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' => 'HOM05D001124', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '548', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02520' => 'bna', 'A03p06630' => 'bna', 'A05p44460' => 'bna', 'A06p08710' => 'bna', 'A06p41090' => 'bna', 'A07p32320' => 'bna', 'A08p32520' => 'bna', 'A09p10360' => 'bna', 'A10p24080' => 'bna', 'Aa31LG11G15250' => 'aar', 'Aa31LG1G1800' => 'aar', 'Aa31LG2G5120' => 'aar', 'Aa31LG2G6070' => 'aar', 'Aa31LG5G10770' => 'aar', 'Aa31sc61G90' => 'aar', 'Actinidia01352' => 'ach', 'Actinidia05983' => 'ach', 'Actinidia08133' => 'ach', 'Actinidia15101' => 'ach', 'Actinidia26379' => 'ach', 'Actinidia35778' => 'ach', 'Actinidia36123' => 'ach', 'Actinidia37436' => 'ach', 'Actinidia38730' => 'ach', 'Ah.02g128210' => 'amhyb', 'Ah.03g132990' => 'amhyb', 'Ah.14g079410' => 'amhyb', 'AL1G24640' => 'aly', 'AL2G26680' => 'aly', 'AL3G10530' => 'aly', 'AL3G45230' => 'aly', 'AL5G15230' => 'aly', 'AL5G16960' => 'aly', 'AL6G25210' => 'aly', 'Aqoxy2G00441' => 'aox', 'Aqoxy3G01236' => 'aox', 'Aqoxy5G03746' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3RQ047' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C7GMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9C8JER' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MBL6KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YXCZ83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZANX40' => 'arhy', 'AT1G12990' => 'ath', 'AT1G67880' => 'ath', 'AT2G13290' => 'ath', 'AT3G01620' => 'ath', 'AT3G26445' => 'ath', 'AT3G27540' => 'ath', 'AT5G14480' => 'ath', 'ATR0824G026' => 'atr', 'ATR1098G019' => 'atr', 'Atru.chr11.2145' => 'acertr', 'Atru.chr2.3636' => 'acertr', 'Atru.chr2.3644' => 'acertr', 'Atru.chr6.2422' => 'acertr', 'Atru.chr7.1112' => 'acertr', 'AUR62005469' => 'cqu', 'AUR62011166' => 'cqu', 'AUR62013319' => 'cqu', 'AUR62024273' => 'cqu', 'AUR62028420' => 'cqu', 'AUR62041942' => 'cqu', 'BcaB01g04969' => 'bca', 'BcaB01g06371' => 'bca', 'BcaB02g11494' => 'bca', 'BcaB03g15382' => 'bca', 'BcaB08g36994' => 'bca', 'BcaC03g13477' => 'bca', 'BcaC03g13478' => 'bca', 'BcaC03g13480' => 'bca', 'BcaC03g13481' => 'bca', 'BcaC03g13486' => 'bca', 'BcaC04g19031' => 'bca', 'BcaC04g23085' => 'bca', 'BcaC05g25094' => 'bca', 'BcaC05g25096' => 'bca', 'BcaC05g25138' => 'bca', 'BcaC05g30416' => 'bca', 'BcaC05g30455' => 'bca', 'BcaC06g30979' => 'bca', 'BcaC06g33805' => 'bca', 'BcaC08g46021' => 'bca', 'BcaNung03154' => 'bca', 'BolC2t06623H' => 'bol', 'BolC2t06632H' => 'bol', 'BolC2t06635H' => 'bol', 'BolC2t06638H' => 'bol', 'BolC3t13266H' => 'bol', 'BolC5t29776H' => 'bol', 'BolC6t38912H' => 'bol', 'BolC7t44183H' => 'bol', 'BolC9t54123H' => 'bol', 'BolC9t59107H' => 'bol', 'BraA02t05221Z' => 'bra', 'BraA03t09996Z' => 'bra', 'BraA05t23210Z' => 'bra', 'BraA06t24068Z' => 'bra', 'BraA06t27032Z' => 'bra', 'BraA08t35176Z' => 'bra', 'BraA09t36680Z' => 'bra', 'BraA10t44471Z' => 'bra', 'C02p06760' => 'bna', 'C02p06890' => 'bna', 'C02p07010' => 'bna', 'C03p07660' => 'bna', 'C05p10300' => 'bna', 'C06p38150' => 'bna', 'C07p36650' => 'bna', 'C08p15770' => 'bna', 'C09p12300' => 'bna', 'C09p62700' => 'bna', 'C09p75040' => 'bna', 'CAN.G13.1' => 'can', 'CAN.G138.4' => 'can', 'CAN.G44.6' => 'can', 'CAN.G473.19' => 'can', 'CANSAT01G0835' => 'cansat', 'CANSAT11G0246' => 'cansat', 'CANSAT11G1766' => 'cansat', 'CANSAT64G1954' => 'cansat', 'CARHR013330' => 'chi', 'CARHR060530' => 'chi', 'CARHR075300' => 'chi', 'CARHR105120' => 'chi', 'CARHR148910' => 'chi', 'CARHR198830' => 'chi', 'Carub.0001s1275' => 'cru', 'Carub.0002s1437' => 'cru', 'Carub.0003s0044' => 'cru', 'Carub.0003s2787' => 'cru', 'Carub.0005s0597' => 'cru', 'Carub.0006s1266' => 'cru', 'Ca_06935_v3' => 'car', 'Ca_13559_v3' => 'car', 'Ca_16941_v3' => 'car', 'Ca_16960_v3' => 'car', 'Ca_17775_v3' => 'car', 'Ca_30464_v3' => 'car', 'Cc06_g08160' => 'ccan', 'Cc07_g01520' => 'ccan', 'Cc11_g15810' => 'ccan', 'CDE02G2840' => 'cde', 'CDE03G0093' => 'cde', 'CDE04G2127' => 'cde', 'CDE07G1857' => 'cde', 'CDE09G1246' => 'cde', 'Cfa003412' => 'cfa', 'Cfa007341' => 'cfa', 'Cfa009220' => 'cfa', 'Ciclev10008737m.g' => 'ccl', 'Ciclev10015565m.g' => 'ccl', 'Ciclev10031761m.g' => 'ccl', 'CiPaw.03G045300' => 'cil', 'CiPaw.03G247200' => 'cil', 'CiPaw.04G029500' => 'cil', 'CiPaw.04G174000' => 'cil', 'CiPaw.05G181200' => 'cil', 'CiPaw.06G067100' => 'cil', 'ClCG05G025800' => 'cla', 'ClCG06G011400' => 'cla', 'ClCG09G019360' => 'cla', 'COL.COLO4_04827' => 'col', 'COL.COLO4_29170' => 'col', 'COL.COLO4_35131' => 'col', 'COL.COLO4_35132' => 'col', 'Cpa.g.sc33.32' => 'cpa', 'Cpa.g.sc46.29' => 'cpa', 'Cpa.g.sc796.1' => 'cpa', 'CsaV3_1G030420' => 'csa', 'CsaV3_5G027050' => 'csa', 'CsaV3_5G031040' => 'csa', 'CsaV3_UNG023130' => 'csa', 'CSS0007726' => 'camsi', 'CSS0016433' => 'camsi', 'CSS0017656' => 'camsi', 'CSS0025364' => 'camsi', 'CSS0027582' => 'camsi', 'CSS0047288' => 'camsi', 'CSS0049950' => 'camsi', 'DCAR_003843' => 'dca', 'DCAR_007052' => 'dca', 'DCAR_020884' => 'dca', 'DCAR_021730' => 'dca', 'DCAR_024423' => 'dca', 'DCAR_026509' => 'dca', 'DCAR_031158' => 'dca', 'Dinv14728' => 'din', 'Dinv15219' => 'din', 'Dinv25728' => 'din', 'Dinv33428' => 'din', 'Dinv36489' => 'din', 'Dinv41486' => 'din', 'Duzib147G0469' => 'dzi', 'Duzib168G0060' => 'dzi', 'Duzib187G1215' => 'dzi', 'Duzib248G0692' => 'dzi', 'Duzib251G0767' => 'dzi', 'Duzib264G0446' => 'dzi', 'Duzib268G0691' => 'dzi', 'ECA232G4767' => 'eca', 'ECA233G2838' => 'eca', 'ECA234G0391' => 'eca', 'ECA234G0857' => 'eca', 'ECA236G1593' => 'eca', 'ECA238G0565' => 'eca', 'ECA246G1027' => 'eca', 'ECA246G3223' => 'eca', 'ECA246G3470' => 'eca', 'EL10Ac6g13829' => 'bvu', 'EL10Ac6g14093' => 'bvu', 'EL10Ac8g18707' => 'bvu', 'Eucgr.C01369' => 'egr', 'Eucgr.H02492' => 'egr', 'Eucgr.I01733' => 'egr', 'Eucgr.J02255' => 'egr', 'Eucgr.J02257' => 'egr', 'Eucgr.J02258' => 'egr', 'FAN02G1601' => 'fan', 'FAN03G1586' => 'fan', 'FAN03G2986' => 'fan', 'FAN05G4837' => 'fan', 'FAN06G0146' => 'fan', 'FAN07G0858' => 'fan', 'FAN09G3179' => 'fan', 'FAN10G0669' => 'fan', 'FAN12G2358' => 'fan', 'FAN14G4198' => 'fan', 'FAN14G5112' => 'fan', 'FAN17G0342' => 'fan', 'FAN19G0342' => 'fan', 'FAN19G0962' => 'fan', 'FAN19G1101' => 'fan', 'FAN19G1872' => 'fan', 'FAN22G0356' => 'fan', 'FAN23G0744' => 'fan', 'FAN23G1914' => 'fan', 'FAN26G0032' => 'fan', 'FAN28G0625' => 'fan', 'FvH4_1g02710' => 'fve', 'FvH4_1g02720' => 'fve', 'FvH4_4g25670' => 'fve', 'FvH4_6g51700' => 'fve', 'FvH4_7g20170' => 'fve', 'Glyma.05G175000' => 'gma', 'Glyma.08G132300' => 'gma', 'Glyma.11G243000' => 'gma', 'Glyma.13G158900' => 'gma', 'Glyma.17G112400' => 'gma', 'Glyma.18G014100' => 'gma', 'Glyma.19G003100' => 'gma', 'Glyma.19G056500' => 'gma', 'Gohir.A01G158900' => 'ghi', 'Gohir.A05G312600' => 'ghi', 'Gohir.A05G354900' => 'ghi', 'Gohir.A07G037200' => 'ghi', 'Gohir.A09G030000' => 'ghi', 'Gohir.A12G145200' => 'ghi', 'Gohir.D01G151500' => 'ghi', 'Gohir.D04G058300' => 'ghi', 'Gohir.D05G314100' => 'ghi', 'Gohir.D07G041400' => 'ghi', 'Gohir.D09G029700' => 'ghi', 'Gohir.D12G149700' => 'ghi', 'Gorai.001G043800' => 'gra', 'Gorai.002G187800' => 'gra', 'Gorai.006G034700' => 'gra', 'Gorai.008G161200' => 'gra', 'Gorai.009G335700' => 'gra', 'Gorai.012G065000' => 'gra', 'GSVIVG01000535001' => 'vvi', 'GSVIVG01015572001' => 'vvi', 'GSVIVG01032386001' => 'vvi', 'HanXRQChr05g0138531' => 'han', 'HanXRQChr06g0174391' => 'han', 'HanXRQChr07g0199021' => 'han', 'HanXRQChr08g0208211' => 'han', 'HanXRQChr09g0255471' => 'han', 'HanXRQChr10g0315791' => 'han', 'HanXRQChr12g0371991' => 'han', 'HanXRQChr15g0475251' => 'han', 'HanXRQChr17g0540001' => 'han', 'HanXRQChr17g0548631' => 'han', 'HanXRQChr17g0569561' => 'han', 'Haze_12256' => 'cav', 'Haze_14756' => 'cav', 'Haze_25528' => 'cav', 'Hma1.2p1_0079F.1_g041020' => 'hma', 'Hma1.2p1_0818F.1_g223260' => 'hma', 'Hma1.2p1_1747F.1_g300530' => 'hma', 'HPP92_004607' => 'vpl', 'HPP92_004608' => 'vpl', 'HPP92_006181' => 'vpl', 'HPP92_012192' => 'vpl', 'HPP92_015680' => 'vpl', 'HPP92_020249' => 'vpl', 'HPP92_021376' => 'vpl', 'HPP92_024275' => 'vpl', 'Hund06031' => 'sun', 'Hund25391' => 'sun', 'Lalb_Chr07g0185371' => 'lal', 'Lalb_Chr07g0185381' => 'lal', 'Lalb_Chr12g0204011' => 'lal', 'Lalb_Chr13g0301671' => 'lal', 'Lalb_Chr14g0362851' => 'lal', 'Lalb_Chr24g0403581' => 'lal', 'Lj1g0000233' => 'lja', 'Lj2g0018120' => 'lja', 'Lj3C621T0' => 'lonja', 'Lj3P1059T14' => 'lonja', 'Lj3P611T9' => 'lonja', 'Lj3P614T13' => 'lonja', 'Lj3P615T5' => 'lonja', 'Lj4g0012315' => 'lja', 'Lj4g0026182' => 'lja', 'Lj6P813T16' => 'lonja', 'Lj7C427T7' => 'lonja', 'Lj7C427T8' => 'lonja', 'Lj7P600T41' => 'lonja', 'Lju41C42G17' => 'lonja', 'Lsat_1_v5_gn_0_47300' => 'lsa', 'Lsat_1_v5_gn_2_91280' => 'lsa', 'Lsat_1_v5_gn_3_30561' => 'lsa', 'Lsat_1_v5_gn_4_184321' => 'lsa', 'Lsat_1_v5_gn_4_4041' => 'lsa', 'Lsat_1_v5_gn_5_92000' => 'lsa', 'Lsat_1_v5_gn_8_152940' => 'lsa', 'Lsat_1_v5_gn_8_62401' => 'lsa', 'Manes.06G055900' => 'mes', 'Manes.12G022200' => 'mes', 'Manes.13G023300' => 'mes', 'Manes.14G115000' => 'mes', 'Manes.15G151700' => 'mes', 'Manes.17G111300' => 'mes', 'Mapoly0226s0009' => 'mpo', 'MBI02_g25363_MAGBIO' => 'mbi', 'MBI06_g00027_MAGBIO' => 'mbi', 'MBI10_g13034_MAGBIO' => 'mbi', 'MD09G1023400' => 'mdo', 'MD13G1100100' => 'mdo', 'MD15G1169200' => 'mdo', 'MD16G1101100' => 'mdo', 'MD17G1022900' => 'mdo', 'Medtr3g096150' => 'mtr', 'Medtr4g115070' => 'mtr', 'Medtr7g033325' => 'mtr', 'Medtr8g089840' => 'mtr', 'MELO3C010319.2' => 'cme', 'MELO3C011944.2' => 'cme', 'MELO3C021589.2' => 'cme', 'Migut.E00207' => 'egut', 'Migut.H00067' => 'egut', 'Migut.K00433' => 'egut', 'Migut.K00606' => 'egut', 'Migut.K01410' => 'egut', 'MSTRG.13347' => 'ama', 'MSTRG.24045' => 'ama', 'MSTRG.2428' => 'ama', 'MSTRG.26410' => 'ama', 'MSTRG.3139' => 'ama', 'MSTRG.3286' => 'ama', 'MSTRG.563' => 'ama', 'MSTRG.7941' => 'ama', 'Nitab4.5_0000028g0060' => 'nta', 'Nitab4.5_0000065g0260' => 'nta', 'Nitab4.5_0000112g0060' => 'nta', 'Nitab4.5_0000489g0120' => 'nta', 'Nitab4.5_0001776g0050' => 'nta', 'Nitab4.5_0001854g0010' => 'nta', 'Nitab4.5_0001860g0020' => 'nta', 'Nitab4.5_0004352g0010' => 'nta', 'Nitab4.5_0008716g0020' => 'nta', 'Nitab4.5_0008922g0010' => 'nta', 'Nn3g16693' => 'nnu', 'Nn4g22596' => 'nnu', 'Nn7g37639' => 'nnu', 'Oeu001701.1' => 'oeu', 'Oeu018149.1' => 'oeu', 'Oeu026220.1' => 'oeu', 'Oeu038635.1' => 'oeu', 'Oeu049176.1' => 'oeu', 'Oeu056706.1' => 'oeu', 'Oeu056937.1' => 'oeu', 'Oeu057540.1' => 'oeu', 'Os02g0594900' => 'osa', 'Os02g0595100' => 'osa', 'Os04g0477500' => 'osa', 'Os12g0611900' => 'osa', 'Peaxi162Scf00076g00020' => 'pax', 'Peaxi162Scf00128g00217' => 'pax', 'Peaxi162Scf00129g01640' => 'pax', 'Peaxi162Scf00669g00007' => 'pax', 'Peaxi162Scf00700g00421' => 'pax', 'Peaxi162Scf00801g00038' => 'pax', 'Peaxi162Scf00891g00025' => 'pax', 'PGR083G0909' => 'pgr', 'PGR119G1005' => 'pgr', 'PGR142G2236' => 'pgr', 'PGR142G3388' => 'pgr', 'PGSC0003DMG400004514' => 'stu', 'PGSC0003DMG400012635' => 'stu', 'PGSC0003DMG400015730' => 'stu', 'PGSC0003DMG400018611' => 'stu', 'PGSC0003DMG400030897' => 'stu', 'Phvul.001G254800' => 'pvu', 'Phvul.002G260100' => 'pvu', 'Phvul.003G167600' => 'pvu', 'Phvul.004G005100' => 'pvu', 'Potri.001G343600' => 'ptr', 'Potri.006G066700' => 'ptr', 'Potri.008G186000' => 'ptr', 'Potri.010G046900' => 'ptr', 'Potri.018G127900' => 'ptr', 'Pp3c20_17750' => 'ppa', 'Pp3c24_4380' => 'ppa', 'Prupe.1G245800' => 'ppe', 'Prupe.3G293400' => 'ppe', 'Prupe.7G247400' => 'ppe', 'Psat0s145g0120' => 'psa', 'Psat0s595g0040' => 'psa', 'Psat0s595g0120' => 'psa', 'Psat3g175040' => 'psa', 'Psat7g058120' => 'psa', 'PSO017G0428' => 'pso', 'PSO063G7510' => 'pso', 'PSO067G0046' => 'pso', 'PSO478G1073' => 'pso', 'PSO675G3677' => 'pso', 'PSO675G6558' => 'pso', 'PSO675G7520' => 'pso', 'PSO675G8959' => 'pso', 'QL02p074089' => 'qlo', 'QL02p089614' => 'qlo', 'QL03p057736' => 'qlo', 'RcHm_v2.0_Chr1g0364131' => 'rch', 'RcHm_v2.0_Chr2g0087801' => 'rch', 'RcHm_v2.0_Chr2g0087821' => 'rch', 'RcHm_v2.0_Chr2g0173231' => 'rch', 'RcHm_v2.0_Chr4g0433111' => 'rch', 'Rhsim03G0250300' => 'rsi', 'Rhsim08G0048400' => 'rsi', 'Rhsim10G0014800' => 'rsi', 'Rhsim12G0040100' => 'rsi', 'Rhsim12G0109700' => 'rsi', 'Sabra06G0049600' => 'sbr', 'Sabra08G0141000' => 'sbr', 'Sabra10G0021400' => 'sbr', 'Sabra16G0222900' => 'sbr', 'Sabra18G0108600' => 'sbr', 'SalBow1G0433' => 'sbo', 'SalBow1G2038' => 'sbo', 'SalBow1G5003' => 'sbo', 'SalBow7G1197' => 'sbo', 'SalBow8G3506' => 'sbo', 'Sc03g0007300' => 'sci', 'Sc11g0000950' => 'sci', 'Sc14g0008750' => 'sci', 'Sc18g0000420' => 'sci', 'Sed0006754' => 'sed', 'Sed0008741' => 'sed', 'Sed0017172' => 'sed', 'Sed0018925' => 'sed', 'Sed0023326' => 'sed', 'Sed0025909' => 'sed', 'SEGI_05333' => 'sgi', 'SEGI_10362' => 'sgi', 'SEGI_13380' => 'sgi', 'SEGI_24306' => 'sgi', 'SEGI_29077' => 'sgi', 'SEGI_29095' => 'sgi', 'SEGI_36534' => 'sgi', 'SEGI_37506' => 'sgi', 'SEGI_38321' => 'sgi', 'SGA_v2.0_scaffold307G48031' => 'sas', 'SGA_v2.0_scaffold47G17507' => 'sas', 'SGA_v2.0_scaffold63G21736' => 'sas', 'SGA_v2.0_scaffold87G27070' => 'sas', 'SHI17794' => 'shi', 'SHI28851' => 'shi', 'SMO165G0155' => 'smo', 'SMO340G0217' => 'smo', 'SMO367G1210' => 'smo', 'Solyc02g093430.3' => 'sly', 'Solyc05g013580.4' => 'sly', 'Solyc07g008030.3' => 'sly', 'Solyc12g035470.2' => 'sly', 'Sopen02g038020' => 'spe', 'Sopen05g008490' => 'spe', 'Sopen07g003910' => 'spe', 'Sopen12g015240' => 'spe', 'Sp1g11550' => 'spa', 'Sp2g16710' => 'spa', 'Sp3g00430' => 'spa', 'Sp3g26780' => 'spa', 'Sp5g22900' => 'spa', 'Sp6g29530' => 'spa', 'TAR371G0794' => 'tar', 'TAR374G0164' => 'tar', 'TAR622G0165' => 'tar', 'TAR626G0929' => 'tar', 'TAR629G2155' => 'tar', 'THA.LOC104805282' => 'tha', 'THA.LOC104805363' => 'tha', 'THA.LOC104808968' => 'tha', 'THA.LOC104821093' => 'tha', 'THA.LOC104823953' => 'tha', 'THA.LOC104825562' => 'tha', 'THA.LOC104825665' => 'tha', 'Thecc.02G261400' => 'tca', 'Thecc.04G019200' => 'tca', 'Thecc.09G130400' => 'tca', 'Thhalv10004374m.g' => 'esa', 'Thhalv10007850m.g' => 'esa', 'Thhalv10013782m.g' => 'esa', 'Thhalv10018686m.g' => 'esa', 'Thhalv10020899m.g' => 'esa', 'Thhalv10022755m.g' => 'esa', 'TPR.G23851' => 'tpr', 'TPR.G26500' => 'tpr', 'TPR.G27267' => 'tpr', 'TPR.G32001' => 'tpr', 'TPR.G6251' => 'tpr', 'TPR.G8167' => 'tpr', 'TWI12G1330' => 'twi', 'TWI18G1239' => 'twi', 'TWI34G0979' => 'twi', 'TWI36G0670' => 'twi', 'TWI36G0707' => 'twi', 'TWI56G0233' => 'twi', 'TWI75G1809' => 'twi', 'unitig_21.g20874' => 'ugi', 'unitig_26.g10343' => 'ugi', 'unitig_46.g18392' => 'ugi', 'unitig_52.g17178' => 'ugi', 'unitig_8.g2934' => 'ugi', 'vmacro01122' => 'vma', 'vmacro05875' => 'vma', 'vmacro06147' => 'vma', 'vmacro16191' => 'vma', 'vmacro18293' => 'vma', 'VMungo0251G3707' => 'vmu', 'VMungo0464G1521' => 'vmu', 'VMungo1215G0205' => 'vmu', 'VMungo1383G2484' => 'vmu', 'Zm00001eb079610' => 'zma', 'Zm00001eb135990' => 'zma', 'Zm00001eb183710' => 'zma', 'Zm00001eb246020' => 'zma' ), 'gf_id' => 'HOM05D001124', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001124' ), 'data_identifier' => 'HOM05D001124', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001124', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '548', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02520' => 'bna', 'A03p06630' => 'bna', 'A05p44460' => 'bna', 'A06p08710' => 'bna', 'A06p41090' => 'bna', 'A07p32320' => 'bna', 'A08p32520' => 'bna', 'A09p10360' => 'bna', 'A10p24080' => 'bna', 'Aa31LG11G15250' => 'aar', 'Aa31LG1G1800' => 'aar', 'Aa31LG2G5120' => 'aar', 'Aa31LG2G6070' => 'aar', 'Aa31LG5G10770' => 'aar', 'Aa31sc61G90' => 'aar', 'Actinidia01352' => 'ach', 'Actinidia05983' => 'ach', 'Actinidia08133' => 'ach', 'Actinidia15101' => 'ach', 'Actinidia26379' => 'ach', 'Actinidia35778' => 'ach', 'Actinidia36123' => 'ach', 'Actinidia37436' => 'ach', 'Actinidia38730' => 'ach', 'Ah.02g128210' => 'amhyb', 'Ah.03g132990' => 'amhyb', 'Ah.14g079410' => 'amhyb', 'AL1G24640' => 'aly', 'AL2G26680' => 'aly', 'AL3G10530' => 'aly', 'AL3G45230' => 'aly', 'AL5G15230' => 'aly', 'AL5G16960' => 'aly', 'AL6G25210' => 'aly', 'Aqoxy2G00441' => 'aox', 'Aqoxy3G01236' => 'aox', 'Aqoxy5G03746' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3RQ047' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C7GMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9C8JER' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MBL6KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YXCZ83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZANX40' => 'arhy', 'AT1G12990' => 'ath', 'AT1G67880' => 'ath', 'AT2G13290' => 'ath', 'AT3G01620' => 'ath', 'AT3G26445' => 'ath', 'AT3G27540' => 'ath', 'AT5G14480' => 'ath', 'ATR0824G026' => 'atr', 'ATR1098G019' => 'atr', 'Atru.chr11.2145' => 'acertr', 'Atru.chr2.3636' => 'acertr', 'Atru.chr2.3644' => 'acertr', 'Atru.chr6.2422' => 'acertr', 'Atru.chr7.1112' => 'acertr', 'AUR62005469' => 'cqu', 'AUR62011166' => 'cqu', 'AUR62013319' => 'cqu', 'AUR62024273' => 'cqu', 'AUR62028420' => 'cqu', 'AUR62041942' => 'cqu', 'BcaB01g04969' => 'bca', 'BcaB01g06371' => 'bca', 'BcaB02g11494' => 'bca', 'BcaB03g15382' => 'bca', 'BcaB08g36994' => 'bca', 'BcaC03g13477' => 'bca', 'BcaC03g13478' => 'bca', 'BcaC03g13480' => 'bca', 'BcaC03g13481' => 'bca', 'BcaC03g13486' => 'bca', 'BcaC04g19031' => 'bca', 'BcaC04g23085' => 'bca', 'BcaC05g25094' => 'bca', 'BcaC05g25096' => 'bca', 'BcaC05g25138' => 'bca', 'BcaC05g30416' => 'bca', 'BcaC05g30455' => 'bca', 'BcaC06g30979' => 'bca', 'BcaC06g33805' => 'bca', 'BcaC08g46021' => 'bca', 'BcaNung03154' => 'bca', 'BolC2t06623H' => 'bol', 'BolC2t06632H' => 'bol', 'BolC2t06635H' => 'bol', 'BolC2t06638H' => 'bol', 'BolC3t13266H' => 'bol', 'BolC5t29776H' => 'bol', 'BolC6t38912H' => 'bol', 'BolC7t44183H' => 'bol', 'BolC9t54123H' => 'bol', 'BolC9t59107H' => 'bol', 'BraA02t05221Z' => 'bra', 'BraA03t09996Z' => 'bra', 'BraA05t23210Z' => 'bra', 'BraA06t24068Z' => 'bra', 'BraA06t27032Z' => 'bra', 'BraA08t35176Z' => 'bra', 'BraA09t36680Z' => 'bra', 'BraA10t44471Z' => 'bra', 'C02p06760' => 'bna', 'C02p06890' => 'bna', 'C02p07010' => 'bna', 'C03p07660' => 'bna', 'C05p10300' => 'bna', 'C06p38150' => 'bna', 'C07p36650' => 'bna', 'C08p15770' => 'bna', 'C09p12300' => 'bna', 'C09p62700' => 'bna', 'C09p75040' => 'bna', 'CAN.G13.1' => 'can', 'CAN.G138.4' => 'can', 'CAN.G44.6' => 'can', 'CAN.G473.19' => 'can', 'CANSAT01G0835' => 'cansat', 'CANSAT11G0246' => 'cansat', 'CANSAT11G1766' => 'cansat', 'CANSAT64G1954' => 'cansat', 'CARHR013330' => 'chi', 'CARHR060530' => 'chi', 'CARHR075300' => 'chi', 'CARHR105120' => 'chi', 'CARHR148910' => 'chi', 'CARHR198830' => 'chi', 'Carub.0001s1275' => 'cru', 'Carub.0002s1437' => 'cru', 'Carub.0003s0044' => 'cru', 'Carub.0003s2787' => 'cru', 'Carub.0005s0597' => 'cru', 'Carub.0006s1266' => 'cru', 'Ca_06935_v3' => 'car', 'Ca_13559_v3' => 'car', 'Ca_16941_v3' => 'car', 'Ca_16960_v3' => 'car', 'Ca_17775_v3' => 'car', 'Ca_30464_v3' => 'car', 'Cc06_g08160' => 'ccan', 'Cc07_g01520' => 'ccan', 'Cc11_g15810' => 'ccan', 'CDE02G2840' => 'cde', 'CDE03G0093' => 'cde', 'CDE04G2127' => 'cde', 'CDE07G1857' => 'cde', 'CDE09G1246' => 'cde', 'Cfa003412' => 'cfa', 'Cfa007341' => 'cfa', 'Cfa009220' => 'cfa', 'Ciclev10008737m.g' => 'ccl', 'Ciclev10015565m.g' => 'ccl', 'Ciclev10031761m.g' => 'ccl', 'CiPaw.03G045300' => 'cil', 'CiPaw.03G247200' => 'cil', 'CiPaw.04G029500' => 'cil', 'CiPaw.04G174000' => 'cil', 'CiPaw.05G181200' => 'cil', 'CiPaw.06G067100' => 'cil', 'ClCG05G025800' => 'cla', 'ClCG06G011400' => 'cla', 'ClCG09G019360' => 'cla', 'COL.COLO4_04827' => 'col', 'COL.COLO4_29170' => 'col', 'COL.COLO4_35131' => 'col', 'COL.COLO4_35132' => 'col', 'Cpa.g.sc33.32' => 'cpa', 'Cpa.g.sc46.29' => 'cpa', 'Cpa.g.sc796.1' => 'cpa', 'CsaV3_1G030420' => 'csa', 'CsaV3_5G027050' => 'csa', 'CsaV3_5G031040' => 'csa', 'CsaV3_UNG023130' => 'csa', 'CSS0007726' => 'camsi', 'CSS0016433' => 'camsi', 'CSS0017656' => 'camsi', 'CSS0025364' => 'camsi', 'CSS0027582' => 'camsi', 'CSS0047288' => 'camsi', 'CSS0049950' => 'camsi', 'DCAR_003843' => 'dca', 'DCAR_007052' => 'dca', 'DCAR_020884' => 'dca', 'DCAR_021730' => 'dca', 'DCAR_024423' => 'dca', 'DCAR_026509' => 'dca', 'DCAR_031158' => 'dca', 'Dinv14728' => 'din', 'Dinv15219' => 'din', 'Dinv25728' => 'din', 'Dinv33428' => 'din', 'Dinv36489' => 'din', 'Dinv41486' => 'din', 'Duzib147G0469' => 'dzi', 'Duzib168G0060' => 'dzi', 'Duzib187G1215' => 'dzi', 'Duzib248G0692' => 'dzi', 'Duzib251G0767' => 'dzi', 'Duzib264G0446' => 'dzi', 'Duzib268G0691' => 'dzi', 'ECA232G4767' => 'eca', 'ECA233G2838' => 'eca', 'ECA234G0391' => 'eca', 'ECA234G0857' => 'eca', 'ECA236G1593' => 'eca', 'ECA238G0565' => 'eca', 'ECA246G1027' => 'eca', 'ECA246G3223' => 'eca', 'ECA246G3470' => 'eca', 'EL10Ac6g13829' => 'bvu', 'EL10Ac6g14093' => 'bvu', 'EL10Ac8g18707' => 'bvu', 'Eucgr.C01369' => 'egr', 'Eucgr.H02492' => 'egr', 'Eucgr.I01733' => 'egr', 'Eucgr.J02255' => 'egr', 'Eucgr.J02257' => 'egr', 'Eucgr.J02258' => 'egr', 'FAN02G1601' => 'fan', 'FAN03G1586' => 'fan', 'FAN03G2986' => 'fan', 'FAN05G4837' => 'fan', 'FAN06G0146' => 'fan', 'FAN07G0858' => 'fan', 'FAN09G3179' => 'fan', 'FAN10G0669' => 'fan', 'FAN12G2358' => 'fan', 'FAN14G4198' => 'fan', 'FAN14G5112' => 'fan', 'FAN17G0342' => 'fan', 'FAN19G0342' => 'fan', 'FAN19G0962' => 'fan', 'FAN19G1101' => 'fan', 'FAN19G1872' => 'fan', 'FAN22G0356' => 'fan', 'FAN23G0744' => 'fan', 'FAN23G1914' => 'fan', 'FAN26G0032' => 'fan', 'FAN28G0625' => 'fan', 'FvH4_1g02710' => 'fve', 'FvH4_1g02720' => 'fve', 'FvH4_4g25670' => 'fve', 'FvH4_6g51700' => 'fve', 'FvH4_7g20170' => 'fve', 'Glyma.05G175000' => 'gma', 'Glyma.08G132300' => 'gma', 'Glyma.11G243000' => 'gma', 'Glyma.13G158900' => 'gma', 'Glyma.17G112400' => 'gma', 'Glyma.18G014100' => 'gma', 'Glyma.19G003100' => 'gma', 'Glyma.19G056500' => 'gma', 'Gohir.A01G158900' => 'ghi', 'Gohir.A05G312600' => 'ghi', 'Gohir.A05G354900' => 'ghi', 'Gohir.A07G037200' => 'ghi', 'Gohir.A09G030000' => 'ghi', 'Gohir.A12G145200' => 'ghi', 'Gohir.D01G151500' => 'ghi', 'Gohir.D04G058300' => 'ghi', 'Gohir.D05G314100' => 'ghi', 'Gohir.D07G041400' => 'ghi', 'Gohir.D09G029700' => 'ghi', 'Gohir.D12G149700' => 'ghi', 'Gorai.001G043800' => 'gra', 'Gorai.002G187800' => 'gra', 'Gorai.006G034700' => 'gra', 'Gorai.008G161200' => 'gra', 'Gorai.009G335700' => 'gra', 'Gorai.012G065000' => 'gra', 'GSVIVG01000535001' => 'vvi', 'GSVIVG01015572001' => 'vvi', 'GSVIVG01032386001' => 'vvi', 'HanXRQChr05g0138531' => 'han', 'HanXRQChr06g0174391' => 'han', 'HanXRQChr07g0199021' => 'han', 'HanXRQChr08g0208211' => 'han', 'HanXRQChr09g0255471' => 'han', 'HanXRQChr10g0315791' => 'han', 'HanXRQChr12g0371991' => 'han', 'HanXRQChr15g0475251' => 'han', 'HanXRQChr17g0540001' => 'han', 'HanXRQChr17g0548631' => 'han', 'HanXRQChr17g0569561' => 'han', 'Haze_12256' => 'cav', 'Haze_14756' => 'cav', 'Haze_25528' => 'cav', 'Hma1.2p1_0079F.1_g041020' => 'hma', 'Hma1.2p1_0818F.1_g223260' => 'hma', 'Hma1.2p1_1747F.1_g300530' => 'hma', 'HPP92_004607' => 'vpl', 'HPP92_004608' => 'vpl', 'HPP92_006181' => 'vpl', 'HPP92_012192' => 'vpl', 'HPP92_015680' => 'vpl', 'HPP92_020249' => 'vpl', 'HPP92_021376' => 'vpl', 'HPP92_024275' => 'vpl', 'Hund06031' => 'sun', 'Hund25391' => 'sun', 'Lalb_Chr07g0185371' => 'lal', 'Lalb_Chr07g0185381' => 'lal', 'Lalb_Chr12g0204011' => 'lal', 'Lalb_Chr13g0301671' => 'lal', 'Lalb_Chr14g0362851' => 'lal', 'Lalb_Chr24g0403581' => 'lal', 'Lj1g0000233' => 'lja', 'Lj2g0018120' => 'lja', 'Lj3C621T0' => 'lonja', 'Lj3P1059T14' => 'lonja', 'Lj3P611T9' => 'lonja', 'Lj3P614T13' => 'lonja', 'Lj3P615T5' => 'lonja', 'Lj4g0012315' => 'lja', 'Lj4g0026182' => 'lja', 'Lj6P813T16' => 'lonja', 'Lj7C427T7' => 'lonja', 'Lj7C427T8' => 'lonja', 'Lj7P600T41' => 'lonja', 'Lju41C42G17' => 'lonja', 'Lsat_1_v5_gn_0_47300' => 'lsa', 'Lsat_1_v5_gn_2_91280' => 'lsa', 'Lsat_1_v5_gn_3_30561' => 'lsa', 'Lsat_1_v5_gn_4_184321' => 'lsa', 'Lsat_1_v5_gn_4_4041' => 'lsa', 'Lsat_1_v5_gn_5_92000' => 'lsa', 'Lsat_1_v5_gn_8_152940' => 'lsa', 'Lsat_1_v5_gn_8_62401' => 'lsa', 'Manes.06G055900' => 'mes', 'Manes.12G022200' => 'mes', 'Manes.13G023300' => 'mes', 'Manes.14G115000' => 'mes', 'Manes.15G151700' => 'mes', 'Manes.17G111300' => 'mes', 'Mapoly0226s0009' => 'mpo', 'MBI02_g25363_MAGBIO' => 'mbi', 'MBI06_g00027_MAGBIO' => 'mbi', 'MBI10_g13034_MAGBIO' => 'mbi', 'MD09G1023400' => 'mdo', 'MD13G1100100' => 'mdo', 'MD15G1169200' => 'mdo', 'MD16G1101100' => 'mdo', 'MD17G1022900' => 'mdo', 'Medtr3g096150' => 'mtr', 'Medtr4g115070' => 'mtr', 'Medtr7g033325' => 'mtr', 'Medtr8g089840' => 'mtr', 'MELO3C010319.2' => 'cme', 'MELO3C011944.2' => 'cme', 'MELO3C021589.2' => 'cme', 'Migut.E00207' => 'egut', 'Migut.H00067' => 'egut', 'Migut.K00433' => 'egut', 'Migut.K00606' => 'egut', 'Migut.K01410' => 'egut', 'MSTRG.13347' => 'ama', 'MSTRG.24045' => 'ama', 'MSTRG.2428' => 'ama', 'MSTRG.26410' => 'ama', 'MSTRG.3139' => 'ama', 'MSTRG.3286' => 'ama', 'MSTRG.563' => 'ama', 'MSTRG.7941' => 'ama', 'Nitab4.5_0000028g0060' => 'nta', 'Nitab4.5_0000065g0260' => 'nta', 'Nitab4.5_0000112g0060' => 'nta', 'Nitab4.5_0000489g0120' => 'nta', 'Nitab4.5_0001776g0050' => 'nta', 'Nitab4.5_0001854g0010' => 'nta', 'Nitab4.5_0001860g0020' => 'nta', 'Nitab4.5_0004352g0010' => 'nta', 'Nitab4.5_0008716g0020' => 'nta', 'Nitab4.5_0008922g0010' => 'nta', 'Nn3g16693' => 'nnu', 'Nn4g22596' => 'nnu', 'Nn7g37639' => 'nnu', 'Oeu001701.1' => 'oeu', 'Oeu018149.1' => 'oeu', 'Oeu026220.1' => 'oeu', 'Oeu038635.1' => 'oeu', 'Oeu049176.1' => 'oeu', 'Oeu056706.1' => 'oeu', 'Oeu056937.1' => 'oeu', 'Oeu057540.1' => 'oeu', 'Os02g0594900' => 'osa', 'Os02g0595100' => 'osa', 'Os04g0477500' => 'osa', 'Os12g0611900' => 'osa', 'Peaxi162Scf00076g00020' => 'pax', 'Peaxi162Scf00128g00217' => 'pax', 'Peaxi162Scf00129g01640' => 'pax', 'Peaxi162Scf00669g00007' => 'pax', 'Peaxi162Scf00700g00421' => 'pax', 'Peaxi162Scf00801g00038' => 'pax', 'Peaxi162Scf00891g00025' => 'pax', 'PGR083G0909' => 'pgr', 'PGR119G1005' => 'pgr', 'PGR142G2236' => 'pgr', 'PGR142G3388' => 'pgr', 'PGSC0003DMG400004514' => 'stu', 'PGSC0003DMG400012635' => 'stu', 'PGSC0003DMG400015730' => 'stu', 'PGSC0003DMG400018611' => 'stu', 'PGSC0003DMG400030897' => 'stu', 'Phvul.001G254800' => 'pvu', 'Phvul.002G260100' => 'pvu', 'Phvul.003G167600' => 'pvu', 'Phvul.004G005100' => 'pvu', 'Potri.001G343600' => 'ptr', 'Potri.006G066700' => 'ptr', 'Potri.008G186000' => 'ptr', 'Potri.010G046900' => 'ptr', 'Potri.018G127900' => 'ptr', 'Pp3c20_17750' => 'ppa', 'Pp3c24_4380' => 'ppa', 'Prupe.1G245800' => 'ppe', 'Prupe.3G293400' => 'ppe', 'Prupe.7G247400' => 'ppe', 'Psat0s145g0120' => 'psa', 'Psat0s595g0040' => 'psa', 'Psat0s595g0120' => 'psa', 'Psat3g175040' => 'psa', 'Psat7g058120' => 'psa', 'PSO017G0428' => 'pso', 'PSO063G7510' => 'pso', 'PSO067G0046' => 'pso', 'PSO478G1073' => 'pso', 'PSO675G3677' => 'pso', 'PSO675G6558' => 'pso', 'PSO675G7520' => 'pso', 'PSO675G8959' => 'pso', 'QL02p074089' => 'qlo', 'QL02p089614' => 'qlo', 'QL03p057736' => 'qlo', 'RcHm_v2.0_Chr1g0364131' => 'rch', 'RcHm_v2.0_Chr2g0087801' => 'rch', 'RcHm_v2.0_Chr2g0087821' => 'rch', 'RcHm_v2.0_Chr2g0173231' => 'rch', 'RcHm_v2.0_Chr4g0433111' => 'rch', 'Rhsim03G0250300' => 'rsi', 'Rhsim08G0048400' => 'rsi', 'Rhsim10G0014800' => 'rsi', 'Rhsim12G0040100' => 'rsi', 'Rhsim12G0109700' => 'rsi', 'Sabra06G0049600' => 'sbr', 'Sabra08G0141000' => 'sbr', 'Sabra10G0021400' => 'sbr', 'Sabra16G0222900' => 'sbr', 'Sabra18G0108600' => 'sbr', 'SalBow1G0433' => 'sbo', 'SalBow1G2038' => 'sbo', 'SalBow1G5003' => 'sbo', 'SalBow7G1197' => 'sbo', 'SalBow8G3506' => 'sbo', 'Sc03g0007300' => 'sci', 'Sc11g0000950' => 'sci', 'Sc14g0008750' => 'sci', 'Sc18g0000420' => 'sci', 'Sed0006754' => 'sed', 'Sed0008741' => 'sed', 'Sed0017172' => 'sed', 'Sed0018925' => 'sed', 'Sed0023326' => 'sed', 'Sed0025909' => 'sed', 'SEGI_05333' => 'sgi', 'SEGI_10362' => 'sgi', 'SEGI_13380' => 'sgi', 'SEGI_24306' => 'sgi', 'SEGI_29077' => 'sgi', 'SEGI_29095' => 'sgi', 'SEGI_36534' => 'sgi', 'SEGI_37506' => 'sgi', 'SEGI_38321' => 'sgi', 'SGA_v2.0_scaffold307G48031' => 'sas', 'SGA_v2.0_scaffold47G17507' => 'sas', 'SGA_v2.0_scaffold63G21736' => 'sas', 'SGA_v2.0_scaffold87G27070' => 'sas', 'SHI17794' => 'shi', 'SHI28851' => 'shi', 'SMO165G0155' => 'smo', 'SMO340G0217' => 'smo', 'SMO367G1210' => 'smo', 'Solyc02g093430.3' => 'sly', 'Solyc05g013580.4' => 'sly', 'Solyc07g008030.3' => 'sly', 'Solyc12g035470.2' => 'sly', 'Sopen02g038020' => 'spe', 'Sopen05g008490' => 'spe', 'Sopen07g003910' => 'spe', 'Sopen12g015240' => 'spe', 'Sp1g11550' => 'spa', 'Sp2g16710' => 'spa', 'Sp3g00430' => 'spa', 'Sp3g26780' => 'spa', 'Sp5g22900' => 'spa', 'Sp6g29530' => 'spa', 'TAR371G0794' => 'tar', 'TAR374G0164' => 'tar', 'TAR622G0165' => 'tar', 'TAR626G0929' => 'tar', 'TAR629G2155' => 'tar', 'THA.LOC104805282' => 'tha', 'THA.LOC104805363' => 'tha', 'THA.LOC104808968' => 'tha', 'THA.LOC104821093' => 'tha', 'THA.LOC104823953' => 'tha', 'THA.LOC104825562' => 'tha', 'THA.LOC104825665' => 'tha', 'Thecc.02G261400' => 'tca', 'Thecc.04G019200' => 'tca', 'Thecc.09G130400' => 'tca', 'Thhalv10004374m.g' => 'esa', 'Thhalv10007850m.g' => 'esa', 'Thhalv10013782m.g' => 'esa', 'Thhalv10018686m.g' => 'esa', 'Thhalv10020899m.g' => 'esa', 'Thhalv10022755m.g' => 'esa', 'TPR.G23851' => 'tpr', 'TPR.G26500' => 'tpr', 'TPR.G27267' => 'tpr', 'TPR.G32001' => 'tpr', 'TPR.G6251' => 'tpr', 'TPR.G8167' => 'tpr', 'TWI12G1330' => 'twi', 'TWI18G1239' => 'twi', 'TWI34G0979' => 'twi', 'TWI36G0670' => 'twi', 'TWI36G0707' => 'twi', 'TWI56G0233' => 'twi', 'TWI75G1809' => 'twi', 'unitig_21.g20874' => 'ugi', 'unitig_26.g10343' => 'ugi', 'unitig_46.g18392' => 'ugi', 'unitig_52.g17178' => 'ugi', 'unitig_8.g2934' => 'ugi', 'vmacro01122' => 'vma', 'vmacro05875' => 'vma', 'vmacro06147' => 'vma', 'vmacro16191' => 'vma', 'vmacro18293' => 'vma', 'VMungo0251G3707' => 'vmu', 'VMungo0464G1521' => 'vmu', 'VMungo1215G0205' => 'vmu', 'VMungo1383G2484' => 'vmu', 'Zm00001eb079610' => 'zma', 'Zm00001eb135990' => 'zma', 'Zm00001eb183710' => 'zma', 'Zm00001eb246020' => 'zma' ) $gf_id = 'HOM05D001124' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001124' ) $data_identifier = 'HOM05D001124' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 6, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 7, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 21, 'bol' => (int) 10, 'bra' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 6, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 9, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 21, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 8, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 10, 'lsa' => (int) 8, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 8, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 9, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb246020' $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' => 'HOM05D001124', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '548', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02520' => 'bna', 'A03p06630' => 'bna', 'A05p44460' => 'bna', 'A06p08710' => 'bna', 'A06p41090' => 'bna', 'A07p32320' => 'bna', 'A08p32520' => 'bna', 'A09p10360' => 'bna', 'A10p24080' => 'bna', 'Aa31LG11G15250' => 'aar', 'Aa31LG1G1800' => 'aar', 'Aa31LG2G5120' => 'aar', 'Aa31LG2G6070' => 'aar', 'Aa31LG5G10770' => 'aar', 'Aa31sc61G90' => 'aar', 'Actinidia01352' => 'ach', 'Actinidia05983' => 'ach', 'Actinidia08133' => 'ach', 'Actinidia15101' => 'ach', 'Actinidia26379' => 'ach', 'Actinidia35778' => 'ach', 'Actinidia36123' => 'ach', 'Actinidia37436' => 'ach', 'Actinidia38730' => 'ach', 'Ah.02g128210' => 'amhyb', 'Ah.03g132990' => 'amhyb', 'Ah.14g079410' => 'amhyb', 'AL1G24640' => 'aly', 'AL2G26680' => 'aly', 'AL3G10530' => 'aly', 'AL3G45230' => 'aly', 'AL5G15230' => 'aly', 'AL5G16960' => 'aly', 'AL6G25210' => 'aly', 'Aqoxy2G00441' => 'aox', 'Aqoxy3G01236' => 'aox', 'Aqoxy5G03746' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3RQ047' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C7GMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9C8JER' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MBL6KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YXCZ83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZANX40' => 'arhy', 'AT1G12990' => 'ath', 'AT1G67880' => 'ath', 'AT2G13290' => 'ath', 'AT3G01620' => 'ath', 'AT3G26445' => 'ath', 'AT3G27540' => 'ath', 'AT5G14480' => 'ath', 'ATR0824G026' => 'atr', 'ATR1098G019' => 'atr', 'Atru.chr11.2145' => 'acertr', 'Atru.chr2.3636' => 'acertr', 'Atru.chr2.3644' => 'acertr', 'Atru.chr6.2422' => 'acertr', 'Atru.chr7.1112' => 'acertr', 'AUR62005469' => 'cqu', 'AUR62011166' => 'cqu', 'AUR62013319' => 'cqu', 'AUR62024273' => 'cqu', 'AUR62028420' => 'cqu', 'AUR62041942' => 'cqu', 'BcaB01g04969' => 'bca', 'BcaB01g06371' => 'bca', 'BcaB02g11494' => 'bca', 'BcaB03g15382' => 'bca', 'BcaB08g36994' => 'bca', 'BcaC03g13477' => 'bca', 'BcaC03g13478' => 'bca', 'BcaC03g13480' => 'bca', 'BcaC03g13481' => 'bca', 'BcaC03g13486' => 'bca', 'BcaC04g19031' => 'bca', 'BcaC04g23085' => 'bca', 'BcaC05g25094' => 'bca', 'BcaC05g25096' => 'bca', 'BcaC05g25138' => 'bca', 'BcaC05g30416' => 'bca', 'BcaC05g30455' => 'bca', 'BcaC06g30979' => 'bca', 'BcaC06g33805' => 'bca', 'BcaC08g46021' => 'bca', 'BcaNung03154' => 'bca', 'BolC2t06623H' => 'bol', 'BolC2t06632H' => 'bol', 'BolC2t06635H' => 'bol', 'BolC2t06638H' => 'bol', 'BolC3t13266H' => 'bol', 'BolC5t29776H' => 'bol', 'BolC6t38912H' => 'bol', 'BolC7t44183H' => 'bol', 'BolC9t54123H' => 'bol', 'BolC9t59107H' => 'bol', 'BraA02t05221Z' => 'bra', 'BraA03t09996Z' => 'bra', 'BraA05t23210Z' => 'bra', 'BraA06t24068Z' => 'bra', 'BraA06t27032Z' => 'bra', 'BraA08t35176Z' => 'bra', 'BraA09t36680Z' => 'bra', 'BraA10t44471Z' => 'bra', 'C02p06760' => 'bna', 'C02p06890' => 'bna', 'C02p07010' => 'bna', 'C03p07660' => 'bna', 'C05p10300' => 'bna', 'C06p38150' => 'bna', 'C07p36650' => 'bna', 'C08p15770' => 'bna', 'C09p12300' => 'bna', 'C09p62700' => 'bna', 'C09p75040' => 'bna', 'CAN.G13.1' => 'can', 'CAN.G138.4' => 'can', 'CAN.G44.6' => 'can', 'CAN.G473.19' => 'can', 'CANSAT01G0835' => 'cansat', 'CANSAT11G0246' => 'cansat', 'CANSAT11G1766' => 'cansat', 'CANSAT64G1954' => 'cansat', 'CARHR013330' => 'chi', 'CARHR060530' => 'chi', 'CARHR075300' => 'chi', 'CARHR105120' => 'chi', 'CARHR148910' => 'chi', 'CARHR198830' => 'chi', 'Carub.0001s1275' => 'cru', 'Carub.0002s1437' => 'cru', 'Carub.0003s0044' => 'cru', 'Carub.0003s2787' => 'cru', 'Carub.0005s0597' => 'cru', 'Carub.0006s1266' => 'cru', 'Ca_06935_v3' => 'car', 'Ca_13559_v3' => 'car', 'Ca_16941_v3' => 'car', 'Ca_16960_v3' => 'car', 'Ca_17775_v3' => 'car', 'Ca_30464_v3' => 'car', 'Cc06_g08160' => 'ccan', 'Cc07_g01520' => 'ccan', 'Cc11_g15810' => 'ccan', 'CDE02G2840' => 'cde', 'CDE03G0093' => 'cde', 'CDE04G2127' => 'cde', 'CDE07G1857' => 'cde', 'CDE09G1246' => 'cde', 'Cfa003412' => 'cfa', 'Cfa007341' => 'cfa', 'Cfa009220' => 'cfa', 'Ciclev10008737m.g' => 'ccl', 'Ciclev10015565m.g' => 'ccl', 'Ciclev10031761m.g' => 'ccl', 'CiPaw.03G045300' => 'cil', 'CiPaw.03G247200' => 'cil', 'CiPaw.04G029500' => 'cil', 'CiPaw.04G174000' => 'cil', 'CiPaw.05G181200' => 'cil', 'CiPaw.06G067100' => 'cil', 'ClCG05G025800' => 'cla', 'ClCG06G011400' => 'cla', 'ClCG09G019360' => 'cla', 'COL.COLO4_04827' => 'col', 'COL.COLO4_29170' => 'col', 'COL.COLO4_35131' => 'col', 'COL.COLO4_35132' => 'col', 'Cpa.g.sc33.32' => 'cpa', 'Cpa.g.sc46.29' => 'cpa', 'Cpa.g.sc796.1' => 'cpa', 'CsaV3_1G030420' => 'csa', 'CsaV3_5G027050' => 'csa', 'CsaV3_5G031040' => 'csa', 'CsaV3_UNG023130' => 'csa', 'CSS0007726' => 'camsi', 'CSS0016433' => 'camsi', 'CSS0017656' => 'camsi', 'CSS0025364' => 'camsi', 'CSS0027582' => 'camsi', 'CSS0047288' => 'camsi', 'CSS0049950' => 'camsi', 'DCAR_003843' => 'dca', 'DCAR_007052' => 'dca', 'DCAR_020884' => 'dca', 'DCAR_021730' => 'dca', 'DCAR_024423' => 'dca', 'DCAR_026509' => 'dca', 'DCAR_031158' => 'dca', 'Dinv14728' => 'din', 'Dinv15219' => 'din', 'Dinv25728' => 'din', 'Dinv33428' => 'din', 'Dinv36489' => 'din', 'Dinv41486' => 'din', 'Duzib147G0469' => 'dzi', 'Duzib168G0060' => 'dzi', 'Duzib187G1215' => 'dzi', 'Duzib248G0692' => 'dzi', 'Duzib251G0767' => 'dzi', 'Duzib264G0446' => 'dzi', 'Duzib268G0691' => 'dzi', 'ECA232G4767' => 'eca', 'ECA233G2838' => 'eca', 'ECA234G0391' => 'eca', 'ECA234G0857' => 'eca', 'ECA236G1593' => 'eca', 'ECA238G0565' => 'eca', 'ECA246G1027' => 'eca', 'ECA246G3223' => 'eca', 'ECA246G3470' => 'eca', 'EL10Ac6g13829' => 'bvu', 'EL10Ac6g14093' => 'bvu', 'EL10Ac8g18707' => 'bvu', 'Eucgr.C01369' => 'egr', 'Eucgr.H02492' => 'egr', 'Eucgr.I01733' => 'egr', 'Eucgr.J02255' => 'egr', 'Eucgr.J02257' => 'egr', 'Eucgr.J02258' => 'egr', 'FAN02G1601' => 'fan', 'FAN03G1586' => 'fan', 'FAN03G2986' => 'fan', 'FAN05G4837' => 'fan', 'FAN06G0146' => 'fan', 'FAN07G0858' => 'fan', 'FAN09G3179' => 'fan', 'FAN10G0669' => 'fan', 'FAN12G2358' => 'fan', 'FAN14G4198' => 'fan', 'FAN14G5112' => 'fan', 'FAN17G0342' => 'fan', 'FAN19G0342' => 'fan', 'FAN19G0962' => 'fan', 'FAN19G1101' => 'fan', 'FAN19G1872' => 'fan', 'FAN22G0356' => 'fan', 'FAN23G0744' => 'fan', 'FAN23G1914' => 'fan', 'FAN26G0032' => 'fan', 'FAN28G0625' => 'fan', 'FvH4_1g02710' => 'fve', 'FvH4_1g02720' => 'fve', 'FvH4_4g25670' => 'fve', 'FvH4_6g51700' => 'fve', 'FvH4_7g20170' => 'fve', 'Glyma.05G175000' => 'gma', 'Glyma.08G132300' => 'gma', 'Glyma.11G243000' => 'gma', 'Glyma.13G158900' => 'gma', 'Glyma.17G112400' => 'gma', 'Glyma.18G014100' => 'gma', 'Glyma.19G003100' => 'gma', 'Glyma.19G056500' => 'gma', 'Gohir.A01G158900' => 'ghi', 'Gohir.A05G312600' => 'ghi', 'Gohir.A05G354900' => 'ghi', 'Gohir.A07G037200' => 'ghi', 'Gohir.A09G030000' => 'ghi', 'Gohir.A12G145200' => 'ghi', 'Gohir.D01G151500' => 'ghi', 'Gohir.D04G058300' => 'ghi', 'Gohir.D05G314100' => 'ghi', 'Gohir.D07G041400' => 'ghi', 'Gohir.D09G029700' => 'ghi', 'Gohir.D12G149700' => 'ghi', 'Gorai.001G043800' => 'gra', 'Gorai.002G187800' => 'gra', 'Gorai.006G034700' => 'gra', 'Gorai.008G161200' => 'gra', 'Gorai.009G335700' => 'gra', 'Gorai.012G065000' => 'gra', 'GSVIVG01000535001' => 'vvi', 'GSVIVG01015572001' => 'vvi', 'GSVIVG01032386001' => 'vvi', 'HanXRQChr05g0138531' => 'han', 'HanXRQChr06g0174391' => 'han', 'HanXRQChr07g0199021' => 'han', 'HanXRQChr08g0208211' => 'han', 'HanXRQChr09g0255471' => 'han', 'HanXRQChr10g0315791' => 'han', 'HanXRQChr12g0371991' => 'han', 'HanXRQChr15g0475251' => 'han', 'HanXRQChr17g0540001' => 'han', 'HanXRQChr17g0548631' => 'han', 'HanXRQChr17g0569561' => 'han', 'Haze_12256' => 'cav', 'Haze_14756' => 'cav', 'Haze_25528' => 'cav', 'Hma1.2p1_0079F.1_g041020' => 'hma', 'Hma1.2p1_0818F.1_g223260' => 'hma', 'Hma1.2p1_1747F.1_g300530' => 'hma', 'HPP92_004607' => 'vpl', 'HPP92_004608' => 'vpl', 'HPP92_006181' => 'vpl', 'HPP92_012192' => 'vpl', 'HPP92_015680' => 'vpl', 'HPP92_020249' => 'vpl', 'HPP92_021376' => 'vpl', 'HPP92_024275' => 'vpl', 'Hund06031' => 'sun', 'Hund25391' => 'sun', 'Lalb_Chr07g0185371' => 'lal', 'Lalb_Chr07g0185381' => 'lal', 'Lalb_Chr12g0204011' => 'lal', 'Lalb_Chr13g0301671' => 'lal', 'Lalb_Chr14g0362851' => 'lal', 'Lalb_Chr24g0403581' => 'lal', 'Lj1g0000233' => 'lja', 'Lj2g0018120' => 'lja', 'Lj3C621T0' => 'lonja', 'Lj3P1059T14' => 'lonja', 'Lj3P611T9' => 'lonja', 'Lj3P614T13' => 'lonja', 'Lj3P615T5' => 'lonja', 'Lj4g0012315' => 'lja', 'Lj4g0026182' => 'lja', 'Lj6P813T16' => 'lonja', 'Lj7C427T7' => 'lonja', 'Lj7C427T8' => 'lonja', 'Lj7P600T41' => 'lonja', 'Lju41C42G17' => 'lonja', 'Lsat_1_v5_gn_0_47300' => 'lsa', 'Lsat_1_v5_gn_2_91280' => 'lsa', 'Lsat_1_v5_gn_3_30561' => 'lsa', 'Lsat_1_v5_gn_4_184321' => 'lsa', 'Lsat_1_v5_gn_4_4041' => 'lsa', 'Lsat_1_v5_gn_5_92000' => 'lsa', 'Lsat_1_v5_gn_8_152940' => 'lsa', 'Lsat_1_v5_gn_8_62401' => 'lsa', 'Manes.06G055900' => 'mes', 'Manes.12G022200' => 'mes', 'Manes.13G023300' => 'mes', 'Manes.14G115000' => 'mes', 'Manes.15G151700' => 'mes', 'Manes.17G111300' => 'mes', 'Mapoly0226s0009' => 'mpo', 'MBI02_g25363_MAGBIO' => 'mbi', 'MBI06_g00027_MAGBIO' => 'mbi', 'MBI10_g13034_MAGBIO' => 'mbi', 'MD09G1023400' => 'mdo', 'MD13G1100100' => 'mdo', 'MD15G1169200' => 'mdo', 'MD16G1101100' => 'mdo', 'MD17G1022900' => 'mdo', 'Medtr3g096150' => 'mtr', 'Medtr4g115070' => 'mtr', 'Medtr7g033325' => 'mtr', 'Medtr8g089840' => 'mtr', 'MELO3C010319.2' => 'cme', 'MELO3C011944.2' => 'cme', 'MELO3C021589.2' => 'cme', 'Migut.E00207' => 'egut', 'Migut.H00067' => 'egut', 'Migut.K00433' => 'egut', 'Migut.K00606' => 'egut', 'Migut.K01410' => 'egut', 'MSTRG.13347' => 'ama', 'MSTRG.24045' => 'ama', 'MSTRG.2428' => 'ama', 'MSTRG.26410' => 'ama', 'MSTRG.3139' => 'ama', 'MSTRG.3286' => 'ama', 'MSTRG.563' => 'ama', 'MSTRG.7941' => 'ama', 'Nitab4.5_0000028g0060' => 'nta', 'Nitab4.5_0000065g0260' => 'nta', 'Nitab4.5_0000112g0060' => 'nta', 'Nitab4.5_0000489g0120' => 'nta', 'Nitab4.5_0001776g0050' => 'nta', 'Nitab4.5_0001854g0010' => 'nta', 'Nitab4.5_0001860g0020' => 'nta', 'Nitab4.5_0004352g0010' => 'nta', 'Nitab4.5_0008716g0020' => 'nta', 'Nitab4.5_0008922g0010' => 'nta', 'Nn3g16693' => 'nnu', 'Nn4g22596' => 'nnu', 'Nn7g37639' => 'nnu', 'Oeu001701.1' => 'oeu', 'Oeu018149.1' => 'oeu', 'Oeu026220.1' => 'oeu', 'Oeu038635.1' => 'oeu', 'Oeu049176.1' => 'oeu', 'Oeu056706.1' => 'oeu', 'Oeu056937.1' => 'oeu', 'Oeu057540.1' => 'oeu', 'Os02g0594900' => 'osa', 'Os02g0595100' => 'osa', 'Os04g0477500' => 'osa', 'Os12g0611900' => 'osa', 'Peaxi162Scf00076g00020' => 'pax', 'Peaxi162Scf00128g00217' => 'pax', 'Peaxi162Scf00129g01640' => 'pax', 'Peaxi162Scf00669g00007' => 'pax', 'Peaxi162Scf00700g00421' => 'pax', 'Peaxi162Scf00801g00038' => 'pax', 'Peaxi162Scf00891g00025' => 'pax', 'PGR083G0909' => 'pgr', 'PGR119G1005' => 'pgr', 'PGR142G2236' => 'pgr', 'PGR142G3388' => 'pgr', 'PGSC0003DMG400004514' => 'stu', 'PGSC0003DMG400012635' => 'stu', 'PGSC0003DMG400015730' => 'stu', 'PGSC0003DMG400018611' => 'stu', 'PGSC0003DMG400030897' => 'stu', 'Phvul.001G254800' => 'pvu', 'Phvul.002G260100' => 'pvu', 'Phvul.003G167600' => 'pvu', 'Phvul.004G005100' => 'pvu', 'Potri.001G343600' => 'ptr', 'Potri.006G066700' => 'ptr', 'Potri.008G186000' => 'ptr', 'Potri.010G046900' => 'ptr', 'Potri.018G127900' => 'ptr', 'Pp3c20_17750' => 'ppa', 'Pp3c24_4380' => 'ppa', 'Prupe.1G245800' => 'ppe', 'Prupe.3G293400' => 'ppe', 'Prupe.7G247400' => 'ppe', 'Psat0s145g0120' => 'psa', 'Psat0s595g0040' => 'psa', 'Psat0s595g0120' => 'psa', 'Psat3g175040' => 'psa', 'Psat7g058120' => 'psa', 'PSO017G0428' => 'pso', 'PSO063G7510' => 'pso', 'PSO067G0046' => 'pso', 'PSO478G1073' => 'pso', 'PSO675G3677' => 'pso', 'PSO675G6558' => 'pso', 'PSO675G7520' => 'pso', 'PSO675G8959' => 'pso', 'QL02p074089' => 'qlo', 'QL02p089614' => 'qlo', 'QL03p057736' => 'qlo', 'RcHm_v2.0_Chr1g0364131' => 'rch', 'RcHm_v2.0_Chr2g0087801' => 'rch', 'RcHm_v2.0_Chr2g0087821' => 'rch', 'RcHm_v2.0_Chr2g0173231' => 'rch', 'RcHm_v2.0_Chr4g0433111' => 'rch', 'Rhsim03G0250300' => 'rsi', 'Rhsim08G0048400' => 'rsi', 'Rhsim10G0014800' => 'rsi', 'Rhsim12G0040100' => 'rsi', 'Rhsim12G0109700' => 'rsi', 'Sabra06G0049600' => 'sbr', 'Sabra08G0141000' => 'sbr', 'Sabra10G0021400' => 'sbr', 'Sabra16G0222900' => 'sbr', 'Sabra18G0108600' => 'sbr', 'SalBow1G0433' => 'sbo', 'SalBow1G2038' => 'sbo', 'SalBow1G5003' => 'sbo', 'SalBow7G1197' => 'sbo', 'SalBow8G3506' => 'sbo', 'Sc03g0007300' => 'sci', 'Sc11g0000950' => 'sci', 'Sc14g0008750' => 'sci', 'Sc18g0000420' => 'sci', 'Sed0006754' => 'sed', 'Sed0008741' => 'sed', 'Sed0017172' => 'sed', 'Sed0018925' => 'sed', 'Sed0023326' => 'sed', 'Sed0025909' => 'sed', 'SEGI_05333' => 'sgi', 'SEGI_10362' => 'sgi', 'SEGI_13380' => 'sgi', 'SEGI_24306' => 'sgi', 'SEGI_29077' => 'sgi', 'SEGI_29095' => 'sgi', 'SEGI_36534' => 'sgi', 'SEGI_37506' => 'sgi', 'SEGI_38321' => 'sgi', 'SGA_v2.0_scaffold307G48031' => 'sas', 'SGA_v2.0_scaffold47G17507' => 'sas', 'SGA_v2.0_scaffold63G21736' => 'sas', 'SGA_v2.0_scaffold87G27070' => 'sas', 'SHI17794' => 'shi', 'SHI28851' => 'shi', 'SMO165G0155' => 'smo', 'SMO340G0217' => 'smo', 'SMO367G1210' => 'smo', 'Solyc02g093430.3' => 'sly', 'Solyc05g013580.4' => 'sly', 'Solyc07g008030.3' => 'sly', 'Solyc12g035470.2' => 'sly', 'Sopen02g038020' => 'spe', 'Sopen05g008490' => 'spe', 'Sopen07g003910' => 'spe', 'Sopen12g015240' => 'spe', 'Sp1g11550' => 'spa', 'Sp2g16710' => 'spa', 'Sp3g00430' => 'spa', 'Sp3g26780' => 'spa', 'Sp5g22900' => 'spa', 'Sp6g29530' => 'spa', 'TAR371G0794' => 'tar', 'TAR374G0164' => 'tar', 'TAR622G0165' => 'tar', 'TAR626G0929' => 'tar', 'TAR629G2155' => 'tar', 'THA.LOC104805282' => 'tha', 'THA.LOC104805363' => 'tha', 'THA.LOC104808968' => 'tha', 'THA.LOC104821093' => 'tha', 'THA.LOC104823953' => 'tha', 'THA.LOC104825562' => 'tha', 'THA.LOC104825665' => 'tha', 'Thecc.02G261400' => 'tca', 'Thecc.04G019200' => 'tca', 'Thecc.09G130400' => 'tca', 'Thhalv10004374m.g' => 'esa', 'Thhalv10007850m.g' => 'esa', 'Thhalv10013782m.g' => 'esa', 'Thhalv10018686m.g' => 'esa', 'Thhalv10020899m.g' => 'esa', 'Thhalv10022755m.g' => 'esa', 'TPR.G23851' => 'tpr', 'TPR.G26500' => 'tpr', 'TPR.G27267' => 'tpr', 'TPR.G32001' => 'tpr', 'TPR.G6251' => 'tpr', 'TPR.G8167' => 'tpr', 'TWI12G1330' => 'twi', 'TWI18G1239' => 'twi', 'TWI34G0979' => 'twi', 'TWI36G0670' => 'twi', 'TWI36G0707' => 'twi', 'TWI56G0233' => 'twi', 'TWI75G1809' => 'twi', 'unitig_21.g20874' => 'ugi', 'unitig_26.g10343' => 'ugi', 'unitig_46.g18392' => 'ugi', 'unitig_52.g17178' => 'ugi', 'unitig_8.g2934' => 'ugi', 'vmacro01122' => 'vma', 'vmacro05875' => 'vma', 'vmacro06147' => 'vma', 'vmacro16191' => 'vma', 'vmacro18293' => 'vma', 'VMungo0251G3707' => 'vmu', 'VMungo0464G1521' => 'vmu', 'VMungo1215G0205' => 'vmu', 'VMungo1383G2484' => 'vmu', 'Zm00001eb079610' => 'zma', 'Zm00001eb135990' => 'zma', 'Zm00001eb183710' => 'zma', 'Zm00001eb246020' => 'zma' ), 'gf_id' => 'HOM05D001124', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001124' ), 'data_identifier' => 'HOM05D001124', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001124', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '548', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02520' => 'bna', 'A03p06630' => 'bna', 'A05p44460' => 'bna', 'A06p08710' => 'bna', 'A06p41090' => 'bna', 'A07p32320' => 'bna', 'A08p32520' => 'bna', 'A09p10360' => 'bna', 'A10p24080' => 'bna', 'Aa31LG11G15250' => 'aar', 'Aa31LG1G1800' => 'aar', 'Aa31LG2G5120' => 'aar', 'Aa31LG2G6070' => 'aar', 'Aa31LG5G10770' => 'aar', 'Aa31sc61G90' => 'aar', 'Actinidia01352' => 'ach', 'Actinidia05983' => 'ach', 'Actinidia08133' => 'ach', 'Actinidia15101' => 'ach', 'Actinidia26379' => 'ach', 'Actinidia35778' => 'ach', 'Actinidia36123' => 'ach', 'Actinidia37436' => 'ach', 'Actinidia38730' => 'ach', 'Ah.02g128210' => 'amhyb', 'Ah.03g132990' => 'amhyb', 'Ah.14g079410' => 'amhyb', 'AL1G24640' => 'aly', 'AL2G26680' => 'aly', 'AL3G10530' => 'aly', 'AL3G45230' => 'aly', 'AL5G15230' => 'aly', 'AL5G16960' => 'aly', 'AL6G25210' => 'aly', 'Aqoxy2G00441' => 'aox', 'Aqoxy3G01236' => 'aox', 'Aqoxy5G03746' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3RQ047' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C7GMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9C8JER' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MBL6KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YXCZ83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZANX40' => 'arhy', 'AT1G12990' => 'ath', 'AT1G67880' => 'ath', 'AT2G13290' => 'ath', 'AT3G01620' => 'ath', 'AT3G26445' => 'ath', 'AT3G27540' => 'ath', 'AT5G14480' => 'ath', 'ATR0824G026' => 'atr', 'ATR1098G019' => 'atr', 'Atru.chr11.2145' => 'acertr', 'Atru.chr2.3636' => 'acertr', 'Atru.chr2.3644' => 'acertr', 'Atru.chr6.2422' => 'acertr', 'Atru.chr7.1112' => 'acertr', 'AUR62005469' => 'cqu', 'AUR62011166' => 'cqu', 'AUR62013319' => 'cqu', 'AUR62024273' => 'cqu', 'AUR62028420' => 'cqu', 'AUR62041942' => 'cqu', 'BcaB01g04969' => 'bca', 'BcaB01g06371' => 'bca', 'BcaB02g11494' => 'bca', 'BcaB03g15382' => 'bca', 'BcaB08g36994' => 'bca', 'BcaC03g13477' => 'bca', 'BcaC03g13478' => 'bca', 'BcaC03g13480' => 'bca', 'BcaC03g13481' => 'bca', 'BcaC03g13486' => 'bca', 'BcaC04g19031' => 'bca', 'BcaC04g23085' => 'bca', 'BcaC05g25094' => 'bca', 'BcaC05g25096' => 'bca', 'BcaC05g25138' => 'bca', 'BcaC05g30416' => 'bca', 'BcaC05g30455' => 'bca', 'BcaC06g30979' => 'bca', 'BcaC06g33805' => 'bca', 'BcaC08g46021' => 'bca', 'BcaNung03154' => 'bca', 'BolC2t06623H' => 'bol', 'BolC2t06632H' => 'bol', 'BolC2t06635H' => 'bol', 'BolC2t06638H' => 'bol', 'BolC3t13266H' => 'bol', 'BolC5t29776H' => 'bol', 'BolC6t38912H' => 'bol', 'BolC7t44183H' => 'bol', 'BolC9t54123H' => 'bol', 'BolC9t59107H' => 'bol', 'BraA02t05221Z' => 'bra', 'BraA03t09996Z' => 'bra', 'BraA05t23210Z' => 'bra', 'BraA06t24068Z' => 'bra', 'BraA06t27032Z' => 'bra', 'BraA08t35176Z' => 'bra', 'BraA09t36680Z' => 'bra', 'BraA10t44471Z' => 'bra', 'C02p06760' => 'bna', 'C02p06890' => 'bna', 'C02p07010' => 'bna', 'C03p07660' => 'bna', 'C05p10300' => 'bna', 'C06p38150' => 'bna', 'C07p36650' => 'bna', 'C08p15770' => 'bna', 'C09p12300' => 'bna', 'C09p62700' => 'bna', 'C09p75040' => 'bna', 'CAN.G13.1' => 'can', 'CAN.G138.4' => 'can', 'CAN.G44.6' => 'can', 'CAN.G473.19' => 'can', 'CANSAT01G0835' => 'cansat', 'CANSAT11G0246' => 'cansat', 'CANSAT11G1766' => 'cansat', 'CANSAT64G1954' => 'cansat', 'CARHR013330' => 'chi', 'CARHR060530' => 'chi', 'CARHR075300' => 'chi', 'CARHR105120' => 'chi', 'CARHR148910' => 'chi', 'CARHR198830' => 'chi', 'Carub.0001s1275' => 'cru', 'Carub.0002s1437' => 'cru', 'Carub.0003s0044' => 'cru', 'Carub.0003s2787' => 'cru', 'Carub.0005s0597' => 'cru', 'Carub.0006s1266' => 'cru', 'Ca_06935_v3' => 'car', 'Ca_13559_v3' => 'car', 'Ca_16941_v3' => 'car', 'Ca_16960_v3' => 'car', 'Ca_17775_v3' => 'car', 'Ca_30464_v3' => 'car', 'Cc06_g08160' => 'ccan', 'Cc07_g01520' => 'ccan', 'Cc11_g15810' => 'ccan', 'CDE02G2840' => 'cde', 'CDE03G0093' => 'cde', 'CDE04G2127' => 'cde', 'CDE07G1857' => 'cde', 'CDE09G1246' => 'cde', 'Cfa003412' => 'cfa', 'Cfa007341' => 'cfa', 'Cfa009220' => 'cfa', 'Ciclev10008737m.g' => 'ccl', 'Ciclev10015565m.g' => 'ccl', 'Ciclev10031761m.g' => 'ccl', 'CiPaw.03G045300' => 'cil', 'CiPaw.03G247200' => 'cil', 'CiPaw.04G029500' => 'cil', 'CiPaw.04G174000' => 'cil', 'CiPaw.05G181200' => 'cil', 'CiPaw.06G067100' => 'cil', 'ClCG05G025800' => 'cla', 'ClCG06G011400' => 'cla', 'ClCG09G019360' => 'cla', 'COL.COLO4_04827' => 'col', 'COL.COLO4_29170' => 'col', 'COL.COLO4_35131' => 'col', 'COL.COLO4_35132' => 'col', 'Cpa.g.sc33.32' => 'cpa', 'Cpa.g.sc46.29' => 'cpa', 'Cpa.g.sc796.1' => 'cpa', 'CsaV3_1G030420' => 'csa', 'CsaV3_5G027050' => 'csa', 'CsaV3_5G031040' => 'csa', 'CsaV3_UNG023130' => 'csa', 'CSS0007726' => 'camsi', 'CSS0016433' => 'camsi', 'CSS0017656' => 'camsi', 'CSS0025364' => 'camsi', 'CSS0027582' => 'camsi', 'CSS0047288' => 'camsi', 'CSS0049950' => 'camsi', 'DCAR_003843' => 'dca', 'DCAR_007052' => 'dca', 'DCAR_020884' => 'dca', 'DCAR_021730' => 'dca', 'DCAR_024423' => 'dca', 'DCAR_026509' => 'dca', 'DCAR_031158' => 'dca', 'Dinv14728' => 'din', 'Dinv15219' => 'din', 'Dinv25728' => 'din', 'Dinv33428' => 'din', 'Dinv36489' => 'din', 'Dinv41486' => 'din', 'Duzib147G0469' => 'dzi', 'Duzib168G0060' => 'dzi', 'Duzib187G1215' => 'dzi', 'Duzib248G0692' => 'dzi', 'Duzib251G0767' => 'dzi', 'Duzib264G0446' => 'dzi', 'Duzib268G0691' => 'dzi', 'ECA232G4767' => 'eca', 'ECA233G2838' => 'eca', 'ECA234G0391' => 'eca', 'ECA234G0857' => 'eca', 'ECA236G1593' => 'eca', 'ECA238G0565' => 'eca', 'ECA246G1027' => 'eca', 'ECA246G3223' => 'eca', 'ECA246G3470' => 'eca', 'EL10Ac6g13829' => 'bvu', 'EL10Ac6g14093' => 'bvu', 'EL10Ac8g18707' => 'bvu', 'Eucgr.C01369' => 'egr', 'Eucgr.H02492' => 'egr', 'Eucgr.I01733' => 'egr', 'Eucgr.J02255' => 'egr', 'Eucgr.J02257' => 'egr', 'Eucgr.J02258' => 'egr', 'FAN02G1601' => 'fan', 'FAN03G1586' => 'fan', 'FAN03G2986' => 'fan', 'FAN05G4837' => 'fan', 'FAN06G0146' => 'fan', 'FAN07G0858' => 'fan', 'FAN09G3179' => 'fan', 'FAN10G0669' => 'fan', 'FAN12G2358' => 'fan', 'FAN14G4198' => 'fan', 'FAN14G5112' => 'fan', 'FAN17G0342' => 'fan', 'FAN19G0342' => 'fan', 'FAN19G0962' => 'fan', 'FAN19G1101' => 'fan', 'FAN19G1872' => 'fan', 'FAN22G0356' => 'fan', 'FAN23G0744' => 'fan', 'FAN23G1914' => 'fan', 'FAN26G0032' => 'fan', 'FAN28G0625' => 'fan', 'FvH4_1g02710' => 'fve', 'FvH4_1g02720' => 'fve', 'FvH4_4g25670' => 'fve', 'FvH4_6g51700' => 'fve', 'FvH4_7g20170' => 'fve', 'Glyma.05G175000' => 'gma', 'Glyma.08G132300' => 'gma', 'Glyma.11G243000' => 'gma', 'Glyma.13G158900' => 'gma', 'Glyma.17G112400' => 'gma', 'Glyma.18G014100' => 'gma', 'Glyma.19G003100' => 'gma', 'Glyma.19G056500' => 'gma', 'Gohir.A01G158900' => 'ghi', 'Gohir.A05G312600' => 'ghi', 'Gohir.A05G354900' => 'ghi', 'Gohir.A07G037200' => 'ghi', 'Gohir.A09G030000' => 'ghi', 'Gohir.A12G145200' => 'ghi', 'Gohir.D01G151500' => 'ghi', 'Gohir.D04G058300' => 'ghi', 'Gohir.D05G314100' => 'ghi', 'Gohir.D07G041400' => 'ghi', 'Gohir.D09G029700' => 'ghi', 'Gohir.D12G149700' => 'ghi', 'Gorai.001G043800' => 'gra', 'Gorai.002G187800' => 'gra', 'Gorai.006G034700' => 'gra', 'Gorai.008G161200' => 'gra', 'Gorai.009G335700' => 'gra', 'Gorai.012G065000' => 'gra', 'GSVIVG01000535001' => 'vvi', 'GSVIVG01015572001' => 'vvi', 'GSVIVG01032386001' => 'vvi', 'HanXRQChr05g0138531' => 'han', 'HanXRQChr06g0174391' => 'han', 'HanXRQChr07g0199021' => 'han', 'HanXRQChr08g0208211' => 'han', 'HanXRQChr09g0255471' => 'han', 'HanXRQChr10g0315791' => 'han', 'HanXRQChr12g0371991' => 'han', 'HanXRQChr15g0475251' => 'han', 'HanXRQChr17g0540001' => 'han', 'HanXRQChr17g0548631' => 'han', 'HanXRQChr17g0569561' => 'han', 'Haze_12256' => 'cav', 'Haze_14756' => 'cav', 'Haze_25528' => 'cav', 'Hma1.2p1_0079F.1_g041020' => 'hma', 'Hma1.2p1_0818F.1_g223260' => 'hma', 'Hma1.2p1_1747F.1_g300530' => 'hma', 'HPP92_004607' => 'vpl', 'HPP92_004608' => 'vpl', 'HPP92_006181' => 'vpl', 'HPP92_012192' => 'vpl', 'HPP92_015680' => 'vpl', 'HPP92_020249' => 'vpl', 'HPP92_021376' => 'vpl', 'HPP92_024275' => 'vpl', 'Hund06031' => 'sun', 'Hund25391' => 'sun', 'Lalb_Chr07g0185371' => 'lal', 'Lalb_Chr07g0185381' => 'lal', 'Lalb_Chr12g0204011' => 'lal', 'Lalb_Chr13g0301671' => 'lal', 'Lalb_Chr14g0362851' => 'lal', 'Lalb_Chr24g0403581' => 'lal', 'Lj1g0000233' => 'lja', 'Lj2g0018120' => 'lja', 'Lj3C621T0' => 'lonja', 'Lj3P1059T14' => 'lonja', 'Lj3P611T9' => 'lonja', 'Lj3P614T13' => 'lonja', 'Lj3P615T5' => 'lonja', 'Lj4g0012315' => 'lja', 'Lj4g0026182' => 'lja', 'Lj6P813T16' => 'lonja', 'Lj7C427T7' => 'lonja', 'Lj7C427T8' => 'lonja', 'Lj7P600T41' => 'lonja', 'Lju41C42G17' => 'lonja', 'Lsat_1_v5_gn_0_47300' => 'lsa', 'Lsat_1_v5_gn_2_91280' => 'lsa', 'Lsat_1_v5_gn_3_30561' => 'lsa', 'Lsat_1_v5_gn_4_184321' => 'lsa', 'Lsat_1_v5_gn_4_4041' => 'lsa', 'Lsat_1_v5_gn_5_92000' => 'lsa', 'Lsat_1_v5_gn_8_152940' => 'lsa', 'Lsat_1_v5_gn_8_62401' => 'lsa', 'Manes.06G055900' => 'mes', 'Manes.12G022200' => 'mes', 'Manes.13G023300' => 'mes', 'Manes.14G115000' => 'mes', 'Manes.15G151700' => 'mes', 'Manes.17G111300' => 'mes', 'Mapoly0226s0009' => 'mpo', 'MBI02_g25363_MAGBIO' => 'mbi', 'MBI06_g00027_MAGBIO' => 'mbi', 'MBI10_g13034_MAGBIO' => 'mbi', 'MD09G1023400' => 'mdo', 'MD13G1100100' => 'mdo', 'MD15G1169200' => 'mdo', 'MD16G1101100' => 'mdo', 'MD17G1022900' => 'mdo', 'Medtr3g096150' => 'mtr', 'Medtr4g115070' => 'mtr', 'Medtr7g033325' => 'mtr', 'Medtr8g089840' => 'mtr', 'MELO3C010319.2' => 'cme', 'MELO3C011944.2' => 'cme', 'MELO3C021589.2' => 'cme', 'Migut.E00207' => 'egut', 'Migut.H00067' => 'egut', 'Migut.K00433' => 'egut', 'Migut.K00606' => 'egut', 'Migut.K01410' => 'egut', 'MSTRG.13347' => 'ama', 'MSTRG.24045' => 'ama', 'MSTRG.2428' => 'ama', 'MSTRG.26410' => 'ama', 'MSTRG.3139' => 'ama', 'MSTRG.3286' => 'ama', 'MSTRG.563' => 'ama', 'MSTRG.7941' => 'ama', 'Nitab4.5_0000028g0060' => 'nta', 'Nitab4.5_0000065g0260' => 'nta', 'Nitab4.5_0000112g0060' => 'nta', 'Nitab4.5_0000489g0120' => 'nta', 'Nitab4.5_0001776g0050' => 'nta', 'Nitab4.5_0001854g0010' => 'nta', 'Nitab4.5_0001860g0020' => 'nta', 'Nitab4.5_0004352g0010' => 'nta', 'Nitab4.5_0008716g0020' => 'nta', 'Nitab4.5_0008922g0010' => 'nta', 'Nn3g16693' => 'nnu', 'Nn4g22596' => 'nnu', 'Nn7g37639' => 'nnu', 'Oeu001701.1' => 'oeu', 'Oeu018149.1' => 'oeu', 'Oeu026220.1' => 'oeu', 'Oeu038635.1' => 'oeu', 'Oeu049176.1' => 'oeu', 'Oeu056706.1' => 'oeu', 'Oeu056937.1' => 'oeu', 'Oeu057540.1' => 'oeu', 'Os02g0594900' => 'osa', 'Os02g0595100' => 'osa', 'Os04g0477500' => 'osa', 'Os12g0611900' => 'osa', 'Peaxi162Scf00076g00020' => 'pax', 'Peaxi162Scf00128g00217' => 'pax', 'Peaxi162Scf00129g01640' => 'pax', 'Peaxi162Scf00669g00007' => 'pax', 'Peaxi162Scf00700g00421' => 'pax', 'Peaxi162Scf00801g00038' => 'pax', 'Peaxi162Scf00891g00025' => 'pax', 'PGR083G0909' => 'pgr', 'PGR119G1005' => 'pgr', 'PGR142G2236' => 'pgr', 'PGR142G3388' => 'pgr', 'PGSC0003DMG400004514' => 'stu', 'PGSC0003DMG400012635' => 'stu', 'PGSC0003DMG400015730' => 'stu', 'PGSC0003DMG400018611' => 'stu', 'PGSC0003DMG400030897' => 'stu', 'Phvul.001G254800' => 'pvu', 'Phvul.002G260100' => 'pvu', 'Phvul.003G167600' => 'pvu', 'Phvul.004G005100' => 'pvu', 'Potri.001G343600' => 'ptr', 'Potri.006G066700' => 'ptr', 'Potri.008G186000' => 'ptr', 'Potri.010G046900' => 'ptr', 'Potri.018G127900' => 'ptr', 'Pp3c20_17750' => 'ppa', 'Pp3c24_4380' => 'ppa', 'Prupe.1G245800' => 'ppe', 'Prupe.3G293400' => 'ppe', 'Prupe.7G247400' => 'ppe', 'Psat0s145g0120' => 'psa', 'Psat0s595g0040' => 'psa', 'Psat0s595g0120' => 'psa', 'Psat3g175040' => 'psa', 'Psat7g058120' => 'psa', 'PSO017G0428' => 'pso', 'PSO063G7510' => 'pso', 'PSO067G0046' => 'pso', 'PSO478G1073' => 'pso', 'PSO675G3677' => 'pso', 'PSO675G6558' => 'pso', 'PSO675G7520' => 'pso', 'PSO675G8959' => 'pso', 'QL02p074089' => 'qlo', 'QL02p089614' => 'qlo', 'QL03p057736' => 'qlo', 'RcHm_v2.0_Chr1g0364131' => 'rch', 'RcHm_v2.0_Chr2g0087801' => 'rch', 'RcHm_v2.0_Chr2g0087821' => 'rch', 'RcHm_v2.0_Chr2g0173231' => 'rch', 'RcHm_v2.0_Chr4g0433111' => 'rch', 'Rhsim03G0250300' => 'rsi', 'Rhsim08G0048400' => 'rsi', 'Rhsim10G0014800' => 'rsi', 'Rhsim12G0040100' => 'rsi', 'Rhsim12G0109700' => 'rsi', 'Sabra06G0049600' => 'sbr', 'Sabra08G0141000' => 'sbr', 'Sabra10G0021400' => 'sbr', 'Sabra16G0222900' => 'sbr', 'Sabra18G0108600' => 'sbr', 'SalBow1G0433' => 'sbo', 'SalBow1G2038' => 'sbo', 'SalBow1G5003' => 'sbo', 'SalBow7G1197' => 'sbo', 'SalBow8G3506' => 'sbo', 'Sc03g0007300' => 'sci', 'Sc11g0000950' => 'sci', 'Sc14g0008750' => 'sci', 'Sc18g0000420' => 'sci', 'Sed0006754' => 'sed', 'Sed0008741' => 'sed', 'Sed0017172' => 'sed', 'Sed0018925' => 'sed', 'Sed0023326' => 'sed', 'Sed0025909' => 'sed', 'SEGI_05333' => 'sgi', 'SEGI_10362' => 'sgi', 'SEGI_13380' => 'sgi', 'SEGI_24306' => 'sgi', 'SEGI_29077' => 'sgi', 'SEGI_29095' => 'sgi', 'SEGI_36534' => 'sgi', 'SEGI_37506' => 'sgi', 'SEGI_38321' => 'sgi', 'SGA_v2.0_scaffold307G48031' => 'sas', 'SGA_v2.0_scaffold47G17507' => 'sas', 'SGA_v2.0_scaffold63G21736' => 'sas', 'SGA_v2.0_scaffold87G27070' => 'sas', 'SHI17794' => 'shi', 'SHI28851' => 'shi', 'SMO165G0155' => 'smo', 'SMO340G0217' => 'smo', 'SMO367G1210' => 'smo', 'Solyc02g093430.3' => 'sly', 'Solyc05g013580.4' => 'sly', 'Solyc07g008030.3' => 'sly', 'Solyc12g035470.2' => 'sly', 'Sopen02g038020' => 'spe', 'Sopen05g008490' => 'spe', 'Sopen07g003910' => 'spe', 'Sopen12g015240' => 'spe', 'Sp1g11550' => 'spa', 'Sp2g16710' => 'spa', 'Sp3g00430' => 'spa', 'Sp3g26780' => 'spa', 'Sp5g22900' => 'spa', 'Sp6g29530' => 'spa', 'TAR371G0794' => 'tar', 'TAR374G0164' => 'tar', 'TAR622G0165' => 'tar', 'TAR626G0929' => 'tar', 'TAR629G2155' => 'tar', 'THA.LOC104805282' => 'tha', 'THA.LOC104805363' => 'tha', 'THA.LOC104808968' => 'tha', 'THA.LOC104821093' => 'tha', 'THA.LOC104823953' => 'tha', 'THA.LOC104825562' => 'tha', 'THA.LOC104825665' => 'tha', 'Thecc.02G261400' => 'tca', 'Thecc.04G019200' => 'tca', 'Thecc.09G130400' => 'tca', 'Thhalv10004374m.g' => 'esa', 'Thhalv10007850m.g' => 'esa', 'Thhalv10013782m.g' => 'esa', 'Thhalv10018686m.g' => 'esa', 'Thhalv10020899m.g' => 'esa', 'Thhalv10022755m.g' => 'esa', 'TPR.G23851' => 'tpr', 'TPR.G26500' => 'tpr', 'TPR.G27267' => 'tpr', 'TPR.G32001' => 'tpr', 'TPR.G6251' => 'tpr', 'TPR.G8167' => 'tpr', 'TWI12G1330' => 'twi', 'TWI18G1239' => 'twi', 'TWI34G0979' => 'twi', 'TWI36G0670' => 'twi', 'TWI36G0707' => 'twi', 'TWI56G0233' => 'twi', 'TWI75G1809' => 'twi', 'unitig_21.g20874' => 'ugi', 'unitig_26.g10343' => 'ugi', 'unitig_46.g18392' => 'ugi', 'unitig_52.g17178' => 'ugi', 'unitig_8.g2934' => 'ugi', 'vmacro01122' => 'vma', 'vmacro05875' => 'vma', 'vmacro06147' => 'vma', 'vmacro16191' => 'vma', 'vmacro18293' => 'vma', 'VMungo0251G3707' => 'vmu', 'VMungo0464G1521' => 'vmu', 'VMungo1215G0205' => 'vmu', 'VMungo1383G2484' => 'vmu', 'Zm00001eb079610' => 'zma', 'Zm00001eb135990' => 'zma', 'Zm00001eb183710' => 'zma', 'Zm00001eb246020' => 'zma' ) $gf_id = 'HOM05D001124' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001124' ) $data_identifier = 'HOM05D001124' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 6, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 7, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 21, 'bol' => (int) 10, 'bra' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 6, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 9, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 21, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 8, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 10, 'lsa' => (int) 8, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 8, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 9, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb246020' $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' => 'HOM05D001124', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '548', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02520' => 'bna', 'A03p06630' => 'bna', 'A05p44460' => 'bna', 'A06p08710' => 'bna', 'A06p41090' => 'bna', 'A07p32320' => 'bna', 'A08p32520' => 'bna', 'A09p10360' => 'bna', 'A10p24080' => 'bna', 'Aa31LG11G15250' => 'aar', 'Aa31LG1G1800' => 'aar', 'Aa31LG2G5120' => 'aar', 'Aa31LG2G6070' => 'aar', 'Aa31LG5G10770' => 'aar', 'Aa31sc61G90' => 'aar', 'Actinidia01352' => 'ach', 'Actinidia05983' => 'ach', 'Actinidia08133' => 'ach', 'Actinidia15101' => 'ach', 'Actinidia26379' => 'ach', 'Actinidia35778' => 'ach', 'Actinidia36123' => 'ach', 'Actinidia37436' => 'ach', 'Actinidia38730' => 'ach', 'Ah.02g128210' => 'amhyb', 'Ah.03g132990' => 'amhyb', 'Ah.14g079410' => 'amhyb', 'AL1G24640' => 'aly', 'AL2G26680' => 'aly', 'AL3G10530' => 'aly', 'AL3G45230' => 'aly', 'AL5G15230' => 'aly', 'AL5G16960' => 'aly', 'AL6G25210' => 'aly', 'Aqoxy2G00441' => 'aox', 'Aqoxy3G01236' => 'aox', 'Aqoxy5G03746' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3RQ047' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C7GMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9C8JER' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MBL6KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YXCZ83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZANX40' => 'arhy', 'AT1G12990' => 'ath', 'AT1G67880' => 'ath', 'AT2G13290' => 'ath', 'AT3G01620' => 'ath', 'AT3G26445' => 'ath', 'AT3G27540' => 'ath', 'AT5G14480' => 'ath', 'ATR0824G026' => 'atr', 'ATR1098G019' => 'atr', 'Atru.chr11.2145' => 'acertr', 'Atru.chr2.3636' => 'acertr', 'Atru.chr2.3644' => 'acertr', 'Atru.chr6.2422' => 'acertr', 'Atru.chr7.1112' => 'acertr', 'AUR62005469' => 'cqu', 'AUR62011166' => 'cqu', 'AUR62013319' => 'cqu', 'AUR62024273' => 'cqu', 'AUR62028420' => 'cqu', 'AUR62041942' => 'cqu', 'BcaB01g04969' => 'bca', 'BcaB01g06371' => 'bca', 'BcaB02g11494' => 'bca', 'BcaB03g15382' => 'bca', 'BcaB08g36994' => 'bca', 'BcaC03g13477' => 'bca', 'BcaC03g13478' => 'bca', 'BcaC03g13480' => 'bca', 'BcaC03g13481' => 'bca', 'BcaC03g13486' => 'bca', 'BcaC04g19031' => 'bca', 'BcaC04g23085' => 'bca', 'BcaC05g25094' => 'bca', 'BcaC05g25096' => 'bca', 'BcaC05g25138' => 'bca', 'BcaC05g30416' => 'bca', 'BcaC05g30455' => 'bca', 'BcaC06g30979' => 'bca', 'BcaC06g33805' => 'bca', 'BcaC08g46021' => 'bca', 'BcaNung03154' => 'bca', 'BolC2t06623H' => 'bol', 'BolC2t06632H' => 'bol', 'BolC2t06635H' => 'bol', 'BolC2t06638H' => 'bol', 'BolC3t13266H' => 'bol', 'BolC5t29776H' => 'bol', 'BolC6t38912H' => 'bol', 'BolC7t44183H' => 'bol', 'BolC9t54123H' => 'bol', 'BolC9t59107H' => 'bol', 'BraA02t05221Z' => 'bra', 'BraA03t09996Z' => 'bra', 'BraA05t23210Z' => 'bra', 'BraA06t24068Z' => 'bra', 'BraA06t27032Z' => 'bra', 'BraA08t35176Z' => 'bra', 'BraA09t36680Z' => 'bra', 'BraA10t44471Z' => 'bra', 'C02p06760' => 'bna', 'C02p06890' => 'bna', 'C02p07010' => 'bna', 'C03p07660' => 'bna', 'C05p10300' => 'bna', 'C06p38150' => 'bna', 'C07p36650' => 'bna', 'C08p15770' => 'bna', 'C09p12300' => 'bna', 'C09p62700' => 'bna', 'C09p75040' => 'bna', 'CAN.G13.1' => 'can', 'CAN.G138.4' => 'can', 'CAN.G44.6' => 'can', 'CAN.G473.19' => 'can', 'CANSAT01G0835' => 'cansat', 'CANSAT11G0246' => 'cansat', 'CANSAT11G1766' => 'cansat', 'CANSAT64G1954' => 'cansat', 'CARHR013330' => 'chi', 'CARHR060530' => 'chi', 'CARHR075300' => 'chi', 'CARHR105120' => 'chi', 'CARHR148910' => 'chi', 'CARHR198830' => 'chi', 'Carub.0001s1275' => 'cru', 'Carub.0002s1437' => 'cru', 'Carub.0003s0044' => 'cru', 'Carub.0003s2787' => 'cru', 'Carub.0005s0597' => 'cru', 'Carub.0006s1266' => 'cru', 'Ca_06935_v3' => 'car', 'Ca_13559_v3' => 'car', 'Ca_16941_v3' => 'car', 'Ca_16960_v3' => 'car', 'Ca_17775_v3' => 'car', 'Ca_30464_v3' => 'car', 'Cc06_g08160' => 'ccan', 'Cc07_g01520' => 'ccan', 'Cc11_g15810' => 'ccan', 'CDE02G2840' => 'cde', 'CDE03G0093' => 'cde', 'CDE04G2127' => 'cde', 'CDE07G1857' => 'cde', 'CDE09G1246' => 'cde', 'Cfa003412' => 'cfa', 'Cfa007341' => 'cfa', 'Cfa009220' => 'cfa', 'Ciclev10008737m.g' => 'ccl', 'Ciclev10015565m.g' => 'ccl', 'Ciclev10031761m.g' => 'ccl', 'CiPaw.03G045300' => 'cil', 'CiPaw.03G247200' => 'cil', 'CiPaw.04G029500' => 'cil', 'CiPaw.04G174000' => 'cil', 'CiPaw.05G181200' => 'cil', 'CiPaw.06G067100' => 'cil', 'ClCG05G025800' => 'cla', 'ClCG06G011400' => 'cla', 'ClCG09G019360' => 'cla', 'COL.COLO4_04827' => 'col', 'COL.COLO4_29170' => 'col', 'COL.COLO4_35131' => 'col', 'COL.COLO4_35132' => 'col', 'Cpa.g.sc33.32' => 'cpa', 'Cpa.g.sc46.29' => 'cpa', 'Cpa.g.sc796.1' => 'cpa', 'CsaV3_1G030420' => 'csa', 'CsaV3_5G027050' => 'csa', 'CsaV3_5G031040' => 'csa', 'CsaV3_UNG023130' => 'csa', 'CSS0007726' => 'camsi', 'CSS0016433' => 'camsi', 'CSS0017656' => 'camsi', 'CSS0025364' => 'camsi', 'CSS0027582' => 'camsi', 'CSS0047288' => 'camsi', 'CSS0049950' => 'camsi', 'DCAR_003843' => 'dca', 'DCAR_007052' => 'dca', 'DCAR_020884' => 'dca', 'DCAR_021730' => 'dca', 'DCAR_024423' => 'dca', 'DCAR_026509' => 'dca', 'DCAR_031158' => 'dca', 'Dinv14728' => 'din', 'Dinv15219' => 'din', 'Dinv25728' => 'din', 'Dinv33428' => 'din', 'Dinv36489' => 'din', 'Dinv41486' => 'din', 'Duzib147G0469' => 'dzi', 'Duzib168G0060' => 'dzi', 'Duzib187G1215' => 'dzi', 'Duzib248G0692' => 'dzi', 'Duzib251G0767' => 'dzi', 'Duzib264G0446' => 'dzi', 'Duzib268G0691' => 'dzi', 'ECA232G4767' => 'eca', 'ECA233G2838' => 'eca', 'ECA234G0391' => 'eca', 'ECA234G0857' => 'eca', 'ECA236G1593' => 'eca', 'ECA238G0565' => 'eca', 'ECA246G1027' => 'eca', 'ECA246G3223' => 'eca', 'ECA246G3470' => 'eca', 'EL10Ac6g13829' => 'bvu', 'EL10Ac6g14093' => 'bvu', 'EL10Ac8g18707' => 'bvu', 'Eucgr.C01369' => 'egr', 'Eucgr.H02492' => 'egr', 'Eucgr.I01733' => 'egr', 'Eucgr.J02255' => 'egr', 'Eucgr.J02257' => 'egr', 'Eucgr.J02258' => 'egr', 'FAN02G1601' => 'fan', 'FAN03G1586' => 'fan', 'FAN03G2986' => 'fan', 'FAN05G4837' => 'fan', 'FAN06G0146' => 'fan', 'FAN07G0858' => 'fan', 'FAN09G3179' => 'fan', 'FAN10G0669' => 'fan', 'FAN12G2358' => 'fan', 'FAN14G4198' => 'fan', 'FAN14G5112' => 'fan', 'FAN17G0342' => 'fan', 'FAN19G0342' => 'fan', 'FAN19G0962' => 'fan', 'FAN19G1101' => 'fan', 'FAN19G1872' => 'fan', 'FAN22G0356' => 'fan', 'FAN23G0744' => 'fan', 'FAN23G1914' => 'fan', 'FAN26G0032' => 'fan', 'FAN28G0625' => 'fan', 'FvH4_1g02710' => 'fve', 'FvH4_1g02720' => 'fve', 'FvH4_4g25670' => 'fve', 'FvH4_6g51700' => 'fve', 'FvH4_7g20170' => 'fve', 'Glyma.05G175000' => 'gma', 'Glyma.08G132300' => 'gma', 'Glyma.11G243000' => 'gma', 'Glyma.13G158900' => 'gma', 'Glyma.17G112400' => 'gma', 'Glyma.18G014100' => 'gma', 'Glyma.19G003100' => 'gma', 'Glyma.19G056500' => 'gma', 'Gohir.A01G158900' => 'ghi', 'Gohir.A05G312600' => 'ghi', 'Gohir.A05G354900' => 'ghi', 'Gohir.A07G037200' => 'ghi', 'Gohir.A09G030000' => 'ghi', 'Gohir.A12G145200' => 'ghi', 'Gohir.D01G151500' => 'ghi', 'Gohir.D04G058300' => 'ghi', 'Gohir.D05G314100' => 'ghi', 'Gohir.D07G041400' => 'ghi', 'Gohir.D09G029700' => 'ghi', 'Gohir.D12G149700' => 'ghi', 'Gorai.001G043800' => 'gra', 'Gorai.002G187800' => 'gra', 'Gorai.006G034700' => 'gra', 'Gorai.008G161200' => 'gra', 'Gorai.009G335700' => 'gra', 'Gorai.012G065000' => 'gra', 'GSVIVG01000535001' => 'vvi', 'GSVIVG01015572001' => 'vvi', 'GSVIVG01032386001' => 'vvi', 'HanXRQChr05g0138531' => 'han', 'HanXRQChr06g0174391' => 'han', 'HanXRQChr07g0199021' => 'han', 'HanXRQChr08g0208211' => 'han', 'HanXRQChr09g0255471' => 'han', 'HanXRQChr10g0315791' => 'han', 'HanXRQChr12g0371991' => 'han', 'HanXRQChr15g0475251' => 'han', 'HanXRQChr17g0540001' => 'han', 'HanXRQChr17g0548631' => 'han', 'HanXRQChr17g0569561' => 'han', 'Haze_12256' => 'cav', 'Haze_14756' => 'cav', 'Haze_25528' => 'cav', 'Hma1.2p1_0079F.1_g041020' => 'hma', 'Hma1.2p1_0818F.1_g223260' => 'hma', 'Hma1.2p1_1747F.1_g300530' => 'hma', 'HPP92_004607' => 'vpl', 'HPP92_004608' => 'vpl', 'HPP92_006181' => 'vpl', 'HPP92_012192' => 'vpl', 'HPP92_015680' => 'vpl', 'HPP92_020249' => 'vpl', 'HPP92_021376' => 'vpl', 'HPP92_024275' => 'vpl', 'Hund06031' => 'sun', 'Hund25391' => 'sun', 'Lalb_Chr07g0185371' => 'lal', 'Lalb_Chr07g0185381' => 'lal', 'Lalb_Chr12g0204011' => 'lal', 'Lalb_Chr13g0301671' => 'lal', 'Lalb_Chr14g0362851' => 'lal', 'Lalb_Chr24g0403581' => 'lal', 'Lj1g0000233' => 'lja', 'Lj2g0018120' => 'lja', 'Lj3C621T0' => 'lonja', 'Lj3P1059T14' => 'lonja', 'Lj3P611T9' => 'lonja', 'Lj3P614T13' => 'lonja', 'Lj3P615T5' => 'lonja', 'Lj4g0012315' => 'lja', 'Lj4g0026182' => 'lja', 'Lj6P813T16' => 'lonja', 'Lj7C427T7' => 'lonja', 'Lj7C427T8' => 'lonja', 'Lj7P600T41' => 'lonja', 'Lju41C42G17' => 'lonja', 'Lsat_1_v5_gn_0_47300' => 'lsa', 'Lsat_1_v5_gn_2_91280' => 'lsa', 'Lsat_1_v5_gn_3_30561' => 'lsa', 'Lsat_1_v5_gn_4_184321' => 'lsa', 'Lsat_1_v5_gn_4_4041' => 'lsa', 'Lsat_1_v5_gn_5_92000' => 'lsa', 'Lsat_1_v5_gn_8_152940' => 'lsa', 'Lsat_1_v5_gn_8_62401' => 'lsa', 'Manes.06G055900' => 'mes', 'Manes.12G022200' => 'mes', 'Manes.13G023300' => 'mes', 'Manes.14G115000' => 'mes', 'Manes.15G151700' => 'mes', 'Manes.17G111300' => 'mes', 'Mapoly0226s0009' => 'mpo', 'MBI02_g25363_MAGBIO' => 'mbi', 'MBI06_g00027_MAGBIO' => 'mbi', 'MBI10_g13034_MAGBIO' => 'mbi', 'MD09G1023400' => 'mdo', 'MD13G1100100' => 'mdo', 'MD15G1169200' => 'mdo', 'MD16G1101100' => 'mdo', 'MD17G1022900' => 'mdo', 'Medtr3g096150' => 'mtr', 'Medtr4g115070' => 'mtr', 'Medtr7g033325' => 'mtr', 'Medtr8g089840' => 'mtr', 'MELO3C010319.2' => 'cme', 'MELO3C011944.2' => 'cme', 'MELO3C021589.2' => 'cme', 'Migut.E00207' => 'egut', 'Migut.H00067' => 'egut', 'Migut.K00433' => 'egut', 'Migut.K00606' => 'egut', 'Migut.K01410' => 'egut', 'MSTRG.13347' => 'ama', 'MSTRG.24045' => 'ama', 'MSTRG.2428' => 'ama', 'MSTRG.26410' => 'ama', 'MSTRG.3139' => 'ama', 'MSTRG.3286' => 'ama', 'MSTRG.563' => 'ama', 'MSTRG.7941' => 'ama', 'Nitab4.5_0000028g0060' => 'nta', 'Nitab4.5_0000065g0260' => 'nta', 'Nitab4.5_0000112g0060' => 'nta', 'Nitab4.5_0000489g0120' => 'nta', 'Nitab4.5_0001776g0050' => 'nta', 'Nitab4.5_0001854g0010' => 'nta', 'Nitab4.5_0001860g0020' => 'nta', 'Nitab4.5_0004352g0010' => 'nta', 'Nitab4.5_0008716g0020' => 'nta', 'Nitab4.5_0008922g0010' => 'nta', 'Nn3g16693' => 'nnu', 'Nn4g22596' => 'nnu', 'Nn7g37639' => 'nnu', 'Oeu001701.1' => 'oeu', 'Oeu018149.1' => 'oeu', 'Oeu026220.1' => 'oeu', 'Oeu038635.1' => 'oeu', 'Oeu049176.1' => 'oeu', 'Oeu056706.1' => 'oeu', 'Oeu056937.1' => 'oeu', 'Oeu057540.1' => 'oeu', 'Os02g0594900' => 'osa', 'Os02g0595100' => 'osa', 'Os04g0477500' => 'osa', 'Os12g0611900' => 'osa', 'Peaxi162Scf00076g00020' => 'pax', 'Peaxi162Scf00128g00217' => 'pax', 'Peaxi162Scf00129g01640' => 'pax', 'Peaxi162Scf00669g00007' => 'pax', 'Peaxi162Scf00700g00421' => 'pax', 'Peaxi162Scf00801g00038' => 'pax', 'Peaxi162Scf00891g00025' => 'pax', 'PGR083G0909' => 'pgr', 'PGR119G1005' => 'pgr', 'PGR142G2236' => 'pgr', 'PGR142G3388' => 'pgr', 'PGSC0003DMG400004514' => 'stu', 'PGSC0003DMG400012635' => 'stu', 'PGSC0003DMG400015730' => 'stu', 'PGSC0003DMG400018611' => 'stu', 'PGSC0003DMG400030897' => 'stu', 'Phvul.001G254800' => 'pvu', 'Phvul.002G260100' => 'pvu', 'Phvul.003G167600' => 'pvu', 'Phvul.004G005100' => 'pvu', 'Potri.001G343600' => 'ptr', 'Potri.006G066700' => 'ptr', 'Potri.008G186000' => 'ptr', 'Potri.010G046900' => 'ptr', 'Potri.018G127900' => 'ptr', 'Pp3c20_17750' => 'ppa', 'Pp3c24_4380' => 'ppa', 'Prupe.1G245800' => 'ppe', 'Prupe.3G293400' => 'ppe', 'Prupe.7G247400' => 'ppe', 'Psat0s145g0120' => 'psa', 'Psat0s595g0040' => 'psa', 'Psat0s595g0120' => 'psa', 'Psat3g175040' => 'psa', 'Psat7g058120' => 'psa', 'PSO017G0428' => 'pso', 'PSO063G7510' => 'pso', 'PSO067G0046' => 'pso', 'PSO478G1073' => 'pso', 'PSO675G3677' => 'pso', 'PSO675G6558' => 'pso', 'PSO675G7520' => 'pso', 'PSO675G8959' => 'pso', 'QL02p074089' => 'qlo', 'QL02p089614' => 'qlo', 'QL03p057736' => 'qlo', 'RcHm_v2.0_Chr1g0364131' => 'rch', 'RcHm_v2.0_Chr2g0087801' => 'rch', 'RcHm_v2.0_Chr2g0087821' => 'rch', 'RcHm_v2.0_Chr2g0173231' => 'rch', 'RcHm_v2.0_Chr4g0433111' => 'rch', 'Rhsim03G0250300' => 'rsi', 'Rhsim08G0048400' => 'rsi', 'Rhsim10G0014800' => 'rsi', 'Rhsim12G0040100' => 'rsi', 'Rhsim12G0109700' => 'rsi', 'Sabra06G0049600' => 'sbr', 'Sabra08G0141000' => 'sbr', 'Sabra10G0021400' => 'sbr', 'Sabra16G0222900' => 'sbr', 'Sabra18G0108600' => 'sbr', 'SalBow1G0433' => 'sbo', 'SalBow1G2038' => 'sbo', 'SalBow1G5003' => 'sbo', 'SalBow7G1197' => 'sbo', 'SalBow8G3506' => 'sbo', 'Sc03g0007300' => 'sci', 'Sc11g0000950' => 'sci', 'Sc14g0008750' => 'sci', 'Sc18g0000420' => 'sci', 'Sed0006754' => 'sed', 'Sed0008741' => 'sed', 'Sed0017172' => 'sed', 'Sed0018925' => 'sed', 'Sed0023326' => 'sed', 'Sed0025909' => 'sed', 'SEGI_05333' => 'sgi', 'SEGI_10362' => 'sgi', 'SEGI_13380' => 'sgi', 'SEGI_24306' => 'sgi', 'SEGI_29077' => 'sgi', 'SEGI_29095' => 'sgi', 'SEGI_36534' => 'sgi', 'SEGI_37506' => 'sgi', 'SEGI_38321' => 'sgi', 'SGA_v2.0_scaffold307G48031' => 'sas', 'SGA_v2.0_scaffold47G17507' => 'sas', 'SGA_v2.0_scaffold63G21736' => 'sas', 'SGA_v2.0_scaffold87G27070' => 'sas', 'SHI17794' => 'shi', 'SHI28851' => 'shi', 'SMO165G0155' => 'smo', 'SMO340G0217' => 'smo', 'SMO367G1210' => 'smo', 'Solyc02g093430.3' => 'sly', 'Solyc05g013580.4' => 'sly', 'Solyc07g008030.3' => 'sly', 'Solyc12g035470.2' => 'sly', 'Sopen02g038020' => 'spe', 'Sopen05g008490' => 'spe', 'Sopen07g003910' => 'spe', 'Sopen12g015240' => 'spe', 'Sp1g11550' => 'spa', 'Sp2g16710' => 'spa', 'Sp3g00430' => 'spa', 'Sp3g26780' => 'spa', 'Sp5g22900' => 'spa', 'Sp6g29530' => 'spa', 'TAR371G0794' => 'tar', 'TAR374G0164' => 'tar', 'TAR622G0165' => 'tar', 'TAR626G0929' => 'tar', 'TAR629G2155' => 'tar', 'THA.LOC104805282' => 'tha', 'THA.LOC104805363' => 'tha', 'THA.LOC104808968' => 'tha', 'THA.LOC104821093' => 'tha', 'THA.LOC104823953' => 'tha', 'THA.LOC104825562' => 'tha', 'THA.LOC104825665' => 'tha', 'Thecc.02G261400' => 'tca', 'Thecc.04G019200' => 'tca', 'Thecc.09G130400' => 'tca', 'Thhalv10004374m.g' => 'esa', 'Thhalv10007850m.g' => 'esa', 'Thhalv10013782m.g' => 'esa', 'Thhalv10018686m.g' => 'esa', 'Thhalv10020899m.g' => 'esa', 'Thhalv10022755m.g' => 'esa', 'TPR.G23851' => 'tpr', 'TPR.G26500' => 'tpr', 'TPR.G27267' => 'tpr', 'TPR.G32001' => 'tpr', 'TPR.G6251' => 'tpr', 'TPR.G8167' => 'tpr', 'TWI12G1330' => 'twi', 'TWI18G1239' => 'twi', 'TWI34G0979' => 'twi', 'TWI36G0670' => 'twi', 'TWI36G0707' => 'twi', 'TWI56G0233' => 'twi', 'TWI75G1809' => 'twi', 'unitig_21.g20874' => 'ugi', 'unitig_26.g10343' => 'ugi', 'unitig_46.g18392' => 'ugi', 'unitig_52.g17178' => 'ugi', 'unitig_8.g2934' => 'ugi', 'vmacro01122' => 'vma', 'vmacro05875' => 'vma', 'vmacro06147' => 'vma', 'vmacro16191' => 'vma', 'vmacro18293' => 'vma', 'VMungo0251G3707' => 'vmu', 'VMungo0464G1521' => 'vmu', 'VMungo1215G0205' => 'vmu', 'VMungo1383G2484' => 'vmu', 'Zm00001eb079610' => 'zma', 'Zm00001eb135990' => 'zma', 'Zm00001eb183710' => 'zma', 'Zm00001eb246020' => 'zma' ), 'gf_id' => 'HOM05D001124', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001124' ), 'data_identifier' => 'HOM05D001124', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001124', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '548', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02520' => 'bna', 'A03p06630' => 'bna', 'A05p44460' => 'bna', 'A06p08710' => 'bna', 'A06p41090' => 'bna', 'A07p32320' => 'bna', 'A08p32520' => 'bna', 'A09p10360' => 'bna', 'A10p24080' => 'bna', 'Aa31LG11G15250' => 'aar', 'Aa31LG1G1800' => 'aar', 'Aa31LG2G5120' => 'aar', 'Aa31LG2G6070' => 'aar', 'Aa31LG5G10770' => 'aar', 'Aa31sc61G90' => 'aar', 'Actinidia01352' => 'ach', 'Actinidia05983' => 'ach', 'Actinidia08133' => 'ach', 'Actinidia15101' => 'ach', 'Actinidia26379' => 'ach', 'Actinidia35778' => 'ach', 'Actinidia36123' => 'ach', 'Actinidia37436' => 'ach', 'Actinidia38730' => 'ach', 'Ah.02g128210' => 'amhyb', 'Ah.03g132990' => 'amhyb', 'Ah.14g079410' => 'amhyb', 'AL1G24640' => 'aly', 'AL2G26680' => 'aly', 'AL3G10530' => 'aly', 'AL3G45230' => 'aly', 'AL5G15230' => 'aly', 'AL5G16960' => 'aly', 'AL6G25210' => 'aly', 'Aqoxy2G00441' => 'aox', 'Aqoxy3G01236' => 'aox', 'Aqoxy5G03746' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3RQ047' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C7GMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9C8JER' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MBL6KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YXCZ83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZANX40' => 'arhy', 'AT1G12990' => 'ath', 'AT1G67880' => 'ath', 'AT2G13290' => 'ath', 'AT3G01620' => 'ath', 'AT3G26445' => 'ath', 'AT3G27540' => 'ath', 'AT5G14480' => 'ath', 'ATR0824G026' => 'atr', 'ATR1098G019' => 'atr', 'Atru.chr11.2145' => 'acertr', 'Atru.chr2.3636' => 'acertr', 'Atru.chr2.3644' => 'acertr', 'Atru.chr6.2422' => 'acertr', 'Atru.chr7.1112' => 'acertr', 'AUR62005469' => 'cqu', 'AUR62011166' => 'cqu', 'AUR62013319' => 'cqu', 'AUR62024273' => 'cqu', 'AUR62028420' => 'cqu', 'AUR62041942' => 'cqu', 'BcaB01g04969' => 'bca', 'BcaB01g06371' => 'bca', 'BcaB02g11494' => 'bca', 'BcaB03g15382' => 'bca', 'BcaB08g36994' => 'bca', 'BcaC03g13477' => 'bca', 'BcaC03g13478' => 'bca', 'BcaC03g13480' => 'bca', 'BcaC03g13481' => 'bca', 'BcaC03g13486' => 'bca', 'BcaC04g19031' => 'bca', 'BcaC04g23085' => 'bca', 'BcaC05g25094' => 'bca', 'BcaC05g25096' => 'bca', 'BcaC05g25138' => 'bca', 'BcaC05g30416' => 'bca', 'BcaC05g30455' => 'bca', 'BcaC06g30979' => 'bca', 'BcaC06g33805' => 'bca', 'BcaC08g46021' => 'bca', 'BcaNung03154' => 'bca', 'BolC2t06623H' => 'bol', 'BolC2t06632H' => 'bol', 'BolC2t06635H' => 'bol', 'BolC2t06638H' => 'bol', 'BolC3t13266H' => 'bol', 'BolC5t29776H' => 'bol', 'BolC6t38912H' => 'bol', 'BolC7t44183H' => 'bol', 'BolC9t54123H' => 'bol', 'BolC9t59107H' => 'bol', 'BraA02t05221Z' => 'bra', 'BraA03t09996Z' => 'bra', 'BraA05t23210Z' => 'bra', 'BraA06t24068Z' => 'bra', 'BraA06t27032Z' => 'bra', 'BraA08t35176Z' => 'bra', 'BraA09t36680Z' => 'bra', 'BraA10t44471Z' => 'bra', 'C02p06760' => 'bna', 'C02p06890' => 'bna', 'C02p07010' => 'bna', 'C03p07660' => 'bna', 'C05p10300' => 'bna', 'C06p38150' => 'bna', 'C07p36650' => 'bna', 'C08p15770' => 'bna', 'C09p12300' => 'bna', 'C09p62700' => 'bna', 'C09p75040' => 'bna', 'CAN.G13.1' => 'can', 'CAN.G138.4' => 'can', 'CAN.G44.6' => 'can', 'CAN.G473.19' => 'can', 'CANSAT01G0835' => 'cansat', 'CANSAT11G0246' => 'cansat', 'CANSAT11G1766' => 'cansat', 'CANSAT64G1954' => 'cansat', 'CARHR013330' => 'chi', 'CARHR060530' => 'chi', 'CARHR075300' => 'chi', 'CARHR105120' => 'chi', 'CARHR148910' => 'chi', 'CARHR198830' => 'chi', 'Carub.0001s1275' => 'cru', 'Carub.0002s1437' => 'cru', 'Carub.0003s0044' => 'cru', 'Carub.0003s2787' => 'cru', 'Carub.0005s0597' => 'cru', 'Carub.0006s1266' => 'cru', 'Ca_06935_v3' => 'car', 'Ca_13559_v3' => 'car', 'Ca_16941_v3' => 'car', 'Ca_16960_v3' => 'car', 'Ca_17775_v3' => 'car', 'Ca_30464_v3' => 'car', 'Cc06_g08160' => 'ccan', 'Cc07_g01520' => 'ccan', 'Cc11_g15810' => 'ccan', 'CDE02G2840' => 'cde', 'CDE03G0093' => 'cde', 'CDE04G2127' => 'cde', 'CDE07G1857' => 'cde', 'CDE09G1246' => 'cde', 'Cfa003412' => 'cfa', 'Cfa007341' => 'cfa', 'Cfa009220' => 'cfa', 'Ciclev10008737m.g' => 'ccl', 'Ciclev10015565m.g' => 'ccl', 'Ciclev10031761m.g' => 'ccl', 'CiPaw.03G045300' => 'cil', 'CiPaw.03G247200' => 'cil', 'CiPaw.04G029500' => 'cil', 'CiPaw.04G174000' => 'cil', 'CiPaw.05G181200' => 'cil', 'CiPaw.06G067100' => 'cil', 'ClCG05G025800' => 'cla', 'ClCG06G011400' => 'cla', 'ClCG09G019360' => 'cla', 'COL.COLO4_04827' => 'col', 'COL.COLO4_29170' => 'col', 'COL.COLO4_35131' => 'col', 'COL.COLO4_35132' => 'col', 'Cpa.g.sc33.32' => 'cpa', 'Cpa.g.sc46.29' => 'cpa', 'Cpa.g.sc796.1' => 'cpa', 'CsaV3_1G030420' => 'csa', 'CsaV3_5G027050' => 'csa', 'CsaV3_5G031040' => 'csa', 'CsaV3_UNG023130' => 'csa', 'CSS0007726' => 'camsi', 'CSS0016433' => 'camsi', 'CSS0017656' => 'camsi', 'CSS0025364' => 'camsi', 'CSS0027582' => 'camsi', 'CSS0047288' => 'camsi', 'CSS0049950' => 'camsi', 'DCAR_003843' => 'dca', 'DCAR_007052' => 'dca', 'DCAR_020884' => 'dca', 'DCAR_021730' => 'dca', 'DCAR_024423' => 'dca', 'DCAR_026509' => 'dca', 'DCAR_031158' => 'dca', 'Dinv14728' => 'din', 'Dinv15219' => 'din', 'Dinv25728' => 'din', 'Dinv33428' => 'din', 'Dinv36489' => 'din', 'Dinv41486' => 'din', 'Duzib147G0469' => 'dzi', 'Duzib168G0060' => 'dzi', 'Duzib187G1215' => 'dzi', 'Duzib248G0692' => 'dzi', 'Duzib251G0767' => 'dzi', 'Duzib264G0446' => 'dzi', 'Duzib268G0691' => 'dzi', 'ECA232G4767' => 'eca', 'ECA233G2838' => 'eca', 'ECA234G0391' => 'eca', 'ECA234G0857' => 'eca', 'ECA236G1593' => 'eca', 'ECA238G0565' => 'eca', 'ECA246G1027' => 'eca', 'ECA246G3223' => 'eca', 'ECA246G3470' => 'eca', 'EL10Ac6g13829' => 'bvu', 'EL10Ac6g14093' => 'bvu', 'EL10Ac8g18707' => 'bvu', 'Eucgr.C01369' => 'egr', 'Eucgr.H02492' => 'egr', 'Eucgr.I01733' => 'egr', 'Eucgr.J02255' => 'egr', 'Eucgr.J02257' => 'egr', 'Eucgr.J02258' => 'egr', 'FAN02G1601' => 'fan', 'FAN03G1586' => 'fan', 'FAN03G2986' => 'fan', 'FAN05G4837' => 'fan', 'FAN06G0146' => 'fan', 'FAN07G0858' => 'fan', 'FAN09G3179' => 'fan', 'FAN10G0669' => 'fan', 'FAN12G2358' => 'fan', 'FAN14G4198' => 'fan', 'FAN14G5112' => 'fan', 'FAN17G0342' => 'fan', 'FAN19G0342' => 'fan', 'FAN19G0962' => 'fan', 'FAN19G1101' => 'fan', 'FAN19G1872' => 'fan', 'FAN22G0356' => 'fan', 'FAN23G0744' => 'fan', 'FAN23G1914' => 'fan', 'FAN26G0032' => 'fan', 'FAN28G0625' => 'fan', 'FvH4_1g02710' => 'fve', 'FvH4_1g02720' => 'fve', 'FvH4_4g25670' => 'fve', 'FvH4_6g51700' => 'fve', 'FvH4_7g20170' => 'fve', 'Glyma.05G175000' => 'gma', 'Glyma.08G132300' => 'gma', 'Glyma.11G243000' => 'gma', 'Glyma.13G158900' => 'gma', 'Glyma.17G112400' => 'gma', 'Glyma.18G014100' => 'gma', 'Glyma.19G003100' => 'gma', 'Glyma.19G056500' => 'gma', 'Gohir.A01G158900' => 'ghi', 'Gohir.A05G312600' => 'ghi', 'Gohir.A05G354900' => 'ghi', 'Gohir.A07G037200' => 'ghi', 'Gohir.A09G030000' => 'ghi', 'Gohir.A12G145200' => 'ghi', 'Gohir.D01G151500' => 'ghi', 'Gohir.D04G058300' => 'ghi', 'Gohir.D05G314100' => 'ghi', 'Gohir.D07G041400' => 'ghi', 'Gohir.D09G029700' => 'ghi', 'Gohir.D12G149700' => 'ghi', 'Gorai.001G043800' => 'gra', 'Gorai.002G187800' => 'gra', 'Gorai.006G034700' => 'gra', 'Gorai.008G161200' => 'gra', 'Gorai.009G335700' => 'gra', 'Gorai.012G065000' => 'gra', 'GSVIVG01000535001' => 'vvi', 'GSVIVG01015572001' => 'vvi', 'GSVIVG01032386001' => 'vvi', 'HanXRQChr05g0138531' => 'han', 'HanXRQChr06g0174391' => 'han', 'HanXRQChr07g0199021' => 'han', 'HanXRQChr08g0208211' => 'han', 'HanXRQChr09g0255471' => 'han', 'HanXRQChr10g0315791' => 'han', 'HanXRQChr12g0371991' => 'han', 'HanXRQChr15g0475251' => 'han', 'HanXRQChr17g0540001' => 'han', 'HanXRQChr17g0548631' => 'han', 'HanXRQChr17g0569561' => 'han', 'Haze_12256' => 'cav', 'Haze_14756' => 'cav', 'Haze_25528' => 'cav', 'Hma1.2p1_0079F.1_g041020' => 'hma', 'Hma1.2p1_0818F.1_g223260' => 'hma', 'Hma1.2p1_1747F.1_g300530' => 'hma', 'HPP92_004607' => 'vpl', 'HPP92_004608' => 'vpl', 'HPP92_006181' => 'vpl', 'HPP92_012192' => 'vpl', 'HPP92_015680' => 'vpl', 'HPP92_020249' => 'vpl', 'HPP92_021376' => 'vpl', 'HPP92_024275' => 'vpl', 'Hund06031' => 'sun', 'Hund25391' => 'sun', 'Lalb_Chr07g0185371' => 'lal', 'Lalb_Chr07g0185381' => 'lal', 'Lalb_Chr12g0204011' => 'lal', 'Lalb_Chr13g0301671' => 'lal', 'Lalb_Chr14g0362851' => 'lal', 'Lalb_Chr24g0403581' => 'lal', 'Lj1g0000233' => 'lja', 'Lj2g0018120' => 'lja', 'Lj3C621T0' => 'lonja', 'Lj3P1059T14' => 'lonja', 'Lj3P611T9' => 'lonja', 'Lj3P614T13' => 'lonja', 'Lj3P615T5' => 'lonja', 'Lj4g0012315' => 'lja', 'Lj4g0026182' => 'lja', 'Lj6P813T16' => 'lonja', 'Lj7C427T7' => 'lonja', 'Lj7C427T8' => 'lonja', 'Lj7P600T41' => 'lonja', 'Lju41C42G17' => 'lonja', 'Lsat_1_v5_gn_0_47300' => 'lsa', 'Lsat_1_v5_gn_2_91280' => 'lsa', 'Lsat_1_v5_gn_3_30561' => 'lsa', 'Lsat_1_v5_gn_4_184321' => 'lsa', 'Lsat_1_v5_gn_4_4041' => 'lsa', 'Lsat_1_v5_gn_5_92000' => 'lsa', 'Lsat_1_v5_gn_8_152940' => 'lsa', 'Lsat_1_v5_gn_8_62401' => 'lsa', 'Manes.06G055900' => 'mes', 'Manes.12G022200' => 'mes', 'Manes.13G023300' => 'mes', 'Manes.14G115000' => 'mes', 'Manes.15G151700' => 'mes', 'Manes.17G111300' => 'mes', 'Mapoly0226s0009' => 'mpo', 'MBI02_g25363_MAGBIO' => 'mbi', 'MBI06_g00027_MAGBIO' => 'mbi', 'MBI10_g13034_MAGBIO' => 'mbi', 'MD09G1023400' => 'mdo', 'MD13G1100100' => 'mdo', 'MD15G1169200' => 'mdo', 'MD16G1101100' => 'mdo', 'MD17G1022900' => 'mdo', 'Medtr3g096150' => 'mtr', 'Medtr4g115070' => 'mtr', 'Medtr7g033325' => 'mtr', 'Medtr8g089840' => 'mtr', 'MELO3C010319.2' => 'cme', 'MELO3C011944.2' => 'cme', 'MELO3C021589.2' => 'cme', 'Migut.E00207' => 'egut', 'Migut.H00067' => 'egut', 'Migut.K00433' => 'egut', 'Migut.K00606' => 'egut', 'Migut.K01410' => 'egut', 'MSTRG.13347' => 'ama', 'MSTRG.24045' => 'ama', 'MSTRG.2428' => 'ama', 'MSTRG.26410' => 'ama', 'MSTRG.3139' => 'ama', 'MSTRG.3286' => 'ama', 'MSTRG.563' => 'ama', 'MSTRG.7941' => 'ama', 'Nitab4.5_0000028g0060' => 'nta', 'Nitab4.5_0000065g0260' => 'nta', 'Nitab4.5_0000112g0060' => 'nta', 'Nitab4.5_0000489g0120' => 'nta', 'Nitab4.5_0001776g0050' => 'nta', 'Nitab4.5_0001854g0010' => 'nta', 'Nitab4.5_0001860g0020' => 'nta', 'Nitab4.5_0004352g0010' => 'nta', 'Nitab4.5_0008716g0020' => 'nta', 'Nitab4.5_0008922g0010' => 'nta', 'Nn3g16693' => 'nnu', 'Nn4g22596' => 'nnu', 'Nn7g37639' => 'nnu', 'Oeu001701.1' => 'oeu', 'Oeu018149.1' => 'oeu', 'Oeu026220.1' => 'oeu', 'Oeu038635.1' => 'oeu', 'Oeu049176.1' => 'oeu', 'Oeu056706.1' => 'oeu', 'Oeu056937.1' => 'oeu', 'Oeu057540.1' => 'oeu', 'Os02g0594900' => 'osa', 'Os02g0595100' => 'osa', 'Os04g0477500' => 'osa', 'Os12g0611900' => 'osa', 'Peaxi162Scf00076g00020' => 'pax', 'Peaxi162Scf00128g00217' => 'pax', 'Peaxi162Scf00129g01640' => 'pax', 'Peaxi162Scf00669g00007' => 'pax', 'Peaxi162Scf00700g00421' => 'pax', 'Peaxi162Scf00801g00038' => 'pax', 'Peaxi162Scf00891g00025' => 'pax', 'PGR083G0909' => 'pgr', 'PGR119G1005' => 'pgr', 'PGR142G2236' => 'pgr', 'PGR142G3388' => 'pgr', 'PGSC0003DMG400004514' => 'stu', 'PGSC0003DMG400012635' => 'stu', 'PGSC0003DMG400015730' => 'stu', 'PGSC0003DMG400018611' => 'stu', 'PGSC0003DMG400030897' => 'stu', 'Phvul.001G254800' => 'pvu', 'Phvul.002G260100' => 'pvu', 'Phvul.003G167600' => 'pvu', 'Phvul.004G005100' => 'pvu', 'Potri.001G343600' => 'ptr', 'Potri.006G066700' => 'ptr', 'Potri.008G186000' => 'ptr', 'Potri.010G046900' => 'ptr', 'Potri.018G127900' => 'ptr', 'Pp3c20_17750' => 'ppa', 'Pp3c24_4380' => 'ppa', 'Prupe.1G245800' => 'ppe', 'Prupe.3G293400' => 'ppe', 'Prupe.7G247400' => 'ppe', 'Psat0s145g0120' => 'psa', 'Psat0s595g0040' => 'psa', 'Psat0s595g0120' => 'psa', 'Psat3g175040' => 'psa', 'Psat7g058120' => 'psa', 'PSO017G0428' => 'pso', 'PSO063G7510' => 'pso', 'PSO067G0046' => 'pso', 'PSO478G1073' => 'pso', 'PSO675G3677' => 'pso', 'PSO675G6558' => 'pso', 'PSO675G7520' => 'pso', 'PSO675G8959' => 'pso', 'QL02p074089' => 'qlo', 'QL02p089614' => 'qlo', 'QL03p057736' => 'qlo', 'RcHm_v2.0_Chr1g0364131' => 'rch', 'RcHm_v2.0_Chr2g0087801' => 'rch', 'RcHm_v2.0_Chr2g0087821' => 'rch', 'RcHm_v2.0_Chr2g0173231' => 'rch', 'RcHm_v2.0_Chr4g0433111' => 'rch', 'Rhsim03G0250300' => 'rsi', 'Rhsim08G0048400' => 'rsi', 'Rhsim10G0014800' => 'rsi', 'Rhsim12G0040100' => 'rsi', 'Rhsim12G0109700' => 'rsi', 'Sabra06G0049600' => 'sbr', 'Sabra08G0141000' => 'sbr', 'Sabra10G0021400' => 'sbr', 'Sabra16G0222900' => 'sbr', 'Sabra18G0108600' => 'sbr', 'SalBow1G0433' => 'sbo', 'SalBow1G2038' => 'sbo', 'SalBow1G5003' => 'sbo', 'SalBow7G1197' => 'sbo', 'SalBow8G3506' => 'sbo', 'Sc03g0007300' => 'sci', 'Sc11g0000950' => 'sci', 'Sc14g0008750' => 'sci', 'Sc18g0000420' => 'sci', 'Sed0006754' => 'sed', 'Sed0008741' => 'sed', 'Sed0017172' => 'sed', 'Sed0018925' => 'sed', 'Sed0023326' => 'sed', 'Sed0025909' => 'sed', 'SEGI_05333' => 'sgi', 'SEGI_10362' => 'sgi', 'SEGI_13380' => 'sgi', 'SEGI_24306' => 'sgi', 'SEGI_29077' => 'sgi', 'SEGI_29095' => 'sgi', 'SEGI_36534' => 'sgi', 'SEGI_37506' => 'sgi', 'SEGI_38321' => 'sgi', 'SGA_v2.0_scaffold307G48031' => 'sas', 'SGA_v2.0_scaffold47G17507' => 'sas', 'SGA_v2.0_scaffold63G21736' => 'sas', 'SGA_v2.0_scaffold87G27070' => 'sas', 'SHI17794' => 'shi', 'SHI28851' => 'shi', 'SMO165G0155' => 'smo', 'SMO340G0217' => 'smo', 'SMO367G1210' => 'smo', 'Solyc02g093430.3' => 'sly', 'Solyc05g013580.4' => 'sly', 'Solyc07g008030.3' => 'sly', 'Solyc12g035470.2' => 'sly', 'Sopen02g038020' => 'spe', 'Sopen05g008490' => 'spe', 'Sopen07g003910' => 'spe', 'Sopen12g015240' => 'spe', 'Sp1g11550' => 'spa', 'Sp2g16710' => 'spa', 'Sp3g00430' => 'spa', 'Sp3g26780' => 'spa', 'Sp5g22900' => 'spa', 'Sp6g29530' => 'spa', 'TAR371G0794' => 'tar', 'TAR374G0164' => 'tar', 'TAR622G0165' => 'tar', 'TAR626G0929' => 'tar', 'TAR629G2155' => 'tar', 'THA.LOC104805282' => 'tha', 'THA.LOC104805363' => 'tha', 'THA.LOC104808968' => 'tha', 'THA.LOC104821093' => 'tha', 'THA.LOC104823953' => 'tha', 'THA.LOC104825562' => 'tha', 'THA.LOC104825665' => 'tha', 'Thecc.02G261400' => 'tca', 'Thecc.04G019200' => 'tca', 'Thecc.09G130400' => 'tca', 'Thhalv10004374m.g' => 'esa', 'Thhalv10007850m.g' => 'esa', 'Thhalv10013782m.g' => 'esa', 'Thhalv10018686m.g' => 'esa', 'Thhalv10020899m.g' => 'esa', 'Thhalv10022755m.g' => 'esa', 'TPR.G23851' => 'tpr', 'TPR.G26500' => 'tpr', 'TPR.G27267' => 'tpr', 'TPR.G32001' => 'tpr', 'TPR.G6251' => 'tpr', 'TPR.G8167' => 'tpr', 'TWI12G1330' => 'twi', 'TWI18G1239' => 'twi', 'TWI34G0979' => 'twi', 'TWI36G0670' => 'twi', 'TWI36G0707' => 'twi', 'TWI56G0233' => 'twi', 'TWI75G1809' => 'twi', 'unitig_21.g20874' => 'ugi', 'unitig_26.g10343' => 'ugi', 'unitig_46.g18392' => 'ugi', 'unitig_52.g17178' => 'ugi', 'unitig_8.g2934' => 'ugi', 'vmacro01122' => 'vma', 'vmacro05875' => 'vma', 'vmacro06147' => 'vma', 'vmacro16191' => 'vma', 'vmacro18293' => 'vma', 'VMungo0251G3707' => 'vmu', 'VMungo0464G1521' => 'vmu', 'VMungo1215G0205' => 'vmu', 'VMungo1383G2484' => 'vmu', 'Zm00001eb079610' => 'zma', 'Zm00001eb135990' => 'zma', 'Zm00001eb183710' => 'zma', 'Zm00001eb246020' => 'zma' ) $gf_id = 'HOM05D001124' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001124' ) $data_identifier = 'HOM05D001124' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 6, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 7, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 21, 'bol' => (int) 10, 'bra' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 6, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 9, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 21, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 8, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 10, 'lsa' => (int) 8, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 8, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 9, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb246020' $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' => 'HOM05D001124', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '548', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02520' => 'bna', 'A03p06630' => 'bna', 'A05p44460' => 'bna', 'A06p08710' => 'bna', 'A06p41090' => 'bna', 'A07p32320' => 'bna', 'A08p32520' => 'bna', 'A09p10360' => 'bna', 'A10p24080' => 'bna', 'Aa31LG11G15250' => 'aar', 'Aa31LG1G1800' => 'aar', 'Aa31LG2G5120' => 'aar', 'Aa31LG2G6070' => 'aar', 'Aa31LG5G10770' => 'aar', 'Aa31sc61G90' => 'aar', 'Actinidia01352' => 'ach', 'Actinidia05983' => 'ach', 'Actinidia08133' => 'ach', 'Actinidia15101' => 'ach', 'Actinidia26379' => 'ach', 'Actinidia35778' => 'ach', 'Actinidia36123' => 'ach', 'Actinidia37436' => 'ach', 'Actinidia38730' => 'ach', 'Ah.02g128210' => 'amhyb', 'Ah.03g132990' => 'amhyb', 'Ah.14g079410' => 'amhyb', 'AL1G24640' => 'aly', 'AL2G26680' => 'aly', 'AL3G10530' => 'aly', 'AL3G45230' => 'aly', 'AL5G15230' => 'aly', 'AL5G16960' => 'aly', 'AL6G25210' => 'aly', 'Aqoxy2G00441' => 'aox', 'Aqoxy3G01236' => 'aox', 'Aqoxy5G03746' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3RQ047' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C7GMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9C8JER' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MBL6KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YXCZ83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZANX40' => 'arhy', 'AT1G12990' => 'ath', 'AT1G67880' => 'ath', 'AT2G13290' => 'ath', 'AT3G01620' => 'ath', 'AT3G26445' => 'ath', 'AT3G27540' => 'ath', 'AT5G14480' => 'ath', 'ATR0824G026' => 'atr', 'ATR1098G019' => 'atr', 'Atru.chr11.2145' => 'acertr', 'Atru.chr2.3636' => 'acertr', 'Atru.chr2.3644' => 'acertr', 'Atru.chr6.2422' => 'acertr', 'Atru.chr7.1112' => 'acertr', 'AUR62005469' => 'cqu', 'AUR62011166' => 'cqu', 'AUR62013319' => 'cqu', 'AUR62024273' => 'cqu', 'AUR62028420' => 'cqu', 'AUR62041942' => 'cqu', 'BcaB01g04969' => 'bca', 'BcaB01g06371' => 'bca', 'BcaB02g11494' => 'bca', 'BcaB03g15382' => 'bca', 'BcaB08g36994' => 'bca', 'BcaC03g13477' => 'bca', 'BcaC03g13478' => 'bca', 'BcaC03g13480' => 'bca', 'BcaC03g13481' => 'bca', 'BcaC03g13486' => 'bca', 'BcaC04g19031' => 'bca', 'BcaC04g23085' => 'bca', 'BcaC05g25094' => 'bca', 'BcaC05g25096' => 'bca', 'BcaC05g25138' => 'bca', 'BcaC05g30416' => 'bca', 'BcaC05g30455' => 'bca', 'BcaC06g30979' => 'bca', 'BcaC06g33805' => 'bca', 'BcaC08g46021' => 'bca', 'BcaNung03154' => 'bca', 'BolC2t06623H' => 'bol', 'BolC2t06632H' => 'bol', 'BolC2t06635H' => 'bol', 'BolC2t06638H' => 'bol', 'BolC3t13266H' => 'bol', 'BolC5t29776H' => 'bol', 'BolC6t38912H' => 'bol', 'BolC7t44183H' => 'bol', 'BolC9t54123H' => 'bol', 'BolC9t59107H' => 'bol', 'BraA02t05221Z' => 'bra', 'BraA03t09996Z' => 'bra', 'BraA05t23210Z' => 'bra', 'BraA06t24068Z' => 'bra', 'BraA06t27032Z' => 'bra', 'BraA08t35176Z' => 'bra', 'BraA09t36680Z' => 'bra', 'BraA10t44471Z' => 'bra', 'C02p06760' => 'bna', 'C02p06890' => 'bna', 'C02p07010' => 'bna', 'C03p07660' => 'bna', 'C05p10300' => 'bna', 'C06p38150' => 'bna', 'C07p36650' => 'bna', 'C08p15770' => 'bna', 'C09p12300' => 'bna', 'C09p62700' => 'bna', 'C09p75040' => 'bna', 'CAN.G13.1' => 'can', 'CAN.G138.4' => 'can', 'CAN.G44.6' => 'can', 'CAN.G473.19' => 'can', 'CANSAT01G0835' => 'cansat', 'CANSAT11G0246' => 'cansat', 'CANSAT11G1766' => 'cansat', 'CANSAT64G1954' => 'cansat', 'CARHR013330' => 'chi', 'CARHR060530' => 'chi', 'CARHR075300' => 'chi', 'CARHR105120' => 'chi', 'CARHR148910' => 'chi', 'CARHR198830' => 'chi', 'Carub.0001s1275' => 'cru', 'Carub.0002s1437' => 'cru', 'Carub.0003s0044' => 'cru', 'Carub.0003s2787' => 'cru', 'Carub.0005s0597' => 'cru', 'Carub.0006s1266' => 'cru', 'Ca_06935_v3' => 'car', 'Ca_13559_v3' => 'car', 'Ca_16941_v3' => 'car', 'Ca_16960_v3' => 'car', 'Ca_17775_v3' => 'car', 'Ca_30464_v3' => 'car', 'Cc06_g08160' => 'ccan', 'Cc07_g01520' => 'ccan', 'Cc11_g15810' => 'ccan', 'CDE02G2840' => 'cde', 'CDE03G0093' => 'cde', 'CDE04G2127' => 'cde', 'CDE07G1857' => 'cde', 'CDE09G1246' => 'cde', 'Cfa003412' => 'cfa', 'Cfa007341' => 'cfa', 'Cfa009220' => 'cfa', 'Ciclev10008737m.g' => 'ccl', 'Ciclev10015565m.g' => 'ccl', 'Ciclev10031761m.g' => 'ccl', 'CiPaw.03G045300' => 'cil', 'CiPaw.03G247200' => 'cil', 'CiPaw.04G029500' => 'cil', 'CiPaw.04G174000' => 'cil', 'CiPaw.05G181200' => 'cil', 'CiPaw.06G067100' => 'cil', 'ClCG05G025800' => 'cla', 'ClCG06G011400' => 'cla', 'ClCG09G019360' => 'cla', 'COL.COLO4_04827' => 'col', 'COL.COLO4_29170' => 'col', 'COL.COLO4_35131' => 'col', 'COL.COLO4_35132' => 'col', 'Cpa.g.sc33.32' => 'cpa', 'Cpa.g.sc46.29' => 'cpa', 'Cpa.g.sc796.1' => 'cpa', 'CsaV3_1G030420' => 'csa', 'CsaV3_5G027050' => 'csa', 'CsaV3_5G031040' => 'csa', 'CsaV3_UNG023130' => 'csa', 'CSS0007726' => 'camsi', 'CSS0016433' => 'camsi', 'CSS0017656' => 'camsi', 'CSS0025364' => 'camsi', 'CSS0027582' => 'camsi', 'CSS0047288' => 'camsi', 'CSS0049950' => 'camsi', 'DCAR_003843' => 'dca', 'DCAR_007052' => 'dca', 'DCAR_020884' => 'dca', 'DCAR_021730' => 'dca', 'DCAR_024423' => 'dca', 'DCAR_026509' => 'dca', 'DCAR_031158' => 'dca', 'Dinv14728' => 'din', 'Dinv15219' => 'din', 'Dinv25728' => 'din', 'Dinv33428' => 'din', 'Dinv36489' => 'din', 'Dinv41486' => 'din', 'Duzib147G0469' => 'dzi', 'Duzib168G0060' => 'dzi', 'Duzib187G1215' => 'dzi', 'Duzib248G0692' => 'dzi', 'Duzib251G0767' => 'dzi', 'Duzib264G0446' => 'dzi', 'Duzib268G0691' => 'dzi', 'ECA232G4767' => 'eca', 'ECA233G2838' => 'eca', 'ECA234G0391' => 'eca', 'ECA234G0857' => 'eca', 'ECA236G1593' => 'eca', 'ECA238G0565' => 'eca', 'ECA246G1027' => 'eca', 'ECA246G3223' => 'eca', 'ECA246G3470' => 'eca', 'EL10Ac6g13829' => 'bvu', 'EL10Ac6g14093' => 'bvu', 'EL10Ac8g18707' => 'bvu', 'Eucgr.C01369' => 'egr', 'Eucgr.H02492' => 'egr', 'Eucgr.I01733' => 'egr', 'Eucgr.J02255' => 'egr', 'Eucgr.J02257' => 'egr', 'Eucgr.J02258' => 'egr', 'FAN02G1601' => 'fan', 'FAN03G1586' => 'fan', 'FAN03G2986' => 'fan', 'FAN05G4837' => 'fan', 'FAN06G0146' => 'fan', 'FAN07G0858' => 'fan', 'FAN09G3179' => 'fan', 'FAN10G0669' => 'fan', 'FAN12G2358' => 'fan', 'FAN14G4198' => 'fan', 'FAN14G5112' => 'fan', 'FAN17G0342' => 'fan', 'FAN19G0342' => 'fan', 'FAN19G0962' => 'fan', 'FAN19G1101' => 'fan', 'FAN19G1872' => 'fan', 'FAN22G0356' => 'fan', 'FAN23G0744' => 'fan', 'FAN23G1914' => 'fan', 'FAN26G0032' => 'fan', 'FAN28G0625' => 'fan', 'FvH4_1g02710' => 'fve', 'FvH4_1g02720' => 'fve', 'FvH4_4g25670' => 'fve', 'FvH4_6g51700' => 'fve', 'FvH4_7g20170' => 'fve', 'Glyma.05G175000' => 'gma', 'Glyma.08G132300' => 'gma', 'Glyma.11G243000' => 'gma', 'Glyma.13G158900' => 'gma', 'Glyma.17G112400' => 'gma', 'Glyma.18G014100' => 'gma', 'Glyma.19G003100' => 'gma', 'Glyma.19G056500' => 'gma', 'Gohir.A01G158900' => 'ghi', 'Gohir.A05G312600' => 'ghi', 'Gohir.A05G354900' => 'ghi', 'Gohir.A07G037200' => 'ghi', 'Gohir.A09G030000' => 'ghi', 'Gohir.A12G145200' => 'ghi', 'Gohir.D01G151500' => 'ghi', 'Gohir.D04G058300' => 'ghi', 'Gohir.D05G314100' => 'ghi', 'Gohir.D07G041400' => 'ghi', 'Gohir.D09G029700' => 'ghi', 'Gohir.D12G149700' => 'ghi', 'Gorai.001G043800' => 'gra', 'Gorai.002G187800' => 'gra', 'Gorai.006G034700' => 'gra', 'Gorai.008G161200' => 'gra', 'Gorai.009G335700' => 'gra', 'Gorai.012G065000' => 'gra', 'GSVIVG01000535001' => 'vvi', 'GSVIVG01015572001' => 'vvi', 'GSVIVG01032386001' => 'vvi', 'HanXRQChr05g0138531' => 'han', 'HanXRQChr06g0174391' => 'han', 'HanXRQChr07g0199021' => 'han', 'HanXRQChr08g0208211' => 'han', 'HanXRQChr09g0255471' => 'han', 'HanXRQChr10g0315791' => 'han', 'HanXRQChr12g0371991' => 'han', 'HanXRQChr15g0475251' => 'han', 'HanXRQChr17g0540001' => 'han', 'HanXRQChr17g0548631' => 'han', 'HanXRQChr17g0569561' => 'han', 'Haze_12256' => 'cav', 'Haze_14756' => 'cav', 'Haze_25528' => 'cav', 'Hma1.2p1_0079F.1_g041020' => 'hma', 'Hma1.2p1_0818F.1_g223260' => 'hma', 'Hma1.2p1_1747F.1_g300530' => 'hma', 'HPP92_004607' => 'vpl', 'HPP92_004608' => 'vpl', 'HPP92_006181' => 'vpl', 'HPP92_012192' => 'vpl', 'HPP92_015680' => 'vpl', 'HPP92_020249' => 'vpl', 'HPP92_021376' => 'vpl', 'HPP92_024275' => 'vpl', 'Hund06031' => 'sun', 'Hund25391' => 'sun', 'Lalb_Chr07g0185371' => 'lal', 'Lalb_Chr07g0185381' => 'lal', 'Lalb_Chr12g0204011' => 'lal', 'Lalb_Chr13g0301671' => 'lal', 'Lalb_Chr14g0362851' => 'lal', 'Lalb_Chr24g0403581' => 'lal', 'Lj1g0000233' => 'lja', 'Lj2g0018120' => 'lja', 'Lj3C621T0' => 'lonja', 'Lj3P1059T14' => 'lonja', 'Lj3P611T9' => 'lonja', 'Lj3P614T13' => 'lonja', 'Lj3P615T5' => 'lonja', 'Lj4g0012315' => 'lja', 'Lj4g0026182' => 'lja', 'Lj6P813T16' => 'lonja', 'Lj7C427T7' => 'lonja', 'Lj7C427T8' => 'lonja', 'Lj7P600T41' => 'lonja', 'Lju41C42G17' => 'lonja', 'Lsat_1_v5_gn_0_47300' => 'lsa', 'Lsat_1_v5_gn_2_91280' => 'lsa', 'Lsat_1_v5_gn_3_30561' => 'lsa', 'Lsat_1_v5_gn_4_184321' => 'lsa', 'Lsat_1_v5_gn_4_4041' => 'lsa', 'Lsat_1_v5_gn_5_92000' => 'lsa', 'Lsat_1_v5_gn_8_152940' => 'lsa', 'Lsat_1_v5_gn_8_62401' => 'lsa', 'Manes.06G055900' => 'mes', 'Manes.12G022200' => 'mes', 'Manes.13G023300' => 'mes', 'Manes.14G115000' => 'mes', 'Manes.15G151700' => 'mes', 'Manes.17G111300' => 'mes', 'Mapoly0226s0009' => 'mpo', 'MBI02_g25363_MAGBIO' => 'mbi', 'MBI06_g00027_MAGBIO' => 'mbi', 'MBI10_g13034_MAGBIO' => 'mbi', 'MD09G1023400' => 'mdo', 'MD13G1100100' => 'mdo', 'MD15G1169200' => 'mdo', 'MD16G1101100' => 'mdo', 'MD17G1022900' => 'mdo', 'Medtr3g096150' => 'mtr', 'Medtr4g115070' => 'mtr', 'Medtr7g033325' => 'mtr', 'Medtr8g089840' => 'mtr', 'MELO3C010319.2' => 'cme', 'MELO3C011944.2' => 'cme', 'MELO3C021589.2' => 'cme', 'Migut.E00207' => 'egut', 'Migut.H00067' => 'egut', 'Migut.K00433' => 'egut', 'Migut.K00606' => 'egut', 'Migut.K01410' => 'egut', 'MSTRG.13347' => 'ama', 'MSTRG.24045' => 'ama', 'MSTRG.2428' => 'ama', 'MSTRG.26410' => 'ama', 'MSTRG.3139' => 'ama', 'MSTRG.3286' => 'ama', 'MSTRG.563' => 'ama', 'MSTRG.7941' => 'ama', 'Nitab4.5_0000028g0060' => 'nta', 'Nitab4.5_0000065g0260' => 'nta', 'Nitab4.5_0000112g0060' => 'nta', 'Nitab4.5_0000489g0120' => 'nta', 'Nitab4.5_0001776g0050' => 'nta', 'Nitab4.5_0001854g0010' => 'nta', 'Nitab4.5_0001860g0020' => 'nta', 'Nitab4.5_0004352g0010' => 'nta', 'Nitab4.5_0008716g0020' => 'nta', 'Nitab4.5_0008922g0010' => 'nta', 'Nn3g16693' => 'nnu', 'Nn4g22596' => 'nnu', 'Nn7g37639' => 'nnu', 'Oeu001701.1' => 'oeu', 'Oeu018149.1' => 'oeu', 'Oeu026220.1' => 'oeu', 'Oeu038635.1' => 'oeu', 'Oeu049176.1' => 'oeu', 'Oeu056706.1' => 'oeu', 'Oeu056937.1' => 'oeu', 'Oeu057540.1' => 'oeu', 'Os02g0594900' => 'osa', 'Os02g0595100' => 'osa', 'Os04g0477500' => 'osa', 'Os12g0611900' => 'osa', 'Peaxi162Scf00076g00020' => 'pax', 'Peaxi162Scf00128g00217' => 'pax', 'Peaxi162Scf00129g01640' => 'pax', 'Peaxi162Scf00669g00007' => 'pax', 'Peaxi162Scf00700g00421' => 'pax', 'Peaxi162Scf00801g00038' => 'pax', 'Peaxi162Scf00891g00025' => 'pax', 'PGR083G0909' => 'pgr', 'PGR119G1005' => 'pgr', 'PGR142G2236' => 'pgr', 'PGR142G3388' => 'pgr', 'PGSC0003DMG400004514' => 'stu', 'PGSC0003DMG400012635' => 'stu', 'PGSC0003DMG400015730' => 'stu', 'PGSC0003DMG400018611' => 'stu', 'PGSC0003DMG400030897' => 'stu', 'Phvul.001G254800' => 'pvu', 'Phvul.002G260100' => 'pvu', 'Phvul.003G167600' => 'pvu', 'Phvul.004G005100' => 'pvu', 'Potri.001G343600' => 'ptr', 'Potri.006G066700' => 'ptr', 'Potri.008G186000' => 'ptr', 'Potri.010G046900' => 'ptr', 'Potri.018G127900' => 'ptr', 'Pp3c20_17750' => 'ppa', 'Pp3c24_4380' => 'ppa', 'Prupe.1G245800' => 'ppe', 'Prupe.3G293400' => 'ppe', 'Prupe.7G247400' => 'ppe', 'Psat0s145g0120' => 'psa', 'Psat0s595g0040' => 'psa', 'Psat0s595g0120' => 'psa', 'Psat3g175040' => 'psa', 'Psat7g058120' => 'psa', 'PSO017G0428' => 'pso', 'PSO063G7510' => 'pso', 'PSO067G0046' => 'pso', 'PSO478G1073' => 'pso', 'PSO675G3677' => 'pso', 'PSO675G6558' => 'pso', 'PSO675G7520' => 'pso', 'PSO675G8959' => 'pso', 'QL02p074089' => 'qlo', 'QL02p089614' => 'qlo', 'QL03p057736' => 'qlo', 'RcHm_v2.0_Chr1g0364131' => 'rch', 'RcHm_v2.0_Chr2g0087801' => 'rch', 'RcHm_v2.0_Chr2g0087821' => 'rch', 'RcHm_v2.0_Chr2g0173231' => 'rch', 'RcHm_v2.0_Chr4g0433111' => 'rch', 'Rhsim03G0250300' => 'rsi', 'Rhsim08G0048400' => 'rsi', 'Rhsim10G0014800' => 'rsi', 'Rhsim12G0040100' => 'rsi', 'Rhsim12G0109700' => 'rsi', 'Sabra06G0049600' => 'sbr', 'Sabra08G0141000' => 'sbr', 'Sabra10G0021400' => 'sbr', 'Sabra16G0222900' => 'sbr', 'Sabra18G0108600' => 'sbr', 'SalBow1G0433' => 'sbo', 'SalBow1G2038' => 'sbo', 'SalBow1G5003' => 'sbo', 'SalBow7G1197' => 'sbo', 'SalBow8G3506' => 'sbo', 'Sc03g0007300' => 'sci', 'Sc11g0000950' => 'sci', 'Sc14g0008750' => 'sci', 'Sc18g0000420' => 'sci', 'Sed0006754' => 'sed', 'Sed0008741' => 'sed', 'Sed0017172' => 'sed', 'Sed0018925' => 'sed', 'Sed0023326' => 'sed', 'Sed0025909' => 'sed', 'SEGI_05333' => 'sgi', 'SEGI_10362' => 'sgi', 'SEGI_13380' => 'sgi', 'SEGI_24306' => 'sgi', 'SEGI_29077' => 'sgi', 'SEGI_29095' => 'sgi', 'SEGI_36534' => 'sgi', 'SEGI_37506' => 'sgi', 'SEGI_38321' => 'sgi', 'SGA_v2.0_scaffold307G48031' => 'sas', 'SGA_v2.0_scaffold47G17507' => 'sas', 'SGA_v2.0_scaffold63G21736' => 'sas', 'SGA_v2.0_scaffold87G27070' => 'sas', 'SHI17794' => 'shi', 'SHI28851' => 'shi', 'SMO165G0155' => 'smo', 'SMO340G0217' => 'smo', 'SMO367G1210' => 'smo', 'Solyc02g093430.3' => 'sly', 'Solyc05g013580.4' => 'sly', 'Solyc07g008030.3' => 'sly', 'Solyc12g035470.2' => 'sly', 'Sopen02g038020' => 'spe', 'Sopen05g008490' => 'spe', 'Sopen07g003910' => 'spe', 'Sopen12g015240' => 'spe', 'Sp1g11550' => 'spa', 'Sp2g16710' => 'spa', 'Sp3g00430' => 'spa', 'Sp3g26780' => 'spa', 'Sp5g22900' => 'spa', 'Sp6g29530' => 'spa', 'TAR371G0794' => 'tar', 'TAR374G0164' => 'tar', 'TAR622G0165' => 'tar', 'TAR626G0929' => 'tar', 'TAR629G2155' => 'tar', 'THA.LOC104805282' => 'tha', 'THA.LOC104805363' => 'tha', 'THA.LOC104808968' => 'tha', 'THA.LOC104821093' => 'tha', 'THA.LOC104823953' => 'tha', 'THA.LOC104825562' => 'tha', 'THA.LOC104825665' => 'tha', 'Thecc.02G261400' => 'tca', 'Thecc.04G019200' => 'tca', 'Thecc.09G130400' => 'tca', 'Thhalv10004374m.g' => 'esa', 'Thhalv10007850m.g' => 'esa', 'Thhalv10013782m.g' => 'esa', 'Thhalv10018686m.g' => 'esa', 'Thhalv10020899m.g' => 'esa', 'Thhalv10022755m.g' => 'esa', 'TPR.G23851' => 'tpr', 'TPR.G26500' => 'tpr', 'TPR.G27267' => 'tpr', 'TPR.G32001' => 'tpr', 'TPR.G6251' => 'tpr', 'TPR.G8167' => 'tpr', 'TWI12G1330' => 'twi', 'TWI18G1239' => 'twi', 'TWI34G0979' => 'twi', 'TWI36G0670' => 'twi', 'TWI36G0707' => 'twi', 'TWI56G0233' => 'twi', 'TWI75G1809' => 'twi', 'unitig_21.g20874' => 'ugi', 'unitig_26.g10343' => 'ugi', 'unitig_46.g18392' => 'ugi', 'unitig_52.g17178' => 'ugi', 'unitig_8.g2934' => 'ugi', 'vmacro01122' => 'vma', 'vmacro05875' => 'vma', 'vmacro06147' => 'vma', 'vmacro16191' => 'vma', 'vmacro18293' => 'vma', 'VMungo0251G3707' => 'vmu', 'VMungo0464G1521' => 'vmu', 'VMungo1215G0205' => 'vmu', 'VMungo1383G2484' => 'vmu', 'Zm00001eb079610' => 'zma', 'Zm00001eb135990' => 'zma', 'Zm00001eb183710' => 'zma', 'Zm00001eb246020' => 'zma' ), 'gf_id' => 'HOM05D001124', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001124' ), 'data_identifier' => 'HOM05D001124', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001124', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '548', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02520' => 'bna', 'A03p06630' => 'bna', 'A05p44460' => 'bna', 'A06p08710' => 'bna', 'A06p41090' => 'bna', 'A07p32320' => 'bna', 'A08p32520' => 'bna', 'A09p10360' => 'bna', 'A10p24080' => 'bna', 'Aa31LG11G15250' => 'aar', 'Aa31LG1G1800' => 'aar', 'Aa31LG2G5120' => 'aar', 'Aa31LG2G6070' => 'aar', 'Aa31LG5G10770' => 'aar', 'Aa31sc61G90' => 'aar', 'Actinidia01352' => 'ach', 'Actinidia05983' => 'ach', 'Actinidia08133' => 'ach', 'Actinidia15101' => 'ach', 'Actinidia26379' => 'ach', 'Actinidia35778' => 'ach', 'Actinidia36123' => 'ach', 'Actinidia37436' => 'ach', 'Actinidia38730' => 'ach', 'Ah.02g128210' => 'amhyb', 'Ah.03g132990' => 'amhyb', 'Ah.14g079410' => 'amhyb', 'AL1G24640' => 'aly', 'AL2G26680' => 'aly', 'AL3G10530' => 'aly', 'AL3G45230' => 'aly', 'AL5G15230' => 'aly', 'AL5G16960' => 'aly', 'AL6G25210' => 'aly', 'Aqoxy2G00441' => 'aox', 'Aqoxy3G01236' => 'aox', 'Aqoxy5G03746' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3RQ047' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C7GMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9C8JER' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MBL6KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YXCZ83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZANX40' => 'arhy', 'AT1G12990' => 'ath', 'AT1G67880' => 'ath', 'AT2G13290' => 'ath', 'AT3G01620' => 'ath', 'AT3G26445' => 'ath', 'AT3G27540' => 'ath', 'AT5G14480' => 'ath', 'ATR0824G026' => 'atr', 'ATR1098G019' => 'atr', 'Atru.chr11.2145' => 'acertr', 'Atru.chr2.3636' => 'acertr', 'Atru.chr2.3644' => 'acertr', 'Atru.chr6.2422' => 'acertr', 'Atru.chr7.1112' => 'acertr', 'AUR62005469' => 'cqu', 'AUR62011166' => 'cqu', 'AUR62013319' => 'cqu', 'AUR62024273' => 'cqu', 'AUR62028420' => 'cqu', 'AUR62041942' => 'cqu', 'BcaB01g04969' => 'bca', 'BcaB01g06371' => 'bca', 'BcaB02g11494' => 'bca', 'BcaB03g15382' => 'bca', 'BcaB08g36994' => 'bca', 'BcaC03g13477' => 'bca', 'BcaC03g13478' => 'bca', 'BcaC03g13480' => 'bca', 'BcaC03g13481' => 'bca', 'BcaC03g13486' => 'bca', 'BcaC04g19031' => 'bca', 'BcaC04g23085' => 'bca', 'BcaC05g25094' => 'bca', 'BcaC05g25096' => 'bca', 'BcaC05g25138' => 'bca', 'BcaC05g30416' => 'bca', 'BcaC05g30455' => 'bca', 'BcaC06g30979' => 'bca', 'BcaC06g33805' => 'bca', 'BcaC08g46021' => 'bca', 'BcaNung03154' => 'bca', 'BolC2t06623H' => 'bol', 'BolC2t06632H' => 'bol', 'BolC2t06635H' => 'bol', 'BolC2t06638H' => 'bol', 'BolC3t13266H' => 'bol', 'BolC5t29776H' => 'bol', 'BolC6t38912H' => 'bol', 'BolC7t44183H' => 'bol', 'BolC9t54123H' => 'bol', 'BolC9t59107H' => 'bol', 'BraA02t05221Z' => 'bra', 'BraA03t09996Z' => 'bra', 'BraA05t23210Z' => 'bra', 'BraA06t24068Z' => 'bra', 'BraA06t27032Z' => 'bra', 'BraA08t35176Z' => 'bra', 'BraA09t36680Z' => 'bra', 'BraA10t44471Z' => 'bra', 'C02p06760' => 'bna', 'C02p06890' => 'bna', 'C02p07010' => 'bna', 'C03p07660' => 'bna', 'C05p10300' => 'bna', 'C06p38150' => 'bna', 'C07p36650' => 'bna', 'C08p15770' => 'bna', 'C09p12300' => 'bna', 'C09p62700' => 'bna', 'C09p75040' => 'bna', 'CAN.G13.1' => 'can', 'CAN.G138.4' => 'can', 'CAN.G44.6' => 'can', 'CAN.G473.19' => 'can', 'CANSAT01G0835' => 'cansat', 'CANSAT11G0246' => 'cansat', 'CANSAT11G1766' => 'cansat', 'CANSAT64G1954' => 'cansat', 'CARHR013330' => 'chi', 'CARHR060530' => 'chi', 'CARHR075300' => 'chi', 'CARHR105120' => 'chi', 'CARHR148910' => 'chi', 'CARHR198830' => 'chi', 'Carub.0001s1275' => 'cru', 'Carub.0002s1437' => 'cru', 'Carub.0003s0044' => 'cru', 'Carub.0003s2787' => 'cru', 'Carub.0005s0597' => 'cru', 'Carub.0006s1266' => 'cru', 'Ca_06935_v3' => 'car', 'Ca_13559_v3' => 'car', 'Ca_16941_v3' => 'car', 'Ca_16960_v3' => 'car', 'Ca_17775_v3' => 'car', 'Ca_30464_v3' => 'car', 'Cc06_g08160' => 'ccan', 'Cc07_g01520' => 'ccan', 'Cc11_g15810' => 'ccan', 'CDE02G2840' => 'cde', 'CDE03G0093' => 'cde', 'CDE04G2127' => 'cde', 'CDE07G1857' => 'cde', 'CDE09G1246' => 'cde', 'Cfa003412' => 'cfa', 'Cfa007341' => 'cfa', 'Cfa009220' => 'cfa', 'Ciclev10008737m.g' => 'ccl', 'Ciclev10015565m.g' => 'ccl', 'Ciclev10031761m.g' => 'ccl', 'CiPaw.03G045300' => 'cil', 'CiPaw.03G247200' => 'cil', 'CiPaw.04G029500' => 'cil', 'CiPaw.04G174000' => 'cil', 'CiPaw.05G181200' => 'cil', 'CiPaw.06G067100' => 'cil', 'ClCG05G025800' => 'cla', 'ClCG06G011400' => 'cla', 'ClCG09G019360' => 'cla', 'COL.COLO4_04827' => 'col', 'COL.COLO4_29170' => 'col', 'COL.COLO4_35131' => 'col', 'COL.COLO4_35132' => 'col', 'Cpa.g.sc33.32' => 'cpa', 'Cpa.g.sc46.29' => 'cpa', 'Cpa.g.sc796.1' => 'cpa', 'CsaV3_1G030420' => 'csa', 'CsaV3_5G027050' => 'csa', 'CsaV3_5G031040' => 'csa', 'CsaV3_UNG023130' => 'csa', 'CSS0007726' => 'camsi', 'CSS0016433' => 'camsi', 'CSS0017656' => 'camsi', 'CSS0025364' => 'camsi', 'CSS0027582' => 'camsi', 'CSS0047288' => 'camsi', 'CSS0049950' => 'camsi', 'DCAR_003843' => 'dca', 'DCAR_007052' => 'dca', 'DCAR_020884' => 'dca', 'DCAR_021730' => 'dca', 'DCAR_024423' => 'dca', 'DCAR_026509' => 'dca', 'DCAR_031158' => 'dca', 'Dinv14728' => 'din', 'Dinv15219' => 'din', 'Dinv25728' => 'din', 'Dinv33428' => 'din', 'Dinv36489' => 'din', 'Dinv41486' => 'din', 'Duzib147G0469' => 'dzi', 'Duzib168G0060' => 'dzi', 'Duzib187G1215' => 'dzi', 'Duzib248G0692' => 'dzi', 'Duzib251G0767' => 'dzi', 'Duzib264G0446' => 'dzi', 'Duzib268G0691' => 'dzi', 'ECA232G4767' => 'eca', 'ECA233G2838' => 'eca', 'ECA234G0391' => 'eca', 'ECA234G0857' => 'eca', 'ECA236G1593' => 'eca', 'ECA238G0565' => 'eca', 'ECA246G1027' => 'eca', 'ECA246G3223' => 'eca', 'ECA246G3470' => 'eca', 'EL10Ac6g13829' => 'bvu', 'EL10Ac6g14093' => 'bvu', 'EL10Ac8g18707' => 'bvu', 'Eucgr.C01369' => 'egr', 'Eucgr.H02492' => 'egr', 'Eucgr.I01733' => 'egr', 'Eucgr.J02255' => 'egr', 'Eucgr.J02257' => 'egr', 'Eucgr.J02258' => 'egr', 'FAN02G1601' => 'fan', 'FAN03G1586' => 'fan', 'FAN03G2986' => 'fan', 'FAN05G4837' => 'fan', 'FAN06G0146' => 'fan', 'FAN07G0858' => 'fan', 'FAN09G3179' => 'fan', 'FAN10G0669' => 'fan', 'FAN12G2358' => 'fan', 'FAN14G4198' => 'fan', 'FAN14G5112' => 'fan', 'FAN17G0342' => 'fan', 'FAN19G0342' => 'fan', 'FAN19G0962' => 'fan', 'FAN19G1101' => 'fan', 'FAN19G1872' => 'fan', 'FAN22G0356' => 'fan', 'FAN23G0744' => 'fan', 'FAN23G1914' => 'fan', 'FAN26G0032' => 'fan', 'FAN28G0625' => 'fan', 'FvH4_1g02710' => 'fve', 'FvH4_1g02720' => 'fve', 'FvH4_4g25670' => 'fve', 'FvH4_6g51700' => 'fve', 'FvH4_7g20170' => 'fve', 'Glyma.05G175000' => 'gma', 'Glyma.08G132300' => 'gma', 'Glyma.11G243000' => 'gma', 'Glyma.13G158900' => 'gma', 'Glyma.17G112400' => 'gma', 'Glyma.18G014100' => 'gma', 'Glyma.19G003100' => 'gma', 'Glyma.19G056500' => 'gma', 'Gohir.A01G158900' => 'ghi', 'Gohir.A05G312600' => 'ghi', 'Gohir.A05G354900' => 'ghi', 'Gohir.A07G037200' => 'ghi', 'Gohir.A09G030000' => 'ghi', 'Gohir.A12G145200' => 'ghi', 'Gohir.D01G151500' => 'ghi', 'Gohir.D04G058300' => 'ghi', 'Gohir.D05G314100' => 'ghi', 'Gohir.D07G041400' => 'ghi', 'Gohir.D09G029700' => 'ghi', 'Gohir.D12G149700' => 'ghi', 'Gorai.001G043800' => 'gra', 'Gorai.002G187800' => 'gra', 'Gorai.006G034700' => 'gra', 'Gorai.008G161200' => 'gra', 'Gorai.009G335700' => 'gra', 'Gorai.012G065000' => 'gra', 'GSVIVG01000535001' => 'vvi', 'GSVIVG01015572001' => 'vvi', 'GSVIVG01032386001' => 'vvi', 'HanXRQChr05g0138531' => 'han', 'HanXRQChr06g0174391' => 'han', 'HanXRQChr07g0199021' => 'han', 'HanXRQChr08g0208211' => 'han', 'HanXRQChr09g0255471' => 'han', 'HanXRQChr10g0315791' => 'han', 'HanXRQChr12g0371991' => 'han', 'HanXRQChr15g0475251' => 'han', 'HanXRQChr17g0540001' => 'han', 'HanXRQChr17g0548631' => 'han', 'HanXRQChr17g0569561' => 'han', 'Haze_12256' => 'cav', 'Haze_14756' => 'cav', 'Haze_25528' => 'cav', 'Hma1.2p1_0079F.1_g041020' => 'hma', 'Hma1.2p1_0818F.1_g223260' => 'hma', 'Hma1.2p1_1747F.1_g300530' => 'hma', 'HPP92_004607' => 'vpl', 'HPP92_004608' => 'vpl', 'HPP92_006181' => 'vpl', 'HPP92_012192' => 'vpl', 'HPP92_015680' => 'vpl', 'HPP92_020249' => 'vpl', 'HPP92_021376' => 'vpl', 'HPP92_024275' => 'vpl', 'Hund06031' => 'sun', 'Hund25391' => 'sun', 'Lalb_Chr07g0185371' => 'lal', 'Lalb_Chr07g0185381' => 'lal', 'Lalb_Chr12g0204011' => 'lal', 'Lalb_Chr13g0301671' => 'lal', 'Lalb_Chr14g0362851' => 'lal', 'Lalb_Chr24g0403581' => 'lal', 'Lj1g0000233' => 'lja', 'Lj2g0018120' => 'lja', 'Lj3C621T0' => 'lonja', 'Lj3P1059T14' => 'lonja', 'Lj3P611T9' => 'lonja', 'Lj3P614T13' => 'lonja', 'Lj3P615T5' => 'lonja', 'Lj4g0012315' => 'lja', 'Lj4g0026182' => 'lja', 'Lj6P813T16' => 'lonja', 'Lj7C427T7' => 'lonja', 'Lj7C427T8' => 'lonja', 'Lj7P600T41' => 'lonja', 'Lju41C42G17' => 'lonja', 'Lsat_1_v5_gn_0_47300' => 'lsa', 'Lsat_1_v5_gn_2_91280' => 'lsa', 'Lsat_1_v5_gn_3_30561' => 'lsa', 'Lsat_1_v5_gn_4_184321' => 'lsa', 'Lsat_1_v5_gn_4_4041' => 'lsa', 'Lsat_1_v5_gn_5_92000' => 'lsa', 'Lsat_1_v5_gn_8_152940' => 'lsa', 'Lsat_1_v5_gn_8_62401' => 'lsa', 'Manes.06G055900' => 'mes', 'Manes.12G022200' => 'mes', 'Manes.13G023300' => 'mes', 'Manes.14G115000' => 'mes', 'Manes.15G151700' => 'mes', 'Manes.17G111300' => 'mes', 'Mapoly0226s0009' => 'mpo', 'MBI02_g25363_MAGBIO' => 'mbi', 'MBI06_g00027_MAGBIO' => 'mbi', 'MBI10_g13034_MAGBIO' => 'mbi', 'MD09G1023400' => 'mdo', 'MD13G1100100' => 'mdo', 'MD15G1169200' => 'mdo', 'MD16G1101100' => 'mdo', 'MD17G1022900' => 'mdo', 'Medtr3g096150' => 'mtr', 'Medtr4g115070' => 'mtr', 'Medtr7g033325' => 'mtr', 'Medtr8g089840' => 'mtr', 'MELO3C010319.2' => 'cme', 'MELO3C011944.2' => 'cme', 'MELO3C021589.2' => 'cme', 'Migut.E00207' => 'egut', 'Migut.H00067' => 'egut', 'Migut.K00433' => 'egut', 'Migut.K00606' => 'egut', 'Migut.K01410' => 'egut', 'MSTRG.13347' => 'ama', 'MSTRG.24045' => 'ama', 'MSTRG.2428' => 'ama', 'MSTRG.26410' => 'ama', 'MSTRG.3139' => 'ama', 'MSTRG.3286' => 'ama', 'MSTRG.563' => 'ama', 'MSTRG.7941' => 'ama', 'Nitab4.5_0000028g0060' => 'nta', 'Nitab4.5_0000065g0260' => 'nta', 'Nitab4.5_0000112g0060' => 'nta', 'Nitab4.5_0000489g0120' => 'nta', 'Nitab4.5_0001776g0050' => 'nta', 'Nitab4.5_0001854g0010' => 'nta', 'Nitab4.5_0001860g0020' => 'nta', 'Nitab4.5_0004352g0010' => 'nta', 'Nitab4.5_0008716g0020' => 'nta', 'Nitab4.5_0008922g0010' => 'nta', 'Nn3g16693' => 'nnu', 'Nn4g22596' => 'nnu', 'Nn7g37639' => 'nnu', 'Oeu001701.1' => 'oeu', 'Oeu018149.1' => 'oeu', 'Oeu026220.1' => 'oeu', 'Oeu038635.1' => 'oeu', 'Oeu049176.1' => 'oeu', 'Oeu056706.1' => 'oeu', 'Oeu056937.1' => 'oeu', 'Oeu057540.1' => 'oeu', 'Os02g0594900' => 'osa', 'Os02g0595100' => 'osa', 'Os04g0477500' => 'osa', 'Os12g0611900' => 'osa', 'Peaxi162Scf00076g00020' => 'pax', 'Peaxi162Scf00128g00217' => 'pax', 'Peaxi162Scf00129g01640' => 'pax', 'Peaxi162Scf00669g00007' => 'pax', 'Peaxi162Scf00700g00421' => 'pax', 'Peaxi162Scf00801g00038' => 'pax', 'Peaxi162Scf00891g00025' => 'pax', 'PGR083G0909' => 'pgr', 'PGR119G1005' => 'pgr', 'PGR142G2236' => 'pgr', 'PGR142G3388' => 'pgr', 'PGSC0003DMG400004514' => 'stu', 'PGSC0003DMG400012635' => 'stu', 'PGSC0003DMG400015730' => 'stu', 'PGSC0003DMG400018611' => 'stu', 'PGSC0003DMG400030897' => 'stu', 'Phvul.001G254800' => 'pvu', 'Phvul.002G260100' => 'pvu', 'Phvul.003G167600' => 'pvu', 'Phvul.004G005100' => 'pvu', 'Potri.001G343600' => 'ptr', 'Potri.006G066700' => 'ptr', 'Potri.008G186000' => 'ptr', 'Potri.010G046900' => 'ptr', 'Potri.018G127900' => 'ptr', 'Pp3c20_17750' => 'ppa', 'Pp3c24_4380' => 'ppa', 'Prupe.1G245800' => 'ppe', 'Prupe.3G293400' => 'ppe', 'Prupe.7G247400' => 'ppe', 'Psat0s145g0120' => 'psa', 'Psat0s595g0040' => 'psa', 'Psat0s595g0120' => 'psa', 'Psat3g175040' => 'psa', 'Psat7g058120' => 'psa', 'PSO017G0428' => 'pso', 'PSO063G7510' => 'pso', 'PSO067G0046' => 'pso', 'PSO478G1073' => 'pso', 'PSO675G3677' => 'pso', 'PSO675G6558' => 'pso', 'PSO675G7520' => 'pso', 'PSO675G8959' => 'pso', 'QL02p074089' => 'qlo', 'QL02p089614' => 'qlo', 'QL03p057736' => 'qlo', 'RcHm_v2.0_Chr1g0364131' => 'rch', 'RcHm_v2.0_Chr2g0087801' => 'rch', 'RcHm_v2.0_Chr2g0087821' => 'rch', 'RcHm_v2.0_Chr2g0173231' => 'rch', 'RcHm_v2.0_Chr4g0433111' => 'rch', 'Rhsim03G0250300' => 'rsi', 'Rhsim08G0048400' => 'rsi', 'Rhsim10G0014800' => 'rsi', 'Rhsim12G0040100' => 'rsi', 'Rhsim12G0109700' => 'rsi', 'Sabra06G0049600' => 'sbr', 'Sabra08G0141000' => 'sbr', 'Sabra10G0021400' => 'sbr', 'Sabra16G0222900' => 'sbr', 'Sabra18G0108600' => 'sbr', 'SalBow1G0433' => 'sbo', 'SalBow1G2038' => 'sbo', 'SalBow1G5003' => 'sbo', 'SalBow7G1197' => 'sbo', 'SalBow8G3506' => 'sbo', 'Sc03g0007300' => 'sci', 'Sc11g0000950' => 'sci', 'Sc14g0008750' => 'sci', 'Sc18g0000420' => 'sci', 'Sed0006754' => 'sed', 'Sed0008741' => 'sed', 'Sed0017172' => 'sed', 'Sed0018925' => 'sed', 'Sed0023326' => 'sed', 'Sed0025909' => 'sed', 'SEGI_05333' => 'sgi', 'SEGI_10362' => 'sgi', 'SEGI_13380' => 'sgi', 'SEGI_24306' => 'sgi', 'SEGI_29077' => 'sgi', 'SEGI_29095' => 'sgi', 'SEGI_36534' => 'sgi', 'SEGI_37506' => 'sgi', 'SEGI_38321' => 'sgi', 'SGA_v2.0_scaffold307G48031' => 'sas', 'SGA_v2.0_scaffold47G17507' => 'sas', 'SGA_v2.0_scaffold63G21736' => 'sas', 'SGA_v2.0_scaffold87G27070' => 'sas', 'SHI17794' => 'shi', 'SHI28851' => 'shi', 'SMO165G0155' => 'smo', 'SMO340G0217' => 'smo', 'SMO367G1210' => 'smo', 'Solyc02g093430.3' => 'sly', 'Solyc05g013580.4' => 'sly', 'Solyc07g008030.3' => 'sly', 'Solyc12g035470.2' => 'sly', 'Sopen02g038020' => 'spe', 'Sopen05g008490' => 'spe', 'Sopen07g003910' => 'spe', 'Sopen12g015240' => 'spe', 'Sp1g11550' => 'spa', 'Sp2g16710' => 'spa', 'Sp3g00430' => 'spa', 'Sp3g26780' => 'spa', 'Sp5g22900' => 'spa', 'Sp6g29530' => 'spa', 'TAR371G0794' => 'tar', 'TAR374G0164' => 'tar', 'TAR622G0165' => 'tar', 'TAR626G0929' => 'tar', 'TAR629G2155' => 'tar', 'THA.LOC104805282' => 'tha', 'THA.LOC104805363' => 'tha', 'THA.LOC104808968' => 'tha', 'THA.LOC104821093' => 'tha', 'THA.LOC104823953' => 'tha', 'THA.LOC104825562' => 'tha', 'THA.LOC104825665' => 'tha', 'Thecc.02G261400' => 'tca', 'Thecc.04G019200' => 'tca', 'Thecc.09G130400' => 'tca', 'Thhalv10004374m.g' => 'esa', 'Thhalv10007850m.g' => 'esa', 'Thhalv10013782m.g' => 'esa', 'Thhalv10018686m.g' => 'esa', 'Thhalv10020899m.g' => 'esa', 'Thhalv10022755m.g' => 'esa', 'TPR.G23851' => 'tpr', 'TPR.G26500' => 'tpr', 'TPR.G27267' => 'tpr', 'TPR.G32001' => 'tpr', 'TPR.G6251' => 'tpr', 'TPR.G8167' => 'tpr', 'TWI12G1330' => 'twi', 'TWI18G1239' => 'twi', 'TWI34G0979' => 'twi', 'TWI36G0670' => 'twi', 'TWI36G0707' => 'twi', 'TWI56G0233' => 'twi', 'TWI75G1809' => 'twi', 'unitig_21.g20874' => 'ugi', 'unitig_26.g10343' => 'ugi', 'unitig_46.g18392' => 'ugi', 'unitig_52.g17178' => 'ugi', 'unitig_8.g2934' => 'ugi', 'vmacro01122' => 'vma', 'vmacro05875' => 'vma', 'vmacro06147' => 'vma', 'vmacro16191' => 'vma', 'vmacro18293' => 'vma', 'VMungo0251G3707' => 'vmu', 'VMungo0464G1521' => 'vmu', 'VMungo1215G0205' => 'vmu', 'VMungo1383G2484' => 'vmu', 'Zm00001eb079610' => 'zma', 'Zm00001eb135990' => 'zma', 'Zm00001eb183710' => 'zma', 'Zm00001eb246020' => 'zma' ) $gf_id = 'HOM05D001124' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001124' ) $data_identifier = 'HOM05D001124' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 6, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 7, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 21, 'bol' => (int) 10, 'bra' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 6, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 9, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 21, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 8, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 10, 'lsa' => (int) 8, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 8, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 9, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb246020' $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' => 'HOM05D001124', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '548', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02520' => 'bna', 'A03p06630' => 'bna', 'A05p44460' => 'bna', 'A06p08710' => 'bna', 'A06p41090' => 'bna', 'A07p32320' => 'bna', 'A08p32520' => 'bna', 'A09p10360' => 'bna', 'A10p24080' => 'bna', 'Aa31LG11G15250' => 'aar', 'Aa31LG1G1800' => 'aar', 'Aa31LG2G5120' => 'aar', 'Aa31LG2G6070' => 'aar', 'Aa31LG5G10770' => 'aar', 'Aa31sc61G90' => 'aar', 'Actinidia01352' => 'ach', 'Actinidia05983' => 'ach', 'Actinidia08133' => 'ach', 'Actinidia15101' => 'ach', 'Actinidia26379' => 'ach', 'Actinidia35778' => 'ach', 'Actinidia36123' => 'ach', 'Actinidia37436' => 'ach', 'Actinidia38730' => 'ach', 'Ah.02g128210' => 'amhyb', 'Ah.03g132990' => 'amhyb', 'Ah.14g079410' => 'amhyb', 'AL1G24640' => 'aly', 'AL2G26680' => 'aly', 'AL3G10530' => 'aly', 'AL3G45230' => 'aly', 'AL5G15230' => 'aly', 'AL5G16960' => 'aly', 'AL6G25210' => 'aly', 'Aqoxy2G00441' => 'aox', 'Aqoxy3G01236' => 'aox', 'Aqoxy5G03746' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3RQ047' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C7GMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9C8JER' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MBL6KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YXCZ83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZANX40' => 'arhy', 'AT1G12990' => 'ath', 'AT1G67880' => 'ath', 'AT2G13290' => 'ath', 'AT3G01620' => 'ath', 'AT3G26445' => 'ath', 'AT3G27540' => 'ath', 'AT5G14480' => 'ath', 'ATR0824G026' => 'atr', 'ATR1098G019' => 'atr', 'Atru.chr11.2145' => 'acertr', 'Atru.chr2.3636' => 'acertr', 'Atru.chr2.3644' => 'acertr', 'Atru.chr6.2422' => 'acertr', 'Atru.chr7.1112' => 'acertr', 'AUR62005469' => 'cqu', 'AUR62011166' => 'cqu', 'AUR62013319' => 'cqu', 'AUR62024273' => 'cqu', 'AUR62028420' => 'cqu', 'AUR62041942' => 'cqu', 'BcaB01g04969' => 'bca', 'BcaB01g06371' => 'bca', 'BcaB02g11494' => 'bca', 'BcaB03g15382' => 'bca', 'BcaB08g36994' => 'bca', 'BcaC03g13477' => 'bca', 'BcaC03g13478' => 'bca', 'BcaC03g13480' => 'bca', 'BcaC03g13481' => 'bca', 'BcaC03g13486' => 'bca', 'BcaC04g19031' => 'bca', 'BcaC04g23085' => 'bca', 'BcaC05g25094' => 'bca', 'BcaC05g25096' => 'bca', 'BcaC05g25138' => 'bca', 'BcaC05g30416' => 'bca', 'BcaC05g30455' => 'bca', 'BcaC06g30979' => 'bca', 'BcaC06g33805' => 'bca', 'BcaC08g46021' => 'bca', 'BcaNung03154' => 'bca', 'BolC2t06623H' => 'bol', 'BolC2t06632H' => 'bol', 'BolC2t06635H' => 'bol', 'BolC2t06638H' => 'bol', 'BolC3t13266H' => 'bol', 'BolC5t29776H' => 'bol', 'BolC6t38912H' => 'bol', 'BolC7t44183H' => 'bol', 'BolC9t54123H' => 'bol', 'BolC9t59107H' => 'bol', 'BraA02t05221Z' => 'bra', 'BraA03t09996Z' => 'bra', 'BraA05t23210Z' => 'bra', 'BraA06t24068Z' => 'bra', 'BraA06t27032Z' => 'bra', 'BraA08t35176Z' => 'bra', 'BraA09t36680Z' => 'bra', 'BraA10t44471Z' => 'bra', 'C02p06760' => 'bna', 'C02p06890' => 'bna', 'C02p07010' => 'bna', 'C03p07660' => 'bna', 'C05p10300' => 'bna', 'C06p38150' => 'bna', 'C07p36650' => 'bna', 'C08p15770' => 'bna', 'C09p12300' => 'bna', 'C09p62700' => 'bna', 'C09p75040' => 'bna', 'CAN.G13.1' => 'can', 'CAN.G138.4' => 'can', 'CAN.G44.6' => 'can', 'CAN.G473.19' => 'can', 'CANSAT01G0835' => 'cansat', 'CANSAT11G0246' => 'cansat', 'CANSAT11G1766' => 'cansat', 'CANSAT64G1954' => 'cansat', 'CARHR013330' => 'chi', 'CARHR060530' => 'chi', 'CARHR075300' => 'chi', 'CARHR105120' => 'chi', 'CARHR148910' => 'chi', 'CARHR198830' => 'chi', 'Carub.0001s1275' => 'cru', 'Carub.0002s1437' => 'cru', 'Carub.0003s0044' => 'cru', 'Carub.0003s2787' => 'cru', 'Carub.0005s0597' => 'cru', 'Carub.0006s1266' => 'cru', 'Ca_06935_v3' => 'car', 'Ca_13559_v3' => 'car', 'Ca_16941_v3' => 'car', 'Ca_16960_v3' => 'car', 'Ca_17775_v3' => 'car', 'Ca_30464_v3' => 'car', 'Cc06_g08160' => 'ccan', 'Cc07_g01520' => 'ccan', 'Cc11_g15810' => 'ccan', 'CDE02G2840' => 'cde', 'CDE03G0093' => 'cde', 'CDE04G2127' => 'cde', 'CDE07G1857' => 'cde', 'CDE09G1246' => 'cde', 'Cfa003412' => 'cfa', 'Cfa007341' => 'cfa', 'Cfa009220' => 'cfa', 'Ciclev10008737m.g' => 'ccl', 'Ciclev10015565m.g' => 'ccl', 'Ciclev10031761m.g' => 'ccl', 'CiPaw.03G045300' => 'cil', 'CiPaw.03G247200' => 'cil', 'CiPaw.04G029500' => 'cil', 'CiPaw.04G174000' => 'cil', 'CiPaw.05G181200' => 'cil', 'CiPaw.06G067100' => 'cil', 'ClCG05G025800' => 'cla', 'ClCG06G011400' => 'cla', 'ClCG09G019360' => 'cla', 'COL.COLO4_04827' => 'col', 'COL.COLO4_29170' => 'col', 'COL.COLO4_35131' => 'col', 'COL.COLO4_35132' => 'col', 'Cpa.g.sc33.32' => 'cpa', 'Cpa.g.sc46.29' => 'cpa', 'Cpa.g.sc796.1' => 'cpa', 'CsaV3_1G030420' => 'csa', 'CsaV3_5G027050' => 'csa', 'CsaV3_5G031040' => 'csa', 'CsaV3_UNG023130' => 'csa', 'CSS0007726' => 'camsi', 'CSS0016433' => 'camsi', 'CSS0017656' => 'camsi', 'CSS0025364' => 'camsi', 'CSS0027582' => 'camsi', 'CSS0047288' => 'camsi', 'CSS0049950' => 'camsi', 'DCAR_003843' => 'dca', 'DCAR_007052' => 'dca', 'DCAR_020884' => 'dca', 'DCAR_021730' => 'dca', 'DCAR_024423' => 'dca', 'DCAR_026509' => 'dca', 'DCAR_031158' => 'dca', 'Dinv14728' => 'din', 'Dinv15219' => 'din', 'Dinv25728' => 'din', 'Dinv33428' => 'din', 'Dinv36489' => 'din', 'Dinv41486' => 'din', 'Duzib147G0469' => 'dzi', 'Duzib168G0060' => 'dzi', 'Duzib187G1215' => 'dzi', 'Duzib248G0692' => 'dzi', 'Duzib251G0767' => 'dzi', 'Duzib264G0446' => 'dzi', 'Duzib268G0691' => 'dzi', 'ECA232G4767' => 'eca', 'ECA233G2838' => 'eca', 'ECA234G0391' => 'eca', 'ECA234G0857' => 'eca', 'ECA236G1593' => 'eca', 'ECA238G0565' => 'eca', 'ECA246G1027' => 'eca', 'ECA246G3223' => 'eca', 'ECA246G3470' => 'eca', 'EL10Ac6g13829' => 'bvu', 'EL10Ac6g14093' => 'bvu', 'EL10Ac8g18707' => 'bvu', 'Eucgr.C01369' => 'egr', 'Eucgr.H02492' => 'egr', 'Eucgr.I01733' => 'egr', 'Eucgr.J02255' => 'egr', 'Eucgr.J02257' => 'egr', 'Eucgr.J02258' => 'egr', 'FAN02G1601' => 'fan', 'FAN03G1586' => 'fan', 'FAN03G2986' => 'fan', 'FAN05G4837' => 'fan', 'FAN06G0146' => 'fan', 'FAN07G0858' => 'fan', 'FAN09G3179' => 'fan', 'FAN10G0669' => 'fan', 'FAN12G2358' => 'fan', 'FAN14G4198' => 'fan', 'FAN14G5112' => 'fan', 'FAN17G0342' => 'fan', 'FAN19G0342' => 'fan', 'FAN19G0962' => 'fan', 'FAN19G1101' => 'fan', 'FAN19G1872' => 'fan', 'FAN22G0356' => 'fan', 'FAN23G0744' => 'fan', 'FAN23G1914' => 'fan', 'FAN26G0032' => 'fan', 'FAN28G0625' => 'fan', 'FvH4_1g02710' => 'fve', 'FvH4_1g02720' => 'fve', 'FvH4_4g25670' => 'fve', 'FvH4_6g51700' => 'fve', 'FvH4_7g20170' => 'fve', 'Glyma.05G175000' => 'gma', 'Glyma.08G132300' => 'gma', 'Glyma.11G243000' => 'gma', 'Glyma.13G158900' => 'gma', 'Glyma.17G112400' => 'gma', 'Glyma.18G014100' => 'gma', 'Glyma.19G003100' => 'gma', 'Glyma.19G056500' => 'gma', 'Gohir.A01G158900' => 'ghi', 'Gohir.A05G312600' => 'ghi', 'Gohir.A05G354900' => 'ghi', 'Gohir.A07G037200' => 'ghi', 'Gohir.A09G030000' => 'ghi', 'Gohir.A12G145200' => 'ghi', 'Gohir.D01G151500' => 'ghi', 'Gohir.D04G058300' => 'ghi', 'Gohir.D05G314100' => 'ghi', 'Gohir.D07G041400' => 'ghi', 'Gohir.D09G029700' => 'ghi', 'Gohir.D12G149700' => 'ghi', 'Gorai.001G043800' => 'gra', 'Gorai.002G187800' => 'gra', 'Gorai.006G034700' => 'gra', 'Gorai.008G161200' => 'gra', 'Gorai.009G335700' => 'gra', 'Gorai.012G065000' => 'gra', 'GSVIVG01000535001' => 'vvi', 'GSVIVG01015572001' => 'vvi', 'GSVIVG01032386001' => 'vvi', 'HanXRQChr05g0138531' => 'han', 'HanXRQChr06g0174391' => 'han', 'HanXRQChr07g0199021' => 'han', 'HanXRQChr08g0208211' => 'han', 'HanXRQChr09g0255471' => 'han', 'HanXRQChr10g0315791' => 'han', 'HanXRQChr12g0371991' => 'han', 'HanXRQChr15g0475251' => 'han', 'HanXRQChr17g0540001' => 'han', 'HanXRQChr17g0548631' => 'han', 'HanXRQChr17g0569561' => 'han', 'Haze_12256' => 'cav', 'Haze_14756' => 'cav', 'Haze_25528' => 'cav', 'Hma1.2p1_0079F.1_g041020' => 'hma', 'Hma1.2p1_0818F.1_g223260' => 'hma', 'Hma1.2p1_1747F.1_g300530' => 'hma', 'HPP92_004607' => 'vpl', 'HPP92_004608' => 'vpl', 'HPP92_006181' => 'vpl', 'HPP92_012192' => 'vpl', 'HPP92_015680' => 'vpl', 'HPP92_020249' => 'vpl', 'HPP92_021376' => 'vpl', 'HPP92_024275' => 'vpl', 'Hund06031' => 'sun', 'Hund25391' => 'sun', 'Lalb_Chr07g0185371' => 'lal', 'Lalb_Chr07g0185381' => 'lal', 'Lalb_Chr12g0204011' => 'lal', 'Lalb_Chr13g0301671' => 'lal', 'Lalb_Chr14g0362851' => 'lal', 'Lalb_Chr24g0403581' => 'lal', 'Lj1g0000233' => 'lja', 'Lj2g0018120' => 'lja', 'Lj3C621T0' => 'lonja', 'Lj3P1059T14' => 'lonja', 'Lj3P611T9' => 'lonja', 'Lj3P614T13' => 'lonja', 'Lj3P615T5' => 'lonja', 'Lj4g0012315' => 'lja', 'Lj4g0026182' => 'lja', 'Lj6P813T16' => 'lonja', 'Lj7C427T7' => 'lonja', 'Lj7C427T8' => 'lonja', 'Lj7P600T41' => 'lonja', 'Lju41C42G17' => 'lonja', 'Lsat_1_v5_gn_0_47300' => 'lsa', 'Lsat_1_v5_gn_2_91280' => 'lsa', 'Lsat_1_v5_gn_3_30561' => 'lsa', 'Lsat_1_v5_gn_4_184321' => 'lsa', 'Lsat_1_v5_gn_4_4041' => 'lsa', 'Lsat_1_v5_gn_5_92000' => 'lsa', 'Lsat_1_v5_gn_8_152940' => 'lsa', 'Lsat_1_v5_gn_8_62401' => 'lsa', 'Manes.06G055900' => 'mes', 'Manes.12G022200' => 'mes', 'Manes.13G023300' => 'mes', 'Manes.14G115000' => 'mes', 'Manes.15G151700' => 'mes', 'Manes.17G111300' => 'mes', 'Mapoly0226s0009' => 'mpo', 'MBI02_g25363_MAGBIO' => 'mbi', 'MBI06_g00027_MAGBIO' => 'mbi', 'MBI10_g13034_MAGBIO' => 'mbi', 'MD09G1023400' => 'mdo', 'MD13G1100100' => 'mdo', 'MD15G1169200' => 'mdo', 'MD16G1101100' => 'mdo', 'MD17G1022900' => 'mdo', 'Medtr3g096150' => 'mtr', 'Medtr4g115070' => 'mtr', 'Medtr7g033325' => 'mtr', 'Medtr8g089840' => 'mtr', 'MELO3C010319.2' => 'cme', 'MELO3C011944.2' => 'cme', 'MELO3C021589.2' => 'cme', 'Migut.E00207' => 'egut', 'Migut.H00067' => 'egut', 'Migut.K00433' => 'egut', 'Migut.K00606' => 'egut', 'Migut.K01410' => 'egut', 'MSTRG.13347' => 'ama', 'MSTRG.24045' => 'ama', 'MSTRG.2428' => 'ama', 'MSTRG.26410' => 'ama', 'MSTRG.3139' => 'ama', 'MSTRG.3286' => 'ama', 'MSTRG.563' => 'ama', 'MSTRG.7941' => 'ama', 'Nitab4.5_0000028g0060' => 'nta', 'Nitab4.5_0000065g0260' => 'nta', 'Nitab4.5_0000112g0060' => 'nta', 'Nitab4.5_0000489g0120' => 'nta', 'Nitab4.5_0001776g0050' => 'nta', 'Nitab4.5_0001854g0010' => 'nta', 'Nitab4.5_0001860g0020' => 'nta', 'Nitab4.5_0004352g0010' => 'nta', 'Nitab4.5_0008716g0020' => 'nta', 'Nitab4.5_0008922g0010' => 'nta', 'Nn3g16693' => 'nnu', 'Nn4g22596' => 'nnu', 'Nn7g37639' => 'nnu', 'Oeu001701.1' => 'oeu', 'Oeu018149.1' => 'oeu', 'Oeu026220.1' => 'oeu', 'Oeu038635.1' => 'oeu', 'Oeu049176.1' => 'oeu', 'Oeu056706.1' => 'oeu', 'Oeu056937.1' => 'oeu', 'Oeu057540.1' => 'oeu', 'Os02g0594900' => 'osa', 'Os02g0595100' => 'osa', 'Os04g0477500' => 'osa', 'Os12g0611900' => 'osa', 'Peaxi162Scf00076g00020' => 'pax', 'Peaxi162Scf00128g00217' => 'pax', 'Peaxi162Scf00129g01640' => 'pax', 'Peaxi162Scf00669g00007' => 'pax', 'Peaxi162Scf00700g00421' => 'pax', 'Peaxi162Scf00801g00038' => 'pax', 'Peaxi162Scf00891g00025' => 'pax', 'PGR083G0909' => 'pgr', 'PGR119G1005' => 'pgr', 'PGR142G2236' => 'pgr', 'PGR142G3388' => 'pgr', 'PGSC0003DMG400004514' => 'stu', 'PGSC0003DMG400012635' => 'stu', 'PGSC0003DMG400015730' => 'stu', 'PGSC0003DMG400018611' => 'stu', 'PGSC0003DMG400030897' => 'stu', 'Phvul.001G254800' => 'pvu', 'Phvul.002G260100' => 'pvu', 'Phvul.003G167600' => 'pvu', 'Phvul.004G005100' => 'pvu', 'Potri.001G343600' => 'ptr', 'Potri.006G066700' => 'ptr', 'Potri.008G186000' => 'ptr', 'Potri.010G046900' => 'ptr', 'Potri.018G127900' => 'ptr', 'Pp3c20_17750' => 'ppa', 'Pp3c24_4380' => 'ppa', 'Prupe.1G245800' => 'ppe', 'Prupe.3G293400' => 'ppe', 'Prupe.7G247400' => 'ppe', 'Psat0s145g0120' => 'psa', 'Psat0s595g0040' => 'psa', 'Psat0s595g0120' => 'psa', 'Psat3g175040' => 'psa', 'Psat7g058120' => 'psa', 'PSO017G0428' => 'pso', 'PSO063G7510' => 'pso', 'PSO067G0046' => 'pso', 'PSO478G1073' => 'pso', 'PSO675G3677' => 'pso', 'PSO675G6558' => 'pso', 'PSO675G7520' => 'pso', 'PSO675G8959' => 'pso', 'QL02p074089' => 'qlo', 'QL02p089614' => 'qlo', 'QL03p057736' => 'qlo', 'RcHm_v2.0_Chr1g0364131' => 'rch', 'RcHm_v2.0_Chr2g0087801' => 'rch', 'RcHm_v2.0_Chr2g0087821' => 'rch', 'RcHm_v2.0_Chr2g0173231' => 'rch', 'RcHm_v2.0_Chr4g0433111' => 'rch', 'Rhsim03G0250300' => 'rsi', 'Rhsim08G0048400' => 'rsi', 'Rhsim10G0014800' => 'rsi', 'Rhsim12G0040100' => 'rsi', 'Rhsim12G0109700' => 'rsi', 'Sabra06G0049600' => 'sbr', 'Sabra08G0141000' => 'sbr', 'Sabra10G0021400' => 'sbr', 'Sabra16G0222900' => 'sbr', 'Sabra18G0108600' => 'sbr', 'SalBow1G0433' => 'sbo', 'SalBow1G2038' => 'sbo', 'SalBow1G5003' => 'sbo', 'SalBow7G1197' => 'sbo', 'SalBow8G3506' => 'sbo', 'Sc03g0007300' => 'sci', 'Sc11g0000950' => 'sci', 'Sc14g0008750' => 'sci', 'Sc18g0000420' => 'sci', 'Sed0006754' => 'sed', 'Sed0008741' => 'sed', 'Sed0017172' => 'sed', 'Sed0018925' => 'sed', 'Sed0023326' => 'sed', 'Sed0025909' => 'sed', 'SEGI_05333' => 'sgi', 'SEGI_10362' => 'sgi', 'SEGI_13380' => 'sgi', 'SEGI_24306' => 'sgi', 'SEGI_29077' => 'sgi', 'SEGI_29095' => 'sgi', 'SEGI_36534' => 'sgi', 'SEGI_37506' => 'sgi', 'SEGI_38321' => 'sgi', 'SGA_v2.0_scaffold307G48031' => 'sas', 'SGA_v2.0_scaffold47G17507' => 'sas', 'SGA_v2.0_scaffold63G21736' => 'sas', 'SGA_v2.0_scaffold87G27070' => 'sas', 'SHI17794' => 'shi', 'SHI28851' => 'shi', 'SMO165G0155' => 'smo', 'SMO340G0217' => 'smo', 'SMO367G1210' => 'smo', 'Solyc02g093430.3' => 'sly', 'Solyc05g013580.4' => 'sly', 'Solyc07g008030.3' => 'sly', 'Solyc12g035470.2' => 'sly', 'Sopen02g038020' => 'spe', 'Sopen05g008490' => 'spe', 'Sopen07g003910' => 'spe', 'Sopen12g015240' => 'spe', 'Sp1g11550' => 'spa', 'Sp2g16710' => 'spa', 'Sp3g00430' => 'spa', 'Sp3g26780' => 'spa', 'Sp5g22900' => 'spa', 'Sp6g29530' => 'spa', 'TAR371G0794' => 'tar', 'TAR374G0164' => 'tar', 'TAR622G0165' => 'tar', 'TAR626G0929' => 'tar', 'TAR629G2155' => 'tar', 'THA.LOC104805282' => 'tha', 'THA.LOC104805363' => 'tha', 'THA.LOC104808968' => 'tha', 'THA.LOC104821093' => 'tha', 'THA.LOC104823953' => 'tha', 'THA.LOC104825562' => 'tha', 'THA.LOC104825665' => 'tha', 'Thecc.02G261400' => 'tca', 'Thecc.04G019200' => 'tca', 'Thecc.09G130400' => 'tca', 'Thhalv10004374m.g' => 'esa', 'Thhalv10007850m.g' => 'esa', 'Thhalv10013782m.g' => 'esa', 'Thhalv10018686m.g' => 'esa', 'Thhalv10020899m.g' => 'esa', 'Thhalv10022755m.g' => 'esa', 'TPR.G23851' => 'tpr', 'TPR.G26500' => 'tpr', 'TPR.G27267' => 'tpr', 'TPR.G32001' => 'tpr', 'TPR.G6251' => 'tpr', 'TPR.G8167' => 'tpr', 'TWI12G1330' => 'twi', 'TWI18G1239' => 'twi', 'TWI34G0979' => 'twi', 'TWI36G0670' => 'twi', 'TWI36G0707' => 'twi', 'TWI56G0233' => 'twi', 'TWI75G1809' => 'twi', 'unitig_21.g20874' => 'ugi', 'unitig_26.g10343' => 'ugi', 'unitig_46.g18392' => 'ugi', 'unitig_52.g17178' => 'ugi', 'unitig_8.g2934' => 'ugi', 'vmacro01122' => 'vma', 'vmacro05875' => 'vma', 'vmacro06147' => 'vma', 'vmacro16191' => 'vma', 'vmacro18293' => 'vma', 'VMungo0251G3707' => 'vmu', 'VMungo0464G1521' => 'vmu', 'VMungo1215G0205' => 'vmu', 'VMungo1383G2484' => 'vmu', 'Zm00001eb079610' => 'zma', 'Zm00001eb135990' => 'zma', 'Zm00001eb183710' => 'zma', 'Zm00001eb246020' => 'zma' ), 'gf_id' => 'HOM05D001124', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001124' ), 'data_identifier' => 'HOM05D001124', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001124', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '548', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02520' => 'bna', 'A03p06630' => 'bna', 'A05p44460' => 'bna', 'A06p08710' => 'bna', 'A06p41090' => 'bna', 'A07p32320' => 'bna', 'A08p32520' => 'bna', 'A09p10360' => 'bna', 'A10p24080' => 'bna', 'Aa31LG11G15250' => 'aar', 'Aa31LG1G1800' => 'aar', 'Aa31LG2G5120' => 'aar', 'Aa31LG2G6070' => 'aar', 'Aa31LG5G10770' => 'aar', 'Aa31sc61G90' => 'aar', 'Actinidia01352' => 'ach', 'Actinidia05983' => 'ach', 'Actinidia08133' => 'ach', 'Actinidia15101' => 'ach', 'Actinidia26379' => 'ach', 'Actinidia35778' => 'ach', 'Actinidia36123' => 'ach', 'Actinidia37436' => 'ach', 'Actinidia38730' => 'ach', 'Ah.02g128210' => 'amhyb', 'Ah.03g132990' => 'amhyb', 'Ah.14g079410' => 'amhyb', 'AL1G24640' => 'aly', 'AL2G26680' => 'aly', 'AL3G10530' => 'aly', 'AL3G45230' => 'aly', 'AL5G15230' => 'aly', 'AL5G16960' => 'aly', 'AL6G25210' => 'aly', 'Aqoxy2G00441' => 'aox', 'Aqoxy3G01236' => 'aox', 'Aqoxy5G03746' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3RQ047' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C7GMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9C8JER' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MBL6KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YXCZ83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZANX40' => 'arhy', 'AT1G12990' => 'ath', 'AT1G67880' => 'ath', 'AT2G13290' => 'ath', 'AT3G01620' => 'ath', 'AT3G26445' => 'ath', 'AT3G27540' => 'ath', 'AT5G14480' => 'ath', 'ATR0824G026' => 'atr', 'ATR1098G019' => 'atr', 'Atru.chr11.2145' => 'acertr', 'Atru.chr2.3636' => 'acertr', 'Atru.chr2.3644' => 'acertr', 'Atru.chr6.2422' => 'acertr', 'Atru.chr7.1112' => 'acertr', 'AUR62005469' => 'cqu', 'AUR62011166' => 'cqu', 'AUR62013319' => 'cqu', 'AUR62024273' => 'cqu', 'AUR62028420' => 'cqu', 'AUR62041942' => 'cqu', 'BcaB01g04969' => 'bca', 'BcaB01g06371' => 'bca', 'BcaB02g11494' => 'bca', 'BcaB03g15382' => 'bca', 'BcaB08g36994' => 'bca', 'BcaC03g13477' => 'bca', 'BcaC03g13478' => 'bca', 'BcaC03g13480' => 'bca', 'BcaC03g13481' => 'bca', 'BcaC03g13486' => 'bca', 'BcaC04g19031' => 'bca', 'BcaC04g23085' => 'bca', 'BcaC05g25094' => 'bca', 'BcaC05g25096' => 'bca', 'BcaC05g25138' => 'bca', 'BcaC05g30416' => 'bca', 'BcaC05g30455' => 'bca', 'BcaC06g30979' => 'bca', 'BcaC06g33805' => 'bca', 'BcaC08g46021' => 'bca', 'BcaNung03154' => 'bca', 'BolC2t06623H' => 'bol', 'BolC2t06632H' => 'bol', 'BolC2t06635H' => 'bol', 'BolC2t06638H' => 'bol', 'BolC3t13266H' => 'bol', 'BolC5t29776H' => 'bol', 'BolC6t38912H' => 'bol', 'BolC7t44183H' => 'bol', 'BolC9t54123H' => 'bol', 'BolC9t59107H' => 'bol', 'BraA02t05221Z' => 'bra', 'BraA03t09996Z' => 'bra', 'BraA05t23210Z' => 'bra', 'BraA06t24068Z' => 'bra', 'BraA06t27032Z' => 'bra', 'BraA08t35176Z' => 'bra', 'BraA09t36680Z' => 'bra', 'BraA10t44471Z' => 'bra', 'C02p06760' => 'bna', 'C02p06890' => 'bna', 'C02p07010' => 'bna', 'C03p07660' => 'bna', 'C05p10300' => 'bna', 'C06p38150' => 'bna', 'C07p36650' => 'bna', 'C08p15770' => 'bna', 'C09p12300' => 'bna', 'C09p62700' => 'bna', 'C09p75040' => 'bna', 'CAN.G13.1' => 'can', 'CAN.G138.4' => 'can', 'CAN.G44.6' => 'can', 'CAN.G473.19' => 'can', 'CANSAT01G0835' => 'cansat', 'CANSAT11G0246' => 'cansat', 'CANSAT11G1766' => 'cansat', 'CANSAT64G1954' => 'cansat', 'CARHR013330' => 'chi', 'CARHR060530' => 'chi', 'CARHR075300' => 'chi', 'CARHR105120' => 'chi', 'CARHR148910' => 'chi', 'CARHR198830' => 'chi', 'Carub.0001s1275' => 'cru', 'Carub.0002s1437' => 'cru', 'Carub.0003s0044' => 'cru', 'Carub.0003s2787' => 'cru', 'Carub.0005s0597' => 'cru', 'Carub.0006s1266' => 'cru', 'Ca_06935_v3' => 'car', 'Ca_13559_v3' => 'car', 'Ca_16941_v3' => 'car', 'Ca_16960_v3' => 'car', 'Ca_17775_v3' => 'car', 'Ca_30464_v3' => 'car', 'Cc06_g08160' => 'ccan', 'Cc07_g01520' => 'ccan', 'Cc11_g15810' => 'ccan', 'CDE02G2840' => 'cde', 'CDE03G0093' => 'cde', 'CDE04G2127' => 'cde', 'CDE07G1857' => 'cde', 'CDE09G1246' => 'cde', 'Cfa003412' => 'cfa', 'Cfa007341' => 'cfa', 'Cfa009220' => 'cfa', 'Ciclev10008737m.g' => 'ccl', 'Ciclev10015565m.g' => 'ccl', 'Ciclev10031761m.g' => 'ccl', 'CiPaw.03G045300' => 'cil', 'CiPaw.03G247200' => 'cil', 'CiPaw.04G029500' => 'cil', 'CiPaw.04G174000' => 'cil', 'CiPaw.05G181200' => 'cil', 'CiPaw.06G067100' => 'cil', 'ClCG05G025800' => 'cla', 'ClCG06G011400' => 'cla', 'ClCG09G019360' => 'cla', 'COL.COLO4_04827' => 'col', 'COL.COLO4_29170' => 'col', 'COL.COLO4_35131' => 'col', 'COL.COLO4_35132' => 'col', 'Cpa.g.sc33.32' => 'cpa', 'Cpa.g.sc46.29' => 'cpa', 'Cpa.g.sc796.1' => 'cpa', 'CsaV3_1G030420' => 'csa', 'CsaV3_5G027050' => 'csa', 'CsaV3_5G031040' => 'csa', 'CsaV3_UNG023130' => 'csa', 'CSS0007726' => 'camsi', 'CSS0016433' => 'camsi', 'CSS0017656' => 'camsi', 'CSS0025364' => 'camsi', 'CSS0027582' => 'camsi', 'CSS0047288' => 'camsi', 'CSS0049950' => 'camsi', 'DCAR_003843' => 'dca', 'DCAR_007052' => 'dca', 'DCAR_020884' => 'dca', 'DCAR_021730' => 'dca', 'DCAR_024423' => 'dca', 'DCAR_026509' => 'dca', 'DCAR_031158' => 'dca', 'Dinv14728' => 'din', 'Dinv15219' => 'din', 'Dinv25728' => 'din', 'Dinv33428' => 'din', 'Dinv36489' => 'din', 'Dinv41486' => 'din', 'Duzib147G0469' => 'dzi', 'Duzib168G0060' => 'dzi', 'Duzib187G1215' => 'dzi', 'Duzib248G0692' => 'dzi', 'Duzib251G0767' => 'dzi', 'Duzib264G0446' => 'dzi', 'Duzib268G0691' => 'dzi', 'ECA232G4767' => 'eca', 'ECA233G2838' => 'eca', 'ECA234G0391' => 'eca', 'ECA234G0857' => 'eca', 'ECA236G1593' => 'eca', 'ECA238G0565' => 'eca', 'ECA246G1027' => 'eca', 'ECA246G3223' => 'eca', 'ECA246G3470' => 'eca', 'EL10Ac6g13829' => 'bvu', 'EL10Ac6g14093' => 'bvu', 'EL10Ac8g18707' => 'bvu', 'Eucgr.C01369' => 'egr', 'Eucgr.H02492' => 'egr', 'Eucgr.I01733' => 'egr', 'Eucgr.J02255' => 'egr', 'Eucgr.J02257' => 'egr', 'Eucgr.J02258' => 'egr', 'FAN02G1601' => 'fan', 'FAN03G1586' => 'fan', 'FAN03G2986' => 'fan', 'FAN05G4837' => 'fan', 'FAN06G0146' => 'fan', 'FAN07G0858' => 'fan', 'FAN09G3179' => 'fan', 'FAN10G0669' => 'fan', 'FAN12G2358' => 'fan', 'FAN14G4198' => 'fan', 'FAN14G5112' => 'fan', 'FAN17G0342' => 'fan', 'FAN19G0342' => 'fan', 'FAN19G0962' => 'fan', 'FAN19G1101' => 'fan', 'FAN19G1872' => 'fan', 'FAN22G0356' => 'fan', 'FAN23G0744' => 'fan', 'FAN23G1914' => 'fan', 'FAN26G0032' => 'fan', 'FAN28G0625' => 'fan', 'FvH4_1g02710' => 'fve', 'FvH4_1g02720' => 'fve', 'FvH4_4g25670' => 'fve', 'FvH4_6g51700' => 'fve', 'FvH4_7g20170' => 'fve', 'Glyma.05G175000' => 'gma', 'Glyma.08G132300' => 'gma', 'Glyma.11G243000' => 'gma', 'Glyma.13G158900' => 'gma', 'Glyma.17G112400' => 'gma', 'Glyma.18G014100' => 'gma', 'Glyma.19G003100' => 'gma', 'Glyma.19G056500' => 'gma', 'Gohir.A01G158900' => 'ghi', 'Gohir.A05G312600' => 'ghi', 'Gohir.A05G354900' => 'ghi', 'Gohir.A07G037200' => 'ghi', 'Gohir.A09G030000' => 'ghi', 'Gohir.A12G145200' => 'ghi', 'Gohir.D01G151500' => 'ghi', 'Gohir.D04G058300' => 'ghi', 'Gohir.D05G314100' => 'ghi', 'Gohir.D07G041400' => 'ghi', 'Gohir.D09G029700' => 'ghi', 'Gohir.D12G149700' => 'ghi', 'Gorai.001G043800' => 'gra', 'Gorai.002G187800' => 'gra', 'Gorai.006G034700' => 'gra', 'Gorai.008G161200' => 'gra', 'Gorai.009G335700' => 'gra', 'Gorai.012G065000' => 'gra', 'GSVIVG01000535001' => 'vvi', 'GSVIVG01015572001' => 'vvi', 'GSVIVG01032386001' => 'vvi', 'HanXRQChr05g0138531' => 'han', 'HanXRQChr06g0174391' => 'han', 'HanXRQChr07g0199021' => 'han', 'HanXRQChr08g0208211' => 'han', 'HanXRQChr09g0255471' => 'han', 'HanXRQChr10g0315791' => 'han', 'HanXRQChr12g0371991' => 'han', 'HanXRQChr15g0475251' => 'han', 'HanXRQChr17g0540001' => 'han', 'HanXRQChr17g0548631' => 'han', 'HanXRQChr17g0569561' => 'han', 'Haze_12256' => 'cav', 'Haze_14756' => 'cav', 'Haze_25528' => 'cav', 'Hma1.2p1_0079F.1_g041020' => 'hma', 'Hma1.2p1_0818F.1_g223260' => 'hma', 'Hma1.2p1_1747F.1_g300530' => 'hma', 'HPP92_004607' => 'vpl', 'HPP92_004608' => 'vpl', 'HPP92_006181' => 'vpl', 'HPP92_012192' => 'vpl', 'HPP92_015680' => 'vpl', 'HPP92_020249' => 'vpl', 'HPP92_021376' => 'vpl', 'HPP92_024275' => 'vpl', 'Hund06031' => 'sun', 'Hund25391' => 'sun', 'Lalb_Chr07g0185371' => 'lal', 'Lalb_Chr07g0185381' => 'lal', 'Lalb_Chr12g0204011' => 'lal', 'Lalb_Chr13g0301671' => 'lal', 'Lalb_Chr14g0362851' => 'lal', 'Lalb_Chr24g0403581' => 'lal', 'Lj1g0000233' => 'lja', 'Lj2g0018120' => 'lja', 'Lj3C621T0' => 'lonja', 'Lj3P1059T14' => 'lonja', 'Lj3P611T9' => 'lonja', 'Lj3P614T13' => 'lonja', 'Lj3P615T5' => 'lonja', 'Lj4g0012315' => 'lja', 'Lj4g0026182' => 'lja', 'Lj6P813T16' => 'lonja', 'Lj7C427T7' => 'lonja', 'Lj7C427T8' => 'lonja', 'Lj7P600T41' => 'lonja', 'Lju41C42G17' => 'lonja', 'Lsat_1_v5_gn_0_47300' => 'lsa', 'Lsat_1_v5_gn_2_91280' => 'lsa', 'Lsat_1_v5_gn_3_30561' => 'lsa', 'Lsat_1_v5_gn_4_184321' => 'lsa', 'Lsat_1_v5_gn_4_4041' => 'lsa', 'Lsat_1_v5_gn_5_92000' => 'lsa', 'Lsat_1_v5_gn_8_152940' => 'lsa', 'Lsat_1_v5_gn_8_62401' => 'lsa', 'Manes.06G055900' => 'mes', 'Manes.12G022200' => 'mes', 'Manes.13G023300' => 'mes', 'Manes.14G115000' => 'mes', 'Manes.15G151700' => 'mes', 'Manes.17G111300' => 'mes', 'Mapoly0226s0009' => 'mpo', 'MBI02_g25363_MAGBIO' => 'mbi', 'MBI06_g00027_MAGBIO' => 'mbi', 'MBI10_g13034_MAGBIO' => 'mbi', 'MD09G1023400' => 'mdo', 'MD13G1100100' => 'mdo', 'MD15G1169200' => 'mdo', 'MD16G1101100' => 'mdo', 'MD17G1022900' => 'mdo', 'Medtr3g096150' => 'mtr', 'Medtr4g115070' => 'mtr', 'Medtr7g033325' => 'mtr', 'Medtr8g089840' => 'mtr', 'MELO3C010319.2' => 'cme', 'MELO3C011944.2' => 'cme', 'MELO3C021589.2' => 'cme', 'Migut.E00207' => 'egut', 'Migut.H00067' => 'egut', 'Migut.K00433' => 'egut', 'Migut.K00606' => 'egut', 'Migut.K01410' => 'egut', 'MSTRG.13347' => 'ama', 'MSTRG.24045' => 'ama', 'MSTRG.2428' => 'ama', 'MSTRG.26410' => 'ama', 'MSTRG.3139' => 'ama', 'MSTRG.3286' => 'ama', 'MSTRG.563' => 'ama', 'MSTRG.7941' => 'ama', 'Nitab4.5_0000028g0060' => 'nta', 'Nitab4.5_0000065g0260' => 'nta', 'Nitab4.5_0000112g0060' => 'nta', 'Nitab4.5_0000489g0120' => 'nta', 'Nitab4.5_0001776g0050' => 'nta', 'Nitab4.5_0001854g0010' => 'nta', 'Nitab4.5_0001860g0020' => 'nta', 'Nitab4.5_0004352g0010' => 'nta', 'Nitab4.5_0008716g0020' => 'nta', 'Nitab4.5_0008922g0010' => 'nta', 'Nn3g16693' => 'nnu', 'Nn4g22596' => 'nnu', 'Nn7g37639' => 'nnu', 'Oeu001701.1' => 'oeu', 'Oeu018149.1' => 'oeu', 'Oeu026220.1' => 'oeu', 'Oeu038635.1' => 'oeu', 'Oeu049176.1' => 'oeu', 'Oeu056706.1' => 'oeu', 'Oeu056937.1' => 'oeu', 'Oeu057540.1' => 'oeu', 'Os02g0594900' => 'osa', 'Os02g0595100' => 'osa', 'Os04g0477500' => 'osa', 'Os12g0611900' => 'osa', 'Peaxi162Scf00076g00020' => 'pax', 'Peaxi162Scf00128g00217' => 'pax', 'Peaxi162Scf00129g01640' => 'pax', 'Peaxi162Scf00669g00007' => 'pax', 'Peaxi162Scf00700g00421' => 'pax', 'Peaxi162Scf00801g00038' => 'pax', 'Peaxi162Scf00891g00025' => 'pax', 'PGR083G0909' => 'pgr', 'PGR119G1005' => 'pgr', 'PGR142G2236' => 'pgr', 'PGR142G3388' => 'pgr', 'PGSC0003DMG400004514' => 'stu', 'PGSC0003DMG400012635' => 'stu', 'PGSC0003DMG400015730' => 'stu', 'PGSC0003DMG400018611' => 'stu', 'PGSC0003DMG400030897' => 'stu', 'Phvul.001G254800' => 'pvu', 'Phvul.002G260100' => 'pvu', 'Phvul.003G167600' => 'pvu', 'Phvul.004G005100' => 'pvu', 'Potri.001G343600' => 'ptr', 'Potri.006G066700' => 'ptr', 'Potri.008G186000' => 'ptr', 'Potri.010G046900' => 'ptr', 'Potri.018G127900' => 'ptr', 'Pp3c20_17750' => 'ppa', 'Pp3c24_4380' => 'ppa', 'Prupe.1G245800' => 'ppe', 'Prupe.3G293400' => 'ppe', 'Prupe.7G247400' => 'ppe', 'Psat0s145g0120' => 'psa', 'Psat0s595g0040' => 'psa', 'Psat0s595g0120' => 'psa', 'Psat3g175040' => 'psa', 'Psat7g058120' => 'psa', 'PSO017G0428' => 'pso', 'PSO063G7510' => 'pso', 'PSO067G0046' => 'pso', 'PSO478G1073' => 'pso', 'PSO675G3677' => 'pso', 'PSO675G6558' => 'pso', 'PSO675G7520' => 'pso', 'PSO675G8959' => 'pso', 'QL02p074089' => 'qlo', 'QL02p089614' => 'qlo', 'QL03p057736' => 'qlo', 'RcHm_v2.0_Chr1g0364131' => 'rch', 'RcHm_v2.0_Chr2g0087801' => 'rch', 'RcHm_v2.0_Chr2g0087821' => 'rch', 'RcHm_v2.0_Chr2g0173231' => 'rch', 'RcHm_v2.0_Chr4g0433111' => 'rch', 'Rhsim03G0250300' => 'rsi', 'Rhsim08G0048400' => 'rsi', 'Rhsim10G0014800' => 'rsi', 'Rhsim12G0040100' => 'rsi', 'Rhsim12G0109700' => 'rsi', 'Sabra06G0049600' => 'sbr', 'Sabra08G0141000' => 'sbr', 'Sabra10G0021400' => 'sbr', 'Sabra16G0222900' => 'sbr', 'Sabra18G0108600' => 'sbr', 'SalBow1G0433' => 'sbo', 'SalBow1G2038' => 'sbo', 'SalBow1G5003' => 'sbo', 'SalBow7G1197' => 'sbo', 'SalBow8G3506' => 'sbo', 'Sc03g0007300' => 'sci', 'Sc11g0000950' => 'sci', 'Sc14g0008750' => 'sci', 'Sc18g0000420' => 'sci', 'Sed0006754' => 'sed', 'Sed0008741' => 'sed', 'Sed0017172' => 'sed', 'Sed0018925' => 'sed', 'Sed0023326' => 'sed', 'Sed0025909' => 'sed', 'SEGI_05333' => 'sgi', 'SEGI_10362' => 'sgi', 'SEGI_13380' => 'sgi', 'SEGI_24306' => 'sgi', 'SEGI_29077' => 'sgi', 'SEGI_29095' => 'sgi', 'SEGI_36534' => 'sgi', 'SEGI_37506' => 'sgi', 'SEGI_38321' => 'sgi', 'SGA_v2.0_scaffold307G48031' => 'sas', 'SGA_v2.0_scaffold47G17507' => 'sas', 'SGA_v2.0_scaffold63G21736' => 'sas', 'SGA_v2.0_scaffold87G27070' => 'sas', 'SHI17794' => 'shi', 'SHI28851' => 'shi', 'SMO165G0155' => 'smo', 'SMO340G0217' => 'smo', 'SMO367G1210' => 'smo', 'Solyc02g093430.3' => 'sly', 'Solyc05g013580.4' => 'sly', 'Solyc07g008030.3' => 'sly', 'Solyc12g035470.2' => 'sly', 'Sopen02g038020' => 'spe', 'Sopen05g008490' => 'spe', 'Sopen07g003910' => 'spe', 'Sopen12g015240' => 'spe', 'Sp1g11550' => 'spa', 'Sp2g16710' => 'spa', 'Sp3g00430' => 'spa', 'Sp3g26780' => 'spa', 'Sp5g22900' => 'spa', 'Sp6g29530' => 'spa', 'TAR371G0794' => 'tar', 'TAR374G0164' => 'tar', 'TAR622G0165' => 'tar', 'TAR626G0929' => 'tar', 'TAR629G2155' => 'tar', 'THA.LOC104805282' => 'tha', 'THA.LOC104805363' => 'tha', 'THA.LOC104808968' => 'tha', 'THA.LOC104821093' => 'tha', 'THA.LOC104823953' => 'tha', 'THA.LOC104825562' => 'tha', 'THA.LOC104825665' => 'tha', 'Thecc.02G261400' => 'tca', 'Thecc.04G019200' => 'tca', 'Thecc.09G130400' => 'tca', 'Thhalv10004374m.g' => 'esa', 'Thhalv10007850m.g' => 'esa', 'Thhalv10013782m.g' => 'esa', 'Thhalv10018686m.g' => 'esa', 'Thhalv10020899m.g' => 'esa', 'Thhalv10022755m.g' => 'esa', 'TPR.G23851' => 'tpr', 'TPR.G26500' => 'tpr', 'TPR.G27267' => 'tpr', 'TPR.G32001' => 'tpr', 'TPR.G6251' => 'tpr', 'TPR.G8167' => 'tpr', 'TWI12G1330' => 'twi', 'TWI18G1239' => 'twi', 'TWI34G0979' => 'twi', 'TWI36G0670' => 'twi', 'TWI36G0707' => 'twi', 'TWI56G0233' => 'twi', 'TWI75G1809' => 'twi', 'unitig_21.g20874' => 'ugi', 'unitig_26.g10343' => 'ugi', 'unitig_46.g18392' => 'ugi', 'unitig_52.g17178' => 'ugi', 'unitig_8.g2934' => 'ugi', 'vmacro01122' => 'vma', 'vmacro05875' => 'vma', 'vmacro06147' => 'vma', 'vmacro16191' => 'vma', 'vmacro18293' => 'vma', 'VMungo0251G3707' => 'vmu', 'VMungo0464G1521' => 'vmu', 'VMungo1215G0205' => 'vmu', 'VMungo1383G2484' => 'vmu', 'Zm00001eb079610' => 'zma', 'Zm00001eb135990' => 'zma', 'Zm00001eb183710' => 'zma', 'Zm00001eb246020' => 'zma' ) $gf_id = 'HOM05D001124' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001124' ) $data_identifier = 'HOM05D001124' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 6, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 7, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 21, 'bol' => (int) 10, 'bra' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 6, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 9, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 21, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 8, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 10, 'lsa' => (int) 8, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 8, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 9, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb246020' $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' => 'HOM05D001124', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '548', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02520' => 'bna', 'A03p06630' => 'bna', 'A05p44460' => 'bna', 'A06p08710' => 'bna', 'A06p41090' => 'bna', 'A07p32320' => 'bna', 'A08p32520' => 'bna', 'A09p10360' => 'bna', 'A10p24080' => 'bna', 'Aa31LG11G15250' => 'aar', 'Aa31LG1G1800' => 'aar', 'Aa31LG2G5120' => 'aar', 'Aa31LG2G6070' => 'aar', 'Aa31LG5G10770' => 'aar', 'Aa31sc61G90' => 'aar', 'Actinidia01352' => 'ach', 'Actinidia05983' => 'ach', 'Actinidia08133' => 'ach', 'Actinidia15101' => 'ach', 'Actinidia26379' => 'ach', 'Actinidia35778' => 'ach', 'Actinidia36123' => 'ach', 'Actinidia37436' => 'ach', 'Actinidia38730' => 'ach', 'Ah.02g128210' => 'amhyb', 'Ah.03g132990' => 'amhyb', 'Ah.14g079410' => 'amhyb', 'AL1G24640' => 'aly', 'AL2G26680' => 'aly', 'AL3G10530' => 'aly', 'AL3G45230' => 'aly', 'AL5G15230' => 'aly', 'AL5G16960' => 'aly', 'AL6G25210' => 'aly', 'Aqoxy2G00441' => 'aox', 'Aqoxy3G01236' => 'aox', 'Aqoxy5G03746' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3RQ047' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C7GMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9C8JER' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MBL6KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YXCZ83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZANX40' => 'arhy', 'AT1G12990' => 'ath', 'AT1G67880' => 'ath', 'AT2G13290' => 'ath', 'AT3G01620' => 'ath', 'AT3G26445' => 'ath', 'AT3G27540' => 'ath', 'AT5G14480' => 'ath', 'ATR0824G026' => 'atr', 'ATR1098G019' => 'atr', 'Atru.chr11.2145' => 'acertr', 'Atru.chr2.3636' => 'acertr', 'Atru.chr2.3644' => 'acertr', 'Atru.chr6.2422' => 'acertr', 'Atru.chr7.1112' => 'acertr', 'AUR62005469' => 'cqu', 'AUR62011166' => 'cqu', 'AUR62013319' => 'cqu', 'AUR62024273' => 'cqu', 'AUR62028420' => 'cqu', 'AUR62041942' => 'cqu', 'BcaB01g04969' => 'bca', 'BcaB01g06371' => 'bca', 'BcaB02g11494' => 'bca', 'BcaB03g15382' => 'bca', 'BcaB08g36994' => 'bca', 'BcaC03g13477' => 'bca', 'BcaC03g13478' => 'bca', 'BcaC03g13480' => 'bca', 'BcaC03g13481' => 'bca', 'BcaC03g13486' => 'bca', 'BcaC04g19031' => 'bca', 'BcaC04g23085' => 'bca', 'BcaC05g25094' => 'bca', 'BcaC05g25096' => 'bca', 'BcaC05g25138' => 'bca', 'BcaC05g30416' => 'bca', 'BcaC05g30455' => 'bca', 'BcaC06g30979' => 'bca', 'BcaC06g33805' => 'bca', 'BcaC08g46021' => 'bca', 'BcaNung03154' => 'bca', 'BolC2t06623H' => 'bol', 'BolC2t06632H' => 'bol', 'BolC2t06635H' => 'bol', 'BolC2t06638H' => 'bol', 'BolC3t13266H' => 'bol', 'BolC5t29776H' => 'bol', 'BolC6t38912H' => 'bol', 'BolC7t44183H' => 'bol', 'BolC9t54123H' => 'bol', 'BolC9t59107H' => 'bol', 'BraA02t05221Z' => 'bra', 'BraA03t09996Z' => 'bra', 'BraA05t23210Z' => 'bra', 'BraA06t24068Z' => 'bra', 'BraA06t27032Z' => 'bra', 'BraA08t35176Z' => 'bra', 'BraA09t36680Z' => 'bra', 'BraA10t44471Z' => 'bra', 'C02p06760' => 'bna', 'C02p06890' => 'bna', 'C02p07010' => 'bna', 'C03p07660' => 'bna', 'C05p10300' => 'bna', 'C06p38150' => 'bna', 'C07p36650' => 'bna', 'C08p15770' => 'bna', 'C09p12300' => 'bna', 'C09p62700' => 'bna', 'C09p75040' => 'bna', 'CAN.G13.1' => 'can', 'CAN.G138.4' => 'can', 'CAN.G44.6' => 'can', 'CAN.G473.19' => 'can', 'CANSAT01G0835' => 'cansat', 'CANSAT11G0246' => 'cansat', 'CANSAT11G1766' => 'cansat', 'CANSAT64G1954' => 'cansat', 'CARHR013330' => 'chi', 'CARHR060530' => 'chi', 'CARHR075300' => 'chi', 'CARHR105120' => 'chi', 'CARHR148910' => 'chi', 'CARHR198830' => 'chi', 'Carub.0001s1275' => 'cru', 'Carub.0002s1437' => 'cru', 'Carub.0003s0044' => 'cru', 'Carub.0003s2787' => 'cru', 'Carub.0005s0597' => 'cru', 'Carub.0006s1266' => 'cru', 'Ca_06935_v3' => 'car', 'Ca_13559_v3' => 'car', 'Ca_16941_v3' => 'car', 'Ca_16960_v3' => 'car', 'Ca_17775_v3' => 'car', 'Ca_30464_v3' => 'car', 'Cc06_g08160' => 'ccan', 'Cc07_g01520' => 'ccan', 'Cc11_g15810' => 'ccan', 'CDE02G2840' => 'cde', 'CDE03G0093' => 'cde', 'CDE04G2127' => 'cde', 'CDE07G1857' => 'cde', 'CDE09G1246' => 'cde', 'Cfa003412' => 'cfa', 'Cfa007341' => 'cfa', 'Cfa009220' => 'cfa', 'Ciclev10008737m.g' => 'ccl', 'Ciclev10015565m.g' => 'ccl', 'Ciclev10031761m.g' => 'ccl', 'CiPaw.03G045300' => 'cil', 'CiPaw.03G247200' => 'cil', 'CiPaw.04G029500' => 'cil', 'CiPaw.04G174000' => 'cil', 'CiPaw.05G181200' => 'cil', 'CiPaw.06G067100' => 'cil', 'ClCG05G025800' => 'cla', 'ClCG06G011400' => 'cla', 'ClCG09G019360' => 'cla', 'COL.COLO4_04827' => 'col', 'COL.COLO4_29170' => 'col', 'COL.COLO4_35131' => 'col', 'COL.COLO4_35132' => 'col', 'Cpa.g.sc33.32' => 'cpa', 'Cpa.g.sc46.29' => 'cpa', 'Cpa.g.sc796.1' => 'cpa', 'CsaV3_1G030420' => 'csa', 'CsaV3_5G027050' => 'csa', 'CsaV3_5G031040' => 'csa', 'CsaV3_UNG023130' => 'csa', 'CSS0007726' => 'camsi', 'CSS0016433' => 'camsi', 'CSS0017656' => 'camsi', 'CSS0025364' => 'camsi', 'CSS0027582' => 'camsi', 'CSS0047288' => 'camsi', 'CSS0049950' => 'camsi', 'DCAR_003843' => 'dca', 'DCAR_007052' => 'dca', 'DCAR_020884' => 'dca', 'DCAR_021730' => 'dca', 'DCAR_024423' => 'dca', 'DCAR_026509' => 'dca', 'DCAR_031158' => 'dca', 'Dinv14728' => 'din', 'Dinv15219' => 'din', 'Dinv25728' => 'din', 'Dinv33428' => 'din', 'Dinv36489' => 'din', 'Dinv41486' => 'din', 'Duzib147G0469' => 'dzi', 'Duzib168G0060' => 'dzi', 'Duzib187G1215' => 'dzi', 'Duzib248G0692' => 'dzi', 'Duzib251G0767' => 'dzi', 'Duzib264G0446' => 'dzi', 'Duzib268G0691' => 'dzi', 'ECA232G4767' => 'eca', 'ECA233G2838' => 'eca', 'ECA234G0391' => 'eca', 'ECA234G0857' => 'eca', 'ECA236G1593' => 'eca', 'ECA238G0565' => 'eca', 'ECA246G1027' => 'eca', 'ECA246G3223' => 'eca', 'ECA246G3470' => 'eca', 'EL10Ac6g13829' => 'bvu', 'EL10Ac6g14093' => 'bvu', 'EL10Ac8g18707' => 'bvu', 'Eucgr.C01369' => 'egr', 'Eucgr.H02492' => 'egr', 'Eucgr.I01733' => 'egr', 'Eucgr.J02255' => 'egr', 'Eucgr.J02257' => 'egr', 'Eucgr.J02258' => 'egr', 'FAN02G1601' => 'fan', 'FAN03G1586' => 'fan', 'FAN03G2986' => 'fan', 'FAN05G4837' => 'fan', 'FAN06G0146' => 'fan', 'FAN07G0858' => 'fan', 'FAN09G3179' => 'fan', 'FAN10G0669' => 'fan', 'FAN12G2358' => 'fan', 'FAN14G4198' => 'fan', 'FAN14G5112' => 'fan', 'FAN17G0342' => 'fan', 'FAN19G0342' => 'fan', 'FAN19G0962' => 'fan', 'FAN19G1101' => 'fan', 'FAN19G1872' => 'fan', 'FAN22G0356' => 'fan', 'FAN23G0744' => 'fan', 'FAN23G1914' => 'fan', 'FAN26G0032' => 'fan', 'FAN28G0625' => 'fan', 'FvH4_1g02710' => 'fve', 'FvH4_1g02720' => 'fve', 'FvH4_4g25670' => 'fve', 'FvH4_6g51700' => 'fve', 'FvH4_7g20170' => 'fve', 'Glyma.05G175000' => 'gma', 'Glyma.08G132300' => 'gma', 'Glyma.11G243000' => 'gma', 'Glyma.13G158900' => 'gma', 'Glyma.17G112400' => 'gma', 'Glyma.18G014100' => 'gma', 'Glyma.19G003100' => 'gma', 'Glyma.19G056500' => 'gma', 'Gohir.A01G158900' => 'ghi', 'Gohir.A05G312600' => 'ghi', 'Gohir.A05G354900' => 'ghi', 'Gohir.A07G037200' => 'ghi', 'Gohir.A09G030000' => 'ghi', 'Gohir.A12G145200' => 'ghi', 'Gohir.D01G151500' => 'ghi', 'Gohir.D04G058300' => 'ghi', 'Gohir.D05G314100' => 'ghi', 'Gohir.D07G041400' => 'ghi', 'Gohir.D09G029700' => 'ghi', 'Gohir.D12G149700' => 'ghi', 'Gorai.001G043800' => 'gra', 'Gorai.002G187800' => 'gra', 'Gorai.006G034700' => 'gra', 'Gorai.008G161200' => 'gra', 'Gorai.009G335700' => 'gra', 'Gorai.012G065000' => 'gra', 'GSVIVG01000535001' => 'vvi', 'GSVIVG01015572001' => 'vvi', 'GSVIVG01032386001' => 'vvi', 'HanXRQChr05g0138531' => 'han', 'HanXRQChr06g0174391' => 'han', 'HanXRQChr07g0199021' => 'han', 'HanXRQChr08g0208211' => 'han', 'HanXRQChr09g0255471' => 'han', 'HanXRQChr10g0315791' => 'han', 'HanXRQChr12g0371991' => 'han', 'HanXRQChr15g0475251' => 'han', 'HanXRQChr17g0540001' => 'han', 'HanXRQChr17g0548631' => 'han', 'HanXRQChr17g0569561' => 'han', 'Haze_12256' => 'cav', 'Haze_14756' => 'cav', 'Haze_25528' => 'cav', 'Hma1.2p1_0079F.1_g041020' => 'hma', 'Hma1.2p1_0818F.1_g223260' => 'hma', 'Hma1.2p1_1747F.1_g300530' => 'hma', 'HPP92_004607' => 'vpl', 'HPP92_004608' => 'vpl', 'HPP92_006181' => 'vpl', 'HPP92_012192' => 'vpl', 'HPP92_015680' => 'vpl', 'HPP92_020249' => 'vpl', 'HPP92_021376' => 'vpl', 'HPP92_024275' => 'vpl', 'Hund06031' => 'sun', 'Hund25391' => 'sun', 'Lalb_Chr07g0185371' => 'lal', 'Lalb_Chr07g0185381' => 'lal', 'Lalb_Chr12g0204011' => 'lal', 'Lalb_Chr13g0301671' => 'lal', 'Lalb_Chr14g0362851' => 'lal', 'Lalb_Chr24g0403581' => 'lal', 'Lj1g0000233' => 'lja', 'Lj2g0018120' => 'lja', 'Lj3C621T0' => 'lonja', 'Lj3P1059T14' => 'lonja', 'Lj3P611T9' => 'lonja', 'Lj3P614T13' => 'lonja', 'Lj3P615T5' => 'lonja', 'Lj4g0012315' => 'lja', 'Lj4g0026182' => 'lja', 'Lj6P813T16' => 'lonja', 'Lj7C427T7' => 'lonja', 'Lj7C427T8' => 'lonja', 'Lj7P600T41' => 'lonja', 'Lju41C42G17' => 'lonja', 'Lsat_1_v5_gn_0_47300' => 'lsa', 'Lsat_1_v5_gn_2_91280' => 'lsa', 'Lsat_1_v5_gn_3_30561' => 'lsa', 'Lsat_1_v5_gn_4_184321' => 'lsa', 'Lsat_1_v5_gn_4_4041' => 'lsa', 'Lsat_1_v5_gn_5_92000' => 'lsa', 'Lsat_1_v5_gn_8_152940' => 'lsa', 'Lsat_1_v5_gn_8_62401' => 'lsa', 'Manes.06G055900' => 'mes', 'Manes.12G022200' => 'mes', 'Manes.13G023300' => 'mes', 'Manes.14G115000' => 'mes', 'Manes.15G151700' => 'mes', 'Manes.17G111300' => 'mes', 'Mapoly0226s0009' => 'mpo', 'MBI02_g25363_MAGBIO' => 'mbi', 'MBI06_g00027_MAGBIO' => 'mbi', 'MBI10_g13034_MAGBIO' => 'mbi', 'MD09G1023400' => 'mdo', 'MD13G1100100' => 'mdo', 'MD15G1169200' => 'mdo', 'MD16G1101100' => 'mdo', 'MD17G1022900' => 'mdo', 'Medtr3g096150' => 'mtr', 'Medtr4g115070' => 'mtr', 'Medtr7g033325' => 'mtr', 'Medtr8g089840' => 'mtr', 'MELO3C010319.2' => 'cme', 'MELO3C011944.2' => 'cme', 'MELO3C021589.2' => 'cme', 'Migut.E00207' => 'egut', 'Migut.H00067' => 'egut', 'Migut.K00433' => 'egut', 'Migut.K00606' => 'egut', 'Migut.K01410' => 'egut', 'MSTRG.13347' => 'ama', 'MSTRG.24045' => 'ama', 'MSTRG.2428' => 'ama', 'MSTRG.26410' => 'ama', 'MSTRG.3139' => 'ama', 'MSTRG.3286' => 'ama', 'MSTRG.563' => 'ama', 'MSTRG.7941' => 'ama', 'Nitab4.5_0000028g0060' => 'nta', 'Nitab4.5_0000065g0260' => 'nta', 'Nitab4.5_0000112g0060' => 'nta', 'Nitab4.5_0000489g0120' => 'nta', 'Nitab4.5_0001776g0050' => 'nta', 'Nitab4.5_0001854g0010' => 'nta', 'Nitab4.5_0001860g0020' => 'nta', 'Nitab4.5_0004352g0010' => 'nta', 'Nitab4.5_0008716g0020' => 'nta', 'Nitab4.5_0008922g0010' => 'nta', 'Nn3g16693' => 'nnu', 'Nn4g22596' => 'nnu', 'Nn7g37639' => 'nnu', 'Oeu001701.1' => 'oeu', 'Oeu018149.1' => 'oeu', 'Oeu026220.1' => 'oeu', 'Oeu038635.1' => 'oeu', 'Oeu049176.1' => 'oeu', 'Oeu056706.1' => 'oeu', 'Oeu056937.1' => 'oeu', 'Oeu057540.1' => 'oeu', 'Os02g0594900' => 'osa', 'Os02g0595100' => 'osa', 'Os04g0477500' => 'osa', 'Os12g0611900' => 'osa', 'Peaxi162Scf00076g00020' => 'pax', 'Peaxi162Scf00128g00217' => 'pax', 'Peaxi162Scf00129g01640' => 'pax', 'Peaxi162Scf00669g00007' => 'pax', 'Peaxi162Scf00700g00421' => 'pax', 'Peaxi162Scf00801g00038' => 'pax', 'Peaxi162Scf00891g00025' => 'pax', 'PGR083G0909' => 'pgr', 'PGR119G1005' => 'pgr', 'PGR142G2236' => 'pgr', 'PGR142G3388' => 'pgr', 'PGSC0003DMG400004514' => 'stu', 'PGSC0003DMG400012635' => 'stu', 'PGSC0003DMG400015730' => 'stu', 'PGSC0003DMG400018611' => 'stu', 'PGSC0003DMG400030897' => 'stu', 'Phvul.001G254800' => 'pvu', 'Phvul.002G260100' => 'pvu', 'Phvul.003G167600' => 'pvu', 'Phvul.004G005100' => 'pvu', 'Potri.001G343600' => 'ptr', 'Potri.006G066700' => 'ptr', 'Potri.008G186000' => 'ptr', 'Potri.010G046900' => 'ptr', 'Potri.018G127900' => 'ptr', 'Pp3c20_17750' => 'ppa', 'Pp3c24_4380' => 'ppa', 'Prupe.1G245800' => 'ppe', 'Prupe.3G293400' => 'ppe', 'Prupe.7G247400' => 'ppe', 'Psat0s145g0120' => 'psa', 'Psat0s595g0040' => 'psa', 'Psat0s595g0120' => 'psa', 'Psat3g175040' => 'psa', 'Psat7g058120' => 'psa', 'PSO017G0428' => 'pso', 'PSO063G7510' => 'pso', 'PSO067G0046' => 'pso', 'PSO478G1073' => 'pso', 'PSO675G3677' => 'pso', 'PSO675G6558' => 'pso', 'PSO675G7520' => 'pso', 'PSO675G8959' => 'pso', 'QL02p074089' => 'qlo', 'QL02p089614' => 'qlo', 'QL03p057736' => 'qlo', 'RcHm_v2.0_Chr1g0364131' => 'rch', 'RcHm_v2.0_Chr2g0087801' => 'rch', 'RcHm_v2.0_Chr2g0087821' => 'rch', 'RcHm_v2.0_Chr2g0173231' => 'rch', 'RcHm_v2.0_Chr4g0433111' => 'rch', 'Rhsim03G0250300' => 'rsi', 'Rhsim08G0048400' => 'rsi', 'Rhsim10G0014800' => 'rsi', 'Rhsim12G0040100' => 'rsi', 'Rhsim12G0109700' => 'rsi', 'Sabra06G0049600' => 'sbr', 'Sabra08G0141000' => 'sbr', 'Sabra10G0021400' => 'sbr', 'Sabra16G0222900' => 'sbr', 'Sabra18G0108600' => 'sbr', 'SalBow1G0433' => 'sbo', 'SalBow1G2038' => 'sbo', 'SalBow1G5003' => 'sbo', 'SalBow7G1197' => 'sbo', 'SalBow8G3506' => 'sbo', 'Sc03g0007300' => 'sci', 'Sc11g0000950' => 'sci', 'Sc14g0008750' => 'sci', 'Sc18g0000420' => 'sci', 'Sed0006754' => 'sed', 'Sed0008741' => 'sed', 'Sed0017172' => 'sed', 'Sed0018925' => 'sed', 'Sed0023326' => 'sed', 'Sed0025909' => 'sed', 'SEGI_05333' => 'sgi', 'SEGI_10362' => 'sgi', 'SEGI_13380' => 'sgi', 'SEGI_24306' => 'sgi', 'SEGI_29077' => 'sgi', 'SEGI_29095' => 'sgi', 'SEGI_36534' => 'sgi', 'SEGI_37506' => 'sgi', 'SEGI_38321' => 'sgi', 'SGA_v2.0_scaffold307G48031' => 'sas', 'SGA_v2.0_scaffold47G17507' => 'sas', 'SGA_v2.0_scaffold63G21736' => 'sas', 'SGA_v2.0_scaffold87G27070' => 'sas', 'SHI17794' => 'shi', 'SHI28851' => 'shi', 'SMO165G0155' => 'smo', 'SMO340G0217' => 'smo', 'SMO367G1210' => 'smo', 'Solyc02g093430.3' => 'sly', 'Solyc05g013580.4' => 'sly', 'Solyc07g008030.3' => 'sly', 'Solyc12g035470.2' => 'sly', 'Sopen02g038020' => 'spe', 'Sopen05g008490' => 'spe', 'Sopen07g003910' => 'spe', 'Sopen12g015240' => 'spe', 'Sp1g11550' => 'spa', 'Sp2g16710' => 'spa', 'Sp3g00430' => 'spa', 'Sp3g26780' => 'spa', 'Sp5g22900' => 'spa', 'Sp6g29530' => 'spa', 'TAR371G0794' => 'tar', 'TAR374G0164' => 'tar', 'TAR622G0165' => 'tar', 'TAR626G0929' => 'tar', 'TAR629G2155' => 'tar', 'THA.LOC104805282' => 'tha', 'THA.LOC104805363' => 'tha', 'THA.LOC104808968' => 'tha', 'THA.LOC104821093' => 'tha', 'THA.LOC104823953' => 'tha', 'THA.LOC104825562' => 'tha', 'THA.LOC104825665' => 'tha', 'Thecc.02G261400' => 'tca', 'Thecc.04G019200' => 'tca', 'Thecc.09G130400' => 'tca', 'Thhalv10004374m.g' => 'esa', 'Thhalv10007850m.g' => 'esa', 'Thhalv10013782m.g' => 'esa', 'Thhalv10018686m.g' => 'esa', 'Thhalv10020899m.g' => 'esa', 'Thhalv10022755m.g' => 'esa', 'TPR.G23851' => 'tpr', 'TPR.G26500' => 'tpr', 'TPR.G27267' => 'tpr', 'TPR.G32001' => 'tpr', 'TPR.G6251' => 'tpr', 'TPR.G8167' => 'tpr', 'TWI12G1330' => 'twi', 'TWI18G1239' => 'twi', 'TWI34G0979' => 'twi', 'TWI36G0670' => 'twi', 'TWI36G0707' => 'twi', 'TWI56G0233' => 'twi', 'TWI75G1809' => 'twi', 'unitig_21.g20874' => 'ugi', 'unitig_26.g10343' => 'ugi', 'unitig_46.g18392' => 'ugi', 'unitig_52.g17178' => 'ugi', 'unitig_8.g2934' => 'ugi', 'vmacro01122' => 'vma', 'vmacro05875' => 'vma', 'vmacro06147' => 'vma', 'vmacro16191' => 'vma', 'vmacro18293' => 'vma', 'VMungo0251G3707' => 'vmu', 'VMungo0464G1521' => 'vmu', 'VMungo1215G0205' => 'vmu', 'VMungo1383G2484' => 'vmu', 'Zm00001eb079610' => 'zma', 'Zm00001eb135990' => 'zma', 'Zm00001eb183710' => 'zma', 'Zm00001eb246020' => 'zma' ), 'gf_id' => 'HOM05D001124', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001124' ), 'data_identifier' => 'HOM05D001124', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001124', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '548', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02520' => 'bna', 'A03p06630' => 'bna', 'A05p44460' => 'bna', 'A06p08710' => 'bna', 'A06p41090' => 'bna', 'A07p32320' => 'bna', 'A08p32520' => 'bna', 'A09p10360' => 'bna', 'A10p24080' => 'bna', 'Aa31LG11G15250' => 'aar', 'Aa31LG1G1800' => 'aar', 'Aa31LG2G5120' => 'aar', 'Aa31LG2G6070' => 'aar', 'Aa31LG5G10770' => 'aar', 'Aa31sc61G90' => 'aar', 'Actinidia01352' => 'ach', 'Actinidia05983' => 'ach', 'Actinidia08133' => 'ach', 'Actinidia15101' => 'ach', 'Actinidia26379' => 'ach', 'Actinidia35778' => 'ach', 'Actinidia36123' => 'ach', 'Actinidia37436' => 'ach', 'Actinidia38730' => 'ach', 'Ah.02g128210' => 'amhyb', 'Ah.03g132990' => 'amhyb', 'Ah.14g079410' => 'amhyb', 'AL1G24640' => 'aly', 'AL2G26680' => 'aly', 'AL3G10530' => 'aly', 'AL3G45230' => 'aly', 'AL5G15230' => 'aly', 'AL5G16960' => 'aly', 'AL6G25210' => 'aly', 'Aqoxy2G00441' => 'aox', 'Aqoxy3G01236' => 'aox', 'Aqoxy5G03746' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3RQ047' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C7GMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9C8JER' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MBL6KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YXCZ83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZANX40' => 'arhy', 'AT1G12990' => 'ath', 'AT1G67880' => 'ath', 'AT2G13290' => 'ath', 'AT3G01620' => 'ath', 'AT3G26445' => 'ath', 'AT3G27540' => 'ath', 'AT5G14480' => 'ath', 'ATR0824G026' => 'atr', 'ATR1098G019' => 'atr', 'Atru.chr11.2145' => 'acertr', 'Atru.chr2.3636' => 'acertr', 'Atru.chr2.3644' => 'acertr', 'Atru.chr6.2422' => 'acertr', 'Atru.chr7.1112' => 'acertr', 'AUR62005469' => 'cqu', 'AUR62011166' => 'cqu', 'AUR62013319' => 'cqu', 'AUR62024273' => 'cqu', 'AUR62028420' => 'cqu', 'AUR62041942' => 'cqu', 'BcaB01g04969' => 'bca', 'BcaB01g06371' => 'bca', 'BcaB02g11494' => 'bca', 'BcaB03g15382' => 'bca', 'BcaB08g36994' => 'bca', 'BcaC03g13477' => 'bca', 'BcaC03g13478' => 'bca', 'BcaC03g13480' => 'bca', 'BcaC03g13481' => 'bca', 'BcaC03g13486' => 'bca', 'BcaC04g19031' => 'bca', 'BcaC04g23085' => 'bca', 'BcaC05g25094' => 'bca', 'BcaC05g25096' => 'bca', 'BcaC05g25138' => 'bca', 'BcaC05g30416' => 'bca', 'BcaC05g30455' => 'bca', 'BcaC06g30979' => 'bca', 'BcaC06g33805' => 'bca', 'BcaC08g46021' => 'bca', 'BcaNung03154' => 'bca', 'BolC2t06623H' => 'bol', 'BolC2t06632H' => 'bol', 'BolC2t06635H' => 'bol', 'BolC2t06638H' => 'bol', 'BolC3t13266H' => 'bol', 'BolC5t29776H' => 'bol', 'BolC6t38912H' => 'bol', 'BolC7t44183H' => 'bol', 'BolC9t54123H' => 'bol', 'BolC9t59107H' => 'bol', 'BraA02t05221Z' => 'bra', 'BraA03t09996Z' => 'bra', 'BraA05t23210Z' => 'bra', 'BraA06t24068Z' => 'bra', 'BraA06t27032Z' => 'bra', 'BraA08t35176Z' => 'bra', 'BraA09t36680Z' => 'bra', 'BraA10t44471Z' => 'bra', 'C02p06760' => 'bna', 'C02p06890' => 'bna', 'C02p07010' => 'bna', 'C03p07660' => 'bna', 'C05p10300' => 'bna', 'C06p38150' => 'bna', 'C07p36650' => 'bna', 'C08p15770' => 'bna', 'C09p12300' => 'bna', 'C09p62700' => 'bna', 'C09p75040' => 'bna', 'CAN.G13.1' => 'can', 'CAN.G138.4' => 'can', 'CAN.G44.6' => 'can', 'CAN.G473.19' => 'can', 'CANSAT01G0835' => 'cansat', 'CANSAT11G0246' => 'cansat', 'CANSAT11G1766' => 'cansat', 'CANSAT64G1954' => 'cansat', 'CARHR013330' => 'chi', 'CARHR060530' => 'chi', 'CARHR075300' => 'chi', 'CARHR105120' => 'chi', 'CARHR148910' => 'chi', 'CARHR198830' => 'chi', 'Carub.0001s1275' => 'cru', 'Carub.0002s1437' => 'cru', 'Carub.0003s0044' => 'cru', 'Carub.0003s2787' => 'cru', 'Carub.0005s0597' => 'cru', 'Carub.0006s1266' => 'cru', 'Ca_06935_v3' => 'car', 'Ca_13559_v3' => 'car', 'Ca_16941_v3' => 'car', 'Ca_16960_v3' => 'car', 'Ca_17775_v3' => 'car', 'Ca_30464_v3' => 'car', 'Cc06_g08160' => 'ccan', 'Cc07_g01520' => 'ccan', 'Cc11_g15810' => 'ccan', 'CDE02G2840' => 'cde', 'CDE03G0093' => 'cde', 'CDE04G2127' => 'cde', 'CDE07G1857' => 'cde', 'CDE09G1246' => 'cde', 'Cfa003412' => 'cfa', 'Cfa007341' => 'cfa', 'Cfa009220' => 'cfa', 'Ciclev10008737m.g' => 'ccl', 'Ciclev10015565m.g' => 'ccl', 'Ciclev10031761m.g' => 'ccl', 'CiPaw.03G045300' => 'cil', 'CiPaw.03G247200' => 'cil', 'CiPaw.04G029500' => 'cil', 'CiPaw.04G174000' => 'cil', 'CiPaw.05G181200' => 'cil', 'CiPaw.06G067100' => 'cil', 'ClCG05G025800' => 'cla', 'ClCG06G011400' => 'cla', 'ClCG09G019360' => 'cla', 'COL.COLO4_04827' => 'col', 'COL.COLO4_29170' => 'col', 'COL.COLO4_35131' => 'col', 'COL.COLO4_35132' => 'col', 'Cpa.g.sc33.32' => 'cpa', 'Cpa.g.sc46.29' => 'cpa', 'Cpa.g.sc796.1' => 'cpa', 'CsaV3_1G030420' => 'csa', 'CsaV3_5G027050' => 'csa', 'CsaV3_5G031040' => 'csa', 'CsaV3_UNG023130' => 'csa', 'CSS0007726' => 'camsi', 'CSS0016433' => 'camsi', 'CSS0017656' => 'camsi', 'CSS0025364' => 'camsi', 'CSS0027582' => 'camsi', 'CSS0047288' => 'camsi', 'CSS0049950' => 'camsi', 'DCAR_003843' => 'dca', 'DCAR_007052' => 'dca', 'DCAR_020884' => 'dca', 'DCAR_021730' => 'dca', 'DCAR_024423' => 'dca', 'DCAR_026509' => 'dca', 'DCAR_031158' => 'dca', 'Dinv14728' => 'din', 'Dinv15219' => 'din', 'Dinv25728' => 'din', 'Dinv33428' => 'din', 'Dinv36489' => 'din', 'Dinv41486' => 'din', 'Duzib147G0469' => 'dzi', 'Duzib168G0060' => 'dzi', 'Duzib187G1215' => 'dzi', 'Duzib248G0692' => 'dzi', 'Duzib251G0767' => 'dzi', 'Duzib264G0446' => 'dzi', 'Duzib268G0691' => 'dzi', 'ECA232G4767' => 'eca', 'ECA233G2838' => 'eca', 'ECA234G0391' => 'eca', 'ECA234G0857' => 'eca', 'ECA236G1593' => 'eca', 'ECA238G0565' => 'eca', 'ECA246G1027' => 'eca', 'ECA246G3223' => 'eca', 'ECA246G3470' => 'eca', 'EL10Ac6g13829' => 'bvu', 'EL10Ac6g14093' => 'bvu', 'EL10Ac8g18707' => 'bvu', 'Eucgr.C01369' => 'egr', 'Eucgr.H02492' => 'egr', 'Eucgr.I01733' => 'egr', 'Eucgr.J02255' => 'egr', 'Eucgr.J02257' => 'egr', 'Eucgr.J02258' => 'egr', 'FAN02G1601' => 'fan', 'FAN03G1586' => 'fan', 'FAN03G2986' => 'fan', 'FAN05G4837' => 'fan', 'FAN06G0146' => 'fan', 'FAN07G0858' => 'fan', 'FAN09G3179' => 'fan', 'FAN10G0669' => 'fan', 'FAN12G2358' => 'fan', 'FAN14G4198' => 'fan', 'FAN14G5112' => 'fan', 'FAN17G0342' => 'fan', 'FAN19G0342' => 'fan', 'FAN19G0962' => 'fan', 'FAN19G1101' => 'fan', 'FAN19G1872' => 'fan', 'FAN22G0356' => 'fan', 'FAN23G0744' => 'fan', 'FAN23G1914' => 'fan', 'FAN26G0032' => 'fan', 'FAN28G0625' => 'fan', 'FvH4_1g02710' => 'fve', 'FvH4_1g02720' => 'fve', 'FvH4_4g25670' => 'fve', 'FvH4_6g51700' => 'fve', 'FvH4_7g20170' => 'fve', 'Glyma.05G175000' => 'gma', 'Glyma.08G132300' => 'gma', 'Glyma.11G243000' => 'gma', 'Glyma.13G158900' => 'gma', 'Glyma.17G112400' => 'gma', 'Glyma.18G014100' => 'gma', 'Glyma.19G003100' => 'gma', 'Glyma.19G056500' => 'gma', 'Gohir.A01G158900' => 'ghi', 'Gohir.A05G312600' => 'ghi', 'Gohir.A05G354900' => 'ghi', 'Gohir.A07G037200' => 'ghi', 'Gohir.A09G030000' => 'ghi', 'Gohir.A12G145200' => 'ghi', 'Gohir.D01G151500' => 'ghi', 'Gohir.D04G058300' => 'ghi', 'Gohir.D05G314100' => 'ghi', 'Gohir.D07G041400' => 'ghi', 'Gohir.D09G029700' => 'ghi', 'Gohir.D12G149700' => 'ghi', 'Gorai.001G043800' => 'gra', 'Gorai.002G187800' => 'gra', 'Gorai.006G034700' => 'gra', 'Gorai.008G161200' => 'gra', 'Gorai.009G335700' => 'gra', 'Gorai.012G065000' => 'gra', 'GSVIVG01000535001' => 'vvi', 'GSVIVG01015572001' => 'vvi', 'GSVIVG01032386001' => 'vvi', 'HanXRQChr05g0138531' => 'han', 'HanXRQChr06g0174391' => 'han', 'HanXRQChr07g0199021' => 'han', 'HanXRQChr08g0208211' => 'han', 'HanXRQChr09g0255471' => 'han', 'HanXRQChr10g0315791' => 'han', 'HanXRQChr12g0371991' => 'han', 'HanXRQChr15g0475251' => 'han', 'HanXRQChr17g0540001' => 'han', 'HanXRQChr17g0548631' => 'han', 'HanXRQChr17g0569561' => 'han', 'Haze_12256' => 'cav', 'Haze_14756' => 'cav', 'Haze_25528' => 'cav', 'Hma1.2p1_0079F.1_g041020' => 'hma', 'Hma1.2p1_0818F.1_g223260' => 'hma', 'Hma1.2p1_1747F.1_g300530' => 'hma', 'HPP92_004607' => 'vpl', 'HPP92_004608' => 'vpl', 'HPP92_006181' => 'vpl', 'HPP92_012192' => 'vpl', 'HPP92_015680' => 'vpl', 'HPP92_020249' => 'vpl', 'HPP92_021376' => 'vpl', 'HPP92_024275' => 'vpl', 'Hund06031' => 'sun', 'Hund25391' => 'sun', 'Lalb_Chr07g0185371' => 'lal', 'Lalb_Chr07g0185381' => 'lal', 'Lalb_Chr12g0204011' => 'lal', 'Lalb_Chr13g0301671' => 'lal', 'Lalb_Chr14g0362851' => 'lal', 'Lalb_Chr24g0403581' => 'lal', 'Lj1g0000233' => 'lja', 'Lj2g0018120' => 'lja', 'Lj3C621T0' => 'lonja', 'Lj3P1059T14' => 'lonja', 'Lj3P611T9' => 'lonja', 'Lj3P614T13' => 'lonja', 'Lj3P615T5' => 'lonja', 'Lj4g0012315' => 'lja', 'Lj4g0026182' => 'lja', 'Lj6P813T16' => 'lonja', 'Lj7C427T7' => 'lonja', 'Lj7C427T8' => 'lonja', 'Lj7P600T41' => 'lonja', 'Lju41C42G17' => 'lonja', 'Lsat_1_v5_gn_0_47300' => 'lsa', 'Lsat_1_v5_gn_2_91280' => 'lsa', 'Lsat_1_v5_gn_3_30561' => 'lsa', 'Lsat_1_v5_gn_4_184321' => 'lsa', 'Lsat_1_v5_gn_4_4041' => 'lsa', 'Lsat_1_v5_gn_5_92000' => 'lsa', 'Lsat_1_v5_gn_8_152940' => 'lsa', 'Lsat_1_v5_gn_8_62401' => 'lsa', 'Manes.06G055900' => 'mes', 'Manes.12G022200' => 'mes', 'Manes.13G023300' => 'mes', 'Manes.14G115000' => 'mes', 'Manes.15G151700' => 'mes', 'Manes.17G111300' => 'mes', 'Mapoly0226s0009' => 'mpo', 'MBI02_g25363_MAGBIO' => 'mbi', 'MBI06_g00027_MAGBIO' => 'mbi', 'MBI10_g13034_MAGBIO' => 'mbi', 'MD09G1023400' => 'mdo', 'MD13G1100100' => 'mdo', 'MD15G1169200' => 'mdo', 'MD16G1101100' => 'mdo', 'MD17G1022900' => 'mdo', 'Medtr3g096150' => 'mtr', 'Medtr4g115070' => 'mtr', 'Medtr7g033325' => 'mtr', 'Medtr8g089840' => 'mtr', 'MELO3C010319.2' => 'cme', 'MELO3C011944.2' => 'cme', 'MELO3C021589.2' => 'cme', 'Migut.E00207' => 'egut', 'Migut.H00067' => 'egut', 'Migut.K00433' => 'egut', 'Migut.K00606' => 'egut', 'Migut.K01410' => 'egut', 'MSTRG.13347' => 'ama', 'MSTRG.24045' => 'ama', 'MSTRG.2428' => 'ama', 'MSTRG.26410' => 'ama', 'MSTRG.3139' => 'ama', 'MSTRG.3286' => 'ama', 'MSTRG.563' => 'ama', 'MSTRG.7941' => 'ama', 'Nitab4.5_0000028g0060' => 'nta', 'Nitab4.5_0000065g0260' => 'nta', 'Nitab4.5_0000112g0060' => 'nta', 'Nitab4.5_0000489g0120' => 'nta', 'Nitab4.5_0001776g0050' => 'nta', 'Nitab4.5_0001854g0010' => 'nta', 'Nitab4.5_0001860g0020' => 'nta', 'Nitab4.5_0004352g0010' => 'nta', 'Nitab4.5_0008716g0020' => 'nta', 'Nitab4.5_0008922g0010' => 'nta', 'Nn3g16693' => 'nnu', 'Nn4g22596' => 'nnu', 'Nn7g37639' => 'nnu', 'Oeu001701.1' => 'oeu', 'Oeu018149.1' => 'oeu', 'Oeu026220.1' => 'oeu', 'Oeu038635.1' => 'oeu', 'Oeu049176.1' => 'oeu', 'Oeu056706.1' => 'oeu', 'Oeu056937.1' => 'oeu', 'Oeu057540.1' => 'oeu', 'Os02g0594900' => 'osa', 'Os02g0595100' => 'osa', 'Os04g0477500' => 'osa', 'Os12g0611900' => 'osa', 'Peaxi162Scf00076g00020' => 'pax', 'Peaxi162Scf00128g00217' => 'pax', 'Peaxi162Scf00129g01640' => 'pax', 'Peaxi162Scf00669g00007' => 'pax', 'Peaxi162Scf00700g00421' => 'pax', 'Peaxi162Scf00801g00038' => 'pax', 'Peaxi162Scf00891g00025' => 'pax', 'PGR083G0909' => 'pgr', 'PGR119G1005' => 'pgr', 'PGR142G2236' => 'pgr', 'PGR142G3388' => 'pgr', 'PGSC0003DMG400004514' => 'stu', 'PGSC0003DMG400012635' => 'stu', 'PGSC0003DMG400015730' => 'stu', 'PGSC0003DMG400018611' => 'stu', 'PGSC0003DMG400030897' => 'stu', 'Phvul.001G254800' => 'pvu', 'Phvul.002G260100' => 'pvu', 'Phvul.003G167600' => 'pvu', 'Phvul.004G005100' => 'pvu', 'Potri.001G343600' => 'ptr', 'Potri.006G066700' => 'ptr', 'Potri.008G186000' => 'ptr', 'Potri.010G046900' => 'ptr', 'Potri.018G127900' => 'ptr', 'Pp3c20_17750' => 'ppa', 'Pp3c24_4380' => 'ppa', 'Prupe.1G245800' => 'ppe', 'Prupe.3G293400' => 'ppe', 'Prupe.7G247400' => 'ppe', 'Psat0s145g0120' => 'psa', 'Psat0s595g0040' => 'psa', 'Psat0s595g0120' => 'psa', 'Psat3g175040' => 'psa', 'Psat7g058120' => 'psa', 'PSO017G0428' => 'pso', 'PSO063G7510' => 'pso', 'PSO067G0046' => 'pso', 'PSO478G1073' => 'pso', 'PSO675G3677' => 'pso', 'PSO675G6558' => 'pso', 'PSO675G7520' => 'pso', 'PSO675G8959' => 'pso', 'QL02p074089' => 'qlo', 'QL02p089614' => 'qlo', 'QL03p057736' => 'qlo', 'RcHm_v2.0_Chr1g0364131' => 'rch', 'RcHm_v2.0_Chr2g0087801' => 'rch', 'RcHm_v2.0_Chr2g0087821' => 'rch', 'RcHm_v2.0_Chr2g0173231' => 'rch', 'RcHm_v2.0_Chr4g0433111' => 'rch', 'Rhsim03G0250300' => 'rsi', 'Rhsim08G0048400' => 'rsi', 'Rhsim10G0014800' => 'rsi', 'Rhsim12G0040100' => 'rsi', 'Rhsim12G0109700' => 'rsi', 'Sabra06G0049600' => 'sbr', 'Sabra08G0141000' => 'sbr', 'Sabra10G0021400' => 'sbr', 'Sabra16G0222900' => 'sbr', 'Sabra18G0108600' => 'sbr', 'SalBow1G0433' => 'sbo', 'SalBow1G2038' => 'sbo', 'SalBow1G5003' => 'sbo', 'SalBow7G1197' => 'sbo', 'SalBow8G3506' => 'sbo', 'Sc03g0007300' => 'sci', 'Sc11g0000950' => 'sci', 'Sc14g0008750' => 'sci', 'Sc18g0000420' => 'sci', 'Sed0006754' => 'sed', 'Sed0008741' => 'sed', 'Sed0017172' => 'sed', 'Sed0018925' => 'sed', 'Sed0023326' => 'sed', 'Sed0025909' => 'sed', 'SEGI_05333' => 'sgi', 'SEGI_10362' => 'sgi', 'SEGI_13380' => 'sgi', 'SEGI_24306' => 'sgi', 'SEGI_29077' => 'sgi', 'SEGI_29095' => 'sgi', 'SEGI_36534' => 'sgi', 'SEGI_37506' => 'sgi', 'SEGI_38321' => 'sgi', 'SGA_v2.0_scaffold307G48031' => 'sas', 'SGA_v2.0_scaffold47G17507' => 'sas', 'SGA_v2.0_scaffold63G21736' => 'sas', 'SGA_v2.0_scaffold87G27070' => 'sas', 'SHI17794' => 'shi', 'SHI28851' => 'shi', 'SMO165G0155' => 'smo', 'SMO340G0217' => 'smo', 'SMO367G1210' => 'smo', 'Solyc02g093430.3' => 'sly', 'Solyc05g013580.4' => 'sly', 'Solyc07g008030.3' => 'sly', 'Solyc12g035470.2' => 'sly', 'Sopen02g038020' => 'spe', 'Sopen05g008490' => 'spe', 'Sopen07g003910' => 'spe', 'Sopen12g015240' => 'spe', 'Sp1g11550' => 'spa', 'Sp2g16710' => 'spa', 'Sp3g00430' => 'spa', 'Sp3g26780' => 'spa', 'Sp5g22900' => 'spa', 'Sp6g29530' => 'spa', 'TAR371G0794' => 'tar', 'TAR374G0164' => 'tar', 'TAR622G0165' => 'tar', 'TAR626G0929' => 'tar', 'TAR629G2155' => 'tar', 'THA.LOC104805282' => 'tha', 'THA.LOC104805363' => 'tha', 'THA.LOC104808968' => 'tha', 'THA.LOC104821093' => 'tha', 'THA.LOC104823953' => 'tha', 'THA.LOC104825562' => 'tha', 'THA.LOC104825665' => 'tha', 'Thecc.02G261400' => 'tca', 'Thecc.04G019200' => 'tca', 'Thecc.09G130400' => 'tca', 'Thhalv10004374m.g' => 'esa', 'Thhalv10007850m.g' => 'esa', 'Thhalv10013782m.g' => 'esa', 'Thhalv10018686m.g' => 'esa', 'Thhalv10020899m.g' => 'esa', 'Thhalv10022755m.g' => 'esa', 'TPR.G23851' => 'tpr', 'TPR.G26500' => 'tpr', 'TPR.G27267' => 'tpr', 'TPR.G32001' => 'tpr', 'TPR.G6251' => 'tpr', 'TPR.G8167' => 'tpr', 'TWI12G1330' => 'twi', 'TWI18G1239' => 'twi', 'TWI34G0979' => 'twi', 'TWI36G0670' => 'twi', 'TWI36G0707' => 'twi', 'TWI56G0233' => 'twi', 'TWI75G1809' => 'twi', 'unitig_21.g20874' => 'ugi', 'unitig_26.g10343' => 'ugi', 'unitig_46.g18392' => 'ugi', 'unitig_52.g17178' => 'ugi', 'unitig_8.g2934' => 'ugi', 'vmacro01122' => 'vma', 'vmacro05875' => 'vma', 'vmacro06147' => 'vma', 'vmacro16191' => 'vma', 'vmacro18293' => 'vma', 'VMungo0251G3707' => 'vmu', 'VMungo0464G1521' => 'vmu', 'VMungo1215G0205' => 'vmu', 'VMungo1383G2484' => 'vmu', 'Zm00001eb079610' => 'zma', 'Zm00001eb135990' => 'zma', 'Zm00001eb183710' => 'zma', 'Zm00001eb246020' => 'zma' ) $gf_id = 'HOM05D001124' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001124' ) $data_identifier = 'HOM05D001124' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 6, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 7, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 21, 'bol' => (int) 10, 'bra' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 6, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 9, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 21, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 8, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 10, 'lsa' => (int) 8, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 8, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 9, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb246020' $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' => 'HOM05D001124', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '548', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02520' => 'bna', 'A03p06630' => 'bna', 'A05p44460' => 'bna', 'A06p08710' => 'bna', 'A06p41090' => 'bna', 'A07p32320' => 'bna', 'A08p32520' => 'bna', 'A09p10360' => 'bna', 'A10p24080' => 'bna', 'Aa31LG11G15250' => 'aar', 'Aa31LG1G1800' => 'aar', 'Aa31LG2G5120' => 'aar', 'Aa31LG2G6070' => 'aar', 'Aa31LG5G10770' => 'aar', 'Aa31sc61G90' => 'aar', 'Actinidia01352' => 'ach', 'Actinidia05983' => 'ach', 'Actinidia08133' => 'ach', 'Actinidia15101' => 'ach', 'Actinidia26379' => 'ach', 'Actinidia35778' => 'ach', 'Actinidia36123' => 'ach', 'Actinidia37436' => 'ach', 'Actinidia38730' => 'ach', 'Ah.02g128210' => 'amhyb', 'Ah.03g132990' => 'amhyb', 'Ah.14g079410' => 'amhyb', 'AL1G24640' => 'aly', 'AL2G26680' => 'aly', 'AL3G10530' => 'aly', 'AL3G45230' => 'aly', 'AL5G15230' => 'aly', 'AL5G16960' => 'aly', 'AL6G25210' => 'aly', 'Aqoxy2G00441' => 'aox', 'Aqoxy3G01236' => 'aox', 'Aqoxy5G03746' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3RQ047' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C7GMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9C8JER' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MBL6KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YXCZ83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZANX40' => 'arhy', 'AT1G12990' => 'ath', 'AT1G67880' => 'ath', 'AT2G13290' => 'ath', 'AT3G01620' => 'ath', 'AT3G26445' => 'ath', 'AT3G27540' => 'ath', 'AT5G14480' => 'ath', 'ATR0824G026' => 'atr', 'ATR1098G019' => 'atr', 'Atru.chr11.2145' => 'acertr', 'Atru.chr2.3636' => 'acertr', 'Atru.chr2.3644' => 'acertr', 'Atru.chr6.2422' => 'acertr', 'Atru.chr7.1112' => 'acertr', 'AUR62005469' => 'cqu', 'AUR62011166' => 'cqu', 'AUR62013319' => 'cqu', 'AUR62024273' => 'cqu', 'AUR62028420' => 'cqu', 'AUR62041942' => 'cqu', 'BcaB01g04969' => 'bca', 'BcaB01g06371' => 'bca', 'BcaB02g11494' => 'bca', 'BcaB03g15382' => 'bca', 'BcaB08g36994' => 'bca', 'BcaC03g13477' => 'bca', 'BcaC03g13478' => 'bca', 'BcaC03g13480' => 'bca', 'BcaC03g13481' => 'bca', 'BcaC03g13486' => 'bca', 'BcaC04g19031' => 'bca', 'BcaC04g23085' => 'bca', 'BcaC05g25094' => 'bca', 'BcaC05g25096' => 'bca', 'BcaC05g25138' => 'bca', 'BcaC05g30416' => 'bca', 'BcaC05g30455' => 'bca', 'BcaC06g30979' => 'bca', 'BcaC06g33805' => 'bca', 'BcaC08g46021' => 'bca', 'BcaNung03154' => 'bca', 'BolC2t06623H' => 'bol', 'BolC2t06632H' => 'bol', 'BolC2t06635H' => 'bol', 'BolC2t06638H' => 'bol', 'BolC3t13266H' => 'bol', 'BolC5t29776H' => 'bol', 'BolC6t38912H' => 'bol', 'BolC7t44183H' => 'bol', 'BolC9t54123H' => 'bol', 'BolC9t59107H' => 'bol', 'BraA02t05221Z' => 'bra', 'BraA03t09996Z' => 'bra', 'BraA05t23210Z' => 'bra', 'BraA06t24068Z' => 'bra', 'BraA06t27032Z' => 'bra', 'BraA08t35176Z' => 'bra', 'BraA09t36680Z' => 'bra', 'BraA10t44471Z' => 'bra', 'C02p06760' => 'bna', 'C02p06890' => 'bna', 'C02p07010' => 'bna', 'C03p07660' => 'bna', 'C05p10300' => 'bna', 'C06p38150' => 'bna', 'C07p36650' => 'bna', 'C08p15770' => 'bna', 'C09p12300' => 'bna', 'C09p62700' => 'bna', 'C09p75040' => 'bna', 'CAN.G13.1' => 'can', 'CAN.G138.4' => 'can', 'CAN.G44.6' => 'can', 'CAN.G473.19' => 'can', 'CANSAT01G0835' => 'cansat', 'CANSAT11G0246' => 'cansat', 'CANSAT11G1766' => 'cansat', 'CANSAT64G1954' => 'cansat', 'CARHR013330' => 'chi', 'CARHR060530' => 'chi', 'CARHR075300' => 'chi', 'CARHR105120' => 'chi', 'CARHR148910' => 'chi', 'CARHR198830' => 'chi', 'Carub.0001s1275' => 'cru', 'Carub.0002s1437' => 'cru', 'Carub.0003s0044' => 'cru', 'Carub.0003s2787' => 'cru', 'Carub.0005s0597' => 'cru', 'Carub.0006s1266' => 'cru', 'Ca_06935_v3' => 'car', 'Ca_13559_v3' => 'car', 'Ca_16941_v3' => 'car', 'Ca_16960_v3' => 'car', 'Ca_17775_v3' => 'car', 'Ca_30464_v3' => 'car', 'Cc06_g08160' => 'ccan', 'Cc07_g01520' => 'ccan', 'Cc11_g15810' => 'ccan', 'CDE02G2840' => 'cde', 'CDE03G0093' => 'cde', 'CDE04G2127' => 'cde', 'CDE07G1857' => 'cde', 'CDE09G1246' => 'cde', 'Cfa003412' => 'cfa', 'Cfa007341' => 'cfa', 'Cfa009220' => 'cfa', 'Ciclev10008737m.g' => 'ccl', 'Ciclev10015565m.g' => 'ccl', 'Ciclev10031761m.g' => 'ccl', 'CiPaw.03G045300' => 'cil', 'CiPaw.03G247200' => 'cil', 'CiPaw.04G029500' => 'cil', 'CiPaw.04G174000' => 'cil', 'CiPaw.05G181200' => 'cil', 'CiPaw.06G067100' => 'cil', 'ClCG05G025800' => 'cla', 'ClCG06G011400' => 'cla', 'ClCG09G019360' => 'cla', 'COL.COLO4_04827' => 'col', 'COL.COLO4_29170' => 'col', 'COL.COLO4_35131' => 'col', 'COL.COLO4_35132' => 'col', 'Cpa.g.sc33.32' => 'cpa', 'Cpa.g.sc46.29' => 'cpa', 'Cpa.g.sc796.1' => 'cpa', 'CsaV3_1G030420' => 'csa', 'CsaV3_5G027050' => 'csa', 'CsaV3_5G031040' => 'csa', 'CsaV3_UNG023130' => 'csa', 'CSS0007726' => 'camsi', 'CSS0016433' => 'camsi', 'CSS0017656' => 'camsi', 'CSS0025364' => 'camsi', 'CSS0027582' => 'camsi', 'CSS0047288' => 'camsi', 'CSS0049950' => 'camsi', 'DCAR_003843' => 'dca', 'DCAR_007052' => 'dca', 'DCAR_020884' => 'dca', 'DCAR_021730' => 'dca', 'DCAR_024423' => 'dca', 'DCAR_026509' => 'dca', 'DCAR_031158' => 'dca', 'Dinv14728' => 'din', 'Dinv15219' => 'din', 'Dinv25728' => 'din', 'Dinv33428' => 'din', 'Dinv36489' => 'din', 'Dinv41486' => 'din', 'Duzib147G0469' => 'dzi', 'Duzib168G0060' => 'dzi', 'Duzib187G1215' => 'dzi', 'Duzib248G0692' => 'dzi', 'Duzib251G0767' => 'dzi', 'Duzib264G0446' => 'dzi', 'Duzib268G0691' => 'dzi', 'ECA232G4767' => 'eca', 'ECA233G2838' => 'eca', 'ECA234G0391' => 'eca', 'ECA234G0857' => 'eca', 'ECA236G1593' => 'eca', 'ECA238G0565' => 'eca', 'ECA246G1027' => 'eca', 'ECA246G3223' => 'eca', 'ECA246G3470' => 'eca', 'EL10Ac6g13829' => 'bvu', 'EL10Ac6g14093' => 'bvu', 'EL10Ac8g18707' => 'bvu', 'Eucgr.C01369' => 'egr', 'Eucgr.H02492' => 'egr', 'Eucgr.I01733' => 'egr', 'Eucgr.J02255' => 'egr', 'Eucgr.J02257' => 'egr', 'Eucgr.J02258' => 'egr', 'FAN02G1601' => 'fan', 'FAN03G1586' => 'fan', 'FAN03G2986' => 'fan', 'FAN05G4837' => 'fan', 'FAN06G0146' => 'fan', 'FAN07G0858' => 'fan', 'FAN09G3179' => 'fan', 'FAN10G0669' => 'fan', 'FAN12G2358' => 'fan', 'FAN14G4198' => 'fan', 'FAN14G5112' => 'fan', 'FAN17G0342' => 'fan', 'FAN19G0342' => 'fan', 'FAN19G0962' => 'fan', 'FAN19G1101' => 'fan', 'FAN19G1872' => 'fan', 'FAN22G0356' => 'fan', 'FAN23G0744' => 'fan', 'FAN23G1914' => 'fan', 'FAN26G0032' => 'fan', 'FAN28G0625' => 'fan', 'FvH4_1g02710' => 'fve', 'FvH4_1g02720' => 'fve', 'FvH4_4g25670' => 'fve', 'FvH4_6g51700' => 'fve', 'FvH4_7g20170' => 'fve', 'Glyma.05G175000' => 'gma', 'Glyma.08G132300' => 'gma', 'Glyma.11G243000' => 'gma', 'Glyma.13G158900' => 'gma', 'Glyma.17G112400' => 'gma', 'Glyma.18G014100' => 'gma', 'Glyma.19G003100' => 'gma', 'Glyma.19G056500' => 'gma', 'Gohir.A01G158900' => 'ghi', 'Gohir.A05G312600' => 'ghi', 'Gohir.A05G354900' => 'ghi', 'Gohir.A07G037200' => 'ghi', 'Gohir.A09G030000' => 'ghi', 'Gohir.A12G145200' => 'ghi', 'Gohir.D01G151500' => 'ghi', 'Gohir.D04G058300' => 'ghi', 'Gohir.D05G314100' => 'ghi', 'Gohir.D07G041400' => 'ghi', 'Gohir.D09G029700' => 'ghi', 'Gohir.D12G149700' => 'ghi', 'Gorai.001G043800' => 'gra', 'Gorai.002G187800' => 'gra', 'Gorai.006G034700' => 'gra', 'Gorai.008G161200' => 'gra', 'Gorai.009G335700' => 'gra', 'Gorai.012G065000' => 'gra', 'GSVIVG01000535001' => 'vvi', 'GSVIVG01015572001' => 'vvi', 'GSVIVG01032386001' => 'vvi', 'HanXRQChr05g0138531' => 'han', 'HanXRQChr06g0174391' => 'han', 'HanXRQChr07g0199021' => 'han', 'HanXRQChr08g0208211' => 'han', 'HanXRQChr09g0255471' => 'han', 'HanXRQChr10g0315791' => 'han', 'HanXRQChr12g0371991' => 'han', 'HanXRQChr15g0475251' => 'han', 'HanXRQChr17g0540001' => 'han', 'HanXRQChr17g0548631' => 'han', 'HanXRQChr17g0569561' => 'han', 'Haze_12256' => 'cav', 'Haze_14756' => 'cav', 'Haze_25528' => 'cav', 'Hma1.2p1_0079F.1_g041020' => 'hma', 'Hma1.2p1_0818F.1_g223260' => 'hma', 'Hma1.2p1_1747F.1_g300530' => 'hma', 'HPP92_004607' => 'vpl', 'HPP92_004608' => 'vpl', 'HPP92_006181' => 'vpl', 'HPP92_012192' => 'vpl', 'HPP92_015680' => 'vpl', 'HPP92_020249' => 'vpl', 'HPP92_021376' => 'vpl', 'HPP92_024275' => 'vpl', 'Hund06031' => 'sun', 'Hund25391' => 'sun', 'Lalb_Chr07g0185371' => 'lal', 'Lalb_Chr07g0185381' => 'lal', 'Lalb_Chr12g0204011' => 'lal', 'Lalb_Chr13g0301671' => 'lal', 'Lalb_Chr14g0362851' => 'lal', 'Lalb_Chr24g0403581' => 'lal', 'Lj1g0000233' => 'lja', 'Lj2g0018120' => 'lja', 'Lj3C621T0' => 'lonja', 'Lj3P1059T14' => 'lonja', 'Lj3P611T9' => 'lonja', 'Lj3P614T13' => 'lonja', 'Lj3P615T5' => 'lonja', 'Lj4g0012315' => 'lja', 'Lj4g0026182' => 'lja', 'Lj6P813T16' => 'lonja', 'Lj7C427T7' => 'lonja', 'Lj7C427T8' => 'lonja', 'Lj7P600T41' => 'lonja', 'Lju41C42G17' => 'lonja', 'Lsat_1_v5_gn_0_47300' => 'lsa', 'Lsat_1_v5_gn_2_91280' => 'lsa', 'Lsat_1_v5_gn_3_30561' => 'lsa', 'Lsat_1_v5_gn_4_184321' => 'lsa', 'Lsat_1_v5_gn_4_4041' => 'lsa', 'Lsat_1_v5_gn_5_92000' => 'lsa', 'Lsat_1_v5_gn_8_152940' => 'lsa', 'Lsat_1_v5_gn_8_62401' => 'lsa', 'Manes.06G055900' => 'mes', 'Manes.12G022200' => 'mes', 'Manes.13G023300' => 'mes', 'Manes.14G115000' => 'mes', 'Manes.15G151700' => 'mes', 'Manes.17G111300' => 'mes', 'Mapoly0226s0009' => 'mpo', 'MBI02_g25363_MAGBIO' => 'mbi', 'MBI06_g00027_MAGBIO' => 'mbi', 'MBI10_g13034_MAGBIO' => 'mbi', 'MD09G1023400' => 'mdo', 'MD13G1100100' => 'mdo', 'MD15G1169200' => 'mdo', 'MD16G1101100' => 'mdo', 'MD17G1022900' => 'mdo', 'Medtr3g096150' => 'mtr', 'Medtr4g115070' => 'mtr', 'Medtr7g033325' => 'mtr', 'Medtr8g089840' => 'mtr', 'MELO3C010319.2' => 'cme', 'MELO3C011944.2' => 'cme', 'MELO3C021589.2' => 'cme', 'Migut.E00207' => 'egut', 'Migut.H00067' => 'egut', 'Migut.K00433' => 'egut', 'Migut.K00606' => 'egut', 'Migut.K01410' => 'egut', 'MSTRG.13347' => 'ama', 'MSTRG.24045' => 'ama', 'MSTRG.2428' => 'ama', 'MSTRG.26410' => 'ama', 'MSTRG.3139' => 'ama', 'MSTRG.3286' => 'ama', 'MSTRG.563' => 'ama', 'MSTRG.7941' => 'ama', 'Nitab4.5_0000028g0060' => 'nta', 'Nitab4.5_0000065g0260' => 'nta', 'Nitab4.5_0000112g0060' => 'nta', 'Nitab4.5_0000489g0120' => 'nta', 'Nitab4.5_0001776g0050' => 'nta', 'Nitab4.5_0001854g0010' => 'nta', 'Nitab4.5_0001860g0020' => 'nta', 'Nitab4.5_0004352g0010' => 'nta', 'Nitab4.5_0008716g0020' => 'nta', 'Nitab4.5_0008922g0010' => 'nta', 'Nn3g16693' => 'nnu', 'Nn4g22596' => 'nnu', 'Nn7g37639' => 'nnu', 'Oeu001701.1' => 'oeu', 'Oeu018149.1' => 'oeu', 'Oeu026220.1' => 'oeu', 'Oeu038635.1' => 'oeu', 'Oeu049176.1' => 'oeu', 'Oeu056706.1' => 'oeu', 'Oeu056937.1' => 'oeu', 'Oeu057540.1' => 'oeu', 'Os02g0594900' => 'osa', 'Os02g0595100' => 'osa', 'Os04g0477500' => 'osa', 'Os12g0611900' => 'osa', 'Peaxi162Scf00076g00020' => 'pax', 'Peaxi162Scf00128g00217' => 'pax', 'Peaxi162Scf00129g01640' => 'pax', 'Peaxi162Scf00669g00007' => 'pax', 'Peaxi162Scf00700g00421' => 'pax', 'Peaxi162Scf00801g00038' => 'pax', 'Peaxi162Scf00891g00025' => 'pax', 'PGR083G0909' => 'pgr', 'PGR119G1005' => 'pgr', 'PGR142G2236' => 'pgr', 'PGR142G3388' => 'pgr', 'PGSC0003DMG400004514' => 'stu', 'PGSC0003DMG400012635' => 'stu', 'PGSC0003DMG400015730' => 'stu', 'PGSC0003DMG400018611' => 'stu', 'PGSC0003DMG400030897' => 'stu', 'Phvul.001G254800' => 'pvu', 'Phvul.002G260100' => 'pvu', 'Phvul.003G167600' => 'pvu', 'Phvul.004G005100' => 'pvu', 'Potri.001G343600' => 'ptr', 'Potri.006G066700' => 'ptr', 'Potri.008G186000' => 'ptr', 'Potri.010G046900' => 'ptr', 'Potri.018G127900' => 'ptr', 'Pp3c20_17750' => 'ppa', 'Pp3c24_4380' => 'ppa', 'Prupe.1G245800' => 'ppe', 'Prupe.3G293400' => 'ppe', 'Prupe.7G247400' => 'ppe', 'Psat0s145g0120' => 'psa', 'Psat0s595g0040' => 'psa', 'Psat0s595g0120' => 'psa', 'Psat3g175040' => 'psa', 'Psat7g058120' => 'psa', 'PSO017G0428' => 'pso', 'PSO063G7510' => 'pso', 'PSO067G0046' => 'pso', 'PSO478G1073' => 'pso', 'PSO675G3677' => 'pso', 'PSO675G6558' => 'pso', 'PSO675G7520' => 'pso', 'PSO675G8959' => 'pso', 'QL02p074089' => 'qlo', 'QL02p089614' => 'qlo', 'QL03p057736' => 'qlo', 'RcHm_v2.0_Chr1g0364131' => 'rch', 'RcHm_v2.0_Chr2g0087801' => 'rch', 'RcHm_v2.0_Chr2g0087821' => 'rch', 'RcHm_v2.0_Chr2g0173231' => 'rch', 'RcHm_v2.0_Chr4g0433111' => 'rch', 'Rhsim03G0250300' => 'rsi', 'Rhsim08G0048400' => 'rsi', 'Rhsim10G0014800' => 'rsi', 'Rhsim12G0040100' => 'rsi', 'Rhsim12G0109700' => 'rsi', 'Sabra06G0049600' => 'sbr', 'Sabra08G0141000' => 'sbr', 'Sabra10G0021400' => 'sbr', 'Sabra16G0222900' => 'sbr', 'Sabra18G0108600' => 'sbr', 'SalBow1G0433' => 'sbo', 'SalBow1G2038' => 'sbo', 'SalBow1G5003' => 'sbo', 'SalBow7G1197' => 'sbo', 'SalBow8G3506' => 'sbo', 'Sc03g0007300' => 'sci', 'Sc11g0000950' => 'sci', 'Sc14g0008750' => 'sci', 'Sc18g0000420' => 'sci', 'Sed0006754' => 'sed', 'Sed0008741' => 'sed', 'Sed0017172' => 'sed', 'Sed0018925' => 'sed', 'Sed0023326' => 'sed', 'Sed0025909' => 'sed', 'SEGI_05333' => 'sgi', 'SEGI_10362' => 'sgi', 'SEGI_13380' => 'sgi', 'SEGI_24306' => 'sgi', 'SEGI_29077' => 'sgi', 'SEGI_29095' => 'sgi', 'SEGI_36534' => 'sgi', 'SEGI_37506' => 'sgi', 'SEGI_38321' => 'sgi', 'SGA_v2.0_scaffold307G48031' => 'sas', 'SGA_v2.0_scaffold47G17507' => 'sas', 'SGA_v2.0_scaffold63G21736' => 'sas', 'SGA_v2.0_scaffold87G27070' => 'sas', 'SHI17794' => 'shi', 'SHI28851' => 'shi', 'SMO165G0155' => 'smo', 'SMO340G0217' => 'smo', 'SMO367G1210' => 'smo', 'Solyc02g093430.3' => 'sly', 'Solyc05g013580.4' => 'sly', 'Solyc07g008030.3' => 'sly', 'Solyc12g035470.2' => 'sly', 'Sopen02g038020' => 'spe', 'Sopen05g008490' => 'spe', 'Sopen07g003910' => 'spe', 'Sopen12g015240' => 'spe', 'Sp1g11550' => 'spa', 'Sp2g16710' => 'spa', 'Sp3g00430' => 'spa', 'Sp3g26780' => 'spa', 'Sp5g22900' => 'spa', 'Sp6g29530' => 'spa', 'TAR371G0794' => 'tar', 'TAR374G0164' => 'tar', 'TAR622G0165' => 'tar', 'TAR626G0929' => 'tar', 'TAR629G2155' => 'tar', 'THA.LOC104805282' => 'tha', 'THA.LOC104805363' => 'tha', 'THA.LOC104808968' => 'tha', 'THA.LOC104821093' => 'tha', 'THA.LOC104823953' => 'tha', 'THA.LOC104825562' => 'tha', 'THA.LOC104825665' => 'tha', 'Thecc.02G261400' => 'tca', 'Thecc.04G019200' => 'tca', 'Thecc.09G130400' => 'tca', 'Thhalv10004374m.g' => 'esa', 'Thhalv10007850m.g' => 'esa', 'Thhalv10013782m.g' => 'esa', 'Thhalv10018686m.g' => 'esa', 'Thhalv10020899m.g' => 'esa', 'Thhalv10022755m.g' => 'esa', 'TPR.G23851' => 'tpr', 'TPR.G26500' => 'tpr', 'TPR.G27267' => 'tpr', 'TPR.G32001' => 'tpr', 'TPR.G6251' => 'tpr', 'TPR.G8167' => 'tpr', 'TWI12G1330' => 'twi', 'TWI18G1239' => 'twi', 'TWI34G0979' => 'twi', 'TWI36G0670' => 'twi', 'TWI36G0707' => 'twi', 'TWI56G0233' => 'twi', 'TWI75G1809' => 'twi', 'unitig_21.g20874' => 'ugi', 'unitig_26.g10343' => 'ugi', 'unitig_46.g18392' => 'ugi', 'unitig_52.g17178' => 'ugi', 'unitig_8.g2934' => 'ugi', 'vmacro01122' => 'vma', 'vmacro05875' => 'vma', 'vmacro06147' => 'vma', 'vmacro16191' => 'vma', 'vmacro18293' => 'vma', 'VMungo0251G3707' => 'vmu', 'VMungo0464G1521' => 'vmu', 'VMungo1215G0205' => 'vmu', 'VMungo1383G2484' => 'vmu', 'Zm00001eb079610' => 'zma', 'Zm00001eb135990' => 'zma', 'Zm00001eb183710' => 'zma', 'Zm00001eb246020' => 'zma' ), 'gf_id' => 'HOM05D001124', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001124' ), 'data_identifier' => 'HOM05D001124', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001124', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '548', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02520' => 'bna', 'A03p06630' => 'bna', 'A05p44460' => 'bna', 'A06p08710' => 'bna', 'A06p41090' => 'bna', 'A07p32320' => 'bna', 'A08p32520' => 'bna', 'A09p10360' => 'bna', 'A10p24080' => 'bna', 'Aa31LG11G15250' => 'aar', 'Aa31LG1G1800' => 'aar', 'Aa31LG2G5120' => 'aar', 'Aa31LG2G6070' => 'aar', 'Aa31LG5G10770' => 'aar', 'Aa31sc61G90' => 'aar', 'Actinidia01352' => 'ach', 'Actinidia05983' => 'ach', 'Actinidia08133' => 'ach', 'Actinidia15101' => 'ach', 'Actinidia26379' => 'ach', 'Actinidia35778' => 'ach', 'Actinidia36123' => 'ach', 'Actinidia37436' => 'ach', 'Actinidia38730' => 'ach', 'Ah.02g128210' => 'amhyb', 'Ah.03g132990' => 'amhyb', 'Ah.14g079410' => 'amhyb', 'AL1G24640' => 'aly', 'AL2G26680' => 'aly', 'AL3G10530' => 'aly', 'AL3G45230' => 'aly', 'AL5G15230' => 'aly', 'AL5G16960' => 'aly', 'AL6G25210' => 'aly', 'Aqoxy2G00441' => 'aox', 'Aqoxy3G01236' => 'aox', 'Aqoxy5G03746' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3RQ047' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C7GMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9C8JER' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MBL6KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YXCZ83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZANX40' => 'arhy', 'AT1G12990' => 'ath', 'AT1G67880' => 'ath', 'AT2G13290' => 'ath', 'AT3G01620' => 'ath', 'AT3G26445' => 'ath', 'AT3G27540' => 'ath', 'AT5G14480' => 'ath', 'ATR0824G026' => 'atr', 'ATR1098G019' => 'atr', 'Atru.chr11.2145' => 'acertr', 'Atru.chr2.3636' => 'acertr', 'Atru.chr2.3644' => 'acertr', 'Atru.chr6.2422' => 'acertr', 'Atru.chr7.1112' => 'acertr', 'AUR62005469' => 'cqu', 'AUR62011166' => 'cqu', 'AUR62013319' => 'cqu', 'AUR62024273' => 'cqu', 'AUR62028420' => 'cqu', 'AUR62041942' => 'cqu', 'BcaB01g04969' => 'bca', 'BcaB01g06371' => 'bca', 'BcaB02g11494' => 'bca', 'BcaB03g15382' => 'bca', 'BcaB08g36994' => 'bca', 'BcaC03g13477' => 'bca', 'BcaC03g13478' => 'bca', 'BcaC03g13480' => 'bca', 'BcaC03g13481' => 'bca', 'BcaC03g13486' => 'bca', 'BcaC04g19031' => 'bca', 'BcaC04g23085' => 'bca', 'BcaC05g25094' => 'bca', 'BcaC05g25096' => 'bca', 'BcaC05g25138' => 'bca', 'BcaC05g30416' => 'bca', 'BcaC05g30455' => 'bca', 'BcaC06g30979' => 'bca', 'BcaC06g33805' => 'bca', 'BcaC08g46021' => 'bca', 'BcaNung03154' => 'bca', 'BolC2t06623H' => 'bol', 'BolC2t06632H' => 'bol', 'BolC2t06635H' => 'bol', 'BolC2t06638H' => 'bol', 'BolC3t13266H' => 'bol', 'BolC5t29776H' => 'bol', 'BolC6t38912H' => 'bol', 'BolC7t44183H' => 'bol', 'BolC9t54123H' => 'bol', 'BolC9t59107H' => 'bol', 'BraA02t05221Z' => 'bra', 'BraA03t09996Z' => 'bra', 'BraA05t23210Z' => 'bra', 'BraA06t24068Z' => 'bra', 'BraA06t27032Z' => 'bra', 'BraA08t35176Z' => 'bra', 'BraA09t36680Z' => 'bra', 'BraA10t44471Z' => 'bra', 'C02p06760' => 'bna', 'C02p06890' => 'bna', 'C02p07010' => 'bna', 'C03p07660' => 'bna', 'C05p10300' => 'bna', 'C06p38150' => 'bna', 'C07p36650' => 'bna', 'C08p15770' => 'bna', 'C09p12300' => 'bna', 'C09p62700' => 'bna', 'C09p75040' => 'bna', 'CAN.G13.1' => 'can', 'CAN.G138.4' => 'can', 'CAN.G44.6' => 'can', 'CAN.G473.19' => 'can', 'CANSAT01G0835' => 'cansat', 'CANSAT11G0246' => 'cansat', 'CANSAT11G1766' => 'cansat', 'CANSAT64G1954' => 'cansat', 'CARHR013330' => 'chi', 'CARHR060530' => 'chi', 'CARHR075300' => 'chi', 'CARHR105120' => 'chi', 'CARHR148910' => 'chi', 'CARHR198830' => 'chi', 'Carub.0001s1275' => 'cru', 'Carub.0002s1437' => 'cru', 'Carub.0003s0044' => 'cru', 'Carub.0003s2787' => 'cru', 'Carub.0005s0597' => 'cru', 'Carub.0006s1266' => 'cru', 'Ca_06935_v3' => 'car', 'Ca_13559_v3' => 'car', 'Ca_16941_v3' => 'car', 'Ca_16960_v3' => 'car', 'Ca_17775_v3' => 'car', 'Ca_30464_v3' => 'car', 'Cc06_g08160' => 'ccan', 'Cc07_g01520' => 'ccan', 'Cc11_g15810' => 'ccan', 'CDE02G2840' => 'cde', 'CDE03G0093' => 'cde', 'CDE04G2127' => 'cde', 'CDE07G1857' => 'cde', 'CDE09G1246' => 'cde', 'Cfa003412' => 'cfa', 'Cfa007341' => 'cfa', 'Cfa009220' => 'cfa', 'Ciclev10008737m.g' => 'ccl', 'Ciclev10015565m.g' => 'ccl', 'Ciclev10031761m.g' => 'ccl', 'CiPaw.03G045300' => 'cil', 'CiPaw.03G247200' => 'cil', 'CiPaw.04G029500' => 'cil', 'CiPaw.04G174000' => 'cil', 'CiPaw.05G181200' => 'cil', 'CiPaw.06G067100' => 'cil', 'ClCG05G025800' => 'cla', 'ClCG06G011400' => 'cla', 'ClCG09G019360' => 'cla', 'COL.COLO4_04827' => 'col', 'COL.COLO4_29170' => 'col', 'COL.COLO4_35131' => 'col', 'COL.COLO4_35132' => 'col', 'Cpa.g.sc33.32' => 'cpa', 'Cpa.g.sc46.29' => 'cpa', 'Cpa.g.sc796.1' => 'cpa', 'CsaV3_1G030420' => 'csa', 'CsaV3_5G027050' => 'csa', 'CsaV3_5G031040' => 'csa', 'CsaV3_UNG023130' => 'csa', 'CSS0007726' => 'camsi', 'CSS0016433' => 'camsi', 'CSS0017656' => 'camsi', 'CSS0025364' => 'camsi', 'CSS0027582' => 'camsi', 'CSS0047288' => 'camsi', 'CSS0049950' => 'camsi', 'DCAR_003843' => 'dca', 'DCAR_007052' => 'dca', 'DCAR_020884' => 'dca', 'DCAR_021730' => 'dca', 'DCAR_024423' => 'dca', 'DCAR_026509' => 'dca', 'DCAR_031158' => 'dca', 'Dinv14728' => 'din', 'Dinv15219' => 'din', 'Dinv25728' => 'din', 'Dinv33428' => 'din', 'Dinv36489' => 'din', 'Dinv41486' => 'din', 'Duzib147G0469' => 'dzi', 'Duzib168G0060' => 'dzi', 'Duzib187G1215' => 'dzi', 'Duzib248G0692' => 'dzi', 'Duzib251G0767' => 'dzi', 'Duzib264G0446' => 'dzi', 'Duzib268G0691' => 'dzi', 'ECA232G4767' => 'eca', 'ECA233G2838' => 'eca', 'ECA234G0391' => 'eca', 'ECA234G0857' => 'eca', 'ECA236G1593' => 'eca', 'ECA238G0565' => 'eca', 'ECA246G1027' => 'eca', 'ECA246G3223' => 'eca', 'ECA246G3470' => 'eca', 'EL10Ac6g13829' => 'bvu', 'EL10Ac6g14093' => 'bvu', 'EL10Ac8g18707' => 'bvu', 'Eucgr.C01369' => 'egr', 'Eucgr.H02492' => 'egr', 'Eucgr.I01733' => 'egr', 'Eucgr.J02255' => 'egr', 'Eucgr.J02257' => 'egr', 'Eucgr.J02258' => 'egr', 'FAN02G1601' => 'fan', 'FAN03G1586' => 'fan', 'FAN03G2986' => 'fan', 'FAN05G4837' => 'fan', 'FAN06G0146' => 'fan', 'FAN07G0858' => 'fan', 'FAN09G3179' => 'fan', 'FAN10G0669' => 'fan', 'FAN12G2358' => 'fan', 'FAN14G4198' => 'fan', 'FAN14G5112' => 'fan', 'FAN17G0342' => 'fan', 'FAN19G0342' => 'fan', 'FAN19G0962' => 'fan', 'FAN19G1101' => 'fan', 'FAN19G1872' => 'fan', 'FAN22G0356' => 'fan', 'FAN23G0744' => 'fan', 'FAN23G1914' => 'fan', 'FAN26G0032' => 'fan', 'FAN28G0625' => 'fan', 'FvH4_1g02710' => 'fve', 'FvH4_1g02720' => 'fve', 'FvH4_4g25670' => 'fve', 'FvH4_6g51700' => 'fve', 'FvH4_7g20170' => 'fve', 'Glyma.05G175000' => 'gma', 'Glyma.08G132300' => 'gma', 'Glyma.11G243000' => 'gma', 'Glyma.13G158900' => 'gma', 'Glyma.17G112400' => 'gma', 'Glyma.18G014100' => 'gma', 'Glyma.19G003100' => 'gma', 'Glyma.19G056500' => 'gma', 'Gohir.A01G158900' => 'ghi', 'Gohir.A05G312600' => 'ghi', 'Gohir.A05G354900' => 'ghi', 'Gohir.A07G037200' => 'ghi', 'Gohir.A09G030000' => 'ghi', 'Gohir.A12G145200' => 'ghi', 'Gohir.D01G151500' => 'ghi', 'Gohir.D04G058300' => 'ghi', 'Gohir.D05G314100' => 'ghi', 'Gohir.D07G041400' => 'ghi', 'Gohir.D09G029700' => 'ghi', 'Gohir.D12G149700' => 'ghi', 'Gorai.001G043800' => 'gra', 'Gorai.002G187800' => 'gra', 'Gorai.006G034700' => 'gra', 'Gorai.008G161200' => 'gra', 'Gorai.009G335700' => 'gra', 'Gorai.012G065000' => 'gra', 'GSVIVG01000535001' => 'vvi', 'GSVIVG01015572001' => 'vvi', 'GSVIVG01032386001' => 'vvi', 'HanXRQChr05g0138531' => 'han', 'HanXRQChr06g0174391' => 'han', 'HanXRQChr07g0199021' => 'han', 'HanXRQChr08g0208211' => 'han', 'HanXRQChr09g0255471' => 'han', 'HanXRQChr10g0315791' => 'han', 'HanXRQChr12g0371991' => 'han', 'HanXRQChr15g0475251' => 'han', 'HanXRQChr17g0540001' => 'han', 'HanXRQChr17g0548631' => 'han', 'HanXRQChr17g0569561' => 'han', 'Haze_12256' => 'cav', 'Haze_14756' => 'cav', 'Haze_25528' => 'cav', 'Hma1.2p1_0079F.1_g041020' => 'hma', 'Hma1.2p1_0818F.1_g223260' => 'hma', 'Hma1.2p1_1747F.1_g300530' => 'hma', 'HPP92_004607' => 'vpl', 'HPP92_004608' => 'vpl', 'HPP92_006181' => 'vpl', 'HPP92_012192' => 'vpl', 'HPP92_015680' => 'vpl', 'HPP92_020249' => 'vpl', 'HPP92_021376' => 'vpl', 'HPP92_024275' => 'vpl', 'Hund06031' => 'sun', 'Hund25391' => 'sun', 'Lalb_Chr07g0185371' => 'lal', 'Lalb_Chr07g0185381' => 'lal', 'Lalb_Chr12g0204011' => 'lal', 'Lalb_Chr13g0301671' => 'lal', 'Lalb_Chr14g0362851' => 'lal', 'Lalb_Chr24g0403581' => 'lal', 'Lj1g0000233' => 'lja', 'Lj2g0018120' => 'lja', 'Lj3C621T0' => 'lonja', 'Lj3P1059T14' => 'lonja', 'Lj3P611T9' => 'lonja', 'Lj3P614T13' => 'lonja', 'Lj3P615T5' => 'lonja', 'Lj4g0012315' => 'lja', 'Lj4g0026182' => 'lja', 'Lj6P813T16' => 'lonja', 'Lj7C427T7' => 'lonja', 'Lj7C427T8' => 'lonja', 'Lj7P600T41' => 'lonja', 'Lju41C42G17' => 'lonja', 'Lsat_1_v5_gn_0_47300' => 'lsa', 'Lsat_1_v5_gn_2_91280' => 'lsa', 'Lsat_1_v5_gn_3_30561' => 'lsa', 'Lsat_1_v5_gn_4_184321' => 'lsa', 'Lsat_1_v5_gn_4_4041' => 'lsa', 'Lsat_1_v5_gn_5_92000' => 'lsa', 'Lsat_1_v5_gn_8_152940' => 'lsa', 'Lsat_1_v5_gn_8_62401' => 'lsa', 'Manes.06G055900' => 'mes', 'Manes.12G022200' => 'mes', 'Manes.13G023300' => 'mes', 'Manes.14G115000' => 'mes', 'Manes.15G151700' => 'mes', 'Manes.17G111300' => 'mes', 'Mapoly0226s0009' => 'mpo', 'MBI02_g25363_MAGBIO' => 'mbi', 'MBI06_g00027_MAGBIO' => 'mbi', 'MBI10_g13034_MAGBIO' => 'mbi', 'MD09G1023400' => 'mdo', 'MD13G1100100' => 'mdo', 'MD15G1169200' => 'mdo', 'MD16G1101100' => 'mdo', 'MD17G1022900' => 'mdo', 'Medtr3g096150' => 'mtr', 'Medtr4g115070' => 'mtr', 'Medtr7g033325' => 'mtr', 'Medtr8g089840' => 'mtr', 'MELO3C010319.2' => 'cme', 'MELO3C011944.2' => 'cme', 'MELO3C021589.2' => 'cme', 'Migut.E00207' => 'egut', 'Migut.H00067' => 'egut', 'Migut.K00433' => 'egut', 'Migut.K00606' => 'egut', 'Migut.K01410' => 'egut', 'MSTRG.13347' => 'ama', 'MSTRG.24045' => 'ama', 'MSTRG.2428' => 'ama', 'MSTRG.26410' => 'ama', 'MSTRG.3139' => 'ama', 'MSTRG.3286' => 'ama', 'MSTRG.563' => 'ama', 'MSTRG.7941' => 'ama', 'Nitab4.5_0000028g0060' => 'nta', 'Nitab4.5_0000065g0260' => 'nta', 'Nitab4.5_0000112g0060' => 'nta', 'Nitab4.5_0000489g0120' => 'nta', 'Nitab4.5_0001776g0050' => 'nta', 'Nitab4.5_0001854g0010' => 'nta', 'Nitab4.5_0001860g0020' => 'nta', 'Nitab4.5_0004352g0010' => 'nta', 'Nitab4.5_0008716g0020' => 'nta', 'Nitab4.5_0008922g0010' => 'nta', 'Nn3g16693' => 'nnu', 'Nn4g22596' => 'nnu', 'Nn7g37639' => 'nnu', 'Oeu001701.1' => 'oeu', 'Oeu018149.1' => 'oeu', 'Oeu026220.1' => 'oeu', 'Oeu038635.1' => 'oeu', 'Oeu049176.1' => 'oeu', 'Oeu056706.1' => 'oeu', 'Oeu056937.1' => 'oeu', 'Oeu057540.1' => 'oeu', 'Os02g0594900' => 'osa', 'Os02g0595100' => 'osa', 'Os04g0477500' => 'osa', 'Os12g0611900' => 'osa', 'Peaxi162Scf00076g00020' => 'pax', 'Peaxi162Scf00128g00217' => 'pax', 'Peaxi162Scf00129g01640' => 'pax', 'Peaxi162Scf00669g00007' => 'pax', 'Peaxi162Scf00700g00421' => 'pax', 'Peaxi162Scf00801g00038' => 'pax', 'Peaxi162Scf00891g00025' => 'pax', 'PGR083G0909' => 'pgr', 'PGR119G1005' => 'pgr', 'PGR142G2236' => 'pgr', 'PGR142G3388' => 'pgr', 'PGSC0003DMG400004514' => 'stu', 'PGSC0003DMG400012635' => 'stu', 'PGSC0003DMG400015730' => 'stu', 'PGSC0003DMG400018611' => 'stu', 'PGSC0003DMG400030897' => 'stu', 'Phvul.001G254800' => 'pvu', 'Phvul.002G260100' => 'pvu', 'Phvul.003G167600' => 'pvu', 'Phvul.004G005100' => 'pvu', 'Potri.001G343600' => 'ptr', 'Potri.006G066700' => 'ptr', 'Potri.008G186000' => 'ptr', 'Potri.010G046900' => 'ptr', 'Potri.018G127900' => 'ptr', 'Pp3c20_17750' => 'ppa', 'Pp3c24_4380' => 'ppa', 'Prupe.1G245800' => 'ppe', 'Prupe.3G293400' => 'ppe', 'Prupe.7G247400' => 'ppe', 'Psat0s145g0120' => 'psa', 'Psat0s595g0040' => 'psa', 'Psat0s595g0120' => 'psa', 'Psat3g175040' => 'psa', 'Psat7g058120' => 'psa', 'PSO017G0428' => 'pso', 'PSO063G7510' => 'pso', 'PSO067G0046' => 'pso', 'PSO478G1073' => 'pso', 'PSO675G3677' => 'pso', 'PSO675G6558' => 'pso', 'PSO675G7520' => 'pso', 'PSO675G8959' => 'pso', 'QL02p074089' => 'qlo', 'QL02p089614' => 'qlo', 'QL03p057736' => 'qlo', 'RcHm_v2.0_Chr1g0364131' => 'rch', 'RcHm_v2.0_Chr2g0087801' => 'rch', 'RcHm_v2.0_Chr2g0087821' => 'rch', 'RcHm_v2.0_Chr2g0173231' => 'rch', 'RcHm_v2.0_Chr4g0433111' => 'rch', 'Rhsim03G0250300' => 'rsi', 'Rhsim08G0048400' => 'rsi', 'Rhsim10G0014800' => 'rsi', 'Rhsim12G0040100' => 'rsi', 'Rhsim12G0109700' => 'rsi', 'Sabra06G0049600' => 'sbr', 'Sabra08G0141000' => 'sbr', 'Sabra10G0021400' => 'sbr', 'Sabra16G0222900' => 'sbr', 'Sabra18G0108600' => 'sbr', 'SalBow1G0433' => 'sbo', 'SalBow1G2038' => 'sbo', 'SalBow1G5003' => 'sbo', 'SalBow7G1197' => 'sbo', 'SalBow8G3506' => 'sbo', 'Sc03g0007300' => 'sci', 'Sc11g0000950' => 'sci', 'Sc14g0008750' => 'sci', 'Sc18g0000420' => 'sci', 'Sed0006754' => 'sed', 'Sed0008741' => 'sed', 'Sed0017172' => 'sed', 'Sed0018925' => 'sed', 'Sed0023326' => 'sed', 'Sed0025909' => 'sed', 'SEGI_05333' => 'sgi', 'SEGI_10362' => 'sgi', 'SEGI_13380' => 'sgi', 'SEGI_24306' => 'sgi', 'SEGI_29077' => 'sgi', 'SEGI_29095' => 'sgi', 'SEGI_36534' => 'sgi', 'SEGI_37506' => 'sgi', 'SEGI_38321' => 'sgi', 'SGA_v2.0_scaffold307G48031' => 'sas', 'SGA_v2.0_scaffold47G17507' => 'sas', 'SGA_v2.0_scaffold63G21736' => 'sas', 'SGA_v2.0_scaffold87G27070' => 'sas', 'SHI17794' => 'shi', 'SHI28851' => 'shi', 'SMO165G0155' => 'smo', 'SMO340G0217' => 'smo', 'SMO367G1210' => 'smo', 'Solyc02g093430.3' => 'sly', 'Solyc05g013580.4' => 'sly', 'Solyc07g008030.3' => 'sly', 'Solyc12g035470.2' => 'sly', 'Sopen02g038020' => 'spe', 'Sopen05g008490' => 'spe', 'Sopen07g003910' => 'spe', 'Sopen12g015240' => 'spe', 'Sp1g11550' => 'spa', 'Sp2g16710' => 'spa', 'Sp3g00430' => 'spa', 'Sp3g26780' => 'spa', 'Sp5g22900' => 'spa', 'Sp6g29530' => 'spa', 'TAR371G0794' => 'tar', 'TAR374G0164' => 'tar', 'TAR622G0165' => 'tar', 'TAR626G0929' => 'tar', 'TAR629G2155' => 'tar', 'THA.LOC104805282' => 'tha', 'THA.LOC104805363' => 'tha', 'THA.LOC104808968' => 'tha', 'THA.LOC104821093' => 'tha', 'THA.LOC104823953' => 'tha', 'THA.LOC104825562' => 'tha', 'THA.LOC104825665' => 'tha', 'Thecc.02G261400' => 'tca', 'Thecc.04G019200' => 'tca', 'Thecc.09G130400' => 'tca', 'Thhalv10004374m.g' => 'esa', 'Thhalv10007850m.g' => 'esa', 'Thhalv10013782m.g' => 'esa', 'Thhalv10018686m.g' => 'esa', 'Thhalv10020899m.g' => 'esa', 'Thhalv10022755m.g' => 'esa', 'TPR.G23851' => 'tpr', 'TPR.G26500' => 'tpr', 'TPR.G27267' => 'tpr', 'TPR.G32001' => 'tpr', 'TPR.G6251' => 'tpr', 'TPR.G8167' => 'tpr', 'TWI12G1330' => 'twi', 'TWI18G1239' => 'twi', 'TWI34G0979' => 'twi', 'TWI36G0670' => 'twi', 'TWI36G0707' => 'twi', 'TWI56G0233' => 'twi', 'TWI75G1809' => 'twi', 'unitig_21.g20874' => 'ugi', 'unitig_26.g10343' => 'ugi', 'unitig_46.g18392' => 'ugi', 'unitig_52.g17178' => 'ugi', 'unitig_8.g2934' => 'ugi', 'vmacro01122' => 'vma', 'vmacro05875' => 'vma', 'vmacro06147' => 'vma', 'vmacro16191' => 'vma', 'vmacro18293' => 'vma', 'VMungo0251G3707' => 'vmu', 'VMungo0464G1521' => 'vmu', 'VMungo1215G0205' => 'vmu', 'VMungo1383G2484' => 'vmu', 'Zm00001eb079610' => 'zma', 'Zm00001eb135990' => 'zma', 'Zm00001eb183710' => 'zma', 'Zm00001eb246020' => 'zma' ) $gf_id = 'HOM05D001124' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001124' ) $data_identifier = 'HOM05D001124' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 6, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 7, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 21, 'bol' => (int) 10, 'bra' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 6, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 9, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 21, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 8, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 10, 'lsa' => (int) 8, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 8, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 9, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb246020' $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' => 'HOM05D001124', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '548', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02520' => 'bna', 'A03p06630' => 'bna', 'A05p44460' => 'bna', 'A06p08710' => 'bna', 'A06p41090' => 'bna', 'A07p32320' => 'bna', 'A08p32520' => 'bna', 'A09p10360' => 'bna', 'A10p24080' => 'bna', 'Aa31LG11G15250' => 'aar', 'Aa31LG1G1800' => 'aar', 'Aa31LG2G5120' => 'aar', 'Aa31LG2G6070' => 'aar', 'Aa31LG5G10770' => 'aar', 'Aa31sc61G90' => 'aar', 'Actinidia01352' => 'ach', 'Actinidia05983' => 'ach', 'Actinidia08133' => 'ach', 'Actinidia15101' => 'ach', 'Actinidia26379' => 'ach', 'Actinidia35778' => 'ach', 'Actinidia36123' => 'ach', 'Actinidia37436' => 'ach', 'Actinidia38730' => 'ach', 'Ah.02g128210' => 'amhyb', 'Ah.03g132990' => 'amhyb', 'Ah.14g079410' => 'amhyb', 'AL1G24640' => 'aly', 'AL2G26680' => 'aly', 'AL3G10530' => 'aly', 'AL3G45230' => 'aly', 'AL5G15230' => 'aly', 'AL5G16960' => 'aly', 'AL6G25210' => 'aly', 'Aqoxy2G00441' => 'aox', 'Aqoxy3G01236' => 'aox', 'Aqoxy5G03746' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3RQ047' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C7GMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9C8JER' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MBL6KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YXCZ83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZANX40' => 'arhy', 'AT1G12990' => 'ath', 'AT1G67880' => 'ath', 'AT2G13290' => 'ath', 'AT3G01620' => 'ath', 'AT3G26445' => 'ath', 'AT3G27540' => 'ath', 'AT5G14480' => 'ath', 'ATR0824G026' => 'atr', 'ATR1098G019' => 'atr', 'Atru.chr11.2145' => 'acertr', 'Atru.chr2.3636' => 'acertr', 'Atru.chr2.3644' => 'acertr', 'Atru.chr6.2422' => 'acertr', 'Atru.chr7.1112' => 'acertr', 'AUR62005469' => 'cqu', 'AUR62011166' => 'cqu', 'AUR62013319' => 'cqu', 'AUR62024273' => 'cqu', 'AUR62028420' => 'cqu', 'AUR62041942' => 'cqu', 'BcaB01g04969' => 'bca', 'BcaB01g06371' => 'bca', 'BcaB02g11494' => 'bca', 'BcaB03g15382' => 'bca', 'BcaB08g36994' => 'bca', 'BcaC03g13477' => 'bca', 'BcaC03g13478' => 'bca', 'BcaC03g13480' => 'bca', 'BcaC03g13481' => 'bca', 'BcaC03g13486' => 'bca', 'BcaC04g19031' => 'bca', 'BcaC04g23085' => 'bca', 'BcaC05g25094' => 'bca', 'BcaC05g25096' => 'bca', 'BcaC05g25138' => 'bca', 'BcaC05g30416' => 'bca', 'BcaC05g30455' => 'bca', 'BcaC06g30979' => 'bca', 'BcaC06g33805' => 'bca', 'BcaC08g46021' => 'bca', 'BcaNung03154' => 'bca', 'BolC2t06623H' => 'bol', 'BolC2t06632H' => 'bol', 'BolC2t06635H' => 'bol', 'BolC2t06638H' => 'bol', 'BolC3t13266H' => 'bol', 'BolC5t29776H' => 'bol', 'BolC6t38912H' => 'bol', 'BolC7t44183H' => 'bol', 'BolC9t54123H' => 'bol', 'BolC9t59107H' => 'bol', 'BraA02t05221Z' => 'bra', 'BraA03t09996Z' => 'bra', 'BraA05t23210Z' => 'bra', 'BraA06t24068Z' => 'bra', 'BraA06t27032Z' => 'bra', 'BraA08t35176Z' => 'bra', 'BraA09t36680Z' => 'bra', 'BraA10t44471Z' => 'bra', 'C02p06760' => 'bna', 'C02p06890' => 'bna', 'C02p07010' => 'bna', 'C03p07660' => 'bna', 'C05p10300' => 'bna', 'C06p38150' => 'bna', 'C07p36650' => 'bna', 'C08p15770' => 'bna', 'C09p12300' => 'bna', 'C09p62700' => 'bna', 'C09p75040' => 'bna', 'CAN.G13.1' => 'can', 'CAN.G138.4' => 'can', 'CAN.G44.6' => 'can', 'CAN.G473.19' => 'can', 'CANSAT01G0835' => 'cansat', 'CANSAT11G0246' => 'cansat', 'CANSAT11G1766' => 'cansat', 'CANSAT64G1954' => 'cansat', 'CARHR013330' => 'chi', 'CARHR060530' => 'chi', 'CARHR075300' => 'chi', 'CARHR105120' => 'chi', 'CARHR148910' => 'chi', 'CARHR198830' => 'chi', 'Carub.0001s1275' => 'cru', 'Carub.0002s1437' => 'cru', 'Carub.0003s0044' => 'cru', 'Carub.0003s2787' => 'cru', 'Carub.0005s0597' => 'cru', 'Carub.0006s1266' => 'cru', 'Ca_06935_v3' => 'car', 'Ca_13559_v3' => 'car', 'Ca_16941_v3' => 'car', 'Ca_16960_v3' => 'car', 'Ca_17775_v3' => 'car', 'Ca_30464_v3' => 'car', 'Cc06_g08160' => 'ccan', 'Cc07_g01520' => 'ccan', 'Cc11_g15810' => 'ccan', 'CDE02G2840' => 'cde', 'CDE03G0093' => 'cde', 'CDE04G2127' => 'cde', 'CDE07G1857' => 'cde', 'CDE09G1246' => 'cde', 'Cfa003412' => 'cfa', 'Cfa007341' => 'cfa', 'Cfa009220' => 'cfa', 'Ciclev10008737m.g' => 'ccl', 'Ciclev10015565m.g' => 'ccl', 'Ciclev10031761m.g' => 'ccl', 'CiPaw.03G045300' => 'cil', 'CiPaw.03G247200' => 'cil', 'CiPaw.04G029500' => 'cil', 'CiPaw.04G174000' => 'cil', 'CiPaw.05G181200' => 'cil', 'CiPaw.06G067100' => 'cil', 'ClCG05G025800' => 'cla', 'ClCG06G011400' => 'cla', 'ClCG09G019360' => 'cla', 'COL.COLO4_04827' => 'col', 'COL.COLO4_29170' => 'col', 'COL.COLO4_35131' => 'col', 'COL.COLO4_35132' => 'col', 'Cpa.g.sc33.32' => 'cpa', 'Cpa.g.sc46.29' => 'cpa', 'Cpa.g.sc796.1' => 'cpa', 'CsaV3_1G030420' => 'csa', 'CsaV3_5G027050' => 'csa', 'CsaV3_5G031040' => 'csa', 'CsaV3_UNG023130' => 'csa', 'CSS0007726' => 'camsi', 'CSS0016433' => 'camsi', 'CSS0017656' => 'camsi', 'CSS0025364' => 'camsi', 'CSS0027582' => 'camsi', 'CSS0047288' => 'camsi', 'CSS0049950' => 'camsi', 'DCAR_003843' => 'dca', 'DCAR_007052' => 'dca', 'DCAR_020884' => 'dca', 'DCAR_021730' => 'dca', 'DCAR_024423' => 'dca', 'DCAR_026509' => 'dca', 'DCAR_031158' => 'dca', 'Dinv14728' => 'din', 'Dinv15219' => 'din', 'Dinv25728' => 'din', 'Dinv33428' => 'din', 'Dinv36489' => 'din', 'Dinv41486' => 'din', 'Duzib147G0469' => 'dzi', 'Duzib168G0060' => 'dzi', 'Duzib187G1215' => 'dzi', 'Duzib248G0692' => 'dzi', 'Duzib251G0767' => 'dzi', 'Duzib264G0446' => 'dzi', 'Duzib268G0691' => 'dzi', 'ECA232G4767' => 'eca', 'ECA233G2838' => 'eca', 'ECA234G0391' => 'eca', 'ECA234G0857' => 'eca', 'ECA236G1593' => 'eca', 'ECA238G0565' => 'eca', 'ECA246G1027' => 'eca', 'ECA246G3223' => 'eca', 'ECA246G3470' => 'eca', 'EL10Ac6g13829' => 'bvu', 'EL10Ac6g14093' => 'bvu', 'EL10Ac8g18707' => 'bvu', 'Eucgr.C01369' => 'egr', 'Eucgr.H02492' => 'egr', 'Eucgr.I01733' => 'egr', 'Eucgr.J02255' => 'egr', 'Eucgr.J02257' => 'egr', 'Eucgr.J02258' => 'egr', 'FAN02G1601' => 'fan', 'FAN03G1586' => 'fan', 'FAN03G2986' => 'fan', 'FAN05G4837' => 'fan', 'FAN06G0146' => 'fan', 'FAN07G0858' => 'fan', 'FAN09G3179' => 'fan', 'FAN10G0669' => 'fan', 'FAN12G2358' => 'fan', 'FAN14G4198' => 'fan', 'FAN14G5112' => 'fan', 'FAN17G0342' => 'fan', 'FAN19G0342' => 'fan', 'FAN19G0962' => 'fan', 'FAN19G1101' => 'fan', 'FAN19G1872' => 'fan', 'FAN22G0356' => 'fan', 'FAN23G0744' => 'fan', 'FAN23G1914' => 'fan', 'FAN26G0032' => 'fan', 'FAN28G0625' => 'fan', 'FvH4_1g02710' => 'fve', 'FvH4_1g02720' => 'fve', 'FvH4_4g25670' => 'fve', 'FvH4_6g51700' => 'fve', 'FvH4_7g20170' => 'fve', 'Glyma.05G175000' => 'gma', 'Glyma.08G132300' => 'gma', 'Glyma.11G243000' => 'gma', 'Glyma.13G158900' => 'gma', 'Glyma.17G112400' => 'gma', 'Glyma.18G014100' => 'gma', 'Glyma.19G003100' => 'gma', 'Glyma.19G056500' => 'gma', 'Gohir.A01G158900' => 'ghi', 'Gohir.A05G312600' => 'ghi', 'Gohir.A05G354900' => 'ghi', 'Gohir.A07G037200' => 'ghi', 'Gohir.A09G030000' => 'ghi', 'Gohir.A12G145200' => 'ghi', 'Gohir.D01G151500' => 'ghi', 'Gohir.D04G058300' => 'ghi', 'Gohir.D05G314100' => 'ghi', 'Gohir.D07G041400' => 'ghi', 'Gohir.D09G029700' => 'ghi', 'Gohir.D12G149700' => 'ghi', 'Gorai.001G043800' => 'gra', 'Gorai.002G187800' => 'gra', 'Gorai.006G034700' => 'gra', 'Gorai.008G161200' => 'gra', 'Gorai.009G335700' => 'gra', 'Gorai.012G065000' => 'gra', 'GSVIVG01000535001' => 'vvi', 'GSVIVG01015572001' => 'vvi', 'GSVIVG01032386001' => 'vvi', 'HanXRQChr05g0138531' => 'han', 'HanXRQChr06g0174391' => 'han', 'HanXRQChr07g0199021' => 'han', 'HanXRQChr08g0208211' => 'han', 'HanXRQChr09g0255471' => 'han', 'HanXRQChr10g0315791' => 'han', 'HanXRQChr12g0371991' => 'han', 'HanXRQChr15g0475251' => 'han', 'HanXRQChr17g0540001' => 'han', 'HanXRQChr17g0548631' => 'han', 'HanXRQChr17g0569561' => 'han', 'Haze_12256' => 'cav', 'Haze_14756' => 'cav', 'Haze_25528' => 'cav', 'Hma1.2p1_0079F.1_g041020' => 'hma', 'Hma1.2p1_0818F.1_g223260' => 'hma', 'Hma1.2p1_1747F.1_g300530' => 'hma', 'HPP92_004607' => 'vpl', 'HPP92_004608' => 'vpl', 'HPP92_006181' => 'vpl', 'HPP92_012192' => 'vpl', 'HPP92_015680' => 'vpl', 'HPP92_020249' => 'vpl', 'HPP92_021376' => 'vpl', 'HPP92_024275' => 'vpl', 'Hund06031' => 'sun', 'Hund25391' => 'sun', 'Lalb_Chr07g0185371' => 'lal', 'Lalb_Chr07g0185381' => 'lal', 'Lalb_Chr12g0204011' => 'lal', 'Lalb_Chr13g0301671' => 'lal', 'Lalb_Chr14g0362851' => 'lal', 'Lalb_Chr24g0403581' => 'lal', 'Lj1g0000233' => 'lja', 'Lj2g0018120' => 'lja', 'Lj3C621T0' => 'lonja', 'Lj3P1059T14' => 'lonja', 'Lj3P611T9' => 'lonja', 'Lj3P614T13' => 'lonja', 'Lj3P615T5' => 'lonja', 'Lj4g0012315' => 'lja', 'Lj4g0026182' => 'lja', 'Lj6P813T16' => 'lonja', 'Lj7C427T7' => 'lonja', 'Lj7C427T8' => 'lonja', 'Lj7P600T41' => 'lonja', 'Lju41C42G17' => 'lonja', 'Lsat_1_v5_gn_0_47300' => 'lsa', 'Lsat_1_v5_gn_2_91280' => 'lsa', 'Lsat_1_v5_gn_3_30561' => 'lsa', 'Lsat_1_v5_gn_4_184321' => 'lsa', 'Lsat_1_v5_gn_4_4041' => 'lsa', 'Lsat_1_v5_gn_5_92000' => 'lsa', 'Lsat_1_v5_gn_8_152940' => 'lsa', 'Lsat_1_v5_gn_8_62401' => 'lsa', 'Manes.06G055900' => 'mes', 'Manes.12G022200' => 'mes', 'Manes.13G023300' => 'mes', 'Manes.14G115000' => 'mes', 'Manes.15G151700' => 'mes', 'Manes.17G111300' => 'mes', 'Mapoly0226s0009' => 'mpo', 'MBI02_g25363_MAGBIO' => 'mbi', 'MBI06_g00027_MAGBIO' => 'mbi', 'MBI10_g13034_MAGBIO' => 'mbi', 'MD09G1023400' => 'mdo', 'MD13G1100100' => 'mdo', 'MD15G1169200' => 'mdo', 'MD16G1101100' => 'mdo', 'MD17G1022900' => 'mdo', 'Medtr3g096150' => 'mtr', 'Medtr4g115070' => 'mtr', 'Medtr7g033325' => 'mtr', 'Medtr8g089840' => 'mtr', 'MELO3C010319.2' => 'cme', 'MELO3C011944.2' => 'cme', 'MELO3C021589.2' => 'cme', 'Migut.E00207' => 'egut', 'Migut.H00067' => 'egut', 'Migut.K00433' => 'egut', 'Migut.K00606' => 'egut', 'Migut.K01410' => 'egut', 'MSTRG.13347' => 'ama', 'MSTRG.24045' => 'ama', 'MSTRG.2428' => 'ama', 'MSTRG.26410' => 'ama', 'MSTRG.3139' => 'ama', 'MSTRG.3286' => 'ama', 'MSTRG.563' => 'ama', 'MSTRG.7941' => 'ama', 'Nitab4.5_0000028g0060' => 'nta', 'Nitab4.5_0000065g0260' => 'nta', 'Nitab4.5_0000112g0060' => 'nta', 'Nitab4.5_0000489g0120' => 'nta', 'Nitab4.5_0001776g0050' => 'nta', 'Nitab4.5_0001854g0010' => 'nta', 'Nitab4.5_0001860g0020' => 'nta', 'Nitab4.5_0004352g0010' => 'nta', 'Nitab4.5_0008716g0020' => 'nta', 'Nitab4.5_0008922g0010' => 'nta', 'Nn3g16693' => 'nnu', 'Nn4g22596' => 'nnu', 'Nn7g37639' => 'nnu', 'Oeu001701.1' => 'oeu', 'Oeu018149.1' => 'oeu', 'Oeu026220.1' => 'oeu', 'Oeu038635.1' => 'oeu', 'Oeu049176.1' => 'oeu', 'Oeu056706.1' => 'oeu', 'Oeu056937.1' => 'oeu', 'Oeu057540.1' => 'oeu', 'Os02g0594900' => 'osa', 'Os02g0595100' => 'osa', 'Os04g0477500' => 'osa', 'Os12g0611900' => 'osa', 'Peaxi162Scf00076g00020' => 'pax', 'Peaxi162Scf00128g00217' => 'pax', 'Peaxi162Scf00129g01640' => 'pax', 'Peaxi162Scf00669g00007' => 'pax', 'Peaxi162Scf00700g00421' => 'pax', 'Peaxi162Scf00801g00038' => 'pax', 'Peaxi162Scf00891g00025' => 'pax', 'PGR083G0909' => 'pgr', 'PGR119G1005' => 'pgr', 'PGR142G2236' => 'pgr', 'PGR142G3388' => 'pgr', 'PGSC0003DMG400004514' => 'stu', 'PGSC0003DMG400012635' => 'stu', 'PGSC0003DMG400015730' => 'stu', 'PGSC0003DMG400018611' => 'stu', 'PGSC0003DMG400030897' => 'stu', 'Phvul.001G254800' => 'pvu', 'Phvul.002G260100' => 'pvu', 'Phvul.003G167600' => 'pvu', 'Phvul.004G005100' => 'pvu', 'Potri.001G343600' => 'ptr', 'Potri.006G066700' => 'ptr', 'Potri.008G186000' => 'ptr', 'Potri.010G046900' => 'ptr', 'Potri.018G127900' => 'ptr', 'Pp3c20_17750' => 'ppa', 'Pp3c24_4380' => 'ppa', 'Prupe.1G245800' => 'ppe', 'Prupe.3G293400' => 'ppe', 'Prupe.7G247400' => 'ppe', 'Psat0s145g0120' => 'psa', 'Psat0s595g0040' => 'psa', 'Psat0s595g0120' => 'psa', 'Psat3g175040' => 'psa', 'Psat7g058120' => 'psa', 'PSO017G0428' => 'pso', 'PSO063G7510' => 'pso', 'PSO067G0046' => 'pso', 'PSO478G1073' => 'pso', 'PSO675G3677' => 'pso', 'PSO675G6558' => 'pso', 'PSO675G7520' => 'pso', 'PSO675G8959' => 'pso', 'QL02p074089' => 'qlo', 'QL02p089614' => 'qlo', 'QL03p057736' => 'qlo', 'RcHm_v2.0_Chr1g0364131' => 'rch', 'RcHm_v2.0_Chr2g0087801' => 'rch', 'RcHm_v2.0_Chr2g0087821' => 'rch', 'RcHm_v2.0_Chr2g0173231' => 'rch', 'RcHm_v2.0_Chr4g0433111' => 'rch', 'Rhsim03G0250300' => 'rsi', 'Rhsim08G0048400' => 'rsi', 'Rhsim10G0014800' => 'rsi', 'Rhsim12G0040100' => 'rsi', 'Rhsim12G0109700' => 'rsi', 'Sabra06G0049600' => 'sbr', 'Sabra08G0141000' => 'sbr', 'Sabra10G0021400' => 'sbr', 'Sabra16G0222900' => 'sbr', 'Sabra18G0108600' => 'sbr', 'SalBow1G0433' => 'sbo', 'SalBow1G2038' => 'sbo', 'SalBow1G5003' => 'sbo', 'SalBow7G1197' => 'sbo', 'SalBow8G3506' => 'sbo', 'Sc03g0007300' => 'sci', 'Sc11g0000950' => 'sci', 'Sc14g0008750' => 'sci', 'Sc18g0000420' => 'sci', 'Sed0006754' => 'sed', 'Sed0008741' => 'sed', 'Sed0017172' => 'sed', 'Sed0018925' => 'sed', 'Sed0023326' => 'sed', 'Sed0025909' => 'sed', 'SEGI_05333' => 'sgi', 'SEGI_10362' => 'sgi', 'SEGI_13380' => 'sgi', 'SEGI_24306' => 'sgi', 'SEGI_29077' => 'sgi', 'SEGI_29095' => 'sgi', 'SEGI_36534' => 'sgi', 'SEGI_37506' => 'sgi', 'SEGI_38321' => 'sgi', 'SGA_v2.0_scaffold307G48031' => 'sas', 'SGA_v2.0_scaffold47G17507' => 'sas', 'SGA_v2.0_scaffold63G21736' => 'sas', 'SGA_v2.0_scaffold87G27070' => 'sas', 'SHI17794' => 'shi', 'SHI28851' => 'shi', 'SMO165G0155' => 'smo', 'SMO340G0217' => 'smo', 'SMO367G1210' => 'smo', 'Solyc02g093430.3' => 'sly', 'Solyc05g013580.4' => 'sly', 'Solyc07g008030.3' => 'sly', 'Solyc12g035470.2' => 'sly', 'Sopen02g038020' => 'spe', 'Sopen05g008490' => 'spe', 'Sopen07g003910' => 'spe', 'Sopen12g015240' => 'spe', 'Sp1g11550' => 'spa', 'Sp2g16710' => 'spa', 'Sp3g00430' => 'spa', 'Sp3g26780' => 'spa', 'Sp5g22900' => 'spa', 'Sp6g29530' => 'spa', 'TAR371G0794' => 'tar', 'TAR374G0164' => 'tar', 'TAR622G0165' => 'tar', 'TAR626G0929' => 'tar', 'TAR629G2155' => 'tar', 'THA.LOC104805282' => 'tha', 'THA.LOC104805363' => 'tha', 'THA.LOC104808968' => 'tha', 'THA.LOC104821093' => 'tha', 'THA.LOC104823953' => 'tha', 'THA.LOC104825562' => 'tha', 'THA.LOC104825665' => 'tha', 'Thecc.02G261400' => 'tca', 'Thecc.04G019200' => 'tca', 'Thecc.09G130400' => 'tca', 'Thhalv10004374m.g' => 'esa', 'Thhalv10007850m.g' => 'esa', 'Thhalv10013782m.g' => 'esa', 'Thhalv10018686m.g' => 'esa', 'Thhalv10020899m.g' => 'esa', 'Thhalv10022755m.g' => 'esa', 'TPR.G23851' => 'tpr', 'TPR.G26500' => 'tpr', 'TPR.G27267' => 'tpr', 'TPR.G32001' => 'tpr', 'TPR.G6251' => 'tpr', 'TPR.G8167' => 'tpr', 'TWI12G1330' => 'twi', 'TWI18G1239' => 'twi', 'TWI34G0979' => 'twi', 'TWI36G0670' => 'twi', 'TWI36G0707' => 'twi', 'TWI56G0233' => 'twi', 'TWI75G1809' => 'twi', 'unitig_21.g20874' => 'ugi', 'unitig_26.g10343' => 'ugi', 'unitig_46.g18392' => 'ugi', 'unitig_52.g17178' => 'ugi', 'unitig_8.g2934' => 'ugi', 'vmacro01122' => 'vma', 'vmacro05875' => 'vma', 'vmacro06147' => 'vma', 'vmacro16191' => 'vma', 'vmacro18293' => 'vma', 'VMungo0251G3707' => 'vmu', 'VMungo0464G1521' => 'vmu', 'VMungo1215G0205' => 'vmu', 'VMungo1383G2484' => 'vmu', 'Zm00001eb079610' => 'zma', 'Zm00001eb135990' => 'zma', 'Zm00001eb183710' => 'zma', 'Zm00001eb246020' => 'zma' ), 'gf_id' => 'HOM05D001124', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001124' ), 'data_identifier' => 'HOM05D001124', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001124', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '548', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02520' => 'bna', 'A03p06630' => 'bna', 'A05p44460' => 'bna', 'A06p08710' => 'bna', 'A06p41090' => 'bna', 'A07p32320' => 'bna', 'A08p32520' => 'bna', 'A09p10360' => 'bna', 'A10p24080' => 'bna', 'Aa31LG11G15250' => 'aar', 'Aa31LG1G1800' => 'aar', 'Aa31LG2G5120' => 'aar', 'Aa31LG2G6070' => 'aar', 'Aa31LG5G10770' => 'aar', 'Aa31sc61G90' => 'aar', 'Actinidia01352' => 'ach', 'Actinidia05983' => 'ach', 'Actinidia08133' => 'ach', 'Actinidia15101' => 'ach', 'Actinidia26379' => 'ach', 'Actinidia35778' => 'ach', 'Actinidia36123' => 'ach', 'Actinidia37436' => 'ach', 'Actinidia38730' => 'ach', 'Ah.02g128210' => 'amhyb', 'Ah.03g132990' => 'amhyb', 'Ah.14g079410' => 'amhyb', 'AL1G24640' => 'aly', 'AL2G26680' => 'aly', 'AL3G10530' => 'aly', 'AL3G45230' => 'aly', 'AL5G15230' => 'aly', 'AL5G16960' => 'aly', 'AL6G25210' => 'aly', 'Aqoxy2G00441' => 'aox', 'Aqoxy3G01236' => 'aox', 'Aqoxy5G03746' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3RQ047' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C7GMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9C8JER' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MBL6KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YXCZ83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZANX40' => 'arhy', 'AT1G12990' => 'ath', 'AT1G67880' => 'ath', 'AT2G13290' => 'ath', 'AT3G01620' => 'ath', 'AT3G26445' => 'ath', 'AT3G27540' => 'ath', 'AT5G14480' => 'ath', 'ATR0824G026' => 'atr', 'ATR1098G019' => 'atr', 'Atru.chr11.2145' => 'acertr', 'Atru.chr2.3636' => 'acertr', 'Atru.chr2.3644' => 'acertr', 'Atru.chr6.2422' => 'acertr', 'Atru.chr7.1112' => 'acertr', 'AUR62005469' => 'cqu', 'AUR62011166' => 'cqu', 'AUR62013319' => 'cqu', 'AUR62024273' => 'cqu', 'AUR62028420' => 'cqu', 'AUR62041942' => 'cqu', 'BcaB01g04969' => 'bca', 'BcaB01g06371' => 'bca', 'BcaB02g11494' => 'bca', 'BcaB03g15382' => 'bca', 'BcaB08g36994' => 'bca', 'BcaC03g13477' => 'bca', 'BcaC03g13478' => 'bca', 'BcaC03g13480' => 'bca', 'BcaC03g13481' => 'bca', 'BcaC03g13486' => 'bca', 'BcaC04g19031' => 'bca', 'BcaC04g23085' => 'bca', 'BcaC05g25094' => 'bca', 'BcaC05g25096' => 'bca', 'BcaC05g25138' => 'bca', 'BcaC05g30416' => 'bca', 'BcaC05g30455' => 'bca', 'BcaC06g30979' => 'bca', 'BcaC06g33805' => 'bca', 'BcaC08g46021' => 'bca', 'BcaNung03154' => 'bca', 'BolC2t06623H' => 'bol', 'BolC2t06632H' => 'bol', 'BolC2t06635H' => 'bol', 'BolC2t06638H' => 'bol', 'BolC3t13266H' => 'bol', 'BolC5t29776H' => 'bol', 'BolC6t38912H' => 'bol', 'BolC7t44183H' => 'bol', 'BolC9t54123H' => 'bol', 'BolC9t59107H' => 'bol', 'BraA02t05221Z' => 'bra', 'BraA03t09996Z' => 'bra', 'BraA05t23210Z' => 'bra', 'BraA06t24068Z' => 'bra', 'BraA06t27032Z' => 'bra', 'BraA08t35176Z' => 'bra', 'BraA09t36680Z' => 'bra', 'BraA10t44471Z' => 'bra', 'C02p06760' => 'bna', 'C02p06890' => 'bna', 'C02p07010' => 'bna', 'C03p07660' => 'bna', 'C05p10300' => 'bna', 'C06p38150' => 'bna', 'C07p36650' => 'bna', 'C08p15770' => 'bna', 'C09p12300' => 'bna', 'C09p62700' => 'bna', 'C09p75040' => 'bna', 'CAN.G13.1' => 'can', 'CAN.G138.4' => 'can', 'CAN.G44.6' => 'can', 'CAN.G473.19' => 'can', 'CANSAT01G0835' => 'cansat', 'CANSAT11G0246' => 'cansat', 'CANSAT11G1766' => 'cansat', 'CANSAT64G1954' => 'cansat', 'CARHR013330' => 'chi', 'CARHR060530' => 'chi', 'CARHR075300' => 'chi', 'CARHR105120' => 'chi', 'CARHR148910' => 'chi', 'CARHR198830' => 'chi', 'Carub.0001s1275' => 'cru', 'Carub.0002s1437' => 'cru', 'Carub.0003s0044' => 'cru', 'Carub.0003s2787' => 'cru', 'Carub.0005s0597' => 'cru', 'Carub.0006s1266' => 'cru', 'Ca_06935_v3' => 'car', 'Ca_13559_v3' => 'car', 'Ca_16941_v3' => 'car', 'Ca_16960_v3' => 'car', 'Ca_17775_v3' => 'car', 'Ca_30464_v3' => 'car', 'Cc06_g08160' => 'ccan', 'Cc07_g01520' => 'ccan', 'Cc11_g15810' => 'ccan', 'CDE02G2840' => 'cde', 'CDE03G0093' => 'cde', 'CDE04G2127' => 'cde', 'CDE07G1857' => 'cde', 'CDE09G1246' => 'cde', 'Cfa003412' => 'cfa', 'Cfa007341' => 'cfa', 'Cfa009220' => 'cfa', 'Ciclev10008737m.g' => 'ccl', 'Ciclev10015565m.g' => 'ccl', 'Ciclev10031761m.g' => 'ccl', 'CiPaw.03G045300' => 'cil', 'CiPaw.03G247200' => 'cil', 'CiPaw.04G029500' => 'cil', 'CiPaw.04G174000' => 'cil', 'CiPaw.05G181200' => 'cil', 'CiPaw.06G067100' => 'cil', 'ClCG05G025800' => 'cla', 'ClCG06G011400' => 'cla', 'ClCG09G019360' => 'cla', 'COL.COLO4_04827' => 'col', 'COL.COLO4_29170' => 'col', 'COL.COLO4_35131' => 'col', 'COL.COLO4_35132' => 'col', 'Cpa.g.sc33.32' => 'cpa', 'Cpa.g.sc46.29' => 'cpa', 'Cpa.g.sc796.1' => 'cpa', 'CsaV3_1G030420' => 'csa', 'CsaV3_5G027050' => 'csa', 'CsaV3_5G031040' => 'csa', 'CsaV3_UNG023130' => 'csa', 'CSS0007726' => 'camsi', 'CSS0016433' => 'camsi', 'CSS0017656' => 'camsi', 'CSS0025364' => 'camsi', 'CSS0027582' => 'camsi', 'CSS0047288' => 'camsi', 'CSS0049950' => 'camsi', 'DCAR_003843' => 'dca', 'DCAR_007052' => 'dca', 'DCAR_020884' => 'dca', 'DCAR_021730' => 'dca', 'DCAR_024423' => 'dca', 'DCAR_026509' => 'dca', 'DCAR_031158' => 'dca', 'Dinv14728' => 'din', 'Dinv15219' => 'din', 'Dinv25728' => 'din', 'Dinv33428' => 'din', 'Dinv36489' => 'din', 'Dinv41486' => 'din', 'Duzib147G0469' => 'dzi', 'Duzib168G0060' => 'dzi', 'Duzib187G1215' => 'dzi', 'Duzib248G0692' => 'dzi', 'Duzib251G0767' => 'dzi', 'Duzib264G0446' => 'dzi', 'Duzib268G0691' => 'dzi', 'ECA232G4767' => 'eca', 'ECA233G2838' => 'eca', 'ECA234G0391' => 'eca', 'ECA234G0857' => 'eca', 'ECA236G1593' => 'eca', 'ECA238G0565' => 'eca', 'ECA246G1027' => 'eca', 'ECA246G3223' => 'eca', 'ECA246G3470' => 'eca', 'EL10Ac6g13829' => 'bvu', 'EL10Ac6g14093' => 'bvu', 'EL10Ac8g18707' => 'bvu', 'Eucgr.C01369' => 'egr', 'Eucgr.H02492' => 'egr', 'Eucgr.I01733' => 'egr', 'Eucgr.J02255' => 'egr', 'Eucgr.J02257' => 'egr', 'Eucgr.J02258' => 'egr', 'FAN02G1601' => 'fan', 'FAN03G1586' => 'fan', 'FAN03G2986' => 'fan', 'FAN05G4837' => 'fan', 'FAN06G0146' => 'fan', 'FAN07G0858' => 'fan', 'FAN09G3179' => 'fan', 'FAN10G0669' => 'fan', 'FAN12G2358' => 'fan', 'FAN14G4198' => 'fan', 'FAN14G5112' => 'fan', 'FAN17G0342' => 'fan', 'FAN19G0342' => 'fan', 'FAN19G0962' => 'fan', 'FAN19G1101' => 'fan', 'FAN19G1872' => 'fan', 'FAN22G0356' => 'fan', 'FAN23G0744' => 'fan', 'FAN23G1914' => 'fan', 'FAN26G0032' => 'fan', 'FAN28G0625' => 'fan', 'FvH4_1g02710' => 'fve', 'FvH4_1g02720' => 'fve', 'FvH4_4g25670' => 'fve', 'FvH4_6g51700' => 'fve', 'FvH4_7g20170' => 'fve', 'Glyma.05G175000' => 'gma', 'Glyma.08G132300' => 'gma', 'Glyma.11G243000' => 'gma', 'Glyma.13G158900' => 'gma', 'Glyma.17G112400' => 'gma', 'Glyma.18G014100' => 'gma', 'Glyma.19G003100' => 'gma', 'Glyma.19G056500' => 'gma', 'Gohir.A01G158900' => 'ghi', 'Gohir.A05G312600' => 'ghi', 'Gohir.A05G354900' => 'ghi', 'Gohir.A07G037200' => 'ghi', 'Gohir.A09G030000' => 'ghi', 'Gohir.A12G145200' => 'ghi', 'Gohir.D01G151500' => 'ghi', 'Gohir.D04G058300' => 'ghi', 'Gohir.D05G314100' => 'ghi', 'Gohir.D07G041400' => 'ghi', 'Gohir.D09G029700' => 'ghi', 'Gohir.D12G149700' => 'ghi', 'Gorai.001G043800' => 'gra', 'Gorai.002G187800' => 'gra', 'Gorai.006G034700' => 'gra', 'Gorai.008G161200' => 'gra', 'Gorai.009G335700' => 'gra', 'Gorai.012G065000' => 'gra', 'GSVIVG01000535001' => 'vvi', 'GSVIVG01015572001' => 'vvi', 'GSVIVG01032386001' => 'vvi', 'HanXRQChr05g0138531' => 'han', 'HanXRQChr06g0174391' => 'han', 'HanXRQChr07g0199021' => 'han', 'HanXRQChr08g0208211' => 'han', 'HanXRQChr09g0255471' => 'han', 'HanXRQChr10g0315791' => 'han', 'HanXRQChr12g0371991' => 'han', 'HanXRQChr15g0475251' => 'han', 'HanXRQChr17g0540001' => 'han', 'HanXRQChr17g0548631' => 'han', 'HanXRQChr17g0569561' => 'han', 'Haze_12256' => 'cav', 'Haze_14756' => 'cav', 'Haze_25528' => 'cav', 'Hma1.2p1_0079F.1_g041020' => 'hma', 'Hma1.2p1_0818F.1_g223260' => 'hma', 'Hma1.2p1_1747F.1_g300530' => 'hma', 'HPP92_004607' => 'vpl', 'HPP92_004608' => 'vpl', 'HPP92_006181' => 'vpl', 'HPP92_012192' => 'vpl', 'HPP92_015680' => 'vpl', 'HPP92_020249' => 'vpl', 'HPP92_021376' => 'vpl', 'HPP92_024275' => 'vpl', 'Hund06031' => 'sun', 'Hund25391' => 'sun', 'Lalb_Chr07g0185371' => 'lal', 'Lalb_Chr07g0185381' => 'lal', 'Lalb_Chr12g0204011' => 'lal', 'Lalb_Chr13g0301671' => 'lal', 'Lalb_Chr14g0362851' => 'lal', 'Lalb_Chr24g0403581' => 'lal', 'Lj1g0000233' => 'lja', 'Lj2g0018120' => 'lja', 'Lj3C621T0' => 'lonja', 'Lj3P1059T14' => 'lonja', 'Lj3P611T9' => 'lonja', 'Lj3P614T13' => 'lonja', 'Lj3P615T5' => 'lonja', 'Lj4g0012315' => 'lja', 'Lj4g0026182' => 'lja', 'Lj6P813T16' => 'lonja', 'Lj7C427T7' => 'lonja', 'Lj7C427T8' => 'lonja', 'Lj7P600T41' => 'lonja', 'Lju41C42G17' => 'lonja', 'Lsat_1_v5_gn_0_47300' => 'lsa', 'Lsat_1_v5_gn_2_91280' => 'lsa', 'Lsat_1_v5_gn_3_30561' => 'lsa', 'Lsat_1_v5_gn_4_184321' => 'lsa', 'Lsat_1_v5_gn_4_4041' => 'lsa', 'Lsat_1_v5_gn_5_92000' => 'lsa', 'Lsat_1_v5_gn_8_152940' => 'lsa', 'Lsat_1_v5_gn_8_62401' => 'lsa', 'Manes.06G055900' => 'mes', 'Manes.12G022200' => 'mes', 'Manes.13G023300' => 'mes', 'Manes.14G115000' => 'mes', 'Manes.15G151700' => 'mes', 'Manes.17G111300' => 'mes', 'Mapoly0226s0009' => 'mpo', 'MBI02_g25363_MAGBIO' => 'mbi', 'MBI06_g00027_MAGBIO' => 'mbi', 'MBI10_g13034_MAGBIO' => 'mbi', 'MD09G1023400' => 'mdo', 'MD13G1100100' => 'mdo', 'MD15G1169200' => 'mdo', 'MD16G1101100' => 'mdo', 'MD17G1022900' => 'mdo', 'Medtr3g096150' => 'mtr', 'Medtr4g115070' => 'mtr', 'Medtr7g033325' => 'mtr', 'Medtr8g089840' => 'mtr', 'MELO3C010319.2' => 'cme', 'MELO3C011944.2' => 'cme', 'MELO3C021589.2' => 'cme', 'Migut.E00207' => 'egut', 'Migut.H00067' => 'egut', 'Migut.K00433' => 'egut', 'Migut.K00606' => 'egut', 'Migut.K01410' => 'egut', 'MSTRG.13347' => 'ama', 'MSTRG.24045' => 'ama', 'MSTRG.2428' => 'ama', 'MSTRG.26410' => 'ama', 'MSTRG.3139' => 'ama', 'MSTRG.3286' => 'ama', 'MSTRG.563' => 'ama', 'MSTRG.7941' => 'ama', 'Nitab4.5_0000028g0060' => 'nta', 'Nitab4.5_0000065g0260' => 'nta', 'Nitab4.5_0000112g0060' => 'nta', 'Nitab4.5_0000489g0120' => 'nta', 'Nitab4.5_0001776g0050' => 'nta', 'Nitab4.5_0001854g0010' => 'nta', 'Nitab4.5_0001860g0020' => 'nta', 'Nitab4.5_0004352g0010' => 'nta', 'Nitab4.5_0008716g0020' => 'nta', 'Nitab4.5_0008922g0010' => 'nta', 'Nn3g16693' => 'nnu', 'Nn4g22596' => 'nnu', 'Nn7g37639' => 'nnu', 'Oeu001701.1' => 'oeu', 'Oeu018149.1' => 'oeu', 'Oeu026220.1' => 'oeu', 'Oeu038635.1' => 'oeu', 'Oeu049176.1' => 'oeu', 'Oeu056706.1' => 'oeu', 'Oeu056937.1' => 'oeu', 'Oeu057540.1' => 'oeu', 'Os02g0594900' => 'osa', 'Os02g0595100' => 'osa', 'Os04g0477500' => 'osa', 'Os12g0611900' => 'osa', 'Peaxi162Scf00076g00020' => 'pax', 'Peaxi162Scf00128g00217' => 'pax', 'Peaxi162Scf00129g01640' => 'pax', 'Peaxi162Scf00669g00007' => 'pax', 'Peaxi162Scf00700g00421' => 'pax', 'Peaxi162Scf00801g00038' => 'pax', 'Peaxi162Scf00891g00025' => 'pax', 'PGR083G0909' => 'pgr', 'PGR119G1005' => 'pgr', 'PGR142G2236' => 'pgr', 'PGR142G3388' => 'pgr', 'PGSC0003DMG400004514' => 'stu', 'PGSC0003DMG400012635' => 'stu', 'PGSC0003DMG400015730' => 'stu', 'PGSC0003DMG400018611' => 'stu', 'PGSC0003DMG400030897' => 'stu', 'Phvul.001G254800' => 'pvu', 'Phvul.002G260100' => 'pvu', 'Phvul.003G167600' => 'pvu', 'Phvul.004G005100' => 'pvu', 'Potri.001G343600' => 'ptr', 'Potri.006G066700' => 'ptr', 'Potri.008G186000' => 'ptr', 'Potri.010G046900' => 'ptr', 'Potri.018G127900' => 'ptr', 'Pp3c20_17750' => 'ppa', 'Pp3c24_4380' => 'ppa', 'Prupe.1G245800' => 'ppe', 'Prupe.3G293400' => 'ppe', 'Prupe.7G247400' => 'ppe', 'Psat0s145g0120' => 'psa', 'Psat0s595g0040' => 'psa', 'Psat0s595g0120' => 'psa', 'Psat3g175040' => 'psa', 'Psat7g058120' => 'psa', 'PSO017G0428' => 'pso', 'PSO063G7510' => 'pso', 'PSO067G0046' => 'pso', 'PSO478G1073' => 'pso', 'PSO675G3677' => 'pso', 'PSO675G6558' => 'pso', 'PSO675G7520' => 'pso', 'PSO675G8959' => 'pso', 'QL02p074089' => 'qlo', 'QL02p089614' => 'qlo', 'QL03p057736' => 'qlo', 'RcHm_v2.0_Chr1g0364131' => 'rch', 'RcHm_v2.0_Chr2g0087801' => 'rch', 'RcHm_v2.0_Chr2g0087821' => 'rch', 'RcHm_v2.0_Chr2g0173231' => 'rch', 'RcHm_v2.0_Chr4g0433111' => 'rch', 'Rhsim03G0250300' => 'rsi', 'Rhsim08G0048400' => 'rsi', 'Rhsim10G0014800' => 'rsi', 'Rhsim12G0040100' => 'rsi', 'Rhsim12G0109700' => 'rsi', 'Sabra06G0049600' => 'sbr', 'Sabra08G0141000' => 'sbr', 'Sabra10G0021400' => 'sbr', 'Sabra16G0222900' => 'sbr', 'Sabra18G0108600' => 'sbr', 'SalBow1G0433' => 'sbo', 'SalBow1G2038' => 'sbo', 'SalBow1G5003' => 'sbo', 'SalBow7G1197' => 'sbo', 'SalBow8G3506' => 'sbo', 'Sc03g0007300' => 'sci', 'Sc11g0000950' => 'sci', 'Sc14g0008750' => 'sci', 'Sc18g0000420' => 'sci', 'Sed0006754' => 'sed', 'Sed0008741' => 'sed', 'Sed0017172' => 'sed', 'Sed0018925' => 'sed', 'Sed0023326' => 'sed', 'Sed0025909' => 'sed', 'SEGI_05333' => 'sgi', 'SEGI_10362' => 'sgi', 'SEGI_13380' => 'sgi', 'SEGI_24306' => 'sgi', 'SEGI_29077' => 'sgi', 'SEGI_29095' => 'sgi', 'SEGI_36534' => 'sgi', 'SEGI_37506' => 'sgi', 'SEGI_38321' => 'sgi', 'SGA_v2.0_scaffold307G48031' => 'sas', 'SGA_v2.0_scaffold47G17507' => 'sas', 'SGA_v2.0_scaffold63G21736' => 'sas', 'SGA_v2.0_scaffold87G27070' => 'sas', 'SHI17794' => 'shi', 'SHI28851' => 'shi', 'SMO165G0155' => 'smo', 'SMO340G0217' => 'smo', 'SMO367G1210' => 'smo', 'Solyc02g093430.3' => 'sly', 'Solyc05g013580.4' => 'sly', 'Solyc07g008030.3' => 'sly', 'Solyc12g035470.2' => 'sly', 'Sopen02g038020' => 'spe', 'Sopen05g008490' => 'spe', 'Sopen07g003910' => 'spe', 'Sopen12g015240' => 'spe', 'Sp1g11550' => 'spa', 'Sp2g16710' => 'spa', 'Sp3g00430' => 'spa', 'Sp3g26780' => 'spa', 'Sp5g22900' => 'spa', 'Sp6g29530' => 'spa', 'TAR371G0794' => 'tar', 'TAR374G0164' => 'tar', 'TAR622G0165' => 'tar', 'TAR626G0929' => 'tar', 'TAR629G2155' => 'tar', 'THA.LOC104805282' => 'tha', 'THA.LOC104805363' => 'tha', 'THA.LOC104808968' => 'tha', 'THA.LOC104821093' => 'tha', 'THA.LOC104823953' => 'tha', 'THA.LOC104825562' => 'tha', 'THA.LOC104825665' => 'tha', 'Thecc.02G261400' => 'tca', 'Thecc.04G019200' => 'tca', 'Thecc.09G130400' => 'tca', 'Thhalv10004374m.g' => 'esa', 'Thhalv10007850m.g' => 'esa', 'Thhalv10013782m.g' => 'esa', 'Thhalv10018686m.g' => 'esa', 'Thhalv10020899m.g' => 'esa', 'Thhalv10022755m.g' => 'esa', 'TPR.G23851' => 'tpr', 'TPR.G26500' => 'tpr', 'TPR.G27267' => 'tpr', 'TPR.G32001' => 'tpr', 'TPR.G6251' => 'tpr', 'TPR.G8167' => 'tpr', 'TWI12G1330' => 'twi', 'TWI18G1239' => 'twi', 'TWI34G0979' => 'twi', 'TWI36G0670' => 'twi', 'TWI36G0707' => 'twi', 'TWI56G0233' => 'twi', 'TWI75G1809' => 'twi', 'unitig_21.g20874' => 'ugi', 'unitig_26.g10343' => 'ugi', 'unitig_46.g18392' => 'ugi', 'unitig_52.g17178' => 'ugi', 'unitig_8.g2934' => 'ugi', 'vmacro01122' => 'vma', 'vmacro05875' => 'vma', 'vmacro06147' => 'vma', 'vmacro16191' => 'vma', 'vmacro18293' => 'vma', 'VMungo0251G3707' => 'vmu', 'VMungo0464G1521' => 'vmu', 'VMungo1215G0205' => 'vmu', 'VMungo1383G2484' => 'vmu', 'Zm00001eb079610' => 'zma', 'Zm00001eb135990' => 'zma', 'Zm00001eb183710' => 'zma', 'Zm00001eb246020' => 'zma' ) $gf_id = 'HOM05D001124' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001124' ) $data_identifier = 'HOM05D001124' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 6, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 7, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 21, 'bol' => (int) 10, 'bra' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 6, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 9, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 21, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 8, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 10, 'lsa' => (int) 8, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 8, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 9, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb246020' $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' => 'HOM05D001124', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '548', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02520' => 'bna', 'A03p06630' => 'bna', 'A05p44460' => 'bna', 'A06p08710' => 'bna', 'A06p41090' => 'bna', 'A07p32320' => 'bna', 'A08p32520' => 'bna', 'A09p10360' => 'bna', 'A10p24080' => 'bna', 'Aa31LG11G15250' => 'aar', 'Aa31LG1G1800' => 'aar', 'Aa31LG2G5120' => 'aar', 'Aa31LG2G6070' => 'aar', 'Aa31LG5G10770' => 'aar', 'Aa31sc61G90' => 'aar', 'Actinidia01352' => 'ach', 'Actinidia05983' => 'ach', 'Actinidia08133' => 'ach', 'Actinidia15101' => 'ach', 'Actinidia26379' => 'ach', 'Actinidia35778' => 'ach', 'Actinidia36123' => 'ach', 'Actinidia37436' => 'ach', 'Actinidia38730' => 'ach', 'Ah.02g128210' => 'amhyb', 'Ah.03g132990' => 'amhyb', 'Ah.14g079410' => 'amhyb', 'AL1G24640' => 'aly', 'AL2G26680' => 'aly', 'AL3G10530' => 'aly', 'AL3G45230' => 'aly', 'AL5G15230' => 'aly', 'AL5G16960' => 'aly', 'AL6G25210' => 'aly', 'Aqoxy2G00441' => 'aox', 'Aqoxy3G01236' => 'aox', 'Aqoxy5G03746' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3RQ047' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C7GMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9C8JER' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MBL6KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YXCZ83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZANX40' => 'arhy', 'AT1G12990' => 'ath', 'AT1G67880' => 'ath', 'AT2G13290' => 'ath', 'AT3G01620' => 'ath', 'AT3G26445' => 'ath', 'AT3G27540' => 'ath', 'AT5G14480' => 'ath', 'ATR0824G026' => 'atr', 'ATR1098G019' => 'atr', 'Atru.chr11.2145' => 'acertr', 'Atru.chr2.3636' => 'acertr', 'Atru.chr2.3644' => 'acertr', 'Atru.chr6.2422' => 'acertr', 'Atru.chr7.1112' => 'acertr', 'AUR62005469' => 'cqu', 'AUR62011166' => 'cqu', 'AUR62013319' => 'cqu', 'AUR62024273' => 'cqu', 'AUR62028420' => 'cqu', 'AUR62041942' => 'cqu', 'BcaB01g04969' => 'bca', 'BcaB01g06371' => 'bca', 'BcaB02g11494' => 'bca', 'BcaB03g15382' => 'bca', 'BcaB08g36994' => 'bca', 'BcaC03g13477' => 'bca', 'BcaC03g13478' => 'bca', 'BcaC03g13480' => 'bca', 'BcaC03g13481' => 'bca', 'BcaC03g13486' => 'bca', 'BcaC04g19031' => 'bca', 'BcaC04g23085' => 'bca', 'BcaC05g25094' => 'bca', 'BcaC05g25096' => 'bca', 'BcaC05g25138' => 'bca', 'BcaC05g30416' => 'bca', 'BcaC05g30455' => 'bca', 'BcaC06g30979' => 'bca', 'BcaC06g33805' => 'bca', 'BcaC08g46021' => 'bca', 'BcaNung03154' => 'bca', 'BolC2t06623H' => 'bol', 'BolC2t06632H' => 'bol', 'BolC2t06635H' => 'bol', 'BolC2t06638H' => 'bol', 'BolC3t13266H' => 'bol', 'BolC5t29776H' => 'bol', 'BolC6t38912H' => 'bol', 'BolC7t44183H' => 'bol', 'BolC9t54123H' => 'bol', 'BolC9t59107H' => 'bol', 'BraA02t05221Z' => 'bra', 'BraA03t09996Z' => 'bra', 'BraA05t23210Z' => 'bra', 'BraA06t24068Z' => 'bra', 'BraA06t27032Z' => 'bra', 'BraA08t35176Z' => 'bra', 'BraA09t36680Z' => 'bra', 'BraA10t44471Z' => 'bra', 'C02p06760' => 'bna', 'C02p06890' => 'bna', 'C02p07010' => 'bna', 'C03p07660' => 'bna', 'C05p10300' => 'bna', 'C06p38150' => 'bna', 'C07p36650' => 'bna', 'C08p15770' => 'bna', 'C09p12300' => 'bna', 'C09p62700' => 'bna', 'C09p75040' => 'bna', 'CAN.G13.1' => 'can', 'CAN.G138.4' => 'can', 'CAN.G44.6' => 'can', 'CAN.G473.19' => 'can', 'CANSAT01G0835' => 'cansat', 'CANSAT11G0246' => 'cansat', 'CANSAT11G1766' => 'cansat', 'CANSAT64G1954' => 'cansat', 'CARHR013330' => 'chi', 'CARHR060530' => 'chi', 'CARHR075300' => 'chi', 'CARHR105120' => 'chi', 'CARHR148910' => 'chi', 'CARHR198830' => 'chi', 'Carub.0001s1275' => 'cru', 'Carub.0002s1437' => 'cru', 'Carub.0003s0044' => 'cru', 'Carub.0003s2787' => 'cru', 'Carub.0005s0597' => 'cru', 'Carub.0006s1266' => 'cru', 'Ca_06935_v3' => 'car', 'Ca_13559_v3' => 'car', 'Ca_16941_v3' => 'car', 'Ca_16960_v3' => 'car', 'Ca_17775_v3' => 'car', 'Ca_30464_v3' => 'car', 'Cc06_g08160' => 'ccan', 'Cc07_g01520' => 'ccan', 'Cc11_g15810' => 'ccan', 'CDE02G2840' => 'cde', 'CDE03G0093' => 'cde', 'CDE04G2127' => 'cde', 'CDE07G1857' => 'cde', 'CDE09G1246' => 'cde', 'Cfa003412' => 'cfa', 'Cfa007341' => 'cfa', 'Cfa009220' => 'cfa', 'Ciclev10008737m.g' => 'ccl', 'Ciclev10015565m.g' => 'ccl', 'Ciclev10031761m.g' => 'ccl', 'CiPaw.03G045300' => 'cil', 'CiPaw.03G247200' => 'cil', 'CiPaw.04G029500' => 'cil', 'CiPaw.04G174000' => 'cil', 'CiPaw.05G181200' => 'cil', 'CiPaw.06G067100' => 'cil', 'ClCG05G025800' => 'cla', 'ClCG06G011400' => 'cla', 'ClCG09G019360' => 'cla', 'COL.COLO4_04827' => 'col', 'COL.COLO4_29170' => 'col', 'COL.COLO4_35131' => 'col', 'COL.COLO4_35132' => 'col', 'Cpa.g.sc33.32' => 'cpa', 'Cpa.g.sc46.29' => 'cpa', 'Cpa.g.sc796.1' => 'cpa', 'CsaV3_1G030420' => 'csa', 'CsaV3_5G027050' => 'csa', 'CsaV3_5G031040' => 'csa', 'CsaV3_UNG023130' => 'csa', 'CSS0007726' => 'camsi', 'CSS0016433' => 'camsi', 'CSS0017656' => 'camsi', 'CSS0025364' => 'camsi', 'CSS0027582' => 'camsi', 'CSS0047288' => 'camsi', 'CSS0049950' => 'camsi', 'DCAR_003843' => 'dca', 'DCAR_007052' => 'dca', 'DCAR_020884' => 'dca', 'DCAR_021730' => 'dca', 'DCAR_024423' => 'dca', 'DCAR_026509' => 'dca', 'DCAR_031158' => 'dca', 'Dinv14728' => 'din', 'Dinv15219' => 'din', 'Dinv25728' => 'din', 'Dinv33428' => 'din', 'Dinv36489' => 'din', 'Dinv41486' => 'din', 'Duzib147G0469' => 'dzi', 'Duzib168G0060' => 'dzi', 'Duzib187G1215' => 'dzi', 'Duzib248G0692' => 'dzi', 'Duzib251G0767' => 'dzi', 'Duzib264G0446' => 'dzi', 'Duzib268G0691' => 'dzi', 'ECA232G4767' => 'eca', 'ECA233G2838' => 'eca', 'ECA234G0391' => 'eca', 'ECA234G0857' => 'eca', 'ECA236G1593' => 'eca', 'ECA238G0565' => 'eca', 'ECA246G1027' => 'eca', 'ECA246G3223' => 'eca', 'ECA246G3470' => 'eca', 'EL10Ac6g13829' => 'bvu', 'EL10Ac6g14093' => 'bvu', 'EL10Ac8g18707' => 'bvu', 'Eucgr.C01369' => 'egr', 'Eucgr.H02492' => 'egr', 'Eucgr.I01733' => 'egr', 'Eucgr.J02255' => 'egr', 'Eucgr.J02257' => 'egr', 'Eucgr.J02258' => 'egr', 'FAN02G1601' => 'fan', 'FAN03G1586' => 'fan', 'FAN03G2986' => 'fan', 'FAN05G4837' => 'fan', 'FAN06G0146' => 'fan', 'FAN07G0858' => 'fan', 'FAN09G3179' => 'fan', 'FAN10G0669' => 'fan', 'FAN12G2358' => 'fan', 'FAN14G4198' => 'fan', 'FAN14G5112' => 'fan', 'FAN17G0342' => 'fan', 'FAN19G0342' => 'fan', 'FAN19G0962' => 'fan', 'FAN19G1101' => 'fan', 'FAN19G1872' => 'fan', 'FAN22G0356' => 'fan', 'FAN23G0744' => 'fan', 'FAN23G1914' => 'fan', 'FAN26G0032' => 'fan', 'FAN28G0625' => 'fan', 'FvH4_1g02710' => 'fve', 'FvH4_1g02720' => 'fve', 'FvH4_4g25670' => 'fve', 'FvH4_6g51700' => 'fve', 'FvH4_7g20170' => 'fve', 'Glyma.05G175000' => 'gma', 'Glyma.08G132300' => 'gma', 'Glyma.11G243000' => 'gma', 'Glyma.13G158900' => 'gma', 'Glyma.17G112400' => 'gma', 'Glyma.18G014100' => 'gma', 'Glyma.19G003100' => 'gma', 'Glyma.19G056500' => 'gma', 'Gohir.A01G158900' => 'ghi', 'Gohir.A05G312600' => 'ghi', 'Gohir.A05G354900' => 'ghi', 'Gohir.A07G037200' => 'ghi', 'Gohir.A09G030000' => 'ghi', 'Gohir.A12G145200' => 'ghi', 'Gohir.D01G151500' => 'ghi', 'Gohir.D04G058300' => 'ghi', 'Gohir.D05G314100' => 'ghi', 'Gohir.D07G041400' => 'ghi', 'Gohir.D09G029700' => 'ghi', 'Gohir.D12G149700' => 'ghi', 'Gorai.001G043800' => 'gra', 'Gorai.002G187800' => 'gra', 'Gorai.006G034700' => 'gra', 'Gorai.008G161200' => 'gra', 'Gorai.009G335700' => 'gra', 'Gorai.012G065000' => 'gra', 'GSVIVG01000535001' => 'vvi', 'GSVIVG01015572001' => 'vvi', 'GSVIVG01032386001' => 'vvi', 'HanXRQChr05g0138531' => 'han', 'HanXRQChr06g0174391' => 'han', 'HanXRQChr07g0199021' => 'han', 'HanXRQChr08g0208211' => 'han', 'HanXRQChr09g0255471' => 'han', 'HanXRQChr10g0315791' => 'han', 'HanXRQChr12g0371991' => 'han', 'HanXRQChr15g0475251' => 'han', 'HanXRQChr17g0540001' => 'han', 'HanXRQChr17g0548631' => 'han', 'HanXRQChr17g0569561' => 'han', 'Haze_12256' => 'cav', 'Haze_14756' => 'cav', 'Haze_25528' => 'cav', 'Hma1.2p1_0079F.1_g041020' => 'hma', 'Hma1.2p1_0818F.1_g223260' => 'hma', 'Hma1.2p1_1747F.1_g300530' => 'hma', 'HPP92_004607' => 'vpl', 'HPP92_004608' => 'vpl', 'HPP92_006181' => 'vpl', 'HPP92_012192' => 'vpl', 'HPP92_015680' => 'vpl', 'HPP92_020249' => 'vpl', 'HPP92_021376' => 'vpl', 'HPP92_024275' => 'vpl', 'Hund06031' => 'sun', 'Hund25391' => 'sun', 'Lalb_Chr07g0185371' => 'lal', 'Lalb_Chr07g0185381' => 'lal', 'Lalb_Chr12g0204011' => 'lal', 'Lalb_Chr13g0301671' => 'lal', 'Lalb_Chr14g0362851' => 'lal', 'Lalb_Chr24g0403581' => 'lal', 'Lj1g0000233' => 'lja', 'Lj2g0018120' => 'lja', 'Lj3C621T0' => 'lonja', 'Lj3P1059T14' => 'lonja', 'Lj3P611T9' => 'lonja', 'Lj3P614T13' => 'lonja', 'Lj3P615T5' => 'lonja', 'Lj4g0012315' => 'lja', 'Lj4g0026182' => 'lja', 'Lj6P813T16' => 'lonja', 'Lj7C427T7' => 'lonja', 'Lj7C427T8' => 'lonja', 'Lj7P600T41' => 'lonja', 'Lju41C42G17' => 'lonja', 'Lsat_1_v5_gn_0_47300' => 'lsa', 'Lsat_1_v5_gn_2_91280' => 'lsa', 'Lsat_1_v5_gn_3_30561' => 'lsa', 'Lsat_1_v5_gn_4_184321' => 'lsa', 'Lsat_1_v5_gn_4_4041' => 'lsa', 'Lsat_1_v5_gn_5_92000' => 'lsa', 'Lsat_1_v5_gn_8_152940' => 'lsa', 'Lsat_1_v5_gn_8_62401' => 'lsa', 'Manes.06G055900' => 'mes', 'Manes.12G022200' => 'mes', 'Manes.13G023300' => 'mes', 'Manes.14G115000' => 'mes', 'Manes.15G151700' => 'mes', 'Manes.17G111300' => 'mes', 'Mapoly0226s0009' => 'mpo', 'MBI02_g25363_MAGBIO' => 'mbi', 'MBI06_g00027_MAGBIO' => 'mbi', 'MBI10_g13034_MAGBIO' => 'mbi', 'MD09G1023400' => 'mdo', 'MD13G1100100' => 'mdo', 'MD15G1169200' => 'mdo', 'MD16G1101100' => 'mdo', 'MD17G1022900' => 'mdo', 'Medtr3g096150' => 'mtr', 'Medtr4g115070' => 'mtr', 'Medtr7g033325' => 'mtr', 'Medtr8g089840' => 'mtr', 'MELO3C010319.2' => 'cme', 'MELO3C011944.2' => 'cme', 'MELO3C021589.2' => 'cme', 'Migut.E00207' => 'egut', 'Migut.H00067' => 'egut', 'Migut.K00433' => 'egut', 'Migut.K00606' => 'egut', 'Migut.K01410' => 'egut', 'MSTRG.13347' => 'ama', 'MSTRG.24045' => 'ama', 'MSTRG.2428' => 'ama', 'MSTRG.26410' => 'ama', 'MSTRG.3139' => 'ama', 'MSTRG.3286' => 'ama', 'MSTRG.563' => 'ama', 'MSTRG.7941' => 'ama', 'Nitab4.5_0000028g0060' => 'nta', 'Nitab4.5_0000065g0260' => 'nta', 'Nitab4.5_0000112g0060' => 'nta', 'Nitab4.5_0000489g0120' => 'nta', 'Nitab4.5_0001776g0050' => 'nta', 'Nitab4.5_0001854g0010' => 'nta', 'Nitab4.5_0001860g0020' => 'nta', 'Nitab4.5_0004352g0010' => 'nta', 'Nitab4.5_0008716g0020' => 'nta', 'Nitab4.5_0008922g0010' => 'nta', 'Nn3g16693' => 'nnu', 'Nn4g22596' => 'nnu', 'Nn7g37639' => 'nnu', 'Oeu001701.1' => 'oeu', 'Oeu018149.1' => 'oeu', 'Oeu026220.1' => 'oeu', 'Oeu038635.1' => 'oeu', 'Oeu049176.1' => 'oeu', 'Oeu056706.1' => 'oeu', 'Oeu056937.1' => 'oeu', 'Oeu057540.1' => 'oeu', 'Os02g0594900' => 'osa', 'Os02g0595100' => 'osa', 'Os04g0477500' => 'osa', 'Os12g0611900' => 'osa', 'Peaxi162Scf00076g00020' => 'pax', 'Peaxi162Scf00128g00217' => 'pax', 'Peaxi162Scf00129g01640' => 'pax', 'Peaxi162Scf00669g00007' => 'pax', 'Peaxi162Scf00700g00421' => 'pax', 'Peaxi162Scf00801g00038' => 'pax', 'Peaxi162Scf00891g00025' => 'pax', 'PGR083G0909' => 'pgr', 'PGR119G1005' => 'pgr', 'PGR142G2236' => 'pgr', 'PGR142G3388' => 'pgr', 'PGSC0003DMG400004514' => 'stu', 'PGSC0003DMG400012635' => 'stu', 'PGSC0003DMG400015730' => 'stu', 'PGSC0003DMG400018611' => 'stu', 'PGSC0003DMG400030897' => 'stu', 'Phvul.001G254800' => 'pvu', 'Phvul.002G260100' => 'pvu', 'Phvul.003G167600' => 'pvu', 'Phvul.004G005100' => 'pvu', 'Potri.001G343600' => 'ptr', 'Potri.006G066700' => 'ptr', 'Potri.008G186000' => 'ptr', 'Potri.010G046900' => 'ptr', 'Potri.018G127900' => 'ptr', 'Pp3c20_17750' => 'ppa', 'Pp3c24_4380' => 'ppa', 'Prupe.1G245800' => 'ppe', 'Prupe.3G293400' => 'ppe', 'Prupe.7G247400' => 'ppe', 'Psat0s145g0120' => 'psa', 'Psat0s595g0040' => 'psa', 'Psat0s595g0120' => 'psa', 'Psat3g175040' => 'psa', 'Psat7g058120' => 'psa', 'PSO017G0428' => 'pso', 'PSO063G7510' => 'pso', 'PSO067G0046' => 'pso', 'PSO478G1073' => 'pso', 'PSO675G3677' => 'pso', 'PSO675G6558' => 'pso', 'PSO675G7520' => 'pso', 'PSO675G8959' => 'pso', 'QL02p074089' => 'qlo', 'QL02p089614' => 'qlo', 'QL03p057736' => 'qlo', 'RcHm_v2.0_Chr1g0364131' => 'rch', 'RcHm_v2.0_Chr2g0087801' => 'rch', 'RcHm_v2.0_Chr2g0087821' => 'rch', 'RcHm_v2.0_Chr2g0173231' => 'rch', 'RcHm_v2.0_Chr4g0433111' => 'rch', 'Rhsim03G0250300' => 'rsi', 'Rhsim08G0048400' => 'rsi', 'Rhsim10G0014800' => 'rsi', 'Rhsim12G0040100' => 'rsi', 'Rhsim12G0109700' => 'rsi', 'Sabra06G0049600' => 'sbr', 'Sabra08G0141000' => 'sbr', 'Sabra10G0021400' => 'sbr', 'Sabra16G0222900' => 'sbr', 'Sabra18G0108600' => 'sbr', 'SalBow1G0433' => 'sbo', 'SalBow1G2038' => 'sbo', 'SalBow1G5003' => 'sbo', 'SalBow7G1197' => 'sbo', 'SalBow8G3506' => 'sbo', 'Sc03g0007300' => 'sci', 'Sc11g0000950' => 'sci', 'Sc14g0008750' => 'sci', 'Sc18g0000420' => 'sci', 'Sed0006754' => 'sed', 'Sed0008741' => 'sed', 'Sed0017172' => 'sed', 'Sed0018925' => 'sed', 'Sed0023326' => 'sed', 'Sed0025909' => 'sed', 'SEGI_05333' => 'sgi', 'SEGI_10362' => 'sgi', 'SEGI_13380' => 'sgi', 'SEGI_24306' => 'sgi', 'SEGI_29077' => 'sgi', 'SEGI_29095' => 'sgi', 'SEGI_36534' => 'sgi', 'SEGI_37506' => 'sgi', 'SEGI_38321' => 'sgi', 'SGA_v2.0_scaffold307G48031' => 'sas', 'SGA_v2.0_scaffold47G17507' => 'sas', 'SGA_v2.0_scaffold63G21736' => 'sas', 'SGA_v2.0_scaffold87G27070' => 'sas', 'SHI17794' => 'shi', 'SHI28851' => 'shi', 'SMO165G0155' => 'smo', 'SMO340G0217' => 'smo', 'SMO367G1210' => 'smo', 'Solyc02g093430.3' => 'sly', 'Solyc05g013580.4' => 'sly', 'Solyc07g008030.3' => 'sly', 'Solyc12g035470.2' => 'sly', 'Sopen02g038020' => 'spe', 'Sopen05g008490' => 'spe', 'Sopen07g003910' => 'spe', 'Sopen12g015240' => 'spe', 'Sp1g11550' => 'spa', 'Sp2g16710' => 'spa', 'Sp3g00430' => 'spa', 'Sp3g26780' => 'spa', 'Sp5g22900' => 'spa', 'Sp6g29530' => 'spa', 'TAR371G0794' => 'tar', 'TAR374G0164' => 'tar', 'TAR622G0165' => 'tar', 'TAR626G0929' => 'tar', 'TAR629G2155' => 'tar', 'THA.LOC104805282' => 'tha', 'THA.LOC104805363' => 'tha', 'THA.LOC104808968' => 'tha', 'THA.LOC104821093' => 'tha', 'THA.LOC104823953' => 'tha', 'THA.LOC104825562' => 'tha', 'THA.LOC104825665' => 'tha', 'Thecc.02G261400' => 'tca', 'Thecc.04G019200' => 'tca', 'Thecc.09G130400' => 'tca', 'Thhalv10004374m.g' => 'esa', 'Thhalv10007850m.g' => 'esa', 'Thhalv10013782m.g' => 'esa', 'Thhalv10018686m.g' => 'esa', 'Thhalv10020899m.g' => 'esa', 'Thhalv10022755m.g' => 'esa', 'TPR.G23851' => 'tpr', 'TPR.G26500' => 'tpr', 'TPR.G27267' => 'tpr', 'TPR.G32001' => 'tpr', 'TPR.G6251' => 'tpr', 'TPR.G8167' => 'tpr', 'TWI12G1330' => 'twi', 'TWI18G1239' => 'twi', 'TWI34G0979' => 'twi', 'TWI36G0670' => 'twi', 'TWI36G0707' => 'twi', 'TWI56G0233' => 'twi', 'TWI75G1809' => 'twi', 'unitig_21.g20874' => 'ugi', 'unitig_26.g10343' => 'ugi', 'unitig_46.g18392' => 'ugi', 'unitig_52.g17178' => 'ugi', 'unitig_8.g2934' => 'ugi', 'vmacro01122' => 'vma', 'vmacro05875' => 'vma', 'vmacro06147' => 'vma', 'vmacro16191' => 'vma', 'vmacro18293' => 'vma', 'VMungo0251G3707' => 'vmu', 'VMungo0464G1521' => 'vmu', 'VMungo1215G0205' => 'vmu', 'VMungo1383G2484' => 'vmu', 'Zm00001eb079610' => 'zma', 'Zm00001eb135990' => 'zma', 'Zm00001eb183710' => 'zma', 'Zm00001eb246020' => 'zma' ), 'gf_id' => 'HOM05D001124', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001124' ), 'data_identifier' => 'HOM05D001124', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001124', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '548', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02520' => 'bna', 'A03p06630' => 'bna', 'A05p44460' => 'bna', 'A06p08710' => 'bna', 'A06p41090' => 'bna', 'A07p32320' => 'bna', 'A08p32520' => 'bna', 'A09p10360' => 'bna', 'A10p24080' => 'bna', 'Aa31LG11G15250' => 'aar', 'Aa31LG1G1800' => 'aar', 'Aa31LG2G5120' => 'aar', 'Aa31LG2G6070' => 'aar', 'Aa31LG5G10770' => 'aar', 'Aa31sc61G90' => 'aar', 'Actinidia01352' => 'ach', 'Actinidia05983' => 'ach', 'Actinidia08133' => 'ach', 'Actinidia15101' => 'ach', 'Actinidia26379' => 'ach', 'Actinidia35778' => 'ach', 'Actinidia36123' => 'ach', 'Actinidia37436' => 'ach', 'Actinidia38730' => 'ach', 'Ah.02g128210' => 'amhyb', 'Ah.03g132990' => 'amhyb', 'Ah.14g079410' => 'amhyb', 'AL1G24640' => 'aly', 'AL2G26680' => 'aly', 'AL3G10530' => 'aly', 'AL3G45230' => 'aly', 'AL5G15230' => 'aly', 'AL5G16960' => 'aly', 'AL6G25210' => 'aly', 'Aqoxy2G00441' => 'aox', 'Aqoxy3G01236' => 'aox', 'Aqoxy5G03746' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3RQ047' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C7GMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9C8JER' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MBL6KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YXCZ83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZANX40' => 'arhy', 'AT1G12990' => 'ath', 'AT1G67880' => 'ath', 'AT2G13290' => 'ath', 'AT3G01620' => 'ath', 'AT3G26445' => 'ath', 'AT3G27540' => 'ath', 'AT5G14480' => 'ath', 'ATR0824G026' => 'atr', 'ATR1098G019' => 'atr', 'Atru.chr11.2145' => 'acertr', 'Atru.chr2.3636' => 'acertr', 'Atru.chr2.3644' => 'acertr', 'Atru.chr6.2422' => 'acertr', 'Atru.chr7.1112' => 'acertr', 'AUR62005469' => 'cqu', 'AUR62011166' => 'cqu', 'AUR62013319' => 'cqu', 'AUR62024273' => 'cqu', 'AUR62028420' => 'cqu', 'AUR62041942' => 'cqu', 'BcaB01g04969' => 'bca', 'BcaB01g06371' => 'bca', 'BcaB02g11494' => 'bca', 'BcaB03g15382' => 'bca', 'BcaB08g36994' => 'bca', 'BcaC03g13477' => 'bca', 'BcaC03g13478' => 'bca', 'BcaC03g13480' => 'bca', 'BcaC03g13481' => 'bca', 'BcaC03g13486' => 'bca', 'BcaC04g19031' => 'bca', 'BcaC04g23085' => 'bca', 'BcaC05g25094' => 'bca', 'BcaC05g25096' => 'bca', 'BcaC05g25138' => 'bca', 'BcaC05g30416' => 'bca', 'BcaC05g30455' => 'bca', 'BcaC06g30979' => 'bca', 'BcaC06g33805' => 'bca', 'BcaC08g46021' => 'bca', 'BcaNung03154' => 'bca', 'BolC2t06623H' => 'bol', 'BolC2t06632H' => 'bol', 'BolC2t06635H' => 'bol', 'BolC2t06638H' => 'bol', 'BolC3t13266H' => 'bol', 'BolC5t29776H' => 'bol', 'BolC6t38912H' => 'bol', 'BolC7t44183H' => 'bol', 'BolC9t54123H' => 'bol', 'BolC9t59107H' => 'bol', 'BraA02t05221Z' => 'bra', 'BraA03t09996Z' => 'bra', 'BraA05t23210Z' => 'bra', 'BraA06t24068Z' => 'bra', 'BraA06t27032Z' => 'bra', 'BraA08t35176Z' => 'bra', 'BraA09t36680Z' => 'bra', 'BraA10t44471Z' => 'bra', 'C02p06760' => 'bna', 'C02p06890' => 'bna', 'C02p07010' => 'bna', 'C03p07660' => 'bna', 'C05p10300' => 'bna', 'C06p38150' => 'bna', 'C07p36650' => 'bna', 'C08p15770' => 'bna', 'C09p12300' => 'bna', 'C09p62700' => 'bna', 'C09p75040' => 'bna', 'CAN.G13.1' => 'can', 'CAN.G138.4' => 'can', 'CAN.G44.6' => 'can', 'CAN.G473.19' => 'can', 'CANSAT01G0835' => 'cansat', 'CANSAT11G0246' => 'cansat', 'CANSAT11G1766' => 'cansat', 'CANSAT64G1954' => 'cansat', 'CARHR013330' => 'chi', 'CARHR060530' => 'chi', 'CARHR075300' => 'chi', 'CARHR105120' => 'chi', 'CARHR148910' => 'chi', 'CARHR198830' => 'chi', 'Carub.0001s1275' => 'cru', 'Carub.0002s1437' => 'cru', 'Carub.0003s0044' => 'cru', 'Carub.0003s2787' => 'cru', 'Carub.0005s0597' => 'cru', 'Carub.0006s1266' => 'cru', 'Ca_06935_v3' => 'car', 'Ca_13559_v3' => 'car', 'Ca_16941_v3' => 'car', 'Ca_16960_v3' => 'car', 'Ca_17775_v3' => 'car', 'Ca_30464_v3' => 'car', 'Cc06_g08160' => 'ccan', 'Cc07_g01520' => 'ccan', 'Cc11_g15810' => 'ccan', 'CDE02G2840' => 'cde', 'CDE03G0093' => 'cde', 'CDE04G2127' => 'cde', 'CDE07G1857' => 'cde', 'CDE09G1246' => 'cde', 'Cfa003412' => 'cfa', 'Cfa007341' => 'cfa', 'Cfa009220' => 'cfa', 'Ciclev10008737m.g' => 'ccl', 'Ciclev10015565m.g' => 'ccl', 'Ciclev10031761m.g' => 'ccl', 'CiPaw.03G045300' => 'cil', 'CiPaw.03G247200' => 'cil', 'CiPaw.04G029500' => 'cil', 'CiPaw.04G174000' => 'cil', 'CiPaw.05G181200' => 'cil', 'CiPaw.06G067100' => 'cil', 'ClCG05G025800' => 'cla', 'ClCG06G011400' => 'cla', 'ClCG09G019360' => 'cla', 'COL.COLO4_04827' => 'col', 'COL.COLO4_29170' => 'col', 'COL.COLO4_35131' => 'col', 'COL.COLO4_35132' => 'col', 'Cpa.g.sc33.32' => 'cpa', 'Cpa.g.sc46.29' => 'cpa', 'Cpa.g.sc796.1' => 'cpa', 'CsaV3_1G030420' => 'csa', 'CsaV3_5G027050' => 'csa', 'CsaV3_5G031040' => 'csa', 'CsaV3_UNG023130' => 'csa', 'CSS0007726' => 'camsi', 'CSS0016433' => 'camsi', 'CSS0017656' => 'camsi', 'CSS0025364' => 'camsi', 'CSS0027582' => 'camsi', 'CSS0047288' => 'camsi', 'CSS0049950' => 'camsi', 'DCAR_003843' => 'dca', 'DCAR_007052' => 'dca', 'DCAR_020884' => 'dca', 'DCAR_021730' => 'dca', 'DCAR_024423' => 'dca', 'DCAR_026509' => 'dca', 'DCAR_031158' => 'dca', 'Dinv14728' => 'din', 'Dinv15219' => 'din', 'Dinv25728' => 'din', 'Dinv33428' => 'din', 'Dinv36489' => 'din', 'Dinv41486' => 'din', 'Duzib147G0469' => 'dzi', 'Duzib168G0060' => 'dzi', 'Duzib187G1215' => 'dzi', 'Duzib248G0692' => 'dzi', 'Duzib251G0767' => 'dzi', 'Duzib264G0446' => 'dzi', 'Duzib268G0691' => 'dzi', 'ECA232G4767' => 'eca', 'ECA233G2838' => 'eca', 'ECA234G0391' => 'eca', 'ECA234G0857' => 'eca', 'ECA236G1593' => 'eca', 'ECA238G0565' => 'eca', 'ECA246G1027' => 'eca', 'ECA246G3223' => 'eca', 'ECA246G3470' => 'eca', 'EL10Ac6g13829' => 'bvu', 'EL10Ac6g14093' => 'bvu', 'EL10Ac8g18707' => 'bvu', 'Eucgr.C01369' => 'egr', 'Eucgr.H02492' => 'egr', 'Eucgr.I01733' => 'egr', 'Eucgr.J02255' => 'egr', 'Eucgr.J02257' => 'egr', 'Eucgr.J02258' => 'egr', 'FAN02G1601' => 'fan', 'FAN03G1586' => 'fan', 'FAN03G2986' => 'fan', 'FAN05G4837' => 'fan', 'FAN06G0146' => 'fan', 'FAN07G0858' => 'fan', 'FAN09G3179' => 'fan', 'FAN10G0669' => 'fan', 'FAN12G2358' => 'fan', 'FAN14G4198' => 'fan', 'FAN14G5112' => 'fan', 'FAN17G0342' => 'fan', 'FAN19G0342' => 'fan', 'FAN19G0962' => 'fan', 'FAN19G1101' => 'fan', 'FAN19G1872' => 'fan', 'FAN22G0356' => 'fan', 'FAN23G0744' => 'fan', 'FAN23G1914' => 'fan', 'FAN26G0032' => 'fan', 'FAN28G0625' => 'fan', 'FvH4_1g02710' => 'fve', 'FvH4_1g02720' => 'fve', 'FvH4_4g25670' => 'fve', 'FvH4_6g51700' => 'fve', 'FvH4_7g20170' => 'fve', 'Glyma.05G175000' => 'gma', 'Glyma.08G132300' => 'gma', 'Glyma.11G243000' => 'gma', 'Glyma.13G158900' => 'gma', 'Glyma.17G112400' => 'gma', 'Glyma.18G014100' => 'gma', 'Glyma.19G003100' => 'gma', 'Glyma.19G056500' => 'gma', 'Gohir.A01G158900' => 'ghi', 'Gohir.A05G312600' => 'ghi', 'Gohir.A05G354900' => 'ghi', 'Gohir.A07G037200' => 'ghi', 'Gohir.A09G030000' => 'ghi', 'Gohir.A12G145200' => 'ghi', 'Gohir.D01G151500' => 'ghi', 'Gohir.D04G058300' => 'ghi', 'Gohir.D05G314100' => 'ghi', 'Gohir.D07G041400' => 'ghi', 'Gohir.D09G029700' => 'ghi', 'Gohir.D12G149700' => 'ghi', 'Gorai.001G043800' => 'gra', 'Gorai.002G187800' => 'gra', 'Gorai.006G034700' => 'gra', 'Gorai.008G161200' => 'gra', 'Gorai.009G335700' => 'gra', 'Gorai.012G065000' => 'gra', 'GSVIVG01000535001' => 'vvi', 'GSVIVG01015572001' => 'vvi', 'GSVIVG01032386001' => 'vvi', 'HanXRQChr05g0138531' => 'han', 'HanXRQChr06g0174391' => 'han', 'HanXRQChr07g0199021' => 'han', 'HanXRQChr08g0208211' => 'han', 'HanXRQChr09g0255471' => 'han', 'HanXRQChr10g0315791' => 'han', 'HanXRQChr12g0371991' => 'han', 'HanXRQChr15g0475251' => 'han', 'HanXRQChr17g0540001' => 'han', 'HanXRQChr17g0548631' => 'han', 'HanXRQChr17g0569561' => 'han', 'Haze_12256' => 'cav', 'Haze_14756' => 'cav', 'Haze_25528' => 'cav', 'Hma1.2p1_0079F.1_g041020' => 'hma', 'Hma1.2p1_0818F.1_g223260' => 'hma', 'Hma1.2p1_1747F.1_g300530' => 'hma', 'HPP92_004607' => 'vpl', 'HPP92_004608' => 'vpl', 'HPP92_006181' => 'vpl', 'HPP92_012192' => 'vpl', 'HPP92_015680' => 'vpl', 'HPP92_020249' => 'vpl', 'HPP92_021376' => 'vpl', 'HPP92_024275' => 'vpl', 'Hund06031' => 'sun', 'Hund25391' => 'sun', 'Lalb_Chr07g0185371' => 'lal', 'Lalb_Chr07g0185381' => 'lal', 'Lalb_Chr12g0204011' => 'lal', 'Lalb_Chr13g0301671' => 'lal', 'Lalb_Chr14g0362851' => 'lal', 'Lalb_Chr24g0403581' => 'lal', 'Lj1g0000233' => 'lja', 'Lj2g0018120' => 'lja', 'Lj3C621T0' => 'lonja', 'Lj3P1059T14' => 'lonja', 'Lj3P611T9' => 'lonja', 'Lj3P614T13' => 'lonja', 'Lj3P615T5' => 'lonja', 'Lj4g0012315' => 'lja', 'Lj4g0026182' => 'lja', 'Lj6P813T16' => 'lonja', 'Lj7C427T7' => 'lonja', 'Lj7C427T8' => 'lonja', 'Lj7P600T41' => 'lonja', 'Lju41C42G17' => 'lonja', 'Lsat_1_v5_gn_0_47300' => 'lsa', 'Lsat_1_v5_gn_2_91280' => 'lsa', 'Lsat_1_v5_gn_3_30561' => 'lsa', 'Lsat_1_v5_gn_4_184321' => 'lsa', 'Lsat_1_v5_gn_4_4041' => 'lsa', 'Lsat_1_v5_gn_5_92000' => 'lsa', 'Lsat_1_v5_gn_8_152940' => 'lsa', 'Lsat_1_v5_gn_8_62401' => 'lsa', 'Manes.06G055900' => 'mes', 'Manes.12G022200' => 'mes', 'Manes.13G023300' => 'mes', 'Manes.14G115000' => 'mes', 'Manes.15G151700' => 'mes', 'Manes.17G111300' => 'mes', 'Mapoly0226s0009' => 'mpo', 'MBI02_g25363_MAGBIO' => 'mbi', 'MBI06_g00027_MAGBIO' => 'mbi', 'MBI10_g13034_MAGBIO' => 'mbi', 'MD09G1023400' => 'mdo', 'MD13G1100100' => 'mdo', 'MD15G1169200' => 'mdo', 'MD16G1101100' => 'mdo', 'MD17G1022900' => 'mdo', 'Medtr3g096150' => 'mtr', 'Medtr4g115070' => 'mtr', 'Medtr7g033325' => 'mtr', 'Medtr8g089840' => 'mtr', 'MELO3C010319.2' => 'cme', 'MELO3C011944.2' => 'cme', 'MELO3C021589.2' => 'cme', 'Migut.E00207' => 'egut', 'Migut.H00067' => 'egut', 'Migut.K00433' => 'egut', 'Migut.K00606' => 'egut', 'Migut.K01410' => 'egut', 'MSTRG.13347' => 'ama', 'MSTRG.24045' => 'ama', 'MSTRG.2428' => 'ama', 'MSTRG.26410' => 'ama', 'MSTRG.3139' => 'ama', 'MSTRG.3286' => 'ama', 'MSTRG.563' => 'ama', 'MSTRG.7941' => 'ama', 'Nitab4.5_0000028g0060' => 'nta', 'Nitab4.5_0000065g0260' => 'nta', 'Nitab4.5_0000112g0060' => 'nta', 'Nitab4.5_0000489g0120' => 'nta', 'Nitab4.5_0001776g0050' => 'nta', 'Nitab4.5_0001854g0010' => 'nta', 'Nitab4.5_0001860g0020' => 'nta', 'Nitab4.5_0004352g0010' => 'nta', 'Nitab4.5_0008716g0020' => 'nta', 'Nitab4.5_0008922g0010' => 'nta', 'Nn3g16693' => 'nnu', 'Nn4g22596' => 'nnu', 'Nn7g37639' => 'nnu', 'Oeu001701.1' => 'oeu', 'Oeu018149.1' => 'oeu', 'Oeu026220.1' => 'oeu', 'Oeu038635.1' => 'oeu', 'Oeu049176.1' => 'oeu', 'Oeu056706.1' => 'oeu', 'Oeu056937.1' => 'oeu', 'Oeu057540.1' => 'oeu', 'Os02g0594900' => 'osa', 'Os02g0595100' => 'osa', 'Os04g0477500' => 'osa', 'Os12g0611900' => 'osa', 'Peaxi162Scf00076g00020' => 'pax', 'Peaxi162Scf00128g00217' => 'pax', 'Peaxi162Scf00129g01640' => 'pax', 'Peaxi162Scf00669g00007' => 'pax', 'Peaxi162Scf00700g00421' => 'pax', 'Peaxi162Scf00801g00038' => 'pax', 'Peaxi162Scf00891g00025' => 'pax', 'PGR083G0909' => 'pgr', 'PGR119G1005' => 'pgr', 'PGR142G2236' => 'pgr', 'PGR142G3388' => 'pgr', 'PGSC0003DMG400004514' => 'stu', 'PGSC0003DMG400012635' => 'stu', 'PGSC0003DMG400015730' => 'stu', 'PGSC0003DMG400018611' => 'stu', 'PGSC0003DMG400030897' => 'stu', 'Phvul.001G254800' => 'pvu', 'Phvul.002G260100' => 'pvu', 'Phvul.003G167600' => 'pvu', 'Phvul.004G005100' => 'pvu', 'Potri.001G343600' => 'ptr', 'Potri.006G066700' => 'ptr', 'Potri.008G186000' => 'ptr', 'Potri.010G046900' => 'ptr', 'Potri.018G127900' => 'ptr', 'Pp3c20_17750' => 'ppa', 'Pp3c24_4380' => 'ppa', 'Prupe.1G245800' => 'ppe', 'Prupe.3G293400' => 'ppe', 'Prupe.7G247400' => 'ppe', 'Psat0s145g0120' => 'psa', 'Psat0s595g0040' => 'psa', 'Psat0s595g0120' => 'psa', 'Psat3g175040' => 'psa', 'Psat7g058120' => 'psa', 'PSO017G0428' => 'pso', 'PSO063G7510' => 'pso', 'PSO067G0046' => 'pso', 'PSO478G1073' => 'pso', 'PSO675G3677' => 'pso', 'PSO675G6558' => 'pso', 'PSO675G7520' => 'pso', 'PSO675G8959' => 'pso', 'QL02p074089' => 'qlo', 'QL02p089614' => 'qlo', 'QL03p057736' => 'qlo', 'RcHm_v2.0_Chr1g0364131' => 'rch', 'RcHm_v2.0_Chr2g0087801' => 'rch', 'RcHm_v2.0_Chr2g0087821' => 'rch', 'RcHm_v2.0_Chr2g0173231' => 'rch', 'RcHm_v2.0_Chr4g0433111' => 'rch', 'Rhsim03G0250300' => 'rsi', 'Rhsim08G0048400' => 'rsi', 'Rhsim10G0014800' => 'rsi', 'Rhsim12G0040100' => 'rsi', 'Rhsim12G0109700' => 'rsi', 'Sabra06G0049600' => 'sbr', 'Sabra08G0141000' => 'sbr', 'Sabra10G0021400' => 'sbr', 'Sabra16G0222900' => 'sbr', 'Sabra18G0108600' => 'sbr', 'SalBow1G0433' => 'sbo', 'SalBow1G2038' => 'sbo', 'SalBow1G5003' => 'sbo', 'SalBow7G1197' => 'sbo', 'SalBow8G3506' => 'sbo', 'Sc03g0007300' => 'sci', 'Sc11g0000950' => 'sci', 'Sc14g0008750' => 'sci', 'Sc18g0000420' => 'sci', 'Sed0006754' => 'sed', 'Sed0008741' => 'sed', 'Sed0017172' => 'sed', 'Sed0018925' => 'sed', 'Sed0023326' => 'sed', 'Sed0025909' => 'sed', 'SEGI_05333' => 'sgi', 'SEGI_10362' => 'sgi', 'SEGI_13380' => 'sgi', 'SEGI_24306' => 'sgi', 'SEGI_29077' => 'sgi', 'SEGI_29095' => 'sgi', 'SEGI_36534' => 'sgi', 'SEGI_37506' => 'sgi', 'SEGI_38321' => 'sgi', 'SGA_v2.0_scaffold307G48031' => 'sas', 'SGA_v2.0_scaffold47G17507' => 'sas', 'SGA_v2.0_scaffold63G21736' => 'sas', 'SGA_v2.0_scaffold87G27070' => 'sas', 'SHI17794' => 'shi', 'SHI28851' => 'shi', 'SMO165G0155' => 'smo', 'SMO340G0217' => 'smo', 'SMO367G1210' => 'smo', 'Solyc02g093430.3' => 'sly', 'Solyc05g013580.4' => 'sly', 'Solyc07g008030.3' => 'sly', 'Solyc12g035470.2' => 'sly', 'Sopen02g038020' => 'spe', 'Sopen05g008490' => 'spe', 'Sopen07g003910' => 'spe', 'Sopen12g015240' => 'spe', 'Sp1g11550' => 'spa', 'Sp2g16710' => 'spa', 'Sp3g00430' => 'spa', 'Sp3g26780' => 'spa', 'Sp5g22900' => 'spa', 'Sp6g29530' => 'spa', 'TAR371G0794' => 'tar', 'TAR374G0164' => 'tar', 'TAR622G0165' => 'tar', 'TAR626G0929' => 'tar', 'TAR629G2155' => 'tar', 'THA.LOC104805282' => 'tha', 'THA.LOC104805363' => 'tha', 'THA.LOC104808968' => 'tha', 'THA.LOC104821093' => 'tha', 'THA.LOC104823953' => 'tha', 'THA.LOC104825562' => 'tha', 'THA.LOC104825665' => 'tha', 'Thecc.02G261400' => 'tca', 'Thecc.04G019200' => 'tca', 'Thecc.09G130400' => 'tca', 'Thhalv10004374m.g' => 'esa', 'Thhalv10007850m.g' => 'esa', 'Thhalv10013782m.g' => 'esa', 'Thhalv10018686m.g' => 'esa', 'Thhalv10020899m.g' => 'esa', 'Thhalv10022755m.g' => 'esa', 'TPR.G23851' => 'tpr', 'TPR.G26500' => 'tpr', 'TPR.G27267' => 'tpr', 'TPR.G32001' => 'tpr', 'TPR.G6251' => 'tpr', 'TPR.G8167' => 'tpr', 'TWI12G1330' => 'twi', 'TWI18G1239' => 'twi', 'TWI34G0979' => 'twi', 'TWI36G0670' => 'twi', 'TWI36G0707' => 'twi', 'TWI56G0233' => 'twi', 'TWI75G1809' => 'twi', 'unitig_21.g20874' => 'ugi', 'unitig_26.g10343' => 'ugi', 'unitig_46.g18392' => 'ugi', 'unitig_52.g17178' => 'ugi', 'unitig_8.g2934' => 'ugi', 'vmacro01122' => 'vma', 'vmacro05875' => 'vma', 'vmacro06147' => 'vma', 'vmacro16191' => 'vma', 'vmacro18293' => 'vma', 'VMungo0251G3707' => 'vmu', 'VMungo0464G1521' => 'vmu', 'VMungo1215G0205' => 'vmu', 'VMungo1383G2484' => 'vmu', 'Zm00001eb079610' => 'zma', 'Zm00001eb135990' => 'zma', 'Zm00001eb183710' => 'zma', 'Zm00001eb246020' => 'zma' ) $gf_id = 'HOM05D001124' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001124' ) $data_identifier = 'HOM05D001124' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 6, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 7, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 21, 'bol' => (int) 10, 'bra' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 6, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 9, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 21, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 8, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 10, 'lsa' => (int) 8, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 8, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 9, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb246020' $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' => 'HOM05D001124', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '548', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02520' => 'bna', 'A03p06630' => 'bna', 'A05p44460' => 'bna', 'A06p08710' => 'bna', 'A06p41090' => 'bna', 'A07p32320' => 'bna', 'A08p32520' => 'bna', 'A09p10360' => 'bna', 'A10p24080' => 'bna', 'Aa31LG11G15250' => 'aar', 'Aa31LG1G1800' => 'aar', 'Aa31LG2G5120' => 'aar', 'Aa31LG2G6070' => 'aar', 'Aa31LG5G10770' => 'aar', 'Aa31sc61G90' => 'aar', 'Actinidia01352' => 'ach', 'Actinidia05983' => 'ach', 'Actinidia08133' => 'ach', 'Actinidia15101' => 'ach', 'Actinidia26379' => 'ach', 'Actinidia35778' => 'ach', 'Actinidia36123' => 'ach', 'Actinidia37436' => 'ach', 'Actinidia38730' => 'ach', 'Ah.02g128210' => 'amhyb', 'Ah.03g132990' => 'amhyb', 'Ah.14g079410' => 'amhyb', 'AL1G24640' => 'aly', 'AL2G26680' => 'aly', 'AL3G10530' => 'aly', 'AL3G45230' => 'aly', 'AL5G15230' => 'aly', 'AL5G16960' => 'aly', 'AL6G25210' => 'aly', 'Aqoxy2G00441' => 'aox', 'Aqoxy3G01236' => 'aox', 'Aqoxy5G03746' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3RQ047' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C7GMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9C8JER' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MBL6KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YXCZ83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZANX40' => 'arhy', 'AT1G12990' => 'ath', 'AT1G67880' => 'ath', 'AT2G13290' => 'ath', 'AT3G01620' => 'ath', 'AT3G26445' => 'ath', 'AT3G27540' => 'ath', 'AT5G14480' => 'ath', 'ATR0824G026' => 'atr', 'ATR1098G019' => 'atr', 'Atru.chr11.2145' => 'acertr', 'Atru.chr2.3636' => 'acertr', 'Atru.chr2.3644' => 'acertr', 'Atru.chr6.2422' => 'acertr', 'Atru.chr7.1112' => 'acertr', 'AUR62005469' => 'cqu', 'AUR62011166' => 'cqu', 'AUR62013319' => 'cqu', 'AUR62024273' => 'cqu', 'AUR62028420' => 'cqu', 'AUR62041942' => 'cqu', 'BcaB01g04969' => 'bca', 'BcaB01g06371' => 'bca', 'BcaB02g11494' => 'bca', 'BcaB03g15382' => 'bca', 'BcaB08g36994' => 'bca', 'BcaC03g13477' => 'bca', 'BcaC03g13478' => 'bca', 'BcaC03g13480' => 'bca', 'BcaC03g13481' => 'bca', 'BcaC03g13486' => 'bca', 'BcaC04g19031' => 'bca', 'BcaC04g23085' => 'bca', 'BcaC05g25094' => 'bca', 'BcaC05g25096' => 'bca', 'BcaC05g25138' => 'bca', 'BcaC05g30416' => 'bca', 'BcaC05g30455' => 'bca', 'BcaC06g30979' => 'bca', 'BcaC06g33805' => 'bca', 'BcaC08g46021' => 'bca', 'BcaNung03154' => 'bca', 'BolC2t06623H' => 'bol', 'BolC2t06632H' => 'bol', 'BolC2t06635H' => 'bol', 'BolC2t06638H' => 'bol', 'BolC3t13266H' => 'bol', 'BolC5t29776H' => 'bol', 'BolC6t38912H' => 'bol', 'BolC7t44183H' => 'bol', 'BolC9t54123H' => 'bol', 'BolC9t59107H' => 'bol', 'BraA02t05221Z' => 'bra', 'BraA03t09996Z' => 'bra', 'BraA05t23210Z' => 'bra', 'BraA06t24068Z' => 'bra', 'BraA06t27032Z' => 'bra', 'BraA08t35176Z' => 'bra', 'BraA09t36680Z' => 'bra', 'BraA10t44471Z' => 'bra', 'C02p06760' => 'bna', 'C02p06890' => 'bna', 'C02p07010' => 'bna', 'C03p07660' => 'bna', 'C05p10300' => 'bna', 'C06p38150' => 'bna', 'C07p36650' => 'bna', 'C08p15770' => 'bna', 'C09p12300' => 'bna', 'C09p62700' => 'bna', 'C09p75040' => 'bna', 'CAN.G13.1' => 'can', 'CAN.G138.4' => 'can', 'CAN.G44.6' => 'can', 'CAN.G473.19' => 'can', 'CANSAT01G0835' => 'cansat', 'CANSAT11G0246' => 'cansat', 'CANSAT11G1766' => 'cansat', 'CANSAT64G1954' => 'cansat', 'CARHR013330' => 'chi', 'CARHR060530' => 'chi', 'CARHR075300' => 'chi', 'CARHR105120' => 'chi', 'CARHR148910' => 'chi', 'CARHR198830' => 'chi', 'Carub.0001s1275' => 'cru', 'Carub.0002s1437' => 'cru', 'Carub.0003s0044' => 'cru', 'Carub.0003s2787' => 'cru', 'Carub.0005s0597' => 'cru', 'Carub.0006s1266' => 'cru', 'Ca_06935_v3' => 'car', 'Ca_13559_v3' => 'car', 'Ca_16941_v3' => 'car', 'Ca_16960_v3' => 'car', 'Ca_17775_v3' => 'car', 'Ca_30464_v3' => 'car', 'Cc06_g08160' => 'ccan', 'Cc07_g01520' => 'ccan', 'Cc11_g15810' => 'ccan', 'CDE02G2840' => 'cde', 'CDE03G0093' => 'cde', 'CDE04G2127' => 'cde', 'CDE07G1857' => 'cde', 'CDE09G1246' => 'cde', 'Cfa003412' => 'cfa', 'Cfa007341' => 'cfa', 'Cfa009220' => 'cfa', 'Ciclev10008737m.g' => 'ccl', 'Ciclev10015565m.g' => 'ccl', 'Ciclev10031761m.g' => 'ccl', 'CiPaw.03G045300' => 'cil', 'CiPaw.03G247200' => 'cil', 'CiPaw.04G029500' => 'cil', 'CiPaw.04G174000' => 'cil', 'CiPaw.05G181200' => 'cil', 'CiPaw.06G067100' => 'cil', 'ClCG05G025800' => 'cla', 'ClCG06G011400' => 'cla', 'ClCG09G019360' => 'cla', 'COL.COLO4_04827' => 'col', 'COL.COLO4_29170' => 'col', 'COL.COLO4_35131' => 'col', 'COL.COLO4_35132' => 'col', 'Cpa.g.sc33.32' => 'cpa', 'Cpa.g.sc46.29' => 'cpa', 'Cpa.g.sc796.1' => 'cpa', 'CsaV3_1G030420' => 'csa', 'CsaV3_5G027050' => 'csa', 'CsaV3_5G031040' => 'csa', 'CsaV3_UNG023130' => 'csa', 'CSS0007726' => 'camsi', 'CSS0016433' => 'camsi', 'CSS0017656' => 'camsi', 'CSS0025364' => 'camsi', 'CSS0027582' => 'camsi', 'CSS0047288' => 'camsi', 'CSS0049950' => 'camsi', 'DCAR_003843' => 'dca', 'DCAR_007052' => 'dca', 'DCAR_020884' => 'dca', 'DCAR_021730' => 'dca', 'DCAR_024423' => 'dca', 'DCAR_026509' => 'dca', 'DCAR_031158' => 'dca', 'Dinv14728' => 'din', 'Dinv15219' => 'din', 'Dinv25728' => 'din', 'Dinv33428' => 'din', 'Dinv36489' => 'din', 'Dinv41486' => 'din', 'Duzib147G0469' => 'dzi', 'Duzib168G0060' => 'dzi', 'Duzib187G1215' => 'dzi', 'Duzib248G0692' => 'dzi', 'Duzib251G0767' => 'dzi', 'Duzib264G0446' => 'dzi', 'Duzib268G0691' => 'dzi', 'ECA232G4767' => 'eca', 'ECA233G2838' => 'eca', 'ECA234G0391' => 'eca', 'ECA234G0857' => 'eca', 'ECA236G1593' => 'eca', 'ECA238G0565' => 'eca', 'ECA246G1027' => 'eca', 'ECA246G3223' => 'eca', 'ECA246G3470' => 'eca', 'EL10Ac6g13829' => 'bvu', 'EL10Ac6g14093' => 'bvu', 'EL10Ac8g18707' => 'bvu', 'Eucgr.C01369' => 'egr', 'Eucgr.H02492' => 'egr', 'Eucgr.I01733' => 'egr', 'Eucgr.J02255' => 'egr', 'Eucgr.J02257' => 'egr', 'Eucgr.J02258' => 'egr', 'FAN02G1601' => 'fan', 'FAN03G1586' => 'fan', 'FAN03G2986' => 'fan', 'FAN05G4837' => 'fan', 'FAN06G0146' => 'fan', 'FAN07G0858' => 'fan', 'FAN09G3179' => 'fan', 'FAN10G0669' => 'fan', 'FAN12G2358' => 'fan', 'FAN14G4198' => 'fan', 'FAN14G5112' => 'fan', 'FAN17G0342' => 'fan', 'FAN19G0342' => 'fan', 'FAN19G0962' => 'fan', 'FAN19G1101' => 'fan', 'FAN19G1872' => 'fan', 'FAN22G0356' => 'fan', 'FAN23G0744' => 'fan', 'FAN23G1914' => 'fan', 'FAN26G0032' => 'fan', 'FAN28G0625' => 'fan', 'FvH4_1g02710' => 'fve', 'FvH4_1g02720' => 'fve', 'FvH4_4g25670' => 'fve', 'FvH4_6g51700' => 'fve', 'FvH4_7g20170' => 'fve', 'Glyma.05G175000' => 'gma', 'Glyma.08G132300' => 'gma', 'Glyma.11G243000' => 'gma', 'Glyma.13G158900' => 'gma', 'Glyma.17G112400' => 'gma', 'Glyma.18G014100' => 'gma', 'Glyma.19G003100' => 'gma', 'Glyma.19G056500' => 'gma', 'Gohir.A01G158900' => 'ghi', 'Gohir.A05G312600' => 'ghi', 'Gohir.A05G354900' => 'ghi', 'Gohir.A07G037200' => 'ghi', 'Gohir.A09G030000' => 'ghi', 'Gohir.A12G145200' => 'ghi', 'Gohir.D01G151500' => 'ghi', 'Gohir.D04G058300' => 'ghi', 'Gohir.D05G314100' => 'ghi', 'Gohir.D07G041400' => 'ghi', 'Gohir.D09G029700' => 'ghi', 'Gohir.D12G149700' => 'ghi', 'Gorai.001G043800' => 'gra', 'Gorai.002G187800' => 'gra', 'Gorai.006G034700' => 'gra', 'Gorai.008G161200' => 'gra', 'Gorai.009G335700' => 'gra', 'Gorai.012G065000' => 'gra', 'GSVIVG01000535001' => 'vvi', 'GSVIVG01015572001' => 'vvi', 'GSVIVG01032386001' => 'vvi', 'HanXRQChr05g0138531' => 'han', 'HanXRQChr06g0174391' => 'han', 'HanXRQChr07g0199021' => 'han', 'HanXRQChr08g0208211' => 'han', 'HanXRQChr09g0255471' => 'han', 'HanXRQChr10g0315791' => 'han', 'HanXRQChr12g0371991' => 'han', 'HanXRQChr15g0475251' => 'han', 'HanXRQChr17g0540001' => 'han', 'HanXRQChr17g0548631' => 'han', 'HanXRQChr17g0569561' => 'han', 'Haze_12256' => 'cav', 'Haze_14756' => 'cav', 'Haze_25528' => 'cav', 'Hma1.2p1_0079F.1_g041020' => 'hma', 'Hma1.2p1_0818F.1_g223260' => 'hma', 'Hma1.2p1_1747F.1_g300530' => 'hma', 'HPP92_004607' => 'vpl', 'HPP92_004608' => 'vpl', 'HPP92_006181' => 'vpl', 'HPP92_012192' => 'vpl', 'HPP92_015680' => 'vpl', 'HPP92_020249' => 'vpl', 'HPP92_021376' => 'vpl', 'HPP92_024275' => 'vpl', 'Hund06031' => 'sun', 'Hund25391' => 'sun', 'Lalb_Chr07g0185371' => 'lal', 'Lalb_Chr07g0185381' => 'lal', 'Lalb_Chr12g0204011' => 'lal', 'Lalb_Chr13g0301671' => 'lal', 'Lalb_Chr14g0362851' => 'lal', 'Lalb_Chr24g0403581' => 'lal', 'Lj1g0000233' => 'lja', 'Lj2g0018120' => 'lja', 'Lj3C621T0' => 'lonja', 'Lj3P1059T14' => 'lonja', 'Lj3P611T9' => 'lonja', 'Lj3P614T13' => 'lonja', 'Lj3P615T5' => 'lonja', 'Lj4g0012315' => 'lja', 'Lj4g0026182' => 'lja', 'Lj6P813T16' => 'lonja', 'Lj7C427T7' => 'lonja', 'Lj7C427T8' => 'lonja', 'Lj7P600T41' => 'lonja', 'Lju41C42G17' => 'lonja', 'Lsat_1_v5_gn_0_47300' => 'lsa', 'Lsat_1_v5_gn_2_91280' => 'lsa', 'Lsat_1_v5_gn_3_30561' => 'lsa', 'Lsat_1_v5_gn_4_184321' => 'lsa', 'Lsat_1_v5_gn_4_4041' => 'lsa', 'Lsat_1_v5_gn_5_92000' => 'lsa', 'Lsat_1_v5_gn_8_152940' => 'lsa', 'Lsat_1_v5_gn_8_62401' => 'lsa', 'Manes.06G055900' => 'mes', 'Manes.12G022200' => 'mes', 'Manes.13G023300' => 'mes', 'Manes.14G115000' => 'mes', 'Manes.15G151700' => 'mes', 'Manes.17G111300' => 'mes', 'Mapoly0226s0009' => 'mpo', 'MBI02_g25363_MAGBIO' => 'mbi', 'MBI06_g00027_MAGBIO' => 'mbi', 'MBI10_g13034_MAGBIO' => 'mbi', 'MD09G1023400' => 'mdo', 'MD13G1100100' => 'mdo', 'MD15G1169200' => 'mdo', 'MD16G1101100' => 'mdo', 'MD17G1022900' => 'mdo', 'Medtr3g096150' => 'mtr', 'Medtr4g115070' => 'mtr', 'Medtr7g033325' => 'mtr', 'Medtr8g089840' => 'mtr', 'MELO3C010319.2' => 'cme', 'MELO3C011944.2' => 'cme', 'MELO3C021589.2' => 'cme', 'Migut.E00207' => 'egut', 'Migut.H00067' => 'egut', 'Migut.K00433' => 'egut', 'Migut.K00606' => 'egut', 'Migut.K01410' => 'egut', 'MSTRG.13347' => 'ama', 'MSTRG.24045' => 'ama', 'MSTRG.2428' => 'ama', 'MSTRG.26410' => 'ama', 'MSTRG.3139' => 'ama', 'MSTRG.3286' => 'ama', 'MSTRG.563' => 'ama', 'MSTRG.7941' => 'ama', 'Nitab4.5_0000028g0060' => 'nta', 'Nitab4.5_0000065g0260' => 'nta', 'Nitab4.5_0000112g0060' => 'nta', 'Nitab4.5_0000489g0120' => 'nta', 'Nitab4.5_0001776g0050' => 'nta', 'Nitab4.5_0001854g0010' => 'nta', 'Nitab4.5_0001860g0020' => 'nta', 'Nitab4.5_0004352g0010' => 'nta', 'Nitab4.5_0008716g0020' => 'nta', 'Nitab4.5_0008922g0010' => 'nta', 'Nn3g16693' => 'nnu', 'Nn4g22596' => 'nnu', 'Nn7g37639' => 'nnu', 'Oeu001701.1' => 'oeu', 'Oeu018149.1' => 'oeu', 'Oeu026220.1' => 'oeu', 'Oeu038635.1' => 'oeu', 'Oeu049176.1' => 'oeu', 'Oeu056706.1' => 'oeu', 'Oeu056937.1' => 'oeu', 'Oeu057540.1' => 'oeu', 'Os02g0594900' => 'osa', 'Os02g0595100' => 'osa', 'Os04g0477500' => 'osa', 'Os12g0611900' => 'osa', 'Peaxi162Scf00076g00020' => 'pax', 'Peaxi162Scf00128g00217' => 'pax', 'Peaxi162Scf00129g01640' => 'pax', 'Peaxi162Scf00669g00007' => 'pax', 'Peaxi162Scf00700g00421' => 'pax', 'Peaxi162Scf00801g00038' => 'pax', 'Peaxi162Scf00891g00025' => 'pax', 'PGR083G0909' => 'pgr', 'PGR119G1005' => 'pgr', 'PGR142G2236' => 'pgr', 'PGR142G3388' => 'pgr', 'PGSC0003DMG400004514' => 'stu', 'PGSC0003DMG400012635' => 'stu', 'PGSC0003DMG400015730' => 'stu', 'PGSC0003DMG400018611' => 'stu', 'PGSC0003DMG400030897' => 'stu', 'Phvul.001G254800' => 'pvu', 'Phvul.002G260100' => 'pvu', 'Phvul.003G167600' => 'pvu', 'Phvul.004G005100' => 'pvu', 'Potri.001G343600' => 'ptr', 'Potri.006G066700' => 'ptr', 'Potri.008G186000' => 'ptr', 'Potri.010G046900' => 'ptr', 'Potri.018G127900' => 'ptr', 'Pp3c20_17750' => 'ppa', 'Pp3c24_4380' => 'ppa', 'Prupe.1G245800' => 'ppe', 'Prupe.3G293400' => 'ppe', 'Prupe.7G247400' => 'ppe', 'Psat0s145g0120' => 'psa', 'Psat0s595g0040' => 'psa', 'Psat0s595g0120' => 'psa', 'Psat3g175040' => 'psa', 'Psat7g058120' => 'psa', 'PSO017G0428' => 'pso', 'PSO063G7510' => 'pso', 'PSO067G0046' => 'pso', 'PSO478G1073' => 'pso', 'PSO675G3677' => 'pso', 'PSO675G6558' => 'pso', 'PSO675G7520' => 'pso', 'PSO675G8959' => 'pso', 'QL02p074089' => 'qlo', 'QL02p089614' => 'qlo', 'QL03p057736' => 'qlo', 'RcHm_v2.0_Chr1g0364131' => 'rch', 'RcHm_v2.0_Chr2g0087801' => 'rch', 'RcHm_v2.0_Chr2g0087821' => 'rch', 'RcHm_v2.0_Chr2g0173231' => 'rch', 'RcHm_v2.0_Chr4g0433111' => 'rch', 'Rhsim03G0250300' => 'rsi', 'Rhsim08G0048400' => 'rsi', 'Rhsim10G0014800' => 'rsi', 'Rhsim12G0040100' => 'rsi', 'Rhsim12G0109700' => 'rsi', 'Sabra06G0049600' => 'sbr', 'Sabra08G0141000' => 'sbr', 'Sabra10G0021400' => 'sbr', 'Sabra16G0222900' => 'sbr', 'Sabra18G0108600' => 'sbr', 'SalBow1G0433' => 'sbo', 'SalBow1G2038' => 'sbo', 'SalBow1G5003' => 'sbo', 'SalBow7G1197' => 'sbo', 'SalBow8G3506' => 'sbo', 'Sc03g0007300' => 'sci', 'Sc11g0000950' => 'sci', 'Sc14g0008750' => 'sci', 'Sc18g0000420' => 'sci', 'Sed0006754' => 'sed', 'Sed0008741' => 'sed', 'Sed0017172' => 'sed', 'Sed0018925' => 'sed', 'Sed0023326' => 'sed', 'Sed0025909' => 'sed', 'SEGI_05333' => 'sgi', 'SEGI_10362' => 'sgi', 'SEGI_13380' => 'sgi', 'SEGI_24306' => 'sgi', 'SEGI_29077' => 'sgi', 'SEGI_29095' => 'sgi', 'SEGI_36534' => 'sgi', 'SEGI_37506' => 'sgi', 'SEGI_38321' => 'sgi', 'SGA_v2.0_scaffold307G48031' => 'sas', 'SGA_v2.0_scaffold47G17507' => 'sas', 'SGA_v2.0_scaffold63G21736' => 'sas', 'SGA_v2.0_scaffold87G27070' => 'sas', 'SHI17794' => 'shi', 'SHI28851' => 'shi', 'SMO165G0155' => 'smo', 'SMO340G0217' => 'smo', 'SMO367G1210' => 'smo', 'Solyc02g093430.3' => 'sly', 'Solyc05g013580.4' => 'sly', 'Solyc07g008030.3' => 'sly', 'Solyc12g035470.2' => 'sly', 'Sopen02g038020' => 'spe', 'Sopen05g008490' => 'spe', 'Sopen07g003910' => 'spe', 'Sopen12g015240' => 'spe', 'Sp1g11550' => 'spa', 'Sp2g16710' => 'spa', 'Sp3g00430' => 'spa', 'Sp3g26780' => 'spa', 'Sp5g22900' => 'spa', 'Sp6g29530' => 'spa', 'TAR371G0794' => 'tar', 'TAR374G0164' => 'tar', 'TAR622G0165' => 'tar', 'TAR626G0929' => 'tar', 'TAR629G2155' => 'tar', 'THA.LOC104805282' => 'tha', 'THA.LOC104805363' => 'tha', 'THA.LOC104808968' => 'tha', 'THA.LOC104821093' => 'tha', 'THA.LOC104823953' => 'tha', 'THA.LOC104825562' => 'tha', 'THA.LOC104825665' => 'tha', 'Thecc.02G261400' => 'tca', 'Thecc.04G019200' => 'tca', 'Thecc.09G130400' => 'tca', 'Thhalv10004374m.g' => 'esa', 'Thhalv10007850m.g' => 'esa', 'Thhalv10013782m.g' => 'esa', 'Thhalv10018686m.g' => 'esa', 'Thhalv10020899m.g' => 'esa', 'Thhalv10022755m.g' => 'esa', 'TPR.G23851' => 'tpr', 'TPR.G26500' => 'tpr', 'TPR.G27267' => 'tpr', 'TPR.G32001' => 'tpr', 'TPR.G6251' => 'tpr', 'TPR.G8167' => 'tpr', 'TWI12G1330' => 'twi', 'TWI18G1239' => 'twi', 'TWI34G0979' => 'twi', 'TWI36G0670' => 'twi', 'TWI36G0707' => 'twi', 'TWI56G0233' => 'twi', 'TWI75G1809' => 'twi', 'unitig_21.g20874' => 'ugi', 'unitig_26.g10343' => 'ugi', 'unitig_46.g18392' => 'ugi', 'unitig_52.g17178' => 'ugi', 'unitig_8.g2934' => 'ugi', 'vmacro01122' => 'vma', 'vmacro05875' => 'vma', 'vmacro06147' => 'vma', 'vmacro16191' => 'vma', 'vmacro18293' => 'vma', 'VMungo0251G3707' => 'vmu', 'VMungo0464G1521' => 'vmu', 'VMungo1215G0205' => 'vmu', 'VMungo1383G2484' => 'vmu', 'Zm00001eb079610' => 'zma', 'Zm00001eb135990' => 'zma', 'Zm00001eb183710' => 'zma', 'Zm00001eb246020' => 'zma' ), 'gf_id' => 'HOM05D001124', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001124' ), 'data_identifier' => 'HOM05D001124', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001124', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '548', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02520' => 'bna', 'A03p06630' => 'bna', 'A05p44460' => 'bna', 'A06p08710' => 'bna', 'A06p41090' => 'bna', 'A07p32320' => 'bna', 'A08p32520' => 'bna', 'A09p10360' => 'bna', 'A10p24080' => 'bna', 'Aa31LG11G15250' => 'aar', 'Aa31LG1G1800' => 'aar', 'Aa31LG2G5120' => 'aar', 'Aa31LG2G6070' => 'aar', 'Aa31LG5G10770' => 'aar', 'Aa31sc61G90' => 'aar', 'Actinidia01352' => 'ach', 'Actinidia05983' => 'ach', 'Actinidia08133' => 'ach', 'Actinidia15101' => 'ach', 'Actinidia26379' => 'ach', 'Actinidia35778' => 'ach', 'Actinidia36123' => 'ach', 'Actinidia37436' => 'ach', 'Actinidia38730' => 'ach', 'Ah.02g128210' => 'amhyb', 'Ah.03g132990' => 'amhyb', 'Ah.14g079410' => 'amhyb', 'AL1G24640' => 'aly', 'AL2G26680' => 'aly', 'AL3G10530' => 'aly', 'AL3G45230' => 'aly', 'AL5G15230' => 'aly', 'AL5G16960' => 'aly', 'AL6G25210' => 'aly', 'Aqoxy2G00441' => 'aox', 'Aqoxy3G01236' => 'aox', 'Aqoxy5G03746' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3RQ047' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C7GMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9C8JER' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MBL6KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YXCZ83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZANX40' => 'arhy', 'AT1G12990' => 'ath', 'AT1G67880' => 'ath', 'AT2G13290' => 'ath', 'AT3G01620' => 'ath', 'AT3G26445' => 'ath', 'AT3G27540' => 'ath', 'AT5G14480' => 'ath', 'ATR0824G026' => 'atr', 'ATR1098G019' => 'atr', 'Atru.chr11.2145' => 'acertr', 'Atru.chr2.3636' => 'acertr', 'Atru.chr2.3644' => 'acertr', 'Atru.chr6.2422' => 'acertr', 'Atru.chr7.1112' => 'acertr', 'AUR62005469' => 'cqu', 'AUR62011166' => 'cqu', 'AUR62013319' => 'cqu', 'AUR62024273' => 'cqu', 'AUR62028420' => 'cqu', 'AUR62041942' => 'cqu', 'BcaB01g04969' => 'bca', 'BcaB01g06371' => 'bca', 'BcaB02g11494' => 'bca', 'BcaB03g15382' => 'bca', 'BcaB08g36994' => 'bca', 'BcaC03g13477' => 'bca', 'BcaC03g13478' => 'bca', 'BcaC03g13480' => 'bca', 'BcaC03g13481' => 'bca', 'BcaC03g13486' => 'bca', 'BcaC04g19031' => 'bca', 'BcaC04g23085' => 'bca', 'BcaC05g25094' => 'bca', 'BcaC05g25096' => 'bca', 'BcaC05g25138' => 'bca', 'BcaC05g30416' => 'bca', 'BcaC05g30455' => 'bca', 'BcaC06g30979' => 'bca', 'BcaC06g33805' => 'bca', 'BcaC08g46021' => 'bca', 'BcaNung03154' => 'bca', 'BolC2t06623H' => 'bol', 'BolC2t06632H' => 'bol', 'BolC2t06635H' => 'bol', 'BolC2t06638H' => 'bol', 'BolC3t13266H' => 'bol', 'BolC5t29776H' => 'bol', 'BolC6t38912H' => 'bol', 'BolC7t44183H' => 'bol', 'BolC9t54123H' => 'bol', 'BolC9t59107H' => 'bol', 'BraA02t05221Z' => 'bra', 'BraA03t09996Z' => 'bra', 'BraA05t23210Z' => 'bra', 'BraA06t24068Z' => 'bra', 'BraA06t27032Z' => 'bra', 'BraA08t35176Z' => 'bra', 'BraA09t36680Z' => 'bra', 'BraA10t44471Z' => 'bra', 'C02p06760' => 'bna', 'C02p06890' => 'bna', 'C02p07010' => 'bna', 'C03p07660' => 'bna', 'C05p10300' => 'bna', 'C06p38150' => 'bna', 'C07p36650' => 'bna', 'C08p15770' => 'bna', 'C09p12300' => 'bna', 'C09p62700' => 'bna', 'C09p75040' => 'bna', 'CAN.G13.1' => 'can', 'CAN.G138.4' => 'can', 'CAN.G44.6' => 'can', 'CAN.G473.19' => 'can', 'CANSAT01G0835' => 'cansat', 'CANSAT11G0246' => 'cansat', 'CANSAT11G1766' => 'cansat', 'CANSAT64G1954' => 'cansat', 'CARHR013330' => 'chi', 'CARHR060530' => 'chi', 'CARHR075300' => 'chi', 'CARHR105120' => 'chi', 'CARHR148910' => 'chi', 'CARHR198830' => 'chi', 'Carub.0001s1275' => 'cru', 'Carub.0002s1437' => 'cru', 'Carub.0003s0044' => 'cru', 'Carub.0003s2787' => 'cru', 'Carub.0005s0597' => 'cru', 'Carub.0006s1266' => 'cru', 'Ca_06935_v3' => 'car', 'Ca_13559_v3' => 'car', 'Ca_16941_v3' => 'car', 'Ca_16960_v3' => 'car', 'Ca_17775_v3' => 'car', 'Ca_30464_v3' => 'car', 'Cc06_g08160' => 'ccan', 'Cc07_g01520' => 'ccan', 'Cc11_g15810' => 'ccan', 'CDE02G2840' => 'cde', 'CDE03G0093' => 'cde', 'CDE04G2127' => 'cde', 'CDE07G1857' => 'cde', 'CDE09G1246' => 'cde', 'Cfa003412' => 'cfa', 'Cfa007341' => 'cfa', 'Cfa009220' => 'cfa', 'Ciclev10008737m.g' => 'ccl', 'Ciclev10015565m.g' => 'ccl', 'Ciclev10031761m.g' => 'ccl', 'CiPaw.03G045300' => 'cil', 'CiPaw.03G247200' => 'cil', 'CiPaw.04G029500' => 'cil', 'CiPaw.04G174000' => 'cil', 'CiPaw.05G181200' => 'cil', 'CiPaw.06G067100' => 'cil', 'ClCG05G025800' => 'cla', 'ClCG06G011400' => 'cla', 'ClCG09G019360' => 'cla', 'COL.COLO4_04827' => 'col', 'COL.COLO4_29170' => 'col', 'COL.COLO4_35131' => 'col', 'COL.COLO4_35132' => 'col', 'Cpa.g.sc33.32' => 'cpa', 'Cpa.g.sc46.29' => 'cpa', 'Cpa.g.sc796.1' => 'cpa', 'CsaV3_1G030420' => 'csa', 'CsaV3_5G027050' => 'csa', 'CsaV3_5G031040' => 'csa', 'CsaV3_UNG023130' => 'csa', 'CSS0007726' => 'camsi', 'CSS0016433' => 'camsi', 'CSS0017656' => 'camsi', 'CSS0025364' => 'camsi', 'CSS0027582' => 'camsi', 'CSS0047288' => 'camsi', 'CSS0049950' => 'camsi', 'DCAR_003843' => 'dca', 'DCAR_007052' => 'dca', 'DCAR_020884' => 'dca', 'DCAR_021730' => 'dca', 'DCAR_024423' => 'dca', 'DCAR_026509' => 'dca', 'DCAR_031158' => 'dca', 'Dinv14728' => 'din', 'Dinv15219' => 'din', 'Dinv25728' => 'din', 'Dinv33428' => 'din', 'Dinv36489' => 'din', 'Dinv41486' => 'din', 'Duzib147G0469' => 'dzi', 'Duzib168G0060' => 'dzi', 'Duzib187G1215' => 'dzi', 'Duzib248G0692' => 'dzi', 'Duzib251G0767' => 'dzi', 'Duzib264G0446' => 'dzi', 'Duzib268G0691' => 'dzi', 'ECA232G4767' => 'eca', 'ECA233G2838' => 'eca', 'ECA234G0391' => 'eca', 'ECA234G0857' => 'eca', 'ECA236G1593' => 'eca', 'ECA238G0565' => 'eca', 'ECA246G1027' => 'eca', 'ECA246G3223' => 'eca', 'ECA246G3470' => 'eca', 'EL10Ac6g13829' => 'bvu', 'EL10Ac6g14093' => 'bvu', 'EL10Ac8g18707' => 'bvu', 'Eucgr.C01369' => 'egr', 'Eucgr.H02492' => 'egr', 'Eucgr.I01733' => 'egr', 'Eucgr.J02255' => 'egr', 'Eucgr.J02257' => 'egr', 'Eucgr.J02258' => 'egr', 'FAN02G1601' => 'fan', 'FAN03G1586' => 'fan', 'FAN03G2986' => 'fan', 'FAN05G4837' => 'fan', 'FAN06G0146' => 'fan', 'FAN07G0858' => 'fan', 'FAN09G3179' => 'fan', 'FAN10G0669' => 'fan', 'FAN12G2358' => 'fan', 'FAN14G4198' => 'fan', 'FAN14G5112' => 'fan', 'FAN17G0342' => 'fan', 'FAN19G0342' => 'fan', 'FAN19G0962' => 'fan', 'FAN19G1101' => 'fan', 'FAN19G1872' => 'fan', 'FAN22G0356' => 'fan', 'FAN23G0744' => 'fan', 'FAN23G1914' => 'fan', 'FAN26G0032' => 'fan', 'FAN28G0625' => 'fan', 'FvH4_1g02710' => 'fve', 'FvH4_1g02720' => 'fve', 'FvH4_4g25670' => 'fve', 'FvH4_6g51700' => 'fve', 'FvH4_7g20170' => 'fve', 'Glyma.05G175000' => 'gma', 'Glyma.08G132300' => 'gma', 'Glyma.11G243000' => 'gma', 'Glyma.13G158900' => 'gma', 'Glyma.17G112400' => 'gma', 'Glyma.18G014100' => 'gma', 'Glyma.19G003100' => 'gma', 'Glyma.19G056500' => 'gma', 'Gohir.A01G158900' => 'ghi', 'Gohir.A05G312600' => 'ghi', 'Gohir.A05G354900' => 'ghi', 'Gohir.A07G037200' => 'ghi', 'Gohir.A09G030000' => 'ghi', 'Gohir.A12G145200' => 'ghi', 'Gohir.D01G151500' => 'ghi', 'Gohir.D04G058300' => 'ghi', 'Gohir.D05G314100' => 'ghi', 'Gohir.D07G041400' => 'ghi', 'Gohir.D09G029700' => 'ghi', 'Gohir.D12G149700' => 'ghi', 'Gorai.001G043800' => 'gra', 'Gorai.002G187800' => 'gra', 'Gorai.006G034700' => 'gra', 'Gorai.008G161200' => 'gra', 'Gorai.009G335700' => 'gra', 'Gorai.012G065000' => 'gra', 'GSVIVG01000535001' => 'vvi', 'GSVIVG01015572001' => 'vvi', 'GSVIVG01032386001' => 'vvi', 'HanXRQChr05g0138531' => 'han', 'HanXRQChr06g0174391' => 'han', 'HanXRQChr07g0199021' => 'han', 'HanXRQChr08g0208211' => 'han', 'HanXRQChr09g0255471' => 'han', 'HanXRQChr10g0315791' => 'han', 'HanXRQChr12g0371991' => 'han', 'HanXRQChr15g0475251' => 'han', 'HanXRQChr17g0540001' => 'han', 'HanXRQChr17g0548631' => 'han', 'HanXRQChr17g0569561' => 'han', 'Haze_12256' => 'cav', 'Haze_14756' => 'cav', 'Haze_25528' => 'cav', 'Hma1.2p1_0079F.1_g041020' => 'hma', 'Hma1.2p1_0818F.1_g223260' => 'hma', 'Hma1.2p1_1747F.1_g300530' => 'hma', 'HPP92_004607' => 'vpl', 'HPP92_004608' => 'vpl', 'HPP92_006181' => 'vpl', 'HPP92_012192' => 'vpl', 'HPP92_015680' => 'vpl', 'HPP92_020249' => 'vpl', 'HPP92_021376' => 'vpl', 'HPP92_024275' => 'vpl', 'Hund06031' => 'sun', 'Hund25391' => 'sun', 'Lalb_Chr07g0185371' => 'lal', 'Lalb_Chr07g0185381' => 'lal', 'Lalb_Chr12g0204011' => 'lal', 'Lalb_Chr13g0301671' => 'lal', 'Lalb_Chr14g0362851' => 'lal', 'Lalb_Chr24g0403581' => 'lal', 'Lj1g0000233' => 'lja', 'Lj2g0018120' => 'lja', 'Lj3C621T0' => 'lonja', 'Lj3P1059T14' => 'lonja', 'Lj3P611T9' => 'lonja', 'Lj3P614T13' => 'lonja', 'Lj3P615T5' => 'lonja', 'Lj4g0012315' => 'lja', 'Lj4g0026182' => 'lja', 'Lj6P813T16' => 'lonja', 'Lj7C427T7' => 'lonja', 'Lj7C427T8' => 'lonja', 'Lj7P600T41' => 'lonja', 'Lju41C42G17' => 'lonja', 'Lsat_1_v5_gn_0_47300' => 'lsa', 'Lsat_1_v5_gn_2_91280' => 'lsa', 'Lsat_1_v5_gn_3_30561' => 'lsa', 'Lsat_1_v5_gn_4_184321' => 'lsa', 'Lsat_1_v5_gn_4_4041' => 'lsa', 'Lsat_1_v5_gn_5_92000' => 'lsa', 'Lsat_1_v5_gn_8_152940' => 'lsa', 'Lsat_1_v5_gn_8_62401' => 'lsa', 'Manes.06G055900' => 'mes', 'Manes.12G022200' => 'mes', 'Manes.13G023300' => 'mes', 'Manes.14G115000' => 'mes', 'Manes.15G151700' => 'mes', 'Manes.17G111300' => 'mes', 'Mapoly0226s0009' => 'mpo', 'MBI02_g25363_MAGBIO' => 'mbi', 'MBI06_g00027_MAGBIO' => 'mbi', 'MBI10_g13034_MAGBIO' => 'mbi', 'MD09G1023400' => 'mdo', 'MD13G1100100' => 'mdo', 'MD15G1169200' => 'mdo', 'MD16G1101100' => 'mdo', 'MD17G1022900' => 'mdo', 'Medtr3g096150' => 'mtr', 'Medtr4g115070' => 'mtr', 'Medtr7g033325' => 'mtr', 'Medtr8g089840' => 'mtr', 'MELO3C010319.2' => 'cme', 'MELO3C011944.2' => 'cme', 'MELO3C021589.2' => 'cme', 'Migut.E00207' => 'egut', 'Migut.H00067' => 'egut', 'Migut.K00433' => 'egut', 'Migut.K00606' => 'egut', 'Migut.K01410' => 'egut', 'MSTRG.13347' => 'ama', 'MSTRG.24045' => 'ama', 'MSTRG.2428' => 'ama', 'MSTRG.26410' => 'ama', 'MSTRG.3139' => 'ama', 'MSTRG.3286' => 'ama', 'MSTRG.563' => 'ama', 'MSTRG.7941' => 'ama', 'Nitab4.5_0000028g0060' => 'nta', 'Nitab4.5_0000065g0260' => 'nta', 'Nitab4.5_0000112g0060' => 'nta', 'Nitab4.5_0000489g0120' => 'nta', 'Nitab4.5_0001776g0050' => 'nta', 'Nitab4.5_0001854g0010' => 'nta', 'Nitab4.5_0001860g0020' => 'nta', 'Nitab4.5_0004352g0010' => 'nta', 'Nitab4.5_0008716g0020' => 'nta', 'Nitab4.5_0008922g0010' => 'nta', 'Nn3g16693' => 'nnu', 'Nn4g22596' => 'nnu', 'Nn7g37639' => 'nnu', 'Oeu001701.1' => 'oeu', 'Oeu018149.1' => 'oeu', 'Oeu026220.1' => 'oeu', 'Oeu038635.1' => 'oeu', 'Oeu049176.1' => 'oeu', 'Oeu056706.1' => 'oeu', 'Oeu056937.1' => 'oeu', 'Oeu057540.1' => 'oeu', 'Os02g0594900' => 'osa', 'Os02g0595100' => 'osa', 'Os04g0477500' => 'osa', 'Os12g0611900' => 'osa', 'Peaxi162Scf00076g00020' => 'pax', 'Peaxi162Scf00128g00217' => 'pax', 'Peaxi162Scf00129g01640' => 'pax', 'Peaxi162Scf00669g00007' => 'pax', 'Peaxi162Scf00700g00421' => 'pax', 'Peaxi162Scf00801g00038' => 'pax', 'Peaxi162Scf00891g00025' => 'pax', 'PGR083G0909' => 'pgr', 'PGR119G1005' => 'pgr', 'PGR142G2236' => 'pgr', 'PGR142G3388' => 'pgr', 'PGSC0003DMG400004514' => 'stu', 'PGSC0003DMG400012635' => 'stu', 'PGSC0003DMG400015730' => 'stu', 'PGSC0003DMG400018611' => 'stu', 'PGSC0003DMG400030897' => 'stu', 'Phvul.001G254800' => 'pvu', 'Phvul.002G260100' => 'pvu', 'Phvul.003G167600' => 'pvu', 'Phvul.004G005100' => 'pvu', 'Potri.001G343600' => 'ptr', 'Potri.006G066700' => 'ptr', 'Potri.008G186000' => 'ptr', 'Potri.010G046900' => 'ptr', 'Potri.018G127900' => 'ptr', 'Pp3c20_17750' => 'ppa', 'Pp3c24_4380' => 'ppa', 'Prupe.1G245800' => 'ppe', 'Prupe.3G293400' => 'ppe', 'Prupe.7G247400' => 'ppe', 'Psat0s145g0120' => 'psa', 'Psat0s595g0040' => 'psa', 'Psat0s595g0120' => 'psa', 'Psat3g175040' => 'psa', 'Psat7g058120' => 'psa', 'PSO017G0428' => 'pso', 'PSO063G7510' => 'pso', 'PSO067G0046' => 'pso', 'PSO478G1073' => 'pso', 'PSO675G3677' => 'pso', 'PSO675G6558' => 'pso', 'PSO675G7520' => 'pso', 'PSO675G8959' => 'pso', 'QL02p074089' => 'qlo', 'QL02p089614' => 'qlo', 'QL03p057736' => 'qlo', 'RcHm_v2.0_Chr1g0364131' => 'rch', 'RcHm_v2.0_Chr2g0087801' => 'rch', 'RcHm_v2.0_Chr2g0087821' => 'rch', 'RcHm_v2.0_Chr2g0173231' => 'rch', 'RcHm_v2.0_Chr4g0433111' => 'rch', 'Rhsim03G0250300' => 'rsi', 'Rhsim08G0048400' => 'rsi', 'Rhsim10G0014800' => 'rsi', 'Rhsim12G0040100' => 'rsi', 'Rhsim12G0109700' => 'rsi', 'Sabra06G0049600' => 'sbr', 'Sabra08G0141000' => 'sbr', 'Sabra10G0021400' => 'sbr', 'Sabra16G0222900' => 'sbr', 'Sabra18G0108600' => 'sbr', 'SalBow1G0433' => 'sbo', 'SalBow1G2038' => 'sbo', 'SalBow1G5003' => 'sbo', 'SalBow7G1197' => 'sbo', 'SalBow8G3506' => 'sbo', 'Sc03g0007300' => 'sci', 'Sc11g0000950' => 'sci', 'Sc14g0008750' => 'sci', 'Sc18g0000420' => 'sci', 'Sed0006754' => 'sed', 'Sed0008741' => 'sed', 'Sed0017172' => 'sed', 'Sed0018925' => 'sed', 'Sed0023326' => 'sed', 'Sed0025909' => 'sed', 'SEGI_05333' => 'sgi', 'SEGI_10362' => 'sgi', 'SEGI_13380' => 'sgi', 'SEGI_24306' => 'sgi', 'SEGI_29077' => 'sgi', 'SEGI_29095' => 'sgi', 'SEGI_36534' => 'sgi', 'SEGI_37506' => 'sgi', 'SEGI_38321' => 'sgi', 'SGA_v2.0_scaffold307G48031' => 'sas', 'SGA_v2.0_scaffold47G17507' => 'sas', 'SGA_v2.0_scaffold63G21736' => 'sas', 'SGA_v2.0_scaffold87G27070' => 'sas', 'SHI17794' => 'shi', 'SHI28851' => 'shi', 'SMO165G0155' => 'smo', 'SMO340G0217' => 'smo', 'SMO367G1210' => 'smo', 'Solyc02g093430.3' => 'sly', 'Solyc05g013580.4' => 'sly', 'Solyc07g008030.3' => 'sly', 'Solyc12g035470.2' => 'sly', 'Sopen02g038020' => 'spe', 'Sopen05g008490' => 'spe', 'Sopen07g003910' => 'spe', 'Sopen12g015240' => 'spe', 'Sp1g11550' => 'spa', 'Sp2g16710' => 'spa', 'Sp3g00430' => 'spa', 'Sp3g26780' => 'spa', 'Sp5g22900' => 'spa', 'Sp6g29530' => 'spa', 'TAR371G0794' => 'tar', 'TAR374G0164' => 'tar', 'TAR622G0165' => 'tar', 'TAR626G0929' => 'tar', 'TAR629G2155' => 'tar', 'THA.LOC104805282' => 'tha', 'THA.LOC104805363' => 'tha', 'THA.LOC104808968' => 'tha', 'THA.LOC104821093' => 'tha', 'THA.LOC104823953' => 'tha', 'THA.LOC104825562' => 'tha', 'THA.LOC104825665' => 'tha', 'Thecc.02G261400' => 'tca', 'Thecc.04G019200' => 'tca', 'Thecc.09G130400' => 'tca', 'Thhalv10004374m.g' => 'esa', 'Thhalv10007850m.g' => 'esa', 'Thhalv10013782m.g' => 'esa', 'Thhalv10018686m.g' => 'esa', 'Thhalv10020899m.g' => 'esa', 'Thhalv10022755m.g' => 'esa', 'TPR.G23851' => 'tpr', 'TPR.G26500' => 'tpr', 'TPR.G27267' => 'tpr', 'TPR.G32001' => 'tpr', 'TPR.G6251' => 'tpr', 'TPR.G8167' => 'tpr', 'TWI12G1330' => 'twi', 'TWI18G1239' => 'twi', 'TWI34G0979' => 'twi', 'TWI36G0670' => 'twi', 'TWI36G0707' => 'twi', 'TWI56G0233' => 'twi', 'TWI75G1809' => 'twi', 'unitig_21.g20874' => 'ugi', 'unitig_26.g10343' => 'ugi', 'unitig_46.g18392' => 'ugi', 'unitig_52.g17178' => 'ugi', 'unitig_8.g2934' => 'ugi', 'vmacro01122' => 'vma', 'vmacro05875' => 'vma', 'vmacro06147' => 'vma', 'vmacro16191' => 'vma', 'vmacro18293' => 'vma', 'VMungo0251G3707' => 'vmu', 'VMungo0464G1521' => 'vmu', 'VMungo1215G0205' => 'vmu', 'VMungo1383G2484' => 'vmu', 'Zm00001eb079610' => 'zma', 'Zm00001eb135990' => 'zma', 'Zm00001eb183710' => 'zma', 'Zm00001eb246020' => 'zma' ) $gf_id = 'HOM05D001124' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001124' ) $data_identifier = 'HOM05D001124' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 6, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 7, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 21, 'bol' => (int) 10, 'bra' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 6, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 9, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 21, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 8, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 10, 'lsa' => (int) 8, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 8, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 9, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb246020' $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' => 'HOM05D001124', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '548', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02520' => 'bna', 'A03p06630' => 'bna', 'A05p44460' => 'bna', 'A06p08710' => 'bna', 'A06p41090' => 'bna', 'A07p32320' => 'bna', 'A08p32520' => 'bna', 'A09p10360' => 'bna', 'A10p24080' => 'bna', 'Aa31LG11G15250' => 'aar', 'Aa31LG1G1800' => 'aar', 'Aa31LG2G5120' => 'aar', 'Aa31LG2G6070' => 'aar', 'Aa31LG5G10770' => 'aar', 'Aa31sc61G90' => 'aar', 'Actinidia01352' => 'ach', 'Actinidia05983' => 'ach', 'Actinidia08133' => 'ach', 'Actinidia15101' => 'ach', 'Actinidia26379' => 'ach', 'Actinidia35778' => 'ach', 'Actinidia36123' => 'ach', 'Actinidia37436' => 'ach', 'Actinidia38730' => 'ach', 'Ah.02g128210' => 'amhyb', 'Ah.03g132990' => 'amhyb', 'Ah.14g079410' => 'amhyb', 'AL1G24640' => 'aly', 'AL2G26680' => 'aly', 'AL3G10530' => 'aly', 'AL3G45230' => 'aly', 'AL5G15230' => 'aly', 'AL5G16960' => 'aly', 'AL6G25210' => 'aly', 'Aqoxy2G00441' => 'aox', 'Aqoxy3G01236' => 'aox', 'Aqoxy5G03746' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3RQ047' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C7GMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9C8JER' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MBL6KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YXCZ83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZANX40' => 'arhy', 'AT1G12990' => 'ath', 'AT1G67880' => 'ath', 'AT2G13290' => 'ath', 'AT3G01620' => 'ath', 'AT3G26445' => 'ath', 'AT3G27540' => 'ath', 'AT5G14480' => 'ath', 'ATR0824G026' => 'atr', 'ATR1098G019' => 'atr', 'Atru.chr11.2145' => 'acertr', 'Atru.chr2.3636' => 'acertr', 'Atru.chr2.3644' => 'acertr', 'Atru.chr6.2422' => 'acertr', 'Atru.chr7.1112' => 'acertr', 'AUR62005469' => 'cqu', 'AUR62011166' => 'cqu', 'AUR62013319' => 'cqu', 'AUR62024273' => 'cqu', 'AUR62028420' => 'cqu', 'AUR62041942' => 'cqu', 'BcaB01g04969' => 'bca', 'BcaB01g06371' => 'bca', 'BcaB02g11494' => 'bca', 'BcaB03g15382' => 'bca', 'BcaB08g36994' => 'bca', 'BcaC03g13477' => 'bca', 'BcaC03g13478' => 'bca', 'BcaC03g13480' => 'bca', 'BcaC03g13481' => 'bca', 'BcaC03g13486' => 'bca', 'BcaC04g19031' => 'bca', 'BcaC04g23085' => 'bca', 'BcaC05g25094' => 'bca', 'BcaC05g25096' => 'bca', 'BcaC05g25138' => 'bca', 'BcaC05g30416' => 'bca', 'BcaC05g30455' => 'bca', 'BcaC06g30979' => 'bca', 'BcaC06g33805' => 'bca', 'BcaC08g46021' => 'bca', 'BcaNung03154' => 'bca', 'BolC2t06623H' => 'bol', 'BolC2t06632H' => 'bol', 'BolC2t06635H' => 'bol', 'BolC2t06638H' => 'bol', 'BolC3t13266H' => 'bol', 'BolC5t29776H' => 'bol', 'BolC6t38912H' => 'bol', 'BolC7t44183H' => 'bol', 'BolC9t54123H' => 'bol', 'BolC9t59107H' => 'bol', 'BraA02t05221Z' => 'bra', 'BraA03t09996Z' => 'bra', 'BraA05t23210Z' => 'bra', 'BraA06t24068Z' => 'bra', 'BraA06t27032Z' => 'bra', 'BraA08t35176Z' => 'bra', 'BraA09t36680Z' => 'bra', 'BraA10t44471Z' => 'bra', 'C02p06760' => 'bna', 'C02p06890' => 'bna', 'C02p07010' => 'bna', 'C03p07660' => 'bna', 'C05p10300' => 'bna', 'C06p38150' => 'bna', 'C07p36650' => 'bna', 'C08p15770' => 'bna', 'C09p12300' => 'bna', 'C09p62700' => 'bna', 'C09p75040' => 'bna', 'CAN.G13.1' => 'can', 'CAN.G138.4' => 'can', 'CAN.G44.6' => 'can', 'CAN.G473.19' => 'can', 'CANSAT01G0835' => 'cansat', 'CANSAT11G0246' => 'cansat', 'CANSAT11G1766' => 'cansat', 'CANSAT64G1954' => 'cansat', 'CARHR013330' => 'chi', 'CARHR060530' => 'chi', 'CARHR075300' => 'chi', 'CARHR105120' => 'chi', 'CARHR148910' => 'chi', 'CARHR198830' => 'chi', 'Carub.0001s1275' => 'cru', 'Carub.0002s1437' => 'cru', 'Carub.0003s0044' => 'cru', 'Carub.0003s2787' => 'cru', 'Carub.0005s0597' => 'cru', 'Carub.0006s1266' => 'cru', 'Ca_06935_v3' => 'car', 'Ca_13559_v3' => 'car', 'Ca_16941_v3' => 'car', 'Ca_16960_v3' => 'car', 'Ca_17775_v3' => 'car', 'Ca_30464_v3' => 'car', 'Cc06_g08160' => 'ccan', 'Cc07_g01520' => 'ccan', 'Cc11_g15810' => 'ccan', 'CDE02G2840' => 'cde', 'CDE03G0093' => 'cde', 'CDE04G2127' => 'cde', 'CDE07G1857' => 'cde', 'CDE09G1246' => 'cde', 'Cfa003412' => 'cfa', 'Cfa007341' => 'cfa', 'Cfa009220' => 'cfa', 'Ciclev10008737m.g' => 'ccl', 'Ciclev10015565m.g' => 'ccl', 'Ciclev10031761m.g' => 'ccl', 'CiPaw.03G045300' => 'cil', 'CiPaw.03G247200' => 'cil', 'CiPaw.04G029500' => 'cil', 'CiPaw.04G174000' => 'cil', 'CiPaw.05G181200' => 'cil', 'CiPaw.06G067100' => 'cil', 'ClCG05G025800' => 'cla', 'ClCG06G011400' => 'cla', 'ClCG09G019360' => 'cla', 'COL.COLO4_04827' => 'col', 'COL.COLO4_29170' => 'col', 'COL.COLO4_35131' => 'col', 'COL.COLO4_35132' => 'col', 'Cpa.g.sc33.32' => 'cpa', 'Cpa.g.sc46.29' => 'cpa', 'Cpa.g.sc796.1' => 'cpa', 'CsaV3_1G030420' => 'csa', 'CsaV3_5G027050' => 'csa', 'CsaV3_5G031040' => 'csa', 'CsaV3_UNG023130' => 'csa', 'CSS0007726' => 'camsi', 'CSS0016433' => 'camsi', 'CSS0017656' => 'camsi', 'CSS0025364' => 'camsi', 'CSS0027582' => 'camsi', 'CSS0047288' => 'camsi', 'CSS0049950' => 'camsi', 'DCAR_003843' => 'dca', 'DCAR_007052' => 'dca', 'DCAR_020884' => 'dca', 'DCAR_021730' => 'dca', 'DCAR_024423' => 'dca', 'DCAR_026509' => 'dca', 'DCAR_031158' => 'dca', 'Dinv14728' => 'din', 'Dinv15219' => 'din', 'Dinv25728' => 'din', 'Dinv33428' => 'din', 'Dinv36489' => 'din', 'Dinv41486' => 'din', 'Duzib147G0469' => 'dzi', 'Duzib168G0060' => 'dzi', 'Duzib187G1215' => 'dzi', 'Duzib248G0692' => 'dzi', 'Duzib251G0767' => 'dzi', 'Duzib264G0446' => 'dzi', 'Duzib268G0691' => 'dzi', 'ECA232G4767' => 'eca', 'ECA233G2838' => 'eca', 'ECA234G0391' => 'eca', 'ECA234G0857' => 'eca', 'ECA236G1593' => 'eca', 'ECA238G0565' => 'eca', 'ECA246G1027' => 'eca', 'ECA246G3223' => 'eca', 'ECA246G3470' => 'eca', 'EL10Ac6g13829' => 'bvu', 'EL10Ac6g14093' => 'bvu', 'EL10Ac8g18707' => 'bvu', 'Eucgr.C01369' => 'egr', 'Eucgr.H02492' => 'egr', 'Eucgr.I01733' => 'egr', 'Eucgr.J02255' => 'egr', 'Eucgr.J02257' => 'egr', 'Eucgr.J02258' => 'egr', 'FAN02G1601' => 'fan', 'FAN03G1586' => 'fan', 'FAN03G2986' => 'fan', 'FAN05G4837' => 'fan', 'FAN06G0146' => 'fan', 'FAN07G0858' => 'fan', 'FAN09G3179' => 'fan', 'FAN10G0669' => 'fan', 'FAN12G2358' => 'fan', 'FAN14G4198' => 'fan', 'FAN14G5112' => 'fan', 'FAN17G0342' => 'fan', 'FAN19G0342' => 'fan', 'FAN19G0962' => 'fan', 'FAN19G1101' => 'fan', 'FAN19G1872' => 'fan', 'FAN22G0356' => 'fan', 'FAN23G0744' => 'fan', 'FAN23G1914' => 'fan', 'FAN26G0032' => 'fan', 'FAN28G0625' => 'fan', 'FvH4_1g02710' => 'fve', 'FvH4_1g02720' => 'fve', 'FvH4_4g25670' => 'fve', 'FvH4_6g51700' => 'fve', 'FvH4_7g20170' => 'fve', 'Glyma.05G175000' => 'gma', 'Glyma.08G132300' => 'gma', 'Glyma.11G243000' => 'gma', 'Glyma.13G158900' => 'gma', 'Glyma.17G112400' => 'gma', 'Glyma.18G014100' => 'gma', 'Glyma.19G003100' => 'gma', 'Glyma.19G056500' => 'gma', 'Gohir.A01G158900' => 'ghi', 'Gohir.A05G312600' => 'ghi', 'Gohir.A05G354900' => 'ghi', 'Gohir.A07G037200' => 'ghi', 'Gohir.A09G030000' => 'ghi', 'Gohir.A12G145200' => 'ghi', 'Gohir.D01G151500' => 'ghi', 'Gohir.D04G058300' => 'ghi', 'Gohir.D05G314100' => 'ghi', 'Gohir.D07G041400' => 'ghi', 'Gohir.D09G029700' => 'ghi', 'Gohir.D12G149700' => 'ghi', 'Gorai.001G043800' => 'gra', 'Gorai.002G187800' => 'gra', 'Gorai.006G034700' => 'gra', 'Gorai.008G161200' => 'gra', 'Gorai.009G335700' => 'gra', 'Gorai.012G065000' => 'gra', 'GSVIVG01000535001' => 'vvi', 'GSVIVG01015572001' => 'vvi', 'GSVIVG01032386001' => 'vvi', 'HanXRQChr05g0138531' => 'han', 'HanXRQChr06g0174391' => 'han', 'HanXRQChr07g0199021' => 'han', 'HanXRQChr08g0208211' => 'han', 'HanXRQChr09g0255471' => 'han', 'HanXRQChr10g0315791' => 'han', 'HanXRQChr12g0371991' => 'han', 'HanXRQChr15g0475251' => 'han', 'HanXRQChr17g0540001' => 'han', 'HanXRQChr17g0548631' => 'han', 'HanXRQChr17g0569561' => 'han', 'Haze_12256' => 'cav', 'Haze_14756' => 'cav', 'Haze_25528' => 'cav', 'Hma1.2p1_0079F.1_g041020' => 'hma', 'Hma1.2p1_0818F.1_g223260' => 'hma', 'Hma1.2p1_1747F.1_g300530' => 'hma', 'HPP92_004607' => 'vpl', 'HPP92_004608' => 'vpl', 'HPP92_006181' => 'vpl', 'HPP92_012192' => 'vpl', 'HPP92_015680' => 'vpl', 'HPP92_020249' => 'vpl', 'HPP92_021376' => 'vpl', 'HPP92_024275' => 'vpl', 'Hund06031' => 'sun', 'Hund25391' => 'sun', 'Lalb_Chr07g0185371' => 'lal', 'Lalb_Chr07g0185381' => 'lal', 'Lalb_Chr12g0204011' => 'lal', 'Lalb_Chr13g0301671' => 'lal', 'Lalb_Chr14g0362851' => 'lal', 'Lalb_Chr24g0403581' => 'lal', 'Lj1g0000233' => 'lja', 'Lj2g0018120' => 'lja', 'Lj3C621T0' => 'lonja', 'Lj3P1059T14' => 'lonja', 'Lj3P611T9' => 'lonja', 'Lj3P614T13' => 'lonja', 'Lj3P615T5' => 'lonja', 'Lj4g0012315' => 'lja', 'Lj4g0026182' => 'lja', 'Lj6P813T16' => 'lonja', 'Lj7C427T7' => 'lonja', 'Lj7C427T8' => 'lonja', 'Lj7P600T41' => 'lonja', 'Lju41C42G17' => 'lonja', 'Lsat_1_v5_gn_0_47300' => 'lsa', 'Lsat_1_v5_gn_2_91280' => 'lsa', 'Lsat_1_v5_gn_3_30561' => 'lsa', 'Lsat_1_v5_gn_4_184321' => 'lsa', 'Lsat_1_v5_gn_4_4041' => 'lsa', 'Lsat_1_v5_gn_5_92000' => 'lsa', 'Lsat_1_v5_gn_8_152940' => 'lsa', 'Lsat_1_v5_gn_8_62401' => 'lsa', 'Manes.06G055900' => 'mes', 'Manes.12G022200' => 'mes', 'Manes.13G023300' => 'mes', 'Manes.14G115000' => 'mes', 'Manes.15G151700' => 'mes', 'Manes.17G111300' => 'mes', 'Mapoly0226s0009' => 'mpo', 'MBI02_g25363_MAGBIO' => 'mbi', 'MBI06_g00027_MAGBIO' => 'mbi', 'MBI10_g13034_MAGBIO' => 'mbi', 'MD09G1023400' => 'mdo', 'MD13G1100100' => 'mdo', 'MD15G1169200' => 'mdo', 'MD16G1101100' => 'mdo', 'MD17G1022900' => 'mdo', 'Medtr3g096150' => 'mtr', 'Medtr4g115070' => 'mtr', 'Medtr7g033325' => 'mtr', 'Medtr8g089840' => 'mtr', 'MELO3C010319.2' => 'cme', 'MELO3C011944.2' => 'cme', 'MELO3C021589.2' => 'cme', 'Migut.E00207' => 'egut', 'Migut.H00067' => 'egut', 'Migut.K00433' => 'egut', 'Migut.K00606' => 'egut', 'Migut.K01410' => 'egut', 'MSTRG.13347' => 'ama', 'MSTRG.24045' => 'ama', 'MSTRG.2428' => 'ama', 'MSTRG.26410' => 'ama', 'MSTRG.3139' => 'ama', 'MSTRG.3286' => 'ama', 'MSTRG.563' => 'ama', 'MSTRG.7941' => 'ama', 'Nitab4.5_0000028g0060' => 'nta', 'Nitab4.5_0000065g0260' => 'nta', 'Nitab4.5_0000112g0060' => 'nta', 'Nitab4.5_0000489g0120' => 'nta', 'Nitab4.5_0001776g0050' => 'nta', 'Nitab4.5_0001854g0010' => 'nta', 'Nitab4.5_0001860g0020' => 'nta', 'Nitab4.5_0004352g0010' => 'nta', 'Nitab4.5_0008716g0020' => 'nta', 'Nitab4.5_0008922g0010' => 'nta', 'Nn3g16693' => 'nnu', 'Nn4g22596' => 'nnu', 'Nn7g37639' => 'nnu', 'Oeu001701.1' => 'oeu', 'Oeu018149.1' => 'oeu', 'Oeu026220.1' => 'oeu', 'Oeu038635.1' => 'oeu', 'Oeu049176.1' => 'oeu', 'Oeu056706.1' => 'oeu', 'Oeu056937.1' => 'oeu', 'Oeu057540.1' => 'oeu', 'Os02g0594900' => 'osa', 'Os02g0595100' => 'osa', 'Os04g0477500' => 'osa', 'Os12g0611900' => 'osa', 'Peaxi162Scf00076g00020' => 'pax', 'Peaxi162Scf00128g00217' => 'pax', 'Peaxi162Scf00129g01640' => 'pax', 'Peaxi162Scf00669g00007' => 'pax', 'Peaxi162Scf00700g00421' => 'pax', 'Peaxi162Scf00801g00038' => 'pax', 'Peaxi162Scf00891g00025' => 'pax', 'PGR083G0909' => 'pgr', 'PGR119G1005' => 'pgr', 'PGR142G2236' => 'pgr', 'PGR142G3388' => 'pgr', 'PGSC0003DMG400004514' => 'stu', 'PGSC0003DMG400012635' => 'stu', 'PGSC0003DMG400015730' => 'stu', 'PGSC0003DMG400018611' => 'stu', 'PGSC0003DMG400030897' => 'stu', 'Phvul.001G254800' => 'pvu', 'Phvul.002G260100' => 'pvu', 'Phvul.003G167600' => 'pvu', 'Phvul.004G005100' => 'pvu', 'Potri.001G343600' => 'ptr', 'Potri.006G066700' => 'ptr', 'Potri.008G186000' => 'ptr', 'Potri.010G046900' => 'ptr', 'Potri.018G127900' => 'ptr', 'Pp3c20_17750' => 'ppa', 'Pp3c24_4380' => 'ppa', 'Prupe.1G245800' => 'ppe', 'Prupe.3G293400' => 'ppe', 'Prupe.7G247400' => 'ppe', 'Psat0s145g0120' => 'psa', 'Psat0s595g0040' => 'psa', 'Psat0s595g0120' => 'psa', 'Psat3g175040' => 'psa', 'Psat7g058120' => 'psa', 'PSO017G0428' => 'pso', 'PSO063G7510' => 'pso', 'PSO067G0046' => 'pso', 'PSO478G1073' => 'pso', 'PSO675G3677' => 'pso', 'PSO675G6558' => 'pso', 'PSO675G7520' => 'pso', 'PSO675G8959' => 'pso', 'QL02p074089' => 'qlo', 'QL02p089614' => 'qlo', 'QL03p057736' => 'qlo', 'RcHm_v2.0_Chr1g0364131' => 'rch', 'RcHm_v2.0_Chr2g0087801' => 'rch', 'RcHm_v2.0_Chr2g0087821' => 'rch', 'RcHm_v2.0_Chr2g0173231' => 'rch', 'RcHm_v2.0_Chr4g0433111' => 'rch', 'Rhsim03G0250300' => 'rsi', 'Rhsim08G0048400' => 'rsi', 'Rhsim10G0014800' => 'rsi', 'Rhsim12G0040100' => 'rsi', 'Rhsim12G0109700' => 'rsi', 'Sabra06G0049600' => 'sbr', 'Sabra08G0141000' => 'sbr', 'Sabra10G0021400' => 'sbr', 'Sabra16G0222900' => 'sbr', 'Sabra18G0108600' => 'sbr', 'SalBow1G0433' => 'sbo', 'SalBow1G2038' => 'sbo', 'SalBow1G5003' => 'sbo', 'SalBow7G1197' => 'sbo', 'SalBow8G3506' => 'sbo', 'Sc03g0007300' => 'sci', 'Sc11g0000950' => 'sci', 'Sc14g0008750' => 'sci', 'Sc18g0000420' => 'sci', 'Sed0006754' => 'sed', 'Sed0008741' => 'sed', 'Sed0017172' => 'sed', 'Sed0018925' => 'sed', 'Sed0023326' => 'sed', 'Sed0025909' => 'sed', 'SEGI_05333' => 'sgi', 'SEGI_10362' => 'sgi', 'SEGI_13380' => 'sgi', 'SEGI_24306' => 'sgi', 'SEGI_29077' => 'sgi', 'SEGI_29095' => 'sgi', 'SEGI_36534' => 'sgi', 'SEGI_37506' => 'sgi', 'SEGI_38321' => 'sgi', 'SGA_v2.0_scaffold307G48031' => 'sas', 'SGA_v2.0_scaffold47G17507' => 'sas', 'SGA_v2.0_scaffold63G21736' => 'sas', 'SGA_v2.0_scaffold87G27070' => 'sas', 'SHI17794' => 'shi', 'SHI28851' => 'shi', 'SMO165G0155' => 'smo', 'SMO340G0217' => 'smo', 'SMO367G1210' => 'smo', 'Solyc02g093430.3' => 'sly', 'Solyc05g013580.4' => 'sly', 'Solyc07g008030.3' => 'sly', 'Solyc12g035470.2' => 'sly', 'Sopen02g038020' => 'spe', 'Sopen05g008490' => 'spe', 'Sopen07g003910' => 'spe', 'Sopen12g015240' => 'spe', 'Sp1g11550' => 'spa', 'Sp2g16710' => 'spa', 'Sp3g00430' => 'spa', 'Sp3g26780' => 'spa', 'Sp5g22900' => 'spa', 'Sp6g29530' => 'spa', 'TAR371G0794' => 'tar', 'TAR374G0164' => 'tar', 'TAR622G0165' => 'tar', 'TAR626G0929' => 'tar', 'TAR629G2155' => 'tar', 'THA.LOC104805282' => 'tha', 'THA.LOC104805363' => 'tha', 'THA.LOC104808968' => 'tha', 'THA.LOC104821093' => 'tha', 'THA.LOC104823953' => 'tha', 'THA.LOC104825562' => 'tha', 'THA.LOC104825665' => 'tha', 'Thecc.02G261400' => 'tca', 'Thecc.04G019200' => 'tca', 'Thecc.09G130400' => 'tca', 'Thhalv10004374m.g' => 'esa', 'Thhalv10007850m.g' => 'esa', 'Thhalv10013782m.g' => 'esa', 'Thhalv10018686m.g' => 'esa', 'Thhalv10020899m.g' => 'esa', 'Thhalv10022755m.g' => 'esa', 'TPR.G23851' => 'tpr', 'TPR.G26500' => 'tpr', 'TPR.G27267' => 'tpr', 'TPR.G32001' => 'tpr', 'TPR.G6251' => 'tpr', 'TPR.G8167' => 'tpr', 'TWI12G1330' => 'twi', 'TWI18G1239' => 'twi', 'TWI34G0979' => 'twi', 'TWI36G0670' => 'twi', 'TWI36G0707' => 'twi', 'TWI56G0233' => 'twi', 'TWI75G1809' => 'twi', 'unitig_21.g20874' => 'ugi', 'unitig_26.g10343' => 'ugi', 'unitig_46.g18392' => 'ugi', 'unitig_52.g17178' => 'ugi', 'unitig_8.g2934' => 'ugi', 'vmacro01122' => 'vma', 'vmacro05875' => 'vma', 'vmacro06147' => 'vma', 'vmacro16191' => 'vma', 'vmacro18293' => 'vma', 'VMungo0251G3707' => 'vmu', 'VMungo0464G1521' => 'vmu', 'VMungo1215G0205' => 'vmu', 'VMungo1383G2484' => 'vmu', 'Zm00001eb079610' => 'zma', 'Zm00001eb135990' => 'zma', 'Zm00001eb183710' => 'zma', 'Zm00001eb246020' => 'zma' ), 'gf_id' => 'HOM05D001124', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001124' ), 'data_identifier' => 'HOM05D001124', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001124', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '548', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02520' => 'bna', 'A03p06630' => 'bna', 'A05p44460' => 'bna', 'A06p08710' => 'bna', 'A06p41090' => 'bna', 'A07p32320' => 'bna', 'A08p32520' => 'bna', 'A09p10360' => 'bna', 'A10p24080' => 'bna', 'Aa31LG11G15250' => 'aar', 'Aa31LG1G1800' => 'aar', 'Aa31LG2G5120' => 'aar', 'Aa31LG2G6070' => 'aar', 'Aa31LG5G10770' => 'aar', 'Aa31sc61G90' => 'aar', 'Actinidia01352' => 'ach', 'Actinidia05983' => 'ach', 'Actinidia08133' => 'ach', 'Actinidia15101' => 'ach', 'Actinidia26379' => 'ach', 'Actinidia35778' => 'ach', 'Actinidia36123' => 'ach', 'Actinidia37436' => 'ach', 'Actinidia38730' => 'ach', 'Ah.02g128210' => 'amhyb', 'Ah.03g132990' => 'amhyb', 'Ah.14g079410' => 'amhyb', 'AL1G24640' => 'aly', 'AL2G26680' => 'aly', 'AL3G10530' => 'aly', 'AL3G45230' => 'aly', 'AL5G15230' => 'aly', 'AL5G16960' => 'aly', 'AL6G25210' => 'aly', 'Aqoxy2G00441' => 'aox', 'Aqoxy3G01236' => 'aox', 'Aqoxy5G03746' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3RQ047' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C7GMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9C8JER' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MBL6KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YXCZ83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZANX40' => 'arhy', 'AT1G12990' => 'ath', 'AT1G67880' => 'ath', 'AT2G13290' => 'ath', 'AT3G01620' => 'ath', 'AT3G26445' => 'ath', 'AT3G27540' => 'ath', 'AT5G14480' => 'ath', 'ATR0824G026' => 'atr', 'ATR1098G019' => 'atr', 'Atru.chr11.2145' => 'acertr', 'Atru.chr2.3636' => 'acertr', 'Atru.chr2.3644' => 'acertr', 'Atru.chr6.2422' => 'acertr', 'Atru.chr7.1112' => 'acertr', 'AUR62005469' => 'cqu', 'AUR62011166' => 'cqu', 'AUR62013319' => 'cqu', 'AUR62024273' => 'cqu', 'AUR62028420' => 'cqu', 'AUR62041942' => 'cqu', 'BcaB01g04969' => 'bca', 'BcaB01g06371' => 'bca', 'BcaB02g11494' => 'bca', 'BcaB03g15382' => 'bca', 'BcaB08g36994' => 'bca', 'BcaC03g13477' => 'bca', 'BcaC03g13478' => 'bca', 'BcaC03g13480' => 'bca', 'BcaC03g13481' => 'bca', 'BcaC03g13486' => 'bca', 'BcaC04g19031' => 'bca', 'BcaC04g23085' => 'bca', 'BcaC05g25094' => 'bca', 'BcaC05g25096' => 'bca', 'BcaC05g25138' => 'bca', 'BcaC05g30416' => 'bca', 'BcaC05g30455' => 'bca', 'BcaC06g30979' => 'bca', 'BcaC06g33805' => 'bca', 'BcaC08g46021' => 'bca', 'BcaNung03154' => 'bca', 'BolC2t06623H' => 'bol', 'BolC2t06632H' => 'bol', 'BolC2t06635H' => 'bol', 'BolC2t06638H' => 'bol', 'BolC3t13266H' => 'bol', 'BolC5t29776H' => 'bol', 'BolC6t38912H' => 'bol', 'BolC7t44183H' => 'bol', 'BolC9t54123H' => 'bol', 'BolC9t59107H' => 'bol', 'BraA02t05221Z' => 'bra', 'BraA03t09996Z' => 'bra', 'BraA05t23210Z' => 'bra', 'BraA06t24068Z' => 'bra', 'BraA06t27032Z' => 'bra', 'BraA08t35176Z' => 'bra', 'BraA09t36680Z' => 'bra', 'BraA10t44471Z' => 'bra', 'C02p06760' => 'bna', 'C02p06890' => 'bna', 'C02p07010' => 'bna', 'C03p07660' => 'bna', 'C05p10300' => 'bna', 'C06p38150' => 'bna', 'C07p36650' => 'bna', 'C08p15770' => 'bna', 'C09p12300' => 'bna', 'C09p62700' => 'bna', 'C09p75040' => 'bna', 'CAN.G13.1' => 'can', 'CAN.G138.4' => 'can', 'CAN.G44.6' => 'can', 'CAN.G473.19' => 'can', 'CANSAT01G0835' => 'cansat', 'CANSAT11G0246' => 'cansat', 'CANSAT11G1766' => 'cansat', 'CANSAT64G1954' => 'cansat', 'CARHR013330' => 'chi', 'CARHR060530' => 'chi', 'CARHR075300' => 'chi', 'CARHR105120' => 'chi', 'CARHR148910' => 'chi', 'CARHR198830' => 'chi', 'Carub.0001s1275' => 'cru', 'Carub.0002s1437' => 'cru', 'Carub.0003s0044' => 'cru', 'Carub.0003s2787' => 'cru', 'Carub.0005s0597' => 'cru', 'Carub.0006s1266' => 'cru', 'Ca_06935_v3' => 'car', 'Ca_13559_v3' => 'car', 'Ca_16941_v3' => 'car', 'Ca_16960_v3' => 'car', 'Ca_17775_v3' => 'car', 'Ca_30464_v3' => 'car', 'Cc06_g08160' => 'ccan', 'Cc07_g01520' => 'ccan', 'Cc11_g15810' => 'ccan', 'CDE02G2840' => 'cde', 'CDE03G0093' => 'cde', 'CDE04G2127' => 'cde', 'CDE07G1857' => 'cde', 'CDE09G1246' => 'cde', 'Cfa003412' => 'cfa', 'Cfa007341' => 'cfa', 'Cfa009220' => 'cfa', 'Ciclev10008737m.g' => 'ccl', 'Ciclev10015565m.g' => 'ccl', 'Ciclev10031761m.g' => 'ccl', 'CiPaw.03G045300' => 'cil', 'CiPaw.03G247200' => 'cil', 'CiPaw.04G029500' => 'cil', 'CiPaw.04G174000' => 'cil', 'CiPaw.05G181200' => 'cil', 'CiPaw.06G067100' => 'cil', 'ClCG05G025800' => 'cla', 'ClCG06G011400' => 'cla', 'ClCG09G019360' => 'cla', 'COL.COLO4_04827' => 'col', 'COL.COLO4_29170' => 'col', 'COL.COLO4_35131' => 'col', 'COL.COLO4_35132' => 'col', 'Cpa.g.sc33.32' => 'cpa', 'Cpa.g.sc46.29' => 'cpa', 'Cpa.g.sc796.1' => 'cpa', 'CsaV3_1G030420' => 'csa', 'CsaV3_5G027050' => 'csa', 'CsaV3_5G031040' => 'csa', 'CsaV3_UNG023130' => 'csa', 'CSS0007726' => 'camsi', 'CSS0016433' => 'camsi', 'CSS0017656' => 'camsi', 'CSS0025364' => 'camsi', 'CSS0027582' => 'camsi', 'CSS0047288' => 'camsi', 'CSS0049950' => 'camsi', 'DCAR_003843' => 'dca', 'DCAR_007052' => 'dca', 'DCAR_020884' => 'dca', 'DCAR_021730' => 'dca', 'DCAR_024423' => 'dca', 'DCAR_026509' => 'dca', 'DCAR_031158' => 'dca', 'Dinv14728' => 'din', 'Dinv15219' => 'din', 'Dinv25728' => 'din', 'Dinv33428' => 'din', 'Dinv36489' => 'din', 'Dinv41486' => 'din', 'Duzib147G0469' => 'dzi', 'Duzib168G0060' => 'dzi', 'Duzib187G1215' => 'dzi', 'Duzib248G0692' => 'dzi', 'Duzib251G0767' => 'dzi', 'Duzib264G0446' => 'dzi', 'Duzib268G0691' => 'dzi', 'ECA232G4767' => 'eca', 'ECA233G2838' => 'eca', 'ECA234G0391' => 'eca', 'ECA234G0857' => 'eca', 'ECA236G1593' => 'eca', 'ECA238G0565' => 'eca', 'ECA246G1027' => 'eca', 'ECA246G3223' => 'eca', 'ECA246G3470' => 'eca', 'EL10Ac6g13829' => 'bvu', 'EL10Ac6g14093' => 'bvu', 'EL10Ac8g18707' => 'bvu', 'Eucgr.C01369' => 'egr', 'Eucgr.H02492' => 'egr', 'Eucgr.I01733' => 'egr', 'Eucgr.J02255' => 'egr', 'Eucgr.J02257' => 'egr', 'Eucgr.J02258' => 'egr', 'FAN02G1601' => 'fan', 'FAN03G1586' => 'fan', 'FAN03G2986' => 'fan', 'FAN05G4837' => 'fan', 'FAN06G0146' => 'fan', 'FAN07G0858' => 'fan', 'FAN09G3179' => 'fan', 'FAN10G0669' => 'fan', 'FAN12G2358' => 'fan', 'FAN14G4198' => 'fan', 'FAN14G5112' => 'fan', 'FAN17G0342' => 'fan', 'FAN19G0342' => 'fan', 'FAN19G0962' => 'fan', 'FAN19G1101' => 'fan', 'FAN19G1872' => 'fan', 'FAN22G0356' => 'fan', 'FAN23G0744' => 'fan', 'FAN23G1914' => 'fan', 'FAN26G0032' => 'fan', 'FAN28G0625' => 'fan', 'FvH4_1g02710' => 'fve', 'FvH4_1g02720' => 'fve', 'FvH4_4g25670' => 'fve', 'FvH4_6g51700' => 'fve', 'FvH4_7g20170' => 'fve', 'Glyma.05G175000' => 'gma', 'Glyma.08G132300' => 'gma', 'Glyma.11G243000' => 'gma', 'Glyma.13G158900' => 'gma', 'Glyma.17G112400' => 'gma', 'Glyma.18G014100' => 'gma', 'Glyma.19G003100' => 'gma', 'Glyma.19G056500' => 'gma', 'Gohir.A01G158900' => 'ghi', 'Gohir.A05G312600' => 'ghi', 'Gohir.A05G354900' => 'ghi', 'Gohir.A07G037200' => 'ghi', 'Gohir.A09G030000' => 'ghi', 'Gohir.A12G145200' => 'ghi', 'Gohir.D01G151500' => 'ghi', 'Gohir.D04G058300' => 'ghi', 'Gohir.D05G314100' => 'ghi', 'Gohir.D07G041400' => 'ghi', 'Gohir.D09G029700' => 'ghi', 'Gohir.D12G149700' => 'ghi', 'Gorai.001G043800' => 'gra', 'Gorai.002G187800' => 'gra', 'Gorai.006G034700' => 'gra', 'Gorai.008G161200' => 'gra', 'Gorai.009G335700' => 'gra', 'Gorai.012G065000' => 'gra', 'GSVIVG01000535001' => 'vvi', 'GSVIVG01015572001' => 'vvi', 'GSVIVG01032386001' => 'vvi', 'HanXRQChr05g0138531' => 'han', 'HanXRQChr06g0174391' => 'han', 'HanXRQChr07g0199021' => 'han', 'HanXRQChr08g0208211' => 'han', 'HanXRQChr09g0255471' => 'han', 'HanXRQChr10g0315791' => 'han', 'HanXRQChr12g0371991' => 'han', 'HanXRQChr15g0475251' => 'han', 'HanXRQChr17g0540001' => 'han', 'HanXRQChr17g0548631' => 'han', 'HanXRQChr17g0569561' => 'han', 'Haze_12256' => 'cav', 'Haze_14756' => 'cav', 'Haze_25528' => 'cav', 'Hma1.2p1_0079F.1_g041020' => 'hma', 'Hma1.2p1_0818F.1_g223260' => 'hma', 'Hma1.2p1_1747F.1_g300530' => 'hma', 'HPP92_004607' => 'vpl', 'HPP92_004608' => 'vpl', 'HPP92_006181' => 'vpl', 'HPP92_012192' => 'vpl', 'HPP92_015680' => 'vpl', 'HPP92_020249' => 'vpl', 'HPP92_021376' => 'vpl', 'HPP92_024275' => 'vpl', 'Hund06031' => 'sun', 'Hund25391' => 'sun', 'Lalb_Chr07g0185371' => 'lal', 'Lalb_Chr07g0185381' => 'lal', 'Lalb_Chr12g0204011' => 'lal', 'Lalb_Chr13g0301671' => 'lal', 'Lalb_Chr14g0362851' => 'lal', 'Lalb_Chr24g0403581' => 'lal', 'Lj1g0000233' => 'lja', 'Lj2g0018120' => 'lja', 'Lj3C621T0' => 'lonja', 'Lj3P1059T14' => 'lonja', 'Lj3P611T9' => 'lonja', 'Lj3P614T13' => 'lonja', 'Lj3P615T5' => 'lonja', 'Lj4g0012315' => 'lja', 'Lj4g0026182' => 'lja', 'Lj6P813T16' => 'lonja', 'Lj7C427T7' => 'lonja', 'Lj7C427T8' => 'lonja', 'Lj7P600T41' => 'lonja', 'Lju41C42G17' => 'lonja', 'Lsat_1_v5_gn_0_47300' => 'lsa', 'Lsat_1_v5_gn_2_91280' => 'lsa', 'Lsat_1_v5_gn_3_30561' => 'lsa', 'Lsat_1_v5_gn_4_184321' => 'lsa', 'Lsat_1_v5_gn_4_4041' => 'lsa', 'Lsat_1_v5_gn_5_92000' => 'lsa', 'Lsat_1_v5_gn_8_152940' => 'lsa', 'Lsat_1_v5_gn_8_62401' => 'lsa', 'Manes.06G055900' => 'mes', 'Manes.12G022200' => 'mes', 'Manes.13G023300' => 'mes', 'Manes.14G115000' => 'mes', 'Manes.15G151700' => 'mes', 'Manes.17G111300' => 'mes', 'Mapoly0226s0009' => 'mpo', 'MBI02_g25363_MAGBIO' => 'mbi', 'MBI06_g00027_MAGBIO' => 'mbi', 'MBI10_g13034_MAGBIO' => 'mbi', 'MD09G1023400' => 'mdo', 'MD13G1100100' => 'mdo', 'MD15G1169200' => 'mdo', 'MD16G1101100' => 'mdo', 'MD17G1022900' => 'mdo', 'Medtr3g096150' => 'mtr', 'Medtr4g115070' => 'mtr', 'Medtr7g033325' => 'mtr', 'Medtr8g089840' => 'mtr', 'MELO3C010319.2' => 'cme', 'MELO3C011944.2' => 'cme', 'MELO3C021589.2' => 'cme', 'Migut.E00207' => 'egut', 'Migut.H00067' => 'egut', 'Migut.K00433' => 'egut', 'Migut.K00606' => 'egut', 'Migut.K01410' => 'egut', 'MSTRG.13347' => 'ama', 'MSTRG.24045' => 'ama', 'MSTRG.2428' => 'ama', 'MSTRG.26410' => 'ama', 'MSTRG.3139' => 'ama', 'MSTRG.3286' => 'ama', 'MSTRG.563' => 'ama', 'MSTRG.7941' => 'ama', 'Nitab4.5_0000028g0060' => 'nta', 'Nitab4.5_0000065g0260' => 'nta', 'Nitab4.5_0000112g0060' => 'nta', 'Nitab4.5_0000489g0120' => 'nta', 'Nitab4.5_0001776g0050' => 'nta', 'Nitab4.5_0001854g0010' => 'nta', 'Nitab4.5_0001860g0020' => 'nta', 'Nitab4.5_0004352g0010' => 'nta', 'Nitab4.5_0008716g0020' => 'nta', 'Nitab4.5_0008922g0010' => 'nta', 'Nn3g16693' => 'nnu', 'Nn4g22596' => 'nnu', 'Nn7g37639' => 'nnu', 'Oeu001701.1' => 'oeu', 'Oeu018149.1' => 'oeu', 'Oeu026220.1' => 'oeu', 'Oeu038635.1' => 'oeu', 'Oeu049176.1' => 'oeu', 'Oeu056706.1' => 'oeu', 'Oeu056937.1' => 'oeu', 'Oeu057540.1' => 'oeu', 'Os02g0594900' => 'osa', 'Os02g0595100' => 'osa', 'Os04g0477500' => 'osa', 'Os12g0611900' => 'osa', 'Peaxi162Scf00076g00020' => 'pax', 'Peaxi162Scf00128g00217' => 'pax', 'Peaxi162Scf00129g01640' => 'pax', 'Peaxi162Scf00669g00007' => 'pax', 'Peaxi162Scf00700g00421' => 'pax', 'Peaxi162Scf00801g00038' => 'pax', 'Peaxi162Scf00891g00025' => 'pax', 'PGR083G0909' => 'pgr', 'PGR119G1005' => 'pgr', 'PGR142G2236' => 'pgr', 'PGR142G3388' => 'pgr', 'PGSC0003DMG400004514' => 'stu', 'PGSC0003DMG400012635' => 'stu', 'PGSC0003DMG400015730' => 'stu', 'PGSC0003DMG400018611' => 'stu', 'PGSC0003DMG400030897' => 'stu', 'Phvul.001G254800' => 'pvu', 'Phvul.002G260100' => 'pvu', 'Phvul.003G167600' => 'pvu', 'Phvul.004G005100' => 'pvu', 'Potri.001G343600' => 'ptr', 'Potri.006G066700' => 'ptr', 'Potri.008G186000' => 'ptr', 'Potri.010G046900' => 'ptr', 'Potri.018G127900' => 'ptr', 'Pp3c20_17750' => 'ppa', 'Pp3c24_4380' => 'ppa', 'Prupe.1G245800' => 'ppe', 'Prupe.3G293400' => 'ppe', 'Prupe.7G247400' => 'ppe', 'Psat0s145g0120' => 'psa', 'Psat0s595g0040' => 'psa', 'Psat0s595g0120' => 'psa', 'Psat3g175040' => 'psa', 'Psat7g058120' => 'psa', 'PSO017G0428' => 'pso', 'PSO063G7510' => 'pso', 'PSO067G0046' => 'pso', 'PSO478G1073' => 'pso', 'PSO675G3677' => 'pso', 'PSO675G6558' => 'pso', 'PSO675G7520' => 'pso', 'PSO675G8959' => 'pso', 'QL02p074089' => 'qlo', 'QL02p089614' => 'qlo', 'QL03p057736' => 'qlo', 'RcHm_v2.0_Chr1g0364131' => 'rch', 'RcHm_v2.0_Chr2g0087801' => 'rch', 'RcHm_v2.0_Chr2g0087821' => 'rch', 'RcHm_v2.0_Chr2g0173231' => 'rch', 'RcHm_v2.0_Chr4g0433111' => 'rch', 'Rhsim03G0250300' => 'rsi', 'Rhsim08G0048400' => 'rsi', 'Rhsim10G0014800' => 'rsi', 'Rhsim12G0040100' => 'rsi', 'Rhsim12G0109700' => 'rsi', 'Sabra06G0049600' => 'sbr', 'Sabra08G0141000' => 'sbr', 'Sabra10G0021400' => 'sbr', 'Sabra16G0222900' => 'sbr', 'Sabra18G0108600' => 'sbr', 'SalBow1G0433' => 'sbo', 'SalBow1G2038' => 'sbo', 'SalBow1G5003' => 'sbo', 'SalBow7G1197' => 'sbo', 'SalBow8G3506' => 'sbo', 'Sc03g0007300' => 'sci', 'Sc11g0000950' => 'sci', 'Sc14g0008750' => 'sci', 'Sc18g0000420' => 'sci', 'Sed0006754' => 'sed', 'Sed0008741' => 'sed', 'Sed0017172' => 'sed', 'Sed0018925' => 'sed', 'Sed0023326' => 'sed', 'Sed0025909' => 'sed', 'SEGI_05333' => 'sgi', 'SEGI_10362' => 'sgi', 'SEGI_13380' => 'sgi', 'SEGI_24306' => 'sgi', 'SEGI_29077' => 'sgi', 'SEGI_29095' => 'sgi', 'SEGI_36534' => 'sgi', 'SEGI_37506' => 'sgi', 'SEGI_38321' => 'sgi', 'SGA_v2.0_scaffold307G48031' => 'sas', 'SGA_v2.0_scaffold47G17507' => 'sas', 'SGA_v2.0_scaffold63G21736' => 'sas', 'SGA_v2.0_scaffold87G27070' => 'sas', 'SHI17794' => 'shi', 'SHI28851' => 'shi', 'SMO165G0155' => 'smo', 'SMO340G0217' => 'smo', 'SMO367G1210' => 'smo', 'Solyc02g093430.3' => 'sly', 'Solyc05g013580.4' => 'sly', 'Solyc07g008030.3' => 'sly', 'Solyc12g035470.2' => 'sly', 'Sopen02g038020' => 'spe', 'Sopen05g008490' => 'spe', 'Sopen07g003910' => 'spe', 'Sopen12g015240' => 'spe', 'Sp1g11550' => 'spa', 'Sp2g16710' => 'spa', 'Sp3g00430' => 'spa', 'Sp3g26780' => 'spa', 'Sp5g22900' => 'spa', 'Sp6g29530' => 'spa', 'TAR371G0794' => 'tar', 'TAR374G0164' => 'tar', 'TAR622G0165' => 'tar', 'TAR626G0929' => 'tar', 'TAR629G2155' => 'tar', 'THA.LOC104805282' => 'tha', 'THA.LOC104805363' => 'tha', 'THA.LOC104808968' => 'tha', 'THA.LOC104821093' => 'tha', 'THA.LOC104823953' => 'tha', 'THA.LOC104825562' => 'tha', 'THA.LOC104825665' => 'tha', 'Thecc.02G261400' => 'tca', 'Thecc.04G019200' => 'tca', 'Thecc.09G130400' => 'tca', 'Thhalv10004374m.g' => 'esa', 'Thhalv10007850m.g' => 'esa', 'Thhalv10013782m.g' => 'esa', 'Thhalv10018686m.g' => 'esa', 'Thhalv10020899m.g' => 'esa', 'Thhalv10022755m.g' => 'esa', 'TPR.G23851' => 'tpr', 'TPR.G26500' => 'tpr', 'TPR.G27267' => 'tpr', 'TPR.G32001' => 'tpr', 'TPR.G6251' => 'tpr', 'TPR.G8167' => 'tpr', 'TWI12G1330' => 'twi', 'TWI18G1239' => 'twi', 'TWI34G0979' => 'twi', 'TWI36G0670' => 'twi', 'TWI36G0707' => 'twi', 'TWI56G0233' => 'twi', 'TWI75G1809' => 'twi', 'unitig_21.g20874' => 'ugi', 'unitig_26.g10343' => 'ugi', 'unitig_46.g18392' => 'ugi', 'unitig_52.g17178' => 'ugi', 'unitig_8.g2934' => 'ugi', 'vmacro01122' => 'vma', 'vmacro05875' => 'vma', 'vmacro06147' => 'vma', 'vmacro16191' => 'vma', 'vmacro18293' => 'vma', 'VMungo0251G3707' => 'vmu', 'VMungo0464G1521' => 'vmu', 'VMungo1215G0205' => 'vmu', 'VMungo1383G2484' => 'vmu', 'Zm00001eb079610' => 'zma', 'Zm00001eb135990' => 'zma', 'Zm00001eb183710' => 'zma', 'Zm00001eb246020' => 'zma' ) $gf_id = 'HOM05D001124' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001124' ) $data_identifier = 'HOM05D001124' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 6, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 7, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 21, 'bol' => (int) 10, 'bra' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 6, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 9, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 21, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 8, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 10, 'lsa' => (int) 8, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 8, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 9, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb246020' $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' => 'HOM05D001124', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '548', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02520' => 'bna', 'A03p06630' => 'bna', 'A05p44460' => 'bna', 'A06p08710' => 'bna', 'A06p41090' => 'bna', 'A07p32320' => 'bna', 'A08p32520' => 'bna', 'A09p10360' => 'bna', 'A10p24080' => 'bna', 'Aa31LG11G15250' => 'aar', 'Aa31LG1G1800' => 'aar', 'Aa31LG2G5120' => 'aar', 'Aa31LG2G6070' => 'aar', 'Aa31LG5G10770' => 'aar', 'Aa31sc61G90' => 'aar', 'Actinidia01352' => 'ach', 'Actinidia05983' => 'ach', 'Actinidia08133' => 'ach', 'Actinidia15101' => 'ach', 'Actinidia26379' => 'ach', 'Actinidia35778' => 'ach', 'Actinidia36123' => 'ach', 'Actinidia37436' => 'ach', 'Actinidia38730' => 'ach', 'Ah.02g128210' => 'amhyb', 'Ah.03g132990' => 'amhyb', 'Ah.14g079410' => 'amhyb', 'AL1G24640' => 'aly', 'AL2G26680' => 'aly', 'AL3G10530' => 'aly', 'AL3G45230' => 'aly', 'AL5G15230' => 'aly', 'AL5G16960' => 'aly', 'AL6G25210' => 'aly', 'Aqoxy2G00441' => 'aox', 'Aqoxy3G01236' => 'aox', 'Aqoxy5G03746' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3RQ047' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C7GMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9C8JER' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MBL6KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YXCZ83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZANX40' => 'arhy', 'AT1G12990' => 'ath', 'AT1G67880' => 'ath', 'AT2G13290' => 'ath', 'AT3G01620' => 'ath', 'AT3G26445' => 'ath', 'AT3G27540' => 'ath', 'AT5G14480' => 'ath', 'ATR0824G026' => 'atr', 'ATR1098G019' => 'atr', 'Atru.chr11.2145' => 'acertr', 'Atru.chr2.3636' => 'acertr', 'Atru.chr2.3644' => 'acertr', 'Atru.chr6.2422' => 'acertr', 'Atru.chr7.1112' => 'acertr', 'AUR62005469' => 'cqu', 'AUR62011166' => 'cqu', 'AUR62013319' => 'cqu', 'AUR62024273' => 'cqu', 'AUR62028420' => 'cqu', 'AUR62041942' => 'cqu', 'BcaB01g04969' => 'bca', 'BcaB01g06371' => 'bca', 'BcaB02g11494' => 'bca', 'BcaB03g15382' => 'bca', 'BcaB08g36994' => 'bca', 'BcaC03g13477' => 'bca', 'BcaC03g13478' => 'bca', 'BcaC03g13480' => 'bca', 'BcaC03g13481' => 'bca', 'BcaC03g13486' => 'bca', 'BcaC04g19031' => 'bca', 'BcaC04g23085' => 'bca', 'BcaC05g25094' => 'bca', 'BcaC05g25096' => 'bca', 'BcaC05g25138' => 'bca', 'BcaC05g30416' => 'bca', 'BcaC05g30455' => 'bca', 'BcaC06g30979' => 'bca', 'BcaC06g33805' => 'bca', 'BcaC08g46021' => 'bca', 'BcaNung03154' => 'bca', 'BolC2t06623H' => 'bol', 'BolC2t06632H' => 'bol', 'BolC2t06635H' => 'bol', 'BolC2t06638H' => 'bol', 'BolC3t13266H' => 'bol', 'BolC5t29776H' => 'bol', 'BolC6t38912H' => 'bol', 'BolC7t44183H' => 'bol', 'BolC9t54123H' => 'bol', 'BolC9t59107H' => 'bol', 'BraA02t05221Z' => 'bra', 'BraA03t09996Z' => 'bra', 'BraA05t23210Z' => 'bra', 'BraA06t24068Z' => 'bra', 'BraA06t27032Z' => 'bra', 'BraA08t35176Z' => 'bra', 'BraA09t36680Z' => 'bra', 'BraA10t44471Z' => 'bra', 'C02p06760' => 'bna', 'C02p06890' => 'bna', 'C02p07010' => 'bna', 'C03p07660' => 'bna', 'C05p10300' => 'bna', 'C06p38150' => 'bna', 'C07p36650' => 'bna', 'C08p15770' => 'bna', 'C09p12300' => 'bna', 'C09p62700' => 'bna', 'C09p75040' => 'bna', 'CAN.G13.1' => 'can', 'CAN.G138.4' => 'can', 'CAN.G44.6' => 'can', 'CAN.G473.19' => 'can', 'CANSAT01G0835' => 'cansat', 'CANSAT11G0246' => 'cansat', 'CANSAT11G1766' => 'cansat', 'CANSAT64G1954' => 'cansat', 'CARHR013330' => 'chi', 'CARHR060530' => 'chi', 'CARHR075300' => 'chi', 'CARHR105120' => 'chi', 'CARHR148910' => 'chi', 'CARHR198830' => 'chi', 'Carub.0001s1275' => 'cru', 'Carub.0002s1437' => 'cru', 'Carub.0003s0044' => 'cru', 'Carub.0003s2787' => 'cru', 'Carub.0005s0597' => 'cru', 'Carub.0006s1266' => 'cru', 'Ca_06935_v3' => 'car', 'Ca_13559_v3' => 'car', 'Ca_16941_v3' => 'car', 'Ca_16960_v3' => 'car', 'Ca_17775_v3' => 'car', 'Ca_30464_v3' => 'car', 'Cc06_g08160' => 'ccan', 'Cc07_g01520' => 'ccan', 'Cc11_g15810' => 'ccan', 'CDE02G2840' => 'cde', 'CDE03G0093' => 'cde', 'CDE04G2127' => 'cde', 'CDE07G1857' => 'cde', 'CDE09G1246' => 'cde', 'Cfa003412' => 'cfa', 'Cfa007341' => 'cfa', 'Cfa009220' => 'cfa', 'Ciclev10008737m.g' => 'ccl', 'Ciclev10015565m.g' => 'ccl', 'Ciclev10031761m.g' => 'ccl', 'CiPaw.03G045300' => 'cil', 'CiPaw.03G247200' => 'cil', 'CiPaw.04G029500' => 'cil', 'CiPaw.04G174000' => 'cil', 'CiPaw.05G181200' => 'cil', 'CiPaw.06G067100' => 'cil', 'ClCG05G025800' => 'cla', 'ClCG06G011400' => 'cla', 'ClCG09G019360' => 'cla', 'COL.COLO4_04827' => 'col', 'COL.COLO4_29170' => 'col', 'COL.COLO4_35131' => 'col', 'COL.COLO4_35132' => 'col', 'Cpa.g.sc33.32' => 'cpa', 'Cpa.g.sc46.29' => 'cpa', 'Cpa.g.sc796.1' => 'cpa', 'CsaV3_1G030420' => 'csa', 'CsaV3_5G027050' => 'csa', 'CsaV3_5G031040' => 'csa', 'CsaV3_UNG023130' => 'csa', 'CSS0007726' => 'camsi', 'CSS0016433' => 'camsi', 'CSS0017656' => 'camsi', 'CSS0025364' => 'camsi', 'CSS0027582' => 'camsi', 'CSS0047288' => 'camsi', 'CSS0049950' => 'camsi', 'DCAR_003843' => 'dca', 'DCAR_007052' => 'dca', 'DCAR_020884' => 'dca', 'DCAR_021730' => 'dca', 'DCAR_024423' => 'dca', 'DCAR_026509' => 'dca', 'DCAR_031158' => 'dca', 'Dinv14728' => 'din', 'Dinv15219' => 'din', 'Dinv25728' => 'din', 'Dinv33428' => 'din', 'Dinv36489' => 'din', 'Dinv41486' => 'din', 'Duzib147G0469' => 'dzi', 'Duzib168G0060' => 'dzi', 'Duzib187G1215' => 'dzi', 'Duzib248G0692' => 'dzi', 'Duzib251G0767' => 'dzi', 'Duzib264G0446' => 'dzi', 'Duzib268G0691' => 'dzi', 'ECA232G4767' => 'eca', 'ECA233G2838' => 'eca', 'ECA234G0391' => 'eca', 'ECA234G0857' => 'eca', 'ECA236G1593' => 'eca', 'ECA238G0565' => 'eca', 'ECA246G1027' => 'eca', 'ECA246G3223' => 'eca', 'ECA246G3470' => 'eca', 'EL10Ac6g13829' => 'bvu', 'EL10Ac6g14093' => 'bvu', 'EL10Ac8g18707' => 'bvu', 'Eucgr.C01369' => 'egr', 'Eucgr.H02492' => 'egr', 'Eucgr.I01733' => 'egr', 'Eucgr.J02255' => 'egr', 'Eucgr.J02257' => 'egr', 'Eucgr.J02258' => 'egr', 'FAN02G1601' => 'fan', 'FAN03G1586' => 'fan', 'FAN03G2986' => 'fan', 'FAN05G4837' => 'fan', 'FAN06G0146' => 'fan', 'FAN07G0858' => 'fan', 'FAN09G3179' => 'fan', 'FAN10G0669' => 'fan', 'FAN12G2358' => 'fan', 'FAN14G4198' => 'fan', 'FAN14G5112' => 'fan', 'FAN17G0342' => 'fan', 'FAN19G0342' => 'fan', 'FAN19G0962' => 'fan', 'FAN19G1101' => 'fan', 'FAN19G1872' => 'fan', 'FAN22G0356' => 'fan', 'FAN23G0744' => 'fan', 'FAN23G1914' => 'fan', 'FAN26G0032' => 'fan', 'FAN28G0625' => 'fan', 'FvH4_1g02710' => 'fve', 'FvH4_1g02720' => 'fve', 'FvH4_4g25670' => 'fve', 'FvH4_6g51700' => 'fve', 'FvH4_7g20170' => 'fve', 'Glyma.05G175000' => 'gma', 'Glyma.08G132300' => 'gma', 'Glyma.11G243000' => 'gma', 'Glyma.13G158900' => 'gma', 'Glyma.17G112400' => 'gma', 'Glyma.18G014100' => 'gma', 'Glyma.19G003100' => 'gma', 'Glyma.19G056500' => 'gma', 'Gohir.A01G158900' => 'ghi', 'Gohir.A05G312600' => 'ghi', 'Gohir.A05G354900' => 'ghi', 'Gohir.A07G037200' => 'ghi', 'Gohir.A09G030000' => 'ghi', 'Gohir.A12G145200' => 'ghi', 'Gohir.D01G151500' => 'ghi', 'Gohir.D04G058300' => 'ghi', 'Gohir.D05G314100' => 'ghi', 'Gohir.D07G041400' => 'ghi', 'Gohir.D09G029700' => 'ghi', 'Gohir.D12G149700' => 'ghi', 'Gorai.001G043800' => 'gra', 'Gorai.002G187800' => 'gra', 'Gorai.006G034700' => 'gra', 'Gorai.008G161200' => 'gra', 'Gorai.009G335700' => 'gra', 'Gorai.012G065000' => 'gra', 'GSVIVG01000535001' => 'vvi', 'GSVIVG01015572001' => 'vvi', 'GSVIVG01032386001' => 'vvi', 'HanXRQChr05g0138531' => 'han', 'HanXRQChr06g0174391' => 'han', 'HanXRQChr07g0199021' => 'han', 'HanXRQChr08g0208211' => 'han', 'HanXRQChr09g0255471' => 'han', 'HanXRQChr10g0315791' => 'han', 'HanXRQChr12g0371991' => 'han', 'HanXRQChr15g0475251' => 'han', 'HanXRQChr17g0540001' => 'han', 'HanXRQChr17g0548631' => 'han', 'HanXRQChr17g0569561' => 'han', 'Haze_12256' => 'cav', 'Haze_14756' => 'cav', 'Haze_25528' => 'cav', 'Hma1.2p1_0079F.1_g041020' => 'hma', 'Hma1.2p1_0818F.1_g223260' => 'hma', 'Hma1.2p1_1747F.1_g300530' => 'hma', 'HPP92_004607' => 'vpl', 'HPP92_004608' => 'vpl', 'HPP92_006181' => 'vpl', 'HPP92_012192' => 'vpl', 'HPP92_015680' => 'vpl', 'HPP92_020249' => 'vpl', 'HPP92_021376' => 'vpl', 'HPP92_024275' => 'vpl', 'Hund06031' => 'sun', 'Hund25391' => 'sun', 'Lalb_Chr07g0185371' => 'lal', 'Lalb_Chr07g0185381' => 'lal', 'Lalb_Chr12g0204011' => 'lal', 'Lalb_Chr13g0301671' => 'lal', 'Lalb_Chr14g0362851' => 'lal', 'Lalb_Chr24g0403581' => 'lal', 'Lj1g0000233' => 'lja', 'Lj2g0018120' => 'lja', 'Lj3C621T0' => 'lonja', 'Lj3P1059T14' => 'lonja', 'Lj3P611T9' => 'lonja', 'Lj3P614T13' => 'lonja', 'Lj3P615T5' => 'lonja', 'Lj4g0012315' => 'lja', 'Lj4g0026182' => 'lja', 'Lj6P813T16' => 'lonja', 'Lj7C427T7' => 'lonja', 'Lj7C427T8' => 'lonja', 'Lj7P600T41' => 'lonja', 'Lju41C42G17' => 'lonja', 'Lsat_1_v5_gn_0_47300' => 'lsa', 'Lsat_1_v5_gn_2_91280' => 'lsa', 'Lsat_1_v5_gn_3_30561' => 'lsa', 'Lsat_1_v5_gn_4_184321' => 'lsa', 'Lsat_1_v5_gn_4_4041' => 'lsa', 'Lsat_1_v5_gn_5_92000' => 'lsa', 'Lsat_1_v5_gn_8_152940' => 'lsa', 'Lsat_1_v5_gn_8_62401' => 'lsa', 'Manes.06G055900' => 'mes', 'Manes.12G022200' => 'mes', 'Manes.13G023300' => 'mes', 'Manes.14G115000' => 'mes', 'Manes.15G151700' => 'mes', 'Manes.17G111300' => 'mes', 'Mapoly0226s0009' => 'mpo', 'MBI02_g25363_MAGBIO' => 'mbi', 'MBI06_g00027_MAGBIO' => 'mbi', 'MBI10_g13034_MAGBIO' => 'mbi', 'MD09G1023400' => 'mdo', 'MD13G1100100' => 'mdo', 'MD15G1169200' => 'mdo', 'MD16G1101100' => 'mdo', 'MD17G1022900' => 'mdo', 'Medtr3g096150' => 'mtr', 'Medtr4g115070' => 'mtr', 'Medtr7g033325' => 'mtr', 'Medtr8g089840' => 'mtr', 'MELO3C010319.2' => 'cme', 'MELO3C011944.2' => 'cme', 'MELO3C021589.2' => 'cme', 'Migut.E00207' => 'egut', 'Migut.H00067' => 'egut', 'Migut.K00433' => 'egut', 'Migut.K00606' => 'egut', 'Migut.K01410' => 'egut', 'MSTRG.13347' => 'ama', 'MSTRG.24045' => 'ama', 'MSTRG.2428' => 'ama', 'MSTRG.26410' => 'ama', 'MSTRG.3139' => 'ama', 'MSTRG.3286' => 'ama', 'MSTRG.563' => 'ama', 'MSTRG.7941' => 'ama', 'Nitab4.5_0000028g0060' => 'nta', 'Nitab4.5_0000065g0260' => 'nta', 'Nitab4.5_0000112g0060' => 'nta', 'Nitab4.5_0000489g0120' => 'nta', 'Nitab4.5_0001776g0050' => 'nta', 'Nitab4.5_0001854g0010' => 'nta', 'Nitab4.5_0001860g0020' => 'nta', 'Nitab4.5_0004352g0010' => 'nta', 'Nitab4.5_0008716g0020' => 'nta', 'Nitab4.5_0008922g0010' => 'nta', 'Nn3g16693' => 'nnu', 'Nn4g22596' => 'nnu', 'Nn7g37639' => 'nnu', 'Oeu001701.1' => 'oeu', 'Oeu018149.1' => 'oeu', 'Oeu026220.1' => 'oeu', 'Oeu038635.1' => 'oeu', 'Oeu049176.1' => 'oeu', 'Oeu056706.1' => 'oeu', 'Oeu056937.1' => 'oeu', 'Oeu057540.1' => 'oeu', 'Os02g0594900' => 'osa', 'Os02g0595100' => 'osa', 'Os04g0477500' => 'osa', 'Os12g0611900' => 'osa', 'Peaxi162Scf00076g00020' => 'pax', 'Peaxi162Scf00128g00217' => 'pax', 'Peaxi162Scf00129g01640' => 'pax', 'Peaxi162Scf00669g00007' => 'pax', 'Peaxi162Scf00700g00421' => 'pax', 'Peaxi162Scf00801g00038' => 'pax', 'Peaxi162Scf00891g00025' => 'pax', 'PGR083G0909' => 'pgr', 'PGR119G1005' => 'pgr', 'PGR142G2236' => 'pgr', 'PGR142G3388' => 'pgr', 'PGSC0003DMG400004514' => 'stu', 'PGSC0003DMG400012635' => 'stu', 'PGSC0003DMG400015730' => 'stu', 'PGSC0003DMG400018611' => 'stu', 'PGSC0003DMG400030897' => 'stu', 'Phvul.001G254800' => 'pvu', 'Phvul.002G260100' => 'pvu', 'Phvul.003G167600' => 'pvu', 'Phvul.004G005100' => 'pvu', 'Potri.001G343600' => 'ptr', 'Potri.006G066700' => 'ptr', 'Potri.008G186000' => 'ptr', 'Potri.010G046900' => 'ptr', 'Potri.018G127900' => 'ptr', 'Pp3c20_17750' => 'ppa', 'Pp3c24_4380' => 'ppa', 'Prupe.1G245800' => 'ppe', 'Prupe.3G293400' => 'ppe', 'Prupe.7G247400' => 'ppe', 'Psat0s145g0120' => 'psa', 'Psat0s595g0040' => 'psa', 'Psat0s595g0120' => 'psa', 'Psat3g175040' => 'psa', 'Psat7g058120' => 'psa', 'PSO017G0428' => 'pso', 'PSO063G7510' => 'pso', 'PSO067G0046' => 'pso', 'PSO478G1073' => 'pso', 'PSO675G3677' => 'pso', 'PSO675G6558' => 'pso', 'PSO675G7520' => 'pso', 'PSO675G8959' => 'pso', 'QL02p074089' => 'qlo', 'QL02p089614' => 'qlo', 'QL03p057736' => 'qlo', 'RcHm_v2.0_Chr1g0364131' => 'rch', 'RcHm_v2.0_Chr2g0087801' => 'rch', 'RcHm_v2.0_Chr2g0087821' => 'rch', 'RcHm_v2.0_Chr2g0173231' => 'rch', 'RcHm_v2.0_Chr4g0433111' => 'rch', 'Rhsim03G0250300' => 'rsi', 'Rhsim08G0048400' => 'rsi', 'Rhsim10G0014800' => 'rsi', 'Rhsim12G0040100' => 'rsi', 'Rhsim12G0109700' => 'rsi', 'Sabra06G0049600' => 'sbr', 'Sabra08G0141000' => 'sbr', 'Sabra10G0021400' => 'sbr', 'Sabra16G0222900' => 'sbr', 'Sabra18G0108600' => 'sbr', 'SalBow1G0433' => 'sbo', 'SalBow1G2038' => 'sbo', 'SalBow1G5003' => 'sbo', 'SalBow7G1197' => 'sbo', 'SalBow8G3506' => 'sbo', 'Sc03g0007300' => 'sci', 'Sc11g0000950' => 'sci', 'Sc14g0008750' => 'sci', 'Sc18g0000420' => 'sci', 'Sed0006754' => 'sed', 'Sed0008741' => 'sed', 'Sed0017172' => 'sed', 'Sed0018925' => 'sed', 'Sed0023326' => 'sed', 'Sed0025909' => 'sed', 'SEGI_05333' => 'sgi', 'SEGI_10362' => 'sgi', 'SEGI_13380' => 'sgi', 'SEGI_24306' => 'sgi', 'SEGI_29077' => 'sgi', 'SEGI_29095' => 'sgi', 'SEGI_36534' => 'sgi', 'SEGI_37506' => 'sgi', 'SEGI_38321' => 'sgi', 'SGA_v2.0_scaffold307G48031' => 'sas', 'SGA_v2.0_scaffold47G17507' => 'sas', 'SGA_v2.0_scaffold63G21736' => 'sas', 'SGA_v2.0_scaffold87G27070' => 'sas', 'SHI17794' => 'shi', 'SHI28851' => 'shi', 'SMO165G0155' => 'smo', 'SMO340G0217' => 'smo', 'SMO367G1210' => 'smo', 'Solyc02g093430.3' => 'sly', 'Solyc05g013580.4' => 'sly', 'Solyc07g008030.3' => 'sly', 'Solyc12g035470.2' => 'sly', 'Sopen02g038020' => 'spe', 'Sopen05g008490' => 'spe', 'Sopen07g003910' => 'spe', 'Sopen12g015240' => 'spe', 'Sp1g11550' => 'spa', 'Sp2g16710' => 'spa', 'Sp3g00430' => 'spa', 'Sp3g26780' => 'spa', 'Sp5g22900' => 'spa', 'Sp6g29530' => 'spa', 'TAR371G0794' => 'tar', 'TAR374G0164' => 'tar', 'TAR622G0165' => 'tar', 'TAR626G0929' => 'tar', 'TAR629G2155' => 'tar', 'THA.LOC104805282' => 'tha', 'THA.LOC104805363' => 'tha', 'THA.LOC104808968' => 'tha', 'THA.LOC104821093' => 'tha', 'THA.LOC104823953' => 'tha', 'THA.LOC104825562' => 'tha', 'THA.LOC104825665' => 'tha', 'Thecc.02G261400' => 'tca', 'Thecc.04G019200' => 'tca', 'Thecc.09G130400' => 'tca', 'Thhalv10004374m.g' => 'esa', 'Thhalv10007850m.g' => 'esa', 'Thhalv10013782m.g' => 'esa', 'Thhalv10018686m.g' => 'esa', 'Thhalv10020899m.g' => 'esa', 'Thhalv10022755m.g' => 'esa', 'TPR.G23851' => 'tpr', 'TPR.G26500' => 'tpr', 'TPR.G27267' => 'tpr', 'TPR.G32001' => 'tpr', 'TPR.G6251' => 'tpr', 'TPR.G8167' => 'tpr', 'TWI12G1330' => 'twi', 'TWI18G1239' => 'twi', 'TWI34G0979' => 'twi', 'TWI36G0670' => 'twi', 'TWI36G0707' => 'twi', 'TWI56G0233' => 'twi', 'TWI75G1809' => 'twi', 'unitig_21.g20874' => 'ugi', 'unitig_26.g10343' => 'ugi', 'unitig_46.g18392' => 'ugi', 'unitig_52.g17178' => 'ugi', 'unitig_8.g2934' => 'ugi', 'vmacro01122' => 'vma', 'vmacro05875' => 'vma', 'vmacro06147' => 'vma', 'vmacro16191' => 'vma', 'vmacro18293' => 'vma', 'VMungo0251G3707' => 'vmu', 'VMungo0464G1521' => 'vmu', 'VMungo1215G0205' => 'vmu', 'VMungo1383G2484' => 'vmu', 'Zm00001eb079610' => 'zma', 'Zm00001eb135990' => 'zma', 'Zm00001eb183710' => 'zma', 'Zm00001eb246020' => 'zma' ), 'gf_id' => 'HOM05D001124', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001124' ), 'data_identifier' => 'HOM05D001124', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001124', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '548', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02520' => 'bna', 'A03p06630' => 'bna', 'A05p44460' => 'bna', 'A06p08710' => 'bna', 'A06p41090' => 'bna', 'A07p32320' => 'bna', 'A08p32520' => 'bna', 'A09p10360' => 'bna', 'A10p24080' => 'bna', 'Aa31LG11G15250' => 'aar', 'Aa31LG1G1800' => 'aar', 'Aa31LG2G5120' => 'aar', 'Aa31LG2G6070' => 'aar', 'Aa31LG5G10770' => 'aar', 'Aa31sc61G90' => 'aar', 'Actinidia01352' => 'ach', 'Actinidia05983' => 'ach', 'Actinidia08133' => 'ach', 'Actinidia15101' => 'ach', 'Actinidia26379' => 'ach', 'Actinidia35778' => 'ach', 'Actinidia36123' => 'ach', 'Actinidia37436' => 'ach', 'Actinidia38730' => 'ach', 'Ah.02g128210' => 'amhyb', 'Ah.03g132990' => 'amhyb', 'Ah.14g079410' => 'amhyb', 'AL1G24640' => 'aly', 'AL2G26680' => 'aly', 'AL3G10530' => 'aly', 'AL3G45230' => 'aly', 'AL5G15230' => 'aly', 'AL5G16960' => 'aly', 'AL6G25210' => 'aly', 'Aqoxy2G00441' => 'aox', 'Aqoxy3G01236' => 'aox', 'Aqoxy5G03746' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3RQ047' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C7GMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9C8JER' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MBL6KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YXCZ83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZANX40' => 'arhy', 'AT1G12990' => 'ath', 'AT1G67880' => 'ath', 'AT2G13290' => 'ath', 'AT3G01620' => 'ath', 'AT3G26445' => 'ath', 'AT3G27540' => 'ath', 'AT5G14480' => 'ath', 'ATR0824G026' => 'atr', 'ATR1098G019' => 'atr', 'Atru.chr11.2145' => 'acertr', 'Atru.chr2.3636' => 'acertr', 'Atru.chr2.3644' => 'acertr', 'Atru.chr6.2422' => 'acertr', 'Atru.chr7.1112' => 'acertr', 'AUR62005469' => 'cqu', 'AUR62011166' => 'cqu', 'AUR62013319' => 'cqu', 'AUR62024273' => 'cqu', 'AUR62028420' => 'cqu', 'AUR62041942' => 'cqu', 'BcaB01g04969' => 'bca', 'BcaB01g06371' => 'bca', 'BcaB02g11494' => 'bca', 'BcaB03g15382' => 'bca', 'BcaB08g36994' => 'bca', 'BcaC03g13477' => 'bca', 'BcaC03g13478' => 'bca', 'BcaC03g13480' => 'bca', 'BcaC03g13481' => 'bca', 'BcaC03g13486' => 'bca', 'BcaC04g19031' => 'bca', 'BcaC04g23085' => 'bca', 'BcaC05g25094' => 'bca', 'BcaC05g25096' => 'bca', 'BcaC05g25138' => 'bca', 'BcaC05g30416' => 'bca', 'BcaC05g30455' => 'bca', 'BcaC06g30979' => 'bca', 'BcaC06g33805' => 'bca', 'BcaC08g46021' => 'bca', 'BcaNung03154' => 'bca', 'BolC2t06623H' => 'bol', 'BolC2t06632H' => 'bol', 'BolC2t06635H' => 'bol', 'BolC2t06638H' => 'bol', 'BolC3t13266H' => 'bol', 'BolC5t29776H' => 'bol', 'BolC6t38912H' => 'bol', 'BolC7t44183H' => 'bol', 'BolC9t54123H' => 'bol', 'BolC9t59107H' => 'bol', 'BraA02t05221Z' => 'bra', 'BraA03t09996Z' => 'bra', 'BraA05t23210Z' => 'bra', 'BraA06t24068Z' => 'bra', 'BraA06t27032Z' => 'bra', 'BraA08t35176Z' => 'bra', 'BraA09t36680Z' => 'bra', 'BraA10t44471Z' => 'bra', 'C02p06760' => 'bna', 'C02p06890' => 'bna', 'C02p07010' => 'bna', 'C03p07660' => 'bna', 'C05p10300' => 'bna', 'C06p38150' => 'bna', 'C07p36650' => 'bna', 'C08p15770' => 'bna', 'C09p12300' => 'bna', 'C09p62700' => 'bna', 'C09p75040' => 'bna', 'CAN.G13.1' => 'can', 'CAN.G138.4' => 'can', 'CAN.G44.6' => 'can', 'CAN.G473.19' => 'can', 'CANSAT01G0835' => 'cansat', 'CANSAT11G0246' => 'cansat', 'CANSAT11G1766' => 'cansat', 'CANSAT64G1954' => 'cansat', 'CARHR013330' => 'chi', 'CARHR060530' => 'chi', 'CARHR075300' => 'chi', 'CARHR105120' => 'chi', 'CARHR148910' => 'chi', 'CARHR198830' => 'chi', 'Carub.0001s1275' => 'cru', 'Carub.0002s1437' => 'cru', 'Carub.0003s0044' => 'cru', 'Carub.0003s2787' => 'cru', 'Carub.0005s0597' => 'cru', 'Carub.0006s1266' => 'cru', 'Ca_06935_v3' => 'car', 'Ca_13559_v3' => 'car', 'Ca_16941_v3' => 'car', 'Ca_16960_v3' => 'car', 'Ca_17775_v3' => 'car', 'Ca_30464_v3' => 'car', 'Cc06_g08160' => 'ccan', 'Cc07_g01520' => 'ccan', 'Cc11_g15810' => 'ccan', 'CDE02G2840' => 'cde', 'CDE03G0093' => 'cde', 'CDE04G2127' => 'cde', 'CDE07G1857' => 'cde', 'CDE09G1246' => 'cde', 'Cfa003412' => 'cfa', 'Cfa007341' => 'cfa', 'Cfa009220' => 'cfa', 'Ciclev10008737m.g' => 'ccl', 'Ciclev10015565m.g' => 'ccl', 'Ciclev10031761m.g' => 'ccl', 'CiPaw.03G045300' => 'cil', 'CiPaw.03G247200' => 'cil', 'CiPaw.04G029500' => 'cil', 'CiPaw.04G174000' => 'cil', 'CiPaw.05G181200' => 'cil', 'CiPaw.06G067100' => 'cil', 'ClCG05G025800' => 'cla', 'ClCG06G011400' => 'cla', 'ClCG09G019360' => 'cla', 'COL.COLO4_04827' => 'col', 'COL.COLO4_29170' => 'col', 'COL.COLO4_35131' => 'col', 'COL.COLO4_35132' => 'col', 'Cpa.g.sc33.32' => 'cpa', 'Cpa.g.sc46.29' => 'cpa', 'Cpa.g.sc796.1' => 'cpa', 'CsaV3_1G030420' => 'csa', 'CsaV3_5G027050' => 'csa', 'CsaV3_5G031040' => 'csa', 'CsaV3_UNG023130' => 'csa', 'CSS0007726' => 'camsi', 'CSS0016433' => 'camsi', 'CSS0017656' => 'camsi', 'CSS0025364' => 'camsi', 'CSS0027582' => 'camsi', 'CSS0047288' => 'camsi', 'CSS0049950' => 'camsi', 'DCAR_003843' => 'dca', 'DCAR_007052' => 'dca', 'DCAR_020884' => 'dca', 'DCAR_021730' => 'dca', 'DCAR_024423' => 'dca', 'DCAR_026509' => 'dca', 'DCAR_031158' => 'dca', 'Dinv14728' => 'din', 'Dinv15219' => 'din', 'Dinv25728' => 'din', 'Dinv33428' => 'din', 'Dinv36489' => 'din', 'Dinv41486' => 'din', 'Duzib147G0469' => 'dzi', 'Duzib168G0060' => 'dzi', 'Duzib187G1215' => 'dzi', 'Duzib248G0692' => 'dzi', 'Duzib251G0767' => 'dzi', 'Duzib264G0446' => 'dzi', 'Duzib268G0691' => 'dzi', 'ECA232G4767' => 'eca', 'ECA233G2838' => 'eca', 'ECA234G0391' => 'eca', 'ECA234G0857' => 'eca', 'ECA236G1593' => 'eca', 'ECA238G0565' => 'eca', 'ECA246G1027' => 'eca', 'ECA246G3223' => 'eca', 'ECA246G3470' => 'eca', 'EL10Ac6g13829' => 'bvu', 'EL10Ac6g14093' => 'bvu', 'EL10Ac8g18707' => 'bvu', 'Eucgr.C01369' => 'egr', 'Eucgr.H02492' => 'egr', 'Eucgr.I01733' => 'egr', 'Eucgr.J02255' => 'egr', 'Eucgr.J02257' => 'egr', 'Eucgr.J02258' => 'egr', 'FAN02G1601' => 'fan', 'FAN03G1586' => 'fan', 'FAN03G2986' => 'fan', 'FAN05G4837' => 'fan', 'FAN06G0146' => 'fan', 'FAN07G0858' => 'fan', 'FAN09G3179' => 'fan', 'FAN10G0669' => 'fan', 'FAN12G2358' => 'fan', 'FAN14G4198' => 'fan', 'FAN14G5112' => 'fan', 'FAN17G0342' => 'fan', 'FAN19G0342' => 'fan', 'FAN19G0962' => 'fan', 'FAN19G1101' => 'fan', 'FAN19G1872' => 'fan', 'FAN22G0356' => 'fan', 'FAN23G0744' => 'fan', 'FAN23G1914' => 'fan', 'FAN26G0032' => 'fan', 'FAN28G0625' => 'fan', 'FvH4_1g02710' => 'fve', 'FvH4_1g02720' => 'fve', 'FvH4_4g25670' => 'fve', 'FvH4_6g51700' => 'fve', 'FvH4_7g20170' => 'fve', 'Glyma.05G175000' => 'gma', 'Glyma.08G132300' => 'gma', 'Glyma.11G243000' => 'gma', 'Glyma.13G158900' => 'gma', 'Glyma.17G112400' => 'gma', 'Glyma.18G014100' => 'gma', 'Glyma.19G003100' => 'gma', 'Glyma.19G056500' => 'gma', 'Gohir.A01G158900' => 'ghi', 'Gohir.A05G312600' => 'ghi', 'Gohir.A05G354900' => 'ghi', 'Gohir.A07G037200' => 'ghi', 'Gohir.A09G030000' => 'ghi', 'Gohir.A12G145200' => 'ghi', 'Gohir.D01G151500' => 'ghi', 'Gohir.D04G058300' => 'ghi', 'Gohir.D05G314100' => 'ghi', 'Gohir.D07G041400' => 'ghi', 'Gohir.D09G029700' => 'ghi', 'Gohir.D12G149700' => 'ghi', 'Gorai.001G043800' => 'gra', 'Gorai.002G187800' => 'gra', 'Gorai.006G034700' => 'gra', 'Gorai.008G161200' => 'gra', 'Gorai.009G335700' => 'gra', 'Gorai.012G065000' => 'gra', 'GSVIVG01000535001' => 'vvi', 'GSVIVG01015572001' => 'vvi', 'GSVIVG01032386001' => 'vvi', 'HanXRQChr05g0138531' => 'han', 'HanXRQChr06g0174391' => 'han', 'HanXRQChr07g0199021' => 'han', 'HanXRQChr08g0208211' => 'han', 'HanXRQChr09g0255471' => 'han', 'HanXRQChr10g0315791' => 'han', 'HanXRQChr12g0371991' => 'han', 'HanXRQChr15g0475251' => 'han', 'HanXRQChr17g0540001' => 'han', 'HanXRQChr17g0548631' => 'han', 'HanXRQChr17g0569561' => 'han', 'Haze_12256' => 'cav', 'Haze_14756' => 'cav', 'Haze_25528' => 'cav', 'Hma1.2p1_0079F.1_g041020' => 'hma', 'Hma1.2p1_0818F.1_g223260' => 'hma', 'Hma1.2p1_1747F.1_g300530' => 'hma', 'HPP92_004607' => 'vpl', 'HPP92_004608' => 'vpl', 'HPP92_006181' => 'vpl', 'HPP92_012192' => 'vpl', 'HPP92_015680' => 'vpl', 'HPP92_020249' => 'vpl', 'HPP92_021376' => 'vpl', 'HPP92_024275' => 'vpl', 'Hund06031' => 'sun', 'Hund25391' => 'sun', 'Lalb_Chr07g0185371' => 'lal', 'Lalb_Chr07g0185381' => 'lal', 'Lalb_Chr12g0204011' => 'lal', 'Lalb_Chr13g0301671' => 'lal', 'Lalb_Chr14g0362851' => 'lal', 'Lalb_Chr24g0403581' => 'lal', 'Lj1g0000233' => 'lja', 'Lj2g0018120' => 'lja', 'Lj3C621T0' => 'lonja', 'Lj3P1059T14' => 'lonja', 'Lj3P611T9' => 'lonja', 'Lj3P614T13' => 'lonja', 'Lj3P615T5' => 'lonja', 'Lj4g0012315' => 'lja', 'Lj4g0026182' => 'lja', 'Lj6P813T16' => 'lonja', 'Lj7C427T7' => 'lonja', 'Lj7C427T8' => 'lonja', 'Lj7P600T41' => 'lonja', 'Lju41C42G17' => 'lonja', 'Lsat_1_v5_gn_0_47300' => 'lsa', 'Lsat_1_v5_gn_2_91280' => 'lsa', 'Lsat_1_v5_gn_3_30561' => 'lsa', 'Lsat_1_v5_gn_4_184321' => 'lsa', 'Lsat_1_v5_gn_4_4041' => 'lsa', 'Lsat_1_v5_gn_5_92000' => 'lsa', 'Lsat_1_v5_gn_8_152940' => 'lsa', 'Lsat_1_v5_gn_8_62401' => 'lsa', 'Manes.06G055900' => 'mes', 'Manes.12G022200' => 'mes', 'Manes.13G023300' => 'mes', 'Manes.14G115000' => 'mes', 'Manes.15G151700' => 'mes', 'Manes.17G111300' => 'mes', 'Mapoly0226s0009' => 'mpo', 'MBI02_g25363_MAGBIO' => 'mbi', 'MBI06_g00027_MAGBIO' => 'mbi', 'MBI10_g13034_MAGBIO' => 'mbi', 'MD09G1023400' => 'mdo', 'MD13G1100100' => 'mdo', 'MD15G1169200' => 'mdo', 'MD16G1101100' => 'mdo', 'MD17G1022900' => 'mdo', 'Medtr3g096150' => 'mtr', 'Medtr4g115070' => 'mtr', 'Medtr7g033325' => 'mtr', 'Medtr8g089840' => 'mtr', 'MELO3C010319.2' => 'cme', 'MELO3C011944.2' => 'cme', 'MELO3C021589.2' => 'cme', 'Migut.E00207' => 'egut', 'Migut.H00067' => 'egut', 'Migut.K00433' => 'egut', 'Migut.K00606' => 'egut', 'Migut.K01410' => 'egut', 'MSTRG.13347' => 'ama', 'MSTRG.24045' => 'ama', 'MSTRG.2428' => 'ama', 'MSTRG.26410' => 'ama', 'MSTRG.3139' => 'ama', 'MSTRG.3286' => 'ama', 'MSTRG.563' => 'ama', 'MSTRG.7941' => 'ama', 'Nitab4.5_0000028g0060' => 'nta', 'Nitab4.5_0000065g0260' => 'nta', 'Nitab4.5_0000112g0060' => 'nta', 'Nitab4.5_0000489g0120' => 'nta', 'Nitab4.5_0001776g0050' => 'nta', 'Nitab4.5_0001854g0010' => 'nta', 'Nitab4.5_0001860g0020' => 'nta', 'Nitab4.5_0004352g0010' => 'nta', 'Nitab4.5_0008716g0020' => 'nta', 'Nitab4.5_0008922g0010' => 'nta', 'Nn3g16693' => 'nnu', 'Nn4g22596' => 'nnu', 'Nn7g37639' => 'nnu', 'Oeu001701.1' => 'oeu', 'Oeu018149.1' => 'oeu', 'Oeu026220.1' => 'oeu', 'Oeu038635.1' => 'oeu', 'Oeu049176.1' => 'oeu', 'Oeu056706.1' => 'oeu', 'Oeu056937.1' => 'oeu', 'Oeu057540.1' => 'oeu', 'Os02g0594900' => 'osa', 'Os02g0595100' => 'osa', 'Os04g0477500' => 'osa', 'Os12g0611900' => 'osa', 'Peaxi162Scf00076g00020' => 'pax', 'Peaxi162Scf00128g00217' => 'pax', 'Peaxi162Scf00129g01640' => 'pax', 'Peaxi162Scf00669g00007' => 'pax', 'Peaxi162Scf00700g00421' => 'pax', 'Peaxi162Scf00801g00038' => 'pax', 'Peaxi162Scf00891g00025' => 'pax', 'PGR083G0909' => 'pgr', 'PGR119G1005' => 'pgr', 'PGR142G2236' => 'pgr', 'PGR142G3388' => 'pgr', 'PGSC0003DMG400004514' => 'stu', 'PGSC0003DMG400012635' => 'stu', 'PGSC0003DMG400015730' => 'stu', 'PGSC0003DMG400018611' => 'stu', 'PGSC0003DMG400030897' => 'stu', 'Phvul.001G254800' => 'pvu', 'Phvul.002G260100' => 'pvu', 'Phvul.003G167600' => 'pvu', 'Phvul.004G005100' => 'pvu', 'Potri.001G343600' => 'ptr', 'Potri.006G066700' => 'ptr', 'Potri.008G186000' => 'ptr', 'Potri.010G046900' => 'ptr', 'Potri.018G127900' => 'ptr', 'Pp3c20_17750' => 'ppa', 'Pp3c24_4380' => 'ppa', 'Prupe.1G245800' => 'ppe', 'Prupe.3G293400' => 'ppe', 'Prupe.7G247400' => 'ppe', 'Psat0s145g0120' => 'psa', 'Psat0s595g0040' => 'psa', 'Psat0s595g0120' => 'psa', 'Psat3g175040' => 'psa', 'Psat7g058120' => 'psa', 'PSO017G0428' => 'pso', 'PSO063G7510' => 'pso', 'PSO067G0046' => 'pso', 'PSO478G1073' => 'pso', 'PSO675G3677' => 'pso', 'PSO675G6558' => 'pso', 'PSO675G7520' => 'pso', 'PSO675G8959' => 'pso', 'QL02p074089' => 'qlo', 'QL02p089614' => 'qlo', 'QL03p057736' => 'qlo', 'RcHm_v2.0_Chr1g0364131' => 'rch', 'RcHm_v2.0_Chr2g0087801' => 'rch', 'RcHm_v2.0_Chr2g0087821' => 'rch', 'RcHm_v2.0_Chr2g0173231' => 'rch', 'RcHm_v2.0_Chr4g0433111' => 'rch', 'Rhsim03G0250300' => 'rsi', 'Rhsim08G0048400' => 'rsi', 'Rhsim10G0014800' => 'rsi', 'Rhsim12G0040100' => 'rsi', 'Rhsim12G0109700' => 'rsi', 'Sabra06G0049600' => 'sbr', 'Sabra08G0141000' => 'sbr', 'Sabra10G0021400' => 'sbr', 'Sabra16G0222900' => 'sbr', 'Sabra18G0108600' => 'sbr', 'SalBow1G0433' => 'sbo', 'SalBow1G2038' => 'sbo', 'SalBow1G5003' => 'sbo', 'SalBow7G1197' => 'sbo', 'SalBow8G3506' => 'sbo', 'Sc03g0007300' => 'sci', 'Sc11g0000950' => 'sci', 'Sc14g0008750' => 'sci', 'Sc18g0000420' => 'sci', 'Sed0006754' => 'sed', 'Sed0008741' => 'sed', 'Sed0017172' => 'sed', 'Sed0018925' => 'sed', 'Sed0023326' => 'sed', 'Sed0025909' => 'sed', 'SEGI_05333' => 'sgi', 'SEGI_10362' => 'sgi', 'SEGI_13380' => 'sgi', 'SEGI_24306' => 'sgi', 'SEGI_29077' => 'sgi', 'SEGI_29095' => 'sgi', 'SEGI_36534' => 'sgi', 'SEGI_37506' => 'sgi', 'SEGI_38321' => 'sgi', 'SGA_v2.0_scaffold307G48031' => 'sas', 'SGA_v2.0_scaffold47G17507' => 'sas', 'SGA_v2.0_scaffold63G21736' => 'sas', 'SGA_v2.0_scaffold87G27070' => 'sas', 'SHI17794' => 'shi', 'SHI28851' => 'shi', 'SMO165G0155' => 'smo', 'SMO340G0217' => 'smo', 'SMO367G1210' => 'smo', 'Solyc02g093430.3' => 'sly', 'Solyc05g013580.4' => 'sly', 'Solyc07g008030.3' => 'sly', 'Solyc12g035470.2' => 'sly', 'Sopen02g038020' => 'spe', 'Sopen05g008490' => 'spe', 'Sopen07g003910' => 'spe', 'Sopen12g015240' => 'spe', 'Sp1g11550' => 'spa', 'Sp2g16710' => 'spa', 'Sp3g00430' => 'spa', 'Sp3g26780' => 'spa', 'Sp5g22900' => 'spa', 'Sp6g29530' => 'spa', 'TAR371G0794' => 'tar', 'TAR374G0164' => 'tar', 'TAR622G0165' => 'tar', 'TAR626G0929' => 'tar', 'TAR629G2155' => 'tar', 'THA.LOC104805282' => 'tha', 'THA.LOC104805363' => 'tha', 'THA.LOC104808968' => 'tha', 'THA.LOC104821093' => 'tha', 'THA.LOC104823953' => 'tha', 'THA.LOC104825562' => 'tha', 'THA.LOC104825665' => 'tha', 'Thecc.02G261400' => 'tca', 'Thecc.04G019200' => 'tca', 'Thecc.09G130400' => 'tca', 'Thhalv10004374m.g' => 'esa', 'Thhalv10007850m.g' => 'esa', 'Thhalv10013782m.g' => 'esa', 'Thhalv10018686m.g' => 'esa', 'Thhalv10020899m.g' => 'esa', 'Thhalv10022755m.g' => 'esa', 'TPR.G23851' => 'tpr', 'TPR.G26500' => 'tpr', 'TPR.G27267' => 'tpr', 'TPR.G32001' => 'tpr', 'TPR.G6251' => 'tpr', 'TPR.G8167' => 'tpr', 'TWI12G1330' => 'twi', 'TWI18G1239' => 'twi', 'TWI34G0979' => 'twi', 'TWI36G0670' => 'twi', 'TWI36G0707' => 'twi', 'TWI56G0233' => 'twi', 'TWI75G1809' => 'twi', 'unitig_21.g20874' => 'ugi', 'unitig_26.g10343' => 'ugi', 'unitig_46.g18392' => 'ugi', 'unitig_52.g17178' => 'ugi', 'unitig_8.g2934' => 'ugi', 'vmacro01122' => 'vma', 'vmacro05875' => 'vma', 'vmacro06147' => 'vma', 'vmacro16191' => 'vma', 'vmacro18293' => 'vma', 'VMungo0251G3707' => 'vmu', 'VMungo0464G1521' => 'vmu', 'VMungo1215G0205' => 'vmu', 'VMungo1383G2484' => 'vmu', 'Zm00001eb079610' => 'zma', 'Zm00001eb135990' => 'zma', 'Zm00001eb183710' => 'zma', 'Zm00001eb246020' => 'zma' ) $gf_id = 'HOM05D001124' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001124' ) $data_identifier = 'HOM05D001124' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 6, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 7, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 21, 'bol' => (int) 10, 'bra' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 6, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 9, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 21, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 8, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 10, 'lsa' => (int) 8, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 8, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 9, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb246020' $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' => 'HOM05D001124', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '548', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02520' => 'bna', 'A03p06630' => 'bna', 'A05p44460' => 'bna', 'A06p08710' => 'bna', 'A06p41090' => 'bna', 'A07p32320' => 'bna', 'A08p32520' => 'bna', 'A09p10360' => 'bna', 'A10p24080' => 'bna', 'Aa31LG11G15250' => 'aar', 'Aa31LG1G1800' => 'aar', 'Aa31LG2G5120' => 'aar', 'Aa31LG2G6070' => 'aar', 'Aa31LG5G10770' => 'aar', 'Aa31sc61G90' => 'aar', 'Actinidia01352' => 'ach', 'Actinidia05983' => 'ach', 'Actinidia08133' => 'ach', 'Actinidia15101' => 'ach', 'Actinidia26379' => 'ach', 'Actinidia35778' => 'ach', 'Actinidia36123' => 'ach', 'Actinidia37436' => 'ach', 'Actinidia38730' => 'ach', 'Ah.02g128210' => 'amhyb', 'Ah.03g132990' => 'amhyb', 'Ah.14g079410' => 'amhyb', 'AL1G24640' => 'aly', 'AL2G26680' => 'aly', 'AL3G10530' => 'aly', 'AL3G45230' => 'aly', 'AL5G15230' => 'aly', 'AL5G16960' => 'aly', 'AL6G25210' => 'aly', 'Aqoxy2G00441' => 'aox', 'Aqoxy3G01236' => 'aox', 'Aqoxy5G03746' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3RQ047' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C7GMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9C8JER' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MBL6KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YXCZ83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZANX40' => 'arhy', 'AT1G12990' => 'ath', 'AT1G67880' => 'ath', 'AT2G13290' => 'ath', 'AT3G01620' => 'ath', 'AT3G26445' => 'ath', 'AT3G27540' => 'ath', 'AT5G14480' => 'ath', 'ATR0824G026' => 'atr', 'ATR1098G019' => 'atr', 'Atru.chr11.2145' => 'acertr', 'Atru.chr2.3636' => 'acertr', 'Atru.chr2.3644' => 'acertr', 'Atru.chr6.2422' => 'acertr', 'Atru.chr7.1112' => 'acertr', 'AUR62005469' => 'cqu', 'AUR62011166' => 'cqu', 'AUR62013319' => 'cqu', 'AUR62024273' => 'cqu', 'AUR62028420' => 'cqu', 'AUR62041942' => 'cqu', 'BcaB01g04969' => 'bca', 'BcaB01g06371' => 'bca', 'BcaB02g11494' => 'bca', 'BcaB03g15382' => 'bca', 'BcaB08g36994' => 'bca', 'BcaC03g13477' => 'bca', 'BcaC03g13478' => 'bca', 'BcaC03g13480' => 'bca', 'BcaC03g13481' => 'bca', 'BcaC03g13486' => 'bca', 'BcaC04g19031' => 'bca', 'BcaC04g23085' => 'bca', 'BcaC05g25094' => 'bca', 'BcaC05g25096' => 'bca', 'BcaC05g25138' => 'bca', 'BcaC05g30416' => 'bca', 'BcaC05g30455' => 'bca', 'BcaC06g30979' => 'bca', 'BcaC06g33805' => 'bca', 'BcaC08g46021' => 'bca', 'BcaNung03154' => 'bca', 'BolC2t06623H' => 'bol', 'BolC2t06632H' => 'bol', 'BolC2t06635H' => 'bol', 'BolC2t06638H' => 'bol', 'BolC3t13266H' => 'bol', 'BolC5t29776H' => 'bol', 'BolC6t38912H' => 'bol', 'BolC7t44183H' => 'bol', 'BolC9t54123H' => 'bol', 'BolC9t59107H' => 'bol', 'BraA02t05221Z' => 'bra', 'BraA03t09996Z' => 'bra', 'BraA05t23210Z' => 'bra', 'BraA06t24068Z' => 'bra', 'BraA06t27032Z' => 'bra', 'BraA08t35176Z' => 'bra', 'BraA09t36680Z' => 'bra', 'BraA10t44471Z' => 'bra', 'C02p06760' => 'bna', 'C02p06890' => 'bna', 'C02p07010' => 'bna', 'C03p07660' => 'bna', 'C05p10300' => 'bna', 'C06p38150' => 'bna', 'C07p36650' => 'bna', 'C08p15770' => 'bna', 'C09p12300' => 'bna', 'C09p62700' => 'bna', 'C09p75040' => 'bna', 'CAN.G13.1' => 'can', 'CAN.G138.4' => 'can', 'CAN.G44.6' => 'can', 'CAN.G473.19' => 'can', 'CANSAT01G0835' => 'cansat', 'CANSAT11G0246' => 'cansat', 'CANSAT11G1766' => 'cansat', 'CANSAT64G1954' => 'cansat', 'CARHR013330' => 'chi', 'CARHR060530' => 'chi', 'CARHR075300' => 'chi', 'CARHR105120' => 'chi', 'CARHR148910' => 'chi', 'CARHR198830' => 'chi', 'Carub.0001s1275' => 'cru', 'Carub.0002s1437' => 'cru', 'Carub.0003s0044' => 'cru', 'Carub.0003s2787' => 'cru', 'Carub.0005s0597' => 'cru', 'Carub.0006s1266' => 'cru', 'Ca_06935_v3' => 'car', 'Ca_13559_v3' => 'car', 'Ca_16941_v3' => 'car', 'Ca_16960_v3' => 'car', 'Ca_17775_v3' => 'car', 'Ca_30464_v3' => 'car', 'Cc06_g08160' => 'ccan', 'Cc07_g01520' => 'ccan', 'Cc11_g15810' => 'ccan', 'CDE02G2840' => 'cde', 'CDE03G0093' => 'cde', 'CDE04G2127' => 'cde', 'CDE07G1857' => 'cde', 'CDE09G1246' => 'cde', 'Cfa003412' => 'cfa', 'Cfa007341' => 'cfa', 'Cfa009220' => 'cfa', 'Ciclev10008737m.g' => 'ccl', 'Ciclev10015565m.g' => 'ccl', 'Ciclev10031761m.g' => 'ccl', 'CiPaw.03G045300' => 'cil', 'CiPaw.03G247200' => 'cil', 'CiPaw.04G029500' => 'cil', 'CiPaw.04G174000' => 'cil', 'CiPaw.05G181200' => 'cil', 'CiPaw.06G067100' => 'cil', 'ClCG05G025800' => 'cla', 'ClCG06G011400' => 'cla', 'ClCG09G019360' => 'cla', 'COL.COLO4_04827' => 'col', 'COL.COLO4_29170' => 'col', 'COL.COLO4_35131' => 'col', 'COL.COLO4_35132' => 'col', 'Cpa.g.sc33.32' => 'cpa', 'Cpa.g.sc46.29' => 'cpa', 'Cpa.g.sc796.1' => 'cpa', 'CsaV3_1G030420' => 'csa', 'CsaV3_5G027050' => 'csa', 'CsaV3_5G031040' => 'csa', 'CsaV3_UNG023130' => 'csa', 'CSS0007726' => 'camsi', 'CSS0016433' => 'camsi', 'CSS0017656' => 'camsi', 'CSS0025364' => 'camsi', 'CSS0027582' => 'camsi', 'CSS0047288' => 'camsi', 'CSS0049950' => 'camsi', 'DCAR_003843' => 'dca', 'DCAR_007052' => 'dca', 'DCAR_020884' => 'dca', 'DCAR_021730' => 'dca', 'DCAR_024423' => 'dca', 'DCAR_026509' => 'dca', 'DCAR_031158' => 'dca', 'Dinv14728' => 'din', 'Dinv15219' => 'din', 'Dinv25728' => 'din', 'Dinv33428' => 'din', 'Dinv36489' => 'din', 'Dinv41486' => 'din', 'Duzib147G0469' => 'dzi', 'Duzib168G0060' => 'dzi', 'Duzib187G1215' => 'dzi', 'Duzib248G0692' => 'dzi', 'Duzib251G0767' => 'dzi', 'Duzib264G0446' => 'dzi', 'Duzib268G0691' => 'dzi', 'ECA232G4767' => 'eca', 'ECA233G2838' => 'eca', 'ECA234G0391' => 'eca', 'ECA234G0857' => 'eca', 'ECA236G1593' => 'eca', 'ECA238G0565' => 'eca', 'ECA246G1027' => 'eca', 'ECA246G3223' => 'eca', 'ECA246G3470' => 'eca', 'EL10Ac6g13829' => 'bvu', 'EL10Ac6g14093' => 'bvu', 'EL10Ac8g18707' => 'bvu', 'Eucgr.C01369' => 'egr', 'Eucgr.H02492' => 'egr', 'Eucgr.I01733' => 'egr', 'Eucgr.J02255' => 'egr', 'Eucgr.J02257' => 'egr', 'Eucgr.J02258' => 'egr', 'FAN02G1601' => 'fan', 'FAN03G1586' => 'fan', 'FAN03G2986' => 'fan', 'FAN05G4837' => 'fan', 'FAN06G0146' => 'fan', 'FAN07G0858' => 'fan', 'FAN09G3179' => 'fan', 'FAN10G0669' => 'fan', 'FAN12G2358' => 'fan', 'FAN14G4198' => 'fan', 'FAN14G5112' => 'fan', 'FAN17G0342' => 'fan', 'FAN19G0342' => 'fan', 'FAN19G0962' => 'fan', 'FAN19G1101' => 'fan', 'FAN19G1872' => 'fan', 'FAN22G0356' => 'fan', 'FAN23G0744' => 'fan', 'FAN23G1914' => 'fan', 'FAN26G0032' => 'fan', 'FAN28G0625' => 'fan', 'FvH4_1g02710' => 'fve', 'FvH4_1g02720' => 'fve', 'FvH4_4g25670' => 'fve', 'FvH4_6g51700' => 'fve', 'FvH4_7g20170' => 'fve', 'Glyma.05G175000' => 'gma', 'Glyma.08G132300' => 'gma', 'Glyma.11G243000' => 'gma', 'Glyma.13G158900' => 'gma', 'Glyma.17G112400' => 'gma', 'Glyma.18G014100' => 'gma', 'Glyma.19G003100' => 'gma', 'Glyma.19G056500' => 'gma', 'Gohir.A01G158900' => 'ghi', 'Gohir.A05G312600' => 'ghi', 'Gohir.A05G354900' => 'ghi', 'Gohir.A07G037200' => 'ghi', 'Gohir.A09G030000' => 'ghi', 'Gohir.A12G145200' => 'ghi', 'Gohir.D01G151500' => 'ghi', 'Gohir.D04G058300' => 'ghi', 'Gohir.D05G314100' => 'ghi', 'Gohir.D07G041400' => 'ghi', 'Gohir.D09G029700' => 'ghi', 'Gohir.D12G149700' => 'ghi', 'Gorai.001G043800' => 'gra', 'Gorai.002G187800' => 'gra', 'Gorai.006G034700' => 'gra', 'Gorai.008G161200' => 'gra', 'Gorai.009G335700' => 'gra', 'Gorai.012G065000' => 'gra', 'GSVIVG01000535001' => 'vvi', 'GSVIVG01015572001' => 'vvi', 'GSVIVG01032386001' => 'vvi', 'HanXRQChr05g0138531' => 'han', 'HanXRQChr06g0174391' => 'han', 'HanXRQChr07g0199021' => 'han', 'HanXRQChr08g0208211' => 'han', 'HanXRQChr09g0255471' => 'han', 'HanXRQChr10g0315791' => 'han', 'HanXRQChr12g0371991' => 'han', 'HanXRQChr15g0475251' => 'han', 'HanXRQChr17g0540001' => 'han', 'HanXRQChr17g0548631' => 'han', 'HanXRQChr17g0569561' => 'han', 'Haze_12256' => 'cav', 'Haze_14756' => 'cav', 'Haze_25528' => 'cav', 'Hma1.2p1_0079F.1_g041020' => 'hma', 'Hma1.2p1_0818F.1_g223260' => 'hma', 'Hma1.2p1_1747F.1_g300530' => 'hma', 'HPP92_004607' => 'vpl', 'HPP92_004608' => 'vpl', 'HPP92_006181' => 'vpl', 'HPP92_012192' => 'vpl', 'HPP92_015680' => 'vpl', 'HPP92_020249' => 'vpl', 'HPP92_021376' => 'vpl', 'HPP92_024275' => 'vpl', 'Hund06031' => 'sun', 'Hund25391' => 'sun', 'Lalb_Chr07g0185371' => 'lal', 'Lalb_Chr07g0185381' => 'lal', 'Lalb_Chr12g0204011' => 'lal', 'Lalb_Chr13g0301671' => 'lal', 'Lalb_Chr14g0362851' => 'lal', 'Lalb_Chr24g0403581' => 'lal', 'Lj1g0000233' => 'lja', 'Lj2g0018120' => 'lja', 'Lj3C621T0' => 'lonja', 'Lj3P1059T14' => 'lonja', 'Lj3P611T9' => 'lonja', 'Lj3P614T13' => 'lonja', 'Lj3P615T5' => 'lonja', 'Lj4g0012315' => 'lja', 'Lj4g0026182' => 'lja', 'Lj6P813T16' => 'lonja', 'Lj7C427T7' => 'lonja', 'Lj7C427T8' => 'lonja', 'Lj7P600T41' => 'lonja', 'Lju41C42G17' => 'lonja', 'Lsat_1_v5_gn_0_47300' => 'lsa', 'Lsat_1_v5_gn_2_91280' => 'lsa', 'Lsat_1_v5_gn_3_30561' => 'lsa', 'Lsat_1_v5_gn_4_184321' => 'lsa', 'Lsat_1_v5_gn_4_4041' => 'lsa', 'Lsat_1_v5_gn_5_92000' => 'lsa', 'Lsat_1_v5_gn_8_152940' => 'lsa', 'Lsat_1_v5_gn_8_62401' => 'lsa', 'Manes.06G055900' => 'mes', 'Manes.12G022200' => 'mes', 'Manes.13G023300' => 'mes', 'Manes.14G115000' => 'mes', 'Manes.15G151700' => 'mes', 'Manes.17G111300' => 'mes', 'Mapoly0226s0009' => 'mpo', 'MBI02_g25363_MAGBIO' => 'mbi', 'MBI06_g00027_MAGBIO' => 'mbi', 'MBI10_g13034_MAGBIO' => 'mbi', 'MD09G1023400' => 'mdo', 'MD13G1100100' => 'mdo', 'MD15G1169200' => 'mdo', 'MD16G1101100' => 'mdo', 'MD17G1022900' => 'mdo', 'Medtr3g096150' => 'mtr', 'Medtr4g115070' => 'mtr', 'Medtr7g033325' => 'mtr', 'Medtr8g089840' => 'mtr', 'MELO3C010319.2' => 'cme', 'MELO3C011944.2' => 'cme', 'MELO3C021589.2' => 'cme', 'Migut.E00207' => 'egut', 'Migut.H00067' => 'egut', 'Migut.K00433' => 'egut', 'Migut.K00606' => 'egut', 'Migut.K01410' => 'egut', 'MSTRG.13347' => 'ama', 'MSTRG.24045' => 'ama', 'MSTRG.2428' => 'ama', 'MSTRG.26410' => 'ama', 'MSTRG.3139' => 'ama', 'MSTRG.3286' => 'ama', 'MSTRG.563' => 'ama', 'MSTRG.7941' => 'ama', 'Nitab4.5_0000028g0060' => 'nta', 'Nitab4.5_0000065g0260' => 'nta', 'Nitab4.5_0000112g0060' => 'nta', 'Nitab4.5_0000489g0120' => 'nta', 'Nitab4.5_0001776g0050' => 'nta', 'Nitab4.5_0001854g0010' => 'nta', 'Nitab4.5_0001860g0020' => 'nta', 'Nitab4.5_0004352g0010' => 'nta', 'Nitab4.5_0008716g0020' => 'nta', 'Nitab4.5_0008922g0010' => 'nta', 'Nn3g16693' => 'nnu', 'Nn4g22596' => 'nnu', 'Nn7g37639' => 'nnu', 'Oeu001701.1' => 'oeu', 'Oeu018149.1' => 'oeu', 'Oeu026220.1' => 'oeu', 'Oeu038635.1' => 'oeu', 'Oeu049176.1' => 'oeu', 'Oeu056706.1' => 'oeu', 'Oeu056937.1' => 'oeu', 'Oeu057540.1' => 'oeu', 'Os02g0594900' => 'osa', 'Os02g0595100' => 'osa', 'Os04g0477500' => 'osa', 'Os12g0611900' => 'osa', 'Peaxi162Scf00076g00020' => 'pax', 'Peaxi162Scf00128g00217' => 'pax', 'Peaxi162Scf00129g01640' => 'pax', 'Peaxi162Scf00669g00007' => 'pax', 'Peaxi162Scf00700g00421' => 'pax', 'Peaxi162Scf00801g00038' => 'pax', 'Peaxi162Scf00891g00025' => 'pax', 'PGR083G0909' => 'pgr', 'PGR119G1005' => 'pgr', 'PGR142G2236' => 'pgr', 'PGR142G3388' => 'pgr', 'PGSC0003DMG400004514' => 'stu', 'PGSC0003DMG400012635' => 'stu', 'PGSC0003DMG400015730' => 'stu', 'PGSC0003DMG400018611' => 'stu', 'PGSC0003DMG400030897' => 'stu', 'Phvul.001G254800' => 'pvu', 'Phvul.002G260100' => 'pvu', 'Phvul.003G167600' => 'pvu', 'Phvul.004G005100' => 'pvu', 'Potri.001G343600' => 'ptr', 'Potri.006G066700' => 'ptr', 'Potri.008G186000' => 'ptr', 'Potri.010G046900' => 'ptr', 'Potri.018G127900' => 'ptr', 'Pp3c20_17750' => 'ppa', 'Pp3c24_4380' => 'ppa', 'Prupe.1G245800' => 'ppe', 'Prupe.3G293400' => 'ppe', 'Prupe.7G247400' => 'ppe', 'Psat0s145g0120' => 'psa', 'Psat0s595g0040' => 'psa', 'Psat0s595g0120' => 'psa', 'Psat3g175040' => 'psa', 'Psat7g058120' => 'psa', 'PSO017G0428' => 'pso', 'PSO063G7510' => 'pso', 'PSO067G0046' => 'pso', 'PSO478G1073' => 'pso', 'PSO675G3677' => 'pso', 'PSO675G6558' => 'pso', 'PSO675G7520' => 'pso', 'PSO675G8959' => 'pso', 'QL02p074089' => 'qlo', 'QL02p089614' => 'qlo', 'QL03p057736' => 'qlo', 'RcHm_v2.0_Chr1g0364131' => 'rch', 'RcHm_v2.0_Chr2g0087801' => 'rch', 'RcHm_v2.0_Chr2g0087821' => 'rch', 'RcHm_v2.0_Chr2g0173231' => 'rch', 'RcHm_v2.0_Chr4g0433111' => 'rch', 'Rhsim03G0250300' => 'rsi', 'Rhsim08G0048400' => 'rsi', 'Rhsim10G0014800' => 'rsi', 'Rhsim12G0040100' => 'rsi', 'Rhsim12G0109700' => 'rsi', 'Sabra06G0049600' => 'sbr', 'Sabra08G0141000' => 'sbr', 'Sabra10G0021400' => 'sbr', 'Sabra16G0222900' => 'sbr', 'Sabra18G0108600' => 'sbr', 'SalBow1G0433' => 'sbo', 'SalBow1G2038' => 'sbo', 'SalBow1G5003' => 'sbo', 'SalBow7G1197' => 'sbo', 'SalBow8G3506' => 'sbo', 'Sc03g0007300' => 'sci', 'Sc11g0000950' => 'sci', 'Sc14g0008750' => 'sci', 'Sc18g0000420' => 'sci', 'Sed0006754' => 'sed', 'Sed0008741' => 'sed', 'Sed0017172' => 'sed', 'Sed0018925' => 'sed', 'Sed0023326' => 'sed', 'Sed0025909' => 'sed', 'SEGI_05333' => 'sgi', 'SEGI_10362' => 'sgi', 'SEGI_13380' => 'sgi', 'SEGI_24306' => 'sgi', 'SEGI_29077' => 'sgi', 'SEGI_29095' => 'sgi', 'SEGI_36534' => 'sgi', 'SEGI_37506' => 'sgi', 'SEGI_38321' => 'sgi', 'SGA_v2.0_scaffold307G48031' => 'sas', 'SGA_v2.0_scaffold47G17507' => 'sas', 'SGA_v2.0_scaffold63G21736' => 'sas', 'SGA_v2.0_scaffold87G27070' => 'sas', 'SHI17794' => 'shi', 'SHI28851' => 'shi', 'SMO165G0155' => 'smo', 'SMO340G0217' => 'smo', 'SMO367G1210' => 'smo', 'Solyc02g093430.3' => 'sly', 'Solyc05g013580.4' => 'sly', 'Solyc07g008030.3' => 'sly', 'Solyc12g035470.2' => 'sly', 'Sopen02g038020' => 'spe', 'Sopen05g008490' => 'spe', 'Sopen07g003910' => 'spe', 'Sopen12g015240' => 'spe', 'Sp1g11550' => 'spa', 'Sp2g16710' => 'spa', 'Sp3g00430' => 'spa', 'Sp3g26780' => 'spa', 'Sp5g22900' => 'spa', 'Sp6g29530' => 'spa', 'TAR371G0794' => 'tar', 'TAR374G0164' => 'tar', 'TAR622G0165' => 'tar', 'TAR626G0929' => 'tar', 'TAR629G2155' => 'tar', 'THA.LOC104805282' => 'tha', 'THA.LOC104805363' => 'tha', 'THA.LOC104808968' => 'tha', 'THA.LOC104821093' => 'tha', 'THA.LOC104823953' => 'tha', 'THA.LOC104825562' => 'tha', 'THA.LOC104825665' => 'tha', 'Thecc.02G261400' => 'tca', 'Thecc.04G019200' => 'tca', 'Thecc.09G130400' => 'tca', 'Thhalv10004374m.g' => 'esa', 'Thhalv10007850m.g' => 'esa', 'Thhalv10013782m.g' => 'esa', 'Thhalv10018686m.g' => 'esa', 'Thhalv10020899m.g' => 'esa', 'Thhalv10022755m.g' => 'esa', 'TPR.G23851' => 'tpr', 'TPR.G26500' => 'tpr', 'TPR.G27267' => 'tpr', 'TPR.G32001' => 'tpr', 'TPR.G6251' => 'tpr', 'TPR.G8167' => 'tpr', 'TWI12G1330' => 'twi', 'TWI18G1239' => 'twi', 'TWI34G0979' => 'twi', 'TWI36G0670' => 'twi', 'TWI36G0707' => 'twi', 'TWI56G0233' => 'twi', 'TWI75G1809' => 'twi', 'unitig_21.g20874' => 'ugi', 'unitig_26.g10343' => 'ugi', 'unitig_46.g18392' => 'ugi', 'unitig_52.g17178' => 'ugi', 'unitig_8.g2934' => 'ugi', 'vmacro01122' => 'vma', 'vmacro05875' => 'vma', 'vmacro06147' => 'vma', 'vmacro16191' => 'vma', 'vmacro18293' => 'vma', 'VMungo0251G3707' => 'vmu', 'VMungo0464G1521' => 'vmu', 'VMungo1215G0205' => 'vmu', 'VMungo1383G2484' => 'vmu', 'Zm00001eb079610' => 'zma', 'Zm00001eb135990' => 'zma', 'Zm00001eb183710' => 'zma', 'Zm00001eb246020' => 'zma' ), 'gf_id' => 'HOM05D001124', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001124' ), 'data_identifier' => 'HOM05D001124', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001124', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '548', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02520' => 'bna', 'A03p06630' => 'bna', 'A05p44460' => 'bna', 'A06p08710' => 'bna', 'A06p41090' => 'bna', 'A07p32320' => 'bna', 'A08p32520' => 'bna', 'A09p10360' => 'bna', 'A10p24080' => 'bna', 'Aa31LG11G15250' => 'aar', 'Aa31LG1G1800' => 'aar', 'Aa31LG2G5120' => 'aar', 'Aa31LG2G6070' => 'aar', 'Aa31LG5G10770' => 'aar', 'Aa31sc61G90' => 'aar', 'Actinidia01352' => 'ach', 'Actinidia05983' => 'ach', 'Actinidia08133' => 'ach', 'Actinidia15101' => 'ach', 'Actinidia26379' => 'ach', 'Actinidia35778' => 'ach', 'Actinidia36123' => 'ach', 'Actinidia37436' => 'ach', 'Actinidia38730' => 'ach', 'Ah.02g128210' => 'amhyb', 'Ah.03g132990' => 'amhyb', 'Ah.14g079410' => 'amhyb', 'AL1G24640' => 'aly', 'AL2G26680' => 'aly', 'AL3G10530' => 'aly', 'AL3G45230' => 'aly', 'AL5G15230' => 'aly', 'AL5G16960' => 'aly', 'AL6G25210' => 'aly', 'Aqoxy2G00441' => 'aox', 'Aqoxy3G01236' => 'aox', 'Aqoxy5G03746' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3RQ047' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C7GMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9C8JER' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MBL6KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YXCZ83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZANX40' => 'arhy', 'AT1G12990' => 'ath', 'AT1G67880' => 'ath', 'AT2G13290' => 'ath', 'AT3G01620' => 'ath', 'AT3G26445' => 'ath', 'AT3G27540' => 'ath', 'AT5G14480' => 'ath', 'ATR0824G026' => 'atr', 'ATR1098G019' => 'atr', 'Atru.chr11.2145' => 'acertr', 'Atru.chr2.3636' => 'acertr', 'Atru.chr2.3644' => 'acertr', 'Atru.chr6.2422' => 'acertr', 'Atru.chr7.1112' => 'acertr', 'AUR62005469' => 'cqu', 'AUR62011166' => 'cqu', 'AUR62013319' => 'cqu', 'AUR62024273' => 'cqu', 'AUR62028420' => 'cqu', 'AUR62041942' => 'cqu', 'BcaB01g04969' => 'bca', 'BcaB01g06371' => 'bca', 'BcaB02g11494' => 'bca', 'BcaB03g15382' => 'bca', 'BcaB08g36994' => 'bca', 'BcaC03g13477' => 'bca', 'BcaC03g13478' => 'bca', 'BcaC03g13480' => 'bca', 'BcaC03g13481' => 'bca', 'BcaC03g13486' => 'bca', 'BcaC04g19031' => 'bca', 'BcaC04g23085' => 'bca', 'BcaC05g25094' => 'bca', 'BcaC05g25096' => 'bca', 'BcaC05g25138' => 'bca', 'BcaC05g30416' => 'bca', 'BcaC05g30455' => 'bca', 'BcaC06g30979' => 'bca', 'BcaC06g33805' => 'bca', 'BcaC08g46021' => 'bca', 'BcaNung03154' => 'bca', 'BolC2t06623H' => 'bol', 'BolC2t06632H' => 'bol', 'BolC2t06635H' => 'bol', 'BolC2t06638H' => 'bol', 'BolC3t13266H' => 'bol', 'BolC5t29776H' => 'bol', 'BolC6t38912H' => 'bol', 'BolC7t44183H' => 'bol', 'BolC9t54123H' => 'bol', 'BolC9t59107H' => 'bol', 'BraA02t05221Z' => 'bra', 'BraA03t09996Z' => 'bra', 'BraA05t23210Z' => 'bra', 'BraA06t24068Z' => 'bra', 'BraA06t27032Z' => 'bra', 'BraA08t35176Z' => 'bra', 'BraA09t36680Z' => 'bra', 'BraA10t44471Z' => 'bra', 'C02p06760' => 'bna', 'C02p06890' => 'bna', 'C02p07010' => 'bna', 'C03p07660' => 'bna', 'C05p10300' => 'bna', 'C06p38150' => 'bna', 'C07p36650' => 'bna', 'C08p15770' => 'bna', 'C09p12300' => 'bna', 'C09p62700' => 'bna', 'C09p75040' => 'bna', 'CAN.G13.1' => 'can', 'CAN.G138.4' => 'can', 'CAN.G44.6' => 'can', 'CAN.G473.19' => 'can', 'CANSAT01G0835' => 'cansat', 'CANSAT11G0246' => 'cansat', 'CANSAT11G1766' => 'cansat', 'CANSAT64G1954' => 'cansat', 'CARHR013330' => 'chi', 'CARHR060530' => 'chi', 'CARHR075300' => 'chi', 'CARHR105120' => 'chi', 'CARHR148910' => 'chi', 'CARHR198830' => 'chi', 'Carub.0001s1275' => 'cru', 'Carub.0002s1437' => 'cru', 'Carub.0003s0044' => 'cru', 'Carub.0003s2787' => 'cru', 'Carub.0005s0597' => 'cru', 'Carub.0006s1266' => 'cru', 'Ca_06935_v3' => 'car', 'Ca_13559_v3' => 'car', 'Ca_16941_v3' => 'car', 'Ca_16960_v3' => 'car', 'Ca_17775_v3' => 'car', 'Ca_30464_v3' => 'car', 'Cc06_g08160' => 'ccan', 'Cc07_g01520' => 'ccan', 'Cc11_g15810' => 'ccan', 'CDE02G2840' => 'cde', 'CDE03G0093' => 'cde', 'CDE04G2127' => 'cde', 'CDE07G1857' => 'cde', 'CDE09G1246' => 'cde', 'Cfa003412' => 'cfa', 'Cfa007341' => 'cfa', 'Cfa009220' => 'cfa', 'Ciclev10008737m.g' => 'ccl', 'Ciclev10015565m.g' => 'ccl', 'Ciclev10031761m.g' => 'ccl', 'CiPaw.03G045300' => 'cil', 'CiPaw.03G247200' => 'cil', 'CiPaw.04G029500' => 'cil', 'CiPaw.04G174000' => 'cil', 'CiPaw.05G181200' => 'cil', 'CiPaw.06G067100' => 'cil', 'ClCG05G025800' => 'cla', 'ClCG06G011400' => 'cla', 'ClCG09G019360' => 'cla', 'COL.COLO4_04827' => 'col', 'COL.COLO4_29170' => 'col', 'COL.COLO4_35131' => 'col', 'COL.COLO4_35132' => 'col', 'Cpa.g.sc33.32' => 'cpa', 'Cpa.g.sc46.29' => 'cpa', 'Cpa.g.sc796.1' => 'cpa', 'CsaV3_1G030420' => 'csa', 'CsaV3_5G027050' => 'csa', 'CsaV3_5G031040' => 'csa', 'CsaV3_UNG023130' => 'csa', 'CSS0007726' => 'camsi', 'CSS0016433' => 'camsi', 'CSS0017656' => 'camsi', 'CSS0025364' => 'camsi', 'CSS0027582' => 'camsi', 'CSS0047288' => 'camsi', 'CSS0049950' => 'camsi', 'DCAR_003843' => 'dca', 'DCAR_007052' => 'dca', 'DCAR_020884' => 'dca', 'DCAR_021730' => 'dca', 'DCAR_024423' => 'dca', 'DCAR_026509' => 'dca', 'DCAR_031158' => 'dca', 'Dinv14728' => 'din', 'Dinv15219' => 'din', 'Dinv25728' => 'din', 'Dinv33428' => 'din', 'Dinv36489' => 'din', 'Dinv41486' => 'din', 'Duzib147G0469' => 'dzi', 'Duzib168G0060' => 'dzi', 'Duzib187G1215' => 'dzi', 'Duzib248G0692' => 'dzi', 'Duzib251G0767' => 'dzi', 'Duzib264G0446' => 'dzi', 'Duzib268G0691' => 'dzi', 'ECA232G4767' => 'eca', 'ECA233G2838' => 'eca', 'ECA234G0391' => 'eca', 'ECA234G0857' => 'eca', 'ECA236G1593' => 'eca', 'ECA238G0565' => 'eca', 'ECA246G1027' => 'eca', 'ECA246G3223' => 'eca', 'ECA246G3470' => 'eca', 'EL10Ac6g13829' => 'bvu', 'EL10Ac6g14093' => 'bvu', 'EL10Ac8g18707' => 'bvu', 'Eucgr.C01369' => 'egr', 'Eucgr.H02492' => 'egr', 'Eucgr.I01733' => 'egr', 'Eucgr.J02255' => 'egr', 'Eucgr.J02257' => 'egr', 'Eucgr.J02258' => 'egr', 'FAN02G1601' => 'fan', 'FAN03G1586' => 'fan', 'FAN03G2986' => 'fan', 'FAN05G4837' => 'fan', 'FAN06G0146' => 'fan', 'FAN07G0858' => 'fan', 'FAN09G3179' => 'fan', 'FAN10G0669' => 'fan', 'FAN12G2358' => 'fan', 'FAN14G4198' => 'fan', 'FAN14G5112' => 'fan', 'FAN17G0342' => 'fan', 'FAN19G0342' => 'fan', 'FAN19G0962' => 'fan', 'FAN19G1101' => 'fan', 'FAN19G1872' => 'fan', 'FAN22G0356' => 'fan', 'FAN23G0744' => 'fan', 'FAN23G1914' => 'fan', 'FAN26G0032' => 'fan', 'FAN28G0625' => 'fan', 'FvH4_1g02710' => 'fve', 'FvH4_1g02720' => 'fve', 'FvH4_4g25670' => 'fve', 'FvH4_6g51700' => 'fve', 'FvH4_7g20170' => 'fve', 'Glyma.05G175000' => 'gma', 'Glyma.08G132300' => 'gma', 'Glyma.11G243000' => 'gma', 'Glyma.13G158900' => 'gma', 'Glyma.17G112400' => 'gma', 'Glyma.18G014100' => 'gma', 'Glyma.19G003100' => 'gma', 'Glyma.19G056500' => 'gma', 'Gohir.A01G158900' => 'ghi', 'Gohir.A05G312600' => 'ghi', 'Gohir.A05G354900' => 'ghi', 'Gohir.A07G037200' => 'ghi', 'Gohir.A09G030000' => 'ghi', 'Gohir.A12G145200' => 'ghi', 'Gohir.D01G151500' => 'ghi', 'Gohir.D04G058300' => 'ghi', 'Gohir.D05G314100' => 'ghi', 'Gohir.D07G041400' => 'ghi', 'Gohir.D09G029700' => 'ghi', 'Gohir.D12G149700' => 'ghi', 'Gorai.001G043800' => 'gra', 'Gorai.002G187800' => 'gra', 'Gorai.006G034700' => 'gra', 'Gorai.008G161200' => 'gra', 'Gorai.009G335700' => 'gra', 'Gorai.012G065000' => 'gra', 'GSVIVG01000535001' => 'vvi', 'GSVIVG01015572001' => 'vvi', 'GSVIVG01032386001' => 'vvi', 'HanXRQChr05g0138531' => 'han', 'HanXRQChr06g0174391' => 'han', 'HanXRQChr07g0199021' => 'han', 'HanXRQChr08g0208211' => 'han', 'HanXRQChr09g0255471' => 'han', 'HanXRQChr10g0315791' => 'han', 'HanXRQChr12g0371991' => 'han', 'HanXRQChr15g0475251' => 'han', 'HanXRQChr17g0540001' => 'han', 'HanXRQChr17g0548631' => 'han', 'HanXRQChr17g0569561' => 'han', 'Haze_12256' => 'cav', 'Haze_14756' => 'cav', 'Haze_25528' => 'cav', 'Hma1.2p1_0079F.1_g041020' => 'hma', 'Hma1.2p1_0818F.1_g223260' => 'hma', 'Hma1.2p1_1747F.1_g300530' => 'hma', 'HPP92_004607' => 'vpl', 'HPP92_004608' => 'vpl', 'HPP92_006181' => 'vpl', 'HPP92_012192' => 'vpl', 'HPP92_015680' => 'vpl', 'HPP92_020249' => 'vpl', 'HPP92_021376' => 'vpl', 'HPP92_024275' => 'vpl', 'Hund06031' => 'sun', 'Hund25391' => 'sun', 'Lalb_Chr07g0185371' => 'lal', 'Lalb_Chr07g0185381' => 'lal', 'Lalb_Chr12g0204011' => 'lal', 'Lalb_Chr13g0301671' => 'lal', 'Lalb_Chr14g0362851' => 'lal', 'Lalb_Chr24g0403581' => 'lal', 'Lj1g0000233' => 'lja', 'Lj2g0018120' => 'lja', 'Lj3C621T0' => 'lonja', 'Lj3P1059T14' => 'lonja', 'Lj3P611T9' => 'lonja', 'Lj3P614T13' => 'lonja', 'Lj3P615T5' => 'lonja', 'Lj4g0012315' => 'lja', 'Lj4g0026182' => 'lja', 'Lj6P813T16' => 'lonja', 'Lj7C427T7' => 'lonja', 'Lj7C427T8' => 'lonja', 'Lj7P600T41' => 'lonja', 'Lju41C42G17' => 'lonja', 'Lsat_1_v5_gn_0_47300' => 'lsa', 'Lsat_1_v5_gn_2_91280' => 'lsa', 'Lsat_1_v5_gn_3_30561' => 'lsa', 'Lsat_1_v5_gn_4_184321' => 'lsa', 'Lsat_1_v5_gn_4_4041' => 'lsa', 'Lsat_1_v5_gn_5_92000' => 'lsa', 'Lsat_1_v5_gn_8_152940' => 'lsa', 'Lsat_1_v5_gn_8_62401' => 'lsa', 'Manes.06G055900' => 'mes', 'Manes.12G022200' => 'mes', 'Manes.13G023300' => 'mes', 'Manes.14G115000' => 'mes', 'Manes.15G151700' => 'mes', 'Manes.17G111300' => 'mes', 'Mapoly0226s0009' => 'mpo', 'MBI02_g25363_MAGBIO' => 'mbi', 'MBI06_g00027_MAGBIO' => 'mbi', 'MBI10_g13034_MAGBIO' => 'mbi', 'MD09G1023400' => 'mdo', 'MD13G1100100' => 'mdo', 'MD15G1169200' => 'mdo', 'MD16G1101100' => 'mdo', 'MD17G1022900' => 'mdo', 'Medtr3g096150' => 'mtr', 'Medtr4g115070' => 'mtr', 'Medtr7g033325' => 'mtr', 'Medtr8g089840' => 'mtr', 'MELO3C010319.2' => 'cme', 'MELO3C011944.2' => 'cme', 'MELO3C021589.2' => 'cme', 'Migut.E00207' => 'egut', 'Migut.H00067' => 'egut', 'Migut.K00433' => 'egut', 'Migut.K00606' => 'egut', 'Migut.K01410' => 'egut', 'MSTRG.13347' => 'ama', 'MSTRG.24045' => 'ama', 'MSTRG.2428' => 'ama', 'MSTRG.26410' => 'ama', 'MSTRG.3139' => 'ama', 'MSTRG.3286' => 'ama', 'MSTRG.563' => 'ama', 'MSTRG.7941' => 'ama', 'Nitab4.5_0000028g0060' => 'nta', 'Nitab4.5_0000065g0260' => 'nta', 'Nitab4.5_0000112g0060' => 'nta', 'Nitab4.5_0000489g0120' => 'nta', 'Nitab4.5_0001776g0050' => 'nta', 'Nitab4.5_0001854g0010' => 'nta', 'Nitab4.5_0001860g0020' => 'nta', 'Nitab4.5_0004352g0010' => 'nta', 'Nitab4.5_0008716g0020' => 'nta', 'Nitab4.5_0008922g0010' => 'nta', 'Nn3g16693' => 'nnu', 'Nn4g22596' => 'nnu', 'Nn7g37639' => 'nnu', 'Oeu001701.1' => 'oeu', 'Oeu018149.1' => 'oeu', 'Oeu026220.1' => 'oeu', 'Oeu038635.1' => 'oeu', 'Oeu049176.1' => 'oeu', 'Oeu056706.1' => 'oeu', 'Oeu056937.1' => 'oeu', 'Oeu057540.1' => 'oeu', 'Os02g0594900' => 'osa', 'Os02g0595100' => 'osa', 'Os04g0477500' => 'osa', 'Os12g0611900' => 'osa', 'Peaxi162Scf00076g00020' => 'pax', 'Peaxi162Scf00128g00217' => 'pax', 'Peaxi162Scf00129g01640' => 'pax', 'Peaxi162Scf00669g00007' => 'pax', 'Peaxi162Scf00700g00421' => 'pax', 'Peaxi162Scf00801g00038' => 'pax', 'Peaxi162Scf00891g00025' => 'pax', 'PGR083G0909' => 'pgr', 'PGR119G1005' => 'pgr', 'PGR142G2236' => 'pgr', 'PGR142G3388' => 'pgr', 'PGSC0003DMG400004514' => 'stu', 'PGSC0003DMG400012635' => 'stu', 'PGSC0003DMG400015730' => 'stu', 'PGSC0003DMG400018611' => 'stu', 'PGSC0003DMG400030897' => 'stu', 'Phvul.001G254800' => 'pvu', 'Phvul.002G260100' => 'pvu', 'Phvul.003G167600' => 'pvu', 'Phvul.004G005100' => 'pvu', 'Potri.001G343600' => 'ptr', 'Potri.006G066700' => 'ptr', 'Potri.008G186000' => 'ptr', 'Potri.010G046900' => 'ptr', 'Potri.018G127900' => 'ptr', 'Pp3c20_17750' => 'ppa', 'Pp3c24_4380' => 'ppa', 'Prupe.1G245800' => 'ppe', 'Prupe.3G293400' => 'ppe', 'Prupe.7G247400' => 'ppe', 'Psat0s145g0120' => 'psa', 'Psat0s595g0040' => 'psa', 'Psat0s595g0120' => 'psa', 'Psat3g175040' => 'psa', 'Psat7g058120' => 'psa', 'PSO017G0428' => 'pso', 'PSO063G7510' => 'pso', 'PSO067G0046' => 'pso', 'PSO478G1073' => 'pso', 'PSO675G3677' => 'pso', 'PSO675G6558' => 'pso', 'PSO675G7520' => 'pso', 'PSO675G8959' => 'pso', 'QL02p074089' => 'qlo', 'QL02p089614' => 'qlo', 'QL03p057736' => 'qlo', 'RcHm_v2.0_Chr1g0364131' => 'rch', 'RcHm_v2.0_Chr2g0087801' => 'rch', 'RcHm_v2.0_Chr2g0087821' => 'rch', 'RcHm_v2.0_Chr2g0173231' => 'rch', 'RcHm_v2.0_Chr4g0433111' => 'rch', 'Rhsim03G0250300' => 'rsi', 'Rhsim08G0048400' => 'rsi', 'Rhsim10G0014800' => 'rsi', 'Rhsim12G0040100' => 'rsi', 'Rhsim12G0109700' => 'rsi', 'Sabra06G0049600' => 'sbr', 'Sabra08G0141000' => 'sbr', 'Sabra10G0021400' => 'sbr', 'Sabra16G0222900' => 'sbr', 'Sabra18G0108600' => 'sbr', 'SalBow1G0433' => 'sbo', 'SalBow1G2038' => 'sbo', 'SalBow1G5003' => 'sbo', 'SalBow7G1197' => 'sbo', 'SalBow8G3506' => 'sbo', 'Sc03g0007300' => 'sci', 'Sc11g0000950' => 'sci', 'Sc14g0008750' => 'sci', 'Sc18g0000420' => 'sci', 'Sed0006754' => 'sed', 'Sed0008741' => 'sed', 'Sed0017172' => 'sed', 'Sed0018925' => 'sed', 'Sed0023326' => 'sed', 'Sed0025909' => 'sed', 'SEGI_05333' => 'sgi', 'SEGI_10362' => 'sgi', 'SEGI_13380' => 'sgi', 'SEGI_24306' => 'sgi', 'SEGI_29077' => 'sgi', 'SEGI_29095' => 'sgi', 'SEGI_36534' => 'sgi', 'SEGI_37506' => 'sgi', 'SEGI_38321' => 'sgi', 'SGA_v2.0_scaffold307G48031' => 'sas', 'SGA_v2.0_scaffold47G17507' => 'sas', 'SGA_v2.0_scaffold63G21736' => 'sas', 'SGA_v2.0_scaffold87G27070' => 'sas', 'SHI17794' => 'shi', 'SHI28851' => 'shi', 'SMO165G0155' => 'smo', 'SMO340G0217' => 'smo', 'SMO367G1210' => 'smo', 'Solyc02g093430.3' => 'sly', 'Solyc05g013580.4' => 'sly', 'Solyc07g008030.3' => 'sly', 'Solyc12g035470.2' => 'sly', 'Sopen02g038020' => 'spe', 'Sopen05g008490' => 'spe', 'Sopen07g003910' => 'spe', 'Sopen12g015240' => 'spe', 'Sp1g11550' => 'spa', 'Sp2g16710' => 'spa', 'Sp3g00430' => 'spa', 'Sp3g26780' => 'spa', 'Sp5g22900' => 'spa', 'Sp6g29530' => 'spa', 'TAR371G0794' => 'tar', 'TAR374G0164' => 'tar', 'TAR622G0165' => 'tar', 'TAR626G0929' => 'tar', 'TAR629G2155' => 'tar', 'THA.LOC104805282' => 'tha', 'THA.LOC104805363' => 'tha', 'THA.LOC104808968' => 'tha', 'THA.LOC104821093' => 'tha', 'THA.LOC104823953' => 'tha', 'THA.LOC104825562' => 'tha', 'THA.LOC104825665' => 'tha', 'Thecc.02G261400' => 'tca', 'Thecc.04G019200' => 'tca', 'Thecc.09G130400' => 'tca', 'Thhalv10004374m.g' => 'esa', 'Thhalv10007850m.g' => 'esa', 'Thhalv10013782m.g' => 'esa', 'Thhalv10018686m.g' => 'esa', 'Thhalv10020899m.g' => 'esa', 'Thhalv10022755m.g' => 'esa', 'TPR.G23851' => 'tpr', 'TPR.G26500' => 'tpr', 'TPR.G27267' => 'tpr', 'TPR.G32001' => 'tpr', 'TPR.G6251' => 'tpr', 'TPR.G8167' => 'tpr', 'TWI12G1330' => 'twi', 'TWI18G1239' => 'twi', 'TWI34G0979' => 'twi', 'TWI36G0670' => 'twi', 'TWI36G0707' => 'twi', 'TWI56G0233' => 'twi', 'TWI75G1809' => 'twi', 'unitig_21.g20874' => 'ugi', 'unitig_26.g10343' => 'ugi', 'unitig_46.g18392' => 'ugi', 'unitig_52.g17178' => 'ugi', 'unitig_8.g2934' => 'ugi', 'vmacro01122' => 'vma', 'vmacro05875' => 'vma', 'vmacro06147' => 'vma', 'vmacro16191' => 'vma', 'vmacro18293' => 'vma', 'VMungo0251G3707' => 'vmu', 'VMungo0464G1521' => 'vmu', 'VMungo1215G0205' => 'vmu', 'VMungo1383G2484' => 'vmu', 'Zm00001eb079610' => 'zma', 'Zm00001eb135990' => 'zma', 'Zm00001eb183710' => 'zma', 'Zm00001eb246020' => 'zma' ) $gf_id = 'HOM05D001124' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001124' ) $data_identifier = 'HOM05D001124' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 6, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 7, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 21, 'bol' => (int) 10, 'bra' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 6, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 9, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 21, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 8, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 10, 'lsa' => (int) 8, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 8, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 9, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb246020' $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' => 'HOM05D001124', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '548', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02520' => 'bna', 'A03p06630' => 'bna', 'A05p44460' => 'bna', 'A06p08710' => 'bna', 'A06p41090' => 'bna', 'A07p32320' => 'bna', 'A08p32520' => 'bna', 'A09p10360' => 'bna', 'A10p24080' => 'bna', 'Aa31LG11G15250' => 'aar', 'Aa31LG1G1800' => 'aar', 'Aa31LG2G5120' => 'aar', 'Aa31LG2G6070' => 'aar', 'Aa31LG5G10770' => 'aar', 'Aa31sc61G90' => 'aar', 'Actinidia01352' => 'ach', 'Actinidia05983' => 'ach', 'Actinidia08133' => 'ach', 'Actinidia15101' => 'ach', 'Actinidia26379' => 'ach', 'Actinidia35778' => 'ach', 'Actinidia36123' => 'ach', 'Actinidia37436' => 'ach', 'Actinidia38730' => 'ach', 'Ah.02g128210' => 'amhyb', 'Ah.03g132990' => 'amhyb', 'Ah.14g079410' => 'amhyb', 'AL1G24640' => 'aly', 'AL2G26680' => 'aly', 'AL3G10530' => 'aly', 'AL3G45230' => 'aly', 'AL5G15230' => 'aly', 'AL5G16960' => 'aly', 'AL6G25210' => 'aly', 'Aqoxy2G00441' => 'aox', 'Aqoxy3G01236' => 'aox', 'Aqoxy5G03746' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3RQ047' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C7GMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9C8JER' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MBL6KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YXCZ83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZANX40' => 'arhy', 'AT1G12990' => 'ath', 'AT1G67880' => 'ath', 'AT2G13290' => 'ath', 'AT3G01620' => 'ath', 'AT3G26445' => 'ath', 'AT3G27540' => 'ath', 'AT5G14480' => 'ath', 'ATR0824G026' => 'atr', 'ATR1098G019' => 'atr', 'Atru.chr11.2145' => 'acertr', 'Atru.chr2.3636' => 'acertr', 'Atru.chr2.3644' => 'acertr', 'Atru.chr6.2422' => 'acertr', 'Atru.chr7.1112' => 'acertr', 'AUR62005469' => 'cqu', 'AUR62011166' => 'cqu', 'AUR62013319' => 'cqu', 'AUR62024273' => 'cqu', 'AUR62028420' => 'cqu', 'AUR62041942' => 'cqu', 'BcaB01g04969' => 'bca', 'BcaB01g06371' => 'bca', 'BcaB02g11494' => 'bca', 'BcaB03g15382' => 'bca', 'BcaB08g36994' => 'bca', 'BcaC03g13477' => 'bca', 'BcaC03g13478' => 'bca', 'BcaC03g13480' => 'bca', 'BcaC03g13481' => 'bca', 'BcaC03g13486' => 'bca', 'BcaC04g19031' => 'bca', 'BcaC04g23085' => 'bca', 'BcaC05g25094' => 'bca', 'BcaC05g25096' => 'bca', 'BcaC05g25138' => 'bca', 'BcaC05g30416' => 'bca', 'BcaC05g30455' => 'bca', 'BcaC06g30979' => 'bca', 'BcaC06g33805' => 'bca', 'BcaC08g46021' => 'bca', 'BcaNung03154' => 'bca', 'BolC2t06623H' => 'bol', 'BolC2t06632H' => 'bol', 'BolC2t06635H' => 'bol', 'BolC2t06638H' => 'bol', 'BolC3t13266H' => 'bol', 'BolC5t29776H' => 'bol', 'BolC6t38912H' => 'bol', 'BolC7t44183H' => 'bol', 'BolC9t54123H' => 'bol', 'BolC9t59107H' => 'bol', 'BraA02t05221Z' => 'bra', 'BraA03t09996Z' => 'bra', 'BraA05t23210Z' => 'bra', 'BraA06t24068Z' => 'bra', 'BraA06t27032Z' => 'bra', 'BraA08t35176Z' => 'bra', 'BraA09t36680Z' => 'bra', 'BraA10t44471Z' => 'bra', 'C02p06760' => 'bna', 'C02p06890' => 'bna', 'C02p07010' => 'bna', 'C03p07660' => 'bna', 'C05p10300' => 'bna', 'C06p38150' => 'bna', 'C07p36650' => 'bna', 'C08p15770' => 'bna', 'C09p12300' => 'bna', 'C09p62700' => 'bna', 'C09p75040' => 'bna', 'CAN.G13.1' => 'can', 'CAN.G138.4' => 'can', 'CAN.G44.6' => 'can', 'CAN.G473.19' => 'can', 'CANSAT01G0835' => 'cansat', 'CANSAT11G0246' => 'cansat', 'CANSAT11G1766' => 'cansat', 'CANSAT64G1954' => 'cansat', 'CARHR013330' => 'chi', 'CARHR060530' => 'chi', 'CARHR075300' => 'chi', 'CARHR105120' => 'chi', 'CARHR148910' => 'chi', 'CARHR198830' => 'chi', 'Carub.0001s1275' => 'cru', 'Carub.0002s1437' => 'cru', 'Carub.0003s0044' => 'cru', 'Carub.0003s2787' => 'cru', 'Carub.0005s0597' => 'cru', 'Carub.0006s1266' => 'cru', 'Ca_06935_v3' => 'car', 'Ca_13559_v3' => 'car', 'Ca_16941_v3' => 'car', 'Ca_16960_v3' => 'car', 'Ca_17775_v3' => 'car', 'Ca_30464_v3' => 'car', 'Cc06_g08160' => 'ccan', 'Cc07_g01520' => 'ccan', 'Cc11_g15810' => 'ccan', 'CDE02G2840' => 'cde', 'CDE03G0093' => 'cde', 'CDE04G2127' => 'cde', 'CDE07G1857' => 'cde', 'CDE09G1246' => 'cde', 'Cfa003412' => 'cfa', 'Cfa007341' => 'cfa', 'Cfa009220' => 'cfa', 'Ciclev10008737m.g' => 'ccl', 'Ciclev10015565m.g' => 'ccl', 'Ciclev10031761m.g' => 'ccl', 'CiPaw.03G045300' => 'cil', 'CiPaw.03G247200' => 'cil', 'CiPaw.04G029500' => 'cil', 'CiPaw.04G174000' => 'cil', 'CiPaw.05G181200' => 'cil', 'CiPaw.06G067100' => 'cil', 'ClCG05G025800' => 'cla', 'ClCG06G011400' => 'cla', 'ClCG09G019360' => 'cla', 'COL.COLO4_04827' => 'col', 'COL.COLO4_29170' => 'col', 'COL.COLO4_35131' => 'col', 'COL.COLO4_35132' => 'col', 'Cpa.g.sc33.32' => 'cpa', 'Cpa.g.sc46.29' => 'cpa', 'Cpa.g.sc796.1' => 'cpa', 'CsaV3_1G030420' => 'csa', 'CsaV3_5G027050' => 'csa', 'CsaV3_5G031040' => 'csa', 'CsaV3_UNG023130' => 'csa', 'CSS0007726' => 'camsi', 'CSS0016433' => 'camsi', 'CSS0017656' => 'camsi', 'CSS0025364' => 'camsi', 'CSS0027582' => 'camsi', 'CSS0047288' => 'camsi', 'CSS0049950' => 'camsi', 'DCAR_003843' => 'dca', 'DCAR_007052' => 'dca', 'DCAR_020884' => 'dca', 'DCAR_021730' => 'dca', 'DCAR_024423' => 'dca', 'DCAR_026509' => 'dca', 'DCAR_031158' => 'dca', 'Dinv14728' => 'din', 'Dinv15219' => 'din', 'Dinv25728' => 'din', 'Dinv33428' => 'din', 'Dinv36489' => 'din', 'Dinv41486' => 'din', 'Duzib147G0469' => 'dzi', 'Duzib168G0060' => 'dzi', 'Duzib187G1215' => 'dzi', 'Duzib248G0692' => 'dzi', 'Duzib251G0767' => 'dzi', 'Duzib264G0446' => 'dzi', 'Duzib268G0691' => 'dzi', 'ECA232G4767' => 'eca', 'ECA233G2838' => 'eca', 'ECA234G0391' => 'eca', 'ECA234G0857' => 'eca', 'ECA236G1593' => 'eca', 'ECA238G0565' => 'eca', 'ECA246G1027' => 'eca', 'ECA246G3223' => 'eca', 'ECA246G3470' => 'eca', 'EL10Ac6g13829' => 'bvu', 'EL10Ac6g14093' => 'bvu', 'EL10Ac8g18707' => 'bvu', 'Eucgr.C01369' => 'egr', 'Eucgr.H02492' => 'egr', 'Eucgr.I01733' => 'egr', 'Eucgr.J02255' => 'egr', 'Eucgr.J02257' => 'egr', 'Eucgr.J02258' => 'egr', 'FAN02G1601' => 'fan', 'FAN03G1586' => 'fan', 'FAN03G2986' => 'fan', 'FAN05G4837' => 'fan', 'FAN06G0146' => 'fan', 'FAN07G0858' => 'fan', 'FAN09G3179' => 'fan', 'FAN10G0669' => 'fan', 'FAN12G2358' => 'fan', 'FAN14G4198' => 'fan', 'FAN14G5112' => 'fan', 'FAN17G0342' => 'fan', 'FAN19G0342' => 'fan', 'FAN19G0962' => 'fan', 'FAN19G1101' => 'fan', 'FAN19G1872' => 'fan', 'FAN22G0356' => 'fan', 'FAN23G0744' => 'fan', 'FAN23G1914' => 'fan', 'FAN26G0032' => 'fan', 'FAN28G0625' => 'fan', 'FvH4_1g02710' => 'fve', 'FvH4_1g02720' => 'fve', 'FvH4_4g25670' => 'fve', 'FvH4_6g51700' => 'fve', 'FvH4_7g20170' => 'fve', 'Glyma.05G175000' => 'gma', 'Glyma.08G132300' => 'gma', 'Glyma.11G243000' => 'gma', 'Glyma.13G158900' => 'gma', 'Glyma.17G112400' => 'gma', 'Glyma.18G014100' => 'gma', 'Glyma.19G003100' => 'gma', 'Glyma.19G056500' => 'gma', 'Gohir.A01G158900' => 'ghi', 'Gohir.A05G312600' => 'ghi', 'Gohir.A05G354900' => 'ghi', 'Gohir.A07G037200' => 'ghi', 'Gohir.A09G030000' => 'ghi', 'Gohir.A12G145200' => 'ghi', 'Gohir.D01G151500' => 'ghi', 'Gohir.D04G058300' => 'ghi', 'Gohir.D05G314100' => 'ghi', 'Gohir.D07G041400' => 'ghi', 'Gohir.D09G029700' => 'ghi', 'Gohir.D12G149700' => 'ghi', 'Gorai.001G043800' => 'gra', 'Gorai.002G187800' => 'gra', 'Gorai.006G034700' => 'gra', 'Gorai.008G161200' => 'gra', 'Gorai.009G335700' => 'gra', 'Gorai.012G065000' => 'gra', 'GSVIVG01000535001' => 'vvi', 'GSVIVG01015572001' => 'vvi', 'GSVIVG01032386001' => 'vvi', 'HanXRQChr05g0138531' => 'han', 'HanXRQChr06g0174391' => 'han', 'HanXRQChr07g0199021' => 'han', 'HanXRQChr08g0208211' => 'han', 'HanXRQChr09g0255471' => 'han', 'HanXRQChr10g0315791' => 'han', 'HanXRQChr12g0371991' => 'han', 'HanXRQChr15g0475251' => 'han', 'HanXRQChr17g0540001' => 'han', 'HanXRQChr17g0548631' => 'han', 'HanXRQChr17g0569561' => 'han', 'Haze_12256' => 'cav', 'Haze_14756' => 'cav', 'Haze_25528' => 'cav', 'Hma1.2p1_0079F.1_g041020' => 'hma', 'Hma1.2p1_0818F.1_g223260' => 'hma', 'Hma1.2p1_1747F.1_g300530' => 'hma', 'HPP92_004607' => 'vpl', 'HPP92_004608' => 'vpl', 'HPP92_006181' => 'vpl', 'HPP92_012192' => 'vpl', 'HPP92_015680' => 'vpl', 'HPP92_020249' => 'vpl', 'HPP92_021376' => 'vpl', 'HPP92_024275' => 'vpl', 'Hund06031' => 'sun', 'Hund25391' => 'sun', 'Lalb_Chr07g0185371' => 'lal', 'Lalb_Chr07g0185381' => 'lal', 'Lalb_Chr12g0204011' => 'lal', 'Lalb_Chr13g0301671' => 'lal', 'Lalb_Chr14g0362851' => 'lal', 'Lalb_Chr24g0403581' => 'lal', 'Lj1g0000233' => 'lja', 'Lj2g0018120' => 'lja', 'Lj3C621T0' => 'lonja', 'Lj3P1059T14' => 'lonja', 'Lj3P611T9' => 'lonja', 'Lj3P614T13' => 'lonja', 'Lj3P615T5' => 'lonja', 'Lj4g0012315' => 'lja', 'Lj4g0026182' => 'lja', 'Lj6P813T16' => 'lonja', 'Lj7C427T7' => 'lonja', 'Lj7C427T8' => 'lonja', 'Lj7P600T41' => 'lonja', 'Lju41C42G17' => 'lonja', 'Lsat_1_v5_gn_0_47300' => 'lsa', 'Lsat_1_v5_gn_2_91280' => 'lsa', 'Lsat_1_v5_gn_3_30561' => 'lsa', 'Lsat_1_v5_gn_4_184321' => 'lsa', 'Lsat_1_v5_gn_4_4041' => 'lsa', 'Lsat_1_v5_gn_5_92000' => 'lsa', 'Lsat_1_v5_gn_8_152940' => 'lsa', 'Lsat_1_v5_gn_8_62401' => 'lsa', 'Manes.06G055900' => 'mes', 'Manes.12G022200' => 'mes', 'Manes.13G023300' => 'mes', 'Manes.14G115000' => 'mes', 'Manes.15G151700' => 'mes', 'Manes.17G111300' => 'mes', 'Mapoly0226s0009' => 'mpo', 'MBI02_g25363_MAGBIO' => 'mbi', 'MBI06_g00027_MAGBIO' => 'mbi', 'MBI10_g13034_MAGBIO' => 'mbi', 'MD09G1023400' => 'mdo', 'MD13G1100100' => 'mdo', 'MD15G1169200' => 'mdo', 'MD16G1101100' => 'mdo', 'MD17G1022900' => 'mdo', 'Medtr3g096150' => 'mtr', 'Medtr4g115070' => 'mtr', 'Medtr7g033325' => 'mtr', 'Medtr8g089840' => 'mtr', 'MELO3C010319.2' => 'cme', 'MELO3C011944.2' => 'cme', 'MELO3C021589.2' => 'cme', 'Migut.E00207' => 'egut', 'Migut.H00067' => 'egut', 'Migut.K00433' => 'egut', 'Migut.K00606' => 'egut', 'Migut.K01410' => 'egut', 'MSTRG.13347' => 'ama', 'MSTRG.24045' => 'ama', 'MSTRG.2428' => 'ama', 'MSTRG.26410' => 'ama', 'MSTRG.3139' => 'ama', 'MSTRG.3286' => 'ama', 'MSTRG.563' => 'ama', 'MSTRG.7941' => 'ama', 'Nitab4.5_0000028g0060' => 'nta', 'Nitab4.5_0000065g0260' => 'nta', 'Nitab4.5_0000112g0060' => 'nta', 'Nitab4.5_0000489g0120' => 'nta', 'Nitab4.5_0001776g0050' => 'nta', 'Nitab4.5_0001854g0010' => 'nta', 'Nitab4.5_0001860g0020' => 'nta', 'Nitab4.5_0004352g0010' => 'nta', 'Nitab4.5_0008716g0020' => 'nta', 'Nitab4.5_0008922g0010' => 'nta', 'Nn3g16693' => 'nnu', 'Nn4g22596' => 'nnu', 'Nn7g37639' => 'nnu', 'Oeu001701.1' => 'oeu', 'Oeu018149.1' => 'oeu', 'Oeu026220.1' => 'oeu', 'Oeu038635.1' => 'oeu', 'Oeu049176.1' => 'oeu', 'Oeu056706.1' => 'oeu', 'Oeu056937.1' => 'oeu', 'Oeu057540.1' => 'oeu', 'Os02g0594900' => 'osa', 'Os02g0595100' => 'osa', 'Os04g0477500' => 'osa', 'Os12g0611900' => 'osa', 'Peaxi162Scf00076g00020' => 'pax', 'Peaxi162Scf00128g00217' => 'pax', 'Peaxi162Scf00129g01640' => 'pax', 'Peaxi162Scf00669g00007' => 'pax', 'Peaxi162Scf00700g00421' => 'pax', 'Peaxi162Scf00801g00038' => 'pax', 'Peaxi162Scf00891g00025' => 'pax', 'PGR083G0909' => 'pgr', 'PGR119G1005' => 'pgr', 'PGR142G2236' => 'pgr', 'PGR142G3388' => 'pgr', 'PGSC0003DMG400004514' => 'stu', 'PGSC0003DMG400012635' => 'stu', 'PGSC0003DMG400015730' => 'stu', 'PGSC0003DMG400018611' => 'stu', 'PGSC0003DMG400030897' => 'stu', 'Phvul.001G254800' => 'pvu', 'Phvul.002G260100' => 'pvu', 'Phvul.003G167600' => 'pvu', 'Phvul.004G005100' => 'pvu', 'Potri.001G343600' => 'ptr', 'Potri.006G066700' => 'ptr', 'Potri.008G186000' => 'ptr', 'Potri.010G046900' => 'ptr', 'Potri.018G127900' => 'ptr', 'Pp3c20_17750' => 'ppa', 'Pp3c24_4380' => 'ppa', 'Prupe.1G245800' => 'ppe', 'Prupe.3G293400' => 'ppe', 'Prupe.7G247400' => 'ppe', 'Psat0s145g0120' => 'psa', 'Psat0s595g0040' => 'psa', 'Psat0s595g0120' => 'psa', 'Psat3g175040' => 'psa', 'Psat7g058120' => 'psa', 'PSO017G0428' => 'pso', 'PSO063G7510' => 'pso', 'PSO067G0046' => 'pso', 'PSO478G1073' => 'pso', 'PSO675G3677' => 'pso', 'PSO675G6558' => 'pso', 'PSO675G7520' => 'pso', 'PSO675G8959' => 'pso', 'QL02p074089' => 'qlo', 'QL02p089614' => 'qlo', 'QL03p057736' => 'qlo', 'RcHm_v2.0_Chr1g0364131' => 'rch', 'RcHm_v2.0_Chr2g0087801' => 'rch', 'RcHm_v2.0_Chr2g0087821' => 'rch', 'RcHm_v2.0_Chr2g0173231' => 'rch', 'RcHm_v2.0_Chr4g0433111' => 'rch', 'Rhsim03G0250300' => 'rsi', 'Rhsim08G0048400' => 'rsi', 'Rhsim10G0014800' => 'rsi', 'Rhsim12G0040100' => 'rsi', 'Rhsim12G0109700' => 'rsi', 'Sabra06G0049600' => 'sbr', 'Sabra08G0141000' => 'sbr', 'Sabra10G0021400' => 'sbr', 'Sabra16G0222900' => 'sbr', 'Sabra18G0108600' => 'sbr', 'SalBow1G0433' => 'sbo', 'SalBow1G2038' => 'sbo', 'SalBow1G5003' => 'sbo', 'SalBow7G1197' => 'sbo', 'SalBow8G3506' => 'sbo', 'Sc03g0007300' => 'sci', 'Sc11g0000950' => 'sci', 'Sc14g0008750' => 'sci', 'Sc18g0000420' => 'sci', 'Sed0006754' => 'sed', 'Sed0008741' => 'sed', 'Sed0017172' => 'sed', 'Sed0018925' => 'sed', 'Sed0023326' => 'sed', 'Sed0025909' => 'sed', 'SEGI_05333' => 'sgi', 'SEGI_10362' => 'sgi', 'SEGI_13380' => 'sgi', 'SEGI_24306' => 'sgi', 'SEGI_29077' => 'sgi', 'SEGI_29095' => 'sgi', 'SEGI_36534' => 'sgi', 'SEGI_37506' => 'sgi', 'SEGI_38321' => 'sgi', 'SGA_v2.0_scaffold307G48031' => 'sas', 'SGA_v2.0_scaffold47G17507' => 'sas', 'SGA_v2.0_scaffold63G21736' => 'sas', 'SGA_v2.0_scaffold87G27070' => 'sas', 'SHI17794' => 'shi', 'SHI28851' => 'shi', 'SMO165G0155' => 'smo', 'SMO340G0217' => 'smo', 'SMO367G1210' => 'smo', 'Solyc02g093430.3' => 'sly', 'Solyc05g013580.4' => 'sly', 'Solyc07g008030.3' => 'sly', 'Solyc12g035470.2' => 'sly', 'Sopen02g038020' => 'spe', 'Sopen05g008490' => 'spe', 'Sopen07g003910' => 'spe', 'Sopen12g015240' => 'spe', 'Sp1g11550' => 'spa', 'Sp2g16710' => 'spa', 'Sp3g00430' => 'spa', 'Sp3g26780' => 'spa', 'Sp5g22900' => 'spa', 'Sp6g29530' => 'spa', 'TAR371G0794' => 'tar', 'TAR374G0164' => 'tar', 'TAR622G0165' => 'tar', 'TAR626G0929' => 'tar', 'TAR629G2155' => 'tar', 'THA.LOC104805282' => 'tha', 'THA.LOC104805363' => 'tha', 'THA.LOC104808968' => 'tha', 'THA.LOC104821093' => 'tha', 'THA.LOC104823953' => 'tha', 'THA.LOC104825562' => 'tha', 'THA.LOC104825665' => 'tha', 'Thecc.02G261400' => 'tca', 'Thecc.04G019200' => 'tca', 'Thecc.09G130400' => 'tca', 'Thhalv10004374m.g' => 'esa', 'Thhalv10007850m.g' => 'esa', 'Thhalv10013782m.g' => 'esa', 'Thhalv10018686m.g' => 'esa', 'Thhalv10020899m.g' => 'esa', 'Thhalv10022755m.g' => 'esa', 'TPR.G23851' => 'tpr', 'TPR.G26500' => 'tpr', 'TPR.G27267' => 'tpr', 'TPR.G32001' => 'tpr', 'TPR.G6251' => 'tpr', 'TPR.G8167' => 'tpr', 'TWI12G1330' => 'twi', 'TWI18G1239' => 'twi', 'TWI34G0979' => 'twi', 'TWI36G0670' => 'twi', 'TWI36G0707' => 'twi', 'TWI56G0233' => 'twi', 'TWI75G1809' => 'twi', 'unitig_21.g20874' => 'ugi', 'unitig_26.g10343' => 'ugi', 'unitig_46.g18392' => 'ugi', 'unitig_52.g17178' => 'ugi', 'unitig_8.g2934' => 'ugi', 'vmacro01122' => 'vma', 'vmacro05875' => 'vma', 'vmacro06147' => 'vma', 'vmacro16191' => 'vma', 'vmacro18293' => 'vma', 'VMungo0251G3707' => 'vmu', 'VMungo0464G1521' => 'vmu', 'VMungo1215G0205' => 'vmu', 'VMungo1383G2484' => 'vmu', 'Zm00001eb079610' => 'zma', 'Zm00001eb135990' => 'zma', 'Zm00001eb183710' => 'zma', 'Zm00001eb246020' => 'zma' ), 'gf_id' => 'HOM05D001124', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001124' ), 'data_identifier' => 'HOM05D001124', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001124', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '548', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02520' => 'bna', 'A03p06630' => 'bna', 'A05p44460' => 'bna', 'A06p08710' => 'bna', 'A06p41090' => 'bna', 'A07p32320' => 'bna', 'A08p32520' => 'bna', 'A09p10360' => 'bna', 'A10p24080' => 'bna', 'Aa31LG11G15250' => 'aar', 'Aa31LG1G1800' => 'aar', 'Aa31LG2G5120' => 'aar', 'Aa31LG2G6070' => 'aar', 'Aa31LG5G10770' => 'aar', 'Aa31sc61G90' => 'aar', 'Actinidia01352' => 'ach', 'Actinidia05983' => 'ach', 'Actinidia08133' => 'ach', 'Actinidia15101' => 'ach', 'Actinidia26379' => 'ach', 'Actinidia35778' => 'ach', 'Actinidia36123' => 'ach', 'Actinidia37436' => 'ach', 'Actinidia38730' => 'ach', 'Ah.02g128210' => 'amhyb', 'Ah.03g132990' => 'amhyb', 'Ah.14g079410' => 'amhyb', 'AL1G24640' => 'aly', 'AL2G26680' => 'aly', 'AL3G10530' => 'aly', 'AL3G45230' => 'aly', 'AL5G15230' => 'aly', 'AL5G16960' => 'aly', 'AL6G25210' => 'aly', 'Aqoxy2G00441' => 'aox', 'Aqoxy3G01236' => 'aox', 'Aqoxy5G03746' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3RQ047' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C7GMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9C8JER' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MBL6KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YXCZ83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZANX40' => 'arhy', 'AT1G12990' => 'ath', 'AT1G67880' => 'ath', 'AT2G13290' => 'ath', 'AT3G01620' => 'ath', 'AT3G26445' => 'ath', 'AT3G27540' => 'ath', 'AT5G14480' => 'ath', 'ATR0824G026' => 'atr', 'ATR1098G019' => 'atr', 'Atru.chr11.2145' => 'acertr', 'Atru.chr2.3636' => 'acertr', 'Atru.chr2.3644' => 'acertr', 'Atru.chr6.2422' => 'acertr', 'Atru.chr7.1112' => 'acertr', 'AUR62005469' => 'cqu', 'AUR62011166' => 'cqu', 'AUR62013319' => 'cqu', 'AUR62024273' => 'cqu', 'AUR62028420' => 'cqu', 'AUR62041942' => 'cqu', 'BcaB01g04969' => 'bca', 'BcaB01g06371' => 'bca', 'BcaB02g11494' => 'bca', 'BcaB03g15382' => 'bca', 'BcaB08g36994' => 'bca', 'BcaC03g13477' => 'bca', 'BcaC03g13478' => 'bca', 'BcaC03g13480' => 'bca', 'BcaC03g13481' => 'bca', 'BcaC03g13486' => 'bca', 'BcaC04g19031' => 'bca', 'BcaC04g23085' => 'bca', 'BcaC05g25094' => 'bca', 'BcaC05g25096' => 'bca', 'BcaC05g25138' => 'bca', 'BcaC05g30416' => 'bca', 'BcaC05g30455' => 'bca', 'BcaC06g30979' => 'bca', 'BcaC06g33805' => 'bca', 'BcaC08g46021' => 'bca', 'BcaNung03154' => 'bca', 'BolC2t06623H' => 'bol', 'BolC2t06632H' => 'bol', 'BolC2t06635H' => 'bol', 'BolC2t06638H' => 'bol', 'BolC3t13266H' => 'bol', 'BolC5t29776H' => 'bol', 'BolC6t38912H' => 'bol', 'BolC7t44183H' => 'bol', 'BolC9t54123H' => 'bol', 'BolC9t59107H' => 'bol', 'BraA02t05221Z' => 'bra', 'BraA03t09996Z' => 'bra', 'BraA05t23210Z' => 'bra', 'BraA06t24068Z' => 'bra', 'BraA06t27032Z' => 'bra', 'BraA08t35176Z' => 'bra', 'BraA09t36680Z' => 'bra', 'BraA10t44471Z' => 'bra', 'C02p06760' => 'bna', 'C02p06890' => 'bna', 'C02p07010' => 'bna', 'C03p07660' => 'bna', 'C05p10300' => 'bna', 'C06p38150' => 'bna', 'C07p36650' => 'bna', 'C08p15770' => 'bna', 'C09p12300' => 'bna', 'C09p62700' => 'bna', 'C09p75040' => 'bna', 'CAN.G13.1' => 'can', 'CAN.G138.4' => 'can', 'CAN.G44.6' => 'can', 'CAN.G473.19' => 'can', 'CANSAT01G0835' => 'cansat', 'CANSAT11G0246' => 'cansat', 'CANSAT11G1766' => 'cansat', 'CANSAT64G1954' => 'cansat', 'CARHR013330' => 'chi', 'CARHR060530' => 'chi', 'CARHR075300' => 'chi', 'CARHR105120' => 'chi', 'CARHR148910' => 'chi', 'CARHR198830' => 'chi', 'Carub.0001s1275' => 'cru', 'Carub.0002s1437' => 'cru', 'Carub.0003s0044' => 'cru', 'Carub.0003s2787' => 'cru', 'Carub.0005s0597' => 'cru', 'Carub.0006s1266' => 'cru', 'Ca_06935_v3' => 'car', 'Ca_13559_v3' => 'car', 'Ca_16941_v3' => 'car', 'Ca_16960_v3' => 'car', 'Ca_17775_v3' => 'car', 'Ca_30464_v3' => 'car', 'Cc06_g08160' => 'ccan', 'Cc07_g01520' => 'ccan', 'Cc11_g15810' => 'ccan', 'CDE02G2840' => 'cde', 'CDE03G0093' => 'cde', 'CDE04G2127' => 'cde', 'CDE07G1857' => 'cde', 'CDE09G1246' => 'cde', 'Cfa003412' => 'cfa', 'Cfa007341' => 'cfa', 'Cfa009220' => 'cfa', 'Ciclev10008737m.g' => 'ccl', 'Ciclev10015565m.g' => 'ccl', 'Ciclev10031761m.g' => 'ccl', 'CiPaw.03G045300' => 'cil', 'CiPaw.03G247200' => 'cil', 'CiPaw.04G029500' => 'cil', 'CiPaw.04G174000' => 'cil', 'CiPaw.05G181200' => 'cil', 'CiPaw.06G067100' => 'cil', 'ClCG05G025800' => 'cla', 'ClCG06G011400' => 'cla', 'ClCG09G019360' => 'cla', 'COL.COLO4_04827' => 'col', 'COL.COLO4_29170' => 'col', 'COL.COLO4_35131' => 'col', 'COL.COLO4_35132' => 'col', 'Cpa.g.sc33.32' => 'cpa', 'Cpa.g.sc46.29' => 'cpa', 'Cpa.g.sc796.1' => 'cpa', 'CsaV3_1G030420' => 'csa', 'CsaV3_5G027050' => 'csa', 'CsaV3_5G031040' => 'csa', 'CsaV3_UNG023130' => 'csa', 'CSS0007726' => 'camsi', 'CSS0016433' => 'camsi', 'CSS0017656' => 'camsi', 'CSS0025364' => 'camsi', 'CSS0027582' => 'camsi', 'CSS0047288' => 'camsi', 'CSS0049950' => 'camsi', 'DCAR_003843' => 'dca', 'DCAR_007052' => 'dca', 'DCAR_020884' => 'dca', 'DCAR_021730' => 'dca', 'DCAR_024423' => 'dca', 'DCAR_026509' => 'dca', 'DCAR_031158' => 'dca', 'Dinv14728' => 'din', 'Dinv15219' => 'din', 'Dinv25728' => 'din', 'Dinv33428' => 'din', 'Dinv36489' => 'din', 'Dinv41486' => 'din', 'Duzib147G0469' => 'dzi', 'Duzib168G0060' => 'dzi', 'Duzib187G1215' => 'dzi', 'Duzib248G0692' => 'dzi', 'Duzib251G0767' => 'dzi', 'Duzib264G0446' => 'dzi', 'Duzib268G0691' => 'dzi', 'ECA232G4767' => 'eca', 'ECA233G2838' => 'eca', 'ECA234G0391' => 'eca', 'ECA234G0857' => 'eca', 'ECA236G1593' => 'eca', 'ECA238G0565' => 'eca', 'ECA246G1027' => 'eca', 'ECA246G3223' => 'eca', 'ECA246G3470' => 'eca', 'EL10Ac6g13829' => 'bvu', 'EL10Ac6g14093' => 'bvu', 'EL10Ac8g18707' => 'bvu', 'Eucgr.C01369' => 'egr', 'Eucgr.H02492' => 'egr', 'Eucgr.I01733' => 'egr', 'Eucgr.J02255' => 'egr', 'Eucgr.J02257' => 'egr', 'Eucgr.J02258' => 'egr', 'FAN02G1601' => 'fan', 'FAN03G1586' => 'fan', 'FAN03G2986' => 'fan', 'FAN05G4837' => 'fan', 'FAN06G0146' => 'fan', 'FAN07G0858' => 'fan', 'FAN09G3179' => 'fan', 'FAN10G0669' => 'fan', 'FAN12G2358' => 'fan', 'FAN14G4198' => 'fan', 'FAN14G5112' => 'fan', 'FAN17G0342' => 'fan', 'FAN19G0342' => 'fan', 'FAN19G0962' => 'fan', 'FAN19G1101' => 'fan', 'FAN19G1872' => 'fan', 'FAN22G0356' => 'fan', 'FAN23G0744' => 'fan', 'FAN23G1914' => 'fan', 'FAN26G0032' => 'fan', 'FAN28G0625' => 'fan', 'FvH4_1g02710' => 'fve', 'FvH4_1g02720' => 'fve', 'FvH4_4g25670' => 'fve', 'FvH4_6g51700' => 'fve', 'FvH4_7g20170' => 'fve', 'Glyma.05G175000' => 'gma', 'Glyma.08G132300' => 'gma', 'Glyma.11G243000' => 'gma', 'Glyma.13G158900' => 'gma', 'Glyma.17G112400' => 'gma', 'Glyma.18G014100' => 'gma', 'Glyma.19G003100' => 'gma', 'Glyma.19G056500' => 'gma', 'Gohir.A01G158900' => 'ghi', 'Gohir.A05G312600' => 'ghi', 'Gohir.A05G354900' => 'ghi', 'Gohir.A07G037200' => 'ghi', 'Gohir.A09G030000' => 'ghi', 'Gohir.A12G145200' => 'ghi', 'Gohir.D01G151500' => 'ghi', 'Gohir.D04G058300' => 'ghi', 'Gohir.D05G314100' => 'ghi', 'Gohir.D07G041400' => 'ghi', 'Gohir.D09G029700' => 'ghi', 'Gohir.D12G149700' => 'ghi', 'Gorai.001G043800' => 'gra', 'Gorai.002G187800' => 'gra', 'Gorai.006G034700' => 'gra', 'Gorai.008G161200' => 'gra', 'Gorai.009G335700' => 'gra', 'Gorai.012G065000' => 'gra', 'GSVIVG01000535001' => 'vvi', 'GSVIVG01015572001' => 'vvi', 'GSVIVG01032386001' => 'vvi', 'HanXRQChr05g0138531' => 'han', 'HanXRQChr06g0174391' => 'han', 'HanXRQChr07g0199021' => 'han', 'HanXRQChr08g0208211' => 'han', 'HanXRQChr09g0255471' => 'han', 'HanXRQChr10g0315791' => 'han', 'HanXRQChr12g0371991' => 'han', 'HanXRQChr15g0475251' => 'han', 'HanXRQChr17g0540001' => 'han', 'HanXRQChr17g0548631' => 'han', 'HanXRQChr17g0569561' => 'han', 'Haze_12256' => 'cav', 'Haze_14756' => 'cav', 'Haze_25528' => 'cav', 'Hma1.2p1_0079F.1_g041020' => 'hma', 'Hma1.2p1_0818F.1_g223260' => 'hma', 'Hma1.2p1_1747F.1_g300530' => 'hma', 'HPP92_004607' => 'vpl', 'HPP92_004608' => 'vpl', 'HPP92_006181' => 'vpl', 'HPP92_012192' => 'vpl', 'HPP92_015680' => 'vpl', 'HPP92_020249' => 'vpl', 'HPP92_021376' => 'vpl', 'HPP92_024275' => 'vpl', 'Hund06031' => 'sun', 'Hund25391' => 'sun', 'Lalb_Chr07g0185371' => 'lal', 'Lalb_Chr07g0185381' => 'lal', 'Lalb_Chr12g0204011' => 'lal', 'Lalb_Chr13g0301671' => 'lal', 'Lalb_Chr14g0362851' => 'lal', 'Lalb_Chr24g0403581' => 'lal', 'Lj1g0000233' => 'lja', 'Lj2g0018120' => 'lja', 'Lj3C621T0' => 'lonja', 'Lj3P1059T14' => 'lonja', 'Lj3P611T9' => 'lonja', 'Lj3P614T13' => 'lonja', 'Lj3P615T5' => 'lonja', 'Lj4g0012315' => 'lja', 'Lj4g0026182' => 'lja', 'Lj6P813T16' => 'lonja', 'Lj7C427T7' => 'lonja', 'Lj7C427T8' => 'lonja', 'Lj7P600T41' => 'lonja', 'Lju41C42G17' => 'lonja', 'Lsat_1_v5_gn_0_47300' => 'lsa', 'Lsat_1_v5_gn_2_91280' => 'lsa', 'Lsat_1_v5_gn_3_30561' => 'lsa', 'Lsat_1_v5_gn_4_184321' => 'lsa', 'Lsat_1_v5_gn_4_4041' => 'lsa', 'Lsat_1_v5_gn_5_92000' => 'lsa', 'Lsat_1_v5_gn_8_152940' => 'lsa', 'Lsat_1_v5_gn_8_62401' => 'lsa', 'Manes.06G055900' => 'mes', 'Manes.12G022200' => 'mes', 'Manes.13G023300' => 'mes', 'Manes.14G115000' => 'mes', 'Manes.15G151700' => 'mes', 'Manes.17G111300' => 'mes', 'Mapoly0226s0009' => 'mpo', 'MBI02_g25363_MAGBIO' => 'mbi', 'MBI06_g00027_MAGBIO' => 'mbi', 'MBI10_g13034_MAGBIO' => 'mbi', 'MD09G1023400' => 'mdo', 'MD13G1100100' => 'mdo', 'MD15G1169200' => 'mdo', 'MD16G1101100' => 'mdo', 'MD17G1022900' => 'mdo', 'Medtr3g096150' => 'mtr', 'Medtr4g115070' => 'mtr', 'Medtr7g033325' => 'mtr', 'Medtr8g089840' => 'mtr', 'MELO3C010319.2' => 'cme', 'MELO3C011944.2' => 'cme', 'MELO3C021589.2' => 'cme', 'Migut.E00207' => 'egut', 'Migut.H00067' => 'egut', 'Migut.K00433' => 'egut', 'Migut.K00606' => 'egut', 'Migut.K01410' => 'egut', 'MSTRG.13347' => 'ama', 'MSTRG.24045' => 'ama', 'MSTRG.2428' => 'ama', 'MSTRG.26410' => 'ama', 'MSTRG.3139' => 'ama', 'MSTRG.3286' => 'ama', 'MSTRG.563' => 'ama', 'MSTRG.7941' => 'ama', 'Nitab4.5_0000028g0060' => 'nta', 'Nitab4.5_0000065g0260' => 'nta', 'Nitab4.5_0000112g0060' => 'nta', 'Nitab4.5_0000489g0120' => 'nta', 'Nitab4.5_0001776g0050' => 'nta', 'Nitab4.5_0001854g0010' => 'nta', 'Nitab4.5_0001860g0020' => 'nta', 'Nitab4.5_0004352g0010' => 'nta', 'Nitab4.5_0008716g0020' => 'nta', 'Nitab4.5_0008922g0010' => 'nta', 'Nn3g16693' => 'nnu', 'Nn4g22596' => 'nnu', 'Nn7g37639' => 'nnu', 'Oeu001701.1' => 'oeu', 'Oeu018149.1' => 'oeu', 'Oeu026220.1' => 'oeu', 'Oeu038635.1' => 'oeu', 'Oeu049176.1' => 'oeu', 'Oeu056706.1' => 'oeu', 'Oeu056937.1' => 'oeu', 'Oeu057540.1' => 'oeu', 'Os02g0594900' => 'osa', 'Os02g0595100' => 'osa', 'Os04g0477500' => 'osa', 'Os12g0611900' => 'osa', 'Peaxi162Scf00076g00020' => 'pax', 'Peaxi162Scf00128g00217' => 'pax', 'Peaxi162Scf00129g01640' => 'pax', 'Peaxi162Scf00669g00007' => 'pax', 'Peaxi162Scf00700g00421' => 'pax', 'Peaxi162Scf00801g00038' => 'pax', 'Peaxi162Scf00891g00025' => 'pax', 'PGR083G0909' => 'pgr', 'PGR119G1005' => 'pgr', 'PGR142G2236' => 'pgr', 'PGR142G3388' => 'pgr', 'PGSC0003DMG400004514' => 'stu', 'PGSC0003DMG400012635' => 'stu', 'PGSC0003DMG400015730' => 'stu', 'PGSC0003DMG400018611' => 'stu', 'PGSC0003DMG400030897' => 'stu', 'Phvul.001G254800' => 'pvu', 'Phvul.002G260100' => 'pvu', 'Phvul.003G167600' => 'pvu', 'Phvul.004G005100' => 'pvu', 'Potri.001G343600' => 'ptr', 'Potri.006G066700' => 'ptr', 'Potri.008G186000' => 'ptr', 'Potri.010G046900' => 'ptr', 'Potri.018G127900' => 'ptr', 'Pp3c20_17750' => 'ppa', 'Pp3c24_4380' => 'ppa', 'Prupe.1G245800' => 'ppe', 'Prupe.3G293400' => 'ppe', 'Prupe.7G247400' => 'ppe', 'Psat0s145g0120' => 'psa', 'Psat0s595g0040' => 'psa', 'Psat0s595g0120' => 'psa', 'Psat3g175040' => 'psa', 'Psat7g058120' => 'psa', 'PSO017G0428' => 'pso', 'PSO063G7510' => 'pso', 'PSO067G0046' => 'pso', 'PSO478G1073' => 'pso', 'PSO675G3677' => 'pso', 'PSO675G6558' => 'pso', 'PSO675G7520' => 'pso', 'PSO675G8959' => 'pso', 'QL02p074089' => 'qlo', 'QL02p089614' => 'qlo', 'QL03p057736' => 'qlo', 'RcHm_v2.0_Chr1g0364131' => 'rch', 'RcHm_v2.0_Chr2g0087801' => 'rch', 'RcHm_v2.0_Chr2g0087821' => 'rch', 'RcHm_v2.0_Chr2g0173231' => 'rch', 'RcHm_v2.0_Chr4g0433111' => 'rch', 'Rhsim03G0250300' => 'rsi', 'Rhsim08G0048400' => 'rsi', 'Rhsim10G0014800' => 'rsi', 'Rhsim12G0040100' => 'rsi', 'Rhsim12G0109700' => 'rsi', 'Sabra06G0049600' => 'sbr', 'Sabra08G0141000' => 'sbr', 'Sabra10G0021400' => 'sbr', 'Sabra16G0222900' => 'sbr', 'Sabra18G0108600' => 'sbr', 'SalBow1G0433' => 'sbo', 'SalBow1G2038' => 'sbo', 'SalBow1G5003' => 'sbo', 'SalBow7G1197' => 'sbo', 'SalBow8G3506' => 'sbo', 'Sc03g0007300' => 'sci', 'Sc11g0000950' => 'sci', 'Sc14g0008750' => 'sci', 'Sc18g0000420' => 'sci', 'Sed0006754' => 'sed', 'Sed0008741' => 'sed', 'Sed0017172' => 'sed', 'Sed0018925' => 'sed', 'Sed0023326' => 'sed', 'Sed0025909' => 'sed', 'SEGI_05333' => 'sgi', 'SEGI_10362' => 'sgi', 'SEGI_13380' => 'sgi', 'SEGI_24306' => 'sgi', 'SEGI_29077' => 'sgi', 'SEGI_29095' => 'sgi', 'SEGI_36534' => 'sgi', 'SEGI_37506' => 'sgi', 'SEGI_38321' => 'sgi', 'SGA_v2.0_scaffold307G48031' => 'sas', 'SGA_v2.0_scaffold47G17507' => 'sas', 'SGA_v2.0_scaffold63G21736' => 'sas', 'SGA_v2.0_scaffold87G27070' => 'sas', 'SHI17794' => 'shi', 'SHI28851' => 'shi', 'SMO165G0155' => 'smo', 'SMO340G0217' => 'smo', 'SMO367G1210' => 'smo', 'Solyc02g093430.3' => 'sly', 'Solyc05g013580.4' => 'sly', 'Solyc07g008030.3' => 'sly', 'Solyc12g035470.2' => 'sly', 'Sopen02g038020' => 'spe', 'Sopen05g008490' => 'spe', 'Sopen07g003910' => 'spe', 'Sopen12g015240' => 'spe', 'Sp1g11550' => 'spa', 'Sp2g16710' => 'spa', 'Sp3g00430' => 'spa', 'Sp3g26780' => 'spa', 'Sp5g22900' => 'spa', 'Sp6g29530' => 'spa', 'TAR371G0794' => 'tar', 'TAR374G0164' => 'tar', 'TAR622G0165' => 'tar', 'TAR626G0929' => 'tar', 'TAR629G2155' => 'tar', 'THA.LOC104805282' => 'tha', 'THA.LOC104805363' => 'tha', 'THA.LOC104808968' => 'tha', 'THA.LOC104821093' => 'tha', 'THA.LOC104823953' => 'tha', 'THA.LOC104825562' => 'tha', 'THA.LOC104825665' => 'tha', 'Thecc.02G261400' => 'tca', 'Thecc.04G019200' => 'tca', 'Thecc.09G130400' => 'tca', 'Thhalv10004374m.g' => 'esa', 'Thhalv10007850m.g' => 'esa', 'Thhalv10013782m.g' => 'esa', 'Thhalv10018686m.g' => 'esa', 'Thhalv10020899m.g' => 'esa', 'Thhalv10022755m.g' => 'esa', 'TPR.G23851' => 'tpr', 'TPR.G26500' => 'tpr', 'TPR.G27267' => 'tpr', 'TPR.G32001' => 'tpr', 'TPR.G6251' => 'tpr', 'TPR.G8167' => 'tpr', 'TWI12G1330' => 'twi', 'TWI18G1239' => 'twi', 'TWI34G0979' => 'twi', 'TWI36G0670' => 'twi', 'TWI36G0707' => 'twi', 'TWI56G0233' => 'twi', 'TWI75G1809' => 'twi', 'unitig_21.g20874' => 'ugi', 'unitig_26.g10343' => 'ugi', 'unitig_46.g18392' => 'ugi', 'unitig_52.g17178' => 'ugi', 'unitig_8.g2934' => 'ugi', 'vmacro01122' => 'vma', 'vmacro05875' => 'vma', 'vmacro06147' => 'vma', 'vmacro16191' => 'vma', 'vmacro18293' => 'vma', 'VMungo0251G3707' => 'vmu', 'VMungo0464G1521' => 'vmu', 'VMungo1215G0205' => 'vmu', 'VMungo1383G2484' => 'vmu', 'Zm00001eb079610' => 'zma', 'Zm00001eb135990' => 'zma', 'Zm00001eb183710' => 'zma', 'Zm00001eb246020' => 'zma' ) $gf_id = 'HOM05D001124' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001124' ) $data_identifier = 'HOM05D001124' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 6, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 7, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 21, 'bol' => (int) 10, 'bra' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 6, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 9, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 21, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 8, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 10, 'lsa' => (int) 8, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 8, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 9, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb246020' $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' => 'HOM05D001124', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '548', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02520' => 'bna', 'A03p06630' => 'bna', 'A05p44460' => 'bna', 'A06p08710' => 'bna', 'A06p41090' => 'bna', 'A07p32320' => 'bna', 'A08p32520' => 'bna', 'A09p10360' => 'bna', 'A10p24080' => 'bna', 'Aa31LG11G15250' => 'aar', 'Aa31LG1G1800' => 'aar', 'Aa31LG2G5120' => 'aar', 'Aa31LG2G6070' => 'aar', 'Aa31LG5G10770' => 'aar', 'Aa31sc61G90' => 'aar', 'Actinidia01352' => 'ach', 'Actinidia05983' => 'ach', 'Actinidia08133' => 'ach', 'Actinidia15101' => 'ach', 'Actinidia26379' => 'ach', 'Actinidia35778' => 'ach', 'Actinidia36123' => 'ach', 'Actinidia37436' => 'ach', 'Actinidia38730' => 'ach', 'Ah.02g128210' => 'amhyb', 'Ah.03g132990' => 'amhyb', 'Ah.14g079410' => 'amhyb', 'AL1G24640' => 'aly', 'AL2G26680' => 'aly', 'AL3G10530' => 'aly', 'AL3G45230' => 'aly', 'AL5G15230' => 'aly', 'AL5G16960' => 'aly', 'AL6G25210' => 'aly', 'Aqoxy2G00441' => 'aox', 'Aqoxy3G01236' => 'aox', 'Aqoxy5G03746' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3RQ047' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C7GMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9C8JER' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MBL6KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YXCZ83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZANX40' => 'arhy', 'AT1G12990' => 'ath', 'AT1G67880' => 'ath', 'AT2G13290' => 'ath', 'AT3G01620' => 'ath', 'AT3G26445' => 'ath', 'AT3G27540' => 'ath', 'AT5G14480' => 'ath', 'ATR0824G026' => 'atr', 'ATR1098G019' => 'atr', 'Atru.chr11.2145' => 'acertr', 'Atru.chr2.3636' => 'acertr', 'Atru.chr2.3644' => 'acertr', 'Atru.chr6.2422' => 'acertr', 'Atru.chr7.1112' => 'acertr', 'AUR62005469' => 'cqu', 'AUR62011166' => 'cqu', 'AUR62013319' => 'cqu', 'AUR62024273' => 'cqu', 'AUR62028420' => 'cqu', 'AUR62041942' => 'cqu', 'BcaB01g04969' => 'bca', 'BcaB01g06371' => 'bca', 'BcaB02g11494' => 'bca', 'BcaB03g15382' => 'bca', 'BcaB08g36994' => 'bca', 'BcaC03g13477' => 'bca', 'BcaC03g13478' => 'bca', 'BcaC03g13480' => 'bca', 'BcaC03g13481' => 'bca', 'BcaC03g13486' => 'bca', 'BcaC04g19031' => 'bca', 'BcaC04g23085' => 'bca', 'BcaC05g25094' => 'bca', 'BcaC05g25096' => 'bca', 'BcaC05g25138' => 'bca', 'BcaC05g30416' => 'bca', 'BcaC05g30455' => 'bca', 'BcaC06g30979' => 'bca', 'BcaC06g33805' => 'bca', 'BcaC08g46021' => 'bca', 'BcaNung03154' => 'bca', 'BolC2t06623H' => 'bol', 'BolC2t06632H' => 'bol', 'BolC2t06635H' => 'bol', 'BolC2t06638H' => 'bol', 'BolC3t13266H' => 'bol', 'BolC5t29776H' => 'bol', 'BolC6t38912H' => 'bol', 'BolC7t44183H' => 'bol', 'BolC9t54123H' => 'bol', 'BolC9t59107H' => 'bol', 'BraA02t05221Z' => 'bra', 'BraA03t09996Z' => 'bra', 'BraA05t23210Z' => 'bra', 'BraA06t24068Z' => 'bra', 'BraA06t27032Z' => 'bra', 'BraA08t35176Z' => 'bra', 'BraA09t36680Z' => 'bra', 'BraA10t44471Z' => 'bra', 'C02p06760' => 'bna', 'C02p06890' => 'bna', 'C02p07010' => 'bna', 'C03p07660' => 'bna', 'C05p10300' => 'bna', 'C06p38150' => 'bna', 'C07p36650' => 'bna', 'C08p15770' => 'bna', 'C09p12300' => 'bna', 'C09p62700' => 'bna', 'C09p75040' => 'bna', 'CAN.G13.1' => 'can', 'CAN.G138.4' => 'can', 'CAN.G44.6' => 'can', 'CAN.G473.19' => 'can', 'CANSAT01G0835' => 'cansat', 'CANSAT11G0246' => 'cansat', 'CANSAT11G1766' => 'cansat', 'CANSAT64G1954' => 'cansat', 'CARHR013330' => 'chi', 'CARHR060530' => 'chi', 'CARHR075300' => 'chi', 'CARHR105120' => 'chi', 'CARHR148910' => 'chi', 'CARHR198830' => 'chi', 'Carub.0001s1275' => 'cru', 'Carub.0002s1437' => 'cru', 'Carub.0003s0044' => 'cru', 'Carub.0003s2787' => 'cru', 'Carub.0005s0597' => 'cru', 'Carub.0006s1266' => 'cru', 'Ca_06935_v3' => 'car', 'Ca_13559_v3' => 'car', 'Ca_16941_v3' => 'car', 'Ca_16960_v3' => 'car', 'Ca_17775_v3' => 'car', 'Ca_30464_v3' => 'car', 'Cc06_g08160' => 'ccan', 'Cc07_g01520' => 'ccan', 'Cc11_g15810' => 'ccan', 'CDE02G2840' => 'cde', 'CDE03G0093' => 'cde', 'CDE04G2127' => 'cde', 'CDE07G1857' => 'cde', 'CDE09G1246' => 'cde', 'Cfa003412' => 'cfa', 'Cfa007341' => 'cfa', 'Cfa009220' => 'cfa', 'Ciclev10008737m.g' => 'ccl', 'Ciclev10015565m.g' => 'ccl', 'Ciclev10031761m.g' => 'ccl', 'CiPaw.03G045300' => 'cil', 'CiPaw.03G247200' => 'cil', 'CiPaw.04G029500' => 'cil', 'CiPaw.04G174000' => 'cil', 'CiPaw.05G181200' => 'cil', 'CiPaw.06G067100' => 'cil', 'ClCG05G025800' => 'cla', 'ClCG06G011400' => 'cla', 'ClCG09G019360' => 'cla', 'COL.COLO4_04827' => 'col', 'COL.COLO4_29170' => 'col', 'COL.COLO4_35131' => 'col', 'COL.COLO4_35132' => 'col', 'Cpa.g.sc33.32' => 'cpa', 'Cpa.g.sc46.29' => 'cpa', 'Cpa.g.sc796.1' => 'cpa', 'CsaV3_1G030420' => 'csa', 'CsaV3_5G027050' => 'csa', 'CsaV3_5G031040' => 'csa', 'CsaV3_UNG023130' => 'csa', 'CSS0007726' => 'camsi', 'CSS0016433' => 'camsi', 'CSS0017656' => 'camsi', 'CSS0025364' => 'camsi', 'CSS0027582' => 'camsi', 'CSS0047288' => 'camsi', 'CSS0049950' => 'camsi', 'DCAR_003843' => 'dca', 'DCAR_007052' => 'dca', 'DCAR_020884' => 'dca', 'DCAR_021730' => 'dca', 'DCAR_024423' => 'dca', 'DCAR_026509' => 'dca', 'DCAR_031158' => 'dca', 'Dinv14728' => 'din', 'Dinv15219' => 'din', 'Dinv25728' => 'din', 'Dinv33428' => 'din', 'Dinv36489' => 'din', 'Dinv41486' => 'din', 'Duzib147G0469' => 'dzi', 'Duzib168G0060' => 'dzi', 'Duzib187G1215' => 'dzi', 'Duzib248G0692' => 'dzi', 'Duzib251G0767' => 'dzi', 'Duzib264G0446' => 'dzi', 'Duzib268G0691' => 'dzi', 'ECA232G4767' => 'eca', 'ECA233G2838' => 'eca', 'ECA234G0391' => 'eca', 'ECA234G0857' => 'eca', 'ECA236G1593' => 'eca', 'ECA238G0565' => 'eca', 'ECA246G1027' => 'eca', 'ECA246G3223' => 'eca', 'ECA246G3470' => 'eca', 'EL10Ac6g13829' => 'bvu', 'EL10Ac6g14093' => 'bvu', 'EL10Ac8g18707' => 'bvu', 'Eucgr.C01369' => 'egr', 'Eucgr.H02492' => 'egr', 'Eucgr.I01733' => 'egr', 'Eucgr.J02255' => 'egr', 'Eucgr.J02257' => 'egr', 'Eucgr.J02258' => 'egr', 'FAN02G1601' => 'fan', 'FAN03G1586' => 'fan', 'FAN03G2986' => 'fan', 'FAN05G4837' => 'fan', 'FAN06G0146' => 'fan', 'FAN07G0858' => 'fan', 'FAN09G3179' => 'fan', 'FAN10G0669' => 'fan', 'FAN12G2358' => 'fan', 'FAN14G4198' => 'fan', 'FAN14G5112' => 'fan', 'FAN17G0342' => 'fan', 'FAN19G0342' => 'fan', 'FAN19G0962' => 'fan', 'FAN19G1101' => 'fan', 'FAN19G1872' => 'fan', 'FAN22G0356' => 'fan', 'FAN23G0744' => 'fan', 'FAN23G1914' => 'fan', 'FAN26G0032' => 'fan', 'FAN28G0625' => 'fan', 'FvH4_1g02710' => 'fve', 'FvH4_1g02720' => 'fve', 'FvH4_4g25670' => 'fve', 'FvH4_6g51700' => 'fve', 'FvH4_7g20170' => 'fve', 'Glyma.05G175000' => 'gma', 'Glyma.08G132300' => 'gma', 'Glyma.11G243000' => 'gma', 'Glyma.13G158900' => 'gma', 'Glyma.17G112400' => 'gma', 'Glyma.18G014100' => 'gma', 'Glyma.19G003100' => 'gma', 'Glyma.19G056500' => 'gma', 'Gohir.A01G158900' => 'ghi', 'Gohir.A05G312600' => 'ghi', 'Gohir.A05G354900' => 'ghi', 'Gohir.A07G037200' => 'ghi', 'Gohir.A09G030000' => 'ghi', 'Gohir.A12G145200' => 'ghi', 'Gohir.D01G151500' => 'ghi', 'Gohir.D04G058300' => 'ghi', 'Gohir.D05G314100' => 'ghi', 'Gohir.D07G041400' => 'ghi', 'Gohir.D09G029700' => 'ghi', 'Gohir.D12G149700' => 'ghi', 'Gorai.001G043800' => 'gra', 'Gorai.002G187800' => 'gra', 'Gorai.006G034700' => 'gra', 'Gorai.008G161200' => 'gra', 'Gorai.009G335700' => 'gra', 'Gorai.012G065000' => 'gra', 'GSVIVG01000535001' => 'vvi', 'GSVIVG01015572001' => 'vvi', 'GSVIVG01032386001' => 'vvi', 'HanXRQChr05g0138531' => 'han', 'HanXRQChr06g0174391' => 'han', 'HanXRQChr07g0199021' => 'han', 'HanXRQChr08g0208211' => 'han', 'HanXRQChr09g0255471' => 'han', 'HanXRQChr10g0315791' => 'han', 'HanXRQChr12g0371991' => 'han', 'HanXRQChr15g0475251' => 'han', 'HanXRQChr17g0540001' => 'han', 'HanXRQChr17g0548631' => 'han', 'HanXRQChr17g0569561' => 'han', 'Haze_12256' => 'cav', 'Haze_14756' => 'cav', 'Haze_25528' => 'cav', 'Hma1.2p1_0079F.1_g041020' => 'hma', 'Hma1.2p1_0818F.1_g223260' => 'hma', 'Hma1.2p1_1747F.1_g300530' => 'hma', 'HPP92_004607' => 'vpl', 'HPP92_004608' => 'vpl', 'HPP92_006181' => 'vpl', 'HPP92_012192' => 'vpl', 'HPP92_015680' => 'vpl', 'HPP92_020249' => 'vpl', 'HPP92_021376' => 'vpl', 'HPP92_024275' => 'vpl', 'Hund06031' => 'sun', 'Hund25391' => 'sun', 'Lalb_Chr07g0185371' => 'lal', 'Lalb_Chr07g0185381' => 'lal', 'Lalb_Chr12g0204011' => 'lal', 'Lalb_Chr13g0301671' => 'lal', 'Lalb_Chr14g0362851' => 'lal', 'Lalb_Chr24g0403581' => 'lal', 'Lj1g0000233' => 'lja', 'Lj2g0018120' => 'lja', 'Lj3C621T0' => 'lonja', 'Lj3P1059T14' => 'lonja', 'Lj3P611T9' => 'lonja', 'Lj3P614T13' => 'lonja', 'Lj3P615T5' => 'lonja', 'Lj4g0012315' => 'lja', 'Lj4g0026182' => 'lja', 'Lj6P813T16' => 'lonja', 'Lj7C427T7' => 'lonja', 'Lj7C427T8' => 'lonja', 'Lj7P600T41' => 'lonja', 'Lju41C42G17' => 'lonja', 'Lsat_1_v5_gn_0_47300' => 'lsa', 'Lsat_1_v5_gn_2_91280' => 'lsa', 'Lsat_1_v5_gn_3_30561' => 'lsa', 'Lsat_1_v5_gn_4_184321' => 'lsa', 'Lsat_1_v5_gn_4_4041' => 'lsa', 'Lsat_1_v5_gn_5_92000' => 'lsa', 'Lsat_1_v5_gn_8_152940' => 'lsa', 'Lsat_1_v5_gn_8_62401' => 'lsa', 'Manes.06G055900' => 'mes', 'Manes.12G022200' => 'mes', 'Manes.13G023300' => 'mes', 'Manes.14G115000' => 'mes', 'Manes.15G151700' => 'mes', 'Manes.17G111300' => 'mes', 'Mapoly0226s0009' => 'mpo', 'MBI02_g25363_MAGBIO' => 'mbi', 'MBI06_g00027_MAGBIO' => 'mbi', 'MBI10_g13034_MAGBIO' => 'mbi', 'MD09G1023400' => 'mdo', 'MD13G1100100' => 'mdo', 'MD15G1169200' => 'mdo', 'MD16G1101100' => 'mdo', 'MD17G1022900' => 'mdo', 'Medtr3g096150' => 'mtr', 'Medtr4g115070' => 'mtr', 'Medtr7g033325' => 'mtr', 'Medtr8g089840' => 'mtr', 'MELO3C010319.2' => 'cme', 'MELO3C011944.2' => 'cme', 'MELO3C021589.2' => 'cme', 'Migut.E00207' => 'egut', 'Migut.H00067' => 'egut', 'Migut.K00433' => 'egut', 'Migut.K00606' => 'egut', 'Migut.K01410' => 'egut', 'MSTRG.13347' => 'ama', 'MSTRG.24045' => 'ama', 'MSTRG.2428' => 'ama', 'MSTRG.26410' => 'ama', 'MSTRG.3139' => 'ama', 'MSTRG.3286' => 'ama', 'MSTRG.563' => 'ama', 'MSTRG.7941' => 'ama', 'Nitab4.5_0000028g0060' => 'nta', 'Nitab4.5_0000065g0260' => 'nta', 'Nitab4.5_0000112g0060' => 'nta', 'Nitab4.5_0000489g0120' => 'nta', 'Nitab4.5_0001776g0050' => 'nta', 'Nitab4.5_0001854g0010' => 'nta', 'Nitab4.5_0001860g0020' => 'nta', 'Nitab4.5_0004352g0010' => 'nta', 'Nitab4.5_0008716g0020' => 'nta', 'Nitab4.5_0008922g0010' => 'nta', 'Nn3g16693' => 'nnu', 'Nn4g22596' => 'nnu', 'Nn7g37639' => 'nnu', 'Oeu001701.1' => 'oeu', 'Oeu018149.1' => 'oeu', 'Oeu026220.1' => 'oeu', 'Oeu038635.1' => 'oeu', 'Oeu049176.1' => 'oeu', 'Oeu056706.1' => 'oeu', 'Oeu056937.1' => 'oeu', 'Oeu057540.1' => 'oeu', 'Os02g0594900' => 'osa', 'Os02g0595100' => 'osa', 'Os04g0477500' => 'osa', 'Os12g0611900' => 'osa', 'Peaxi162Scf00076g00020' => 'pax', 'Peaxi162Scf00128g00217' => 'pax', 'Peaxi162Scf00129g01640' => 'pax', 'Peaxi162Scf00669g00007' => 'pax', 'Peaxi162Scf00700g00421' => 'pax', 'Peaxi162Scf00801g00038' => 'pax', 'Peaxi162Scf00891g00025' => 'pax', 'PGR083G0909' => 'pgr', 'PGR119G1005' => 'pgr', 'PGR142G2236' => 'pgr', 'PGR142G3388' => 'pgr', 'PGSC0003DMG400004514' => 'stu', 'PGSC0003DMG400012635' => 'stu', 'PGSC0003DMG400015730' => 'stu', 'PGSC0003DMG400018611' => 'stu', 'PGSC0003DMG400030897' => 'stu', 'Phvul.001G254800' => 'pvu', 'Phvul.002G260100' => 'pvu', 'Phvul.003G167600' => 'pvu', 'Phvul.004G005100' => 'pvu', 'Potri.001G343600' => 'ptr', 'Potri.006G066700' => 'ptr', 'Potri.008G186000' => 'ptr', 'Potri.010G046900' => 'ptr', 'Potri.018G127900' => 'ptr', 'Pp3c20_17750' => 'ppa', 'Pp3c24_4380' => 'ppa', 'Prupe.1G245800' => 'ppe', 'Prupe.3G293400' => 'ppe', 'Prupe.7G247400' => 'ppe', 'Psat0s145g0120' => 'psa', 'Psat0s595g0040' => 'psa', 'Psat0s595g0120' => 'psa', 'Psat3g175040' => 'psa', 'Psat7g058120' => 'psa', 'PSO017G0428' => 'pso', 'PSO063G7510' => 'pso', 'PSO067G0046' => 'pso', 'PSO478G1073' => 'pso', 'PSO675G3677' => 'pso', 'PSO675G6558' => 'pso', 'PSO675G7520' => 'pso', 'PSO675G8959' => 'pso', 'QL02p074089' => 'qlo', 'QL02p089614' => 'qlo', 'QL03p057736' => 'qlo', 'RcHm_v2.0_Chr1g0364131' => 'rch', 'RcHm_v2.0_Chr2g0087801' => 'rch', 'RcHm_v2.0_Chr2g0087821' => 'rch', 'RcHm_v2.0_Chr2g0173231' => 'rch', 'RcHm_v2.0_Chr4g0433111' => 'rch', 'Rhsim03G0250300' => 'rsi', 'Rhsim08G0048400' => 'rsi', 'Rhsim10G0014800' => 'rsi', 'Rhsim12G0040100' => 'rsi', 'Rhsim12G0109700' => 'rsi', 'Sabra06G0049600' => 'sbr', 'Sabra08G0141000' => 'sbr', 'Sabra10G0021400' => 'sbr', 'Sabra16G0222900' => 'sbr', 'Sabra18G0108600' => 'sbr', 'SalBow1G0433' => 'sbo', 'SalBow1G2038' => 'sbo', 'SalBow1G5003' => 'sbo', 'SalBow7G1197' => 'sbo', 'SalBow8G3506' => 'sbo', 'Sc03g0007300' => 'sci', 'Sc11g0000950' => 'sci', 'Sc14g0008750' => 'sci', 'Sc18g0000420' => 'sci', 'Sed0006754' => 'sed', 'Sed0008741' => 'sed', 'Sed0017172' => 'sed', 'Sed0018925' => 'sed', 'Sed0023326' => 'sed', 'Sed0025909' => 'sed', 'SEGI_05333' => 'sgi', 'SEGI_10362' => 'sgi', 'SEGI_13380' => 'sgi', 'SEGI_24306' => 'sgi', 'SEGI_29077' => 'sgi', 'SEGI_29095' => 'sgi', 'SEGI_36534' => 'sgi', 'SEGI_37506' => 'sgi', 'SEGI_38321' => 'sgi', 'SGA_v2.0_scaffold307G48031' => 'sas', 'SGA_v2.0_scaffold47G17507' => 'sas', 'SGA_v2.0_scaffold63G21736' => 'sas', 'SGA_v2.0_scaffold87G27070' => 'sas', 'SHI17794' => 'shi', 'SHI28851' => 'shi', 'SMO165G0155' => 'smo', 'SMO340G0217' => 'smo', 'SMO367G1210' => 'smo', 'Solyc02g093430.3' => 'sly', 'Solyc05g013580.4' => 'sly', 'Solyc07g008030.3' => 'sly', 'Solyc12g035470.2' => 'sly', 'Sopen02g038020' => 'spe', 'Sopen05g008490' => 'spe', 'Sopen07g003910' => 'spe', 'Sopen12g015240' => 'spe', 'Sp1g11550' => 'spa', 'Sp2g16710' => 'spa', 'Sp3g00430' => 'spa', 'Sp3g26780' => 'spa', 'Sp5g22900' => 'spa', 'Sp6g29530' => 'spa', 'TAR371G0794' => 'tar', 'TAR374G0164' => 'tar', 'TAR622G0165' => 'tar', 'TAR626G0929' => 'tar', 'TAR629G2155' => 'tar', 'THA.LOC104805282' => 'tha', 'THA.LOC104805363' => 'tha', 'THA.LOC104808968' => 'tha', 'THA.LOC104821093' => 'tha', 'THA.LOC104823953' => 'tha', 'THA.LOC104825562' => 'tha', 'THA.LOC104825665' => 'tha', 'Thecc.02G261400' => 'tca', 'Thecc.04G019200' => 'tca', 'Thecc.09G130400' => 'tca', 'Thhalv10004374m.g' => 'esa', 'Thhalv10007850m.g' => 'esa', 'Thhalv10013782m.g' => 'esa', 'Thhalv10018686m.g' => 'esa', 'Thhalv10020899m.g' => 'esa', 'Thhalv10022755m.g' => 'esa', 'TPR.G23851' => 'tpr', 'TPR.G26500' => 'tpr', 'TPR.G27267' => 'tpr', 'TPR.G32001' => 'tpr', 'TPR.G6251' => 'tpr', 'TPR.G8167' => 'tpr', 'TWI12G1330' => 'twi', 'TWI18G1239' => 'twi', 'TWI34G0979' => 'twi', 'TWI36G0670' => 'twi', 'TWI36G0707' => 'twi', 'TWI56G0233' => 'twi', 'TWI75G1809' => 'twi', 'unitig_21.g20874' => 'ugi', 'unitig_26.g10343' => 'ugi', 'unitig_46.g18392' => 'ugi', 'unitig_52.g17178' => 'ugi', 'unitig_8.g2934' => 'ugi', 'vmacro01122' => 'vma', 'vmacro05875' => 'vma', 'vmacro06147' => 'vma', 'vmacro16191' => 'vma', 'vmacro18293' => 'vma', 'VMungo0251G3707' => 'vmu', 'VMungo0464G1521' => 'vmu', 'VMungo1215G0205' => 'vmu', 'VMungo1383G2484' => 'vmu', 'Zm00001eb079610' => 'zma', 'Zm00001eb135990' => 'zma', 'Zm00001eb183710' => 'zma', 'Zm00001eb246020' => 'zma' ), 'gf_id' => 'HOM05D001124', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001124' ), 'data_identifier' => 'HOM05D001124', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001124', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '548', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02520' => 'bna', 'A03p06630' => 'bna', 'A05p44460' => 'bna', 'A06p08710' => 'bna', 'A06p41090' => 'bna', 'A07p32320' => 'bna', 'A08p32520' => 'bna', 'A09p10360' => 'bna', 'A10p24080' => 'bna', 'Aa31LG11G15250' => 'aar', 'Aa31LG1G1800' => 'aar', 'Aa31LG2G5120' => 'aar', 'Aa31LG2G6070' => 'aar', 'Aa31LG5G10770' => 'aar', 'Aa31sc61G90' => 'aar', 'Actinidia01352' => 'ach', 'Actinidia05983' => 'ach', 'Actinidia08133' => 'ach', 'Actinidia15101' => 'ach', 'Actinidia26379' => 'ach', 'Actinidia35778' => 'ach', 'Actinidia36123' => 'ach', 'Actinidia37436' => 'ach', 'Actinidia38730' => 'ach', 'Ah.02g128210' => 'amhyb', 'Ah.03g132990' => 'amhyb', 'Ah.14g079410' => 'amhyb', 'AL1G24640' => 'aly', 'AL2G26680' => 'aly', 'AL3G10530' => 'aly', 'AL3G45230' => 'aly', 'AL5G15230' => 'aly', 'AL5G16960' => 'aly', 'AL6G25210' => 'aly', 'Aqoxy2G00441' => 'aox', 'Aqoxy3G01236' => 'aox', 'Aqoxy5G03746' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3RQ047' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C7GMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9C8JER' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MBL6KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YXCZ83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZANX40' => 'arhy', 'AT1G12990' => 'ath', 'AT1G67880' => 'ath', 'AT2G13290' => 'ath', 'AT3G01620' => 'ath', 'AT3G26445' => 'ath', 'AT3G27540' => 'ath', 'AT5G14480' => 'ath', 'ATR0824G026' => 'atr', 'ATR1098G019' => 'atr', 'Atru.chr11.2145' => 'acertr', 'Atru.chr2.3636' => 'acertr', 'Atru.chr2.3644' => 'acertr', 'Atru.chr6.2422' => 'acertr', 'Atru.chr7.1112' => 'acertr', 'AUR62005469' => 'cqu', 'AUR62011166' => 'cqu', 'AUR62013319' => 'cqu', 'AUR62024273' => 'cqu', 'AUR62028420' => 'cqu', 'AUR62041942' => 'cqu', 'BcaB01g04969' => 'bca', 'BcaB01g06371' => 'bca', 'BcaB02g11494' => 'bca', 'BcaB03g15382' => 'bca', 'BcaB08g36994' => 'bca', 'BcaC03g13477' => 'bca', 'BcaC03g13478' => 'bca', 'BcaC03g13480' => 'bca', 'BcaC03g13481' => 'bca', 'BcaC03g13486' => 'bca', 'BcaC04g19031' => 'bca', 'BcaC04g23085' => 'bca', 'BcaC05g25094' => 'bca', 'BcaC05g25096' => 'bca', 'BcaC05g25138' => 'bca', 'BcaC05g30416' => 'bca', 'BcaC05g30455' => 'bca', 'BcaC06g30979' => 'bca', 'BcaC06g33805' => 'bca', 'BcaC08g46021' => 'bca', 'BcaNung03154' => 'bca', 'BolC2t06623H' => 'bol', 'BolC2t06632H' => 'bol', 'BolC2t06635H' => 'bol', 'BolC2t06638H' => 'bol', 'BolC3t13266H' => 'bol', 'BolC5t29776H' => 'bol', 'BolC6t38912H' => 'bol', 'BolC7t44183H' => 'bol', 'BolC9t54123H' => 'bol', 'BolC9t59107H' => 'bol', 'BraA02t05221Z' => 'bra', 'BraA03t09996Z' => 'bra', 'BraA05t23210Z' => 'bra', 'BraA06t24068Z' => 'bra', 'BraA06t27032Z' => 'bra', 'BraA08t35176Z' => 'bra', 'BraA09t36680Z' => 'bra', 'BraA10t44471Z' => 'bra', 'C02p06760' => 'bna', 'C02p06890' => 'bna', 'C02p07010' => 'bna', 'C03p07660' => 'bna', 'C05p10300' => 'bna', 'C06p38150' => 'bna', 'C07p36650' => 'bna', 'C08p15770' => 'bna', 'C09p12300' => 'bna', 'C09p62700' => 'bna', 'C09p75040' => 'bna', 'CAN.G13.1' => 'can', 'CAN.G138.4' => 'can', 'CAN.G44.6' => 'can', 'CAN.G473.19' => 'can', 'CANSAT01G0835' => 'cansat', 'CANSAT11G0246' => 'cansat', 'CANSAT11G1766' => 'cansat', 'CANSAT64G1954' => 'cansat', 'CARHR013330' => 'chi', 'CARHR060530' => 'chi', 'CARHR075300' => 'chi', 'CARHR105120' => 'chi', 'CARHR148910' => 'chi', 'CARHR198830' => 'chi', 'Carub.0001s1275' => 'cru', 'Carub.0002s1437' => 'cru', 'Carub.0003s0044' => 'cru', 'Carub.0003s2787' => 'cru', 'Carub.0005s0597' => 'cru', 'Carub.0006s1266' => 'cru', 'Ca_06935_v3' => 'car', 'Ca_13559_v3' => 'car', 'Ca_16941_v3' => 'car', 'Ca_16960_v3' => 'car', 'Ca_17775_v3' => 'car', 'Ca_30464_v3' => 'car', 'Cc06_g08160' => 'ccan', 'Cc07_g01520' => 'ccan', 'Cc11_g15810' => 'ccan', 'CDE02G2840' => 'cde', 'CDE03G0093' => 'cde', 'CDE04G2127' => 'cde', 'CDE07G1857' => 'cde', 'CDE09G1246' => 'cde', 'Cfa003412' => 'cfa', 'Cfa007341' => 'cfa', 'Cfa009220' => 'cfa', 'Ciclev10008737m.g' => 'ccl', 'Ciclev10015565m.g' => 'ccl', 'Ciclev10031761m.g' => 'ccl', 'CiPaw.03G045300' => 'cil', 'CiPaw.03G247200' => 'cil', 'CiPaw.04G029500' => 'cil', 'CiPaw.04G174000' => 'cil', 'CiPaw.05G181200' => 'cil', 'CiPaw.06G067100' => 'cil', 'ClCG05G025800' => 'cla', 'ClCG06G011400' => 'cla', 'ClCG09G019360' => 'cla', 'COL.COLO4_04827' => 'col', 'COL.COLO4_29170' => 'col', 'COL.COLO4_35131' => 'col', 'COL.COLO4_35132' => 'col', 'Cpa.g.sc33.32' => 'cpa', 'Cpa.g.sc46.29' => 'cpa', 'Cpa.g.sc796.1' => 'cpa', 'CsaV3_1G030420' => 'csa', 'CsaV3_5G027050' => 'csa', 'CsaV3_5G031040' => 'csa', 'CsaV3_UNG023130' => 'csa', 'CSS0007726' => 'camsi', 'CSS0016433' => 'camsi', 'CSS0017656' => 'camsi', 'CSS0025364' => 'camsi', 'CSS0027582' => 'camsi', 'CSS0047288' => 'camsi', 'CSS0049950' => 'camsi', 'DCAR_003843' => 'dca', 'DCAR_007052' => 'dca', 'DCAR_020884' => 'dca', 'DCAR_021730' => 'dca', 'DCAR_024423' => 'dca', 'DCAR_026509' => 'dca', 'DCAR_031158' => 'dca', 'Dinv14728' => 'din', 'Dinv15219' => 'din', 'Dinv25728' => 'din', 'Dinv33428' => 'din', 'Dinv36489' => 'din', 'Dinv41486' => 'din', 'Duzib147G0469' => 'dzi', 'Duzib168G0060' => 'dzi', 'Duzib187G1215' => 'dzi', 'Duzib248G0692' => 'dzi', 'Duzib251G0767' => 'dzi', 'Duzib264G0446' => 'dzi', 'Duzib268G0691' => 'dzi', 'ECA232G4767' => 'eca', 'ECA233G2838' => 'eca', 'ECA234G0391' => 'eca', 'ECA234G0857' => 'eca', 'ECA236G1593' => 'eca', 'ECA238G0565' => 'eca', 'ECA246G1027' => 'eca', 'ECA246G3223' => 'eca', 'ECA246G3470' => 'eca', 'EL10Ac6g13829' => 'bvu', 'EL10Ac6g14093' => 'bvu', 'EL10Ac8g18707' => 'bvu', 'Eucgr.C01369' => 'egr', 'Eucgr.H02492' => 'egr', 'Eucgr.I01733' => 'egr', 'Eucgr.J02255' => 'egr', 'Eucgr.J02257' => 'egr', 'Eucgr.J02258' => 'egr', 'FAN02G1601' => 'fan', 'FAN03G1586' => 'fan', 'FAN03G2986' => 'fan', 'FAN05G4837' => 'fan', 'FAN06G0146' => 'fan', 'FAN07G0858' => 'fan', 'FAN09G3179' => 'fan', 'FAN10G0669' => 'fan', 'FAN12G2358' => 'fan', 'FAN14G4198' => 'fan', 'FAN14G5112' => 'fan', 'FAN17G0342' => 'fan', 'FAN19G0342' => 'fan', 'FAN19G0962' => 'fan', 'FAN19G1101' => 'fan', 'FAN19G1872' => 'fan', 'FAN22G0356' => 'fan', 'FAN23G0744' => 'fan', 'FAN23G1914' => 'fan', 'FAN26G0032' => 'fan', 'FAN28G0625' => 'fan', 'FvH4_1g02710' => 'fve', 'FvH4_1g02720' => 'fve', 'FvH4_4g25670' => 'fve', 'FvH4_6g51700' => 'fve', 'FvH4_7g20170' => 'fve', 'Glyma.05G175000' => 'gma', 'Glyma.08G132300' => 'gma', 'Glyma.11G243000' => 'gma', 'Glyma.13G158900' => 'gma', 'Glyma.17G112400' => 'gma', 'Glyma.18G014100' => 'gma', 'Glyma.19G003100' => 'gma', 'Glyma.19G056500' => 'gma', 'Gohir.A01G158900' => 'ghi', 'Gohir.A05G312600' => 'ghi', 'Gohir.A05G354900' => 'ghi', 'Gohir.A07G037200' => 'ghi', 'Gohir.A09G030000' => 'ghi', 'Gohir.A12G145200' => 'ghi', 'Gohir.D01G151500' => 'ghi', 'Gohir.D04G058300' => 'ghi', 'Gohir.D05G314100' => 'ghi', 'Gohir.D07G041400' => 'ghi', 'Gohir.D09G029700' => 'ghi', 'Gohir.D12G149700' => 'ghi', 'Gorai.001G043800' => 'gra', 'Gorai.002G187800' => 'gra', 'Gorai.006G034700' => 'gra', 'Gorai.008G161200' => 'gra', 'Gorai.009G335700' => 'gra', 'Gorai.012G065000' => 'gra', 'GSVIVG01000535001' => 'vvi', 'GSVIVG01015572001' => 'vvi', 'GSVIVG01032386001' => 'vvi', 'HanXRQChr05g0138531' => 'han', 'HanXRQChr06g0174391' => 'han', 'HanXRQChr07g0199021' => 'han', 'HanXRQChr08g0208211' => 'han', 'HanXRQChr09g0255471' => 'han', 'HanXRQChr10g0315791' => 'han', 'HanXRQChr12g0371991' => 'han', 'HanXRQChr15g0475251' => 'han', 'HanXRQChr17g0540001' => 'han', 'HanXRQChr17g0548631' => 'han', 'HanXRQChr17g0569561' => 'han', 'Haze_12256' => 'cav', 'Haze_14756' => 'cav', 'Haze_25528' => 'cav', 'Hma1.2p1_0079F.1_g041020' => 'hma', 'Hma1.2p1_0818F.1_g223260' => 'hma', 'Hma1.2p1_1747F.1_g300530' => 'hma', 'HPP92_004607' => 'vpl', 'HPP92_004608' => 'vpl', 'HPP92_006181' => 'vpl', 'HPP92_012192' => 'vpl', 'HPP92_015680' => 'vpl', 'HPP92_020249' => 'vpl', 'HPP92_021376' => 'vpl', 'HPP92_024275' => 'vpl', 'Hund06031' => 'sun', 'Hund25391' => 'sun', 'Lalb_Chr07g0185371' => 'lal', 'Lalb_Chr07g0185381' => 'lal', 'Lalb_Chr12g0204011' => 'lal', 'Lalb_Chr13g0301671' => 'lal', 'Lalb_Chr14g0362851' => 'lal', 'Lalb_Chr24g0403581' => 'lal', 'Lj1g0000233' => 'lja', 'Lj2g0018120' => 'lja', 'Lj3C621T0' => 'lonja', 'Lj3P1059T14' => 'lonja', 'Lj3P611T9' => 'lonja', 'Lj3P614T13' => 'lonja', 'Lj3P615T5' => 'lonja', 'Lj4g0012315' => 'lja', 'Lj4g0026182' => 'lja', 'Lj6P813T16' => 'lonja', 'Lj7C427T7' => 'lonja', 'Lj7C427T8' => 'lonja', 'Lj7P600T41' => 'lonja', 'Lju41C42G17' => 'lonja', 'Lsat_1_v5_gn_0_47300' => 'lsa', 'Lsat_1_v5_gn_2_91280' => 'lsa', 'Lsat_1_v5_gn_3_30561' => 'lsa', 'Lsat_1_v5_gn_4_184321' => 'lsa', 'Lsat_1_v5_gn_4_4041' => 'lsa', 'Lsat_1_v5_gn_5_92000' => 'lsa', 'Lsat_1_v5_gn_8_152940' => 'lsa', 'Lsat_1_v5_gn_8_62401' => 'lsa', 'Manes.06G055900' => 'mes', 'Manes.12G022200' => 'mes', 'Manes.13G023300' => 'mes', 'Manes.14G115000' => 'mes', 'Manes.15G151700' => 'mes', 'Manes.17G111300' => 'mes', 'Mapoly0226s0009' => 'mpo', 'MBI02_g25363_MAGBIO' => 'mbi', 'MBI06_g00027_MAGBIO' => 'mbi', 'MBI10_g13034_MAGBIO' => 'mbi', 'MD09G1023400' => 'mdo', 'MD13G1100100' => 'mdo', 'MD15G1169200' => 'mdo', 'MD16G1101100' => 'mdo', 'MD17G1022900' => 'mdo', 'Medtr3g096150' => 'mtr', 'Medtr4g115070' => 'mtr', 'Medtr7g033325' => 'mtr', 'Medtr8g089840' => 'mtr', 'MELO3C010319.2' => 'cme', 'MELO3C011944.2' => 'cme', 'MELO3C021589.2' => 'cme', 'Migut.E00207' => 'egut', 'Migut.H00067' => 'egut', 'Migut.K00433' => 'egut', 'Migut.K00606' => 'egut', 'Migut.K01410' => 'egut', 'MSTRG.13347' => 'ama', 'MSTRG.24045' => 'ama', 'MSTRG.2428' => 'ama', 'MSTRG.26410' => 'ama', 'MSTRG.3139' => 'ama', 'MSTRG.3286' => 'ama', 'MSTRG.563' => 'ama', 'MSTRG.7941' => 'ama', 'Nitab4.5_0000028g0060' => 'nta', 'Nitab4.5_0000065g0260' => 'nta', 'Nitab4.5_0000112g0060' => 'nta', 'Nitab4.5_0000489g0120' => 'nta', 'Nitab4.5_0001776g0050' => 'nta', 'Nitab4.5_0001854g0010' => 'nta', 'Nitab4.5_0001860g0020' => 'nta', 'Nitab4.5_0004352g0010' => 'nta', 'Nitab4.5_0008716g0020' => 'nta', 'Nitab4.5_0008922g0010' => 'nta', 'Nn3g16693' => 'nnu', 'Nn4g22596' => 'nnu', 'Nn7g37639' => 'nnu', 'Oeu001701.1' => 'oeu', 'Oeu018149.1' => 'oeu', 'Oeu026220.1' => 'oeu', 'Oeu038635.1' => 'oeu', 'Oeu049176.1' => 'oeu', 'Oeu056706.1' => 'oeu', 'Oeu056937.1' => 'oeu', 'Oeu057540.1' => 'oeu', 'Os02g0594900' => 'osa', 'Os02g0595100' => 'osa', 'Os04g0477500' => 'osa', 'Os12g0611900' => 'osa', 'Peaxi162Scf00076g00020' => 'pax', 'Peaxi162Scf00128g00217' => 'pax', 'Peaxi162Scf00129g01640' => 'pax', 'Peaxi162Scf00669g00007' => 'pax', 'Peaxi162Scf00700g00421' => 'pax', 'Peaxi162Scf00801g00038' => 'pax', 'Peaxi162Scf00891g00025' => 'pax', 'PGR083G0909' => 'pgr', 'PGR119G1005' => 'pgr', 'PGR142G2236' => 'pgr', 'PGR142G3388' => 'pgr', 'PGSC0003DMG400004514' => 'stu', 'PGSC0003DMG400012635' => 'stu', 'PGSC0003DMG400015730' => 'stu', 'PGSC0003DMG400018611' => 'stu', 'PGSC0003DMG400030897' => 'stu', 'Phvul.001G254800' => 'pvu', 'Phvul.002G260100' => 'pvu', 'Phvul.003G167600' => 'pvu', 'Phvul.004G005100' => 'pvu', 'Potri.001G343600' => 'ptr', 'Potri.006G066700' => 'ptr', 'Potri.008G186000' => 'ptr', 'Potri.010G046900' => 'ptr', 'Potri.018G127900' => 'ptr', 'Pp3c20_17750' => 'ppa', 'Pp3c24_4380' => 'ppa', 'Prupe.1G245800' => 'ppe', 'Prupe.3G293400' => 'ppe', 'Prupe.7G247400' => 'ppe', 'Psat0s145g0120' => 'psa', 'Psat0s595g0040' => 'psa', 'Psat0s595g0120' => 'psa', 'Psat3g175040' => 'psa', 'Psat7g058120' => 'psa', 'PSO017G0428' => 'pso', 'PSO063G7510' => 'pso', 'PSO067G0046' => 'pso', 'PSO478G1073' => 'pso', 'PSO675G3677' => 'pso', 'PSO675G6558' => 'pso', 'PSO675G7520' => 'pso', 'PSO675G8959' => 'pso', 'QL02p074089' => 'qlo', 'QL02p089614' => 'qlo', 'QL03p057736' => 'qlo', 'RcHm_v2.0_Chr1g0364131' => 'rch', 'RcHm_v2.0_Chr2g0087801' => 'rch', 'RcHm_v2.0_Chr2g0087821' => 'rch', 'RcHm_v2.0_Chr2g0173231' => 'rch', 'RcHm_v2.0_Chr4g0433111' => 'rch', 'Rhsim03G0250300' => 'rsi', 'Rhsim08G0048400' => 'rsi', 'Rhsim10G0014800' => 'rsi', 'Rhsim12G0040100' => 'rsi', 'Rhsim12G0109700' => 'rsi', 'Sabra06G0049600' => 'sbr', 'Sabra08G0141000' => 'sbr', 'Sabra10G0021400' => 'sbr', 'Sabra16G0222900' => 'sbr', 'Sabra18G0108600' => 'sbr', 'SalBow1G0433' => 'sbo', 'SalBow1G2038' => 'sbo', 'SalBow1G5003' => 'sbo', 'SalBow7G1197' => 'sbo', 'SalBow8G3506' => 'sbo', 'Sc03g0007300' => 'sci', 'Sc11g0000950' => 'sci', 'Sc14g0008750' => 'sci', 'Sc18g0000420' => 'sci', 'Sed0006754' => 'sed', 'Sed0008741' => 'sed', 'Sed0017172' => 'sed', 'Sed0018925' => 'sed', 'Sed0023326' => 'sed', 'Sed0025909' => 'sed', 'SEGI_05333' => 'sgi', 'SEGI_10362' => 'sgi', 'SEGI_13380' => 'sgi', 'SEGI_24306' => 'sgi', 'SEGI_29077' => 'sgi', 'SEGI_29095' => 'sgi', 'SEGI_36534' => 'sgi', 'SEGI_37506' => 'sgi', 'SEGI_38321' => 'sgi', 'SGA_v2.0_scaffold307G48031' => 'sas', 'SGA_v2.0_scaffold47G17507' => 'sas', 'SGA_v2.0_scaffold63G21736' => 'sas', 'SGA_v2.0_scaffold87G27070' => 'sas', 'SHI17794' => 'shi', 'SHI28851' => 'shi', 'SMO165G0155' => 'smo', 'SMO340G0217' => 'smo', 'SMO367G1210' => 'smo', 'Solyc02g093430.3' => 'sly', 'Solyc05g013580.4' => 'sly', 'Solyc07g008030.3' => 'sly', 'Solyc12g035470.2' => 'sly', 'Sopen02g038020' => 'spe', 'Sopen05g008490' => 'spe', 'Sopen07g003910' => 'spe', 'Sopen12g015240' => 'spe', 'Sp1g11550' => 'spa', 'Sp2g16710' => 'spa', 'Sp3g00430' => 'spa', 'Sp3g26780' => 'spa', 'Sp5g22900' => 'spa', 'Sp6g29530' => 'spa', 'TAR371G0794' => 'tar', 'TAR374G0164' => 'tar', 'TAR622G0165' => 'tar', 'TAR626G0929' => 'tar', 'TAR629G2155' => 'tar', 'THA.LOC104805282' => 'tha', 'THA.LOC104805363' => 'tha', 'THA.LOC104808968' => 'tha', 'THA.LOC104821093' => 'tha', 'THA.LOC104823953' => 'tha', 'THA.LOC104825562' => 'tha', 'THA.LOC104825665' => 'tha', 'Thecc.02G261400' => 'tca', 'Thecc.04G019200' => 'tca', 'Thecc.09G130400' => 'tca', 'Thhalv10004374m.g' => 'esa', 'Thhalv10007850m.g' => 'esa', 'Thhalv10013782m.g' => 'esa', 'Thhalv10018686m.g' => 'esa', 'Thhalv10020899m.g' => 'esa', 'Thhalv10022755m.g' => 'esa', 'TPR.G23851' => 'tpr', 'TPR.G26500' => 'tpr', 'TPR.G27267' => 'tpr', 'TPR.G32001' => 'tpr', 'TPR.G6251' => 'tpr', 'TPR.G8167' => 'tpr', 'TWI12G1330' => 'twi', 'TWI18G1239' => 'twi', 'TWI34G0979' => 'twi', 'TWI36G0670' => 'twi', 'TWI36G0707' => 'twi', 'TWI56G0233' => 'twi', 'TWI75G1809' => 'twi', 'unitig_21.g20874' => 'ugi', 'unitig_26.g10343' => 'ugi', 'unitig_46.g18392' => 'ugi', 'unitig_52.g17178' => 'ugi', 'unitig_8.g2934' => 'ugi', 'vmacro01122' => 'vma', 'vmacro05875' => 'vma', 'vmacro06147' => 'vma', 'vmacro16191' => 'vma', 'vmacro18293' => 'vma', 'VMungo0251G3707' => 'vmu', 'VMungo0464G1521' => 'vmu', 'VMungo1215G0205' => 'vmu', 'VMungo1383G2484' => 'vmu', 'Zm00001eb079610' => 'zma', 'Zm00001eb135990' => 'zma', 'Zm00001eb183710' => 'zma', 'Zm00001eb246020' => 'zma' ) $gf_id = 'HOM05D001124' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001124' ) $data_identifier = 'HOM05D001124' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 6, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 7, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 21, 'bol' => (int) 10, 'bra' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 6, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 9, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 21, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 8, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 10, 'lsa' => (int) 8, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 8, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 9, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb246020' $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' => 'HOM05D001124', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '548', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02520' => 'bna', 'A03p06630' => 'bna', 'A05p44460' => 'bna', 'A06p08710' => 'bna', 'A06p41090' => 'bna', 'A07p32320' => 'bna', 'A08p32520' => 'bna', 'A09p10360' => 'bna', 'A10p24080' => 'bna', 'Aa31LG11G15250' => 'aar', 'Aa31LG1G1800' => 'aar', 'Aa31LG2G5120' => 'aar', 'Aa31LG2G6070' => 'aar', 'Aa31LG5G10770' => 'aar', 'Aa31sc61G90' => 'aar', 'Actinidia01352' => 'ach', 'Actinidia05983' => 'ach', 'Actinidia08133' => 'ach', 'Actinidia15101' => 'ach', 'Actinidia26379' => 'ach', 'Actinidia35778' => 'ach', 'Actinidia36123' => 'ach', 'Actinidia37436' => 'ach', 'Actinidia38730' => 'ach', 'Ah.02g128210' => 'amhyb', 'Ah.03g132990' => 'amhyb', 'Ah.14g079410' => 'amhyb', 'AL1G24640' => 'aly', 'AL2G26680' => 'aly', 'AL3G10530' => 'aly', 'AL3G45230' => 'aly', 'AL5G15230' => 'aly', 'AL5G16960' => 'aly', 'AL6G25210' => 'aly', 'Aqoxy2G00441' => 'aox', 'Aqoxy3G01236' => 'aox', 'Aqoxy5G03746' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3RQ047' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C7GMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9C8JER' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MBL6KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YXCZ83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZANX40' => 'arhy', 'AT1G12990' => 'ath', 'AT1G67880' => 'ath', 'AT2G13290' => 'ath', 'AT3G01620' => 'ath', 'AT3G26445' => 'ath', 'AT3G27540' => 'ath', 'AT5G14480' => 'ath', 'ATR0824G026' => 'atr', 'ATR1098G019' => 'atr', 'Atru.chr11.2145' => 'acertr', 'Atru.chr2.3636' => 'acertr', 'Atru.chr2.3644' => 'acertr', 'Atru.chr6.2422' => 'acertr', 'Atru.chr7.1112' => 'acertr', 'AUR62005469' => 'cqu', 'AUR62011166' => 'cqu', 'AUR62013319' => 'cqu', 'AUR62024273' => 'cqu', 'AUR62028420' => 'cqu', 'AUR62041942' => 'cqu', 'BcaB01g04969' => 'bca', 'BcaB01g06371' => 'bca', 'BcaB02g11494' => 'bca', 'BcaB03g15382' => 'bca', 'BcaB08g36994' => 'bca', 'BcaC03g13477' => 'bca', 'BcaC03g13478' => 'bca', 'BcaC03g13480' => 'bca', 'BcaC03g13481' => 'bca', 'BcaC03g13486' => 'bca', 'BcaC04g19031' => 'bca', 'BcaC04g23085' => 'bca', 'BcaC05g25094' => 'bca', 'BcaC05g25096' => 'bca', 'BcaC05g25138' => 'bca', 'BcaC05g30416' => 'bca', 'BcaC05g30455' => 'bca', 'BcaC06g30979' => 'bca', 'BcaC06g33805' => 'bca', 'BcaC08g46021' => 'bca', 'BcaNung03154' => 'bca', 'BolC2t06623H' => 'bol', 'BolC2t06632H' => 'bol', 'BolC2t06635H' => 'bol', 'BolC2t06638H' => 'bol', 'BolC3t13266H' => 'bol', 'BolC5t29776H' => 'bol', 'BolC6t38912H' => 'bol', 'BolC7t44183H' => 'bol', 'BolC9t54123H' => 'bol', 'BolC9t59107H' => 'bol', 'BraA02t05221Z' => 'bra', 'BraA03t09996Z' => 'bra', 'BraA05t23210Z' => 'bra', 'BraA06t24068Z' => 'bra', 'BraA06t27032Z' => 'bra', 'BraA08t35176Z' => 'bra', 'BraA09t36680Z' => 'bra', 'BraA10t44471Z' => 'bra', 'C02p06760' => 'bna', 'C02p06890' => 'bna', 'C02p07010' => 'bna', 'C03p07660' => 'bna', 'C05p10300' => 'bna', 'C06p38150' => 'bna', 'C07p36650' => 'bna', 'C08p15770' => 'bna', 'C09p12300' => 'bna', 'C09p62700' => 'bna', 'C09p75040' => 'bna', 'CAN.G13.1' => 'can', 'CAN.G138.4' => 'can', 'CAN.G44.6' => 'can', 'CAN.G473.19' => 'can', 'CANSAT01G0835' => 'cansat', 'CANSAT11G0246' => 'cansat', 'CANSAT11G1766' => 'cansat', 'CANSAT64G1954' => 'cansat', 'CARHR013330' => 'chi', 'CARHR060530' => 'chi', 'CARHR075300' => 'chi', 'CARHR105120' => 'chi', 'CARHR148910' => 'chi', 'CARHR198830' => 'chi', 'Carub.0001s1275' => 'cru', 'Carub.0002s1437' => 'cru', 'Carub.0003s0044' => 'cru', 'Carub.0003s2787' => 'cru', 'Carub.0005s0597' => 'cru', 'Carub.0006s1266' => 'cru', 'Ca_06935_v3' => 'car', 'Ca_13559_v3' => 'car', 'Ca_16941_v3' => 'car', 'Ca_16960_v3' => 'car', 'Ca_17775_v3' => 'car', 'Ca_30464_v3' => 'car', 'Cc06_g08160' => 'ccan', 'Cc07_g01520' => 'ccan', 'Cc11_g15810' => 'ccan', 'CDE02G2840' => 'cde', 'CDE03G0093' => 'cde', 'CDE04G2127' => 'cde', 'CDE07G1857' => 'cde', 'CDE09G1246' => 'cde', 'Cfa003412' => 'cfa', 'Cfa007341' => 'cfa', 'Cfa009220' => 'cfa', 'Ciclev10008737m.g' => 'ccl', 'Ciclev10015565m.g' => 'ccl', 'Ciclev10031761m.g' => 'ccl', 'CiPaw.03G045300' => 'cil', 'CiPaw.03G247200' => 'cil', 'CiPaw.04G029500' => 'cil', 'CiPaw.04G174000' => 'cil', 'CiPaw.05G181200' => 'cil', 'CiPaw.06G067100' => 'cil', 'ClCG05G025800' => 'cla', 'ClCG06G011400' => 'cla', 'ClCG09G019360' => 'cla', 'COL.COLO4_04827' => 'col', 'COL.COLO4_29170' => 'col', 'COL.COLO4_35131' => 'col', 'COL.COLO4_35132' => 'col', 'Cpa.g.sc33.32' => 'cpa', 'Cpa.g.sc46.29' => 'cpa', 'Cpa.g.sc796.1' => 'cpa', 'CsaV3_1G030420' => 'csa', 'CsaV3_5G027050' => 'csa', 'CsaV3_5G031040' => 'csa', 'CsaV3_UNG023130' => 'csa', 'CSS0007726' => 'camsi', 'CSS0016433' => 'camsi', 'CSS0017656' => 'camsi', 'CSS0025364' => 'camsi', 'CSS0027582' => 'camsi', 'CSS0047288' => 'camsi', 'CSS0049950' => 'camsi', 'DCAR_003843' => 'dca', 'DCAR_007052' => 'dca', 'DCAR_020884' => 'dca', 'DCAR_021730' => 'dca', 'DCAR_024423' => 'dca', 'DCAR_026509' => 'dca', 'DCAR_031158' => 'dca', 'Dinv14728' => 'din', 'Dinv15219' => 'din', 'Dinv25728' => 'din', 'Dinv33428' => 'din', 'Dinv36489' => 'din', 'Dinv41486' => 'din', 'Duzib147G0469' => 'dzi', 'Duzib168G0060' => 'dzi', 'Duzib187G1215' => 'dzi', 'Duzib248G0692' => 'dzi', 'Duzib251G0767' => 'dzi', 'Duzib264G0446' => 'dzi', 'Duzib268G0691' => 'dzi', 'ECA232G4767' => 'eca', 'ECA233G2838' => 'eca', 'ECA234G0391' => 'eca', 'ECA234G0857' => 'eca', 'ECA236G1593' => 'eca', 'ECA238G0565' => 'eca', 'ECA246G1027' => 'eca', 'ECA246G3223' => 'eca', 'ECA246G3470' => 'eca', 'EL10Ac6g13829' => 'bvu', 'EL10Ac6g14093' => 'bvu', 'EL10Ac8g18707' => 'bvu', 'Eucgr.C01369' => 'egr', 'Eucgr.H02492' => 'egr', 'Eucgr.I01733' => 'egr', 'Eucgr.J02255' => 'egr', 'Eucgr.J02257' => 'egr', 'Eucgr.J02258' => 'egr', 'FAN02G1601' => 'fan', 'FAN03G1586' => 'fan', 'FAN03G2986' => 'fan', 'FAN05G4837' => 'fan', 'FAN06G0146' => 'fan', 'FAN07G0858' => 'fan', 'FAN09G3179' => 'fan', 'FAN10G0669' => 'fan', 'FAN12G2358' => 'fan', 'FAN14G4198' => 'fan', 'FAN14G5112' => 'fan', 'FAN17G0342' => 'fan', 'FAN19G0342' => 'fan', 'FAN19G0962' => 'fan', 'FAN19G1101' => 'fan', 'FAN19G1872' => 'fan', 'FAN22G0356' => 'fan', 'FAN23G0744' => 'fan', 'FAN23G1914' => 'fan', 'FAN26G0032' => 'fan', 'FAN28G0625' => 'fan', 'FvH4_1g02710' => 'fve', 'FvH4_1g02720' => 'fve', 'FvH4_4g25670' => 'fve', 'FvH4_6g51700' => 'fve', 'FvH4_7g20170' => 'fve', 'Glyma.05G175000' => 'gma', 'Glyma.08G132300' => 'gma', 'Glyma.11G243000' => 'gma', 'Glyma.13G158900' => 'gma', 'Glyma.17G112400' => 'gma', 'Glyma.18G014100' => 'gma', 'Glyma.19G003100' => 'gma', 'Glyma.19G056500' => 'gma', 'Gohir.A01G158900' => 'ghi', 'Gohir.A05G312600' => 'ghi', 'Gohir.A05G354900' => 'ghi', 'Gohir.A07G037200' => 'ghi', 'Gohir.A09G030000' => 'ghi', 'Gohir.A12G145200' => 'ghi', 'Gohir.D01G151500' => 'ghi', 'Gohir.D04G058300' => 'ghi', 'Gohir.D05G314100' => 'ghi', 'Gohir.D07G041400' => 'ghi', 'Gohir.D09G029700' => 'ghi', 'Gohir.D12G149700' => 'ghi', 'Gorai.001G043800' => 'gra', 'Gorai.002G187800' => 'gra', 'Gorai.006G034700' => 'gra', 'Gorai.008G161200' => 'gra', 'Gorai.009G335700' => 'gra', 'Gorai.012G065000' => 'gra', 'GSVIVG01000535001' => 'vvi', 'GSVIVG01015572001' => 'vvi', 'GSVIVG01032386001' => 'vvi', 'HanXRQChr05g0138531' => 'han', 'HanXRQChr06g0174391' => 'han', 'HanXRQChr07g0199021' => 'han', 'HanXRQChr08g0208211' => 'han', 'HanXRQChr09g0255471' => 'han', 'HanXRQChr10g0315791' => 'han', 'HanXRQChr12g0371991' => 'han', 'HanXRQChr15g0475251' => 'han', 'HanXRQChr17g0540001' => 'han', 'HanXRQChr17g0548631' => 'han', 'HanXRQChr17g0569561' => 'han', 'Haze_12256' => 'cav', 'Haze_14756' => 'cav', 'Haze_25528' => 'cav', 'Hma1.2p1_0079F.1_g041020' => 'hma', 'Hma1.2p1_0818F.1_g223260' => 'hma', 'Hma1.2p1_1747F.1_g300530' => 'hma', 'HPP92_004607' => 'vpl', 'HPP92_004608' => 'vpl', 'HPP92_006181' => 'vpl', 'HPP92_012192' => 'vpl', 'HPP92_015680' => 'vpl', 'HPP92_020249' => 'vpl', 'HPP92_021376' => 'vpl', 'HPP92_024275' => 'vpl', 'Hund06031' => 'sun', 'Hund25391' => 'sun', 'Lalb_Chr07g0185371' => 'lal', 'Lalb_Chr07g0185381' => 'lal', 'Lalb_Chr12g0204011' => 'lal', 'Lalb_Chr13g0301671' => 'lal', 'Lalb_Chr14g0362851' => 'lal', 'Lalb_Chr24g0403581' => 'lal', 'Lj1g0000233' => 'lja', 'Lj2g0018120' => 'lja', 'Lj3C621T0' => 'lonja', 'Lj3P1059T14' => 'lonja', 'Lj3P611T9' => 'lonja', 'Lj3P614T13' => 'lonja', 'Lj3P615T5' => 'lonja', 'Lj4g0012315' => 'lja', 'Lj4g0026182' => 'lja', 'Lj6P813T16' => 'lonja', 'Lj7C427T7' => 'lonja', 'Lj7C427T8' => 'lonja', 'Lj7P600T41' => 'lonja', 'Lju41C42G17' => 'lonja', 'Lsat_1_v5_gn_0_47300' => 'lsa', 'Lsat_1_v5_gn_2_91280' => 'lsa', 'Lsat_1_v5_gn_3_30561' => 'lsa', 'Lsat_1_v5_gn_4_184321' => 'lsa', 'Lsat_1_v5_gn_4_4041' => 'lsa', 'Lsat_1_v5_gn_5_92000' => 'lsa', 'Lsat_1_v5_gn_8_152940' => 'lsa', 'Lsat_1_v5_gn_8_62401' => 'lsa', 'Manes.06G055900' => 'mes', 'Manes.12G022200' => 'mes', 'Manes.13G023300' => 'mes', 'Manes.14G115000' => 'mes', 'Manes.15G151700' => 'mes', 'Manes.17G111300' => 'mes', 'Mapoly0226s0009' => 'mpo', 'MBI02_g25363_MAGBIO' => 'mbi', 'MBI06_g00027_MAGBIO' => 'mbi', 'MBI10_g13034_MAGBIO' => 'mbi', 'MD09G1023400' => 'mdo', 'MD13G1100100' => 'mdo', 'MD15G1169200' => 'mdo', 'MD16G1101100' => 'mdo', 'MD17G1022900' => 'mdo', 'Medtr3g096150' => 'mtr', 'Medtr4g115070' => 'mtr', 'Medtr7g033325' => 'mtr', 'Medtr8g089840' => 'mtr', 'MELO3C010319.2' => 'cme', 'MELO3C011944.2' => 'cme', 'MELO3C021589.2' => 'cme', 'Migut.E00207' => 'egut', 'Migut.H00067' => 'egut', 'Migut.K00433' => 'egut', 'Migut.K00606' => 'egut', 'Migut.K01410' => 'egut', 'MSTRG.13347' => 'ama', 'MSTRG.24045' => 'ama', 'MSTRG.2428' => 'ama', 'MSTRG.26410' => 'ama', 'MSTRG.3139' => 'ama', 'MSTRG.3286' => 'ama', 'MSTRG.563' => 'ama', 'MSTRG.7941' => 'ama', 'Nitab4.5_0000028g0060' => 'nta', 'Nitab4.5_0000065g0260' => 'nta', 'Nitab4.5_0000112g0060' => 'nta', 'Nitab4.5_0000489g0120' => 'nta', 'Nitab4.5_0001776g0050' => 'nta', 'Nitab4.5_0001854g0010' => 'nta', 'Nitab4.5_0001860g0020' => 'nta', 'Nitab4.5_0004352g0010' => 'nta', 'Nitab4.5_0008716g0020' => 'nta', 'Nitab4.5_0008922g0010' => 'nta', 'Nn3g16693' => 'nnu', 'Nn4g22596' => 'nnu', 'Nn7g37639' => 'nnu', 'Oeu001701.1' => 'oeu', 'Oeu018149.1' => 'oeu', 'Oeu026220.1' => 'oeu', 'Oeu038635.1' => 'oeu', 'Oeu049176.1' => 'oeu', 'Oeu056706.1' => 'oeu', 'Oeu056937.1' => 'oeu', 'Oeu057540.1' => 'oeu', 'Os02g0594900' => 'osa', 'Os02g0595100' => 'osa', 'Os04g0477500' => 'osa', 'Os12g0611900' => 'osa', 'Peaxi162Scf00076g00020' => 'pax', 'Peaxi162Scf00128g00217' => 'pax', 'Peaxi162Scf00129g01640' => 'pax', 'Peaxi162Scf00669g00007' => 'pax', 'Peaxi162Scf00700g00421' => 'pax', 'Peaxi162Scf00801g00038' => 'pax', 'Peaxi162Scf00891g00025' => 'pax', 'PGR083G0909' => 'pgr', 'PGR119G1005' => 'pgr', 'PGR142G2236' => 'pgr', 'PGR142G3388' => 'pgr', 'PGSC0003DMG400004514' => 'stu', 'PGSC0003DMG400012635' => 'stu', 'PGSC0003DMG400015730' => 'stu', 'PGSC0003DMG400018611' => 'stu', 'PGSC0003DMG400030897' => 'stu', 'Phvul.001G254800' => 'pvu', 'Phvul.002G260100' => 'pvu', 'Phvul.003G167600' => 'pvu', 'Phvul.004G005100' => 'pvu', 'Potri.001G343600' => 'ptr', 'Potri.006G066700' => 'ptr', 'Potri.008G186000' => 'ptr', 'Potri.010G046900' => 'ptr', 'Potri.018G127900' => 'ptr', 'Pp3c20_17750' => 'ppa', 'Pp3c24_4380' => 'ppa', 'Prupe.1G245800' => 'ppe', 'Prupe.3G293400' => 'ppe', 'Prupe.7G247400' => 'ppe', 'Psat0s145g0120' => 'psa', 'Psat0s595g0040' => 'psa', 'Psat0s595g0120' => 'psa', 'Psat3g175040' => 'psa', 'Psat7g058120' => 'psa', 'PSO017G0428' => 'pso', 'PSO063G7510' => 'pso', 'PSO067G0046' => 'pso', 'PSO478G1073' => 'pso', 'PSO675G3677' => 'pso', 'PSO675G6558' => 'pso', 'PSO675G7520' => 'pso', 'PSO675G8959' => 'pso', 'QL02p074089' => 'qlo', 'QL02p089614' => 'qlo', 'QL03p057736' => 'qlo', 'RcHm_v2.0_Chr1g0364131' => 'rch', 'RcHm_v2.0_Chr2g0087801' => 'rch', 'RcHm_v2.0_Chr2g0087821' => 'rch', 'RcHm_v2.0_Chr2g0173231' => 'rch', 'RcHm_v2.0_Chr4g0433111' => 'rch', 'Rhsim03G0250300' => 'rsi', 'Rhsim08G0048400' => 'rsi', 'Rhsim10G0014800' => 'rsi', 'Rhsim12G0040100' => 'rsi', 'Rhsim12G0109700' => 'rsi', 'Sabra06G0049600' => 'sbr', 'Sabra08G0141000' => 'sbr', 'Sabra10G0021400' => 'sbr', 'Sabra16G0222900' => 'sbr', 'Sabra18G0108600' => 'sbr', 'SalBow1G0433' => 'sbo', 'SalBow1G2038' => 'sbo', 'SalBow1G5003' => 'sbo', 'SalBow7G1197' => 'sbo', 'SalBow8G3506' => 'sbo', 'Sc03g0007300' => 'sci', 'Sc11g0000950' => 'sci', 'Sc14g0008750' => 'sci', 'Sc18g0000420' => 'sci', 'Sed0006754' => 'sed', 'Sed0008741' => 'sed', 'Sed0017172' => 'sed', 'Sed0018925' => 'sed', 'Sed0023326' => 'sed', 'Sed0025909' => 'sed', 'SEGI_05333' => 'sgi', 'SEGI_10362' => 'sgi', 'SEGI_13380' => 'sgi', 'SEGI_24306' => 'sgi', 'SEGI_29077' => 'sgi', 'SEGI_29095' => 'sgi', 'SEGI_36534' => 'sgi', 'SEGI_37506' => 'sgi', 'SEGI_38321' => 'sgi', 'SGA_v2.0_scaffold307G48031' => 'sas', 'SGA_v2.0_scaffold47G17507' => 'sas', 'SGA_v2.0_scaffold63G21736' => 'sas', 'SGA_v2.0_scaffold87G27070' => 'sas', 'SHI17794' => 'shi', 'SHI28851' => 'shi', 'SMO165G0155' => 'smo', 'SMO340G0217' => 'smo', 'SMO367G1210' => 'smo', 'Solyc02g093430.3' => 'sly', 'Solyc05g013580.4' => 'sly', 'Solyc07g008030.3' => 'sly', 'Solyc12g035470.2' => 'sly', 'Sopen02g038020' => 'spe', 'Sopen05g008490' => 'spe', 'Sopen07g003910' => 'spe', 'Sopen12g015240' => 'spe', 'Sp1g11550' => 'spa', 'Sp2g16710' => 'spa', 'Sp3g00430' => 'spa', 'Sp3g26780' => 'spa', 'Sp5g22900' => 'spa', 'Sp6g29530' => 'spa', 'TAR371G0794' => 'tar', 'TAR374G0164' => 'tar', 'TAR622G0165' => 'tar', 'TAR626G0929' => 'tar', 'TAR629G2155' => 'tar', 'THA.LOC104805282' => 'tha', 'THA.LOC104805363' => 'tha', 'THA.LOC104808968' => 'tha', 'THA.LOC104821093' => 'tha', 'THA.LOC104823953' => 'tha', 'THA.LOC104825562' => 'tha', 'THA.LOC104825665' => 'tha', 'Thecc.02G261400' => 'tca', 'Thecc.04G019200' => 'tca', 'Thecc.09G130400' => 'tca', 'Thhalv10004374m.g' => 'esa', 'Thhalv10007850m.g' => 'esa', 'Thhalv10013782m.g' => 'esa', 'Thhalv10018686m.g' => 'esa', 'Thhalv10020899m.g' => 'esa', 'Thhalv10022755m.g' => 'esa', 'TPR.G23851' => 'tpr', 'TPR.G26500' => 'tpr', 'TPR.G27267' => 'tpr', 'TPR.G32001' => 'tpr', 'TPR.G6251' => 'tpr', 'TPR.G8167' => 'tpr', 'TWI12G1330' => 'twi', 'TWI18G1239' => 'twi', 'TWI34G0979' => 'twi', 'TWI36G0670' => 'twi', 'TWI36G0707' => 'twi', 'TWI56G0233' => 'twi', 'TWI75G1809' => 'twi', 'unitig_21.g20874' => 'ugi', 'unitig_26.g10343' => 'ugi', 'unitig_46.g18392' => 'ugi', 'unitig_52.g17178' => 'ugi', 'unitig_8.g2934' => 'ugi', 'vmacro01122' => 'vma', 'vmacro05875' => 'vma', 'vmacro06147' => 'vma', 'vmacro16191' => 'vma', 'vmacro18293' => 'vma', 'VMungo0251G3707' => 'vmu', 'VMungo0464G1521' => 'vmu', 'VMungo1215G0205' => 'vmu', 'VMungo1383G2484' => 'vmu', 'Zm00001eb079610' => 'zma', 'Zm00001eb135990' => 'zma', 'Zm00001eb183710' => 'zma', 'Zm00001eb246020' => 'zma' ), 'gf_id' => 'HOM05D001124', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001124' ), 'data_identifier' => 'HOM05D001124', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001124', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '548', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02520' => 'bna', 'A03p06630' => 'bna', 'A05p44460' => 'bna', 'A06p08710' => 'bna', 'A06p41090' => 'bna', 'A07p32320' => 'bna', 'A08p32520' => 'bna', 'A09p10360' => 'bna', 'A10p24080' => 'bna', 'Aa31LG11G15250' => 'aar', 'Aa31LG1G1800' => 'aar', 'Aa31LG2G5120' => 'aar', 'Aa31LG2G6070' => 'aar', 'Aa31LG5G10770' => 'aar', 'Aa31sc61G90' => 'aar', 'Actinidia01352' => 'ach', 'Actinidia05983' => 'ach', 'Actinidia08133' => 'ach', 'Actinidia15101' => 'ach', 'Actinidia26379' => 'ach', 'Actinidia35778' => 'ach', 'Actinidia36123' => 'ach', 'Actinidia37436' => 'ach', 'Actinidia38730' => 'ach', 'Ah.02g128210' => 'amhyb', 'Ah.03g132990' => 'amhyb', 'Ah.14g079410' => 'amhyb', 'AL1G24640' => 'aly', 'AL2G26680' => 'aly', 'AL3G10530' => 'aly', 'AL3G45230' => 'aly', 'AL5G15230' => 'aly', 'AL5G16960' => 'aly', 'AL6G25210' => 'aly', 'Aqoxy2G00441' => 'aox', 'Aqoxy3G01236' => 'aox', 'Aqoxy5G03746' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3RQ047' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C7GMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9C8JER' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MBL6KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YXCZ83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZANX40' => 'arhy', 'AT1G12990' => 'ath', 'AT1G67880' => 'ath', 'AT2G13290' => 'ath', 'AT3G01620' => 'ath', 'AT3G26445' => 'ath', 'AT3G27540' => 'ath', 'AT5G14480' => 'ath', 'ATR0824G026' => 'atr', 'ATR1098G019' => 'atr', 'Atru.chr11.2145' => 'acertr', 'Atru.chr2.3636' => 'acertr', 'Atru.chr2.3644' => 'acertr', 'Atru.chr6.2422' => 'acertr', 'Atru.chr7.1112' => 'acertr', 'AUR62005469' => 'cqu', 'AUR62011166' => 'cqu', 'AUR62013319' => 'cqu', 'AUR62024273' => 'cqu', 'AUR62028420' => 'cqu', 'AUR62041942' => 'cqu', 'BcaB01g04969' => 'bca', 'BcaB01g06371' => 'bca', 'BcaB02g11494' => 'bca', 'BcaB03g15382' => 'bca', 'BcaB08g36994' => 'bca', 'BcaC03g13477' => 'bca', 'BcaC03g13478' => 'bca', 'BcaC03g13480' => 'bca', 'BcaC03g13481' => 'bca', 'BcaC03g13486' => 'bca', 'BcaC04g19031' => 'bca', 'BcaC04g23085' => 'bca', 'BcaC05g25094' => 'bca', 'BcaC05g25096' => 'bca', 'BcaC05g25138' => 'bca', 'BcaC05g30416' => 'bca', 'BcaC05g30455' => 'bca', 'BcaC06g30979' => 'bca', 'BcaC06g33805' => 'bca', 'BcaC08g46021' => 'bca', 'BcaNung03154' => 'bca', 'BolC2t06623H' => 'bol', 'BolC2t06632H' => 'bol', 'BolC2t06635H' => 'bol', 'BolC2t06638H' => 'bol', 'BolC3t13266H' => 'bol', 'BolC5t29776H' => 'bol', 'BolC6t38912H' => 'bol', 'BolC7t44183H' => 'bol', 'BolC9t54123H' => 'bol', 'BolC9t59107H' => 'bol', 'BraA02t05221Z' => 'bra', 'BraA03t09996Z' => 'bra', 'BraA05t23210Z' => 'bra', 'BraA06t24068Z' => 'bra', 'BraA06t27032Z' => 'bra', 'BraA08t35176Z' => 'bra', 'BraA09t36680Z' => 'bra', 'BraA10t44471Z' => 'bra', 'C02p06760' => 'bna', 'C02p06890' => 'bna', 'C02p07010' => 'bna', 'C03p07660' => 'bna', 'C05p10300' => 'bna', 'C06p38150' => 'bna', 'C07p36650' => 'bna', 'C08p15770' => 'bna', 'C09p12300' => 'bna', 'C09p62700' => 'bna', 'C09p75040' => 'bna', 'CAN.G13.1' => 'can', 'CAN.G138.4' => 'can', 'CAN.G44.6' => 'can', 'CAN.G473.19' => 'can', 'CANSAT01G0835' => 'cansat', 'CANSAT11G0246' => 'cansat', 'CANSAT11G1766' => 'cansat', 'CANSAT64G1954' => 'cansat', 'CARHR013330' => 'chi', 'CARHR060530' => 'chi', 'CARHR075300' => 'chi', 'CARHR105120' => 'chi', 'CARHR148910' => 'chi', 'CARHR198830' => 'chi', 'Carub.0001s1275' => 'cru', 'Carub.0002s1437' => 'cru', 'Carub.0003s0044' => 'cru', 'Carub.0003s2787' => 'cru', 'Carub.0005s0597' => 'cru', 'Carub.0006s1266' => 'cru', 'Ca_06935_v3' => 'car', 'Ca_13559_v3' => 'car', 'Ca_16941_v3' => 'car', 'Ca_16960_v3' => 'car', 'Ca_17775_v3' => 'car', 'Ca_30464_v3' => 'car', 'Cc06_g08160' => 'ccan', 'Cc07_g01520' => 'ccan', 'Cc11_g15810' => 'ccan', 'CDE02G2840' => 'cde', 'CDE03G0093' => 'cde', 'CDE04G2127' => 'cde', 'CDE07G1857' => 'cde', 'CDE09G1246' => 'cde', 'Cfa003412' => 'cfa', 'Cfa007341' => 'cfa', 'Cfa009220' => 'cfa', 'Ciclev10008737m.g' => 'ccl', 'Ciclev10015565m.g' => 'ccl', 'Ciclev10031761m.g' => 'ccl', 'CiPaw.03G045300' => 'cil', 'CiPaw.03G247200' => 'cil', 'CiPaw.04G029500' => 'cil', 'CiPaw.04G174000' => 'cil', 'CiPaw.05G181200' => 'cil', 'CiPaw.06G067100' => 'cil', 'ClCG05G025800' => 'cla', 'ClCG06G011400' => 'cla', 'ClCG09G019360' => 'cla', 'COL.COLO4_04827' => 'col', 'COL.COLO4_29170' => 'col', 'COL.COLO4_35131' => 'col', 'COL.COLO4_35132' => 'col', 'Cpa.g.sc33.32' => 'cpa', 'Cpa.g.sc46.29' => 'cpa', 'Cpa.g.sc796.1' => 'cpa', 'CsaV3_1G030420' => 'csa', 'CsaV3_5G027050' => 'csa', 'CsaV3_5G031040' => 'csa', 'CsaV3_UNG023130' => 'csa', 'CSS0007726' => 'camsi', 'CSS0016433' => 'camsi', 'CSS0017656' => 'camsi', 'CSS0025364' => 'camsi', 'CSS0027582' => 'camsi', 'CSS0047288' => 'camsi', 'CSS0049950' => 'camsi', 'DCAR_003843' => 'dca', 'DCAR_007052' => 'dca', 'DCAR_020884' => 'dca', 'DCAR_021730' => 'dca', 'DCAR_024423' => 'dca', 'DCAR_026509' => 'dca', 'DCAR_031158' => 'dca', 'Dinv14728' => 'din', 'Dinv15219' => 'din', 'Dinv25728' => 'din', 'Dinv33428' => 'din', 'Dinv36489' => 'din', 'Dinv41486' => 'din', 'Duzib147G0469' => 'dzi', 'Duzib168G0060' => 'dzi', 'Duzib187G1215' => 'dzi', 'Duzib248G0692' => 'dzi', 'Duzib251G0767' => 'dzi', 'Duzib264G0446' => 'dzi', 'Duzib268G0691' => 'dzi', 'ECA232G4767' => 'eca', 'ECA233G2838' => 'eca', 'ECA234G0391' => 'eca', 'ECA234G0857' => 'eca', 'ECA236G1593' => 'eca', 'ECA238G0565' => 'eca', 'ECA246G1027' => 'eca', 'ECA246G3223' => 'eca', 'ECA246G3470' => 'eca', 'EL10Ac6g13829' => 'bvu', 'EL10Ac6g14093' => 'bvu', 'EL10Ac8g18707' => 'bvu', 'Eucgr.C01369' => 'egr', 'Eucgr.H02492' => 'egr', 'Eucgr.I01733' => 'egr', 'Eucgr.J02255' => 'egr', 'Eucgr.J02257' => 'egr', 'Eucgr.J02258' => 'egr', 'FAN02G1601' => 'fan', 'FAN03G1586' => 'fan', 'FAN03G2986' => 'fan', 'FAN05G4837' => 'fan', 'FAN06G0146' => 'fan', 'FAN07G0858' => 'fan', 'FAN09G3179' => 'fan', 'FAN10G0669' => 'fan', 'FAN12G2358' => 'fan', 'FAN14G4198' => 'fan', 'FAN14G5112' => 'fan', 'FAN17G0342' => 'fan', 'FAN19G0342' => 'fan', 'FAN19G0962' => 'fan', 'FAN19G1101' => 'fan', 'FAN19G1872' => 'fan', 'FAN22G0356' => 'fan', 'FAN23G0744' => 'fan', 'FAN23G1914' => 'fan', 'FAN26G0032' => 'fan', 'FAN28G0625' => 'fan', 'FvH4_1g02710' => 'fve', 'FvH4_1g02720' => 'fve', 'FvH4_4g25670' => 'fve', 'FvH4_6g51700' => 'fve', 'FvH4_7g20170' => 'fve', 'Glyma.05G175000' => 'gma', 'Glyma.08G132300' => 'gma', 'Glyma.11G243000' => 'gma', 'Glyma.13G158900' => 'gma', 'Glyma.17G112400' => 'gma', 'Glyma.18G014100' => 'gma', 'Glyma.19G003100' => 'gma', 'Glyma.19G056500' => 'gma', 'Gohir.A01G158900' => 'ghi', 'Gohir.A05G312600' => 'ghi', 'Gohir.A05G354900' => 'ghi', 'Gohir.A07G037200' => 'ghi', 'Gohir.A09G030000' => 'ghi', 'Gohir.A12G145200' => 'ghi', 'Gohir.D01G151500' => 'ghi', 'Gohir.D04G058300' => 'ghi', 'Gohir.D05G314100' => 'ghi', 'Gohir.D07G041400' => 'ghi', 'Gohir.D09G029700' => 'ghi', 'Gohir.D12G149700' => 'ghi', 'Gorai.001G043800' => 'gra', 'Gorai.002G187800' => 'gra', 'Gorai.006G034700' => 'gra', 'Gorai.008G161200' => 'gra', 'Gorai.009G335700' => 'gra', 'Gorai.012G065000' => 'gra', 'GSVIVG01000535001' => 'vvi', 'GSVIVG01015572001' => 'vvi', 'GSVIVG01032386001' => 'vvi', 'HanXRQChr05g0138531' => 'han', 'HanXRQChr06g0174391' => 'han', 'HanXRQChr07g0199021' => 'han', 'HanXRQChr08g0208211' => 'han', 'HanXRQChr09g0255471' => 'han', 'HanXRQChr10g0315791' => 'han', 'HanXRQChr12g0371991' => 'han', 'HanXRQChr15g0475251' => 'han', 'HanXRQChr17g0540001' => 'han', 'HanXRQChr17g0548631' => 'han', 'HanXRQChr17g0569561' => 'han', 'Haze_12256' => 'cav', 'Haze_14756' => 'cav', 'Haze_25528' => 'cav', 'Hma1.2p1_0079F.1_g041020' => 'hma', 'Hma1.2p1_0818F.1_g223260' => 'hma', 'Hma1.2p1_1747F.1_g300530' => 'hma', 'HPP92_004607' => 'vpl', 'HPP92_004608' => 'vpl', 'HPP92_006181' => 'vpl', 'HPP92_012192' => 'vpl', 'HPP92_015680' => 'vpl', 'HPP92_020249' => 'vpl', 'HPP92_021376' => 'vpl', 'HPP92_024275' => 'vpl', 'Hund06031' => 'sun', 'Hund25391' => 'sun', 'Lalb_Chr07g0185371' => 'lal', 'Lalb_Chr07g0185381' => 'lal', 'Lalb_Chr12g0204011' => 'lal', 'Lalb_Chr13g0301671' => 'lal', 'Lalb_Chr14g0362851' => 'lal', 'Lalb_Chr24g0403581' => 'lal', 'Lj1g0000233' => 'lja', 'Lj2g0018120' => 'lja', 'Lj3C621T0' => 'lonja', 'Lj3P1059T14' => 'lonja', 'Lj3P611T9' => 'lonja', 'Lj3P614T13' => 'lonja', 'Lj3P615T5' => 'lonja', 'Lj4g0012315' => 'lja', 'Lj4g0026182' => 'lja', 'Lj6P813T16' => 'lonja', 'Lj7C427T7' => 'lonja', 'Lj7C427T8' => 'lonja', 'Lj7P600T41' => 'lonja', 'Lju41C42G17' => 'lonja', 'Lsat_1_v5_gn_0_47300' => 'lsa', 'Lsat_1_v5_gn_2_91280' => 'lsa', 'Lsat_1_v5_gn_3_30561' => 'lsa', 'Lsat_1_v5_gn_4_184321' => 'lsa', 'Lsat_1_v5_gn_4_4041' => 'lsa', 'Lsat_1_v5_gn_5_92000' => 'lsa', 'Lsat_1_v5_gn_8_152940' => 'lsa', 'Lsat_1_v5_gn_8_62401' => 'lsa', 'Manes.06G055900' => 'mes', 'Manes.12G022200' => 'mes', 'Manes.13G023300' => 'mes', 'Manes.14G115000' => 'mes', 'Manes.15G151700' => 'mes', 'Manes.17G111300' => 'mes', 'Mapoly0226s0009' => 'mpo', 'MBI02_g25363_MAGBIO' => 'mbi', 'MBI06_g00027_MAGBIO' => 'mbi', 'MBI10_g13034_MAGBIO' => 'mbi', 'MD09G1023400' => 'mdo', 'MD13G1100100' => 'mdo', 'MD15G1169200' => 'mdo', 'MD16G1101100' => 'mdo', 'MD17G1022900' => 'mdo', 'Medtr3g096150' => 'mtr', 'Medtr4g115070' => 'mtr', 'Medtr7g033325' => 'mtr', 'Medtr8g089840' => 'mtr', 'MELO3C010319.2' => 'cme', 'MELO3C011944.2' => 'cme', 'MELO3C021589.2' => 'cme', 'Migut.E00207' => 'egut', 'Migut.H00067' => 'egut', 'Migut.K00433' => 'egut', 'Migut.K00606' => 'egut', 'Migut.K01410' => 'egut', 'MSTRG.13347' => 'ama', 'MSTRG.24045' => 'ama', 'MSTRG.2428' => 'ama', 'MSTRG.26410' => 'ama', 'MSTRG.3139' => 'ama', 'MSTRG.3286' => 'ama', 'MSTRG.563' => 'ama', 'MSTRG.7941' => 'ama', 'Nitab4.5_0000028g0060' => 'nta', 'Nitab4.5_0000065g0260' => 'nta', 'Nitab4.5_0000112g0060' => 'nta', 'Nitab4.5_0000489g0120' => 'nta', 'Nitab4.5_0001776g0050' => 'nta', 'Nitab4.5_0001854g0010' => 'nta', 'Nitab4.5_0001860g0020' => 'nta', 'Nitab4.5_0004352g0010' => 'nta', 'Nitab4.5_0008716g0020' => 'nta', 'Nitab4.5_0008922g0010' => 'nta', 'Nn3g16693' => 'nnu', 'Nn4g22596' => 'nnu', 'Nn7g37639' => 'nnu', 'Oeu001701.1' => 'oeu', 'Oeu018149.1' => 'oeu', 'Oeu026220.1' => 'oeu', 'Oeu038635.1' => 'oeu', 'Oeu049176.1' => 'oeu', 'Oeu056706.1' => 'oeu', 'Oeu056937.1' => 'oeu', 'Oeu057540.1' => 'oeu', 'Os02g0594900' => 'osa', 'Os02g0595100' => 'osa', 'Os04g0477500' => 'osa', 'Os12g0611900' => 'osa', 'Peaxi162Scf00076g00020' => 'pax', 'Peaxi162Scf00128g00217' => 'pax', 'Peaxi162Scf00129g01640' => 'pax', 'Peaxi162Scf00669g00007' => 'pax', 'Peaxi162Scf00700g00421' => 'pax', 'Peaxi162Scf00801g00038' => 'pax', 'Peaxi162Scf00891g00025' => 'pax', 'PGR083G0909' => 'pgr', 'PGR119G1005' => 'pgr', 'PGR142G2236' => 'pgr', 'PGR142G3388' => 'pgr', 'PGSC0003DMG400004514' => 'stu', 'PGSC0003DMG400012635' => 'stu', 'PGSC0003DMG400015730' => 'stu', 'PGSC0003DMG400018611' => 'stu', 'PGSC0003DMG400030897' => 'stu', 'Phvul.001G254800' => 'pvu', 'Phvul.002G260100' => 'pvu', 'Phvul.003G167600' => 'pvu', 'Phvul.004G005100' => 'pvu', 'Potri.001G343600' => 'ptr', 'Potri.006G066700' => 'ptr', 'Potri.008G186000' => 'ptr', 'Potri.010G046900' => 'ptr', 'Potri.018G127900' => 'ptr', 'Pp3c20_17750' => 'ppa', 'Pp3c24_4380' => 'ppa', 'Prupe.1G245800' => 'ppe', 'Prupe.3G293400' => 'ppe', 'Prupe.7G247400' => 'ppe', 'Psat0s145g0120' => 'psa', 'Psat0s595g0040' => 'psa', 'Psat0s595g0120' => 'psa', 'Psat3g175040' => 'psa', 'Psat7g058120' => 'psa', 'PSO017G0428' => 'pso', 'PSO063G7510' => 'pso', 'PSO067G0046' => 'pso', 'PSO478G1073' => 'pso', 'PSO675G3677' => 'pso', 'PSO675G6558' => 'pso', 'PSO675G7520' => 'pso', 'PSO675G8959' => 'pso', 'QL02p074089' => 'qlo', 'QL02p089614' => 'qlo', 'QL03p057736' => 'qlo', 'RcHm_v2.0_Chr1g0364131' => 'rch', 'RcHm_v2.0_Chr2g0087801' => 'rch', 'RcHm_v2.0_Chr2g0087821' => 'rch', 'RcHm_v2.0_Chr2g0173231' => 'rch', 'RcHm_v2.0_Chr4g0433111' => 'rch', 'Rhsim03G0250300' => 'rsi', 'Rhsim08G0048400' => 'rsi', 'Rhsim10G0014800' => 'rsi', 'Rhsim12G0040100' => 'rsi', 'Rhsim12G0109700' => 'rsi', 'Sabra06G0049600' => 'sbr', 'Sabra08G0141000' => 'sbr', 'Sabra10G0021400' => 'sbr', 'Sabra16G0222900' => 'sbr', 'Sabra18G0108600' => 'sbr', 'SalBow1G0433' => 'sbo', 'SalBow1G2038' => 'sbo', 'SalBow1G5003' => 'sbo', 'SalBow7G1197' => 'sbo', 'SalBow8G3506' => 'sbo', 'Sc03g0007300' => 'sci', 'Sc11g0000950' => 'sci', 'Sc14g0008750' => 'sci', 'Sc18g0000420' => 'sci', 'Sed0006754' => 'sed', 'Sed0008741' => 'sed', 'Sed0017172' => 'sed', 'Sed0018925' => 'sed', 'Sed0023326' => 'sed', 'Sed0025909' => 'sed', 'SEGI_05333' => 'sgi', 'SEGI_10362' => 'sgi', 'SEGI_13380' => 'sgi', 'SEGI_24306' => 'sgi', 'SEGI_29077' => 'sgi', 'SEGI_29095' => 'sgi', 'SEGI_36534' => 'sgi', 'SEGI_37506' => 'sgi', 'SEGI_38321' => 'sgi', 'SGA_v2.0_scaffold307G48031' => 'sas', 'SGA_v2.0_scaffold47G17507' => 'sas', 'SGA_v2.0_scaffold63G21736' => 'sas', 'SGA_v2.0_scaffold87G27070' => 'sas', 'SHI17794' => 'shi', 'SHI28851' => 'shi', 'SMO165G0155' => 'smo', 'SMO340G0217' => 'smo', 'SMO367G1210' => 'smo', 'Solyc02g093430.3' => 'sly', 'Solyc05g013580.4' => 'sly', 'Solyc07g008030.3' => 'sly', 'Solyc12g035470.2' => 'sly', 'Sopen02g038020' => 'spe', 'Sopen05g008490' => 'spe', 'Sopen07g003910' => 'spe', 'Sopen12g015240' => 'spe', 'Sp1g11550' => 'spa', 'Sp2g16710' => 'spa', 'Sp3g00430' => 'spa', 'Sp3g26780' => 'spa', 'Sp5g22900' => 'spa', 'Sp6g29530' => 'spa', 'TAR371G0794' => 'tar', 'TAR374G0164' => 'tar', 'TAR622G0165' => 'tar', 'TAR626G0929' => 'tar', 'TAR629G2155' => 'tar', 'THA.LOC104805282' => 'tha', 'THA.LOC104805363' => 'tha', 'THA.LOC104808968' => 'tha', 'THA.LOC104821093' => 'tha', 'THA.LOC104823953' => 'tha', 'THA.LOC104825562' => 'tha', 'THA.LOC104825665' => 'tha', 'Thecc.02G261400' => 'tca', 'Thecc.04G019200' => 'tca', 'Thecc.09G130400' => 'tca', 'Thhalv10004374m.g' => 'esa', 'Thhalv10007850m.g' => 'esa', 'Thhalv10013782m.g' => 'esa', 'Thhalv10018686m.g' => 'esa', 'Thhalv10020899m.g' => 'esa', 'Thhalv10022755m.g' => 'esa', 'TPR.G23851' => 'tpr', 'TPR.G26500' => 'tpr', 'TPR.G27267' => 'tpr', 'TPR.G32001' => 'tpr', 'TPR.G6251' => 'tpr', 'TPR.G8167' => 'tpr', 'TWI12G1330' => 'twi', 'TWI18G1239' => 'twi', 'TWI34G0979' => 'twi', 'TWI36G0670' => 'twi', 'TWI36G0707' => 'twi', 'TWI56G0233' => 'twi', 'TWI75G1809' => 'twi', 'unitig_21.g20874' => 'ugi', 'unitig_26.g10343' => 'ugi', 'unitig_46.g18392' => 'ugi', 'unitig_52.g17178' => 'ugi', 'unitig_8.g2934' => 'ugi', 'vmacro01122' => 'vma', 'vmacro05875' => 'vma', 'vmacro06147' => 'vma', 'vmacro16191' => 'vma', 'vmacro18293' => 'vma', 'VMungo0251G3707' => 'vmu', 'VMungo0464G1521' => 'vmu', 'VMungo1215G0205' => 'vmu', 'VMungo1383G2484' => 'vmu', 'Zm00001eb079610' => 'zma', 'Zm00001eb135990' => 'zma', 'Zm00001eb183710' => 'zma', 'Zm00001eb246020' => 'zma' ) $gf_id = 'HOM05D001124' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001124' ) $data_identifier = 'HOM05D001124' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 6, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 7, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 21, 'bol' => (int) 10, 'bra' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 6, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 9, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 21, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 8, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 10, 'lsa' => (int) 8, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 8, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 9, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb246020' $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' => 'HOM05D001124', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '548', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02520' => 'bna', 'A03p06630' => 'bna', 'A05p44460' => 'bna', 'A06p08710' => 'bna', 'A06p41090' => 'bna', 'A07p32320' => 'bna', 'A08p32520' => 'bna', 'A09p10360' => 'bna', 'A10p24080' => 'bna', 'Aa31LG11G15250' => 'aar', 'Aa31LG1G1800' => 'aar', 'Aa31LG2G5120' => 'aar', 'Aa31LG2G6070' => 'aar', 'Aa31LG5G10770' => 'aar', 'Aa31sc61G90' => 'aar', 'Actinidia01352' => 'ach', 'Actinidia05983' => 'ach', 'Actinidia08133' => 'ach', 'Actinidia15101' => 'ach', 'Actinidia26379' => 'ach', 'Actinidia35778' => 'ach', 'Actinidia36123' => 'ach', 'Actinidia37436' => 'ach', 'Actinidia38730' => 'ach', 'Ah.02g128210' => 'amhyb', 'Ah.03g132990' => 'amhyb', 'Ah.14g079410' => 'amhyb', 'AL1G24640' => 'aly', 'AL2G26680' => 'aly', 'AL3G10530' => 'aly', 'AL3G45230' => 'aly', 'AL5G15230' => 'aly', 'AL5G16960' => 'aly', 'AL6G25210' => 'aly', 'Aqoxy2G00441' => 'aox', 'Aqoxy3G01236' => 'aox', 'Aqoxy5G03746' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3RQ047' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C7GMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9C8JER' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MBL6KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YXCZ83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZANX40' => 'arhy', 'AT1G12990' => 'ath', 'AT1G67880' => 'ath', 'AT2G13290' => 'ath', 'AT3G01620' => 'ath', 'AT3G26445' => 'ath', 'AT3G27540' => 'ath', 'AT5G14480' => 'ath', 'ATR0824G026' => 'atr', 'ATR1098G019' => 'atr', 'Atru.chr11.2145' => 'acertr', 'Atru.chr2.3636' => 'acertr', 'Atru.chr2.3644' => 'acertr', 'Atru.chr6.2422' => 'acertr', 'Atru.chr7.1112' => 'acertr', 'AUR62005469' => 'cqu', 'AUR62011166' => 'cqu', 'AUR62013319' => 'cqu', 'AUR62024273' => 'cqu', 'AUR62028420' => 'cqu', 'AUR62041942' => 'cqu', 'BcaB01g04969' => 'bca', 'BcaB01g06371' => 'bca', 'BcaB02g11494' => 'bca', 'BcaB03g15382' => 'bca', 'BcaB08g36994' => 'bca', 'BcaC03g13477' => 'bca', 'BcaC03g13478' => 'bca', 'BcaC03g13480' => 'bca', 'BcaC03g13481' => 'bca', 'BcaC03g13486' => 'bca', 'BcaC04g19031' => 'bca', 'BcaC04g23085' => 'bca', 'BcaC05g25094' => 'bca', 'BcaC05g25096' => 'bca', 'BcaC05g25138' => 'bca', 'BcaC05g30416' => 'bca', 'BcaC05g30455' => 'bca', 'BcaC06g30979' => 'bca', 'BcaC06g33805' => 'bca', 'BcaC08g46021' => 'bca', 'BcaNung03154' => 'bca', 'BolC2t06623H' => 'bol', 'BolC2t06632H' => 'bol', 'BolC2t06635H' => 'bol', 'BolC2t06638H' => 'bol', 'BolC3t13266H' => 'bol', 'BolC5t29776H' => 'bol', 'BolC6t38912H' => 'bol', 'BolC7t44183H' => 'bol', 'BolC9t54123H' => 'bol', 'BolC9t59107H' => 'bol', 'BraA02t05221Z' => 'bra', 'BraA03t09996Z' => 'bra', 'BraA05t23210Z' => 'bra', 'BraA06t24068Z' => 'bra', 'BraA06t27032Z' => 'bra', 'BraA08t35176Z' => 'bra', 'BraA09t36680Z' => 'bra', 'BraA10t44471Z' => 'bra', 'C02p06760' => 'bna', 'C02p06890' => 'bna', 'C02p07010' => 'bna', 'C03p07660' => 'bna', 'C05p10300' => 'bna', 'C06p38150' => 'bna', 'C07p36650' => 'bna', 'C08p15770' => 'bna', 'C09p12300' => 'bna', 'C09p62700' => 'bna', 'C09p75040' => 'bna', 'CAN.G13.1' => 'can', 'CAN.G138.4' => 'can', 'CAN.G44.6' => 'can', 'CAN.G473.19' => 'can', 'CANSAT01G0835' => 'cansat', 'CANSAT11G0246' => 'cansat', 'CANSAT11G1766' => 'cansat', 'CANSAT64G1954' => 'cansat', 'CARHR013330' => 'chi', 'CARHR060530' => 'chi', 'CARHR075300' => 'chi', 'CARHR105120' => 'chi', 'CARHR148910' => 'chi', 'CARHR198830' => 'chi', 'Carub.0001s1275' => 'cru', 'Carub.0002s1437' => 'cru', 'Carub.0003s0044' => 'cru', 'Carub.0003s2787' => 'cru', 'Carub.0005s0597' => 'cru', 'Carub.0006s1266' => 'cru', 'Ca_06935_v3' => 'car', 'Ca_13559_v3' => 'car', 'Ca_16941_v3' => 'car', 'Ca_16960_v3' => 'car', 'Ca_17775_v3' => 'car', 'Ca_30464_v3' => 'car', 'Cc06_g08160' => 'ccan', 'Cc07_g01520' => 'ccan', 'Cc11_g15810' => 'ccan', 'CDE02G2840' => 'cde', 'CDE03G0093' => 'cde', 'CDE04G2127' => 'cde', 'CDE07G1857' => 'cde', 'CDE09G1246' => 'cde', 'Cfa003412' => 'cfa', 'Cfa007341' => 'cfa', 'Cfa009220' => 'cfa', 'Ciclev10008737m.g' => 'ccl', 'Ciclev10015565m.g' => 'ccl', 'Ciclev10031761m.g' => 'ccl', 'CiPaw.03G045300' => 'cil', 'CiPaw.03G247200' => 'cil', 'CiPaw.04G029500' => 'cil', 'CiPaw.04G174000' => 'cil', 'CiPaw.05G181200' => 'cil', 'CiPaw.06G067100' => 'cil', 'ClCG05G025800' => 'cla', 'ClCG06G011400' => 'cla', 'ClCG09G019360' => 'cla', 'COL.COLO4_04827' => 'col', 'COL.COLO4_29170' => 'col', 'COL.COLO4_35131' => 'col', 'COL.COLO4_35132' => 'col', 'Cpa.g.sc33.32' => 'cpa', 'Cpa.g.sc46.29' => 'cpa', 'Cpa.g.sc796.1' => 'cpa', 'CsaV3_1G030420' => 'csa', 'CsaV3_5G027050' => 'csa', 'CsaV3_5G031040' => 'csa', 'CsaV3_UNG023130' => 'csa', 'CSS0007726' => 'camsi', 'CSS0016433' => 'camsi', 'CSS0017656' => 'camsi', 'CSS0025364' => 'camsi', 'CSS0027582' => 'camsi', 'CSS0047288' => 'camsi', 'CSS0049950' => 'camsi', 'DCAR_003843' => 'dca', 'DCAR_007052' => 'dca', 'DCAR_020884' => 'dca', 'DCAR_021730' => 'dca', 'DCAR_024423' => 'dca', 'DCAR_026509' => 'dca', 'DCAR_031158' => 'dca', 'Dinv14728' => 'din', 'Dinv15219' => 'din', 'Dinv25728' => 'din', 'Dinv33428' => 'din', 'Dinv36489' => 'din', 'Dinv41486' => 'din', 'Duzib147G0469' => 'dzi', 'Duzib168G0060' => 'dzi', 'Duzib187G1215' => 'dzi', 'Duzib248G0692' => 'dzi', 'Duzib251G0767' => 'dzi', 'Duzib264G0446' => 'dzi', 'Duzib268G0691' => 'dzi', 'ECA232G4767' => 'eca', 'ECA233G2838' => 'eca', 'ECA234G0391' => 'eca', 'ECA234G0857' => 'eca', 'ECA236G1593' => 'eca', 'ECA238G0565' => 'eca', 'ECA246G1027' => 'eca', 'ECA246G3223' => 'eca', 'ECA246G3470' => 'eca', 'EL10Ac6g13829' => 'bvu', 'EL10Ac6g14093' => 'bvu', 'EL10Ac8g18707' => 'bvu', 'Eucgr.C01369' => 'egr', 'Eucgr.H02492' => 'egr', 'Eucgr.I01733' => 'egr', 'Eucgr.J02255' => 'egr', 'Eucgr.J02257' => 'egr', 'Eucgr.J02258' => 'egr', 'FAN02G1601' => 'fan', 'FAN03G1586' => 'fan', 'FAN03G2986' => 'fan', 'FAN05G4837' => 'fan', 'FAN06G0146' => 'fan', 'FAN07G0858' => 'fan', 'FAN09G3179' => 'fan', 'FAN10G0669' => 'fan', 'FAN12G2358' => 'fan', 'FAN14G4198' => 'fan', 'FAN14G5112' => 'fan', 'FAN17G0342' => 'fan', 'FAN19G0342' => 'fan', 'FAN19G0962' => 'fan', 'FAN19G1101' => 'fan', 'FAN19G1872' => 'fan', 'FAN22G0356' => 'fan', 'FAN23G0744' => 'fan', 'FAN23G1914' => 'fan', 'FAN26G0032' => 'fan', 'FAN28G0625' => 'fan', 'FvH4_1g02710' => 'fve', 'FvH4_1g02720' => 'fve', 'FvH4_4g25670' => 'fve', 'FvH4_6g51700' => 'fve', 'FvH4_7g20170' => 'fve', 'Glyma.05G175000' => 'gma', 'Glyma.08G132300' => 'gma', 'Glyma.11G243000' => 'gma', 'Glyma.13G158900' => 'gma', 'Glyma.17G112400' => 'gma', 'Glyma.18G014100' => 'gma', 'Glyma.19G003100' => 'gma', 'Glyma.19G056500' => 'gma', 'Gohir.A01G158900' => 'ghi', 'Gohir.A05G312600' => 'ghi', 'Gohir.A05G354900' => 'ghi', 'Gohir.A07G037200' => 'ghi', 'Gohir.A09G030000' => 'ghi', 'Gohir.A12G145200' => 'ghi', 'Gohir.D01G151500' => 'ghi', 'Gohir.D04G058300' => 'ghi', 'Gohir.D05G314100' => 'ghi', 'Gohir.D07G041400' => 'ghi', 'Gohir.D09G029700' => 'ghi', 'Gohir.D12G149700' => 'ghi', 'Gorai.001G043800' => 'gra', 'Gorai.002G187800' => 'gra', 'Gorai.006G034700' => 'gra', 'Gorai.008G161200' => 'gra', 'Gorai.009G335700' => 'gra', 'Gorai.012G065000' => 'gra', 'GSVIVG01000535001' => 'vvi', 'GSVIVG01015572001' => 'vvi', 'GSVIVG01032386001' => 'vvi', 'HanXRQChr05g0138531' => 'han', 'HanXRQChr06g0174391' => 'han', 'HanXRQChr07g0199021' => 'han', 'HanXRQChr08g0208211' => 'han', 'HanXRQChr09g0255471' => 'han', 'HanXRQChr10g0315791' => 'han', 'HanXRQChr12g0371991' => 'han', 'HanXRQChr15g0475251' => 'han', 'HanXRQChr17g0540001' => 'han', 'HanXRQChr17g0548631' => 'han', 'HanXRQChr17g0569561' => 'han', 'Haze_12256' => 'cav', 'Haze_14756' => 'cav', 'Haze_25528' => 'cav', 'Hma1.2p1_0079F.1_g041020' => 'hma', 'Hma1.2p1_0818F.1_g223260' => 'hma', 'Hma1.2p1_1747F.1_g300530' => 'hma', 'HPP92_004607' => 'vpl', 'HPP92_004608' => 'vpl', 'HPP92_006181' => 'vpl', 'HPP92_012192' => 'vpl', 'HPP92_015680' => 'vpl', 'HPP92_020249' => 'vpl', 'HPP92_021376' => 'vpl', 'HPP92_024275' => 'vpl', 'Hund06031' => 'sun', 'Hund25391' => 'sun', 'Lalb_Chr07g0185371' => 'lal', 'Lalb_Chr07g0185381' => 'lal', 'Lalb_Chr12g0204011' => 'lal', 'Lalb_Chr13g0301671' => 'lal', 'Lalb_Chr14g0362851' => 'lal', 'Lalb_Chr24g0403581' => 'lal', 'Lj1g0000233' => 'lja', 'Lj2g0018120' => 'lja', 'Lj3C621T0' => 'lonja', 'Lj3P1059T14' => 'lonja', 'Lj3P611T9' => 'lonja', 'Lj3P614T13' => 'lonja', 'Lj3P615T5' => 'lonja', 'Lj4g0012315' => 'lja', 'Lj4g0026182' => 'lja', 'Lj6P813T16' => 'lonja', 'Lj7C427T7' => 'lonja', 'Lj7C427T8' => 'lonja', 'Lj7P600T41' => 'lonja', 'Lju41C42G17' => 'lonja', 'Lsat_1_v5_gn_0_47300' => 'lsa', 'Lsat_1_v5_gn_2_91280' => 'lsa', 'Lsat_1_v5_gn_3_30561' => 'lsa', 'Lsat_1_v5_gn_4_184321' => 'lsa', 'Lsat_1_v5_gn_4_4041' => 'lsa', 'Lsat_1_v5_gn_5_92000' => 'lsa', 'Lsat_1_v5_gn_8_152940' => 'lsa', 'Lsat_1_v5_gn_8_62401' => 'lsa', 'Manes.06G055900' => 'mes', 'Manes.12G022200' => 'mes', 'Manes.13G023300' => 'mes', 'Manes.14G115000' => 'mes', 'Manes.15G151700' => 'mes', 'Manes.17G111300' => 'mes', 'Mapoly0226s0009' => 'mpo', 'MBI02_g25363_MAGBIO' => 'mbi', 'MBI06_g00027_MAGBIO' => 'mbi', 'MBI10_g13034_MAGBIO' => 'mbi', 'MD09G1023400' => 'mdo', 'MD13G1100100' => 'mdo', 'MD15G1169200' => 'mdo', 'MD16G1101100' => 'mdo', 'MD17G1022900' => 'mdo', 'Medtr3g096150' => 'mtr', 'Medtr4g115070' => 'mtr', 'Medtr7g033325' => 'mtr', 'Medtr8g089840' => 'mtr', 'MELO3C010319.2' => 'cme', 'MELO3C011944.2' => 'cme', 'MELO3C021589.2' => 'cme', 'Migut.E00207' => 'egut', 'Migut.H00067' => 'egut', 'Migut.K00433' => 'egut', 'Migut.K00606' => 'egut', 'Migut.K01410' => 'egut', 'MSTRG.13347' => 'ama', 'MSTRG.24045' => 'ama', 'MSTRG.2428' => 'ama', 'MSTRG.26410' => 'ama', 'MSTRG.3139' => 'ama', 'MSTRG.3286' => 'ama', 'MSTRG.563' => 'ama', 'MSTRG.7941' => 'ama', 'Nitab4.5_0000028g0060' => 'nta', 'Nitab4.5_0000065g0260' => 'nta', 'Nitab4.5_0000112g0060' => 'nta', 'Nitab4.5_0000489g0120' => 'nta', 'Nitab4.5_0001776g0050' => 'nta', 'Nitab4.5_0001854g0010' => 'nta', 'Nitab4.5_0001860g0020' => 'nta', 'Nitab4.5_0004352g0010' => 'nta', 'Nitab4.5_0008716g0020' => 'nta', 'Nitab4.5_0008922g0010' => 'nta', 'Nn3g16693' => 'nnu', 'Nn4g22596' => 'nnu', 'Nn7g37639' => 'nnu', 'Oeu001701.1' => 'oeu', 'Oeu018149.1' => 'oeu', 'Oeu026220.1' => 'oeu', 'Oeu038635.1' => 'oeu', 'Oeu049176.1' => 'oeu', 'Oeu056706.1' => 'oeu', 'Oeu056937.1' => 'oeu', 'Oeu057540.1' => 'oeu', 'Os02g0594900' => 'osa', 'Os02g0595100' => 'osa', 'Os04g0477500' => 'osa', 'Os12g0611900' => 'osa', 'Peaxi162Scf00076g00020' => 'pax', 'Peaxi162Scf00128g00217' => 'pax', 'Peaxi162Scf00129g01640' => 'pax', 'Peaxi162Scf00669g00007' => 'pax', 'Peaxi162Scf00700g00421' => 'pax', 'Peaxi162Scf00801g00038' => 'pax', 'Peaxi162Scf00891g00025' => 'pax', 'PGR083G0909' => 'pgr', 'PGR119G1005' => 'pgr', 'PGR142G2236' => 'pgr', 'PGR142G3388' => 'pgr', 'PGSC0003DMG400004514' => 'stu', 'PGSC0003DMG400012635' => 'stu', 'PGSC0003DMG400015730' => 'stu', 'PGSC0003DMG400018611' => 'stu', 'PGSC0003DMG400030897' => 'stu', 'Phvul.001G254800' => 'pvu', 'Phvul.002G260100' => 'pvu', 'Phvul.003G167600' => 'pvu', 'Phvul.004G005100' => 'pvu', 'Potri.001G343600' => 'ptr', 'Potri.006G066700' => 'ptr', 'Potri.008G186000' => 'ptr', 'Potri.010G046900' => 'ptr', 'Potri.018G127900' => 'ptr', 'Pp3c20_17750' => 'ppa', 'Pp3c24_4380' => 'ppa', 'Prupe.1G245800' => 'ppe', 'Prupe.3G293400' => 'ppe', 'Prupe.7G247400' => 'ppe', 'Psat0s145g0120' => 'psa', 'Psat0s595g0040' => 'psa', 'Psat0s595g0120' => 'psa', 'Psat3g175040' => 'psa', 'Psat7g058120' => 'psa', 'PSO017G0428' => 'pso', 'PSO063G7510' => 'pso', 'PSO067G0046' => 'pso', 'PSO478G1073' => 'pso', 'PSO675G3677' => 'pso', 'PSO675G6558' => 'pso', 'PSO675G7520' => 'pso', 'PSO675G8959' => 'pso', 'QL02p074089' => 'qlo', 'QL02p089614' => 'qlo', 'QL03p057736' => 'qlo', 'RcHm_v2.0_Chr1g0364131' => 'rch', 'RcHm_v2.0_Chr2g0087801' => 'rch', 'RcHm_v2.0_Chr2g0087821' => 'rch', 'RcHm_v2.0_Chr2g0173231' => 'rch', 'RcHm_v2.0_Chr4g0433111' => 'rch', 'Rhsim03G0250300' => 'rsi', 'Rhsim08G0048400' => 'rsi', 'Rhsim10G0014800' => 'rsi', 'Rhsim12G0040100' => 'rsi', 'Rhsim12G0109700' => 'rsi', 'Sabra06G0049600' => 'sbr', 'Sabra08G0141000' => 'sbr', 'Sabra10G0021400' => 'sbr', 'Sabra16G0222900' => 'sbr', 'Sabra18G0108600' => 'sbr', 'SalBow1G0433' => 'sbo', 'SalBow1G2038' => 'sbo', 'SalBow1G5003' => 'sbo', 'SalBow7G1197' => 'sbo', 'SalBow8G3506' => 'sbo', 'Sc03g0007300' => 'sci', 'Sc11g0000950' => 'sci', 'Sc14g0008750' => 'sci', 'Sc18g0000420' => 'sci', 'Sed0006754' => 'sed', 'Sed0008741' => 'sed', 'Sed0017172' => 'sed', 'Sed0018925' => 'sed', 'Sed0023326' => 'sed', 'Sed0025909' => 'sed', 'SEGI_05333' => 'sgi', 'SEGI_10362' => 'sgi', 'SEGI_13380' => 'sgi', 'SEGI_24306' => 'sgi', 'SEGI_29077' => 'sgi', 'SEGI_29095' => 'sgi', 'SEGI_36534' => 'sgi', 'SEGI_37506' => 'sgi', 'SEGI_38321' => 'sgi', 'SGA_v2.0_scaffold307G48031' => 'sas', 'SGA_v2.0_scaffold47G17507' => 'sas', 'SGA_v2.0_scaffold63G21736' => 'sas', 'SGA_v2.0_scaffold87G27070' => 'sas', 'SHI17794' => 'shi', 'SHI28851' => 'shi', 'SMO165G0155' => 'smo', 'SMO340G0217' => 'smo', 'SMO367G1210' => 'smo', 'Solyc02g093430.3' => 'sly', 'Solyc05g013580.4' => 'sly', 'Solyc07g008030.3' => 'sly', 'Solyc12g035470.2' => 'sly', 'Sopen02g038020' => 'spe', 'Sopen05g008490' => 'spe', 'Sopen07g003910' => 'spe', 'Sopen12g015240' => 'spe', 'Sp1g11550' => 'spa', 'Sp2g16710' => 'spa', 'Sp3g00430' => 'spa', 'Sp3g26780' => 'spa', 'Sp5g22900' => 'spa', 'Sp6g29530' => 'spa', 'TAR371G0794' => 'tar', 'TAR374G0164' => 'tar', 'TAR622G0165' => 'tar', 'TAR626G0929' => 'tar', 'TAR629G2155' => 'tar', 'THA.LOC104805282' => 'tha', 'THA.LOC104805363' => 'tha', 'THA.LOC104808968' => 'tha', 'THA.LOC104821093' => 'tha', 'THA.LOC104823953' => 'tha', 'THA.LOC104825562' => 'tha', 'THA.LOC104825665' => 'tha', 'Thecc.02G261400' => 'tca', 'Thecc.04G019200' => 'tca', 'Thecc.09G130400' => 'tca', 'Thhalv10004374m.g' => 'esa', 'Thhalv10007850m.g' => 'esa', 'Thhalv10013782m.g' => 'esa', 'Thhalv10018686m.g' => 'esa', 'Thhalv10020899m.g' => 'esa', 'Thhalv10022755m.g' => 'esa', 'TPR.G23851' => 'tpr', 'TPR.G26500' => 'tpr', 'TPR.G27267' => 'tpr', 'TPR.G32001' => 'tpr', 'TPR.G6251' => 'tpr', 'TPR.G8167' => 'tpr', 'TWI12G1330' => 'twi', 'TWI18G1239' => 'twi', 'TWI34G0979' => 'twi', 'TWI36G0670' => 'twi', 'TWI36G0707' => 'twi', 'TWI56G0233' => 'twi', 'TWI75G1809' => 'twi', 'unitig_21.g20874' => 'ugi', 'unitig_26.g10343' => 'ugi', 'unitig_46.g18392' => 'ugi', 'unitig_52.g17178' => 'ugi', 'unitig_8.g2934' => 'ugi', 'vmacro01122' => 'vma', 'vmacro05875' => 'vma', 'vmacro06147' => 'vma', 'vmacro16191' => 'vma', 'vmacro18293' => 'vma', 'VMungo0251G3707' => 'vmu', 'VMungo0464G1521' => 'vmu', 'VMungo1215G0205' => 'vmu', 'VMungo1383G2484' => 'vmu', 'Zm00001eb079610' => 'zma', 'Zm00001eb135990' => 'zma', 'Zm00001eb183710' => 'zma', 'Zm00001eb246020' => 'zma' ), 'gf_id' => 'HOM05D001124', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001124' ), 'data_identifier' => 'HOM05D001124', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001124', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '548', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02520' => 'bna', 'A03p06630' => 'bna', 'A05p44460' => 'bna', 'A06p08710' => 'bna', 'A06p41090' => 'bna', 'A07p32320' => 'bna', 'A08p32520' => 'bna', 'A09p10360' => 'bna', 'A10p24080' => 'bna', 'Aa31LG11G15250' => 'aar', 'Aa31LG1G1800' => 'aar', 'Aa31LG2G5120' => 'aar', 'Aa31LG2G6070' => 'aar', 'Aa31LG5G10770' => 'aar', 'Aa31sc61G90' => 'aar', 'Actinidia01352' => 'ach', 'Actinidia05983' => 'ach', 'Actinidia08133' => 'ach', 'Actinidia15101' => 'ach', 'Actinidia26379' => 'ach', 'Actinidia35778' => 'ach', 'Actinidia36123' => 'ach', 'Actinidia37436' => 'ach', 'Actinidia38730' => 'ach', 'Ah.02g128210' => 'amhyb', 'Ah.03g132990' => 'amhyb', 'Ah.14g079410' => 'amhyb', 'AL1G24640' => 'aly', 'AL2G26680' => 'aly', 'AL3G10530' => 'aly', 'AL3G45230' => 'aly', 'AL5G15230' => 'aly', 'AL5G16960' => 'aly', 'AL6G25210' => 'aly', 'Aqoxy2G00441' => 'aox', 'Aqoxy3G01236' => 'aox', 'Aqoxy5G03746' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3RQ047' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C7GMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9C8JER' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MBL6KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YXCZ83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZANX40' => 'arhy', 'AT1G12990' => 'ath', 'AT1G67880' => 'ath', 'AT2G13290' => 'ath', 'AT3G01620' => 'ath', 'AT3G26445' => 'ath', 'AT3G27540' => 'ath', 'AT5G14480' => 'ath', 'ATR0824G026' => 'atr', 'ATR1098G019' => 'atr', 'Atru.chr11.2145' => 'acertr', 'Atru.chr2.3636' => 'acertr', 'Atru.chr2.3644' => 'acertr', 'Atru.chr6.2422' => 'acertr', 'Atru.chr7.1112' => 'acertr', 'AUR62005469' => 'cqu', 'AUR62011166' => 'cqu', 'AUR62013319' => 'cqu', 'AUR62024273' => 'cqu', 'AUR62028420' => 'cqu', 'AUR62041942' => 'cqu', 'BcaB01g04969' => 'bca', 'BcaB01g06371' => 'bca', 'BcaB02g11494' => 'bca', 'BcaB03g15382' => 'bca', 'BcaB08g36994' => 'bca', 'BcaC03g13477' => 'bca', 'BcaC03g13478' => 'bca', 'BcaC03g13480' => 'bca', 'BcaC03g13481' => 'bca', 'BcaC03g13486' => 'bca', 'BcaC04g19031' => 'bca', 'BcaC04g23085' => 'bca', 'BcaC05g25094' => 'bca', 'BcaC05g25096' => 'bca', 'BcaC05g25138' => 'bca', 'BcaC05g30416' => 'bca', 'BcaC05g30455' => 'bca', 'BcaC06g30979' => 'bca', 'BcaC06g33805' => 'bca', 'BcaC08g46021' => 'bca', 'BcaNung03154' => 'bca', 'BolC2t06623H' => 'bol', 'BolC2t06632H' => 'bol', 'BolC2t06635H' => 'bol', 'BolC2t06638H' => 'bol', 'BolC3t13266H' => 'bol', 'BolC5t29776H' => 'bol', 'BolC6t38912H' => 'bol', 'BolC7t44183H' => 'bol', 'BolC9t54123H' => 'bol', 'BolC9t59107H' => 'bol', 'BraA02t05221Z' => 'bra', 'BraA03t09996Z' => 'bra', 'BraA05t23210Z' => 'bra', 'BraA06t24068Z' => 'bra', 'BraA06t27032Z' => 'bra', 'BraA08t35176Z' => 'bra', 'BraA09t36680Z' => 'bra', 'BraA10t44471Z' => 'bra', 'C02p06760' => 'bna', 'C02p06890' => 'bna', 'C02p07010' => 'bna', 'C03p07660' => 'bna', 'C05p10300' => 'bna', 'C06p38150' => 'bna', 'C07p36650' => 'bna', 'C08p15770' => 'bna', 'C09p12300' => 'bna', 'C09p62700' => 'bna', 'C09p75040' => 'bna', 'CAN.G13.1' => 'can', 'CAN.G138.4' => 'can', 'CAN.G44.6' => 'can', 'CAN.G473.19' => 'can', 'CANSAT01G0835' => 'cansat', 'CANSAT11G0246' => 'cansat', 'CANSAT11G1766' => 'cansat', 'CANSAT64G1954' => 'cansat', 'CARHR013330' => 'chi', 'CARHR060530' => 'chi', 'CARHR075300' => 'chi', 'CARHR105120' => 'chi', 'CARHR148910' => 'chi', 'CARHR198830' => 'chi', 'Carub.0001s1275' => 'cru', 'Carub.0002s1437' => 'cru', 'Carub.0003s0044' => 'cru', 'Carub.0003s2787' => 'cru', 'Carub.0005s0597' => 'cru', 'Carub.0006s1266' => 'cru', 'Ca_06935_v3' => 'car', 'Ca_13559_v3' => 'car', 'Ca_16941_v3' => 'car', 'Ca_16960_v3' => 'car', 'Ca_17775_v3' => 'car', 'Ca_30464_v3' => 'car', 'Cc06_g08160' => 'ccan', 'Cc07_g01520' => 'ccan', 'Cc11_g15810' => 'ccan', 'CDE02G2840' => 'cde', 'CDE03G0093' => 'cde', 'CDE04G2127' => 'cde', 'CDE07G1857' => 'cde', 'CDE09G1246' => 'cde', 'Cfa003412' => 'cfa', 'Cfa007341' => 'cfa', 'Cfa009220' => 'cfa', 'Ciclev10008737m.g' => 'ccl', 'Ciclev10015565m.g' => 'ccl', 'Ciclev10031761m.g' => 'ccl', 'CiPaw.03G045300' => 'cil', 'CiPaw.03G247200' => 'cil', 'CiPaw.04G029500' => 'cil', 'CiPaw.04G174000' => 'cil', 'CiPaw.05G181200' => 'cil', 'CiPaw.06G067100' => 'cil', 'ClCG05G025800' => 'cla', 'ClCG06G011400' => 'cla', 'ClCG09G019360' => 'cla', 'COL.COLO4_04827' => 'col', 'COL.COLO4_29170' => 'col', 'COL.COLO4_35131' => 'col', 'COL.COLO4_35132' => 'col', 'Cpa.g.sc33.32' => 'cpa', 'Cpa.g.sc46.29' => 'cpa', 'Cpa.g.sc796.1' => 'cpa', 'CsaV3_1G030420' => 'csa', 'CsaV3_5G027050' => 'csa', 'CsaV3_5G031040' => 'csa', 'CsaV3_UNG023130' => 'csa', 'CSS0007726' => 'camsi', 'CSS0016433' => 'camsi', 'CSS0017656' => 'camsi', 'CSS0025364' => 'camsi', 'CSS0027582' => 'camsi', 'CSS0047288' => 'camsi', 'CSS0049950' => 'camsi', 'DCAR_003843' => 'dca', 'DCAR_007052' => 'dca', 'DCAR_020884' => 'dca', 'DCAR_021730' => 'dca', 'DCAR_024423' => 'dca', 'DCAR_026509' => 'dca', 'DCAR_031158' => 'dca', 'Dinv14728' => 'din', 'Dinv15219' => 'din', 'Dinv25728' => 'din', 'Dinv33428' => 'din', 'Dinv36489' => 'din', 'Dinv41486' => 'din', 'Duzib147G0469' => 'dzi', 'Duzib168G0060' => 'dzi', 'Duzib187G1215' => 'dzi', 'Duzib248G0692' => 'dzi', 'Duzib251G0767' => 'dzi', 'Duzib264G0446' => 'dzi', 'Duzib268G0691' => 'dzi', 'ECA232G4767' => 'eca', 'ECA233G2838' => 'eca', 'ECA234G0391' => 'eca', 'ECA234G0857' => 'eca', 'ECA236G1593' => 'eca', 'ECA238G0565' => 'eca', 'ECA246G1027' => 'eca', 'ECA246G3223' => 'eca', 'ECA246G3470' => 'eca', 'EL10Ac6g13829' => 'bvu', 'EL10Ac6g14093' => 'bvu', 'EL10Ac8g18707' => 'bvu', 'Eucgr.C01369' => 'egr', 'Eucgr.H02492' => 'egr', 'Eucgr.I01733' => 'egr', 'Eucgr.J02255' => 'egr', 'Eucgr.J02257' => 'egr', 'Eucgr.J02258' => 'egr', 'FAN02G1601' => 'fan', 'FAN03G1586' => 'fan', 'FAN03G2986' => 'fan', 'FAN05G4837' => 'fan', 'FAN06G0146' => 'fan', 'FAN07G0858' => 'fan', 'FAN09G3179' => 'fan', 'FAN10G0669' => 'fan', 'FAN12G2358' => 'fan', 'FAN14G4198' => 'fan', 'FAN14G5112' => 'fan', 'FAN17G0342' => 'fan', 'FAN19G0342' => 'fan', 'FAN19G0962' => 'fan', 'FAN19G1101' => 'fan', 'FAN19G1872' => 'fan', 'FAN22G0356' => 'fan', 'FAN23G0744' => 'fan', 'FAN23G1914' => 'fan', 'FAN26G0032' => 'fan', 'FAN28G0625' => 'fan', 'FvH4_1g02710' => 'fve', 'FvH4_1g02720' => 'fve', 'FvH4_4g25670' => 'fve', 'FvH4_6g51700' => 'fve', 'FvH4_7g20170' => 'fve', 'Glyma.05G175000' => 'gma', 'Glyma.08G132300' => 'gma', 'Glyma.11G243000' => 'gma', 'Glyma.13G158900' => 'gma', 'Glyma.17G112400' => 'gma', 'Glyma.18G014100' => 'gma', 'Glyma.19G003100' => 'gma', 'Glyma.19G056500' => 'gma', 'Gohir.A01G158900' => 'ghi', 'Gohir.A05G312600' => 'ghi', 'Gohir.A05G354900' => 'ghi', 'Gohir.A07G037200' => 'ghi', 'Gohir.A09G030000' => 'ghi', 'Gohir.A12G145200' => 'ghi', 'Gohir.D01G151500' => 'ghi', 'Gohir.D04G058300' => 'ghi', 'Gohir.D05G314100' => 'ghi', 'Gohir.D07G041400' => 'ghi', 'Gohir.D09G029700' => 'ghi', 'Gohir.D12G149700' => 'ghi', 'Gorai.001G043800' => 'gra', 'Gorai.002G187800' => 'gra', 'Gorai.006G034700' => 'gra', 'Gorai.008G161200' => 'gra', 'Gorai.009G335700' => 'gra', 'Gorai.012G065000' => 'gra', 'GSVIVG01000535001' => 'vvi', 'GSVIVG01015572001' => 'vvi', 'GSVIVG01032386001' => 'vvi', 'HanXRQChr05g0138531' => 'han', 'HanXRQChr06g0174391' => 'han', 'HanXRQChr07g0199021' => 'han', 'HanXRQChr08g0208211' => 'han', 'HanXRQChr09g0255471' => 'han', 'HanXRQChr10g0315791' => 'han', 'HanXRQChr12g0371991' => 'han', 'HanXRQChr15g0475251' => 'han', 'HanXRQChr17g0540001' => 'han', 'HanXRQChr17g0548631' => 'han', 'HanXRQChr17g0569561' => 'han', 'Haze_12256' => 'cav', 'Haze_14756' => 'cav', 'Haze_25528' => 'cav', 'Hma1.2p1_0079F.1_g041020' => 'hma', 'Hma1.2p1_0818F.1_g223260' => 'hma', 'Hma1.2p1_1747F.1_g300530' => 'hma', 'HPP92_004607' => 'vpl', 'HPP92_004608' => 'vpl', 'HPP92_006181' => 'vpl', 'HPP92_012192' => 'vpl', 'HPP92_015680' => 'vpl', 'HPP92_020249' => 'vpl', 'HPP92_021376' => 'vpl', 'HPP92_024275' => 'vpl', 'Hund06031' => 'sun', 'Hund25391' => 'sun', 'Lalb_Chr07g0185371' => 'lal', 'Lalb_Chr07g0185381' => 'lal', 'Lalb_Chr12g0204011' => 'lal', 'Lalb_Chr13g0301671' => 'lal', 'Lalb_Chr14g0362851' => 'lal', 'Lalb_Chr24g0403581' => 'lal', 'Lj1g0000233' => 'lja', 'Lj2g0018120' => 'lja', 'Lj3C621T0' => 'lonja', 'Lj3P1059T14' => 'lonja', 'Lj3P611T9' => 'lonja', 'Lj3P614T13' => 'lonja', 'Lj3P615T5' => 'lonja', 'Lj4g0012315' => 'lja', 'Lj4g0026182' => 'lja', 'Lj6P813T16' => 'lonja', 'Lj7C427T7' => 'lonja', 'Lj7C427T8' => 'lonja', 'Lj7P600T41' => 'lonja', 'Lju41C42G17' => 'lonja', 'Lsat_1_v5_gn_0_47300' => 'lsa', 'Lsat_1_v5_gn_2_91280' => 'lsa', 'Lsat_1_v5_gn_3_30561' => 'lsa', 'Lsat_1_v5_gn_4_184321' => 'lsa', 'Lsat_1_v5_gn_4_4041' => 'lsa', 'Lsat_1_v5_gn_5_92000' => 'lsa', 'Lsat_1_v5_gn_8_152940' => 'lsa', 'Lsat_1_v5_gn_8_62401' => 'lsa', 'Manes.06G055900' => 'mes', 'Manes.12G022200' => 'mes', 'Manes.13G023300' => 'mes', 'Manes.14G115000' => 'mes', 'Manes.15G151700' => 'mes', 'Manes.17G111300' => 'mes', 'Mapoly0226s0009' => 'mpo', 'MBI02_g25363_MAGBIO' => 'mbi', 'MBI06_g00027_MAGBIO' => 'mbi', 'MBI10_g13034_MAGBIO' => 'mbi', 'MD09G1023400' => 'mdo', 'MD13G1100100' => 'mdo', 'MD15G1169200' => 'mdo', 'MD16G1101100' => 'mdo', 'MD17G1022900' => 'mdo', 'Medtr3g096150' => 'mtr', 'Medtr4g115070' => 'mtr', 'Medtr7g033325' => 'mtr', 'Medtr8g089840' => 'mtr', 'MELO3C010319.2' => 'cme', 'MELO3C011944.2' => 'cme', 'MELO3C021589.2' => 'cme', 'Migut.E00207' => 'egut', 'Migut.H00067' => 'egut', 'Migut.K00433' => 'egut', 'Migut.K00606' => 'egut', 'Migut.K01410' => 'egut', 'MSTRG.13347' => 'ama', 'MSTRG.24045' => 'ama', 'MSTRG.2428' => 'ama', 'MSTRG.26410' => 'ama', 'MSTRG.3139' => 'ama', 'MSTRG.3286' => 'ama', 'MSTRG.563' => 'ama', 'MSTRG.7941' => 'ama', 'Nitab4.5_0000028g0060' => 'nta', 'Nitab4.5_0000065g0260' => 'nta', 'Nitab4.5_0000112g0060' => 'nta', 'Nitab4.5_0000489g0120' => 'nta', 'Nitab4.5_0001776g0050' => 'nta', 'Nitab4.5_0001854g0010' => 'nta', 'Nitab4.5_0001860g0020' => 'nta', 'Nitab4.5_0004352g0010' => 'nta', 'Nitab4.5_0008716g0020' => 'nta', 'Nitab4.5_0008922g0010' => 'nta', 'Nn3g16693' => 'nnu', 'Nn4g22596' => 'nnu', 'Nn7g37639' => 'nnu', 'Oeu001701.1' => 'oeu', 'Oeu018149.1' => 'oeu', 'Oeu026220.1' => 'oeu', 'Oeu038635.1' => 'oeu', 'Oeu049176.1' => 'oeu', 'Oeu056706.1' => 'oeu', 'Oeu056937.1' => 'oeu', 'Oeu057540.1' => 'oeu', 'Os02g0594900' => 'osa', 'Os02g0595100' => 'osa', 'Os04g0477500' => 'osa', 'Os12g0611900' => 'osa', 'Peaxi162Scf00076g00020' => 'pax', 'Peaxi162Scf00128g00217' => 'pax', 'Peaxi162Scf00129g01640' => 'pax', 'Peaxi162Scf00669g00007' => 'pax', 'Peaxi162Scf00700g00421' => 'pax', 'Peaxi162Scf00801g00038' => 'pax', 'Peaxi162Scf00891g00025' => 'pax', 'PGR083G0909' => 'pgr', 'PGR119G1005' => 'pgr', 'PGR142G2236' => 'pgr', 'PGR142G3388' => 'pgr', 'PGSC0003DMG400004514' => 'stu', 'PGSC0003DMG400012635' => 'stu', 'PGSC0003DMG400015730' => 'stu', 'PGSC0003DMG400018611' => 'stu', 'PGSC0003DMG400030897' => 'stu', 'Phvul.001G254800' => 'pvu', 'Phvul.002G260100' => 'pvu', 'Phvul.003G167600' => 'pvu', 'Phvul.004G005100' => 'pvu', 'Potri.001G343600' => 'ptr', 'Potri.006G066700' => 'ptr', 'Potri.008G186000' => 'ptr', 'Potri.010G046900' => 'ptr', 'Potri.018G127900' => 'ptr', 'Pp3c20_17750' => 'ppa', 'Pp3c24_4380' => 'ppa', 'Prupe.1G245800' => 'ppe', 'Prupe.3G293400' => 'ppe', 'Prupe.7G247400' => 'ppe', 'Psat0s145g0120' => 'psa', 'Psat0s595g0040' => 'psa', 'Psat0s595g0120' => 'psa', 'Psat3g175040' => 'psa', 'Psat7g058120' => 'psa', 'PSO017G0428' => 'pso', 'PSO063G7510' => 'pso', 'PSO067G0046' => 'pso', 'PSO478G1073' => 'pso', 'PSO675G3677' => 'pso', 'PSO675G6558' => 'pso', 'PSO675G7520' => 'pso', 'PSO675G8959' => 'pso', 'QL02p074089' => 'qlo', 'QL02p089614' => 'qlo', 'QL03p057736' => 'qlo', 'RcHm_v2.0_Chr1g0364131' => 'rch', 'RcHm_v2.0_Chr2g0087801' => 'rch', 'RcHm_v2.0_Chr2g0087821' => 'rch', 'RcHm_v2.0_Chr2g0173231' => 'rch', 'RcHm_v2.0_Chr4g0433111' => 'rch', 'Rhsim03G0250300' => 'rsi', 'Rhsim08G0048400' => 'rsi', 'Rhsim10G0014800' => 'rsi', 'Rhsim12G0040100' => 'rsi', 'Rhsim12G0109700' => 'rsi', 'Sabra06G0049600' => 'sbr', 'Sabra08G0141000' => 'sbr', 'Sabra10G0021400' => 'sbr', 'Sabra16G0222900' => 'sbr', 'Sabra18G0108600' => 'sbr', 'SalBow1G0433' => 'sbo', 'SalBow1G2038' => 'sbo', 'SalBow1G5003' => 'sbo', 'SalBow7G1197' => 'sbo', 'SalBow8G3506' => 'sbo', 'Sc03g0007300' => 'sci', 'Sc11g0000950' => 'sci', 'Sc14g0008750' => 'sci', 'Sc18g0000420' => 'sci', 'Sed0006754' => 'sed', 'Sed0008741' => 'sed', 'Sed0017172' => 'sed', 'Sed0018925' => 'sed', 'Sed0023326' => 'sed', 'Sed0025909' => 'sed', 'SEGI_05333' => 'sgi', 'SEGI_10362' => 'sgi', 'SEGI_13380' => 'sgi', 'SEGI_24306' => 'sgi', 'SEGI_29077' => 'sgi', 'SEGI_29095' => 'sgi', 'SEGI_36534' => 'sgi', 'SEGI_37506' => 'sgi', 'SEGI_38321' => 'sgi', 'SGA_v2.0_scaffold307G48031' => 'sas', 'SGA_v2.0_scaffold47G17507' => 'sas', 'SGA_v2.0_scaffold63G21736' => 'sas', 'SGA_v2.0_scaffold87G27070' => 'sas', 'SHI17794' => 'shi', 'SHI28851' => 'shi', 'SMO165G0155' => 'smo', 'SMO340G0217' => 'smo', 'SMO367G1210' => 'smo', 'Solyc02g093430.3' => 'sly', 'Solyc05g013580.4' => 'sly', 'Solyc07g008030.3' => 'sly', 'Solyc12g035470.2' => 'sly', 'Sopen02g038020' => 'spe', 'Sopen05g008490' => 'spe', 'Sopen07g003910' => 'spe', 'Sopen12g015240' => 'spe', 'Sp1g11550' => 'spa', 'Sp2g16710' => 'spa', 'Sp3g00430' => 'spa', 'Sp3g26780' => 'spa', 'Sp5g22900' => 'spa', 'Sp6g29530' => 'spa', 'TAR371G0794' => 'tar', 'TAR374G0164' => 'tar', 'TAR622G0165' => 'tar', 'TAR626G0929' => 'tar', 'TAR629G2155' => 'tar', 'THA.LOC104805282' => 'tha', 'THA.LOC104805363' => 'tha', 'THA.LOC104808968' => 'tha', 'THA.LOC104821093' => 'tha', 'THA.LOC104823953' => 'tha', 'THA.LOC104825562' => 'tha', 'THA.LOC104825665' => 'tha', 'Thecc.02G261400' => 'tca', 'Thecc.04G019200' => 'tca', 'Thecc.09G130400' => 'tca', 'Thhalv10004374m.g' => 'esa', 'Thhalv10007850m.g' => 'esa', 'Thhalv10013782m.g' => 'esa', 'Thhalv10018686m.g' => 'esa', 'Thhalv10020899m.g' => 'esa', 'Thhalv10022755m.g' => 'esa', 'TPR.G23851' => 'tpr', 'TPR.G26500' => 'tpr', 'TPR.G27267' => 'tpr', 'TPR.G32001' => 'tpr', 'TPR.G6251' => 'tpr', 'TPR.G8167' => 'tpr', 'TWI12G1330' => 'twi', 'TWI18G1239' => 'twi', 'TWI34G0979' => 'twi', 'TWI36G0670' => 'twi', 'TWI36G0707' => 'twi', 'TWI56G0233' => 'twi', 'TWI75G1809' => 'twi', 'unitig_21.g20874' => 'ugi', 'unitig_26.g10343' => 'ugi', 'unitig_46.g18392' => 'ugi', 'unitig_52.g17178' => 'ugi', 'unitig_8.g2934' => 'ugi', 'vmacro01122' => 'vma', 'vmacro05875' => 'vma', 'vmacro06147' => 'vma', 'vmacro16191' => 'vma', 'vmacro18293' => 'vma', 'VMungo0251G3707' => 'vmu', 'VMungo0464G1521' => 'vmu', 'VMungo1215G0205' => 'vmu', 'VMungo1383G2484' => 'vmu', 'Zm00001eb079610' => 'zma', 'Zm00001eb135990' => 'zma', 'Zm00001eb183710' => 'zma', 'Zm00001eb246020' => 'zma' ) $gf_id = 'HOM05D001124' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001124' ) $data_identifier = 'HOM05D001124' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 6, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 7, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 21, 'bol' => (int) 10, 'bra' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 6, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 9, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 21, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 8, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 10, 'lsa' => (int) 8, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 8, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 9, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb246020' $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' => 'HOM05D001124', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '548', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02520' => 'bna', 'A03p06630' => 'bna', 'A05p44460' => 'bna', 'A06p08710' => 'bna', 'A06p41090' => 'bna', 'A07p32320' => 'bna', 'A08p32520' => 'bna', 'A09p10360' => 'bna', 'A10p24080' => 'bna', 'Aa31LG11G15250' => 'aar', 'Aa31LG1G1800' => 'aar', 'Aa31LG2G5120' => 'aar', 'Aa31LG2G6070' => 'aar', 'Aa31LG5G10770' => 'aar', 'Aa31sc61G90' => 'aar', 'Actinidia01352' => 'ach', 'Actinidia05983' => 'ach', 'Actinidia08133' => 'ach', 'Actinidia15101' => 'ach', 'Actinidia26379' => 'ach', 'Actinidia35778' => 'ach', 'Actinidia36123' => 'ach', 'Actinidia37436' => 'ach', 'Actinidia38730' => 'ach', 'Ah.02g128210' => 'amhyb', 'Ah.03g132990' => 'amhyb', 'Ah.14g079410' => 'amhyb', 'AL1G24640' => 'aly', 'AL2G26680' => 'aly', 'AL3G10530' => 'aly', 'AL3G45230' => 'aly', 'AL5G15230' => 'aly', 'AL5G16960' => 'aly', 'AL6G25210' => 'aly', 'Aqoxy2G00441' => 'aox', 'Aqoxy3G01236' => 'aox', 'Aqoxy5G03746' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3RQ047' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C7GMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9C8JER' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MBL6KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YXCZ83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZANX40' => 'arhy', 'AT1G12990' => 'ath', 'AT1G67880' => 'ath', 'AT2G13290' => 'ath', 'AT3G01620' => 'ath', 'AT3G26445' => 'ath', 'AT3G27540' => 'ath', 'AT5G14480' => 'ath', 'ATR0824G026' => 'atr', 'ATR1098G019' => 'atr', 'Atru.chr11.2145' => 'acertr', 'Atru.chr2.3636' => 'acertr', 'Atru.chr2.3644' => 'acertr', 'Atru.chr6.2422' => 'acertr', 'Atru.chr7.1112' => 'acertr', 'AUR62005469' => 'cqu', 'AUR62011166' => 'cqu', 'AUR62013319' => 'cqu', 'AUR62024273' => 'cqu', 'AUR62028420' => 'cqu', 'AUR62041942' => 'cqu', 'BcaB01g04969' => 'bca', 'BcaB01g06371' => 'bca', 'BcaB02g11494' => 'bca', 'BcaB03g15382' => 'bca', 'BcaB08g36994' => 'bca', 'BcaC03g13477' => 'bca', 'BcaC03g13478' => 'bca', 'BcaC03g13480' => 'bca', 'BcaC03g13481' => 'bca', 'BcaC03g13486' => 'bca', 'BcaC04g19031' => 'bca', 'BcaC04g23085' => 'bca', 'BcaC05g25094' => 'bca', 'BcaC05g25096' => 'bca', 'BcaC05g25138' => 'bca', 'BcaC05g30416' => 'bca', 'BcaC05g30455' => 'bca', 'BcaC06g30979' => 'bca', 'BcaC06g33805' => 'bca', 'BcaC08g46021' => 'bca', 'BcaNung03154' => 'bca', 'BolC2t06623H' => 'bol', 'BolC2t06632H' => 'bol', 'BolC2t06635H' => 'bol', 'BolC2t06638H' => 'bol', 'BolC3t13266H' => 'bol', 'BolC5t29776H' => 'bol', 'BolC6t38912H' => 'bol', 'BolC7t44183H' => 'bol', 'BolC9t54123H' => 'bol', 'BolC9t59107H' => 'bol', 'BraA02t05221Z' => 'bra', 'BraA03t09996Z' => 'bra', 'BraA05t23210Z' => 'bra', 'BraA06t24068Z' => 'bra', 'BraA06t27032Z' => 'bra', 'BraA08t35176Z' => 'bra', 'BraA09t36680Z' => 'bra', 'BraA10t44471Z' => 'bra', 'C02p06760' => 'bna', 'C02p06890' => 'bna', 'C02p07010' => 'bna', 'C03p07660' => 'bna', 'C05p10300' => 'bna', 'C06p38150' => 'bna', 'C07p36650' => 'bna', 'C08p15770' => 'bna', 'C09p12300' => 'bna', 'C09p62700' => 'bna', 'C09p75040' => 'bna', 'CAN.G13.1' => 'can', 'CAN.G138.4' => 'can', 'CAN.G44.6' => 'can', 'CAN.G473.19' => 'can', 'CANSAT01G0835' => 'cansat', 'CANSAT11G0246' => 'cansat', 'CANSAT11G1766' => 'cansat', 'CANSAT64G1954' => 'cansat', 'CARHR013330' => 'chi', 'CARHR060530' => 'chi', 'CARHR075300' => 'chi', 'CARHR105120' => 'chi', 'CARHR148910' => 'chi', 'CARHR198830' => 'chi', 'Carub.0001s1275' => 'cru', 'Carub.0002s1437' => 'cru', 'Carub.0003s0044' => 'cru', 'Carub.0003s2787' => 'cru', 'Carub.0005s0597' => 'cru', 'Carub.0006s1266' => 'cru', 'Ca_06935_v3' => 'car', 'Ca_13559_v3' => 'car', 'Ca_16941_v3' => 'car', 'Ca_16960_v3' => 'car', 'Ca_17775_v3' => 'car', 'Ca_30464_v3' => 'car', 'Cc06_g08160' => 'ccan', 'Cc07_g01520' => 'ccan', 'Cc11_g15810' => 'ccan', 'CDE02G2840' => 'cde', 'CDE03G0093' => 'cde', 'CDE04G2127' => 'cde', 'CDE07G1857' => 'cde', 'CDE09G1246' => 'cde', 'Cfa003412' => 'cfa', 'Cfa007341' => 'cfa', 'Cfa009220' => 'cfa', 'Ciclev10008737m.g' => 'ccl', 'Ciclev10015565m.g' => 'ccl', 'Ciclev10031761m.g' => 'ccl', 'CiPaw.03G045300' => 'cil', 'CiPaw.03G247200' => 'cil', 'CiPaw.04G029500' => 'cil', 'CiPaw.04G174000' => 'cil', 'CiPaw.05G181200' => 'cil', 'CiPaw.06G067100' => 'cil', 'ClCG05G025800' => 'cla', 'ClCG06G011400' => 'cla', 'ClCG09G019360' => 'cla', 'COL.COLO4_04827' => 'col', 'COL.COLO4_29170' => 'col', 'COL.COLO4_35131' => 'col', 'COL.COLO4_35132' => 'col', 'Cpa.g.sc33.32' => 'cpa', 'Cpa.g.sc46.29' => 'cpa', 'Cpa.g.sc796.1' => 'cpa', 'CsaV3_1G030420' => 'csa', 'CsaV3_5G027050' => 'csa', 'CsaV3_5G031040' => 'csa', 'CsaV3_UNG023130' => 'csa', 'CSS0007726' => 'camsi', 'CSS0016433' => 'camsi', 'CSS0017656' => 'camsi', 'CSS0025364' => 'camsi', 'CSS0027582' => 'camsi', 'CSS0047288' => 'camsi', 'CSS0049950' => 'camsi', 'DCAR_003843' => 'dca', 'DCAR_007052' => 'dca', 'DCAR_020884' => 'dca', 'DCAR_021730' => 'dca', 'DCAR_024423' => 'dca', 'DCAR_026509' => 'dca', 'DCAR_031158' => 'dca', 'Dinv14728' => 'din', 'Dinv15219' => 'din', 'Dinv25728' => 'din', 'Dinv33428' => 'din', 'Dinv36489' => 'din', 'Dinv41486' => 'din', 'Duzib147G0469' => 'dzi', 'Duzib168G0060' => 'dzi', 'Duzib187G1215' => 'dzi', 'Duzib248G0692' => 'dzi', 'Duzib251G0767' => 'dzi', 'Duzib264G0446' => 'dzi', 'Duzib268G0691' => 'dzi', 'ECA232G4767' => 'eca', 'ECA233G2838' => 'eca', 'ECA234G0391' => 'eca', 'ECA234G0857' => 'eca', 'ECA236G1593' => 'eca', 'ECA238G0565' => 'eca', 'ECA246G1027' => 'eca', 'ECA246G3223' => 'eca', 'ECA246G3470' => 'eca', 'EL10Ac6g13829' => 'bvu', 'EL10Ac6g14093' => 'bvu', 'EL10Ac8g18707' => 'bvu', 'Eucgr.C01369' => 'egr', 'Eucgr.H02492' => 'egr', 'Eucgr.I01733' => 'egr', 'Eucgr.J02255' => 'egr', 'Eucgr.J02257' => 'egr', 'Eucgr.J02258' => 'egr', 'FAN02G1601' => 'fan', 'FAN03G1586' => 'fan', 'FAN03G2986' => 'fan', 'FAN05G4837' => 'fan', 'FAN06G0146' => 'fan', 'FAN07G0858' => 'fan', 'FAN09G3179' => 'fan', 'FAN10G0669' => 'fan', 'FAN12G2358' => 'fan', 'FAN14G4198' => 'fan', 'FAN14G5112' => 'fan', 'FAN17G0342' => 'fan', 'FAN19G0342' => 'fan', 'FAN19G0962' => 'fan', 'FAN19G1101' => 'fan', 'FAN19G1872' => 'fan', 'FAN22G0356' => 'fan', 'FAN23G0744' => 'fan', 'FAN23G1914' => 'fan', 'FAN26G0032' => 'fan', 'FAN28G0625' => 'fan', 'FvH4_1g02710' => 'fve', 'FvH4_1g02720' => 'fve', 'FvH4_4g25670' => 'fve', 'FvH4_6g51700' => 'fve', 'FvH4_7g20170' => 'fve', 'Glyma.05G175000' => 'gma', 'Glyma.08G132300' => 'gma', 'Glyma.11G243000' => 'gma', 'Glyma.13G158900' => 'gma', 'Glyma.17G112400' => 'gma', 'Glyma.18G014100' => 'gma', 'Glyma.19G003100' => 'gma', 'Glyma.19G056500' => 'gma', 'Gohir.A01G158900' => 'ghi', 'Gohir.A05G312600' => 'ghi', 'Gohir.A05G354900' => 'ghi', 'Gohir.A07G037200' => 'ghi', 'Gohir.A09G030000' => 'ghi', 'Gohir.A12G145200' => 'ghi', 'Gohir.D01G151500' => 'ghi', 'Gohir.D04G058300' => 'ghi', 'Gohir.D05G314100' => 'ghi', 'Gohir.D07G041400' => 'ghi', 'Gohir.D09G029700' => 'ghi', 'Gohir.D12G149700' => 'ghi', 'Gorai.001G043800' => 'gra', 'Gorai.002G187800' => 'gra', 'Gorai.006G034700' => 'gra', 'Gorai.008G161200' => 'gra', 'Gorai.009G335700' => 'gra', 'Gorai.012G065000' => 'gra', 'GSVIVG01000535001' => 'vvi', 'GSVIVG01015572001' => 'vvi', 'GSVIVG01032386001' => 'vvi', 'HanXRQChr05g0138531' => 'han', 'HanXRQChr06g0174391' => 'han', 'HanXRQChr07g0199021' => 'han', 'HanXRQChr08g0208211' => 'han', 'HanXRQChr09g0255471' => 'han', 'HanXRQChr10g0315791' => 'han', 'HanXRQChr12g0371991' => 'han', 'HanXRQChr15g0475251' => 'han', 'HanXRQChr17g0540001' => 'han', 'HanXRQChr17g0548631' => 'han', 'HanXRQChr17g0569561' => 'han', 'Haze_12256' => 'cav', 'Haze_14756' => 'cav', 'Haze_25528' => 'cav', 'Hma1.2p1_0079F.1_g041020' => 'hma', 'Hma1.2p1_0818F.1_g223260' => 'hma', 'Hma1.2p1_1747F.1_g300530' => 'hma', 'HPP92_004607' => 'vpl', 'HPP92_004608' => 'vpl', 'HPP92_006181' => 'vpl', 'HPP92_012192' => 'vpl', 'HPP92_015680' => 'vpl', 'HPP92_020249' => 'vpl', 'HPP92_021376' => 'vpl', 'HPP92_024275' => 'vpl', 'Hund06031' => 'sun', 'Hund25391' => 'sun', 'Lalb_Chr07g0185371' => 'lal', 'Lalb_Chr07g0185381' => 'lal', 'Lalb_Chr12g0204011' => 'lal', 'Lalb_Chr13g0301671' => 'lal', 'Lalb_Chr14g0362851' => 'lal', 'Lalb_Chr24g0403581' => 'lal', 'Lj1g0000233' => 'lja', 'Lj2g0018120' => 'lja', 'Lj3C621T0' => 'lonja', 'Lj3P1059T14' => 'lonja', 'Lj3P611T9' => 'lonja', 'Lj3P614T13' => 'lonja', 'Lj3P615T5' => 'lonja', 'Lj4g0012315' => 'lja', 'Lj4g0026182' => 'lja', 'Lj6P813T16' => 'lonja', 'Lj7C427T7' => 'lonja', 'Lj7C427T8' => 'lonja', 'Lj7P600T41' => 'lonja', 'Lju41C42G17' => 'lonja', 'Lsat_1_v5_gn_0_47300' => 'lsa', 'Lsat_1_v5_gn_2_91280' => 'lsa', 'Lsat_1_v5_gn_3_30561' => 'lsa', 'Lsat_1_v5_gn_4_184321' => 'lsa', 'Lsat_1_v5_gn_4_4041' => 'lsa', 'Lsat_1_v5_gn_5_92000' => 'lsa', 'Lsat_1_v5_gn_8_152940' => 'lsa', 'Lsat_1_v5_gn_8_62401' => 'lsa', 'Manes.06G055900' => 'mes', 'Manes.12G022200' => 'mes', 'Manes.13G023300' => 'mes', 'Manes.14G115000' => 'mes', 'Manes.15G151700' => 'mes', 'Manes.17G111300' => 'mes', 'Mapoly0226s0009' => 'mpo', 'MBI02_g25363_MAGBIO' => 'mbi', 'MBI06_g00027_MAGBIO' => 'mbi', 'MBI10_g13034_MAGBIO' => 'mbi', 'MD09G1023400' => 'mdo', 'MD13G1100100' => 'mdo', 'MD15G1169200' => 'mdo', 'MD16G1101100' => 'mdo', 'MD17G1022900' => 'mdo', 'Medtr3g096150' => 'mtr', 'Medtr4g115070' => 'mtr', 'Medtr7g033325' => 'mtr', 'Medtr8g089840' => 'mtr', 'MELO3C010319.2' => 'cme', 'MELO3C011944.2' => 'cme', 'MELO3C021589.2' => 'cme', 'Migut.E00207' => 'egut', 'Migut.H00067' => 'egut', 'Migut.K00433' => 'egut', 'Migut.K00606' => 'egut', 'Migut.K01410' => 'egut', 'MSTRG.13347' => 'ama', 'MSTRG.24045' => 'ama', 'MSTRG.2428' => 'ama', 'MSTRG.26410' => 'ama', 'MSTRG.3139' => 'ama', 'MSTRG.3286' => 'ama', 'MSTRG.563' => 'ama', 'MSTRG.7941' => 'ama', 'Nitab4.5_0000028g0060' => 'nta', 'Nitab4.5_0000065g0260' => 'nta', 'Nitab4.5_0000112g0060' => 'nta', 'Nitab4.5_0000489g0120' => 'nta', 'Nitab4.5_0001776g0050' => 'nta', 'Nitab4.5_0001854g0010' => 'nta', 'Nitab4.5_0001860g0020' => 'nta', 'Nitab4.5_0004352g0010' => 'nta', 'Nitab4.5_0008716g0020' => 'nta', 'Nitab4.5_0008922g0010' => 'nta', 'Nn3g16693' => 'nnu', 'Nn4g22596' => 'nnu', 'Nn7g37639' => 'nnu', 'Oeu001701.1' => 'oeu', 'Oeu018149.1' => 'oeu', 'Oeu026220.1' => 'oeu', 'Oeu038635.1' => 'oeu', 'Oeu049176.1' => 'oeu', 'Oeu056706.1' => 'oeu', 'Oeu056937.1' => 'oeu', 'Oeu057540.1' => 'oeu', 'Os02g0594900' => 'osa', 'Os02g0595100' => 'osa', 'Os04g0477500' => 'osa', 'Os12g0611900' => 'osa', 'Peaxi162Scf00076g00020' => 'pax', 'Peaxi162Scf00128g00217' => 'pax', 'Peaxi162Scf00129g01640' => 'pax', 'Peaxi162Scf00669g00007' => 'pax', 'Peaxi162Scf00700g00421' => 'pax', 'Peaxi162Scf00801g00038' => 'pax', 'Peaxi162Scf00891g00025' => 'pax', 'PGR083G0909' => 'pgr', 'PGR119G1005' => 'pgr', 'PGR142G2236' => 'pgr', 'PGR142G3388' => 'pgr', 'PGSC0003DMG400004514' => 'stu', 'PGSC0003DMG400012635' => 'stu', 'PGSC0003DMG400015730' => 'stu', 'PGSC0003DMG400018611' => 'stu', 'PGSC0003DMG400030897' => 'stu', 'Phvul.001G254800' => 'pvu', 'Phvul.002G260100' => 'pvu', 'Phvul.003G167600' => 'pvu', 'Phvul.004G005100' => 'pvu', 'Potri.001G343600' => 'ptr', 'Potri.006G066700' => 'ptr', 'Potri.008G186000' => 'ptr', 'Potri.010G046900' => 'ptr', 'Potri.018G127900' => 'ptr', 'Pp3c20_17750' => 'ppa', 'Pp3c24_4380' => 'ppa', 'Prupe.1G245800' => 'ppe', 'Prupe.3G293400' => 'ppe', 'Prupe.7G247400' => 'ppe', 'Psat0s145g0120' => 'psa', 'Psat0s595g0040' => 'psa', 'Psat0s595g0120' => 'psa', 'Psat3g175040' => 'psa', 'Psat7g058120' => 'psa', 'PSO017G0428' => 'pso', 'PSO063G7510' => 'pso', 'PSO067G0046' => 'pso', 'PSO478G1073' => 'pso', 'PSO675G3677' => 'pso', 'PSO675G6558' => 'pso', 'PSO675G7520' => 'pso', 'PSO675G8959' => 'pso', 'QL02p074089' => 'qlo', 'QL02p089614' => 'qlo', 'QL03p057736' => 'qlo', 'RcHm_v2.0_Chr1g0364131' => 'rch', 'RcHm_v2.0_Chr2g0087801' => 'rch', 'RcHm_v2.0_Chr2g0087821' => 'rch', 'RcHm_v2.0_Chr2g0173231' => 'rch', 'RcHm_v2.0_Chr4g0433111' => 'rch', 'Rhsim03G0250300' => 'rsi', 'Rhsim08G0048400' => 'rsi', 'Rhsim10G0014800' => 'rsi', 'Rhsim12G0040100' => 'rsi', 'Rhsim12G0109700' => 'rsi', 'Sabra06G0049600' => 'sbr', 'Sabra08G0141000' => 'sbr', 'Sabra10G0021400' => 'sbr', 'Sabra16G0222900' => 'sbr', 'Sabra18G0108600' => 'sbr', 'SalBow1G0433' => 'sbo', 'SalBow1G2038' => 'sbo', 'SalBow1G5003' => 'sbo', 'SalBow7G1197' => 'sbo', 'SalBow8G3506' => 'sbo', 'Sc03g0007300' => 'sci', 'Sc11g0000950' => 'sci', 'Sc14g0008750' => 'sci', 'Sc18g0000420' => 'sci', 'Sed0006754' => 'sed', 'Sed0008741' => 'sed', 'Sed0017172' => 'sed', 'Sed0018925' => 'sed', 'Sed0023326' => 'sed', 'Sed0025909' => 'sed', 'SEGI_05333' => 'sgi', 'SEGI_10362' => 'sgi', 'SEGI_13380' => 'sgi', 'SEGI_24306' => 'sgi', 'SEGI_29077' => 'sgi', 'SEGI_29095' => 'sgi', 'SEGI_36534' => 'sgi', 'SEGI_37506' => 'sgi', 'SEGI_38321' => 'sgi', 'SGA_v2.0_scaffold307G48031' => 'sas', 'SGA_v2.0_scaffold47G17507' => 'sas', 'SGA_v2.0_scaffold63G21736' => 'sas', 'SGA_v2.0_scaffold87G27070' => 'sas', 'SHI17794' => 'shi', 'SHI28851' => 'shi', 'SMO165G0155' => 'smo', 'SMO340G0217' => 'smo', 'SMO367G1210' => 'smo', 'Solyc02g093430.3' => 'sly', 'Solyc05g013580.4' => 'sly', 'Solyc07g008030.3' => 'sly', 'Solyc12g035470.2' => 'sly', 'Sopen02g038020' => 'spe', 'Sopen05g008490' => 'spe', 'Sopen07g003910' => 'spe', 'Sopen12g015240' => 'spe', 'Sp1g11550' => 'spa', 'Sp2g16710' => 'spa', 'Sp3g00430' => 'spa', 'Sp3g26780' => 'spa', 'Sp5g22900' => 'spa', 'Sp6g29530' => 'spa', 'TAR371G0794' => 'tar', 'TAR374G0164' => 'tar', 'TAR622G0165' => 'tar', 'TAR626G0929' => 'tar', 'TAR629G2155' => 'tar', 'THA.LOC104805282' => 'tha', 'THA.LOC104805363' => 'tha', 'THA.LOC104808968' => 'tha', 'THA.LOC104821093' => 'tha', 'THA.LOC104823953' => 'tha', 'THA.LOC104825562' => 'tha', 'THA.LOC104825665' => 'tha', 'Thecc.02G261400' => 'tca', 'Thecc.04G019200' => 'tca', 'Thecc.09G130400' => 'tca', 'Thhalv10004374m.g' => 'esa', 'Thhalv10007850m.g' => 'esa', 'Thhalv10013782m.g' => 'esa', 'Thhalv10018686m.g' => 'esa', 'Thhalv10020899m.g' => 'esa', 'Thhalv10022755m.g' => 'esa', 'TPR.G23851' => 'tpr', 'TPR.G26500' => 'tpr', 'TPR.G27267' => 'tpr', 'TPR.G32001' => 'tpr', 'TPR.G6251' => 'tpr', 'TPR.G8167' => 'tpr', 'TWI12G1330' => 'twi', 'TWI18G1239' => 'twi', 'TWI34G0979' => 'twi', 'TWI36G0670' => 'twi', 'TWI36G0707' => 'twi', 'TWI56G0233' => 'twi', 'TWI75G1809' => 'twi', 'unitig_21.g20874' => 'ugi', 'unitig_26.g10343' => 'ugi', 'unitig_46.g18392' => 'ugi', 'unitig_52.g17178' => 'ugi', 'unitig_8.g2934' => 'ugi', 'vmacro01122' => 'vma', 'vmacro05875' => 'vma', 'vmacro06147' => 'vma', 'vmacro16191' => 'vma', 'vmacro18293' => 'vma', 'VMungo0251G3707' => 'vmu', 'VMungo0464G1521' => 'vmu', 'VMungo1215G0205' => 'vmu', 'VMungo1383G2484' => 'vmu', 'Zm00001eb079610' => 'zma', 'Zm00001eb135990' => 'zma', 'Zm00001eb183710' => 'zma', 'Zm00001eb246020' => 'zma' ), 'gf_id' => 'HOM05D001124', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001124' ), 'data_identifier' => 'HOM05D001124', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001124', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '548', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02520' => 'bna', 'A03p06630' => 'bna', 'A05p44460' => 'bna', 'A06p08710' => 'bna', 'A06p41090' => 'bna', 'A07p32320' => 'bna', 'A08p32520' => 'bna', 'A09p10360' => 'bna', 'A10p24080' => 'bna', 'Aa31LG11G15250' => 'aar', 'Aa31LG1G1800' => 'aar', 'Aa31LG2G5120' => 'aar', 'Aa31LG2G6070' => 'aar', 'Aa31LG5G10770' => 'aar', 'Aa31sc61G90' => 'aar', 'Actinidia01352' => 'ach', 'Actinidia05983' => 'ach', 'Actinidia08133' => 'ach', 'Actinidia15101' => 'ach', 'Actinidia26379' => 'ach', 'Actinidia35778' => 'ach', 'Actinidia36123' => 'ach', 'Actinidia37436' => 'ach', 'Actinidia38730' => 'ach', 'Ah.02g128210' => 'amhyb', 'Ah.03g132990' => 'amhyb', 'Ah.14g079410' => 'amhyb', 'AL1G24640' => 'aly', 'AL2G26680' => 'aly', 'AL3G10530' => 'aly', 'AL3G45230' => 'aly', 'AL5G15230' => 'aly', 'AL5G16960' => 'aly', 'AL6G25210' => 'aly', 'Aqoxy2G00441' => 'aox', 'Aqoxy3G01236' => 'aox', 'Aqoxy5G03746' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3RQ047' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C7GMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9C8JER' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MBL6KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YXCZ83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZANX40' => 'arhy', 'AT1G12990' => 'ath', 'AT1G67880' => 'ath', 'AT2G13290' => 'ath', 'AT3G01620' => 'ath', 'AT3G26445' => 'ath', 'AT3G27540' => 'ath', 'AT5G14480' => 'ath', 'ATR0824G026' => 'atr', 'ATR1098G019' => 'atr', 'Atru.chr11.2145' => 'acertr', 'Atru.chr2.3636' => 'acertr', 'Atru.chr2.3644' => 'acertr', 'Atru.chr6.2422' => 'acertr', 'Atru.chr7.1112' => 'acertr', 'AUR62005469' => 'cqu', 'AUR62011166' => 'cqu', 'AUR62013319' => 'cqu', 'AUR62024273' => 'cqu', 'AUR62028420' => 'cqu', 'AUR62041942' => 'cqu', 'BcaB01g04969' => 'bca', 'BcaB01g06371' => 'bca', 'BcaB02g11494' => 'bca', 'BcaB03g15382' => 'bca', 'BcaB08g36994' => 'bca', 'BcaC03g13477' => 'bca', 'BcaC03g13478' => 'bca', 'BcaC03g13480' => 'bca', 'BcaC03g13481' => 'bca', 'BcaC03g13486' => 'bca', 'BcaC04g19031' => 'bca', 'BcaC04g23085' => 'bca', 'BcaC05g25094' => 'bca', 'BcaC05g25096' => 'bca', 'BcaC05g25138' => 'bca', 'BcaC05g30416' => 'bca', 'BcaC05g30455' => 'bca', 'BcaC06g30979' => 'bca', 'BcaC06g33805' => 'bca', 'BcaC08g46021' => 'bca', 'BcaNung03154' => 'bca', 'BolC2t06623H' => 'bol', 'BolC2t06632H' => 'bol', 'BolC2t06635H' => 'bol', 'BolC2t06638H' => 'bol', 'BolC3t13266H' => 'bol', 'BolC5t29776H' => 'bol', 'BolC6t38912H' => 'bol', 'BolC7t44183H' => 'bol', 'BolC9t54123H' => 'bol', 'BolC9t59107H' => 'bol', 'BraA02t05221Z' => 'bra', 'BraA03t09996Z' => 'bra', 'BraA05t23210Z' => 'bra', 'BraA06t24068Z' => 'bra', 'BraA06t27032Z' => 'bra', 'BraA08t35176Z' => 'bra', 'BraA09t36680Z' => 'bra', 'BraA10t44471Z' => 'bra', 'C02p06760' => 'bna', 'C02p06890' => 'bna', 'C02p07010' => 'bna', 'C03p07660' => 'bna', 'C05p10300' => 'bna', 'C06p38150' => 'bna', 'C07p36650' => 'bna', 'C08p15770' => 'bna', 'C09p12300' => 'bna', 'C09p62700' => 'bna', 'C09p75040' => 'bna', 'CAN.G13.1' => 'can', 'CAN.G138.4' => 'can', 'CAN.G44.6' => 'can', 'CAN.G473.19' => 'can', 'CANSAT01G0835' => 'cansat', 'CANSAT11G0246' => 'cansat', 'CANSAT11G1766' => 'cansat', 'CANSAT64G1954' => 'cansat', 'CARHR013330' => 'chi', 'CARHR060530' => 'chi', 'CARHR075300' => 'chi', 'CARHR105120' => 'chi', 'CARHR148910' => 'chi', 'CARHR198830' => 'chi', 'Carub.0001s1275' => 'cru', 'Carub.0002s1437' => 'cru', 'Carub.0003s0044' => 'cru', 'Carub.0003s2787' => 'cru', 'Carub.0005s0597' => 'cru', 'Carub.0006s1266' => 'cru', 'Ca_06935_v3' => 'car', 'Ca_13559_v3' => 'car', 'Ca_16941_v3' => 'car', 'Ca_16960_v3' => 'car', 'Ca_17775_v3' => 'car', 'Ca_30464_v3' => 'car', 'Cc06_g08160' => 'ccan', 'Cc07_g01520' => 'ccan', 'Cc11_g15810' => 'ccan', 'CDE02G2840' => 'cde', 'CDE03G0093' => 'cde', 'CDE04G2127' => 'cde', 'CDE07G1857' => 'cde', 'CDE09G1246' => 'cde', 'Cfa003412' => 'cfa', 'Cfa007341' => 'cfa', 'Cfa009220' => 'cfa', 'Ciclev10008737m.g' => 'ccl', 'Ciclev10015565m.g' => 'ccl', 'Ciclev10031761m.g' => 'ccl', 'CiPaw.03G045300' => 'cil', 'CiPaw.03G247200' => 'cil', 'CiPaw.04G029500' => 'cil', 'CiPaw.04G174000' => 'cil', 'CiPaw.05G181200' => 'cil', 'CiPaw.06G067100' => 'cil', 'ClCG05G025800' => 'cla', 'ClCG06G011400' => 'cla', 'ClCG09G019360' => 'cla', 'COL.COLO4_04827' => 'col', 'COL.COLO4_29170' => 'col', 'COL.COLO4_35131' => 'col', 'COL.COLO4_35132' => 'col', 'Cpa.g.sc33.32' => 'cpa', 'Cpa.g.sc46.29' => 'cpa', 'Cpa.g.sc796.1' => 'cpa', 'CsaV3_1G030420' => 'csa', 'CsaV3_5G027050' => 'csa', 'CsaV3_5G031040' => 'csa', 'CsaV3_UNG023130' => 'csa', 'CSS0007726' => 'camsi', 'CSS0016433' => 'camsi', 'CSS0017656' => 'camsi', 'CSS0025364' => 'camsi', 'CSS0027582' => 'camsi', 'CSS0047288' => 'camsi', 'CSS0049950' => 'camsi', 'DCAR_003843' => 'dca', 'DCAR_007052' => 'dca', 'DCAR_020884' => 'dca', 'DCAR_021730' => 'dca', 'DCAR_024423' => 'dca', 'DCAR_026509' => 'dca', 'DCAR_031158' => 'dca', 'Dinv14728' => 'din', 'Dinv15219' => 'din', 'Dinv25728' => 'din', 'Dinv33428' => 'din', 'Dinv36489' => 'din', 'Dinv41486' => 'din', 'Duzib147G0469' => 'dzi', 'Duzib168G0060' => 'dzi', 'Duzib187G1215' => 'dzi', 'Duzib248G0692' => 'dzi', 'Duzib251G0767' => 'dzi', 'Duzib264G0446' => 'dzi', 'Duzib268G0691' => 'dzi', 'ECA232G4767' => 'eca', 'ECA233G2838' => 'eca', 'ECA234G0391' => 'eca', 'ECA234G0857' => 'eca', 'ECA236G1593' => 'eca', 'ECA238G0565' => 'eca', 'ECA246G1027' => 'eca', 'ECA246G3223' => 'eca', 'ECA246G3470' => 'eca', 'EL10Ac6g13829' => 'bvu', 'EL10Ac6g14093' => 'bvu', 'EL10Ac8g18707' => 'bvu', 'Eucgr.C01369' => 'egr', 'Eucgr.H02492' => 'egr', 'Eucgr.I01733' => 'egr', 'Eucgr.J02255' => 'egr', 'Eucgr.J02257' => 'egr', 'Eucgr.J02258' => 'egr', 'FAN02G1601' => 'fan', 'FAN03G1586' => 'fan', 'FAN03G2986' => 'fan', 'FAN05G4837' => 'fan', 'FAN06G0146' => 'fan', 'FAN07G0858' => 'fan', 'FAN09G3179' => 'fan', 'FAN10G0669' => 'fan', 'FAN12G2358' => 'fan', 'FAN14G4198' => 'fan', 'FAN14G5112' => 'fan', 'FAN17G0342' => 'fan', 'FAN19G0342' => 'fan', 'FAN19G0962' => 'fan', 'FAN19G1101' => 'fan', 'FAN19G1872' => 'fan', 'FAN22G0356' => 'fan', 'FAN23G0744' => 'fan', 'FAN23G1914' => 'fan', 'FAN26G0032' => 'fan', 'FAN28G0625' => 'fan', 'FvH4_1g02710' => 'fve', 'FvH4_1g02720' => 'fve', 'FvH4_4g25670' => 'fve', 'FvH4_6g51700' => 'fve', 'FvH4_7g20170' => 'fve', 'Glyma.05G175000' => 'gma', 'Glyma.08G132300' => 'gma', 'Glyma.11G243000' => 'gma', 'Glyma.13G158900' => 'gma', 'Glyma.17G112400' => 'gma', 'Glyma.18G014100' => 'gma', 'Glyma.19G003100' => 'gma', 'Glyma.19G056500' => 'gma', 'Gohir.A01G158900' => 'ghi', 'Gohir.A05G312600' => 'ghi', 'Gohir.A05G354900' => 'ghi', 'Gohir.A07G037200' => 'ghi', 'Gohir.A09G030000' => 'ghi', 'Gohir.A12G145200' => 'ghi', 'Gohir.D01G151500' => 'ghi', 'Gohir.D04G058300' => 'ghi', 'Gohir.D05G314100' => 'ghi', 'Gohir.D07G041400' => 'ghi', 'Gohir.D09G029700' => 'ghi', 'Gohir.D12G149700' => 'ghi', 'Gorai.001G043800' => 'gra', 'Gorai.002G187800' => 'gra', 'Gorai.006G034700' => 'gra', 'Gorai.008G161200' => 'gra', 'Gorai.009G335700' => 'gra', 'Gorai.012G065000' => 'gra', 'GSVIVG01000535001' => 'vvi', 'GSVIVG01015572001' => 'vvi', 'GSVIVG01032386001' => 'vvi', 'HanXRQChr05g0138531' => 'han', 'HanXRQChr06g0174391' => 'han', 'HanXRQChr07g0199021' => 'han', 'HanXRQChr08g0208211' => 'han', 'HanXRQChr09g0255471' => 'han', 'HanXRQChr10g0315791' => 'han', 'HanXRQChr12g0371991' => 'han', 'HanXRQChr15g0475251' => 'han', 'HanXRQChr17g0540001' => 'han', 'HanXRQChr17g0548631' => 'han', 'HanXRQChr17g0569561' => 'han', 'Haze_12256' => 'cav', 'Haze_14756' => 'cav', 'Haze_25528' => 'cav', 'Hma1.2p1_0079F.1_g041020' => 'hma', 'Hma1.2p1_0818F.1_g223260' => 'hma', 'Hma1.2p1_1747F.1_g300530' => 'hma', 'HPP92_004607' => 'vpl', 'HPP92_004608' => 'vpl', 'HPP92_006181' => 'vpl', 'HPP92_012192' => 'vpl', 'HPP92_015680' => 'vpl', 'HPP92_020249' => 'vpl', 'HPP92_021376' => 'vpl', 'HPP92_024275' => 'vpl', 'Hund06031' => 'sun', 'Hund25391' => 'sun', 'Lalb_Chr07g0185371' => 'lal', 'Lalb_Chr07g0185381' => 'lal', 'Lalb_Chr12g0204011' => 'lal', 'Lalb_Chr13g0301671' => 'lal', 'Lalb_Chr14g0362851' => 'lal', 'Lalb_Chr24g0403581' => 'lal', 'Lj1g0000233' => 'lja', 'Lj2g0018120' => 'lja', 'Lj3C621T0' => 'lonja', 'Lj3P1059T14' => 'lonja', 'Lj3P611T9' => 'lonja', 'Lj3P614T13' => 'lonja', 'Lj3P615T5' => 'lonja', 'Lj4g0012315' => 'lja', 'Lj4g0026182' => 'lja', 'Lj6P813T16' => 'lonja', 'Lj7C427T7' => 'lonja', 'Lj7C427T8' => 'lonja', 'Lj7P600T41' => 'lonja', 'Lju41C42G17' => 'lonja', 'Lsat_1_v5_gn_0_47300' => 'lsa', 'Lsat_1_v5_gn_2_91280' => 'lsa', 'Lsat_1_v5_gn_3_30561' => 'lsa', 'Lsat_1_v5_gn_4_184321' => 'lsa', 'Lsat_1_v5_gn_4_4041' => 'lsa', 'Lsat_1_v5_gn_5_92000' => 'lsa', 'Lsat_1_v5_gn_8_152940' => 'lsa', 'Lsat_1_v5_gn_8_62401' => 'lsa', 'Manes.06G055900' => 'mes', 'Manes.12G022200' => 'mes', 'Manes.13G023300' => 'mes', 'Manes.14G115000' => 'mes', 'Manes.15G151700' => 'mes', 'Manes.17G111300' => 'mes', 'Mapoly0226s0009' => 'mpo', 'MBI02_g25363_MAGBIO' => 'mbi', 'MBI06_g00027_MAGBIO' => 'mbi', 'MBI10_g13034_MAGBIO' => 'mbi', 'MD09G1023400' => 'mdo', 'MD13G1100100' => 'mdo', 'MD15G1169200' => 'mdo', 'MD16G1101100' => 'mdo', 'MD17G1022900' => 'mdo', 'Medtr3g096150' => 'mtr', 'Medtr4g115070' => 'mtr', 'Medtr7g033325' => 'mtr', 'Medtr8g089840' => 'mtr', 'MELO3C010319.2' => 'cme', 'MELO3C011944.2' => 'cme', 'MELO3C021589.2' => 'cme', 'Migut.E00207' => 'egut', 'Migut.H00067' => 'egut', 'Migut.K00433' => 'egut', 'Migut.K00606' => 'egut', 'Migut.K01410' => 'egut', 'MSTRG.13347' => 'ama', 'MSTRG.24045' => 'ama', 'MSTRG.2428' => 'ama', 'MSTRG.26410' => 'ama', 'MSTRG.3139' => 'ama', 'MSTRG.3286' => 'ama', 'MSTRG.563' => 'ama', 'MSTRG.7941' => 'ama', 'Nitab4.5_0000028g0060' => 'nta', 'Nitab4.5_0000065g0260' => 'nta', 'Nitab4.5_0000112g0060' => 'nta', 'Nitab4.5_0000489g0120' => 'nta', 'Nitab4.5_0001776g0050' => 'nta', 'Nitab4.5_0001854g0010' => 'nta', 'Nitab4.5_0001860g0020' => 'nta', 'Nitab4.5_0004352g0010' => 'nta', 'Nitab4.5_0008716g0020' => 'nta', 'Nitab4.5_0008922g0010' => 'nta', 'Nn3g16693' => 'nnu', 'Nn4g22596' => 'nnu', 'Nn7g37639' => 'nnu', 'Oeu001701.1' => 'oeu', 'Oeu018149.1' => 'oeu', 'Oeu026220.1' => 'oeu', 'Oeu038635.1' => 'oeu', 'Oeu049176.1' => 'oeu', 'Oeu056706.1' => 'oeu', 'Oeu056937.1' => 'oeu', 'Oeu057540.1' => 'oeu', 'Os02g0594900' => 'osa', 'Os02g0595100' => 'osa', 'Os04g0477500' => 'osa', 'Os12g0611900' => 'osa', 'Peaxi162Scf00076g00020' => 'pax', 'Peaxi162Scf00128g00217' => 'pax', 'Peaxi162Scf00129g01640' => 'pax', 'Peaxi162Scf00669g00007' => 'pax', 'Peaxi162Scf00700g00421' => 'pax', 'Peaxi162Scf00801g00038' => 'pax', 'Peaxi162Scf00891g00025' => 'pax', 'PGR083G0909' => 'pgr', 'PGR119G1005' => 'pgr', 'PGR142G2236' => 'pgr', 'PGR142G3388' => 'pgr', 'PGSC0003DMG400004514' => 'stu', 'PGSC0003DMG400012635' => 'stu', 'PGSC0003DMG400015730' => 'stu', 'PGSC0003DMG400018611' => 'stu', 'PGSC0003DMG400030897' => 'stu', 'Phvul.001G254800' => 'pvu', 'Phvul.002G260100' => 'pvu', 'Phvul.003G167600' => 'pvu', 'Phvul.004G005100' => 'pvu', 'Potri.001G343600' => 'ptr', 'Potri.006G066700' => 'ptr', 'Potri.008G186000' => 'ptr', 'Potri.010G046900' => 'ptr', 'Potri.018G127900' => 'ptr', 'Pp3c20_17750' => 'ppa', 'Pp3c24_4380' => 'ppa', 'Prupe.1G245800' => 'ppe', 'Prupe.3G293400' => 'ppe', 'Prupe.7G247400' => 'ppe', 'Psat0s145g0120' => 'psa', 'Psat0s595g0040' => 'psa', 'Psat0s595g0120' => 'psa', 'Psat3g175040' => 'psa', 'Psat7g058120' => 'psa', 'PSO017G0428' => 'pso', 'PSO063G7510' => 'pso', 'PSO067G0046' => 'pso', 'PSO478G1073' => 'pso', 'PSO675G3677' => 'pso', 'PSO675G6558' => 'pso', 'PSO675G7520' => 'pso', 'PSO675G8959' => 'pso', 'QL02p074089' => 'qlo', 'QL02p089614' => 'qlo', 'QL03p057736' => 'qlo', 'RcHm_v2.0_Chr1g0364131' => 'rch', 'RcHm_v2.0_Chr2g0087801' => 'rch', 'RcHm_v2.0_Chr2g0087821' => 'rch', 'RcHm_v2.0_Chr2g0173231' => 'rch', 'RcHm_v2.0_Chr4g0433111' => 'rch', 'Rhsim03G0250300' => 'rsi', 'Rhsim08G0048400' => 'rsi', 'Rhsim10G0014800' => 'rsi', 'Rhsim12G0040100' => 'rsi', 'Rhsim12G0109700' => 'rsi', 'Sabra06G0049600' => 'sbr', 'Sabra08G0141000' => 'sbr', 'Sabra10G0021400' => 'sbr', 'Sabra16G0222900' => 'sbr', 'Sabra18G0108600' => 'sbr', 'SalBow1G0433' => 'sbo', 'SalBow1G2038' => 'sbo', 'SalBow1G5003' => 'sbo', 'SalBow7G1197' => 'sbo', 'SalBow8G3506' => 'sbo', 'Sc03g0007300' => 'sci', 'Sc11g0000950' => 'sci', 'Sc14g0008750' => 'sci', 'Sc18g0000420' => 'sci', 'Sed0006754' => 'sed', 'Sed0008741' => 'sed', 'Sed0017172' => 'sed', 'Sed0018925' => 'sed', 'Sed0023326' => 'sed', 'Sed0025909' => 'sed', 'SEGI_05333' => 'sgi', 'SEGI_10362' => 'sgi', 'SEGI_13380' => 'sgi', 'SEGI_24306' => 'sgi', 'SEGI_29077' => 'sgi', 'SEGI_29095' => 'sgi', 'SEGI_36534' => 'sgi', 'SEGI_37506' => 'sgi', 'SEGI_38321' => 'sgi', 'SGA_v2.0_scaffold307G48031' => 'sas', 'SGA_v2.0_scaffold47G17507' => 'sas', 'SGA_v2.0_scaffold63G21736' => 'sas', 'SGA_v2.0_scaffold87G27070' => 'sas', 'SHI17794' => 'shi', 'SHI28851' => 'shi', 'SMO165G0155' => 'smo', 'SMO340G0217' => 'smo', 'SMO367G1210' => 'smo', 'Solyc02g093430.3' => 'sly', 'Solyc05g013580.4' => 'sly', 'Solyc07g008030.3' => 'sly', 'Solyc12g035470.2' => 'sly', 'Sopen02g038020' => 'spe', 'Sopen05g008490' => 'spe', 'Sopen07g003910' => 'spe', 'Sopen12g015240' => 'spe', 'Sp1g11550' => 'spa', 'Sp2g16710' => 'spa', 'Sp3g00430' => 'spa', 'Sp3g26780' => 'spa', 'Sp5g22900' => 'spa', 'Sp6g29530' => 'spa', 'TAR371G0794' => 'tar', 'TAR374G0164' => 'tar', 'TAR622G0165' => 'tar', 'TAR626G0929' => 'tar', 'TAR629G2155' => 'tar', 'THA.LOC104805282' => 'tha', 'THA.LOC104805363' => 'tha', 'THA.LOC104808968' => 'tha', 'THA.LOC104821093' => 'tha', 'THA.LOC104823953' => 'tha', 'THA.LOC104825562' => 'tha', 'THA.LOC104825665' => 'tha', 'Thecc.02G261400' => 'tca', 'Thecc.04G019200' => 'tca', 'Thecc.09G130400' => 'tca', 'Thhalv10004374m.g' => 'esa', 'Thhalv10007850m.g' => 'esa', 'Thhalv10013782m.g' => 'esa', 'Thhalv10018686m.g' => 'esa', 'Thhalv10020899m.g' => 'esa', 'Thhalv10022755m.g' => 'esa', 'TPR.G23851' => 'tpr', 'TPR.G26500' => 'tpr', 'TPR.G27267' => 'tpr', 'TPR.G32001' => 'tpr', 'TPR.G6251' => 'tpr', 'TPR.G8167' => 'tpr', 'TWI12G1330' => 'twi', 'TWI18G1239' => 'twi', 'TWI34G0979' => 'twi', 'TWI36G0670' => 'twi', 'TWI36G0707' => 'twi', 'TWI56G0233' => 'twi', 'TWI75G1809' => 'twi', 'unitig_21.g20874' => 'ugi', 'unitig_26.g10343' => 'ugi', 'unitig_46.g18392' => 'ugi', 'unitig_52.g17178' => 'ugi', 'unitig_8.g2934' => 'ugi', 'vmacro01122' => 'vma', 'vmacro05875' => 'vma', 'vmacro06147' => 'vma', 'vmacro16191' => 'vma', 'vmacro18293' => 'vma', 'VMungo0251G3707' => 'vmu', 'VMungo0464G1521' => 'vmu', 'VMungo1215G0205' => 'vmu', 'VMungo1383G2484' => 'vmu', 'Zm00001eb079610' => 'zma', 'Zm00001eb135990' => 'zma', 'Zm00001eb183710' => 'zma', 'Zm00001eb246020' => 'zma' ) $gf_id = 'HOM05D001124' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001124' ) $data_identifier = 'HOM05D001124' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 6, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 7, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 21, 'bol' => (int) 10, 'bra' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 6, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 9, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 21, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 8, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 10, 'lsa' => (int) 8, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 8, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 9, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb246020' $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' => 'HOM05D001124', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '548', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02520' => 'bna', 'A03p06630' => 'bna', 'A05p44460' => 'bna', 'A06p08710' => 'bna', 'A06p41090' => 'bna', 'A07p32320' => 'bna', 'A08p32520' => 'bna', 'A09p10360' => 'bna', 'A10p24080' => 'bna', 'Aa31LG11G15250' => 'aar', 'Aa31LG1G1800' => 'aar', 'Aa31LG2G5120' => 'aar', 'Aa31LG2G6070' => 'aar', 'Aa31LG5G10770' => 'aar', 'Aa31sc61G90' => 'aar', 'Actinidia01352' => 'ach', 'Actinidia05983' => 'ach', 'Actinidia08133' => 'ach', 'Actinidia15101' => 'ach', 'Actinidia26379' => 'ach', 'Actinidia35778' => 'ach', 'Actinidia36123' => 'ach', 'Actinidia37436' => 'ach', 'Actinidia38730' => 'ach', 'Ah.02g128210' => 'amhyb', 'Ah.03g132990' => 'amhyb', 'Ah.14g079410' => 'amhyb', 'AL1G24640' => 'aly', 'AL2G26680' => 'aly', 'AL3G10530' => 'aly', 'AL3G45230' => 'aly', 'AL5G15230' => 'aly', 'AL5G16960' => 'aly', 'AL6G25210' => 'aly', 'Aqoxy2G00441' => 'aox', 'Aqoxy3G01236' => 'aox', 'Aqoxy5G03746' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3RQ047' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C7GMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9C8JER' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MBL6KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YXCZ83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZANX40' => 'arhy', 'AT1G12990' => 'ath', 'AT1G67880' => 'ath', 'AT2G13290' => 'ath', 'AT3G01620' => 'ath', 'AT3G26445' => 'ath', 'AT3G27540' => 'ath', 'AT5G14480' => 'ath', 'ATR0824G026' => 'atr', 'ATR1098G019' => 'atr', 'Atru.chr11.2145' => 'acertr', 'Atru.chr2.3636' => 'acertr', 'Atru.chr2.3644' => 'acertr', 'Atru.chr6.2422' => 'acertr', 'Atru.chr7.1112' => 'acertr', 'AUR62005469' => 'cqu', 'AUR62011166' => 'cqu', 'AUR62013319' => 'cqu', 'AUR62024273' => 'cqu', 'AUR62028420' => 'cqu', 'AUR62041942' => 'cqu', 'BcaB01g04969' => 'bca', 'BcaB01g06371' => 'bca', 'BcaB02g11494' => 'bca', 'BcaB03g15382' => 'bca', 'BcaB08g36994' => 'bca', 'BcaC03g13477' => 'bca', 'BcaC03g13478' => 'bca', 'BcaC03g13480' => 'bca', 'BcaC03g13481' => 'bca', 'BcaC03g13486' => 'bca', 'BcaC04g19031' => 'bca', 'BcaC04g23085' => 'bca', 'BcaC05g25094' => 'bca', 'BcaC05g25096' => 'bca', 'BcaC05g25138' => 'bca', 'BcaC05g30416' => 'bca', 'BcaC05g30455' => 'bca', 'BcaC06g30979' => 'bca', 'BcaC06g33805' => 'bca', 'BcaC08g46021' => 'bca', 'BcaNung03154' => 'bca', 'BolC2t06623H' => 'bol', 'BolC2t06632H' => 'bol', 'BolC2t06635H' => 'bol', 'BolC2t06638H' => 'bol', 'BolC3t13266H' => 'bol', 'BolC5t29776H' => 'bol', 'BolC6t38912H' => 'bol', 'BolC7t44183H' => 'bol', 'BolC9t54123H' => 'bol', 'BolC9t59107H' => 'bol', 'BraA02t05221Z' => 'bra', 'BraA03t09996Z' => 'bra', 'BraA05t23210Z' => 'bra', 'BraA06t24068Z' => 'bra', 'BraA06t27032Z' => 'bra', 'BraA08t35176Z' => 'bra', 'BraA09t36680Z' => 'bra', 'BraA10t44471Z' => 'bra', 'C02p06760' => 'bna', 'C02p06890' => 'bna', 'C02p07010' => 'bna', 'C03p07660' => 'bna', 'C05p10300' => 'bna', 'C06p38150' => 'bna', 'C07p36650' => 'bna', 'C08p15770' => 'bna', 'C09p12300' => 'bna', 'C09p62700' => 'bna', 'C09p75040' => 'bna', 'CAN.G13.1' => 'can', 'CAN.G138.4' => 'can', 'CAN.G44.6' => 'can', 'CAN.G473.19' => 'can', 'CANSAT01G0835' => 'cansat', 'CANSAT11G0246' => 'cansat', 'CANSAT11G1766' => 'cansat', 'CANSAT64G1954' => 'cansat', 'CARHR013330' => 'chi', 'CARHR060530' => 'chi', 'CARHR075300' => 'chi', 'CARHR105120' => 'chi', 'CARHR148910' => 'chi', 'CARHR198830' => 'chi', 'Carub.0001s1275' => 'cru', 'Carub.0002s1437' => 'cru', 'Carub.0003s0044' => 'cru', 'Carub.0003s2787' => 'cru', 'Carub.0005s0597' => 'cru', 'Carub.0006s1266' => 'cru', 'Ca_06935_v3' => 'car', 'Ca_13559_v3' => 'car', 'Ca_16941_v3' => 'car', 'Ca_16960_v3' => 'car', 'Ca_17775_v3' => 'car', 'Ca_30464_v3' => 'car', 'Cc06_g08160' => 'ccan', 'Cc07_g01520' => 'ccan', 'Cc11_g15810' => 'ccan', 'CDE02G2840' => 'cde', 'CDE03G0093' => 'cde', 'CDE04G2127' => 'cde', 'CDE07G1857' => 'cde', 'CDE09G1246' => 'cde', 'Cfa003412' => 'cfa', 'Cfa007341' => 'cfa', 'Cfa009220' => 'cfa', 'Ciclev10008737m.g' => 'ccl', 'Ciclev10015565m.g' => 'ccl', 'Ciclev10031761m.g' => 'ccl', 'CiPaw.03G045300' => 'cil', 'CiPaw.03G247200' => 'cil', 'CiPaw.04G029500' => 'cil', 'CiPaw.04G174000' => 'cil', 'CiPaw.05G181200' => 'cil', 'CiPaw.06G067100' => 'cil', 'ClCG05G025800' => 'cla', 'ClCG06G011400' => 'cla', 'ClCG09G019360' => 'cla', 'COL.COLO4_04827' => 'col', 'COL.COLO4_29170' => 'col', 'COL.COLO4_35131' => 'col', 'COL.COLO4_35132' => 'col', 'Cpa.g.sc33.32' => 'cpa', 'Cpa.g.sc46.29' => 'cpa', 'Cpa.g.sc796.1' => 'cpa', 'CsaV3_1G030420' => 'csa', 'CsaV3_5G027050' => 'csa', 'CsaV3_5G031040' => 'csa', 'CsaV3_UNG023130' => 'csa', 'CSS0007726' => 'camsi', 'CSS0016433' => 'camsi', 'CSS0017656' => 'camsi', 'CSS0025364' => 'camsi', 'CSS0027582' => 'camsi', 'CSS0047288' => 'camsi', 'CSS0049950' => 'camsi', 'DCAR_003843' => 'dca', 'DCAR_007052' => 'dca', 'DCAR_020884' => 'dca', 'DCAR_021730' => 'dca', 'DCAR_024423' => 'dca', 'DCAR_026509' => 'dca', 'DCAR_031158' => 'dca', 'Dinv14728' => 'din', 'Dinv15219' => 'din', 'Dinv25728' => 'din', 'Dinv33428' => 'din', 'Dinv36489' => 'din', 'Dinv41486' => 'din', 'Duzib147G0469' => 'dzi', 'Duzib168G0060' => 'dzi', 'Duzib187G1215' => 'dzi', 'Duzib248G0692' => 'dzi', 'Duzib251G0767' => 'dzi', 'Duzib264G0446' => 'dzi', 'Duzib268G0691' => 'dzi', 'ECA232G4767' => 'eca', 'ECA233G2838' => 'eca', 'ECA234G0391' => 'eca', 'ECA234G0857' => 'eca', 'ECA236G1593' => 'eca', 'ECA238G0565' => 'eca', 'ECA246G1027' => 'eca', 'ECA246G3223' => 'eca', 'ECA246G3470' => 'eca', 'EL10Ac6g13829' => 'bvu', 'EL10Ac6g14093' => 'bvu', 'EL10Ac8g18707' => 'bvu', 'Eucgr.C01369' => 'egr', 'Eucgr.H02492' => 'egr', 'Eucgr.I01733' => 'egr', 'Eucgr.J02255' => 'egr', 'Eucgr.J02257' => 'egr', 'Eucgr.J02258' => 'egr', 'FAN02G1601' => 'fan', 'FAN03G1586' => 'fan', 'FAN03G2986' => 'fan', 'FAN05G4837' => 'fan', 'FAN06G0146' => 'fan', 'FAN07G0858' => 'fan', 'FAN09G3179' => 'fan', 'FAN10G0669' => 'fan', 'FAN12G2358' => 'fan', 'FAN14G4198' => 'fan', 'FAN14G5112' => 'fan', 'FAN17G0342' => 'fan', 'FAN19G0342' => 'fan', 'FAN19G0962' => 'fan', 'FAN19G1101' => 'fan', 'FAN19G1872' => 'fan', 'FAN22G0356' => 'fan', 'FAN23G0744' => 'fan', 'FAN23G1914' => 'fan', 'FAN26G0032' => 'fan', 'FAN28G0625' => 'fan', 'FvH4_1g02710' => 'fve', 'FvH4_1g02720' => 'fve', 'FvH4_4g25670' => 'fve', 'FvH4_6g51700' => 'fve', 'FvH4_7g20170' => 'fve', 'Glyma.05G175000' => 'gma', 'Glyma.08G132300' => 'gma', 'Glyma.11G243000' => 'gma', 'Glyma.13G158900' => 'gma', 'Glyma.17G112400' => 'gma', 'Glyma.18G014100' => 'gma', 'Glyma.19G003100' => 'gma', 'Glyma.19G056500' => 'gma', 'Gohir.A01G158900' => 'ghi', 'Gohir.A05G312600' => 'ghi', 'Gohir.A05G354900' => 'ghi', 'Gohir.A07G037200' => 'ghi', 'Gohir.A09G030000' => 'ghi', 'Gohir.A12G145200' => 'ghi', 'Gohir.D01G151500' => 'ghi', 'Gohir.D04G058300' => 'ghi', 'Gohir.D05G314100' => 'ghi', 'Gohir.D07G041400' => 'ghi', 'Gohir.D09G029700' => 'ghi', 'Gohir.D12G149700' => 'ghi', 'Gorai.001G043800' => 'gra', 'Gorai.002G187800' => 'gra', 'Gorai.006G034700' => 'gra', 'Gorai.008G161200' => 'gra', 'Gorai.009G335700' => 'gra', 'Gorai.012G065000' => 'gra', 'GSVIVG01000535001' => 'vvi', 'GSVIVG01015572001' => 'vvi', 'GSVIVG01032386001' => 'vvi', 'HanXRQChr05g0138531' => 'han', 'HanXRQChr06g0174391' => 'han', 'HanXRQChr07g0199021' => 'han', 'HanXRQChr08g0208211' => 'han', 'HanXRQChr09g0255471' => 'han', 'HanXRQChr10g0315791' => 'han', 'HanXRQChr12g0371991' => 'han', 'HanXRQChr15g0475251' => 'han', 'HanXRQChr17g0540001' => 'han', 'HanXRQChr17g0548631' => 'han', 'HanXRQChr17g0569561' => 'han', 'Haze_12256' => 'cav', 'Haze_14756' => 'cav', 'Haze_25528' => 'cav', 'Hma1.2p1_0079F.1_g041020' => 'hma', 'Hma1.2p1_0818F.1_g223260' => 'hma', 'Hma1.2p1_1747F.1_g300530' => 'hma', 'HPP92_004607' => 'vpl', 'HPP92_004608' => 'vpl', 'HPP92_006181' => 'vpl', 'HPP92_012192' => 'vpl', 'HPP92_015680' => 'vpl', 'HPP92_020249' => 'vpl', 'HPP92_021376' => 'vpl', 'HPP92_024275' => 'vpl', 'Hund06031' => 'sun', 'Hund25391' => 'sun', 'Lalb_Chr07g0185371' => 'lal', 'Lalb_Chr07g0185381' => 'lal', 'Lalb_Chr12g0204011' => 'lal', 'Lalb_Chr13g0301671' => 'lal', 'Lalb_Chr14g0362851' => 'lal', 'Lalb_Chr24g0403581' => 'lal', 'Lj1g0000233' => 'lja', 'Lj2g0018120' => 'lja', 'Lj3C621T0' => 'lonja', 'Lj3P1059T14' => 'lonja', 'Lj3P611T9' => 'lonja', 'Lj3P614T13' => 'lonja', 'Lj3P615T5' => 'lonja', 'Lj4g0012315' => 'lja', 'Lj4g0026182' => 'lja', 'Lj6P813T16' => 'lonja', 'Lj7C427T7' => 'lonja', 'Lj7C427T8' => 'lonja', 'Lj7P600T41' => 'lonja', 'Lju41C42G17' => 'lonja', 'Lsat_1_v5_gn_0_47300' => 'lsa', 'Lsat_1_v5_gn_2_91280' => 'lsa', 'Lsat_1_v5_gn_3_30561' => 'lsa', 'Lsat_1_v5_gn_4_184321' => 'lsa', 'Lsat_1_v5_gn_4_4041' => 'lsa', 'Lsat_1_v5_gn_5_92000' => 'lsa', 'Lsat_1_v5_gn_8_152940' => 'lsa', 'Lsat_1_v5_gn_8_62401' => 'lsa', 'Manes.06G055900' => 'mes', 'Manes.12G022200' => 'mes', 'Manes.13G023300' => 'mes', 'Manes.14G115000' => 'mes', 'Manes.15G151700' => 'mes', 'Manes.17G111300' => 'mes', 'Mapoly0226s0009' => 'mpo', 'MBI02_g25363_MAGBIO' => 'mbi', 'MBI06_g00027_MAGBIO' => 'mbi', 'MBI10_g13034_MAGBIO' => 'mbi', 'MD09G1023400' => 'mdo', 'MD13G1100100' => 'mdo', 'MD15G1169200' => 'mdo', 'MD16G1101100' => 'mdo', 'MD17G1022900' => 'mdo', 'Medtr3g096150' => 'mtr', 'Medtr4g115070' => 'mtr', 'Medtr7g033325' => 'mtr', 'Medtr8g089840' => 'mtr', 'MELO3C010319.2' => 'cme', 'MELO3C011944.2' => 'cme', 'MELO3C021589.2' => 'cme', 'Migut.E00207' => 'egut', 'Migut.H00067' => 'egut', 'Migut.K00433' => 'egut', 'Migut.K00606' => 'egut', 'Migut.K01410' => 'egut', 'MSTRG.13347' => 'ama', 'MSTRG.24045' => 'ama', 'MSTRG.2428' => 'ama', 'MSTRG.26410' => 'ama', 'MSTRG.3139' => 'ama', 'MSTRG.3286' => 'ama', 'MSTRG.563' => 'ama', 'MSTRG.7941' => 'ama', 'Nitab4.5_0000028g0060' => 'nta', 'Nitab4.5_0000065g0260' => 'nta', 'Nitab4.5_0000112g0060' => 'nta', 'Nitab4.5_0000489g0120' => 'nta', 'Nitab4.5_0001776g0050' => 'nta', 'Nitab4.5_0001854g0010' => 'nta', 'Nitab4.5_0001860g0020' => 'nta', 'Nitab4.5_0004352g0010' => 'nta', 'Nitab4.5_0008716g0020' => 'nta', 'Nitab4.5_0008922g0010' => 'nta', 'Nn3g16693' => 'nnu', 'Nn4g22596' => 'nnu', 'Nn7g37639' => 'nnu', 'Oeu001701.1' => 'oeu', 'Oeu018149.1' => 'oeu', 'Oeu026220.1' => 'oeu', 'Oeu038635.1' => 'oeu', 'Oeu049176.1' => 'oeu', 'Oeu056706.1' => 'oeu', 'Oeu056937.1' => 'oeu', 'Oeu057540.1' => 'oeu', 'Os02g0594900' => 'osa', 'Os02g0595100' => 'osa', 'Os04g0477500' => 'osa', 'Os12g0611900' => 'osa', 'Peaxi162Scf00076g00020' => 'pax', 'Peaxi162Scf00128g00217' => 'pax', 'Peaxi162Scf00129g01640' => 'pax', 'Peaxi162Scf00669g00007' => 'pax', 'Peaxi162Scf00700g00421' => 'pax', 'Peaxi162Scf00801g00038' => 'pax', 'Peaxi162Scf00891g00025' => 'pax', 'PGR083G0909' => 'pgr', 'PGR119G1005' => 'pgr', 'PGR142G2236' => 'pgr', 'PGR142G3388' => 'pgr', 'PGSC0003DMG400004514' => 'stu', 'PGSC0003DMG400012635' => 'stu', 'PGSC0003DMG400015730' => 'stu', 'PGSC0003DMG400018611' => 'stu', 'PGSC0003DMG400030897' => 'stu', 'Phvul.001G254800' => 'pvu', 'Phvul.002G260100' => 'pvu', 'Phvul.003G167600' => 'pvu', 'Phvul.004G005100' => 'pvu', 'Potri.001G343600' => 'ptr', 'Potri.006G066700' => 'ptr', 'Potri.008G186000' => 'ptr', 'Potri.010G046900' => 'ptr', 'Potri.018G127900' => 'ptr', 'Pp3c20_17750' => 'ppa', 'Pp3c24_4380' => 'ppa', 'Prupe.1G245800' => 'ppe', 'Prupe.3G293400' => 'ppe', 'Prupe.7G247400' => 'ppe', 'Psat0s145g0120' => 'psa', 'Psat0s595g0040' => 'psa', 'Psat0s595g0120' => 'psa', 'Psat3g175040' => 'psa', 'Psat7g058120' => 'psa', 'PSO017G0428' => 'pso', 'PSO063G7510' => 'pso', 'PSO067G0046' => 'pso', 'PSO478G1073' => 'pso', 'PSO675G3677' => 'pso', 'PSO675G6558' => 'pso', 'PSO675G7520' => 'pso', 'PSO675G8959' => 'pso', 'QL02p074089' => 'qlo', 'QL02p089614' => 'qlo', 'QL03p057736' => 'qlo', 'RcHm_v2.0_Chr1g0364131' => 'rch', 'RcHm_v2.0_Chr2g0087801' => 'rch', 'RcHm_v2.0_Chr2g0087821' => 'rch', 'RcHm_v2.0_Chr2g0173231' => 'rch', 'RcHm_v2.0_Chr4g0433111' => 'rch', 'Rhsim03G0250300' => 'rsi', 'Rhsim08G0048400' => 'rsi', 'Rhsim10G0014800' => 'rsi', 'Rhsim12G0040100' => 'rsi', 'Rhsim12G0109700' => 'rsi', 'Sabra06G0049600' => 'sbr', 'Sabra08G0141000' => 'sbr', 'Sabra10G0021400' => 'sbr', 'Sabra16G0222900' => 'sbr', 'Sabra18G0108600' => 'sbr', 'SalBow1G0433' => 'sbo', 'SalBow1G2038' => 'sbo', 'SalBow1G5003' => 'sbo', 'SalBow7G1197' => 'sbo', 'SalBow8G3506' => 'sbo', 'Sc03g0007300' => 'sci', 'Sc11g0000950' => 'sci', 'Sc14g0008750' => 'sci', 'Sc18g0000420' => 'sci', 'Sed0006754' => 'sed', 'Sed0008741' => 'sed', 'Sed0017172' => 'sed', 'Sed0018925' => 'sed', 'Sed0023326' => 'sed', 'Sed0025909' => 'sed', 'SEGI_05333' => 'sgi', 'SEGI_10362' => 'sgi', 'SEGI_13380' => 'sgi', 'SEGI_24306' => 'sgi', 'SEGI_29077' => 'sgi', 'SEGI_29095' => 'sgi', 'SEGI_36534' => 'sgi', 'SEGI_37506' => 'sgi', 'SEGI_38321' => 'sgi', 'SGA_v2.0_scaffold307G48031' => 'sas', 'SGA_v2.0_scaffold47G17507' => 'sas', 'SGA_v2.0_scaffold63G21736' => 'sas', 'SGA_v2.0_scaffold87G27070' => 'sas', 'SHI17794' => 'shi', 'SHI28851' => 'shi', 'SMO165G0155' => 'smo', 'SMO340G0217' => 'smo', 'SMO367G1210' => 'smo', 'Solyc02g093430.3' => 'sly', 'Solyc05g013580.4' => 'sly', 'Solyc07g008030.3' => 'sly', 'Solyc12g035470.2' => 'sly', 'Sopen02g038020' => 'spe', 'Sopen05g008490' => 'spe', 'Sopen07g003910' => 'spe', 'Sopen12g015240' => 'spe', 'Sp1g11550' => 'spa', 'Sp2g16710' => 'spa', 'Sp3g00430' => 'spa', 'Sp3g26780' => 'spa', 'Sp5g22900' => 'spa', 'Sp6g29530' => 'spa', 'TAR371G0794' => 'tar', 'TAR374G0164' => 'tar', 'TAR622G0165' => 'tar', 'TAR626G0929' => 'tar', 'TAR629G2155' => 'tar', 'THA.LOC104805282' => 'tha', 'THA.LOC104805363' => 'tha', 'THA.LOC104808968' => 'tha', 'THA.LOC104821093' => 'tha', 'THA.LOC104823953' => 'tha', 'THA.LOC104825562' => 'tha', 'THA.LOC104825665' => 'tha', 'Thecc.02G261400' => 'tca', 'Thecc.04G019200' => 'tca', 'Thecc.09G130400' => 'tca', 'Thhalv10004374m.g' => 'esa', 'Thhalv10007850m.g' => 'esa', 'Thhalv10013782m.g' => 'esa', 'Thhalv10018686m.g' => 'esa', 'Thhalv10020899m.g' => 'esa', 'Thhalv10022755m.g' => 'esa', 'TPR.G23851' => 'tpr', 'TPR.G26500' => 'tpr', 'TPR.G27267' => 'tpr', 'TPR.G32001' => 'tpr', 'TPR.G6251' => 'tpr', 'TPR.G8167' => 'tpr', 'TWI12G1330' => 'twi', 'TWI18G1239' => 'twi', 'TWI34G0979' => 'twi', 'TWI36G0670' => 'twi', 'TWI36G0707' => 'twi', 'TWI56G0233' => 'twi', 'TWI75G1809' => 'twi', 'unitig_21.g20874' => 'ugi', 'unitig_26.g10343' => 'ugi', 'unitig_46.g18392' => 'ugi', 'unitig_52.g17178' => 'ugi', 'unitig_8.g2934' => 'ugi', 'vmacro01122' => 'vma', 'vmacro05875' => 'vma', 'vmacro06147' => 'vma', 'vmacro16191' => 'vma', 'vmacro18293' => 'vma', 'VMungo0251G3707' => 'vmu', 'VMungo0464G1521' => 'vmu', 'VMungo1215G0205' => 'vmu', 'VMungo1383G2484' => 'vmu', 'Zm00001eb079610' => 'zma', 'Zm00001eb135990' => 'zma', 'Zm00001eb183710' => 'zma', 'Zm00001eb246020' => 'zma' ), 'gf_id' => 'HOM05D001124', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001124' ), 'data_identifier' => 'HOM05D001124', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001124', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '548', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02520' => 'bna', 'A03p06630' => 'bna', 'A05p44460' => 'bna', 'A06p08710' => 'bna', 'A06p41090' => 'bna', 'A07p32320' => 'bna', 'A08p32520' => 'bna', 'A09p10360' => 'bna', 'A10p24080' => 'bna', 'Aa31LG11G15250' => 'aar', 'Aa31LG1G1800' => 'aar', 'Aa31LG2G5120' => 'aar', 'Aa31LG2G6070' => 'aar', 'Aa31LG5G10770' => 'aar', 'Aa31sc61G90' => 'aar', 'Actinidia01352' => 'ach', 'Actinidia05983' => 'ach', 'Actinidia08133' => 'ach', 'Actinidia15101' => 'ach', 'Actinidia26379' => 'ach', 'Actinidia35778' => 'ach', 'Actinidia36123' => 'ach', 'Actinidia37436' => 'ach', 'Actinidia38730' => 'ach', 'Ah.02g128210' => 'amhyb', 'Ah.03g132990' => 'amhyb', 'Ah.14g079410' => 'amhyb', 'AL1G24640' => 'aly', 'AL2G26680' => 'aly', 'AL3G10530' => 'aly', 'AL3G45230' => 'aly', 'AL5G15230' => 'aly', 'AL5G16960' => 'aly', 'AL6G25210' => 'aly', 'Aqoxy2G00441' => 'aox', 'Aqoxy3G01236' => 'aox', 'Aqoxy5G03746' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3RQ047' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C7GMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9C8JER' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MBL6KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YXCZ83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZANX40' => 'arhy', 'AT1G12990' => 'ath', 'AT1G67880' => 'ath', 'AT2G13290' => 'ath', 'AT3G01620' => 'ath', 'AT3G26445' => 'ath', 'AT3G27540' => 'ath', 'AT5G14480' => 'ath', 'ATR0824G026' => 'atr', 'ATR1098G019' => 'atr', 'Atru.chr11.2145' => 'acertr', 'Atru.chr2.3636' => 'acertr', 'Atru.chr2.3644' => 'acertr', 'Atru.chr6.2422' => 'acertr', 'Atru.chr7.1112' => 'acertr', 'AUR62005469' => 'cqu', 'AUR62011166' => 'cqu', 'AUR62013319' => 'cqu', 'AUR62024273' => 'cqu', 'AUR62028420' => 'cqu', 'AUR62041942' => 'cqu', 'BcaB01g04969' => 'bca', 'BcaB01g06371' => 'bca', 'BcaB02g11494' => 'bca', 'BcaB03g15382' => 'bca', 'BcaB08g36994' => 'bca', 'BcaC03g13477' => 'bca', 'BcaC03g13478' => 'bca', 'BcaC03g13480' => 'bca', 'BcaC03g13481' => 'bca', 'BcaC03g13486' => 'bca', 'BcaC04g19031' => 'bca', 'BcaC04g23085' => 'bca', 'BcaC05g25094' => 'bca', 'BcaC05g25096' => 'bca', 'BcaC05g25138' => 'bca', 'BcaC05g30416' => 'bca', 'BcaC05g30455' => 'bca', 'BcaC06g30979' => 'bca', 'BcaC06g33805' => 'bca', 'BcaC08g46021' => 'bca', 'BcaNung03154' => 'bca', 'BolC2t06623H' => 'bol', 'BolC2t06632H' => 'bol', 'BolC2t06635H' => 'bol', 'BolC2t06638H' => 'bol', 'BolC3t13266H' => 'bol', 'BolC5t29776H' => 'bol', 'BolC6t38912H' => 'bol', 'BolC7t44183H' => 'bol', 'BolC9t54123H' => 'bol', 'BolC9t59107H' => 'bol', 'BraA02t05221Z' => 'bra', 'BraA03t09996Z' => 'bra', 'BraA05t23210Z' => 'bra', 'BraA06t24068Z' => 'bra', 'BraA06t27032Z' => 'bra', 'BraA08t35176Z' => 'bra', 'BraA09t36680Z' => 'bra', 'BraA10t44471Z' => 'bra', 'C02p06760' => 'bna', 'C02p06890' => 'bna', 'C02p07010' => 'bna', 'C03p07660' => 'bna', 'C05p10300' => 'bna', 'C06p38150' => 'bna', 'C07p36650' => 'bna', 'C08p15770' => 'bna', 'C09p12300' => 'bna', 'C09p62700' => 'bna', 'C09p75040' => 'bna', 'CAN.G13.1' => 'can', 'CAN.G138.4' => 'can', 'CAN.G44.6' => 'can', 'CAN.G473.19' => 'can', 'CANSAT01G0835' => 'cansat', 'CANSAT11G0246' => 'cansat', 'CANSAT11G1766' => 'cansat', 'CANSAT64G1954' => 'cansat', 'CARHR013330' => 'chi', 'CARHR060530' => 'chi', 'CARHR075300' => 'chi', 'CARHR105120' => 'chi', 'CARHR148910' => 'chi', 'CARHR198830' => 'chi', 'Carub.0001s1275' => 'cru', 'Carub.0002s1437' => 'cru', 'Carub.0003s0044' => 'cru', 'Carub.0003s2787' => 'cru', 'Carub.0005s0597' => 'cru', 'Carub.0006s1266' => 'cru', 'Ca_06935_v3' => 'car', 'Ca_13559_v3' => 'car', 'Ca_16941_v3' => 'car', 'Ca_16960_v3' => 'car', 'Ca_17775_v3' => 'car', 'Ca_30464_v3' => 'car', 'Cc06_g08160' => 'ccan', 'Cc07_g01520' => 'ccan', 'Cc11_g15810' => 'ccan', 'CDE02G2840' => 'cde', 'CDE03G0093' => 'cde', 'CDE04G2127' => 'cde', 'CDE07G1857' => 'cde', 'CDE09G1246' => 'cde', 'Cfa003412' => 'cfa', 'Cfa007341' => 'cfa', 'Cfa009220' => 'cfa', 'Ciclev10008737m.g' => 'ccl', 'Ciclev10015565m.g' => 'ccl', 'Ciclev10031761m.g' => 'ccl', 'CiPaw.03G045300' => 'cil', 'CiPaw.03G247200' => 'cil', 'CiPaw.04G029500' => 'cil', 'CiPaw.04G174000' => 'cil', 'CiPaw.05G181200' => 'cil', 'CiPaw.06G067100' => 'cil', 'ClCG05G025800' => 'cla', 'ClCG06G011400' => 'cla', 'ClCG09G019360' => 'cla', 'COL.COLO4_04827' => 'col', 'COL.COLO4_29170' => 'col', 'COL.COLO4_35131' => 'col', 'COL.COLO4_35132' => 'col', 'Cpa.g.sc33.32' => 'cpa', 'Cpa.g.sc46.29' => 'cpa', 'Cpa.g.sc796.1' => 'cpa', 'CsaV3_1G030420' => 'csa', 'CsaV3_5G027050' => 'csa', 'CsaV3_5G031040' => 'csa', 'CsaV3_UNG023130' => 'csa', 'CSS0007726' => 'camsi', 'CSS0016433' => 'camsi', 'CSS0017656' => 'camsi', 'CSS0025364' => 'camsi', 'CSS0027582' => 'camsi', 'CSS0047288' => 'camsi', 'CSS0049950' => 'camsi', 'DCAR_003843' => 'dca', 'DCAR_007052' => 'dca', 'DCAR_020884' => 'dca', 'DCAR_021730' => 'dca', 'DCAR_024423' => 'dca', 'DCAR_026509' => 'dca', 'DCAR_031158' => 'dca', 'Dinv14728' => 'din', 'Dinv15219' => 'din', 'Dinv25728' => 'din', 'Dinv33428' => 'din', 'Dinv36489' => 'din', 'Dinv41486' => 'din', 'Duzib147G0469' => 'dzi', 'Duzib168G0060' => 'dzi', 'Duzib187G1215' => 'dzi', 'Duzib248G0692' => 'dzi', 'Duzib251G0767' => 'dzi', 'Duzib264G0446' => 'dzi', 'Duzib268G0691' => 'dzi', 'ECA232G4767' => 'eca', 'ECA233G2838' => 'eca', 'ECA234G0391' => 'eca', 'ECA234G0857' => 'eca', 'ECA236G1593' => 'eca', 'ECA238G0565' => 'eca', 'ECA246G1027' => 'eca', 'ECA246G3223' => 'eca', 'ECA246G3470' => 'eca', 'EL10Ac6g13829' => 'bvu', 'EL10Ac6g14093' => 'bvu', 'EL10Ac8g18707' => 'bvu', 'Eucgr.C01369' => 'egr', 'Eucgr.H02492' => 'egr', 'Eucgr.I01733' => 'egr', 'Eucgr.J02255' => 'egr', 'Eucgr.J02257' => 'egr', 'Eucgr.J02258' => 'egr', 'FAN02G1601' => 'fan', 'FAN03G1586' => 'fan', 'FAN03G2986' => 'fan', 'FAN05G4837' => 'fan', 'FAN06G0146' => 'fan', 'FAN07G0858' => 'fan', 'FAN09G3179' => 'fan', 'FAN10G0669' => 'fan', 'FAN12G2358' => 'fan', 'FAN14G4198' => 'fan', 'FAN14G5112' => 'fan', 'FAN17G0342' => 'fan', 'FAN19G0342' => 'fan', 'FAN19G0962' => 'fan', 'FAN19G1101' => 'fan', 'FAN19G1872' => 'fan', 'FAN22G0356' => 'fan', 'FAN23G0744' => 'fan', 'FAN23G1914' => 'fan', 'FAN26G0032' => 'fan', 'FAN28G0625' => 'fan', 'FvH4_1g02710' => 'fve', 'FvH4_1g02720' => 'fve', 'FvH4_4g25670' => 'fve', 'FvH4_6g51700' => 'fve', 'FvH4_7g20170' => 'fve', 'Glyma.05G175000' => 'gma', 'Glyma.08G132300' => 'gma', 'Glyma.11G243000' => 'gma', 'Glyma.13G158900' => 'gma', 'Glyma.17G112400' => 'gma', 'Glyma.18G014100' => 'gma', 'Glyma.19G003100' => 'gma', 'Glyma.19G056500' => 'gma', 'Gohir.A01G158900' => 'ghi', 'Gohir.A05G312600' => 'ghi', 'Gohir.A05G354900' => 'ghi', 'Gohir.A07G037200' => 'ghi', 'Gohir.A09G030000' => 'ghi', 'Gohir.A12G145200' => 'ghi', 'Gohir.D01G151500' => 'ghi', 'Gohir.D04G058300' => 'ghi', 'Gohir.D05G314100' => 'ghi', 'Gohir.D07G041400' => 'ghi', 'Gohir.D09G029700' => 'ghi', 'Gohir.D12G149700' => 'ghi', 'Gorai.001G043800' => 'gra', 'Gorai.002G187800' => 'gra', 'Gorai.006G034700' => 'gra', 'Gorai.008G161200' => 'gra', 'Gorai.009G335700' => 'gra', 'Gorai.012G065000' => 'gra', 'GSVIVG01000535001' => 'vvi', 'GSVIVG01015572001' => 'vvi', 'GSVIVG01032386001' => 'vvi', 'HanXRQChr05g0138531' => 'han', 'HanXRQChr06g0174391' => 'han', 'HanXRQChr07g0199021' => 'han', 'HanXRQChr08g0208211' => 'han', 'HanXRQChr09g0255471' => 'han', 'HanXRQChr10g0315791' => 'han', 'HanXRQChr12g0371991' => 'han', 'HanXRQChr15g0475251' => 'han', 'HanXRQChr17g0540001' => 'han', 'HanXRQChr17g0548631' => 'han', 'HanXRQChr17g0569561' => 'han', 'Haze_12256' => 'cav', 'Haze_14756' => 'cav', 'Haze_25528' => 'cav', 'Hma1.2p1_0079F.1_g041020' => 'hma', 'Hma1.2p1_0818F.1_g223260' => 'hma', 'Hma1.2p1_1747F.1_g300530' => 'hma', 'HPP92_004607' => 'vpl', 'HPP92_004608' => 'vpl', 'HPP92_006181' => 'vpl', 'HPP92_012192' => 'vpl', 'HPP92_015680' => 'vpl', 'HPP92_020249' => 'vpl', 'HPP92_021376' => 'vpl', 'HPP92_024275' => 'vpl', 'Hund06031' => 'sun', 'Hund25391' => 'sun', 'Lalb_Chr07g0185371' => 'lal', 'Lalb_Chr07g0185381' => 'lal', 'Lalb_Chr12g0204011' => 'lal', 'Lalb_Chr13g0301671' => 'lal', 'Lalb_Chr14g0362851' => 'lal', 'Lalb_Chr24g0403581' => 'lal', 'Lj1g0000233' => 'lja', 'Lj2g0018120' => 'lja', 'Lj3C621T0' => 'lonja', 'Lj3P1059T14' => 'lonja', 'Lj3P611T9' => 'lonja', 'Lj3P614T13' => 'lonja', 'Lj3P615T5' => 'lonja', 'Lj4g0012315' => 'lja', 'Lj4g0026182' => 'lja', 'Lj6P813T16' => 'lonja', 'Lj7C427T7' => 'lonja', 'Lj7C427T8' => 'lonja', 'Lj7P600T41' => 'lonja', 'Lju41C42G17' => 'lonja', 'Lsat_1_v5_gn_0_47300' => 'lsa', 'Lsat_1_v5_gn_2_91280' => 'lsa', 'Lsat_1_v5_gn_3_30561' => 'lsa', 'Lsat_1_v5_gn_4_184321' => 'lsa', 'Lsat_1_v5_gn_4_4041' => 'lsa', 'Lsat_1_v5_gn_5_92000' => 'lsa', 'Lsat_1_v5_gn_8_152940' => 'lsa', 'Lsat_1_v5_gn_8_62401' => 'lsa', 'Manes.06G055900' => 'mes', 'Manes.12G022200' => 'mes', 'Manes.13G023300' => 'mes', 'Manes.14G115000' => 'mes', 'Manes.15G151700' => 'mes', 'Manes.17G111300' => 'mes', 'Mapoly0226s0009' => 'mpo', 'MBI02_g25363_MAGBIO' => 'mbi', 'MBI06_g00027_MAGBIO' => 'mbi', 'MBI10_g13034_MAGBIO' => 'mbi', 'MD09G1023400' => 'mdo', 'MD13G1100100' => 'mdo', 'MD15G1169200' => 'mdo', 'MD16G1101100' => 'mdo', 'MD17G1022900' => 'mdo', 'Medtr3g096150' => 'mtr', 'Medtr4g115070' => 'mtr', 'Medtr7g033325' => 'mtr', 'Medtr8g089840' => 'mtr', 'MELO3C010319.2' => 'cme', 'MELO3C011944.2' => 'cme', 'MELO3C021589.2' => 'cme', 'Migut.E00207' => 'egut', 'Migut.H00067' => 'egut', 'Migut.K00433' => 'egut', 'Migut.K00606' => 'egut', 'Migut.K01410' => 'egut', 'MSTRG.13347' => 'ama', 'MSTRG.24045' => 'ama', 'MSTRG.2428' => 'ama', 'MSTRG.26410' => 'ama', 'MSTRG.3139' => 'ama', 'MSTRG.3286' => 'ama', 'MSTRG.563' => 'ama', 'MSTRG.7941' => 'ama', 'Nitab4.5_0000028g0060' => 'nta', 'Nitab4.5_0000065g0260' => 'nta', 'Nitab4.5_0000112g0060' => 'nta', 'Nitab4.5_0000489g0120' => 'nta', 'Nitab4.5_0001776g0050' => 'nta', 'Nitab4.5_0001854g0010' => 'nta', 'Nitab4.5_0001860g0020' => 'nta', 'Nitab4.5_0004352g0010' => 'nta', 'Nitab4.5_0008716g0020' => 'nta', 'Nitab4.5_0008922g0010' => 'nta', 'Nn3g16693' => 'nnu', 'Nn4g22596' => 'nnu', 'Nn7g37639' => 'nnu', 'Oeu001701.1' => 'oeu', 'Oeu018149.1' => 'oeu', 'Oeu026220.1' => 'oeu', 'Oeu038635.1' => 'oeu', 'Oeu049176.1' => 'oeu', 'Oeu056706.1' => 'oeu', 'Oeu056937.1' => 'oeu', 'Oeu057540.1' => 'oeu', 'Os02g0594900' => 'osa', 'Os02g0595100' => 'osa', 'Os04g0477500' => 'osa', 'Os12g0611900' => 'osa', 'Peaxi162Scf00076g00020' => 'pax', 'Peaxi162Scf00128g00217' => 'pax', 'Peaxi162Scf00129g01640' => 'pax', 'Peaxi162Scf00669g00007' => 'pax', 'Peaxi162Scf00700g00421' => 'pax', 'Peaxi162Scf00801g00038' => 'pax', 'Peaxi162Scf00891g00025' => 'pax', 'PGR083G0909' => 'pgr', 'PGR119G1005' => 'pgr', 'PGR142G2236' => 'pgr', 'PGR142G3388' => 'pgr', 'PGSC0003DMG400004514' => 'stu', 'PGSC0003DMG400012635' => 'stu', 'PGSC0003DMG400015730' => 'stu', 'PGSC0003DMG400018611' => 'stu', 'PGSC0003DMG400030897' => 'stu', 'Phvul.001G254800' => 'pvu', 'Phvul.002G260100' => 'pvu', 'Phvul.003G167600' => 'pvu', 'Phvul.004G005100' => 'pvu', 'Potri.001G343600' => 'ptr', 'Potri.006G066700' => 'ptr', 'Potri.008G186000' => 'ptr', 'Potri.010G046900' => 'ptr', 'Potri.018G127900' => 'ptr', 'Pp3c20_17750' => 'ppa', 'Pp3c24_4380' => 'ppa', 'Prupe.1G245800' => 'ppe', 'Prupe.3G293400' => 'ppe', 'Prupe.7G247400' => 'ppe', 'Psat0s145g0120' => 'psa', 'Psat0s595g0040' => 'psa', 'Psat0s595g0120' => 'psa', 'Psat3g175040' => 'psa', 'Psat7g058120' => 'psa', 'PSO017G0428' => 'pso', 'PSO063G7510' => 'pso', 'PSO067G0046' => 'pso', 'PSO478G1073' => 'pso', 'PSO675G3677' => 'pso', 'PSO675G6558' => 'pso', 'PSO675G7520' => 'pso', 'PSO675G8959' => 'pso', 'QL02p074089' => 'qlo', 'QL02p089614' => 'qlo', 'QL03p057736' => 'qlo', 'RcHm_v2.0_Chr1g0364131' => 'rch', 'RcHm_v2.0_Chr2g0087801' => 'rch', 'RcHm_v2.0_Chr2g0087821' => 'rch', 'RcHm_v2.0_Chr2g0173231' => 'rch', 'RcHm_v2.0_Chr4g0433111' => 'rch', 'Rhsim03G0250300' => 'rsi', 'Rhsim08G0048400' => 'rsi', 'Rhsim10G0014800' => 'rsi', 'Rhsim12G0040100' => 'rsi', 'Rhsim12G0109700' => 'rsi', 'Sabra06G0049600' => 'sbr', 'Sabra08G0141000' => 'sbr', 'Sabra10G0021400' => 'sbr', 'Sabra16G0222900' => 'sbr', 'Sabra18G0108600' => 'sbr', 'SalBow1G0433' => 'sbo', 'SalBow1G2038' => 'sbo', 'SalBow1G5003' => 'sbo', 'SalBow7G1197' => 'sbo', 'SalBow8G3506' => 'sbo', 'Sc03g0007300' => 'sci', 'Sc11g0000950' => 'sci', 'Sc14g0008750' => 'sci', 'Sc18g0000420' => 'sci', 'Sed0006754' => 'sed', 'Sed0008741' => 'sed', 'Sed0017172' => 'sed', 'Sed0018925' => 'sed', 'Sed0023326' => 'sed', 'Sed0025909' => 'sed', 'SEGI_05333' => 'sgi', 'SEGI_10362' => 'sgi', 'SEGI_13380' => 'sgi', 'SEGI_24306' => 'sgi', 'SEGI_29077' => 'sgi', 'SEGI_29095' => 'sgi', 'SEGI_36534' => 'sgi', 'SEGI_37506' => 'sgi', 'SEGI_38321' => 'sgi', 'SGA_v2.0_scaffold307G48031' => 'sas', 'SGA_v2.0_scaffold47G17507' => 'sas', 'SGA_v2.0_scaffold63G21736' => 'sas', 'SGA_v2.0_scaffold87G27070' => 'sas', 'SHI17794' => 'shi', 'SHI28851' => 'shi', 'SMO165G0155' => 'smo', 'SMO340G0217' => 'smo', 'SMO367G1210' => 'smo', 'Solyc02g093430.3' => 'sly', 'Solyc05g013580.4' => 'sly', 'Solyc07g008030.3' => 'sly', 'Solyc12g035470.2' => 'sly', 'Sopen02g038020' => 'spe', 'Sopen05g008490' => 'spe', 'Sopen07g003910' => 'spe', 'Sopen12g015240' => 'spe', 'Sp1g11550' => 'spa', 'Sp2g16710' => 'spa', 'Sp3g00430' => 'spa', 'Sp3g26780' => 'spa', 'Sp5g22900' => 'spa', 'Sp6g29530' => 'spa', 'TAR371G0794' => 'tar', 'TAR374G0164' => 'tar', 'TAR622G0165' => 'tar', 'TAR626G0929' => 'tar', 'TAR629G2155' => 'tar', 'THA.LOC104805282' => 'tha', 'THA.LOC104805363' => 'tha', 'THA.LOC104808968' => 'tha', 'THA.LOC104821093' => 'tha', 'THA.LOC104823953' => 'tha', 'THA.LOC104825562' => 'tha', 'THA.LOC104825665' => 'tha', 'Thecc.02G261400' => 'tca', 'Thecc.04G019200' => 'tca', 'Thecc.09G130400' => 'tca', 'Thhalv10004374m.g' => 'esa', 'Thhalv10007850m.g' => 'esa', 'Thhalv10013782m.g' => 'esa', 'Thhalv10018686m.g' => 'esa', 'Thhalv10020899m.g' => 'esa', 'Thhalv10022755m.g' => 'esa', 'TPR.G23851' => 'tpr', 'TPR.G26500' => 'tpr', 'TPR.G27267' => 'tpr', 'TPR.G32001' => 'tpr', 'TPR.G6251' => 'tpr', 'TPR.G8167' => 'tpr', 'TWI12G1330' => 'twi', 'TWI18G1239' => 'twi', 'TWI34G0979' => 'twi', 'TWI36G0670' => 'twi', 'TWI36G0707' => 'twi', 'TWI56G0233' => 'twi', 'TWI75G1809' => 'twi', 'unitig_21.g20874' => 'ugi', 'unitig_26.g10343' => 'ugi', 'unitig_46.g18392' => 'ugi', 'unitig_52.g17178' => 'ugi', 'unitig_8.g2934' => 'ugi', 'vmacro01122' => 'vma', 'vmacro05875' => 'vma', 'vmacro06147' => 'vma', 'vmacro16191' => 'vma', 'vmacro18293' => 'vma', 'VMungo0251G3707' => 'vmu', 'VMungo0464G1521' => 'vmu', 'VMungo1215G0205' => 'vmu', 'VMungo1383G2484' => 'vmu', 'Zm00001eb079610' => 'zma', 'Zm00001eb135990' => 'zma', 'Zm00001eb183710' => 'zma', 'Zm00001eb246020' => 'zma' ) $gf_id = 'HOM05D001124' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001124' ) $data_identifier = 'HOM05D001124' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 6, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 7, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 21, 'bol' => (int) 10, 'bra' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 6, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 9, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 21, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 8, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 10, 'lsa' => (int) 8, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 8, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 9, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb246020' $species_info = array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ) $local_species = 'ama' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001124', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '548', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02520' => 'bna', 'A03p06630' => 'bna', 'A05p44460' => 'bna', 'A06p08710' => 'bna', 'A06p41090' => 'bna', 'A07p32320' => 'bna', 'A08p32520' => 'bna', 'A09p10360' => 'bna', 'A10p24080' => 'bna', 'Aa31LG11G15250' => 'aar', 'Aa31LG1G1800' => 'aar', 'Aa31LG2G5120' => 'aar', 'Aa31LG2G6070' => 'aar', 'Aa31LG5G10770' => 'aar', 'Aa31sc61G90' => 'aar', 'Actinidia01352' => 'ach', 'Actinidia05983' => 'ach', 'Actinidia08133' => 'ach', 'Actinidia15101' => 'ach', 'Actinidia26379' => 'ach', 'Actinidia35778' => 'ach', 'Actinidia36123' => 'ach', 'Actinidia37436' => 'ach', 'Actinidia38730' => 'ach', 'Ah.02g128210' => 'amhyb', 'Ah.03g132990' => 'amhyb', 'Ah.14g079410' => 'amhyb', 'AL1G24640' => 'aly', 'AL2G26680' => 'aly', 'AL3G10530' => 'aly', 'AL3G45230' => 'aly', 'AL5G15230' => 'aly', 'AL5G16960' => 'aly', 'AL6G25210' => 'aly', 'Aqoxy2G00441' => 'aox', 'Aqoxy3G01236' => 'aox', 'Aqoxy5G03746' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3RQ047' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C7GMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9C8JER' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MBL6KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YXCZ83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZANX40' => 'arhy', 'AT1G12990' => 'ath', 'AT1G67880' => 'ath', 'AT2G13290' => 'ath', 'AT3G01620' => 'ath', 'AT3G26445' => 'ath', 'AT3G27540' => 'ath', 'AT5G14480' => 'ath', 'ATR0824G026' => 'atr', 'ATR1098G019' => 'atr', 'Atru.chr11.2145' => 'acertr', 'Atru.chr2.3636' => 'acertr', 'Atru.chr2.3644' => 'acertr', 'Atru.chr6.2422' => 'acertr', 'Atru.chr7.1112' => 'acertr', 'AUR62005469' => 'cqu', 'AUR62011166' => 'cqu', 'AUR62013319' => 'cqu', 'AUR62024273' => 'cqu', 'AUR62028420' => 'cqu', 'AUR62041942' => 'cqu', 'BcaB01g04969' => 'bca', 'BcaB01g06371' => 'bca', 'BcaB02g11494' => 'bca', 'BcaB03g15382' => 'bca', 'BcaB08g36994' => 'bca', 'BcaC03g13477' => 'bca', 'BcaC03g13478' => 'bca', 'BcaC03g13480' => 'bca', 'BcaC03g13481' => 'bca', 'BcaC03g13486' => 'bca', 'BcaC04g19031' => 'bca', 'BcaC04g23085' => 'bca', 'BcaC05g25094' => 'bca', 'BcaC05g25096' => 'bca', 'BcaC05g25138' => 'bca', 'BcaC05g30416' => 'bca', 'BcaC05g30455' => 'bca', 'BcaC06g30979' => 'bca', 'BcaC06g33805' => 'bca', 'BcaC08g46021' => 'bca', 'BcaNung03154' => 'bca', 'BolC2t06623H' => 'bol', 'BolC2t06632H' => 'bol', 'BolC2t06635H' => 'bol', 'BolC2t06638H' => 'bol', 'BolC3t13266H' => 'bol', 'BolC5t29776H' => 'bol', 'BolC6t38912H' => 'bol', 'BolC7t44183H' => 'bol', 'BolC9t54123H' => 'bol', 'BolC9t59107H' => 'bol', 'BraA02t05221Z' => 'bra', 'BraA03t09996Z' => 'bra', 'BraA05t23210Z' => 'bra', 'BraA06t24068Z' => 'bra', 'BraA06t27032Z' => 'bra', 'BraA08t35176Z' => 'bra', 'BraA09t36680Z' => 'bra', 'BraA10t44471Z' => 'bra', 'C02p06760' => 'bna', 'C02p06890' => 'bna', 'C02p07010' => 'bna', 'C03p07660' => 'bna', 'C05p10300' => 'bna', 'C06p38150' => 'bna', 'C07p36650' => 'bna', 'C08p15770' => 'bna', 'C09p12300' => 'bna', 'C09p62700' => 'bna', 'C09p75040' => 'bna', 'CAN.G13.1' => 'can', 'CAN.G138.4' => 'can', 'CAN.G44.6' => 'can', 'CAN.G473.19' => 'can', 'CANSAT01G0835' => 'cansat', 'CANSAT11G0246' => 'cansat', 'CANSAT11G1766' => 'cansat', 'CANSAT64G1954' => 'cansat', 'CARHR013330' => 'chi', 'CARHR060530' => 'chi', 'CARHR075300' => 'chi', 'CARHR105120' => 'chi', 'CARHR148910' => 'chi', 'CARHR198830' => 'chi', 'Carub.0001s1275' => 'cru', 'Carub.0002s1437' => 'cru', 'Carub.0003s0044' => 'cru', 'Carub.0003s2787' => 'cru', 'Carub.0005s0597' => 'cru', 'Carub.0006s1266' => 'cru', 'Ca_06935_v3' => 'car', 'Ca_13559_v3' => 'car', 'Ca_16941_v3' => 'car', 'Ca_16960_v3' => 'car', 'Ca_17775_v3' => 'car', 'Ca_30464_v3' => 'car', 'Cc06_g08160' => 'ccan', 'Cc07_g01520' => 'ccan', 'Cc11_g15810' => 'ccan', 'CDE02G2840' => 'cde', 'CDE03G0093' => 'cde', 'CDE04G2127' => 'cde', 'CDE07G1857' => 'cde', 'CDE09G1246' => 'cde', 'Cfa003412' => 'cfa', 'Cfa007341' => 'cfa', 'Cfa009220' => 'cfa', 'Ciclev10008737m.g' => 'ccl', 'Ciclev10015565m.g' => 'ccl', 'Ciclev10031761m.g' => 'ccl', 'CiPaw.03G045300' => 'cil', 'CiPaw.03G247200' => 'cil', 'CiPaw.04G029500' => 'cil', 'CiPaw.04G174000' => 'cil', 'CiPaw.05G181200' => 'cil', 'CiPaw.06G067100' => 'cil', 'ClCG05G025800' => 'cla', 'ClCG06G011400' => 'cla', 'ClCG09G019360' => 'cla', 'COL.COLO4_04827' => 'col', 'COL.COLO4_29170' => 'col', 'COL.COLO4_35131' => 'col', 'COL.COLO4_35132' => 'col', 'Cpa.g.sc33.32' => 'cpa', 'Cpa.g.sc46.29' => 'cpa', 'Cpa.g.sc796.1' => 'cpa', 'CsaV3_1G030420' => 'csa', 'CsaV3_5G027050' => 'csa', 'CsaV3_5G031040' => 'csa', 'CsaV3_UNG023130' => 'csa', 'CSS0007726' => 'camsi', 'CSS0016433' => 'camsi', 'CSS0017656' => 'camsi', 'CSS0025364' => 'camsi', 'CSS0027582' => 'camsi', 'CSS0047288' => 'camsi', 'CSS0049950' => 'camsi', 'DCAR_003843' => 'dca', 'DCAR_007052' => 'dca', 'DCAR_020884' => 'dca', 'DCAR_021730' => 'dca', 'DCAR_024423' => 'dca', 'DCAR_026509' => 'dca', 'DCAR_031158' => 'dca', 'Dinv14728' => 'din', 'Dinv15219' => 'din', 'Dinv25728' => 'din', 'Dinv33428' => 'din', 'Dinv36489' => 'din', 'Dinv41486' => 'din', 'Duzib147G0469' => 'dzi', 'Duzib168G0060' => 'dzi', 'Duzib187G1215' => 'dzi', 'Duzib248G0692' => 'dzi', 'Duzib251G0767' => 'dzi', 'Duzib264G0446' => 'dzi', 'Duzib268G0691' => 'dzi', 'ECA232G4767' => 'eca', 'ECA233G2838' => 'eca', 'ECA234G0391' => 'eca', 'ECA234G0857' => 'eca', 'ECA236G1593' => 'eca', 'ECA238G0565' => 'eca', 'ECA246G1027' => 'eca', 'ECA246G3223' => 'eca', 'ECA246G3470' => 'eca', 'EL10Ac6g13829' => 'bvu', 'EL10Ac6g14093' => 'bvu', 'EL10Ac8g18707' => 'bvu', 'Eucgr.C01369' => 'egr', 'Eucgr.H02492' => 'egr', 'Eucgr.I01733' => 'egr', 'Eucgr.J02255' => 'egr', 'Eucgr.J02257' => 'egr', 'Eucgr.J02258' => 'egr', 'FAN02G1601' => 'fan', 'FAN03G1586' => 'fan', 'FAN03G2986' => 'fan', 'FAN05G4837' => 'fan', 'FAN06G0146' => 'fan', 'FAN07G0858' => 'fan', 'FAN09G3179' => 'fan', 'FAN10G0669' => 'fan', 'FAN12G2358' => 'fan', 'FAN14G4198' => 'fan', 'FAN14G5112' => 'fan', 'FAN17G0342' => 'fan', 'FAN19G0342' => 'fan', 'FAN19G0962' => 'fan', 'FAN19G1101' => 'fan', 'FAN19G1872' => 'fan', 'FAN22G0356' => 'fan', 'FAN23G0744' => 'fan', 'FAN23G1914' => 'fan', 'FAN26G0032' => 'fan', 'FAN28G0625' => 'fan', 'FvH4_1g02710' => 'fve', 'FvH4_1g02720' => 'fve', 'FvH4_4g25670' => 'fve', 'FvH4_6g51700' => 'fve', 'FvH4_7g20170' => 'fve', 'Glyma.05G175000' => 'gma', 'Glyma.08G132300' => 'gma', 'Glyma.11G243000' => 'gma', 'Glyma.13G158900' => 'gma', 'Glyma.17G112400' => 'gma', 'Glyma.18G014100' => 'gma', 'Glyma.19G003100' => 'gma', 'Glyma.19G056500' => 'gma', 'Gohir.A01G158900' => 'ghi', 'Gohir.A05G312600' => 'ghi', 'Gohir.A05G354900' => 'ghi', 'Gohir.A07G037200' => 'ghi', 'Gohir.A09G030000' => 'ghi', 'Gohir.A12G145200' => 'ghi', 'Gohir.D01G151500' => 'ghi', 'Gohir.D04G058300' => 'ghi', 'Gohir.D05G314100' => 'ghi', 'Gohir.D07G041400' => 'ghi', 'Gohir.D09G029700' => 'ghi', 'Gohir.D12G149700' => 'ghi', 'Gorai.001G043800' => 'gra', 'Gorai.002G187800' => 'gra', 'Gorai.006G034700' => 'gra', 'Gorai.008G161200' => 'gra', 'Gorai.009G335700' => 'gra', 'Gorai.012G065000' => 'gra', 'GSVIVG01000535001' => 'vvi', 'GSVIVG01015572001' => 'vvi', 'GSVIVG01032386001' => 'vvi', 'HanXRQChr05g0138531' => 'han', 'HanXRQChr06g0174391' => 'han', 'HanXRQChr07g0199021' => 'han', 'HanXRQChr08g0208211' => 'han', 'HanXRQChr09g0255471' => 'han', 'HanXRQChr10g0315791' => 'han', 'HanXRQChr12g0371991' => 'han', 'HanXRQChr15g0475251' => 'han', 'HanXRQChr17g0540001' => 'han', 'HanXRQChr17g0548631' => 'han', 'HanXRQChr17g0569561' => 'han', 'Haze_12256' => 'cav', 'Haze_14756' => 'cav', 'Haze_25528' => 'cav', 'Hma1.2p1_0079F.1_g041020' => 'hma', 'Hma1.2p1_0818F.1_g223260' => 'hma', 'Hma1.2p1_1747F.1_g300530' => 'hma', 'HPP92_004607' => 'vpl', 'HPP92_004608' => 'vpl', 'HPP92_006181' => 'vpl', 'HPP92_012192' => 'vpl', 'HPP92_015680' => 'vpl', 'HPP92_020249' => 'vpl', 'HPP92_021376' => 'vpl', 'HPP92_024275' => 'vpl', 'Hund06031' => 'sun', 'Hund25391' => 'sun', 'Lalb_Chr07g0185371' => 'lal', 'Lalb_Chr07g0185381' => 'lal', 'Lalb_Chr12g0204011' => 'lal', 'Lalb_Chr13g0301671' => 'lal', 'Lalb_Chr14g0362851' => 'lal', 'Lalb_Chr24g0403581' => 'lal', 'Lj1g0000233' => 'lja', 'Lj2g0018120' => 'lja', 'Lj3C621T0' => 'lonja', 'Lj3P1059T14' => 'lonja', 'Lj3P611T9' => 'lonja', 'Lj3P614T13' => 'lonja', 'Lj3P615T5' => 'lonja', 'Lj4g0012315' => 'lja', 'Lj4g0026182' => 'lja', 'Lj6P813T16' => 'lonja', 'Lj7C427T7' => 'lonja', 'Lj7C427T8' => 'lonja', 'Lj7P600T41' => 'lonja', 'Lju41C42G17' => 'lonja', 'Lsat_1_v5_gn_0_47300' => 'lsa', 'Lsat_1_v5_gn_2_91280' => 'lsa', 'Lsat_1_v5_gn_3_30561' => 'lsa', 'Lsat_1_v5_gn_4_184321' => 'lsa', 'Lsat_1_v5_gn_4_4041' => 'lsa', 'Lsat_1_v5_gn_5_92000' => 'lsa', 'Lsat_1_v5_gn_8_152940' => 'lsa', 'Lsat_1_v5_gn_8_62401' => 'lsa', 'Manes.06G055900' => 'mes', 'Manes.12G022200' => 'mes', 'Manes.13G023300' => 'mes', 'Manes.14G115000' => 'mes', 'Manes.15G151700' => 'mes', 'Manes.17G111300' => 'mes', 'Mapoly0226s0009' => 'mpo', 'MBI02_g25363_MAGBIO' => 'mbi', 'MBI06_g00027_MAGBIO' => 'mbi', 'MBI10_g13034_MAGBIO' => 'mbi', 'MD09G1023400' => 'mdo', 'MD13G1100100' => 'mdo', 'MD15G1169200' => 'mdo', 'MD16G1101100' => 'mdo', 'MD17G1022900' => 'mdo', 'Medtr3g096150' => 'mtr', 'Medtr4g115070' => 'mtr', 'Medtr7g033325' => 'mtr', 'Medtr8g089840' => 'mtr', 'MELO3C010319.2' => 'cme', 'MELO3C011944.2' => 'cme', 'MELO3C021589.2' => 'cme', 'Migut.E00207' => 'egut', 'Migut.H00067' => 'egut', 'Migut.K00433' => 'egut', 'Migut.K00606' => 'egut', 'Migut.K01410' => 'egut', 'MSTRG.13347' => 'ama', 'MSTRG.24045' => 'ama', 'MSTRG.2428' => 'ama', 'MSTRG.26410' => 'ama', 'MSTRG.3139' => 'ama', 'MSTRG.3286' => 'ama', 'MSTRG.563' => 'ama', 'MSTRG.7941' => 'ama', 'Nitab4.5_0000028g0060' => 'nta', 'Nitab4.5_0000065g0260' => 'nta', 'Nitab4.5_0000112g0060' => 'nta', 'Nitab4.5_0000489g0120' => 'nta', 'Nitab4.5_0001776g0050' => 'nta', 'Nitab4.5_0001854g0010' => 'nta', 'Nitab4.5_0001860g0020' => 'nta', 'Nitab4.5_0004352g0010' => 'nta', 'Nitab4.5_0008716g0020' => 'nta', 'Nitab4.5_0008922g0010' => 'nta', 'Nn3g16693' => 'nnu', 'Nn4g22596' => 'nnu', 'Nn7g37639' => 'nnu', 'Oeu001701.1' => 'oeu', 'Oeu018149.1' => 'oeu', 'Oeu026220.1' => 'oeu', 'Oeu038635.1' => 'oeu', 'Oeu049176.1' => 'oeu', 'Oeu056706.1' => 'oeu', 'Oeu056937.1' => 'oeu', 'Oeu057540.1' => 'oeu', 'Os02g0594900' => 'osa', 'Os02g0595100' => 'osa', 'Os04g0477500' => 'osa', 'Os12g0611900' => 'osa', 'Peaxi162Scf00076g00020' => 'pax', 'Peaxi162Scf00128g00217' => 'pax', 'Peaxi162Scf00129g01640' => 'pax', 'Peaxi162Scf00669g00007' => 'pax', 'Peaxi162Scf00700g00421' => 'pax', 'Peaxi162Scf00801g00038' => 'pax', 'Peaxi162Scf00891g00025' => 'pax', 'PGR083G0909' => 'pgr', 'PGR119G1005' => 'pgr', 'PGR142G2236' => 'pgr', 'PGR142G3388' => 'pgr', 'PGSC0003DMG400004514' => 'stu', 'PGSC0003DMG400012635' => 'stu', 'PGSC0003DMG400015730' => 'stu', 'PGSC0003DMG400018611' => 'stu', 'PGSC0003DMG400030897' => 'stu', 'Phvul.001G254800' => 'pvu', 'Phvul.002G260100' => 'pvu', 'Phvul.003G167600' => 'pvu', 'Phvul.004G005100' => 'pvu', 'Potri.001G343600' => 'ptr', 'Potri.006G066700' => 'ptr', 'Potri.008G186000' => 'ptr', 'Potri.010G046900' => 'ptr', 'Potri.018G127900' => 'ptr', 'Pp3c20_17750' => 'ppa', 'Pp3c24_4380' => 'ppa', 'Prupe.1G245800' => 'ppe', 'Prupe.3G293400' => 'ppe', 'Prupe.7G247400' => 'ppe', 'Psat0s145g0120' => 'psa', 'Psat0s595g0040' => 'psa', 'Psat0s595g0120' => 'psa', 'Psat3g175040' => 'psa', 'Psat7g058120' => 'psa', 'PSO017G0428' => 'pso', 'PSO063G7510' => 'pso', 'PSO067G0046' => 'pso', 'PSO478G1073' => 'pso', 'PSO675G3677' => 'pso', 'PSO675G6558' => 'pso', 'PSO675G7520' => 'pso', 'PSO675G8959' => 'pso', 'QL02p074089' => 'qlo', 'QL02p089614' => 'qlo', 'QL03p057736' => 'qlo', 'RcHm_v2.0_Chr1g0364131' => 'rch', 'RcHm_v2.0_Chr2g0087801' => 'rch', 'RcHm_v2.0_Chr2g0087821' => 'rch', 'RcHm_v2.0_Chr2g0173231' => 'rch', 'RcHm_v2.0_Chr4g0433111' => 'rch', 'Rhsim03G0250300' => 'rsi', 'Rhsim08G0048400' => 'rsi', 'Rhsim10G0014800' => 'rsi', 'Rhsim12G0040100' => 'rsi', 'Rhsim12G0109700' => 'rsi', 'Sabra06G0049600' => 'sbr', 'Sabra08G0141000' => 'sbr', 'Sabra10G0021400' => 'sbr', 'Sabra16G0222900' => 'sbr', 'Sabra18G0108600' => 'sbr', 'SalBow1G0433' => 'sbo', 'SalBow1G2038' => 'sbo', 'SalBow1G5003' => 'sbo', 'SalBow7G1197' => 'sbo', 'SalBow8G3506' => 'sbo', 'Sc03g0007300' => 'sci', 'Sc11g0000950' => 'sci', 'Sc14g0008750' => 'sci', 'Sc18g0000420' => 'sci', 'Sed0006754' => 'sed', 'Sed0008741' => 'sed', 'Sed0017172' => 'sed', 'Sed0018925' => 'sed', 'Sed0023326' => 'sed', 'Sed0025909' => 'sed', 'SEGI_05333' => 'sgi', 'SEGI_10362' => 'sgi', 'SEGI_13380' => 'sgi', 'SEGI_24306' => 'sgi', 'SEGI_29077' => 'sgi', 'SEGI_29095' => 'sgi', 'SEGI_36534' => 'sgi', 'SEGI_37506' => 'sgi', 'SEGI_38321' => 'sgi', 'SGA_v2.0_scaffold307G48031' => 'sas', 'SGA_v2.0_scaffold47G17507' => 'sas', 'SGA_v2.0_scaffold63G21736' => 'sas', 'SGA_v2.0_scaffold87G27070' => 'sas', 'SHI17794' => 'shi', 'SHI28851' => 'shi', 'SMO165G0155' => 'smo', 'SMO340G0217' => 'smo', 'SMO367G1210' => 'smo', 'Solyc02g093430.3' => 'sly', 'Solyc05g013580.4' => 'sly', 'Solyc07g008030.3' => 'sly', 'Solyc12g035470.2' => 'sly', 'Sopen02g038020' => 'spe', 'Sopen05g008490' => 'spe', 'Sopen07g003910' => 'spe', 'Sopen12g015240' => 'spe', 'Sp1g11550' => 'spa', 'Sp2g16710' => 'spa', 'Sp3g00430' => 'spa', 'Sp3g26780' => 'spa', 'Sp5g22900' => 'spa', 'Sp6g29530' => 'spa', 'TAR371G0794' => 'tar', 'TAR374G0164' => 'tar', 'TAR622G0165' => 'tar', 'TAR626G0929' => 'tar', 'TAR629G2155' => 'tar', 'THA.LOC104805282' => 'tha', 'THA.LOC104805363' => 'tha', 'THA.LOC104808968' => 'tha', 'THA.LOC104821093' => 'tha', 'THA.LOC104823953' => 'tha', 'THA.LOC104825562' => 'tha', 'THA.LOC104825665' => 'tha', 'Thecc.02G261400' => 'tca', 'Thecc.04G019200' => 'tca', 'Thecc.09G130400' => 'tca', 'Thhalv10004374m.g' => 'esa', 'Thhalv10007850m.g' => 'esa', 'Thhalv10013782m.g' => 'esa', 'Thhalv10018686m.g' => 'esa', 'Thhalv10020899m.g' => 'esa', 'Thhalv10022755m.g' => 'esa', 'TPR.G23851' => 'tpr', 'TPR.G26500' => 'tpr', 'TPR.G27267' => 'tpr', 'TPR.G32001' => 'tpr', 'TPR.G6251' => 'tpr', 'TPR.G8167' => 'tpr', 'TWI12G1330' => 'twi', 'TWI18G1239' => 'twi', 'TWI34G0979' => 'twi', 'TWI36G0670' => 'twi', 'TWI36G0707' => 'twi', 'TWI56G0233' => 'twi', 'TWI75G1809' => 'twi', 'unitig_21.g20874' => 'ugi', 'unitig_26.g10343' => 'ugi', 'unitig_46.g18392' => 'ugi', 'unitig_52.g17178' => 'ugi', 'unitig_8.g2934' => 'ugi', 'vmacro01122' => 'vma', 'vmacro05875' => 'vma', 'vmacro06147' => 'vma', 'vmacro16191' => 'vma', 'vmacro18293' => 'vma', 'VMungo0251G3707' => 'vmu', 'VMungo0464G1521' => 'vmu', 'VMungo1215G0205' => 'vmu', 'VMungo1383G2484' => 'vmu', 'Zm00001eb079610' => 'zma', 'Zm00001eb135990' => 'zma', 'Zm00001eb183710' => 'zma', 'Zm00001eb246020' => 'zma' ), 'gf_id' => 'HOM05D001124', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001124' ), 'data_identifier' => 'HOM05D001124', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001124', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '548', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02520' => 'bna', 'A03p06630' => 'bna', 'A05p44460' => 'bna', 'A06p08710' => 'bna', 'A06p41090' => 'bna', 'A07p32320' => 'bna', 'A08p32520' => 'bna', 'A09p10360' => 'bna', 'A10p24080' => 'bna', 'Aa31LG11G15250' => 'aar', 'Aa31LG1G1800' => 'aar', 'Aa31LG2G5120' => 'aar', 'Aa31LG2G6070' => 'aar', 'Aa31LG5G10770' => 'aar', 'Aa31sc61G90' => 'aar', 'Actinidia01352' => 'ach', 'Actinidia05983' => 'ach', 'Actinidia08133' => 'ach', 'Actinidia15101' => 'ach', 'Actinidia26379' => 'ach', 'Actinidia35778' => 'ach', 'Actinidia36123' => 'ach', 'Actinidia37436' => 'ach', 'Actinidia38730' => 'ach', 'Ah.02g128210' => 'amhyb', 'Ah.03g132990' => 'amhyb', 'Ah.14g079410' => 'amhyb', 'AL1G24640' => 'aly', 'AL2G26680' => 'aly', 'AL3G10530' => 'aly', 'AL3G45230' => 'aly', 'AL5G15230' => 'aly', 'AL5G16960' => 'aly', 'AL6G25210' => 'aly', 'Aqoxy2G00441' => 'aox', 'Aqoxy3G01236' => 'aox', 'Aqoxy5G03746' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3RQ047' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C7GMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9C8JER' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MBL6KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YXCZ83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZANX40' => 'arhy', 'AT1G12990' => 'ath', 'AT1G67880' => 'ath', 'AT2G13290' => 'ath', 'AT3G01620' => 'ath', 'AT3G26445' => 'ath', 'AT3G27540' => 'ath', 'AT5G14480' => 'ath', 'ATR0824G026' => 'atr', 'ATR1098G019' => 'atr', 'Atru.chr11.2145' => 'acertr', 'Atru.chr2.3636' => 'acertr', 'Atru.chr2.3644' => 'acertr', 'Atru.chr6.2422' => 'acertr', 'Atru.chr7.1112' => 'acertr', 'AUR62005469' => 'cqu', 'AUR62011166' => 'cqu', 'AUR62013319' => 'cqu', 'AUR62024273' => 'cqu', 'AUR62028420' => 'cqu', 'AUR62041942' => 'cqu', 'BcaB01g04969' => 'bca', 'BcaB01g06371' => 'bca', 'BcaB02g11494' => 'bca', 'BcaB03g15382' => 'bca', 'BcaB08g36994' => 'bca', 'BcaC03g13477' => 'bca', 'BcaC03g13478' => 'bca', 'BcaC03g13480' => 'bca', 'BcaC03g13481' => 'bca', 'BcaC03g13486' => 'bca', 'BcaC04g19031' => 'bca', 'BcaC04g23085' => 'bca', 'BcaC05g25094' => 'bca', 'BcaC05g25096' => 'bca', 'BcaC05g25138' => 'bca', 'BcaC05g30416' => 'bca', 'BcaC05g30455' => 'bca', 'BcaC06g30979' => 'bca', 'BcaC06g33805' => 'bca', 'BcaC08g46021' => 'bca', 'BcaNung03154' => 'bca', 'BolC2t06623H' => 'bol', 'BolC2t06632H' => 'bol', 'BolC2t06635H' => 'bol', 'BolC2t06638H' => 'bol', 'BolC3t13266H' => 'bol', 'BolC5t29776H' => 'bol', 'BolC6t38912H' => 'bol', 'BolC7t44183H' => 'bol', 'BolC9t54123H' => 'bol', 'BolC9t59107H' => 'bol', 'BraA02t05221Z' => 'bra', 'BraA03t09996Z' => 'bra', 'BraA05t23210Z' => 'bra', 'BraA06t24068Z' => 'bra', 'BraA06t27032Z' => 'bra', 'BraA08t35176Z' => 'bra', 'BraA09t36680Z' => 'bra', 'BraA10t44471Z' => 'bra', 'C02p06760' => 'bna', 'C02p06890' => 'bna', 'C02p07010' => 'bna', 'C03p07660' => 'bna', 'C05p10300' => 'bna', 'C06p38150' => 'bna', 'C07p36650' => 'bna', 'C08p15770' => 'bna', 'C09p12300' => 'bna', 'C09p62700' => 'bna', 'C09p75040' => 'bna', 'CAN.G13.1' => 'can', 'CAN.G138.4' => 'can', 'CAN.G44.6' => 'can', 'CAN.G473.19' => 'can', 'CANSAT01G0835' => 'cansat', 'CANSAT11G0246' => 'cansat', 'CANSAT11G1766' => 'cansat', 'CANSAT64G1954' => 'cansat', 'CARHR013330' => 'chi', 'CARHR060530' => 'chi', 'CARHR075300' => 'chi', 'CARHR105120' => 'chi', 'CARHR148910' => 'chi', 'CARHR198830' => 'chi', 'Carub.0001s1275' => 'cru', 'Carub.0002s1437' => 'cru', 'Carub.0003s0044' => 'cru', 'Carub.0003s2787' => 'cru', 'Carub.0005s0597' => 'cru', 'Carub.0006s1266' => 'cru', 'Ca_06935_v3' => 'car', 'Ca_13559_v3' => 'car', 'Ca_16941_v3' => 'car', 'Ca_16960_v3' => 'car', 'Ca_17775_v3' => 'car', 'Ca_30464_v3' => 'car', 'Cc06_g08160' => 'ccan', 'Cc07_g01520' => 'ccan', 'Cc11_g15810' => 'ccan', 'CDE02G2840' => 'cde', 'CDE03G0093' => 'cde', 'CDE04G2127' => 'cde', 'CDE07G1857' => 'cde', 'CDE09G1246' => 'cde', 'Cfa003412' => 'cfa', 'Cfa007341' => 'cfa', 'Cfa009220' => 'cfa', 'Ciclev10008737m.g' => 'ccl', 'Ciclev10015565m.g' => 'ccl', 'Ciclev10031761m.g' => 'ccl', 'CiPaw.03G045300' => 'cil', 'CiPaw.03G247200' => 'cil', 'CiPaw.04G029500' => 'cil', 'CiPaw.04G174000' => 'cil', 'CiPaw.05G181200' => 'cil', 'CiPaw.06G067100' => 'cil', 'ClCG05G025800' => 'cla', 'ClCG06G011400' => 'cla', 'ClCG09G019360' => 'cla', 'COL.COLO4_04827' => 'col', 'COL.COLO4_29170' => 'col', 'COL.COLO4_35131' => 'col', 'COL.COLO4_35132' => 'col', 'Cpa.g.sc33.32' => 'cpa', 'Cpa.g.sc46.29' => 'cpa', 'Cpa.g.sc796.1' => 'cpa', 'CsaV3_1G030420' => 'csa', 'CsaV3_5G027050' => 'csa', 'CsaV3_5G031040' => 'csa', 'CsaV3_UNG023130' => 'csa', 'CSS0007726' => 'camsi', 'CSS0016433' => 'camsi', 'CSS0017656' => 'camsi', 'CSS0025364' => 'camsi', 'CSS0027582' => 'camsi', 'CSS0047288' => 'camsi', 'CSS0049950' => 'camsi', 'DCAR_003843' => 'dca', 'DCAR_007052' => 'dca', 'DCAR_020884' => 'dca', 'DCAR_021730' => 'dca', 'DCAR_024423' => 'dca', 'DCAR_026509' => 'dca', 'DCAR_031158' => 'dca', 'Dinv14728' => 'din', 'Dinv15219' => 'din', 'Dinv25728' => 'din', 'Dinv33428' => 'din', 'Dinv36489' => 'din', 'Dinv41486' => 'din', 'Duzib147G0469' => 'dzi', 'Duzib168G0060' => 'dzi', 'Duzib187G1215' => 'dzi', 'Duzib248G0692' => 'dzi', 'Duzib251G0767' => 'dzi', 'Duzib264G0446' => 'dzi', 'Duzib268G0691' => 'dzi', 'ECA232G4767' => 'eca', 'ECA233G2838' => 'eca', 'ECA234G0391' => 'eca', 'ECA234G0857' => 'eca', 'ECA236G1593' => 'eca', 'ECA238G0565' => 'eca', 'ECA246G1027' => 'eca', 'ECA246G3223' => 'eca', 'ECA246G3470' => 'eca', 'EL10Ac6g13829' => 'bvu', 'EL10Ac6g14093' => 'bvu', 'EL10Ac8g18707' => 'bvu', 'Eucgr.C01369' => 'egr', 'Eucgr.H02492' => 'egr', 'Eucgr.I01733' => 'egr', 'Eucgr.J02255' => 'egr', 'Eucgr.J02257' => 'egr', 'Eucgr.J02258' => 'egr', 'FAN02G1601' => 'fan', 'FAN03G1586' => 'fan', 'FAN03G2986' => 'fan', 'FAN05G4837' => 'fan', 'FAN06G0146' => 'fan', 'FAN07G0858' => 'fan', 'FAN09G3179' => 'fan', 'FAN10G0669' => 'fan', 'FAN12G2358' => 'fan', 'FAN14G4198' => 'fan', 'FAN14G5112' => 'fan', 'FAN17G0342' => 'fan', 'FAN19G0342' => 'fan', 'FAN19G0962' => 'fan', 'FAN19G1101' => 'fan', 'FAN19G1872' => 'fan', 'FAN22G0356' => 'fan', 'FAN23G0744' => 'fan', 'FAN23G1914' => 'fan', 'FAN26G0032' => 'fan', 'FAN28G0625' => 'fan', 'FvH4_1g02710' => 'fve', 'FvH4_1g02720' => 'fve', 'FvH4_4g25670' => 'fve', 'FvH4_6g51700' => 'fve', 'FvH4_7g20170' => 'fve', 'Glyma.05G175000' => 'gma', 'Glyma.08G132300' => 'gma', 'Glyma.11G243000' => 'gma', 'Glyma.13G158900' => 'gma', 'Glyma.17G112400' => 'gma', 'Glyma.18G014100' => 'gma', 'Glyma.19G003100' => 'gma', 'Glyma.19G056500' => 'gma', 'Gohir.A01G158900' => 'ghi', 'Gohir.A05G312600' => 'ghi', 'Gohir.A05G354900' => 'ghi', 'Gohir.A07G037200' => 'ghi', 'Gohir.A09G030000' => 'ghi', 'Gohir.A12G145200' => 'ghi', 'Gohir.D01G151500' => 'ghi', 'Gohir.D04G058300' => 'ghi', 'Gohir.D05G314100' => 'ghi', 'Gohir.D07G041400' => 'ghi', 'Gohir.D09G029700' => 'ghi', 'Gohir.D12G149700' => 'ghi', 'Gorai.001G043800' => 'gra', 'Gorai.002G187800' => 'gra', 'Gorai.006G034700' => 'gra', 'Gorai.008G161200' => 'gra', 'Gorai.009G335700' => 'gra', 'Gorai.012G065000' => 'gra', 'GSVIVG01000535001' => 'vvi', 'GSVIVG01015572001' => 'vvi', 'GSVIVG01032386001' => 'vvi', 'HanXRQChr05g0138531' => 'han', 'HanXRQChr06g0174391' => 'han', 'HanXRQChr07g0199021' => 'han', 'HanXRQChr08g0208211' => 'han', 'HanXRQChr09g0255471' => 'han', 'HanXRQChr10g0315791' => 'han', 'HanXRQChr12g0371991' => 'han', 'HanXRQChr15g0475251' => 'han', 'HanXRQChr17g0540001' => 'han', 'HanXRQChr17g0548631' => 'han', 'HanXRQChr17g0569561' => 'han', 'Haze_12256' => 'cav', 'Haze_14756' => 'cav', 'Haze_25528' => 'cav', 'Hma1.2p1_0079F.1_g041020' => 'hma', 'Hma1.2p1_0818F.1_g223260' => 'hma', 'Hma1.2p1_1747F.1_g300530' => 'hma', 'HPP92_004607' => 'vpl', 'HPP92_004608' => 'vpl', 'HPP92_006181' => 'vpl', 'HPP92_012192' => 'vpl', 'HPP92_015680' => 'vpl', 'HPP92_020249' => 'vpl', 'HPP92_021376' => 'vpl', 'HPP92_024275' => 'vpl', 'Hund06031' => 'sun', 'Hund25391' => 'sun', 'Lalb_Chr07g0185371' => 'lal', 'Lalb_Chr07g0185381' => 'lal', 'Lalb_Chr12g0204011' => 'lal', 'Lalb_Chr13g0301671' => 'lal', 'Lalb_Chr14g0362851' => 'lal', 'Lalb_Chr24g0403581' => 'lal', 'Lj1g0000233' => 'lja', 'Lj2g0018120' => 'lja', 'Lj3C621T0' => 'lonja', 'Lj3P1059T14' => 'lonja', 'Lj3P611T9' => 'lonja', 'Lj3P614T13' => 'lonja', 'Lj3P615T5' => 'lonja', 'Lj4g0012315' => 'lja', 'Lj4g0026182' => 'lja', 'Lj6P813T16' => 'lonja', 'Lj7C427T7' => 'lonja', 'Lj7C427T8' => 'lonja', 'Lj7P600T41' => 'lonja', 'Lju41C42G17' => 'lonja', 'Lsat_1_v5_gn_0_47300' => 'lsa', 'Lsat_1_v5_gn_2_91280' => 'lsa', 'Lsat_1_v5_gn_3_30561' => 'lsa', 'Lsat_1_v5_gn_4_184321' => 'lsa', 'Lsat_1_v5_gn_4_4041' => 'lsa', 'Lsat_1_v5_gn_5_92000' => 'lsa', 'Lsat_1_v5_gn_8_152940' => 'lsa', 'Lsat_1_v5_gn_8_62401' => 'lsa', 'Manes.06G055900' => 'mes', 'Manes.12G022200' => 'mes', 'Manes.13G023300' => 'mes', 'Manes.14G115000' => 'mes', 'Manes.15G151700' => 'mes', 'Manes.17G111300' => 'mes', 'Mapoly0226s0009' => 'mpo', 'MBI02_g25363_MAGBIO' => 'mbi', 'MBI06_g00027_MAGBIO' => 'mbi', 'MBI10_g13034_MAGBIO' => 'mbi', 'MD09G1023400' => 'mdo', 'MD13G1100100' => 'mdo', 'MD15G1169200' => 'mdo', 'MD16G1101100' => 'mdo', 'MD17G1022900' => 'mdo', 'Medtr3g096150' => 'mtr', 'Medtr4g115070' => 'mtr', 'Medtr7g033325' => 'mtr', 'Medtr8g089840' => 'mtr', 'MELO3C010319.2' => 'cme', 'MELO3C011944.2' => 'cme', 'MELO3C021589.2' => 'cme', 'Migut.E00207' => 'egut', 'Migut.H00067' => 'egut', 'Migut.K00433' => 'egut', 'Migut.K00606' => 'egut', 'Migut.K01410' => 'egut', 'MSTRG.13347' => 'ama', 'MSTRG.24045' => 'ama', 'MSTRG.2428' => 'ama', 'MSTRG.26410' => 'ama', 'MSTRG.3139' => 'ama', 'MSTRG.3286' => 'ama', 'MSTRG.563' => 'ama', 'MSTRG.7941' => 'ama', 'Nitab4.5_0000028g0060' => 'nta', 'Nitab4.5_0000065g0260' => 'nta', 'Nitab4.5_0000112g0060' => 'nta', 'Nitab4.5_0000489g0120' => 'nta', 'Nitab4.5_0001776g0050' => 'nta', 'Nitab4.5_0001854g0010' => 'nta', 'Nitab4.5_0001860g0020' => 'nta', 'Nitab4.5_0004352g0010' => 'nta', 'Nitab4.5_0008716g0020' => 'nta', 'Nitab4.5_0008922g0010' => 'nta', 'Nn3g16693' => 'nnu', 'Nn4g22596' => 'nnu', 'Nn7g37639' => 'nnu', 'Oeu001701.1' => 'oeu', 'Oeu018149.1' => 'oeu', 'Oeu026220.1' => 'oeu', 'Oeu038635.1' => 'oeu', 'Oeu049176.1' => 'oeu', 'Oeu056706.1' => 'oeu', 'Oeu056937.1' => 'oeu', 'Oeu057540.1' => 'oeu', 'Os02g0594900' => 'osa', 'Os02g0595100' => 'osa', 'Os04g0477500' => 'osa', 'Os12g0611900' => 'osa', 'Peaxi162Scf00076g00020' => 'pax', 'Peaxi162Scf00128g00217' => 'pax', 'Peaxi162Scf00129g01640' => 'pax', 'Peaxi162Scf00669g00007' => 'pax', 'Peaxi162Scf00700g00421' => 'pax', 'Peaxi162Scf00801g00038' => 'pax', 'Peaxi162Scf00891g00025' => 'pax', 'PGR083G0909' => 'pgr', 'PGR119G1005' => 'pgr', 'PGR142G2236' => 'pgr', 'PGR142G3388' => 'pgr', 'PGSC0003DMG400004514' => 'stu', 'PGSC0003DMG400012635' => 'stu', 'PGSC0003DMG400015730' => 'stu', 'PGSC0003DMG400018611' => 'stu', 'PGSC0003DMG400030897' => 'stu', 'Phvul.001G254800' => 'pvu', 'Phvul.002G260100' => 'pvu', 'Phvul.003G167600' => 'pvu', 'Phvul.004G005100' => 'pvu', 'Potri.001G343600' => 'ptr', 'Potri.006G066700' => 'ptr', 'Potri.008G186000' => 'ptr', 'Potri.010G046900' => 'ptr', 'Potri.018G127900' => 'ptr', 'Pp3c20_17750' => 'ppa', 'Pp3c24_4380' => 'ppa', 'Prupe.1G245800' => 'ppe', 'Prupe.3G293400' => 'ppe', 'Prupe.7G247400' => 'ppe', 'Psat0s145g0120' => 'psa', 'Psat0s595g0040' => 'psa', 'Psat0s595g0120' => 'psa', 'Psat3g175040' => 'psa', 'Psat7g058120' => 'psa', 'PSO017G0428' => 'pso', 'PSO063G7510' => 'pso', 'PSO067G0046' => 'pso', 'PSO478G1073' => 'pso', 'PSO675G3677' => 'pso', 'PSO675G6558' => 'pso', 'PSO675G7520' => 'pso', 'PSO675G8959' => 'pso', 'QL02p074089' => 'qlo', 'QL02p089614' => 'qlo', 'QL03p057736' => 'qlo', 'RcHm_v2.0_Chr1g0364131' => 'rch', 'RcHm_v2.0_Chr2g0087801' => 'rch', 'RcHm_v2.0_Chr2g0087821' => 'rch', 'RcHm_v2.0_Chr2g0173231' => 'rch', 'RcHm_v2.0_Chr4g0433111' => 'rch', 'Rhsim03G0250300' => 'rsi', 'Rhsim08G0048400' => 'rsi', 'Rhsim10G0014800' => 'rsi', 'Rhsim12G0040100' => 'rsi', 'Rhsim12G0109700' => 'rsi', 'Sabra06G0049600' => 'sbr', 'Sabra08G0141000' => 'sbr', 'Sabra10G0021400' => 'sbr', 'Sabra16G0222900' => 'sbr', 'Sabra18G0108600' => 'sbr', 'SalBow1G0433' => 'sbo', 'SalBow1G2038' => 'sbo', 'SalBow1G5003' => 'sbo', 'SalBow7G1197' => 'sbo', 'SalBow8G3506' => 'sbo', 'Sc03g0007300' => 'sci', 'Sc11g0000950' => 'sci', 'Sc14g0008750' => 'sci', 'Sc18g0000420' => 'sci', 'Sed0006754' => 'sed', 'Sed0008741' => 'sed', 'Sed0017172' => 'sed', 'Sed0018925' => 'sed', 'Sed0023326' => 'sed', 'Sed0025909' => 'sed', 'SEGI_05333' => 'sgi', 'SEGI_10362' => 'sgi', 'SEGI_13380' => 'sgi', 'SEGI_24306' => 'sgi', 'SEGI_29077' => 'sgi', 'SEGI_29095' => 'sgi', 'SEGI_36534' => 'sgi', 'SEGI_37506' => 'sgi', 'SEGI_38321' => 'sgi', 'SGA_v2.0_scaffold307G48031' => 'sas', 'SGA_v2.0_scaffold47G17507' => 'sas', 'SGA_v2.0_scaffold63G21736' => 'sas', 'SGA_v2.0_scaffold87G27070' => 'sas', 'SHI17794' => 'shi', 'SHI28851' => 'shi', 'SMO165G0155' => 'smo', 'SMO340G0217' => 'smo', 'SMO367G1210' => 'smo', 'Solyc02g093430.3' => 'sly', 'Solyc05g013580.4' => 'sly', 'Solyc07g008030.3' => 'sly', 'Solyc12g035470.2' => 'sly', 'Sopen02g038020' => 'spe', 'Sopen05g008490' => 'spe', 'Sopen07g003910' => 'spe', 'Sopen12g015240' => 'spe', 'Sp1g11550' => 'spa', 'Sp2g16710' => 'spa', 'Sp3g00430' => 'spa', 'Sp3g26780' => 'spa', 'Sp5g22900' => 'spa', 'Sp6g29530' => 'spa', 'TAR371G0794' => 'tar', 'TAR374G0164' => 'tar', 'TAR622G0165' => 'tar', 'TAR626G0929' => 'tar', 'TAR629G2155' => 'tar', 'THA.LOC104805282' => 'tha', 'THA.LOC104805363' => 'tha', 'THA.LOC104808968' => 'tha', 'THA.LOC104821093' => 'tha', 'THA.LOC104823953' => 'tha', 'THA.LOC104825562' => 'tha', 'THA.LOC104825665' => 'tha', 'Thecc.02G261400' => 'tca', 'Thecc.04G019200' => 'tca', 'Thecc.09G130400' => 'tca', 'Thhalv10004374m.g' => 'esa', 'Thhalv10007850m.g' => 'esa', 'Thhalv10013782m.g' => 'esa', 'Thhalv10018686m.g' => 'esa', 'Thhalv10020899m.g' => 'esa', 'Thhalv10022755m.g' => 'esa', 'TPR.G23851' => 'tpr', 'TPR.G26500' => 'tpr', 'TPR.G27267' => 'tpr', 'TPR.G32001' => 'tpr', 'TPR.G6251' => 'tpr', 'TPR.G8167' => 'tpr', 'TWI12G1330' => 'twi', 'TWI18G1239' => 'twi', 'TWI34G0979' => 'twi', 'TWI36G0670' => 'twi', 'TWI36G0707' => 'twi', 'TWI56G0233' => 'twi', 'TWI75G1809' => 'twi', 'unitig_21.g20874' => 'ugi', 'unitig_26.g10343' => 'ugi', 'unitig_46.g18392' => 'ugi', 'unitig_52.g17178' => 'ugi', 'unitig_8.g2934' => 'ugi', 'vmacro01122' => 'vma', 'vmacro05875' => 'vma', 'vmacro06147' => 'vma', 'vmacro16191' => 'vma', 'vmacro18293' => 'vma', 'VMungo0251G3707' => 'vmu', 'VMungo0464G1521' => 'vmu', 'VMungo1215G0205' => 'vmu', 'VMungo1383G2484' => 'vmu', 'Zm00001eb079610' => 'zma', 'Zm00001eb135990' => 'zma', 'Zm00001eb183710' => 'zma', 'Zm00001eb246020' => 'zma' ) $gf_id = 'HOM05D001124' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001124' ) $data_identifier = 'HOM05D001124' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 6, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 7, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 21, 'bol' => (int) 10, 'bra' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 6, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 9, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 21, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 8, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 10, 'lsa' => (int) 8, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 8, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 9, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb246020' $species_info = array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ) $local_species = 'ama' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001124', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '548', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02520' => 'bna', 'A03p06630' => 'bna', 'A05p44460' => 'bna', 'A06p08710' => 'bna', 'A06p41090' => 'bna', 'A07p32320' => 'bna', 'A08p32520' => 'bna', 'A09p10360' => 'bna', 'A10p24080' => 'bna', 'Aa31LG11G15250' => 'aar', 'Aa31LG1G1800' => 'aar', 'Aa31LG2G5120' => 'aar', 'Aa31LG2G6070' => 'aar', 'Aa31LG5G10770' => 'aar', 'Aa31sc61G90' => 'aar', 'Actinidia01352' => 'ach', 'Actinidia05983' => 'ach', 'Actinidia08133' => 'ach', 'Actinidia15101' => 'ach', 'Actinidia26379' => 'ach', 'Actinidia35778' => 'ach', 'Actinidia36123' => 'ach', 'Actinidia37436' => 'ach', 'Actinidia38730' => 'ach', 'Ah.02g128210' => 'amhyb', 'Ah.03g132990' => 'amhyb', 'Ah.14g079410' => 'amhyb', 'AL1G24640' => 'aly', 'AL2G26680' => 'aly', 'AL3G10530' => 'aly', 'AL3G45230' => 'aly', 'AL5G15230' => 'aly', 'AL5G16960' => 'aly', 'AL6G25210' => 'aly', 'Aqoxy2G00441' => 'aox', 'Aqoxy3G01236' => 'aox', 'Aqoxy5G03746' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3RQ047' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C7GMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9C8JER' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MBL6KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YXCZ83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZANX40' => 'arhy', 'AT1G12990' => 'ath', 'AT1G67880' => 'ath', 'AT2G13290' => 'ath', 'AT3G01620' => 'ath', 'AT3G26445' => 'ath', 'AT3G27540' => 'ath', 'AT5G14480' => 'ath', 'ATR0824G026' => 'atr', 'ATR1098G019' => 'atr', 'Atru.chr11.2145' => 'acertr', 'Atru.chr2.3636' => 'acertr', 'Atru.chr2.3644' => 'acertr', 'Atru.chr6.2422' => 'acertr', 'Atru.chr7.1112' => 'acertr', 'AUR62005469' => 'cqu', 'AUR62011166' => 'cqu', 'AUR62013319' => 'cqu', 'AUR62024273' => 'cqu', 'AUR62028420' => 'cqu', 'AUR62041942' => 'cqu', 'BcaB01g04969' => 'bca', 'BcaB01g06371' => 'bca', 'BcaB02g11494' => 'bca', 'BcaB03g15382' => 'bca', 'BcaB08g36994' => 'bca', 'BcaC03g13477' => 'bca', 'BcaC03g13478' => 'bca', 'BcaC03g13480' => 'bca', 'BcaC03g13481' => 'bca', 'BcaC03g13486' => 'bca', 'BcaC04g19031' => 'bca', 'BcaC04g23085' => 'bca', 'BcaC05g25094' => 'bca', 'BcaC05g25096' => 'bca', 'BcaC05g25138' => 'bca', 'BcaC05g30416' => 'bca', 'BcaC05g30455' => 'bca', 'BcaC06g30979' => 'bca', 'BcaC06g33805' => 'bca', 'BcaC08g46021' => 'bca', 'BcaNung03154' => 'bca', 'BolC2t06623H' => 'bol', 'BolC2t06632H' => 'bol', 'BolC2t06635H' => 'bol', 'BolC2t06638H' => 'bol', 'BolC3t13266H' => 'bol', 'BolC5t29776H' => 'bol', 'BolC6t38912H' => 'bol', 'BolC7t44183H' => 'bol', 'BolC9t54123H' => 'bol', 'BolC9t59107H' => 'bol', 'BraA02t05221Z' => 'bra', 'BraA03t09996Z' => 'bra', 'BraA05t23210Z' => 'bra', 'BraA06t24068Z' => 'bra', 'BraA06t27032Z' => 'bra', 'BraA08t35176Z' => 'bra', 'BraA09t36680Z' => 'bra', 'BraA10t44471Z' => 'bra', 'C02p06760' => 'bna', 'C02p06890' => 'bna', 'C02p07010' => 'bna', 'C03p07660' => 'bna', 'C05p10300' => 'bna', 'C06p38150' => 'bna', 'C07p36650' => 'bna', 'C08p15770' => 'bna', 'C09p12300' => 'bna', 'C09p62700' => 'bna', 'C09p75040' => 'bna', 'CAN.G13.1' => 'can', 'CAN.G138.4' => 'can', 'CAN.G44.6' => 'can', 'CAN.G473.19' => 'can', 'CANSAT01G0835' => 'cansat', 'CANSAT11G0246' => 'cansat', 'CANSAT11G1766' => 'cansat', 'CANSAT64G1954' => 'cansat', 'CARHR013330' => 'chi', 'CARHR060530' => 'chi', 'CARHR075300' => 'chi', 'CARHR105120' => 'chi', 'CARHR148910' => 'chi', 'CARHR198830' => 'chi', 'Carub.0001s1275' => 'cru', 'Carub.0002s1437' => 'cru', 'Carub.0003s0044' => 'cru', 'Carub.0003s2787' => 'cru', 'Carub.0005s0597' => 'cru', 'Carub.0006s1266' => 'cru', 'Ca_06935_v3' => 'car', 'Ca_13559_v3' => 'car', 'Ca_16941_v3' => 'car', 'Ca_16960_v3' => 'car', 'Ca_17775_v3' => 'car', 'Ca_30464_v3' => 'car', 'Cc06_g08160' => 'ccan', 'Cc07_g01520' => 'ccan', 'Cc11_g15810' => 'ccan', 'CDE02G2840' => 'cde', 'CDE03G0093' => 'cde', 'CDE04G2127' => 'cde', 'CDE07G1857' => 'cde', 'CDE09G1246' => 'cde', 'Cfa003412' => 'cfa', 'Cfa007341' => 'cfa', 'Cfa009220' => 'cfa', 'Ciclev10008737m.g' => 'ccl', 'Ciclev10015565m.g' => 'ccl', 'Ciclev10031761m.g' => 'ccl', 'CiPaw.03G045300' => 'cil', 'CiPaw.03G247200' => 'cil', 'CiPaw.04G029500' => 'cil', 'CiPaw.04G174000' => 'cil', 'CiPaw.05G181200' => 'cil', 'CiPaw.06G067100' => 'cil', 'ClCG05G025800' => 'cla', 'ClCG06G011400' => 'cla', 'ClCG09G019360' => 'cla', 'COL.COLO4_04827' => 'col', 'COL.COLO4_29170' => 'col', 'COL.COLO4_35131' => 'col', 'COL.COLO4_35132' => 'col', 'Cpa.g.sc33.32' => 'cpa', 'Cpa.g.sc46.29' => 'cpa', 'Cpa.g.sc796.1' => 'cpa', 'CsaV3_1G030420' => 'csa', 'CsaV3_5G027050' => 'csa', 'CsaV3_5G031040' => 'csa', 'CsaV3_UNG023130' => 'csa', 'CSS0007726' => 'camsi', 'CSS0016433' => 'camsi', 'CSS0017656' => 'camsi', 'CSS0025364' => 'camsi', 'CSS0027582' => 'camsi', 'CSS0047288' => 'camsi', 'CSS0049950' => 'camsi', 'DCAR_003843' => 'dca', 'DCAR_007052' => 'dca', 'DCAR_020884' => 'dca', 'DCAR_021730' => 'dca', 'DCAR_024423' => 'dca', 'DCAR_026509' => 'dca', 'DCAR_031158' => 'dca', 'Dinv14728' => 'din', 'Dinv15219' => 'din', 'Dinv25728' => 'din', 'Dinv33428' => 'din', 'Dinv36489' => 'din', 'Dinv41486' => 'din', 'Duzib147G0469' => 'dzi', 'Duzib168G0060' => 'dzi', 'Duzib187G1215' => 'dzi', 'Duzib248G0692' => 'dzi', 'Duzib251G0767' => 'dzi', 'Duzib264G0446' => 'dzi', 'Duzib268G0691' => 'dzi', 'ECA232G4767' => 'eca', 'ECA233G2838' => 'eca', 'ECA234G0391' => 'eca', 'ECA234G0857' => 'eca', 'ECA236G1593' => 'eca', 'ECA238G0565' => 'eca', 'ECA246G1027' => 'eca', 'ECA246G3223' => 'eca', 'ECA246G3470' => 'eca', 'EL10Ac6g13829' => 'bvu', 'EL10Ac6g14093' => 'bvu', 'EL10Ac8g18707' => 'bvu', 'Eucgr.C01369' => 'egr', 'Eucgr.H02492' => 'egr', 'Eucgr.I01733' => 'egr', 'Eucgr.J02255' => 'egr', 'Eucgr.J02257' => 'egr', 'Eucgr.J02258' => 'egr', 'FAN02G1601' => 'fan', 'FAN03G1586' => 'fan', 'FAN03G2986' => 'fan', 'FAN05G4837' => 'fan', 'FAN06G0146' => 'fan', 'FAN07G0858' => 'fan', 'FAN09G3179' => 'fan', 'FAN10G0669' => 'fan', 'FAN12G2358' => 'fan', 'FAN14G4198' => 'fan', 'FAN14G5112' => 'fan', 'FAN17G0342' => 'fan', 'FAN19G0342' => 'fan', 'FAN19G0962' => 'fan', 'FAN19G1101' => 'fan', 'FAN19G1872' => 'fan', 'FAN22G0356' => 'fan', 'FAN23G0744' => 'fan', 'FAN23G1914' => 'fan', 'FAN26G0032' => 'fan', 'FAN28G0625' => 'fan', 'FvH4_1g02710' => 'fve', 'FvH4_1g02720' => 'fve', 'FvH4_4g25670' => 'fve', 'FvH4_6g51700' => 'fve', 'FvH4_7g20170' => 'fve', 'Glyma.05G175000' => 'gma', 'Glyma.08G132300' => 'gma', 'Glyma.11G243000' => 'gma', 'Glyma.13G158900' => 'gma', 'Glyma.17G112400' => 'gma', 'Glyma.18G014100' => 'gma', 'Glyma.19G003100' => 'gma', 'Glyma.19G056500' => 'gma', 'Gohir.A01G158900' => 'ghi', 'Gohir.A05G312600' => 'ghi', 'Gohir.A05G354900' => 'ghi', 'Gohir.A07G037200' => 'ghi', 'Gohir.A09G030000' => 'ghi', 'Gohir.A12G145200' => 'ghi', 'Gohir.D01G151500' => 'ghi', 'Gohir.D04G058300' => 'ghi', 'Gohir.D05G314100' => 'ghi', 'Gohir.D07G041400' => 'ghi', 'Gohir.D09G029700' => 'ghi', 'Gohir.D12G149700' => 'ghi', 'Gorai.001G043800' => 'gra', 'Gorai.002G187800' => 'gra', 'Gorai.006G034700' => 'gra', 'Gorai.008G161200' => 'gra', 'Gorai.009G335700' => 'gra', 'Gorai.012G065000' => 'gra', 'GSVIVG01000535001' => 'vvi', 'GSVIVG01015572001' => 'vvi', 'GSVIVG01032386001' => 'vvi', 'HanXRQChr05g0138531' => 'han', 'HanXRQChr06g0174391' => 'han', 'HanXRQChr07g0199021' => 'han', 'HanXRQChr08g0208211' => 'han', 'HanXRQChr09g0255471' => 'han', 'HanXRQChr10g0315791' => 'han', 'HanXRQChr12g0371991' => 'han', 'HanXRQChr15g0475251' => 'han', 'HanXRQChr17g0540001' => 'han', 'HanXRQChr17g0548631' => 'han', 'HanXRQChr17g0569561' => 'han', 'Haze_12256' => 'cav', 'Haze_14756' => 'cav', 'Haze_25528' => 'cav', 'Hma1.2p1_0079F.1_g041020' => 'hma', 'Hma1.2p1_0818F.1_g223260' => 'hma', 'Hma1.2p1_1747F.1_g300530' => 'hma', 'HPP92_004607' => 'vpl', 'HPP92_004608' => 'vpl', 'HPP92_006181' => 'vpl', 'HPP92_012192' => 'vpl', 'HPP92_015680' => 'vpl', 'HPP92_020249' => 'vpl', 'HPP92_021376' => 'vpl', 'HPP92_024275' => 'vpl', 'Hund06031' => 'sun', 'Hund25391' => 'sun', 'Lalb_Chr07g0185371' => 'lal', 'Lalb_Chr07g0185381' => 'lal', 'Lalb_Chr12g0204011' => 'lal', 'Lalb_Chr13g0301671' => 'lal', 'Lalb_Chr14g0362851' => 'lal', 'Lalb_Chr24g0403581' => 'lal', 'Lj1g0000233' => 'lja', 'Lj2g0018120' => 'lja', 'Lj3C621T0' => 'lonja', 'Lj3P1059T14' => 'lonja', 'Lj3P611T9' => 'lonja', 'Lj3P614T13' => 'lonja', 'Lj3P615T5' => 'lonja', 'Lj4g0012315' => 'lja', 'Lj4g0026182' => 'lja', 'Lj6P813T16' => 'lonja', 'Lj7C427T7' => 'lonja', 'Lj7C427T8' => 'lonja', 'Lj7P600T41' => 'lonja', 'Lju41C42G17' => 'lonja', 'Lsat_1_v5_gn_0_47300' => 'lsa', 'Lsat_1_v5_gn_2_91280' => 'lsa', 'Lsat_1_v5_gn_3_30561' => 'lsa', 'Lsat_1_v5_gn_4_184321' => 'lsa', 'Lsat_1_v5_gn_4_4041' => 'lsa', 'Lsat_1_v5_gn_5_92000' => 'lsa', 'Lsat_1_v5_gn_8_152940' => 'lsa', 'Lsat_1_v5_gn_8_62401' => 'lsa', 'Manes.06G055900' => 'mes', 'Manes.12G022200' => 'mes', 'Manes.13G023300' => 'mes', 'Manes.14G115000' => 'mes', 'Manes.15G151700' => 'mes', 'Manes.17G111300' => 'mes', 'Mapoly0226s0009' => 'mpo', 'MBI02_g25363_MAGBIO' => 'mbi', 'MBI06_g00027_MAGBIO' => 'mbi', 'MBI10_g13034_MAGBIO' => 'mbi', 'MD09G1023400' => 'mdo', 'MD13G1100100' => 'mdo', 'MD15G1169200' => 'mdo', 'MD16G1101100' => 'mdo', 'MD17G1022900' => 'mdo', 'Medtr3g096150' => 'mtr', 'Medtr4g115070' => 'mtr', 'Medtr7g033325' => 'mtr', 'Medtr8g089840' => 'mtr', 'MELO3C010319.2' => 'cme', 'MELO3C011944.2' => 'cme', 'MELO3C021589.2' => 'cme', 'Migut.E00207' => 'egut', 'Migut.H00067' => 'egut', 'Migut.K00433' => 'egut', 'Migut.K00606' => 'egut', 'Migut.K01410' => 'egut', 'MSTRG.13347' => 'ama', 'MSTRG.24045' => 'ama', 'MSTRG.2428' => 'ama', 'MSTRG.26410' => 'ama', 'MSTRG.3139' => 'ama', 'MSTRG.3286' => 'ama', 'MSTRG.563' => 'ama', 'MSTRG.7941' => 'ama', 'Nitab4.5_0000028g0060' => 'nta', 'Nitab4.5_0000065g0260' => 'nta', 'Nitab4.5_0000112g0060' => 'nta', 'Nitab4.5_0000489g0120' => 'nta', 'Nitab4.5_0001776g0050' => 'nta', 'Nitab4.5_0001854g0010' => 'nta', 'Nitab4.5_0001860g0020' => 'nta', 'Nitab4.5_0004352g0010' => 'nta', 'Nitab4.5_0008716g0020' => 'nta', 'Nitab4.5_0008922g0010' => 'nta', 'Nn3g16693' => 'nnu', 'Nn4g22596' => 'nnu', 'Nn7g37639' => 'nnu', 'Oeu001701.1' => 'oeu', 'Oeu018149.1' => 'oeu', 'Oeu026220.1' => 'oeu', 'Oeu038635.1' => 'oeu', 'Oeu049176.1' => 'oeu', 'Oeu056706.1' => 'oeu', 'Oeu056937.1' => 'oeu', 'Oeu057540.1' => 'oeu', 'Os02g0594900' => 'osa', 'Os02g0595100' => 'osa', 'Os04g0477500' => 'osa', 'Os12g0611900' => 'osa', 'Peaxi162Scf00076g00020' => 'pax', 'Peaxi162Scf00128g00217' => 'pax', 'Peaxi162Scf00129g01640' => 'pax', 'Peaxi162Scf00669g00007' => 'pax', 'Peaxi162Scf00700g00421' => 'pax', 'Peaxi162Scf00801g00038' => 'pax', 'Peaxi162Scf00891g00025' => 'pax', 'PGR083G0909' => 'pgr', 'PGR119G1005' => 'pgr', 'PGR142G2236' => 'pgr', 'PGR142G3388' => 'pgr', 'PGSC0003DMG400004514' => 'stu', 'PGSC0003DMG400012635' => 'stu', 'PGSC0003DMG400015730' => 'stu', 'PGSC0003DMG400018611' => 'stu', 'PGSC0003DMG400030897' => 'stu', 'Phvul.001G254800' => 'pvu', 'Phvul.002G260100' => 'pvu', 'Phvul.003G167600' => 'pvu', 'Phvul.004G005100' => 'pvu', 'Potri.001G343600' => 'ptr', 'Potri.006G066700' => 'ptr', 'Potri.008G186000' => 'ptr', 'Potri.010G046900' => 'ptr', 'Potri.018G127900' => 'ptr', 'Pp3c20_17750' => 'ppa', 'Pp3c24_4380' => 'ppa', 'Prupe.1G245800' => 'ppe', 'Prupe.3G293400' => 'ppe', 'Prupe.7G247400' => 'ppe', 'Psat0s145g0120' => 'psa', 'Psat0s595g0040' => 'psa', 'Psat0s595g0120' => 'psa', 'Psat3g175040' => 'psa', 'Psat7g058120' => 'psa', 'PSO017G0428' => 'pso', 'PSO063G7510' => 'pso', 'PSO067G0046' => 'pso', 'PSO478G1073' => 'pso', 'PSO675G3677' => 'pso', 'PSO675G6558' => 'pso', 'PSO675G7520' => 'pso', 'PSO675G8959' => 'pso', 'QL02p074089' => 'qlo', 'QL02p089614' => 'qlo', 'QL03p057736' => 'qlo', 'RcHm_v2.0_Chr1g0364131' => 'rch', 'RcHm_v2.0_Chr2g0087801' => 'rch', 'RcHm_v2.0_Chr2g0087821' => 'rch', 'RcHm_v2.0_Chr2g0173231' => 'rch', 'RcHm_v2.0_Chr4g0433111' => 'rch', 'Rhsim03G0250300' => 'rsi', 'Rhsim08G0048400' => 'rsi', 'Rhsim10G0014800' => 'rsi', 'Rhsim12G0040100' => 'rsi', 'Rhsim12G0109700' => 'rsi', 'Sabra06G0049600' => 'sbr', 'Sabra08G0141000' => 'sbr', 'Sabra10G0021400' => 'sbr', 'Sabra16G0222900' => 'sbr', 'Sabra18G0108600' => 'sbr', 'SalBow1G0433' => 'sbo', 'SalBow1G2038' => 'sbo', 'SalBow1G5003' => 'sbo', 'SalBow7G1197' => 'sbo', 'SalBow8G3506' => 'sbo', 'Sc03g0007300' => 'sci', 'Sc11g0000950' => 'sci', 'Sc14g0008750' => 'sci', 'Sc18g0000420' => 'sci', 'Sed0006754' => 'sed', 'Sed0008741' => 'sed', 'Sed0017172' => 'sed', 'Sed0018925' => 'sed', 'Sed0023326' => 'sed', 'Sed0025909' => 'sed', 'SEGI_05333' => 'sgi', 'SEGI_10362' => 'sgi', 'SEGI_13380' => 'sgi', 'SEGI_24306' => 'sgi', 'SEGI_29077' => 'sgi', 'SEGI_29095' => 'sgi', 'SEGI_36534' => 'sgi', 'SEGI_37506' => 'sgi', 'SEGI_38321' => 'sgi', 'SGA_v2.0_scaffold307G48031' => 'sas', 'SGA_v2.0_scaffold47G17507' => 'sas', 'SGA_v2.0_scaffold63G21736' => 'sas', 'SGA_v2.0_scaffold87G27070' => 'sas', 'SHI17794' => 'shi', 'SHI28851' => 'shi', 'SMO165G0155' => 'smo', 'SMO340G0217' => 'smo', 'SMO367G1210' => 'smo', 'Solyc02g093430.3' => 'sly', 'Solyc05g013580.4' => 'sly', 'Solyc07g008030.3' => 'sly', 'Solyc12g035470.2' => 'sly', 'Sopen02g038020' => 'spe', 'Sopen05g008490' => 'spe', 'Sopen07g003910' => 'spe', 'Sopen12g015240' => 'spe', 'Sp1g11550' => 'spa', 'Sp2g16710' => 'spa', 'Sp3g00430' => 'spa', 'Sp3g26780' => 'spa', 'Sp5g22900' => 'spa', 'Sp6g29530' => 'spa', 'TAR371G0794' => 'tar', 'TAR374G0164' => 'tar', 'TAR622G0165' => 'tar', 'TAR626G0929' => 'tar', 'TAR629G2155' => 'tar', 'THA.LOC104805282' => 'tha', 'THA.LOC104805363' => 'tha', 'THA.LOC104808968' => 'tha', 'THA.LOC104821093' => 'tha', 'THA.LOC104823953' => 'tha', 'THA.LOC104825562' => 'tha', 'THA.LOC104825665' => 'tha', 'Thecc.02G261400' => 'tca', 'Thecc.04G019200' => 'tca', 'Thecc.09G130400' => 'tca', 'Thhalv10004374m.g' => 'esa', 'Thhalv10007850m.g' => 'esa', 'Thhalv10013782m.g' => 'esa', 'Thhalv10018686m.g' => 'esa', 'Thhalv10020899m.g' => 'esa', 'Thhalv10022755m.g' => 'esa', 'TPR.G23851' => 'tpr', 'TPR.G26500' => 'tpr', 'TPR.G27267' => 'tpr', 'TPR.G32001' => 'tpr', 'TPR.G6251' => 'tpr', 'TPR.G8167' => 'tpr', 'TWI12G1330' => 'twi', 'TWI18G1239' => 'twi', 'TWI34G0979' => 'twi', 'TWI36G0670' => 'twi', 'TWI36G0707' => 'twi', 'TWI56G0233' => 'twi', 'TWI75G1809' => 'twi', 'unitig_21.g20874' => 'ugi', 'unitig_26.g10343' => 'ugi', 'unitig_46.g18392' => 'ugi', 'unitig_52.g17178' => 'ugi', 'unitig_8.g2934' => 'ugi', 'vmacro01122' => 'vma', 'vmacro05875' => 'vma', 'vmacro06147' => 'vma', 'vmacro16191' => 'vma', 'vmacro18293' => 'vma', 'VMungo0251G3707' => 'vmu', 'VMungo0464G1521' => 'vmu', 'VMungo1215G0205' => 'vmu', 'VMungo1383G2484' => 'vmu', 'Zm00001eb079610' => 'zma', 'Zm00001eb135990' => 'zma', 'Zm00001eb183710' => 'zma', 'Zm00001eb246020' => 'zma' ), 'gf_id' => 'HOM05D001124', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001124' ), 'data_identifier' => 'HOM05D001124', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001124', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '548', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02520' => 'bna', 'A03p06630' => 'bna', 'A05p44460' => 'bna', 'A06p08710' => 'bna', 'A06p41090' => 'bna', 'A07p32320' => 'bna', 'A08p32520' => 'bna', 'A09p10360' => 'bna', 'A10p24080' => 'bna', 'Aa31LG11G15250' => 'aar', 'Aa31LG1G1800' => 'aar', 'Aa31LG2G5120' => 'aar', 'Aa31LG2G6070' => 'aar', 'Aa31LG5G10770' => 'aar', 'Aa31sc61G90' => 'aar', 'Actinidia01352' => 'ach', 'Actinidia05983' => 'ach', 'Actinidia08133' => 'ach', 'Actinidia15101' => 'ach', 'Actinidia26379' => 'ach', 'Actinidia35778' => 'ach', 'Actinidia36123' => 'ach', 'Actinidia37436' => 'ach', 'Actinidia38730' => 'ach', 'Ah.02g128210' => 'amhyb', 'Ah.03g132990' => 'amhyb', 'Ah.14g079410' => 'amhyb', 'AL1G24640' => 'aly', 'AL2G26680' => 'aly', 'AL3G10530' => 'aly', 'AL3G45230' => 'aly', 'AL5G15230' => 'aly', 'AL5G16960' => 'aly', 'AL6G25210' => 'aly', 'Aqoxy2G00441' => 'aox', 'Aqoxy3G01236' => 'aox', 'Aqoxy5G03746' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3RQ047' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C7GMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9C8JER' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MBL6KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YXCZ83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZANX40' => 'arhy', 'AT1G12990' => 'ath', 'AT1G67880' => 'ath', 'AT2G13290' => 'ath', 'AT3G01620' => 'ath', 'AT3G26445' => 'ath', 'AT3G27540' => 'ath', 'AT5G14480' => 'ath', 'ATR0824G026' => 'atr', 'ATR1098G019' => 'atr', 'Atru.chr11.2145' => 'acertr', 'Atru.chr2.3636' => 'acertr', 'Atru.chr2.3644' => 'acertr', 'Atru.chr6.2422' => 'acertr', 'Atru.chr7.1112' => 'acertr', 'AUR62005469' => 'cqu', 'AUR62011166' => 'cqu', 'AUR62013319' => 'cqu', 'AUR62024273' => 'cqu', 'AUR62028420' => 'cqu', 'AUR62041942' => 'cqu', 'BcaB01g04969' => 'bca', 'BcaB01g06371' => 'bca', 'BcaB02g11494' => 'bca', 'BcaB03g15382' => 'bca', 'BcaB08g36994' => 'bca', 'BcaC03g13477' => 'bca', 'BcaC03g13478' => 'bca', 'BcaC03g13480' => 'bca', 'BcaC03g13481' => 'bca', 'BcaC03g13486' => 'bca', 'BcaC04g19031' => 'bca', 'BcaC04g23085' => 'bca', 'BcaC05g25094' => 'bca', 'BcaC05g25096' => 'bca', 'BcaC05g25138' => 'bca', 'BcaC05g30416' => 'bca', 'BcaC05g30455' => 'bca', 'BcaC06g30979' => 'bca', 'BcaC06g33805' => 'bca', 'BcaC08g46021' => 'bca', 'BcaNung03154' => 'bca', 'BolC2t06623H' => 'bol', 'BolC2t06632H' => 'bol', 'BolC2t06635H' => 'bol', 'BolC2t06638H' => 'bol', 'BolC3t13266H' => 'bol', 'BolC5t29776H' => 'bol', 'BolC6t38912H' => 'bol', 'BolC7t44183H' => 'bol', 'BolC9t54123H' => 'bol', 'BolC9t59107H' => 'bol', 'BraA02t05221Z' => 'bra', 'BraA03t09996Z' => 'bra', 'BraA05t23210Z' => 'bra', 'BraA06t24068Z' => 'bra', 'BraA06t27032Z' => 'bra', 'BraA08t35176Z' => 'bra', 'BraA09t36680Z' => 'bra', 'BraA10t44471Z' => 'bra', 'C02p06760' => 'bna', 'C02p06890' => 'bna', 'C02p07010' => 'bna', 'C03p07660' => 'bna', 'C05p10300' => 'bna', 'C06p38150' => 'bna', 'C07p36650' => 'bna', 'C08p15770' => 'bna', 'C09p12300' => 'bna', 'C09p62700' => 'bna', 'C09p75040' => 'bna', 'CAN.G13.1' => 'can', 'CAN.G138.4' => 'can', 'CAN.G44.6' => 'can', 'CAN.G473.19' => 'can', 'CANSAT01G0835' => 'cansat', 'CANSAT11G0246' => 'cansat', 'CANSAT11G1766' => 'cansat', 'CANSAT64G1954' => 'cansat', 'CARHR013330' => 'chi', 'CARHR060530' => 'chi', 'CARHR075300' => 'chi', 'CARHR105120' => 'chi', 'CARHR148910' => 'chi', 'CARHR198830' => 'chi', 'Carub.0001s1275' => 'cru', 'Carub.0002s1437' => 'cru', 'Carub.0003s0044' => 'cru', 'Carub.0003s2787' => 'cru', 'Carub.0005s0597' => 'cru', 'Carub.0006s1266' => 'cru', 'Ca_06935_v3' => 'car', 'Ca_13559_v3' => 'car', 'Ca_16941_v3' => 'car', 'Ca_16960_v3' => 'car', 'Ca_17775_v3' => 'car', 'Ca_30464_v3' => 'car', 'Cc06_g08160' => 'ccan', 'Cc07_g01520' => 'ccan', 'Cc11_g15810' => 'ccan', 'CDE02G2840' => 'cde', 'CDE03G0093' => 'cde', 'CDE04G2127' => 'cde', 'CDE07G1857' => 'cde', 'CDE09G1246' => 'cde', 'Cfa003412' => 'cfa', 'Cfa007341' => 'cfa', 'Cfa009220' => 'cfa', 'Ciclev10008737m.g' => 'ccl', 'Ciclev10015565m.g' => 'ccl', 'Ciclev10031761m.g' => 'ccl', 'CiPaw.03G045300' => 'cil', 'CiPaw.03G247200' => 'cil', 'CiPaw.04G029500' => 'cil', 'CiPaw.04G174000' => 'cil', 'CiPaw.05G181200' => 'cil', 'CiPaw.06G067100' => 'cil', 'ClCG05G025800' => 'cla', 'ClCG06G011400' => 'cla', 'ClCG09G019360' => 'cla', 'COL.COLO4_04827' => 'col', 'COL.COLO4_29170' => 'col', 'COL.COLO4_35131' => 'col', 'COL.COLO4_35132' => 'col', 'Cpa.g.sc33.32' => 'cpa', 'Cpa.g.sc46.29' => 'cpa', 'Cpa.g.sc796.1' => 'cpa', 'CsaV3_1G030420' => 'csa', 'CsaV3_5G027050' => 'csa', 'CsaV3_5G031040' => 'csa', 'CsaV3_UNG023130' => 'csa', 'CSS0007726' => 'camsi', 'CSS0016433' => 'camsi', 'CSS0017656' => 'camsi', 'CSS0025364' => 'camsi', 'CSS0027582' => 'camsi', 'CSS0047288' => 'camsi', 'CSS0049950' => 'camsi', 'DCAR_003843' => 'dca', 'DCAR_007052' => 'dca', 'DCAR_020884' => 'dca', 'DCAR_021730' => 'dca', 'DCAR_024423' => 'dca', 'DCAR_026509' => 'dca', 'DCAR_031158' => 'dca', 'Dinv14728' => 'din', 'Dinv15219' => 'din', 'Dinv25728' => 'din', 'Dinv33428' => 'din', 'Dinv36489' => 'din', 'Dinv41486' => 'din', 'Duzib147G0469' => 'dzi', 'Duzib168G0060' => 'dzi', 'Duzib187G1215' => 'dzi', 'Duzib248G0692' => 'dzi', 'Duzib251G0767' => 'dzi', 'Duzib264G0446' => 'dzi', 'Duzib268G0691' => 'dzi', 'ECA232G4767' => 'eca', 'ECA233G2838' => 'eca', 'ECA234G0391' => 'eca', 'ECA234G0857' => 'eca', 'ECA236G1593' => 'eca', 'ECA238G0565' => 'eca', 'ECA246G1027' => 'eca', 'ECA246G3223' => 'eca', 'ECA246G3470' => 'eca', 'EL10Ac6g13829' => 'bvu', 'EL10Ac6g14093' => 'bvu', 'EL10Ac8g18707' => 'bvu', 'Eucgr.C01369' => 'egr', 'Eucgr.H02492' => 'egr', 'Eucgr.I01733' => 'egr', 'Eucgr.J02255' => 'egr', 'Eucgr.J02257' => 'egr', 'Eucgr.J02258' => 'egr', 'FAN02G1601' => 'fan', 'FAN03G1586' => 'fan', 'FAN03G2986' => 'fan', 'FAN05G4837' => 'fan', 'FAN06G0146' => 'fan', 'FAN07G0858' => 'fan', 'FAN09G3179' => 'fan', 'FAN10G0669' => 'fan', 'FAN12G2358' => 'fan', 'FAN14G4198' => 'fan', 'FAN14G5112' => 'fan', 'FAN17G0342' => 'fan', 'FAN19G0342' => 'fan', 'FAN19G0962' => 'fan', 'FAN19G1101' => 'fan', 'FAN19G1872' => 'fan', 'FAN22G0356' => 'fan', 'FAN23G0744' => 'fan', 'FAN23G1914' => 'fan', 'FAN26G0032' => 'fan', 'FAN28G0625' => 'fan', 'FvH4_1g02710' => 'fve', 'FvH4_1g02720' => 'fve', 'FvH4_4g25670' => 'fve', 'FvH4_6g51700' => 'fve', 'FvH4_7g20170' => 'fve', 'Glyma.05G175000' => 'gma', 'Glyma.08G132300' => 'gma', 'Glyma.11G243000' => 'gma', 'Glyma.13G158900' => 'gma', 'Glyma.17G112400' => 'gma', 'Glyma.18G014100' => 'gma', 'Glyma.19G003100' => 'gma', 'Glyma.19G056500' => 'gma', 'Gohir.A01G158900' => 'ghi', 'Gohir.A05G312600' => 'ghi', 'Gohir.A05G354900' => 'ghi', 'Gohir.A07G037200' => 'ghi', 'Gohir.A09G030000' => 'ghi', 'Gohir.A12G145200' => 'ghi', 'Gohir.D01G151500' => 'ghi', 'Gohir.D04G058300' => 'ghi', 'Gohir.D05G314100' => 'ghi', 'Gohir.D07G041400' => 'ghi', 'Gohir.D09G029700' => 'ghi', 'Gohir.D12G149700' => 'ghi', 'Gorai.001G043800' => 'gra', 'Gorai.002G187800' => 'gra', 'Gorai.006G034700' => 'gra', 'Gorai.008G161200' => 'gra', 'Gorai.009G335700' => 'gra', 'Gorai.012G065000' => 'gra', 'GSVIVG01000535001' => 'vvi', 'GSVIVG01015572001' => 'vvi', 'GSVIVG01032386001' => 'vvi', 'HanXRQChr05g0138531' => 'han', 'HanXRQChr06g0174391' => 'han', 'HanXRQChr07g0199021' => 'han', 'HanXRQChr08g0208211' => 'han', 'HanXRQChr09g0255471' => 'han', 'HanXRQChr10g0315791' => 'han', 'HanXRQChr12g0371991' => 'han', 'HanXRQChr15g0475251' => 'han', 'HanXRQChr17g0540001' => 'han', 'HanXRQChr17g0548631' => 'han', 'HanXRQChr17g0569561' => 'han', 'Haze_12256' => 'cav', 'Haze_14756' => 'cav', 'Haze_25528' => 'cav', 'Hma1.2p1_0079F.1_g041020' => 'hma', 'Hma1.2p1_0818F.1_g223260' => 'hma', 'Hma1.2p1_1747F.1_g300530' => 'hma', 'HPP92_004607' => 'vpl', 'HPP92_004608' => 'vpl', 'HPP92_006181' => 'vpl', 'HPP92_012192' => 'vpl', 'HPP92_015680' => 'vpl', 'HPP92_020249' => 'vpl', 'HPP92_021376' => 'vpl', 'HPP92_024275' => 'vpl', 'Hund06031' => 'sun', 'Hund25391' => 'sun', 'Lalb_Chr07g0185371' => 'lal', 'Lalb_Chr07g0185381' => 'lal', 'Lalb_Chr12g0204011' => 'lal', 'Lalb_Chr13g0301671' => 'lal', 'Lalb_Chr14g0362851' => 'lal', 'Lalb_Chr24g0403581' => 'lal', 'Lj1g0000233' => 'lja', 'Lj2g0018120' => 'lja', 'Lj3C621T0' => 'lonja', 'Lj3P1059T14' => 'lonja', 'Lj3P611T9' => 'lonja', 'Lj3P614T13' => 'lonja', 'Lj3P615T5' => 'lonja', 'Lj4g0012315' => 'lja', 'Lj4g0026182' => 'lja', 'Lj6P813T16' => 'lonja', 'Lj7C427T7' => 'lonja', 'Lj7C427T8' => 'lonja', 'Lj7P600T41' => 'lonja', 'Lju41C42G17' => 'lonja', 'Lsat_1_v5_gn_0_47300' => 'lsa', 'Lsat_1_v5_gn_2_91280' => 'lsa', 'Lsat_1_v5_gn_3_30561' => 'lsa', 'Lsat_1_v5_gn_4_184321' => 'lsa', 'Lsat_1_v5_gn_4_4041' => 'lsa', 'Lsat_1_v5_gn_5_92000' => 'lsa', 'Lsat_1_v5_gn_8_152940' => 'lsa', 'Lsat_1_v5_gn_8_62401' => 'lsa', 'Manes.06G055900' => 'mes', 'Manes.12G022200' => 'mes', 'Manes.13G023300' => 'mes', 'Manes.14G115000' => 'mes', 'Manes.15G151700' => 'mes', 'Manes.17G111300' => 'mes', 'Mapoly0226s0009' => 'mpo', 'MBI02_g25363_MAGBIO' => 'mbi', 'MBI06_g00027_MAGBIO' => 'mbi', 'MBI10_g13034_MAGBIO' => 'mbi', 'MD09G1023400' => 'mdo', 'MD13G1100100' => 'mdo', 'MD15G1169200' => 'mdo', 'MD16G1101100' => 'mdo', 'MD17G1022900' => 'mdo', 'Medtr3g096150' => 'mtr', 'Medtr4g115070' => 'mtr', 'Medtr7g033325' => 'mtr', 'Medtr8g089840' => 'mtr', 'MELO3C010319.2' => 'cme', 'MELO3C011944.2' => 'cme', 'MELO3C021589.2' => 'cme', 'Migut.E00207' => 'egut', 'Migut.H00067' => 'egut', 'Migut.K00433' => 'egut', 'Migut.K00606' => 'egut', 'Migut.K01410' => 'egut', 'MSTRG.13347' => 'ama', 'MSTRG.24045' => 'ama', 'MSTRG.2428' => 'ama', 'MSTRG.26410' => 'ama', 'MSTRG.3139' => 'ama', 'MSTRG.3286' => 'ama', 'MSTRG.563' => 'ama', 'MSTRG.7941' => 'ama', 'Nitab4.5_0000028g0060' => 'nta', 'Nitab4.5_0000065g0260' => 'nta', 'Nitab4.5_0000112g0060' => 'nta', 'Nitab4.5_0000489g0120' => 'nta', 'Nitab4.5_0001776g0050' => 'nta', 'Nitab4.5_0001854g0010' => 'nta', 'Nitab4.5_0001860g0020' => 'nta', 'Nitab4.5_0004352g0010' => 'nta', 'Nitab4.5_0008716g0020' => 'nta', 'Nitab4.5_0008922g0010' => 'nta', 'Nn3g16693' => 'nnu', 'Nn4g22596' => 'nnu', 'Nn7g37639' => 'nnu', 'Oeu001701.1' => 'oeu', 'Oeu018149.1' => 'oeu', 'Oeu026220.1' => 'oeu', 'Oeu038635.1' => 'oeu', 'Oeu049176.1' => 'oeu', 'Oeu056706.1' => 'oeu', 'Oeu056937.1' => 'oeu', 'Oeu057540.1' => 'oeu', 'Os02g0594900' => 'osa', 'Os02g0595100' => 'osa', 'Os04g0477500' => 'osa', 'Os12g0611900' => 'osa', 'Peaxi162Scf00076g00020' => 'pax', 'Peaxi162Scf00128g00217' => 'pax', 'Peaxi162Scf00129g01640' => 'pax', 'Peaxi162Scf00669g00007' => 'pax', 'Peaxi162Scf00700g00421' => 'pax', 'Peaxi162Scf00801g00038' => 'pax', 'Peaxi162Scf00891g00025' => 'pax', 'PGR083G0909' => 'pgr', 'PGR119G1005' => 'pgr', 'PGR142G2236' => 'pgr', 'PGR142G3388' => 'pgr', 'PGSC0003DMG400004514' => 'stu', 'PGSC0003DMG400012635' => 'stu', 'PGSC0003DMG400015730' => 'stu', 'PGSC0003DMG400018611' => 'stu', 'PGSC0003DMG400030897' => 'stu', 'Phvul.001G254800' => 'pvu', 'Phvul.002G260100' => 'pvu', 'Phvul.003G167600' => 'pvu', 'Phvul.004G005100' => 'pvu', 'Potri.001G343600' => 'ptr', 'Potri.006G066700' => 'ptr', 'Potri.008G186000' => 'ptr', 'Potri.010G046900' => 'ptr', 'Potri.018G127900' => 'ptr', 'Pp3c20_17750' => 'ppa', 'Pp3c24_4380' => 'ppa', 'Prupe.1G245800' => 'ppe', 'Prupe.3G293400' => 'ppe', 'Prupe.7G247400' => 'ppe', 'Psat0s145g0120' => 'psa', 'Psat0s595g0040' => 'psa', 'Psat0s595g0120' => 'psa', 'Psat3g175040' => 'psa', 'Psat7g058120' => 'psa', 'PSO017G0428' => 'pso', 'PSO063G7510' => 'pso', 'PSO067G0046' => 'pso', 'PSO478G1073' => 'pso', 'PSO675G3677' => 'pso', 'PSO675G6558' => 'pso', 'PSO675G7520' => 'pso', 'PSO675G8959' => 'pso', 'QL02p074089' => 'qlo', 'QL02p089614' => 'qlo', 'QL03p057736' => 'qlo', 'RcHm_v2.0_Chr1g0364131' => 'rch', 'RcHm_v2.0_Chr2g0087801' => 'rch', 'RcHm_v2.0_Chr2g0087821' => 'rch', 'RcHm_v2.0_Chr2g0173231' => 'rch', 'RcHm_v2.0_Chr4g0433111' => 'rch', 'Rhsim03G0250300' => 'rsi', 'Rhsim08G0048400' => 'rsi', 'Rhsim10G0014800' => 'rsi', 'Rhsim12G0040100' => 'rsi', 'Rhsim12G0109700' => 'rsi', 'Sabra06G0049600' => 'sbr', 'Sabra08G0141000' => 'sbr', 'Sabra10G0021400' => 'sbr', 'Sabra16G0222900' => 'sbr', 'Sabra18G0108600' => 'sbr', 'SalBow1G0433' => 'sbo', 'SalBow1G2038' => 'sbo', 'SalBow1G5003' => 'sbo', 'SalBow7G1197' => 'sbo', 'SalBow8G3506' => 'sbo', 'Sc03g0007300' => 'sci', 'Sc11g0000950' => 'sci', 'Sc14g0008750' => 'sci', 'Sc18g0000420' => 'sci', 'Sed0006754' => 'sed', 'Sed0008741' => 'sed', 'Sed0017172' => 'sed', 'Sed0018925' => 'sed', 'Sed0023326' => 'sed', 'Sed0025909' => 'sed', 'SEGI_05333' => 'sgi', 'SEGI_10362' => 'sgi', 'SEGI_13380' => 'sgi', 'SEGI_24306' => 'sgi', 'SEGI_29077' => 'sgi', 'SEGI_29095' => 'sgi', 'SEGI_36534' => 'sgi', 'SEGI_37506' => 'sgi', 'SEGI_38321' => 'sgi', 'SGA_v2.0_scaffold307G48031' => 'sas', 'SGA_v2.0_scaffold47G17507' => 'sas', 'SGA_v2.0_scaffold63G21736' => 'sas', 'SGA_v2.0_scaffold87G27070' => 'sas', 'SHI17794' => 'shi', 'SHI28851' => 'shi', 'SMO165G0155' => 'smo', 'SMO340G0217' => 'smo', 'SMO367G1210' => 'smo', 'Solyc02g093430.3' => 'sly', 'Solyc05g013580.4' => 'sly', 'Solyc07g008030.3' => 'sly', 'Solyc12g035470.2' => 'sly', 'Sopen02g038020' => 'spe', 'Sopen05g008490' => 'spe', 'Sopen07g003910' => 'spe', 'Sopen12g015240' => 'spe', 'Sp1g11550' => 'spa', 'Sp2g16710' => 'spa', 'Sp3g00430' => 'spa', 'Sp3g26780' => 'spa', 'Sp5g22900' => 'spa', 'Sp6g29530' => 'spa', 'TAR371G0794' => 'tar', 'TAR374G0164' => 'tar', 'TAR622G0165' => 'tar', 'TAR626G0929' => 'tar', 'TAR629G2155' => 'tar', 'THA.LOC104805282' => 'tha', 'THA.LOC104805363' => 'tha', 'THA.LOC104808968' => 'tha', 'THA.LOC104821093' => 'tha', 'THA.LOC104823953' => 'tha', 'THA.LOC104825562' => 'tha', 'THA.LOC104825665' => 'tha', 'Thecc.02G261400' => 'tca', 'Thecc.04G019200' => 'tca', 'Thecc.09G130400' => 'tca', 'Thhalv10004374m.g' => 'esa', 'Thhalv10007850m.g' => 'esa', 'Thhalv10013782m.g' => 'esa', 'Thhalv10018686m.g' => 'esa', 'Thhalv10020899m.g' => 'esa', 'Thhalv10022755m.g' => 'esa', 'TPR.G23851' => 'tpr', 'TPR.G26500' => 'tpr', 'TPR.G27267' => 'tpr', 'TPR.G32001' => 'tpr', 'TPR.G6251' => 'tpr', 'TPR.G8167' => 'tpr', 'TWI12G1330' => 'twi', 'TWI18G1239' => 'twi', 'TWI34G0979' => 'twi', 'TWI36G0670' => 'twi', 'TWI36G0707' => 'twi', 'TWI56G0233' => 'twi', 'TWI75G1809' => 'twi', 'unitig_21.g20874' => 'ugi', 'unitig_26.g10343' => 'ugi', 'unitig_46.g18392' => 'ugi', 'unitig_52.g17178' => 'ugi', 'unitig_8.g2934' => 'ugi', 'vmacro01122' => 'vma', 'vmacro05875' => 'vma', 'vmacro06147' => 'vma', 'vmacro16191' => 'vma', 'vmacro18293' => 'vma', 'VMungo0251G3707' => 'vmu', 'VMungo0464G1521' => 'vmu', 'VMungo1215G0205' => 'vmu', 'VMungo1383G2484' => 'vmu', 'Zm00001eb079610' => 'zma', 'Zm00001eb135990' => 'zma', 'Zm00001eb183710' => 'zma', 'Zm00001eb246020' => 'zma' ) $gf_id = 'HOM05D001124' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001124' ) $data_identifier = 'HOM05D001124' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 6, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 7, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 21, 'bol' => (int) 10, 'bra' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 6, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 9, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 21, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 8, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 10, 'lsa' => (int) 8, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 8, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 9, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb246020' $species_info = array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ) $local_species = 'bvu' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001124', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '548', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02520' => 'bna', 'A03p06630' => 'bna', 'A05p44460' => 'bna', 'A06p08710' => 'bna', 'A06p41090' => 'bna', 'A07p32320' => 'bna', 'A08p32520' => 'bna', 'A09p10360' => 'bna', 'A10p24080' => 'bna', 'Aa31LG11G15250' => 'aar', 'Aa31LG1G1800' => 'aar', 'Aa31LG2G5120' => 'aar', 'Aa31LG2G6070' => 'aar', 'Aa31LG5G10770' => 'aar', 'Aa31sc61G90' => 'aar', 'Actinidia01352' => 'ach', 'Actinidia05983' => 'ach', 'Actinidia08133' => 'ach', 'Actinidia15101' => 'ach', 'Actinidia26379' => 'ach', 'Actinidia35778' => 'ach', 'Actinidia36123' => 'ach', 'Actinidia37436' => 'ach', 'Actinidia38730' => 'ach', 'Ah.02g128210' => 'amhyb', 'Ah.03g132990' => 'amhyb', 'Ah.14g079410' => 'amhyb', 'AL1G24640' => 'aly', 'AL2G26680' => 'aly', 'AL3G10530' => 'aly', 'AL3G45230' => 'aly', 'AL5G15230' => 'aly', 'AL5G16960' => 'aly', 'AL6G25210' => 'aly', 'Aqoxy2G00441' => 'aox', 'Aqoxy3G01236' => 'aox', 'Aqoxy5G03746' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3RQ047' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C7GMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9C8JER' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MBL6KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YXCZ83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZANX40' => 'arhy', 'AT1G12990' => 'ath', 'AT1G67880' => 'ath', 'AT2G13290' => 'ath', 'AT3G01620' => 'ath', 'AT3G26445' => 'ath', 'AT3G27540' => 'ath', 'AT5G14480' => 'ath', 'ATR0824G026' => 'atr', 'ATR1098G019' => 'atr', 'Atru.chr11.2145' => 'acertr', 'Atru.chr2.3636' => 'acertr', 'Atru.chr2.3644' => 'acertr', 'Atru.chr6.2422' => 'acertr', 'Atru.chr7.1112' => 'acertr', 'AUR62005469' => 'cqu', 'AUR62011166' => 'cqu', 'AUR62013319' => 'cqu', 'AUR62024273' => 'cqu', 'AUR62028420' => 'cqu', 'AUR62041942' => 'cqu', 'BcaB01g04969' => 'bca', 'BcaB01g06371' => 'bca', 'BcaB02g11494' => 'bca', 'BcaB03g15382' => 'bca', 'BcaB08g36994' => 'bca', 'BcaC03g13477' => 'bca', 'BcaC03g13478' => 'bca', 'BcaC03g13480' => 'bca', 'BcaC03g13481' => 'bca', 'BcaC03g13486' => 'bca', 'BcaC04g19031' => 'bca', 'BcaC04g23085' => 'bca', 'BcaC05g25094' => 'bca', 'BcaC05g25096' => 'bca', 'BcaC05g25138' => 'bca', 'BcaC05g30416' => 'bca', 'BcaC05g30455' => 'bca', 'BcaC06g30979' => 'bca', 'BcaC06g33805' => 'bca', 'BcaC08g46021' => 'bca', 'BcaNung03154' => 'bca', 'BolC2t06623H' => 'bol', 'BolC2t06632H' => 'bol', 'BolC2t06635H' => 'bol', 'BolC2t06638H' => 'bol', 'BolC3t13266H' => 'bol', 'BolC5t29776H' => 'bol', 'BolC6t38912H' => 'bol', 'BolC7t44183H' => 'bol', 'BolC9t54123H' => 'bol', 'BolC9t59107H' => 'bol', 'BraA02t05221Z' => 'bra', 'BraA03t09996Z' => 'bra', 'BraA05t23210Z' => 'bra', 'BraA06t24068Z' => 'bra', 'BraA06t27032Z' => 'bra', 'BraA08t35176Z' => 'bra', 'BraA09t36680Z' => 'bra', 'BraA10t44471Z' => 'bra', 'C02p06760' => 'bna', 'C02p06890' => 'bna', 'C02p07010' => 'bna', 'C03p07660' => 'bna', 'C05p10300' => 'bna', 'C06p38150' => 'bna', 'C07p36650' => 'bna', 'C08p15770' => 'bna', 'C09p12300' => 'bna', 'C09p62700' => 'bna', 'C09p75040' => 'bna', 'CAN.G13.1' => 'can', 'CAN.G138.4' => 'can', 'CAN.G44.6' => 'can', 'CAN.G473.19' => 'can', 'CANSAT01G0835' => 'cansat', 'CANSAT11G0246' => 'cansat', 'CANSAT11G1766' => 'cansat', 'CANSAT64G1954' => 'cansat', 'CARHR013330' => 'chi', 'CARHR060530' => 'chi', 'CARHR075300' => 'chi', 'CARHR105120' => 'chi', 'CARHR148910' => 'chi', 'CARHR198830' => 'chi', 'Carub.0001s1275' => 'cru', 'Carub.0002s1437' => 'cru', 'Carub.0003s0044' => 'cru', 'Carub.0003s2787' => 'cru', 'Carub.0005s0597' => 'cru', 'Carub.0006s1266' => 'cru', 'Ca_06935_v3' => 'car', 'Ca_13559_v3' => 'car', 'Ca_16941_v3' => 'car', 'Ca_16960_v3' => 'car', 'Ca_17775_v3' => 'car', 'Ca_30464_v3' => 'car', 'Cc06_g08160' => 'ccan', 'Cc07_g01520' => 'ccan', 'Cc11_g15810' => 'ccan', 'CDE02G2840' => 'cde', 'CDE03G0093' => 'cde', 'CDE04G2127' => 'cde', 'CDE07G1857' => 'cde', 'CDE09G1246' => 'cde', 'Cfa003412' => 'cfa', 'Cfa007341' => 'cfa', 'Cfa009220' => 'cfa', 'Ciclev10008737m.g' => 'ccl', 'Ciclev10015565m.g' => 'ccl', 'Ciclev10031761m.g' => 'ccl', 'CiPaw.03G045300' => 'cil', 'CiPaw.03G247200' => 'cil', 'CiPaw.04G029500' => 'cil', 'CiPaw.04G174000' => 'cil', 'CiPaw.05G181200' => 'cil', 'CiPaw.06G067100' => 'cil', 'ClCG05G025800' => 'cla', 'ClCG06G011400' => 'cla', 'ClCG09G019360' => 'cla', 'COL.COLO4_04827' => 'col', 'COL.COLO4_29170' => 'col', 'COL.COLO4_35131' => 'col', 'COL.COLO4_35132' => 'col', 'Cpa.g.sc33.32' => 'cpa', 'Cpa.g.sc46.29' => 'cpa', 'Cpa.g.sc796.1' => 'cpa', 'CsaV3_1G030420' => 'csa', 'CsaV3_5G027050' => 'csa', 'CsaV3_5G031040' => 'csa', 'CsaV3_UNG023130' => 'csa', 'CSS0007726' => 'camsi', 'CSS0016433' => 'camsi', 'CSS0017656' => 'camsi', 'CSS0025364' => 'camsi', 'CSS0027582' => 'camsi', 'CSS0047288' => 'camsi', 'CSS0049950' => 'camsi', 'DCAR_003843' => 'dca', 'DCAR_007052' => 'dca', 'DCAR_020884' => 'dca', 'DCAR_021730' => 'dca', 'DCAR_024423' => 'dca', 'DCAR_026509' => 'dca', 'DCAR_031158' => 'dca', 'Dinv14728' => 'din', 'Dinv15219' => 'din', 'Dinv25728' => 'din', 'Dinv33428' => 'din', 'Dinv36489' => 'din', 'Dinv41486' => 'din', 'Duzib147G0469' => 'dzi', 'Duzib168G0060' => 'dzi', 'Duzib187G1215' => 'dzi', 'Duzib248G0692' => 'dzi', 'Duzib251G0767' => 'dzi', 'Duzib264G0446' => 'dzi', 'Duzib268G0691' => 'dzi', 'ECA232G4767' => 'eca', 'ECA233G2838' => 'eca', 'ECA234G0391' => 'eca', 'ECA234G0857' => 'eca', 'ECA236G1593' => 'eca', 'ECA238G0565' => 'eca', 'ECA246G1027' => 'eca', 'ECA246G3223' => 'eca', 'ECA246G3470' => 'eca', 'EL10Ac6g13829' => 'bvu', 'EL10Ac6g14093' => 'bvu', 'EL10Ac8g18707' => 'bvu', 'Eucgr.C01369' => 'egr', 'Eucgr.H02492' => 'egr', 'Eucgr.I01733' => 'egr', 'Eucgr.J02255' => 'egr', 'Eucgr.J02257' => 'egr', 'Eucgr.J02258' => 'egr', 'FAN02G1601' => 'fan', 'FAN03G1586' => 'fan', 'FAN03G2986' => 'fan', 'FAN05G4837' => 'fan', 'FAN06G0146' => 'fan', 'FAN07G0858' => 'fan', 'FAN09G3179' => 'fan', 'FAN10G0669' => 'fan', 'FAN12G2358' => 'fan', 'FAN14G4198' => 'fan', 'FAN14G5112' => 'fan', 'FAN17G0342' => 'fan', 'FAN19G0342' => 'fan', 'FAN19G0962' => 'fan', 'FAN19G1101' => 'fan', 'FAN19G1872' => 'fan', 'FAN22G0356' => 'fan', 'FAN23G0744' => 'fan', 'FAN23G1914' => 'fan', 'FAN26G0032' => 'fan', 'FAN28G0625' => 'fan', 'FvH4_1g02710' => 'fve', 'FvH4_1g02720' => 'fve', 'FvH4_4g25670' => 'fve', 'FvH4_6g51700' => 'fve', 'FvH4_7g20170' => 'fve', 'Glyma.05G175000' => 'gma', 'Glyma.08G132300' => 'gma', 'Glyma.11G243000' => 'gma', 'Glyma.13G158900' => 'gma', 'Glyma.17G112400' => 'gma', 'Glyma.18G014100' => 'gma', 'Glyma.19G003100' => 'gma', 'Glyma.19G056500' => 'gma', 'Gohir.A01G158900' => 'ghi', 'Gohir.A05G312600' => 'ghi', 'Gohir.A05G354900' => 'ghi', 'Gohir.A07G037200' => 'ghi', 'Gohir.A09G030000' => 'ghi', 'Gohir.A12G145200' => 'ghi', 'Gohir.D01G151500' => 'ghi', 'Gohir.D04G058300' => 'ghi', 'Gohir.D05G314100' => 'ghi', 'Gohir.D07G041400' => 'ghi', 'Gohir.D09G029700' => 'ghi', 'Gohir.D12G149700' => 'ghi', 'Gorai.001G043800' => 'gra', 'Gorai.002G187800' => 'gra', 'Gorai.006G034700' => 'gra', 'Gorai.008G161200' => 'gra', 'Gorai.009G335700' => 'gra', 'Gorai.012G065000' => 'gra', 'GSVIVG01000535001' => 'vvi', 'GSVIVG01015572001' => 'vvi', 'GSVIVG01032386001' => 'vvi', 'HanXRQChr05g0138531' => 'han', 'HanXRQChr06g0174391' => 'han', 'HanXRQChr07g0199021' => 'han', 'HanXRQChr08g0208211' => 'han', 'HanXRQChr09g0255471' => 'han', 'HanXRQChr10g0315791' => 'han', 'HanXRQChr12g0371991' => 'han', 'HanXRQChr15g0475251' => 'han', 'HanXRQChr17g0540001' => 'han', 'HanXRQChr17g0548631' => 'han', 'HanXRQChr17g0569561' => 'han', 'Haze_12256' => 'cav', 'Haze_14756' => 'cav', 'Haze_25528' => 'cav', 'Hma1.2p1_0079F.1_g041020' => 'hma', 'Hma1.2p1_0818F.1_g223260' => 'hma', 'Hma1.2p1_1747F.1_g300530' => 'hma', 'HPP92_004607' => 'vpl', 'HPP92_004608' => 'vpl', 'HPP92_006181' => 'vpl', 'HPP92_012192' => 'vpl', 'HPP92_015680' => 'vpl', 'HPP92_020249' => 'vpl', 'HPP92_021376' => 'vpl', 'HPP92_024275' => 'vpl', 'Hund06031' => 'sun', 'Hund25391' => 'sun', 'Lalb_Chr07g0185371' => 'lal', 'Lalb_Chr07g0185381' => 'lal', 'Lalb_Chr12g0204011' => 'lal', 'Lalb_Chr13g0301671' => 'lal', 'Lalb_Chr14g0362851' => 'lal', 'Lalb_Chr24g0403581' => 'lal', 'Lj1g0000233' => 'lja', 'Lj2g0018120' => 'lja', 'Lj3C621T0' => 'lonja', 'Lj3P1059T14' => 'lonja', 'Lj3P611T9' => 'lonja', 'Lj3P614T13' => 'lonja', 'Lj3P615T5' => 'lonja', 'Lj4g0012315' => 'lja', 'Lj4g0026182' => 'lja', 'Lj6P813T16' => 'lonja', 'Lj7C427T7' => 'lonja', 'Lj7C427T8' => 'lonja', 'Lj7P600T41' => 'lonja', 'Lju41C42G17' => 'lonja', 'Lsat_1_v5_gn_0_47300' => 'lsa', 'Lsat_1_v5_gn_2_91280' => 'lsa', 'Lsat_1_v5_gn_3_30561' => 'lsa', 'Lsat_1_v5_gn_4_184321' => 'lsa', 'Lsat_1_v5_gn_4_4041' => 'lsa', 'Lsat_1_v5_gn_5_92000' => 'lsa', 'Lsat_1_v5_gn_8_152940' => 'lsa', 'Lsat_1_v5_gn_8_62401' => 'lsa', 'Manes.06G055900' => 'mes', 'Manes.12G022200' => 'mes', 'Manes.13G023300' => 'mes', 'Manes.14G115000' => 'mes', 'Manes.15G151700' => 'mes', 'Manes.17G111300' => 'mes', 'Mapoly0226s0009' => 'mpo', 'MBI02_g25363_MAGBIO' => 'mbi', 'MBI06_g00027_MAGBIO' => 'mbi', 'MBI10_g13034_MAGBIO' => 'mbi', 'MD09G1023400' => 'mdo', 'MD13G1100100' => 'mdo', 'MD15G1169200' => 'mdo', 'MD16G1101100' => 'mdo', 'MD17G1022900' => 'mdo', 'Medtr3g096150' => 'mtr', 'Medtr4g115070' => 'mtr', 'Medtr7g033325' => 'mtr', 'Medtr8g089840' => 'mtr', 'MELO3C010319.2' => 'cme', 'MELO3C011944.2' => 'cme', 'MELO3C021589.2' => 'cme', 'Migut.E00207' => 'egut', 'Migut.H00067' => 'egut', 'Migut.K00433' => 'egut', 'Migut.K00606' => 'egut', 'Migut.K01410' => 'egut', 'MSTRG.13347' => 'ama', 'MSTRG.24045' => 'ama', 'MSTRG.2428' => 'ama', 'MSTRG.26410' => 'ama', 'MSTRG.3139' => 'ama', 'MSTRG.3286' => 'ama', 'MSTRG.563' => 'ama', 'MSTRG.7941' => 'ama', 'Nitab4.5_0000028g0060' => 'nta', 'Nitab4.5_0000065g0260' => 'nta', 'Nitab4.5_0000112g0060' => 'nta', 'Nitab4.5_0000489g0120' => 'nta', 'Nitab4.5_0001776g0050' => 'nta', 'Nitab4.5_0001854g0010' => 'nta', 'Nitab4.5_0001860g0020' => 'nta', 'Nitab4.5_0004352g0010' => 'nta', 'Nitab4.5_0008716g0020' => 'nta', 'Nitab4.5_0008922g0010' => 'nta', 'Nn3g16693' => 'nnu', 'Nn4g22596' => 'nnu', 'Nn7g37639' => 'nnu', 'Oeu001701.1' => 'oeu', 'Oeu018149.1' => 'oeu', 'Oeu026220.1' => 'oeu', 'Oeu038635.1' => 'oeu', 'Oeu049176.1' => 'oeu', 'Oeu056706.1' => 'oeu', 'Oeu056937.1' => 'oeu', 'Oeu057540.1' => 'oeu', 'Os02g0594900' => 'osa', 'Os02g0595100' => 'osa', 'Os04g0477500' => 'osa', 'Os12g0611900' => 'osa', 'Peaxi162Scf00076g00020' => 'pax', 'Peaxi162Scf00128g00217' => 'pax', 'Peaxi162Scf00129g01640' => 'pax', 'Peaxi162Scf00669g00007' => 'pax', 'Peaxi162Scf00700g00421' => 'pax', 'Peaxi162Scf00801g00038' => 'pax', 'Peaxi162Scf00891g00025' => 'pax', 'PGR083G0909' => 'pgr', 'PGR119G1005' => 'pgr', 'PGR142G2236' => 'pgr', 'PGR142G3388' => 'pgr', 'PGSC0003DMG400004514' => 'stu', 'PGSC0003DMG400012635' => 'stu', 'PGSC0003DMG400015730' => 'stu', 'PGSC0003DMG400018611' => 'stu', 'PGSC0003DMG400030897' => 'stu', 'Phvul.001G254800' => 'pvu', 'Phvul.002G260100' => 'pvu', 'Phvul.003G167600' => 'pvu', 'Phvul.004G005100' => 'pvu', 'Potri.001G343600' => 'ptr', 'Potri.006G066700' => 'ptr', 'Potri.008G186000' => 'ptr', 'Potri.010G046900' => 'ptr', 'Potri.018G127900' => 'ptr', 'Pp3c20_17750' => 'ppa', 'Pp3c24_4380' => 'ppa', 'Prupe.1G245800' => 'ppe', 'Prupe.3G293400' => 'ppe', 'Prupe.7G247400' => 'ppe', 'Psat0s145g0120' => 'psa', 'Psat0s595g0040' => 'psa', 'Psat0s595g0120' => 'psa', 'Psat3g175040' => 'psa', 'Psat7g058120' => 'psa', 'PSO017G0428' => 'pso', 'PSO063G7510' => 'pso', 'PSO067G0046' => 'pso', 'PSO478G1073' => 'pso', 'PSO675G3677' => 'pso', 'PSO675G6558' => 'pso', 'PSO675G7520' => 'pso', 'PSO675G8959' => 'pso', 'QL02p074089' => 'qlo', 'QL02p089614' => 'qlo', 'QL03p057736' => 'qlo', 'RcHm_v2.0_Chr1g0364131' => 'rch', 'RcHm_v2.0_Chr2g0087801' => 'rch', 'RcHm_v2.0_Chr2g0087821' => 'rch', 'RcHm_v2.0_Chr2g0173231' => 'rch', 'RcHm_v2.0_Chr4g0433111' => 'rch', 'Rhsim03G0250300' => 'rsi', 'Rhsim08G0048400' => 'rsi', 'Rhsim10G0014800' => 'rsi', 'Rhsim12G0040100' => 'rsi', 'Rhsim12G0109700' => 'rsi', 'Sabra06G0049600' => 'sbr', 'Sabra08G0141000' => 'sbr', 'Sabra10G0021400' => 'sbr', 'Sabra16G0222900' => 'sbr', 'Sabra18G0108600' => 'sbr', 'SalBow1G0433' => 'sbo', 'SalBow1G2038' => 'sbo', 'SalBow1G5003' => 'sbo', 'SalBow7G1197' => 'sbo', 'SalBow8G3506' => 'sbo', 'Sc03g0007300' => 'sci', 'Sc11g0000950' => 'sci', 'Sc14g0008750' => 'sci', 'Sc18g0000420' => 'sci', 'Sed0006754' => 'sed', 'Sed0008741' => 'sed', 'Sed0017172' => 'sed', 'Sed0018925' => 'sed', 'Sed0023326' => 'sed', 'Sed0025909' => 'sed', 'SEGI_05333' => 'sgi', 'SEGI_10362' => 'sgi', 'SEGI_13380' => 'sgi', 'SEGI_24306' => 'sgi', 'SEGI_29077' => 'sgi', 'SEGI_29095' => 'sgi', 'SEGI_36534' => 'sgi', 'SEGI_37506' => 'sgi', 'SEGI_38321' => 'sgi', 'SGA_v2.0_scaffold307G48031' => 'sas', 'SGA_v2.0_scaffold47G17507' => 'sas', 'SGA_v2.0_scaffold63G21736' => 'sas', 'SGA_v2.0_scaffold87G27070' => 'sas', 'SHI17794' => 'shi', 'SHI28851' => 'shi', 'SMO165G0155' => 'smo', 'SMO340G0217' => 'smo', 'SMO367G1210' => 'smo', 'Solyc02g093430.3' => 'sly', 'Solyc05g013580.4' => 'sly', 'Solyc07g008030.3' => 'sly', 'Solyc12g035470.2' => 'sly', 'Sopen02g038020' => 'spe', 'Sopen05g008490' => 'spe', 'Sopen07g003910' => 'spe', 'Sopen12g015240' => 'spe', 'Sp1g11550' => 'spa', 'Sp2g16710' => 'spa', 'Sp3g00430' => 'spa', 'Sp3g26780' => 'spa', 'Sp5g22900' => 'spa', 'Sp6g29530' => 'spa', 'TAR371G0794' => 'tar', 'TAR374G0164' => 'tar', 'TAR622G0165' => 'tar', 'TAR626G0929' => 'tar', 'TAR629G2155' => 'tar', 'THA.LOC104805282' => 'tha', 'THA.LOC104805363' => 'tha', 'THA.LOC104808968' => 'tha', 'THA.LOC104821093' => 'tha', 'THA.LOC104823953' => 'tha', 'THA.LOC104825562' => 'tha', 'THA.LOC104825665' => 'tha', 'Thecc.02G261400' => 'tca', 'Thecc.04G019200' => 'tca', 'Thecc.09G130400' => 'tca', 'Thhalv10004374m.g' => 'esa', 'Thhalv10007850m.g' => 'esa', 'Thhalv10013782m.g' => 'esa', 'Thhalv10018686m.g' => 'esa', 'Thhalv10020899m.g' => 'esa', 'Thhalv10022755m.g' => 'esa', 'TPR.G23851' => 'tpr', 'TPR.G26500' => 'tpr', 'TPR.G27267' => 'tpr', 'TPR.G32001' => 'tpr', 'TPR.G6251' => 'tpr', 'TPR.G8167' => 'tpr', 'TWI12G1330' => 'twi', 'TWI18G1239' => 'twi', 'TWI34G0979' => 'twi', 'TWI36G0670' => 'twi', 'TWI36G0707' => 'twi', 'TWI56G0233' => 'twi', 'TWI75G1809' => 'twi', 'unitig_21.g20874' => 'ugi', 'unitig_26.g10343' => 'ugi', 'unitig_46.g18392' => 'ugi', 'unitig_52.g17178' => 'ugi', 'unitig_8.g2934' => 'ugi', 'vmacro01122' => 'vma', 'vmacro05875' => 'vma', 'vmacro06147' => 'vma', 'vmacro16191' => 'vma', 'vmacro18293' => 'vma', 'VMungo0251G3707' => 'vmu', 'VMungo0464G1521' => 'vmu', 'VMungo1215G0205' => 'vmu', 'VMungo1383G2484' => 'vmu', 'Zm00001eb079610' => 'zma', 'Zm00001eb135990' => 'zma', 'Zm00001eb183710' => 'zma', 'Zm00001eb246020' => 'zma' ), 'gf_id' => 'HOM05D001124', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001124' ), 'data_identifier' => 'HOM05D001124', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001124', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '548', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02520' => 'bna', 'A03p06630' => 'bna', 'A05p44460' => 'bna', 'A06p08710' => 'bna', 'A06p41090' => 'bna', 'A07p32320' => 'bna', 'A08p32520' => 'bna', 'A09p10360' => 'bna', 'A10p24080' => 'bna', 'Aa31LG11G15250' => 'aar', 'Aa31LG1G1800' => 'aar', 'Aa31LG2G5120' => 'aar', 'Aa31LG2G6070' => 'aar', 'Aa31LG5G10770' => 'aar', 'Aa31sc61G90' => 'aar', 'Actinidia01352' => 'ach', 'Actinidia05983' => 'ach', 'Actinidia08133' => 'ach', 'Actinidia15101' => 'ach', 'Actinidia26379' => 'ach', 'Actinidia35778' => 'ach', 'Actinidia36123' => 'ach', 'Actinidia37436' => 'ach', 'Actinidia38730' => 'ach', 'Ah.02g128210' => 'amhyb', 'Ah.03g132990' => 'amhyb', 'Ah.14g079410' => 'amhyb', 'AL1G24640' => 'aly', 'AL2G26680' => 'aly', 'AL3G10530' => 'aly', 'AL3G45230' => 'aly', 'AL5G15230' => 'aly', 'AL5G16960' => 'aly', 'AL6G25210' => 'aly', 'Aqoxy2G00441' => 'aox', 'Aqoxy3G01236' => 'aox', 'Aqoxy5G03746' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3RQ047' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C7GMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9C8JER' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MBL6KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YXCZ83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZANX40' => 'arhy', 'AT1G12990' => 'ath', 'AT1G67880' => 'ath', 'AT2G13290' => 'ath', 'AT3G01620' => 'ath', 'AT3G26445' => 'ath', 'AT3G27540' => 'ath', 'AT5G14480' => 'ath', 'ATR0824G026' => 'atr', 'ATR1098G019' => 'atr', 'Atru.chr11.2145' => 'acertr', 'Atru.chr2.3636' => 'acertr', 'Atru.chr2.3644' => 'acertr', 'Atru.chr6.2422' => 'acertr', 'Atru.chr7.1112' => 'acertr', 'AUR62005469' => 'cqu', 'AUR62011166' => 'cqu', 'AUR62013319' => 'cqu', 'AUR62024273' => 'cqu', 'AUR62028420' => 'cqu', 'AUR62041942' => 'cqu', 'BcaB01g04969' => 'bca', 'BcaB01g06371' => 'bca', 'BcaB02g11494' => 'bca', 'BcaB03g15382' => 'bca', 'BcaB08g36994' => 'bca', 'BcaC03g13477' => 'bca', 'BcaC03g13478' => 'bca', 'BcaC03g13480' => 'bca', 'BcaC03g13481' => 'bca', 'BcaC03g13486' => 'bca', 'BcaC04g19031' => 'bca', 'BcaC04g23085' => 'bca', 'BcaC05g25094' => 'bca', 'BcaC05g25096' => 'bca', 'BcaC05g25138' => 'bca', 'BcaC05g30416' => 'bca', 'BcaC05g30455' => 'bca', 'BcaC06g30979' => 'bca', 'BcaC06g33805' => 'bca', 'BcaC08g46021' => 'bca', 'BcaNung03154' => 'bca', 'BolC2t06623H' => 'bol', 'BolC2t06632H' => 'bol', 'BolC2t06635H' => 'bol', 'BolC2t06638H' => 'bol', 'BolC3t13266H' => 'bol', 'BolC5t29776H' => 'bol', 'BolC6t38912H' => 'bol', 'BolC7t44183H' => 'bol', 'BolC9t54123H' => 'bol', 'BolC9t59107H' => 'bol', 'BraA02t05221Z' => 'bra', 'BraA03t09996Z' => 'bra', 'BraA05t23210Z' => 'bra', 'BraA06t24068Z' => 'bra', 'BraA06t27032Z' => 'bra', 'BraA08t35176Z' => 'bra', 'BraA09t36680Z' => 'bra', 'BraA10t44471Z' => 'bra', 'C02p06760' => 'bna', 'C02p06890' => 'bna', 'C02p07010' => 'bna', 'C03p07660' => 'bna', 'C05p10300' => 'bna', 'C06p38150' => 'bna', 'C07p36650' => 'bna', 'C08p15770' => 'bna', 'C09p12300' => 'bna', 'C09p62700' => 'bna', 'C09p75040' => 'bna', 'CAN.G13.1' => 'can', 'CAN.G138.4' => 'can', 'CAN.G44.6' => 'can', 'CAN.G473.19' => 'can', 'CANSAT01G0835' => 'cansat', 'CANSAT11G0246' => 'cansat', 'CANSAT11G1766' => 'cansat', 'CANSAT64G1954' => 'cansat', 'CARHR013330' => 'chi', 'CARHR060530' => 'chi', 'CARHR075300' => 'chi', 'CARHR105120' => 'chi', 'CARHR148910' => 'chi', 'CARHR198830' => 'chi', 'Carub.0001s1275' => 'cru', 'Carub.0002s1437' => 'cru', 'Carub.0003s0044' => 'cru', 'Carub.0003s2787' => 'cru', 'Carub.0005s0597' => 'cru', 'Carub.0006s1266' => 'cru', 'Ca_06935_v3' => 'car', 'Ca_13559_v3' => 'car', 'Ca_16941_v3' => 'car', 'Ca_16960_v3' => 'car', 'Ca_17775_v3' => 'car', 'Ca_30464_v3' => 'car', 'Cc06_g08160' => 'ccan', 'Cc07_g01520' => 'ccan', 'Cc11_g15810' => 'ccan', 'CDE02G2840' => 'cde', 'CDE03G0093' => 'cde', 'CDE04G2127' => 'cde', 'CDE07G1857' => 'cde', 'CDE09G1246' => 'cde', 'Cfa003412' => 'cfa', 'Cfa007341' => 'cfa', 'Cfa009220' => 'cfa', 'Ciclev10008737m.g' => 'ccl', 'Ciclev10015565m.g' => 'ccl', 'Ciclev10031761m.g' => 'ccl', 'CiPaw.03G045300' => 'cil', 'CiPaw.03G247200' => 'cil', 'CiPaw.04G029500' => 'cil', 'CiPaw.04G174000' => 'cil', 'CiPaw.05G181200' => 'cil', 'CiPaw.06G067100' => 'cil', 'ClCG05G025800' => 'cla', 'ClCG06G011400' => 'cla', 'ClCG09G019360' => 'cla', 'COL.COLO4_04827' => 'col', 'COL.COLO4_29170' => 'col', 'COL.COLO4_35131' => 'col', 'COL.COLO4_35132' => 'col', 'Cpa.g.sc33.32' => 'cpa', 'Cpa.g.sc46.29' => 'cpa', 'Cpa.g.sc796.1' => 'cpa', 'CsaV3_1G030420' => 'csa', 'CsaV3_5G027050' => 'csa', 'CsaV3_5G031040' => 'csa', 'CsaV3_UNG023130' => 'csa', 'CSS0007726' => 'camsi', 'CSS0016433' => 'camsi', 'CSS0017656' => 'camsi', 'CSS0025364' => 'camsi', 'CSS0027582' => 'camsi', 'CSS0047288' => 'camsi', 'CSS0049950' => 'camsi', 'DCAR_003843' => 'dca', 'DCAR_007052' => 'dca', 'DCAR_020884' => 'dca', 'DCAR_021730' => 'dca', 'DCAR_024423' => 'dca', 'DCAR_026509' => 'dca', 'DCAR_031158' => 'dca', 'Dinv14728' => 'din', 'Dinv15219' => 'din', 'Dinv25728' => 'din', 'Dinv33428' => 'din', 'Dinv36489' => 'din', 'Dinv41486' => 'din', 'Duzib147G0469' => 'dzi', 'Duzib168G0060' => 'dzi', 'Duzib187G1215' => 'dzi', 'Duzib248G0692' => 'dzi', 'Duzib251G0767' => 'dzi', 'Duzib264G0446' => 'dzi', 'Duzib268G0691' => 'dzi', 'ECA232G4767' => 'eca', 'ECA233G2838' => 'eca', 'ECA234G0391' => 'eca', 'ECA234G0857' => 'eca', 'ECA236G1593' => 'eca', 'ECA238G0565' => 'eca', 'ECA246G1027' => 'eca', 'ECA246G3223' => 'eca', 'ECA246G3470' => 'eca', 'EL10Ac6g13829' => 'bvu', 'EL10Ac6g14093' => 'bvu', 'EL10Ac8g18707' => 'bvu', 'Eucgr.C01369' => 'egr', 'Eucgr.H02492' => 'egr', 'Eucgr.I01733' => 'egr', 'Eucgr.J02255' => 'egr', 'Eucgr.J02257' => 'egr', 'Eucgr.J02258' => 'egr', 'FAN02G1601' => 'fan', 'FAN03G1586' => 'fan', 'FAN03G2986' => 'fan', 'FAN05G4837' => 'fan', 'FAN06G0146' => 'fan', 'FAN07G0858' => 'fan', 'FAN09G3179' => 'fan', 'FAN10G0669' => 'fan', 'FAN12G2358' => 'fan', 'FAN14G4198' => 'fan', 'FAN14G5112' => 'fan', 'FAN17G0342' => 'fan', 'FAN19G0342' => 'fan', 'FAN19G0962' => 'fan', 'FAN19G1101' => 'fan', 'FAN19G1872' => 'fan', 'FAN22G0356' => 'fan', 'FAN23G0744' => 'fan', 'FAN23G1914' => 'fan', 'FAN26G0032' => 'fan', 'FAN28G0625' => 'fan', 'FvH4_1g02710' => 'fve', 'FvH4_1g02720' => 'fve', 'FvH4_4g25670' => 'fve', 'FvH4_6g51700' => 'fve', 'FvH4_7g20170' => 'fve', 'Glyma.05G175000' => 'gma', 'Glyma.08G132300' => 'gma', 'Glyma.11G243000' => 'gma', 'Glyma.13G158900' => 'gma', 'Glyma.17G112400' => 'gma', 'Glyma.18G014100' => 'gma', 'Glyma.19G003100' => 'gma', 'Glyma.19G056500' => 'gma', 'Gohir.A01G158900' => 'ghi', 'Gohir.A05G312600' => 'ghi', 'Gohir.A05G354900' => 'ghi', 'Gohir.A07G037200' => 'ghi', 'Gohir.A09G030000' => 'ghi', 'Gohir.A12G145200' => 'ghi', 'Gohir.D01G151500' => 'ghi', 'Gohir.D04G058300' => 'ghi', 'Gohir.D05G314100' => 'ghi', 'Gohir.D07G041400' => 'ghi', 'Gohir.D09G029700' => 'ghi', 'Gohir.D12G149700' => 'ghi', 'Gorai.001G043800' => 'gra', 'Gorai.002G187800' => 'gra', 'Gorai.006G034700' => 'gra', 'Gorai.008G161200' => 'gra', 'Gorai.009G335700' => 'gra', 'Gorai.012G065000' => 'gra', 'GSVIVG01000535001' => 'vvi', 'GSVIVG01015572001' => 'vvi', 'GSVIVG01032386001' => 'vvi', 'HanXRQChr05g0138531' => 'han', 'HanXRQChr06g0174391' => 'han', 'HanXRQChr07g0199021' => 'han', 'HanXRQChr08g0208211' => 'han', 'HanXRQChr09g0255471' => 'han', 'HanXRQChr10g0315791' => 'han', 'HanXRQChr12g0371991' => 'han', 'HanXRQChr15g0475251' => 'han', 'HanXRQChr17g0540001' => 'han', 'HanXRQChr17g0548631' => 'han', 'HanXRQChr17g0569561' => 'han', 'Haze_12256' => 'cav', 'Haze_14756' => 'cav', 'Haze_25528' => 'cav', 'Hma1.2p1_0079F.1_g041020' => 'hma', 'Hma1.2p1_0818F.1_g223260' => 'hma', 'Hma1.2p1_1747F.1_g300530' => 'hma', 'HPP92_004607' => 'vpl', 'HPP92_004608' => 'vpl', 'HPP92_006181' => 'vpl', 'HPP92_012192' => 'vpl', 'HPP92_015680' => 'vpl', 'HPP92_020249' => 'vpl', 'HPP92_021376' => 'vpl', 'HPP92_024275' => 'vpl', 'Hund06031' => 'sun', 'Hund25391' => 'sun', 'Lalb_Chr07g0185371' => 'lal', 'Lalb_Chr07g0185381' => 'lal', 'Lalb_Chr12g0204011' => 'lal', 'Lalb_Chr13g0301671' => 'lal', 'Lalb_Chr14g0362851' => 'lal', 'Lalb_Chr24g0403581' => 'lal', 'Lj1g0000233' => 'lja', 'Lj2g0018120' => 'lja', 'Lj3C621T0' => 'lonja', 'Lj3P1059T14' => 'lonja', 'Lj3P611T9' => 'lonja', 'Lj3P614T13' => 'lonja', 'Lj3P615T5' => 'lonja', 'Lj4g0012315' => 'lja', 'Lj4g0026182' => 'lja', 'Lj6P813T16' => 'lonja', 'Lj7C427T7' => 'lonja', 'Lj7C427T8' => 'lonja', 'Lj7P600T41' => 'lonja', 'Lju41C42G17' => 'lonja', 'Lsat_1_v5_gn_0_47300' => 'lsa', 'Lsat_1_v5_gn_2_91280' => 'lsa', 'Lsat_1_v5_gn_3_30561' => 'lsa', 'Lsat_1_v5_gn_4_184321' => 'lsa', 'Lsat_1_v5_gn_4_4041' => 'lsa', 'Lsat_1_v5_gn_5_92000' => 'lsa', 'Lsat_1_v5_gn_8_152940' => 'lsa', 'Lsat_1_v5_gn_8_62401' => 'lsa', 'Manes.06G055900' => 'mes', 'Manes.12G022200' => 'mes', 'Manes.13G023300' => 'mes', 'Manes.14G115000' => 'mes', 'Manes.15G151700' => 'mes', 'Manes.17G111300' => 'mes', 'Mapoly0226s0009' => 'mpo', 'MBI02_g25363_MAGBIO' => 'mbi', 'MBI06_g00027_MAGBIO' => 'mbi', 'MBI10_g13034_MAGBIO' => 'mbi', 'MD09G1023400' => 'mdo', 'MD13G1100100' => 'mdo', 'MD15G1169200' => 'mdo', 'MD16G1101100' => 'mdo', 'MD17G1022900' => 'mdo', 'Medtr3g096150' => 'mtr', 'Medtr4g115070' => 'mtr', 'Medtr7g033325' => 'mtr', 'Medtr8g089840' => 'mtr', 'MELO3C010319.2' => 'cme', 'MELO3C011944.2' => 'cme', 'MELO3C021589.2' => 'cme', 'Migut.E00207' => 'egut', 'Migut.H00067' => 'egut', 'Migut.K00433' => 'egut', 'Migut.K00606' => 'egut', 'Migut.K01410' => 'egut', 'MSTRG.13347' => 'ama', 'MSTRG.24045' => 'ama', 'MSTRG.2428' => 'ama', 'MSTRG.26410' => 'ama', 'MSTRG.3139' => 'ama', 'MSTRG.3286' => 'ama', 'MSTRG.563' => 'ama', 'MSTRG.7941' => 'ama', 'Nitab4.5_0000028g0060' => 'nta', 'Nitab4.5_0000065g0260' => 'nta', 'Nitab4.5_0000112g0060' => 'nta', 'Nitab4.5_0000489g0120' => 'nta', 'Nitab4.5_0001776g0050' => 'nta', 'Nitab4.5_0001854g0010' => 'nta', 'Nitab4.5_0001860g0020' => 'nta', 'Nitab4.5_0004352g0010' => 'nta', 'Nitab4.5_0008716g0020' => 'nta', 'Nitab4.5_0008922g0010' => 'nta', 'Nn3g16693' => 'nnu', 'Nn4g22596' => 'nnu', 'Nn7g37639' => 'nnu', 'Oeu001701.1' => 'oeu', 'Oeu018149.1' => 'oeu', 'Oeu026220.1' => 'oeu', 'Oeu038635.1' => 'oeu', 'Oeu049176.1' => 'oeu', 'Oeu056706.1' => 'oeu', 'Oeu056937.1' => 'oeu', 'Oeu057540.1' => 'oeu', 'Os02g0594900' => 'osa', 'Os02g0595100' => 'osa', 'Os04g0477500' => 'osa', 'Os12g0611900' => 'osa', 'Peaxi162Scf00076g00020' => 'pax', 'Peaxi162Scf00128g00217' => 'pax', 'Peaxi162Scf00129g01640' => 'pax', 'Peaxi162Scf00669g00007' => 'pax', 'Peaxi162Scf00700g00421' => 'pax', 'Peaxi162Scf00801g00038' => 'pax', 'Peaxi162Scf00891g00025' => 'pax', 'PGR083G0909' => 'pgr', 'PGR119G1005' => 'pgr', 'PGR142G2236' => 'pgr', 'PGR142G3388' => 'pgr', 'PGSC0003DMG400004514' => 'stu', 'PGSC0003DMG400012635' => 'stu', 'PGSC0003DMG400015730' => 'stu', 'PGSC0003DMG400018611' => 'stu', 'PGSC0003DMG400030897' => 'stu', 'Phvul.001G254800' => 'pvu', 'Phvul.002G260100' => 'pvu', 'Phvul.003G167600' => 'pvu', 'Phvul.004G005100' => 'pvu', 'Potri.001G343600' => 'ptr', 'Potri.006G066700' => 'ptr', 'Potri.008G186000' => 'ptr', 'Potri.010G046900' => 'ptr', 'Potri.018G127900' => 'ptr', 'Pp3c20_17750' => 'ppa', 'Pp3c24_4380' => 'ppa', 'Prupe.1G245800' => 'ppe', 'Prupe.3G293400' => 'ppe', 'Prupe.7G247400' => 'ppe', 'Psat0s145g0120' => 'psa', 'Psat0s595g0040' => 'psa', 'Psat0s595g0120' => 'psa', 'Psat3g175040' => 'psa', 'Psat7g058120' => 'psa', 'PSO017G0428' => 'pso', 'PSO063G7510' => 'pso', 'PSO067G0046' => 'pso', 'PSO478G1073' => 'pso', 'PSO675G3677' => 'pso', 'PSO675G6558' => 'pso', 'PSO675G7520' => 'pso', 'PSO675G8959' => 'pso', 'QL02p074089' => 'qlo', 'QL02p089614' => 'qlo', 'QL03p057736' => 'qlo', 'RcHm_v2.0_Chr1g0364131' => 'rch', 'RcHm_v2.0_Chr2g0087801' => 'rch', 'RcHm_v2.0_Chr2g0087821' => 'rch', 'RcHm_v2.0_Chr2g0173231' => 'rch', 'RcHm_v2.0_Chr4g0433111' => 'rch', 'Rhsim03G0250300' => 'rsi', 'Rhsim08G0048400' => 'rsi', 'Rhsim10G0014800' => 'rsi', 'Rhsim12G0040100' => 'rsi', 'Rhsim12G0109700' => 'rsi', 'Sabra06G0049600' => 'sbr', 'Sabra08G0141000' => 'sbr', 'Sabra10G0021400' => 'sbr', 'Sabra16G0222900' => 'sbr', 'Sabra18G0108600' => 'sbr', 'SalBow1G0433' => 'sbo', 'SalBow1G2038' => 'sbo', 'SalBow1G5003' => 'sbo', 'SalBow7G1197' => 'sbo', 'SalBow8G3506' => 'sbo', 'Sc03g0007300' => 'sci', 'Sc11g0000950' => 'sci', 'Sc14g0008750' => 'sci', 'Sc18g0000420' => 'sci', 'Sed0006754' => 'sed', 'Sed0008741' => 'sed', 'Sed0017172' => 'sed', 'Sed0018925' => 'sed', 'Sed0023326' => 'sed', 'Sed0025909' => 'sed', 'SEGI_05333' => 'sgi', 'SEGI_10362' => 'sgi', 'SEGI_13380' => 'sgi', 'SEGI_24306' => 'sgi', 'SEGI_29077' => 'sgi', 'SEGI_29095' => 'sgi', 'SEGI_36534' => 'sgi', 'SEGI_37506' => 'sgi', 'SEGI_38321' => 'sgi', 'SGA_v2.0_scaffold307G48031' => 'sas', 'SGA_v2.0_scaffold47G17507' => 'sas', 'SGA_v2.0_scaffold63G21736' => 'sas', 'SGA_v2.0_scaffold87G27070' => 'sas', 'SHI17794' => 'shi', 'SHI28851' => 'shi', 'SMO165G0155' => 'smo', 'SMO340G0217' => 'smo', 'SMO367G1210' => 'smo', 'Solyc02g093430.3' => 'sly', 'Solyc05g013580.4' => 'sly', 'Solyc07g008030.3' => 'sly', 'Solyc12g035470.2' => 'sly', 'Sopen02g038020' => 'spe', 'Sopen05g008490' => 'spe', 'Sopen07g003910' => 'spe', 'Sopen12g015240' => 'spe', 'Sp1g11550' => 'spa', 'Sp2g16710' => 'spa', 'Sp3g00430' => 'spa', 'Sp3g26780' => 'spa', 'Sp5g22900' => 'spa', 'Sp6g29530' => 'spa', 'TAR371G0794' => 'tar', 'TAR374G0164' => 'tar', 'TAR622G0165' => 'tar', 'TAR626G0929' => 'tar', 'TAR629G2155' => 'tar', 'THA.LOC104805282' => 'tha', 'THA.LOC104805363' => 'tha', 'THA.LOC104808968' => 'tha', 'THA.LOC104821093' => 'tha', 'THA.LOC104823953' => 'tha', 'THA.LOC104825562' => 'tha', 'THA.LOC104825665' => 'tha', 'Thecc.02G261400' => 'tca', 'Thecc.04G019200' => 'tca', 'Thecc.09G130400' => 'tca', 'Thhalv10004374m.g' => 'esa', 'Thhalv10007850m.g' => 'esa', 'Thhalv10013782m.g' => 'esa', 'Thhalv10018686m.g' => 'esa', 'Thhalv10020899m.g' => 'esa', 'Thhalv10022755m.g' => 'esa', 'TPR.G23851' => 'tpr', 'TPR.G26500' => 'tpr', 'TPR.G27267' => 'tpr', 'TPR.G32001' => 'tpr', 'TPR.G6251' => 'tpr', 'TPR.G8167' => 'tpr', 'TWI12G1330' => 'twi', 'TWI18G1239' => 'twi', 'TWI34G0979' => 'twi', 'TWI36G0670' => 'twi', 'TWI36G0707' => 'twi', 'TWI56G0233' => 'twi', 'TWI75G1809' => 'twi', 'unitig_21.g20874' => 'ugi', 'unitig_26.g10343' => 'ugi', 'unitig_46.g18392' => 'ugi', 'unitig_52.g17178' => 'ugi', 'unitig_8.g2934' => 'ugi', 'vmacro01122' => 'vma', 'vmacro05875' => 'vma', 'vmacro06147' => 'vma', 'vmacro16191' => 'vma', 'vmacro18293' => 'vma', 'VMungo0251G3707' => 'vmu', 'VMungo0464G1521' => 'vmu', 'VMungo1215G0205' => 'vmu', 'VMungo1383G2484' => 'vmu', 'Zm00001eb079610' => 'zma', 'Zm00001eb135990' => 'zma', 'Zm00001eb183710' => 'zma', 'Zm00001eb246020' => 'zma' ) $gf_id = 'HOM05D001124' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001124' ) $data_identifier = 'HOM05D001124' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 6, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 7, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 21, 'bol' => (int) 10, 'bra' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 6, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 9, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 21, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 8, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 10, 'lsa' => (int) 8, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 8, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 9, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb246020' $species_info = array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ) $local_species = 'bvu' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001124', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '548', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02520' => 'bna', 'A03p06630' => 'bna', 'A05p44460' => 'bna', 'A06p08710' => 'bna', 'A06p41090' => 'bna', 'A07p32320' => 'bna', 'A08p32520' => 'bna', 'A09p10360' => 'bna', 'A10p24080' => 'bna', 'Aa31LG11G15250' => 'aar', 'Aa31LG1G1800' => 'aar', 'Aa31LG2G5120' => 'aar', 'Aa31LG2G6070' => 'aar', 'Aa31LG5G10770' => 'aar', 'Aa31sc61G90' => 'aar', 'Actinidia01352' => 'ach', 'Actinidia05983' => 'ach', 'Actinidia08133' => 'ach', 'Actinidia15101' => 'ach', 'Actinidia26379' => 'ach', 'Actinidia35778' => 'ach', 'Actinidia36123' => 'ach', 'Actinidia37436' => 'ach', 'Actinidia38730' => 'ach', 'Ah.02g128210' => 'amhyb', 'Ah.03g132990' => 'amhyb', 'Ah.14g079410' => 'amhyb', 'AL1G24640' => 'aly', 'AL2G26680' => 'aly', 'AL3G10530' => 'aly', 'AL3G45230' => 'aly', 'AL5G15230' => 'aly', 'AL5G16960' => 'aly', 'AL6G25210' => 'aly', 'Aqoxy2G00441' => 'aox', 'Aqoxy3G01236' => 'aox', 'Aqoxy5G03746' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3RQ047' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C7GMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9C8JER' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MBL6KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YXCZ83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZANX40' => 'arhy', 'AT1G12990' => 'ath', 'AT1G67880' => 'ath', 'AT2G13290' => 'ath', 'AT3G01620' => 'ath', 'AT3G26445' => 'ath', 'AT3G27540' => 'ath', 'AT5G14480' => 'ath', 'ATR0824G026' => 'atr', 'ATR1098G019' => 'atr', 'Atru.chr11.2145' => 'acertr', 'Atru.chr2.3636' => 'acertr', 'Atru.chr2.3644' => 'acertr', 'Atru.chr6.2422' => 'acertr', 'Atru.chr7.1112' => 'acertr', 'AUR62005469' => 'cqu', 'AUR62011166' => 'cqu', 'AUR62013319' => 'cqu', 'AUR62024273' => 'cqu', 'AUR62028420' => 'cqu', 'AUR62041942' => 'cqu', 'BcaB01g04969' => 'bca', 'BcaB01g06371' => 'bca', 'BcaB02g11494' => 'bca', 'BcaB03g15382' => 'bca', 'BcaB08g36994' => 'bca', 'BcaC03g13477' => 'bca', 'BcaC03g13478' => 'bca', 'BcaC03g13480' => 'bca', 'BcaC03g13481' => 'bca', 'BcaC03g13486' => 'bca', 'BcaC04g19031' => 'bca', 'BcaC04g23085' => 'bca', 'BcaC05g25094' => 'bca', 'BcaC05g25096' => 'bca', 'BcaC05g25138' => 'bca', 'BcaC05g30416' => 'bca', 'BcaC05g30455' => 'bca', 'BcaC06g30979' => 'bca', 'BcaC06g33805' => 'bca', 'BcaC08g46021' => 'bca', 'BcaNung03154' => 'bca', 'BolC2t06623H' => 'bol', 'BolC2t06632H' => 'bol', 'BolC2t06635H' => 'bol', 'BolC2t06638H' => 'bol', 'BolC3t13266H' => 'bol', 'BolC5t29776H' => 'bol', 'BolC6t38912H' => 'bol', 'BolC7t44183H' => 'bol', 'BolC9t54123H' => 'bol', 'BolC9t59107H' => 'bol', 'BraA02t05221Z' => 'bra', 'BraA03t09996Z' => 'bra', 'BraA05t23210Z' => 'bra', 'BraA06t24068Z' => 'bra', 'BraA06t27032Z' => 'bra', 'BraA08t35176Z' => 'bra', 'BraA09t36680Z' => 'bra', 'BraA10t44471Z' => 'bra', 'C02p06760' => 'bna', 'C02p06890' => 'bna', 'C02p07010' => 'bna', 'C03p07660' => 'bna', 'C05p10300' => 'bna', 'C06p38150' => 'bna', 'C07p36650' => 'bna', 'C08p15770' => 'bna', 'C09p12300' => 'bna', 'C09p62700' => 'bna', 'C09p75040' => 'bna', 'CAN.G13.1' => 'can', 'CAN.G138.4' => 'can', 'CAN.G44.6' => 'can', 'CAN.G473.19' => 'can', 'CANSAT01G0835' => 'cansat', 'CANSAT11G0246' => 'cansat', 'CANSAT11G1766' => 'cansat', 'CANSAT64G1954' => 'cansat', 'CARHR013330' => 'chi', 'CARHR060530' => 'chi', 'CARHR075300' => 'chi', 'CARHR105120' => 'chi', 'CARHR148910' => 'chi', 'CARHR198830' => 'chi', 'Carub.0001s1275' => 'cru', 'Carub.0002s1437' => 'cru', 'Carub.0003s0044' => 'cru', 'Carub.0003s2787' => 'cru', 'Carub.0005s0597' => 'cru', 'Carub.0006s1266' => 'cru', 'Ca_06935_v3' => 'car', 'Ca_13559_v3' => 'car', 'Ca_16941_v3' => 'car', 'Ca_16960_v3' => 'car', 'Ca_17775_v3' => 'car', 'Ca_30464_v3' => 'car', 'Cc06_g08160' => 'ccan', 'Cc07_g01520' => 'ccan', 'Cc11_g15810' => 'ccan', 'CDE02G2840' => 'cde', 'CDE03G0093' => 'cde', 'CDE04G2127' => 'cde', 'CDE07G1857' => 'cde', 'CDE09G1246' => 'cde', 'Cfa003412' => 'cfa', 'Cfa007341' => 'cfa', 'Cfa009220' => 'cfa', 'Ciclev10008737m.g' => 'ccl', 'Ciclev10015565m.g' => 'ccl', 'Ciclev10031761m.g' => 'ccl', 'CiPaw.03G045300' => 'cil', 'CiPaw.03G247200' => 'cil', 'CiPaw.04G029500' => 'cil', 'CiPaw.04G174000' => 'cil', 'CiPaw.05G181200' => 'cil', 'CiPaw.06G067100' => 'cil', 'ClCG05G025800' => 'cla', 'ClCG06G011400' => 'cla', 'ClCG09G019360' => 'cla', 'COL.COLO4_04827' => 'col', 'COL.COLO4_29170' => 'col', 'COL.COLO4_35131' => 'col', 'COL.COLO4_35132' => 'col', 'Cpa.g.sc33.32' => 'cpa', 'Cpa.g.sc46.29' => 'cpa', 'Cpa.g.sc796.1' => 'cpa', 'CsaV3_1G030420' => 'csa', 'CsaV3_5G027050' => 'csa', 'CsaV3_5G031040' => 'csa', 'CsaV3_UNG023130' => 'csa', 'CSS0007726' => 'camsi', 'CSS0016433' => 'camsi', 'CSS0017656' => 'camsi', 'CSS0025364' => 'camsi', 'CSS0027582' => 'camsi', 'CSS0047288' => 'camsi', 'CSS0049950' => 'camsi', 'DCAR_003843' => 'dca', 'DCAR_007052' => 'dca', 'DCAR_020884' => 'dca', 'DCAR_021730' => 'dca', 'DCAR_024423' => 'dca', 'DCAR_026509' => 'dca', 'DCAR_031158' => 'dca', 'Dinv14728' => 'din', 'Dinv15219' => 'din', 'Dinv25728' => 'din', 'Dinv33428' => 'din', 'Dinv36489' => 'din', 'Dinv41486' => 'din', 'Duzib147G0469' => 'dzi', 'Duzib168G0060' => 'dzi', 'Duzib187G1215' => 'dzi', 'Duzib248G0692' => 'dzi', 'Duzib251G0767' => 'dzi', 'Duzib264G0446' => 'dzi', 'Duzib268G0691' => 'dzi', 'ECA232G4767' => 'eca', 'ECA233G2838' => 'eca', 'ECA234G0391' => 'eca', 'ECA234G0857' => 'eca', 'ECA236G1593' => 'eca', 'ECA238G0565' => 'eca', 'ECA246G1027' => 'eca', 'ECA246G3223' => 'eca', 'ECA246G3470' => 'eca', 'EL10Ac6g13829' => 'bvu', 'EL10Ac6g14093' => 'bvu', 'EL10Ac8g18707' => 'bvu', 'Eucgr.C01369' => 'egr', 'Eucgr.H02492' => 'egr', 'Eucgr.I01733' => 'egr', 'Eucgr.J02255' => 'egr', 'Eucgr.J02257' => 'egr', 'Eucgr.J02258' => 'egr', 'FAN02G1601' => 'fan', 'FAN03G1586' => 'fan', 'FAN03G2986' => 'fan', 'FAN05G4837' => 'fan', 'FAN06G0146' => 'fan', 'FAN07G0858' => 'fan', 'FAN09G3179' => 'fan', 'FAN10G0669' => 'fan', 'FAN12G2358' => 'fan', 'FAN14G4198' => 'fan', 'FAN14G5112' => 'fan', 'FAN17G0342' => 'fan', 'FAN19G0342' => 'fan', 'FAN19G0962' => 'fan', 'FAN19G1101' => 'fan', 'FAN19G1872' => 'fan', 'FAN22G0356' => 'fan', 'FAN23G0744' => 'fan', 'FAN23G1914' => 'fan', 'FAN26G0032' => 'fan', 'FAN28G0625' => 'fan', 'FvH4_1g02710' => 'fve', 'FvH4_1g02720' => 'fve', 'FvH4_4g25670' => 'fve', 'FvH4_6g51700' => 'fve', 'FvH4_7g20170' => 'fve', 'Glyma.05G175000' => 'gma', 'Glyma.08G132300' => 'gma', 'Glyma.11G243000' => 'gma', 'Glyma.13G158900' => 'gma', 'Glyma.17G112400' => 'gma', 'Glyma.18G014100' => 'gma', 'Glyma.19G003100' => 'gma', 'Glyma.19G056500' => 'gma', 'Gohir.A01G158900' => 'ghi', 'Gohir.A05G312600' => 'ghi', 'Gohir.A05G354900' => 'ghi', 'Gohir.A07G037200' => 'ghi', 'Gohir.A09G030000' => 'ghi', 'Gohir.A12G145200' => 'ghi', 'Gohir.D01G151500' => 'ghi', 'Gohir.D04G058300' => 'ghi', 'Gohir.D05G314100' => 'ghi', 'Gohir.D07G041400' => 'ghi', 'Gohir.D09G029700' => 'ghi', 'Gohir.D12G149700' => 'ghi', 'Gorai.001G043800' => 'gra', 'Gorai.002G187800' => 'gra', 'Gorai.006G034700' => 'gra', 'Gorai.008G161200' => 'gra', 'Gorai.009G335700' => 'gra', 'Gorai.012G065000' => 'gra', 'GSVIVG01000535001' => 'vvi', 'GSVIVG01015572001' => 'vvi', 'GSVIVG01032386001' => 'vvi', 'HanXRQChr05g0138531' => 'han', 'HanXRQChr06g0174391' => 'han', 'HanXRQChr07g0199021' => 'han', 'HanXRQChr08g0208211' => 'han', 'HanXRQChr09g0255471' => 'han', 'HanXRQChr10g0315791' => 'han', 'HanXRQChr12g0371991' => 'han', 'HanXRQChr15g0475251' => 'han', 'HanXRQChr17g0540001' => 'han', 'HanXRQChr17g0548631' => 'han', 'HanXRQChr17g0569561' => 'han', 'Haze_12256' => 'cav', 'Haze_14756' => 'cav', 'Haze_25528' => 'cav', 'Hma1.2p1_0079F.1_g041020' => 'hma', 'Hma1.2p1_0818F.1_g223260' => 'hma', 'Hma1.2p1_1747F.1_g300530' => 'hma', 'HPP92_004607' => 'vpl', 'HPP92_004608' => 'vpl', 'HPP92_006181' => 'vpl', 'HPP92_012192' => 'vpl', 'HPP92_015680' => 'vpl', 'HPP92_020249' => 'vpl', 'HPP92_021376' => 'vpl', 'HPP92_024275' => 'vpl', 'Hund06031' => 'sun', 'Hund25391' => 'sun', 'Lalb_Chr07g0185371' => 'lal', 'Lalb_Chr07g0185381' => 'lal', 'Lalb_Chr12g0204011' => 'lal', 'Lalb_Chr13g0301671' => 'lal', 'Lalb_Chr14g0362851' => 'lal', 'Lalb_Chr24g0403581' => 'lal', 'Lj1g0000233' => 'lja', 'Lj2g0018120' => 'lja', 'Lj3C621T0' => 'lonja', 'Lj3P1059T14' => 'lonja', 'Lj3P611T9' => 'lonja', 'Lj3P614T13' => 'lonja', 'Lj3P615T5' => 'lonja', 'Lj4g0012315' => 'lja', 'Lj4g0026182' => 'lja', 'Lj6P813T16' => 'lonja', 'Lj7C427T7' => 'lonja', 'Lj7C427T8' => 'lonja', 'Lj7P600T41' => 'lonja', 'Lju41C42G17' => 'lonja', 'Lsat_1_v5_gn_0_47300' => 'lsa', 'Lsat_1_v5_gn_2_91280' => 'lsa', 'Lsat_1_v5_gn_3_30561' => 'lsa', 'Lsat_1_v5_gn_4_184321' => 'lsa', 'Lsat_1_v5_gn_4_4041' => 'lsa', 'Lsat_1_v5_gn_5_92000' => 'lsa', 'Lsat_1_v5_gn_8_152940' => 'lsa', 'Lsat_1_v5_gn_8_62401' => 'lsa', 'Manes.06G055900' => 'mes', 'Manes.12G022200' => 'mes', 'Manes.13G023300' => 'mes', 'Manes.14G115000' => 'mes', 'Manes.15G151700' => 'mes', 'Manes.17G111300' => 'mes', 'Mapoly0226s0009' => 'mpo', 'MBI02_g25363_MAGBIO' => 'mbi', 'MBI06_g00027_MAGBIO' => 'mbi', 'MBI10_g13034_MAGBIO' => 'mbi', 'MD09G1023400' => 'mdo', 'MD13G1100100' => 'mdo', 'MD15G1169200' => 'mdo', 'MD16G1101100' => 'mdo', 'MD17G1022900' => 'mdo', 'Medtr3g096150' => 'mtr', 'Medtr4g115070' => 'mtr', 'Medtr7g033325' => 'mtr', 'Medtr8g089840' => 'mtr', 'MELO3C010319.2' => 'cme', 'MELO3C011944.2' => 'cme', 'MELO3C021589.2' => 'cme', 'Migut.E00207' => 'egut', 'Migut.H00067' => 'egut', 'Migut.K00433' => 'egut', 'Migut.K00606' => 'egut', 'Migut.K01410' => 'egut', 'MSTRG.13347' => 'ama', 'MSTRG.24045' => 'ama', 'MSTRG.2428' => 'ama', 'MSTRG.26410' => 'ama', 'MSTRG.3139' => 'ama', 'MSTRG.3286' => 'ama', 'MSTRG.563' => 'ama', 'MSTRG.7941' => 'ama', 'Nitab4.5_0000028g0060' => 'nta', 'Nitab4.5_0000065g0260' => 'nta', 'Nitab4.5_0000112g0060' => 'nta', 'Nitab4.5_0000489g0120' => 'nta', 'Nitab4.5_0001776g0050' => 'nta', 'Nitab4.5_0001854g0010' => 'nta', 'Nitab4.5_0001860g0020' => 'nta', 'Nitab4.5_0004352g0010' => 'nta', 'Nitab4.5_0008716g0020' => 'nta', 'Nitab4.5_0008922g0010' => 'nta', 'Nn3g16693' => 'nnu', 'Nn4g22596' => 'nnu', 'Nn7g37639' => 'nnu', 'Oeu001701.1' => 'oeu', 'Oeu018149.1' => 'oeu', 'Oeu026220.1' => 'oeu', 'Oeu038635.1' => 'oeu', 'Oeu049176.1' => 'oeu', 'Oeu056706.1' => 'oeu', 'Oeu056937.1' => 'oeu', 'Oeu057540.1' => 'oeu', 'Os02g0594900' => 'osa', 'Os02g0595100' => 'osa', 'Os04g0477500' => 'osa', 'Os12g0611900' => 'osa', 'Peaxi162Scf00076g00020' => 'pax', 'Peaxi162Scf00128g00217' => 'pax', 'Peaxi162Scf00129g01640' => 'pax', 'Peaxi162Scf00669g00007' => 'pax', 'Peaxi162Scf00700g00421' => 'pax', 'Peaxi162Scf00801g00038' => 'pax', 'Peaxi162Scf00891g00025' => 'pax', 'PGR083G0909' => 'pgr', 'PGR119G1005' => 'pgr', 'PGR142G2236' => 'pgr', 'PGR142G3388' => 'pgr', 'PGSC0003DMG400004514' => 'stu', 'PGSC0003DMG400012635' => 'stu', 'PGSC0003DMG400015730' => 'stu', 'PGSC0003DMG400018611' => 'stu', 'PGSC0003DMG400030897' => 'stu', 'Phvul.001G254800' => 'pvu', 'Phvul.002G260100' => 'pvu', 'Phvul.003G167600' => 'pvu', 'Phvul.004G005100' => 'pvu', 'Potri.001G343600' => 'ptr', 'Potri.006G066700' => 'ptr', 'Potri.008G186000' => 'ptr', 'Potri.010G046900' => 'ptr', 'Potri.018G127900' => 'ptr', 'Pp3c20_17750' => 'ppa', 'Pp3c24_4380' => 'ppa', 'Prupe.1G245800' => 'ppe', 'Prupe.3G293400' => 'ppe', 'Prupe.7G247400' => 'ppe', 'Psat0s145g0120' => 'psa', 'Psat0s595g0040' => 'psa', 'Psat0s595g0120' => 'psa', 'Psat3g175040' => 'psa', 'Psat7g058120' => 'psa', 'PSO017G0428' => 'pso', 'PSO063G7510' => 'pso', 'PSO067G0046' => 'pso', 'PSO478G1073' => 'pso', 'PSO675G3677' => 'pso', 'PSO675G6558' => 'pso', 'PSO675G7520' => 'pso', 'PSO675G8959' => 'pso', 'QL02p074089' => 'qlo', 'QL02p089614' => 'qlo', 'QL03p057736' => 'qlo', 'RcHm_v2.0_Chr1g0364131' => 'rch', 'RcHm_v2.0_Chr2g0087801' => 'rch', 'RcHm_v2.0_Chr2g0087821' => 'rch', 'RcHm_v2.0_Chr2g0173231' => 'rch', 'RcHm_v2.0_Chr4g0433111' => 'rch', 'Rhsim03G0250300' => 'rsi', 'Rhsim08G0048400' => 'rsi', 'Rhsim10G0014800' => 'rsi', 'Rhsim12G0040100' => 'rsi', 'Rhsim12G0109700' => 'rsi', 'Sabra06G0049600' => 'sbr', 'Sabra08G0141000' => 'sbr', 'Sabra10G0021400' => 'sbr', 'Sabra16G0222900' => 'sbr', 'Sabra18G0108600' => 'sbr', 'SalBow1G0433' => 'sbo', 'SalBow1G2038' => 'sbo', 'SalBow1G5003' => 'sbo', 'SalBow7G1197' => 'sbo', 'SalBow8G3506' => 'sbo', 'Sc03g0007300' => 'sci', 'Sc11g0000950' => 'sci', 'Sc14g0008750' => 'sci', 'Sc18g0000420' => 'sci', 'Sed0006754' => 'sed', 'Sed0008741' => 'sed', 'Sed0017172' => 'sed', 'Sed0018925' => 'sed', 'Sed0023326' => 'sed', 'Sed0025909' => 'sed', 'SEGI_05333' => 'sgi', 'SEGI_10362' => 'sgi', 'SEGI_13380' => 'sgi', 'SEGI_24306' => 'sgi', 'SEGI_29077' => 'sgi', 'SEGI_29095' => 'sgi', 'SEGI_36534' => 'sgi', 'SEGI_37506' => 'sgi', 'SEGI_38321' => 'sgi', 'SGA_v2.0_scaffold307G48031' => 'sas', 'SGA_v2.0_scaffold47G17507' => 'sas', 'SGA_v2.0_scaffold63G21736' => 'sas', 'SGA_v2.0_scaffold87G27070' => 'sas', 'SHI17794' => 'shi', 'SHI28851' => 'shi', 'SMO165G0155' => 'smo', 'SMO340G0217' => 'smo', 'SMO367G1210' => 'smo', 'Solyc02g093430.3' => 'sly', 'Solyc05g013580.4' => 'sly', 'Solyc07g008030.3' => 'sly', 'Solyc12g035470.2' => 'sly', 'Sopen02g038020' => 'spe', 'Sopen05g008490' => 'spe', 'Sopen07g003910' => 'spe', 'Sopen12g015240' => 'spe', 'Sp1g11550' => 'spa', 'Sp2g16710' => 'spa', 'Sp3g00430' => 'spa', 'Sp3g26780' => 'spa', 'Sp5g22900' => 'spa', 'Sp6g29530' => 'spa', 'TAR371G0794' => 'tar', 'TAR374G0164' => 'tar', 'TAR622G0165' => 'tar', 'TAR626G0929' => 'tar', 'TAR629G2155' => 'tar', 'THA.LOC104805282' => 'tha', 'THA.LOC104805363' => 'tha', 'THA.LOC104808968' => 'tha', 'THA.LOC104821093' => 'tha', 'THA.LOC104823953' => 'tha', 'THA.LOC104825562' => 'tha', 'THA.LOC104825665' => 'tha', 'Thecc.02G261400' => 'tca', 'Thecc.04G019200' => 'tca', 'Thecc.09G130400' => 'tca', 'Thhalv10004374m.g' => 'esa', 'Thhalv10007850m.g' => 'esa', 'Thhalv10013782m.g' => 'esa', 'Thhalv10018686m.g' => 'esa', 'Thhalv10020899m.g' => 'esa', 'Thhalv10022755m.g' => 'esa', 'TPR.G23851' => 'tpr', 'TPR.G26500' => 'tpr', 'TPR.G27267' => 'tpr', 'TPR.G32001' => 'tpr', 'TPR.G6251' => 'tpr', 'TPR.G8167' => 'tpr', 'TWI12G1330' => 'twi', 'TWI18G1239' => 'twi', 'TWI34G0979' => 'twi', 'TWI36G0670' => 'twi', 'TWI36G0707' => 'twi', 'TWI56G0233' => 'twi', 'TWI75G1809' => 'twi', 'unitig_21.g20874' => 'ugi', 'unitig_26.g10343' => 'ugi', 'unitig_46.g18392' => 'ugi', 'unitig_52.g17178' => 'ugi', 'unitig_8.g2934' => 'ugi', 'vmacro01122' => 'vma', 'vmacro05875' => 'vma', 'vmacro06147' => 'vma', 'vmacro16191' => 'vma', 'vmacro18293' => 'vma', 'VMungo0251G3707' => 'vmu', 'VMungo0464G1521' => 'vmu', 'VMungo1215G0205' => 'vmu', 'VMungo1383G2484' => 'vmu', 'Zm00001eb079610' => 'zma', 'Zm00001eb135990' => 'zma', 'Zm00001eb183710' => 'zma', 'Zm00001eb246020' => 'zma' ), 'gf_id' => 'HOM05D001124', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001124' ), 'data_identifier' => 'HOM05D001124', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001124', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '548', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02520' => 'bna', 'A03p06630' => 'bna', 'A05p44460' => 'bna', 'A06p08710' => 'bna', 'A06p41090' => 'bna', 'A07p32320' => 'bna', 'A08p32520' => 'bna', 'A09p10360' => 'bna', 'A10p24080' => 'bna', 'Aa31LG11G15250' => 'aar', 'Aa31LG1G1800' => 'aar', 'Aa31LG2G5120' => 'aar', 'Aa31LG2G6070' => 'aar', 'Aa31LG5G10770' => 'aar', 'Aa31sc61G90' => 'aar', 'Actinidia01352' => 'ach', 'Actinidia05983' => 'ach', 'Actinidia08133' => 'ach', 'Actinidia15101' => 'ach', 'Actinidia26379' => 'ach', 'Actinidia35778' => 'ach', 'Actinidia36123' => 'ach', 'Actinidia37436' => 'ach', 'Actinidia38730' => 'ach', 'Ah.02g128210' => 'amhyb', 'Ah.03g132990' => 'amhyb', 'Ah.14g079410' => 'amhyb', 'AL1G24640' => 'aly', 'AL2G26680' => 'aly', 'AL3G10530' => 'aly', 'AL3G45230' => 'aly', 'AL5G15230' => 'aly', 'AL5G16960' => 'aly', 'AL6G25210' => 'aly', 'Aqoxy2G00441' => 'aox', 'Aqoxy3G01236' => 'aox', 'Aqoxy5G03746' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3RQ047' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C7GMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9C8JER' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MBL6KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YXCZ83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZANX40' => 'arhy', 'AT1G12990' => 'ath', 'AT1G67880' => 'ath', 'AT2G13290' => 'ath', 'AT3G01620' => 'ath', 'AT3G26445' => 'ath', 'AT3G27540' => 'ath', 'AT5G14480' => 'ath', 'ATR0824G026' => 'atr', 'ATR1098G019' => 'atr', 'Atru.chr11.2145' => 'acertr', 'Atru.chr2.3636' => 'acertr', 'Atru.chr2.3644' => 'acertr', 'Atru.chr6.2422' => 'acertr', 'Atru.chr7.1112' => 'acertr', 'AUR62005469' => 'cqu', 'AUR62011166' => 'cqu', 'AUR62013319' => 'cqu', 'AUR62024273' => 'cqu', 'AUR62028420' => 'cqu', 'AUR62041942' => 'cqu', 'BcaB01g04969' => 'bca', 'BcaB01g06371' => 'bca', 'BcaB02g11494' => 'bca', 'BcaB03g15382' => 'bca', 'BcaB08g36994' => 'bca', 'BcaC03g13477' => 'bca', 'BcaC03g13478' => 'bca', 'BcaC03g13480' => 'bca', 'BcaC03g13481' => 'bca', 'BcaC03g13486' => 'bca', 'BcaC04g19031' => 'bca', 'BcaC04g23085' => 'bca', 'BcaC05g25094' => 'bca', 'BcaC05g25096' => 'bca', 'BcaC05g25138' => 'bca', 'BcaC05g30416' => 'bca', 'BcaC05g30455' => 'bca', 'BcaC06g30979' => 'bca', 'BcaC06g33805' => 'bca', 'BcaC08g46021' => 'bca', 'BcaNung03154' => 'bca', 'BolC2t06623H' => 'bol', 'BolC2t06632H' => 'bol', 'BolC2t06635H' => 'bol', 'BolC2t06638H' => 'bol', 'BolC3t13266H' => 'bol', 'BolC5t29776H' => 'bol', 'BolC6t38912H' => 'bol', 'BolC7t44183H' => 'bol', 'BolC9t54123H' => 'bol', 'BolC9t59107H' => 'bol', 'BraA02t05221Z' => 'bra', 'BraA03t09996Z' => 'bra', 'BraA05t23210Z' => 'bra', 'BraA06t24068Z' => 'bra', 'BraA06t27032Z' => 'bra', 'BraA08t35176Z' => 'bra', 'BraA09t36680Z' => 'bra', 'BraA10t44471Z' => 'bra', 'C02p06760' => 'bna', 'C02p06890' => 'bna', 'C02p07010' => 'bna', 'C03p07660' => 'bna', 'C05p10300' => 'bna', 'C06p38150' => 'bna', 'C07p36650' => 'bna', 'C08p15770' => 'bna', 'C09p12300' => 'bna', 'C09p62700' => 'bna', 'C09p75040' => 'bna', 'CAN.G13.1' => 'can', 'CAN.G138.4' => 'can', 'CAN.G44.6' => 'can', 'CAN.G473.19' => 'can', 'CANSAT01G0835' => 'cansat', 'CANSAT11G0246' => 'cansat', 'CANSAT11G1766' => 'cansat', 'CANSAT64G1954' => 'cansat', 'CARHR013330' => 'chi', 'CARHR060530' => 'chi', 'CARHR075300' => 'chi', 'CARHR105120' => 'chi', 'CARHR148910' => 'chi', 'CARHR198830' => 'chi', 'Carub.0001s1275' => 'cru', 'Carub.0002s1437' => 'cru', 'Carub.0003s0044' => 'cru', 'Carub.0003s2787' => 'cru', 'Carub.0005s0597' => 'cru', 'Carub.0006s1266' => 'cru', 'Ca_06935_v3' => 'car', 'Ca_13559_v3' => 'car', 'Ca_16941_v3' => 'car', 'Ca_16960_v3' => 'car', 'Ca_17775_v3' => 'car', 'Ca_30464_v3' => 'car', 'Cc06_g08160' => 'ccan', 'Cc07_g01520' => 'ccan', 'Cc11_g15810' => 'ccan', 'CDE02G2840' => 'cde', 'CDE03G0093' => 'cde', 'CDE04G2127' => 'cde', 'CDE07G1857' => 'cde', 'CDE09G1246' => 'cde', 'Cfa003412' => 'cfa', 'Cfa007341' => 'cfa', 'Cfa009220' => 'cfa', 'Ciclev10008737m.g' => 'ccl', 'Ciclev10015565m.g' => 'ccl', 'Ciclev10031761m.g' => 'ccl', 'CiPaw.03G045300' => 'cil', 'CiPaw.03G247200' => 'cil', 'CiPaw.04G029500' => 'cil', 'CiPaw.04G174000' => 'cil', 'CiPaw.05G181200' => 'cil', 'CiPaw.06G067100' => 'cil', 'ClCG05G025800' => 'cla', 'ClCG06G011400' => 'cla', 'ClCG09G019360' => 'cla', 'COL.COLO4_04827' => 'col', 'COL.COLO4_29170' => 'col', 'COL.COLO4_35131' => 'col', 'COL.COLO4_35132' => 'col', 'Cpa.g.sc33.32' => 'cpa', 'Cpa.g.sc46.29' => 'cpa', 'Cpa.g.sc796.1' => 'cpa', 'CsaV3_1G030420' => 'csa', 'CsaV3_5G027050' => 'csa', 'CsaV3_5G031040' => 'csa', 'CsaV3_UNG023130' => 'csa', 'CSS0007726' => 'camsi', 'CSS0016433' => 'camsi', 'CSS0017656' => 'camsi', 'CSS0025364' => 'camsi', 'CSS0027582' => 'camsi', 'CSS0047288' => 'camsi', 'CSS0049950' => 'camsi', 'DCAR_003843' => 'dca', 'DCAR_007052' => 'dca', 'DCAR_020884' => 'dca', 'DCAR_021730' => 'dca', 'DCAR_024423' => 'dca', 'DCAR_026509' => 'dca', 'DCAR_031158' => 'dca', 'Dinv14728' => 'din', 'Dinv15219' => 'din', 'Dinv25728' => 'din', 'Dinv33428' => 'din', 'Dinv36489' => 'din', 'Dinv41486' => 'din', 'Duzib147G0469' => 'dzi', 'Duzib168G0060' => 'dzi', 'Duzib187G1215' => 'dzi', 'Duzib248G0692' => 'dzi', 'Duzib251G0767' => 'dzi', 'Duzib264G0446' => 'dzi', 'Duzib268G0691' => 'dzi', 'ECA232G4767' => 'eca', 'ECA233G2838' => 'eca', 'ECA234G0391' => 'eca', 'ECA234G0857' => 'eca', 'ECA236G1593' => 'eca', 'ECA238G0565' => 'eca', 'ECA246G1027' => 'eca', 'ECA246G3223' => 'eca', 'ECA246G3470' => 'eca', 'EL10Ac6g13829' => 'bvu', 'EL10Ac6g14093' => 'bvu', 'EL10Ac8g18707' => 'bvu', 'Eucgr.C01369' => 'egr', 'Eucgr.H02492' => 'egr', 'Eucgr.I01733' => 'egr', 'Eucgr.J02255' => 'egr', 'Eucgr.J02257' => 'egr', 'Eucgr.J02258' => 'egr', 'FAN02G1601' => 'fan', 'FAN03G1586' => 'fan', 'FAN03G2986' => 'fan', 'FAN05G4837' => 'fan', 'FAN06G0146' => 'fan', 'FAN07G0858' => 'fan', 'FAN09G3179' => 'fan', 'FAN10G0669' => 'fan', 'FAN12G2358' => 'fan', 'FAN14G4198' => 'fan', 'FAN14G5112' => 'fan', 'FAN17G0342' => 'fan', 'FAN19G0342' => 'fan', 'FAN19G0962' => 'fan', 'FAN19G1101' => 'fan', 'FAN19G1872' => 'fan', 'FAN22G0356' => 'fan', 'FAN23G0744' => 'fan', 'FAN23G1914' => 'fan', 'FAN26G0032' => 'fan', 'FAN28G0625' => 'fan', 'FvH4_1g02710' => 'fve', 'FvH4_1g02720' => 'fve', 'FvH4_4g25670' => 'fve', 'FvH4_6g51700' => 'fve', 'FvH4_7g20170' => 'fve', 'Glyma.05G175000' => 'gma', 'Glyma.08G132300' => 'gma', 'Glyma.11G243000' => 'gma', 'Glyma.13G158900' => 'gma', 'Glyma.17G112400' => 'gma', 'Glyma.18G014100' => 'gma', 'Glyma.19G003100' => 'gma', 'Glyma.19G056500' => 'gma', 'Gohir.A01G158900' => 'ghi', 'Gohir.A05G312600' => 'ghi', 'Gohir.A05G354900' => 'ghi', 'Gohir.A07G037200' => 'ghi', 'Gohir.A09G030000' => 'ghi', 'Gohir.A12G145200' => 'ghi', 'Gohir.D01G151500' => 'ghi', 'Gohir.D04G058300' => 'ghi', 'Gohir.D05G314100' => 'ghi', 'Gohir.D07G041400' => 'ghi', 'Gohir.D09G029700' => 'ghi', 'Gohir.D12G149700' => 'ghi', 'Gorai.001G043800' => 'gra', 'Gorai.002G187800' => 'gra', 'Gorai.006G034700' => 'gra', 'Gorai.008G161200' => 'gra', 'Gorai.009G335700' => 'gra', 'Gorai.012G065000' => 'gra', 'GSVIVG01000535001' => 'vvi', 'GSVIVG01015572001' => 'vvi', 'GSVIVG01032386001' => 'vvi', 'HanXRQChr05g0138531' => 'han', 'HanXRQChr06g0174391' => 'han', 'HanXRQChr07g0199021' => 'han', 'HanXRQChr08g0208211' => 'han', 'HanXRQChr09g0255471' => 'han', 'HanXRQChr10g0315791' => 'han', 'HanXRQChr12g0371991' => 'han', 'HanXRQChr15g0475251' => 'han', 'HanXRQChr17g0540001' => 'han', 'HanXRQChr17g0548631' => 'han', 'HanXRQChr17g0569561' => 'han', 'Haze_12256' => 'cav', 'Haze_14756' => 'cav', 'Haze_25528' => 'cav', 'Hma1.2p1_0079F.1_g041020' => 'hma', 'Hma1.2p1_0818F.1_g223260' => 'hma', 'Hma1.2p1_1747F.1_g300530' => 'hma', 'HPP92_004607' => 'vpl', 'HPP92_004608' => 'vpl', 'HPP92_006181' => 'vpl', 'HPP92_012192' => 'vpl', 'HPP92_015680' => 'vpl', 'HPP92_020249' => 'vpl', 'HPP92_021376' => 'vpl', 'HPP92_024275' => 'vpl', 'Hund06031' => 'sun', 'Hund25391' => 'sun', 'Lalb_Chr07g0185371' => 'lal', 'Lalb_Chr07g0185381' => 'lal', 'Lalb_Chr12g0204011' => 'lal', 'Lalb_Chr13g0301671' => 'lal', 'Lalb_Chr14g0362851' => 'lal', 'Lalb_Chr24g0403581' => 'lal', 'Lj1g0000233' => 'lja', 'Lj2g0018120' => 'lja', 'Lj3C621T0' => 'lonja', 'Lj3P1059T14' => 'lonja', 'Lj3P611T9' => 'lonja', 'Lj3P614T13' => 'lonja', 'Lj3P615T5' => 'lonja', 'Lj4g0012315' => 'lja', 'Lj4g0026182' => 'lja', 'Lj6P813T16' => 'lonja', 'Lj7C427T7' => 'lonja', 'Lj7C427T8' => 'lonja', 'Lj7P600T41' => 'lonja', 'Lju41C42G17' => 'lonja', 'Lsat_1_v5_gn_0_47300' => 'lsa', 'Lsat_1_v5_gn_2_91280' => 'lsa', 'Lsat_1_v5_gn_3_30561' => 'lsa', 'Lsat_1_v5_gn_4_184321' => 'lsa', 'Lsat_1_v5_gn_4_4041' => 'lsa', 'Lsat_1_v5_gn_5_92000' => 'lsa', 'Lsat_1_v5_gn_8_152940' => 'lsa', 'Lsat_1_v5_gn_8_62401' => 'lsa', 'Manes.06G055900' => 'mes', 'Manes.12G022200' => 'mes', 'Manes.13G023300' => 'mes', 'Manes.14G115000' => 'mes', 'Manes.15G151700' => 'mes', 'Manes.17G111300' => 'mes', 'Mapoly0226s0009' => 'mpo', 'MBI02_g25363_MAGBIO' => 'mbi', 'MBI06_g00027_MAGBIO' => 'mbi', 'MBI10_g13034_MAGBIO' => 'mbi', 'MD09G1023400' => 'mdo', 'MD13G1100100' => 'mdo', 'MD15G1169200' => 'mdo', 'MD16G1101100' => 'mdo', 'MD17G1022900' => 'mdo', 'Medtr3g096150' => 'mtr', 'Medtr4g115070' => 'mtr', 'Medtr7g033325' => 'mtr', 'Medtr8g089840' => 'mtr', 'MELO3C010319.2' => 'cme', 'MELO3C011944.2' => 'cme', 'MELO3C021589.2' => 'cme', 'Migut.E00207' => 'egut', 'Migut.H00067' => 'egut', 'Migut.K00433' => 'egut', 'Migut.K00606' => 'egut', 'Migut.K01410' => 'egut', 'MSTRG.13347' => 'ama', 'MSTRG.24045' => 'ama', 'MSTRG.2428' => 'ama', 'MSTRG.26410' => 'ama', 'MSTRG.3139' => 'ama', 'MSTRG.3286' => 'ama', 'MSTRG.563' => 'ama', 'MSTRG.7941' => 'ama', 'Nitab4.5_0000028g0060' => 'nta', 'Nitab4.5_0000065g0260' => 'nta', 'Nitab4.5_0000112g0060' => 'nta', 'Nitab4.5_0000489g0120' => 'nta', 'Nitab4.5_0001776g0050' => 'nta', 'Nitab4.5_0001854g0010' => 'nta', 'Nitab4.5_0001860g0020' => 'nta', 'Nitab4.5_0004352g0010' => 'nta', 'Nitab4.5_0008716g0020' => 'nta', 'Nitab4.5_0008922g0010' => 'nta', 'Nn3g16693' => 'nnu', 'Nn4g22596' => 'nnu', 'Nn7g37639' => 'nnu', 'Oeu001701.1' => 'oeu', 'Oeu018149.1' => 'oeu', 'Oeu026220.1' => 'oeu', 'Oeu038635.1' => 'oeu', 'Oeu049176.1' => 'oeu', 'Oeu056706.1' => 'oeu', 'Oeu056937.1' => 'oeu', 'Oeu057540.1' => 'oeu', 'Os02g0594900' => 'osa', 'Os02g0595100' => 'osa', 'Os04g0477500' => 'osa', 'Os12g0611900' => 'osa', 'Peaxi162Scf00076g00020' => 'pax', 'Peaxi162Scf00128g00217' => 'pax', 'Peaxi162Scf00129g01640' => 'pax', 'Peaxi162Scf00669g00007' => 'pax', 'Peaxi162Scf00700g00421' => 'pax', 'Peaxi162Scf00801g00038' => 'pax', 'Peaxi162Scf00891g00025' => 'pax', 'PGR083G0909' => 'pgr', 'PGR119G1005' => 'pgr', 'PGR142G2236' => 'pgr', 'PGR142G3388' => 'pgr', 'PGSC0003DMG400004514' => 'stu', 'PGSC0003DMG400012635' => 'stu', 'PGSC0003DMG400015730' => 'stu', 'PGSC0003DMG400018611' => 'stu', 'PGSC0003DMG400030897' => 'stu', 'Phvul.001G254800' => 'pvu', 'Phvul.002G260100' => 'pvu', 'Phvul.003G167600' => 'pvu', 'Phvul.004G005100' => 'pvu', 'Potri.001G343600' => 'ptr', 'Potri.006G066700' => 'ptr', 'Potri.008G186000' => 'ptr', 'Potri.010G046900' => 'ptr', 'Potri.018G127900' => 'ptr', 'Pp3c20_17750' => 'ppa', 'Pp3c24_4380' => 'ppa', 'Prupe.1G245800' => 'ppe', 'Prupe.3G293400' => 'ppe', 'Prupe.7G247400' => 'ppe', 'Psat0s145g0120' => 'psa', 'Psat0s595g0040' => 'psa', 'Psat0s595g0120' => 'psa', 'Psat3g175040' => 'psa', 'Psat7g058120' => 'psa', 'PSO017G0428' => 'pso', 'PSO063G7510' => 'pso', 'PSO067G0046' => 'pso', 'PSO478G1073' => 'pso', 'PSO675G3677' => 'pso', 'PSO675G6558' => 'pso', 'PSO675G7520' => 'pso', 'PSO675G8959' => 'pso', 'QL02p074089' => 'qlo', 'QL02p089614' => 'qlo', 'QL03p057736' => 'qlo', 'RcHm_v2.0_Chr1g0364131' => 'rch', 'RcHm_v2.0_Chr2g0087801' => 'rch', 'RcHm_v2.0_Chr2g0087821' => 'rch', 'RcHm_v2.0_Chr2g0173231' => 'rch', 'RcHm_v2.0_Chr4g0433111' => 'rch', 'Rhsim03G0250300' => 'rsi', 'Rhsim08G0048400' => 'rsi', 'Rhsim10G0014800' => 'rsi', 'Rhsim12G0040100' => 'rsi', 'Rhsim12G0109700' => 'rsi', 'Sabra06G0049600' => 'sbr', 'Sabra08G0141000' => 'sbr', 'Sabra10G0021400' => 'sbr', 'Sabra16G0222900' => 'sbr', 'Sabra18G0108600' => 'sbr', 'SalBow1G0433' => 'sbo', 'SalBow1G2038' => 'sbo', 'SalBow1G5003' => 'sbo', 'SalBow7G1197' => 'sbo', 'SalBow8G3506' => 'sbo', 'Sc03g0007300' => 'sci', 'Sc11g0000950' => 'sci', 'Sc14g0008750' => 'sci', 'Sc18g0000420' => 'sci', 'Sed0006754' => 'sed', 'Sed0008741' => 'sed', 'Sed0017172' => 'sed', 'Sed0018925' => 'sed', 'Sed0023326' => 'sed', 'Sed0025909' => 'sed', 'SEGI_05333' => 'sgi', 'SEGI_10362' => 'sgi', 'SEGI_13380' => 'sgi', 'SEGI_24306' => 'sgi', 'SEGI_29077' => 'sgi', 'SEGI_29095' => 'sgi', 'SEGI_36534' => 'sgi', 'SEGI_37506' => 'sgi', 'SEGI_38321' => 'sgi', 'SGA_v2.0_scaffold307G48031' => 'sas', 'SGA_v2.0_scaffold47G17507' => 'sas', 'SGA_v2.0_scaffold63G21736' => 'sas', 'SGA_v2.0_scaffold87G27070' => 'sas', 'SHI17794' => 'shi', 'SHI28851' => 'shi', 'SMO165G0155' => 'smo', 'SMO340G0217' => 'smo', 'SMO367G1210' => 'smo', 'Solyc02g093430.3' => 'sly', 'Solyc05g013580.4' => 'sly', 'Solyc07g008030.3' => 'sly', 'Solyc12g035470.2' => 'sly', 'Sopen02g038020' => 'spe', 'Sopen05g008490' => 'spe', 'Sopen07g003910' => 'spe', 'Sopen12g015240' => 'spe', 'Sp1g11550' => 'spa', 'Sp2g16710' => 'spa', 'Sp3g00430' => 'spa', 'Sp3g26780' => 'spa', 'Sp5g22900' => 'spa', 'Sp6g29530' => 'spa', 'TAR371G0794' => 'tar', 'TAR374G0164' => 'tar', 'TAR622G0165' => 'tar', 'TAR626G0929' => 'tar', 'TAR629G2155' => 'tar', 'THA.LOC104805282' => 'tha', 'THA.LOC104805363' => 'tha', 'THA.LOC104808968' => 'tha', 'THA.LOC104821093' => 'tha', 'THA.LOC104823953' => 'tha', 'THA.LOC104825562' => 'tha', 'THA.LOC104825665' => 'tha', 'Thecc.02G261400' => 'tca', 'Thecc.04G019200' => 'tca', 'Thecc.09G130400' => 'tca', 'Thhalv10004374m.g' => 'esa', 'Thhalv10007850m.g' => 'esa', 'Thhalv10013782m.g' => 'esa', 'Thhalv10018686m.g' => 'esa', 'Thhalv10020899m.g' => 'esa', 'Thhalv10022755m.g' => 'esa', 'TPR.G23851' => 'tpr', 'TPR.G26500' => 'tpr', 'TPR.G27267' => 'tpr', 'TPR.G32001' => 'tpr', 'TPR.G6251' => 'tpr', 'TPR.G8167' => 'tpr', 'TWI12G1330' => 'twi', 'TWI18G1239' => 'twi', 'TWI34G0979' => 'twi', 'TWI36G0670' => 'twi', 'TWI36G0707' => 'twi', 'TWI56G0233' => 'twi', 'TWI75G1809' => 'twi', 'unitig_21.g20874' => 'ugi', 'unitig_26.g10343' => 'ugi', 'unitig_46.g18392' => 'ugi', 'unitig_52.g17178' => 'ugi', 'unitig_8.g2934' => 'ugi', 'vmacro01122' => 'vma', 'vmacro05875' => 'vma', 'vmacro06147' => 'vma', 'vmacro16191' => 'vma', 'vmacro18293' => 'vma', 'VMungo0251G3707' => 'vmu', 'VMungo0464G1521' => 'vmu', 'VMungo1215G0205' => 'vmu', 'VMungo1383G2484' => 'vmu', 'Zm00001eb079610' => 'zma', 'Zm00001eb135990' => 'zma', 'Zm00001eb183710' => 'zma', 'Zm00001eb246020' => 'zma' ) $gf_id = 'HOM05D001124' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001124' ) $data_identifier = 'HOM05D001124' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 6, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 7, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 21, 'bol' => (int) 10, 'bra' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 6, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 9, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 21, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 8, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 10, 'lsa' => (int) 8, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 8, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 9, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb246020' $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' => 'HOM05D001124', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '548', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02520' => 'bna', 'A03p06630' => 'bna', 'A05p44460' => 'bna', 'A06p08710' => 'bna', 'A06p41090' => 'bna', 'A07p32320' => 'bna', 'A08p32520' => 'bna', 'A09p10360' => 'bna', 'A10p24080' => 'bna', 'Aa31LG11G15250' => 'aar', 'Aa31LG1G1800' => 'aar', 'Aa31LG2G5120' => 'aar', 'Aa31LG2G6070' => 'aar', 'Aa31LG5G10770' => 'aar', 'Aa31sc61G90' => 'aar', 'Actinidia01352' => 'ach', 'Actinidia05983' => 'ach', 'Actinidia08133' => 'ach', 'Actinidia15101' => 'ach', 'Actinidia26379' => 'ach', 'Actinidia35778' => 'ach', 'Actinidia36123' => 'ach', 'Actinidia37436' => 'ach', 'Actinidia38730' => 'ach', 'Ah.02g128210' => 'amhyb', 'Ah.03g132990' => 'amhyb', 'Ah.14g079410' => 'amhyb', 'AL1G24640' => 'aly', 'AL2G26680' => 'aly', 'AL3G10530' => 'aly', 'AL3G45230' => 'aly', 'AL5G15230' => 'aly', 'AL5G16960' => 'aly', 'AL6G25210' => 'aly', 'Aqoxy2G00441' => 'aox', 'Aqoxy3G01236' => 'aox', 'Aqoxy5G03746' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3RQ047' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C7GMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9C8JER' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MBL6KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YXCZ83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZANX40' => 'arhy', 'AT1G12990' => 'ath', 'AT1G67880' => 'ath', 'AT2G13290' => 'ath', 'AT3G01620' => 'ath', 'AT3G26445' => 'ath', 'AT3G27540' => 'ath', 'AT5G14480' => 'ath', 'ATR0824G026' => 'atr', 'ATR1098G019' => 'atr', 'Atru.chr11.2145' => 'acertr', 'Atru.chr2.3636' => 'acertr', 'Atru.chr2.3644' => 'acertr', 'Atru.chr6.2422' => 'acertr', 'Atru.chr7.1112' => 'acertr', 'AUR62005469' => 'cqu', 'AUR62011166' => 'cqu', 'AUR62013319' => 'cqu', 'AUR62024273' => 'cqu', 'AUR62028420' => 'cqu', 'AUR62041942' => 'cqu', 'BcaB01g04969' => 'bca', 'BcaB01g06371' => 'bca', 'BcaB02g11494' => 'bca', 'BcaB03g15382' => 'bca', 'BcaB08g36994' => 'bca', 'BcaC03g13477' => 'bca', 'BcaC03g13478' => 'bca', 'BcaC03g13480' => 'bca', 'BcaC03g13481' => 'bca', 'BcaC03g13486' => 'bca', 'BcaC04g19031' => 'bca', 'BcaC04g23085' => 'bca', 'BcaC05g25094' => 'bca', 'BcaC05g25096' => 'bca', 'BcaC05g25138' => 'bca', 'BcaC05g30416' => 'bca', 'BcaC05g30455' => 'bca', 'BcaC06g30979' => 'bca', 'BcaC06g33805' => 'bca', 'BcaC08g46021' => 'bca', 'BcaNung03154' => 'bca', 'BolC2t06623H' => 'bol', 'BolC2t06632H' => 'bol', 'BolC2t06635H' => 'bol', 'BolC2t06638H' => 'bol', 'BolC3t13266H' => 'bol', 'BolC5t29776H' => 'bol', 'BolC6t38912H' => 'bol', 'BolC7t44183H' => 'bol', 'BolC9t54123H' => 'bol', 'BolC9t59107H' => 'bol', 'BraA02t05221Z' => 'bra', 'BraA03t09996Z' => 'bra', 'BraA05t23210Z' => 'bra', 'BraA06t24068Z' => 'bra', 'BraA06t27032Z' => 'bra', 'BraA08t35176Z' => 'bra', 'BraA09t36680Z' => 'bra', 'BraA10t44471Z' => 'bra', 'C02p06760' => 'bna', 'C02p06890' => 'bna', 'C02p07010' => 'bna', 'C03p07660' => 'bna', 'C05p10300' => 'bna', 'C06p38150' => 'bna', 'C07p36650' => 'bna', 'C08p15770' => 'bna', 'C09p12300' => 'bna', 'C09p62700' => 'bna', 'C09p75040' => 'bna', 'CAN.G13.1' => 'can', 'CAN.G138.4' => 'can', 'CAN.G44.6' => 'can', 'CAN.G473.19' => 'can', 'CANSAT01G0835' => 'cansat', 'CANSAT11G0246' => 'cansat', 'CANSAT11G1766' => 'cansat', 'CANSAT64G1954' => 'cansat', 'CARHR013330' => 'chi', 'CARHR060530' => 'chi', 'CARHR075300' => 'chi', 'CARHR105120' => 'chi', 'CARHR148910' => 'chi', 'CARHR198830' => 'chi', 'Carub.0001s1275' => 'cru', 'Carub.0002s1437' => 'cru', 'Carub.0003s0044' => 'cru', 'Carub.0003s2787' => 'cru', 'Carub.0005s0597' => 'cru', 'Carub.0006s1266' => 'cru', 'Ca_06935_v3' => 'car', 'Ca_13559_v3' => 'car', 'Ca_16941_v3' => 'car', 'Ca_16960_v3' => 'car', 'Ca_17775_v3' => 'car', 'Ca_30464_v3' => 'car', 'Cc06_g08160' => 'ccan', 'Cc07_g01520' => 'ccan', 'Cc11_g15810' => 'ccan', 'CDE02G2840' => 'cde', 'CDE03G0093' => 'cde', 'CDE04G2127' => 'cde', 'CDE07G1857' => 'cde', 'CDE09G1246' => 'cde', 'Cfa003412' => 'cfa', 'Cfa007341' => 'cfa', 'Cfa009220' => 'cfa', 'Ciclev10008737m.g' => 'ccl', 'Ciclev10015565m.g' => 'ccl', 'Ciclev10031761m.g' => 'ccl', 'CiPaw.03G045300' => 'cil', 'CiPaw.03G247200' => 'cil', 'CiPaw.04G029500' => 'cil', 'CiPaw.04G174000' => 'cil', 'CiPaw.05G181200' => 'cil', 'CiPaw.06G067100' => 'cil', 'ClCG05G025800' => 'cla', 'ClCG06G011400' => 'cla', 'ClCG09G019360' => 'cla', 'COL.COLO4_04827' => 'col', 'COL.COLO4_29170' => 'col', 'COL.COLO4_35131' => 'col', 'COL.COLO4_35132' => 'col', 'Cpa.g.sc33.32' => 'cpa', 'Cpa.g.sc46.29' => 'cpa', 'Cpa.g.sc796.1' => 'cpa', 'CsaV3_1G030420' => 'csa', 'CsaV3_5G027050' => 'csa', 'CsaV3_5G031040' => 'csa', 'CsaV3_UNG023130' => 'csa', 'CSS0007726' => 'camsi', 'CSS0016433' => 'camsi', 'CSS0017656' => 'camsi', 'CSS0025364' => 'camsi', 'CSS0027582' => 'camsi', 'CSS0047288' => 'camsi', 'CSS0049950' => 'camsi', 'DCAR_003843' => 'dca', 'DCAR_007052' => 'dca', 'DCAR_020884' => 'dca', 'DCAR_021730' => 'dca', 'DCAR_024423' => 'dca', 'DCAR_026509' => 'dca', 'DCAR_031158' => 'dca', 'Dinv14728' => 'din', 'Dinv15219' => 'din', 'Dinv25728' => 'din', 'Dinv33428' => 'din', 'Dinv36489' => 'din', 'Dinv41486' => 'din', 'Duzib147G0469' => 'dzi', 'Duzib168G0060' => 'dzi', 'Duzib187G1215' => 'dzi', 'Duzib248G0692' => 'dzi', 'Duzib251G0767' => 'dzi', 'Duzib264G0446' => 'dzi', 'Duzib268G0691' => 'dzi', 'ECA232G4767' => 'eca', 'ECA233G2838' => 'eca', 'ECA234G0391' => 'eca', 'ECA234G0857' => 'eca', 'ECA236G1593' => 'eca', 'ECA238G0565' => 'eca', 'ECA246G1027' => 'eca', 'ECA246G3223' => 'eca', 'ECA246G3470' => 'eca', 'EL10Ac6g13829' => 'bvu', 'EL10Ac6g14093' => 'bvu', 'EL10Ac8g18707' => 'bvu', 'Eucgr.C01369' => 'egr', 'Eucgr.H02492' => 'egr', 'Eucgr.I01733' => 'egr', 'Eucgr.J02255' => 'egr', 'Eucgr.J02257' => 'egr', 'Eucgr.J02258' => 'egr', 'FAN02G1601' => 'fan', 'FAN03G1586' => 'fan', 'FAN03G2986' => 'fan', 'FAN05G4837' => 'fan', 'FAN06G0146' => 'fan', 'FAN07G0858' => 'fan', 'FAN09G3179' => 'fan', 'FAN10G0669' => 'fan', 'FAN12G2358' => 'fan', 'FAN14G4198' => 'fan', 'FAN14G5112' => 'fan', 'FAN17G0342' => 'fan', 'FAN19G0342' => 'fan', 'FAN19G0962' => 'fan', 'FAN19G1101' => 'fan', 'FAN19G1872' => 'fan', 'FAN22G0356' => 'fan', 'FAN23G0744' => 'fan', 'FAN23G1914' => 'fan', 'FAN26G0032' => 'fan', 'FAN28G0625' => 'fan', 'FvH4_1g02710' => 'fve', 'FvH4_1g02720' => 'fve', 'FvH4_4g25670' => 'fve', 'FvH4_6g51700' => 'fve', 'FvH4_7g20170' => 'fve', 'Glyma.05G175000' => 'gma', 'Glyma.08G132300' => 'gma', 'Glyma.11G243000' => 'gma', 'Glyma.13G158900' => 'gma', 'Glyma.17G112400' => 'gma', 'Glyma.18G014100' => 'gma', 'Glyma.19G003100' => 'gma', 'Glyma.19G056500' => 'gma', 'Gohir.A01G158900' => 'ghi', 'Gohir.A05G312600' => 'ghi', 'Gohir.A05G354900' => 'ghi', 'Gohir.A07G037200' => 'ghi', 'Gohir.A09G030000' => 'ghi', 'Gohir.A12G145200' => 'ghi', 'Gohir.D01G151500' => 'ghi', 'Gohir.D04G058300' => 'ghi', 'Gohir.D05G314100' => 'ghi', 'Gohir.D07G041400' => 'ghi', 'Gohir.D09G029700' => 'ghi', 'Gohir.D12G149700' => 'ghi', 'Gorai.001G043800' => 'gra', 'Gorai.002G187800' => 'gra', 'Gorai.006G034700' => 'gra', 'Gorai.008G161200' => 'gra', 'Gorai.009G335700' => 'gra', 'Gorai.012G065000' => 'gra', 'GSVIVG01000535001' => 'vvi', 'GSVIVG01015572001' => 'vvi', 'GSVIVG01032386001' => 'vvi', 'HanXRQChr05g0138531' => 'han', 'HanXRQChr06g0174391' => 'han', 'HanXRQChr07g0199021' => 'han', 'HanXRQChr08g0208211' => 'han', 'HanXRQChr09g0255471' => 'han', 'HanXRQChr10g0315791' => 'han', 'HanXRQChr12g0371991' => 'han', 'HanXRQChr15g0475251' => 'han', 'HanXRQChr17g0540001' => 'han', 'HanXRQChr17g0548631' => 'han', 'HanXRQChr17g0569561' => 'han', 'Haze_12256' => 'cav', 'Haze_14756' => 'cav', 'Haze_25528' => 'cav', 'Hma1.2p1_0079F.1_g041020' => 'hma', 'Hma1.2p1_0818F.1_g223260' => 'hma', 'Hma1.2p1_1747F.1_g300530' => 'hma', 'HPP92_004607' => 'vpl', 'HPP92_004608' => 'vpl', 'HPP92_006181' => 'vpl', 'HPP92_012192' => 'vpl', 'HPP92_015680' => 'vpl', 'HPP92_020249' => 'vpl', 'HPP92_021376' => 'vpl', 'HPP92_024275' => 'vpl', 'Hund06031' => 'sun', 'Hund25391' => 'sun', 'Lalb_Chr07g0185371' => 'lal', 'Lalb_Chr07g0185381' => 'lal', 'Lalb_Chr12g0204011' => 'lal', 'Lalb_Chr13g0301671' => 'lal', 'Lalb_Chr14g0362851' => 'lal', 'Lalb_Chr24g0403581' => 'lal', 'Lj1g0000233' => 'lja', 'Lj2g0018120' => 'lja', 'Lj3C621T0' => 'lonja', 'Lj3P1059T14' => 'lonja', 'Lj3P611T9' => 'lonja', 'Lj3P614T13' => 'lonja', 'Lj3P615T5' => 'lonja', 'Lj4g0012315' => 'lja', 'Lj4g0026182' => 'lja', 'Lj6P813T16' => 'lonja', 'Lj7C427T7' => 'lonja', 'Lj7C427T8' => 'lonja', 'Lj7P600T41' => 'lonja', 'Lju41C42G17' => 'lonja', 'Lsat_1_v5_gn_0_47300' => 'lsa', 'Lsat_1_v5_gn_2_91280' => 'lsa', 'Lsat_1_v5_gn_3_30561' => 'lsa', 'Lsat_1_v5_gn_4_184321' => 'lsa', 'Lsat_1_v5_gn_4_4041' => 'lsa', 'Lsat_1_v5_gn_5_92000' => 'lsa', 'Lsat_1_v5_gn_8_152940' => 'lsa', 'Lsat_1_v5_gn_8_62401' => 'lsa', 'Manes.06G055900' => 'mes', 'Manes.12G022200' => 'mes', 'Manes.13G023300' => 'mes', 'Manes.14G115000' => 'mes', 'Manes.15G151700' => 'mes', 'Manes.17G111300' => 'mes', 'Mapoly0226s0009' => 'mpo', 'MBI02_g25363_MAGBIO' => 'mbi', 'MBI06_g00027_MAGBIO' => 'mbi', 'MBI10_g13034_MAGBIO' => 'mbi', 'MD09G1023400' => 'mdo', 'MD13G1100100' => 'mdo', 'MD15G1169200' => 'mdo', 'MD16G1101100' => 'mdo', 'MD17G1022900' => 'mdo', 'Medtr3g096150' => 'mtr', 'Medtr4g115070' => 'mtr', 'Medtr7g033325' => 'mtr', 'Medtr8g089840' => 'mtr', 'MELO3C010319.2' => 'cme', 'MELO3C011944.2' => 'cme', 'MELO3C021589.2' => 'cme', 'Migut.E00207' => 'egut', 'Migut.H00067' => 'egut', 'Migut.K00433' => 'egut', 'Migut.K00606' => 'egut', 'Migut.K01410' => 'egut', 'MSTRG.13347' => 'ama', 'MSTRG.24045' => 'ama', 'MSTRG.2428' => 'ama', 'MSTRG.26410' => 'ama', 'MSTRG.3139' => 'ama', 'MSTRG.3286' => 'ama', 'MSTRG.563' => 'ama', 'MSTRG.7941' => 'ama', 'Nitab4.5_0000028g0060' => 'nta', 'Nitab4.5_0000065g0260' => 'nta', 'Nitab4.5_0000112g0060' => 'nta', 'Nitab4.5_0000489g0120' => 'nta', 'Nitab4.5_0001776g0050' => 'nta', 'Nitab4.5_0001854g0010' => 'nta', 'Nitab4.5_0001860g0020' => 'nta', 'Nitab4.5_0004352g0010' => 'nta', 'Nitab4.5_0008716g0020' => 'nta', 'Nitab4.5_0008922g0010' => 'nta', 'Nn3g16693' => 'nnu', 'Nn4g22596' => 'nnu', 'Nn7g37639' => 'nnu', 'Oeu001701.1' => 'oeu', 'Oeu018149.1' => 'oeu', 'Oeu026220.1' => 'oeu', 'Oeu038635.1' => 'oeu', 'Oeu049176.1' => 'oeu', 'Oeu056706.1' => 'oeu', 'Oeu056937.1' => 'oeu', 'Oeu057540.1' => 'oeu', 'Os02g0594900' => 'osa', 'Os02g0595100' => 'osa', 'Os04g0477500' => 'osa', 'Os12g0611900' => 'osa', 'Peaxi162Scf00076g00020' => 'pax', 'Peaxi162Scf00128g00217' => 'pax', 'Peaxi162Scf00129g01640' => 'pax', 'Peaxi162Scf00669g00007' => 'pax', 'Peaxi162Scf00700g00421' => 'pax', 'Peaxi162Scf00801g00038' => 'pax', 'Peaxi162Scf00891g00025' => 'pax', 'PGR083G0909' => 'pgr', 'PGR119G1005' => 'pgr', 'PGR142G2236' => 'pgr', 'PGR142G3388' => 'pgr', 'PGSC0003DMG400004514' => 'stu', 'PGSC0003DMG400012635' => 'stu', 'PGSC0003DMG400015730' => 'stu', 'PGSC0003DMG400018611' => 'stu', 'PGSC0003DMG400030897' => 'stu', 'Phvul.001G254800' => 'pvu', 'Phvul.002G260100' => 'pvu', 'Phvul.003G167600' => 'pvu', 'Phvul.004G005100' => 'pvu', 'Potri.001G343600' => 'ptr', 'Potri.006G066700' => 'ptr', 'Potri.008G186000' => 'ptr', 'Potri.010G046900' => 'ptr', 'Potri.018G127900' => 'ptr', 'Pp3c20_17750' => 'ppa', 'Pp3c24_4380' => 'ppa', 'Prupe.1G245800' => 'ppe', 'Prupe.3G293400' => 'ppe', 'Prupe.7G247400' => 'ppe', 'Psat0s145g0120' => 'psa', 'Psat0s595g0040' => 'psa', 'Psat0s595g0120' => 'psa', 'Psat3g175040' => 'psa', 'Psat7g058120' => 'psa', 'PSO017G0428' => 'pso', 'PSO063G7510' => 'pso', 'PSO067G0046' => 'pso', 'PSO478G1073' => 'pso', 'PSO675G3677' => 'pso', 'PSO675G6558' => 'pso', 'PSO675G7520' => 'pso', 'PSO675G8959' => 'pso', 'QL02p074089' => 'qlo', 'QL02p089614' => 'qlo', 'QL03p057736' => 'qlo', 'RcHm_v2.0_Chr1g0364131' => 'rch', 'RcHm_v2.0_Chr2g0087801' => 'rch', 'RcHm_v2.0_Chr2g0087821' => 'rch', 'RcHm_v2.0_Chr2g0173231' => 'rch', 'RcHm_v2.0_Chr4g0433111' => 'rch', 'Rhsim03G0250300' => 'rsi', 'Rhsim08G0048400' => 'rsi', 'Rhsim10G0014800' => 'rsi', 'Rhsim12G0040100' => 'rsi', 'Rhsim12G0109700' => 'rsi', 'Sabra06G0049600' => 'sbr', 'Sabra08G0141000' => 'sbr', 'Sabra10G0021400' => 'sbr', 'Sabra16G0222900' => 'sbr', 'Sabra18G0108600' => 'sbr', 'SalBow1G0433' => 'sbo', 'SalBow1G2038' => 'sbo', 'SalBow1G5003' => 'sbo', 'SalBow7G1197' => 'sbo', 'SalBow8G3506' => 'sbo', 'Sc03g0007300' => 'sci', 'Sc11g0000950' => 'sci', 'Sc14g0008750' => 'sci', 'Sc18g0000420' => 'sci', 'Sed0006754' => 'sed', 'Sed0008741' => 'sed', 'Sed0017172' => 'sed', 'Sed0018925' => 'sed', 'Sed0023326' => 'sed', 'Sed0025909' => 'sed', 'SEGI_05333' => 'sgi', 'SEGI_10362' => 'sgi', 'SEGI_13380' => 'sgi', 'SEGI_24306' => 'sgi', 'SEGI_29077' => 'sgi', 'SEGI_29095' => 'sgi', 'SEGI_36534' => 'sgi', 'SEGI_37506' => 'sgi', 'SEGI_38321' => 'sgi', 'SGA_v2.0_scaffold307G48031' => 'sas', 'SGA_v2.0_scaffold47G17507' => 'sas', 'SGA_v2.0_scaffold63G21736' => 'sas', 'SGA_v2.0_scaffold87G27070' => 'sas', 'SHI17794' => 'shi', 'SHI28851' => 'shi', 'SMO165G0155' => 'smo', 'SMO340G0217' => 'smo', 'SMO367G1210' => 'smo', 'Solyc02g093430.3' => 'sly', 'Solyc05g013580.4' => 'sly', 'Solyc07g008030.3' => 'sly', 'Solyc12g035470.2' => 'sly', 'Sopen02g038020' => 'spe', 'Sopen05g008490' => 'spe', 'Sopen07g003910' => 'spe', 'Sopen12g015240' => 'spe', 'Sp1g11550' => 'spa', 'Sp2g16710' => 'spa', 'Sp3g00430' => 'spa', 'Sp3g26780' => 'spa', 'Sp5g22900' => 'spa', 'Sp6g29530' => 'spa', 'TAR371G0794' => 'tar', 'TAR374G0164' => 'tar', 'TAR622G0165' => 'tar', 'TAR626G0929' => 'tar', 'TAR629G2155' => 'tar', 'THA.LOC104805282' => 'tha', 'THA.LOC104805363' => 'tha', 'THA.LOC104808968' => 'tha', 'THA.LOC104821093' => 'tha', 'THA.LOC104823953' => 'tha', 'THA.LOC104825562' => 'tha', 'THA.LOC104825665' => 'tha', 'Thecc.02G261400' => 'tca', 'Thecc.04G019200' => 'tca', 'Thecc.09G130400' => 'tca', 'Thhalv10004374m.g' => 'esa', 'Thhalv10007850m.g' => 'esa', 'Thhalv10013782m.g' => 'esa', 'Thhalv10018686m.g' => 'esa', 'Thhalv10020899m.g' => 'esa', 'Thhalv10022755m.g' => 'esa', 'TPR.G23851' => 'tpr', 'TPR.G26500' => 'tpr', 'TPR.G27267' => 'tpr', 'TPR.G32001' => 'tpr', 'TPR.G6251' => 'tpr', 'TPR.G8167' => 'tpr', 'TWI12G1330' => 'twi', 'TWI18G1239' => 'twi', 'TWI34G0979' => 'twi', 'TWI36G0670' => 'twi', 'TWI36G0707' => 'twi', 'TWI56G0233' => 'twi', 'TWI75G1809' => 'twi', 'unitig_21.g20874' => 'ugi', 'unitig_26.g10343' => 'ugi', 'unitig_46.g18392' => 'ugi', 'unitig_52.g17178' => 'ugi', 'unitig_8.g2934' => 'ugi', 'vmacro01122' => 'vma', 'vmacro05875' => 'vma', 'vmacro06147' => 'vma', 'vmacro16191' => 'vma', 'vmacro18293' => 'vma', 'VMungo0251G3707' => 'vmu', 'VMungo0464G1521' => 'vmu', 'VMungo1215G0205' => 'vmu', 'VMungo1383G2484' => 'vmu', 'Zm00001eb079610' => 'zma', 'Zm00001eb135990' => 'zma', 'Zm00001eb183710' => 'zma', 'Zm00001eb246020' => 'zma' ), 'gf_id' => 'HOM05D001124', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001124' ), 'data_identifier' => 'HOM05D001124', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001124', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '548', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02520' => 'bna', 'A03p06630' => 'bna', 'A05p44460' => 'bna', 'A06p08710' => 'bna', 'A06p41090' => 'bna', 'A07p32320' => 'bna', 'A08p32520' => 'bna', 'A09p10360' => 'bna', 'A10p24080' => 'bna', 'Aa31LG11G15250' => 'aar', 'Aa31LG1G1800' => 'aar', 'Aa31LG2G5120' => 'aar', 'Aa31LG2G6070' => 'aar', 'Aa31LG5G10770' => 'aar', 'Aa31sc61G90' => 'aar', 'Actinidia01352' => 'ach', 'Actinidia05983' => 'ach', 'Actinidia08133' => 'ach', 'Actinidia15101' => 'ach', 'Actinidia26379' => 'ach', 'Actinidia35778' => 'ach', 'Actinidia36123' => 'ach', 'Actinidia37436' => 'ach', 'Actinidia38730' => 'ach', 'Ah.02g128210' => 'amhyb', 'Ah.03g132990' => 'amhyb', 'Ah.14g079410' => 'amhyb', 'AL1G24640' => 'aly', 'AL2G26680' => 'aly', 'AL3G10530' => 'aly', 'AL3G45230' => 'aly', 'AL5G15230' => 'aly', 'AL5G16960' => 'aly', 'AL6G25210' => 'aly', 'Aqoxy2G00441' => 'aox', 'Aqoxy3G01236' => 'aox', 'Aqoxy5G03746' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3RQ047' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C7GMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9C8JER' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MBL6KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YXCZ83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZANX40' => 'arhy', 'AT1G12990' => 'ath', 'AT1G67880' => 'ath', 'AT2G13290' => 'ath', 'AT3G01620' => 'ath', 'AT3G26445' => 'ath', 'AT3G27540' => 'ath', 'AT5G14480' => 'ath', 'ATR0824G026' => 'atr', 'ATR1098G019' => 'atr', 'Atru.chr11.2145' => 'acertr', 'Atru.chr2.3636' => 'acertr', 'Atru.chr2.3644' => 'acertr', 'Atru.chr6.2422' => 'acertr', 'Atru.chr7.1112' => 'acertr', 'AUR62005469' => 'cqu', 'AUR62011166' => 'cqu', 'AUR62013319' => 'cqu', 'AUR62024273' => 'cqu', 'AUR62028420' => 'cqu', 'AUR62041942' => 'cqu', 'BcaB01g04969' => 'bca', 'BcaB01g06371' => 'bca', 'BcaB02g11494' => 'bca', 'BcaB03g15382' => 'bca', 'BcaB08g36994' => 'bca', 'BcaC03g13477' => 'bca', 'BcaC03g13478' => 'bca', 'BcaC03g13480' => 'bca', 'BcaC03g13481' => 'bca', 'BcaC03g13486' => 'bca', 'BcaC04g19031' => 'bca', 'BcaC04g23085' => 'bca', 'BcaC05g25094' => 'bca', 'BcaC05g25096' => 'bca', 'BcaC05g25138' => 'bca', 'BcaC05g30416' => 'bca', 'BcaC05g30455' => 'bca', 'BcaC06g30979' => 'bca', 'BcaC06g33805' => 'bca', 'BcaC08g46021' => 'bca', 'BcaNung03154' => 'bca', 'BolC2t06623H' => 'bol', 'BolC2t06632H' => 'bol', 'BolC2t06635H' => 'bol', 'BolC2t06638H' => 'bol', 'BolC3t13266H' => 'bol', 'BolC5t29776H' => 'bol', 'BolC6t38912H' => 'bol', 'BolC7t44183H' => 'bol', 'BolC9t54123H' => 'bol', 'BolC9t59107H' => 'bol', 'BraA02t05221Z' => 'bra', 'BraA03t09996Z' => 'bra', 'BraA05t23210Z' => 'bra', 'BraA06t24068Z' => 'bra', 'BraA06t27032Z' => 'bra', 'BraA08t35176Z' => 'bra', 'BraA09t36680Z' => 'bra', 'BraA10t44471Z' => 'bra', 'C02p06760' => 'bna', 'C02p06890' => 'bna', 'C02p07010' => 'bna', 'C03p07660' => 'bna', 'C05p10300' => 'bna', 'C06p38150' => 'bna', 'C07p36650' => 'bna', 'C08p15770' => 'bna', 'C09p12300' => 'bna', 'C09p62700' => 'bna', 'C09p75040' => 'bna', 'CAN.G13.1' => 'can', 'CAN.G138.4' => 'can', 'CAN.G44.6' => 'can', 'CAN.G473.19' => 'can', 'CANSAT01G0835' => 'cansat', 'CANSAT11G0246' => 'cansat', 'CANSAT11G1766' => 'cansat', 'CANSAT64G1954' => 'cansat', 'CARHR013330' => 'chi', 'CARHR060530' => 'chi', 'CARHR075300' => 'chi', 'CARHR105120' => 'chi', 'CARHR148910' => 'chi', 'CARHR198830' => 'chi', 'Carub.0001s1275' => 'cru', 'Carub.0002s1437' => 'cru', 'Carub.0003s0044' => 'cru', 'Carub.0003s2787' => 'cru', 'Carub.0005s0597' => 'cru', 'Carub.0006s1266' => 'cru', 'Ca_06935_v3' => 'car', 'Ca_13559_v3' => 'car', 'Ca_16941_v3' => 'car', 'Ca_16960_v3' => 'car', 'Ca_17775_v3' => 'car', 'Ca_30464_v3' => 'car', 'Cc06_g08160' => 'ccan', 'Cc07_g01520' => 'ccan', 'Cc11_g15810' => 'ccan', 'CDE02G2840' => 'cde', 'CDE03G0093' => 'cde', 'CDE04G2127' => 'cde', 'CDE07G1857' => 'cde', 'CDE09G1246' => 'cde', 'Cfa003412' => 'cfa', 'Cfa007341' => 'cfa', 'Cfa009220' => 'cfa', 'Ciclev10008737m.g' => 'ccl', 'Ciclev10015565m.g' => 'ccl', 'Ciclev10031761m.g' => 'ccl', 'CiPaw.03G045300' => 'cil', 'CiPaw.03G247200' => 'cil', 'CiPaw.04G029500' => 'cil', 'CiPaw.04G174000' => 'cil', 'CiPaw.05G181200' => 'cil', 'CiPaw.06G067100' => 'cil', 'ClCG05G025800' => 'cla', 'ClCG06G011400' => 'cla', 'ClCG09G019360' => 'cla', 'COL.COLO4_04827' => 'col', 'COL.COLO4_29170' => 'col', 'COL.COLO4_35131' => 'col', 'COL.COLO4_35132' => 'col', 'Cpa.g.sc33.32' => 'cpa', 'Cpa.g.sc46.29' => 'cpa', 'Cpa.g.sc796.1' => 'cpa', 'CsaV3_1G030420' => 'csa', 'CsaV3_5G027050' => 'csa', 'CsaV3_5G031040' => 'csa', 'CsaV3_UNG023130' => 'csa', 'CSS0007726' => 'camsi', 'CSS0016433' => 'camsi', 'CSS0017656' => 'camsi', 'CSS0025364' => 'camsi', 'CSS0027582' => 'camsi', 'CSS0047288' => 'camsi', 'CSS0049950' => 'camsi', 'DCAR_003843' => 'dca', 'DCAR_007052' => 'dca', 'DCAR_020884' => 'dca', 'DCAR_021730' => 'dca', 'DCAR_024423' => 'dca', 'DCAR_026509' => 'dca', 'DCAR_031158' => 'dca', 'Dinv14728' => 'din', 'Dinv15219' => 'din', 'Dinv25728' => 'din', 'Dinv33428' => 'din', 'Dinv36489' => 'din', 'Dinv41486' => 'din', 'Duzib147G0469' => 'dzi', 'Duzib168G0060' => 'dzi', 'Duzib187G1215' => 'dzi', 'Duzib248G0692' => 'dzi', 'Duzib251G0767' => 'dzi', 'Duzib264G0446' => 'dzi', 'Duzib268G0691' => 'dzi', 'ECA232G4767' => 'eca', 'ECA233G2838' => 'eca', 'ECA234G0391' => 'eca', 'ECA234G0857' => 'eca', 'ECA236G1593' => 'eca', 'ECA238G0565' => 'eca', 'ECA246G1027' => 'eca', 'ECA246G3223' => 'eca', 'ECA246G3470' => 'eca', 'EL10Ac6g13829' => 'bvu', 'EL10Ac6g14093' => 'bvu', 'EL10Ac8g18707' => 'bvu', 'Eucgr.C01369' => 'egr', 'Eucgr.H02492' => 'egr', 'Eucgr.I01733' => 'egr', 'Eucgr.J02255' => 'egr', 'Eucgr.J02257' => 'egr', 'Eucgr.J02258' => 'egr', 'FAN02G1601' => 'fan', 'FAN03G1586' => 'fan', 'FAN03G2986' => 'fan', 'FAN05G4837' => 'fan', 'FAN06G0146' => 'fan', 'FAN07G0858' => 'fan', 'FAN09G3179' => 'fan', 'FAN10G0669' => 'fan', 'FAN12G2358' => 'fan', 'FAN14G4198' => 'fan', 'FAN14G5112' => 'fan', 'FAN17G0342' => 'fan', 'FAN19G0342' => 'fan', 'FAN19G0962' => 'fan', 'FAN19G1101' => 'fan', 'FAN19G1872' => 'fan', 'FAN22G0356' => 'fan', 'FAN23G0744' => 'fan', 'FAN23G1914' => 'fan', 'FAN26G0032' => 'fan', 'FAN28G0625' => 'fan', 'FvH4_1g02710' => 'fve', 'FvH4_1g02720' => 'fve', 'FvH4_4g25670' => 'fve', 'FvH4_6g51700' => 'fve', 'FvH4_7g20170' => 'fve', 'Glyma.05G175000' => 'gma', 'Glyma.08G132300' => 'gma', 'Glyma.11G243000' => 'gma', 'Glyma.13G158900' => 'gma', 'Glyma.17G112400' => 'gma', 'Glyma.18G014100' => 'gma', 'Glyma.19G003100' => 'gma', 'Glyma.19G056500' => 'gma', 'Gohir.A01G158900' => 'ghi', 'Gohir.A05G312600' => 'ghi', 'Gohir.A05G354900' => 'ghi', 'Gohir.A07G037200' => 'ghi', 'Gohir.A09G030000' => 'ghi', 'Gohir.A12G145200' => 'ghi', 'Gohir.D01G151500' => 'ghi', 'Gohir.D04G058300' => 'ghi', 'Gohir.D05G314100' => 'ghi', 'Gohir.D07G041400' => 'ghi', 'Gohir.D09G029700' => 'ghi', 'Gohir.D12G149700' => 'ghi', 'Gorai.001G043800' => 'gra', 'Gorai.002G187800' => 'gra', 'Gorai.006G034700' => 'gra', 'Gorai.008G161200' => 'gra', 'Gorai.009G335700' => 'gra', 'Gorai.012G065000' => 'gra', 'GSVIVG01000535001' => 'vvi', 'GSVIVG01015572001' => 'vvi', 'GSVIVG01032386001' => 'vvi', 'HanXRQChr05g0138531' => 'han', 'HanXRQChr06g0174391' => 'han', 'HanXRQChr07g0199021' => 'han', 'HanXRQChr08g0208211' => 'han', 'HanXRQChr09g0255471' => 'han', 'HanXRQChr10g0315791' => 'han', 'HanXRQChr12g0371991' => 'han', 'HanXRQChr15g0475251' => 'han', 'HanXRQChr17g0540001' => 'han', 'HanXRQChr17g0548631' => 'han', 'HanXRQChr17g0569561' => 'han', 'Haze_12256' => 'cav', 'Haze_14756' => 'cav', 'Haze_25528' => 'cav', 'Hma1.2p1_0079F.1_g041020' => 'hma', 'Hma1.2p1_0818F.1_g223260' => 'hma', 'Hma1.2p1_1747F.1_g300530' => 'hma', 'HPP92_004607' => 'vpl', 'HPP92_004608' => 'vpl', 'HPP92_006181' => 'vpl', 'HPP92_012192' => 'vpl', 'HPP92_015680' => 'vpl', 'HPP92_020249' => 'vpl', 'HPP92_021376' => 'vpl', 'HPP92_024275' => 'vpl', 'Hund06031' => 'sun', 'Hund25391' => 'sun', 'Lalb_Chr07g0185371' => 'lal', 'Lalb_Chr07g0185381' => 'lal', 'Lalb_Chr12g0204011' => 'lal', 'Lalb_Chr13g0301671' => 'lal', 'Lalb_Chr14g0362851' => 'lal', 'Lalb_Chr24g0403581' => 'lal', 'Lj1g0000233' => 'lja', 'Lj2g0018120' => 'lja', 'Lj3C621T0' => 'lonja', 'Lj3P1059T14' => 'lonja', 'Lj3P611T9' => 'lonja', 'Lj3P614T13' => 'lonja', 'Lj3P615T5' => 'lonja', 'Lj4g0012315' => 'lja', 'Lj4g0026182' => 'lja', 'Lj6P813T16' => 'lonja', 'Lj7C427T7' => 'lonja', 'Lj7C427T8' => 'lonja', 'Lj7P600T41' => 'lonja', 'Lju41C42G17' => 'lonja', 'Lsat_1_v5_gn_0_47300' => 'lsa', 'Lsat_1_v5_gn_2_91280' => 'lsa', 'Lsat_1_v5_gn_3_30561' => 'lsa', 'Lsat_1_v5_gn_4_184321' => 'lsa', 'Lsat_1_v5_gn_4_4041' => 'lsa', 'Lsat_1_v5_gn_5_92000' => 'lsa', 'Lsat_1_v5_gn_8_152940' => 'lsa', 'Lsat_1_v5_gn_8_62401' => 'lsa', 'Manes.06G055900' => 'mes', 'Manes.12G022200' => 'mes', 'Manes.13G023300' => 'mes', 'Manes.14G115000' => 'mes', 'Manes.15G151700' => 'mes', 'Manes.17G111300' => 'mes', 'Mapoly0226s0009' => 'mpo', 'MBI02_g25363_MAGBIO' => 'mbi', 'MBI06_g00027_MAGBIO' => 'mbi', 'MBI10_g13034_MAGBIO' => 'mbi', 'MD09G1023400' => 'mdo', 'MD13G1100100' => 'mdo', 'MD15G1169200' => 'mdo', 'MD16G1101100' => 'mdo', 'MD17G1022900' => 'mdo', 'Medtr3g096150' => 'mtr', 'Medtr4g115070' => 'mtr', 'Medtr7g033325' => 'mtr', 'Medtr8g089840' => 'mtr', 'MELO3C010319.2' => 'cme', 'MELO3C011944.2' => 'cme', 'MELO3C021589.2' => 'cme', 'Migut.E00207' => 'egut', 'Migut.H00067' => 'egut', 'Migut.K00433' => 'egut', 'Migut.K00606' => 'egut', 'Migut.K01410' => 'egut', 'MSTRG.13347' => 'ama', 'MSTRG.24045' => 'ama', 'MSTRG.2428' => 'ama', 'MSTRG.26410' => 'ama', 'MSTRG.3139' => 'ama', 'MSTRG.3286' => 'ama', 'MSTRG.563' => 'ama', 'MSTRG.7941' => 'ama', 'Nitab4.5_0000028g0060' => 'nta', 'Nitab4.5_0000065g0260' => 'nta', 'Nitab4.5_0000112g0060' => 'nta', 'Nitab4.5_0000489g0120' => 'nta', 'Nitab4.5_0001776g0050' => 'nta', 'Nitab4.5_0001854g0010' => 'nta', 'Nitab4.5_0001860g0020' => 'nta', 'Nitab4.5_0004352g0010' => 'nta', 'Nitab4.5_0008716g0020' => 'nta', 'Nitab4.5_0008922g0010' => 'nta', 'Nn3g16693' => 'nnu', 'Nn4g22596' => 'nnu', 'Nn7g37639' => 'nnu', 'Oeu001701.1' => 'oeu', 'Oeu018149.1' => 'oeu', 'Oeu026220.1' => 'oeu', 'Oeu038635.1' => 'oeu', 'Oeu049176.1' => 'oeu', 'Oeu056706.1' => 'oeu', 'Oeu056937.1' => 'oeu', 'Oeu057540.1' => 'oeu', 'Os02g0594900' => 'osa', 'Os02g0595100' => 'osa', 'Os04g0477500' => 'osa', 'Os12g0611900' => 'osa', 'Peaxi162Scf00076g00020' => 'pax', 'Peaxi162Scf00128g00217' => 'pax', 'Peaxi162Scf00129g01640' => 'pax', 'Peaxi162Scf00669g00007' => 'pax', 'Peaxi162Scf00700g00421' => 'pax', 'Peaxi162Scf00801g00038' => 'pax', 'Peaxi162Scf00891g00025' => 'pax', 'PGR083G0909' => 'pgr', 'PGR119G1005' => 'pgr', 'PGR142G2236' => 'pgr', 'PGR142G3388' => 'pgr', 'PGSC0003DMG400004514' => 'stu', 'PGSC0003DMG400012635' => 'stu', 'PGSC0003DMG400015730' => 'stu', 'PGSC0003DMG400018611' => 'stu', 'PGSC0003DMG400030897' => 'stu', 'Phvul.001G254800' => 'pvu', 'Phvul.002G260100' => 'pvu', 'Phvul.003G167600' => 'pvu', 'Phvul.004G005100' => 'pvu', 'Potri.001G343600' => 'ptr', 'Potri.006G066700' => 'ptr', 'Potri.008G186000' => 'ptr', 'Potri.010G046900' => 'ptr', 'Potri.018G127900' => 'ptr', 'Pp3c20_17750' => 'ppa', 'Pp3c24_4380' => 'ppa', 'Prupe.1G245800' => 'ppe', 'Prupe.3G293400' => 'ppe', 'Prupe.7G247400' => 'ppe', 'Psat0s145g0120' => 'psa', 'Psat0s595g0040' => 'psa', 'Psat0s595g0120' => 'psa', 'Psat3g175040' => 'psa', 'Psat7g058120' => 'psa', 'PSO017G0428' => 'pso', 'PSO063G7510' => 'pso', 'PSO067G0046' => 'pso', 'PSO478G1073' => 'pso', 'PSO675G3677' => 'pso', 'PSO675G6558' => 'pso', 'PSO675G7520' => 'pso', 'PSO675G8959' => 'pso', 'QL02p074089' => 'qlo', 'QL02p089614' => 'qlo', 'QL03p057736' => 'qlo', 'RcHm_v2.0_Chr1g0364131' => 'rch', 'RcHm_v2.0_Chr2g0087801' => 'rch', 'RcHm_v2.0_Chr2g0087821' => 'rch', 'RcHm_v2.0_Chr2g0173231' => 'rch', 'RcHm_v2.0_Chr4g0433111' => 'rch', 'Rhsim03G0250300' => 'rsi', 'Rhsim08G0048400' => 'rsi', 'Rhsim10G0014800' => 'rsi', 'Rhsim12G0040100' => 'rsi', 'Rhsim12G0109700' => 'rsi', 'Sabra06G0049600' => 'sbr', 'Sabra08G0141000' => 'sbr', 'Sabra10G0021400' => 'sbr', 'Sabra16G0222900' => 'sbr', 'Sabra18G0108600' => 'sbr', 'SalBow1G0433' => 'sbo', 'SalBow1G2038' => 'sbo', 'SalBow1G5003' => 'sbo', 'SalBow7G1197' => 'sbo', 'SalBow8G3506' => 'sbo', 'Sc03g0007300' => 'sci', 'Sc11g0000950' => 'sci', 'Sc14g0008750' => 'sci', 'Sc18g0000420' => 'sci', 'Sed0006754' => 'sed', 'Sed0008741' => 'sed', 'Sed0017172' => 'sed', 'Sed0018925' => 'sed', 'Sed0023326' => 'sed', 'Sed0025909' => 'sed', 'SEGI_05333' => 'sgi', 'SEGI_10362' => 'sgi', 'SEGI_13380' => 'sgi', 'SEGI_24306' => 'sgi', 'SEGI_29077' => 'sgi', 'SEGI_29095' => 'sgi', 'SEGI_36534' => 'sgi', 'SEGI_37506' => 'sgi', 'SEGI_38321' => 'sgi', 'SGA_v2.0_scaffold307G48031' => 'sas', 'SGA_v2.0_scaffold47G17507' => 'sas', 'SGA_v2.0_scaffold63G21736' => 'sas', 'SGA_v2.0_scaffold87G27070' => 'sas', 'SHI17794' => 'shi', 'SHI28851' => 'shi', 'SMO165G0155' => 'smo', 'SMO340G0217' => 'smo', 'SMO367G1210' => 'smo', 'Solyc02g093430.3' => 'sly', 'Solyc05g013580.4' => 'sly', 'Solyc07g008030.3' => 'sly', 'Solyc12g035470.2' => 'sly', 'Sopen02g038020' => 'spe', 'Sopen05g008490' => 'spe', 'Sopen07g003910' => 'spe', 'Sopen12g015240' => 'spe', 'Sp1g11550' => 'spa', 'Sp2g16710' => 'spa', 'Sp3g00430' => 'spa', 'Sp3g26780' => 'spa', 'Sp5g22900' => 'spa', 'Sp6g29530' => 'spa', 'TAR371G0794' => 'tar', 'TAR374G0164' => 'tar', 'TAR622G0165' => 'tar', 'TAR626G0929' => 'tar', 'TAR629G2155' => 'tar', 'THA.LOC104805282' => 'tha', 'THA.LOC104805363' => 'tha', 'THA.LOC104808968' => 'tha', 'THA.LOC104821093' => 'tha', 'THA.LOC104823953' => 'tha', 'THA.LOC104825562' => 'tha', 'THA.LOC104825665' => 'tha', 'Thecc.02G261400' => 'tca', 'Thecc.04G019200' => 'tca', 'Thecc.09G130400' => 'tca', 'Thhalv10004374m.g' => 'esa', 'Thhalv10007850m.g' => 'esa', 'Thhalv10013782m.g' => 'esa', 'Thhalv10018686m.g' => 'esa', 'Thhalv10020899m.g' => 'esa', 'Thhalv10022755m.g' => 'esa', 'TPR.G23851' => 'tpr', 'TPR.G26500' => 'tpr', 'TPR.G27267' => 'tpr', 'TPR.G32001' => 'tpr', 'TPR.G6251' => 'tpr', 'TPR.G8167' => 'tpr', 'TWI12G1330' => 'twi', 'TWI18G1239' => 'twi', 'TWI34G0979' => 'twi', 'TWI36G0670' => 'twi', 'TWI36G0707' => 'twi', 'TWI56G0233' => 'twi', 'TWI75G1809' => 'twi', 'unitig_21.g20874' => 'ugi', 'unitig_26.g10343' => 'ugi', 'unitig_46.g18392' => 'ugi', 'unitig_52.g17178' => 'ugi', 'unitig_8.g2934' => 'ugi', 'vmacro01122' => 'vma', 'vmacro05875' => 'vma', 'vmacro06147' => 'vma', 'vmacro16191' => 'vma', 'vmacro18293' => 'vma', 'VMungo0251G3707' => 'vmu', 'VMungo0464G1521' => 'vmu', 'VMungo1215G0205' => 'vmu', 'VMungo1383G2484' => 'vmu', 'Zm00001eb079610' => 'zma', 'Zm00001eb135990' => 'zma', 'Zm00001eb183710' => 'zma', 'Zm00001eb246020' => 'zma' ) $gf_id = 'HOM05D001124' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001124' ) $data_identifier = 'HOM05D001124' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 6, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 7, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 21, 'bol' => (int) 10, 'bra' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 6, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 9, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 21, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 8, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 10, 'lsa' => (int) 8, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 8, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 9, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb246020' $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' => 'HOM05D001124', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '548', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02520' => 'bna', 'A03p06630' => 'bna', 'A05p44460' => 'bna', 'A06p08710' => 'bna', 'A06p41090' => 'bna', 'A07p32320' => 'bna', 'A08p32520' => 'bna', 'A09p10360' => 'bna', 'A10p24080' => 'bna', 'Aa31LG11G15250' => 'aar', 'Aa31LG1G1800' => 'aar', 'Aa31LG2G5120' => 'aar', 'Aa31LG2G6070' => 'aar', 'Aa31LG5G10770' => 'aar', 'Aa31sc61G90' => 'aar', 'Actinidia01352' => 'ach', 'Actinidia05983' => 'ach', 'Actinidia08133' => 'ach', 'Actinidia15101' => 'ach', 'Actinidia26379' => 'ach', 'Actinidia35778' => 'ach', 'Actinidia36123' => 'ach', 'Actinidia37436' => 'ach', 'Actinidia38730' => 'ach', 'Ah.02g128210' => 'amhyb', 'Ah.03g132990' => 'amhyb', 'Ah.14g079410' => 'amhyb', 'AL1G24640' => 'aly', 'AL2G26680' => 'aly', 'AL3G10530' => 'aly', 'AL3G45230' => 'aly', 'AL5G15230' => 'aly', 'AL5G16960' => 'aly', 'AL6G25210' => 'aly', 'Aqoxy2G00441' => 'aox', 'Aqoxy3G01236' => 'aox', 'Aqoxy5G03746' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3RQ047' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C7GMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9C8JER' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MBL6KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YXCZ83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZANX40' => 'arhy', 'AT1G12990' => 'ath', 'AT1G67880' => 'ath', 'AT2G13290' => 'ath', 'AT3G01620' => 'ath', 'AT3G26445' => 'ath', 'AT3G27540' => 'ath', 'AT5G14480' => 'ath', 'ATR0824G026' => 'atr', 'ATR1098G019' => 'atr', 'Atru.chr11.2145' => 'acertr', 'Atru.chr2.3636' => 'acertr', 'Atru.chr2.3644' => 'acertr', 'Atru.chr6.2422' => 'acertr', 'Atru.chr7.1112' => 'acertr', 'AUR62005469' => 'cqu', 'AUR62011166' => 'cqu', 'AUR62013319' => 'cqu', 'AUR62024273' => 'cqu', 'AUR62028420' => 'cqu', 'AUR62041942' => 'cqu', 'BcaB01g04969' => 'bca', 'BcaB01g06371' => 'bca', 'BcaB02g11494' => 'bca', 'BcaB03g15382' => 'bca', 'BcaB08g36994' => 'bca', 'BcaC03g13477' => 'bca', 'BcaC03g13478' => 'bca', 'BcaC03g13480' => 'bca', 'BcaC03g13481' => 'bca', 'BcaC03g13486' => 'bca', 'BcaC04g19031' => 'bca', 'BcaC04g23085' => 'bca', 'BcaC05g25094' => 'bca', 'BcaC05g25096' => 'bca', 'BcaC05g25138' => 'bca', 'BcaC05g30416' => 'bca', 'BcaC05g30455' => 'bca', 'BcaC06g30979' => 'bca', 'BcaC06g33805' => 'bca', 'BcaC08g46021' => 'bca', 'BcaNung03154' => 'bca', 'BolC2t06623H' => 'bol', 'BolC2t06632H' => 'bol', 'BolC2t06635H' => 'bol', 'BolC2t06638H' => 'bol', 'BolC3t13266H' => 'bol', 'BolC5t29776H' => 'bol', 'BolC6t38912H' => 'bol', 'BolC7t44183H' => 'bol', 'BolC9t54123H' => 'bol', 'BolC9t59107H' => 'bol', 'BraA02t05221Z' => 'bra', 'BraA03t09996Z' => 'bra', 'BraA05t23210Z' => 'bra', 'BraA06t24068Z' => 'bra', 'BraA06t27032Z' => 'bra', 'BraA08t35176Z' => 'bra', 'BraA09t36680Z' => 'bra', 'BraA10t44471Z' => 'bra', 'C02p06760' => 'bna', 'C02p06890' => 'bna', 'C02p07010' => 'bna', 'C03p07660' => 'bna', 'C05p10300' => 'bna', 'C06p38150' => 'bna', 'C07p36650' => 'bna', 'C08p15770' => 'bna', 'C09p12300' => 'bna', 'C09p62700' => 'bna', 'C09p75040' => 'bna', 'CAN.G13.1' => 'can', 'CAN.G138.4' => 'can', 'CAN.G44.6' => 'can', 'CAN.G473.19' => 'can', 'CANSAT01G0835' => 'cansat', 'CANSAT11G0246' => 'cansat', 'CANSAT11G1766' => 'cansat', 'CANSAT64G1954' => 'cansat', 'CARHR013330' => 'chi', 'CARHR060530' => 'chi', 'CARHR075300' => 'chi', 'CARHR105120' => 'chi', 'CARHR148910' => 'chi', 'CARHR198830' => 'chi', 'Carub.0001s1275' => 'cru', 'Carub.0002s1437' => 'cru', 'Carub.0003s0044' => 'cru', 'Carub.0003s2787' => 'cru', 'Carub.0005s0597' => 'cru', 'Carub.0006s1266' => 'cru', 'Ca_06935_v3' => 'car', 'Ca_13559_v3' => 'car', 'Ca_16941_v3' => 'car', 'Ca_16960_v3' => 'car', 'Ca_17775_v3' => 'car', 'Ca_30464_v3' => 'car', 'Cc06_g08160' => 'ccan', 'Cc07_g01520' => 'ccan', 'Cc11_g15810' => 'ccan', 'CDE02G2840' => 'cde', 'CDE03G0093' => 'cde', 'CDE04G2127' => 'cde', 'CDE07G1857' => 'cde', 'CDE09G1246' => 'cde', 'Cfa003412' => 'cfa', 'Cfa007341' => 'cfa', 'Cfa009220' => 'cfa', 'Ciclev10008737m.g' => 'ccl', 'Ciclev10015565m.g' => 'ccl', 'Ciclev10031761m.g' => 'ccl', 'CiPaw.03G045300' => 'cil', 'CiPaw.03G247200' => 'cil', 'CiPaw.04G029500' => 'cil', 'CiPaw.04G174000' => 'cil', 'CiPaw.05G181200' => 'cil', 'CiPaw.06G067100' => 'cil', 'ClCG05G025800' => 'cla', 'ClCG06G011400' => 'cla', 'ClCG09G019360' => 'cla', 'COL.COLO4_04827' => 'col', 'COL.COLO4_29170' => 'col', 'COL.COLO4_35131' => 'col', 'COL.COLO4_35132' => 'col', 'Cpa.g.sc33.32' => 'cpa', 'Cpa.g.sc46.29' => 'cpa', 'Cpa.g.sc796.1' => 'cpa', 'CsaV3_1G030420' => 'csa', 'CsaV3_5G027050' => 'csa', 'CsaV3_5G031040' => 'csa', 'CsaV3_UNG023130' => 'csa', 'CSS0007726' => 'camsi', 'CSS0016433' => 'camsi', 'CSS0017656' => 'camsi', 'CSS0025364' => 'camsi', 'CSS0027582' => 'camsi', 'CSS0047288' => 'camsi', 'CSS0049950' => 'camsi', 'DCAR_003843' => 'dca', 'DCAR_007052' => 'dca', 'DCAR_020884' => 'dca', 'DCAR_021730' => 'dca', 'DCAR_024423' => 'dca', 'DCAR_026509' => 'dca', 'DCAR_031158' => 'dca', 'Dinv14728' => 'din', 'Dinv15219' => 'din', 'Dinv25728' => 'din', 'Dinv33428' => 'din', 'Dinv36489' => 'din', 'Dinv41486' => 'din', 'Duzib147G0469' => 'dzi', 'Duzib168G0060' => 'dzi', 'Duzib187G1215' => 'dzi', 'Duzib248G0692' => 'dzi', 'Duzib251G0767' => 'dzi', 'Duzib264G0446' => 'dzi', 'Duzib268G0691' => 'dzi', 'ECA232G4767' => 'eca', 'ECA233G2838' => 'eca', 'ECA234G0391' => 'eca', 'ECA234G0857' => 'eca', 'ECA236G1593' => 'eca', 'ECA238G0565' => 'eca', 'ECA246G1027' => 'eca', 'ECA246G3223' => 'eca', 'ECA246G3470' => 'eca', 'EL10Ac6g13829' => 'bvu', 'EL10Ac6g14093' => 'bvu', 'EL10Ac8g18707' => 'bvu', 'Eucgr.C01369' => 'egr', 'Eucgr.H02492' => 'egr', 'Eucgr.I01733' => 'egr', 'Eucgr.J02255' => 'egr', 'Eucgr.J02257' => 'egr', 'Eucgr.J02258' => 'egr', 'FAN02G1601' => 'fan', 'FAN03G1586' => 'fan', 'FAN03G2986' => 'fan', 'FAN05G4837' => 'fan', 'FAN06G0146' => 'fan', 'FAN07G0858' => 'fan', 'FAN09G3179' => 'fan', 'FAN10G0669' => 'fan', 'FAN12G2358' => 'fan', 'FAN14G4198' => 'fan', 'FAN14G5112' => 'fan', 'FAN17G0342' => 'fan', 'FAN19G0342' => 'fan', 'FAN19G0962' => 'fan', 'FAN19G1101' => 'fan', 'FAN19G1872' => 'fan', 'FAN22G0356' => 'fan', 'FAN23G0744' => 'fan', 'FAN23G1914' => 'fan', 'FAN26G0032' => 'fan', 'FAN28G0625' => 'fan', 'FvH4_1g02710' => 'fve', 'FvH4_1g02720' => 'fve', 'FvH4_4g25670' => 'fve', 'FvH4_6g51700' => 'fve', 'FvH4_7g20170' => 'fve', 'Glyma.05G175000' => 'gma', 'Glyma.08G132300' => 'gma', 'Glyma.11G243000' => 'gma', 'Glyma.13G158900' => 'gma', 'Glyma.17G112400' => 'gma', 'Glyma.18G014100' => 'gma', 'Glyma.19G003100' => 'gma', 'Glyma.19G056500' => 'gma', 'Gohir.A01G158900' => 'ghi', 'Gohir.A05G312600' => 'ghi', 'Gohir.A05G354900' => 'ghi', 'Gohir.A07G037200' => 'ghi', 'Gohir.A09G030000' => 'ghi', 'Gohir.A12G145200' => 'ghi', 'Gohir.D01G151500' => 'ghi', 'Gohir.D04G058300' => 'ghi', 'Gohir.D05G314100' => 'ghi', 'Gohir.D07G041400' => 'ghi', 'Gohir.D09G029700' => 'ghi', 'Gohir.D12G149700' => 'ghi', 'Gorai.001G043800' => 'gra', 'Gorai.002G187800' => 'gra', 'Gorai.006G034700' => 'gra', 'Gorai.008G161200' => 'gra', 'Gorai.009G335700' => 'gra', 'Gorai.012G065000' => 'gra', 'GSVIVG01000535001' => 'vvi', 'GSVIVG01015572001' => 'vvi', 'GSVIVG01032386001' => 'vvi', 'HanXRQChr05g0138531' => 'han', 'HanXRQChr06g0174391' => 'han', 'HanXRQChr07g0199021' => 'han', 'HanXRQChr08g0208211' => 'han', 'HanXRQChr09g0255471' => 'han', 'HanXRQChr10g0315791' => 'han', 'HanXRQChr12g0371991' => 'han', 'HanXRQChr15g0475251' => 'han', 'HanXRQChr17g0540001' => 'han', 'HanXRQChr17g0548631' => 'han', 'HanXRQChr17g0569561' => 'han', 'Haze_12256' => 'cav', 'Haze_14756' => 'cav', 'Haze_25528' => 'cav', 'Hma1.2p1_0079F.1_g041020' => 'hma', 'Hma1.2p1_0818F.1_g223260' => 'hma', 'Hma1.2p1_1747F.1_g300530' => 'hma', 'HPP92_004607' => 'vpl', 'HPP92_004608' => 'vpl', 'HPP92_006181' => 'vpl', 'HPP92_012192' => 'vpl', 'HPP92_015680' => 'vpl', 'HPP92_020249' => 'vpl', 'HPP92_021376' => 'vpl', 'HPP92_024275' => 'vpl', 'Hund06031' => 'sun', 'Hund25391' => 'sun', 'Lalb_Chr07g0185371' => 'lal', 'Lalb_Chr07g0185381' => 'lal', 'Lalb_Chr12g0204011' => 'lal', 'Lalb_Chr13g0301671' => 'lal', 'Lalb_Chr14g0362851' => 'lal', 'Lalb_Chr24g0403581' => 'lal', 'Lj1g0000233' => 'lja', 'Lj2g0018120' => 'lja', 'Lj3C621T0' => 'lonja', 'Lj3P1059T14' => 'lonja', 'Lj3P611T9' => 'lonja', 'Lj3P614T13' => 'lonja', 'Lj3P615T5' => 'lonja', 'Lj4g0012315' => 'lja', 'Lj4g0026182' => 'lja', 'Lj6P813T16' => 'lonja', 'Lj7C427T7' => 'lonja', 'Lj7C427T8' => 'lonja', 'Lj7P600T41' => 'lonja', 'Lju41C42G17' => 'lonja', 'Lsat_1_v5_gn_0_47300' => 'lsa', 'Lsat_1_v5_gn_2_91280' => 'lsa', 'Lsat_1_v5_gn_3_30561' => 'lsa', 'Lsat_1_v5_gn_4_184321' => 'lsa', 'Lsat_1_v5_gn_4_4041' => 'lsa', 'Lsat_1_v5_gn_5_92000' => 'lsa', 'Lsat_1_v5_gn_8_152940' => 'lsa', 'Lsat_1_v5_gn_8_62401' => 'lsa', 'Manes.06G055900' => 'mes', 'Manes.12G022200' => 'mes', 'Manes.13G023300' => 'mes', 'Manes.14G115000' => 'mes', 'Manes.15G151700' => 'mes', 'Manes.17G111300' => 'mes', 'Mapoly0226s0009' => 'mpo', 'MBI02_g25363_MAGBIO' => 'mbi', 'MBI06_g00027_MAGBIO' => 'mbi', 'MBI10_g13034_MAGBIO' => 'mbi', 'MD09G1023400' => 'mdo', 'MD13G1100100' => 'mdo', 'MD15G1169200' => 'mdo', 'MD16G1101100' => 'mdo', 'MD17G1022900' => 'mdo', 'Medtr3g096150' => 'mtr', 'Medtr4g115070' => 'mtr', 'Medtr7g033325' => 'mtr', 'Medtr8g089840' => 'mtr', 'MELO3C010319.2' => 'cme', 'MELO3C011944.2' => 'cme', 'MELO3C021589.2' => 'cme', 'Migut.E00207' => 'egut', 'Migut.H00067' => 'egut', 'Migut.K00433' => 'egut', 'Migut.K00606' => 'egut', 'Migut.K01410' => 'egut', 'MSTRG.13347' => 'ama', 'MSTRG.24045' => 'ama', 'MSTRG.2428' => 'ama', 'MSTRG.26410' => 'ama', 'MSTRG.3139' => 'ama', 'MSTRG.3286' => 'ama', 'MSTRG.563' => 'ama', 'MSTRG.7941' => 'ama', 'Nitab4.5_0000028g0060' => 'nta', 'Nitab4.5_0000065g0260' => 'nta', 'Nitab4.5_0000112g0060' => 'nta', 'Nitab4.5_0000489g0120' => 'nta', 'Nitab4.5_0001776g0050' => 'nta', 'Nitab4.5_0001854g0010' => 'nta', 'Nitab4.5_0001860g0020' => 'nta', 'Nitab4.5_0004352g0010' => 'nta', 'Nitab4.5_0008716g0020' => 'nta', 'Nitab4.5_0008922g0010' => 'nta', 'Nn3g16693' => 'nnu', 'Nn4g22596' => 'nnu', 'Nn7g37639' => 'nnu', 'Oeu001701.1' => 'oeu', 'Oeu018149.1' => 'oeu', 'Oeu026220.1' => 'oeu', 'Oeu038635.1' => 'oeu', 'Oeu049176.1' => 'oeu', 'Oeu056706.1' => 'oeu', 'Oeu056937.1' => 'oeu', 'Oeu057540.1' => 'oeu', 'Os02g0594900' => 'osa', 'Os02g0595100' => 'osa', 'Os04g0477500' => 'osa', 'Os12g0611900' => 'osa', 'Peaxi162Scf00076g00020' => 'pax', 'Peaxi162Scf00128g00217' => 'pax', 'Peaxi162Scf00129g01640' => 'pax', 'Peaxi162Scf00669g00007' => 'pax', 'Peaxi162Scf00700g00421' => 'pax', 'Peaxi162Scf00801g00038' => 'pax', 'Peaxi162Scf00891g00025' => 'pax', 'PGR083G0909' => 'pgr', 'PGR119G1005' => 'pgr', 'PGR142G2236' => 'pgr', 'PGR142G3388' => 'pgr', 'PGSC0003DMG400004514' => 'stu', 'PGSC0003DMG400012635' => 'stu', 'PGSC0003DMG400015730' => 'stu', 'PGSC0003DMG400018611' => 'stu', 'PGSC0003DMG400030897' => 'stu', 'Phvul.001G254800' => 'pvu', 'Phvul.002G260100' => 'pvu', 'Phvul.003G167600' => 'pvu', 'Phvul.004G005100' => 'pvu', 'Potri.001G343600' => 'ptr', 'Potri.006G066700' => 'ptr', 'Potri.008G186000' => 'ptr', 'Potri.010G046900' => 'ptr', 'Potri.018G127900' => 'ptr', 'Pp3c20_17750' => 'ppa', 'Pp3c24_4380' => 'ppa', 'Prupe.1G245800' => 'ppe', 'Prupe.3G293400' => 'ppe', 'Prupe.7G247400' => 'ppe', 'Psat0s145g0120' => 'psa', 'Psat0s595g0040' => 'psa', 'Psat0s595g0120' => 'psa', 'Psat3g175040' => 'psa', 'Psat7g058120' => 'psa', 'PSO017G0428' => 'pso', 'PSO063G7510' => 'pso', 'PSO067G0046' => 'pso', 'PSO478G1073' => 'pso', 'PSO675G3677' => 'pso', 'PSO675G6558' => 'pso', 'PSO675G7520' => 'pso', 'PSO675G8959' => 'pso', 'QL02p074089' => 'qlo', 'QL02p089614' => 'qlo', 'QL03p057736' => 'qlo', 'RcHm_v2.0_Chr1g0364131' => 'rch', 'RcHm_v2.0_Chr2g0087801' => 'rch', 'RcHm_v2.0_Chr2g0087821' => 'rch', 'RcHm_v2.0_Chr2g0173231' => 'rch', 'RcHm_v2.0_Chr4g0433111' => 'rch', 'Rhsim03G0250300' => 'rsi', 'Rhsim08G0048400' => 'rsi', 'Rhsim10G0014800' => 'rsi', 'Rhsim12G0040100' => 'rsi', 'Rhsim12G0109700' => 'rsi', 'Sabra06G0049600' => 'sbr', 'Sabra08G0141000' => 'sbr', 'Sabra10G0021400' => 'sbr', 'Sabra16G0222900' => 'sbr', 'Sabra18G0108600' => 'sbr', 'SalBow1G0433' => 'sbo', 'SalBow1G2038' => 'sbo', 'SalBow1G5003' => 'sbo', 'SalBow7G1197' => 'sbo', 'SalBow8G3506' => 'sbo', 'Sc03g0007300' => 'sci', 'Sc11g0000950' => 'sci', 'Sc14g0008750' => 'sci', 'Sc18g0000420' => 'sci', 'Sed0006754' => 'sed', 'Sed0008741' => 'sed', 'Sed0017172' => 'sed', 'Sed0018925' => 'sed', 'Sed0023326' => 'sed', 'Sed0025909' => 'sed', 'SEGI_05333' => 'sgi', 'SEGI_10362' => 'sgi', 'SEGI_13380' => 'sgi', 'SEGI_24306' => 'sgi', 'SEGI_29077' => 'sgi', 'SEGI_29095' => 'sgi', 'SEGI_36534' => 'sgi', 'SEGI_37506' => 'sgi', 'SEGI_38321' => 'sgi', 'SGA_v2.0_scaffold307G48031' => 'sas', 'SGA_v2.0_scaffold47G17507' => 'sas', 'SGA_v2.0_scaffold63G21736' => 'sas', 'SGA_v2.0_scaffold87G27070' => 'sas', 'SHI17794' => 'shi', 'SHI28851' => 'shi', 'SMO165G0155' => 'smo', 'SMO340G0217' => 'smo', 'SMO367G1210' => 'smo', 'Solyc02g093430.3' => 'sly', 'Solyc05g013580.4' => 'sly', 'Solyc07g008030.3' => 'sly', 'Solyc12g035470.2' => 'sly', 'Sopen02g038020' => 'spe', 'Sopen05g008490' => 'spe', 'Sopen07g003910' => 'spe', 'Sopen12g015240' => 'spe', 'Sp1g11550' => 'spa', 'Sp2g16710' => 'spa', 'Sp3g00430' => 'spa', 'Sp3g26780' => 'spa', 'Sp5g22900' => 'spa', 'Sp6g29530' => 'spa', 'TAR371G0794' => 'tar', 'TAR374G0164' => 'tar', 'TAR622G0165' => 'tar', 'TAR626G0929' => 'tar', 'TAR629G2155' => 'tar', 'THA.LOC104805282' => 'tha', 'THA.LOC104805363' => 'tha', 'THA.LOC104808968' => 'tha', 'THA.LOC104821093' => 'tha', 'THA.LOC104823953' => 'tha', 'THA.LOC104825562' => 'tha', 'THA.LOC104825665' => 'tha', 'Thecc.02G261400' => 'tca', 'Thecc.04G019200' => 'tca', 'Thecc.09G130400' => 'tca', 'Thhalv10004374m.g' => 'esa', 'Thhalv10007850m.g' => 'esa', 'Thhalv10013782m.g' => 'esa', 'Thhalv10018686m.g' => 'esa', 'Thhalv10020899m.g' => 'esa', 'Thhalv10022755m.g' => 'esa', 'TPR.G23851' => 'tpr', 'TPR.G26500' => 'tpr', 'TPR.G27267' => 'tpr', 'TPR.G32001' => 'tpr', 'TPR.G6251' => 'tpr', 'TPR.G8167' => 'tpr', 'TWI12G1330' => 'twi', 'TWI18G1239' => 'twi', 'TWI34G0979' => 'twi', 'TWI36G0670' => 'twi', 'TWI36G0707' => 'twi', 'TWI56G0233' => 'twi', 'TWI75G1809' => 'twi', 'unitig_21.g20874' => 'ugi', 'unitig_26.g10343' => 'ugi', 'unitig_46.g18392' => 'ugi', 'unitig_52.g17178' => 'ugi', 'unitig_8.g2934' => 'ugi', 'vmacro01122' => 'vma', 'vmacro05875' => 'vma', 'vmacro06147' => 'vma', 'vmacro16191' => 'vma', 'vmacro18293' => 'vma', 'VMungo0251G3707' => 'vmu', 'VMungo0464G1521' => 'vmu', 'VMungo1215G0205' => 'vmu', 'VMungo1383G2484' => 'vmu', 'Zm00001eb079610' => 'zma', 'Zm00001eb135990' => 'zma', 'Zm00001eb183710' => 'zma', 'Zm00001eb246020' => 'zma' ), 'gf_id' => 'HOM05D001124', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001124' ), 'data_identifier' => 'HOM05D001124', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001124', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '548', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02520' => 'bna', 'A03p06630' => 'bna', 'A05p44460' => 'bna', 'A06p08710' => 'bna', 'A06p41090' => 'bna', 'A07p32320' => 'bna', 'A08p32520' => 'bna', 'A09p10360' => 'bna', 'A10p24080' => 'bna', 'Aa31LG11G15250' => 'aar', 'Aa31LG1G1800' => 'aar', 'Aa31LG2G5120' => 'aar', 'Aa31LG2G6070' => 'aar', 'Aa31LG5G10770' => 'aar', 'Aa31sc61G90' => 'aar', 'Actinidia01352' => 'ach', 'Actinidia05983' => 'ach', 'Actinidia08133' => 'ach', 'Actinidia15101' => 'ach', 'Actinidia26379' => 'ach', 'Actinidia35778' => 'ach', 'Actinidia36123' => 'ach', 'Actinidia37436' => 'ach', 'Actinidia38730' => 'ach', 'Ah.02g128210' => 'amhyb', 'Ah.03g132990' => 'amhyb', 'Ah.14g079410' => 'amhyb', 'AL1G24640' => 'aly', 'AL2G26680' => 'aly', 'AL3G10530' => 'aly', 'AL3G45230' => 'aly', 'AL5G15230' => 'aly', 'AL5G16960' => 'aly', 'AL6G25210' => 'aly', 'Aqoxy2G00441' => 'aox', 'Aqoxy3G01236' => 'aox', 'Aqoxy5G03746' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3RQ047' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C7GMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9C8JER' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MBL6KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YXCZ83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZANX40' => 'arhy', 'AT1G12990' => 'ath', 'AT1G67880' => 'ath', 'AT2G13290' => 'ath', 'AT3G01620' => 'ath', 'AT3G26445' => 'ath', 'AT3G27540' => 'ath', 'AT5G14480' => 'ath', 'ATR0824G026' => 'atr', 'ATR1098G019' => 'atr', 'Atru.chr11.2145' => 'acertr', 'Atru.chr2.3636' => 'acertr', 'Atru.chr2.3644' => 'acertr', 'Atru.chr6.2422' => 'acertr', 'Atru.chr7.1112' => 'acertr', 'AUR62005469' => 'cqu', 'AUR62011166' => 'cqu', 'AUR62013319' => 'cqu', 'AUR62024273' => 'cqu', 'AUR62028420' => 'cqu', 'AUR62041942' => 'cqu', 'BcaB01g04969' => 'bca', 'BcaB01g06371' => 'bca', 'BcaB02g11494' => 'bca', 'BcaB03g15382' => 'bca', 'BcaB08g36994' => 'bca', 'BcaC03g13477' => 'bca', 'BcaC03g13478' => 'bca', 'BcaC03g13480' => 'bca', 'BcaC03g13481' => 'bca', 'BcaC03g13486' => 'bca', 'BcaC04g19031' => 'bca', 'BcaC04g23085' => 'bca', 'BcaC05g25094' => 'bca', 'BcaC05g25096' => 'bca', 'BcaC05g25138' => 'bca', 'BcaC05g30416' => 'bca', 'BcaC05g30455' => 'bca', 'BcaC06g30979' => 'bca', 'BcaC06g33805' => 'bca', 'BcaC08g46021' => 'bca', 'BcaNung03154' => 'bca', 'BolC2t06623H' => 'bol', 'BolC2t06632H' => 'bol', 'BolC2t06635H' => 'bol', 'BolC2t06638H' => 'bol', 'BolC3t13266H' => 'bol', 'BolC5t29776H' => 'bol', 'BolC6t38912H' => 'bol', 'BolC7t44183H' => 'bol', 'BolC9t54123H' => 'bol', 'BolC9t59107H' => 'bol', 'BraA02t05221Z' => 'bra', 'BraA03t09996Z' => 'bra', 'BraA05t23210Z' => 'bra', 'BraA06t24068Z' => 'bra', 'BraA06t27032Z' => 'bra', 'BraA08t35176Z' => 'bra', 'BraA09t36680Z' => 'bra', 'BraA10t44471Z' => 'bra', 'C02p06760' => 'bna', 'C02p06890' => 'bna', 'C02p07010' => 'bna', 'C03p07660' => 'bna', 'C05p10300' => 'bna', 'C06p38150' => 'bna', 'C07p36650' => 'bna', 'C08p15770' => 'bna', 'C09p12300' => 'bna', 'C09p62700' => 'bna', 'C09p75040' => 'bna', 'CAN.G13.1' => 'can', 'CAN.G138.4' => 'can', 'CAN.G44.6' => 'can', 'CAN.G473.19' => 'can', 'CANSAT01G0835' => 'cansat', 'CANSAT11G0246' => 'cansat', 'CANSAT11G1766' => 'cansat', 'CANSAT64G1954' => 'cansat', 'CARHR013330' => 'chi', 'CARHR060530' => 'chi', 'CARHR075300' => 'chi', 'CARHR105120' => 'chi', 'CARHR148910' => 'chi', 'CARHR198830' => 'chi', 'Carub.0001s1275' => 'cru', 'Carub.0002s1437' => 'cru', 'Carub.0003s0044' => 'cru', 'Carub.0003s2787' => 'cru', 'Carub.0005s0597' => 'cru', 'Carub.0006s1266' => 'cru', 'Ca_06935_v3' => 'car', 'Ca_13559_v3' => 'car', 'Ca_16941_v3' => 'car', 'Ca_16960_v3' => 'car', 'Ca_17775_v3' => 'car', 'Ca_30464_v3' => 'car', 'Cc06_g08160' => 'ccan', 'Cc07_g01520' => 'ccan', 'Cc11_g15810' => 'ccan', 'CDE02G2840' => 'cde', 'CDE03G0093' => 'cde', 'CDE04G2127' => 'cde', 'CDE07G1857' => 'cde', 'CDE09G1246' => 'cde', 'Cfa003412' => 'cfa', 'Cfa007341' => 'cfa', 'Cfa009220' => 'cfa', 'Ciclev10008737m.g' => 'ccl', 'Ciclev10015565m.g' => 'ccl', 'Ciclev10031761m.g' => 'ccl', 'CiPaw.03G045300' => 'cil', 'CiPaw.03G247200' => 'cil', 'CiPaw.04G029500' => 'cil', 'CiPaw.04G174000' => 'cil', 'CiPaw.05G181200' => 'cil', 'CiPaw.06G067100' => 'cil', 'ClCG05G025800' => 'cla', 'ClCG06G011400' => 'cla', 'ClCG09G019360' => 'cla', 'COL.COLO4_04827' => 'col', 'COL.COLO4_29170' => 'col', 'COL.COLO4_35131' => 'col', 'COL.COLO4_35132' => 'col', 'Cpa.g.sc33.32' => 'cpa', 'Cpa.g.sc46.29' => 'cpa', 'Cpa.g.sc796.1' => 'cpa', 'CsaV3_1G030420' => 'csa', 'CsaV3_5G027050' => 'csa', 'CsaV3_5G031040' => 'csa', 'CsaV3_UNG023130' => 'csa', 'CSS0007726' => 'camsi', 'CSS0016433' => 'camsi', 'CSS0017656' => 'camsi', 'CSS0025364' => 'camsi', 'CSS0027582' => 'camsi', 'CSS0047288' => 'camsi', 'CSS0049950' => 'camsi', 'DCAR_003843' => 'dca', 'DCAR_007052' => 'dca', 'DCAR_020884' => 'dca', 'DCAR_021730' => 'dca', 'DCAR_024423' => 'dca', 'DCAR_026509' => 'dca', 'DCAR_031158' => 'dca', 'Dinv14728' => 'din', 'Dinv15219' => 'din', 'Dinv25728' => 'din', 'Dinv33428' => 'din', 'Dinv36489' => 'din', 'Dinv41486' => 'din', 'Duzib147G0469' => 'dzi', 'Duzib168G0060' => 'dzi', 'Duzib187G1215' => 'dzi', 'Duzib248G0692' => 'dzi', 'Duzib251G0767' => 'dzi', 'Duzib264G0446' => 'dzi', 'Duzib268G0691' => 'dzi', 'ECA232G4767' => 'eca', 'ECA233G2838' => 'eca', 'ECA234G0391' => 'eca', 'ECA234G0857' => 'eca', 'ECA236G1593' => 'eca', 'ECA238G0565' => 'eca', 'ECA246G1027' => 'eca', 'ECA246G3223' => 'eca', 'ECA246G3470' => 'eca', 'EL10Ac6g13829' => 'bvu', 'EL10Ac6g14093' => 'bvu', 'EL10Ac8g18707' => 'bvu', 'Eucgr.C01369' => 'egr', 'Eucgr.H02492' => 'egr', 'Eucgr.I01733' => 'egr', 'Eucgr.J02255' => 'egr', 'Eucgr.J02257' => 'egr', 'Eucgr.J02258' => 'egr', 'FAN02G1601' => 'fan', 'FAN03G1586' => 'fan', 'FAN03G2986' => 'fan', 'FAN05G4837' => 'fan', 'FAN06G0146' => 'fan', 'FAN07G0858' => 'fan', 'FAN09G3179' => 'fan', 'FAN10G0669' => 'fan', 'FAN12G2358' => 'fan', 'FAN14G4198' => 'fan', 'FAN14G5112' => 'fan', 'FAN17G0342' => 'fan', 'FAN19G0342' => 'fan', 'FAN19G0962' => 'fan', 'FAN19G1101' => 'fan', 'FAN19G1872' => 'fan', 'FAN22G0356' => 'fan', 'FAN23G0744' => 'fan', 'FAN23G1914' => 'fan', 'FAN26G0032' => 'fan', 'FAN28G0625' => 'fan', 'FvH4_1g02710' => 'fve', 'FvH4_1g02720' => 'fve', 'FvH4_4g25670' => 'fve', 'FvH4_6g51700' => 'fve', 'FvH4_7g20170' => 'fve', 'Glyma.05G175000' => 'gma', 'Glyma.08G132300' => 'gma', 'Glyma.11G243000' => 'gma', 'Glyma.13G158900' => 'gma', 'Glyma.17G112400' => 'gma', 'Glyma.18G014100' => 'gma', 'Glyma.19G003100' => 'gma', 'Glyma.19G056500' => 'gma', 'Gohir.A01G158900' => 'ghi', 'Gohir.A05G312600' => 'ghi', 'Gohir.A05G354900' => 'ghi', 'Gohir.A07G037200' => 'ghi', 'Gohir.A09G030000' => 'ghi', 'Gohir.A12G145200' => 'ghi', 'Gohir.D01G151500' => 'ghi', 'Gohir.D04G058300' => 'ghi', 'Gohir.D05G314100' => 'ghi', 'Gohir.D07G041400' => 'ghi', 'Gohir.D09G029700' => 'ghi', 'Gohir.D12G149700' => 'ghi', 'Gorai.001G043800' => 'gra', 'Gorai.002G187800' => 'gra', 'Gorai.006G034700' => 'gra', 'Gorai.008G161200' => 'gra', 'Gorai.009G335700' => 'gra', 'Gorai.012G065000' => 'gra', 'GSVIVG01000535001' => 'vvi', 'GSVIVG01015572001' => 'vvi', 'GSVIVG01032386001' => 'vvi', 'HanXRQChr05g0138531' => 'han', 'HanXRQChr06g0174391' => 'han', 'HanXRQChr07g0199021' => 'han', 'HanXRQChr08g0208211' => 'han', 'HanXRQChr09g0255471' => 'han', 'HanXRQChr10g0315791' => 'han', 'HanXRQChr12g0371991' => 'han', 'HanXRQChr15g0475251' => 'han', 'HanXRQChr17g0540001' => 'han', 'HanXRQChr17g0548631' => 'han', 'HanXRQChr17g0569561' => 'han', 'Haze_12256' => 'cav', 'Haze_14756' => 'cav', 'Haze_25528' => 'cav', 'Hma1.2p1_0079F.1_g041020' => 'hma', 'Hma1.2p1_0818F.1_g223260' => 'hma', 'Hma1.2p1_1747F.1_g300530' => 'hma', 'HPP92_004607' => 'vpl', 'HPP92_004608' => 'vpl', 'HPP92_006181' => 'vpl', 'HPP92_012192' => 'vpl', 'HPP92_015680' => 'vpl', 'HPP92_020249' => 'vpl', 'HPP92_021376' => 'vpl', 'HPP92_024275' => 'vpl', 'Hund06031' => 'sun', 'Hund25391' => 'sun', 'Lalb_Chr07g0185371' => 'lal', 'Lalb_Chr07g0185381' => 'lal', 'Lalb_Chr12g0204011' => 'lal', 'Lalb_Chr13g0301671' => 'lal', 'Lalb_Chr14g0362851' => 'lal', 'Lalb_Chr24g0403581' => 'lal', 'Lj1g0000233' => 'lja', 'Lj2g0018120' => 'lja', 'Lj3C621T0' => 'lonja', 'Lj3P1059T14' => 'lonja', 'Lj3P611T9' => 'lonja', 'Lj3P614T13' => 'lonja', 'Lj3P615T5' => 'lonja', 'Lj4g0012315' => 'lja', 'Lj4g0026182' => 'lja', 'Lj6P813T16' => 'lonja', 'Lj7C427T7' => 'lonja', 'Lj7C427T8' => 'lonja', 'Lj7P600T41' => 'lonja', 'Lju41C42G17' => 'lonja', 'Lsat_1_v5_gn_0_47300' => 'lsa', 'Lsat_1_v5_gn_2_91280' => 'lsa', 'Lsat_1_v5_gn_3_30561' => 'lsa', 'Lsat_1_v5_gn_4_184321' => 'lsa', 'Lsat_1_v5_gn_4_4041' => 'lsa', 'Lsat_1_v5_gn_5_92000' => 'lsa', 'Lsat_1_v5_gn_8_152940' => 'lsa', 'Lsat_1_v5_gn_8_62401' => 'lsa', 'Manes.06G055900' => 'mes', 'Manes.12G022200' => 'mes', 'Manes.13G023300' => 'mes', 'Manes.14G115000' => 'mes', 'Manes.15G151700' => 'mes', 'Manes.17G111300' => 'mes', 'Mapoly0226s0009' => 'mpo', 'MBI02_g25363_MAGBIO' => 'mbi', 'MBI06_g00027_MAGBIO' => 'mbi', 'MBI10_g13034_MAGBIO' => 'mbi', 'MD09G1023400' => 'mdo', 'MD13G1100100' => 'mdo', 'MD15G1169200' => 'mdo', 'MD16G1101100' => 'mdo', 'MD17G1022900' => 'mdo', 'Medtr3g096150' => 'mtr', 'Medtr4g115070' => 'mtr', 'Medtr7g033325' => 'mtr', 'Medtr8g089840' => 'mtr', 'MELO3C010319.2' => 'cme', 'MELO3C011944.2' => 'cme', 'MELO3C021589.2' => 'cme', 'Migut.E00207' => 'egut', 'Migut.H00067' => 'egut', 'Migut.K00433' => 'egut', 'Migut.K00606' => 'egut', 'Migut.K01410' => 'egut', 'MSTRG.13347' => 'ama', 'MSTRG.24045' => 'ama', 'MSTRG.2428' => 'ama', 'MSTRG.26410' => 'ama', 'MSTRG.3139' => 'ama', 'MSTRG.3286' => 'ama', 'MSTRG.563' => 'ama', 'MSTRG.7941' => 'ama', 'Nitab4.5_0000028g0060' => 'nta', 'Nitab4.5_0000065g0260' => 'nta', 'Nitab4.5_0000112g0060' => 'nta', 'Nitab4.5_0000489g0120' => 'nta', 'Nitab4.5_0001776g0050' => 'nta', 'Nitab4.5_0001854g0010' => 'nta', 'Nitab4.5_0001860g0020' => 'nta', 'Nitab4.5_0004352g0010' => 'nta', 'Nitab4.5_0008716g0020' => 'nta', 'Nitab4.5_0008922g0010' => 'nta', 'Nn3g16693' => 'nnu', 'Nn4g22596' => 'nnu', 'Nn7g37639' => 'nnu', 'Oeu001701.1' => 'oeu', 'Oeu018149.1' => 'oeu', 'Oeu026220.1' => 'oeu', 'Oeu038635.1' => 'oeu', 'Oeu049176.1' => 'oeu', 'Oeu056706.1' => 'oeu', 'Oeu056937.1' => 'oeu', 'Oeu057540.1' => 'oeu', 'Os02g0594900' => 'osa', 'Os02g0595100' => 'osa', 'Os04g0477500' => 'osa', 'Os12g0611900' => 'osa', 'Peaxi162Scf00076g00020' => 'pax', 'Peaxi162Scf00128g00217' => 'pax', 'Peaxi162Scf00129g01640' => 'pax', 'Peaxi162Scf00669g00007' => 'pax', 'Peaxi162Scf00700g00421' => 'pax', 'Peaxi162Scf00801g00038' => 'pax', 'Peaxi162Scf00891g00025' => 'pax', 'PGR083G0909' => 'pgr', 'PGR119G1005' => 'pgr', 'PGR142G2236' => 'pgr', 'PGR142G3388' => 'pgr', 'PGSC0003DMG400004514' => 'stu', 'PGSC0003DMG400012635' => 'stu', 'PGSC0003DMG400015730' => 'stu', 'PGSC0003DMG400018611' => 'stu', 'PGSC0003DMG400030897' => 'stu', 'Phvul.001G254800' => 'pvu', 'Phvul.002G260100' => 'pvu', 'Phvul.003G167600' => 'pvu', 'Phvul.004G005100' => 'pvu', 'Potri.001G343600' => 'ptr', 'Potri.006G066700' => 'ptr', 'Potri.008G186000' => 'ptr', 'Potri.010G046900' => 'ptr', 'Potri.018G127900' => 'ptr', 'Pp3c20_17750' => 'ppa', 'Pp3c24_4380' => 'ppa', 'Prupe.1G245800' => 'ppe', 'Prupe.3G293400' => 'ppe', 'Prupe.7G247400' => 'ppe', 'Psat0s145g0120' => 'psa', 'Psat0s595g0040' => 'psa', 'Psat0s595g0120' => 'psa', 'Psat3g175040' => 'psa', 'Psat7g058120' => 'psa', 'PSO017G0428' => 'pso', 'PSO063G7510' => 'pso', 'PSO067G0046' => 'pso', 'PSO478G1073' => 'pso', 'PSO675G3677' => 'pso', 'PSO675G6558' => 'pso', 'PSO675G7520' => 'pso', 'PSO675G8959' => 'pso', 'QL02p074089' => 'qlo', 'QL02p089614' => 'qlo', 'QL03p057736' => 'qlo', 'RcHm_v2.0_Chr1g0364131' => 'rch', 'RcHm_v2.0_Chr2g0087801' => 'rch', 'RcHm_v2.0_Chr2g0087821' => 'rch', 'RcHm_v2.0_Chr2g0173231' => 'rch', 'RcHm_v2.0_Chr4g0433111' => 'rch', 'Rhsim03G0250300' => 'rsi', 'Rhsim08G0048400' => 'rsi', 'Rhsim10G0014800' => 'rsi', 'Rhsim12G0040100' => 'rsi', 'Rhsim12G0109700' => 'rsi', 'Sabra06G0049600' => 'sbr', 'Sabra08G0141000' => 'sbr', 'Sabra10G0021400' => 'sbr', 'Sabra16G0222900' => 'sbr', 'Sabra18G0108600' => 'sbr', 'SalBow1G0433' => 'sbo', 'SalBow1G2038' => 'sbo', 'SalBow1G5003' => 'sbo', 'SalBow7G1197' => 'sbo', 'SalBow8G3506' => 'sbo', 'Sc03g0007300' => 'sci', 'Sc11g0000950' => 'sci', 'Sc14g0008750' => 'sci', 'Sc18g0000420' => 'sci', 'Sed0006754' => 'sed', 'Sed0008741' => 'sed', 'Sed0017172' => 'sed', 'Sed0018925' => 'sed', 'Sed0023326' => 'sed', 'Sed0025909' => 'sed', 'SEGI_05333' => 'sgi', 'SEGI_10362' => 'sgi', 'SEGI_13380' => 'sgi', 'SEGI_24306' => 'sgi', 'SEGI_29077' => 'sgi', 'SEGI_29095' => 'sgi', 'SEGI_36534' => 'sgi', 'SEGI_37506' => 'sgi', 'SEGI_38321' => 'sgi', 'SGA_v2.0_scaffold307G48031' => 'sas', 'SGA_v2.0_scaffold47G17507' => 'sas', 'SGA_v2.0_scaffold63G21736' => 'sas', 'SGA_v2.0_scaffold87G27070' => 'sas', 'SHI17794' => 'shi', 'SHI28851' => 'shi', 'SMO165G0155' => 'smo', 'SMO340G0217' => 'smo', 'SMO367G1210' => 'smo', 'Solyc02g093430.3' => 'sly', 'Solyc05g013580.4' => 'sly', 'Solyc07g008030.3' => 'sly', 'Solyc12g035470.2' => 'sly', 'Sopen02g038020' => 'spe', 'Sopen05g008490' => 'spe', 'Sopen07g003910' => 'spe', 'Sopen12g015240' => 'spe', 'Sp1g11550' => 'spa', 'Sp2g16710' => 'spa', 'Sp3g00430' => 'spa', 'Sp3g26780' => 'spa', 'Sp5g22900' => 'spa', 'Sp6g29530' => 'spa', 'TAR371G0794' => 'tar', 'TAR374G0164' => 'tar', 'TAR622G0165' => 'tar', 'TAR626G0929' => 'tar', 'TAR629G2155' => 'tar', 'THA.LOC104805282' => 'tha', 'THA.LOC104805363' => 'tha', 'THA.LOC104808968' => 'tha', 'THA.LOC104821093' => 'tha', 'THA.LOC104823953' => 'tha', 'THA.LOC104825562' => 'tha', 'THA.LOC104825665' => 'tha', 'Thecc.02G261400' => 'tca', 'Thecc.04G019200' => 'tca', 'Thecc.09G130400' => 'tca', 'Thhalv10004374m.g' => 'esa', 'Thhalv10007850m.g' => 'esa', 'Thhalv10013782m.g' => 'esa', 'Thhalv10018686m.g' => 'esa', 'Thhalv10020899m.g' => 'esa', 'Thhalv10022755m.g' => 'esa', 'TPR.G23851' => 'tpr', 'TPR.G26500' => 'tpr', 'TPR.G27267' => 'tpr', 'TPR.G32001' => 'tpr', 'TPR.G6251' => 'tpr', 'TPR.G8167' => 'tpr', 'TWI12G1330' => 'twi', 'TWI18G1239' => 'twi', 'TWI34G0979' => 'twi', 'TWI36G0670' => 'twi', 'TWI36G0707' => 'twi', 'TWI56G0233' => 'twi', 'TWI75G1809' => 'twi', 'unitig_21.g20874' => 'ugi', 'unitig_26.g10343' => 'ugi', 'unitig_46.g18392' => 'ugi', 'unitig_52.g17178' => 'ugi', 'unitig_8.g2934' => 'ugi', 'vmacro01122' => 'vma', 'vmacro05875' => 'vma', 'vmacro06147' => 'vma', 'vmacro16191' => 'vma', 'vmacro18293' => 'vma', 'VMungo0251G3707' => 'vmu', 'VMungo0464G1521' => 'vmu', 'VMungo1215G0205' => 'vmu', 'VMungo1383G2484' => 'vmu', 'Zm00001eb079610' => 'zma', 'Zm00001eb135990' => 'zma', 'Zm00001eb183710' => 'zma', 'Zm00001eb246020' => 'zma' ) $gf_id = 'HOM05D001124' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001124' ) $data_identifier = 'HOM05D001124' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 6, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 7, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 21, 'bol' => (int) 10, 'bra' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 6, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 9, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 21, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 8, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 10, 'lsa' => (int) 8, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 8, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 9, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb246020' $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' => 'HOM05D001124', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '548', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02520' => 'bna', 'A03p06630' => 'bna', 'A05p44460' => 'bna', 'A06p08710' => 'bna', 'A06p41090' => 'bna', 'A07p32320' => 'bna', 'A08p32520' => 'bna', 'A09p10360' => 'bna', 'A10p24080' => 'bna', 'Aa31LG11G15250' => 'aar', 'Aa31LG1G1800' => 'aar', 'Aa31LG2G5120' => 'aar', 'Aa31LG2G6070' => 'aar', 'Aa31LG5G10770' => 'aar', 'Aa31sc61G90' => 'aar', 'Actinidia01352' => 'ach', 'Actinidia05983' => 'ach', 'Actinidia08133' => 'ach', 'Actinidia15101' => 'ach', 'Actinidia26379' => 'ach', 'Actinidia35778' => 'ach', 'Actinidia36123' => 'ach', 'Actinidia37436' => 'ach', 'Actinidia38730' => 'ach', 'Ah.02g128210' => 'amhyb', 'Ah.03g132990' => 'amhyb', 'Ah.14g079410' => 'amhyb', 'AL1G24640' => 'aly', 'AL2G26680' => 'aly', 'AL3G10530' => 'aly', 'AL3G45230' => 'aly', 'AL5G15230' => 'aly', 'AL5G16960' => 'aly', 'AL6G25210' => 'aly', 'Aqoxy2G00441' => 'aox', 'Aqoxy3G01236' => 'aox', 'Aqoxy5G03746' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3RQ047' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C7GMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9C8JER' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MBL6KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YXCZ83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZANX40' => 'arhy', 'AT1G12990' => 'ath', 'AT1G67880' => 'ath', 'AT2G13290' => 'ath', 'AT3G01620' => 'ath', 'AT3G26445' => 'ath', 'AT3G27540' => 'ath', 'AT5G14480' => 'ath', 'ATR0824G026' => 'atr', 'ATR1098G019' => 'atr', 'Atru.chr11.2145' => 'acertr', 'Atru.chr2.3636' => 'acertr', 'Atru.chr2.3644' => 'acertr', 'Atru.chr6.2422' => 'acertr', 'Atru.chr7.1112' => 'acertr', 'AUR62005469' => 'cqu', 'AUR62011166' => 'cqu', 'AUR62013319' => 'cqu', 'AUR62024273' => 'cqu', 'AUR62028420' => 'cqu', 'AUR62041942' => 'cqu', 'BcaB01g04969' => 'bca', 'BcaB01g06371' => 'bca', 'BcaB02g11494' => 'bca', 'BcaB03g15382' => 'bca', 'BcaB08g36994' => 'bca', 'BcaC03g13477' => 'bca', 'BcaC03g13478' => 'bca', 'BcaC03g13480' => 'bca', 'BcaC03g13481' => 'bca', 'BcaC03g13486' => 'bca', 'BcaC04g19031' => 'bca', 'BcaC04g23085' => 'bca', 'BcaC05g25094' => 'bca', 'BcaC05g25096' => 'bca', 'BcaC05g25138' => 'bca', 'BcaC05g30416' => 'bca', 'BcaC05g30455' => 'bca', 'BcaC06g30979' => 'bca', 'BcaC06g33805' => 'bca', 'BcaC08g46021' => 'bca', 'BcaNung03154' => 'bca', 'BolC2t06623H' => 'bol', 'BolC2t06632H' => 'bol', 'BolC2t06635H' => 'bol', 'BolC2t06638H' => 'bol', 'BolC3t13266H' => 'bol', 'BolC5t29776H' => 'bol', 'BolC6t38912H' => 'bol', 'BolC7t44183H' => 'bol', 'BolC9t54123H' => 'bol', 'BolC9t59107H' => 'bol', 'BraA02t05221Z' => 'bra', 'BraA03t09996Z' => 'bra', 'BraA05t23210Z' => 'bra', 'BraA06t24068Z' => 'bra', 'BraA06t27032Z' => 'bra', 'BraA08t35176Z' => 'bra', 'BraA09t36680Z' => 'bra', 'BraA10t44471Z' => 'bra', 'C02p06760' => 'bna', 'C02p06890' => 'bna', 'C02p07010' => 'bna', 'C03p07660' => 'bna', 'C05p10300' => 'bna', 'C06p38150' => 'bna', 'C07p36650' => 'bna', 'C08p15770' => 'bna', 'C09p12300' => 'bna', 'C09p62700' => 'bna', 'C09p75040' => 'bna', 'CAN.G13.1' => 'can', 'CAN.G138.4' => 'can', 'CAN.G44.6' => 'can', 'CAN.G473.19' => 'can', 'CANSAT01G0835' => 'cansat', 'CANSAT11G0246' => 'cansat', 'CANSAT11G1766' => 'cansat', 'CANSAT64G1954' => 'cansat', 'CARHR013330' => 'chi', 'CARHR060530' => 'chi', 'CARHR075300' => 'chi', 'CARHR105120' => 'chi', 'CARHR148910' => 'chi', 'CARHR198830' => 'chi', 'Carub.0001s1275' => 'cru', 'Carub.0002s1437' => 'cru', 'Carub.0003s0044' => 'cru', 'Carub.0003s2787' => 'cru', 'Carub.0005s0597' => 'cru', 'Carub.0006s1266' => 'cru', 'Ca_06935_v3' => 'car', 'Ca_13559_v3' => 'car', 'Ca_16941_v3' => 'car', 'Ca_16960_v3' => 'car', 'Ca_17775_v3' => 'car', 'Ca_30464_v3' => 'car', 'Cc06_g08160' => 'ccan', 'Cc07_g01520' => 'ccan', 'Cc11_g15810' => 'ccan', 'CDE02G2840' => 'cde', 'CDE03G0093' => 'cde', 'CDE04G2127' => 'cde', 'CDE07G1857' => 'cde', 'CDE09G1246' => 'cde', 'Cfa003412' => 'cfa', 'Cfa007341' => 'cfa', 'Cfa009220' => 'cfa', 'Ciclev10008737m.g' => 'ccl', 'Ciclev10015565m.g' => 'ccl', 'Ciclev10031761m.g' => 'ccl', 'CiPaw.03G045300' => 'cil', 'CiPaw.03G247200' => 'cil', 'CiPaw.04G029500' => 'cil', 'CiPaw.04G174000' => 'cil', 'CiPaw.05G181200' => 'cil', 'CiPaw.06G067100' => 'cil', 'ClCG05G025800' => 'cla', 'ClCG06G011400' => 'cla', 'ClCG09G019360' => 'cla', 'COL.COLO4_04827' => 'col', 'COL.COLO4_29170' => 'col', 'COL.COLO4_35131' => 'col', 'COL.COLO4_35132' => 'col', 'Cpa.g.sc33.32' => 'cpa', 'Cpa.g.sc46.29' => 'cpa', 'Cpa.g.sc796.1' => 'cpa', 'CsaV3_1G030420' => 'csa', 'CsaV3_5G027050' => 'csa', 'CsaV3_5G031040' => 'csa', 'CsaV3_UNG023130' => 'csa', 'CSS0007726' => 'camsi', 'CSS0016433' => 'camsi', 'CSS0017656' => 'camsi', 'CSS0025364' => 'camsi', 'CSS0027582' => 'camsi', 'CSS0047288' => 'camsi', 'CSS0049950' => 'camsi', 'DCAR_003843' => 'dca', 'DCAR_007052' => 'dca', 'DCAR_020884' => 'dca', 'DCAR_021730' => 'dca', 'DCAR_024423' => 'dca', 'DCAR_026509' => 'dca', 'DCAR_031158' => 'dca', 'Dinv14728' => 'din', 'Dinv15219' => 'din', 'Dinv25728' => 'din', 'Dinv33428' => 'din', 'Dinv36489' => 'din', 'Dinv41486' => 'din', 'Duzib147G0469' => 'dzi', 'Duzib168G0060' => 'dzi', 'Duzib187G1215' => 'dzi', 'Duzib248G0692' => 'dzi', 'Duzib251G0767' => 'dzi', 'Duzib264G0446' => 'dzi', 'Duzib268G0691' => 'dzi', 'ECA232G4767' => 'eca', 'ECA233G2838' => 'eca', 'ECA234G0391' => 'eca', 'ECA234G0857' => 'eca', 'ECA236G1593' => 'eca', 'ECA238G0565' => 'eca', 'ECA246G1027' => 'eca', 'ECA246G3223' => 'eca', 'ECA246G3470' => 'eca', 'EL10Ac6g13829' => 'bvu', 'EL10Ac6g14093' => 'bvu', 'EL10Ac8g18707' => 'bvu', 'Eucgr.C01369' => 'egr', 'Eucgr.H02492' => 'egr', 'Eucgr.I01733' => 'egr', 'Eucgr.J02255' => 'egr', 'Eucgr.J02257' => 'egr', 'Eucgr.J02258' => 'egr', 'FAN02G1601' => 'fan', 'FAN03G1586' => 'fan', 'FAN03G2986' => 'fan', 'FAN05G4837' => 'fan', 'FAN06G0146' => 'fan', 'FAN07G0858' => 'fan', 'FAN09G3179' => 'fan', 'FAN10G0669' => 'fan', 'FAN12G2358' => 'fan', 'FAN14G4198' => 'fan', 'FAN14G5112' => 'fan', 'FAN17G0342' => 'fan', 'FAN19G0342' => 'fan', 'FAN19G0962' => 'fan', 'FAN19G1101' => 'fan', 'FAN19G1872' => 'fan', 'FAN22G0356' => 'fan', 'FAN23G0744' => 'fan', 'FAN23G1914' => 'fan', 'FAN26G0032' => 'fan', 'FAN28G0625' => 'fan', 'FvH4_1g02710' => 'fve', 'FvH4_1g02720' => 'fve', 'FvH4_4g25670' => 'fve', 'FvH4_6g51700' => 'fve', 'FvH4_7g20170' => 'fve', 'Glyma.05G175000' => 'gma', 'Glyma.08G132300' => 'gma', 'Glyma.11G243000' => 'gma', 'Glyma.13G158900' => 'gma', 'Glyma.17G112400' => 'gma', 'Glyma.18G014100' => 'gma', 'Glyma.19G003100' => 'gma', 'Glyma.19G056500' => 'gma', 'Gohir.A01G158900' => 'ghi', 'Gohir.A05G312600' => 'ghi', 'Gohir.A05G354900' => 'ghi', 'Gohir.A07G037200' => 'ghi', 'Gohir.A09G030000' => 'ghi', 'Gohir.A12G145200' => 'ghi', 'Gohir.D01G151500' => 'ghi', 'Gohir.D04G058300' => 'ghi', 'Gohir.D05G314100' => 'ghi', 'Gohir.D07G041400' => 'ghi', 'Gohir.D09G029700' => 'ghi', 'Gohir.D12G149700' => 'ghi', 'Gorai.001G043800' => 'gra', 'Gorai.002G187800' => 'gra', 'Gorai.006G034700' => 'gra', 'Gorai.008G161200' => 'gra', 'Gorai.009G335700' => 'gra', 'Gorai.012G065000' => 'gra', 'GSVIVG01000535001' => 'vvi', 'GSVIVG01015572001' => 'vvi', 'GSVIVG01032386001' => 'vvi', 'HanXRQChr05g0138531' => 'han', 'HanXRQChr06g0174391' => 'han', 'HanXRQChr07g0199021' => 'han', 'HanXRQChr08g0208211' => 'han', 'HanXRQChr09g0255471' => 'han', 'HanXRQChr10g0315791' => 'han', 'HanXRQChr12g0371991' => 'han', 'HanXRQChr15g0475251' => 'han', 'HanXRQChr17g0540001' => 'han', 'HanXRQChr17g0548631' => 'han', 'HanXRQChr17g0569561' => 'han', 'Haze_12256' => 'cav', 'Haze_14756' => 'cav', 'Haze_25528' => 'cav', 'Hma1.2p1_0079F.1_g041020' => 'hma', 'Hma1.2p1_0818F.1_g223260' => 'hma', 'Hma1.2p1_1747F.1_g300530' => 'hma', 'HPP92_004607' => 'vpl', 'HPP92_004608' => 'vpl', 'HPP92_006181' => 'vpl', 'HPP92_012192' => 'vpl', 'HPP92_015680' => 'vpl', 'HPP92_020249' => 'vpl', 'HPP92_021376' => 'vpl', 'HPP92_024275' => 'vpl', 'Hund06031' => 'sun', 'Hund25391' => 'sun', 'Lalb_Chr07g0185371' => 'lal', 'Lalb_Chr07g0185381' => 'lal', 'Lalb_Chr12g0204011' => 'lal', 'Lalb_Chr13g0301671' => 'lal', 'Lalb_Chr14g0362851' => 'lal', 'Lalb_Chr24g0403581' => 'lal', 'Lj1g0000233' => 'lja', 'Lj2g0018120' => 'lja', 'Lj3C621T0' => 'lonja', 'Lj3P1059T14' => 'lonja', 'Lj3P611T9' => 'lonja', 'Lj3P614T13' => 'lonja', 'Lj3P615T5' => 'lonja', 'Lj4g0012315' => 'lja', 'Lj4g0026182' => 'lja', 'Lj6P813T16' => 'lonja', 'Lj7C427T7' => 'lonja', 'Lj7C427T8' => 'lonja', 'Lj7P600T41' => 'lonja', 'Lju41C42G17' => 'lonja', 'Lsat_1_v5_gn_0_47300' => 'lsa', 'Lsat_1_v5_gn_2_91280' => 'lsa', 'Lsat_1_v5_gn_3_30561' => 'lsa', 'Lsat_1_v5_gn_4_184321' => 'lsa', 'Lsat_1_v5_gn_4_4041' => 'lsa', 'Lsat_1_v5_gn_5_92000' => 'lsa', 'Lsat_1_v5_gn_8_152940' => 'lsa', 'Lsat_1_v5_gn_8_62401' => 'lsa', 'Manes.06G055900' => 'mes', 'Manes.12G022200' => 'mes', 'Manes.13G023300' => 'mes', 'Manes.14G115000' => 'mes', 'Manes.15G151700' => 'mes', 'Manes.17G111300' => 'mes', 'Mapoly0226s0009' => 'mpo', 'MBI02_g25363_MAGBIO' => 'mbi', 'MBI06_g00027_MAGBIO' => 'mbi', 'MBI10_g13034_MAGBIO' => 'mbi', 'MD09G1023400' => 'mdo', 'MD13G1100100' => 'mdo', 'MD15G1169200' => 'mdo', 'MD16G1101100' => 'mdo', 'MD17G1022900' => 'mdo', 'Medtr3g096150' => 'mtr', 'Medtr4g115070' => 'mtr', 'Medtr7g033325' => 'mtr', 'Medtr8g089840' => 'mtr', 'MELO3C010319.2' => 'cme', 'MELO3C011944.2' => 'cme', 'MELO3C021589.2' => 'cme', 'Migut.E00207' => 'egut', 'Migut.H00067' => 'egut', 'Migut.K00433' => 'egut', 'Migut.K00606' => 'egut', 'Migut.K01410' => 'egut', 'MSTRG.13347' => 'ama', 'MSTRG.24045' => 'ama', 'MSTRG.2428' => 'ama', 'MSTRG.26410' => 'ama', 'MSTRG.3139' => 'ama', 'MSTRG.3286' => 'ama', 'MSTRG.563' => 'ama', 'MSTRG.7941' => 'ama', 'Nitab4.5_0000028g0060' => 'nta', 'Nitab4.5_0000065g0260' => 'nta', 'Nitab4.5_0000112g0060' => 'nta', 'Nitab4.5_0000489g0120' => 'nta', 'Nitab4.5_0001776g0050' => 'nta', 'Nitab4.5_0001854g0010' => 'nta', 'Nitab4.5_0001860g0020' => 'nta', 'Nitab4.5_0004352g0010' => 'nta', 'Nitab4.5_0008716g0020' => 'nta', 'Nitab4.5_0008922g0010' => 'nta', 'Nn3g16693' => 'nnu', 'Nn4g22596' => 'nnu', 'Nn7g37639' => 'nnu', 'Oeu001701.1' => 'oeu', 'Oeu018149.1' => 'oeu', 'Oeu026220.1' => 'oeu', 'Oeu038635.1' => 'oeu', 'Oeu049176.1' => 'oeu', 'Oeu056706.1' => 'oeu', 'Oeu056937.1' => 'oeu', 'Oeu057540.1' => 'oeu', 'Os02g0594900' => 'osa', 'Os02g0595100' => 'osa', 'Os04g0477500' => 'osa', 'Os12g0611900' => 'osa', 'Peaxi162Scf00076g00020' => 'pax', 'Peaxi162Scf00128g00217' => 'pax', 'Peaxi162Scf00129g01640' => 'pax', 'Peaxi162Scf00669g00007' => 'pax', 'Peaxi162Scf00700g00421' => 'pax', 'Peaxi162Scf00801g00038' => 'pax', 'Peaxi162Scf00891g00025' => 'pax', 'PGR083G0909' => 'pgr', 'PGR119G1005' => 'pgr', 'PGR142G2236' => 'pgr', 'PGR142G3388' => 'pgr', 'PGSC0003DMG400004514' => 'stu', 'PGSC0003DMG400012635' => 'stu', 'PGSC0003DMG400015730' => 'stu', 'PGSC0003DMG400018611' => 'stu', 'PGSC0003DMG400030897' => 'stu', 'Phvul.001G254800' => 'pvu', 'Phvul.002G260100' => 'pvu', 'Phvul.003G167600' => 'pvu', 'Phvul.004G005100' => 'pvu', 'Potri.001G343600' => 'ptr', 'Potri.006G066700' => 'ptr', 'Potri.008G186000' => 'ptr', 'Potri.010G046900' => 'ptr', 'Potri.018G127900' => 'ptr', 'Pp3c20_17750' => 'ppa', 'Pp3c24_4380' => 'ppa', 'Prupe.1G245800' => 'ppe', 'Prupe.3G293400' => 'ppe', 'Prupe.7G247400' => 'ppe', 'Psat0s145g0120' => 'psa', 'Psat0s595g0040' => 'psa', 'Psat0s595g0120' => 'psa', 'Psat3g175040' => 'psa', 'Psat7g058120' => 'psa', 'PSO017G0428' => 'pso', 'PSO063G7510' => 'pso', 'PSO067G0046' => 'pso', 'PSO478G1073' => 'pso', 'PSO675G3677' => 'pso', 'PSO675G6558' => 'pso', 'PSO675G7520' => 'pso', 'PSO675G8959' => 'pso', 'QL02p074089' => 'qlo', 'QL02p089614' => 'qlo', 'QL03p057736' => 'qlo', 'RcHm_v2.0_Chr1g0364131' => 'rch', 'RcHm_v2.0_Chr2g0087801' => 'rch', 'RcHm_v2.0_Chr2g0087821' => 'rch', 'RcHm_v2.0_Chr2g0173231' => 'rch', 'RcHm_v2.0_Chr4g0433111' => 'rch', 'Rhsim03G0250300' => 'rsi', 'Rhsim08G0048400' => 'rsi', 'Rhsim10G0014800' => 'rsi', 'Rhsim12G0040100' => 'rsi', 'Rhsim12G0109700' => 'rsi', 'Sabra06G0049600' => 'sbr', 'Sabra08G0141000' => 'sbr', 'Sabra10G0021400' => 'sbr', 'Sabra16G0222900' => 'sbr', 'Sabra18G0108600' => 'sbr', 'SalBow1G0433' => 'sbo', 'SalBow1G2038' => 'sbo', 'SalBow1G5003' => 'sbo', 'SalBow7G1197' => 'sbo', 'SalBow8G3506' => 'sbo', 'Sc03g0007300' => 'sci', 'Sc11g0000950' => 'sci', 'Sc14g0008750' => 'sci', 'Sc18g0000420' => 'sci', 'Sed0006754' => 'sed', 'Sed0008741' => 'sed', 'Sed0017172' => 'sed', 'Sed0018925' => 'sed', 'Sed0023326' => 'sed', 'Sed0025909' => 'sed', 'SEGI_05333' => 'sgi', 'SEGI_10362' => 'sgi', 'SEGI_13380' => 'sgi', 'SEGI_24306' => 'sgi', 'SEGI_29077' => 'sgi', 'SEGI_29095' => 'sgi', 'SEGI_36534' => 'sgi', 'SEGI_37506' => 'sgi', 'SEGI_38321' => 'sgi', 'SGA_v2.0_scaffold307G48031' => 'sas', 'SGA_v2.0_scaffold47G17507' => 'sas', 'SGA_v2.0_scaffold63G21736' => 'sas', 'SGA_v2.0_scaffold87G27070' => 'sas', 'SHI17794' => 'shi', 'SHI28851' => 'shi', 'SMO165G0155' => 'smo', 'SMO340G0217' => 'smo', 'SMO367G1210' => 'smo', 'Solyc02g093430.3' => 'sly', 'Solyc05g013580.4' => 'sly', 'Solyc07g008030.3' => 'sly', 'Solyc12g035470.2' => 'sly', 'Sopen02g038020' => 'spe', 'Sopen05g008490' => 'spe', 'Sopen07g003910' => 'spe', 'Sopen12g015240' => 'spe', 'Sp1g11550' => 'spa', 'Sp2g16710' => 'spa', 'Sp3g00430' => 'spa', 'Sp3g26780' => 'spa', 'Sp5g22900' => 'spa', 'Sp6g29530' => 'spa', 'TAR371G0794' => 'tar', 'TAR374G0164' => 'tar', 'TAR622G0165' => 'tar', 'TAR626G0929' => 'tar', 'TAR629G2155' => 'tar', 'THA.LOC104805282' => 'tha', 'THA.LOC104805363' => 'tha', 'THA.LOC104808968' => 'tha', 'THA.LOC104821093' => 'tha', 'THA.LOC104823953' => 'tha', 'THA.LOC104825562' => 'tha', 'THA.LOC104825665' => 'tha', 'Thecc.02G261400' => 'tca', 'Thecc.04G019200' => 'tca', 'Thecc.09G130400' => 'tca', 'Thhalv10004374m.g' => 'esa', 'Thhalv10007850m.g' => 'esa', 'Thhalv10013782m.g' => 'esa', 'Thhalv10018686m.g' => 'esa', 'Thhalv10020899m.g' => 'esa', 'Thhalv10022755m.g' => 'esa', 'TPR.G23851' => 'tpr', 'TPR.G26500' => 'tpr', 'TPR.G27267' => 'tpr', 'TPR.G32001' => 'tpr', 'TPR.G6251' => 'tpr', 'TPR.G8167' => 'tpr', 'TWI12G1330' => 'twi', 'TWI18G1239' => 'twi', 'TWI34G0979' => 'twi', 'TWI36G0670' => 'twi', 'TWI36G0707' => 'twi', 'TWI56G0233' => 'twi', 'TWI75G1809' => 'twi', 'unitig_21.g20874' => 'ugi', 'unitig_26.g10343' => 'ugi', 'unitig_46.g18392' => 'ugi', 'unitig_52.g17178' => 'ugi', 'unitig_8.g2934' => 'ugi', 'vmacro01122' => 'vma', 'vmacro05875' => 'vma', 'vmacro06147' => 'vma', 'vmacro16191' => 'vma', 'vmacro18293' => 'vma', 'VMungo0251G3707' => 'vmu', 'VMungo0464G1521' => 'vmu', 'VMungo1215G0205' => 'vmu', 'VMungo1383G2484' => 'vmu', 'Zm00001eb079610' => 'zma', 'Zm00001eb135990' => 'zma', 'Zm00001eb183710' => 'zma', 'Zm00001eb246020' => 'zma' ), 'gf_id' => 'HOM05D001124', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001124' ), 'data_identifier' => 'HOM05D001124', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001124', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '548', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02520' => 'bna', 'A03p06630' => 'bna', 'A05p44460' => 'bna', 'A06p08710' => 'bna', 'A06p41090' => 'bna', 'A07p32320' => 'bna', 'A08p32520' => 'bna', 'A09p10360' => 'bna', 'A10p24080' => 'bna', 'Aa31LG11G15250' => 'aar', 'Aa31LG1G1800' => 'aar', 'Aa31LG2G5120' => 'aar', 'Aa31LG2G6070' => 'aar', 'Aa31LG5G10770' => 'aar', 'Aa31sc61G90' => 'aar', 'Actinidia01352' => 'ach', 'Actinidia05983' => 'ach', 'Actinidia08133' => 'ach', 'Actinidia15101' => 'ach', 'Actinidia26379' => 'ach', 'Actinidia35778' => 'ach', 'Actinidia36123' => 'ach', 'Actinidia37436' => 'ach', 'Actinidia38730' => 'ach', 'Ah.02g128210' => 'amhyb', 'Ah.03g132990' => 'amhyb', 'Ah.14g079410' => 'amhyb', 'AL1G24640' => 'aly', 'AL2G26680' => 'aly', 'AL3G10530' => 'aly', 'AL3G45230' => 'aly', 'AL5G15230' => 'aly', 'AL5G16960' => 'aly', 'AL6G25210' => 'aly', 'Aqoxy2G00441' => 'aox', 'Aqoxy3G01236' => 'aox', 'Aqoxy5G03746' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3RQ047' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C7GMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9C8JER' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MBL6KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YXCZ83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZANX40' => 'arhy', 'AT1G12990' => 'ath', 'AT1G67880' => 'ath', 'AT2G13290' => 'ath', 'AT3G01620' => 'ath', 'AT3G26445' => 'ath', 'AT3G27540' => 'ath', 'AT5G14480' => 'ath', 'ATR0824G026' => 'atr', 'ATR1098G019' => 'atr', 'Atru.chr11.2145' => 'acertr', 'Atru.chr2.3636' => 'acertr', 'Atru.chr2.3644' => 'acertr', 'Atru.chr6.2422' => 'acertr', 'Atru.chr7.1112' => 'acertr', 'AUR62005469' => 'cqu', 'AUR62011166' => 'cqu', 'AUR62013319' => 'cqu', 'AUR62024273' => 'cqu', 'AUR62028420' => 'cqu', 'AUR62041942' => 'cqu', 'BcaB01g04969' => 'bca', 'BcaB01g06371' => 'bca', 'BcaB02g11494' => 'bca', 'BcaB03g15382' => 'bca', 'BcaB08g36994' => 'bca', 'BcaC03g13477' => 'bca', 'BcaC03g13478' => 'bca', 'BcaC03g13480' => 'bca', 'BcaC03g13481' => 'bca', 'BcaC03g13486' => 'bca', 'BcaC04g19031' => 'bca', 'BcaC04g23085' => 'bca', 'BcaC05g25094' => 'bca', 'BcaC05g25096' => 'bca', 'BcaC05g25138' => 'bca', 'BcaC05g30416' => 'bca', 'BcaC05g30455' => 'bca', 'BcaC06g30979' => 'bca', 'BcaC06g33805' => 'bca', 'BcaC08g46021' => 'bca', 'BcaNung03154' => 'bca', 'BolC2t06623H' => 'bol', 'BolC2t06632H' => 'bol', 'BolC2t06635H' => 'bol', 'BolC2t06638H' => 'bol', 'BolC3t13266H' => 'bol', 'BolC5t29776H' => 'bol', 'BolC6t38912H' => 'bol', 'BolC7t44183H' => 'bol', 'BolC9t54123H' => 'bol', 'BolC9t59107H' => 'bol', 'BraA02t05221Z' => 'bra', 'BraA03t09996Z' => 'bra', 'BraA05t23210Z' => 'bra', 'BraA06t24068Z' => 'bra', 'BraA06t27032Z' => 'bra', 'BraA08t35176Z' => 'bra', 'BraA09t36680Z' => 'bra', 'BraA10t44471Z' => 'bra', 'C02p06760' => 'bna', 'C02p06890' => 'bna', 'C02p07010' => 'bna', 'C03p07660' => 'bna', 'C05p10300' => 'bna', 'C06p38150' => 'bna', 'C07p36650' => 'bna', 'C08p15770' => 'bna', 'C09p12300' => 'bna', 'C09p62700' => 'bna', 'C09p75040' => 'bna', 'CAN.G13.1' => 'can', 'CAN.G138.4' => 'can', 'CAN.G44.6' => 'can', 'CAN.G473.19' => 'can', 'CANSAT01G0835' => 'cansat', 'CANSAT11G0246' => 'cansat', 'CANSAT11G1766' => 'cansat', 'CANSAT64G1954' => 'cansat', 'CARHR013330' => 'chi', 'CARHR060530' => 'chi', 'CARHR075300' => 'chi', 'CARHR105120' => 'chi', 'CARHR148910' => 'chi', 'CARHR198830' => 'chi', 'Carub.0001s1275' => 'cru', 'Carub.0002s1437' => 'cru', 'Carub.0003s0044' => 'cru', 'Carub.0003s2787' => 'cru', 'Carub.0005s0597' => 'cru', 'Carub.0006s1266' => 'cru', 'Ca_06935_v3' => 'car', 'Ca_13559_v3' => 'car', 'Ca_16941_v3' => 'car', 'Ca_16960_v3' => 'car', 'Ca_17775_v3' => 'car', 'Ca_30464_v3' => 'car', 'Cc06_g08160' => 'ccan', 'Cc07_g01520' => 'ccan', 'Cc11_g15810' => 'ccan', 'CDE02G2840' => 'cde', 'CDE03G0093' => 'cde', 'CDE04G2127' => 'cde', 'CDE07G1857' => 'cde', 'CDE09G1246' => 'cde', 'Cfa003412' => 'cfa', 'Cfa007341' => 'cfa', 'Cfa009220' => 'cfa', 'Ciclev10008737m.g' => 'ccl', 'Ciclev10015565m.g' => 'ccl', 'Ciclev10031761m.g' => 'ccl', 'CiPaw.03G045300' => 'cil', 'CiPaw.03G247200' => 'cil', 'CiPaw.04G029500' => 'cil', 'CiPaw.04G174000' => 'cil', 'CiPaw.05G181200' => 'cil', 'CiPaw.06G067100' => 'cil', 'ClCG05G025800' => 'cla', 'ClCG06G011400' => 'cla', 'ClCG09G019360' => 'cla', 'COL.COLO4_04827' => 'col', 'COL.COLO4_29170' => 'col', 'COL.COLO4_35131' => 'col', 'COL.COLO4_35132' => 'col', 'Cpa.g.sc33.32' => 'cpa', 'Cpa.g.sc46.29' => 'cpa', 'Cpa.g.sc796.1' => 'cpa', 'CsaV3_1G030420' => 'csa', 'CsaV3_5G027050' => 'csa', 'CsaV3_5G031040' => 'csa', 'CsaV3_UNG023130' => 'csa', 'CSS0007726' => 'camsi', 'CSS0016433' => 'camsi', 'CSS0017656' => 'camsi', 'CSS0025364' => 'camsi', 'CSS0027582' => 'camsi', 'CSS0047288' => 'camsi', 'CSS0049950' => 'camsi', 'DCAR_003843' => 'dca', 'DCAR_007052' => 'dca', 'DCAR_020884' => 'dca', 'DCAR_021730' => 'dca', 'DCAR_024423' => 'dca', 'DCAR_026509' => 'dca', 'DCAR_031158' => 'dca', 'Dinv14728' => 'din', 'Dinv15219' => 'din', 'Dinv25728' => 'din', 'Dinv33428' => 'din', 'Dinv36489' => 'din', 'Dinv41486' => 'din', 'Duzib147G0469' => 'dzi', 'Duzib168G0060' => 'dzi', 'Duzib187G1215' => 'dzi', 'Duzib248G0692' => 'dzi', 'Duzib251G0767' => 'dzi', 'Duzib264G0446' => 'dzi', 'Duzib268G0691' => 'dzi', 'ECA232G4767' => 'eca', 'ECA233G2838' => 'eca', 'ECA234G0391' => 'eca', 'ECA234G0857' => 'eca', 'ECA236G1593' => 'eca', 'ECA238G0565' => 'eca', 'ECA246G1027' => 'eca', 'ECA246G3223' => 'eca', 'ECA246G3470' => 'eca', 'EL10Ac6g13829' => 'bvu', 'EL10Ac6g14093' => 'bvu', 'EL10Ac8g18707' => 'bvu', 'Eucgr.C01369' => 'egr', 'Eucgr.H02492' => 'egr', 'Eucgr.I01733' => 'egr', 'Eucgr.J02255' => 'egr', 'Eucgr.J02257' => 'egr', 'Eucgr.J02258' => 'egr', 'FAN02G1601' => 'fan', 'FAN03G1586' => 'fan', 'FAN03G2986' => 'fan', 'FAN05G4837' => 'fan', 'FAN06G0146' => 'fan', 'FAN07G0858' => 'fan', 'FAN09G3179' => 'fan', 'FAN10G0669' => 'fan', 'FAN12G2358' => 'fan', 'FAN14G4198' => 'fan', 'FAN14G5112' => 'fan', 'FAN17G0342' => 'fan', 'FAN19G0342' => 'fan', 'FAN19G0962' => 'fan', 'FAN19G1101' => 'fan', 'FAN19G1872' => 'fan', 'FAN22G0356' => 'fan', 'FAN23G0744' => 'fan', 'FAN23G1914' => 'fan', 'FAN26G0032' => 'fan', 'FAN28G0625' => 'fan', 'FvH4_1g02710' => 'fve', 'FvH4_1g02720' => 'fve', 'FvH4_4g25670' => 'fve', 'FvH4_6g51700' => 'fve', 'FvH4_7g20170' => 'fve', 'Glyma.05G175000' => 'gma', 'Glyma.08G132300' => 'gma', 'Glyma.11G243000' => 'gma', 'Glyma.13G158900' => 'gma', 'Glyma.17G112400' => 'gma', 'Glyma.18G014100' => 'gma', 'Glyma.19G003100' => 'gma', 'Glyma.19G056500' => 'gma', 'Gohir.A01G158900' => 'ghi', 'Gohir.A05G312600' => 'ghi', 'Gohir.A05G354900' => 'ghi', 'Gohir.A07G037200' => 'ghi', 'Gohir.A09G030000' => 'ghi', 'Gohir.A12G145200' => 'ghi', 'Gohir.D01G151500' => 'ghi', 'Gohir.D04G058300' => 'ghi', 'Gohir.D05G314100' => 'ghi', 'Gohir.D07G041400' => 'ghi', 'Gohir.D09G029700' => 'ghi', 'Gohir.D12G149700' => 'ghi', 'Gorai.001G043800' => 'gra', 'Gorai.002G187800' => 'gra', 'Gorai.006G034700' => 'gra', 'Gorai.008G161200' => 'gra', 'Gorai.009G335700' => 'gra', 'Gorai.012G065000' => 'gra', 'GSVIVG01000535001' => 'vvi', 'GSVIVG01015572001' => 'vvi', 'GSVIVG01032386001' => 'vvi', 'HanXRQChr05g0138531' => 'han', 'HanXRQChr06g0174391' => 'han', 'HanXRQChr07g0199021' => 'han', 'HanXRQChr08g0208211' => 'han', 'HanXRQChr09g0255471' => 'han', 'HanXRQChr10g0315791' => 'han', 'HanXRQChr12g0371991' => 'han', 'HanXRQChr15g0475251' => 'han', 'HanXRQChr17g0540001' => 'han', 'HanXRQChr17g0548631' => 'han', 'HanXRQChr17g0569561' => 'han', 'Haze_12256' => 'cav', 'Haze_14756' => 'cav', 'Haze_25528' => 'cav', 'Hma1.2p1_0079F.1_g041020' => 'hma', 'Hma1.2p1_0818F.1_g223260' => 'hma', 'Hma1.2p1_1747F.1_g300530' => 'hma', 'HPP92_004607' => 'vpl', 'HPP92_004608' => 'vpl', 'HPP92_006181' => 'vpl', 'HPP92_012192' => 'vpl', 'HPP92_015680' => 'vpl', 'HPP92_020249' => 'vpl', 'HPP92_021376' => 'vpl', 'HPP92_024275' => 'vpl', 'Hund06031' => 'sun', 'Hund25391' => 'sun', 'Lalb_Chr07g0185371' => 'lal', 'Lalb_Chr07g0185381' => 'lal', 'Lalb_Chr12g0204011' => 'lal', 'Lalb_Chr13g0301671' => 'lal', 'Lalb_Chr14g0362851' => 'lal', 'Lalb_Chr24g0403581' => 'lal', 'Lj1g0000233' => 'lja', 'Lj2g0018120' => 'lja', 'Lj3C621T0' => 'lonja', 'Lj3P1059T14' => 'lonja', 'Lj3P611T9' => 'lonja', 'Lj3P614T13' => 'lonja', 'Lj3P615T5' => 'lonja', 'Lj4g0012315' => 'lja', 'Lj4g0026182' => 'lja', 'Lj6P813T16' => 'lonja', 'Lj7C427T7' => 'lonja', 'Lj7C427T8' => 'lonja', 'Lj7P600T41' => 'lonja', 'Lju41C42G17' => 'lonja', 'Lsat_1_v5_gn_0_47300' => 'lsa', 'Lsat_1_v5_gn_2_91280' => 'lsa', 'Lsat_1_v5_gn_3_30561' => 'lsa', 'Lsat_1_v5_gn_4_184321' => 'lsa', 'Lsat_1_v5_gn_4_4041' => 'lsa', 'Lsat_1_v5_gn_5_92000' => 'lsa', 'Lsat_1_v5_gn_8_152940' => 'lsa', 'Lsat_1_v5_gn_8_62401' => 'lsa', 'Manes.06G055900' => 'mes', 'Manes.12G022200' => 'mes', 'Manes.13G023300' => 'mes', 'Manes.14G115000' => 'mes', 'Manes.15G151700' => 'mes', 'Manes.17G111300' => 'mes', 'Mapoly0226s0009' => 'mpo', 'MBI02_g25363_MAGBIO' => 'mbi', 'MBI06_g00027_MAGBIO' => 'mbi', 'MBI10_g13034_MAGBIO' => 'mbi', 'MD09G1023400' => 'mdo', 'MD13G1100100' => 'mdo', 'MD15G1169200' => 'mdo', 'MD16G1101100' => 'mdo', 'MD17G1022900' => 'mdo', 'Medtr3g096150' => 'mtr', 'Medtr4g115070' => 'mtr', 'Medtr7g033325' => 'mtr', 'Medtr8g089840' => 'mtr', 'MELO3C010319.2' => 'cme', 'MELO3C011944.2' => 'cme', 'MELO3C021589.2' => 'cme', 'Migut.E00207' => 'egut', 'Migut.H00067' => 'egut', 'Migut.K00433' => 'egut', 'Migut.K00606' => 'egut', 'Migut.K01410' => 'egut', 'MSTRG.13347' => 'ama', 'MSTRG.24045' => 'ama', 'MSTRG.2428' => 'ama', 'MSTRG.26410' => 'ama', 'MSTRG.3139' => 'ama', 'MSTRG.3286' => 'ama', 'MSTRG.563' => 'ama', 'MSTRG.7941' => 'ama', 'Nitab4.5_0000028g0060' => 'nta', 'Nitab4.5_0000065g0260' => 'nta', 'Nitab4.5_0000112g0060' => 'nta', 'Nitab4.5_0000489g0120' => 'nta', 'Nitab4.5_0001776g0050' => 'nta', 'Nitab4.5_0001854g0010' => 'nta', 'Nitab4.5_0001860g0020' => 'nta', 'Nitab4.5_0004352g0010' => 'nta', 'Nitab4.5_0008716g0020' => 'nta', 'Nitab4.5_0008922g0010' => 'nta', 'Nn3g16693' => 'nnu', 'Nn4g22596' => 'nnu', 'Nn7g37639' => 'nnu', 'Oeu001701.1' => 'oeu', 'Oeu018149.1' => 'oeu', 'Oeu026220.1' => 'oeu', 'Oeu038635.1' => 'oeu', 'Oeu049176.1' => 'oeu', 'Oeu056706.1' => 'oeu', 'Oeu056937.1' => 'oeu', 'Oeu057540.1' => 'oeu', 'Os02g0594900' => 'osa', 'Os02g0595100' => 'osa', 'Os04g0477500' => 'osa', 'Os12g0611900' => 'osa', 'Peaxi162Scf00076g00020' => 'pax', 'Peaxi162Scf00128g00217' => 'pax', 'Peaxi162Scf00129g01640' => 'pax', 'Peaxi162Scf00669g00007' => 'pax', 'Peaxi162Scf00700g00421' => 'pax', 'Peaxi162Scf00801g00038' => 'pax', 'Peaxi162Scf00891g00025' => 'pax', 'PGR083G0909' => 'pgr', 'PGR119G1005' => 'pgr', 'PGR142G2236' => 'pgr', 'PGR142G3388' => 'pgr', 'PGSC0003DMG400004514' => 'stu', 'PGSC0003DMG400012635' => 'stu', 'PGSC0003DMG400015730' => 'stu', 'PGSC0003DMG400018611' => 'stu', 'PGSC0003DMG400030897' => 'stu', 'Phvul.001G254800' => 'pvu', 'Phvul.002G260100' => 'pvu', 'Phvul.003G167600' => 'pvu', 'Phvul.004G005100' => 'pvu', 'Potri.001G343600' => 'ptr', 'Potri.006G066700' => 'ptr', 'Potri.008G186000' => 'ptr', 'Potri.010G046900' => 'ptr', 'Potri.018G127900' => 'ptr', 'Pp3c20_17750' => 'ppa', 'Pp3c24_4380' => 'ppa', 'Prupe.1G245800' => 'ppe', 'Prupe.3G293400' => 'ppe', 'Prupe.7G247400' => 'ppe', 'Psat0s145g0120' => 'psa', 'Psat0s595g0040' => 'psa', 'Psat0s595g0120' => 'psa', 'Psat3g175040' => 'psa', 'Psat7g058120' => 'psa', 'PSO017G0428' => 'pso', 'PSO063G7510' => 'pso', 'PSO067G0046' => 'pso', 'PSO478G1073' => 'pso', 'PSO675G3677' => 'pso', 'PSO675G6558' => 'pso', 'PSO675G7520' => 'pso', 'PSO675G8959' => 'pso', 'QL02p074089' => 'qlo', 'QL02p089614' => 'qlo', 'QL03p057736' => 'qlo', 'RcHm_v2.0_Chr1g0364131' => 'rch', 'RcHm_v2.0_Chr2g0087801' => 'rch', 'RcHm_v2.0_Chr2g0087821' => 'rch', 'RcHm_v2.0_Chr2g0173231' => 'rch', 'RcHm_v2.0_Chr4g0433111' => 'rch', 'Rhsim03G0250300' => 'rsi', 'Rhsim08G0048400' => 'rsi', 'Rhsim10G0014800' => 'rsi', 'Rhsim12G0040100' => 'rsi', 'Rhsim12G0109700' => 'rsi', 'Sabra06G0049600' => 'sbr', 'Sabra08G0141000' => 'sbr', 'Sabra10G0021400' => 'sbr', 'Sabra16G0222900' => 'sbr', 'Sabra18G0108600' => 'sbr', 'SalBow1G0433' => 'sbo', 'SalBow1G2038' => 'sbo', 'SalBow1G5003' => 'sbo', 'SalBow7G1197' => 'sbo', 'SalBow8G3506' => 'sbo', 'Sc03g0007300' => 'sci', 'Sc11g0000950' => 'sci', 'Sc14g0008750' => 'sci', 'Sc18g0000420' => 'sci', 'Sed0006754' => 'sed', 'Sed0008741' => 'sed', 'Sed0017172' => 'sed', 'Sed0018925' => 'sed', 'Sed0023326' => 'sed', 'Sed0025909' => 'sed', 'SEGI_05333' => 'sgi', 'SEGI_10362' => 'sgi', 'SEGI_13380' => 'sgi', 'SEGI_24306' => 'sgi', 'SEGI_29077' => 'sgi', 'SEGI_29095' => 'sgi', 'SEGI_36534' => 'sgi', 'SEGI_37506' => 'sgi', 'SEGI_38321' => 'sgi', 'SGA_v2.0_scaffold307G48031' => 'sas', 'SGA_v2.0_scaffold47G17507' => 'sas', 'SGA_v2.0_scaffold63G21736' => 'sas', 'SGA_v2.0_scaffold87G27070' => 'sas', 'SHI17794' => 'shi', 'SHI28851' => 'shi', 'SMO165G0155' => 'smo', 'SMO340G0217' => 'smo', 'SMO367G1210' => 'smo', 'Solyc02g093430.3' => 'sly', 'Solyc05g013580.4' => 'sly', 'Solyc07g008030.3' => 'sly', 'Solyc12g035470.2' => 'sly', 'Sopen02g038020' => 'spe', 'Sopen05g008490' => 'spe', 'Sopen07g003910' => 'spe', 'Sopen12g015240' => 'spe', 'Sp1g11550' => 'spa', 'Sp2g16710' => 'spa', 'Sp3g00430' => 'spa', 'Sp3g26780' => 'spa', 'Sp5g22900' => 'spa', 'Sp6g29530' => 'spa', 'TAR371G0794' => 'tar', 'TAR374G0164' => 'tar', 'TAR622G0165' => 'tar', 'TAR626G0929' => 'tar', 'TAR629G2155' => 'tar', 'THA.LOC104805282' => 'tha', 'THA.LOC104805363' => 'tha', 'THA.LOC104808968' => 'tha', 'THA.LOC104821093' => 'tha', 'THA.LOC104823953' => 'tha', 'THA.LOC104825562' => 'tha', 'THA.LOC104825665' => 'tha', 'Thecc.02G261400' => 'tca', 'Thecc.04G019200' => 'tca', 'Thecc.09G130400' => 'tca', 'Thhalv10004374m.g' => 'esa', 'Thhalv10007850m.g' => 'esa', 'Thhalv10013782m.g' => 'esa', 'Thhalv10018686m.g' => 'esa', 'Thhalv10020899m.g' => 'esa', 'Thhalv10022755m.g' => 'esa', 'TPR.G23851' => 'tpr', 'TPR.G26500' => 'tpr', 'TPR.G27267' => 'tpr', 'TPR.G32001' => 'tpr', 'TPR.G6251' => 'tpr', 'TPR.G8167' => 'tpr', 'TWI12G1330' => 'twi', 'TWI18G1239' => 'twi', 'TWI34G0979' => 'twi', 'TWI36G0670' => 'twi', 'TWI36G0707' => 'twi', 'TWI56G0233' => 'twi', 'TWI75G1809' => 'twi', 'unitig_21.g20874' => 'ugi', 'unitig_26.g10343' => 'ugi', 'unitig_46.g18392' => 'ugi', 'unitig_52.g17178' => 'ugi', 'unitig_8.g2934' => 'ugi', 'vmacro01122' => 'vma', 'vmacro05875' => 'vma', 'vmacro06147' => 'vma', 'vmacro16191' => 'vma', 'vmacro18293' => 'vma', 'VMungo0251G3707' => 'vmu', 'VMungo0464G1521' => 'vmu', 'VMungo1215G0205' => 'vmu', 'VMungo1383G2484' => 'vmu', 'Zm00001eb079610' => 'zma', 'Zm00001eb135990' => 'zma', 'Zm00001eb183710' => 'zma', 'Zm00001eb246020' => 'zma' ) $gf_id = 'HOM05D001124' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001124' ) $data_identifier = 'HOM05D001124' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 6, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 7, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 21, 'bol' => (int) 10, 'bra' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 6, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 9, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 21, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 8, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 10, 'lsa' => (int) 8, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 8, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 9, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb246020' $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' => 'HOM05D001124', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '548', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02520' => 'bna', 'A03p06630' => 'bna', 'A05p44460' => 'bna', 'A06p08710' => 'bna', 'A06p41090' => 'bna', 'A07p32320' => 'bna', 'A08p32520' => 'bna', 'A09p10360' => 'bna', 'A10p24080' => 'bna', 'Aa31LG11G15250' => 'aar', 'Aa31LG1G1800' => 'aar', 'Aa31LG2G5120' => 'aar', 'Aa31LG2G6070' => 'aar', 'Aa31LG5G10770' => 'aar', 'Aa31sc61G90' => 'aar', 'Actinidia01352' => 'ach', 'Actinidia05983' => 'ach', 'Actinidia08133' => 'ach', 'Actinidia15101' => 'ach', 'Actinidia26379' => 'ach', 'Actinidia35778' => 'ach', 'Actinidia36123' => 'ach', 'Actinidia37436' => 'ach', 'Actinidia38730' => 'ach', 'Ah.02g128210' => 'amhyb', 'Ah.03g132990' => 'amhyb', 'Ah.14g079410' => 'amhyb', 'AL1G24640' => 'aly', 'AL2G26680' => 'aly', 'AL3G10530' => 'aly', 'AL3G45230' => 'aly', 'AL5G15230' => 'aly', 'AL5G16960' => 'aly', 'AL6G25210' => 'aly', 'Aqoxy2G00441' => 'aox', 'Aqoxy3G01236' => 'aox', 'Aqoxy5G03746' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3RQ047' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C7GMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9C8JER' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MBL6KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YXCZ83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZANX40' => 'arhy', 'AT1G12990' => 'ath', 'AT1G67880' => 'ath', 'AT2G13290' => 'ath', 'AT3G01620' => 'ath', 'AT3G26445' => 'ath', 'AT3G27540' => 'ath', 'AT5G14480' => 'ath', 'ATR0824G026' => 'atr', 'ATR1098G019' => 'atr', 'Atru.chr11.2145' => 'acertr', 'Atru.chr2.3636' => 'acertr', 'Atru.chr2.3644' => 'acertr', 'Atru.chr6.2422' => 'acertr', 'Atru.chr7.1112' => 'acertr', 'AUR62005469' => 'cqu', 'AUR62011166' => 'cqu', 'AUR62013319' => 'cqu', 'AUR62024273' => 'cqu', 'AUR62028420' => 'cqu', 'AUR62041942' => 'cqu', 'BcaB01g04969' => 'bca', 'BcaB01g06371' => 'bca', 'BcaB02g11494' => 'bca', 'BcaB03g15382' => 'bca', 'BcaB08g36994' => 'bca', 'BcaC03g13477' => 'bca', 'BcaC03g13478' => 'bca', 'BcaC03g13480' => 'bca', 'BcaC03g13481' => 'bca', 'BcaC03g13486' => 'bca', 'BcaC04g19031' => 'bca', 'BcaC04g23085' => 'bca', 'BcaC05g25094' => 'bca', 'BcaC05g25096' => 'bca', 'BcaC05g25138' => 'bca', 'BcaC05g30416' => 'bca', 'BcaC05g30455' => 'bca', 'BcaC06g30979' => 'bca', 'BcaC06g33805' => 'bca', 'BcaC08g46021' => 'bca', 'BcaNung03154' => 'bca', 'BolC2t06623H' => 'bol', 'BolC2t06632H' => 'bol', 'BolC2t06635H' => 'bol', 'BolC2t06638H' => 'bol', 'BolC3t13266H' => 'bol', 'BolC5t29776H' => 'bol', 'BolC6t38912H' => 'bol', 'BolC7t44183H' => 'bol', 'BolC9t54123H' => 'bol', 'BolC9t59107H' => 'bol', 'BraA02t05221Z' => 'bra', 'BraA03t09996Z' => 'bra', 'BraA05t23210Z' => 'bra', 'BraA06t24068Z' => 'bra', 'BraA06t27032Z' => 'bra', 'BraA08t35176Z' => 'bra', 'BraA09t36680Z' => 'bra', 'BraA10t44471Z' => 'bra', 'C02p06760' => 'bna', 'C02p06890' => 'bna', 'C02p07010' => 'bna', 'C03p07660' => 'bna', 'C05p10300' => 'bna', 'C06p38150' => 'bna', 'C07p36650' => 'bna', 'C08p15770' => 'bna', 'C09p12300' => 'bna', 'C09p62700' => 'bna', 'C09p75040' => 'bna', 'CAN.G13.1' => 'can', 'CAN.G138.4' => 'can', 'CAN.G44.6' => 'can', 'CAN.G473.19' => 'can', 'CANSAT01G0835' => 'cansat', 'CANSAT11G0246' => 'cansat', 'CANSAT11G1766' => 'cansat', 'CANSAT64G1954' => 'cansat', 'CARHR013330' => 'chi', 'CARHR060530' => 'chi', 'CARHR075300' => 'chi', 'CARHR105120' => 'chi', 'CARHR148910' => 'chi', 'CARHR198830' => 'chi', 'Carub.0001s1275' => 'cru', 'Carub.0002s1437' => 'cru', 'Carub.0003s0044' => 'cru', 'Carub.0003s2787' => 'cru', 'Carub.0005s0597' => 'cru', 'Carub.0006s1266' => 'cru', 'Ca_06935_v3' => 'car', 'Ca_13559_v3' => 'car', 'Ca_16941_v3' => 'car', 'Ca_16960_v3' => 'car', 'Ca_17775_v3' => 'car', 'Ca_30464_v3' => 'car', 'Cc06_g08160' => 'ccan', 'Cc07_g01520' => 'ccan', 'Cc11_g15810' => 'ccan', 'CDE02G2840' => 'cde', 'CDE03G0093' => 'cde', 'CDE04G2127' => 'cde', 'CDE07G1857' => 'cde', 'CDE09G1246' => 'cde', 'Cfa003412' => 'cfa', 'Cfa007341' => 'cfa', 'Cfa009220' => 'cfa', 'Ciclev10008737m.g' => 'ccl', 'Ciclev10015565m.g' => 'ccl', 'Ciclev10031761m.g' => 'ccl', 'CiPaw.03G045300' => 'cil', 'CiPaw.03G247200' => 'cil', 'CiPaw.04G029500' => 'cil', 'CiPaw.04G174000' => 'cil', 'CiPaw.05G181200' => 'cil', 'CiPaw.06G067100' => 'cil', 'ClCG05G025800' => 'cla', 'ClCG06G011400' => 'cla', 'ClCG09G019360' => 'cla', 'COL.COLO4_04827' => 'col', 'COL.COLO4_29170' => 'col', 'COL.COLO4_35131' => 'col', 'COL.COLO4_35132' => 'col', 'Cpa.g.sc33.32' => 'cpa', 'Cpa.g.sc46.29' => 'cpa', 'Cpa.g.sc796.1' => 'cpa', 'CsaV3_1G030420' => 'csa', 'CsaV3_5G027050' => 'csa', 'CsaV3_5G031040' => 'csa', 'CsaV3_UNG023130' => 'csa', 'CSS0007726' => 'camsi', 'CSS0016433' => 'camsi', 'CSS0017656' => 'camsi', 'CSS0025364' => 'camsi', 'CSS0027582' => 'camsi', 'CSS0047288' => 'camsi', 'CSS0049950' => 'camsi', 'DCAR_003843' => 'dca', 'DCAR_007052' => 'dca', 'DCAR_020884' => 'dca', 'DCAR_021730' => 'dca', 'DCAR_024423' => 'dca', 'DCAR_026509' => 'dca', 'DCAR_031158' => 'dca', 'Dinv14728' => 'din', 'Dinv15219' => 'din', 'Dinv25728' => 'din', 'Dinv33428' => 'din', 'Dinv36489' => 'din', 'Dinv41486' => 'din', 'Duzib147G0469' => 'dzi', 'Duzib168G0060' => 'dzi', 'Duzib187G1215' => 'dzi', 'Duzib248G0692' => 'dzi', 'Duzib251G0767' => 'dzi', 'Duzib264G0446' => 'dzi', 'Duzib268G0691' => 'dzi', 'ECA232G4767' => 'eca', 'ECA233G2838' => 'eca', 'ECA234G0391' => 'eca', 'ECA234G0857' => 'eca', 'ECA236G1593' => 'eca', 'ECA238G0565' => 'eca', 'ECA246G1027' => 'eca', 'ECA246G3223' => 'eca', 'ECA246G3470' => 'eca', 'EL10Ac6g13829' => 'bvu', 'EL10Ac6g14093' => 'bvu', 'EL10Ac8g18707' => 'bvu', 'Eucgr.C01369' => 'egr', 'Eucgr.H02492' => 'egr', 'Eucgr.I01733' => 'egr', 'Eucgr.J02255' => 'egr', 'Eucgr.J02257' => 'egr', 'Eucgr.J02258' => 'egr', 'FAN02G1601' => 'fan', 'FAN03G1586' => 'fan', 'FAN03G2986' => 'fan', 'FAN05G4837' => 'fan', 'FAN06G0146' => 'fan', 'FAN07G0858' => 'fan', 'FAN09G3179' => 'fan', 'FAN10G0669' => 'fan', 'FAN12G2358' => 'fan', 'FAN14G4198' => 'fan', 'FAN14G5112' => 'fan', 'FAN17G0342' => 'fan', 'FAN19G0342' => 'fan', 'FAN19G0962' => 'fan', 'FAN19G1101' => 'fan', 'FAN19G1872' => 'fan', 'FAN22G0356' => 'fan', 'FAN23G0744' => 'fan', 'FAN23G1914' => 'fan', 'FAN26G0032' => 'fan', 'FAN28G0625' => 'fan', 'FvH4_1g02710' => 'fve', 'FvH4_1g02720' => 'fve', 'FvH4_4g25670' => 'fve', 'FvH4_6g51700' => 'fve', 'FvH4_7g20170' => 'fve', 'Glyma.05G175000' => 'gma', 'Glyma.08G132300' => 'gma', 'Glyma.11G243000' => 'gma', 'Glyma.13G158900' => 'gma', 'Glyma.17G112400' => 'gma', 'Glyma.18G014100' => 'gma', 'Glyma.19G003100' => 'gma', 'Glyma.19G056500' => 'gma', 'Gohir.A01G158900' => 'ghi', 'Gohir.A05G312600' => 'ghi', 'Gohir.A05G354900' => 'ghi', 'Gohir.A07G037200' => 'ghi', 'Gohir.A09G030000' => 'ghi', 'Gohir.A12G145200' => 'ghi', 'Gohir.D01G151500' => 'ghi', 'Gohir.D04G058300' => 'ghi', 'Gohir.D05G314100' => 'ghi', 'Gohir.D07G041400' => 'ghi', 'Gohir.D09G029700' => 'ghi', 'Gohir.D12G149700' => 'ghi', 'Gorai.001G043800' => 'gra', 'Gorai.002G187800' => 'gra', 'Gorai.006G034700' => 'gra', 'Gorai.008G161200' => 'gra', 'Gorai.009G335700' => 'gra', 'Gorai.012G065000' => 'gra', 'GSVIVG01000535001' => 'vvi', 'GSVIVG01015572001' => 'vvi', 'GSVIVG01032386001' => 'vvi', 'HanXRQChr05g0138531' => 'han', 'HanXRQChr06g0174391' => 'han', 'HanXRQChr07g0199021' => 'han', 'HanXRQChr08g0208211' => 'han', 'HanXRQChr09g0255471' => 'han', 'HanXRQChr10g0315791' => 'han', 'HanXRQChr12g0371991' => 'han', 'HanXRQChr15g0475251' => 'han', 'HanXRQChr17g0540001' => 'han', 'HanXRQChr17g0548631' => 'han', 'HanXRQChr17g0569561' => 'han', 'Haze_12256' => 'cav', 'Haze_14756' => 'cav', 'Haze_25528' => 'cav', 'Hma1.2p1_0079F.1_g041020' => 'hma', 'Hma1.2p1_0818F.1_g223260' => 'hma', 'Hma1.2p1_1747F.1_g300530' => 'hma', 'HPP92_004607' => 'vpl', 'HPP92_004608' => 'vpl', 'HPP92_006181' => 'vpl', 'HPP92_012192' => 'vpl', 'HPP92_015680' => 'vpl', 'HPP92_020249' => 'vpl', 'HPP92_021376' => 'vpl', 'HPP92_024275' => 'vpl', 'Hund06031' => 'sun', 'Hund25391' => 'sun', 'Lalb_Chr07g0185371' => 'lal', 'Lalb_Chr07g0185381' => 'lal', 'Lalb_Chr12g0204011' => 'lal', 'Lalb_Chr13g0301671' => 'lal', 'Lalb_Chr14g0362851' => 'lal', 'Lalb_Chr24g0403581' => 'lal', 'Lj1g0000233' => 'lja', 'Lj2g0018120' => 'lja', 'Lj3C621T0' => 'lonja', 'Lj3P1059T14' => 'lonja', 'Lj3P611T9' => 'lonja', 'Lj3P614T13' => 'lonja', 'Lj3P615T5' => 'lonja', 'Lj4g0012315' => 'lja', 'Lj4g0026182' => 'lja', 'Lj6P813T16' => 'lonja', 'Lj7C427T7' => 'lonja', 'Lj7C427T8' => 'lonja', 'Lj7P600T41' => 'lonja', 'Lju41C42G17' => 'lonja', 'Lsat_1_v5_gn_0_47300' => 'lsa', 'Lsat_1_v5_gn_2_91280' => 'lsa', 'Lsat_1_v5_gn_3_30561' => 'lsa', 'Lsat_1_v5_gn_4_184321' => 'lsa', 'Lsat_1_v5_gn_4_4041' => 'lsa', 'Lsat_1_v5_gn_5_92000' => 'lsa', 'Lsat_1_v5_gn_8_152940' => 'lsa', 'Lsat_1_v5_gn_8_62401' => 'lsa', 'Manes.06G055900' => 'mes', 'Manes.12G022200' => 'mes', 'Manes.13G023300' => 'mes', 'Manes.14G115000' => 'mes', 'Manes.15G151700' => 'mes', 'Manes.17G111300' => 'mes', 'Mapoly0226s0009' => 'mpo', 'MBI02_g25363_MAGBIO' => 'mbi', 'MBI06_g00027_MAGBIO' => 'mbi', 'MBI10_g13034_MAGBIO' => 'mbi', 'MD09G1023400' => 'mdo', 'MD13G1100100' => 'mdo', 'MD15G1169200' => 'mdo', 'MD16G1101100' => 'mdo', 'MD17G1022900' => 'mdo', 'Medtr3g096150' => 'mtr', 'Medtr4g115070' => 'mtr', 'Medtr7g033325' => 'mtr', 'Medtr8g089840' => 'mtr', 'MELO3C010319.2' => 'cme', 'MELO3C011944.2' => 'cme', 'MELO3C021589.2' => 'cme', 'Migut.E00207' => 'egut', 'Migut.H00067' => 'egut', 'Migut.K00433' => 'egut', 'Migut.K00606' => 'egut', 'Migut.K01410' => 'egut', 'MSTRG.13347' => 'ama', 'MSTRG.24045' => 'ama', 'MSTRG.2428' => 'ama', 'MSTRG.26410' => 'ama', 'MSTRG.3139' => 'ama', 'MSTRG.3286' => 'ama', 'MSTRG.563' => 'ama', 'MSTRG.7941' => 'ama', 'Nitab4.5_0000028g0060' => 'nta', 'Nitab4.5_0000065g0260' => 'nta', 'Nitab4.5_0000112g0060' => 'nta', 'Nitab4.5_0000489g0120' => 'nta', 'Nitab4.5_0001776g0050' => 'nta', 'Nitab4.5_0001854g0010' => 'nta', 'Nitab4.5_0001860g0020' => 'nta', 'Nitab4.5_0004352g0010' => 'nta', 'Nitab4.5_0008716g0020' => 'nta', 'Nitab4.5_0008922g0010' => 'nta', 'Nn3g16693' => 'nnu', 'Nn4g22596' => 'nnu', 'Nn7g37639' => 'nnu', 'Oeu001701.1' => 'oeu', 'Oeu018149.1' => 'oeu', 'Oeu026220.1' => 'oeu', 'Oeu038635.1' => 'oeu', 'Oeu049176.1' => 'oeu', 'Oeu056706.1' => 'oeu', 'Oeu056937.1' => 'oeu', 'Oeu057540.1' => 'oeu', 'Os02g0594900' => 'osa', 'Os02g0595100' => 'osa', 'Os04g0477500' => 'osa', 'Os12g0611900' => 'osa', 'Peaxi162Scf00076g00020' => 'pax', 'Peaxi162Scf00128g00217' => 'pax', 'Peaxi162Scf00129g01640' => 'pax', 'Peaxi162Scf00669g00007' => 'pax', 'Peaxi162Scf00700g00421' => 'pax', 'Peaxi162Scf00801g00038' => 'pax', 'Peaxi162Scf00891g00025' => 'pax', 'PGR083G0909' => 'pgr', 'PGR119G1005' => 'pgr', 'PGR142G2236' => 'pgr', 'PGR142G3388' => 'pgr', 'PGSC0003DMG400004514' => 'stu', 'PGSC0003DMG400012635' => 'stu', 'PGSC0003DMG400015730' => 'stu', 'PGSC0003DMG400018611' => 'stu', 'PGSC0003DMG400030897' => 'stu', 'Phvul.001G254800' => 'pvu', 'Phvul.002G260100' => 'pvu', 'Phvul.003G167600' => 'pvu', 'Phvul.004G005100' => 'pvu', 'Potri.001G343600' => 'ptr', 'Potri.006G066700' => 'ptr', 'Potri.008G186000' => 'ptr', 'Potri.010G046900' => 'ptr', 'Potri.018G127900' => 'ptr', 'Pp3c20_17750' => 'ppa', 'Pp3c24_4380' => 'ppa', 'Prupe.1G245800' => 'ppe', 'Prupe.3G293400' => 'ppe', 'Prupe.7G247400' => 'ppe', 'Psat0s145g0120' => 'psa', 'Psat0s595g0040' => 'psa', 'Psat0s595g0120' => 'psa', 'Psat3g175040' => 'psa', 'Psat7g058120' => 'psa', 'PSO017G0428' => 'pso', 'PSO063G7510' => 'pso', 'PSO067G0046' => 'pso', 'PSO478G1073' => 'pso', 'PSO675G3677' => 'pso', 'PSO675G6558' => 'pso', 'PSO675G7520' => 'pso', 'PSO675G8959' => 'pso', 'QL02p074089' => 'qlo', 'QL02p089614' => 'qlo', 'QL03p057736' => 'qlo', 'RcHm_v2.0_Chr1g0364131' => 'rch', 'RcHm_v2.0_Chr2g0087801' => 'rch', 'RcHm_v2.0_Chr2g0087821' => 'rch', 'RcHm_v2.0_Chr2g0173231' => 'rch', 'RcHm_v2.0_Chr4g0433111' => 'rch', 'Rhsim03G0250300' => 'rsi', 'Rhsim08G0048400' => 'rsi', 'Rhsim10G0014800' => 'rsi', 'Rhsim12G0040100' => 'rsi', 'Rhsim12G0109700' => 'rsi', 'Sabra06G0049600' => 'sbr', 'Sabra08G0141000' => 'sbr', 'Sabra10G0021400' => 'sbr', 'Sabra16G0222900' => 'sbr', 'Sabra18G0108600' => 'sbr', 'SalBow1G0433' => 'sbo', 'SalBow1G2038' => 'sbo', 'SalBow1G5003' => 'sbo', 'SalBow7G1197' => 'sbo', 'SalBow8G3506' => 'sbo', 'Sc03g0007300' => 'sci', 'Sc11g0000950' => 'sci', 'Sc14g0008750' => 'sci', 'Sc18g0000420' => 'sci', 'Sed0006754' => 'sed', 'Sed0008741' => 'sed', 'Sed0017172' => 'sed', 'Sed0018925' => 'sed', 'Sed0023326' => 'sed', 'Sed0025909' => 'sed', 'SEGI_05333' => 'sgi', 'SEGI_10362' => 'sgi', 'SEGI_13380' => 'sgi', 'SEGI_24306' => 'sgi', 'SEGI_29077' => 'sgi', 'SEGI_29095' => 'sgi', 'SEGI_36534' => 'sgi', 'SEGI_37506' => 'sgi', 'SEGI_38321' => 'sgi', 'SGA_v2.0_scaffold307G48031' => 'sas', 'SGA_v2.0_scaffold47G17507' => 'sas', 'SGA_v2.0_scaffold63G21736' => 'sas', 'SGA_v2.0_scaffold87G27070' => 'sas', 'SHI17794' => 'shi', 'SHI28851' => 'shi', 'SMO165G0155' => 'smo', 'SMO340G0217' => 'smo', 'SMO367G1210' => 'smo', 'Solyc02g093430.3' => 'sly', 'Solyc05g013580.4' => 'sly', 'Solyc07g008030.3' => 'sly', 'Solyc12g035470.2' => 'sly', 'Sopen02g038020' => 'spe', 'Sopen05g008490' => 'spe', 'Sopen07g003910' => 'spe', 'Sopen12g015240' => 'spe', 'Sp1g11550' => 'spa', 'Sp2g16710' => 'spa', 'Sp3g00430' => 'spa', 'Sp3g26780' => 'spa', 'Sp5g22900' => 'spa', 'Sp6g29530' => 'spa', 'TAR371G0794' => 'tar', 'TAR374G0164' => 'tar', 'TAR622G0165' => 'tar', 'TAR626G0929' => 'tar', 'TAR629G2155' => 'tar', 'THA.LOC104805282' => 'tha', 'THA.LOC104805363' => 'tha', 'THA.LOC104808968' => 'tha', 'THA.LOC104821093' => 'tha', 'THA.LOC104823953' => 'tha', 'THA.LOC104825562' => 'tha', 'THA.LOC104825665' => 'tha', 'Thecc.02G261400' => 'tca', 'Thecc.04G019200' => 'tca', 'Thecc.09G130400' => 'tca', 'Thhalv10004374m.g' => 'esa', 'Thhalv10007850m.g' => 'esa', 'Thhalv10013782m.g' => 'esa', 'Thhalv10018686m.g' => 'esa', 'Thhalv10020899m.g' => 'esa', 'Thhalv10022755m.g' => 'esa', 'TPR.G23851' => 'tpr', 'TPR.G26500' => 'tpr', 'TPR.G27267' => 'tpr', 'TPR.G32001' => 'tpr', 'TPR.G6251' => 'tpr', 'TPR.G8167' => 'tpr', 'TWI12G1330' => 'twi', 'TWI18G1239' => 'twi', 'TWI34G0979' => 'twi', 'TWI36G0670' => 'twi', 'TWI36G0707' => 'twi', 'TWI56G0233' => 'twi', 'TWI75G1809' => 'twi', 'unitig_21.g20874' => 'ugi', 'unitig_26.g10343' => 'ugi', 'unitig_46.g18392' => 'ugi', 'unitig_52.g17178' => 'ugi', 'unitig_8.g2934' => 'ugi', 'vmacro01122' => 'vma', 'vmacro05875' => 'vma', 'vmacro06147' => 'vma', 'vmacro16191' => 'vma', 'vmacro18293' => 'vma', 'VMungo0251G3707' => 'vmu', 'VMungo0464G1521' => 'vmu', 'VMungo1215G0205' => 'vmu', 'VMungo1383G2484' => 'vmu', 'Zm00001eb079610' => 'zma', 'Zm00001eb135990' => 'zma', 'Zm00001eb183710' => 'zma', 'Zm00001eb246020' => 'zma' ), 'gf_id' => 'HOM05D001124', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001124' ), 'data_identifier' => 'HOM05D001124', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001124', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '548', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02520' => 'bna', 'A03p06630' => 'bna', 'A05p44460' => 'bna', 'A06p08710' => 'bna', 'A06p41090' => 'bna', 'A07p32320' => 'bna', 'A08p32520' => 'bna', 'A09p10360' => 'bna', 'A10p24080' => 'bna', 'Aa31LG11G15250' => 'aar', 'Aa31LG1G1800' => 'aar', 'Aa31LG2G5120' => 'aar', 'Aa31LG2G6070' => 'aar', 'Aa31LG5G10770' => 'aar', 'Aa31sc61G90' => 'aar', 'Actinidia01352' => 'ach', 'Actinidia05983' => 'ach', 'Actinidia08133' => 'ach', 'Actinidia15101' => 'ach', 'Actinidia26379' => 'ach', 'Actinidia35778' => 'ach', 'Actinidia36123' => 'ach', 'Actinidia37436' => 'ach', 'Actinidia38730' => 'ach', 'Ah.02g128210' => 'amhyb', 'Ah.03g132990' => 'amhyb', 'Ah.14g079410' => 'amhyb', 'AL1G24640' => 'aly', 'AL2G26680' => 'aly', 'AL3G10530' => 'aly', 'AL3G45230' => 'aly', 'AL5G15230' => 'aly', 'AL5G16960' => 'aly', 'AL6G25210' => 'aly', 'Aqoxy2G00441' => 'aox', 'Aqoxy3G01236' => 'aox', 'Aqoxy5G03746' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3RQ047' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C7GMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9C8JER' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MBL6KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YXCZ83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZANX40' => 'arhy', 'AT1G12990' => 'ath', 'AT1G67880' => 'ath', 'AT2G13290' => 'ath', 'AT3G01620' => 'ath', 'AT3G26445' => 'ath', 'AT3G27540' => 'ath', 'AT5G14480' => 'ath', 'ATR0824G026' => 'atr', 'ATR1098G019' => 'atr', 'Atru.chr11.2145' => 'acertr', 'Atru.chr2.3636' => 'acertr', 'Atru.chr2.3644' => 'acertr', 'Atru.chr6.2422' => 'acertr', 'Atru.chr7.1112' => 'acertr', 'AUR62005469' => 'cqu', 'AUR62011166' => 'cqu', 'AUR62013319' => 'cqu', 'AUR62024273' => 'cqu', 'AUR62028420' => 'cqu', 'AUR62041942' => 'cqu', 'BcaB01g04969' => 'bca', 'BcaB01g06371' => 'bca', 'BcaB02g11494' => 'bca', 'BcaB03g15382' => 'bca', 'BcaB08g36994' => 'bca', 'BcaC03g13477' => 'bca', 'BcaC03g13478' => 'bca', 'BcaC03g13480' => 'bca', 'BcaC03g13481' => 'bca', 'BcaC03g13486' => 'bca', 'BcaC04g19031' => 'bca', 'BcaC04g23085' => 'bca', 'BcaC05g25094' => 'bca', 'BcaC05g25096' => 'bca', 'BcaC05g25138' => 'bca', 'BcaC05g30416' => 'bca', 'BcaC05g30455' => 'bca', 'BcaC06g30979' => 'bca', 'BcaC06g33805' => 'bca', 'BcaC08g46021' => 'bca', 'BcaNung03154' => 'bca', 'BolC2t06623H' => 'bol', 'BolC2t06632H' => 'bol', 'BolC2t06635H' => 'bol', 'BolC2t06638H' => 'bol', 'BolC3t13266H' => 'bol', 'BolC5t29776H' => 'bol', 'BolC6t38912H' => 'bol', 'BolC7t44183H' => 'bol', 'BolC9t54123H' => 'bol', 'BolC9t59107H' => 'bol', 'BraA02t05221Z' => 'bra', 'BraA03t09996Z' => 'bra', 'BraA05t23210Z' => 'bra', 'BraA06t24068Z' => 'bra', 'BraA06t27032Z' => 'bra', 'BraA08t35176Z' => 'bra', 'BraA09t36680Z' => 'bra', 'BraA10t44471Z' => 'bra', 'C02p06760' => 'bna', 'C02p06890' => 'bna', 'C02p07010' => 'bna', 'C03p07660' => 'bna', 'C05p10300' => 'bna', 'C06p38150' => 'bna', 'C07p36650' => 'bna', 'C08p15770' => 'bna', 'C09p12300' => 'bna', 'C09p62700' => 'bna', 'C09p75040' => 'bna', 'CAN.G13.1' => 'can', 'CAN.G138.4' => 'can', 'CAN.G44.6' => 'can', 'CAN.G473.19' => 'can', 'CANSAT01G0835' => 'cansat', 'CANSAT11G0246' => 'cansat', 'CANSAT11G1766' => 'cansat', 'CANSAT64G1954' => 'cansat', 'CARHR013330' => 'chi', 'CARHR060530' => 'chi', 'CARHR075300' => 'chi', 'CARHR105120' => 'chi', 'CARHR148910' => 'chi', 'CARHR198830' => 'chi', 'Carub.0001s1275' => 'cru', 'Carub.0002s1437' => 'cru', 'Carub.0003s0044' => 'cru', 'Carub.0003s2787' => 'cru', 'Carub.0005s0597' => 'cru', 'Carub.0006s1266' => 'cru', 'Ca_06935_v3' => 'car', 'Ca_13559_v3' => 'car', 'Ca_16941_v3' => 'car', 'Ca_16960_v3' => 'car', 'Ca_17775_v3' => 'car', 'Ca_30464_v3' => 'car', 'Cc06_g08160' => 'ccan', 'Cc07_g01520' => 'ccan', 'Cc11_g15810' => 'ccan', 'CDE02G2840' => 'cde', 'CDE03G0093' => 'cde', 'CDE04G2127' => 'cde', 'CDE07G1857' => 'cde', 'CDE09G1246' => 'cde', 'Cfa003412' => 'cfa', 'Cfa007341' => 'cfa', 'Cfa009220' => 'cfa', 'Ciclev10008737m.g' => 'ccl', 'Ciclev10015565m.g' => 'ccl', 'Ciclev10031761m.g' => 'ccl', 'CiPaw.03G045300' => 'cil', 'CiPaw.03G247200' => 'cil', 'CiPaw.04G029500' => 'cil', 'CiPaw.04G174000' => 'cil', 'CiPaw.05G181200' => 'cil', 'CiPaw.06G067100' => 'cil', 'ClCG05G025800' => 'cla', 'ClCG06G011400' => 'cla', 'ClCG09G019360' => 'cla', 'COL.COLO4_04827' => 'col', 'COL.COLO4_29170' => 'col', 'COL.COLO4_35131' => 'col', 'COL.COLO4_35132' => 'col', 'Cpa.g.sc33.32' => 'cpa', 'Cpa.g.sc46.29' => 'cpa', 'Cpa.g.sc796.1' => 'cpa', 'CsaV3_1G030420' => 'csa', 'CsaV3_5G027050' => 'csa', 'CsaV3_5G031040' => 'csa', 'CsaV3_UNG023130' => 'csa', 'CSS0007726' => 'camsi', 'CSS0016433' => 'camsi', 'CSS0017656' => 'camsi', 'CSS0025364' => 'camsi', 'CSS0027582' => 'camsi', 'CSS0047288' => 'camsi', 'CSS0049950' => 'camsi', 'DCAR_003843' => 'dca', 'DCAR_007052' => 'dca', 'DCAR_020884' => 'dca', 'DCAR_021730' => 'dca', 'DCAR_024423' => 'dca', 'DCAR_026509' => 'dca', 'DCAR_031158' => 'dca', 'Dinv14728' => 'din', 'Dinv15219' => 'din', 'Dinv25728' => 'din', 'Dinv33428' => 'din', 'Dinv36489' => 'din', 'Dinv41486' => 'din', 'Duzib147G0469' => 'dzi', 'Duzib168G0060' => 'dzi', 'Duzib187G1215' => 'dzi', 'Duzib248G0692' => 'dzi', 'Duzib251G0767' => 'dzi', 'Duzib264G0446' => 'dzi', 'Duzib268G0691' => 'dzi', 'ECA232G4767' => 'eca', 'ECA233G2838' => 'eca', 'ECA234G0391' => 'eca', 'ECA234G0857' => 'eca', 'ECA236G1593' => 'eca', 'ECA238G0565' => 'eca', 'ECA246G1027' => 'eca', 'ECA246G3223' => 'eca', 'ECA246G3470' => 'eca', 'EL10Ac6g13829' => 'bvu', 'EL10Ac6g14093' => 'bvu', 'EL10Ac8g18707' => 'bvu', 'Eucgr.C01369' => 'egr', 'Eucgr.H02492' => 'egr', 'Eucgr.I01733' => 'egr', 'Eucgr.J02255' => 'egr', 'Eucgr.J02257' => 'egr', 'Eucgr.J02258' => 'egr', 'FAN02G1601' => 'fan', 'FAN03G1586' => 'fan', 'FAN03G2986' => 'fan', 'FAN05G4837' => 'fan', 'FAN06G0146' => 'fan', 'FAN07G0858' => 'fan', 'FAN09G3179' => 'fan', 'FAN10G0669' => 'fan', 'FAN12G2358' => 'fan', 'FAN14G4198' => 'fan', 'FAN14G5112' => 'fan', 'FAN17G0342' => 'fan', 'FAN19G0342' => 'fan', 'FAN19G0962' => 'fan', 'FAN19G1101' => 'fan', 'FAN19G1872' => 'fan', 'FAN22G0356' => 'fan', 'FAN23G0744' => 'fan', 'FAN23G1914' => 'fan', 'FAN26G0032' => 'fan', 'FAN28G0625' => 'fan', 'FvH4_1g02710' => 'fve', 'FvH4_1g02720' => 'fve', 'FvH4_4g25670' => 'fve', 'FvH4_6g51700' => 'fve', 'FvH4_7g20170' => 'fve', 'Glyma.05G175000' => 'gma', 'Glyma.08G132300' => 'gma', 'Glyma.11G243000' => 'gma', 'Glyma.13G158900' => 'gma', 'Glyma.17G112400' => 'gma', 'Glyma.18G014100' => 'gma', 'Glyma.19G003100' => 'gma', 'Glyma.19G056500' => 'gma', 'Gohir.A01G158900' => 'ghi', 'Gohir.A05G312600' => 'ghi', 'Gohir.A05G354900' => 'ghi', 'Gohir.A07G037200' => 'ghi', 'Gohir.A09G030000' => 'ghi', 'Gohir.A12G145200' => 'ghi', 'Gohir.D01G151500' => 'ghi', 'Gohir.D04G058300' => 'ghi', 'Gohir.D05G314100' => 'ghi', 'Gohir.D07G041400' => 'ghi', 'Gohir.D09G029700' => 'ghi', 'Gohir.D12G149700' => 'ghi', 'Gorai.001G043800' => 'gra', 'Gorai.002G187800' => 'gra', 'Gorai.006G034700' => 'gra', 'Gorai.008G161200' => 'gra', 'Gorai.009G335700' => 'gra', 'Gorai.012G065000' => 'gra', 'GSVIVG01000535001' => 'vvi', 'GSVIVG01015572001' => 'vvi', 'GSVIVG01032386001' => 'vvi', 'HanXRQChr05g0138531' => 'han', 'HanXRQChr06g0174391' => 'han', 'HanXRQChr07g0199021' => 'han', 'HanXRQChr08g0208211' => 'han', 'HanXRQChr09g0255471' => 'han', 'HanXRQChr10g0315791' => 'han', 'HanXRQChr12g0371991' => 'han', 'HanXRQChr15g0475251' => 'han', 'HanXRQChr17g0540001' => 'han', 'HanXRQChr17g0548631' => 'han', 'HanXRQChr17g0569561' => 'han', 'Haze_12256' => 'cav', 'Haze_14756' => 'cav', 'Haze_25528' => 'cav', 'Hma1.2p1_0079F.1_g041020' => 'hma', 'Hma1.2p1_0818F.1_g223260' => 'hma', 'Hma1.2p1_1747F.1_g300530' => 'hma', 'HPP92_004607' => 'vpl', 'HPP92_004608' => 'vpl', 'HPP92_006181' => 'vpl', 'HPP92_012192' => 'vpl', 'HPP92_015680' => 'vpl', 'HPP92_020249' => 'vpl', 'HPP92_021376' => 'vpl', 'HPP92_024275' => 'vpl', 'Hund06031' => 'sun', 'Hund25391' => 'sun', 'Lalb_Chr07g0185371' => 'lal', 'Lalb_Chr07g0185381' => 'lal', 'Lalb_Chr12g0204011' => 'lal', 'Lalb_Chr13g0301671' => 'lal', 'Lalb_Chr14g0362851' => 'lal', 'Lalb_Chr24g0403581' => 'lal', 'Lj1g0000233' => 'lja', 'Lj2g0018120' => 'lja', 'Lj3C621T0' => 'lonja', 'Lj3P1059T14' => 'lonja', 'Lj3P611T9' => 'lonja', 'Lj3P614T13' => 'lonja', 'Lj3P615T5' => 'lonja', 'Lj4g0012315' => 'lja', 'Lj4g0026182' => 'lja', 'Lj6P813T16' => 'lonja', 'Lj7C427T7' => 'lonja', 'Lj7C427T8' => 'lonja', 'Lj7P600T41' => 'lonja', 'Lju41C42G17' => 'lonja', 'Lsat_1_v5_gn_0_47300' => 'lsa', 'Lsat_1_v5_gn_2_91280' => 'lsa', 'Lsat_1_v5_gn_3_30561' => 'lsa', 'Lsat_1_v5_gn_4_184321' => 'lsa', 'Lsat_1_v5_gn_4_4041' => 'lsa', 'Lsat_1_v5_gn_5_92000' => 'lsa', 'Lsat_1_v5_gn_8_152940' => 'lsa', 'Lsat_1_v5_gn_8_62401' => 'lsa', 'Manes.06G055900' => 'mes', 'Manes.12G022200' => 'mes', 'Manes.13G023300' => 'mes', 'Manes.14G115000' => 'mes', 'Manes.15G151700' => 'mes', 'Manes.17G111300' => 'mes', 'Mapoly0226s0009' => 'mpo', 'MBI02_g25363_MAGBIO' => 'mbi', 'MBI06_g00027_MAGBIO' => 'mbi', 'MBI10_g13034_MAGBIO' => 'mbi', 'MD09G1023400' => 'mdo', 'MD13G1100100' => 'mdo', 'MD15G1169200' => 'mdo', 'MD16G1101100' => 'mdo', 'MD17G1022900' => 'mdo', 'Medtr3g096150' => 'mtr', 'Medtr4g115070' => 'mtr', 'Medtr7g033325' => 'mtr', 'Medtr8g089840' => 'mtr', 'MELO3C010319.2' => 'cme', 'MELO3C011944.2' => 'cme', 'MELO3C021589.2' => 'cme', 'Migut.E00207' => 'egut', 'Migut.H00067' => 'egut', 'Migut.K00433' => 'egut', 'Migut.K00606' => 'egut', 'Migut.K01410' => 'egut', 'MSTRG.13347' => 'ama', 'MSTRG.24045' => 'ama', 'MSTRG.2428' => 'ama', 'MSTRG.26410' => 'ama', 'MSTRG.3139' => 'ama', 'MSTRG.3286' => 'ama', 'MSTRG.563' => 'ama', 'MSTRG.7941' => 'ama', 'Nitab4.5_0000028g0060' => 'nta', 'Nitab4.5_0000065g0260' => 'nta', 'Nitab4.5_0000112g0060' => 'nta', 'Nitab4.5_0000489g0120' => 'nta', 'Nitab4.5_0001776g0050' => 'nta', 'Nitab4.5_0001854g0010' => 'nta', 'Nitab4.5_0001860g0020' => 'nta', 'Nitab4.5_0004352g0010' => 'nta', 'Nitab4.5_0008716g0020' => 'nta', 'Nitab4.5_0008922g0010' => 'nta', 'Nn3g16693' => 'nnu', 'Nn4g22596' => 'nnu', 'Nn7g37639' => 'nnu', 'Oeu001701.1' => 'oeu', 'Oeu018149.1' => 'oeu', 'Oeu026220.1' => 'oeu', 'Oeu038635.1' => 'oeu', 'Oeu049176.1' => 'oeu', 'Oeu056706.1' => 'oeu', 'Oeu056937.1' => 'oeu', 'Oeu057540.1' => 'oeu', 'Os02g0594900' => 'osa', 'Os02g0595100' => 'osa', 'Os04g0477500' => 'osa', 'Os12g0611900' => 'osa', 'Peaxi162Scf00076g00020' => 'pax', 'Peaxi162Scf00128g00217' => 'pax', 'Peaxi162Scf00129g01640' => 'pax', 'Peaxi162Scf00669g00007' => 'pax', 'Peaxi162Scf00700g00421' => 'pax', 'Peaxi162Scf00801g00038' => 'pax', 'Peaxi162Scf00891g00025' => 'pax', 'PGR083G0909' => 'pgr', 'PGR119G1005' => 'pgr', 'PGR142G2236' => 'pgr', 'PGR142G3388' => 'pgr', 'PGSC0003DMG400004514' => 'stu', 'PGSC0003DMG400012635' => 'stu', 'PGSC0003DMG400015730' => 'stu', 'PGSC0003DMG400018611' => 'stu', 'PGSC0003DMG400030897' => 'stu', 'Phvul.001G254800' => 'pvu', 'Phvul.002G260100' => 'pvu', 'Phvul.003G167600' => 'pvu', 'Phvul.004G005100' => 'pvu', 'Potri.001G343600' => 'ptr', 'Potri.006G066700' => 'ptr', 'Potri.008G186000' => 'ptr', 'Potri.010G046900' => 'ptr', 'Potri.018G127900' => 'ptr', 'Pp3c20_17750' => 'ppa', 'Pp3c24_4380' => 'ppa', 'Prupe.1G245800' => 'ppe', 'Prupe.3G293400' => 'ppe', 'Prupe.7G247400' => 'ppe', 'Psat0s145g0120' => 'psa', 'Psat0s595g0040' => 'psa', 'Psat0s595g0120' => 'psa', 'Psat3g175040' => 'psa', 'Psat7g058120' => 'psa', 'PSO017G0428' => 'pso', 'PSO063G7510' => 'pso', 'PSO067G0046' => 'pso', 'PSO478G1073' => 'pso', 'PSO675G3677' => 'pso', 'PSO675G6558' => 'pso', 'PSO675G7520' => 'pso', 'PSO675G8959' => 'pso', 'QL02p074089' => 'qlo', 'QL02p089614' => 'qlo', 'QL03p057736' => 'qlo', 'RcHm_v2.0_Chr1g0364131' => 'rch', 'RcHm_v2.0_Chr2g0087801' => 'rch', 'RcHm_v2.0_Chr2g0087821' => 'rch', 'RcHm_v2.0_Chr2g0173231' => 'rch', 'RcHm_v2.0_Chr4g0433111' => 'rch', 'Rhsim03G0250300' => 'rsi', 'Rhsim08G0048400' => 'rsi', 'Rhsim10G0014800' => 'rsi', 'Rhsim12G0040100' => 'rsi', 'Rhsim12G0109700' => 'rsi', 'Sabra06G0049600' => 'sbr', 'Sabra08G0141000' => 'sbr', 'Sabra10G0021400' => 'sbr', 'Sabra16G0222900' => 'sbr', 'Sabra18G0108600' => 'sbr', 'SalBow1G0433' => 'sbo', 'SalBow1G2038' => 'sbo', 'SalBow1G5003' => 'sbo', 'SalBow7G1197' => 'sbo', 'SalBow8G3506' => 'sbo', 'Sc03g0007300' => 'sci', 'Sc11g0000950' => 'sci', 'Sc14g0008750' => 'sci', 'Sc18g0000420' => 'sci', 'Sed0006754' => 'sed', 'Sed0008741' => 'sed', 'Sed0017172' => 'sed', 'Sed0018925' => 'sed', 'Sed0023326' => 'sed', 'Sed0025909' => 'sed', 'SEGI_05333' => 'sgi', 'SEGI_10362' => 'sgi', 'SEGI_13380' => 'sgi', 'SEGI_24306' => 'sgi', 'SEGI_29077' => 'sgi', 'SEGI_29095' => 'sgi', 'SEGI_36534' => 'sgi', 'SEGI_37506' => 'sgi', 'SEGI_38321' => 'sgi', 'SGA_v2.0_scaffold307G48031' => 'sas', 'SGA_v2.0_scaffold47G17507' => 'sas', 'SGA_v2.0_scaffold63G21736' => 'sas', 'SGA_v2.0_scaffold87G27070' => 'sas', 'SHI17794' => 'shi', 'SHI28851' => 'shi', 'SMO165G0155' => 'smo', 'SMO340G0217' => 'smo', 'SMO367G1210' => 'smo', 'Solyc02g093430.3' => 'sly', 'Solyc05g013580.4' => 'sly', 'Solyc07g008030.3' => 'sly', 'Solyc12g035470.2' => 'sly', 'Sopen02g038020' => 'spe', 'Sopen05g008490' => 'spe', 'Sopen07g003910' => 'spe', 'Sopen12g015240' => 'spe', 'Sp1g11550' => 'spa', 'Sp2g16710' => 'spa', 'Sp3g00430' => 'spa', 'Sp3g26780' => 'spa', 'Sp5g22900' => 'spa', 'Sp6g29530' => 'spa', 'TAR371G0794' => 'tar', 'TAR374G0164' => 'tar', 'TAR622G0165' => 'tar', 'TAR626G0929' => 'tar', 'TAR629G2155' => 'tar', 'THA.LOC104805282' => 'tha', 'THA.LOC104805363' => 'tha', 'THA.LOC104808968' => 'tha', 'THA.LOC104821093' => 'tha', 'THA.LOC104823953' => 'tha', 'THA.LOC104825562' => 'tha', 'THA.LOC104825665' => 'tha', 'Thecc.02G261400' => 'tca', 'Thecc.04G019200' => 'tca', 'Thecc.09G130400' => 'tca', 'Thhalv10004374m.g' => 'esa', 'Thhalv10007850m.g' => 'esa', 'Thhalv10013782m.g' => 'esa', 'Thhalv10018686m.g' => 'esa', 'Thhalv10020899m.g' => 'esa', 'Thhalv10022755m.g' => 'esa', 'TPR.G23851' => 'tpr', 'TPR.G26500' => 'tpr', 'TPR.G27267' => 'tpr', 'TPR.G32001' => 'tpr', 'TPR.G6251' => 'tpr', 'TPR.G8167' => 'tpr', 'TWI12G1330' => 'twi', 'TWI18G1239' => 'twi', 'TWI34G0979' => 'twi', 'TWI36G0670' => 'twi', 'TWI36G0707' => 'twi', 'TWI56G0233' => 'twi', 'TWI75G1809' => 'twi', 'unitig_21.g20874' => 'ugi', 'unitig_26.g10343' => 'ugi', 'unitig_46.g18392' => 'ugi', 'unitig_52.g17178' => 'ugi', 'unitig_8.g2934' => 'ugi', 'vmacro01122' => 'vma', 'vmacro05875' => 'vma', 'vmacro06147' => 'vma', 'vmacro16191' => 'vma', 'vmacro18293' => 'vma', 'VMungo0251G3707' => 'vmu', 'VMungo0464G1521' => 'vmu', 'VMungo1215G0205' => 'vmu', 'VMungo1383G2484' => 'vmu', 'Zm00001eb079610' => 'zma', 'Zm00001eb135990' => 'zma', 'Zm00001eb183710' => 'zma', 'Zm00001eb246020' => 'zma' ) $gf_id = 'HOM05D001124' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001124' ) $data_identifier = 'HOM05D001124' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 6, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 7, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 21, 'bol' => (int) 10, 'bra' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 6, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 9, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 21, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 8, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 10, 'lsa' => (int) 8, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 8, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 9, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb246020' $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' => 'HOM05D001124', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '548', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02520' => 'bna', 'A03p06630' => 'bna', 'A05p44460' => 'bna', 'A06p08710' => 'bna', 'A06p41090' => 'bna', 'A07p32320' => 'bna', 'A08p32520' => 'bna', 'A09p10360' => 'bna', 'A10p24080' => 'bna', 'Aa31LG11G15250' => 'aar', 'Aa31LG1G1800' => 'aar', 'Aa31LG2G5120' => 'aar', 'Aa31LG2G6070' => 'aar', 'Aa31LG5G10770' => 'aar', 'Aa31sc61G90' => 'aar', 'Actinidia01352' => 'ach', 'Actinidia05983' => 'ach', 'Actinidia08133' => 'ach', 'Actinidia15101' => 'ach', 'Actinidia26379' => 'ach', 'Actinidia35778' => 'ach', 'Actinidia36123' => 'ach', 'Actinidia37436' => 'ach', 'Actinidia38730' => 'ach', 'Ah.02g128210' => 'amhyb', 'Ah.03g132990' => 'amhyb', 'Ah.14g079410' => 'amhyb', 'AL1G24640' => 'aly', 'AL2G26680' => 'aly', 'AL3G10530' => 'aly', 'AL3G45230' => 'aly', 'AL5G15230' => 'aly', 'AL5G16960' => 'aly', 'AL6G25210' => 'aly', 'Aqoxy2G00441' => 'aox', 'Aqoxy3G01236' => 'aox', 'Aqoxy5G03746' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3RQ047' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C7GMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9C8JER' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MBL6KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YXCZ83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZANX40' => 'arhy', 'AT1G12990' => 'ath', 'AT1G67880' => 'ath', 'AT2G13290' => 'ath', 'AT3G01620' => 'ath', 'AT3G26445' => 'ath', 'AT3G27540' => 'ath', 'AT5G14480' => 'ath', 'ATR0824G026' => 'atr', 'ATR1098G019' => 'atr', 'Atru.chr11.2145' => 'acertr', 'Atru.chr2.3636' => 'acertr', 'Atru.chr2.3644' => 'acertr', 'Atru.chr6.2422' => 'acertr', 'Atru.chr7.1112' => 'acertr', 'AUR62005469' => 'cqu', 'AUR62011166' => 'cqu', 'AUR62013319' => 'cqu', 'AUR62024273' => 'cqu', 'AUR62028420' => 'cqu', 'AUR62041942' => 'cqu', 'BcaB01g04969' => 'bca', 'BcaB01g06371' => 'bca', 'BcaB02g11494' => 'bca', 'BcaB03g15382' => 'bca', 'BcaB08g36994' => 'bca', 'BcaC03g13477' => 'bca', 'BcaC03g13478' => 'bca', 'BcaC03g13480' => 'bca', 'BcaC03g13481' => 'bca', 'BcaC03g13486' => 'bca', 'BcaC04g19031' => 'bca', 'BcaC04g23085' => 'bca', 'BcaC05g25094' => 'bca', 'BcaC05g25096' => 'bca', 'BcaC05g25138' => 'bca', 'BcaC05g30416' => 'bca', 'BcaC05g30455' => 'bca', 'BcaC06g30979' => 'bca', 'BcaC06g33805' => 'bca', 'BcaC08g46021' => 'bca', 'BcaNung03154' => 'bca', 'BolC2t06623H' => 'bol', 'BolC2t06632H' => 'bol', 'BolC2t06635H' => 'bol', 'BolC2t06638H' => 'bol', 'BolC3t13266H' => 'bol', 'BolC5t29776H' => 'bol', 'BolC6t38912H' => 'bol', 'BolC7t44183H' => 'bol', 'BolC9t54123H' => 'bol', 'BolC9t59107H' => 'bol', 'BraA02t05221Z' => 'bra', 'BraA03t09996Z' => 'bra', 'BraA05t23210Z' => 'bra', 'BraA06t24068Z' => 'bra', 'BraA06t27032Z' => 'bra', 'BraA08t35176Z' => 'bra', 'BraA09t36680Z' => 'bra', 'BraA10t44471Z' => 'bra', 'C02p06760' => 'bna', 'C02p06890' => 'bna', 'C02p07010' => 'bna', 'C03p07660' => 'bna', 'C05p10300' => 'bna', 'C06p38150' => 'bna', 'C07p36650' => 'bna', 'C08p15770' => 'bna', 'C09p12300' => 'bna', 'C09p62700' => 'bna', 'C09p75040' => 'bna', 'CAN.G13.1' => 'can', 'CAN.G138.4' => 'can', 'CAN.G44.6' => 'can', 'CAN.G473.19' => 'can', 'CANSAT01G0835' => 'cansat', 'CANSAT11G0246' => 'cansat', 'CANSAT11G1766' => 'cansat', 'CANSAT64G1954' => 'cansat', 'CARHR013330' => 'chi', 'CARHR060530' => 'chi', 'CARHR075300' => 'chi', 'CARHR105120' => 'chi', 'CARHR148910' => 'chi', 'CARHR198830' => 'chi', 'Carub.0001s1275' => 'cru', 'Carub.0002s1437' => 'cru', 'Carub.0003s0044' => 'cru', 'Carub.0003s2787' => 'cru', 'Carub.0005s0597' => 'cru', 'Carub.0006s1266' => 'cru', 'Ca_06935_v3' => 'car', 'Ca_13559_v3' => 'car', 'Ca_16941_v3' => 'car', 'Ca_16960_v3' => 'car', 'Ca_17775_v3' => 'car', 'Ca_30464_v3' => 'car', 'Cc06_g08160' => 'ccan', 'Cc07_g01520' => 'ccan', 'Cc11_g15810' => 'ccan', 'CDE02G2840' => 'cde', 'CDE03G0093' => 'cde', 'CDE04G2127' => 'cde', 'CDE07G1857' => 'cde', 'CDE09G1246' => 'cde', 'Cfa003412' => 'cfa', 'Cfa007341' => 'cfa', 'Cfa009220' => 'cfa', 'Ciclev10008737m.g' => 'ccl', 'Ciclev10015565m.g' => 'ccl', 'Ciclev10031761m.g' => 'ccl', 'CiPaw.03G045300' => 'cil', 'CiPaw.03G247200' => 'cil', 'CiPaw.04G029500' => 'cil', 'CiPaw.04G174000' => 'cil', 'CiPaw.05G181200' => 'cil', 'CiPaw.06G067100' => 'cil', 'ClCG05G025800' => 'cla', 'ClCG06G011400' => 'cla', 'ClCG09G019360' => 'cla', 'COL.COLO4_04827' => 'col', 'COL.COLO4_29170' => 'col', 'COL.COLO4_35131' => 'col', 'COL.COLO4_35132' => 'col', 'Cpa.g.sc33.32' => 'cpa', 'Cpa.g.sc46.29' => 'cpa', 'Cpa.g.sc796.1' => 'cpa', 'CsaV3_1G030420' => 'csa', 'CsaV3_5G027050' => 'csa', 'CsaV3_5G031040' => 'csa', 'CsaV3_UNG023130' => 'csa', 'CSS0007726' => 'camsi', 'CSS0016433' => 'camsi', 'CSS0017656' => 'camsi', 'CSS0025364' => 'camsi', 'CSS0027582' => 'camsi', 'CSS0047288' => 'camsi', 'CSS0049950' => 'camsi', 'DCAR_003843' => 'dca', 'DCAR_007052' => 'dca', 'DCAR_020884' => 'dca', 'DCAR_021730' => 'dca', 'DCAR_024423' => 'dca', 'DCAR_026509' => 'dca', 'DCAR_031158' => 'dca', 'Dinv14728' => 'din', 'Dinv15219' => 'din', 'Dinv25728' => 'din', 'Dinv33428' => 'din', 'Dinv36489' => 'din', 'Dinv41486' => 'din', 'Duzib147G0469' => 'dzi', 'Duzib168G0060' => 'dzi', 'Duzib187G1215' => 'dzi', 'Duzib248G0692' => 'dzi', 'Duzib251G0767' => 'dzi', 'Duzib264G0446' => 'dzi', 'Duzib268G0691' => 'dzi', 'ECA232G4767' => 'eca', 'ECA233G2838' => 'eca', 'ECA234G0391' => 'eca', 'ECA234G0857' => 'eca', 'ECA236G1593' => 'eca', 'ECA238G0565' => 'eca', 'ECA246G1027' => 'eca', 'ECA246G3223' => 'eca', 'ECA246G3470' => 'eca', 'EL10Ac6g13829' => 'bvu', 'EL10Ac6g14093' => 'bvu', 'EL10Ac8g18707' => 'bvu', 'Eucgr.C01369' => 'egr', 'Eucgr.H02492' => 'egr', 'Eucgr.I01733' => 'egr', 'Eucgr.J02255' => 'egr', 'Eucgr.J02257' => 'egr', 'Eucgr.J02258' => 'egr', 'FAN02G1601' => 'fan', 'FAN03G1586' => 'fan', 'FAN03G2986' => 'fan', 'FAN05G4837' => 'fan', 'FAN06G0146' => 'fan', 'FAN07G0858' => 'fan', 'FAN09G3179' => 'fan', 'FAN10G0669' => 'fan', 'FAN12G2358' => 'fan', 'FAN14G4198' => 'fan', 'FAN14G5112' => 'fan', 'FAN17G0342' => 'fan', 'FAN19G0342' => 'fan', 'FAN19G0962' => 'fan', 'FAN19G1101' => 'fan', 'FAN19G1872' => 'fan', 'FAN22G0356' => 'fan', 'FAN23G0744' => 'fan', 'FAN23G1914' => 'fan', 'FAN26G0032' => 'fan', 'FAN28G0625' => 'fan', 'FvH4_1g02710' => 'fve', 'FvH4_1g02720' => 'fve', 'FvH4_4g25670' => 'fve', 'FvH4_6g51700' => 'fve', 'FvH4_7g20170' => 'fve', 'Glyma.05G175000' => 'gma', 'Glyma.08G132300' => 'gma', 'Glyma.11G243000' => 'gma', 'Glyma.13G158900' => 'gma', 'Glyma.17G112400' => 'gma', 'Glyma.18G014100' => 'gma', 'Glyma.19G003100' => 'gma', 'Glyma.19G056500' => 'gma', 'Gohir.A01G158900' => 'ghi', 'Gohir.A05G312600' => 'ghi', 'Gohir.A05G354900' => 'ghi', 'Gohir.A07G037200' => 'ghi', 'Gohir.A09G030000' => 'ghi', 'Gohir.A12G145200' => 'ghi', 'Gohir.D01G151500' => 'ghi', 'Gohir.D04G058300' => 'ghi', 'Gohir.D05G314100' => 'ghi', 'Gohir.D07G041400' => 'ghi', 'Gohir.D09G029700' => 'ghi', 'Gohir.D12G149700' => 'ghi', 'Gorai.001G043800' => 'gra', 'Gorai.002G187800' => 'gra', 'Gorai.006G034700' => 'gra', 'Gorai.008G161200' => 'gra', 'Gorai.009G335700' => 'gra', 'Gorai.012G065000' => 'gra', 'GSVIVG01000535001' => 'vvi', 'GSVIVG01015572001' => 'vvi', 'GSVIVG01032386001' => 'vvi', 'HanXRQChr05g0138531' => 'han', 'HanXRQChr06g0174391' => 'han', 'HanXRQChr07g0199021' => 'han', 'HanXRQChr08g0208211' => 'han', 'HanXRQChr09g0255471' => 'han', 'HanXRQChr10g0315791' => 'han', 'HanXRQChr12g0371991' => 'han', 'HanXRQChr15g0475251' => 'han', 'HanXRQChr17g0540001' => 'han', 'HanXRQChr17g0548631' => 'han', 'HanXRQChr17g0569561' => 'han', 'Haze_12256' => 'cav', 'Haze_14756' => 'cav', 'Haze_25528' => 'cav', 'Hma1.2p1_0079F.1_g041020' => 'hma', 'Hma1.2p1_0818F.1_g223260' => 'hma', 'Hma1.2p1_1747F.1_g300530' => 'hma', 'HPP92_004607' => 'vpl', 'HPP92_004608' => 'vpl', 'HPP92_006181' => 'vpl', 'HPP92_012192' => 'vpl', 'HPP92_015680' => 'vpl', 'HPP92_020249' => 'vpl', 'HPP92_021376' => 'vpl', 'HPP92_024275' => 'vpl', 'Hund06031' => 'sun', 'Hund25391' => 'sun', 'Lalb_Chr07g0185371' => 'lal', 'Lalb_Chr07g0185381' => 'lal', 'Lalb_Chr12g0204011' => 'lal', 'Lalb_Chr13g0301671' => 'lal', 'Lalb_Chr14g0362851' => 'lal', 'Lalb_Chr24g0403581' => 'lal', 'Lj1g0000233' => 'lja', 'Lj2g0018120' => 'lja', 'Lj3C621T0' => 'lonja', 'Lj3P1059T14' => 'lonja', 'Lj3P611T9' => 'lonja', 'Lj3P614T13' => 'lonja', 'Lj3P615T5' => 'lonja', 'Lj4g0012315' => 'lja', 'Lj4g0026182' => 'lja', 'Lj6P813T16' => 'lonja', 'Lj7C427T7' => 'lonja', 'Lj7C427T8' => 'lonja', 'Lj7P600T41' => 'lonja', 'Lju41C42G17' => 'lonja', 'Lsat_1_v5_gn_0_47300' => 'lsa', 'Lsat_1_v5_gn_2_91280' => 'lsa', 'Lsat_1_v5_gn_3_30561' => 'lsa', 'Lsat_1_v5_gn_4_184321' => 'lsa', 'Lsat_1_v5_gn_4_4041' => 'lsa', 'Lsat_1_v5_gn_5_92000' => 'lsa', 'Lsat_1_v5_gn_8_152940' => 'lsa', 'Lsat_1_v5_gn_8_62401' => 'lsa', 'Manes.06G055900' => 'mes', 'Manes.12G022200' => 'mes', 'Manes.13G023300' => 'mes', 'Manes.14G115000' => 'mes', 'Manes.15G151700' => 'mes', 'Manes.17G111300' => 'mes', 'Mapoly0226s0009' => 'mpo', 'MBI02_g25363_MAGBIO' => 'mbi', 'MBI06_g00027_MAGBIO' => 'mbi', 'MBI10_g13034_MAGBIO' => 'mbi', 'MD09G1023400' => 'mdo', 'MD13G1100100' => 'mdo', 'MD15G1169200' => 'mdo', 'MD16G1101100' => 'mdo', 'MD17G1022900' => 'mdo', 'Medtr3g096150' => 'mtr', 'Medtr4g115070' => 'mtr', 'Medtr7g033325' => 'mtr', 'Medtr8g089840' => 'mtr', 'MELO3C010319.2' => 'cme', 'MELO3C011944.2' => 'cme', 'MELO3C021589.2' => 'cme', 'Migut.E00207' => 'egut', 'Migut.H00067' => 'egut', 'Migut.K00433' => 'egut', 'Migut.K00606' => 'egut', 'Migut.K01410' => 'egut', 'MSTRG.13347' => 'ama', 'MSTRG.24045' => 'ama', 'MSTRG.2428' => 'ama', 'MSTRG.26410' => 'ama', 'MSTRG.3139' => 'ama', 'MSTRG.3286' => 'ama', 'MSTRG.563' => 'ama', 'MSTRG.7941' => 'ama', 'Nitab4.5_0000028g0060' => 'nta', 'Nitab4.5_0000065g0260' => 'nta', 'Nitab4.5_0000112g0060' => 'nta', 'Nitab4.5_0000489g0120' => 'nta', 'Nitab4.5_0001776g0050' => 'nta', 'Nitab4.5_0001854g0010' => 'nta', 'Nitab4.5_0001860g0020' => 'nta', 'Nitab4.5_0004352g0010' => 'nta', 'Nitab4.5_0008716g0020' => 'nta', 'Nitab4.5_0008922g0010' => 'nta', 'Nn3g16693' => 'nnu', 'Nn4g22596' => 'nnu', 'Nn7g37639' => 'nnu', 'Oeu001701.1' => 'oeu', 'Oeu018149.1' => 'oeu', 'Oeu026220.1' => 'oeu', 'Oeu038635.1' => 'oeu', 'Oeu049176.1' => 'oeu', 'Oeu056706.1' => 'oeu', 'Oeu056937.1' => 'oeu', 'Oeu057540.1' => 'oeu', 'Os02g0594900' => 'osa', 'Os02g0595100' => 'osa', 'Os04g0477500' => 'osa', 'Os12g0611900' => 'osa', 'Peaxi162Scf00076g00020' => 'pax', 'Peaxi162Scf00128g00217' => 'pax', 'Peaxi162Scf00129g01640' => 'pax', 'Peaxi162Scf00669g00007' => 'pax', 'Peaxi162Scf00700g00421' => 'pax', 'Peaxi162Scf00801g00038' => 'pax', 'Peaxi162Scf00891g00025' => 'pax', 'PGR083G0909' => 'pgr', 'PGR119G1005' => 'pgr', 'PGR142G2236' => 'pgr', 'PGR142G3388' => 'pgr', 'PGSC0003DMG400004514' => 'stu', 'PGSC0003DMG400012635' => 'stu', 'PGSC0003DMG400015730' => 'stu', 'PGSC0003DMG400018611' => 'stu', 'PGSC0003DMG400030897' => 'stu', 'Phvul.001G254800' => 'pvu', 'Phvul.002G260100' => 'pvu', 'Phvul.003G167600' => 'pvu', 'Phvul.004G005100' => 'pvu', 'Potri.001G343600' => 'ptr', 'Potri.006G066700' => 'ptr', 'Potri.008G186000' => 'ptr', 'Potri.010G046900' => 'ptr', 'Potri.018G127900' => 'ptr', 'Pp3c20_17750' => 'ppa', 'Pp3c24_4380' => 'ppa', 'Prupe.1G245800' => 'ppe', 'Prupe.3G293400' => 'ppe', 'Prupe.7G247400' => 'ppe', 'Psat0s145g0120' => 'psa', 'Psat0s595g0040' => 'psa', 'Psat0s595g0120' => 'psa', 'Psat3g175040' => 'psa', 'Psat7g058120' => 'psa', 'PSO017G0428' => 'pso', 'PSO063G7510' => 'pso', 'PSO067G0046' => 'pso', 'PSO478G1073' => 'pso', 'PSO675G3677' => 'pso', 'PSO675G6558' => 'pso', 'PSO675G7520' => 'pso', 'PSO675G8959' => 'pso', 'QL02p074089' => 'qlo', 'QL02p089614' => 'qlo', 'QL03p057736' => 'qlo', 'RcHm_v2.0_Chr1g0364131' => 'rch', 'RcHm_v2.0_Chr2g0087801' => 'rch', 'RcHm_v2.0_Chr2g0087821' => 'rch', 'RcHm_v2.0_Chr2g0173231' => 'rch', 'RcHm_v2.0_Chr4g0433111' => 'rch', 'Rhsim03G0250300' => 'rsi', 'Rhsim08G0048400' => 'rsi', 'Rhsim10G0014800' => 'rsi', 'Rhsim12G0040100' => 'rsi', 'Rhsim12G0109700' => 'rsi', 'Sabra06G0049600' => 'sbr', 'Sabra08G0141000' => 'sbr', 'Sabra10G0021400' => 'sbr', 'Sabra16G0222900' => 'sbr', 'Sabra18G0108600' => 'sbr', 'SalBow1G0433' => 'sbo', 'SalBow1G2038' => 'sbo', 'SalBow1G5003' => 'sbo', 'SalBow7G1197' => 'sbo', 'SalBow8G3506' => 'sbo', 'Sc03g0007300' => 'sci', 'Sc11g0000950' => 'sci', 'Sc14g0008750' => 'sci', 'Sc18g0000420' => 'sci', 'Sed0006754' => 'sed', 'Sed0008741' => 'sed', 'Sed0017172' => 'sed', 'Sed0018925' => 'sed', 'Sed0023326' => 'sed', 'Sed0025909' => 'sed', 'SEGI_05333' => 'sgi', 'SEGI_10362' => 'sgi', 'SEGI_13380' => 'sgi', 'SEGI_24306' => 'sgi', 'SEGI_29077' => 'sgi', 'SEGI_29095' => 'sgi', 'SEGI_36534' => 'sgi', 'SEGI_37506' => 'sgi', 'SEGI_38321' => 'sgi', 'SGA_v2.0_scaffold307G48031' => 'sas', 'SGA_v2.0_scaffold47G17507' => 'sas', 'SGA_v2.0_scaffold63G21736' => 'sas', 'SGA_v2.0_scaffold87G27070' => 'sas', 'SHI17794' => 'shi', 'SHI28851' => 'shi', 'SMO165G0155' => 'smo', 'SMO340G0217' => 'smo', 'SMO367G1210' => 'smo', 'Solyc02g093430.3' => 'sly', 'Solyc05g013580.4' => 'sly', 'Solyc07g008030.3' => 'sly', 'Solyc12g035470.2' => 'sly', 'Sopen02g038020' => 'spe', 'Sopen05g008490' => 'spe', 'Sopen07g003910' => 'spe', 'Sopen12g015240' => 'spe', 'Sp1g11550' => 'spa', 'Sp2g16710' => 'spa', 'Sp3g00430' => 'spa', 'Sp3g26780' => 'spa', 'Sp5g22900' => 'spa', 'Sp6g29530' => 'spa', 'TAR371G0794' => 'tar', 'TAR374G0164' => 'tar', 'TAR622G0165' => 'tar', 'TAR626G0929' => 'tar', 'TAR629G2155' => 'tar', 'THA.LOC104805282' => 'tha', 'THA.LOC104805363' => 'tha', 'THA.LOC104808968' => 'tha', 'THA.LOC104821093' => 'tha', 'THA.LOC104823953' => 'tha', 'THA.LOC104825562' => 'tha', 'THA.LOC104825665' => 'tha', 'Thecc.02G261400' => 'tca', 'Thecc.04G019200' => 'tca', 'Thecc.09G130400' => 'tca', 'Thhalv10004374m.g' => 'esa', 'Thhalv10007850m.g' => 'esa', 'Thhalv10013782m.g' => 'esa', 'Thhalv10018686m.g' => 'esa', 'Thhalv10020899m.g' => 'esa', 'Thhalv10022755m.g' => 'esa', 'TPR.G23851' => 'tpr', 'TPR.G26500' => 'tpr', 'TPR.G27267' => 'tpr', 'TPR.G32001' => 'tpr', 'TPR.G6251' => 'tpr', 'TPR.G8167' => 'tpr', 'TWI12G1330' => 'twi', 'TWI18G1239' => 'twi', 'TWI34G0979' => 'twi', 'TWI36G0670' => 'twi', 'TWI36G0707' => 'twi', 'TWI56G0233' => 'twi', 'TWI75G1809' => 'twi', 'unitig_21.g20874' => 'ugi', 'unitig_26.g10343' => 'ugi', 'unitig_46.g18392' => 'ugi', 'unitig_52.g17178' => 'ugi', 'unitig_8.g2934' => 'ugi', 'vmacro01122' => 'vma', 'vmacro05875' => 'vma', 'vmacro06147' => 'vma', 'vmacro16191' => 'vma', 'vmacro18293' => 'vma', 'VMungo0251G3707' => 'vmu', 'VMungo0464G1521' => 'vmu', 'VMungo1215G0205' => 'vmu', 'VMungo1383G2484' => 'vmu', 'Zm00001eb079610' => 'zma', 'Zm00001eb135990' => 'zma', 'Zm00001eb183710' => 'zma', 'Zm00001eb246020' => 'zma' ), 'gf_id' => 'HOM05D001124', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001124' ), 'data_identifier' => 'HOM05D001124', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001124', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '548', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02520' => 'bna', 'A03p06630' => 'bna', 'A05p44460' => 'bna', 'A06p08710' => 'bna', 'A06p41090' => 'bna', 'A07p32320' => 'bna', 'A08p32520' => 'bna', 'A09p10360' => 'bna', 'A10p24080' => 'bna', 'Aa31LG11G15250' => 'aar', 'Aa31LG1G1800' => 'aar', 'Aa31LG2G5120' => 'aar', 'Aa31LG2G6070' => 'aar', 'Aa31LG5G10770' => 'aar', 'Aa31sc61G90' => 'aar', 'Actinidia01352' => 'ach', 'Actinidia05983' => 'ach', 'Actinidia08133' => 'ach', 'Actinidia15101' => 'ach', 'Actinidia26379' => 'ach', 'Actinidia35778' => 'ach', 'Actinidia36123' => 'ach', 'Actinidia37436' => 'ach', 'Actinidia38730' => 'ach', 'Ah.02g128210' => 'amhyb', 'Ah.03g132990' => 'amhyb', 'Ah.14g079410' => 'amhyb', 'AL1G24640' => 'aly', 'AL2G26680' => 'aly', 'AL3G10530' => 'aly', 'AL3G45230' => 'aly', 'AL5G15230' => 'aly', 'AL5G16960' => 'aly', 'AL6G25210' => 'aly', 'Aqoxy2G00441' => 'aox', 'Aqoxy3G01236' => 'aox', 'Aqoxy5G03746' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3RQ047' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C7GMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9C8JER' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MBL6KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YXCZ83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZANX40' => 'arhy', 'AT1G12990' => 'ath', 'AT1G67880' => 'ath', 'AT2G13290' => 'ath', 'AT3G01620' => 'ath', 'AT3G26445' => 'ath', 'AT3G27540' => 'ath', 'AT5G14480' => 'ath', 'ATR0824G026' => 'atr', 'ATR1098G019' => 'atr', 'Atru.chr11.2145' => 'acertr', 'Atru.chr2.3636' => 'acertr', 'Atru.chr2.3644' => 'acertr', 'Atru.chr6.2422' => 'acertr', 'Atru.chr7.1112' => 'acertr', 'AUR62005469' => 'cqu', 'AUR62011166' => 'cqu', 'AUR62013319' => 'cqu', 'AUR62024273' => 'cqu', 'AUR62028420' => 'cqu', 'AUR62041942' => 'cqu', 'BcaB01g04969' => 'bca', 'BcaB01g06371' => 'bca', 'BcaB02g11494' => 'bca', 'BcaB03g15382' => 'bca', 'BcaB08g36994' => 'bca', 'BcaC03g13477' => 'bca', 'BcaC03g13478' => 'bca', 'BcaC03g13480' => 'bca', 'BcaC03g13481' => 'bca', 'BcaC03g13486' => 'bca', 'BcaC04g19031' => 'bca', 'BcaC04g23085' => 'bca', 'BcaC05g25094' => 'bca', 'BcaC05g25096' => 'bca', 'BcaC05g25138' => 'bca', 'BcaC05g30416' => 'bca', 'BcaC05g30455' => 'bca', 'BcaC06g30979' => 'bca', 'BcaC06g33805' => 'bca', 'BcaC08g46021' => 'bca', 'BcaNung03154' => 'bca', 'BolC2t06623H' => 'bol', 'BolC2t06632H' => 'bol', 'BolC2t06635H' => 'bol', 'BolC2t06638H' => 'bol', 'BolC3t13266H' => 'bol', 'BolC5t29776H' => 'bol', 'BolC6t38912H' => 'bol', 'BolC7t44183H' => 'bol', 'BolC9t54123H' => 'bol', 'BolC9t59107H' => 'bol', 'BraA02t05221Z' => 'bra', 'BraA03t09996Z' => 'bra', 'BraA05t23210Z' => 'bra', 'BraA06t24068Z' => 'bra', 'BraA06t27032Z' => 'bra', 'BraA08t35176Z' => 'bra', 'BraA09t36680Z' => 'bra', 'BraA10t44471Z' => 'bra', 'C02p06760' => 'bna', 'C02p06890' => 'bna', 'C02p07010' => 'bna', 'C03p07660' => 'bna', 'C05p10300' => 'bna', 'C06p38150' => 'bna', 'C07p36650' => 'bna', 'C08p15770' => 'bna', 'C09p12300' => 'bna', 'C09p62700' => 'bna', 'C09p75040' => 'bna', 'CAN.G13.1' => 'can', 'CAN.G138.4' => 'can', 'CAN.G44.6' => 'can', 'CAN.G473.19' => 'can', 'CANSAT01G0835' => 'cansat', 'CANSAT11G0246' => 'cansat', 'CANSAT11G1766' => 'cansat', 'CANSAT64G1954' => 'cansat', 'CARHR013330' => 'chi', 'CARHR060530' => 'chi', 'CARHR075300' => 'chi', 'CARHR105120' => 'chi', 'CARHR148910' => 'chi', 'CARHR198830' => 'chi', 'Carub.0001s1275' => 'cru', 'Carub.0002s1437' => 'cru', 'Carub.0003s0044' => 'cru', 'Carub.0003s2787' => 'cru', 'Carub.0005s0597' => 'cru', 'Carub.0006s1266' => 'cru', 'Ca_06935_v3' => 'car', 'Ca_13559_v3' => 'car', 'Ca_16941_v3' => 'car', 'Ca_16960_v3' => 'car', 'Ca_17775_v3' => 'car', 'Ca_30464_v3' => 'car', 'Cc06_g08160' => 'ccan', 'Cc07_g01520' => 'ccan', 'Cc11_g15810' => 'ccan', 'CDE02G2840' => 'cde', 'CDE03G0093' => 'cde', 'CDE04G2127' => 'cde', 'CDE07G1857' => 'cde', 'CDE09G1246' => 'cde', 'Cfa003412' => 'cfa', 'Cfa007341' => 'cfa', 'Cfa009220' => 'cfa', 'Ciclev10008737m.g' => 'ccl', 'Ciclev10015565m.g' => 'ccl', 'Ciclev10031761m.g' => 'ccl', 'CiPaw.03G045300' => 'cil', 'CiPaw.03G247200' => 'cil', 'CiPaw.04G029500' => 'cil', 'CiPaw.04G174000' => 'cil', 'CiPaw.05G181200' => 'cil', 'CiPaw.06G067100' => 'cil', 'ClCG05G025800' => 'cla', 'ClCG06G011400' => 'cla', 'ClCG09G019360' => 'cla', 'COL.COLO4_04827' => 'col', 'COL.COLO4_29170' => 'col', 'COL.COLO4_35131' => 'col', 'COL.COLO4_35132' => 'col', 'Cpa.g.sc33.32' => 'cpa', 'Cpa.g.sc46.29' => 'cpa', 'Cpa.g.sc796.1' => 'cpa', 'CsaV3_1G030420' => 'csa', 'CsaV3_5G027050' => 'csa', 'CsaV3_5G031040' => 'csa', 'CsaV3_UNG023130' => 'csa', 'CSS0007726' => 'camsi', 'CSS0016433' => 'camsi', 'CSS0017656' => 'camsi', 'CSS0025364' => 'camsi', 'CSS0027582' => 'camsi', 'CSS0047288' => 'camsi', 'CSS0049950' => 'camsi', 'DCAR_003843' => 'dca', 'DCAR_007052' => 'dca', 'DCAR_020884' => 'dca', 'DCAR_021730' => 'dca', 'DCAR_024423' => 'dca', 'DCAR_026509' => 'dca', 'DCAR_031158' => 'dca', 'Dinv14728' => 'din', 'Dinv15219' => 'din', 'Dinv25728' => 'din', 'Dinv33428' => 'din', 'Dinv36489' => 'din', 'Dinv41486' => 'din', 'Duzib147G0469' => 'dzi', 'Duzib168G0060' => 'dzi', 'Duzib187G1215' => 'dzi', 'Duzib248G0692' => 'dzi', 'Duzib251G0767' => 'dzi', 'Duzib264G0446' => 'dzi', 'Duzib268G0691' => 'dzi', 'ECA232G4767' => 'eca', 'ECA233G2838' => 'eca', 'ECA234G0391' => 'eca', 'ECA234G0857' => 'eca', 'ECA236G1593' => 'eca', 'ECA238G0565' => 'eca', 'ECA246G1027' => 'eca', 'ECA246G3223' => 'eca', 'ECA246G3470' => 'eca', 'EL10Ac6g13829' => 'bvu', 'EL10Ac6g14093' => 'bvu', 'EL10Ac8g18707' => 'bvu', 'Eucgr.C01369' => 'egr', 'Eucgr.H02492' => 'egr', 'Eucgr.I01733' => 'egr', 'Eucgr.J02255' => 'egr', 'Eucgr.J02257' => 'egr', 'Eucgr.J02258' => 'egr', 'FAN02G1601' => 'fan', 'FAN03G1586' => 'fan', 'FAN03G2986' => 'fan', 'FAN05G4837' => 'fan', 'FAN06G0146' => 'fan', 'FAN07G0858' => 'fan', 'FAN09G3179' => 'fan', 'FAN10G0669' => 'fan', 'FAN12G2358' => 'fan', 'FAN14G4198' => 'fan', 'FAN14G5112' => 'fan', 'FAN17G0342' => 'fan', 'FAN19G0342' => 'fan', 'FAN19G0962' => 'fan', 'FAN19G1101' => 'fan', 'FAN19G1872' => 'fan', 'FAN22G0356' => 'fan', 'FAN23G0744' => 'fan', 'FAN23G1914' => 'fan', 'FAN26G0032' => 'fan', 'FAN28G0625' => 'fan', 'FvH4_1g02710' => 'fve', 'FvH4_1g02720' => 'fve', 'FvH4_4g25670' => 'fve', 'FvH4_6g51700' => 'fve', 'FvH4_7g20170' => 'fve', 'Glyma.05G175000' => 'gma', 'Glyma.08G132300' => 'gma', 'Glyma.11G243000' => 'gma', 'Glyma.13G158900' => 'gma', 'Glyma.17G112400' => 'gma', 'Glyma.18G014100' => 'gma', 'Glyma.19G003100' => 'gma', 'Glyma.19G056500' => 'gma', 'Gohir.A01G158900' => 'ghi', 'Gohir.A05G312600' => 'ghi', 'Gohir.A05G354900' => 'ghi', 'Gohir.A07G037200' => 'ghi', 'Gohir.A09G030000' => 'ghi', 'Gohir.A12G145200' => 'ghi', 'Gohir.D01G151500' => 'ghi', 'Gohir.D04G058300' => 'ghi', 'Gohir.D05G314100' => 'ghi', 'Gohir.D07G041400' => 'ghi', 'Gohir.D09G029700' => 'ghi', 'Gohir.D12G149700' => 'ghi', 'Gorai.001G043800' => 'gra', 'Gorai.002G187800' => 'gra', 'Gorai.006G034700' => 'gra', 'Gorai.008G161200' => 'gra', 'Gorai.009G335700' => 'gra', 'Gorai.012G065000' => 'gra', 'GSVIVG01000535001' => 'vvi', 'GSVIVG01015572001' => 'vvi', 'GSVIVG01032386001' => 'vvi', 'HanXRQChr05g0138531' => 'han', 'HanXRQChr06g0174391' => 'han', 'HanXRQChr07g0199021' => 'han', 'HanXRQChr08g0208211' => 'han', 'HanXRQChr09g0255471' => 'han', 'HanXRQChr10g0315791' => 'han', 'HanXRQChr12g0371991' => 'han', 'HanXRQChr15g0475251' => 'han', 'HanXRQChr17g0540001' => 'han', 'HanXRQChr17g0548631' => 'han', 'HanXRQChr17g0569561' => 'han', 'Haze_12256' => 'cav', 'Haze_14756' => 'cav', 'Haze_25528' => 'cav', 'Hma1.2p1_0079F.1_g041020' => 'hma', 'Hma1.2p1_0818F.1_g223260' => 'hma', 'Hma1.2p1_1747F.1_g300530' => 'hma', 'HPP92_004607' => 'vpl', 'HPP92_004608' => 'vpl', 'HPP92_006181' => 'vpl', 'HPP92_012192' => 'vpl', 'HPP92_015680' => 'vpl', 'HPP92_020249' => 'vpl', 'HPP92_021376' => 'vpl', 'HPP92_024275' => 'vpl', 'Hund06031' => 'sun', 'Hund25391' => 'sun', 'Lalb_Chr07g0185371' => 'lal', 'Lalb_Chr07g0185381' => 'lal', 'Lalb_Chr12g0204011' => 'lal', 'Lalb_Chr13g0301671' => 'lal', 'Lalb_Chr14g0362851' => 'lal', 'Lalb_Chr24g0403581' => 'lal', 'Lj1g0000233' => 'lja', 'Lj2g0018120' => 'lja', 'Lj3C621T0' => 'lonja', 'Lj3P1059T14' => 'lonja', 'Lj3P611T9' => 'lonja', 'Lj3P614T13' => 'lonja', 'Lj3P615T5' => 'lonja', 'Lj4g0012315' => 'lja', 'Lj4g0026182' => 'lja', 'Lj6P813T16' => 'lonja', 'Lj7C427T7' => 'lonja', 'Lj7C427T8' => 'lonja', 'Lj7P600T41' => 'lonja', 'Lju41C42G17' => 'lonja', 'Lsat_1_v5_gn_0_47300' => 'lsa', 'Lsat_1_v5_gn_2_91280' => 'lsa', 'Lsat_1_v5_gn_3_30561' => 'lsa', 'Lsat_1_v5_gn_4_184321' => 'lsa', 'Lsat_1_v5_gn_4_4041' => 'lsa', 'Lsat_1_v5_gn_5_92000' => 'lsa', 'Lsat_1_v5_gn_8_152940' => 'lsa', 'Lsat_1_v5_gn_8_62401' => 'lsa', 'Manes.06G055900' => 'mes', 'Manes.12G022200' => 'mes', 'Manes.13G023300' => 'mes', 'Manes.14G115000' => 'mes', 'Manes.15G151700' => 'mes', 'Manes.17G111300' => 'mes', 'Mapoly0226s0009' => 'mpo', 'MBI02_g25363_MAGBIO' => 'mbi', 'MBI06_g00027_MAGBIO' => 'mbi', 'MBI10_g13034_MAGBIO' => 'mbi', 'MD09G1023400' => 'mdo', 'MD13G1100100' => 'mdo', 'MD15G1169200' => 'mdo', 'MD16G1101100' => 'mdo', 'MD17G1022900' => 'mdo', 'Medtr3g096150' => 'mtr', 'Medtr4g115070' => 'mtr', 'Medtr7g033325' => 'mtr', 'Medtr8g089840' => 'mtr', 'MELO3C010319.2' => 'cme', 'MELO3C011944.2' => 'cme', 'MELO3C021589.2' => 'cme', 'Migut.E00207' => 'egut', 'Migut.H00067' => 'egut', 'Migut.K00433' => 'egut', 'Migut.K00606' => 'egut', 'Migut.K01410' => 'egut', 'MSTRG.13347' => 'ama', 'MSTRG.24045' => 'ama', 'MSTRG.2428' => 'ama', 'MSTRG.26410' => 'ama', 'MSTRG.3139' => 'ama', 'MSTRG.3286' => 'ama', 'MSTRG.563' => 'ama', 'MSTRG.7941' => 'ama', 'Nitab4.5_0000028g0060' => 'nta', 'Nitab4.5_0000065g0260' => 'nta', 'Nitab4.5_0000112g0060' => 'nta', 'Nitab4.5_0000489g0120' => 'nta', 'Nitab4.5_0001776g0050' => 'nta', 'Nitab4.5_0001854g0010' => 'nta', 'Nitab4.5_0001860g0020' => 'nta', 'Nitab4.5_0004352g0010' => 'nta', 'Nitab4.5_0008716g0020' => 'nta', 'Nitab4.5_0008922g0010' => 'nta', 'Nn3g16693' => 'nnu', 'Nn4g22596' => 'nnu', 'Nn7g37639' => 'nnu', 'Oeu001701.1' => 'oeu', 'Oeu018149.1' => 'oeu', 'Oeu026220.1' => 'oeu', 'Oeu038635.1' => 'oeu', 'Oeu049176.1' => 'oeu', 'Oeu056706.1' => 'oeu', 'Oeu056937.1' => 'oeu', 'Oeu057540.1' => 'oeu', 'Os02g0594900' => 'osa', 'Os02g0595100' => 'osa', 'Os04g0477500' => 'osa', 'Os12g0611900' => 'osa', 'Peaxi162Scf00076g00020' => 'pax', 'Peaxi162Scf00128g00217' => 'pax', 'Peaxi162Scf00129g01640' => 'pax', 'Peaxi162Scf00669g00007' => 'pax', 'Peaxi162Scf00700g00421' => 'pax', 'Peaxi162Scf00801g00038' => 'pax', 'Peaxi162Scf00891g00025' => 'pax', 'PGR083G0909' => 'pgr', 'PGR119G1005' => 'pgr', 'PGR142G2236' => 'pgr', 'PGR142G3388' => 'pgr', 'PGSC0003DMG400004514' => 'stu', 'PGSC0003DMG400012635' => 'stu', 'PGSC0003DMG400015730' => 'stu', 'PGSC0003DMG400018611' => 'stu', 'PGSC0003DMG400030897' => 'stu', 'Phvul.001G254800' => 'pvu', 'Phvul.002G260100' => 'pvu', 'Phvul.003G167600' => 'pvu', 'Phvul.004G005100' => 'pvu', 'Potri.001G343600' => 'ptr', 'Potri.006G066700' => 'ptr', 'Potri.008G186000' => 'ptr', 'Potri.010G046900' => 'ptr', 'Potri.018G127900' => 'ptr', 'Pp3c20_17750' => 'ppa', 'Pp3c24_4380' => 'ppa', 'Prupe.1G245800' => 'ppe', 'Prupe.3G293400' => 'ppe', 'Prupe.7G247400' => 'ppe', 'Psat0s145g0120' => 'psa', 'Psat0s595g0040' => 'psa', 'Psat0s595g0120' => 'psa', 'Psat3g175040' => 'psa', 'Psat7g058120' => 'psa', 'PSO017G0428' => 'pso', 'PSO063G7510' => 'pso', 'PSO067G0046' => 'pso', 'PSO478G1073' => 'pso', 'PSO675G3677' => 'pso', 'PSO675G6558' => 'pso', 'PSO675G7520' => 'pso', 'PSO675G8959' => 'pso', 'QL02p074089' => 'qlo', 'QL02p089614' => 'qlo', 'QL03p057736' => 'qlo', 'RcHm_v2.0_Chr1g0364131' => 'rch', 'RcHm_v2.0_Chr2g0087801' => 'rch', 'RcHm_v2.0_Chr2g0087821' => 'rch', 'RcHm_v2.0_Chr2g0173231' => 'rch', 'RcHm_v2.0_Chr4g0433111' => 'rch', 'Rhsim03G0250300' => 'rsi', 'Rhsim08G0048400' => 'rsi', 'Rhsim10G0014800' => 'rsi', 'Rhsim12G0040100' => 'rsi', 'Rhsim12G0109700' => 'rsi', 'Sabra06G0049600' => 'sbr', 'Sabra08G0141000' => 'sbr', 'Sabra10G0021400' => 'sbr', 'Sabra16G0222900' => 'sbr', 'Sabra18G0108600' => 'sbr', 'SalBow1G0433' => 'sbo', 'SalBow1G2038' => 'sbo', 'SalBow1G5003' => 'sbo', 'SalBow7G1197' => 'sbo', 'SalBow8G3506' => 'sbo', 'Sc03g0007300' => 'sci', 'Sc11g0000950' => 'sci', 'Sc14g0008750' => 'sci', 'Sc18g0000420' => 'sci', 'Sed0006754' => 'sed', 'Sed0008741' => 'sed', 'Sed0017172' => 'sed', 'Sed0018925' => 'sed', 'Sed0023326' => 'sed', 'Sed0025909' => 'sed', 'SEGI_05333' => 'sgi', 'SEGI_10362' => 'sgi', 'SEGI_13380' => 'sgi', 'SEGI_24306' => 'sgi', 'SEGI_29077' => 'sgi', 'SEGI_29095' => 'sgi', 'SEGI_36534' => 'sgi', 'SEGI_37506' => 'sgi', 'SEGI_38321' => 'sgi', 'SGA_v2.0_scaffold307G48031' => 'sas', 'SGA_v2.0_scaffold47G17507' => 'sas', 'SGA_v2.0_scaffold63G21736' => 'sas', 'SGA_v2.0_scaffold87G27070' => 'sas', 'SHI17794' => 'shi', 'SHI28851' => 'shi', 'SMO165G0155' => 'smo', 'SMO340G0217' => 'smo', 'SMO367G1210' => 'smo', 'Solyc02g093430.3' => 'sly', 'Solyc05g013580.4' => 'sly', 'Solyc07g008030.3' => 'sly', 'Solyc12g035470.2' => 'sly', 'Sopen02g038020' => 'spe', 'Sopen05g008490' => 'spe', 'Sopen07g003910' => 'spe', 'Sopen12g015240' => 'spe', 'Sp1g11550' => 'spa', 'Sp2g16710' => 'spa', 'Sp3g00430' => 'spa', 'Sp3g26780' => 'spa', 'Sp5g22900' => 'spa', 'Sp6g29530' => 'spa', 'TAR371G0794' => 'tar', 'TAR374G0164' => 'tar', 'TAR622G0165' => 'tar', 'TAR626G0929' => 'tar', 'TAR629G2155' => 'tar', 'THA.LOC104805282' => 'tha', 'THA.LOC104805363' => 'tha', 'THA.LOC104808968' => 'tha', 'THA.LOC104821093' => 'tha', 'THA.LOC104823953' => 'tha', 'THA.LOC104825562' => 'tha', 'THA.LOC104825665' => 'tha', 'Thecc.02G261400' => 'tca', 'Thecc.04G019200' => 'tca', 'Thecc.09G130400' => 'tca', 'Thhalv10004374m.g' => 'esa', 'Thhalv10007850m.g' => 'esa', 'Thhalv10013782m.g' => 'esa', 'Thhalv10018686m.g' => 'esa', 'Thhalv10020899m.g' => 'esa', 'Thhalv10022755m.g' => 'esa', 'TPR.G23851' => 'tpr', 'TPR.G26500' => 'tpr', 'TPR.G27267' => 'tpr', 'TPR.G32001' => 'tpr', 'TPR.G6251' => 'tpr', 'TPR.G8167' => 'tpr', 'TWI12G1330' => 'twi', 'TWI18G1239' => 'twi', 'TWI34G0979' => 'twi', 'TWI36G0670' => 'twi', 'TWI36G0707' => 'twi', 'TWI56G0233' => 'twi', 'TWI75G1809' => 'twi', 'unitig_21.g20874' => 'ugi', 'unitig_26.g10343' => 'ugi', 'unitig_46.g18392' => 'ugi', 'unitig_52.g17178' => 'ugi', 'unitig_8.g2934' => 'ugi', 'vmacro01122' => 'vma', 'vmacro05875' => 'vma', 'vmacro06147' => 'vma', 'vmacro16191' => 'vma', 'vmacro18293' => 'vma', 'VMungo0251G3707' => 'vmu', 'VMungo0464G1521' => 'vmu', 'VMungo1215G0205' => 'vmu', 'VMungo1383G2484' => 'vmu', 'Zm00001eb079610' => 'zma', 'Zm00001eb135990' => 'zma', 'Zm00001eb183710' => 'zma', 'Zm00001eb246020' => 'zma' ) $gf_id = 'HOM05D001124' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001124' ) $data_identifier = 'HOM05D001124' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 6, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 7, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 21, 'bol' => (int) 10, 'bra' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 6, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 9, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 21, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 8, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 10, 'lsa' => (int) 8, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 8, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 9, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb246020' $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' => 'HOM05D001124', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '548', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02520' => 'bna', 'A03p06630' => 'bna', 'A05p44460' => 'bna', 'A06p08710' => 'bna', 'A06p41090' => 'bna', 'A07p32320' => 'bna', 'A08p32520' => 'bna', 'A09p10360' => 'bna', 'A10p24080' => 'bna', 'Aa31LG11G15250' => 'aar', 'Aa31LG1G1800' => 'aar', 'Aa31LG2G5120' => 'aar', 'Aa31LG2G6070' => 'aar', 'Aa31LG5G10770' => 'aar', 'Aa31sc61G90' => 'aar', 'Actinidia01352' => 'ach', 'Actinidia05983' => 'ach', 'Actinidia08133' => 'ach', 'Actinidia15101' => 'ach', 'Actinidia26379' => 'ach', 'Actinidia35778' => 'ach', 'Actinidia36123' => 'ach', 'Actinidia37436' => 'ach', 'Actinidia38730' => 'ach', 'Ah.02g128210' => 'amhyb', 'Ah.03g132990' => 'amhyb', 'Ah.14g079410' => 'amhyb', 'AL1G24640' => 'aly', 'AL2G26680' => 'aly', 'AL3G10530' => 'aly', 'AL3G45230' => 'aly', 'AL5G15230' => 'aly', 'AL5G16960' => 'aly', 'AL6G25210' => 'aly', 'Aqoxy2G00441' => 'aox', 'Aqoxy3G01236' => 'aox', 'Aqoxy5G03746' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3RQ047' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C7GMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9C8JER' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MBL6KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YXCZ83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZANX40' => 'arhy', 'AT1G12990' => 'ath', 'AT1G67880' => 'ath', 'AT2G13290' => 'ath', 'AT3G01620' => 'ath', 'AT3G26445' => 'ath', 'AT3G27540' => 'ath', 'AT5G14480' => 'ath', 'ATR0824G026' => 'atr', 'ATR1098G019' => 'atr', 'Atru.chr11.2145' => 'acertr', 'Atru.chr2.3636' => 'acertr', 'Atru.chr2.3644' => 'acertr', 'Atru.chr6.2422' => 'acertr', 'Atru.chr7.1112' => 'acertr', 'AUR62005469' => 'cqu', 'AUR62011166' => 'cqu', 'AUR62013319' => 'cqu', 'AUR62024273' => 'cqu', 'AUR62028420' => 'cqu', 'AUR62041942' => 'cqu', 'BcaB01g04969' => 'bca', 'BcaB01g06371' => 'bca', 'BcaB02g11494' => 'bca', 'BcaB03g15382' => 'bca', 'BcaB08g36994' => 'bca', 'BcaC03g13477' => 'bca', 'BcaC03g13478' => 'bca', 'BcaC03g13480' => 'bca', 'BcaC03g13481' => 'bca', 'BcaC03g13486' => 'bca', 'BcaC04g19031' => 'bca', 'BcaC04g23085' => 'bca', 'BcaC05g25094' => 'bca', 'BcaC05g25096' => 'bca', 'BcaC05g25138' => 'bca', 'BcaC05g30416' => 'bca', 'BcaC05g30455' => 'bca', 'BcaC06g30979' => 'bca', 'BcaC06g33805' => 'bca', 'BcaC08g46021' => 'bca', 'BcaNung03154' => 'bca', 'BolC2t06623H' => 'bol', 'BolC2t06632H' => 'bol', 'BolC2t06635H' => 'bol', 'BolC2t06638H' => 'bol', 'BolC3t13266H' => 'bol', 'BolC5t29776H' => 'bol', 'BolC6t38912H' => 'bol', 'BolC7t44183H' => 'bol', 'BolC9t54123H' => 'bol', 'BolC9t59107H' => 'bol', 'BraA02t05221Z' => 'bra', 'BraA03t09996Z' => 'bra', 'BraA05t23210Z' => 'bra', 'BraA06t24068Z' => 'bra', 'BraA06t27032Z' => 'bra', 'BraA08t35176Z' => 'bra', 'BraA09t36680Z' => 'bra', 'BraA10t44471Z' => 'bra', 'C02p06760' => 'bna', 'C02p06890' => 'bna', 'C02p07010' => 'bna', 'C03p07660' => 'bna', 'C05p10300' => 'bna', 'C06p38150' => 'bna', 'C07p36650' => 'bna', 'C08p15770' => 'bna', 'C09p12300' => 'bna', 'C09p62700' => 'bna', 'C09p75040' => 'bna', 'CAN.G13.1' => 'can', 'CAN.G138.4' => 'can', 'CAN.G44.6' => 'can', 'CAN.G473.19' => 'can', 'CANSAT01G0835' => 'cansat', 'CANSAT11G0246' => 'cansat', 'CANSAT11G1766' => 'cansat', 'CANSAT64G1954' => 'cansat', 'CARHR013330' => 'chi', 'CARHR060530' => 'chi', 'CARHR075300' => 'chi', 'CARHR105120' => 'chi', 'CARHR148910' => 'chi', 'CARHR198830' => 'chi', 'Carub.0001s1275' => 'cru', 'Carub.0002s1437' => 'cru', 'Carub.0003s0044' => 'cru', 'Carub.0003s2787' => 'cru', 'Carub.0005s0597' => 'cru', 'Carub.0006s1266' => 'cru', 'Ca_06935_v3' => 'car', 'Ca_13559_v3' => 'car', 'Ca_16941_v3' => 'car', 'Ca_16960_v3' => 'car', 'Ca_17775_v3' => 'car', 'Ca_30464_v3' => 'car', 'Cc06_g08160' => 'ccan', 'Cc07_g01520' => 'ccan', 'Cc11_g15810' => 'ccan', 'CDE02G2840' => 'cde', 'CDE03G0093' => 'cde', 'CDE04G2127' => 'cde', 'CDE07G1857' => 'cde', 'CDE09G1246' => 'cde', 'Cfa003412' => 'cfa', 'Cfa007341' => 'cfa', 'Cfa009220' => 'cfa', 'Ciclev10008737m.g' => 'ccl', 'Ciclev10015565m.g' => 'ccl', 'Ciclev10031761m.g' => 'ccl', 'CiPaw.03G045300' => 'cil', 'CiPaw.03G247200' => 'cil', 'CiPaw.04G029500' => 'cil', 'CiPaw.04G174000' => 'cil', 'CiPaw.05G181200' => 'cil', 'CiPaw.06G067100' => 'cil', 'ClCG05G025800' => 'cla', 'ClCG06G011400' => 'cla', 'ClCG09G019360' => 'cla', 'COL.COLO4_04827' => 'col', 'COL.COLO4_29170' => 'col', 'COL.COLO4_35131' => 'col', 'COL.COLO4_35132' => 'col', 'Cpa.g.sc33.32' => 'cpa', 'Cpa.g.sc46.29' => 'cpa', 'Cpa.g.sc796.1' => 'cpa', 'CsaV3_1G030420' => 'csa', 'CsaV3_5G027050' => 'csa', 'CsaV3_5G031040' => 'csa', 'CsaV3_UNG023130' => 'csa', 'CSS0007726' => 'camsi', 'CSS0016433' => 'camsi', 'CSS0017656' => 'camsi', 'CSS0025364' => 'camsi', 'CSS0027582' => 'camsi', 'CSS0047288' => 'camsi', 'CSS0049950' => 'camsi', 'DCAR_003843' => 'dca', 'DCAR_007052' => 'dca', 'DCAR_020884' => 'dca', 'DCAR_021730' => 'dca', 'DCAR_024423' => 'dca', 'DCAR_026509' => 'dca', 'DCAR_031158' => 'dca', 'Dinv14728' => 'din', 'Dinv15219' => 'din', 'Dinv25728' => 'din', 'Dinv33428' => 'din', 'Dinv36489' => 'din', 'Dinv41486' => 'din', 'Duzib147G0469' => 'dzi', 'Duzib168G0060' => 'dzi', 'Duzib187G1215' => 'dzi', 'Duzib248G0692' => 'dzi', 'Duzib251G0767' => 'dzi', 'Duzib264G0446' => 'dzi', 'Duzib268G0691' => 'dzi', 'ECA232G4767' => 'eca', 'ECA233G2838' => 'eca', 'ECA234G0391' => 'eca', 'ECA234G0857' => 'eca', 'ECA236G1593' => 'eca', 'ECA238G0565' => 'eca', 'ECA246G1027' => 'eca', 'ECA246G3223' => 'eca', 'ECA246G3470' => 'eca', 'EL10Ac6g13829' => 'bvu', 'EL10Ac6g14093' => 'bvu', 'EL10Ac8g18707' => 'bvu', 'Eucgr.C01369' => 'egr', 'Eucgr.H02492' => 'egr', 'Eucgr.I01733' => 'egr', 'Eucgr.J02255' => 'egr', 'Eucgr.J02257' => 'egr', 'Eucgr.J02258' => 'egr', 'FAN02G1601' => 'fan', 'FAN03G1586' => 'fan', 'FAN03G2986' => 'fan', 'FAN05G4837' => 'fan', 'FAN06G0146' => 'fan', 'FAN07G0858' => 'fan', 'FAN09G3179' => 'fan', 'FAN10G0669' => 'fan', 'FAN12G2358' => 'fan', 'FAN14G4198' => 'fan', 'FAN14G5112' => 'fan', 'FAN17G0342' => 'fan', 'FAN19G0342' => 'fan', 'FAN19G0962' => 'fan', 'FAN19G1101' => 'fan', 'FAN19G1872' => 'fan', 'FAN22G0356' => 'fan', 'FAN23G0744' => 'fan', 'FAN23G1914' => 'fan', 'FAN26G0032' => 'fan', 'FAN28G0625' => 'fan', 'FvH4_1g02710' => 'fve', 'FvH4_1g02720' => 'fve', 'FvH4_4g25670' => 'fve', 'FvH4_6g51700' => 'fve', 'FvH4_7g20170' => 'fve', 'Glyma.05G175000' => 'gma', 'Glyma.08G132300' => 'gma', 'Glyma.11G243000' => 'gma', 'Glyma.13G158900' => 'gma', 'Glyma.17G112400' => 'gma', 'Glyma.18G014100' => 'gma', 'Glyma.19G003100' => 'gma', 'Glyma.19G056500' => 'gma', 'Gohir.A01G158900' => 'ghi', 'Gohir.A05G312600' => 'ghi', 'Gohir.A05G354900' => 'ghi', 'Gohir.A07G037200' => 'ghi', 'Gohir.A09G030000' => 'ghi', 'Gohir.A12G145200' => 'ghi', 'Gohir.D01G151500' => 'ghi', 'Gohir.D04G058300' => 'ghi', 'Gohir.D05G314100' => 'ghi', 'Gohir.D07G041400' => 'ghi', 'Gohir.D09G029700' => 'ghi', 'Gohir.D12G149700' => 'ghi', 'Gorai.001G043800' => 'gra', 'Gorai.002G187800' => 'gra', 'Gorai.006G034700' => 'gra', 'Gorai.008G161200' => 'gra', 'Gorai.009G335700' => 'gra', 'Gorai.012G065000' => 'gra', 'GSVIVG01000535001' => 'vvi', 'GSVIVG01015572001' => 'vvi', 'GSVIVG01032386001' => 'vvi', 'HanXRQChr05g0138531' => 'han', 'HanXRQChr06g0174391' => 'han', 'HanXRQChr07g0199021' => 'han', 'HanXRQChr08g0208211' => 'han', 'HanXRQChr09g0255471' => 'han', 'HanXRQChr10g0315791' => 'han', 'HanXRQChr12g0371991' => 'han', 'HanXRQChr15g0475251' => 'han', 'HanXRQChr17g0540001' => 'han', 'HanXRQChr17g0548631' => 'han', 'HanXRQChr17g0569561' => 'han', 'Haze_12256' => 'cav', 'Haze_14756' => 'cav', 'Haze_25528' => 'cav', 'Hma1.2p1_0079F.1_g041020' => 'hma', 'Hma1.2p1_0818F.1_g223260' => 'hma', 'Hma1.2p1_1747F.1_g300530' => 'hma', 'HPP92_004607' => 'vpl', 'HPP92_004608' => 'vpl', 'HPP92_006181' => 'vpl', 'HPP92_012192' => 'vpl', 'HPP92_015680' => 'vpl', 'HPP92_020249' => 'vpl', 'HPP92_021376' => 'vpl', 'HPP92_024275' => 'vpl', 'Hund06031' => 'sun', 'Hund25391' => 'sun', 'Lalb_Chr07g0185371' => 'lal', 'Lalb_Chr07g0185381' => 'lal', 'Lalb_Chr12g0204011' => 'lal', 'Lalb_Chr13g0301671' => 'lal', 'Lalb_Chr14g0362851' => 'lal', 'Lalb_Chr24g0403581' => 'lal', 'Lj1g0000233' => 'lja', 'Lj2g0018120' => 'lja', 'Lj3C621T0' => 'lonja', 'Lj3P1059T14' => 'lonja', 'Lj3P611T9' => 'lonja', 'Lj3P614T13' => 'lonja', 'Lj3P615T5' => 'lonja', 'Lj4g0012315' => 'lja', 'Lj4g0026182' => 'lja', 'Lj6P813T16' => 'lonja', 'Lj7C427T7' => 'lonja', 'Lj7C427T8' => 'lonja', 'Lj7P600T41' => 'lonja', 'Lju41C42G17' => 'lonja', 'Lsat_1_v5_gn_0_47300' => 'lsa', 'Lsat_1_v5_gn_2_91280' => 'lsa', 'Lsat_1_v5_gn_3_30561' => 'lsa', 'Lsat_1_v5_gn_4_184321' => 'lsa', 'Lsat_1_v5_gn_4_4041' => 'lsa', 'Lsat_1_v5_gn_5_92000' => 'lsa', 'Lsat_1_v5_gn_8_152940' => 'lsa', 'Lsat_1_v5_gn_8_62401' => 'lsa', 'Manes.06G055900' => 'mes', 'Manes.12G022200' => 'mes', 'Manes.13G023300' => 'mes', 'Manes.14G115000' => 'mes', 'Manes.15G151700' => 'mes', 'Manes.17G111300' => 'mes', 'Mapoly0226s0009' => 'mpo', 'MBI02_g25363_MAGBIO' => 'mbi', 'MBI06_g00027_MAGBIO' => 'mbi', 'MBI10_g13034_MAGBIO' => 'mbi', 'MD09G1023400' => 'mdo', 'MD13G1100100' => 'mdo', 'MD15G1169200' => 'mdo', 'MD16G1101100' => 'mdo', 'MD17G1022900' => 'mdo', 'Medtr3g096150' => 'mtr', 'Medtr4g115070' => 'mtr', 'Medtr7g033325' => 'mtr', 'Medtr8g089840' => 'mtr', 'MELO3C010319.2' => 'cme', 'MELO3C011944.2' => 'cme', 'MELO3C021589.2' => 'cme', 'Migut.E00207' => 'egut', 'Migut.H00067' => 'egut', 'Migut.K00433' => 'egut', 'Migut.K00606' => 'egut', 'Migut.K01410' => 'egut', 'MSTRG.13347' => 'ama', 'MSTRG.24045' => 'ama', 'MSTRG.2428' => 'ama', 'MSTRG.26410' => 'ama', 'MSTRG.3139' => 'ama', 'MSTRG.3286' => 'ama', 'MSTRG.563' => 'ama', 'MSTRG.7941' => 'ama', 'Nitab4.5_0000028g0060' => 'nta', 'Nitab4.5_0000065g0260' => 'nta', 'Nitab4.5_0000112g0060' => 'nta', 'Nitab4.5_0000489g0120' => 'nta', 'Nitab4.5_0001776g0050' => 'nta', 'Nitab4.5_0001854g0010' => 'nta', 'Nitab4.5_0001860g0020' => 'nta', 'Nitab4.5_0004352g0010' => 'nta', 'Nitab4.5_0008716g0020' => 'nta', 'Nitab4.5_0008922g0010' => 'nta', 'Nn3g16693' => 'nnu', 'Nn4g22596' => 'nnu', 'Nn7g37639' => 'nnu', 'Oeu001701.1' => 'oeu', 'Oeu018149.1' => 'oeu', 'Oeu026220.1' => 'oeu', 'Oeu038635.1' => 'oeu', 'Oeu049176.1' => 'oeu', 'Oeu056706.1' => 'oeu', 'Oeu056937.1' => 'oeu', 'Oeu057540.1' => 'oeu', 'Os02g0594900' => 'osa', 'Os02g0595100' => 'osa', 'Os04g0477500' => 'osa', 'Os12g0611900' => 'osa', 'Peaxi162Scf00076g00020' => 'pax', 'Peaxi162Scf00128g00217' => 'pax', 'Peaxi162Scf00129g01640' => 'pax', 'Peaxi162Scf00669g00007' => 'pax', 'Peaxi162Scf00700g00421' => 'pax', 'Peaxi162Scf00801g00038' => 'pax', 'Peaxi162Scf00891g00025' => 'pax', 'PGR083G0909' => 'pgr', 'PGR119G1005' => 'pgr', 'PGR142G2236' => 'pgr', 'PGR142G3388' => 'pgr', 'PGSC0003DMG400004514' => 'stu', 'PGSC0003DMG400012635' => 'stu', 'PGSC0003DMG400015730' => 'stu', 'PGSC0003DMG400018611' => 'stu', 'PGSC0003DMG400030897' => 'stu', 'Phvul.001G254800' => 'pvu', 'Phvul.002G260100' => 'pvu', 'Phvul.003G167600' => 'pvu', 'Phvul.004G005100' => 'pvu', 'Potri.001G343600' => 'ptr', 'Potri.006G066700' => 'ptr', 'Potri.008G186000' => 'ptr', 'Potri.010G046900' => 'ptr', 'Potri.018G127900' => 'ptr', 'Pp3c20_17750' => 'ppa', 'Pp3c24_4380' => 'ppa', 'Prupe.1G245800' => 'ppe', 'Prupe.3G293400' => 'ppe', 'Prupe.7G247400' => 'ppe', 'Psat0s145g0120' => 'psa', 'Psat0s595g0040' => 'psa', 'Psat0s595g0120' => 'psa', 'Psat3g175040' => 'psa', 'Psat7g058120' => 'psa', 'PSO017G0428' => 'pso', 'PSO063G7510' => 'pso', 'PSO067G0046' => 'pso', 'PSO478G1073' => 'pso', 'PSO675G3677' => 'pso', 'PSO675G6558' => 'pso', 'PSO675G7520' => 'pso', 'PSO675G8959' => 'pso', 'QL02p074089' => 'qlo', 'QL02p089614' => 'qlo', 'QL03p057736' => 'qlo', 'RcHm_v2.0_Chr1g0364131' => 'rch', 'RcHm_v2.0_Chr2g0087801' => 'rch', 'RcHm_v2.0_Chr2g0087821' => 'rch', 'RcHm_v2.0_Chr2g0173231' => 'rch', 'RcHm_v2.0_Chr4g0433111' => 'rch', 'Rhsim03G0250300' => 'rsi', 'Rhsim08G0048400' => 'rsi', 'Rhsim10G0014800' => 'rsi', 'Rhsim12G0040100' => 'rsi', 'Rhsim12G0109700' => 'rsi', 'Sabra06G0049600' => 'sbr', 'Sabra08G0141000' => 'sbr', 'Sabra10G0021400' => 'sbr', 'Sabra16G0222900' => 'sbr', 'Sabra18G0108600' => 'sbr', 'SalBow1G0433' => 'sbo', 'SalBow1G2038' => 'sbo', 'SalBow1G5003' => 'sbo', 'SalBow7G1197' => 'sbo', 'SalBow8G3506' => 'sbo', 'Sc03g0007300' => 'sci', 'Sc11g0000950' => 'sci', 'Sc14g0008750' => 'sci', 'Sc18g0000420' => 'sci', 'Sed0006754' => 'sed', 'Sed0008741' => 'sed', 'Sed0017172' => 'sed', 'Sed0018925' => 'sed', 'Sed0023326' => 'sed', 'Sed0025909' => 'sed', 'SEGI_05333' => 'sgi', 'SEGI_10362' => 'sgi', 'SEGI_13380' => 'sgi', 'SEGI_24306' => 'sgi', 'SEGI_29077' => 'sgi', 'SEGI_29095' => 'sgi', 'SEGI_36534' => 'sgi', 'SEGI_37506' => 'sgi', 'SEGI_38321' => 'sgi', 'SGA_v2.0_scaffold307G48031' => 'sas', 'SGA_v2.0_scaffold47G17507' => 'sas', 'SGA_v2.0_scaffold63G21736' => 'sas', 'SGA_v2.0_scaffold87G27070' => 'sas', 'SHI17794' => 'shi', 'SHI28851' => 'shi', 'SMO165G0155' => 'smo', 'SMO340G0217' => 'smo', 'SMO367G1210' => 'smo', 'Solyc02g093430.3' => 'sly', 'Solyc05g013580.4' => 'sly', 'Solyc07g008030.3' => 'sly', 'Solyc12g035470.2' => 'sly', 'Sopen02g038020' => 'spe', 'Sopen05g008490' => 'spe', 'Sopen07g003910' => 'spe', 'Sopen12g015240' => 'spe', 'Sp1g11550' => 'spa', 'Sp2g16710' => 'spa', 'Sp3g00430' => 'spa', 'Sp3g26780' => 'spa', 'Sp5g22900' => 'spa', 'Sp6g29530' => 'spa', 'TAR371G0794' => 'tar', 'TAR374G0164' => 'tar', 'TAR622G0165' => 'tar', 'TAR626G0929' => 'tar', 'TAR629G2155' => 'tar', 'THA.LOC104805282' => 'tha', 'THA.LOC104805363' => 'tha', 'THA.LOC104808968' => 'tha', 'THA.LOC104821093' => 'tha', 'THA.LOC104823953' => 'tha', 'THA.LOC104825562' => 'tha', 'THA.LOC104825665' => 'tha', 'Thecc.02G261400' => 'tca', 'Thecc.04G019200' => 'tca', 'Thecc.09G130400' => 'tca', 'Thhalv10004374m.g' => 'esa', 'Thhalv10007850m.g' => 'esa', 'Thhalv10013782m.g' => 'esa', 'Thhalv10018686m.g' => 'esa', 'Thhalv10020899m.g' => 'esa', 'Thhalv10022755m.g' => 'esa', 'TPR.G23851' => 'tpr', 'TPR.G26500' => 'tpr', 'TPR.G27267' => 'tpr', 'TPR.G32001' => 'tpr', 'TPR.G6251' => 'tpr', 'TPR.G8167' => 'tpr', 'TWI12G1330' => 'twi', 'TWI18G1239' => 'twi', 'TWI34G0979' => 'twi', 'TWI36G0670' => 'twi', 'TWI36G0707' => 'twi', 'TWI56G0233' => 'twi', 'TWI75G1809' => 'twi', 'unitig_21.g20874' => 'ugi', 'unitig_26.g10343' => 'ugi', 'unitig_46.g18392' => 'ugi', 'unitig_52.g17178' => 'ugi', 'unitig_8.g2934' => 'ugi', 'vmacro01122' => 'vma', 'vmacro05875' => 'vma', 'vmacro06147' => 'vma', 'vmacro16191' => 'vma', 'vmacro18293' => 'vma', 'VMungo0251G3707' => 'vmu', 'VMungo0464G1521' => 'vmu', 'VMungo1215G0205' => 'vmu', 'VMungo1383G2484' => 'vmu', 'Zm00001eb079610' => 'zma', 'Zm00001eb135990' => 'zma', 'Zm00001eb183710' => 'zma', 'Zm00001eb246020' => 'zma' ), 'gf_id' => 'HOM05D001124', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001124' ), 'data_identifier' => 'HOM05D001124', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001124', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '548', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02520' => 'bna', 'A03p06630' => 'bna', 'A05p44460' => 'bna', 'A06p08710' => 'bna', 'A06p41090' => 'bna', 'A07p32320' => 'bna', 'A08p32520' => 'bna', 'A09p10360' => 'bna', 'A10p24080' => 'bna', 'Aa31LG11G15250' => 'aar', 'Aa31LG1G1800' => 'aar', 'Aa31LG2G5120' => 'aar', 'Aa31LG2G6070' => 'aar', 'Aa31LG5G10770' => 'aar', 'Aa31sc61G90' => 'aar', 'Actinidia01352' => 'ach', 'Actinidia05983' => 'ach', 'Actinidia08133' => 'ach', 'Actinidia15101' => 'ach', 'Actinidia26379' => 'ach', 'Actinidia35778' => 'ach', 'Actinidia36123' => 'ach', 'Actinidia37436' => 'ach', 'Actinidia38730' => 'ach', 'Ah.02g128210' => 'amhyb', 'Ah.03g132990' => 'amhyb', 'Ah.14g079410' => 'amhyb', 'AL1G24640' => 'aly', 'AL2G26680' => 'aly', 'AL3G10530' => 'aly', 'AL3G45230' => 'aly', 'AL5G15230' => 'aly', 'AL5G16960' => 'aly', 'AL6G25210' => 'aly', 'Aqoxy2G00441' => 'aox', 'Aqoxy3G01236' => 'aox', 'Aqoxy5G03746' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3RQ047' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C7GMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9C8JER' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MBL6KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YXCZ83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZANX40' => 'arhy', 'AT1G12990' => 'ath', 'AT1G67880' => 'ath', 'AT2G13290' => 'ath', 'AT3G01620' => 'ath', 'AT3G26445' => 'ath', 'AT3G27540' => 'ath', 'AT5G14480' => 'ath', 'ATR0824G026' => 'atr', 'ATR1098G019' => 'atr', 'Atru.chr11.2145' => 'acertr', 'Atru.chr2.3636' => 'acertr', 'Atru.chr2.3644' => 'acertr', 'Atru.chr6.2422' => 'acertr', 'Atru.chr7.1112' => 'acertr', 'AUR62005469' => 'cqu', 'AUR62011166' => 'cqu', 'AUR62013319' => 'cqu', 'AUR62024273' => 'cqu', 'AUR62028420' => 'cqu', 'AUR62041942' => 'cqu', 'BcaB01g04969' => 'bca', 'BcaB01g06371' => 'bca', 'BcaB02g11494' => 'bca', 'BcaB03g15382' => 'bca', 'BcaB08g36994' => 'bca', 'BcaC03g13477' => 'bca', 'BcaC03g13478' => 'bca', 'BcaC03g13480' => 'bca', 'BcaC03g13481' => 'bca', 'BcaC03g13486' => 'bca', 'BcaC04g19031' => 'bca', 'BcaC04g23085' => 'bca', 'BcaC05g25094' => 'bca', 'BcaC05g25096' => 'bca', 'BcaC05g25138' => 'bca', 'BcaC05g30416' => 'bca', 'BcaC05g30455' => 'bca', 'BcaC06g30979' => 'bca', 'BcaC06g33805' => 'bca', 'BcaC08g46021' => 'bca', 'BcaNung03154' => 'bca', 'BolC2t06623H' => 'bol', 'BolC2t06632H' => 'bol', 'BolC2t06635H' => 'bol', 'BolC2t06638H' => 'bol', 'BolC3t13266H' => 'bol', 'BolC5t29776H' => 'bol', 'BolC6t38912H' => 'bol', 'BolC7t44183H' => 'bol', 'BolC9t54123H' => 'bol', 'BolC9t59107H' => 'bol', 'BraA02t05221Z' => 'bra', 'BraA03t09996Z' => 'bra', 'BraA05t23210Z' => 'bra', 'BraA06t24068Z' => 'bra', 'BraA06t27032Z' => 'bra', 'BraA08t35176Z' => 'bra', 'BraA09t36680Z' => 'bra', 'BraA10t44471Z' => 'bra', 'C02p06760' => 'bna', 'C02p06890' => 'bna', 'C02p07010' => 'bna', 'C03p07660' => 'bna', 'C05p10300' => 'bna', 'C06p38150' => 'bna', 'C07p36650' => 'bna', 'C08p15770' => 'bna', 'C09p12300' => 'bna', 'C09p62700' => 'bna', 'C09p75040' => 'bna', 'CAN.G13.1' => 'can', 'CAN.G138.4' => 'can', 'CAN.G44.6' => 'can', 'CAN.G473.19' => 'can', 'CANSAT01G0835' => 'cansat', 'CANSAT11G0246' => 'cansat', 'CANSAT11G1766' => 'cansat', 'CANSAT64G1954' => 'cansat', 'CARHR013330' => 'chi', 'CARHR060530' => 'chi', 'CARHR075300' => 'chi', 'CARHR105120' => 'chi', 'CARHR148910' => 'chi', 'CARHR198830' => 'chi', 'Carub.0001s1275' => 'cru', 'Carub.0002s1437' => 'cru', 'Carub.0003s0044' => 'cru', 'Carub.0003s2787' => 'cru', 'Carub.0005s0597' => 'cru', 'Carub.0006s1266' => 'cru', 'Ca_06935_v3' => 'car', 'Ca_13559_v3' => 'car', 'Ca_16941_v3' => 'car', 'Ca_16960_v3' => 'car', 'Ca_17775_v3' => 'car', 'Ca_30464_v3' => 'car', 'Cc06_g08160' => 'ccan', 'Cc07_g01520' => 'ccan', 'Cc11_g15810' => 'ccan', 'CDE02G2840' => 'cde', 'CDE03G0093' => 'cde', 'CDE04G2127' => 'cde', 'CDE07G1857' => 'cde', 'CDE09G1246' => 'cde', 'Cfa003412' => 'cfa', 'Cfa007341' => 'cfa', 'Cfa009220' => 'cfa', 'Ciclev10008737m.g' => 'ccl', 'Ciclev10015565m.g' => 'ccl', 'Ciclev10031761m.g' => 'ccl', 'CiPaw.03G045300' => 'cil', 'CiPaw.03G247200' => 'cil', 'CiPaw.04G029500' => 'cil', 'CiPaw.04G174000' => 'cil', 'CiPaw.05G181200' => 'cil', 'CiPaw.06G067100' => 'cil', 'ClCG05G025800' => 'cla', 'ClCG06G011400' => 'cla', 'ClCG09G019360' => 'cla', 'COL.COLO4_04827' => 'col', 'COL.COLO4_29170' => 'col', 'COL.COLO4_35131' => 'col', 'COL.COLO4_35132' => 'col', 'Cpa.g.sc33.32' => 'cpa', 'Cpa.g.sc46.29' => 'cpa', 'Cpa.g.sc796.1' => 'cpa', 'CsaV3_1G030420' => 'csa', 'CsaV3_5G027050' => 'csa', 'CsaV3_5G031040' => 'csa', 'CsaV3_UNG023130' => 'csa', 'CSS0007726' => 'camsi', 'CSS0016433' => 'camsi', 'CSS0017656' => 'camsi', 'CSS0025364' => 'camsi', 'CSS0027582' => 'camsi', 'CSS0047288' => 'camsi', 'CSS0049950' => 'camsi', 'DCAR_003843' => 'dca', 'DCAR_007052' => 'dca', 'DCAR_020884' => 'dca', 'DCAR_021730' => 'dca', 'DCAR_024423' => 'dca', 'DCAR_026509' => 'dca', 'DCAR_031158' => 'dca', 'Dinv14728' => 'din', 'Dinv15219' => 'din', 'Dinv25728' => 'din', 'Dinv33428' => 'din', 'Dinv36489' => 'din', 'Dinv41486' => 'din', 'Duzib147G0469' => 'dzi', 'Duzib168G0060' => 'dzi', 'Duzib187G1215' => 'dzi', 'Duzib248G0692' => 'dzi', 'Duzib251G0767' => 'dzi', 'Duzib264G0446' => 'dzi', 'Duzib268G0691' => 'dzi', 'ECA232G4767' => 'eca', 'ECA233G2838' => 'eca', 'ECA234G0391' => 'eca', 'ECA234G0857' => 'eca', 'ECA236G1593' => 'eca', 'ECA238G0565' => 'eca', 'ECA246G1027' => 'eca', 'ECA246G3223' => 'eca', 'ECA246G3470' => 'eca', 'EL10Ac6g13829' => 'bvu', 'EL10Ac6g14093' => 'bvu', 'EL10Ac8g18707' => 'bvu', 'Eucgr.C01369' => 'egr', 'Eucgr.H02492' => 'egr', 'Eucgr.I01733' => 'egr', 'Eucgr.J02255' => 'egr', 'Eucgr.J02257' => 'egr', 'Eucgr.J02258' => 'egr', 'FAN02G1601' => 'fan', 'FAN03G1586' => 'fan', 'FAN03G2986' => 'fan', 'FAN05G4837' => 'fan', 'FAN06G0146' => 'fan', 'FAN07G0858' => 'fan', 'FAN09G3179' => 'fan', 'FAN10G0669' => 'fan', 'FAN12G2358' => 'fan', 'FAN14G4198' => 'fan', 'FAN14G5112' => 'fan', 'FAN17G0342' => 'fan', 'FAN19G0342' => 'fan', 'FAN19G0962' => 'fan', 'FAN19G1101' => 'fan', 'FAN19G1872' => 'fan', 'FAN22G0356' => 'fan', 'FAN23G0744' => 'fan', 'FAN23G1914' => 'fan', 'FAN26G0032' => 'fan', 'FAN28G0625' => 'fan', 'FvH4_1g02710' => 'fve', 'FvH4_1g02720' => 'fve', 'FvH4_4g25670' => 'fve', 'FvH4_6g51700' => 'fve', 'FvH4_7g20170' => 'fve', 'Glyma.05G175000' => 'gma', 'Glyma.08G132300' => 'gma', 'Glyma.11G243000' => 'gma', 'Glyma.13G158900' => 'gma', 'Glyma.17G112400' => 'gma', 'Glyma.18G014100' => 'gma', 'Glyma.19G003100' => 'gma', 'Glyma.19G056500' => 'gma', 'Gohir.A01G158900' => 'ghi', 'Gohir.A05G312600' => 'ghi', 'Gohir.A05G354900' => 'ghi', 'Gohir.A07G037200' => 'ghi', 'Gohir.A09G030000' => 'ghi', 'Gohir.A12G145200' => 'ghi', 'Gohir.D01G151500' => 'ghi', 'Gohir.D04G058300' => 'ghi', 'Gohir.D05G314100' => 'ghi', 'Gohir.D07G041400' => 'ghi', 'Gohir.D09G029700' => 'ghi', 'Gohir.D12G149700' => 'ghi', 'Gorai.001G043800' => 'gra', 'Gorai.002G187800' => 'gra', 'Gorai.006G034700' => 'gra', 'Gorai.008G161200' => 'gra', 'Gorai.009G335700' => 'gra', 'Gorai.012G065000' => 'gra', 'GSVIVG01000535001' => 'vvi', 'GSVIVG01015572001' => 'vvi', 'GSVIVG01032386001' => 'vvi', 'HanXRQChr05g0138531' => 'han', 'HanXRQChr06g0174391' => 'han', 'HanXRQChr07g0199021' => 'han', 'HanXRQChr08g0208211' => 'han', 'HanXRQChr09g0255471' => 'han', 'HanXRQChr10g0315791' => 'han', 'HanXRQChr12g0371991' => 'han', 'HanXRQChr15g0475251' => 'han', 'HanXRQChr17g0540001' => 'han', 'HanXRQChr17g0548631' => 'han', 'HanXRQChr17g0569561' => 'han', 'Haze_12256' => 'cav', 'Haze_14756' => 'cav', 'Haze_25528' => 'cav', 'Hma1.2p1_0079F.1_g041020' => 'hma', 'Hma1.2p1_0818F.1_g223260' => 'hma', 'Hma1.2p1_1747F.1_g300530' => 'hma', 'HPP92_004607' => 'vpl', 'HPP92_004608' => 'vpl', 'HPP92_006181' => 'vpl', 'HPP92_012192' => 'vpl', 'HPP92_015680' => 'vpl', 'HPP92_020249' => 'vpl', 'HPP92_021376' => 'vpl', 'HPP92_024275' => 'vpl', 'Hund06031' => 'sun', 'Hund25391' => 'sun', 'Lalb_Chr07g0185371' => 'lal', 'Lalb_Chr07g0185381' => 'lal', 'Lalb_Chr12g0204011' => 'lal', 'Lalb_Chr13g0301671' => 'lal', 'Lalb_Chr14g0362851' => 'lal', 'Lalb_Chr24g0403581' => 'lal', 'Lj1g0000233' => 'lja', 'Lj2g0018120' => 'lja', 'Lj3C621T0' => 'lonja', 'Lj3P1059T14' => 'lonja', 'Lj3P611T9' => 'lonja', 'Lj3P614T13' => 'lonja', 'Lj3P615T5' => 'lonja', 'Lj4g0012315' => 'lja', 'Lj4g0026182' => 'lja', 'Lj6P813T16' => 'lonja', 'Lj7C427T7' => 'lonja', 'Lj7C427T8' => 'lonja', 'Lj7P600T41' => 'lonja', 'Lju41C42G17' => 'lonja', 'Lsat_1_v5_gn_0_47300' => 'lsa', 'Lsat_1_v5_gn_2_91280' => 'lsa', 'Lsat_1_v5_gn_3_30561' => 'lsa', 'Lsat_1_v5_gn_4_184321' => 'lsa', 'Lsat_1_v5_gn_4_4041' => 'lsa', 'Lsat_1_v5_gn_5_92000' => 'lsa', 'Lsat_1_v5_gn_8_152940' => 'lsa', 'Lsat_1_v5_gn_8_62401' => 'lsa', 'Manes.06G055900' => 'mes', 'Manes.12G022200' => 'mes', 'Manes.13G023300' => 'mes', 'Manes.14G115000' => 'mes', 'Manes.15G151700' => 'mes', 'Manes.17G111300' => 'mes', 'Mapoly0226s0009' => 'mpo', 'MBI02_g25363_MAGBIO' => 'mbi', 'MBI06_g00027_MAGBIO' => 'mbi', 'MBI10_g13034_MAGBIO' => 'mbi', 'MD09G1023400' => 'mdo', 'MD13G1100100' => 'mdo', 'MD15G1169200' => 'mdo', 'MD16G1101100' => 'mdo', 'MD17G1022900' => 'mdo', 'Medtr3g096150' => 'mtr', 'Medtr4g115070' => 'mtr', 'Medtr7g033325' => 'mtr', 'Medtr8g089840' => 'mtr', 'MELO3C010319.2' => 'cme', 'MELO3C011944.2' => 'cme', 'MELO3C021589.2' => 'cme', 'Migut.E00207' => 'egut', 'Migut.H00067' => 'egut', 'Migut.K00433' => 'egut', 'Migut.K00606' => 'egut', 'Migut.K01410' => 'egut', 'MSTRG.13347' => 'ama', 'MSTRG.24045' => 'ama', 'MSTRG.2428' => 'ama', 'MSTRG.26410' => 'ama', 'MSTRG.3139' => 'ama', 'MSTRG.3286' => 'ama', 'MSTRG.563' => 'ama', 'MSTRG.7941' => 'ama', 'Nitab4.5_0000028g0060' => 'nta', 'Nitab4.5_0000065g0260' => 'nta', 'Nitab4.5_0000112g0060' => 'nta', 'Nitab4.5_0000489g0120' => 'nta', 'Nitab4.5_0001776g0050' => 'nta', 'Nitab4.5_0001854g0010' => 'nta', 'Nitab4.5_0001860g0020' => 'nta', 'Nitab4.5_0004352g0010' => 'nta', 'Nitab4.5_0008716g0020' => 'nta', 'Nitab4.5_0008922g0010' => 'nta', 'Nn3g16693' => 'nnu', 'Nn4g22596' => 'nnu', 'Nn7g37639' => 'nnu', 'Oeu001701.1' => 'oeu', 'Oeu018149.1' => 'oeu', 'Oeu026220.1' => 'oeu', 'Oeu038635.1' => 'oeu', 'Oeu049176.1' => 'oeu', 'Oeu056706.1' => 'oeu', 'Oeu056937.1' => 'oeu', 'Oeu057540.1' => 'oeu', 'Os02g0594900' => 'osa', 'Os02g0595100' => 'osa', 'Os04g0477500' => 'osa', 'Os12g0611900' => 'osa', 'Peaxi162Scf00076g00020' => 'pax', 'Peaxi162Scf00128g00217' => 'pax', 'Peaxi162Scf00129g01640' => 'pax', 'Peaxi162Scf00669g00007' => 'pax', 'Peaxi162Scf00700g00421' => 'pax', 'Peaxi162Scf00801g00038' => 'pax', 'Peaxi162Scf00891g00025' => 'pax', 'PGR083G0909' => 'pgr', 'PGR119G1005' => 'pgr', 'PGR142G2236' => 'pgr', 'PGR142G3388' => 'pgr', 'PGSC0003DMG400004514' => 'stu', 'PGSC0003DMG400012635' => 'stu', 'PGSC0003DMG400015730' => 'stu', 'PGSC0003DMG400018611' => 'stu', 'PGSC0003DMG400030897' => 'stu', 'Phvul.001G254800' => 'pvu', 'Phvul.002G260100' => 'pvu', 'Phvul.003G167600' => 'pvu', 'Phvul.004G005100' => 'pvu', 'Potri.001G343600' => 'ptr', 'Potri.006G066700' => 'ptr', 'Potri.008G186000' => 'ptr', 'Potri.010G046900' => 'ptr', 'Potri.018G127900' => 'ptr', 'Pp3c20_17750' => 'ppa', 'Pp3c24_4380' => 'ppa', 'Prupe.1G245800' => 'ppe', 'Prupe.3G293400' => 'ppe', 'Prupe.7G247400' => 'ppe', 'Psat0s145g0120' => 'psa', 'Psat0s595g0040' => 'psa', 'Psat0s595g0120' => 'psa', 'Psat3g175040' => 'psa', 'Psat7g058120' => 'psa', 'PSO017G0428' => 'pso', 'PSO063G7510' => 'pso', 'PSO067G0046' => 'pso', 'PSO478G1073' => 'pso', 'PSO675G3677' => 'pso', 'PSO675G6558' => 'pso', 'PSO675G7520' => 'pso', 'PSO675G8959' => 'pso', 'QL02p074089' => 'qlo', 'QL02p089614' => 'qlo', 'QL03p057736' => 'qlo', 'RcHm_v2.0_Chr1g0364131' => 'rch', 'RcHm_v2.0_Chr2g0087801' => 'rch', 'RcHm_v2.0_Chr2g0087821' => 'rch', 'RcHm_v2.0_Chr2g0173231' => 'rch', 'RcHm_v2.0_Chr4g0433111' => 'rch', 'Rhsim03G0250300' => 'rsi', 'Rhsim08G0048400' => 'rsi', 'Rhsim10G0014800' => 'rsi', 'Rhsim12G0040100' => 'rsi', 'Rhsim12G0109700' => 'rsi', 'Sabra06G0049600' => 'sbr', 'Sabra08G0141000' => 'sbr', 'Sabra10G0021400' => 'sbr', 'Sabra16G0222900' => 'sbr', 'Sabra18G0108600' => 'sbr', 'SalBow1G0433' => 'sbo', 'SalBow1G2038' => 'sbo', 'SalBow1G5003' => 'sbo', 'SalBow7G1197' => 'sbo', 'SalBow8G3506' => 'sbo', 'Sc03g0007300' => 'sci', 'Sc11g0000950' => 'sci', 'Sc14g0008750' => 'sci', 'Sc18g0000420' => 'sci', 'Sed0006754' => 'sed', 'Sed0008741' => 'sed', 'Sed0017172' => 'sed', 'Sed0018925' => 'sed', 'Sed0023326' => 'sed', 'Sed0025909' => 'sed', 'SEGI_05333' => 'sgi', 'SEGI_10362' => 'sgi', 'SEGI_13380' => 'sgi', 'SEGI_24306' => 'sgi', 'SEGI_29077' => 'sgi', 'SEGI_29095' => 'sgi', 'SEGI_36534' => 'sgi', 'SEGI_37506' => 'sgi', 'SEGI_38321' => 'sgi', 'SGA_v2.0_scaffold307G48031' => 'sas', 'SGA_v2.0_scaffold47G17507' => 'sas', 'SGA_v2.0_scaffold63G21736' => 'sas', 'SGA_v2.0_scaffold87G27070' => 'sas', 'SHI17794' => 'shi', 'SHI28851' => 'shi', 'SMO165G0155' => 'smo', 'SMO340G0217' => 'smo', 'SMO367G1210' => 'smo', 'Solyc02g093430.3' => 'sly', 'Solyc05g013580.4' => 'sly', 'Solyc07g008030.3' => 'sly', 'Solyc12g035470.2' => 'sly', 'Sopen02g038020' => 'spe', 'Sopen05g008490' => 'spe', 'Sopen07g003910' => 'spe', 'Sopen12g015240' => 'spe', 'Sp1g11550' => 'spa', 'Sp2g16710' => 'spa', 'Sp3g00430' => 'spa', 'Sp3g26780' => 'spa', 'Sp5g22900' => 'spa', 'Sp6g29530' => 'spa', 'TAR371G0794' => 'tar', 'TAR374G0164' => 'tar', 'TAR622G0165' => 'tar', 'TAR626G0929' => 'tar', 'TAR629G2155' => 'tar', 'THA.LOC104805282' => 'tha', 'THA.LOC104805363' => 'tha', 'THA.LOC104808968' => 'tha', 'THA.LOC104821093' => 'tha', 'THA.LOC104823953' => 'tha', 'THA.LOC104825562' => 'tha', 'THA.LOC104825665' => 'tha', 'Thecc.02G261400' => 'tca', 'Thecc.04G019200' => 'tca', 'Thecc.09G130400' => 'tca', 'Thhalv10004374m.g' => 'esa', 'Thhalv10007850m.g' => 'esa', 'Thhalv10013782m.g' => 'esa', 'Thhalv10018686m.g' => 'esa', 'Thhalv10020899m.g' => 'esa', 'Thhalv10022755m.g' => 'esa', 'TPR.G23851' => 'tpr', 'TPR.G26500' => 'tpr', 'TPR.G27267' => 'tpr', 'TPR.G32001' => 'tpr', 'TPR.G6251' => 'tpr', 'TPR.G8167' => 'tpr', 'TWI12G1330' => 'twi', 'TWI18G1239' => 'twi', 'TWI34G0979' => 'twi', 'TWI36G0670' => 'twi', 'TWI36G0707' => 'twi', 'TWI56G0233' => 'twi', 'TWI75G1809' => 'twi', 'unitig_21.g20874' => 'ugi', 'unitig_26.g10343' => 'ugi', 'unitig_46.g18392' => 'ugi', 'unitig_52.g17178' => 'ugi', 'unitig_8.g2934' => 'ugi', 'vmacro01122' => 'vma', 'vmacro05875' => 'vma', 'vmacro06147' => 'vma', 'vmacro16191' => 'vma', 'vmacro18293' => 'vma', 'VMungo0251G3707' => 'vmu', 'VMungo0464G1521' => 'vmu', 'VMungo1215G0205' => 'vmu', 'VMungo1383G2484' => 'vmu', 'Zm00001eb079610' => 'zma', 'Zm00001eb135990' => 'zma', 'Zm00001eb183710' => 'zma', 'Zm00001eb246020' => 'zma' ) $gf_id = 'HOM05D001124' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001124' ) $data_identifier = 'HOM05D001124' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 6, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 7, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 21, 'bol' => (int) 10, 'bra' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 6, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 9, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 21, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 8, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 10, 'lsa' => (int) 8, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 8, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 9, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb246020' $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' => 'HOM05D001124', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '548', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02520' => 'bna', 'A03p06630' => 'bna', 'A05p44460' => 'bna', 'A06p08710' => 'bna', 'A06p41090' => 'bna', 'A07p32320' => 'bna', 'A08p32520' => 'bna', 'A09p10360' => 'bna', 'A10p24080' => 'bna', 'Aa31LG11G15250' => 'aar', 'Aa31LG1G1800' => 'aar', 'Aa31LG2G5120' => 'aar', 'Aa31LG2G6070' => 'aar', 'Aa31LG5G10770' => 'aar', 'Aa31sc61G90' => 'aar', 'Actinidia01352' => 'ach', 'Actinidia05983' => 'ach', 'Actinidia08133' => 'ach', 'Actinidia15101' => 'ach', 'Actinidia26379' => 'ach', 'Actinidia35778' => 'ach', 'Actinidia36123' => 'ach', 'Actinidia37436' => 'ach', 'Actinidia38730' => 'ach', 'Ah.02g128210' => 'amhyb', 'Ah.03g132990' => 'amhyb', 'Ah.14g079410' => 'amhyb', 'AL1G24640' => 'aly', 'AL2G26680' => 'aly', 'AL3G10530' => 'aly', 'AL3G45230' => 'aly', 'AL5G15230' => 'aly', 'AL5G16960' => 'aly', 'AL6G25210' => 'aly', 'Aqoxy2G00441' => 'aox', 'Aqoxy3G01236' => 'aox', 'Aqoxy5G03746' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3RQ047' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C7GMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9C8JER' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MBL6KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YXCZ83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZANX40' => 'arhy', 'AT1G12990' => 'ath', 'AT1G67880' => 'ath', 'AT2G13290' => 'ath', 'AT3G01620' => 'ath', 'AT3G26445' => 'ath', 'AT3G27540' => 'ath', 'AT5G14480' => 'ath', 'ATR0824G026' => 'atr', 'ATR1098G019' => 'atr', 'Atru.chr11.2145' => 'acertr', 'Atru.chr2.3636' => 'acertr', 'Atru.chr2.3644' => 'acertr', 'Atru.chr6.2422' => 'acertr', 'Atru.chr7.1112' => 'acertr', 'AUR62005469' => 'cqu', 'AUR62011166' => 'cqu', 'AUR62013319' => 'cqu', 'AUR62024273' => 'cqu', 'AUR62028420' => 'cqu', 'AUR62041942' => 'cqu', 'BcaB01g04969' => 'bca', 'BcaB01g06371' => 'bca', 'BcaB02g11494' => 'bca', 'BcaB03g15382' => 'bca', 'BcaB08g36994' => 'bca', 'BcaC03g13477' => 'bca', 'BcaC03g13478' => 'bca', 'BcaC03g13480' => 'bca', 'BcaC03g13481' => 'bca', 'BcaC03g13486' => 'bca', 'BcaC04g19031' => 'bca', 'BcaC04g23085' => 'bca', 'BcaC05g25094' => 'bca', 'BcaC05g25096' => 'bca', 'BcaC05g25138' => 'bca', 'BcaC05g30416' => 'bca', 'BcaC05g30455' => 'bca', 'BcaC06g30979' => 'bca', 'BcaC06g33805' => 'bca', 'BcaC08g46021' => 'bca', 'BcaNung03154' => 'bca', 'BolC2t06623H' => 'bol', 'BolC2t06632H' => 'bol', 'BolC2t06635H' => 'bol', 'BolC2t06638H' => 'bol', 'BolC3t13266H' => 'bol', 'BolC5t29776H' => 'bol', 'BolC6t38912H' => 'bol', 'BolC7t44183H' => 'bol', 'BolC9t54123H' => 'bol', 'BolC9t59107H' => 'bol', 'BraA02t05221Z' => 'bra', 'BraA03t09996Z' => 'bra', 'BraA05t23210Z' => 'bra', 'BraA06t24068Z' => 'bra', 'BraA06t27032Z' => 'bra', 'BraA08t35176Z' => 'bra', 'BraA09t36680Z' => 'bra', 'BraA10t44471Z' => 'bra', 'C02p06760' => 'bna', 'C02p06890' => 'bna', 'C02p07010' => 'bna', 'C03p07660' => 'bna', 'C05p10300' => 'bna', 'C06p38150' => 'bna', 'C07p36650' => 'bna', 'C08p15770' => 'bna', 'C09p12300' => 'bna', 'C09p62700' => 'bna', 'C09p75040' => 'bna', 'CAN.G13.1' => 'can', 'CAN.G138.4' => 'can', 'CAN.G44.6' => 'can', 'CAN.G473.19' => 'can', 'CANSAT01G0835' => 'cansat', 'CANSAT11G0246' => 'cansat', 'CANSAT11G1766' => 'cansat', 'CANSAT64G1954' => 'cansat', 'CARHR013330' => 'chi', 'CARHR060530' => 'chi', 'CARHR075300' => 'chi', 'CARHR105120' => 'chi', 'CARHR148910' => 'chi', 'CARHR198830' => 'chi', 'Carub.0001s1275' => 'cru', 'Carub.0002s1437' => 'cru', 'Carub.0003s0044' => 'cru', 'Carub.0003s2787' => 'cru', 'Carub.0005s0597' => 'cru', 'Carub.0006s1266' => 'cru', 'Ca_06935_v3' => 'car', 'Ca_13559_v3' => 'car', 'Ca_16941_v3' => 'car', 'Ca_16960_v3' => 'car', 'Ca_17775_v3' => 'car', 'Ca_30464_v3' => 'car', 'Cc06_g08160' => 'ccan', 'Cc07_g01520' => 'ccan', 'Cc11_g15810' => 'ccan', 'CDE02G2840' => 'cde', 'CDE03G0093' => 'cde', 'CDE04G2127' => 'cde', 'CDE07G1857' => 'cde', 'CDE09G1246' => 'cde', 'Cfa003412' => 'cfa', 'Cfa007341' => 'cfa', 'Cfa009220' => 'cfa', 'Ciclev10008737m.g' => 'ccl', 'Ciclev10015565m.g' => 'ccl', 'Ciclev10031761m.g' => 'ccl', 'CiPaw.03G045300' => 'cil', 'CiPaw.03G247200' => 'cil', 'CiPaw.04G029500' => 'cil', 'CiPaw.04G174000' => 'cil', 'CiPaw.05G181200' => 'cil', 'CiPaw.06G067100' => 'cil', 'ClCG05G025800' => 'cla', 'ClCG06G011400' => 'cla', 'ClCG09G019360' => 'cla', 'COL.COLO4_04827' => 'col', 'COL.COLO4_29170' => 'col', 'COL.COLO4_35131' => 'col', 'COL.COLO4_35132' => 'col', 'Cpa.g.sc33.32' => 'cpa', 'Cpa.g.sc46.29' => 'cpa', 'Cpa.g.sc796.1' => 'cpa', 'CsaV3_1G030420' => 'csa', 'CsaV3_5G027050' => 'csa', 'CsaV3_5G031040' => 'csa', 'CsaV3_UNG023130' => 'csa', 'CSS0007726' => 'camsi', 'CSS0016433' => 'camsi', 'CSS0017656' => 'camsi', 'CSS0025364' => 'camsi', 'CSS0027582' => 'camsi', 'CSS0047288' => 'camsi', 'CSS0049950' => 'camsi', 'DCAR_003843' => 'dca', 'DCAR_007052' => 'dca', 'DCAR_020884' => 'dca', 'DCAR_021730' => 'dca', 'DCAR_024423' => 'dca', 'DCAR_026509' => 'dca', 'DCAR_031158' => 'dca', 'Dinv14728' => 'din', 'Dinv15219' => 'din', 'Dinv25728' => 'din', 'Dinv33428' => 'din', 'Dinv36489' => 'din', 'Dinv41486' => 'din', 'Duzib147G0469' => 'dzi', 'Duzib168G0060' => 'dzi', 'Duzib187G1215' => 'dzi', 'Duzib248G0692' => 'dzi', 'Duzib251G0767' => 'dzi', 'Duzib264G0446' => 'dzi', 'Duzib268G0691' => 'dzi', 'ECA232G4767' => 'eca', 'ECA233G2838' => 'eca', 'ECA234G0391' => 'eca', 'ECA234G0857' => 'eca', 'ECA236G1593' => 'eca', 'ECA238G0565' => 'eca', 'ECA246G1027' => 'eca', 'ECA246G3223' => 'eca', 'ECA246G3470' => 'eca', 'EL10Ac6g13829' => 'bvu', 'EL10Ac6g14093' => 'bvu', 'EL10Ac8g18707' => 'bvu', 'Eucgr.C01369' => 'egr', 'Eucgr.H02492' => 'egr', 'Eucgr.I01733' => 'egr', 'Eucgr.J02255' => 'egr', 'Eucgr.J02257' => 'egr', 'Eucgr.J02258' => 'egr', 'FAN02G1601' => 'fan', 'FAN03G1586' => 'fan', 'FAN03G2986' => 'fan', 'FAN05G4837' => 'fan', 'FAN06G0146' => 'fan', 'FAN07G0858' => 'fan', 'FAN09G3179' => 'fan', 'FAN10G0669' => 'fan', 'FAN12G2358' => 'fan', 'FAN14G4198' => 'fan', 'FAN14G5112' => 'fan', 'FAN17G0342' => 'fan', 'FAN19G0342' => 'fan', 'FAN19G0962' => 'fan', 'FAN19G1101' => 'fan', 'FAN19G1872' => 'fan', 'FAN22G0356' => 'fan', 'FAN23G0744' => 'fan', 'FAN23G1914' => 'fan', 'FAN26G0032' => 'fan', 'FAN28G0625' => 'fan', 'FvH4_1g02710' => 'fve', 'FvH4_1g02720' => 'fve', 'FvH4_4g25670' => 'fve', 'FvH4_6g51700' => 'fve', 'FvH4_7g20170' => 'fve', 'Glyma.05G175000' => 'gma', 'Glyma.08G132300' => 'gma', 'Glyma.11G243000' => 'gma', 'Glyma.13G158900' => 'gma', 'Glyma.17G112400' => 'gma', 'Glyma.18G014100' => 'gma', 'Glyma.19G003100' => 'gma', 'Glyma.19G056500' => 'gma', 'Gohir.A01G158900' => 'ghi', 'Gohir.A05G312600' => 'ghi', 'Gohir.A05G354900' => 'ghi', 'Gohir.A07G037200' => 'ghi', 'Gohir.A09G030000' => 'ghi', 'Gohir.A12G145200' => 'ghi', 'Gohir.D01G151500' => 'ghi', 'Gohir.D04G058300' => 'ghi', 'Gohir.D05G314100' => 'ghi', 'Gohir.D07G041400' => 'ghi', 'Gohir.D09G029700' => 'ghi', 'Gohir.D12G149700' => 'ghi', 'Gorai.001G043800' => 'gra', 'Gorai.002G187800' => 'gra', 'Gorai.006G034700' => 'gra', 'Gorai.008G161200' => 'gra', 'Gorai.009G335700' => 'gra', 'Gorai.012G065000' => 'gra', 'GSVIVG01000535001' => 'vvi', 'GSVIVG01015572001' => 'vvi', 'GSVIVG01032386001' => 'vvi', 'HanXRQChr05g0138531' => 'han', 'HanXRQChr06g0174391' => 'han', 'HanXRQChr07g0199021' => 'han', 'HanXRQChr08g0208211' => 'han', 'HanXRQChr09g0255471' => 'han', 'HanXRQChr10g0315791' => 'han', 'HanXRQChr12g0371991' => 'han', 'HanXRQChr15g0475251' => 'han', 'HanXRQChr17g0540001' => 'han', 'HanXRQChr17g0548631' => 'han', 'HanXRQChr17g0569561' => 'han', 'Haze_12256' => 'cav', 'Haze_14756' => 'cav', 'Haze_25528' => 'cav', 'Hma1.2p1_0079F.1_g041020' => 'hma', 'Hma1.2p1_0818F.1_g223260' => 'hma', 'Hma1.2p1_1747F.1_g300530' => 'hma', 'HPP92_004607' => 'vpl', 'HPP92_004608' => 'vpl', 'HPP92_006181' => 'vpl', 'HPP92_012192' => 'vpl', 'HPP92_015680' => 'vpl', 'HPP92_020249' => 'vpl', 'HPP92_021376' => 'vpl', 'HPP92_024275' => 'vpl', 'Hund06031' => 'sun', 'Hund25391' => 'sun', 'Lalb_Chr07g0185371' => 'lal', 'Lalb_Chr07g0185381' => 'lal', 'Lalb_Chr12g0204011' => 'lal', 'Lalb_Chr13g0301671' => 'lal', 'Lalb_Chr14g0362851' => 'lal', 'Lalb_Chr24g0403581' => 'lal', 'Lj1g0000233' => 'lja', 'Lj2g0018120' => 'lja', 'Lj3C621T0' => 'lonja', 'Lj3P1059T14' => 'lonja', 'Lj3P611T9' => 'lonja', 'Lj3P614T13' => 'lonja', 'Lj3P615T5' => 'lonja', 'Lj4g0012315' => 'lja', 'Lj4g0026182' => 'lja', 'Lj6P813T16' => 'lonja', 'Lj7C427T7' => 'lonja', 'Lj7C427T8' => 'lonja', 'Lj7P600T41' => 'lonja', 'Lju41C42G17' => 'lonja', 'Lsat_1_v5_gn_0_47300' => 'lsa', 'Lsat_1_v5_gn_2_91280' => 'lsa', 'Lsat_1_v5_gn_3_30561' => 'lsa', 'Lsat_1_v5_gn_4_184321' => 'lsa', 'Lsat_1_v5_gn_4_4041' => 'lsa', 'Lsat_1_v5_gn_5_92000' => 'lsa', 'Lsat_1_v5_gn_8_152940' => 'lsa', 'Lsat_1_v5_gn_8_62401' => 'lsa', 'Manes.06G055900' => 'mes', 'Manes.12G022200' => 'mes', 'Manes.13G023300' => 'mes', 'Manes.14G115000' => 'mes', 'Manes.15G151700' => 'mes', 'Manes.17G111300' => 'mes', 'Mapoly0226s0009' => 'mpo', 'MBI02_g25363_MAGBIO' => 'mbi', 'MBI06_g00027_MAGBIO' => 'mbi', 'MBI10_g13034_MAGBIO' => 'mbi', 'MD09G1023400' => 'mdo', 'MD13G1100100' => 'mdo', 'MD15G1169200' => 'mdo', 'MD16G1101100' => 'mdo', 'MD17G1022900' => 'mdo', 'Medtr3g096150' => 'mtr', 'Medtr4g115070' => 'mtr', 'Medtr7g033325' => 'mtr', 'Medtr8g089840' => 'mtr', 'MELO3C010319.2' => 'cme', 'MELO3C011944.2' => 'cme', 'MELO3C021589.2' => 'cme', 'Migut.E00207' => 'egut', 'Migut.H00067' => 'egut', 'Migut.K00433' => 'egut', 'Migut.K00606' => 'egut', 'Migut.K01410' => 'egut', 'MSTRG.13347' => 'ama', 'MSTRG.24045' => 'ama', 'MSTRG.2428' => 'ama', 'MSTRG.26410' => 'ama', 'MSTRG.3139' => 'ama', 'MSTRG.3286' => 'ama', 'MSTRG.563' => 'ama', 'MSTRG.7941' => 'ama', 'Nitab4.5_0000028g0060' => 'nta', 'Nitab4.5_0000065g0260' => 'nta', 'Nitab4.5_0000112g0060' => 'nta', 'Nitab4.5_0000489g0120' => 'nta', 'Nitab4.5_0001776g0050' => 'nta', 'Nitab4.5_0001854g0010' => 'nta', 'Nitab4.5_0001860g0020' => 'nta', 'Nitab4.5_0004352g0010' => 'nta', 'Nitab4.5_0008716g0020' => 'nta', 'Nitab4.5_0008922g0010' => 'nta', 'Nn3g16693' => 'nnu', 'Nn4g22596' => 'nnu', 'Nn7g37639' => 'nnu', 'Oeu001701.1' => 'oeu', 'Oeu018149.1' => 'oeu', 'Oeu026220.1' => 'oeu', 'Oeu038635.1' => 'oeu', 'Oeu049176.1' => 'oeu', 'Oeu056706.1' => 'oeu', 'Oeu056937.1' => 'oeu', 'Oeu057540.1' => 'oeu', 'Os02g0594900' => 'osa', 'Os02g0595100' => 'osa', 'Os04g0477500' => 'osa', 'Os12g0611900' => 'osa', 'Peaxi162Scf00076g00020' => 'pax', 'Peaxi162Scf00128g00217' => 'pax', 'Peaxi162Scf00129g01640' => 'pax', 'Peaxi162Scf00669g00007' => 'pax', 'Peaxi162Scf00700g00421' => 'pax', 'Peaxi162Scf00801g00038' => 'pax', 'Peaxi162Scf00891g00025' => 'pax', 'PGR083G0909' => 'pgr', 'PGR119G1005' => 'pgr', 'PGR142G2236' => 'pgr', 'PGR142G3388' => 'pgr', 'PGSC0003DMG400004514' => 'stu', 'PGSC0003DMG400012635' => 'stu', 'PGSC0003DMG400015730' => 'stu', 'PGSC0003DMG400018611' => 'stu', 'PGSC0003DMG400030897' => 'stu', 'Phvul.001G254800' => 'pvu', 'Phvul.002G260100' => 'pvu', 'Phvul.003G167600' => 'pvu', 'Phvul.004G005100' => 'pvu', 'Potri.001G343600' => 'ptr', 'Potri.006G066700' => 'ptr', 'Potri.008G186000' => 'ptr', 'Potri.010G046900' => 'ptr', 'Potri.018G127900' => 'ptr', 'Pp3c20_17750' => 'ppa', 'Pp3c24_4380' => 'ppa', 'Prupe.1G245800' => 'ppe', 'Prupe.3G293400' => 'ppe', 'Prupe.7G247400' => 'ppe', 'Psat0s145g0120' => 'psa', 'Psat0s595g0040' => 'psa', 'Psat0s595g0120' => 'psa', 'Psat3g175040' => 'psa', 'Psat7g058120' => 'psa', 'PSO017G0428' => 'pso', 'PSO063G7510' => 'pso', 'PSO067G0046' => 'pso', 'PSO478G1073' => 'pso', 'PSO675G3677' => 'pso', 'PSO675G6558' => 'pso', 'PSO675G7520' => 'pso', 'PSO675G8959' => 'pso', 'QL02p074089' => 'qlo', 'QL02p089614' => 'qlo', 'QL03p057736' => 'qlo', 'RcHm_v2.0_Chr1g0364131' => 'rch', 'RcHm_v2.0_Chr2g0087801' => 'rch', 'RcHm_v2.0_Chr2g0087821' => 'rch', 'RcHm_v2.0_Chr2g0173231' => 'rch', 'RcHm_v2.0_Chr4g0433111' => 'rch', 'Rhsim03G0250300' => 'rsi', 'Rhsim08G0048400' => 'rsi', 'Rhsim10G0014800' => 'rsi', 'Rhsim12G0040100' => 'rsi', 'Rhsim12G0109700' => 'rsi', 'Sabra06G0049600' => 'sbr', 'Sabra08G0141000' => 'sbr', 'Sabra10G0021400' => 'sbr', 'Sabra16G0222900' => 'sbr', 'Sabra18G0108600' => 'sbr', 'SalBow1G0433' => 'sbo', 'SalBow1G2038' => 'sbo', 'SalBow1G5003' => 'sbo', 'SalBow7G1197' => 'sbo', 'SalBow8G3506' => 'sbo', 'Sc03g0007300' => 'sci', 'Sc11g0000950' => 'sci', 'Sc14g0008750' => 'sci', 'Sc18g0000420' => 'sci', 'Sed0006754' => 'sed', 'Sed0008741' => 'sed', 'Sed0017172' => 'sed', 'Sed0018925' => 'sed', 'Sed0023326' => 'sed', 'Sed0025909' => 'sed', 'SEGI_05333' => 'sgi', 'SEGI_10362' => 'sgi', 'SEGI_13380' => 'sgi', 'SEGI_24306' => 'sgi', 'SEGI_29077' => 'sgi', 'SEGI_29095' => 'sgi', 'SEGI_36534' => 'sgi', 'SEGI_37506' => 'sgi', 'SEGI_38321' => 'sgi', 'SGA_v2.0_scaffold307G48031' => 'sas', 'SGA_v2.0_scaffold47G17507' => 'sas', 'SGA_v2.0_scaffold63G21736' => 'sas', 'SGA_v2.0_scaffold87G27070' => 'sas', 'SHI17794' => 'shi', 'SHI28851' => 'shi', 'SMO165G0155' => 'smo', 'SMO340G0217' => 'smo', 'SMO367G1210' => 'smo', 'Solyc02g093430.3' => 'sly', 'Solyc05g013580.4' => 'sly', 'Solyc07g008030.3' => 'sly', 'Solyc12g035470.2' => 'sly', 'Sopen02g038020' => 'spe', 'Sopen05g008490' => 'spe', 'Sopen07g003910' => 'spe', 'Sopen12g015240' => 'spe', 'Sp1g11550' => 'spa', 'Sp2g16710' => 'spa', 'Sp3g00430' => 'spa', 'Sp3g26780' => 'spa', 'Sp5g22900' => 'spa', 'Sp6g29530' => 'spa', 'TAR371G0794' => 'tar', 'TAR374G0164' => 'tar', 'TAR622G0165' => 'tar', 'TAR626G0929' => 'tar', 'TAR629G2155' => 'tar', 'THA.LOC104805282' => 'tha', 'THA.LOC104805363' => 'tha', 'THA.LOC104808968' => 'tha', 'THA.LOC104821093' => 'tha', 'THA.LOC104823953' => 'tha', 'THA.LOC104825562' => 'tha', 'THA.LOC104825665' => 'tha', 'Thecc.02G261400' => 'tca', 'Thecc.04G019200' => 'tca', 'Thecc.09G130400' => 'tca', 'Thhalv10004374m.g' => 'esa', 'Thhalv10007850m.g' => 'esa', 'Thhalv10013782m.g' => 'esa', 'Thhalv10018686m.g' => 'esa', 'Thhalv10020899m.g' => 'esa', 'Thhalv10022755m.g' => 'esa', 'TPR.G23851' => 'tpr', 'TPR.G26500' => 'tpr', 'TPR.G27267' => 'tpr', 'TPR.G32001' => 'tpr', 'TPR.G6251' => 'tpr', 'TPR.G8167' => 'tpr', 'TWI12G1330' => 'twi', 'TWI18G1239' => 'twi', 'TWI34G0979' => 'twi', 'TWI36G0670' => 'twi', 'TWI36G0707' => 'twi', 'TWI56G0233' => 'twi', 'TWI75G1809' => 'twi', 'unitig_21.g20874' => 'ugi', 'unitig_26.g10343' => 'ugi', 'unitig_46.g18392' => 'ugi', 'unitig_52.g17178' => 'ugi', 'unitig_8.g2934' => 'ugi', 'vmacro01122' => 'vma', 'vmacro05875' => 'vma', 'vmacro06147' => 'vma', 'vmacro16191' => 'vma', 'vmacro18293' => 'vma', 'VMungo0251G3707' => 'vmu', 'VMungo0464G1521' => 'vmu', 'VMungo1215G0205' => 'vmu', 'VMungo1383G2484' => 'vmu', 'Zm00001eb079610' => 'zma', 'Zm00001eb135990' => 'zma', 'Zm00001eb183710' => 'zma', 'Zm00001eb246020' => 'zma' ), 'gf_id' => 'HOM05D001124', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001124' ), 'data_identifier' => 'HOM05D001124', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001124', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '548', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02520' => 'bna', 'A03p06630' => 'bna', 'A05p44460' => 'bna', 'A06p08710' => 'bna', 'A06p41090' => 'bna', 'A07p32320' => 'bna', 'A08p32520' => 'bna', 'A09p10360' => 'bna', 'A10p24080' => 'bna', 'Aa31LG11G15250' => 'aar', 'Aa31LG1G1800' => 'aar', 'Aa31LG2G5120' => 'aar', 'Aa31LG2G6070' => 'aar', 'Aa31LG5G10770' => 'aar', 'Aa31sc61G90' => 'aar', 'Actinidia01352' => 'ach', 'Actinidia05983' => 'ach', 'Actinidia08133' => 'ach', 'Actinidia15101' => 'ach', 'Actinidia26379' => 'ach', 'Actinidia35778' => 'ach', 'Actinidia36123' => 'ach', 'Actinidia37436' => 'ach', 'Actinidia38730' => 'ach', 'Ah.02g128210' => 'amhyb', 'Ah.03g132990' => 'amhyb', 'Ah.14g079410' => 'amhyb', 'AL1G24640' => 'aly', 'AL2G26680' => 'aly', 'AL3G10530' => 'aly', 'AL3G45230' => 'aly', 'AL5G15230' => 'aly', 'AL5G16960' => 'aly', 'AL6G25210' => 'aly', 'Aqoxy2G00441' => 'aox', 'Aqoxy3G01236' => 'aox', 'Aqoxy5G03746' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3RQ047' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C7GMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9C8JER' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MBL6KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YXCZ83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZANX40' => 'arhy', 'AT1G12990' => 'ath', 'AT1G67880' => 'ath', 'AT2G13290' => 'ath', 'AT3G01620' => 'ath', 'AT3G26445' => 'ath', 'AT3G27540' => 'ath', 'AT5G14480' => 'ath', 'ATR0824G026' => 'atr', 'ATR1098G019' => 'atr', 'Atru.chr11.2145' => 'acertr', 'Atru.chr2.3636' => 'acertr', 'Atru.chr2.3644' => 'acertr', 'Atru.chr6.2422' => 'acertr', 'Atru.chr7.1112' => 'acertr', 'AUR62005469' => 'cqu', 'AUR62011166' => 'cqu', 'AUR62013319' => 'cqu', 'AUR62024273' => 'cqu', 'AUR62028420' => 'cqu', 'AUR62041942' => 'cqu', 'BcaB01g04969' => 'bca', 'BcaB01g06371' => 'bca', 'BcaB02g11494' => 'bca', 'BcaB03g15382' => 'bca', 'BcaB08g36994' => 'bca', 'BcaC03g13477' => 'bca', 'BcaC03g13478' => 'bca', 'BcaC03g13480' => 'bca', 'BcaC03g13481' => 'bca', 'BcaC03g13486' => 'bca', 'BcaC04g19031' => 'bca', 'BcaC04g23085' => 'bca', 'BcaC05g25094' => 'bca', 'BcaC05g25096' => 'bca', 'BcaC05g25138' => 'bca', 'BcaC05g30416' => 'bca', 'BcaC05g30455' => 'bca', 'BcaC06g30979' => 'bca', 'BcaC06g33805' => 'bca', 'BcaC08g46021' => 'bca', 'BcaNung03154' => 'bca', 'BolC2t06623H' => 'bol', 'BolC2t06632H' => 'bol', 'BolC2t06635H' => 'bol', 'BolC2t06638H' => 'bol', 'BolC3t13266H' => 'bol', 'BolC5t29776H' => 'bol', 'BolC6t38912H' => 'bol', 'BolC7t44183H' => 'bol', 'BolC9t54123H' => 'bol', 'BolC9t59107H' => 'bol', 'BraA02t05221Z' => 'bra', 'BraA03t09996Z' => 'bra', 'BraA05t23210Z' => 'bra', 'BraA06t24068Z' => 'bra', 'BraA06t27032Z' => 'bra', 'BraA08t35176Z' => 'bra', 'BraA09t36680Z' => 'bra', 'BraA10t44471Z' => 'bra', 'C02p06760' => 'bna', 'C02p06890' => 'bna', 'C02p07010' => 'bna', 'C03p07660' => 'bna', 'C05p10300' => 'bna', 'C06p38150' => 'bna', 'C07p36650' => 'bna', 'C08p15770' => 'bna', 'C09p12300' => 'bna', 'C09p62700' => 'bna', 'C09p75040' => 'bna', 'CAN.G13.1' => 'can', 'CAN.G138.4' => 'can', 'CAN.G44.6' => 'can', 'CAN.G473.19' => 'can', 'CANSAT01G0835' => 'cansat', 'CANSAT11G0246' => 'cansat', 'CANSAT11G1766' => 'cansat', 'CANSAT64G1954' => 'cansat', 'CARHR013330' => 'chi', 'CARHR060530' => 'chi', 'CARHR075300' => 'chi', 'CARHR105120' => 'chi', 'CARHR148910' => 'chi', 'CARHR198830' => 'chi', 'Carub.0001s1275' => 'cru', 'Carub.0002s1437' => 'cru', 'Carub.0003s0044' => 'cru', 'Carub.0003s2787' => 'cru', 'Carub.0005s0597' => 'cru', 'Carub.0006s1266' => 'cru', 'Ca_06935_v3' => 'car', 'Ca_13559_v3' => 'car', 'Ca_16941_v3' => 'car', 'Ca_16960_v3' => 'car', 'Ca_17775_v3' => 'car', 'Ca_30464_v3' => 'car', 'Cc06_g08160' => 'ccan', 'Cc07_g01520' => 'ccan', 'Cc11_g15810' => 'ccan', 'CDE02G2840' => 'cde', 'CDE03G0093' => 'cde', 'CDE04G2127' => 'cde', 'CDE07G1857' => 'cde', 'CDE09G1246' => 'cde', 'Cfa003412' => 'cfa', 'Cfa007341' => 'cfa', 'Cfa009220' => 'cfa', 'Ciclev10008737m.g' => 'ccl', 'Ciclev10015565m.g' => 'ccl', 'Ciclev10031761m.g' => 'ccl', 'CiPaw.03G045300' => 'cil', 'CiPaw.03G247200' => 'cil', 'CiPaw.04G029500' => 'cil', 'CiPaw.04G174000' => 'cil', 'CiPaw.05G181200' => 'cil', 'CiPaw.06G067100' => 'cil', 'ClCG05G025800' => 'cla', 'ClCG06G011400' => 'cla', 'ClCG09G019360' => 'cla', 'COL.COLO4_04827' => 'col', 'COL.COLO4_29170' => 'col', 'COL.COLO4_35131' => 'col', 'COL.COLO4_35132' => 'col', 'Cpa.g.sc33.32' => 'cpa', 'Cpa.g.sc46.29' => 'cpa', 'Cpa.g.sc796.1' => 'cpa', 'CsaV3_1G030420' => 'csa', 'CsaV3_5G027050' => 'csa', 'CsaV3_5G031040' => 'csa', 'CsaV3_UNG023130' => 'csa', 'CSS0007726' => 'camsi', 'CSS0016433' => 'camsi', 'CSS0017656' => 'camsi', 'CSS0025364' => 'camsi', 'CSS0027582' => 'camsi', 'CSS0047288' => 'camsi', 'CSS0049950' => 'camsi', 'DCAR_003843' => 'dca', 'DCAR_007052' => 'dca', 'DCAR_020884' => 'dca', 'DCAR_021730' => 'dca', 'DCAR_024423' => 'dca', 'DCAR_026509' => 'dca', 'DCAR_031158' => 'dca', 'Dinv14728' => 'din', 'Dinv15219' => 'din', 'Dinv25728' => 'din', 'Dinv33428' => 'din', 'Dinv36489' => 'din', 'Dinv41486' => 'din', 'Duzib147G0469' => 'dzi', 'Duzib168G0060' => 'dzi', 'Duzib187G1215' => 'dzi', 'Duzib248G0692' => 'dzi', 'Duzib251G0767' => 'dzi', 'Duzib264G0446' => 'dzi', 'Duzib268G0691' => 'dzi', 'ECA232G4767' => 'eca', 'ECA233G2838' => 'eca', 'ECA234G0391' => 'eca', 'ECA234G0857' => 'eca', 'ECA236G1593' => 'eca', 'ECA238G0565' => 'eca', 'ECA246G1027' => 'eca', 'ECA246G3223' => 'eca', 'ECA246G3470' => 'eca', 'EL10Ac6g13829' => 'bvu', 'EL10Ac6g14093' => 'bvu', 'EL10Ac8g18707' => 'bvu', 'Eucgr.C01369' => 'egr', 'Eucgr.H02492' => 'egr', 'Eucgr.I01733' => 'egr', 'Eucgr.J02255' => 'egr', 'Eucgr.J02257' => 'egr', 'Eucgr.J02258' => 'egr', 'FAN02G1601' => 'fan', 'FAN03G1586' => 'fan', 'FAN03G2986' => 'fan', 'FAN05G4837' => 'fan', 'FAN06G0146' => 'fan', 'FAN07G0858' => 'fan', 'FAN09G3179' => 'fan', 'FAN10G0669' => 'fan', 'FAN12G2358' => 'fan', 'FAN14G4198' => 'fan', 'FAN14G5112' => 'fan', 'FAN17G0342' => 'fan', 'FAN19G0342' => 'fan', 'FAN19G0962' => 'fan', 'FAN19G1101' => 'fan', 'FAN19G1872' => 'fan', 'FAN22G0356' => 'fan', 'FAN23G0744' => 'fan', 'FAN23G1914' => 'fan', 'FAN26G0032' => 'fan', 'FAN28G0625' => 'fan', 'FvH4_1g02710' => 'fve', 'FvH4_1g02720' => 'fve', 'FvH4_4g25670' => 'fve', 'FvH4_6g51700' => 'fve', 'FvH4_7g20170' => 'fve', 'Glyma.05G175000' => 'gma', 'Glyma.08G132300' => 'gma', 'Glyma.11G243000' => 'gma', 'Glyma.13G158900' => 'gma', 'Glyma.17G112400' => 'gma', 'Glyma.18G014100' => 'gma', 'Glyma.19G003100' => 'gma', 'Glyma.19G056500' => 'gma', 'Gohir.A01G158900' => 'ghi', 'Gohir.A05G312600' => 'ghi', 'Gohir.A05G354900' => 'ghi', 'Gohir.A07G037200' => 'ghi', 'Gohir.A09G030000' => 'ghi', 'Gohir.A12G145200' => 'ghi', 'Gohir.D01G151500' => 'ghi', 'Gohir.D04G058300' => 'ghi', 'Gohir.D05G314100' => 'ghi', 'Gohir.D07G041400' => 'ghi', 'Gohir.D09G029700' => 'ghi', 'Gohir.D12G149700' => 'ghi', 'Gorai.001G043800' => 'gra', 'Gorai.002G187800' => 'gra', 'Gorai.006G034700' => 'gra', 'Gorai.008G161200' => 'gra', 'Gorai.009G335700' => 'gra', 'Gorai.012G065000' => 'gra', 'GSVIVG01000535001' => 'vvi', 'GSVIVG01015572001' => 'vvi', 'GSVIVG01032386001' => 'vvi', 'HanXRQChr05g0138531' => 'han', 'HanXRQChr06g0174391' => 'han', 'HanXRQChr07g0199021' => 'han', 'HanXRQChr08g0208211' => 'han', 'HanXRQChr09g0255471' => 'han', 'HanXRQChr10g0315791' => 'han', 'HanXRQChr12g0371991' => 'han', 'HanXRQChr15g0475251' => 'han', 'HanXRQChr17g0540001' => 'han', 'HanXRQChr17g0548631' => 'han', 'HanXRQChr17g0569561' => 'han', 'Haze_12256' => 'cav', 'Haze_14756' => 'cav', 'Haze_25528' => 'cav', 'Hma1.2p1_0079F.1_g041020' => 'hma', 'Hma1.2p1_0818F.1_g223260' => 'hma', 'Hma1.2p1_1747F.1_g300530' => 'hma', 'HPP92_004607' => 'vpl', 'HPP92_004608' => 'vpl', 'HPP92_006181' => 'vpl', 'HPP92_012192' => 'vpl', 'HPP92_015680' => 'vpl', 'HPP92_020249' => 'vpl', 'HPP92_021376' => 'vpl', 'HPP92_024275' => 'vpl', 'Hund06031' => 'sun', 'Hund25391' => 'sun', 'Lalb_Chr07g0185371' => 'lal', 'Lalb_Chr07g0185381' => 'lal', 'Lalb_Chr12g0204011' => 'lal', 'Lalb_Chr13g0301671' => 'lal', 'Lalb_Chr14g0362851' => 'lal', 'Lalb_Chr24g0403581' => 'lal', 'Lj1g0000233' => 'lja', 'Lj2g0018120' => 'lja', 'Lj3C621T0' => 'lonja', 'Lj3P1059T14' => 'lonja', 'Lj3P611T9' => 'lonja', 'Lj3P614T13' => 'lonja', 'Lj3P615T5' => 'lonja', 'Lj4g0012315' => 'lja', 'Lj4g0026182' => 'lja', 'Lj6P813T16' => 'lonja', 'Lj7C427T7' => 'lonja', 'Lj7C427T8' => 'lonja', 'Lj7P600T41' => 'lonja', 'Lju41C42G17' => 'lonja', 'Lsat_1_v5_gn_0_47300' => 'lsa', 'Lsat_1_v5_gn_2_91280' => 'lsa', 'Lsat_1_v5_gn_3_30561' => 'lsa', 'Lsat_1_v5_gn_4_184321' => 'lsa', 'Lsat_1_v5_gn_4_4041' => 'lsa', 'Lsat_1_v5_gn_5_92000' => 'lsa', 'Lsat_1_v5_gn_8_152940' => 'lsa', 'Lsat_1_v5_gn_8_62401' => 'lsa', 'Manes.06G055900' => 'mes', 'Manes.12G022200' => 'mes', 'Manes.13G023300' => 'mes', 'Manes.14G115000' => 'mes', 'Manes.15G151700' => 'mes', 'Manes.17G111300' => 'mes', 'Mapoly0226s0009' => 'mpo', 'MBI02_g25363_MAGBIO' => 'mbi', 'MBI06_g00027_MAGBIO' => 'mbi', 'MBI10_g13034_MAGBIO' => 'mbi', 'MD09G1023400' => 'mdo', 'MD13G1100100' => 'mdo', 'MD15G1169200' => 'mdo', 'MD16G1101100' => 'mdo', 'MD17G1022900' => 'mdo', 'Medtr3g096150' => 'mtr', 'Medtr4g115070' => 'mtr', 'Medtr7g033325' => 'mtr', 'Medtr8g089840' => 'mtr', 'MELO3C010319.2' => 'cme', 'MELO3C011944.2' => 'cme', 'MELO3C021589.2' => 'cme', 'Migut.E00207' => 'egut', 'Migut.H00067' => 'egut', 'Migut.K00433' => 'egut', 'Migut.K00606' => 'egut', 'Migut.K01410' => 'egut', 'MSTRG.13347' => 'ama', 'MSTRG.24045' => 'ama', 'MSTRG.2428' => 'ama', 'MSTRG.26410' => 'ama', 'MSTRG.3139' => 'ama', 'MSTRG.3286' => 'ama', 'MSTRG.563' => 'ama', 'MSTRG.7941' => 'ama', 'Nitab4.5_0000028g0060' => 'nta', 'Nitab4.5_0000065g0260' => 'nta', 'Nitab4.5_0000112g0060' => 'nta', 'Nitab4.5_0000489g0120' => 'nta', 'Nitab4.5_0001776g0050' => 'nta', 'Nitab4.5_0001854g0010' => 'nta', 'Nitab4.5_0001860g0020' => 'nta', 'Nitab4.5_0004352g0010' => 'nta', 'Nitab4.5_0008716g0020' => 'nta', 'Nitab4.5_0008922g0010' => 'nta', 'Nn3g16693' => 'nnu', 'Nn4g22596' => 'nnu', 'Nn7g37639' => 'nnu', 'Oeu001701.1' => 'oeu', 'Oeu018149.1' => 'oeu', 'Oeu026220.1' => 'oeu', 'Oeu038635.1' => 'oeu', 'Oeu049176.1' => 'oeu', 'Oeu056706.1' => 'oeu', 'Oeu056937.1' => 'oeu', 'Oeu057540.1' => 'oeu', 'Os02g0594900' => 'osa', 'Os02g0595100' => 'osa', 'Os04g0477500' => 'osa', 'Os12g0611900' => 'osa', 'Peaxi162Scf00076g00020' => 'pax', 'Peaxi162Scf00128g00217' => 'pax', 'Peaxi162Scf00129g01640' => 'pax', 'Peaxi162Scf00669g00007' => 'pax', 'Peaxi162Scf00700g00421' => 'pax', 'Peaxi162Scf00801g00038' => 'pax', 'Peaxi162Scf00891g00025' => 'pax', 'PGR083G0909' => 'pgr', 'PGR119G1005' => 'pgr', 'PGR142G2236' => 'pgr', 'PGR142G3388' => 'pgr', 'PGSC0003DMG400004514' => 'stu', 'PGSC0003DMG400012635' => 'stu', 'PGSC0003DMG400015730' => 'stu', 'PGSC0003DMG400018611' => 'stu', 'PGSC0003DMG400030897' => 'stu', 'Phvul.001G254800' => 'pvu', 'Phvul.002G260100' => 'pvu', 'Phvul.003G167600' => 'pvu', 'Phvul.004G005100' => 'pvu', 'Potri.001G343600' => 'ptr', 'Potri.006G066700' => 'ptr', 'Potri.008G186000' => 'ptr', 'Potri.010G046900' => 'ptr', 'Potri.018G127900' => 'ptr', 'Pp3c20_17750' => 'ppa', 'Pp3c24_4380' => 'ppa', 'Prupe.1G245800' => 'ppe', 'Prupe.3G293400' => 'ppe', 'Prupe.7G247400' => 'ppe', 'Psat0s145g0120' => 'psa', 'Psat0s595g0040' => 'psa', 'Psat0s595g0120' => 'psa', 'Psat3g175040' => 'psa', 'Psat7g058120' => 'psa', 'PSO017G0428' => 'pso', 'PSO063G7510' => 'pso', 'PSO067G0046' => 'pso', 'PSO478G1073' => 'pso', 'PSO675G3677' => 'pso', 'PSO675G6558' => 'pso', 'PSO675G7520' => 'pso', 'PSO675G8959' => 'pso', 'QL02p074089' => 'qlo', 'QL02p089614' => 'qlo', 'QL03p057736' => 'qlo', 'RcHm_v2.0_Chr1g0364131' => 'rch', 'RcHm_v2.0_Chr2g0087801' => 'rch', 'RcHm_v2.0_Chr2g0087821' => 'rch', 'RcHm_v2.0_Chr2g0173231' => 'rch', 'RcHm_v2.0_Chr4g0433111' => 'rch', 'Rhsim03G0250300' => 'rsi', 'Rhsim08G0048400' => 'rsi', 'Rhsim10G0014800' => 'rsi', 'Rhsim12G0040100' => 'rsi', 'Rhsim12G0109700' => 'rsi', 'Sabra06G0049600' => 'sbr', 'Sabra08G0141000' => 'sbr', 'Sabra10G0021400' => 'sbr', 'Sabra16G0222900' => 'sbr', 'Sabra18G0108600' => 'sbr', 'SalBow1G0433' => 'sbo', 'SalBow1G2038' => 'sbo', 'SalBow1G5003' => 'sbo', 'SalBow7G1197' => 'sbo', 'SalBow8G3506' => 'sbo', 'Sc03g0007300' => 'sci', 'Sc11g0000950' => 'sci', 'Sc14g0008750' => 'sci', 'Sc18g0000420' => 'sci', 'Sed0006754' => 'sed', 'Sed0008741' => 'sed', 'Sed0017172' => 'sed', 'Sed0018925' => 'sed', 'Sed0023326' => 'sed', 'Sed0025909' => 'sed', 'SEGI_05333' => 'sgi', 'SEGI_10362' => 'sgi', 'SEGI_13380' => 'sgi', 'SEGI_24306' => 'sgi', 'SEGI_29077' => 'sgi', 'SEGI_29095' => 'sgi', 'SEGI_36534' => 'sgi', 'SEGI_37506' => 'sgi', 'SEGI_38321' => 'sgi', 'SGA_v2.0_scaffold307G48031' => 'sas', 'SGA_v2.0_scaffold47G17507' => 'sas', 'SGA_v2.0_scaffold63G21736' => 'sas', 'SGA_v2.0_scaffold87G27070' => 'sas', 'SHI17794' => 'shi', 'SHI28851' => 'shi', 'SMO165G0155' => 'smo', 'SMO340G0217' => 'smo', 'SMO367G1210' => 'smo', 'Solyc02g093430.3' => 'sly', 'Solyc05g013580.4' => 'sly', 'Solyc07g008030.3' => 'sly', 'Solyc12g035470.2' => 'sly', 'Sopen02g038020' => 'spe', 'Sopen05g008490' => 'spe', 'Sopen07g003910' => 'spe', 'Sopen12g015240' => 'spe', 'Sp1g11550' => 'spa', 'Sp2g16710' => 'spa', 'Sp3g00430' => 'spa', 'Sp3g26780' => 'spa', 'Sp5g22900' => 'spa', 'Sp6g29530' => 'spa', 'TAR371G0794' => 'tar', 'TAR374G0164' => 'tar', 'TAR622G0165' => 'tar', 'TAR626G0929' => 'tar', 'TAR629G2155' => 'tar', 'THA.LOC104805282' => 'tha', 'THA.LOC104805363' => 'tha', 'THA.LOC104808968' => 'tha', 'THA.LOC104821093' => 'tha', 'THA.LOC104823953' => 'tha', 'THA.LOC104825562' => 'tha', 'THA.LOC104825665' => 'tha', 'Thecc.02G261400' => 'tca', 'Thecc.04G019200' => 'tca', 'Thecc.09G130400' => 'tca', 'Thhalv10004374m.g' => 'esa', 'Thhalv10007850m.g' => 'esa', 'Thhalv10013782m.g' => 'esa', 'Thhalv10018686m.g' => 'esa', 'Thhalv10020899m.g' => 'esa', 'Thhalv10022755m.g' => 'esa', 'TPR.G23851' => 'tpr', 'TPR.G26500' => 'tpr', 'TPR.G27267' => 'tpr', 'TPR.G32001' => 'tpr', 'TPR.G6251' => 'tpr', 'TPR.G8167' => 'tpr', 'TWI12G1330' => 'twi', 'TWI18G1239' => 'twi', 'TWI34G0979' => 'twi', 'TWI36G0670' => 'twi', 'TWI36G0707' => 'twi', 'TWI56G0233' => 'twi', 'TWI75G1809' => 'twi', 'unitig_21.g20874' => 'ugi', 'unitig_26.g10343' => 'ugi', 'unitig_46.g18392' => 'ugi', 'unitig_52.g17178' => 'ugi', 'unitig_8.g2934' => 'ugi', 'vmacro01122' => 'vma', 'vmacro05875' => 'vma', 'vmacro06147' => 'vma', 'vmacro16191' => 'vma', 'vmacro18293' => 'vma', 'VMungo0251G3707' => 'vmu', 'VMungo0464G1521' => 'vmu', 'VMungo1215G0205' => 'vmu', 'VMungo1383G2484' => 'vmu', 'Zm00001eb079610' => 'zma', 'Zm00001eb135990' => 'zma', 'Zm00001eb183710' => 'zma', 'Zm00001eb246020' => 'zma' ) $gf_id = 'HOM05D001124' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001124' ) $data_identifier = 'HOM05D001124' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 6, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 7, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 21, 'bol' => (int) 10, 'bra' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 6, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 9, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 21, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 8, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 10, 'lsa' => (int) 8, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 8, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 9, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb246020' $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' => 'HOM05D001124', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '548', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02520' => 'bna', 'A03p06630' => 'bna', 'A05p44460' => 'bna', 'A06p08710' => 'bna', 'A06p41090' => 'bna', 'A07p32320' => 'bna', 'A08p32520' => 'bna', 'A09p10360' => 'bna', 'A10p24080' => 'bna', 'Aa31LG11G15250' => 'aar', 'Aa31LG1G1800' => 'aar', 'Aa31LG2G5120' => 'aar', 'Aa31LG2G6070' => 'aar', 'Aa31LG5G10770' => 'aar', 'Aa31sc61G90' => 'aar', 'Actinidia01352' => 'ach', 'Actinidia05983' => 'ach', 'Actinidia08133' => 'ach', 'Actinidia15101' => 'ach', 'Actinidia26379' => 'ach', 'Actinidia35778' => 'ach', 'Actinidia36123' => 'ach', 'Actinidia37436' => 'ach', 'Actinidia38730' => 'ach', 'Ah.02g128210' => 'amhyb', 'Ah.03g132990' => 'amhyb', 'Ah.14g079410' => 'amhyb', 'AL1G24640' => 'aly', 'AL2G26680' => 'aly', 'AL3G10530' => 'aly', 'AL3G45230' => 'aly', 'AL5G15230' => 'aly', 'AL5G16960' => 'aly', 'AL6G25210' => 'aly', 'Aqoxy2G00441' => 'aox', 'Aqoxy3G01236' => 'aox', 'Aqoxy5G03746' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3RQ047' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C7GMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9C8JER' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MBL6KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YXCZ83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZANX40' => 'arhy', 'AT1G12990' => 'ath', 'AT1G67880' => 'ath', 'AT2G13290' => 'ath', 'AT3G01620' => 'ath', 'AT3G26445' => 'ath', 'AT3G27540' => 'ath', 'AT5G14480' => 'ath', 'ATR0824G026' => 'atr', 'ATR1098G019' => 'atr', 'Atru.chr11.2145' => 'acertr', 'Atru.chr2.3636' => 'acertr', 'Atru.chr2.3644' => 'acertr', 'Atru.chr6.2422' => 'acertr', 'Atru.chr7.1112' => 'acertr', 'AUR62005469' => 'cqu', 'AUR62011166' => 'cqu', 'AUR62013319' => 'cqu', 'AUR62024273' => 'cqu', 'AUR62028420' => 'cqu', 'AUR62041942' => 'cqu', 'BcaB01g04969' => 'bca', 'BcaB01g06371' => 'bca', 'BcaB02g11494' => 'bca', 'BcaB03g15382' => 'bca', 'BcaB08g36994' => 'bca', 'BcaC03g13477' => 'bca', 'BcaC03g13478' => 'bca', 'BcaC03g13480' => 'bca', 'BcaC03g13481' => 'bca', 'BcaC03g13486' => 'bca', 'BcaC04g19031' => 'bca', 'BcaC04g23085' => 'bca', 'BcaC05g25094' => 'bca', 'BcaC05g25096' => 'bca', 'BcaC05g25138' => 'bca', 'BcaC05g30416' => 'bca', 'BcaC05g30455' => 'bca', 'BcaC06g30979' => 'bca', 'BcaC06g33805' => 'bca', 'BcaC08g46021' => 'bca', 'BcaNung03154' => 'bca', 'BolC2t06623H' => 'bol', 'BolC2t06632H' => 'bol', 'BolC2t06635H' => 'bol', 'BolC2t06638H' => 'bol', 'BolC3t13266H' => 'bol', 'BolC5t29776H' => 'bol', 'BolC6t38912H' => 'bol', 'BolC7t44183H' => 'bol', 'BolC9t54123H' => 'bol', 'BolC9t59107H' => 'bol', 'BraA02t05221Z' => 'bra', 'BraA03t09996Z' => 'bra', 'BraA05t23210Z' => 'bra', 'BraA06t24068Z' => 'bra', 'BraA06t27032Z' => 'bra', 'BraA08t35176Z' => 'bra', 'BraA09t36680Z' => 'bra', 'BraA10t44471Z' => 'bra', 'C02p06760' => 'bna', 'C02p06890' => 'bna', 'C02p07010' => 'bna', 'C03p07660' => 'bna', 'C05p10300' => 'bna', 'C06p38150' => 'bna', 'C07p36650' => 'bna', 'C08p15770' => 'bna', 'C09p12300' => 'bna', 'C09p62700' => 'bna', 'C09p75040' => 'bna', 'CAN.G13.1' => 'can', 'CAN.G138.4' => 'can', 'CAN.G44.6' => 'can', 'CAN.G473.19' => 'can', 'CANSAT01G0835' => 'cansat', 'CANSAT11G0246' => 'cansat', 'CANSAT11G1766' => 'cansat', 'CANSAT64G1954' => 'cansat', 'CARHR013330' => 'chi', 'CARHR060530' => 'chi', 'CARHR075300' => 'chi', 'CARHR105120' => 'chi', 'CARHR148910' => 'chi', 'CARHR198830' => 'chi', 'Carub.0001s1275' => 'cru', 'Carub.0002s1437' => 'cru', 'Carub.0003s0044' => 'cru', 'Carub.0003s2787' => 'cru', 'Carub.0005s0597' => 'cru', 'Carub.0006s1266' => 'cru', 'Ca_06935_v3' => 'car', 'Ca_13559_v3' => 'car', 'Ca_16941_v3' => 'car', 'Ca_16960_v3' => 'car', 'Ca_17775_v3' => 'car', 'Ca_30464_v3' => 'car', 'Cc06_g08160' => 'ccan', 'Cc07_g01520' => 'ccan', 'Cc11_g15810' => 'ccan', 'CDE02G2840' => 'cde', 'CDE03G0093' => 'cde', 'CDE04G2127' => 'cde', 'CDE07G1857' => 'cde', 'CDE09G1246' => 'cde', 'Cfa003412' => 'cfa', 'Cfa007341' => 'cfa', 'Cfa009220' => 'cfa', 'Ciclev10008737m.g' => 'ccl', 'Ciclev10015565m.g' => 'ccl', 'Ciclev10031761m.g' => 'ccl', 'CiPaw.03G045300' => 'cil', 'CiPaw.03G247200' => 'cil', 'CiPaw.04G029500' => 'cil', 'CiPaw.04G174000' => 'cil', 'CiPaw.05G181200' => 'cil', 'CiPaw.06G067100' => 'cil', 'ClCG05G025800' => 'cla', 'ClCG06G011400' => 'cla', 'ClCG09G019360' => 'cla', 'COL.COLO4_04827' => 'col', 'COL.COLO4_29170' => 'col', 'COL.COLO4_35131' => 'col', 'COL.COLO4_35132' => 'col', 'Cpa.g.sc33.32' => 'cpa', 'Cpa.g.sc46.29' => 'cpa', 'Cpa.g.sc796.1' => 'cpa', 'CsaV3_1G030420' => 'csa', 'CsaV3_5G027050' => 'csa', 'CsaV3_5G031040' => 'csa', 'CsaV3_UNG023130' => 'csa', 'CSS0007726' => 'camsi', 'CSS0016433' => 'camsi', 'CSS0017656' => 'camsi', 'CSS0025364' => 'camsi', 'CSS0027582' => 'camsi', 'CSS0047288' => 'camsi', 'CSS0049950' => 'camsi', 'DCAR_003843' => 'dca', 'DCAR_007052' => 'dca', 'DCAR_020884' => 'dca', 'DCAR_021730' => 'dca', 'DCAR_024423' => 'dca', 'DCAR_026509' => 'dca', 'DCAR_031158' => 'dca', 'Dinv14728' => 'din', 'Dinv15219' => 'din', 'Dinv25728' => 'din', 'Dinv33428' => 'din', 'Dinv36489' => 'din', 'Dinv41486' => 'din', 'Duzib147G0469' => 'dzi', 'Duzib168G0060' => 'dzi', 'Duzib187G1215' => 'dzi', 'Duzib248G0692' => 'dzi', 'Duzib251G0767' => 'dzi', 'Duzib264G0446' => 'dzi', 'Duzib268G0691' => 'dzi', 'ECA232G4767' => 'eca', 'ECA233G2838' => 'eca', 'ECA234G0391' => 'eca', 'ECA234G0857' => 'eca', 'ECA236G1593' => 'eca', 'ECA238G0565' => 'eca', 'ECA246G1027' => 'eca', 'ECA246G3223' => 'eca', 'ECA246G3470' => 'eca', 'EL10Ac6g13829' => 'bvu', 'EL10Ac6g14093' => 'bvu', 'EL10Ac8g18707' => 'bvu', 'Eucgr.C01369' => 'egr', 'Eucgr.H02492' => 'egr', 'Eucgr.I01733' => 'egr', 'Eucgr.J02255' => 'egr', 'Eucgr.J02257' => 'egr', 'Eucgr.J02258' => 'egr', 'FAN02G1601' => 'fan', 'FAN03G1586' => 'fan', 'FAN03G2986' => 'fan', 'FAN05G4837' => 'fan', 'FAN06G0146' => 'fan', 'FAN07G0858' => 'fan', 'FAN09G3179' => 'fan', 'FAN10G0669' => 'fan', 'FAN12G2358' => 'fan', 'FAN14G4198' => 'fan', 'FAN14G5112' => 'fan', 'FAN17G0342' => 'fan', 'FAN19G0342' => 'fan', 'FAN19G0962' => 'fan', 'FAN19G1101' => 'fan', 'FAN19G1872' => 'fan', 'FAN22G0356' => 'fan', 'FAN23G0744' => 'fan', 'FAN23G1914' => 'fan', 'FAN26G0032' => 'fan', 'FAN28G0625' => 'fan', 'FvH4_1g02710' => 'fve', 'FvH4_1g02720' => 'fve', 'FvH4_4g25670' => 'fve', 'FvH4_6g51700' => 'fve', 'FvH4_7g20170' => 'fve', 'Glyma.05G175000' => 'gma', 'Glyma.08G132300' => 'gma', 'Glyma.11G243000' => 'gma', 'Glyma.13G158900' => 'gma', 'Glyma.17G112400' => 'gma', 'Glyma.18G014100' => 'gma', 'Glyma.19G003100' => 'gma', 'Glyma.19G056500' => 'gma', 'Gohir.A01G158900' => 'ghi', 'Gohir.A05G312600' => 'ghi', 'Gohir.A05G354900' => 'ghi', 'Gohir.A07G037200' => 'ghi', 'Gohir.A09G030000' => 'ghi', 'Gohir.A12G145200' => 'ghi', 'Gohir.D01G151500' => 'ghi', 'Gohir.D04G058300' => 'ghi', 'Gohir.D05G314100' => 'ghi', 'Gohir.D07G041400' => 'ghi', 'Gohir.D09G029700' => 'ghi', 'Gohir.D12G149700' => 'ghi', 'Gorai.001G043800' => 'gra', 'Gorai.002G187800' => 'gra', 'Gorai.006G034700' => 'gra', 'Gorai.008G161200' => 'gra', 'Gorai.009G335700' => 'gra', 'Gorai.012G065000' => 'gra', 'GSVIVG01000535001' => 'vvi', 'GSVIVG01015572001' => 'vvi', 'GSVIVG01032386001' => 'vvi', 'HanXRQChr05g0138531' => 'han', 'HanXRQChr06g0174391' => 'han', 'HanXRQChr07g0199021' => 'han', 'HanXRQChr08g0208211' => 'han', 'HanXRQChr09g0255471' => 'han', 'HanXRQChr10g0315791' => 'han', 'HanXRQChr12g0371991' => 'han', 'HanXRQChr15g0475251' => 'han', 'HanXRQChr17g0540001' => 'han', 'HanXRQChr17g0548631' => 'han', 'HanXRQChr17g0569561' => 'han', 'Haze_12256' => 'cav', 'Haze_14756' => 'cav', 'Haze_25528' => 'cav', 'Hma1.2p1_0079F.1_g041020' => 'hma', 'Hma1.2p1_0818F.1_g223260' => 'hma', 'Hma1.2p1_1747F.1_g300530' => 'hma', 'HPP92_004607' => 'vpl', 'HPP92_004608' => 'vpl', 'HPP92_006181' => 'vpl', 'HPP92_012192' => 'vpl', 'HPP92_015680' => 'vpl', 'HPP92_020249' => 'vpl', 'HPP92_021376' => 'vpl', 'HPP92_024275' => 'vpl', 'Hund06031' => 'sun', 'Hund25391' => 'sun', 'Lalb_Chr07g0185371' => 'lal', 'Lalb_Chr07g0185381' => 'lal', 'Lalb_Chr12g0204011' => 'lal', 'Lalb_Chr13g0301671' => 'lal', 'Lalb_Chr14g0362851' => 'lal', 'Lalb_Chr24g0403581' => 'lal', 'Lj1g0000233' => 'lja', 'Lj2g0018120' => 'lja', 'Lj3C621T0' => 'lonja', 'Lj3P1059T14' => 'lonja', 'Lj3P611T9' => 'lonja', 'Lj3P614T13' => 'lonja', 'Lj3P615T5' => 'lonja', 'Lj4g0012315' => 'lja', 'Lj4g0026182' => 'lja', 'Lj6P813T16' => 'lonja', 'Lj7C427T7' => 'lonja', 'Lj7C427T8' => 'lonja', 'Lj7P600T41' => 'lonja', 'Lju41C42G17' => 'lonja', 'Lsat_1_v5_gn_0_47300' => 'lsa', 'Lsat_1_v5_gn_2_91280' => 'lsa', 'Lsat_1_v5_gn_3_30561' => 'lsa', 'Lsat_1_v5_gn_4_184321' => 'lsa', 'Lsat_1_v5_gn_4_4041' => 'lsa', 'Lsat_1_v5_gn_5_92000' => 'lsa', 'Lsat_1_v5_gn_8_152940' => 'lsa', 'Lsat_1_v5_gn_8_62401' => 'lsa', 'Manes.06G055900' => 'mes', 'Manes.12G022200' => 'mes', 'Manes.13G023300' => 'mes', 'Manes.14G115000' => 'mes', 'Manes.15G151700' => 'mes', 'Manes.17G111300' => 'mes', 'Mapoly0226s0009' => 'mpo', 'MBI02_g25363_MAGBIO' => 'mbi', 'MBI06_g00027_MAGBIO' => 'mbi', 'MBI10_g13034_MAGBIO' => 'mbi', 'MD09G1023400' => 'mdo', 'MD13G1100100' => 'mdo', 'MD15G1169200' => 'mdo', 'MD16G1101100' => 'mdo', 'MD17G1022900' => 'mdo', 'Medtr3g096150' => 'mtr', 'Medtr4g115070' => 'mtr', 'Medtr7g033325' => 'mtr', 'Medtr8g089840' => 'mtr', 'MELO3C010319.2' => 'cme', 'MELO3C011944.2' => 'cme', 'MELO3C021589.2' => 'cme', 'Migut.E00207' => 'egut', 'Migut.H00067' => 'egut', 'Migut.K00433' => 'egut', 'Migut.K00606' => 'egut', 'Migut.K01410' => 'egut', 'MSTRG.13347' => 'ama', 'MSTRG.24045' => 'ama', 'MSTRG.2428' => 'ama', 'MSTRG.26410' => 'ama', 'MSTRG.3139' => 'ama', 'MSTRG.3286' => 'ama', 'MSTRG.563' => 'ama', 'MSTRG.7941' => 'ama', 'Nitab4.5_0000028g0060' => 'nta', 'Nitab4.5_0000065g0260' => 'nta', 'Nitab4.5_0000112g0060' => 'nta', 'Nitab4.5_0000489g0120' => 'nta', 'Nitab4.5_0001776g0050' => 'nta', 'Nitab4.5_0001854g0010' => 'nta', 'Nitab4.5_0001860g0020' => 'nta', 'Nitab4.5_0004352g0010' => 'nta', 'Nitab4.5_0008716g0020' => 'nta', 'Nitab4.5_0008922g0010' => 'nta', 'Nn3g16693' => 'nnu', 'Nn4g22596' => 'nnu', 'Nn7g37639' => 'nnu', 'Oeu001701.1' => 'oeu', 'Oeu018149.1' => 'oeu', 'Oeu026220.1' => 'oeu', 'Oeu038635.1' => 'oeu', 'Oeu049176.1' => 'oeu', 'Oeu056706.1' => 'oeu', 'Oeu056937.1' => 'oeu', 'Oeu057540.1' => 'oeu', 'Os02g0594900' => 'osa', 'Os02g0595100' => 'osa', 'Os04g0477500' => 'osa', 'Os12g0611900' => 'osa', 'Peaxi162Scf00076g00020' => 'pax', 'Peaxi162Scf00128g00217' => 'pax', 'Peaxi162Scf00129g01640' => 'pax', 'Peaxi162Scf00669g00007' => 'pax', 'Peaxi162Scf00700g00421' => 'pax', 'Peaxi162Scf00801g00038' => 'pax', 'Peaxi162Scf00891g00025' => 'pax', 'PGR083G0909' => 'pgr', 'PGR119G1005' => 'pgr', 'PGR142G2236' => 'pgr', 'PGR142G3388' => 'pgr', 'PGSC0003DMG400004514' => 'stu', 'PGSC0003DMG400012635' => 'stu', 'PGSC0003DMG400015730' => 'stu', 'PGSC0003DMG400018611' => 'stu', 'PGSC0003DMG400030897' => 'stu', 'Phvul.001G254800' => 'pvu', 'Phvul.002G260100' => 'pvu', 'Phvul.003G167600' => 'pvu', 'Phvul.004G005100' => 'pvu', 'Potri.001G343600' => 'ptr', 'Potri.006G066700' => 'ptr', 'Potri.008G186000' => 'ptr', 'Potri.010G046900' => 'ptr', 'Potri.018G127900' => 'ptr', 'Pp3c20_17750' => 'ppa', 'Pp3c24_4380' => 'ppa', 'Prupe.1G245800' => 'ppe', 'Prupe.3G293400' => 'ppe', 'Prupe.7G247400' => 'ppe', 'Psat0s145g0120' => 'psa', 'Psat0s595g0040' => 'psa', 'Psat0s595g0120' => 'psa', 'Psat3g175040' => 'psa', 'Psat7g058120' => 'psa', 'PSO017G0428' => 'pso', 'PSO063G7510' => 'pso', 'PSO067G0046' => 'pso', 'PSO478G1073' => 'pso', 'PSO675G3677' => 'pso', 'PSO675G6558' => 'pso', 'PSO675G7520' => 'pso', 'PSO675G8959' => 'pso', 'QL02p074089' => 'qlo', 'QL02p089614' => 'qlo', 'QL03p057736' => 'qlo', 'RcHm_v2.0_Chr1g0364131' => 'rch', 'RcHm_v2.0_Chr2g0087801' => 'rch', 'RcHm_v2.0_Chr2g0087821' => 'rch', 'RcHm_v2.0_Chr2g0173231' => 'rch', 'RcHm_v2.0_Chr4g0433111' => 'rch', 'Rhsim03G0250300' => 'rsi', 'Rhsim08G0048400' => 'rsi', 'Rhsim10G0014800' => 'rsi', 'Rhsim12G0040100' => 'rsi', 'Rhsim12G0109700' => 'rsi', 'Sabra06G0049600' => 'sbr', 'Sabra08G0141000' => 'sbr', 'Sabra10G0021400' => 'sbr', 'Sabra16G0222900' => 'sbr', 'Sabra18G0108600' => 'sbr', 'SalBow1G0433' => 'sbo', 'SalBow1G2038' => 'sbo', 'SalBow1G5003' => 'sbo', 'SalBow7G1197' => 'sbo', 'SalBow8G3506' => 'sbo', 'Sc03g0007300' => 'sci', 'Sc11g0000950' => 'sci', 'Sc14g0008750' => 'sci', 'Sc18g0000420' => 'sci', 'Sed0006754' => 'sed', 'Sed0008741' => 'sed', 'Sed0017172' => 'sed', 'Sed0018925' => 'sed', 'Sed0023326' => 'sed', 'Sed0025909' => 'sed', 'SEGI_05333' => 'sgi', 'SEGI_10362' => 'sgi', 'SEGI_13380' => 'sgi', 'SEGI_24306' => 'sgi', 'SEGI_29077' => 'sgi', 'SEGI_29095' => 'sgi', 'SEGI_36534' => 'sgi', 'SEGI_37506' => 'sgi', 'SEGI_38321' => 'sgi', 'SGA_v2.0_scaffold307G48031' => 'sas', 'SGA_v2.0_scaffold47G17507' => 'sas', 'SGA_v2.0_scaffold63G21736' => 'sas', 'SGA_v2.0_scaffold87G27070' => 'sas', 'SHI17794' => 'shi', 'SHI28851' => 'shi', 'SMO165G0155' => 'smo', 'SMO340G0217' => 'smo', 'SMO367G1210' => 'smo', 'Solyc02g093430.3' => 'sly', 'Solyc05g013580.4' => 'sly', 'Solyc07g008030.3' => 'sly', 'Solyc12g035470.2' => 'sly', 'Sopen02g038020' => 'spe', 'Sopen05g008490' => 'spe', 'Sopen07g003910' => 'spe', 'Sopen12g015240' => 'spe', 'Sp1g11550' => 'spa', 'Sp2g16710' => 'spa', 'Sp3g00430' => 'spa', 'Sp3g26780' => 'spa', 'Sp5g22900' => 'spa', 'Sp6g29530' => 'spa', 'TAR371G0794' => 'tar', 'TAR374G0164' => 'tar', 'TAR622G0165' => 'tar', 'TAR626G0929' => 'tar', 'TAR629G2155' => 'tar', 'THA.LOC104805282' => 'tha', 'THA.LOC104805363' => 'tha', 'THA.LOC104808968' => 'tha', 'THA.LOC104821093' => 'tha', 'THA.LOC104823953' => 'tha', 'THA.LOC104825562' => 'tha', 'THA.LOC104825665' => 'tha', 'Thecc.02G261400' => 'tca', 'Thecc.04G019200' => 'tca', 'Thecc.09G130400' => 'tca', 'Thhalv10004374m.g' => 'esa', 'Thhalv10007850m.g' => 'esa', 'Thhalv10013782m.g' => 'esa', 'Thhalv10018686m.g' => 'esa', 'Thhalv10020899m.g' => 'esa', 'Thhalv10022755m.g' => 'esa', 'TPR.G23851' => 'tpr', 'TPR.G26500' => 'tpr', 'TPR.G27267' => 'tpr', 'TPR.G32001' => 'tpr', 'TPR.G6251' => 'tpr', 'TPR.G8167' => 'tpr', 'TWI12G1330' => 'twi', 'TWI18G1239' => 'twi', 'TWI34G0979' => 'twi', 'TWI36G0670' => 'twi', 'TWI36G0707' => 'twi', 'TWI56G0233' => 'twi', 'TWI75G1809' => 'twi', 'unitig_21.g20874' => 'ugi', 'unitig_26.g10343' => 'ugi', 'unitig_46.g18392' => 'ugi', 'unitig_52.g17178' => 'ugi', 'unitig_8.g2934' => 'ugi', 'vmacro01122' => 'vma', 'vmacro05875' => 'vma', 'vmacro06147' => 'vma', 'vmacro16191' => 'vma', 'vmacro18293' => 'vma', 'VMungo0251G3707' => 'vmu', 'VMungo0464G1521' => 'vmu', 'VMungo1215G0205' => 'vmu', 'VMungo1383G2484' => 'vmu', 'Zm00001eb079610' => 'zma', 'Zm00001eb135990' => 'zma', 'Zm00001eb183710' => 'zma', 'Zm00001eb246020' => 'zma' ), 'gf_id' => 'HOM05D001124', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001124' ), 'data_identifier' => 'HOM05D001124', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001124', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '548', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02520' => 'bna', 'A03p06630' => 'bna', 'A05p44460' => 'bna', 'A06p08710' => 'bna', 'A06p41090' => 'bna', 'A07p32320' => 'bna', 'A08p32520' => 'bna', 'A09p10360' => 'bna', 'A10p24080' => 'bna', 'Aa31LG11G15250' => 'aar', 'Aa31LG1G1800' => 'aar', 'Aa31LG2G5120' => 'aar', 'Aa31LG2G6070' => 'aar', 'Aa31LG5G10770' => 'aar', 'Aa31sc61G90' => 'aar', 'Actinidia01352' => 'ach', 'Actinidia05983' => 'ach', 'Actinidia08133' => 'ach', 'Actinidia15101' => 'ach', 'Actinidia26379' => 'ach', 'Actinidia35778' => 'ach', 'Actinidia36123' => 'ach', 'Actinidia37436' => 'ach', 'Actinidia38730' => 'ach', 'Ah.02g128210' => 'amhyb', 'Ah.03g132990' => 'amhyb', 'Ah.14g079410' => 'amhyb', 'AL1G24640' => 'aly', 'AL2G26680' => 'aly', 'AL3G10530' => 'aly', 'AL3G45230' => 'aly', 'AL5G15230' => 'aly', 'AL5G16960' => 'aly', 'AL6G25210' => 'aly', 'Aqoxy2G00441' => 'aox', 'Aqoxy3G01236' => 'aox', 'Aqoxy5G03746' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3RQ047' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C7GMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9C8JER' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MBL6KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YXCZ83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZANX40' => 'arhy', 'AT1G12990' => 'ath', 'AT1G67880' => 'ath', 'AT2G13290' => 'ath', 'AT3G01620' => 'ath', 'AT3G26445' => 'ath', 'AT3G27540' => 'ath', 'AT5G14480' => 'ath', 'ATR0824G026' => 'atr', 'ATR1098G019' => 'atr', 'Atru.chr11.2145' => 'acertr', 'Atru.chr2.3636' => 'acertr', 'Atru.chr2.3644' => 'acertr', 'Atru.chr6.2422' => 'acertr', 'Atru.chr7.1112' => 'acertr', 'AUR62005469' => 'cqu', 'AUR62011166' => 'cqu', 'AUR62013319' => 'cqu', 'AUR62024273' => 'cqu', 'AUR62028420' => 'cqu', 'AUR62041942' => 'cqu', 'BcaB01g04969' => 'bca', 'BcaB01g06371' => 'bca', 'BcaB02g11494' => 'bca', 'BcaB03g15382' => 'bca', 'BcaB08g36994' => 'bca', 'BcaC03g13477' => 'bca', 'BcaC03g13478' => 'bca', 'BcaC03g13480' => 'bca', 'BcaC03g13481' => 'bca', 'BcaC03g13486' => 'bca', 'BcaC04g19031' => 'bca', 'BcaC04g23085' => 'bca', 'BcaC05g25094' => 'bca', 'BcaC05g25096' => 'bca', 'BcaC05g25138' => 'bca', 'BcaC05g30416' => 'bca', 'BcaC05g30455' => 'bca', 'BcaC06g30979' => 'bca', 'BcaC06g33805' => 'bca', 'BcaC08g46021' => 'bca', 'BcaNung03154' => 'bca', 'BolC2t06623H' => 'bol', 'BolC2t06632H' => 'bol', 'BolC2t06635H' => 'bol', 'BolC2t06638H' => 'bol', 'BolC3t13266H' => 'bol', 'BolC5t29776H' => 'bol', 'BolC6t38912H' => 'bol', 'BolC7t44183H' => 'bol', 'BolC9t54123H' => 'bol', 'BolC9t59107H' => 'bol', 'BraA02t05221Z' => 'bra', 'BraA03t09996Z' => 'bra', 'BraA05t23210Z' => 'bra', 'BraA06t24068Z' => 'bra', 'BraA06t27032Z' => 'bra', 'BraA08t35176Z' => 'bra', 'BraA09t36680Z' => 'bra', 'BraA10t44471Z' => 'bra', 'C02p06760' => 'bna', 'C02p06890' => 'bna', 'C02p07010' => 'bna', 'C03p07660' => 'bna', 'C05p10300' => 'bna', 'C06p38150' => 'bna', 'C07p36650' => 'bna', 'C08p15770' => 'bna', 'C09p12300' => 'bna', 'C09p62700' => 'bna', 'C09p75040' => 'bna', 'CAN.G13.1' => 'can', 'CAN.G138.4' => 'can', 'CAN.G44.6' => 'can', 'CAN.G473.19' => 'can', 'CANSAT01G0835' => 'cansat', 'CANSAT11G0246' => 'cansat', 'CANSAT11G1766' => 'cansat', 'CANSAT64G1954' => 'cansat', 'CARHR013330' => 'chi', 'CARHR060530' => 'chi', 'CARHR075300' => 'chi', 'CARHR105120' => 'chi', 'CARHR148910' => 'chi', 'CARHR198830' => 'chi', 'Carub.0001s1275' => 'cru', 'Carub.0002s1437' => 'cru', 'Carub.0003s0044' => 'cru', 'Carub.0003s2787' => 'cru', 'Carub.0005s0597' => 'cru', 'Carub.0006s1266' => 'cru', 'Ca_06935_v3' => 'car', 'Ca_13559_v3' => 'car', 'Ca_16941_v3' => 'car', 'Ca_16960_v3' => 'car', 'Ca_17775_v3' => 'car', 'Ca_30464_v3' => 'car', 'Cc06_g08160' => 'ccan', 'Cc07_g01520' => 'ccan', 'Cc11_g15810' => 'ccan', 'CDE02G2840' => 'cde', 'CDE03G0093' => 'cde', 'CDE04G2127' => 'cde', 'CDE07G1857' => 'cde', 'CDE09G1246' => 'cde', 'Cfa003412' => 'cfa', 'Cfa007341' => 'cfa', 'Cfa009220' => 'cfa', 'Ciclev10008737m.g' => 'ccl', 'Ciclev10015565m.g' => 'ccl', 'Ciclev10031761m.g' => 'ccl', 'CiPaw.03G045300' => 'cil', 'CiPaw.03G247200' => 'cil', 'CiPaw.04G029500' => 'cil', 'CiPaw.04G174000' => 'cil', 'CiPaw.05G181200' => 'cil', 'CiPaw.06G067100' => 'cil', 'ClCG05G025800' => 'cla', 'ClCG06G011400' => 'cla', 'ClCG09G019360' => 'cla', 'COL.COLO4_04827' => 'col', 'COL.COLO4_29170' => 'col', 'COL.COLO4_35131' => 'col', 'COL.COLO4_35132' => 'col', 'Cpa.g.sc33.32' => 'cpa', 'Cpa.g.sc46.29' => 'cpa', 'Cpa.g.sc796.1' => 'cpa', 'CsaV3_1G030420' => 'csa', 'CsaV3_5G027050' => 'csa', 'CsaV3_5G031040' => 'csa', 'CsaV3_UNG023130' => 'csa', 'CSS0007726' => 'camsi', 'CSS0016433' => 'camsi', 'CSS0017656' => 'camsi', 'CSS0025364' => 'camsi', 'CSS0027582' => 'camsi', 'CSS0047288' => 'camsi', 'CSS0049950' => 'camsi', 'DCAR_003843' => 'dca', 'DCAR_007052' => 'dca', 'DCAR_020884' => 'dca', 'DCAR_021730' => 'dca', 'DCAR_024423' => 'dca', 'DCAR_026509' => 'dca', 'DCAR_031158' => 'dca', 'Dinv14728' => 'din', 'Dinv15219' => 'din', 'Dinv25728' => 'din', 'Dinv33428' => 'din', 'Dinv36489' => 'din', 'Dinv41486' => 'din', 'Duzib147G0469' => 'dzi', 'Duzib168G0060' => 'dzi', 'Duzib187G1215' => 'dzi', 'Duzib248G0692' => 'dzi', 'Duzib251G0767' => 'dzi', 'Duzib264G0446' => 'dzi', 'Duzib268G0691' => 'dzi', 'ECA232G4767' => 'eca', 'ECA233G2838' => 'eca', 'ECA234G0391' => 'eca', 'ECA234G0857' => 'eca', 'ECA236G1593' => 'eca', 'ECA238G0565' => 'eca', 'ECA246G1027' => 'eca', 'ECA246G3223' => 'eca', 'ECA246G3470' => 'eca', 'EL10Ac6g13829' => 'bvu', 'EL10Ac6g14093' => 'bvu', 'EL10Ac8g18707' => 'bvu', 'Eucgr.C01369' => 'egr', 'Eucgr.H02492' => 'egr', 'Eucgr.I01733' => 'egr', 'Eucgr.J02255' => 'egr', 'Eucgr.J02257' => 'egr', 'Eucgr.J02258' => 'egr', 'FAN02G1601' => 'fan', 'FAN03G1586' => 'fan', 'FAN03G2986' => 'fan', 'FAN05G4837' => 'fan', 'FAN06G0146' => 'fan', 'FAN07G0858' => 'fan', 'FAN09G3179' => 'fan', 'FAN10G0669' => 'fan', 'FAN12G2358' => 'fan', 'FAN14G4198' => 'fan', 'FAN14G5112' => 'fan', 'FAN17G0342' => 'fan', 'FAN19G0342' => 'fan', 'FAN19G0962' => 'fan', 'FAN19G1101' => 'fan', 'FAN19G1872' => 'fan', 'FAN22G0356' => 'fan', 'FAN23G0744' => 'fan', 'FAN23G1914' => 'fan', 'FAN26G0032' => 'fan', 'FAN28G0625' => 'fan', 'FvH4_1g02710' => 'fve', 'FvH4_1g02720' => 'fve', 'FvH4_4g25670' => 'fve', 'FvH4_6g51700' => 'fve', 'FvH4_7g20170' => 'fve', 'Glyma.05G175000' => 'gma', 'Glyma.08G132300' => 'gma', 'Glyma.11G243000' => 'gma', 'Glyma.13G158900' => 'gma', 'Glyma.17G112400' => 'gma', 'Glyma.18G014100' => 'gma', 'Glyma.19G003100' => 'gma', 'Glyma.19G056500' => 'gma', 'Gohir.A01G158900' => 'ghi', 'Gohir.A05G312600' => 'ghi', 'Gohir.A05G354900' => 'ghi', 'Gohir.A07G037200' => 'ghi', 'Gohir.A09G030000' => 'ghi', 'Gohir.A12G145200' => 'ghi', 'Gohir.D01G151500' => 'ghi', 'Gohir.D04G058300' => 'ghi', 'Gohir.D05G314100' => 'ghi', 'Gohir.D07G041400' => 'ghi', 'Gohir.D09G029700' => 'ghi', 'Gohir.D12G149700' => 'ghi', 'Gorai.001G043800' => 'gra', 'Gorai.002G187800' => 'gra', 'Gorai.006G034700' => 'gra', 'Gorai.008G161200' => 'gra', 'Gorai.009G335700' => 'gra', 'Gorai.012G065000' => 'gra', 'GSVIVG01000535001' => 'vvi', 'GSVIVG01015572001' => 'vvi', 'GSVIVG01032386001' => 'vvi', 'HanXRQChr05g0138531' => 'han', 'HanXRQChr06g0174391' => 'han', 'HanXRQChr07g0199021' => 'han', 'HanXRQChr08g0208211' => 'han', 'HanXRQChr09g0255471' => 'han', 'HanXRQChr10g0315791' => 'han', 'HanXRQChr12g0371991' => 'han', 'HanXRQChr15g0475251' => 'han', 'HanXRQChr17g0540001' => 'han', 'HanXRQChr17g0548631' => 'han', 'HanXRQChr17g0569561' => 'han', 'Haze_12256' => 'cav', 'Haze_14756' => 'cav', 'Haze_25528' => 'cav', 'Hma1.2p1_0079F.1_g041020' => 'hma', 'Hma1.2p1_0818F.1_g223260' => 'hma', 'Hma1.2p1_1747F.1_g300530' => 'hma', 'HPP92_004607' => 'vpl', 'HPP92_004608' => 'vpl', 'HPP92_006181' => 'vpl', 'HPP92_012192' => 'vpl', 'HPP92_015680' => 'vpl', 'HPP92_020249' => 'vpl', 'HPP92_021376' => 'vpl', 'HPP92_024275' => 'vpl', 'Hund06031' => 'sun', 'Hund25391' => 'sun', 'Lalb_Chr07g0185371' => 'lal', 'Lalb_Chr07g0185381' => 'lal', 'Lalb_Chr12g0204011' => 'lal', 'Lalb_Chr13g0301671' => 'lal', 'Lalb_Chr14g0362851' => 'lal', 'Lalb_Chr24g0403581' => 'lal', 'Lj1g0000233' => 'lja', 'Lj2g0018120' => 'lja', 'Lj3C621T0' => 'lonja', 'Lj3P1059T14' => 'lonja', 'Lj3P611T9' => 'lonja', 'Lj3P614T13' => 'lonja', 'Lj3P615T5' => 'lonja', 'Lj4g0012315' => 'lja', 'Lj4g0026182' => 'lja', 'Lj6P813T16' => 'lonja', 'Lj7C427T7' => 'lonja', 'Lj7C427T8' => 'lonja', 'Lj7P600T41' => 'lonja', 'Lju41C42G17' => 'lonja', 'Lsat_1_v5_gn_0_47300' => 'lsa', 'Lsat_1_v5_gn_2_91280' => 'lsa', 'Lsat_1_v5_gn_3_30561' => 'lsa', 'Lsat_1_v5_gn_4_184321' => 'lsa', 'Lsat_1_v5_gn_4_4041' => 'lsa', 'Lsat_1_v5_gn_5_92000' => 'lsa', 'Lsat_1_v5_gn_8_152940' => 'lsa', 'Lsat_1_v5_gn_8_62401' => 'lsa', 'Manes.06G055900' => 'mes', 'Manes.12G022200' => 'mes', 'Manes.13G023300' => 'mes', 'Manes.14G115000' => 'mes', 'Manes.15G151700' => 'mes', 'Manes.17G111300' => 'mes', 'Mapoly0226s0009' => 'mpo', 'MBI02_g25363_MAGBIO' => 'mbi', 'MBI06_g00027_MAGBIO' => 'mbi', 'MBI10_g13034_MAGBIO' => 'mbi', 'MD09G1023400' => 'mdo', 'MD13G1100100' => 'mdo', 'MD15G1169200' => 'mdo', 'MD16G1101100' => 'mdo', 'MD17G1022900' => 'mdo', 'Medtr3g096150' => 'mtr', 'Medtr4g115070' => 'mtr', 'Medtr7g033325' => 'mtr', 'Medtr8g089840' => 'mtr', 'MELO3C010319.2' => 'cme', 'MELO3C011944.2' => 'cme', 'MELO3C021589.2' => 'cme', 'Migut.E00207' => 'egut', 'Migut.H00067' => 'egut', 'Migut.K00433' => 'egut', 'Migut.K00606' => 'egut', 'Migut.K01410' => 'egut', 'MSTRG.13347' => 'ama', 'MSTRG.24045' => 'ama', 'MSTRG.2428' => 'ama', 'MSTRG.26410' => 'ama', 'MSTRG.3139' => 'ama', 'MSTRG.3286' => 'ama', 'MSTRG.563' => 'ama', 'MSTRG.7941' => 'ama', 'Nitab4.5_0000028g0060' => 'nta', 'Nitab4.5_0000065g0260' => 'nta', 'Nitab4.5_0000112g0060' => 'nta', 'Nitab4.5_0000489g0120' => 'nta', 'Nitab4.5_0001776g0050' => 'nta', 'Nitab4.5_0001854g0010' => 'nta', 'Nitab4.5_0001860g0020' => 'nta', 'Nitab4.5_0004352g0010' => 'nta', 'Nitab4.5_0008716g0020' => 'nta', 'Nitab4.5_0008922g0010' => 'nta', 'Nn3g16693' => 'nnu', 'Nn4g22596' => 'nnu', 'Nn7g37639' => 'nnu', 'Oeu001701.1' => 'oeu', 'Oeu018149.1' => 'oeu', 'Oeu026220.1' => 'oeu', 'Oeu038635.1' => 'oeu', 'Oeu049176.1' => 'oeu', 'Oeu056706.1' => 'oeu', 'Oeu056937.1' => 'oeu', 'Oeu057540.1' => 'oeu', 'Os02g0594900' => 'osa', 'Os02g0595100' => 'osa', 'Os04g0477500' => 'osa', 'Os12g0611900' => 'osa', 'Peaxi162Scf00076g00020' => 'pax', 'Peaxi162Scf00128g00217' => 'pax', 'Peaxi162Scf00129g01640' => 'pax', 'Peaxi162Scf00669g00007' => 'pax', 'Peaxi162Scf00700g00421' => 'pax', 'Peaxi162Scf00801g00038' => 'pax', 'Peaxi162Scf00891g00025' => 'pax', 'PGR083G0909' => 'pgr', 'PGR119G1005' => 'pgr', 'PGR142G2236' => 'pgr', 'PGR142G3388' => 'pgr', 'PGSC0003DMG400004514' => 'stu', 'PGSC0003DMG400012635' => 'stu', 'PGSC0003DMG400015730' => 'stu', 'PGSC0003DMG400018611' => 'stu', 'PGSC0003DMG400030897' => 'stu', 'Phvul.001G254800' => 'pvu', 'Phvul.002G260100' => 'pvu', 'Phvul.003G167600' => 'pvu', 'Phvul.004G005100' => 'pvu', 'Potri.001G343600' => 'ptr', 'Potri.006G066700' => 'ptr', 'Potri.008G186000' => 'ptr', 'Potri.010G046900' => 'ptr', 'Potri.018G127900' => 'ptr', 'Pp3c20_17750' => 'ppa', 'Pp3c24_4380' => 'ppa', 'Prupe.1G245800' => 'ppe', 'Prupe.3G293400' => 'ppe', 'Prupe.7G247400' => 'ppe', 'Psat0s145g0120' => 'psa', 'Psat0s595g0040' => 'psa', 'Psat0s595g0120' => 'psa', 'Psat3g175040' => 'psa', 'Psat7g058120' => 'psa', 'PSO017G0428' => 'pso', 'PSO063G7510' => 'pso', 'PSO067G0046' => 'pso', 'PSO478G1073' => 'pso', 'PSO675G3677' => 'pso', 'PSO675G6558' => 'pso', 'PSO675G7520' => 'pso', 'PSO675G8959' => 'pso', 'QL02p074089' => 'qlo', 'QL02p089614' => 'qlo', 'QL03p057736' => 'qlo', 'RcHm_v2.0_Chr1g0364131' => 'rch', 'RcHm_v2.0_Chr2g0087801' => 'rch', 'RcHm_v2.0_Chr2g0087821' => 'rch', 'RcHm_v2.0_Chr2g0173231' => 'rch', 'RcHm_v2.0_Chr4g0433111' => 'rch', 'Rhsim03G0250300' => 'rsi', 'Rhsim08G0048400' => 'rsi', 'Rhsim10G0014800' => 'rsi', 'Rhsim12G0040100' => 'rsi', 'Rhsim12G0109700' => 'rsi', 'Sabra06G0049600' => 'sbr', 'Sabra08G0141000' => 'sbr', 'Sabra10G0021400' => 'sbr', 'Sabra16G0222900' => 'sbr', 'Sabra18G0108600' => 'sbr', 'SalBow1G0433' => 'sbo', 'SalBow1G2038' => 'sbo', 'SalBow1G5003' => 'sbo', 'SalBow7G1197' => 'sbo', 'SalBow8G3506' => 'sbo', 'Sc03g0007300' => 'sci', 'Sc11g0000950' => 'sci', 'Sc14g0008750' => 'sci', 'Sc18g0000420' => 'sci', 'Sed0006754' => 'sed', 'Sed0008741' => 'sed', 'Sed0017172' => 'sed', 'Sed0018925' => 'sed', 'Sed0023326' => 'sed', 'Sed0025909' => 'sed', 'SEGI_05333' => 'sgi', 'SEGI_10362' => 'sgi', 'SEGI_13380' => 'sgi', 'SEGI_24306' => 'sgi', 'SEGI_29077' => 'sgi', 'SEGI_29095' => 'sgi', 'SEGI_36534' => 'sgi', 'SEGI_37506' => 'sgi', 'SEGI_38321' => 'sgi', 'SGA_v2.0_scaffold307G48031' => 'sas', 'SGA_v2.0_scaffold47G17507' => 'sas', 'SGA_v2.0_scaffold63G21736' => 'sas', 'SGA_v2.0_scaffold87G27070' => 'sas', 'SHI17794' => 'shi', 'SHI28851' => 'shi', 'SMO165G0155' => 'smo', 'SMO340G0217' => 'smo', 'SMO367G1210' => 'smo', 'Solyc02g093430.3' => 'sly', 'Solyc05g013580.4' => 'sly', 'Solyc07g008030.3' => 'sly', 'Solyc12g035470.2' => 'sly', 'Sopen02g038020' => 'spe', 'Sopen05g008490' => 'spe', 'Sopen07g003910' => 'spe', 'Sopen12g015240' => 'spe', 'Sp1g11550' => 'spa', 'Sp2g16710' => 'spa', 'Sp3g00430' => 'spa', 'Sp3g26780' => 'spa', 'Sp5g22900' => 'spa', 'Sp6g29530' => 'spa', 'TAR371G0794' => 'tar', 'TAR374G0164' => 'tar', 'TAR622G0165' => 'tar', 'TAR626G0929' => 'tar', 'TAR629G2155' => 'tar', 'THA.LOC104805282' => 'tha', 'THA.LOC104805363' => 'tha', 'THA.LOC104808968' => 'tha', 'THA.LOC104821093' => 'tha', 'THA.LOC104823953' => 'tha', 'THA.LOC104825562' => 'tha', 'THA.LOC104825665' => 'tha', 'Thecc.02G261400' => 'tca', 'Thecc.04G019200' => 'tca', 'Thecc.09G130400' => 'tca', 'Thhalv10004374m.g' => 'esa', 'Thhalv10007850m.g' => 'esa', 'Thhalv10013782m.g' => 'esa', 'Thhalv10018686m.g' => 'esa', 'Thhalv10020899m.g' => 'esa', 'Thhalv10022755m.g' => 'esa', 'TPR.G23851' => 'tpr', 'TPR.G26500' => 'tpr', 'TPR.G27267' => 'tpr', 'TPR.G32001' => 'tpr', 'TPR.G6251' => 'tpr', 'TPR.G8167' => 'tpr', 'TWI12G1330' => 'twi', 'TWI18G1239' => 'twi', 'TWI34G0979' => 'twi', 'TWI36G0670' => 'twi', 'TWI36G0707' => 'twi', 'TWI56G0233' => 'twi', 'TWI75G1809' => 'twi', 'unitig_21.g20874' => 'ugi', 'unitig_26.g10343' => 'ugi', 'unitig_46.g18392' => 'ugi', 'unitig_52.g17178' => 'ugi', 'unitig_8.g2934' => 'ugi', 'vmacro01122' => 'vma', 'vmacro05875' => 'vma', 'vmacro06147' => 'vma', 'vmacro16191' => 'vma', 'vmacro18293' => 'vma', 'VMungo0251G3707' => 'vmu', 'VMungo0464G1521' => 'vmu', 'VMungo1215G0205' => 'vmu', 'VMungo1383G2484' => 'vmu', 'Zm00001eb079610' => 'zma', 'Zm00001eb135990' => 'zma', 'Zm00001eb183710' => 'zma', 'Zm00001eb246020' => 'zma' ) $gf_id = 'HOM05D001124' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001124' ) $data_identifier = 'HOM05D001124' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 6, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 7, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 21, 'bol' => (int) 10, 'bra' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 6, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 9, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 21, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 8, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 10, 'lsa' => (int) 8, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 8, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 9, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb246020' $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' => 'HOM05D001124', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '548', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02520' => 'bna', 'A03p06630' => 'bna', 'A05p44460' => 'bna', 'A06p08710' => 'bna', 'A06p41090' => 'bna', 'A07p32320' => 'bna', 'A08p32520' => 'bna', 'A09p10360' => 'bna', 'A10p24080' => 'bna', 'Aa31LG11G15250' => 'aar', 'Aa31LG1G1800' => 'aar', 'Aa31LG2G5120' => 'aar', 'Aa31LG2G6070' => 'aar', 'Aa31LG5G10770' => 'aar', 'Aa31sc61G90' => 'aar', 'Actinidia01352' => 'ach', 'Actinidia05983' => 'ach', 'Actinidia08133' => 'ach', 'Actinidia15101' => 'ach', 'Actinidia26379' => 'ach', 'Actinidia35778' => 'ach', 'Actinidia36123' => 'ach', 'Actinidia37436' => 'ach', 'Actinidia38730' => 'ach', 'Ah.02g128210' => 'amhyb', 'Ah.03g132990' => 'amhyb', 'Ah.14g079410' => 'amhyb', 'AL1G24640' => 'aly', 'AL2G26680' => 'aly', 'AL3G10530' => 'aly', 'AL3G45230' => 'aly', 'AL5G15230' => 'aly', 'AL5G16960' => 'aly', 'AL6G25210' => 'aly', 'Aqoxy2G00441' => 'aox', 'Aqoxy3G01236' => 'aox', 'Aqoxy5G03746' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3RQ047' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C7GMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9C8JER' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MBL6KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YXCZ83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZANX40' => 'arhy', 'AT1G12990' => 'ath', 'AT1G67880' => 'ath', 'AT2G13290' => 'ath', 'AT3G01620' => 'ath', 'AT3G26445' => 'ath', 'AT3G27540' => 'ath', 'AT5G14480' => 'ath', 'ATR0824G026' => 'atr', 'ATR1098G019' => 'atr', 'Atru.chr11.2145' => 'acertr', 'Atru.chr2.3636' => 'acertr', 'Atru.chr2.3644' => 'acertr', 'Atru.chr6.2422' => 'acertr', 'Atru.chr7.1112' => 'acertr', 'AUR62005469' => 'cqu', 'AUR62011166' => 'cqu', 'AUR62013319' => 'cqu', 'AUR62024273' => 'cqu', 'AUR62028420' => 'cqu', 'AUR62041942' => 'cqu', 'BcaB01g04969' => 'bca', 'BcaB01g06371' => 'bca', 'BcaB02g11494' => 'bca', 'BcaB03g15382' => 'bca', 'BcaB08g36994' => 'bca', 'BcaC03g13477' => 'bca', 'BcaC03g13478' => 'bca', 'BcaC03g13480' => 'bca', 'BcaC03g13481' => 'bca', 'BcaC03g13486' => 'bca', 'BcaC04g19031' => 'bca', 'BcaC04g23085' => 'bca', 'BcaC05g25094' => 'bca', 'BcaC05g25096' => 'bca', 'BcaC05g25138' => 'bca', 'BcaC05g30416' => 'bca', 'BcaC05g30455' => 'bca', 'BcaC06g30979' => 'bca', 'BcaC06g33805' => 'bca', 'BcaC08g46021' => 'bca', 'BcaNung03154' => 'bca', 'BolC2t06623H' => 'bol', 'BolC2t06632H' => 'bol', 'BolC2t06635H' => 'bol', 'BolC2t06638H' => 'bol', 'BolC3t13266H' => 'bol', 'BolC5t29776H' => 'bol', 'BolC6t38912H' => 'bol', 'BolC7t44183H' => 'bol', 'BolC9t54123H' => 'bol', 'BolC9t59107H' => 'bol', 'BraA02t05221Z' => 'bra', 'BraA03t09996Z' => 'bra', 'BraA05t23210Z' => 'bra', 'BraA06t24068Z' => 'bra', 'BraA06t27032Z' => 'bra', 'BraA08t35176Z' => 'bra', 'BraA09t36680Z' => 'bra', 'BraA10t44471Z' => 'bra', 'C02p06760' => 'bna', 'C02p06890' => 'bna', 'C02p07010' => 'bna', 'C03p07660' => 'bna', 'C05p10300' => 'bna', 'C06p38150' => 'bna', 'C07p36650' => 'bna', 'C08p15770' => 'bna', 'C09p12300' => 'bna', 'C09p62700' => 'bna', 'C09p75040' => 'bna', 'CAN.G13.1' => 'can', 'CAN.G138.4' => 'can', 'CAN.G44.6' => 'can', 'CAN.G473.19' => 'can', 'CANSAT01G0835' => 'cansat', 'CANSAT11G0246' => 'cansat', 'CANSAT11G1766' => 'cansat', 'CANSAT64G1954' => 'cansat', 'CARHR013330' => 'chi', 'CARHR060530' => 'chi', 'CARHR075300' => 'chi', 'CARHR105120' => 'chi', 'CARHR148910' => 'chi', 'CARHR198830' => 'chi', 'Carub.0001s1275' => 'cru', 'Carub.0002s1437' => 'cru', 'Carub.0003s0044' => 'cru', 'Carub.0003s2787' => 'cru', 'Carub.0005s0597' => 'cru', 'Carub.0006s1266' => 'cru', 'Ca_06935_v3' => 'car', 'Ca_13559_v3' => 'car', 'Ca_16941_v3' => 'car', 'Ca_16960_v3' => 'car', 'Ca_17775_v3' => 'car', 'Ca_30464_v3' => 'car', 'Cc06_g08160' => 'ccan', 'Cc07_g01520' => 'ccan', 'Cc11_g15810' => 'ccan', 'CDE02G2840' => 'cde', 'CDE03G0093' => 'cde', 'CDE04G2127' => 'cde', 'CDE07G1857' => 'cde', 'CDE09G1246' => 'cde', 'Cfa003412' => 'cfa', 'Cfa007341' => 'cfa', 'Cfa009220' => 'cfa', 'Ciclev10008737m.g' => 'ccl', 'Ciclev10015565m.g' => 'ccl', 'Ciclev10031761m.g' => 'ccl', 'CiPaw.03G045300' => 'cil', 'CiPaw.03G247200' => 'cil', 'CiPaw.04G029500' => 'cil', 'CiPaw.04G174000' => 'cil', 'CiPaw.05G181200' => 'cil', 'CiPaw.06G067100' => 'cil', 'ClCG05G025800' => 'cla', 'ClCG06G011400' => 'cla', 'ClCG09G019360' => 'cla', 'COL.COLO4_04827' => 'col', 'COL.COLO4_29170' => 'col', 'COL.COLO4_35131' => 'col', 'COL.COLO4_35132' => 'col', 'Cpa.g.sc33.32' => 'cpa', 'Cpa.g.sc46.29' => 'cpa', 'Cpa.g.sc796.1' => 'cpa', 'CsaV3_1G030420' => 'csa', 'CsaV3_5G027050' => 'csa', 'CsaV3_5G031040' => 'csa', 'CsaV3_UNG023130' => 'csa', 'CSS0007726' => 'camsi', 'CSS0016433' => 'camsi', 'CSS0017656' => 'camsi', 'CSS0025364' => 'camsi', 'CSS0027582' => 'camsi', 'CSS0047288' => 'camsi', 'CSS0049950' => 'camsi', 'DCAR_003843' => 'dca', 'DCAR_007052' => 'dca', 'DCAR_020884' => 'dca', 'DCAR_021730' => 'dca', 'DCAR_024423' => 'dca', 'DCAR_026509' => 'dca', 'DCAR_031158' => 'dca', 'Dinv14728' => 'din', 'Dinv15219' => 'din', 'Dinv25728' => 'din', 'Dinv33428' => 'din', 'Dinv36489' => 'din', 'Dinv41486' => 'din', 'Duzib147G0469' => 'dzi', 'Duzib168G0060' => 'dzi', 'Duzib187G1215' => 'dzi', 'Duzib248G0692' => 'dzi', 'Duzib251G0767' => 'dzi', 'Duzib264G0446' => 'dzi', 'Duzib268G0691' => 'dzi', 'ECA232G4767' => 'eca', 'ECA233G2838' => 'eca', 'ECA234G0391' => 'eca', 'ECA234G0857' => 'eca', 'ECA236G1593' => 'eca', 'ECA238G0565' => 'eca', 'ECA246G1027' => 'eca', 'ECA246G3223' => 'eca', 'ECA246G3470' => 'eca', 'EL10Ac6g13829' => 'bvu', 'EL10Ac6g14093' => 'bvu', 'EL10Ac8g18707' => 'bvu', 'Eucgr.C01369' => 'egr', 'Eucgr.H02492' => 'egr', 'Eucgr.I01733' => 'egr', 'Eucgr.J02255' => 'egr', 'Eucgr.J02257' => 'egr', 'Eucgr.J02258' => 'egr', 'FAN02G1601' => 'fan', 'FAN03G1586' => 'fan', 'FAN03G2986' => 'fan', 'FAN05G4837' => 'fan', 'FAN06G0146' => 'fan', 'FAN07G0858' => 'fan', 'FAN09G3179' => 'fan', 'FAN10G0669' => 'fan', 'FAN12G2358' => 'fan', 'FAN14G4198' => 'fan', 'FAN14G5112' => 'fan', 'FAN17G0342' => 'fan', 'FAN19G0342' => 'fan', 'FAN19G0962' => 'fan', 'FAN19G1101' => 'fan', 'FAN19G1872' => 'fan', 'FAN22G0356' => 'fan', 'FAN23G0744' => 'fan', 'FAN23G1914' => 'fan', 'FAN26G0032' => 'fan', 'FAN28G0625' => 'fan', 'FvH4_1g02710' => 'fve', 'FvH4_1g02720' => 'fve', 'FvH4_4g25670' => 'fve', 'FvH4_6g51700' => 'fve', 'FvH4_7g20170' => 'fve', 'Glyma.05G175000' => 'gma', 'Glyma.08G132300' => 'gma', 'Glyma.11G243000' => 'gma', 'Glyma.13G158900' => 'gma', 'Glyma.17G112400' => 'gma', 'Glyma.18G014100' => 'gma', 'Glyma.19G003100' => 'gma', 'Glyma.19G056500' => 'gma', 'Gohir.A01G158900' => 'ghi', 'Gohir.A05G312600' => 'ghi', 'Gohir.A05G354900' => 'ghi', 'Gohir.A07G037200' => 'ghi', 'Gohir.A09G030000' => 'ghi', 'Gohir.A12G145200' => 'ghi', 'Gohir.D01G151500' => 'ghi', 'Gohir.D04G058300' => 'ghi', 'Gohir.D05G314100' => 'ghi', 'Gohir.D07G041400' => 'ghi', 'Gohir.D09G029700' => 'ghi', 'Gohir.D12G149700' => 'ghi', 'Gorai.001G043800' => 'gra', 'Gorai.002G187800' => 'gra', 'Gorai.006G034700' => 'gra', 'Gorai.008G161200' => 'gra', 'Gorai.009G335700' => 'gra', 'Gorai.012G065000' => 'gra', 'GSVIVG01000535001' => 'vvi', 'GSVIVG01015572001' => 'vvi', 'GSVIVG01032386001' => 'vvi', 'HanXRQChr05g0138531' => 'han', 'HanXRQChr06g0174391' => 'han', 'HanXRQChr07g0199021' => 'han', 'HanXRQChr08g0208211' => 'han', 'HanXRQChr09g0255471' => 'han', 'HanXRQChr10g0315791' => 'han', 'HanXRQChr12g0371991' => 'han', 'HanXRQChr15g0475251' => 'han', 'HanXRQChr17g0540001' => 'han', 'HanXRQChr17g0548631' => 'han', 'HanXRQChr17g0569561' => 'han', 'Haze_12256' => 'cav', 'Haze_14756' => 'cav', 'Haze_25528' => 'cav', 'Hma1.2p1_0079F.1_g041020' => 'hma', 'Hma1.2p1_0818F.1_g223260' => 'hma', 'Hma1.2p1_1747F.1_g300530' => 'hma', 'HPP92_004607' => 'vpl', 'HPP92_004608' => 'vpl', 'HPP92_006181' => 'vpl', 'HPP92_012192' => 'vpl', 'HPP92_015680' => 'vpl', 'HPP92_020249' => 'vpl', 'HPP92_021376' => 'vpl', 'HPP92_024275' => 'vpl', 'Hund06031' => 'sun', 'Hund25391' => 'sun', 'Lalb_Chr07g0185371' => 'lal', 'Lalb_Chr07g0185381' => 'lal', 'Lalb_Chr12g0204011' => 'lal', 'Lalb_Chr13g0301671' => 'lal', 'Lalb_Chr14g0362851' => 'lal', 'Lalb_Chr24g0403581' => 'lal', 'Lj1g0000233' => 'lja', 'Lj2g0018120' => 'lja', 'Lj3C621T0' => 'lonja', 'Lj3P1059T14' => 'lonja', 'Lj3P611T9' => 'lonja', 'Lj3P614T13' => 'lonja', 'Lj3P615T5' => 'lonja', 'Lj4g0012315' => 'lja', 'Lj4g0026182' => 'lja', 'Lj6P813T16' => 'lonja', 'Lj7C427T7' => 'lonja', 'Lj7C427T8' => 'lonja', 'Lj7P600T41' => 'lonja', 'Lju41C42G17' => 'lonja', 'Lsat_1_v5_gn_0_47300' => 'lsa', 'Lsat_1_v5_gn_2_91280' => 'lsa', 'Lsat_1_v5_gn_3_30561' => 'lsa', 'Lsat_1_v5_gn_4_184321' => 'lsa', 'Lsat_1_v5_gn_4_4041' => 'lsa', 'Lsat_1_v5_gn_5_92000' => 'lsa', 'Lsat_1_v5_gn_8_152940' => 'lsa', 'Lsat_1_v5_gn_8_62401' => 'lsa', 'Manes.06G055900' => 'mes', 'Manes.12G022200' => 'mes', 'Manes.13G023300' => 'mes', 'Manes.14G115000' => 'mes', 'Manes.15G151700' => 'mes', 'Manes.17G111300' => 'mes', 'Mapoly0226s0009' => 'mpo', 'MBI02_g25363_MAGBIO' => 'mbi', 'MBI06_g00027_MAGBIO' => 'mbi', 'MBI10_g13034_MAGBIO' => 'mbi', 'MD09G1023400' => 'mdo', 'MD13G1100100' => 'mdo', 'MD15G1169200' => 'mdo', 'MD16G1101100' => 'mdo', 'MD17G1022900' => 'mdo', 'Medtr3g096150' => 'mtr', 'Medtr4g115070' => 'mtr', 'Medtr7g033325' => 'mtr', 'Medtr8g089840' => 'mtr', 'MELO3C010319.2' => 'cme', 'MELO3C011944.2' => 'cme', 'MELO3C021589.2' => 'cme', 'Migut.E00207' => 'egut', 'Migut.H00067' => 'egut', 'Migut.K00433' => 'egut', 'Migut.K00606' => 'egut', 'Migut.K01410' => 'egut', 'MSTRG.13347' => 'ama', 'MSTRG.24045' => 'ama', 'MSTRG.2428' => 'ama', 'MSTRG.26410' => 'ama', 'MSTRG.3139' => 'ama', 'MSTRG.3286' => 'ama', 'MSTRG.563' => 'ama', 'MSTRG.7941' => 'ama', 'Nitab4.5_0000028g0060' => 'nta', 'Nitab4.5_0000065g0260' => 'nta', 'Nitab4.5_0000112g0060' => 'nta', 'Nitab4.5_0000489g0120' => 'nta', 'Nitab4.5_0001776g0050' => 'nta', 'Nitab4.5_0001854g0010' => 'nta', 'Nitab4.5_0001860g0020' => 'nta', 'Nitab4.5_0004352g0010' => 'nta', 'Nitab4.5_0008716g0020' => 'nta', 'Nitab4.5_0008922g0010' => 'nta', 'Nn3g16693' => 'nnu', 'Nn4g22596' => 'nnu', 'Nn7g37639' => 'nnu', 'Oeu001701.1' => 'oeu', 'Oeu018149.1' => 'oeu', 'Oeu026220.1' => 'oeu', 'Oeu038635.1' => 'oeu', 'Oeu049176.1' => 'oeu', 'Oeu056706.1' => 'oeu', 'Oeu056937.1' => 'oeu', 'Oeu057540.1' => 'oeu', 'Os02g0594900' => 'osa', 'Os02g0595100' => 'osa', 'Os04g0477500' => 'osa', 'Os12g0611900' => 'osa', 'Peaxi162Scf00076g00020' => 'pax', 'Peaxi162Scf00128g00217' => 'pax', 'Peaxi162Scf00129g01640' => 'pax', 'Peaxi162Scf00669g00007' => 'pax', 'Peaxi162Scf00700g00421' => 'pax', 'Peaxi162Scf00801g00038' => 'pax', 'Peaxi162Scf00891g00025' => 'pax', 'PGR083G0909' => 'pgr', 'PGR119G1005' => 'pgr', 'PGR142G2236' => 'pgr', 'PGR142G3388' => 'pgr', 'PGSC0003DMG400004514' => 'stu', 'PGSC0003DMG400012635' => 'stu', 'PGSC0003DMG400015730' => 'stu', 'PGSC0003DMG400018611' => 'stu', 'PGSC0003DMG400030897' => 'stu', 'Phvul.001G254800' => 'pvu', 'Phvul.002G260100' => 'pvu', 'Phvul.003G167600' => 'pvu', 'Phvul.004G005100' => 'pvu', 'Potri.001G343600' => 'ptr', 'Potri.006G066700' => 'ptr', 'Potri.008G186000' => 'ptr', 'Potri.010G046900' => 'ptr', 'Potri.018G127900' => 'ptr', 'Pp3c20_17750' => 'ppa', 'Pp3c24_4380' => 'ppa', 'Prupe.1G245800' => 'ppe', 'Prupe.3G293400' => 'ppe', 'Prupe.7G247400' => 'ppe', 'Psat0s145g0120' => 'psa', 'Psat0s595g0040' => 'psa', 'Psat0s595g0120' => 'psa', 'Psat3g175040' => 'psa', 'Psat7g058120' => 'psa', 'PSO017G0428' => 'pso', 'PSO063G7510' => 'pso', 'PSO067G0046' => 'pso', 'PSO478G1073' => 'pso', 'PSO675G3677' => 'pso', 'PSO675G6558' => 'pso', 'PSO675G7520' => 'pso', 'PSO675G8959' => 'pso', 'QL02p074089' => 'qlo', 'QL02p089614' => 'qlo', 'QL03p057736' => 'qlo', 'RcHm_v2.0_Chr1g0364131' => 'rch', 'RcHm_v2.0_Chr2g0087801' => 'rch', 'RcHm_v2.0_Chr2g0087821' => 'rch', 'RcHm_v2.0_Chr2g0173231' => 'rch', 'RcHm_v2.0_Chr4g0433111' => 'rch', 'Rhsim03G0250300' => 'rsi', 'Rhsim08G0048400' => 'rsi', 'Rhsim10G0014800' => 'rsi', 'Rhsim12G0040100' => 'rsi', 'Rhsim12G0109700' => 'rsi', 'Sabra06G0049600' => 'sbr', 'Sabra08G0141000' => 'sbr', 'Sabra10G0021400' => 'sbr', 'Sabra16G0222900' => 'sbr', 'Sabra18G0108600' => 'sbr', 'SalBow1G0433' => 'sbo', 'SalBow1G2038' => 'sbo', 'SalBow1G5003' => 'sbo', 'SalBow7G1197' => 'sbo', 'SalBow8G3506' => 'sbo', 'Sc03g0007300' => 'sci', 'Sc11g0000950' => 'sci', 'Sc14g0008750' => 'sci', 'Sc18g0000420' => 'sci', 'Sed0006754' => 'sed', 'Sed0008741' => 'sed', 'Sed0017172' => 'sed', 'Sed0018925' => 'sed', 'Sed0023326' => 'sed', 'Sed0025909' => 'sed', 'SEGI_05333' => 'sgi', 'SEGI_10362' => 'sgi', 'SEGI_13380' => 'sgi', 'SEGI_24306' => 'sgi', 'SEGI_29077' => 'sgi', 'SEGI_29095' => 'sgi', 'SEGI_36534' => 'sgi', 'SEGI_37506' => 'sgi', 'SEGI_38321' => 'sgi', 'SGA_v2.0_scaffold307G48031' => 'sas', 'SGA_v2.0_scaffold47G17507' => 'sas', 'SGA_v2.0_scaffold63G21736' => 'sas', 'SGA_v2.0_scaffold87G27070' => 'sas', 'SHI17794' => 'shi', 'SHI28851' => 'shi', 'SMO165G0155' => 'smo', 'SMO340G0217' => 'smo', 'SMO367G1210' => 'smo', 'Solyc02g093430.3' => 'sly', 'Solyc05g013580.4' => 'sly', 'Solyc07g008030.3' => 'sly', 'Solyc12g035470.2' => 'sly', 'Sopen02g038020' => 'spe', 'Sopen05g008490' => 'spe', 'Sopen07g003910' => 'spe', 'Sopen12g015240' => 'spe', 'Sp1g11550' => 'spa', 'Sp2g16710' => 'spa', 'Sp3g00430' => 'spa', 'Sp3g26780' => 'spa', 'Sp5g22900' => 'spa', 'Sp6g29530' => 'spa', 'TAR371G0794' => 'tar', 'TAR374G0164' => 'tar', 'TAR622G0165' => 'tar', 'TAR626G0929' => 'tar', 'TAR629G2155' => 'tar', 'THA.LOC104805282' => 'tha', 'THA.LOC104805363' => 'tha', 'THA.LOC104808968' => 'tha', 'THA.LOC104821093' => 'tha', 'THA.LOC104823953' => 'tha', 'THA.LOC104825562' => 'tha', 'THA.LOC104825665' => 'tha', 'Thecc.02G261400' => 'tca', 'Thecc.04G019200' => 'tca', 'Thecc.09G130400' => 'tca', 'Thhalv10004374m.g' => 'esa', 'Thhalv10007850m.g' => 'esa', 'Thhalv10013782m.g' => 'esa', 'Thhalv10018686m.g' => 'esa', 'Thhalv10020899m.g' => 'esa', 'Thhalv10022755m.g' => 'esa', 'TPR.G23851' => 'tpr', 'TPR.G26500' => 'tpr', 'TPR.G27267' => 'tpr', 'TPR.G32001' => 'tpr', 'TPR.G6251' => 'tpr', 'TPR.G8167' => 'tpr', 'TWI12G1330' => 'twi', 'TWI18G1239' => 'twi', 'TWI34G0979' => 'twi', 'TWI36G0670' => 'twi', 'TWI36G0707' => 'twi', 'TWI56G0233' => 'twi', 'TWI75G1809' => 'twi', 'unitig_21.g20874' => 'ugi', 'unitig_26.g10343' => 'ugi', 'unitig_46.g18392' => 'ugi', 'unitig_52.g17178' => 'ugi', 'unitig_8.g2934' => 'ugi', 'vmacro01122' => 'vma', 'vmacro05875' => 'vma', 'vmacro06147' => 'vma', 'vmacro16191' => 'vma', 'vmacro18293' => 'vma', 'VMungo0251G3707' => 'vmu', 'VMungo0464G1521' => 'vmu', 'VMungo1215G0205' => 'vmu', 'VMungo1383G2484' => 'vmu', 'Zm00001eb079610' => 'zma', 'Zm00001eb135990' => 'zma', 'Zm00001eb183710' => 'zma', 'Zm00001eb246020' => 'zma' ), 'gf_id' => 'HOM05D001124', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001124' ), 'data_identifier' => 'HOM05D001124', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001124', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '548', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02520' => 'bna', 'A03p06630' => 'bna', 'A05p44460' => 'bna', 'A06p08710' => 'bna', 'A06p41090' => 'bna', 'A07p32320' => 'bna', 'A08p32520' => 'bna', 'A09p10360' => 'bna', 'A10p24080' => 'bna', 'Aa31LG11G15250' => 'aar', 'Aa31LG1G1800' => 'aar', 'Aa31LG2G5120' => 'aar', 'Aa31LG2G6070' => 'aar', 'Aa31LG5G10770' => 'aar', 'Aa31sc61G90' => 'aar', 'Actinidia01352' => 'ach', 'Actinidia05983' => 'ach', 'Actinidia08133' => 'ach', 'Actinidia15101' => 'ach', 'Actinidia26379' => 'ach', 'Actinidia35778' => 'ach', 'Actinidia36123' => 'ach', 'Actinidia37436' => 'ach', 'Actinidia38730' => 'ach', 'Ah.02g128210' => 'amhyb', 'Ah.03g132990' => 'amhyb', 'Ah.14g079410' => 'amhyb', 'AL1G24640' => 'aly', 'AL2G26680' => 'aly', 'AL3G10530' => 'aly', 'AL3G45230' => 'aly', 'AL5G15230' => 'aly', 'AL5G16960' => 'aly', 'AL6G25210' => 'aly', 'Aqoxy2G00441' => 'aox', 'Aqoxy3G01236' => 'aox', 'Aqoxy5G03746' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3RQ047' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C7GMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9C8JER' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MBL6KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YXCZ83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZANX40' => 'arhy', 'AT1G12990' => 'ath', 'AT1G67880' => 'ath', 'AT2G13290' => 'ath', 'AT3G01620' => 'ath', 'AT3G26445' => 'ath', 'AT3G27540' => 'ath', 'AT5G14480' => 'ath', 'ATR0824G026' => 'atr', 'ATR1098G019' => 'atr', 'Atru.chr11.2145' => 'acertr', 'Atru.chr2.3636' => 'acertr', 'Atru.chr2.3644' => 'acertr', 'Atru.chr6.2422' => 'acertr', 'Atru.chr7.1112' => 'acertr', 'AUR62005469' => 'cqu', 'AUR62011166' => 'cqu', 'AUR62013319' => 'cqu', 'AUR62024273' => 'cqu', 'AUR62028420' => 'cqu', 'AUR62041942' => 'cqu', 'BcaB01g04969' => 'bca', 'BcaB01g06371' => 'bca', 'BcaB02g11494' => 'bca', 'BcaB03g15382' => 'bca', 'BcaB08g36994' => 'bca', 'BcaC03g13477' => 'bca', 'BcaC03g13478' => 'bca', 'BcaC03g13480' => 'bca', 'BcaC03g13481' => 'bca', 'BcaC03g13486' => 'bca', 'BcaC04g19031' => 'bca', 'BcaC04g23085' => 'bca', 'BcaC05g25094' => 'bca', 'BcaC05g25096' => 'bca', 'BcaC05g25138' => 'bca', 'BcaC05g30416' => 'bca', 'BcaC05g30455' => 'bca', 'BcaC06g30979' => 'bca', 'BcaC06g33805' => 'bca', 'BcaC08g46021' => 'bca', 'BcaNung03154' => 'bca', 'BolC2t06623H' => 'bol', 'BolC2t06632H' => 'bol', 'BolC2t06635H' => 'bol', 'BolC2t06638H' => 'bol', 'BolC3t13266H' => 'bol', 'BolC5t29776H' => 'bol', 'BolC6t38912H' => 'bol', 'BolC7t44183H' => 'bol', 'BolC9t54123H' => 'bol', 'BolC9t59107H' => 'bol', 'BraA02t05221Z' => 'bra', 'BraA03t09996Z' => 'bra', 'BraA05t23210Z' => 'bra', 'BraA06t24068Z' => 'bra', 'BraA06t27032Z' => 'bra', 'BraA08t35176Z' => 'bra', 'BraA09t36680Z' => 'bra', 'BraA10t44471Z' => 'bra', 'C02p06760' => 'bna', 'C02p06890' => 'bna', 'C02p07010' => 'bna', 'C03p07660' => 'bna', 'C05p10300' => 'bna', 'C06p38150' => 'bna', 'C07p36650' => 'bna', 'C08p15770' => 'bna', 'C09p12300' => 'bna', 'C09p62700' => 'bna', 'C09p75040' => 'bna', 'CAN.G13.1' => 'can', 'CAN.G138.4' => 'can', 'CAN.G44.6' => 'can', 'CAN.G473.19' => 'can', 'CANSAT01G0835' => 'cansat', 'CANSAT11G0246' => 'cansat', 'CANSAT11G1766' => 'cansat', 'CANSAT64G1954' => 'cansat', 'CARHR013330' => 'chi', 'CARHR060530' => 'chi', 'CARHR075300' => 'chi', 'CARHR105120' => 'chi', 'CARHR148910' => 'chi', 'CARHR198830' => 'chi', 'Carub.0001s1275' => 'cru', 'Carub.0002s1437' => 'cru', 'Carub.0003s0044' => 'cru', 'Carub.0003s2787' => 'cru', 'Carub.0005s0597' => 'cru', 'Carub.0006s1266' => 'cru', 'Ca_06935_v3' => 'car', 'Ca_13559_v3' => 'car', 'Ca_16941_v3' => 'car', 'Ca_16960_v3' => 'car', 'Ca_17775_v3' => 'car', 'Ca_30464_v3' => 'car', 'Cc06_g08160' => 'ccan', 'Cc07_g01520' => 'ccan', 'Cc11_g15810' => 'ccan', 'CDE02G2840' => 'cde', 'CDE03G0093' => 'cde', 'CDE04G2127' => 'cde', 'CDE07G1857' => 'cde', 'CDE09G1246' => 'cde', 'Cfa003412' => 'cfa', 'Cfa007341' => 'cfa', 'Cfa009220' => 'cfa', 'Ciclev10008737m.g' => 'ccl', 'Ciclev10015565m.g' => 'ccl', 'Ciclev10031761m.g' => 'ccl', 'CiPaw.03G045300' => 'cil', 'CiPaw.03G247200' => 'cil', 'CiPaw.04G029500' => 'cil', 'CiPaw.04G174000' => 'cil', 'CiPaw.05G181200' => 'cil', 'CiPaw.06G067100' => 'cil', 'ClCG05G025800' => 'cla', 'ClCG06G011400' => 'cla', 'ClCG09G019360' => 'cla', 'COL.COLO4_04827' => 'col', 'COL.COLO4_29170' => 'col', 'COL.COLO4_35131' => 'col', 'COL.COLO4_35132' => 'col', 'Cpa.g.sc33.32' => 'cpa', 'Cpa.g.sc46.29' => 'cpa', 'Cpa.g.sc796.1' => 'cpa', 'CsaV3_1G030420' => 'csa', 'CsaV3_5G027050' => 'csa', 'CsaV3_5G031040' => 'csa', 'CsaV3_UNG023130' => 'csa', 'CSS0007726' => 'camsi', 'CSS0016433' => 'camsi', 'CSS0017656' => 'camsi', 'CSS0025364' => 'camsi', 'CSS0027582' => 'camsi', 'CSS0047288' => 'camsi', 'CSS0049950' => 'camsi', 'DCAR_003843' => 'dca', 'DCAR_007052' => 'dca', 'DCAR_020884' => 'dca', 'DCAR_021730' => 'dca', 'DCAR_024423' => 'dca', 'DCAR_026509' => 'dca', 'DCAR_031158' => 'dca', 'Dinv14728' => 'din', 'Dinv15219' => 'din', 'Dinv25728' => 'din', 'Dinv33428' => 'din', 'Dinv36489' => 'din', 'Dinv41486' => 'din', 'Duzib147G0469' => 'dzi', 'Duzib168G0060' => 'dzi', 'Duzib187G1215' => 'dzi', 'Duzib248G0692' => 'dzi', 'Duzib251G0767' => 'dzi', 'Duzib264G0446' => 'dzi', 'Duzib268G0691' => 'dzi', 'ECA232G4767' => 'eca', 'ECA233G2838' => 'eca', 'ECA234G0391' => 'eca', 'ECA234G0857' => 'eca', 'ECA236G1593' => 'eca', 'ECA238G0565' => 'eca', 'ECA246G1027' => 'eca', 'ECA246G3223' => 'eca', 'ECA246G3470' => 'eca', 'EL10Ac6g13829' => 'bvu', 'EL10Ac6g14093' => 'bvu', 'EL10Ac8g18707' => 'bvu', 'Eucgr.C01369' => 'egr', 'Eucgr.H02492' => 'egr', 'Eucgr.I01733' => 'egr', 'Eucgr.J02255' => 'egr', 'Eucgr.J02257' => 'egr', 'Eucgr.J02258' => 'egr', 'FAN02G1601' => 'fan', 'FAN03G1586' => 'fan', 'FAN03G2986' => 'fan', 'FAN05G4837' => 'fan', 'FAN06G0146' => 'fan', 'FAN07G0858' => 'fan', 'FAN09G3179' => 'fan', 'FAN10G0669' => 'fan', 'FAN12G2358' => 'fan', 'FAN14G4198' => 'fan', 'FAN14G5112' => 'fan', 'FAN17G0342' => 'fan', 'FAN19G0342' => 'fan', 'FAN19G0962' => 'fan', 'FAN19G1101' => 'fan', 'FAN19G1872' => 'fan', 'FAN22G0356' => 'fan', 'FAN23G0744' => 'fan', 'FAN23G1914' => 'fan', 'FAN26G0032' => 'fan', 'FAN28G0625' => 'fan', 'FvH4_1g02710' => 'fve', 'FvH4_1g02720' => 'fve', 'FvH4_4g25670' => 'fve', 'FvH4_6g51700' => 'fve', 'FvH4_7g20170' => 'fve', 'Glyma.05G175000' => 'gma', 'Glyma.08G132300' => 'gma', 'Glyma.11G243000' => 'gma', 'Glyma.13G158900' => 'gma', 'Glyma.17G112400' => 'gma', 'Glyma.18G014100' => 'gma', 'Glyma.19G003100' => 'gma', 'Glyma.19G056500' => 'gma', 'Gohir.A01G158900' => 'ghi', 'Gohir.A05G312600' => 'ghi', 'Gohir.A05G354900' => 'ghi', 'Gohir.A07G037200' => 'ghi', 'Gohir.A09G030000' => 'ghi', 'Gohir.A12G145200' => 'ghi', 'Gohir.D01G151500' => 'ghi', 'Gohir.D04G058300' => 'ghi', 'Gohir.D05G314100' => 'ghi', 'Gohir.D07G041400' => 'ghi', 'Gohir.D09G029700' => 'ghi', 'Gohir.D12G149700' => 'ghi', 'Gorai.001G043800' => 'gra', 'Gorai.002G187800' => 'gra', 'Gorai.006G034700' => 'gra', 'Gorai.008G161200' => 'gra', 'Gorai.009G335700' => 'gra', 'Gorai.012G065000' => 'gra', 'GSVIVG01000535001' => 'vvi', 'GSVIVG01015572001' => 'vvi', 'GSVIVG01032386001' => 'vvi', 'HanXRQChr05g0138531' => 'han', 'HanXRQChr06g0174391' => 'han', 'HanXRQChr07g0199021' => 'han', 'HanXRQChr08g0208211' => 'han', 'HanXRQChr09g0255471' => 'han', 'HanXRQChr10g0315791' => 'han', 'HanXRQChr12g0371991' => 'han', 'HanXRQChr15g0475251' => 'han', 'HanXRQChr17g0540001' => 'han', 'HanXRQChr17g0548631' => 'han', 'HanXRQChr17g0569561' => 'han', 'Haze_12256' => 'cav', 'Haze_14756' => 'cav', 'Haze_25528' => 'cav', 'Hma1.2p1_0079F.1_g041020' => 'hma', 'Hma1.2p1_0818F.1_g223260' => 'hma', 'Hma1.2p1_1747F.1_g300530' => 'hma', 'HPP92_004607' => 'vpl', 'HPP92_004608' => 'vpl', 'HPP92_006181' => 'vpl', 'HPP92_012192' => 'vpl', 'HPP92_015680' => 'vpl', 'HPP92_020249' => 'vpl', 'HPP92_021376' => 'vpl', 'HPP92_024275' => 'vpl', 'Hund06031' => 'sun', 'Hund25391' => 'sun', 'Lalb_Chr07g0185371' => 'lal', 'Lalb_Chr07g0185381' => 'lal', 'Lalb_Chr12g0204011' => 'lal', 'Lalb_Chr13g0301671' => 'lal', 'Lalb_Chr14g0362851' => 'lal', 'Lalb_Chr24g0403581' => 'lal', 'Lj1g0000233' => 'lja', 'Lj2g0018120' => 'lja', 'Lj3C621T0' => 'lonja', 'Lj3P1059T14' => 'lonja', 'Lj3P611T9' => 'lonja', 'Lj3P614T13' => 'lonja', 'Lj3P615T5' => 'lonja', 'Lj4g0012315' => 'lja', 'Lj4g0026182' => 'lja', 'Lj6P813T16' => 'lonja', 'Lj7C427T7' => 'lonja', 'Lj7C427T8' => 'lonja', 'Lj7P600T41' => 'lonja', 'Lju41C42G17' => 'lonja', 'Lsat_1_v5_gn_0_47300' => 'lsa', 'Lsat_1_v5_gn_2_91280' => 'lsa', 'Lsat_1_v5_gn_3_30561' => 'lsa', 'Lsat_1_v5_gn_4_184321' => 'lsa', 'Lsat_1_v5_gn_4_4041' => 'lsa', 'Lsat_1_v5_gn_5_92000' => 'lsa', 'Lsat_1_v5_gn_8_152940' => 'lsa', 'Lsat_1_v5_gn_8_62401' => 'lsa', 'Manes.06G055900' => 'mes', 'Manes.12G022200' => 'mes', 'Manes.13G023300' => 'mes', 'Manes.14G115000' => 'mes', 'Manes.15G151700' => 'mes', 'Manes.17G111300' => 'mes', 'Mapoly0226s0009' => 'mpo', 'MBI02_g25363_MAGBIO' => 'mbi', 'MBI06_g00027_MAGBIO' => 'mbi', 'MBI10_g13034_MAGBIO' => 'mbi', 'MD09G1023400' => 'mdo', 'MD13G1100100' => 'mdo', 'MD15G1169200' => 'mdo', 'MD16G1101100' => 'mdo', 'MD17G1022900' => 'mdo', 'Medtr3g096150' => 'mtr', 'Medtr4g115070' => 'mtr', 'Medtr7g033325' => 'mtr', 'Medtr8g089840' => 'mtr', 'MELO3C010319.2' => 'cme', 'MELO3C011944.2' => 'cme', 'MELO3C021589.2' => 'cme', 'Migut.E00207' => 'egut', 'Migut.H00067' => 'egut', 'Migut.K00433' => 'egut', 'Migut.K00606' => 'egut', 'Migut.K01410' => 'egut', 'MSTRG.13347' => 'ama', 'MSTRG.24045' => 'ama', 'MSTRG.2428' => 'ama', 'MSTRG.26410' => 'ama', 'MSTRG.3139' => 'ama', 'MSTRG.3286' => 'ama', 'MSTRG.563' => 'ama', 'MSTRG.7941' => 'ama', 'Nitab4.5_0000028g0060' => 'nta', 'Nitab4.5_0000065g0260' => 'nta', 'Nitab4.5_0000112g0060' => 'nta', 'Nitab4.5_0000489g0120' => 'nta', 'Nitab4.5_0001776g0050' => 'nta', 'Nitab4.5_0001854g0010' => 'nta', 'Nitab4.5_0001860g0020' => 'nta', 'Nitab4.5_0004352g0010' => 'nta', 'Nitab4.5_0008716g0020' => 'nta', 'Nitab4.5_0008922g0010' => 'nta', 'Nn3g16693' => 'nnu', 'Nn4g22596' => 'nnu', 'Nn7g37639' => 'nnu', 'Oeu001701.1' => 'oeu', 'Oeu018149.1' => 'oeu', 'Oeu026220.1' => 'oeu', 'Oeu038635.1' => 'oeu', 'Oeu049176.1' => 'oeu', 'Oeu056706.1' => 'oeu', 'Oeu056937.1' => 'oeu', 'Oeu057540.1' => 'oeu', 'Os02g0594900' => 'osa', 'Os02g0595100' => 'osa', 'Os04g0477500' => 'osa', 'Os12g0611900' => 'osa', 'Peaxi162Scf00076g00020' => 'pax', 'Peaxi162Scf00128g00217' => 'pax', 'Peaxi162Scf00129g01640' => 'pax', 'Peaxi162Scf00669g00007' => 'pax', 'Peaxi162Scf00700g00421' => 'pax', 'Peaxi162Scf00801g00038' => 'pax', 'Peaxi162Scf00891g00025' => 'pax', 'PGR083G0909' => 'pgr', 'PGR119G1005' => 'pgr', 'PGR142G2236' => 'pgr', 'PGR142G3388' => 'pgr', 'PGSC0003DMG400004514' => 'stu', 'PGSC0003DMG400012635' => 'stu', 'PGSC0003DMG400015730' => 'stu', 'PGSC0003DMG400018611' => 'stu', 'PGSC0003DMG400030897' => 'stu', 'Phvul.001G254800' => 'pvu', 'Phvul.002G260100' => 'pvu', 'Phvul.003G167600' => 'pvu', 'Phvul.004G005100' => 'pvu', 'Potri.001G343600' => 'ptr', 'Potri.006G066700' => 'ptr', 'Potri.008G186000' => 'ptr', 'Potri.010G046900' => 'ptr', 'Potri.018G127900' => 'ptr', 'Pp3c20_17750' => 'ppa', 'Pp3c24_4380' => 'ppa', 'Prupe.1G245800' => 'ppe', 'Prupe.3G293400' => 'ppe', 'Prupe.7G247400' => 'ppe', 'Psat0s145g0120' => 'psa', 'Psat0s595g0040' => 'psa', 'Psat0s595g0120' => 'psa', 'Psat3g175040' => 'psa', 'Psat7g058120' => 'psa', 'PSO017G0428' => 'pso', 'PSO063G7510' => 'pso', 'PSO067G0046' => 'pso', 'PSO478G1073' => 'pso', 'PSO675G3677' => 'pso', 'PSO675G6558' => 'pso', 'PSO675G7520' => 'pso', 'PSO675G8959' => 'pso', 'QL02p074089' => 'qlo', 'QL02p089614' => 'qlo', 'QL03p057736' => 'qlo', 'RcHm_v2.0_Chr1g0364131' => 'rch', 'RcHm_v2.0_Chr2g0087801' => 'rch', 'RcHm_v2.0_Chr2g0087821' => 'rch', 'RcHm_v2.0_Chr2g0173231' => 'rch', 'RcHm_v2.0_Chr4g0433111' => 'rch', 'Rhsim03G0250300' => 'rsi', 'Rhsim08G0048400' => 'rsi', 'Rhsim10G0014800' => 'rsi', 'Rhsim12G0040100' => 'rsi', 'Rhsim12G0109700' => 'rsi', 'Sabra06G0049600' => 'sbr', 'Sabra08G0141000' => 'sbr', 'Sabra10G0021400' => 'sbr', 'Sabra16G0222900' => 'sbr', 'Sabra18G0108600' => 'sbr', 'SalBow1G0433' => 'sbo', 'SalBow1G2038' => 'sbo', 'SalBow1G5003' => 'sbo', 'SalBow7G1197' => 'sbo', 'SalBow8G3506' => 'sbo', 'Sc03g0007300' => 'sci', 'Sc11g0000950' => 'sci', 'Sc14g0008750' => 'sci', 'Sc18g0000420' => 'sci', 'Sed0006754' => 'sed', 'Sed0008741' => 'sed', 'Sed0017172' => 'sed', 'Sed0018925' => 'sed', 'Sed0023326' => 'sed', 'Sed0025909' => 'sed', 'SEGI_05333' => 'sgi', 'SEGI_10362' => 'sgi', 'SEGI_13380' => 'sgi', 'SEGI_24306' => 'sgi', 'SEGI_29077' => 'sgi', 'SEGI_29095' => 'sgi', 'SEGI_36534' => 'sgi', 'SEGI_37506' => 'sgi', 'SEGI_38321' => 'sgi', 'SGA_v2.0_scaffold307G48031' => 'sas', 'SGA_v2.0_scaffold47G17507' => 'sas', 'SGA_v2.0_scaffold63G21736' => 'sas', 'SGA_v2.0_scaffold87G27070' => 'sas', 'SHI17794' => 'shi', 'SHI28851' => 'shi', 'SMO165G0155' => 'smo', 'SMO340G0217' => 'smo', 'SMO367G1210' => 'smo', 'Solyc02g093430.3' => 'sly', 'Solyc05g013580.4' => 'sly', 'Solyc07g008030.3' => 'sly', 'Solyc12g035470.2' => 'sly', 'Sopen02g038020' => 'spe', 'Sopen05g008490' => 'spe', 'Sopen07g003910' => 'spe', 'Sopen12g015240' => 'spe', 'Sp1g11550' => 'spa', 'Sp2g16710' => 'spa', 'Sp3g00430' => 'spa', 'Sp3g26780' => 'spa', 'Sp5g22900' => 'spa', 'Sp6g29530' => 'spa', 'TAR371G0794' => 'tar', 'TAR374G0164' => 'tar', 'TAR622G0165' => 'tar', 'TAR626G0929' => 'tar', 'TAR629G2155' => 'tar', 'THA.LOC104805282' => 'tha', 'THA.LOC104805363' => 'tha', 'THA.LOC104808968' => 'tha', 'THA.LOC104821093' => 'tha', 'THA.LOC104823953' => 'tha', 'THA.LOC104825562' => 'tha', 'THA.LOC104825665' => 'tha', 'Thecc.02G261400' => 'tca', 'Thecc.04G019200' => 'tca', 'Thecc.09G130400' => 'tca', 'Thhalv10004374m.g' => 'esa', 'Thhalv10007850m.g' => 'esa', 'Thhalv10013782m.g' => 'esa', 'Thhalv10018686m.g' => 'esa', 'Thhalv10020899m.g' => 'esa', 'Thhalv10022755m.g' => 'esa', 'TPR.G23851' => 'tpr', 'TPR.G26500' => 'tpr', 'TPR.G27267' => 'tpr', 'TPR.G32001' => 'tpr', 'TPR.G6251' => 'tpr', 'TPR.G8167' => 'tpr', 'TWI12G1330' => 'twi', 'TWI18G1239' => 'twi', 'TWI34G0979' => 'twi', 'TWI36G0670' => 'twi', 'TWI36G0707' => 'twi', 'TWI56G0233' => 'twi', 'TWI75G1809' => 'twi', 'unitig_21.g20874' => 'ugi', 'unitig_26.g10343' => 'ugi', 'unitig_46.g18392' => 'ugi', 'unitig_52.g17178' => 'ugi', 'unitig_8.g2934' => 'ugi', 'vmacro01122' => 'vma', 'vmacro05875' => 'vma', 'vmacro06147' => 'vma', 'vmacro16191' => 'vma', 'vmacro18293' => 'vma', 'VMungo0251G3707' => 'vmu', 'VMungo0464G1521' => 'vmu', 'VMungo1215G0205' => 'vmu', 'VMungo1383G2484' => 'vmu', 'Zm00001eb079610' => 'zma', 'Zm00001eb135990' => 'zma', 'Zm00001eb183710' => 'zma', 'Zm00001eb246020' => 'zma' ) $gf_id = 'HOM05D001124' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001124' ) $data_identifier = 'HOM05D001124' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 6, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 7, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 21, 'bol' => (int) 10, 'bra' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 6, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 9, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 21, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 8, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 10, 'lsa' => (int) 8, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 8, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 9, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb246020' $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' => 'HOM05D001124', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '548', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02520' => 'bna', 'A03p06630' => 'bna', 'A05p44460' => 'bna', 'A06p08710' => 'bna', 'A06p41090' => 'bna', 'A07p32320' => 'bna', 'A08p32520' => 'bna', 'A09p10360' => 'bna', 'A10p24080' => 'bna', 'Aa31LG11G15250' => 'aar', 'Aa31LG1G1800' => 'aar', 'Aa31LG2G5120' => 'aar', 'Aa31LG2G6070' => 'aar', 'Aa31LG5G10770' => 'aar', 'Aa31sc61G90' => 'aar', 'Actinidia01352' => 'ach', 'Actinidia05983' => 'ach', 'Actinidia08133' => 'ach', 'Actinidia15101' => 'ach', 'Actinidia26379' => 'ach', 'Actinidia35778' => 'ach', 'Actinidia36123' => 'ach', 'Actinidia37436' => 'ach', 'Actinidia38730' => 'ach', 'Ah.02g128210' => 'amhyb', 'Ah.03g132990' => 'amhyb', 'Ah.14g079410' => 'amhyb', 'AL1G24640' => 'aly', 'AL2G26680' => 'aly', 'AL3G10530' => 'aly', 'AL3G45230' => 'aly', 'AL5G15230' => 'aly', 'AL5G16960' => 'aly', 'AL6G25210' => 'aly', 'Aqoxy2G00441' => 'aox', 'Aqoxy3G01236' => 'aox', 'Aqoxy5G03746' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3RQ047' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C7GMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9C8JER' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MBL6KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YXCZ83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZANX40' => 'arhy', 'AT1G12990' => 'ath', 'AT1G67880' => 'ath', 'AT2G13290' => 'ath', 'AT3G01620' => 'ath', 'AT3G26445' => 'ath', 'AT3G27540' => 'ath', 'AT5G14480' => 'ath', 'ATR0824G026' => 'atr', 'ATR1098G019' => 'atr', 'Atru.chr11.2145' => 'acertr', 'Atru.chr2.3636' => 'acertr', 'Atru.chr2.3644' => 'acertr', 'Atru.chr6.2422' => 'acertr', 'Atru.chr7.1112' => 'acertr', 'AUR62005469' => 'cqu', 'AUR62011166' => 'cqu', 'AUR62013319' => 'cqu', 'AUR62024273' => 'cqu', 'AUR62028420' => 'cqu', 'AUR62041942' => 'cqu', 'BcaB01g04969' => 'bca', 'BcaB01g06371' => 'bca', 'BcaB02g11494' => 'bca', 'BcaB03g15382' => 'bca', 'BcaB08g36994' => 'bca', 'BcaC03g13477' => 'bca', 'BcaC03g13478' => 'bca', 'BcaC03g13480' => 'bca', 'BcaC03g13481' => 'bca', 'BcaC03g13486' => 'bca', 'BcaC04g19031' => 'bca', 'BcaC04g23085' => 'bca', 'BcaC05g25094' => 'bca', 'BcaC05g25096' => 'bca', 'BcaC05g25138' => 'bca', 'BcaC05g30416' => 'bca', 'BcaC05g30455' => 'bca', 'BcaC06g30979' => 'bca', 'BcaC06g33805' => 'bca', 'BcaC08g46021' => 'bca', 'BcaNung03154' => 'bca', 'BolC2t06623H' => 'bol', 'BolC2t06632H' => 'bol', 'BolC2t06635H' => 'bol', 'BolC2t06638H' => 'bol', 'BolC3t13266H' => 'bol', 'BolC5t29776H' => 'bol', 'BolC6t38912H' => 'bol', 'BolC7t44183H' => 'bol', 'BolC9t54123H' => 'bol', 'BolC9t59107H' => 'bol', 'BraA02t05221Z' => 'bra', 'BraA03t09996Z' => 'bra', 'BraA05t23210Z' => 'bra', 'BraA06t24068Z' => 'bra', 'BraA06t27032Z' => 'bra', 'BraA08t35176Z' => 'bra', 'BraA09t36680Z' => 'bra', 'BraA10t44471Z' => 'bra', 'C02p06760' => 'bna', 'C02p06890' => 'bna', 'C02p07010' => 'bna', 'C03p07660' => 'bna', 'C05p10300' => 'bna', 'C06p38150' => 'bna', 'C07p36650' => 'bna', 'C08p15770' => 'bna', 'C09p12300' => 'bna', 'C09p62700' => 'bna', 'C09p75040' => 'bna', 'CAN.G13.1' => 'can', 'CAN.G138.4' => 'can', 'CAN.G44.6' => 'can', 'CAN.G473.19' => 'can', 'CANSAT01G0835' => 'cansat', 'CANSAT11G0246' => 'cansat', 'CANSAT11G1766' => 'cansat', 'CANSAT64G1954' => 'cansat', 'CARHR013330' => 'chi', 'CARHR060530' => 'chi', 'CARHR075300' => 'chi', 'CARHR105120' => 'chi', 'CARHR148910' => 'chi', 'CARHR198830' => 'chi', 'Carub.0001s1275' => 'cru', 'Carub.0002s1437' => 'cru', 'Carub.0003s0044' => 'cru', 'Carub.0003s2787' => 'cru', 'Carub.0005s0597' => 'cru', 'Carub.0006s1266' => 'cru', 'Ca_06935_v3' => 'car', 'Ca_13559_v3' => 'car', 'Ca_16941_v3' => 'car', 'Ca_16960_v3' => 'car', 'Ca_17775_v3' => 'car', 'Ca_30464_v3' => 'car', 'Cc06_g08160' => 'ccan', 'Cc07_g01520' => 'ccan', 'Cc11_g15810' => 'ccan', 'CDE02G2840' => 'cde', 'CDE03G0093' => 'cde', 'CDE04G2127' => 'cde', 'CDE07G1857' => 'cde', 'CDE09G1246' => 'cde', 'Cfa003412' => 'cfa', 'Cfa007341' => 'cfa', 'Cfa009220' => 'cfa', 'Ciclev10008737m.g' => 'ccl', 'Ciclev10015565m.g' => 'ccl', 'Ciclev10031761m.g' => 'ccl', 'CiPaw.03G045300' => 'cil', 'CiPaw.03G247200' => 'cil', 'CiPaw.04G029500' => 'cil', 'CiPaw.04G174000' => 'cil', 'CiPaw.05G181200' => 'cil', 'CiPaw.06G067100' => 'cil', 'ClCG05G025800' => 'cla', 'ClCG06G011400' => 'cla', 'ClCG09G019360' => 'cla', 'COL.COLO4_04827' => 'col', 'COL.COLO4_29170' => 'col', 'COL.COLO4_35131' => 'col', 'COL.COLO4_35132' => 'col', 'Cpa.g.sc33.32' => 'cpa', 'Cpa.g.sc46.29' => 'cpa', 'Cpa.g.sc796.1' => 'cpa', 'CsaV3_1G030420' => 'csa', 'CsaV3_5G027050' => 'csa', 'CsaV3_5G031040' => 'csa', 'CsaV3_UNG023130' => 'csa', 'CSS0007726' => 'camsi', 'CSS0016433' => 'camsi', 'CSS0017656' => 'camsi', 'CSS0025364' => 'camsi', 'CSS0027582' => 'camsi', 'CSS0047288' => 'camsi', 'CSS0049950' => 'camsi', 'DCAR_003843' => 'dca', 'DCAR_007052' => 'dca', 'DCAR_020884' => 'dca', 'DCAR_021730' => 'dca', 'DCAR_024423' => 'dca', 'DCAR_026509' => 'dca', 'DCAR_031158' => 'dca', 'Dinv14728' => 'din', 'Dinv15219' => 'din', 'Dinv25728' => 'din', 'Dinv33428' => 'din', 'Dinv36489' => 'din', 'Dinv41486' => 'din', 'Duzib147G0469' => 'dzi', 'Duzib168G0060' => 'dzi', 'Duzib187G1215' => 'dzi', 'Duzib248G0692' => 'dzi', 'Duzib251G0767' => 'dzi', 'Duzib264G0446' => 'dzi', 'Duzib268G0691' => 'dzi', 'ECA232G4767' => 'eca', 'ECA233G2838' => 'eca', 'ECA234G0391' => 'eca', 'ECA234G0857' => 'eca', 'ECA236G1593' => 'eca', 'ECA238G0565' => 'eca', 'ECA246G1027' => 'eca', 'ECA246G3223' => 'eca', 'ECA246G3470' => 'eca', 'EL10Ac6g13829' => 'bvu', 'EL10Ac6g14093' => 'bvu', 'EL10Ac8g18707' => 'bvu', 'Eucgr.C01369' => 'egr', 'Eucgr.H02492' => 'egr', 'Eucgr.I01733' => 'egr', 'Eucgr.J02255' => 'egr', 'Eucgr.J02257' => 'egr', 'Eucgr.J02258' => 'egr', 'FAN02G1601' => 'fan', 'FAN03G1586' => 'fan', 'FAN03G2986' => 'fan', 'FAN05G4837' => 'fan', 'FAN06G0146' => 'fan', 'FAN07G0858' => 'fan', 'FAN09G3179' => 'fan', 'FAN10G0669' => 'fan', 'FAN12G2358' => 'fan', 'FAN14G4198' => 'fan', 'FAN14G5112' => 'fan', 'FAN17G0342' => 'fan', 'FAN19G0342' => 'fan', 'FAN19G0962' => 'fan', 'FAN19G1101' => 'fan', 'FAN19G1872' => 'fan', 'FAN22G0356' => 'fan', 'FAN23G0744' => 'fan', 'FAN23G1914' => 'fan', 'FAN26G0032' => 'fan', 'FAN28G0625' => 'fan', 'FvH4_1g02710' => 'fve', 'FvH4_1g02720' => 'fve', 'FvH4_4g25670' => 'fve', 'FvH4_6g51700' => 'fve', 'FvH4_7g20170' => 'fve', 'Glyma.05G175000' => 'gma', 'Glyma.08G132300' => 'gma', 'Glyma.11G243000' => 'gma', 'Glyma.13G158900' => 'gma', 'Glyma.17G112400' => 'gma', 'Glyma.18G014100' => 'gma', 'Glyma.19G003100' => 'gma', 'Glyma.19G056500' => 'gma', 'Gohir.A01G158900' => 'ghi', 'Gohir.A05G312600' => 'ghi', 'Gohir.A05G354900' => 'ghi', 'Gohir.A07G037200' => 'ghi', 'Gohir.A09G030000' => 'ghi', 'Gohir.A12G145200' => 'ghi', 'Gohir.D01G151500' => 'ghi', 'Gohir.D04G058300' => 'ghi', 'Gohir.D05G314100' => 'ghi', 'Gohir.D07G041400' => 'ghi', 'Gohir.D09G029700' => 'ghi', 'Gohir.D12G149700' => 'ghi', 'Gorai.001G043800' => 'gra', 'Gorai.002G187800' => 'gra', 'Gorai.006G034700' => 'gra', 'Gorai.008G161200' => 'gra', 'Gorai.009G335700' => 'gra', 'Gorai.012G065000' => 'gra', 'GSVIVG01000535001' => 'vvi', 'GSVIVG01015572001' => 'vvi', 'GSVIVG01032386001' => 'vvi', 'HanXRQChr05g0138531' => 'han', 'HanXRQChr06g0174391' => 'han', 'HanXRQChr07g0199021' => 'han', 'HanXRQChr08g0208211' => 'han', 'HanXRQChr09g0255471' => 'han', 'HanXRQChr10g0315791' => 'han', 'HanXRQChr12g0371991' => 'han', 'HanXRQChr15g0475251' => 'han', 'HanXRQChr17g0540001' => 'han', 'HanXRQChr17g0548631' => 'han', 'HanXRQChr17g0569561' => 'han', 'Haze_12256' => 'cav', 'Haze_14756' => 'cav', 'Haze_25528' => 'cav', 'Hma1.2p1_0079F.1_g041020' => 'hma', 'Hma1.2p1_0818F.1_g223260' => 'hma', 'Hma1.2p1_1747F.1_g300530' => 'hma', 'HPP92_004607' => 'vpl', 'HPP92_004608' => 'vpl', 'HPP92_006181' => 'vpl', 'HPP92_012192' => 'vpl', 'HPP92_015680' => 'vpl', 'HPP92_020249' => 'vpl', 'HPP92_021376' => 'vpl', 'HPP92_024275' => 'vpl', 'Hund06031' => 'sun', 'Hund25391' => 'sun', 'Lalb_Chr07g0185371' => 'lal', 'Lalb_Chr07g0185381' => 'lal', 'Lalb_Chr12g0204011' => 'lal', 'Lalb_Chr13g0301671' => 'lal', 'Lalb_Chr14g0362851' => 'lal', 'Lalb_Chr24g0403581' => 'lal', 'Lj1g0000233' => 'lja', 'Lj2g0018120' => 'lja', 'Lj3C621T0' => 'lonja', 'Lj3P1059T14' => 'lonja', 'Lj3P611T9' => 'lonja', 'Lj3P614T13' => 'lonja', 'Lj3P615T5' => 'lonja', 'Lj4g0012315' => 'lja', 'Lj4g0026182' => 'lja', 'Lj6P813T16' => 'lonja', 'Lj7C427T7' => 'lonja', 'Lj7C427T8' => 'lonja', 'Lj7P600T41' => 'lonja', 'Lju41C42G17' => 'lonja', 'Lsat_1_v5_gn_0_47300' => 'lsa', 'Lsat_1_v5_gn_2_91280' => 'lsa', 'Lsat_1_v5_gn_3_30561' => 'lsa', 'Lsat_1_v5_gn_4_184321' => 'lsa', 'Lsat_1_v5_gn_4_4041' => 'lsa', 'Lsat_1_v5_gn_5_92000' => 'lsa', 'Lsat_1_v5_gn_8_152940' => 'lsa', 'Lsat_1_v5_gn_8_62401' => 'lsa', 'Manes.06G055900' => 'mes', 'Manes.12G022200' => 'mes', 'Manes.13G023300' => 'mes', 'Manes.14G115000' => 'mes', 'Manes.15G151700' => 'mes', 'Manes.17G111300' => 'mes', 'Mapoly0226s0009' => 'mpo', 'MBI02_g25363_MAGBIO' => 'mbi', 'MBI06_g00027_MAGBIO' => 'mbi', 'MBI10_g13034_MAGBIO' => 'mbi', 'MD09G1023400' => 'mdo', 'MD13G1100100' => 'mdo', 'MD15G1169200' => 'mdo', 'MD16G1101100' => 'mdo', 'MD17G1022900' => 'mdo', 'Medtr3g096150' => 'mtr', 'Medtr4g115070' => 'mtr', 'Medtr7g033325' => 'mtr', 'Medtr8g089840' => 'mtr', 'MELO3C010319.2' => 'cme', 'MELO3C011944.2' => 'cme', 'MELO3C021589.2' => 'cme', 'Migut.E00207' => 'egut', 'Migut.H00067' => 'egut', 'Migut.K00433' => 'egut', 'Migut.K00606' => 'egut', 'Migut.K01410' => 'egut', 'MSTRG.13347' => 'ama', 'MSTRG.24045' => 'ama', 'MSTRG.2428' => 'ama', 'MSTRG.26410' => 'ama', 'MSTRG.3139' => 'ama', 'MSTRG.3286' => 'ama', 'MSTRG.563' => 'ama', 'MSTRG.7941' => 'ama', 'Nitab4.5_0000028g0060' => 'nta', 'Nitab4.5_0000065g0260' => 'nta', 'Nitab4.5_0000112g0060' => 'nta', 'Nitab4.5_0000489g0120' => 'nta', 'Nitab4.5_0001776g0050' => 'nta', 'Nitab4.5_0001854g0010' => 'nta', 'Nitab4.5_0001860g0020' => 'nta', 'Nitab4.5_0004352g0010' => 'nta', 'Nitab4.5_0008716g0020' => 'nta', 'Nitab4.5_0008922g0010' => 'nta', 'Nn3g16693' => 'nnu', 'Nn4g22596' => 'nnu', 'Nn7g37639' => 'nnu', 'Oeu001701.1' => 'oeu', 'Oeu018149.1' => 'oeu', 'Oeu026220.1' => 'oeu', 'Oeu038635.1' => 'oeu', 'Oeu049176.1' => 'oeu', 'Oeu056706.1' => 'oeu', 'Oeu056937.1' => 'oeu', 'Oeu057540.1' => 'oeu', 'Os02g0594900' => 'osa', 'Os02g0595100' => 'osa', 'Os04g0477500' => 'osa', 'Os12g0611900' => 'osa', 'Peaxi162Scf00076g00020' => 'pax', 'Peaxi162Scf00128g00217' => 'pax', 'Peaxi162Scf00129g01640' => 'pax', 'Peaxi162Scf00669g00007' => 'pax', 'Peaxi162Scf00700g00421' => 'pax', 'Peaxi162Scf00801g00038' => 'pax', 'Peaxi162Scf00891g00025' => 'pax', 'PGR083G0909' => 'pgr', 'PGR119G1005' => 'pgr', 'PGR142G2236' => 'pgr', 'PGR142G3388' => 'pgr', 'PGSC0003DMG400004514' => 'stu', 'PGSC0003DMG400012635' => 'stu', 'PGSC0003DMG400015730' => 'stu', 'PGSC0003DMG400018611' => 'stu', 'PGSC0003DMG400030897' => 'stu', 'Phvul.001G254800' => 'pvu', 'Phvul.002G260100' => 'pvu', 'Phvul.003G167600' => 'pvu', 'Phvul.004G005100' => 'pvu', 'Potri.001G343600' => 'ptr', 'Potri.006G066700' => 'ptr', 'Potri.008G186000' => 'ptr', 'Potri.010G046900' => 'ptr', 'Potri.018G127900' => 'ptr', 'Pp3c20_17750' => 'ppa', 'Pp3c24_4380' => 'ppa', 'Prupe.1G245800' => 'ppe', 'Prupe.3G293400' => 'ppe', 'Prupe.7G247400' => 'ppe', 'Psat0s145g0120' => 'psa', 'Psat0s595g0040' => 'psa', 'Psat0s595g0120' => 'psa', 'Psat3g175040' => 'psa', 'Psat7g058120' => 'psa', 'PSO017G0428' => 'pso', 'PSO063G7510' => 'pso', 'PSO067G0046' => 'pso', 'PSO478G1073' => 'pso', 'PSO675G3677' => 'pso', 'PSO675G6558' => 'pso', 'PSO675G7520' => 'pso', 'PSO675G8959' => 'pso', 'QL02p074089' => 'qlo', 'QL02p089614' => 'qlo', 'QL03p057736' => 'qlo', 'RcHm_v2.0_Chr1g0364131' => 'rch', 'RcHm_v2.0_Chr2g0087801' => 'rch', 'RcHm_v2.0_Chr2g0087821' => 'rch', 'RcHm_v2.0_Chr2g0173231' => 'rch', 'RcHm_v2.0_Chr4g0433111' => 'rch', 'Rhsim03G0250300' => 'rsi', 'Rhsim08G0048400' => 'rsi', 'Rhsim10G0014800' => 'rsi', 'Rhsim12G0040100' => 'rsi', 'Rhsim12G0109700' => 'rsi', 'Sabra06G0049600' => 'sbr', 'Sabra08G0141000' => 'sbr', 'Sabra10G0021400' => 'sbr', 'Sabra16G0222900' => 'sbr', 'Sabra18G0108600' => 'sbr', 'SalBow1G0433' => 'sbo', 'SalBow1G2038' => 'sbo', 'SalBow1G5003' => 'sbo', 'SalBow7G1197' => 'sbo', 'SalBow8G3506' => 'sbo', 'Sc03g0007300' => 'sci', 'Sc11g0000950' => 'sci', 'Sc14g0008750' => 'sci', 'Sc18g0000420' => 'sci', 'Sed0006754' => 'sed', 'Sed0008741' => 'sed', 'Sed0017172' => 'sed', 'Sed0018925' => 'sed', 'Sed0023326' => 'sed', 'Sed0025909' => 'sed', 'SEGI_05333' => 'sgi', 'SEGI_10362' => 'sgi', 'SEGI_13380' => 'sgi', 'SEGI_24306' => 'sgi', 'SEGI_29077' => 'sgi', 'SEGI_29095' => 'sgi', 'SEGI_36534' => 'sgi', 'SEGI_37506' => 'sgi', 'SEGI_38321' => 'sgi', 'SGA_v2.0_scaffold307G48031' => 'sas', 'SGA_v2.0_scaffold47G17507' => 'sas', 'SGA_v2.0_scaffold63G21736' => 'sas', 'SGA_v2.0_scaffold87G27070' => 'sas', 'SHI17794' => 'shi', 'SHI28851' => 'shi', 'SMO165G0155' => 'smo', 'SMO340G0217' => 'smo', 'SMO367G1210' => 'smo', 'Solyc02g093430.3' => 'sly', 'Solyc05g013580.4' => 'sly', 'Solyc07g008030.3' => 'sly', 'Solyc12g035470.2' => 'sly', 'Sopen02g038020' => 'spe', 'Sopen05g008490' => 'spe', 'Sopen07g003910' => 'spe', 'Sopen12g015240' => 'spe', 'Sp1g11550' => 'spa', 'Sp2g16710' => 'spa', 'Sp3g00430' => 'spa', 'Sp3g26780' => 'spa', 'Sp5g22900' => 'spa', 'Sp6g29530' => 'spa', 'TAR371G0794' => 'tar', 'TAR374G0164' => 'tar', 'TAR622G0165' => 'tar', 'TAR626G0929' => 'tar', 'TAR629G2155' => 'tar', 'THA.LOC104805282' => 'tha', 'THA.LOC104805363' => 'tha', 'THA.LOC104808968' => 'tha', 'THA.LOC104821093' => 'tha', 'THA.LOC104823953' => 'tha', 'THA.LOC104825562' => 'tha', 'THA.LOC104825665' => 'tha', 'Thecc.02G261400' => 'tca', 'Thecc.04G019200' => 'tca', 'Thecc.09G130400' => 'tca', 'Thhalv10004374m.g' => 'esa', 'Thhalv10007850m.g' => 'esa', 'Thhalv10013782m.g' => 'esa', 'Thhalv10018686m.g' => 'esa', 'Thhalv10020899m.g' => 'esa', 'Thhalv10022755m.g' => 'esa', 'TPR.G23851' => 'tpr', 'TPR.G26500' => 'tpr', 'TPR.G27267' => 'tpr', 'TPR.G32001' => 'tpr', 'TPR.G6251' => 'tpr', 'TPR.G8167' => 'tpr', 'TWI12G1330' => 'twi', 'TWI18G1239' => 'twi', 'TWI34G0979' => 'twi', 'TWI36G0670' => 'twi', 'TWI36G0707' => 'twi', 'TWI56G0233' => 'twi', 'TWI75G1809' => 'twi', 'unitig_21.g20874' => 'ugi', 'unitig_26.g10343' => 'ugi', 'unitig_46.g18392' => 'ugi', 'unitig_52.g17178' => 'ugi', 'unitig_8.g2934' => 'ugi', 'vmacro01122' => 'vma', 'vmacro05875' => 'vma', 'vmacro06147' => 'vma', 'vmacro16191' => 'vma', 'vmacro18293' => 'vma', 'VMungo0251G3707' => 'vmu', 'VMungo0464G1521' => 'vmu', 'VMungo1215G0205' => 'vmu', 'VMungo1383G2484' => 'vmu', 'Zm00001eb079610' => 'zma', 'Zm00001eb135990' => 'zma', 'Zm00001eb183710' => 'zma', 'Zm00001eb246020' => 'zma' ), 'gf_id' => 'HOM05D001124', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001124' ), 'data_identifier' => 'HOM05D001124', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001124', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '548', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02520' => 'bna', 'A03p06630' => 'bna', 'A05p44460' => 'bna', 'A06p08710' => 'bna', 'A06p41090' => 'bna', 'A07p32320' => 'bna', 'A08p32520' => 'bna', 'A09p10360' => 'bna', 'A10p24080' => 'bna', 'Aa31LG11G15250' => 'aar', 'Aa31LG1G1800' => 'aar', 'Aa31LG2G5120' => 'aar', 'Aa31LG2G6070' => 'aar', 'Aa31LG5G10770' => 'aar', 'Aa31sc61G90' => 'aar', 'Actinidia01352' => 'ach', 'Actinidia05983' => 'ach', 'Actinidia08133' => 'ach', 'Actinidia15101' => 'ach', 'Actinidia26379' => 'ach', 'Actinidia35778' => 'ach', 'Actinidia36123' => 'ach', 'Actinidia37436' => 'ach', 'Actinidia38730' => 'ach', 'Ah.02g128210' => 'amhyb', 'Ah.03g132990' => 'amhyb', 'Ah.14g079410' => 'amhyb', 'AL1G24640' => 'aly', 'AL2G26680' => 'aly', 'AL3G10530' => 'aly', 'AL3G45230' => 'aly', 'AL5G15230' => 'aly', 'AL5G16960' => 'aly', 'AL6G25210' => 'aly', 'Aqoxy2G00441' => 'aox', 'Aqoxy3G01236' => 'aox', 'Aqoxy5G03746' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3RQ047' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C7GMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9C8JER' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MBL6KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YXCZ83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZANX40' => 'arhy', 'AT1G12990' => 'ath', 'AT1G67880' => 'ath', 'AT2G13290' => 'ath', 'AT3G01620' => 'ath', 'AT3G26445' => 'ath', 'AT3G27540' => 'ath', 'AT5G14480' => 'ath', 'ATR0824G026' => 'atr', 'ATR1098G019' => 'atr', 'Atru.chr11.2145' => 'acertr', 'Atru.chr2.3636' => 'acertr', 'Atru.chr2.3644' => 'acertr', 'Atru.chr6.2422' => 'acertr', 'Atru.chr7.1112' => 'acertr', 'AUR62005469' => 'cqu', 'AUR62011166' => 'cqu', 'AUR62013319' => 'cqu', 'AUR62024273' => 'cqu', 'AUR62028420' => 'cqu', 'AUR62041942' => 'cqu', 'BcaB01g04969' => 'bca', 'BcaB01g06371' => 'bca', 'BcaB02g11494' => 'bca', 'BcaB03g15382' => 'bca', 'BcaB08g36994' => 'bca', 'BcaC03g13477' => 'bca', 'BcaC03g13478' => 'bca', 'BcaC03g13480' => 'bca', 'BcaC03g13481' => 'bca', 'BcaC03g13486' => 'bca', 'BcaC04g19031' => 'bca', 'BcaC04g23085' => 'bca', 'BcaC05g25094' => 'bca', 'BcaC05g25096' => 'bca', 'BcaC05g25138' => 'bca', 'BcaC05g30416' => 'bca', 'BcaC05g30455' => 'bca', 'BcaC06g30979' => 'bca', 'BcaC06g33805' => 'bca', 'BcaC08g46021' => 'bca', 'BcaNung03154' => 'bca', 'BolC2t06623H' => 'bol', 'BolC2t06632H' => 'bol', 'BolC2t06635H' => 'bol', 'BolC2t06638H' => 'bol', 'BolC3t13266H' => 'bol', 'BolC5t29776H' => 'bol', 'BolC6t38912H' => 'bol', 'BolC7t44183H' => 'bol', 'BolC9t54123H' => 'bol', 'BolC9t59107H' => 'bol', 'BraA02t05221Z' => 'bra', 'BraA03t09996Z' => 'bra', 'BraA05t23210Z' => 'bra', 'BraA06t24068Z' => 'bra', 'BraA06t27032Z' => 'bra', 'BraA08t35176Z' => 'bra', 'BraA09t36680Z' => 'bra', 'BraA10t44471Z' => 'bra', 'C02p06760' => 'bna', 'C02p06890' => 'bna', 'C02p07010' => 'bna', 'C03p07660' => 'bna', 'C05p10300' => 'bna', 'C06p38150' => 'bna', 'C07p36650' => 'bna', 'C08p15770' => 'bna', 'C09p12300' => 'bna', 'C09p62700' => 'bna', 'C09p75040' => 'bna', 'CAN.G13.1' => 'can', 'CAN.G138.4' => 'can', 'CAN.G44.6' => 'can', 'CAN.G473.19' => 'can', 'CANSAT01G0835' => 'cansat', 'CANSAT11G0246' => 'cansat', 'CANSAT11G1766' => 'cansat', 'CANSAT64G1954' => 'cansat', 'CARHR013330' => 'chi', 'CARHR060530' => 'chi', 'CARHR075300' => 'chi', 'CARHR105120' => 'chi', 'CARHR148910' => 'chi', 'CARHR198830' => 'chi', 'Carub.0001s1275' => 'cru', 'Carub.0002s1437' => 'cru', 'Carub.0003s0044' => 'cru', 'Carub.0003s2787' => 'cru', 'Carub.0005s0597' => 'cru', 'Carub.0006s1266' => 'cru', 'Ca_06935_v3' => 'car', 'Ca_13559_v3' => 'car', 'Ca_16941_v3' => 'car', 'Ca_16960_v3' => 'car', 'Ca_17775_v3' => 'car', 'Ca_30464_v3' => 'car', 'Cc06_g08160' => 'ccan', 'Cc07_g01520' => 'ccan', 'Cc11_g15810' => 'ccan', 'CDE02G2840' => 'cde', 'CDE03G0093' => 'cde', 'CDE04G2127' => 'cde', 'CDE07G1857' => 'cde', 'CDE09G1246' => 'cde', 'Cfa003412' => 'cfa', 'Cfa007341' => 'cfa', 'Cfa009220' => 'cfa', 'Ciclev10008737m.g' => 'ccl', 'Ciclev10015565m.g' => 'ccl', 'Ciclev10031761m.g' => 'ccl', 'CiPaw.03G045300' => 'cil', 'CiPaw.03G247200' => 'cil', 'CiPaw.04G029500' => 'cil', 'CiPaw.04G174000' => 'cil', 'CiPaw.05G181200' => 'cil', 'CiPaw.06G067100' => 'cil', 'ClCG05G025800' => 'cla', 'ClCG06G011400' => 'cla', 'ClCG09G019360' => 'cla', 'COL.COLO4_04827' => 'col', 'COL.COLO4_29170' => 'col', 'COL.COLO4_35131' => 'col', 'COL.COLO4_35132' => 'col', 'Cpa.g.sc33.32' => 'cpa', 'Cpa.g.sc46.29' => 'cpa', 'Cpa.g.sc796.1' => 'cpa', 'CsaV3_1G030420' => 'csa', 'CsaV3_5G027050' => 'csa', 'CsaV3_5G031040' => 'csa', 'CsaV3_UNG023130' => 'csa', 'CSS0007726' => 'camsi', 'CSS0016433' => 'camsi', 'CSS0017656' => 'camsi', 'CSS0025364' => 'camsi', 'CSS0027582' => 'camsi', 'CSS0047288' => 'camsi', 'CSS0049950' => 'camsi', 'DCAR_003843' => 'dca', 'DCAR_007052' => 'dca', 'DCAR_020884' => 'dca', 'DCAR_021730' => 'dca', 'DCAR_024423' => 'dca', 'DCAR_026509' => 'dca', 'DCAR_031158' => 'dca', 'Dinv14728' => 'din', 'Dinv15219' => 'din', 'Dinv25728' => 'din', 'Dinv33428' => 'din', 'Dinv36489' => 'din', 'Dinv41486' => 'din', 'Duzib147G0469' => 'dzi', 'Duzib168G0060' => 'dzi', 'Duzib187G1215' => 'dzi', 'Duzib248G0692' => 'dzi', 'Duzib251G0767' => 'dzi', 'Duzib264G0446' => 'dzi', 'Duzib268G0691' => 'dzi', 'ECA232G4767' => 'eca', 'ECA233G2838' => 'eca', 'ECA234G0391' => 'eca', 'ECA234G0857' => 'eca', 'ECA236G1593' => 'eca', 'ECA238G0565' => 'eca', 'ECA246G1027' => 'eca', 'ECA246G3223' => 'eca', 'ECA246G3470' => 'eca', 'EL10Ac6g13829' => 'bvu', 'EL10Ac6g14093' => 'bvu', 'EL10Ac8g18707' => 'bvu', 'Eucgr.C01369' => 'egr', 'Eucgr.H02492' => 'egr', 'Eucgr.I01733' => 'egr', 'Eucgr.J02255' => 'egr', 'Eucgr.J02257' => 'egr', 'Eucgr.J02258' => 'egr', 'FAN02G1601' => 'fan', 'FAN03G1586' => 'fan', 'FAN03G2986' => 'fan', 'FAN05G4837' => 'fan', 'FAN06G0146' => 'fan', 'FAN07G0858' => 'fan', 'FAN09G3179' => 'fan', 'FAN10G0669' => 'fan', 'FAN12G2358' => 'fan', 'FAN14G4198' => 'fan', 'FAN14G5112' => 'fan', 'FAN17G0342' => 'fan', 'FAN19G0342' => 'fan', 'FAN19G0962' => 'fan', 'FAN19G1101' => 'fan', 'FAN19G1872' => 'fan', 'FAN22G0356' => 'fan', 'FAN23G0744' => 'fan', 'FAN23G1914' => 'fan', 'FAN26G0032' => 'fan', 'FAN28G0625' => 'fan', 'FvH4_1g02710' => 'fve', 'FvH4_1g02720' => 'fve', 'FvH4_4g25670' => 'fve', 'FvH4_6g51700' => 'fve', 'FvH4_7g20170' => 'fve', 'Glyma.05G175000' => 'gma', 'Glyma.08G132300' => 'gma', 'Glyma.11G243000' => 'gma', 'Glyma.13G158900' => 'gma', 'Glyma.17G112400' => 'gma', 'Glyma.18G014100' => 'gma', 'Glyma.19G003100' => 'gma', 'Glyma.19G056500' => 'gma', 'Gohir.A01G158900' => 'ghi', 'Gohir.A05G312600' => 'ghi', 'Gohir.A05G354900' => 'ghi', 'Gohir.A07G037200' => 'ghi', 'Gohir.A09G030000' => 'ghi', 'Gohir.A12G145200' => 'ghi', 'Gohir.D01G151500' => 'ghi', 'Gohir.D04G058300' => 'ghi', 'Gohir.D05G314100' => 'ghi', 'Gohir.D07G041400' => 'ghi', 'Gohir.D09G029700' => 'ghi', 'Gohir.D12G149700' => 'ghi', 'Gorai.001G043800' => 'gra', 'Gorai.002G187800' => 'gra', 'Gorai.006G034700' => 'gra', 'Gorai.008G161200' => 'gra', 'Gorai.009G335700' => 'gra', 'Gorai.012G065000' => 'gra', 'GSVIVG01000535001' => 'vvi', 'GSVIVG01015572001' => 'vvi', 'GSVIVG01032386001' => 'vvi', 'HanXRQChr05g0138531' => 'han', 'HanXRQChr06g0174391' => 'han', 'HanXRQChr07g0199021' => 'han', 'HanXRQChr08g0208211' => 'han', 'HanXRQChr09g0255471' => 'han', 'HanXRQChr10g0315791' => 'han', 'HanXRQChr12g0371991' => 'han', 'HanXRQChr15g0475251' => 'han', 'HanXRQChr17g0540001' => 'han', 'HanXRQChr17g0548631' => 'han', 'HanXRQChr17g0569561' => 'han', 'Haze_12256' => 'cav', 'Haze_14756' => 'cav', 'Haze_25528' => 'cav', 'Hma1.2p1_0079F.1_g041020' => 'hma', 'Hma1.2p1_0818F.1_g223260' => 'hma', 'Hma1.2p1_1747F.1_g300530' => 'hma', 'HPP92_004607' => 'vpl', 'HPP92_004608' => 'vpl', 'HPP92_006181' => 'vpl', 'HPP92_012192' => 'vpl', 'HPP92_015680' => 'vpl', 'HPP92_020249' => 'vpl', 'HPP92_021376' => 'vpl', 'HPP92_024275' => 'vpl', 'Hund06031' => 'sun', 'Hund25391' => 'sun', 'Lalb_Chr07g0185371' => 'lal', 'Lalb_Chr07g0185381' => 'lal', 'Lalb_Chr12g0204011' => 'lal', 'Lalb_Chr13g0301671' => 'lal', 'Lalb_Chr14g0362851' => 'lal', 'Lalb_Chr24g0403581' => 'lal', 'Lj1g0000233' => 'lja', 'Lj2g0018120' => 'lja', 'Lj3C621T0' => 'lonja', 'Lj3P1059T14' => 'lonja', 'Lj3P611T9' => 'lonja', 'Lj3P614T13' => 'lonja', 'Lj3P615T5' => 'lonja', 'Lj4g0012315' => 'lja', 'Lj4g0026182' => 'lja', 'Lj6P813T16' => 'lonja', 'Lj7C427T7' => 'lonja', 'Lj7C427T8' => 'lonja', 'Lj7P600T41' => 'lonja', 'Lju41C42G17' => 'lonja', 'Lsat_1_v5_gn_0_47300' => 'lsa', 'Lsat_1_v5_gn_2_91280' => 'lsa', 'Lsat_1_v5_gn_3_30561' => 'lsa', 'Lsat_1_v5_gn_4_184321' => 'lsa', 'Lsat_1_v5_gn_4_4041' => 'lsa', 'Lsat_1_v5_gn_5_92000' => 'lsa', 'Lsat_1_v5_gn_8_152940' => 'lsa', 'Lsat_1_v5_gn_8_62401' => 'lsa', 'Manes.06G055900' => 'mes', 'Manes.12G022200' => 'mes', 'Manes.13G023300' => 'mes', 'Manes.14G115000' => 'mes', 'Manes.15G151700' => 'mes', 'Manes.17G111300' => 'mes', 'Mapoly0226s0009' => 'mpo', 'MBI02_g25363_MAGBIO' => 'mbi', 'MBI06_g00027_MAGBIO' => 'mbi', 'MBI10_g13034_MAGBIO' => 'mbi', 'MD09G1023400' => 'mdo', 'MD13G1100100' => 'mdo', 'MD15G1169200' => 'mdo', 'MD16G1101100' => 'mdo', 'MD17G1022900' => 'mdo', 'Medtr3g096150' => 'mtr', 'Medtr4g115070' => 'mtr', 'Medtr7g033325' => 'mtr', 'Medtr8g089840' => 'mtr', 'MELO3C010319.2' => 'cme', 'MELO3C011944.2' => 'cme', 'MELO3C021589.2' => 'cme', 'Migut.E00207' => 'egut', 'Migut.H00067' => 'egut', 'Migut.K00433' => 'egut', 'Migut.K00606' => 'egut', 'Migut.K01410' => 'egut', 'MSTRG.13347' => 'ama', 'MSTRG.24045' => 'ama', 'MSTRG.2428' => 'ama', 'MSTRG.26410' => 'ama', 'MSTRG.3139' => 'ama', 'MSTRG.3286' => 'ama', 'MSTRG.563' => 'ama', 'MSTRG.7941' => 'ama', 'Nitab4.5_0000028g0060' => 'nta', 'Nitab4.5_0000065g0260' => 'nta', 'Nitab4.5_0000112g0060' => 'nta', 'Nitab4.5_0000489g0120' => 'nta', 'Nitab4.5_0001776g0050' => 'nta', 'Nitab4.5_0001854g0010' => 'nta', 'Nitab4.5_0001860g0020' => 'nta', 'Nitab4.5_0004352g0010' => 'nta', 'Nitab4.5_0008716g0020' => 'nta', 'Nitab4.5_0008922g0010' => 'nta', 'Nn3g16693' => 'nnu', 'Nn4g22596' => 'nnu', 'Nn7g37639' => 'nnu', 'Oeu001701.1' => 'oeu', 'Oeu018149.1' => 'oeu', 'Oeu026220.1' => 'oeu', 'Oeu038635.1' => 'oeu', 'Oeu049176.1' => 'oeu', 'Oeu056706.1' => 'oeu', 'Oeu056937.1' => 'oeu', 'Oeu057540.1' => 'oeu', 'Os02g0594900' => 'osa', 'Os02g0595100' => 'osa', 'Os04g0477500' => 'osa', 'Os12g0611900' => 'osa', 'Peaxi162Scf00076g00020' => 'pax', 'Peaxi162Scf00128g00217' => 'pax', 'Peaxi162Scf00129g01640' => 'pax', 'Peaxi162Scf00669g00007' => 'pax', 'Peaxi162Scf00700g00421' => 'pax', 'Peaxi162Scf00801g00038' => 'pax', 'Peaxi162Scf00891g00025' => 'pax', 'PGR083G0909' => 'pgr', 'PGR119G1005' => 'pgr', 'PGR142G2236' => 'pgr', 'PGR142G3388' => 'pgr', 'PGSC0003DMG400004514' => 'stu', 'PGSC0003DMG400012635' => 'stu', 'PGSC0003DMG400015730' => 'stu', 'PGSC0003DMG400018611' => 'stu', 'PGSC0003DMG400030897' => 'stu', 'Phvul.001G254800' => 'pvu', 'Phvul.002G260100' => 'pvu', 'Phvul.003G167600' => 'pvu', 'Phvul.004G005100' => 'pvu', 'Potri.001G343600' => 'ptr', 'Potri.006G066700' => 'ptr', 'Potri.008G186000' => 'ptr', 'Potri.010G046900' => 'ptr', 'Potri.018G127900' => 'ptr', 'Pp3c20_17750' => 'ppa', 'Pp3c24_4380' => 'ppa', 'Prupe.1G245800' => 'ppe', 'Prupe.3G293400' => 'ppe', 'Prupe.7G247400' => 'ppe', 'Psat0s145g0120' => 'psa', 'Psat0s595g0040' => 'psa', 'Psat0s595g0120' => 'psa', 'Psat3g175040' => 'psa', 'Psat7g058120' => 'psa', 'PSO017G0428' => 'pso', 'PSO063G7510' => 'pso', 'PSO067G0046' => 'pso', 'PSO478G1073' => 'pso', 'PSO675G3677' => 'pso', 'PSO675G6558' => 'pso', 'PSO675G7520' => 'pso', 'PSO675G8959' => 'pso', 'QL02p074089' => 'qlo', 'QL02p089614' => 'qlo', 'QL03p057736' => 'qlo', 'RcHm_v2.0_Chr1g0364131' => 'rch', 'RcHm_v2.0_Chr2g0087801' => 'rch', 'RcHm_v2.0_Chr2g0087821' => 'rch', 'RcHm_v2.0_Chr2g0173231' => 'rch', 'RcHm_v2.0_Chr4g0433111' => 'rch', 'Rhsim03G0250300' => 'rsi', 'Rhsim08G0048400' => 'rsi', 'Rhsim10G0014800' => 'rsi', 'Rhsim12G0040100' => 'rsi', 'Rhsim12G0109700' => 'rsi', 'Sabra06G0049600' => 'sbr', 'Sabra08G0141000' => 'sbr', 'Sabra10G0021400' => 'sbr', 'Sabra16G0222900' => 'sbr', 'Sabra18G0108600' => 'sbr', 'SalBow1G0433' => 'sbo', 'SalBow1G2038' => 'sbo', 'SalBow1G5003' => 'sbo', 'SalBow7G1197' => 'sbo', 'SalBow8G3506' => 'sbo', 'Sc03g0007300' => 'sci', 'Sc11g0000950' => 'sci', 'Sc14g0008750' => 'sci', 'Sc18g0000420' => 'sci', 'Sed0006754' => 'sed', 'Sed0008741' => 'sed', 'Sed0017172' => 'sed', 'Sed0018925' => 'sed', 'Sed0023326' => 'sed', 'Sed0025909' => 'sed', 'SEGI_05333' => 'sgi', 'SEGI_10362' => 'sgi', 'SEGI_13380' => 'sgi', 'SEGI_24306' => 'sgi', 'SEGI_29077' => 'sgi', 'SEGI_29095' => 'sgi', 'SEGI_36534' => 'sgi', 'SEGI_37506' => 'sgi', 'SEGI_38321' => 'sgi', 'SGA_v2.0_scaffold307G48031' => 'sas', 'SGA_v2.0_scaffold47G17507' => 'sas', 'SGA_v2.0_scaffold63G21736' => 'sas', 'SGA_v2.0_scaffold87G27070' => 'sas', 'SHI17794' => 'shi', 'SHI28851' => 'shi', 'SMO165G0155' => 'smo', 'SMO340G0217' => 'smo', 'SMO367G1210' => 'smo', 'Solyc02g093430.3' => 'sly', 'Solyc05g013580.4' => 'sly', 'Solyc07g008030.3' => 'sly', 'Solyc12g035470.2' => 'sly', 'Sopen02g038020' => 'spe', 'Sopen05g008490' => 'spe', 'Sopen07g003910' => 'spe', 'Sopen12g015240' => 'spe', 'Sp1g11550' => 'spa', 'Sp2g16710' => 'spa', 'Sp3g00430' => 'spa', 'Sp3g26780' => 'spa', 'Sp5g22900' => 'spa', 'Sp6g29530' => 'spa', 'TAR371G0794' => 'tar', 'TAR374G0164' => 'tar', 'TAR622G0165' => 'tar', 'TAR626G0929' => 'tar', 'TAR629G2155' => 'tar', 'THA.LOC104805282' => 'tha', 'THA.LOC104805363' => 'tha', 'THA.LOC104808968' => 'tha', 'THA.LOC104821093' => 'tha', 'THA.LOC104823953' => 'tha', 'THA.LOC104825562' => 'tha', 'THA.LOC104825665' => 'tha', 'Thecc.02G261400' => 'tca', 'Thecc.04G019200' => 'tca', 'Thecc.09G130400' => 'tca', 'Thhalv10004374m.g' => 'esa', 'Thhalv10007850m.g' => 'esa', 'Thhalv10013782m.g' => 'esa', 'Thhalv10018686m.g' => 'esa', 'Thhalv10020899m.g' => 'esa', 'Thhalv10022755m.g' => 'esa', 'TPR.G23851' => 'tpr', 'TPR.G26500' => 'tpr', 'TPR.G27267' => 'tpr', 'TPR.G32001' => 'tpr', 'TPR.G6251' => 'tpr', 'TPR.G8167' => 'tpr', 'TWI12G1330' => 'twi', 'TWI18G1239' => 'twi', 'TWI34G0979' => 'twi', 'TWI36G0670' => 'twi', 'TWI36G0707' => 'twi', 'TWI56G0233' => 'twi', 'TWI75G1809' => 'twi', 'unitig_21.g20874' => 'ugi', 'unitig_26.g10343' => 'ugi', 'unitig_46.g18392' => 'ugi', 'unitig_52.g17178' => 'ugi', 'unitig_8.g2934' => 'ugi', 'vmacro01122' => 'vma', 'vmacro05875' => 'vma', 'vmacro06147' => 'vma', 'vmacro16191' => 'vma', 'vmacro18293' => 'vma', 'VMungo0251G3707' => 'vmu', 'VMungo0464G1521' => 'vmu', 'VMungo1215G0205' => 'vmu', 'VMungo1383G2484' => 'vmu', 'Zm00001eb079610' => 'zma', 'Zm00001eb135990' => 'zma', 'Zm00001eb183710' => 'zma', 'Zm00001eb246020' => 'zma' ) $gf_id = 'HOM05D001124' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001124' ) $data_identifier = 'HOM05D001124' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 6, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 7, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 21, 'bol' => (int) 10, 'bra' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 6, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 9, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 21, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 8, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 10, 'lsa' => (int) 8, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 8, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 9, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb246020' $species_info = array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ) $local_species = 'cansat' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001124', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '548', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02520' => 'bna', 'A03p06630' => 'bna', 'A05p44460' => 'bna', 'A06p08710' => 'bna', 'A06p41090' => 'bna', 'A07p32320' => 'bna', 'A08p32520' => 'bna', 'A09p10360' => 'bna', 'A10p24080' => 'bna', 'Aa31LG11G15250' => 'aar', 'Aa31LG1G1800' => 'aar', 'Aa31LG2G5120' => 'aar', 'Aa31LG2G6070' => 'aar', 'Aa31LG5G10770' => 'aar', 'Aa31sc61G90' => 'aar', 'Actinidia01352' => 'ach', 'Actinidia05983' => 'ach', 'Actinidia08133' => 'ach', 'Actinidia15101' => 'ach', 'Actinidia26379' => 'ach', 'Actinidia35778' => 'ach', 'Actinidia36123' => 'ach', 'Actinidia37436' => 'ach', 'Actinidia38730' => 'ach', 'Ah.02g128210' => 'amhyb', 'Ah.03g132990' => 'amhyb', 'Ah.14g079410' => 'amhyb', 'AL1G24640' => 'aly', 'AL2G26680' => 'aly', 'AL3G10530' => 'aly', 'AL3G45230' => 'aly', 'AL5G15230' => 'aly', 'AL5G16960' => 'aly', 'AL6G25210' => 'aly', 'Aqoxy2G00441' => 'aox', 'Aqoxy3G01236' => 'aox', 'Aqoxy5G03746' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3RQ047' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C7GMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9C8JER' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MBL6KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YXCZ83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZANX40' => 'arhy', 'AT1G12990' => 'ath', 'AT1G67880' => 'ath', 'AT2G13290' => 'ath', 'AT3G01620' => 'ath', 'AT3G26445' => 'ath', 'AT3G27540' => 'ath', 'AT5G14480' => 'ath', 'ATR0824G026' => 'atr', 'ATR1098G019' => 'atr', 'Atru.chr11.2145' => 'acertr', 'Atru.chr2.3636' => 'acertr', 'Atru.chr2.3644' => 'acertr', 'Atru.chr6.2422' => 'acertr', 'Atru.chr7.1112' => 'acertr', 'AUR62005469' => 'cqu', 'AUR62011166' => 'cqu', 'AUR62013319' => 'cqu', 'AUR62024273' => 'cqu', 'AUR62028420' => 'cqu', 'AUR62041942' => 'cqu', 'BcaB01g04969' => 'bca', 'BcaB01g06371' => 'bca', 'BcaB02g11494' => 'bca', 'BcaB03g15382' => 'bca', 'BcaB08g36994' => 'bca', 'BcaC03g13477' => 'bca', 'BcaC03g13478' => 'bca', 'BcaC03g13480' => 'bca', 'BcaC03g13481' => 'bca', 'BcaC03g13486' => 'bca', 'BcaC04g19031' => 'bca', 'BcaC04g23085' => 'bca', 'BcaC05g25094' => 'bca', 'BcaC05g25096' => 'bca', 'BcaC05g25138' => 'bca', 'BcaC05g30416' => 'bca', 'BcaC05g30455' => 'bca', 'BcaC06g30979' => 'bca', 'BcaC06g33805' => 'bca', 'BcaC08g46021' => 'bca', 'BcaNung03154' => 'bca', 'BolC2t06623H' => 'bol', 'BolC2t06632H' => 'bol', 'BolC2t06635H' => 'bol', 'BolC2t06638H' => 'bol', 'BolC3t13266H' => 'bol', 'BolC5t29776H' => 'bol', 'BolC6t38912H' => 'bol', 'BolC7t44183H' => 'bol', 'BolC9t54123H' => 'bol', 'BolC9t59107H' => 'bol', 'BraA02t05221Z' => 'bra', 'BraA03t09996Z' => 'bra', 'BraA05t23210Z' => 'bra', 'BraA06t24068Z' => 'bra', 'BraA06t27032Z' => 'bra', 'BraA08t35176Z' => 'bra', 'BraA09t36680Z' => 'bra', 'BraA10t44471Z' => 'bra', 'C02p06760' => 'bna', 'C02p06890' => 'bna', 'C02p07010' => 'bna', 'C03p07660' => 'bna', 'C05p10300' => 'bna', 'C06p38150' => 'bna', 'C07p36650' => 'bna', 'C08p15770' => 'bna', 'C09p12300' => 'bna', 'C09p62700' => 'bna', 'C09p75040' => 'bna', 'CAN.G13.1' => 'can', 'CAN.G138.4' => 'can', 'CAN.G44.6' => 'can', 'CAN.G473.19' => 'can', 'CANSAT01G0835' => 'cansat', 'CANSAT11G0246' => 'cansat', 'CANSAT11G1766' => 'cansat', 'CANSAT64G1954' => 'cansat', 'CARHR013330' => 'chi', 'CARHR060530' => 'chi', 'CARHR075300' => 'chi', 'CARHR105120' => 'chi', 'CARHR148910' => 'chi', 'CARHR198830' => 'chi', 'Carub.0001s1275' => 'cru', 'Carub.0002s1437' => 'cru', 'Carub.0003s0044' => 'cru', 'Carub.0003s2787' => 'cru', 'Carub.0005s0597' => 'cru', 'Carub.0006s1266' => 'cru', 'Ca_06935_v3' => 'car', 'Ca_13559_v3' => 'car', 'Ca_16941_v3' => 'car', 'Ca_16960_v3' => 'car', 'Ca_17775_v3' => 'car', 'Ca_30464_v3' => 'car', 'Cc06_g08160' => 'ccan', 'Cc07_g01520' => 'ccan', 'Cc11_g15810' => 'ccan', 'CDE02G2840' => 'cde', 'CDE03G0093' => 'cde', 'CDE04G2127' => 'cde', 'CDE07G1857' => 'cde', 'CDE09G1246' => 'cde', 'Cfa003412' => 'cfa', 'Cfa007341' => 'cfa', 'Cfa009220' => 'cfa', 'Ciclev10008737m.g' => 'ccl', 'Ciclev10015565m.g' => 'ccl', 'Ciclev10031761m.g' => 'ccl', 'CiPaw.03G045300' => 'cil', 'CiPaw.03G247200' => 'cil', 'CiPaw.04G029500' => 'cil', 'CiPaw.04G174000' => 'cil', 'CiPaw.05G181200' => 'cil', 'CiPaw.06G067100' => 'cil', 'ClCG05G025800' => 'cla', 'ClCG06G011400' => 'cla', 'ClCG09G019360' => 'cla', 'COL.COLO4_04827' => 'col', 'COL.COLO4_29170' => 'col', 'COL.COLO4_35131' => 'col', 'COL.COLO4_35132' => 'col', 'Cpa.g.sc33.32' => 'cpa', 'Cpa.g.sc46.29' => 'cpa', 'Cpa.g.sc796.1' => 'cpa', 'CsaV3_1G030420' => 'csa', 'CsaV3_5G027050' => 'csa', 'CsaV3_5G031040' => 'csa', 'CsaV3_UNG023130' => 'csa', 'CSS0007726' => 'camsi', 'CSS0016433' => 'camsi', 'CSS0017656' => 'camsi', 'CSS0025364' => 'camsi', 'CSS0027582' => 'camsi', 'CSS0047288' => 'camsi', 'CSS0049950' => 'camsi', 'DCAR_003843' => 'dca', 'DCAR_007052' => 'dca', 'DCAR_020884' => 'dca', 'DCAR_021730' => 'dca', 'DCAR_024423' => 'dca', 'DCAR_026509' => 'dca', 'DCAR_031158' => 'dca', 'Dinv14728' => 'din', 'Dinv15219' => 'din', 'Dinv25728' => 'din', 'Dinv33428' => 'din', 'Dinv36489' => 'din', 'Dinv41486' => 'din', 'Duzib147G0469' => 'dzi', 'Duzib168G0060' => 'dzi', 'Duzib187G1215' => 'dzi', 'Duzib248G0692' => 'dzi', 'Duzib251G0767' => 'dzi', 'Duzib264G0446' => 'dzi', 'Duzib268G0691' => 'dzi', 'ECA232G4767' => 'eca', 'ECA233G2838' => 'eca', 'ECA234G0391' => 'eca', 'ECA234G0857' => 'eca', 'ECA236G1593' => 'eca', 'ECA238G0565' => 'eca', 'ECA246G1027' => 'eca', 'ECA246G3223' => 'eca', 'ECA246G3470' => 'eca', 'EL10Ac6g13829' => 'bvu', 'EL10Ac6g14093' => 'bvu', 'EL10Ac8g18707' => 'bvu', 'Eucgr.C01369' => 'egr', 'Eucgr.H02492' => 'egr', 'Eucgr.I01733' => 'egr', 'Eucgr.J02255' => 'egr', 'Eucgr.J02257' => 'egr', 'Eucgr.J02258' => 'egr', 'FAN02G1601' => 'fan', 'FAN03G1586' => 'fan', 'FAN03G2986' => 'fan', 'FAN05G4837' => 'fan', 'FAN06G0146' => 'fan', 'FAN07G0858' => 'fan', 'FAN09G3179' => 'fan', 'FAN10G0669' => 'fan', 'FAN12G2358' => 'fan', 'FAN14G4198' => 'fan', 'FAN14G5112' => 'fan', 'FAN17G0342' => 'fan', 'FAN19G0342' => 'fan', 'FAN19G0962' => 'fan', 'FAN19G1101' => 'fan', 'FAN19G1872' => 'fan', 'FAN22G0356' => 'fan', 'FAN23G0744' => 'fan', 'FAN23G1914' => 'fan', 'FAN26G0032' => 'fan', 'FAN28G0625' => 'fan', 'FvH4_1g02710' => 'fve', 'FvH4_1g02720' => 'fve', 'FvH4_4g25670' => 'fve', 'FvH4_6g51700' => 'fve', 'FvH4_7g20170' => 'fve', 'Glyma.05G175000' => 'gma', 'Glyma.08G132300' => 'gma', 'Glyma.11G243000' => 'gma', 'Glyma.13G158900' => 'gma', 'Glyma.17G112400' => 'gma', 'Glyma.18G014100' => 'gma', 'Glyma.19G003100' => 'gma', 'Glyma.19G056500' => 'gma', 'Gohir.A01G158900' => 'ghi', 'Gohir.A05G312600' => 'ghi', 'Gohir.A05G354900' => 'ghi', 'Gohir.A07G037200' => 'ghi', 'Gohir.A09G030000' => 'ghi', 'Gohir.A12G145200' => 'ghi', 'Gohir.D01G151500' => 'ghi', 'Gohir.D04G058300' => 'ghi', 'Gohir.D05G314100' => 'ghi', 'Gohir.D07G041400' => 'ghi', 'Gohir.D09G029700' => 'ghi', 'Gohir.D12G149700' => 'ghi', 'Gorai.001G043800' => 'gra', 'Gorai.002G187800' => 'gra', 'Gorai.006G034700' => 'gra', 'Gorai.008G161200' => 'gra', 'Gorai.009G335700' => 'gra', 'Gorai.012G065000' => 'gra', 'GSVIVG01000535001' => 'vvi', 'GSVIVG01015572001' => 'vvi', 'GSVIVG01032386001' => 'vvi', 'HanXRQChr05g0138531' => 'han', 'HanXRQChr06g0174391' => 'han', 'HanXRQChr07g0199021' => 'han', 'HanXRQChr08g0208211' => 'han', 'HanXRQChr09g0255471' => 'han', 'HanXRQChr10g0315791' => 'han', 'HanXRQChr12g0371991' => 'han', 'HanXRQChr15g0475251' => 'han', 'HanXRQChr17g0540001' => 'han', 'HanXRQChr17g0548631' => 'han', 'HanXRQChr17g0569561' => 'han', 'Haze_12256' => 'cav', 'Haze_14756' => 'cav', 'Haze_25528' => 'cav', 'Hma1.2p1_0079F.1_g041020' => 'hma', 'Hma1.2p1_0818F.1_g223260' => 'hma', 'Hma1.2p1_1747F.1_g300530' => 'hma', 'HPP92_004607' => 'vpl', 'HPP92_004608' => 'vpl', 'HPP92_006181' => 'vpl', 'HPP92_012192' => 'vpl', 'HPP92_015680' => 'vpl', 'HPP92_020249' => 'vpl', 'HPP92_021376' => 'vpl', 'HPP92_024275' => 'vpl', 'Hund06031' => 'sun', 'Hund25391' => 'sun', 'Lalb_Chr07g0185371' => 'lal', 'Lalb_Chr07g0185381' => 'lal', 'Lalb_Chr12g0204011' => 'lal', 'Lalb_Chr13g0301671' => 'lal', 'Lalb_Chr14g0362851' => 'lal', 'Lalb_Chr24g0403581' => 'lal', 'Lj1g0000233' => 'lja', 'Lj2g0018120' => 'lja', 'Lj3C621T0' => 'lonja', 'Lj3P1059T14' => 'lonja', 'Lj3P611T9' => 'lonja', 'Lj3P614T13' => 'lonja', 'Lj3P615T5' => 'lonja', 'Lj4g0012315' => 'lja', 'Lj4g0026182' => 'lja', 'Lj6P813T16' => 'lonja', 'Lj7C427T7' => 'lonja', 'Lj7C427T8' => 'lonja', 'Lj7P600T41' => 'lonja', 'Lju41C42G17' => 'lonja', 'Lsat_1_v5_gn_0_47300' => 'lsa', 'Lsat_1_v5_gn_2_91280' => 'lsa', 'Lsat_1_v5_gn_3_30561' => 'lsa', 'Lsat_1_v5_gn_4_184321' => 'lsa', 'Lsat_1_v5_gn_4_4041' => 'lsa', 'Lsat_1_v5_gn_5_92000' => 'lsa', 'Lsat_1_v5_gn_8_152940' => 'lsa', 'Lsat_1_v5_gn_8_62401' => 'lsa', 'Manes.06G055900' => 'mes', 'Manes.12G022200' => 'mes', 'Manes.13G023300' => 'mes', 'Manes.14G115000' => 'mes', 'Manes.15G151700' => 'mes', 'Manes.17G111300' => 'mes', 'Mapoly0226s0009' => 'mpo', 'MBI02_g25363_MAGBIO' => 'mbi', 'MBI06_g00027_MAGBIO' => 'mbi', 'MBI10_g13034_MAGBIO' => 'mbi', 'MD09G1023400' => 'mdo', 'MD13G1100100' => 'mdo', 'MD15G1169200' => 'mdo', 'MD16G1101100' => 'mdo', 'MD17G1022900' => 'mdo', 'Medtr3g096150' => 'mtr', 'Medtr4g115070' => 'mtr', 'Medtr7g033325' => 'mtr', 'Medtr8g089840' => 'mtr', 'MELO3C010319.2' => 'cme', 'MELO3C011944.2' => 'cme', 'MELO3C021589.2' => 'cme', 'Migut.E00207' => 'egut', 'Migut.H00067' => 'egut', 'Migut.K00433' => 'egut', 'Migut.K00606' => 'egut', 'Migut.K01410' => 'egut', 'MSTRG.13347' => 'ama', 'MSTRG.24045' => 'ama', 'MSTRG.2428' => 'ama', 'MSTRG.26410' => 'ama', 'MSTRG.3139' => 'ama', 'MSTRG.3286' => 'ama', 'MSTRG.563' => 'ama', 'MSTRG.7941' => 'ama', 'Nitab4.5_0000028g0060' => 'nta', 'Nitab4.5_0000065g0260' => 'nta', 'Nitab4.5_0000112g0060' => 'nta', 'Nitab4.5_0000489g0120' => 'nta', 'Nitab4.5_0001776g0050' => 'nta', 'Nitab4.5_0001854g0010' => 'nta', 'Nitab4.5_0001860g0020' => 'nta', 'Nitab4.5_0004352g0010' => 'nta', 'Nitab4.5_0008716g0020' => 'nta', 'Nitab4.5_0008922g0010' => 'nta', 'Nn3g16693' => 'nnu', 'Nn4g22596' => 'nnu', 'Nn7g37639' => 'nnu', 'Oeu001701.1' => 'oeu', 'Oeu018149.1' => 'oeu', 'Oeu026220.1' => 'oeu', 'Oeu038635.1' => 'oeu', 'Oeu049176.1' => 'oeu', 'Oeu056706.1' => 'oeu', 'Oeu056937.1' => 'oeu', 'Oeu057540.1' => 'oeu', 'Os02g0594900' => 'osa', 'Os02g0595100' => 'osa', 'Os04g0477500' => 'osa', 'Os12g0611900' => 'osa', 'Peaxi162Scf00076g00020' => 'pax', 'Peaxi162Scf00128g00217' => 'pax', 'Peaxi162Scf00129g01640' => 'pax', 'Peaxi162Scf00669g00007' => 'pax', 'Peaxi162Scf00700g00421' => 'pax', 'Peaxi162Scf00801g00038' => 'pax', 'Peaxi162Scf00891g00025' => 'pax', 'PGR083G0909' => 'pgr', 'PGR119G1005' => 'pgr', 'PGR142G2236' => 'pgr', 'PGR142G3388' => 'pgr', 'PGSC0003DMG400004514' => 'stu', 'PGSC0003DMG400012635' => 'stu', 'PGSC0003DMG400015730' => 'stu', 'PGSC0003DMG400018611' => 'stu', 'PGSC0003DMG400030897' => 'stu', 'Phvul.001G254800' => 'pvu', 'Phvul.002G260100' => 'pvu', 'Phvul.003G167600' => 'pvu', 'Phvul.004G005100' => 'pvu', 'Potri.001G343600' => 'ptr', 'Potri.006G066700' => 'ptr', 'Potri.008G186000' => 'ptr', 'Potri.010G046900' => 'ptr', 'Potri.018G127900' => 'ptr', 'Pp3c20_17750' => 'ppa', 'Pp3c24_4380' => 'ppa', 'Prupe.1G245800' => 'ppe', 'Prupe.3G293400' => 'ppe', 'Prupe.7G247400' => 'ppe', 'Psat0s145g0120' => 'psa', 'Psat0s595g0040' => 'psa', 'Psat0s595g0120' => 'psa', 'Psat3g175040' => 'psa', 'Psat7g058120' => 'psa', 'PSO017G0428' => 'pso', 'PSO063G7510' => 'pso', 'PSO067G0046' => 'pso', 'PSO478G1073' => 'pso', 'PSO675G3677' => 'pso', 'PSO675G6558' => 'pso', 'PSO675G7520' => 'pso', 'PSO675G8959' => 'pso', 'QL02p074089' => 'qlo', 'QL02p089614' => 'qlo', 'QL03p057736' => 'qlo', 'RcHm_v2.0_Chr1g0364131' => 'rch', 'RcHm_v2.0_Chr2g0087801' => 'rch', 'RcHm_v2.0_Chr2g0087821' => 'rch', 'RcHm_v2.0_Chr2g0173231' => 'rch', 'RcHm_v2.0_Chr4g0433111' => 'rch', 'Rhsim03G0250300' => 'rsi', 'Rhsim08G0048400' => 'rsi', 'Rhsim10G0014800' => 'rsi', 'Rhsim12G0040100' => 'rsi', 'Rhsim12G0109700' => 'rsi', 'Sabra06G0049600' => 'sbr', 'Sabra08G0141000' => 'sbr', 'Sabra10G0021400' => 'sbr', 'Sabra16G0222900' => 'sbr', 'Sabra18G0108600' => 'sbr', 'SalBow1G0433' => 'sbo', 'SalBow1G2038' => 'sbo', 'SalBow1G5003' => 'sbo', 'SalBow7G1197' => 'sbo', 'SalBow8G3506' => 'sbo', 'Sc03g0007300' => 'sci', 'Sc11g0000950' => 'sci', 'Sc14g0008750' => 'sci', 'Sc18g0000420' => 'sci', 'Sed0006754' => 'sed', 'Sed0008741' => 'sed', 'Sed0017172' => 'sed', 'Sed0018925' => 'sed', 'Sed0023326' => 'sed', 'Sed0025909' => 'sed', 'SEGI_05333' => 'sgi', 'SEGI_10362' => 'sgi', 'SEGI_13380' => 'sgi', 'SEGI_24306' => 'sgi', 'SEGI_29077' => 'sgi', 'SEGI_29095' => 'sgi', 'SEGI_36534' => 'sgi', 'SEGI_37506' => 'sgi', 'SEGI_38321' => 'sgi', 'SGA_v2.0_scaffold307G48031' => 'sas', 'SGA_v2.0_scaffold47G17507' => 'sas', 'SGA_v2.0_scaffold63G21736' => 'sas', 'SGA_v2.0_scaffold87G27070' => 'sas', 'SHI17794' => 'shi', 'SHI28851' => 'shi', 'SMO165G0155' => 'smo', 'SMO340G0217' => 'smo', 'SMO367G1210' => 'smo', 'Solyc02g093430.3' => 'sly', 'Solyc05g013580.4' => 'sly', 'Solyc07g008030.3' => 'sly', 'Solyc12g035470.2' => 'sly', 'Sopen02g038020' => 'spe', 'Sopen05g008490' => 'spe', 'Sopen07g003910' => 'spe', 'Sopen12g015240' => 'spe', 'Sp1g11550' => 'spa', 'Sp2g16710' => 'spa', 'Sp3g00430' => 'spa', 'Sp3g26780' => 'spa', 'Sp5g22900' => 'spa', 'Sp6g29530' => 'spa', 'TAR371G0794' => 'tar', 'TAR374G0164' => 'tar', 'TAR622G0165' => 'tar', 'TAR626G0929' => 'tar', 'TAR629G2155' => 'tar', 'THA.LOC104805282' => 'tha', 'THA.LOC104805363' => 'tha', 'THA.LOC104808968' => 'tha', 'THA.LOC104821093' => 'tha', 'THA.LOC104823953' => 'tha', 'THA.LOC104825562' => 'tha', 'THA.LOC104825665' => 'tha', 'Thecc.02G261400' => 'tca', 'Thecc.04G019200' => 'tca', 'Thecc.09G130400' => 'tca', 'Thhalv10004374m.g' => 'esa', 'Thhalv10007850m.g' => 'esa', 'Thhalv10013782m.g' => 'esa', 'Thhalv10018686m.g' => 'esa', 'Thhalv10020899m.g' => 'esa', 'Thhalv10022755m.g' => 'esa', 'TPR.G23851' => 'tpr', 'TPR.G26500' => 'tpr', 'TPR.G27267' => 'tpr', 'TPR.G32001' => 'tpr', 'TPR.G6251' => 'tpr', 'TPR.G8167' => 'tpr', 'TWI12G1330' => 'twi', 'TWI18G1239' => 'twi', 'TWI34G0979' => 'twi', 'TWI36G0670' => 'twi', 'TWI36G0707' => 'twi', 'TWI56G0233' => 'twi', 'TWI75G1809' => 'twi', 'unitig_21.g20874' => 'ugi', 'unitig_26.g10343' => 'ugi', 'unitig_46.g18392' => 'ugi', 'unitig_52.g17178' => 'ugi', 'unitig_8.g2934' => 'ugi', 'vmacro01122' => 'vma', 'vmacro05875' => 'vma', 'vmacro06147' => 'vma', 'vmacro16191' => 'vma', 'vmacro18293' => 'vma', 'VMungo0251G3707' => 'vmu', 'VMungo0464G1521' => 'vmu', 'VMungo1215G0205' => 'vmu', 'VMungo1383G2484' => 'vmu', 'Zm00001eb079610' => 'zma', 'Zm00001eb135990' => 'zma', 'Zm00001eb183710' => 'zma', 'Zm00001eb246020' => 'zma' ), 'gf_id' => 'HOM05D001124', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001124' ), 'data_identifier' => 'HOM05D001124', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001124', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '548', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02520' => 'bna', 'A03p06630' => 'bna', 'A05p44460' => 'bna', 'A06p08710' => 'bna', 'A06p41090' => 'bna', 'A07p32320' => 'bna', 'A08p32520' => 'bna', 'A09p10360' => 'bna', 'A10p24080' => 'bna', 'Aa31LG11G15250' => 'aar', 'Aa31LG1G1800' => 'aar', 'Aa31LG2G5120' => 'aar', 'Aa31LG2G6070' => 'aar', 'Aa31LG5G10770' => 'aar', 'Aa31sc61G90' => 'aar', 'Actinidia01352' => 'ach', 'Actinidia05983' => 'ach', 'Actinidia08133' => 'ach', 'Actinidia15101' => 'ach', 'Actinidia26379' => 'ach', 'Actinidia35778' => 'ach', 'Actinidia36123' => 'ach', 'Actinidia37436' => 'ach', 'Actinidia38730' => 'ach', 'Ah.02g128210' => 'amhyb', 'Ah.03g132990' => 'amhyb', 'Ah.14g079410' => 'amhyb', 'AL1G24640' => 'aly', 'AL2G26680' => 'aly', 'AL3G10530' => 'aly', 'AL3G45230' => 'aly', 'AL5G15230' => 'aly', 'AL5G16960' => 'aly', 'AL6G25210' => 'aly', 'Aqoxy2G00441' => 'aox', 'Aqoxy3G01236' => 'aox', 'Aqoxy5G03746' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3RQ047' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C7GMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9C8JER' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MBL6KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YXCZ83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZANX40' => 'arhy', 'AT1G12990' => 'ath', 'AT1G67880' => 'ath', 'AT2G13290' => 'ath', 'AT3G01620' => 'ath', 'AT3G26445' => 'ath', 'AT3G27540' => 'ath', 'AT5G14480' => 'ath', 'ATR0824G026' => 'atr', 'ATR1098G019' => 'atr', 'Atru.chr11.2145' => 'acertr', 'Atru.chr2.3636' => 'acertr', 'Atru.chr2.3644' => 'acertr', 'Atru.chr6.2422' => 'acertr', 'Atru.chr7.1112' => 'acertr', 'AUR62005469' => 'cqu', 'AUR62011166' => 'cqu', 'AUR62013319' => 'cqu', 'AUR62024273' => 'cqu', 'AUR62028420' => 'cqu', 'AUR62041942' => 'cqu', 'BcaB01g04969' => 'bca', 'BcaB01g06371' => 'bca', 'BcaB02g11494' => 'bca', 'BcaB03g15382' => 'bca', 'BcaB08g36994' => 'bca', 'BcaC03g13477' => 'bca', 'BcaC03g13478' => 'bca', 'BcaC03g13480' => 'bca', 'BcaC03g13481' => 'bca', 'BcaC03g13486' => 'bca', 'BcaC04g19031' => 'bca', 'BcaC04g23085' => 'bca', 'BcaC05g25094' => 'bca', 'BcaC05g25096' => 'bca', 'BcaC05g25138' => 'bca', 'BcaC05g30416' => 'bca', 'BcaC05g30455' => 'bca', 'BcaC06g30979' => 'bca', 'BcaC06g33805' => 'bca', 'BcaC08g46021' => 'bca', 'BcaNung03154' => 'bca', 'BolC2t06623H' => 'bol', 'BolC2t06632H' => 'bol', 'BolC2t06635H' => 'bol', 'BolC2t06638H' => 'bol', 'BolC3t13266H' => 'bol', 'BolC5t29776H' => 'bol', 'BolC6t38912H' => 'bol', 'BolC7t44183H' => 'bol', 'BolC9t54123H' => 'bol', 'BolC9t59107H' => 'bol', 'BraA02t05221Z' => 'bra', 'BraA03t09996Z' => 'bra', 'BraA05t23210Z' => 'bra', 'BraA06t24068Z' => 'bra', 'BraA06t27032Z' => 'bra', 'BraA08t35176Z' => 'bra', 'BraA09t36680Z' => 'bra', 'BraA10t44471Z' => 'bra', 'C02p06760' => 'bna', 'C02p06890' => 'bna', 'C02p07010' => 'bna', 'C03p07660' => 'bna', 'C05p10300' => 'bna', 'C06p38150' => 'bna', 'C07p36650' => 'bna', 'C08p15770' => 'bna', 'C09p12300' => 'bna', 'C09p62700' => 'bna', 'C09p75040' => 'bna', 'CAN.G13.1' => 'can', 'CAN.G138.4' => 'can', 'CAN.G44.6' => 'can', 'CAN.G473.19' => 'can', 'CANSAT01G0835' => 'cansat', 'CANSAT11G0246' => 'cansat', 'CANSAT11G1766' => 'cansat', 'CANSAT64G1954' => 'cansat', 'CARHR013330' => 'chi', 'CARHR060530' => 'chi', 'CARHR075300' => 'chi', 'CARHR105120' => 'chi', 'CARHR148910' => 'chi', 'CARHR198830' => 'chi', 'Carub.0001s1275' => 'cru', 'Carub.0002s1437' => 'cru', 'Carub.0003s0044' => 'cru', 'Carub.0003s2787' => 'cru', 'Carub.0005s0597' => 'cru', 'Carub.0006s1266' => 'cru', 'Ca_06935_v3' => 'car', 'Ca_13559_v3' => 'car', 'Ca_16941_v3' => 'car', 'Ca_16960_v3' => 'car', 'Ca_17775_v3' => 'car', 'Ca_30464_v3' => 'car', 'Cc06_g08160' => 'ccan', 'Cc07_g01520' => 'ccan', 'Cc11_g15810' => 'ccan', 'CDE02G2840' => 'cde', 'CDE03G0093' => 'cde', 'CDE04G2127' => 'cde', 'CDE07G1857' => 'cde', 'CDE09G1246' => 'cde', 'Cfa003412' => 'cfa', 'Cfa007341' => 'cfa', 'Cfa009220' => 'cfa', 'Ciclev10008737m.g' => 'ccl', 'Ciclev10015565m.g' => 'ccl', 'Ciclev10031761m.g' => 'ccl', 'CiPaw.03G045300' => 'cil', 'CiPaw.03G247200' => 'cil', 'CiPaw.04G029500' => 'cil', 'CiPaw.04G174000' => 'cil', 'CiPaw.05G181200' => 'cil', 'CiPaw.06G067100' => 'cil', 'ClCG05G025800' => 'cla', 'ClCG06G011400' => 'cla', 'ClCG09G019360' => 'cla', 'COL.COLO4_04827' => 'col', 'COL.COLO4_29170' => 'col', 'COL.COLO4_35131' => 'col', 'COL.COLO4_35132' => 'col', 'Cpa.g.sc33.32' => 'cpa', 'Cpa.g.sc46.29' => 'cpa', 'Cpa.g.sc796.1' => 'cpa', 'CsaV3_1G030420' => 'csa', 'CsaV3_5G027050' => 'csa', 'CsaV3_5G031040' => 'csa', 'CsaV3_UNG023130' => 'csa', 'CSS0007726' => 'camsi', 'CSS0016433' => 'camsi', 'CSS0017656' => 'camsi', 'CSS0025364' => 'camsi', 'CSS0027582' => 'camsi', 'CSS0047288' => 'camsi', 'CSS0049950' => 'camsi', 'DCAR_003843' => 'dca', 'DCAR_007052' => 'dca', 'DCAR_020884' => 'dca', 'DCAR_021730' => 'dca', 'DCAR_024423' => 'dca', 'DCAR_026509' => 'dca', 'DCAR_031158' => 'dca', 'Dinv14728' => 'din', 'Dinv15219' => 'din', 'Dinv25728' => 'din', 'Dinv33428' => 'din', 'Dinv36489' => 'din', 'Dinv41486' => 'din', 'Duzib147G0469' => 'dzi', 'Duzib168G0060' => 'dzi', 'Duzib187G1215' => 'dzi', 'Duzib248G0692' => 'dzi', 'Duzib251G0767' => 'dzi', 'Duzib264G0446' => 'dzi', 'Duzib268G0691' => 'dzi', 'ECA232G4767' => 'eca', 'ECA233G2838' => 'eca', 'ECA234G0391' => 'eca', 'ECA234G0857' => 'eca', 'ECA236G1593' => 'eca', 'ECA238G0565' => 'eca', 'ECA246G1027' => 'eca', 'ECA246G3223' => 'eca', 'ECA246G3470' => 'eca', 'EL10Ac6g13829' => 'bvu', 'EL10Ac6g14093' => 'bvu', 'EL10Ac8g18707' => 'bvu', 'Eucgr.C01369' => 'egr', 'Eucgr.H02492' => 'egr', 'Eucgr.I01733' => 'egr', 'Eucgr.J02255' => 'egr', 'Eucgr.J02257' => 'egr', 'Eucgr.J02258' => 'egr', 'FAN02G1601' => 'fan', 'FAN03G1586' => 'fan', 'FAN03G2986' => 'fan', 'FAN05G4837' => 'fan', 'FAN06G0146' => 'fan', 'FAN07G0858' => 'fan', 'FAN09G3179' => 'fan', 'FAN10G0669' => 'fan', 'FAN12G2358' => 'fan', 'FAN14G4198' => 'fan', 'FAN14G5112' => 'fan', 'FAN17G0342' => 'fan', 'FAN19G0342' => 'fan', 'FAN19G0962' => 'fan', 'FAN19G1101' => 'fan', 'FAN19G1872' => 'fan', 'FAN22G0356' => 'fan', 'FAN23G0744' => 'fan', 'FAN23G1914' => 'fan', 'FAN26G0032' => 'fan', 'FAN28G0625' => 'fan', 'FvH4_1g02710' => 'fve', 'FvH4_1g02720' => 'fve', 'FvH4_4g25670' => 'fve', 'FvH4_6g51700' => 'fve', 'FvH4_7g20170' => 'fve', 'Glyma.05G175000' => 'gma', 'Glyma.08G132300' => 'gma', 'Glyma.11G243000' => 'gma', 'Glyma.13G158900' => 'gma', 'Glyma.17G112400' => 'gma', 'Glyma.18G014100' => 'gma', 'Glyma.19G003100' => 'gma', 'Glyma.19G056500' => 'gma', 'Gohir.A01G158900' => 'ghi', 'Gohir.A05G312600' => 'ghi', 'Gohir.A05G354900' => 'ghi', 'Gohir.A07G037200' => 'ghi', 'Gohir.A09G030000' => 'ghi', 'Gohir.A12G145200' => 'ghi', 'Gohir.D01G151500' => 'ghi', 'Gohir.D04G058300' => 'ghi', 'Gohir.D05G314100' => 'ghi', 'Gohir.D07G041400' => 'ghi', 'Gohir.D09G029700' => 'ghi', 'Gohir.D12G149700' => 'ghi', 'Gorai.001G043800' => 'gra', 'Gorai.002G187800' => 'gra', 'Gorai.006G034700' => 'gra', 'Gorai.008G161200' => 'gra', 'Gorai.009G335700' => 'gra', 'Gorai.012G065000' => 'gra', 'GSVIVG01000535001' => 'vvi', 'GSVIVG01015572001' => 'vvi', 'GSVIVG01032386001' => 'vvi', 'HanXRQChr05g0138531' => 'han', 'HanXRQChr06g0174391' => 'han', 'HanXRQChr07g0199021' => 'han', 'HanXRQChr08g0208211' => 'han', 'HanXRQChr09g0255471' => 'han', 'HanXRQChr10g0315791' => 'han', 'HanXRQChr12g0371991' => 'han', 'HanXRQChr15g0475251' => 'han', 'HanXRQChr17g0540001' => 'han', 'HanXRQChr17g0548631' => 'han', 'HanXRQChr17g0569561' => 'han', 'Haze_12256' => 'cav', 'Haze_14756' => 'cav', 'Haze_25528' => 'cav', 'Hma1.2p1_0079F.1_g041020' => 'hma', 'Hma1.2p1_0818F.1_g223260' => 'hma', 'Hma1.2p1_1747F.1_g300530' => 'hma', 'HPP92_004607' => 'vpl', 'HPP92_004608' => 'vpl', 'HPP92_006181' => 'vpl', 'HPP92_012192' => 'vpl', 'HPP92_015680' => 'vpl', 'HPP92_020249' => 'vpl', 'HPP92_021376' => 'vpl', 'HPP92_024275' => 'vpl', 'Hund06031' => 'sun', 'Hund25391' => 'sun', 'Lalb_Chr07g0185371' => 'lal', 'Lalb_Chr07g0185381' => 'lal', 'Lalb_Chr12g0204011' => 'lal', 'Lalb_Chr13g0301671' => 'lal', 'Lalb_Chr14g0362851' => 'lal', 'Lalb_Chr24g0403581' => 'lal', 'Lj1g0000233' => 'lja', 'Lj2g0018120' => 'lja', 'Lj3C621T0' => 'lonja', 'Lj3P1059T14' => 'lonja', 'Lj3P611T9' => 'lonja', 'Lj3P614T13' => 'lonja', 'Lj3P615T5' => 'lonja', 'Lj4g0012315' => 'lja', 'Lj4g0026182' => 'lja', 'Lj6P813T16' => 'lonja', 'Lj7C427T7' => 'lonja', 'Lj7C427T8' => 'lonja', 'Lj7P600T41' => 'lonja', 'Lju41C42G17' => 'lonja', 'Lsat_1_v5_gn_0_47300' => 'lsa', 'Lsat_1_v5_gn_2_91280' => 'lsa', 'Lsat_1_v5_gn_3_30561' => 'lsa', 'Lsat_1_v5_gn_4_184321' => 'lsa', 'Lsat_1_v5_gn_4_4041' => 'lsa', 'Lsat_1_v5_gn_5_92000' => 'lsa', 'Lsat_1_v5_gn_8_152940' => 'lsa', 'Lsat_1_v5_gn_8_62401' => 'lsa', 'Manes.06G055900' => 'mes', 'Manes.12G022200' => 'mes', 'Manes.13G023300' => 'mes', 'Manes.14G115000' => 'mes', 'Manes.15G151700' => 'mes', 'Manes.17G111300' => 'mes', 'Mapoly0226s0009' => 'mpo', 'MBI02_g25363_MAGBIO' => 'mbi', 'MBI06_g00027_MAGBIO' => 'mbi', 'MBI10_g13034_MAGBIO' => 'mbi', 'MD09G1023400' => 'mdo', 'MD13G1100100' => 'mdo', 'MD15G1169200' => 'mdo', 'MD16G1101100' => 'mdo', 'MD17G1022900' => 'mdo', 'Medtr3g096150' => 'mtr', 'Medtr4g115070' => 'mtr', 'Medtr7g033325' => 'mtr', 'Medtr8g089840' => 'mtr', 'MELO3C010319.2' => 'cme', 'MELO3C011944.2' => 'cme', 'MELO3C021589.2' => 'cme', 'Migut.E00207' => 'egut', 'Migut.H00067' => 'egut', 'Migut.K00433' => 'egut', 'Migut.K00606' => 'egut', 'Migut.K01410' => 'egut', 'MSTRG.13347' => 'ama', 'MSTRG.24045' => 'ama', 'MSTRG.2428' => 'ama', 'MSTRG.26410' => 'ama', 'MSTRG.3139' => 'ama', 'MSTRG.3286' => 'ama', 'MSTRG.563' => 'ama', 'MSTRG.7941' => 'ama', 'Nitab4.5_0000028g0060' => 'nta', 'Nitab4.5_0000065g0260' => 'nta', 'Nitab4.5_0000112g0060' => 'nta', 'Nitab4.5_0000489g0120' => 'nta', 'Nitab4.5_0001776g0050' => 'nta', 'Nitab4.5_0001854g0010' => 'nta', 'Nitab4.5_0001860g0020' => 'nta', 'Nitab4.5_0004352g0010' => 'nta', 'Nitab4.5_0008716g0020' => 'nta', 'Nitab4.5_0008922g0010' => 'nta', 'Nn3g16693' => 'nnu', 'Nn4g22596' => 'nnu', 'Nn7g37639' => 'nnu', 'Oeu001701.1' => 'oeu', 'Oeu018149.1' => 'oeu', 'Oeu026220.1' => 'oeu', 'Oeu038635.1' => 'oeu', 'Oeu049176.1' => 'oeu', 'Oeu056706.1' => 'oeu', 'Oeu056937.1' => 'oeu', 'Oeu057540.1' => 'oeu', 'Os02g0594900' => 'osa', 'Os02g0595100' => 'osa', 'Os04g0477500' => 'osa', 'Os12g0611900' => 'osa', 'Peaxi162Scf00076g00020' => 'pax', 'Peaxi162Scf00128g00217' => 'pax', 'Peaxi162Scf00129g01640' => 'pax', 'Peaxi162Scf00669g00007' => 'pax', 'Peaxi162Scf00700g00421' => 'pax', 'Peaxi162Scf00801g00038' => 'pax', 'Peaxi162Scf00891g00025' => 'pax', 'PGR083G0909' => 'pgr', 'PGR119G1005' => 'pgr', 'PGR142G2236' => 'pgr', 'PGR142G3388' => 'pgr', 'PGSC0003DMG400004514' => 'stu', 'PGSC0003DMG400012635' => 'stu', 'PGSC0003DMG400015730' => 'stu', 'PGSC0003DMG400018611' => 'stu', 'PGSC0003DMG400030897' => 'stu', 'Phvul.001G254800' => 'pvu', 'Phvul.002G260100' => 'pvu', 'Phvul.003G167600' => 'pvu', 'Phvul.004G005100' => 'pvu', 'Potri.001G343600' => 'ptr', 'Potri.006G066700' => 'ptr', 'Potri.008G186000' => 'ptr', 'Potri.010G046900' => 'ptr', 'Potri.018G127900' => 'ptr', 'Pp3c20_17750' => 'ppa', 'Pp3c24_4380' => 'ppa', 'Prupe.1G245800' => 'ppe', 'Prupe.3G293400' => 'ppe', 'Prupe.7G247400' => 'ppe', 'Psat0s145g0120' => 'psa', 'Psat0s595g0040' => 'psa', 'Psat0s595g0120' => 'psa', 'Psat3g175040' => 'psa', 'Psat7g058120' => 'psa', 'PSO017G0428' => 'pso', 'PSO063G7510' => 'pso', 'PSO067G0046' => 'pso', 'PSO478G1073' => 'pso', 'PSO675G3677' => 'pso', 'PSO675G6558' => 'pso', 'PSO675G7520' => 'pso', 'PSO675G8959' => 'pso', 'QL02p074089' => 'qlo', 'QL02p089614' => 'qlo', 'QL03p057736' => 'qlo', 'RcHm_v2.0_Chr1g0364131' => 'rch', 'RcHm_v2.0_Chr2g0087801' => 'rch', 'RcHm_v2.0_Chr2g0087821' => 'rch', 'RcHm_v2.0_Chr2g0173231' => 'rch', 'RcHm_v2.0_Chr4g0433111' => 'rch', 'Rhsim03G0250300' => 'rsi', 'Rhsim08G0048400' => 'rsi', 'Rhsim10G0014800' => 'rsi', 'Rhsim12G0040100' => 'rsi', 'Rhsim12G0109700' => 'rsi', 'Sabra06G0049600' => 'sbr', 'Sabra08G0141000' => 'sbr', 'Sabra10G0021400' => 'sbr', 'Sabra16G0222900' => 'sbr', 'Sabra18G0108600' => 'sbr', 'SalBow1G0433' => 'sbo', 'SalBow1G2038' => 'sbo', 'SalBow1G5003' => 'sbo', 'SalBow7G1197' => 'sbo', 'SalBow8G3506' => 'sbo', 'Sc03g0007300' => 'sci', 'Sc11g0000950' => 'sci', 'Sc14g0008750' => 'sci', 'Sc18g0000420' => 'sci', 'Sed0006754' => 'sed', 'Sed0008741' => 'sed', 'Sed0017172' => 'sed', 'Sed0018925' => 'sed', 'Sed0023326' => 'sed', 'Sed0025909' => 'sed', 'SEGI_05333' => 'sgi', 'SEGI_10362' => 'sgi', 'SEGI_13380' => 'sgi', 'SEGI_24306' => 'sgi', 'SEGI_29077' => 'sgi', 'SEGI_29095' => 'sgi', 'SEGI_36534' => 'sgi', 'SEGI_37506' => 'sgi', 'SEGI_38321' => 'sgi', 'SGA_v2.0_scaffold307G48031' => 'sas', 'SGA_v2.0_scaffold47G17507' => 'sas', 'SGA_v2.0_scaffold63G21736' => 'sas', 'SGA_v2.0_scaffold87G27070' => 'sas', 'SHI17794' => 'shi', 'SHI28851' => 'shi', 'SMO165G0155' => 'smo', 'SMO340G0217' => 'smo', 'SMO367G1210' => 'smo', 'Solyc02g093430.3' => 'sly', 'Solyc05g013580.4' => 'sly', 'Solyc07g008030.3' => 'sly', 'Solyc12g035470.2' => 'sly', 'Sopen02g038020' => 'spe', 'Sopen05g008490' => 'spe', 'Sopen07g003910' => 'spe', 'Sopen12g015240' => 'spe', 'Sp1g11550' => 'spa', 'Sp2g16710' => 'spa', 'Sp3g00430' => 'spa', 'Sp3g26780' => 'spa', 'Sp5g22900' => 'spa', 'Sp6g29530' => 'spa', 'TAR371G0794' => 'tar', 'TAR374G0164' => 'tar', 'TAR622G0165' => 'tar', 'TAR626G0929' => 'tar', 'TAR629G2155' => 'tar', 'THA.LOC104805282' => 'tha', 'THA.LOC104805363' => 'tha', 'THA.LOC104808968' => 'tha', 'THA.LOC104821093' => 'tha', 'THA.LOC104823953' => 'tha', 'THA.LOC104825562' => 'tha', 'THA.LOC104825665' => 'tha', 'Thecc.02G261400' => 'tca', 'Thecc.04G019200' => 'tca', 'Thecc.09G130400' => 'tca', 'Thhalv10004374m.g' => 'esa', 'Thhalv10007850m.g' => 'esa', 'Thhalv10013782m.g' => 'esa', 'Thhalv10018686m.g' => 'esa', 'Thhalv10020899m.g' => 'esa', 'Thhalv10022755m.g' => 'esa', 'TPR.G23851' => 'tpr', 'TPR.G26500' => 'tpr', 'TPR.G27267' => 'tpr', 'TPR.G32001' => 'tpr', 'TPR.G6251' => 'tpr', 'TPR.G8167' => 'tpr', 'TWI12G1330' => 'twi', 'TWI18G1239' => 'twi', 'TWI34G0979' => 'twi', 'TWI36G0670' => 'twi', 'TWI36G0707' => 'twi', 'TWI56G0233' => 'twi', 'TWI75G1809' => 'twi', 'unitig_21.g20874' => 'ugi', 'unitig_26.g10343' => 'ugi', 'unitig_46.g18392' => 'ugi', 'unitig_52.g17178' => 'ugi', 'unitig_8.g2934' => 'ugi', 'vmacro01122' => 'vma', 'vmacro05875' => 'vma', 'vmacro06147' => 'vma', 'vmacro16191' => 'vma', 'vmacro18293' => 'vma', 'VMungo0251G3707' => 'vmu', 'VMungo0464G1521' => 'vmu', 'VMungo1215G0205' => 'vmu', 'VMungo1383G2484' => 'vmu', 'Zm00001eb079610' => 'zma', 'Zm00001eb135990' => 'zma', 'Zm00001eb183710' => 'zma', 'Zm00001eb246020' => 'zma' ) $gf_id = 'HOM05D001124' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001124' ) $data_identifier = 'HOM05D001124' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 6, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 7, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 21, 'bol' => (int) 10, 'bra' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 6, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 9, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 21, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 8, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 10, 'lsa' => (int) 8, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 8, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 9, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb246020' $species_info = array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ) $local_species = 'cansat' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001124', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '548', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02520' => 'bna', 'A03p06630' => 'bna', 'A05p44460' => 'bna', 'A06p08710' => 'bna', 'A06p41090' => 'bna', 'A07p32320' => 'bna', 'A08p32520' => 'bna', 'A09p10360' => 'bna', 'A10p24080' => 'bna', 'Aa31LG11G15250' => 'aar', 'Aa31LG1G1800' => 'aar', 'Aa31LG2G5120' => 'aar', 'Aa31LG2G6070' => 'aar', 'Aa31LG5G10770' => 'aar', 'Aa31sc61G90' => 'aar', 'Actinidia01352' => 'ach', 'Actinidia05983' => 'ach', 'Actinidia08133' => 'ach', 'Actinidia15101' => 'ach', 'Actinidia26379' => 'ach', 'Actinidia35778' => 'ach', 'Actinidia36123' => 'ach', 'Actinidia37436' => 'ach', 'Actinidia38730' => 'ach', 'Ah.02g128210' => 'amhyb', 'Ah.03g132990' => 'amhyb', 'Ah.14g079410' => 'amhyb', 'AL1G24640' => 'aly', 'AL2G26680' => 'aly', 'AL3G10530' => 'aly', 'AL3G45230' => 'aly', 'AL5G15230' => 'aly', 'AL5G16960' => 'aly', 'AL6G25210' => 'aly', 'Aqoxy2G00441' => 'aox', 'Aqoxy3G01236' => 'aox', 'Aqoxy5G03746' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3RQ047' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C7GMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9C8JER' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MBL6KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YXCZ83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZANX40' => 'arhy', 'AT1G12990' => 'ath', 'AT1G67880' => 'ath', 'AT2G13290' => 'ath', 'AT3G01620' => 'ath', 'AT3G26445' => 'ath', 'AT3G27540' => 'ath', 'AT5G14480' => 'ath', 'ATR0824G026' => 'atr', 'ATR1098G019' => 'atr', 'Atru.chr11.2145' => 'acertr', 'Atru.chr2.3636' => 'acertr', 'Atru.chr2.3644' => 'acertr', 'Atru.chr6.2422' => 'acertr', 'Atru.chr7.1112' => 'acertr', 'AUR62005469' => 'cqu', 'AUR62011166' => 'cqu', 'AUR62013319' => 'cqu', 'AUR62024273' => 'cqu', 'AUR62028420' => 'cqu', 'AUR62041942' => 'cqu', 'BcaB01g04969' => 'bca', 'BcaB01g06371' => 'bca', 'BcaB02g11494' => 'bca', 'BcaB03g15382' => 'bca', 'BcaB08g36994' => 'bca', 'BcaC03g13477' => 'bca', 'BcaC03g13478' => 'bca', 'BcaC03g13480' => 'bca', 'BcaC03g13481' => 'bca', 'BcaC03g13486' => 'bca', 'BcaC04g19031' => 'bca', 'BcaC04g23085' => 'bca', 'BcaC05g25094' => 'bca', 'BcaC05g25096' => 'bca', 'BcaC05g25138' => 'bca', 'BcaC05g30416' => 'bca', 'BcaC05g30455' => 'bca', 'BcaC06g30979' => 'bca', 'BcaC06g33805' => 'bca', 'BcaC08g46021' => 'bca', 'BcaNung03154' => 'bca', 'BolC2t06623H' => 'bol', 'BolC2t06632H' => 'bol', 'BolC2t06635H' => 'bol', 'BolC2t06638H' => 'bol', 'BolC3t13266H' => 'bol', 'BolC5t29776H' => 'bol', 'BolC6t38912H' => 'bol', 'BolC7t44183H' => 'bol', 'BolC9t54123H' => 'bol', 'BolC9t59107H' => 'bol', 'BraA02t05221Z' => 'bra', 'BraA03t09996Z' => 'bra', 'BraA05t23210Z' => 'bra', 'BraA06t24068Z' => 'bra', 'BraA06t27032Z' => 'bra', 'BraA08t35176Z' => 'bra', 'BraA09t36680Z' => 'bra', 'BraA10t44471Z' => 'bra', 'C02p06760' => 'bna', 'C02p06890' => 'bna', 'C02p07010' => 'bna', 'C03p07660' => 'bna', 'C05p10300' => 'bna', 'C06p38150' => 'bna', 'C07p36650' => 'bna', 'C08p15770' => 'bna', 'C09p12300' => 'bna', 'C09p62700' => 'bna', 'C09p75040' => 'bna', 'CAN.G13.1' => 'can', 'CAN.G138.4' => 'can', 'CAN.G44.6' => 'can', 'CAN.G473.19' => 'can', 'CANSAT01G0835' => 'cansat', 'CANSAT11G0246' => 'cansat', 'CANSAT11G1766' => 'cansat', 'CANSAT64G1954' => 'cansat', 'CARHR013330' => 'chi', 'CARHR060530' => 'chi', 'CARHR075300' => 'chi', 'CARHR105120' => 'chi', 'CARHR148910' => 'chi', 'CARHR198830' => 'chi', 'Carub.0001s1275' => 'cru', 'Carub.0002s1437' => 'cru', 'Carub.0003s0044' => 'cru', 'Carub.0003s2787' => 'cru', 'Carub.0005s0597' => 'cru', 'Carub.0006s1266' => 'cru', 'Ca_06935_v3' => 'car', 'Ca_13559_v3' => 'car', 'Ca_16941_v3' => 'car', 'Ca_16960_v3' => 'car', 'Ca_17775_v3' => 'car', 'Ca_30464_v3' => 'car', 'Cc06_g08160' => 'ccan', 'Cc07_g01520' => 'ccan', 'Cc11_g15810' => 'ccan', 'CDE02G2840' => 'cde', 'CDE03G0093' => 'cde', 'CDE04G2127' => 'cde', 'CDE07G1857' => 'cde', 'CDE09G1246' => 'cde', 'Cfa003412' => 'cfa', 'Cfa007341' => 'cfa', 'Cfa009220' => 'cfa', 'Ciclev10008737m.g' => 'ccl', 'Ciclev10015565m.g' => 'ccl', 'Ciclev10031761m.g' => 'ccl', 'CiPaw.03G045300' => 'cil', 'CiPaw.03G247200' => 'cil', 'CiPaw.04G029500' => 'cil', 'CiPaw.04G174000' => 'cil', 'CiPaw.05G181200' => 'cil', 'CiPaw.06G067100' => 'cil', 'ClCG05G025800' => 'cla', 'ClCG06G011400' => 'cla', 'ClCG09G019360' => 'cla', 'COL.COLO4_04827' => 'col', 'COL.COLO4_29170' => 'col', 'COL.COLO4_35131' => 'col', 'COL.COLO4_35132' => 'col', 'Cpa.g.sc33.32' => 'cpa', 'Cpa.g.sc46.29' => 'cpa', 'Cpa.g.sc796.1' => 'cpa', 'CsaV3_1G030420' => 'csa', 'CsaV3_5G027050' => 'csa', 'CsaV3_5G031040' => 'csa', 'CsaV3_UNG023130' => 'csa', 'CSS0007726' => 'camsi', 'CSS0016433' => 'camsi', 'CSS0017656' => 'camsi', 'CSS0025364' => 'camsi', 'CSS0027582' => 'camsi', 'CSS0047288' => 'camsi', 'CSS0049950' => 'camsi', 'DCAR_003843' => 'dca', 'DCAR_007052' => 'dca', 'DCAR_020884' => 'dca', 'DCAR_021730' => 'dca', 'DCAR_024423' => 'dca', 'DCAR_026509' => 'dca', 'DCAR_031158' => 'dca', 'Dinv14728' => 'din', 'Dinv15219' => 'din', 'Dinv25728' => 'din', 'Dinv33428' => 'din', 'Dinv36489' => 'din', 'Dinv41486' => 'din', 'Duzib147G0469' => 'dzi', 'Duzib168G0060' => 'dzi', 'Duzib187G1215' => 'dzi', 'Duzib248G0692' => 'dzi', 'Duzib251G0767' => 'dzi', 'Duzib264G0446' => 'dzi', 'Duzib268G0691' => 'dzi', 'ECA232G4767' => 'eca', 'ECA233G2838' => 'eca', 'ECA234G0391' => 'eca', 'ECA234G0857' => 'eca', 'ECA236G1593' => 'eca', 'ECA238G0565' => 'eca', 'ECA246G1027' => 'eca', 'ECA246G3223' => 'eca', 'ECA246G3470' => 'eca', 'EL10Ac6g13829' => 'bvu', 'EL10Ac6g14093' => 'bvu', 'EL10Ac8g18707' => 'bvu', 'Eucgr.C01369' => 'egr', 'Eucgr.H02492' => 'egr', 'Eucgr.I01733' => 'egr', 'Eucgr.J02255' => 'egr', 'Eucgr.J02257' => 'egr', 'Eucgr.J02258' => 'egr', 'FAN02G1601' => 'fan', 'FAN03G1586' => 'fan', 'FAN03G2986' => 'fan', 'FAN05G4837' => 'fan', 'FAN06G0146' => 'fan', 'FAN07G0858' => 'fan', 'FAN09G3179' => 'fan', 'FAN10G0669' => 'fan', 'FAN12G2358' => 'fan', 'FAN14G4198' => 'fan', 'FAN14G5112' => 'fan', 'FAN17G0342' => 'fan', 'FAN19G0342' => 'fan', 'FAN19G0962' => 'fan', 'FAN19G1101' => 'fan', 'FAN19G1872' => 'fan', 'FAN22G0356' => 'fan', 'FAN23G0744' => 'fan', 'FAN23G1914' => 'fan', 'FAN26G0032' => 'fan', 'FAN28G0625' => 'fan', 'FvH4_1g02710' => 'fve', 'FvH4_1g02720' => 'fve', 'FvH4_4g25670' => 'fve', 'FvH4_6g51700' => 'fve', 'FvH4_7g20170' => 'fve', 'Glyma.05G175000' => 'gma', 'Glyma.08G132300' => 'gma', 'Glyma.11G243000' => 'gma', 'Glyma.13G158900' => 'gma', 'Glyma.17G112400' => 'gma', 'Glyma.18G014100' => 'gma', 'Glyma.19G003100' => 'gma', 'Glyma.19G056500' => 'gma', 'Gohir.A01G158900' => 'ghi', 'Gohir.A05G312600' => 'ghi', 'Gohir.A05G354900' => 'ghi', 'Gohir.A07G037200' => 'ghi', 'Gohir.A09G030000' => 'ghi', 'Gohir.A12G145200' => 'ghi', 'Gohir.D01G151500' => 'ghi', 'Gohir.D04G058300' => 'ghi', 'Gohir.D05G314100' => 'ghi', 'Gohir.D07G041400' => 'ghi', 'Gohir.D09G029700' => 'ghi', 'Gohir.D12G149700' => 'ghi', 'Gorai.001G043800' => 'gra', 'Gorai.002G187800' => 'gra', 'Gorai.006G034700' => 'gra', 'Gorai.008G161200' => 'gra', 'Gorai.009G335700' => 'gra', 'Gorai.012G065000' => 'gra', 'GSVIVG01000535001' => 'vvi', 'GSVIVG01015572001' => 'vvi', 'GSVIVG01032386001' => 'vvi', 'HanXRQChr05g0138531' => 'han', 'HanXRQChr06g0174391' => 'han', 'HanXRQChr07g0199021' => 'han', 'HanXRQChr08g0208211' => 'han', 'HanXRQChr09g0255471' => 'han', 'HanXRQChr10g0315791' => 'han', 'HanXRQChr12g0371991' => 'han', 'HanXRQChr15g0475251' => 'han', 'HanXRQChr17g0540001' => 'han', 'HanXRQChr17g0548631' => 'han', 'HanXRQChr17g0569561' => 'han', 'Haze_12256' => 'cav', 'Haze_14756' => 'cav', 'Haze_25528' => 'cav', 'Hma1.2p1_0079F.1_g041020' => 'hma', 'Hma1.2p1_0818F.1_g223260' => 'hma', 'Hma1.2p1_1747F.1_g300530' => 'hma', 'HPP92_004607' => 'vpl', 'HPP92_004608' => 'vpl', 'HPP92_006181' => 'vpl', 'HPP92_012192' => 'vpl', 'HPP92_015680' => 'vpl', 'HPP92_020249' => 'vpl', 'HPP92_021376' => 'vpl', 'HPP92_024275' => 'vpl', 'Hund06031' => 'sun', 'Hund25391' => 'sun', 'Lalb_Chr07g0185371' => 'lal', 'Lalb_Chr07g0185381' => 'lal', 'Lalb_Chr12g0204011' => 'lal', 'Lalb_Chr13g0301671' => 'lal', 'Lalb_Chr14g0362851' => 'lal', 'Lalb_Chr24g0403581' => 'lal', 'Lj1g0000233' => 'lja', 'Lj2g0018120' => 'lja', 'Lj3C621T0' => 'lonja', 'Lj3P1059T14' => 'lonja', 'Lj3P611T9' => 'lonja', 'Lj3P614T13' => 'lonja', 'Lj3P615T5' => 'lonja', 'Lj4g0012315' => 'lja', 'Lj4g0026182' => 'lja', 'Lj6P813T16' => 'lonja', 'Lj7C427T7' => 'lonja', 'Lj7C427T8' => 'lonja', 'Lj7P600T41' => 'lonja', 'Lju41C42G17' => 'lonja', 'Lsat_1_v5_gn_0_47300' => 'lsa', 'Lsat_1_v5_gn_2_91280' => 'lsa', 'Lsat_1_v5_gn_3_30561' => 'lsa', 'Lsat_1_v5_gn_4_184321' => 'lsa', 'Lsat_1_v5_gn_4_4041' => 'lsa', 'Lsat_1_v5_gn_5_92000' => 'lsa', 'Lsat_1_v5_gn_8_152940' => 'lsa', 'Lsat_1_v5_gn_8_62401' => 'lsa', 'Manes.06G055900' => 'mes', 'Manes.12G022200' => 'mes', 'Manes.13G023300' => 'mes', 'Manes.14G115000' => 'mes', 'Manes.15G151700' => 'mes', 'Manes.17G111300' => 'mes', 'Mapoly0226s0009' => 'mpo', 'MBI02_g25363_MAGBIO' => 'mbi', 'MBI06_g00027_MAGBIO' => 'mbi', 'MBI10_g13034_MAGBIO' => 'mbi', 'MD09G1023400' => 'mdo', 'MD13G1100100' => 'mdo', 'MD15G1169200' => 'mdo', 'MD16G1101100' => 'mdo', 'MD17G1022900' => 'mdo', 'Medtr3g096150' => 'mtr', 'Medtr4g115070' => 'mtr', 'Medtr7g033325' => 'mtr', 'Medtr8g089840' => 'mtr', 'MELO3C010319.2' => 'cme', 'MELO3C011944.2' => 'cme', 'MELO3C021589.2' => 'cme', 'Migut.E00207' => 'egut', 'Migut.H00067' => 'egut', 'Migut.K00433' => 'egut', 'Migut.K00606' => 'egut', 'Migut.K01410' => 'egut', 'MSTRG.13347' => 'ama', 'MSTRG.24045' => 'ama', 'MSTRG.2428' => 'ama', 'MSTRG.26410' => 'ama', 'MSTRG.3139' => 'ama', 'MSTRG.3286' => 'ama', 'MSTRG.563' => 'ama', 'MSTRG.7941' => 'ama', 'Nitab4.5_0000028g0060' => 'nta', 'Nitab4.5_0000065g0260' => 'nta', 'Nitab4.5_0000112g0060' => 'nta', 'Nitab4.5_0000489g0120' => 'nta', 'Nitab4.5_0001776g0050' => 'nta', 'Nitab4.5_0001854g0010' => 'nta', 'Nitab4.5_0001860g0020' => 'nta', 'Nitab4.5_0004352g0010' => 'nta', 'Nitab4.5_0008716g0020' => 'nta', 'Nitab4.5_0008922g0010' => 'nta', 'Nn3g16693' => 'nnu', 'Nn4g22596' => 'nnu', 'Nn7g37639' => 'nnu', 'Oeu001701.1' => 'oeu', 'Oeu018149.1' => 'oeu', 'Oeu026220.1' => 'oeu', 'Oeu038635.1' => 'oeu', 'Oeu049176.1' => 'oeu', 'Oeu056706.1' => 'oeu', 'Oeu056937.1' => 'oeu', 'Oeu057540.1' => 'oeu', 'Os02g0594900' => 'osa', 'Os02g0595100' => 'osa', 'Os04g0477500' => 'osa', 'Os12g0611900' => 'osa', 'Peaxi162Scf00076g00020' => 'pax', 'Peaxi162Scf00128g00217' => 'pax', 'Peaxi162Scf00129g01640' => 'pax', 'Peaxi162Scf00669g00007' => 'pax', 'Peaxi162Scf00700g00421' => 'pax', 'Peaxi162Scf00801g00038' => 'pax', 'Peaxi162Scf00891g00025' => 'pax', 'PGR083G0909' => 'pgr', 'PGR119G1005' => 'pgr', 'PGR142G2236' => 'pgr', 'PGR142G3388' => 'pgr', 'PGSC0003DMG400004514' => 'stu', 'PGSC0003DMG400012635' => 'stu', 'PGSC0003DMG400015730' => 'stu', 'PGSC0003DMG400018611' => 'stu', 'PGSC0003DMG400030897' => 'stu', 'Phvul.001G254800' => 'pvu', 'Phvul.002G260100' => 'pvu', 'Phvul.003G167600' => 'pvu', 'Phvul.004G005100' => 'pvu', 'Potri.001G343600' => 'ptr', 'Potri.006G066700' => 'ptr', 'Potri.008G186000' => 'ptr', 'Potri.010G046900' => 'ptr', 'Potri.018G127900' => 'ptr', 'Pp3c20_17750' => 'ppa', 'Pp3c24_4380' => 'ppa', 'Prupe.1G245800' => 'ppe', 'Prupe.3G293400' => 'ppe', 'Prupe.7G247400' => 'ppe', 'Psat0s145g0120' => 'psa', 'Psat0s595g0040' => 'psa', 'Psat0s595g0120' => 'psa', 'Psat3g175040' => 'psa', 'Psat7g058120' => 'psa', 'PSO017G0428' => 'pso', 'PSO063G7510' => 'pso', 'PSO067G0046' => 'pso', 'PSO478G1073' => 'pso', 'PSO675G3677' => 'pso', 'PSO675G6558' => 'pso', 'PSO675G7520' => 'pso', 'PSO675G8959' => 'pso', 'QL02p074089' => 'qlo', 'QL02p089614' => 'qlo', 'QL03p057736' => 'qlo', 'RcHm_v2.0_Chr1g0364131' => 'rch', 'RcHm_v2.0_Chr2g0087801' => 'rch', 'RcHm_v2.0_Chr2g0087821' => 'rch', 'RcHm_v2.0_Chr2g0173231' => 'rch', 'RcHm_v2.0_Chr4g0433111' => 'rch', 'Rhsim03G0250300' => 'rsi', 'Rhsim08G0048400' => 'rsi', 'Rhsim10G0014800' => 'rsi', 'Rhsim12G0040100' => 'rsi', 'Rhsim12G0109700' => 'rsi', 'Sabra06G0049600' => 'sbr', 'Sabra08G0141000' => 'sbr', 'Sabra10G0021400' => 'sbr', 'Sabra16G0222900' => 'sbr', 'Sabra18G0108600' => 'sbr', 'SalBow1G0433' => 'sbo', 'SalBow1G2038' => 'sbo', 'SalBow1G5003' => 'sbo', 'SalBow7G1197' => 'sbo', 'SalBow8G3506' => 'sbo', 'Sc03g0007300' => 'sci', 'Sc11g0000950' => 'sci', 'Sc14g0008750' => 'sci', 'Sc18g0000420' => 'sci', 'Sed0006754' => 'sed', 'Sed0008741' => 'sed', 'Sed0017172' => 'sed', 'Sed0018925' => 'sed', 'Sed0023326' => 'sed', 'Sed0025909' => 'sed', 'SEGI_05333' => 'sgi', 'SEGI_10362' => 'sgi', 'SEGI_13380' => 'sgi', 'SEGI_24306' => 'sgi', 'SEGI_29077' => 'sgi', 'SEGI_29095' => 'sgi', 'SEGI_36534' => 'sgi', 'SEGI_37506' => 'sgi', 'SEGI_38321' => 'sgi', 'SGA_v2.0_scaffold307G48031' => 'sas', 'SGA_v2.0_scaffold47G17507' => 'sas', 'SGA_v2.0_scaffold63G21736' => 'sas', 'SGA_v2.0_scaffold87G27070' => 'sas', 'SHI17794' => 'shi', 'SHI28851' => 'shi', 'SMO165G0155' => 'smo', 'SMO340G0217' => 'smo', 'SMO367G1210' => 'smo', 'Solyc02g093430.3' => 'sly', 'Solyc05g013580.4' => 'sly', 'Solyc07g008030.3' => 'sly', 'Solyc12g035470.2' => 'sly', 'Sopen02g038020' => 'spe', 'Sopen05g008490' => 'spe', 'Sopen07g003910' => 'spe', 'Sopen12g015240' => 'spe', 'Sp1g11550' => 'spa', 'Sp2g16710' => 'spa', 'Sp3g00430' => 'spa', 'Sp3g26780' => 'spa', 'Sp5g22900' => 'spa', 'Sp6g29530' => 'spa', 'TAR371G0794' => 'tar', 'TAR374G0164' => 'tar', 'TAR622G0165' => 'tar', 'TAR626G0929' => 'tar', 'TAR629G2155' => 'tar', 'THA.LOC104805282' => 'tha', 'THA.LOC104805363' => 'tha', 'THA.LOC104808968' => 'tha', 'THA.LOC104821093' => 'tha', 'THA.LOC104823953' => 'tha', 'THA.LOC104825562' => 'tha', 'THA.LOC104825665' => 'tha', 'Thecc.02G261400' => 'tca', 'Thecc.04G019200' => 'tca', 'Thecc.09G130400' => 'tca', 'Thhalv10004374m.g' => 'esa', 'Thhalv10007850m.g' => 'esa', 'Thhalv10013782m.g' => 'esa', 'Thhalv10018686m.g' => 'esa', 'Thhalv10020899m.g' => 'esa', 'Thhalv10022755m.g' => 'esa', 'TPR.G23851' => 'tpr', 'TPR.G26500' => 'tpr', 'TPR.G27267' => 'tpr', 'TPR.G32001' => 'tpr', 'TPR.G6251' => 'tpr', 'TPR.G8167' => 'tpr', 'TWI12G1330' => 'twi', 'TWI18G1239' => 'twi', 'TWI34G0979' => 'twi', 'TWI36G0670' => 'twi', 'TWI36G0707' => 'twi', 'TWI56G0233' => 'twi', 'TWI75G1809' => 'twi', 'unitig_21.g20874' => 'ugi', 'unitig_26.g10343' => 'ugi', 'unitig_46.g18392' => 'ugi', 'unitig_52.g17178' => 'ugi', 'unitig_8.g2934' => 'ugi', 'vmacro01122' => 'vma', 'vmacro05875' => 'vma', 'vmacro06147' => 'vma', 'vmacro16191' => 'vma', 'vmacro18293' => 'vma', 'VMungo0251G3707' => 'vmu', 'VMungo0464G1521' => 'vmu', 'VMungo1215G0205' => 'vmu', 'VMungo1383G2484' => 'vmu', 'Zm00001eb079610' => 'zma', 'Zm00001eb135990' => 'zma', 'Zm00001eb183710' => 'zma', 'Zm00001eb246020' => 'zma' ), 'gf_id' => 'HOM05D001124', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001124' ), 'data_identifier' => 'HOM05D001124', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001124', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '548', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02520' => 'bna', 'A03p06630' => 'bna', 'A05p44460' => 'bna', 'A06p08710' => 'bna', 'A06p41090' => 'bna', 'A07p32320' => 'bna', 'A08p32520' => 'bna', 'A09p10360' => 'bna', 'A10p24080' => 'bna', 'Aa31LG11G15250' => 'aar', 'Aa31LG1G1800' => 'aar', 'Aa31LG2G5120' => 'aar', 'Aa31LG2G6070' => 'aar', 'Aa31LG5G10770' => 'aar', 'Aa31sc61G90' => 'aar', 'Actinidia01352' => 'ach', 'Actinidia05983' => 'ach', 'Actinidia08133' => 'ach', 'Actinidia15101' => 'ach', 'Actinidia26379' => 'ach', 'Actinidia35778' => 'ach', 'Actinidia36123' => 'ach', 'Actinidia37436' => 'ach', 'Actinidia38730' => 'ach', 'Ah.02g128210' => 'amhyb', 'Ah.03g132990' => 'amhyb', 'Ah.14g079410' => 'amhyb', 'AL1G24640' => 'aly', 'AL2G26680' => 'aly', 'AL3G10530' => 'aly', 'AL3G45230' => 'aly', 'AL5G15230' => 'aly', 'AL5G16960' => 'aly', 'AL6G25210' => 'aly', 'Aqoxy2G00441' => 'aox', 'Aqoxy3G01236' => 'aox', 'Aqoxy5G03746' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3RQ047' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C7GMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9C8JER' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MBL6KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YXCZ83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZANX40' => 'arhy', 'AT1G12990' => 'ath', 'AT1G67880' => 'ath', 'AT2G13290' => 'ath', 'AT3G01620' => 'ath', 'AT3G26445' => 'ath', 'AT3G27540' => 'ath', 'AT5G14480' => 'ath', 'ATR0824G026' => 'atr', 'ATR1098G019' => 'atr', 'Atru.chr11.2145' => 'acertr', 'Atru.chr2.3636' => 'acertr', 'Atru.chr2.3644' => 'acertr', 'Atru.chr6.2422' => 'acertr', 'Atru.chr7.1112' => 'acertr', 'AUR62005469' => 'cqu', 'AUR62011166' => 'cqu', 'AUR62013319' => 'cqu', 'AUR62024273' => 'cqu', 'AUR62028420' => 'cqu', 'AUR62041942' => 'cqu', 'BcaB01g04969' => 'bca', 'BcaB01g06371' => 'bca', 'BcaB02g11494' => 'bca', 'BcaB03g15382' => 'bca', 'BcaB08g36994' => 'bca', 'BcaC03g13477' => 'bca', 'BcaC03g13478' => 'bca', 'BcaC03g13480' => 'bca', 'BcaC03g13481' => 'bca', 'BcaC03g13486' => 'bca', 'BcaC04g19031' => 'bca', 'BcaC04g23085' => 'bca', 'BcaC05g25094' => 'bca', 'BcaC05g25096' => 'bca', 'BcaC05g25138' => 'bca', 'BcaC05g30416' => 'bca', 'BcaC05g30455' => 'bca', 'BcaC06g30979' => 'bca', 'BcaC06g33805' => 'bca', 'BcaC08g46021' => 'bca', 'BcaNung03154' => 'bca', 'BolC2t06623H' => 'bol', 'BolC2t06632H' => 'bol', 'BolC2t06635H' => 'bol', 'BolC2t06638H' => 'bol', 'BolC3t13266H' => 'bol', 'BolC5t29776H' => 'bol', 'BolC6t38912H' => 'bol', 'BolC7t44183H' => 'bol', 'BolC9t54123H' => 'bol', 'BolC9t59107H' => 'bol', 'BraA02t05221Z' => 'bra', 'BraA03t09996Z' => 'bra', 'BraA05t23210Z' => 'bra', 'BraA06t24068Z' => 'bra', 'BraA06t27032Z' => 'bra', 'BraA08t35176Z' => 'bra', 'BraA09t36680Z' => 'bra', 'BraA10t44471Z' => 'bra', 'C02p06760' => 'bna', 'C02p06890' => 'bna', 'C02p07010' => 'bna', 'C03p07660' => 'bna', 'C05p10300' => 'bna', 'C06p38150' => 'bna', 'C07p36650' => 'bna', 'C08p15770' => 'bna', 'C09p12300' => 'bna', 'C09p62700' => 'bna', 'C09p75040' => 'bna', 'CAN.G13.1' => 'can', 'CAN.G138.4' => 'can', 'CAN.G44.6' => 'can', 'CAN.G473.19' => 'can', 'CANSAT01G0835' => 'cansat', 'CANSAT11G0246' => 'cansat', 'CANSAT11G1766' => 'cansat', 'CANSAT64G1954' => 'cansat', 'CARHR013330' => 'chi', 'CARHR060530' => 'chi', 'CARHR075300' => 'chi', 'CARHR105120' => 'chi', 'CARHR148910' => 'chi', 'CARHR198830' => 'chi', 'Carub.0001s1275' => 'cru', 'Carub.0002s1437' => 'cru', 'Carub.0003s0044' => 'cru', 'Carub.0003s2787' => 'cru', 'Carub.0005s0597' => 'cru', 'Carub.0006s1266' => 'cru', 'Ca_06935_v3' => 'car', 'Ca_13559_v3' => 'car', 'Ca_16941_v3' => 'car', 'Ca_16960_v3' => 'car', 'Ca_17775_v3' => 'car', 'Ca_30464_v3' => 'car', 'Cc06_g08160' => 'ccan', 'Cc07_g01520' => 'ccan', 'Cc11_g15810' => 'ccan', 'CDE02G2840' => 'cde', 'CDE03G0093' => 'cde', 'CDE04G2127' => 'cde', 'CDE07G1857' => 'cde', 'CDE09G1246' => 'cde', 'Cfa003412' => 'cfa', 'Cfa007341' => 'cfa', 'Cfa009220' => 'cfa', 'Ciclev10008737m.g' => 'ccl', 'Ciclev10015565m.g' => 'ccl', 'Ciclev10031761m.g' => 'ccl', 'CiPaw.03G045300' => 'cil', 'CiPaw.03G247200' => 'cil', 'CiPaw.04G029500' => 'cil', 'CiPaw.04G174000' => 'cil', 'CiPaw.05G181200' => 'cil', 'CiPaw.06G067100' => 'cil', 'ClCG05G025800' => 'cla', 'ClCG06G011400' => 'cla', 'ClCG09G019360' => 'cla', 'COL.COLO4_04827' => 'col', 'COL.COLO4_29170' => 'col', 'COL.COLO4_35131' => 'col', 'COL.COLO4_35132' => 'col', 'Cpa.g.sc33.32' => 'cpa', 'Cpa.g.sc46.29' => 'cpa', 'Cpa.g.sc796.1' => 'cpa', 'CsaV3_1G030420' => 'csa', 'CsaV3_5G027050' => 'csa', 'CsaV3_5G031040' => 'csa', 'CsaV3_UNG023130' => 'csa', 'CSS0007726' => 'camsi', 'CSS0016433' => 'camsi', 'CSS0017656' => 'camsi', 'CSS0025364' => 'camsi', 'CSS0027582' => 'camsi', 'CSS0047288' => 'camsi', 'CSS0049950' => 'camsi', 'DCAR_003843' => 'dca', 'DCAR_007052' => 'dca', 'DCAR_020884' => 'dca', 'DCAR_021730' => 'dca', 'DCAR_024423' => 'dca', 'DCAR_026509' => 'dca', 'DCAR_031158' => 'dca', 'Dinv14728' => 'din', 'Dinv15219' => 'din', 'Dinv25728' => 'din', 'Dinv33428' => 'din', 'Dinv36489' => 'din', 'Dinv41486' => 'din', 'Duzib147G0469' => 'dzi', 'Duzib168G0060' => 'dzi', 'Duzib187G1215' => 'dzi', 'Duzib248G0692' => 'dzi', 'Duzib251G0767' => 'dzi', 'Duzib264G0446' => 'dzi', 'Duzib268G0691' => 'dzi', 'ECA232G4767' => 'eca', 'ECA233G2838' => 'eca', 'ECA234G0391' => 'eca', 'ECA234G0857' => 'eca', 'ECA236G1593' => 'eca', 'ECA238G0565' => 'eca', 'ECA246G1027' => 'eca', 'ECA246G3223' => 'eca', 'ECA246G3470' => 'eca', 'EL10Ac6g13829' => 'bvu', 'EL10Ac6g14093' => 'bvu', 'EL10Ac8g18707' => 'bvu', 'Eucgr.C01369' => 'egr', 'Eucgr.H02492' => 'egr', 'Eucgr.I01733' => 'egr', 'Eucgr.J02255' => 'egr', 'Eucgr.J02257' => 'egr', 'Eucgr.J02258' => 'egr', 'FAN02G1601' => 'fan', 'FAN03G1586' => 'fan', 'FAN03G2986' => 'fan', 'FAN05G4837' => 'fan', 'FAN06G0146' => 'fan', 'FAN07G0858' => 'fan', 'FAN09G3179' => 'fan', 'FAN10G0669' => 'fan', 'FAN12G2358' => 'fan', 'FAN14G4198' => 'fan', 'FAN14G5112' => 'fan', 'FAN17G0342' => 'fan', 'FAN19G0342' => 'fan', 'FAN19G0962' => 'fan', 'FAN19G1101' => 'fan', 'FAN19G1872' => 'fan', 'FAN22G0356' => 'fan', 'FAN23G0744' => 'fan', 'FAN23G1914' => 'fan', 'FAN26G0032' => 'fan', 'FAN28G0625' => 'fan', 'FvH4_1g02710' => 'fve', 'FvH4_1g02720' => 'fve', 'FvH4_4g25670' => 'fve', 'FvH4_6g51700' => 'fve', 'FvH4_7g20170' => 'fve', 'Glyma.05G175000' => 'gma', 'Glyma.08G132300' => 'gma', 'Glyma.11G243000' => 'gma', 'Glyma.13G158900' => 'gma', 'Glyma.17G112400' => 'gma', 'Glyma.18G014100' => 'gma', 'Glyma.19G003100' => 'gma', 'Glyma.19G056500' => 'gma', 'Gohir.A01G158900' => 'ghi', 'Gohir.A05G312600' => 'ghi', 'Gohir.A05G354900' => 'ghi', 'Gohir.A07G037200' => 'ghi', 'Gohir.A09G030000' => 'ghi', 'Gohir.A12G145200' => 'ghi', 'Gohir.D01G151500' => 'ghi', 'Gohir.D04G058300' => 'ghi', 'Gohir.D05G314100' => 'ghi', 'Gohir.D07G041400' => 'ghi', 'Gohir.D09G029700' => 'ghi', 'Gohir.D12G149700' => 'ghi', 'Gorai.001G043800' => 'gra', 'Gorai.002G187800' => 'gra', 'Gorai.006G034700' => 'gra', 'Gorai.008G161200' => 'gra', 'Gorai.009G335700' => 'gra', 'Gorai.012G065000' => 'gra', 'GSVIVG01000535001' => 'vvi', 'GSVIVG01015572001' => 'vvi', 'GSVIVG01032386001' => 'vvi', 'HanXRQChr05g0138531' => 'han', 'HanXRQChr06g0174391' => 'han', 'HanXRQChr07g0199021' => 'han', 'HanXRQChr08g0208211' => 'han', 'HanXRQChr09g0255471' => 'han', 'HanXRQChr10g0315791' => 'han', 'HanXRQChr12g0371991' => 'han', 'HanXRQChr15g0475251' => 'han', 'HanXRQChr17g0540001' => 'han', 'HanXRQChr17g0548631' => 'han', 'HanXRQChr17g0569561' => 'han', 'Haze_12256' => 'cav', 'Haze_14756' => 'cav', 'Haze_25528' => 'cav', 'Hma1.2p1_0079F.1_g041020' => 'hma', 'Hma1.2p1_0818F.1_g223260' => 'hma', 'Hma1.2p1_1747F.1_g300530' => 'hma', 'HPP92_004607' => 'vpl', 'HPP92_004608' => 'vpl', 'HPP92_006181' => 'vpl', 'HPP92_012192' => 'vpl', 'HPP92_015680' => 'vpl', 'HPP92_020249' => 'vpl', 'HPP92_021376' => 'vpl', 'HPP92_024275' => 'vpl', 'Hund06031' => 'sun', 'Hund25391' => 'sun', 'Lalb_Chr07g0185371' => 'lal', 'Lalb_Chr07g0185381' => 'lal', 'Lalb_Chr12g0204011' => 'lal', 'Lalb_Chr13g0301671' => 'lal', 'Lalb_Chr14g0362851' => 'lal', 'Lalb_Chr24g0403581' => 'lal', 'Lj1g0000233' => 'lja', 'Lj2g0018120' => 'lja', 'Lj3C621T0' => 'lonja', 'Lj3P1059T14' => 'lonja', 'Lj3P611T9' => 'lonja', 'Lj3P614T13' => 'lonja', 'Lj3P615T5' => 'lonja', 'Lj4g0012315' => 'lja', 'Lj4g0026182' => 'lja', 'Lj6P813T16' => 'lonja', 'Lj7C427T7' => 'lonja', 'Lj7C427T8' => 'lonja', 'Lj7P600T41' => 'lonja', 'Lju41C42G17' => 'lonja', 'Lsat_1_v5_gn_0_47300' => 'lsa', 'Lsat_1_v5_gn_2_91280' => 'lsa', 'Lsat_1_v5_gn_3_30561' => 'lsa', 'Lsat_1_v5_gn_4_184321' => 'lsa', 'Lsat_1_v5_gn_4_4041' => 'lsa', 'Lsat_1_v5_gn_5_92000' => 'lsa', 'Lsat_1_v5_gn_8_152940' => 'lsa', 'Lsat_1_v5_gn_8_62401' => 'lsa', 'Manes.06G055900' => 'mes', 'Manes.12G022200' => 'mes', 'Manes.13G023300' => 'mes', 'Manes.14G115000' => 'mes', 'Manes.15G151700' => 'mes', 'Manes.17G111300' => 'mes', 'Mapoly0226s0009' => 'mpo', 'MBI02_g25363_MAGBIO' => 'mbi', 'MBI06_g00027_MAGBIO' => 'mbi', 'MBI10_g13034_MAGBIO' => 'mbi', 'MD09G1023400' => 'mdo', 'MD13G1100100' => 'mdo', 'MD15G1169200' => 'mdo', 'MD16G1101100' => 'mdo', 'MD17G1022900' => 'mdo', 'Medtr3g096150' => 'mtr', 'Medtr4g115070' => 'mtr', 'Medtr7g033325' => 'mtr', 'Medtr8g089840' => 'mtr', 'MELO3C010319.2' => 'cme', 'MELO3C011944.2' => 'cme', 'MELO3C021589.2' => 'cme', 'Migut.E00207' => 'egut', 'Migut.H00067' => 'egut', 'Migut.K00433' => 'egut', 'Migut.K00606' => 'egut', 'Migut.K01410' => 'egut', 'MSTRG.13347' => 'ama', 'MSTRG.24045' => 'ama', 'MSTRG.2428' => 'ama', 'MSTRG.26410' => 'ama', 'MSTRG.3139' => 'ama', 'MSTRG.3286' => 'ama', 'MSTRG.563' => 'ama', 'MSTRG.7941' => 'ama', 'Nitab4.5_0000028g0060' => 'nta', 'Nitab4.5_0000065g0260' => 'nta', 'Nitab4.5_0000112g0060' => 'nta', 'Nitab4.5_0000489g0120' => 'nta', 'Nitab4.5_0001776g0050' => 'nta', 'Nitab4.5_0001854g0010' => 'nta', 'Nitab4.5_0001860g0020' => 'nta', 'Nitab4.5_0004352g0010' => 'nta', 'Nitab4.5_0008716g0020' => 'nta', 'Nitab4.5_0008922g0010' => 'nta', 'Nn3g16693' => 'nnu', 'Nn4g22596' => 'nnu', 'Nn7g37639' => 'nnu', 'Oeu001701.1' => 'oeu', 'Oeu018149.1' => 'oeu', 'Oeu026220.1' => 'oeu', 'Oeu038635.1' => 'oeu', 'Oeu049176.1' => 'oeu', 'Oeu056706.1' => 'oeu', 'Oeu056937.1' => 'oeu', 'Oeu057540.1' => 'oeu', 'Os02g0594900' => 'osa', 'Os02g0595100' => 'osa', 'Os04g0477500' => 'osa', 'Os12g0611900' => 'osa', 'Peaxi162Scf00076g00020' => 'pax', 'Peaxi162Scf00128g00217' => 'pax', 'Peaxi162Scf00129g01640' => 'pax', 'Peaxi162Scf00669g00007' => 'pax', 'Peaxi162Scf00700g00421' => 'pax', 'Peaxi162Scf00801g00038' => 'pax', 'Peaxi162Scf00891g00025' => 'pax', 'PGR083G0909' => 'pgr', 'PGR119G1005' => 'pgr', 'PGR142G2236' => 'pgr', 'PGR142G3388' => 'pgr', 'PGSC0003DMG400004514' => 'stu', 'PGSC0003DMG400012635' => 'stu', 'PGSC0003DMG400015730' => 'stu', 'PGSC0003DMG400018611' => 'stu', 'PGSC0003DMG400030897' => 'stu', 'Phvul.001G254800' => 'pvu', 'Phvul.002G260100' => 'pvu', 'Phvul.003G167600' => 'pvu', 'Phvul.004G005100' => 'pvu', 'Potri.001G343600' => 'ptr', 'Potri.006G066700' => 'ptr', 'Potri.008G186000' => 'ptr', 'Potri.010G046900' => 'ptr', 'Potri.018G127900' => 'ptr', 'Pp3c20_17750' => 'ppa', 'Pp3c24_4380' => 'ppa', 'Prupe.1G245800' => 'ppe', 'Prupe.3G293400' => 'ppe', 'Prupe.7G247400' => 'ppe', 'Psat0s145g0120' => 'psa', 'Psat0s595g0040' => 'psa', 'Psat0s595g0120' => 'psa', 'Psat3g175040' => 'psa', 'Psat7g058120' => 'psa', 'PSO017G0428' => 'pso', 'PSO063G7510' => 'pso', 'PSO067G0046' => 'pso', 'PSO478G1073' => 'pso', 'PSO675G3677' => 'pso', 'PSO675G6558' => 'pso', 'PSO675G7520' => 'pso', 'PSO675G8959' => 'pso', 'QL02p074089' => 'qlo', 'QL02p089614' => 'qlo', 'QL03p057736' => 'qlo', 'RcHm_v2.0_Chr1g0364131' => 'rch', 'RcHm_v2.0_Chr2g0087801' => 'rch', 'RcHm_v2.0_Chr2g0087821' => 'rch', 'RcHm_v2.0_Chr2g0173231' => 'rch', 'RcHm_v2.0_Chr4g0433111' => 'rch', 'Rhsim03G0250300' => 'rsi', 'Rhsim08G0048400' => 'rsi', 'Rhsim10G0014800' => 'rsi', 'Rhsim12G0040100' => 'rsi', 'Rhsim12G0109700' => 'rsi', 'Sabra06G0049600' => 'sbr', 'Sabra08G0141000' => 'sbr', 'Sabra10G0021400' => 'sbr', 'Sabra16G0222900' => 'sbr', 'Sabra18G0108600' => 'sbr', 'SalBow1G0433' => 'sbo', 'SalBow1G2038' => 'sbo', 'SalBow1G5003' => 'sbo', 'SalBow7G1197' => 'sbo', 'SalBow8G3506' => 'sbo', 'Sc03g0007300' => 'sci', 'Sc11g0000950' => 'sci', 'Sc14g0008750' => 'sci', 'Sc18g0000420' => 'sci', 'Sed0006754' => 'sed', 'Sed0008741' => 'sed', 'Sed0017172' => 'sed', 'Sed0018925' => 'sed', 'Sed0023326' => 'sed', 'Sed0025909' => 'sed', 'SEGI_05333' => 'sgi', 'SEGI_10362' => 'sgi', 'SEGI_13380' => 'sgi', 'SEGI_24306' => 'sgi', 'SEGI_29077' => 'sgi', 'SEGI_29095' => 'sgi', 'SEGI_36534' => 'sgi', 'SEGI_37506' => 'sgi', 'SEGI_38321' => 'sgi', 'SGA_v2.0_scaffold307G48031' => 'sas', 'SGA_v2.0_scaffold47G17507' => 'sas', 'SGA_v2.0_scaffold63G21736' => 'sas', 'SGA_v2.0_scaffold87G27070' => 'sas', 'SHI17794' => 'shi', 'SHI28851' => 'shi', 'SMO165G0155' => 'smo', 'SMO340G0217' => 'smo', 'SMO367G1210' => 'smo', 'Solyc02g093430.3' => 'sly', 'Solyc05g013580.4' => 'sly', 'Solyc07g008030.3' => 'sly', 'Solyc12g035470.2' => 'sly', 'Sopen02g038020' => 'spe', 'Sopen05g008490' => 'spe', 'Sopen07g003910' => 'spe', 'Sopen12g015240' => 'spe', 'Sp1g11550' => 'spa', 'Sp2g16710' => 'spa', 'Sp3g00430' => 'spa', 'Sp3g26780' => 'spa', 'Sp5g22900' => 'spa', 'Sp6g29530' => 'spa', 'TAR371G0794' => 'tar', 'TAR374G0164' => 'tar', 'TAR622G0165' => 'tar', 'TAR626G0929' => 'tar', 'TAR629G2155' => 'tar', 'THA.LOC104805282' => 'tha', 'THA.LOC104805363' => 'tha', 'THA.LOC104808968' => 'tha', 'THA.LOC104821093' => 'tha', 'THA.LOC104823953' => 'tha', 'THA.LOC104825562' => 'tha', 'THA.LOC104825665' => 'tha', 'Thecc.02G261400' => 'tca', 'Thecc.04G019200' => 'tca', 'Thecc.09G130400' => 'tca', 'Thhalv10004374m.g' => 'esa', 'Thhalv10007850m.g' => 'esa', 'Thhalv10013782m.g' => 'esa', 'Thhalv10018686m.g' => 'esa', 'Thhalv10020899m.g' => 'esa', 'Thhalv10022755m.g' => 'esa', 'TPR.G23851' => 'tpr', 'TPR.G26500' => 'tpr', 'TPR.G27267' => 'tpr', 'TPR.G32001' => 'tpr', 'TPR.G6251' => 'tpr', 'TPR.G8167' => 'tpr', 'TWI12G1330' => 'twi', 'TWI18G1239' => 'twi', 'TWI34G0979' => 'twi', 'TWI36G0670' => 'twi', 'TWI36G0707' => 'twi', 'TWI56G0233' => 'twi', 'TWI75G1809' => 'twi', 'unitig_21.g20874' => 'ugi', 'unitig_26.g10343' => 'ugi', 'unitig_46.g18392' => 'ugi', 'unitig_52.g17178' => 'ugi', 'unitig_8.g2934' => 'ugi', 'vmacro01122' => 'vma', 'vmacro05875' => 'vma', 'vmacro06147' => 'vma', 'vmacro16191' => 'vma', 'vmacro18293' => 'vma', 'VMungo0251G3707' => 'vmu', 'VMungo0464G1521' => 'vmu', 'VMungo1215G0205' => 'vmu', 'VMungo1383G2484' => 'vmu', 'Zm00001eb079610' => 'zma', 'Zm00001eb135990' => 'zma', 'Zm00001eb183710' => 'zma', 'Zm00001eb246020' => 'zma' ) $gf_id = 'HOM05D001124' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001124' ) $data_identifier = 'HOM05D001124' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 6, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 7, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 21, 'bol' => (int) 10, 'bra' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 6, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 9, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 21, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 8, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 10, 'lsa' => (int) 8, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 8, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 9, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb246020' $species_info = array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ) $local_species = 'cru' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001124', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '548', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02520' => 'bna', 'A03p06630' => 'bna', 'A05p44460' => 'bna', 'A06p08710' => 'bna', 'A06p41090' => 'bna', 'A07p32320' => 'bna', 'A08p32520' => 'bna', 'A09p10360' => 'bna', 'A10p24080' => 'bna', 'Aa31LG11G15250' => 'aar', 'Aa31LG1G1800' => 'aar', 'Aa31LG2G5120' => 'aar', 'Aa31LG2G6070' => 'aar', 'Aa31LG5G10770' => 'aar', 'Aa31sc61G90' => 'aar', 'Actinidia01352' => 'ach', 'Actinidia05983' => 'ach', 'Actinidia08133' => 'ach', 'Actinidia15101' => 'ach', 'Actinidia26379' => 'ach', 'Actinidia35778' => 'ach', 'Actinidia36123' => 'ach', 'Actinidia37436' => 'ach', 'Actinidia38730' => 'ach', 'Ah.02g128210' => 'amhyb', 'Ah.03g132990' => 'amhyb', 'Ah.14g079410' => 'amhyb', 'AL1G24640' => 'aly', 'AL2G26680' => 'aly', 'AL3G10530' => 'aly', 'AL3G45230' => 'aly', 'AL5G15230' => 'aly', 'AL5G16960' => 'aly', 'AL6G25210' => 'aly', 'Aqoxy2G00441' => 'aox', 'Aqoxy3G01236' => 'aox', 'Aqoxy5G03746' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3RQ047' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C7GMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9C8JER' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MBL6KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YXCZ83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZANX40' => 'arhy', 'AT1G12990' => 'ath', 'AT1G67880' => 'ath', 'AT2G13290' => 'ath', 'AT3G01620' => 'ath', 'AT3G26445' => 'ath', 'AT3G27540' => 'ath', 'AT5G14480' => 'ath', 'ATR0824G026' => 'atr', 'ATR1098G019' => 'atr', 'Atru.chr11.2145' => 'acertr', 'Atru.chr2.3636' => 'acertr', 'Atru.chr2.3644' => 'acertr', 'Atru.chr6.2422' => 'acertr', 'Atru.chr7.1112' => 'acertr', 'AUR62005469' => 'cqu', 'AUR62011166' => 'cqu', 'AUR62013319' => 'cqu', 'AUR62024273' => 'cqu', 'AUR62028420' => 'cqu', 'AUR62041942' => 'cqu', 'BcaB01g04969' => 'bca', 'BcaB01g06371' => 'bca', 'BcaB02g11494' => 'bca', 'BcaB03g15382' => 'bca', 'BcaB08g36994' => 'bca', 'BcaC03g13477' => 'bca', 'BcaC03g13478' => 'bca', 'BcaC03g13480' => 'bca', 'BcaC03g13481' => 'bca', 'BcaC03g13486' => 'bca', 'BcaC04g19031' => 'bca', 'BcaC04g23085' => 'bca', 'BcaC05g25094' => 'bca', 'BcaC05g25096' => 'bca', 'BcaC05g25138' => 'bca', 'BcaC05g30416' => 'bca', 'BcaC05g30455' => 'bca', 'BcaC06g30979' => 'bca', 'BcaC06g33805' => 'bca', 'BcaC08g46021' => 'bca', 'BcaNung03154' => 'bca', 'BolC2t06623H' => 'bol', 'BolC2t06632H' => 'bol', 'BolC2t06635H' => 'bol', 'BolC2t06638H' => 'bol', 'BolC3t13266H' => 'bol', 'BolC5t29776H' => 'bol', 'BolC6t38912H' => 'bol', 'BolC7t44183H' => 'bol', 'BolC9t54123H' => 'bol', 'BolC9t59107H' => 'bol', 'BraA02t05221Z' => 'bra', 'BraA03t09996Z' => 'bra', 'BraA05t23210Z' => 'bra', 'BraA06t24068Z' => 'bra', 'BraA06t27032Z' => 'bra', 'BraA08t35176Z' => 'bra', 'BraA09t36680Z' => 'bra', 'BraA10t44471Z' => 'bra', 'C02p06760' => 'bna', 'C02p06890' => 'bna', 'C02p07010' => 'bna', 'C03p07660' => 'bna', 'C05p10300' => 'bna', 'C06p38150' => 'bna', 'C07p36650' => 'bna', 'C08p15770' => 'bna', 'C09p12300' => 'bna', 'C09p62700' => 'bna', 'C09p75040' => 'bna', 'CAN.G13.1' => 'can', 'CAN.G138.4' => 'can', 'CAN.G44.6' => 'can', 'CAN.G473.19' => 'can', 'CANSAT01G0835' => 'cansat', 'CANSAT11G0246' => 'cansat', 'CANSAT11G1766' => 'cansat', 'CANSAT64G1954' => 'cansat', 'CARHR013330' => 'chi', 'CARHR060530' => 'chi', 'CARHR075300' => 'chi', 'CARHR105120' => 'chi', 'CARHR148910' => 'chi', 'CARHR198830' => 'chi', 'Carub.0001s1275' => 'cru', 'Carub.0002s1437' => 'cru', 'Carub.0003s0044' => 'cru', 'Carub.0003s2787' => 'cru', 'Carub.0005s0597' => 'cru', 'Carub.0006s1266' => 'cru', 'Ca_06935_v3' => 'car', 'Ca_13559_v3' => 'car', 'Ca_16941_v3' => 'car', 'Ca_16960_v3' => 'car', 'Ca_17775_v3' => 'car', 'Ca_30464_v3' => 'car', 'Cc06_g08160' => 'ccan', 'Cc07_g01520' => 'ccan', 'Cc11_g15810' => 'ccan', 'CDE02G2840' => 'cde', 'CDE03G0093' => 'cde', 'CDE04G2127' => 'cde', 'CDE07G1857' => 'cde', 'CDE09G1246' => 'cde', 'Cfa003412' => 'cfa', 'Cfa007341' => 'cfa', 'Cfa009220' => 'cfa', 'Ciclev10008737m.g' => 'ccl', 'Ciclev10015565m.g' => 'ccl', 'Ciclev10031761m.g' => 'ccl', 'CiPaw.03G045300' => 'cil', 'CiPaw.03G247200' => 'cil', 'CiPaw.04G029500' => 'cil', 'CiPaw.04G174000' => 'cil', 'CiPaw.05G181200' => 'cil', 'CiPaw.06G067100' => 'cil', 'ClCG05G025800' => 'cla', 'ClCG06G011400' => 'cla', 'ClCG09G019360' => 'cla', 'COL.COLO4_04827' => 'col', 'COL.COLO4_29170' => 'col', 'COL.COLO4_35131' => 'col', 'COL.COLO4_35132' => 'col', 'Cpa.g.sc33.32' => 'cpa', 'Cpa.g.sc46.29' => 'cpa', 'Cpa.g.sc796.1' => 'cpa', 'CsaV3_1G030420' => 'csa', 'CsaV3_5G027050' => 'csa', 'CsaV3_5G031040' => 'csa', 'CsaV3_UNG023130' => 'csa', 'CSS0007726' => 'camsi', 'CSS0016433' => 'camsi', 'CSS0017656' => 'camsi', 'CSS0025364' => 'camsi', 'CSS0027582' => 'camsi', 'CSS0047288' => 'camsi', 'CSS0049950' => 'camsi', 'DCAR_003843' => 'dca', 'DCAR_007052' => 'dca', 'DCAR_020884' => 'dca', 'DCAR_021730' => 'dca', 'DCAR_024423' => 'dca', 'DCAR_026509' => 'dca', 'DCAR_031158' => 'dca', 'Dinv14728' => 'din', 'Dinv15219' => 'din', 'Dinv25728' => 'din', 'Dinv33428' => 'din', 'Dinv36489' => 'din', 'Dinv41486' => 'din', 'Duzib147G0469' => 'dzi', 'Duzib168G0060' => 'dzi', 'Duzib187G1215' => 'dzi', 'Duzib248G0692' => 'dzi', 'Duzib251G0767' => 'dzi', 'Duzib264G0446' => 'dzi', 'Duzib268G0691' => 'dzi', 'ECA232G4767' => 'eca', 'ECA233G2838' => 'eca', 'ECA234G0391' => 'eca', 'ECA234G0857' => 'eca', 'ECA236G1593' => 'eca', 'ECA238G0565' => 'eca', 'ECA246G1027' => 'eca', 'ECA246G3223' => 'eca', 'ECA246G3470' => 'eca', 'EL10Ac6g13829' => 'bvu', 'EL10Ac6g14093' => 'bvu', 'EL10Ac8g18707' => 'bvu', 'Eucgr.C01369' => 'egr', 'Eucgr.H02492' => 'egr', 'Eucgr.I01733' => 'egr', 'Eucgr.J02255' => 'egr', 'Eucgr.J02257' => 'egr', 'Eucgr.J02258' => 'egr', 'FAN02G1601' => 'fan', 'FAN03G1586' => 'fan', 'FAN03G2986' => 'fan', 'FAN05G4837' => 'fan', 'FAN06G0146' => 'fan', 'FAN07G0858' => 'fan', 'FAN09G3179' => 'fan', 'FAN10G0669' => 'fan', 'FAN12G2358' => 'fan', 'FAN14G4198' => 'fan', 'FAN14G5112' => 'fan', 'FAN17G0342' => 'fan', 'FAN19G0342' => 'fan', 'FAN19G0962' => 'fan', 'FAN19G1101' => 'fan', 'FAN19G1872' => 'fan', 'FAN22G0356' => 'fan', 'FAN23G0744' => 'fan', 'FAN23G1914' => 'fan', 'FAN26G0032' => 'fan', 'FAN28G0625' => 'fan', 'FvH4_1g02710' => 'fve', 'FvH4_1g02720' => 'fve', 'FvH4_4g25670' => 'fve', 'FvH4_6g51700' => 'fve', 'FvH4_7g20170' => 'fve', 'Glyma.05G175000' => 'gma', 'Glyma.08G132300' => 'gma', 'Glyma.11G243000' => 'gma', 'Glyma.13G158900' => 'gma', 'Glyma.17G112400' => 'gma', 'Glyma.18G014100' => 'gma', 'Glyma.19G003100' => 'gma', 'Glyma.19G056500' => 'gma', 'Gohir.A01G158900' => 'ghi', 'Gohir.A05G312600' => 'ghi', 'Gohir.A05G354900' => 'ghi', 'Gohir.A07G037200' => 'ghi', 'Gohir.A09G030000' => 'ghi', 'Gohir.A12G145200' => 'ghi', 'Gohir.D01G151500' => 'ghi', 'Gohir.D04G058300' => 'ghi', 'Gohir.D05G314100' => 'ghi', 'Gohir.D07G041400' => 'ghi', 'Gohir.D09G029700' => 'ghi', 'Gohir.D12G149700' => 'ghi', 'Gorai.001G043800' => 'gra', 'Gorai.002G187800' => 'gra', 'Gorai.006G034700' => 'gra', 'Gorai.008G161200' => 'gra', 'Gorai.009G335700' => 'gra', 'Gorai.012G065000' => 'gra', 'GSVIVG01000535001' => 'vvi', 'GSVIVG01015572001' => 'vvi', 'GSVIVG01032386001' => 'vvi', 'HanXRQChr05g0138531' => 'han', 'HanXRQChr06g0174391' => 'han', 'HanXRQChr07g0199021' => 'han', 'HanXRQChr08g0208211' => 'han', 'HanXRQChr09g0255471' => 'han', 'HanXRQChr10g0315791' => 'han', 'HanXRQChr12g0371991' => 'han', 'HanXRQChr15g0475251' => 'han', 'HanXRQChr17g0540001' => 'han', 'HanXRQChr17g0548631' => 'han', 'HanXRQChr17g0569561' => 'han', 'Haze_12256' => 'cav', 'Haze_14756' => 'cav', 'Haze_25528' => 'cav', 'Hma1.2p1_0079F.1_g041020' => 'hma', 'Hma1.2p1_0818F.1_g223260' => 'hma', 'Hma1.2p1_1747F.1_g300530' => 'hma', 'HPP92_004607' => 'vpl', 'HPP92_004608' => 'vpl', 'HPP92_006181' => 'vpl', 'HPP92_012192' => 'vpl', 'HPP92_015680' => 'vpl', 'HPP92_020249' => 'vpl', 'HPP92_021376' => 'vpl', 'HPP92_024275' => 'vpl', 'Hund06031' => 'sun', 'Hund25391' => 'sun', 'Lalb_Chr07g0185371' => 'lal', 'Lalb_Chr07g0185381' => 'lal', 'Lalb_Chr12g0204011' => 'lal', 'Lalb_Chr13g0301671' => 'lal', 'Lalb_Chr14g0362851' => 'lal', 'Lalb_Chr24g0403581' => 'lal', 'Lj1g0000233' => 'lja', 'Lj2g0018120' => 'lja', 'Lj3C621T0' => 'lonja', 'Lj3P1059T14' => 'lonja', 'Lj3P611T9' => 'lonja', 'Lj3P614T13' => 'lonja', 'Lj3P615T5' => 'lonja', 'Lj4g0012315' => 'lja', 'Lj4g0026182' => 'lja', 'Lj6P813T16' => 'lonja', 'Lj7C427T7' => 'lonja', 'Lj7C427T8' => 'lonja', 'Lj7P600T41' => 'lonja', 'Lju41C42G17' => 'lonja', 'Lsat_1_v5_gn_0_47300' => 'lsa', 'Lsat_1_v5_gn_2_91280' => 'lsa', 'Lsat_1_v5_gn_3_30561' => 'lsa', 'Lsat_1_v5_gn_4_184321' => 'lsa', 'Lsat_1_v5_gn_4_4041' => 'lsa', 'Lsat_1_v5_gn_5_92000' => 'lsa', 'Lsat_1_v5_gn_8_152940' => 'lsa', 'Lsat_1_v5_gn_8_62401' => 'lsa', 'Manes.06G055900' => 'mes', 'Manes.12G022200' => 'mes', 'Manes.13G023300' => 'mes', 'Manes.14G115000' => 'mes', 'Manes.15G151700' => 'mes', 'Manes.17G111300' => 'mes', 'Mapoly0226s0009' => 'mpo', 'MBI02_g25363_MAGBIO' => 'mbi', 'MBI06_g00027_MAGBIO' => 'mbi', 'MBI10_g13034_MAGBIO' => 'mbi', 'MD09G1023400' => 'mdo', 'MD13G1100100' => 'mdo', 'MD15G1169200' => 'mdo', 'MD16G1101100' => 'mdo', 'MD17G1022900' => 'mdo', 'Medtr3g096150' => 'mtr', 'Medtr4g115070' => 'mtr', 'Medtr7g033325' => 'mtr', 'Medtr8g089840' => 'mtr', 'MELO3C010319.2' => 'cme', 'MELO3C011944.2' => 'cme', 'MELO3C021589.2' => 'cme', 'Migut.E00207' => 'egut', 'Migut.H00067' => 'egut', 'Migut.K00433' => 'egut', 'Migut.K00606' => 'egut', 'Migut.K01410' => 'egut', 'MSTRG.13347' => 'ama', 'MSTRG.24045' => 'ama', 'MSTRG.2428' => 'ama', 'MSTRG.26410' => 'ama', 'MSTRG.3139' => 'ama', 'MSTRG.3286' => 'ama', 'MSTRG.563' => 'ama', 'MSTRG.7941' => 'ama', 'Nitab4.5_0000028g0060' => 'nta', 'Nitab4.5_0000065g0260' => 'nta', 'Nitab4.5_0000112g0060' => 'nta', 'Nitab4.5_0000489g0120' => 'nta', 'Nitab4.5_0001776g0050' => 'nta', 'Nitab4.5_0001854g0010' => 'nta', 'Nitab4.5_0001860g0020' => 'nta', 'Nitab4.5_0004352g0010' => 'nta', 'Nitab4.5_0008716g0020' => 'nta', 'Nitab4.5_0008922g0010' => 'nta', 'Nn3g16693' => 'nnu', 'Nn4g22596' => 'nnu', 'Nn7g37639' => 'nnu', 'Oeu001701.1' => 'oeu', 'Oeu018149.1' => 'oeu', 'Oeu026220.1' => 'oeu', 'Oeu038635.1' => 'oeu', 'Oeu049176.1' => 'oeu', 'Oeu056706.1' => 'oeu', 'Oeu056937.1' => 'oeu', 'Oeu057540.1' => 'oeu', 'Os02g0594900' => 'osa', 'Os02g0595100' => 'osa', 'Os04g0477500' => 'osa', 'Os12g0611900' => 'osa', 'Peaxi162Scf00076g00020' => 'pax', 'Peaxi162Scf00128g00217' => 'pax', 'Peaxi162Scf00129g01640' => 'pax', 'Peaxi162Scf00669g00007' => 'pax', 'Peaxi162Scf00700g00421' => 'pax', 'Peaxi162Scf00801g00038' => 'pax', 'Peaxi162Scf00891g00025' => 'pax', 'PGR083G0909' => 'pgr', 'PGR119G1005' => 'pgr', 'PGR142G2236' => 'pgr', 'PGR142G3388' => 'pgr', 'PGSC0003DMG400004514' => 'stu', 'PGSC0003DMG400012635' => 'stu', 'PGSC0003DMG400015730' => 'stu', 'PGSC0003DMG400018611' => 'stu', 'PGSC0003DMG400030897' => 'stu', 'Phvul.001G254800' => 'pvu', 'Phvul.002G260100' => 'pvu', 'Phvul.003G167600' => 'pvu', 'Phvul.004G005100' => 'pvu', 'Potri.001G343600' => 'ptr', 'Potri.006G066700' => 'ptr', 'Potri.008G186000' => 'ptr', 'Potri.010G046900' => 'ptr', 'Potri.018G127900' => 'ptr', 'Pp3c20_17750' => 'ppa', 'Pp3c24_4380' => 'ppa', 'Prupe.1G245800' => 'ppe', 'Prupe.3G293400' => 'ppe', 'Prupe.7G247400' => 'ppe', 'Psat0s145g0120' => 'psa', 'Psat0s595g0040' => 'psa', 'Psat0s595g0120' => 'psa', 'Psat3g175040' => 'psa', 'Psat7g058120' => 'psa', 'PSO017G0428' => 'pso', 'PSO063G7510' => 'pso', 'PSO067G0046' => 'pso', 'PSO478G1073' => 'pso', 'PSO675G3677' => 'pso', 'PSO675G6558' => 'pso', 'PSO675G7520' => 'pso', 'PSO675G8959' => 'pso', 'QL02p074089' => 'qlo', 'QL02p089614' => 'qlo', 'QL03p057736' => 'qlo', 'RcHm_v2.0_Chr1g0364131' => 'rch', 'RcHm_v2.0_Chr2g0087801' => 'rch', 'RcHm_v2.0_Chr2g0087821' => 'rch', 'RcHm_v2.0_Chr2g0173231' => 'rch', 'RcHm_v2.0_Chr4g0433111' => 'rch', 'Rhsim03G0250300' => 'rsi', 'Rhsim08G0048400' => 'rsi', 'Rhsim10G0014800' => 'rsi', 'Rhsim12G0040100' => 'rsi', 'Rhsim12G0109700' => 'rsi', 'Sabra06G0049600' => 'sbr', 'Sabra08G0141000' => 'sbr', 'Sabra10G0021400' => 'sbr', 'Sabra16G0222900' => 'sbr', 'Sabra18G0108600' => 'sbr', 'SalBow1G0433' => 'sbo', 'SalBow1G2038' => 'sbo', 'SalBow1G5003' => 'sbo', 'SalBow7G1197' => 'sbo', 'SalBow8G3506' => 'sbo', 'Sc03g0007300' => 'sci', 'Sc11g0000950' => 'sci', 'Sc14g0008750' => 'sci', 'Sc18g0000420' => 'sci', 'Sed0006754' => 'sed', 'Sed0008741' => 'sed', 'Sed0017172' => 'sed', 'Sed0018925' => 'sed', 'Sed0023326' => 'sed', 'Sed0025909' => 'sed', 'SEGI_05333' => 'sgi', 'SEGI_10362' => 'sgi', 'SEGI_13380' => 'sgi', 'SEGI_24306' => 'sgi', 'SEGI_29077' => 'sgi', 'SEGI_29095' => 'sgi', 'SEGI_36534' => 'sgi', 'SEGI_37506' => 'sgi', 'SEGI_38321' => 'sgi', 'SGA_v2.0_scaffold307G48031' => 'sas', 'SGA_v2.0_scaffold47G17507' => 'sas', 'SGA_v2.0_scaffold63G21736' => 'sas', 'SGA_v2.0_scaffold87G27070' => 'sas', 'SHI17794' => 'shi', 'SHI28851' => 'shi', 'SMO165G0155' => 'smo', 'SMO340G0217' => 'smo', 'SMO367G1210' => 'smo', 'Solyc02g093430.3' => 'sly', 'Solyc05g013580.4' => 'sly', 'Solyc07g008030.3' => 'sly', 'Solyc12g035470.2' => 'sly', 'Sopen02g038020' => 'spe', 'Sopen05g008490' => 'spe', 'Sopen07g003910' => 'spe', 'Sopen12g015240' => 'spe', 'Sp1g11550' => 'spa', 'Sp2g16710' => 'spa', 'Sp3g00430' => 'spa', 'Sp3g26780' => 'spa', 'Sp5g22900' => 'spa', 'Sp6g29530' => 'spa', 'TAR371G0794' => 'tar', 'TAR374G0164' => 'tar', 'TAR622G0165' => 'tar', 'TAR626G0929' => 'tar', 'TAR629G2155' => 'tar', 'THA.LOC104805282' => 'tha', 'THA.LOC104805363' => 'tha', 'THA.LOC104808968' => 'tha', 'THA.LOC104821093' => 'tha', 'THA.LOC104823953' => 'tha', 'THA.LOC104825562' => 'tha', 'THA.LOC104825665' => 'tha', 'Thecc.02G261400' => 'tca', 'Thecc.04G019200' => 'tca', 'Thecc.09G130400' => 'tca', 'Thhalv10004374m.g' => 'esa', 'Thhalv10007850m.g' => 'esa', 'Thhalv10013782m.g' => 'esa', 'Thhalv10018686m.g' => 'esa', 'Thhalv10020899m.g' => 'esa', 'Thhalv10022755m.g' => 'esa', 'TPR.G23851' => 'tpr', 'TPR.G26500' => 'tpr', 'TPR.G27267' => 'tpr', 'TPR.G32001' => 'tpr', 'TPR.G6251' => 'tpr', 'TPR.G8167' => 'tpr', 'TWI12G1330' => 'twi', 'TWI18G1239' => 'twi', 'TWI34G0979' => 'twi', 'TWI36G0670' => 'twi', 'TWI36G0707' => 'twi', 'TWI56G0233' => 'twi', 'TWI75G1809' => 'twi', 'unitig_21.g20874' => 'ugi', 'unitig_26.g10343' => 'ugi', 'unitig_46.g18392' => 'ugi', 'unitig_52.g17178' => 'ugi', 'unitig_8.g2934' => 'ugi', 'vmacro01122' => 'vma', 'vmacro05875' => 'vma', 'vmacro06147' => 'vma', 'vmacro16191' => 'vma', 'vmacro18293' => 'vma', 'VMungo0251G3707' => 'vmu', 'VMungo0464G1521' => 'vmu', 'VMungo1215G0205' => 'vmu', 'VMungo1383G2484' => 'vmu', 'Zm00001eb079610' => 'zma', 'Zm00001eb135990' => 'zma', 'Zm00001eb183710' => 'zma', 'Zm00001eb246020' => 'zma' ), 'gf_id' => 'HOM05D001124', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001124' ), 'data_identifier' => 'HOM05D001124', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001124', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '548', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02520' => 'bna', 'A03p06630' => 'bna', 'A05p44460' => 'bna', 'A06p08710' => 'bna', 'A06p41090' => 'bna', 'A07p32320' => 'bna', 'A08p32520' => 'bna', 'A09p10360' => 'bna', 'A10p24080' => 'bna', 'Aa31LG11G15250' => 'aar', 'Aa31LG1G1800' => 'aar', 'Aa31LG2G5120' => 'aar', 'Aa31LG2G6070' => 'aar', 'Aa31LG5G10770' => 'aar', 'Aa31sc61G90' => 'aar', 'Actinidia01352' => 'ach', 'Actinidia05983' => 'ach', 'Actinidia08133' => 'ach', 'Actinidia15101' => 'ach', 'Actinidia26379' => 'ach', 'Actinidia35778' => 'ach', 'Actinidia36123' => 'ach', 'Actinidia37436' => 'ach', 'Actinidia38730' => 'ach', 'Ah.02g128210' => 'amhyb', 'Ah.03g132990' => 'amhyb', 'Ah.14g079410' => 'amhyb', 'AL1G24640' => 'aly', 'AL2G26680' => 'aly', 'AL3G10530' => 'aly', 'AL3G45230' => 'aly', 'AL5G15230' => 'aly', 'AL5G16960' => 'aly', 'AL6G25210' => 'aly', 'Aqoxy2G00441' => 'aox', 'Aqoxy3G01236' => 'aox', 'Aqoxy5G03746' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3RQ047' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C7GMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9C8JER' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MBL6KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YXCZ83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZANX40' => 'arhy', 'AT1G12990' => 'ath', 'AT1G67880' => 'ath', 'AT2G13290' => 'ath', 'AT3G01620' => 'ath', 'AT3G26445' => 'ath', 'AT3G27540' => 'ath', 'AT5G14480' => 'ath', 'ATR0824G026' => 'atr', 'ATR1098G019' => 'atr', 'Atru.chr11.2145' => 'acertr', 'Atru.chr2.3636' => 'acertr', 'Atru.chr2.3644' => 'acertr', 'Atru.chr6.2422' => 'acertr', 'Atru.chr7.1112' => 'acertr', 'AUR62005469' => 'cqu', 'AUR62011166' => 'cqu', 'AUR62013319' => 'cqu', 'AUR62024273' => 'cqu', 'AUR62028420' => 'cqu', 'AUR62041942' => 'cqu', 'BcaB01g04969' => 'bca', 'BcaB01g06371' => 'bca', 'BcaB02g11494' => 'bca', 'BcaB03g15382' => 'bca', 'BcaB08g36994' => 'bca', 'BcaC03g13477' => 'bca', 'BcaC03g13478' => 'bca', 'BcaC03g13480' => 'bca', 'BcaC03g13481' => 'bca', 'BcaC03g13486' => 'bca', 'BcaC04g19031' => 'bca', 'BcaC04g23085' => 'bca', 'BcaC05g25094' => 'bca', 'BcaC05g25096' => 'bca', 'BcaC05g25138' => 'bca', 'BcaC05g30416' => 'bca', 'BcaC05g30455' => 'bca', 'BcaC06g30979' => 'bca', 'BcaC06g33805' => 'bca', 'BcaC08g46021' => 'bca', 'BcaNung03154' => 'bca', 'BolC2t06623H' => 'bol', 'BolC2t06632H' => 'bol', 'BolC2t06635H' => 'bol', 'BolC2t06638H' => 'bol', 'BolC3t13266H' => 'bol', 'BolC5t29776H' => 'bol', 'BolC6t38912H' => 'bol', 'BolC7t44183H' => 'bol', 'BolC9t54123H' => 'bol', 'BolC9t59107H' => 'bol', 'BraA02t05221Z' => 'bra', 'BraA03t09996Z' => 'bra', 'BraA05t23210Z' => 'bra', 'BraA06t24068Z' => 'bra', 'BraA06t27032Z' => 'bra', 'BraA08t35176Z' => 'bra', 'BraA09t36680Z' => 'bra', 'BraA10t44471Z' => 'bra', 'C02p06760' => 'bna', 'C02p06890' => 'bna', 'C02p07010' => 'bna', 'C03p07660' => 'bna', 'C05p10300' => 'bna', 'C06p38150' => 'bna', 'C07p36650' => 'bna', 'C08p15770' => 'bna', 'C09p12300' => 'bna', 'C09p62700' => 'bna', 'C09p75040' => 'bna', 'CAN.G13.1' => 'can', 'CAN.G138.4' => 'can', 'CAN.G44.6' => 'can', 'CAN.G473.19' => 'can', 'CANSAT01G0835' => 'cansat', 'CANSAT11G0246' => 'cansat', 'CANSAT11G1766' => 'cansat', 'CANSAT64G1954' => 'cansat', 'CARHR013330' => 'chi', 'CARHR060530' => 'chi', 'CARHR075300' => 'chi', 'CARHR105120' => 'chi', 'CARHR148910' => 'chi', 'CARHR198830' => 'chi', 'Carub.0001s1275' => 'cru', 'Carub.0002s1437' => 'cru', 'Carub.0003s0044' => 'cru', 'Carub.0003s2787' => 'cru', 'Carub.0005s0597' => 'cru', 'Carub.0006s1266' => 'cru', 'Ca_06935_v3' => 'car', 'Ca_13559_v3' => 'car', 'Ca_16941_v3' => 'car', 'Ca_16960_v3' => 'car', 'Ca_17775_v3' => 'car', 'Ca_30464_v3' => 'car', 'Cc06_g08160' => 'ccan', 'Cc07_g01520' => 'ccan', 'Cc11_g15810' => 'ccan', 'CDE02G2840' => 'cde', 'CDE03G0093' => 'cde', 'CDE04G2127' => 'cde', 'CDE07G1857' => 'cde', 'CDE09G1246' => 'cde', 'Cfa003412' => 'cfa', 'Cfa007341' => 'cfa', 'Cfa009220' => 'cfa', 'Ciclev10008737m.g' => 'ccl', 'Ciclev10015565m.g' => 'ccl', 'Ciclev10031761m.g' => 'ccl', 'CiPaw.03G045300' => 'cil', 'CiPaw.03G247200' => 'cil', 'CiPaw.04G029500' => 'cil', 'CiPaw.04G174000' => 'cil', 'CiPaw.05G181200' => 'cil', 'CiPaw.06G067100' => 'cil', 'ClCG05G025800' => 'cla', 'ClCG06G011400' => 'cla', 'ClCG09G019360' => 'cla', 'COL.COLO4_04827' => 'col', 'COL.COLO4_29170' => 'col', 'COL.COLO4_35131' => 'col', 'COL.COLO4_35132' => 'col', 'Cpa.g.sc33.32' => 'cpa', 'Cpa.g.sc46.29' => 'cpa', 'Cpa.g.sc796.1' => 'cpa', 'CsaV3_1G030420' => 'csa', 'CsaV3_5G027050' => 'csa', 'CsaV3_5G031040' => 'csa', 'CsaV3_UNG023130' => 'csa', 'CSS0007726' => 'camsi', 'CSS0016433' => 'camsi', 'CSS0017656' => 'camsi', 'CSS0025364' => 'camsi', 'CSS0027582' => 'camsi', 'CSS0047288' => 'camsi', 'CSS0049950' => 'camsi', 'DCAR_003843' => 'dca', 'DCAR_007052' => 'dca', 'DCAR_020884' => 'dca', 'DCAR_021730' => 'dca', 'DCAR_024423' => 'dca', 'DCAR_026509' => 'dca', 'DCAR_031158' => 'dca', 'Dinv14728' => 'din', 'Dinv15219' => 'din', 'Dinv25728' => 'din', 'Dinv33428' => 'din', 'Dinv36489' => 'din', 'Dinv41486' => 'din', 'Duzib147G0469' => 'dzi', 'Duzib168G0060' => 'dzi', 'Duzib187G1215' => 'dzi', 'Duzib248G0692' => 'dzi', 'Duzib251G0767' => 'dzi', 'Duzib264G0446' => 'dzi', 'Duzib268G0691' => 'dzi', 'ECA232G4767' => 'eca', 'ECA233G2838' => 'eca', 'ECA234G0391' => 'eca', 'ECA234G0857' => 'eca', 'ECA236G1593' => 'eca', 'ECA238G0565' => 'eca', 'ECA246G1027' => 'eca', 'ECA246G3223' => 'eca', 'ECA246G3470' => 'eca', 'EL10Ac6g13829' => 'bvu', 'EL10Ac6g14093' => 'bvu', 'EL10Ac8g18707' => 'bvu', 'Eucgr.C01369' => 'egr', 'Eucgr.H02492' => 'egr', 'Eucgr.I01733' => 'egr', 'Eucgr.J02255' => 'egr', 'Eucgr.J02257' => 'egr', 'Eucgr.J02258' => 'egr', 'FAN02G1601' => 'fan', 'FAN03G1586' => 'fan', 'FAN03G2986' => 'fan', 'FAN05G4837' => 'fan', 'FAN06G0146' => 'fan', 'FAN07G0858' => 'fan', 'FAN09G3179' => 'fan', 'FAN10G0669' => 'fan', 'FAN12G2358' => 'fan', 'FAN14G4198' => 'fan', 'FAN14G5112' => 'fan', 'FAN17G0342' => 'fan', 'FAN19G0342' => 'fan', 'FAN19G0962' => 'fan', 'FAN19G1101' => 'fan', 'FAN19G1872' => 'fan', 'FAN22G0356' => 'fan', 'FAN23G0744' => 'fan', 'FAN23G1914' => 'fan', 'FAN26G0032' => 'fan', 'FAN28G0625' => 'fan', 'FvH4_1g02710' => 'fve', 'FvH4_1g02720' => 'fve', 'FvH4_4g25670' => 'fve', 'FvH4_6g51700' => 'fve', 'FvH4_7g20170' => 'fve', 'Glyma.05G175000' => 'gma', 'Glyma.08G132300' => 'gma', 'Glyma.11G243000' => 'gma', 'Glyma.13G158900' => 'gma', 'Glyma.17G112400' => 'gma', 'Glyma.18G014100' => 'gma', 'Glyma.19G003100' => 'gma', 'Glyma.19G056500' => 'gma', 'Gohir.A01G158900' => 'ghi', 'Gohir.A05G312600' => 'ghi', 'Gohir.A05G354900' => 'ghi', 'Gohir.A07G037200' => 'ghi', 'Gohir.A09G030000' => 'ghi', 'Gohir.A12G145200' => 'ghi', 'Gohir.D01G151500' => 'ghi', 'Gohir.D04G058300' => 'ghi', 'Gohir.D05G314100' => 'ghi', 'Gohir.D07G041400' => 'ghi', 'Gohir.D09G029700' => 'ghi', 'Gohir.D12G149700' => 'ghi', 'Gorai.001G043800' => 'gra', 'Gorai.002G187800' => 'gra', 'Gorai.006G034700' => 'gra', 'Gorai.008G161200' => 'gra', 'Gorai.009G335700' => 'gra', 'Gorai.012G065000' => 'gra', 'GSVIVG01000535001' => 'vvi', 'GSVIVG01015572001' => 'vvi', 'GSVIVG01032386001' => 'vvi', 'HanXRQChr05g0138531' => 'han', 'HanXRQChr06g0174391' => 'han', 'HanXRQChr07g0199021' => 'han', 'HanXRQChr08g0208211' => 'han', 'HanXRQChr09g0255471' => 'han', 'HanXRQChr10g0315791' => 'han', 'HanXRQChr12g0371991' => 'han', 'HanXRQChr15g0475251' => 'han', 'HanXRQChr17g0540001' => 'han', 'HanXRQChr17g0548631' => 'han', 'HanXRQChr17g0569561' => 'han', 'Haze_12256' => 'cav', 'Haze_14756' => 'cav', 'Haze_25528' => 'cav', 'Hma1.2p1_0079F.1_g041020' => 'hma', 'Hma1.2p1_0818F.1_g223260' => 'hma', 'Hma1.2p1_1747F.1_g300530' => 'hma', 'HPP92_004607' => 'vpl', 'HPP92_004608' => 'vpl', 'HPP92_006181' => 'vpl', 'HPP92_012192' => 'vpl', 'HPP92_015680' => 'vpl', 'HPP92_020249' => 'vpl', 'HPP92_021376' => 'vpl', 'HPP92_024275' => 'vpl', 'Hund06031' => 'sun', 'Hund25391' => 'sun', 'Lalb_Chr07g0185371' => 'lal', 'Lalb_Chr07g0185381' => 'lal', 'Lalb_Chr12g0204011' => 'lal', 'Lalb_Chr13g0301671' => 'lal', 'Lalb_Chr14g0362851' => 'lal', 'Lalb_Chr24g0403581' => 'lal', 'Lj1g0000233' => 'lja', 'Lj2g0018120' => 'lja', 'Lj3C621T0' => 'lonja', 'Lj3P1059T14' => 'lonja', 'Lj3P611T9' => 'lonja', 'Lj3P614T13' => 'lonja', 'Lj3P615T5' => 'lonja', 'Lj4g0012315' => 'lja', 'Lj4g0026182' => 'lja', 'Lj6P813T16' => 'lonja', 'Lj7C427T7' => 'lonja', 'Lj7C427T8' => 'lonja', 'Lj7P600T41' => 'lonja', 'Lju41C42G17' => 'lonja', 'Lsat_1_v5_gn_0_47300' => 'lsa', 'Lsat_1_v5_gn_2_91280' => 'lsa', 'Lsat_1_v5_gn_3_30561' => 'lsa', 'Lsat_1_v5_gn_4_184321' => 'lsa', 'Lsat_1_v5_gn_4_4041' => 'lsa', 'Lsat_1_v5_gn_5_92000' => 'lsa', 'Lsat_1_v5_gn_8_152940' => 'lsa', 'Lsat_1_v5_gn_8_62401' => 'lsa', 'Manes.06G055900' => 'mes', 'Manes.12G022200' => 'mes', 'Manes.13G023300' => 'mes', 'Manes.14G115000' => 'mes', 'Manes.15G151700' => 'mes', 'Manes.17G111300' => 'mes', 'Mapoly0226s0009' => 'mpo', 'MBI02_g25363_MAGBIO' => 'mbi', 'MBI06_g00027_MAGBIO' => 'mbi', 'MBI10_g13034_MAGBIO' => 'mbi', 'MD09G1023400' => 'mdo', 'MD13G1100100' => 'mdo', 'MD15G1169200' => 'mdo', 'MD16G1101100' => 'mdo', 'MD17G1022900' => 'mdo', 'Medtr3g096150' => 'mtr', 'Medtr4g115070' => 'mtr', 'Medtr7g033325' => 'mtr', 'Medtr8g089840' => 'mtr', 'MELO3C010319.2' => 'cme', 'MELO3C011944.2' => 'cme', 'MELO3C021589.2' => 'cme', 'Migut.E00207' => 'egut', 'Migut.H00067' => 'egut', 'Migut.K00433' => 'egut', 'Migut.K00606' => 'egut', 'Migut.K01410' => 'egut', 'MSTRG.13347' => 'ama', 'MSTRG.24045' => 'ama', 'MSTRG.2428' => 'ama', 'MSTRG.26410' => 'ama', 'MSTRG.3139' => 'ama', 'MSTRG.3286' => 'ama', 'MSTRG.563' => 'ama', 'MSTRG.7941' => 'ama', 'Nitab4.5_0000028g0060' => 'nta', 'Nitab4.5_0000065g0260' => 'nta', 'Nitab4.5_0000112g0060' => 'nta', 'Nitab4.5_0000489g0120' => 'nta', 'Nitab4.5_0001776g0050' => 'nta', 'Nitab4.5_0001854g0010' => 'nta', 'Nitab4.5_0001860g0020' => 'nta', 'Nitab4.5_0004352g0010' => 'nta', 'Nitab4.5_0008716g0020' => 'nta', 'Nitab4.5_0008922g0010' => 'nta', 'Nn3g16693' => 'nnu', 'Nn4g22596' => 'nnu', 'Nn7g37639' => 'nnu', 'Oeu001701.1' => 'oeu', 'Oeu018149.1' => 'oeu', 'Oeu026220.1' => 'oeu', 'Oeu038635.1' => 'oeu', 'Oeu049176.1' => 'oeu', 'Oeu056706.1' => 'oeu', 'Oeu056937.1' => 'oeu', 'Oeu057540.1' => 'oeu', 'Os02g0594900' => 'osa', 'Os02g0595100' => 'osa', 'Os04g0477500' => 'osa', 'Os12g0611900' => 'osa', 'Peaxi162Scf00076g00020' => 'pax', 'Peaxi162Scf00128g00217' => 'pax', 'Peaxi162Scf00129g01640' => 'pax', 'Peaxi162Scf00669g00007' => 'pax', 'Peaxi162Scf00700g00421' => 'pax', 'Peaxi162Scf00801g00038' => 'pax', 'Peaxi162Scf00891g00025' => 'pax', 'PGR083G0909' => 'pgr', 'PGR119G1005' => 'pgr', 'PGR142G2236' => 'pgr', 'PGR142G3388' => 'pgr', 'PGSC0003DMG400004514' => 'stu', 'PGSC0003DMG400012635' => 'stu', 'PGSC0003DMG400015730' => 'stu', 'PGSC0003DMG400018611' => 'stu', 'PGSC0003DMG400030897' => 'stu', 'Phvul.001G254800' => 'pvu', 'Phvul.002G260100' => 'pvu', 'Phvul.003G167600' => 'pvu', 'Phvul.004G005100' => 'pvu', 'Potri.001G343600' => 'ptr', 'Potri.006G066700' => 'ptr', 'Potri.008G186000' => 'ptr', 'Potri.010G046900' => 'ptr', 'Potri.018G127900' => 'ptr', 'Pp3c20_17750' => 'ppa', 'Pp3c24_4380' => 'ppa', 'Prupe.1G245800' => 'ppe', 'Prupe.3G293400' => 'ppe', 'Prupe.7G247400' => 'ppe', 'Psat0s145g0120' => 'psa', 'Psat0s595g0040' => 'psa', 'Psat0s595g0120' => 'psa', 'Psat3g175040' => 'psa', 'Psat7g058120' => 'psa', 'PSO017G0428' => 'pso', 'PSO063G7510' => 'pso', 'PSO067G0046' => 'pso', 'PSO478G1073' => 'pso', 'PSO675G3677' => 'pso', 'PSO675G6558' => 'pso', 'PSO675G7520' => 'pso', 'PSO675G8959' => 'pso', 'QL02p074089' => 'qlo', 'QL02p089614' => 'qlo', 'QL03p057736' => 'qlo', 'RcHm_v2.0_Chr1g0364131' => 'rch', 'RcHm_v2.0_Chr2g0087801' => 'rch', 'RcHm_v2.0_Chr2g0087821' => 'rch', 'RcHm_v2.0_Chr2g0173231' => 'rch', 'RcHm_v2.0_Chr4g0433111' => 'rch', 'Rhsim03G0250300' => 'rsi', 'Rhsim08G0048400' => 'rsi', 'Rhsim10G0014800' => 'rsi', 'Rhsim12G0040100' => 'rsi', 'Rhsim12G0109700' => 'rsi', 'Sabra06G0049600' => 'sbr', 'Sabra08G0141000' => 'sbr', 'Sabra10G0021400' => 'sbr', 'Sabra16G0222900' => 'sbr', 'Sabra18G0108600' => 'sbr', 'SalBow1G0433' => 'sbo', 'SalBow1G2038' => 'sbo', 'SalBow1G5003' => 'sbo', 'SalBow7G1197' => 'sbo', 'SalBow8G3506' => 'sbo', 'Sc03g0007300' => 'sci', 'Sc11g0000950' => 'sci', 'Sc14g0008750' => 'sci', 'Sc18g0000420' => 'sci', 'Sed0006754' => 'sed', 'Sed0008741' => 'sed', 'Sed0017172' => 'sed', 'Sed0018925' => 'sed', 'Sed0023326' => 'sed', 'Sed0025909' => 'sed', 'SEGI_05333' => 'sgi', 'SEGI_10362' => 'sgi', 'SEGI_13380' => 'sgi', 'SEGI_24306' => 'sgi', 'SEGI_29077' => 'sgi', 'SEGI_29095' => 'sgi', 'SEGI_36534' => 'sgi', 'SEGI_37506' => 'sgi', 'SEGI_38321' => 'sgi', 'SGA_v2.0_scaffold307G48031' => 'sas', 'SGA_v2.0_scaffold47G17507' => 'sas', 'SGA_v2.0_scaffold63G21736' => 'sas', 'SGA_v2.0_scaffold87G27070' => 'sas', 'SHI17794' => 'shi', 'SHI28851' => 'shi', 'SMO165G0155' => 'smo', 'SMO340G0217' => 'smo', 'SMO367G1210' => 'smo', 'Solyc02g093430.3' => 'sly', 'Solyc05g013580.4' => 'sly', 'Solyc07g008030.3' => 'sly', 'Solyc12g035470.2' => 'sly', 'Sopen02g038020' => 'spe', 'Sopen05g008490' => 'spe', 'Sopen07g003910' => 'spe', 'Sopen12g015240' => 'spe', 'Sp1g11550' => 'spa', 'Sp2g16710' => 'spa', 'Sp3g00430' => 'spa', 'Sp3g26780' => 'spa', 'Sp5g22900' => 'spa', 'Sp6g29530' => 'spa', 'TAR371G0794' => 'tar', 'TAR374G0164' => 'tar', 'TAR622G0165' => 'tar', 'TAR626G0929' => 'tar', 'TAR629G2155' => 'tar', 'THA.LOC104805282' => 'tha', 'THA.LOC104805363' => 'tha', 'THA.LOC104808968' => 'tha', 'THA.LOC104821093' => 'tha', 'THA.LOC104823953' => 'tha', 'THA.LOC104825562' => 'tha', 'THA.LOC104825665' => 'tha', 'Thecc.02G261400' => 'tca', 'Thecc.04G019200' => 'tca', 'Thecc.09G130400' => 'tca', 'Thhalv10004374m.g' => 'esa', 'Thhalv10007850m.g' => 'esa', 'Thhalv10013782m.g' => 'esa', 'Thhalv10018686m.g' => 'esa', 'Thhalv10020899m.g' => 'esa', 'Thhalv10022755m.g' => 'esa', 'TPR.G23851' => 'tpr', 'TPR.G26500' => 'tpr', 'TPR.G27267' => 'tpr', 'TPR.G32001' => 'tpr', 'TPR.G6251' => 'tpr', 'TPR.G8167' => 'tpr', 'TWI12G1330' => 'twi', 'TWI18G1239' => 'twi', 'TWI34G0979' => 'twi', 'TWI36G0670' => 'twi', 'TWI36G0707' => 'twi', 'TWI56G0233' => 'twi', 'TWI75G1809' => 'twi', 'unitig_21.g20874' => 'ugi', 'unitig_26.g10343' => 'ugi', 'unitig_46.g18392' => 'ugi', 'unitig_52.g17178' => 'ugi', 'unitig_8.g2934' => 'ugi', 'vmacro01122' => 'vma', 'vmacro05875' => 'vma', 'vmacro06147' => 'vma', 'vmacro16191' => 'vma', 'vmacro18293' => 'vma', 'VMungo0251G3707' => 'vmu', 'VMungo0464G1521' => 'vmu', 'VMungo1215G0205' => 'vmu', 'VMungo1383G2484' => 'vmu', 'Zm00001eb079610' => 'zma', 'Zm00001eb135990' => 'zma', 'Zm00001eb183710' => 'zma', 'Zm00001eb246020' => 'zma' ) $gf_id = 'HOM05D001124' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001124' ) $data_identifier = 'HOM05D001124' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 6, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 7, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 21, 'bol' => (int) 10, 'bra' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 6, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 9, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 21, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 8, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 10, 'lsa' => (int) 8, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 8, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 9, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb246020' $species_info = array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ) $local_species = 'cru' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001124', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '548', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02520' => 'bna', 'A03p06630' => 'bna', 'A05p44460' => 'bna', 'A06p08710' => 'bna', 'A06p41090' => 'bna', 'A07p32320' => 'bna', 'A08p32520' => 'bna', 'A09p10360' => 'bna', 'A10p24080' => 'bna', 'Aa31LG11G15250' => 'aar', 'Aa31LG1G1800' => 'aar', 'Aa31LG2G5120' => 'aar', 'Aa31LG2G6070' => 'aar', 'Aa31LG5G10770' => 'aar', 'Aa31sc61G90' => 'aar', 'Actinidia01352' => 'ach', 'Actinidia05983' => 'ach', 'Actinidia08133' => 'ach', 'Actinidia15101' => 'ach', 'Actinidia26379' => 'ach', 'Actinidia35778' => 'ach', 'Actinidia36123' => 'ach', 'Actinidia37436' => 'ach', 'Actinidia38730' => 'ach', 'Ah.02g128210' => 'amhyb', 'Ah.03g132990' => 'amhyb', 'Ah.14g079410' => 'amhyb', 'AL1G24640' => 'aly', 'AL2G26680' => 'aly', 'AL3G10530' => 'aly', 'AL3G45230' => 'aly', 'AL5G15230' => 'aly', 'AL5G16960' => 'aly', 'AL6G25210' => 'aly', 'Aqoxy2G00441' => 'aox', 'Aqoxy3G01236' => 'aox', 'Aqoxy5G03746' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3RQ047' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C7GMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9C8JER' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MBL6KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YXCZ83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZANX40' => 'arhy', 'AT1G12990' => 'ath', 'AT1G67880' => 'ath', 'AT2G13290' => 'ath', 'AT3G01620' => 'ath', 'AT3G26445' => 'ath', 'AT3G27540' => 'ath', 'AT5G14480' => 'ath', 'ATR0824G026' => 'atr', 'ATR1098G019' => 'atr', 'Atru.chr11.2145' => 'acertr', 'Atru.chr2.3636' => 'acertr', 'Atru.chr2.3644' => 'acertr', 'Atru.chr6.2422' => 'acertr', 'Atru.chr7.1112' => 'acertr', 'AUR62005469' => 'cqu', 'AUR62011166' => 'cqu', 'AUR62013319' => 'cqu', 'AUR62024273' => 'cqu', 'AUR62028420' => 'cqu', 'AUR62041942' => 'cqu', 'BcaB01g04969' => 'bca', 'BcaB01g06371' => 'bca', 'BcaB02g11494' => 'bca', 'BcaB03g15382' => 'bca', 'BcaB08g36994' => 'bca', 'BcaC03g13477' => 'bca', 'BcaC03g13478' => 'bca', 'BcaC03g13480' => 'bca', 'BcaC03g13481' => 'bca', 'BcaC03g13486' => 'bca', 'BcaC04g19031' => 'bca', 'BcaC04g23085' => 'bca', 'BcaC05g25094' => 'bca', 'BcaC05g25096' => 'bca', 'BcaC05g25138' => 'bca', 'BcaC05g30416' => 'bca', 'BcaC05g30455' => 'bca', 'BcaC06g30979' => 'bca', 'BcaC06g33805' => 'bca', 'BcaC08g46021' => 'bca', 'BcaNung03154' => 'bca', 'BolC2t06623H' => 'bol', 'BolC2t06632H' => 'bol', 'BolC2t06635H' => 'bol', 'BolC2t06638H' => 'bol', 'BolC3t13266H' => 'bol', 'BolC5t29776H' => 'bol', 'BolC6t38912H' => 'bol', 'BolC7t44183H' => 'bol', 'BolC9t54123H' => 'bol', 'BolC9t59107H' => 'bol', 'BraA02t05221Z' => 'bra', 'BraA03t09996Z' => 'bra', 'BraA05t23210Z' => 'bra', 'BraA06t24068Z' => 'bra', 'BraA06t27032Z' => 'bra', 'BraA08t35176Z' => 'bra', 'BraA09t36680Z' => 'bra', 'BraA10t44471Z' => 'bra', 'C02p06760' => 'bna', 'C02p06890' => 'bna', 'C02p07010' => 'bna', 'C03p07660' => 'bna', 'C05p10300' => 'bna', 'C06p38150' => 'bna', 'C07p36650' => 'bna', 'C08p15770' => 'bna', 'C09p12300' => 'bna', 'C09p62700' => 'bna', 'C09p75040' => 'bna', 'CAN.G13.1' => 'can', 'CAN.G138.4' => 'can', 'CAN.G44.6' => 'can', 'CAN.G473.19' => 'can', 'CANSAT01G0835' => 'cansat', 'CANSAT11G0246' => 'cansat', 'CANSAT11G1766' => 'cansat', 'CANSAT64G1954' => 'cansat', 'CARHR013330' => 'chi', 'CARHR060530' => 'chi', 'CARHR075300' => 'chi', 'CARHR105120' => 'chi', 'CARHR148910' => 'chi', 'CARHR198830' => 'chi', 'Carub.0001s1275' => 'cru', 'Carub.0002s1437' => 'cru', 'Carub.0003s0044' => 'cru', 'Carub.0003s2787' => 'cru', 'Carub.0005s0597' => 'cru', 'Carub.0006s1266' => 'cru', 'Ca_06935_v3' => 'car', 'Ca_13559_v3' => 'car', 'Ca_16941_v3' => 'car', 'Ca_16960_v3' => 'car', 'Ca_17775_v3' => 'car', 'Ca_30464_v3' => 'car', 'Cc06_g08160' => 'ccan', 'Cc07_g01520' => 'ccan', 'Cc11_g15810' => 'ccan', 'CDE02G2840' => 'cde', 'CDE03G0093' => 'cde', 'CDE04G2127' => 'cde', 'CDE07G1857' => 'cde', 'CDE09G1246' => 'cde', 'Cfa003412' => 'cfa', 'Cfa007341' => 'cfa', 'Cfa009220' => 'cfa', 'Ciclev10008737m.g' => 'ccl', 'Ciclev10015565m.g' => 'ccl', 'Ciclev10031761m.g' => 'ccl', 'CiPaw.03G045300' => 'cil', 'CiPaw.03G247200' => 'cil', 'CiPaw.04G029500' => 'cil', 'CiPaw.04G174000' => 'cil', 'CiPaw.05G181200' => 'cil', 'CiPaw.06G067100' => 'cil', 'ClCG05G025800' => 'cla', 'ClCG06G011400' => 'cla', 'ClCG09G019360' => 'cla', 'COL.COLO4_04827' => 'col', 'COL.COLO4_29170' => 'col', 'COL.COLO4_35131' => 'col', 'COL.COLO4_35132' => 'col', 'Cpa.g.sc33.32' => 'cpa', 'Cpa.g.sc46.29' => 'cpa', 'Cpa.g.sc796.1' => 'cpa', 'CsaV3_1G030420' => 'csa', 'CsaV3_5G027050' => 'csa', 'CsaV3_5G031040' => 'csa', 'CsaV3_UNG023130' => 'csa', 'CSS0007726' => 'camsi', 'CSS0016433' => 'camsi', 'CSS0017656' => 'camsi', 'CSS0025364' => 'camsi', 'CSS0027582' => 'camsi', 'CSS0047288' => 'camsi', 'CSS0049950' => 'camsi', 'DCAR_003843' => 'dca', 'DCAR_007052' => 'dca', 'DCAR_020884' => 'dca', 'DCAR_021730' => 'dca', 'DCAR_024423' => 'dca', 'DCAR_026509' => 'dca', 'DCAR_031158' => 'dca', 'Dinv14728' => 'din', 'Dinv15219' => 'din', 'Dinv25728' => 'din', 'Dinv33428' => 'din', 'Dinv36489' => 'din', 'Dinv41486' => 'din', 'Duzib147G0469' => 'dzi', 'Duzib168G0060' => 'dzi', 'Duzib187G1215' => 'dzi', 'Duzib248G0692' => 'dzi', 'Duzib251G0767' => 'dzi', 'Duzib264G0446' => 'dzi', 'Duzib268G0691' => 'dzi', 'ECA232G4767' => 'eca', 'ECA233G2838' => 'eca', 'ECA234G0391' => 'eca', 'ECA234G0857' => 'eca', 'ECA236G1593' => 'eca', 'ECA238G0565' => 'eca', 'ECA246G1027' => 'eca', 'ECA246G3223' => 'eca', 'ECA246G3470' => 'eca', 'EL10Ac6g13829' => 'bvu', 'EL10Ac6g14093' => 'bvu', 'EL10Ac8g18707' => 'bvu', 'Eucgr.C01369' => 'egr', 'Eucgr.H02492' => 'egr', 'Eucgr.I01733' => 'egr', 'Eucgr.J02255' => 'egr', 'Eucgr.J02257' => 'egr', 'Eucgr.J02258' => 'egr', 'FAN02G1601' => 'fan', 'FAN03G1586' => 'fan', 'FAN03G2986' => 'fan', 'FAN05G4837' => 'fan', 'FAN06G0146' => 'fan', 'FAN07G0858' => 'fan', 'FAN09G3179' => 'fan', 'FAN10G0669' => 'fan', 'FAN12G2358' => 'fan', 'FAN14G4198' => 'fan', 'FAN14G5112' => 'fan', 'FAN17G0342' => 'fan', 'FAN19G0342' => 'fan', 'FAN19G0962' => 'fan', 'FAN19G1101' => 'fan', 'FAN19G1872' => 'fan', 'FAN22G0356' => 'fan', 'FAN23G0744' => 'fan', 'FAN23G1914' => 'fan', 'FAN26G0032' => 'fan', 'FAN28G0625' => 'fan', 'FvH4_1g02710' => 'fve', 'FvH4_1g02720' => 'fve', 'FvH4_4g25670' => 'fve', 'FvH4_6g51700' => 'fve', 'FvH4_7g20170' => 'fve', 'Glyma.05G175000' => 'gma', 'Glyma.08G132300' => 'gma', 'Glyma.11G243000' => 'gma', 'Glyma.13G158900' => 'gma', 'Glyma.17G112400' => 'gma', 'Glyma.18G014100' => 'gma', 'Glyma.19G003100' => 'gma', 'Glyma.19G056500' => 'gma', 'Gohir.A01G158900' => 'ghi', 'Gohir.A05G312600' => 'ghi', 'Gohir.A05G354900' => 'ghi', 'Gohir.A07G037200' => 'ghi', 'Gohir.A09G030000' => 'ghi', 'Gohir.A12G145200' => 'ghi', 'Gohir.D01G151500' => 'ghi', 'Gohir.D04G058300' => 'ghi', 'Gohir.D05G314100' => 'ghi', 'Gohir.D07G041400' => 'ghi', 'Gohir.D09G029700' => 'ghi', 'Gohir.D12G149700' => 'ghi', 'Gorai.001G043800' => 'gra', 'Gorai.002G187800' => 'gra', 'Gorai.006G034700' => 'gra', 'Gorai.008G161200' => 'gra', 'Gorai.009G335700' => 'gra', 'Gorai.012G065000' => 'gra', 'GSVIVG01000535001' => 'vvi', 'GSVIVG01015572001' => 'vvi', 'GSVIVG01032386001' => 'vvi', 'HanXRQChr05g0138531' => 'han', 'HanXRQChr06g0174391' => 'han', 'HanXRQChr07g0199021' => 'han', 'HanXRQChr08g0208211' => 'han', 'HanXRQChr09g0255471' => 'han', 'HanXRQChr10g0315791' => 'han', 'HanXRQChr12g0371991' => 'han', 'HanXRQChr15g0475251' => 'han', 'HanXRQChr17g0540001' => 'han', 'HanXRQChr17g0548631' => 'han', 'HanXRQChr17g0569561' => 'han', 'Haze_12256' => 'cav', 'Haze_14756' => 'cav', 'Haze_25528' => 'cav', 'Hma1.2p1_0079F.1_g041020' => 'hma', 'Hma1.2p1_0818F.1_g223260' => 'hma', 'Hma1.2p1_1747F.1_g300530' => 'hma', 'HPP92_004607' => 'vpl', 'HPP92_004608' => 'vpl', 'HPP92_006181' => 'vpl', 'HPP92_012192' => 'vpl', 'HPP92_015680' => 'vpl', 'HPP92_020249' => 'vpl', 'HPP92_021376' => 'vpl', 'HPP92_024275' => 'vpl', 'Hund06031' => 'sun', 'Hund25391' => 'sun', 'Lalb_Chr07g0185371' => 'lal', 'Lalb_Chr07g0185381' => 'lal', 'Lalb_Chr12g0204011' => 'lal', 'Lalb_Chr13g0301671' => 'lal', 'Lalb_Chr14g0362851' => 'lal', 'Lalb_Chr24g0403581' => 'lal', 'Lj1g0000233' => 'lja', 'Lj2g0018120' => 'lja', 'Lj3C621T0' => 'lonja', 'Lj3P1059T14' => 'lonja', 'Lj3P611T9' => 'lonja', 'Lj3P614T13' => 'lonja', 'Lj3P615T5' => 'lonja', 'Lj4g0012315' => 'lja', 'Lj4g0026182' => 'lja', 'Lj6P813T16' => 'lonja', 'Lj7C427T7' => 'lonja', 'Lj7C427T8' => 'lonja', 'Lj7P600T41' => 'lonja', 'Lju41C42G17' => 'lonja', 'Lsat_1_v5_gn_0_47300' => 'lsa', 'Lsat_1_v5_gn_2_91280' => 'lsa', 'Lsat_1_v5_gn_3_30561' => 'lsa', 'Lsat_1_v5_gn_4_184321' => 'lsa', 'Lsat_1_v5_gn_4_4041' => 'lsa', 'Lsat_1_v5_gn_5_92000' => 'lsa', 'Lsat_1_v5_gn_8_152940' => 'lsa', 'Lsat_1_v5_gn_8_62401' => 'lsa', 'Manes.06G055900' => 'mes', 'Manes.12G022200' => 'mes', 'Manes.13G023300' => 'mes', 'Manes.14G115000' => 'mes', 'Manes.15G151700' => 'mes', 'Manes.17G111300' => 'mes', 'Mapoly0226s0009' => 'mpo', 'MBI02_g25363_MAGBIO' => 'mbi', 'MBI06_g00027_MAGBIO' => 'mbi', 'MBI10_g13034_MAGBIO' => 'mbi', 'MD09G1023400' => 'mdo', 'MD13G1100100' => 'mdo', 'MD15G1169200' => 'mdo', 'MD16G1101100' => 'mdo', 'MD17G1022900' => 'mdo', 'Medtr3g096150' => 'mtr', 'Medtr4g115070' => 'mtr', 'Medtr7g033325' => 'mtr', 'Medtr8g089840' => 'mtr', 'MELO3C010319.2' => 'cme', 'MELO3C011944.2' => 'cme', 'MELO3C021589.2' => 'cme', 'Migut.E00207' => 'egut', 'Migut.H00067' => 'egut', 'Migut.K00433' => 'egut', 'Migut.K00606' => 'egut', 'Migut.K01410' => 'egut', 'MSTRG.13347' => 'ama', 'MSTRG.24045' => 'ama', 'MSTRG.2428' => 'ama', 'MSTRG.26410' => 'ama', 'MSTRG.3139' => 'ama', 'MSTRG.3286' => 'ama', 'MSTRG.563' => 'ama', 'MSTRG.7941' => 'ama', 'Nitab4.5_0000028g0060' => 'nta', 'Nitab4.5_0000065g0260' => 'nta', 'Nitab4.5_0000112g0060' => 'nta', 'Nitab4.5_0000489g0120' => 'nta', 'Nitab4.5_0001776g0050' => 'nta', 'Nitab4.5_0001854g0010' => 'nta', 'Nitab4.5_0001860g0020' => 'nta', 'Nitab4.5_0004352g0010' => 'nta', 'Nitab4.5_0008716g0020' => 'nta', 'Nitab4.5_0008922g0010' => 'nta', 'Nn3g16693' => 'nnu', 'Nn4g22596' => 'nnu', 'Nn7g37639' => 'nnu', 'Oeu001701.1' => 'oeu', 'Oeu018149.1' => 'oeu', 'Oeu026220.1' => 'oeu', 'Oeu038635.1' => 'oeu', 'Oeu049176.1' => 'oeu', 'Oeu056706.1' => 'oeu', 'Oeu056937.1' => 'oeu', 'Oeu057540.1' => 'oeu', 'Os02g0594900' => 'osa', 'Os02g0595100' => 'osa', 'Os04g0477500' => 'osa', 'Os12g0611900' => 'osa', 'Peaxi162Scf00076g00020' => 'pax', 'Peaxi162Scf00128g00217' => 'pax', 'Peaxi162Scf00129g01640' => 'pax', 'Peaxi162Scf00669g00007' => 'pax', 'Peaxi162Scf00700g00421' => 'pax', 'Peaxi162Scf00801g00038' => 'pax', 'Peaxi162Scf00891g00025' => 'pax', 'PGR083G0909' => 'pgr', 'PGR119G1005' => 'pgr', 'PGR142G2236' => 'pgr', 'PGR142G3388' => 'pgr', 'PGSC0003DMG400004514' => 'stu', 'PGSC0003DMG400012635' => 'stu', 'PGSC0003DMG400015730' => 'stu', 'PGSC0003DMG400018611' => 'stu', 'PGSC0003DMG400030897' => 'stu', 'Phvul.001G254800' => 'pvu', 'Phvul.002G260100' => 'pvu', 'Phvul.003G167600' => 'pvu', 'Phvul.004G005100' => 'pvu', 'Potri.001G343600' => 'ptr', 'Potri.006G066700' => 'ptr', 'Potri.008G186000' => 'ptr', 'Potri.010G046900' => 'ptr', 'Potri.018G127900' => 'ptr', 'Pp3c20_17750' => 'ppa', 'Pp3c24_4380' => 'ppa', 'Prupe.1G245800' => 'ppe', 'Prupe.3G293400' => 'ppe', 'Prupe.7G247400' => 'ppe', 'Psat0s145g0120' => 'psa', 'Psat0s595g0040' => 'psa', 'Psat0s595g0120' => 'psa', 'Psat3g175040' => 'psa', 'Psat7g058120' => 'psa', 'PSO017G0428' => 'pso', 'PSO063G7510' => 'pso', 'PSO067G0046' => 'pso', 'PSO478G1073' => 'pso', 'PSO675G3677' => 'pso', 'PSO675G6558' => 'pso', 'PSO675G7520' => 'pso', 'PSO675G8959' => 'pso', 'QL02p074089' => 'qlo', 'QL02p089614' => 'qlo', 'QL03p057736' => 'qlo', 'RcHm_v2.0_Chr1g0364131' => 'rch', 'RcHm_v2.0_Chr2g0087801' => 'rch', 'RcHm_v2.0_Chr2g0087821' => 'rch', 'RcHm_v2.0_Chr2g0173231' => 'rch', 'RcHm_v2.0_Chr4g0433111' => 'rch', 'Rhsim03G0250300' => 'rsi', 'Rhsim08G0048400' => 'rsi', 'Rhsim10G0014800' => 'rsi', 'Rhsim12G0040100' => 'rsi', 'Rhsim12G0109700' => 'rsi', 'Sabra06G0049600' => 'sbr', 'Sabra08G0141000' => 'sbr', 'Sabra10G0021400' => 'sbr', 'Sabra16G0222900' => 'sbr', 'Sabra18G0108600' => 'sbr', 'SalBow1G0433' => 'sbo', 'SalBow1G2038' => 'sbo', 'SalBow1G5003' => 'sbo', 'SalBow7G1197' => 'sbo', 'SalBow8G3506' => 'sbo', 'Sc03g0007300' => 'sci', 'Sc11g0000950' => 'sci', 'Sc14g0008750' => 'sci', 'Sc18g0000420' => 'sci', 'Sed0006754' => 'sed', 'Sed0008741' => 'sed', 'Sed0017172' => 'sed', 'Sed0018925' => 'sed', 'Sed0023326' => 'sed', 'Sed0025909' => 'sed', 'SEGI_05333' => 'sgi', 'SEGI_10362' => 'sgi', 'SEGI_13380' => 'sgi', 'SEGI_24306' => 'sgi', 'SEGI_29077' => 'sgi', 'SEGI_29095' => 'sgi', 'SEGI_36534' => 'sgi', 'SEGI_37506' => 'sgi', 'SEGI_38321' => 'sgi', 'SGA_v2.0_scaffold307G48031' => 'sas', 'SGA_v2.0_scaffold47G17507' => 'sas', 'SGA_v2.0_scaffold63G21736' => 'sas', 'SGA_v2.0_scaffold87G27070' => 'sas', 'SHI17794' => 'shi', 'SHI28851' => 'shi', 'SMO165G0155' => 'smo', 'SMO340G0217' => 'smo', 'SMO367G1210' => 'smo', 'Solyc02g093430.3' => 'sly', 'Solyc05g013580.4' => 'sly', 'Solyc07g008030.3' => 'sly', 'Solyc12g035470.2' => 'sly', 'Sopen02g038020' => 'spe', 'Sopen05g008490' => 'spe', 'Sopen07g003910' => 'spe', 'Sopen12g015240' => 'spe', 'Sp1g11550' => 'spa', 'Sp2g16710' => 'spa', 'Sp3g00430' => 'spa', 'Sp3g26780' => 'spa', 'Sp5g22900' => 'spa', 'Sp6g29530' => 'spa', 'TAR371G0794' => 'tar', 'TAR374G0164' => 'tar', 'TAR622G0165' => 'tar', 'TAR626G0929' => 'tar', 'TAR629G2155' => 'tar', 'THA.LOC104805282' => 'tha', 'THA.LOC104805363' => 'tha', 'THA.LOC104808968' => 'tha', 'THA.LOC104821093' => 'tha', 'THA.LOC104823953' => 'tha', 'THA.LOC104825562' => 'tha', 'THA.LOC104825665' => 'tha', 'Thecc.02G261400' => 'tca', 'Thecc.04G019200' => 'tca', 'Thecc.09G130400' => 'tca', 'Thhalv10004374m.g' => 'esa', 'Thhalv10007850m.g' => 'esa', 'Thhalv10013782m.g' => 'esa', 'Thhalv10018686m.g' => 'esa', 'Thhalv10020899m.g' => 'esa', 'Thhalv10022755m.g' => 'esa', 'TPR.G23851' => 'tpr', 'TPR.G26500' => 'tpr', 'TPR.G27267' => 'tpr', 'TPR.G32001' => 'tpr', 'TPR.G6251' => 'tpr', 'TPR.G8167' => 'tpr', 'TWI12G1330' => 'twi', 'TWI18G1239' => 'twi', 'TWI34G0979' => 'twi', 'TWI36G0670' => 'twi', 'TWI36G0707' => 'twi', 'TWI56G0233' => 'twi', 'TWI75G1809' => 'twi', 'unitig_21.g20874' => 'ugi', 'unitig_26.g10343' => 'ugi', 'unitig_46.g18392' => 'ugi', 'unitig_52.g17178' => 'ugi', 'unitig_8.g2934' => 'ugi', 'vmacro01122' => 'vma', 'vmacro05875' => 'vma', 'vmacro06147' => 'vma', 'vmacro16191' => 'vma', 'vmacro18293' => 'vma', 'VMungo0251G3707' => 'vmu', 'VMungo0464G1521' => 'vmu', 'VMungo1215G0205' => 'vmu', 'VMungo1383G2484' => 'vmu', 'Zm00001eb079610' => 'zma', 'Zm00001eb135990' => 'zma', 'Zm00001eb183710' => 'zma', 'Zm00001eb246020' => 'zma' ), 'gf_id' => 'HOM05D001124', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001124' ), 'data_identifier' => 'HOM05D001124', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001124', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '548', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02520' => 'bna', 'A03p06630' => 'bna', 'A05p44460' => 'bna', 'A06p08710' => 'bna', 'A06p41090' => 'bna', 'A07p32320' => 'bna', 'A08p32520' => 'bna', 'A09p10360' => 'bna', 'A10p24080' => 'bna', 'Aa31LG11G15250' => 'aar', 'Aa31LG1G1800' => 'aar', 'Aa31LG2G5120' => 'aar', 'Aa31LG2G6070' => 'aar', 'Aa31LG5G10770' => 'aar', 'Aa31sc61G90' => 'aar', 'Actinidia01352' => 'ach', 'Actinidia05983' => 'ach', 'Actinidia08133' => 'ach', 'Actinidia15101' => 'ach', 'Actinidia26379' => 'ach', 'Actinidia35778' => 'ach', 'Actinidia36123' => 'ach', 'Actinidia37436' => 'ach', 'Actinidia38730' => 'ach', 'Ah.02g128210' => 'amhyb', 'Ah.03g132990' => 'amhyb', 'Ah.14g079410' => 'amhyb', 'AL1G24640' => 'aly', 'AL2G26680' => 'aly', 'AL3G10530' => 'aly', 'AL3G45230' => 'aly', 'AL5G15230' => 'aly', 'AL5G16960' => 'aly', 'AL6G25210' => 'aly', 'Aqoxy2G00441' => 'aox', 'Aqoxy3G01236' => 'aox', 'Aqoxy5G03746' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3RQ047' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C7GMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9C8JER' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MBL6KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YXCZ83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZANX40' => 'arhy', 'AT1G12990' => 'ath', 'AT1G67880' => 'ath', 'AT2G13290' => 'ath', 'AT3G01620' => 'ath', 'AT3G26445' => 'ath', 'AT3G27540' => 'ath', 'AT5G14480' => 'ath', 'ATR0824G026' => 'atr', 'ATR1098G019' => 'atr', 'Atru.chr11.2145' => 'acertr', 'Atru.chr2.3636' => 'acertr', 'Atru.chr2.3644' => 'acertr', 'Atru.chr6.2422' => 'acertr', 'Atru.chr7.1112' => 'acertr', 'AUR62005469' => 'cqu', 'AUR62011166' => 'cqu', 'AUR62013319' => 'cqu', 'AUR62024273' => 'cqu', 'AUR62028420' => 'cqu', 'AUR62041942' => 'cqu', 'BcaB01g04969' => 'bca', 'BcaB01g06371' => 'bca', 'BcaB02g11494' => 'bca', 'BcaB03g15382' => 'bca', 'BcaB08g36994' => 'bca', 'BcaC03g13477' => 'bca', 'BcaC03g13478' => 'bca', 'BcaC03g13480' => 'bca', 'BcaC03g13481' => 'bca', 'BcaC03g13486' => 'bca', 'BcaC04g19031' => 'bca', 'BcaC04g23085' => 'bca', 'BcaC05g25094' => 'bca', 'BcaC05g25096' => 'bca', 'BcaC05g25138' => 'bca', 'BcaC05g30416' => 'bca', 'BcaC05g30455' => 'bca', 'BcaC06g30979' => 'bca', 'BcaC06g33805' => 'bca', 'BcaC08g46021' => 'bca', 'BcaNung03154' => 'bca', 'BolC2t06623H' => 'bol', 'BolC2t06632H' => 'bol', 'BolC2t06635H' => 'bol', 'BolC2t06638H' => 'bol', 'BolC3t13266H' => 'bol', 'BolC5t29776H' => 'bol', 'BolC6t38912H' => 'bol', 'BolC7t44183H' => 'bol', 'BolC9t54123H' => 'bol', 'BolC9t59107H' => 'bol', 'BraA02t05221Z' => 'bra', 'BraA03t09996Z' => 'bra', 'BraA05t23210Z' => 'bra', 'BraA06t24068Z' => 'bra', 'BraA06t27032Z' => 'bra', 'BraA08t35176Z' => 'bra', 'BraA09t36680Z' => 'bra', 'BraA10t44471Z' => 'bra', 'C02p06760' => 'bna', 'C02p06890' => 'bna', 'C02p07010' => 'bna', 'C03p07660' => 'bna', 'C05p10300' => 'bna', 'C06p38150' => 'bna', 'C07p36650' => 'bna', 'C08p15770' => 'bna', 'C09p12300' => 'bna', 'C09p62700' => 'bna', 'C09p75040' => 'bna', 'CAN.G13.1' => 'can', 'CAN.G138.4' => 'can', 'CAN.G44.6' => 'can', 'CAN.G473.19' => 'can', 'CANSAT01G0835' => 'cansat', 'CANSAT11G0246' => 'cansat', 'CANSAT11G1766' => 'cansat', 'CANSAT64G1954' => 'cansat', 'CARHR013330' => 'chi', 'CARHR060530' => 'chi', 'CARHR075300' => 'chi', 'CARHR105120' => 'chi', 'CARHR148910' => 'chi', 'CARHR198830' => 'chi', 'Carub.0001s1275' => 'cru', 'Carub.0002s1437' => 'cru', 'Carub.0003s0044' => 'cru', 'Carub.0003s2787' => 'cru', 'Carub.0005s0597' => 'cru', 'Carub.0006s1266' => 'cru', 'Ca_06935_v3' => 'car', 'Ca_13559_v3' => 'car', 'Ca_16941_v3' => 'car', 'Ca_16960_v3' => 'car', 'Ca_17775_v3' => 'car', 'Ca_30464_v3' => 'car', 'Cc06_g08160' => 'ccan', 'Cc07_g01520' => 'ccan', 'Cc11_g15810' => 'ccan', 'CDE02G2840' => 'cde', 'CDE03G0093' => 'cde', 'CDE04G2127' => 'cde', 'CDE07G1857' => 'cde', 'CDE09G1246' => 'cde', 'Cfa003412' => 'cfa', 'Cfa007341' => 'cfa', 'Cfa009220' => 'cfa', 'Ciclev10008737m.g' => 'ccl', 'Ciclev10015565m.g' => 'ccl', 'Ciclev10031761m.g' => 'ccl', 'CiPaw.03G045300' => 'cil', 'CiPaw.03G247200' => 'cil', 'CiPaw.04G029500' => 'cil', 'CiPaw.04G174000' => 'cil', 'CiPaw.05G181200' => 'cil', 'CiPaw.06G067100' => 'cil', 'ClCG05G025800' => 'cla', 'ClCG06G011400' => 'cla', 'ClCG09G019360' => 'cla', 'COL.COLO4_04827' => 'col', 'COL.COLO4_29170' => 'col', 'COL.COLO4_35131' => 'col', 'COL.COLO4_35132' => 'col', 'Cpa.g.sc33.32' => 'cpa', 'Cpa.g.sc46.29' => 'cpa', 'Cpa.g.sc796.1' => 'cpa', 'CsaV3_1G030420' => 'csa', 'CsaV3_5G027050' => 'csa', 'CsaV3_5G031040' => 'csa', 'CsaV3_UNG023130' => 'csa', 'CSS0007726' => 'camsi', 'CSS0016433' => 'camsi', 'CSS0017656' => 'camsi', 'CSS0025364' => 'camsi', 'CSS0027582' => 'camsi', 'CSS0047288' => 'camsi', 'CSS0049950' => 'camsi', 'DCAR_003843' => 'dca', 'DCAR_007052' => 'dca', 'DCAR_020884' => 'dca', 'DCAR_021730' => 'dca', 'DCAR_024423' => 'dca', 'DCAR_026509' => 'dca', 'DCAR_031158' => 'dca', 'Dinv14728' => 'din', 'Dinv15219' => 'din', 'Dinv25728' => 'din', 'Dinv33428' => 'din', 'Dinv36489' => 'din', 'Dinv41486' => 'din', 'Duzib147G0469' => 'dzi', 'Duzib168G0060' => 'dzi', 'Duzib187G1215' => 'dzi', 'Duzib248G0692' => 'dzi', 'Duzib251G0767' => 'dzi', 'Duzib264G0446' => 'dzi', 'Duzib268G0691' => 'dzi', 'ECA232G4767' => 'eca', 'ECA233G2838' => 'eca', 'ECA234G0391' => 'eca', 'ECA234G0857' => 'eca', 'ECA236G1593' => 'eca', 'ECA238G0565' => 'eca', 'ECA246G1027' => 'eca', 'ECA246G3223' => 'eca', 'ECA246G3470' => 'eca', 'EL10Ac6g13829' => 'bvu', 'EL10Ac6g14093' => 'bvu', 'EL10Ac8g18707' => 'bvu', 'Eucgr.C01369' => 'egr', 'Eucgr.H02492' => 'egr', 'Eucgr.I01733' => 'egr', 'Eucgr.J02255' => 'egr', 'Eucgr.J02257' => 'egr', 'Eucgr.J02258' => 'egr', 'FAN02G1601' => 'fan', 'FAN03G1586' => 'fan', 'FAN03G2986' => 'fan', 'FAN05G4837' => 'fan', 'FAN06G0146' => 'fan', 'FAN07G0858' => 'fan', 'FAN09G3179' => 'fan', 'FAN10G0669' => 'fan', 'FAN12G2358' => 'fan', 'FAN14G4198' => 'fan', 'FAN14G5112' => 'fan', 'FAN17G0342' => 'fan', 'FAN19G0342' => 'fan', 'FAN19G0962' => 'fan', 'FAN19G1101' => 'fan', 'FAN19G1872' => 'fan', 'FAN22G0356' => 'fan', 'FAN23G0744' => 'fan', 'FAN23G1914' => 'fan', 'FAN26G0032' => 'fan', 'FAN28G0625' => 'fan', 'FvH4_1g02710' => 'fve', 'FvH4_1g02720' => 'fve', 'FvH4_4g25670' => 'fve', 'FvH4_6g51700' => 'fve', 'FvH4_7g20170' => 'fve', 'Glyma.05G175000' => 'gma', 'Glyma.08G132300' => 'gma', 'Glyma.11G243000' => 'gma', 'Glyma.13G158900' => 'gma', 'Glyma.17G112400' => 'gma', 'Glyma.18G014100' => 'gma', 'Glyma.19G003100' => 'gma', 'Glyma.19G056500' => 'gma', 'Gohir.A01G158900' => 'ghi', 'Gohir.A05G312600' => 'ghi', 'Gohir.A05G354900' => 'ghi', 'Gohir.A07G037200' => 'ghi', 'Gohir.A09G030000' => 'ghi', 'Gohir.A12G145200' => 'ghi', 'Gohir.D01G151500' => 'ghi', 'Gohir.D04G058300' => 'ghi', 'Gohir.D05G314100' => 'ghi', 'Gohir.D07G041400' => 'ghi', 'Gohir.D09G029700' => 'ghi', 'Gohir.D12G149700' => 'ghi', 'Gorai.001G043800' => 'gra', 'Gorai.002G187800' => 'gra', 'Gorai.006G034700' => 'gra', 'Gorai.008G161200' => 'gra', 'Gorai.009G335700' => 'gra', 'Gorai.012G065000' => 'gra', 'GSVIVG01000535001' => 'vvi', 'GSVIVG01015572001' => 'vvi', 'GSVIVG01032386001' => 'vvi', 'HanXRQChr05g0138531' => 'han', 'HanXRQChr06g0174391' => 'han', 'HanXRQChr07g0199021' => 'han', 'HanXRQChr08g0208211' => 'han', 'HanXRQChr09g0255471' => 'han', 'HanXRQChr10g0315791' => 'han', 'HanXRQChr12g0371991' => 'han', 'HanXRQChr15g0475251' => 'han', 'HanXRQChr17g0540001' => 'han', 'HanXRQChr17g0548631' => 'han', 'HanXRQChr17g0569561' => 'han', 'Haze_12256' => 'cav', 'Haze_14756' => 'cav', 'Haze_25528' => 'cav', 'Hma1.2p1_0079F.1_g041020' => 'hma', 'Hma1.2p1_0818F.1_g223260' => 'hma', 'Hma1.2p1_1747F.1_g300530' => 'hma', 'HPP92_004607' => 'vpl', 'HPP92_004608' => 'vpl', 'HPP92_006181' => 'vpl', 'HPP92_012192' => 'vpl', 'HPP92_015680' => 'vpl', 'HPP92_020249' => 'vpl', 'HPP92_021376' => 'vpl', 'HPP92_024275' => 'vpl', 'Hund06031' => 'sun', 'Hund25391' => 'sun', 'Lalb_Chr07g0185371' => 'lal', 'Lalb_Chr07g0185381' => 'lal', 'Lalb_Chr12g0204011' => 'lal', 'Lalb_Chr13g0301671' => 'lal', 'Lalb_Chr14g0362851' => 'lal', 'Lalb_Chr24g0403581' => 'lal', 'Lj1g0000233' => 'lja', 'Lj2g0018120' => 'lja', 'Lj3C621T0' => 'lonja', 'Lj3P1059T14' => 'lonja', 'Lj3P611T9' => 'lonja', 'Lj3P614T13' => 'lonja', 'Lj3P615T5' => 'lonja', 'Lj4g0012315' => 'lja', 'Lj4g0026182' => 'lja', 'Lj6P813T16' => 'lonja', 'Lj7C427T7' => 'lonja', 'Lj7C427T8' => 'lonja', 'Lj7P600T41' => 'lonja', 'Lju41C42G17' => 'lonja', 'Lsat_1_v5_gn_0_47300' => 'lsa', 'Lsat_1_v5_gn_2_91280' => 'lsa', 'Lsat_1_v5_gn_3_30561' => 'lsa', 'Lsat_1_v5_gn_4_184321' => 'lsa', 'Lsat_1_v5_gn_4_4041' => 'lsa', 'Lsat_1_v5_gn_5_92000' => 'lsa', 'Lsat_1_v5_gn_8_152940' => 'lsa', 'Lsat_1_v5_gn_8_62401' => 'lsa', 'Manes.06G055900' => 'mes', 'Manes.12G022200' => 'mes', 'Manes.13G023300' => 'mes', 'Manes.14G115000' => 'mes', 'Manes.15G151700' => 'mes', 'Manes.17G111300' => 'mes', 'Mapoly0226s0009' => 'mpo', 'MBI02_g25363_MAGBIO' => 'mbi', 'MBI06_g00027_MAGBIO' => 'mbi', 'MBI10_g13034_MAGBIO' => 'mbi', 'MD09G1023400' => 'mdo', 'MD13G1100100' => 'mdo', 'MD15G1169200' => 'mdo', 'MD16G1101100' => 'mdo', 'MD17G1022900' => 'mdo', 'Medtr3g096150' => 'mtr', 'Medtr4g115070' => 'mtr', 'Medtr7g033325' => 'mtr', 'Medtr8g089840' => 'mtr', 'MELO3C010319.2' => 'cme', 'MELO3C011944.2' => 'cme', 'MELO3C021589.2' => 'cme', 'Migut.E00207' => 'egut', 'Migut.H00067' => 'egut', 'Migut.K00433' => 'egut', 'Migut.K00606' => 'egut', 'Migut.K01410' => 'egut', 'MSTRG.13347' => 'ama', 'MSTRG.24045' => 'ama', 'MSTRG.2428' => 'ama', 'MSTRG.26410' => 'ama', 'MSTRG.3139' => 'ama', 'MSTRG.3286' => 'ama', 'MSTRG.563' => 'ama', 'MSTRG.7941' => 'ama', 'Nitab4.5_0000028g0060' => 'nta', 'Nitab4.5_0000065g0260' => 'nta', 'Nitab4.5_0000112g0060' => 'nta', 'Nitab4.5_0000489g0120' => 'nta', 'Nitab4.5_0001776g0050' => 'nta', 'Nitab4.5_0001854g0010' => 'nta', 'Nitab4.5_0001860g0020' => 'nta', 'Nitab4.5_0004352g0010' => 'nta', 'Nitab4.5_0008716g0020' => 'nta', 'Nitab4.5_0008922g0010' => 'nta', 'Nn3g16693' => 'nnu', 'Nn4g22596' => 'nnu', 'Nn7g37639' => 'nnu', 'Oeu001701.1' => 'oeu', 'Oeu018149.1' => 'oeu', 'Oeu026220.1' => 'oeu', 'Oeu038635.1' => 'oeu', 'Oeu049176.1' => 'oeu', 'Oeu056706.1' => 'oeu', 'Oeu056937.1' => 'oeu', 'Oeu057540.1' => 'oeu', 'Os02g0594900' => 'osa', 'Os02g0595100' => 'osa', 'Os04g0477500' => 'osa', 'Os12g0611900' => 'osa', 'Peaxi162Scf00076g00020' => 'pax', 'Peaxi162Scf00128g00217' => 'pax', 'Peaxi162Scf00129g01640' => 'pax', 'Peaxi162Scf00669g00007' => 'pax', 'Peaxi162Scf00700g00421' => 'pax', 'Peaxi162Scf00801g00038' => 'pax', 'Peaxi162Scf00891g00025' => 'pax', 'PGR083G0909' => 'pgr', 'PGR119G1005' => 'pgr', 'PGR142G2236' => 'pgr', 'PGR142G3388' => 'pgr', 'PGSC0003DMG400004514' => 'stu', 'PGSC0003DMG400012635' => 'stu', 'PGSC0003DMG400015730' => 'stu', 'PGSC0003DMG400018611' => 'stu', 'PGSC0003DMG400030897' => 'stu', 'Phvul.001G254800' => 'pvu', 'Phvul.002G260100' => 'pvu', 'Phvul.003G167600' => 'pvu', 'Phvul.004G005100' => 'pvu', 'Potri.001G343600' => 'ptr', 'Potri.006G066700' => 'ptr', 'Potri.008G186000' => 'ptr', 'Potri.010G046900' => 'ptr', 'Potri.018G127900' => 'ptr', 'Pp3c20_17750' => 'ppa', 'Pp3c24_4380' => 'ppa', 'Prupe.1G245800' => 'ppe', 'Prupe.3G293400' => 'ppe', 'Prupe.7G247400' => 'ppe', 'Psat0s145g0120' => 'psa', 'Psat0s595g0040' => 'psa', 'Psat0s595g0120' => 'psa', 'Psat3g175040' => 'psa', 'Psat7g058120' => 'psa', 'PSO017G0428' => 'pso', 'PSO063G7510' => 'pso', 'PSO067G0046' => 'pso', 'PSO478G1073' => 'pso', 'PSO675G3677' => 'pso', 'PSO675G6558' => 'pso', 'PSO675G7520' => 'pso', 'PSO675G8959' => 'pso', 'QL02p074089' => 'qlo', 'QL02p089614' => 'qlo', 'QL03p057736' => 'qlo', 'RcHm_v2.0_Chr1g0364131' => 'rch', 'RcHm_v2.0_Chr2g0087801' => 'rch', 'RcHm_v2.0_Chr2g0087821' => 'rch', 'RcHm_v2.0_Chr2g0173231' => 'rch', 'RcHm_v2.0_Chr4g0433111' => 'rch', 'Rhsim03G0250300' => 'rsi', 'Rhsim08G0048400' => 'rsi', 'Rhsim10G0014800' => 'rsi', 'Rhsim12G0040100' => 'rsi', 'Rhsim12G0109700' => 'rsi', 'Sabra06G0049600' => 'sbr', 'Sabra08G0141000' => 'sbr', 'Sabra10G0021400' => 'sbr', 'Sabra16G0222900' => 'sbr', 'Sabra18G0108600' => 'sbr', 'SalBow1G0433' => 'sbo', 'SalBow1G2038' => 'sbo', 'SalBow1G5003' => 'sbo', 'SalBow7G1197' => 'sbo', 'SalBow8G3506' => 'sbo', 'Sc03g0007300' => 'sci', 'Sc11g0000950' => 'sci', 'Sc14g0008750' => 'sci', 'Sc18g0000420' => 'sci', 'Sed0006754' => 'sed', 'Sed0008741' => 'sed', 'Sed0017172' => 'sed', 'Sed0018925' => 'sed', 'Sed0023326' => 'sed', 'Sed0025909' => 'sed', 'SEGI_05333' => 'sgi', 'SEGI_10362' => 'sgi', 'SEGI_13380' => 'sgi', 'SEGI_24306' => 'sgi', 'SEGI_29077' => 'sgi', 'SEGI_29095' => 'sgi', 'SEGI_36534' => 'sgi', 'SEGI_37506' => 'sgi', 'SEGI_38321' => 'sgi', 'SGA_v2.0_scaffold307G48031' => 'sas', 'SGA_v2.0_scaffold47G17507' => 'sas', 'SGA_v2.0_scaffold63G21736' => 'sas', 'SGA_v2.0_scaffold87G27070' => 'sas', 'SHI17794' => 'shi', 'SHI28851' => 'shi', 'SMO165G0155' => 'smo', 'SMO340G0217' => 'smo', 'SMO367G1210' => 'smo', 'Solyc02g093430.3' => 'sly', 'Solyc05g013580.4' => 'sly', 'Solyc07g008030.3' => 'sly', 'Solyc12g035470.2' => 'sly', 'Sopen02g038020' => 'spe', 'Sopen05g008490' => 'spe', 'Sopen07g003910' => 'spe', 'Sopen12g015240' => 'spe', 'Sp1g11550' => 'spa', 'Sp2g16710' => 'spa', 'Sp3g00430' => 'spa', 'Sp3g26780' => 'spa', 'Sp5g22900' => 'spa', 'Sp6g29530' => 'spa', 'TAR371G0794' => 'tar', 'TAR374G0164' => 'tar', 'TAR622G0165' => 'tar', 'TAR626G0929' => 'tar', 'TAR629G2155' => 'tar', 'THA.LOC104805282' => 'tha', 'THA.LOC104805363' => 'tha', 'THA.LOC104808968' => 'tha', 'THA.LOC104821093' => 'tha', 'THA.LOC104823953' => 'tha', 'THA.LOC104825562' => 'tha', 'THA.LOC104825665' => 'tha', 'Thecc.02G261400' => 'tca', 'Thecc.04G019200' => 'tca', 'Thecc.09G130400' => 'tca', 'Thhalv10004374m.g' => 'esa', 'Thhalv10007850m.g' => 'esa', 'Thhalv10013782m.g' => 'esa', 'Thhalv10018686m.g' => 'esa', 'Thhalv10020899m.g' => 'esa', 'Thhalv10022755m.g' => 'esa', 'TPR.G23851' => 'tpr', 'TPR.G26500' => 'tpr', 'TPR.G27267' => 'tpr', 'TPR.G32001' => 'tpr', 'TPR.G6251' => 'tpr', 'TPR.G8167' => 'tpr', 'TWI12G1330' => 'twi', 'TWI18G1239' => 'twi', 'TWI34G0979' => 'twi', 'TWI36G0670' => 'twi', 'TWI36G0707' => 'twi', 'TWI56G0233' => 'twi', 'TWI75G1809' => 'twi', 'unitig_21.g20874' => 'ugi', 'unitig_26.g10343' => 'ugi', 'unitig_46.g18392' => 'ugi', 'unitig_52.g17178' => 'ugi', 'unitig_8.g2934' => 'ugi', 'vmacro01122' => 'vma', 'vmacro05875' => 'vma', 'vmacro06147' => 'vma', 'vmacro16191' => 'vma', 'vmacro18293' => 'vma', 'VMungo0251G3707' => 'vmu', 'VMungo0464G1521' => 'vmu', 'VMungo1215G0205' => 'vmu', 'VMungo1383G2484' => 'vmu', 'Zm00001eb079610' => 'zma', 'Zm00001eb135990' => 'zma', 'Zm00001eb183710' => 'zma', 'Zm00001eb246020' => 'zma' ) $gf_id = 'HOM05D001124' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001124' ) $data_identifier = 'HOM05D001124' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 6, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 7, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 21, 'bol' => (int) 10, 'bra' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 6, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 9, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 21, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 8, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 10, 'lsa' => (int) 8, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 8, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 9, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb246020' $species_info = array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ) $local_species = 'can' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001124', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '548', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02520' => 'bna', 'A03p06630' => 'bna', 'A05p44460' => 'bna', 'A06p08710' => 'bna', 'A06p41090' => 'bna', 'A07p32320' => 'bna', 'A08p32520' => 'bna', 'A09p10360' => 'bna', 'A10p24080' => 'bna', 'Aa31LG11G15250' => 'aar', 'Aa31LG1G1800' => 'aar', 'Aa31LG2G5120' => 'aar', 'Aa31LG2G6070' => 'aar', 'Aa31LG5G10770' => 'aar', 'Aa31sc61G90' => 'aar', 'Actinidia01352' => 'ach', 'Actinidia05983' => 'ach', 'Actinidia08133' => 'ach', 'Actinidia15101' => 'ach', 'Actinidia26379' => 'ach', 'Actinidia35778' => 'ach', 'Actinidia36123' => 'ach', 'Actinidia37436' => 'ach', 'Actinidia38730' => 'ach', 'Ah.02g128210' => 'amhyb', 'Ah.03g132990' => 'amhyb', 'Ah.14g079410' => 'amhyb', 'AL1G24640' => 'aly', 'AL2G26680' => 'aly', 'AL3G10530' => 'aly', 'AL3G45230' => 'aly', 'AL5G15230' => 'aly', 'AL5G16960' => 'aly', 'AL6G25210' => 'aly', 'Aqoxy2G00441' => 'aox', 'Aqoxy3G01236' => 'aox', 'Aqoxy5G03746' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3RQ047' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C7GMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9C8JER' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MBL6KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YXCZ83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZANX40' => 'arhy', 'AT1G12990' => 'ath', 'AT1G67880' => 'ath', 'AT2G13290' => 'ath', 'AT3G01620' => 'ath', 'AT3G26445' => 'ath', 'AT3G27540' => 'ath', 'AT5G14480' => 'ath', 'ATR0824G026' => 'atr', 'ATR1098G019' => 'atr', 'Atru.chr11.2145' => 'acertr', 'Atru.chr2.3636' => 'acertr', 'Atru.chr2.3644' => 'acertr', 'Atru.chr6.2422' => 'acertr', 'Atru.chr7.1112' => 'acertr', 'AUR62005469' => 'cqu', 'AUR62011166' => 'cqu', 'AUR62013319' => 'cqu', 'AUR62024273' => 'cqu', 'AUR62028420' => 'cqu', 'AUR62041942' => 'cqu', 'BcaB01g04969' => 'bca', 'BcaB01g06371' => 'bca', 'BcaB02g11494' => 'bca', 'BcaB03g15382' => 'bca', 'BcaB08g36994' => 'bca', 'BcaC03g13477' => 'bca', 'BcaC03g13478' => 'bca', 'BcaC03g13480' => 'bca', 'BcaC03g13481' => 'bca', 'BcaC03g13486' => 'bca', 'BcaC04g19031' => 'bca', 'BcaC04g23085' => 'bca', 'BcaC05g25094' => 'bca', 'BcaC05g25096' => 'bca', 'BcaC05g25138' => 'bca', 'BcaC05g30416' => 'bca', 'BcaC05g30455' => 'bca', 'BcaC06g30979' => 'bca', 'BcaC06g33805' => 'bca', 'BcaC08g46021' => 'bca', 'BcaNung03154' => 'bca', 'BolC2t06623H' => 'bol', 'BolC2t06632H' => 'bol', 'BolC2t06635H' => 'bol', 'BolC2t06638H' => 'bol', 'BolC3t13266H' => 'bol', 'BolC5t29776H' => 'bol', 'BolC6t38912H' => 'bol', 'BolC7t44183H' => 'bol', 'BolC9t54123H' => 'bol', 'BolC9t59107H' => 'bol', 'BraA02t05221Z' => 'bra', 'BraA03t09996Z' => 'bra', 'BraA05t23210Z' => 'bra', 'BraA06t24068Z' => 'bra', 'BraA06t27032Z' => 'bra', 'BraA08t35176Z' => 'bra', 'BraA09t36680Z' => 'bra', 'BraA10t44471Z' => 'bra', 'C02p06760' => 'bna', 'C02p06890' => 'bna', 'C02p07010' => 'bna', 'C03p07660' => 'bna', 'C05p10300' => 'bna', 'C06p38150' => 'bna', 'C07p36650' => 'bna', 'C08p15770' => 'bna', 'C09p12300' => 'bna', 'C09p62700' => 'bna', 'C09p75040' => 'bna', 'CAN.G13.1' => 'can', 'CAN.G138.4' => 'can', 'CAN.G44.6' => 'can', 'CAN.G473.19' => 'can', 'CANSAT01G0835' => 'cansat', 'CANSAT11G0246' => 'cansat', 'CANSAT11G1766' => 'cansat', 'CANSAT64G1954' => 'cansat', 'CARHR013330' => 'chi', 'CARHR060530' => 'chi', 'CARHR075300' => 'chi', 'CARHR105120' => 'chi', 'CARHR148910' => 'chi', 'CARHR198830' => 'chi', 'Carub.0001s1275' => 'cru', 'Carub.0002s1437' => 'cru', 'Carub.0003s0044' => 'cru', 'Carub.0003s2787' => 'cru', 'Carub.0005s0597' => 'cru', 'Carub.0006s1266' => 'cru', 'Ca_06935_v3' => 'car', 'Ca_13559_v3' => 'car', 'Ca_16941_v3' => 'car', 'Ca_16960_v3' => 'car', 'Ca_17775_v3' => 'car', 'Ca_30464_v3' => 'car', 'Cc06_g08160' => 'ccan', 'Cc07_g01520' => 'ccan', 'Cc11_g15810' => 'ccan', 'CDE02G2840' => 'cde', 'CDE03G0093' => 'cde', 'CDE04G2127' => 'cde', 'CDE07G1857' => 'cde', 'CDE09G1246' => 'cde', 'Cfa003412' => 'cfa', 'Cfa007341' => 'cfa', 'Cfa009220' => 'cfa', 'Ciclev10008737m.g' => 'ccl', 'Ciclev10015565m.g' => 'ccl', 'Ciclev10031761m.g' => 'ccl', 'CiPaw.03G045300' => 'cil', 'CiPaw.03G247200' => 'cil', 'CiPaw.04G029500' => 'cil', 'CiPaw.04G174000' => 'cil', 'CiPaw.05G181200' => 'cil', 'CiPaw.06G067100' => 'cil', 'ClCG05G025800' => 'cla', 'ClCG06G011400' => 'cla', 'ClCG09G019360' => 'cla', 'COL.COLO4_04827' => 'col', 'COL.COLO4_29170' => 'col', 'COL.COLO4_35131' => 'col', 'COL.COLO4_35132' => 'col', 'Cpa.g.sc33.32' => 'cpa', 'Cpa.g.sc46.29' => 'cpa', 'Cpa.g.sc796.1' => 'cpa', 'CsaV3_1G030420' => 'csa', 'CsaV3_5G027050' => 'csa', 'CsaV3_5G031040' => 'csa', 'CsaV3_UNG023130' => 'csa', 'CSS0007726' => 'camsi', 'CSS0016433' => 'camsi', 'CSS0017656' => 'camsi', 'CSS0025364' => 'camsi', 'CSS0027582' => 'camsi', 'CSS0047288' => 'camsi', 'CSS0049950' => 'camsi', 'DCAR_003843' => 'dca', 'DCAR_007052' => 'dca', 'DCAR_020884' => 'dca', 'DCAR_021730' => 'dca', 'DCAR_024423' => 'dca', 'DCAR_026509' => 'dca', 'DCAR_031158' => 'dca', 'Dinv14728' => 'din', 'Dinv15219' => 'din', 'Dinv25728' => 'din', 'Dinv33428' => 'din', 'Dinv36489' => 'din', 'Dinv41486' => 'din', 'Duzib147G0469' => 'dzi', 'Duzib168G0060' => 'dzi', 'Duzib187G1215' => 'dzi', 'Duzib248G0692' => 'dzi', 'Duzib251G0767' => 'dzi', 'Duzib264G0446' => 'dzi', 'Duzib268G0691' => 'dzi', 'ECA232G4767' => 'eca', 'ECA233G2838' => 'eca', 'ECA234G0391' => 'eca', 'ECA234G0857' => 'eca', 'ECA236G1593' => 'eca', 'ECA238G0565' => 'eca', 'ECA246G1027' => 'eca', 'ECA246G3223' => 'eca', 'ECA246G3470' => 'eca', 'EL10Ac6g13829' => 'bvu', 'EL10Ac6g14093' => 'bvu', 'EL10Ac8g18707' => 'bvu', 'Eucgr.C01369' => 'egr', 'Eucgr.H02492' => 'egr', 'Eucgr.I01733' => 'egr', 'Eucgr.J02255' => 'egr', 'Eucgr.J02257' => 'egr', 'Eucgr.J02258' => 'egr', 'FAN02G1601' => 'fan', 'FAN03G1586' => 'fan', 'FAN03G2986' => 'fan', 'FAN05G4837' => 'fan', 'FAN06G0146' => 'fan', 'FAN07G0858' => 'fan', 'FAN09G3179' => 'fan', 'FAN10G0669' => 'fan', 'FAN12G2358' => 'fan', 'FAN14G4198' => 'fan', 'FAN14G5112' => 'fan', 'FAN17G0342' => 'fan', 'FAN19G0342' => 'fan', 'FAN19G0962' => 'fan', 'FAN19G1101' => 'fan', 'FAN19G1872' => 'fan', 'FAN22G0356' => 'fan', 'FAN23G0744' => 'fan', 'FAN23G1914' => 'fan', 'FAN26G0032' => 'fan', 'FAN28G0625' => 'fan', 'FvH4_1g02710' => 'fve', 'FvH4_1g02720' => 'fve', 'FvH4_4g25670' => 'fve', 'FvH4_6g51700' => 'fve', 'FvH4_7g20170' => 'fve', 'Glyma.05G175000' => 'gma', 'Glyma.08G132300' => 'gma', 'Glyma.11G243000' => 'gma', 'Glyma.13G158900' => 'gma', 'Glyma.17G112400' => 'gma', 'Glyma.18G014100' => 'gma', 'Glyma.19G003100' => 'gma', 'Glyma.19G056500' => 'gma', 'Gohir.A01G158900' => 'ghi', 'Gohir.A05G312600' => 'ghi', 'Gohir.A05G354900' => 'ghi', 'Gohir.A07G037200' => 'ghi', 'Gohir.A09G030000' => 'ghi', 'Gohir.A12G145200' => 'ghi', 'Gohir.D01G151500' => 'ghi', 'Gohir.D04G058300' => 'ghi', 'Gohir.D05G314100' => 'ghi', 'Gohir.D07G041400' => 'ghi', 'Gohir.D09G029700' => 'ghi', 'Gohir.D12G149700' => 'ghi', 'Gorai.001G043800' => 'gra', 'Gorai.002G187800' => 'gra', 'Gorai.006G034700' => 'gra', 'Gorai.008G161200' => 'gra', 'Gorai.009G335700' => 'gra', 'Gorai.012G065000' => 'gra', 'GSVIVG01000535001' => 'vvi', 'GSVIVG01015572001' => 'vvi', 'GSVIVG01032386001' => 'vvi', 'HanXRQChr05g0138531' => 'han', 'HanXRQChr06g0174391' => 'han', 'HanXRQChr07g0199021' => 'han', 'HanXRQChr08g0208211' => 'han', 'HanXRQChr09g0255471' => 'han', 'HanXRQChr10g0315791' => 'han', 'HanXRQChr12g0371991' => 'han', 'HanXRQChr15g0475251' => 'han', 'HanXRQChr17g0540001' => 'han', 'HanXRQChr17g0548631' => 'han', 'HanXRQChr17g0569561' => 'han', 'Haze_12256' => 'cav', 'Haze_14756' => 'cav', 'Haze_25528' => 'cav', 'Hma1.2p1_0079F.1_g041020' => 'hma', 'Hma1.2p1_0818F.1_g223260' => 'hma', 'Hma1.2p1_1747F.1_g300530' => 'hma', 'HPP92_004607' => 'vpl', 'HPP92_004608' => 'vpl', 'HPP92_006181' => 'vpl', 'HPP92_012192' => 'vpl', 'HPP92_015680' => 'vpl', 'HPP92_020249' => 'vpl', 'HPP92_021376' => 'vpl', 'HPP92_024275' => 'vpl', 'Hund06031' => 'sun', 'Hund25391' => 'sun', 'Lalb_Chr07g0185371' => 'lal', 'Lalb_Chr07g0185381' => 'lal', 'Lalb_Chr12g0204011' => 'lal', 'Lalb_Chr13g0301671' => 'lal', 'Lalb_Chr14g0362851' => 'lal', 'Lalb_Chr24g0403581' => 'lal', 'Lj1g0000233' => 'lja', 'Lj2g0018120' => 'lja', 'Lj3C621T0' => 'lonja', 'Lj3P1059T14' => 'lonja', 'Lj3P611T9' => 'lonja', 'Lj3P614T13' => 'lonja', 'Lj3P615T5' => 'lonja', 'Lj4g0012315' => 'lja', 'Lj4g0026182' => 'lja', 'Lj6P813T16' => 'lonja', 'Lj7C427T7' => 'lonja', 'Lj7C427T8' => 'lonja', 'Lj7P600T41' => 'lonja', 'Lju41C42G17' => 'lonja', 'Lsat_1_v5_gn_0_47300' => 'lsa', 'Lsat_1_v5_gn_2_91280' => 'lsa', 'Lsat_1_v5_gn_3_30561' => 'lsa', 'Lsat_1_v5_gn_4_184321' => 'lsa', 'Lsat_1_v5_gn_4_4041' => 'lsa', 'Lsat_1_v5_gn_5_92000' => 'lsa', 'Lsat_1_v5_gn_8_152940' => 'lsa', 'Lsat_1_v5_gn_8_62401' => 'lsa', 'Manes.06G055900' => 'mes', 'Manes.12G022200' => 'mes', 'Manes.13G023300' => 'mes', 'Manes.14G115000' => 'mes', 'Manes.15G151700' => 'mes', 'Manes.17G111300' => 'mes', 'Mapoly0226s0009' => 'mpo', 'MBI02_g25363_MAGBIO' => 'mbi', 'MBI06_g00027_MAGBIO' => 'mbi', 'MBI10_g13034_MAGBIO' => 'mbi', 'MD09G1023400' => 'mdo', 'MD13G1100100' => 'mdo', 'MD15G1169200' => 'mdo', 'MD16G1101100' => 'mdo', 'MD17G1022900' => 'mdo', 'Medtr3g096150' => 'mtr', 'Medtr4g115070' => 'mtr', 'Medtr7g033325' => 'mtr', 'Medtr8g089840' => 'mtr', 'MELO3C010319.2' => 'cme', 'MELO3C011944.2' => 'cme', 'MELO3C021589.2' => 'cme', 'Migut.E00207' => 'egut', 'Migut.H00067' => 'egut', 'Migut.K00433' => 'egut', 'Migut.K00606' => 'egut', 'Migut.K01410' => 'egut', 'MSTRG.13347' => 'ama', 'MSTRG.24045' => 'ama', 'MSTRG.2428' => 'ama', 'MSTRG.26410' => 'ama', 'MSTRG.3139' => 'ama', 'MSTRG.3286' => 'ama', 'MSTRG.563' => 'ama', 'MSTRG.7941' => 'ama', 'Nitab4.5_0000028g0060' => 'nta', 'Nitab4.5_0000065g0260' => 'nta', 'Nitab4.5_0000112g0060' => 'nta', 'Nitab4.5_0000489g0120' => 'nta', 'Nitab4.5_0001776g0050' => 'nta', 'Nitab4.5_0001854g0010' => 'nta', 'Nitab4.5_0001860g0020' => 'nta', 'Nitab4.5_0004352g0010' => 'nta', 'Nitab4.5_0008716g0020' => 'nta', 'Nitab4.5_0008922g0010' => 'nta', 'Nn3g16693' => 'nnu', 'Nn4g22596' => 'nnu', 'Nn7g37639' => 'nnu', 'Oeu001701.1' => 'oeu', 'Oeu018149.1' => 'oeu', 'Oeu026220.1' => 'oeu', 'Oeu038635.1' => 'oeu', 'Oeu049176.1' => 'oeu', 'Oeu056706.1' => 'oeu', 'Oeu056937.1' => 'oeu', 'Oeu057540.1' => 'oeu', 'Os02g0594900' => 'osa', 'Os02g0595100' => 'osa', 'Os04g0477500' => 'osa', 'Os12g0611900' => 'osa', 'Peaxi162Scf00076g00020' => 'pax', 'Peaxi162Scf00128g00217' => 'pax', 'Peaxi162Scf00129g01640' => 'pax', 'Peaxi162Scf00669g00007' => 'pax', 'Peaxi162Scf00700g00421' => 'pax', 'Peaxi162Scf00801g00038' => 'pax', 'Peaxi162Scf00891g00025' => 'pax', 'PGR083G0909' => 'pgr', 'PGR119G1005' => 'pgr', 'PGR142G2236' => 'pgr', 'PGR142G3388' => 'pgr', 'PGSC0003DMG400004514' => 'stu', 'PGSC0003DMG400012635' => 'stu', 'PGSC0003DMG400015730' => 'stu', 'PGSC0003DMG400018611' => 'stu', 'PGSC0003DMG400030897' => 'stu', 'Phvul.001G254800' => 'pvu', 'Phvul.002G260100' => 'pvu', 'Phvul.003G167600' => 'pvu', 'Phvul.004G005100' => 'pvu', 'Potri.001G343600' => 'ptr', 'Potri.006G066700' => 'ptr', 'Potri.008G186000' => 'ptr', 'Potri.010G046900' => 'ptr', 'Potri.018G127900' => 'ptr', 'Pp3c20_17750' => 'ppa', 'Pp3c24_4380' => 'ppa', 'Prupe.1G245800' => 'ppe', 'Prupe.3G293400' => 'ppe', 'Prupe.7G247400' => 'ppe', 'Psat0s145g0120' => 'psa', 'Psat0s595g0040' => 'psa', 'Psat0s595g0120' => 'psa', 'Psat3g175040' => 'psa', 'Psat7g058120' => 'psa', 'PSO017G0428' => 'pso', 'PSO063G7510' => 'pso', 'PSO067G0046' => 'pso', 'PSO478G1073' => 'pso', 'PSO675G3677' => 'pso', 'PSO675G6558' => 'pso', 'PSO675G7520' => 'pso', 'PSO675G8959' => 'pso', 'QL02p074089' => 'qlo', 'QL02p089614' => 'qlo', 'QL03p057736' => 'qlo', 'RcHm_v2.0_Chr1g0364131' => 'rch', 'RcHm_v2.0_Chr2g0087801' => 'rch', 'RcHm_v2.0_Chr2g0087821' => 'rch', 'RcHm_v2.0_Chr2g0173231' => 'rch', 'RcHm_v2.0_Chr4g0433111' => 'rch', 'Rhsim03G0250300' => 'rsi', 'Rhsim08G0048400' => 'rsi', 'Rhsim10G0014800' => 'rsi', 'Rhsim12G0040100' => 'rsi', 'Rhsim12G0109700' => 'rsi', 'Sabra06G0049600' => 'sbr', 'Sabra08G0141000' => 'sbr', 'Sabra10G0021400' => 'sbr', 'Sabra16G0222900' => 'sbr', 'Sabra18G0108600' => 'sbr', 'SalBow1G0433' => 'sbo', 'SalBow1G2038' => 'sbo', 'SalBow1G5003' => 'sbo', 'SalBow7G1197' => 'sbo', 'SalBow8G3506' => 'sbo', 'Sc03g0007300' => 'sci', 'Sc11g0000950' => 'sci', 'Sc14g0008750' => 'sci', 'Sc18g0000420' => 'sci', 'Sed0006754' => 'sed', 'Sed0008741' => 'sed', 'Sed0017172' => 'sed', 'Sed0018925' => 'sed', 'Sed0023326' => 'sed', 'Sed0025909' => 'sed', 'SEGI_05333' => 'sgi', 'SEGI_10362' => 'sgi', 'SEGI_13380' => 'sgi', 'SEGI_24306' => 'sgi', 'SEGI_29077' => 'sgi', 'SEGI_29095' => 'sgi', 'SEGI_36534' => 'sgi', 'SEGI_37506' => 'sgi', 'SEGI_38321' => 'sgi', 'SGA_v2.0_scaffold307G48031' => 'sas', 'SGA_v2.0_scaffold47G17507' => 'sas', 'SGA_v2.0_scaffold63G21736' => 'sas', 'SGA_v2.0_scaffold87G27070' => 'sas', 'SHI17794' => 'shi', 'SHI28851' => 'shi', 'SMO165G0155' => 'smo', 'SMO340G0217' => 'smo', 'SMO367G1210' => 'smo', 'Solyc02g093430.3' => 'sly', 'Solyc05g013580.4' => 'sly', 'Solyc07g008030.3' => 'sly', 'Solyc12g035470.2' => 'sly', 'Sopen02g038020' => 'spe', 'Sopen05g008490' => 'spe', 'Sopen07g003910' => 'spe', 'Sopen12g015240' => 'spe', 'Sp1g11550' => 'spa', 'Sp2g16710' => 'spa', 'Sp3g00430' => 'spa', 'Sp3g26780' => 'spa', 'Sp5g22900' => 'spa', 'Sp6g29530' => 'spa', 'TAR371G0794' => 'tar', 'TAR374G0164' => 'tar', 'TAR622G0165' => 'tar', 'TAR626G0929' => 'tar', 'TAR629G2155' => 'tar', 'THA.LOC104805282' => 'tha', 'THA.LOC104805363' => 'tha', 'THA.LOC104808968' => 'tha', 'THA.LOC104821093' => 'tha', 'THA.LOC104823953' => 'tha', 'THA.LOC104825562' => 'tha', 'THA.LOC104825665' => 'tha', 'Thecc.02G261400' => 'tca', 'Thecc.04G019200' => 'tca', 'Thecc.09G130400' => 'tca', 'Thhalv10004374m.g' => 'esa', 'Thhalv10007850m.g' => 'esa', 'Thhalv10013782m.g' => 'esa', 'Thhalv10018686m.g' => 'esa', 'Thhalv10020899m.g' => 'esa', 'Thhalv10022755m.g' => 'esa', 'TPR.G23851' => 'tpr', 'TPR.G26500' => 'tpr', 'TPR.G27267' => 'tpr', 'TPR.G32001' => 'tpr', 'TPR.G6251' => 'tpr', 'TPR.G8167' => 'tpr', 'TWI12G1330' => 'twi', 'TWI18G1239' => 'twi', 'TWI34G0979' => 'twi', 'TWI36G0670' => 'twi', 'TWI36G0707' => 'twi', 'TWI56G0233' => 'twi', 'TWI75G1809' => 'twi', 'unitig_21.g20874' => 'ugi', 'unitig_26.g10343' => 'ugi', 'unitig_46.g18392' => 'ugi', 'unitig_52.g17178' => 'ugi', 'unitig_8.g2934' => 'ugi', 'vmacro01122' => 'vma', 'vmacro05875' => 'vma', 'vmacro06147' => 'vma', 'vmacro16191' => 'vma', 'vmacro18293' => 'vma', 'VMungo0251G3707' => 'vmu', 'VMungo0464G1521' => 'vmu', 'VMungo1215G0205' => 'vmu', 'VMungo1383G2484' => 'vmu', 'Zm00001eb079610' => 'zma', 'Zm00001eb135990' => 'zma', 'Zm00001eb183710' => 'zma', 'Zm00001eb246020' => 'zma' ), 'gf_id' => 'HOM05D001124', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001124' ), 'data_identifier' => 'HOM05D001124', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001124', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '548', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02520' => 'bna', 'A03p06630' => 'bna', 'A05p44460' => 'bna', 'A06p08710' => 'bna', 'A06p41090' => 'bna', 'A07p32320' => 'bna', 'A08p32520' => 'bna', 'A09p10360' => 'bna', 'A10p24080' => 'bna', 'Aa31LG11G15250' => 'aar', 'Aa31LG1G1800' => 'aar', 'Aa31LG2G5120' => 'aar', 'Aa31LG2G6070' => 'aar', 'Aa31LG5G10770' => 'aar', 'Aa31sc61G90' => 'aar', 'Actinidia01352' => 'ach', 'Actinidia05983' => 'ach', 'Actinidia08133' => 'ach', 'Actinidia15101' => 'ach', 'Actinidia26379' => 'ach', 'Actinidia35778' => 'ach', 'Actinidia36123' => 'ach', 'Actinidia37436' => 'ach', 'Actinidia38730' => 'ach', 'Ah.02g128210' => 'amhyb', 'Ah.03g132990' => 'amhyb', 'Ah.14g079410' => 'amhyb', 'AL1G24640' => 'aly', 'AL2G26680' => 'aly', 'AL3G10530' => 'aly', 'AL3G45230' => 'aly', 'AL5G15230' => 'aly', 'AL5G16960' => 'aly', 'AL6G25210' => 'aly', 'Aqoxy2G00441' => 'aox', 'Aqoxy3G01236' => 'aox', 'Aqoxy5G03746' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3RQ047' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C7GMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9C8JER' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MBL6KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YXCZ83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZANX40' => 'arhy', 'AT1G12990' => 'ath', 'AT1G67880' => 'ath', 'AT2G13290' => 'ath', 'AT3G01620' => 'ath', 'AT3G26445' => 'ath', 'AT3G27540' => 'ath', 'AT5G14480' => 'ath', 'ATR0824G026' => 'atr', 'ATR1098G019' => 'atr', 'Atru.chr11.2145' => 'acertr', 'Atru.chr2.3636' => 'acertr', 'Atru.chr2.3644' => 'acertr', 'Atru.chr6.2422' => 'acertr', 'Atru.chr7.1112' => 'acertr', 'AUR62005469' => 'cqu', 'AUR62011166' => 'cqu', 'AUR62013319' => 'cqu', 'AUR62024273' => 'cqu', 'AUR62028420' => 'cqu', 'AUR62041942' => 'cqu', 'BcaB01g04969' => 'bca', 'BcaB01g06371' => 'bca', 'BcaB02g11494' => 'bca', 'BcaB03g15382' => 'bca', 'BcaB08g36994' => 'bca', 'BcaC03g13477' => 'bca', 'BcaC03g13478' => 'bca', 'BcaC03g13480' => 'bca', 'BcaC03g13481' => 'bca', 'BcaC03g13486' => 'bca', 'BcaC04g19031' => 'bca', 'BcaC04g23085' => 'bca', 'BcaC05g25094' => 'bca', 'BcaC05g25096' => 'bca', 'BcaC05g25138' => 'bca', 'BcaC05g30416' => 'bca', 'BcaC05g30455' => 'bca', 'BcaC06g30979' => 'bca', 'BcaC06g33805' => 'bca', 'BcaC08g46021' => 'bca', 'BcaNung03154' => 'bca', 'BolC2t06623H' => 'bol', 'BolC2t06632H' => 'bol', 'BolC2t06635H' => 'bol', 'BolC2t06638H' => 'bol', 'BolC3t13266H' => 'bol', 'BolC5t29776H' => 'bol', 'BolC6t38912H' => 'bol', 'BolC7t44183H' => 'bol', 'BolC9t54123H' => 'bol', 'BolC9t59107H' => 'bol', 'BraA02t05221Z' => 'bra', 'BraA03t09996Z' => 'bra', 'BraA05t23210Z' => 'bra', 'BraA06t24068Z' => 'bra', 'BraA06t27032Z' => 'bra', 'BraA08t35176Z' => 'bra', 'BraA09t36680Z' => 'bra', 'BraA10t44471Z' => 'bra', 'C02p06760' => 'bna', 'C02p06890' => 'bna', 'C02p07010' => 'bna', 'C03p07660' => 'bna', 'C05p10300' => 'bna', 'C06p38150' => 'bna', 'C07p36650' => 'bna', 'C08p15770' => 'bna', 'C09p12300' => 'bna', 'C09p62700' => 'bna', 'C09p75040' => 'bna', 'CAN.G13.1' => 'can', 'CAN.G138.4' => 'can', 'CAN.G44.6' => 'can', 'CAN.G473.19' => 'can', 'CANSAT01G0835' => 'cansat', 'CANSAT11G0246' => 'cansat', 'CANSAT11G1766' => 'cansat', 'CANSAT64G1954' => 'cansat', 'CARHR013330' => 'chi', 'CARHR060530' => 'chi', 'CARHR075300' => 'chi', 'CARHR105120' => 'chi', 'CARHR148910' => 'chi', 'CARHR198830' => 'chi', 'Carub.0001s1275' => 'cru', 'Carub.0002s1437' => 'cru', 'Carub.0003s0044' => 'cru', 'Carub.0003s2787' => 'cru', 'Carub.0005s0597' => 'cru', 'Carub.0006s1266' => 'cru', 'Ca_06935_v3' => 'car', 'Ca_13559_v3' => 'car', 'Ca_16941_v3' => 'car', 'Ca_16960_v3' => 'car', 'Ca_17775_v3' => 'car', 'Ca_30464_v3' => 'car', 'Cc06_g08160' => 'ccan', 'Cc07_g01520' => 'ccan', 'Cc11_g15810' => 'ccan', 'CDE02G2840' => 'cde', 'CDE03G0093' => 'cde', 'CDE04G2127' => 'cde', 'CDE07G1857' => 'cde', 'CDE09G1246' => 'cde', 'Cfa003412' => 'cfa', 'Cfa007341' => 'cfa', 'Cfa009220' => 'cfa', 'Ciclev10008737m.g' => 'ccl', 'Ciclev10015565m.g' => 'ccl', 'Ciclev10031761m.g' => 'ccl', 'CiPaw.03G045300' => 'cil', 'CiPaw.03G247200' => 'cil', 'CiPaw.04G029500' => 'cil', 'CiPaw.04G174000' => 'cil', 'CiPaw.05G181200' => 'cil', 'CiPaw.06G067100' => 'cil', 'ClCG05G025800' => 'cla', 'ClCG06G011400' => 'cla', 'ClCG09G019360' => 'cla', 'COL.COLO4_04827' => 'col', 'COL.COLO4_29170' => 'col', 'COL.COLO4_35131' => 'col', 'COL.COLO4_35132' => 'col', 'Cpa.g.sc33.32' => 'cpa', 'Cpa.g.sc46.29' => 'cpa', 'Cpa.g.sc796.1' => 'cpa', 'CsaV3_1G030420' => 'csa', 'CsaV3_5G027050' => 'csa', 'CsaV3_5G031040' => 'csa', 'CsaV3_UNG023130' => 'csa', 'CSS0007726' => 'camsi', 'CSS0016433' => 'camsi', 'CSS0017656' => 'camsi', 'CSS0025364' => 'camsi', 'CSS0027582' => 'camsi', 'CSS0047288' => 'camsi', 'CSS0049950' => 'camsi', 'DCAR_003843' => 'dca', 'DCAR_007052' => 'dca', 'DCAR_020884' => 'dca', 'DCAR_021730' => 'dca', 'DCAR_024423' => 'dca', 'DCAR_026509' => 'dca', 'DCAR_031158' => 'dca', 'Dinv14728' => 'din', 'Dinv15219' => 'din', 'Dinv25728' => 'din', 'Dinv33428' => 'din', 'Dinv36489' => 'din', 'Dinv41486' => 'din', 'Duzib147G0469' => 'dzi', 'Duzib168G0060' => 'dzi', 'Duzib187G1215' => 'dzi', 'Duzib248G0692' => 'dzi', 'Duzib251G0767' => 'dzi', 'Duzib264G0446' => 'dzi', 'Duzib268G0691' => 'dzi', 'ECA232G4767' => 'eca', 'ECA233G2838' => 'eca', 'ECA234G0391' => 'eca', 'ECA234G0857' => 'eca', 'ECA236G1593' => 'eca', 'ECA238G0565' => 'eca', 'ECA246G1027' => 'eca', 'ECA246G3223' => 'eca', 'ECA246G3470' => 'eca', 'EL10Ac6g13829' => 'bvu', 'EL10Ac6g14093' => 'bvu', 'EL10Ac8g18707' => 'bvu', 'Eucgr.C01369' => 'egr', 'Eucgr.H02492' => 'egr', 'Eucgr.I01733' => 'egr', 'Eucgr.J02255' => 'egr', 'Eucgr.J02257' => 'egr', 'Eucgr.J02258' => 'egr', 'FAN02G1601' => 'fan', 'FAN03G1586' => 'fan', 'FAN03G2986' => 'fan', 'FAN05G4837' => 'fan', 'FAN06G0146' => 'fan', 'FAN07G0858' => 'fan', 'FAN09G3179' => 'fan', 'FAN10G0669' => 'fan', 'FAN12G2358' => 'fan', 'FAN14G4198' => 'fan', 'FAN14G5112' => 'fan', 'FAN17G0342' => 'fan', 'FAN19G0342' => 'fan', 'FAN19G0962' => 'fan', 'FAN19G1101' => 'fan', 'FAN19G1872' => 'fan', 'FAN22G0356' => 'fan', 'FAN23G0744' => 'fan', 'FAN23G1914' => 'fan', 'FAN26G0032' => 'fan', 'FAN28G0625' => 'fan', 'FvH4_1g02710' => 'fve', 'FvH4_1g02720' => 'fve', 'FvH4_4g25670' => 'fve', 'FvH4_6g51700' => 'fve', 'FvH4_7g20170' => 'fve', 'Glyma.05G175000' => 'gma', 'Glyma.08G132300' => 'gma', 'Glyma.11G243000' => 'gma', 'Glyma.13G158900' => 'gma', 'Glyma.17G112400' => 'gma', 'Glyma.18G014100' => 'gma', 'Glyma.19G003100' => 'gma', 'Glyma.19G056500' => 'gma', 'Gohir.A01G158900' => 'ghi', 'Gohir.A05G312600' => 'ghi', 'Gohir.A05G354900' => 'ghi', 'Gohir.A07G037200' => 'ghi', 'Gohir.A09G030000' => 'ghi', 'Gohir.A12G145200' => 'ghi', 'Gohir.D01G151500' => 'ghi', 'Gohir.D04G058300' => 'ghi', 'Gohir.D05G314100' => 'ghi', 'Gohir.D07G041400' => 'ghi', 'Gohir.D09G029700' => 'ghi', 'Gohir.D12G149700' => 'ghi', 'Gorai.001G043800' => 'gra', 'Gorai.002G187800' => 'gra', 'Gorai.006G034700' => 'gra', 'Gorai.008G161200' => 'gra', 'Gorai.009G335700' => 'gra', 'Gorai.012G065000' => 'gra', 'GSVIVG01000535001' => 'vvi', 'GSVIVG01015572001' => 'vvi', 'GSVIVG01032386001' => 'vvi', 'HanXRQChr05g0138531' => 'han', 'HanXRQChr06g0174391' => 'han', 'HanXRQChr07g0199021' => 'han', 'HanXRQChr08g0208211' => 'han', 'HanXRQChr09g0255471' => 'han', 'HanXRQChr10g0315791' => 'han', 'HanXRQChr12g0371991' => 'han', 'HanXRQChr15g0475251' => 'han', 'HanXRQChr17g0540001' => 'han', 'HanXRQChr17g0548631' => 'han', 'HanXRQChr17g0569561' => 'han', 'Haze_12256' => 'cav', 'Haze_14756' => 'cav', 'Haze_25528' => 'cav', 'Hma1.2p1_0079F.1_g041020' => 'hma', 'Hma1.2p1_0818F.1_g223260' => 'hma', 'Hma1.2p1_1747F.1_g300530' => 'hma', 'HPP92_004607' => 'vpl', 'HPP92_004608' => 'vpl', 'HPP92_006181' => 'vpl', 'HPP92_012192' => 'vpl', 'HPP92_015680' => 'vpl', 'HPP92_020249' => 'vpl', 'HPP92_021376' => 'vpl', 'HPP92_024275' => 'vpl', 'Hund06031' => 'sun', 'Hund25391' => 'sun', 'Lalb_Chr07g0185371' => 'lal', 'Lalb_Chr07g0185381' => 'lal', 'Lalb_Chr12g0204011' => 'lal', 'Lalb_Chr13g0301671' => 'lal', 'Lalb_Chr14g0362851' => 'lal', 'Lalb_Chr24g0403581' => 'lal', 'Lj1g0000233' => 'lja', 'Lj2g0018120' => 'lja', 'Lj3C621T0' => 'lonja', 'Lj3P1059T14' => 'lonja', 'Lj3P611T9' => 'lonja', 'Lj3P614T13' => 'lonja', 'Lj3P615T5' => 'lonja', 'Lj4g0012315' => 'lja', 'Lj4g0026182' => 'lja', 'Lj6P813T16' => 'lonja', 'Lj7C427T7' => 'lonja', 'Lj7C427T8' => 'lonja', 'Lj7P600T41' => 'lonja', 'Lju41C42G17' => 'lonja', 'Lsat_1_v5_gn_0_47300' => 'lsa', 'Lsat_1_v5_gn_2_91280' => 'lsa', 'Lsat_1_v5_gn_3_30561' => 'lsa', 'Lsat_1_v5_gn_4_184321' => 'lsa', 'Lsat_1_v5_gn_4_4041' => 'lsa', 'Lsat_1_v5_gn_5_92000' => 'lsa', 'Lsat_1_v5_gn_8_152940' => 'lsa', 'Lsat_1_v5_gn_8_62401' => 'lsa', 'Manes.06G055900' => 'mes', 'Manes.12G022200' => 'mes', 'Manes.13G023300' => 'mes', 'Manes.14G115000' => 'mes', 'Manes.15G151700' => 'mes', 'Manes.17G111300' => 'mes', 'Mapoly0226s0009' => 'mpo', 'MBI02_g25363_MAGBIO' => 'mbi', 'MBI06_g00027_MAGBIO' => 'mbi', 'MBI10_g13034_MAGBIO' => 'mbi', 'MD09G1023400' => 'mdo', 'MD13G1100100' => 'mdo', 'MD15G1169200' => 'mdo', 'MD16G1101100' => 'mdo', 'MD17G1022900' => 'mdo', 'Medtr3g096150' => 'mtr', 'Medtr4g115070' => 'mtr', 'Medtr7g033325' => 'mtr', 'Medtr8g089840' => 'mtr', 'MELO3C010319.2' => 'cme', 'MELO3C011944.2' => 'cme', 'MELO3C021589.2' => 'cme', 'Migut.E00207' => 'egut', 'Migut.H00067' => 'egut', 'Migut.K00433' => 'egut', 'Migut.K00606' => 'egut', 'Migut.K01410' => 'egut', 'MSTRG.13347' => 'ama', 'MSTRG.24045' => 'ama', 'MSTRG.2428' => 'ama', 'MSTRG.26410' => 'ama', 'MSTRG.3139' => 'ama', 'MSTRG.3286' => 'ama', 'MSTRG.563' => 'ama', 'MSTRG.7941' => 'ama', 'Nitab4.5_0000028g0060' => 'nta', 'Nitab4.5_0000065g0260' => 'nta', 'Nitab4.5_0000112g0060' => 'nta', 'Nitab4.5_0000489g0120' => 'nta', 'Nitab4.5_0001776g0050' => 'nta', 'Nitab4.5_0001854g0010' => 'nta', 'Nitab4.5_0001860g0020' => 'nta', 'Nitab4.5_0004352g0010' => 'nta', 'Nitab4.5_0008716g0020' => 'nta', 'Nitab4.5_0008922g0010' => 'nta', 'Nn3g16693' => 'nnu', 'Nn4g22596' => 'nnu', 'Nn7g37639' => 'nnu', 'Oeu001701.1' => 'oeu', 'Oeu018149.1' => 'oeu', 'Oeu026220.1' => 'oeu', 'Oeu038635.1' => 'oeu', 'Oeu049176.1' => 'oeu', 'Oeu056706.1' => 'oeu', 'Oeu056937.1' => 'oeu', 'Oeu057540.1' => 'oeu', 'Os02g0594900' => 'osa', 'Os02g0595100' => 'osa', 'Os04g0477500' => 'osa', 'Os12g0611900' => 'osa', 'Peaxi162Scf00076g00020' => 'pax', 'Peaxi162Scf00128g00217' => 'pax', 'Peaxi162Scf00129g01640' => 'pax', 'Peaxi162Scf00669g00007' => 'pax', 'Peaxi162Scf00700g00421' => 'pax', 'Peaxi162Scf00801g00038' => 'pax', 'Peaxi162Scf00891g00025' => 'pax', 'PGR083G0909' => 'pgr', 'PGR119G1005' => 'pgr', 'PGR142G2236' => 'pgr', 'PGR142G3388' => 'pgr', 'PGSC0003DMG400004514' => 'stu', 'PGSC0003DMG400012635' => 'stu', 'PGSC0003DMG400015730' => 'stu', 'PGSC0003DMG400018611' => 'stu', 'PGSC0003DMG400030897' => 'stu', 'Phvul.001G254800' => 'pvu', 'Phvul.002G260100' => 'pvu', 'Phvul.003G167600' => 'pvu', 'Phvul.004G005100' => 'pvu', 'Potri.001G343600' => 'ptr', 'Potri.006G066700' => 'ptr', 'Potri.008G186000' => 'ptr', 'Potri.010G046900' => 'ptr', 'Potri.018G127900' => 'ptr', 'Pp3c20_17750' => 'ppa', 'Pp3c24_4380' => 'ppa', 'Prupe.1G245800' => 'ppe', 'Prupe.3G293400' => 'ppe', 'Prupe.7G247400' => 'ppe', 'Psat0s145g0120' => 'psa', 'Psat0s595g0040' => 'psa', 'Psat0s595g0120' => 'psa', 'Psat3g175040' => 'psa', 'Psat7g058120' => 'psa', 'PSO017G0428' => 'pso', 'PSO063G7510' => 'pso', 'PSO067G0046' => 'pso', 'PSO478G1073' => 'pso', 'PSO675G3677' => 'pso', 'PSO675G6558' => 'pso', 'PSO675G7520' => 'pso', 'PSO675G8959' => 'pso', 'QL02p074089' => 'qlo', 'QL02p089614' => 'qlo', 'QL03p057736' => 'qlo', 'RcHm_v2.0_Chr1g0364131' => 'rch', 'RcHm_v2.0_Chr2g0087801' => 'rch', 'RcHm_v2.0_Chr2g0087821' => 'rch', 'RcHm_v2.0_Chr2g0173231' => 'rch', 'RcHm_v2.0_Chr4g0433111' => 'rch', 'Rhsim03G0250300' => 'rsi', 'Rhsim08G0048400' => 'rsi', 'Rhsim10G0014800' => 'rsi', 'Rhsim12G0040100' => 'rsi', 'Rhsim12G0109700' => 'rsi', 'Sabra06G0049600' => 'sbr', 'Sabra08G0141000' => 'sbr', 'Sabra10G0021400' => 'sbr', 'Sabra16G0222900' => 'sbr', 'Sabra18G0108600' => 'sbr', 'SalBow1G0433' => 'sbo', 'SalBow1G2038' => 'sbo', 'SalBow1G5003' => 'sbo', 'SalBow7G1197' => 'sbo', 'SalBow8G3506' => 'sbo', 'Sc03g0007300' => 'sci', 'Sc11g0000950' => 'sci', 'Sc14g0008750' => 'sci', 'Sc18g0000420' => 'sci', 'Sed0006754' => 'sed', 'Sed0008741' => 'sed', 'Sed0017172' => 'sed', 'Sed0018925' => 'sed', 'Sed0023326' => 'sed', 'Sed0025909' => 'sed', 'SEGI_05333' => 'sgi', 'SEGI_10362' => 'sgi', 'SEGI_13380' => 'sgi', 'SEGI_24306' => 'sgi', 'SEGI_29077' => 'sgi', 'SEGI_29095' => 'sgi', 'SEGI_36534' => 'sgi', 'SEGI_37506' => 'sgi', 'SEGI_38321' => 'sgi', 'SGA_v2.0_scaffold307G48031' => 'sas', 'SGA_v2.0_scaffold47G17507' => 'sas', 'SGA_v2.0_scaffold63G21736' => 'sas', 'SGA_v2.0_scaffold87G27070' => 'sas', 'SHI17794' => 'shi', 'SHI28851' => 'shi', 'SMO165G0155' => 'smo', 'SMO340G0217' => 'smo', 'SMO367G1210' => 'smo', 'Solyc02g093430.3' => 'sly', 'Solyc05g013580.4' => 'sly', 'Solyc07g008030.3' => 'sly', 'Solyc12g035470.2' => 'sly', 'Sopen02g038020' => 'spe', 'Sopen05g008490' => 'spe', 'Sopen07g003910' => 'spe', 'Sopen12g015240' => 'spe', 'Sp1g11550' => 'spa', 'Sp2g16710' => 'spa', 'Sp3g00430' => 'spa', 'Sp3g26780' => 'spa', 'Sp5g22900' => 'spa', 'Sp6g29530' => 'spa', 'TAR371G0794' => 'tar', 'TAR374G0164' => 'tar', 'TAR622G0165' => 'tar', 'TAR626G0929' => 'tar', 'TAR629G2155' => 'tar', 'THA.LOC104805282' => 'tha', 'THA.LOC104805363' => 'tha', 'THA.LOC104808968' => 'tha', 'THA.LOC104821093' => 'tha', 'THA.LOC104823953' => 'tha', 'THA.LOC104825562' => 'tha', 'THA.LOC104825665' => 'tha', 'Thecc.02G261400' => 'tca', 'Thecc.04G019200' => 'tca', 'Thecc.09G130400' => 'tca', 'Thhalv10004374m.g' => 'esa', 'Thhalv10007850m.g' => 'esa', 'Thhalv10013782m.g' => 'esa', 'Thhalv10018686m.g' => 'esa', 'Thhalv10020899m.g' => 'esa', 'Thhalv10022755m.g' => 'esa', 'TPR.G23851' => 'tpr', 'TPR.G26500' => 'tpr', 'TPR.G27267' => 'tpr', 'TPR.G32001' => 'tpr', 'TPR.G6251' => 'tpr', 'TPR.G8167' => 'tpr', 'TWI12G1330' => 'twi', 'TWI18G1239' => 'twi', 'TWI34G0979' => 'twi', 'TWI36G0670' => 'twi', 'TWI36G0707' => 'twi', 'TWI56G0233' => 'twi', 'TWI75G1809' => 'twi', 'unitig_21.g20874' => 'ugi', 'unitig_26.g10343' => 'ugi', 'unitig_46.g18392' => 'ugi', 'unitig_52.g17178' => 'ugi', 'unitig_8.g2934' => 'ugi', 'vmacro01122' => 'vma', 'vmacro05875' => 'vma', 'vmacro06147' => 'vma', 'vmacro16191' => 'vma', 'vmacro18293' => 'vma', 'VMungo0251G3707' => 'vmu', 'VMungo0464G1521' => 'vmu', 'VMungo1215G0205' => 'vmu', 'VMungo1383G2484' => 'vmu', 'Zm00001eb079610' => 'zma', 'Zm00001eb135990' => 'zma', 'Zm00001eb183710' => 'zma', 'Zm00001eb246020' => 'zma' ) $gf_id = 'HOM05D001124' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001124' ) $data_identifier = 'HOM05D001124' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 6, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 7, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 21, 'bol' => (int) 10, 'bra' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 6, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 9, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 21, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 8, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 10, 'lsa' => (int) 8, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 8, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 9, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb246020' $species_info = array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ) $local_species = 'can' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001124', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '548', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02520' => 'bna', 'A03p06630' => 'bna', 'A05p44460' => 'bna', 'A06p08710' => 'bna', 'A06p41090' => 'bna', 'A07p32320' => 'bna', 'A08p32520' => 'bna', 'A09p10360' => 'bna', 'A10p24080' => 'bna', 'Aa31LG11G15250' => 'aar', 'Aa31LG1G1800' => 'aar', 'Aa31LG2G5120' => 'aar', 'Aa31LG2G6070' => 'aar', 'Aa31LG5G10770' => 'aar', 'Aa31sc61G90' => 'aar', 'Actinidia01352' => 'ach', 'Actinidia05983' => 'ach', 'Actinidia08133' => 'ach', 'Actinidia15101' => 'ach', 'Actinidia26379' => 'ach', 'Actinidia35778' => 'ach', 'Actinidia36123' => 'ach', 'Actinidia37436' => 'ach', 'Actinidia38730' => 'ach', 'Ah.02g128210' => 'amhyb', 'Ah.03g132990' => 'amhyb', 'Ah.14g079410' => 'amhyb', 'AL1G24640' => 'aly', 'AL2G26680' => 'aly', 'AL3G10530' => 'aly', 'AL3G45230' => 'aly', 'AL5G15230' => 'aly', 'AL5G16960' => 'aly', 'AL6G25210' => 'aly', 'Aqoxy2G00441' => 'aox', 'Aqoxy3G01236' => 'aox', 'Aqoxy5G03746' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3RQ047' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C7GMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9C8JER' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MBL6KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YXCZ83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZANX40' => 'arhy', 'AT1G12990' => 'ath', 'AT1G67880' => 'ath', 'AT2G13290' => 'ath', 'AT3G01620' => 'ath', 'AT3G26445' => 'ath', 'AT3G27540' => 'ath', 'AT5G14480' => 'ath', 'ATR0824G026' => 'atr', 'ATR1098G019' => 'atr', 'Atru.chr11.2145' => 'acertr', 'Atru.chr2.3636' => 'acertr', 'Atru.chr2.3644' => 'acertr', 'Atru.chr6.2422' => 'acertr', 'Atru.chr7.1112' => 'acertr', 'AUR62005469' => 'cqu', 'AUR62011166' => 'cqu', 'AUR62013319' => 'cqu', 'AUR62024273' => 'cqu', 'AUR62028420' => 'cqu', 'AUR62041942' => 'cqu', 'BcaB01g04969' => 'bca', 'BcaB01g06371' => 'bca', 'BcaB02g11494' => 'bca', 'BcaB03g15382' => 'bca', 'BcaB08g36994' => 'bca', 'BcaC03g13477' => 'bca', 'BcaC03g13478' => 'bca', 'BcaC03g13480' => 'bca', 'BcaC03g13481' => 'bca', 'BcaC03g13486' => 'bca', 'BcaC04g19031' => 'bca', 'BcaC04g23085' => 'bca', 'BcaC05g25094' => 'bca', 'BcaC05g25096' => 'bca', 'BcaC05g25138' => 'bca', 'BcaC05g30416' => 'bca', 'BcaC05g30455' => 'bca', 'BcaC06g30979' => 'bca', 'BcaC06g33805' => 'bca', 'BcaC08g46021' => 'bca', 'BcaNung03154' => 'bca', 'BolC2t06623H' => 'bol', 'BolC2t06632H' => 'bol', 'BolC2t06635H' => 'bol', 'BolC2t06638H' => 'bol', 'BolC3t13266H' => 'bol', 'BolC5t29776H' => 'bol', 'BolC6t38912H' => 'bol', 'BolC7t44183H' => 'bol', 'BolC9t54123H' => 'bol', 'BolC9t59107H' => 'bol', 'BraA02t05221Z' => 'bra', 'BraA03t09996Z' => 'bra', 'BraA05t23210Z' => 'bra', 'BraA06t24068Z' => 'bra', 'BraA06t27032Z' => 'bra', 'BraA08t35176Z' => 'bra', 'BraA09t36680Z' => 'bra', 'BraA10t44471Z' => 'bra', 'C02p06760' => 'bna', 'C02p06890' => 'bna', 'C02p07010' => 'bna', 'C03p07660' => 'bna', 'C05p10300' => 'bna', 'C06p38150' => 'bna', 'C07p36650' => 'bna', 'C08p15770' => 'bna', 'C09p12300' => 'bna', 'C09p62700' => 'bna', 'C09p75040' => 'bna', 'CAN.G13.1' => 'can', 'CAN.G138.4' => 'can', 'CAN.G44.6' => 'can', 'CAN.G473.19' => 'can', 'CANSAT01G0835' => 'cansat', 'CANSAT11G0246' => 'cansat', 'CANSAT11G1766' => 'cansat', 'CANSAT64G1954' => 'cansat', 'CARHR013330' => 'chi', 'CARHR060530' => 'chi', 'CARHR075300' => 'chi', 'CARHR105120' => 'chi', 'CARHR148910' => 'chi', 'CARHR198830' => 'chi', 'Carub.0001s1275' => 'cru', 'Carub.0002s1437' => 'cru', 'Carub.0003s0044' => 'cru', 'Carub.0003s2787' => 'cru', 'Carub.0005s0597' => 'cru', 'Carub.0006s1266' => 'cru', 'Ca_06935_v3' => 'car', 'Ca_13559_v3' => 'car', 'Ca_16941_v3' => 'car', 'Ca_16960_v3' => 'car', 'Ca_17775_v3' => 'car', 'Ca_30464_v3' => 'car', 'Cc06_g08160' => 'ccan', 'Cc07_g01520' => 'ccan', 'Cc11_g15810' => 'ccan', 'CDE02G2840' => 'cde', 'CDE03G0093' => 'cde', 'CDE04G2127' => 'cde', 'CDE07G1857' => 'cde', 'CDE09G1246' => 'cde', 'Cfa003412' => 'cfa', 'Cfa007341' => 'cfa', 'Cfa009220' => 'cfa', 'Ciclev10008737m.g' => 'ccl', 'Ciclev10015565m.g' => 'ccl', 'Ciclev10031761m.g' => 'ccl', 'CiPaw.03G045300' => 'cil', 'CiPaw.03G247200' => 'cil', 'CiPaw.04G029500' => 'cil', 'CiPaw.04G174000' => 'cil', 'CiPaw.05G181200' => 'cil', 'CiPaw.06G067100' => 'cil', 'ClCG05G025800' => 'cla', 'ClCG06G011400' => 'cla', 'ClCG09G019360' => 'cla', 'COL.COLO4_04827' => 'col', 'COL.COLO4_29170' => 'col', 'COL.COLO4_35131' => 'col', 'COL.COLO4_35132' => 'col', 'Cpa.g.sc33.32' => 'cpa', 'Cpa.g.sc46.29' => 'cpa', 'Cpa.g.sc796.1' => 'cpa', 'CsaV3_1G030420' => 'csa', 'CsaV3_5G027050' => 'csa', 'CsaV3_5G031040' => 'csa', 'CsaV3_UNG023130' => 'csa', 'CSS0007726' => 'camsi', 'CSS0016433' => 'camsi', 'CSS0017656' => 'camsi', 'CSS0025364' => 'camsi', 'CSS0027582' => 'camsi', 'CSS0047288' => 'camsi', 'CSS0049950' => 'camsi', 'DCAR_003843' => 'dca', 'DCAR_007052' => 'dca', 'DCAR_020884' => 'dca', 'DCAR_021730' => 'dca', 'DCAR_024423' => 'dca', 'DCAR_026509' => 'dca', 'DCAR_031158' => 'dca', 'Dinv14728' => 'din', 'Dinv15219' => 'din', 'Dinv25728' => 'din', 'Dinv33428' => 'din', 'Dinv36489' => 'din', 'Dinv41486' => 'din', 'Duzib147G0469' => 'dzi', 'Duzib168G0060' => 'dzi', 'Duzib187G1215' => 'dzi', 'Duzib248G0692' => 'dzi', 'Duzib251G0767' => 'dzi', 'Duzib264G0446' => 'dzi', 'Duzib268G0691' => 'dzi', 'ECA232G4767' => 'eca', 'ECA233G2838' => 'eca', 'ECA234G0391' => 'eca', 'ECA234G0857' => 'eca', 'ECA236G1593' => 'eca', 'ECA238G0565' => 'eca', 'ECA246G1027' => 'eca', 'ECA246G3223' => 'eca', 'ECA246G3470' => 'eca', 'EL10Ac6g13829' => 'bvu', 'EL10Ac6g14093' => 'bvu', 'EL10Ac8g18707' => 'bvu', 'Eucgr.C01369' => 'egr', 'Eucgr.H02492' => 'egr', 'Eucgr.I01733' => 'egr', 'Eucgr.J02255' => 'egr', 'Eucgr.J02257' => 'egr', 'Eucgr.J02258' => 'egr', 'FAN02G1601' => 'fan', 'FAN03G1586' => 'fan', 'FAN03G2986' => 'fan', 'FAN05G4837' => 'fan', 'FAN06G0146' => 'fan', 'FAN07G0858' => 'fan', 'FAN09G3179' => 'fan', 'FAN10G0669' => 'fan', 'FAN12G2358' => 'fan', 'FAN14G4198' => 'fan', 'FAN14G5112' => 'fan', 'FAN17G0342' => 'fan', 'FAN19G0342' => 'fan', 'FAN19G0962' => 'fan', 'FAN19G1101' => 'fan', 'FAN19G1872' => 'fan', 'FAN22G0356' => 'fan', 'FAN23G0744' => 'fan', 'FAN23G1914' => 'fan', 'FAN26G0032' => 'fan', 'FAN28G0625' => 'fan', 'FvH4_1g02710' => 'fve', 'FvH4_1g02720' => 'fve', 'FvH4_4g25670' => 'fve', 'FvH4_6g51700' => 'fve', 'FvH4_7g20170' => 'fve', 'Glyma.05G175000' => 'gma', 'Glyma.08G132300' => 'gma', 'Glyma.11G243000' => 'gma', 'Glyma.13G158900' => 'gma', 'Glyma.17G112400' => 'gma', 'Glyma.18G014100' => 'gma', 'Glyma.19G003100' => 'gma', 'Glyma.19G056500' => 'gma', 'Gohir.A01G158900' => 'ghi', 'Gohir.A05G312600' => 'ghi', 'Gohir.A05G354900' => 'ghi', 'Gohir.A07G037200' => 'ghi', 'Gohir.A09G030000' => 'ghi', 'Gohir.A12G145200' => 'ghi', 'Gohir.D01G151500' => 'ghi', 'Gohir.D04G058300' => 'ghi', 'Gohir.D05G314100' => 'ghi', 'Gohir.D07G041400' => 'ghi', 'Gohir.D09G029700' => 'ghi', 'Gohir.D12G149700' => 'ghi', 'Gorai.001G043800' => 'gra', 'Gorai.002G187800' => 'gra', 'Gorai.006G034700' => 'gra', 'Gorai.008G161200' => 'gra', 'Gorai.009G335700' => 'gra', 'Gorai.012G065000' => 'gra', 'GSVIVG01000535001' => 'vvi', 'GSVIVG01015572001' => 'vvi', 'GSVIVG01032386001' => 'vvi', 'HanXRQChr05g0138531' => 'han', 'HanXRQChr06g0174391' => 'han', 'HanXRQChr07g0199021' => 'han', 'HanXRQChr08g0208211' => 'han', 'HanXRQChr09g0255471' => 'han', 'HanXRQChr10g0315791' => 'han', 'HanXRQChr12g0371991' => 'han', 'HanXRQChr15g0475251' => 'han', 'HanXRQChr17g0540001' => 'han', 'HanXRQChr17g0548631' => 'han', 'HanXRQChr17g0569561' => 'han', 'Haze_12256' => 'cav', 'Haze_14756' => 'cav', 'Haze_25528' => 'cav', 'Hma1.2p1_0079F.1_g041020' => 'hma', 'Hma1.2p1_0818F.1_g223260' => 'hma', 'Hma1.2p1_1747F.1_g300530' => 'hma', 'HPP92_004607' => 'vpl', 'HPP92_004608' => 'vpl', 'HPP92_006181' => 'vpl', 'HPP92_012192' => 'vpl', 'HPP92_015680' => 'vpl', 'HPP92_020249' => 'vpl', 'HPP92_021376' => 'vpl', 'HPP92_024275' => 'vpl', 'Hund06031' => 'sun', 'Hund25391' => 'sun', 'Lalb_Chr07g0185371' => 'lal', 'Lalb_Chr07g0185381' => 'lal', 'Lalb_Chr12g0204011' => 'lal', 'Lalb_Chr13g0301671' => 'lal', 'Lalb_Chr14g0362851' => 'lal', 'Lalb_Chr24g0403581' => 'lal', 'Lj1g0000233' => 'lja', 'Lj2g0018120' => 'lja', 'Lj3C621T0' => 'lonja', 'Lj3P1059T14' => 'lonja', 'Lj3P611T9' => 'lonja', 'Lj3P614T13' => 'lonja', 'Lj3P615T5' => 'lonja', 'Lj4g0012315' => 'lja', 'Lj4g0026182' => 'lja', 'Lj6P813T16' => 'lonja', 'Lj7C427T7' => 'lonja', 'Lj7C427T8' => 'lonja', 'Lj7P600T41' => 'lonja', 'Lju41C42G17' => 'lonja', 'Lsat_1_v5_gn_0_47300' => 'lsa', 'Lsat_1_v5_gn_2_91280' => 'lsa', 'Lsat_1_v5_gn_3_30561' => 'lsa', 'Lsat_1_v5_gn_4_184321' => 'lsa', 'Lsat_1_v5_gn_4_4041' => 'lsa', 'Lsat_1_v5_gn_5_92000' => 'lsa', 'Lsat_1_v5_gn_8_152940' => 'lsa', 'Lsat_1_v5_gn_8_62401' => 'lsa', 'Manes.06G055900' => 'mes', 'Manes.12G022200' => 'mes', 'Manes.13G023300' => 'mes', 'Manes.14G115000' => 'mes', 'Manes.15G151700' => 'mes', 'Manes.17G111300' => 'mes', 'Mapoly0226s0009' => 'mpo', 'MBI02_g25363_MAGBIO' => 'mbi', 'MBI06_g00027_MAGBIO' => 'mbi', 'MBI10_g13034_MAGBIO' => 'mbi', 'MD09G1023400' => 'mdo', 'MD13G1100100' => 'mdo', 'MD15G1169200' => 'mdo', 'MD16G1101100' => 'mdo', 'MD17G1022900' => 'mdo', 'Medtr3g096150' => 'mtr', 'Medtr4g115070' => 'mtr', 'Medtr7g033325' => 'mtr', 'Medtr8g089840' => 'mtr', 'MELO3C010319.2' => 'cme', 'MELO3C011944.2' => 'cme', 'MELO3C021589.2' => 'cme', 'Migut.E00207' => 'egut', 'Migut.H00067' => 'egut', 'Migut.K00433' => 'egut', 'Migut.K00606' => 'egut', 'Migut.K01410' => 'egut', 'MSTRG.13347' => 'ama', 'MSTRG.24045' => 'ama', 'MSTRG.2428' => 'ama', 'MSTRG.26410' => 'ama', 'MSTRG.3139' => 'ama', 'MSTRG.3286' => 'ama', 'MSTRG.563' => 'ama', 'MSTRG.7941' => 'ama', 'Nitab4.5_0000028g0060' => 'nta', 'Nitab4.5_0000065g0260' => 'nta', 'Nitab4.5_0000112g0060' => 'nta', 'Nitab4.5_0000489g0120' => 'nta', 'Nitab4.5_0001776g0050' => 'nta', 'Nitab4.5_0001854g0010' => 'nta', 'Nitab4.5_0001860g0020' => 'nta', 'Nitab4.5_0004352g0010' => 'nta', 'Nitab4.5_0008716g0020' => 'nta', 'Nitab4.5_0008922g0010' => 'nta', 'Nn3g16693' => 'nnu', 'Nn4g22596' => 'nnu', 'Nn7g37639' => 'nnu', 'Oeu001701.1' => 'oeu', 'Oeu018149.1' => 'oeu', 'Oeu026220.1' => 'oeu', 'Oeu038635.1' => 'oeu', 'Oeu049176.1' => 'oeu', 'Oeu056706.1' => 'oeu', 'Oeu056937.1' => 'oeu', 'Oeu057540.1' => 'oeu', 'Os02g0594900' => 'osa', 'Os02g0595100' => 'osa', 'Os04g0477500' => 'osa', 'Os12g0611900' => 'osa', 'Peaxi162Scf00076g00020' => 'pax', 'Peaxi162Scf00128g00217' => 'pax', 'Peaxi162Scf00129g01640' => 'pax', 'Peaxi162Scf00669g00007' => 'pax', 'Peaxi162Scf00700g00421' => 'pax', 'Peaxi162Scf00801g00038' => 'pax', 'Peaxi162Scf00891g00025' => 'pax', 'PGR083G0909' => 'pgr', 'PGR119G1005' => 'pgr', 'PGR142G2236' => 'pgr', 'PGR142G3388' => 'pgr', 'PGSC0003DMG400004514' => 'stu', 'PGSC0003DMG400012635' => 'stu', 'PGSC0003DMG400015730' => 'stu', 'PGSC0003DMG400018611' => 'stu', 'PGSC0003DMG400030897' => 'stu', 'Phvul.001G254800' => 'pvu', 'Phvul.002G260100' => 'pvu', 'Phvul.003G167600' => 'pvu', 'Phvul.004G005100' => 'pvu', 'Potri.001G343600' => 'ptr', 'Potri.006G066700' => 'ptr', 'Potri.008G186000' => 'ptr', 'Potri.010G046900' => 'ptr', 'Potri.018G127900' => 'ptr', 'Pp3c20_17750' => 'ppa', 'Pp3c24_4380' => 'ppa', 'Prupe.1G245800' => 'ppe', 'Prupe.3G293400' => 'ppe', 'Prupe.7G247400' => 'ppe', 'Psat0s145g0120' => 'psa', 'Psat0s595g0040' => 'psa', 'Psat0s595g0120' => 'psa', 'Psat3g175040' => 'psa', 'Psat7g058120' => 'psa', 'PSO017G0428' => 'pso', 'PSO063G7510' => 'pso', 'PSO067G0046' => 'pso', 'PSO478G1073' => 'pso', 'PSO675G3677' => 'pso', 'PSO675G6558' => 'pso', 'PSO675G7520' => 'pso', 'PSO675G8959' => 'pso', 'QL02p074089' => 'qlo', 'QL02p089614' => 'qlo', 'QL03p057736' => 'qlo', 'RcHm_v2.0_Chr1g0364131' => 'rch', 'RcHm_v2.0_Chr2g0087801' => 'rch', 'RcHm_v2.0_Chr2g0087821' => 'rch', 'RcHm_v2.0_Chr2g0173231' => 'rch', 'RcHm_v2.0_Chr4g0433111' => 'rch', 'Rhsim03G0250300' => 'rsi', 'Rhsim08G0048400' => 'rsi', 'Rhsim10G0014800' => 'rsi', 'Rhsim12G0040100' => 'rsi', 'Rhsim12G0109700' => 'rsi', 'Sabra06G0049600' => 'sbr', 'Sabra08G0141000' => 'sbr', 'Sabra10G0021400' => 'sbr', 'Sabra16G0222900' => 'sbr', 'Sabra18G0108600' => 'sbr', 'SalBow1G0433' => 'sbo', 'SalBow1G2038' => 'sbo', 'SalBow1G5003' => 'sbo', 'SalBow7G1197' => 'sbo', 'SalBow8G3506' => 'sbo', 'Sc03g0007300' => 'sci', 'Sc11g0000950' => 'sci', 'Sc14g0008750' => 'sci', 'Sc18g0000420' => 'sci', 'Sed0006754' => 'sed', 'Sed0008741' => 'sed', 'Sed0017172' => 'sed', 'Sed0018925' => 'sed', 'Sed0023326' => 'sed', 'Sed0025909' => 'sed', 'SEGI_05333' => 'sgi', 'SEGI_10362' => 'sgi', 'SEGI_13380' => 'sgi', 'SEGI_24306' => 'sgi', 'SEGI_29077' => 'sgi', 'SEGI_29095' => 'sgi', 'SEGI_36534' => 'sgi', 'SEGI_37506' => 'sgi', 'SEGI_38321' => 'sgi', 'SGA_v2.0_scaffold307G48031' => 'sas', 'SGA_v2.0_scaffold47G17507' => 'sas', 'SGA_v2.0_scaffold63G21736' => 'sas', 'SGA_v2.0_scaffold87G27070' => 'sas', 'SHI17794' => 'shi', 'SHI28851' => 'shi', 'SMO165G0155' => 'smo', 'SMO340G0217' => 'smo', 'SMO367G1210' => 'smo', 'Solyc02g093430.3' => 'sly', 'Solyc05g013580.4' => 'sly', 'Solyc07g008030.3' => 'sly', 'Solyc12g035470.2' => 'sly', 'Sopen02g038020' => 'spe', 'Sopen05g008490' => 'spe', 'Sopen07g003910' => 'spe', 'Sopen12g015240' => 'spe', 'Sp1g11550' => 'spa', 'Sp2g16710' => 'spa', 'Sp3g00430' => 'spa', 'Sp3g26780' => 'spa', 'Sp5g22900' => 'spa', 'Sp6g29530' => 'spa', 'TAR371G0794' => 'tar', 'TAR374G0164' => 'tar', 'TAR622G0165' => 'tar', 'TAR626G0929' => 'tar', 'TAR629G2155' => 'tar', 'THA.LOC104805282' => 'tha', 'THA.LOC104805363' => 'tha', 'THA.LOC104808968' => 'tha', 'THA.LOC104821093' => 'tha', 'THA.LOC104823953' => 'tha', 'THA.LOC104825562' => 'tha', 'THA.LOC104825665' => 'tha', 'Thecc.02G261400' => 'tca', 'Thecc.04G019200' => 'tca', 'Thecc.09G130400' => 'tca', 'Thhalv10004374m.g' => 'esa', 'Thhalv10007850m.g' => 'esa', 'Thhalv10013782m.g' => 'esa', 'Thhalv10018686m.g' => 'esa', 'Thhalv10020899m.g' => 'esa', 'Thhalv10022755m.g' => 'esa', 'TPR.G23851' => 'tpr', 'TPR.G26500' => 'tpr', 'TPR.G27267' => 'tpr', 'TPR.G32001' => 'tpr', 'TPR.G6251' => 'tpr', 'TPR.G8167' => 'tpr', 'TWI12G1330' => 'twi', 'TWI18G1239' => 'twi', 'TWI34G0979' => 'twi', 'TWI36G0670' => 'twi', 'TWI36G0707' => 'twi', 'TWI56G0233' => 'twi', 'TWI75G1809' => 'twi', 'unitig_21.g20874' => 'ugi', 'unitig_26.g10343' => 'ugi', 'unitig_46.g18392' => 'ugi', 'unitig_52.g17178' => 'ugi', 'unitig_8.g2934' => 'ugi', 'vmacro01122' => 'vma', 'vmacro05875' => 'vma', 'vmacro06147' => 'vma', 'vmacro16191' => 'vma', 'vmacro18293' => 'vma', 'VMungo0251G3707' => 'vmu', 'VMungo0464G1521' => 'vmu', 'VMungo1215G0205' => 'vmu', 'VMungo1383G2484' => 'vmu', 'Zm00001eb079610' => 'zma', 'Zm00001eb135990' => 'zma', 'Zm00001eb183710' => 'zma', 'Zm00001eb246020' => 'zma' ), 'gf_id' => 'HOM05D001124', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001124' ), 'data_identifier' => 'HOM05D001124', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001124', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '548', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02520' => 'bna', 'A03p06630' => 'bna', 'A05p44460' => 'bna', 'A06p08710' => 'bna', 'A06p41090' => 'bna', 'A07p32320' => 'bna', 'A08p32520' => 'bna', 'A09p10360' => 'bna', 'A10p24080' => 'bna', 'Aa31LG11G15250' => 'aar', 'Aa31LG1G1800' => 'aar', 'Aa31LG2G5120' => 'aar', 'Aa31LG2G6070' => 'aar', 'Aa31LG5G10770' => 'aar', 'Aa31sc61G90' => 'aar', 'Actinidia01352' => 'ach', 'Actinidia05983' => 'ach', 'Actinidia08133' => 'ach', 'Actinidia15101' => 'ach', 'Actinidia26379' => 'ach', 'Actinidia35778' => 'ach', 'Actinidia36123' => 'ach', 'Actinidia37436' => 'ach', 'Actinidia38730' => 'ach', 'Ah.02g128210' => 'amhyb', 'Ah.03g132990' => 'amhyb', 'Ah.14g079410' => 'amhyb', 'AL1G24640' => 'aly', 'AL2G26680' => 'aly', 'AL3G10530' => 'aly', 'AL3G45230' => 'aly', 'AL5G15230' => 'aly', 'AL5G16960' => 'aly', 'AL6G25210' => 'aly', 'Aqoxy2G00441' => 'aox', 'Aqoxy3G01236' => 'aox', 'Aqoxy5G03746' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3RQ047' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C7GMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9C8JER' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MBL6KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YXCZ83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZANX40' => 'arhy', 'AT1G12990' => 'ath', 'AT1G67880' => 'ath', 'AT2G13290' => 'ath', 'AT3G01620' => 'ath', 'AT3G26445' => 'ath', 'AT3G27540' => 'ath', 'AT5G14480' => 'ath', 'ATR0824G026' => 'atr', 'ATR1098G019' => 'atr', 'Atru.chr11.2145' => 'acertr', 'Atru.chr2.3636' => 'acertr', 'Atru.chr2.3644' => 'acertr', 'Atru.chr6.2422' => 'acertr', 'Atru.chr7.1112' => 'acertr', 'AUR62005469' => 'cqu', 'AUR62011166' => 'cqu', 'AUR62013319' => 'cqu', 'AUR62024273' => 'cqu', 'AUR62028420' => 'cqu', 'AUR62041942' => 'cqu', 'BcaB01g04969' => 'bca', 'BcaB01g06371' => 'bca', 'BcaB02g11494' => 'bca', 'BcaB03g15382' => 'bca', 'BcaB08g36994' => 'bca', 'BcaC03g13477' => 'bca', 'BcaC03g13478' => 'bca', 'BcaC03g13480' => 'bca', 'BcaC03g13481' => 'bca', 'BcaC03g13486' => 'bca', 'BcaC04g19031' => 'bca', 'BcaC04g23085' => 'bca', 'BcaC05g25094' => 'bca', 'BcaC05g25096' => 'bca', 'BcaC05g25138' => 'bca', 'BcaC05g30416' => 'bca', 'BcaC05g30455' => 'bca', 'BcaC06g30979' => 'bca', 'BcaC06g33805' => 'bca', 'BcaC08g46021' => 'bca', 'BcaNung03154' => 'bca', 'BolC2t06623H' => 'bol', 'BolC2t06632H' => 'bol', 'BolC2t06635H' => 'bol', 'BolC2t06638H' => 'bol', 'BolC3t13266H' => 'bol', 'BolC5t29776H' => 'bol', 'BolC6t38912H' => 'bol', 'BolC7t44183H' => 'bol', 'BolC9t54123H' => 'bol', 'BolC9t59107H' => 'bol', 'BraA02t05221Z' => 'bra', 'BraA03t09996Z' => 'bra', 'BraA05t23210Z' => 'bra', 'BraA06t24068Z' => 'bra', 'BraA06t27032Z' => 'bra', 'BraA08t35176Z' => 'bra', 'BraA09t36680Z' => 'bra', 'BraA10t44471Z' => 'bra', 'C02p06760' => 'bna', 'C02p06890' => 'bna', 'C02p07010' => 'bna', 'C03p07660' => 'bna', 'C05p10300' => 'bna', 'C06p38150' => 'bna', 'C07p36650' => 'bna', 'C08p15770' => 'bna', 'C09p12300' => 'bna', 'C09p62700' => 'bna', 'C09p75040' => 'bna', 'CAN.G13.1' => 'can', 'CAN.G138.4' => 'can', 'CAN.G44.6' => 'can', 'CAN.G473.19' => 'can', 'CANSAT01G0835' => 'cansat', 'CANSAT11G0246' => 'cansat', 'CANSAT11G1766' => 'cansat', 'CANSAT64G1954' => 'cansat', 'CARHR013330' => 'chi', 'CARHR060530' => 'chi', 'CARHR075300' => 'chi', 'CARHR105120' => 'chi', 'CARHR148910' => 'chi', 'CARHR198830' => 'chi', 'Carub.0001s1275' => 'cru', 'Carub.0002s1437' => 'cru', 'Carub.0003s0044' => 'cru', 'Carub.0003s2787' => 'cru', 'Carub.0005s0597' => 'cru', 'Carub.0006s1266' => 'cru', 'Ca_06935_v3' => 'car', 'Ca_13559_v3' => 'car', 'Ca_16941_v3' => 'car', 'Ca_16960_v3' => 'car', 'Ca_17775_v3' => 'car', 'Ca_30464_v3' => 'car', 'Cc06_g08160' => 'ccan', 'Cc07_g01520' => 'ccan', 'Cc11_g15810' => 'ccan', 'CDE02G2840' => 'cde', 'CDE03G0093' => 'cde', 'CDE04G2127' => 'cde', 'CDE07G1857' => 'cde', 'CDE09G1246' => 'cde', 'Cfa003412' => 'cfa', 'Cfa007341' => 'cfa', 'Cfa009220' => 'cfa', 'Ciclev10008737m.g' => 'ccl', 'Ciclev10015565m.g' => 'ccl', 'Ciclev10031761m.g' => 'ccl', 'CiPaw.03G045300' => 'cil', 'CiPaw.03G247200' => 'cil', 'CiPaw.04G029500' => 'cil', 'CiPaw.04G174000' => 'cil', 'CiPaw.05G181200' => 'cil', 'CiPaw.06G067100' => 'cil', 'ClCG05G025800' => 'cla', 'ClCG06G011400' => 'cla', 'ClCG09G019360' => 'cla', 'COL.COLO4_04827' => 'col', 'COL.COLO4_29170' => 'col', 'COL.COLO4_35131' => 'col', 'COL.COLO4_35132' => 'col', 'Cpa.g.sc33.32' => 'cpa', 'Cpa.g.sc46.29' => 'cpa', 'Cpa.g.sc796.1' => 'cpa', 'CsaV3_1G030420' => 'csa', 'CsaV3_5G027050' => 'csa', 'CsaV3_5G031040' => 'csa', 'CsaV3_UNG023130' => 'csa', 'CSS0007726' => 'camsi', 'CSS0016433' => 'camsi', 'CSS0017656' => 'camsi', 'CSS0025364' => 'camsi', 'CSS0027582' => 'camsi', 'CSS0047288' => 'camsi', 'CSS0049950' => 'camsi', 'DCAR_003843' => 'dca', 'DCAR_007052' => 'dca', 'DCAR_020884' => 'dca', 'DCAR_021730' => 'dca', 'DCAR_024423' => 'dca', 'DCAR_026509' => 'dca', 'DCAR_031158' => 'dca', 'Dinv14728' => 'din', 'Dinv15219' => 'din', 'Dinv25728' => 'din', 'Dinv33428' => 'din', 'Dinv36489' => 'din', 'Dinv41486' => 'din', 'Duzib147G0469' => 'dzi', 'Duzib168G0060' => 'dzi', 'Duzib187G1215' => 'dzi', 'Duzib248G0692' => 'dzi', 'Duzib251G0767' => 'dzi', 'Duzib264G0446' => 'dzi', 'Duzib268G0691' => 'dzi', 'ECA232G4767' => 'eca', 'ECA233G2838' => 'eca', 'ECA234G0391' => 'eca', 'ECA234G0857' => 'eca', 'ECA236G1593' => 'eca', 'ECA238G0565' => 'eca', 'ECA246G1027' => 'eca', 'ECA246G3223' => 'eca', 'ECA246G3470' => 'eca', 'EL10Ac6g13829' => 'bvu', 'EL10Ac6g14093' => 'bvu', 'EL10Ac8g18707' => 'bvu', 'Eucgr.C01369' => 'egr', 'Eucgr.H02492' => 'egr', 'Eucgr.I01733' => 'egr', 'Eucgr.J02255' => 'egr', 'Eucgr.J02257' => 'egr', 'Eucgr.J02258' => 'egr', 'FAN02G1601' => 'fan', 'FAN03G1586' => 'fan', 'FAN03G2986' => 'fan', 'FAN05G4837' => 'fan', 'FAN06G0146' => 'fan', 'FAN07G0858' => 'fan', 'FAN09G3179' => 'fan', 'FAN10G0669' => 'fan', 'FAN12G2358' => 'fan', 'FAN14G4198' => 'fan', 'FAN14G5112' => 'fan', 'FAN17G0342' => 'fan', 'FAN19G0342' => 'fan', 'FAN19G0962' => 'fan', 'FAN19G1101' => 'fan', 'FAN19G1872' => 'fan', 'FAN22G0356' => 'fan', 'FAN23G0744' => 'fan', 'FAN23G1914' => 'fan', 'FAN26G0032' => 'fan', 'FAN28G0625' => 'fan', 'FvH4_1g02710' => 'fve', 'FvH4_1g02720' => 'fve', 'FvH4_4g25670' => 'fve', 'FvH4_6g51700' => 'fve', 'FvH4_7g20170' => 'fve', 'Glyma.05G175000' => 'gma', 'Glyma.08G132300' => 'gma', 'Glyma.11G243000' => 'gma', 'Glyma.13G158900' => 'gma', 'Glyma.17G112400' => 'gma', 'Glyma.18G014100' => 'gma', 'Glyma.19G003100' => 'gma', 'Glyma.19G056500' => 'gma', 'Gohir.A01G158900' => 'ghi', 'Gohir.A05G312600' => 'ghi', 'Gohir.A05G354900' => 'ghi', 'Gohir.A07G037200' => 'ghi', 'Gohir.A09G030000' => 'ghi', 'Gohir.A12G145200' => 'ghi', 'Gohir.D01G151500' => 'ghi', 'Gohir.D04G058300' => 'ghi', 'Gohir.D05G314100' => 'ghi', 'Gohir.D07G041400' => 'ghi', 'Gohir.D09G029700' => 'ghi', 'Gohir.D12G149700' => 'ghi', 'Gorai.001G043800' => 'gra', 'Gorai.002G187800' => 'gra', 'Gorai.006G034700' => 'gra', 'Gorai.008G161200' => 'gra', 'Gorai.009G335700' => 'gra', 'Gorai.012G065000' => 'gra', 'GSVIVG01000535001' => 'vvi', 'GSVIVG01015572001' => 'vvi', 'GSVIVG01032386001' => 'vvi', 'HanXRQChr05g0138531' => 'han', 'HanXRQChr06g0174391' => 'han', 'HanXRQChr07g0199021' => 'han', 'HanXRQChr08g0208211' => 'han', 'HanXRQChr09g0255471' => 'han', 'HanXRQChr10g0315791' => 'han', 'HanXRQChr12g0371991' => 'han', 'HanXRQChr15g0475251' => 'han', 'HanXRQChr17g0540001' => 'han', 'HanXRQChr17g0548631' => 'han', 'HanXRQChr17g0569561' => 'han', 'Haze_12256' => 'cav', 'Haze_14756' => 'cav', 'Haze_25528' => 'cav', 'Hma1.2p1_0079F.1_g041020' => 'hma', 'Hma1.2p1_0818F.1_g223260' => 'hma', 'Hma1.2p1_1747F.1_g300530' => 'hma', 'HPP92_004607' => 'vpl', 'HPP92_004608' => 'vpl', 'HPP92_006181' => 'vpl', 'HPP92_012192' => 'vpl', 'HPP92_015680' => 'vpl', 'HPP92_020249' => 'vpl', 'HPP92_021376' => 'vpl', 'HPP92_024275' => 'vpl', 'Hund06031' => 'sun', 'Hund25391' => 'sun', 'Lalb_Chr07g0185371' => 'lal', 'Lalb_Chr07g0185381' => 'lal', 'Lalb_Chr12g0204011' => 'lal', 'Lalb_Chr13g0301671' => 'lal', 'Lalb_Chr14g0362851' => 'lal', 'Lalb_Chr24g0403581' => 'lal', 'Lj1g0000233' => 'lja', 'Lj2g0018120' => 'lja', 'Lj3C621T0' => 'lonja', 'Lj3P1059T14' => 'lonja', 'Lj3P611T9' => 'lonja', 'Lj3P614T13' => 'lonja', 'Lj3P615T5' => 'lonja', 'Lj4g0012315' => 'lja', 'Lj4g0026182' => 'lja', 'Lj6P813T16' => 'lonja', 'Lj7C427T7' => 'lonja', 'Lj7C427T8' => 'lonja', 'Lj7P600T41' => 'lonja', 'Lju41C42G17' => 'lonja', 'Lsat_1_v5_gn_0_47300' => 'lsa', 'Lsat_1_v5_gn_2_91280' => 'lsa', 'Lsat_1_v5_gn_3_30561' => 'lsa', 'Lsat_1_v5_gn_4_184321' => 'lsa', 'Lsat_1_v5_gn_4_4041' => 'lsa', 'Lsat_1_v5_gn_5_92000' => 'lsa', 'Lsat_1_v5_gn_8_152940' => 'lsa', 'Lsat_1_v5_gn_8_62401' => 'lsa', 'Manes.06G055900' => 'mes', 'Manes.12G022200' => 'mes', 'Manes.13G023300' => 'mes', 'Manes.14G115000' => 'mes', 'Manes.15G151700' => 'mes', 'Manes.17G111300' => 'mes', 'Mapoly0226s0009' => 'mpo', 'MBI02_g25363_MAGBIO' => 'mbi', 'MBI06_g00027_MAGBIO' => 'mbi', 'MBI10_g13034_MAGBIO' => 'mbi', 'MD09G1023400' => 'mdo', 'MD13G1100100' => 'mdo', 'MD15G1169200' => 'mdo', 'MD16G1101100' => 'mdo', 'MD17G1022900' => 'mdo', 'Medtr3g096150' => 'mtr', 'Medtr4g115070' => 'mtr', 'Medtr7g033325' => 'mtr', 'Medtr8g089840' => 'mtr', 'MELO3C010319.2' => 'cme', 'MELO3C011944.2' => 'cme', 'MELO3C021589.2' => 'cme', 'Migut.E00207' => 'egut', 'Migut.H00067' => 'egut', 'Migut.K00433' => 'egut', 'Migut.K00606' => 'egut', 'Migut.K01410' => 'egut', 'MSTRG.13347' => 'ama', 'MSTRG.24045' => 'ama', 'MSTRG.2428' => 'ama', 'MSTRG.26410' => 'ama', 'MSTRG.3139' => 'ama', 'MSTRG.3286' => 'ama', 'MSTRG.563' => 'ama', 'MSTRG.7941' => 'ama', 'Nitab4.5_0000028g0060' => 'nta', 'Nitab4.5_0000065g0260' => 'nta', 'Nitab4.5_0000112g0060' => 'nta', 'Nitab4.5_0000489g0120' => 'nta', 'Nitab4.5_0001776g0050' => 'nta', 'Nitab4.5_0001854g0010' => 'nta', 'Nitab4.5_0001860g0020' => 'nta', 'Nitab4.5_0004352g0010' => 'nta', 'Nitab4.5_0008716g0020' => 'nta', 'Nitab4.5_0008922g0010' => 'nta', 'Nn3g16693' => 'nnu', 'Nn4g22596' => 'nnu', 'Nn7g37639' => 'nnu', 'Oeu001701.1' => 'oeu', 'Oeu018149.1' => 'oeu', 'Oeu026220.1' => 'oeu', 'Oeu038635.1' => 'oeu', 'Oeu049176.1' => 'oeu', 'Oeu056706.1' => 'oeu', 'Oeu056937.1' => 'oeu', 'Oeu057540.1' => 'oeu', 'Os02g0594900' => 'osa', 'Os02g0595100' => 'osa', 'Os04g0477500' => 'osa', 'Os12g0611900' => 'osa', 'Peaxi162Scf00076g00020' => 'pax', 'Peaxi162Scf00128g00217' => 'pax', 'Peaxi162Scf00129g01640' => 'pax', 'Peaxi162Scf00669g00007' => 'pax', 'Peaxi162Scf00700g00421' => 'pax', 'Peaxi162Scf00801g00038' => 'pax', 'Peaxi162Scf00891g00025' => 'pax', 'PGR083G0909' => 'pgr', 'PGR119G1005' => 'pgr', 'PGR142G2236' => 'pgr', 'PGR142G3388' => 'pgr', 'PGSC0003DMG400004514' => 'stu', 'PGSC0003DMG400012635' => 'stu', 'PGSC0003DMG400015730' => 'stu', 'PGSC0003DMG400018611' => 'stu', 'PGSC0003DMG400030897' => 'stu', 'Phvul.001G254800' => 'pvu', 'Phvul.002G260100' => 'pvu', 'Phvul.003G167600' => 'pvu', 'Phvul.004G005100' => 'pvu', 'Potri.001G343600' => 'ptr', 'Potri.006G066700' => 'ptr', 'Potri.008G186000' => 'ptr', 'Potri.010G046900' => 'ptr', 'Potri.018G127900' => 'ptr', 'Pp3c20_17750' => 'ppa', 'Pp3c24_4380' => 'ppa', 'Prupe.1G245800' => 'ppe', 'Prupe.3G293400' => 'ppe', 'Prupe.7G247400' => 'ppe', 'Psat0s145g0120' => 'psa', 'Psat0s595g0040' => 'psa', 'Psat0s595g0120' => 'psa', 'Psat3g175040' => 'psa', 'Psat7g058120' => 'psa', 'PSO017G0428' => 'pso', 'PSO063G7510' => 'pso', 'PSO067G0046' => 'pso', 'PSO478G1073' => 'pso', 'PSO675G3677' => 'pso', 'PSO675G6558' => 'pso', 'PSO675G7520' => 'pso', 'PSO675G8959' => 'pso', 'QL02p074089' => 'qlo', 'QL02p089614' => 'qlo', 'QL03p057736' => 'qlo', 'RcHm_v2.0_Chr1g0364131' => 'rch', 'RcHm_v2.0_Chr2g0087801' => 'rch', 'RcHm_v2.0_Chr2g0087821' => 'rch', 'RcHm_v2.0_Chr2g0173231' => 'rch', 'RcHm_v2.0_Chr4g0433111' => 'rch', 'Rhsim03G0250300' => 'rsi', 'Rhsim08G0048400' => 'rsi', 'Rhsim10G0014800' => 'rsi', 'Rhsim12G0040100' => 'rsi', 'Rhsim12G0109700' => 'rsi', 'Sabra06G0049600' => 'sbr', 'Sabra08G0141000' => 'sbr', 'Sabra10G0021400' => 'sbr', 'Sabra16G0222900' => 'sbr', 'Sabra18G0108600' => 'sbr', 'SalBow1G0433' => 'sbo', 'SalBow1G2038' => 'sbo', 'SalBow1G5003' => 'sbo', 'SalBow7G1197' => 'sbo', 'SalBow8G3506' => 'sbo', 'Sc03g0007300' => 'sci', 'Sc11g0000950' => 'sci', 'Sc14g0008750' => 'sci', 'Sc18g0000420' => 'sci', 'Sed0006754' => 'sed', 'Sed0008741' => 'sed', 'Sed0017172' => 'sed', 'Sed0018925' => 'sed', 'Sed0023326' => 'sed', 'Sed0025909' => 'sed', 'SEGI_05333' => 'sgi', 'SEGI_10362' => 'sgi', 'SEGI_13380' => 'sgi', 'SEGI_24306' => 'sgi', 'SEGI_29077' => 'sgi', 'SEGI_29095' => 'sgi', 'SEGI_36534' => 'sgi', 'SEGI_37506' => 'sgi', 'SEGI_38321' => 'sgi', 'SGA_v2.0_scaffold307G48031' => 'sas', 'SGA_v2.0_scaffold47G17507' => 'sas', 'SGA_v2.0_scaffold63G21736' => 'sas', 'SGA_v2.0_scaffold87G27070' => 'sas', 'SHI17794' => 'shi', 'SHI28851' => 'shi', 'SMO165G0155' => 'smo', 'SMO340G0217' => 'smo', 'SMO367G1210' => 'smo', 'Solyc02g093430.3' => 'sly', 'Solyc05g013580.4' => 'sly', 'Solyc07g008030.3' => 'sly', 'Solyc12g035470.2' => 'sly', 'Sopen02g038020' => 'spe', 'Sopen05g008490' => 'spe', 'Sopen07g003910' => 'spe', 'Sopen12g015240' => 'spe', 'Sp1g11550' => 'spa', 'Sp2g16710' => 'spa', 'Sp3g00430' => 'spa', 'Sp3g26780' => 'spa', 'Sp5g22900' => 'spa', 'Sp6g29530' => 'spa', 'TAR371G0794' => 'tar', 'TAR374G0164' => 'tar', 'TAR622G0165' => 'tar', 'TAR626G0929' => 'tar', 'TAR629G2155' => 'tar', 'THA.LOC104805282' => 'tha', 'THA.LOC104805363' => 'tha', 'THA.LOC104808968' => 'tha', 'THA.LOC104821093' => 'tha', 'THA.LOC104823953' => 'tha', 'THA.LOC104825562' => 'tha', 'THA.LOC104825665' => 'tha', 'Thecc.02G261400' => 'tca', 'Thecc.04G019200' => 'tca', 'Thecc.09G130400' => 'tca', 'Thhalv10004374m.g' => 'esa', 'Thhalv10007850m.g' => 'esa', 'Thhalv10013782m.g' => 'esa', 'Thhalv10018686m.g' => 'esa', 'Thhalv10020899m.g' => 'esa', 'Thhalv10022755m.g' => 'esa', 'TPR.G23851' => 'tpr', 'TPR.G26500' => 'tpr', 'TPR.G27267' => 'tpr', 'TPR.G32001' => 'tpr', 'TPR.G6251' => 'tpr', 'TPR.G8167' => 'tpr', 'TWI12G1330' => 'twi', 'TWI18G1239' => 'twi', 'TWI34G0979' => 'twi', 'TWI36G0670' => 'twi', 'TWI36G0707' => 'twi', 'TWI56G0233' => 'twi', 'TWI75G1809' => 'twi', 'unitig_21.g20874' => 'ugi', 'unitig_26.g10343' => 'ugi', 'unitig_46.g18392' => 'ugi', 'unitig_52.g17178' => 'ugi', 'unitig_8.g2934' => 'ugi', 'vmacro01122' => 'vma', 'vmacro05875' => 'vma', 'vmacro06147' => 'vma', 'vmacro16191' => 'vma', 'vmacro18293' => 'vma', 'VMungo0251G3707' => 'vmu', 'VMungo0464G1521' => 'vmu', 'VMungo1215G0205' => 'vmu', 'VMungo1383G2484' => 'vmu', 'Zm00001eb079610' => 'zma', 'Zm00001eb135990' => 'zma', 'Zm00001eb183710' => 'zma', 'Zm00001eb246020' => 'zma' ) $gf_id = 'HOM05D001124' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001124' ) $data_identifier = 'HOM05D001124' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 6, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 7, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 21, 'bol' => (int) 10, 'bra' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 6, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 9, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 21, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 8, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 10, 'lsa' => (int) 8, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 8, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 9, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb246020' $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' => 'HOM05D001124', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '548', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02520' => 'bna', 'A03p06630' => 'bna', 'A05p44460' => 'bna', 'A06p08710' => 'bna', 'A06p41090' => 'bna', 'A07p32320' => 'bna', 'A08p32520' => 'bna', 'A09p10360' => 'bna', 'A10p24080' => 'bna', 'Aa31LG11G15250' => 'aar', 'Aa31LG1G1800' => 'aar', 'Aa31LG2G5120' => 'aar', 'Aa31LG2G6070' => 'aar', 'Aa31LG5G10770' => 'aar', 'Aa31sc61G90' => 'aar', 'Actinidia01352' => 'ach', 'Actinidia05983' => 'ach', 'Actinidia08133' => 'ach', 'Actinidia15101' => 'ach', 'Actinidia26379' => 'ach', 'Actinidia35778' => 'ach', 'Actinidia36123' => 'ach', 'Actinidia37436' => 'ach', 'Actinidia38730' => 'ach', 'Ah.02g128210' => 'amhyb', 'Ah.03g132990' => 'amhyb', 'Ah.14g079410' => 'amhyb', 'AL1G24640' => 'aly', 'AL2G26680' => 'aly', 'AL3G10530' => 'aly', 'AL3G45230' => 'aly', 'AL5G15230' => 'aly', 'AL5G16960' => 'aly', 'AL6G25210' => 'aly', 'Aqoxy2G00441' => 'aox', 'Aqoxy3G01236' => 'aox', 'Aqoxy5G03746' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3RQ047' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C7GMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9C8JER' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MBL6KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YXCZ83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZANX40' => 'arhy', 'AT1G12990' => 'ath', 'AT1G67880' => 'ath', 'AT2G13290' => 'ath', 'AT3G01620' => 'ath', 'AT3G26445' => 'ath', 'AT3G27540' => 'ath', 'AT5G14480' => 'ath', 'ATR0824G026' => 'atr', 'ATR1098G019' => 'atr', 'Atru.chr11.2145' => 'acertr', 'Atru.chr2.3636' => 'acertr', 'Atru.chr2.3644' => 'acertr', 'Atru.chr6.2422' => 'acertr', 'Atru.chr7.1112' => 'acertr', 'AUR62005469' => 'cqu', 'AUR62011166' => 'cqu', 'AUR62013319' => 'cqu', 'AUR62024273' => 'cqu', 'AUR62028420' => 'cqu', 'AUR62041942' => 'cqu', 'BcaB01g04969' => 'bca', 'BcaB01g06371' => 'bca', 'BcaB02g11494' => 'bca', 'BcaB03g15382' => 'bca', 'BcaB08g36994' => 'bca', 'BcaC03g13477' => 'bca', 'BcaC03g13478' => 'bca', 'BcaC03g13480' => 'bca', 'BcaC03g13481' => 'bca', 'BcaC03g13486' => 'bca', 'BcaC04g19031' => 'bca', 'BcaC04g23085' => 'bca', 'BcaC05g25094' => 'bca', 'BcaC05g25096' => 'bca', 'BcaC05g25138' => 'bca', 'BcaC05g30416' => 'bca', 'BcaC05g30455' => 'bca', 'BcaC06g30979' => 'bca', 'BcaC06g33805' => 'bca', 'BcaC08g46021' => 'bca', 'BcaNung03154' => 'bca', 'BolC2t06623H' => 'bol', 'BolC2t06632H' => 'bol', 'BolC2t06635H' => 'bol', 'BolC2t06638H' => 'bol', 'BolC3t13266H' => 'bol', 'BolC5t29776H' => 'bol', 'BolC6t38912H' => 'bol', 'BolC7t44183H' => 'bol', 'BolC9t54123H' => 'bol', 'BolC9t59107H' => 'bol', 'BraA02t05221Z' => 'bra', 'BraA03t09996Z' => 'bra', 'BraA05t23210Z' => 'bra', 'BraA06t24068Z' => 'bra', 'BraA06t27032Z' => 'bra', 'BraA08t35176Z' => 'bra', 'BraA09t36680Z' => 'bra', 'BraA10t44471Z' => 'bra', 'C02p06760' => 'bna', 'C02p06890' => 'bna', 'C02p07010' => 'bna', 'C03p07660' => 'bna', 'C05p10300' => 'bna', 'C06p38150' => 'bna', 'C07p36650' => 'bna', 'C08p15770' => 'bna', 'C09p12300' => 'bna', 'C09p62700' => 'bna', 'C09p75040' => 'bna', 'CAN.G13.1' => 'can', 'CAN.G138.4' => 'can', 'CAN.G44.6' => 'can', 'CAN.G473.19' => 'can', 'CANSAT01G0835' => 'cansat', 'CANSAT11G0246' => 'cansat', 'CANSAT11G1766' => 'cansat', 'CANSAT64G1954' => 'cansat', 'CARHR013330' => 'chi', 'CARHR060530' => 'chi', 'CARHR075300' => 'chi', 'CARHR105120' => 'chi', 'CARHR148910' => 'chi', 'CARHR198830' => 'chi', 'Carub.0001s1275' => 'cru', 'Carub.0002s1437' => 'cru', 'Carub.0003s0044' => 'cru', 'Carub.0003s2787' => 'cru', 'Carub.0005s0597' => 'cru', 'Carub.0006s1266' => 'cru', 'Ca_06935_v3' => 'car', 'Ca_13559_v3' => 'car', 'Ca_16941_v3' => 'car', 'Ca_16960_v3' => 'car', 'Ca_17775_v3' => 'car', 'Ca_30464_v3' => 'car', 'Cc06_g08160' => 'ccan', 'Cc07_g01520' => 'ccan', 'Cc11_g15810' => 'ccan', 'CDE02G2840' => 'cde', 'CDE03G0093' => 'cde', 'CDE04G2127' => 'cde', 'CDE07G1857' => 'cde', 'CDE09G1246' => 'cde', 'Cfa003412' => 'cfa', 'Cfa007341' => 'cfa', 'Cfa009220' => 'cfa', 'Ciclev10008737m.g' => 'ccl', 'Ciclev10015565m.g' => 'ccl', 'Ciclev10031761m.g' => 'ccl', 'CiPaw.03G045300' => 'cil', 'CiPaw.03G247200' => 'cil', 'CiPaw.04G029500' => 'cil', 'CiPaw.04G174000' => 'cil', 'CiPaw.05G181200' => 'cil', 'CiPaw.06G067100' => 'cil', 'ClCG05G025800' => 'cla', 'ClCG06G011400' => 'cla', 'ClCG09G019360' => 'cla', 'COL.COLO4_04827' => 'col', 'COL.COLO4_29170' => 'col', 'COL.COLO4_35131' => 'col', 'COL.COLO4_35132' => 'col', 'Cpa.g.sc33.32' => 'cpa', 'Cpa.g.sc46.29' => 'cpa', 'Cpa.g.sc796.1' => 'cpa', 'CsaV3_1G030420' => 'csa', 'CsaV3_5G027050' => 'csa', 'CsaV3_5G031040' => 'csa', 'CsaV3_UNG023130' => 'csa', 'CSS0007726' => 'camsi', 'CSS0016433' => 'camsi', 'CSS0017656' => 'camsi', 'CSS0025364' => 'camsi', 'CSS0027582' => 'camsi', 'CSS0047288' => 'camsi', 'CSS0049950' => 'camsi', 'DCAR_003843' => 'dca', 'DCAR_007052' => 'dca', 'DCAR_020884' => 'dca', 'DCAR_021730' => 'dca', 'DCAR_024423' => 'dca', 'DCAR_026509' => 'dca', 'DCAR_031158' => 'dca', 'Dinv14728' => 'din', 'Dinv15219' => 'din', 'Dinv25728' => 'din', 'Dinv33428' => 'din', 'Dinv36489' => 'din', 'Dinv41486' => 'din', 'Duzib147G0469' => 'dzi', 'Duzib168G0060' => 'dzi', 'Duzib187G1215' => 'dzi', 'Duzib248G0692' => 'dzi', 'Duzib251G0767' => 'dzi', 'Duzib264G0446' => 'dzi', 'Duzib268G0691' => 'dzi', 'ECA232G4767' => 'eca', 'ECA233G2838' => 'eca', 'ECA234G0391' => 'eca', 'ECA234G0857' => 'eca', 'ECA236G1593' => 'eca', 'ECA238G0565' => 'eca', 'ECA246G1027' => 'eca', 'ECA246G3223' => 'eca', 'ECA246G3470' => 'eca', 'EL10Ac6g13829' => 'bvu', 'EL10Ac6g14093' => 'bvu', 'EL10Ac8g18707' => 'bvu', 'Eucgr.C01369' => 'egr', 'Eucgr.H02492' => 'egr', 'Eucgr.I01733' => 'egr', 'Eucgr.J02255' => 'egr', 'Eucgr.J02257' => 'egr', 'Eucgr.J02258' => 'egr', 'FAN02G1601' => 'fan', 'FAN03G1586' => 'fan', 'FAN03G2986' => 'fan', 'FAN05G4837' => 'fan', 'FAN06G0146' => 'fan', 'FAN07G0858' => 'fan', 'FAN09G3179' => 'fan', 'FAN10G0669' => 'fan', 'FAN12G2358' => 'fan', 'FAN14G4198' => 'fan', 'FAN14G5112' => 'fan', 'FAN17G0342' => 'fan', 'FAN19G0342' => 'fan', 'FAN19G0962' => 'fan', 'FAN19G1101' => 'fan', 'FAN19G1872' => 'fan', 'FAN22G0356' => 'fan', 'FAN23G0744' => 'fan', 'FAN23G1914' => 'fan', 'FAN26G0032' => 'fan', 'FAN28G0625' => 'fan', 'FvH4_1g02710' => 'fve', 'FvH4_1g02720' => 'fve', 'FvH4_4g25670' => 'fve', 'FvH4_6g51700' => 'fve', 'FvH4_7g20170' => 'fve', 'Glyma.05G175000' => 'gma', 'Glyma.08G132300' => 'gma', 'Glyma.11G243000' => 'gma', 'Glyma.13G158900' => 'gma', 'Glyma.17G112400' => 'gma', 'Glyma.18G014100' => 'gma', 'Glyma.19G003100' => 'gma', 'Glyma.19G056500' => 'gma', 'Gohir.A01G158900' => 'ghi', 'Gohir.A05G312600' => 'ghi', 'Gohir.A05G354900' => 'ghi', 'Gohir.A07G037200' => 'ghi', 'Gohir.A09G030000' => 'ghi', 'Gohir.A12G145200' => 'ghi', 'Gohir.D01G151500' => 'ghi', 'Gohir.D04G058300' => 'ghi', 'Gohir.D05G314100' => 'ghi', 'Gohir.D07G041400' => 'ghi', 'Gohir.D09G029700' => 'ghi', 'Gohir.D12G149700' => 'ghi', 'Gorai.001G043800' => 'gra', 'Gorai.002G187800' => 'gra', 'Gorai.006G034700' => 'gra', 'Gorai.008G161200' => 'gra', 'Gorai.009G335700' => 'gra', 'Gorai.012G065000' => 'gra', 'GSVIVG01000535001' => 'vvi', 'GSVIVG01015572001' => 'vvi', 'GSVIVG01032386001' => 'vvi', 'HanXRQChr05g0138531' => 'han', 'HanXRQChr06g0174391' => 'han', 'HanXRQChr07g0199021' => 'han', 'HanXRQChr08g0208211' => 'han', 'HanXRQChr09g0255471' => 'han', 'HanXRQChr10g0315791' => 'han', 'HanXRQChr12g0371991' => 'han', 'HanXRQChr15g0475251' => 'han', 'HanXRQChr17g0540001' => 'han', 'HanXRQChr17g0548631' => 'han', 'HanXRQChr17g0569561' => 'han', 'Haze_12256' => 'cav', 'Haze_14756' => 'cav', 'Haze_25528' => 'cav', 'Hma1.2p1_0079F.1_g041020' => 'hma', 'Hma1.2p1_0818F.1_g223260' => 'hma', 'Hma1.2p1_1747F.1_g300530' => 'hma', 'HPP92_004607' => 'vpl', 'HPP92_004608' => 'vpl', 'HPP92_006181' => 'vpl', 'HPP92_012192' => 'vpl', 'HPP92_015680' => 'vpl', 'HPP92_020249' => 'vpl', 'HPP92_021376' => 'vpl', 'HPP92_024275' => 'vpl', 'Hund06031' => 'sun', 'Hund25391' => 'sun', 'Lalb_Chr07g0185371' => 'lal', 'Lalb_Chr07g0185381' => 'lal', 'Lalb_Chr12g0204011' => 'lal', 'Lalb_Chr13g0301671' => 'lal', 'Lalb_Chr14g0362851' => 'lal', 'Lalb_Chr24g0403581' => 'lal', 'Lj1g0000233' => 'lja', 'Lj2g0018120' => 'lja', 'Lj3C621T0' => 'lonja', 'Lj3P1059T14' => 'lonja', 'Lj3P611T9' => 'lonja', 'Lj3P614T13' => 'lonja', 'Lj3P615T5' => 'lonja', 'Lj4g0012315' => 'lja', 'Lj4g0026182' => 'lja', 'Lj6P813T16' => 'lonja', 'Lj7C427T7' => 'lonja', 'Lj7C427T8' => 'lonja', 'Lj7P600T41' => 'lonja', 'Lju41C42G17' => 'lonja', 'Lsat_1_v5_gn_0_47300' => 'lsa', 'Lsat_1_v5_gn_2_91280' => 'lsa', 'Lsat_1_v5_gn_3_30561' => 'lsa', 'Lsat_1_v5_gn_4_184321' => 'lsa', 'Lsat_1_v5_gn_4_4041' => 'lsa', 'Lsat_1_v5_gn_5_92000' => 'lsa', 'Lsat_1_v5_gn_8_152940' => 'lsa', 'Lsat_1_v5_gn_8_62401' => 'lsa', 'Manes.06G055900' => 'mes', 'Manes.12G022200' => 'mes', 'Manes.13G023300' => 'mes', 'Manes.14G115000' => 'mes', 'Manes.15G151700' => 'mes', 'Manes.17G111300' => 'mes', 'Mapoly0226s0009' => 'mpo', 'MBI02_g25363_MAGBIO' => 'mbi', 'MBI06_g00027_MAGBIO' => 'mbi', 'MBI10_g13034_MAGBIO' => 'mbi', 'MD09G1023400' => 'mdo', 'MD13G1100100' => 'mdo', 'MD15G1169200' => 'mdo', 'MD16G1101100' => 'mdo', 'MD17G1022900' => 'mdo', 'Medtr3g096150' => 'mtr', 'Medtr4g115070' => 'mtr', 'Medtr7g033325' => 'mtr', 'Medtr8g089840' => 'mtr', 'MELO3C010319.2' => 'cme', 'MELO3C011944.2' => 'cme', 'MELO3C021589.2' => 'cme', 'Migut.E00207' => 'egut', 'Migut.H00067' => 'egut', 'Migut.K00433' => 'egut', 'Migut.K00606' => 'egut', 'Migut.K01410' => 'egut', 'MSTRG.13347' => 'ama', 'MSTRG.24045' => 'ama', 'MSTRG.2428' => 'ama', 'MSTRG.26410' => 'ama', 'MSTRG.3139' => 'ama', 'MSTRG.3286' => 'ama', 'MSTRG.563' => 'ama', 'MSTRG.7941' => 'ama', 'Nitab4.5_0000028g0060' => 'nta', 'Nitab4.5_0000065g0260' => 'nta', 'Nitab4.5_0000112g0060' => 'nta', 'Nitab4.5_0000489g0120' => 'nta', 'Nitab4.5_0001776g0050' => 'nta', 'Nitab4.5_0001854g0010' => 'nta', 'Nitab4.5_0001860g0020' => 'nta', 'Nitab4.5_0004352g0010' => 'nta', 'Nitab4.5_0008716g0020' => 'nta', 'Nitab4.5_0008922g0010' => 'nta', 'Nn3g16693' => 'nnu', 'Nn4g22596' => 'nnu', 'Nn7g37639' => 'nnu', 'Oeu001701.1' => 'oeu', 'Oeu018149.1' => 'oeu', 'Oeu026220.1' => 'oeu', 'Oeu038635.1' => 'oeu', 'Oeu049176.1' => 'oeu', 'Oeu056706.1' => 'oeu', 'Oeu056937.1' => 'oeu', 'Oeu057540.1' => 'oeu', 'Os02g0594900' => 'osa', 'Os02g0595100' => 'osa', 'Os04g0477500' => 'osa', 'Os12g0611900' => 'osa', 'Peaxi162Scf00076g00020' => 'pax', 'Peaxi162Scf00128g00217' => 'pax', 'Peaxi162Scf00129g01640' => 'pax', 'Peaxi162Scf00669g00007' => 'pax', 'Peaxi162Scf00700g00421' => 'pax', 'Peaxi162Scf00801g00038' => 'pax', 'Peaxi162Scf00891g00025' => 'pax', 'PGR083G0909' => 'pgr', 'PGR119G1005' => 'pgr', 'PGR142G2236' => 'pgr', 'PGR142G3388' => 'pgr', 'PGSC0003DMG400004514' => 'stu', 'PGSC0003DMG400012635' => 'stu', 'PGSC0003DMG400015730' => 'stu', 'PGSC0003DMG400018611' => 'stu', 'PGSC0003DMG400030897' => 'stu', 'Phvul.001G254800' => 'pvu', 'Phvul.002G260100' => 'pvu', 'Phvul.003G167600' => 'pvu', 'Phvul.004G005100' => 'pvu', 'Potri.001G343600' => 'ptr', 'Potri.006G066700' => 'ptr', 'Potri.008G186000' => 'ptr', 'Potri.010G046900' => 'ptr', 'Potri.018G127900' => 'ptr', 'Pp3c20_17750' => 'ppa', 'Pp3c24_4380' => 'ppa', 'Prupe.1G245800' => 'ppe', 'Prupe.3G293400' => 'ppe', 'Prupe.7G247400' => 'ppe', 'Psat0s145g0120' => 'psa', 'Psat0s595g0040' => 'psa', 'Psat0s595g0120' => 'psa', 'Psat3g175040' => 'psa', 'Psat7g058120' => 'psa', 'PSO017G0428' => 'pso', 'PSO063G7510' => 'pso', 'PSO067G0046' => 'pso', 'PSO478G1073' => 'pso', 'PSO675G3677' => 'pso', 'PSO675G6558' => 'pso', 'PSO675G7520' => 'pso', 'PSO675G8959' => 'pso', 'QL02p074089' => 'qlo', 'QL02p089614' => 'qlo', 'QL03p057736' => 'qlo', 'RcHm_v2.0_Chr1g0364131' => 'rch', 'RcHm_v2.0_Chr2g0087801' => 'rch', 'RcHm_v2.0_Chr2g0087821' => 'rch', 'RcHm_v2.0_Chr2g0173231' => 'rch', 'RcHm_v2.0_Chr4g0433111' => 'rch', 'Rhsim03G0250300' => 'rsi', 'Rhsim08G0048400' => 'rsi', 'Rhsim10G0014800' => 'rsi', 'Rhsim12G0040100' => 'rsi', 'Rhsim12G0109700' => 'rsi', 'Sabra06G0049600' => 'sbr', 'Sabra08G0141000' => 'sbr', 'Sabra10G0021400' => 'sbr', 'Sabra16G0222900' => 'sbr', 'Sabra18G0108600' => 'sbr', 'SalBow1G0433' => 'sbo', 'SalBow1G2038' => 'sbo', 'SalBow1G5003' => 'sbo', 'SalBow7G1197' => 'sbo', 'SalBow8G3506' => 'sbo', 'Sc03g0007300' => 'sci', 'Sc11g0000950' => 'sci', 'Sc14g0008750' => 'sci', 'Sc18g0000420' => 'sci', 'Sed0006754' => 'sed', 'Sed0008741' => 'sed', 'Sed0017172' => 'sed', 'Sed0018925' => 'sed', 'Sed0023326' => 'sed', 'Sed0025909' => 'sed', 'SEGI_05333' => 'sgi', 'SEGI_10362' => 'sgi', 'SEGI_13380' => 'sgi', 'SEGI_24306' => 'sgi', 'SEGI_29077' => 'sgi', 'SEGI_29095' => 'sgi', 'SEGI_36534' => 'sgi', 'SEGI_37506' => 'sgi', 'SEGI_38321' => 'sgi', 'SGA_v2.0_scaffold307G48031' => 'sas', 'SGA_v2.0_scaffold47G17507' => 'sas', 'SGA_v2.0_scaffold63G21736' => 'sas', 'SGA_v2.0_scaffold87G27070' => 'sas', 'SHI17794' => 'shi', 'SHI28851' => 'shi', 'SMO165G0155' => 'smo', 'SMO340G0217' => 'smo', 'SMO367G1210' => 'smo', 'Solyc02g093430.3' => 'sly', 'Solyc05g013580.4' => 'sly', 'Solyc07g008030.3' => 'sly', 'Solyc12g035470.2' => 'sly', 'Sopen02g038020' => 'spe', 'Sopen05g008490' => 'spe', 'Sopen07g003910' => 'spe', 'Sopen12g015240' => 'spe', 'Sp1g11550' => 'spa', 'Sp2g16710' => 'spa', 'Sp3g00430' => 'spa', 'Sp3g26780' => 'spa', 'Sp5g22900' => 'spa', 'Sp6g29530' => 'spa', 'TAR371G0794' => 'tar', 'TAR374G0164' => 'tar', 'TAR622G0165' => 'tar', 'TAR626G0929' => 'tar', 'TAR629G2155' => 'tar', 'THA.LOC104805282' => 'tha', 'THA.LOC104805363' => 'tha', 'THA.LOC104808968' => 'tha', 'THA.LOC104821093' => 'tha', 'THA.LOC104823953' => 'tha', 'THA.LOC104825562' => 'tha', 'THA.LOC104825665' => 'tha', 'Thecc.02G261400' => 'tca', 'Thecc.04G019200' => 'tca', 'Thecc.09G130400' => 'tca', 'Thhalv10004374m.g' => 'esa', 'Thhalv10007850m.g' => 'esa', 'Thhalv10013782m.g' => 'esa', 'Thhalv10018686m.g' => 'esa', 'Thhalv10020899m.g' => 'esa', 'Thhalv10022755m.g' => 'esa', 'TPR.G23851' => 'tpr', 'TPR.G26500' => 'tpr', 'TPR.G27267' => 'tpr', 'TPR.G32001' => 'tpr', 'TPR.G6251' => 'tpr', 'TPR.G8167' => 'tpr', 'TWI12G1330' => 'twi', 'TWI18G1239' => 'twi', 'TWI34G0979' => 'twi', 'TWI36G0670' => 'twi', 'TWI36G0707' => 'twi', 'TWI56G0233' => 'twi', 'TWI75G1809' => 'twi', 'unitig_21.g20874' => 'ugi', 'unitig_26.g10343' => 'ugi', 'unitig_46.g18392' => 'ugi', 'unitig_52.g17178' => 'ugi', 'unitig_8.g2934' => 'ugi', 'vmacro01122' => 'vma', 'vmacro05875' => 'vma', 'vmacro06147' => 'vma', 'vmacro16191' => 'vma', 'vmacro18293' => 'vma', 'VMungo0251G3707' => 'vmu', 'VMungo0464G1521' => 'vmu', 'VMungo1215G0205' => 'vmu', 'VMungo1383G2484' => 'vmu', 'Zm00001eb079610' => 'zma', 'Zm00001eb135990' => 'zma', 'Zm00001eb183710' => 'zma', 'Zm00001eb246020' => 'zma' ), 'gf_id' => 'HOM05D001124', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001124' ), 'data_identifier' => 'HOM05D001124', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001124', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '548', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02520' => 'bna', 'A03p06630' => 'bna', 'A05p44460' => 'bna', 'A06p08710' => 'bna', 'A06p41090' => 'bna', 'A07p32320' => 'bna', 'A08p32520' => 'bna', 'A09p10360' => 'bna', 'A10p24080' => 'bna', 'Aa31LG11G15250' => 'aar', 'Aa31LG1G1800' => 'aar', 'Aa31LG2G5120' => 'aar', 'Aa31LG2G6070' => 'aar', 'Aa31LG5G10770' => 'aar', 'Aa31sc61G90' => 'aar', 'Actinidia01352' => 'ach', 'Actinidia05983' => 'ach', 'Actinidia08133' => 'ach', 'Actinidia15101' => 'ach', 'Actinidia26379' => 'ach', 'Actinidia35778' => 'ach', 'Actinidia36123' => 'ach', 'Actinidia37436' => 'ach', 'Actinidia38730' => 'ach', 'Ah.02g128210' => 'amhyb', 'Ah.03g132990' => 'amhyb', 'Ah.14g079410' => 'amhyb', 'AL1G24640' => 'aly', 'AL2G26680' => 'aly', 'AL3G10530' => 'aly', 'AL3G45230' => 'aly', 'AL5G15230' => 'aly', 'AL5G16960' => 'aly', 'AL6G25210' => 'aly', 'Aqoxy2G00441' => 'aox', 'Aqoxy3G01236' => 'aox', 'Aqoxy5G03746' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3RQ047' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C7GMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9C8JER' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MBL6KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YXCZ83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZANX40' => 'arhy', 'AT1G12990' => 'ath', 'AT1G67880' => 'ath', 'AT2G13290' => 'ath', 'AT3G01620' => 'ath', 'AT3G26445' => 'ath', 'AT3G27540' => 'ath', 'AT5G14480' => 'ath', 'ATR0824G026' => 'atr', 'ATR1098G019' => 'atr', 'Atru.chr11.2145' => 'acertr', 'Atru.chr2.3636' => 'acertr', 'Atru.chr2.3644' => 'acertr', 'Atru.chr6.2422' => 'acertr', 'Atru.chr7.1112' => 'acertr', 'AUR62005469' => 'cqu', 'AUR62011166' => 'cqu', 'AUR62013319' => 'cqu', 'AUR62024273' => 'cqu', 'AUR62028420' => 'cqu', 'AUR62041942' => 'cqu', 'BcaB01g04969' => 'bca', 'BcaB01g06371' => 'bca', 'BcaB02g11494' => 'bca', 'BcaB03g15382' => 'bca', 'BcaB08g36994' => 'bca', 'BcaC03g13477' => 'bca', 'BcaC03g13478' => 'bca', 'BcaC03g13480' => 'bca', 'BcaC03g13481' => 'bca', 'BcaC03g13486' => 'bca', 'BcaC04g19031' => 'bca', 'BcaC04g23085' => 'bca', 'BcaC05g25094' => 'bca', 'BcaC05g25096' => 'bca', 'BcaC05g25138' => 'bca', 'BcaC05g30416' => 'bca', 'BcaC05g30455' => 'bca', 'BcaC06g30979' => 'bca', 'BcaC06g33805' => 'bca', 'BcaC08g46021' => 'bca', 'BcaNung03154' => 'bca', 'BolC2t06623H' => 'bol', 'BolC2t06632H' => 'bol', 'BolC2t06635H' => 'bol', 'BolC2t06638H' => 'bol', 'BolC3t13266H' => 'bol', 'BolC5t29776H' => 'bol', 'BolC6t38912H' => 'bol', 'BolC7t44183H' => 'bol', 'BolC9t54123H' => 'bol', 'BolC9t59107H' => 'bol', 'BraA02t05221Z' => 'bra', 'BraA03t09996Z' => 'bra', 'BraA05t23210Z' => 'bra', 'BraA06t24068Z' => 'bra', 'BraA06t27032Z' => 'bra', 'BraA08t35176Z' => 'bra', 'BraA09t36680Z' => 'bra', 'BraA10t44471Z' => 'bra', 'C02p06760' => 'bna', 'C02p06890' => 'bna', 'C02p07010' => 'bna', 'C03p07660' => 'bna', 'C05p10300' => 'bna', 'C06p38150' => 'bna', 'C07p36650' => 'bna', 'C08p15770' => 'bna', 'C09p12300' => 'bna', 'C09p62700' => 'bna', 'C09p75040' => 'bna', 'CAN.G13.1' => 'can', 'CAN.G138.4' => 'can', 'CAN.G44.6' => 'can', 'CAN.G473.19' => 'can', 'CANSAT01G0835' => 'cansat', 'CANSAT11G0246' => 'cansat', 'CANSAT11G1766' => 'cansat', 'CANSAT64G1954' => 'cansat', 'CARHR013330' => 'chi', 'CARHR060530' => 'chi', 'CARHR075300' => 'chi', 'CARHR105120' => 'chi', 'CARHR148910' => 'chi', 'CARHR198830' => 'chi', 'Carub.0001s1275' => 'cru', 'Carub.0002s1437' => 'cru', 'Carub.0003s0044' => 'cru', 'Carub.0003s2787' => 'cru', 'Carub.0005s0597' => 'cru', 'Carub.0006s1266' => 'cru', 'Ca_06935_v3' => 'car', 'Ca_13559_v3' => 'car', 'Ca_16941_v3' => 'car', 'Ca_16960_v3' => 'car', 'Ca_17775_v3' => 'car', 'Ca_30464_v3' => 'car', 'Cc06_g08160' => 'ccan', 'Cc07_g01520' => 'ccan', 'Cc11_g15810' => 'ccan', 'CDE02G2840' => 'cde', 'CDE03G0093' => 'cde', 'CDE04G2127' => 'cde', 'CDE07G1857' => 'cde', 'CDE09G1246' => 'cde', 'Cfa003412' => 'cfa', 'Cfa007341' => 'cfa', 'Cfa009220' => 'cfa', 'Ciclev10008737m.g' => 'ccl', 'Ciclev10015565m.g' => 'ccl', 'Ciclev10031761m.g' => 'ccl', 'CiPaw.03G045300' => 'cil', 'CiPaw.03G247200' => 'cil', 'CiPaw.04G029500' => 'cil', 'CiPaw.04G174000' => 'cil', 'CiPaw.05G181200' => 'cil', 'CiPaw.06G067100' => 'cil', 'ClCG05G025800' => 'cla', 'ClCG06G011400' => 'cla', 'ClCG09G019360' => 'cla', 'COL.COLO4_04827' => 'col', 'COL.COLO4_29170' => 'col', 'COL.COLO4_35131' => 'col', 'COL.COLO4_35132' => 'col', 'Cpa.g.sc33.32' => 'cpa', 'Cpa.g.sc46.29' => 'cpa', 'Cpa.g.sc796.1' => 'cpa', 'CsaV3_1G030420' => 'csa', 'CsaV3_5G027050' => 'csa', 'CsaV3_5G031040' => 'csa', 'CsaV3_UNG023130' => 'csa', 'CSS0007726' => 'camsi', 'CSS0016433' => 'camsi', 'CSS0017656' => 'camsi', 'CSS0025364' => 'camsi', 'CSS0027582' => 'camsi', 'CSS0047288' => 'camsi', 'CSS0049950' => 'camsi', 'DCAR_003843' => 'dca', 'DCAR_007052' => 'dca', 'DCAR_020884' => 'dca', 'DCAR_021730' => 'dca', 'DCAR_024423' => 'dca', 'DCAR_026509' => 'dca', 'DCAR_031158' => 'dca', 'Dinv14728' => 'din', 'Dinv15219' => 'din', 'Dinv25728' => 'din', 'Dinv33428' => 'din', 'Dinv36489' => 'din', 'Dinv41486' => 'din', 'Duzib147G0469' => 'dzi', 'Duzib168G0060' => 'dzi', 'Duzib187G1215' => 'dzi', 'Duzib248G0692' => 'dzi', 'Duzib251G0767' => 'dzi', 'Duzib264G0446' => 'dzi', 'Duzib268G0691' => 'dzi', 'ECA232G4767' => 'eca', 'ECA233G2838' => 'eca', 'ECA234G0391' => 'eca', 'ECA234G0857' => 'eca', 'ECA236G1593' => 'eca', 'ECA238G0565' => 'eca', 'ECA246G1027' => 'eca', 'ECA246G3223' => 'eca', 'ECA246G3470' => 'eca', 'EL10Ac6g13829' => 'bvu', 'EL10Ac6g14093' => 'bvu', 'EL10Ac8g18707' => 'bvu', 'Eucgr.C01369' => 'egr', 'Eucgr.H02492' => 'egr', 'Eucgr.I01733' => 'egr', 'Eucgr.J02255' => 'egr', 'Eucgr.J02257' => 'egr', 'Eucgr.J02258' => 'egr', 'FAN02G1601' => 'fan', 'FAN03G1586' => 'fan', 'FAN03G2986' => 'fan', 'FAN05G4837' => 'fan', 'FAN06G0146' => 'fan', 'FAN07G0858' => 'fan', 'FAN09G3179' => 'fan', 'FAN10G0669' => 'fan', 'FAN12G2358' => 'fan', 'FAN14G4198' => 'fan', 'FAN14G5112' => 'fan', 'FAN17G0342' => 'fan', 'FAN19G0342' => 'fan', 'FAN19G0962' => 'fan', 'FAN19G1101' => 'fan', 'FAN19G1872' => 'fan', 'FAN22G0356' => 'fan', 'FAN23G0744' => 'fan', 'FAN23G1914' => 'fan', 'FAN26G0032' => 'fan', 'FAN28G0625' => 'fan', 'FvH4_1g02710' => 'fve', 'FvH4_1g02720' => 'fve', 'FvH4_4g25670' => 'fve', 'FvH4_6g51700' => 'fve', 'FvH4_7g20170' => 'fve', 'Glyma.05G175000' => 'gma', 'Glyma.08G132300' => 'gma', 'Glyma.11G243000' => 'gma', 'Glyma.13G158900' => 'gma', 'Glyma.17G112400' => 'gma', 'Glyma.18G014100' => 'gma', 'Glyma.19G003100' => 'gma', 'Glyma.19G056500' => 'gma', 'Gohir.A01G158900' => 'ghi', 'Gohir.A05G312600' => 'ghi', 'Gohir.A05G354900' => 'ghi', 'Gohir.A07G037200' => 'ghi', 'Gohir.A09G030000' => 'ghi', 'Gohir.A12G145200' => 'ghi', 'Gohir.D01G151500' => 'ghi', 'Gohir.D04G058300' => 'ghi', 'Gohir.D05G314100' => 'ghi', 'Gohir.D07G041400' => 'ghi', 'Gohir.D09G029700' => 'ghi', 'Gohir.D12G149700' => 'ghi', 'Gorai.001G043800' => 'gra', 'Gorai.002G187800' => 'gra', 'Gorai.006G034700' => 'gra', 'Gorai.008G161200' => 'gra', 'Gorai.009G335700' => 'gra', 'Gorai.012G065000' => 'gra', 'GSVIVG01000535001' => 'vvi', 'GSVIVG01015572001' => 'vvi', 'GSVIVG01032386001' => 'vvi', 'HanXRQChr05g0138531' => 'han', 'HanXRQChr06g0174391' => 'han', 'HanXRQChr07g0199021' => 'han', 'HanXRQChr08g0208211' => 'han', 'HanXRQChr09g0255471' => 'han', 'HanXRQChr10g0315791' => 'han', 'HanXRQChr12g0371991' => 'han', 'HanXRQChr15g0475251' => 'han', 'HanXRQChr17g0540001' => 'han', 'HanXRQChr17g0548631' => 'han', 'HanXRQChr17g0569561' => 'han', 'Haze_12256' => 'cav', 'Haze_14756' => 'cav', 'Haze_25528' => 'cav', 'Hma1.2p1_0079F.1_g041020' => 'hma', 'Hma1.2p1_0818F.1_g223260' => 'hma', 'Hma1.2p1_1747F.1_g300530' => 'hma', 'HPP92_004607' => 'vpl', 'HPP92_004608' => 'vpl', 'HPP92_006181' => 'vpl', 'HPP92_012192' => 'vpl', 'HPP92_015680' => 'vpl', 'HPP92_020249' => 'vpl', 'HPP92_021376' => 'vpl', 'HPP92_024275' => 'vpl', 'Hund06031' => 'sun', 'Hund25391' => 'sun', 'Lalb_Chr07g0185371' => 'lal', 'Lalb_Chr07g0185381' => 'lal', 'Lalb_Chr12g0204011' => 'lal', 'Lalb_Chr13g0301671' => 'lal', 'Lalb_Chr14g0362851' => 'lal', 'Lalb_Chr24g0403581' => 'lal', 'Lj1g0000233' => 'lja', 'Lj2g0018120' => 'lja', 'Lj3C621T0' => 'lonja', 'Lj3P1059T14' => 'lonja', 'Lj3P611T9' => 'lonja', 'Lj3P614T13' => 'lonja', 'Lj3P615T5' => 'lonja', 'Lj4g0012315' => 'lja', 'Lj4g0026182' => 'lja', 'Lj6P813T16' => 'lonja', 'Lj7C427T7' => 'lonja', 'Lj7C427T8' => 'lonja', 'Lj7P600T41' => 'lonja', 'Lju41C42G17' => 'lonja', 'Lsat_1_v5_gn_0_47300' => 'lsa', 'Lsat_1_v5_gn_2_91280' => 'lsa', 'Lsat_1_v5_gn_3_30561' => 'lsa', 'Lsat_1_v5_gn_4_184321' => 'lsa', 'Lsat_1_v5_gn_4_4041' => 'lsa', 'Lsat_1_v5_gn_5_92000' => 'lsa', 'Lsat_1_v5_gn_8_152940' => 'lsa', 'Lsat_1_v5_gn_8_62401' => 'lsa', 'Manes.06G055900' => 'mes', 'Manes.12G022200' => 'mes', 'Manes.13G023300' => 'mes', 'Manes.14G115000' => 'mes', 'Manes.15G151700' => 'mes', 'Manes.17G111300' => 'mes', 'Mapoly0226s0009' => 'mpo', 'MBI02_g25363_MAGBIO' => 'mbi', 'MBI06_g00027_MAGBIO' => 'mbi', 'MBI10_g13034_MAGBIO' => 'mbi', 'MD09G1023400' => 'mdo', 'MD13G1100100' => 'mdo', 'MD15G1169200' => 'mdo', 'MD16G1101100' => 'mdo', 'MD17G1022900' => 'mdo', 'Medtr3g096150' => 'mtr', 'Medtr4g115070' => 'mtr', 'Medtr7g033325' => 'mtr', 'Medtr8g089840' => 'mtr', 'MELO3C010319.2' => 'cme', 'MELO3C011944.2' => 'cme', 'MELO3C021589.2' => 'cme', 'Migut.E00207' => 'egut', 'Migut.H00067' => 'egut', 'Migut.K00433' => 'egut', 'Migut.K00606' => 'egut', 'Migut.K01410' => 'egut', 'MSTRG.13347' => 'ama', 'MSTRG.24045' => 'ama', 'MSTRG.2428' => 'ama', 'MSTRG.26410' => 'ama', 'MSTRG.3139' => 'ama', 'MSTRG.3286' => 'ama', 'MSTRG.563' => 'ama', 'MSTRG.7941' => 'ama', 'Nitab4.5_0000028g0060' => 'nta', 'Nitab4.5_0000065g0260' => 'nta', 'Nitab4.5_0000112g0060' => 'nta', 'Nitab4.5_0000489g0120' => 'nta', 'Nitab4.5_0001776g0050' => 'nta', 'Nitab4.5_0001854g0010' => 'nta', 'Nitab4.5_0001860g0020' => 'nta', 'Nitab4.5_0004352g0010' => 'nta', 'Nitab4.5_0008716g0020' => 'nta', 'Nitab4.5_0008922g0010' => 'nta', 'Nn3g16693' => 'nnu', 'Nn4g22596' => 'nnu', 'Nn7g37639' => 'nnu', 'Oeu001701.1' => 'oeu', 'Oeu018149.1' => 'oeu', 'Oeu026220.1' => 'oeu', 'Oeu038635.1' => 'oeu', 'Oeu049176.1' => 'oeu', 'Oeu056706.1' => 'oeu', 'Oeu056937.1' => 'oeu', 'Oeu057540.1' => 'oeu', 'Os02g0594900' => 'osa', 'Os02g0595100' => 'osa', 'Os04g0477500' => 'osa', 'Os12g0611900' => 'osa', 'Peaxi162Scf00076g00020' => 'pax', 'Peaxi162Scf00128g00217' => 'pax', 'Peaxi162Scf00129g01640' => 'pax', 'Peaxi162Scf00669g00007' => 'pax', 'Peaxi162Scf00700g00421' => 'pax', 'Peaxi162Scf00801g00038' => 'pax', 'Peaxi162Scf00891g00025' => 'pax', 'PGR083G0909' => 'pgr', 'PGR119G1005' => 'pgr', 'PGR142G2236' => 'pgr', 'PGR142G3388' => 'pgr', 'PGSC0003DMG400004514' => 'stu', 'PGSC0003DMG400012635' => 'stu', 'PGSC0003DMG400015730' => 'stu', 'PGSC0003DMG400018611' => 'stu', 'PGSC0003DMG400030897' => 'stu', 'Phvul.001G254800' => 'pvu', 'Phvul.002G260100' => 'pvu', 'Phvul.003G167600' => 'pvu', 'Phvul.004G005100' => 'pvu', 'Potri.001G343600' => 'ptr', 'Potri.006G066700' => 'ptr', 'Potri.008G186000' => 'ptr', 'Potri.010G046900' => 'ptr', 'Potri.018G127900' => 'ptr', 'Pp3c20_17750' => 'ppa', 'Pp3c24_4380' => 'ppa', 'Prupe.1G245800' => 'ppe', 'Prupe.3G293400' => 'ppe', 'Prupe.7G247400' => 'ppe', 'Psat0s145g0120' => 'psa', 'Psat0s595g0040' => 'psa', 'Psat0s595g0120' => 'psa', 'Psat3g175040' => 'psa', 'Psat7g058120' => 'psa', 'PSO017G0428' => 'pso', 'PSO063G7510' => 'pso', 'PSO067G0046' => 'pso', 'PSO478G1073' => 'pso', 'PSO675G3677' => 'pso', 'PSO675G6558' => 'pso', 'PSO675G7520' => 'pso', 'PSO675G8959' => 'pso', 'QL02p074089' => 'qlo', 'QL02p089614' => 'qlo', 'QL03p057736' => 'qlo', 'RcHm_v2.0_Chr1g0364131' => 'rch', 'RcHm_v2.0_Chr2g0087801' => 'rch', 'RcHm_v2.0_Chr2g0087821' => 'rch', 'RcHm_v2.0_Chr2g0173231' => 'rch', 'RcHm_v2.0_Chr4g0433111' => 'rch', 'Rhsim03G0250300' => 'rsi', 'Rhsim08G0048400' => 'rsi', 'Rhsim10G0014800' => 'rsi', 'Rhsim12G0040100' => 'rsi', 'Rhsim12G0109700' => 'rsi', 'Sabra06G0049600' => 'sbr', 'Sabra08G0141000' => 'sbr', 'Sabra10G0021400' => 'sbr', 'Sabra16G0222900' => 'sbr', 'Sabra18G0108600' => 'sbr', 'SalBow1G0433' => 'sbo', 'SalBow1G2038' => 'sbo', 'SalBow1G5003' => 'sbo', 'SalBow7G1197' => 'sbo', 'SalBow8G3506' => 'sbo', 'Sc03g0007300' => 'sci', 'Sc11g0000950' => 'sci', 'Sc14g0008750' => 'sci', 'Sc18g0000420' => 'sci', 'Sed0006754' => 'sed', 'Sed0008741' => 'sed', 'Sed0017172' => 'sed', 'Sed0018925' => 'sed', 'Sed0023326' => 'sed', 'Sed0025909' => 'sed', 'SEGI_05333' => 'sgi', 'SEGI_10362' => 'sgi', 'SEGI_13380' => 'sgi', 'SEGI_24306' => 'sgi', 'SEGI_29077' => 'sgi', 'SEGI_29095' => 'sgi', 'SEGI_36534' => 'sgi', 'SEGI_37506' => 'sgi', 'SEGI_38321' => 'sgi', 'SGA_v2.0_scaffold307G48031' => 'sas', 'SGA_v2.0_scaffold47G17507' => 'sas', 'SGA_v2.0_scaffold63G21736' => 'sas', 'SGA_v2.0_scaffold87G27070' => 'sas', 'SHI17794' => 'shi', 'SHI28851' => 'shi', 'SMO165G0155' => 'smo', 'SMO340G0217' => 'smo', 'SMO367G1210' => 'smo', 'Solyc02g093430.3' => 'sly', 'Solyc05g013580.4' => 'sly', 'Solyc07g008030.3' => 'sly', 'Solyc12g035470.2' => 'sly', 'Sopen02g038020' => 'spe', 'Sopen05g008490' => 'spe', 'Sopen07g003910' => 'spe', 'Sopen12g015240' => 'spe', 'Sp1g11550' => 'spa', 'Sp2g16710' => 'spa', 'Sp3g00430' => 'spa', 'Sp3g26780' => 'spa', 'Sp5g22900' => 'spa', 'Sp6g29530' => 'spa', 'TAR371G0794' => 'tar', 'TAR374G0164' => 'tar', 'TAR622G0165' => 'tar', 'TAR626G0929' => 'tar', 'TAR629G2155' => 'tar', 'THA.LOC104805282' => 'tha', 'THA.LOC104805363' => 'tha', 'THA.LOC104808968' => 'tha', 'THA.LOC104821093' => 'tha', 'THA.LOC104823953' => 'tha', 'THA.LOC104825562' => 'tha', 'THA.LOC104825665' => 'tha', 'Thecc.02G261400' => 'tca', 'Thecc.04G019200' => 'tca', 'Thecc.09G130400' => 'tca', 'Thhalv10004374m.g' => 'esa', 'Thhalv10007850m.g' => 'esa', 'Thhalv10013782m.g' => 'esa', 'Thhalv10018686m.g' => 'esa', 'Thhalv10020899m.g' => 'esa', 'Thhalv10022755m.g' => 'esa', 'TPR.G23851' => 'tpr', 'TPR.G26500' => 'tpr', 'TPR.G27267' => 'tpr', 'TPR.G32001' => 'tpr', 'TPR.G6251' => 'tpr', 'TPR.G8167' => 'tpr', 'TWI12G1330' => 'twi', 'TWI18G1239' => 'twi', 'TWI34G0979' => 'twi', 'TWI36G0670' => 'twi', 'TWI36G0707' => 'twi', 'TWI56G0233' => 'twi', 'TWI75G1809' => 'twi', 'unitig_21.g20874' => 'ugi', 'unitig_26.g10343' => 'ugi', 'unitig_46.g18392' => 'ugi', 'unitig_52.g17178' => 'ugi', 'unitig_8.g2934' => 'ugi', 'vmacro01122' => 'vma', 'vmacro05875' => 'vma', 'vmacro06147' => 'vma', 'vmacro16191' => 'vma', 'vmacro18293' => 'vma', 'VMungo0251G3707' => 'vmu', 'VMungo0464G1521' => 'vmu', 'VMungo1215G0205' => 'vmu', 'VMungo1383G2484' => 'vmu', 'Zm00001eb079610' => 'zma', 'Zm00001eb135990' => 'zma', 'Zm00001eb183710' => 'zma', 'Zm00001eb246020' => 'zma' ) $gf_id = 'HOM05D001124' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001124' ) $data_identifier = 'HOM05D001124' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 6, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 7, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 21, 'bol' => (int) 10, 'bra' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 6, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 9, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 21, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 8, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 10, 'lsa' => (int) 8, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 8, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 9, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb246020' $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' => 'HOM05D001124', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '548', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02520' => 'bna', 'A03p06630' => 'bna', 'A05p44460' => 'bna', 'A06p08710' => 'bna', 'A06p41090' => 'bna', 'A07p32320' => 'bna', 'A08p32520' => 'bna', 'A09p10360' => 'bna', 'A10p24080' => 'bna', 'Aa31LG11G15250' => 'aar', 'Aa31LG1G1800' => 'aar', 'Aa31LG2G5120' => 'aar', 'Aa31LG2G6070' => 'aar', 'Aa31LG5G10770' => 'aar', 'Aa31sc61G90' => 'aar', 'Actinidia01352' => 'ach', 'Actinidia05983' => 'ach', 'Actinidia08133' => 'ach', 'Actinidia15101' => 'ach', 'Actinidia26379' => 'ach', 'Actinidia35778' => 'ach', 'Actinidia36123' => 'ach', 'Actinidia37436' => 'ach', 'Actinidia38730' => 'ach', 'Ah.02g128210' => 'amhyb', 'Ah.03g132990' => 'amhyb', 'Ah.14g079410' => 'amhyb', 'AL1G24640' => 'aly', 'AL2G26680' => 'aly', 'AL3G10530' => 'aly', 'AL3G45230' => 'aly', 'AL5G15230' => 'aly', 'AL5G16960' => 'aly', 'AL6G25210' => 'aly', 'Aqoxy2G00441' => 'aox', 'Aqoxy3G01236' => 'aox', 'Aqoxy5G03746' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3RQ047' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C7GMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9C8JER' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MBL6KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YXCZ83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZANX40' => 'arhy', 'AT1G12990' => 'ath', 'AT1G67880' => 'ath', 'AT2G13290' => 'ath', 'AT3G01620' => 'ath', 'AT3G26445' => 'ath', 'AT3G27540' => 'ath', 'AT5G14480' => 'ath', 'ATR0824G026' => 'atr', 'ATR1098G019' => 'atr', 'Atru.chr11.2145' => 'acertr', 'Atru.chr2.3636' => 'acertr', 'Atru.chr2.3644' => 'acertr', 'Atru.chr6.2422' => 'acertr', 'Atru.chr7.1112' => 'acertr', 'AUR62005469' => 'cqu', 'AUR62011166' => 'cqu', 'AUR62013319' => 'cqu', 'AUR62024273' => 'cqu', 'AUR62028420' => 'cqu', 'AUR62041942' => 'cqu', 'BcaB01g04969' => 'bca', 'BcaB01g06371' => 'bca', 'BcaB02g11494' => 'bca', 'BcaB03g15382' => 'bca', 'BcaB08g36994' => 'bca', 'BcaC03g13477' => 'bca', 'BcaC03g13478' => 'bca', 'BcaC03g13480' => 'bca', 'BcaC03g13481' => 'bca', 'BcaC03g13486' => 'bca', 'BcaC04g19031' => 'bca', 'BcaC04g23085' => 'bca', 'BcaC05g25094' => 'bca', 'BcaC05g25096' => 'bca', 'BcaC05g25138' => 'bca', 'BcaC05g30416' => 'bca', 'BcaC05g30455' => 'bca', 'BcaC06g30979' => 'bca', 'BcaC06g33805' => 'bca', 'BcaC08g46021' => 'bca', 'BcaNung03154' => 'bca', 'BolC2t06623H' => 'bol', 'BolC2t06632H' => 'bol', 'BolC2t06635H' => 'bol', 'BolC2t06638H' => 'bol', 'BolC3t13266H' => 'bol', 'BolC5t29776H' => 'bol', 'BolC6t38912H' => 'bol', 'BolC7t44183H' => 'bol', 'BolC9t54123H' => 'bol', 'BolC9t59107H' => 'bol', 'BraA02t05221Z' => 'bra', 'BraA03t09996Z' => 'bra', 'BraA05t23210Z' => 'bra', 'BraA06t24068Z' => 'bra', 'BraA06t27032Z' => 'bra', 'BraA08t35176Z' => 'bra', 'BraA09t36680Z' => 'bra', 'BraA10t44471Z' => 'bra', 'C02p06760' => 'bna', 'C02p06890' => 'bna', 'C02p07010' => 'bna', 'C03p07660' => 'bna', 'C05p10300' => 'bna', 'C06p38150' => 'bna', 'C07p36650' => 'bna', 'C08p15770' => 'bna', 'C09p12300' => 'bna', 'C09p62700' => 'bna', 'C09p75040' => 'bna', 'CAN.G13.1' => 'can', 'CAN.G138.4' => 'can', 'CAN.G44.6' => 'can', 'CAN.G473.19' => 'can', 'CANSAT01G0835' => 'cansat', 'CANSAT11G0246' => 'cansat', 'CANSAT11G1766' => 'cansat', 'CANSAT64G1954' => 'cansat', 'CARHR013330' => 'chi', 'CARHR060530' => 'chi', 'CARHR075300' => 'chi', 'CARHR105120' => 'chi', 'CARHR148910' => 'chi', 'CARHR198830' => 'chi', 'Carub.0001s1275' => 'cru', 'Carub.0002s1437' => 'cru', 'Carub.0003s0044' => 'cru', 'Carub.0003s2787' => 'cru', 'Carub.0005s0597' => 'cru', 'Carub.0006s1266' => 'cru', 'Ca_06935_v3' => 'car', 'Ca_13559_v3' => 'car', 'Ca_16941_v3' => 'car', 'Ca_16960_v3' => 'car', 'Ca_17775_v3' => 'car', 'Ca_30464_v3' => 'car', 'Cc06_g08160' => 'ccan', 'Cc07_g01520' => 'ccan', 'Cc11_g15810' => 'ccan', 'CDE02G2840' => 'cde', 'CDE03G0093' => 'cde', 'CDE04G2127' => 'cde', 'CDE07G1857' => 'cde', 'CDE09G1246' => 'cde', 'Cfa003412' => 'cfa', 'Cfa007341' => 'cfa', 'Cfa009220' => 'cfa', 'Ciclev10008737m.g' => 'ccl', 'Ciclev10015565m.g' => 'ccl', 'Ciclev10031761m.g' => 'ccl', 'CiPaw.03G045300' => 'cil', 'CiPaw.03G247200' => 'cil', 'CiPaw.04G029500' => 'cil', 'CiPaw.04G174000' => 'cil', 'CiPaw.05G181200' => 'cil', 'CiPaw.06G067100' => 'cil', 'ClCG05G025800' => 'cla', 'ClCG06G011400' => 'cla', 'ClCG09G019360' => 'cla', 'COL.COLO4_04827' => 'col', 'COL.COLO4_29170' => 'col', 'COL.COLO4_35131' => 'col', 'COL.COLO4_35132' => 'col', 'Cpa.g.sc33.32' => 'cpa', 'Cpa.g.sc46.29' => 'cpa', 'Cpa.g.sc796.1' => 'cpa', 'CsaV3_1G030420' => 'csa', 'CsaV3_5G027050' => 'csa', 'CsaV3_5G031040' => 'csa', 'CsaV3_UNG023130' => 'csa', 'CSS0007726' => 'camsi', 'CSS0016433' => 'camsi', 'CSS0017656' => 'camsi', 'CSS0025364' => 'camsi', 'CSS0027582' => 'camsi', 'CSS0047288' => 'camsi', 'CSS0049950' => 'camsi', 'DCAR_003843' => 'dca', 'DCAR_007052' => 'dca', 'DCAR_020884' => 'dca', 'DCAR_021730' => 'dca', 'DCAR_024423' => 'dca', 'DCAR_026509' => 'dca', 'DCAR_031158' => 'dca', 'Dinv14728' => 'din', 'Dinv15219' => 'din', 'Dinv25728' => 'din', 'Dinv33428' => 'din', 'Dinv36489' => 'din', 'Dinv41486' => 'din', 'Duzib147G0469' => 'dzi', 'Duzib168G0060' => 'dzi', 'Duzib187G1215' => 'dzi', 'Duzib248G0692' => 'dzi', 'Duzib251G0767' => 'dzi', 'Duzib264G0446' => 'dzi', 'Duzib268G0691' => 'dzi', 'ECA232G4767' => 'eca', 'ECA233G2838' => 'eca', 'ECA234G0391' => 'eca', 'ECA234G0857' => 'eca', 'ECA236G1593' => 'eca', 'ECA238G0565' => 'eca', 'ECA246G1027' => 'eca', 'ECA246G3223' => 'eca', 'ECA246G3470' => 'eca', 'EL10Ac6g13829' => 'bvu', 'EL10Ac6g14093' => 'bvu', 'EL10Ac8g18707' => 'bvu', 'Eucgr.C01369' => 'egr', 'Eucgr.H02492' => 'egr', 'Eucgr.I01733' => 'egr', 'Eucgr.J02255' => 'egr', 'Eucgr.J02257' => 'egr', 'Eucgr.J02258' => 'egr', 'FAN02G1601' => 'fan', 'FAN03G1586' => 'fan', 'FAN03G2986' => 'fan', 'FAN05G4837' => 'fan', 'FAN06G0146' => 'fan', 'FAN07G0858' => 'fan', 'FAN09G3179' => 'fan', 'FAN10G0669' => 'fan', 'FAN12G2358' => 'fan', 'FAN14G4198' => 'fan', 'FAN14G5112' => 'fan', 'FAN17G0342' => 'fan', 'FAN19G0342' => 'fan', 'FAN19G0962' => 'fan', 'FAN19G1101' => 'fan', 'FAN19G1872' => 'fan', 'FAN22G0356' => 'fan', 'FAN23G0744' => 'fan', 'FAN23G1914' => 'fan', 'FAN26G0032' => 'fan', 'FAN28G0625' => 'fan', 'FvH4_1g02710' => 'fve', 'FvH4_1g02720' => 'fve', 'FvH4_4g25670' => 'fve', 'FvH4_6g51700' => 'fve', 'FvH4_7g20170' => 'fve', 'Glyma.05G175000' => 'gma', 'Glyma.08G132300' => 'gma', 'Glyma.11G243000' => 'gma', 'Glyma.13G158900' => 'gma', 'Glyma.17G112400' => 'gma', 'Glyma.18G014100' => 'gma', 'Glyma.19G003100' => 'gma', 'Glyma.19G056500' => 'gma', 'Gohir.A01G158900' => 'ghi', 'Gohir.A05G312600' => 'ghi', 'Gohir.A05G354900' => 'ghi', 'Gohir.A07G037200' => 'ghi', 'Gohir.A09G030000' => 'ghi', 'Gohir.A12G145200' => 'ghi', 'Gohir.D01G151500' => 'ghi', 'Gohir.D04G058300' => 'ghi', 'Gohir.D05G314100' => 'ghi', 'Gohir.D07G041400' => 'ghi', 'Gohir.D09G029700' => 'ghi', 'Gohir.D12G149700' => 'ghi', 'Gorai.001G043800' => 'gra', 'Gorai.002G187800' => 'gra', 'Gorai.006G034700' => 'gra', 'Gorai.008G161200' => 'gra', 'Gorai.009G335700' => 'gra', 'Gorai.012G065000' => 'gra', 'GSVIVG01000535001' => 'vvi', 'GSVIVG01015572001' => 'vvi', 'GSVIVG01032386001' => 'vvi', 'HanXRQChr05g0138531' => 'han', 'HanXRQChr06g0174391' => 'han', 'HanXRQChr07g0199021' => 'han', 'HanXRQChr08g0208211' => 'han', 'HanXRQChr09g0255471' => 'han', 'HanXRQChr10g0315791' => 'han', 'HanXRQChr12g0371991' => 'han', 'HanXRQChr15g0475251' => 'han', 'HanXRQChr17g0540001' => 'han', 'HanXRQChr17g0548631' => 'han', 'HanXRQChr17g0569561' => 'han', 'Haze_12256' => 'cav', 'Haze_14756' => 'cav', 'Haze_25528' => 'cav', 'Hma1.2p1_0079F.1_g041020' => 'hma', 'Hma1.2p1_0818F.1_g223260' => 'hma', 'Hma1.2p1_1747F.1_g300530' => 'hma', 'HPP92_004607' => 'vpl', 'HPP92_004608' => 'vpl', 'HPP92_006181' => 'vpl', 'HPP92_012192' => 'vpl', 'HPP92_015680' => 'vpl', 'HPP92_020249' => 'vpl', 'HPP92_021376' => 'vpl', 'HPP92_024275' => 'vpl', 'Hund06031' => 'sun', 'Hund25391' => 'sun', 'Lalb_Chr07g0185371' => 'lal', 'Lalb_Chr07g0185381' => 'lal', 'Lalb_Chr12g0204011' => 'lal', 'Lalb_Chr13g0301671' => 'lal', 'Lalb_Chr14g0362851' => 'lal', 'Lalb_Chr24g0403581' => 'lal', 'Lj1g0000233' => 'lja', 'Lj2g0018120' => 'lja', 'Lj3C621T0' => 'lonja', 'Lj3P1059T14' => 'lonja', 'Lj3P611T9' => 'lonja', 'Lj3P614T13' => 'lonja', 'Lj3P615T5' => 'lonja', 'Lj4g0012315' => 'lja', 'Lj4g0026182' => 'lja', 'Lj6P813T16' => 'lonja', 'Lj7C427T7' => 'lonja', 'Lj7C427T8' => 'lonja', 'Lj7P600T41' => 'lonja', 'Lju41C42G17' => 'lonja', 'Lsat_1_v5_gn_0_47300' => 'lsa', 'Lsat_1_v5_gn_2_91280' => 'lsa', 'Lsat_1_v5_gn_3_30561' => 'lsa', 'Lsat_1_v5_gn_4_184321' => 'lsa', 'Lsat_1_v5_gn_4_4041' => 'lsa', 'Lsat_1_v5_gn_5_92000' => 'lsa', 'Lsat_1_v5_gn_8_152940' => 'lsa', 'Lsat_1_v5_gn_8_62401' => 'lsa', 'Manes.06G055900' => 'mes', 'Manes.12G022200' => 'mes', 'Manes.13G023300' => 'mes', 'Manes.14G115000' => 'mes', 'Manes.15G151700' => 'mes', 'Manes.17G111300' => 'mes', 'Mapoly0226s0009' => 'mpo', 'MBI02_g25363_MAGBIO' => 'mbi', 'MBI06_g00027_MAGBIO' => 'mbi', 'MBI10_g13034_MAGBIO' => 'mbi', 'MD09G1023400' => 'mdo', 'MD13G1100100' => 'mdo', 'MD15G1169200' => 'mdo', 'MD16G1101100' => 'mdo', 'MD17G1022900' => 'mdo', 'Medtr3g096150' => 'mtr', 'Medtr4g115070' => 'mtr', 'Medtr7g033325' => 'mtr', 'Medtr8g089840' => 'mtr', 'MELO3C010319.2' => 'cme', 'MELO3C011944.2' => 'cme', 'MELO3C021589.2' => 'cme', 'Migut.E00207' => 'egut', 'Migut.H00067' => 'egut', 'Migut.K00433' => 'egut', 'Migut.K00606' => 'egut', 'Migut.K01410' => 'egut', 'MSTRG.13347' => 'ama', 'MSTRG.24045' => 'ama', 'MSTRG.2428' => 'ama', 'MSTRG.26410' => 'ama', 'MSTRG.3139' => 'ama', 'MSTRG.3286' => 'ama', 'MSTRG.563' => 'ama', 'MSTRG.7941' => 'ama', 'Nitab4.5_0000028g0060' => 'nta', 'Nitab4.5_0000065g0260' => 'nta', 'Nitab4.5_0000112g0060' => 'nta', 'Nitab4.5_0000489g0120' => 'nta', 'Nitab4.5_0001776g0050' => 'nta', 'Nitab4.5_0001854g0010' => 'nta', 'Nitab4.5_0001860g0020' => 'nta', 'Nitab4.5_0004352g0010' => 'nta', 'Nitab4.5_0008716g0020' => 'nta', 'Nitab4.5_0008922g0010' => 'nta', 'Nn3g16693' => 'nnu', 'Nn4g22596' => 'nnu', 'Nn7g37639' => 'nnu', 'Oeu001701.1' => 'oeu', 'Oeu018149.1' => 'oeu', 'Oeu026220.1' => 'oeu', 'Oeu038635.1' => 'oeu', 'Oeu049176.1' => 'oeu', 'Oeu056706.1' => 'oeu', 'Oeu056937.1' => 'oeu', 'Oeu057540.1' => 'oeu', 'Os02g0594900' => 'osa', 'Os02g0595100' => 'osa', 'Os04g0477500' => 'osa', 'Os12g0611900' => 'osa', 'Peaxi162Scf00076g00020' => 'pax', 'Peaxi162Scf00128g00217' => 'pax', 'Peaxi162Scf00129g01640' => 'pax', 'Peaxi162Scf00669g00007' => 'pax', 'Peaxi162Scf00700g00421' => 'pax', 'Peaxi162Scf00801g00038' => 'pax', 'Peaxi162Scf00891g00025' => 'pax', 'PGR083G0909' => 'pgr', 'PGR119G1005' => 'pgr', 'PGR142G2236' => 'pgr', 'PGR142G3388' => 'pgr', 'PGSC0003DMG400004514' => 'stu', 'PGSC0003DMG400012635' => 'stu', 'PGSC0003DMG400015730' => 'stu', 'PGSC0003DMG400018611' => 'stu', 'PGSC0003DMG400030897' => 'stu', 'Phvul.001G254800' => 'pvu', 'Phvul.002G260100' => 'pvu', 'Phvul.003G167600' => 'pvu', 'Phvul.004G005100' => 'pvu', 'Potri.001G343600' => 'ptr', 'Potri.006G066700' => 'ptr', 'Potri.008G186000' => 'ptr', 'Potri.010G046900' => 'ptr', 'Potri.018G127900' => 'ptr', 'Pp3c20_17750' => 'ppa', 'Pp3c24_4380' => 'ppa', 'Prupe.1G245800' => 'ppe', 'Prupe.3G293400' => 'ppe', 'Prupe.7G247400' => 'ppe', 'Psat0s145g0120' => 'psa', 'Psat0s595g0040' => 'psa', 'Psat0s595g0120' => 'psa', 'Psat3g175040' => 'psa', 'Psat7g058120' => 'psa', 'PSO017G0428' => 'pso', 'PSO063G7510' => 'pso', 'PSO067G0046' => 'pso', 'PSO478G1073' => 'pso', 'PSO675G3677' => 'pso', 'PSO675G6558' => 'pso', 'PSO675G7520' => 'pso', 'PSO675G8959' => 'pso', 'QL02p074089' => 'qlo', 'QL02p089614' => 'qlo', 'QL03p057736' => 'qlo', 'RcHm_v2.0_Chr1g0364131' => 'rch', 'RcHm_v2.0_Chr2g0087801' => 'rch', 'RcHm_v2.0_Chr2g0087821' => 'rch', 'RcHm_v2.0_Chr2g0173231' => 'rch', 'RcHm_v2.0_Chr4g0433111' => 'rch', 'Rhsim03G0250300' => 'rsi', 'Rhsim08G0048400' => 'rsi', 'Rhsim10G0014800' => 'rsi', 'Rhsim12G0040100' => 'rsi', 'Rhsim12G0109700' => 'rsi', 'Sabra06G0049600' => 'sbr', 'Sabra08G0141000' => 'sbr', 'Sabra10G0021400' => 'sbr', 'Sabra16G0222900' => 'sbr', 'Sabra18G0108600' => 'sbr', 'SalBow1G0433' => 'sbo', 'SalBow1G2038' => 'sbo', 'SalBow1G5003' => 'sbo', 'SalBow7G1197' => 'sbo', 'SalBow8G3506' => 'sbo', 'Sc03g0007300' => 'sci', 'Sc11g0000950' => 'sci', 'Sc14g0008750' => 'sci', 'Sc18g0000420' => 'sci', 'Sed0006754' => 'sed', 'Sed0008741' => 'sed', 'Sed0017172' => 'sed', 'Sed0018925' => 'sed', 'Sed0023326' => 'sed', 'Sed0025909' => 'sed', 'SEGI_05333' => 'sgi', 'SEGI_10362' => 'sgi', 'SEGI_13380' => 'sgi', 'SEGI_24306' => 'sgi', 'SEGI_29077' => 'sgi', 'SEGI_29095' => 'sgi', 'SEGI_36534' => 'sgi', 'SEGI_37506' => 'sgi', 'SEGI_38321' => 'sgi', 'SGA_v2.0_scaffold307G48031' => 'sas', 'SGA_v2.0_scaffold47G17507' => 'sas', 'SGA_v2.0_scaffold63G21736' => 'sas', 'SGA_v2.0_scaffold87G27070' => 'sas', 'SHI17794' => 'shi', 'SHI28851' => 'shi', 'SMO165G0155' => 'smo', 'SMO340G0217' => 'smo', 'SMO367G1210' => 'smo', 'Solyc02g093430.3' => 'sly', 'Solyc05g013580.4' => 'sly', 'Solyc07g008030.3' => 'sly', 'Solyc12g035470.2' => 'sly', 'Sopen02g038020' => 'spe', 'Sopen05g008490' => 'spe', 'Sopen07g003910' => 'spe', 'Sopen12g015240' => 'spe', 'Sp1g11550' => 'spa', 'Sp2g16710' => 'spa', 'Sp3g00430' => 'spa', 'Sp3g26780' => 'spa', 'Sp5g22900' => 'spa', 'Sp6g29530' => 'spa', 'TAR371G0794' => 'tar', 'TAR374G0164' => 'tar', 'TAR622G0165' => 'tar', 'TAR626G0929' => 'tar', 'TAR629G2155' => 'tar', 'THA.LOC104805282' => 'tha', 'THA.LOC104805363' => 'tha', 'THA.LOC104808968' => 'tha', 'THA.LOC104821093' => 'tha', 'THA.LOC104823953' => 'tha', 'THA.LOC104825562' => 'tha', 'THA.LOC104825665' => 'tha', 'Thecc.02G261400' => 'tca', 'Thecc.04G019200' => 'tca', 'Thecc.09G130400' => 'tca', 'Thhalv10004374m.g' => 'esa', 'Thhalv10007850m.g' => 'esa', 'Thhalv10013782m.g' => 'esa', 'Thhalv10018686m.g' => 'esa', 'Thhalv10020899m.g' => 'esa', 'Thhalv10022755m.g' => 'esa', 'TPR.G23851' => 'tpr', 'TPR.G26500' => 'tpr', 'TPR.G27267' => 'tpr', 'TPR.G32001' => 'tpr', 'TPR.G6251' => 'tpr', 'TPR.G8167' => 'tpr', 'TWI12G1330' => 'twi', 'TWI18G1239' => 'twi', 'TWI34G0979' => 'twi', 'TWI36G0670' => 'twi', 'TWI36G0707' => 'twi', 'TWI56G0233' => 'twi', 'TWI75G1809' => 'twi', 'unitig_21.g20874' => 'ugi', 'unitig_26.g10343' => 'ugi', 'unitig_46.g18392' => 'ugi', 'unitig_52.g17178' => 'ugi', 'unitig_8.g2934' => 'ugi', 'vmacro01122' => 'vma', 'vmacro05875' => 'vma', 'vmacro06147' => 'vma', 'vmacro16191' => 'vma', 'vmacro18293' => 'vma', 'VMungo0251G3707' => 'vmu', 'VMungo0464G1521' => 'vmu', 'VMungo1215G0205' => 'vmu', 'VMungo1383G2484' => 'vmu', 'Zm00001eb079610' => 'zma', 'Zm00001eb135990' => 'zma', 'Zm00001eb183710' => 'zma', 'Zm00001eb246020' => 'zma' ), 'gf_id' => 'HOM05D001124', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001124' ), 'data_identifier' => 'HOM05D001124', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001124', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '548', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02520' => 'bna', 'A03p06630' => 'bna', 'A05p44460' => 'bna', 'A06p08710' => 'bna', 'A06p41090' => 'bna', 'A07p32320' => 'bna', 'A08p32520' => 'bna', 'A09p10360' => 'bna', 'A10p24080' => 'bna', 'Aa31LG11G15250' => 'aar', 'Aa31LG1G1800' => 'aar', 'Aa31LG2G5120' => 'aar', 'Aa31LG2G6070' => 'aar', 'Aa31LG5G10770' => 'aar', 'Aa31sc61G90' => 'aar', 'Actinidia01352' => 'ach', 'Actinidia05983' => 'ach', 'Actinidia08133' => 'ach', 'Actinidia15101' => 'ach', 'Actinidia26379' => 'ach', 'Actinidia35778' => 'ach', 'Actinidia36123' => 'ach', 'Actinidia37436' => 'ach', 'Actinidia38730' => 'ach', 'Ah.02g128210' => 'amhyb', 'Ah.03g132990' => 'amhyb', 'Ah.14g079410' => 'amhyb', 'AL1G24640' => 'aly', 'AL2G26680' => 'aly', 'AL3G10530' => 'aly', 'AL3G45230' => 'aly', 'AL5G15230' => 'aly', 'AL5G16960' => 'aly', 'AL6G25210' => 'aly', 'Aqoxy2G00441' => 'aox', 'Aqoxy3G01236' => 'aox', 'Aqoxy5G03746' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3RQ047' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C7GMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9C8JER' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MBL6KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YXCZ83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZANX40' => 'arhy', 'AT1G12990' => 'ath', 'AT1G67880' => 'ath', 'AT2G13290' => 'ath', 'AT3G01620' => 'ath', 'AT3G26445' => 'ath', 'AT3G27540' => 'ath', 'AT5G14480' => 'ath', 'ATR0824G026' => 'atr', 'ATR1098G019' => 'atr', 'Atru.chr11.2145' => 'acertr', 'Atru.chr2.3636' => 'acertr', 'Atru.chr2.3644' => 'acertr', 'Atru.chr6.2422' => 'acertr', 'Atru.chr7.1112' => 'acertr', 'AUR62005469' => 'cqu', 'AUR62011166' => 'cqu', 'AUR62013319' => 'cqu', 'AUR62024273' => 'cqu', 'AUR62028420' => 'cqu', 'AUR62041942' => 'cqu', 'BcaB01g04969' => 'bca', 'BcaB01g06371' => 'bca', 'BcaB02g11494' => 'bca', 'BcaB03g15382' => 'bca', 'BcaB08g36994' => 'bca', 'BcaC03g13477' => 'bca', 'BcaC03g13478' => 'bca', 'BcaC03g13480' => 'bca', 'BcaC03g13481' => 'bca', 'BcaC03g13486' => 'bca', 'BcaC04g19031' => 'bca', 'BcaC04g23085' => 'bca', 'BcaC05g25094' => 'bca', 'BcaC05g25096' => 'bca', 'BcaC05g25138' => 'bca', 'BcaC05g30416' => 'bca', 'BcaC05g30455' => 'bca', 'BcaC06g30979' => 'bca', 'BcaC06g33805' => 'bca', 'BcaC08g46021' => 'bca', 'BcaNung03154' => 'bca', 'BolC2t06623H' => 'bol', 'BolC2t06632H' => 'bol', 'BolC2t06635H' => 'bol', 'BolC2t06638H' => 'bol', 'BolC3t13266H' => 'bol', 'BolC5t29776H' => 'bol', 'BolC6t38912H' => 'bol', 'BolC7t44183H' => 'bol', 'BolC9t54123H' => 'bol', 'BolC9t59107H' => 'bol', 'BraA02t05221Z' => 'bra', 'BraA03t09996Z' => 'bra', 'BraA05t23210Z' => 'bra', 'BraA06t24068Z' => 'bra', 'BraA06t27032Z' => 'bra', 'BraA08t35176Z' => 'bra', 'BraA09t36680Z' => 'bra', 'BraA10t44471Z' => 'bra', 'C02p06760' => 'bna', 'C02p06890' => 'bna', 'C02p07010' => 'bna', 'C03p07660' => 'bna', 'C05p10300' => 'bna', 'C06p38150' => 'bna', 'C07p36650' => 'bna', 'C08p15770' => 'bna', 'C09p12300' => 'bna', 'C09p62700' => 'bna', 'C09p75040' => 'bna', 'CAN.G13.1' => 'can', 'CAN.G138.4' => 'can', 'CAN.G44.6' => 'can', 'CAN.G473.19' => 'can', 'CANSAT01G0835' => 'cansat', 'CANSAT11G0246' => 'cansat', 'CANSAT11G1766' => 'cansat', 'CANSAT64G1954' => 'cansat', 'CARHR013330' => 'chi', 'CARHR060530' => 'chi', 'CARHR075300' => 'chi', 'CARHR105120' => 'chi', 'CARHR148910' => 'chi', 'CARHR198830' => 'chi', 'Carub.0001s1275' => 'cru', 'Carub.0002s1437' => 'cru', 'Carub.0003s0044' => 'cru', 'Carub.0003s2787' => 'cru', 'Carub.0005s0597' => 'cru', 'Carub.0006s1266' => 'cru', 'Ca_06935_v3' => 'car', 'Ca_13559_v3' => 'car', 'Ca_16941_v3' => 'car', 'Ca_16960_v3' => 'car', 'Ca_17775_v3' => 'car', 'Ca_30464_v3' => 'car', 'Cc06_g08160' => 'ccan', 'Cc07_g01520' => 'ccan', 'Cc11_g15810' => 'ccan', 'CDE02G2840' => 'cde', 'CDE03G0093' => 'cde', 'CDE04G2127' => 'cde', 'CDE07G1857' => 'cde', 'CDE09G1246' => 'cde', 'Cfa003412' => 'cfa', 'Cfa007341' => 'cfa', 'Cfa009220' => 'cfa', 'Ciclev10008737m.g' => 'ccl', 'Ciclev10015565m.g' => 'ccl', 'Ciclev10031761m.g' => 'ccl', 'CiPaw.03G045300' => 'cil', 'CiPaw.03G247200' => 'cil', 'CiPaw.04G029500' => 'cil', 'CiPaw.04G174000' => 'cil', 'CiPaw.05G181200' => 'cil', 'CiPaw.06G067100' => 'cil', 'ClCG05G025800' => 'cla', 'ClCG06G011400' => 'cla', 'ClCG09G019360' => 'cla', 'COL.COLO4_04827' => 'col', 'COL.COLO4_29170' => 'col', 'COL.COLO4_35131' => 'col', 'COL.COLO4_35132' => 'col', 'Cpa.g.sc33.32' => 'cpa', 'Cpa.g.sc46.29' => 'cpa', 'Cpa.g.sc796.1' => 'cpa', 'CsaV3_1G030420' => 'csa', 'CsaV3_5G027050' => 'csa', 'CsaV3_5G031040' => 'csa', 'CsaV3_UNG023130' => 'csa', 'CSS0007726' => 'camsi', 'CSS0016433' => 'camsi', 'CSS0017656' => 'camsi', 'CSS0025364' => 'camsi', 'CSS0027582' => 'camsi', 'CSS0047288' => 'camsi', 'CSS0049950' => 'camsi', 'DCAR_003843' => 'dca', 'DCAR_007052' => 'dca', 'DCAR_020884' => 'dca', 'DCAR_021730' => 'dca', 'DCAR_024423' => 'dca', 'DCAR_026509' => 'dca', 'DCAR_031158' => 'dca', 'Dinv14728' => 'din', 'Dinv15219' => 'din', 'Dinv25728' => 'din', 'Dinv33428' => 'din', 'Dinv36489' => 'din', 'Dinv41486' => 'din', 'Duzib147G0469' => 'dzi', 'Duzib168G0060' => 'dzi', 'Duzib187G1215' => 'dzi', 'Duzib248G0692' => 'dzi', 'Duzib251G0767' => 'dzi', 'Duzib264G0446' => 'dzi', 'Duzib268G0691' => 'dzi', 'ECA232G4767' => 'eca', 'ECA233G2838' => 'eca', 'ECA234G0391' => 'eca', 'ECA234G0857' => 'eca', 'ECA236G1593' => 'eca', 'ECA238G0565' => 'eca', 'ECA246G1027' => 'eca', 'ECA246G3223' => 'eca', 'ECA246G3470' => 'eca', 'EL10Ac6g13829' => 'bvu', 'EL10Ac6g14093' => 'bvu', 'EL10Ac8g18707' => 'bvu', 'Eucgr.C01369' => 'egr', 'Eucgr.H02492' => 'egr', 'Eucgr.I01733' => 'egr', 'Eucgr.J02255' => 'egr', 'Eucgr.J02257' => 'egr', 'Eucgr.J02258' => 'egr', 'FAN02G1601' => 'fan', 'FAN03G1586' => 'fan', 'FAN03G2986' => 'fan', 'FAN05G4837' => 'fan', 'FAN06G0146' => 'fan', 'FAN07G0858' => 'fan', 'FAN09G3179' => 'fan', 'FAN10G0669' => 'fan', 'FAN12G2358' => 'fan', 'FAN14G4198' => 'fan', 'FAN14G5112' => 'fan', 'FAN17G0342' => 'fan', 'FAN19G0342' => 'fan', 'FAN19G0962' => 'fan', 'FAN19G1101' => 'fan', 'FAN19G1872' => 'fan', 'FAN22G0356' => 'fan', 'FAN23G0744' => 'fan', 'FAN23G1914' => 'fan', 'FAN26G0032' => 'fan', 'FAN28G0625' => 'fan', 'FvH4_1g02710' => 'fve', 'FvH4_1g02720' => 'fve', 'FvH4_4g25670' => 'fve', 'FvH4_6g51700' => 'fve', 'FvH4_7g20170' => 'fve', 'Glyma.05G175000' => 'gma', 'Glyma.08G132300' => 'gma', 'Glyma.11G243000' => 'gma', 'Glyma.13G158900' => 'gma', 'Glyma.17G112400' => 'gma', 'Glyma.18G014100' => 'gma', 'Glyma.19G003100' => 'gma', 'Glyma.19G056500' => 'gma', 'Gohir.A01G158900' => 'ghi', 'Gohir.A05G312600' => 'ghi', 'Gohir.A05G354900' => 'ghi', 'Gohir.A07G037200' => 'ghi', 'Gohir.A09G030000' => 'ghi', 'Gohir.A12G145200' => 'ghi', 'Gohir.D01G151500' => 'ghi', 'Gohir.D04G058300' => 'ghi', 'Gohir.D05G314100' => 'ghi', 'Gohir.D07G041400' => 'ghi', 'Gohir.D09G029700' => 'ghi', 'Gohir.D12G149700' => 'ghi', 'Gorai.001G043800' => 'gra', 'Gorai.002G187800' => 'gra', 'Gorai.006G034700' => 'gra', 'Gorai.008G161200' => 'gra', 'Gorai.009G335700' => 'gra', 'Gorai.012G065000' => 'gra', 'GSVIVG01000535001' => 'vvi', 'GSVIVG01015572001' => 'vvi', 'GSVIVG01032386001' => 'vvi', 'HanXRQChr05g0138531' => 'han', 'HanXRQChr06g0174391' => 'han', 'HanXRQChr07g0199021' => 'han', 'HanXRQChr08g0208211' => 'han', 'HanXRQChr09g0255471' => 'han', 'HanXRQChr10g0315791' => 'han', 'HanXRQChr12g0371991' => 'han', 'HanXRQChr15g0475251' => 'han', 'HanXRQChr17g0540001' => 'han', 'HanXRQChr17g0548631' => 'han', 'HanXRQChr17g0569561' => 'han', 'Haze_12256' => 'cav', 'Haze_14756' => 'cav', 'Haze_25528' => 'cav', 'Hma1.2p1_0079F.1_g041020' => 'hma', 'Hma1.2p1_0818F.1_g223260' => 'hma', 'Hma1.2p1_1747F.1_g300530' => 'hma', 'HPP92_004607' => 'vpl', 'HPP92_004608' => 'vpl', 'HPP92_006181' => 'vpl', 'HPP92_012192' => 'vpl', 'HPP92_015680' => 'vpl', 'HPP92_020249' => 'vpl', 'HPP92_021376' => 'vpl', 'HPP92_024275' => 'vpl', 'Hund06031' => 'sun', 'Hund25391' => 'sun', 'Lalb_Chr07g0185371' => 'lal', 'Lalb_Chr07g0185381' => 'lal', 'Lalb_Chr12g0204011' => 'lal', 'Lalb_Chr13g0301671' => 'lal', 'Lalb_Chr14g0362851' => 'lal', 'Lalb_Chr24g0403581' => 'lal', 'Lj1g0000233' => 'lja', 'Lj2g0018120' => 'lja', 'Lj3C621T0' => 'lonja', 'Lj3P1059T14' => 'lonja', 'Lj3P611T9' => 'lonja', 'Lj3P614T13' => 'lonja', 'Lj3P615T5' => 'lonja', 'Lj4g0012315' => 'lja', 'Lj4g0026182' => 'lja', 'Lj6P813T16' => 'lonja', 'Lj7C427T7' => 'lonja', 'Lj7C427T8' => 'lonja', 'Lj7P600T41' => 'lonja', 'Lju41C42G17' => 'lonja', 'Lsat_1_v5_gn_0_47300' => 'lsa', 'Lsat_1_v5_gn_2_91280' => 'lsa', 'Lsat_1_v5_gn_3_30561' => 'lsa', 'Lsat_1_v5_gn_4_184321' => 'lsa', 'Lsat_1_v5_gn_4_4041' => 'lsa', 'Lsat_1_v5_gn_5_92000' => 'lsa', 'Lsat_1_v5_gn_8_152940' => 'lsa', 'Lsat_1_v5_gn_8_62401' => 'lsa', 'Manes.06G055900' => 'mes', 'Manes.12G022200' => 'mes', 'Manes.13G023300' => 'mes', 'Manes.14G115000' => 'mes', 'Manes.15G151700' => 'mes', 'Manes.17G111300' => 'mes', 'Mapoly0226s0009' => 'mpo', 'MBI02_g25363_MAGBIO' => 'mbi', 'MBI06_g00027_MAGBIO' => 'mbi', 'MBI10_g13034_MAGBIO' => 'mbi', 'MD09G1023400' => 'mdo', 'MD13G1100100' => 'mdo', 'MD15G1169200' => 'mdo', 'MD16G1101100' => 'mdo', 'MD17G1022900' => 'mdo', 'Medtr3g096150' => 'mtr', 'Medtr4g115070' => 'mtr', 'Medtr7g033325' => 'mtr', 'Medtr8g089840' => 'mtr', 'MELO3C010319.2' => 'cme', 'MELO3C011944.2' => 'cme', 'MELO3C021589.2' => 'cme', 'Migut.E00207' => 'egut', 'Migut.H00067' => 'egut', 'Migut.K00433' => 'egut', 'Migut.K00606' => 'egut', 'Migut.K01410' => 'egut', 'MSTRG.13347' => 'ama', 'MSTRG.24045' => 'ama', 'MSTRG.2428' => 'ama', 'MSTRG.26410' => 'ama', 'MSTRG.3139' => 'ama', 'MSTRG.3286' => 'ama', 'MSTRG.563' => 'ama', 'MSTRG.7941' => 'ama', 'Nitab4.5_0000028g0060' => 'nta', 'Nitab4.5_0000065g0260' => 'nta', 'Nitab4.5_0000112g0060' => 'nta', 'Nitab4.5_0000489g0120' => 'nta', 'Nitab4.5_0001776g0050' => 'nta', 'Nitab4.5_0001854g0010' => 'nta', 'Nitab4.5_0001860g0020' => 'nta', 'Nitab4.5_0004352g0010' => 'nta', 'Nitab4.5_0008716g0020' => 'nta', 'Nitab4.5_0008922g0010' => 'nta', 'Nn3g16693' => 'nnu', 'Nn4g22596' => 'nnu', 'Nn7g37639' => 'nnu', 'Oeu001701.1' => 'oeu', 'Oeu018149.1' => 'oeu', 'Oeu026220.1' => 'oeu', 'Oeu038635.1' => 'oeu', 'Oeu049176.1' => 'oeu', 'Oeu056706.1' => 'oeu', 'Oeu056937.1' => 'oeu', 'Oeu057540.1' => 'oeu', 'Os02g0594900' => 'osa', 'Os02g0595100' => 'osa', 'Os04g0477500' => 'osa', 'Os12g0611900' => 'osa', 'Peaxi162Scf00076g00020' => 'pax', 'Peaxi162Scf00128g00217' => 'pax', 'Peaxi162Scf00129g01640' => 'pax', 'Peaxi162Scf00669g00007' => 'pax', 'Peaxi162Scf00700g00421' => 'pax', 'Peaxi162Scf00801g00038' => 'pax', 'Peaxi162Scf00891g00025' => 'pax', 'PGR083G0909' => 'pgr', 'PGR119G1005' => 'pgr', 'PGR142G2236' => 'pgr', 'PGR142G3388' => 'pgr', 'PGSC0003DMG400004514' => 'stu', 'PGSC0003DMG400012635' => 'stu', 'PGSC0003DMG400015730' => 'stu', 'PGSC0003DMG400018611' => 'stu', 'PGSC0003DMG400030897' => 'stu', 'Phvul.001G254800' => 'pvu', 'Phvul.002G260100' => 'pvu', 'Phvul.003G167600' => 'pvu', 'Phvul.004G005100' => 'pvu', 'Potri.001G343600' => 'ptr', 'Potri.006G066700' => 'ptr', 'Potri.008G186000' => 'ptr', 'Potri.010G046900' => 'ptr', 'Potri.018G127900' => 'ptr', 'Pp3c20_17750' => 'ppa', 'Pp3c24_4380' => 'ppa', 'Prupe.1G245800' => 'ppe', 'Prupe.3G293400' => 'ppe', 'Prupe.7G247400' => 'ppe', 'Psat0s145g0120' => 'psa', 'Psat0s595g0040' => 'psa', 'Psat0s595g0120' => 'psa', 'Psat3g175040' => 'psa', 'Psat7g058120' => 'psa', 'PSO017G0428' => 'pso', 'PSO063G7510' => 'pso', 'PSO067G0046' => 'pso', 'PSO478G1073' => 'pso', 'PSO675G3677' => 'pso', 'PSO675G6558' => 'pso', 'PSO675G7520' => 'pso', 'PSO675G8959' => 'pso', 'QL02p074089' => 'qlo', 'QL02p089614' => 'qlo', 'QL03p057736' => 'qlo', 'RcHm_v2.0_Chr1g0364131' => 'rch', 'RcHm_v2.0_Chr2g0087801' => 'rch', 'RcHm_v2.0_Chr2g0087821' => 'rch', 'RcHm_v2.0_Chr2g0173231' => 'rch', 'RcHm_v2.0_Chr4g0433111' => 'rch', 'Rhsim03G0250300' => 'rsi', 'Rhsim08G0048400' => 'rsi', 'Rhsim10G0014800' => 'rsi', 'Rhsim12G0040100' => 'rsi', 'Rhsim12G0109700' => 'rsi', 'Sabra06G0049600' => 'sbr', 'Sabra08G0141000' => 'sbr', 'Sabra10G0021400' => 'sbr', 'Sabra16G0222900' => 'sbr', 'Sabra18G0108600' => 'sbr', 'SalBow1G0433' => 'sbo', 'SalBow1G2038' => 'sbo', 'SalBow1G5003' => 'sbo', 'SalBow7G1197' => 'sbo', 'SalBow8G3506' => 'sbo', 'Sc03g0007300' => 'sci', 'Sc11g0000950' => 'sci', 'Sc14g0008750' => 'sci', 'Sc18g0000420' => 'sci', 'Sed0006754' => 'sed', 'Sed0008741' => 'sed', 'Sed0017172' => 'sed', 'Sed0018925' => 'sed', 'Sed0023326' => 'sed', 'Sed0025909' => 'sed', 'SEGI_05333' => 'sgi', 'SEGI_10362' => 'sgi', 'SEGI_13380' => 'sgi', 'SEGI_24306' => 'sgi', 'SEGI_29077' => 'sgi', 'SEGI_29095' => 'sgi', 'SEGI_36534' => 'sgi', 'SEGI_37506' => 'sgi', 'SEGI_38321' => 'sgi', 'SGA_v2.0_scaffold307G48031' => 'sas', 'SGA_v2.0_scaffold47G17507' => 'sas', 'SGA_v2.0_scaffold63G21736' => 'sas', 'SGA_v2.0_scaffold87G27070' => 'sas', 'SHI17794' => 'shi', 'SHI28851' => 'shi', 'SMO165G0155' => 'smo', 'SMO340G0217' => 'smo', 'SMO367G1210' => 'smo', 'Solyc02g093430.3' => 'sly', 'Solyc05g013580.4' => 'sly', 'Solyc07g008030.3' => 'sly', 'Solyc12g035470.2' => 'sly', 'Sopen02g038020' => 'spe', 'Sopen05g008490' => 'spe', 'Sopen07g003910' => 'spe', 'Sopen12g015240' => 'spe', 'Sp1g11550' => 'spa', 'Sp2g16710' => 'spa', 'Sp3g00430' => 'spa', 'Sp3g26780' => 'spa', 'Sp5g22900' => 'spa', 'Sp6g29530' => 'spa', 'TAR371G0794' => 'tar', 'TAR374G0164' => 'tar', 'TAR622G0165' => 'tar', 'TAR626G0929' => 'tar', 'TAR629G2155' => 'tar', 'THA.LOC104805282' => 'tha', 'THA.LOC104805363' => 'tha', 'THA.LOC104808968' => 'tha', 'THA.LOC104821093' => 'tha', 'THA.LOC104823953' => 'tha', 'THA.LOC104825562' => 'tha', 'THA.LOC104825665' => 'tha', 'Thecc.02G261400' => 'tca', 'Thecc.04G019200' => 'tca', 'Thecc.09G130400' => 'tca', 'Thhalv10004374m.g' => 'esa', 'Thhalv10007850m.g' => 'esa', 'Thhalv10013782m.g' => 'esa', 'Thhalv10018686m.g' => 'esa', 'Thhalv10020899m.g' => 'esa', 'Thhalv10022755m.g' => 'esa', 'TPR.G23851' => 'tpr', 'TPR.G26500' => 'tpr', 'TPR.G27267' => 'tpr', 'TPR.G32001' => 'tpr', 'TPR.G6251' => 'tpr', 'TPR.G8167' => 'tpr', 'TWI12G1330' => 'twi', 'TWI18G1239' => 'twi', 'TWI34G0979' => 'twi', 'TWI36G0670' => 'twi', 'TWI36G0707' => 'twi', 'TWI56G0233' => 'twi', 'TWI75G1809' => 'twi', 'unitig_21.g20874' => 'ugi', 'unitig_26.g10343' => 'ugi', 'unitig_46.g18392' => 'ugi', 'unitig_52.g17178' => 'ugi', 'unitig_8.g2934' => 'ugi', 'vmacro01122' => 'vma', 'vmacro05875' => 'vma', 'vmacro06147' => 'vma', 'vmacro16191' => 'vma', 'vmacro18293' => 'vma', 'VMungo0251G3707' => 'vmu', 'VMungo0464G1521' => 'vmu', 'VMungo1215G0205' => 'vmu', 'VMungo1383G2484' => 'vmu', 'Zm00001eb079610' => 'zma', 'Zm00001eb135990' => 'zma', 'Zm00001eb183710' => 'zma', 'Zm00001eb246020' => 'zma' ) $gf_id = 'HOM05D001124' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001124' ) $data_identifier = 'HOM05D001124' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 6, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 7, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 21, 'bol' => (int) 10, 'bra' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 6, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 9, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 21, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 8, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 10, 'lsa' => (int) 8, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 8, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 9, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb246020' $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' => 'HOM05D001124', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '548', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02520' => 'bna', 'A03p06630' => 'bna', 'A05p44460' => 'bna', 'A06p08710' => 'bna', 'A06p41090' => 'bna', 'A07p32320' => 'bna', 'A08p32520' => 'bna', 'A09p10360' => 'bna', 'A10p24080' => 'bna', 'Aa31LG11G15250' => 'aar', 'Aa31LG1G1800' => 'aar', 'Aa31LG2G5120' => 'aar', 'Aa31LG2G6070' => 'aar', 'Aa31LG5G10770' => 'aar', 'Aa31sc61G90' => 'aar', 'Actinidia01352' => 'ach', 'Actinidia05983' => 'ach', 'Actinidia08133' => 'ach', 'Actinidia15101' => 'ach', 'Actinidia26379' => 'ach', 'Actinidia35778' => 'ach', 'Actinidia36123' => 'ach', 'Actinidia37436' => 'ach', 'Actinidia38730' => 'ach', 'Ah.02g128210' => 'amhyb', 'Ah.03g132990' => 'amhyb', 'Ah.14g079410' => 'amhyb', 'AL1G24640' => 'aly', 'AL2G26680' => 'aly', 'AL3G10530' => 'aly', 'AL3G45230' => 'aly', 'AL5G15230' => 'aly', 'AL5G16960' => 'aly', 'AL6G25210' => 'aly', 'Aqoxy2G00441' => 'aox', 'Aqoxy3G01236' => 'aox', 'Aqoxy5G03746' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3RQ047' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C7GMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9C8JER' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MBL6KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YXCZ83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZANX40' => 'arhy', 'AT1G12990' => 'ath', 'AT1G67880' => 'ath', 'AT2G13290' => 'ath', 'AT3G01620' => 'ath', 'AT3G26445' => 'ath', 'AT3G27540' => 'ath', 'AT5G14480' => 'ath', 'ATR0824G026' => 'atr', 'ATR1098G019' => 'atr', 'Atru.chr11.2145' => 'acertr', 'Atru.chr2.3636' => 'acertr', 'Atru.chr2.3644' => 'acertr', 'Atru.chr6.2422' => 'acertr', 'Atru.chr7.1112' => 'acertr', 'AUR62005469' => 'cqu', 'AUR62011166' => 'cqu', 'AUR62013319' => 'cqu', 'AUR62024273' => 'cqu', 'AUR62028420' => 'cqu', 'AUR62041942' => 'cqu', 'BcaB01g04969' => 'bca', 'BcaB01g06371' => 'bca', 'BcaB02g11494' => 'bca', 'BcaB03g15382' => 'bca', 'BcaB08g36994' => 'bca', 'BcaC03g13477' => 'bca', 'BcaC03g13478' => 'bca', 'BcaC03g13480' => 'bca', 'BcaC03g13481' => 'bca', 'BcaC03g13486' => 'bca', 'BcaC04g19031' => 'bca', 'BcaC04g23085' => 'bca', 'BcaC05g25094' => 'bca', 'BcaC05g25096' => 'bca', 'BcaC05g25138' => 'bca', 'BcaC05g30416' => 'bca', 'BcaC05g30455' => 'bca', 'BcaC06g30979' => 'bca', 'BcaC06g33805' => 'bca', 'BcaC08g46021' => 'bca', 'BcaNung03154' => 'bca', 'BolC2t06623H' => 'bol', 'BolC2t06632H' => 'bol', 'BolC2t06635H' => 'bol', 'BolC2t06638H' => 'bol', 'BolC3t13266H' => 'bol', 'BolC5t29776H' => 'bol', 'BolC6t38912H' => 'bol', 'BolC7t44183H' => 'bol', 'BolC9t54123H' => 'bol', 'BolC9t59107H' => 'bol', 'BraA02t05221Z' => 'bra', 'BraA03t09996Z' => 'bra', 'BraA05t23210Z' => 'bra', 'BraA06t24068Z' => 'bra', 'BraA06t27032Z' => 'bra', 'BraA08t35176Z' => 'bra', 'BraA09t36680Z' => 'bra', 'BraA10t44471Z' => 'bra', 'C02p06760' => 'bna', 'C02p06890' => 'bna', 'C02p07010' => 'bna', 'C03p07660' => 'bna', 'C05p10300' => 'bna', 'C06p38150' => 'bna', 'C07p36650' => 'bna', 'C08p15770' => 'bna', 'C09p12300' => 'bna', 'C09p62700' => 'bna', 'C09p75040' => 'bna', 'CAN.G13.1' => 'can', 'CAN.G138.4' => 'can', 'CAN.G44.6' => 'can', 'CAN.G473.19' => 'can', 'CANSAT01G0835' => 'cansat', 'CANSAT11G0246' => 'cansat', 'CANSAT11G1766' => 'cansat', 'CANSAT64G1954' => 'cansat', 'CARHR013330' => 'chi', 'CARHR060530' => 'chi', 'CARHR075300' => 'chi', 'CARHR105120' => 'chi', 'CARHR148910' => 'chi', 'CARHR198830' => 'chi', 'Carub.0001s1275' => 'cru', 'Carub.0002s1437' => 'cru', 'Carub.0003s0044' => 'cru', 'Carub.0003s2787' => 'cru', 'Carub.0005s0597' => 'cru', 'Carub.0006s1266' => 'cru', 'Ca_06935_v3' => 'car', 'Ca_13559_v3' => 'car', 'Ca_16941_v3' => 'car', 'Ca_16960_v3' => 'car', 'Ca_17775_v3' => 'car', 'Ca_30464_v3' => 'car', 'Cc06_g08160' => 'ccan', 'Cc07_g01520' => 'ccan', 'Cc11_g15810' => 'ccan', 'CDE02G2840' => 'cde', 'CDE03G0093' => 'cde', 'CDE04G2127' => 'cde', 'CDE07G1857' => 'cde', 'CDE09G1246' => 'cde', 'Cfa003412' => 'cfa', 'Cfa007341' => 'cfa', 'Cfa009220' => 'cfa', 'Ciclev10008737m.g' => 'ccl', 'Ciclev10015565m.g' => 'ccl', 'Ciclev10031761m.g' => 'ccl', 'CiPaw.03G045300' => 'cil', 'CiPaw.03G247200' => 'cil', 'CiPaw.04G029500' => 'cil', 'CiPaw.04G174000' => 'cil', 'CiPaw.05G181200' => 'cil', 'CiPaw.06G067100' => 'cil', 'ClCG05G025800' => 'cla', 'ClCG06G011400' => 'cla', 'ClCG09G019360' => 'cla', 'COL.COLO4_04827' => 'col', 'COL.COLO4_29170' => 'col', 'COL.COLO4_35131' => 'col', 'COL.COLO4_35132' => 'col', 'Cpa.g.sc33.32' => 'cpa', 'Cpa.g.sc46.29' => 'cpa', 'Cpa.g.sc796.1' => 'cpa', 'CsaV3_1G030420' => 'csa', 'CsaV3_5G027050' => 'csa', 'CsaV3_5G031040' => 'csa', 'CsaV3_UNG023130' => 'csa', 'CSS0007726' => 'camsi', 'CSS0016433' => 'camsi', 'CSS0017656' => 'camsi', 'CSS0025364' => 'camsi', 'CSS0027582' => 'camsi', 'CSS0047288' => 'camsi', 'CSS0049950' => 'camsi', 'DCAR_003843' => 'dca', 'DCAR_007052' => 'dca', 'DCAR_020884' => 'dca', 'DCAR_021730' => 'dca', 'DCAR_024423' => 'dca', 'DCAR_026509' => 'dca', 'DCAR_031158' => 'dca', 'Dinv14728' => 'din', 'Dinv15219' => 'din', 'Dinv25728' => 'din', 'Dinv33428' => 'din', 'Dinv36489' => 'din', 'Dinv41486' => 'din', 'Duzib147G0469' => 'dzi', 'Duzib168G0060' => 'dzi', 'Duzib187G1215' => 'dzi', 'Duzib248G0692' => 'dzi', 'Duzib251G0767' => 'dzi', 'Duzib264G0446' => 'dzi', 'Duzib268G0691' => 'dzi', 'ECA232G4767' => 'eca', 'ECA233G2838' => 'eca', 'ECA234G0391' => 'eca', 'ECA234G0857' => 'eca', 'ECA236G1593' => 'eca', 'ECA238G0565' => 'eca', 'ECA246G1027' => 'eca', 'ECA246G3223' => 'eca', 'ECA246G3470' => 'eca', 'EL10Ac6g13829' => 'bvu', 'EL10Ac6g14093' => 'bvu', 'EL10Ac8g18707' => 'bvu', 'Eucgr.C01369' => 'egr', 'Eucgr.H02492' => 'egr', 'Eucgr.I01733' => 'egr', 'Eucgr.J02255' => 'egr', 'Eucgr.J02257' => 'egr', 'Eucgr.J02258' => 'egr', 'FAN02G1601' => 'fan', 'FAN03G1586' => 'fan', 'FAN03G2986' => 'fan', 'FAN05G4837' => 'fan', 'FAN06G0146' => 'fan', 'FAN07G0858' => 'fan', 'FAN09G3179' => 'fan', 'FAN10G0669' => 'fan', 'FAN12G2358' => 'fan', 'FAN14G4198' => 'fan', 'FAN14G5112' => 'fan', 'FAN17G0342' => 'fan', 'FAN19G0342' => 'fan', 'FAN19G0962' => 'fan', 'FAN19G1101' => 'fan', 'FAN19G1872' => 'fan', 'FAN22G0356' => 'fan', 'FAN23G0744' => 'fan', 'FAN23G1914' => 'fan', 'FAN26G0032' => 'fan', 'FAN28G0625' => 'fan', 'FvH4_1g02710' => 'fve', 'FvH4_1g02720' => 'fve', 'FvH4_4g25670' => 'fve', 'FvH4_6g51700' => 'fve', 'FvH4_7g20170' => 'fve', 'Glyma.05G175000' => 'gma', 'Glyma.08G132300' => 'gma', 'Glyma.11G243000' => 'gma', 'Glyma.13G158900' => 'gma', 'Glyma.17G112400' => 'gma', 'Glyma.18G014100' => 'gma', 'Glyma.19G003100' => 'gma', 'Glyma.19G056500' => 'gma', 'Gohir.A01G158900' => 'ghi', 'Gohir.A05G312600' => 'ghi', 'Gohir.A05G354900' => 'ghi', 'Gohir.A07G037200' => 'ghi', 'Gohir.A09G030000' => 'ghi', 'Gohir.A12G145200' => 'ghi', 'Gohir.D01G151500' => 'ghi', 'Gohir.D04G058300' => 'ghi', 'Gohir.D05G314100' => 'ghi', 'Gohir.D07G041400' => 'ghi', 'Gohir.D09G029700' => 'ghi', 'Gohir.D12G149700' => 'ghi', 'Gorai.001G043800' => 'gra', 'Gorai.002G187800' => 'gra', 'Gorai.006G034700' => 'gra', 'Gorai.008G161200' => 'gra', 'Gorai.009G335700' => 'gra', 'Gorai.012G065000' => 'gra', 'GSVIVG01000535001' => 'vvi', 'GSVIVG01015572001' => 'vvi', 'GSVIVG01032386001' => 'vvi', 'HanXRQChr05g0138531' => 'han', 'HanXRQChr06g0174391' => 'han', 'HanXRQChr07g0199021' => 'han', 'HanXRQChr08g0208211' => 'han', 'HanXRQChr09g0255471' => 'han', 'HanXRQChr10g0315791' => 'han', 'HanXRQChr12g0371991' => 'han', 'HanXRQChr15g0475251' => 'han', 'HanXRQChr17g0540001' => 'han', 'HanXRQChr17g0548631' => 'han', 'HanXRQChr17g0569561' => 'han', 'Haze_12256' => 'cav', 'Haze_14756' => 'cav', 'Haze_25528' => 'cav', 'Hma1.2p1_0079F.1_g041020' => 'hma', 'Hma1.2p1_0818F.1_g223260' => 'hma', 'Hma1.2p1_1747F.1_g300530' => 'hma', 'HPP92_004607' => 'vpl', 'HPP92_004608' => 'vpl', 'HPP92_006181' => 'vpl', 'HPP92_012192' => 'vpl', 'HPP92_015680' => 'vpl', 'HPP92_020249' => 'vpl', 'HPP92_021376' => 'vpl', 'HPP92_024275' => 'vpl', 'Hund06031' => 'sun', 'Hund25391' => 'sun', 'Lalb_Chr07g0185371' => 'lal', 'Lalb_Chr07g0185381' => 'lal', 'Lalb_Chr12g0204011' => 'lal', 'Lalb_Chr13g0301671' => 'lal', 'Lalb_Chr14g0362851' => 'lal', 'Lalb_Chr24g0403581' => 'lal', 'Lj1g0000233' => 'lja', 'Lj2g0018120' => 'lja', 'Lj3C621T0' => 'lonja', 'Lj3P1059T14' => 'lonja', 'Lj3P611T9' => 'lonja', 'Lj3P614T13' => 'lonja', 'Lj3P615T5' => 'lonja', 'Lj4g0012315' => 'lja', 'Lj4g0026182' => 'lja', 'Lj6P813T16' => 'lonja', 'Lj7C427T7' => 'lonja', 'Lj7C427T8' => 'lonja', 'Lj7P600T41' => 'lonja', 'Lju41C42G17' => 'lonja', 'Lsat_1_v5_gn_0_47300' => 'lsa', 'Lsat_1_v5_gn_2_91280' => 'lsa', 'Lsat_1_v5_gn_3_30561' => 'lsa', 'Lsat_1_v5_gn_4_184321' => 'lsa', 'Lsat_1_v5_gn_4_4041' => 'lsa', 'Lsat_1_v5_gn_5_92000' => 'lsa', 'Lsat_1_v5_gn_8_152940' => 'lsa', 'Lsat_1_v5_gn_8_62401' => 'lsa', 'Manes.06G055900' => 'mes', 'Manes.12G022200' => 'mes', 'Manes.13G023300' => 'mes', 'Manes.14G115000' => 'mes', 'Manes.15G151700' => 'mes', 'Manes.17G111300' => 'mes', 'Mapoly0226s0009' => 'mpo', 'MBI02_g25363_MAGBIO' => 'mbi', 'MBI06_g00027_MAGBIO' => 'mbi', 'MBI10_g13034_MAGBIO' => 'mbi', 'MD09G1023400' => 'mdo', 'MD13G1100100' => 'mdo', 'MD15G1169200' => 'mdo', 'MD16G1101100' => 'mdo', 'MD17G1022900' => 'mdo', 'Medtr3g096150' => 'mtr', 'Medtr4g115070' => 'mtr', 'Medtr7g033325' => 'mtr', 'Medtr8g089840' => 'mtr', 'MELO3C010319.2' => 'cme', 'MELO3C011944.2' => 'cme', 'MELO3C021589.2' => 'cme', 'Migut.E00207' => 'egut', 'Migut.H00067' => 'egut', 'Migut.K00433' => 'egut', 'Migut.K00606' => 'egut', 'Migut.K01410' => 'egut', 'MSTRG.13347' => 'ama', 'MSTRG.24045' => 'ama', 'MSTRG.2428' => 'ama', 'MSTRG.26410' => 'ama', 'MSTRG.3139' => 'ama', 'MSTRG.3286' => 'ama', 'MSTRG.563' => 'ama', 'MSTRG.7941' => 'ama', 'Nitab4.5_0000028g0060' => 'nta', 'Nitab4.5_0000065g0260' => 'nta', 'Nitab4.5_0000112g0060' => 'nta', 'Nitab4.5_0000489g0120' => 'nta', 'Nitab4.5_0001776g0050' => 'nta', 'Nitab4.5_0001854g0010' => 'nta', 'Nitab4.5_0001860g0020' => 'nta', 'Nitab4.5_0004352g0010' => 'nta', 'Nitab4.5_0008716g0020' => 'nta', 'Nitab4.5_0008922g0010' => 'nta', 'Nn3g16693' => 'nnu', 'Nn4g22596' => 'nnu', 'Nn7g37639' => 'nnu', 'Oeu001701.1' => 'oeu', 'Oeu018149.1' => 'oeu', 'Oeu026220.1' => 'oeu', 'Oeu038635.1' => 'oeu', 'Oeu049176.1' => 'oeu', 'Oeu056706.1' => 'oeu', 'Oeu056937.1' => 'oeu', 'Oeu057540.1' => 'oeu', 'Os02g0594900' => 'osa', 'Os02g0595100' => 'osa', 'Os04g0477500' => 'osa', 'Os12g0611900' => 'osa', 'Peaxi162Scf00076g00020' => 'pax', 'Peaxi162Scf00128g00217' => 'pax', 'Peaxi162Scf00129g01640' => 'pax', 'Peaxi162Scf00669g00007' => 'pax', 'Peaxi162Scf00700g00421' => 'pax', 'Peaxi162Scf00801g00038' => 'pax', 'Peaxi162Scf00891g00025' => 'pax', 'PGR083G0909' => 'pgr', 'PGR119G1005' => 'pgr', 'PGR142G2236' => 'pgr', 'PGR142G3388' => 'pgr', 'PGSC0003DMG400004514' => 'stu', 'PGSC0003DMG400012635' => 'stu', 'PGSC0003DMG400015730' => 'stu', 'PGSC0003DMG400018611' => 'stu', 'PGSC0003DMG400030897' => 'stu', 'Phvul.001G254800' => 'pvu', 'Phvul.002G260100' => 'pvu', 'Phvul.003G167600' => 'pvu', 'Phvul.004G005100' => 'pvu', 'Potri.001G343600' => 'ptr', 'Potri.006G066700' => 'ptr', 'Potri.008G186000' => 'ptr', 'Potri.010G046900' => 'ptr', 'Potri.018G127900' => 'ptr', 'Pp3c20_17750' => 'ppa', 'Pp3c24_4380' => 'ppa', 'Prupe.1G245800' => 'ppe', 'Prupe.3G293400' => 'ppe', 'Prupe.7G247400' => 'ppe', 'Psat0s145g0120' => 'psa', 'Psat0s595g0040' => 'psa', 'Psat0s595g0120' => 'psa', 'Psat3g175040' => 'psa', 'Psat7g058120' => 'psa', 'PSO017G0428' => 'pso', 'PSO063G7510' => 'pso', 'PSO067G0046' => 'pso', 'PSO478G1073' => 'pso', 'PSO675G3677' => 'pso', 'PSO675G6558' => 'pso', 'PSO675G7520' => 'pso', 'PSO675G8959' => 'pso', 'QL02p074089' => 'qlo', 'QL02p089614' => 'qlo', 'QL03p057736' => 'qlo', 'RcHm_v2.0_Chr1g0364131' => 'rch', 'RcHm_v2.0_Chr2g0087801' => 'rch', 'RcHm_v2.0_Chr2g0087821' => 'rch', 'RcHm_v2.0_Chr2g0173231' => 'rch', 'RcHm_v2.0_Chr4g0433111' => 'rch', 'Rhsim03G0250300' => 'rsi', 'Rhsim08G0048400' => 'rsi', 'Rhsim10G0014800' => 'rsi', 'Rhsim12G0040100' => 'rsi', 'Rhsim12G0109700' => 'rsi', 'Sabra06G0049600' => 'sbr', 'Sabra08G0141000' => 'sbr', 'Sabra10G0021400' => 'sbr', 'Sabra16G0222900' => 'sbr', 'Sabra18G0108600' => 'sbr', 'SalBow1G0433' => 'sbo', 'SalBow1G2038' => 'sbo', 'SalBow1G5003' => 'sbo', 'SalBow7G1197' => 'sbo', 'SalBow8G3506' => 'sbo', 'Sc03g0007300' => 'sci', 'Sc11g0000950' => 'sci', 'Sc14g0008750' => 'sci', 'Sc18g0000420' => 'sci', 'Sed0006754' => 'sed', 'Sed0008741' => 'sed', 'Sed0017172' => 'sed', 'Sed0018925' => 'sed', 'Sed0023326' => 'sed', 'Sed0025909' => 'sed', 'SEGI_05333' => 'sgi', 'SEGI_10362' => 'sgi', 'SEGI_13380' => 'sgi', 'SEGI_24306' => 'sgi', 'SEGI_29077' => 'sgi', 'SEGI_29095' => 'sgi', 'SEGI_36534' => 'sgi', 'SEGI_37506' => 'sgi', 'SEGI_38321' => 'sgi', 'SGA_v2.0_scaffold307G48031' => 'sas', 'SGA_v2.0_scaffold47G17507' => 'sas', 'SGA_v2.0_scaffold63G21736' => 'sas', 'SGA_v2.0_scaffold87G27070' => 'sas', 'SHI17794' => 'shi', 'SHI28851' => 'shi', 'SMO165G0155' => 'smo', 'SMO340G0217' => 'smo', 'SMO367G1210' => 'smo', 'Solyc02g093430.3' => 'sly', 'Solyc05g013580.4' => 'sly', 'Solyc07g008030.3' => 'sly', 'Solyc12g035470.2' => 'sly', 'Sopen02g038020' => 'spe', 'Sopen05g008490' => 'spe', 'Sopen07g003910' => 'spe', 'Sopen12g015240' => 'spe', 'Sp1g11550' => 'spa', 'Sp2g16710' => 'spa', 'Sp3g00430' => 'spa', 'Sp3g26780' => 'spa', 'Sp5g22900' => 'spa', 'Sp6g29530' => 'spa', 'TAR371G0794' => 'tar', 'TAR374G0164' => 'tar', 'TAR622G0165' => 'tar', 'TAR626G0929' => 'tar', 'TAR629G2155' => 'tar', 'THA.LOC104805282' => 'tha', 'THA.LOC104805363' => 'tha', 'THA.LOC104808968' => 'tha', 'THA.LOC104821093' => 'tha', 'THA.LOC104823953' => 'tha', 'THA.LOC104825562' => 'tha', 'THA.LOC104825665' => 'tha', 'Thecc.02G261400' => 'tca', 'Thecc.04G019200' => 'tca', 'Thecc.09G130400' => 'tca', 'Thhalv10004374m.g' => 'esa', 'Thhalv10007850m.g' => 'esa', 'Thhalv10013782m.g' => 'esa', 'Thhalv10018686m.g' => 'esa', 'Thhalv10020899m.g' => 'esa', 'Thhalv10022755m.g' => 'esa', 'TPR.G23851' => 'tpr', 'TPR.G26500' => 'tpr', 'TPR.G27267' => 'tpr', 'TPR.G32001' => 'tpr', 'TPR.G6251' => 'tpr', 'TPR.G8167' => 'tpr', 'TWI12G1330' => 'twi', 'TWI18G1239' => 'twi', 'TWI34G0979' => 'twi', 'TWI36G0670' => 'twi', 'TWI36G0707' => 'twi', 'TWI56G0233' => 'twi', 'TWI75G1809' => 'twi', 'unitig_21.g20874' => 'ugi', 'unitig_26.g10343' => 'ugi', 'unitig_46.g18392' => 'ugi', 'unitig_52.g17178' => 'ugi', 'unitig_8.g2934' => 'ugi', 'vmacro01122' => 'vma', 'vmacro05875' => 'vma', 'vmacro06147' => 'vma', 'vmacro16191' => 'vma', 'vmacro18293' => 'vma', 'VMungo0251G3707' => 'vmu', 'VMungo0464G1521' => 'vmu', 'VMungo1215G0205' => 'vmu', 'VMungo1383G2484' => 'vmu', 'Zm00001eb079610' => 'zma', 'Zm00001eb135990' => 'zma', 'Zm00001eb183710' => 'zma', 'Zm00001eb246020' => 'zma' ), 'gf_id' => 'HOM05D001124', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001124' ), 'data_identifier' => 'HOM05D001124', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001124', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '548', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02520' => 'bna', 'A03p06630' => 'bna', 'A05p44460' => 'bna', 'A06p08710' => 'bna', 'A06p41090' => 'bna', 'A07p32320' => 'bna', 'A08p32520' => 'bna', 'A09p10360' => 'bna', 'A10p24080' => 'bna', 'Aa31LG11G15250' => 'aar', 'Aa31LG1G1800' => 'aar', 'Aa31LG2G5120' => 'aar', 'Aa31LG2G6070' => 'aar', 'Aa31LG5G10770' => 'aar', 'Aa31sc61G90' => 'aar', 'Actinidia01352' => 'ach', 'Actinidia05983' => 'ach', 'Actinidia08133' => 'ach', 'Actinidia15101' => 'ach', 'Actinidia26379' => 'ach', 'Actinidia35778' => 'ach', 'Actinidia36123' => 'ach', 'Actinidia37436' => 'ach', 'Actinidia38730' => 'ach', 'Ah.02g128210' => 'amhyb', 'Ah.03g132990' => 'amhyb', 'Ah.14g079410' => 'amhyb', 'AL1G24640' => 'aly', 'AL2G26680' => 'aly', 'AL3G10530' => 'aly', 'AL3G45230' => 'aly', 'AL5G15230' => 'aly', 'AL5G16960' => 'aly', 'AL6G25210' => 'aly', 'Aqoxy2G00441' => 'aox', 'Aqoxy3G01236' => 'aox', 'Aqoxy5G03746' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3RQ047' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C7GMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9C8JER' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MBL6KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YXCZ83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZANX40' => 'arhy', 'AT1G12990' => 'ath', 'AT1G67880' => 'ath', 'AT2G13290' => 'ath', 'AT3G01620' => 'ath', 'AT3G26445' => 'ath', 'AT3G27540' => 'ath', 'AT5G14480' => 'ath', 'ATR0824G026' => 'atr', 'ATR1098G019' => 'atr', 'Atru.chr11.2145' => 'acertr', 'Atru.chr2.3636' => 'acertr', 'Atru.chr2.3644' => 'acertr', 'Atru.chr6.2422' => 'acertr', 'Atru.chr7.1112' => 'acertr', 'AUR62005469' => 'cqu', 'AUR62011166' => 'cqu', 'AUR62013319' => 'cqu', 'AUR62024273' => 'cqu', 'AUR62028420' => 'cqu', 'AUR62041942' => 'cqu', 'BcaB01g04969' => 'bca', 'BcaB01g06371' => 'bca', 'BcaB02g11494' => 'bca', 'BcaB03g15382' => 'bca', 'BcaB08g36994' => 'bca', 'BcaC03g13477' => 'bca', 'BcaC03g13478' => 'bca', 'BcaC03g13480' => 'bca', 'BcaC03g13481' => 'bca', 'BcaC03g13486' => 'bca', 'BcaC04g19031' => 'bca', 'BcaC04g23085' => 'bca', 'BcaC05g25094' => 'bca', 'BcaC05g25096' => 'bca', 'BcaC05g25138' => 'bca', 'BcaC05g30416' => 'bca', 'BcaC05g30455' => 'bca', 'BcaC06g30979' => 'bca', 'BcaC06g33805' => 'bca', 'BcaC08g46021' => 'bca', 'BcaNung03154' => 'bca', 'BolC2t06623H' => 'bol', 'BolC2t06632H' => 'bol', 'BolC2t06635H' => 'bol', 'BolC2t06638H' => 'bol', 'BolC3t13266H' => 'bol', 'BolC5t29776H' => 'bol', 'BolC6t38912H' => 'bol', 'BolC7t44183H' => 'bol', 'BolC9t54123H' => 'bol', 'BolC9t59107H' => 'bol', 'BraA02t05221Z' => 'bra', 'BraA03t09996Z' => 'bra', 'BraA05t23210Z' => 'bra', 'BraA06t24068Z' => 'bra', 'BraA06t27032Z' => 'bra', 'BraA08t35176Z' => 'bra', 'BraA09t36680Z' => 'bra', 'BraA10t44471Z' => 'bra', 'C02p06760' => 'bna', 'C02p06890' => 'bna', 'C02p07010' => 'bna', 'C03p07660' => 'bna', 'C05p10300' => 'bna', 'C06p38150' => 'bna', 'C07p36650' => 'bna', 'C08p15770' => 'bna', 'C09p12300' => 'bna', 'C09p62700' => 'bna', 'C09p75040' => 'bna', 'CAN.G13.1' => 'can', 'CAN.G138.4' => 'can', 'CAN.G44.6' => 'can', 'CAN.G473.19' => 'can', 'CANSAT01G0835' => 'cansat', 'CANSAT11G0246' => 'cansat', 'CANSAT11G1766' => 'cansat', 'CANSAT64G1954' => 'cansat', 'CARHR013330' => 'chi', 'CARHR060530' => 'chi', 'CARHR075300' => 'chi', 'CARHR105120' => 'chi', 'CARHR148910' => 'chi', 'CARHR198830' => 'chi', 'Carub.0001s1275' => 'cru', 'Carub.0002s1437' => 'cru', 'Carub.0003s0044' => 'cru', 'Carub.0003s2787' => 'cru', 'Carub.0005s0597' => 'cru', 'Carub.0006s1266' => 'cru', 'Ca_06935_v3' => 'car', 'Ca_13559_v3' => 'car', 'Ca_16941_v3' => 'car', 'Ca_16960_v3' => 'car', 'Ca_17775_v3' => 'car', 'Ca_30464_v3' => 'car', 'Cc06_g08160' => 'ccan', 'Cc07_g01520' => 'ccan', 'Cc11_g15810' => 'ccan', 'CDE02G2840' => 'cde', 'CDE03G0093' => 'cde', 'CDE04G2127' => 'cde', 'CDE07G1857' => 'cde', 'CDE09G1246' => 'cde', 'Cfa003412' => 'cfa', 'Cfa007341' => 'cfa', 'Cfa009220' => 'cfa', 'Ciclev10008737m.g' => 'ccl', 'Ciclev10015565m.g' => 'ccl', 'Ciclev10031761m.g' => 'ccl', 'CiPaw.03G045300' => 'cil', 'CiPaw.03G247200' => 'cil', 'CiPaw.04G029500' => 'cil', 'CiPaw.04G174000' => 'cil', 'CiPaw.05G181200' => 'cil', 'CiPaw.06G067100' => 'cil', 'ClCG05G025800' => 'cla', 'ClCG06G011400' => 'cla', 'ClCG09G019360' => 'cla', 'COL.COLO4_04827' => 'col', 'COL.COLO4_29170' => 'col', 'COL.COLO4_35131' => 'col', 'COL.COLO4_35132' => 'col', 'Cpa.g.sc33.32' => 'cpa', 'Cpa.g.sc46.29' => 'cpa', 'Cpa.g.sc796.1' => 'cpa', 'CsaV3_1G030420' => 'csa', 'CsaV3_5G027050' => 'csa', 'CsaV3_5G031040' => 'csa', 'CsaV3_UNG023130' => 'csa', 'CSS0007726' => 'camsi', 'CSS0016433' => 'camsi', 'CSS0017656' => 'camsi', 'CSS0025364' => 'camsi', 'CSS0027582' => 'camsi', 'CSS0047288' => 'camsi', 'CSS0049950' => 'camsi', 'DCAR_003843' => 'dca', 'DCAR_007052' => 'dca', 'DCAR_020884' => 'dca', 'DCAR_021730' => 'dca', 'DCAR_024423' => 'dca', 'DCAR_026509' => 'dca', 'DCAR_031158' => 'dca', 'Dinv14728' => 'din', 'Dinv15219' => 'din', 'Dinv25728' => 'din', 'Dinv33428' => 'din', 'Dinv36489' => 'din', 'Dinv41486' => 'din', 'Duzib147G0469' => 'dzi', 'Duzib168G0060' => 'dzi', 'Duzib187G1215' => 'dzi', 'Duzib248G0692' => 'dzi', 'Duzib251G0767' => 'dzi', 'Duzib264G0446' => 'dzi', 'Duzib268G0691' => 'dzi', 'ECA232G4767' => 'eca', 'ECA233G2838' => 'eca', 'ECA234G0391' => 'eca', 'ECA234G0857' => 'eca', 'ECA236G1593' => 'eca', 'ECA238G0565' => 'eca', 'ECA246G1027' => 'eca', 'ECA246G3223' => 'eca', 'ECA246G3470' => 'eca', 'EL10Ac6g13829' => 'bvu', 'EL10Ac6g14093' => 'bvu', 'EL10Ac8g18707' => 'bvu', 'Eucgr.C01369' => 'egr', 'Eucgr.H02492' => 'egr', 'Eucgr.I01733' => 'egr', 'Eucgr.J02255' => 'egr', 'Eucgr.J02257' => 'egr', 'Eucgr.J02258' => 'egr', 'FAN02G1601' => 'fan', 'FAN03G1586' => 'fan', 'FAN03G2986' => 'fan', 'FAN05G4837' => 'fan', 'FAN06G0146' => 'fan', 'FAN07G0858' => 'fan', 'FAN09G3179' => 'fan', 'FAN10G0669' => 'fan', 'FAN12G2358' => 'fan', 'FAN14G4198' => 'fan', 'FAN14G5112' => 'fan', 'FAN17G0342' => 'fan', 'FAN19G0342' => 'fan', 'FAN19G0962' => 'fan', 'FAN19G1101' => 'fan', 'FAN19G1872' => 'fan', 'FAN22G0356' => 'fan', 'FAN23G0744' => 'fan', 'FAN23G1914' => 'fan', 'FAN26G0032' => 'fan', 'FAN28G0625' => 'fan', 'FvH4_1g02710' => 'fve', 'FvH4_1g02720' => 'fve', 'FvH4_4g25670' => 'fve', 'FvH4_6g51700' => 'fve', 'FvH4_7g20170' => 'fve', 'Glyma.05G175000' => 'gma', 'Glyma.08G132300' => 'gma', 'Glyma.11G243000' => 'gma', 'Glyma.13G158900' => 'gma', 'Glyma.17G112400' => 'gma', 'Glyma.18G014100' => 'gma', 'Glyma.19G003100' => 'gma', 'Glyma.19G056500' => 'gma', 'Gohir.A01G158900' => 'ghi', 'Gohir.A05G312600' => 'ghi', 'Gohir.A05G354900' => 'ghi', 'Gohir.A07G037200' => 'ghi', 'Gohir.A09G030000' => 'ghi', 'Gohir.A12G145200' => 'ghi', 'Gohir.D01G151500' => 'ghi', 'Gohir.D04G058300' => 'ghi', 'Gohir.D05G314100' => 'ghi', 'Gohir.D07G041400' => 'ghi', 'Gohir.D09G029700' => 'ghi', 'Gohir.D12G149700' => 'ghi', 'Gorai.001G043800' => 'gra', 'Gorai.002G187800' => 'gra', 'Gorai.006G034700' => 'gra', 'Gorai.008G161200' => 'gra', 'Gorai.009G335700' => 'gra', 'Gorai.012G065000' => 'gra', 'GSVIVG01000535001' => 'vvi', 'GSVIVG01015572001' => 'vvi', 'GSVIVG01032386001' => 'vvi', 'HanXRQChr05g0138531' => 'han', 'HanXRQChr06g0174391' => 'han', 'HanXRQChr07g0199021' => 'han', 'HanXRQChr08g0208211' => 'han', 'HanXRQChr09g0255471' => 'han', 'HanXRQChr10g0315791' => 'han', 'HanXRQChr12g0371991' => 'han', 'HanXRQChr15g0475251' => 'han', 'HanXRQChr17g0540001' => 'han', 'HanXRQChr17g0548631' => 'han', 'HanXRQChr17g0569561' => 'han', 'Haze_12256' => 'cav', 'Haze_14756' => 'cav', 'Haze_25528' => 'cav', 'Hma1.2p1_0079F.1_g041020' => 'hma', 'Hma1.2p1_0818F.1_g223260' => 'hma', 'Hma1.2p1_1747F.1_g300530' => 'hma', 'HPP92_004607' => 'vpl', 'HPP92_004608' => 'vpl', 'HPP92_006181' => 'vpl', 'HPP92_012192' => 'vpl', 'HPP92_015680' => 'vpl', 'HPP92_020249' => 'vpl', 'HPP92_021376' => 'vpl', 'HPP92_024275' => 'vpl', 'Hund06031' => 'sun', 'Hund25391' => 'sun', 'Lalb_Chr07g0185371' => 'lal', 'Lalb_Chr07g0185381' => 'lal', 'Lalb_Chr12g0204011' => 'lal', 'Lalb_Chr13g0301671' => 'lal', 'Lalb_Chr14g0362851' => 'lal', 'Lalb_Chr24g0403581' => 'lal', 'Lj1g0000233' => 'lja', 'Lj2g0018120' => 'lja', 'Lj3C621T0' => 'lonja', 'Lj3P1059T14' => 'lonja', 'Lj3P611T9' => 'lonja', 'Lj3P614T13' => 'lonja', 'Lj3P615T5' => 'lonja', 'Lj4g0012315' => 'lja', 'Lj4g0026182' => 'lja', 'Lj6P813T16' => 'lonja', 'Lj7C427T7' => 'lonja', 'Lj7C427T8' => 'lonja', 'Lj7P600T41' => 'lonja', 'Lju41C42G17' => 'lonja', 'Lsat_1_v5_gn_0_47300' => 'lsa', 'Lsat_1_v5_gn_2_91280' => 'lsa', 'Lsat_1_v5_gn_3_30561' => 'lsa', 'Lsat_1_v5_gn_4_184321' => 'lsa', 'Lsat_1_v5_gn_4_4041' => 'lsa', 'Lsat_1_v5_gn_5_92000' => 'lsa', 'Lsat_1_v5_gn_8_152940' => 'lsa', 'Lsat_1_v5_gn_8_62401' => 'lsa', 'Manes.06G055900' => 'mes', 'Manes.12G022200' => 'mes', 'Manes.13G023300' => 'mes', 'Manes.14G115000' => 'mes', 'Manes.15G151700' => 'mes', 'Manes.17G111300' => 'mes', 'Mapoly0226s0009' => 'mpo', 'MBI02_g25363_MAGBIO' => 'mbi', 'MBI06_g00027_MAGBIO' => 'mbi', 'MBI10_g13034_MAGBIO' => 'mbi', 'MD09G1023400' => 'mdo', 'MD13G1100100' => 'mdo', 'MD15G1169200' => 'mdo', 'MD16G1101100' => 'mdo', 'MD17G1022900' => 'mdo', 'Medtr3g096150' => 'mtr', 'Medtr4g115070' => 'mtr', 'Medtr7g033325' => 'mtr', 'Medtr8g089840' => 'mtr', 'MELO3C010319.2' => 'cme', 'MELO3C011944.2' => 'cme', 'MELO3C021589.2' => 'cme', 'Migut.E00207' => 'egut', 'Migut.H00067' => 'egut', 'Migut.K00433' => 'egut', 'Migut.K00606' => 'egut', 'Migut.K01410' => 'egut', 'MSTRG.13347' => 'ama', 'MSTRG.24045' => 'ama', 'MSTRG.2428' => 'ama', 'MSTRG.26410' => 'ama', 'MSTRG.3139' => 'ama', 'MSTRG.3286' => 'ama', 'MSTRG.563' => 'ama', 'MSTRG.7941' => 'ama', 'Nitab4.5_0000028g0060' => 'nta', 'Nitab4.5_0000065g0260' => 'nta', 'Nitab4.5_0000112g0060' => 'nta', 'Nitab4.5_0000489g0120' => 'nta', 'Nitab4.5_0001776g0050' => 'nta', 'Nitab4.5_0001854g0010' => 'nta', 'Nitab4.5_0001860g0020' => 'nta', 'Nitab4.5_0004352g0010' => 'nta', 'Nitab4.5_0008716g0020' => 'nta', 'Nitab4.5_0008922g0010' => 'nta', 'Nn3g16693' => 'nnu', 'Nn4g22596' => 'nnu', 'Nn7g37639' => 'nnu', 'Oeu001701.1' => 'oeu', 'Oeu018149.1' => 'oeu', 'Oeu026220.1' => 'oeu', 'Oeu038635.1' => 'oeu', 'Oeu049176.1' => 'oeu', 'Oeu056706.1' => 'oeu', 'Oeu056937.1' => 'oeu', 'Oeu057540.1' => 'oeu', 'Os02g0594900' => 'osa', 'Os02g0595100' => 'osa', 'Os04g0477500' => 'osa', 'Os12g0611900' => 'osa', 'Peaxi162Scf00076g00020' => 'pax', 'Peaxi162Scf00128g00217' => 'pax', 'Peaxi162Scf00129g01640' => 'pax', 'Peaxi162Scf00669g00007' => 'pax', 'Peaxi162Scf00700g00421' => 'pax', 'Peaxi162Scf00801g00038' => 'pax', 'Peaxi162Scf00891g00025' => 'pax', 'PGR083G0909' => 'pgr', 'PGR119G1005' => 'pgr', 'PGR142G2236' => 'pgr', 'PGR142G3388' => 'pgr', 'PGSC0003DMG400004514' => 'stu', 'PGSC0003DMG400012635' => 'stu', 'PGSC0003DMG400015730' => 'stu', 'PGSC0003DMG400018611' => 'stu', 'PGSC0003DMG400030897' => 'stu', 'Phvul.001G254800' => 'pvu', 'Phvul.002G260100' => 'pvu', 'Phvul.003G167600' => 'pvu', 'Phvul.004G005100' => 'pvu', 'Potri.001G343600' => 'ptr', 'Potri.006G066700' => 'ptr', 'Potri.008G186000' => 'ptr', 'Potri.010G046900' => 'ptr', 'Potri.018G127900' => 'ptr', 'Pp3c20_17750' => 'ppa', 'Pp3c24_4380' => 'ppa', 'Prupe.1G245800' => 'ppe', 'Prupe.3G293400' => 'ppe', 'Prupe.7G247400' => 'ppe', 'Psat0s145g0120' => 'psa', 'Psat0s595g0040' => 'psa', 'Psat0s595g0120' => 'psa', 'Psat3g175040' => 'psa', 'Psat7g058120' => 'psa', 'PSO017G0428' => 'pso', 'PSO063G7510' => 'pso', 'PSO067G0046' => 'pso', 'PSO478G1073' => 'pso', 'PSO675G3677' => 'pso', 'PSO675G6558' => 'pso', 'PSO675G7520' => 'pso', 'PSO675G8959' => 'pso', 'QL02p074089' => 'qlo', 'QL02p089614' => 'qlo', 'QL03p057736' => 'qlo', 'RcHm_v2.0_Chr1g0364131' => 'rch', 'RcHm_v2.0_Chr2g0087801' => 'rch', 'RcHm_v2.0_Chr2g0087821' => 'rch', 'RcHm_v2.0_Chr2g0173231' => 'rch', 'RcHm_v2.0_Chr4g0433111' => 'rch', 'Rhsim03G0250300' => 'rsi', 'Rhsim08G0048400' => 'rsi', 'Rhsim10G0014800' => 'rsi', 'Rhsim12G0040100' => 'rsi', 'Rhsim12G0109700' => 'rsi', 'Sabra06G0049600' => 'sbr', 'Sabra08G0141000' => 'sbr', 'Sabra10G0021400' => 'sbr', 'Sabra16G0222900' => 'sbr', 'Sabra18G0108600' => 'sbr', 'SalBow1G0433' => 'sbo', 'SalBow1G2038' => 'sbo', 'SalBow1G5003' => 'sbo', 'SalBow7G1197' => 'sbo', 'SalBow8G3506' => 'sbo', 'Sc03g0007300' => 'sci', 'Sc11g0000950' => 'sci', 'Sc14g0008750' => 'sci', 'Sc18g0000420' => 'sci', 'Sed0006754' => 'sed', 'Sed0008741' => 'sed', 'Sed0017172' => 'sed', 'Sed0018925' => 'sed', 'Sed0023326' => 'sed', 'Sed0025909' => 'sed', 'SEGI_05333' => 'sgi', 'SEGI_10362' => 'sgi', 'SEGI_13380' => 'sgi', 'SEGI_24306' => 'sgi', 'SEGI_29077' => 'sgi', 'SEGI_29095' => 'sgi', 'SEGI_36534' => 'sgi', 'SEGI_37506' => 'sgi', 'SEGI_38321' => 'sgi', 'SGA_v2.0_scaffold307G48031' => 'sas', 'SGA_v2.0_scaffold47G17507' => 'sas', 'SGA_v2.0_scaffold63G21736' => 'sas', 'SGA_v2.0_scaffold87G27070' => 'sas', 'SHI17794' => 'shi', 'SHI28851' => 'shi', 'SMO165G0155' => 'smo', 'SMO340G0217' => 'smo', 'SMO367G1210' => 'smo', 'Solyc02g093430.3' => 'sly', 'Solyc05g013580.4' => 'sly', 'Solyc07g008030.3' => 'sly', 'Solyc12g035470.2' => 'sly', 'Sopen02g038020' => 'spe', 'Sopen05g008490' => 'spe', 'Sopen07g003910' => 'spe', 'Sopen12g015240' => 'spe', 'Sp1g11550' => 'spa', 'Sp2g16710' => 'spa', 'Sp3g00430' => 'spa', 'Sp3g26780' => 'spa', 'Sp5g22900' => 'spa', 'Sp6g29530' => 'spa', 'TAR371G0794' => 'tar', 'TAR374G0164' => 'tar', 'TAR622G0165' => 'tar', 'TAR626G0929' => 'tar', 'TAR629G2155' => 'tar', 'THA.LOC104805282' => 'tha', 'THA.LOC104805363' => 'tha', 'THA.LOC104808968' => 'tha', 'THA.LOC104821093' => 'tha', 'THA.LOC104823953' => 'tha', 'THA.LOC104825562' => 'tha', 'THA.LOC104825665' => 'tha', 'Thecc.02G261400' => 'tca', 'Thecc.04G019200' => 'tca', 'Thecc.09G130400' => 'tca', 'Thhalv10004374m.g' => 'esa', 'Thhalv10007850m.g' => 'esa', 'Thhalv10013782m.g' => 'esa', 'Thhalv10018686m.g' => 'esa', 'Thhalv10020899m.g' => 'esa', 'Thhalv10022755m.g' => 'esa', 'TPR.G23851' => 'tpr', 'TPR.G26500' => 'tpr', 'TPR.G27267' => 'tpr', 'TPR.G32001' => 'tpr', 'TPR.G6251' => 'tpr', 'TPR.G8167' => 'tpr', 'TWI12G1330' => 'twi', 'TWI18G1239' => 'twi', 'TWI34G0979' => 'twi', 'TWI36G0670' => 'twi', 'TWI36G0707' => 'twi', 'TWI56G0233' => 'twi', 'TWI75G1809' => 'twi', 'unitig_21.g20874' => 'ugi', 'unitig_26.g10343' => 'ugi', 'unitig_46.g18392' => 'ugi', 'unitig_52.g17178' => 'ugi', 'unitig_8.g2934' => 'ugi', 'vmacro01122' => 'vma', 'vmacro05875' => 'vma', 'vmacro06147' => 'vma', 'vmacro16191' => 'vma', 'vmacro18293' => 'vma', 'VMungo0251G3707' => 'vmu', 'VMungo0464G1521' => 'vmu', 'VMungo1215G0205' => 'vmu', 'VMungo1383G2484' => 'vmu', 'Zm00001eb079610' => 'zma', 'Zm00001eb135990' => 'zma', 'Zm00001eb183710' => 'zma', 'Zm00001eb246020' => 'zma' ) $gf_id = 'HOM05D001124' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001124' ) $data_identifier = 'HOM05D001124' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 6, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 7, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 21, 'bol' => (int) 10, 'bra' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 6, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 9, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 21, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 8, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 10, 'lsa' => (int) 8, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 8, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 9, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb246020' $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' => 'HOM05D001124', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '548', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02520' => 'bna', 'A03p06630' => 'bna', 'A05p44460' => 'bna', 'A06p08710' => 'bna', 'A06p41090' => 'bna', 'A07p32320' => 'bna', 'A08p32520' => 'bna', 'A09p10360' => 'bna', 'A10p24080' => 'bna', 'Aa31LG11G15250' => 'aar', 'Aa31LG1G1800' => 'aar', 'Aa31LG2G5120' => 'aar', 'Aa31LG2G6070' => 'aar', 'Aa31LG5G10770' => 'aar', 'Aa31sc61G90' => 'aar', 'Actinidia01352' => 'ach', 'Actinidia05983' => 'ach', 'Actinidia08133' => 'ach', 'Actinidia15101' => 'ach', 'Actinidia26379' => 'ach', 'Actinidia35778' => 'ach', 'Actinidia36123' => 'ach', 'Actinidia37436' => 'ach', 'Actinidia38730' => 'ach', 'Ah.02g128210' => 'amhyb', 'Ah.03g132990' => 'amhyb', 'Ah.14g079410' => 'amhyb', 'AL1G24640' => 'aly', 'AL2G26680' => 'aly', 'AL3G10530' => 'aly', 'AL3G45230' => 'aly', 'AL5G15230' => 'aly', 'AL5G16960' => 'aly', 'AL6G25210' => 'aly', 'Aqoxy2G00441' => 'aox', 'Aqoxy3G01236' => 'aox', 'Aqoxy5G03746' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3RQ047' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C7GMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9C8JER' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MBL6KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YXCZ83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZANX40' => 'arhy', 'AT1G12990' => 'ath', 'AT1G67880' => 'ath', 'AT2G13290' => 'ath', 'AT3G01620' => 'ath', 'AT3G26445' => 'ath', 'AT3G27540' => 'ath', 'AT5G14480' => 'ath', 'ATR0824G026' => 'atr', 'ATR1098G019' => 'atr', 'Atru.chr11.2145' => 'acertr', 'Atru.chr2.3636' => 'acertr', 'Atru.chr2.3644' => 'acertr', 'Atru.chr6.2422' => 'acertr', 'Atru.chr7.1112' => 'acertr', 'AUR62005469' => 'cqu', 'AUR62011166' => 'cqu', 'AUR62013319' => 'cqu', 'AUR62024273' => 'cqu', 'AUR62028420' => 'cqu', 'AUR62041942' => 'cqu', 'BcaB01g04969' => 'bca', 'BcaB01g06371' => 'bca', 'BcaB02g11494' => 'bca', 'BcaB03g15382' => 'bca', 'BcaB08g36994' => 'bca', 'BcaC03g13477' => 'bca', 'BcaC03g13478' => 'bca', 'BcaC03g13480' => 'bca', 'BcaC03g13481' => 'bca', 'BcaC03g13486' => 'bca', 'BcaC04g19031' => 'bca', 'BcaC04g23085' => 'bca', 'BcaC05g25094' => 'bca', 'BcaC05g25096' => 'bca', 'BcaC05g25138' => 'bca', 'BcaC05g30416' => 'bca', 'BcaC05g30455' => 'bca', 'BcaC06g30979' => 'bca', 'BcaC06g33805' => 'bca', 'BcaC08g46021' => 'bca', 'BcaNung03154' => 'bca', 'BolC2t06623H' => 'bol', 'BolC2t06632H' => 'bol', 'BolC2t06635H' => 'bol', 'BolC2t06638H' => 'bol', 'BolC3t13266H' => 'bol', 'BolC5t29776H' => 'bol', 'BolC6t38912H' => 'bol', 'BolC7t44183H' => 'bol', 'BolC9t54123H' => 'bol', 'BolC9t59107H' => 'bol', 'BraA02t05221Z' => 'bra', 'BraA03t09996Z' => 'bra', 'BraA05t23210Z' => 'bra', 'BraA06t24068Z' => 'bra', 'BraA06t27032Z' => 'bra', 'BraA08t35176Z' => 'bra', 'BraA09t36680Z' => 'bra', 'BraA10t44471Z' => 'bra', 'C02p06760' => 'bna', 'C02p06890' => 'bna', 'C02p07010' => 'bna', 'C03p07660' => 'bna', 'C05p10300' => 'bna', 'C06p38150' => 'bna', 'C07p36650' => 'bna', 'C08p15770' => 'bna', 'C09p12300' => 'bna', 'C09p62700' => 'bna', 'C09p75040' => 'bna', 'CAN.G13.1' => 'can', 'CAN.G138.4' => 'can', 'CAN.G44.6' => 'can', 'CAN.G473.19' => 'can', 'CANSAT01G0835' => 'cansat', 'CANSAT11G0246' => 'cansat', 'CANSAT11G1766' => 'cansat', 'CANSAT64G1954' => 'cansat', 'CARHR013330' => 'chi', 'CARHR060530' => 'chi', 'CARHR075300' => 'chi', 'CARHR105120' => 'chi', 'CARHR148910' => 'chi', 'CARHR198830' => 'chi', 'Carub.0001s1275' => 'cru', 'Carub.0002s1437' => 'cru', 'Carub.0003s0044' => 'cru', 'Carub.0003s2787' => 'cru', 'Carub.0005s0597' => 'cru', 'Carub.0006s1266' => 'cru', 'Ca_06935_v3' => 'car', 'Ca_13559_v3' => 'car', 'Ca_16941_v3' => 'car', 'Ca_16960_v3' => 'car', 'Ca_17775_v3' => 'car', 'Ca_30464_v3' => 'car', 'Cc06_g08160' => 'ccan', 'Cc07_g01520' => 'ccan', 'Cc11_g15810' => 'ccan', 'CDE02G2840' => 'cde', 'CDE03G0093' => 'cde', 'CDE04G2127' => 'cde', 'CDE07G1857' => 'cde', 'CDE09G1246' => 'cde', 'Cfa003412' => 'cfa', 'Cfa007341' => 'cfa', 'Cfa009220' => 'cfa', 'Ciclev10008737m.g' => 'ccl', 'Ciclev10015565m.g' => 'ccl', 'Ciclev10031761m.g' => 'ccl', 'CiPaw.03G045300' => 'cil', 'CiPaw.03G247200' => 'cil', 'CiPaw.04G029500' => 'cil', 'CiPaw.04G174000' => 'cil', 'CiPaw.05G181200' => 'cil', 'CiPaw.06G067100' => 'cil', 'ClCG05G025800' => 'cla', 'ClCG06G011400' => 'cla', 'ClCG09G019360' => 'cla', 'COL.COLO4_04827' => 'col', 'COL.COLO4_29170' => 'col', 'COL.COLO4_35131' => 'col', 'COL.COLO4_35132' => 'col', 'Cpa.g.sc33.32' => 'cpa', 'Cpa.g.sc46.29' => 'cpa', 'Cpa.g.sc796.1' => 'cpa', 'CsaV3_1G030420' => 'csa', 'CsaV3_5G027050' => 'csa', 'CsaV3_5G031040' => 'csa', 'CsaV3_UNG023130' => 'csa', 'CSS0007726' => 'camsi', 'CSS0016433' => 'camsi', 'CSS0017656' => 'camsi', 'CSS0025364' => 'camsi', 'CSS0027582' => 'camsi', 'CSS0047288' => 'camsi', 'CSS0049950' => 'camsi', 'DCAR_003843' => 'dca', 'DCAR_007052' => 'dca', 'DCAR_020884' => 'dca', 'DCAR_021730' => 'dca', 'DCAR_024423' => 'dca', 'DCAR_026509' => 'dca', 'DCAR_031158' => 'dca', 'Dinv14728' => 'din', 'Dinv15219' => 'din', 'Dinv25728' => 'din', 'Dinv33428' => 'din', 'Dinv36489' => 'din', 'Dinv41486' => 'din', 'Duzib147G0469' => 'dzi', 'Duzib168G0060' => 'dzi', 'Duzib187G1215' => 'dzi', 'Duzib248G0692' => 'dzi', 'Duzib251G0767' => 'dzi', 'Duzib264G0446' => 'dzi', 'Duzib268G0691' => 'dzi', 'ECA232G4767' => 'eca', 'ECA233G2838' => 'eca', 'ECA234G0391' => 'eca', 'ECA234G0857' => 'eca', 'ECA236G1593' => 'eca', 'ECA238G0565' => 'eca', 'ECA246G1027' => 'eca', 'ECA246G3223' => 'eca', 'ECA246G3470' => 'eca', 'EL10Ac6g13829' => 'bvu', 'EL10Ac6g14093' => 'bvu', 'EL10Ac8g18707' => 'bvu', 'Eucgr.C01369' => 'egr', 'Eucgr.H02492' => 'egr', 'Eucgr.I01733' => 'egr', 'Eucgr.J02255' => 'egr', 'Eucgr.J02257' => 'egr', 'Eucgr.J02258' => 'egr', 'FAN02G1601' => 'fan', 'FAN03G1586' => 'fan', 'FAN03G2986' => 'fan', 'FAN05G4837' => 'fan', 'FAN06G0146' => 'fan', 'FAN07G0858' => 'fan', 'FAN09G3179' => 'fan', 'FAN10G0669' => 'fan', 'FAN12G2358' => 'fan', 'FAN14G4198' => 'fan', 'FAN14G5112' => 'fan', 'FAN17G0342' => 'fan', 'FAN19G0342' => 'fan', 'FAN19G0962' => 'fan', 'FAN19G1101' => 'fan', 'FAN19G1872' => 'fan', 'FAN22G0356' => 'fan', 'FAN23G0744' => 'fan', 'FAN23G1914' => 'fan', 'FAN26G0032' => 'fan', 'FAN28G0625' => 'fan', 'FvH4_1g02710' => 'fve', 'FvH4_1g02720' => 'fve', 'FvH4_4g25670' => 'fve', 'FvH4_6g51700' => 'fve', 'FvH4_7g20170' => 'fve', 'Glyma.05G175000' => 'gma', 'Glyma.08G132300' => 'gma', 'Glyma.11G243000' => 'gma', 'Glyma.13G158900' => 'gma', 'Glyma.17G112400' => 'gma', 'Glyma.18G014100' => 'gma', 'Glyma.19G003100' => 'gma', 'Glyma.19G056500' => 'gma', 'Gohir.A01G158900' => 'ghi', 'Gohir.A05G312600' => 'ghi', 'Gohir.A05G354900' => 'ghi', 'Gohir.A07G037200' => 'ghi', 'Gohir.A09G030000' => 'ghi', 'Gohir.A12G145200' => 'ghi', 'Gohir.D01G151500' => 'ghi', 'Gohir.D04G058300' => 'ghi', 'Gohir.D05G314100' => 'ghi', 'Gohir.D07G041400' => 'ghi', 'Gohir.D09G029700' => 'ghi', 'Gohir.D12G149700' => 'ghi', 'Gorai.001G043800' => 'gra', 'Gorai.002G187800' => 'gra', 'Gorai.006G034700' => 'gra', 'Gorai.008G161200' => 'gra', 'Gorai.009G335700' => 'gra', 'Gorai.012G065000' => 'gra', 'GSVIVG01000535001' => 'vvi', 'GSVIVG01015572001' => 'vvi', 'GSVIVG01032386001' => 'vvi', 'HanXRQChr05g0138531' => 'han', 'HanXRQChr06g0174391' => 'han', 'HanXRQChr07g0199021' => 'han', 'HanXRQChr08g0208211' => 'han', 'HanXRQChr09g0255471' => 'han', 'HanXRQChr10g0315791' => 'han', 'HanXRQChr12g0371991' => 'han', 'HanXRQChr15g0475251' => 'han', 'HanXRQChr17g0540001' => 'han', 'HanXRQChr17g0548631' => 'han', 'HanXRQChr17g0569561' => 'han', 'Haze_12256' => 'cav', 'Haze_14756' => 'cav', 'Haze_25528' => 'cav', 'Hma1.2p1_0079F.1_g041020' => 'hma', 'Hma1.2p1_0818F.1_g223260' => 'hma', 'Hma1.2p1_1747F.1_g300530' => 'hma', 'HPP92_004607' => 'vpl', 'HPP92_004608' => 'vpl', 'HPP92_006181' => 'vpl', 'HPP92_012192' => 'vpl', 'HPP92_015680' => 'vpl', 'HPP92_020249' => 'vpl', 'HPP92_021376' => 'vpl', 'HPP92_024275' => 'vpl', 'Hund06031' => 'sun', 'Hund25391' => 'sun', 'Lalb_Chr07g0185371' => 'lal', 'Lalb_Chr07g0185381' => 'lal', 'Lalb_Chr12g0204011' => 'lal', 'Lalb_Chr13g0301671' => 'lal', 'Lalb_Chr14g0362851' => 'lal', 'Lalb_Chr24g0403581' => 'lal', 'Lj1g0000233' => 'lja', 'Lj2g0018120' => 'lja', 'Lj3C621T0' => 'lonja', 'Lj3P1059T14' => 'lonja', 'Lj3P611T9' => 'lonja', 'Lj3P614T13' => 'lonja', 'Lj3P615T5' => 'lonja', 'Lj4g0012315' => 'lja', 'Lj4g0026182' => 'lja', 'Lj6P813T16' => 'lonja', 'Lj7C427T7' => 'lonja', 'Lj7C427T8' => 'lonja', 'Lj7P600T41' => 'lonja', 'Lju41C42G17' => 'lonja', 'Lsat_1_v5_gn_0_47300' => 'lsa', 'Lsat_1_v5_gn_2_91280' => 'lsa', 'Lsat_1_v5_gn_3_30561' => 'lsa', 'Lsat_1_v5_gn_4_184321' => 'lsa', 'Lsat_1_v5_gn_4_4041' => 'lsa', 'Lsat_1_v5_gn_5_92000' => 'lsa', 'Lsat_1_v5_gn_8_152940' => 'lsa', 'Lsat_1_v5_gn_8_62401' => 'lsa', 'Manes.06G055900' => 'mes', 'Manes.12G022200' => 'mes', 'Manes.13G023300' => 'mes', 'Manes.14G115000' => 'mes', 'Manes.15G151700' => 'mes', 'Manes.17G111300' => 'mes', 'Mapoly0226s0009' => 'mpo', 'MBI02_g25363_MAGBIO' => 'mbi', 'MBI06_g00027_MAGBIO' => 'mbi', 'MBI10_g13034_MAGBIO' => 'mbi', 'MD09G1023400' => 'mdo', 'MD13G1100100' => 'mdo', 'MD15G1169200' => 'mdo', 'MD16G1101100' => 'mdo', 'MD17G1022900' => 'mdo', 'Medtr3g096150' => 'mtr', 'Medtr4g115070' => 'mtr', 'Medtr7g033325' => 'mtr', 'Medtr8g089840' => 'mtr', 'MELO3C010319.2' => 'cme', 'MELO3C011944.2' => 'cme', 'MELO3C021589.2' => 'cme', 'Migut.E00207' => 'egut', 'Migut.H00067' => 'egut', 'Migut.K00433' => 'egut', 'Migut.K00606' => 'egut', 'Migut.K01410' => 'egut', 'MSTRG.13347' => 'ama', 'MSTRG.24045' => 'ama', 'MSTRG.2428' => 'ama', 'MSTRG.26410' => 'ama', 'MSTRG.3139' => 'ama', 'MSTRG.3286' => 'ama', 'MSTRG.563' => 'ama', 'MSTRG.7941' => 'ama', 'Nitab4.5_0000028g0060' => 'nta', 'Nitab4.5_0000065g0260' => 'nta', 'Nitab4.5_0000112g0060' => 'nta', 'Nitab4.5_0000489g0120' => 'nta', 'Nitab4.5_0001776g0050' => 'nta', 'Nitab4.5_0001854g0010' => 'nta', 'Nitab4.5_0001860g0020' => 'nta', 'Nitab4.5_0004352g0010' => 'nta', 'Nitab4.5_0008716g0020' => 'nta', 'Nitab4.5_0008922g0010' => 'nta', 'Nn3g16693' => 'nnu', 'Nn4g22596' => 'nnu', 'Nn7g37639' => 'nnu', 'Oeu001701.1' => 'oeu', 'Oeu018149.1' => 'oeu', 'Oeu026220.1' => 'oeu', 'Oeu038635.1' => 'oeu', 'Oeu049176.1' => 'oeu', 'Oeu056706.1' => 'oeu', 'Oeu056937.1' => 'oeu', 'Oeu057540.1' => 'oeu', 'Os02g0594900' => 'osa', 'Os02g0595100' => 'osa', 'Os04g0477500' => 'osa', 'Os12g0611900' => 'osa', 'Peaxi162Scf00076g00020' => 'pax', 'Peaxi162Scf00128g00217' => 'pax', 'Peaxi162Scf00129g01640' => 'pax', 'Peaxi162Scf00669g00007' => 'pax', 'Peaxi162Scf00700g00421' => 'pax', 'Peaxi162Scf00801g00038' => 'pax', 'Peaxi162Scf00891g00025' => 'pax', 'PGR083G0909' => 'pgr', 'PGR119G1005' => 'pgr', 'PGR142G2236' => 'pgr', 'PGR142G3388' => 'pgr', 'PGSC0003DMG400004514' => 'stu', 'PGSC0003DMG400012635' => 'stu', 'PGSC0003DMG400015730' => 'stu', 'PGSC0003DMG400018611' => 'stu', 'PGSC0003DMG400030897' => 'stu', 'Phvul.001G254800' => 'pvu', 'Phvul.002G260100' => 'pvu', 'Phvul.003G167600' => 'pvu', 'Phvul.004G005100' => 'pvu', 'Potri.001G343600' => 'ptr', 'Potri.006G066700' => 'ptr', 'Potri.008G186000' => 'ptr', 'Potri.010G046900' => 'ptr', 'Potri.018G127900' => 'ptr', 'Pp3c20_17750' => 'ppa', 'Pp3c24_4380' => 'ppa', 'Prupe.1G245800' => 'ppe', 'Prupe.3G293400' => 'ppe', 'Prupe.7G247400' => 'ppe', 'Psat0s145g0120' => 'psa', 'Psat0s595g0040' => 'psa', 'Psat0s595g0120' => 'psa', 'Psat3g175040' => 'psa', 'Psat7g058120' => 'psa', 'PSO017G0428' => 'pso', 'PSO063G7510' => 'pso', 'PSO067G0046' => 'pso', 'PSO478G1073' => 'pso', 'PSO675G3677' => 'pso', 'PSO675G6558' => 'pso', 'PSO675G7520' => 'pso', 'PSO675G8959' => 'pso', 'QL02p074089' => 'qlo', 'QL02p089614' => 'qlo', 'QL03p057736' => 'qlo', 'RcHm_v2.0_Chr1g0364131' => 'rch', 'RcHm_v2.0_Chr2g0087801' => 'rch', 'RcHm_v2.0_Chr2g0087821' => 'rch', 'RcHm_v2.0_Chr2g0173231' => 'rch', 'RcHm_v2.0_Chr4g0433111' => 'rch', 'Rhsim03G0250300' => 'rsi', 'Rhsim08G0048400' => 'rsi', 'Rhsim10G0014800' => 'rsi', 'Rhsim12G0040100' => 'rsi', 'Rhsim12G0109700' => 'rsi', 'Sabra06G0049600' => 'sbr', 'Sabra08G0141000' => 'sbr', 'Sabra10G0021400' => 'sbr', 'Sabra16G0222900' => 'sbr', 'Sabra18G0108600' => 'sbr', 'SalBow1G0433' => 'sbo', 'SalBow1G2038' => 'sbo', 'SalBow1G5003' => 'sbo', 'SalBow7G1197' => 'sbo', 'SalBow8G3506' => 'sbo', 'Sc03g0007300' => 'sci', 'Sc11g0000950' => 'sci', 'Sc14g0008750' => 'sci', 'Sc18g0000420' => 'sci', 'Sed0006754' => 'sed', 'Sed0008741' => 'sed', 'Sed0017172' => 'sed', 'Sed0018925' => 'sed', 'Sed0023326' => 'sed', 'Sed0025909' => 'sed', 'SEGI_05333' => 'sgi', 'SEGI_10362' => 'sgi', 'SEGI_13380' => 'sgi', 'SEGI_24306' => 'sgi', 'SEGI_29077' => 'sgi', 'SEGI_29095' => 'sgi', 'SEGI_36534' => 'sgi', 'SEGI_37506' => 'sgi', 'SEGI_38321' => 'sgi', 'SGA_v2.0_scaffold307G48031' => 'sas', 'SGA_v2.0_scaffold47G17507' => 'sas', 'SGA_v2.0_scaffold63G21736' => 'sas', 'SGA_v2.0_scaffold87G27070' => 'sas', 'SHI17794' => 'shi', 'SHI28851' => 'shi', 'SMO165G0155' => 'smo', 'SMO340G0217' => 'smo', 'SMO367G1210' => 'smo', 'Solyc02g093430.3' => 'sly', 'Solyc05g013580.4' => 'sly', 'Solyc07g008030.3' => 'sly', 'Solyc12g035470.2' => 'sly', 'Sopen02g038020' => 'spe', 'Sopen05g008490' => 'spe', 'Sopen07g003910' => 'spe', 'Sopen12g015240' => 'spe', 'Sp1g11550' => 'spa', 'Sp2g16710' => 'spa', 'Sp3g00430' => 'spa', 'Sp3g26780' => 'spa', 'Sp5g22900' => 'spa', 'Sp6g29530' => 'spa', 'TAR371G0794' => 'tar', 'TAR374G0164' => 'tar', 'TAR622G0165' => 'tar', 'TAR626G0929' => 'tar', 'TAR629G2155' => 'tar', 'THA.LOC104805282' => 'tha', 'THA.LOC104805363' => 'tha', 'THA.LOC104808968' => 'tha', 'THA.LOC104821093' => 'tha', 'THA.LOC104823953' => 'tha', 'THA.LOC104825562' => 'tha', 'THA.LOC104825665' => 'tha', 'Thecc.02G261400' => 'tca', 'Thecc.04G019200' => 'tca', 'Thecc.09G130400' => 'tca', 'Thhalv10004374m.g' => 'esa', 'Thhalv10007850m.g' => 'esa', 'Thhalv10013782m.g' => 'esa', 'Thhalv10018686m.g' => 'esa', 'Thhalv10020899m.g' => 'esa', 'Thhalv10022755m.g' => 'esa', 'TPR.G23851' => 'tpr', 'TPR.G26500' => 'tpr', 'TPR.G27267' => 'tpr', 'TPR.G32001' => 'tpr', 'TPR.G6251' => 'tpr', 'TPR.G8167' => 'tpr', 'TWI12G1330' => 'twi', 'TWI18G1239' => 'twi', 'TWI34G0979' => 'twi', 'TWI36G0670' => 'twi', 'TWI36G0707' => 'twi', 'TWI56G0233' => 'twi', 'TWI75G1809' => 'twi', 'unitig_21.g20874' => 'ugi', 'unitig_26.g10343' => 'ugi', 'unitig_46.g18392' => 'ugi', 'unitig_52.g17178' => 'ugi', 'unitig_8.g2934' => 'ugi', 'vmacro01122' => 'vma', 'vmacro05875' => 'vma', 'vmacro06147' => 'vma', 'vmacro16191' => 'vma', 'vmacro18293' => 'vma', 'VMungo0251G3707' => 'vmu', 'VMungo0464G1521' => 'vmu', 'VMungo1215G0205' => 'vmu', 'VMungo1383G2484' => 'vmu', 'Zm00001eb079610' => 'zma', 'Zm00001eb135990' => 'zma', 'Zm00001eb183710' => 'zma', 'Zm00001eb246020' => 'zma' ), 'gf_id' => 'HOM05D001124', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001124' ), 'data_identifier' => 'HOM05D001124', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001124', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '548', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02520' => 'bna', 'A03p06630' => 'bna', 'A05p44460' => 'bna', 'A06p08710' => 'bna', 'A06p41090' => 'bna', 'A07p32320' => 'bna', 'A08p32520' => 'bna', 'A09p10360' => 'bna', 'A10p24080' => 'bna', 'Aa31LG11G15250' => 'aar', 'Aa31LG1G1800' => 'aar', 'Aa31LG2G5120' => 'aar', 'Aa31LG2G6070' => 'aar', 'Aa31LG5G10770' => 'aar', 'Aa31sc61G90' => 'aar', 'Actinidia01352' => 'ach', 'Actinidia05983' => 'ach', 'Actinidia08133' => 'ach', 'Actinidia15101' => 'ach', 'Actinidia26379' => 'ach', 'Actinidia35778' => 'ach', 'Actinidia36123' => 'ach', 'Actinidia37436' => 'ach', 'Actinidia38730' => 'ach', 'Ah.02g128210' => 'amhyb', 'Ah.03g132990' => 'amhyb', 'Ah.14g079410' => 'amhyb', 'AL1G24640' => 'aly', 'AL2G26680' => 'aly', 'AL3G10530' => 'aly', 'AL3G45230' => 'aly', 'AL5G15230' => 'aly', 'AL5G16960' => 'aly', 'AL6G25210' => 'aly', 'Aqoxy2G00441' => 'aox', 'Aqoxy3G01236' => 'aox', 'Aqoxy5G03746' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3RQ047' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C7GMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9C8JER' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MBL6KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YXCZ83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZANX40' => 'arhy', 'AT1G12990' => 'ath', 'AT1G67880' => 'ath', 'AT2G13290' => 'ath', 'AT3G01620' => 'ath', 'AT3G26445' => 'ath', 'AT3G27540' => 'ath', 'AT5G14480' => 'ath', 'ATR0824G026' => 'atr', 'ATR1098G019' => 'atr', 'Atru.chr11.2145' => 'acertr', 'Atru.chr2.3636' => 'acertr', 'Atru.chr2.3644' => 'acertr', 'Atru.chr6.2422' => 'acertr', 'Atru.chr7.1112' => 'acertr', 'AUR62005469' => 'cqu', 'AUR62011166' => 'cqu', 'AUR62013319' => 'cqu', 'AUR62024273' => 'cqu', 'AUR62028420' => 'cqu', 'AUR62041942' => 'cqu', 'BcaB01g04969' => 'bca', 'BcaB01g06371' => 'bca', 'BcaB02g11494' => 'bca', 'BcaB03g15382' => 'bca', 'BcaB08g36994' => 'bca', 'BcaC03g13477' => 'bca', 'BcaC03g13478' => 'bca', 'BcaC03g13480' => 'bca', 'BcaC03g13481' => 'bca', 'BcaC03g13486' => 'bca', 'BcaC04g19031' => 'bca', 'BcaC04g23085' => 'bca', 'BcaC05g25094' => 'bca', 'BcaC05g25096' => 'bca', 'BcaC05g25138' => 'bca', 'BcaC05g30416' => 'bca', 'BcaC05g30455' => 'bca', 'BcaC06g30979' => 'bca', 'BcaC06g33805' => 'bca', 'BcaC08g46021' => 'bca', 'BcaNung03154' => 'bca', 'BolC2t06623H' => 'bol', 'BolC2t06632H' => 'bol', 'BolC2t06635H' => 'bol', 'BolC2t06638H' => 'bol', 'BolC3t13266H' => 'bol', 'BolC5t29776H' => 'bol', 'BolC6t38912H' => 'bol', 'BolC7t44183H' => 'bol', 'BolC9t54123H' => 'bol', 'BolC9t59107H' => 'bol', 'BraA02t05221Z' => 'bra', 'BraA03t09996Z' => 'bra', 'BraA05t23210Z' => 'bra', 'BraA06t24068Z' => 'bra', 'BraA06t27032Z' => 'bra', 'BraA08t35176Z' => 'bra', 'BraA09t36680Z' => 'bra', 'BraA10t44471Z' => 'bra', 'C02p06760' => 'bna', 'C02p06890' => 'bna', 'C02p07010' => 'bna', 'C03p07660' => 'bna', 'C05p10300' => 'bna', 'C06p38150' => 'bna', 'C07p36650' => 'bna', 'C08p15770' => 'bna', 'C09p12300' => 'bna', 'C09p62700' => 'bna', 'C09p75040' => 'bna', 'CAN.G13.1' => 'can', 'CAN.G138.4' => 'can', 'CAN.G44.6' => 'can', 'CAN.G473.19' => 'can', 'CANSAT01G0835' => 'cansat', 'CANSAT11G0246' => 'cansat', 'CANSAT11G1766' => 'cansat', 'CANSAT64G1954' => 'cansat', 'CARHR013330' => 'chi', 'CARHR060530' => 'chi', 'CARHR075300' => 'chi', 'CARHR105120' => 'chi', 'CARHR148910' => 'chi', 'CARHR198830' => 'chi', 'Carub.0001s1275' => 'cru', 'Carub.0002s1437' => 'cru', 'Carub.0003s0044' => 'cru', 'Carub.0003s2787' => 'cru', 'Carub.0005s0597' => 'cru', 'Carub.0006s1266' => 'cru', 'Ca_06935_v3' => 'car', 'Ca_13559_v3' => 'car', 'Ca_16941_v3' => 'car', 'Ca_16960_v3' => 'car', 'Ca_17775_v3' => 'car', 'Ca_30464_v3' => 'car', 'Cc06_g08160' => 'ccan', 'Cc07_g01520' => 'ccan', 'Cc11_g15810' => 'ccan', 'CDE02G2840' => 'cde', 'CDE03G0093' => 'cde', 'CDE04G2127' => 'cde', 'CDE07G1857' => 'cde', 'CDE09G1246' => 'cde', 'Cfa003412' => 'cfa', 'Cfa007341' => 'cfa', 'Cfa009220' => 'cfa', 'Ciclev10008737m.g' => 'ccl', 'Ciclev10015565m.g' => 'ccl', 'Ciclev10031761m.g' => 'ccl', 'CiPaw.03G045300' => 'cil', 'CiPaw.03G247200' => 'cil', 'CiPaw.04G029500' => 'cil', 'CiPaw.04G174000' => 'cil', 'CiPaw.05G181200' => 'cil', 'CiPaw.06G067100' => 'cil', 'ClCG05G025800' => 'cla', 'ClCG06G011400' => 'cla', 'ClCG09G019360' => 'cla', 'COL.COLO4_04827' => 'col', 'COL.COLO4_29170' => 'col', 'COL.COLO4_35131' => 'col', 'COL.COLO4_35132' => 'col', 'Cpa.g.sc33.32' => 'cpa', 'Cpa.g.sc46.29' => 'cpa', 'Cpa.g.sc796.1' => 'cpa', 'CsaV3_1G030420' => 'csa', 'CsaV3_5G027050' => 'csa', 'CsaV3_5G031040' => 'csa', 'CsaV3_UNG023130' => 'csa', 'CSS0007726' => 'camsi', 'CSS0016433' => 'camsi', 'CSS0017656' => 'camsi', 'CSS0025364' => 'camsi', 'CSS0027582' => 'camsi', 'CSS0047288' => 'camsi', 'CSS0049950' => 'camsi', 'DCAR_003843' => 'dca', 'DCAR_007052' => 'dca', 'DCAR_020884' => 'dca', 'DCAR_021730' => 'dca', 'DCAR_024423' => 'dca', 'DCAR_026509' => 'dca', 'DCAR_031158' => 'dca', 'Dinv14728' => 'din', 'Dinv15219' => 'din', 'Dinv25728' => 'din', 'Dinv33428' => 'din', 'Dinv36489' => 'din', 'Dinv41486' => 'din', 'Duzib147G0469' => 'dzi', 'Duzib168G0060' => 'dzi', 'Duzib187G1215' => 'dzi', 'Duzib248G0692' => 'dzi', 'Duzib251G0767' => 'dzi', 'Duzib264G0446' => 'dzi', 'Duzib268G0691' => 'dzi', 'ECA232G4767' => 'eca', 'ECA233G2838' => 'eca', 'ECA234G0391' => 'eca', 'ECA234G0857' => 'eca', 'ECA236G1593' => 'eca', 'ECA238G0565' => 'eca', 'ECA246G1027' => 'eca', 'ECA246G3223' => 'eca', 'ECA246G3470' => 'eca', 'EL10Ac6g13829' => 'bvu', 'EL10Ac6g14093' => 'bvu', 'EL10Ac8g18707' => 'bvu', 'Eucgr.C01369' => 'egr', 'Eucgr.H02492' => 'egr', 'Eucgr.I01733' => 'egr', 'Eucgr.J02255' => 'egr', 'Eucgr.J02257' => 'egr', 'Eucgr.J02258' => 'egr', 'FAN02G1601' => 'fan', 'FAN03G1586' => 'fan', 'FAN03G2986' => 'fan', 'FAN05G4837' => 'fan', 'FAN06G0146' => 'fan', 'FAN07G0858' => 'fan', 'FAN09G3179' => 'fan', 'FAN10G0669' => 'fan', 'FAN12G2358' => 'fan', 'FAN14G4198' => 'fan', 'FAN14G5112' => 'fan', 'FAN17G0342' => 'fan', 'FAN19G0342' => 'fan', 'FAN19G0962' => 'fan', 'FAN19G1101' => 'fan', 'FAN19G1872' => 'fan', 'FAN22G0356' => 'fan', 'FAN23G0744' => 'fan', 'FAN23G1914' => 'fan', 'FAN26G0032' => 'fan', 'FAN28G0625' => 'fan', 'FvH4_1g02710' => 'fve', 'FvH4_1g02720' => 'fve', 'FvH4_4g25670' => 'fve', 'FvH4_6g51700' => 'fve', 'FvH4_7g20170' => 'fve', 'Glyma.05G175000' => 'gma', 'Glyma.08G132300' => 'gma', 'Glyma.11G243000' => 'gma', 'Glyma.13G158900' => 'gma', 'Glyma.17G112400' => 'gma', 'Glyma.18G014100' => 'gma', 'Glyma.19G003100' => 'gma', 'Glyma.19G056500' => 'gma', 'Gohir.A01G158900' => 'ghi', 'Gohir.A05G312600' => 'ghi', 'Gohir.A05G354900' => 'ghi', 'Gohir.A07G037200' => 'ghi', 'Gohir.A09G030000' => 'ghi', 'Gohir.A12G145200' => 'ghi', 'Gohir.D01G151500' => 'ghi', 'Gohir.D04G058300' => 'ghi', 'Gohir.D05G314100' => 'ghi', 'Gohir.D07G041400' => 'ghi', 'Gohir.D09G029700' => 'ghi', 'Gohir.D12G149700' => 'ghi', 'Gorai.001G043800' => 'gra', 'Gorai.002G187800' => 'gra', 'Gorai.006G034700' => 'gra', 'Gorai.008G161200' => 'gra', 'Gorai.009G335700' => 'gra', 'Gorai.012G065000' => 'gra', 'GSVIVG01000535001' => 'vvi', 'GSVIVG01015572001' => 'vvi', 'GSVIVG01032386001' => 'vvi', 'HanXRQChr05g0138531' => 'han', 'HanXRQChr06g0174391' => 'han', 'HanXRQChr07g0199021' => 'han', 'HanXRQChr08g0208211' => 'han', 'HanXRQChr09g0255471' => 'han', 'HanXRQChr10g0315791' => 'han', 'HanXRQChr12g0371991' => 'han', 'HanXRQChr15g0475251' => 'han', 'HanXRQChr17g0540001' => 'han', 'HanXRQChr17g0548631' => 'han', 'HanXRQChr17g0569561' => 'han', 'Haze_12256' => 'cav', 'Haze_14756' => 'cav', 'Haze_25528' => 'cav', 'Hma1.2p1_0079F.1_g041020' => 'hma', 'Hma1.2p1_0818F.1_g223260' => 'hma', 'Hma1.2p1_1747F.1_g300530' => 'hma', 'HPP92_004607' => 'vpl', 'HPP92_004608' => 'vpl', 'HPP92_006181' => 'vpl', 'HPP92_012192' => 'vpl', 'HPP92_015680' => 'vpl', 'HPP92_020249' => 'vpl', 'HPP92_021376' => 'vpl', 'HPP92_024275' => 'vpl', 'Hund06031' => 'sun', 'Hund25391' => 'sun', 'Lalb_Chr07g0185371' => 'lal', 'Lalb_Chr07g0185381' => 'lal', 'Lalb_Chr12g0204011' => 'lal', 'Lalb_Chr13g0301671' => 'lal', 'Lalb_Chr14g0362851' => 'lal', 'Lalb_Chr24g0403581' => 'lal', 'Lj1g0000233' => 'lja', 'Lj2g0018120' => 'lja', 'Lj3C621T0' => 'lonja', 'Lj3P1059T14' => 'lonja', 'Lj3P611T9' => 'lonja', 'Lj3P614T13' => 'lonja', 'Lj3P615T5' => 'lonja', 'Lj4g0012315' => 'lja', 'Lj4g0026182' => 'lja', 'Lj6P813T16' => 'lonja', 'Lj7C427T7' => 'lonja', 'Lj7C427T8' => 'lonja', 'Lj7P600T41' => 'lonja', 'Lju41C42G17' => 'lonja', 'Lsat_1_v5_gn_0_47300' => 'lsa', 'Lsat_1_v5_gn_2_91280' => 'lsa', 'Lsat_1_v5_gn_3_30561' => 'lsa', 'Lsat_1_v5_gn_4_184321' => 'lsa', 'Lsat_1_v5_gn_4_4041' => 'lsa', 'Lsat_1_v5_gn_5_92000' => 'lsa', 'Lsat_1_v5_gn_8_152940' => 'lsa', 'Lsat_1_v5_gn_8_62401' => 'lsa', 'Manes.06G055900' => 'mes', 'Manes.12G022200' => 'mes', 'Manes.13G023300' => 'mes', 'Manes.14G115000' => 'mes', 'Manes.15G151700' => 'mes', 'Manes.17G111300' => 'mes', 'Mapoly0226s0009' => 'mpo', 'MBI02_g25363_MAGBIO' => 'mbi', 'MBI06_g00027_MAGBIO' => 'mbi', 'MBI10_g13034_MAGBIO' => 'mbi', 'MD09G1023400' => 'mdo', 'MD13G1100100' => 'mdo', 'MD15G1169200' => 'mdo', 'MD16G1101100' => 'mdo', 'MD17G1022900' => 'mdo', 'Medtr3g096150' => 'mtr', 'Medtr4g115070' => 'mtr', 'Medtr7g033325' => 'mtr', 'Medtr8g089840' => 'mtr', 'MELO3C010319.2' => 'cme', 'MELO3C011944.2' => 'cme', 'MELO3C021589.2' => 'cme', 'Migut.E00207' => 'egut', 'Migut.H00067' => 'egut', 'Migut.K00433' => 'egut', 'Migut.K00606' => 'egut', 'Migut.K01410' => 'egut', 'MSTRG.13347' => 'ama', 'MSTRG.24045' => 'ama', 'MSTRG.2428' => 'ama', 'MSTRG.26410' => 'ama', 'MSTRG.3139' => 'ama', 'MSTRG.3286' => 'ama', 'MSTRG.563' => 'ama', 'MSTRG.7941' => 'ama', 'Nitab4.5_0000028g0060' => 'nta', 'Nitab4.5_0000065g0260' => 'nta', 'Nitab4.5_0000112g0060' => 'nta', 'Nitab4.5_0000489g0120' => 'nta', 'Nitab4.5_0001776g0050' => 'nta', 'Nitab4.5_0001854g0010' => 'nta', 'Nitab4.5_0001860g0020' => 'nta', 'Nitab4.5_0004352g0010' => 'nta', 'Nitab4.5_0008716g0020' => 'nta', 'Nitab4.5_0008922g0010' => 'nta', 'Nn3g16693' => 'nnu', 'Nn4g22596' => 'nnu', 'Nn7g37639' => 'nnu', 'Oeu001701.1' => 'oeu', 'Oeu018149.1' => 'oeu', 'Oeu026220.1' => 'oeu', 'Oeu038635.1' => 'oeu', 'Oeu049176.1' => 'oeu', 'Oeu056706.1' => 'oeu', 'Oeu056937.1' => 'oeu', 'Oeu057540.1' => 'oeu', 'Os02g0594900' => 'osa', 'Os02g0595100' => 'osa', 'Os04g0477500' => 'osa', 'Os12g0611900' => 'osa', 'Peaxi162Scf00076g00020' => 'pax', 'Peaxi162Scf00128g00217' => 'pax', 'Peaxi162Scf00129g01640' => 'pax', 'Peaxi162Scf00669g00007' => 'pax', 'Peaxi162Scf00700g00421' => 'pax', 'Peaxi162Scf00801g00038' => 'pax', 'Peaxi162Scf00891g00025' => 'pax', 'PGR083G0909' => 'pgr', 'PGR119G1005' => 'pgr', 'PGR142G2236' => 'pgr', 'PGR142G3388' => 'pgr', 'PGSC0003DMG400004514' => 'stu', 'PGSC0003DMG400012635' => 'stu', 'PGSC0003DMG400015730' => 'stu', 'PGSC0003DMG400018611' => 'stu', 'PGSC0003DMG400030897' => 'stu', 'Phvul.001G254800' => 'pvu', 'Phvul.002G260100' => 'pvu', 'Phvul.003G167600' => 'pvu', 'Phvul.004G005100' => 'pvu', 'Potri.001G343600' => 'ptr', 'Potri.006G066700' => 'ptr', 'Potri.008G186000' => 'ptr', 'Potri.010G046900' => 'ptr', 'Potri.018G127900' => 'ptr', 'Pp3c20_17750' => 'ppa', 'Pp3c24_4380' => 'ppa', 'Prupe.1G245800' => 'ppe', 'Prupe.3G293400' => 'ppe', 'Prupe.7G247400' => 'ppe', 'Psat0s145g0120' => 'psa', 'Psat0s595g0040' => 'psa', 'Psat0s595g0120' => 'psa', 'Psat3g175040' => 'psa', 'Psat7g058120' => 'psa', 'PSO017G0428' => 'pso', 'PSO063G7510' => 'pso', 'PSO067G0046' => 'pso', 'PSO478G1073' => 'pso', 'PSO675G3677' => 'pso', 'PSO675G6558' => 'pso', 'PSO675G7520' => 'pso', 'PSO675G8959' => 'pso', 'QL02p074089' => 'qlo', 'QL02p089614' => 'qlo', 'QL03p057736' => 'qlo', 'RcHm_v2.0_Chr1g0364131' => 'rch', 'RcHm_v2.0_Chr2g0087801' => 'rch', 'RcHm_v2.0_Chr2g0087821' => 'rch', 'RcHm_v2.0_Chr2g0173231' => 'rch', 'RcHm_v2.0_Chr4g0433111' => 'rch', 'Rhsim03G0250300' => 'rsi', 'Rhsim08G0048400' => 'rsi', 'Rhsim10G0014800' => 'rsi', 'Rhsim12G0040100' => 'rsi', 'Rhsim12G0109700' => 'rsi', 'Sabra06G0049600' => 'sbr', 'Sabra08G0141000' => 'sbr', 'Sabra10G0021400' => 'sbr', 'Sabra16G0222900' => 'sbr', 'Sabra18G0108600' => 'sbr', 'SalBow1G0433' => 'sbo', 'SalBow1G2038' => 'sbo', 'SalBow1G5003' => 'sbo', 'SalBow7G1197' => 'sbo', 'SalBow8G3506' => 'sbo', 'Sc03g0007300' => 'sci', 'Sc11g0000950' => 'sci', 'Sc14g0008750' => 'sci', 'Sc18g0000420' => 'sci', 'Sed0006754' => 'sed', 'Sed0008741' => 'sed', 'Sed0017172' => 'sed', 'Sed0018925' => 'sed', 'Sed0023326' => 'sed', 'Sed0025909' => 'sed', 'SEGI_05333' => 'sgi', 'SEGI_10362' => 'sgi', 'SEGI_13380' => 'sgi', 'SEGI_24306' => 'sgi', 'SEGI_29077' => 'sgi', 'SEGI_29095' => 'sgi', 'SEGI_36534' => 'sgi', 'SEGI_37506' => 'sgi', 'SEGI_38321' => 'sgi', 'SGA_v2.0_scaffold307G48031' => 'sas', 'SGA_v2.0_scaffold47G17507' => 'sas', 'SGA_v2.0_scaffold63G21736' => 'sas', 'SGA_v2.0_scaffold87G27070' => 'sas', 'SHI17794' => 'shi', 'SHI28851' => 'shi', 'SMO165G0155' => 'smo', 'SMO340G0217' => 'smo', 'SMO367G1210' => 'smo', 'Solyc02g093430.3' => 'sly', 'Solyc05g013580.4' => 'sly', 'Solyc07g008030.3' => 'sly', 'Solyc12g035470.2' => 'sly', 'Sopen02g038020' => 'spe', 'Sopen05g008490' => 'spe', 'Sopen07g003910' => 'spe', 'Sopen12g015240' => 'spe', 'Sp1g11550' => 'spa', 'Sp2g16710' => 'spa', 'Sp3g00430' => 'spa', 'Sp3g26780' => 'spa', 'Sp5g22900' => 'spa', 'Sp6g29530' => 'spa', 'TAR371G0794' => 'tar', 'TAR374G0164' => 'tar', 'TAR622G0165' => 'tar', 'TAR626G0929' => 'tar', 'TAR629G2155' => 'tar', 'THA.LOC104805282' => 'tha', 'THA.LOC104805363' => 'tha', 'THA.LOC104808968' => 'tha', 'THA.LOC104821093' => 'tha', 'THA.LOC104823953' => 'tha', 'THA.LOC104825562' => 'tha', 'THA.LOC104825665' => 'tha', 'Thecc.02G261400' => 'tca', 'Thecc.04G019200' => 'tca', 'Thecc.09G130400' => 'tca', 'Thhalv10004374m.g' => 'esa', 'Thhalv10007850m.g' => 'esa', 'Thhalv10013782m.g' => 'esa', 'Thhalv10018686m.g' => 'esa', 'Thhalv10020899m.g' => 'esa', 'Thhalv10022755m.g' => 'esa', 'TPR.G23851' => 'tpr', 'TPR.G26500' => 'tpr', 'TPR.G27267' => 'tpr', 'TPR.G32001' => 'tpr', 'TPR.G6251' => 'tpr', 'TPR.G8167' => 'tpr', 'TWI12G1330' => 'twi', 'TWI18G1239' => 'twi', 'TWI34G0979' => 'twi', 'TWI36G0670' => 'twi', 'TWI36G0707' => 'twi', 'TWI56G0233' => 'twi', 'TWI75G1809' => 'twi', 'unitig_21.g20874' => 'ugi', 'unitig_26.g10343' => 'ugi', 'unitig_46.g18392' => 'ugi', 'unitig_52.g17178' => 'ugi', 'unitig_8.g2934' => 'ugi', 'vmacro01122' => 'vma', 'vmacro05875' => 'vma', 'vmacro06147' => 'vma', 'vmacro16191' => 'vma', 'vmacro18293' => 'vma', 'VMungo0251G3707' => 'vmu', 'VMungo0464G1521' => 'vmu', 'VMungo1215G0205' => 'vmu', 'VMungo1383G2484' => 'vmu', 'Zm00001eb079610' => 'zma', 'Zm00001eb135990' => 'zma', 'Zm00001eb183710' => 'zma', 'Zm00001eb246020' => 'zma' ) $gf_id = 'HOM05D001124' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001124' ) $data_identifier = 'HOM05D001124' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 6, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 7, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 21, 'bol' => (int) 10, 'bra' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 6, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 9, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 21, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 8, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 10, 'lsa' => (int) 8, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 8, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 9, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb246020' $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' => 'HOM05D001124', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '548', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02520' => 'bna', 'A03p06630' => 'bna', 'A05p44460' => 'bna', 'A06p08710' => 'bna', 'A06p41090' => 'bna', 'A07p32320' => 'bna', 'A08p32520' => 'bna', 'A09p10360' => 'bna', 'A10p24080' => 'bna', 'Aa31LG11G15250' => 'aar', 'Aa31LG1G1800' => 'aar', 'Aa31LG2G5120' => 'aar', 'Aa31LG2G6070' => 'aar', 'Aa31LG5G10770' => 'aar', 'Aa31sc61G90' => 'aar', 'Actinidia01352' => 'ach', 'Actinidia05983' => 'ach', 'Actinidia08133' => 'ach', 'Actinidia15101' => 'ach', 'Actinidia26379' => 'ach', 'Actinidia35778' => 'ach', 'Actinidia36123' => 'ach', 'Actinidia37436' => 'ach', 'Actinidia38730' => 'ach', 'Ah.02g128210' => 'amhyb', 'Ah.03g132990' => 'amhyb', 'Ah.14g079410' => 'amhyb', 'AL1G24640' => 'aly', 'AL2G26680' => 'aly', 'AL3G10530' => 'aly', 'AL3G45230' => 'aly', 'AL5G15230' => 'aly', 'AL5G16960' => 'aly', 'AL6G25210' => 'aly', 'Aqoxy2G00441' => 'aox', 'Aqoxy3G01236' => 'aox', 'Aqoxy5G03746' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3RQ047' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C7GMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9C8JER' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MBL6KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YXCZ83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZANX40' => 'arhy', 'AT1G12990' => 'ath', 'AT1G67880' => 'ath', 'AT2G13290' => 'ath', 'AT3G01620' => 'ath', 'AT3G26445' => 'ath', 'AT3G27540' => 'ath', 'AT5G14480' => 'ath', 'ATR0824G026' => 'atr', 'ATR1098G019' => 'atr', 'Atru.chr11.2145' => 'acertr', 'Atru.chr2.3636' => 'acertr', 'Atru.chr2.3644' => 'acertr', 'Atru.chr6.2422' => 'acertr', 'Atru.chr7.1112' => 'acertr', 'AUR62005469' => 'cqu', 'AUR62011166' => 'cqu', 'AUR62013319' => 'cqu', 'AUR62024273' => 'cqu', 'AUR62028420' => 'cqu', 'AUR62041942' => 'cqu', 'BcaB01g04969' => 'bca', 'BcaB01g06371' => 'bca', 'BcaB02g11494' => 'bca', 'BcaB03g15382' => 'bca', 'BcaB08g36994' => 'bca', 'BcaC03g13477' => 'bca', 'BcaC03g13478' => 'bca', 'BcaC03g13480' => 'bca', 'BcaC03g13481' => 'bca', 'BcaC03g13486' => 'bca', 'BcaC04g19031' => 'bca', 'BcaC04g23085' => 'bca', 'BcaC05g25094' => 'bca', 'BcaC05g25096' => 'bca', 'BcaC05g25138' => 'bca', 'BcaC05g30416' => 'bca', 'BcaC05g30455' => 'bca', 'BcaC06g30979' => 'bca', 'BcaC06g33805' => 'bca', 'BcaC08g46021' => 'bca', 'BcaNung03154' => 'bca', 'BolC2t06623H' => 'bol', 'BolC2t06632H' => 'bol', 'BolC2t06635H' => 'bol', 'BolC2t06638H' => 'bol', 'BolC3t13266H' => 'bol', 'BolC5t29776H' => 'bol', 'BolC6t38912H' => 'bol', 'BolC7t44183H' => 'bol', 'BolC9t54123H' => 'bol', 'BolC9t59107H' => 'bol', 'BraA02t05221Z' => 'bra', 'BraA03t09996Z' => 'bra', 'BraA05t23210Z' => 'bra', 'BraA06t24068Z' => 'bra', 'BraA06t27032Z' => 'bra', 'BraA08t35176Z' => 'bra', 'BraA09t36680Z' => 'bra', 'BraA10t44471Z' => 'bra', 'C02p06760' => 'bna', 'C02p06890' => 'bna', 'C02p07010' => 'bna', 'C03p07660' => 'bna', 'C05p10300' => 'bna', 'C06p38150' => 'bna', 'C07p36650' => 'bna', 'C08p15770' => 'bna', 'C09p12300' => 'bna', 'C09p62700' => 'bna', 'C09p75040' => 'bna', 'CAN.G13.1' => 'can', 'CAN.G138.4' => 'can', 'CAN.G44.6' => 'can', 'CAN.G473.19' => 'can', 'CANSAT01G0835' => 'cansat', 'CANSAT11G0246' => 'cansat', 'CANSAT11G1766' => 'cansat', 'CANSAT64G1954' => 'cansat', 'CARHR013330' => 'chi', 'CARHR060530' => 'chi', 'CARHR075300' => 'chi', 'CARHR105120' => 'chi', 'CARHR148910' => 'chi', 'CARHR198830' => 'chi', 'Carub.0001s1275' => 'cru', 'Carub.0002s1437' => 'cru', 'Carub.0003s0044' => 'cru', 'Carub.0003s2787' => 'cru', 'Carub.0005s0597' => 'cru', 'Carub.0006s1266' => 'cru', 'Ca_06935_v3' => 'car', 'Ca_13559_v3' => 'car', 'Ca_16941_v3' => 'car', 'Ca_16960_v3' => 'car', 'Ca_17775_v3' => 'car', 'Ca_30464_v3' => 'car', 'Cc06_g08160' => 'ccan', 'Cc07_g01520' => 'ccan', 'Cc11_g15810' => 'ccan', 'CDE02G2840' => 'cde', 'CDE03G0093' => 'cde', 'CDE04G2127' => 'cde', 'CDE07G1857' => 'cde', 'CDE09G1246' => 'cde', 'Cfa003412' => 'cfa', 'Cfa007341' => 'cfa', 'Cfa009220' => 'cfa', 'Ciclev10008737m.g' => 'ccl', 'Ciclev10015565m.g' => 'ccl', 'Ciclev10031761m.g' => 'ccl', 'CiPaw.03G045300' => 'cil', 'CiPaw.03G247200' => 'cil', 'CiPaw.04G029500' => 'cil', 'CiPaw.04G174000' => 'cil', 'CiPaw.05G181200' => 'cil', 'CiPaw.06G067100' => 'cil', 'ClCG05G025800' => 'cla', 'ClCG06G011400' => 'cla', 'ClCG09G019360' => 'cla', 'COL.COLO4_04827' => 'col', 'COL.COLO4_29170' => 'col', 'COL.COLO4_35131' => 'col', 'COL.COLO4_35132' => 'col', 'Cpa.g.sc33.32' => 'cpa', 'Cpa.g.sc46.29' => 'cpa', 'Cpa.g.sc796.1' => 'cpa', 'CsaV3_1G030420' => 'csa', 'CsaV3_5G027050' => 'csa', 'CsaV3_5G031040' => 'csa', 'CsaV3_UNG023130' => 'csa', 'CSS0007726' => 'camsi', 'CSS0016433' => 'camsi', 'CSS0017656' => 'camsi', 'CSS0025364' => 'camsi', 'CSS0027582' => 'camsi', 'CSS0047288' => 'camsi', 'CSS0049950' => 'camsi', 'DCAR_003843' => 'dca', 'DCAR_007052' => 'dca', 'DCAR_020884' => 'dca', 'DCAR_021730' => 'dca', 'DCAR_024423' => 'dca', 'DCAR_026509' => 'dca', 'DCAR_031158' => 'dca', 'Dinv14728' => 'din', 'Dinv15219' => 'din', 'Dinv25728' => 'din', 'Dinv33428' => 'din', 'Dinv36489' => 'din', 'Dinv41486' => 'din', 'Duzib147G0469' => 'dzi', 'Duzib168G0060' => 'dzi', 'Duzib187G1215' => 'dzi', 'Duzib248G0692' => 'dzi', 'Duzib251G0767' => 'dzi', 'Duzib264G0446' => 'dzi', 'Duzib268G0691' => 'dzi', 'ECA232G4767' => 'eca', 'ECA233G2838' => 'eca', 'ECA234G0391' => 'eca', 'ECA234G0857' => 'eca', 'ECA236G1593' => 'eca', 'ECA238G0565' => 'eca', 'ECA246G1027' => 'eca', 'ECA246G3223' => 'eca', 'ECA246G3470' => 'eca', 'EL10Ac6g13829' => 'bvu', 'EL10Ac6g14093' => 'bvu', 'EL10Ac8g18707' => 'bvu', 'Eucgr.C01369' => 'egr', 'Eucgr.H02492' => 'egr', 'Eucgr.I01733' => 'egr', 'Eucgr.J02255' => 'egr', 'Eucgr.J02257' => 'egr', 'Eucgr.J02258' => 'egr', 'FAN02G1601' => 'fan', 'FAN03G1586' => 'fan', 'FAN03G2986' => 'fan', 'FAN05G4837' => 'fan', 'FAN06G0146' => 'fan', 'FAN07G0858' => 'fan', 'FAN09G3179' => 'fan', 'FAN10G0669' => 'fan', 'FAN12G2358' => 'fan', 'FAN14G4198' => 'fan', 'FAN14G5112' => 'fan', 'FAN17G0342' => 'fan', 'FAN19G0342' => 'fan', 'FAN19G0962' => 'fan', 'FAN19G1101' => 'fan', 'FAN19G1872' => 'fan', 'FAN22G0356' => 'fan', 'FAN23G0744' => 'fan', 'FAN23G1914' => 'fan', 'FAN26G0032' => 'fan', 'FAN28G0625' => 'fan', 'FvH4_1g02710' => 'fve', 'FvH4_1g02720' => 'fve', 'FvH4_4g25670' => 'fve', 'FvH4_6g51700' => 'fve', 'FvH4_7g20170' => 'fve', 'Glyma.05G175000' => 'gma', 'Glyma.08G132300' => 'gma', 'Glyma.11G243000' => 'gma', 'Glyma.13G158900' => 'gma', 'Glyma.17G112400' => 'gma', 'Glyma.18G014100' => 'gma', 'Glyma.19G003100' => 'gma', 'Glyma.19G056500' => 'gma', 'Gohir.A01G158900' => 'ghi', 'Gohir.A05G312600' => 'ghi', 'Gohir.A05G354900' => 'ghi', 'Gohir.A07G037200' => 'ghi', 'Gohir.A09G030000' => 'ghi', 'Gohir.A12G145200' => 'ghi', 'Gohir.D01G151500' => 'ghi', 'Gohir.D04G058300' => 'ghi', 'Gohir.D05G314100' => 'ghi', 'Gohir.D07G041400' => 'ghi', 'Gohir.D09G029700' => 'ghi', 'Gohir.D12G149700' => 'ghi', 'Gorai.001G043800' => 'gra', 'Gorai.002G187800' => 'gra', 'Gorai.006G034700' => 'gra', 'Gorai.008G161200' => 'gra', 'Gorai.009G335700' => 'gra', 'Gorai.012G065000' => 'gra', 'GSVIVG01000535001' => 'vvi', 'GSVIVG01015572001' => 'vvi', 'GSVIVG01032386001' => 'vvi', 'HanXRQChr05g0138531' => 'han', 'HanXRQChr06g0174391' => 'han', 'HanXRQChr07g0199021' => 'han', 'HanXRQChr08g0208211' => 'han', 'HanXRQChr09g0255471' => 'han', 'HanXRQChr10g0315791' => 'han', 'HanXRQChr12g0371991' => 'han', 'HanXRQChr15g0475251' => 'han', 'HanXRQChr17g0540001' => 'han', 'HanXRQChr17g0548631' => 'han', 'HanXRQChr17g0569561' => 'han', 'Haze_12256' => 'cav', 'Haze_14756' => 'cav', 'Haze_25528' => 'cav', 'Hma1.2p1_0079F.1_g041020' => 'hma', 'Hma1.2p1_0818F.1_g223260' => 'hma', 'Hma1.2p1_1747F.1_g300530' => 'hma', 'HPP92_004607' => 'vpl', 'HPP92_004608' => 'vpl', 'HPP92_006181' => 'vpl', 'HPP92_012192' => 'vpl', 'HPP92_015680' => 'vpl', 'HPP92_020249' => 'vpl', 'HPP92_021376' => 'vpl', 'HPP92_024275' => 'vpl', 'Hund06031' => 'sun', 'Hund25391' => 'sun', 'Lalb_Chr07g0185371' => 'lal', 'Lalb_Chr07g0185381' => 'lal', 'Lalb_Chr12g0204011' => 'lal', 'Lalb_Chr13g0301671' => 'lal', 'Lalb_Chr14g0362851' => 'lal', 'Lalb_Chr24g0403581' => 'lal', 'Lj1g0000233' => 'lja', 'Lj2g0018120' => 'lja', 'Lj3C621T0' => 'lonja', 'Lj3P1059T14' => 'lonja', 'Lj3P611T9' => 'lonja', 'Lj3P614T13' => 'lonja', 'Lj3P615T5' => 'lonja', 'Lj4g0012315' => 'lja', 'Lj4g0026182' => 'lja', 'Lj6P813T16' => 'lonja', 'Lj7C427T7' => 'lonja', 'Lj7C427T8' => 'lonja', 'Lj7P600T41' => 'lonja', 'Lju41C42G17' => 'lonja', 'Lsat_1_v5_gn_0_47300' => 'lsa', 'Lsat_1_v5_gn_2_91280' => 'lsa', 'Lsat_1_v5_gn_3_30561' => 'lsa', 'Lsat_1_v5_gn_4_184321' => 'lsa', 'Lsat_1_v5_gn_4_4041' => 'lsa', 'Lsat_1_v5_gn_5_92000' => 'lsa', 'Lsat_1_v5_gn_8_152940' => 'lsa', 'Lsat_1_v5_gn_8_62401' => 'lsa', 'Manes.06G055900' => 'mes', 'Manes.12G022200' => 'mes', 'Manes.13G023300' => 'mes', 'Manes.14G115000' => 'mes', 'Manes.15G151700' => 'mes', 'Manes.17G111300' => 'mes', 'Mapoly0226s0009' => 'mpo', 'MBI02_g25363_MAGBIO' => 'mbi', 'MBI06_g00027_MAGBIO' => 'mbi', 'MBI10_g13034_MAGBIO' => 'mbi', 'MD09G1023400' => 'mdo', 'MD13G1100100' => 'mdo', 'MD15G1169200' => 'mdo', 'MD16G1101100' => 'mdo', 'MD17G1022900' => 'mdo', 'Medtr3g096150' => 'mtr', 'Medtr4g115070' => 'mtr', 'Medtr7g033325' => 'mtr', 'Medtr8g089840' => 'mtr', 'MELO3C010319.2' => 'cme', 'MELO3C011944.2' => 'cme', 'MELO3C021589.2' => 'cme', 'Migut.E00207' => 'egut', 'Migut.H00067' => 'egut', 'Migut.K00433' => 'egut', 'Migut.K00606' => 'egut', 'Migut.K01410' => 'egut', 'MSTRG.13347' => 'ama', 'MSTRG.24045' => 'ama', 'MSTRG.2428' => 'ama', 'MSTRG.26410' => 'ama', 'MSTRG.3139' => 'ama', 'MSTRG.3286' => 'ama', 'MSTRG.563' => 'ama', 'MSTRG.7941' => 'ama', 'Nitab4.5_0000028g0060' => 'nta', 'Nitab4.5_0000065g0260' => 'nta', 'Nitab4.5_0000112g0060' => 'nta', 'Nitab4.5_0000489g0120' => 'nta', 'Nitab4.5_0001776g0050' => 'nta', 'Nitab4.5_0001854g0010' => 'nta', 'Nitab4.5_0001860g0020' => 'nta', 'Nitab4.5_0004352g0010' => 'nta', 'Nitab4.5_0008716g0020' => 'nta', 'Nitab4.5_0008922g0010' => 'nta', 'Nn3g16693' => 'nnu', 'Nn4g22596' => 'nnu', 'Nn7g37639' => 'nnu', 'Oeu001701.1' => 'oeu', 'Oeu018149.1' => 'oeu', 'Oeu026220.1' => 'oeu', 'Oeu038635.1' => 'oeu', 'Oeu049176.1' => 'oeu', 'Oeu056706.1' => 'oeu', 'Oeu056937.1' => 'oeu', 'Oeu057540.1' => 'oeu', 'Os02g0594900' => 'osa', 'Os02g0595100' => 'osa', 'Os04g0477500' => 'osa', 'Os12g0611900' => 'osa', 'Peaxi162Scf00076g00020' => 'pax', 'Peaxi162Scf00128g00217' => 'pax', 'Peaxi162Scf00129g01640' => 'pax', 'Peaxi162Scf00669g00007' => 'pax', 'Peaxi162Scf00700g00421' => 'pax', 'Peaxi162Scf00801g00038' => 'pax', 'Peaxi162Scf00891g00025' => 'pax', 'PGR083G0909' => 'pgr', 'PGR119G1005' => 'pgr', 'PGR142G2236' => 'pgr', 'PGR142G3388' => 'pgr', 'PGSC0003DMG400004514' => 'stu', 'PGSC0003DMG400012635' => 'stu', 'PGSC0003DMG400015730' => 'stu', 'PGSC0003DMG400018611' => 'stu', 'PGSC0003DMG400030897' => 'stu', 'Phvul.001G254800' => 'pvu', 'Phvul.002G260100' => 'pvu', 'Phvul.003G167600' => 'pvu', 'Phvul.004G005100' => 'pvu', 'Potri.001G343600' => 'ptr', 'Potri.006G066700' => 'ptr', 'Potri.008G186000' => 'ptr', 'Potri.010G046900' => 'ptr', 'Potri.018G127900' => 'ptr', 'Pp3c20_17750' => 'ppa', 'Pp3c24_4380' => 'ppa', 'Prupe.1G245800' => 'ppe', 'Prupe.3G293400' => 'ppe', 'Prupe.7G247400' => 'ppe', 'Psat0s145g0120' => 'psa', 'Psat0s595g0040' => 'psa', 'Psat0s595g0120' => 'psa', 'Psat3g175040' => 'psa', 'Psat7g058120' => 'psa', 'PSO017G0428' => 'pso', 'PSO063G7510' => 'pso', 'PSO067G0046' => 'pso', 'PSO478G1073' => 'pso', 'PSO675G3677' => 'pso', 'PSO675G6558' => 'pso', 'PSO675G7520' => 'pso', 'PSO675G8959' => 'pso', 'QL02p074089' => 'qlo', 'QL02p089614' => 'qlo', 'QL03p057736' => 'qlo', 'RcHm_v2.0_Chr1g0364131' => 'rch', 'RcHm_v2.0_Chr2g0087801' => 'rch', 'RcHm_v2.0_Chr2g0087821' => 'rch', 'RcHm_v2.0_Chr2g0173231' => 'rch', 'RcHm_v2.0_Chr4g0433111' => 'rch', 'Rhsim03G0250300' => 'rsi', 'Rhsim08G0048400' => 'rsi', 'Rhsim10G0014800' => 'rsi', 'Rhsim12G0040100' => 'rsi', 'Rhsim12G0109700' => 'rsi', 'Sabra06G0049600' => 'sbr', 'Sabra08G0141000' => 'sbr', 'Sabra10G0021400' => 'sbr', 'Sabra16G0222900' => 'sbr', 'Sabra18G0108600' => 'sbr', 'SalBow1G0433' => 'sbo', 'SalBow1G2038' => 'sbo', 'SalBow1G5003' => 'sbo', 'SalBow7G1197' => 'sbo', 'SalBow8G3506' => 'sbo', 'Sc03g0007300' => 'sci', 'Sc11g0000950' => 'sci', 'Sc14g0008750' => 'sci', 'Sc18g0000420' => 'sci', 'Sed0006754' => 'sed', 'Sed0008741' => 'sed', 'Sed0017172' => 'sed', 'Sed0018925' => 'sed', 'Sed0023326' => 'sed', 'Sed0025909' => 'sed', 'SEGI_05333' => 'sgi', 'SEGI_10362' => 'sgi', 'SEGI_13380' => 'sgi', 'SEGI_24306' => 'sgi', 'SEGI_29077' => 'sgi', 'SEGI_29095' => 'sgi', 'SEGI_36534' => 'sgi', 'SEGI_37506' => 'sgi', 'SEGI_38321' => 'sgi', 'SGA_v2.0_scaffold307G48031' => 'sas', 'SGA_v2.0_scaffold47G17507' => 'sas', 'SGA_v2.0_scaffold63G21736' => 'sas', 'SGA_v2.0_scaffold87G27070' => 'sas', 'SHI17794' => 'shi', 'SHI28851' => 'shi', 'SMO165G0155' => 'smo', 'SMO340G0217' => 'smo', 'SMO367G1210' => 'smo', 'Solyc02g093430.3' => 'sly', 'Solyc05g013580.4' => 'sly', 'Solyc07g008030.3' => 'sly', 'Solyc12g035470.2' => 'sly', 'Sopen02g038020' => 'spe', 'Sopen05g008490' => 'spe', 'Sopen07g003910' => 'spe', 'Sopen12g015240' => 'spe', 'Sp1g11550' => 'spa', 'Sp2g16710' => 'spa', 'Sp3g00430' => 'spa', 'Sp3g26780' => 'spa', 'Sp5g22900' => 'spa', 'Sp6g29530' => 'spa', 'TAR371G0794' => 'tar', 'TAR374G0164' => 'tar', 'TAR622G0165' => 'tar', 'TAR626G0929' => 'tar', 'TAR629G2155' => 'tar', 'THA.LOC104805282' => 'tha', 'THA.LOC104805363' => 'tha', 'THA.LOC104808968' => 'tha', 'THA.LOC104821093' => 'tha', 'THA.LOC104823953' => 'tha', 'THA.LOC104825562' => 'tha', 'THA.LOC104825665' => 'tha', 'Thecc.02G261400' => 'tca', 'Thecc.04G019200' => 'tca', 'Thecc.09G130400' => 'tca', 'Thhalv10004374m.g' => 'esa', 'Thhalv10007850m.g' => 'esa', 'Thhalv10013782m.g' => 'esa', 'Thhalv10018686m.g' => 'esa', 'Thhalv10020899m.g' => 'esa', 'Thhalv10022755m.g' => 'esa', 'TPR.G23851' => 'tpr', 'TPR.G26500' => 'tpr', 'TPR.G27267' => 'tpr', 'TPR.G32001' => 'tpr', 'TPR.G6251' => 'tpr', 'TPR.G8167' => 'tpr', 'TWI12G1330' => 'twi', 'TWI18G1239' => 'twi', 'TWI34G0979' => 'twi', 'TWI36G0670' => 'twi', 'TWI36G0707' => 'twi', 'TWI56G0233' => 'twi', 'TWI75G1809' => 'twi', 'unitig_21.g20874' => 'ugi', 'unitig_26.g10343' => 'ugi', 'unitig_46.g18392' => 'ugi', 'unitig_52.g17178' => 'ugi', 'unitig_8.g2934' => 'ugi', 'vmacro01122' => 'vma', 'vmacro05875' => 'vma', 'vmacro06147' => 'vma', 'vmacro16191' => 'vma', 'vmacro18293' => 'vma', 'VMungo0251G3707' => 'vmu', 'VMungo0464G1521' => 'vmu', 'VMungo1215G0205' => 'vmu', 'VMungo1383G2484' => 'vmu', 'Zm00001eb079610' => 'zma', 'Zm00001eb135990' => 'zma', 'Zm00001eb183710' => 'zma', 'Zm00001eb246020' => 'zma' ), 'gf_id' => 'HOM05D001124', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001124' ), 'data_identifier' => 'HOM05D001124', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001124', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '548', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02520' => 'bna', 'A03p06630' => 'bna', 'A05p44460' => 'bna', 'A06p08710' => 'bna', 'A06p41090' => 'bna', 'A07p32320' => 'bna', 'A08p32520' => 'bna', 'A09p10360' => 'bna', 'A10p24080' => 'bna', 'Aa31LG11G15250' => 'aar', 'Aa31LG1G1800' => 'aar', 'Aa31LG2G5120' => 'aar', 'Aa31LG2G6070' => 'aar', 'Aa31LG5G10770' => 'aar', 'Aa31sc61G90' => 'aar', 'Actinidia01352' => 'ach', 'Actinidia05983' => 'ach', 'Actinidia08133' => 'ach', 'Actinidia15101' => 'ach', 'Actinidia26379' => 'ach', 'Actinidia35778' => 'ach', 'Actinidia36123' => 'ach', 'Actinidia37436' => 'ach', 'Actinidia38730' => 'ach', 'Ah.02g128210' => 'amhyb', 'Ah.03g132990' => 'amhyb', 'Ah.14g079410' => 'amhyb', 'AL1G24640' => 'aly', 'AL2G26680' => 'aly', 'AL3G10530' => 'aly', 'AL3G45230' => 'aly', 'AL5G15230' => 'aly', 'AL5G16960' => 'aly', 'AL6G25210' => 'aly', 'Aqoxy2G00441' => 'aox', 'Aqoxy3G01236' => 'aox', 'Aqoxy5G03746' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3RQ047' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C7GMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9C8JER' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MBL6KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YXCZ83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZANX40' => 'arhy', 'AT1G12990' => 'ath', 'AT1G67880' => 'ath', 'AT2G13290' => 'ath', 'AT3G01620' => 'ath', 'AT3G26445' => 'ath', 'AT3G27540' => 'ath', 'AT5G14480' => 'ath', 'ATR0824G026' => 'atr', 'ATR1098G019' => 'atr', 'Atru.chr11.2145' => 'acertr', 'Atru.chr2.3636' => 'acertr', 'Atru.chr2.3644' => 'acertr', 'Atru.chr6.2422' => 'acertr', 'Atru.chr7.1112' => 'acertr', 'AUR62005469' => 'cqu', 'AUR62011166' => 'cqu', 'AUR62013319' => 'cqu', 'AUR62024273' => 'cqu', 'AUR62028420' => 'cqu', 'AUR62041942' => 'cqu', 'BcaB01g04969' => 'bca', 'BcaB01g06371' => 'bca', 'BcaB02g11494' => 'bca', 'BcaB03g15382' => 'bca', 'BcaB08g36994' => 'bca', 'BcaC03g13477' => 'bca', 'BcaC03g13478' => 'bca', 'BcaC03g13480' => 'bca', 'BcaC03g13481' => 'bca', 'BcaC03g13486' => 'bca', 'BcaC04g19031' => 'bca', 'BcaC04g23085' => 'bca', 'BcaC05g25094' => 'bca', 'BcaC05g25096' => 'bca', 'BcaC05g25138' => 'bca', 'BcaC05g30416' => 'bca', 'BcaC05g30455' => 'bca', 'BcaC06g30979' => 'bca', 'BcaC06g33805' => 'bca', 'BcaC08g46021' => 'bca', 'BcaNung03154' => 'bca', 'BolC2t06623H' => 'bol', 'BolC2t06632H' => 'bol', 'BolC2t06635H' => 'bol', 'BolC2t06638H' => 'bol', 'BolC3t13266H' => 'bol', 'BolC5t29776H' => 'bol', 'BolC6t38912H' => 'bol', 'BolC7t44183H' => 'bol', 'BolC9t54123H' => 'bol', 'BolC9t59107H' => 'bol', 'BraA02t05221Z' => 'bra', 'BraA03t09996Z' => 'bra', 'BraA05t23210Z' => 'bra', 'BraA06t24068Z' => 'bra', 'BraA06t27032Z' => 'bra', 'BraA08t35176Z' => 'bra', 'BraA09t36680Z' => 'bra', 'BraA10t44471Z' => 'bra', 'C02p06760' => 'bna', 'C02p06890' => 'bna', 'C02p07010' => 'bna', 'C03p07660' => 'bna', 'C05p10300' => 'bna', 'C06p38150' => 'bna', 'C07p36650' => 'bna', 'C08p15770' => 'bna', 'C09p12300' => 'bna', 'C09p62700' => 'bna', 'C09p75040' => 'bna', 'CAN.G13.1' => 'can', 'CAN.G138.4' => 'can', 'CAN.G44.6' => 'can', 'CAN.G473.19' => 'can', 'CANSAT01G0835' => 'cansat', 'CANSAT11G0246' => 'cansat', 'CANSAT11G1766' => 'cansat', 'CANSAT64G1954' => 'cansat', 'CARHR013330' => 'chi', 'CARHR060530' => 'chi', 'CARHR075300' => 'chi', 'CARHR105120' => 'chi', 'CARHR148910' => 'chi', 'CARHR198830' => 'chi', 'Carub.0001s1275' => 'cru', 'Carub.0002s1437' => 'cru', 'Carub.0003s0044' => 'cru', 'Carub.0003s2787' => 'cru', 'Carub.0005s0597' => 'cru', 'Carub.0006s1266' => 'cru', 'Ca_06935_v3' => 'car', 'Ca_13559_v3' => 'car', 'Ca_16941_v3' => 'car', 'Ca_16960_v3' => 'car', 'Ca_17775_v3' => 'car', 'Ca_30464_v3' => 'car', 'Cc06_g08160' => 'ccan', 'Cc07_g01520' => 'ccan', 'Cc11_g15810' => 'ccan', 'CDE02G2840' => 'cde', 'CDE03G0093' => 'cde', 'CDE04G2127' => 'cde', 'CDE07G1857' => 'cde', 'CDE09G1246' => 'cde', 'Cfa003412' => 'cfa', 'Cfa007341' => 'cfa', 'Cfa009220' => 'cfa', 'Ciclev10008737m.g' => 'ccl', 'Ciclev10015565m.g' => 'ccl', 'Ciclev10031761m.g' => 'ccl', 'CiPaw.03G045300' => 'cil', 'CiPaw.03G247200' => 'cil', 'CiPaw.04G029500' => 'cil', 'CiPaw.04G174000' => 'cil', 'CiPaw.05G181200' => 'cil', 'CiPaw.06G067100' => 'cil', 'ClCG05G025800' => 'cla', 'ClCG06G011400' => 'cla', 'ClCG09G019360' => 'cla', 'COL.COLO4_04827' => 'col', 'COL.COLO4_29170' => 'col', 'COL.COLO4_35131' => 'col', 'COL.COLO4_35132' => 'col', 'Cpa.g.sc33.32' => 'cpa', 'Cpa.g.sc46.29' => 'cpa', 'Cpa.g.sc796.1' => 'cpa', 'CsaV3_1G030420' => 'csa', 'CsaV3_5G027050' => 'csa', 'CsaV3_5G031040' => 'csa', 'CsaV3_UNG023130' => 'csa', 'CSS0007726' => 'camsi', 'CSS0016433' => 'camsi', 'CSS0017656' => 'camsi', 'CSS0025364' => 'camsi', 'CSS0027582' => 'camsi', 'CSS0047288' => 'camsi', 'CSS0049950' => 'camsi', 'DCAR_003843' => 'dca', 'DCAR_007052' => 'dca', 'DCAR_020884' => 'dca', 'DCAR_021730' => 'dca', 'DCAR_024423' => 'dca', 'DCAR_026509' => 'dca', 'DCAR_031158' => 'dca', 'Dinv14728' => 'din', 'Dinv15219' => 'din', 'Dinv25728' => 'din', 'Dinv33428' => 'din', 'Dinv36489' => 'din', 'Dinv41486' => 'din', 'Duzib147G0469' => 'dzi', 'Duzib168G0060' => 'dzi', 'Duzib187G1215' => 'dzi', 'Duzib248G0692' => 'dzi', 'Duzib251G0767' => 'dzi', 'Duzib264G0446' => 'dzi', 'Duzib268G0691' => 'dzi', 'ECA232G4767' => 'eca', 'ECA233G2838' => 'eca', 'ECA234G0391' => 'eca', 'ECA234G0857' => 'eca', 'ECA236G1593' => 'eca', 'ECA238G0565' => 'eca', 'ECA246G1027' => 'eca', 'ECA246G3223' => 'eca', 'ECA246G3470' => 'eca', 'EL10Ac6g13829' => 'bvu', 'EL10Ac6g14093' => 'bvu', 'EL10Ac8g18707' => 'bvu', 'Eucgr.C01369' => 'egr', 'Eucgr.H02492' => 'egr', 'Eucgr.I01733' => 'egr', 'Eucgr.J02255' => 'egr', 'Eucgr.J02257' => 'egr', 'Eucgr.J02258' => 'egr', 'FAN02G1601' => 'fan', 'FAN03G1586' => 'fan', 'FAN03G2986' => 'fan', 'FAN05G4837' => 'fan', 'FAN06G0146' => 'fan', 'FAN07G0858' => 'fan', 'FAN09G3179' => 'fan', 'FAN10G0669' => 'fan', 'FAN12G2358' => 'fan', 'FAN14G4198' => 'fan', 'FAN14G5112' => 'fan', 'FAN17G0342' => 'fan', 'FAN19G0342' => 'fan', 'FAN19G0962' => 'fan', 'FAN19G1101' => 'fan', 'FAN19G1872' => 'fan', 'FAN22G0356' => 'fan', 'FAN23G0744' => 'fan', 'FAN23G1914' => 'fan', 'FAN26G0032' => 'fan', 'FAN28G0625' => 'fan', 'FvH4_1g02710' => 'fve', 'FvH4_1g02720' => 'fve', 'FvH4_4g25670' => 'fve', 'FvH4_6g51700' => 'fve', 'FvH4_7g20170' => 'fve', 'Glyma.05G175000' => 'gma', 'Glyma.08G132300' => 'gma', 'Glyma.11G243000' => 'gma', 'Glyma.13G158900' => 'gma', 'Glyma.17G112400' => 'gma', 'Glyma.18G014100' => 'gma', 'Glyma.19G003100' => 'gma', 'Glyma.19G056500' => 'gma', 'Gohir.A01G158900' => 'ghi', 'Gohir.A05G312600' => 'ghi', 'Gohir.A05G354900' => 'ghi', 'Gohir.A07G037200' => 'ghi', 'Gohir.A09G030000' => 'ghi', 'Gohir.A12G145200' => 'ghi', 'Gohir.D01G151500' => 'ghi', 'Gohir.D04G058300' => 'ghi', 'Gohir.D05G314100' => 'ghi', 'Gohir.D07G041400' => 'ghi', 'Gohir.D09G029700' => 'ghi', 'Gohir.D12G149700' => 'ghi', 'Gorai.001G043800' => 'gra', 'Gorai.002G187800' => 'gra', 'Gorai.006G034700' => 'gra', 'Gorai.008G161200' => 'gra', 'Gorai.009G335700' => 'gra', 'Gorai.012G065000' => 'gra', 'GSVIVG01000535001' => 'vvi', 'GSVIVG01015572001' => 'vvi', 'GSVIVG01032386001' => 'vvi', 'HanXRQChr05g0138531' => 'han', 'HanXRQChr06g0174391' => 'han', 'HanXRQChr07g0199021' => 'han', 'HanXRQChr08g0208211' => 'han', 'HanXRQChr09g0255471' => 'han', 'HanXRQChr10g0315791' => 'han', 'HanXRQChr12g0371991' => 'han', 'HanXRQChr15g0475251' => 'han', 'HanXRQChr17g0540001' => 'han', 'HanXRQChr17g0548631' => 'han', 'HanXRQChr17g0569561' => 'han', 'Haze_12256' => 'cav', 'Haze_14756' => 'cav', 'Haze_25528' => 'cav', 'Hma1.2p1_0079F.1_g041020' => 'hma', 'Hma1.2p1_0818F.1_g223260' => 'hma', 'Hma1.2p1_1747F.1_g300530' => 'hma', 'HPP92_004607' => 'vpl', 'HPP92_004608' => 'vpl', 'HPP92_006181' => 'vpl', 'HPP92_012192' => 'vpl', 'HPP92_015680' => 'vpl', 'HPP92_020249' => 'vpl', 'HPP92_021376' => 'vpl', 'HPP92_024275' => 'vpl', 'Hund06031' => 'sun', 'Hund25391' => 'sun', 'Lalb_Chr07g0185371' => 'lal', 'Lalb_Chr07g0185381' => 'lal', 'Lalb_Chr12g0204011' => 'lal', 'Lalb_Chr13g0301671' => 'lal', 'Lalb_Chr14g0362851' => 'lal', 'Lalb_Chr24g0403581' => 'lal', 'Lj1g0000233' => 'lja', 'Lj2g0018120' => 'lja', 'Lj3C621T0' => 'lonja', 'Lj3P1059T14' => 'lonja', 'Lj3P611T9' => 'lonja', 'Lj3P614T13' => 'lonja', 'Lj3P615T5' => 'lonja', 'Lj4g0012315' => 'lja', 'Lj4g0026182' => 'lja', 'Lj6P813T16' => 'lonja', 'Lj7C427T7' => 'lonja', 'Lj7C427T8' => 'lonja', 'Lj7P600T41' => 'lonja', 'Lju41C42G17' => 'lonja', 'Lsat_1_v5_gn_0_47300' => 'lsa', 'Lsat_1_v5_gn_2_91280' => 'lsa', 'Lsat_1_v5_gn_3_30561' => 'lsa', 'Lsat_1_v5_gn_4_184321' => 'lsa', 'Lsat_1_v5_gn_4_4041' => 'lsa', 'Lsat_1_v5_gn_5_92000' => 'lsa', 'Lsat_1_v5_gn_8_152940' => 'lsa', 'Lsat_1_v5_gn_8_62401' => 'lsa', 'Manes.06G055900' => 'mes', 'Manes.12G022200' => 'mes', 'Manes.13G023300' => 'mes', 'Manes.14G115000' => 'mes', 'Manes.15G151700' => 'mes', 'Manes.17G111300' => 'mes', 'Mapoly0226s0009' => 'mpo', 'MBI02_g25363_MAGBIO' => 'mbi', 'MBI06_g00027_MAGBIO' => 'mbi', 'MBI10_g13034_MAGBIO' => 'mbi', 'MD09G1023400' => 'mdo', 'MD13G1100100' => 'mdo', 'MD15G1169200' => 'mdo', 'MD16G1101100' => 'mdo', 'MD17G1022900' => 'mdo', 'Medtr3g096150' => 'mtr', 'Medtr4g115070' => 'mtr', 'Medtr7g033325' => 'mtr', 'Medtr8g089840' => 'mtr', 'MELO3C010319.2' => 'cme', 'MELO3C011944.2' => 'cme', 'MELO3C021589.2' => 'cme', 'Migut.E00207' => 'egut', 'Migut.H00067' => 'egut', 'Migut.K00433' => 'egut', 'Migut.K00606' => 'egut', 'Migut.K01410' => 'egut', 'MSTRG.13347' => 'ama', 'MSTRG.24045' => 'ama', 'MSTRG.2428' => 'ama', 'MSTRG.26410' => 'ama', 'MSTRG.3139' => 'ama', 'MSTRG.3286' => 'ama', 'MSTRG.563' => 'ama', 'MSTRG.7941' => 'ama', 'Nitab4.5_0000028g0060' => 'nta', 'Nitab4.5_0000065g0260' => 'nta', 'Nitab4.5_0000112g0060' => 'nta', 'Nitab4.5_0000489g0120' => 'nta', 'Nitab4.5_0001776g0050' => 'nta', 'Nitab4.5_0001854g0010' => 'nta', 'Nitab4.5_0001860g0020' => 'nta', 'Nitab4.5_0004352g0010' => 'nta', 'Nitab4.5_0008716g0020' => 'nta', 'Nitab4.5_0008922g0010' => 'nta', 'Nn3g16693' => 'nnu', 'Nn4g22596' => 'nnu', 'Nn7g37639' => 'nnu', 'Oeu001701.1' => 'oeu', 'Oeu018149.1' => 'oeu', 'Oeu026220.1' => 'oeu', 'Oeu038635.1' => 'oeu', 'Oeu049176.1' => 'oeu', 'Oeu056706.1' => 'oeu', 'Oeu056937.1' => 'oeu', 'Oeu057540.1' => 'oeu', 'Os02g0594900' => 'osa', 'Os02g0595100' => 'osa', 'Os04g0477500' => 'osa', 'Os12g0611900' => 'osa', 'Peaxi162Scf00076g00020' => 'pax', 'Peaxi162Scf00128g00217' => 'pax', 'Peaxi162Scf00129g01640' => 'pax', 'Peaxi162Scf00669g00007' => 'pax', 'Peaxi162Scf00700g00421' => 'pax', 'Peaxi162Scf00801g00038' => 'pax', 'Peaxi162Scf00891g00025' => 'pax', 'PGR083G0909' => 'pgr', 'PGR119G1005' => 'pgr', 'PGR142G2236' => 'pgr', 'PGR142G3388' => 'pgr', 'PGSC0003DMG400004514' => 'stu', 'PGSC0003DMG400012635' => 'stu', 'PGSC0003DMG400015730' => 'stu', 'PGSC0003DMG400018611' => 'stu', 'PGSC0003DMG400030897' => 'stu', 'Phvul.001G254800' => 'pvu', 'Phvul.002G260100' => 'pvu', 'Phvul.003G167600' => 'pvu', 'Phvul.004G005100' => 'pvu', 'Potri.001G343600' => 'ptr', 'Potri.006G066700' => 'ptr', 'Potri.008G186000' => 'ptr', 'Potri.010G046900' => 'ptr', 'Potri.018G127900' => 'ptr', 'Pp3c20_17750' => 'ppa', 'Pp3c24_4380' => 'ppa', 'Prupe.1G245800' => 'ppe', 'Prupe.3G293400' => 'ppe', 'Prupe.7G247400' => 'ppe', 'Psat0s145g0120' => 'psa', 'Psat0s595g0040' => 'psa', 'Psat0s595g0120' => 'psa', 'Psat3g175040' => 'psa', 'Psat7g058120' => 'psa', 'PSO017G0428' => 'pso', 'PSO063G7510' => 'pso', 'PSO067G0046' => 'pso', 'PSO478G1073' => 'pso', 'PSO675G3677' => 'pso', 'PSO675G6558' => 'pso', 'PSO675G7520' => 'pso', 'PSO675G8959' => 'pso', 'QL02p074089' => 'qlo', 'QL02p089614' => 'qlo', 'QL03p057736' => 'qlo', 'RcHm_v2.0_Chr1g0364131' => 'rch', 'RcHm_v2.0_Chr2g0087801' => 'rch', 'RcHm_v2.0_Chr2g0087821' => 'rch', 'RcHm_v2.0_Chr2g0173231' => 'rch', 'RcHm_v2.0_Chr4g0433111' => 'rch', 'Rhsim03G0250300' => 'rsi', 'Rhsim08G0048400' => 'rsi', 'Rhsim10G0014800' => 'rsi', 'Rhsim12G0040100' => 'rsi', 'Rhsim12G0109700' => 'rsi', 'Sabra06G0049600' => 'sbr', 'Sabra08G0141000' => 'sbr', 'Sabra10G0021400' => 'sbr', 'Sabra16G0222900' => 'sbr', 'Sabra18G0108600' => 'sbr', 'SalBow1G0433' => 'sbo', 'SalBow1G2038' => 'sbo', 'SalBow1G5003' => 'sbo', 'SalBow7G1197' => 'sbo', 'SalBow8G3506' => 'sbo', 'Sc03g0007300' => 'sci', 'Sc11g0000950' => 'sci', 'Sc14g0008750' => 'sci', 'Sc18g0000420' => 'sci', 'Sed0006754' => 'sed', 'Sed0008741' => 'sed', 'Sed0017172' => 'sed', 'Sed0018925' => 'sed', 'Sed0023326' => 'sed', 'Sed0025909' => 'sed', 'SEGI_05333' => 'sgi', 'SEGI_10362' => 'sgi', 'SEGI_13380' => 'sgi', 'SEGI_24306' => 'sgi', 'SEGI_29077' => 'sgi', 'SEGI_29095' => 'sgi', 'SEGI_36534' => 'sgi', 'SEGI_37506' => 'sgi', 'SEGI_38321' => 'sgi', 'SGA_v2.0_scaffold307G48031' => 'sas', 'SGA_v2.0_scaffold47G17507' => 'sas', 'SGA_v2.0_scaffold63G21736' => 'sas', 'SGA_v2.0_scaffold87G27070' => 'sas', 'SHI17794' => 'shi', 'SHI28851' => 'shi', 'SMO165G0155' => 'smo', 'SMO340G0217' => 'smo', 'SMO367G1210' => 'smo', 'Solyc02g093430.3' => 'sly', 'Solyc05g013580.4' => 'sly', 'Solyc07g008030.3' => 'sly', 'Solyc12g035470.2' => 'sly', 'Sopen02g038020' => 'spe', 'Sopen05g008490' => 'spe', 'Sopen07g003910' => 'spe', 'Sopen12g015240' => 'spe', 'Sp1g11550' => 'spa', 'Sp2g16710' => 'spa', 'Sp3g00430' => 'spa', 'Sp3g26780' => 'spa', 'Sp5g22900' => 'spa', 'Sp6g29530' => 'spa', 'TAR371G0794' => 'tar', 'TAR374G0164' => 'tar', 'TAR622G0165' => 'tar', 'TAR626G0929' => 'tar', 'TAR629G2155' => 'tar', 'THA.LOC104805282' => 'tha', 'THA.LOC104805363' => 'tha', 'THA.LOC104808968' => 'tha', 'THA.LOC104821093' => 'tha', 'THA.LOC104823953' => 'tha', 'THA.LOC104825562' => 'tha', 'THA.LOC104825665' => 'tha', 'Thecc.02G261400' => 'tca', 'Thecc.04G019200' => 'tca', 'Thecc.09G130400' => 'tca', 'Thhalv10004374m.g' => 'esa', 'Thhalv10007850m.g' => 'esa', 'Thhalv10013782m.g' => 'esa', 'Thhalv10018686m.g' => 'esa', 'Thhalv10020899m.g' => 'esa', 'Thhalv10022755m.g' => 'esa', 'TPR.G23851' => 'tpr', 'TPR.G26500' => 'tpr', 'TPR.G27267' => 'tpr', 'TPR.G32001' => 'tpr', 'TPR.G6251' => 'tpr', 'TPR.G8167' => 'tpr', 'TWI12G1330' => 'twi', 'TWI18G1239' => 'twi', 'TWI34G0979' => 'twi', 'TWI36G0670' => 'twi', 'TWI36G0707' => 'twi', 'TWI56G0233' => 'twi', 'TWI75G1809' => 'twi', 'unitig_21.g20874' => 'ugi', 'unitig_26.g10343' => 'ugi', 'unitig_46.g18392' => 'ugi', 'unitig_52.g17178' => 'ugi', 'unitig_8.g2934' => 'ugi', 'vmacro01122' => 'vma', 'vmacro05875' => 'vma', 'vmacro06147' => 'vma', 'vmacro16191' => 'vma', 'vmacro18293' => 'vma', 'VMungo0251G3707' => 'vmu', 'VMungo0464G1521' => 'vmu', 'VMungo1215G0205' => 'vmu', 'VMungo1383G2484' => 'vmu', 'Zm00001eb079610' => 'zma', 'Zm00001eb135990' => 'zma', 'Zm00001eb183710' => 'zma', 'Zm00001eb246020' => 'zma' ) $gf_id = 'HOM05D001124' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001124' ) $data_identifier = 'HOM05D001124' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 6, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 7, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 21, 'bol' => (int) 10, 'bra' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 6, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 9, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 21, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 8, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 10, 'lsa' => (int) 8, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 8, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 9, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb246020' $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' => 'HOM05D001124', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '548', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02520' => 'bna', 'A03p06630' => 'bna', 'A05p44460' => 'bna', 'A06p08710' => 'bna', 'A06p41090' => 'bna', 'A07p32320' => 'bna', 'A08p32520' => 'bna', 'A09p10360' => 'bna', 'A10p24080' => 'bna', 'Aa31LG11G15250' => 'aar', 'Aa31LG1G1800' => 'aar', 'Aa31LG2G5120' => 'aar', 'Aa31LG2G6070' => 'aar', 'Aa31LG5G10770' => 'aar', 'Aa31sc61G90' => 'aar', 'Actinidia01352' => 'ach', 'Actinidia05983' => 'ach', 'Actinidia08133' => 'ach', 'Actinidia15101' => 'ach', 'Actinidia26379' => 'ach', 'Actinidia35778' => 'ach', 'Actinidia36123' => 'ach', 'Actinidia37436' => 'ach', 'Actinidia38730' => 'ach', 'Ah.02g128210' => 'amhyb', 'Ah.03g132990' => 'amhyb', 'Ah.14g079410' => 'amhyb', 'AL1G24640' => 'aly', 'AL2G26680' => 'aly', 'AL3G10530' => 'aly', 'AL3G45230' => 'aly', 'AL5G15230' => 'aly', 'AL5G16960' => 'aly', 'AL6G25210' => 'aly', 'Aqoxy2G00441' => 'aox', 'Aqoxy3G01236' => 'aox', 'Aqoxy5G03746' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3RQ047' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C7GMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9C8JER' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MBL6KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YXCZ83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZANX40' => 'arhy', 'AT1G12990' => 'ath', 'AT1G67880' => 'ath', 'AT2G13290' => 'ath', 'AT3G01620' => 'ath', 'AT3G26445' => 'ath', 'AT3G27540' => 'ath', 'AT5G14480' => 'ath', 'ATR0824G026' => 'atr', 'ATR1098G019' => 'atr', 'Atru.chr11.2145' => 'acertr', 'Atru.chr2.3636' => 'acertr', 'Atru.chr2.3644' => 'acertr', 'Atru.chr6.2422' => 'acertr', 'Atru.chr7.1112' => 'acertr', 'AUR62005469' => 'cqu', 'AUR62011166' => 'cqu', 'AUR62013319' => 'cqu', 'AUR62024273' => 'cqu', 'AUR62028420' => 'cqu', 'AUR62041942' => 'cqu', 'BcaB01g04969' => 'bca', 'BcaB01g06371' => 'bca', 'BcaB02g11494' => 'bca', 'BcaB03g15382' => 'bca', 'BcaB08g36994' => 'bca', 'BcaC03g13477' => 'bca', 'BcaC03g13478' => 'bca', 'BcaC03g13480' => 'bca', 'BcaC03g13481' => 'bca', 'BcaC03g13486' => 'bca', 'BcaC04g19031' => 'bca', 'BcaC04g23085' => 'bca', 'BcaC05g25094' => 'bca', 'BcaC05g25096' => 'bca', 'BcaC05g25138' => 'bca', 'BcaC05g30416' => 'bca', 'BcaC05g30455' => 'bca', 'BcaC06g30979' => 'bca', 'BcaC06g33805' => 'bca', 'BcaC08g46021' => 'bca', 'BcaNung03154' => 'bca', 'BolC2t06623H' => 'bol', 'BolC2t06632H' => 'bol', 'BolC2t06635H' => 'bol', 'BolC2t06638H' => 'bol', 'BolC3t13266H' => 'bol', 'BolC5t29776H' => 'bol', 'BolC6t38912H' => 'bol', 'BolC7t44183H' => 'bol', 'BolC9t54123H' => 'bol', 'BolC9t59107H' => 'bol', 'BraA02t05221Z' => 'bra', 'BraA03t09996Z' => 'bra', 'BraA05t23210Z' => 'bra', 'BraA06t24068Z' => 'bra', 'BraA06t27032Z' => 'bra', 'BraA08t35176Z' => 'bra', 'BraA09t36680Z' => 'bra', 'BraA10t44471Z' => 'bra', 'C02p06760' => 'bna', 'C02p06890' => 'bna', 'C02p07010' => 'bna', 'C03p07660' => 'bna', 'C05p10300' => 'bna', 'C06p38150' => 'bna', 'C07p36650' => 'bna', 'C08p15770' => 'bna', 'C09p12300' => 'bna', 'C09p62700' => 'bna', 'C09p75040' => 'bna', 'CAN.G13.1' => 'can', 'CAN.G138.4' => 'can', 'CAN.G44.6' => 'can', 'CAN.G473.19' => 'can', 'CANSAT01G0835' => 'cansat', 'CANSAT11G0246' => 'cansat', 'CANSAT11G1766' => 'cansat', 'CANSAT64G1954' => 'cansat', 'CARHR013330' => 'chi', 'CARHR060530' => 'chi', 'CARHR075300' => 'chi', 'CARHR105120' => 'chi', 'CARHR148910' => 'chi', 'CARHR198830' => 'chi', 'Carub.0001s1275' => 'cru', 'Carub.0002s1437' => 'cru', 'Carub.0003s0044' => 'cru', 'Carub.0003s2787' => 'cru', 'Carub.0005s0597' => 'cru', 'Carub.0006s1266' => 'cru', 'Ca_06935_v3' => 'car', 'Ca_13559_v3' => 'car', 'Ca_16941_v3' => 'car', 'Ca_16960_v3' => 'car', 'Ca_17775_v3' => 'car', 'Ca_30464_v3' => 'car', 'Cc06_g08160' => 'ccan', 'Cc07_g01520' => 'ccan', 'Cc11_g15810' => 'ccan', 'CDE02G2840' => 'cde', 'CDE03G0093' => 'cde', 'CDE04G2127' => 'cde', 'CDE07G1857' => 'cde', 'CDE09G1246' => 'cde', 'Cfa003412' => 'cfa', 'Cfa007341' => 'cfa', 'Cfa009220' => 'cfa', 'Ciclev10008737m.g' => 'ccl', 'Ciclev10015565m.g' => 'ccl', 'Ciclev10031761m.g' => 'ccl', 'CiPaw.03G045300' => 'cil', 'CiPaw.03G247200' => 'cil', 'CiPaw.04G029500' => 'cil', 'CiPaw.04G174000' => 'cil', 'CiPaw.05G181200' => 'cil', 'CiPaw.06G067100' => 'cil', 'ClCG05G025800' => 'cla', 'ClCG06G011400' => 'cla', 'ClCG09G019360' => 'cla', 'COL.COLO4_04827' => 'col', 'COL.COLO4_29170' => 'col', 'COL.COLO4_35131' => 'col', 'COL.COLO4_35132' => 'col', 'Cpa.g.sc33.32' => 'cpa', 'Cpa.g.sc46.29' => 'cpa', 'Cpa.g.sc796.1' => 'cpa', 'CsaV3_1G030420' => 'csa', 'CsaV3_5G027050' => 'csa', 'CsaV3_5G031040' => 'csa', 'CsaV3_UNG023130' => 'csa', 'CSS0007726' => 'camsi', 'CSS0016433' => 'camsi', 'CSS0017656' => 'camsi', 'CSS0025364' => 'camsi', 'CSS0027582' => 'camsi', 'CSS0047288' => 'camsi', 'CSS0049950' => 'camsi', 'DCAR_003843' => 'dca', 'DCAR_007052' => 'dca', 'DCAR_020884' => 'dca', 'DCAR_021730' => 'dca', 'DCAR_024423' => 'dca', 'DCAR_026509' => 'dca', 'DCAR_031158' => 'dca', 'Dinv14728' => 'din', 'Dinv15219' => 'din', 'Dinv25728' => 'din', 'Dinv33428' => 'din', 'Dinv36489' => 'din', 'Dinv41486' => 'din', 'Duzib147G0469' => 'dzi', 'Duzib168G0060' => 'dzi', 'Duzib187G1215' => 'dzi', 'Duzib248G0692' => 'dzi', 'Duzib251G0767' => 'dzi', 'Duzib264G0446' => 'dzi', 'Duzib268G0691' => 'dzi', 'ECA232G4767' => 'eca', 'ECA233G2838' => 'eca', 'ECA234G0391' => 'eca', 'ECA234G0857' => 'eca', 'ECA236G1593' => 'eca', 'ECA238G0565' => 'eca', 'ECA246G1027' => 'eca', 'ECA246G3223' => 'eca', 'ECA246G3470' => 'eca', 'EL10Ac6g13829' => 'bvu', 'EL10Ac6g14093' => 'bvu', 'EL10Ac8g18707' => 'bvu', 'Eucgr.C01369' => 'egr', 'Eucgr.H02492' => 'egr', 'Eucgr.I01733' => 'egr', 'Eucgr.J02255' => 'egr', 'Eucgr.J02257' => 'egr', 'Eucgr.J02258' => 'egr', 'FAN02G1601' => 'fan', 'FAN03G1586' => 'fan', 'FAN03G2986' => 'fan', 'FAN05G4837' => 'fan', 'FAN06G0146' => 'fan', 'FAN07G0858' => 'fan', 'FAN09G3179' => 'fan', 'FAN10G0669' => 'fan', 'FAN12G2358' => 'fan', 'FAN14G4198' => 'fan', 'FAN14G5112' => 'fan', 'FAN17G0342' => 'fan', 'FAN19G0342' => 'fan', 'FAN19G0962' => 'fan', 'FAN19G1101' => 'fan', 'FAN19G1872' => 'fan', 'FAN22G0356' => 'fan', 'FAN23G0744' => 'fan', 'FAN23G1914' => 'fan', 'FAN26G0032' => 'fan', 'FAN28G0625' => 'fan', 'FvH4_1g02710' => 'fve', 'FvH4_1g02720' => 'fve', 'FvH4_4g25670' => 'fve', 'FvH4_6g51700' => 'fve', 'FvH4_7g20170' => 'fve', 'Glyma.05G175000' => 'gma', 'Glyma.08G132300' => 'gma', 'Glyma.11G243000' => 'gma', 'Glyma.13G158900' => 'gma', 'Glyma.17G112400' => 'gma', 'Glyma.18G014100' => 'gma', 'Glyma.19G003100' => 'gma', 'Glyma.19G056500' => 'gma', 'Gohir.A01G158900' => 'ghi', 'Gohir.A05G312600' => 'ghi', 'Gohir.A05G354900' => 'ghi', 'Gohir.A07G037200' => 'ghi', 'Gohir.A09G030000' => 'ghi', 'Gohir.A12G145200' => 'ghi', 'Gohir.D01G151500' => 'ghi', 'Gohir.D04G058300' => 'ghi', 'Gohir.D05G314100' => 'ghi', 'Gohir.D07G041400' => 'ghi', 'Gohir.D09G029700' => 'ghi', 'Gohir.D12G149700' => 'ghi', 'Gorai.001G043800' => 'gra', 'Gorai.002G187800' => 'gra', 'Gorai.006G034700' => 'gra', 'Gorai.008G161200' => 'gra', 'Gorai.009G335700' => 'gra', 'Gorai.012G065000' => 'gra', 'GSVIVG01000535001' => 'vvi', 'GSVIVG01015572001' => 'vvi', 'GSVIVG01032386001' => 'vvi', 'HanXRQChr05g0138531' => 'han', 'HanXRQChr06g0174391' => 'han', 'HanXRQChr07g0199021' => 'han', 'HanXRQChr08g0208211' => 'han', 'HanXRQChr09g0255471' => 'han', 'HanXRQChr10g0315791' => 'han', 'HanXRQChr12g0371991' => 'han', 'HanXRQChr15g0475251' => 'han', 'HanXRQChr17g0540001' => 'han', 'HanXRQChr17g0548631' => 'han', 'HanXRQChr17g0569561' => 'han', 'Haze_12256' => 'cav', 'Haze_14756' => 'cav', 'Haze_25528' => 'cav', 'Hma1.2p1_0079F.1_g041020' => 'hma', 'Hma1.2p1_0818F.1_g223260' => 'hma', 'Hma1.2p1_1747F.1_g300530' => 'hma', 'HPP92_004607' => 'vpl', 'HPP92_004608' => 'vpl', 'HPP92_006181' => 'vpl', 'HPP92_012192' => 'vpl', 'HPP92_015680' => 'vpl', 'HPP92_020249' => 'vpl', 'HPP92_021376' => 'vpl', 'HPP92_024275' => 'vpl', 'Hund06031' => 'sun', 'Hund25391' => 'sun', 'Lalb_Chr07g0185371' => 'lal', 'Lalb_Chr07g0185381' => 'lal', 'Lalb_Chr12g0204011' => 'lal', 'Lalb_Chr13g0301671' => 'lal', 'Lalb_Chr14g0362851' => 'lal', 'Lalb_Chr24g0403581' => 'lal', 'Lj1g0000233' => 'lja', 'Lj2g0018120' => 'lja', 'Lj3C621T0' => 'lonja', 'Lj3P1059T14' => 'lonja', 'Lj3P611T9' => 'lonja', 'Lj3P614T13' => 'lonja', 'Lj3P615T5' => 'lonja', 'Lj4g0012315' => 'lja', 'Lj4g0026182' => 'lja', 'Lj6P813T16' => 'lonja', 'Lj7C427T7' => 'lonja', 'Lj7C427T8' => 'lonja', 'Lj7P600T41' => 'lonja', 'Lju41C42G17' => 'lonja', 'Lsat_1_v5_gn_0_47300' => 'lsa', 'Lsat_1_v5_gn_2_91280' => 'lsa', 'Lsat_1_v5_gn_3_30561' => 'lsa', 'Lsat_1_v5_gn_4_184321' => 'lsa', 'Lsat_1_v5_gn_4_4041' => 'lsa', 'Lsat_1_v5_gn_5_92000' => 'lsa', 'Lsat_1_v5_gn_8_152940' => 'lsa', 'Lsat_1_v5_gn_8_62401' => 'lsa', 'Manes.06G055900' => 'mes', 'Manes.12G022200' => 'mes', 'Manes.13G023300' => 'mes', 'Manes.14G115000' => 'mes', 'Manes.15G151700' => 'mes', 'Manes.17G111300' => 'mes', 'Mapoly0226s0009' => 'mpo', 'MBI02_g25363_MAGBIO' => 'mbi', 'MBI06_g00027_MAGBIO' => 'mbi', 'MBI10_g13034_MAGBIO' => 'mbi', 'MD09G1023400' => 'mdo', 'MD13G1100100' => 'mdo', 'MD15G1169200' => 'mdo', 'MD16G1101100' => 'mdo', 'MD17G1022900' => 'mdo', 'Medtr3g096150' => 'mtr', 'Medtr4g115070' => 'mtr', 'Medtr7g033325' => 'mtr', 'Medtr8g089840' => 'mtr', 'MELO3C010319.2' => 'cme', 'MELO3C011944.2' => 'cme', 'MELO3C021589.2' => 'cme', 'Migut.E00207' => 'egut', 'Migut.H00067' => 'egut', 'Migut.K00433' => 'egut', 'Migut.K00606' => 'egut', 'Migut.K01410' => 'egut', 'MSTRG.13347' => 'ama', 'MSTRG.24045' => 'ama', 'MSTRG.2428' => 'ama', 'MSTRG.26410' => 'ama', 'MSTRG.3139' => 'ama', 'MSTRG.3286' => 'ama', 'MSTRG.563' => 'ama', 'MSTRG.7941' => 'ama', 'Nitab4.5_0000028g0060' => 'nta', 'Nitab4.5_0000065g0260' => 'nta', 'Nitab4.5_0000112g0060' => 'nta', 'Nitab4.5_0000489g0120' => 'nta', 'Nitab4.5_0001776g0050' => 'nta', 'Nitab4.5_0001854g0010' => 'nta', 'Nitab4.5_0001860g0020' => 'nta', 'Nitab4.5_0004352g0010' => 'nta', 'Nitab4.5_0008716g0020' => 'nta', 'Nitab4.5_0008922g0010' => 'nta', 'Nn3g16693' => 'nnu', 'Nn4g22596' => 'nnu', 'Nn7g37639' => 'nnu', 'Oeu001701.1' => 'oeu', 'Oeu018149.1' => 'oeu', 'Oeu026220.1' => 'oeu', 'Oeu038635.1' => 'oeu', 'Oeu049176.1' => 'oeu', 'Oeu056706.1' => 'oeu', 'Oeu056937.1' => 'oeu', 'Oeu057540.1' => 'oeu', 'Os02g0594900' => 'osa', 'Os02g0595100' => 'osa', 'Os04g0477500' => 'osa', 'Os12g0611900' => 'osa', 'Peaxi162Scf00076g00020' => 'pax', 'Peaxi162Scf00128g00217' => 'pax', 'Peaxi162Scf00129g01640' => 'pax', 'Peaxi162Scf00669g00007' => 'pax', 'Peaxi162Scf00700g00421' => 'pax', 'Peaxi162Scf00801g00038' => 'pax', 'Peaxi162Scf00891g00025' => 'pax', 'PGR083G0909' => 'pgr', 'PGR119G1005' => 'pgr', 'PGR142G2236' => 'pgr', 'PGR142G3388' => 'pgr', 'PGSC0003DMG400004514' => 'stu', 'PGSC0003DMG400012635' => 'stu', 'PGSC0003DMG400015730' => 'stu', 'PGSC0003DMG400018611' => 'stu', 'PGSC0003DMG400030897' => 'stu', 'Phvul.001G254800' => 'pvu', 'Phvul.002G260100' => 'pvu', 'Phvul.003G167600' => 'pvu', 'Phvul.004G005100' => 'pvu', 'Potri.001G343600' => 'ptr', 'Potri.006G066700' => 'ptr', 'Potri.008G186000' => 'ptr', 'Potri.010G046900' => 'ptr', 'Potri.018G127900' => 'ptr', 'Pp3c20_17750' => 'ppa', 'Pp3c24_4380' => 'ppa', 'Prupe.1G245800' => 'ppe', 'Prupe.3G293400' => 'ppe', 'Prupe.7G247400' => 'ppe', 'Psat0s145g0120' => 'psa', 'Psat0s595g0040' => 'psa', 'Psat0s595g0120' => 'psa', 'Psat3g175040' => 'psa', 'Psat7g058120' => 'psa', 'PSO017G0428' => 'pso', 'PSO063G7510' => 'pso', 'PSO067G0046' => 'pso', 'PSO478G1073' => 'pso', 'PSO675G3677' => 'pso', 'PSO675G6558' => 'pso', 'PSO675G7520' => 'pso', 'PSO675G8959' => 'pso', 'QL02p074089' => 'qlo', 'QL02p089614' => 'qlo', 'QL03p057736' => 'qlo', 'RcHm_v2.0_Chr1g0364131' => 'rch', 'RcHm_v2.0_Chr2g0087801' => 'rch', 'RcHm_v2.0_Chr2g0087821' => 'rch', 'RcHm_v2.0_Chr2g0173231' => 'rch', 'RcHm_v2.0_Chr4g0433111' => 'rch', 'Rhsim03G0250300' => 'rsi', 'Rhsim08G0048400' => 'rsi', 'Rhsim10G0014800' => 'rsi', 'Rhsim12G0040100' => 'rsi', 'Rhsim12G0109700' => 'rsi', 'Sabra06G0049600' => 'sbr', 'Sabra08G0141000' => 'sbr', 'Sabra10G0021400' => 'sbr', 'Sabra16G0222900' => 'sbr', 'Sabra18G0108600' => 'sbr', 'SalBow1G0433' => 'sbo', 'SalBow1G2038' => 'sbo', 'SalBow1G5003' => 'sbo', 'SalBow7G1197' => 'sbo', 'SalBow8G3506' => 'sbo', 'Sc03g0007300' => 'sci', 'Sc11g0000950' => 'sci', 'Sc14g0008750' => 'sci', 'Sc18g0000420' => 'sci', 'Sed0006754' => 'sed', 'Sed0008741' => 'sed', 'Sed0017172' => 'sed', 'Sed0018925' => 'sed', 'Sed0023326' => 'sed', 'Sed0025909' => 'sed', 'SEGI_05333' => 'sgi', 'SEGI_10362' => 'sgi', 'SEGI_13380' => 'sgi', 'SEGI_24306' => 'sgi', 'SEGI_29077' => 'sgi', 'SEGI_29095' => 'sgi', 'SEGI_36534' => 'sgi', 'SEGI_37506' => 'sgi', 'SEGI_38321' => 'sgi', 'SGA_v2.0_scaffold307G48031' => 'sas', 'SGA_v2.0_scaffold47G17507' => 'sas', 'SGA_v2.0_scaffold63G21736' => 'sas', 'SGA_v2.0_scaffold87G27070' => 'sas', 'SHI17794' => 'shi', 'SHI28851' => 'shi', 'SMO165G0155' => 'smo', 'SMO340G0217' => 'smo', 'SMO367G1210' => 'smo', 'Solyc02g093430.3' => 'sly', 'Solyc05g013580.4' => 'sly', 'Solyc07g008030.3' => 'sly', 'Solyc12g035470.2' => 'sly', 'Sopen02g038020' => 'spe', 'Sopen05g008490' => 'spe', 'Sopen07g003910' => 'spe', 'Sopen12g015240' => 'spe', 'Sp1g11550' => 'spa', 'Sp2g16710' => 'spa', 'Sp3g00430' => 'spa', 'Sp3g26780' => 'spa', 'Sp5g22900' => 'spa', 'Sp6g29530' => 'spa', 'TAR371G0794' => 'tar', 'TAR374G0164' => 'tar', 'TAR622G0165' => 'tar', 'TAR626G0929' => 'tar', 'TAR629G2155' => 'tar', 'THA.LOC104805282' => 'tha', 'THA.LOC104805363' => 'tha', 'THA.LOC104808968' => 'tha', 'THA.LOC104821093' => 'tha', 'THA.LOC104823953' => 'tha', 'THA.LOC104825562' => 'tha', 'THA.LOC104825665' => 'tha', 'Thecc.02G261400' => 'tca', 'Thecc.04G019200' => 'tca', 'Thecc.09G130400' => 'tca', 'Thhalv10004374m.g' => 'esa', 'Thhalv10007850m.g' => 'esa', 'Thhalv10013782m.g' => 'esa', 'Thhalv10018686m.g' => 'esa', 'Thhalv10020899m.g' => 'esa', 'Thhalv10022755m.g' => 'esa', 'TPR.G23851' => 'tpr', 'TPR.G26500' => 'tpr', 'TPR.G27267' => 'tpr', 'TPR.G32001' => 'tpr', 'TPR.G6251' => 'tpr', 'TPR.G8167' => 'tpr', 'TWI12G1330' => 'twi', 'TWI18G1239' => 'twi', 'TWI34G0979' => 'twi', 'TWI36G0670' => 'twi', 'TWI36G0707' => 'twi', 'TWI56G0233' => 'twi', 'TWI75G1809' => 'twi', 'unitig_21.g20874' => 'ugi', 'unitig_26.g10343' => 'ugi', 'unitig_46.g18392' => 'ugi', 'unitig_52.g17178' => 'ugi', 'unitig_8.g2934' => 'ugi', 'vmacro01122' => 'vma', 'vmacro05875' => 'vma', 'vmacro06147' => 'vma', 'vmacro16191' => 'vma', 'vmacro18293' => 'vma', 'VMungo0251G3707' => 'vmu', 'VMungo0464G1521' => 'vmu', 'VMungo1215G0205' => 'vmu', 'VMungo1383G2484' => 'vmu', 'Zm00001eb079610' => 'zma', 'Zm00001eb135990' => 'zma', 'Zm00001eb183710' => 'zma', 'Zm00001eb246020' => 'zma' ), 'gf_id' => 'HOM05D001124', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001124' ), 'data_identifier' => 'HOM05D001124', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001124', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '548', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02520' => 'bna', 'A03p06630' => 'bna', 'A05p44460' => 'bna', 'A06p08710' => 'bna', 'A06p41090' => 'bna', 'A07p32320' => 'bna', 'A08p32520' => 'bna', 'A09p10360' => 'bna', 'A10p24080' => 'bna', 'Aa31LG11G15250' => 'aar', 'Aa31LG1G1800' => 'aar', 'Aa31LG2G5120' => 'aar', 'Aa31LG2G6070' => 'aar', 'Aa31LG5G10770' => 'aar', 'Aa31sc61G90' => 'aar', 'Actinidia01352' => 'ach', 'Actinidia05983' => 'ach', 'Actinidia08133' => 'ach', 'Actinidia15101' => 'ach', 'Actinidia26379' => 'ach', 'Actinidia35778' => 'ach', 'Actinidia36123' => 'ach', 'Actinidia37436' => 'ach', 'Actinidia38730' => 'ach', 'Ah.02g128210' => 'amhyb', 'Ah.03g132990' => 'amhyb', 'Ah.14g079410' => 'amhyb', 'AL1G24640' => 'aly', 'AL2G26680' => 'aly', 'AL3G10530' => 'aly', 'AL3G45230' => 'aly', 'AL5G15230' => 'aly', 'AL5G16960' => 'aly', 'AL6G25210' => 'aly', 'Aqoxy2G00441' => 'aox', 'Aqoxy3G01236' => 'aox', 'Aqoxy5G03746' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3RQ047' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C7GMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9C8JER' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MBL6KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YXCZ83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZANX40' => 'arhy', 'AT1G12990' => 'ath', 'AT1G67880' => 'ath', 'AT2G13290' => 'ath', 'AT3G01620' => 'ath', 'AT3G26445' => 'ath', 'AT3G27540' => 'ath', 'AT5G14480' => 'ath', 'ATR0824G026' => 'atr', 'ATR1098G019' => 'atr', 'Atru.chr11.2145' => 'acertr', 'Atru.chr2.3636' => 'acertr', 'Atru.chr2.3644' => 'acertr', 'Atru.chr6.2422' => 'acertr', 'Atru.chr7.1112' => 'acertr', 'AUR62005469' => 'cqu', 'AUR62011166' => 'cqu', 'AUR62013319' => 'cqu', 'AUR62024273' => 'cqu', 'AUR62028420' => 'cqu', 'AUR62041942' => 'cqu', 'BcaB01g04969' => 'bca', 'BcaB01g06371' => 'bca', 'BcaB02g11494' => 'bca', 'BcaB03g15382' => 'bca', 'BcaB08g36994' => 'bca', 'BcaC03g13477' => 'bca', 'BcaC03g13478' => 'bca', 'BcaC03g13480' => 'bca', 'BcaC03g13481' => 'bca', 'BcaC03g13486' => 'bca', 'BcaC04g19031' => 'bca', 'BcaC04g23085' => 'bca', 'BcaC05g25094' => 'bca', 'BcaC05g25096' => 'bca', 'BcaC05g25138' => 'bca', 'BcaC05g30416' => 'bca', 'BcaC05g30455' => 'bca', 'BcaC06g30979' => 'bca', 'BcaC06g33805' => 'bca', 'BcaC08g46021' => 'bca', 'BcaNung03154' => 'bca', 'BolC2t06623H' => 'bol', 'BolC2t06632H' => 'bol', 'BolC2t06635H' => 'bol', 'BolC2t06638H' => 'bol', 'BolC3t13266H' => 'bol', 'BolC5t29776H' => 'bol', 'BolC6t38912H' => 'bol', 'BolC7t44183H' => 'bol', 'BolC9t54123H' => 'bol', 'BolC9t59107H' => 'bol', 'BraA02t05221Z' => 'bra', 'BraA03t09996Z' => 'bra', 'BraA05t23210Z' => 'bra', 'BraA06t24068Z' => 'bra', 'BraA06t27032Z' => 'bra', 'BraA08t35176Z' => 'bra', 'BraA09t36680Z' => 'bra', 'BraA10t44471Z' => 'bra', 'C02p06760' => 'bna', 'C02p06890' => 'bna', 'C02p07010' => 'bna', 'C03p07660' => 'bna', 'C05p10300' => 'bna', 'C06p38150' => 'bna', 'C07p36650' => 'bna', 'C08p15770' => 'bna', 'C09p12300' => 'bna', 'C09p62700' => 'bna', 'C09p75040' => 'bna', 'CAN.G13.1' => 'can', 'CAN.G138.4' => 'can', 'CAN.G44.6' => 'can', 'CAN.G473.19' => 'can', 'CANSAT01G0835' => 'cansat', 'CANSAT11G0246' => 'cansat', 'CANSAT11G1766' => 'cansat', 'CANSAT64G1954' => 'cansat', 'CARHR013330' => 'chi', 'CARHR060530' => 'chi', 'CARHR075300' => 'chi', 'CARHR105120' => 'chi', 'CARHR148910' => 'chi', 'CARHR198830' => 'chi', 'Carub.0001s1275' => 'cru', 'Carub.0002s1437' => 'cru', 'Carub.0003s0044' => 'cru', 'Carub.0003s2787' => 'cru', 'Carub.0005s0597' => 'cru', 'Carub.0006s1266' => 'cru', 'Ca_06935_v3' => 'car', 'Ca_13559_v3' => 'car', 'Ca_16941_v3' => 'car', 'Ca_16960_v3' => 'car', 'Ca_17775_v3' => 'car', 'Ca_30464_v3' => 'car', 'Cc06_g08160' => 'ccan', 'Cc07_g01520' => 'ccan', 'Cc11_g15810' => 'ccan', 'CDE02G2840' => 'cde', 'CDE03G0093' => 'cde', 'CDE04G2127' => 'cde', 'CDE07G1857' => 'cde', 'CDE09G1246' => 'cde', 'Cfa003412' => 'cfa', 'Cfa007341' => 'cfa', 'Cfa009220' => 'cfa', 'Ciclev10008737m.g' => 'ccl', 'Ciclev10015565m.g' => 'ccl', 'Ciclev10031761m.g' => 'ccl', 'CiPaw.03G045300' => 'cil', 'CiPaw.03G247200' => 'cil', 'CiPaw.04G029500' => 'cil', 'CiPaw.04G174000' => 'cil', 'CiPaw.05G181200' => 'cil', 'CiPaw.06G067100' => 'cil', 'ClCG05G025800' => 'cla', 'ClCG06G011400' => 'cla', 'ClCG09G019360' => 'cla', 'COL.COLO4_04827' => 'col', 'COL.COLO4_29170' => 'col', 'COL.COLO4_35131' => 'col', 'COL.COLO4_35132' => 'col', 'Cpa.g.sc33.32' => 'cpa', 'Cpa.g.sc46.29' => 'cpa', 'Cpa.g.sc796.1' => 'cpa', 'CsaV3_1G030420' => 'csa', 'CsaV3_5G027050' => 'csa', 'CsaV3_5G031040' => 'csa', 'CsaV3_UNG023130' => 'csa', 'CSS0007726' => 'camsi', 'CSS0016433' => 'camsi', 'CSS0017656' => 'camsi', 'CSS0025364' => 'camsi', 'CSS0027582' => 'camsi', 'CSS0047288' => 'camsi', 'CSS0049950' => 'camsi', 'DCAR_003843' => 'dca', 'DCAR_007052' => 'dca', 'DCAR_020884' => 'dca', 'DCAR_021730' => 'dca', 'DCAR_024423' => 'dca', 'DCAR_026509' => 'dca', 'DCAR_031158' => 'dca', 'Dinv14728' => 'din', 'Dinv15219' => 'din', 'Dinv25728' => 'din', 'Dinv33428' => 'din', 'Dinv36489' => 'din', 'Dinv41486' => 'din', 'Duzib147G0469' => 'dzi', 'Duzib168G0060' => 'dzi', 'Duzib187G1215' => 'dzi', 'Duzib248G0692' => 'dzi', 'Duzib251G0767' => 'dzi', 'Duzib264G0446' => 'dzi', 'Duzib268G0691' => 'dzi', 'ECA232G4767' => 'eca', 'ECA233G2838' => 'eca', 'ECA234G0391' => 'eca', 'ECA234G0857' => 'eca', 'ECA236G1593' => 'eca', 'ECA238G0565' => 'eca', 'ECA246G1027' => 'eca', 'ECA246G3223' => 'eca', 'ECA246G3470' => 'eca', 'EL10Ac6g13829' => 'bvu', 'EL10Ac6g14093' => 'bvu', 'EL10Ac8g18707' => 'bvu', 'Eucgr.C01369' => 'egr', 'Eucgr.H02492' => 'egr', 'Eucgr.I01733' => 'egr', 'Eucgr.J02255' => 'egr', 'Eucgr.J02257' => 'egr', 'Eucgr.J02258' => 'egr', 'FAN02G1601' => 'fan', 'FAN03G1586' => 'fan', 'FAN03G2986' => 'fan', 'FAN05G4837' => 'fan', 'FAN06G0146' => 'fan', 'FAN07G0858' => 'fan', 'FAN09G3179' => 'fan', 'FAN10G0669' => 'fan', 'FAN12G2358' => 'fan', 'FAN14G4198' => 'fan', 'FAN14G5112' => 'fan', 'FAN17G0342' => 'fan', 'FAN19G0342' => 'fan', 'FAN19G0962' => 'fan', 'FAN19G1101' => 'fan', 'FAN19G1872' => 'fan', 'FAN22G0356' => 'fan', 'FAN23G0744' => 'fan', 'FAN23G1914' => 'fan', 'FAN26G0032' => 'fan', 'FAN28G0625' => 'fan', 'FvH4_1g02710' => 'fve', 'FvH4_1g02720' => 'fve', 'FvH4_4g25670' => 'fve', 'FvH4_6g51700' => 'fve', 'FvH4_7g20170' => 'fve', 'Glyma.05G175000' => 'gma', 'Glyma.08G132300' => 'gma', 'Glyma.11G243000' => 'gma', 'Glyma.13G158900' => 'gma', 'Glyma.17G112400' => 'gma', 'Glyma.18G014100' => 'gma', 'Glyma.19G003100' => 'gma', 'Glyma.19G056500' => 'gma', 'Gohir.A01G158900' => 'ghi', 'Gohir.A05G312600' => 'ghi', 'Gohir.A05G354900' => 'ghi', 'Gohir.A07G037200' => 'ghi', 'Gohir.A09G030000' => 'ghi', 'Gohir.A12G145200' => 'ghi', 'Gohir.D01G151500' => 'ghi', 'Gohir.D04G058300' => 'ghi', 'Gohir.D05G314100' => 'ghi', 'Gohir.D07G041400' => 'ghi', 'Gohir.D09G029700' => 'ghi', 'Gohir.D12G149700' => 'ghi', 'Gorai.001G043800' => 'gra', 'Gorai.002G187800' => 'gra', 'Gorai.006G034700' => 'gra', 'Gorai.008G161200' => 'gra', 'Gorai.009G335700' => 'gra', 'Gorai.012G065000' => 'gra', 'GSVIVG01000535001' => 'vvi', 'GSVIVG01015572001' => 'vvi', 'GSVIVG01032386001' => 'vvi', 'HanXRQChr05g0138531' => 'han', 'HanXRQChr06g0174391' => 'han', 'HanXRQChr07g0199021' => 'han', 'HanXRQChr08g0208211' => 'han', 'HanXRQChr09g0255471' => 'han', 'HanXRQChr10g0315791' => 'han', 'HanXRQChr12g0371991' => 'han', 'HanXRQChr15g0475251' => 'han', 'HanXRQChr17g0540001' => 'han', 'HanXRQChr17g0548631' => 'han', 'HanXRQChr17g0569561' => 'han', 'Haze_12256' => 'cav', 'Haze_14756' => 'cav', 'Haze_25528' => 'cav', 'Hma1.2p1_0079F.1_g041020' => 'hma', 'Hma1.2p1_0818F.1_g223260' => 'hma', 'Hma1.2p1_1747F.1_g300530' => 'hma', 'HPP92_004607' => 'vpl', 'HPP92_004608' => 'vpl', 'HPP92_006181' => 'vpl', 'HPP92_012192' => 'vpl', 'HPP92_015680' => 'vpl', 'HPP92_020249' => 'vpl', 'HPP92_021376' => 'vpl', 'HPP92_024275' => 'vpl', 'Hund06031' => 'sun', 'Hund25391' => 'sun', 'Lalb_Chr07g0185371' => 'lal', 'Lalb_Chr07g0185381' => 'lal', 'Lalb_Chr12g0204011' => 'lal', 'Lalb_Chr13g0301671' => 'lal', 'Lalb_Chr14g0362851' => 'lal', 'Lalb_Chr24g0403581' => 'lal', 'Lj1g0000233' => 'lja', 'Lj2g0018120' => 'lja', 'Lj3C621T0' => 'lonja', 'Lj3P1059T14' => 'lonja', 'Lj3P611T9' => 'lonja', 'Lj3P614T13' => 'lonja', 'Lj3P615T5' => 'lonja', 'Lj4g0012315' => 'lja', 'Lj4g0026182' => 'lja', 'Lj6P813T16' => 'lonja', 'Lj7C427T7' => 'lonja', 'Lj7C427T8' => 'lonja', 'Lj7P600T41' => 'lonja', 'Lju41C42G17' => 'lonja', 'Lsat_1_v5_gn_0_47300' => 'lsa', 'Lsat_1_v5_gn_2_91280' => 'lsa', 'Lsat_1_v5_gn_3_30561' => 'lsa', 'Lsat_1_v5_gn_4_184321' => 'lsa', 'Lsat_1_v5_gn_4_4041' => 'lsa', 'Lsat_1_v5_gn_5_92000' => 'lsa', 'Lsat_1_v5_gn_8_152940' => 'lsa', 'Lsat_1_v5_gn_8_62401' => 'lsa', 'Manes.06G055900' => 'mes', 'Manes.12G022200' => 'mes', 'Manes.13G023300' => 'mes', 'Manes.14G115000' => 'mes', 'Manes.15G151700' => 'mes', 'Manes.17G111300' => 'mes', 'Mapoly0226s0009' => 'mpo', 'MBI02_g25363_MAGBIO' => 'mbi', 'MBI06_g00027_MAGBIO' => 'mbi', 'MBI10_g13034_MAGBIO' => 'mbi', 'MD09G1023400' => 'mdo', 'MD13G1100100' => 'mdo', 'MD15G1169200' => 'mdo', 'MD16G1101100' => 'mdo', 'MD17G1022900' => 'mdo', 'Medtr3g096150' => 'mtr', 'Medtr4g115070' => 'mtr', 'Medtr7g033325' => 'mtr', 'Medtr8g089840' => 'mtr', 'MELO3C010319.2' => 'cme', 'MELO3C011944.2' => 'cme', 'MELO3C021589.2' => 'cme', 'Migut.E00207' => 'egut', 'Migut.H00067' => 'egut', 'Migut.K00433' => 'egut', 'Migut.K00606' => 'egut', 'Migut.K01410' => 'egut', 'MSTRG.13347' => 'ama', 'MSTRG.24045' => 'ama', 'MSTRG.2428' => 'ama', 'MSTRG.26410' => 'ama', 'MSTRG.3139' => 'ama', 'MSTRG.3286' => 'ama', 'MSTRG.563' => 'ama', 'MSTRG.7941' => 'ama', 'Nitab4.5_0000028g0060' => 'nta', 'Nitab4.5_0000065g0260' => 'nta', 'Nitab4.5_0000112g0060' => 'nta', 'Nitab4.5_0000489g0120' => 'nta', 'Nitab4.5_0001776g0050' => 'nta', 'Nitab4.5_0001854g0010' => 'nta', 'Nitab4.5_0001860g0020' => 'nta', 'Nitab4.5_0004352g0010' => 'nta', 'Nitab4.5_0008716g0020' => 'nta', 'Nitab4.5_0008922g0010' => 'nta', 'Nn3g16693' => 'nnu', 'Nn4g22596' => 'nnu', 'Nn7g37639' => 'nnu', 'Oeu001701.1' => 'oeu', 'Oeu018149.1' => 'oeu', 'Oeu026220.1' => 'oeu', 'Oeu038635.1' => 'oeu', 'Oeu049176.1' => 'oeu', 'Oeu056706.1' => 'oeu', 'Oeu056937.1' => 'oeu', 'Oeu057540.1' => 'oeu', 'Os02g0594900' => 'osa', 'Os02g0595100' => 'osa', 'Os04g0477500' => 'osa', 'Os12g0611900' => 'osa', 'Peaxi162Scf00076g00020' => 'pax', 'Peaxi162Scf00128g00217' => 'pax', 'Peaxi162Scf00129g01640' => 'pax', 'Peaxi162Scf00669g00007' => 'pax', 'Peaxi162Scf00700g00421' => 'pax', 'Peaxi162Scf00801g00038' => 'pax', 'Peaxi162Scf00891g00025' => 'pax', 'PGR083G0909' => 'pgr', 'PGR119G1005' => 'pgr', 'PGR142G2236' => 'pgr', 'PGR142G3388' => 'pgr', 'PGSC0003DMG400004514' => 'stu', 'PGSC0003DMG400012635' => 'stu', 'PGSC0003DMG400015730' => 'stu', 'PGSC0003DMG400018611' => 'stu', 'PGSC0003DMG400030897' => 'stu', 'Phvul.001G254800' => 'pvu', 'Phvul.002G260100' => 'pvu', 'Phvul.003G167600' => 'pvu', 'Phvul.004G005100' => 'pvu', 'Potri.001G343600' => 'ptr', 'Potri.006G066700' => 'ptr', 'Potri.008G186000' => 'ptr', 'Potri.010G046900' => 'ptr', 'Potri.018G127900' => 'ptr', 'Pp3c20_17750' => 'ppa', 'Pp3c24_4380' => 'ppa', 'Prupe.1G245800' => 'ppe', 'Prupe.3G293400' => 'ppe', 'Prupe.7G247400' => 'ppe', 'Psat0s145g0120' => 'psa', 'Psat0s595g0040' => 'psa', 'Psat0s595g0120' => 'psa', 'Psat3g175040' => 'psa', 'Psat7g058120' => 'psa', 'PSO017G0428' => 'pso', 'PSO063G7510' => 'pso', 'PSO067G0046' => 'pso', 'PSO478G1073' => 'pso', 'PSO675G3677' => 'pso', 'PSO675G6558' => 'pso', 'PSO675G7520' => 'pso', 'PSO675G8959' => 'pso', 'QL02p074089' => 'qlo', 'QL02p089614' => 'qlo', 'QL03p057736' => 'qlo', 'RcHm_v2.0_Chr1g0364131' => 'rch', 'RcHm_v2.0_Chr2g0087801' => 'rch', 'RcHm_v2.0_Chr2g0087821' => 'rch', 'RcHm_v2.0_Chr2g0173231' => 'rch', 'RcHm_v2.0_Chr4g0433111' => 'rch', 'Rhsim03G0250300' => 'rsi', 'Rhsim08G0048400' => 'rsi', 'Rhsim10G0014800' => 'rsi', 'Rhsim12G0040100' => 'rsi', 'Rhsim12G0109700' => 'rsi', 'Sabra06G0049600' => 'sbr', 'Sabra08G0141000' => 'sbr', 'Sabra10G0021400' => 'sbr', 'Sabra16G0222900' => 'sbr', 'Sabra18G0108600' => 'sbr', 'SalBow1G0433' => 'sbo', 'SalBow1G2038' => 'sbo', 'SalBow1G5003' => 'sbo', 'SalBow7G1197' => 'sbo', 'SalBow8G3506' => 'sbo', 'Sc03g0007300' => 'sci', 'Sc11g0000950' => 'sci', 'Sc14g0008750' => 'sci', 'Sc18g0000420' => 'sci', 'Sed0006754' => 'sed', 'Sed0008741' => 'sed', 'Sed0017172' => 'sed', 'Sed0018925' => 'sed', 'Sed0023326' => 'sed', 'Sed0025909' => 'sed', 'SEGI_05333' => 'sgi', 'SEGI_10362' => 'sgi', 'SEGI_13380' => 'sgi', 'SEGI_24306' => 'sgi', 'SEGI_29077' => 'sgi', 'SEGI_29095' => 'sgi', 'SEGI_36534' => 'sgi', 'SEGI_37506' => 'sgi', 'SEGI_38321' => 'sgi', 'SGA_v2.0_scaffold307G48031' => 'sas', 'SGA_v2.0_scaffold47G17507' => 'sas', 'SGA_v2.0_scaffold63G21736' => 'sas', 'SGA_v2.0_scaffold87G27070' => 'sas', 'SHI17794' => 'shi', 'SHI28851' => 'shi', 'SMO165G0155' => 'smo', 'SMO340G0217' => 'smo', 'SMO367G1210' => 'smo', 'Solyc02g093430.3' => 'sly', 'Solyc05g013580.4' => 'sly', 'Solyc07g008030.3' => 'sly', 'Solyc12g035470.2' => 'sly', 'Sopen02g038020' => 'spe', 'Sopen05g008490' => 'spe', 'Sopen07g003910' => 'spe', 'Sopen12g015240' => 'spe', 'Sp1g11550' => 'spa', 'Sp2g16710' => 'spa', 'Sp3g00430' => 'spa', 'Sp3g26780' => 'spa', 'Sp5g22900' => 'spa', 'Sp6g29530' => 'spa', 'TAR371G0794' => 'tar', 'TAR374G0164' => 'tar', 'TAR622G0165' => 'tar', 'TAR626G0929' => 'tar', 'TAR629G2155' => 'tar', 'THA.LOC104805282' => 'tha', 'THA.LOC104805363' => 'tha', 'THA.LOC104808968' => 'tha', 'THA.LOC104821093' => 'tha', 'THA.LOC104823953' => 'tha', 'THA.LOC104825562' => 'tha', 'THA.LOC104825665' => 'tha', 'Thecc.02G261400' => 'tca', 'Thecc.04G019200' => 'tca', 'Thecc.09G130400' => 'tca', 'Thhalv10004374m.g' => 'esa', 'Thhalv10007850m.g' => 'esa', 'Thhalv10013782m.g' => 'esa', 'Thhalv10018686m.g' => 'esa', 'Thhalv10020899m.g' => 'esa', 'Thhalv10022755m.g' => 'esa', 'TPR.G23851' => 'tpr', 'TPR.G26500' => 'tpr', 'TPR.G27267' => 'tpr', 'TPR.G32001' => 'tpr', 'TPR.G6251' => 'tpr', 'TPR.G8167' => 'tpr', 'TWI12G1330' => 'twi', 'TWI18G1239' => 'twi', 'TWI34G0979' => 'twi', 'TWI36G0670' => 'twi', 'TWI36G0707' => 'twi', 'TWI56G0233' => 'twi', 'TWI75G1809' => 'twi', 'unitig_21.g20874' => 'ugi', 'unitig_26.g10343' => 'ugi', 'unitig_46.g18392' => 'ugi', 'unitig_52.g17178' => 'ugi', 'unitig_8.g2934' => 'ugi', 'vmacro01122' => 'vma', 'vmacro05875' => 'vma', 'vmacro06147' => 'vma', 'vmacro16191' => 'vma', 'vmacro18293' => 'vma', 'VMungo0251G3707' => 'vmu', 'VMungo0464G1521' => 'vmu', 'VMungo1215G0205' => 'vmu', 'VMungo1383G2484' => 'vmu', 'Zm00001eb079610' => 'zma', 'Zm00001eb135990' => 'zma', 'Zm00001eb183710' => 'zma', 'Zm00001eb246020' => 'zma' ) $gf_id = 'HOM05D001124' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001124' ) $data_identifier = 'HOM05D001124' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 6, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 7, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 21, 'bol' => (int) 10, 'bra' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 6, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 9, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 21, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 8, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 10, 'lsa' => (int) 8, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 8, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 9, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb246020' $species_info = array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ) $local_species = 'cil' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001124', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '548', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02520' => 'bna', 'A03p06630' => 'bna', 'A05p44460' => 'bna', 'A06p08710' => 'bna', 'A06p41090' => 'bna', 'A07p32320' => 'bna', 'A08p32520' => 'bna', 'A09p10360' => 'bna', 'A10p24080' => 'bna', 'Aa31LG11G15250' => 'aar', 'Aa31LG1G1800' => 'aar', 'Aa31LG2G5120' => 'aar', 'Aa31LG2G6070' => 'aar', 'Aa31LG5G10770' => 'aar', 'Aa31sc61G90' => 'aar', 'Actinidia01352' => 'ach', 'Actinidia05983' => 'ach', 'Actinidia08133' => 'ach', 'Actinidia15101' => 'ach', 'Actinidia26379' => 'ach', 'Actinidia35778' => 'ach', 'Actinidia36123' => 'ach', 'Actinidia37436' => 'ach', 'Actinidia38730' => 'ach', 'Ah.02g128210' => 'amhyb', 'Ah.03g132990' => 'amhyb', 'Ah.14g079410' => 'amhyb', 'AL1G24640' => 'aly', 'AL2G26680' => 'aly', 'AL3G10530' => 'aly', 'AL3G45230' => 'aly', 'AL5G15230' => 'aly', 'AL5G16960' => 'aly', 'AL6G25210' => 'aly', 'Aqoxy2G00441' => 'aox', 'Aqoxy3G01236' => 'aox', 'Aqoxy5G03746' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3RQ047' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C7GMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9C8JER' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MBL6KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YXCZ83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZANX40' => 'arhy', 'AT1G12990' => 'ath', 'AT1G67880' => 'ath', 'AT2G13290' => 'ath', 'AT3G01620' => 'ath', 'AT3G26445' => 'ath', 'AT3G27540' => 'ath', 'AT5G14480' => 'ath', 'ATR0824G026' => 'atr', 'ATR1098G019' => 'atr', 'Atru.chr11.2145' => 'acertr', 'Atru.chr2.3636' => 'acertr', 'Atru.chr2.3644' => 'acertr', 'Atru.chr6.2422' => 'acertr', 'Atru.chr7.1112' => 'acertr', 'AUR62005469' => 'cqu', 'AUR62011166' => 'cqu', 'AUR62013319' => 'cqu', 'AUR62024273' => 'cqu', 'AUR62028420' => 'cqu', 'AUR62041942' => 'cqu', 'BcaB01g04969' => 'bca', 'BcaB01g06371' => 'bca', 'BcaB02g11494' => 'bca', 'BcaB03g15382' => 'bca', 'BcaB08g36994' => 'bca', 'BcaC03g13477' => 'bca', 'BcaC03g13478' => 'bca', 'BcaC03g13480' => 'bca', 'BcaC03g13481' => 'bca', 'BcaC03g13486' => 'bca', 'BcaC04g19031' => 'bca', 'BcaC04g23085' => 'bca', 'BcaC05g25094' => 'bca', 'BcaC05g25096' => 'bca', 'BcaC05g25138' => 'bca', 'BcaC05g30416' => 'bca', 'BcaC05g30455' => 'bca', 'BcaC06g30979' => 'bca', 'BcaC06g33805' => 'bca', 'BcaC08g46021' => 'bca', 'BcaNung03154' => 'bca', 'BolC2t06623H' => 'bol', 'BolC2t06632H' => 'bol', 'BolC2t06635H' => 'bol', 'BolC2t06638H' => 'bol', 'BolC3t13266H' => 'bol', 'BolC5t29776H' => 'bol', 'BolC6t38912H' => 'bol', 'BolC7t44183H' => 'bol', 'BolC9t54123H' => 'bol', 'BolC9t59107H' => 'bol', 'BraA02t05221Z' => 'bra', 'BraA03t09996Z' => 'bra', 'BraA05t23210Z' => 'bra', 'BraA06t24068Z' => 'bra', 'BraA06t27032Z' => 'bra', 'BraA08t35176Z' => 'bra', 'BraA09t36680Z' => 'bra', 'BraA10t44471Z' => 'bra', 'C02p06760' => 'bna', 'C02p06890' => 'bna', 'C02p07010' => 'bna', 'C03p07660' => 'bna', 'C05p10300' => 'bna', 'C06p38150' => 'bna', 'C07p36650' => 'bna', 'C08p15770' => 'bna', 'C09p12300' => 'bna', 'C09p62700' => 'bna', 'C09p75040' => 'bna', 'CAN.G13.1' => 'can', 'CAN.G138.4' => 'can', 'CAN.G44.6' => 'can', 'CAN.G473.19' => 'can', 'CANSAT01G0835' => 'cansat', 'CANSAT11G0246' => 'cansat', 'CANSAT11G1766' => 'cansat', 'CANSAT64G1954' => 'cansat', 'CARHR013330' => 'chi', 'CARHR060530' => 'chi', 'CARHR075300' => 'chi', 'CARHR105120' => 'chi', 'CARHR148910' => 'chi', 'CARHR198830' => 'chi', 'Carub.0001s1275' => 'cru', 'Carub.0002s1437' => 'cru', 'Carub.0003s0044' => 'cru', 'Carub.0003s2787' => 'cru', 'Carub.0005s0597' => 'cru', 'Carub.0006s1266' => 'cru', 'Ca_06935_v3' => 'car', 'Ca_13559_v3' => 'car', 'Ca_16941_v3' => 'car', 'Ca_16960_v3' => 'car', 'Ca_17775_v3' => 'car', 'Ca_30464_v3' => 'car', 'Cc06_g08160' => 'ccan', 'Cc07_g01520' => 'ccan', 'Cc11_g15810' => 'ccan', 'CDE02G2840' => 'cde', 'CDE03G0093' => 'cde', 'CDE04G2127' => 'cde', 'CDE07G1857' => 'cde', 'CDE09G1246' => 'cde', 'Cfa003412' => 'cfa', 'Cfa007341' => 'cfa', 'Cfa009220' => 'cfa', 'Ciclev10008737m.g' => 'ccl', 'Ciclev10015565m.g' => 'ccl', 'Ciclev10031761m.g' => 'ccl', 'CiPaw.03G045300' => 'cil', 'CiPaw.03G247200' => 'cil', 'CiPaw.04G029500' => 'cil', 'CiPaw.04G174000' => 'cil', 'CiPaw.05G181200' => 'cil', 'CiPaw.06G067100' => 'cil', 'ClCG05G025800' => 'cla', 'ClCG06G011400' => 'cla', 'ClCG09G019360' => 'cla', 'COL.COLO4_04827' => 'col', 'COL.COLO4_29170' => 'col', 'COL.COLO4_35131' => 'col', 'COL.COLO4_35132' => 'col', 'Cpa.g.sc33.32' => 'cpa', 'Cpa.g.sc46.29' => 'cpa', 'Cpa.g.sc796.1' => 'cpa', 'CsaV3_1G030420' => 'csa', 'CsaV3_5G027050' => 'csa', 'CsaV3_5G031040' => 'csa', 'CsaV3_UNG023130' => 'csa', 'CSS0007726' => 'camsi', 'CSS0016433' => 'camsi', 'CSS0017656' => 'camsi', 'CSS0025364' => 'camsi', 'CSS0027582' => 'camsi', 'CSS0047288' => 'camsi', 'CSS0049950' => 'camsi', 'DCAR_003843' => 'dca', 'DCAR_007052' => 'dca', 'DCAR_020884' => 'dca', 'DCAR_021730' => 'dca', 'DCAR_024423' => 'dca', 'DCAR_026509' => 'dca', 'DCAR_031158' => 'dca', 'Dinv14728' => 'din', 'Dinv15219' => 'din', 'Dinv25728' => 'din', 'Dinv33428' => 'din', 'Dinv36489' => 'din', 'Dinv41486' => 'din', 'Duzib147G0469' => 'dzi', 'Duzib168G0060' => 'dzi', 'Duzib187G1215' => 'dzi', 'Duzib248G0692' => 'dzi', 'Duzib251G0767' => 'dzi', 'Duzib264G0446' => 'dzi', 'Duzib268G0691' => 'dzi', 'ECA232G4767' => 'eca', 'ECA233G2838' => 'eca', 'ECA234G0391' => 'eca', 'ECA234G0857' => 'eca', 'ECA236G1593' => 'eca', 'ECA238G0565' => 'eca', 'ECA246G1027' => 'eca', 'ECA246G3223' => 'eca', 'ECA246G3470' => 'eca', 'EL10Ac6g13829' => 'bvu', 'EL10Ac6g14093' => 'bvu', 'EL10Ac8g18707' => 'bvu', 'Eucgr.C01369' => 'egr', 'Eucgr.H02492' => 'egr', 'Eucgr.I01733' => 'egr', 'Eucgr.J02255' => 'egr', 'Eucgr.J02257' => 'egr', 'Eucgr.J02258' => 'egr', 'FAN02G1601' => 'fan', 'FAN03G1586' => 'fan', 'FAN03G2986' => 'fan', 'FAN05G4837' => 'fan', 'FAN06G0146' => 'fan', 'FAN07G0858' => 'fan', 'FAN09G3179' => 'fan', 'FAN10G0669' => 'fan', 'FAN12G2358' => 'fan', 'FAN14G4198' => 'fan', 'FAN14G5112' => 'fan', 'FAN17G0342' => 'fan', 'FAN19G0342' => 'fan', 'FAN19G0962' => 'fan', 'FAN19G1101' => 'fan', 'FAN19G1872' => 'fan', 'FAN22G0356' => 'fan', 'FAN23G0744' => 'fan', 'FAN23G1914' => 'fan', 'FAN26G0032' => 'fan', 'FAN28G0625' => 'fan', 'FvH4_1g02710' => 'fve', 'FvH4_1g02720' => 'fve', 'FvH4_4g25670' => 'fve', 'FvH4_6g51700' => 'fve', 'FvH4_7g20170' => 'fve', 'Glyma.05G175000' => 'gma', 'Glyma.08G132300' => 'gma', 'Glyma.11G243000' => 'gma', 'Glyma.13G158900' => 'gma', 'Glyma.17G112400' => 'gma', 'Glyma.18G014100' => 'gma', 'Glyma.19G003100' => 'gma', 'Glyma.19G056500' => 'gma', 'Gohir.A01G158900' => 'ghi', 'Gohir.A05G312600' => 'ghi', 'Gohir.A05G354900' => 'ghi', 'Gohir.A07G037200' => 'ghi', 'Gohir.A09G030000' => 'ghi', 'Gohir.A12G145200' => 'ghi', 'Gohir.D01G151500' => 'ghi', 'Gohir.D04G058300' => 'ghi', 'Gohir.D05G314100' => 'ghi', 'Gohir.D07G041400' => 'ghi', 'Gohir.D09G029700' => 'ghi', 'Gohir.D12G149700' => 'ghi', 'Gorai.001G043800' => 'gra', 'Gorai.002G187800' => 'gra', 'Gorai.006G034700' => 'gra', 'Gorai.008G161200' => 'gra', 'Gorai.009G335700' => 'gra', 'Gorai.012G065000' => 'gra', 'GSVIVG01000535001' => 'vvi', 'GSVIVG01015572001' => 'vvi', 'GSVIVG01032386001' => 'vvi', 'HanXRQChr05g0138531' => 'han', 'HanXRQChr06g0174391' => 'han', 'HanXRQChr07g0199021' => 'han', 'HanXRQChr08g0208211' => 'han', 'HanXRQChr09g0255471' => 'han', 'HanXRQChr10g0315791' => 'han', 'HanXRQChr12g0371991' => 'han', 'HanXRQChr15g0475251' => 'han', 'HanXRQChr17g0540001' => 'han', 'HanXRQChr17g0548631' => 'han', 'HanXRQChr17g0569561' => 'han', 'Haze_12256' => 'cav', 'Haze_14756' => 'cav', 'Haze_25528' => 'cav', 'Hma1.2p1_0079F.1_g041020' => 'hma', 'Hma1.2p1_0818F.1_g223260' => 'hma', 'Hma1.2p1_1747F.1_g300530' => 'hma', 'HPP92_004607' => 'vpl', 'HPP92_004608' => 'vpl', 'HPP92_006181' => 'vpl', 'HPP92_012192' => 'vpl', 'HPP92_015680' => 'vpl', 'HPP92_020249' => 'vpl', 'HPP92_021376' => 'vpl', 'HPP92_024275' => 'vpl', 'Hund06031' => 'sun', 'Hund25391' => 'sun', 'Lalb_Chr07g0185371' => 'lal', 'Lalb_Chr07g0185381' => 'lal', 'Lalb_Chr12g0204011' => 'lal', 'Lalb_Chr13g0301671' => 'lal', 'Lalb_Chr14g0362851' => 'lal', 'Lalb_Chr24g0403581' => 'lal', 'Lj1g0000233' => 'lja', 'Lj2g0018120' => 'lja', 'Lj3C621T0' => 'lonja', 'Lj3P1059T14' => 'lonja', 'Lj3P611T9' => 'lonja', 'Lj3P614T13' => 'lonja', 'Lj3P615T5' => 'lonja', 'Lj4g0012315' => 'lja', 'Lj4g0026182' => 'lja', 'Lj6P813T16' => 'lonja', 'Lj7C427T7' => 'lonja', 'Lj7C427T8' => 'lonja', 'Lj7P600T41' => 'lonja', 'Lju41C42G17' => 'lonja', 'Lsat_1_v5_gn_0_47300' => 'lsa', 'Lsat_1_v5_gn_2_91280' => 'lsa', 'Lsat_1_v5_gn_3_30561' => 'lsa', 'Lsat_1_v5_gn_4_184321' => 'lsa', 'Lsat_1_v5_gn_4_4041' => 'lsa', 'Lsat_1_v5_gn_5_92000' => 'lsa', 'Lsat_1_v5_gn_8_152940' => 'lsa', 'Lsat_1_v5_gn_8_62401' => 'lsa', 'Manes.06G055900' => 'mes', 'Manes.12G022200' => 'mes', 'Manes.13G023300' => 'mes', 'Manes.14G115000' => 'mes', 'Manes.15G151700' => 'mes', 'Manes.17G111300' => 'mes', 'Mapoly0226s0009' => 'mpo', 'MBI02_g25363_MAGBIO' => 'mbi', 'MBI06_g00027_MAGBIO' => 'mbi', 'MBI10_g13034_MAGBIO' => 'mbi', 'MD09G1023400' => 'mdo', 'MD13G1100100' => 'mdo', 'MD15G1169200' => 'mdo', 'MD16G1101100' => 'mdo', 'MD17G1022900' => 'mdo', 'Medtr3g096150' => 'mtr', 'Medtr4g115070' => 'mtr', 'Medtr7g033325' => 'mtr', 'Medtr8g089840' => 'mtr', 'MELO3C010319.2' => 'cme', 'MELO3C011944.2' => 'cme', 'MELO3C021589.2' => 'cme', 'Migut.E00207' => 'egut', 'Migut.H00067' => 'egut', 'Migut.K00433' => 'egut', 'Migut.K00606' => 'egut', 'Migut.K01410' => 'egut', 'MSTRG.13347' => 'ama', 'MSTRG.24045' => 'ama', 'MSTRG.2428' => 'ama', 'MSTRG.26410' => 'ama', 'MSTRG.3139' => 'ama', 'MSTRG.3286' => 'ama', 'MSTRG.563' => 'ama', 'MSTRG.7941' => 'ama', 'Nitab4.5_0000028g0060' => 'nta', 'Nitab4.5_0000065g0260' => 'nta', 'Nitab4.5_0000112g0060' => 'nta', 'Nitab4.5_0000489g0120' => 'nta', 'Nitab4.5_0001776g0050' => 'nta', 'Nitab4.5_0001854g0010' => 'nta', 'Nitab4.5_0001860g0020' => 'nta', 'Nitab4.5_0004352g0010' => 'nta', 'Nitab4.5_0008716g0020' => 'nta', 'Nitab4.5_0008922g0010' => 'nta', 'Nn3g16693' => 'nnu', 'Nn4g22596' => 'nnu', 'Nn7g37639' => 'nnu', 'Oeu001701.1' => 'oeu', 'Oeu018149.1' => 'oeu', 'Oeu026220.1' => 'oeu', 'Oeu038635.1' => 'oeu', 'Oeu049176.1' => 'oeu', 'Oeu056706.1' => 'oeu', 'Oeu056937.1' => 'oeu', 'Oeu057540.1' => 'oeu', 'Os02g0594900' => 'osa', 'Os02g0595100' => 'osa', 'Os04g0477500' => 'osa', 'Os12g0611900' => 'osa', 'Peaxi162Scf00076g00020' => 'pax', 'Peaxi162Scf00128g00217' => 'pax', 'Peaxi162Scf00129g01640' => 'pax', 'Peaxi162Scf00669g00007' => 'pax', 'Peaxi162Scf00700g00421' => 'pax', 'Peaxi162Scf00801g00038' => 'pax', 'Peaxi162Scf00891g00025' => 'pax', 'PGR083G0909' => 'pgr', 'PGR119G1005' => 'pgr', 'PGR142G2236' => 'pgr', 'PGR142G3388' => 'pgr', 'PGSC0003DMG400004514' => 'stu', 'PGSC0003DMG400012635' => 'stu', 'PGSC0003DMG400015730' => 'stu', 'PGSC0003DMG400018611' => 'stu', 'PGSC0003DMG400030897' => 'stu', 'Phvul.001G254800' => 'pvu', 'Phvul.002G260100' => 'pvu', 'Phvul.003G167600' => 'pvu', 'Phvul.004G005100' => 'pvu', 'Potri.001G343600' => 'ptr', 'Potri.006G066700' => 'ptr', 'Potri.008G186000' => 'ptr', 'Potri.010G046900' => 'ptr', 'Potri.018G127900' => 'ptr', 'Pp3c20_17750' => 'ppa', 'Pp3c24_4380' => 'ppa', 'Prupe.1G245800' => 'ppe', 'Prupe.3G293400' => 'ppe', 'Prupe.7G247400' => 'ppe', 'Psat0s145g0120' => 'psa', 'Psat0s595g0040' => 'psa', 'Psat0s595g0120' => 'psa', 'Psat3g175040' => 'psa', 'Psat7g058120' => 'psa', 'PSO017G0428' => 'pso', 'PSO063G7510' => 'pso', 'PSO067G0046' => 'pso', 'PSO478G1073' => 'pso', 'PSO675G3677' => 'pso', 'PSO675G6558' => 'pso', 'PSO675G7520' => 'pso', 'PSO675G8959' => 'pso', 'QL02p074089' => 'qlo', 'QL02p089614' => 'qlo', 'QL03p057736' => 'qlo', 'RcHm_v2.0_Chr1g0364131' => 'rch', 'RcHm_v2.0_Chr2g0087801' => 'rch', 'RcHm_v2.0_Chr2g0087821' => 'rch', 'RcHm_v2.0_Chr2g0173231' => 'rch', 'RcHm_v2.0_Chr4g0433111' => 'rch', 'Rhsim03G0250300' => 'rsi', 'Rhsim08G0048400' => 'rsi', 'Rhsim10G0014800' => 'rsi', 'Rhsim12G0040100' => 'rsi', 'Rhsim12G0109700' => 'rsi', 'Sabra06G0049600' => 'sbr', 'Sabra08G0141000' => 'sbr', 'Sabra10G0021400' => 'sbr', 'Sabra16G0222900' => 'sbr', 'Sabra18G0108600' => 'sbr', 'SalBow1G0433' => 'sbo', 'SalBow1G2038' => 'sbo', 'SalBow1G5003' => 'sbo', 'SalBow7G1197' => 'sbo', 'SalBow8G3506' => 'sbo', 'Sc03g0007300' => 'sci', 'Sc11g0000950' => 'sci', 'Sc14g0008750' => 'sci', 'Sc18g0000420' => 'sci', 'Sed0006754' => 'sed', 'Sed0008741' => 'sed', 'Sed0017172' => 'sed', 'Sed0018925' => 'sed', 'Sed0023326' => 'sed', 'Sed0025909' => 'sed', 'SEGI_05333' => 'sgi', 'SEGI_10362' => 'sgi', 'SEGI_13380' => 'sgi', 'SEGI_24306' => 'sgi', 'SEGI_29077' => 'sgi', 'SEGI_29095' => 'sgi', 'SEGI_36534' => 'sgi', 'SEGI_37506' => 'sgi', 'SEGI_38321' => 'sgi', 'SGA_v2.0_scaffold307G48031' => 'sas', 'SGA_v2.0_scaffold47G17507' => 'sas', 'SGA_v2.0_scaffold63G21736' => 'sas', 'SGA_v2.0_scaffold87G27070' => 'sas', 'SHI17794' => 'shi', 'SHI28851' => 'shi', 'SMO165G0155' => 'smo', 'SMO340G0217' => 'smo', 'SMO367G1210' => 'smo', 'Solyc02g093430.3' => 'sly', 'Solyc05g013580.4' => 'sly', 'Solyc07g008030.3' => 'sly', 'Solyc12g035470.2' => 'sly', 'Sopen02g038020' => 'spe', 'Sopen05g008490' => 'spe', 'Sopen07g003910' => 'spe', 'Sopen12g015240' => 'spe', 'Sp1g11550' => 'spa', 'Sp2g16710' => 'spa', 'Sp3g00430' => 'spa', 'Sp3g26780' => 'spa', 'Sp5g22900' => 'spa', 'Sp6g29530' => 'spa', 'TAR371G0794' => 'tar', 'TAR374G0164' => 'tar', 'TAR622G0165' => 'tar', 'TAR626G0929' => 'tar', 'TAR629G2155' => 'tar', 'THA.LOC104805282' => 'tha', 'THA.LOC104805363' => 'tha', 'THA.LOC104808968' => 'tha', 'THA.LOC104821093' => 'tha', 'THA.LOC104823953' => 'tha', 'THA.LOC104825562' => 'tha', 'THA.LOC104825665' => 'tha', 'Thecc.02G261400' => 'tca', 'Thecc.04G019200' => 'tca', 'Thecc.09G130400' => 'tca', 'Thhalv10004374m.g' => 'esa', 'Thhalv10007850m.g' => 'esa', 'Thhalv10013782m.g' => 'esa', 'Thhalv10018686m.g' => 'esa', 'Thhalv10020899m.g' => 'esa', 'Thhalv10022755m.g' => 'esa', 'TPR.G23851' => 'tpr', 'TPR.G26500' => 'tpr', 'TPR.G27267' => 'tpr', 'TPR.G32001' => 'tpr', 'TPR.G6251' => 'tpr', 'TPR.G8167' => 'tpr', 'TWI12G1330' => 'twi', 'TWI18G1239' => 'twi', 'TWI34G0979' => 'twi', 'TWI36G0670' => 'twi', 'TWI36G0707' => 'twi', 'TWI56G0233' => 'twi', 'TWI75G1809' => 'twi', 'unitig_21.g20874' => 'ugi', 'unitig_26.g10343' => 'ugi', 'unitig_46.g18392' => 'ugi', 'unitig_52.g17178' => 'ugi', 'unitig_8.g2934' => 'ugi', 'vmacro01122' => 'vma', 'vmacro05875' => 'vma', 'vmacro06147' => 'vma', 'vmacro16191' => 'vma', 'vmacro18293' => 'vma', 'VMungo0251G3707' => 'vmu', 'VMungo0464G1521' => 'vmu', 'VMungo1215G0205' => 'vmu', 'VMungo1383G2484' => 'vmu', 'Zm00001eb079610' => 'zma', 'Zm00001eb135990' => 'zma', 'Zm00001eb183710' => 'zma', 'Zm00001eb246020' => 'zma' ), 'gf_id' => 'HOM05D001124', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001124' ), 'data_identifier' => 'HOM05D001124', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001124', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '548', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02520' => 'bna', 'A03p06630' => 'bna', 'A05p44460' => 'bna', 'A06p08710' => 'bna', 'A06p41090' => 'bna', 'A07p32320' => 'bna', 'A08p32520' => 'bna', 'A09p10360' => 'bna', 'A10p24080' => 'bna', 'Aa31LG11G15250' => 'aar', 'Aa31LG1G1800' => 'aar', 'Aa31LG2G5120' => 'aar', 'Aa31LG2G6070' => 'aar', 'Aa31LG5G10770' => 'aar', 'Aa31sc61G90' => 'aar', 'Actinidia01352' => 'ach', 'Actinidia05983' => 'ach', 'Actinidia08133' => 'ach', 'Actinidia15101' => 'ach', 'Actinidia26379' => 'ach', 'Actinidia35778' => 'ach', 'Actinidia36123' => 'ach', 'Actinidia37436' => 'ach', 'Actinidia38730' => 'ach', 'Ah.02g128210' => 'amhyb', 'Ah.03g132990' => 'amhyb', 'Ah.14g079410' => 'amhyb', 'AL1G24640' => 'aly', 'AL2G26680' => 'aly', 'AL3G10530' => 'aly', 'AL3G45230' => 'aly', 'AL5G15230' => 'aly', 'AL5G16960' => 'aly', 'AL6G25210' => 'aly', 'Aqoxy2G00441' => 'aox', 'Aqoxy3G01236' => 'aox', 'Aqoxy5G03746' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3RQ047' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C7GMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9C8JER' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MBL6KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YXCZ83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZANX40' => 'arhy', 'AT1G12990' => 'ath', 'AT1G67880' => 'ath', 'AT2G13290' => 'ath', 'AT3G01620' => 'ath', 'AT3G26445' => 'ath', 'AT3G27540' => 'ath', 'AT5G14480' => 'ath', 'ATR0824G026' => 'atr', 'ATR1098G019' => 'atr', 'Atru.chr11.2145' => 'acertr', 'Atru.chr2.3636' => 'acertr', 'Atru.chr2.3644' => 'acertr', 'Atru.chr6.2422' => 'acertr', 'Atru.chr7.1112' => 'acertr', 'AUR62005469' => 'cqu', 'AUR62011166' => 'cqu', 'AUR62013319' => 'cqu', 'AUR62024273' => 'cqu', 'AUR62028420' => 'cqu', 'AUR62041942' => 'cqu', 'BcaB01g04969' => 'bca', 'BcaB01g06371' => 'bca', 'BcaB02g11494' => 'bca', 'BcaB03g15382' => 'bca', 'BcaB08g36994' => 'bca', 'BcaC03g13477' => 'bca', 'BcaC03g13478' => 'bca', 'BcaC03g13480' => 'bca', 'BcaC03g13481' => 'bca', 'BcaC03g13486' => 'bca', 'BcaC04g19031' => 'bca', 'BcaC04g23085' => 'bca', 'BcaC05g25094' => 'bca', 'BcaC05g25096' => 'bca', 'BcaC05g25138' => 'bca', 'BcaC05g30416' => 'bca', 'BcaC05g30455' => 'bca', 'BcaC06g30979' => 'bca', 'BcaC06g33805' => 'bca', 'BcaC08g46021' => 'bca', 'BcaNung03154' => 'bca', 'BolC2t06623H' => 'bol', 'BolC2t06632H' => 'bol', 'BolC2t06635H' => 'bol', 'BolC2t06638H' => 'bol', 'BolC3t13266H' => 'bol', 'BolC5t29776H' => 'bol', 'BolC6t38912H' => 'bol', 'BolC7t44183H' => 'bol', 'BolC9t54123H' => 'bol', 'BolC9t59107H' => 'bol', 'BraA02t05221Z' => 'bra', 'BraA03t09996Z' => 'bra', 'BraA05t23210Z' => 'bra', 'BraA06t24068Z' => 'bra', 'BraA06t27032Z' => 'bra', 'BraA08t35176Z' => 'bra', 'BraA09t36680Z' => 'bra', 'BraA10t44471Z' => 'bra', 'C02p06760' => 'bna', 'C02p06890' => 'bna', 'C02p07010' => 'bna', 'C03p07660' => 'bna', 'C05p10300' => 'bna', 'C06p38150' => 'bna', 'C07p36650' => 'bna', 'C08p15770' => 'bna', 'C09p12300' => 'bna', 'C09p62700' => 'bna', 'C09p75040' => 'bna', 'CAN.G13.1' => 'can', 'CAN.G138.4' => 'can', 'CAN.G44.6' => 'can', 'CAN.G473.19' => 'can', 'CANSAT01G0835' => 'cansat', 'CANSAT11G0246' => 'cansat', 'CANSAT11G1766' => 'cansat', 'CANSAT64G1954' => 'cansat', 'CARHR013330' => 'chi', 'CARHR060530' => 'chi', 'CARHR075300' => 'chi', 'CARHR105120' => 'chi', 'CARHR148910' => 'chi', 'CARHR198830' => 'chi', 'Carub.0001s1275' => 'cru', 'Carub.0002s1437' => 'cru', 'Carub.0003s0044' => 'cru', 'Carub.0003s2787' => 'cru', 'Carub.0005s0597' => 'cru', 'Carub.0006s1266' => 'cru', 'Ca_06935_v3' => 'car', 'Ca_13559_v3' => 'car', 'Ca_16941_v3' => 'car', 'Ca_16960_v3' => 'car', 'Ca_17775_v3' => 'car', 'Ca_30464_v3' => 'car', 'Cc06_g08160' => 'ccan', 'Cc07_g01520' => 'ccan', 'Cc11_g15810' => 'ccan', 'CDE02G2840' => 'cde', 'CDE03G0093' => 'cde', 'CDE04G2127' => 'cde', 'CDE07G1857' => 'cde', 'CDE09G1246' => 'cde', 'Cfa003412' => 'cfa', 'Cfa007341' => 'cfa', 'Cfa009220' => 'cfa', 'Ciclev10008737m.g' => 'ccl', 'Ciclev10015565m.g' => 'ccl', 'Ciclev10031761m.g' => 'ccl', 'CiPaw.03G045300' => 'cil', 'CiPaw.03G247200' => 'cil', 'CiPaw.04G029500' => 'cil', 'CiPaw.04G174000' => 'cil', 'CiPaw.05G181200' => 'cil', 'CiPaw.06G067100' => 'cil', 'ClCG05G025800' => 'cla', 'ClCG06G011400' => 'cla', 'ClCG09G019360' => 'cla', 'COL.COLO4_04827' => 'col', 'COL.COLO4_29170' => 'col', 'COL.COLO4_35131' => 'col', 'COL.COLO4_35132' => 'col', 'Cpa.g.sc33.32' => 'cpa', 'Cpa.g.sc46.29' => 'cpa', 'Cpa.g.sc796.1' => 'cpa', 'CsaV3_1G030420' => 'csa', 'CsaV3_5G027050' => 'csa', 'CsaV3_5G031040' => 'csa', 'CsaV3_UNG023130' => 'csa', 'CSS0007726' => 'camsi', 'CSS0016433' => 'camsi', 'CSS0017656' => 'camsi', 'CSS0025364' => 'camsi', 'CSS0027582' => 'camsi', 'CSS0047288' => 'camsi', 'CSS0049950' => 'camsi', 'DCAR_003843' => 'dca', 'DCAR_007052' => 'dca', 'DCAR_020884' => 'dca', 'DCAR_021730' => 'dca', 'DCAR_024423' => 'dca', 'DCAR_026509' => 'dca', 'DCAR_031158' => 'dca', 'Dinv14728' => 'din', 'Dinv15219' => 'din', 'Dinv25728' => 'din', 'Dinv33428' => 'din', 'Dinv36489' => 'din', 'Dinv41486' => 'din', 'Duzib147G0469' => 'dzi', 'Duzib168G0060' => 'dzi', 'Duzib187G1215' => 'dzi', 'Duzib248G0692' => 'dzi', 'Duzib251G0767' => 'dzi', 'Duzib264G0446' => 'dzi', 'Duzib268G0691' => 'dzi', 'ECA232G4767' => 'eca', 'ECA233G2838' => 'eca', 'ECA234G0391' => 'eca', 'ECA234G0857' => 'eca', 'ECA236G1593' => 'eca', 'ECA238G0565' => 'eca', 'ECA246G1027' => 'eca', 'ECA246G3223' => 'eca', 'ECA246G3470' => 'eca', 'EL10Ac6g13829' => 'bvu', 'EL10Ac6g14093' => 'bvu', 'EL10Ac8g18707' => 'bvu', 'Eucgr.C01369' => 'egr', 'Eucgr.H02492' => 'egr', 'Eucgr.I01733' => 'egr', 'Eucgr.J02255' => 'egr', 'Eucgr.J02257' => 'egr', 'Eucgr.J02258' => 'egr', 'FAN02G1601' => 'fan', 'FAN03G1586' => 'fan', 'FAN03G2986' => 'fan', 'FAN05G4837' => 'fan', 'FAN06G0146' => 'fan', 'FAN07G0858' => 'fan', 'FAN09G3179' => 'fan', 'FAN10G0669' => 'fan', 'FAN12G2358' => 'fan', 'FAN14G4198' => 'fan', 'FAN14G5112' => 'fan', 'FAN17G0342' => 'fan', 'FAN19G0342' => 'fan', 'FAN19G0962' => 'fan', 'FAN19G1101' => 'fan', 'FAN19G1872' => 'fan', 'FAN22G0356' => 'fan', 'FAN23G0744' => 'fan', 'FAN23G1914' => 'fan', 'FAN26G0032' => 'fan', 'FAN28G0625' => 'fan', 'FvH4_1g02710' => 'fve', 'FvH4_1g02720' => 'fve', 'FvH4_4g25670' => 'fve', 'FvH4_6g51700' => 'fve', 'FvH4_7g20170' => 'fve', 'Glyma.05G175000' => 'gma', 'Glyma.08G132300' => 'gma', 'Glyma.11G243000' => 'gma', 'Glyma.13G158900' => 'gma', 'Glyma.17G112400' => 'gma', 'Glyma.18G014100' => 'gma', 'Glyma.19G003100' => 'gma', 'Glyma.19G056500' => 'gma', 'Gohir.A01G158900' => 'ghi', 'Gohir.A05G312600' => 'ghi', 'Gohir.A05G354900' => 'ghi', 'Gohir.A07G037200' => 'ghi', 'Gohir.A09G030000' => 'ghi', 'Gohir.A12G145200' => 'ghi', 'Gohir.D01G151500' => 'ghi', 'Gohir.D04G058300' => 'ghi', 'Gohir.D05G314100' => 'ghi', 'Gohir.D07G041400' => 'ghi', 'Gohir.D09G029700' => 'ghi', 'Gohir.D12G149700' => 'ghi', 'Gorai.001G043800' => 'gra', 'Gorai.002G187800' => 'gra', 'Gorai.006G034700' => 'gra', 'Gorai.008G161200' => 'gra', 'Gorai.009G335700' => 'gra', 'Gorai.012G065000' => 'gra', 'GSVIVG01000535001' => 'vvi', 'GSVIVG01015572001' => 'vvi', 'GSVIVG01032386001' => 'vvi', 'HanXRQChr05g0138531' => 'han', 'HanXRQChr06g0174391' => 'han', 'HanXRQChr07g0199021' => 'han', 'HanXRQChr08g0208211' => 'han', 'HanXRQChr09g0255471' => 'han', 'HanXRQChr10g0315791' => 'han', 'HanXRQChr12g0371991' => 'han', 'HanXRQChr15g0475251' => 'han', 'HanXRQChr17g0540001' => 'han', 'HanXRQChr17g0548631' => 'han', 'HanXRQChr17g0569561' => 'han', 'Haze_12256' => 'cav', 'Haze_14756' => 'cav', 'Haze_25528' => 'cav', 'Hma1.2p1_0079F.1_g041020' => 'hma', 'Hma1.2p1_0818F.1_g223260' => 'hma', 'Hma1.2p1_1747F.1_g300530' => 'hma', 'HPP92_004607' => 'vpl', 'HPP92_004608' => 'vpl', 'HPP92_006181' => 'vpl', 'HPP92_012192' => 'vpl', 'HPP92_015680' => 'vpl', 'HPP92_020249' => 'vpl', 'HPP92_021376' => 'vpl', 'HPP92_024275' => 'vpl', 'Hund06031' => 'sun', 'Hund25391' => 'sun', 'Lalb_Chr07g0185371' => 'lal', 'Lalb_Chr07g0185381' => 'lal', 'Lalb_Chr12g0204011' => 'lal', 'Lalb_Chr13g0301671' => 'lal', 'Lalb_Chr14g0362851' => 'lal', 'Lalb_Chr24g0403581' => 'lal', 'Lj1g0000233' => 'lja', 'Lj2g0018120' => 'lja', 'Lj3C621T0' => 'lonja', 'Lj3P1059T14' => 'lonja', 'Lj3P611T9' => 'lonja', 'Lj3P614T13' => 'lonja', 'Lj3P615T5' => 'lonja', 'Lj4g0012315' => 'lja', 'Lj4g0026182' => 'lja', 'Lj6P813T16' => 'lonja', 'Lj7C427T7' => 'lonja', 'Lj7C427T8' => 'lonja', 'Lj7P600T41' => 'lonja', 'Lju41C42G17' => 'lonja', 'Lsat_1_v5_gn_0_47300' => 'lsa', 'Lsat_1_v5_gn_2_91280' => 'lsa', 'Lsat_1_v5_gn_3_30561' => 'lsa', 'Lsat_1_v5_gn_4_184321' => 'lsa', 'Lsat_1_v5_gn_4_4041' => 'lsa', 'Lsat_1_v5_gn_5_92000' => 'lsa', 'Lsat_1_v5_gn_8_152940' => 'lsa', 'Lsat_1_v5_gn_8_62401' => 'lsa', 'Manes.06G055900' => 'mes', 'Manes.12G022200' => 'mes', 'Manes.13G023300' => 'mes', 'Manes.14G115000' => 'mes', 'Manes.15G151700' => 'mes', 'Manes.17G111300' => 'mes', 'Mapoly0226s0009' => 'mpo', 'MBI02_g25363_MAGBIO' => 'mbi', 'MBI06_g00027_MAGBIO' => 'mbi', 'MBI10_g13034_MAGBIO' => 'mbi', 'MD09G1023400' => 'mdo', 'MD13G1100100' => 'mdo', 'MD15G1169200' => 'mdo', 'MD16G1101100' => 'mdo', 'MD17G1022900' => 'mdo', 'Medtr3g096150' => 'mtr', 'Medtr4g115070' => 'mtr', 'Medtr7g033325' => 'mtr', 'Medtr8g089840' => 'mtr', 'MELO3C010319.2' => 'cme', 'MELO3C011944.2' => 'cme', 'MELO3C021589.2' => 'cme', 'Migut.E00207' => 'egut', 'Migut.H00067' => 'egut', 'Migut.K00433' => 'egut', 'Migut.K00606' => 'egut', 'Migut.K01410' => 'egut', 'MSTRG.13347' => 'ama', 'MSTRG.24045' => 'ama', 'MSTRG.2428' => 'ama', 'MSTRG.26410' => 'ama', 'MSTRG.3139' => 'ama', 'MSTRG.3286' => 'ama', 'MSTRG.563' => 'ama', 'MSTRG.7941' => 'ama', 'Nitab4.5_0000028g0060' => 'nta', 'Nitab4.5_0000065g0260' => 'nta', 'Nitab4.5_0000112g0060' => 'nta', 'Nitab4.5_0000489g0120' => 'nta', 'Nitab4.5_0001776g0050' => 'nta', 'Nitab4.5_0001854g0010' => 'nta', 'Nitab4.5_0001860g0020' => 'nta', 'Nitab4.5_0004352g0010' => 'nta', 'Nitab4.5_0008716g0020' => 'nta', 'Nitab4.5_0008922g0010' => 'nta', 'Nn3g16693' => 'nnu', 'Nn4g22596' => 'nnu', 'Nn7g37639' => 'nnu', 'Oeu001701.1' => 'oeu', 'Oeu018149.1' => 'oeu', 'Oeu026220.1' => 'oeu', 'Oeu038635.1' => 'oeu', 'Oeu049176.1' => 'oeu', 'Oeu056706.1' => 'oeu', 'Oeu056937.1' => 'oeu', 'Oeu057540.1' => 'oeu', 'Os02g0594900' => 'osa', 'Os02g0595100' => 'osa', 'Os04g0477500' => 'osa', 'Os12g0611900' => 'osa', 'Peaxi162Scf00076g00020' => 'pax', 'Peaxi162Scf00128g00217' => 'pax', 'Peaxi162Scf00129g01640' => 'pax', 'Peaxi162Scf00669g00007' => 'pax', 'Peaxi162Scf00700g00421' => 'pax', 'Peaxi162Scf00801g00038' => 'pax', 'Peaxi162Scf00891g00025' => 'pax', 'PGR083G0909' => 'pgr', 'PGR119G1005' => 'pgr', 'PGR142G2236' => 'pgr', 'PGR142G3388' => 'pgr', 'PGSC0003DMG400004514' => 'stu', 'PGSC0003DMG400012635' => 'stu', 'PGSC0003DMG400015730' => 'stu', 'PGSC0003DMG400018611' => 'stu', 'PGSC0003DMG400030897' => 'stu', 'Phvul.001G254800' => 'pvu', 'Phvul.002G260100' => 'pvu', 'Phvul.003G167600' => 'pvu', 'Phvul.004G005100' => 'pvu', 'Potri.001G343600' => 'ptr', 'Potri.006G066700' => 'ptr', 'Potri.008G186000' => 'ptr', 'Potri.010G046900' => 'ptr', 'Potri.018G127900' => 'ptr', 'Pp3c20_17750' => 'ppa', 'Pp3c24_4380' => 'ppa', 'Prupe.1G245800' => 'ppe', 'Prupe.3G293400' => 'ppe', 'Prupe.7G247400' => 'ppe', 'Psat0s145g0120' => 'psa', 'Psat0s595g0040' => 'psa', 'Psat0s595g0120' => 'psa', 'Psat3g175040' => 'psa', 'Psat7g058120' => 'psa', 'PSO017G0428' => 'pso', 'PSO063G7510' => 'pso', 'PSO067G0046' => 'pso', 'PSO478G1073' => 'pso', 'PSO675G3677' => 'pso', 'PSO675G6558' => 'pso', 'PSO675G7520' => 'pso', 'PSO675G8959' => 'pso', 'QL02p074089' => 'qlo', 'QL02p089614' => 'qlo', 'QL03p057736' => 'qlo', 'RcHm_v2.0_Chr1g0364131' => 'rch', 'RcHm_v2.0_Chr2g0087801' => 'rch', 'RcHm_v2.0_Chr2g0087821' => 'rch', 'RcHm_v2.0_Chr2g0173231' => 'rch', 'RcHm_v2.0_Chr4g0433111' => 'rch', 'Rhsim03G0250300' => 'rsi', 'Rhsim08G0048400' => 'rsi', 'Rhsim10G0014800' => 'rsi', 'Rhsim12G0040100' => 'rsi', 'Rhsim12G0109700' => 'rsi', 'Sabra06G0049600' => 'sbr', 'Sabra08G0141000' => 'sbr', 'Sabra10G0021400' => 'sbr', 'Sabra16G0222900' => 'sbr', 'Sabra18G0108600' => 'sbr', 'SalBow1G0433' => 'sbo', 'SalBow1G2038' => 'sbo', 'SalBow1G5003' => 'sbo', 'SalBow7G1197' => 'sbo', 'SalBow8G3506' => 'sbo', 'Sc03g0007300' => 'sci', 'Sc11g0000950' => 'sci', 'Sc14g0008750' => 'sci', 'Sc18g0000420' => 'sci', 'Sed0006754' => 'sed', 'Sed0008741' => 'sed', 'Sed0017172' => 'sed', 'Sed0018925' => 'sed', 'Sed0023326' => 'sed', 'Sed0025909' => 'sed', 'SEGI_05333' => 'sgi', 'SEGI_10362' => 'sgi', 'SEGI_13380' => 'sgi', 'SEGI_24306' => 'sgi', 'SEGI_29077' => 'sgi', 'SEGI_29095' => 'sgi', 'SEGI_36534' => 'sgi', 'SEGI_37506' => 'sgi', 'SEGI_38321' => 'sgi', 'SGA_v2.0_scaffold307G48031' => 'sas', 'SGA_v2.0_scaffold47G17507' => 'sas', 'SGA_v2.0_scaffold63G21736' => 'sas', 'SGA_v2.0_scaffold87G27070' => 'sas', 'SHI17794' => 'shi', 'SHI28851' => 'shi', 'SMO165G0155' => 'smo', 'SMO340G0217' => 'smo', 'SMO367G1210' => 'smo', 'Solyc02g093430.3' => 'sly', 'Solyc05g013580.4' => 'sly', 'Solyc07g008030.3' => 'sly', 'Solyc12g035470.2' => 'sly', 'Sopen02g038020' => 'spe', 'Sopen05g008490' => 'spe', 'Sopen07g003910' => 'spe', 'Sopen12g015240' => 'spe', 'Sp1g11550' => 'spa', 'Sp2g16710' => 'spa', 'Sp3g00430' => 'spa', 'Sp3g26780' => 'spa', 'Sp5g22900' => 'spa', 'Sp6g29530' => 'spa', 'TAR371G0794' => 'tar', 'TAR374G0164' => 'tar', 'TAR622G0165' => 'tar', 'TAR626G0929' => 'tar', 'TAR629G2155' => 'tar', 'THA.LOC104805282' => 'tha', 'THA.LOC104805363' => 'tha', 'THA.LOC104808968' => 'tha', 'THA.LOC104821093' => 'tha', 'THA.LOC104823953' => 'tha', 'THA.LOC104825562' => 'tha', 'THA.LOC104825665' => 'tha', 'Thecc.02G261400' => 'tca', 'Thecc.04G019200' => 'tca', 'Thecc.09G130400' => 'tca', 'Thhalv10004374m.g' => 'esa', 'Thhalv10007850m.g' => 'esa', 'Thhalv10013782m.g' => 'esa', 'Thhalv10018686m.g' => 'esa', 'Thhalv10020899m.g' => 'esa', 'Thhalv10022755m.g' => 'esa', 'TPR.G23851' => 'tpr', 'TPR.G26500' => 'tpr', 'TPR.G27267' => 'tpr', 'TPR.G32001' => 'tpr', 'TPR.G6251' => 'tpr', 'TPR.G8167' => 'tpr', 'TWI12G1330' => 'twi', 'TWI18G1239' => 'twi', 'TWI34G0979' => 'twi', 'TWI36G0670' => 'twi', 'TWI36G0707' => 'twi', 'TWI56G0233' => 'twi', 'TWI75G1809' => 'twi', 'unitig_21.g20874' => 'ugi', 'unitig_26.g10343' => 'ugi', 'unitig_46.g18392' => 'ugi', 'unitig_52.g17178' => 'ugi', 'unitig_8.g2934' => 'ugi', 'vmacro01122' => 'vma', 'vmacro05875' => 'vma', 'vmacro06147' => 'vma', 'vmacro16191' => 'vma', 'vmacro18293' => 'vma', 'VMungo0251G3707' => 'vmu', 'VMungo0464G1521' => 'vmu', 'VMungo1215G0205' => 'vmu', 'VMungo1383G2484' => 'vmu', 'Zm00001eb079610' => 'zma', 'Zm00001eb135990' => 'zma', 'Zm00001eb183710' => 'zma', 'Zm00001eb246020' => 'zma' ) $gf_id = 'HOM05D001124' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001124' ) $data_identifier = 'HOM05D001124' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 6, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 7, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 21, 'bol' => (int) 10, 'bra' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 6, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 9, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 21, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 8, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 10, 'lsa' => (int) 8, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 8, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 9, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb246020' $species_info = array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ) $local_species = 'cil' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001124', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '548', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02520' => 'bna', 'A03p06630' => 'bna', 'A05p44460' => 'bna', 'A06p08710' => 'bna', 'A06p41090' => 'bna', 'A07p32320' => 'bna', 'A08p32520' => 'bna', 'A09p10360' => 'bna', 'A10p24080' => 'bna', 'Aa31LG11G15250' => 'aar', 'Aa31LG1G1800' => 'aar', 'Aa31LG2G5120' => 'aar', 'Aa31LG2G6070' => 'aar', 'Aa31LG5G10770' => 'aar', 'Aa31sc61G90' => 'aar', 'Actinidia01352' => 'ach', 'Actinidia05983' => 'ach', 'Actinidia08133' => 'ach', 'Actinidia15101' => 'ach', 'Actinidia26379' => 'ach', 'Actinidia35778' => 'ach', 'Actinidia36123' => 'ach', 'Actinidia37436' => 'ach', 'Actinidia38730' => 'ach', 'Ah.02g128210' => 'amhyb', 'Ah.03g132990' => 'amhyb', 'Ah.14g079410' => 'amhyb', 'AL1G24640' => 'aly', 'AL2G26680' => 'aly', 'AL3G10530' => 'aly', 'AL3G45230' => 'aly', 'AL5G15230' => 'aly', 'AL5G16960' => 'aly', 'AL6G25210' => 'aly', 'Aqoxy2G00441' => 'aox', 'Aqoxy3G01236' => 'aox', 'Aqoxy5G03746' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3RQ047' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C7GMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9C8JER' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MBL6KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YXCZ83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZANX40' => 'arhy', 'AT1G12990' => 'ath', 'AT1G67880' => 'ath', 'AT2G13290' => 'ath', 'AT3G01620' => 'ath', 'AT3G26445' => 'ath', 'AT3G27540' => 'ath', 'AT5G14480' => 'ath', 'ATR0824G026' => 'atr', 'ATR1098G019' => 'atr', 'Atru.chr11.2145' => 'acertr', 'Atru.chr2.3636' => 'acertr', 'Atru.chr2.3644' => 'acertr', 'Atru.chr6.2422' => 'acertr', 'Atru.chr7.1112' => 'acertr', 'AUR62005469' => 'cqu', 'AUR62011166' => 'cqu', 'AUR62013319' => 'cqu', 'AUR62024273' => 'cqu', 'AUR62028420' => 'cqu', 'AUR62041942' => 'cqu', 'BcaB01g04969' => 'bca', 'BcaB01g06371' => 'bca', 'BcaB02g11494' => 'bca', 'BcaB03g15382' => 'bca', 'BcaB08g36994' => 'bca', 'BcaC03g13477' => 'bca', 'BcaC03g13478' => 'bca', 'BcaC03g13480' => 'bca', 'BcaC03g13481' => 'bca', 'BcaC03g13486' => 'bca', 'BcaC04g19031' => 'bca', 'BcaC04g23085' => 'bca', 'BcaC05g25094' => 'bca', 'BcaC05g25096' => 'bca', 'BcaC05g25138' => 'bca', 'BcaC05g30416' => 'bca', 'BcaC05g30455' => 'bca', 'BcaC06g30979' => 'bca', 'BcaC06g33805' => 'bca', 'BcaC08g46021' => 'bca', 'BcaNung03154' => 'bca', 'BolC2t06623H' => 'bol', 'BolC2t06632H' => 'bol', 'BolC2t06635H' => 'bol', 'BolC2t06638H' => 'bol', 'BolC3t13266H' => 'bol', 'BolC5t29776H' => 'bol', 'BolC6t38912H' => 'bol', 'BolC7t44183H' => 'bol', 'BolC9t54123H' => 'bol', 'BolC9t59107H' => 'bol', 'BraA02t05221Z' => 'bra', 'BraA03t09996Z' => 'bra', 'BraA05t23210Z' => 'bra', 'BraA06t24068Z' => 'bra', 'BraA06t27032Z' => 'bra', 'BraA08t35176Z' => 'bra', 'BraA09t36680Z' => 'bra', 'BraA10t44471Z' => 'bra', 'C02p06760' => 'bna', 'C02p06890' => 'bna', 'C02p07010' => 'bna', 'C03p07660' => 'bna', 'C05p10300' => 'bna', 'C06p38150' => 'bna', 'C07p36650' => 'bna', 'C08p15770' => 'bna', 'C09p12300' => 'bna', 'C09p62700' => 'bna', 'C09p75040' => 'bna', 'CAN.G13.1' => 'can', 'CAN.G138.4' => 'can', 'CAN.G44.6' => 'can', 'CAN.G473.19' => 'can', 'CANSAT01G0835' => 'cansat', 'CANSAT11G0246' => 'cansat', 'CANSAT11G1766' => 'cansat', 'CANSAT64G1954' => 'cansat', 'CARHR013330' => 'chi', 'CARHR060530' => 'chi', 'CARHR075300' => 'chi', 'CARHR105120' => 'chi', 'CARHR148910' => 'chi', 'CARHR198830' => 'chi', 'Carub.0001s1275' => 'cru', 'Carub.0002s1437' => 'cru', 'Carub.0003s0044' => 'cru', 'Carub.0003s2787' => 'cru', 'Carub.0005s0597' => 'cru', 'Carub.0006s1266' => 'cru', 'Ca_06935_v3' => 'car', 'Ca_13559_v3' => 'car', 'Ca_16941_v3' => 'car', 'Ca_16960_v3' => 'car', 'Ca_17775_v3' => 'car', 'Ca_30464_v3' => 'car', 'Cc06_g08160' => 'ccan', 'Cc07_g01520' => 'ccan', 'Cc11_g15810' => 'ccan', 'CDE02G2840' => 'cde', 'CDE03G0093' => 'cde', 'CDE04G2127' => 'cde', 'CDE07G1857' => 'cde', 'CDE09G1246' => 'cde', 'Cfa003412' => 'cfa', 'Cfa007341' => 'cfa', 'Cfa009220' => 'cfa', 'Ciclev10008737m.g' => 'ccl', 'Ciclev10015565m.g' => 'ccl', 'Ciclev10031761m.g' => 'ccl', 'CiPaw.03G045300' => 'cil', 'CiPaw.03G247200' => 'cil', 'CiPaw.04G029500' => 'cil', 'CiPaw.04G174000' => 'cil', 'CiPaw.05G181200' => 'cil', 'CiPaw.06G067100' => 'cil', 'ClCG05G025800' => 'cla', 'ClCG06G011400' => 'cla', 'ClCG09G019360' => 'cla', 'COL.COLO4_04827' => 'col', 'COL.COLO4_29170' => 'col', 'COL.COLO4_35131' => 'col', 'COL.COLO4_35132' => 'col', 'Cpa.g.sc33.32' => 'cpa', 'Cpa.g.sc46.29' => 'cpa', 'Cpa.g.sc796.1' => 'cpa', 'CsaV3_1G030420' => 'csa', 'CsaV3_5G027050' => 'csa', 'CsaV3_5G031040' => 'csa', 'CsaV3_UNG023130' => 'csa', 'CSS0007726' => 'camsi', 'CSS0016433' => 'camsi', 'CSS0017656' => 'camsi', 'CSS0025364' => 'camsi', 'CSS0027582' => 'camsi', 'CSS0047288' => 'camsi', 'CSS0049950' => 'camsi', 'DCAR_003843' => 'dca', 'DCAR_007052' => 'dca', 'DCAR_020884' => 'dca', 'DCAR_021730' => 'dca', 'DCAR_024423' => 'dca', 'DCAR_026509' => 'dca', 'DCAR_031158' => 'dca', 'Dinv14728' => 'din', 'Dinv15219' => 'din', 'Dinv25728' => 'din', 'Dinv33428' => 'din', 'Dinv36489' => 'din', 'Dinv41486' => 'din', 'Duzib147G0469' => 'dzi', 'Duzib168G0060' => 'dzi', 'Duzib187G1215' => 'dzi', 'Duzib248G0692' => 'dzi', 'Duzib251G0767' => 'dzi', 'Duzib264G0446' => 'dzi', 'Duzib268G0691' => 'dzi', 'ECA232G4767' => 'eca', 'ECA233G2838' => 'eca', 'ECA234G0391' => 'eca', 'ECA234G0857' => 'eca', 'ECA236G1593' => 'eca', 'ECA238G0565' => 'eca', 'ECA246G1027' => 'eca', 'ECA246G3223' => 'eca', 'ECA246G3470' => 'eca', 'EL10Ac6g13829' => 'bvu', 'EL10Ac6g14093' => 'bvu', 'EL10Ac8g18707' => 'bvu', 'Eucgr.C01369' => 'egr', 'Eucgr.H02492' => 'egr', 'Eucgr.I01733' => 'egr', 'Eucgr.J02255' => 'egr', 'Eucgr.J02257' => 'egr', 'Eucgr.J02258' => 'egr', 'FAN02G1601' => 'fan', 'FAN03G1586' => 'fan', 'FAN03G2986' => 'fan', 'FAN05G4837' => 'fan', 'FAN06G0146' => 'fan', 'FAN07G0858' => 'fan', 'FAN09G3179' => 'fan', 'FAN10G0669' => 'fan', 'FAN12G2358' => 'fan', 'FAN14G4198' => 'fan', 'FAN14G5112' => 'fan', 'FAN17G0342' => 'fan', 'FAN19G0342' => 'fan', 'FAN19G0962' => 'fan', 'FAN19G1101' => 'fan', 'FAN19G1872' => 'fan', 'FAN22G0356' => 'fan', 'FAN23G0744' => 'fan', 'FAN23G1914' => 'fan', 'FAN26G0032' => 'fan', 'FAN28G0625' => 'fan', 'FvH4_1g02710' => 'fve', 'FvH4_1g02720' => 'fve', 'FvH4_4g25670' => 'fve', 'FvH4_6g51700' => 'fve', 'FvH4_7g20170' => 'fve', 'Glyma.05G175000' => 'gma', 'Glyma.08G132300' => 'gma', 'Glyma.11G243000' => 'gma', 'Glyma.13G158900' => 'gma', 'Glyma.17G112400' => 'gma', 'Glyma.18G014100' => 'gma', 'Glyma.19G003100' => 'gma', 'Glyma.19G056500' => 'gma', 'Gohir.A01G158900' => 'ghi', 'Gohir.A05G312600' => 'ghi', 'Gohir.A05G354900' => 'ghi', 'Gohir.A07G037200' => 'ghi', 'Gohir.A09G030000' => 'ghi', 'Gohir.A12G145200' => 'ghi', 'Gohir.D01G151500' => 'ghi', 'Gohir.D04G058300' => 'ghi', 'Gohir.D05G314100' => 'ghi', 'Gohir.D07G041400' => 'ghi', 'Gohir.D09G029700' => 'ghi', 'Gohir.D12G149700' => 'ghi', 'Gorai.001G043800' => 'gra', 'Gorai.002G187800' => 'gra', 'Gorai.006G034700' => 'gra', 'Gorai.008G161200' => 'gra', 'Gorai.009G335700' => 'gra', 'Gorai.012G065000' => 'gra', 'GSVIVG01000535001' => 'vvi', 'GSVIVG01015572001' => 'vvi', 'GSVIVG01032386001' => 'vvi', 'HanXRQChr05g0138531' => 'han', 'HanXRQChr06g0174391' => 'han', 'HanXRQChr07g0199021' => 'han', 'HanXRQChr08g0208211' => 'han', 'HanXRQChr09g0255471' => 'han', 'HanXRQChr10g0315791' => 'han', 'HanXRQChr12g0371991' => 'han', 'HanXRQChr15g0475251' => 'han', 'HanXRQChr17g0540001' => 'han', 'HanXRQChr17g0548631' => 'han', 'HanXRQChr17g0569561' => 'han', 'Haze_12256' => 'cav', 'Haze_14756' => 'cav', 'Haze_25528' => 'cav', 'Hma1.2p1_0079F.1_g041020' => 'hma', 'Hma1.2p1_0818F.1_g223260' => 'hma', 'Hma1.2p1_1747F.1_g300530' => 'hma', 'HPP92_004607' => 'vpl', 'HPP92_004608' => 'vpl', 'HPP92_006181' => 'vpl', 'HPP92_012192' => 'vpl', 'HPP92_015680' => 'vpl', 'HPP92_020249' => 'vpl', 'HPP92_021376' => 'vpl', 'HPP92_024275' => 'vpl', 'Hund06031' => 'sun', 'Hund25391' => 'sun', 'Lalb_Chr07g0185371' => 'lal', 'Lalb_Chr07g0185381' => 'lal', 'Lalb_Chr12g0204011' => 'lal', 'Lalb_Chr13g0301671' => 'lal', 'Lalb_Chr14g0362851' => 'lal', 'Lalb_Chr24g0403581' => 'lal', 'Lj1g0000233' => 'lja', 'Lj2g0018120' => 'lja', 'Lj3C621T0' => 'lonja', 'Lj3P1059T14' => 'lonja', 'Lj3P611T9' => 'lonja', 'Lj3P614T13' => 'lonja', 'Lj3P615T5' => 'lonja', 'Lj4g0012315' => 'lja', 'Lj4g0026182' => 'lja', 'Lj6P813T16' => 'lonja', 'Lj7C427T7' => 'lonja', 'Lj7C427T8' => 'lonja', 'Lj7P600T41' => 'lonja', 'Lju41C42G17' => 'lonja', 'Lsat_1_v5_gn_0_47300' => 'lsa', 'Lsat_1_v5_gn_2_91280' => 'lsa', 'Lsat_1_v5_gn_3_30561' => 'lsa', 'Lsat_1_v5_gn_4_184321' => 'lsa', 'Lsat_1_v5_gn_4_4041' => 'lsa', 'Lsat_1_v5_gn_5_92000' => 'lsa', 'Lsat_1_v5_gn_8_152940' => 'lsa', 'Lsat_1_v5_gn_8_62401' => 'lsa', 'Manes.06G055900' => 'mes', 'Manes.12G022200' => 'mes', 'Manes.13G023300' => 'mes', 'Manes.14G115000' => 'mes', 'Manes.15G151700' => 'mes', 'Manes.17G111300' => 'mes', 'Mapoly0226s0009' => 'mpo', 'MBI02_g25363_MAGBIO' => 'mbi', 'MBI06_g00027_MAGBIO' => 'mbi', 'MBI10_g13034_MAGBIO' => 'mbi', 'MD09G1023400' => 'mdo', 'MD13G1100100' => 'mdo', 'MD15G1169200' => 'mdo', 'MD16G1101100' => 'mdo', 'MD17G1022900' => 'mdo', 'Medtr3g096150' => 'mtr', 'Medtr4g115070' => 'mtr', 'Medtr7g033325' => 'mtr', 'Medtr8g089840' => 'mtr', 'MELO3C010319.2' => 'cme', 'MELO3C011944.2' => 'cme', 'MELO3C021589.2' => 'cme', 'Migut.E00207' => 'egut', 'Migut.H00067' => 'egut', 'Migut.K00433' => 'egut', 'Migut.K00606' => 'egut', 'Migut.K01410' => 'egut', 'MSTRG.13347' => 'ama', 'MSTRG.24045' => 'ama', 'MSTRG.2428' => 'ama', 'MSTRG.26410' => 'ama', 'MSTRG.3139' => 'ama', 'MSTRG.3286' => 'ama', 'MSTRG.563' => 'ama', 'MSTRG.7941' => 'ama', 'Nitab4.5_0000028g0060' => 'nta', 'Nitab4.5_0000065g0260' => 'nta', 'Nitab4.5_0000112g0060' => 'nta', 'Nitab4.5_0000489g0120' => 'nta', 'Nitab4.5_0001776g0050' => 'nta', 'Nitab4.5_0001854g0010' => 'nta', 'Nitab4.5_0001860g0020' => 'nta', 'Nitab4.5_0004352g0010' => 'nta', 'Nitab4.5_0008716g0020' => 'nta', 'Nitab4.5_0008922g0010' => 'nta', 'Nn3g16693' => 'nnu', 'Nn4g22596' => 'nnu', 'Nn7g37639' => 'nnu', 'Oeu001701.1' => 'oeu', 'Oeu018149.1' => 'oeu', 'Oeu026220.1' => 'oeu', 'Oeu038635.1' => 'oeu', 'Oeu049176.1' => 'oeu', 'Oeu056706.1' => 'oeu', 'Oeu056937.1' => 'oeu', 'Oeu057540.1' => 'oeu', 'Os02g0594900' => 'osa', 'Os02g0595100' => 'osa', 'Os04g0477500' => 'osa', 'Os12g0611900' => 'osa', 'Peaxi162Scf00076g00020' => 'pax', 'Peaxi162Scf00128g00217' => 'pax', 'Peaxi162Scf00129g01640' => 'pax', 'Peaxi162Scf00669g00007' => 'pax', 'Peaxi162Scf00700g00421' => 'pax', 'Peaxi162Scf00801g00038' => 'pax', 'Peaxi162Scf00891g00025' => 'pax', 'PGR083G0909' => 'pgr', 'PGR119G1005' => 'pgr', 'PGR142G2236' => 'pgr', 'PGR142G3388' => 'pgr', 'PGSC0003DMG400004514' => 'stu', 'PGSC0003DMG400012635' => 'stu', 'PGSC0003DMG400015730' => 'stu', 'PGSC0003DMG400018611' => 'stu', 'PGSC0003DMG400030897' => 'stu', 'Phvul.001G254800' => 'pvu', 'Phvul.002G260100' => 'pvu', 'Phvul.003G167600' => 'pvu', 'Phvul.004G005100' => 'pvu', 'Potri.001G343600' => 'ptr', 'Potri.006G066700' => 'ptr', 'Potri.008G186000' => 'ptr', 'Potri.010G046900' => 'ptr', 'Potri.018G127900' => 'ptr', 'Pp3c20_17750' => 'ppa', 'Pp3c24_4380' => 'ppa', 'Prupe.1G245800' => 'ppe', 'Prupe.3G293400' => 'ppe', 'Prupe.7G247400' => 'ppe', 'Psat0s145g0120' => 'psa', 'Psat0s595g0040' => 'psa', 'Psat0s595g0120' => 'psa', 'Psat3g175040' => 'psa', 'Psat7g058120' => 'psa', 'PSO017G0428' => 'pso', 'PSO063G7510' => 'pso', 'PSO067G0046' => 'pso', 'PSO478G1073' => 'pso', 'PSO675G3677' => 'pso', 'PSO675G6558' => 'pso', 'PSO675G7520' => 'pso', 'PSO675G8959' => 'pso', 'QL02p074089' => 'qlo', 'QL02p089614' => 'qlo', 'QL03p057736' => 'qlo', 'RcHm_v2.0_Chr1g0364131' => 'rch', 'RcHm_v2.0_Chr2g0087801' => 'rch', 'RcHm_v2.0_Chr2g0087821' => 'rch', 'RcHm_v2.0_Chr2g0173231' => 'rch', 'RcHm_v2.0_Chr4g0433111' => 'rch', 'Rhsim03G0250300' => 'rsi', 'Rhsim08G0048400' => 'rsi', 'Rhsim10G0014800' => 'rsi', 'Rhsim12G0040100' => 'rsi', 'Rhsim12G0109700' => 'rsi', 'Sabra06G0049600' => 'sbr', 'Sabra08G0141000' => 'sbr', 'Sabra10G0021400' => 'sbr', 'Sabra16G0222900' => 'sbr', 'Sabra18G0108600' => 'sbr', 'SalBow1G0433' => 'sbo', 'SalBow1G2038' => 'sbo', 'SalBow1G5003' => 'sbo', 'SalBow7G1197' => 'sbo', 'SalBow8G3506' => 'sbo', 'Sc03g0007300' => 'sci', 'Sc11g0000950' => 'sci', 'Sc14g0008750' => 'sci', 'Sc18g0000420' => 'sci', 'Sed0006754' => 'sed', 'Sed0008741' => 'sed', 'Sed0017172' => 'sed', 'Sed0018925' => 'sed', 'Sed0023326' => 'sed', 'Sed0025909' => 'sed', 'SEGI_05333' => 'sgi', 'SEGI_10362' => 'sgi', 'SEGI_13380' => 'sgi', 'SEGI_24306' => 'sgi', 'SEGI_29077' => 'sgi', 'SEGI_29095' => 'sgi', 'SEGI_36534' => 'sgi', 'SEGI_37506' => 'sgi', 'SEGI_38321' => 'sgi', 'SGA_v2.0_scaffold307G48031' => 'sas', 'SGA_v2.0_scaffold47G17507' => 'sas', 'SGA_v2.0_scaffold63G21736' => 'sas', 'SGA_v2.0_scaffold87G27070' => 'sas', 'SHI17794' => 'shi', 'SHI28851' => 'shi', 'SMO165G0155' => 'smo', 'SMO340G0217' => 'smo', 'SMO367G1210' => 'smo', 'Solyc02g093430.3' => 'sly', 'Solyc05g013580.4' => 'sly', 'Solyc07g008030.3' => 'sly', 'Solyc12g035470.2' => 'sly', 'Sopen02g038020' => 'spe', 'Sopen05g008490' => 'spe', 'Sopen07g003910' => 'spe', 'Sopen12g015240' => 'spe', 'Sp1g11550' => 'spa', 'Sp2g16710' => 'spa', 'Sp3g00430' => 'spa', 'Sp3g26780' => 'spa', 'Sp5g22900' => 'spa', 'Sp6g29530' => 'spa', 'TAR371G0794' => 'tar', 'TAR374G0164' => 'tar', 'TAR622G0165' => 'tar', 'TAR626G0929' => 'tar', 'TAR629G2155' => 'tar', 'THA.LOC104805282' => 'tha', 'THA.LOC104805363' => 'tha', 'THA.LOC104808968' => 'tha', 'THA.LOC104821093' => 'tha', 'THA.LOC104823953' => 'tha', 'THA.LOC104825562' => 'tha', 'THA.LOC104825665' => 'tha', 'Thecc.02G261400' => 'tca', 'Thecc.04G019200' => 'tca', 'Thecc.09G130400' => 'tca', 'Thhalv10004374m.g' => 'esa', 'Thhalv10007850m.g' => 'esa', 'Thhalv10013782m.g' => 'esa', 'Thhalv10018686m.g' => 'esa', 'Thhalv10020899m.g' => 'esa', 'Thhalv10022755m.g' => 'esa', 'TPR.G23851' => 'tpr', 'TPR.G26500' => 'tpr', 'TPR.G27267' => 'tpr', 'TPR.G32001' => 'tpr', 'TPR.G6251' => 'tpr', 'TPR.G8167' => 'tpr', 'TWI12G1330' => 'twi', 'TWI18G1239' => 'twi', 'TWI34G0979' => 'twi', 'TWI36G0670' => 'twi', 'TWI36G0707' => 'twi', 'TWI56G0233' => 'twi', 'TWI75G1809' => 'twi', 'unitig_21.g20874' => 'ugi', 'unitig_26.g10343' => 'ugi', 'unitig_46.g18392' => 'ugi', 'unitig_52.g17178' => 'ugi', 'unitig_8.g2934' => 'ugi', 'vmacro01122' => 'vma', 'vmacro05875' => 'vma', 'vmacro06147' => 'vma', 'vmacro16191' => 'vma', 'vmacro18293' => 'vma', 'VMungo0251G3707' => 'vmu', 'VMungo0464G1521' => 'vmu', 'VMungo1215G0205' => 'vmu', 'VMungo1383G2484' => 'vmu', 'Zm00001eb079610' => 'zma', 'Zm00001eb135990' => 'zma', 'Zm00001eb183710' => 'zma', 'Zm00001eb246020' => 'zma' ), 'gf_id' => 'HOM05D001124', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001124' ), 'data_identifier' => 'HOM05D001124', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001124', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '548', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02520' => 'bna', 'A03p06630' => 'bna', 'A05p44460' => 'bna', 'A06p08710' => 'bna', 'A06p41090' => 'bna', 'A07p32320' => 'bna', 'A08p32520' => 'bna', 'A09p10360' => 'bna', 'A10p24080' => 'bna', 'Aa31LG11G15250' => 'aar', 'Aa31LG1G1800' => 'aar', 'Aa31LG2G5120' => 'aar', 'Aa31LG2G6070' => 'aar', 'Aa31LG5G10770' => 'aar', 'Aa31sc61G90' => 'aar', 'Actinidia01352' => 'ach', 'Actinidia05983' => 'ach', 'Actinidia08133' => 'ach', 'Actinidia15101' => 'ach', 'Actinidia26379' => 'ach', 'Actinidia35778' => 'ach', 'Actinidia36123' => 'ach', 'Actinidia37436' => 'ach', 'Actinidia38730' => 'ach', 'Ah.02g128210' => 'amhyb', 'Ah.03g132990' => 'amhyb', 'Ah.14g079410' => 'amhyb', 'AL1G24640' => 'aly', 'AL2G26680' => 'aly', 'AL3G10530' => 'aly', 'AL3G45230' => 'aly', 'AL5G15230' => 'aly', 'AL5G16960' => 'aly', 'AL6G25210' => 'aly', 'Aqoxy2G00441' => 'aox', 'Aqoxy3G01236' => 'aox', 'Aqoxy5G03746' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3RQ047' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C7GMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9C8JER' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MBL6KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YXCZ83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZANX40' => 'arhy', 'AT1G12990' => 'ath', 'AT1G67880' => 'ath', 'AT2G13290' => 'ath', 'AT3G01620' => 'ath', 'AT3G26445' => 'ath', 'AT3G27540' => 'ath', 'AT5G14480' => 'ath', 'ATR0824G026' => 'atr', 'ATR1098G019' => 'atr', 'Atru.chr11.2145' => 'acertr', 'Atru.chr2.3636' => 'acertr', 'Atru.chr2.3644' => 'acertr', 'Atru.chr6.2422' => 'acertr', 'Atru.chr7.1112' => 'acertr', 'AUR62005469' => 'cqu', 'AUR62011166' => 'cqu', 'AUR62013319' => 'cqu', 'AUR62024273' => 'cqu', 'AUR62028420' => 'cqu', 'AUR62041942' => 'cqu', 'BcaB01g04969' => 'bca', 'BcaB01g06371' => 'bca', 'BcaB02g11494' => 'bca', 'BcaB03g15382' => 'bca', 'BcaB08g36994' => 'bca', 'BcaC03g13477' => 'bca', 'BcaC03g13478' => 'bca', 'BcaC03g13480' => 'bca', 'BcaC03g13481' => 'bca', 'BcaC03g13486' => 'bca', 'BcaC04g19031' => 'bca', 'BcaC04g23085' => 'bca', 'BcaC05g25094' => 'bca', 'BcaC05g25096' => 'bca', 'BcaC05g25138' => 'bca', 'BcaC05g30416' => 'bca', 'BcaC05g30455' => 'bca', 'BcaC06g30979' => 'bca', 'BcaC06g33805' => 'bca', 'BcaC08g46021' => 'bca', 'BcaNung03154' => 'bca', 'BolC2t06623H' => 'bol', 'BolC2t06632H' => 'bol', 'BolC2t06635H' => 'bol', 'BolC2t06638H' => 'bol', 'BolC3t13266H' => 'bol', 'BolC5t29776H' => 'bol', 'BolC6t38912H' => 'bol', 'BolC7t44183H' => 'bol', 'BolC9t54123H' => 'bol', 'BolC9t59107H' => 'bol', 'BraA02t05221Z' => 'bra', 'BraA03t09996Z' => 'bra', 'BraA05t23210Z' => 'bra', 'BraA06t24068Z' => 'bra', 'BraA06t27032Z' => 'bra', 'BraA08t35176Z' => 'bra', 'BraA09t36680Z' => 'bra', 'BraA10t44471Z' => 'bra', 'C02p06760' => 'bna', 'C02p06890' => 'bna', 'C02p07010' => 'bna', 'C03p07660' => 'bna', 'C05p10300' => 'bna', 'C06p38150' => 'bna', 'C07p36650' => 'bna', 'C08p15770' => 'bna', 'C09p12300' => 'bna', 'C09p62700' => 'bna', 'C09p75040' => 'bna', 'CAN.G13.1' => 'can', 'CAN.G138.4' => 'can', 'CAN.G44.6' => 'can', 'CAN.G473.19' => 'can', 'CANSAT01G0835' => 'cansat', 'CANSAT11G0246' => 'cansat', 'CANSAT11G1766' => 'cansat', 'CANSAT64G1954' => 'cansat', 'CARHR013330' => 'chi', 'CARHR060530' => 'chi', 'CARHR075300' => 'chi', 'CARHR105120' => 'chi', 'CARHR148910' => 'chi', 'CARHR198830' => 'chi', 'Carub.0001s1275' => 'cru', 'Carub.0002s1437' => 'cru', 'Carub.0003s0044' => 'cru', 'Carub.0003s2787' => 'cru', 'Carub.0005s0597' => 'cru', 'Carub.0006s1266' => 'cru', 'Ca_06935_v3' => 'car', 'Ca_13559_v3' => 'car', 'Ca_16941_v3' => 'car', 'Ca_16960_v3' => 'car', 'Ca_17775_v3' => 'car', 'Ca_30464_v3' => 'car', 'Cc06_g08160' => 'ccan', 'Cc07_g01520' => 'ccan', 'Cc11_g15810' => 'ccan', 'CDE02G2840' => 'cde', 'CDE03G0093' => 'cde', 'CDE04G2127' => 'cde', 'CDE07G1857' => 'cde', 'CDE09G1246' => 'cde', 'Cfa003412' => 'cfa', 'Cfa007341' => 'cfa', 'Cfa009220' => 'cfa', 'Ciclev10008737m.g' => 'ccl', 'Ciclev10015565m.g' => 'ccl', 'Ciclev10031761m.g' => 'ccl', 'CiPaw.03G045300' => 'cil', 'CiPaw.03G247200' => 'cil', 'CiPaw.04G029500' => 'cil', 'CiPaw.04G174000' => 'cil', 'CiPaw.05G181200' => 'cil', 'CiPaw.06G067100' => 'cil', 'ClCG05G025800' => 'cla', 'ClCG06G011400' => 'cla', 'ClCG09G019360' => 'cla', 'COL.COLO4_04827' => 'col', 'COL.COLO4_29170' => 'col', 'COL.COLO4_35131' => 'col', 'COL.COLO4_35132' => 'col', 'Cpa.g.sc33.32' => 'cpa', 'Cpa.g.sc46.29' => 'cpa', 'Cpa.g.sc796.1' => 'cpa', 'CsaV3_1G030420' => 'csa', 'CsaV3_5G027050' => 'csa', 'CsaV3_5G031040' => 'csa', 'CsaV3_UNG023130' => 'csa', 'CSS0007726' => 'camsi', 'CSS0016433' => 'camsi', 'CSS0017656' => 'camsi', 'CSS0025364' => 'camsi', 'CSS0027582' => 'camsi', 'CSS0047288' => 'camsi', 'CSS0049950' => 'camsi', 'DCAR_003843' => 'dca', 'DCAR_007052' => 'dca', 'DCAR_020884' => 'dca', 'DCAR_021730' => 'dca', 'DCAR_024423' => 'dca', 'DCAR_026509' => 'dca', 'DCAR_031158' => 'dca', 'Dinv14728' => 'din', 'Dinv15219' => 'din', 'Dinv25728' => 'din', 'Dinv33428' => 'din', 'Dinv36489' => 'din', 'Dinv41486' => 'din', 'Duzib147G0469' => 'dzi', 'Duzib168G0060' => 'dzi', 'Duzib187G1215' => 'dzi', 'Duzib248G0692' => 'dzi', 'Duzib251G0767' => 'dzi', 'Duzib264G0446' => 'dzi', 'Duzib268G0691' => 'dzi', 'ECA232G4767' => 'eca', 'ECA233G2838' => 'eca', 'ECA234G0391' => 'eca', 'ECA234G0857' => 'eca', 'ECA236G1593' => 'eca', 'ECA238G0565' => 'eca', 'ECA246G1027' => 'eca', 'ECA246G3223' => 'eca', 'ECA246G3470' => 'eca', 'EL10Ac6g13829' => 'bvu', 'EL10Ac6g14093' => 'bvu', 'EL10Ac8g18707' => 'bvu', 'Eucgr.C01369' => 'egr', 'Eucgr.H02492' => 'egr', 'Eucgr.I01733' => 'egr', 'Eucgr.J02255' => 'egr', 'Eucgr.J02257' => 'egr', 'Eucgr.J02258' => 'egr', 'FAN02G1601' => 'fan', 'FAN03G1586' => 'fan', 'FAN03G2986' => 'fan', 'FAN05G4837' => 'fan', 'FAN06G0146' => 'fan', 'FAN07G0858' => 'fan', 'FAN09G3179' => 'fan', 'FAN10G0669' => 'fan', 'FAN12G2358' => 'fan', 'FAN14G4198' => 'fan', 'FAN14G5112' => 'fan', 'FAN17G0342' => 'fan', 'FAN19G0342' => 'fan', 'FAN19G0962' => 'fan', 'FAN19G1101' => 'fan', 'FAN19G1872' => 'fan', 'FAN22G0356' => 'fan', 'FAN23G0744' => 'fan', 'FAN23G1914' => 'fan', 'FAN26G0032' => 'fan', 'FAN28G0625' => 'fan', 'FvH4_1g02710' => 'fve', 'FvH4_1g02720' => 'fve', 'FvH4_4g25670' => 'fve', 'FvH4_6g51700' => 'fve', 'FvH4_7g20170' => 'fve', 'Glyma.05G175000' => 'gma', 'Glyma.08G132300' => 'gma', 'Glyma.11G243000' => 'gma', 'Glyma.13G158900' => 'gma', 'Glyma.17G112400' => 'gma', 'Glyma.18G014100' => 'gma', 'Glyma.19G003100' => 'gma', 'Glyma.19G056500' => 'gma', 'Gohir.A01G158900' => 'ghi', 'Gohir.A05G312600' => 'ghi', 'Gohir.A05G354900' => 'ghi', 'Gohir.A07G037200' => 'ghi', 'Gohir.A09G030000' => 'ghi', 'Gohir.A12G145200' => 'ghi', 'Gohir.D01G151500' => 'ghi', 'Gohir.D04G058300' => 'ghi', 'Gohir.D05G314100' => 'ghi', 'Gohir.D07G041400' => 'ghi', 'Gohir.D09G029700' => 'ghi', 'Gohir.D12G149700' => 'ghi', 'Gorai.001G043800' => 'gra', 'Gorai.002G187800' => 'gra', 'Gorai.006G034700' => 'gra', 'Gorai.008G161200' => 'gra', 'Gorai.009G335700' => 'gra', 'Gorai.012G065000' => 'gra', 'GSVIVG01000535001' => 'vvi', 'GSVIVG01015572001' => 'vvi', 'GSVIVG01032386001' => 'vvi', 'HanXRQChr05g0138531' => 'han', 'HanXRQChr06g0174391' => 'han', 'HanXRQChr07g0199021' => 'han', 'HanXRQChr08g0208211' => 'han', 'HanXRQChr09g0255471' => 'han', 'HanXRQChr10g0315791' => 'han', 'HanXRQChr12g0371991' => 'han', 'HanXRQChr15g0475251' => 'han', 'HanXRQChr17g0540001' => 'han', 'HanXRQChr17g0548631' => 'han', 'HanXRQChr17g0569561' => 'han', 'Haze_12256' => 'cav', 'Haze_14756' => 'cav', 'Haze_25528' => 'cav', 'Hma1.2p1_0079F.1_g041020' => 'hma', 'Hma1.2p1_0818F.1_g223260' => 'hma', 'Hma1.2p1_1747F.1_g300530' => 'hma', 'HPP92_004607' => 'vpl', 'HPP92_004608' => 'vpl', 'HPP92_006181' => 'vpl', 'HPP92_012192' => 'vpl', 'HPP92_015680' => 'vpl', 'HPP92_020249' => 'vpl', 'HPP92_021376' => 'vpl', 'HPP92_024275' => 'vpl', 'Hund06031' => 'sun', 'Hund25391' => 'sun', 'Lalb_Chr07g0185371' => 'lal', 'Lalb_Chr07g0185381' => 'lal', 'Lalb_Chr12g0204011' => 'lal', 'Lalb_Chr13g0301671' => 'lal', 'Lalb_Chr14g0362851' => 'lal', 'Lalb_Chr24g0403581' => 'lal', 'Lj1g0000233' => 'lja', 'Lj2g0018120' => 'lja', 'Lj3C621T0' => 'lonja', 'Lj3P1059T14' => 'lonja', 'Lj3P611T9' => 'lonja', 'Lj3P614T13' => 'lonja', 'Lj3P615T5' => 'lonja', 'Lj4g0012315' => 'lja', 'Lj4g0026182' => 'lja', 'Lj6P813T16' => 'lonja', 'Lj7C427T7' => 'lonja', 'Lj7C427T8' => 'lonja', 'Lj7P600T41' => 'lonja', 'Lju41C42G17' => 'lonja', 'Lsat_1_v5_gn_0_47300' => 'lsa', 'Lsat_1_v5_gn_2_91280' => 'lsa', 'Lsat_1_v5_gn_3_30561' => 'lsa', 'Lsat_1_v5_gn_4_184321' => 'lsa', 'Lsat_1_v5_gn_4_4041' => 'lsa', 'Lsat_1_v5_gn_5_92000' => 'lsa', 'Lsat_1_v5_gn_8_152940' => 'lsa', 'Lsat_1_v5_gn_8_62401' => 'lsa', 'Manes.06G055900' => 'mes', 'Manes.12G022200' => 'mes', 'Manes.13G023300' => 'mes', 'Manes.14G115000' => 'mes', 'Manes.15G151700' => 'mes', 'Manes.17G111300' => 'mes', 'Mapoly0226s0009' => 'mpo', 'MBI02_g25363_MAGBIO' => 'mbi', 'MBI06_g00027_MAGBIO' => 'mbi', 'MBI10_g13034_MAGBIO' => 'mbi', 'MD09G1023400' => 'mdo', 'MD13G1100100' => 'mdo', 'MD15G1169200' => 'mdo', 'MD16G1101100' => 'mdo', 'MD17G1022900' => 'mdo', 'Medtr3g096150' => 'mtr', 'Medtr4g115070' => 'mtr', 'Medtr7g033325' => 'mtr', 'Medtr8g089840' => 'mtr', 'MELO3C010319.2' => 'cme', 'MELO3C011944.2' => 'cme', 'MELO3C021589.2' => 'cme', 'Migut.E00207' => 'egut', 'Migut.H00067' => 'egut', 'Migut.K00433' => 'egut', 'Migut.K00606' => 'egut', 'Migut.K01410' => 'egut', 'MSTRG.13347' => 'ama', 'MSTRG.24045' => 'ama', 'MSTRG.2428' => 'ama', 'MSTRG.26410' => 'ama', 'MSTRG.3139' => 'ama', 'MSTRG.3286' => 'ama', 'MSTRG.563' => 'ama', 'MSTRG.7941' => 'ama', 'Nitab4.5_0000028g0060' => 'nta', 'Nitab4.5_0000065g0260' => 'nta', 'Nitab4.5_0000112g0060' => 'nta', 'Nitab4.5_0000489g0120' => 'nta', 'Nitab4.5_0001776g0050' => 'nta', 'Nitab4.5_0001854g0010' => 'nta', 'Nitab4.5_0001860g0020' => 'nta', 'Nitab4.5_0004352g0010' => 'nta', 'Nitab4.5_0008716g0020' => 'nta', 'Nitab4.5_0008922g0010' => 'nta', 'Nn3g16693' => 'nnu', 'Nn4g22596' => 'nnu', 'Nn7g37639' => 'nnu', 'Oeu001701.1' => 'oeu', 'Oeu018149.1' => 'oeu', 'Oeu026220.1' => 'oeu', 'Oeu038635.1' => 'oeu', 'Oeu049176.1' => 'oeu', 'Oeu056706.1' => 'oeu', 'Oeu056937.1' => 'oeu', 'Oeu057540.1' => 'oeu', 'Os02g0594900' => 'osa', 'Os02g0595100' => 'osa', 'Os04g0477500' => 'osa', 'Os12g0611900' => 'osa', 'Peaxi162Scf00076g00020' => 'pax', 'Peaxi162Scf00128g00217' => 'pax', 'Peaxi162Scf00129g01640' => 'pax', 'Peaxi162Scf00669g00007' => 'pax', 'Peaxi162Scf00700g00421' => 'pax', 'Peaxi162Scf00801g00038' => 'pax', 'Peaxi162Scf00891g00025' => 'pax', 'PGR083G0909' => 'pgr', 'PGR119G1005' => 'pgr', 'PGR142G2236' => 'pgr', 'PGR142G3388' => 'pgr', 'PGSC0003DMG400004514' => 'stu', 'PGSC0003DMG400012635' => 'stu', 'PGSC0003DMG400015730' => 'stu', 'PGSC0003DMG400018611' => 'stu', 'PGSC0003DMG400030897' => 'stu', 'Phvul.001G254800' => 'pvu', 'Phvul.002G260100' => 'pvu', 'Phvul.003G167600' => 'pvu', 'Phvul.004G005100' => 'pvu', 'Potri.001G343600' => 'ptr', 'Potri.006G066700' => 'ptr', 'Potri.008G186000' => 'ptr', 'Potri.010G046900' => 'ptr', 'Potri.018G127900' => 'ptr', 'Pp3c20_17750' => 'ppa', 'Pp3c24_4380' => 'ppa', 'Prupe.1G245800' => 'ppe', 'Prupe.3G293400' => 'ppe', 'Prupe.7G247400' => 'ppe', 'Psat0s145g0120' => 'psa', 'Psat0s595g0040' => 'psa', 'Psat0s595g0120' => 'psa', 'Psat3g175040' => 'psa', 'Psat7g058120' => 'psa', 'PSO017G0428' => 'pso', 'PSO063G7510' => 'pso', 'PSO067G0046' => 'pso', 'PSO478G1073' => 'pso', 'PSO675G3677' => 'pso', 'PSO675G6558' => 'pso', 'PSO675G7520' => 'pso', 'PSO675G8959' => 'pso', 'QL02p074089' => 'qlo', 'QL02p089614' => 'qlo', 'QL03p057736' => 'qlo', 'RcHm_v2.0_Chr1g0364131' => 'rch', 'RcHm_v2.0_Chr2g0087801' => 'rch', 'RcHm_v2.0_Chr2g0087821' => 'rch', 'RcHm_v2.0_Chr2g0173231' => 'rch', 'RcHm_v2.0_Chr4g0433111' => 'rch', 'Rhsim03G0250300' => 'rsi', 'Rhsim08G0048400' => 'rsi', 'Rhsim10G0014800' => 'rsi', 'Rhsim12G0040100' => 'rsi', 'Rhsim12G0109700' => 'rsi', 'Sabra06G0049600' => 'sbr', 'Sabra08G0141000' => 'sbr', 'Sabra10G0021400' => 'sbr', 'Sabra16G0222900' => 'sbr', 'Sabra18G0108600' => 'sbr', 'SalBow1G0433' => 'sbo', 'SalBow1G2038' => 'sbo', 'SalBow1G5003' => 'sbo', 'SalBow7G1197' => 'sbo', 'SalBow8G3506' => 'sbo', 'Sc03g0007300' => 'sci', 'Sc11g0000950' => 'sci', 'Sc14g0008750' => 'sci', 'Sc18g0000420' => 'sci', 'Sed0006754' => 'sed', 'Sed0008741' => 'sed', 'Sed0017172' => 'sed', 'Sed0018925' => 'sed', 'Sed0023326' => 'sed', 'Sed0025909' => 'sed', 'SEGI_05333' => 'sgi', 'SEGI_10362' => 'sgi', 'SEGI_13380' => 'sgi', 'SEGI_24306' => 'sgi', 'SEGI_29077' => 'sgi', 'SEGI_29095' => 'sgi', 'SEGI_36534' => 'sgi', 'SEGI_37506' => 'sgi', 'SEGI_38321' => 'sgi', 'SGA_v2.0_scaffold307G48031' => 'sas', 'SGA_v2.0_scaffold47G17507' => 'sas', 'SGA_v2.0_scaffold63G21736' => 'sas', 'SGA_v2.0_scaffold87G27070' => 'sas', 'SHI17794' => 'shi', 'SHI28851' => 'shi', 'SMO165G0155' => 'smo', 'SMO340G0217' => 'smo', 'SMO367G1210' => 'smo', 'Solyc02g093430.3' => 'sly', 'Solyc05g013580.4' => 'sly', 'Solyc07g008030.3' => 'sly', 'Solyc12g035470.2' => 'sly', 'Sopen02g038020' => 'spe', 'Sopen05g008490' => 'spe', 'Sopen07g003910' => 'spe', 'Sopen12g015240' => 'spe', 'Sp1g11550' => 'spa', 'Sp2g16710' => 'spa', 'Sp3g00430' => 'spa', 'Sp3g26780' => 'spa', 'Sp5g22900' => 'spa', 'Sp6g29530' => 'spa', 'TAR371G0794' => 'tar', 'TAR374G0164' => 'tar', 'TAR622G0165' => 'tar', 'TAR626G0929' => 'tar', 'TAR629G2155' => 'tar', 'THA.LOC104805282' => 'tha', 'THA.LOC104805363' => 'tha', 'THA.LOC104808968' => 'tha', 'THA.LOC104821093' => 'tha', 'THA.LOC104823953' => 'tha', 'THA.LOC104825562' => 'tha', 'THA.LOC104825665' => 'tha', 'Thecc.02G261400' => 'tca', 'Thecc.04G019200' => 'tca', 'Thecc.09G130400' => 'tca', 'Thhalv10004374m.g' => 'esa', 'Thhalv10007850m.g' => 'esa', 'Thhalv10013782m.g' => 'esa', 'Thhalv10018686m.g' => 'esa', 'Thhalv10020899m.g' => 'esa', 'Thhalv10022755m.g' => 'esa', 'TPR.G23851' => 'tpr', 'TPR.G26500' => 'tpr', 'TPR.G27267' => 'tpr', 'TPR.G32001' => 'tpr', 'TPR.G6251' => 'tpr', 'TPR.G8167' => 'tpr', 'TWI12G1330' => 'twi', 'TWI18G1239' => 'twi', 'TWI34G0979' => 'twi', 'TWI36G0670' => 'twi', 'TWI36G0707' => 'twi', 'TWI56G0233' => 'twi', 'TWI75G1809' => 'twi', 'unitig_21.g20874' => 'ugi', 'unitig_26.g10343' => 'ugi', 'unitig_46.g18392' => 'ugi', 'unitig_52.g17178' => 'ugi', 'unitig_8.g2934' => 'ugi', 'vmacro01122' => 'vma', 'vmacro05875' => 'vma', 'vmacro06147' => 'vma', 'vmacro16191' => 'vma', 'vmacro18293' => 'vma', 'VMungo0251G3707' => 'vmu', 'VMungo0464G1521' => 'vmu', 'VMungo1215G0205' => 'vmu', 'VMungo1383G2484' => 'vmu', 'Zm00001eb079610' => 'zma', 'Zm00001eb135990' => 'zma', 'Zm00001eb183710' => 'zma', 'Zm00001eb246020' => 'zma' ) $gf_id = 'HOM05D001124' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001124' ) $data_identifier = 'HOM05D001124' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 6, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 7, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 21, 'bol' => (int) 10, 'bra' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 6, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 9, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 21, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 8, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 10, 'lsa' => (int) 8, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 8, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 9, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb246020' $species_info = array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ) $local_species = 'cde' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001124', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '548', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02520' => 'bna', 'A03p06630' => 'bna', 'A05p44460' => 'bna', 'A06p08710' => 'bna', 'A06p41090' => 'bna', 'A07p32320' => 'bna', 'A08p32520' => 'bna', 'A09p10360' => 'bna', 'A10p24080' => 'bna', 'Aa31LG11G15250' => 'aar', 'Aa31LG1G1800' => 'aar', 'Aa31LG2G5120' => 'aar', 'Aa31LG2G6070' => 'aar', 'Aa31LG5G10770' => 'aar', 'Aa31sc61G90' => 'aar', 'Actinidia01352' => 'ach', 'Actinidia05983' => 'ach', 'Actinidia08133' => 'ach', 'Actinidia15101' => 'ach', 'Actinidia26379' => 'ach', 'Actinidia35778' => 'ach', 'Actinidia36123' => 'ach', 'Actinidia37436' => 'ach', 'Actinidia38730' => 'ach', 'Ah.02g128210' => 'amhyb', 'Ah.03g132990' => 'amhyb', 'Ah.14g079410' => 'amhyb', 'AL1G24640' => 'aly', 'AL2G26680' => 'aly', 'AL3G10530' => 'aly', 'AL3G45230' => 'aly', 'AL5G15230' => 'aly', 'AL5G16960' => 'aly', 'AL6G25210' => 'aly', 'Aqoxy2G00441' => 'aox', 'Aqoxy3G01236' => 'aox', 'Aqoxy5G03746' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3RQ047' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C7GMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9C8JER' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MBL6KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YXCZ83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZANX40' => 'arhy', 'AT1G12990' => 'ath', 'AT1G67880' => 'ath', 'AT2G13290' => 'ath', 'AT3G01620' => 'ath', 'AT3G26445' => 'ath', 'AT3G27540' => 'ath', 'AT5G14480' => 'ath', 'ATR0824G026' => 'atr', 'ATR1098G019' => 'atr', 'Atru.chr11.2145' => 'acertr', 'Atru.chr2.3636' => 'acertr', 'Atru.chr2.3644' => 'acertr', 'Atru.chr6.2422' => 'acertr', 'Atru.chr7.1112' => 'acertr', 'AUR62005469' => 'cqu', 'AUR62011166' => 'cqu', 'AUR62013319' => 'cqu', 'AUR62024273' => 'cqu', 'AUR62028420' => 'cqu', 'AUR62041942' => 'cqu', 'BcaB01g04969' => 'bca', 'BcaB01g06371' => 'bca', 'BcaB02g11494' => 'bca', 'BcaB03g15382' => 'bca', 'BcaB08g36994' => 'bca', 'BcaC03g13477' => 'bca', 'BcaC03g13478' => 'bca', 'BcaC03g13480' => 'bca', 'BcaC03g13481' => 'bca', 'BcaC03g13486' => 'bca', 'BcaC04g19031' => 'bca', 'BcaC04g23085' => 'bca', 'BcaC05g25094' => 'bca', 'BcaC05g25096' => 'bca', 'BcaC05g25138' => 'bca', 'BcaC05g30416' => 'bca', 'BcaC05g30455' => 'bca', 'BcaC06g30979' => 'bca', 'BcaC06g33805' => 'bca', 'BcaC08g46021' => 'bca', 'BcaNung03154' => 'bca', 'BolC2t06623H' => 'bol', 'BolC2t06632H' => 'bol', 'BolC2t06635H' => 'bol', 'BolC2t06638H' => 'bol', 'BolC3t13266H' => 'bol', 'BolC5t29776H' => 'bol', 'BolC6t38912H' => 'bol', 'BolC7t44183H' => 'bol', 'BolC9t54123H' => 'bol', 'BolC9t59107H' => 'bol', 'BraA02t05221Z' => 'bra', 'BraA03t09996Z' => 'bra', 'BraA05t23210Z' => 'bra', 'BraA06t24068Z' => 'bra', 'BraA06t27032Z' => 'bra', 'BraA08t35176Z' => 'bra', 'BraA09t36680Z' => 'bra', 'BraA10t44471Z' => 'bra', 'C02p06760' => 'bna', 'C02p06890' => 'bna', 'C02p07010' => 'bna', 'C03p07660' => 'bna', 'C05p10300' => 'bna', 'C06p38150' => 'bna', 'C07p36650' => 'bna', 'C08p15770' => 'bna', 'C09p12300' => 'bna', 'C09p62700' => 'bna', 'C09p75040' => 'bna', 'CAN.G13.1' => 'can', 'CAN.G138.4' => 'can', 'CAN.G44.6' => 'can', 'CAN.G473.19' => 'can', 'CANSAT01G0835' => 'cansat', 'CANSAT11G0246' => 'cansat', 'CANSAT11G1766' => 'cansat', 'CANSAT64G1954' => 'cansat', 'CARHR013330' => 'chi', 'CARHR060530' => 'chi', 'CARHR075300' => 'chi', 'CARHR105120' => 'chi', 'CARHR148910' => 'chi', 'CARHR198830' => 'chi', 'Carub.0001s1275' => 'cru', 'Carub.0002s1437' => 'cru', 'Carub.0003s0044' => 'cru', 'Carub.0003s2787' => 'cru', 'Carub.0005s0597' => 'cru', 'Carub.0006s1266' => 'cru', 'Ca_06935_v3' => 'car', 'Ca_13559_v3' => 'car', 'Ca_16941_v3' => 'car', 'Ca_16960_v3' => 'car', 'Ca_17775_v3' => 'car', 'Ca_30464_v3' => 'car', 'Cc06_g08160' => 'ccan', 'Cc07_g01520' => 'ccan', 'Cc11_g15810' => 'ccan', 'CDE02G2840' => 'cde', 'CDE03G0093' => 'cde', 'CDE04G2127' => 'cde', 'CDE07G1857' => 'cde', 'CDE09G1246' => 'cde', 'Cfa003412' => 'cfa', 'Cfa007341' => 'cfa', 'Cfa009220' => 'cfa', 'Ciclev10008737m.g' => 'ccl', 'Ciclev10015565m.g' => 'ccl', 'Ciclev10031761m.g' => 'ccl', 'CiPaw.03G045300' => 'cil', 'CiPaw.03G247200' => 'cil', 'CiPaw.04G029500' => 'cil', 'CiPaw.04G174000' => 'cil', 'CiPaw.05G181200' => 'cil', 'CiPaw.06G067100' => 'cil', 'ClCG05G025800' => 'cla', 'ClCG06G011400' => 'cla', 'ClCG09G019360' => 'cla', 'COL.COLO4_04827' => 'col', 'COL.COLO4_29170' => 'col', 'COL.COLO4_35131' => 'col', 'COL.COLO4_35132' => 'col', 'Cpa.g.sc33.32' => 'cpa', 'Cpa.g.sc46.29' => 'cpa', 'Cpa.g.sc796.1' => 'cpa', 'CsaV3_1G030420' => 'csa', 'CsaV3_5G027050' => 'csa', 'CsaV3_5G031040' => 'csa', 'CsaV3_UNG023130' => 'csa', 'CSS0007726' => 'camsi', 'CSS0016433' => 'camsi', 'CSS0017656' => 'camsi', 'CSS0025364' => 'camsi', 'CSS0027582' => 'camsi', 'CSS0047288' => 'camsi', 'CSS0049950' => 'camsi', 'DCAR_003843' => 'dca', 'DCAR_007052' => 'dca', 'DCAR_020884' => 'dca', 'DCAR_021730' => 'dca', 'DCAR_024423' => 'dca', 'DCAR_026509' => 'dca', 'DCAR_031158' => 'dca', 'Dinv14728' => 'din', 'Dinv15219' => 'din', 'Dinv25728' => 'din', 'Dinv33428' => 'din', 'Dinv36489' => 'din', 'Dinv41486' => 'din', 'Duzib147G0469' => 'dzi', 'Duzib168G0060' => 'dzi', 'Duzib187G1215' => 'dzi', 'Duzib248G0692' => 'dzi', 'Duzib251G0767' => 'dzi', 'Duzib264G0446' => 'dzi', 'Duzib268G0691' => 'dzi', 'ECA232G4767' => 'eca', 'ECA233G2838' => 'eca', 'ECA234G0391' => 'eca', 'ECA234G0857' => 'eca', 'ECA236G1593' => 'eca', 'ECA238G0565' => 'eca', 'ECA246G1027' => 'eca', 'ECA246G3223' => 'eca', 'ECA246G3470' => 'eca', 'EL10Ac6g13829' => 'bvu', 'EL10Ac6g14093' => 'bvu', 'EL10Ac8g18707' => 'bvu', 'Eucgr.C01369' => 'egr', 'Eucgr.H02492' => 'egr', 'Eucgr.I01733' => 'egr', 'Eucgr.J02255' => 'egr', 'Eucgr.J02257' => 'egr', 'Eucgr.J02258' => 'egr', 'FAN02G1601' => 'fan', 'FAN03G1586' => 'fan', 'FAN03G2986' => 'fan', 'FAN05G4837' => 'fan', 'FAN06G0146' => 'fan', 'FAN07G0858' => 'fan', 'FAN09G3179' => 'fan', 'FAN10G0669' => 'fan', 'FAN12G2358' => 'fan', 'FAN14G4198' => 'fan', 'FAN14G5112' => 'fan', 'FAN17G0342' => 'fan', 'FAN19G0342' => 'fan', 'FAN19G0962' => 'fan', 'FAN19G1101' => 'fan', 'FAN19G1872' => 'fan', 'FAN22G0356' => 'fan', 'FAN23G0744' => 'fan', 'FAN23G1914' => 'fan', 'FAN26G0032' => 'fan', 'FAN28G0625' => 'fan', 'FvH4_1g02710' => 'fve', 'FvH4_1g02720' => 'fve', 'FvH4_4g25670' => 'fve', 'FvH4_6g51700' => 'fve', 'FvH4_7g20170' => 'fve', 'Glyma.05G175000' => 'gma', 'Glyma.08G132300' => 'gma', 'Glyma.11G243000' => 'gma', 'Glyma.13G158900' => 'gma', 'Glyma.17G112400' => 'gma', 'Glyma.18G014100' => 'gma', 'Glyma.19G003100' => 'gma', 'Glyma.19G056500' => 'gma', 'Gohir.A01G158900' => 'ghi', 'Gohir.A05G312600' => 'ghi', 'Gohir.A05G354900' => 'ghi', 'Gohir.A07G037200' => 'ghi', 'Gohir.A09G030000' => 'ghi', 'Gohir.A12G145200' => 'ghi', 'Gohir.D01G151500' => 'ghi', 'Gohir.D04G058300' => 'ghi', 'Gohir.D05G314100' => 'ghi', 'Gohir.D07G041400' => 'ghi', 'Gohir.D09G029700' => 'ghi', 'Gohir.D12G149700' => 'ghi', 'Gorai.001G043800' => 'gra', 'Gorai.002G187800' => 'gra', 'Gorai.006G034700' => 'gra', 'Gorai.008G161200' => 'gra', 'Gorai.009G335700' => 'gra', 'Gorai.012G065000' => 'gra', 'GSVIVG01000535001' => 'vvi', 'GSVIVG01015572001' => 'vvi', 'GSVIVG01032386001' => 'vvi', 'HanXRQChr05g0138531' => 'han', 'HanXRQChr06g0174391' => 'han', 'HanXRQChr07g0199021' => 'han', 'HanXRQChr08g0208211' => 'han', 'HanXRQChr09g0255471' => 'han', 'HanXRQChr10g0315791' => 'han', 'HanXRQChr12g0371991' => 'han', 'HanXRQChr15g0475251' => 'han', 'HanXRQChr17g0540001' => 'han', 'HanXRQChr17g0548631' => 'han', 'HanXRQChr17g0569561' => 'han', 'Haze_12256' => 'cav', 'Haze_14756' => 'cav', 'Haze_25528' => 'cav', 'Hma1.2p1_0079F.1_g041020' => 'hma', 'Hma1.2p1_0818F.1_g223260' => 'hma', 'Hma1.2p1_1747F.1_g300530' => 'hma', 'HPP92_004607' => 'vpl', 'HPP92_004608' => 'vpl', 'HPP92_006181' => 'vpl', 'HPP92_012192' => 'vpl', 'HPP92_015680' => 'vpl', 'HPP92_020249' => 'vpl', 'HPP92_021376' => 'vpl', 'HPP92_024275' => 'vpl', 'Hund06031' => 'sun', 'Hund25391' => 'sun', 'Lalb_Chr07g0185371' => 'lal', 'Lalb_Chr07g0185381' => 'lal', 'Lalb_Chr12g0204011' => 'lal', 'Lalb_Chr13g0301671' => 'lal', 'Lalb_Chr14g0362851' => 'lal', 'Lalb_Chr24g0403581' => 'lal', 'Lj1g0000233' => 'lja', 'Lj2g0018120' => 'lja', 'Lj3C621T0' => 'lonja', 'Lj3P1059T14' => 'lonja', 'Lj3P611T9' => 'lonja', 'Lj3P614T13' => 'lonja', 'Lj3P615T5' => 'lonja', 'Lj4g0012315' => 'lja', 'Lj4g0026182' => 'lja', 'Lj6P813T16' => 'lonja', 'Lj7C427T7' => 'lonja', 'Lj7C427T8' => 'lonja', 'Lj7P600T41' => 'lonja', 'Lju41C42G17' => 'lonja', 'Lsat_1_v5_gn_0_47300' => 'lsa', 'Lsat_1_v5_gn_2_91280' => 'lsa', 'Lsat_1_v5_gn_3_30561' => 'lsa', 'Lsat_1_v5_gn_4_184321' => 'lsa', 'Lsat_1_v5_gn_4_4041' => 'lsa', 'Lsat_1_v5_gn_5_92000' => 'lsa', 'Lsat_1_v5_gn_8_152940' => 'lsa', 'Lsat_1_v5_gn_8_62401' => 'lsa', 'Manes.06G055900' => 'mes', 'Manes.12G022200' => 'mes', 'Manes.13G023300' => 'mes', 'Manes.14G115000' => 'mes', 'Manes.15G151700' => 'mes', 'Manes.17G111300' => 'mes', 'Mapoly0226s0009' => 'mpo', 'MBI02_g25363_MAGBIO' => 'mbi', 'MBI06_g00027_MAGBIO' => 'mbi', 'MBI10_g13034_MAGBIO' => 'mbi', 'MD09G1023400' => 'mdo', 'MD13G1100100' => 'mdo', 'MD15G1169200' => 'mdo', 'MD16G1101100' => 'mdo', 'MD17G1022900' => 'mdo', 'Medtr3g096150' => 'mtr', 'Medtr4g115070' => 'mtr', 'Medtr7g033325' => 'mtr', 'Medtr8g089840' => 'mtr', 'MELO3C010319.2' => 'cme', 'MELO3C011944.2' => 'cme', 'MELO3C021589.2' => 'cme', 'Migut.E00207' => 'egut', 'Migut.H00067' => 'egut', 'Migut.K00433' => 'egut', 'Migut.K00606' => 'egut', 'Migut.K01410' => 'egut', 'MSTRG.13347' => 'ama', 'MSTRG.24045' => 'ama', 'MSTRG.2428' => 'ama', 'MSTRG.26410' => 'ama', 'MSTRG.3139' => 'ama', 'MSTRG.3286' => 'ama', 'MSTRG.563' => 'ama', 'MSTRG.7941' => 'ama', 'Nitab4.5_0000028g0060' => 'nta', 'Nitab4.5_0000065g0260' => 'nta', 'Nitab4.5_0000112g0060' => 'nta', 'Nitab4.5_0000489g0120' => 'nta', 'Nitab4.5_0001776g0050' => 'nta', 'Nitab4.5_0001854g0010' => 'nta', 'Nitab4.5_0001860g0020' => 'nta', 'Nitab4.5_0004352g0010' => 'nta', 'Nitab4.5_0008716g0020' => 'nta', 'Nitab4.5_0008922g0010' => 'nta', 'Nn3g16693' => 'nnu', 'Nn4g22596' => 'nnu', 'Nn7g37639' => 'nnu', 'Oeu001701.1' => 'oeu', 'Oeu018149.1' => 'oeu', 'Oeu026220.1' => 'oeu', 'Oeu038635.1' => 'oeu', 'Oeu049176.1' => 'oeu', 'Oeu056706.1' => 'oeu', 'Oeu056937.1' => 'oeu', 'Oeu057540.1' => 'oeu', 'Os02g0594900' => 'osa', 'Os02g0595100' => 'osa', 'Os04g0477500' => 'osa', 'Os12g0611900' => 'osa', 'Peaxi162Scf00076g00020' => 'pax', 'Peaxi162Scf00128g00217' => 'pax', 'Peaxi162Scf00129g01640' => 'pax', 'Peaxi162Scf00669g00007' => 'pax', 'Peaxi162Scf00700g00421' => 'pax', 'Peaxi162Scf00801g00038' => 'pax', 'Peaxi162Scf00891g00025' => 'pax', 'PGR083G0909' => 'pgr', 'PGR119G1005' => 'pgr', 'PGR142G2236' => 'pgr', 'PGR142G3388' => 'pgr', 'PGSC0003DMG400004514' => 'stu', 'PGSC0003DMG400012635' => 'stu', 'PGSC0003DMG400015730' => 'stu', 'PGSC0003DMG400018611' => 'stu', 'PGSC0003DMG400030897' => 'stu', 'Phvul.001G254800' => 'pvu', 'Phvul.002G260100' => 'pvu', 'Phvul.003G167600' => 'pvu', 'Phvul.004G005100' => 'pvu', 'Potri.001G343600' => 'ptr', 'Potri.006G066700' => 'ptr', 'Potri.008G186000' => 'ptr', 'Potri.010G046900' => 'ptr', 'Potri.018G127900' => 'ptr', 'Pp3c20_17750' => 'ppa', 'Pp3c24_4380' => 'ppa', 'Prupe.1G245800' => 'ppe', 'Prupe.3G293400' => 'ppe', 'Prupe.7G247400' => 'ppe', 'Psat0s145g0120' => 'psa', 'Psat0s595g0040' => 'psa', 'Psat0s595g0120' => 'psa', 'Psat3g175040' => 'psa', 'Psat7g058120' => 'psa', 'PSO017G0428' => 'pso', 'PSO063G7510' => 'pso', 'PSO067G0046' => 'pso', 'PSO478G1073' => 'pso', 'PSO675G3677' => 'pso', 'PSO675G6558' => 'pso', 'PSO675G7520' => 'pso', 'PSO675G8959' => 'pso', 'QL02p074089' => 'qlo', 'QL02p089614' => 'qlo', 'QL03p057736' => 'qlo', 'RcHm_v2.0_Chr1g0364131' => 'rch', 'RcHm_v2.0_Chr2g0087801' => 'rch', 'RcHm_v2.0_Chr2g0087821' => 'rch', 'RcHm_v2.0_Chr2g0173231' => 'rch', 'RcHm_v2.0_Chr4g0433111' => 'rch', 'Rhsim03G0250300' => 'rsi', 'Rhsim08G0048400' => 'rsi', 'Rhsim10G0014800' => 'rsi', 'Rhsim12G0040100' => 'rsi', 'Rhsim12G0109700' => 'rsi', 'Sabra06G0049600' => 'sbr', 'Sabra08G0141000' => 'sbr', 'Sabra10G0021400' => 'sbr', 'Sabra16G0222900' => 'sbr', 'Sabra18G0108600' => 'sbr', 'SalBow1G0433' => 'sbo', 'SalBow1G2038' => 'sbo', 'SalBow1G5003' => 'sbo', 'SalBow7G1197' => 'sbo', 'SalBow8G3506' => 'sbo', 'Sc03g0007300' => 'sci', 'Sc11g0000950' => 'sci', 'Sc14g0008750' => 'sci', 'Sc18g0000420' => 'sci', 'Sed0006754' => 'sed', 'Sed0008741' => 'sed', 'Sed0017172' => 'sed', 'Sed0018925' => 'sed', 'Sed0023326' => 'sed', 'Sed0025909' => 'sed', 'SEGI_05333' => 'sgi', 'SEGI_10362' => 'sgi', 'SEGI_13380' => 'sgi', 'SEGI_24306' => 'sgi', 'SEGI_29077' => 'sgi', 'SEGI_29095' => 'sgi', 'SEGI_36534' => 'sgi', 'SEGI_37506' => 'sgi', 'SEGI_38321' => 'sgi', 'SGA_v2.0_scaffold307G48031' => 'sas', 'SGA_v2.0_scaffold47G17507' => 'sas', 'SGA_v2.0_scaffold63G21736' => 'sas', 'SGA_v2.0_scaffold87G27070' => 'sas', 'SHI17794' => 'shi', 'SHI28851' => 'shi', 'SMO165G0155' => 'smo', 'SMO340G0217' => 'smo', 'SMO367G1210' => 'smo', 'Solyc02g093430.3' => 'sly', 'Solyc05g013580.4' => 'sly', 'Solyc07g008030.3' => 'sly', 'Solyc12g035470.2' => 'sly', 'Sopen02g038020' => 'spe', 'Sopen05g008490' => 'spe', 'Sopen07g003910' => 'spe', 'Sopen12g015240' => 'spe', 'Sp1g11550' => 'spa', 'Sp2g16710' => 'spa', 'Sp3g00430' => 'spa', 'Sp3g26780' => 'spa', 'Sp5g22900' => 'spa', 'Sp6g29530' => 'spa', 'TAR371G0794' => 'tar', 'TAR374G0164' => 'tar', 'TAR622G0165' => 'tar', 'TAR626G0929' => 'tar', 'TAR629G2155' => 'tar', 'THA.LOC104805282' => 'tha', 'THA.LOC104805363' => 'tha', 'THA.LOC104808968' => 'tha', 'THA.LOC104821093' => 'tha', 'THA.LOC104823953' => 'tha', 'THA.LOC104825562' => 'tha', 'THA.LOC104825665' => 'tha', 'Thecc.02G261400' => 'tca', 'Thecc.04G019200' => 'tca', 'Thecc.09G130400' => 'tca', 'Thhalv10004374m.g' => 'esa', 'Thhalv10007850m.g' => 'esa', 'Thhalv10013782m.g' => 'esa', 'Thhalv10018686m.g' => 'esa', 'Thhalv10020899m.g' => 'esa', 'Thhalv10022755m.g' => 'esa', 'TPR.G23851' => 'tpr', 'TPR.G26500' => 'tpr', 'TPR.G27267' => 'tpr', 'TPR.G32001' => 'tpr', 'TPR.G6251' => 'tpr', 'TPR.G8167' => 'tpr', 'TWI12G1330' => 'twi', 'TWI18G1239' => 'twi', 'TWI34G0979' => 'twi', 'TWI36G0670' => 'twi', 'TWI36G0707' => 'twi', 'TWI56G0233' => 'twi', 'TWI75G1809' => 'twi', 'unitig_21.g20874' => 'ugi', 'unitig_26.g10343' => 'ugi', 'unitig_46.g18392' => 'ugi', 'unitig_52.g17178' => 'ugi', 'unitig_8.g2934' => 'ugi', 'vmacro01122' => 'vma', 'vmacro05875' => 'vma', 'vmacro06147' => 'vma', 'vmacro16191' => 'vma', 'vmacro18293' => 'vma', 'VMungo0251G3707' => 'vmu', 'VMungo0464G1521' => 'vmu', 'VMungo1215G0205' => 'vmu', 'VMungo1383G2484' => 'vmu', 'Zm00001eb079610' => 'zma', 'Zm00001eb135990' => 'zma', 'Zm00001eb183710' => 'zma', 'Zm00001eb246020' => 'zma' ), 'gf_id' => 'HOM05D001124', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001124' ), 'data_identifier' => 'HOM05D001124', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001124', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '548', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02520' => 'bna', 'A03p06630' => 'bna', 'A05p44460' => 'bna', 'A06p08710' => 'bna', 'A06p41090' => 'bna', 'A07p32320' => 'bna', 'A08p32520' => 'bna', 'A09p10360' => 'bna', 'A10p24080' => 'bna', 'Aa31LG11G15250' => 'aar', 'Aa31LG1G1800' => 'aar', 'Aa31LG2G5120' => 'aar', 'Aa31LG2G6070' => 'aar', 'Aa31LG5G10770' => 'aar', 'Aa31sc61G90' => 'aar', 'Actinidia01352' => 'ach', 'Actinidia05983' => 'ach', 'Actinidia08133' => 'ach', 'Actinidia15101' => 'ach', 'Actinidia26379' => 'ach', 'Actinidia35778' => 'ach', 'Actinidia36123' => 'ach', 'Actinidia37436' => 'ach', 'Actinidia38730' => 'ach', 'Ah.02g128210' => 'amhyb', 'Ah.03g132990' => 'amhyb', 'Ah.14g079410' => 'amhyb', 'AL1G24640' => 'aly', 'AL2G26680' => 'aly', 'AL3G10530' => 'aly', 'AL3G45230' => 'aly', 'AL5G15230' => 'aly', 'AL5G16960' => 'aly', 'AL6G25210' => 'aly', 'Aqoxy2G00441' => 'aox', 'Aqoxy3G01236' => 'aox', 'Aqoxy5G03746' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3RQ047' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C7GMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9C8JER' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MBL6KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YXCZ83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZANX40' => 'arhy', 'AT1G12990' => 'ath', 'AT1G67880' => 'ath', 'AT2G13290' => 'ath', 'AT3G01620' => 'ath', 'AT3G26445' => 'ath', 'AT3G27540' => 'ath', 'AT5G14480' => 'ath', 'ATR0824G026' => 'atr', 'ATR1098G019' => 'atr', 'Atru.chr11.2145' => 'acertr', 'Atru.chr2.3636' => 'acertr', 'Atru.chr2.3644' => 'acertr', 'Atru.chr6.2422' => 'acertr', 'Atru.chr7.1112' => 'acertr', 'AUR62005469' => 'cqu', 'AUR62011166' => 'cqu', 'AUR62013319' => 'cqu', 'AUR62024273' => 'cqu', 'AUR62028420' => 'cqu', 'AUR62041942' => 'cqu', 'BcaB01g04969' => 'bca', 'BcaB01g06371' => 'bca', 'BcaB02g11494' => 'bca', 'BcaB03g15382' => 'bca', 'BcaB08g36994' => 'bca', 'BcaC03g13477' => 'bca', 'BcaC03g13478' => 'bca', 'BcaC03g13480' => 'bca', 'BcaC03g13481' => 'bca', 'BcaC03g13486' => 'bca', 'BcaC04g19031' => 'bca', 'BcaC04g23085' => 'bca', 'BcaC05g25094' => 'bca', 'BcaC05g25096' => 'bca', 'BcaC05g25138' => 'bca', 'BcaC05g30416' => 'bca', 'BcaC05g30455' => 'bca', 'BcaC06g30979' => 'bca', 'BcaC06g33805' => 'bca', 'BcaC08g46021' => 'bca', 'BcaNung03154' => 'bca', 'BolC2t06623H' => 'bol', 'BolC2t06632H' => 'bol', 'BolC2t06635H' => 'bol', 'BolC2t06638H' => 'bol', 'BolC3t13266H' => 'bol', 'BolC5t29776H' => 'bol', 'BolC6t38912H' => 'bol', 'BolC7t44183H' => 'bol', 'BolC9t54123H' => 'bol', 'BolC9t59107H' => 'bol', 'BraA02t05221Z' => 'bra', 'BraA03t09996Z' => 'bra', 'BraA05t23210Z' => 'bra', 'BraA06t24068Z' => 'bra', 'BraA06t27032Z' => 'bra', 'BraA08t35176Z' => 'bra', 'BraA09t36680Z' => 'bra', 'BraA10t44471Z' => 'bra', 'C02p06760' => 'bna', 'C02p06890' => 'bna', 'C02p07010' => 'bna', 'C03p07660' => 'bna', 'C05p10300' => 'bna', 'C06p38150' => 'bna', 'C07p36650' => 'bna', 'C08p15770' => 'bna', 'C09p12300' => 'bna', 'C09p62700' => 'bna', 'C09p75040' => 'bna', 'CAN.G13.1' => 'can', 'CAN.G138.4' => 'can', 'CAN.G44.6' => 'can', 'CAN.G473.19' => 'can', 'CANSAT01G0835' => 'cansat', 'CANSAT11G0246' => 'cansat', 'CANSAT11G1766' => 'cansat', 'CANSAT64G1954' => 'cansat', 'CARHR013330' => 'chi', 'CARHR060530' => 'chi', 'CARHR075300' => 'chi', 'CARHR105120' => 'chi', 'CARHR148910' => 'chi', 'CARHR198830' => 'chi', 'Carub.0001s1275' => 'cru', 'Carub.0002s1437' => 'cru', 'Carub.0003s0044' => 'cru', 'Carub.0003s2787' => 'cru', 'Carub.0005s0597' => 'cru', 'Carub.0006s1266' => 'cru', 'Ca_06935_v3' => 'car', 'Ca_13559_v3' => 'car', 'Ca_16941_v3' => 'car', 'Ca_16960_v3' => 'car', 'Ca_17775_v3' => 'car', 'Ca_30464_v3' => 'car', 'Cc06_g08160' => 'ccan', 'Cc07_g01520' => 'ccan', 'Cc11_g15810' => 'ccan', 'CDE02G2840' => 'cde', 'CDE03G0093' => 'cde', 'CDE04G2127' => 'cde', 'CDE07G1857' => 'cde', 'CDE09G1246' => 'cde', 'Cfa003412' => 'cfa', 'Cfa007341' => 'cfa', 'Cfa009220' => 'cfa', 'Ciclev10008737m.g' => 'ccl', 'Ciclev10015565m.g' => 'ccl', 'Ciclev10031761m.g' => 'ccl', 'CiPaw.03G045300' => 'cil', 'CiPaw.03G247200' => 'cil', 'CiPaw.04G029500' => 'cil', 'CiPaw.04G174000' => 'cil', 'CiPaw.05G181200' => 'cil', 'CiPaw.06G067100' => 'cil', 'ClCG05G025800' => 'cla', 'ClCG06G011400' => 'cla', 'ClCG09G019360' => 'cla', 'COL.COLO4_04827' => 'col', 'COL.COLO4_29170' => 'col', 'COL.COLO4_35131' => 'col', 'COL.COLO4_35132' => 'col', 'Cpa.g.sc33.32' => 'cpa', 'Cpa.g.sc46.29' => 'cpa', 'Cpa.g.sc796.1' => 'cpa', 'CsaV3_1G030420' => 'csa', 'CsaV3_5G027050' => 'csa', 'CsaV3_5G031040' => 'csa', 'CsaV3_UNG023130' => 'csa', 'CSS0007726' => 'camsi', 'CSS0016433' => 'camsi', 'CSS0017656' => 'camsi', 'CSS0025364' => 'camsi', 'CSS0027582' => 'camsi', 'CSS0047288' => 'camsi', 'CSS0049950' => 'camsi', 'DCAR_003843' => 'dca', 'DCAR_007052' => 'dca', 'DCAR_020884' => 'dca', 'DCAR_021730' => 'dca', 'DCAR_024423' => 'dca', 'DCAR_026509' => 'dca', 'DCAR_031158' => 'dca', 'Dinv14728' => 'din', 'Dinv15219' => 'din', 'Dinv25728' => 'din', 'Dinv33428' => 'din', 'Dinv36489' => 'din', 'Dinv41486' => 'din', 'Duzib147G0469' => 'dzi', 'Duzib168G0060' => 'dzi', 'Duzib187G1215' => 'dzi', 'Duzib248G0692' => 'dzi', 'Duzib251G0767' => 'dzi', 'Duzib264G0446' => 'dzi', 'Duzib268G0691' => 'dzi', 'ECA232G4767' => 'eca', 'ECA233G2838' => 'eca', 'ECA234G0391' => 'eca', 'ECA234G0857' => 'eca', 'ECA236G1593' => 'eca', 'ECA238G0565' => 'eca', 'ECA246G1027' => 'eca', 'ECA246G3223' => 'eca', 'ECA246G3470' => 'eca', 'EL10Ac6g13829' => 'bvu', 'EL10Ac6g14093' => 'bvu', 'EL10Ac8g18707' => 'bvu', 'Eucgr.C01369' => 'egr', 'Eucgr.H02492' => 'egr', 'Eucgr.I01733' => 'egr', 'Eucgr.J02255' => 'egr', 'Eucgr.J02257' => 'egr', 'Eucgr.J02258' => 'egr', 'FAN02G1601' => 'fan', 'FAN03G1586' => 'fan', 'FAN03G2986' => 'fan', 'FAN05G4837' => 'fan', 'FAN06G0146' => 'fan', 'FAN07G0858' => 'fan', 'FAN09G3179' => 'fan', 'FAN10G0669' => 'fan', 'FAN12G2358' => 'fan', 'FAN14G4198' => 'fan', 'FAN14G5112' => 'fan', 'FAN17G0342' => 'fan', 'FAN19G0342' => 'fan', 'FAN19G0962' => 'fan', 'FAN19G1101' => 'fan', 'FAN19G1872' => 'fan', 'FAN22G0356' => 'fan', 'FAN23G0744' => 'fan', 'FAN23G1914' => 'fan', 'FAN26G0032' => 'fan', 'FAN28G0625' => 'fan', 'FvH4_1g02710' => 'fve', 'FvH4_1g02720' => 'fve', 'FvH4_4g25670' => 'fve', 'FvH4_6g51700' => 'fve', 'FvH4_7g20170' => 'fve', 'Glyma.05G175000' => 'gma', 'Glyma.08G132300' => 'gma', 'Glyma.11G243000' => 'gma', 'Glyma.13G158900' => 'gma', 'Glyma.17G112400' => 'gma', 'Glyma.18G014100' => 'gma', 'Glyma.19G003100' => 'gma', 'Glyma.19G056500' => 'gma', 'Gohir.A01G158900' => 'ghi', 'Gohir.A05G312600' => 'ghi', 'Gohir.A05G354900' => 'ghi', 'Gohir.A07G037200' => 'ghi', 'Gohir.A09G030000' => 'ghi', 'Gohir.A12G145200' => 'ghi', 'Gohir.D01G151500' => 'ghi', 'Gohir.D04G058300' => 'ghi', 'Gohir.D05G314100' => 'ghi', 'Gohir.D07G041400' => 'ghi', 'Gohir.D09G029700' => 'ghi', 'Gohir.D12G149700' => 'ghi', 'Gorai.001G043800' => 'gra', 'Gorai.002G187800' => 'gra', 'Gorai.006G034700' => 'gra', 'Gorai.008G161200' => 'gra', 'Gorai.009G335700' => 'gra', 'Gorai.012G065000' => 'gra', 'GSVIVG01000535001' => 'vvi', 'GSVIVG01015572001' => 'vvi', 'GSVIVG01032386001' => 'vvi', 'HanXRQChr05g0138531' => 'han', 'HanXRQChr06g0174391' => 'han', 'HanXRQChr07g0199021' => 'han', 'HanXRQChr08g0208211' => 'han', 'HanXRQChr09g0255471' => 'han', 'HanXRQChr10g0315791' => 'han', 'HanXRQChr12g0371991' => 'han', 'HanXRQChr15g0475251' => 'han', 'HanXRQChr17g0540001' => 'han', 'HanXRQChr17g0548631' => 'han', 'HanXRQChr17g0569561' => 'han', 'Haze_12256' => 'cav', 'Haze_14756' => 'cav', 'Haze_25528' => 'cav', 'Hma1.2p1_0079F.1_g041020' => 'hma', 'Hma1.2p1_0818F.1_g223260' => 'hma', 'Hma1.2p1_1747F.1_g300530' => 'hma', 'HPP92_004607' => 'vpl', 'HPP92_004608' => 'vpl', 'HPP92_006181' => 'vpl', 'HPP92_012192' => 'vpl', 'HPP92_015680' => 'vpl', 'HPP92_020249' => 'vpl', 'HPP92_021376' => 'vpl', 'HPP92_024275' => 'vpl', 'Hund06031' => 'sun', 'Hund25391' => 'sun', 'Lalb_Chr07g0185371' => 'lal', 'Lalb_Chr07g0185381' => 'lal', 'Lalb_Chr12g0204011' => 'lal', 'Lalb_Chr13g0301671' => 'lal', 'Lalb_Chr14g0362851' => 'lal', 'Lalb_Chr24g0403581' => 'lal', 'Lj1g0000233' => 'lja', 'Lj2g0018120' => 'lja', 'Lj3C621T0' => 'lonja', 'Lj3P1059T14' => 'lonja', 'Lj3P611T9' => 'lonja', 'Lj3P614T13' => 'lonja', 'Lj3P615T5' => 'lonja', 'Lj4g0012315' => 'lja', 'Lj4g0026182' => 'lja', 'Lj6P813T16' => 'lonja', 'Lj7C427T7' => 'lonja', 'Lj7C427T8' => 'lonja', 'Lj7P600T41' => 'lonja', 'Lju41C42G17' => 'lonja', 'Lsat_1_v5_gn_0_47300' => 'lsa', 'Lsat_1_v5_gn_2_91280' => 'lsa', 'Lsat_1_v5_gn_3_30561' => 'lsa', 'Lsat_1_v5_gn_4_184321' => 'lsa', 'Lsat_1_v5_gn_4_4041' => 'lsa', 'Lsat_1_v5_gn_5_92000' => 'lsa', 'Lsat_1_v5_gn_8_152940' => 'lsa', 'Lsat_1_v5_gn_8_62401' => 'lsa', 'Manes.06G055900' => 'mes', 'Manes.12G022200' => 'mes', 'Manes.13G023300' => 'mes', 'Manes.14G115000' => 'mes', 'Manes.15G151700' => 'mes', 'Manes.17G111300' => 'mes', 'Mapoly0226s0009' => 'mpo', 'MBI02_g25363_MAGBIO' => 'mbi', 'MBI06_g00027_MAGBIO' => 'mbi', 'MBI10_g13034_MAGBIO' => 'mbi', 'MD09G1023400' => 'mdo', 'MD13G1100100' => 'mdo', 'MD15G1169200' => 'mdo', 'MD16G1101100' => 'mdo', 'MD17G1022900' => 'mdo', 'Medtr3g096150' => 'mtr', 'Medtr4g115070' => 'mtr', 'Medtr7g033325' => 'mtr', 'Medtr8g089840' => 'mtr', 'MELO3C010319.2' => 'cme', 'MELO3C011944.2' => 'cme', 'MELO3C021589.2' => 'cme', 'Migut.E00207' => 'egut', 'Migut.H00067' => 'egut', 'Migut.K00433' => 'egut', 'Migut.K00606' => 'egut', 'Migut.K01410' => 'egut', 'MSTRG.13347' => 'ama', 'MSTRG.24045' => 'ama', 'MSTRG.2428' => 'ama', 'MSTRG.26410' => 'ama', 'MSTRG.3139' => 'ama', 'MSTRG.3286' => 'ama', 'MSTRG.563' => 'ama', 'MSTRG.7941' => 'ama', 'Nitab4.5_0000028g0060' => 'nta', 'Nitab4.5_0000065g0260' => 'nta', 'Nitab4.5_0000112g0060' => 'nta', 'Nitab4.5_0000489g0120' => 'nta', 'Nitab4.5_0001776g0050' => 'nta', 'Nitab4.5_0001854g0010' => 'nta', 'Nitab4.5_0001860g0020' => 'nta', 'Nitab4.5_0004352g0010' => 'nta', 'Nitab4.5_0008716g0020' => 'nta', 'Nitab4.5_0008922g0010' => 'nta', 'Nn3g16693' => 'nnu', 'Nn4g22596' => 'nnu', 'Nn7g37639' => 'nnu', 'Oeu001701.1' => 'oeu', 'Oeu018149.1' => 'oeu', 'Oeu026220.1' => 'oeu', 'Oeu038635.1' => 'oeu', 'Oeu049176.1' => 'oeu', 'Oeu056706.1' => 'oeu', 'Oeu056937.1' => 'oeu', 'Oeu057540.1' => 'oeu', 'Os02g0594900' => 'osa', 'Os02g0595100' => 'osa', 'Os04g0477500' => 'osa', 'Os12g0611900' => 'osa', 'Peaxi162Scf00076g00020' => 'pax', 'Peaxi162Scf00128g00217' => 'pax', 'Peaxi162Scf00129g01640' => 'pax', 'Peaxi162Scf00669g00007' => 'pax', 'Peaxi162Scf00700g00421' => 'pax', 'Peaxi162Scf00801g00038' => 'pax', 'Peaxi162Scf00891g00025' => 'pax', 'PGR083G0909' => 'pgr', 'PGR119G1005' => 'pgr', 'PGR142G2236' => 'pgr', 'PGR142G3388' => 'pgr', 'PGSC0003DMG400004514' => 'stu', 'PGSC0003DMG400012635' => 'stu', 'PGSC0003DMG400015730' => 'stu', 'PGSC0003DMG400018611' => 'stu', 'PGSC0003DMG400030897' => 'stu', 'Phvul.001G254800' => 'pvu', 'Phvul.002G260100' => 'pvu', 'Phvul.003G167600' => 'pvu', 'Phvul.004G005100' => 'pvu', 'Potri.001G343600' => 'ptr', 'Potri.006G066700' => 'ptr', 'Potri.008G186000' => 'ptr', 'Potri.010G046900' => 'ptr', 'Potri.018G127900' => 'ptr', 'Pp3c20_17750' => 'ppa', 'Pp3c24_4380' => 'ppa', 'Prupe.1G245800' => 'ppe', 'Prupe.3G293400' => 'ppe', 'Prupe.7G247400' => 'ppe', 'Psat0s145g0120' => 'psa', 'Psat0s595g0040' => 'psa', 'Psat0s595g0120' => 'psa', 'Psat3g175040' => 'psa', 'Psat7g058120' => 'psa', 'PSO017G0428' => 'pso', 'PSO063G7510' => 'pso', 'PSO067G0046' => 'pso', 'PSO478G1073' => 'pso', 'PSO675G3677' => 'pso', 'PSO675G6558' => 'pso', 'PSO675G7520' => 'pso', 'PSO675G8959' => 'pso', 'QL02p074089' => 'qlo', 'QL02p089614' => 'qlo', 'QL03p057736' => 'qlo', 'RcHm_v2.0_Chr1g0364131' => 'rch', 'RcHm_v2.0_Chr2g0087801' => 'rch', 'RcHm_v2.0_Chr2g0087821' => 'rch', 'RcHm_v2.0_Chr2g0173231' => 'rch', 'RcHm_v2.0_Chr4g0433111' => 'rch', 'Rhsim03G0250300' => 'rsi', 'Rhsim08G0048400' => 'rsi', 'Rhsim10G0014800' => 'rsi', 'Rhsim12G0040100' => 'rsi', 'Rhsim12G0109700' => 'rsi', 'Sabra06G0049600' => 'sbr', 'Sabra08G0141000' => 'sbr', 'Sabra10G0021400' => 'sbr', 'Sabra16G0222900' => 'sbr', 'Sabra18G0108600' => 'sbr', 'SalBow1G0433' => 'sbo', 'SalBow1G2038' => 'sbo', 'SalBow1G5003' => 'sbo', 'SalBow7G1197' => 'sbo', 'SalBow8G3506' => 'sbo', 'Sc03g0007300' => 'sci', 'Sc11g0000950' => 'sci', 'Sc14g0008750' => 'sci', 'Sc18g0000420' => 'sci', 'Sed0006754' => 'sed', 'Sed0008741' => 'sed', 'Sed0017172' => 'sed', 'Sed0018925' => 'sed', 'Sed0023326' => 'sed', 'Sed0025909' => 'sed', 'SEGI_05333' => 'sgi', 'SEGI_10362' => 'sgi', 'SEGI_13380' => 'sgi', 'SEGI_24306' => 'sgi', 'SEGI_29077' => 'sgi', 'SEGI_29095' => 'sgi', 'SEGI_36534' => 'sgi', 'SEGI_37506' => 'sgi', 'SEGI_38321' => 'sgi', 'SGA_v2.0_scaffold307G48031' => 'sas', 'SGA_v2.0_scaffold47G17507' => 'sas', 'SGA_v2.0_scaffold63G21736' => 'sas', 'SGA_v2.0_scaffold87G27070' => 'sas', 'SHI17794' => 'shi', 'SHI28851' => 'shi', 'SMO165G0155' => 'smo', 'SMO340G0217' => 'smo', 'SMO367G1210' => 'smo', 'Solyc02g093430.3' => 'sly', 'Solyc05g013580.4' => 'sly', 'Solyc07g008030.3' => 'sly', 'Solyc12g035470.2' => 'sly', 'Sopen02g038020' => 'spe', 'Sopen05g008490' => 'spe', 'Sopen07g003910' => 'spe', 'Sopen12g015240' => 'spe', 'Sp1g11550' => 'spa', 'Sp2g16710' => 'spa', 'Sp3g00430' => 'spa', 'Sp3g26780' => 'spa', 'Sp5g22900' => 'spa', 'Sp6g29530' => 'spa', 'TAR371G0794' => 'tar', 'TAR374G0164' => 'tar', 'TAR622G0165' => 'tar', 'TAR626G0929' => 'tar', 'TAR629G2155' => 'tar', 'THA.LOC104805282' => 'tha', 'THA.LOC104805363' => 'tha', 'THA.LOC104808968' => 'tha', 'THA.LOC104821093' => 'tha', 'THA.LOC104823953' => 'tha', 'THA.LOC104825562' => 'tha', 'THA.LOC104825665' => 'tha', 'Thecc.02G261400' => 'tca', 'Thecc.04G019200' => 'tca', 'Thecc.09G130400' => 'tca', 'Thhalv10004374m.g' => 'esa', 'Thhalv10007850m.g' => 'esa', 'Thhalv10013782m.g' => 'esa', 'Thhalv10018686m.g' => 'esa', 'Thhalv10020899m.g' => 'esa', 'Thhalv10022755m.g' => 'esa', 'TPR.G23851' => 'tpr', 'TPR.G26500' => 'tpr', 'TPR.G27267' => 'tpr', 'TPR.G32001' => 'tpr', 'TPR.G6251' => 'tpr', 'TPR.G8167' => 'tpr', 'TWI12G1330' => 'twi', 'TWI18G1239' => 'twi', 'TWI34G0979' => 'twi', 'TWI36G0670' => 'twi', 'TWI36G0707' => 'twi', 'TWI56G0233' => 'twi', 'TWI75G1809' => 'twi', 'unitig_21.g20874' => 'ugi', 'unitig_26.g10343' => 'ugi', 'unitig_46.g18392' => 'ugi', 'unitig_52.g17178' => 'ugi', 'unitig_8.g2934' => 'ugi', 'vmacro01122' => 'vma', 'vmacro05875' => 'vma', 'vmacro06147' => 'vma', 'vmacro16191' => 'vma', 'vmacro18293' => 'vma', 'VMungo0251G3707' => 'vmu', 'VMungo0464G1521' => 'vmu', 'VMungo1215G0205' => 'vmu', 'VMungo1383G2484' => 'vmu', 'Zm00001eb079610' => 'zma', 'Zm00001eb135990' => 'zma', 'Zm00001eb183710' => 'zma', 'Zm00001eb246020' => 'zma' ) $gf_id = 'HOM05D001124' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001124' ) $data_identifier = 'HOM05D001124' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 6, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 7, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 21, 'bol' => (int) 10, 'bra' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 6, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 9, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 21, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 8, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 10, 'lsa' => (int) 8, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 8, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 9, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb246020' $species_info = array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ) $local_species = 'cde' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001124', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '548', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02520' => 'bna', 'A03p06630' => 'bna', 'A05p44460' => 'bna', 'A06p08710' => 'bna', 'A06p41090' => 'bna', 'A07p32320' => 'bna', 'A08p32520' => 'bna', 'A09p10360' => 'bna', 'A10p24080' => 'bna', 'Aa31LG11G15250' => 'aar', 'Aa31LG1G1800' => 'aar', 'Aa31LG2G5120' => 'aar', 'Aa31LG2G6070' => 'aar', 'Aa31LG5G10770' => 'aar', 'Aa31sc61G90' => 'aar', 'Actinidia01352' => 'ach', 'Actinidia05983' => 'ach', 'Actinidia08133' => 'ach', 'Actinidia15101' => 'ach', 'Actinidia26379' => 'ach', 'Actinidia35778' => 'ach', 'Actinidia36123' => 'ach', 'Actinidia37436' => 'ach', 'Actinidia38730' => 'ach', 'Ah.02g128210' => 'amhyb', 'Ah.03g132990' => 'amhyb', 'Ah.14g079410' => 'amhyb', 'AL1G24640' => 'aly', 'AL2G26680' => 'aly', 'AL3G10530' => 'aly', 'AL3G45230' => 'aly', 'AL5G15230' => 'aly', 'AL5G16960' => 'aly', 'AL6G25210' => 'aly', 'Aqoxy2G00441' => 'aox', 'Aqoxy3G01236' => 'aox', 'Aqoxy5G03746' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3RQ047' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C7GMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9C8JER' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MBL6KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YXCZ83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZANX40' => 'arhy', 'AT1G12990' => 'ath', 'AT1G67880' => 'ath', 'AT2G13290' => 'ath', 'AT3G01620' => 'ath', 'AT3G26445' => 'ath', 'AT3G27540' => 'ath', 'AT5G14480' => 'ath', 'ATR0824G026' => 'atr', 'ATR1098G019' => 'atr', 'Atru.chr11.2145' => 'acertr', 'Atru.chr2.3636' => 'acertr', 'Atru.chr2.3644' => 'acertr', 'Atru.chr6.2422' => 'acertr', 'Atru.chr7.1112' => 'acertr', 'AUR62005469' => 'cqu', 'AUR62011166' => 'cqu', 'AUR62013319' => 'cqu', 'AUR62024273' => 'cqu', 'AUR62028420' => 'cqu', 'AUR62041942' => 'cqu', 'BcaB01g04969' => 'bca', 'BcaB01g06371' => 'bca', 'BcaB02g11494' => 'bca', 'BcaB03g15382' => 'bca', 'BcaB08g36994' => 'bca', 'BcaC03g13477' => 'bca', 'BcaC03g13478' => 'bca', 'BcaC03g13480' => 'bca', 'BcaC03g13481' => 'bca', 'BcaC03g13486' => 'bca', 'BcaC04g19031' => 'bca', 'BcaC04g23085' => 'bca', 'BcaC05g25094' => 'bca', 'BcaC05g25096' => 'bca', 'BcaC05g25138' => 'bca', 'BcaC05g30416' => 'bca', 'BcaC05g30455' => 'bca', 'BcaC06g30979' => 'bca', 'BcaC06g33805' => 'bca', 'BcaC08g46021' => 'bca', 'BcaNung03154' => 'bca', 'BolC2t06623H' => 'bol', 'BolC2t06632H' => 'bol', 'BolC2t06635H' => 'bol', 'BolC2t06638H' => 'bol', 'BolC3t13266H' => 'bol', 'BolC5t29776H' => 'bol', 'BolC6t38912H' => 'bol', 'BolC7t44183H' => 'bol', 'BolC9t54123H' => 'bol', 'BolC9t59107H' => 'bol', 'BraA02t05221Z' => 'bra', 'BraA03t09996Z' => 'bra', 'BraA05t23210Z' => 'bra', 'BraA06t24068Z' => 'bra', 'BraA06t27032Z' => 'bra', 'BraA08t35176Z' => 'bra', 'BraA09t36680Z' => 'bra', 'BraA10t44471Z' => 'bra', 'C02p06760' => 'bna', 'C02p06890' => 'bna', 'C02p07010' => 'bna', 'C03p07660' => 'bna', 'C05p10300' => 'bna', 'C06p38150' => 'bna', 'C07p36650' => 'bna', 'C08p15770' => 'bna', 'C09p12300' => 'bna', 'C09p62700' => 'bna', 'C09p75040' => 'bna', 'CAN.G13.1' => 'can', 'CAN.G138.4' => 'can', 'CAN.G44.6' => 'can', 'CAN.G473.19' => 'can', 'CANSAT01G0835' => 'cansat', 'CANSAT11G0246' => 'cansat', 'CANSAT11G1766' => 'cansat', 'CANSAT64G1954' => 'cansat', 'CARHR013330' => 'chi', 'CARHR060530' => 'chi', 'CARHR075300' => 'chi', 'CARHR105120' => 'chi', 'CARHR148910' => 'chi', 'CARHR198830' => 'chi', 'Carub.0001s1275' => 'cru', 'Carub.0002s1437' => 'cru', 'Carub.0003s0044' => 'cru', 'Carub.0003s2787' => 'cru', 'Carub.0005s0597' => 'cru', 'Carub.0006s1266' => 'cru', 'Ca_06935_v3' => 'car', 'Ca_13559_v3' => 'car', 'Ca_16941_v3' => 'car', 'Ca_16960_v3' => 'car', 'Ca_17775_v3' => 'car', 'Ca_30464_v3' => 'car', 'Cc06_g08160' => 'ccan', 'Cc07_g01520' => 'ccan', 'Cc11_g15810' => 'ccan', 'CDE02G2840' => 'cde', 'CDE03G0093' => 'cde', 'CDE04G2127' => 'cde', 'CDE07G1857' => 'cde', 'CDE09G1246' => 'cde', 'Cfa003412' => 'cfa', 'Cfa007341' => 'cfa', 'Cfa009220' => 'cfa', 'Ciclev10008737m.g' => 'ccl', 'Ciclev10015565m.g' => 'ccl', 'Ciclev10031761m.g' => 'ccl', 'CiPaw.03G045300' => 'cil', 'CiPaw.03G247200' => 'cil', 'CiPaw.04G029500' => 'cil', 'CiPaw.04G174000' => 'cil', 'CiPaw.05G181200' => 'cil', 'CiPaw.06G067100' => 'cil', 'ClCG05G025800' => 'cla', 'ClCG06G011400' => 'cla', 'ClCG09G019360' => 'cla', 'COL.COLO4_04827' => 'col', 'COL.COLO4_29170' => 'col', 'COL.COLO4_35131' => 'col', 'COL.COLO4_35132' => 'col', 'Cpa.g.sc33.32' => 'cpa', 'Cpa.g.sc46.29' => 'cpa', 'Cpa.g.sc796.1' => 'cpa', 'CsaV3_1G030420' => 'csa', 'CsaV3_5G027050' => 'csa', 'CsaV3_5G031040' => 'csa', 'CsaV3_UNG023130' => 'csa', 'CSS0007726' => 'camsi', 'CSS0016433' => 'camsi', 'CSS0017656' => 'camsi', 'CSS0025364' => 'camsi', 'CSS0027582' => 'camsi', 'CSS0047288' => 'camsi', 'CSS0049950' => 'camsi', 'DCAR_003843' => 'dca', 'DCAR_007052' => 'dca', 'DCAR_020884' => 'dca', 'DCAR_021730' => 'dca', 'DCAR_024423' => 'dca', 'DCAR_026509' => 'dca', 'DCAR_031158' => 'dca', 'Dinv14728' => 'din', 'Dinv15219' => 'din', 'Dinv25728' => 'din', 'Dinv33428' => 'din', 'Dinv36489' => 'din', 'Dinv41486' => 'din', 'Duzib147G0469' => 'dzi', 'Duzib168G0060' => 'dzi', 'Duzib187G1215' => 'dzi', 'Duzib248G0692' => 'dzi', 'Duzib251G0767' => 'dzi', 'Duzib264G0446' => 'dzi', 'Duzib268G0691' => 'dzi', 'ECA232G4767' => 'eca', 'ECA233G2838' => 'eca', 'ECA234G0391' => 'eca', 'ECA234G0857' => 'eca', 'ECA236G1593' => 'eca', 'ECA238G0565' => 'eca', 'ECA246G1027' => 'eca', 'ECA246G3223' => 'eca', 'ECA246G3470' => 'eca', 'EL10Ac6g13829' => 'bvu', 'EL10Ac6g14093' => 'bvu', 'EL10Ac8g18707' => 'bvu', 'Eucgr.C01369' => 'egr', 'Eucgr.H02492' => 'egr', 'Eucgr.I01733' => 'egr', 'Eucgr.J02255' => 'egr', 'Eucgr.J02257' => 'egr', 'Eucgr.J02258' => 'egr', 'FAN02G1601' => 'fan', 'FAN03G1586' => 'fan', 'FAN03G2986' => 'fan', 'FAN05G4837' => 'fan', 'FAN06G0146' => 'fan', 'FAN07G0858' => 'fan', 'FAN09G3179' => 'fan', 'FAN10G0669' => 'fan', 'FAN12G2358' => 'fan', 'FAN14G4198' => 'fan', 'FAN14G5112' => 'fan', 'FAN17G0342' => 'fan', 'FAN19G0342' => 'fan', 'FAN19G0962' => 'fan', 'FAN19G1101' => 'fan', 'FAN19G1872' => 'fan', 'FAN22G0356' => 'fan', 'FAN23G0744' => 'fan', 'FAN23G1914' => 'fan', 'FAN26G0032' => 'fan', 'FAN28G0625' => 'fan', 'FvH4_1g02710' => 'fve', 'FvH4_1g02720' => 'fve', 'FvH4_4g25670' => 'fve', 'FvH4_6g51700' => 'fve', 'FvH4_7g20170' => 'fve', 'Glyma.05G175000' => 'gma', 'Glyma.08G132300' => 'gma', 'Glyma.11G243000' => 'gma', 'Glyma.13G158900' => 'gma', 'Glyma.17G112400' => 'gma', 'Glyma.18G014100' => 'gma', 'Glyma.19G003100' => 'gma', 'Glyma.19G056500' => 'gma', 'Gohir.A01G158900' => 'ghi', 'Gohir.A05G312600' => 'ghi', 'Gohir.A05G354900' => 'ghi', 'Gohir.A07G037200' => 'ghi', 'Gohir.A09G030000' => 'ghi', 'Gohir.A12G145200' => 'ghi', 'Gohir.D01G151500' => 'ghi', 'Gohir.D04G058300' => 'ghi', 'Gohir.D05G314100' => 'ghi', 'Gohir.D07G041400' => 'ghi', 'Gohir.D09G029700' => 'ghi', 'Gohir.D12G149700' => 'ghi', 'Gorai.001G043800' => 'gra', 'Gorai.002G187800' => 'gra', 'Gorai.006G034700' => 'gra', 'Gorai.008G161200' => 'gra', 'Gorai.009G335700' => 'gra', 'Gorai.012G065000' => 'gra', 'GSVIVG01000535001' => 'vvi', 'GSVIVG01015572001' => 'vvi', 'GSVIVG01032386001' => 'vvi', 'HanXRQChr05g0138531' => 'han', 'HanXRQChr06g0174391' => 'han', 'HanXRQChr07g0199021' => 'han', 'HanXRQChr08g0208211' => 'han', 'HanXRQChr09g0255471' => 'han', 'HanXRQChr10g0315791' => 'han', 'HanXRQChr12g0371991' => 'han', 'HanXRQChr15g0475251' => 'han', 'HanXRQChr17g0540001' => 'han', 'HanXRQChr17g0548631' => 'han', 'HanXRQChr17g0569561' => 'han', 'Haze_12256' => 'cav', 'Haze_14756' => 'cav', 'Haze_25528' => 'cav', 'Hma1.2p1_0079F.1_g041020' => 'hma', 'Hma1.2p1_0818F.1_g223260' => 'hma', 'Hma1.2p1_1747F.1_g300530' => 'hma', 'HPP92_004607' => 'vpl', 'HPP92_004608' => 'vpl', 'HPP92_006181' => 'vpl', 'HPP92_012192' => 'vpl', 'HPP92_015680' => 'vpl', 'HPP92_020249' => 'vpl', 'HPP92_021376' => 'vpl', 'HPP92_024275' => 'vpl', 'Hund06031' => 'sun', 'Hund25391' => 'sun', 'Lalb_Chr07g0185371' => 'lal', 'Lalb_Chr07g0185381' => 'lal', 'Lalb_Chr12g0204011' => 'lal', 'Lalb_Chr13g0301671' => 'lal', 'Lalb_Chr14g0362851' => 'lal', 'Lalb_Chr24g0403581' => 'lal', 'Lj1g0000233' => 'lja', 'Lj2g0018120' => 'lja', 'Lj3C621T0' => 'lonja', 'Lj3P1059T14' => 'lonja', 'Lj3P611T9' => 'lonja', 'Lj3P614T13' => 'lonja', 'Lj3P615T5' => 'lonja', 'Lj4g0012315' => 'lja', 'Lj4g0026182' => 'lja', 'Lj6P813T16' => 'lonja', 'Lj7C427T7' => 'lonja', 'Lj7C427T8' => 'lonja', 'Lj7P600T41' => 'lonja', 'Lju41C42G17' => 'lonja', 'Lsat_1_v5_gn_0_47300' => 'lsa', 'Lsat_1_v5_gn_2_91280' => 'lsa', 'Lsat_1_v5_gn_3_30561' => 'lsa', 'Lsat_1_v5_gn_4_184321' => 'lsa', 'Lsat_1_v5_gn_4_4041' => 'lsa', 'Lsat_1_v5_gn_5_92000' => 'lsa', 'Lsat_1_v5_gn_8_152940' => 'lsa', 'Lsat_1_v5_gn_8_62401' => 'lsa', 'Manes.06G055900' => 'mes', 'Manes.12G022200' => 'mes', 'Manes.13G023300' => 'mes', 'Manes.14G115000' => 'mes', 'Manes.15G151700' => 'mes', 'Manes.17G111300' => 'mes', 'Mapoly0226s0009' => 'mpo', 'MBI02_g25363_MAGBIO' => 'mbi', 'MBI06_g00027_MAGBIO' => 'mbi', 'MBI10_g13034_MAGBIO' => 'mbi', 'MD09G1023400' => 'mdo', 'MD13G1100100' => 'mdo', 'MD15G1169200' => 'mdo', 'MD16G1101100' => 'mdo', 'MD17G1022900' => 'mdo', 'Medtr3g096150' => 'mtr', 'Medtr4g115070' => 'mtr', 'Medtr7g033325' => 'mtr', 'Medtr8g089840' => 'mtr', 'MELO3C010319.2' => 'cme', 'MELO3C011944.2' => 'cme', 'MELO3C021589.2' => 'cme', 'Migut.E00207' => 'egut', 'Migut.H00067' => 'egut', 'Migut.K00433' => 'egut', 'Migut.K00606' => 'egut', 'Migut.K01410' => 'egut', 'MSTRG.13347' => 'ama', 'MSTRG.24045' => 'ama', 'MSTRG.2428' => 'ama', 'MSTRG.26410' => 'ama', 'MSTRG.3139' => 'ama', 'MSTRG.3286' => 'ama', 'MSTRG.563' => 'ama', 'MSTRG.7941' => 'ama', 'Nitab4.5_0000028g0060' => 'nta', 'Nitab4.5_0000065g0260' => 'nta', 'Nitab4.5_0000112g0060' => 'nta', 'Nitab4.5_0000489g0120' => 'nta', 'Nitab4.5_0001776g0050' => 'nta', 'Nitab4.5_0001854g0010' => 'nta', 'Nitab4.5_0001860g0020' => 'nta', 'Nitab4.5_0004352g0010' => 'nta', 'Nitab4.5_0008716g0020' => 'nta', 'Nitab4.5_0008922g0010' => 'nta', 'Nn3g16693' => 'nnu', 'Nn4g22596' => 'nnu', 'Nn7g37639' => 'nnu', 'Oeu001701.1' => 'oeu', 'Oeu018149.1' => 'oeu', 'Oeu026220.1' => 'oeu', 'Oeu038635.1' => 'oeu', 'Oeu049176.1' => 'oeu', 'Oeu056706.1' => 'oeu', 'Oeu056937.1' => 'oeu', 'Oeu057540.1' => 'oeu', 'Os02g0594900' => 'osa', 'Os02g0595100' => 'osa', 'Os04g0477500' => 'osa', 'Os12g0611900' => 'osa', 'Peaxi162Scf00076g00020' => 'pax', 'Peaxi162Scf00128g00217' => 'pax', 'Peaxi162Scf00129g01640' => 'pax', 'Peaxi162Scf00669g00007' => 'pax', 'Peaxi162Scf00700g00421' => 'pax', 'Peaxi162Scf00801g00038' => 'pax', 'Peaxi162Scf00891g00025' => 'pax', 'PGR083G0909' => 'pgr', 'PGR119G1005' => 'pgr', 'PGR142G2236' => 'pgr', 'PGR142G3388' => 'pgr', 'PGSC0003DMG400004514' => 'stu', 'PGSC0003DMG400012635' => 'stu', 'PGSC0003DMG400015730' => 'stu', 'PGSC0003DMG400018611' => 'stu', 'PGSC0003DMG400030897' => 'stu', 'Phvul.001G254800' => 'pvu', 'Phvul.002G260100' => 'pvu', 'Phvul.003G167600' => 'pvu', 'Phvul.004G005100' => 'pvu', 'Potri.001G343600' => 'ptr', 'Potri.006G066700' => 'ptr', 'Potri.008G186000' => 'ptr', 'Potri.010G046900' => 'ptr', 'Potri.018G127900' => 'ptr', 'Pp3c20_17750' => 'ppa', 'Pp3c24_4380' => 'ppa', 'Prupe.1G245800' => 'ppe', 'Prupe.3G293400' => 'ppe', 'Prupe.7G247400' => 'ppe', 'Psat0s145g0120' => 'psa', 'Psat0s595g0040' => 'psa', 'Psat0s595g0120' => 'psa', 'Psat3g175040' => 'psa', 'Psat7g058120' => 'psa', 'PSO017G0428' => 'pso', 'PSO063G7510' => 'pso', 'PSO067G0046' => 'pso', 'PSO478G1073' => 'pso', 'PSO675G3677' => 'pso', 'PSO675G6558' => 'pso', 'PSO675G7520' => 'pso', 'PSO675G8959' => 'pso', 'QL02p074089' => 'qlo', 'QL02p089614' => 'qlo', 'QL03p057736' => 'qlo', 'RcHm_v2.0_Chr1g0364131' => 'rch', 'RcHm_v2.0_Chr2g0087801' => 'rch', 'RcHm_v2.0_Chr2g0087821' => 'rch', 'RcHm_v2.0_Chr2g0173231' => 'rch', 'RcHm_v2.0_Chr4g0433111' => 'rch', 'Rhsim03G0250300' => 'rsi', 'Rhsim08G0048400' => 'rsi', 'Rhsim10G0014800' => 'rsi', 'Rhsim12G0040100' => 'rsi', 'Rhsim12G0109700' => 'rsi', 'Sabra06G0049600' => 'sbr', 'Sabra08G0141000' => 'sbr', 'Sabra10G0021400' => 'sbr', 'Sabra16G0222900' => 'sbr', 'Sabra18G0108600' => 'sbr', 'SalBow1G0433' => 'sbo', 'SalBow1G2038' => 'sbo', 'SalBow1G5003' => 'sbo', 'SalBow7G1197' => 'sbo', 'SalBow8G3506' => 'sbo', 'Sc03g0007300' => 'sci', 'Sc11g0000950' => 'sci', 'Sc14g0008750' => 'sci', 'Sc18g0000420' => 'sci', 'Sed0006754' => 'sed', 'Sed0008741' => 'sed', 'Sed0017172' => 'sed', 'Sed0018925' => 'sed', 'Sed0023326' => 'sed', 'Sed0025909' => 'sed', 'SEGI_05333' => 'sgi', 'SEGI_10362' => 'sgi', 'SEGI_13380' => 'sgi', 'SEGI_24306' => 'sgi', 'SEGI_29077' => 'sgi', 'SEGI_29095' => 'sgi', 'SEGI_36534' => 'sgi', 'SEGI_37506' => 'sgi', 'SEGI_38321' => 'sgi', 'SGA_v2.0_scaffold307G48031' => 'sas', 'SGA_v2.0_scaffold47G17507' => 'sas', 'SGA_v2.0_scaffold63G21736' => 'sas', 'SGA_v2.0_scaffold87G27070' => 'sas', 'SHI17794' => 'shi', 'SHI28851' => 'shi', 'SMO165G0155' => 'smo', 'SMO340G0217' => 'smo', 'SMO367G1210' => 'smo', 'Solyc02g093430.3' => 'sly', 'Solyc05g013580.4' => 'sly', 'Solyc07g008030.3' => 'sly', 'Solyc12g035470.2' => 'sly', 'Sopen02g038020' => 'spe', 'Sopen05g008490' => 'spe', 'Sopen07g003910' => 'spe', 'Sopen12g015240' => 'spe', 'Sp1g11550' => 'spa', 'Sp2g16710' => 'spa', 'Sp3g00430' => 'spa', 'Sp3g26780' => 'spa', 'Sp5g22900' => 'spa', 'Sp6g29530' => 'spa', 'TAR371G0794' => 'tar', 'TAR374G0164' => 'tar', 'TAR622G0165' => 'tar', 'TAR626G0929' => 'tar', 'TAR629G2155' => 'tar', 'THA.LOC104805282' => 'tha', 'THA.LOC104805363' => 'tha', 'THA.LOC104808968' => 'tha', 'THA.LOC104821093' => 'tha', 'THA.LOC104823953' => 'tha', 'THA.LOC104825562' => 'tha', 'THA.LOC104825665' => 'tha', 'Thecc.02G261400' => 'tca', 'Thecc.04G019200' => 'tca', 'Thecc.09G130400' => 'tca', 'Thhalv10004374m.g' => 'esa', 'Thhalv10007850m.g' => 'esa', 'Thhalv10013782m.g' => 'esa', 'Thhalv10018686m.g' => 'esa', 'Thhalv10020899m.g' => 'esa', 'Thhalv10022755m.g' => 'esa', 'TPR.G23851' => 'tpr', 'TPR.G26500' => 'tpr', 'TPR.G27267' => 'tpr', 'TPR.G32001' => 'tpr', 'TPR.G6251' => 'tpr', 'TPR.G8167' => 'tpr', 'TWI12G1330' => 'twi', 'TWI18G1239' => 'twi', 'TWI34G0979' => 'twi', 'TWI36G0670' => 'twi', 'TWI36G0707' => 'twi', 'TWI56G0233' => 'twi', 'TWI75G1809' => 'twi', 'unitig_21.g20874' => 'ugi', 'unitig_26.g10343' => 'ugi', 'unitig_46.g18392' => 'ugi', 'unitig_52.g17178' => 'ugi', 'unitig_8.g2934' => 'ugi', 'vmacro01122' => 'vma', 'vmacro05875' => 'vma', 'vmacro06147' => 'vma', 'vmacro16191' => 'vma', 'vmacro18293' => 'vma', 'VMungo0251G3707' => 'vmu', 'VMungo0464G1521' => 'vmu', 'VMungo1215G0205' => 'vmu', 'VMungo1383G2484' => 'vmu', 'Zm00001eb079610' => 'zma', 'Zm00001eb135990' => 'zma', 'Zm00001eb183710' => 'zma', 'Zm00001eb246020' => 'zma' ), 'gf_id' => 'HOM05D001124', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001124' ), 'data_identifier' => 'HOM05D001124', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001124', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '548', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02520' => 'bna', 'A03p06630' => 'bna', 'A05p44460' => 'bna', 'A06p08710' => 'bna', 'A06p41090' => 'bna', 'A07p32320' => 'bna', 'A08p32520' => 'bna', 'A09p10360' => 'bna', 'A10p24080' => 'bna', 'Aa31LG11G15250' => 'aar', 'Aa31LG1G1800' => 'aar', 'Aa31LG2G5120' => 'aar', 'Aa31LG2G6070' => 'aar', 'Aa31LG5G10770' => 'aar', 'Aa31sc61G90' => 'aar', 'Actinidia01352' => 'ach', 'Actinidia05983' => 'ach', 'Actinidia08133' => 'ach', 'Actinidia15101' => 'ach', 'Actinidia26379' => 'ach', 'Actinidia35778' => 'ach', 'Actinidia36123' => 'ach', 'Actinidia37436' => 'ach', 'Actinidia38730' => 'ach', 'Ah.02g128210' => 'amhyb', 'Ah.03g132990' => 'amhyb', 'Ah.14g079410' => 'amhyb', 'AL1G24640' => 'aly', 'AL2G26680' => 'aly', 'AL3G10530' => 'aly', 'AL3G45230' => 'aly', 'AL5G15230' => 'aly', 'AL5G16960' => 'aly', 'AL6G25210' => 'aly', 'Aqoxy2G00441' => 'aox', 'Aqoxy3G01236' => 'aox', 'Aqoxy5G03746' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3RQ047' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C7GMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9C8JER' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MBL6KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YXCZ83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZANX40' => 'arhy', 'AT1G12990' => 'ath', 'AT1G67880' => 'ath', 'AT2G13290' => 'ath', 'AT3G01620' => 'ath', 'AT3G26445' => 'ath', 'AT3G27540' => 'ath', 'AT5G14480' => 'ath', 'ATR0824G026' => 'atr', 'ATR1098G019' => 'atr', 'Atru.chr11.2145' => 'acertr', 'Atru.chr2.3636' => 'acertr', 'Atru.chr2.3644' => 'acertr', 'Atru.chr6.2422' => 'acertr', 'Atru.chr7.1112' => 'acertr', 'AUR62005469' => 'cqu', 'AUR62011166' => 'cqu', 'AUR62013319' => 'cqu', 'AUR62024273' => 'cqu', 'AUR62028420' => 'cqu', 'AUR62041942' => 'cqu', 'BcaB01g04969' => 'bca', 'BcaB01g06371' => 'bca', 'BcaB02g11494' => 'bca', 'BcaB03g15382' => 'bca', 'BcaB08g36994' => 'bca', 'BcaC03g13477' => 'bca', 'BcaC03g13478' => 'bca', 'BcaC03g13480' => 'bca', 'BcaC03g13481' => 'bca', 'BcaC03g13486' => 'bca', 'BcaC04g19031' => 'bca', 'BcaC04g23085' => 'bca', 'BcaC05g25094' => 'bca', 'BcaC05g25096' => 'bca', 'BcaC05g25138' => 'bca', 'BcaC05g30416' => 'bca', 'BcaC05g30455' => 'bca', 'BcaC06g30979' => 'bca', 'BcaC06g33805' => 'bca', 'BcaC08g46021' => 'bca', 'BcaNung03154' => 'bca', 'BolC2t06623H' => 'bol', 'BolC2t06632H' => 'bol', 'BolC2t06635H' => 'bol', 'BolC2t06638H' => 'bol', 'BolC3t13266H' => 'bol', 'BolC5t29776H' => 'bol', 'BolC6t38912H' => 'bol', 'BolC7t44183H' => 'bol', 'BolC9t54123H' => 'bol', 'BolC9t59107H' => 'bol', 'BraA02t05221Z' => 'bra', 'BraA03t09996Z' => 'bra', 'BraA05t23210Z' => 'bra', 'BraA06t24068Z' => 'bra', 'BraA06t27032Z' => 'bra', 'BraA08t35176Z' => 'bra', 'BraA09t36680Z' => 'bra', 'BraA10t44471Z' => 'bra', 'C02p06760' => 'bna', 'C02p06890' => 'bna', 'C02p07010' => 'bna', 'C03p07660' => 'bna', 'C05p10300' => 'bna', 'C06p38150' => 'bna', 'C07p36650' => 'bna', 'C08p15770' => 'bna', 'C09p12300' => 'bna', 'C09p62700' => 'bna', 'C09p75040' => 'bna', 'CAN.G13.1' => 'can', 'CAN.G138.4' => 'can', 'CAN.G44.6' => 'can', 'CAN.G473.19' => 'can', 'CANSAT01G0835' => 'cansat', 'CANSAT11G0246' => 'cansat', 'CANSAT11G1766' => 'cansat', 'CANSAT64G1954' => 'cansat', 'CARHR013330' => 'chi', 'CARHR060530' => 'chi', 'CARHR075300' => 'chi', 'CARHR105120' => 'chi', 'CARHR148910' => 'chi', 'CARHR198830' => 'chi', 'Carub.0001s1275' => 'cru', 'Carub.0002s1437' => 'cru', 'Carub.0003s0044' => 'cru', 'Carub.0003s2787' => 'cru', 'Carub.0005s0597' => 'cru', 'Carub.0006s1266' => 'cru', 'Ca_06935_v3' => 'car', 'Ca_13559_v3' => 'car', 'Ca_16941_v3' => 'car', 'Ca_16960_v3' => 'car', 'Ca_17775_v3' => 'car', 'Ca_30464_v3' => 'car', 'Cc06_g08160' => 'ccan', 'Cc07_g01520' => 'ccan', 'Cc11_g15810' => 'ccan', 'CDE02G2840' => 'cde', 'CDE03G0093' => 'cde', 'CDE04G2127' => 'cde', 'CDE07G1857' => 'cde', 'CDE09G1246' => 'cde', 'Cfa003412' => 'cfa', 'Cfa007341' => 'cfa', 'Cfa009220' => 'cfa', 'Ciclev10008737m.g' => 'ccl', 'Ciclev10015565m.g' => 'ccl', 'Ciclev10031761m.g' => 'ccl', 'CiPaw.03G045300' => 'cil', 'CiPaw.03G247200' => 'cil', 'CiPaw.04G029500' => 'cil', 'CiPaw.04G174000' => 'cil', 'CiPaw.05G181200' => 'cil', 'CiPaw.06G067100' => 'cil', 'ClCG05G025800' => 'cla', 'ClCG06G011400' => 'cla', 'ClCG09G019360' => 'cla', 'COL.COLO4_04827' => 'col', 'COL.COLO4_29170' => 'col', 'COL.COLO4_35131' => 'col', 'COL.COLO4_35132' => 'col', 'Cpa.g.sc33.32' => 'cpa', 'Cpa.g.sc46.29' => 'cpa', 'Cpa.g.sc796.1' => 'cpa', 'CsaV3_1G030420' => 'csa', 'CsaV3_5G027050' => 'csa', 'CsaV3_5G031040' => 'csa', 'CsaV3_UNG023130' => 'csa', 'CSS0007726' => 'camsi', 'CSS0016433' => 'camsi', 'CSS0017656' => 'camsi', 'CSS0025364' => 'camsi', 'CSS0027582' => 'camsi', 'CSS0047288' => 'camsi', 'CSS0049950' => 'camsi', 'DCAR_003843' => 'dca', 'DCAR_007052' => 'dca', 'DCAR_020884' => 'dca', 'DCAR_021730' => 'dca', 'DCAR_024423' => 'dca', 'DCAR_026509' => 'dca', 'DCAR_031158' => 'dca', 'Dinv14728' => 'din', 'Dinv15219' => 'din', 'Dinv25728' => 'din', 'Dinv33428' => 'din', 'Dinv36489' => 'din', 'Dinv41486' => 'din', 'Duzib147G0469' => 'dzi', 'Duzib168G0060' => 'dzi', 'Duzib187G1215' => 'dzi', 'Duzib248G0692' => 'dzi', 'Duzib251G0767' => 'dzi', 'Duzib264G0446' => 'dzi', 'Duzib268G0691' => 'dzi', 'ECA232G4767' => 'eca', 'ECA233G2838' => 'eca', 'ECA234G0391' => 'eca', 'ECA234G0857' => 'eca', 'ECA236G1593' => 'eca', 'ECA238G0565' => 'eca', 'ECA246G1027' => 'eca', 'ECA246G3223' => 'eca', 'ECA246G3470' => 'eca', 'EL10Ac6g13829' => 'bvu', 'EL10Ac6g14093' => 'bvu', 'EL10Ac8g18707' => 'bvu', 'Eucgr.C01369' => 'egr', 'Eucgr.H02492' => 'egr', 'Eucgr.I01733' => 'egr', 'Eucgr.J02255' => 'egr', 'Eucgr.J02257' => 'egr', 'Eucgr.J02258' => 'egr', 'FAN02G1601' => 'fan', 'FAN03G1586' => 'fan', 'FAN03G2986' => 'fan', 'FAN05G4837' => 'fan', 'FAN06G0146' => 'fan', 'FAN07G0858' => 'fan', 'FAN09G3179' => 'fan', 'FAN10G0669' => 'fan', 'FAN12G2358' => 'fan', 'FAN14G4198' => 'fan', 'FAN14G5112' => 'fan', 'FAN17G0342' => 'fan', 'FAN19G0342' => 'fan', 'FAN19G0962' => 'fan', 'FAN19G1101' => 'fan', 'FAN19G1872' => 'fan', 'FAN22G0356' => 'fan', 'FAN23G0744' => 'fan', 'FAN23G1914' => 'fan', 'FAN26G0032' => 'fan', 'FAN28G0625' => 'fan', 'FvH4_1g02710' => 'fve', 'FvH4_1g02720' => 'fve', 'FvH4_4g25670' => 'fve', 'FvH4_6g51700' => 'fve', 'FvH4_7g20170' => 'fve', 'Glyma.05G175000' => 'gma', 'Glyma.08G132300' => 'gma', 'Glyma.11G243000' => 'gma', 'Glyma.13G158900' => 'gma', 'Glyma.17G112400' => 'gma', 'Glyma.18G014100' => 'gma', 'Glyma.19G003100' => 'gma', 'Glyma.19G056500' => 'gma', 'Gohir.A01G158900' => 'ghi', 'Gohir.A05G312600' => 'ghi', 'Gohir.A05G354900' => 'ghi', 'Gohir.A07G037200' => 'ghi', 'Gohir.A09G030000' => 'ghi', 'Gohir.A12G145200' => 'ghi', 'Gohir.D01G151500' => 'ghi', 'Gohir.D04G058300' => 'ghi', 'Gohir.D05G314100' => 'ghi', 'Gohir.D07G041400' => 'ghi', 'Gohir.D09G029700' => 'ghi', 'Gohir.D12G149700' => 'ghi', 'Gorai.001G043800' => 'gra', 'Gorai.002G187800' => 'gra', 'Gorai.006G034700' => 'gra', 'Gorai.008G161200' => 'gra', 'Gorai.009G335700' => 'gra', 'Gorai.012G065000' => 'gra', 'GSVIVG01000535001' => 'vvi', 'GSVIVG01015572001' => 'vvi', 'GSVIVG01032386001' => 'vvi', 'HanXRQChr05g0138531' => 'han', 'HanXRQChr06g0174391' => 'han', 'HanXRQChr07g0199021' => 'han', 'HanXRQChr08g0208211' => 'han', 'HanXRQChr09g0255471' => 'han', 'HanXRQChr10g0315791' => 'han', 'HanXRQChr12g0371991' => 'han', 'HanXRQChr15g0475251' => 'han', 'HanXRQChr17g0540001' => 'han', 'HanXRQChr17g0548631' => 'han', 'HanXRQChr17g0569561' => 'han', 'Haze_12256' => 'cav', 'Haze_14756' => 'cav', 'Haze_25528' => 'cav', 'Hma1.2p1_0079F.1_g041020' => 'hma', 'Hma1.2p1_0818F.1_g223260' => 'hma', 'Hma1.2p1_1747F.1_g300530' => 'hma', 'HPP92_004607' => 'vpl', 'HPP92_004608' => 'vpl', 'HPP92_006181' => 'vpl', 'HPP92_012192' => 'vpl', 'HPP92_015680' => 'vpl', 'HPP92_020249' => 'vpl', 'HPP92_021376' => 'vpl', 'HPP92_024275' => 'vpl', 'Hund06031' => 'sun', 'Hund25391' => 'sun', 'Lalb_Chr07g0185371' => 'lal', 'Lalb_Chr07g0185381' => 'lal', 'Lalb_Chr12g0204011' => 'lal', 'Lalb_Chr13g0301671' => 'lal', 'Lalb_Chr14g0362851' => 'lal', 'Lalb_Chr24g0403581' => 'lal', 'Lj1g0000233' => 'lja', 'Lj2g0018120' => 'lja', 'Lj3C621T0' => 'lonja', 'Lj3P1059T14' => 'lonja', 'Lj3P611T9' => 'lonja', 'Lj3P614T13' => 'lonja', 'Lj3P615T5' => 'lonja', 'Lj4g0012315' => 'lja', 'Lj4g0026182' => 'lja', 'Lj6P813T16' => 'lonja', 'Lj7C427T7' => 'lonja', 'Lj7C427T8' => 'lonja', 'Lj7P600T41' => 'lonja', 'Lju41C42G17' => 'lonja', 'Lsat_1_v5_gn_0_47300' => 'lsa', 'Lsat_1_v5_gn_2_91280' => 'lsa', 'Lsat_1_v5_gn_3_30561' => 'lsa', 'Lsat_1_v5_gn_4_184321' => 'lsa', 'Lsat_1_v5_gn_4_4041' => 'lsa', 'Lsat_1_v5_gn_5_92000' => 'lsa', 'Lsat_1_v5_gn_8_152940' => 'lsa', 'Lsat_1_v5_gn_8_62401' => 'lsa', 'Manes.06G055900' => 'mes', 'Manes.12G022200' => 'mes', 'Manes.13G023300' => 'mes', 'Manes.14G115000' => 'mes', 'Manes.15G151700' => 'mes', 'Manes.17G111300' => 'mes', 'Mapoly0226s0009' => 'mpo', 'MBI02_g25363_MAGBIO' => 'mbi', 'MBI06_g00027_MAGBIO' => 'mbi', 'MBI10_g13034_MAGBIO' => 'mbi', 'MD09G1023400' => 'mdo', 'MD13G1100100' => 'mdo', 'MD15G1169200' => 'mdo', 'MD16G1101100' => 'mdo', 'MD17G1022900' => 'mdo', 'Medtr3g096150' => 'mtr', 'Medtr4g115070' => 'mtr', 'Medtr7g033325' => 'mtr', 'Medtr8g089840' => 'mtr', 'MELO3C010319.2' => 'cme', 'MELO3C011944.2' => 'cme', 'MELO3C021589.2' => 'cme', 'Migut.E00207' => 'egut', 'Migut.H00067' => 'egut', 'Migut.K00433' => 'egut', 'Migut.K00606' => 'egut', 'Migut.K01410' => 'egut', 'MSTRG.13347' => 'ama', 'MSTRG.24045' => 'ama', 'MSTRG.2428' => 'ama', 'MSTRG.26410' => 'ama', 'MSTRG.3139' => 'ama', 'MSTRG.3286' => 'ama', 'MSTRG.563' => 'ama', 'MSTRG.7941' => 'ama', 'Nitab4.5_0000028g0060' => 'nta', 'Nitab4.5_0000065g0260' => 'nta', 'Nitab4.5_0000112g0060' => 'nta', 'Nitab4.5_0000489g0120' => 'nta', 'Nitab4.5_0001776g0050' => 'nta', 'Nitab4.5_0001854g0010' => 'nta', 'Nitab4.5_0001860g0020' => 'nta', 'Nitab4.5_0004352g0010' => 'nta', 'Nitab4.5_0008716g0020' => 'nta', 'Nitab4.5_0008922g0010' => 'nta', 'Nn3g16693' => 'nnu', 'Nn4g22596' => 'nnu', 'Nn7g37639' => 'nnu', 'Oeu001701.1' => 'oeu', 'Oeu018149.1' => 'oeu', 'Oeu026220.1' => 'oeu', 'Oeu038635.1' => 'oeu', 'Oeu049176.1' => 'oeu', 'Oeu056706.1' => 'oeu', 'Oeu056937.1' => 'oeu', 'Oeu057540.1' => 'oeu', 'Os02g0594900' => 'osa', 'Os02g0595100' => 'osa', 'Os04g0477500' => 'osa', 'Os12g0611900' => 'osa', 'Peaxi162Scf00076g00020' => 'pax', 'Peaxi162Scf00128g00217' => 'pax', 'Peaxi162Scf00129g01640' => 'pax', 'Peaxi162Scf00669g00007' => 'pax', 'Peaxi162Scf00700g00421' => 'pax', 'Peaxi162Scf00801g00038' => 'pax', 'Peaxi162Scf00891g00025' => 'pax', 'PGR083G0909' => 'pgr', 'PGR119G1005' => 'pgr', 'PGR142G2236' => 'pgr', 'PGR142G3388' => 'pgr', 'PGSC0003DMG400004514' => 'stu', 'PGSC0003DMG400012635' => 'stu', 'PGSC0003DMG400015730' => 'stu', 'PGSC0003DMG400018611' => 'stu', 'PGSC0003DMG400030897' => 'stu', 'Phvul.001G254800' => 'pvu', 'Phvul.002G260100' => 'pvu', 'Phvul.003G167600' => 'pvu', 'Phvul.004G005100' => 'pvu', 'Potri.001G343600' => 'ptr', 'Potri.006G066700' => 'ptr', 'Potri.008G186000' => 'ptr', 'Potri.010G046900' => 'ptr', 'Potri.018G127900' => 'ptr', 'Pp3c20_17750' => 'ppa', 'Pp3c24_4380' => 'ppa', 'Prupe.1G245800' => 'ppe', 'Prupe.3G293400' => 'ppe', 'Prupe.7G247400' => 'ppe', 'Psat0s145g0120' => 'psa', 'Psat0s595g0040' => 'psa', 'Psat0s595g0120' => 'psa', 'Psat3g175040' => 'psa', 'Psat7g058120' => 'psa', 'PSO017G0428' => 'pso', 'PSO063G7510' => 'pso', 'PSO067G0046' => 'pso', 'PSO478G1073' => 'pso', 'PSO675G3677' => 'pso', 'PSO675G6558' => 'pso', 'PSO675G7520' => 'pso', 'PSO675G8959' => 'pso', 'QL02p074089' => 'qlo', 'QL02p089614' => 'qlo', 'QL03p057736' => 'qlo', 'RcHm_v2.0_Chr1g0364131' => 'rch', 'RcHm_v2.0_Chr2g0087801' => 'rch', 'RcHm_v2.0_Chr2g0087821' => 'rch', 'RcHm_v2.0_Chr2g0173231' => 'rch', 'RcHm_v2.0_Chr4g0433111' => 'rch', 'Rhsim03G0250300' => 'rsi', 'Rhsim08G0048400' => 'rsi', 'Rhsim10G0014800' => 'rsi', 'Rhsim12G0040100' => 'rsi', 'Rhsim12G0109700' => 'rsi', 'Sabra06G0049600' => 'sbr', 'Sabra08G0141000' => 'sbr', 'Sabra10G0021400' => 'sbr', 'Sabra16G0222900' => 'sbr', 'Sabra18G0108600' => 'sbr', 'SalBow1G0433' => 'sbo', 'SalBow1G2038' => 'sbo', 'SalBow1G5003' => 'sbo', 'SalBow7G1197' => 'sbo', 'SalBow8G3506' => 'sbo', 'Sc03g0007300' => 'sci', 'Sc11g0000950' => 'sci', 'Sc14g0008750' => 'sci', 'Sc18g0000420' => 'sci', 'Sed0006754' => 'sed', 'Sed0008741' => 'sed', 'Sed0017172' => 'sed', 'Sed0018925' => 'sed', 'Sed0023326' => 'sed', 'Sed0025909' => 'sed', 'SEGI_05333' => 'sgi', 'SEGI_10362' => 'sgi', 'SEGI_13380' => 'sgi', 'SEGI_24306' => 'sgi', 'SEGI_29077' => 'sgi', 'SEGI_29095' => 'sgi', 'SEGI_36534' => 'sgi', 'SEGI_37506' => 'sgi', 'SEGI_38321' => 'sgi', 'SGA_v2.0_scaffold307G48031' => 'sas', 'SGA_v2.0_scaffold47G17507' => 'sas', 'SGA_v2.0_scaffold63G21736' => 'sas', 'SGA_v2.0_scaffold87G27070' => 'sas', 'SHI17794' => 'shi', 'SHI28851' => 'shi', 'SMO165G0155' => 'smo', 'SMO340G0217' => 'smo', 'SMO367G1210' => 'smo', 'Solyc02g093430.3' => 'sly', 'Solyc05g013580.4' => 'sly', 'Solyc07g008030.3' => 'sly', 'Solyc12g035470.2' => 'sly', 'Sopen02g038020' => 'spe', 'Sopen05g008490' => 'spe', 'Sopen07g003910' => 'spe', 'Sopen12g015240' => 'spe', 'Sp1g11550' => 'spa', 'Sp2g16710' => 'spa', 'Sp3g00430' => 'spa', 'Sp3g26780' => 'spa', 'Sp5g22900' => 'spa', 'Sp6g29530' => 'spa', 'TAR371G0794' => 'tar', 'TAR374G0164' => 'tar', 'TAR622G0165' => 'tar', 'TAR626G0929' => 'tar', 'TAR629G2155' => 'tar', 'THA.LOC104805282' => 'tha', 'THA.LOC104805363' => 'tha', 'THA.LOC104808968' => 'tha', 'THA.LOC104821093' => 'tha', 'THA.LOC104823953' => 'tha', 'THA.LOC104825562' => 'tha', 'THA.LOC104825665' => 'tha', 'Thecc.02G261400' => 'tca', 'Thecc.04G019200' => 'tca', 'Thecc.09G130400' => 'tca', 'Thhalv10004374m.g' => 'esa', 'Thhalv10007850m.g' => 'esa', 'Thhalv10013782m.g' => 'esa', 'Thhalv10018686m.g' => 'esa', 'Thhalv10020899m.g' => 'esa', 'Thhalv10022755m.g' => 'esa', 'TPR.G23851' => 'tpr', 'TPR.G26500' => 'tpr', 'TPR.G27267' => 'tpr', 'TPR.G32001' => 'tpr', 'TPR.G6251' => 'tpr', 'TPR.G8167' => 'tpr', 'TWI12G1330' => 'twi', 'TWI18G1239' => 'twi', 'TWI34G0979' => 'twi', 'TWI36G0670' => 'twi', 'TWI36G0707' => 'twi', 'TWI56G0233' => 'twi', 'TWI75G1809' => 'twi', 'unitig_21.g20874' => 'ugi', 'unitig_26.g10343' => 'ugi', 'unitig_46.g18392' => 'ugi', 'unitig_52.g17178' => 'ugi', 'unitig_8.g2934' => 'ugi', 'vmacro01122' => 'vma', 'vmacro05875' => 'vma', 'vmacro06147' => 'vma', 'vmacro16191' => 'vma', 'vmacro18293' => 'vma', 'VMungo0251G3707' => 'vmu', 'VMungo0464G1521' => 'vmu', 'VMungo1215G0205' => 'vmu', 'VMungo1383G2484' => 'vmu', 'Zm00001eb079610' => 'zma', 'Zm00001eb135990' => 'zma', 'Zm00001eb183710' => 'zma', 'Zm00001eb246020' => 'zma' ) $gf_id = 'HOM05D001124' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001124' ) $data_identifier = 'HOM05D001124' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 6, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 7, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 21, 'bol' => (int) 10, 'bra' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 6, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 9, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 21, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 8, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 10, 'lsa' => (int) 8, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 8, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 9, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb246020' $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' => 'HOM05D001124', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '548', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02520' => 'bna', 'A03p06630' => 'bna', 'A05p44460' => 'bna', 'A06p08710' => 'bna', 'A06p41090' => 'bna', 'A07p32320' => 'bna', 'A08p32520' => 'bna', 'A09p10360' => 'bna', 'A10p24080' => 'bna', 'Aa31LG11G15250' => 'aar', 'Aa31LG1G1800' => 'aar', 'Aa31LG2G5120' => 'aar', 'Aa31LG2G6070' => 'aar', 'Aa31LG5G10770' => 'aar', 'Aa31sc61G90' => 'aar', 'Actinidia01352' => 'ach', 'Actinidia05983' => 'ach', 'Actinidia08133' => 'ach', 'Actinidia15101' => 'ach', 'Actinidia26379' => 'ach', 'Actinidia35778' => 'ach', 'Actinidia36123' => 'ach', 'Actinidia37436' => 'ach', 'Actinidia38730' => 'ach', 'Ah.02g128210' => 'amhyb', 'Ah.03g132990' => 'amhyb', 'Ah.14g079410' => 'amhyb', 'AL1G24640' => 'aly', 'AL2G26680' => 'aly', 'AL3G10530' => 'aly', 'AL3G45230' => 'aly', 'AL5G15230' => 'aly', 'AL5G16960' => 'aly', 'AL6G25210' => 'aly', 'Aqoxy2G00441' => 'aox', 'Aqoxy3G01236' => 'aox', 'Aqoxy5G03746' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3RQ047' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C7GMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9C8JER' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MBL6KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YXCZ83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZANX40' => 'arhy', 'AT1G12990' => 'ath', 'AT1G67880' => 'ath', 'AT2G13290' => 'ath', 'AT3G01620' => 'ath', 'AT3G26445' => 'ath', 'AT3G27540' => 'ath', 'AT5G14480' => 'ath', 'ATR0824G026' => 'atr', 'ATR1098G019' => 'atr', 'Atru.chr11.2145' => 'acertr', 'Atru.chr2.3636' => 'acertr', 'Atru.chr2.3644' => 'acertr', 'Atru.chr6.2422' => 'acertr', 'Atru.chr7.1112' => 'acertr', 'AUR62005469' => 'cqu', 'AUR62011166' => 'cqu', 'AUR62013319' => 'cqu', 'AUR62024273' => 'cqu', 'AUR62028420' => 'cqu', 'AUR62041942' => 'cqu', 'BcaB01g04969' => 'bca', 'BcaB01g06371' => 'bca', 'BcaB02g11494' => 'bca', 'BcaB03g15382' => 'bca', 'BcaB08g36994' => 'bca', 'BcaC03g13477' => 'bca', 'BcaC03g13478' => 'bca', 'BcaC03g13480' => 'bca', 'BcaC03g13481' => 'bca', 'BcaC03g13486' => 'bca', 'BcaC04g19031' => 'bca', 'BcaC04g23085' => 'bca', 'BcaC05g25094' => 'bca', 'BcaC05g25096' => 'bca', 'BcaC05g25138' => 'bca', 'BcaC05g30416' => 'bca', 'BcaC05g30455' => 'bca', 'BcaC06g30979' => 'bca', 'BcaC06g33805' => 'bca', 'BcaC08g46021' => 'bca', 'BcaNung03154' => 'bca', 'BolC2t06623H' => 'bol', 'BolC2t06632H' => 'bol', 'BolC2t06635H' => 'bol', 'BolC2t06638H' => 'bol', 'BolC3t13266H' => 'bol', 'BolC5t29776H' => 'bol', 'BolC6t38912H' => 'bol', 'BolC7t44183H' => 'bol', 'BolC9t54123H' => 'bol', 'BolC9t59107H' => 'bol', 'BraA02t05221Z' => 'bra', 'BraA03t09996Z' => 'bra', 'BraA05t23210Z' => 'bra', 'BraA06t24068Z' => 'bra', 'BraA06t27032Z' => 'bra', 'BraA08t35176Z' => 'bra', 'BraA09t36680Z' => 'bra', 'BraA10t44471Z' => 'bra', 'C02p06760' => 'bna', 'C02p06890' => 'bna', 'C02p07010' => 'bna', 'C03p07660' => 'bna', 'C05p10300' => 'bna', 'C06p38150' => 'bna', 'C07p36650' => 'bna', 'C08p15770' => 'bna', 'C09p12300' => 'bna', 'C09p62700' => 'bna', 'C09p75040' => 'bna', 'CAN.G13.1' => 'can', 'CAN.G138.4' => 'can', 'CAN.G44.6' => 'can', 'CAN.G473.19' => 'can', 'CANSAT01G0835' => 'cansat', 'CANSAT11G0246' => 'cansat', 'CANSAT11G1766' => 'cansat', 'CANSAT64G1954' => 'cansat', 'CARHR013330' => 'chi', 'CARHR060530' => 'chi', 'CARHR075300' => 'chi', 'CARHR105120' => 'chi', 'CARHR148910' => 'chi', 'CARHR198830' => 'chi', 'Carub.0001s1275' => 'cru', 'Carub.0002s1437' => 'cru', 'Carub.0003s0044' => 'cru', 'Carub.0003s2787' => 'cru', 'Carub.0005s0597' => 'cru', 'Carub.0006s1266' => 'cru', 'Ca_06935_v3' => 'car', 'Ca_13559_v3' => 'car', 'Ca_16941_v3' => 'car', 'Ca_16960_v3' => 'car', 'Ca_17775_v3' => 'car', 'Ca_30464_v3' => 'car', 'Cc06_g08160' => 'ccan', 'Cc07_g01520' => 'ccan', 'Cc11_g15810' => 'ccan', 'CDE02G2840' => 'cde', 'CDE03G0093' => 'cde', 'CDE04G2127' => 'cde', 'CDE07G1857' => 'cde', 'CDE09G1246' => 'cde', 'Cfa003412' => 'cfa', 'Cfa007341' => 'cfa', 'Cfa009220' => 'cfa', 'Ciclev10008737m.g' => 'ccl', 'Ciclev10015565m.g' => 'ccl', 'Ciclev10031761m.g' => 'ccl', 'CiPaw.03G045300' => 'cil', 'CiPaw.03G247200' => 'cil', 'CiPaw.04G029500' => 'cil', 'CiPaw.04G174000' => 'cil', 'CiPaw.05G181200' => 'cil', 'CiPaw.06G067100' => 'cil', 'ClCG05G025800' => 'cla', 'ClCG06G011400' => 'cla', 'ClCG09G019360' => 'cla', 'COL.COLO4_04827' => 'col', 'COL.COLO4_29170' => 'col', 'COL.COLO4_35131' => 'col', 'COL.COLO4_35132' => 'col', 'Cpa.g.sc33.32' => 'cpa', 'Cpa.g.sc46.29' => 'cpa', 'Cpa.g.sc796.1' => 'cpa', 'CsaV3_1G030420' => 'csa', 'CsaV3_5G027050' => 'csa', 'CsaV3_5G031040' => 'csa', 'CsaV3_UNG023130' => 'csa', 'CSS0007726' => 'camsi', 'CSS0016433' => 'camsi', 'CSS0017656' => 'camsi', 'CSS0025364' => 'camsi', 'CSS0027582' => 'camsi', 'CSS0047288' => 'camsi', 'CSS0049950' => 'camsi', 'DCAR_003843' => 'dca', 'DCAR_007052' => 'dca', 'DCAR_020884' => 'dca', 'DCAR_021730' => 'dca', 'DCAR_024423' => 'dca', 'DCAR_026509' => 'dca', 'DCAR_031158' => 'dca', 'Dinv14728' => 'din', 'Dinv15219' => 'din', 'Dinv25728' => 'din', 'Dinv33428' => 'din', 'Dinv36489' => 'din', 'Dinv41486' => 'din', 'Duzib147G0469' => 'dzi', 'Duzib168G0060' => 'dzi', 'Duzib187G1215' => 'dzi', 'Duzib248G0692' => 'dzi', 'Duzib251G0767' => 'dzi', 'Duzib264G0446' => 'dzi', 'Duzib268G0691' => 'dzi', 'ECA232G4767' => 'eca', 'ECA233G2838' => 'eca', 'ECA234G0391' => 'eca', 'ECA234G0857' => 'eca', 'ECA236G1593' => 'eca', 'ECA238G0565' => 'eca', 'ECA246G1027' => 'eca', 'ECA246G3223' => 'eca', 'ECA246G3470' => 'eca', 'EL10Ac6g13829' => 'bvu', 'EL10Ac6g14093' => 'bvu', 'EL10Ac8g18707' => 'bvu', 'Eucgr.C01369' => 'egr', 'Eucgr.H02492' => 'egr', 'Eucgr.I01733' => 'egr', 'Eucgr.J02255' => 'egr', 'Eucgr.J02257' => 'egr', 'Eucgr.J02258' => 'egr', 'FAN02G1601' => 'fan', 'FAN03G1586' => 'fan', 'FAN03G2986' => 'fan', 'FAN05G4837' => 'fan', 'FAN06G0146' => 'fan', 'FAN07G0858' => 'fan', 'FAN09G3179' => 'fan', 'FAN10G0669' => 'fan', 'FAN12G2358' => 'fan', 'FAN14G4198' => 'fan', 'FAN14G5112' => 'fan', 'FAN17G0342' => 'fan', 'FAN19G0342' => 'fan', 'FAN19G0962' => 'fan', 'FAN19G1101' => 'fan', 'FAN19G1872' => 'fan', 'FAN22G0356' => 'fan', 'FAN23G0744' => 'fan', 'FAN23G1914' => 'fan', 'FAN26G0032' => 'fan', 'FAN28G0625' => 'fan', 'FvH4_1g02710' => 'fve', 'FvH4_1g02720' => 'fve', 'FvH4_4g25670' => 'fve', 'FvH4_6g51700' => 'fve', 'FvH4_7g20170' => 'fve', 'Glyma.05G175000' => 'gma', 'Glyma.08G132300' => 'gma', 'Glyma.11G243000' => 'gma', 'Glyma.13G158900' => 'gma', 'Glyma.17G112400' => 'gma', 'Glyma.18G014100' => 'gma', 'Glyma.19G003100' => 'gma', 'Glyma.19G056500' => 'gma', 'Gohir.A01G158900' => 'ghi', 'Gohir.A05G312600' => 'ghi', 'Gohir.A05G354900' => 'ghi', 'Gohir.A07G037200' => 'ghi', 'Gohir.A09G030000' => 'ghi', 'Gohir.A12G145200' => 'ghi', 'Gohir.D01G151500' => 'ghi', 'Gohir.D04G058300' => 'ghi', 'Gohir.D05G314100' => 'ghi', 'Gohir.D07G041400' => 'ghi', 'Gohir.D09G029700' => 'ghi', 'Gohir.D12G149700' => 'ghi', 'Gorai.001G043800' => 'gra', 'Gorai.002G187800' => 'gra', 'Gorai.006G034700' => 'gra', 'Gorai.008G161200' => 'gra', 'Gorai.009G335700' => 'gra', 'Gorai.012G065000' => 'gra', 'GSVIVG01000535001' => 'vvi', 'GSVIVG01015572001' => 'vvi', 'GSVIVG01032386001' => 'vvi', 'HanXRQChr05g0138531' => 'han', 'HanXRQChr06g0174391' => 'han', 'HanXRQChr07g0199021' => 'han', 'HanXRQChr08g0208211' => 'han', 'HanXRQChr09g0255471' => 'han', 'HanXRQChr10g0315791' => 'han', 'HanXRQChr12g0371991' => 'han', 'HanXRQChr15g0475251' => 'han', 'HanXRQChr17g0540001' => 'han', 'HanXRQChr17g0548631' => 'han', 'HanXRQChr17g0569561' => 'han', 'Haze_12256' => 'cav', 'Haze_14756' => 'cav', 'Haze_25528' => 'cav', 'Hma1.2p1_0079F.1_g041020' => 'hma', 'Hma1.2p1_0818F.1_g223260' => 'hma', 'Hma1.2p1_1747F.1_g300530' => 'hma', 'HPP92_004607' => 'vpl', 'HPP92_004608' => 'vpl', 'HPP92_006181' => 'vpl', 'HPP92_012192' => 'vpl', 'HPP92_015680' => 'vpl', 'HPP92_020249' => 'vpl', 'HPP92_021376' => 'vpl', 'HPP92_024275' => 'vpl', 'Hund06031' => 'sun', 'Hund25391' => 'sun', 'Lalb_Chr07g0185371' => 'lal', 'Lalb_Chr07g0185381' => 'lal', 'Lalb_Chr12g0204011' => 'lal', 'Lalb_Chr13g0301671' => 'lal', 'Lalb_Chr14g0362851' => 'lal', 'Lalb_Chr24g0403581' => 'lal', 'Lj1g0000233' => 'lja', 'Lj2g0018120' => 'lja', 'Lj3C621T0' => 'lonja', 'Lj3P1059T14' => 'lonja', 'Lj3P611T9' => 'lonja', 'Lj3P614T13' => 'lonja', 'Lj3P615T5' => 'lonja', 'Lj4g0012315' => 'lja', 'Lj4g0026182' => 'lja', 'Lj6P813T16' => 'lonja', 'Lj7C427T7' => 'lonja', 'Lj7C427T8' => 'lonja', 'Lj7P600T41' => 'lonja', 'Lju41C42G17' => 'lonja', 'Lsat_1_v5_gn_0_47300' => 'lsa', 'Lsat_1_v5_gn_2_91280' => 'lsa', 'Lsat_1_v5_gn_3_30561' => 'lsa', 'Lsat_1_v5_gn_4_184321' => 'lsa', 'Lsat_1_v5_gn_4_4041' => 'lsa', 'Lsat_1_v5_gn_5_92000' => 'lsa', 'Lsat_1_v5_gn_8_152940' => 'lsa', 'Lsat_1_v5_gn_8_62401' => 'lsa', 'Manes.06G055900' => 'mes', 'Manes.12G022200' => 'mes', 'Manes.13G023300' => 'mes', 'Manes.14G115000' => 'mes', 'Manes.15G151700' => 'mes', 'Manes.17G111300' => 'mes', 'Mapoly0226s0009' => 'mpo', 'MBI02_g25363_MAGBIO' => 'mbi', 'MBI06_g00027_MAGBIO' => 'mbi', 'MBI10_g13034_MAGBIO' => 'mbi', 'MD09G1023400' => 'mdo', 'MD13G1100100' => 'mdo', 'MD15G1169200' => 'mdo', 'MD16G1101100' => 'mdo', 'MD17G1022900' => 'mdo', 'Medtr3g096150' => 'mtr', 'Medtr4g115070' => 'mtr', 'Medtr7g033325' => 'mtr', 'Medtr8g089840' => 'mtr', 'MELO3C010319.2' => 'cme', 'MELO3C011944.2' => 'cme', 'MELO3C021589.2' => 'cme', 'Migut.E00207' => 'egut', 'Migut.H00067' => 'egut', 'Migut.K00433' => 'egut', 'Migut.K00606' => 'egut', 'Migut.K01410' => 'egut', 'MSTRG.13347' => 'ama', 'MSTRG.24045' => 'ama', 'MSTRG.2428' => 'ama', 'MSTRG.26410' => 'ama', 'MSTRG.3139' => 'ama', 'MSTRG.3286' => 'ama', 'MSTRG.563' => 'ama', 'MSTRG.7941' => 'ama', 'Nitab4.5_0000028g0060' => 'nta', 'Nitab4.5_0000065g0260' => 'nta', 'Nitab4.5_0000112g0060' => 'nta', 'Nitab4.5_0000489g0120' => 'nta', 'Nitab4.5_0001776g0050' => 'nta', 'Nitab4.5_0001854g0010' => 'nta', 'Nitab4.5_0001860g0020' => 'nta', 'Nitab4.5_0004352g0010' => 'nta', 'Nitab4.5_0008716g0020' => 'nta', 'Nitab4.5_0008922g0010' => 'nta', 'Nn3g16693' => 'nnu', 'Nn4g22596' => 'nnu', 'Nn7g37639' => 'nnu', 'Oeu001701.1' => 'oeu', 'Oeu018149.1' => 'oeu', 'Oeu026220.1' => 'oeu', 'Oeu038635.1' => 'oeu', 'Oeu049176.1' => 'oeu', 'Oeu056706.1' => 'oeu', 'Oeu056937.1' => 'oeu', 'Oeu057540.1' => 'oeu', 'Os02g0594900' => 'osa', 'Os02g0595100' => 'osa', 'Os04g0477500' => 'osa', 'Os12g0611900' => 'osa', 'Peaxi162Scf00076g00020' => 'pax', 'Peaxi162Scf00128g00217' => 'pax', 'Peaxi162Scf00129g01640' => 'pax', 'Peaxi162Scf00669g00007' => 'pax', 'Peaxi162Scf00700g00421' => 'pax', 'Peaxi162Scf00801g00038' => 'pax', 'Peaxi162Scf00891g00025' => 'pax', 'PGR083G0909' => 'pgr', 'PGR119G1005' => 'pgr', 'PGR142G2236' => 'pgr', 'PGR142G3388' => 'pgr', 'PGSC0003DMG400004514' => 'stu', 'PGSC0003DMG400012635' => 'stu', 'PGSC0003DMG400015730' => 'stu', 'PGSC0003DMG400018611' => 'stu', 'PGSC0003DMG400030897' => 'stu', 'Phvul.001G254800' => 'pvu', 'Phvul.002G260100' => 'pvu', 'Phvul.003G167600' => 'pvu', 'Phvul.004G005100' => 'pvu', 'Potri.001G343600' => 'ptr', 'Potri.006G066700' => 'ptr', 'Potri.008G186000' => 'ptr', 'Potri.010G046900' => 'ptr', 'Potri.018G127900' => 'ptr', 'Pp3c20_17750' => 'ppa', 'Pp3c24_4380' => 'ppa', 'Prupe.1G245800' => 'ppe', 'Prupe.3G293400' => 'ppe', 'Prupe.7G247400' => 'ppe', 'Psat0s145g0120' => 'psa', 'Psat0s595g0040' => 'psa', 'Psat0s595g0120' => 'psa', 'Psat3g175040' => 'psa', 'Psat7g058120' => 'psa', 'PSO017G0428' => 'pso', 'PSO063G7510' => 'pso', 'PSO067G0046' => 'pso', 'PSO478G1073' => 'pso', 'PSO675G3677' => 'pso', 'PSO675G6558' => 'pso', 'PSO675G7520' => 'pso', 'PSO675G8959' => 'pso', 'QL02p074089' => 'qlo', 'QL02p089614' => 'qlo', 'QL03p057736' => 'qlo', 'RcHm_v2.0_Chr1g0364131' => 'rch', 'RcHm_v2.0_Chr2g0087801' => 'rch', 'RcHm_v2.0_Chr2g0087821' => 'rch', 'RcHm_v2.0_Chr2g0173231' => 'rch', 'RcHm_v2.0_Chr4g0433111' => 'rch', 'Rhsim03G0250300' => 'rsi', 'Rhsim08G0048400' => 'rsi', 'Rhsim10G0014800' => 'rsi', 'Rhsim12G0040100' => 'rsi', 'Rhsim12G0109700' => 'rsi', 'Sabra06G0049600' => 'sbr', 'Sabra08G0141000' => 'sbr', 'Sabra10G0021400' => 'sbr', 'Sabra16G0222900' => 'sbr', 'Sabra18G0108600' => 'sbr', 'SalBow1G0433' => 'sbo', 'SalBow1G2038' => 'sbo', 'SalBow1G5003' => 'sbo', 'SalBow7G1197' => 'sbo', 'SalBow8G3506' => 'sbo', 'Sc03g0007300' => 'sci', 'Sc11g0000950' => 'sci', 'Sc14g0008750' => 'sci', 'Sc18g0000420' => 'sci', 'Sed0006754' => 'sed', 'Sed0008741' => 'sed', 'Sed0017172' => 'sed', 'Sed0018925' => 'sed', 'Sed0023326' => 'sed', 'Sed0025909' => 'sed', 'SEGI_05333' => 'sgi', 'SEGI_10362' => 'sgi', 'SEGI_13380' => 'sgi', 'SEGI_24306' => 'sgi', 'SEGI_29077' => 'sgi', 'SEGI_29095' => 'sgi', 'SEGI_36534' => 'sgi', 'SEGI_37506' => 'sgi', 'SEGI_38321' => 'sgi', 'SGA_v2.0_scaffold307G48031' => 'sas', 'SGA_v2.0_scaffold47G17507' => 'sas', 'SGA_v2.0_scaffold63G21736' => 'sas', 'SGA_v2.0_scaffold87G27070' => 'sas', 'SHI17794' => 'shi', 'SHI28851' => 'shi', 'SMO165G0155' => 'smo', 'SMO340G0217' => 'smo', 'SMO367G1210' => 'smo', 'Solyc02g093430.3' => 'sly', 'Solyc05g013580.4' => 'sly', 'Solyc07g008030.3' => 'sly', 'Solyc12g035470.2' => 'sly', 'Sopen02g038020' => 'spe', 'Sopen05g008490' => 'spe', 'Sopen07g003910' => 'spe', 'Sopen12g015240' => 'spe', 'Sp1g11550' => 'spa', 'Sp2g16710' => 'spa', 'Sp3g00430' => 'spa', 'Sp3g26780' => 'spa', 'Sp5g22900' => 'spa', 'Sp6g29530' => 'spa', 'TAR371G0794' => 'tar', 'TAR374G0164' => 'tar', 'TAR622G0165' => 'tar', 'TAR626G0929' => 'tar', 'TAR629G2155' => 'tar', 'THA.LOC104805282' => 'tha', 'THA.LOC104805363' => 'tha', 'THA.LOC104808968' => 'tha', 'THA.LOC104821093' => 'tha', 'THA.LOC104823953' => 'tha', 'THA.LOC104825562' => 'tha', 'THA.LOC104825665' => 'tha', 'Thecc.02G261400' => 'tca', 'Thecc.04G019200' => 'tca', 'Thecc.09G130400' => 'tca', 'Thhalv10004374m.g' => 'esa', 'Thhalv10007850m.g' => 'esa', 'Thhalv10013782m.g' => 'esa', 'Thhalv10018686m.g' => 'esa', 'Thhalv10020899m.g' => 'esa', 'Thhalv10022755m.g' => 'esa', 'TPR.G23851' => 'tpr', 'TPR.G26500' => 'tpr', 'TPR.G27267' => 'tpr', 'TPR.G32001' => 'tpr', 'TPR.G6251' => 'tpr', 'TPR.G8167' => 'tpr', 'TWI12G1330' => 'twi', 'TWI18G1239' => 'twi', 'TWI34G0979' => 'twi', 'TWI36G0670' => 'twi', 'TWI36G0707' => 'twi', 'TWI56G0233' => 'twi', 'TWI75G1809' => 'twi', 'unitig_21.g20874' => 'ugi', 'unitig_26.g10343' => 'ugi', 'unitig_46.g18392' => 'ugi', 'unitig_52.g17178' => 'ugi', 'unitig_8.g2934' => 'ugi', 'vmacro01122' => 'vma', 'vmacro05875' => 'vma', 'vmacro06147' => 'vma', 'vmacro16191' => 'vma', 'vmacro18293' => 'vma', 'VMungo0251G3707' => 'vmu', 'VMungo0464G1521' => 'vmu', 'VMungo1215G0205' => 'vmu', 'VMungo1383G2484' => 'vmu', 'Zm00001eb079610' => 'zma', 'Zm00001eb135990' => 'zma', 'Zm00001eb183710' => 'zma', 'Zm00001eb246020' => 'zma' ), 'gf_id' => 'HOM05D001124', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001124' ), 'data_identifier' => 'HOM05D001124', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001124', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '548', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02520' => 'bna', 'A03p06630' => 'bna', 'A05p44460' => 'bna', 'A06p08710' => 'bna', 'A06p41090' => 'bna', 'A07p32320' => 'bna', 'A08p32520' => 'bna', 'A09p10360' => 'bna', 'A10p24080' => 'bna', 'Aa31LG11G15250' => 'aar', 'Aa31LG1G1800' => 'aar', 'Aa31LG2G5120' => 'aar', 'Aa31LG2G6070' => 'aar', 'Aa31LG5G10770' => 'aar', 'Aa31sc61G90' => 'aar', 'Actinidia01352' => 'ach', 'Actinidia05983' => 'ach', 'Actinidia08133' => 'ach', 'Actinidia15101' => 'ach', 'Actinidia26379' => 'ach', 'Actinidia35778' => 'ach', 'Actinidia36123' => 'ach', 'Actinidia37436' => 'ach', 'Actinidia38730' => 'ach', 'Ah.02g128210' => 'amhyb', 'Ah.03g132990' => 'amhyb', 'Ah.14g079410' => 'amhyb', 'AL1G24640' => 'aly', 'AL2G26680' => 'aly', 'AL3G10530' => 'aly', 'AL3G45230' => 'aly', 'AL5G15230' => 'aly', 'AL5G16960' => 'aly', 'AL6G25210' => 'aly', 'Aqoxy2G00441' => 'aox', 'Aqoxy3G01236' => 'aox', 'Aqoxy5G03746' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3RQ047' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C7GMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9C8JER' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MBL6KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YXCZ83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZANX40' => 'arhy', 'AT1G12990' => 'ath', 'AT1G67880' => 'ath', 'AT2G13290' => 'ath', 'AT3G01620' => 'ath', 'AT3G26445' => 'ath', 'AT3G27540' => 'ath', 'AT5G14480' => 'ath', 'ATR0824G026' => 'atr', 'ATR1098G019' => 'atr', 'Atru.chr11.2145' => 'acertr', 'Atru.chr2.3636' => 'acertr', 'Atru.chr2.3644' => 'acertr', 'Atru.chr6.2422' => 'acertr', 'Atru.chr7.1112' => 'acertr', 'AUR62005469' => 'cqu', 'AUR62011166' => 'cqu', 'AUR62013319' => 'cqu', 'AUR62024273' => 'cqu', 'AUR62028420' => 'cqu', 'AUR62041942' => 'cqu', 'BcaB01g04969' => 'bca', 'BcaB01g06371' => 'bca', 'BcaB02g11494' => 'bca', 'BcaB03g15382' => 'bca', 'BcaB08g36994' => 'bca', 'BcaC03g13477' => 'bca', 'BcaC03g13478' => 'bca', 'BcaC03g13480' => 'bca', 'BcaC03g13481' => 'bca', 'BcaC03g13486' => 'bca', 'BcaC04g19031' => 'bca', 'BcaC04g23085' => 'bca', 'BcaC05g25094' => 'bca', 'BcaC05g25096' => 'bca', 'BcaC05g25138' => 'bca', 'BcaC05g30416' => 'bca', 'BcaC05g30455' => 'bca', 'BcaC06g30979' => 'bca', 'BcaC06g33805' => 'bca', 'BcaC08g46021' => 'bca', 'BcaNung03154' => 'bca', 'BolC2t06623H' => 'bol', 'BolC2t06632H' => 'bol', 'BolC2t06635H' => 'bol', 'BolC2t06638H' => 'bol', 'BolC3t13266H' => 'bol', 'BolC5t29776H' => 'bol', 'BolC6t38912H' => 'bol', 'BolC7t44183H' => 'bol', 'BolC9t54123H' => 'bol', 'BolC9t59107H' => 'bol', 'BraA02t05221Z' => 'bra', 'BraA03t09996Z' => 'bra', 'BraA05t23210Z' => 'bra', 'BraA06t24068Z' => 'bra', 'BraA06t27032Z' => 'bra', 'BraA08t35176Z' => 'bra', 'BraA09t36680Z' => 'bra', 'BraA10t44471Z' => 'bra', 'C02p06760' => 'bna', 'C02p06890' => 'bna', 'C02p07010' => 'bna', 'C03p07660' => 'bna', 'C05p10300' => 'bna', 'C06p38150' => 'bna', 'C07p36650' => 'bna', 'C08p15770' => 'bna', 'C09p12300' => 'bna', 'C09p62700' => 'bna', 'C09p75040' => 'bna', 'CAN.G13.1' => 'can', 'CAN.G138.4' => 'can', 'CAN.G44.6' => 'can', 'CAN.G473.19' => 'can', 'CANSAT01G0835' => 'cansat', 'CANSAT11G0246' => 'cansat', 'CANSAT11G1766' => 'cansat', 'CANSAT64G1954' => 'cansat', 'CARHR013330' => 'chi', 'CARHR060530' => 'chi', 'CARHR075300' => 'chi', 'CARHR105120' => 'chi', 'CARHR148910' => 'chi', 'CARHR198830' => 'chi', 'Carub.0001s1275' => 'cru', 'Carub.0002s1437' => 'cru', 'Carub.0003s0044' => 'cru', 'Carub.0003s2787' => 'cru', 'Carub.0005s0597' => 'cru', 'Carub.0006s1266' => 'cru', 'Ca_06935_v3' => 'car', 'Ca_13559_v3' => 'car', 'Ca_16941_v3' => 'car', 'Ca_16960_v3' => 'car', 'Ca_17775_v3' => 'car', 'Ca_30464_v3' => 'car', 'Cc06_g08160' => 'ccan', 'Cc07_g01520' => 'ccan', 'Cc11_g15810' => 'ccan', 'CDE02G2840' => 'cde', 'CDE03G0093' => 'cde', 'CDE04G2127' => 'cde', 'CDE07G1857' => 'cde', 'CDE09G1246' => 'cde', 'Cfa003412' => 'cfa', 'Cfa007341' => 'cfa', 'Cfa009220' => 'cfa', 'Ciclev10008737m.g' => 'ccl', 'Ciclev10015565m.g' => 'ccl', 'Ciclev10031761m.g' => 'ccl', 'CiPaw.03G045300' => 'cil', 'CiPaw.03G247200' => 'cil', 'CiPaw.04G029500' => 'cil', 'CiPaw.04G174000' => 'cil', 'CiPaw.05G181200' => 'cil', 'CiPaw.06G067100' => 'cil', 'ClCG05G025800' => 'cla', 'ClCG06G011400' => 'cla', 'ClCG09G019360' => 'cla', 'COL.COLO4_04827' => 'col', 'COL.COLO4_29170' => 'col', 'COL.COLO4_35131' => 'col', 'COL.COLO4_35132' => 'col', 'Cpa.g.sc33.32' => 'cpa', 'Cpa.g.sc46.29' => 'cpa', 'Cpa.g.sc796.1' => 'cpa', 'CsaV3_1G030420' => 'csa', 'CsaV3_5G027050' => 'csa', 'CsaV3_5G031040' => 'csa', 'CsaV3_UNG023130' => 'csa', 'CSS0007726' => 'camsi', 'CSS0016433' => 'camsi', 'CSS0017656' => 'camsi', 'CSS0025364' => 'camsi', 'CSS0027582' => 'camsi', 'CSS0047288' => 'camsi', 'CSS0049950' => 'camsi', 'DCAR_003843' => 'dca', 'DCAR_007052' => 'dca', 'DCAR_020884' => 'dca', 'DCAR_021730' => 'dca', 'DCAR_024423' => 'dca', 'DCAR_026509' => 'dca', 'DCAR_031158' => 'dca', 'Dinv14728' => 'din', 'Dinv15219' => 'din', 'Dinv25728' => 'din', 'Dinv33428' => 'din', 'Dinv36489' => 'din', 'Dinv41486' => 'din', 'Duzib147G0469' => 'dzi', 'Duzib168G0060' => 'dzi', 'Duzib187G1215' => 'dzi', 'Duzib248G0692' => 'dzi', 'Duzib251G0767' => 'dzi', 'Duzib264G0446' => 'dzi', 'Duzib268G0691' => 'dzi', 'ECA232G4767' => 'eca', 'ECA233G2838' => 'eca', 'ECA234G0391' => 'eca', 'ECA234G0857' => 'eca', 'ECA236G1593' => 'eca', 'ECA238G0565' => 'eca', 'ECA246G1027' => 'eca', 'ECA246G3223' => 'eca', 'ECA246G3470' => 'eca', 'EL10Ac6g13829' => 'bvu', 'EL10Ac6g14093' => 'bvu', 'EL10Ac8g18707' => 'bvu', 'Eucgr.C01369' => 'egr', 'Eucgr.H02492' => 'egr', 'Eucgr.I01733' => 'egr', 'Eucgr.J02255' => 'egr', 'Eucgr.J02257' => 'egr', 'Eucgr.J02258' => 'egr', 'FAN02G1601' => 'fan', 'FAN03G1586' => 'fan', 'FAN03G2986' => 'fan', 'FAN05G4837' => 'fan', 'FAN06G0146' => 'fan', 'FAN07G0858' => 'fan', 'FAN09G3179' => 'fan', 'FAN10G0669' => 'fan', 'FAN12G2358' => 'fan', 'FAN14G4198' => 'fan', 'FAN14G5112' => 'fan', 'FAN17G0342' => 'fan', 'FAN19G0342' => 'fan', 'FAN19G0962' => 'fan', 'FAN19G1101' => 'fan', 'FAN19G1872' => 'fan', 'FAN22G0356' => 'fan', 'FAN23G0744' => 'fan', 'FAN23G1914' => 'fan', 'FAN26G0032' => 'fan', 'FAN28G0625' => 'fan', 'FvH4_1g02710' => 'fve', 'FvH4_1g02720' => 'fve', 'FvH4_4g25670' => 'fve', 'FvH4_6g51700' => 'fve', 'FvH4_7g20170' => 'fve', 'Glyma.05G175000' => 'gma', 'Glyma.08G132300' => 'gma', 'Glyma.11G243000' => 'gma', 'Glyma.13G158900' => 'gma', 'Glyma.17G112400' => 'gma', 'Glyma.18G014100' => 'gma', 'Glyma.19G003100' => 'gma', 'Glyma.19G056500' => 'gma', 'Gohir.A01G158900' => 'ghi', 'Gohir.A05G312600' => 'ghi', 'Gohir.A05G354900' => 'ghi', 'Gohir.A07G037200' => 'ghi', 'Gohir.A09G030000' => 'ghi', 'Gohir.A12G145200' => 'ghi', 'Gohir.D01G151500' => 'ghi', 'Gohir.D04G058300' => 'ghi', 'Gohir.D05G314100' => 'ghi', 'Gohir.D07G041400' => 'ghi', 'Gohir.D09G029700' => 'ghi', 'Gohir.D12G149700' => 'ghi', 'Gorai.001G043800' => 'gra', 'Gorai.002G187800' => 'gra', 'Gorai.006G034700' => 'gra', 'Gorai.008G161200' => 'gra', 'Gorai.009G335700' => 'gra', 'Gorai.012G065000' => 'gra', 'GSVIVG01000535001' => 'vvi', 'GSVIVG01015572001' => 'vvi', 'GSVIVG01032386001' => 'vvi', 'HanXRQChr05g0138531' => 'han', 'HanXRQChr06g0174391' => 'han', 'HanXRQChr07g0199021' => 'han', 'HanXRQChr08g0208211' => 'han', 'HanXRQChr09g0255471' => 'han', 'HanXRQChr10g0315791' => 'han', 'HanXRQChr12g0371991' => 'han', 'HanXRQChr15g0475251' => 'han', 'HanXRQChr17g0540001' => 'han', 'HanXRQChr17g0548631' => 'han', 'HanXRQChr17g0569561' => 'han', 'Haze_12256' => 'cav', 'Haze_14756' => 'cav', 'Haze_25528' => 'cav', 'Hma1.2p1_0079F.1_g041020' => 'hma', 'Hma1.2p1_0818F.1_g223260' => 'hma', 'Hma1.2p1_1747F.1_g300530' => 'hma', 'HPP92_004607' => 'vpl', 'HPP92_004608' => 'vpl', 'HPP92_006181' => 'vpl', 'HPP92_012192' => 'vpl', 'HPP92_015680' => 'vpl', 'HPP92_020249' => 'vpl', 'HPP92_021376' => 'vpl', 'HPP92_024275' => 'vpl', 'Hund06031' => 'sun', 'Hund25391' => 'sun', 'Lalb_Chr07g0185371' => 'lal', 'Lalb_Chr07g0185381' => 'lal', 'Lalb_Chr12g0204011' => 'lal', 'Lalb_Chr13g0301671' => 'lal', 'Lalb_Chr14g0362851' => 'lal', 'Lalb_Chr24g0403581' => 'lal', 'Lj1g0000233' => 'lja', 'Lj2g0018120' => 'lja', 'Lj3C621T0' => 'lonja', 'Lj3P1059T14' => 'lonja', 'Lj3P611T9' => 'lonja', 'Lj3P614T13' => 'lonja', 'Lj3P615T5' => 'lonja', 'Lj4g0012315' => 'lja', 'Lj4g0026182' => 'lja', 'Lj6P813T16' => 'lonja', 'Lj7C427T7' => 'lonja', 'Lj7C427T8' => 'lonja', 'Lj7P600T41' => 'lonja', 'Lju41C42G17' => 'lonja', 'Lsat_1_v5_gn_0_47300' => 'lsa', 'Lsat_1_v5_gn_2_91280' => 'lsa', 'Lsat_1_v5_gn_3_30561' => 'lsa', 'Lsat_1_v5_gn_4_184321' => 'lsa', 'Lsat_1_v5_gn_4_4041' => 'lsa', 'Lsat_1_v5_gn_5_92000' => 'lsa', 'Lsat_1_v5_gn_8_152940' => 'lsa', 'Lsat_1_v5_gn_8_62401' => 'lsa', 'Manes.06G055900' => 'mes', 'Manes.12G022200' => 'mes', 'Manes.13G023300' => 'mes', 'Manes.14G115000' => 'mes', 'Manes.15G151700' => 'mes', 'Manes.17G111300' => 'mes', 'Mapoly0226s0009' => 'mpo', 'MBI02_g25363_MAGBIO' => 'mbi', 'MBI06_g00027_MAGBIO' => 'mbi', 'MBI10_g13034_MAGBIO' => 'mbi', 'MD09G1023400' => 'mdo', 'MD13G1100100' => 'mdo', 'MD15G1169200' => 'mdo', 'MD16G1101100' => 'mdo', 'MD17G1022900' => 'mdo', 'Medtr3g096150' => 'mtr', 'Medtr4g115070' => 'mtr', 'Medtr7g033325' => 'mtr', 'Medtr8g089840' => 'mtr', 'MELO3C010319.2' => 'cme', 'MELO3C011944.2' => 'cme', 'MELO3C021589.2' => 'cme', 'Migut.E00207' => 'egut', 'Migut.H00067' => 'egut', 'Migut.K00433' => 'egut', 'Migut.K00606' => 'egut', 'Migut.K01410' => 'egut', 'MSTRG.13347' => 'ama', 'MSTRG.24045' => 'ama', 'MSTRG.2428' => 'ama', 'MSTRG.26410' => 'ama', 'MSTRG.3139' => 'ama', 'MSTRG.3286' => 'ama', 'MSTRG.563' => 'ama', 'MSTRG.7941' => 'ama', 'Nitab4.5_0000028g0060' => 'nta', 'Nitab4.5_0000065g0260' => 'nta', 'Nitab4.5_0000112g0060' => 'nta', 'Nitab4.5_0000489g0120' => 'nta', 'Nitab4.5_0001776g0050' => 'nta', 'Nitab4.5_0001854g0010' => 'nta', 'Nitab4.5_0001860g0020' => 'nta', 'Nitab4.5_0004352g0010' => 'nta', 'Nitab4.5_0008716g0020' => 'nta', 'Nitab4.5_0008922g0010' => 'nta', 'Nn3g16693' => 'nnu', 'Nn4g22596' => 'nnu', 'Nn7g37639' => 'nnu', 'Oeu001701.1' => 'oeu', 'Oeu018149.1' => 'oeu', 'Oeu026220.1' => 'oeu', 'Oeu038635.1' => 'oeu', 'Oeu049176.1' => 'oeu', 'Oeu056706.1' => 'oeu', 'Oeu056937.1' => 'oeu', 'Oeu057540.1' => 'oeu', 'Os02g0594900' => 'osa', 'Os02g0595100' => 'osa', 'Os04g0477500' => 'osa', 'Os12g0611900' => 'osa', 'Peaxi162Scf00076g00020' => 'pax', 'Peaxi162Scf00128g00217' => 'pax', 'Peaxi162Scf00129g01640' => 'pax', 'Peaxi162Scf00669g00007' => 'pax', 'Peaxi162Scf00700g00421' => 'pax', 'Peaxi162Scf00801g00038' => 'pax', 'Peaxi162Scf00891g00025' => 'pax', 'PGR083G0909' => 'pgr', 'PGR119G1005' => 'pgr', 'PGR142G2236' => 'pgr', 'PGR142G3388' => 'pgr', 'PGSC0003DMG400004514' => 'stu', 'PGSC0003DMG400012635' => 'stu', 'PGSC0003DMG400015730' => 'stu', 'PGSC0003DMG400018611' => 'stu', 'PGSC0003DMG400030897' => 'stu', 'Phvul.001G254800' => 'pvu', 'Phvul.002G260100' => 'pvu', 'Phvul.003G167600' => 'pvu', 'Phvul.004G005100' => 'pvu', 'Potri.001G343600' => 'ptr', 'Potri.006G066700' => 'ptr', 'Potri.008G186000' => 'ptr', 'Potri.010G046900' => 'ptr', 'Potri.018G127900' => 'ptr', 'Pp3c20_17750' => 'ppa', 'Pp3c24_4380' => 'ppa', 'Prupe.1G245800' => 'ppe', 'Prupe.3G293400' => 'ppe', 'Prupe.7G247400' => 'ppe', 'Psat0s145g0120' => 'psa', 'Psat0s595g0040' => 'psa', 'Psat0s595g0120' => 'psa', 'Psat3g175040' => 'psa', 'Psat7g058120' => 'psa', 'PSO017G0428' => 'pso', 'PSO063G7510' => 'pso', 'PSO067G0046' => 'pso', 'PSO478G1073' => 'pso', 'PSO675G3677' => 'pso', 'PSO675G6558' => 'pso', 'PSO675G7520' => 'pso', 'PSO675G8959' => 'pso', 'QL02p074089' => 'qlo', 'QL02p089614' => 'qlo', 'QL03p057736' => 'qlo', 'RcHm_v2.0_Chr1g0364131' => 'rch', 'RcHm_v2.0_Chr2g0087801' => 'rch', 'RcHm_v2.0_Chr2g0087821' => 'rch', 'RcHm_v2.0_Chr2g0173231' => 'rch', 'RcHm_v2.0_Chr4g0433111' => 'rch', 'Rhsim03G0250300' => 'rsi', 'Rhsim08G0048400' => 'rsi', 'Rhsim10G0014800' => 'rsi', 'Rhsim12G0040100' => 'rsi', 'Rhsim12G0109700' => 'rsi', 'Sabra06G0049600' => 'sbr', 'Sabra08G0141000' => 'sbr', 'Sabra10G0021400' => 'sbr', 'Sabra16G0222900' => 'sbr', 'Sabra18G0108600' => 'sbr', 'SalBow1G0433' => 'sbo', 'SalBow1G2038' => 'sbo', 'SalBow1G5003' => 'sbo', 'SalBow7G1197' => 'sbo', 'SalBow8G3506' => 'sbo', 'Sc03g0007300' => 'sci', 'Sc11g0000950' => 'sci', 'Sc14g0008750' => 'sci', 'Sc18g0000420' => 'sci', 'Sed0006754' => 'sed', 'Sed0008741' => 'sed', 'Sed0017172' => 'sed', 'Sed0018925' => 'sed', 'Sed0023326' => 'sed', 'Sed0025909' => 'sed', 'SEGI_05333' => 'sgi', 'SEGI_10362' => 'sgi', 'SEGI_13380' => 'sgi', 'SEGI_24306' => 'sgi', 'SEGI_29077' => 'sgi', 'SEGI_29095' => 'sgi', 'SEGI_36534' => 'sgi', 'SEGI_37506' => 'sgi', 'SEGI_38321' => 'sgi', 'SGA_v2.0_scaffold307G48031' => 'sas', 'SGA_v2.0_scaffold47G17507' => 'sas', 'SGA_v2.0_scaffold63G21736' => 'sas', 'SGA_v2.0_scaffold87G27070' => 'sas', 'SHI17794' => 'shi', 'SHI28851' => 'shi', 'SMO165G0155' => 'smo', 'SMO340G0217' => 'smo', 'SMO367G1210' => 'smo', 'Solyc02g093430.3' => 'sly', 'Solyc05g013580.4' => 'sly', 'Solyc07g008030.3' => 'sly', 'Solyc12g035470.2' => 'sly', 'Sopen02g038020' => 'spe', 'Sopen05g008490' => 'spe', 'Sopen07g003910' => 'spe', 'Sopen12g015240' => 'spe', 'Sp1g11550' => 'spa', 'Sp2g16710' => 'spa', 'Sp3g00430' => 'spa', 'Sp3g26780' => 'spa', 'Sp5g22900' => 'spa', 'Sp6g29530' => 'spa', 'TAR371G0794' => 'tar', 'TAR374G0164' => 'tar', 'TAR622G0165' => 'tar', 'TAR626G0929' => 'tar', 'TAR629G2155' => 'tar', 'THA.LOC104805282' => 'tha', 'THA.LOC104805363' => 'tha', 'THA.LOC104808968' => 'tha', 'THA.LOC104821093' => 'tha', 'THA.LOC104823953' => 'tha', 'THA.LOC104825562' => 'tha', 'THA.LOC104825665' => 'tha', 'Thecc.02G261400' => 'tca', 'Thecc.04G019200' => 'tca', 'Thecc.09G130400' => 'tca', 'Thhalv10004374m.g' => 'esa', 'Thhalv10007850m.g' => 'esa', 'Thhalv10013782m.g' => 'esa', 'Thhalv10018686m.g' => 'esa', 'Thhalv10020899m.g' => 'esa', 'Thhalv10022755m.g' => 'esa', 'TPR.G23851' => 'tpr', 'TPR.G26500' => 'tpr', 'TPR.G27267' => 'tpr', 'TPR.G32001' => 'tpr', 'TPR.G6251' => 'tpr', 'TPR.G8167' => 'tpr', 'TWI12G1330' => 'twi', 'TWI18G1239' => 'twi', 'TWI34G0979' => 'twi', 'TWI36G0670' => 'twi', 'TWI36G0707' => 'twi', 'TWI56G0233' => 'twi', 'TWI75G1809' => 'twi', 'unitig_21.g20874' => 'ugi', 'unitig_26.g10343' => 'ugi', 'unitig_46.g18392' => 'ugi', 'unitig_52.g17178' => 'ugi', 'unitig_8.g2934' => 'ugi', 'vmacro01122' => 'vma', 'vmacro05875' => 'vma', 'vmacro06147' => 'vma', 'vmacro16191' => 'vma', 'vmacro18293' => 'vma', 'VMungo0251G3707' => 'vmu', 'VMungo0464G1521' => 'vmu', 'VMungo1215G0205' => 'vmu', 'VMungo1383G2484' => 'vmu', 'Zm00001eb079610' => 'zma', 'Zm00001eb135990' => 'zma', 'Zm00001eb183710' => 'zma', 'Zm00001eb246020' => 'zma' ) $gf_id = 'HOM05D001124' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001124' ) $data_identifier = 'HOM05D001124' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 6, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 7, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 21, 'bol' => (int) 10, 'bra' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 6, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 9, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 21, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 8, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 10, 'lsa' => (int) 8, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 8, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 9, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb246020' $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' => 'HOM05D001124', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '548', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02520' => 'bna', 'A03p06630' => 'bna', 'A05p44460' => 'bna', 'A06p08710' => 'bna', 'A06p41090' => 'bna', 'A07p32320' => 'bna', 'A08p32520' => 'bna', 'A09p10360' => 'bna', 'A10p24080' => 'bna', 'Aa31LG11G15250' => 'aar', 'Aa31LG1G1800' => 'aar', 'Aa31LG2G5120' => 'aar', 'Aa31LG2G6070' => 'aar', 'Aa31LG5G10770' => 'aar', 'Aa31sc61G90' => 'aar', 'Actinidia01352' => 'ach', 'Actinidia05983' => 'ach', 'Actinidia08133' => 'ach', 'Actinidia15101' => 'ach', 'Actinidia26379' => 'ach', 'Actinidia35778' => 'ach', 'Actinidia36123' => 'ach', 'Actinidia37436' => 'ach', 'Actinidia38730' => 'ach', 'Ah.02g128210' => 'amhyb', 'Ah.03g132990' => 'amhyb', 'Ah.14g079410' => 'amhyb', 'AL1G24640' => 'aly', 'AL2G26680' => 'aly', 'AL3G10530' => 'aly', 'AL3G45230' => 'aly', 'AL5G15230' => 'aly', 'AL5G16960' => 'aly', 'AL6G25210' => 'aly', 'Aqoxy2G00441' => 'aox', 'Aqoxy3G01236' => 'aox', 'Aqoxy5G03746' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3RQ047' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C7GMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9C8JER' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MBL6KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YXCZ83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZANX40' => 'arhy', 'AT1G12990' => 'ath', 'AT1G67880' => 'ath', 'AT2G13290' => 'ath', 'AT3G01620' => 'ath', 'AT3G26445' => 'ath', 'AT3G27540' => 'ath', 'AT5G14480' => 'ath', 'ATR0824G026' => 'atr', 'ATR1098G019' => 'atr', 'Atru.chr11.2145' => 'acertr', 'Atru.chr2.3636' => 'acertr', 'Atru.chr2.3644' => 'acertr', 'Atru.chr6.2422' => 'acertr', 'Atru.chr7.1112' => 'acertr', 'AUR62005469' => 'cqu', 'AUR62011166' => 'cqu', 'AUR62013319' => 'cqu', 'AUR62024273' => 'cqu', 'AUR62028420' => 'cqu', 'AUR62041942' => 'cqu', 'BcaB01g04969' => 'bca', 'BcaB01g06371' => 'bca', 'BcaB02g11494' => 'bca', 'BcaB03g15382' => 'bca', 'BcaB08g36994' => 'bca', 'BcaC03g13477' => 'bca', 'BcaC03g13478' => 'bca', 'BcaC03g13480' => 'bca', 'BcaC03g13481' => 'bca', 'BcaC03g13486' => 'bca', 'BcaC04g19031' => 'bca', 'BcaC04g23085' => 'bca', 'BcaC05g25094' => 'bca', 'BcaC05g25096' => 'bca', 'BcaC05g25138' => 'bca', 'BcaC05g30416' => 'bca', 'BcaC05g30455' => 'bca', 'BcaC06g30979' => 'bca', 'BcaC06g33805' => 'bca', 'BcaC08g46021' => 'bca', 'BcaNung03154' => 'bca', 'BolC2t06623H' => 'bol', 'BolC2t06632H' => 'bol', 'BolC2t06635H' => 'bol', 'BolC2t06638H' => 'bol', 'BolC3t13266H' => 'bol', 'BolC5t29776H' => 'bol', 'BolC6t38912H' => 'bol', 'BolC7t44183H' => 'bol', 'BolC9t54123H' => 'bol', 'BolC9t59107H' => 'bol', 'BraA02t05221Z' => 'bra', 'BraA03t09996Z' => 'bra', 'BraA05t23210Z' => 'bra', 'BraA06t24068Z' => 'bra', 'BraA06t27032Z' => 'bra', 'BraA08t35176Z' => 'bra', 'BraA09t36680Z' => 'bra', 'BraA10t44471Z' => 'bra', 'C02p06760' => 'bna', 'C02p06890' => 'bna', 'C02p07010' => 'bna', 'C03p07660' => 'bna', 'C05p10300' => 'bna', 'C06p38150' => 'bna', 'C07p36650' => 'bna', 'C08p15770' => 'bna', 'C09p12300' => 'bna', 'C09p62700' => 'bna', 'C09p75040' => 'bna', 'CAN.G13.1' => 'can', 'CAN.G138.4' => 'can', 'CAN.G44.6' => 'can', 'CAN.G473.19' => 'can', 'CANSAT01G0835' => 'cansat', 'CANSAT11G0246' => 'cansat', 'CANSAT11G1766' => 'cansat', 'CANSAT64G1954' => 'cansat', 'CARHR013330' => 'chi', 'CARHR060530' => 'chi', 'CARHR075300' => 'chi', 'CARHR105120' => 'chi', 'CARHR148910' => 'chi', 'CARHR198830' => 'chi', 'Carub.0001s1275' => 'cru', 'Carub.0002s1437' => 'cru', 'Carub.0003s0044' => 'cru', 'Carub.0003s2787' => 'cru', 'Carub.0005s0597' => 'cru', 'Carub.0006s1266' => 'cru', 'Ca_06935_v3' => 'car', 'Ca_13559_v3' => 'car', 'Ca_16941_v3' => 'car', 'Ca_16960_v3' => 'car', 'Ca_17775_v3' => 'car', 'Ca_30464_v3' => 'car', 'Cc06_g08160' => 'ccan', 'Cc07_g01520' => 'ccan', 'Cc11_g15810' => 'ccan', 'CDE02G2840' => 'cde', 'CDE03G0093' => 'cde', 'CDE04G2127' => 'cde', 'CDE07G1857' => 'cde', 'CDE09G1246' => 'cde', 'Cfa003412' => 'cfa', 'Cfa007341' => 'cfa', 'Cfa009220' => 'cfa', 'Ciclev10008737m.g' => 'ccl', 'Ciclev10015565m.g' => 'ccl', 'Ciclev10031761m.g' => 'ccl', 'CiPaw.03G045300' => 'cil', 'CiPaw.03G247200' => 'cil', 'CiPaw.04G029500' => 'cil', 'CiPaw.04G174000' => 'cil', 'CiPaw.05G181200' => 'cil', 'CiPaw.06G067100' => 'cil', 'ClCG05G025800' => 'cla', 'ClCG06G011400' => 'cla', 'ClCG09G019360' => 'cla', 'COL.COLO4_04827' => 'col', 'COL.COLO4_29170' => 'col', 'COL.COLO4_35131' => 'col', 'COL.COLO4_35132' => 'col', 'Cpa.g.sc33.32' => 'cpa', 'Cpa.g.sc46.29' => 'cpa', 'Cpa.g.sc796.1' => 'cpa', 'CsaV3_1G030420' => 'csa', 'CsaV3_5G027050' => 'csa', 'CsaV3_5G031040' => 'csa', 'CsaV3_UNG023130' => 'csa', 'CSS0007726' => 'camsi', 'CSS0016433' => 'camsi', 'CSS0017656' => 'camsi', 'CSS0025364' => 'camsi', 'CSS0027582' => 'camsi', 'CSS0047288' => 'camsi', 'CSS0049950' => 'camsi', 'DCAR_003843' => 'dca', 'DCAR_007052' => 'dca', 'DCAR_020884' => 'dca', 'DCAR_021730' => 'dca', 'DCAR_024423' => 'dca', 'DCAR_026509' => 'dca', 'DCAR_031158' => 'dca', 'Dinv14728' => 'din', 'Dinv15219' => 'din', 'Dinv25728' => 'din', 'Dinv33428' => 'din', 'Dinv36489' => 'din', 'Dinv41486' => 'din', 'Duzib147G0469' => 'dzi', 'Duzib168G0060' => 'dzi', 'Duzib187G1215' => 'dzi', 'Duzib248G0692' => 'dzi', 'Duzib251G0767' => 'dzi', 'Duzib264G0446' => 'dzi', 'Duzib268G0691' => 'dzi', 'ECA232G4767' => 'eca', 'ECA233G2838' => 'eca', 'ECA234G0391' => 'eca', 'ECA234G0857' => 'eca', 'ECA236G1593' => 'eca', 'ECA238G0565' => 'eca', 'ECA246G1027' => 'eca', 'ECA246G3223' => 'eca', 'ECA246G3470' => 'eca', 'EL10Ac6g13829' => 'bvu', 'EL10Ac6g14093' => 'bvu', 'EL10Ac8g18707' => 'bvu', 'Eucgr.C01369' => 'egr', 'Eucgr.H02492' => 'egr', 'Eucgr.I01733' => 'egr', 'Eucgr.J02255' => 'egr', 'Eucgr.J02257' => 'egr', 'Eucgr.J02258' => 'egr', 'FAN02G1601' => 'fan', 'FAN03G1586' => 'fan', 'FAN03G2986' => 'fan', 'FAN05G4837' => 'fan', 'FAN06G0146' => 'fan', 'FAN07G0858' => 'fan', 'FAN09G3179' => 'fan', 'FAN10G0669' => 'fan', 'FAN12G2358' => 'fan', 'FAN14G4198' => 'fan', 'FAN14G5112' => 'fan', 'FAN17G0342' => 'fan', 'FAN19G0342' => 'fan', 'FAN19G0962' => 'fan', 'FAN19G1101' => 'fan', 'FAN19G1872' => 'fan', 'FAN22G0356' => 'fan', 'FAN23G0744' => 'fan', 'FAN23G1914' => 'fan', 'FAN26G0032' => 'fan', 'FAN28G0625' => 'fan', 'FvH4_1g02710' => 'fve', 'FvH4_1g02720' => 'fve', 'FvH4_4g25670' => 'fve', 'FvH4_6g51700' => 'fve', 'FvH4_7g20170' => 'fve', 'Glyma.05G175000' => 'gma', 'Glyma.08G132300' => 'gma', 'Glyma.11G243000' => 'gma', 'Glyma.13G158900' => 'gma', 'Glyma.17G112400' => 'gma', 'Glyma.18G014100' => 'gma', 'Glyma.19G003100' => 'gma', 'Glyma.19G056500' => 'gma', 'Gohir.A01G158900' => 'ghi', 'Gohir.A05G312600' => 'ghi', 'Gohir.A05G354900' => 'ghi', 'Gohir.A07G037200' => 'ghi', 'Gohir.A09G030000' => 'ghi', 'Gohir.A12G145200' => 'ghi', 'Gohir.D01G151500' => 'ghi', 'Gohir.D04G058300' => 'ghi', 'Gohir.D05G314100' => 'ghi', 'Gohir.D07G041400' => 'ghi', 'Gohir.D09G029700' => 'ghi', 'Gohir.D12G149700' => 'ghi', 'Gorai.001G043800' => 'gra', 'Gorai.002G187800' => 'gra', 'Gorai.006G034700' => 'gra', 'Gorai.008G161200' => 'gra', 'Gorai.009G335700' => 'gra', 'Gorai.012G065000' => 'gra', 'GSVIVG01000535001' => 'vvi', 'GSVIVG01015572001' => 'vvi', 'GSVIVG01032386001' => 'vvi', 'HanXRQChr05g0138531' => 'han', 'HanXRQChr06g0174391' => 'han', 'HanXRQChr07g0199021' => 'han', 'HanXRQChr08g0208211' => 'han', 'HanXRQChr09g0255471' => 'han', 'HanXRQChr10g0315791' => 'han', 'HanXRQChr12g0371991' => 'han', 'HanXRQChr15g0475251' => 'han', 'HanXRQChr17g0540001' => 'han', 'HanXRQChr17g0548631' => 'han', 'HanXRQChr17g0569561' => 'han', 'Haze_12256' => 'cav', 'Haze_14756' => 'cav', 'Haze_25528' => 'cav', 'Hma1.2p1_0079F.1_g041020' => 'hma', 'Hma1.2p1_0818F.1_g223260' => 'hma', 'Hma1.2p1_1747F.1_g300530' => 'hma', 'HPP92_004607' => 'vpl', 'HPP92_004608' => 'vpl', 'HPP92_006181' => 'vpl', 'HPP92_012192' => 'vpl', 'HPP92_015680' => 'vpl', 'HPP92_020249' => 'vpl', 'HPP92_021376' => 'vpl', 'HPP92_024275' => 'vpl', 'Hund06031' => 'sun', 'Hund25391' => 'sun', 'Lalb_Chr07g0185371' => 'lal', 'Lalb_Chr07g0185381' => 'lal', 'Lalb_Chr12g0204011' => 'lal', 'Lalb_Chr13g0301671' => 'lal', 'Lalb_Chr14g0362851' => 'lal', 'Lalb_Chr24g0403581' => 'lal', 'Lj1g0000233' => 'lja', 'Lj2g0018120' => 'lja', 'Lj3C621T0' => 'lonja', 'Lj3P1059T14' => 'lonja', 'Lj3P611T9' => 'lonja', 'Lj3P614T13' => 'lonja', 'Lj3P615T5' => 'lonja', 'Lj4g0012315' => 'lja', 'Lj4g0026182' => 'lja', 'Lj6P813T16' => 'lonja', 'Lj7C427T7' => 'lonja', 'Lj7C427T8' => 'lonja', 'Lj7P600T41' => 'lonja', 'Lju41C42G17' => 'lonja', 'Lsat_1_v5_gn_0_47300' => 'lsa', 'Lsat_1_v5_gn_2_91280' => 'lsa', 'Lsat_1_v5_gn_3_30561' => 'lsa', 'Lsat_1_v5_gn_4_184321' => 'lsa', 'Lsat_1_v5_gn_4_4041' => 'lsa', 'Lsat_1_v5_gn_5_92000' => 'lsa', 'Lsat_1_v5_gn_8_152940' => 'lsa', 'Lsat_1_v5_gn_8_62401' => 'lsa', 'Manes.06G055900' => 'mes', 'Manes.12G022200' => 'mes', 'Manes.13G023300' => 'mes', 'Manes.14G115000' => 'mes', 'Manes.15G151700' => 'mes', 'Manes.17G111300' => 'mes', 'Mapoly0226s0009' => 'mpo', 'MBI02_g25363_MAGBIO' => 'mbi', 'MBI06_g00027_MAGBIO' => 'mbi', 'MBI10_g13034_MAGBIO' => 'mbi', 'MD09G1023400' => 'mdo', 'MD13G1100100' => 'mdo', 'MD15G1169200' => 'mdo', 'MD16G1101100' => 'mdo', 'MD17G1022900' => 'mdo', 'Medtr3g096150' => 'mtr', 'Medtr4g115070' => 'mtr', 'Medtr7g033325' => 'mtr', 'Medtr8g089840' => 'mtr', 'MELO3C010319.2' => 'cme', 'MELO3C011944.2' => 'cme', 'MELO3C021589.2' => 'cme', 'Migut.E00207' => 'egut', 'Migut.H00067' => 'egut', 'Migut.K00433' => 'egut', 'Migut.K00606' => 'egut', 'Migut.K01410' => 'egut', 'MSTRG.13347' => 'ama', 'MSTRG.24045' => 'ama', 'MSTRG.2428' => 'ama', 'MSTRG.26410' => 'ama', 'MSTRG.3139' => 'ama', 'MSTRG.3286' => 'ama', 'MSTRG.563' => 'ama', 'MSTRG.7941' => 'ama', 'Nitab4.5_0000028g0060' => 'nta', 'Nitab4.5_0000065g0260' => 'nta', 'Nitab4.5_0000112g0060' => 'nta', 'Nitab4.5_0000489g0120' => 'nta', 'Nitab4.5_0001776g0050' => 'nta', 'Nitab4.5_0001854g0010' => 'nta', 'Nitab4.5_0001860g0020' => 'nta', 'Nitab4.5_0004352g0010' => 'nta', 'Nitab4.5_0008716g0020' => 'nta', 'Nitab4.5_0008922g0010' => 'nta', 'Nn3g16693' => 'nnu', 'Nn4g22596' => 'nnu', 'Nn7g37639' => 'nnu', 'Oeu001701.1' => 'oeu', 'Oeu018149.1' => 'oeu', 'Oeu026220.1' => 'oeu', 'Oeu038635.1' => 'oeu', 'Oeu049176.1' => 'oeu', 'Oeu056706.1' => 'oeu', 'Oeu056937.1' => 'oeu', 'Oeu057540.1' => 'oeu', 'Os02g0594900' => 'osa', 'Os02g0595100' => 'osa', 'Os04g0477500' => 'osa', 'Os12g0611900' => 'osa', 'Peaxi162Scf00076g00020' => 'pax', 'Peaxi162Scf00128g00217' => 'pax', 'Peaxi162Scf00129g01640' => 'pax', 'Peaxi162Scf00669g00007' => 'pax', 'Peaxi162Scf00700g00421' => 'pax', 'Peaxi162Scf00801g00038' => 'pax', 'Peaxi162Scf00891g00025' => 'pax', 'PGR083G0909' => 'pgr', 'PGR119G1005' => 'pgr', 'PGR142G2236' => 'pgr', 'PGR142G3388' => 'pgr', 'PGSC0003DMG400004514' => 'stu', 'PGSC0003DMG400012635' => 'stu', 'PGSC0003DMG400015730' => 'stu', 'PGSC0003DMG400018611' => 'stu', 'PGSC0003DMG400030897' => 'stu', 'Phvul.001G254800' => 'pvu', 'Phvul.002G260100' => 'pvu', 'Phvul.003G167600' => 'pvu', 'Phvul.004G005100' => 'pvu', 'Potri.001G343600' => 'ptr', 'Potri.006G066700' => 'ptr', 'Potri.008G186000' => 'ptr', 'Potri.010G046900' => 'ptr', 'Potri.018G127900' => 'ptr', 'Pp3c20_17750' => 'ppa', 'Pp3c24_4380' => 'ppa', 'Prupe.1G245800' => 'ppe', 'Prupe.3G293400' => 'ppe', 'Prupe.7G247400' => 'ppe', 'Psat0s145g0120' => 'psa', 'Psat0s595g0040' => 'psa', 'Psat0s595g0120' => 'psa', 'Psat3g175040' => 'psa', 'Psat7g058120' => 'psa', 'PSO017G0428' => 'pso', 'PSO063G7510' => 'pso', 'PSO067G0046' => 'pso', 'PSO478G1073' => 'pso', 'PSO675G3677' => 'pso', 'PSO675G6558' => 'pso', 'PSO675G7520' => 'pso', 'PSO675G8959' => 'pso', 'QL02p074089' => 'qlo', 'QL02p089614' => 'qlo', 'QL03p057736' => 'qlo', 'RcHm_v2.0_Chr1g0364131' => 'rch', 'RcHm_v2.0_Chr2g0087801' => 'rch', 'RcHm_v2.0_Chr2g0087821' => 'rch', 'RcHm_v2.0_Chr2g0173231' => 'rch', 'RcHm_v2.0_Chr4g0433111' => 'rch', 'Rhsim03G0250300' => 'rsi', 'Rhsim08G0048400' => 'rsi', 'Rhsim10G0014800' => 'rsi', 'Rhsim12G0040100' => 'rsi', 'Rhsim12G0109700' => 'rsi', 'Sabra06G0049600' => 'sbr', 'Sabra08G0141000' => 'sbr', 'Sabra10G0021400' => 'sbr', 'Sabra16G0222900' => 'sbr', 'Sabra18G0108600' => 'sbr', 'SalBow1G0433' => 'sbo', 'SalBow1G2038' => 'sbo', 'SalBow1G5003' => 'sbo', 'SalBow7G1197' => 'sbo', 'SalBow8G3506' => 'sbo', 'Sc03g0007300' => 'sci', 'Sc11g0000950' => 'sci', 'Sc14g0008750' => 'sci', 'Sc18g0000420' => 'sci', 'Sed0006754' => 'sed', 'Sed0008741' => 'sed', 'Sed0017172' => 'sed', 'Sed0018925' => 'sed', 'Sed0023326' => 'sed', 'Sed0025909' => 'sed', 'SEGI_05333' => 'sgi', 'SEGI_10362' => 'sgi', 'SEGI_13380' => 'sgi', 'SEGI_24306' => 'sgi', 'SEGI_29077' => 'sgi', 'SEGI_29095' => 'sgi', 'SEGI_36534' => 'sgi', 'SEGI_37506' => 'sgi', 'SEGI_38321' => 'sgi', 'SGA_v2.0_scaffold307G48031' => 'sas', 'SGA_v2.0_scaffold47G17507' => 'sas', 'SGA_v2.0_scaffold63G21736' => 'sas', 'SGA_v2.0_scaffold87G27070' => 'sas', 'SHI17794' => 'shi', 'SHI28851' => 'shi', 'SMO165G0155' => 'smo', 'SMO340G0217' => 'smo', 'SMO367G1210' => 'smo', 'Solyc02g093430.3' => 'sly', 'Solyc05g013580.4' => 'sly', 'Solyc07g008030.3' => 'sly', 'Solyc12g035470.2' => 'sly', 'Sopen02g038020' => 'spe', 'Sopen05g008490' => 'spe', 'Sopen07g003910' => 'spe', 'Sopen12g015240' => 'spe', 'Sp1g11550' => 'spa', 'Sp2g16710' => 'spa', 'Sp3g00430' => 'spa', 'Sp3g26780' => 'spa', 'Sp5g22900' => 'spa', 'Sp6g29530' => 'spa', 'TAR371G0794' => 'tar', 'TAR374G0164' => 'tar', 'TAR622G0165' => 'tar', 'TAR626G0929' => 'tar', 'TAR629G2155' => 'tar', 'THA.LOC104805282' => 'tha', 'THA.LOC104805363' => 'tha', 'THA.LOC104808968' => 'tha', 'THA.LOC104821093' => 'tha', 'THA.LOC104823953' => 'tha', 'THA.LOC104825562' => 'tha', 'THA.LOC104825665' => 'tha', 'Thecc.02G261400' => 'tca', 'Thecc.04G019200' => 'tca', 'Thecc.09G130400' => 'tca', 'Thhalv10004374m.g' => 'esa', 'Thhalv10007850m.g' => 'esa', 'Thhalv10013782m.g' => 'esa', 'Thhalv10018686m.g' => 'esa', 'Thhalv10020899m.g' => 'esa', 'Thhalv10022755m.g' => 'esa', 'TPR.G23851' => 'tpr', 'TPR.G26500' => 'tpr', 'TPR.G27267' => 'tpr', 'TPR.G32001' => 'tpr', 'TPR.G6251' => 'tpr', 'TPR.G8167' => 'tpr', 'TWI12G1330' => 'twi', 'TWI18G1239' => 'twi', 'TWI34G0979' => 'twi', 'TWI36G0670' => 'twi', 'TWI36G0707' => 'twi', 'TWI56G0233' => 'twi', 'TWI75G1809' => 'twi', 'unitig_21.g20874' => 'ugi', 'unitig_26.g10343' => 'ugi', 'unitig_46.g18392' => 'ugi', 'unitig_52.g17178' => 'ugi', 'unitig_8.g2934' => 'ugi', 'vmacro01122' => 'vma', 'vmacro05875' => 'vma', 'vmacro06147' => 'vma', 'vmacro16191' => 'vma', 'vmacro18293' => 'vma', 'VMungo0251G3707' => 'vmu', 'VMungo0464G1521' => 'vmu', 'VMungo1215G0205' => 'vmu', 'VMungo1383G2484' => 'vmu', 'Zm00001eb079610' => 'zma', 'Zm00001eb135990' => 'zma', 'Zm00001eb183710' => 'zma', 'Zm00001eb246020' => 'zma' ), 'gf_id' => 'HOM05D001124', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001124' ), 'data_identifier' => 'HOM05D001124', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001124', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '548', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02520' => 'bna', 'A03p06630' => 'bna', 'A05p44460' => 'bna', 'A06p08710' => 'bna', 'A06p41090' => 'bna', 'A07p32320' => 'bna', 'A08p32520' => 'bna', 'A09p10360' => 'bna', 'A10p24080' => 'bna', 'Aa31LG11G15250' => 'aar', 'Aa31LG1G1800' => 'aar', 'Aa31LG2G5120' => 'aar', 'Aa31LG2G6070' => 'aar', 'Aa31LG5G10770' => 'aar', 'Aa31sc61G90' => 'aar', 'Actinidia01352' => 'ach', 'Actinidia05983' => 'ach', 'Actinidia08133' => 'ach', 'Actinidia15101' => 'ach', 'Actinidia26379' => 'ach', 'Actinidia35778' => 'ach', 'Actinidia36123' => 'ach', 'Actinidia37436' => 'ach', 'Actinidia38730' => 'ach', 'Ah.02g128210' => 'amhyb', 'Ah.03g132990' => 'amhyb', 'Ah.14g079410' => 'amhyb', 'AL1G24640' => 'aly', 'AL2G26680' => 'aly', 'AL3G10530' => 'aly', 'AL3G45230' => 'aly', 'AL5G15230' => 'aly', 'AL5G16960' => 'aly', 'AL6G25210' => 'aly', 'Aqoxy2G00441' => 'aox', 'Aqoxy3G01236' => 'aox', 'Aqoxy5G03746' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3RQ047' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C7GMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9C8JER' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MBL6KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YXCZ83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZANX40' => 'arhy', 'AT1G12990' => 'ath', 'AT1G67880' => 'ath', 'AT2G13290' => 'ath', 'AT3G01620' => 'ath', 'AT3G26445' => 'ath', 'AT3G27540' => 'ath', 'AT5G14480' => 'ath', 'ATR0824G026' => 'atr', 'ATR1098G019' => 'atr', 'Atru.chr11.2145' => 'acertr', 'Atru.chr2.3636' => 'acertr', 'Atru.chr2.3644' => 'acertr', 'Atru.chr6.2422' => 'acertr', 'Atru.chr7.1112' => 'acertr', 'AUR62005469' => 'cqu', 'AUR62011166' => 'cqu', 'AUR62013319' => 'cqu', 'AUR62024273' => 'cqu', 'AUR62028420' => 'cqu', 'AUR62041942' => 'cqu', 'BcaB01g04969' => 'bca', 'BcaB01g06371' => 'bca', 'BcaB02g11494' => 'bca', 'BcaB03g15382' => 'bca', 'BcaB08g36994' => 'bca', 'BcaC03g13477' => 'bca', 'BcaC03g13478' => 'bca', 'BcaC03g13480' => 'bca', 'BcaC03g13481' => 'bca', 'BcaC03g13486' => 'bca', 'BcaC04g19031' => 'bca', 'BcaC04g23085' => 'bca', 'BcaC05g25094' => 'bca', 'BcaC05g25096' => 'bca', 'BcaC05g25138' => 'bca', 'BcaC05g30416' => 'bca', 'BcaC05g30455' => 'bca', 'BcaC06g30979' => 'bca', 'BcaC06g33805' => 'bca', 'BcaC08g46021' => 'bca', 'BcaNung03154' => 'bca', 'BolC2t06623H' => 'bol', 'BolC2t06632H' => 'bol', 'BolC2t06635H' => 'bol', 'BolC2t06638H' => 'bol', 'BolC3t13266H' => 'bol', 'BolC5t29776H' => 'bol', 'BolC6t38912H' => 'bol', 'BolC7t44183H' => 'bol', 'BolC9t54123H' => 'bol', 'BolC9t59107H' => 'bol', 'BraA02t05221Z' => 'bra', 'BraA03t09996Z' => 'bra', 'BraA05t23210Z' => 'bra', 'BraA06t24068Z' => 'bra', 'BraA06t27032Z' => 'bra', 'BraA08t35176Z' => 'bra', 'BraA09t36680Z' => 'bra', 'BraA10t44471Z' => 'bra', 'C02p06760' => 'bna', 'C02p06890' => 'bna', 'C02p07010' => 'bna', 'C03p07660' => 'bna', 'C05p10300' => 'bna', 'C06p38150' => 'bna', 'C07p36650' => 'bna', 'C08p15770' => 'bna', 'C09p12300' => 'bna', 'C09p62700' => 'bna', 'C09p75040' => 'bna', 'CAN.G13.1' => 'can', 'CAN.G138.4' => 'can', 'CAN.G44.6' => 'can', 'CAN.G473.19' => 'can', 'CANSAT01G0835' => 'cansat', 'CANSAT11G0246' => 'cansat', 'CANSAT11G1766' => 'cansat', 'CANSAT64G1954' => 'cansat', 'CARHR013330' => 'chi', 'CARHR060530' => 'chi', 'CARHR075300' => 'chi', 'CARHR105120' => 'chi', 'CARHR148910' => 'chi', 'CARHR198830' => 'chi', 'Carub.0001s1275' => 'cru', 'Carub.0002s1437' => 'cru', 'Carub.0003s0044' => 'cru', 'Carub.0003s2787' => 'cru', 'Carub.0005s0597' => 'cru', 'Carub.0006s1266' => 'cru', 'Ca_06935_v3' => 'car', 'Ca_13559_v3' => 'car', 'Ca_16941_v3' => 'car', 'Ca_16960_v3' => 'car', 'Ca_17775_v3' => 'car', 'Ca_30464_v3' => 'car', 'Cc06_g08160' => 'ccan', 'Cc07_g01520' => 'ccan', 'Cc11_g15810' => 'ccan', 'CDE02G2840' => 'cde', 'CDE03G0093' => 'cde', 'CDE04G2127' => 'cde', 'CDE07G1857' => 'cde', 'CDE09G1246' => 'cde', 'Cfa003412' => 'cfa', 'Cfa007341' => 'cfa', 'Cfa009220' => 'cfa', 'Ciclev10008737m.g' => 'ccl', 'Ciclev10015565m.g' => 'ccl', 'Ciclev10031761m.g' => 'ccl', 'CiPaw.03G045300' => 'cil', 'CiPaw.03G247200' => 'cil', 'CiPaw.04G029500' => 'cil', 'CiPaw.04G174000' => 'cil', 'CiPaw.05G181200' => 'cil', 'CiPaw.06G067100' => 'cil', 'ClCG05G025800' => 'cla', 'ClCG06G011400' => 'cla', 'ClCG09G019360' => 'cla', 'COL.COLO4_04827' => 'col', 'COL.COLO4_29170' => 'col', 'COL.COLO4_35131' => 'col', 'COL.COLO4_35132' => 'col', 'Cpa.g.sc33.32' => 'cpa', 'Cpa.g.sc46.29' => 'cpa', 'Cpa.g.sc796.1' => 'cpa', 'CsaV3_1G030420' => 'csa', 'CsaV3_5G027050' => 'csa', 'CsaV3_5G031040' => 'csa', 'CsaV3_UNG023130' => 'csa', 'CSS0007726' => 'camsi', 'CSS0016433' => 'camsi', 'CSS0017656' => 'camsi', 'CSS0025364' => 'camsi', 'CSS0027582' => 'camsi', 'CSS0047288' => 'camsi', 'CSS0049950' => 'camsi', 'DCAR_003843' => 'dca', 'DCAR_007052' => 'dca', 'DCAR_020884' => 'dca', 'DCAR_021730' => 'dca', 'DCAR_024423' => 'dca', 'DCAR_026509' => 'dca', 'DCAR_031158' => 'dca', 'Dinv14728' => 'din', 'Dinv15219' => 'din', 'Dinv25728' => 'din', 'Dinv33428' => 'din', 'Dinv36489' => 'din', 'Dinv41486' => 'din', 'Duzib147G0469' => 'dzi', 'Duzib168G0060' => 'dzi', 'Duzib187G1215' => 'dzi', 'Duzib248G0692' => 'dzi', 'Duzib251G0767' => 'dzi', 'Duzib264G0446' => 'dzi', 'Duzib268G0691' => 'dzi', 'ECA232G4767' => 'eca', 'ECA233G2838' => 'eca', 'ECA234G0391' => 'eca', 'ECA234G0857' => 'eca', 'ECA236G1593' => 'eca', 'ECA238G0565' => 'eca', 'ECA246G1027' => 'eca', 'ECA246G3223' => 'eca', 'ECA246G3470' => 'eca', 'EL10Ac6g13829' => 'bvu', 'EL10Ac6g14093' => 'bvu', 'EL10Ac8g18707' => 'bvu', 'Eucgr.C01369' => 'egr', 'Eucgr.H02492' => 'egr', 'Eucgr.I01733' => 'egr', 'Eucgr.J02255' => 'egr', 'Eucgr.J02257' => 'egr', 'Eucgr.J02258' => 'egr', 'FAN02G1601' => 'fan', 'FAN03G1586' => 'fan', 'FAN03G2986' => 'fan', 'FAN05G4837' => 'fan', 'FAN06G0146' => 'fan', 'FAN07G0858' => 'fan', 'FAN09G3179' => 'fan', 'FAN10G0669' => 'fan', 'FAN12G2358' => 'fan', 'FAN14G4198' => 'fan', 'FAN14G5112' => 'fan', 'FAN17G0342' => 'fan', 'FAN19G0342' => 'fan', 'FAN19G0962' => 'fan', 'FAN19G1101' => 'fan', 'FAN19G1872' => 'fan', 'FAN22G0356' => 'fan', 'FAN23G0744' => 'fan', 'FAN23G1914' => 'fan', 'FAN26G0032' => 'fan', 'FAN28G0625' => 'fan', 'FvH4_1g02710' => 'fve', 'FvH4_1g02720' => 'fve', 'FvH4_4g25670' => 'fve', 'FvH4_6g51700' => 'fve', 'FvH4_7g20170' => 'fve', 'Glyma.05G175000' => 'gma', 'Glyma.08G132300' => 'gma', 'Glyma.11G243000' => 'gma', 'Glyma.13G158900' => 'gma', 'Glyma.17G112400' => 'gma', 'Glyma.18G014100' => 'gma', 'Glyma.19G003100' => 'gma', 'Glyma.19G056500' => 'gma', 'Gohir.A01G158900' => 'ghi', 'Gohir.A05G312600' => 'ghi', 'Gohir.A05G354900' => 'ghi', 'Gohir.A07G037200' => 'ghi', 'Gohir.A09G030000' => 'ghi', 'Gohir.A12G145200' => 'ghi', 'Gohir.D01G151500' => 'ghi', 'Gohir.D04G058300' => 'ghi', 'Gohir.D05G314100' => 'ghi', 'Gohir.D07G041400' => 'ghi', 'Gohir.D09G029700' => 'ghi', 'Gohir.D12G149700' => 'ghi', 'Gorai.001G043800' => 'gra', 'Gorai.002G187800' => 'gra', 'Gorai.006G034700' => 'gra', 'Gorai.008G161200' => 'gra', 'Gorai.009G335700' => 'gra', 'Gorai.012G065000' => 'gra', 'GSVIVG01000535001' => 'vvi', 'GSVIVG01015572001' => 'vvi', 'GSVIVG01032386001' => 'vvi', 'HanXRQChr05g0138531' => 'han', 'HanXRQChr06g0174391' => 'han', 'HanXRQChr07g0199021' => 'han', 'HanXRQChr08g0208211' => 'han', 'HanXRQChr09g0255471' => 'han', 'HanXRQChr10g0315791' => 'han', 'HanXRQChr12g0371991' => 'han', 'HanXRQChr15g0475251' => 'han', 'HanXRQChr17g0540001' => 'han', 'HanXRQChr17g0548631' => 'han', 'HanXRQChr17g0569561' => 'han', 'Haze_12256' => 'cav', 'Haze_14756' => 'cav', 'Haze_25528' => 'cav', 'Hma1.2p1_0079F.1_g041020' => 'hma', 'Hma1.2p1_0818F.1_g223260' => 'hma', 'Hma1.2p1_1747F.1_g300530' => 'hma', 'HPP92_004607' => 'vpl', 'HPP92_004608' => 'vpl', 'HPP92_006181' => 'vpl', 'HPP92_012192' => 'vpl', 'HPP92_015680' => 'vpl', 'HPP92_020249' => 'vpl', 'HPP92_021376' => 'vpl', 'HPP92_024275' => 'vpl', 'Hund06031' => 'sun', 'Hund25391' => 'sun', 'Lalb_Chr07g0185371' => 'lal', 'Lalb_Chr07g0185381' => 'lal', 'Lalb_Chr12g0204011' => 'lal', 'Lalb_Chr13g0301671' => 'lal', 'Lalb_Chr14g0362851' => 'lal', 'Lalb_Chr24g0403581' => 'lal', 'Lj1g0000233' => 'lja', 'Lj2g0018120' => 'lja', 'Lj3C621T0' => 'lonja', 'Lj3P1059T14' => 'lonja', 'Lj3P611T9' => 'lonja', 'Lj3P614T13' => 'lonja', 'Lj3P615T5' => 'lonja', 'Lj4g0012315' => 'lja', 'Lj4g0026182' => 'lja', 'Lj6P813T16' => 'lonja', 'Lj7C427T7' => 'lonja', 'Lj7C427T8' => 'lonja', 'Lj7P600T41' => 'lonja', 'Lju41C42G17' => 'lonja', 'Lsat_1_v5_gn_0_47300' => 'lsa', 'Lsat_1_v5_gn_2_91280' => 'lsa', 'Lsat_1_v5_gn_3_30561' => 'lsa', 'Lsat_1_v5_gn_4_184321' => 'lsa', 'Lsat_1_v5_gn_4_4041' => 'lsa', 'Lsat_1_v5_gn_5_92000' => 'lsa', 'Lsat_1_v5_gn_8_152940' => 'lsa', 'Lsat_1_v5_gn_8_62401' => 'lsa', 'Manes.06G055900' => 'mes', 'Manes.12G022200' => 'mes', 'Manes.13G023300' => 'mes', 'Manes.14G115000' => 'mes', 'Manes.15G151700' => 'mes', 'Manes.17G111300' => 'mes', 'Mapoly0226s0009' => 'mpo', 'MBI02_g25363_MAGBIO' => 'mbi', 'MBI06_g00027_MAGBIO' => 'mbi', 'MBI10_g13034_MAGBIO' => 'mbi', 'MD09G1023400' => 'mdo', 'MD13G1100100' => 'mdo', 'MD15G1169200' => 'mdo', 'MD16G1101100' => 'mdo', 'MD17G1022900' => 'mdo', 'Medtr3g096150' => 'mtr', 'Medtr4g115070' => 'mtr', 'Medtr7g033325' => 'mtr', 'Medtr8g089840' => 'mtr', 'MELO3C010319.2' => 'cme', 'MELO3C011944.2' => 'cme', 'MELO3C021589.2' => 'cme', 'Migut.E00207' => 'egut', 'Migut.H00067' => 'egut', 'Migut.K00433' => 'egut', 'Migut.K00606' => 'egut', 'Migut.K01410' => 'egut', 'MSTRG.13347' => 'ama', 'MSTRG.24045' => 'ama', 'MSTRG.2428' => 'ama', 'MSTRG.26410' => 'ama', 'MSTRG.3139' => 'ama', 'MSTRG.3286' => 'ama', 'MSTRG.563' => 'ama', 'MSTRG.7941' => 'ama', 'Nitab4.5_0000028g0060' => 'nta', 'Nitab4.5_0000065g0260' => 'nta', 'Nitab4.5_0000112g0060' => 'nta', 'Nitab4.5_0000489g0120' => 'nta', 'Nitab4.5_0001776g0050' => 'nta', 'Nitab4.5_0001854g0010' => 'nta', 'Nitab4.5_0001860g0020' => 'nta', 'Nitab4.5_0004352g0010' => 'nta', 'Nitab4.5_0008716g0020' => 'nta', 'Nitab4.5_0008922g0010' => 'nta', 'Nn3g16693' => 'nnu', 'Nn4g22596' => 'nnu', 'Nn7g37639' => 'nnu', 'Oeu001701.1' => 'oeu', 'Oeu018149.1' => 'oeu', 'Oeu026220.1' => 'oeu', 'Oeu038635.1' => 'oeu', 'Oeu049176.1' => 'oeu', 'Oeu056706.1' => 'oeu', 'Oeu056937.1' => 'oeu', 'Oeu057540.1' => 'oeu', 'Os02g0594900' => 'osa', 'Os02g0595100' => 'osa', 'Os04g0477500' => 'osa', 'Os12g0611900' => 'osa', 'Peaxi162Scf00076g00020' => 'pax', 'Peaxi162Scf00128g00217' => 'pax', 'Peaxi162Scf00129g01640' => 'pax', 'Peaxi162Scf00669g00007' => 'pax', 'Peaxi162Scf00700g00421' => 'pax', 'Peaxi162Scf00801g00038' => 'pax', 'Peaxi162Scf00891g00025' => 'pax', 'PGR083G0909' => 'pgr', 'PGR119G1005' => 'pgr', 'PGR142G2236' => 'pgr', 'PGR142G3388' => 'pgr', 'PGSC0003DMG400004514' => 'stu', 'PGSC0003DMG400012635' => 'stu', 'PGSC0003DMG400015730' => 'stu', 'PGSC0003DMG400018611' => 'stu', 'PGSC0003DMG400030897' => 'stu', 'Phvul.001G254800' => 'pvu', 'Phvul.002G260100' => 'pvu', 'Phvul.003G167600' => 'pvu', 'Phvul.004G005100' => 'pvu', 'Potri.001G343600' => 'ptr', 'Potri.006G066700' => 'ptr', 'Potri.008G186000' => 'ptr', 'Potri.010G046900' => 'ptr', 'Potri.018G127900' => 'ptr', 'Pp3c20_17750' => 'ppa', 'Pp3c24_4380' => 'ppa', 'Prupe.1G245800' => 'ppe', 'Prupe.3G293400' => 'ppe', 'Prupe.7G247400' => 'ppe', 'Psat0s145g0120' => 'psa', 'Psat0s595g0040' => 'psa', 'Psat0s595g0120' => 'psa', 'Psat3g175040' => 'psa', 'Psat7g058120' => 'psa', 'PSO017G0428' => 'pso', 'PSO063G7510' => 'pso', 'PSO067G0046' => 'pso', 'PSO478G1073' => 'pso', 'PSO675G3677' => 'pso', 'PSO675G6558' => 'pso', 'PSO675G7520' => 'pso', 'PSO675G8959' => 'pso', 'QL02p074089' => 'qlo', 'QL02p089614' => 'qlo', 'QL03p057736' => 'qlo', 'RcHm_v2.0_Chr1g0364131' => 'rch', 'RcHm_v2.0_Chr2g0087801' => 'rch', 'RcHm_v2.0_Chr2g0087821' => 'rch', 'RcHm_v2.0_Chr2g0173231' => 'rch', 'RcHm_v2.0_Chr4g0433111' => 'rch', 'Rhsim03G0250300' => 'rsi', 'Rhsim08G0048400' => 'rsi', 'Rhsim10G0014800' => 'rsi', 'Rhsim12G0040100' => 'rsi', 'Rhsim12G0109700' => 'rsi', 'Sabra06G0049600' => 'sbr', 'Sabra08G0141000' => 'sbr', 'Sabra10G0021400' => 'sbr', 'Sabra16G0222900' => 'sbr', 'Sabra18G0108600' => 'sbr', 'SalBow1G0433' => 'sbo', 'SalBow1G2038' => 'sbo', 'SalBow1G5003' => 'sbo', 'SalBow7G1197' => 'sbo', 'SalBow8G3506' => 'sbo', 'Sc03g0007300' => 'sci', 'Sc11g0000950' => 'sci', 'Sc14g0008750' => 'sci', 'Sc18g0000420' => 'sci', 'Sed0006754' => 'sed', 'Sed0008741' => 'sed', 'Sed0017172' => 'sed', 'Sed0018925' => 'sed', 'Sed0023326' => 'sed', 'Sed0025909' => 'sed', 'SEGI_05333' => 'sgi', 'SEGI_10362' => 'sgi', 'SEGI_13380' => 'sgi', 'SEGI_24306' => 'sgi', 'SEGI_29077' => 'sgi', 'SEGI_29095' => 'sgi', 'SEGI_36534' => 'sgi', 'SEGI_37506' => 'sgi', 'SEGI_38321' => 'sgi', 'SGA_v2.0_scaffold307G48031' => 'sas', 'SGA_v2.0_scaffold47G17507' => 'sas', 'SGA_v2.0_scaffold63G21736' => 'sas', 'SGA_v2.0_scaffold87G27070' => 'sas', 'SHI17794' => 'shi', 'SHI28851' => 'shi', 'SMO165G0155' => 'smo', 'SMO340G0217' => 'smo', 'SMO367G1210' => 'smo', 'Solyc02g093430.3' => 'sly', 'Solyc05g013580.4' => 'sly', 'Solyc07g008030.3' => 'sly', 'Solyc12g035470.2' => 'sly', 'Sopen02g038020' => 'spe', 'Sopen05g008490' => 'spe', 'Sopen07g003910' => 'spe', 'Sopen12g015240' => 'spe', 'Sp1g11550' => 'spa', 'Sp2g16710' => 'spa', 'Sp3g00430' => 'spa', 'Sp3g26780' => 'spa', 'Sp5g22900' => 'spa', 'Sp6g29530' => 'spa', 'TAR371G0794' => 'tar', 'TAR374G0164' => 'tar', 'TAR622G0165' => 'tar', 'TAR626G0929' => 'tar', 'TAR629G2155' => 'tar', 'THA.LOC104805282' => 'tha', 'THA.LOC104805363' => 'tha', 'THA.LOC104808968' => 'tha', 'THA.LOC104821093' => 'tha', 'THA.LOC104823953' => 'tha', 'THA.LOC104825562' => 'tha', 'THA.LOC104825665' => 'tha', 'Thecc.02G261400' => 'tca', 'Thecc.04G019200' => 'tca', 'Thecc.09G130400' => 'tca', 'Thhalv10004374m.g' => 'esa', 'Thhalv10007850m.g' => 'esa', 'Thhalv10013782m.g' => 'esa', 'Thhalv10018686m.g' => 'esa', 'Thhalv10020899m.g' => 'esa', 'Thhalv10022755m.g' => 'esa', 'TPR.G23851' => 'tpr', 'TPR.G26500' => 'tpr', 'TPR.G27267' => 'tpr', 'TPR.G32001' => 'tpr', 'TPR.G6251' => 'tpr', 'TPR.G8167' => 'tpr', 'TWI12G1330' => 'twi', 'TWI18G1239' => 'twi', 'TWI34G0979' => 'twi', 'TWI36G0670' => 'twi', 'TWI36G0707' => 'twi', 'TWI56G0233' => 'twi', 'TWI75G1809' => 'twi', 'unitig_21.g20874' => 'ugi', 'unitig_26.g10343' => 'ugi', 'unitig_46.g18392' => 'ugi', 'unitig_52.g17178' => 'ugi', 'unitig_8.g2934' => 'ugi', 'vmacro01122' => 'vma', 'vmacro05875' => 'vma', 'vmacro06147' => 'vma', 'vmacro16191' => 'vma', 'vmacro18293' => 'vma', 'VMungo0251G3707' => 'vmu', 'VMungo0464G1521' => 'vmu', 'VMungo1215G0205' => 'vmu', 'VMungo1383G2484' => 'vmu', 'Zm00001eb079610' => 'zma', 'Zm00001eb135990' => 'zma', 'Zm00001eb183710' => 'zma', 'Zm00001eb246020' => 'zma' ) $gf_id = 'HOM05D001124' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001124' ) $data_identifier = 'HOM05D001124' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 6, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 7, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 21, 'bol' => (int) 10, 'bra' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 6, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 9, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 21, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 8, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 10, 'lsa' => (int) 8, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 8, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 9, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb246020' $species_info = array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ) $local_species = 'car' $disabled = '' $selected = '' $num_hits = (int) 0include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001124', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '548', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02520' => 'bna', 'A03p06630' => 'bna', 'A05p44460' => 'bna', 'A06p08710' => 'bna', 'A06p41090' => 'bna', 'A07p32320' => 'bna', 'A08p32520' => 'bna', 'A09p10360' => 'bna', 'A10p24080' => 'bna', 'Aa31LG11G15250' => 'aar', 'Aa31LG1G1800' => 'aar', 'Aa31LG2G5120' => 'aar', 'Aa31LG2G6070' => 'aar', 'Aa31LG5G10770' => 'aar', 'Aa31sc61G90' => 'aar', 'Actinidia01352' => 'ach', 'Actinidia05983' => 'ach', 'Actinidia08133' => 'ach', 'Actinidia15101' => 'ach', 'Actinidia26379' => 'ach', 'Actinidia35778' => 'ach', 'Actinidia36123' => 'ach', 'Actinidia37436' => 'ach', 'Actinidia38730' => 'ach', 'Ah.02g128210' => 'amhyb', 'Ah.03g132990' => 'amhyb', 'Ah.14g079410' => 'amhyb', 'AL1G24640' => 'aly', 'AL2G26680' => 'aly', 'AL3G10530' => 'aly', 'AL3G45230' => 'aly', 'AL5G15230' => 'aly', 'AL5G16960' => 'aly', 'AL6G25210' => 'aly', 'Aqoxy2G00441' => 'aox', 'Aqoxy3G01236' => 'aox', 'Aqoxy5G03746' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3RQ047' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C7GMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9C8JER' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MBL6KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YXCZ83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZANX40' => 'arhy', 'AT1G12990' => 'ath', 'AT1G67880' => 'ath', 'AT2G13290' => 'ath', 'AT3G01620' => 'ath', 'AT3G26445' => 'ath', 'AT3G27540' => 'ath', 'AT5G14480' => 'ath', 'ATR0824G026' => 'atr', 'ATR1098G019' => 'atr', 'Atru.chr11.2145' => 'acertr', 'Atru.chr2.3636' => 'acertr', 'Atru.chr2.3644' => 'acertr', 'Atru.chr6.2422' => 'acertr', 'Atru.chr7.1112' => 'acertr', 'AUR62005469' => 'cqu', 'AUR62011166' => 'cqu', 'AUR62013319' => 'cqu', 'AUR62024273' => 'cqu', 'AUR62028420' => 'cqu', 'AUR62041942' => 'cqu', 'BcaB01g04969' => 'bca', 'BcaB01g06371' => 'bca', 'BcaB02g11494' => 'bca', 'BcaB03g15382' => 'bca', 'BcaB08g36994' => 'bca', 'BcaC03g13477' => 'bca', 'BcaC03g13478' => 'bca', 'BcaC03g13480' => 'bca', 'BcaC03g13481' => 'bca', 'BcaC03g13486' => 'bca', 'BcaC04g19031' => 'bca', 'BcaC04g23085' => 'bca', 'BcaC05g25094' => 'bca', 'BcaC05g25096' => 'bca', 'BcaC05g25138' => 'bca', 'BcaC05g30416' => 'bca', 'BcaC05g30455' => 'bca', 'BcaC06g30979' => 'bca', 'BcaC06g33805' => 'bca', 'BcaC08g46021' => 'bca', 'BcaNung03154' => 'bca', 'BolC2t06623H' => 'bol', 'BolC2t06632H' => 'bol', 'BolC2t06635H' => 'bol', 'BolC2t06638H' => 'bol', 'BolC3t13266H' => 'bol', 'BolC5t29776H' => 'bol', 'BolC6t38912H' => 'bol', 'BolC7t44183H' => 'bol', 'BolC9t54123H' => 'bol', 'BolC9t59107H' => 'bol', 'BraA02t05221Z' => 'bra', 'BraA03t09996Z' => 'bra', 'BraA05t23210Z' => 'bra', 'BraA06t24068Z' => 'bra', 'BraA06t27032Z' => 'bra', 'BraA08t35176Z' => 'bra', 'BraA09t36680Z' => 'bra', 'BraA10t44471Z' => 'bra', 'C02p06760' => 'bna', 'C02p06890' => 'bna', 'C02p07010' => 'bna', 'C03p07660' => 'bna', 'C05p10300' => 'bna', 'C06p38150' => 'bna', 'C07p36650' => 'bna', 'C08p15770' => 'bna', 'C09p12300' => 'bna', 'C09p62700' => 'bna', 'C09p75040' => 'bna', 'CAN.G13.1' => 'can', 'CAN.G138.4' => 'can', 'CAN.G44.6' => 'can', 'CAN.G473.19' => 'can', 'CANSAT01G0835' => 'cansat', 'CANSAT11G0246' => 'cansat', 'CANSAT11G1766' => 'cansat', 'CANSAT64G1954' => 'cansat', 'CARHR013330' => 'chi', 'CARHR060530' => 'chi', 'CARHR075300' => 'chi', 'CARHR105120' => 'chi', 'CARHR148910' => 'chi', 'CARHR198830' => 'chi', 'Carub.0001s1275' => 'cru', 'Carub.0002s1437' => 'cru', 'Carub.0003s0044' => 'cru', 'Carub.0003s2787' => 'cru', 'Carub.0005s0597' => 'cru', 'Carub.0006s1266' => 'cru', 'Ca_06935_v3' => 'car', 'Ca_13559_v3' => 'car', 'Ca_16941_v3' => 'car', 'Ca_16960_v3' => 'car', 'Ca_17775_v3' => 'car', 'Ca_30464_v3' => 'car', 'Cc06_g08160' => 'ccan', 'Cc07_g01520' => 'ccan', 'Cc11_g15810' => 'ccan', 'CDE02G2840' => 'cde', 'CDE03G0093' => 'cde', 'CDE04G2127' => 'cde', 'CDE07G1857' => 'cde', 'CDE09G1246' => 'cde', 'Cfa003412' => 'cfa', 'Cfa007341' => 'cfa', 'Cfa009220' => 'cfa', 'Ciclev10008737m.g' => 'ccl', 'Ciclev10015565m.g' => 'ccl', 'Ciclev10031761m.g' => 'ccl', 'CiPaw.03G045300' => 'cil', 'CiPaw.03G247200' => 'cil', 'CiPaw.04G029500' => 'cil', 'CiPaw.04G174000' => 'cil', 'CiPaw.05G181200' => 'cil', 'CiPaw.06G067100' => 'cil', 'ClCG05G025800' => 'cla', 'ClCG06G011400' => 'cla', 'ClCG09G019360' => 'cla', 'COL.COLO4_04827' => 'col', 'COL.COLO4_29170' => 'col', 'COL.COLO4_35131' => 'col', 'COL.COLO4_35132' => 'col', 'Cpa.g.sc33.32' => 'cpa', 'Cpa.g.sc46.29' => 'cpa', 'Cpa.g.sc796.1' => 'cpa', 'CsaV3_1G030420' => 'csa', 'CsaV3_5G027050' => 'csa', 'CsaV3_5G031040' => 'csa', 'CsaV3_UNG023130' => 'csa', 'CSS0007726' => 'camsi', 'CSS0016433' => 'camsi', 'CSS0017656' => 'camsi', 'CSS0025364' => 'camsi', 'CSS0027582' => 'camsi', 'CSS0047288' => 'camsi', 'CSS0049950' => 'camsi', 'DCAR_003843' => 'dca', 'DCAR_007052' => 'dca', 'DCAR_020884' => 'dca', 'DCAR_021730' => 'dca', 'DCAR_024423' => 'dca', 'DCAR_026509' => 'dca', 'DCAR_031158' => 'dca', 'Dinv14728' => 'din', 'Dinv15219' => 'din', 'Dinv25728' => 'din', 'Dinv33428' => 'din', 'Dinv36489' => 'din', 'Dinv41486' => 'din', 'Duzib147G0469' => 'dzi', 'Duzib168G0060' => 'dzi', 'Duzib187G1215' => 'dzi', 'Duzib248G0692' => 'dzi', 'Duzib251G0767' => 'dzi', 'Duzib264G0446' => 'dzi', 'Duzib268G0691' => 'dzi', 'ECA232G4767' => 'eca', 'ECA233G2838' => 'eca', 'ECA234G0391' => 'eca', 'ECA234G0857' => 'eca', 'ECA236G1593' => 'eca', 'ECA238G0565' => 'eca', 'ECA246G1027' => 'eca', 'ECA246G3223' => 'eca', 'ECA246G3470' => 'eca', 'EL10Ac6g13829' => 'bvu', 'EL10Ac6g14093' => 'bvu', 'EL10Ac8g18707' => 'bvu', 'Eucgr.C01369' => 'egr', 'Eucgr.H02492' => 'egr', 'Eucgr.I01733' => 'egr', 'Eucgr.J02255' => 'egr', 'Eucgr.J02257' => 'egr', 'Eucgr.J02258' => 'egr', 'FAN02G1601' => 'fan', 'FAN03G1586' => 'fan', 'FAN03G2986' => 'fan', 'FAN05G4837' => 'fan', 'FAN06G0146' => 'fan', 'FAN07G0858' => 'fan', 'FAN09G3179' => 'fan', 'FAN10G0669' => 'fan', 'FAN12G2358' => 'fan', 'FAN14G4198' => 'fan', 'FAN14G5112' => 'fan', 'FAN17G0342' => 'fan', 'FAN19G0342' => 'fan', 'FAN19G0962' => 'fan', 'FAN19G1101' => 'fan', 'FAN19G1872' => 'fan', 'FAN22G0356' => 'fan', 'FAN23G0744' => 'fan', 'FAN23G1914' => 'fan', 'FAN26G0032' => 'fan', 'FAN28G0625' => 'fan', 'FvH4_1g02710' => 'fve', 'FvH4_1g02720' => 'fve', 'FvH4_4g25670' => 'fve', 'FvH4_6g51700' => 'fve', 'FvH4_7g20170' => 'fve', 'Glyma.05G175000' => 'gma', 'Glyma.08G132300' => 'gma', 'Glyma.11G243000' => 'gma', 'Glyma.13G158900' => 'gma', 'Glyma.17G112400' => 'gma', 'Glyma.18G014100' => 'gma', 'Glyma.19G003100' => 'gma', 'Glyma.19G056500' => 'gma', 'Gohir.A01G158900' => 'ghi', 'Gohir.A05G312600' => 'ghi', 'Gohir.A05G354900' => 'ghi', 'Gohir.A07G037200' => 'ghi', 'Gohir.A09G030000' => 'ghi', 'Gohir.A12G145200' => 'ghi', 'Gohir.D01G151500' => 'ghi', 'Gohir.D04G058300' => 'ghi', 'Gohir.D05G314100' => 'ghi', 'Gohir.D07G041400' => 'ghi', 'Gohir.D09G029700' => 'ghi', 'Gohir.D12G149700' => 'ghi', 'Gorai.001G043800' => 'gra', 'Gorai.002G187800' => 'gra', 'Gorai.006G034700' => 'gra', 'Gorai.008G161200' => 'gra', 'Gorai.009G335700' => 'gra', 'Gorai.012G065000' => 'gra', 'GSVIVG01000535001' => 'vvi', 'GSVIVG01015572001' => 'vvi', 'GSVIVG01032386001' => 'vvi', 'HanXRQChr05g0138531' => 'han', 'HanXRQChr06g0174391' => 'han', 'HanXRQChr07g0199021' => 'han', 'HanXRQChr08g0208211' => 'han', 'HanXRQChr09g0255471' => 'han', 'HanXRQChr10g0315791' => 'han', 'HanXRQChr12g0371991' => 'han', 'HanXRQChr15g0475251' => 'han', 'HanXRQChr17g0540001' => 'han', 'HanXRQChr17g0548631' => 'han', 'HanXRQChr17g0569561' => 'han', 'Haze_12256' => 'cav', 'Haze_14756' => 'cav', 'Haze_25528' => 'cav', 'Hma1.2p1_0079F.1_g041020' => 'hma', 'Hma1.2p1_0818F.1_g223260' => 'hma', 'Hma1.2p1_1747F.1_g300530' => 'hma', 'HPP92_004607' => 'vpl', 'HPP92_004608' => 'vpl', 'HPP92_006181' => 'vpl', 'HPP92_012192' => 'vpl', 'HPP92_015680' => 'vpl', 'HPP92_020249' => 'vpl', 'HPP92_021376' => 'vpl', 'HPP92_024275' => 'vpl', 'Hund06031' => 'sun', 'Hund25391' => 'sun', 'Lalb_Chr07g0185371' => 'lal', 'Lalb_Chr07g0185381' => 'lal', 'Lalb_Chr12g0204011' => 'lal', 'Lalb_Chr13g0301671' => 'lal', 'Lalb_Chr14g0362851' => 'lal', 'Lalb_Chr24g0403581' => 'lal', 'Lj1g0000233' => 'lja', 'Lj2g0018120' => 'lja', 'Lj3C621T0' => 'lonja', 'Lj3P1059T14' => 'lonja', 'Lj3P611T9' => 'lonja', 'Lj3P614T13' => 'lonja', 'Lj3P615T5' => 'lonja', 'Lj4g0012315' => 'lja', 'Lj4g0026182' => 'lja', 'Lj6P813T16' => 'lonja', 'Lj7C427T7' => 'lonja', 'Lj7C427T8' => 'lonja', 'Lj7P600T41' => 'lonja', 'Lju41C42G17' => 'lonja', 'Lsat_1_v5_gn_0_47300' => 'lsa', 'Lsat_1_v5_gn_2_91280' => 'lsa', 'Lsat_1_v5_gn_3_30561' => 'lsa', 'Lsat_1_v5_gn_4_184321' => 'lsa', 'Lsat_1_v5_gn_4_4041' => 'lsa', 'Lsat_1_v5_gn_5_92000' => 'lsa', 'Lsat_1_v5_gn_8_152940' => 'lsa', 'Lsat_1_v5_gn_8_62401' => 'lsa', 'Manes.06G055900' => 'mes', 'Manes.12G022200' => 'mes', 'Manes.13G023300' => 'mes', 'Manes.14G115000' => 'mes', 'Manes.15G151700' => 'mes', 'Manes.17G111300' => 'mes', 'Mapoly0226s0009' => 'mpo', 'MBI02_g25363_MAGBIO' => 'mbi', 'MBI06_g00027_MAGBIO' => 'mbi', 'MBI10_g13034_MAGBIO' => 'mbi', 'MD09G1023400' => 'mdo', 'MD13G1100100' => 'mdo', 'MD15G1169200' => 'mdo', 'MD16G1101100' => 'mdo', 'MD17G1022900' => 'mdo', 'Medtr3g096150' => 'mtr', 'Medtr4g115070' => 'mtr', 'Medtr7g033325' => 'mtr', 'Medtr8g089840' => 'mtr', 'MELO3C010319.2' => 'cme', 'MELO3C011944.2' => 'cme', 'MELO3C021589.2' => 'cme', 'Migut.E00207' => 'egut', 'Migut.H00067' => 'egut', 'Migut.K00433' => 'egut', 'Migut.K00606' => 'egut', 'Migut.K01410' => 'egut', 'MSTRG.13347' => 'ama', 'MSTRG.24045' => 'ama', 'MSTRG.2428' => 'ama', 'MSTRG.26410' => 'ama', 'MSTRG.3139' => 'ama', 'MSTRG.3286' => 'ama', 'MSTRG.563' => 'ama', 'MSTRG.7941' => 'ama', 'Nitab4.5_0000028g0060' => 'nta', 'Nitab4.5_0000065g0260' => 'nta', 'Nitab4.5_0000112g0060' => 'nta', 'Nitab4.5_0000489g0120' => 'nta', 'Nitab4.5_0001776g0050' => 'nta', 'Nitab4.5_0001854g0010' => 'nta', 'Nitab4.5_0001860g0020' => 'nta', 'Nitab4.5_0004352g0010' => 'nta', 'Nitab4.5_0008716g0020' => 'nta', 'Nitab4.5_0008922g0010' => 'nta', 'Nn3g16693' => 'nnu', 'Nn4g22596' => 'nnu', 'Nn7g37639' => 'nnu', 'Oeu001701.1' => 'oeu', 'Oeu018149.1' => 'oeu', 'Oeu026220.1' => 'oeu', 'Oeu038635.1' => 'oeu', 'Oeu049176.1' => 'oeu', 'Oeu056706.1' => 'oeu', 'Oeu056937.1' => 'oeu', 'Oeu057540.1' => 'oeu', 'Os02g0594900' => 'osa', 'Os02g0595100' => 'osa', 'Os04g0477500' => 'osa', 'Os12g0611900' => 'osa', 'Peaxi162Scf00076g00020' => 'pax', 'Peaxi162Scf00128g00217' => 'pax', 'Peaxi162Scf00129g01640' => 'pax', 'Peaxi162Scf00669g00007' => 'pax', 'Peaxi162Scf00700g00421' => 'pax', 'Peaxi162Scf00801g00038' => 'pax', 'Peaxi162Scf00891g00025' => 'pax', 'PGR083G0909' => 'pgr', 'PGR119G1005' => 'pgr', 'PGR142G2236' => 'pgr', 'PGR142G3388' => 'pgr', 'PGSC0003DMG400004514' => 'stu', 'PGSC0003DMG400012635' => 'stu', 'PGSC0003DMG400015730' => 'stu', 'PGSC0003DMG400018611' => 'stu', 'PGSC0003DMG400030897' => 'stu', 'Phvul.001G254800' => 'pvu', 'Phvul.002G260100' => 'pvu', 'Phvul.003G167600' => 'pvu', 'Phvul.004G005100' => 'pvu', 'Potri.001G343600' => 'ptr', 'Potri.006G066700' => 'ptr', 'Potri.008G186000' => 'ptr', 'Potri.010G046900' => 'ptr', 'Potri.018G127900' => 'ptr', 'Pp3c20_17750' => 'ppa', 'Pp3c24_4380' => 'ppa', 'Prupe.1G245800' => 'ppe', 'Prupe.3G293400' => 'ppe', 'Prupe.7G247400' => 'ppe', 'Psat0s145g0120' => 'psa', 'Psat0s595g0040' => 'psa', 'Psat0s595g0120' => 'psa', 'Psat3g175040' => 'psa', 'Psat7g058120' => 'psa', 'PSO017G0428' => 'pso', 'PSO063G7510' => 'pso', 'PSO067G0046' => 'pso', 'PSO478G1073' => 'pso', 'PSO675G3677' => 'pso', 'PSO675G6558' => 'pso', 'PSO675G7520' => 'pso', 'PSO675G8959' => 'pso', 'QL02p074089' => 'qlo', 'QL02p089614' => 'qlo', 'QL03p057736' => 'qlo', 'RcHm_v2.0_Chr1g0364131' => 'rch', 'RcHm_v2.0_Chr2g0087801' => 'rch', 'RcHm_v2.0_Chr2g0087821' => 'rch', 'RcHm_v2.0_Chr2g0173231' => 'rch', 'RcHm_v2.0_Chr4g0433111' => 'rch', 'Rhsim03G0250300' => 'rsi', 'Rhsim08G0048400' => 'rsi', 'Rhsim10G0014800' => 'rsi', 'Rhsim12G0040100' => 'rsi', 'Rhsim12G0109700' => 'rsi', 'Sabra06G0049600' => 'sbr', 'Sabra08G0141000' => 'sbr', 'Sabra10G0021400' => 'sbr', 'Sabra16G0222900' => 'sbr', 'Sabra18G0108600' => 'sbr', 'SalBow1G0433' => 'sbo', 'SalBow1G2038' => 'sbo', 'SalBow1G5003' => 'sbo', 'SalBow7G1197' => 'sbo', 'SalBow8G3506' => 'sbo', 'Sc03g0007300' => 'sci', 'Sc11g0000950' => 'sci', 'Sc14g0008750' => 'sci', 'Sc18g0000420' => 'sci', 'Sed0006754' => 'sed', 'Sed0008741' => 'sed', 'Sed0017172' => 'sed', 'Sed0018925' => 'sed', 'Sed0023326' => 'sed', 'Sed0025909' => 'sed', 'SEGI_05333' => 'sgi', 'SEGI_10362' => 'sgi', 'SEGI_13380' => 'sgi', 'SEGI_24306' => 'sgi', 'SEGI_29077' => 'sgi', 'SEGI_29095' => 'sgi', 'SEGI_36534' => 'sgi', 'SEGI_37506' => 'sgi', 'SEGI_38321' => 'sgi', 'SGA_v2.0_scaffold307G48031' => 'sas', 'SGA_v2.0_scaffold47G17507' => 'sas', 'SGA_v2.0_scaffold63G21736' => 'sas', 'SGA_v2.0_scaffold87G27070' => 'sas', 'SHI17794' => 'shi', 'SHI28851' => 'shi', 'SMO165G0155' => 'smo', 'SMO340G0217' => 'smo', 'SMO367G1210' => 'smo', 'Solyc02g093430.3' => 'sly', 'Solyc05g013580.4' => 'sly', 'Solyc07g008030.3' => 'sly', 'Solyc12g035470.2' => 'sly', 'Sopen02g038020' => 'spe', 'Sopen05g008490' => 'spe', 'Sopen07g003910' => 'spe', 'Sopen12g015240' => 'spe', 'Sp1g11550' => 'spa', 'Sp2g16710' => 'spa', 'Sp3g00430' => 'spa', 'Sp3g26780' => 'spa', 'Sp5g22900' => 'spa', 'Sp6g29530' => 'spa', 'TAR371G0794' => 'tar', 'TAR374G0164' => 'tar', 'TAR622G0165' => 'tar', 'TAR626G0929' => 'tar', 'TAR629G2155' => 'tar', 'THA.LOC104805282' => 'tha', 'THA.LOC104805363' => 'tha', 'THA.LOC104808968' => 'tha', 'THA.LOC104821093' => 'tha', 'THA.LOC104823953' => 'tha', 'THA.LOC104825562' => 'tha', 'THA.LOC104825665' => 'tha', 'Thecc.02G261400' => 'tca', 'Thecc.04G019200' => 'tca', 'Thecc.09G130400' => 'tca', 'Thhalv10004374m.g' => 'esa', 'Thhalv10007850m.g' => 'esa', 'Thhalv10013782m.g' => 'esa', 'Thhalv10018686m.g' => 'esa', 'Thhalv10020899m.g' => 'esa', 'Thhalv10022755m.g' => 'esa', 'TPR.G23851' => 'tpr', 'TPR.G26500' => 'tpr', 'TPR.G27267' => 'tpr', 'TPR.G32001' => 'tpr', 'TPR.G6251' => 'tpr', 'TPR.G8167' => 'tpr', 'TWI12G1330' => 'twi', 'TWI18G1239' => 'twi', 'TWI34G0979' => 'twi', 'TWI36G0670' => 'twi', 'TWI36G0707' => 'twi', 'TWI56G0233' => 'twi', 'TWI75G1809' => 'twi', 'unitig_21.g20874' => 'ugi', 'unitig_26.g10343' => 'ugi', 'unitig_46.g18392' => 'ugi', 'unitig_52.g17178' => 'ugi', 'unitig_8.g2934' => 'ugi', 'vmacro01122' => 'vma', 'vmacro05875' => 'vma', 'vmacro06147' => 'vma', 'vmacro16191' => 'vma', 'vmacro18293' => 'vma', 'VMungo0251G3707' => 'vmu', 'VMungo0464G1521' => 'vmu', 'VMungo1215G0205' => 'vmu', 'VMungo1383G2484' => 'vmu', 'Zm00001eb079610' => 'zma', 'Zm00001eb135990' => 'zma', 'Zm00001eb183710' => 'zma', 'Zm00001eb246020' => 'zma' ), 'gf_id' => 'HOM05D001124', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001124' ), 'data_identifier' => 'HOM05D001124', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001124', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '548', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02520' => 'bna', 'A03p06630' => 'bna', 'A05p44460' => 'bna', 'A06p08710' => 'bna', 'A06p41090' => 'bna', 'A07p32320' => 'bna', 'A08p32520' => 'bna', 'A09p10360' => 'bna', 'A10p24080' => 'bna', 'Aa31LG11G15250' => 'aar', 'Aa31LG1G1800' => 'aar', 'Aa31LG2G5120' => 'aar', 'Aa31LG2G6070' => 'aar', 'Aa31LG5G10770' => 'aar', 'Aa31sc61G90' => 'aar', 'Actinidia01352' => 'ach', 'Actinidia05983' => 'ach', 'Actinidia08133' => 'ach', 'Actinidia15101' => 'ach', 'Actinidia26379' => 'ach', 'Actinidia35778' => 'ach', 'Actinidia36123' => 'ach', 'Actinidia37436' => 'ach', 'Actinidia38730' => 'ach', 'Ah.02g128210' => 'amhyb', 'Ah.03g132990' => 'amhyb', 'Ah.14g079410' => 'amhyb', 'AL1G24640' => 'aly', 'AL2G26680' => 'aly', 'AL3G10530' => 'aly', 'AL3G45230' => 'aly', 'AL5G15230' => 'aly', 'AL5G16960' => 'aly', 'AL6G25210' => 'aly', 'Aqoxy2G00441' => 'aox', 'Aqoxy3G01236' => 'aox', 'Aqoxy5G03746' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3RQ047' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C7GMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9C8JER' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MBL6KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YXCZ83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZANX40' => 'arhy', 'AT1G12990' => 'ath', 'AT1G67880' => 'ath', 'AT2G13290' => 'ath', 'AT3G01620' => 'ath', 'AT3G26445' => 'ath', 'AT3G27540' => 'ath', 'AT5G14480' => 'ath', 'ATR0824G026' => 'atr', 'ATR1098G019' => 'atr', 'Atru.chr11.2145' => 'acertr', 'Atru.chr2.3636' => 'acertr', 'Atru.chr2.3644' => 'acertr', 'Atru.chr6.2422' => 'acertr', 'Atru.chr7.1112' => 'acertr', 'AUR62005469' => 'cqu', 'AUR62011166' => 'cqu', 'AUR62013319' => 'cqu', 'AUR62024273' => 'cqu', 'AUR62028420' => 'cqu', 'AUR62041942' => 'cqu', 'BcaB01g04969' => 'bca', 'BcaB01g06371' => 'bca', 'BcaB02g11494' => 'bca', 'BcaB03g15382' => 'bca', 'BcaB08g36994' => 'bca', 'BcaC03g13477' => 'bca', 'BcaC03g13478' => 'bca', 'BcaC03g13480' => 'bca', 'BcaC03g13481' => 'bca', 'BcaC03g13486' => 'bca', 'BcaC04g19031' => 'bca', 'BcaC04g23085' => 'bca', 'BcaC05g25094' => 'bca', 'BcaC05g25096' => 'bca', 'BcaC05g25138' => 'bca', 'BcaC05g30416' => 'bca', 'BcaC05g30455' => 'bca', 'BcaC06g30979' => 'bca', 'BcaC06g33805' => 'bca', 'BcaC08g46021' => 'bca', 'BcaNung03154' => 'bca', 'BolC2t06623H' => 'bol', 'BolC2t06632H' => 'bol', 'BolC2t06635H' => 'bol', 'BolC2t06638H' => 'bol', 'BolC3t13266H' => 'bol', 'BolC5t29776H' => 'bol', 'BolC6t38912H' => 'bol', 'BolC7t44183H' => 'bol', 'BolC9t54123H' => 'bol', 'BolC9t59107H' => 'bol', 'BraA02t05221Z' => 'bra', 'BraA03t09996Z' => 'bra', 'BraA05t23210Z' => 'bra', 'BraA06t24068Z' => 'bra', 'BraA06t27032Z' => 'bra', 'BraA08t35176Z' => 'bra', 'BraA09t36680Z' => 'bra', 'BraA10t44471Z' => 'bra', 'C02p06760' => 'bna', 'C02p06890' => 'bna', 'C02p07010' => 'bna', 'C03p07660' => 'bna', 'C05p10300' => 'bna', 'C06p38150' => 'bna', 'C07p36650' => 'bna', 'C08p15770' => 'bna', 'C09p12300' => 'bna', 'C09p62700' => 'bna', 'C09p75040' => 'bna', 'CAN.G13.1' => 'can', 'CAN.G138.4' => 'can', 'CAN.G44.6' => 'can', 'CAN.G473.19' => 'can', 'CANSAT01G0835' => 'cansat', 'CANSAT11G0246' => 'cansat', 'CANSAT11G1766' => 'cansat', 'CANSAT64G1954' => 'cansat', 'CARHR013330' => 'chi', 'CARHR060530' => 'chi', 'CARHR075300' => 'chi', 'CARHR105120' => 'chi', 'CARHR148910' => 'chi', 'CARHR198830' => 'chi', 'Carub.0001s1275' => 'cru', 'Carub.0002s1437' => 'cru', 'Carub.0003s0044' => 'cru', 'Carub.0003s2787' => 'cru', 'Carub.0005s0597' => 'cru', 'Carub.0006s1266' => 'cru', 'Ca_06935_v3' => 'car', 'Ca_13559_v3' => 'car', 'Ca_16941_v3' => 'car', 'Ca_16960_v3' => 'car', 'Ca_17775_v3' => 'car', 'Ca_30464_v3' => 'car', 'Cc06_g08160' => 'ccan', 'Cc07_g01520' => 'ccan', 'Cc11_g15810' => 'ccan', 'CDE02G2840' => 'cde', 'CDE03G0093' => 'cde', 'CDE04G2127' => 'cde', 'CDE07G1857' => 'cde', 'CDE09G1246' => 'cde', 'Cfa003412' => 'cfa', 'Cfa007341' => 'cfa', 'Cfa009220' => 'cfa', 'Ciclev10008737m.g' => 'ccl', 'Ciclev10015565m.g' => 'ccl', 'Ciclev10031761m.g' => 'ccl', 'CiPaw.03G045300' => 'cil', 'CiPaw.03G247200' => 'cil', 'CiPaw.04G029500' => 'cil', 'CiPaw.04G174000' => 'cil', 'CiPaw.05G181200' => 'cil', 'CiPaw.06G067100' => 'cil', 'ClCG05G025800' => 'cla', 'ClCG06G011400' => 'cla', 'ClCG09G019360' => 'cla', 'COL.COLO4_04827' => 'col', 'COL.COLO4_29170' => 'col', 'COL.COLO4_35131' => 'col', 'COL.COLO4_35132' => 'col', 'Cpa.g.sc33.32' => 'cpa', 'Cpa.g.sc46.29' => 'cpa', 'Cpa.g.sc796.1' => 'cpa', 'CsaV3_1G030420' => 'csa', 'CsaV3_5G027050' => 'csa', 'CsaV3_5G031040' => 'csa', 'CsaV3_UNG023130' => 'csa', 'CSS0007726' => 'camsi', 'CSS0016433' => 'camsi', 'CSS0017656' => 'camsi', 'CSS0025364' => 'camsi', 'CSS0027582' => 'camsi', 'CSS0047288' => 'camsi', 'CSS0049950' => 'camsi', 'DCAR_003843' => 'dca', 'DCAR_007052' => 'dca', 'DCAR_020884' => 'dca', 'DCAR_021730' => 'dca', 'DCAR_024423' => 'dca', 'DCAR_026509' => 'dca', 'DCAR_031158' => 'dca', 'Dinv14728' => 'din', 'Dinv15219' => 'din', 'Dinv25728' => 'din', 'Dinv33428' => 'din', 'Dinv36489' => 'din', 'Dinv41486' => 'din', 'Duzib147G0469' => 'dzi', 'Duzib168G0060' => 'dzi', 'Duzib187G1215' => 'dzi', 'Duzib248G0692' => 'dzi', 'Duzib251G0767' => 'dzi', 'Duzib264G0446' => 'dzi', 'Duzib268G0691' => 'dzi', 'ECA232G4767' => 'eca', 'ECA233G2838' => 'eca', 'ECA234G0391' => 'eca', 'ECA234G0857' => 'eca', 'ECA236G1593' => 'eca', 'ECA238G0565' => 'eca', 'ECA246G1027' => 'eca', 'ECA246G3223' => 'eca', 'ECA246G3470' => 'eca', 'EL10Ac6g13829' => 'bvu', 'EL10Ac6g14093' => 'bvu', 'EL10Ac8g18707' => 'bvu', 'Eucgr.C01369' => 'egr', 'Eucgr.H02492' => 'egr', 'Eucgr.I01733' => 'egr', 'Eucgr.J02255' => 'egr', 'Eucgr.J02257' => 'egr', 'Eucgr.J02258' => 'egr', 'FAN02G1601' => 'fan', 'FAN03G1586' => 'fan', 'FAN03G2986' => 'fan', 'FAN05G4837' => 'fan', 'FAN06G0146' => 'fan', 'FAN07G0858' => 'fan', 'FAN09G3179' => 'fan', 'FAN10G0669' => 'fan', 'FAN12G2358' => 'fan', 'FAN14G4198' => 'fan', 'FAN14G5112' => 'fan', 'FAN17G0342' => 'fan', 'FAN19G0342' => 'fan', 'FAN19G0962' => 'fan', 'FAN19G1101' => 'fan', 'FAN19G1872' => 'fan', 'FAN22G0356' => 'fan', 'FAN23G0744' => 'fan', 'FAN23G1914' => 'fan', 'FAN26G0032' => 'fan', 'FAN28G0625' => 'fan', 'FvH4_1g02710' => 'fve', 'FvH4_1g02720' => 'fve', 'FvH4_4g25670' => 'fve', 'FvH4_6g51700' => 'fve', 'FvH4_7g20170' => 'fve', 'Glyma.05G175000' => 'gma', 'Glyma.08G132300' => 'gma', 'Glyma.11G243000' => 'gma', 'Glyma.13G158900' => 'gma', 'Glyma.17G112400' => 'gma', 'Glyma.18G014100' => 'gma', 'Glyma.19G003100' => 'gma', 'Glyma.19G056500' => 'gma', 'Gohir.A01G158900' => 'ghi', 'Gohir.A05G312600' => 'ghi', 'Gohir.A05G354900' => 'ghi', 'Gohir.A07G037200' => 'ghi', 'Gohir.A09G030000' => 'ghi', 'Gohir.A12G145200' => 'ghi', 'Gohir.D01G151500' => 'ghi', 'Gohir.D04G058300' => 'ghi', 'Gohir.D05G314100' => 'ghi', 'Gohir.D07G041400' => 'ghi', 'Gohir.D09G029700' => 'ghi', 'Gohir.D12G149700' => 'ghi', 'Gorai.001G043800' => 'gra', 'Gorai.002G187800' => 'gra', 'Gorai.006G034700' => 'gra', 'Gorai.008G161200' => 'gra', 'Gorai.009G335700' => 'gra', 'Gorai.012G065000' => 'gra', 'GSVIVG01000535001' => 'vvi', 'GSVIVG01015572001' => 'vvi', 'GSVIVG01032386001' => 'vvi', 'HanXRQChr05g0138531' => 'han', 'HanXRQChr06g0174391' => 'han', 'HanXRQChr07g0199021' => 'han', 'HanXRQChr08g0208211' => 'han', 'HanXRQChr09g0255471' => 'han', 'HanXRQChr10g0315791' => 'han', 'HanXRQChr12g0371991' => 'han', 'HanXRQChr15g0475251' => 'han', 'HanXRQChr17g0540001' => 'han', 'HanXRQChr17g0548631' => 'han', 'HanXRQChr17g0569561' => 'han', 'Haze_12256' => 'cav', 'Haze_14756' => 'cav', 'Haze_25528' => 'cav', 'Hma1.2p1_0079F.1_g041020' => 'hma', 'Hma1.2p1_0818F.1_g223260' => 'hma', 'Hma1.2p1_1747F.1_g300530' => 'hma', 'HPP92_004607' => 'vpl', 'HPP92_004608' => 'vpl', 'HPP92_006181' => 'vpl', 'HPP92_012192' => 'vpl', 'HPP92_015680' => 'vpl', 'HPP92_020249' => 'vpl', 'HPP92_021376' => 'vpl', 'HPP92_024275' => 'vpl', 'Hund06031' => 'sun', 'Hund25391' => 'sun', 'Lalb_Chr07g0185371' => 'lal', 'Lalb_Chr07g0185381' => 'lal', 'Lalb_Chr12g0204011' => 'lal', 'Lalb_Chr13g0301671' => 'lal', 'Lalb_Chr14g0362851' => 'lal', 'Lalb_Chr24g0403581' => 'lal', 'Lj1g0000233' => 'lja', 'Lj2g0018120' => 'lja', 'Lj3C621T0' => 'lonja', 'Lj3P1059T14' => 'lonja', 'Lj3P611T9' => 'lonja', 'Lj3P614T13' => 'lonja', 'Lj3P615T5' => 'lonja', 'Lj4g0012315' => 'lja', 'Lj4g0026182' => 'lja', 'Lj6P813T16' => 'lonja', 'Lj7C427T7' => 'lonja', 'Lj7C427T8' => 'lonja', 'Lj7P600T41' => 'lonja', 'Lju41C42G17' => 'lonja', 'Lsat_1_v5_gn_0_47300' => 'lsa', 'Lsat_1_v5_gn_2_91280' => 'lsa', 'Lsat_1_v5_gn_3_30561' => 'lsa', 'Lsat_1_v5_gn_4_184321' => 'lsa', 'Lsat_1_v5_gn_4_4041' => 'lsa', 'Lsat_1_v5_gn_5_92000' => 'lsa', 'Lsat_1_v5_gn_8_152940' => 'lsa', 'Lsat_1_v5_gn_8_62401' => 'lsa', 'Manes.06G055900' => 'mes', 'Manes.12G022200' => 'mes', 'Manes.13G023300' => 'mes', 'Manes.14G115000' => 'mes', 'Manes.15G151700' => 'mes', 'Manes.17G111300' => 'mes', 'Mapoly0226s0009' => 'mpo', 'MBI02_g25363_MAGBIO' => 'mbi', 'MBI06_g00027_MAGBIO' => 'mbi', 'MBI10_g13034_MAGBIO' => 'mbi', 'MD09G1023400' => 'mdo', 'MD13G1100100' => 'mdo', 'MD15G1169200' => 'mdo', 'MD16G1101100' => 'mdo', 'MD17G1022900' => 'mdo', 'Medtr3g096150' => 'mtr', 'Medtr4g115070' => 'mtr', 'Medtr7g033325' => 'mtr', 'Medtr8g089840' => 'mtr', 'MELO3C010319.2' => 'cme', 'MELO3C011944.2' => 'cme', 'MELO3C021589.2' => 'cme', 'Migut.E00207' => 'egut', 'Migut.H00067' => 'egut', 'Migut.K00433' => 'egut', 'Migut.K00606' => 'egut', 'Migut.K01410' => 'egut', 'MSTRG.13347' => 'ama', 'MSTRG.24045' => 'ama', 'MSTRG.2428' => 'ama', 'MSTRG.26410' => 'ama', 'MSTRG.3139' => 'ama', 'MSTRG.3286' => 'ama', 'MSTRG.563' => 'ama', 'MSTRG.7941' => 'ama', 'Nitab4.5_0000028g0060' => 'nta', 'Nitab4.5_0000065g0260' => 'nta', 'Nitab4.5_0000112g0060' => 'nta', 'Nitab4.5_0000489g0120' => 'nta', 'Nitab4.5_0001776g0050' => 'nta', 'Nitab4.5_0001854g0010' => 'nta', 'Nitab4.5_0001860g0020' => 'nta', 'Nitab4.5_0004352g0010' => 'nta', 'Nitab4.5_0008716g0020' => 'nta', 'Nitab4.5_0008922g0010' => 'nta', 'Nn3g16693' => 'nnu', 'Nn4g22596' => 'nnu', 'Nn7g37639' => 'nnu', 'Oeu001701.1' => 'oeu', 'Oeu018149.1' => 'oeu', 'Oeu026220.1' => 'oeu', 'Oeu038635.1' => 'oeu', 'Oeu049176.1' => 'oeu', 'Oeu056706.1' => 'oeu', 'Oeu056937.1' => 'oeu', 'Oeu057540.1' => 'oeu', 'Os02g0594900' => 'osa', 'Os02g0595100' => 'osa', 'Os04g0477500' => 'osa', 'Os12g0611900' => 'osa', 'Peaxi162Scf00076g00020' => 'pax', 'Peaxi162Scf00128g00217' => 'pax', 'Peaxi162Scf00129g01640' => 'pax', 'Peaxi162Scf00669g00007' => 'pax', 'Peaxi162Scf00700g00421' => 'pax', 'Peaxi162Scf00801g00038' => 'pax', 'Peaxi162Scf00891g00025' => 'pax', 'PGR083G0909' => 'pgr', 'PGR119G1005' => 'pgr', 'PGR142G2236' => 'pgr', 'PGR142G3388' => 'pgr', 'PGSC0003DMG400004514' => 'stu', 'PGSC0003DMG400012635' => 'stu', 'PGSC0003DMG400015730' => 'stu', 'PGSC0003DMG400018611' => 'stu', 'PGSC0003DMG400030897' => 'stu', 'Phvul.001G254800' => 'pvu', 'Phvul.002G260100' => 'pvu', 'Phvul.003G167600' => 'pvu', 'Phvul.004G005100' => 'pvu', 'Potri.001G343600' => 'ptr', 'Potri.006G066700' => 'ptr', 'Potri.008G186000' => 'ptr', 'Potri.010G046900' => 'ptr', 'Potri.018G127900' => 'ptr', 'Pp3c20_17750' => 'ppa', 'Pp3c24_4380' => 'ppa', 'Prupe.1G245800' => 'ppe', 'Prupe.3G293400' => 'ppe', 'Prupe.7G247400' => 'ppe', 'Psat0s145g0120' => 'psa', 'Psat0s595g0040' => 'psa', 'Psat0s595g0120' => 'psa', 'Psat3g175040' => 'psa', 'Psat7g058120' => 'psa', 'PSO017G0428' => 'pso', 'PSO063G7510' => 'pso', 'PSO067G0046' => 'pso', 'PSO478G1073' => 'pso', 'PSO675G3677' => 'pso', 'PSO675G6558' => 'pso', 'PSO675G7520' => 'pso', 'PSO675G8959' => 'pso', 'QL02p074089' => 'qlo', 'QL02p089614' => 'qlo', 'QL03p057736' => 'qlo', 'RcHm_v2.0_Chr1g0364131' => 'rch', 'RcHm_v2.0_Chr2g0087801' => 'rch', 'RcHm_v2.0_Chr2g0087821' => 'rch', 'RcHm_v2.0_Chr2g0173231' => 'rch', 'RcHm_v2.0_Chr4g0433111' => 'rch', 'Rhsim03G0250300' => 'rsi', 'Rhsim08G0048400' => 'rsi', 'Rhsim10G0014800' => 'rsi', 'Rhsim12G0040100' => 'rsi', 'Rhsim12G0109700' => 'rsi', 'Sabra06G0049600' => 'sbr', 'Sabra08G0141000' => 'sbr', 'Sabra10G0021400' => 'sbr', 'Sabra16G0222900' => 'sbr', 'Sabra18G0108600' => 'sbr', 'SalBow1G0433' => 'sbo', 'SalBow1G2038' => 'sbo', 'SalBow1G5003' => 'sbo', 'SalBow7G1197' => 'sbo', 'SalBow8G3506' => 'sbo', 'Sc03g0007300' => 'sci', 'Sc11g0000950' => 'sci', 'Sc14g0008750' => 'sci', 'Sc18g0000420' => 'sci', 'Sed0006754' => 'sed', 'Sed0008741' => 'sed', 'Sed0017172' => 'sed', 'Sed0018925' => 'sed', 'Sed0023326' => 'sed', 'Sed0025909' => 'sed', 'SEGI_05333' => 'sgi', 'SEGI_10362' => 'sgi', 'SEGI_13380' => 'sgi', 'SEGI_24306' => 'sgi', 'SEGI_29077' => 'sgi', 'SEGI_29095' => 'sgi', 'SEGI_36534' => 'sgi', 'SEGI_37506' => 'sgi', 'SEGI_38321' => 'sgi', 'SGA_v2.0_scaffold307G48031' => 'sas', 'SGA_v2.0_scaffold47G17507' => 'sas', 'SGA_v2.0_scaffold63G21736' => 'sas', 'SGA_v2.0_scaffold87G27070' => 'sas', 'SHI17794' => 'shi', 'SHI28851' => 'shi', 'SMO165G0155' => 'smo', 'SMO340G0217' => 'smo', 'SMO367G1210' => 'smo', 'Solyc02g093430.3' => 'sly', 'Solyc05g013580.4' => 'sly', 'Solyc07g008030.3' => 'sly', 'Solyc12g035470.2' => 'sly', 'Sopen02g038020' => 'spe', 'Sopen05g008490' => 'spe', 'Sopen07g003910' => 'spe', 'Sopen12g015240' => 'spe', 'Sp1g11550' => 'spa', 'Sp2g16710' => 'spa', 'Sp3g00430' => 'spa', 'Sp3g26780' => 'spa', 'Sp5g22900' => 'spa', 'Sp6g29530' => 'spa', 'TAR371G0794' => 'tar', 'TAR374G0164' => 'tar', 'TAR622G0165' => 'tar', 'TAR626G0929' => 'tar', 'TAR629G2155' => 'tar', 'THA.LOC104805282' => 'tha', 'THA.LOC104805363' => 'tha', 'THA.LOC104808968' => 'tha', 'THA.LOC104821093' => 'tha', 'THA.LOC104823953' => 'tha', 'THA.LOC104825562' => 'tha', 'THA.LOC104825665' => 'tha', 'Thecc.02G261400' => 'tca', 'Thecc.04G019200' => 'tca', 'Thecc.09G130400' => 'tca', 'Thhalv10004374m.g' => 'esa', 'Thhalv10007850m.g' => 'esa', 'Thhalv10013782m.g' => 'esa', 'Thhalv10018686m.g' => 'esa', 'Thhalv10020899m.g' => 'esa', 'Thhalv10022755m.g' => 'esa', 'TPR.G23851' => 'tpr', 'TPR.G26500' => 'tpr', 'TPR.G27267' => 'tpr', 'TPR.G32001' => 'tpr', 'TPR.G6251' => 'tpr', 'TPR.G8167' => 'tpr', 'TWI12G1330' => 'twi', 'TWI18G1239' => 'twi', 'TWI34G0979' => 'twi', 'TWI36G0670' => 'twi', 'TWI36G0707' => 'twi', 'TWI56G0233' => 'twi', 'TWI75G1809' => 'twi', 'unitig_21.g20874' => 'ugi', 'unitig_26.g10343' => 'ugi', 'unitig_46.g18392' => 'ugi', 'unitig_52.g17178' => 'ugi', 'unitig_8.g2934' => 'ugi', 'vmacro01122' => 'vma', 'vmacro05875' => 'vma', 'vmacro06147' => 'vma', 'vmacro16191' => 'vma', 'vmacro18293' => 'vma', 'VMungo0251G3707' => 'vmu', 'VMungo0464G1521' => 'vmu', 'VMungo1215G0205' => 'vmu', 'VMungo1383G2484' => 'vmu', 'Zm00001eb079610' => 'zma', 'Zm00001eb135990' => 'zma', 'Zm00001eb183710' => 'zma', 'Zm00001eb246020' => 'zma' ) $gf_id = 'HOM05D001124' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001124' ) $data_identifier = 'HOM05D001124' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 6, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 7, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 21, 'bol' => (int) 10, 'bra' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 6, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 9, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 21, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 8, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 10, 'lsa' => (int) 8, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 8, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 9, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb246020' $species_info = array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ) $local_species = 'car' $disabled = '' $selected = '' $num_hits = (int) 0
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001124', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '548', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02520' => 'bna', 'A03p06630' => 'bna', 'A05p44460' => 'bna', 'A06p08710' => 'bna', 'A06p41090' => 'bna', 'A07p32320' => 'bna', 'A08p32520' => 'bna', 'A09p10360' => 'bna', 'A10p24080' => 'bna', 'Aa31LG11G15250' => 'aar', 'Aa31LG1G1800' => 'aar', 'Aa31LG2G5120' => 'aar', 'Aa31LG2G6070' => 'aar', 'Aa31LG5G10770' => 'aar', 'Aa31sc61G90' => 'aar', 'Actinidia01352' => 'ach', 'Actinidia05983' => 'ach', 'Actinidia08133' => 'ach', 'Actinidia15101' => 'ach', 'Actinidia26379' => 'ach', 'Actinidia35778' => 'ach', 'Actinidia36123' => 'ach', 'Actinidia37436' => 'ach', 'Actinidia38730' => 'ach', 'Ah.02g128210' => 'amhyb', 'Ah.03g132990' => 'amhyb', 'Ah.14g079410' => 'amhyb', 'AL1G24640' => 'aly', 'AL2G26680' => 'aly', 'AL3G10530' => 'aly', 'AL3G45230' => 'aly', 'AL5G15230' => 'aly', 'AL5G16960' => 'aly', 'AL6G25210' => 'aly', 'Aqoxy2G00441' => 'aox', 'Aqoxy3G01236' => 'aox', 'Aqoxy5G03746' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3RQ047' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C7GMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9C8JER' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MBL6KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YXCZ83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZANX40' => 'arhy', 'AT1G12990' => 'ath', 'AT1G67880' => 'ath', 'AT2G13290' => 'ath', 'AT3G01620' => 'ath', 'AT3G26445' => 'ath', 'AT3G27540' => 'ath', 'AT5G14480' => 'ath', 'ATR0824G026' => 'atr', 'ATR1098G019' => 'atr', 'Atru.chr11.2145' => 'acertr', 'Atru.chr2.3636' => 'acertr', 'Atru.chr2.3644' => 'acertr', 'Atru.chr6.2422' => 'acertr', 'Atru.chr7.1112' => 'acertr', 'AUR62005469' => 'cqu', 'AUR62011166' => 'cqu', 'AUR62013319' => 'cqu', 'AUR62024273' => 'cqu', 'AUR62028420' => 'cqu', 'AUR62041942' => 'cqu', 'BcaB01g04969' => 'bca', 'BcaB01g06371' => 'bca', 'BcaB02g11494' => 'bca', 'BcaB03g15382' => 'bca', 'BcaB08g36994' => 'bca', 'BcaC03g13477' => 'bca', 'BcaC03g13478' => 'bca', 'BcaC03g13480' => 'bca', 'BcaC03g13481' => 'bca', 'BcaC03g13486' => 'bca', 'BcaC04g19031' => 'bca', 'BcaC04g23085' => 'bca', 'BcaC05g25094' => 'bca', 'BcaC05g25096' => 'bca', 'BcaC05g25138' => 'bca', 'BcaC05g30416' => 'bca', 'BcaC05g30455' => 'bca', 'BcaC06g30979' => 'bca', 'BcaC06g33805' => 'bca', 'BcaC08g46021' => 'bca', 'BcaNung03154' => 'bca', 'BolC2t06623H' => 'bol', 'BolC2t06632H' => 'bol', 'BolC2t06635H' => 'bol', 'BolC2t06638H' => 'bol', 'BolC3t13266H' => 'bol', 'BolC5t29776H' => 'bol', 'BolC6t38912H' => 'bol', 'BolC7t44183H' => 'bol', 'BolC9t54123H' => 'bol', 'BolC9t59107H' => 'bol', 'BraA02t05221Z' => 'bra', 'BraA03t09996Z' => 'bra', 'BraA05t23210Z' => 'bra', 'BraA06t24068Z' => 'bra', 'BraA06t27032Z' => 'bra', 'BraA08t35176Z' => 'bra', 'BraA09t36680Z' => 'bra', 'BraA10t44471Z' => 'bra', 'C02p06760' => 'bna', 'C02p06890' => 'bna', 'C02p07010' => 'bna', 'C03p07660' => 'bna', 'C05p10300' => 'bna', 'C06p38150' => 'bna', 'C07p36650' => 'bna', 'C08p15770' => 'bna', 'C09p12300' => 'bna', 'C09p62700' => 'bna', 'C09p75040' => 'bna', 'CAN.G13.1' => 'can', 'CAN.G138.4' => 'can', 'CAN.G44.6' => 'can', 'CAN.G473.19' => 'can', 'CANSAT01G0835' => 'cansat', 'CANSAT11G0246' => 'cansat', 'CANSAT11G1766' => 'cansat', 'CANSAT64G1954' => 'cansat', 'CARHR013330' => 'chi', 'CARHR060530' => 'chi', 'CARHR075300' => 'chi', 'CARHR105120' => 'chi', 'CARHR148910' => 'chi', 'CARHR198830' => 'chi', 'Carub.0001s1275' => 'cru', 'Carub.0002s1437' => 'cru', 'Carub.0003s0044' => 'cru', 'Carub.0003s2787' => 'cru', 'Carub.0005s0597' => 'cru', 'Carub.0006s1266' => 'cru', 'Ca_06935_v3' => 'car', 'Ca_13559_v3' => 'car', 'Ca_16941_v3' => 'car', 'Ca_16960_v3' => 'car', 'Ca_17775_v3' => 'car', 'Ca_30464_v3' => 'car', 'Cc06_g08160' => 'ccan', 'Cc07_g01520' => 'ccan', 'Cc11_g15810' => 'ccan', 'CDE02G2840' => 'cde', 'CDE03G0093' => 'cde', 'CDE04G2127' => 'cde', 'CDE07G1857' => 'cde', 'CDE09G1246' => 'cde', 'Cfa003412' => 'cfa', 'Cfa007341' => 'cfa', 'Cfa009220' => 'cfa', 'Ciclev10008737m.g' => 'ccl', 'Ciclev10015565m.g' => 'ccl', 'Ciclev10031761m.g' => 'ccl', 'CiPaw.03G045300' => 'cil', 'CiPaw.03G247200' => 'cil', 'CiPaw.04G029500' => 'cil', 'CiPaw.04G174000' => 'cil', 'CiPaw.05G181200' => 'cil', 'CiPaw.06G067100' => 'cil', 'ClCG05G025800' => 'cla', 'ClCG06G011400' => 'cla', 'ClCG09G019360' => 'cla', 'COL.COLO4_04827' => 'col', 'COL.COLO4_29170' => 'col', 'COL.COLO4_35131' => 'col', 'COL.COLO4_35132' => 'col', 'Cpa.g.sc33.32' => 'cpa', 'Cpa.g.sc46.29' => 'cpa', 'Cpa.g.sc796.1' => 'cpa', 'CsaV3_1G030420' => 'csa', 'CsaV3_5G027050' => 'csa', 'CsaV3_5G031040' => 'csa', 'CsaV3_UNG023130' => 'csa', 'CSS0007726' => 'camsi', 'CSS0016433' => 'camsi', 'CSS0017656' => 'camsi', 'CSS0025364' => 'camsi', 'CSS0027582' => 'camsi', 'CSS0047288' => 'camsi', 'CSS0049950' => 'camsi', 'DCAR_003843' => 'dca', 'DCAR_007052' => 'dca', 'DCAR_020884' => 'dca', 'DCAR_021730' => 'dca', 'DCAR_024423' => 'dca', 'DCAR_026509' => 'dca', 'DCAR_031158' => 'dca', 'Dinv14728' => 'din', 'Dinv15219' => 'din', 'Dinv25728' => 'din', 'Dinv33428' => 'din', 'Dinv36489' => 'din', 'Dinv41486' => 'din', 'Duzib147G0469' => 'dzi', 'Duzib168G0060' => 'dzi', 'Duzib187G1215' => 'dzi', 'Duzib248G0692' => 'dzi', 'Duzib251G0767' => 'dzi', 'Duzib264G0446' => 'dzi', 'Duzib268G0691' => 'dzi', 'ECA232G4767' => 'eca', 'ECA233G2838' => 'eca', 'ECA234G0391' => 'eca', 'ECA234G0857' => 'eca', 'ECA236G1593' => 'eca', 'ECA238G0565' => 'eca', 'ECA246G1027' => 'eca', 'ECA246G3223' => 'eca', 'ECA246G3470' => 'eca', 'EL10Ac6g13829' => 'bvu', 'EL10Ac6g14093' => 'bvu', 'EL10Ac8g18707' => 'bvu', 'Eucgr.C01369' => 'egr', 'Eucgr.H02492' => 'egr', 'Eucgr.I01733' => 'egr', 'Eucgr.J02255' => 'egr', 'Eucgr.J02257' => 'egr', 'Eucgr.J02258' => 'egr', 'FAN02G1601' => 'fan', 'FAN03G1586' => 'fan', 'FAN03G2986' => 'fan', 'FAN05G4837' => 'fan', 'FAN06G0146' => 'fan', 'FAN07G0858' => 'fan', 'FAN09G3179' => 'fan', 'FAN10G0669' => 'fan', 'FAN12G2358' => 'fan', 'FAN14G4198' => 'fan', 'FAN14G5112' => 'fan', 'FAN17G0342' => 'fan', 'FAN19G0342' => 'fan', 'FAN19G0962' => 'fan', 'FAN19G1101' => 'fan', 'FAN19G1872' => 'fan', 'FAN22G0356' => 'fan', 'FAN23G0744' => 'fan', 'FAN23G1914' => 'fan', 'FAN26G0032' => 'fan', 'FAN28G0625' => 'fan', 'FvH4_1g02710' => 'fve', 'FvH4_1g02720' => 'fve', 'FvH4_4g25670' => 'fve', 'FvH4_6g51700' => 'fve', 'FvH4_7g20170' => 'fve', 'Glyma.05G175000' => 'gma', 'Glyma.08G132300' => 'gma', 'Glyma.11G243000' => 'gma', 'Glyma.13G158900' => 'gma', 'Glyma.17G112400' => 'gma', 'Glyma.18G014100' => 'gma', 'Glyma.19G003100' => 'gma', 'Glyma.19G056500' => 'gma', 'Gohir.A01G158900' => 'ghi', 'Gohir.A05G312600' => 'ghi', 'Gohir.A05G354900' => 'ghi', 'Gohir.A07G037200' => 'ghi', 'Gohir.A09G030000' => 'ghi', 'Gohir.A12G145200' => 'ghi', 'Gohir.D01G151500' => 'ghi', 'Gohir.D04G058300' => 'ghi', 'Gohir.D05G314100' => 'ghi', 'Gohir.D07G041400' => 'ghi', 'Gohir.D09G029700' => 'ghi', 'Gohir.D12G149700' => 'ghi', 'Gorai.001G043800' => 'gra', 'Gorai.002G187800' => 'gra', 'Gorai.006G034700' => 'gra', 'Gorai.008G161200' => 'gra', 'Gorai.009G335700' => 'gra', 'Gorai.012G065000' => 'gra', 'GSVIVG01000535001' => 'vvi', 'GSVIVG01015572001' => 'vvi', 'GSVIVG01032386001' => 'vvi', 'HanXRQChr05g0138531' => 'han', 'HanXRQChr06g0174391' => 'han', 'HanXRQChr07g0199021' => 'han', 'HanXRQChr08g0208211' => 'han', 'HanXRQChr09g0255471' => 'han', 'HanXRQChr10g0315791' => 'han', 'HanXRQChr12g0371991' => 'han', 'HanXRQChr15g0475251' => 'han', 'HanXRQChr17g0540001' => 'han', 'HanXRQChr17g0548631' => 'han', 'HanXRQChr17g0569561' => 'han', 'Haze_12256' => 'cav', 'Haze_14756' => 'cav', 'Haze_25528' => 'cav', 'Hma1.2p1_0079F.1_g041020' => 'hma', 'Hma1.2p1_0818F.1_g223260' => 'hma', 'Hma1.2p1_1747F.1_g300530' => 'hma', 'HPP92_004607' => 'vpl', 'HPP92_004608' => 'vpl', 'HPP92_006181' => 'vpl', 'HPP92_012192' => 'vpl', 'HPP92_015680' => 'vpl', 'HPP92_020249' => 'vpl', 'HPP92_021376' => 'vpl', 'HPP92_024275' => 'vpl', 'Hund06031' => 'sun', 'Hund25391' => 'sun', 'Lalb_Chr07g0185371' => 'lal', 'Lalb_Chr07g0185381' => 'lal', 'Lalb_Chr12g0204011' => 'lal', 'Lalb_Chr13g0301671' => 'lal', 'Lalb_Chr14g0362851' => 'lal', 'Lalb_Chr24g0403581' => 'lal', 'Lj1g0000233' => 'lja', 'Lj2g0018120' => 'lja', 'Lj3C621T0' => 'lonja', 'Lj3P1059T14' => 'lonja', 'Lj3P611T9' => 'lonja', 'Lj3P614T13' => 'lonja', 'Lj3P615T5' => 'lonja', 'Lj4g0012315' => 'lja', 'Lj4g0026182' => 'lja', 'Lj6P813T16' => 'lonja', 'Lj7C427T7' => 'lonja', 'Lj7C427T8' => 'lonja', 'Lj7P600T41' => 'lonja', 'Lju41C42G17' => 'lonja', 'Lsat_1_v5_gn_0_47300' => 'lsa', 'Lsat_1_v5_gn_2_91280' => 'lsa', 'Lsat_1_v5_gn_3_30561' => 'lsa', 'Lsat_1_v5_gn_4_184321' => 'lsa', 'Lsat_1_v5_gn_4_4041' => 'lsa', 'Lsat_1_v5_gn_5_92000' => 'lsa', 'Lsat_1_v5_gn_8_152940' => 'lsa', 'Lsat_1_v5_gn_8_62401' => 'lsa', 'Manes.06G055900' => 'mes', 'Manes.12G022200' => 'mes', 'Manes.13G023300' => 'mes', 'Manes.14G115000' => 'mes', 'Manes.15G151700' => 'mes', 'Manes.17G111300' => 'mes', 'Mapoly0226s0009' => 'mpo', 'MBI02_g25363_MAGBIO' => 'mbi', 'MBI06_g00027_MAGBIO' => 'mbi', 'MBI10_g13034_MAGBIO' => 'mbi', 'MD09G1023400' => 'mdo', 'MD13G1100100' => 'mdo', 'MD15G1169200' => 'mdo', 'MD16G1101100' => 'mdo', 'MD17G1022900' => 'mdo', 'Medtr3g096150' => 'mtr', 'Medtr4g115070' => 'mtr', 'Medtr7g033325' => 'mtr', 'Medtr8g089840' => 'mtr', 'MELO3C010319.2' => 'cme', 'MELO3C011944.2' => 'cme', 'MELO3C021589.2' => 'cme', 'Migut.E00207' => 'egut', 'Migut.H00067' => 'egut', 'Migut.K00433' => 'egut', 'Migut.K00606' => 'egut', 'Migut.K01410' => 'egut', 'MSTRG.13347' => 'ama', 'MSTRG.24045' => 'ama', 'MSTRG.2428' => 'ama', 'MSTRG.26410' => 'ama', 'MSTRG.3139' => 'ama', 'MSTRG.3286' => 'ama', 'MSTRG.563' => 'ama', 'MSTRG.7941' => 'ama', 'Nitab4.5_0000028g0060' => 'nta', 'Nitab4.5_0000065g0260' => 'nta', 'Nitab4.5_0000112g0060' => 'nta', 'Nitab4.5_0000489g0120' => 'nta', 'Nitab4.5_0001776g0050' => 'nta', 'Nitab4.5_0001854g0010' => 'nta', 'Nitab4.5_0001860g0020' => 'nta', 'Nitab4.5_0004352g0010' => 'nta', 'Nitab4.5_0008716g0020' => 'nta', 'Nitab4.5_0008922g0010' => 'nta', 'Nn3g16693' => 'nnu', 'Nn4g22596' => 'nnu', 'Nn7g37639' => 'nnu', 'Oeu001701.1' => 'oeu', 'Oeu018149.1' => 'oeu', 'Oeu026220.1' => 'oeu', 'Oeu038635.1' => 'oeu', 'Oeu049176.1' => 'oeu', 'Oeu056706.1' => 'oeu', 'Oeu056937.1' => 'oeu', 'Oeu057540.1' => 'oeu', 'Os02g0594900' => 'osa', 'Os02g0595100' => 'osa', 'Os04g0477500' => 'osa', 'Os12g0611900' => 'osa', 'Peaxi162Scf00076g00020' => 'pax', 'Peaxi162Scf00128g00217' => 'pax', 'Peaxi162Scf00129g01640' => 'pax', 'Peaxi162Scf00669g00007' => 'pax', 'Peaxi162Scf00700g00421' => 'pax', 'Peaxi162Scf00801g00038' => 'pax', 'Peaxi162Scf00891g00025' => 'pax', 'PGR083G0909' => 'pgr', 'PGR119G1005' => 'pgr', 'PGR142G2236' => 'pgr', 'PGR142G3388' => 'pgr', 'PGSC0003DMG400004514' => 'stu', 'PGSC0003DMG400012635' => 'stu', 'PGSC0003DMG400015730' => 'stu', 'PGSC0003DMG400018611' => 'stu', 'PGSC0003DMG400030897' => 'stu', 'Phvul.001G254800' => 'pvu', 'Phvul.002G260100' => 'pvu', 'Phvul.003G167600' => 'pvu', 'Phvul.004G005100' => 'pvu', 'Potri.001G343600' => 'ptr', 'Potri.006G066700' => 'ptr', 'Potri.008G186000' => 'ptr', 'Potri.010G046900' => 'ptr', 'Potri.018G127900' => 'ptr', 'Pp3c20_17750' => 'ppa', 'Pp3c24_4380' => 'ppa', 'Prupe.1G245800' => 'ppe', 'Prupe.3G293400' => 'ppe', 'Prupe.7G247400' => 'ppe', 'Psat0s145g0120' => 'psa', 'Psat0s595g0040' => 'psa', 'Psat0s595g0120' => 'psa', 'Psat3g175040' => 'psa', 'Psat7g058120' => 'psa', 'PSO017G0428' => 'pso', 'PSO063G7510' => 'pso', 'PSO067G0046' => 'pso', 'PSO478G1073' => 'pso', 'PSO675G3677' => 'pso', 'PSO675G6558' => 'pso', 'PSO675G7520' => 'pso', 'PSO675G8959' => 'pso', 'QL02p074089' => 'qlo', 'QL02p089614' => 'qlo', 'QL03p057736' => 'qlo', 'RcHm_v2.0_Chr1g0364131' => 'rch', 'RcHm_v2.0_Chr2g0087801' => 'rch', 'RcHm_v2.0_Chr2g0087821' => 'rch', 'RcHm_v2.0_Chr2g0173231' => 'rch', 'RcHm_v2.0_Chr4g0433111' => 'rch', 'Rhsim03G0250300' => 'rsi', 'Rhsim08G0048400' => 'rsi', 'Rhsim10G0014800' => 'rsi', 'Rhsim12G0040100' => 'rsi', 'Rhsim12G0109700' => 'rsi', 'Sabra06G0049600' => 'sbr', 'Sabra08G0141000' => 'sbr', 'Sabra10G0021400' => 'sbr', 'Sabra16G0222900' => 'sbr', 'Sabra18G0108600' => 'sbr', 'SalBow1G0433' => 'sbo', 'SalBow1G2038' => 'sbo', 'SalBow1G5003' => 'sbo', 'SalBow7G1197' => 'sbo', 'SalBow8G3506' => 'sbo', 'Sc03g0007300' => 'sci', 'Sc11g0000950' => 'sci', 'Sc14g0008750' => 'sci', 'Sc18g0000420' => 'sci', 'Sed0006754' => 'sed', 'Sed0008741' => 'sed', 'Sed0017172' => 'sed', 'Sed0018925' => 'sed', 'Sed0023326' => 'sed', 'Sed0025909' => 'sed', 'SEGI_05333' => 'sgi', 'SEGI_10362' => 'sgi', 'SEGI_13380' => 'sgi', 'SEGI_24306' => 'sgi', 'SEGI_29077' => 'sgi', 'SEGI_29095' => 'sgi', 'SEGI_36534' => 'sgi', 'SEGI_37506' => 'sgi', 'SEGI_38321' => 'sgi', 'SGA_v2.0_scaffold307G48031' => 'sas', 'SGA_v2.0_scaffold47G17507' => 'sas', 'SGA_v2.0_scaffold63G21736' => 'sas', 'SGA_v2.0_scaffold87G27070' => 'sas', 'SHI17794' => 'shi', 'SHI28851' => 'shi', 'SMO165G0155' => 'smo', 'SMO340G0217' => 'smo', 'SMO367G1210' => 'smo', 'Solyc02g093430.3' => 'sly', 'Solyc05g013580.4' => 'sly', 'Solyc07g008030.3' => 'sly', 'Solyc12g035470.2' => 'sly', 'Sopen02g038020' => 'spe', 'Sopen05g008490' => 'spe', 'Sopen07g003910' => 'spe', 'Sopen12g015240' => 'spe', 'Sp1g11550' => 'spa', 'Sp2g16710' => 'spa', 'Sp3g00430' => 'spa', 'Sp3g26780' => 'spa', 'Sp5g22900' => 'spa', 'Sp6g29530' => 'spa', 'TAR371G0794' => 'tar', 'TAR374G0164' => 'tar', 'TAR622G0165' => 'tar', 'TAR626G0929' => 'tar', 'TAR629G2155' => 'tar', 'THA.LOC104805282' => 'tha', 'THA.LOC104805363' => 'tha', 'THA.LOC104808968' => 'tha', 'THA.LOC104821093' => 'tha', 'THA.LOC104823953' => 'tha', 'THA.LOC104825562' => 'tha', 'THA.LOC104825665' => 'tha', 'Thecc.02G261400' => 'tca', 'Thecc.04G019200' => 'tca', 'Thecc.09G130400' => 'tca', 'Thhalv10004374m.g' => 'esa', 'Thhalv10007850m.g' => 'esa', 'Thhalv10013782m.g' => 'esa', 'Thhalv10018686m.g' => 'esa', 'Thhalv10020899m.g' => 'esa', 'Thhalv10022755m.g' => 'esa', 'TPR.G23851' => 'tpr', 'TPR.G26500' => 'tpr', 'TPR.G27267' => 'tpr', 'TPR.G32001' => 'tpr', 'TPR.G6251' => 'tpr', 'TPR.G8167' => 'tpr', 'TWI12G1330' => 'twi', 'TWI18G1239' => 'twi', 'TWI34G0979' => 'twi', 'TWI36G0670' => 'twi', 'TWI36G0707' => 'twi', 'TWI56G0233' => 'twi', 'TWI75G1809' => 'twi', 'unitig_21.g20874' => 'ugi', 'unitig_26.g10343' => 'ugi', 'unitig_46.g18392' => 'ugi', 'unitig_52.g17178' => 'ugi', 'unitig_8.g2934' => 'ugi', 'vmacro01122' => 'vma', 'vmacro05875' => 'vma', 'vmacro06147' => 'vma', 'vmacro16191' => 'vma', 'vmacro18293' => 'vma', 'VMungo0251G3707' => 'vmu', 'VMungo0464G1521' => 'vmu', 'VMungo1215G0205' => 'vmu', 'VMungo1383G2484' => 'vmu', 'Zm00001eb079610' => 'zma', 'Zm00001eb135990' => 'zma', 'Zm00001eb183710' => 'zma', 'Zm00001eb246020' => 'zma' ), 'gf_id' => 'HOM05D001124', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001124' ), 'data_identifier' => 'HOM05D001124', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001124', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '548', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02520' => 'bna', 'A03p06630' => 'bna', 'A05p44460' => 'bna', 'A06p08710' => 'bna', 'A06p41090' => 'bna', 'A07p32320' => 'bna', 'A08p32520' => 'bna', 'A09p10360' => 'bna', 'A10p24080' => 'bna', 'Aa31LG11G15250' => 'aar', 'Aa31LG1G1800' => 'aar', 'Aa31LG2G5120' => 'aar', 'Aa31LG2G6070' => 'aar', 'Aa31LG5G10770' => 'aar', 'Aa31sc61G90' => 'aar', 'Actinidia01352' => 'ach', 'Actinidia05983' => 'ach', 'Actinidia08133' => 'ach', 'Actinidia15101' => 'ach', 'Actinidia26379' => 'ach', 'Actinidia35778' => 'ach', 'Actinidia36123' => 'ach', 'Actinidia37436' => 'ach', 'Actinidia38730' => 'ach', 'Ah.02g128210' => 'amhyb', 'Ah.03g132990' => 'amhyb', 'Ah.14g079410' => 'amhyb', 'AL1G24640' => 'aly', 'AL2G26680' => 'aly', 'AL3G10530' => 'aly', 'AL3G45230' => 'aly', 'AL5G15230' => 'aly', 'AL5G16960' => 'aly', 'AL6G25210' => 'aly', 'Aqoxy2G00441' => 'aox', 'Aqoxy3G01236' => 'aox', 'Aqoxy5G03746' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3RQ047' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C7GMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9C8JER' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MBL6KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YXCZ83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZANX40' => 'arhy', 'AT1G12990' => 'ath', 'AT1G67880' => 'ath', 'AT2G13290' => 'ath', 'AT3G01620' => 'ath', 'AT3G26445' => 'ath', 'AT3G27540' => 'ath', 'AT5G14480' => 'ath', 'ATR0824G026' => 'atr', 'ATR1098G019' => 'atr', 'Atru.chr11.2145' => 'acertr', 'Atru.chr2.3636' => 'acertr', 'Atru.chr2.3644' => 'acertr', 'Atru.chr6.2422' => 'acertr', 'Atru.chr7.1112' => 'acertr', 'AUR62005469' => 'cqu', 'AUR62011166' => 'cqu', 'AUR62013319' => 'cqu', 'AUR62024273' => 'cqu', 'AUR62028420' => 'cqu', 'AUR62041942' => 'cqu', 'BcaB01g04969' => 'bca', 'BcaB01g06371' => 'bca', 'BcaB02g11494' => 'bca', 'BcaB03g15382' => 'bca', 'BcaB08g36994' => 'bca', 'BcaC03g13477' => 'bca', 'BcaC03g13478' => 'bca', 'BcaC03g13480' => 'bca', 'BcaC03g13481' => 'bca', 'BcaC03g13486' => 'bca', 'BcaC04g19031' => 'bca', 'BcaC04g23085' => 'bca', 'BcaC05g25094' => 'bca', 'BcaC05g25096' => 'bca', 'BcaC05g25138' => 'bca', 'BcaC05g30416' => 'bca', 'BcaC05g30455' => 'bca', 'BcaC06g30979' => 'bca', 'BcaC06g33805' => 'bca', 'BcaC08g46021' => 'bca', 'BcaNung03154' => 'bca', 'BolC2t06623H' => 'bol', 'BolC2t06632H' => 'bol', 'BolC2t06635H' => 'bol', 'BolC2t06638H' => 'bol', 'BolC3t13266H' => 'bol', 'BolC5t29776H' => 'bol', 'BolC6t38912H' => 'bol', 'BolC7t44183H' => 'bol', 'BolC9t54123H' => 'bol', 'BolC9t59107H' => 'bol', 'BraA02t05221Z' => 'bra', 'BraA03t09996Z' => 'bra', 'BraA05t23210Z' => 'bra', 'BraA06t24068Z' => 'bra', 'BraA06t27032Z' => 'bra', 'BraA08t35176Z' => 'bra', 'BraA09t36680Z' => 'bra', 'BraA10t44471Z' => 'bra', 'C02p06760' => 'bna', 'C02p06890' => 'bna', 'C02p07010' => 'bna', 'C03p07660' => 'bna', 'C05p10300' => 'bna', 'C06p38150' => 'bna', 'C07p36650' => 'bna', 'C08p15770' => 'bna', 'C09p12300' => 'bna', 'C09p62700' => 'bna', 'C09p75040' => 'bna', 'CAN.G13.1' => 'can', 'CAN.G138.4' => 'can', 'CAN.G44.6' => 'can', 'CAN.G473.19' => 'can', 'CANSAT01G0835' => 'cansat', 'CANSAT11G0246' => 'cansat', 'CANSAT11G1766' => 'cansat', 'CANSAT64G1954' => 'cansat', 'CARHR013330' => 'chi', 'CARHR060530' => 'chi', 'CARHR075300' => 'chi', 'CARHR105120' => 'chi', 'CARHR148910' => 'chi', 'CARHR198830' => 'chi', 'Carub.0001s1275' => 'cru', 'Carub.0002s1437' => 'cru', 'Carub.0003s0044' => 'cru', 'Carub.0003s2787' => 'cru', 'Carub.0005s0597' => 'cru', 'Carub.0006s1266' => 'cru', 'Ca_06935_v3' => 'car', 'Ca_13559_v3' => 'car', 'Ca_16941_v3' => 'car', 'Ca_16960_v3' => 'car', 'Ca_17775_v3' => 'car', 'Ca_30464_v3' => 'car', 'Cc06_g08160' => 'ccan', 'Cc07_g01520' => 'ccan', 'Cc11_g15810' => 'ccan', 'CDE02G2840' => 'cde', 'CDE03G0093' => 'cde', 'CDE04G2127' => 'cde', 'CDE07G1857' => 'cde', 'CDE09G1246' => 'cde', 'Cfa003412' => 'cfa', 'Cfa007341' => 'cfa', 'Cfa009220' => 'cfa', 'Ciclev10008737m.g' => 'ccl', 'Ciclev10015565m.g' => 'ccl', 'Ciclev10031761m.g' => 'ccl', 'CiPaw.03G045300' => 'cil', 'CiPaw.03G247200' => 'cil', 'CiPaw.04G029500' => 'cil', 'CiPaw.04G174000' => 'cil', 'CiPaw.05G181200' => 'cil', 'CiPaw.06G067100' => 'cil', 'ClCG05G025800' => 'cla', 'ClCG06G011400' => 'cla', 'ClCG09G019360' => 'cla', 'COL.COLO4_04827' => 'col', 'COL.COLO4_29170' => 'col', 'COL.COLO4_35131' => 'col', 'COL.COLO4_35132' => 'col', 'Cpa.g.sc33.32' => 'cpa', 'Cpa.g.sc46.29' => 'cpa', 'Cpa.g.sc796.1' => 'cpa', 'CsaV3_1G030420' => 'csa', 'CsaV3_5G027050' => 'csa', 'CsaV3_5G031040' => 'csa', 'CsaV3_UNG023130' => 'csa', 'CSS0007726' => 'camsi', 'CSS0016433' => 'camsi', 'CSS0017656' => 'camsi', 'CSS0025364' => 'camsi', 'CSS0027582' => 'camsi', 'CSS0047288' => 'camsi', 'CSS0049950' => 'camsi', 'DCAR_003843' => 'dca', 'DCAR_007052' => 'dca', 'DCAR_020884' => 'dca', 'DCAR_021730' => 'dca', 'DCAR_024423' => 'dca', 'DCAR_026509' => 'dca', 'DCAR_031158' => 'dca', 'Dinv14728' => 'din', 'Dinv15219' => 'din', 'Dinv25728' => 'din', 'Dinv33428' => 'din', 'Dinv36489' => 'din', 'Dinv41486' => 'din', 'Duzib147G0469' => 'dzi', 'Duzib168G0060' => 'dzi', 'Duzib187G1215' => 'dzi', 'Duzib248G0692' => 'dzi', 'Duzib251G0767' => 'dzi', 'Duzib264G0446' => 'dzi', 'Duzib268G0691' => 'dzi', 'ECA232G4767' => 'eca', 'ECA233G2838' => 'eca', 'ECA234G0391' => 'eca', 'ECA234G0857' => 'eca', 'ECA236G1593' => 'eca', 'ECA238G0565' => 'eca', 'ECA246G1027' => 'eca', 'ECA246G3223' => 'eca', 'ECA246G3470' => 'eca', 'EL10Ac6g13829' => 'bvu', 'EL10Ac6g14093' => 'bvu', 'EL10Ac8g18707' => 'bvu', 'Eucgr.C01369' => 'egr', 'Eucgr.H02492' => 'egr', 'Eucgr.I01733' => 'egr', 'Eucgr.J02255' => 'egr', 'Eucgr.J02257' => 'egr', 'Eucgr.J02258' => 'egr', 'FAN02G1601' => 'fan', 'FAN03G1586' => 'fan', 'FAN03G2986' => 'fan', 'FAN05G4837' => 'fan', 'FAN06G0146' => 'fan', 'FAN07G0858' => 'fan', 'FAN09G3179' => 'fan', 'FAN10G0669' => 'fan', 'FAN12G2358' => 'fan', 'FAN14G4198' => 'fan', 'FAN14G5112' => 'fan', 'FAN17G0342' => 'fan', 'FAN19G0342' => 'fan', 'FAN19G0962' => 'fan', 'FAN19G1101' => 'fan', 'FAN19G1872' => 'fan', 'FAN22G0356' => 'fan', 'FAN23G0744' => 'fan', 'FAN23G1914' => 'fan', 'FAN26G0032' => 'fan', 'FAN28G0625' => 'fan', 'FvH4_1g02710' => 'fve', 'FvH4_1g02720' => 'fve', 'FvH4_4g25670' => 'fve', 'FvH4_6g51700' => 'fve', 'FvH4_7g20170' => 'fve', 'Glyma.05G175000' => 'gma', 'Glyma.08G132300' => 'gma', 'Glyma.11G243000' => 'gma', 'Glyma.13G158900' => 'gma', 'Glyma.17G112400' => 'gma', 'Glyma.18G014100' => 'gma', 'Glyma.19G003100' => 'gma', 'Glyma.19G056500' => 'gma', 'Gohir.A01G158900' => 'ghi', 'Gohir.A05G312600' => 'ghi', 'Gohir.A05G354900' => 'ghi', 'Gohir.A07G037200' => 'ghi', 'Gohir.A09G030000' => 'ghi', 'Gohir.A12G145200' => 'ghi', 'Gohir.D01G151500' => 'ghi', 'Gohir.D04G058300' => 'ghi', 'Gohir.D05G314100' => 'ghi', 'Gohir.D07G041400' => 'ghi', 'Gohir.D09G029700' => 'ghi', 'Gohir.D12G149700' => 'ghi', 'Gorai.001G043800' => 'gra', 'Gorai.002G187800' => 'gra', 'Gorai.006G034700' => 'gra', 'Gorai.008G161200' => 'gra', 'Gorai.009G335700' => 'gra', 'Gorai.012G065000' => 'gra', 'GSVIVG01000535001' => 'vvi', 'GSVIVG01015572001' => 'vvi', 'GSVIVG01032386001' => 'vvi', 'HanXRQChr05g0138531' => 'han', 'HanXRQChr06g0174391' => 'han', 'HanXRQChr07g0199021' => 'han', 'HanXRQChr08g0208211' => 'han', 'HanXRQChr09g0255471' => 'han', 'HanXRQChr10g0315791' => 'han', 'HanXRQChr12g0371991' => 'han', 'HanXRQChr15g0475251' => 'han', 'HanXRQChr17g0540001' => 'han', 'HanXRQChr17g0548631' => 'han', 'HanXRQChr17g0569561' => 'han', 'Haze_12256' => 'cav', 'Haze_14756' => 'cav', 'Haze_25528' => 'cav', 'Hma1.2p1_0079F.1_g041020' => 'hma', 'Hma1.2p1_0818F.1_g223260' => 'hma', 'Hma1.2p1_1747F.1_g300530' => 'hma', 'HPP92_004607' => 'vpl', 'HPP92_004608' => 'vpl', 'HPP92_006181' => 'vpl', 'HPP92_012192' => 'vpl', 'HPP92_015680' => 'vpl', 'HPP92_020249' => 'vpl', 'HPP92_021376' => 'vpl', 'HPP92_024275' => 'vpl', 'Hund06031' => 'sun', 'Hund25391' => 'sun', 'Lalb_Chr07g0185371' => 'lal', 'Lalb_Chr07g0185381' => 'lal', 'Lalb_Chr12g0204011' => 'lal', 'Lalb_Chr13g0301671' => 'lal', 'Lalb_Chr14g0362851' => 'lal', 'Lalb_Chr24g0403581' => 'lal', 'Lj1g0000233' => 'lja', 'Lj2g0018120' => 'lja', 'Lj3C621T0' => 'lonja', 'Lj3P1059T14' => 'lonja', 'Lj3P611T9' => 'lonja', 'Lj3P614T13' => 'lonja', 'Lj3P615T5' => 'lonja', 'Lj4g0012315' => 'lja', 'Lj4g0026182' => 'lja', 'Lj6P813T16' => 'lonja', 'Lj7C427T7' => 'lonja', 'Lj7C427T8' => 'lonja', 'Lj7P600T41' => 'lonja', 'Lju41C42G17' => 'lonja', 'Lsat_1_v5_gn_0_47300' => 'lsa', 'Lsat_1_v5_gn_2_91280' => 'lsa', 'Lsat_1_v5_gn_3_30561' => 'lsa', 'Lsat_1_v5_gn_4_184321' => 'lsa', 'Lsat_1_v5_gn_4_4041' => 'lsa', 'Lsat_1_v5_gn_5_92000' => 'lsa', 'Lsat_1_v5_gn_8_152940' => 'lsa', 'Lsat_1_v5_gn_8_62401' => 'lsa', 'Manes.06G055900' => 'mes', 'Manes.12G022200' => 'mes', 'Manes.13G023300' => 'mes', 'Manes.14G115000' => 'mes', 'Manes.15G151700' => 'mes', 'Manes.17G111300' => 'mes', 'Mapoly0226s0009' => 'mpo', 'MBI02_g25363_MAGBIO' => 'mbi', 'MBI06_g00027_MAGBIO' => 'mbi', 'MBI10_g13034_MAGBIO' => 'mbi', 'MD09G1023400' => 'mdo', 'MD13G1100100' => 'mdo', 'MD15G1169200' => 'mdo', 'MD16G1101100' => 'mdo', 'MD17G1022900' => 'mdo', 'Medtr3g096150' => 'mtr', 'Medtr4g115070' => 'mtr', 'Medtr7g033325' => 'mtr', 'Medtr8g089840' => 'mtr', 'MELO3C010319.2' => 'cme', 'MELO3C011944.2' => 'cme', 'MELO3C021589.2' => 'cme', 'Migut.E00207' => 'egut', 'Migut.H00067' => 'egut', 'Migut.K00433' => 'egut', 'Migut.K00606' => 'egut', 'Migut.K01410' => 'egut', 'MSTRG.13347' => 'ama', 'MSTRG.24045' => 'ama', 'MSTRG.2428' => 'ama', 'MSTRG.26410' => 'ama', 'MSTRG.3139' => 'ama', 'MSTRG.3286' => 'ama', 'MSTRG.563' => 'ama', 'MSTRG.7941' => 'ama', 'Nitab4.5_0000028g0060' => 'nta', 'Nitab4.5_0000065g0260' => 'nta', 'Nitab4.5_0000112g0060' => 'nta', 'Nitab4.5_0000489g0120' => 'nta', 'Nitab4.5_0001776g0050' => 'nta', 'Nitab4.5_0001854g0010' => 'nta', 'Nitab4.5_0001860g0020' => 'nta', 'Nitab4.5_0004352g0010' => 'nta', 'Nitab4.5_0008716g0020' => 'nta', 'Nitab4.5_0008922g0010' => 'nta', 'Nn3g16693' => 'nnu', 'Nn4g22596' => 'nnu', 'Nn7g37639' => 'nnu', 'Oeu001701.1' => 'oeu', 'Oeu018149.1' => 'oeu', 'Oeu026220.1' => 'oeu', 'Oeu038635.1' => 'oeu', 'Oeu049176.1' => 'oeu', 'Oeu056706.1' => 'oeu', 'Oeu056937.1' => 'oeu', 'Oeu057540.1' => 'oeu', 'Os02g0594900' => 'osa', 'Os02g0595100' => 'osa', 'Os04g0477500' => 'osa', 'Os12g0611900' => 'osa', 'Peaxi162Scf00076g00020' => 'pax', 'Peaxi162Scf00128g00217' => 'pax', 'Peaxi162Scf00129g01640' => 'pax', 'Peaxi162Scf00669g00007' => 'pax', 'Peaxi162Scf00700g00421' => 'pax', 'Peaxi162Scf00801g00038' => 'pax', 'Peaxi162Scf00891g00025' => 'pax', 'PGR083G0909' => 'pgr', 'PGR119G1005' => 'pgr', 'PGR142G2236' => 'pgr', 'PGR142G3388' => 'pgr', 'PGSC0003DMG400004514' => 'stu', 'PGSC0003DMG400012635' => 'stu', 'PGSC0003DMG400015730' => 'stu', 'PGSC0003DMG400018611' => 'stu', 'PGSC0003DMG400030897' => 'stu', 'Phvul.001G254800' => 'pvu', 'Phvul.002G260100' => 'pvu', 'Phvul.003G167600' => 'pvu', 'Phvul.004G005100' => 'pvu', 'Potri.001G343600' => 'ptr', 'Potri.006G066700' => 'ptr', 'Potri.008G186000' => 'ptr', 'Potri.010G046900' => 'ptr', 'Potri.018G127900' => 'ptr', 'Pp3c20_17750' => 'ppa', 'Pp3c24_4380' => 'ppa', 'Prupe.1G245800' => 'ppe', 'Prupe.3G293400' => 'ppe', 'Prupe.7G247400' => 'ppe', 'Psat0s145g0120' => 'psa', 'Psat0s595g0040' => 'psa', 'Psat0s595g0120' => 'psa', 'Psat3g175040' => 'psa', 'Psat7g058120' => 'psa', 'PSO017G0428' => 'pso', 'PSO063G7510' => 'pso', 'PSO067G0046' => 'pso', 'PSO478G1073' => 'pso', 'PSO675G3677' => 'pso', 'PSO675G6558' => 'pso', 'PSO675G7520' => 'pso', 'PSO675G8959' => 'pso', 'QL02p074089' => 'qlo', 'QL02p089614' => 'qlo', 'QL03p057736' => 'qlo', 'RcHm_v2.0_Chr1g0364131' => 'rch', 'RcHm_v2.0_Chr2g0087801' => 'rch', 'RcHm_v2.0_Chr2g0087821' => 'rch', 'RcHm_v2.0_Chr2g0173231' => 'rch', 'RcHm_v2.0_Chr4g0433111' => 'rch', 'Rhsim03G0250300' => 'rsi', 'Rhsim08G0048400' => 'rsi', 'Rhsim10G0014800' => 'rsi', 'Rhsim12G0040100' => 'rsi', 'Rhsim12G0109700' => 'rsi', 'Sabra06G0049600' => 'sbr', 'Sabra08G0141000' => 'sbr', 'Sabra10G0021400' => 'sbr', 'Sabra16G0222900' => 'sbr', 'Sabra18G0108600' => 'sbr', 'SalBow1G0433' => 'sbo', 'SalBow1G2038' => 'sbo', 'SalBow1G5003' => 'sbo', 'SalBow7G1197' => 'sbo', 'SalBow8G3506' => 'sbo', 'Sc03g0007300' => 'sci', 'Sc11g0000950' => 'sci', 'Sc14g0008750' => 'sci', 'Sc18g0000420' => 'sci', 'Sed0006754' => 'sed', 'Sed0008741' => 'sed', 'Sed0017172' => 'sed', 'Sed0018925' => 'sed', 'Sed0023326' => 'sed', 'Sed0025909' => 'sed', 'SEGI_05333' => 'sgi', 'SEGI_10362' => 'sgi', 'SEGI_13380' => 'sgi', 'SEGI_24306' => 'sgi', 'SEGI_29077' => 'sgi', 'SEGI_29095' => 'sgi', 'SEGI_36534' => 'sgi', 'SEGI_37506' => 'sgi', 'SEGI_38321' => 'sgi', 'SGA_v2.0_scaffold307G48031' => 'sas', 'SGA_v2.0_scaffold47G17507' => 'sas', 'SGA_v2.0_scaffold63G21736' => 'sas', 'SGA_v2.0_scaffold87G27070' => 'sas', 'SHI17794' => 'shi', 'SHI28851' => 'shi', 'SMO165G0155' => 'smo', 'SMO340G0217' => 'smo', 'SMO367G1210' => 'smo', 'Solyc02g093430.3' => 'sly', 'Solyc05g013580.4' => 'sly', 'Solyc07g008030.3' => 'sly', 'Solyc12g035470.2' => 'sly', 'Sopen02g038020' => 'spe', 'Sopen05g008490' => 'spe', 'Sopen07g003910' => 'spe', 'Sopen12g015240' => 'spe', 'Sp1g11550' => 'spa', 'Sp2g16710' => 'spa', 'Sp3g00430' => 'spa', 'Sp3g26780' => 'spa', 'Sp5g22900' => 'spa', 'Sp6g29530' => 'spa', 'TAR371G0794' => 'tar', 'TAR374G0164' => 'tar', 'TAR622G0165' => 'tar', 'TAR626G0929' => 'tar', 'TAR629G2155' => 'tar', 'THA.LOC104805282' => 'tha', 'THA.LOC104805363' => 'tha', 'THA.LOC104808968' => 'tha', 'THA.LOC104821093' => 'tha', 'THA.LOC104823953' => 'tha', 'THA.LOC104825562' => 'tha', 'THA.LOC104825665' => 'tha', 'Thecc.02G261400' => 'tca', 'Thecc.04G019200' => 'tca', 'Thecc.09G130400' => 'tca', 'Thhalv10004374m.g' => 'esa', 'Thhalv10007850m.g' => 'esa', 'Thhalv10013782m.g' => 'esa', 'Thhalv10018686m.g' => 'esa', 'Thhalv10020899m.g' => 'esa', 'Thhalv10022755m.g' => 'esa', 'TPR.G23851' => 'tpr', 'TPR.G26500' => 'tpr', 'TPR.G27267' => 'tpr', 'TPR.G32001' => 'tpr', 'TPR.G6251' => 'tpr', 'TPR.G8167' => 'tpr', 'TWI12G1330' => 'twi', 'TWI18G1239' => 'twi', 'TWI34G0979' => 'twi', 'TWI36G0670' => 'twi', 'TWI36G0707' => 'twi', 'TWI56G0233' => 'twi', 'TWI75G1809' => 'twi', 'unitig_21.g20874' => 'ugi', 'unitig_26.g10343' => 'ugi', 'unitig_46.g18392' => 'ugi', 'unitig_52.g17178' => 'ugi', 'unitig_8.g2934' => 'ugi', 'vmacro01122' => 'vma', 'vmacro05875' => 'vma', 'vmacro06147' => 'vma', 'vmacro16191' => 'vma', 'vmacro18293' => 'vma', 'VMungo0251G3707' => 'vmu', 'VMungo0464G1521' => 'vmu', 'VMungo1215G0205' => 'vmu', 'VMungo1383G2484' => 'vmu', 'Zm00001eb079610' => 'zma', 'Zm00001eb135990' => 'zma', 'Zm00001eb183710' => 'zma', 'Zm00001eb246020' => 'zma' ) $gf_id = 'HOM05D001124' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001124' ) $data_identifier = 'HOM05D001124' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 6, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 7, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 21, 'bol' => (int) 10, 'bra' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 6, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 9, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 21, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 8, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 10, 'lsa' => (int) 8, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 8, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 9, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb246020' $species_info = array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ) $local_species = 'cla' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001124', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '548', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02520' => 'bna', 'A03p06630' => 'bna', 'A05p44460' => 'bna', 'A06p08710' => 'bna', 'A06p41090' => 'bna', 'A07p32320' => 'bna', 'A08p32520' => 'bna', 'A09p10360' => 'bna', 'A10p24080' => 'bna', 'Aa31LG11G15250' => 'aar', 'Aa31LG1G1800' => 'aar', 'Aa31LG2G5120' => 'aar', 'Aa31LG2G6070' => 'aar', 'Aa31LG5G10770' => 'aar', 'Aa31sc61G90' => 'aar', 'Actinidia01352' => 'ach', 'Actinidia05983' => 'ach', 'Actinidia08133' => 'ach', 'Actinidia15101' => 'ach', 'Actinidia26379' => 'ach', 'Actinidia35778' => 'ach', 'Actinidia36123' => 'ach', 'Actinidia37436' => 'ach', 'Actinidia38730' => 'ach', 'Ah.02g128210' => 'amhyb', 'Ah.03g132990' => 'amhyb', 'Ah.14g079410' => 'amhyb', 'AL1G24640' => 'aly', 'AL2G26680' => 'aly', 'AL3G10530' => 'aly', 'AL3G45230' => 'aly', 'AL5G15230' => 'aly', 'AL5G16960' => 'aly', 'AL6G25210' => 'aly', 'Aqoxy2G00441' => 'aox', 'Aqoxy3G01236' => 'aox', 'Aqoxy5G03746' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3RQ047' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C7GMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9C8JER' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MBL6KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YXCZ83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZANX40' => 'arhy', 'AT1G12990' => 'ath', 'AT1G67880' => 'ath', 'AT2G13290' => 'ath', 'AT3G01620' => 'ath', 'AT3G26445' => 'ath', 'AT3G27540' => 'ath', 'AT5G14480' => 'ath', 'ATR0824G026' => 'atr', 'ATR1098G019' => 'atr', 'Atru.chr11.2145' => 'acertr', 'Atru.chr2.3636' => 'acertr', 'Atru.chr2.3644' => 'acertr', 'Atru.chr6.2422' => 'acertr', 'Atru.chr7.1112' => 'acertr', 'AUR62005469' => 'cqu', 'AUR62011166' => 'cqu', 'AUR62013319' => 'cqu', 'AUR62024273' => 'cqu', 'AUR62028420' => 'cqu', 'AUR62041942' => 'cqu', 'BcaB01g04969' => 'bca', 'BcaB01g06371' => 'bca', 'BcaB02g11494' => 'bca', 'BcaB03g15382' => 'bca', 'BcaB08g36994' => 'bca', 'BcaC03g13477' => 'bca', 'BcaC03g13478' => 'bca', 'BcaC03g13480' => 'bca', 'BcaC03g13481' => 'bca', 'BcaC03g13486' => 'bca', 'BcaC04g19031' => 'bca', 'BcaC04g23085' => 'bca', 'BcaC05g25094' => 'bca', 'BcaC05g25096' => 'bca', 'BcaC05g25138' => 'bca', 'BcaC05g30416' => 'bca', 'BcaC05g30455' => 'bca', 'BcaC06g30979' => 'bca', 'BcaC06g33805' => 'bca', 'BcaC08g46021' => 'bca', 'BcaNung03154' => 'bca', 'BolC2t06623H' => 'bol', 'BolC2t06632H' => 'bol', 'BolC2t06635H' => 'bol', 'BolC2t06638H' => 'bol', 'BolC3t13266H' => 'bol', 'BolC5t29776H' => 'bol', 'BolC6t38912H' => 'bol', 'BolC7t44183H' => 'bol', 'BolC9t54123H' => 'bol', 'BolC9t59107H' => 'bol', 'BraA02t05221Z' => 'bra', 'BraA03t09996Z' => 'bra', 'BraA05t23210Z' => 'bra', 'BraA06t24068Z' => 'bra', 'BraA06t27032Z' => 'bra', 'BraA08t35176Z' => 'bra', 'BraA09t36680Z' => 'bra', 'BraA10t44471Z' => 'bra', 'C02p06760' => 'bna', 'C02p06890' => 'bna', 'C02p07010' => 'bna', 'C03p07660' => 'bna', 'C05p10300' => 'bna', 'C06p38150' => 'bna', 'C07p36650' => 'bna', 'C08p15770' => 'bna', 'C09p12300' => 'bna', 'C09p62700' => 'bna', 'C09p75040' => 'bna', 'CAN.G13.1' => 'can', 'CAN.G138.4' => 'can', 'CAN.G44.6' => 'can', 'CAN.G473.19' => 'can', 'CANSAT01G0835' => 'cansat', 'CANSAT11G0246' => 'cansat', 'CANSAT11G1766' => 'cansat', 'CANSAT64G1954' => 'cansat', 'CARHR013330' => 'chi', 'CARHR060530' => 'chi', 'CARHR075300' => 'chi', 'CARHR105120' => 'chi', 'CARHR148910' => 'chi', 'CARHR198830' => 'chi', 'Carub.0001s1275' => 'cru', 'Carub.0002s1437' => 'cru', 'Carub.0003s0044' => 'cru', 'Carub.0003s2787' => 'cru', 'Carub.0005s0597' => 'cru', 'Carub.0006s1266' => 'cru', 'Ca_06935_v3' => 'car', 'Ca_13559_v3' => 'car', 'Ca_16941_v3' => 'car', 'Ca_16960_v3' => 'car', 'Ca_17775_v3' => 'car', 'Ca_30464_v3' => 'car', 'Cc06_g08160' => 'ccan', 'Cc07_g01520' => 'ccan', 'Cc11_g15810' => 'ccan', 'CDE02G2840' => 'cde', 'CDE03G0093' => 'cde', 'CDE04G2127' => 'cde', 'CDE07G1857' => 'cde', 'CDE09G1246' => 'cde', 'Cfa003412' => 'cfa', 'Cfa007341' => 'cfa', 'Cfa009220' => 'cfa', 'Ciclev10008737m.g' => 'ccl', 'Ciclev10015565m.g' => 'ccl', 'Ciclev10031761m.g' => 'ccl', 'CiPaw.03G045300' => 'cil', 'CiPaw.03G247200' => 'cil', 'CiPaw.04G029500' => 'cil', 'CiPaw.04G174000' => 'cil', 'CiPaw.05G181200' => 'cil', 'CiPaw.06G067100' => 'cil', 'ClCG05G025800' => 'cla', 'ClCG06G011400' => 'cla', 'ClCG09G019360' => 'cla', 'COL.COLO4_04827' => 'col', 'COL.COLO4_29170' => 'col', 'COL.COLO4_35131' => 'col', 'COL.COLO4_35132' => 'col', 'Cpa.g.sc33.32' => 'cpa', 'Cpa.g.sc46.29' => 'cpa', 'Cpa.g.sc796.1' => 'cpa', 'CsaV3_1G030420' => 'csa', 'CsaV3_5G027050' => 'csa', 'CsaV3_5G031040' => 'csa', 'CsaV3_UNG023130' => 'csa', 'CSS0007726' => 'camsi', 'CSS0016433' => 'camsi', 'CSS0017656' => 'camsi', 'CSS0025364' => 'camsi', 'CSS0027582' => 'camsi', 'CSS0047288' => 'camsi', 'CSS0049950' => 'camsi', 'DCAR_003843' => 'dca', 'DCAR_007052' => 'dca', 'DCAR_020884' => 'dca', 'DCAR_021730' => 'dca', 'DCAR_024423' => 'dca', 'DCAR_026509' => 'dca', 'DCAR_031158' => 'dca', 'Dinv14728' => 'din', 'Dinv15219' => 'din', 'Dinv25728' => 'din', 'Dinv33428' => 'din', 'Dinv36489' => 'din', 'Dinv41486' => 'din', 'Duzib147G0469' => 'dzi', 'Duzib168G0060' => 'dzi', 'Duzib187G1215' => 'dzi', 'Duzib248G0692' => 'dzi', 'Duzib251G0767' => 'dzi', 'Duzib264G0446' => 'dzi', 'Duzib268G0691' => 'dzi', 'ECA232G4767' => 'eca', 'ECA233G2838' => 'eca', 'ECA234G0391' => 'eca', 'ECA234G0857' => 'eca', 'ECA236G1593' => 'eca', 'ECA238G0565' => 'eca', 'ECA246G1027' => 'eca', 'ECA246G3223' => 'eca', 'ECA246G3470' => 'eca', 'EL10Ac6g13829' => 'bvu', 'EL10Ac6g14093' => 'bvu', 'EL10Ac8g18707' => 'bvu', 'Eucgr.C01369' => 'egr', 'Eucgr.H02492' => 'egr', 'Eucgr.I01733' => 'egr', 'Eucgr.J02255' => 'egr', 'Eucgr.J02257' => 'egr', 'Eucgr.J02258' => 'egr', 'FAN02G1601' => 'fan', 'FAN03G1586' => 'fan', 'FAN03G2986' => 'fan', 'FAN05G4837' => 'fan', 'FAN06G0146' => 'fan', 'FAN07G0858' => 'fan', 'FAN09G3179' => 'fan', 'FAN10G0669' => 'fan', 'FAN12G2358' => 'fan', 'FAN14G4198' => 'fan', 'FAN14G5112' => 'fan', 'FAN17G0342' => 'fan', 'FAN19G0342' => 'fan', 'FAN19G0962' => 'fan', 'FAN19G1101' => 'fan', 'FAN19G1872' => 'fan', 'FAN22G0356' => 'fan', 'FAN23G0744' => 'fan', 'FAN23G1914' => 'fan', 'FAN26G0032' => 'fan', 'FAN28G0625' => 'fan', 'FvH4_1g02710' => 'fve', 'FvH4_1g02720' => 'fve', 'FvH4_4g25670' => 'fve', 'FvH4_6g51700' => 'fve', 'FvH4_7g20170' => 'fve', 'Glyma.05G175000' => 'gma', 'Glyma.08G132300' => 'gma', 'Glyma.11G243000' => 'gma', 'Glyma.13G158900' => 'gma', 'Glyma.17G112400' => 'gma', 'Glyma.18G014100' => 'gma', 'Glyma.19G003100' => 'gma', 'Glyma.19G056500' => 'gma', 'Gohir.A01G158900' => 'ghi', 'Gohir.A05G312600' => 'ghi', 'Gohir.A05G354900' => 'ghi', 'Gohir.A07G037200' => 'ghi', 'Gohir.A09G030000' => 'ghi', 'Gohir.A12G145200' => 'ghi', 'Gohir.D01G151500' => 'ghi', 'Gohir.D04G058300' => 'ghi', 'Gohir.D05G314100' => 'ghi', 'Gohir.D07G041400' => 'ghi', 'Gohir.D09G029700' => 'ghi', 'Gohir.D12G149700' => 'ghi', 'Gorai.001G043800' => 'gra', 'Gorai.002G187800' => 'gra', 'Gorai.006G034700' => 'gra', 'Gorai.008G161200' => 'gra', 'Gorai.009G335700' => 'gra', 'Gorai.012G065000' => 'gra', 'GSVIVG01000535001' => 'vvi', 'GSVIVG01015572001' => 'vvi', 'GSVIVG01032386001' => 'vvi', 'HanXRQChr05g0138531' => 'han', 'HanXRQChr06g0174391' => 'han', 'HanXRQChr07g0199021' => 'han', 'HanXRQChr08g0208211' => 'han', 'HanXRQChr09g0255471' => 'han', 'HanXRQChr10g0315791' => 'han', 'HanXRQChr12g0371991' => 'han', 'HanXRQChr15g0475251' => 'han', 'HanXRQChr17g0540001' => 'han', 'HanXRQChr17g0548631' => 'han', 'HanXRQChr17g0569561' => 'han', 'Haze_12256' => 'cav', 'Haze_14756' => 'cav', 'Haze_25528' => 'cav', 'Hma1.2p1_0079F.1_g041020' => 'hma', 'Hma1.2p1_0818F.1_g223260' => 'hma', 'Hma1.2p1_1747F.1_g300530' => 'hma', 'HPP92_004607' => 'vpl', 'HPP92_004608' => 'vpl', 'HPP92_006181' => 'vpl', 'HPP92_012192' => 'vpl', 'HPP92_015680' => 'vpl', 'HPP92_020249' => 'vpl', 'HPP92_021376' => 'vpl', 'HPP92_024275' => 'vpl', 'Hund06031' => 'sun', 'Hund25391' => 'sun', 'Lalb_Chr07g0185371' => 'lal', 'Lalb_Chr07g0185381' => 'lal', 'Lalb_Chr12g0204011' => 'lal', 'Lalb_Chr13g0301671' => 'lal', 'Lalb_Chr14g0362851' => 'lal', 'Lalb_Chr24g0403581' => 'lal', 'Lj1g0000233' => 'lja', 'Lj2g0018120' => 'lja', 'Lj3C621T0' => 'lonja', 'Lj3P1059T14' => 'lonja', 'Lj3P611T9' => 'lonja', 'Lj3P614T13' => 'lonja', 'Lj3P615T5' => 'lonja', 'Lj4g0012315' => 'lja', 'Lj4g0026182' => 'lja', 'Lj6P813T16' => 'lonja', 'Lj7C427T7' => 'lonja', 'Lj7C427T8' => 'lonja', 'Lj7P600T41' => 'lonja', 'Lju41C42G17' => 'lonja', 'Lsat_1_v5_gn_0_47300' => 'lsa', 'Lsat_1_v5_gn_2_91280' => 'lsa', 'Lsat_1_v5_gn_3_30561' => 'lsa', 'Lsat_1_v5_gn_4_184321' => 'lsa', 'Lsat_1_v5_gn_4_4041' => 'lsa', 'Lsat_1_v5_gn_5_92000' => 'lsa', 'Lsat_1_v5_gn_8_152940' => 'lsa', 'Lsat_1_v5_gn_8_62401' => 'lsa', 'Manes.06G055900' => 'mes', 'Manes.12G022200' => 'mes', 'Manes.13G023300' => 'mes', 'Manes.14G115000' => 'mes', 'Manes.15G151700' => 'mes', 'Manes.17G111300' => 'mes', 'Mapoly0226s0009' => 'mpo', 'MBI02_g25363_MAGBIO' => 'mbi', 'MBI06_g00027_MAGBIO' => 'mbi', 'MBI10_g13034_MAGBIO' => 'mbi', 'MD09G1023400' => 'mdo', 'MD13G1100100' => 'mdo', 'MD15G1169200' => 'mdo', 'MD16G1101100' => 'mdo', 'MD17G1022900' => 'mdo', 'Medtr3g096150' => 'mtr', 'Medtr4g115070' => 'mtr', 'Medtr7g033325' => 'mtr', 'Medtr8g089840' => 'mtr', 'MELO3C010319.2' => 'cme', 'MELO3C011944.2' => 'cme', 'MELO3C021589.2' => 'cme', 'Migut.E00207' => 'egut', 'Migut.H00067' => 'egut', 'Migut.K00433' => 'egut', 'Migut.K00606' => 'egut', 'Migut.K01410' => 'egut', 'MSTRG.13347' => 'ama', 'MSTRG.24045' => 'ama', 'MSTRG.2428' => 'ama', 'MSTRG.26410' => 'ama', 'MSTRG.3139' => 'ama', 'MSTRG.3286' => 'ama', 'MSTRG.563' => 'ama', 'MSTRG.7941' => 'ama', 'Nitab4.5_0000028g0060' => 'nta', 'Nitab4.5_0000065g0260' => 'nta', 'Nitab4.5_0000112g0060' => 'nta', 'Nitab4.5_0000489g0120' => 'nta', 'Nitab4.5_0001776g0050' => 'nta', 'Nitab4.5_0001854g0010' => 'nta', 'Nitab4.5_0001860g0020' => 'nta', 'Nitab4.5_0004352g0010' => 'nta', 'Nitab4.5_0008716g0020' => 'nta', 'Nitab4.5_0008922g0010' => 'nta', 'Nn3g16693' => 'nnu', 'Nn4g22596' => 'nnu', 'Nn7g37639' => 'nnu', 'Oeu001701.1' => 'oeu', 'Oeu018149.1' => 'oeu', 'Oeu026220.1' => 'oeu', 'Oeu038635.1' => 'oeu', 'Oeu049176.1' => 'oeu', 'Oeu056706.1' => 'oeu', 'Oeu056937.1' => 'oeu', 'Oeu057540.1' => 'oeu', 'Os02g0594900' => 'osa', 'Os02g0595100' => 'osa', 'Os04g0477500' => 'osa', 'Os12g0611900' => 'osa', 'Peaxi162Scf00076g00020' => 'pax', 'Peaxi162Scf00128g00217' => 'pax', 'Peaxi162Scf00129g01640' => 'pax', 'Peaxi162Scf00669g00007' => 'pax', 'Peaxi162Scf00700g00421' => 'pax', 'Peaxi162Scf00801g00038' => 'pax', 'Peaxi162Scf00891g00025' => 'pax', 'PGR083G0909' => 'pgr', 'PGR119G1005' => 'pgr', 'PGR142G2236' => 'pgr', 'PGR142G3388' => 'pgr', 'PGSC0003DMG400004514' => 'stu', 'PGSC0003DMG400012635' => 'stu', 'PGSC0003DMG400015730' => 'stu', 'PGSC0003DMG400018611' => 'stu', 'PGSC0003DMG400030897' => 'stu', 'Phvul.001G254800' => 'pvu', 'Phvul.002G260100' => 'pvu', 'Phvul.003G167600' => 'pvu', 'Phvul.004G005100' => 'pvu', 'Potri.001G343600' => 'ptr', 'Potri.006G066700' => 'ptr', 'Potri.008G186000' => 'ptr', 'Potri.010G046900' => 'ptr', 'Potri.018G127900' => 'ptr', 'Pp3c20_17750' => 'ppa', 'Pp3c24_4380' => 'ppa', 'Prupe.1G245800' => 'ppe', 'Prupe.3G293400' => 'ppe', 'Prupe.7G247400' => 'ppe', 'Psat0s145g0120' => 'psa', 'Psat0s595g0040' => 'psa', 'Psat0s595g0120' => 'psa', 'Psat3g175040' => 'psa', 'Psat7g058120' => 'psa', 'PSO017G0428' => 'pso', 'PSO063G7510' => 'pso', 'PSO067G0046' => 'pso', 'PSO478G1073' => 'pso', 'PSO675G3677' => 'pso', 'PSO675G6558' => 'pso', 'PSO675G7520' => 'pso', 'PSO675G8959' => 'pso', 'QL02p074089' => 'qlo', 'QL02p089614' => 'qlo', 'QL03p057736' => 'qlo', 'RcHm_v2.0_Chr1g0364131' => 'rch', 'RcHm_v2.0_Chr2g0087801' => 'rch', 'RcHm_v2.0_Chr2g0087821' => 'rch', 'RcHm_v2.0_Chr2g0173231' => 'rch', 'RcHm_v2.0_Chr4g0433111' => 'rch', 'Rhsim03G0250300' => 'rsi', 'Rhsim08G0048400' => 'rsi', 'Rhsim10G0014800' => 'rsi', 'Rhsim12G0040100' => 'rsi', 'Rhsim12G0109700' => 'rsi', 'Sabra06G0049600' => 'sbr', 'Sabra08G0141000' => 'sbr', 'Sabra10G0021400' => 'sbr', 'Sabra16G0222900' => 'sbr', 'Sabra18G0108600' => 'sbr', 'SalBow1G0433' => 'sbo', 'SalBow1G2038' => 'sbo', 'SalBow1G5003' => 'sbo', 'SalBow7G1197' => 'sbo', 'SalBow8G3506' => 'sbo', 'Sc03g0007300' => 'sci', 'Sc11g0000950' => 'sci', 'Sc14g0008750' => 'sci', 'Sc18g0000420' => 'sci', 'Sed0006754' => 'sed', 'Sed0008741' => 'sed', 'Sed0017172' => 'sed', 'Sed0018925' => 'sed', 'Sed0023326' => 'sed', 'Sed0025909' => 'sed', 'SEGI_05333' => 'sgi', 'SEGI_10362' => 'sgi', 'SEGI_13380' => 'sgi', 'SEGI_24306' => 'sgi', 'SEGI_29077' => 'sgi', 'SEGI_29095' => 'sgi', 'SEGI_36534' => 'sgi', 'SEGI_37506' => 'sgi', 'SEGI_38321' => 'sgi', 'SGA_v2.0_scaffold307G48031' => 'sas', 'SGA_v2.0_scaffold47G17507' => 'sas', 'SGA_v2.0_scaffold63G21736' => 'sas', 'SGA_v2.0_scaffold87G27070' => 'sas', 'SHI17794' => 'shi', 'SHI28851' => 'shi', 'SMO165G0155' => 'smo', 'SMO340G0217' => 'smo', 'SMO367G1210' => 'smo', 'Solyc02g093430.3' => 'sly', 'Solyc05g013580.4' => 'sly', 'Solyc07g008030.3' => 'sly', 'Solyc12g035470.2' => 'sly', 'Sopen02g038020' => 'spe', 'Sopen05g008490' => 'spe', 'Sopen07g003910' => 'spe', 'Sopen12g015240' => 'spe', 'Sp1g11550' => 'spa', 'Sp2g16710' => 'spa', 'Sp3g00430' => 'spa', 'Sp3g26780' => 'spa', 'Sp5g22900' => 'spa', 'Sp6g29530' => 'spa', 'TAR371G0794' => 'tar', 'TAR374G0164' => 'tar', 'TAR622G0165' => 'tar', 'TAR626G0929' => 'tar', 'TAR629G2155' => 'tar', 'THA.LOC104805282' => 'tha', 'THA.LOC104805363' => 'tha', 'THA.LOC104808968' => 'tha', 'THA.LOC104821093' => 'tha', 'THA.LOC104823953' => 'tha', 'THA.LOC104825562' => 'tha', 'THA.LOC104825665' => 'tha', 'Thecc.02G261400' => 'tca', 'Thecc.04G019200' => 'tca', 'Thecc.09G130400' => 'tca', 'Thhalv10004374m.g' => 'esa', 'Thhalv10007850m.g' => 'esa', 'Thhalv10013782m.g' => 'esa', 'Thhalv10018686m.g' => 'esa', 'Thhalv10020899m.g' => 'esa', 'Thhalv10022755m.g' => 'esa', 'TPR.G23851' => 'tpr', 'TPR.G26500' => 'tpr', 'TPR.G27267' => 'tpr', 'TPR.G32001' => 'tpr', 'TPR.G6251' => 'tpr', 'TPR.G8167' => 'tpr', 'TWI12G1330' => 'twi', 'TWI18G1239' => 'twi', 'TWI34G0979' => 'twi', 'TWI36G0670' => 'twi', 'TWI36G0707' => 'twi', 'TWI56G0233' => 'twi', 'TWI75G1809' => 'twi', 'unitig_21.g20874' => 'ugi', 'unitig_26.g10343' => 'ugi', 'unitig_46.g18392' => 'ugi', 'unitig_52.g17178' => 'ugi', 'unitig_8.g2934' => 'ugi', 'vmacro01122' => 'vma', 'vmacro05875' => 'vma', 'vmacro06147' => 'vma', 'vmacro16191' => 'vma', 'vmacro18293' => 'vma', 'VMungo0251G3707' => 'vmu', 'VMungo0464G1521' => 'vmu', 'VMungo1215G0205' => 'vmu', 'VMungo1383G2484' => 'vmu', 'Zm00001eb079610' => 'zma', 'Zm00001eb135990' => 'zma', 'Zm00001eb183710' => 'zma', 'Zm00001eb246020' => 'zma' ), 'gf_id' => 'HOM05D001124', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001124' ), 'data_identifier' => 'HOM05D001124', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001124', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '548', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02520' => 'bna', 'A03p06630' => 'bna', 'A05p44460' => 'bna', 'A06p08710' => 'bna', 'A06p41090' => 'bna', 'A07p32320' => 'bna', 'A08p32520' => 'bna', 'A09p10360' => 'bna', 'A10p24080' => 'bna', 'Aa31LG11G15250' => 'aar', 'Aa31LG1G1800' => 'aar', 'Aa31LG2G5120' => 'aar', 'Aa31LG2G6070' => 'aar', 'Aa31LG5G10770' => 'aar', 'Aa31sc61G90' => 'aar', 'Actinidia01352' => 'ach', 'Actinidia05983' => 'ach', 'Actinidia08133' => 'ach', 'Actinidia15101' => 'ach', 'Actinidia26379' => 'ach', 'Actinidia35778' => 'ach', 'Actinidia36123' => 'ach', 'Actinidia37436' => 'ach', 'Actinidia38730' => 'ach', 'Ah.02g128210' => 'amhyb', 'Ah.03g132990' => 'amhyb', 'Ah.14g079410' => 'amhyb', 'AL1G24640' => 'aly', 'AL2G26680' => 'aly', 'AL3G10530' => 'aly', 'AL3G45230' => 'aly', 'AL5G15230' => 'aly', 'AL5G16960' => 'aly', 'AL6G25210' => 'aly', 'Aqoxy2G00441' => 'aox', 'Aqoxy3G01236' => 'aox', 'Aqoxy5G03746' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3RQ047' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C7GMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9C8JER' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MBL6KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YXCZ83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZANX40' => 'arhy', 'AT1G12990' => 'ath', 'AT1G67880' => 'ath', 'AT2G13290' => 'ath', 'AT3G01620' => 'ath', 'AT3G26445' => 'ath', 'AT3G27540' => 'ath', 'AT5G14480' => 'ath', 'ATR0824G026' => 'atr', 'ATR1098G019' => 'atr', 'Atru.chr11.2145' => 'acertr', 'Atru.chr2.3636' => 'acertr', 'Atru.chr2.3644' => 'acertr', 'Atru.chr6.2422' => 'acertr', 'Atru.chr7.1112' => 'acertr', 'AUR62005469' => 'cqu', 'AUR62011166' => 'cqu', 'AUR62013319' => 'cqu', 'AUR62024273' => 'cqu', 'AUR62028420' => 'cqu', 'AUR62041942' => 'cqu', 'BcaB01g04969' => 'bca', 'BcaB01g06371' => 'bca', 'BcaB02g11494' => 'bca', 'BcaB03g15382' => 'bca', 'BcaB08g36994' => 'bca', 'BcaC03g13477' => 'bca', 'BcaC03g13478' => 'bca', 'BcaC03g13480' => 'bca', 'BcaC03g13481' => 'bca', 'BcaC03g13486' => 'bca', 'BcaC04g19031' => 'bca', 'BcaC04g23085' => 'bca', 'BcaC05g25094' => 'bca', 'BcaC05g25096' => 'bca', 'BcaC05g25138' => 'bca', 'BcaC05g30416' => 'bca', 'BcaC05g30455' => 'bca', 'BcaC06g30979' => 'bca', 'BcaC06g33805' => 'bca', 'BcaC08g46021' => 'bca', 'BcaNung03154' => 'bca', 'BolC2t06623H' => 'bol', 'BolC2t06632H' => 'bol', 'BolC2t06635H' => 'bol', 'BolC2t06638H' => 'bol', 'BolC3t13266H' => 'bol', 'BolC5t29776H' => 'bol', 'BolC6t38912H' => 'bol', 'BolC7t44183H' => 'bol', 'BolC9t54123H' => 'bol', 'BolC9t59107H' => 'bol', 'BraA02t05221Z' => 'bra', 'BraA03t09996Z' => 'bra', 'BraA05t23210Z' => 'bra', 'BraA06t24068Z' => 'bra', 'BraA06t27032Z' => 'bra', 'BraA08t35176Z' => 'bra', 'BraA09t36680Z' => 'bra', 'BraA10t44471Z' => 'bra', 'C02p06760' => 'bna', 'C02p06890' => 'bna', 'C02p07010' => 'bna', 'C03p07660' => 'bna', 'C05p10300' => 'bna', 'C06p38150' => 'bna', 'C07p36650' => 'bna', 'C08p15770' => 'bna', 'C09p12300' => 'bna', 'C09p62700' => 'bna', 'C09p75040' => 'bna', 'CAN.G13.1' => 'can', 'CAN.G138.4' => 'can', 'CAN.G44.6' => 'can', 'CAN.G473.19' => 'can', 'CANSAT01G0835' => 'cansat', 'CANSAT11G0246' => 'cansat', 'CANSAT11G1766' => 'cansat', 'CANSAT64G1954' => 'cansat', 'CARHR013330' => 'chi', 'CARHR060530' => 'chi', 'CARHR075300' => 'chi', 'CARHR105120' => 'chi', 'CARHR148910' => 'chi', 'CARHR198830' => 'chi', 'Carub.0001s1275' => 'cru', 'Carub.0002s1437' => 'cru', 'Carub.0003s0044' => 'cru', 'Carub.0003s2787' => 'cru', 'Carub.0005s0597' => 'cru', 'Carub.0006s1266' => 'cru', 'Ca_06935_v3' => 'car', 'Ca_13559_v3' => 'car', 'Ca_16941_v3' => 'car', 'Ca_16960_v3' => 'car', 'Ca_17775_v3' => 'car', 'Ca_30464_v3' => 'car', 'Cc06_g08160' => 'ccan', 'Cc07_g01520' => 'ccan', 'Cc11_g15810' => 'ccan', 'CDE02G2840' => 'cde', 'CDE03G0093' => 'cde', 'CDE04G2127' => 'cde', 'CDE07G1857' => 'cde', 'CDE09G1246' => 'cde', 'Cfa003412' => 'cfa', 'Cfa007341' => 'cfa', 'Cfa009220' => 'cfa', 'Ciclev10008737m.g' => 'ccl', 'Ciclev10015565m.g' => 'ccl', 'Ciclev10031761m.g' => 'ccl', 'CiPaw.03G045300' => 'cil', 'CiPaw.03G247200' => 'cil', 'CiPaw.04G029500' => 'cil', 'CiPaw.04G174000' => 'cil', 'CiPaw.05G181200' => 'cil', 'CiPaw.06G067100' => 'cil', 'ClCG05G025800' => 'cla', 'ClCG06G011400' => 'cla', 'ClCG09G019360' => 'cla', 'COL.COLO4_04827' => 'col', 'COL.COLO4_29170' => 'col', 'COL.COLO4_35131' => 'col', 'COL.COLO4_35132' => 'col', 'Cpa.g.sc33.32' => 'cpa', 'Cpa.g.sc46.29' => 'cpa', 'Cpa.g.sc796.1' => 'cpa', 'CsaV3_1G030420' => 'csa', 'CsaV3_5G027050' => 'csa', 'CsaV3_5G031040' => 'csa', 'CsaV3_UNG023130' => 'csa', 'CSS0007726' => 'camsi', 'CSS0016433' => 'camsi', 'CSS0017656' => 'camsi', 'CSS0025364' => 'camsi', 'CSS0027582' => 'camsi', 'CSS0047288' => 'camsi', 'CSS0049950' => 'camsi', 'DCAR_003843' => 'dca', 'DCAR_007052' => 'dca', 'DCAR_020884' => 'dca', 'DCAR_021730' => 'dca', 'DCAR_024423' => 'dca', 'DCAR_026509' => 'dca', 'DCAR_031158' => 'dca', 'Dinv14728' => 'din', 'Dinv15219' => 'din', 'Dinv25728' => 'din', 'Dinv33428' => 'din', 'Dinv36489' => 'din', 'Dinv41486' => 'din', 'Duzib147G0469' => 'dzi', 'Duzib168G0060' => 'dzi', 'Duzib187G1215' => 'dzi', 'Duzib248G0692' => 'dzi', 'Duzib251G0767' => 'dzi', 'Duzib264G0446' => 'dzi', 'Duzib268G0691' => 'dzi', 'ECA232G4767' => 'eca', 'ECA233G2838' => 'eca', 'ECA234G0391' => 'eca', 'ECA234G0857' => 'eca', 'ECA236G1593' => 'eca', 'ECA238G0565' => 'eca', 'ECA246G1027' => 'eca', 'ECA246G3223' => 'eca', 'ECA246G3470' => 'eca', 'EL10Ac6g13829' => 'bvu', 'EL10Ac6g14093' => 'bvu', 'EL10Ac8g18707' => 'bvu', 'Eucgr.C01369' => 'egr', 'Eucgr.H02492' => 'egr', 'Eucgr.I01733' => 'egr', 'Eucgr.J02255' => 'egr', 'Eucgr.J02257' => 'egr', 'Eucgr.J02258' => 'egr', 'FAN02G1601' => 'fan', 'FAN03G1586' => 'fan', 'FAN03G2986' => 'fan', 'FAN05G4837' => 'fan', 'FAN06G0146' => 'fan', 'FAN07G0858' => 'fan', 'FAN09G3179' => 'fan', 'FAN10G0669' => 'fan', 'FAN12G2358' => 'fan', 'FAN14G4198' => 'fan', 'FAN14G5112' => 'fan', 'FAN17G0342' => 'fan', 'FAN19G0342' => 'fan', 'FAN19G0962' => 'fan', 'FAN19G1101' => 'fan', 'FAN19G1872' => 'fan', 'FAN22G0356' => 'fan', 'FAN23G0744' => 'fan', 'FAN23G1914' => 'fan', 'FAN26G0032' => 'fan', 'FAN28G0625' => 'fan', 'FvH4_1g02710' => 'fve', 'FvH4_1g02720' => 'fve', 'FvH4_4g25670' => 'fve', 'FvH4_6g51700' => 'fve', 'FvH4_7g20170' => 'fve', 'Glyma.05G175000' => 'gma', 'Glyma.08G132300' => 'gma', 'Glyma.11G243000' => 'gma', 'Glyma.13G158900' => 'gma', 'Glyma.17G112400' => 'gma', 'Glyma.18G014100' => 'gma', 'Glyma.19G003100' => 'gma', 'Glyma.19G056500' => 'gma', 'Gohir.A01G158900' => 'ghi', 'Gohir.A05G312600' => 'ghi', 'Gohir.A05G354900' => 'ghi', 'Gohir.A07G037200' => 'ghi', 'Gohir.A09G030000' => 'ghi', 'Gohir.A12G145200' => 'ghi', 'Gohir.D01G151500' => 'ghi', 'Gohir.D04G058300' => 'ghi', 'Gohir.D05G314100' => 'ghi', 'Gohir.D07G041400' => 'ghi', 'Gohir.D09G029700' => 'ghi', 'Gohir.D12G149700' => 'ghi', 'Gorai.001G043800' => 'gra', 'Gorai.002G187800' => 'gra', 'Gorai.006G034700' => 'gra', 'Gorai.008G161200' => 'gra', 'Gorai.009G335700' => 'gra', 'Gorai.012G065000' => 'gra', 'GSVIVG01000535001' => 'vvi', 'GSVIVG01015572001' => 'vvi', 'GSVIVG01032386001' => 'vvi', 'HanXRQChr05g0138531' => 'han', 'HanXRQChr06g0174391' => 'han', 'HanXRQChr07g0199021' => 'han', 'HanXRQChr08g0208211' => 'han', 'HanXRQChr09g0255471' => 'han', 'HanXRQChr10g0315791' => 'han', 'HanXRQChr12g0371991' => 'han', 'HanXRQChr15g0475251' => 'han', 'HanXRQChr17g0540001' => 'han', 'HanXRQChr17g0548631' => 'han', 'HanXRQChr17g0569561' => 'han', 'Haze_12256' => 'cav', 'Haze_14756' => 'cav', 'Haze_25528' => 'cav', 'Hma1.2p1_0079F.1_g041020' => 'hma', 'Hma1.2p1_0818F.1_g223260' => 'hma', 'Hma1.2p1_1747F.1_g300530' => 'hma', 'HPP92_004607' => 'vpl', 'HPP92_004608' => 'vpl', 'HPP92_006181' => 'vpl', 'HPP92_012192' => 'vpl', 'HPP92_015680' => 'vpl', 'HPP92_020249' => 'vpl', 'HPP92_021376' => 'vpl', 'HPP92_024275' => 'vpl', 'Hund06031' => 'sun', 'Hund25391' => 'sun', 'Lalb_Chr07g0185371' => 'lal', 'Lalb_Chr07g0185381' => 'lal', 'Lalb_Chr12g0204011' => 'lal', 'Lalb_Chr13g0301671' => 'lal', 'Lalb_Chr14g0362851' => 'lal', 'Lalb_Chr24g0403581' => 'lal', 'Lj1g0000233' => 'lja', 'Lj2g0018120' => 'lja', 'Lj3C621T0' => 'lonja', 'Lj3P1059T14' => 'lonja', 'Lj3P611T9' => 'lonja', 'Lj3P614T13' => 'lonja', 'Lj3P615T5' => 'lonja', 'Lj4g0012315' => 'lja', 'Lj4g0026182' => 'lja', 'Lj6P813T16' => 'lonja', 'Lj7C427T7' => 'lonja', 'Lj7C427T8' => 'lonja', 'Lj7P600T41' => 'lonja', 'Lju41C42G17' => 'lonja', 'Lsat_1_v5_gn_0_47300' => 'lsa', 'Lsat_1_v5_gn_2_91280' => 'lsa', 'Lsat_1_v5_gn_3_30561' => 'lsa', 'Lsat_1_v5_gn_4_184321' => 'lsa', 'Lsat_1_v5_gn_4_4041' => 'lsa', 'Lsat_1_v5_gn_5_92000' => 'lsa', 'Lsat_1_v5_gn_8_152940' => 'lsa', 'Lsat_1_v5_gn_8_62401' => 'lsa', 'Manes.06G055900' => 'mes', 'Manes.12G022200' => 'mes', 'Manes.13G023300' => 'mes', 'Manes.14G115000' => 'mes', 'Manes.15G151700' => 'mes', 'Manes.17G111300' => 'mes', 'Mapoly0226s0009' => 'mpo', 'MBI02_g25363_MAGBIO' => 'mbi', 'MBI06_g00027_MAGBIO' => 'mbi', 'MBI10_g13034_MAGBIO' => 'mbi', 'MD09G1023400' => 'mdo', 'MD13G1100100' => 'mdo', 'MD15G1169200' => 'mdo', 'MD16G1101100' => 'mdo', 'MD17G1022900' => 'mdo', 'Medtr3g096150' => 'mtr', 'Medtr4g115070' => 'mtr', 'Medtr7g033325' => 'mtr', 'Medtr8g089840' => 'mtr', 'MELO3C010319.2' => 'cme', 'MELO3C011944.2' => 'cme', 'MELO3C021589.2' => 'cme', 'Migut.E00207' => 'egut', 'Migut.H00067' => 'egut', 'Migut.K00433' => 'egut', 'Migut.K00606' => 'egut', 'Migut.K01410' => 'egut', 'MSTRG.13347' => 'ama', 'MSTRG.24045' => 'ama', 'MSTRG.2428' => 'ama', 'MSTRG.26410' => 'ama', 'MSTRG.3139' => 'ama', 'MSTRG.3286' => 'ama', 'MSTRG.563' => 'ama', 'MSTRG.7941' => 'ama', 'Nitab4.5_0000028g0060' => 'nta', 'Nitab4.5_0000065g0260' => 'nta', 'Nitab4.5_0000112g0060' => 'nta', 'Nitab4.5_0000489g0120' => 'nta', 'Nitab4.5_0001776g0050' => 'nta', 'Nitab4.5_0001854g0010' => 'nta', 'Nitab4.5_0001860g0020' => 'nta', 'Nitab4.5_0004352g0010' => 'nta', 'Nitab4.5_0008716g0020' => 'nta', 'Nitab4.5_0008922g0010' => 'nta', 'Nn3g16693' => 'nnu', 'Nn4g22596' => 'nnu', 'Nn7g37639' => 'nnu', 'Oeu001701.1' => 'oeu', 'Oeu018149.1' => 'oeu', 'Oeu026220.1' => 'oeu', 'Oeu038635.1' => 'oeu', 'Oeu049176.1' => 'oeu', 'Oeu056706.1' => 'oeu', 'Oeu056937.1' => 'oeu', 'Oeu057540.1' => 'oeu', 'Os02g0594900' => 'osa', 'Os02g0595100' => 'osa', 'Os04g0477500' => 'osa', 'Os12g0611900' => 'osa', 'Peaxi162Scf00076g00020' => 'pax', 'Peaxi162Scf00128g00217' => 'pax', 'Peaxi162Scf00129g01640' => 'pax', 'Peaxi162Scf00669g00007' => 'pax', 'Peaxi162Scf00700g00421' => 'pax', 'Peaxi162Scf00801g00038' => 'pax', 'Peaxi162Scf00891g00025' => 'pax', 'PGR083G0909' => 'pgr', 'PGR119G1005' => 'pgr', 'PGR142G2236' => 'pgr', 'PGR142G3388' => 'pgr', 'PGSC0003DMG400004514' => 'stu', 'PGSC0003DMG400012635' => 'stu', 'PGSC0003DMG400015730' => 'stu', 'PGSC0003DMG400018611' => 'stu', 'PGSC0003DMG400030897' => 'stu', 'Phvul.001G254800' => 'pvu', 'Phvul.002G260100' => 'pvu', 'Phvul.003G167600' => 'pvu', 'Phvul.004G005100' => 'pvu', 'Potri.001G343600' => 'ptr', 'Potri.006G066700' => 'ptr', 'Potri.008G186000' => 'ptr', 'Potri.010G046900' => 'ptr', 'Potri.018G127900' => 'ptr', 'Pp3c20_17750' => 'ppa', 'Pp3c24_4380' => 'ppa', 'Prupe.1G245800' => 'ppe', 'Prupe.3G293400' => 'ppe', 'Prupe.7G247400' => 'ppe', 'Psat0s145g0120' => 'psa', 'Psat0s595g0040' => 'psa', 'Psat0s595g0120' => 'psa', 'Psat3g175040' => 'psa', 'Psat7g058120' => 'psa', 'PSO017G0428' => 'pso', 'PSO063G7510' => 'pso', 'PSO067G0046' => 'pso', 'PSO478G1073' => 'pso', 'PSO675G3677' => 'pso', 'PSO675G6558' => 'pso', 'PSO675G7520' => 'pso', 'PSO675G8959' => 'pso', 'QL02p074089' => 'qlo', 'QL02p089614' => 'qlo', 'QL03p057736' => 'qlo', 'RcHm_v2.0_Chr1g0364131' => 'rch', 'RcHm_v2.0_Chr2g0087801' => 'rch', 'RcHm_v2.0_Chr2g0087821' => 'rch', 'RcHm_v2.0_Chr2g0173231' => 'rch', 'RcHm_v2.0_Chr4g0433111' => 'rch', 'Rhsim03G0250300' => 'rsi', 'Rhsim08G0048400' => 'rsi', 'Rhsim10G0014800' => 'rsi', 'Rhsim12G0040100' => 'rsi', 'Rhsim12G0109700' => 'rsi', 'Sabra06G0049600' => 'sbr', 'Sabra08G0141000' => 'sbr', 'Sabra10G0021400' => 'sbr', 'Sabra16G0222900' => 'sbr', 'Sabra18G0108600' => 'sbr', 'SalBow1G0433' => 'sbo', 'SalBow1G2038' => 'sbo', 'SalBow1G5003' => 'sbo', 'SalBow7G1197' => 'sbo', 'SalBow8G3506' => 'sbo', 'Sc03g0007300' => 'sci', 'Sc11g0000950' => 'sci', 'Sc14g0008750' => 'sci', 'Sc18g0000420' => 'sci', 'Sed0006754' => 'sed', 'Sed0008741' => 'sed', 'Sed0017172' => 'sed', 'Sed0018925' => 'sed', 'Sed0023326' => 'sed', 'Sed0025909' => 'sed', 'SEGI_05333' => 'sgi', 'SEGI_10362' => 'sgi', 'SEGI_13380' => 'sgi', 'SEGI_24306' => 'sgi', 'SEGI_29077' => 'sgi', 'SEGI_29095' => 'sgi', 'SEGI_36534' => 'sgi', 'SEGI_37506' => 'sgi', 'SEGI_38321' => 'sgi', 'SGA_v2.0_scaffold307G48031' => 'sas', 'SGA_v2.0_scaffold47G17507' => 'sas', 'SGA_v2.0_scaffold63G21736' => 'sas', 'SGA_v2.0_scaffold87G27070' => 'sas', 'SHI17794' => 'shi', 'SHI28851' => 'shi', 'SMO165G0155' => 'smo', 'SMO340G0217' => 'smo', 'SMO367G1210' => 'smo', 'Solyc02g093430.3' => 'sly', 'Solyc05g013580.4' => 'sly', 'Solyc07g008030.3' => 'sly', 'Solyc12g035470.2' => 'sly', 'Sopen02g038020' => 'spe', 'Sopen05g008490' => 'spe', 'Sopen07g003910' => 'spe', 'Sopen12g015240' => 'spe', 'Sp1g11550' => 'spa', 'Sp2g16710' => 'spa', 'Sp3g00430' => 'spa', 'Sp3g26780' => 'spa', 'Sp5g22900' => 'spa', 'Sp6g29530' => 'spa', 'TAR371G0794' => 'tar', 'TAR374G0164' => 'tar', 'TAR622G0165' => 'tar', 'TAR626G0929' => 'tar', 'TAR629G2155' => 'tar', 'THA.LOC104805282' => 'tha', 'THA.LOC104805363' => 'tha', 'THA.LOC104808968' => 'tha', 'THA.LOC104821093' => 'tha', 'THA.LOC104823953' => 'tha', 'THA.LOC104825562' => 'tha', 'THA.LOC104825665' => 'tha', 'Thecc.02G261400' => 'tca', 'Thecc.04G019200' => 'tca', 'Thecc.09G130400' => 'tca', 'Thhalv10004374m.g' => 'esa', 'Thhalv10007850m.g' => 'esa', 'Thhalv10013782m.g' => 'esa', 'Thhalv10018686m.g' => 'esa', 'Thhalv10020899m.g' => 'esa', 'Thhalv10022755m.g' => 'esa', 'TPR.G23851' => 'tpr', 'TPR.G26500' => 'tpr', 'TPR.G27267' => 'tpr', 'TPR.G32001' => 'tpr', 'TPR.G6251' => 'tpr', 'TPR.G8167' => 'tpr', 'TWI12G1330' => 'twi', 'TWI18G1239' => 'twi', 'TWI34G0979' => 'twi', 'TWI36G0670' => 'twi', 'TWI36G0707' => 'twi', 'TWI56G0233' => 'twi', 'TWI75G1809' => 'twi', 'unitig_21.g20874' => 'ugi', 'unitig_26.g10343' => 'ugi', 'unitig_46.g18392' => 'ugi', 'unitig_52.g17178' => 'ugi', 'unitig_8.g2934' => 'ugi', 'vmacro01122' => 'vma', 'vmacro05875' => 'vma', 'vmacro06147' => 'vma', 'vmacro16191' => 'vma', 'vmacro18293' => 'vma', 'VMungo0251G3707' => 'vmu', 'VMungo0464G1521' => 'vmu', 'VMungo1215G0205' => 'vmu', 'VMungo1383G2484' => 'vmu', 'Zm00001eb079610' => 'zma', 'Zm00001eb135990' => 'zma', 'Zm00001eb183710' => 'zma', 'Zm00001eb246020' => 'zma' ) $gf_id = 'HOM05D001124' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001124' ) $data_identifier = 'HOM05D001124' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 6, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 7, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 21, 'bol' => (int) 10, 'bra' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 6, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 9, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 21, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 8, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 10, 'lsa' => (int) 8, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 8, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 9, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb246020' $species_info = array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ) $local_species = 'cla' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001124', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '548', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02520' => 'bna', 'A03p06630' => 'bna', 'A05p44460' => 'bna', 'A06p08710' => 'bna', 'A06p41090' => 'bna', 'A07p32320' => 'bna', 'A08p32520' => 'bna', 'A09p10360' => 'bna', 'A10p24080' => 'bna', 'Aa31LG11G15250' => 'aar', 'Aa31LG1G1800' => 'aar', 'Aa31LG2G5120' => 'aar', 'Aa31LG2G6070' => 'aar', 'Aa31LG5G10770' => 'aar', 'Aa31sc61G90' => 'aar', 'Actinidia01352' => 'ach', 'Actinidia05983' => 'ach', 'Actinidia08133' => 'ach', 'Actinidia15101' => 'ach', 'Actinidia26379' => 'ach', 'Actinidia35778' => 'ach', 'Actinidia36123' => 'ach', 'Actinidia37436' => 'ach', 'Actinidia38730' => 'ach', 'Ah.02g128210' => 'amhyb', 'Ah.03g132990' => 'amhyb', 'Ah.14g079410' => 'amhyb', 'AL1G24640' => 'aly', 'AL2G26680' => 'aly', 'AL3G10530' => 'aly', 'AL3G45230' => 'aly', 'AL5G15230' => 'aly', 'AL5G16960' => 'aly', 'AL6G25210' => 'aly', 'Aqoxy2G00441' => 'aox', 'Aqoxy3G01236' => 'aox', 'Aqoxy5G03746' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3RQ047' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C7GMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9C8JER' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MBL6KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YXCZ83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZANX40' => 'arhy', 'AT1G12990' => 'ath', 'AT1G67880' => 'ath', 'AT2G13290' => 'ath', 'AT3G01620' => 'ath', 'AT3G26445' => 'ath', 'AT3G27540' => 'ath', 'AT5G14480' => 'ath', 'ATR0824G026' => 'atr', 'ATR1098G019' => 'atr', 'Atru.chr11.2145' => 'acertr', 'Atru.chr2.3636' => 'acertr', 'Atru.chr2.3644' => 'acertr', 'Atru.chr6.2422' => 'acertr', 'Atru.chr7.1112' => 'acertr', 'AUR62005469' => 'cqu', 'AUR62011166' => 'cqu', 'AUR62013319' => 'cqu', 'AUR62024273' => 'cqu', 'AUR62028420' => 'cqu', 'AUR62041942' => 'cqu', 'BcaB01g04969' => 'bca', 'BcaB01g06371' => 'bca', 'BcaB02g11494' => 'bca', 'BcaB03g15382' => 'bca', 'BcaB08g36994' => 'bca', 'BcaC03g13477' => 'bca', 'BcaC03g13478' => 'bca', 'BcaC03g13480' => 'bca', 'BcaC03g13481' => 'bca', 'BcaC03g13486' => 'bca', 'BcaC04g19031' => 'bca', 'BcaC04g23085' => 'bca', 'BcaC05g25094' => 'bca', 'BcaC05g25096' => 'bca', 'BcaC05g25138' => 'bca', 'BcaC05g30416' => 'bca', 'BcaC05g30455' => 'bca', 'BcaC06g30979' => 'bca', 'BcaC06g33805' => 'bca', 'BcaC08g46021' => 'bca', 'BcaNung03154' => 'bca', 'BolC2t06623H' => 'bol', 'BolC2t06632H' => 'bol', 'BolC2t06635H' => 'bol', 'BolC2t06638H' => 'bol', 'BolC3t13266H' => 'bol', 'BolC5t29776H' => 'bol', 'BolC6t38912H' => 'bol', 'BolC7t44183H' => 'bol', 'BolC9t54123H' => 'bol', 'BolC9t59107H' => 'bol', 'BraA02t05221Z' => 'bra', 'BraA03t09996Z' => 'bra', 'BraA05t23210Z' => 'bra', 'BraA06t24068Z' => 'bra', 'BraA06t27032Z' => 'bra', 'BraA08t35176Z' => 'bra', 'BraA09t36680Z' => 'bra', 'BraA10t44471Z' => 'bra', 'C02p06760' => 'bna', 'C02p06890' => 'bna', 'C02p07010' => 'bna', 'C03p07660' => 'bna', 'C05p10300' => 'bna', 'C06p38150' => 'bna', 'C07p36650' => 'bna', 'C08p15770' => 'bna', 'C09p12300' => 'bna', 'C09p62700' => 'bna', 'C09p75040' => 'bna', 'CAN.G13.1' => 'can', 'CAN.G138.4' => 'can', 'CAN.G44.6' => 'can', 'CAN.G473.19' => 'can', 'CANSAT01G0835' => 'cansat', 'CANSAT11G0246' => 'cansat', 'CANSAT11G1766' => 'cansat', 'CANSAT64G1954' => 'cansat', 'CARHR013330' => 'chi', 'CARHR060530' => 'chi', 'CARHR075300' => 'chi', 'CARHR105120' => 'chi', 'CARHR148910' => 'chi', 'CARHR198830' => 'chi', 'Carub.0001s1275' => 'cru', 'Carub.0002s1437' => 'cru', 'Carub.0003s0044' => 'cru', 'Carub.0003s2787' => 'cru', 'Carub.0005s0597' => 'cru', 'Carub.0006s1266' => 'cru', 'Ca_06935_v3' => 'car', 'Ca_13559_v3' => 'car', 'Ca_16941_v3' => 'car', 'Ca_16960_v3' => 'car', 'Ca_17775_v3' => 'car', 'Ca_30464_v3' => 'car', 'Cc06_g08160' => 'ccan', 'Cc07_g01520' => 'ccan', 'Cc11_g15810' => 'ccan', 'CDE02G2840' => 'cde', 'CDE03G0093' => 'cde', 'CDE04G2127' => 'cde', 'CDE07G1857' => 'cde', 'CDE09G1246' => 'cde', 'Cfa003412' => 'cfa', 'Cfa007341' => 'cfa', 'Cfa009220' => 'cfa', 'Ciclev10008737m.g' => 'ccl', 'Ciclev10015565m.g' => 'ccl', 'Ciclev10031761m.g' => 'ccl', 'CiPaw.03G045300' => 'cil', 'CiPaw.03G247200' => 'cil', 'CiPaw.04G029500' => 'cil', 'CiPaw.04G174000' => 'cil', 'CiPaw.05G181200' => 'cil', 'CiPaw.06G067100' => 'cil', 'ClCG05G025800' => 'cla', 'ClCG06G011400' => 'cla', 'ClCG09G019360' => 'cla', 'COL.COLO4_04827' => 'col', 'COL.COLO4_29170' => 'col', 'COL.COLO4_35131' => 'col', 'COL.COLO4_35132' => 'col', 'Cpa.g.sc33.32' => 'cpa', 'Cpa.g.sc46.29' => 'cpa', 'Cpa.g.sc796.1' => 'cpa', 'CsaV3_1G030420' => 'csa', 'CsaV3_5G027050' => 'csa', 'CsaV3_5G031040' => 'csa', 'CsaV3_UNG023130' => 'csa', 'CSS0007726' => 'camsi', 'CSS0016433' => 'camsi', 'CSS0017656' => 'camsi', 'CSS0025364' => 'camsi', 'CSS0027582' => 'camsi', 'CSS0047288' => 'camsi', 'CSS0049950' => 'camsi', 'DCAR_003843' => 'dca', 'DCAR_007052' => 'dca', 'DCAR_020884' => 'dca', 'DCAR_021730' => 'dca', 'DCAR_024423' => 'dca', 'DCAR_026509' => 'dca', 'DCAR_031158' => 'dca', 'Dinv14728' => 'din', 'Dinv15219' => 'din', 'Dinv25728' => 'din', 'Dinv33428' => 'din', 'Dinv36489' => 'din', 'Dinv41486' => 'din', 'Duzib147G0469' => 'dzi', 'Duzib168G0060' => 'dzi', 'Duzib187G1215' => 'dzi', 'Duzib248G0692' => 'dzi', 'Duzib251G0767' => 'dzi', 'Duzib264G0446' => 'dzi', 'Duzib268G0691' => 'dzi', 'ECA232G4767' => 'eca', 'ECA233G2838' => 'eca', 'ECA234G0391' => 'eca', 'ECA234G0857' => 'eca', 'ECA236G1593' => 'eca', 'ECA238G0565' => 'eca', 'ECA246G1027' => 'eca', 'ECA246G3223' => 'eca', 'ECA246G3470' => 'eca', 'EL10Ac6g13829' => 'bvu', 'EL10Ac6g14093' => 'bvu', 'EL10Ac8g18707' => 'bvu', 'Eucgr.C01369' => 'egr', 'Eucgr.H02492' => 'egr', 'Eucgr.I01733' => 'egr', 'Eucgr.J02255' => 'egr', 'Eucgr.J02257' => 'egr', 'Eucgr.J02258' => 'egr', 'FAN02G1601' => 'fan', 'FAN03G1586' => 'fan', 'FAN03G2986' => 'fan', 'FAN05G4837' => 'fan', 'FAN06G0146' => 'fan', 'FAN07G0858' => 'fan', 'FAN09G3179' => 'fan', 'FAN10G0669' => 'fan', 'FAN12G2358' => 'fan', 'FAN14G4198' => 'fan', 'FAN14G5112' => 'fan', 'FAN17G0342' => 'fan', 'FAN19G0342' => 'fan', 'FAN19G0962' => 'fan', 'FAN19G1101' => 'fan', 'FAN19G1872' => 'fan', 'FAN22G0356' => 'fan', 'FAN23G0744' => 'fan', 'FAN23G1914' => 'fan', 'FAN26G0032' => 'fan', 'FAN28G0625' => 'fan', 'FvH4_1g02710' => 'fve', 'FvH4_1g02720' => 'fve', 'FvH4_4g25670' => 'fve', 'FvH4_6g51700' => 'fve', 'FvH4_7g20170' => 'fve', 'Glyma.05G175000' => 'gma', 'Glyma.08G132300' => 'gma', 'Glyma.11G243000' => 'gma', 'Glyma.13G158900' => 'gma', 'Glyma.17G112400' => 'gma', 'Glyma.18G014100' => 'gma', 'Glyma.19G003100' => 'gma', 'Glyma.19G056500' => 'gma', 'Gohir.A01G158900' => 'ghi', 'Gohir.A05G312600' => 'ghi', 'Gohir.A05G354900' => 'ghi', 'Gohir.A07G037200' => 'ghi', 'Gohir.A09G030000' => 'ghi', 'Gohir.A12G145200' => 'ghi', 'Gohir.D01G151500' => 'ghi', 'Gohir.D04G058300' => 'ghi', 'Gohir.D05G314100' => 'ghi', 'Gohir.D07G041400' => 'ghi', 'Gohir.D09G029700' => 'ghi', 'Gohir.D12G149700' => 'ghi', 'Gorai.001G043800' => 'gra', 'Gorai.002G187800' => 'gra', 'Gorai.006G034700' => 'gra', 'Gorai.008G161200' => 'gra', 'Gorai.009G335700' => 'gra', 'Gorai.012G065000' => 'gra', 'GSVIVG01000535001' => 'vvi', 'GSVIVG01015572001' => 'vvi', 'GSVIVG01032386001' => 'vvi', 'HanXRQChr05g0138531' => 'han', 'HanXRQChr06g0174391' => 'han', 'HanXRQChr07g0199021' => 'han', 'HanXRQChr08g0208211' => 'han', 'HanXRQChr09g0255471' => 'han', 'HanXRQChr10g0315791' => 'han', 'HanXRQChr12g0371991' => 'han', 'HanXRQChr15g0475251' => 'han', 'HanXRQChr17g0540001' => 'han', 'HanXRQChr17g0548631' => 'han', 'HanXRQChr17g0569561' => 'han', 'Haze_12256' => 'cav', 'Haze_14756' => 'cav', 'Haze_25528' => 'cav', 'Hma1.2p1_0079F.1_g041020' => 'hma', 'Hma1.2p1_0818F.1_g223260' => 'hma', 'Hma1.2p1_1747F.1_g300530' => 'hma', 'HPP92_004607' => 'vpl', 'HPP92_004608' => 'vpl', 'HPP92_006181' => 'vpl', 'HPP92_012192' => 'vpl', 'HPP92_015680' => 'vpl', 'HPP92_020249' => 'vpl', 'HPP92_021376' => 'vpl', 'HPP92_024275' => 'vpl', 'Hund06031' => 'sun', 'Hund25391' => 'sun', 'Lalb_Chr07g0185371' => 'lal', 'Lalb_Chr07g0185381' => 'lal', 'Lalb_Chr12g0204011' => 'lal', 'Lalb_Chr13g0301671' => 'lal', 'Lalb_Chr14g0362851' => 'lal', 'Lalb_Chr24g0403581' => 'lal', 'Lj1g0000233' => 'lja', 'Lj2g0018120' => 'lja', 'Lj3C621T0' => 'lonja', 'Lj3P1059T14' => 'lonja', 'Lj3P611T9' => 'lonja', 'Lj3P614T13' => 'lonja', 'Lj3P615T5' => 'lonja', 'Lj4g0012315' => 'lja', 'Lj4g0026182' => 'lja', 'Lj6P813T16' => 'lonja', 'Lj7C427T7' => 'lonja', 'Lj7C427T8' => 'lonja', 'Lj7P600T41' => 'lonja', 'Lju41C42G17' => 'lonja', 'Lsat_1_v5_gn_0_47300' => 'lsa', 'Lsat_1_v5_gn_2_91280' => 'lsa', 'Lsat_1_v5_gn_3_30561' => 'lsa', 'Lsat_1_v5_gn_4_184321' => 'lsa', 'Lsat_1_v5_gn_4_4041' => 'lsa', 'Lsat_1_v5_gn_5_92000' => 'lsa', 'Lsat_1_v5_gn_8_152940' => 'lsa', 'Lsat_1_v5_gn_8_62401' => 'lsa', 'Manes.06G055900' => 'mes', 'Manes.12G022200' => 'mes', 'Manes.13G023300' => 'mes', 'Manes.14G115000' => 'mes', 'Manes.15G151700' => 'mes', 'Manes.17G111300' => 'mes', 'Mapoly0226s0009' => 'mpo', 'MBI02_g25363_MAGBIO' => 'mbi', 'MBI06_g00027_MAGBIO' => 'mbi', 'MBI10_g13034_MAGBIO' => 'mbi', 'MD09G1023400' => 'mdo', 'MD13G1100100' => 'mdo', 'MD15G1169200' => 'mdo', 'MD16G1101100' => 'mdo', 'MD17G1022900' => 'mdo', 'Medtr3g096150' => 'mtr', 'Medtr4g115070' => 'mtr', 'Medtr7g033325' => 'mtr', 'Medtr8g089840' => 'mtr', 'MELO3C010319.2' => 'cme', 'MELO3C011944.2' => 'cme', 'MELO3C021589.2' => 'cme', 'Migut.E00207' => 'egut', 'Migut.H00067' => 'egut', 'Migut.K00433' => 'egut', 'Migut.K00606' => 'egut', 'Migut.K01410' => 'egut', 'MSTRG.13347' => 'ama', 'MSTRG.24045' => 'ama', 'MSTRG.2428' => 'ama', 'MSTRG.26410' => 'ama', 'MSTRG.3139' => 'ama', 'MSTRG.3286' => 'ama', 'MSTRG.563' => 'ama', 'MSTRG.7941' => 'ama', 'Nitab4.5_0000028g0060' => 'nta', 'Nitab4.5_0000065g0260' => 'nta', 'Nitab4.5_0000112g0060' => 'nta', 'Nitab4.5_0000489g0120' => 'nta', 'Nitab4.5_0001776g0050' => 'nta', 'Nitab4.5_0001854g0010' => 'nta', 'Nitab4.5_0001860g0020' => 'nta', 'Nitab4.5_0004352g0010' => 'nta', 'Nitab4.5_0008716g0020' => 'nta', 'Nitab4.5_0008922g0010' => 'nta', 'Nn3g16693' => 'nnu', 'Nn4g22596' => 'nnu', 'Nn7g37639' => 'nnu', 'Oeu001701.1' => 'oeu', 'Oeu018149.1' => 'oeu', 'Oeu026220.1' => 'oeu', 'Oeu038635.1' => 'oeu', 'Oeu049176.1' => 'oeu', 'Oeu056706.1' => 'oeu', 'Oeu056937.1' => 'oeu', 'Oeu057540.1' => 'oeu', 'Os02g0594900' => 'osa', 'Os02g0595100' => 'osa', 'Os04g0477500' => 'osa', 'Os12g0611900' => 'osa', 'Peaxi162Scf00076g00020' => 'pax', 'Peaxi162Scf00128g00217' => 'pax', 'Peaxi162Scf00129g01640' => 'pax', 'Peaxi162Scf00669g00007' => 'pax', 'Peaxi162Scf00700g00421' => 'pax', 'Peaxi162Scf00801g00038' => 'pax', 'Peaxi162Scf00891g00025' => 'pax', 'PGR083G0909' => 'pgr', 'PGR119G1005' => 'pgr', 'PGR142G2236' => 'pgr', 'PGR142G3388' => 'pgr', 'PGSC0003DMG400004514' => 'stu', 'PGSC0003DMG400012635' => 'stu', 'PGSC0003DMG400015730' => 'stu', 'PGSC0003DMG400018611' => 'stu', 'PGSC0003DMG400030897' => 'stu', 'Phvul.001G254800' => 'pvu', 'Phvul.002G260100' => 'pvu', 'Phvul.003G167600' => 'pvu', 'Phvul.004G005100' => 'pvu', 'Potri.001G343600' => 'ptr', 'Potri.006G066700' => 'ptr', 'Potri.008G186000' => 'ptr', 'Potri.010G046900' => 'ptr', 'Potri.018G127900' => 'ptr', 'Pp3c20_17750' => 'ppa', 'Pp3c24_4380' => 'ppa', 'Prupe.1G245800' => 'ppe', 'Prupe.3G293400' => 'ppe', 'Prupe.7G247400' => 'ppe', 'Psat0s145g0120' => 'psa', 'Psat0s595g0040' => 'psa', 'Psat0s595g0120' => 'psa', 'Psat3g175040' => 'psa', 'Psat7g058120' => 'psa', 'PSO017G0428' => 'pso', 'PSO063G7510' => 'pso', 'PSO067G0046' => 'pso', 'PSO478G1073' => 'pso', 'PSO675G3677' => 'pso', 'PSO675G6558' => 'pso', 'PSO675G7520' => 'pso', 'PSO675G8959' => 'pso', 'QL02p074089' => 'qlo', 'QL02p089614' => 'qlo', 'QL03p057736' => 'qlo', 'RcHm_v2.0_Chr1g0364131' => 'rch', 'RcHm_v2.0_Chr2g0087801' => 'rch', 'RcHm_v2.0_Chr2g0087821' => 'rch', 'RcHm_v2.0_Chr2g0173231' => 'rch', 'RcHm_v2.0_Chr4g0433111' => 'rch', 'Rhsim03G0250300' => 'rsi', 'Rhsim08G0048400' => 'rsi', 'Rhsim10G0014800' => 'rsi', 'Rhsim12G0040100' => 'rsi', 'Rhsim12G0109700' => 'rsi', 'Sabra06G0049600' => 'sbr', 'Sabra08G0141000' => 'sbr', 'Sabra10G0021400' => 'sbr', 'Sabra16G0222900' => 'sbr', 'Sabra18G0108600' => 'sbr', 'SalBow1G0433' => 'sbo', 'SalBow1G2038' => 'sbo', 'SalBow1G5003' => 'sbo', 'SalBow7G1197' => 'sbo', 'SalBow8G3506' => 'sbo', 'Sc03g0007300' => 'sci', 'Sc11g0000950' => 'sci', 'Sc14g0008750' => 'sci', 'Sc18g0000420' => 'sci', 'Sed0006754' => 'sed', 'Sed0008741' => 'sed', 'Sed0017172' => 'sed', 'Sed0018925' => 'sed', 'Sed0023326' => 'sed', 'Sed0025909' => 'sed', 'SEGI_05333' => 'sgi', 'SEGI_10362' => 'sgi', 'SEGI_13380' => 'sgi', 'SEGI_24306' => 'sgi', 'SEGI_29077' => 'sgi', 'SEGI_29095' => 'sgi', 'SEGI_36534' => 'sgi', 'SEGI_37506' => 'sgi', 'SEGI_38321' => 'sgi', 'SGA_v2.0_scaffold307G48031' => 'sas', 'SGA_v2.0_scaffold47G17507' => 'sas', 'SGA_v2.0_scaffold63G21736' => 'sas', 'SGA_v2.0_scaffold87G27070' => 'sas', 'SHI17794' => 'shi', 'SHI28851' => 'shi', 'SMO165G0155' => 'smo', 'SMO340G0217' => 'smo', 'SMO367G1210' => 'smo', 'Solyc02g093430.3' => 'sly', 'Solyc05g013580.4' => 'sly', 'Solyc07g008030.3' => 'sly', 'Solyc12g035470.2' => 'sly', 'Sopen02g038020' => 'spe', 'Sopen05g008490' => 'spe', 'Sopen07g003910' => 'spe', 'Sopen12g015240' => 'spe', 'Sp1g11550' => 'spa', 'Sp2g16710' => 'spa', 'Sp3g00430' => 'spa', 'Sp3g26780' => 'spa', 'Sp5g22900' => 'spa', 'Sp6g29530' => 'spa', 'TAR371G0794' => 'tar', 'TAR374G0164' => 'tar', 'TAR622G0165' => 'tar', 'TAR626G0929' => 'tar', 'TAR629G2155' => 'tar', 'THA.LOC104805282' => 'tha', 'THA.LOC104805363' => 'tha', 'THA.LOC104808968' => 'tha', 'THA.LOC104821093' => 'tha', 'THA.LOC104823953' => 'tha', 'THA.LOC104825562' => 'tha', 'THA.LOC104825665' => 'tha', 'Thecc.02G261400' => 'tca', 'Thecc.04G019200' => 'tca', 'Thecc.09G130400' => 'tca', 'Thhalv10004374m.g' => 'esa', 'Thhalv10007850m.g' => 'esa', 'Thhalv10013782m.g' => 'esa', 'Thhalv10018686m.g' => 'esa', 'Thhalv10020899m.g' => 'esa', 'Thhalv10022755m.g' => 'esa', 'TPR.G23851' => 'tpr', 'TPR.G26500' => 'tpr', 'TPR.G27267' => 'tpr', 'TPR.G32001' => 'tpr', 'TPR.G6251' => 'tpr', 'TPR.G8167' => 'tpr', 'TWI12G1330' => 'twi', 'TWI18G1239' => 'twi', 'TWI34G0979' => 'twi', 'TWI36G0670' => 'twi', 'TWI36G0707' => 'twi', 'TWI56G0233' => 'twi', 'TWI75G1809' => 'twi', 'unitig_21.g20874' => 'ugi', 'unitig_26.g10343' => 'ugi', 'unitig_46.g18392' => 'ugi', 'unitig_52.g17178' => 'ugi', 'unitig_8.g2934' => 'ugi', 'vmacro01122' => 'vma', 'vmacro05875' => 'vma', 'vmacro06147' => 'vma', 'vmacro16191' => 'vma', 'vmacro18293' => 'vma', 'VMungo0251G3707' => 'vmu', 'VMungo0464G1521' => 'vmu', 'VMungo1215G0205' => 'vmu', 'VMungo1383G2484' => 'vmu', 'Zm00001eb079610' => 'zma', 'Zm00001eb135990' => 'zma', 'Zm00001eb183710' => 'zma', 'Zm00001eb246020' => 'zma' ), 'gf_id' => 'HOM05D001124', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001124' ), 'data_identifier' => 'HOM05D001124', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001124', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '548', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02520' => 'bna', 'A03p06630' => 'bna', 'A05p44460' => 'bna', 'A06p08710' => 'bna', 'A06p41090' => 'bna', 'A07p32320' => 'bna', 'A08p32520' => 'bna', 'A09p10360' => 'bna', 'A10p24080' => 'bna', 'Aa31LG11G15250' => 'aar', 'Aa31LG1G1800' => 'aar', 'Aa31LG2G5120' => 'aar', 'Aa31LG2G6070' => 'aar', 'Aa31LG5G10770' => 'aar', 'Aa31sc61G90' => 'aar', 'Actinidia01352' => 'ach', 'Actinidia05983' => 'ach', 'Actinidia08133' => 'ach', 'Actinidia15101' => 'ach', 'Actinidia26379' => 'ach', 'Actinidia35778' => 'ach', 'Actinidia36123' => 'ach', 'Actinidia37436' => 'ach', 'Actinidia38730' => 'ach', 'Ah.02g128210' => 'amhyb', 'Ah.03g132990' => 'amhyb', 'Ah.14g079410' => 'amhyb', 'AL1G24640' => 'aly', 'AL2G26680' => 'aly', 'AL3G10530' => 'aly', 'AL3G45230' => 'aly', 'AL5G15230' => 'aly', 'AL5G16960' => 'aly', 'AL6G25210' => 'aly', 'Aqoxy2G00441' => 'aox', 'Aqoxy3G01236' => 'aox', 'Aqoxy5G03746' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3RQ047' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C7GMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9C8JER' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MBL6KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YXCZ83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZANX40' => 'arhy', 'AT1G12990' => 'ath', 'AT1G67880' => 'ath', 'AT2G13290' => 'ath', 'AT3G01620' => 'ath', 'AT3G26445' => 'ath', 'AT3G27540' => 'ath', 'AT5G14480' => 'ath', 'ATR0824G026' => 'atr', 'ATR1098G019' => 'atr', 'Atru.chr11.2145' => 'acertr', 'Atru.chr2.3636' => 'acertr', 'Atru.chr2.3644' => 'acertr', 'Atru.chr6.2422' => 'acertr', 'Atru.chr7.1112' => 'acertr', 'AUR62005469' => 'cqu', 'AUR62011166' => 'cqu', 'AUR62013319' => 'cqu', 'AUR62024273' => 'cqu', 'AUR62028420' => 'cqu', 'AUR62041942' => 'cqu', 'BcaB01g04969' => 'bca', 'BcaB01g06371' => 'bca', 'BcaB02g11494' => 'bca', 'BcaB03g15382' => 'bca', 'BcaB08g36994' => 'bca', 'BcaC03g13477' => 'bca', 'BcaC03g13478' => 'bca', 'BcaC03g13480' => 'bca', 'BcaC03g13481' => 'bca', 'BcaC03g13486' => 'bca', 'BcaC04g19031' => 'bca', 'BcaC04g23085' => 'bca', 'BcaC05g25094' => 'bca', 'BcaC05g25096' => 'bca', 'BcaC05g25138' => 'bca', 'BcaC05g30416' => 'bca', 'BcaC05g30455' => 'bca', 'BcaC06g30979' => 'bca', 'BcaC06g33805' => 'bca', 'BcaC08g46021' => 'bca', 'BcaNung03154' => 'bca', 'BolC2t06623H' => 'bol', 'BolC2t06632H' => 'bol', 'BolC2t06635H' => 'bol', 'BolC2t06638H' => 'bol', 'BolC3t13266H' => 'bol', 'BolC5t29776H' => 'bol', 'BolC6t38912H' => 'bol', 'BolC7t44183H' => 'bol', 'BolC9t54123H' => 'bol', 'BolC9t59107H' => 'bol', 'BraA02t05221Z' => 'bra', 'BraA03t09996Z' => 'bra', 'BraA05t23210Z' => 'bra', 'BraA06t24068Z' => 'bra', 'BraA06t27032Z' => 'bra', 'BraA08t35176Z' => 'bra', 'BraA09t36680Z' => 'bra', 'BraA10t44471Z' => 'bra', 'C02p06760' => 'bna', 'C02p06890' => 'bna', 'C02p07010' => 'bna', 'C03p07660' => 'bna', 'C05p10300' => 'bna', 'C06p38150' => 'bna', 'C07p36650' => 'bna', 'C08p15770' => 'bna', 'C09p12300' => 'bna', 'C09p62700' => 'bna', 'C09p75040' => 'bna', 'CAN.G13.1' => 'can', 'CAN.G138.4' => 'can', 'CAN.G44.6' => 'can', 'CAN.G473.19' => 'can', 'CANSAT01G0835' => 'cansat', 'CANSAT11G0246' => 'cansat', 'CANSAT11G1766' => 'cansat', 'CANSAT64G1954' => 'cansat', 'CARHR013330' => 'chi', 'CARHR060530' => 'chi', 'CARHR075300' => 'chi', 'CARHR105120' => 'chi', 'CARHR148910' => 'chi', 'CARHR198830' => 'chi', 'Carub.0001s1275' => 'cru', 'Carub.0002s1437' => 'cru', 'Carub.0003s0044' => 'cru', 'Carub.0003s2787' => 'cru', 'Carub.0005s0597' => 'cru', 'Carub.0006s1266' => 'cru', 'Ca_06935_v3' => 'car', 'Ca_13559_v3' => 'car', 'Ca_16941_v3' => 'car', 'Ca_16960_v3' => 'car', 'Ca_17775_v3' => 'car', 'Ca_30464_v3' => 'car', 'Cc06_g08160' => 'ccan', 'Cc07_g01520' => 'ccan', 'Cc11_g15810' => 'ccan', 'CDE02G2840' => 'cde', 'CDE03G0093' => 'cde', 'CDE04G2127' => 'cde', 'CDE07G1857' => 'cde', 'CDE09G1246' => 'cde', 'Cfa003412' => 'cfa', 'Cfa007341' => 'cfa', 'Cfa009220' => 'cfa', 'Ciclev10008737m.g' => 'ccl', 'Ciclev10015565m.g' => 'ccl', 'Ciclev10031761m.g' => 'ccl', 'CiPaw.03G045300' => 'cil', 'CiPaw.03G247200' => 'cil', 'CiPaw.04G029500' => 'cil', 'CiPaw.04G174000' => 'cil', 'CiPaw.05G181200' => 'cil', 'CiPaw.06G067100' => 'cil', 'ClCG05G025800' => 'cla', 'ClCG06G011400' => 'cla', 'ClCG09G019360' => 'cla', 'COL.COLO4_04827' => 'col', 'COL.COLO4_29170' => 'col', 'COL.COLO4_35131' => 'col', 'COL.COLO4_35132' => 'col', 'Cpa.g.sc33.32' => 'cpa', 'Cpa.g.sc46.29' => 'cpa', 'Cpa.g.sc796.1' => 'cpa', 'CsaV3_1G030420' => 'csa', 'CsaV3_5G027050' => 'csa', 'CsaV3_5G031040' => 'csa', 'CsaV3_UNG023130' => 'csa', 'CSS0007726' => 'camsi', 'CSS0016433' => 'camsi', 'CSS0017656' => 'camsi', 'CSS0025364' => 'camsi', 'CSS0027582' => 'camsi', 'CSS0047288' => 'camsi', 'CSS0049950' => 'camsi', 'DCAR_003843' => 'dca', 'DCAR_007052' => 'dca', 'DCAR_020884' => 'dca', 'DCAR_021730' => 'dca', 'DCAR_024423' => 'dca', 'DCAR_026509' => 'dca', 'DCAR_031158' => 'dca', 'Dinv14728' => 'din', 'Dinv15219' => 'din', 'Dinv25728' => 'din', 'Dinv33428' => 'din', 'Dinv36489' => 'din', 'Dinv41486' => 'din', 'Duzib147G0469' => 'dzi', 'Duzib168G0060' => 'dzi', 'Duzib187G1215' => 'dzi', 'Duzib248G0692' => 'dzi', 'Duzib251G0767' => 'dzi', 'Duzib264G0446' => 'dzi', 'Duzib268G0691' => 'dzi', 'ECA232G4767' => 'eca', 'ECA233G2838' => 'eca', 'ECA234G0391' => 'eca', 'ECA234G0857' => 'eca', 'ECA236G1593' => 'eca', 'ECA238G0565' => 'eca', 'ECA246G1027' => 'eca', 'ECA246G3223' => 'eca', 'ECA246G3470' => 'eca', 'EL10Ac6g13829' => 'bvu', 'EL10Ac6g14093' => 'bvu', 'EL10Ac8g18707' => 'bvu', 'Eucgr.C01369' => 'egr', 'Eucgr.H02492' => 'egr', 'Eucgr.I01733' => 'egr', 'Eucgr.J02255' => 'egr', 'Eucgr.J02257' => 'egr', 'Eucgr.J02258' => 'egr', 'FAN02G1601' => 'fan', 'FAN03G1586' => 'fan', 'FAN03G2986' => 'fan', 'FAN05G4837' => 'fan', 'FAN06G0146' => 'fan', 'FAN07G0858' => 'fan', 'FAN09G3179' => 'fan', 'FAN10G0669' => 'fan', 'FAN12G2358' => 'fan', 'FAN14G4198' => 'fan', 'FAN14G5112' => 'fan', 'FAN17G0342' => 'fan', 'FAN19G0342' => 'fan', 'FAN19G0962' => 'fan', 'FAN19G1101' => 'fan', 'FAN19G1872' => 'fan', 'FAN22G0356' => 'fan', 'FAN23G0744' => 'fan', 'FAN23G1914' => 'fan', 'FAN26G0032' => 'fan', 'FAN28G0625' => 'fan', 'FvH4_1g02710' => 'fve', 'FvH4_1g02720' => 'fve', 'FvH4_4g25670' => 'fve', 'FvH4_6g51700' => 'fve', 'FvH4_7g20170' => 'fve', 'Glyma.05G175000' => 'gma', 'Glyma.08G132300' => 'gma', 'Glyma.11G243000' => 'gma', 'Glyma.13G158900' => 'gma', 'Glyma.17G112400' => 'gma', 'Glyma.18G014100' => 'gma', 'Glyma.19G003100' => 'gma', 'Glyma.19G056500' => 'gma', 'Gohir.A01G158900' => 'ghi', 'Gohir.A05G312600' => 'ghi', 'Gohir.A05G354900' => 'ghi', 'Gohir.A07G037200' => 'ghi', 'Gohir.A09G030000' => 'ghi', 'Gohir.A12G145200' => 'ghi', 'Gohir.D01G151500' => 'ghi', 'Gohir.D04G058300' => 'ghi', 'Gohir.D05G314100' => 'ghi', 'Gohir.D07G041400' => 'ghi', 'Gohir.D09G029700' => 'ghi', 'Gohir.D12G149700' => 'ghi', 'Gorai.001G043800' => 'gra', 'Gorai.002G187800' => 'gra', 'Gorai.006G034700' => 'gra', 'Gorai.008G161200' => 'gra', 'Gorai.009G335700' => 'gra', 'Gorai.012G065000' => 'gra', 'GSVIVG01000535001' => 'vvi', 'GSVIVG01015572001' => 'vvi', 'GSVIVG01032386001' => 'vvi', 'HanXRQChr05g0138531' => 'han', 'HanXRQChr06g0174391' => 'han', 'HanXRQChr07g0199021' => 'han', 'HanXRQChr08g0208211' => 'han', 'HanXRQChr09g0255471' => 'han', 'HanXRQChr10g0315791' => 'han', 'HanXRQChr12g0371991' => 'han', 'HanXRQChr15g0475251' => 'han', 'HanXRQChr17g0540001' => 'han', 'HanXRQChr17g0548631' => 'han', 'HanXRQChr17g0569561' => 'han', 'Haze_12256' => 'cav', 'Haze_14756' => 'cav', 'Haze_25528' => 'cav', 'Hma1.2p1_0079F.1_g041020' => 'hma', 'Hma1.2p1_0818F.1_g223260' => 'hma', 'Hma1.2p1_1747F.1_g300530' => 'hma', 'HPP92_004607' => 'vpl', 'HPP92_004608' => 'vpl', 'HPP92_006181' => 'vpl', 'HPP92_012192' => 'vpl', 'HPP92_015680' => 'vpl', 'HPP92_020249' => 'vpl', 'HPP92_021376' => 'vpl', 'HPP92_024275' => 'vpl', 'Hund06031' => 'sun', 'Hund25391' => 'sun', 'Lalb_Chr07g0185371' => 'lal', 'Lalb_Chr07g0185381' => 'lal', 'Lalb_Chr12g0204011' => 'lal', 'Lalb_Chr13g0301671' => 'lal', 'Lalb_Chr14g0362851' => 'lal', 'Lalb_Chr24g0403581' => 'lal', 'Lj1g0000233' => 'lja', 'Lj2g0018120' => 'lja', 'Lj3C621T0' => 'lonja', 'Lj3P1059T14' => 'lonja', 'Lj3P611T9' => 'lonja', 'Lj3P614T13' => 'lonja', 'Lj3P615T5' => 'lonja', 'Lj4g0012315' => 'lja', 'Lj4g0026182' => 'lja', 'Lj6P813T16' => 'lonja', 'Lj7C427T7' => 'lonja', 'Lj7C427T8' => 'lonja', 'Lj7P600T41' => 'lonja', 'Lju41C42G17' => 'lonja', 'Lsat_1_v5_gn_0_47300' => 'lsa', 'Lsat_1_v5_gn_2_91280' => 'lsa', 'Lsat_1_v5_gn_3_30561' => 'lsa', 'Lsat_1_v5_gn_4_184321' => 'lsa', 'Lsat_1_v5_gn_4_4041' => 'lsa', 'Lsat_1_v5_gn_5_92000' => 'lsa', 'Lsat_1_v5_gn_8_152940' => 'lsa', 'Lsat_1_v5_gn_8_62401' => 'lsa', 'Manes.06G055900' => 'mes', 'Manes.12G022200' => 'mes', 'Manes.13G023300' => 'mes', 'Manes.14G115000' => 'mes', 'Manes.15G151700' => 'mes', 'Manes.17G111300' => 'mes', 'Mapoly0226s0009' => 'mpo', 'MBI02_g25363_MAGBIO' => 'mbi', 'MBI06_g00027_MAGBIO' => 'mbi', 'MBI10_g13034_MAGBIO' => 'mbi', 'MD09G1023400' => 'mdo', 'MD13G1100100' => 'mdo', 'MD15G1169200' => 'mdo', 'MD16G1101100' => 'mdo', 'MD17G1022900' => 'mdo', 'Medtr3g096150' => 'mtr', 'Medtr4g115070' => 'mtr', 'Medtr7g033325' => 'mtr', 'Medtr8g089840' => 'mtr', 'MELO3C010319.2' => 'cme', 'MELO3C011944.2' => 'cme', 'MELO3C021589.2' => 'cme', 'Migut.E00207' => 'egut', 'Migut.H00067' => 'egut', 'Migut.K00433' => 'egut', 'Migut.K00606' => 'egut', 'Migut.K01410' => 'egut', 'MSTRG.13347' => 'ama', 'MSTRG.24045' => 'ama', 'MSTRG.2428' => 'ama', 'MSTRG.26410' => 'ama', 'MSTRG.3139' => 'ama', 'MSTRG.3286' => 'ama', 'MSTRG.563' => 'ama', 'MSTRG.7941' => 'ama', 'Nitab4.5_0000028g0060' => 'nta', 'Nitab4.5_0000065g0260' => 'nta', 'Nitab4.5_0000112g0060' => 'nta', 'Nitab4.5_0000489g0120' => 'nta', 'Nitab4.5_0001776g0050' => 'nta', 'Nitab4.5_0001854g0010' => 'nta', 'Nitab4.5_0001860g0020' => 'nta', 'Nitab4.5_0004352g0010' => 'nta', 'Nitab4.5_0008716g0020' => 'nta', 'Nitab4.5_0008922g0010' => 'nta', 'Nn3g16693' => 'nnu', 'Nn4g22596' => 'nnu', 'Nn7g37639' => 'nnu', 'Oeu001701.1' => 'oeu', 'Oeu018149.1' => 'oeu', 'Oeu026220.1' => 'oeu', 'Oeu038635.1' => 'oeu', 'Oeu049176.1' => 'oeu', 'Oeu056706.1' => 'oeu', 'Oeu056937.1' => 'oeu', 'Oeu057540.1' => 'oeu', 'Os02g0594900' => 'osa', 'Os02g0595100' => 'osa', 'Os04g0477500' => 'osa', 'Os12g0611900' => 'osa', 'Peaxi162Scf00076g00020' => 'pax', 'Peaxi162Scf00128g00217' => 'pax', 'Peaxi162Scf00129g01640' => 'pax', 'Peaxi162Scf00669g00007' => 'pax', 'Peaxi162Scf00700g00421' => 'pax', 'Peaxi162Scf00801g00038' => 'pax', 'Peaxi162Scf00891g00025' => 'pax', 'PGR083G0909' => 'pgr', 'PGR119G1005' => 'pgr', 'PGR142G2236' => 'pgr', 'PGR142G3388' => 'pgr', 'PGSC0003DMG400004514' => 'stu', 'PGSC0003DMG400012635' => 'stu', 'PGSC0003DMG400015730' => 'stu', 'PGSC0003DMG400018611' => 'stu', 'PGSC0003DMG400030897' => 'stu', 'Phvul.001G254800' => 'pvu', 'Phvul.002G260100' => 'pvu', 'Phvul.003G167600' => 'pvu', 'Phvul.004G005100' => 'pvu', 'Potri.001G343600' => 'ptr', 'Potri.006G066700' => 'ptr', 'Potri.008G186000' => 'ptr', 'Potri.010G046900' => 'ptr', 'Potri.018G127900' => 'ptr', 'Pp3c20_17750' => 'ppa', 'Pp3c24_4380' => 'ppa', 'Prupe.1G245800' => 'ppe', 'Prupe.3G293400' => 'ppe', 'Prupe.7G247400' => 'ppe', 'Psat0s145g0120' => 'psa', 'Psat0s595g0040' => 'psa', 'Psat0s595g0120' => 'psa', 'Psat3g175040' => 'psa', 'Psat7g058120' => 'psa', 'PSO017G0428' => 'pso', 'PSO063G7510' => 'pso', 'PSO067G0046' => 'pso', 'PSO478G1073' => 'pso', 'PSO675G3677' => 'pso', 'PSO675G6558' => 'pso', 'PSO675G7520' => 'pso', 'PSO675G8959' => 'pso', 'QL02p074089' => 'qlo', 'QL02p089614' => 'qlo', 'QL03p057736' => 'qlo', 'RcHm_v2.0_Chr1g0364131' => 'rch', 'RcHm_v2.0_Chr2g0087801' => 'rch', 'RcHm_v2.0_Chr2g0087821' => 'rch', 'RcHm_v2.0_Chr2g0173231' => 'rch', 'RcHm_v2.0_Chr4g0433111' => 'rch', 'Rhsim03G0250300' => 'rsi', 'Rhsim08G0048400' => 'rsi', 'Rhsim10G0014800' => 'rsi', 'Rhsim12G0040100' => 'rsi', 'Rhsim12G0109700' => 'rsi', 'Sabra06G0049600' => 'sbr', 'Sabra08G0141000' => 'sbr', 'Sabra10G0021400' => 'sbr', 'Sabra16G0222900' => 'sbr', 'Sabra18G0108600' => 'sbr', 'SalBow1G0433' => 'sbo', 'SalBow1G2038' => 'sbo', 'SalBow1G5003' => 'sbo', 'SalBow7G1197' => 'sbo', 'SalBow8G3506' => 'sbo', 'Sc03g0007300' => 'sci', 'Sc11g0000950' => 'sci', 'Sc14g0008750' => 'sci', 'Sc18g0000420' => 'sci', 'Sed0006754' => 'sed', 'Sed0008741' => 'sed', 'Sed0017172' => 'sed', 'Sed0018925' => 'sed', 'Sed0023326' => 'sed', 'Sed0025909' => 'sed', 'SEGI_05333' => 'sgi', 'SEGI_10362' => 'sgi', 'SEGI_13380' => 'sgi', 'SEGI_24306' => 'sgi', 'SEGI_29077' => 'sgi', 'SEGI_29095' => 'sgi', 'SEGI_36534' => 'sgi', 'SEGI_37506' => 'sgi', 'SEGI_38321' => 'sgi', 'SGA_v2.0_scaffold307G48031' => 'sas', 'SGA_v2.0_scaffold47G17507' => 'sas', 'SGA_v2.0_scaffold63G21736' => 'sas', 'SGA_v2.0_scaffold87G27070' => 'sas', 'SHI17794' => 'shi', 'SHI28851' => 'shi', 'SMO165G0155' => 'smo', 'SMO340G0217' => 'smo', 'SMO367G1210' => 'smo', 'Solyc02g093430.3' => 'sly', 'Solyc05g013580.4' => 'sly', 'Solyc07g008030.3' => 'sly', 'Solyc12g035470.2' => 'sly', 'Sopen02g038020' => 'spe', 'Sopen05g008490' => 'spe', 'Sopen07g003910' => 'spe', 'Sopen12g015240' => 'spe', 'Sp1g11550' => 'spa', 'Sp2g16710' => 'spa', 'Sp3g00430' => 'spa', 'Sp3g26780' => 'spa', 'Sp5g22900' => 'spa', 'Sp6g29530' => 'spa', 'TAR371G0794' => 'tar', 'TAR374G0164' => 'tar', 'TAR622G0165' => 'tar', 'TAR626G0929' => 'tar', 'TAR629G2155' => 'tar', 'THA.LOC104805282' => 'tha', 'THA.LOC104805363' => 'tha', 'THA.LOC104808968' => 'tha', 'THA.LOC104821093' => 'tha', 'THA.LOC104823953' => 'tha', 'THA.LOC104825562' => 'tha', 'THA.LOC104825665' => 'tha', 'Thecc.02G261400' => 'tca', 'Thecc.04G019200' => 'tca', 'Thecc.09G130400' => 'tca', 'Thhalv10004374m.g' => 'esa', 'Thhalv10007850m.g' => 'esa', 'Thhalv10013782m.g' => 'esa', 'Thhalv10018686m.g' => 'esa', 'Thhalv10020899m.g' => 'esa', 'Thhalv10022755m.g' => 'esa', 'TPR.G23851' => 'tpr', 'TPR.G26500' => 'tpr', 'TPR.G27267' => 'tpr', 'TPR.G32001' => 'tpr', 'TPR.G6251' => 'tpr', 'TPR.G8167' => 'tpr', 'TWI12G1330' => 'twi', 'TWI18G1239' => 'twi', 'TWI34G0979' => 'twi', 'TWI36G0670' => 'twi', 'TWI36G0707' => 'twi', 'TWI56G0233' => 'twi', 'TWI75G1809' => 'twi', 'unitig_21.g20874' => 'ugi', 'unitig_26.g10343' => 'ugi', 'unitig_46.g18392' => 'ugi', 'unitig_52.g17178' => 'ugi', 'unitig_8.g2934' => 'ugi', 'vmacro01122' => 'vma', 'vmacro05875' => 'vma', 'vmacro06147' => 'vma', 'vmacro16191' => 'vma', 'vmacro18293' => 'vma', 'VMungo0251G3707' => 'vmu', 'VMungo0464G1521' => 'vmu', 'VMungo1215G0205' => 'vmu', 'VMungo1383G2484' => 'vmu', 'Zm00001eb079610' => 'zma', 'Zm00001eb135990' => 'zma', 'Zm00001eb183710' => 'zma', 'Zm00001eb246020' => 'zma' ) $gf_id = 'HOM05D001124' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001124' ) $data_identifier = 'HOM05D001124' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 6, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 7, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 21, 'bol' => (int) 10, 'bra' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 6, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 9, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 21, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 8, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 10, 'lsa' => (int) 8, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 8, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 9, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb246020' $species_info = array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ) $local_species = 'ccl' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001124', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '548', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02520' => 'bna', 'A03p06630' => 'bna', 'A05p44460' => 'bna', 'A06p08710' => 'bna', 'A06p41090' => 'bna', 'A07p32320' => 'bna', 'A08p32520' => 'bna', 'A09p10360' => 'bna', 'A10p24080' => 'bna', 'Aa31LG11G15250' => 'aar', 'Aa31LG1G1800' => 'aar', 'Aa31LG2G5120' => 'aar', 'Aa31LG2G6070' => 'aar', 'Aa31LG5G10770' => 'aar', 'Aa31sc61G90' => 'aar', 'Actinidia01352' => 'ach', 'Actinidia05983' => 'ach', 'Actinidia08133' => 'ach', 'Actinidia15101' => 'ach', 'Actinidia26379' => 'ach', 'Actinidia35778' => 'ach', 'Actinidia36123' => 'ach', 'Actinidia37436' => 'ach', 'Actinidia38730' => 'ach', 'Ah.02g128210' => 'amhyb', 'Ah.03g132990' => 'amhyb', 'Ah.14g079410' => 'amhyb', 'AL1G24640' => 'aly', 'AL2G26680' => 'aly', 'AL3G10530' => 'aly', 'AL3G45230' => 'aly', 'AL5G15230' => 'aly', 'AL5G16960' => 'aly', 'AL6G25210' => 'aly', 'Aqoxy2G00441' => 'aox', 'Aqoxy3G01236' => 'aox', 'Aqoxy5G03746' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3RQ047' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C7GMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9C8JER' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MBL6KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YXCZ83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZANX40' => 'arhy', 'AT1G12990' => 'ath', 'AT1G67880' => 'ath', 'AT2G13290' => 'ath', 'AT3G01620' => 'ath', 'AT3G26445' => 'ath', 'AT3G27540' => 'ath', 'AT5G14480' => 'ath', 'ATR0824G026' => 'atr', 'ATR1098G019' => 'atr', 'Atru.chr11.2145' => 'acertr', 'Atru.chr2.3636' => 'acertr', 'Atru.chr2.3644' => 'acertr', 'Atru.chr6.2422' => 'acertr', 'Atru.chr7.1112' => 'acertr', 'AUR62005469' => 'cqu', 'AUR62011166' => 'cqu', 'AUR62013319' => 'cqu', 'AUR62024273' => 'cqu', 'AUR62028420' => 'cqu', 'AUR62041942' => 'cqu', 'BcaB01g04969' => 'bca', 'BcaB01g06371' => 'bca', 'BcaB02g11494' => 'bca', 'BcaB03g15382' => 'bca', 'BcaB08g36994' => 'bca', 'BcaC03g13477' => 'bca', 'BcaC03g13478' => 'bca', 'BcaC03g13480' => 'bca', 'BcaC03g13481' => 'bca', 'BcaC03g13486' => 'bca', 'BcaC04g19031' => 'bca', 'BcaC04g23085' => 'bca', 'BcaC05g25094' => 'bca', 'BcaC05g25096' => 'bca', 'BcaC05g25138' => 'bca', 'BcaC05g30416' => 'bca', 'BcaC05g30455' => 'bca', 'BcaC06g30979' => 'bca', 'BcaC06g33805' => 'bca', 'BcaC08g46021' => 'bca', 'BcaNung03154' => 'bca', 'BolC2t06623H' => 'bol', 'BolC2t06632H' => 'bol', 'BolC2t06635H' => 'bol', 'BolC2t06638H' => 'bol', 'BolC3t13266H' => 'bol', 'BolC5t29776H' => 'bol', 'BolC6t38912H' => 'bol', 'BolC7t44183H' => 'bol', 'BolC9t54123H' => 'bol', 'BolC9t59107H' => 'bol', 'BraA02t05221Z' => 'bra', 'BraA03t09996Z' => 'bra', 'BraA05t23210Z' => 'bra', 'BraA06t24068Z' => 'bra', 'BraA06t27032Z' => 'bra', 'BraA08t35176Z' => 'bra', 'BraA09t36680Z' => 'bra', 'BraA10t44471Z' => 'bra', 'C02p06760' => 'bna', 'C02p06890' => 'bna', 'C02p07010' => 'bna', 'C03p07660' => 'bna', 'C05p10300' => 'bna', 'C06p38150' => 'bna', 'C07p36650' => 'bna', 'C08p15770' => 'bna', 'C09p12300' => 'bna', 'C09p62700' => 'bna', 'C09p75040' => 'bna', 'CAN.G13.1' => 'can', 'CAN.G138.4' => 'can', 'CAN.G44.6' => 'can', 'CAN.G473.19' => 'can', 'CANSAT01G0835' => 'cansat', 'CANSAT11G0246' => 'cansat', 'CANSAT11G1766' => 'cansat', 'CANSAT64G1954' => 'cansat', 'CARHR013330' => 'chi', 'CARHR060530' => 'chi', 'CARHR075300' => 'chi', 'CARHR105120' => 'chi', 'CARHR148910' => 'chi', 'CARHR198830' => 'chi', 'Carub.0001s1275' => 'cru', 'Carub.0002s1437' => 'cru', 'Carub.0003s0044' => 'cru', 'Carub.0003s2787' => 'cru', 'Carub.0005s0597' => 'cru', 'Carub.0006s1266' => 'cru', 'Ca_06935_v3' => 'car', 'Ca_13559_v3' => 'car', 'Ca_16941_v3' => 'car', 'Ca_16960_v3' => 'car', 'Ca_17775_v3' => 'car', 'Ca_30464_v3' => 'car', 'Cc06_g08160' => 'ccan', 'Cc07_g01520' => 'ccan', 'Cc11_g15810' => 'ccan', 'CDE02G2840' => 'cde', 'CDE03G0093' => 'cde', 'CDE04G2127' => 'cde', 'CDE07G1857' => 'cde', 'CDE09G1246' => 'cde', 'Cfa003412' => 'cfa', 'Cfa007341' => 'cfa', 'Cfa009220' => 'cfa', 'Ciclev10008737m.g' => 'ccl', 'Ciclev10015565m.g' => 'ccl', 'Ciclev10031761m.g' => 'ccl', 'CiPaw.03G045300' => 'cil', 'CiPaw.03G247200' => 'cil', 'CiPaw.04G029500' => 'cil', 'CiPaw.04G174000' => 'cil', 'CiPaw.05G181200' => 'cil', 'CiPaw.06G067100' => 'cil', 'ClCG05G025800' => 'cla', 'ClCG06G011400' => 'cla', 'ClCG09G019360' => 'cla', 'COL.COLO4_04827' => 'col', 'COL.COLO4_29170' => 'col', 'COL.COLO4_35131' => 'col', 'COL.COLO4_35132' => 'col', 'Cpa.g.sc33.32' => 'cpa', 'Cpa.g.sc46.29' => 'cpa', 'Cpa.g.sc796.1' => 'cpa', 'CsaV3_1G030420' => 'csa', 'CsaV3_5G027050' => 'csa', 'CsaV3_5G031040' => 'csa', 'CsaV3_UNG023130' => 'csa', 'CSS0007726' => 'camsi', 'CSS0016433' => 'camsi', 'CSS0017656' => 'camsi', 'CSS0025364' => 'camsi', 'CSS0027582' => 'camsi', 'CSS0047288' => 'camsi', 'CSS0049950' => 'camsi', 'DCAR_003843' => 'dca', 'DCAR_007052' => 'dca', 'DCAR_020884' => 'dca', 'DCAR_021730' => 'dca', 'DCAR_024423' => 'dca', 'DCAR_026509' => 'dca', 'DCAR_031158' => 'dca', 'Dinv14728' => 'din', 'Dinv15219' => 'din', 'Dinv25728' => 'din', 'Dinv33428' => 'din', 'Dinv36489' => 'din', 'Dinv41486' => 'din', 'Duzib147G0469' => 'dzi', 'Duzib168G0060' => 'dzi', 'Duzib187G1215' => 'dzi', 'Duzib248G0692' => 'dzi', 'Duzib251G0767' => 'dzi', 'Duzib264G0446' => 'dzi', 'Duzib268G0691' => 'dzi', 'ECA232G4767' => 'eca', 'ECA233G2838' => 'eca', 'ECA234G0391' => 'eca', 'ECA234G0857' => 'eca', 'ECA236G1593' => 'eca', 'ECA238G0565' => 'eca', 'ECA246G1027' => 'eca', 'ECA246G3223' => 'eca', 'ECA246G3470' => 'eca', 'EL10Ac6g13829' => 'bvu', 'EL10Ac6g14093' => 'bvu', 'EL10Ac8g18707' => 'bvu', 'Eucgr.C01369' => 'egr', 'Eucgr.H02492' => 'egr', 'Eucgr.I01733' => 'egr', 'Eucgr.J02255' => 'egr', 'Eucgr.J02257' => 'egr', 'Eucgr.J02258' => 'egr', 'FAN02G1601' => 'fan', 'FAN03G1586' => 'fan', 'FAN03G2986' => 'fan', 'FAN05G4837' => 'fan', 'FAN06G0146' => 'fan', 'FAN07G0858' => 'fan', 'FAN09G3179' => 'fan', 'FAN10G0669' => 'fan', 'FAN12G2358' => 'fan', 'FAN14G4198' => 'fan', 'FAN14G5112' => 'fan', 'FAN17G0342' => 'fan', 'FAN19G0342' => 'fan', 'FAN19G0962' => 'fan', 'FAN19G1101' => 'fan', 'FAN19G1872' => 'fan', 'FAN22G0356' => 'fan', 'FAN23G0744' => 'fan', 'FAN23G1914' => 'fan', 'FAN26G0032' => 'fan', 'FAN28G0625' => 'fan', 'FvH4_1g02710' => 'fve', 'FvH4_1g02720' => 'fve', 'FvH4_4g25670' => 'fve', 'FvH4_6g51700' => 'fve', 'FvH4_7g20170' => 'fve', 'Glyma.05G175000' => 'gma', 'Glyma.08G132300' => 'gma', 'Glyma.11G243000' => 'gma', 'Glyma.13G158900' => 'gma', 'Glyma.17G112400' => 'gma', 'Glyma.18G014100' => 'gma', 'Glyma.19G003100' => 'gma', 'Glyma.19G056500' => 'gma', 'Gohir.A01G158900' => 'ghi', 'Gohir.A05G312600' => 'ghi', 'Gohir.A05G354900' => 'ghi', 'Gohir.A07G037200' => 'ghi', 'Gohir.A09G030000' => 'ghi', 'Gohir.A12G145200' => 'ghi', 'Gohir.D01G151500' => 'ghi', 'Gohir.D04G058300' => 'ghi', 'Gohir.D05G314100' => 'ghi', 'Gohir.D07G041400' => 'ghi', 'Gohir.D09G029700' => 'ghi', 'Gohir.D12G149700' => 'ghi', 'Gorai.001G043800' => 'gra', 'Gorai.002G187800' => 'gra', 'Gorai.006G034700' => 'gra', 'Gorai.008G161200' => 'gra', 'Gorai.009G335700' => 'gra', 'Gorai.012G065000' => 'gra', 'GSVIVG01000535001' => 'vvi', 'GSVIVG01015572001' => 'vvi', 'GSVIVG01032386001' => 'vvi', 'HanXRQChr05g0138531' => 'han', 'HanXRQChr06g0174391' => 'han', 'HanXRQChr07g0199021' => 'han', 'HanXRQChr08g0208211' => 'han', 'HanXRQChr09g0255471' => 'han', 'HanXRQChr10g0315791' => 'han', 'HanXRQChr12g0371991' => 'han', 'HanXRQChr15g0475251' => 'han', 'HanXRQChr17g0540001' => 'han', 'HanXRQChr17g0548631' => 'han', 'HanXRQChr17g0569561' => 'han', 'Haze_12256' => 'cav', 'Haze_14756' => 'cav', 'Haze_25528' => 'cav', 'Hma1.2p1_0079F.1_g041020' => 'hma', 'Hma1.2p1_0818F.1_g223260' => 'hma', 'Hma1.2p1_1747F.1_g300530' => 'hma', 'HPP92_004607' => 'vpl', 'HPP92_004608' => 'vpl', 'HPP92_006181' => 'vpl', 'HPP92_012192' => 'vpl', 'HPP92_015680' => 'vpl', 'HPP92_020249' => 'vpl', 'HPP92_021376' => 'vpl', 'HPP92_024275' => 'vpl', 'Hund06031' => 'sun', 'Hund25391' => 'sun', 'Lalb_Chr07g0185371' => 'lal', 'Lalb_Chr07g0185381' => 'lal', 'Lalb_Chr12g0204011' => 'lal', 'Lalb_Chr13g0301671' => 'lal', 'Lalb_Chr14g0362851' => 'lal', 'Lalb_Chr24g0403581' => 'lal', 'Lj1g0000233' => 'lja', 'Lj2g0018120' => 'lja', 'Lj3C621T0' => 'lonja', 'Lj3P1059T14' => 'lonja', 'Lj3P611T9' => 'lonja', 'Lj3P614T13' => 'lonja', 'Lj3P615T5' => 'lonja', 'Lj4g0012315' => 'lja', 'Lj4g0026182' => 'lja', 'Lj6P813T16' => 'lonja', 'Lj7C427T7' => 'lonja', 'Lj7C427T8' => 'lonja', 'Lj7P600T41' => 'lonja', 'Lju41C42G17' => 'lonja', 'Lsat_1_v5_gn_0_47300' => 'lsa', 'Lsat_1_v5_gn_2_91280' => 'lsa', 'Lsat_1_v5_gn_3_30561' => 'lsa', 'Lsat_1_v5_gn_4_184321' => 'lsa', 'Lsat_1_v5_gn_4_4041' => 'lsa', 'Lsat_1_v5_gn_5_92000' => 'lsa', 'Lsat_1_v5_gn_8_152940' => 'lsa', 'Lsat_1_v5_gn_8_62401' => 'lsa', 'Manes.06G055900' => 'mes', 'Manes.12G022200' => 'mes', 'Manes.13G023300' => 'mes', 'Manes.14G115000' => 'mes', 'Manes.15G151700' => 'mes', 'Manes.17G111300' => 'mes', 'Mapoly0226s0009' => 'mpo', 'MBI02_g25363_MAGBIO' => 'mbi', 'MBI06_g00027_MAGBIO' => 'mbi', 'MBI10_g13034_MAGBIO' => 'mbi', 'MD09G1023400' => 'mdo', 'MD13G1100100' => 'mdo', 'MD15G1169200' => 'mdo', 'MD16G1101100' => 'mdo', 'MD17G1022900' => 'mdo', 'Medtr3g096150' => 'mtr', 'Medtr4g115070' => 'mtr', 'Medtr7g033325' => 'mtr', 'Medtr8g089840' => 'mtr', 'MELO3C010319.2' => 'cme', 'MELO3C011944.2' => 'cme', 'MELO3C021589.2' => 'cme', 'Migut.E00207' => 'egut', 'Migut.H00067' => 'egut', 'Migut.K00433' => 'egut', 'Migut.K00606' => 'egut', 'Migut.K01410' => 'egut', 'MSTRG.13347' => 'ama', 'MSTRG.24045' => 'ama', 'MSTRG.2428' => 'ama', 'MSTRG.26410' => 'ama', 'MSTRG.3139' => 'ama', 'MSTRG.3286' => 'ama', 'MSTRG.563' => 'ama', 'MSTRG.7941' => 'ama', 'Nitab4.5_0000028g0060' => 'nta', 'Nitab4.5_0000065g0260' => 'nta', 'Nitab4.5_0000112g0060' => 'nta', 'Nitab4.5_0000489g0120' => 'nta', 'Nitab4.5_0001776g0050' => 'nta', 'Nitab4.5_0001854g0010' => 'nta', 'Nitab4.5_0001860g0020' => 'nta', 'Nitab4.5_0004352g0010' => 'nta', 'Nitab4.5_0008716g0020' => 'nta', 'Nitab4.5_0008922g0010' => 'nta', 'Nn3g16693' => 'nnu', 'Nn4g22596' => 'nnu', 'Nn7g37639' => 'nnu', 'Oeu001701.1' => 'oeu', 'Oeu018149.1' => 'oeu', 'Oeu026220.1' => 'oeu', 'Oeu038635.1' => 'oeu', 'Oeu049176.1' => 'oeu', 'Oeu056706.1' => 'oeu', 'Oeu056937.1' => 'oeu', 'Oeu057540.1' => 'oeu', 'Os02g0594900' => 'osa', 'Os02g0595100' => 'osa', 'Os04g0477500' => 'osa', 'Os12g0611900' => 'osa', 'Peaxi162Scf00076g00020' => 'pax', 'Peaxi162Scf00128g00217' => 'pax', 'Peaxi162Scf00129g01640' => 'pax', 'Peaxi162Scf00669g00007' => 'pax', 'Peaxi162Scf00700g00421' => 'pax', 'Peaxi162Scf00801g00038' => 'pax', 'Peaxi162Scf00891g00025' => 'pax', 'PGR083G0909' => 'pgr', 'PGR119G1005' => 'pgr', 'PGR142G2236' => 'pgr', 'PGR142G3388' => 'pgr', 'PGSC0003DMG400004514' => 'stu', 'PGSC0003DMG400012635' => 'stu', 'PGSC0003DMG400015730' => 'stu', 'PGSC0003DMG400018611' => 'stu', 'PGSC0003DMG400030897' => 'stu', 'Phvul.001G254800' => 'pvu', 'Phvul.002G260100' => 'pvu', 'Phvul.003G167600' => 'pvu', 'Phvul.004G005100' => 'pvu', 'Potri.001G343600' => 'ptr', 'Potri.006G066700' => 'ptr', 'Potri.008G186000' => 'ptr', 'Potri.010G046900' => 'ptr', 'Potri.018G127900' => 'ptr', 'Pp3c20_17750' => 'ppa', 'Pp3c24_4380' => 'ppa', 'Prupe.1G245800' => 'ppe', 'Prupe.3G293400' => 'ppe', 'Prupe.7G247400' => 'ppe', 'Psat0s145g0120' => 'psa', 'Psat0s595g0040' => 'psa', 'Psat0s595g0120' => 'psa', 'Psat3g175040' => 'psa', 'Psat7g058120' => 'psa', 'PSO017G0428' => 'pso', 'PSO063G7510' => 'pso', 'PSO067G0046' => 'pso', 'PSO478G1073' => 'pso', 'PSO675G3677' => 'pso', 'PSO675G6558' => 'pso', 'PSO675G7520' => 'pso', 'PSO675G8959' => 'pso', 'QL02p074089' => 'qlo', 'QL02p089614' => 'qlo', 'QL03p057736' => 'qlo', 'RcHm_v2.0_Chr1g0364131' => 'rch', 'RcHm_v2.0_Chr2g0087801' => 'rch', 'RcHm_v2.0_Chr2g0087821' => 'rch', 'RcHm_v2.0_Chr2g0173231' => 'rch', 'RcHm_v2.0_Chr4g0433111' => 'rch', 'Rhsim03G0250300' => 'rsi', 'Rhsim08G0048400' => 'rsi', 'Rhsim10G0014800' => 'rsi', 'Rhsim12G0040100' => 'rsi', 'Rhsim12G0109700' => 'rsi', 'Sabra06G0049600' => 'sbr', 'Sabra08G0141000' => 'sbr', 'Sabra10G0021400' => 'sbr', 'Sabra16G0222900' => 'sbr', 'Sabra18G0108600' => 'sbr', 'SalBow1G0433' => 'sbo', 'SalBow1G2038' => 'sbo', 'SalBow1G5003' => 'sbo', 'SalBow7G1197' => 'sbo', 'SalBow8G3506' => 'sbo', 'Sc03g0007300' => 'sci', 'Sc11g0000950' => 'sci', 'Sc14g0008750' => 'sci', 'Sc18g0000420' => 'sci', 'Sed0006754' => 'sed', 'Sed0008741' => 'sed', 'Sed0017172' => 'sed', 'Sed0018925' => 'sed', 'Sed0023326' => 'sed', 'Sed0025909' => 'sed', 'SEGI_05333' => 'sgi', 'SEGI_10362' => 'sgi', 'SEGI_13380' => 'sgi', 'SEGI_24306' => 'sgi', 'SEGI_29077' => 'sgi', 'SEGI_29095' => 'sgi', 'SEGI_36534' => 'sgi', 'SEGI_37506' => 'sgi', 'SEGI_38321' => 'sgi', 'SGA_v2.0_scaffold307G48031' => 'sas', 'SGA_v2.0_scaffold47G17507' => 'sas', 'SGA_v2.0_scaffold63G21736' => 'sas', 'SGA_v2.0_scaffold87G27070' => 'sas', 'SHI17794' => 'shi', 'SHI28851' => 'shi', 'SMO165G0155' => 'smo', 'SMO340G0217' => 'smo', 'SMO367G1210' => 'smo', 'Solyc02g093430.3' => 'sly', 'Solyc05g013580.4' => 'sly', 'Solyc07g008030.3' => 'sly', 'Solyc12g035470.2' => 'sly', 'Sopen02g038020' => 'spe', 'Sopen05g008490' => 'spe', 'Sopen07g003910' => 'spe', 'Sopen12g015240' => 'spe', 'Sp1g11550' => 'spa', 'Sp2g16710' => 'spa', 'Sp3g00430' => 'spa', 'Sp3g26780' => 'spa', 'Sp5g22900' => 'spa', 'Sp6g29530' => 'spa', 'TAR371G0794' => 'tar', 'TAR374G0164' => 'tar', 'TAR622G0165' => 'tar', 'TAR626G0929' => 'tar', 'TAR629G2155' => 'tar', 'THA.LOC104805282' => 'tha', 'THA.LOC104805363' => 'tha', 'THA.LOC104808968' => 'tha', 'THA.LOC104821093' => 'tha', 'THA.LOC104823953' => 'tha', 'THA.LOC104825562' => 'tha', 'THA.LOC104825665' => 'tha', 'Thecc.02G261400' => 'tca', 'Thecc.04G019200' => 'tca', 'Thecc.09G130400' => 'tca', 'Thhalv10004374m.g' => 'esa', 'Thhalv10007850m.g' => 'esa', 'Thhalv10013782m.g' => 'esa', 'Thhalv10018686m.g' => 'esa', 'Thhalv10020899m.g' => 'esa', 'Thhalv10022755m.g' => 'esa', 'TPR.G23851' => 'tpr', 'TPR.G26500' => 'tpr', 'TPR.G27267' => 'tpr', 'TPR.G32001' => 'tpr', 'TPR.G6251' => 'tpr', 'TPR.G8167' => 'tpr', 'TWI12G1330' => 'twi', 'TWI18G1239' => 'twi', 'TWI34G0979' => 'twi', 'TWI36G0670' => 'twi', 'TWI36G0707' => 'twi', 'TWI56G0233' => 'twi', 'TWI75G1809' => 'twi', 'unitig_21.g20874' => 'ugi', 'unitig_26.g10343' => 'ugi', 'unitig_46.g18392' => 'ugi', 'unitig_52.g17178' => 'ugi', 'unitig_8.g2934' => 'ugi', 'vmacro01122' => 'vma', 'vmacro05875' => 'vma', 'vmacro06147' => 'vma', 'vmacro16191' => 'vma', 'vmacro18293' => 'vma', 'VMungo0251G3707' => 'vmu', 'VMungo0464G1521' => 'vmu', 'VMungo1215G0205' => 'vmu', 'VMungo1383G2484' => 'vmu', 'Zm00001eb079610' => 'zma', 'Zm00001eb135990' => 'zma', 'Zm00001eb183710' => 'zma', 'Zm00001eb246020' => 'zma' ), 'gf_id' => 'HOM05D001124', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001124' ), 'data_identifier' => 'HOM05D001124', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001124', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '548', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02520' => 'bna', 'A03p06630' => 'bna', 'A05p44460' => 'bna', 'A06p08710' => 'bna', 'A06p41090' => 'bna', 'A07p32320' => 'bna', 'A08p32520' => 'bna', 'A09p10360' => 'bna', 'A10p24080' => 'bna', 'Aa31LG11G15250' => 'aar', 'Aa31LG1G1800' => 'aar', 'Aa31LG2G5120' => 'aar', 'Aa31LG2G6070' => 'aar', 'Aa31LG5G10770' => 'aar', 'Aa31sc61G90' => 'aar', 'Actinidia01352' => 'ach', 'Actinidia05983' => 'ach', 'Actinidia08133' => 'ach', 'Actinidia15101' => 'ach', 'Actinidia26379' => 'ach', 'Actinidia35778' => 'ach', 'Actinidia36123' => 'ach', 'Actinidia37436' => 'ach', 'Actinidia38730' => 'ach', 'Ah.02g128210' => 'amhyb', 'Ah.03g132990' => 'amhyb', 'Ah.14g079410' => 'amhyb', 'AL1G24640' => 'aly', 'AL2G26680' => 'aly', 'AL3G10530' => 'aly', 'AL3G45230' => 'aly', 'AL5G15230' => 'aly', 'AL5G16960' => 'aly', 'AL6G25210' => 'aly', 'Aqoxy2G00441' => 'aox', 'Aqoxy3G01236' => 'aox', 'Aqoxy5G03746' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3RQ047' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C7GMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9C8JER' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MBL6KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YXCZ83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZANX40' => 'arhy', 'AT1G12990' => 'ath', 'AT1G67880' => 'ath', 'AT2G13290' => 'ath', 'AT3G01620' => 'ath', 'AT3G26445' => 'ath', 'AT3G27540' => 'ath', 'AT5G14480' => 'ath', 'ATR0824G026' => 'atr', 'ATR1098G019' => 'atr', 'Atru.chr11.2145' => 'acertr', 'Atru.chr2.3636' => 'acertr', 'Atru.chr2.3644' => 'acertr', 'Atru.chr6.2422' => 'acertr', 'Atru.chr7.1112' => 'acertr', 'AUR62005469' => 'cqu', 'AUR62011166' => 'cqu', 'AUR62013319' => 'cqu', 'AUR62024273' => 'cqu', 'AUR62028420' => 'cqu', 'AUR62041942' => 'cqu', 'BcaB01g04969' => 'bca', 'BcaB01g06371' => 'bca', 'BcaB02g11494' => 'bca', 'BcaB03g15382' => 'bca', 'BcaB08g36994' => 'bca', 'BcaC03g13477' => 'bca', 'BcaC03g13478' => 'bca', 'BcaC03g13480' => 'bca', 'BcaC03g13481' => 'bca', 'BcaC03g13486' => 'bca', 'BcaC04g19031' => 'bca', 'BcaC04g23085' => 'bca', 'BcaC05g25094' => 'bca', 'BcaC05g25096' => 'bca', 'BcaC05g25138' => 'bca', 'BcaC05g30416' => 'bca', 'BcaC05g30455' => 'bca', 'BcaC06g30979' => 'bca', 'BcaC06g33805' => 'bca', 'BcaC08g46021' => 'bca', 'BcaNung03154' => 'bca', 'BolC2t06623H' => 'bol', 'BolC2t06632H' => 'bol', 'BolC2t06635H' => 'bol', 'BolC2t06638H' => 'bol', 'BolC3t13266H' => 'bol', 'BolC5t29776H' => 'bol', 'BolC6t38912H' => 'bol', 'BolC7t44183H' => 'bol', 'BolC9t54123H' => 'bol', 'BolC9t59107H' => 'bol', 'BraA02t05221Z' => 'bra', 'BraA03t09996Z' => 'bra', 'BraA05t23210Z' => 'bra', 'BraA06t24068Z' => 'bra', 'BraA06t27032Z' => 'bra', 'BraA08t35176Z' => 'bra', 'BraA09t36680Z' => 'bra', 'BraA10t44471Z' => 'bra', 'C02p06760' => 'bna', 'C02p06890' => 'bna', 'C02p07010' => 'bna', 'C03p07660' => 'bna', 'C05p10300' => 'bna', 'C06p38150' => 'bna', 'C07p36650' => 'bna', 'C08p15770' => 'bna', 'C09p12300' => 'bna', 'C09p62700' => 'bna', 'C09p75040' => 'bna', 'CAN.G13.1' => 'can', 'CAN.G138.4' => 'can', 'CAN.G44.6' => 'can', 'CAN.G473.19' => 'can', 'CANSAT01G0835' => 'cansat', 'CANSAT11G0246' => 'cansat', 'CANSAT11G1766' => 'cansat', 'CANSAT64G1954' => 'cansat', 'CARHR013330' => 'chi', 'CARHR060530' => 'chi', 'CARHR075300' => 'chi', 'CARHR105120' => 'chi', 'CARHR148910' => 'chi', 'CARHR198830' => 'chi', 'Carub.0001s1275' => 'cru', 'Carub.0002s1437' => 'cru', 'Carub.0003s0044' => 'cru', 'Carub.0003s2787' => 'cru', 'Carub.0005s0597' => 'cru', 'Carub.0006s1266' => 'cru', 'Ca_06935_v3' => 'car', 'Ca_13559_v3' => 'car', 'Ca_16941_v3' => 'car', 'Ca_16960_v3' => 'car', 'Ca_17775_v3' => 'car', 'Ca_30464_v3' => 'car', 'Cc06_g08160' => 'ccan', 'Cc07_g01520' => 'ccan', 'Cc11_g15810' => 'ccan', 'CDE02G2840' => 'cde', 'CDE03G0093' => 'cde', 'CDE04G2127' => 'cde', 'CDE07G1857' => 'cde', 'CDE09G1246' => 'cde', 'Cfa003412' => 'cfa', 'Cfa007341' => 'cfa', 'Cfa009220' => 'cfa', 'Ciclev10008737m.g' => 'ccl', 'Ciclev10015565m.g' => 'ccl', 'Ciclev10031761m.g' => 'ccl', 'CiPaw.03G045300' => 'cil', 'CiPaw.03G247200' => 'cil', 'CiPaw.04G029500' => 'cil', 'CiPaw.04G174000' => 'cil', 'CiPaw.05G181200' => 'cil', 'CiPaw.06G067100' => 'cil', 'ClCG05G025800' => 'cla', 'ClCG06G011400' => 'cla', 'ClCG09G019360' => 'cla', 'COL.COLO4_04827' => 'col', 'COL.COLO4_29170' => 'col', 'COL.COLO4_35131' => 'col', 'COL.COLO4_35132' => 'col', 'Cpa.g.sc33.32' => 'cpa', 'Cpa.g.sc46.29' => 'cpa', 'Cpa.g.sc796.1' => 'cpa', 'CsaV3_1G030420' => 'csa', 'CsaV3_5G027050' => 'csa', 'CsaV3_5G031040' => 'csa', 'CsaV3_UNG023130' => 'csa', 'CSS0007726' => 'camsi', 'CSS0016433' => 'camsi', 'CSS0017656' => 'camsi', 'CSS0025364' => 'camsi', 'CSS0027582' => 'camsi', 'CSS0047288' => 'camsi', 'CSS0049950' => 'camsi', 'DCAR_003843' => 'dca', 'DCAR_007052' => 'dca', 'DCAR_020884' => 'dca', 'DCAR_021730' => 'dca', 'DCAR_024423' => 'dca', 'DCAR_026509' => 'dca', 'DCAR_031158' => 'dca', 'Dinv14728' => 'din', 'Dinv15219' => 'din', 'Dinv25728' => 'din', 'Dinv33428' => 'din', 'Dinv36489' => 'din', 'Dinv41486' => 'din', 'Duzib147G0469' => 'dzi', 'Duzib168G0060' => 'dzi', 'Duzib187G1215' => 'dzi', 'Duzib248G0692' => 'dzi', 'Duzib251G0767' => 'dzi', 'Duzib264G0446' => 'dzi', 'Duzib268G0691' => 'dzi', 'ECA232G4767' => 'eca', 'ECA233G2838' => 'eca', 'ECA234G0391' => 'eca', 'ECA234G0857' => 'eca', 'ECA236G1593' => 'eca', 'ECA238G0565' => 'eca', 'ECA246G1027' => 'eca', 'ECA246G3223' => 'eca', 'ECA246G3470' => 'eca', 'EL10Ac6g13829' => 'bvu', 'EL10Ac6g14093' => 'bvu', 'EL10Ac8g18707' => 'bvu', 'Eucgr.C01369' => 'egr', 'Eucgr.H02492' => 'egr', 'Eucgr.I01733' => 'egr', 'Eucgr.J02255' => 'egr', 'Eucgr.J02257' => 'egr', 'Eucgr.J02258' => 'egr', 'FAN02G1601' => 'fan', 'FAN03G1586' => 'fan', 'FAN03G2986' => 'fan', 'FAN05G4837' => 'fan', 'FAN06G0146' => 'fan', 'FAN07G0858' => 'fan', 'FAN09G3179' => 'fan', 'FAN10G0669' => 'fan', 'FAN12G2358' => 'fan', 'FAN14G4198' => 'fan', 'FAN14G5112' => 'fan', 'FAN17G0342' => 'fan', 'FAN19G0342' => 'fan', 'FAN19G0962' => 'fan', 'FAN19G1101' => 'fan', 'FAN19G1872' => 'fan', 'FAN22G0356' => 'fan', 'FAN23G0744' => 'fan', 'FAN23G1914' => 'fan', 'FAN26G0032' => 'fan', 'FAN28G0625' => 'fan', 'FvH4_1g02710' => 'fve', 'FvH4_1g02720' => 'fve', 'FvH4_4g25670' => 'fve', 'FvH4_6g51700' => 'fve', 'FvH4_7g20170' => 'fve', 'Glyma.05G175000' => 'gma', 'Glyma.08G132300' => 'gma', 'Glyma.11G243000' => 'gma', 'Glyma.13G158900' => 'gma', 'Glyma.17G112400' => 'gma', 'Glyma.18G014100' => 'gma', 'Glyma.19G003100' => 'gma', 'Glyma.19G056500' => 'gma', 'Gohir.A01G158900' => 'ghi', 'Gohir.A05G312600' => 'ghi', 'Gohir.A05G354900' => 'ghi', 'Gohir.A07G037200' => 'ghi', 'Gohir.A09G030000' => 'ghi', 'Gohir.A12G145200' => 'ghi', 'Gohir.D01G151500' => 'ghi', 'Gohir.D04G058300' => 'ghi', 'Gohir.D05G314100' => 'ghi', 'Gohir.D07G041400' => 'ghi', 'Gohir.D09G029700' => 'ghi', 'Gohir.D12G149700' => 'ghi', 'Gorai.001G043800' => 'gra', 'Gorai.002G187800' => 'gra', 'Gorai.006G034700' => 'gra', 'Gorai.008G161200' => 'gra', 'Gorai.009G335700' => 'gra', 'Gorai.012G065000' => 'gra', 'GSVIVG01000535001' => 'vvi', 'GSVIVG01015572001' => 'vvi', 'GSVIVG01032386001' => 'vvi', 'HanXRQChr05g0138531' => 'han', 'HanXRQChr06g0174391' => 'han', 'HanXRQChr07g0199021' => 'han', 'HanXRQChr08g0208211' => 'han', 'HanXRQChr09g0255471' => 'han', 'HanXRQChr10g0315791' => 'han', 'HanXRQChr12g0371991' => 'han', 'HanXRQChr15g0475251' => 'han', 'HanXRQChr17g0540001' => 'han', 'HanXRQChr17g0548631' => 'han', 'HanXRQChr17g0569561' => 'han', 'Haze_12256' => 'cav', 'Haze_14756' => 'cav', 'Haze_25528' => 'cav', 'Hma1.2p1_0079F.1_g041020' => 'hma', 'Hma1.2p1_0818F.1_g223260' => 'hma', 'Hma1.2p1_1747F.1_g300530' => 'hma', 'HPP92_004607' => 'vpl', 'HPP92_004608' => 'vpl', 'HPP92_006181' => 'vpl', 'HPP92_012192' => 'vpl', 'HPP92_015680' => 'vpl', 'HPP92_020249' => 'vpl', 'HPP92_021376' => 'vpl', 'HPP92_024275' => 'vpl', 'Hund06031' => 'sun', 'Hund25391' => 'sun', 'Lalb_Chr07g0185371' => 'lal', 'Lalb_Chr07g0185381' => 'lal', 'Lalb_Chr12g0204011' => 'lal', 'Lalb_Chr13g0301671' => 'lal', 'Lalb_Chr14g0362851' => 'lal', 'Lalb_Chr24g0403581' => 'lal', 'Lj1g0000233' => 'lja', 'Lj2g0018120' => 'lja', 'Lj3C621T0' => 'lonja', 'Lj3P1059T14' => 'lonja', 'Lj3P611T9' => 'lonja', 'Lj3P614T13' => 'lonja', 'Lj3P615T5' => 'lonja', 'Lj4g0012315' => 'lja', 'Lj4g0026182' => 'lja', 'Lj6P813T16' => 'lonja', 'Lj7C427T7' => 'lonja', 'Lj7C427T8' => 'lonja', 'Lj7P600T41' => 'lonja', 'Lju41C42G17' => 'lonja', 'Lsat_1_v5_gn_0_47300' => 'lsa', 'Lsat_1_v5_gn_2_91280' => 'lsa', 'Lsat_1_v5_gn_3_30561' => 'lsa', 'Lsat_1_v5_gn_4_184321' => 'lsa', 'Lsat_1_v5_gn_4_4041' => 'lsa', 'Lsat_1_v5_gn_5_92000' => 'lsa', 'Lsat_1_v5_gn_8_152940' => 'lsa', 'Lsat_1_v5_gn_8_62401' => 'lsa', 'Manes.06G055900' => 'mes', 'Manes.12G022200' => 'mes', 'Manes.13G023300' => 'mes', 'Manes.14G115000' => 'mes', 'Manes.15G151700' => 'mes', 'Manes.17G111300' => 'mes', 'Mapoly0226s0009' => 'mpo', 'MBI02_g25363_MAGBIO' => 'mbi', 'MBI06_g00027_MAGBIO' => 'mbi', 'MBI10_g13034_MAGBIO' => 'mbi', 'MD09G1023400' => 'mdo', 'MD13G1100100' => 'mdo', 'MD15G1169200' => 'mdo', 'MD16G1101100' => 'mdo', 'MD17G1022900' => 'mdo', 'Medtr3g096150' => 'mtr', 'Medtr4g115070' => 'mtr', 'Medtr7g033325' => 'mtr', 'Medtr8g089840' => 'mtr', 'MELO3C010319.2' => 'cme', 'MELO3C011944.2' => 'cme', 'MELO3C021589.2' => 'cme', 'Migut.E00207' => 'egut', 'Migut.H00067' => 'egut', 'Migut.K00433' => 'egut', 'Migut.K00606' => 'egut', 'Migut.K01410' => 'egut', 'MSTRG.13347' => 'ama', 'MSTRG.24045' => 'ama', 'MSTRG.2428' => 'ama', 'MSTRG.26410' => 'ama', 'MSTRG.3139' => 'ama', 'MSTRG.3286' => 'ama', 'MSTRG.563' => 'ama', 'MSTRG.7941' => 'ama', 'Nitab4.5_0000028g0060' => 'nta', 'Nitab4.5_0000065g0260' => 'nta', 'Nitab4.5_0000112g0060' => 'nta', 'Nitab4.5_0000489g0120' => 'nta', 'Nitab4.5_0001776g0050' => 'nta', 'Nitab4.5_0001854g0010' => 'nta', 'Nitab4.5_0001860g0020' => 'nta', 'Nitab4.5_0004352g0010' => 'nta', 'Nitab4.5_0008716g0020' => 'nta', 'Nitab4.5_0008922g0010' => 'nta', 'Nn3g16693' => 'nnu', 'Nn4g22596' => 'nnu', 'Nn7g37639' => 'nnu', 'Oeu001701.1' => 'oeu', 'Oeu018149.1' => 'oeu', 'Oeu026220.1' => 'oeu', 'Oeu038635.1' => 'oeu', 'Oeu049176.1' => 'oeu', 'Oeu056706.1' => 'oeu', 'Oeu056937.1' => 'oeu', 'Oeu057540.1' => 'oeu', 'Os02g0594900' => 'osa', 'Os02g0595100' => 'osa', 'Os04g0477500' => 'osa', 'Os12g0611900' => 'osa', 'Peaxi162Scf00076g00020' => 'pax', 'Peaxi162Scf00128g00217' => 'pax', 'Peaxi162Scf00129g01640' => 'pax', 'Peaxi162Scf00669g00007' => 'pax', 'Peaxi162Scf00700g00421' => 'pax', 'Peaxi162Scf00801g00038' => 'pax', 'Peaxi162Scf00891g00025' => 'pax', 'PGR083G0909' => 'pgr', 'PGR119G1005' => 'pgr', 'PGR142G2236' => 'pgr', 'PGR142G3388' => 'pgr', 'PGSC0003DMG400004514' => 'stu', 'PGSC0003DMG400012635' => 'stu', 'PGSC0003DMG400015730' => 'stu', 'PGSC0003DMG400018611' => 'stu', 'PGSC0003DMG400030897' => 'stu', 'Phvul.001G254800' => 'pvu', 'Phvul.002G260100' => 'pvu', 'Phvul.003G167600' => 'pvu', 'Phvul.004G005100' => 'pvu', 'Potri.001G343600' => 'ptr', 'Potri.006G066700' => 'ptr', 'Potri.008G186000' => 'ptr', 'Potri.010G046900' => 'ptr', 'Potri.018G127900' => 'ptr', 'Pp3c20_17750' => 'ppa', 'Pp3c24_4380' => 'ppa', 'Prupe.1G245800' => 'ppe', 'Prupe.3G293400' => 'ppe', 'Prupe.7G247400' => 'ppe', 'Psat0s145g0120' => 'psa', 'Psat0s595g0040' => 'psa', 'Psat0s595g0120' => 'psa', 'Psat3g175040' => 'psa', 'Psat7g058120' => 'psa', 'PSO017G0428' => 'pso', 'PSO063G7510' => 'pso', 'PSO067G0046' => 'pso', 'PSO478G1073' => 'pso', 'PSO675G3677' => 'pso', 'PSO675G6558' => 'pso', 'PSO675G7520' => 'pso', 'PSO675G8959' => 'pso', 'QL02p074089' => 'qlo', 'QL02p089614' => 'qlo', 'QL03p057736' => 'qlo', 'RcHm_v2.0_Chr1g0364131' => 'rch', 'RcHm_v2.0_Chr2g0087801' => 'rch', 'RcHm_v2.0_Chr2g0087821' => 'rch', 'RcHm_v2.0_Chr2g0173231' => 'rch', 'RcHm_v2.0_Chr4g0433111' => 'rch', 'Rhsim03G0250300' => 'rsi', 'Rhsim08G0048400' => 'rsi', 'Rhsim10G0014800' => 'rsi', 'Rhsim12G0040100' => 'rsi', 'Rhsim12G0109700' => 'rsi', 'Sabra06G0049600' => 'sbr', 'Sabra08G0141000' => 'sbr', 'Sabra10G0021400' => 'sbr', 'Sabra16G0222900' => 'sbr', 'Sabra18G0108600' => 'sbr', 'SalBow1G0433' => 'sbo', 'SalBow1G2038' => 'sbo', 'SalBow1G5003' => 'sbo', 'SalBow7G1197' => 'sbo', 'SalBow8G3506' => 'sbo', 'Sc03g0007300' => 'sci', 'Sc11g0000950' => 'sci', 'Sc14g0008750' => 'sci', 'Sc18g0000420' => 'sci', 'Sed0006754' => 'sed', 'Sed0008741' => 'sed', 'Sed0017172' => 'sed', 'Sed0018925' => 'sed', 'Sed0023326' => 'sed', 'Sed0025909' => 'sed', 'SEGI_05333' => 'sgi', 'SEGI_10362' => 'sgi', 'SEGI_13380' => 'sgi', 'SEGI_24306' => 'sgi', 'SEGI_29077' => 'sgi', 'SEGI_29095' => 'sgi', 'SEGI_36534' => 'sgi', 'SEGI_37506' => 'sgi', 'SEGI_38321' => 'sgi', 'SGA_v2.0_scaffold307G48031' => 'sas', 'SGA_v2.0_scaffold47G17507' => 'sas', 'SGA_v2.0_scaffold63G21736' => 'sas', 'SGA_v2.0_scaffold87G27070' => 'sas', 'SHI17794' => 'shi', 'SHI28851' => 'shi', 'SMO165G0155' => 'smo', 'SMO340G0217' => 'smo', 'SMO367G1210' => 'smo', 'Solyc02g093430.3' => 'sly', 'Solyc05g013580.4' => 'sly', 'Solyc07g008030.3' => 'sly', 'Solyc12g035470.2' => 'sly', 'Sopen02g038020' => 'spe', 'Sopen05g008490' => 'spe', 'Sopen07g003910' => 'spe', 'Sopen12g015240' => 'spe', 'Sp1g11550' => 'spa', 'Sp2g16710' => 'spa', 'Sp3g00430' => 'spa', 'Sp3g26780' => 'spa', 'Sp5g22900' => 'spa', 'Sp6g29530' => 'spa', 'TAR371G0794' => 'tar', 'TAR374G0164' => 'tar', 'TAR622G0165' => 'tar', 'TAR626G0929' => 'tar', 'TAR629G2155' => 'tar', 'THA.LOC104805282' => 'tha', 'THA.LOC104805363' => 'tha', 'THA.LOC104808968' => 'tha', 'THA.LOC104821093' => 'tha', 'THA.LOC104823953' => 'tha', 'THA.LOC104825562' => 'tha', 'THA.LOC104825665' => 'tha', 'Thecc.02G261400' => 'tca', 'Thecc.04G019200' => 'tca', 'Thecc.09G130400' => 'tca', 'Thhalv10004374m.g' => 'esa', 'Thhalv10007850m.g' => 'esa', 'Thhalv10013782m.g' => 'esa', 'Thhalv10018686m.g' => 'esa', 'Thhalv10020899m.g' => 'esa', 'Thhalv10022755m.g' => 'esa', 'TPR.G23851' => 'tpr', 'TPR.G26500' => 'tpr', 'TPR.G27267' => 'tpr', 'TPR.G32001' => 'tpr', 'TPR.G6251' => 'tpr', 'TPR.G8167' => 'tpr', 'TWI12G1330' => 'twi', 'TWI18G1239' => 'twi', 'TWI34G0979' => 'twi', 'TWI36G0670' => 'twi', 'TWI36G0707' => 'twi', 'TWI56G0233' => 'twi', 'TWI75G1809' => 'twi', 'unitig_21.g20874' => 'ugi', 'unitig_26.g10343' => 'ugi', 'unitig_46.g18392' => 'ugi', 'unitig_52.g17178' => 'ugi', 'unitig_8.g2934' => 'ugi', 'vmacro01122' => 'vma', 'vmacro05875' => 'vma', 'vmacro06147' => 'vma', 'vmacro16191' => 'vma', 'vmacro18293' => 'vma', 'VMungo0251G3707' => 'vmu', 'VMungo0464G1521' => 'vmu', 'VMungo1215G0205' => 'vmu', 'VMungo1383G2484' => 'vmu', 'Zm00001eb079610' => 'zma', 'Zm00001eb135990' => 'zma', 'Zm00001eb183710' => 'zma', 'Zm00001eb246020' => 'zma' ) $gf_id = 'HOM05D001124' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001124' ) $data_identifier = 'HOM05D001124' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 6, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 7, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 21, 'bol' => (int) 10, 'bra' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 6, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 9, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 21, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 8, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 10, 'lsa' => (int) 8, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 8, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 9, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb246020' $species_info = array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ) $local_species = 'ccl' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001124', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '548', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02520' => 'bna', 'A03p06630' => 'bna', 'A05p44460' => 'bna', 'A06p08710' => 'bna', 'A06p41090' => 'bna', 'A07p32320' => 'bna', 'A08p32520' => 'bna', 'A09p10360' => 'bna', 'A10p24080' => 'bna', 'Aa31LG11G15250' => 'aar', 'Aa31LG1G1800' => 'aar', 'Aa31LG2G5120' => 'aar', 'Aa31LG2G6070' => 'aar', 'Aa31LG5G10770' => 'aar', 'Aa31sc61G90' => 'aar', 'Actinidia01352' => 'ach', 'Actinidia05983' => 'ach', 'Actinidia08133' => 'ach', 'Actinidia15101' => 'ach', 'Actinidia26379' => 'ach', 'Actinidia35778' => 'ach', 'Actinidia36123' => 'ach', 'Actinidia37436' => 'ach', 'Actinidia38730' => 'ach', 'Ah.02g128210' => 'amhyb', 'Ah.03g132990' => 'amhyb', 'Ah.14g079410' => 'amhyb', 'AL1G24640' => 'aly', 'AL2G26680' => 'aly', 'AL3G10530' => 'aly', 'AL3G45230' => 'aly', 'AL5G15230' => 'aly', 'AL5G16960' => 'aly', 'AL6G25210' => 'aly', 'Aqoxy2G00441' => 'aox', 'Aqoxy3G01236' => 'aox', 'Aqoxy5G03746' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3RQ047' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C7GMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9C8JER' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MBL6KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YXCZ83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZANX40' => 'arhy', 'AT1G12990' => 'ath', 'AT1G67880' => 'ath', 'AT2G13290' => 'ath', 'AT3G01620' => 'ath', 'AT3G26445' => 'ath', 'AT3G27540' => 'ath', 'AT5G14480' => 'ath', 'ATR0824G026' => 'atr', 'ATR1098G019' => 'atr', 'Atru.chr11.2145' => 'acertr', 'Atru.chr2.3636' => 'acertr', 'Atru.chr2.3644' => 'acertr', 'Atru.chr6.2422' => 'acertr', 'Atru.chr7.1112' => 'acertr', 'AUR62005469' => 'cqu', 'AUR62011166' => 'cqu', 'AUR62013319' => 'cqu', 'AUR62024273' => 'cqu', 'AUR62028420' => 'cqu', 'AUR62041942' => 'cqu', 'BcaB01g04969' => 'bca', 'BcaB01g06371' => 'bca', 'BcaB02g11494' => 'bca', 'BcaB03g15382' => 'bca', 'BcaB08g36994' => 'bca', 'BcaC03g13477' => 'bca', 'BcaC03g13478' => 'bca', 'BcaC03g13480' => 'bca', 'BcaC03g13481' => 'bca', 'BcaC03g13486' => 'bca', 'BcaC04g19031' => 'bca', 'BcaC04g23085' => 'bca', 'BcaC05g25094' => 'bca', 'BcaC05g25096' => 'bca', 'BcaC05g25138' => 'bca', 'BcaC05g30416' => 'bca', 'BcaC05g30455' => 'bca', 'BcaC06g30979' => 'bca', 'BcaC06g33805' => 'bca', 'BcaC08g46021' => 'bca', 'BcaNung03154' => 'bca', 'BolC2t06623H' => 'bol', 'BolC2t06632H' => 'bol', 'BolC2t06635H' => 'bol', 'BolC2t06638H' => 'bol', 'BolC3t13266H' => 'bol', 'BolC5t29776H' => 'bol', 'BolC6t38912H' => 'bol', 'BolC7t44183H' => 'bol', 'BolC9t54123H' => 'bol', 'BolC9t59107H' => 'bol', 'BraA02t05221Z' => 'bra', 'BraA03t09996Z' => 'bra', 'BraA05t23210Z' => 'bra', 'BraA06t24068Z' => 'bra', 'BraA06t27032Z' => 'bra', 'BraA08t35176Z' => 'bra', 'BraA09t36680Z' => 'bra', 'BraA10t44471Z' => 'bra', 'C02p06760' => 'bna', 'C02p06890' => 'bna', 'C02p07010' => 'bna', 'C03p07660' => 'bna', 'C05p10300' => 'bna', 'C06p38150' => 'bna', 'C07p36650' => 'bna', 'C08p15770' => 'bna', 'C09p12300' => 'bna', 'C09p62700' => 'bna', 'C09p75040' => 'bna', 'CAN.G13.1' => 'can', 'CAN.G138.4' => 'can', 'CAN.G44.6' => 'can', 'CAN.G473.19' => 'can', 'CANSAT01G0835' => 'cansat', 'CANSAT11G0246' => 'cansat', 'CANSAT11G1766' => 'cansat', 'CANSAT64G1954' => 'cansat', 'CARHR013330' => 'chi', 'CARHR060530' => 'chi', 'CARHR075300' => 'chi', 'CARHR105120' => 'chi', 'CARHR148910' => 'chi', 'CARHR198830' => 'chi', 'Carub.0001s1275' => 'cru', 'Carub.0002s1437' => 'cru', 'Carub.0003s0044' => 'cru', 'Carub.0003s2787' => 'cru', 'Carub.0005s0597' => 'cru', 'Carub.0006s1266' => 'cru', 'Ca_06935_v3' => 'car', 'Ca_13559_v3' => 'car', 'Ca_16941_v3' => 'car', 'Ca_16960_v3' => 'car', 'Ca_17775_v3' => 'car', 'Ca_30464_v3' => 'car', 'Cc06_g08160' => 'ccan', 'Cc07_g01520' => 'ccan', 'Cc11_g15810' => 'ccan', 'CDE02G2840' => 'cde', 'CDE03G0093' => 'cde', 'CDE04G2127' => 'cde', 'CDE07G1857' => 'cde', 'CDE09G1246' => 'cde', 'Cfa003412' => 'cfa', 'Cfa007341' => 'cfa', 'Cfa009220' => 'cfa', 'Ciclev10008737m.g' => 'ccl', 'Ciclev10015565m.g' => 'ccl', 'Ciclev10031761m.g' => 'ccl', 'CiPaw.03G045300' => 'cil', 'CiPaw.03G247200' => 'cil', 'CiPaw.04G029500' => 'cil', 'CiPaw.04G174000' => 'cil', 'CiPaw.05G181200' => 'cil', 'CiPaw.06G067100' => 'cil', 'ClCG05G025800' => 'cla', 'ClCG06G011400' => 'cla', 'ClCG09G019360' => 'cla', 'COL.COLO4_04827' => 'col', 'COL.COLO4_29170' => 'col', 'COL.COLO4_35131' => 'col', 'COL.COLO4_35132' => 'col', 'Cpa.g.sc33.32' => 'cpa', 'Cpa.g.sc46.29' => 'cpa', 'Cpa.g.sc796.1' => 'cpa', 'CsaV3_1G030420' => 'csa', 'CsaV3_5G027050' => 'csa', 'CsaV3_5G031040' => 'csa', 'CsaV3_UNG023130' => 'csa', 'CSS0007726' => 'camsi', 'CSS0016433' => 'camsi', 'CSS0017656' => 'camsi', 'CSS0025364' => 'camsi', 'CSS0027582' => 'camsi', 'CSS0047288' => 'camsi', 'CSS0049950' => 'camsi', 'DCAR_003843' => 'dca', 'DCAR_007052' => 'dca', 'DCAR_020884' => 'dca', 'DCAR_021730' => 'dca', 'DCAR_024423' => 'dca', 'DCAR_026509' => 'dca', 'DCAR_031158' => 'dca', 'Dinv14728' => 'din', 'Dinv15219' => 'din', 'Dinv25728' => 'din', 'Dinv33428' => 'din', 'Dinv36489' => 'din', 'Dinv41486' => 'din', 'Duzib147G0469' => 'dzi', 'Duzib168G0060' => 'dzi', 'Duzib187G1215' => 'dzi', 'Duzib248G0692' => 'dzi', 'Duzib251G0767' => 'dzi', 'Duzib264G0446' => 'dzi', 'Duzib268G0691' => 'dzi', 'ECA232G4767' => 'eca', 'ECA233G2838' => 'eca', 'ECA234G0391' => 'eca', 'ECA234G0857' => 'eca', 'ECA236G1593' => 'eca', 'ECA238G0565' => 'eca', 'ECA246G1027' => 'eca', 'ECA246G3223' => 'eca', 'ECA246G3470' => 'eca', 'EL10Ac6g13829' => 'bvu', 'EL10Ac6g14093' => 'bvu', 'EL10Ac8g18707' => 'bvu', 'Eucgr.C01369' => 'egr', 'Eucgr.H02492' => 'egr', 'Eucgr.I01733' => 'egr', 'Eucgr.J02255' => 'egr', 'Eucgr.J02257' => 'egr', 'Eucgr.J02258' => 'egr', 'FAN02G1601' => 'fan', 'FAN03G1586' => 'fan', 'FAN03G2986' => 'fan', 'FAN05G4837' => 'fan', 'FAN06G0146' => 'fan', 'FAN07G0858' => 'fan', 'FAN09G3179' => 'fan', 'FAN10G0669' => 'fan', 'FAN12G2358' => 'fan', 'FAN14G4198' => 'fan', 'FAN14G5112' => 'fan', 'FAN17G0342' => 'fan', 'FAN19G0342' => 'fan', 'FAN19G0962' => 'fan', 'FAN19G1101' => 'fan', 'FAN19G1872' => 'fan', 'FAN22G0356' => 'fan', 'FAN23G0744' => 'fan', 'FAN23G1914' => 'fan', 'FAN26G0032' => 'fan', 'FAN28G0625' => 'fan', 'FvH4_1g02710' => 'fve', 'FvH4_1g02720' => 'fve', 'FvH4_4g25670' => 'fve', 'FvH4_6g51700' => 'fve', 'FvH4_7g20170' => 'fve', 'Glyma.05G175000' => 'gma', 'Glyma.08G132300' => 'gma', 'Glyma.11G243000' => 'gma', 'Glyma.13G158900' => 'gma', 'Glyma.17G112400' => 'gma', 'Glyma.18G014100' => 'gma', 'Glyma.19G003100' => 'gma', 'Glyma.19G056500' => 'gma', 'Gohir.A01G158900' => 'ghi', 'Gohir.A05G312600' => 'ghi', 'Gohir.A05G354900' => 'ghi', 'Gohir.A07G037200' => 'ghi', 'Gohir.A09G030000' => 'ghi', 'Gohir.A12G145200' => 'ghi', 'Gohir.D01G151500' => 'ghi', 'Gohir.D04G058300' => 'ghi', 'Gohir.D05G314100' => 'ghi', 'Gohir.D07G041400' => 'ghi', 'Gohir.D09G029700' => 'ghi', 'Gohir.D12G149700' => 'ghi', 'Gorai.001G043800' => 'gra', 'Gorai.002G187800' => 'gra', 'Gorai.006G034700' => 'gra', 'Gorai.008G161200' => 'gra', 'Gorai.009G335700' => 'gra', 'Gorai.012G065000' => 'gra', 'GSVIVG01000535001' => 'vvi', 'GSVIVG01015572001' => 'vvi', 'GSVIVG01032386001' => 'vvi', 'HanXRQChr05g0138531' => 'han', 'HanXRQChr06g0174391' => 'han', 'HanXRQChr07g0199021' => 'han', 'HanXRQChr08g0208211' => 'han', 'HanXRQChr09g0255471' => 'han', 'HanXRQChr10g0315791' => 'han', 'HanXRQChr12g0371991' => 'han', 'HanXRQChr15g0475251' => 'han', 'HanXRQChr17g0540001' => 'han', 'HanXRQChr17g0548631' => 'han', 'HanXRQChr17g0569561' => 'han', 'Haze_12256' => 'cav', 'Haze_14756' => 'cav', 'Haze_25528' => 'cav', 'Hma1.2p1_0079F.1_g041020' => 'hma', 'Hma1.2p1_0818F.1_g223260' => 'hma', 'Hma1.2p1_1747F.1_g300530' => 'hma', 'HPP92_004607' => 'vpl', 'HPP92_004608' => 'vpl', 'HPP92_006181' => 'vpl', 'HPP92_012192' => 'vpl', 'HPP92_015680' => 'vpl', 'HPP92_020249' => 'vpl', 'HPP92_021376' => 'vpl', 'HPP92_024275' => 'vpl', 'Hund06031' => 'sun', 'Hund25391' => 'sun', 'Lalb_Chr07g0185371' => 'lal', 'Lalb_Chr07g0185381' => 'lal', 'Lalb_Chr12g0204011' => 'lal', 'Lalb_Chr13g0301671' => 'lal', 'Lalb_Chr14g0362851' => 'lal', 'Lalb_Chr24g0403581' => 'lal', 'Lj1g0000233' => 'lja', 'Lj2g0018120' => 'lja', 'Lj3C621T0' => 'lonja', 'Lj3P1059T14' => 'lonja', 'Lj3P611T9' => 'lonja', 'Lj3P614T13' => 'lonja', 'Lj3P615T5' => 'lonja', 'Lj4g0012315' => 'lja', 'Lj4g0026182' => 'lja', 'Lj6P813T16' => 'lonja', 'Lj7C427T7' => 'lonja', 'Lj7C427T8' => 'lonja', 'Lj7P600T41' => 'lonja', 'Lju41C42G17' => 'lonja', 'Lsat_1_v5_gn_0_47300' => 'lsa', 'Lsat_1_v5_gn_2_91280' => 'lsa', 'Lsat_1_v5_gn_3_30561' => 'lsa', 'Lsat_1_v5_gn_4_184321' => 'lsa', 'Lsat_1_v5_gn_4_4041' => 'lsa', 'Lsat_1_v5_gn_5_92000' => 'lsa', 'Lsat_1_v5_gn_8_152940' => 'lsa', 'Lsat_1_v5_gn_8_62401' => 'lsa', 'Manes.06G055900' => 'mes', 'Manes.12G022200' => 'mes', 'Manes.13G023300' => 'mes', 'Manes.14G115000' => 'mes', 'Manes.15G151700' => 'mes', 'Manes.17G111300' => 'mes', 'Mapoly0226s0009' => 'mpo', 'MBI02_g25363_MAGBIO' => 'mbi', 'MBI06_g00027_MAGBIO' => 'mbi', 'MBI10_g13034_MAGBIO' => 'mbi', 'MD09G1023400' => 'mdo', 'MD13G1100100' => 'mdo', 'MD15G1169200' => 'mdo', 'MD16G1101100' => 'mdo', 'MD17G1022900' => 'mdo', 'Medtr3g096150' => 'mtr', 'Medtr4g115070' => 'mtr', 'Medtr7g033325' => 'mtr', 'Medtr8g089840' => 'mtr', 'MELO3C010319.2' => 'cme', 'MELO3C011944.2' => 'cme', 'MELO3C021589.2' => 'cme', 'Migut.E00207' => 'egut', 'Migut.H00067' => 'egut', 'Migut.K00433' => 'egut', 'Migut.K00606' => 'egut', 'Migut.K01410' => 'egut', 'MSTRG.13347' => 'ama', 'MSTRG.24045' => 'ama', 'MSTRG.2428' => 'ama', 'MSTRG.26410' => 'ama', 'MSTRG.3139' => 'ama', 'MSTRG.3286' => 'ama', 'MSTRG.563' => 'ama', 'MSTRG.7941' => 'ama', 'Nitab4.5_0000028g0060' => 'nta', 'Nitab4.5_0000065g0260' => 'nta', 'Nitab4.5_0000112g0060' => 'nta', 'Nitab4.5_0000489g0120' => 'nta', 'Nitab4.5_0001776g0050' => 'nta', 'Nitab4.5_0001854g0010' => 'nta', 'Nitab4.5_0001860g0020' => 'nta', 'Nitab4.5_0004352g0010' => 'nta', 'Nitab4.5_0008716g0020' => 'nta', 'Nitab4.5_0008922g0010' => 'nta', 'Nn3g16693' => 'nnu', 'Nn4g22596' => 'nnu', 'Nn7g37639' => 'nnu', 'Oeu001701.1' => 'oeu', 'Oeu018149.1' => 'oeu', 'Oeu026220.1' => 'oeu', 'Oeu038635.1' => 'oeu', 'Oeu049176.1' => 'oeu', 'Oeu056706.1' => 'oeu', 'Oeu056937.1' => 'oeu', 'Oeu057540.1' => 'oeu', 'Os02g0594900' => 'osa', 'Os02g0595100' => 'osa', 'Os04g0477500' => 'osa', 'Os12g0611900' => 'osa', 'Peaxi162Scf00076g00020' => 'pax', 'Peaxi162Scf00128g00217' => 'pax', 'Peaxi162Scf00129g01640' => 'pax', 'Peaxi162Scf00669g00007' => 'pax', 'Peaxi162Scf00700g00421' => 'pax', 'Peaxi162Scf00801g00038' => 'pax', 'Peaxi162Scf00891g00025' => 'pax', 'PGR083G0909' => 'pgr', 'PGR119G1005' => 'pgr', 'PGR142G2236' => 'pgr', 'PGR142G3388' => 'pgr', 'PGSC0003DMG400004514' => 'stu', 'PGSC0003DMG400012635' => 'stu', 'PGSC0003DMG400015730' => 'stu', 'PGSC0003DMG400018611' => 'stu', 'PGSC0003DMG400030897' => 'stu', 'Phvul.001G254800' => 'pvu', 'Phvul.002G260100' => 'pvu', 'Phvul.003G167600' => 'pvu', 'Phvul.004G005100' => 'pvu', 'Potri.001G343600' => 'ptr', 'Potri.006G066700' => 'ptr', 'Potri.008G186000' => 'ptr', 'Potri.010G046900' => 'ptr', 'Potri.018G127900' => 'ptr', 'Pp3c20_17750' => 'ppa', 'Pp3c24_4380' => 'ppa', 'Prupe.1G245800' => 'ppe', 'Prupe.3G293400' => 'ppe', 'Prupe.7G247400' => 'ppe', 'Psat0s145g0120' => 'psa', 'Psat0s595g0040' => 'psa', 'Psat0s595g0120' => 'psa', 'Psat3g175040' => 'psa', 'Psat7g058120' => 'psa', 'PSO017G0428' => 'pso', 'PSO063G7510' => 'pso', 'PSO067G0046' => 'pso', 'PSO478G1073' => 'pso', 'PSO675G3677' => 'pso', 'PSO675G6558' => 'pso', 'PSO675G7520' => 'pso', 'PSO675G8959' => 'pso', 'QL02p074089' => 'qlo', 'QL02p089614' => 'qlo', 'QL03p057736' => 'qlo', 'RcHm_v2.0_Chr1g0364131' => 'rch', 'RcHm_v2.0_Chr2g0087801' => 'rch', 'RcHm_v2.0_Chr2g0087821' => 'rch', 'RcHm_v2.0_Chr2g0173231' => 'rch', 'RcHm_v2.0_Chr4g0433111' => 'rch', 'Rhsim03G0250300' => 'rsi', 'Rhsim08G0048400' => 'rsi', 'Rhsim10G0014800' => 'rsi', 'Rhsim12G0040100' => 'rsi', 'Rhsim12G0109700' => 'rsi', 'Sabra06G0049600' => 'sbr', 'Sabra08G0141000' => 'sbr', 'Sabra10G0021400' => 'sbr', 'Sabra16G0222900' => 'sbr', 'Sabra18G0108600' => 'sbr', 'SalBow1G0433' => 'sbo', 'SalBow1G2038' => 'sbo', 'SalBow1G5003' => 'sbo', 'SalBow7G1197' => 'sbo', 'SalBow8G3506' => 'sbo', 'Sc03g0007300' => 'sci', 'Sc11g0000950' => 'sci', 'Sc14g0008750' => 'sci', 'Sc18g0000420' => 'sci', 'Sed0006754' => 'sed', 'Sed0008741' => 'sed', 'Sed0017172' => 'sed', 'Sed0018925' => 'sed', 'Sed0023326' => 'sed', 'Sed0025909' => 'sed', 'SEGI_05333' => 'sgi', 'SEGI_10362' => 'sgi', 'SEGI_13380' => 'sgi', 'SEGI_24306' => 'sgi', 'SEGI_29077' => 'sgi', 'SEGI_29095' => 'sgi', 'SEGI_36534' => 'sgi', 'SEGI_37506' => 'sgi', 'SEGI_38321' => 'sgi', 'SGA_v2.0_scaffold307G48031' => 'sas', 'SGA_v2.0_scaffold47G17507' => 'sas', 'SGA_v2.0_scaffold63G21736' => 'sas', 'SGA_v2.0_scaffold87G27070' => 'sas', 'SHI17794' => 'shi', 'SHI28851' => 'shi', 'SMO165G0155' => 'smo', 'SMO340G0217' => 'smo', 'SMO367G1210' => 'smo', 'Solyc02g093430.3' => 'sly', 'Solyc05g013580.4' => 'sly', 'Solyc07g008030.3' => 'sly', 'Solyc12g035470.2' => 'sly', 'Sopen02g038020' => 'spe', 'Sopen05g008490' => 'spe', 'Sopen07g003910' => 'spe', 'Sopen12g015240' => 'spe', 'Sp1g11550' => 'spa', 'Sp2g16710' => 'spa', 'Sp3g00430' => 'spa', 'Sp3g26780' => 'spa', 'Sp5g22900' => 'spa', 'Sp6g29530' => 'spa', 'TAR371G0794' => 'tar', 'TAR374G0164' => 'tar', 'TAR622G0165' => 'tar', 'TAR626G0929' => 'tar', 'TAR629G2155' => 'tar', 'THA.LOC104805282' => 'tha', 'THA.LOC104805363' => 'tha', 'THA.LOC104808968' => 'tha', 'THA.LOC104821093' => 'tha', 'THA.LOC104823953' => 'tha', 'THA.LOC104825562' => 'tha', 'THA.LOC104825665' => 'tha', 'Thecc.02G261400' => 'tca', 'Thecc.04G019200' => 'tca', 'Thecc.09G130400' => 'tca', 'Thhalv10004374m.g' => 'esa', 'Thhalv10007850m.g' => 'esa', 'Thhalv10013782m.g' => 'esa', 'Thhalv10018686m.g' => 'esa', 'Thhalv10020899m.g' => 'esa', 'Thhalv10022755m.g' => 'esa', 'TPR.G23851' => 'tpr', 'TPR.G26500' => 'tpr', 'TPR.G27267' => 'tpr', 'TPR.G32001' => 'tpr', 'TPR.G6251' => 'tpr', 'TPR.G8167' => 'tpr', 'TWI12G1330' => 'twi', 'TWI18G1239' => 'twi', 'TWI34G0979' => 'twi', 'TWI36G0670' => 'twi', 'TWI36G0707' => 'twi', 'TWI56G0233' => 'twi', 'TWI75G1809' => 'twi', 'unitig_21.g20874' => 'ugi', 'unitig_26.g10343' => 'ugi', 'unitig_46.g18392' => 'ugi', 'unitig_52.g17178' => 'ugi', 'unitig_8.g2934' => 'ugi', 'vmacro01122' => 'vma', 'vmacro05875' => 'vma', 'vmacro06147' => 'vma', 'vmacro16191' => 'vma', 'vmacro18293' => 'vma', 'VMungo0251G3707' => 'vmu', 'VMungo0464G1521' => 'vmu', 'VMungo1215G0205' => 'vmu', 'VMungo1383G2484' => 'vmu', 'Zm00001eb079610' => 'zma', 'Zm00001eb135990' => 'zma', 'Zm00001eb183710' => 'zma', 'Zm00001eb246020' => 'zma' ), 'gf_id' => 'HOM05D001124', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001124' ), 'data_identifier' => 'HOM05D001124', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001124', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '548', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02520' => 'bna', 'A03p06630' => 'bna', 'A05p44460' => 'bna', 'A06p08710' => 'bna', 'A06p41090' => 'bna', 'A07p32320' => 'bna', 'A08p32520' => 'bna', 'A09p10360' => 'bna', 'A10p24080' => 'bna', 'Aa31LG11G15250' => 'aar', 'Aa31LG1G1800' => 'aar', 'Aa31LG2G5120' => 'aar', 'Aa31LG2G6070' => 'aar', 'Aa31LG5G10770' => 'aar', 'Aa31sc61G90' => 'aar', 'Actinidia01352' => 'ach', 'Actinidia05983' => 'ach', 'Actinidia08133' => 'ach', 'Actinidia15101' => 'ach', 'Actinidia26379' => 'ach', 'Actinidia35778' => 'ach', 'Actinidia36123' => 'ach', 'Actinidia37436' => 'ach', 'Actinidia38730' => 'ach', 'Ah.02g128210' => 'amhyb', 'Ah.03g132990' => 'amhyb', 'Ah.14g079410' => 'amhyb', 'AL1G24640' => 'aly', 'AL2G26680' => 'aly', 'AL3G10530' => 'aly', 'AL3G45230' => 'aly', 'AL5G15230' => 'aly', 'AL5G16960' => 'aly', 'AL6G25210' => 'aly', 'Aqoxy2G00441' => 'aox', 'Aqoxy3G01236' => 'aox', 'Aqoxy5G03746' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3RQ047' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C7GMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9C8JER' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MBL6KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YXCZ83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZANX40' => 'arhy', 'AT1G12990' => 'ath', 'AT1G67880' => 'ath', 'AT2G13290' => 'ath', 'AT3G01620' => 'ath', 'AT3G26445' => 'ath', 'AT3G27540' => 'ath', 'AT5G14480' => 'ath', 'ATR0824G026' => 'atr', 'ATR1098G019' => 'atr', 'Atru.chr11.2145' => 'acertr', 'Atru.chr2.3636' => 'acertr', 'Atru.chr2.3644' => 'acertr', 'Atru.chr6.2422' => 'acertr', 'Atru.chr7.1112' => 'acertr', 'AUR62005469' => 'cqu', 'AUR62011166' => 'cqu', 'AUR62013319' => 'cqu', 'AUR62024273' => 'cqu', 'AUR62028420' => 'cqu', 'AUR62041942' => 'cqu', 'BcaB01g04969' => 'bca', 'BcaB01g06371' => 'bca', 'BcaB02g11494' => 'bca', 'BcaB03g15382' => 'bca', 'BcaB08g36994' => 'bca', 'BcaC03g13477' => 'bca', 'BcaC03g13478' => 'bca', 'BcaC03g13480' => 'bca', 'BcaC03g13481' => 'bca', 'BcaC03g13486' => 'bca', 'BcaC04g19031' => 'bca', 'BcaC04g23085' => 'bca', 'BcaC05g25094' => 'bca', 'BcaC05g25096' => 'bca', 'BcaC05g25138' => 'bca', 'BcaC05g30416' => 'bca', 'BcaC05g30455' => 'bca', 'BcaC06g30979' => 'bca', 'BcaC06g33805' => 'bca', 'BcaC08g46021' => 'bca', 'BcaNung03154' => 'bca', 'BolC2t06623H' => 'bol', 'BolC2t06632H' => 'bol', 'BolC2t06635H' => 'bol', 'BolC2t06638H' => 'bol', 'BolC3t13266H' => 'bol', 'BolC5t29776H' => 'bol', 'BolC6t38912H' => 'bol', 'BolC7t44183H' => 'bol', 'BolC9t54123H' => 'bol', 'BolC9t59107H' => 'bol', 'BraA02t05221Z' => 'bra', 'BraA03t09996Z' => 'bra', 'BraA05t23210Z' => 'bra', 'BraA06t24068Z' => 'bra', 'BraA06t27032Z' => 'bra', 'BraA08t35176Z' => 'bra', 'BraA09t36680Z' => 'bra', 'BraA10t44471Z' => 'bra', 'C02p06760' => 'bna', 'C02p06890' => 'bna', 'C02p07010' => 'bna', 'C03p07660' => 'bna', 'C05p10300' => 'bna', 'C06p38150' => 'bna', 'C07p36650' => 'bna', 'C08p15770' => 'bna', 'C09p12300' => 'bna', 'C09p62700' => 'bna', 'C09p75040' => 'bna', 'CAN.G13.1' => 'can', 'CAN.G138.4' => 'can', 'CAN.G44.6' => 'can', 'CAN.G473.19' => 'can', 'CANSAT01G0835' => 'cansat', 'CANSAT11G0246' => 'cansat', 'CANSAT11G1766' => 'cansat', 'CANSAT64G1954' => 'cansat', 'CARHR013330' => 'chi', 'CARHR060530' => 'chi', 'CARHR075300' => 'chi', 'CARHR105120' => 'chi', 'CARHR148910' => 'chi', 'CARHR198830' => 'chi', 'Carub.0001s1275' => 'cru', 'Carub.0002s1437' => 'cru', 'Carub.0003s0044' => 'cru', 'Carub.0003s2787' => 'cru', 'Carub.0005s0597' => 'cru', 'Carub.0006s1266' => 'cru', 'Ca_06935_v3' => 'car', 'Ca_13559_v3' => 'car', 'Ca_16941_v3' => 'car', 'Ca_16960_v3' => 'car', 'Ca_17775_v3' => 'car', 'Ca_30464_v3' => 'car', 'Cc06_g08160' => 'ccan', 'Cc07_g01520' => 'ccan', 'Cc11_g15810' => 'ccan', 'CDE02G2840' => 'cde', 'CDE03G0093' => 'cde', 'CDE04G2127' => 'cde', 'CDE07G1857' => 'cde', 'CDE09G1246' => 'cde', 'Cfa003412' => 'cfa', 'Cfa007341' => 'cfa', 'Cfa009220' => 'cfa', 'Ciclev10008737m.g' => 'ccl', 'Ciclev10015565m.g' => 'ccl', 'Ciclev10031761m.g' => 'ccl', 'CiPaw.03G045300' => 'cil', 'CiPaw.03G247200' => 'cil', 'CiPaw.04G029500' => 'cil', 'CiPaw.04G174000' => 'cil', 'CiPaw.05G181200' => 'cil', 'CiPaw.06G067100' => 'cil', 'ClCG05G025800' => 'cla', 'ClCG06G011400' => 'cla', 'ClCG09G019360' => 'cla', 'COL.COLO4_04827' => 'col', 'COL.COLO4_29170' => 'col', 'COL.COLO4_35131' => 'col', 'COL.COLO4_35132' => 'col', 'Cpa.g.sc33.32' => 'cpa', 'Cpa.g.sc46.29' => 'cpa', 'Cpa.g.sc796.1' => 'cpa', 'CsaV3_1G030420' => 'csa', 'CsaV3_5G027050' => 'csa', 'CsaV3_5G031040' => 'csa', 'CsaV3_UNG023130' => 'csa', 'CSS0007726' => 'camsi', 'CSS0016433' => 'camsi', 'CSS0017656' => 'camsi', 'CSS0025364' => 'camsi', 'CSS0027582' => 'camsi', 'CSS0047288' => 'camsi', 'CSS0049950' => 'camsi', 'DCAR_003843' => 'dca', 'DCAR_007052' => 'dca', 'DCAR_020884' => 'dca', 'DCAR_021730' => 'dca', 'DCAR_024423' => 'dca', 'DCAR_026509' => 'dca', 'DCAR_031158' => 'dca', 'Dinv14728' => 'din', 'Dinv15219' => 'din', 'Dinv25728' => 'din', 'Dinv33428' => 'din', 'Dinv36489' => 'din', 'Dinv41486' => 'din', 'Duzib147G0469' => 'dzi', 'Duzib168G0060' => 'dzi', 'Duzib187G1215' => 'dzi', 'Duzib248G0692' => 'dzi', 'Duzib251G0767' => 'dzi', 'Duzib264G0446' => 'dzi', 'Duzib268G0691' => 'dzi', 'ECA232G4767' => 'eca', 'ECA233G2838' => 'eca', 'ECA234G0391' => 'eca', 'ECA234G0857' => 'eca', 'ECA236G1593' => 'eca', 'ECA238G0565' => 'eca', 'ECA246G1027' => 'eca', 'ECA246G3223' => 'eca', 'ECA246G3470' => 'eca', 'EL10Ac6g13829' => 'bvu', 'EL10Ac6g14093' => 'bvu', 'EL10Ac8g18707' => 'bvu', 'Eucgr.C01369' => 'egr', 'Eucgr.H02492' => 'egr', 'Eucgr.I01733' => 'egr', 'Eucgr.J02255' => 'egr', 'Eucgr.J02257' => 'egr', 'Eucgr.J02258' => 'egr', 'FAN02G1601' => 'fan', 'FAN03G1586' => 'fan', 'FAN03G2986' => 'fan', 'FAN05G4837' => 'fan', 'FAN06G0146' => 'fan', 'FAN07G0858' => 'fan', 'FAN09G3179' => 'fan', 'FAN10G0669' => 'fan', 'FAN12G2358' => 'fan', 'FAN14G4198' => 'fan', 'FAN14G5112' => 'fan', 'FAN17G0342' => 'fan', 'FAN19G0342' => 'fan', 'FAN19G0962' => 'fan', 'FAN19G1101' => 'fan', 'FAN19G1872' => 'fan', 'FAN22G0356' => 'fan', 'FAN23G0744' => 'fan', 'FAN23G1914' => 'fan', 'FAN26G0032' => 'fan', 'FAN28G0625' => 'fan', 'FvH4_1g02710' => 'fve', 'FvH4_1g02720' => 'fve', 'FvH4_4g25670' => 'fve', 'FvH4_6g51700' => 'fve', 'FvH4_7g20170' => 'fve', 'Glyma.05G175000' => 'gma', 'Glyma.08G132300' => 'gma', 'Glyma.11G243000' => 'gma', 'Glyma.13G158900' => 'gma', 'Glyma.17G112400' => 'gma', 'Glyma.18G014100' => 'gma', 'Glyma.19G003100' => 'gma', 'Glyma.19G056500' => 'gma', 'Gohir.A01G158900' => 'ghi', 'Gohir.A05G312600' => 'ghi', 'Gohir.A05G354900' => 'ghi', 'Gohir.A07G037200' => 'ghi', 'Gohir.A09G030000' => 'ghi', 'Gohir.A12G145200' => 'ghi', 'Gohir.D01G151500' => 'ghi', 'Gohir.D04G058300' => 'ghi', 'Gohir.D05G314100' => 'ghi', 'Gohir.D07G041400' => 'ghi', 'Gohir.D09G029700' => 'ghi', 'Gohir.D12G149700' => 'ghi', 'Gorai.001G043800' => 'gra', 'Gorai.002G187800' => 'gra', 'Gorai.006G034700' => 'gra', 'Gorai.008G161200' => 'gra', 'Gorai.009G335700' => 'gra', 'Gorai.012G065000' => 'gra', 'GSVIVG01000535001' => 'vvi', 'GSVIVG01015572001' => 'vvi', 'GSVIVG01032386001' => 'vvi', 'HanXRQChr05g0138531' => 'han', 'HanXRQChr06g0174391' => 'han', 'HanXRQChr07g0199021' => 'han', 'HanXRQChr08g0208211' => 'han', 'HanXRQChr09g0255471' => 'han', 'HanXRQChr10g0315791' => 'han', 'HanXRQChr12g0371991' => 'han', 'HanXRQChr15g0475251' => 'han', 'HanXRQChr17g0540001' => 'han', 'HanXRQChr17g0548631' => 'han', 'HanXRQChr17g0569561' => 'han', 'Haze_12256' => 'cav', 'Haze_14756' => 'cav', 'Haze_25528' => 'cav', 'Hma1.2p1_0079F.1_g041020' => 'hma', 'Hma1.2p1_0818F.1_g223260' => 'hma', 'Hma1.2p1_1747F.1_g300530' => 'hma', 'HPP92_004607' => 'vpl', 'HPP92_004608' => 'vpl', 'HPP92_006181' => 'vpl', 'HPP92_012192' => 'vpl', 'HPP92_015680' => 'vpl', 'HPP92_020249' => 'vpl', 'HPP92_021376' => 'vpl', 'HPP92_024275' => 'vpl', 'Hund06031' => 'sun', 'Hund25391' => 'sun', 'Lalb_Chr07g0185371' => 'lal', 'Lalb_Chr07g0185381' => 'lal', 'Lalb_Chr12g0204011' => 'lal', 'Lalb_Chr13g0301671' => 'lal', 'Lalb_Chr14g0362851' => 'lal', 'Lalb_Chr24g0403581' => 'lal', 'Lj1g0000233' => 'lja', 'Lj2g0018120' => 'lja', 'Lj3C621T0' => 'lonja', 'Lj3P1059T14' => 'lonja', 'Lj3P611T9' => 'lonja', 'Lj3P614T13' => 'lonja', 'Lj3P615T5' => 'lonja', 'Lj4g0012315' => 'lja', 'Lj4g0026182' => 'lja', 'Lj6P813T16' => 'lonja', 'Lj7C427T7' => 'lonja', 'Lj7C427T8' => 'lonja', 'Lj7P600T41' => 'lonja', 'Lju41C42G17' => 'lonja', 'Lsat_1_v5_gn_0_47300' => 'lsa', 'Lsat_1_v5_gn_2_91280' => 'lsa', 'Lsat_1_v5_gn_3_30561' => 'lsa', 'Lsat_1_v5_gn_4_184321' => 'lsa', 'Lsat_1_v5_gn_4_4041' => 'lsa', 'Lsat_1_v5_gn_5_92000' => 'lsa', 'Lsat_1_v5_gn_8_152940' => 'lsa', 'Lsat_1_v5_gn_8_62401' => 'lsa', 'Manes.06G055900' => 'mes', 'Manes.12G022200' => 'mes', 'Manes.13G023300' => 'mes', 'Manes.14G115000' => 'mes', 'Manes.15G151700' => 'mes', 'Manes.17G111300' => 'mes', 'Mapoly0226s0009' => 'mpo', 'MBI02_g25363_MAGBIO' => 'mbi', 'MBI06_g00027_MAGBIO' => 'mbi', 'MBI10_g13034_MAGBIO' => 'mbi', 'MD09G1023400' => 'mdo', 'MD13G1100100' => 'mdo', 'MD15G1169200' => 'mdo', 'MD16G1101100' => 'mdo', 'MD17G1022900' => 'mdo', 'Medtr3g096150' => 'mtr', 'Medtr4g115070' => 'mtr', 'Medtr7g033325' => 'mtr', 'Medtr8g089840' => 'mtr', 'MELO3C010319.2' => 'cme', 'MELO3C011944.2' => 'cme', 'MELO3C021589.2' => 'cme', 'Migut.E00207' => 'egut', 'Migut.H00067' => 'egut', 'Migut.K00433' => 'egut', 'Migut.K00606' => 'egut', 'Migut.K01410' => 'egut', 'MSTRG.13347' => 'ama', 'MSTRG.24045' => 'ama', 'MSTRG.2428' => 'ama', 'MSTRG.26410' => 'ama', 'MSTRG.3139' => 'ama', 'MSTRG.3286' => 'ama', 'MSTRG.563' => 'ama', 'MSTRG.7941' => 'ama', 'Nitab4.5_0000028g0060' => 'nta', 'Nitab4.5_0000065g0260' => 'nta', 'Nitab4.5_0000112g0060' => 'nta', 'Nitab4.5_0000489g0120' => 'nta', 'Nitab4.5_0001776g0050' => 'nta', 'Nitab4.5_0001854g0010' => 'nta', 'Nitab4.5_0001860g0020' => 'nta', 'Nitab4.5_0004352g0010' => 'nta', 'Nitab4.5_0008716g0020' => 'nta', 'Nitab4.5_0008922g0010' => 'nta', 'Nn3g16693' => 'nnu', 'Nn4g22596' => 'nnu', 'Nn7g37639' => 'nnu', 'Oeu001701.1' => 'oeu', 'Oeu018149.1' => 'oeu', 'Oeu026220.1' => 'oeu', 'Oeu038635.1' => 'oeu', 'Oeu049176.1' => 'oeu', 'Oeu056706.1' => 'oeu', 'Oeu056937.1' => 'oeu', 'Oeu057540.1' => 'oeu', 'Os02g0594900' => 'osa', 'Os02g0595100' => 'osa', 'Os04g0477500' => 'osa', 'Os12g0611900' => 'osa', 'Peaxi162Scf00076g00020' => 'pax', 'Peaxi162Scf00128g00217' => 'pax', 'Peaxi162Scf00129g01640' => 'pax', 'Peaxi162Scf00669g00007' => 'pax', 'Peaxi162Scf00700g00421' => 'pax', 'Peaxi162Scf00801g00038' => 'pax', 'Peaxi162Scf00891g00025' => 'pax', 'PGR083G0909' => 'pgr', 'PGR119G1005' => 'pgr', 'PGR142G2236' => 'pgr', 'PGR142G3388' => 'pgr', 'PGSC0003DMG400004514' => 'stu', 'PGSC0003DMG400012635' => 'stu', 'PGSC0003DMG400015730' => 'stu', 'PGSC0003DMG400018611' => 'stu', 'PGSC0003DMG400030897' => 'stu', 'Phvul.001G254800' => 'pvu', 'Phvul.002G260100' => 'pvu', 'Phvul.003G167600' => 'pvu', 'Phvul.004G005100' => 'pvu', 'Potri.001G343600' => 'ptr', 'Potri.006G066700' => 'ptr', 'Potri.008G186000' => 'ptr', 'Potri.010G046900' => 'ptr', 'Potri.018G127900' => 'ptr', 'Pp3c20_17750' => 'ppa', 'Pp3c24_4380' => 'ppa', 'Prupe.1G245800' => 'ppe', 'Prupe.3G293400' => 'ppe', 'Prupe.7G247400' => 'ppe', 'Psat0s145g0120' => 'psa', 'Psat0s595g0040' => 'psa', 'Psat0s595g0120' => 'psa', 'Psat3g175040' => 'psa', 'Psat7g058120' => 'psa', 'PSO017G0428' => 'pso', 'PSO063G7510' => 'pso', 'PSO067G0046' => 'pso', 'PSO478G1073' => 'pso', 'PSO675G3677' => 'pso', 'PSO675G6558' => 'pso', 'PSO675G7520' => 'pso', 'PSO675G8959' => 'pso', 'QL02p074089' => 'qlo', 'QL02p089614' => 'qlo', 'QL03p057736' => 'qlo', 'RcHm_v2.0_Chr1g0364131' => 'rch', 'RcHm_v2.0_Chr2g0087801' => 'rch', 'RcHm_v2.0_Chr2g0087821' => 'rch', 'RcHm_v2.0_Chr2g0173231' => 'rch', 'RcHm_v2.0_Chr4g0433111' => 'rch', 'Rhsim03G0250300' => 'rsi', 'Rhsim08G0048400' => 'rsi', 'Rhsim10G0014800' => 'rsi', 'Rhsim12G0040100' => 'rsi', 'Rhsim12G0109700' => 'rsi', 'Sabra06G0049600' => 'sbr', 'Sabra08G0141000' => 'sbr', 'Sabra10G0021400' => 'sbr', 'Sabra16G0222900' => 'sbr', 'Sabra18G0108600' => 'sbr', 'SalBow1G0433' => 'sbo', 'SalBow1G2038' => 'sbo', 'SalBow1G5003' => 'sbo', 'SalBow7G1197' => 'sbo', 'SalBow8G3506' => 'sbo', 'Sc03g0007300' => 'sci', 'Sc11g0000950' => 'sci', 'Sc14g0008750' => 'sci', 'Sc18g0000420' => 'sci', 'Sed0006754' => 'sed', 'Sed0008741' => 'sed', 'Sed0017172' => 'sed', 'Sed0018925' => 'sed', 'Sed0023326' => 'sed', 'Sed0025909' => 'sed', 'SEGI_05333' => 'sgi', 'SEGI_10362' => 'sgi', 'SEGI_13380' => 'sgi', 'SEGI_24306' => 'sgi', 'SEGI_29077' => 'sgi', 'SEGI_29095' => 'sgi', 'SEGI_36534' => 'sgi', 'SEGI_37506' => 'sgi', 'SEGI_38321' => 'sgi', 'SGA_v2.0_scaffold307G48031' => 'sas', 'SGA_v2.0_scaffold47G17507' => 'sas', 'SGA_v2.0_scaffold63G21736' => 'sas', 'SGA_v2.0_scaffold87G27070' => 'sas', 'SHI17794' => 'shi', 'SHI28851' => 'shi', 'SMO165G0155' => 'smo', 'SMO340G0217' => 'smo', 'SMO367G1210' => 'smo', 'Solyc02g093430.3' => 'sly', 'Solyc05g013580.4' => 'sly', 'Solyc07g008030.3' => 'sly', 'Solyc12g035470.2' => 'sly', 'Sopen02g038020' => 'spe', 'Sopen05g008490' => 'spe', 'Sopen07g003910' => 'spe', 'Sopen12g015240' => 'spe', 'Sp1g11550' => 'spa', 'Sp2g16710' => 'spa', 'Sp3g00430' => 'spa', 'Sp3g26780' => 'spa', 'Sp5g22900' => 'spa', 'Sp6g29530' => 'spa', 'TAR371G0794' => 'tar', 'TAR374G0164' => 'tar', 'TAR622G0165' => 'tar', 'TAR626G0929' => 'tar', 'TAR629G2155' => 'tar', 'THA.LOC104805282' => 'tha', 'THA.LOC104805363' => 'tha', 'THA.LOC104808968' => 'tha', 'THA.LOC104821093' => 'tha', 'THA.LOC104823953' => 'tha', 'THA.LOC104825562' => 'tha', 'THA.LOC104825665' => 'tha', 'Thecc.02G261400' => 'tca', 'Thecc.04G019200' => 'tca', 'Thecc.09G130400' => 'tca', 'Thhalv10004374m.g' => 'esa', 'Thhalv10007850m.g' => 'esa', 'Thhalv10013782m.g' => 'esa', 'Thhalv10018686m.g' => 'esa', 'Thhalv10020899m.g' => 'esa', 'Thhalv10022755m.g' => 'esa', 'TPR.G23851' => 'tpr', 'TPR.G26500' => 'tpr', 'TPR.G27267' => 'tpr', 'TPR.G32001' => 'tpr', 'TPR.G6251' => 'tpr', 'TPR.G8167' => 'tpr', 'TWI12G1330' => 'twi', 'TWI18G1239' => 'twi', 'TWI34G0979' => 'twi', 'TWI36G0670' => 'twi', 'TWI36G0707' => 'twi', 'TWI56G0233' => 'twi', 'TWI75G1809' => 'twi', 'unitig_21.g20874' => 'ugi', 'unitig_26.g10343' => 'ugi', 'unitig_46.g18392' => 'ugi', 'unitig_52.g17178' => 'ugi', 'unitig_8.g2934' => 'ugi', 'vmacro01122' => 'vma', 'vmacro05875' => 'vma', 'vmacro06147' => 'vma', 'vmacro16191' => 'vma', 'vmacro18293' => 'vma', 'VMungo0251G3707' => 'vmu', 'VMungo0464G1521' => 'vmu', 'VMungo1215G0205' => 'vmu', 'VMungo1383G2484' => 'vmu', 'Zm00001eb079610' => 'zma', 'Zm00001eb135990' => 'zma', 'Zm00001eb183710' => 'zma', 'Zm00001eb246020' => 'zma' ) $gf_id = 'HOM05D001124' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001124' ) $data_identifier = 'HOM05D001124' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 6, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 7, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 21, 'bol' => (int) 10, 'bra' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 6, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 9, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 21, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 8, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 10, 'lsa' => (int) 8, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 8, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 9, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb246020' $species_info = array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ) $local_species = 'ccan' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001124', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '548', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02520' => 'bna', 'A03p06630' => 'bna', 'A05p44460' => 'bna', 'A06p08710' => 'bna', 'A06p41090' => 'bna', 'A07p32320' => 'bna', 'A08p32520' => 'bna', 'A09p10360' => 'bna', 'A10p24080' => 'bna', 'Aa31LG11G15250' => 'aar', 'Aa31LG1G1800' => 'aar', 'Aa31LG2G5120' => 'aar', 'Aa31LG2G6070' => 'aar', 'Aa31LG5G10770' => 'aar', 'Aa31sc61G90' => 'aar', 'Actinidia01352' => 'ach', 'Actinidia05983' => 'ach', 'Actinidia08133' => 'ach', 'Actinidia15101' => 'ach', 'Actinidia26379' => 'ach', 'Actinidia35778' => 'ach', 'Actinidia36123' => 'ach', 'Actinidia37436' => 'ach', 'Actinidia38730' => 'ach', 'Ah.02g128210' => 'amhyb', 'Ah.03g132990' => 'amhyb', 'Ah.14g079410' => 'amhyb', 'AL1G24640' => 'aly', 'AL2G26680' => 'aly', 'AL3G10530' => 'aly', 'AL3G45230' => 'aly', 'AL5G15230' => 'aly', 'AL5G16960' => 'aly', 'AL6G25210' => 'aly', 'Aqoxy2G00441' => 'aox', 'Aqoxy3G01236' => 'aox', 'Aqoxy5G03746' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3RQ047' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C7GMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9C8JER' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MBL6KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YXCZ83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZANX40' => 'arhy', 'AT1G12990' => 'ath', 'AT1G67880' => 'ath', 'AT2G13290' => 'ath', 'AT3G01620' => 'ath', 'AT3G26445' => 'ath', 'AT3G27540' => 'ath', 'AT5G14480' => 'ath', 'ATR0824G026' => 'atr', 'ATR1098G019' => 'atr', 'Atru.chr11.2145' => 'acertr', 'Atru.chr2.3636' => 'acertr', 'Atru.chr2.3644' => 'acertr', 'Atru.chr6.2422' => 'acertr', 'Atru.chr7.1112' => 'acertr', 'AUR62005469' => 'cqu', 'AUR62011166' => 'cqu', 'AUR62013319' => 'cqu', 'AUR62024273' => 'cqu', 'AUR62028420' => 'cqu', 'AUR62041942' => 'cqu', 'BcaB01g04969' => 'bca', 'BcaB01g06371' => 'bca', 'BcaB02g11494' => 'bca', 'BcaB03g15382' => 'bca', 'BcaB08g36994' => 'bca', 'BcaC03g13477' => 'bca', 'BcaC03g13478' => 'bca', 'BcaC03g13480' => 'bca', 'BcaC03g13481' => 'bca', 'BcaC03g13486' => 'bca', 'BcaC04g19031' => 'bca', 'BcaC04g23085' => 'bca', 'BcaC05g25094' => 'bca', 'BcaC05g25096' => 'bca', 'BcaC05g25138' => 'bca', 'BcaC05g30416' => 'bca', 'BcaC05g30455' => 'bca', 'BcaC06g30979' => 'bca', 'BcaC06g33805' => 'bca', 'BcaC08g46021' => 'bca', 'BcaNung03154' => 'bca', 'BolC2t06623H' => 'bol', 'BolC2t06632H' => 'bol', 'BolC2t06635H' => 'bol', 'BolC2t06638H' => 'bol', 'BolC3t13266H' => 'bol', 'BolC5t29776H' => 'bol', 'BolC6t38912H' => 'bol', 'BolC7t44183H' => 'bol', 'BolC9t54123H' => 'bol', 'BolC9t59107H' => 'bol', 'BraA02t05221Z' => 'bra', 'BraA03t09996Z' => 'bra', 'BraA05t23210Z' => 'bra', 'BraA06t24068Z' => 'bra', 'BraA06t27032Z' => 'bra', 'BraA08t35176Z' => 'bra', 'BraA09t36680Z' => 'bra', 'BraA10t44471Z' => 'bra', 'C02p06760' => 'bna', 'C02p06890' => 'bna', 'C02p07010' => 'bna', 'C03p07660' => 'bna', 'C05p10300' => 'bna', 'C06p38150' => 'bna', 'C07p36650' => 'bna', 'C08p15770' => 'bna', 'C09p12300' => 'bna', 'C09p62700' => 'bna', 'C09p75040' => 'bna', 'CAN.G13.1' => 'can', 'CAN.G138.4' => 'can', 'CAN.G44.6' => 'can', 'CAN.G473.19' => 'can', 'CANSAT01G0835' => 'cansat', 'CANSAT11G0246' => 'cansat', 'CANSAT11G1766' => 'cansat', 'CANSAT64G1954' => 'cansat', 'CARHR013330' => 'chi', 'CARHR060530' => 'chi', 'CARHR075300' => 'chi', 'CARHR105120' => 'chi', 'CARHR148910' => 'chi', 'CARHR198830' => 'chi', 'Carub.0001s1275' => 'cru', 'Carub.0002s1437' => 'cru', 'Carub.0003s0044' => 'cru', 'Carub.0003s2787' => 'cru', 'Carub.0005s0597' => 'cru', 'Carub.0006s1266' => 'cru', 'Ca_06935_v3' => 'car', 'Ca_13559_v3' => 'car', 'Ca_16941_v3' => 'car', 'Ca_16960_v3' => 'car', 'Ca_17775_v3' => 'car', 'Ca_30464_v3' => 'car', 'Cc06_g08160' => 'ccan', 'Cc07_g01520' => 'ccan', 'Cc11_g15810' => 'ccan', 'CDE02G2840' => 'cde', 'CDE03G0093' => 'cde', 'CDE04G2127' => 'cde', 'CDE07G1857' => 'cde', 'CDE09G1246' => 'cde', 'Cfa003412' => 'cfa', 'Cfa007341' => 'cfa', 'Cfa009220' => 'cfa', 'Ciclev10008737m.g' => 'ccl', 'Ciclev10015565m.g' => 'ccl', 'Ciclev10031761m.g' => 'ccl', 'CiPaw.03G045300' => 'cil', 'CiPaw.03G247200' => 'cil', 'CiPaw.04G029500' => 'cil', 'CiPaw.04G174000' => 'cil', 'CiPaw.05G181200' => 'cil', 'CiPaw.06G067100' => 'cil', 'ClCG05G025800' => 'cla', 'ClCG06G011400' => 'cla', 'ClCG09G019360' => 'cla', 'COL.COLO4_04827' => 'col', 'COL.COLO4_29170' => 'col', 'COL.COLO4_35131' => 'col', 'COL.COLO4_35132' => 'col', 'Cpa.g.sc33.32' => 'cpa', 'Cpa.g.sc46.29' => 'cpa', 'Cpa.g.sc796.1' => 'cpa', 'CsaV3_1G030420' => 'csa', 'CsaV3_5G027050' => 'csa', 'CsaV3_5G031040' => 'csa', 'CsaV3_UNG023130' => 'csa', 'CSS0007726' => 'camsi', 'CSS0016433' => 'camsi', 'CSS0017656' => 'camsi', 'CSS0025364' => 'camsi', 'CSS0027582' => 'camsi', 'CSS0047288' => 'camsi', 'CSS0049950' => 'camsi', 'DCAR_003843' => 'dca', 'DCAR_007052' => 'dca', 'DCAR_020884' => 'dca', 'DCAR_021730' => 'dca', 'DCAR_024423' => 'dca', 'DCAR_026509' => 'dca', 'DCAR_031158' => 'dca', 'Dinv14728' => 'din', 'Dinv15219' => 'din', 'Dinv25728' => 'din', 'Dinv33428' => 'din', 'Dinv36489' => 'din', 'Dinv41486' => 'din', 'Duzib147G0469' => 'dzi', 'Duzib168G0060' => 'dzi', 'Duzib187G1215' => 'dzi', 'Duzib248G0692' => 'dzi', 'Duzib251G0767' => 'dzi', 'Duzib264G0446' => 'dzi', 'Duzib268G0691' => 'dzi', 'ECA232G4767' => 'eca', 'ECA233G2838' => 'eca', 'ECA234G0391' => 'eca', 'ECA234G0857' => 'eca', 'ECA236G1593' => 'eca', 'ECA238G0565' => 'eca', 'ECA246G1027' => 'eca', 'ECA246G3223' => 'eca', 'ECA246G3470' => 'eca', 'EL10Ac6g13829' => 'bvu', 'EL10Ac6g14093' => 'bvu', 'EL10Ac8g18707' => 'bvu', 'Eucgr.C01369' => 'egr', 'Eucgr.H02492' => 'egr', 'Eucgr.I01733' => 'egr', 'Eucgr.J02255' => 'egr', 'Eucgr.J02257' => 'egr', 'Eucgr.J02258' => 'egr', 'FAN02G1601' => 'fan', 'FAN03G1586' => 'fan', 'FAN03G2986' => 'fan', 'FAN05G4837' => 'fan', 'FAN06G0146' => 'fan', 'FAN07G0858' => 'fan', 'FAN09G3179' => 'fan', 'FAN10G0669' => 'fan', 'FAN12G2358' => 'fan', 'FAN14G4198' => 'fan', 'FAN14G5112' => 'fan', 'FAN17G0342' => 'fan', 'FAN19G0342' => 'fan', 'FAN19G0962' => 'fan', 'FAN19G1101' => 'fan', 'FAN19G1872' => 'fan', 'FAN22G0356' => 'fan', 'FAN23G0744' => 'fan', 'FAN23G1914' => 'fan', 'FAN26G0032' => 'fan', 'FAN28G0625' => 'fan', 'FvH4_1g02710' => 'fve', 'FvH4_1g02720' => 'fve', 'FvH4_4g25670' => 'fve', 'FvH4_6g51700' => 'fve', 'FvH4_7g20170' => 'fve', 'Glyma.05G175000' => 'gma', 'Glyma.08G132300' => 'gma', 'Glyma.11G243000' => 'gma', 'Glyma.13G158900' => 'gma', 'Glyma.17G112400' => 'gma', 'Glyma.18G014100' => 'gma', 'Glyma.19G003100' => 'gma', 'Glyma.19G056500' => 'gma', 'Gohir.A01G158900' => 'ghi', 'Gohir.A05G312600' => 'ghi', 'Gohir.A05G354900' => 'ghi', 'Gohir.A07G037200' => 'ghi', 'Gohir.A09G030000' => 'ghi', 'Gohir.A12G145200' => 'ghi', 'Gohir.D01G151500' => 'ghi', 'Gohir.D04G058300' => 'ghi', 'Gohir.D05G314100' => 'ghi', 'Gohir.D07G041400' => 'ghi', 'Gohir.D09G029700' => 'ghi', 'Gohir.D12G149700' => 'ghi', 'Gorai.001G043800' => 'gra', 'Gorai.002G187800' => 'gra', 'Gorai.006G034700' => 'gra', 'Gorai.008G161200' => 'gra', 'Gorai.009G335700' => 'gra', 'Gorai.012G065000' => 'gra', 'GSVIVG01000535001' => 'vvi', 'GSVIVG01015572001' => 'vvi', 'GSVIVG01032386001' => 'vvi', 'HanXRQChr05g0138531' => 'han', 'HanXRQChr06g0174391' => 'han', 'HanXRQChr07g0199021' => 'han', 'HanXRQChr08g0208211' => 'han', 'HanXRQChr09g0255471' => 'han', 'HanXRQChr10g0315791' => 'han', 'HanXRQChr12g0371991' => 'han', 'HanXRQChr15g0475251' => 'han', 'HanXRQChr17g0540001' => 'han', 'HanXRQChr17g0548631' => 'han', 'HanXRQChr17g0569561' => 'han', 'Haze_12256' => 'cav', 'Haze_14756' => 'cav', 'Haze_25528' => 'cav', 'Hma1.2p1_0079F.1_g041020' => 'hma', 'Hma1.2p1_0818F.1_g223260' => 'hma', 'Hma1.2p1_1747F.1_g300530' => 'hma', 'HPP92_004607' => 'vpl', 'HPP92_004608' => 'vpl', 'HPP92_006181' => 'vpl', 'HPP92_012192' => 'vpl', 'HPP92_015680' => 'vpl', 'HPP92_020249' => 'vpl', 'HPP92_021376' => 'vpl', 'HPP92_024275' => 'vpl', 'Hund06031' => 'sun', 'Hund25391' => 'sun', 'Lalb_Chr07g0185371' => 'lal', 'Lalb_Chr07g0185381' => 'lal', 'Lalb_Chr12g0204011' => 'lal', 'Lalb_Chr13g0301671' => 'lal', 'Lalb_Chr14g0362851' => 'lal', 'Lalb_Chr24g0403581' => 'lal', 'Lj1g0000233' => 'lja', 'Lj2g0018120' => 'lja', 'Lj3C621T0' => 'lonja', 'Lj3P1059T14' => 'lonja', 'Lj3P611T9' => 'lonja', 'Lj3P614T13' => 'lonja', 'Lj3P615T5' => 'lonja', 'Lj4g0012315' => 'lja', 'Lj4g0026182' => 'lja', 'Lj6P813T16' => 'lonja', 'Lj7C427T7' => 'lonja', 'Lj7C427T8' => 'lonja', 'Lj7P600T41' => 'lonja', 'Lju41C42G17' => 'lonja', 'Lsat_1_v5_gn_0_47300' => 'lsa', 'Lsat_1_v5_gn_2_91280' => 'lsa', 'Lsat_1_v5_gn_3_30561' => 'lsa', 'Lsat_1_v5_gn_4_184321' => 'lsa', 'Lsat_1_v5_gn_4_4041' => 'lsa', 'Lsat_1_v5_gn_5_92000' => 'lsa', 'Lsat_1_v5_gn_8_152940' => 'lsa', 'Lsat_1_v5_gn_8_62401' => 'lsa', 'Manes.06G055900' => 'mes', 'Manes.12G022200' => 'mes', 'Manes.13G023300' => 'mes', 'Manes.14G115000' => 'mes', 'Manes.15G151700' => 'mes', 'Manes.17G111300' => 'mes', 'Mapoly0226s0009' => 'mpo', 'MBI02_g25363_MAGBIO' => 'mbi', 'MBI06_g00027_MAGBIO' => 'mbi', 'MBI10_g13034_MAGBIO' => 'mbi', 'MD09G1023400' => 'mdo', 'MD13G1100100' => 'mdo', 'MD15G1169200' => 'mdo', 'MD16G1101100' => 'mdo', 'MD17G1022900' => 'mdo', 'Medtr3g096150' => 'mtr', 'Medtr4g115070' => 'mtr', 'Medtr7g033325' => 'mtr', 'Medtr8g089840' => 'mtr', 'MELO3C010319.2' => 'cme', 'MELO3C011944.2' => 'cme', 'MELO3C021589.2' => 'cme', 'Migut.E00207' => 'egut', 'Migut.H00067' => 'egut', 'Migut.K00433' => 'egut', 'Migut.K00606' => 'egut', 'Migut.K01410' => 'egut', 'MSTRG.13347' => 'ama', 'MSTRG.24045' => 'ama', 'MSTRG.2428' => 'ama', 'MSTRG.26410' => 'ama', 'MSTRG.3139' => 'ama', 'MSTRG.3286' => 'ama', 'MSTRG.563' => 'ama', 'MSTRG.7941' => 'ama', 'Nitab4.5_0000028g0060' => 'nta', 'Nitab4.5_0000065g0260' => 'nta', 'Nitab4.5_0000112g0060' => 'nta', 'Nitab4.5_0000489g0120' => 'nta', 'Nitab4.5_0001776g0050' => 'nta', 'Nitab4.5_0001854g0010' => 'nta', 'Nitab4.5_0001860g0020' => 'nta', 'Nitab4.5_0004352g0010' => 'nta', 'Nitab4.5_0008716g0020' => 'nta', 'Nitab4.5_0008922g0010' => 'nta', 'Nn3g16693' => 'nnu', 'Nn4g22596' => 'nnu', 'Nn7g37639' => 'nnu', 'Oeu001701.1' => 'oeu', 'Oeu018149.1' => 'oeu', 'Oeu026220.1' => 'oeu', 'Oeu038635.1' => 'oeu', 'Oeu049176.1' => 'oeu', 'Oeu056706.1' => 'oeu', 'Oeu056937.1' => 'oeu', 'Oeu057540.1' => 'oeu', 'Os02g0594900' => 'osa', 'Os02g0595100' => 'osa', 'Os04g0477500' => 'osa', 'Os12g0611900' => 'osa', 'Peaxi162Scf00076g00020' => 'pax', 'Peaxi162Scf00128g00217' => 'pax', 'Peaxi162Scf00129g01640' => 'pax', 'Peaxi162Scf00669g00007' => 'pax', 'Peaxi162Scf00700g00421' => 'pax', 'Peaxi162Scf00801g00038' => 'pax', 'Peaxi162Scf00891g00025' => 'pax', 'PGR083G0909' => 'pgr', 'PGR119G1005' => 'pgr', 'PGR142G2236' => 'pgr', 'PGR142G3388' => 'pgr', 'PGSC0003DMG400004514' => 'stu', 'PGSC0003DMG400012635' => 'stu', 'PGSC0003DMG400015730' => 'stu', 'PGSC0003DMG400018611' => 'stu', 'PGSC0003DMG400030897' => 'stu', 'Phvul.001G254800' => 'pvu', 'Phvul.002G260100' => 'pvu', 'Phvul.003G167600' => 'pvu', 'Phvul.004G005100' => 'pvu', 'Potri.001G343600' => 'ptr', 'Potri.006G066700' => 'ptr', 'Potri.008G186000' => 'ptr', 'Potri.010G046900' => 'ptr', 'Potri.018G127900' => 'ptr', 'Pp3c20_17750' => 'ppa', 'Pp3c24_4380' => 'ppa', 'Prupe.1G245800' => 'ppe', 'Prupe.3G293400' => 'ppe', 'Prupe.7G247400' => 'ppe', 'Psat0s145g0120' => 'psa', 'Psat0s595g0040' => 'psa', 'Psat0s595g0120' => 'psa', 'Psat3g175040' => 'psa', 'Psat7g058120' => 'psa', 'PSO017G0428' => 'pso', 'PSO063G7510' => 'pso', 'PSO067G0046' => 'pso', 'PSO478G1073' => 'pso', 'PSO675G3677' => 'pso', 'PSO675G6558' => 'pso', 'PSO675G7520' => 'pso', 'PSO675G8959' => 'pso', 'QL02p074089' => 'qlo', 'QL02p089614' => 'qlo', 'QL03p057736' => 'qlo', 'RcHm_v2.0_Chr1g0364131' => 'rch', 'RcHm_v2.0_Chr2g0087801' => 'rch', 'RcHm_v2.0_Chr2g0087821' => 'rch', 'RcHm_v2.0_Chr2g0173231' => 'rch', 'RcHm_v2.0_Chr4g0433111' => 'rch', 'Rhsim03G0250300' => 'rsi', 'Rhsim08G0048400' => 'rsi', 'Rhsim10G0014800' => 'rsi', 'Rhsim12G0040100' => 'rsi', 'Rhsim12G0109700' => 'rsi', 'Sabra06G0049600' => 'sbr', 'Sabra08G0141000' => 'sbr', 'Sabra10G0021400' => 'sbr', 'Sabra16G0222900' => 'sbr', 'Sabra18G0108600' => 'sbr', 'SalBow1G0433' => 'sbo', 'SalBow1G2038' => 'sbo', 'SalBow1G5003' => 'sbo', 'SalBow7G1197' => 'sbo', 'SalBow8G3506' => 'sbo', 'Sc03g0007300' => 'sci', 'Sc11g0000950' => 'sci', 'Sc14g0008750' => 'sci', 'Sc18g0000420' => 'sci', 'Sed0006754' => 'sed', 'Sed0008741' => 'sed', 'Sed0017172' => 'sed', 'Sed0018925' => 'sed', 'Sed0023326' => 'sed', 'Sed0025909' => 'sed', 'SEGI_05333' => 'sgi', 'SEGI_10362' => 'sgi', 'SEGI_13380' => 'sgi', 'SEGI_24306' => 'sgi', 'SEGI_29077' => 'sgi', 'SEGI_29095' => 'sgi', 'SEGI_36534' => 'sgi', 'SEGI_37506' => 'sgi', 'SEGI_38321' => 'sgi', 'SGA_v2.0_scaffold307G48031' => 'sas', 'SGA_v2.0_scaffold47G17507' => 'sas', 'SGA_v2.0_scaffold63G21736' => 'sas', 'SGA_v2.0_scaffold87G27070' => 'sas', 'SHI17794' => 'shi', 'SHI28851' => 'shi', 'SMO165G0155' => 'smo', 'SMO340G0217' => 'smo', 'SMO367G1210' => 'smo', 'Solyc02g093430.3' => 'sly', 'Solyc05g013580.4' => 'sly', 'Solyc07g008030.3' => 'sly', 'Solyc12g035470.2' => 'sly', 'Sopen02g038020' => 'spe', 'Sopen05g008490' => 'spe', 'Sopen07g003910' => 'spe', 'Sopen12g015240' => 'spe', 'Sp1g11550' => 'spa', 'Sp2g16710' => 'spa', 'Sp3g00430' => 'spa', 'Sp3g26780' => 'spa', 'Sp5g22900' => 'spa', 'Sp6g29530' => 'spa', 'TAR371G0794' => 'tar', 'TAR374G0164' => 'tar', 'TAR622G0165' => 'tar', 'TAR626G0929' => 'tar', 'TAR629G2155' => 'tar', 'THA.LOC104805282' => 'tha', 'THA.LOC104805363' => 'tha', 'THA.LOC104808968' => 'tha', 'THA.LOC104821093' => 'tha', 'THA.LOC104823953' => 'tha', 'THA.LOC104825562' => 'tha', 'THA.LOC104825665' => 'tha', 'Thecc.02G261400' => 'tca', 'Thecc.04G019200' => 'tca', 'Thecc.09G130400' => 'tca', 'Thhalv10004374m.g' => 'esa', 'Thhalv10007850m.g' => 'esa', 'Thhalv10013782m.g' => 'esa', 'Thhalv10018686m.g' => 'esa', 'Thhalv10020899m.g' => 'esa', 'Thhalv10022755m.g' => 'esa', 'TPR.G23851' => 'tpr', 'TPR.G26500' => 'tpr', 'TPR.G27267' => 'tpr', 'TPR.G32001' => 'tpr', 'TPR.G6251' => 'tpr', 'TPR.G8167' => 'tpr', 'TWI12G1330' => 'twi', 'TWI18G1239' => 'twi', 'TWI34G0979' => 'twi', 'TWI36G0670' => 'twi', 'TWI36G0707' => 'twi', 'TWI56G0233' => 'twi', 'TWI75G1809' => 'twi', 'unitig_21.g20874' => 'ugi', 'unitig_26.g10343' => 'ugi', 'unitig_46.g18392' => 'ugi', 'unitig_52.g17178' => 'ugi', 'unitig_8.g2934' => 'ugi', 'vmacro01122' => 'vma', 'vmacro05875' => 'vma', 'vmacro06147' => 'vma', 'vmacro16191' => 'vma', 'vmacro18293' => 'vma', 'VMungo0251G3707' => 'vmu', 'VMungo0464G1521' => 'vmu', 'VMungo1215G0205' => 'vmu', 'VMungo1383G2484' => 'vmu', 'Zm00001eb079610' => 'zma', 'Zm00001eb135990' => 'zma', 'Zm00001eb183710' => 'zma', 'Zm00001eb246020' => 'zma' ), 'gf_id' => 'HOM05D001124', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001124' ), 'data_identifier' => 'HOM05D001124', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001124', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '548', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02520' => 'bna', 'A03p06630' => 'bna', 'A05p44460' => 'bna', 'A06p08710' => 'bna', 'A06p41090' => 'bna', 'A07p32320' => 'bna', 'A08p32520' => 'bna', 'A09p10360' => 'bna', 'A10p24080' => 'bna', 'Aa31LG11G15250' => 'aar', 'Aa31LG1G1800' => 'aar', 'Aa31LG2G5120' => 'aar', 'Aa31LG2G6070' => 'aar', 'Aa31LG5G10770' => 'aar', 'Aa31sc61G90' => 'aar', 'Actinidia01352' => 'ach', 'Actinidia05983' => 'ach', 'Actinidia08133' => 'ach', 'Actinidia15101' => 'ach', 'Actinidia26379' => 'ach', 'Actinidia35778' => 'ach', 'Actinidia36123' => 'ach', 'Actinidia37436' => 'ach', 'Actinidia38730' => 'ach', 'Ah.02g128210' => 'amhyb', 'Ah.03g132990' => 'amhyb', 'Ah.14g079410' => 'amhyb', 'AL1G24640' => 'aly', 'AL2G26680' => 'aly', 'AL3G10530' => 'aly', 'AL3G45230' => 'aly', 'AL5G15230' => 'aly', 'AL5G16960' => 'aly', 'AL6G25210' => 'aly', 'Aqoxy2G00441' => 'aox', 'Aqoxy3G01236' => 'aox', 'Aqoxy5G03746' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3RQ047' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C7GMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9C8JER' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MBL6KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YXCZ83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZANX40' => 'arhy', 'AT1G12990' => 'ath', 'AT1G67880' => 'ath', 'AT2G13290' => 'ath', 'AT3G01620' => 'ath', 'AT3G26445' => 'ath', 'AT3G27540' => 'ath', 'AT5G14480' => 'ath', 'ATR0824G026' => 'atr', 'ATR1098G019' => 'atr', 'Atru.chr11.2145' => 'acertr', 'Atru.chr2.3636' => 'acertr', 'Atru.chr2.3644' => 'acertr', 'Atru.chr6.2422' => 'acertr', 'Atru.chr7.1112' => 'acertr', 'AUR62005469' => 'cqu', 'AUR62011166' => 'cqu', 'AUR62013319' => 'cqu', 'AUR62024273' => 'cqu', 'AUR62028420' => 'cqu', 'AUR62041942' => 'cqu', 'BcaB01g04969' => 'bca', 'BcaB01g06371' => 'bca', 'BcaB02g11494' => 'bca', 'BcaB03g15382' => 'bca', 'BcaB08g36994' => 'bca', 'BcaC03g13477' => 'bca', 'BcaC03g13478' => 'bca', 'BcaC03g13480' => 'bca', 'BcaC03g13481' => 'bca', 'BcaC03g13486' => 'bca', 'BcaC04g19031' => 'bca', 'BcaC04g23085' => 'bca', 'BcaC05g25094' => 'bca', 'BcaC05g25096' => 'bca', 'BcaC05g25138' => 'bca', 'BcaC05g30416' => 'bca', 'BcaC05g30455' => 'bca', 'BcaC06g30979' => 'bca', 'BcaC06g33805' => 'bca', 'BcaC08g46021' => 'bca', 'BcaNung03154' => 'bca', 'BolC2t06623H' => 'bol', 'BolC2t06632H' => 'bol', 'BolC2t06635H' => 'bol', 'BolC2t06638H' => 'bol', 'BolC3t13266H' => 'bol', 'BolC5t29776H' => 'bol', 'BolC6t38912H' => 'bol', 'BolC7t44183H' => 'bol', 'BolC9t54123H' => 'bol', 'BolC9t59107H' => 'bol', 'BraA02t05221Z' => 'bra', 'BraA03t09996Z' => 'bra', 'BraA05t23210Z' => 'bra', 'BraA06t24068Z' => 'bra', 'BraA06t27032Z' => 'bra', 'BraA08t35176Z' => 'bra', 'BraA09t36680Z' => 'bra', 'BraA10t44471Z' => 'bra', 'C02p06760' => 'bna', 'C02p06890' => 'bna', 'C02p07010' => 'bna', 'C03p07660' => 'bna', 'C05p10300' => 'bna', 'C06p38150' => 'bna', 'C07p36650' => 'bna', 'C08p15770' => 'bna', 'C09p12300' => 'bna', 'C09p62700' => 'bna', 'C09p75040' => 'bna', 'CAN.G13.1' => 'can', 'CAN.G138.4' => 'can', 'CAN.G44.6' => 'can', 'CAN.G473.19' => 'can', 'CANSAT01G0835' => 'cansat', 'CANSAT11G0246' => 'cansat', 'CANSAT11G1766' => 'cansat', 'CANSAT64G1954' => 'cansat', 'CARHR013330' => 'chi', 'CARHR060530' => 'chi', 'CARHR075300' => 'chi', 'CARHR105120' => 'chi', 'CARHR148910' => 'chi', 'CARHR198830' => 'chi', 'Carub.0001s1275' => 'cru', 'Carub.0002s1437' => 'cru', 'Carub.0003s0044' => 'cru', 'Carub.0003s2787' => 'cru', 'Carub.0005s0597' => 'cru', 'Carub.0006s1266' => 'cru', 'Ca_06935_v3' => 'car', 'Ca_13559_v3' => 'car', 'Ca_16941_v3' => 'car', 'Ca_16960_v3' => 'car', 'Ca_17775_v3' => 'car', 'Ca_30464_v3' => 'car', 'Cc06_g08160' => 'ccan', 'Cc07_g01520' => 'ccan', 'Cc11_g15810' => 'ccan', 'CDE02G2840' => 'cde', 'CDE03G0093' => 'cde', 'CDE04G2127' => 'cde', 'CDE07G1857' => 'cde', 'CDE09G1246' => 'cde', 'Cfa003412' => 'cfa', 'Cfa007341' => 'cfa', 'Cfa009220' => 'cfa', 'Ciclev10008737m.g' => 'ccl', 'Ciclev10015565m.g' => 'ccl', 'Ciclev10031761m.g' => 'ccl', 'CiPaw.03G045300' => 'cil', 'CiPaw.03G247200' => 'cil', 'CiPaw.04G029500' => 'cil', 'CiPaw.04G174000' => 'cil', 'CiPaw.05G181200' => 'cil', 'CiPaw.06G067100' => 'cil', 'ClCG05G025800' => 'cla', 'ClCG06G011400' => 'cla', 'ClCG09G019360' => 'cla', 'COL.COLO4_04827' => 'col', 'COL.COLO4_29170' => 'col', 'COL.COLO4_35131' => 'col', 'COL.COLO4_35132' => 'col', 'Cpa.g.sc33.32' => 'cpa', 'Cpa.g.sc46.29' => 'cpa', 'Cpa.g.sc796.1' => 'cpa', 'CsaV3_1G030420' => 'csa', 'CsaV3_5G027050' => 'csa', 'CsaV3_5G031040' => 'csa', 'CsaV3_UNG023130' => 'csa', 'CSS0007726' => 'camsi', 'CSS0016433' => 'camsi', 'CSS0017656' => 'camsi', 'CSS0025364' => 'camsi', 'CSS0027582' => 'camsi', 'CSS0047288' => 'camsi', 'CSS0049950' => 'camsi', 'DCAR_003843' => 'dca', 'DCAR_007052' => 'dca', 'DCAR_020884' => 'dca', 'DCAR_021730' => 'dca', 'DCAR_024423' => 'dca', 'DCAR_026509' => 'dca', 'DCAR_031158' => 'dca', 'Dinv14728' => 'din', 'Dinv15219' => 'din', 'Dinv25728' => 'din', 'Dinv33428' => 'din', 'Dinv36489' => 'din', 'Dinv41486' => 'din', 'Duzib147G0469' => 'dzi', 'Duzib168G0060' => 'dzi', 'Duzib187G1215' => 'dzi', 'Duzib248G0692' => 'dzi', 'Duzib251G0767' => 'dzi', 'Duzib264G0446' => 'dzi', 'Duzib268G0691' => 'dzi', 'ECA232G4767' => 'eca', 'ECA233G2838' => 'eca', 'ECA234G0391' => 'eca', 'ECA234G0857' => 'eca', 'ECA236G1593' => 'eca', 'ECA238G0565' => 'eca', 'ECA246G1027' => 'eca', 'ECA246G3223' => 'eca', 'ECA246G3470' => 'eca', 'EL10Ac6g13829' => 'bvu', 'EL10Ac6g14093' => 'bvu', 'EL10Ac8g18707' => 'bvu', 'Eucgr.C01369' => 'egr', 'Eucgr.H02492' => 'egr', 'Eucgr.I01733' => 'egr', 'Eucgr.J02255' => 'egr', 'Eucgr.J02257' => 'egr', 'Eucgr.J02258' => 'egr', 'FAN02G1601' => 'fan', 'FAN03G1586' => 'fan', 'FAN03G2986' => 'fan', 'FAN05G4837' => 'fan', 'FAN06G0146' => 'fan', 'FAN07G0858' => 'fan', 'FAN09G3179' => 'fan', 'FAN10G0669' => 'fan', 'FAN12G2358' => 'fan', 'FAN14G4198' => 'fan', 'FAN14G5112' => 'fan', 'FAN17G0342' => 'fan', 'FAN19G0342' => 'fan', 'FAN19G0962' => 'fan', 'FAN19G1101' => 'fan', 'FAN19G1872' => 'fan', 'FAN22G0356' => 'fan', 'FAN23G0744' => 'fan', 'FAN23G1914' => 'fan', 'FAN26G0032' => 'fan', 'FAN28G0625' => 'fan', 'FvH4_1g02710' => 'fve', 'FvH4_1g02720' => 'fve', 'FvH4_4g25670' => 'fve', 'FvH4_6g51700' => 'fve', 'FvH4_7g20170' => 'fve', 'Glyma.05G175000' => 'gma', 'Glyma.08G132300' => 'gma', 'Glyma.11G243000' => 'gma', 'Glyma.13G158900' => 'gma', 'Glyma.17G112400' => 'gma', 'Glyma.18G014100' => 'gma', 'Glyma.19G003100' => 'gma', 'Glyma.19G056500' => 'gma', 'Gohir.A01G158900' => 'ghi', 'Gohir.A05G312600' => 'ghi', 'Gohir.A05G354900' => 'ghi', 'Gohir.A07G037200' => 'ghi', 'Gohir.A09G030000' => 'ghi', 'Gohir.A12G145200' => 'ghi', 'Gohir.D01G151500' => 'ghi', 'Gohir.D04G058300' => 'ghi', 'Gohir.D05G314100' => 'ghi', 'Gohir.D07G041400' => 'ghi', 'Gohir.D09G029700' => 'ghi', 'Gohir.D12G149700' => 'ghi', 'Gorai.001G043800' => 'gra', 'Gorai.002G187800' => 'gra', 'Gorai.006G034700' => 'gra', 'Gorai.008G161200' => 'gra', 'Gorai.009G335700' => 'gra', 'Gorai.012G065000' => 'gra', 'GSVIVG01000535001' => 'vvi', 'GSVIVG01015572001' => 'vvi', 'GSVIVG01032386001' => 'vvi', 'HanXRQChr05g0138531' => 'han', 'HanXRQChr06g0174391' => 'han', 'HanXRQChr07g0199021' => 'han', 'HanXRQChr08g0208211' => 'han', 'HanXRQChr09g0255471' => 'han', 'HanXRQChr10g0315791' => 'han', 'HanXRQChr12g0371991' => 'han', 'HanXRQChr15g0475251' => 'han', 'HanXRQChr17g0540001' => 'han', 'HanXRQChr17g0548631' => 'han', 'HanXRQChr17g0569561' => 'han', 'Haze_12256' => 'cav', 'Haze_14756' => 'cav', 'Haze_25528' => 'cav', 'Hma1.2p1_0079F.1_g041020' => 'hma', 'Hma1.2p1_0818F.1_g223260' => 'hma', 'Hma1.2p1_1747F.1_g300530' => 'hma', 'HPP92_004607' => 'vpl', 'HPP92_004608' => 'vpl', 'HPP92_006181' => 'vpl', 'HPP92_012192' => 'vpl', 'HPP92_015680' => 'vpl', 'HPP92_020249' => 'vpl', 'HPP92_021376' => 'vpl', 'HPP92_024275' => 'vpl', 'Hund06031' => 'sun', 'Hund25391' => 'sun', 'Lalb_Chr07g0185371' => 'lal', 'Lalb_Chr07g0185381' => 'lal', 'Lalb_Chr12g0204011' => 'lal', 'Lalb_Chr13g0301671' => 'lal', 'Lalb_Chr14g0362851' => 'lal', 'Lalb_Chr24g0403581' => 'lal', 'Lj1g0000233' => 'lja', 'Lj2g0018120' => 'lja', 'Lj3C621T0' => 'lonja', 'Lj3P1059T14' => 'lonja', 'Lj3P611T9' => 'lonja', 'Lj3P614T13' => 'lonja', 'Lj3P615T5' => 'lonja', 'Lj4g0012315' => 'lja', 'Lj4g0026182' => 'lja', 'Lj6P813T16' => 'lonja', 'Lj7C427T7' => 'lonja', 'Lj7C427T8' => 'lonja', 'Lj7P600T41' => 'lonja', 'Lju41C42G17' => 'lonja', 'Lsat_1_v5_gn_0_47300' => 'lsa', 'Lsat_1_v5_gn_2_91280' => 'lsa', 'Lsat_1_v5_gn_3_30561' => 'lsa', 'Lsat_1_v5_gn_4_184321' => 'lsa', 'Lsat_1_v5_gn_4_4041' => 'lsa', 'Lsat_1_v5_gn_5_92000' => 'lsa', 'Lsat_1_v5_gn_8_152940' => 'lsa', 'Lsat_1_v5_gn_8_62401' => 'lsa', 'Manes.06G055900' => 'mes', 'Manes.12G022200' => 'mes', 'Manes.13G023300' => 'mes', 'Manes.14G115000' => 'mes', 'Manes.15G151700' => 'mes', 'Manes.17G111300' => 'mes', 'Mapoly0226s0009' => 'mpo', 'MBI02_g25363_MAGBIO' => 'mbi', 'MBI06_g00027_MAGBIO' => 'mbi', 'MBI10_g13034_MAGBIO' => 'mbi', 'MD09G1023400' => 'mdo', 'MD13G1100100' => 'mdo', 'MD15G1169200' => 'mdo', 'MD16G1101100' => 'mdo', 'MD17G1022900' => 'mdo', 'Medtr3g096150' => 'mtr', 'Medtr4g115070' => 'mtr', 'Medtr7g033325' => 'mtr', 'Medtr8g089840' => 'mtr', 'MELO3C010319.2' => 'cme', 'MELO3C011944.2' => 'cme', 'MELO3C021589.2' => 'cme', 'Migut.E00207' => 'egut', 'Migut.H00067' => 'egut', 'Migut.K00433' => 'egut', 'Migut.K00606' => 'egut', 'Migut.K01410' => 'egut', 'MSTRG.13347' => 'ama', 'MSTRG.24045' => 'ama', 'MSTRG.2428' => 'ama', 'MSTRG.26410' => 'ama', 'MSTRG.3139' => 'ama', 'MSTRG.3286' => 'ama', 'MSTRG.563' => 'ama', 'MSTRG.7941' => 'ama', 'Nitab4.5_0000028g0060' => 'nta', 'Nitab4.5_0000065g0260' => 'nta', 'Nitab4.5_0000112g0060' => 'nta', 'Nitab4.5_0000489g0120' => 'nta', 'Nitab4.5_0001776g0050' => 'nta', 'Nitab4.5_0001854g0010' => 'nta', 'Nitab4.5_0001860g0020' => 'nta', 'Nitab4.5_0004352g0010' => 'nta', 'Nitab4.5_0008716g0020' => 'nta', 'Nitab4.5_0008922g0010' => 'nta', 'Nn3g16693' => 'nnu', 'Nn4g22596' => 'nnu', 'Nn7g37639' => 'nnu', 'Oeu001701.1' => 'oeu', 'Oeu018149.1' => 'oeu', 'Oeu026220.1' => 'oeu', 'Oeu038635.1' => 'oeu', 'Oeu049176.1' => 'oeu', 'Oeu056706.1' => 'oeu', 'Oeu056937.1' => 'oeu', 'Oeu057540.1' => 'oeu', 'Os02g0594900' => 'osa', 'Os02g0595100' => 'osa', 'Os04g0477500' => 'osa', 'Os12g0611900' => 'osa', 'Peaxi162Scf00076g00020' => 'pax', 'Peaxi162Scf00128g00217' => 'pax', 'Peaxi162Scf00129g01640' => 'pax', 'Peaxi162Scf00669g00007' => 'pax', 'Peaxi162Scf00700g00421' => 'pax', 'Peaxi162Scf00801g00038' => 'pax', 'Peaxi162Scf00891g00025' => 'pax', 'PGR083G0909' => 'pgr', 'PGR119G1005' => 'pgr', 'PGR142G2236' => 'pgr', 'PGR142G3388' => 'pgr', 'PGSC0003DMG400004514' => 'stu', 'PGSC0003DMG400012635' => 'stu', 'PGSC0003DMG400015730' => 'stu', 'PGSC0003DMG400018611' => 'stu', 'PGSC0003DMG400030897' => 'stu', 'Phvul.001G254800' => 'pvu', 'Phvul.002G260100' => 'pvu', 'Phvul.003G167600' => 'pvu', 'Phvul.004G005100' => 'pvu', 'Potri.001G343600' => 'ptr', 'Potri.006G066700' => 'ptr', 'Potri.008G186000' => 'ptr', 'Potri.010G046900' => 'ptr', 'Potri.018G127900' => 'ptr', 'Pp3c20_17750' => 'ppa', 'Pp3c24_4380' => 'ppa', 'Prupe.1G245800' => 'ppe', 'Prupe.3G293400' => 'ppe', 'Prupe.7G247400' => 'ppe', 'Psat0s145g0120' => 'psa', 'Psat0s595g0040' => 'psa', 'Psat0s595g0120' => 'psa', 'Psat3g175040' => 'psa', 'Psat7g058120' => 'psa', 'PSO017G0428' => 'pso', 'PSO063G7510' => 'pso', 'PSO067G0046' => 'pso', 'PSO478G1073' => 'pso', 'PSO675G3677' => 'pso', 'PSO675G6558' => 'pso', 'PSO675G7520' => 'pso', 'PSO675G8959' => 'pso', 'QL02p074089' => 'qlo', 'QL02p089614' => 'qlo', 'QL03p057736' => 'qlo', 'RcHm_v2.0_Chr1g0364131' => 'rch', 'RcHm_v2.0_Chr2g0087801' => 'rch', 'RcHm_v2.0_Chr2g0087821' => 'rch', 'RcHm_v2.0_Chr2g0173231' => 'rch', 'RcHm_v2.0_Chr4g0433111' => 'rch', 'Rhsim03G0250300' => 'rsi', 'Rhsim08G0048400' => 'rsi', 'Rhsim10G0014800' => 'rsi', 'Rhsim12G0040100' => 'rsi', 'Rhsim12G0109700' => 'rsi', 'Sabra06G0049600' => 'sbr', 'Sabra08G0141000' => 'sbr', 'Sabra10G0021400' => 'sbr', 'Sabra16G0222900' => 'sbr', 'Sabra18G0108600' => 'sbr', 'SalBow1G0433' => 'sbo', 'SalBow1G2038' => 'sbo', 'SalBow1G5003' => 'sbo', 'SalBow7G1197' => 'sbo', 'SalBow8G3506' => 'sbo', 'Sc03g0007300' => 'sci', 'Sc11g0000950' => 'sci', 'Sc14g0008750' => 'sci', 'Sc18g0000420' => 'sci', 'Sed0006754' => 'sed', 'Sed0008741' => 'sed', 'Sed0017172' => 'sed', 'Sed0018925' => 'sed', 'Sed0023326' => 'sed', 'Sed0025909' => 'sed', 'SEGI_05333' => 'sgi', 'SEGI_10362' => 'sgi', 'SEGI_13380' => 'sgi', 'SEGI_24306' => 'sgi', 'SEGI_29077' => 'sgi', 'SEGI_29095' => 'sgi', 'SEGI_36534' => 'sgi', 'SEGI_37506' => 'sgi', 'SEGI_38321' => 'sgi', 'SGA_v2.0_scaffold307G48031' => 'sas', 'SGA_v2.0_scaffold47G17507' => 'sas', 'SGA_v2.0_scaffold63G21736' => 'sas', 'SGA_v2.0_scaffold87G27070' => 'sas', 'SHI17794' => 'shi', 'SHI28851' => 'shi', 'SMO165G0155' => 'smo', 'SMO340G0217' => 'smo', 'SMO367G1210' => 'smo', 'Solyc02g093430.3' => 'sly', 'Solyc05g013580.4' => 'sly', 'Solyc07g008030.3' => 'sly', 'Solyc12g035470.2' => 'sly', 'Sopen02g038020' => 'spe', 'Sopen05g008490' => 'spe', 'Sopen07g003910' => 'spe', 'Sopen12g015240' => 'spe', 'Sp1g11550' => 'spa', 'Sp2g16710' => 'spa', 'Sp3g00430' => 'spa', 'Sp3g26780' => 'spa', 'Sp5g22900' => 'spa', 'Sp6g29530' => 'spa', 'TAR371G0794' => 'tar', 'TAR374G0164' => 'tar', 'TAR622G0165' => 'tar', 'TAR626G0929' => 'tar', 'TAR629G2155' => 'tar', 'THA.LOC104805282' => 'tha', 'THA.LOC104805363' => 'tha', 'THA.LOC104808968' => 'tha', 'THA.LOC104821093' => 'tha', 'THA.LOC104823953' => 'tha', 'THA.LOC104825562' => 'tha', 'THA.LOC104825665' => 'tha', 'Thecc.02G261400' => 'tca', 'Thecc.04G019200' => 'tca', 'Thecc.09G130400' => 'tca', 'Thhalv10004374m.g' => 'esa', 'Thhalv10007850m.g' => 'esa', 'Thhalv10013782m.g' => 'esa', 'Thhalv10018686m.g' => 'esa', 'Thhalv10020899m.g' => 'esa', 'Thhalv10022755m.g' => 'esa', 'TPR.G23851' => 'tpr', 'TPR.G26500' => 'tpr', 'TPR.G27267' => 'tpr', 'TPR.G32001' => 'tpr', 'TPR.G6251' => 'tpr', 'TPR.G8167' => 'tpr', 'TWI12G1330' => 'twi', 'TWI18G1239' => 'twi', 'TWI34G0979' => 'twi', 'TWI36G0670' => 'twi', 'TWI36G0707' => 'twi', 'TWI56G0233' => 'twi', 'TWI75G1809' => 'twi', 'unitig_21.g20874' => 'ugi', 'unitig_26.g10343' => 'ugi', 'unitig_46.g18392' => 'ugi', 'unitig_52.g17178' => 'ugi', 'unitig_8.g2934' => 'ugi', 'vmacro01122' => 'vma', 'vmacro05875' => 'vma', 'vmacro06147' => 'vma', 'vmacro16191' => 'vma', 'vmacro18293' => 'vma', 'VMungo0251G3707' => 'vmu', 'VMungo0464G1521' => 'vmu', 'VMungo1215G0205' => 'vmu', 'VMungo1383G2484' => 'vmu', 'Zm00001eb079610' => 'zma', 'Zm00001eb135990' => 'zma', 'Zm00001eb183710' => 'zma', 'Zm00001eb246020' => 'zma' ) $gf_id = 'HOM05D001124' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001124' ) $data_identifier = 'HOM05D001124' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 6, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 7, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 21, 'bol' => (int) 10, 'bra' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 6, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 9, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 21, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 8, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 10, 'lsa' => (int) 8, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 8, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 9, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb246020' $species_info = array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ) $local_species = 'ccan' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001124', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '548', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02520' => 'bna', 'A03p06630' => 'bna', 'A05p44460' => 'bna', 'A06p08710' => 'bna', 'A06p41090' => 'bna', 'A07p32320' => 'bna', 'A08p32520' => 'bna', 'A09p10360' => 'bna', 'A10p24080' => 'bna', 'Aa31LG11G15250' => 'aar', 'Aa31LG1G1800' => 'aar', 'Aa31LG2G5120' => 'aar', 'Aa31LG2G6070' => 'aar', 'Aa31LG5G10770' => 'aar', 'Aa31sc61G90' => 'aar', 'Actinidia01352' => 'ach', 'Actinidia05983' => 'ach', 'Actinidia08133' => 'ach', 'Actinidia15101' => 'ach', 'Actinidia26379' => 'ach', 'Actinidia35778' => 'ach', 'Actinidia36123' => 'ach', 'Actinidia37436' => 'ach', 'Actinidia38730' => 'ach', 'Ah.02g128210' => 'amhyb', 'Ah.03g132990' => 'amhyb', 'Ah.14g079410' => 'amhyb', 'AL1G24640' => 'aly', 'AL2G26680' => 'aly', 'AL3G10530' => 'aly', 'AL3G45230' => 'aly', 'AL5G15230' => 'aly', 'AL5G16960' => 'aly', 'AL6G25210' => 'aly', 'Aqoxy2G00441' => 'aox', 'Aqoxy3G01236' => 'aox', 'Aqoxy5G03746' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3RQ047' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C7GMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9C8JER' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MBL6KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YXCZ83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZANX40' => 'arhy', 'AT1G12990' => 'ath', 'AT1G67880' => 'ath', 'AT2G13290' => 'ath', 'AT3G01620' => 'ath', 'AT3G26445' => 'ath', 'AT3G27540' => 'ath', 'AT5G14480' => 'ath', 'ATR0824G026' => 'atr', 'ATR1098G019' => 'atr', 'Atru.chr11.2145' => 'acertr', 'Atru.chr2.3636' => 'acertr', 'Atru.chr2.3644' => 'acertr', 'Atru.chr6.2422' => 'acertr', 'Atru.chr7.1112' => 'acertr', 'AUR62005469' => 'cqu', 'AUR62011166' => 'cqu', 'AUR62013319' => 'cqu', 'AUR62024273' => 'cqu', 'AUR62028420' => 'cqu', 'AUR62041942' => 'cqu', 'BcaB01g04969' => 'bca', 'BcaB01g06371' => 'bca', 'BcaB02g11494' => 'bca', 'BcaB03g15382' => 'bca', 'BcaB08g36994' => 'bca', 'BcaC03g13477' => 'bca', 'BcaC03g13478' => 'bca', 'BcaC03g13480' => 'bca', 'BcaC03g13481' => 'bca', 'BcaC03g13486' => 'bca', 'BcaC04g19031' => 'bca', 'BcaC04g23085' => 'bca', 'BcaC05g25094' => 'bca', 'BcaC05g25096' => 'bca', 'BcaC05g25138' => 'bca', 'BcaC05g30416' => 'bca', 'BcaC05g30455' => 'bca', 'BcaC06g30979' => 'bca', 'BcaC06g33805' => 'bca', 'BcaC08g46021' => 'bca', 'BcaNung03154' => 'bca', 'BolC2t06623H' => 'bol', 'BolC2t06632H' => 'bol', 'BolC2t06635H' => 'bol', 'BolC2t06638H' => 'bol', 'BolC3t13266H' => 'bol', 'BolC5t29776H' => 'bol', 'BolC6t38912H' => 'bol', 'BolC7t44183H' => 'bol', 'BolC9t54123H' => 'bol', 'BolC9t59107H' => 'bol', 'BraA02t05221Z' => 'bra', 'BraA03t09996Z' => 'bra', 'BraA05t23210Z' => 'bra', 'BraA06t24068Z' => 'bra', 'BraA06t27032Z' => 'bra', 'BraA08t35176Z' => 'bra', 'BraA09t36680Z' => 'bra', 'BraA10t44471Z' => 'bra', 'C02p06760' => 'bna', 'C02p06890' => 'bna', 'C02p07010' => 'bna', 'C03p07660' => 'bna', 'C05p10300' => 'bna', 'C06p38150' => 'bna', 'C07p36650' => 'bna', 'C08p15770' => 'bna', 'C09p12300' => 'bna', 'C09p62700' => 'bna', 'C09p75040' => 'bna', 'CAN.G13.1' => 'can', 'CAN.G138.4' => 'can', 'CAN.G44.6' => 'can', 'CAN.G473.19' => 'can', 'CANSAT01G0835' => 'cansat', 'CANSAT11G0246' => 'cansat', 'CANSAT11G1766' => 'cansat', 'CANSAT64G1954' => 'cansat', 'CARHR013330' => 'chi', 'CARHR060530' => 'chi', 'CARHR075300' => 'chi', 'CARHR105120' => 'chi', 'CARHR148910' => 'chi', 'CARHR198830' => 'chi', 'Carub.0001s1275' => 'cru', 'Carub.0002s1437' => 'cru', 'Carub.0003s0044' => 'cru', 'Carub.0003s2787' => 'cru', 'Carub.0005s0597' => 'cru', 'Carub.0006s1266' => 'cru', 'Ca_06935_v3' => 'car', 'Ca_13559_v3' => 'car', 'Ca_16941_v3' => 'car', 'Ca_16960_v3' => 'car', 'Ca_17775_v3' => 'car', 'Ca_30464_v3' => 'car', 'Cc06_g08160' => 'ccan', 'Cc07_g01520' => 'ccan', 'Cc11_g15810' => 'ccan', 'CDE02G2840' => 'cde', 'CDE03G0093' => 'cde', 'CDE04G2127' => 'cde', 'CDE07G1857' => 'cde', 'CDE09G1246' => 'cde', 'Cfa003412' => 'cfa', 'Cfa007341' => 'cfa', 'Cfa009220' => 'cfa', 'Ciclev10008737m.g' => 'ccl', 'Ciclev10015565m.g' => 'ccl', 'Ciclev10031761m.g' => 'ccl', 'CiPaw.03G045300' => 'cil', 'CiPaw.03G247200' => 'cil', 'CiPaw.04G029500' => 'cil', 'CiPaw.04G174000' => 'cil', 'CiPaw.05G181200' => 'cil', 'CiPaw.06G067100' => 'cil', 'ClCG05G025800' => 'cla', 'ClCG06G011400' => 'cla', 'ClCG09G019360' => 'cla', 'COL.COLO4_04827' => 'col', 'COL.COLO4_29170' => 'col', 'COL.COLO4_35131' => 'col', 'COL.COLO4_35132' => 'col', 'Cpa.g.sc33.32' => 'cpa', 'Cpa.g.sc46.29' => 'cpa', 'Cpa.g.sc796.1' => 'cpa', 'CsaV3_1G030420' => 'csa', 'CsaV3_5G027050' => 'csa', 'CsaV3_5G031040' => 'csa', 'CsaV3_UNG023130' => 'csa', 'CSS0007726' => 'camsi', 'CSS0016433' => 'camsi', 'CSS0017656' => 'camsi', 'CSS0025364' => 'camsi', 'CSS0027582' => 'camsi', 'CSS0047288' => 'camsi', 'CSS0049950' => 'camsi', 'DCAR_003843' => 'dca', 'DCAR_007052' => 'dca', 'DCAR_020884' => 'dca', 'DCAR_021730' => 'dca', 'DCAR_024423' => 'dca', 'DCAR_026509' => 'dca', 'DCAR_031158' => 'dca', 'Dinv14728' => 'din', 'Dinv15219' => 'din', 'Dinv25728' => 'din', 'Dinv33428' => 'din', 'Dinv36489' => 'din', 'Dinv41486' => 'din', 'Duzib147G0469' => 'dzi', 'Duzib168G0060' => 'dzi', 'Duzib187G1215' => 'dzi', 'Duzib248G0692' => 'dzi', 'Duzib251G0767' => 'dzi', 'Duzib264G0446' => 'dzi', 'Duzib268G0691' => 'dzi', 'ECA232G4767' => 'eca', 'ECA233G2838' => 'eca', 'ECA234G0391' => 'eca', 'ECA234G0857' => 'eca', 'ECA236G1593' => 'eca', 'ECA238G0565' => 'eca', 'ECA246G1027' => 'eca', 'ECA246G3223' => 'eca', 'ECA246G3470' => 'eca', 'EL10Ac6g13829' => 'bvu', 'EL10Ac6g14093' => 'bvu', 'EL10Ac8g18707' => 'bvu', 'Eucgr.C01369' => 'egr', 'Eucgr.H02492' => 'egr', 'Eucgr.I01733' => 'egr', 'Eucgr.J02255' => 'egr', 'Eucgr.J02257' => 'egr', 'Eucgr.J02258' => 'egr', 'FAN02G1601' => 'fan', 'FAN03G1586' => 'fan', 'FAN03G2986' => 'fan', 'FAN05G4837' => 'fan', 'FAN06G0146' => 'fan', 'FAN07G0858' => 'fan', 'FAN09G3179' => 'fan', 'FAN10G0669' => 'fan', 'FAN12G2358' => 'fan', 'FAN14G4198' => 'fan', 'FAN14G5112' => 'fan', 'FAN17G0342' => 'fan', 'FAN19G0342' => 'fan', 'FAN19G0962' => 'fan', 'FAN19G1101' => 'fan', 'FAN19G1872' => 'fan', 'FAN22G0356' => 'fan', 'FAN23G0744' => 'fan', 'FAN23G1914' => 'fan', 'FAN26G0032' => 'fan', 'FAN28G0625' => 'fan', 'FvH4_1g02710' => 'fve', 'FvH4_1g02720' => 'fve', 'FvH4_4g25670' => 'fve', 'FvH4_6g51700' => 'fve', 'FvH4_7g20170' => 'fve', 'Glyma.05G175000' => 'gma', 'Glyma.08G132300' => 'gma', 'Glyma.11G243000' => 'gma', 'Glyma.13G158900' => 'gma', 'Glyma.17G112400' => 'gma', 'Glyma.18G014100' => 'gma', 'Glyma.19G003100' => 'gma', 'Glyma.19G056500' => 'gma', 'Gohir.A01G158900' => 'ghi', 'Gohir.A05G312600' => 'ghi', 'Gohir.A05G354900' => 'ghi', 'Gohir.A07G037200' => 'ghi', 'Gohir.A09G030000' => 'ghi', 'Gohir.A12G145200' => 'ghi', 'Gohir.D01G151500' => 'ghi', 'Gohir.D04G058300' => 'ghi', 'Gohir.D05G314100' => 'ghi', 'Gohir.D07G041400' => 'ghi', 'Gohir.D09G029700' => 'ghi', 'Gohir.D12G149700' => 'ghi', 'Gorai.001G043800' => 'gra', 'Gorai.002G187800' => 'gra', 'Gorai.006G034700' => 'gra', 'Gorai.008G161200' => 'gra', 'Gorai.009G335700' => 'gra', 'Gorai.012G065000' => 'gra', 'GSVIVG01000535001' => 'vvi', 'GSVIVG01015572001' => 'vvi', 'GSVIVG01032386001' => 'vvi', 'HanXRQChr05g0138531' => 'han', 'HanXRQChr06g0174391' => 'han', 'HanXRQChr07g0199021' => 'han', 'HanXRQChr08g0208211' => 'han', 'HanXRQChr09g0255471' => 'han', 'HanXRQChr10g0315791' => 'han', 'HanXRQChr12g0371991' => 'han', 'HanXRQChr15g0475251' => 'han', 'HanXRQChr17g0540001' => 'han', 'HanXRQChr17g0548631' => 'han', 'HanXRQChr17g0569561' => 'han', 'Haze_12256' => 'cav', 'Haze_14756' => 'cav', 'Haze_25528' => 'cav', 'Hma1.2p1_0079F.1_g041020' => 'hma', 'Hma1.2p1_0818F.1_g223260' => 'hma', 'Hma1.2p1_1747F.1_g300530' => 'hma', 'HPP92_004607' => 'vpl', 'HPP92_004608' => 'vpl', 'HPP92_006181' => 'vpl', 'HPP92_012192' => 'vpl', 'HPP92_015680' => 'vpl', 'HPP92_020249' => 'vpl', 'HPP92_021376' => 'vpl', 'HPP92_024275' => 'vpl', 'Hund06031' => 'sun', 'Hund25391' => 'sun', 'Lalb_Chr07g0185371' => 'lal', 'Lalb_Chr07g0185381' => 'lal', 'Lalb_Chr12g0204011' => 'lal', 'Lalb_Chr13g0301671' => 'lal', 'Lalb_Chr14g0362851' => 'lal', 'Lalb_Chr24g0403581' => 'lal', 'Lj1g0000233' => 'lja', 'Lj2g0018120' => 'lja', 'Lj3C621T0' => 'lonja', 'Lj3P1059T14' => 'lonja', 'Lj3P611T9' => 'lonja', 'Lj3P614T13' => 'lonja', 'Lj3P615T5' => 'lonja', 'Lj4g0012315' => 'lja', 'Lj4g0026182' => 'lja', 'Lj6P813T16' => 'lonja', 'Lj7C427T7' => 'lonja', 'Lj7C427T8' => 'lonja', 'Lj7P600T41' => 'lonja', 'Lju41C42G17' => 'lonja', 'Lsat_1_v5_gn_0_47300' => 'lsa', 'Lsat_1_v5_gn_2_91280' => 'lsa', 'Lsat_1_v5_gn_3_30561' => 'lsa', 'Lsat_1_v5_gn_4_184321' => 'lsa', 'Lsat_1_v5_gn_4_4041' => 'lsa', 'Lsat_1_v5_gn_5_92000' => 'lsa', 'Lsat_1_v5_gn_8_152940' => 'lsa', 'Lsat_1_v5_gn_8_62401' => 'lsa', 'Manes.06G055900' => 'mes', 'Manes.12G022200' => 'mes', 'Manes.13G023300' => 'mes', 'Manes.14G115000' => 'mes', 'Manes.15G151700' => 'mes', 'Manes.17G111300' => 'mes', 'Mapoly0226s0009' => 'mpo', 'MBI02_g25363_MAGBIO' => 'mbi', 'MBI06_g00027_MAGBIO' => 'mbi', 'MBI10_g13034_MAGBIO' => 'mbi', 'MD09G1023400' => 'mdo', 'MD13G1100100' => 'mdo', 'MD15G1169200' => 'mdo', 'MD16G1101100' => 'mdo', 'MD17G1022900' => 'mdo', 'Medtr3g096150' => 'mtr', 'Medtr4g115070' => 'mtr', 'Medtr7g033325' => 'mtr', 'Medtr8g089840' => 'mtr', 'MELO3C010319.2' => 'cme', 'MELO3C011944.2' => 'cme', 'MELO3C021589.2' => 'cme', 'Migut.E00207' => 'egut', 'Migut.H00067' => 'egut', 'Migut.K00433' => 'egut', 'Migut.K00606' => 'egut', 'Migut.K01410' => 'egut', 'MSTRG.13347' => 'ama', 'MSTRG.24045' => 'ama', 'MSTRG.2428' => 'ama', 'MSTRG.26410' => 'ama', 'MSTRG.3139' => 'ama', 'MSTRG.3286' => 'ama', 'MSTRG.563' => 'ama', 'MSTRG.7941' => 'ama', 'Nitab4.5_0000028g0060' => 'nta', 'Nitab4.5_0000065g0260' => 'nta', 'Nitab4.5_0000112g0060' => 'nta', 'Nitab4.5_0000489g0120' => 'nta', 'Nitab4.5_0001776g0050' => 'nta', 'Nitab4.5_0001854g0010' => 'nta', 'Nitab4.5_0001860g0020' => 'nta', 'Nitab4.5_0004352g0010' => 'nta', 'Nitab4.5_0008716g0020' => 'nta', 'Nitab4.5_0008922g0010' => 'nta', 'Nn3g16693' => 'nnu', 'Nn4g22596' => 'nnu', 'Nn7g37639' => 'nnu', 'Oeu001701.1' => 'oeu', 'Oeu018149.1' => 'oeu', 'Oeu026220.1' => 'oeu', 'Oeu038635.1' => 'oeu', 'Oeu049176.1' => 'oeu', 'Oeu056706.1' => 'oeu', 'Oeu056937.1' => 'oeu', 'Oeu057540.1' => 'oeu', 'Os02g0594900' => 'osa', 'Os02g0595100' => 'osa', 'Os04g0477500' => 'osa', 'Os12g0611900' => 'osa', 'Peaxi162Scf00076g00020' => 'pax', 'Peaxi162Scf00128g00217' => 'pax', 'Peaxi162Scf00129g01640' => 'pax', 'Peaxi162Scf00669g00007' => 'pax', 'Peaxi162Scf00700g00421' => 'pax', 'Peaxi162Scf00801g00038' => 'pax', 'Peaxi162Scf00891g00025' => 'pax', 'PGR083G0909' => 'pgr', 'PGR119G1005' => 'pgr', 'PGR142G2236' => 'pgr', 'PGR142G3388' => 'pgr', 'PGSC0003DMG400004514' => 'stu', 'PGSC0003DMG400012635' => 'stu', 'PGSC0003DMG400015730' => 'stu', 'PGSC0003DMG400018611' => 'stu', 'PGSC0003DMG400030897' => 'stu', 'Phvul.001G254800' => 'pvu', 'Phvul.002G260100' => 'pvu', 'Phvul.003G167600' => 'pvu', 'Phvul.004G005100' => 'pvu', 'Potri.001G343600' => 'ptr', 'Potri.006G066700' => 'ptr', 'Potri.008G186000' => 'ptr', 'Potri.010G046900' => 'ptr', 'Potri.018G127900' => 'ptr', 'Pp3c20_17750' => 'ppa', 'Pp3c24_4380' => 'ppa', 'Prupe.1G245800' => 'ppe', 'Prupe.3G293400' => 'ppe', 'Prupe.7G247400' => 'ppe', 'Psat0s145g0120' => 'psa', 'Psat0s595g0040' => 'psa', 'Psat0s595g0120' => 'psa', 'Psat3g175040' => 'psa', 'Psat7g058120' => 'psa', 'PSO017G0428' => 'pso', 'PSO063G7510' => 'pso', 'PSO067G0046' => 'pso', 'PSO478G1073' => 'pso', 'PSO675G3677' => 'pso', 'PSO675G6558' => 'pso', 'PSO675G7520' => 'pso', 'PSO675G8959' => 'pso', 'QL02p074089' => 'qlo', 'QL02p089614' => 'qlo', 'QL03p057736' => 'qlo', 'RcHm_v2.0_Chr1g0364131' => 'rch', 'RcHm_v2.0_Chr2g0087801' => 'rch', 'RcHm_v2.0_Chr2g0087821' => 'rch', 'RcHm_v2.0_Chr2g0173231' => 'rch', 'RcHm_v2.0_Chr4g0433111' => 'rch', 'Rhsim03G0250300' => 'rsi', 'Rhsim08G0048400' => 'rsi', 'Rhsim10G0014800' => 'rsi', 'Rhsim12G0040100' => 'rsi', 'Rhsim12G0109700' => 'rsi', 'Sabra06G0049600' => 'sbr', 'Sabra08G0141000' => 'sbr', 'Sabra10G0021400' => 'sbr', 'Sabra16G0222900' => 'sbr', 'Sabra18G0108600' => 'sbr', 'SalBow1G0433' => 'sbo', 'SalBow1G2038' => 'sbo', 'SalBow1G5003' => 'sbo', 'SalBow7G1197' => 'sbo', 'SalBow8G3506' => 'sbo', 'Sc03g0007300' => 'sci', 'Sc11g0000950' => 'sci', 'Sc14g0008750' => 'sci', 'Sc18g0000420' => 'sci', 'Sed0006754' => 'sed', 'Sed0008741' => 'sed', 'Sed0017172' => 'sed', 'Sed0018925' => 'sed', 'Sed0023326' => 'sed', 'Sed0025909' => 'sed', 'SEGI_05333' => 'sgi', 'SEGI_10362' => 'sgi', 'SEGI_13380' => 'sgi', 'SEGI_24306' => 'sgi', 'SEGI_29077' => 'sgi', 'SEGI_29095' => 'sgi', 'SEGI_36534' => 'sgi', 'SEGI_37506' => 'sgi', 'SEGI_38321' => 'sgi', 'SGA_v2.0_scaffold307G48031' => 'sas', 'SGA_v2.0_scaffold47G17507' => 'sas', 'SGA_v2.0_scaffold63G21736' => 'sas', 'SGA_v2.0_scaffold87G27070' => 'sas', 'SHI17794' => 'shi', 'SHI28851' => 'shi', 'SMO165G0155' => 'smo', 'SMO340G0217' => 'smo', 'SMO367G1210' => 'smo', 'Solyc02g093430.3' => 'sly', 'Solyc05g013580.4' => 'sly', 'Solyc07g008030.3' => 'sly', 'Solyc12g035470.2' => 'sly', 'Sopen02g038020' => 'spe', 'Sopen05g008490' => 'spe', 'Sopen07g003910' => 'spe', 'Sopen12g015240' => 'spe', 'Sp1g11550' => 'spa', 'Sp2g16710' => 'spa', 'Sp3g00430' => 'spa', 'Sp3g26780' => 'spa', 'Sp5g22900' => 'spa', 'Sp6g29530' => 'spa', 'TAR371G0794' => 'tar', 'TAR374G0164' => 'tar', 'TAR622G0165' => 'tar', 'TAR626G0929' => 'tar', 'TAR629G2155' => 'tar', 'THA.LOC104805282' => 'tha', 'THA.LOC104805363' => 'tha', 'THA.LOC104808968' => 'tha', 'THA.LOC104821093' => 'tha', 'THA.LOC104823953' => 'tha', 'THA.LOC104825562' => 'tha', 'THA.LOC104825665' => 'tha', 'Thecc.02G261400' => 'tca', 'Thecc.04G019200' => 'tca', 'Thecc.09G130400' => 'tca', 'Thhalv10004374m.g' => 'esa', 'Thhalv10007850m.g' => 'esa', 'Thhalv10013782m.g' => 'esa', 'Thhalv10018686m.g' => 'esa', 'Thhalv10020899m.g' => 'esa', 'Thhalv10022755m.g' => 'esa', 'TPR.G23851' => 'tpr', 'TPR.G26500' => 'tpr', 'TPR.G27267' => 'tpr', 'TPR.G32001' => 'tpr', 'TPR.G6251' => 'tpr', 'TPR.G8167' => 'tpr', 'TWI12G1330' => 'twi', 'TWI18G1239' => 'twi', 'TWI34G0979' => 'twi', 'TWI36G0670' => 'twi', 'TWI36G0707' => 'twi', 'TWI56G0233' => 'twi', 'TWI75G1809' => 'twi', 'unitig_21.g20874' => 'ugi', 'unitig_26.g10343' => 'ugi', 'unitig_46.g18392' => 'ugi', 'unitig_52.g17178' => 'ugi', 'unitig_8.g2934' => 'ugi', 'vmacro01122' => 'vma', 'vmacro05875' => 'vma', 'vmacro06147' => 'vma', 'vmacro16191' => 'vma', 'vmacro18293' => 'vma', 'VMungo0251G3707' => 'vmu', 'VMungo0464G1521' => 'vmu', 'VMungo1215G0205' => 'vmu', 'VMungo1383G2484' => 'vmu', 'Zm00001eb079610' => 'zma', 'Zm00001eb135990' => 'zma', 'Zm00001eb183710' => 'zma', 'Zm00001eb246020' => 'zma' ), 'gf_id' => 'HOM05D001124', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001124' ), 'data_identifier' => 'HOM05D001124', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001124', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '548', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02520' => 'bna', 'A03p06630' => 'bna', 'A05p44460' => 'bna', 'A06p08710' => 'bna', 'A06p41090' => 'bna', 'A07p32320' => 'bna', 'A08p32520' => 'bna', 'A09p10360' => 'bna', 'A10p24080' => 'bna', 'Aa31LG11G15250' => 'aar', 'Aa31LG1G1800' => 'aar', 'Aa31LG2G5120' => 'aar', 'Aa31LG2G6070' => 'aar', 'Aa31LG5G10770' => 'aar', 'Aa31sc61G90' => 'aar', 'Actinidia01352' => 'ach', 'Actinidia05983' => 'ach', 'Actinidia08133' => 'ach', 'Actinidia15101' => 'ach', 'Actinidia26379' => 'ach', 'Actinidia35778' => 'ach', 'Actinidia36123' => 'ach', 'Actinidia37436' => 'ach', 'Actinidia38730' => 'ach', 'Ah.02g128210' => 'amhyb', 'Ah.03g132990' => 'amhyb', 'Ah.14g079410' => 'amhyb', 'AL1G24640' => 'aly', 'AL2G26680' => 'aly', 'AL3G10530' => 'aly', 'AL3G45230' => 'aly', 'AL5G15230' => 'aly', 'AL5G16960' => 'aly', 'AL6G25210' => 'aly', 'Aqoxy2G00441' => 'aox', 'Aqoxy3G01236' => 'aox', 'Aqoxy5G03746' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3RQ047' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C7GMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9C8JER' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MBL6KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YXCZ83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZANX40' => 'arhy', 'AT1G12990' => 'ath', 'AT1G67880' => 'ath', 'AT2G13290' => 'ath', 'AT3G01620' => 'ath', 'AT3G26445' => 'ath', 'AT3G27540' => 'ath', 'AT5G14480' => 'ath', 'ATR0824G026' => 'atr', 'ATR1098G019' => 'atr', 'Atru.chr11.2145' => 'acertr', 'Atru.chr2.3636' => 'acertr', 'Atru.chr2.3644' => 'acertr', 'Atru.chr6.2422' => 'acertr', 'Atru.chr7.1112' => 'acertr', 'AUR62005469' => 'cqu', 'AUR62011166' => 'cqu', 'AUR62013319' => 'cqu', 'AUR62024273' => 'cqu', 'AUR62028420' => 'cqu', 'AUR62041942' => 'cqu', 'BcaB01g04969' => 'bca', 'BcaB01g06371' => 'bca', 'BcaB02g11494' => 'bca', 'BcaB03g15382' => 'bca', 'BcaB08g36994' => 'bca', 'BcaC03g13477' => 'bca', 'BcaC03g13478' => 'bca', 'BcaC03g13480' => 'bca', 'BcaC03g13481' => 'bca', 'BcaC03g13486' => 'bca', 'BcaC04g19031' => 'bca', 'BcaC04g23085' => 'bca', 'BcaC05g25094' => 'bca', 'BcaC05g25096' => 'bca', 'BcaC05g25138' => 'bca', 'BcaC05g30416' => 'bca', 'BcaC05g30455' => 'bca', 'BcaC06g30979' => 'bca', 'BcaC06g33805' => 'bca', 'BcaC08g46021' => 'bca', 'BcaNung03154' => 'bca', 'BolC2t06623H' => 'bol', 'BolC2t06632H' => 'bol', 'BolC2t06635H' => 'bol', 'BolC2t06638H' => 'bol', 'BolC3t13266H' => 'bol', 'BolC5t29776H' => 'bol', 'BolC6t38912H' => 'bol', 'BolC7t44183H' => 'bol', 'BolC9t54123H' => 'bol', 'BolC9t59107H' => 'bol', 'BraA02t05221Z' => 'bra', 'BraA03t09996Z' => 'bra', 'BraA05t23210Z' => 'bra', 'BraA06t24068Z' => 'bra', 'BraA06t27032Z' => 'bra', 'BraA08t35176Z' => 'bra', 'BraA09t36680Z' => 'bra', 'BraA10t44471Z' => 'bra', 'C02p06760' => 'bna', 'C02p06890' => 'bna', 'C02p07010' => 'bna', 'C03p07660' => 'bna', 'C05p10300' => 'bna', 'C06p38150' => 'bna', 'C07p36650' => 'bna', 'C08p15770' => 'bna', 'C09p12300' => 'bna', 'C09p62700' => 'bna', 'C09p75040' => 'bna', 'CAN.G13.1' => 'can', 'CAN.G138.4' => 'can', 'CAN.G44.6' => 'can', 'CAN.G473.19' => 'can', 'CANSAT01G0835' => 'cansat', 'CANSAT11G0246' => 'cansat', 'CANSAT11G1766' => 'cansat', 'CANSAT64G1954' => 'cansat', 'CARHR013330' => 'chi', 'CARHR060530' => 'chi', 'CARHR075300' => 'chi', 'CARHR105120' => 'chi', 'CARHR148910' => 'chi', 'CARHR198830' => 'chi', 'Carub.0001s1275' => 'cru', 'Carub.0002s1437' => 'cru', 'Carub.0003s0044' => 'cru', 'Carub.0003s2787' => 'cru', 'Carub.0005s0597' => 'cru', 'Carub.0006s1266' => 'cru', 'Ca_06935_v3' => 'car', 'Ca_13559_v3' => 'car', 'Ca_16941_v3' => 'car', 'Ca_16960_v3' => 'car', 'Ca_17775_v3' => 'car', 'Ca_30464_v3' => 'car', 'Cc06_g08160' => 'ccan', 'Cc07_g01520' => 'ccan', 'Cc11_g15810' => 'ccan', 'CDE02G2840' => 'cde', 'CDE03G0093' => 'cde', 'CDE04G2127' => 'cde', 'CDE07G1857' => 'cde', 'CDE09G1246' => 'cde', 'Cfa003412' => 'cfa', 'Cfa007341' => 'cfa', 'Cfa009220' => 'cfa', 'Ciclev10008737m.g' => 'ccl', 'Ciclev10015565m.g' => 'ccl', 'Ciclev10031761m.g' => 'ccl', 'CiPaw.03G045300' => 'cil', 'CiPaw.03G247200' => 'cil', 'CiPaw.04G029500' => 'cil', 'CiPaw.04G174000' => 'cil', 'CiPaw.05G181200' => 'cil', 'CiPaw.06G067100' => 'cil', 'ClCG05G025800' => 'cla', 'ClCG06G011400' => 'cla', 'ClCG09G019360' => 'cla', 'COL.COLO4_04827' => 'col', 'COL.COLO4_29170' => 'col', 'COL.COLO4_35131' => 'col', 'COL.COLO4_35132' => 'col', 'Cpa.g.sc33.32' => 'cpa', 'Cpa.g.sc46.29' => 'cpa', 'Cpa.g.sc796.1' => 'cpa', 'CsaV3_1G030420' => 'csa', 'CsaV3_5G027050' => 'csa', 'CsaV3_5G031040' => 'csa', 'CsaV3_UNG023130' => 'csa', 'CSS0007726' => 'camsi', 'CSS0016433' => 'camsi', 'CSS0017656' => 'camsi', 'CSS0025364' => 'camsi', 'CSS0027582' => 'camsi', 'CSS0047288' => 'camsi', 'CSS0049950' => 'camsi', 'DCAR_003843' => 'dca', 'DCAR_007052' => 'dca', 'DCAR_020884' => 'dca', 'DCAR_021730' => 'dca', 'DCAR_024423' => 'dca', 'DCAR_026509' => 'dca', 'DCAR_031158' => 'dca', 'Dinv14728' => 'din', 'Dinv15219' => 'din', 'Dinv25728' => 'din', 'Dinv33428' => 'din', 'Dinv36489' => 'din', 'Dinv41486' => 'din', 'Duzib147G0469' => 'dzi', 'Duzib168G0060' => 'dzi', 'Duzib187G1215' => 'dzi', 'Duzib248G0692' => 'dzi', 'Duzib251G0767' => 'dzi', 'Duzib264G0446' => 'dzi', 'Duzib268G0691' => 'dzi', 'ECA232G4767' => 'eca', 'ECA233G2838' => 'eca', 'ECA234G0391' => 'eca', 'ECA234G0857' => 'eca', 'ECA236G1593' => 'eca', 'ECA238G0565' => 'eca', 'ECA246G1027' => 'eca', 'ECA246G3223' => 'eca', 'ECA246G3470' => 'eca', 'EL10Ac6g13829' => 'bvu', 'EL10Ac6g14093' => 'bvu', 'EL10Ac8g18707' => 'bvu', 'Eucgr.C01369' => 'egr', 'Eucgr.H02492' => 'egr', 'Eucgr.I01733' => 'egr', 'Eucgr.J02255' => 'egr', 'Eucgr.J02257' => 'egr', 'Eucgr.J02258' => 'egr', 'FAN02G1601' => 'fan', 'FAN03G1586' => 'fan', 'FAN03G2986' => 'fan', 'FAN05G4837' => 'fan', 'FAN06G0146' => 'fan', 'FAN07G0858' => 'fan', 'FAN09G3179' => 'fan', 'FAN10G0669' => 'fan', 'FAN12G2358' => 'fan', 'FAN14G4198' => 'fan', 'FAN14G5112' => 'fan', 'FAN17G0342' => 'fan', 'FAN19G0342' => 'fan', 'FAN19G0962' => 'fan', 'FAN19G1101' => 'fan', 'FAN19G1872' => 'fan', 'FAN22G0356' => 'fan', 'FAN23G0744' => 'fan', 'FAN23G1914' => 'fan', 'FAN26G0032' => 'fan', 'FAN28G0625' => 'fan', 'FvH4_1g02710' => 'fve', 'FvH4_1g02720' => 'fve', 'FvH4_4g25670' => 'fve', 'FvH4_6g51700' => 'fve', 'FvH4_7g20170' => 'fve', 'Glyma.05G175000' => 'gma', 'Glyma.08G132300' => 'gma', 'Glyma.11G243000' => 'gma', 'Glyma.13G158900' => 'gma', 'Glyma.17G112400' => 'gma', 'Glyma.18G014100' => 'gma', 'Glyma.19G003100' => 'gma', 'Glyma.19G056500' => 'gma', 'Gohir.A01G158900' => 'ghi', 'Gohir.A05G312600' => 'ghi', 'Gohir.A05G354900' => 'ghi', 'Gohir.A07G037200' => 'ghi', 'Gohir.A09G030000' => 'ghi', 'Gohir.A12G145200' => 'ghi', 'Gohir.D01G151500' => 'ghi', 'Gohir.D04G058300' => 'ghi', 'Gohir.D05G314100' => 'ghi', 'Gohir.D07G041400' => 'ghi', 'Gohir.D09G029700' => 'ghi', 'Gohir.D12G149700' => 'ghi', 'Gorai.001G043800' => 'gra', 'Gorai.002G187800' => 'gra', 'Gorai.006G034700' => 'gra', 'Gorai.008G161200' => 'gra', 'Gorai.009G335700' => 'gra', 'Gorai.012G065000' => 'gra', 'GSVIVG01000535001' => 'vvi', 'GSVIVG01015572001' => 'vvi', 'GSVIVG01032386001' => 'vvi', 'HanXRQChr05g0138531' => 'han', 'HanXRQChr06g0174391' => 'han', 'HanXRQChr07g0199021' => 'han', 'HanXRQChr08g0208211' => 'han', 'HanXRQChr09g0255471' => 'han', 'HanXRQChr10g0315791' => 'han', 'HanXRQChr12g0371991' => 'han', 'HanXRQChr15g0475251' => 'han', 'HanXRQChr17g0540001' => 'han', 'HanXRQChr17g0548631' => 'han', 'HanXRQChr17g0569561' => 'han', 'Haze_12256' => 'cav', 'Haze_14756' => 'cav', 'Haze_25528' => 'cav', 'Hma1.2p1_0079F.1_g041020' => 'hma', 'Hma1.2p1_0818F.1_g223260' => 'hma', 'Hma1.2p1_1747F.1_g300530' => 'hma', 'HPP92_004607' => 'vpl', 'HPP92_004608' => 'vpl', 'HPP92_006181' => 'vpl', 'HPP92_012192' => 'vpl', 'HPP92_015680' => 'vpl', 'HPP92_020249' => 'vpl', 'HPP92_021376' => 'vpl', 'HPP92_024275' => 'vpl', 'Hund06031' => 'sun', 'Hund25391' => 'sun', 'Lalb_Chr07g0185371' => 'lal', 'Lalb_Chr07g0185381' => 'lal', 'Lalb_Chr12g0204011' => 'lal', 'Lalb_Chr13g0301671' => 'lal', 'Lalb_Chr14g0362851' => 'lal', 'Lalb_Chr24g0403581' => 'lal', 'Lj1g0000233' => 'lja', 'Lj2g0018120' => 'lja', 'Lj3C621T0' => 'lonja', 'Lj3P1059T14' => 'lonja', 'Lj3P611T9' => 'lonja', 'Lj3P614T13' => 'lonja', 'Lj3P615T5' => 'lonja', 'Lj4g0012315' => 'lja', 'Lj4g0026182' => 'lja', 'Lj6P813T16' => 'lonja', 'Lj7C427T7' => 'lonja', 'Lj7C427T8' => 'lonja', 'Lj7P600T41' => 'lonja', 'Lju41C42G17' => 'lonja', 'Lsat_1_v5_gn_0_47300' => 'lsa', 'Lsat_1_v5_gn_2_91280' => 'lsa', 'Lsat_1_v5_gn_3_30561' => 'lsa', 'Lsat_1_v5_gn_4_184321' => 'lsa', 'Lsat_1_v5_gn_4_4041' => 'lsa', 'Lsat_1_v5_gn_5_92000' => 'lsa', 'Lsat_1_v5_gn_8_152940' => 'lsa', 'Lsat_1_v5_gn_8_62401' => 'lsa', 'Manes.06G055900' => 'mes', 'Manes.12G022200' => 'mes', 'Manes.13G023300' => 'mes', 'Manes.14G115000' => 'mes', 'Manes.15G151700' => 'mes', 'Manes.17G111300' => 'mes', 'Mapoly0226s0009' => 'mpo', 'MBI02_g25363_MAGBIO' => 'mbi', 'MBI06_g00027_MAGBIO' => 'mbi', 'MBI10_g13034_MAGBIO' => 'mbi', 'MD09G1023400' => 'mdo', 'MD13G1100100' => 'mdo', 'MD15G1169200' => 'mdo', 'MD16G1101100' => 'mdo', 'MD17G1022900' => 'mdo', 'Medtr3g096150' => 'mtr', 'Medtr4g115070' => 'mtr', 'Medtr7g033325' => 'mtr', 'Medtr8g089840' => 'mtr', 'MELO3C010319.2' => 'cme', 'MELO3C011944.2' => 'cme', 'MELO3C021589.2' => 'cme', 'Migut.E00207' => 'egut', 'Migut.H00067' => 'egut', 'Migut.K00433' => 'egut', 'Migut.K00606' => 'egut', 'Migut.K01410' => 'egut', 'MSTRG.13347' => 'ama', 'MSTRG.24045' => 'ama', 'MSTRG.2428' => 'ama', 'MSTRG.26410' => 'ama', 'MSTRG.3139' => 'ama', 'MSTRG.3286' => 'ama', 'MSTRG.563' => 'ama', 'MSTRG.7941' => 'ama', 'Nitab4.5_0000028g0060' => 'nta', 'Nitab4.5_0000065g0260' => 'nta', 'Nitab4.5_0000112g0060' => 'nta', 'Nitab4.5_0000489g0120' => 'nta', 'Nitab4.5_0001776g0050' => 'nta', 'Nitab4.5_0001854g0010' => 'nta', 'Nitab4.5_0001860g0020' => 'nta', 'Nitab4.5_0004352g0010' => 'nta', 'Nitab4.5_0008716g0020' => 'nta', 'Nitab4.5_0008922g0010' => 'nta', 'Nn3g16693' => 'nnu', 'Nn4g22596' => 'nnu', 'Nn7g37639' => 'nnu', 'Oeu001701.1' => 'oeu', 'Oeu018149.1' => 'oeu', 'Oeu026220.1' => 'oeu', 'Oeu038635.1' => 'oeu', 'Oeu049176.1' => 'oeu', 'Oeu056706.1' => 'oeu', 'Oeu056937.1' => 'oeu', 'Oeu057540.1' => 'oeu', 'Os02g0594900' => 'osa', 'Os02g0595100' => 'osa', 'Os04g0477500' => 'osa', 'Os12g0611900' => 'osa', 'Peaxi162Scf00076g00020' => 'pax', 'Peaxi162Scf00128g00217' => 'pax', 'Peaxi162Scf00129g01640' => 'pax', 'Peaxi162Scf00669g00007' => 'pax', 'Peaxi162Scf00700g00421' => 'pax', 'Peaxi162Scf00801g00038' => 'pax', 'Peaxi162Scf00891g00025' => 'pax', 'PGR083G0909' => 'pgr', 'PGR119G1005' => 'pgr', 'PGR142G2236' => 'pgr', 'PGR142G3388' => 'pgr', 'PGSC0003DMG400004514' => 'stu', 'PGSC0003DMG400012635' => 'stu', 'PGSC0003DMG400015730' => 'stu', 'PGSC0003DMG400018611' => 'stu', 'PGSC0003DMG400030897' => 'stu', 'Phvul.001G254800' => 'pvu', 'Phvul.002G260100' => 'pvu', 'Phvul.003G167600' => 'pvu', 'Phvul.004G005100' => 'pvu', 'Potri.001G343600' => 'ptr', 'Potri.006G066700' => 'ptr', 'Potri.008G186000' => 'ptr', 'Potri.010G046900' => 'ptr', 'Potri.018G127900' => 'ptr', 'Pp3c20_17750' => 'ppa', 'Pp3c24_4380' => 'ppa', 'Prupe.1G245800' => 'ppe', 'Prupe.3G293400' => 'ppe', 'Prupe.7G247400' => 'ppe', 'Psat0s145g0120' => 'psa', 'Psat0s595g0040' => 'psa', 'Psat0s595g0120' => 'psa', 'Psat3g175040' => 'psa', 'Psat7g058120' => 'psa', 'PSO017G0428' => 'pso', 'PSO063G7510' => 'pso', 'PSO067G0046' => 'pso', 'PSO478G1073' => 'pso', 'PSO675G3677' => 'pso', 'PSO675G6558' => 'pso', 'PSO675G7520' => 'pso', 'PSO675G8959' => 'pso', 'QL02p074089' => 'qlo', 'QL02p089614' => 'qlo', 'QL03p057736' => 'qlo', 'RcHm_v2.0_Chr1g0364131' => 'rch', 'RcHm_v2.0_Chr2g0087801' => 'rch', 'RcHm_v2.0_Chr2g0087821' => 'rch', 'RcHm_v2.0_Chr2g0173231' => 'rch', 'RcHm_v2.0_Chr4g0433111' => 'rch', 'Rhsim03G0250300' => 'rsi', 'Rhsim08G0048400' => 'rsi', 'Rhsim10G0014800' => 'rsi', 'Rhsim12G0040100' => 'rsi', 'Rhsim12G0109700' => 'rsi', 'Sabra06G0049600' => 'sbr', 'Sabra08G0141000' => 'sbr', 'Sabra10G0021400' => 'sbr', 'Sabra16G0222900' => 'sbr', 'Sabra18G0108600' => 'sbr', 'SalBow1G0433' => 'sbo', 'SalBow1G2038' => 'sbo', 'SalBow1G5003' => 'sbo', 'SalBow7G1197' => 'sbo', 'SalBow8G3506' => 'sbo', 'Sc03g0007300' => 'sci', 'Sc11g0000950' => 'sci', 'Sc14g0008750' => 'sci', 'Sc18g0000420' => 'sci', 'Sed0006754' => 'sed', 'Sed0008741' => 'sed', 'Sed0017172' => 'sed', 'Sed0018925' => 'sed', 'Sed0023326' => 'sed', 'Sed0025909' => 'sed', 'SEGI_05333' => 'sgi', 'SEGI_10362' => 'sgi', 'SEGI_13380' => 'sgi', 'SEGI_24306' => 'sgi', 'SEGI_29077' => 'sgi', 'SEGI_29095' => 'sgi', 'SEGI_36534' => 'sgi', 'SEGI_37506' => 'sgi', 'SEGI_38321' => 'sgi', 'SGA_v2.0_scaffold307G48031' => 'sas', 'SGA_v2.0_scaffold47G17507' => 'sas', 'SGA_v2.0_scaffold63G21736' => 'sas', 'SGA_v2.0_scaffold87G27070' => 'sas', 'SHI17794' => 'shi', 'SHI28851' => 'shi', 'SMO165G0155' => 'smo', 'SMO340G0217' => 'smo', 'SMO367G1210' => 'smo', 'Solyc02g093430.3' => 'sly', 'Solyc05g013580.4' => 'sly', 'Solyc07g008030.3' => 'sly', 'Solyc12g035470.2' => 'sly', 'Sopen02g038020' => 'spe', 'Sopen05g008490' => 'spe', 'Sopen07g003910' => 'spe', 'Sopen12g015240' => 'spe', 'Sp1g11550' => 'spa', 'Sp2g16710' => 'spa', 'Sp3g00430' => 'spa', 'Sp3g26780' => 'spa', 'Sp5g22900' => 'spa', 'Sp6g29530' => 'spa', 'TAR371G0794' => 'tar', 'TAR374G0164' => 'tar', 'TAR622G0165' => 'tar', 'TAR626G0929' => 'tar', 'TAR629G2155' => 'tar', 'THA.LOC104805282' => 'tha', 'THA.LOC104805363' => 'tha', 'THA.LOC104808968' => 'tha', 'THA.LOC104821093' => 'tha', 'THA.LOC104823953' => 'tha', 'THA.LOC104825562' => 'tha', 'THA.LOC104825665' => 'tha', 'Thecc.02G261400' => 'tca', 'Thecc.04G019200' => 'tca', 'Thecc.09G130400' => 'tca', 'Thhalv10004374m.g' => 'esa', 'Thhalv10007850m.g' => 'esa', 'Thhalv10013782m.g' => 'esa', 'Thhalv10018686m.g' => 'esa', 'Thhalv10020899m.g' => 'esa', 'Thhalv10022755m.g' => 'esa', 'TPR.G23851' => 'tpr', 'TPR.G26500' => 'tpr', 'TPR.G27267' => 'tpr', 'TPR.G32001' => 'tpr', 'TPR.G6251' => 'tpr', 'TPR.G8167' => 'tpr', 'TWI12G1330' => 'twi', 'TWI18G1239' => 'twi', 'TWI34G0979' => 'twi', 'TWI36G0670' => 'twi', 'TWI36G0707' => 'twi', 'TWI56G0233' => 'twi', 'TWI75G1809' => 'twi', 'unitig_21.g20874' => 'ugi', 'unitig_26.g10343' => 'ugi', 'unitig_46.g18392' => 'ugi', 'unitig_52.g17178' => 'ugi', 'unitig_8.g2934' => 'ugi', 'vmacro01122' => 'vma', 'vmacro05875' => 'vma', 'vmacro06147' => 'vma', 'vmacro16191' => 'vma', 'vmacro18293' => 'vma', 'VMungo0251G3707' => 'vmu', 'VMungo0464G1521' => 'vmu', 'VMungo1215G0205' => 'vmu', 'VMungo1383G2484' => 'vmu', 'Zm00001eb079610' => 'zma', 'Zm00001eb135990' => 'zma', 'Zm00001eb183710' => 'zma', 'Zm00001eb246020' => 'zma' ) $gf_id = 'HOM05D001124' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001124' ) $data_identifier = 'HOM05D001124' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 6, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 7, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 21, 'bol' => (int) 10, 'bra' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 6, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 9, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 21, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 8, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 10, 'lsa' => (int) 8, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 8, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 9, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb246020' $species_info = array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ) $local_species = 'col' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001124', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '548', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02520' => 'bna', 'A03p06630' => 'bna', 'A05p44460' => 'bna', 'A06p08710' => 'bna', 'A06p41090' => 'bna', 'A07p32320' => 'bna', 'A08p32520' => 'bna', 'A09p10360' => 'bna', 'A10p24080' => 'bna', 'Aa31LG11G15250' => 'aar', 'Aa31LG1G1800' => 'aar', 'Aa31LG2G5120' => 'aar', 'Aa31LG2G6070' => 'aar', 'Aa31LG5G10770' => 'aar', 'Aa31sc61G90' => 'aar', 'Actinidia01352' => 'ach', 'Actinidia05983' => 'ach', 'Actinidia08133' => 'ach', 'Actinidia15101' => 'ach', 'Actinidia26379' => 'ach', 'Actinidia35778' => 'ach', 'Actinidia36123' => 'ach', 'Actinidia37436' => 'ach', 'Actinidia38730' => 'ach', 'Ah.02g128210' => 'amhyb', 'Ah.03g132990' => 'amhyb', 'Ah.14g079410' => 'amhyb', 'AL1G24640' => 'aly', 'AL2G26680' => 'aly', 'AL3G10530' => 'aly', 'AL3G45230' => 'aly', 'AL5G15230' => 'aly', 'AL5G16960' => 'aly', 'AL6G25210' => 'aly', 'Aqoxy2G00441' => 'aox', 'Aqoxy3G01236' => 'aox', 'Aqoxy5G03746' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3RQ047' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C7GMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9C8JER' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MBL6KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YXCZ83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZANX40' => 'arhy', 'AT1G12990' => 'ath', 'AT1G67880' => 'ath', 'AT2G13290' => 'ath', 'AT3G01620' => 'ath', 'AT3G26445' => 'ath', 'AT3G27540' => 'ath', 'AT5G14480' => 'ath', 'ATR0824G026' => 'atr', 'ATR1098G019' => 'atr', 'Atru.chr11.2145' => 'acertr', 'Atru.chr2.3636' => 'acertr', 'Atru.chr2.3644' => 'acertr', 'Atru.chr6.2422' => 'acertr', 'Atru.chr7.1112' => 'acertr', 'AUR62005469' => 'cqu', 'AUR62011166' => 'cqu', 'AUR62013319' => 'cqu', 'AUR62024273' => 'cqu', 'AUR62028420' => 'cqu', 'AUR62041942' => 'cqu', 'BcaB01g04969' => 'bca', 'BcaB01g06371' => 'bca', 'BcaB02g11494' => 'bca', 'BcaB03g15382' => 'bca', 'BcaB08g36994' => 'bca', 'BcaC03g13477' => 'bca', 'BcaC03g13478' => 'bca', 'BcaC03g13480' => 'bca', 'BcaC03g13481' => 'bca', 'BcaC03g13486' => 'bca', 'BcaC04g19031' => 'bca', 'BcaC04g23085' => 'bca', 'BcaC05g25094' => 'bca', 'BcaC05g25096' => 'bca', 'BcaC05g25138' => 'bca', 'BcaC05g30416' => 'bca', 'BcaC05g30455' => 'bca', 'BcaC06g30979' => 'bca', 'BcaC06g33805' => 'bca', 'BcaC08g46021' => 'bca', 'BcaNung03154' => 'bca', 'BolC2t06623H' => 'bol', 'BolC2t06632H' => 'bol', 'BolC2t06635H' => 'bol', 'BolC2t06638H' => 'bol', 'BolC3t13266H' => 'bol', 'BolC5t29776H' => 'bol', 'BolC6t38912H' => 'bol', 'BolC7t44183H' => 'bol', 'BolC9t54123H' => 'bol', 'BolC9t59107H' => 'bol', 'BraA02t05221Z' => 'bra', 'BraA03t09996Z' => 'bra', 'BraA05t23210Z' => 'bra', 'BraA06t24068Z' => 'bra', 'BraA06t27032Z' => 'bra', 'BraA08t35176Z' => 'bra', 'BraA09t36680Z' => 'bra', 'BraA10t44471Z' => 'bra', 'C02p06760' => 'bna', 'C02p06890' => 'bna', 'C02p07010' => 'bna', 'C03p07660' => 'bna', 'C05p10300' => 'bna', 'C06p38150' => 'bna', 'C07p36650' => 'bna', 'C08p15770' => 'bna', 'C09p12300' => 'bna', 'C09p62700' => 'bna', 'C09p75040' => 'bna', 'CAN.G13.1' => 'can', 'CAN.G138.4' => 'can', 'CAN.G44.6' => 'can', 'CAN.G473.19' => 'can', 'CANSAT01G0835' => 'cansat', 'CANSAT11G0246' => 'cansat', 'CANSAT11G1766' => 'cansat', 'CANSAT64G1954' => 'cansat', 'CARHR013330' => 'chi', 'CARHR060530' => 'chi', 'CARHR075300' => 'chi', 'CARHR105120' => 'chi', 'CARHR148910' => 'chi', 'CARHR198830' => 'chi', 'Carub.0001s1275' => 'cru', 'Carub.0002s1437' => 'cru', 'Carub.0003s0044' => 'cru', 'Carub.0003s2787' => 'cru', 'Carub.0005s0597' => 'cru', 'Carub.0006s1266' => 'cru', 'Ca_06935_v3' => 'car', 'Ca_13559_v3' => 'car', 'Ca_16941_v3' => 'car', 'Ca_16960_v3' => 'car', 'Ca_17775_v3' => 'car', 'Ca_30464_v3' => 'car', 'Cc06_g08160' => 'ccan', 'Cc07_g01520' => 'ccan', 'Cc11_g15810' => 'ccan', 'CDE02G2840' => 'cde', 'CDE03G0093' => 'cde', 'CDE04G2127' => 'cde', 'CDE07G1857' => 'cde', 'CDE09G1246' => 'cde', 'Cfa003412' => 'cfa', 'Cfa007341' => 'cfa', 'Cfa009220' => 'cfa', 'Ciclev10008737m.g' => 'ccl', 'Ciclev10015565m.g' => 'ccl', 'Ciclev10031761m.g' => 'ccl', 'CiPaw.03G045300' => 'cil', 'CiPaw.03G247200' => 'cil', 'CiPaw.04G029500' => 'cil', 'CiPaw.04G174000' => 'cil', 'CiPaw.05G181200' => 'cil', 'CiPaw.06G067100' => 'cil', 'ClCG05G025800' => 'cla', 'ClCG06G011400' => 'cla', 'ClCG09G019360' => 'cla', 'COL.COLO4_04827' => 'col', 'COL.COLO4_29170' => 'col', 'COL.COLO4_35131' => 'col', 'COL.COLO4_35132' => 'col', 'Cpa.g.sc33.32' => 'cpa', 'Cpa.g.sc46.29' => 'cpa', 'Cpa.g.sc796.1' => 'cpa', 'CsaV3_1G030420' => 'csa', 'CsaV3_5G027050' => 'csa', 'CsaV3_5G031040' => 'csa', 'CsaV3_UNG023130' => 'csa', 'CSS0007726' => 'camsi', 'CSS0016433' => 'camsi', 'CSS0017656' => 'camsi', 'CSS0025364' => 'camsi', 'CSS0027582' => 'camsi', 'CSS0047288' => 'camsi', 'CSS0049950' => 'camsi', 'DCAR_003843' => 'dca', 'DCAR_007052' => 'dca', 'DCAR_020884' => 'dca', 'DCAR_021730' => 'dca', 'DCAR_024423' => 'dca', 'DCAR_026509' => 'dca', 'DCAR_031158' => 'dca', 'Dinv14728' => 'din', 'Dinv15219' => 'din', 'Dinv25728' => 'din', 'Dinv33428' => 'din', 'Dinv36489' => 'din', 'Dinv41486' => 'din', 'Duzib147G0469' => 'dzi', 'Duzib168G0060' => 'dzi', 'Duzib187G1215' => 'dzi', 'Duzib248G0692' => 'dzi', 'Duzib251G0767' => 'dzi', 'Duzib264G0446' => 'dzi', 'Duzib268G0691' => 'dzi', 'ECA232G4767' => 'eca', 'ECA233G2838' => 'eca', 'ECA234G0391' => 'eca', 'ECA234G0857' => 'eca', 'ECA236G1593' => 'eca', 'ECA238G0565' => 'eca', 'ECA246G1027' => 'eca', 'ECA246G3223' => 'eca', 'ECA246G3470' => 'eca', 'EL10Ac6g13829' => 'bvu', 'EL10Ac6g14093' => 'bvu', 'EL10Ac8g18707' => 'bvu', 'Eucgr.C01369' => 'egr', 'Eucgr.H02492' => 'egr', 'Eucgr.I01733' => 'egr', 'Eucgr.J02255' => 'egr', 'Eucgr.J02257' => 'egr', 'Eucgr.J02258' => 'egr', 'FAN02G1601' => 'fan', 'FAN03G1586' => 'fan', 'FAN03G2986' => 'fan', 'FAN05G4837' => 'fan', 'FAN06G0146' => 'fan', 'FAN07G0858' => 'fan', 'FAN09G3179' => 'fan', 'FAN10G0669' => 'fan', 'FAN12G2358' => 'fan', 'FAN14G4198' => 'fan', 'FAN14G5112' => 'fan', 'FAN17G0342' => 'fan', 'FAN19G0342' => 'fan', 'FAN19G0962' => 'fan', 'FAN19G1101' => 'fan', 'FAN19G1872' => 'fan', 'FAN22G0356' => 'fan', 'FAN23G0744' => 'fan', 'FAN23G1914' => 'fan', 'FAN26G0032' => 'fan', 'FAN28G0625' => 'fan', 'FvH4_1g02710' => 'fve', 'FvH4_1g02720' => 'fve', 'FvH4_4g25670' => 'fve', 'FvH4_6g51700' => 'fve', 'FvH4_7g20170' => 'fve', 'Glyma.05G175000' => 'gma', 'Glyma.08G132300' => 'gma', 'Glyma.11G243000' => 'gma', 'Glyma.13G158900' => 'gma', 'Glyma.17G112400' => 'gma', 'Glyma.18G014100' => 'gma', 'Glyma.19G003100' => 'gma', 'Glyma.19G056500' => 'gma', 'Gohir.A01G158900' => 'ghi', 'Gohir.A05G312600' => 'ghi', 'Gohir.A05G354900' => 'ghi', 'Gohir.A07G037200' => 'ghi', 'Gohir.A09G030000' => 'ghi', 'Gohir.A12G145200' => 'ghi', 'Gohir.D01G151500' => 'ghi', 'Gohir.D04G058300' => 'ghi', 'Gohir.D05G314100' => 'ghi', 'Gohir.D07G041400' => 'ghi', 'Gohir.D09G029700' => 'ghi', 'Gohir.D12G149700' => 'ghi', 'Gorai.001G043800' => 'gra', 'Gorai.002G187800' => 'gra', 'Gorai.006G034700' => 'gra', 'Gorai.008G161200' => 'gra', 'Gorai.009G335700' => 'gra', 'Gorai.012G065000' => 'gra', 'GSVIVG01000535001' => 'vvi', 'GSVIVG01015572001' => 'vvi', 'GSVIVG01032386001' => 'vvi', 'HanXRQChr05g0138531' => 'han', 'HanXRQChr06g0174391' => 'han', 'HanXRQChr07g0199021' => 'han', 'HanXRQChr08g0208211' => 'han', 'HanXRQChr09g0255471' => 'han', 'HanXRQChr10g0315791' => 'han', 'HanXRQChr12g0371991' => 'han', 'HanXRQChr15g0475251' => 'han', 'HanXRQChr17g0540001' => 'han', 'HanXRQChr17g0548631' => 'han', 'HanXRQChr17g0569561' => 'han', 'Haze_12256' => 'cav', 'Haze_14756' => 'cav', 'Haze_25528' => 'cav', 'Hma1.2p1_0079F.1_g041020' => 'hma', 'Hma1.2p1_0818F.1_g223260' => 'hma', 'Hma1.2p1_1747F.1_g300530' => 'hma', 'HPP92_004607' => 'vpl', 'HPP92_004608' => 'vpl', 'HPP92_006181' => 'vpl', 'HPP92_012192' => 'vpl', 'HPP92_015680' => 'vpl', 'HPP92_020249' => 'vpl', 'HPP92_021376' => 'vpl', 'HPP92_024275' => 'vpl', 'Hund06031' => 'sun', 'Hund25391' => 'sun', 'Lalb_Chr07g0185371' => 'lal', 'Lalb_Chr07g0185381' => 'lal', 'Lalb_Chr12g0204011' => 'lal', 'Lalb_Chr13g0301671' => 'lal', 'Lalb_Chr14g0362851' => 'lal', 'Lalb_Chr24g0403581' => 'lal', 'Lj1g0000233' => 'lja', 'Lj2g0018120' => 'lja', 'Lj3C621T0' => 'lonja', 'Lj3P1059T14' => 'lonja', 'Lj3P611T9' => 'lonja', 'Lj3P614T13' => 'lonja', 'Lj3P615T5' => 'lonja', 'Lj4g0012315' => 'lja', 'Lj4g0026182' => 'lja', 'Lj6P813T16' => 'lonja', 'Lj7C427T7' => 'lonja', 'Lj7C427T8' => 'lonja', 'Lj7P600T41' => 'lonja', 'Lju41C42G17' => 'lonja', 'Lsat_1_v5_gn_0_47300' => 'lsa', 'Lsat_1_v5_gn_2_91280' => 'lsa', 'Lsat_1_v5_gn_3_30561' => 'lsa', 'Lsat_1_v5_gn_4_184321' => 'lsa', 'Lsat_1_v5_gn_4_4041' => 'lsa', 'Lsat_1_v5_gn_5_92000' => 'lsa', 'Lsat_1_v5_gn_8_152940' => 'lsa', 'Lsat_1_v5_gn_8_62401' => 'lsa', 'Manes.06G055900' => 'mes', 'Manes.12G022200' => 'mes', 'Manes.13G023300' => 'mes', 'Manes.14G115000' => 'mes', 'Manes.15G151700' => 'mes', 'Manes.17G111300' => 'mes', 'Mapoly0226s0009' => 'mpo', 'MBI02_g25363_MAGBIO' => 'mbi', 'MBI06_g00027_MAGBIO' => 'mbi', 'MBI10_g13034_MAGBIO' => 'mbi', 'MD09G1023400' => 'mdo', 'MD13G1100100' => 'mdo', 'MD15G1169200' => 'mdo', 'MD16G1101100' => 'mdo', 'MD17G1022900' => 'mdo', 'Medtr3g096150' => 'mtr', 'Medtr4g115070' => 'mtr', 'Medtr7g033325' => 'mtr', 'Medtr8g089840' => 'mtr', 'MELO3C010319.2' => 'cme', 'MELO3C011944.2' => 'cme', 'MELO3C021589.2' => 'cme', 'Migut.E00207' => 'egut', 'Migut.H00067' => 'egut', 'Migut.K00433' => 'egut', 'Migut.K00606' => 'egut', 'Migut.K01410' => 'egut', 'MSTRG.13347' => 'ama', 'MSTRG.24045' => 'ama', 'MSTRG.2428' => 'ama', 'MSTRG.26410' => 'ama', 'MSTRG.3139' => 'ama', 'MSTRG.3286' => 'ama', 'MSTRG.563' => 'ama', 'MSTRG.7941' => 'ama', 'Nitab4.5_0000028g0060' => 'nta', 'Nitab4.5_0000065g0260' => 'nta', 'Nitab4.5_0000112g0060' => 'nta', 'Nitab4.5_0000489g0120' => 'nta', 'Nitab4.5_0001776g0050' => 'nta', 'Nitab4.5_0001854g0010' => 'nta', 'Nitab4.5_0001860g0020' => 'nta', 'Nitab4.5_0004352g0010' => 'nta', 'Nitab4.5_0008716g0020' => 'nta', 'Nitab4.5_0008922g0010' => 'nta', 'Nn3g16693' => 'nnu', 'Nn4g22596' => 'nnu', 'Nn7g37639' => 'nnu', 'Oeu001701.1' => 'oeu', 'Oeu018149.1' => 'oeu', 'Oeu026220.1' => 'oeu', 'Oeu038635.1' => 'oeu', 'Oeu049176.1' => 'oeu', 'Oeu056706.1' => 'oeu', 'Oeu056937.1' => 'oeu', 'Oeu057540.1' => 'oeu', 'Os02g0594900' => 'osa', 'Os02g0595100' => 'osa', 'Os04g0477500' => 'osa', 'Os12g0611900' => 'osa', 'Peaxi162Scf00076g00020' => 'pax', 'Peaxi162Scf00128g00217' => 'pax', 'Peaxi162Scf00129g01640' => 'pax', 'Peaxi162Scf00669g00007' => 'pax', 'Peaxi162Scf00700g00421' => 'pax', 'Peaxi162Scf00801g00038' => 'pax', 'Peaxi162Scf00891g00025' => 'pax', 'PGR083G0909' => 'pgr', 'PGR119G1005' => 'pgr', 'PGR142G2236' => 'pgr', 'PGR142G3388' => 'pgr', 'PGSC0003DMG400004514' => 'stu', 'PGSC0003DMG400012635' => 'stu', 'PGSC0003DMG400015730' => 'stu', 'PGSC0003DMG400018611' => 'stu', 'PGSC0003DMG400030897' => 'stu', 'Phvul.001G254800' => 'pvu', 'Phvul.002G260100' => 'pvu', 'Phvul.003G167600' => 'pvu', 'Phvul.004G005100' => 'pvu', 'Potri.001G343600' => 'ptr', 'Potri.006G066700' => 'ptr', 'Potri.008G186000' => 'ptr', 'Potri.010G046900' => 'ptr', 'Potri.018G127900' => 'ptr', 'Pp3c20_17750' => 'ppa', 'Pp3c24_4380' => 'ppa', 'Prupe.1G245800' => 'ppe', 'Prupe.3G293400' => 'ppe', 'Prupe.7G247400' => 'ppe', 'Psat0s145g0120' => 'psa', 'Psat0s595g0040' => 'psa', 'Psat0s595g0120' => 'psa', 'Psat3g175040' => 'psa', 'Psat7g058120' => 'psa', 'PSO017G0428' => 'pso', 'PSO063G7510' => 'pso', 'PSO067G0046' => 'pso', 'PSO478G1073' => 'pso', 'PSO675G3677' => 'pso', 'PSO675G6558' => 'pso', 'PSO675G7520' => 'pso', 'PSO675G8959' => 'pso', 'QL02p074089' => 'qlo', 'QL02p089614' => 'qlo', 'QL03p057736' => 'qlo', 'RcHm_v2.0_Chr1g0364131' => 'rch', 'RcHm_v2.0_Chr2g0087801' => 'rch', 'RcHm_v2.0_Chr2g0087821' => 'rch', 'RcHm_v2.0_Chr2g0173231' => 'rch', 'RcHm_v2.0_Chr4g0433111' => 'rch', 'Rhsim03G0250300' => 'rsi', 'Rhsim08G0048400' => 'rsi', 'Rhsim10G0014800' => 'rsi', 'Rhsim12G0040100' => 'rsi', 'Rhsim12G0109700' => 'rsi', 'Sabra06G0049600' => 'sbr', 'Sabra08G0141000' => 'sbr', 'Sabra10G0021400' => 'sbr', 'Sabra16G0222900' => 'sbr', 'Sabra18G0108600' => 'sbr', 'SalBow1G0433' => 'sbo', 'SalBow1G2038' => 'sbo', 'SalBow1G5003' => 'sbo', 'SalBow7G1197' => 'sbo', 'SalBow8G3506' => 'sbo', 'Sc03g0007300' => 'sci', 'Sc11g0000950' => 'sci', 'Sc14g0008750' => 'sci', 'Sc18g0000420' => 'sci', 'Sed0006754' => 'sed', 'Sed0008741' => 'sed', 'Sed0017172' => 'sed', 'Sed0018925' => 'sed', 'Sed0023326' => 'sed', 'Sed0025909' => 'sed', 'SEGI_05333' => 'sgi', 'SEGI_10362' => 'sgi', 'SEGI_13380' => 'sgi', 'SEGI_24306' => 'sgi', 'SEGI_29077' => 'sgi', 'SEGI_29095' => 'sgi', 'SEGI_36534' => 'sgi', 'SEGI_37506' => 'sgi', 'SEGI_38321' => 'sgi', 'SGA_v2.0_scaffold307G48031' => 'sas', 'SGA_v2.0_scaffold47G17507' => 'sas', 'SGA_v2.0_scaffold63G21736' => 'sas', 'SGA_v2.0_scaffold87G27070' => 'sas', 'SHI17794' => 'shi', 'SHI28851' => 'shi', 'SMO165G0155' => 'smo', 'SMO340G0217' => 'smo', 'SMO367G1210' => 'smo', 'Solyc02g093430.3' => 'sly', 'Solyc05g013580.4' => 'sly', 'Solyc07g008030.3' => 'sly', 'Solyc12g035470.2' => 'sly', 'Sopen02g038020' => 'spe', 'Sopen05g008490' => 'spe', 'Sopen07g003910' => 'spe', 'Sopen12g015240' => 'spe', 'Sp1g11550' => 'spa', 'Sp2g16710' => 'spa', 'Sp3g00430' => 'spa', 'Sp3g26780' => 'spa', 'Sp5g22900' => 'spa', 'Sp6g29530' => 'spa', 'TAR371G0794' => 'tar', 'TAR374G0164' => 'tar', 'TAR622G0165' => 'tar', 'TAR626G0929' => 'tar', 'TAR629G2155' => 'tar', 'THA.LOC104805282' => 'tha', 'THA.LOC104805363' => 'tha', 'THA.LOC104808968' => 'tha', 'THA.LOC104821093' => 'tha', 'THA.LOC104823953' => 'tha', 'THA.LOC104825562' => 'tha', 'THA.LOC104825665' => 'tha', 'Thecc.02G261400' => 'tca', 'Thecc.04G019200' => 'tca', 'Thecc.09G130400' => 'tca', 'Thhalv10004374m.g' => 'esa', 'Thhalv10007850m.g' => 'esa', 'Thhalv10013782m.g' => 'esa', 'Thhalv10018686m.g' => 'esa', 'Thhalv10020899m.g' => 'esa', 'Thhalv10022755m.g' => 'esa', 'TPR.G23851' => 'tpr', 'TPR.G26500' => 'tpr', 'TPR.G27267' => 'tpr', 'TPR.G32001' => 'tpr', 'TPR.G6251' => 'tpr', 'TPR.G8167' => 'tpr', 'TWI12G1330' => 'twi', 'TWI18G1239' => 'twi', 'TWI34G0979' => 'twi', 'TWI36G0670' => 'twi', 'TWI36G0707' => 'twi', 'TWI56G0233' => 'twi', 'TWI75G1809' => 'twi', 'unitig_21.g20874' => 'ugi', 'unitig_26.g10343' => 'ugi', 'unitig_46.g18392' => 'ugi', 'unitig_52.g17178' => 'ugi', 'unitig_8.g2934' => 'ugi', 'vmacro01122' => 'vma', 'vmacro05875' => 'vma', 'vmacro06147' => 'vma', 'vmacro16191' => 'vma', 'vmacro18293' => 'vma', 'VMungo0251G3707' => 'vmu', 'VMungo0464G1521' => 'vmu', 'VMungo1215G0205' => 'vmu', 'VMungo1383G2484' => 'vmu', 'Zm00001eb079610' => 'zma', 'Zm00001eb135990' => 'zma', 'Zm00001eb183710' => 'zma', 'Zm00001eb246020' => 'zma' ), 'gf_id' => 'HOM05D001124', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001124' ), 'data_identifier' => 'HOM05D001124', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001124', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '548', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02520' => 'bna', 'A03p06630' => 'bna', 'A05p44460' => 'bna', 'A06p08710' => 'bna', 'A06p41090' => 'bna', 'A07p32320' => 'bna', 'A08p32520' => 'bna', 'A09p10360' => 'bna', 'A10p24080' => 'bna', 'Aa31LG11G15250' => 'aar', 'Aa31LG1G1800' => 'aar', 'Aa31LG2G5120' => 'aar', 'Aa31LG2G6070' => 'aar', 'Aa31LG5G10770' => 'aar', 'Aa31sc61G90' => 'aar', 'Actinidia01352' => 'ach', 'Actinidia05983' => 'ach', 'Actinidia08133' => 'ach', 'Actinidia15101' => 'ach', 'Actinidia26379' => 'ach', 'Actinidia35778' => 'ach', 'Actinidia36123' => 'ach', 'Actinidia37436' => 'ach', 'Actinidia38730' => 'ach', 'Ah.02g128210' => 'amhyb', 'Ah.03g132990' => 'amhyb', 'Ah.14g079410' => 'amhyb', 'AL1G24640' => 'aly', 'AL2G26680' => 'aly', 'AL3G10530' => 'aly', 'AL3G45230' => 'aly', 'AL5G15230' => 'aly', 'AL5G16960' => 'aly', 'AL6G25210' => 'aly', 'Aqoxy2G00441' => 'aox', 'Aqoxy3G01236' => 'aox', 'Aqoxy5G03746' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3RQ047' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C7GMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9C8JER' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MBL6KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YXCZ83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZANX40' => 'arhy', 'AT1G12990' => 'ath', 'AT1G67880' => 'ath', 'AT2G13290' => 'ath', 'AT3G01620' => 'ath', 'AT3G26445' => 'ath', 'AT3G27540' => 'ath', 'AT5G14480' => 'ath', 'ATR0824G026' => 'atr', 'ATR1098G019' => 'atr', 'Atru.chr11.2145' => 'acertr', 'Atru.chr2.3636' => 'acertr', 'Atru.chr2.3644' => 'acertr', 'Atru.chr6.2422' => 'acertr', 'Atru.chr7.1112' => 'acertr', 'AUR62005469' => 'cqu', 'AUR62011166' => 'cqu', 'AUR62013319' => 'cqu', 'AUR62024273' => 'cqu', 'AUR62028420' => 'cqu', 'AUR62041942' => 'cqu', 'BcaB01g04969' => 'bca', 'BcaB01g06371' => 'bca', 'BcaB02g11494' => 'bca', 'BcaB03g15382' => 'bca', 'BcaB08g36994' => 'bca', 'BcaC03g13477' => 'bca', 'BcaC03g13478' => 'bca', 'BcaC03g13480' => 'bca', 'BcaC03g13481' => 'bca', 'BcaC03g13486' => 'bca', 'BcaC04g19031' => 'bca', 'BcaC04g23085' => 'bca', 'BcaC05g25094' => 'bca', 'BcaC05g25096' => 'bca', 'BcaC05g25138' => 'bca', 'BcaC05g30416' => 'bca', 'BcaC05g30455' => 'bca', 'BcaC06g30979' => 'bca', 'BcaC06g33805' => 'bca', 'BcaC08g46021' => 'bca', 'BcaNung03154' => 'bca', 'BolC2t06623H' => 'bol', 'BolC2t06632H' => 'bol', 'BolC2t06635H' => 'bol', 'BolC2t06638H' => 'bol', 'BolC3t13266H' => 'bol', 'BolC5t29776H' => 'bol', 'BolC6t38912H' => 'bol', 'BolC7t44183H' => 'bol', 'BolC9t54123H' => 'bol', 'BolC9t59107H' => 'bol', 'BraA02t05221Z' => 'bra', 'BraA03t09996Z' => 'bra', 'BraA05t23210Z' => 'bra', 'BraA06t24068Z' => 'bra', 'BraA06t27032Z' => 'bra', 'BraA08t35176Z' => 'bra', 'BraA09t36680Z' => 'bra', 'BraA10t44471Z' => 'bra', 'C02p06760' => 'bna', 'C02p06890' => 'bna', 'C02p07010' => 'bna', 'C03p07660' => 'bna', 'C05p10300' => 'bna', 'C06p38150' => 'bna', 'C07p36650' => 'bna', 'C08p15770' => 'bna', 'C09p12300' => 'bna', 'C09p62700' => 'bna', 'C09p75040' => 'bna', 'CAN.G13.1' => 'can', 'CAN.G138.4' => 'can', 'CAN.G44.6' => 'can', 'CAN.G473.19' => 'can', 'CANSAT01G0835' => 'cansat', 'CANSAT11G0246' => 'cansat', 'CANSAT11G1766' => 'cansat', 'CANSAT64G1954' => 'cansat', 'CARHR013330' => 'chi', 'CARHR060530' => 'chi', 'CARHR075300' => 'chi', 'CARHR105120' => 'chi', 'CARHR148910' => 'chi', 'CARHR198830' => 'chi', 'Carub.0001s1275' => 'cru', 'Carub.0002s1437' => 'cru', 'Carub.0003s0044' => 'cru', 'Carub.0003s2787' => 'cru', 'Carub.0005s0597' => 'cru', 'Carub.0006s1266' => 'cru', 'Ca_06935_v3' => 'car', 'Ca_13559_v3' => 'car', 'Ca_16941_v3' => 'car', 'Ca_16960_v3' => 'car', 'Ca_17775_v3' => 'car', 'Ca_30464_v3' => 'car', 'Cc06_g08160' => 'ccan', 'Cc07_g01520' => 'ccan', 'Cc11_g15810' => 'ccan', 'CDE02G2840' => 'cde', 'CDE03G0093' => 'cde', 'CDE04G2127' => 'cde', 'CDE07G1857' => 'cde', 'CDE09G1246' => 'cde', 'Cfa003412' => 'cfa', 'Cfa007341' => 'cfa', 'Cfa009220' => 'cfa', 'Ciclev10008737m.g' => 'ccl', 'Ciclev10015565m.g' => 'ccl', 'Ciclev10031761m.g' => 'ccl', 'CiPaw.03G045300' => 'cil', 'CiPaw.03G247200' => 'cil', 'CiPaw.04G029500' => 'cil', 'CiPaw.04G174000' => 'cil', 'CiPaw.05G181200' => 'cil', 'CiPaw.06G067100' => 'cil', 'ClCG05G025800' => 'cla', 'ClCG06G011400' => 'cla', 'ClCG09G019360' => 'cla', 'COL.COLO4_04827' => 'col', 'COL.COLO4_29170' => 'col', 'COL.COLO4_35131' => 'col', 'COL.COLO4_35132' => 'col', 'Cpa.g.sc33.32' => 'cpa', 'Cpa.g.sc46.29' => 'cpa', 'Cpa.g.sc796.1' => 'cpa', 'CsaV3_1G030420' => 'csa', 'CsaV3_5G027050' => 'csa', 'CsaV3_5G031040' => 'csa', 'CsaV3_UNG023130' => 'csa', 'CSS0007726' => 'camsi', 'CSS0016433' => 'camsi', 'CSS0017656' => 'camsi', 'CSS0025364' => 'camsi', 'CSS0027582' => 'camsi', 'CSS0047288' => 'camsi', 'CSS0049950' => 'camsi', 'DCAR_003843' => 'dca', 'DCAR_007052' => 'dca', 'DCAR_020884' => 'dca', 'DCAR_021730' => 'dca', 'DCAR_024423' => 'dca', 'DCAR_026509' => 'dca', 'DCAR_031158' => 'dca', 'Dinv14728' => 'din', 'Dinv15219' => 'din', 'Dinv25728' => 'din', 'Dinv33428' => 'din', 'Dinv36489' => 'din', 'Dinv41486' => 'din', 'Duzib147G0469' => 'dzi', 'Duzib168G0060' => 'dzi', 'Duzib187G1215' => 'dzi', 'Duzib248G0692' => 'dzi', 'Duzib251G0767' => 'dzi', 'Duzib264G0446' => 'dzi', 'Duzib268G0691' => 'dzi', 'ECA232G4767' => 'eca', 'ECA233G2838' => 'eca', 'ECA234G0391' => 'eca', 'ECA234G0857' => 'eca', 'ECA236G1593' => 'eca', 'ECA238G0565' => 'eca', 'ECA246G1027' => 'eca', 'ECA246G3223' => 'eca', 'ECA246G3470' => 'eca', 'EL10Ac6g13829' => 'bvu', 'EL10Ac6g14093' => 'bvu', 'EL10Ac8g18707' => 'bvu', 'Eucgr.C01369' => 'egr', 'Eucgr.H02492' => 'egr', 'Eucgr.I01733' => 'egr', 'Eucgr.J02255' => 'egr', 'Eucgr.J02257' => 'egr', 'Eucgr.J02258' => 'egr', 'FAN02G1601' => 'fan', 'FAN03G1586' => 'fan', 'FAN03G2986' => 'fan', 'FAN05G4837' => 'fan', 'FAN06G0146' => 'fan', 'FAN07G0858' => 'fan', 'FAN09G3179' => 'fan', 'FAN10G0669' => 'fan', 'FAN12G2358' => 'fan', 'FAN14G4198' => 'fan', 'FAN14G5112' => 'fan', 'FAN17G0342' => 'fan', 'FAN19G0342' => 'fan', 'FAN19G0962' => 'fan', 'FAN19G1101' => 'fan', 'FAN19G1872' => 'fan', 'FAN22G0356' => 'fan', 'FAN23G0744' => 'fan', 'FAN23G1914' => 'fan', 'FAN26G0032' => 'fan', 'FAN28G0625' => 'fan', 'FvH4_1g02710' => 'fve', 'FvH4_1g02720' => 'fve', 'FvH4_4g25670' => 'fve', 'FvH4_6g51700' => 'fve', 'FvH4_7g20170' => 'fve', 'Glyma.05G175000' => 'gma', 'Glyma.08G132300' => 'gma', 'Glyma.11G243000' => 'gma', 'Glyma.13G158900' => 'gma', 'Glyma.17G112400' => 'gma', 'Glyma.18G014100' => 'gma', 'Glyma.19G003100' => 'gma', 'Glyma.19G056500' => 'gma', 'Gohir.A01G158900' => 'ghi', 'Gohir.A05G312600' => 'ghi', 'Gohir.A05G354900' => 'ghi', 'Gohir.A07G037200' => 'ghi', 'Gohir.A09G030000' => 'ghi', 'Gohir.A12G145200' => 'ghi', 'Gohir.D01G151500' => 'ghi', 'Gohir.D04G058300' => 'ghi', 'Gohir.D05G314100' => 'ghi', 'Gohir.D07G041400' => 'ghi', 'Gohir.D09G029700' => 'ghi', 'Gohir.D12G149700' => 'ghi', 'Gorai.001G043800' => 'gra', 'Gorai.002G187800' => 'gra', 'Gorai.006G034700' => 'gra', 'Gorai.008G161200' => 'gra', 'Gorai.009G335700' => 'gra', 'Gorai.012G065000' => 'gra', 'GSVIVG01000535001' => 'vvi', 'GSVIVG01015572001' => 'vvi', 'GSVIVG01032386001' => 'vvi', 'HanXRQChr05g0138531' => 'han', 'HanXRQChr06g0174391' => 'han', 'HanXRQChr07g0199021' => 'han', 'HanXRQChr08g0208211' => 'han', 'HanXRQChr09g0255471' => 'han', 'HanXRQChr10g0315791' => 'han', 'HanXRQChr12g0371991' => 'han', 'HanXRQChr15g0475251' => 'han', 'HanXRQChr17g0540001' => 'han', 'HanXRQChr17g0548631' => 'han', 'HanXRQChr17g0569561' => 'han', 'Haze_12256' => 'cav', 'Haze_14756' => 'cav', 'Haze_25528' => 'cav', 'Hma1.2p1_0079F.1_g041020' => 'hma', 'Hma1.2p1_0818F.1_g223260' => 'hma', 'Hma1.2p1_1747F.1_g300530' => 'hma', 'HPP92_004607' => 'vpl', 'HPP92_004608' => 'vpl', 'HPP92_006181' => 'vpl', 'HPP92_012192' => 'vpl', 'HPP92_015680' => 'vpl', 'HPP92_020249' => 'vpl', 'HPP92_021376' => 'vpl', 'HPP92_024275' => 'vpl', 'Hund06031' => 'sun', 'Hund25391' => 'sun', 'Lalb_Chr07g0185371' => 'lal', 'Lalb_Chr07g0185381' => 'lal', 'Lalb_Chr12g0204011' => 'lal', 'Lalb_Chr13g0301671' => 'lal', 'Lalb_Chr14g0362851' => 'lal', 'Lalb_Chr24g0403581' => 'lal', 'Lj1g0000233' => 'lja', 'Lj2g0018120' => 'lja', 'Lj3C621T0' => 'lonja', 'Lj3P1059T14' => 'lonja', 'Lj3P611T9' => 'lonja', 'Lj3P614T13' => 'lonja', 'Lj3P615T5' => 'lonja', 'Lj4g0012315' => 'lja', 'Lj4g0026182' => 'lja', 'Lj6P813T16' => 'lonja', 'Lj7C427T7' => 'lonja', 'Lj7C427T8' => 'lonja', 'Lj7P600T41' => 'lonja', 'Lju41C42G17' => 'lonja', 'Lsat_1_v5_gn_0_47300' => 'lsa', 'Lsat_1_v5_gn_2_91280' => 'lsa', 'Lsat_1_v5_gn_3_30561' => 'lsa', 'Lsat_1_v5_gn_4_184321' => 'lsa', 'Lsat_1_v5_gn_4_4041' => 'lsa', 'Lsat_1_v5_gn_5_92000' => 'lsa', 'Lsat_1_v5_gn_8_152940' => 'lsa', 'Lsat_1_v5_gn_8_62401' => 'lsa', 'Manes.06G055900' => 'mes', 'Manes.12G022200' => 'mes', 'Manes.13G023300' => 'mes', 'Manes.14G115000' => 'mes', 'Manes.15G151700' => 'mes', 'Manes.17G111300' => 'mes', 'Mapoly0226s0009' => 'mpo', 'MBI02_g25363_MAGBIO' => 'mbi', 'MBI06_g00027_MAGBIO' => 'mbi', 'MBI10_g13034_MAGBIO' => 'mbi', 'MD09G1023400' => 'mdo', 'MD13G1100100' => 'mdo', 'MD15G1169200' => 'mdo', 'MD16G1101100' => 'mdo', 'MD17G1022900' => 'mdo', 'Medtr3g096150' => 'mtr', 'Medtr4g115070' => 'mtr', 'Medtr7g033325' => 'mtr', 'Medtr8g089840' => 'mtr', 'MELO3C010319.2' => 'cme', 'MELO3C011944.2' => 'cme', 'MELO3C021589.2' => 'cme', 'Migut.E00207' => 'egut', 'Migut.H00067' => 'egut', 'Migut.K00433' => 'egut', 'Migut.K00606' => 'egut', 'Migut.K01410' => 'egut', 'MSTRG.13347' => 'ama', 'MSTRG.24045' => 'ama', 'MSTRG.2428' => 'ama', 'MSTRG.26410' => 'ama', 'MSTRG.3139' => 'ama', 'MSTRG.3286' => 'ama', 'MSTRG.563' => 'ama', 'MSTRG.7941' => 'ama', 'Nitab4.5_0000028g0060' => 'nta', 'Nitab4.5_0000065g0260' => 'nta', 'Nitab4.5_0000112g0060' => 'nta', 'Nitab4.5_0000489g0120' => 'nta', 'Nitab4.5_0001776g0050' => 'nta', 'Nitab4.5_0001854g0010' => 'nta', 'Nitab4.5_0001860g0020' => 'nta', 'Nitab4.5_0004352g0010' => 'nta', 'Nitab4.5_0008716g0020' => 'nta', 'Nitab4.5_0008922g0010' => 'nta', 'Nn3g16693' => 'nnu', 'Nn4g22596' => 'nnu', 'Nn7g37639' => 'nnu', 'Oeu001701.1' => 'oeu', 'Oeu018149.1' => 'oeu', 'Oeu026220.1' => 'oeu', 'Oeu038635.1' => 'oeu', 'Oeu049176.1' => 'oeu', 'Oeu056706.1' => 'oeu', 'Oeu056937.1' => 'oeu', 'Oeu057540.1' => 'oeu', 'Os02g0594900' => 'osa', 'Os02g0595100' => 'osa', 'Os04g0477500' => 'osa', 'Os12g0611900' => 'osa', 'Peaxi162Scf00076g00020' => 'pax', 'Peaxi162Scf00128g00217' => 'pax', 'Peaxi162Scf00129g01640' => 'pax', 'Peaxi162Scf00669g00007' => 'pax', 'Peaxi162Scf00700g00421' => 'pax', 'Peaxi162Scf00801g00038' => 'pax', 'Peaxi162Scf00891g00025' => 'pax', 'PGR083G0909' => 'pgr', 'PGR119G1005' => 'pgr', 'PGR142G2236' => 'pgr', 'PGR142G3388' => 'pgr', 'PGSC0003DMG400004514' => 'stu', 'PGSC0003DMG400012635' => 'stu', 'PGSC0003DMG400015730' => 'stu', 'PGSC0003DMG400018611' => 'stu', 'PGSC0003DMG400030897' => 'stu', 'Phvul.001G254800' => 'pvu', 'Phvul.002G260100' => 'pvu', 'Phvul.003G167600' => 'pvu', 'Phvul.004G005100' => 'pvu', 'Potri.001G343600' => 'ptr', 'Potri.006G066700' => 'ptr', 'Potri.008G186000' => 'ptr', 'Potri.010G046900' => 'ptr', 'Potri.018G127900' => 'ptr', 'Pp3c20_17750' => 'ppa', 'Pp3c24_4380' => 'ppa', 'Prupe.1G245800' => 'ppe', 'Prupe.3G293400' => 'ppe', 'Prupe.7G247400' => 'ppe', 'Psat0s145g0120' => 'psa', 'Psat0s595g0040' => 'psa', 'Psat0s595g0120' => 'psa', 'Psat3g175040' => 'psa', 'Psat7g058120' => 'psa', 'PSO017G0428' => 'pso', 'PSO063G7510' => 'pso', 'PSO067G0046' => 'pso', 'PSO478G1073' => 'pso', 'PSO675G3677' => 'pso', 'PSO675G6558' => 'pso', 'PSO675G7520' => 'pso', 'PSO675G8959' => 'pso', 'QL02p074089' => 'qlo', 'QL02p089614' => 'qlo', 'QL03p057736' => 'qlo', 'RcHm_v2.0_Chr1g0364131' => 'rch', 'RcHm_v2.0_Chr2g0087801' => 'rch', 'RcHm_v2.0_Chr2g0087821' => 'rch', 'RcHm_v2.0_Chr2g0173231' => 'rch', 'RcHm_v2.0_Chr4g0433111' => 'rch', 'Rhsim03G0250300' => 'rsi', 'Rhsim08G0048400' => 'rsi', 'Rhsim10G0014800' => 'rsi', 'Rhsim12G0040100' => 'rsi', 'Rhsim12G0109700' => 'rsi', 'Sabra06G0049600' => 'sbr', 'Sabra08G0141000' => 'sbr', 'Sabra10G0021400' => 'sbr', 'Sabra16G0222900' => 'sbr', 'Sabra18G0108600' => 'sbr', 'SalBow1G0433' => 'sbo', 'SalBow1G2038' => 'sbo', 'SalBow1G5003' => 'sbo', 'SalBow7G1197' => 'sbo', 'SalBow8G3506' => 'sbo', 'Sc03g0007300' => 'sci', 'Sc11g0000950' => 'sci', 'Sc14g0008750' => 'sci', 'Sc18g0000420' => 'sci', 'Sed0006754' => 'sed', 'Sed0008741' => 'sed', 'Sed0017172' => 'sed', 'Sed0018925' => 'sed', 'Sed0023326' => 'sed', 'Sed0025909' => 'sed', 'SEGI_05333' => 'sgi', 'SEGI_10362' => 'sgi', 'SEGI_13380' => 'sgi', 'SEGI_24306' => 'sgi', 'SEGI_29077' => 'sgi', 'SEGI_29095' => 'sgi', 'SEGI_36534' => 'sgi', 'SEGI_37506' => 'sgi', 'SEGI_38321' => 'sgi', 'SGA_v2.0_scaffold307G48031' => 'sas', 'SGA_v2.0_scaffold47G17507' => 'sas', 'SGA_v2.0_scaffold63G21736' => 'sas', 'SGA_v2.0_scaffold87G27070' => 'sas', 'SHI17794' => 'shi', 'SHI28851' => 'shi', 'SMO165G0155' => 'smo', 'SMO340G0217' => 'smo', 'SMO367G1210' => 'smo', 'Solyc02g093430.3' => 'sly', 'Solyc05g013580.4' => 'sly', 'Solyc07g008030.3' => 'sly', 'Solyc12g035470.2' => 'sly', 'Sopen02g038020' => 'spe', 'Sopen05g008490' => 'spe', 'Sopen07g003910' => 'spe', 'Sopen12g015240' => 'spe', 'Sp1g11550' => 'spa', 'Sp2g16710' => 'spa', 'Sp3g00430' => 'spa', 'Sp3g26780' => 'spa', 'Sp5g22900' => 'spa', 'Sp6g29530' => 'spa', 'TAR371G0794' => 'tar', 'TAR374G0164' => 'tar', 'TAR622G0165' => 'tar', 'TAR626G0929' => 'tar', 'TAR629G2155' => 'tar', 'THA.LOC104805282' => 'tha', 'THA.LOC104805363' => 'tha', 'THA.LOC104808968' => 'tha', 'THA.LOC104821093' => 'tha', 'THA.LOC104823953' => 'tha', 'THA.LOC104825562' => 'tha', 'THA.LOC104825665' => 'tha', 'Thecc.02G261400' => 'tca', 'Thecc.04G019200' => 'tca', 'Thecc.09G130400' => 'tca', 'Thhalv10004374m.g' => 'esa', 'Thhalv10007850m.g' => 'esa', 'Thhalv10013782m.g' => 'esa', 'Thhalv10018686m.g' => 'esa', 'Thhalv10020899m.g' => 'esa', 'Thhalv10022755m.g' => 'esa', 'TPR.G23851' => 'tpr', 'TPR.G26500' => 'tpr', 'TPR.G27267' => 'tpr', 'TPR.G32001' => 'tpr', 'TPR.G6251' => 'tpr', 'TPR.G8167' => 'tpr', 'TWI12G1330' => 'twi', 'TWI18G1239' => 'twi', 'TWI34G0979' => 'twi', 'TWI36G0670' => 'twi', 'TWI36G0707' => 'twi', 'TWI56G0233' => 'twi', 'TWI75G1809' => 'twi', 'unitig_21.g20874' => 'ugi', 'unitig_26.g10343' => 'ugi', 'unitig_46.g18392' => 'ugi', 'unitig_52.g17178' => 'ugi', 'unitig_8.g2934' => 'ugi', 'vmacro01122' => 'vma', 'vmacro05875' => 'vma', 'vmacro06147' => 'vma', 'vmacro16191' => 'vma', 'vmacro18293' => 'vma', 'VMungo0251G3707' => 'vmu', 'VMungo0464G1521' => 'vmu', 'VMungo1215G0205' => 'vmu', 'VMungo1383G2484' => 'vmu', 'Zm00001eb079610' => 'zma', 'Zm00001eb135990' => 'zma', 'Zm00001eb183710' => 'zma', 'Zm00001eb246020' => 'zma' ) $gf_id = 'HOM05D001124' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001124' ) $data_identifier = 'HOM05D001124' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 6, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 7, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 21, 'bol' => (int) 10, 'bra' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 6, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 9, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 21, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 8, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 10, 'lsa' => (int) 8, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 8, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 9, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb246020' $species_info = array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ) $local_species = 'col' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001124', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '548', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02520' => 'bna', 'A03p06630' => 'bna', 'A05p44460' => 'bna', 'A06p08710' => 'bna', 'A06p41090' => 'bna', 'A07p32320' => 'bna', 'A08p32520' => 'bna', 'A09p10360' => 'bna', 'A10p24080' => 'bna', 'Aa31LG11G15250' => 'aar', 'Aa31LG1G1800' => 'aar', 'Aa31LG2G5120' => 'aar', 'Aa31LG2G6070' => 'aar', 'Aa31LG5G10770' => 'aar', 'Aa31sc61G90' => 'aar', 'Actinidia01352' => 'ach', 'Actinidia05983' => 'ach', 'Actinidia08133' => 'ach', 'Actinidia15101' => 'ach', 'Actinidia26379' => 'ach', 'Actinidia35778' => 'ach', 'Actinidia36123' => 'ach', 'Actinidia37436' => 'ach', 'Actinidia38730' => 'ach', 'Ah.02g128210' => 'amhyb', 'Ah.03g132990' => 'amhyb', 'Ah.14g079410' => 'amhyb', 'AL1G24640' => 'aly', 'AL2G26680' => 'aly', 'AL3G10530' => 'aly', 'AL3G45230' => 'aly', 'AL5G15230' => 'aly', 'AL5G16960' => 'aly', 'AL6G25210' => 'aly', 'Aqoxy2G00441' => 'aox', 'Aqoxy3G01236' => 'aox', 'Aqoxy5G03746' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3RQ047' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C7GMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9C8JER' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MBL6KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YXCZ83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZANX40' => 'arhy', 'AT1G12990' => 'ath', 'AT1G67880' => 'ath', 'AT2G13290' => 'ath', 'AT3G01620' => 'ath', 'AT3G26445' => 'ath', 'AT3G27540' => 'ath', 'AT5G14480' => 'ath', 'ATR0824G026' => 'atr', 'ATR1098G019' => 'atr', 'Atru.chr11.2145' => 'acertr', 'Atru.chr2.3636' => 'acertr', 'Atru.chr2.3644' => 'acertr', 'Atru.chr6.2422' => 'acertr', 'Atru.chr7.1112' => 'acertr', 'AUR62005469' => 'cqu', 'AUR62011166' => 'cqu', 'AUR62013319' => 'cqu', 'AUR62024273' => 'cqu', 'AUR62028420' => 'cqu', 'AUR62041942' => 'cqu', 'BcaB01g04969' => 'bca', 'BcaB01g06371' => 'bca', 'BcaB02g11494' => 'bca', 'BcaB03g15382' => 'bca', 'BcaB08g36994' => 'bca', 'BcaC03g13477' => 'bca', 'BcaC03g13478' => 'bca', 'BcaC03g13480' => 'bca', 'BcaC03g13481' => 'bca', 'BcaC03g13486' => 'bca', 'BcaC04g19031' => 'bca', 'BcaC04g23085' => 'bca', 'BcaC05g25094' => 'bca', 'BcaC05g25096' => 'bca', 'BcaC05g25138' => 'bca', 'BcaC05g30416' => 'bca', 'BcaC05g30455' => 'bca', 'BcaC06g30979' => 'bca', 'BcaC06g33805' => 'bca', 'BcaC08g46021' => 'bca', 'BcaNung03154' => 'bca', 'BolC2t06623H' => 'bol', 'BolC2t06632H' => 'bol', 'BolC2t06635H' => 'bol', 'BolC2t06638H' => 'bol', 'BolC3t13266H' => 'bol', 'BolC5t29776H' => 'bol', 'BolC6t38912H' => 'bol', 'BolC7t44183H' => 'bol', 'BolC9t54123H' => 'bol', 'BolC9t59107H' => 'bol', 'BraA02t05221Z' => 'bra', 'BraA03t09996Z' => 'bra', 'BraA05t23210Z' => 'bra', 'BraA06t24068Z' => 'bra', 'BraA06t27032Z' => 'bra', 'BraA08t35176Z' => 'bra', 'BraA09t36680Z' => 'bra', 'BraA10t44471Z' => 'bra', 'C02p06760' => 'bna', 'C02p06890' => 'bna', 'C02p07010' => 'bna', 'C03p07660' => 'bna', 'C05p10300' => 'bna', 'C06p38150' => 'bna', 'C07p36650' => 'bna', 'C08p15770' => 'bna', 'C09p12300' => 'bna', 'C09p62700' => 'bna', 'C09p75040' => 'bna', 'CAN.G13.1' => 'can', 'CAN.G138.4' => 'can', 'CAN.G44.6' => 'can', 'CAN.G473.19' => 'can', 'CANSAT01G0835' => 'cansat', 'CANSAT11G0246' => 'cansat', 'CANSAT11G1766' => 'cansat', 'CANSAT64G1954' => 'cansat', 'CARHR013330' => 'chi', 'CARHR060530' => 'chi', 'CARHR075300' => 'chi', 'CARHR105120' => 'chi', 'CARHR148910' => 'chi', 'CARHR198830' => 'chi', 'Carub.0001s1275' => 'cru', 'Carub.0002s1437' => 'cru', 'Carub.0003s0044' => 'cru', 'Carub.0003s2787' => 'cru', 'Carub.0005s0597' => 'cru', 'Carub.0006s1266' => 'cru', 'Ca_06935_v3' => 'car', 'Ca_13559_v3' => 'car', 'Ca_16941_v3' => 'car', 'Ca_16960_v3' => 'car', 'Ca_17775_v3' => 'car', 'Ca_30464_v3' => 'car', 'Cc06_g08160' => 'ccan', 'Cc07_g01520' => 'ccan', 'Cc11_g15810' => 'ccan', 'CDE02G2840' => 'cde', 'CDE03G0093' => 'cde', 'CDE04G2127' => 'cde', 'CDE07G1857' => 'cde', 'CDE09G1246' => 'cde', 'Cfa003412' => 'cfa', 'Cfa007341' => 'cfa', 'Cfa009220' => 'cfa', 'Ciclev10008737m.g' => 'ccl', 'Ciclev10015565m.g' => 'ccl', 'Ciclev10031761m.g' => 'ccl', 'CiPaw.03G045300' => 'cil', 'CiPaw.03G247200' => 'cil', 'CiPaw.04G029500' => 'cil', 'CiPaw.04G174000' => 'cil', 'CiPaw.05G181200' => 'cil', 'CiPaw.06G067100' => 'cil', 'ClCG05G025800' => 'cla', 'ClCG06G011400' => 'cla', 'ClCG09G019360' => 'cla', 'COL.COLO4_04827' => 'col', 'COL.COLO4_29170' => 'col', 'COL.COLO4_35131' => 'col', 'COL.COLO4_35132' => 'col', 'Cpa.g.sc33.32' => 'cpa', 'Cpa.g.sc46.29' => 'cpa', 'Cpa.g.sc796.1' => 'cpa', 'CsaV3_1G030420' => 'csa', 'CsaV3_5G027050' => 'csa', 'CsaV3_5G031040' => 'csa', 'CsaV3_UNG023130' => 'csa', 'CSS0007726' => 'camsi', 'CSS0016433' => 'camsi', 'CSS0017656' => 'camsi', 'CSS0025364' => 'camsi', 'CSS0027582' => 'camsi', 'CSS0047288' => 'camsi', 'CSS0049950' => 'camsi', 'DCAR_003843' => 'dca', 'DCAR_007052' => 'dca', 'DCAR_020884' => 'dca', 'DCAR_021730' => 'dca', 'DCAR_024423' => 'dca', 'DCAR_026509' => 'dca', 'DCAR_031158' => 'dca', 'Dinv14728' => 'din', 'Dinv15219' => 'din', 'Dinv25728' => 'din', 'Dinv33428' => 'din', 'Dinv36489' => 'din', 'Dinv41486' => 'din', 'Duzib147G0469' => 'dzi', 'Duzib168G0060' => 'dzi', 'Duzib187G1215' => 'dzi', 'Duzib248G0692' => 'dzi', 'Duzib251G0767' => 'dzi', 'Duzib264G0446' => 'dzi', 'Duzib268G0691' => 'dzi', 'ECA232G4767' => 'eca', 'ECA233G2838' => 'eca', 'ECA234G0391' => 'eca', 'ECA234G0857' => 'eca', 'ECA236G1593' => 'eca', 'ECA238G0565' => 'eca', 'ECA246G1027' => 'eca', 'ECA246G3223' => 'eca', 'ECA246G3470' => 'eca', 'EL10Ac6g13829' => 'bvu', 'EL10Ac6g14093' => 'bvu', 'EL10Ac8g18707' => 'bvu', 'Eucgr.C01369' => 'egr', 'Eucgr.H02492' => 'egr', 'Eucgr.I01733' => 'egr', 'Eucgr.J02255' => 'egr', 'Eucgr.J02257' => 'egr', 'Eucgr.J02258' => 'egr', 'FAN02G1601' => 'fan', 'FAN03G1586' => 'fan', 'FAN03G2986' => 'fan', 'FAN05G4837' => 'fan', 'FAN06G0146' => 'fan', 'FAN07G0858' => 'fan', 'FAN09G3179' => 'fan', 'FAN10G0669' => 'fan', 'FAN12G2358' => 'fan', 'FAN14G4198' => 'fan', 'FAN14G5112' => 'fan', 'FAN17G0342' => 'fan', 'FAN19G0342' => 'fan', 'FAN19G0962' => 'fan', 'FAN19G1101' => 'fan', 'FAN19G1872' => 'fan', 'FAN22G0356' => 'fan', 'FAN23G0744' => 'fan', 'FAN23G1914' => 'fan', 'FAN26G0032' => 'fan', 'FAN28G0625' => 'fan', 'FvH4_1g02710' => 'fve', 'FvH4_1g02720' => 'fve', 'FvH4_4g25670' => 'fve', 'FvH4_6g51700' => 'fve', 'FvH4_7g20170' => 'fve', 'Glyma.05G175000' => 'gma', 'Glyma.08G132300' => 'gma', 'Glyma.11G243000' => 'gma', 'Glyma.13G158900' => 'gma', 'Glyma.17G112400' => 'gma', 'Glyma.18G014100' => 'gma', 'Glyma.19G003100' => 'gma', 'Glyma.19G056500' => 'gma', 'Gohir.A01G158900' => 'ghi', 'Gohir.A05G312600' => 'ghi', 'Gohir.A05G354900' => 'ghi', 'Gohir.A07G037200' => 'ghi', 'Gohir.A09G030000' => 'ghi', 'Gohir.A12G145200' => 'ghi', 'Gohir.D01G151500' => 'ghi', 'Gohir.D04G058300' => 'ghi', 'Gohir.D05G314100' => 'ghi', 'Gohir.D07G041400' => 'ghi', 'Gohir.D09G029700' => 'ghi', 'Gohir.D12G149700' => 'ghi', 'Gorai.001G043800' => 'gra', 'Gorai.002G187800' => 'gra', 'Gorai.006G034700' => 'gra', 'Gorai.008G161200' => 'gra', 'Gorai.009G335700' => 'gra', 'Gorai.012G065000' => 'gra', 'GSVIVG01000535001' => 'vvi', 'GSVIVG01015572001' => 'vvi', 'GSVIVG01032386001' => 'vvi', 'HanXRQChr05g0138531' => 'han', 'HanXRQChr06g0174391' => 'han', 'HanXRQChr07g0199021' => 'han', 'HanXRQChr08g0208211' => 'han', 'HanXRQChr09g0255471' => 'han', 'HanXRQChr10g0315791' => 'han', 'HanXRQChr12g0371991' => 'han', 'HanXRQChr15g0475251' => 'han', 'HanXRQChr17g0540001' => 'han', 'HanXRQChr17g0548631' => 'han', 'HanXRQChr17g0569561' => 'han', 'Haze_12256' => 'cav', 'Haze_14756' => 'cav', 'Haze_25528' => 'cav', 'Hma1.2p1_0079F.1_g041020' => 'hma', 'Hma1.2p1_0818F.1_g223260' => 'hma', 'Hma1.2p1_1747F.1_g300530' => 'hma', 'HPP92_004607' => 'vpl', 'HPP92_004608' => 'vpl', 'HPP92_006181' => 'vpl', 'HPP92_012192' => 'vpl', 'HPP92_015680' => 'vpl', 'HPP92_020249' => 'vpl', 'HPP92_021376' => 'vpl', 'HPP92_024275' => 'vpl', 'Hund06031' => 'sun', 'Hund25391' => 'sun', 'Lalb_Chr07g0185371' => 'lal', 'Lalb_Chr07g0185381' => 'lal', 'Lalb_Chr12g0204011' => 'lal', 'Lalb_Chr13g0301671' => 'lal', 'Lalb_Chr14g0362851' => 'lal', 'Lalb_Chr24g0403581' => 'lal', 'Lj1g0000233' => 'lja', 'Lj2g0018120' => 'lja', 'Lj3C621T0' => 'lonja', 'Lj3P1059T14' => 'lonja', 'Lj3P611T9' => 'lonja', 'Lj3P614T13' => 'lonja', 'Lj3P615T5' => 'lonja', 'Lj4g0012315' => 'lja', 'Lj4g0026182' => 'lja', 'Lj6P813T16' => 'lonja', 'Lj7C427T7' => 'lonja', 'Lj7C427T8' => 'lonja', 'Lj7P600T41' => 'lonja', 'Lju41C42G17' => 'lonja', 'Lsat_1_v5_gn_0_47300' => 'lsa', 'Lsat_1_v5_gn_2_91280' => 'lsa', 'Lsat_1_v5_gn_3_30561' => 'lsa', 'Lsat_1_v5_gn_4_184321' => 'lsa', 'Lsat_1_v5_gn_4_4041' => 'lsa', 'Lsat_1_v5_gn_5_92000' => 'lsa', 'Lsat_1_v5_gn_8_152940' => 'lsa', 'Lsat_1_v5_gn_8_62401' => 'lsa', 'Manes.06G055900' => 'mes', 'Manes.12G022200' => 'mes', 'Manes.13G023300' => 'mes', 'Manes.14G115000' => 'mes', 'Manes.15G151700' => 'mes', 'Manes.17G111300' => 'mes', 'Mapoly0226s0009' => 'mpo', 'MBI02_g25363_MAGBIO' => 'mbi', 'MBI06_g00027_MAGBIO' => 'mbi', 'MBI10_g13034_MAGBIO' => 'mbi', 'MD09G1023400' => 'mdo', 'MD13G1100100' => 'mdo', 'MD15G1169200' => 'mdo', 'MD16G1101100' => 'mdo', 'MD17G1022900' => 'mdo', 'Medtr3g096150' => 'mtr', 'Medtr4g115070' => 'mtr', 'Medtr7g033325' => 'mtr', 'Medtr8g089840' => 'mtr', 'MELO3C010319.2' => 'cme', 'MELO3C011944.2' => 'cme', 'MELO3C021589.2' => 'cme', 'Migut.E00207' => 'egut', 'Migut.H00067' => 'egut', 'Migut.K00433' => 'egut', 'Migut.K00606' => 'egut', 'Migut.K01410' => 'egut', 'MSTRG.13347' => 'ama', 'MSTRG.24045' => 'ama', 'MSTRG.2428' => 'ama', 'MSTRG.26410' => 'ama', 'MSTRG.3139' => 'ama', 'MSTRG.3286' => 'ama', 'MSTRG.563' => 'ama', 'MSTRG.7941' => 'ama', 'Nitab4.5_0000028g0060' => 'nta', 'Nitab4.5_0000065g0260' => 'nta', 'Nitab4.5_0000112g0060' => 'nta', 'Nitab4.5_0000489g0120' => 'nta', 'Nitab4.5_0001776g0050' => 'nta', 'Nitab4.5_0001854g0010' => 'nta', 'Nitab4.5_0001860g0020' => 'nta', 'Nitab4.5_0004352g0010' => 'nta', 'Nitab4.5_0008716g0020' => 'nta', 'Nitab4.5_0008922g0010' => 'nta', 'Nn3g16693' => 'nnu', 'Nn4g22596' => 'nnu', 'Nn7g37639' => 'nnu', 'Oeu001701.1' => 'oeu', 'Oeu018149.1' => 'oeu', 'Oeu026220.1' => 'oeu', 'Oeu038635.1' => 'oeu', 'Oeu049176.1' => 'oeu', 'Oeu056706.1' => 'oeu', 'Oeu056937.1' => 'oeu', 'Oeu057540.1' => 'oeu', 'Os02g0594900' => 'osa', 'Os02g0595100' => 'osa', 'Os04g0477500' => 'osa', 'Os12g0611900' => 'osa', 'Peaxi162Scf00076g00020' => 'pax', 'Peaxi162Scf00128g00217' => 'pax', 'Peaxi162Scf00129g01640' => 'pax', 'Peaxi162Scf00669g00007' => 'pax', 'Peaxi162Scf00700g00421' => 'pax', 'Peaxi162Scf00801g00038' => 'pax', 'Peaxi162Scf00891g00025' => 'pax', 'PGR083G0909' => 'pgr', 'PGR119G1005' => 'pgr', 'PGR142G2236' => 'pgr', 'PGR142G3388' => 'pgr', 'PGSC0003DMG400004514' => 'stu', 'PGSC0003DMG400012635' => 'stu', 'PGSC0003DMG400015730' => 'stu', 'PGSC0003DMG400018611' => 'stu', 'PGSC0003DMG400030897' => 'stu', 'Phvul.001G254800' => 'pvu', 'Phvul.002G260100' => 'pvu', 'Phvul.003G167600' => 'pvu', 'Phvul.004G005100' => 'pvu', 'Potri.001G343600' => 'ptr', 'Potri.006G066700' => 'ptr', 'Potri.008G186000' => 'ptr', 'Potri.010G046900' => 'ptr', 'Potri.018G127900' => 'ptr', 'Pp3c20_17750' => 'ppa', 'Pp3c24_4380' => 'ppa', 'Prupe.1G245800' => 'ppe', 'Prupe.3G293400' => 'ppe', 'Prupe.7G247400' => 'ppe', 'Psat0s145g0120' => 'psa', 'Psat0s595g0040' => 'psa', 'Psat0s595g0120' => 'psa', 'Psat3g175040' => 'psa', 'Psat7g058120' => 'psa', 'PSO017G0428' => 'pso', 'PSO063G7510' => 'pso', 'PSO067G0046' => 'pso', 'PSO478G1073' => 'pso', 'PSO675G3677' => 'pso', 'PSO675G6558' => 'pso', 'PSO675G7520' => 'pso', 'PSO675G8959' => 'pso', 'QL02p074089' => 'qlo', 'QL02p089614' => 'qlo', 'QL03p057736' => 'qlo', 'RcHm_v2.0_Chr1g0364131' => 'rch', 'RcHm_v2.0_Chr2g0087801' => 'rch', 'RcHm_v2.0_Chr2g0087821' => 'rch', 'RcHm_v2.0_Chr2g0173231' => 'rch', 'RcHm_v2.0_Chr4g0433111' => 'rch', 'Rhsim03G0250300' => 'rsi', 'Rhsim08G0048400' => 'rsi', 'Rhsim10G0014800' => 'rsi', 'Rhsim12G0040100' => 'rsi', 'Rhsim12G0109700' => 'rsi', 'Sabra06G0049600' => 'sbr', 'Sabra08G0141000' => 'sbr', 'Sabra10G0021400' => 'sbr', 'Sabra16G0222900' => 'sbr', 'Sabra18G0108600' => 'sbr', 'SalBow1G0433' => 'sbo', 'SalBow1G2038' => 'sbo', 'SalBow1G5003' => 'sbo', 'SalBow7G1197' => 'sbo', 'SalBow8G3506' => 'sbo', 'Sc03g0007300' => 'sci', 'Sc11g0000950' => 'sci', 'Sc14g0008750' => 'sci', 'Sc18g0000420' => 'sci', 'Sed0006754' => 'sed', 'Sed0008741' => 'sed', 'Sed0017172' => 'sed', 'Sed0018925' => 'sed', 'Sed0023326' => 'sed', 'Sed0025909' => 'sed', 'SEGI_05333' => 'sgi', 'SEGI_10362' => 'sgi', 'SEGI_13380' => 'sgi', 'SEGI_24306' => 'sgi', 'SEGI_29077' => 'sgi', 'SEGI_29095' => 'sgi', 'SEGI_36534' => 'sgi', 'SEGI_37506' => 'sgi', 'SEGI_38321' => 'sgi', 'SGA_v2.0_scaffold307G48031' => 'sas', 'SGA_v2.0_scaffold47G17507' => 'sas', 'SGA_v2.0_scaffold63G21736' => 'sas', 'SGA_v2.0_scaffold87G27070' => 'sas', 'SHI17794' => 'shi', 'SHI28851' => 'shi', 'SMO165G0155' => 'smo', 'SMO340G0217' => 'smo', 'SMO367G1210' => 'smo', 'Solyc02g093430.3' => 'sly', 'Solyc05g013580.4' => 'sly', 'Solyc07g008030.3' => 'sly', 'Solyc12g035470.2' => 'sly', 'Sopen02g038020' => 'spe', 'Sopen05g008490' => 'spe', 'Sopen07g003910' => 'spe', 'Sopen12g015240' => 'spe', 'Sp1g11550' => 'spa', 'Sp2g16710' => 'spa', 'Sp3g00430' => 'spa', 'Sp3g26780' => 'spa', 'Sp5g22900' => 'spa', 'Sp6g29530' => 'spa', 'TAR371G0794' => 'tar', 'TAR374G0164' => 'tar', 'TAR622G0165' => 'tar', 'TAR626G0929' => 'tar', 'TAR629G2155' => 'tar', 'THA.LOC104805282' => 'tha', 'THA.LOC104805363' => 'tha', 'THA.LOC104808968' => 'tha', 'THA.LOC104821093' => 'tha', 'THA.LOC104823953' => 'tha', 'THA.LOC104825562' => 'tha', 'THA.LOC104825665' => 'tha', 'Thecc.02G261400' => 'tca', 'Thecc.04G019200' => 'tca', 'Thecc.09G130400' => 'tca', 'Thhalv10004374m.g' => 'esa', 'Thhalv10007850m.g' => 'esa', 'Thhalv10013782m.g' => 'esa', 'Thhalv10018686m.g' => 'esa', 'Thhalv10020899m.g' => 'esa', 'Thhalv10022755m.g' => 'esa', 'TPR.G23851' => 'tpr', 'TPR.G26500' => 'tpr', 'TPR.G27267' => 'tpr', 'TPR.G32001' => 'tpr', 'TPR.G6251' => 'tpr', 'TPR.G8167' => 'tpr', 'TWI12G1330' => 'twi', 'TWI18G1239' => 'twi', 'TWI34G0979' => 'twi', 'TWI36G0670' => 'twi', 'TWI36G0707' => 'twi', 'TWI56G0233' => 'twi', 'TWI75G1809' => 'twi', 'unitig_21.g20874' => 'ugi', 'unitig_26.g10343' => 'ugi', 'unitig_46.g18392' => 'ugi', 'unitig_52.g17178' => 'ugi', 'unitig_8.g2934' => 'ugi', 'vmacro01122' => 'vma', 'vmacro05875' => 'vma', 'vmacro06147' => 'vma', 'vmacro16191' => 'vma', 'vmacro18293' => 'vma', 'VMungo0251G3707' => 'vmu', 'VMungo0464G1521' => 'vmu', 'VMungo1215G0205' => 'vmu', 'VMungo1383G2484' => 'vmu', 'Zm00001eb079610' => 'zma', 'Zm00001eb135990' => 'zma', 'Zm00001eb183710' => 'zma', 'Zm00001eb246020' => 'zma' ), 'gf_id' => 'HOM05D001124', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001124' ), 'data_identifier' => 'HOM05D001124', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001124', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '548', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02520' => 'bna', 'A03p06630' => 'bna', 'A05p44460' => 'bna', 'A06p08710' => 'bna', 'A06p41090' => 'bna', 'A07p32320' => 'bna', 'A08p32520' => 'bna', 'A09p10360' => 'bna', 'A10p24080' => 'bna', 'Aa31LG11G15250' => 'aar', 'Aa31LG1G1800' => 'aar', 'Aa31LG2G5120' => 'aar', 'Aa31LG2G6070' => 'aar', 'Aa31LG5G10770' => 'aar', 'Aa31sc61G90' => 'aar', 'Actinidia01352' => 'ach', 'Actinidia05983' => 'ach', 'Actinidia08133' => 'ach', 'Actinidia15101' => 'ach', 'Actinidia26379' => 'ach', 'Actinidia35778' => 'ach', 'Actinidia36123' => 'ach', 'Actinidia37436' => 'ach', 'Actinidia38730' => 'ach', 'Ah.02g128210' => 'amhyb', 'Ah.03g132990' => 'amhyb', 'Ah.14g079410' => 'amhyb', 'AL1G24640' => 'aly', 'AL2G26680' => 'aly', 'AL3G10530' => 'aly', 'AL3G45230' => 'aly', 'AL5G15230' => 'aly', 'AL5G16960' => 'aly', 'AL6G25210' => 'aly', 'Aqoxy2G00441' => 'aox', 'Aqoxy3G01236' => 'aox', 'Aqoxy5G03746' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3RQ047' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C7GMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9C8JER' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MBL6KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YXCZ83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZANX40' => 'arhy', 'AT1G12990' => 'ath', 'AT1G67880' => 'ath', 'AT2G13290' => 'ath', 'AT3G01620' => 'ath', 'AT3G26445' => 'ath', 'AT3G27540' => 'ath', 'AT5G14480' => 'ath', 'ATR0824G026' => 'atr', 'ATR1098G019' => 'atr', 'Atru.chr11.2145' => 'acertr', 'Atru.chr2.3636' => 'acertr', 'Atru.chr2.3644' => 'acertr', 'Atru.chr6.2422' => 'acertr', 'Atru.chr7.1112' => 'acertr', 'AUR62005469' => 'cqu', 'AUR62011166' => 'cqu', 'AUR62013319' => 'cqu', 'AUR62024273' => 'cqu', 'AUR62028420' => 'cqu', 'AUR62041942' => 'cqu', 'BcaB01g04969' => 'bca', 'BcaB01g06371' => 'bca', 'BcaB02g11494' => 'bca', 'BcaB03g15382' => 'bca', 'BcaB08g36994' => 'bca', 'BcaC03g13477' => 'bca', 'BcaC03g13478' => 'bca', 'BcaC03g13480' => 'bca', 'BcaC03g13481' => 'bca', 'BcaC03g13486' => 'bca', 'BcaC04g19031' => 'bca', 'BcaC04g23085' => 'bca', 'BcaC05g25094' => 'bca', 'BcaC05g25096' => 'bca', 'BcaC05g25138' => 'bca', 'BcaC05g30416' => 'bca', 'BcaC05g30455' => 'bca', 'BcaC06g30979' => 'bca', 'BcaC06g33805' => 'bca', 'BcaC08g46021' => 'bca', 'BcaNung03154' => 'bca', 'BolC2t06623H' => 'bol', 'BolC2t06632H' => 'bol', 'BolC2t06635H' => 'bol', 'BolC2t06638H' => 'bol', 'BolC3t13266H' => 'bol', 'BolC5t29776H' => 'bol', 'BolC6t38912H' => 'bol', 'BolC7t44183H' => 'bol', 'BolC9t54123H' => 'bol', 'BolC9t59107H' => 'bol', 'BraA02t05221Z' => 'bra', 'BraA03t09996Z' => 'bra', 'BraA05t23210Z' => 'bra', 'BraA06t24068Z' => 'bra', 'BraA06t27032Z' => 'bra', 'BraA08t35176Z' => 'bra', 'BraA09t36680Z' => 'bra', 'BraA10t44471Z' => 'bra', 'C02p06760' => 'bna', 'C02p06890' => 'bna', 'C02p07010' => 'bna', 'C03p07660' => 'bna', 'C05p10300' => 'bna', 'C06p38150' => 'bna', 'C07p36650' => 'bna', 'C08p15770' => 'bna', 'C09p12300' => 'bna', 'C09p62700' => 'bna', 'C09p75040' => 'bna', 'CAN.G13.1' => 'can', 'CAN.G138.4' => 'can', 'CAN.G44.6' => 'can', 'CAN.G473.19' => 'can', 'CANSAT01G0835' => 'cansat', 'CANSAT11G0246' => 'cansat', 'CANSAT11G1766' => 'cansat', 'CANSAT64G1954' => 'cansat', 'CARHR013330' => 'chi', 'CARHR060530' => 'chi', 'CARHR075300' => 'chi', 'CARHR105120' => 'chi', 'CARHR148910' => 'chi', 'CARHR198830' => 'chi', 'Carub.0001s1275' => 'cru', 'Carub.0002s1437' => 'cru', 'Carub.0003s0044' => 'cru', 'Carub.0003s2787' => 'cru', 'Carub.0005s0597' => 'cru', 'Carub.0006s1266' => 'cru', 'Ca_06935_v3' => 'car', 'Ca_13559_v3' => 'car', 'Ca_16941_v3' => 'car', 'Ca_16960_v3' => 'car', 'Ca_17775_v3' => 'car', 'Ca_30464_v3' => 'car', 'Cc06_g08160' => 'ccan', 'Cc07_g01520' => 'ccan', 'Cc11_g15810' => 'ccan', 'CDE02G2840' => 'cde', 'CDE03G0093' => 'cde', 'CDE04G2127' => 'cde', 'CDE07G1857' => 'cde', 'CDE09G1246' => 'cde', 'Cfa003412' => 'cfa', 'Cfa007341' => 'cfa', 'Cfa009220' => 'cfa', 'Ciclev10008737m.g' => 'ccl', 'Ciclev10015565m.g' => 'ccl', 'Ciclev10031761m.g' => 'ccl', 'CiPaw.03G045300' => 'cil', 'CiPaw.03G247200' => 'cil', 'CiPaw.04G029500' => 'cil', 'CiPaw.04G174000' => 'cil', 'CiPaw.05G181200' => 'cil', 'CiPaw.06G067100' => 'cil', 'ClCG05G025800' => 'cla', 'ClCG06G011400' => 'cla', 'ClCG09G019360' => 'cla', 'COL.COLO4_04827' => 'col', 'COL.COLO4_29170' => 'col', 'COL.COLO4_35131' => 'col', 'COL.COLO4_35132' => 'col', 'Cpa.g.sc33.32' => 'cpa', 'Cpa.g.sc46.29' => 'cpa', 'Cpa.g.sc796.1' => 'cpa', 'CsaV3_1G030420' => 'csa', 'CsaV3_5G027050' => 'csa', 'CsaV3_5G031040' => 'csa', 'CsaV3_UNG023130' => 'csa', 'CSS0007726' => 'camsi', 'CSS0016433' => 'camsi', 'CSS0017656' => 'camsi', 'CSS0025364' => 'camsi', 'CSS0027582' => 'camsi', 'CSS0047288' => 'camsi', 'CSS0049950' => 'camsi', 'DCAR_003843' => 'dca', 'DCAR_007052' => 'dca', 'DCAR_020884' => 'dca', 'DCAR_021730' => 'dca', 'DCAR_024423' => 'dca', 'DCAR_026509' => 'dca', 'DCAR_031158' => 'dca', 'Dinv14728' => 'din', 'Dinv15219' => 'din', 'Dinv25728' => 'din', 'Dinv33428' => 'din', 'Dinv36489' => 'din', 'Dinv41486' => 'din', 'Duzib147G0469' => 'dzi', 'Duzib168G0060' => 'dzi', 'Duzib187G1215' => 'dzi', 'Duzib248G0692' => 'dzi', 'Duzib251G0767' => 'dzi', 'Duzib264G0446' => 'dzi', 'Duzib268G0691' => 'dzi', 'ECA232G4767' => 'eca', 'ECA233G2838' => 'eca', 'ECA234G0391' => 'eca', 'ECA234G0857' => 'eca', 'ECA236G1593' => 'eca', 'ECA238G0565' => 'eca', 'ECA246G1027' => 'eca', 'ECA246G3223' => 'eca', 'ECA246G3470' => 'eca', 'EL10Ac6g13829' => 'bvu', 'EL10Ac6g14093' => 'bvu', 'EL10Ac8g18707' => 'bvu', 'Eucgr.C01369' => 'egr', 'Eucgr.H02492' => 'egr', 'Eucgr.I01733' => 'egr', 'Eucgr.J02255' => 'egr', 'Eucgr.J02257' => 'egr', 'Eucgr.J02258' => 'egr', 'FAN02G1601' => 'fan', 'FAN03G1586' => 'fan', 'FAN03G2986' => 'fan', 'FAN05G4837' => 'fan', 'FAN06G0146' => 'fan', 'FAN07G0858' => 'fan', 'FAN09G3179' => 'fan', 'FAN10G0669' => 'fan', 'FAN12G2358' => 'fan', 'FAN14G4198' => 'fan', 'FAN14G5112' => 'fan', 'FAN17G0342' => 'fan', 'FAN19G0342' => 'fan', 'FAN19G0962' => 'fan', 'FAN19G1101' => 'fan', 'FAN19G1872' => 'fan', 'FAN22G0356' => 'fan', 'FAN23G0744' => 'fan', 'FAN23G1914' => 'fan', 'FAN26G0032' => 'fan', 'FAN28G0625' => 'fan', 'FvH4_1g02710' => 'fve', 'FvH4_1g02720' => 'fve', 'FvH4_4g25670' => 'fve', 'FvH4_6g51700' => 'fve', 'FvH4_7g20170' => 'fve', 'Glyma.05G175000' => 'gma', 'Glyma.08G132300' => 'gma', 'Glyma.11G243000' => 'gma', 'Glyma.13G158900' => 'gma', 'Glyma.17G112400' => 'gma', 'Glyma.18G014100' => 'gma', 'Glyma.19G003100' => 'gma', 'Glyma.19G056500' => 'gma', 'Gohir.A01G158900' => 'ghi', 'Gohir.A05G312600' => 'ghi', 'Gohir.A05G354900' => 'ghi', 'Gohir.A07G037200' => 'ghi', 'Gohir.A09G030000' => 'ghi', 'Gohir.A12G145200' => 'ghi', 'Gohir.D01G151500' => 'ghi', 'Gohir.D04G058300' => 'ghi', 'Gohir.D05G314100' => 'ghi', 'Gohir.D07G041400' => 'ghi', 'Gohir.D09G029700' => 'ghi', 'Gohir.D12G149700' => 'ghi', 'Gorai.001G043800' => 'gra', 'Gorai.002G187800' => 'gra', 'Gorai.006G034700' => 'gra', 'Gorai.008G161200' => 'gra', 'Gorai.009G335700' => 'gra', 'Gorai.012G065000' => 'gra', 'GSVIVG01000535001' => 'vvi', 'GSVIVG01015572001' => 'vvi', 'GSVIVG01032386001' => 'vvi', 'HanXRQChr05g0138531' => 'han', 'HanXRQChr06g0174391' => 'han', 'HanXRQChr07g0199021' => 'han', 'HanXRQChr08g0208211' => 'han', 'HanXRQChr09g0255471' => 'han', 'HanXRQChr10g0315791' => 'han', 'HanXRQChr12g0371991' => 'han', 'HanXRQChr15g0475251' => 'han', 'HanXRQChr17g0540001' => 'han', 'HanXRQChr17g0548631' => 'han', 'HanXRQChr17g0569561' => 'han', 'Haze_12256' => 'cav', 'Haze_14756' => 'cav', 'Haze_25528' => 'cav', 'Hma1.2p1_0079F.1_g041020' => 'hma', 'Hma1.2p1_0818F.1_g223260' => 'hma', 'Hma1.2p1_1747F.1_g300530' => 'hma', 'HPP92_004607' => 'vpl', 'HPP92_004608' => 'vpl', 'HPP92_006181' => 'vpl', 'HPP92_012192' => 'vpl', 'HPP92_015680' => 'vpl', 'HPP92_020249' => 'vpl', 'HPP92_021376' => 'vpl', 'HPP92_024275' => 'vpl', 'Hund06031' => 'sun', 'Hund25391' => 'sun', 'Lalb_Chr07g0185371' => 'lal', 'Lalb_Chr07g0185381' => 'lal', 'Lalb_Chr12g0204011' => 'lal', 'Lalb_Chr13g0301671' => 'lal', 'Lalb_Chr14g0362851' => 'lal', 'Lalb_Chr24g0403581' => 'lal', 'Lj1g0000233' => 'lja', 'Lj2g0018120' => 'lja', 'Lj3C621T0' => 'lonja', 'Lj3P1059T14' => 'lonja', 'Lj3P611T9' => 'lonja', 'Lj3P614T13' => 'lonja', 'Lj3P615T5' => 'lonja', 'Lj4g0012315' => 'lja', 'Lj4g0026182' => 'lja', 'Lj6P813T16' => 'lonja', 'Lj7C427T7' => 'lonja', 'Lj7C427T8' => 'lonja', 'Lj7P600T41' => 'lonja', 'Lju41C42G17' => 'lonja', 'Lsat_1_v5_gn_0_47300' => 'lsa', 'Lsat_1_v5_gn_2_91280' => 'lsa', 'Lsat_1_v5_gn_3_30561' => 'lsa', 'Lsat_1_v5_gn_4_184321' => 'lsa', 'Lsat_1_v5_gn_4_4041' => 'lsa', 'Lsat_1_v5_gn_5_92000' => 'lsa', 'Lsat_1_v5_gn_8_152940' => 'lsa', 'Lsat_1_v5_gn_8_62401' => 'lsa', 'Manes.06G055900' => 'mes', 'Manes.12G022200' => 'mes', 'Manes.13G023300' => 'mes', 'Manes.14G115000' => 'mes', 'Manes.15G151700' => 'mes', 'Manes.17G111300' => 'mes', 'Mapoly0226s0009' => 'mpo', 'MBI02_g25363_MAGBIO' => 'mbi', 'MBI06_g00027_MAGBIO' => 'mbi', 'MBI10_g13034_MAGBIO' => 'mbi', 'MD09G1023400' => 'mdo', 'MD13G1100100' => 'mdo', 'MD15G1169200' => 'mdo', 'MD16G1101100' => 'mdo', 'MD17G1022900' => 'mdo', 'Medtr3g096150' => 'mtr', 'Medtr4g115070' => 'mtr', 'Medtr7g033325' => 'mtr', 'Medtr8g089840' => 'mtr', 'MELO3C010319.2' => 'cme', 'MELO3C011944.2' => 'cme', 'MELO3C021589.2' => 'cme', 'Migut.E00207' => 'egut', 'Migut.H00067' => 'egut', 'Migut.K00433' => 'egut', 'Migut.K00606' => 'egut', 'Migut.K01410' => 'egut', 'MSTRG.13347' => 'ama', 'MSTRG.24045' => 'ama', 'MSTRG.2428' => 'ama', 'MSTRG.26410' => 'ama', 'MSTRG.3139' => 'ama', 'MSTRG.3286' => 'ama', 'MSTRG.563' => 'ama', 'MSTRG.7941' => 'ama', 'Nitab4.5_0000028g0060' => 'nta', 'Nitab4.5_0000065g0260' => 'nta', 'Nitab4.5_0000112g0060' => 'nta', 'Nitab4.5_0000489g0120' => 'nta', 'Nitab4.5_0001776g0050' => 'nta', 'Nitab4.5_0001854g0010' => 'nta', 'Nitab4.5_0001860g0020' => 'nta', 'Nitab4.5_0004352g0010' => 'nta', 'Nitab4.5_0008716g0020' => 'nta', 'Nitab4.5_0008922g0010' => 'nta', 'Nn3g16693' => 'nnu', 'Nn4g22596' => 'nnu', 'Nn7g37639' => 'nnu', 'Oeu001701.1' => 'oeu', 'Oeu018149.1' => 'oeu', 'Oeu026220.1' => 'oeu', 'Oeu038635.1' => 'oeu', 'Oeu049176.1' => 'oeu', 'Oeu056706.1' => 'oeu', 'Oeu056937.1' => 'oeu', 'Oeu057540.1' => 'oeu', 'Os02g0594900' => 'osa', 'Os02g0595100' => 'osa', 'Os04g0477500' => 'osa', 'Os12g0611900' => 'osa', 'Peaxi162Scf00076g00020' => 'pax', 'Peaxi162Scf00128g00217' => 'pax', 'Peaxi162Scf00129g01640' => 'pax', 'Peaxi162Scf00669g00007' => 'pax', 'Peaxi162Scf00700g00421' => 'pax', 'Peaxi162Scf00801g00038' => 'pax', 'Peaxi162Scf00891g00025' => 'pax', 'PGR083G0909' => 'pgr', 'PGR119G1005' => 'pgr', 'PGR142G2236' => 'pgr', 'PGR142G3388' => 'pgr', 'PGSC0003DMG400004514' => 'stu', 'PGSC0003DMG400012635' => 'stu', 'PGSC0003DMG400015730' => 'stu', 'PGSC0003DMG400018611' => 'stu', 'PGSC0003DMG400030897' => 'stu', 'Phvul.001G254800' => 'pvu', 'Phvul.002G260100' => 'pvu', 'Phvul.003G167600' => 'pvu', 'Phvul.004G005100' => 'pvu', 'Potri.001G343600' => 'ptr', 'Potri.006G066700' => 'ptr', 'Potri.008G186000' => 'ptr', 'Potri.010G046900' => 'ptr', 'Potri.018G127900' => 'ptr', 'Pp3c20_17750' => 'ppa', 'Pp3c24_4380' => 'ppa', 'Prupe.1G245800' => 'ppe', 'Prupe.3G293400' => 'ppe', 'Prupe.7G247400' => 'ppe', 'Psat0s145g0120' => 'psa', 'Psat0s595g0040' => 'psa', 'Psat0s595g0120' => 'psa', 'Psat3g175040' => 'psa', 'Psat7g058120' => 'psa', 'PSO017G0428' => 'pso', 'PSO063G7510' => 'pso', 'PSO067G0046' => 'pso', 'PSO478G1073' => 'pso', 'PSO675G3677' => 'pso', 'PSO675G6558' => 'pso', 'PSO675G7520' => 'pso', 'PSO675G8959' => 'pso', 'QL02p074089' => 'qlo', 'QL02p089614' => 'qlo', 'QL03p057736' => 'qlo', 'RcHm_v2.0_Chr1g0364131' => 'rch', 'RcHm_v2.0_Chr2g0087801' => 'rch', 'RcHm_v2.0_Chr2g0087821' => 'rch', 'RcHm_v2.0_Chr2g0173231' => 'rch', 'RcHm_v2.0_Chr4g0433111' => 'rch', 'Rhsim03G0250300' => 'rsi', 'Rhsim08G0048400' => 'rsi', 'Rhsim10G0014800' => 'rsi', 'Rhsim12G0040100' => 'rsi', 'Rhsim12G0109700' => 'rsi', 'Sabra06G0049600' => 'sbr', 'Sabra08G0141000' => 'sbr', 'Sabra10G0021400' => 'sbr', 'Sabra16G0222900' => 'sbr', 'Sabra18G0108600' => 'sbr', 'SalBow1G0433' => 'sbo', 'SalBow1G2038' => 'sbo', 'SalBow1G5003' => 'sbo', 'SalBow7G1197' => 'sbo', 'SalBow8G3506' => 'sbo', 'Sc03g0007300' => 'sci', 'Sc11g0000950' => 'sci', 'Sc14g0008750' => 'sci', 'Sc18g0000420' => 'sci', 'Sed0006754' => 'sed', 'Sed0008741' => 'sed', 'Sed0017172' => 'sed', 'Sed0018925' => 'sed', 'Sed0023326' => 'sed', 'Sed0025909' => 'sed', 'SEGI_05333' => 'sgi', 'SEGI_10362' => 'sgi', 'SEGI_13380' => 'sgi', 'SEGI_24306' => 'sgi', 'SEGI_29077' => 'sgi', 'SEGI_29095' => 'sgi', 'SEGI_36534' => 'sgi', 'SEGI_37506' => 'sgi', 'SEGI_38321' => 'sgi', 'SGA_v2.0_scaffold307G48031' => 'sas', 'SGA_v2.0_scaffold47G17507' => 'sas', 'SGA_v2.0_scaffold63G21736' => 'sas', 'SGA_v2.0_scaffold87G27070' => 'sas', 'SHI17794' => 'shi', 'SHI28851' => 'shi', 'SMO165G0155' => 'smo', 'SMO340G0217' => 'smo', 'SMO367G1210' => 'smo', 'Solyc02g093430.3' => 'sly', 'Solyc05g013580.4' => 'sly', 'Solyc07g008030.3' => 'sly', 'Solyc12g035470.2' => 'sly', 'Sopen02g038020' => 'spe', 'Sopen05g008490' => 'spe', 'Sopen07g003910' => 'spe', 'Sopen12g015240' => 'spe', 'Sp1g11550' => 'spa', 'Sp2g16710' => 'spa', 'Sp3g00430' => 'spa', 'Sp3g26780' => 'spa', 'Sp5g22900' => 'spa', 'Sp6g29530' => 'spa', 'TAR371G0794' => 'tar', 'TAR374G0164' => 'tar', 'TAR622G0165' => 'tar', 'TAR626G0929' => 'tar', 'TAR629G2155' => 'tar', 'THA.LOC104805282' => 'tha', 'THA.LOC104805363' => 'tha', 'THA.LOC104808968' => 'tha', 'THA.LOC104821093' => 'tha', 'THA.LOC104823953' => 'tha', 'THA.LOC104825562' => 'tha', 'THA.LOC104825665' => 'tha', 'Thecc.02G261400' => 'tca', 'Thecc.04G019200' => 'tca', 'Thecc.09G130400' => 'tca', 'Thhalv10004374m.g' => 'esa', 'Thhalv10007850m.g' => 'esa', 'Thhalv10013782m.g' => 'esa', 'Thhalv10018686m.g' => 'esa', 'Thhalv10020899m.g' => 'esa', 'Thhalv10022755m.g' => 'esa', 'TPR.G23851' => 'tpr', 'TPR.G26500' => 'tpr', 'TPR.G27267' => 'tpr', 'TPR.G32001' => 'tpr', 'TPR.G6251' => 'tpr', 'TPR.G8167' => 'tpr', 'TWI12G1330' => 'twi', 'TWI18G1239' => 'twi', 'TWI34G0979' => 'twi', 'TWI36G0670' => 'twi', 'TWI36G0707' => 'twi', 'TWI56G0233' => 'twi', 'TWI75G1809' => 'twi', 'unitig_21.g20874' => 'ugi', 'unitig_26.g10343' => 'ugi', 'unitig_46.g18392' => 'ugi', 'unitig_52.g17178' => 'ugi', 'unitig_8.g2934' => 'ugi', 'vmacro01122' => 'vma', 'vmacro05875' => 'vma', 'vmacro06147' => 'vma', 'vmacro16191' => 'vma', 'vmacro18293' => 'vma', 'VMungo0251G3707' => 'vmu', 'VMungo0464G1521' => 'vmu', 'VMungo1215G0205' => 'vmu', 'VMungo1383G2484' => 'vmu', 'Zm00001eb079610' => 'zma', 'Zm00001eb135990' => 'zma', 'Zm00001eb183710' => 'zma', 'Zm00001eb246020' => 'zma' ) $gf_id = 'HOM05D001124' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001124' ) $data_identifier = 'HOM05D001124' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 6, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 7, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 21, 'bol' => (int) 10, 'bra' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 6, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 9, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 21, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 8, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 10, 'lsa' => (int) 8, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 8, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 9, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb246020' $species_info = array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ) $local_species = 'cav' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001124', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '548', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02520' => 'bna', 'A03p06630' => 'bna', 'A05p44460' => 'bna', 'A06p08710' => 'bna', 'A06p41090' => 'bna', 'A07p32320' => 'bna', 'A08p32520' => 'bna', 'A09p10360' => 'bna', 'A10p24080' => 'bna', 'Aa31LG11G15250' => 'aar', 'Aa31LG1G1800' => 'aar', 'Aa31LG2G5120' => 'aar', 'Aa31LG2G6070' => 'aar', 'Aa31LG5G10770' => 'aar', 'Aa31sc61G90' => 'aar', 'Actinidia01352' => 'ach', 'Actinidia05983' => 'ach', 'Actinidia08133' => 'ach', 'Actinidia15101' => 'ach', 'Actinidia26379' => 'ach', 'Actinidia35778' => 'ach', 'Actinidia36123' => 'ach', 'Actinidia37436' => 'ach', 'Actinidia38730' => 'ach', 'Ah.02g128210' => 'amhyb', 'Ah.03g132990' => 'amhyb', 'Ah.14g079410' => 'amhyb', 'AL1G24640' => 'aly', 'AL2G26680' => 'aly', 'AL3G10530' => 'aly', 'AL3G45230' => 'aly', 'AL5G15230' => 'aly', 'AL5G16960' => 'aly', 'AL6G25210' => 'aly', 'Aqoxy2G00441' => 'aox', 'Aqoxy3G01236' => 'aox', 'Aqoxy5G03746' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3RQ047' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C7GMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9C8JER' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MBL6KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YXCZ83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZANX40' => 'arhy', 'AT1G12990' => 'ath', 'AT1G67880' => 'ath', 'AT2G13290' => 'ath', 'AT3G01620' => 'ath', 'AT3G26445' => 'ath', 'AT3G27540' => 'ath', 'AT5G14480' => 'ath', 'ATR0824G026' => 'atr', 'ATR1098G019' => 'atr', 'Atru.chr11.2145' => 'acertr', 'Atru.chr2.3636' => 'acertr', 'Atru.chr2.3644' => 'acertr', 'Atru.chr6.2422' => 'acertr', 'Atru.chr7.1112' => 'acertr', 'AUR62005469' => 'cqu', 'AUR62011166' => 'cqu', 'AUR62013319' => 'cqu', 'AUR62024273' => 'cqu', 'AUR62028420' => 'cqu', 'AUR62041942' => 'cqu', 'BcaB01g04969' => 'bca', 'BcaB01g06371' => 'bca', 'BcaB02g11494' => 'bca', 'BcaB03g15382' => 'bca', 'BcaB08g36994' => 'bca', 'BcaC03g13477' => 'bca', 'BcaC03g13478' => 'bca', 'BcaC03g13480' => 'bca', 'BcaC03g13481' => 'bca', 'BcaC03g13486' => 'bca', 'BcaC04g19031' => 'bca', 'BcaC04g23085' => 'bca', 'BcaC05g25094' => 'bca', 'BcaC05g25096' => 'bca', 'BcaC05g25138' => 'bca', 'BcaC05g30416' => 'bca', 'BcaC05g30455' => 'bca', 'BcaC06g30979' => 'bca', 'BcaC06g33805' => 'bca', 'BcaC08g46021' => 'bca', 'BcaNung03154' => 'bca', 'BolC2t06623H' => 'bol', 'BolC2t06632H' => 'bol', 'BolC2t06635H' => 'bol', 'BolC2t06638H' => 'bol', 'BolC3t13266H' => 'bol', 'BolC5t29776H' => 'bol', 'BolC6t38912H' => 'bol', 'BolC7t44183H' => 'bol', 'BolC9t54123H' => 'bol', 'BolC9t59107H' => 'bol', 'BraA02t05221Z' => 'bra', 'BraA03t09996Z' => 'bra', 'BraA05t23210Z' => 'bra', 'BraA06t24068Z' => 'bra', 'BraA06t27032Z' => 'bra', 'BraA08t35176Z' => 'bra', 'BraA09t36680Z' => 'bra', 'BraA10t44471Z' => 'bra', 'C02p06760' => 'bna', 'C02p06890' => 'bna', 'C02p07010' => 'bna', 'C03p07660' => 'bna', 'C05p10300' => 'bna', 'C06p38150' => 'bna', 'C07p36650' => 'bna', 'C08p15770' => 'bna', 'C09p12300' => 'bna', 'C09p62700' => 'bna', 'C09p75040' => 'bna', 'CAN.G13.1' => 'can', 'CAN.G138.4' => 'can', 'CAN.G44.6' => 'can', 'CAN.G473.19' => 'can', 'CANSAT01G0835' => 'cansat', 'CANSAT11G0246' => 'cansat', 'CANSAT11G1766' => 'cansat', 'CANSAT64G1954' => 'cansat', 'CARHR013330' => 'chi', 'CARHR060530' => 'chi', 'CARHR075300' => 'chi', 'CARHR105120' => 'chi', 'CARHR148910' => 'chi', 'CARHR198830' => 'chi', 'Carub.0001s1275' => 'cru', 'Carub.0002s1437' => 'cru', 'Carub.0003s0044' => 'cru', 'Carub.0003s2787' => 'cru', 'Carub.0005s0597' => 'cru', 'Carub.0006s1266' => 'cru', 'Ca_06935_v3' => 'car', 'Ca_13559_v3' => 'car', 'Ca_16941_v3' => 'car', 'Ca_16960_v3' => 'car', 'Ca_17775_v3' => 'car', 'Ca_30464_v3' => 'car', 'Cc06_g08160' => 'ccan', 'Cc07_g01520' => 'ccan', 'Cc11_g15810' => 'ccan', 'CDE02G2840' => 'cde', 'CDE03G0093' => 'cde', 'CDE04G2127' => 'cde', 'CDE07G1857' => 'cde', 'CDE09G1246' => 'cde', 'Cfa003412' => 'cfa', 'Cfa007341' => 'cfa', 'Cfa009220' => 'cfa', 'Ciclev10008737m.g' => 'ccl', 'Ciclev10015565m.g' => 'ccl', 'Ciclev10031761m.g' => 'ccl', 'CiPaw.03G045300' => 'cil', 'CiPaw.03G247200' => 'cil', 'CiPaw.04G029500' => 'cil', 'CiPaw.04G174000' => 'cil', 'CiPaw.05G181200' => 'cil', 'CiPaw.06G067100' => 'cil', 'ClCG05G025800' => 'cla', 'ClCG06G011400' => 'cla', 'ClCG09G019360' => 'cla', 'COL.COLO4_04827' => 'col', 'COL.COLO4_29170' => 'col', 'COL.COLO4_35131' => 'col', 'COL.COLO4_35132' => 'col', 'Cpa.g.sc33.32' => 'cpa', 'Cpa.g.sc46.29' => 'cpa', 'Cpa.g.sc796.1' => 'cpa', 'CsaV3_1G030420' => 'csa', 'CsaV3_5G027050' => 'csa', 'CsaV3_5G031040' => 'csa', 'CsaV3_UNG023130' => 'csa', 'CSS0007726' => 'camsi', 'CSS0016433' => 'camsi', 'CSS0017656' => 'camsi', 'CSS0025364' => 'camsi', 'CSS0027582' => 'camsi', 'CSS0047288' => 'camsi', 'CSS0049950' => 'camsi', 'DCAR_003843' => 'dca', 'DCAR_007052' => 'dca', 'DCAR_020884' => 'dca', 'DCAR_021730' => 'dca', 'DCAR_024423' => 'dca', 'DCAR_026509' => 'dca', 'DCAR_031158' => 'dca', 'Dinv14728' => 'din', 'Dinv15219' => 'din', 'Dinv25728' => 'din', 'Dinv33428' => 'din', 'Dinv36489' => 'din', 'Dinv41486' => 'din', 'Duzib147G0469' => 'dzi', 'Duzib168G0060' => 'dzi', 'Duzib187G1215' => 'dzi', 'Duzib248G0692' => 'dzi', 'Duzib251G0767' => 'dzi', 'Duzib264G0446' => 'dzi', 'Duzib268G0691' => 'dzi', 'ECA232G4767' => 'eca', 'ECA233G2838' => 'eca', 'ECA234G0391' => 'eca', 'ECA234G0857' => 'eca', 'ECA236G1593' => 'eca', 'ECA238G0565' => 'eca', 'ECA246G1027' => 'eca', 'ECA246G3223' => 'eca', 'ECA246G3470' => 'eca', 'EL10Ac6g13829' => 'bvu', 'EL10Ac6g14093' => 'bvu', 'EL10Ac8g18707' => 'bvu', 'Eucgr.C01369' => 'egr', 'Eucgr.H02492' => 'egr', 'Eucgr.I01733' => 'egr', 'Eucgr.J02255' => 'egr', 'Eucgr.J02257' => 'egr', 'Eucgr.J02258' => 'egr', 'FAN02G1601' => 'fan', 'FAN03G1586' => 'fan', 'FAN03G2986' => 'fan', 'FAN05G4837' => 'fan', 'FAN06G0146' => 'fan', 'FAN07G0858' => 'fan', 'FAN09G3179' => 'fan', 'FAN10G0669' => 'fan', 'FAN12G2358' => 'fan', 'FAN14G4198' => 'fan', 'FAN14G5112' => 'fan', 'FAN17G0342' => 'fan', 'FAN19G0342' => 'fan', 'FAN19G0962' => 'fan', 'FAN19G1101' => 'fan', 'FAN19G1872' => 'fan', 'FAN22G0356' => 'fan', 'FAN23G0744' => 'fan', 'FAN23G1914' => 'fan', 'FAN26G0032' => 'fan', 'FAN28G0625' => 'fan', 'FvH4_1g02710' => 'fve', 'FvH4_1g02720' => 'fve', 'FvH4_4g25670' => 'fve', 'FvH4_6g51700' => 'fve', 'FvH4_7g20170' => 'fve', 'Glyma.05G175000' => 'gma', 'Glyma.08G132300' => 'gma', 'Glyma.11G243000' => 'gma', 'Glyma.13G158900' => 'gma', 'Glyma.17G112400' => 'gma', 'Glyma.18G014100' => 'gma', 'Glyma.19G003100' => 'gma', 'Glyma.19G056500' => 'gma', 'Gohir.A01G158900' => 'ghi', 'Gohir.A05G312600' => 'ghi', 'Gohir.A05G354900' => 'ghi', 'Gohir.A07G037200' => 'ghi', 'Gohir.A09G030000' => 'ghi', 'Gohir.A12G145200' => 'ghi', 'Gohir.D01G151500' => 'ghi', 'Gohir.D04G058300' => 'ghi', 'Gohir.D05G314100' => 'ghi', 'Gohir.D07G041400' => 'ghi', 'Gohir.D09G029700' => 'ghi', 'Gohir.D12G149700' => 'ghi', 'Gorai.001G043800' => 'gra', 'Gorai.002G187800' => 'gra', 'Gorai.006G034700' => 'gra', 'Gorai.008G161200' => 'gra', 'Gorai.009G335700' => 'gra', 'Gorai.012G065000' => 'gra', 'GSVIVG01000535001' => 'vvi', 'GSVIVG01015572001' => 'vvi', 'GSVIVG01032386001' => 'vvi', 'HanXRQChr05g0138531' => 'han', 'HanXRQChr06g0174391' => 'han', 'HanXRQChr07g0199021' => 'han', 'HanXRQChr08g0208211' => 'han', 'HanXRQChr09g0255471' => 'han', 'HanXRQChr10g0315791' => 'han', 'HanXRQChr12g0371991' => 'han', 'HanXRQChr15g0475251' => 'han', 'HanXRQChr17g0540001' => 'han', 'HanXRQChr17g0548631' => 'han', 'HanXRQChr17g0569561' => 'han', 'Haze_12256' => 'cav', 'Haze_14756' => 'cav', 'Haze_25528' => 'cav', 'Hma1.2p1_0079F.1_g041020' => 'hma', 'Hma1.2p1_0818F.1_g223260' => 'hma', 'Hma1.2p1_1747F.1_g300530' => 'hma', 'HPP92_004607' => 'vpl', 'HPP92_004608' => 'vpl', 'HPP92_006181' => 'vpl', 'HPP92_012192' => 'vpl', 'HPP92_015680' => 'vpl', 'HPP92_020249' => 'vpl', 'HPP92_021376' => 'vpl', 'HPP92_024275' => 'vpl', 'Hund06031' => 'sun', 'Hund25391' => 'sun', 'Lalb_Chr07g0185371' => 'lal', 'Lalb_Chr07g0185381' => 'lal', 'Lalb_Chr12g0204011' => 'lal', 'Lalb_Chr13g0301671' => 'lal', 'Lalb_Chr14g0362851' => 'lal', 'Lalb_Chr24g0403581' => 'lal', 'Lj1g0000233' => 'lja', 'Lj2g0018120' => 'lja', 'Lj3C621T0' => 'lonja', 'Lj3P1059T14' => 'lonja', 'Lj3P611T9' => 'lonja', 'Lj3P614T13' => 'lonja', 'Lj3P615T5' => 'lonja', 'Lj4g0012315' => 'lja', 'Lj4g0026182' => 'lja', 'Lj6P813T16' => 'lonja', 'Lj7C427T7' => 'lonja', 'Lj7C427T8' => 'lonja', 'Lj7P600T41' => 'lonja', 'Lju41C42G17' => 'lonja', 'Lsat_1_v5_gn_0_47300' => 'lsa', 'Lsat_1_v5_gn_2_91280' => 'lsa', 'Lsat_1_v5_gn_3_30561' => 'lsa', 'Lsat_1_v5_gn_4_184321' => 'lsa', 'Lsat_1_v5_gn_4_4041' => 'lsa', 'Lsat_1_v5_gn_5_92000' => 'lsa', 'Lsat_1_v5_gn_8_152940' => 'lsa', 'Lsat_1_v5_gn_8_62401' => 'lsa', 'Manes.06G055900' => 'mes', 'Manes.12G022200' => 'mes', 'Manes.13G023300' => 'mes', 'Manes.14G115000' => 'mes', 'Manes.15G151700' => 'mes', 'Manes.17G111300' => 'mes', 'Mapoly0226s0009' => 'mpo', 'MBI02_g25363_MAGBIO' => 'mbi', 'MBI06_g00027_MAGBIO' => 'mbi', 'MBI10_g13034_MAGBIO' => 'mbi', 'MD09G1023400' => 'mdo', 'MD13G1100100' => 'mdo', 'MD15G1169200' => 'mdo', 'MD16G1101100' => 'mdo', 'MD17G1022900' => 'mdo', 'Medtr3g096150' => 'mtr', 'Medtr4g115070' => 'mtr', 'Medtr7g033325' => 'mtr', 'Medtr8g089840' => 'mtr', 'MELO3C010319.2' => 'cme', 'MELO3C011944.2' => 'cme', 'MELO3C021589.2' => 'cme', 'Migut.E00207' => 'egut', 'Migut.H00067' => 'egut', 'Migut.K00433' => 'egut', 'Migut.K00606' => 'egut', 'Migut.K01410' => 'egut', 'MSTRG.13347' => 'ama', 'MSTRG.24045' => 'ama', 'MSTRG.2428' => 'ama', 'MSTRG.26410' => 'ama', 'MSTRG.3139' => 'ama', 'MSTRG.3286' => 'ama', 'MSTRG.563' => 'ama', 'MSTRG.7941' => 'ama', 'Nitab4.5_0000028g0060' => 'nta', 'Nitab4.5_0000065g0260' => 'nta', 'Nitab4.5_0000112g0060' => 'nta', 'Nitab4.5_0000489g0120' => 'nta', 'Nitab4.5_0001776g0050' => 'nta', 'Nitab4.5_0001854g0010' => 'nta', 'Nitab4.5_0001860g0020' => 'nta', 'Nitab4.5_0004352g0010' => 'nta', 'Nitab4.5_0008716g0020' => 'nta', 'Nitab4.5_0008922g0010' => 'nta', 'Nn3g16693' => 'nnu', 'Nn4g22596' => 'nnu', 'Nn7g37639' => 'nnu', 'Oeu001701.1' => 'oeu', 'Oeu018149.1' => 'oeu', 'Oeu026220.1' => 'oeu', 'Oeu038635.1' => 'oeu', 'Oeu049176.1' => 'oeu', 'Oeu056706.1' => 'oeu', 'Oeu056937.1' => 'oeu', 'Oeu057540.1' => 'oeu', 'Os02g0594900' => 'osa', 'Os02g0595100' => 'osa', 'Os04g0477500' => 'osa', 'Os12g0611900' => 'osa', 'Peaxi162Scf00076g00020' => 'pax', 'Peaxi162Scf00128g00217' => 'pax', 'Peaxi162Scf00129g01640' => 'pax', 'Peaxi162Scf00669g00007' => 'pax', 'Peaxi162Scf00700g00421' => 'pax', 'Peaxi162Scf00801g00038' => 'pax', 'Peaxi162Scf00891g00025' => 'pax', 'PGR083G0909' => 'pgr', 'PGR119G1005' => 'pgr', 'PGR142G2236' => 'pgr', 'PGR142G3388' => 'pgr', 'PGSC0003DMG400004514' => 'stu', 'PGSC0003DMG400012635' => 'stu', 'PGSC0003DMG400015730' => 'stu', 'PGSC0003DMG400018611' => 'stu', 'PGSC0003DMG400030897' => 'stu', 'Phvul.001G254800' => 'pvu', 'Phvul.002G260100' => 'pvu', 'Phvul.003G167600' => 'pvu', 'Phvul.004G005100' => 'pvu', 'Potri.001G343600' => 'ptr', 'Potri.006G066700' => 'ptr', 'Potri.008G186000' => 'ptr', 'Potri.010G046900' => 'ptr', 'Potri.018G127900' => 'ptr', 'Pp3c20_17750' => 'ppa', 'Pp3c24_4380' => 'ppa', 'Prupe.1G245800' => 'ppe', 'Prupe.3G293400' => 'ppe', 'Prupe.7G247400' => 'ppe', 'Psat0s145g0120' => 'psa', 'Psat0s595g0040' => 'psa', 'Psat0s595g0120' => 'psa', 'Psat3g175040' => 'psa', 'Psat7g058120' => 'psa', 'PSO017G0428' => 'pso', 'PSO063G7510' => 'pso', 'PSO067G0046' => 'pso', 'PSO478G1073' => 'pso', 'PSO675G3677' => 'pso', 'PSO675G6558' => 'pso', 'PSO675G7520' => 'pso', 'PSO675G8959' => 'pso', 'QL02p074089' => 'qlo', 'QL02p089614' => 'qlo', 'QL03p057736' => 'qlo', 'RcHm_v2.0_Chr1g0364131' => 'rch', 'RcHm_v2.0_Chr2g0087801' => 'rch', 'RcHm_v2.0_Chr2g0087821' => 'rch', 'RcHm_v2.0_Chr2g0173231' => 'rch', 'RcHm_v2.0_Chr4g0433111' => 'rch', 'Rhsim03G0250300' => 'rsi', 'Rhsim08G0048400' => 'rsi', 'Rhsim10G0014800' => 'rsi', 'Rhsim12G0040100' => 'rsi', 'Rhsim12G0109700' => 'rsi', 'Sabra06G0049600' => 'sbr', 'Sabra08G0141000' => 'sbr', 'Sabra10G0021400' => 'sbr', 'Sabra16G0222900' => 'sbr', 'Sabra18G0108600' => 'sbr', 'SalBow1G0433' => 'sbo', 'SalBow1G2038' => 'sbo', 'SalBow1G5003' => 'sbo', 'SalBow7G1197' => 'sbo', 'SalBow8G3506' => 'sbo', 'Sc03g0007300' => 'sci', 'Sc11g0000950' => 'sci', 'Sc14g0008750' => 'sci', 'Sc18g0000420' => 'sci', 'Sed0006754' => 'sed', 'Sed0008741' => 'sed', 'Sed0017172' => 'sed', 'Sed0018925' => 'sed', 'Sed0023326' => 'sed', 'Sed0025909' => 'sed', 'SEGI_05333' => 'sgi', 'SEGI_10362' => 'sgi', 'SEGI_13380' => 'sgi', 'SEGI_24306' => 'sgi', 'SEGI_29077' => 'sgi', 'SEGI_29095' => 'sgi', 'SEGI_36534' => 'sgi', 'SEGI_37506' => 'sgi', 'SEGI_38321' => 'sgi', 'SGA_v2.0_scaffold307G48031' => 'sas', 'SGA_v2.0_scaffold47G17507' => 'sas', 'SGA_v2.0_scaffold63G21736' => 'sas', 'SGA_v2.0_scaffold87G27070' => 'sas', 'SHI17794' => 'shi', 'SHI28851' => 'shi', 'SMO165G0155' => 'smo', 'SMO340G0217' => 'smo', 'SMO367G1210' => 'smo', 'Solyc02g093430.3' => 'sly', 'Solyc05g013580.4' => 'sly', 'Solyc07g008030.3' => 'sly', 'Solyc12g035470.2' => 'sly', 'Sopen02g038020' => 'spe', 'Sopen05g008490' => 'spe', 'Sopen07g003910' => 'spe', 'Sopen12g015240' => 'spe', 'Sp1g11550' => 'spa', 'Sp2g16710' => 'spa', 'Sp3g00430' => 'spa', 'Sp3g26780' => 'spa', 'Sp5g22900' => 'spa', 'Sp6g29530' => 'spa', 'TAR371G0794' => 'tar', 'TAR374G0164' => 'tar', 'TAR622G0165' => 'tar', 'TAR626G0929' => 'tar', 'TAR629G2155' => 'tar', 'THA.LOC104805282' => 'tha', 'THA.LOC104805363' => 'tha', 'THA.LOC104808968' => 'tha', 'THA.LOC104821093' => 'tha', 'THA.LOC104823953' => 'tha', 'THA.LOC104825562' => 'tha', 'THA.LOC104825665' => 'tha', 'Thecc.02G261400' => 'tca', 'Thecc.04G019200' => 'tca', 'Thecc.09G130400' => 'tca', 'Thhalv10004374m.g' => 'esa', 'Thhalv10007850m.g' => 'esa', 'Thhalv10013782m.g' => 'esa', 'Thhalv10018686m.g' => 'esa', 'Thhalv10020899m.g' => 'esa', 'Thhalv10022755m.g' => 'esa', 'TPR.G23851' => 'tpr', 'TPR.G26500' => 'tpr', 'TPR.G27267' => 'tpr', 'TPR.G32001' => 'tpr', 'TPR.G6251' => 'tpr', 'TPR.G8167' => 'tpr', 'TWI12G1330' => 'twi', 'TWI18G1239' => 'twi', 'TWI34G0979' => 'twi', 'TWI36G0670' => 'twi', 'TWI36G0707' => 'twi', 'TWI56G0233' => 'twi', 'TWI75G1809' => 'twi', 'unitig_21.g20874' => 'ugi', 'unitig_26.g10343' => 'ugi', 'unitig_46.g18392' => 'ugi', 'unitig_52.g17178' => 'ugi', 'unitig_8.g2934' => 'ugi', 'vmacro01122' => 'vma', 'vmacro05875' => 'vma', 'vmacro06147' => 'vma', 'vmacro16191' => 'vma', 'vmacro18293' => 'vma', 'VMungo0251G3707' => 'vmu', 'VMungo0464G1521' => 'vmu', 'VMungo1215G0205' => 'vmu', 'VMungo1383G2484' => 'vmu', 'Zm00001eb079610' => 'zma', 'Zm00001eb135990' => 'zma', 'Zm00001eb183710' => 'zma', 'Zm00001eb246020' => 'zma' ), 'gf_id' => 'HOM05D001124', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001124' ), 'data_identifier' => 'HOM05D001124', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001124', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '548', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02520' => 'bna', 'A03p06630' => 'bna', 'A05p44460' => 'bna', 'A06p08710' => 'bna', 'A06p41090' => 'bna', 'A07p32320' => 'bna', 'A08p32520' => 'bna', 'A09p10360' => 'bna', 'A10p24080' => 'bna', 'Aa31LG11G15250' => 'aar', 'Aa31LG1G1800' => 'aar', 'Aa31LG2G5120' => 'aar', 'Aa31LG2G6070' => 'aar', 'Aa31LG5G10770' => 'aar', 'Aa31sc61G90' => 'aar', 'Actinidia01352' => 'ach', 'Actinidia05983' => 'ach', 'Actinidia08133' => 'ach', 'Actinidia15101' => 'ach', 'Actinidia26379' => 'ach', 'Actinidia35778' => 'ach', 'Actinidia36123' => 'ach', 'Actinidia37436' => 'ach', 'Actinidia38730' => 'ach', 'Ah.02g128210' => 'amhyb', 'Ah.03g132990' => 'amhyb', 'Ah.14g079410' => 'amhyb', 'AL1G24640' => 'aly', 'AL2G26680' => 'aly', 'AL3G10530' => 'aly', 'AL3G45230' => 'aly', 'AL5G15230' => 'aly', 'AL5G16960' => 'aly', 'AL6G25210' => 'aly', 'Aqoxy2G00441' => 'aox', 'Aqoxy3G01236' => 'aox', 'Aqoxy5G03746' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3RQ047' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C7GMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9C8JER' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MBL6KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YXCZ83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZANX40' => 'arhy', 'AT1G12990' => 'ath', 'AT1G67880' => 'ath', 'AT2G13290' => 'ath', 'AT3G01620' => 'ath', 'AT3G26445' => 'ath', 'AT3G27540' => 'ath', 'AT5G14480' => 'ath', 'ATR0824G026' => 'atr', 'ATR1098G019' => 'atr', 'Atru.chr11.2145' => 'acertr', 'Atru.chr2.3636' => 'acertr', 'Atru.chr2.3644' => 'acertr', 'Atru.chr6.2422' => 'acertr', 'Atru.chr7.1112' => 'acertr', 'AUR62005469' => 'cqu', 'AUR62011166' => 'cqu', 'AUR62013319' => 'cqu', 'AUR62024273' => 'cqu', 'AUR62028420' => 'cqu', 'AUR62041942' => 'cqu', 'BcaB01g04969' => 'bca', 'BcaB01g06371' => 'bca', 'BcaB02g11494' => 'bca', 'BcaB03g15382' => 'bca', 'BcaB08g36994' => 'bca', 'BcaC03g13477' => 'bca', 'BcaC03g13478' => 'bca', 'BcaC03g13480' => 'bca', 'BcaC03g13481' => 'bca', 'BcaC03g13486' => 'bca', 'BcaC04g19031' => 'bca', 'BcaC04g23085' => 'bca', 'BcaC05g25094' => 'bca', 'BcaC05g25096' => 'bca', 'BcaC05g25138' => 'bca', 'BcaC05g30416' => 'bca', 'BcaC05g30455' => 'bca', 'BcaC06g30979' => 'bca', 'BcaC06g33805' => 'bca', 'BcaC08g46021' => 'bca', 'BcaNung03154' => 'bca', 'BolC2t06623H' => 'bol', 'BolC2t06632H' => 'bol', 'BolC2t06635H' => 'bol', 'BolC2t06638H' => 'bol', 'BolC3t13266H' => 'bol', 'BolC5t29776H' => 'bol', 'BolC6t38912H' => 'bol', 'BolC7t44183H' => 'bol', 'BolC9t54123H' => 'bol', 'BolC9t59107H' => 'bol', 'BraA02t05221Z' => 'bra', 'BraA03t09996Z' => 'bra', 'BraA05t23210Z' => 'bra', 'BraA06t24068Z' => 'bra', 'BraA06t27032Z' => 'bra', 'BraA08t35176Z' => 'bra', 'BraA09t36680Z' => 'bra', 'BraA10t44471Z' => 'bra', 'C02p06760' => 'bna', 'C02p06890' => 'bna', 'C02p07010' => 'bna', 'C03p07660' => 'bna', 'C05p10300' => 'bna', 'C06p38150' => 'bna', 'C07p36650' => 'bna', 'C08p15770' => 'bna', 'C09p12300' => 'bna', 'C09p62700' => 'bna', 'C09p75040' => 'bna', 'CAN.G13.1' => 'can', 'CAN.G138.4' => 'can', 'CAN.G44.6' => 'can', 'CAN.G473.19' => 'can', 'CANSAT01G0835' => 'cansat', 'CANSAT11G0246' => 'cansat', 'CANSAT11G1766' => 'cansat', 'CANSAT64G1954' => 'cansat', 'CARHR013330' => 'chi', 'CARHR060530' => 'chi', 'CARHR075300' => 'chi', 'CARHR105120' => 'chi', 'CARHR148910' => 'chi', 'CARHR198830' => 'chi', 'Carub.0001s1275' => 'cru', 'Carub.0002s1437' => 'cru', 'Carub.0003s0044' => 'cru', 'Carub.0003s2787' => 'cru', 'Carub.0005s0597' => 'cru', 'Carub.0006s1266' => 'cru', 'Ca_06935_v3' => 'car', 'Ca_13559_v3' => 'car', 'Ca_16941_v3' => 'car', 'Ca_16960_v3' => 'car', 'Ca_17775_v3' => 'car', 'Ca_30464_v3' => 'car', 'Cc06_g08160' => 'ccan', 'Cc07_g01520' => 'ccan', 'Cc11_g15810' => 'ccan', 'CDE02G2840' => 'cde', 'CDE03G0093' => 'cde', 'CDE04G2127' => 'cde', 'CDE07G1857' => 'cde', 'CDE09G1246' => 'cde', 'Cfa003412' => 'cfa', 'Cfa007341' => 'cfa', 'Cfa009220' => 'cfa', 'Ciclev10008737m.g' => 'ccl', 'Ciclev10015565m.g' => 'ccl', 'Ciclev10031761m.g' => 'ccl', 'CiPaw.03G045300' => 'cil', 'CiPaw.03G247200' => 'cil', 'CiPaw.04G029500' => 'cil', 'CiPaw.04G174000' => 'cil', 'CiPaw.05G181200' => 'cil', 'CiPaw.06G067100' => 'cil', 'ClCG05G025800' => 'cla', 'ClCG06G011400' => 'cla', 'ClCG09G019360' => 'cla', 'COL.COLO4_04827' => 'col', 'COL.COLO4_29170' => 'col', 'COL.COLO4_35131' => 'col', 'COL.COLO4_35132' => 'col', 'Cpa.g.sc33.32' => 'cpa', 'Cpa.g.sc46.29' => 'cpa', 'Cpa.g.sc796.1' => 'cpa', 'CsaV3_1G030420' => 'csa', 'CsaV3_5G027050' => 'csa', 'CsaV3_5G031040' => 'csa', 'CsaV3_UNG023130' => 'csa', 'CSS0007726' => 'camsi', 'CSS0016433' => 'camsi', 'CSS0017656' => 'camsi', 'CSS0025364' => 'camsi', 'CSS0027582' => 'camsi', 'CSS0047288' => 'camsi', 'CSS0049950' => 'camsi', 'DCAR_003843' => 'dca', 'DCAR_007052' => 'dca', 'DCAR_020884' => 'dca', 'DCAR_021730' => 'dca', 'DCAR_024423' => 'dca', 'DCAR_026509' => 'dca', 'DCAR_031158' => 'dca', 'Dinv14728' => 'din', 'Dinv15219' => 'din', 'Dinv25728' => 'din', 'Dinv33428' => 'din', 'Dinv36489' => 'din', 'Dinv41486' => 'din', 'Duzib147G0469' => 'dzi', 'Duzib168G0060' => 'dzi', 'Duzib187G1215' => 'dzi', 'Duzib248G0692' => 'dzi', 'Duzib251G0767' => 'dzi', 'Duzib264G0446' => 'dzi', 'Duzib268G0691' => 'dzi', 'ECA232G4767' => 'eca', 'ECA233G2838' => 'eca', 'ECA234G0391' => 'eca', 'ECA234G0857' => 'eca', 'ECA236G1593' => 'eca', 'ECA238G0565' => 'eca', 'ECA246G1027' => 'eca', 'ECA246G3223' => 'eca', 'ECA246G3470' => 'eca', 'EL10Ac6g13829' => 'bvu', 'EL10Ac6g14093' => 'bvu', 'EL10Ac8g18707' => 'bvu', 'Eucgr.C01369' => 'egr', 'Eucgr.H02492' => 'egr', 'Eucgr.I01733' => 'egr', 'Eucgr.J02255' => 'egr', 'Eucgr.J02257' => 'egr', 'Eucgr.J02258' => 'egr', 'FAN02G1601' => 'fan', 'FAN03G1586' => 'fan', 'FAN03G2986' => 'fan', 'FAN05G4837' => 'fan', 'FAN06G0146' => 'fan', 'FAN07G0858' => 'fan', 'FAN09G3179' => 'fan', 'FAN10G0669' => 'fan', 'FAN12G2358' => 'fan', 'FAN14G4198' => 'fan', 'FAN14G5112' => 'fan', 'FAN17G0342' => 'fan', 'FAN19G0342' => 'fan', 'FAN19G0962' => 'fan', 'FAN19G1101' => 'fan', 'FAN19G1872' => 'fan', 'FAN22G0356' => 'fan', 'FAN23G0744' => 'fan', 'FAN23G1914' => 'fan', 'FAN26G0032' => 'fan', 'FAN28G0625' => 'fan', 'FvH4_1g02710' => 'fve', 'FvH4_1g02720' => 'fve', 'FvH4_4g25670' => 'fve', 'FvH4_6g51700' => 'fve', 'FvH4_7g20170' => 'fve', 'Glyma.05G175000' => 'gma', 'Glyma.08G132300' => 'gma', 'Glyma.11G243000' => 'gma', 'Glyma.13G158900' => 'gma', 'Glyma.17G112400' => 'gma', 'Glyma.18G014100' => 'gma', 'Glyma.19G003100' => 'gma', 'Glyma.19G056500' => 'gma', 'Gohir.A01G158900' => 'ghi', 'Gohir.A05G312600' => 'ghi', 'Gohir.A05G354900' => 'ghi', 'Gohir.A07G037200' => 'ghi', 'Gohir.A09G030000' => 'ghi', 'Gohir.A12G145200' => 'ghi', 'Gohir.D01G151500' => 'ghi', 'Gohir.D04G058300' => 'ghi', 'Gohir.D05G314100' => 'ghi', 'Gohir.D07G041400' => 'ghi', 'Gohir.D09G029700' => 'ghi', 'Gohir.D12G149700' => 'ghi', 'Gorai.001G043800' => 'gra', 'Gorai.002G187800' => 'gra', 'Gorai.006G034700' => 'gra', 'Gorai.008G161200' => 'gra', 'Gorai.009G335700' => 'gra', 'Gorai.012G065000' => 'gra', 'GSVIVG01000535001' => 'vvi', 'GSVIVG01015572001' => 'vvi', 'GSVIVG01032386001' => 'vvi', 'HanXRQChr05g0138531' => 'han', 'HanXRQChr06g0174391' => 'han', 'HanXRQChr07g0199021' => 'han', 'HanXRQChr08g0208211' => 'han', 'HanXRQChr09g0255471' => 'han', 'HanXRQChr10g0315791' => 'han', 'HanXRQChr12g0371991' => 'han', 'HanXRQChr15g0475251' => 'han', 'HanXRQChr17g0540001' => 'han', 'HanXRQChr17g0548631' => 'han', 'HanXRQChr17g0569561' => 'han', 'Haze_12256' => 'cav', 'Haze_14756' => 'cav', 'Haze_25528' => 'cav', 'Hma1.2p1_0079F.1_g041020' => 'hma', 'Hma1.2p1_0818F.1_g223260' => 'hma', 'Hma1.2p1_1747F.1_g300530' => 'hma', 'HPP92_004607' => 'vpl', 'HPP92_004608' => 'vpl', 'HPP92_006181' => 'vpl', 'HPP92_012192' => 'vpl', 'HPP92_015680' => 'vpl', 'HPP92_020249' => 'vpl', 'HPP92_021376' => 'vpl', 'HPP92_024275' => 'vpl', 'Hund06031' => 'sun', 'Hund25391' => 'sun', 'Lalb_Chr07g0185371' => 'lal', 'Lalb_Chr07g0185381' => 'lal', 'Lalb_Chr12g0204011' => 'lal', 'Lalb_Chr13g0301671' => 'lal', 'Lalb_Chr14g0362851' => 'lal', 'Lalb_Chr24g0403581' => 'lal', 'Lj1g0000233' => 'lja', 'Lj2g0018120' => 'lja', 'Lj3C621T0' => 'lonja', 'Lj3P1059T14' => 'lonja', 'Lj3P611T9' => 'lonja', 'Lj3P614T13' => 'lonja', 'Lj3P615T5' => 'lonja', 'Lj4g0012315' => 'lja', 'Lj4g0026182' => 'lja', 'Lj6P813T16' => 'lonja', 'Lj7C427T7' => 'lonja', 'Lj7C427T8' => 'lonja', 'Lj7P600T41' => 'lonja', 'Lju41C42G17' => 'lonja', 'Lsat_1_v5_gn_0_47300' => 'lsa', 'Lsat_1_v5_gn_2_91280' => 'lsa', 'Lsat_1_v5_gn_3_30561' => 'lsa', 'Lsat_1_v5_gn_4_184321' => 'lsa', 'Lsat_1_v5_gn_4_4041' => 'lsa', 'Lsat_1_v5_gn_5_92000' => 'lsa', 'Lsat_1_v5_gn_8_152940' => 'lsa', 'Lsat_1_v5_gn_8_62401' => 'lsa', 'Manes.06G055900' => 'mes', 'Manes.12G022200' => 'mes', 'Manes.13G023300' => 'mes', 'Manes.14G115000' => 'mes', 'Manes.15G151700' => 'mes', 'Manes.17G111300' => 'mes', 'Mapoly0226s0009' => 'mpo', 'MBI02_g25363_MAGBIO' => 'mbi', 'MBI06_g00027_MAGBIO' => 'mbi', 'MBI10_g13034_MAGBIO' => 'mbi', 'MD09G1023400' => 'mdo', 'MD13G1100100' => 'mdo', 'MD15G1169200' => 'mdo', 'MD16G1101100' => 'mdo', 'MD17G1022900' => 'mdo', 'Medtr3g096150' => 'mtr', 'Medtr4g115070' => 'mtr', 'Medtr7g033325' => 'mtr', 'Medtr8g089840' => 'mtr', 'MELO3C010319.2' => 'cme', 'MELO3C011944.2' => 'cme', 'MELO3C021589.2' => 'cme', 'Migut.E00207' => 'egut', 'Migut.H00067' => 'egut', 'Migut.K00433' => 'egut', 'Migut.K00606' => 'egut', 'Migut.K01410' => 'egut', 'MSTRG.13347' => 'ama', 'MSTRG.24045' => 'ama', 'MSTRG.2428' => 'ama', 'MSTRG.26410' => 'ama', 'MSTRG.3139' => 'ama', 'MSTRG.3286' => 'ama', 'MSTRG.563' => 'ama', 'MSTRG.7941' => 'ama', 'Nitab4.5_0000028g0060' => 'nta', 'Nitab4.5_0000065g0260' => 'nta', 'Nitab4.5_0000112g0060' => 'nta', 'Nitab4.5_0000489g0120' => 'nta', 'Nitab4.5_0001776g0050' => 'nta', 'Nitab4.5_0001854g0010' => 'nta', 'Nitab4.5_0001860g0020' => 'nta', 'Nitab4.5_0004352g0010' => 'nta', 'Nitab4.5_0008716g0020' => 'nta', 'Nitab4.5_0008922g0010' => 'nta', 'Nn3g16693' => 'nnu', 'Nn4g22596' => 'nnu', 'Nn7g37639' => 'nnu', 'Oeu001701.1' => 'oeu', 'Oeu018149.1' => 'oeu', 'Oeu026220.1' => 'oeu', 'Oeu038635.1' => 'oeu', 'Oeu049176.1' => 'oeu', 'Oeu056706.1' => 'oeu', 'Oeu056937.1' => 'oeu', 'Oeu057540.1' => 'oeu', 'Os02g0594900' => 'osa', 'Os02g0595100' => 'osa', 'Os04g0477500' => 'osa', 'Os12g0611900' => 'osa', 'Peaxi162Scf00076g00020' => 'pax', 'Peaxi162Scf00128g00217' => 'pax', 'Peaxi162Scf00129g01640' => 'pax', 'Peaxi162Scf00669g00007' => 'pax', 'Peaxi162Scf00700g00421' => 'pax', 'Peaxi162Scf00801g00038' => 'pax', 'Peaxi162Scf00891g00025' => 'pax', 'PGR083G0909' => 'pgr', 'PGR119G1005' => 'pgr', 'PGR142G2236' => 'pgr', 'PGR142G3388' => 'pgr', 'PGSC0003DMG400004514' => 'stu', 'PGSC0003DMG400012635' => 'stu', 'PGSC0003DMG400015730' => 'stu', 'PGSC0003DMG400018611' => 'stu', 'PGSC0003DMG400030897' => 'stu', 'Phvul.001G254800' => 'pvu', 'Phvul.002G260100' => 'pvu', 'Phvul.003G167600' => 'pvu', 'Phvul.004G005100' => 'pvu', 'Potri.001G343600' => 'ptr', 'Potri.006G066700' => 'ptr', 'Potri.008G186000' => 'ptr', 'Potri.010G046900' => 'ptr', 'Potri.018G127900' => 'ptr', 'Pp3c20_17750' => 'ppa', 'Pp3c24_4380' => 'ppa', 'Prupe.1G245800' => 'ppe', 'Prupe.3G293400' => 'ppe', 'Prupe.7G247400' => 'ppe', 'Psat0s145g0120' => 'psa', 'Psat0s595g0040' => 'psa', 'Psat0s595g0120' => 'psa', 'Psat3g175040' => 'psa', 'Psat7g058120' => 'psa', 'PSO017G0428' => 'pso', 'PSO063G7510' => 'pso', 'PSO067G0046' => 'pso', 'PSO478G1073' => 'pso', 'PSO675G3677' => 'pso', 'PSO675G6558' => 'pso', 'PSO675G7520' => 'pso', 'PSO675G8959' => 'pso', 'QL02p074089' => 'qlo', 'QL02p089614' => 'qlo', 'QL03p057736' => 'qlo', 'RcHm_v2.0_Chr1g0364131' => 'rch', 'RcHm_v2.0_Chr2g0087801' => 'rch', 'RcHm_v2.0_Chr2g0087821' => 'rch', 'RcHm_v2.0_Chr2g0173231' => 'rch', 'RcHm_v2.0_Chr4g0433111' => 'rch', 'Rhsim03G0250300' => 'rsi', 'Rhsim08G0048400' => 'rsi', 'Rhsim10G0014800' => 'rsi', 'Rhsim12G0040100' => 'rsi', 'Rhsim12G0109700' => 'rsi', 'Sabra06G0049600' => 'sbr', 'Sabra08G0141000' => 'sbr', 'Sabra10G0021400' => 'sbr', 'Sabra16G0222900' => 'sbr', 'Sabra18G0108600' => 'sbr', 'SalBow1G0433' => 'sbo', 'SalBow1G2038' => 'sbo', 'SalBow1G5003' => 'sbo', 'SalBow7G1197' => 'sbo', 'SalBow8G3506' => 'sbo', 'Sc03g0007300' => 'sci', 'Sc11g0000950' => 'sci', 'Sc14g0008750' => 'sci', 'Sc18g0000420' => 'sci', 'Sed0006754' => 'sed', 'Sed0008741' => 'sed', 'Sed0017172' => 'sed', 'Sed0018925' => 'sed', 'Sed0023326' => 'sed', 'Sed0025909' => 'sed', 'SEGI_05333' => 'sgi', 'SEGI_10362' => 'sgi', 'SEGI_13380' => 'sgi', 'SEGI_24306' => 'sgi', 'SEGI_29077' => 'sgi', 'SEGI_29095' => 'sgi', 'SEGI_36534' => 'sgi', 'SEGI_37506' => 'sgi', 'SEGI_38321' => 'sgi', 'SGA_v2.0_scaffold307G48031' => 'sas', 'SGA_v2.0_scaffold47G17507' => 'sas', 'SGA_v2.0_scaffold63G21736' => 'sas', 'SGA_v2.0_scaffold87G27070' => 'sas', 'SHI17794' => 'shi', 'SHI28851' => 'shi', 'SMO165G0155' => 'smo', 'SMO340G0217' => 'smo', 'SMO367G1210' => 'smo', 'Solyc02g093430.3' => 'sly', 'Solyc05g013580.4' => 'sly', 'Solyc07g008030.3' => 'sly', 'Solyc12g035470.2' => 'sly', 'Sopen02g038020' => 'spe', 'Sopen05g008490' => 'spe', 'Sopen07g003910' => 'spe', 'Sopen12g015240' => 'spe', 'Sp1g11550' => 'spa', 'Sp2g16710' => 'spa', 'Sp3g00430' => 'spa', 'Sp3g26780' => 'spa', 'Sp5g22900' => 'spa', 'Sp6g29530' => 'spa', 'TAR371G0794' => 'tar', 'TAR374G0164' => 'tar', 'TAR622G0165' => 'tar', 'TAR626G0929' => 'tar', 'TAR629G2155' => 'tar', 'THA.LOC104805282' => 'tha', 'THA.LOC104805363' => 'tha', 'THA.LOC104808968' => 'tha', 'THA.LOC104821093' => 'tha', 'THA.LOC104823953' => 'tha', 'THA.LOC104825562' => 'tha', 'THA.LOC104825665' => 'tha', 'Thecc.02G261400' => 'tca', 'Thecc.04G019200' => 'tca', 'Thecc.09G130400' => 'tca', 'Thhalv10004374m.g' => 'esa', 'Thhalv10007850m.g' => 'esa', 'Thhalv10013782m.g' => 'esa', 'Thhalv10018686m.g' => 'esa', 'Thhalv10020899m.g' => 'esa', 'Thhalv10022755m.g' => 'esa', 'TPR.G23851' => 'tpr', 'TPR.G26500' => 'tpr', 'TPR.G27267' => 'tpr', 'TPR.G32001' => 'tpr', 'TPR.G6251' => 'tpr', 'TPR.G8167' => 'tpr', 'TWI12G1330' => 'twi', 'TWI18G1239' => 'twi', 'TWI34G0979' => 'twi', 'TWI36G0670' => 'twi', 'TWI36G0707' => 'twi', 'TWI56G0233' => 'twi', 'TWI75G1809' => 'twi', 'unitig_21.g20874' => 'ugi', 'unitig_26.g10343' => 'ugi', 'unitig_46.g18392' => 'ugi', 'unitig_52.g17178' => 'ugi', 'unitig_8.g2934' => 'ugi', 'vmacro01122' => 'vma', 'vmacro05875' => 'vma', 'vmacro06147' => 'vma', 'vmacro16191' => 'vma', 'vmacro18293' => 'vma', 'VMungo0251G3707' => 'vmu', 'VMungo0464G1521' => 'vmu', 'VMungo1215G0205' => 'vmu', 'VMungo1383G2484' => 'vmu', 'Zm00001eb079610' => 'zma', 'Zm00001eb135990' => 'zma', 'Zm00001eb183710' => 'zma', 'Zm00001eb246020' => 'zma' ) $gf_id = 'HOM05D001124' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001124' ) $data_identifier = 'HOM05D001124' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 6, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 7, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 21, 'bol' => (int) 10, 'bra' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 6, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 9, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 21, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 8, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 10, 'lsa' => (int) 8, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 8, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 9, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb246020' $species_info = array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ) $local_species = 'cav' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001124', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '548', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02520' => 'bna', 'A03p06630' => 'bna', 'A05p44460' => 'bna', 'A06p08710' => 'bna', 'A06p41090' => 'bna', 'A07p32320' => 'bna', 'A08p32520' => 'bna', 'A09p10360' => 'bna', 'A10p24080' => 'bna', 'Aa31LG11G15250' => 'aar', 'Aa31LG1G1800' => 'aar', 'Aa31LG2G5120' => 'aar', 'Aa31LG2G6070' => 'aar', 'Aa31LG5G10770' => 'aar', 'Aa31sc61G90' => 'aar', 'Actinidia01352' => 'ach', 'Actinidia05983' => 'ach', 'Actinidia08133' => 'ach', 'Actinidia15101' => 'ach', 'Actinidia26379' => 'ach', 'Actinidia35778' => 'ach', 'Actinidia36123' => 'ach', 'Actinidia37436' => 'ach', 'Actinidia38730' => 'ach', 'Ah.02g128210' => 'amhyb', 'Ah.03g132990' => 'amhyb', 'Ah.14g079410' => 'amhyb', 'AL1G24640' => 'aly', 'AL2G26680' => 'aly', 'AL3G10530' => 'aly', 'AL3G45230' => 'aly', 'AL5G15230' => 'aly', 'AL5G16960' => 'aly', 'AL6G25210' => 'aly', 'Aqoxy2G00441' => 'aox', 'Aqoxy3G01236' => 'aox', 'Aqoxy5G03746' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3RQ047' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C7GMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9C8JER' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MBL6KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YXCZ83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZANX40' => 'arhy', 'AT1G12990' => 'ath', 'AT1G67880' => 'ath', 'AT2G13290' => 'ath', 'AT3G01620' => 'ath', 'AT3G26445' => 'ath', 'AT3G27540' => 'ath', 'AT5G14480' => 'ath', 'ATR0824G026' => 'atr', 'ATR1098G019' => 'atr', 'Atru.chr11.2145' => 'acertr', 'Atru.chr2.3636' => 'acertr', 'Atru.chr2.3644' => 'acertr', 'Atru.chr6.2422' => 'acertr', 'Atru.chr7.1112' => 'acertr', 'AUR62005469' => 'cqu', 'AUR62011166' => 'cqu', 'AUR62013319' => 'cqu', 'AUR62024273' => 'cqu', 'AUR62028420' => 'cqu', 'AUR62041942' => 'cqu', 'BcaB01g04969' => 'bca', 'BcaB01g06371' => 'bca', 'BcaB02g11494' => 'bca', 'BcaB03g15382' => 'bca', 'BcaB08g36994' => 'bca', 'BcaC03g13477' => 'bca', 'BcaC03g13478' => 'bca', 'BcaC03g13480' => 'bca', 'BcaC03g13481' => 'bca', 'BcaC03g13486' => 'bca', 'BcaC04g19031' => 'bca', 'BcaC04g23085' => 'bca', 'BcaC05g25094' => 'bca', 'BcaC05g25096' => 'bca', 'BcaC05g25138' => 'bca', 'BcaC05g30416' => 'bca', 'BcaC05g30455' => 'bca', 'BcaC06g30979' => 'bca', 'BcaC06g33805' => 'bca', 'BcaC08g46021' => 'bca', 'BcaNung03154' => 'bca', 'BolC2t06623H' => 'bol', 'BolC2t06632H' => 'bol', 'BolC2t06635H' => 'bol', 'BolC2t06638H' => 'bol', 'BolC3t13266H' => 'bol', 'BolC5t29776H' => 'bol', 'BolC6t38912H' => 'bol', 'BolC7t44183H' => 'bol', 'BolC9t54123H' => 'bol', 'BolC9t59107H' => 'bol', 'BraA02t05221Z' => 'bra', 'BraA03t09996Z' => 'bra', 'BraA05t23210Z' => 'bra', 'BraA06t24068Z' => 'bra', 'BraA06t27032Z' => 'bra', 'BraA08t35176Z' => 'bra', 'BraA09t36680Z' => 'bra', 'BraA10t44471Z' => 'bra', 'C02p06760' => 'bna', 'C02p06890' => 'bna', 'C02p07010' => 'bna', 'C03p07660' => 'bna', 'C05p10300' => 'bna', 'C06p38150' => 'bna', 'C07p36650' => 'bna', 'C08p15770' => 'bna', 'C09p12300' => 'bna', 'C09p62700' => 'bna', 'C09p75040' => 'bna', 'CAN.G13.1' => 'can', 'CAN.G138.4' => 'can', 'CAN.G44.6' => 'can', 'CAN.G473.19' => 'can', 'CANSAT01G0835' => 'cansat', 'CANSAT11G0246' => 'cansat', 'CANSAT11G1766' => 'cansat', 'CANSAT64G1954' => 'cansat', 'CARHR013330' => 'chi', 'CARHR060530' => 'chi', 'CARHR075300' => 'chi', 'CARHR105120' => 'chi', 'CARHR148910' => 'chi', 'CARHR198830' => 'chi', 'Carub.0001s1275' => 'cru', 'Carub.0002s1437' => 'cru', 'Carub.0003s0044' => 'cru', 'Carub.0003s2787' => 'cru', 'Carub.0005s0597' => 'cru', 'Carub.0006s1266' => 'cru', 'Ca_06935_v3' => 'car', 'Ca_13559_v3' => 'car', 'Ca_16941_v3' => 'car', 'Ca_16960_v3' => 'car', 'Ca_17775_v3' => 'car', 'Ca_30464_v3' => 'car', 'Cc06_g08160' => 'ccan', 'Cc07_g01520' => 'ccan', 'Cc11_g15810' => 'ccan', 'CDE02G2840' => 'cde', 'CDE03G0093' => 'cde', 'CDE04G2127' => 'cde', 'CDE07G1857' => 'cde', 'CDE09G1246' => 'cde', 'Cfa003412' => 'cfa', 'Cfa007341' => 'cfa', 'Cfa009220' => 'cfa', 'Ciclev10008737m.g' => 'ccl', 'Ciclev10015565m.g' => 'ccl', 'Ciclev10031761m.g' => 'ccl', 'CiPaw.03G045300' => 'cil', 'CiPaw.03G247200' => 'cil', 'CiPaw.04G029500' => 'cil', 'CiPaw.04G174000' => 'cil', 'CiPaw.05G181200' => 'cil', 'CiPaw.06G067100' => 'cil', 'ClCG05G025800' => 'cla', 'ClCG06G011400' => 'cla', 'ClCG09G019360' => 'cla', 'COL.COLO4_04827' => 'col', 'COL.COLO4_29170' => 'col', 'COL.COLO4_35131' => 'col', 'COL.COLO4_35132' => 'col', 'Cpa.g.sc33.32' => 'cpa', 'Cpa.g.sc46.29' => 'cpa', 'Cpa.g.sc796.1' => 'cpa', 'CsaV3_1G030420' => 'csa', 'CsaV3_5G027050' => 'csa', 'CsaV3_5G031040' => 'csa', 'CsaV3_UNG023130' => 'csa', 'CSS0007726' => 'camsi', 'CSS0016433' => 'camsi', 'CSS0017656' => 'camsi', 'CSS0025364' => 'camsi', 'CSS0027582' => 'camsi', 'CSS0047288' => 'camsi', 'CSS0049950' => 'camsi', 'DCAR_003843' => 'dca', 'DCAR_007052' => 'dca', 'DCAR_020884' => 'dca', 'DCAR_021730' => 'dca', 'DCAR_024423' => 'dca', 'DCAR_026509' => 'dca', 'DCAR_031158' => 'dca', 'Dinv14728' => 'din', 'Dinv15219' => 'din', 'Dinv25728' => 'din', 'Dinv33428' => 'din', 'Dinv36489' => 'din', 'Dinv41486' => 'din', 'Duzib147G0469' => 'dzi', 'Duzib168G0060' => 'dzi', 'Duzib187G1215' => 'dzi', 'Duzib248G0692' => 'dzi', 'Duzib251G0767' => 'dzi', 'Duzib264G0446' => 'dzi', 'Duzib268G0691' => 'dzi', 'ECA232G4767' => 'eca', 'ECA233G2838' => 'eca', 'ECA234G0391' => 'eca', 'ECA234G0857' => 'eca', 'ECA236G1593' => 'eca', 'ECA238G0565' => 'eca', 'ECA246G1027' => 'eca', 'ECA246G3223' => 'eca', 'ECA246G3470' => 'eca', 'EL10Ac6g13829' => 'bvu', 'EL10Ac6g14093' => 'bvu', 'EL10Ac8g18707' => 'bvu', 'Eucgr.C01369' => 'egr', 'Eucgr.H02492' => 'egr', 'Eucgr.I01733' => 'egr', 'Eucgr.J02255' => 'egr', 'Eucgr.J02257' => 'egr', 'Eucgr.J02258' => 'egr', 'FAN02G1601' => 'fan', 'FAN03G1586' => 'fan', 'FAN03G2986' => 'fan', 'FAN05G4837' => 'fan', 'FAN06G0146' => 'fan', 'FAN07G0858' => 'fan', 'FAN09G3179' => 'fan', 'FAN10G0669' => 'fan', 'FAN12G2358' => 'fan', 'FAN14G4198' => 'fan', 'FAN14G5112' => 'fan', 'FAN17G0342' => 'fan', 'FAN19G0342' => 'fan', 'FAN19G0962' => 'fan', 'FAN19G1101' => 'fan', 'FAN19G1872' => 'fan', 'FAN22G0356' => 'fan', 'FAN23G0744' => 'fan', 'FAN23G1914' => 'fan', 'FAN26G0032' => 'fan', 'FAN28G0625' => 'fan', 'FvH4_1g02710' => 'fve', 'FvH4_1g02720' => 'fve', 'FvH4_4g25670' => 'fve', 'FvH4_6g51700' => 'fve', 'FvH4_7g20170' => 'fve', 'Glyma.05G175000' => 'gma', 'Glyma.08G132300' => 'gma', 'Glyma.11G243000' => 'gma', 'Glyma.13G158900' => 'gma', 'Glyma.17G112400' => 'gma', 'Glyma.18G014100' => 'gma', 'Glyma.19G003100' => 'gma', 'Glyma.19G056500' => 'gma', 'Gohir.A01G158900' => 'ghi', 'Gohir.A05G312600' => 'ghi', 'Gohir.A05G354900' => 'ghi', 'Gohir.A07G037200' => 'ghi', 'Gohir.A09G030000' => 'ghi', 'Gohir.A12G145200' => 'ghi', 'Gohir.D01G151500' => 'ghi', 'Gohir.D04G058300' => 'ghi', 'Gohir.D05G314100' => 'ghi', 'Gohir.D07G041400' => 'ghi', 'Gohir.D09G029700' => 'ghi', 'Gohir.D12G149700' => 'ghi', 'Gorai.001G043800' => 'gra', 'Gorai.002G187800' => 'gra', 'Gorai.006G034700' => 'gra', 'Gorai.008G161200' => 'gra', 'Gorai.009G335700' => 'gra', 'Gorai.012G065000' => 'gra', 'GSVIVG01000535001' => 'vvi', 'GSVIVG01015572001' => 'vvi', 'GSVIVG01032386001' => 'vvi', 'HanXRQChr05g0138531' => 'han', 'HanXRQChr06g0174391' => 'han', 'HanXRQChr07g0199021' => 'han', 'HanXRQChr08g0208211' => 'han', 'HanXRQChr09g0255471' => 'han', 'HanXRQChr10g0315791' => 'han', 'HanXRQChr12g0371991' => 'han', 'HanXRQChr15g0475251' => 'han', 'HanXRQChr17g0540001' => 'han', 'HanXRQChr17g0548631' => 'han', 'HanXRQChr17g0569561' => 'han', 'Haze_12256' => 'cav', 'Haze_14756' => 'cav', 'Haze_25528' => 'cav', 'Hma1.2p1_0079F.1_g041020' => 'hma', 'Hma1.2p1_0818F.1_g223260' => 'hma', 'Hma1.2p1_1747F.1_g300530' => 'hma', 'HPP92_004607' => 'vpl', 'HPP92_004608' => 'vpl', 'HPP92_006181' => 'vpl', 'HPP92_012192' => 'vpl', 'HPP92_015680' => 'vpl', 'HPP92_020249' => 'vpl', 'HPP92_021376' => 'vpl', 'HPP92_024275' => 'vpl', 'Hund06031' => 'sun', 'Hund25391' => 'sun', 'Lalb_Chr07g0185371' => 'lal', 'Lalb_Chr07g0185381' => 'lal', 'Lalb_Chr12g0204011' => 'lal', 'Lalb_Chr13g0301671' => 'lal', 'Lalb_Chr14g0362851' => 'lal', 'Lalb_Chr24g0403581' => 'lal', 'Lj1g0000233' => 'lja', 'Lj2g0018120' => 'lja', 'Lj3C621T0' => 'lonja', 'Lj3P1059T14' => 'lonja', 'Lj3P611T9' => 'lonja', 'Lj3P614T13' => 'lonja', 'Lj3P615T5' => 'lonja', 'Lj4g0012315' => 'lja', 'Lj4g0026182' => 'lja', 'Lj6P813T16' => 'lonja', 'Lj7C427T7' => 'lonja', 'Lj7C427T8' => 'lonja', 'Lj7P600T41' => 'lonja', 'Lju41C42G17' => 'lonja', 'Lsat_1_v5_gn_0_47300' => 'lsa', 'Lsat_1_v5_gn_2_91280' => 'lsa', 'Lsat_1_v5_gn_3_30561' => 'lsa', 'Lsat_1_v5_gn_4_184321' => 'lsa', 'Lsat_1_v5_gn_4_4041' => 'lsa', 'Lsat_1_v5_gn_5_92000' => 'lsa', 'Lsat_1_v5_gn_8_152940' => 'lsa', 'Lsat_1_v5_gn_8_62401' => 'lsa', 'Manes.06G055900' => 'mes', 'Manes.12G022200' => 'mes', 'Manes.13G023300' => 'mes', 'Manes.14G115000' => 'mes', 'Manes.15G151700' => 'mes', 'Manes.17G111300' => 'mes', 'Mapoly0226s0009' => 'mpo', 'MBI02_g25363_MAGBIO' => 'mbi', 'MBI06_g00027_MAGBIO' => 'mbi', 'MBI10_g13034_MAGBIO' => 'mbi', 'MD09G1023400' => 'mdo', 'MD13G1100100' => 'mdo', 'MD15G1169200' => 'mdo', 'MD16G1101100' => 'mdo', 'MD17G1022900' => 'mdo', 'Medtr3g096150' => 'mtr', 'Medtr4g115070' => 'mtr', 'Medtr7g033325' => 'mtr', 'Medtr8g089840' => 'mtr', 'MELO3C010319.2' => 'cme', 'MELO3C011944.2' => 'cme', 'MELO3C021589.2' => 'cme', 'Migut.E00207' => 'egut', 'Migut.H00067' => 'egut', 'Migut.K00433' => 'egut', 'Migut.K00606' => 'egut', 'Migut.K01410' => 'egut', 'MSTRG.13347' => 'ama', 'MSTRG.24045' => 'ama', 'MSTRG.2428' => 'ama', 'MSTRG.26410' => 'ama', 'MSTRG.3139' => 'ama', 'MSTRG.3286' => 'ama', 'MSTRG.563' => 'ama', 'MSTRG.7941' => 'ama', 'Nitab4.5_0000028g0060' => 'nta', 'Nitab4.5_0000065g0260' => 'nta', 'Nitab4.5_0000112g0060' => 'nta', 'Nitab4.5_0000489g0120' => 'nta', 'Nitab4.5_0001776g0050' => 'nta', 'Nitab4.5_0001854g0010' => 'nta', 'Nitab4.5_0001860g0020' => 'nta', 'Nitab4.5_0004352g0010' => 'nta', 'Nitab4.5_0008716g0020' => 'nta', 'Nitab4.5_0008922g0010' => 'nta', 'Nn3g16693' => 'nnu', 'Nn4g22596' => 'nnu', 'Nn7g37639' => 'nnu', 'Oeu001701.1' => 'oeu', 'Oeu018149.1' => 'oeu', 'Oeu026220.1' => 'oeu', 'Oeu038635.1' => 'oeu', 'Oeu049176.1' => 'oeu', 'Oeu056706.1' => 'oeu', 'Oeu056937.1' => 'oeu', 'Oeu057540.1' => 'oeu', 'Os02g0594900' => 'osa', 'Os02g0595100' => 'osa', 'Os04g0477500' => 'osa', 'Os12g0611900' => 'osa', 'Peaxi162Scf00076g00020' => 'pax', 'Peaxi162Scf00128g00217' => 'pax', 'Peaxi162Scf00129g01640' => 'pax', 'Peaxi162Scf00669g00007' => 'pax', 'Peaxi162Scf00700g00421' => 'pax', 'Peaxi162Scf00801g00038' => 'pax', 'Peaxi162Scf00891g00025' => 'pax', 'PGR083G0909' => 'pgr', 'PGR119G1005' => 'pgr', 'PGR142G2236' => 'pgr', 'PGR142G3388' => 'pgr', 'PGSC0003DMG400004514' => 'stu', 'PGSC0003DMG400012635' => 'stu', 'PGSC0003DMG400015730' => 'stu', 'PGSC0003DMG400018611' => 'stu', 'PGSC0003DMG400030897' => 'stu', 'Phvul.001G254800' => 'pvu', 'Phvul.002G260100' => 'pvu', 'Phvul.003G167600' => 'pvu', 'Phvul.004G005100' => 'pvu', 'Potri.001G343600' => 'ptr', 'Potri.006G066700' => 'ptr', 'Potri.008G186000' => 'ptr', 'Potri.010G046900' => 'ptr', 'Potri.018G127900' => 'ptr', 'Pp3c20_17750' => 'ppa', 'Pp3c24_4380' => 'ppa', 'Prupe.1G245800' => 'ppe', 'Prupe.3G293400' => 'ppe', 'Prupe.7G247400' => 'ppe', 'Psat0s145g0120' => 'psa', 'Psat0s595g0040' => 'psa', 'Psat0s595g0120' => 'psa', 'Psat3g175040' => 'psa', 'Psat7g058120' => 'psa', 'PSO017G0428' => 'pso', 'PSO063G7510' => 'pso', 'PSO067G0046' => 'pso', 'PSO478G1073' => 'pso', 'PSO675G3677' => 'pso', 'PSO675G6558' => 'pso', 'PSO675G7520' => 'pso', 'PSO675G8959' => 'pso', 'QL02p074089' => 'qlo', 'QL02p089614' => 'qlo', 'QL03p057736' => 'qlo', 'RcHm_v2.0_Chr1g0364131' => 'rch', 'RcHm_v2.0_Chr2g0087801' => 'rch', 'RcHm_v2.0_Chr2g0087821' => 'rch', 'RcHm_v2.0_Chr2g0173231' => 'rch', 'RcHm_v2.0_Chr4g0433111' => 'rch', 'Rhsim03G0250300' => 'rsi', 'Rhsim08G0048400' => 'rsi', 'Rhsim10G0014800' => 'rsi', 'Rhsim12G0040100' => 'rsi', 'Rhsim12G0109700' => 'rsi', 'Sabra06G0049600' => 'sbr', 'Sabra08G0141000' => 'sbr', 'Sabra10G0021400' => 'sbr', 'Sabra16G0222900' => 'sbr', 'Sabra18G0108600' => 'sbr', 'SalBow1G0433' => 'sbo', 'SalBow1G2038' => 'sbo', 'SalBow1G5003' => 'sbo', 'SalBow7G1197' => 'sbo', 'SalBow8G3506' => 'sbo', 'Sc03g0007300' => 'sci', 'Sc11g0000950' => 'sci', 'Sc14g0008750' => 'sci', 'Sc18g0000420' => 'sci', 'Sed0006754' => 'sed', 'Sed0008741' => 'sed', 'Sed0017172' => 'sed', 'Sed0018925' => 'sed', 'Sed0023326' => 'sed', 'Sed0025909' => 'sed', 'SEGI_05333' => 'sgi', 'SEGI_10362' => 'sgi', 'SEGI_13380' => 'sgi', 'SEGI_24306' => 'sgi', 'SEGI_29077' => 'sgi', 'SEGI_29095' => 'sgi', 'SEGI_36534' => 'sgi', 'SEGI_37506' => 'sgi', 'SEGI_38321' => 'sgi', 'SGA_v2.0_scaffold307G48031' => 'sas', 'SGA_v2.0_scaffold47G17507' => 'sas', 'SGA_v2.0_scaffold63G21736' => 'sas', 'SGA_v2.0_scaffold87G27070' => 'sas', 'SHI17794' => 'shi', 'SHI28851' => 'shi', 'SMO165G0155' => 'smo', 'SMO340G0217' => 'smo', 'SMO367G1210' => 'smo', 'Solyc02g093430.3' => 'sly', 'Solyc05g013580.4' => 'sly', 'Solyc07g008030.3' => 'sly', 'Solyc12g035470.2' => 'sly', 'Sopen02g038020' => 'spe', 'Sopen05g008490' => 'spe', 'Sopen07g003910' => 'spe', 'Sopen12g015240' => 'spe', 'Sp1g11550' => 'spa', 'Sp2g16710' => 'spa', 'Sp3g00430' => 'spa', 'Sp3g26780' => 'spa', 'Sp5g22900' => 'spa', 'Sp6g29530' => 'spa', 'TAR371G0794' => 'tar', 'TAR374G0164' => 'tar', 'TAR622G0165' => 'tar', 'TAR626G0929' => 'tar', 'TAR629G2155' => 'tar', 'THA.LOC104805282' => 'tha', 'THA.LOC104805363' => 'tha', 'THA.LOC104808968' => 'tha', 'THA.LOC104821093' => 'tha', 'THA.LOC104823953' => 'tha', 'THA.LOC104825562' => 'tha', 'THA.LOC104825665' => 'tha', 'Thecc.02G261400' => 'tca', 'Thecc.04G019200' => 'tca', 'Thecc.09G130400' => 'tca', 'Thhalv10004374m.g' => 'esa', 'Thhalv10007850m.g' => 'esa', 'Thhalv10013782m.g' => 'esa', 'Thhalv10018686m.g' => 'esa', 'Thhalv10020899m.g' => 'esa', 'Thhalv10022755m.g' => 'esa', 'TPR.G23851' => 'tpr', 'TPR.G26500' => 'tpr', 'TPR.G27267' => 'tpr', 'TPR.G32001' => 'tpr', 'TPR.G6251' => 'tpr', 'TPR.G8167' => 'tpr', 'TWI12G1330' => 'twi', 'TWI18G1239' => 'twi', 'TWI34G0979' => 'twi', 'TWI36G0670' => 'twi', 'TWI36G0707' => 'twi', 'TWI56G0233' => 'twi', 'TWI75G1809' => 'twi', 'unitig_21.g20874' => 'ugi', 'unitig_26.g10343' => 'ugi', 'unitig_46.g18392' => 'ugi', 'unitig_52.g17178' => 'ugi', 'unitig_8.g2934' => 'ugi', 'vmacro01122' => 'vma', 'vmacro05875' => 'vma', 'vmacro06147' => 'vma', 'vmacro16191' => 'vma', 'vmacro18293' => 'vma', 'VMungo0251G3707' => 'vmu', 'VMungo0464G1521' => 'vmu', 'VMungo1215G0205' => 'vmu', 'VMungo1383G2484' => 'vmu', 'Zm00001eb079610' => 'zma', 'Zm00001eb135990' => 'zma', 'Zm00001eb183710' => 'zma', 'Zm00001eb246020' => 'zma' ), 'gf_id' => 'HOM05D001124', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001124' ), 'data_identifier' => 'HOM05D001124', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001124', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '548', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02520' => 'bna', 'A03p06630' => 'bna', 'A05p44460' => 'bna', 'A06p08710' => 'bna', 'A06p41090' => 'bna', 'A07p32320' => 'bna', 'A08p32520' => 'bna', 'A09p10360' => 'bna', 'A10p24080' => 'bna', 'Aa31LG11G15250' => 'aar', 'Aa31LG1G1800' => 'aar', 'Aa31LG2G5120' => 'aar', 'Aa31LG2G6070' => 'aar', 'Aa31LG5G10770' => 'aar', 'Aa31sc61G90' => 'aar', 'Actinidia01352' => 'ach', 'Actinidia05983' => 'ach', 'Actinidia08133' => 'ach', 'Actinidia15101' => 'ach', 'Actinidia26379' => 'ach', 'Actinidia35778' => 'ach', 'Actinidia36123' => 'ach', 'Actinidia37436' => 'ach', 'Actinidia38730' => 'ach', 'Ah.02g128210' => 'amhyb', 'Ah.03g132990' => 'amhyb', 'Ah.14g079410' => 'amhyb', 'AL1G24640' => 'aly', 'AL2G26680' => 'aly', 'AL3G10530' => 'aly', 'AL3G45230' => 'aly', 'AL5G15230' => 'aly', 'AL5G16960' => 'aly', 'AL6G25210' => 'aly', 'Aqoxy2G00441' => 'aox', 'Aqoxy3G01236' => 'aox', 'Aqoxy5G03746' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3RQ047' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C7GMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9C8JER' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MBL6KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YXCZ83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZANX40' => 'arhy', 'AT1G12990' => 'ath', 'AT1G67880' => 'ath', 'AT2G13290' => 'ath', 'AT3G01620' => 'ath', 'AT3G26445' => 'ath', 'AT3G27540' => 'ath', 'AT5G14480' => 'ath', 'ATR0824G026' => 'atr', 'ATR1098G019' => 'atr', 'Atru.chr11.2145' => 'acertr', 'Atru.chr2.3636' => 'acertr', 'Atru.chr2.3644' => 'acertr', 'Atru.chr6.2422' => 'acertr', 'Atru.chr7.1112' => 'acertr', 'AUR62005469' => 'cqu', 'AUR62011166' => 'cqu', 'AUR62013319' => 'cqu', 'AUR62024273' => 'cqu', 'AUR62028420' => 'cqu', 'AUR62041942' => 'cqu', 'BcaB01g04969' => 'bca', 'BcaB01g06371' => 'bca', 'BcaB02g11494' => 'bca', 'BcaB03g15382' => 'bca', 'BcaB08g36994' => 'bca', 'BcaC03g13477' => 'bca', 'BcaC03g13478' => 'bca', 'BcaC03g13480' => 'bca', 'BcaC03g13481' => 'bca', 'BcaC03g13486' => 'bca', 'BcaC04g19031' => 'bca', 'BcaC04g23085' => 'bca', 'BcaC05g25094' => 'bca', 'BcaC05g25096' => 'bca', 'BcaC05g25138' => 'bca', 'BcaC05g30416' => 'bca', 'BcaC05g30455' => 'bca', 'BcaC06g30979' => 'bca', 'BcaC06g33805' => 'bca', 'BcaC08g46021' => 'bca', 'BcaNung03154' => 'bca', 'BolC2t06623H' => 'bol', 'BolC2t06632H' => 'bol', 'BolC2t06635H' => 'bol', 'BolC2t06638H' => 'bol', 'BolC3t13266H' => 'bol', 'BolC5t29776H' => 'bol', 'BolC6t38912H' => 'bol', 'BolC7t44183H' => 'bol', 'BolC9t54123H' => 'bol', 'BolC9t59107H' => 'bol', 'BraA02t05221Z' => 'bra', 'BraA03t09996Z' => 'bra', 'BraA05t23210Z' => 'bra', 'BraA06t24068Z' => 'bra', 'BraA06t27032Z' => 'bra', 'BraA08t35176Z' => 'bra', 'BraA09t36680Z' => 'bra', 'BraA10t44471Z' => 'bra', 'C02p06760' => 'bna', 'C02p06890' => 'bna', 'C02p07010' => 'bna', 'C03p07660' => 'bna', 'C05p10300' => 'bna', 'C06p38150' => 'bna', 'C07p36650' => 'bna', 'C08p15770' => 'bna', 'C09p12300' => 'bna', 'C09p62700' => 'bna', 'C09p75040' => 'bna', 'CAN.G13.1' => 'can', 'CAN.G138.4' => 'can', 'CAN.G44.6' => 'can', 'CAN.G473.19' => 'can', 'CANSAT01G0835' => 'cansat', 'CANSAT11G0246' => 'cansat', 'CANSAT11G1766' => 'cansat', 'CANSAT64G1954' => 'cansat', 'CARHR013330' => 'chi', 'CARHR060530' => 'chi', 'CARHR075300' => 'chi', 'CARHR105120' => 'chi', 'CARHR148910' => 'chi', 'CARHR198830' => 'chi', 'Carub.0001s1275' => 'cru', 'Carub.0002s1437' => 'cru', 'Carub.0003s0044' => 'cru', 'Carub.0003s2787' => 'cru', 'Carub.0005s0597' => 'cru', 'Carub.0006s1266' => 'cru', 'Ca_06935_v3' => 'car', 'Ca_13559_v3' => 'car', 'Ca_16941_v3' => 'car', 'Ca_16960_v3' => 'car', 'Ca_17775_v3' => 'car', 'Ca_30464_v3' => 'car', 'Cc06_g08160' => 'ccan', 'Cc07_g01520' => 'ccan', 'Cc11_g15810' => 'ccan', 'CDE02G2840' => 'cde', 'CDE03G0093' => 'cde', 'CDE04G2127' => 'cde', 'CDE07G1857' => 'cde', 'CDE09G1246' => 'cde', 'Cfa003412' => 'cfa', 'Cfa007341' => 'cfa', 'Cfa009220' => 'cfa', 'Ciclev10008737m.g' => 'ccl', 'Ciclev10015565m.g' => 'ccl', 'Ciclev10031761m.g' => 'ccl', 'CiPaw.03G045300' => 'cil', 'CiPaw.03G247200' => 'cil', 'CiPaw.04G029500' => 'cil', 'CiPaw.04G174000' => 'cil', 'CiPaw.05G181200' => 'cil', 'CiPaw.06G067100' => 'cil', 'ClCG05G025800' => 'cla', 'ClCG06G011400' => 'cla', 'ClCG09G019360' => 'cla', 'COL.COLO4_04827' => 'col', 'COL.COLO4_29170' => 'col', 'COL.COLO4_35131' => 'col', 'COL.COLO4_35132' => 'col', 'Cpa.g.sc33.32' => 'cpa', 'Cpa.g.sc46.29' => 'cpa', 'Cpa.g.sc796.1' => 'cpa', 'CsaV3_1G030420' => 'csa', 'CsaV3_5G027050' => 'csa', 'CsaV3_5G031040' => 'csa', 'CsaV3_UNG023130' => 'csa', 'CSS0007726' => 'camsi', 'CSS0016433' => 'camsi', 'CSS0017656' => 'camsi', 'CSS0025364' => 'camsi', 'CSS0027582' => 'camsi', 'CSS0047288' => 'camsi', 'CSS0049950' => 'camsi', 'DCAR_003843' => 'dca', 'DCAR_007052' => 'dca', 'DCAR_020884' => 'dca', 'DCAR_021730' => 'dca', 'DCAR_024423' => 'dca', 'DCAR_026509' => 'dca', 'DCAR_031158' => 'dca', 'Dinv14728' => 'din', 'Dinv15219' => 'din', 'Dinv25728' => 'din', 'Dinv33428' => 'din', 'Dinv36489' => 'din', 'Dinv41486' => 'din', 'Duzib147G0469' => 'dzi', 'Duzib168G0060' => 'dzi', 'Duzib187G1215' => 'dzi', 'Duzib248G0692' => 'dzi', 'Duzib251G0767' => 'dzi', 'Duzib264G0446' => 'dzi', 'Duzib268G0691' => 'dzi', 'ECA232G4767' => 'eca', 'ECA233G2838' => 'eca', 'ECA234G0391' => 'eca', 'ECA234G0857' => 'eca', 'ECA236G1593' => 'eca', 'ECA238G0565' => 'eca', 'ECA246G1027' => 'eca', 'ECA246G3223' => 'eca', 'ECA246G3470' => 'eca', 'EL10Ac6g13829' => 'bvu', 'EL10Ac6g14093' => 'bvu', 'EL10Ac8g18707' => 'bvu', 'Eucgr.C01369' => 'egr', 'Eucgr.H02492' => 'egr', 'Eucgr.I01733' => 'egr', 'Eucgr.J02255' => 'egr', 'Eucgr.J02257' => 'egr', 'Eucgr.J02258' => 'egr', 'FAN02G1601' => 'fan', 'FAN03G1586' => 'fan', 'FAN03G2986' => 'fan', 'FAN05G4837' => 'fan', 'FAN06G0146' => 'fan', 'FAN07G0858' => 'fan', 'FAN09G3179' => 'fan', 'FAN10G0669' => 'fan', 'FAN12G2358' => 'fan', 'FAN14G4198' => 'fan', 'FAN14G5112' => 'fan', 'FAN17G0342' => 'fan', 'FAN19G0342' => 'fan', 'FAN19G0962' => 'fan', 'FAN19G1101' => 'fan', 'FAN19G1872' => 'fan', 'FAN22G0356' => 'fan', 'FAN23G0744' => 'fan', 'FAN23G1914' => 'fan', 'FAN26G0032' => 'fan', 'FAN28G0625' => 'fan', 'FvH4_1g02710' => 'fve', 'FvH4_1g02720' => 'fve', 'FvH4_4g25670' => 'fve', 'FvH4_6g51700' => 'fve', 'FvH4_7g20170' => 'fve', 'Glyma.05G175000' => 'gma', 'Glyma.08G132300' => 'gma', 'Glyma.11G243000' => 'gma', 'Glyma.13G158900' => 'gma', 'Glyma.17G112400' => 'gma', 'Glyma.18G014100' => 'gma', 'Glyma.19G003100' => 'gma', 'Glyma.19G056500' => 'gma', 'Gohir.A01G158900' => 'ghi', 'Gohir.A05G312600' => 'ghi', 'Gohir.A05G354900' => 'ghi', 'Gohir.A07G037200' => 'ghi', 'Gohir.A09G030000' => 'ghi', 'Gohir.A12G145200' => 'ghi', 'Gohir.D01G151500' => 'ghi', 'Gohir.D04G058300' => 'ghi', 'Gohir.D05G314100' => 'ghi', 'Gohir.D07G041400' => 'ghi', 'Gohir.D09G029700' => 'ghi', 'Gohir.D12G149700' => 'ghi', 'Gorai.001G043800' => 'gra', 'Gorai.002G187800' => 'gra', 'Gorai.006G034700' => 'gra', 'Gorai.008G161200' => 'gra', 'Gorai.009G335700' => 'gra', 'Gorai.012G065000' => 'gra', 'GSVIVG01000535001' => 'vvi', 'GSVIVG01015572001' => 'vvi', 'GSVIVG01032386001' => 'vvi', 'HanXRQChr05g0138531' => 'han', 'HanXRQChr06g0174391' => 'han', 'HanXRQChr07g0199021' => 'han', 'HanXRQChr08g0208211' => 'han', 'HanXRQChr09g0255471' => 'han', 'HanXRQChr10g0315791' => 'han', 'HanXRQChr12g0371991' => 'han', 'HanXRQChr15g0475251' => 'han', 'HanXRQChr17g0540001' => 'han', 'HanXRQChr17g0548631' => 'han', 'HanXRQChr17g0569561' => 'han', 'Haze_12256' => 'cav', 'Haze_14756' => 'cav', 'Haze_25528' => 'cav', 'Hma1.2p1_0079F.1_g041020' => 'hma', 'Hma1.2p1_0818F.1_g223260' => 'hma', 'Hma1.2p1_1747F.1_g300530' => 'hma', 'HPP92_004607' => 'vpl', 'HPP92_004608' => 'vpl', 'HPP92_006181' => 'vpl', 'HPP92_012192' => 'vpl', 'HPP92_015680' => 'vpl', 'HPP92_020249' => 'vpl', 'HPP92_021376' => 'vpl', 'HPP92_024275' => 'vpl', 'Hund06031' => 'sun', 'Hund25391' => 'sun', 'Lalb_Chr07g0185371' => 'lal', 'Lalb_Chr07g0185381' => 'lal', 'Lalb_Chr12g0204011' => 'lal', 'Lalb_Chr13g0301671' => 'lal', 'Lalb_Chr14g0362851' => 'lal', 'Lalb_Chr24g0403581' => 'lal', 'Lj1g0000233' => 'lja', 'Lj2g0018120' => 'lja', 'Lj3C621T0' => 'lonja', 'Lj3P1059T14' => 'lonja', 'Lj3P611T9' => 'lonja', 'Lj3P614T13' => 'lonja', 'Lj3P615T5' => 'lonja', 'Lj4g0012315' => 'lja', 'Lj4g0026182' => 'lja', 'Lj6P813T16' => 'lonja', 'Lj7C427T7' => 'lonja', 'Lj7C427T8' => 'lonja', 'Lj7P600T41' => 'lonja', 'Lju41C42G17' => 'lonja', 'Lsat_1_v5_gn_0_47300' => 'lsa', 'Lsat_1_v5_gn_2_91280' => 'lsa', 'Lsat_1_v5_gn_3_30561' => 'lsa', 'Lsat_1_v5_gn_4_184321' => 'lsa', 'Lsat_1_v5_gn_4_4041' => 'lsa', 'Lsat_1_v5_gn_5_92000' => 'lsa', 'Lsat_1_v5_gn_8_152940' => 'lsa', 'Lsat_1_v5_gn_8_62401' => 'lsa', 'Manes.06G055900' => 'mes', 'Manes.12G022200' => 'mes', 'Manes.13G023300' => 'mes', 'Manes.14G115000' => 'mes', 'Manes.15G151700' => 'mes', 'Manes.17G111300' => 'mes', 'Mapoly0226s0009' => 'mpo', 'MBI02_g25363_MAGBIO' => 'mbi', 'MBI06_g00027_MAGBIO' => 'mbi', 'MBI10_g13034_MAGBIO' => 'mbi', 'MD09G1023400' => 'mdo', 'MD13G1100100' => 'mdo', 'MD15G1169200' => 'mdo', 'MD16G1101100' => 'mdo', 'MD17G1022900' => 'mdo', 'Medtr3g096150' => 'mtr', 'Medtr4g115070' => 'mtr', 'Medtr7g033325' => 'mtr', 'Medtr8g089840' => 'mtr', 'MELO3C010319.2' => 'cme', 'MELO3C011944.2' => 'cme', 'MELO3C021589.2' => 'cme', 'Migut.E00207' => 'egut', 'Migut.H00067' => 'egut', 'Migut.K00433' => 'egut', 'Migut.K00606' => 'egut', 'Migut.K01410' => 'egut', 'MSTRG.13347' => 'ama', 'MSTRG.24045' => 'ama', 'MSTRG.2428' => 'ama', 'MSTRG.26410' => 'ama', 'MSTRG.3139' => 'ama', 'MSTRG.3286' => 'ama', 'MSTRG.563' => 'ama', 'MSTRG.7941' => 'ama', 'Nitab4.5_0000028g0060' => 'nta', 'Nitab4.5_0000065g0260' => 'nta', 'Nitab4.5_0000112g0060' => 'nta', 'Nitab4.5_0000489g0120' => 'nta', 'Nitab4.5_0001776g0050' => 'nta', 'Nitab4.5_0001854g0010' => 'nta', 'Nitab4.5_0001860g0020' => 'nta', 'Nitab4.5_0004352g0010' => 'nta', 'Nitab4.5_0008716g0020' => 'nta', 'Nitab4.5_0008922g0010' => 'nta', 'Nn3g16693' => 'nnu', 'Nn4g22596' => 'nnu', 'Nn7g37639' => 'nnu', 'Oeu001701.1' => 'oeu', 'Oeu018149.1' => 'oeu', 'Oeu026220.1' => 'oeu', 'Oeu038635.1' => 'oeu', 'Oeu049176.1' => 'oeu', 'Oeu056706.1' => 'oeu', 'Oeu056937.1' => 'oeu', 'Oeu057540.1' => 'oeu', 'Os02g0594900' => 'osa', 'Os02g0595100' => 'osa', 'Os04g0477500' => 'osa', 'Os12g0611900' => 'osa', 'Peaxi162Scf00076g00020' => 'pax', 'Peaxi162Scf00128g00217' => 'pax', 'Peaxi162Scf00129g01640' => 'pax', 'Peaxi162Scf00669g00007' => 'pax', 'Peaxi162Scf00700g00421' => 'pax', 'Peaxi162Scf00801g00038' => 'pax', 'Peaxi162Scf00891g00025' => 'pax', 'PGR083G0909' => 'pgr', 'PGR119G1005' => 'pgr', 'PGR142G2236' => 'pgr', 'PGR142G3388' => 'pgr', 'PGSC0003DMG400004514' => 'stu', 'PGSC0003DMG400012635' => 'stu', 'PGSC0003DMG400015730' => 'stu', 'PGSC0003DMG400018611' => 'stu', 'PGSC0003DMG400030897' => 'stu', 'Phvul.001G254800' => 'pvu', 'Phvul.002G260100' => 'pvu', 'Phvul.003G167600' => 'pvu', 'Phvul.004G005100' => 'pvu', 'Potri.001G343600' => 'ptr', 'Potri.006G066700' => 'ptr', 'Potri.008G186000' => 'ptr', 'Potri.010G046900' => 'ptr', 'Potri.018G127900' => 'ptr', 'Pp3c20_17750' => 'ppa', 'Pp3c24_4380' => 'ppa', 'Prupe.1G245800' => 'ppe', 'Prupe.3G293400' => 'ppe', 'Prupe.7G247400' => 'ppe', 'Psat0s145g0120' => 'psa', 'Psat0s595g0040' => 'psa', 'Psat0s595g0120' => 'psa', 'Psat3g175040' => 'psa', 'Psat7g058120' => 'psa', 'PSO017G0428' => 'pso', 'PSO063G7510' => 'pso', 'PSO067G0046' => 'pso', 'PSO478G1073' => 'pso', 'PSO675G3677' => 'pso', 'PSO675G6558' => 'pso', 'PSO675G7520' => 'pso', 'PSO675G8959' => 'pso', 'QL02p074089' => 'qlo', 'QL02p089614' => 'qlo', 'QL03p057736' => 'qlo', 'RcHm_v2.0_Chr1g0364131' => 'rch', 'RcHm_v2.0_Chr2g0087801' => 'rch', 'RcHm_v2.0_Chr2g0087821' => 'rch', 'RcHm_v2.0_Chr2g0173231' => 'rch', 'RcHm_v2.0_Chr4g0433111' => 'rch', 'Rhsim03G0250300' => 'rsi', 'Rhsim08G0048400' => 'rsi', 'Rhsim10G0014800' => 'rsi', 'Rhsim12G0040100' => 'rsi', 'Rhsim12G0109700' => 'rsi', 'Sabra06G0049600' => 'sbr', 'Sabra08G0141000' => 'sbr', 'Sabra10G0021400' => 'sbr', 'Sabra16G0222900' => 'sbr', 'Sabra18G0108600' => 'sbr', 'SalBow1G0433' => 'sbo', 'SalBow1G2038' => 'sbo', 'SalBow1G5003' => 'sbo', 'SalBow7G1197' => 'sbo', 'SalBow8G3506' => 'sbo', 'Sc03g0007300' => 'sci', 'Sc11g0000950' => 'sci', 'Sc14g0008750' => 'sci', 'Sc18g0000420' => 'sci', 'Sed0006754' => 'sed', 'Sed0008741' => 'sed', 'Sed0017172' => 'sed', 'Sed0018925' => 'sed', 'Sed0023326' => 'sed', 'Sed0025909' => 'sed', 'SEGI_05333' => 'sgi', 'SEGI_10362' => 'sgi', 'SEGI_13380' => 'sgi', 'SEGI_24306' => 'sgi', 'SEGI_29077' => 'sgi', 'SEGI_29095' => 'sgi', 'SEGI_36534' => 'sgi', 'SEGI_37506' => 'sgi', 'SEGI_38321' => 'sgi', 'SGA_v2.0_scaffold307G48031' => 'sas', 'SGA_v2.0_scaffold47G17507' => 'sas', 'SGA_v2.0_scaffold63G21736' => 'sas', 'SGA_v2.0_scaffold87G27070' => 'sas', 'SHI17794' => 'shi', 'SHI28851' => 'shi', 'SMO165G0155' => 'smo', 'SMO340G0217' => 'smo', 'SMO367G1210' => 'smo', 'Solyc02g093430.3' => 'sly', 'Solyc05g013580.4' => 'sly', 'Solyc07g008030.3' => 'sly', 'Solyc12g035470.2' => 'sly', 'Sopen02g038020' => 'spe', 'Sopen05g008490' => 'spe', 'Sopen07g003910' => 'spe', 'Sopen12g015240' => 'spe', 'Sp1g11550' => 'spa', 'Sp2g16710' => 'spa', 'Sp3g00430' => 'spa', 'Sp3g26780' => 'spa', 'Sp5g22900' => 'spa', 'Sp6g29530' => 'spa', 'TAR371G0794' => 'tar', 'TAR374G0164' => 'tar', 'TAR622G0165' => 'tar', 'TAR626G0929' => 'tar', 'TAR629G2155' => 'tar', 'THA.LOC104805282' => 'tha', 'THA.LOC104805363' => 'tha', 'THA.LOC104808968' => 'tha', 'THA.LOC104821093' => 'tha', 'THA.LOC104823953' => 'tha', 'THA.LOC104825562' => 'tha', 'THA.LOC104825665' => 'tha', 'Thecc.02G261400' => 'tca', 'Thecc.04G019200' => 'tca', 'Thecc.09G130400' => 'tca', 'Thhalv10004374m.g' => 'esa', 'Thhalv10007850m.g' => 'esa', 'Thhalv10013782m.g' => 'esa', 'Thhalv10018686m.g' => 'esa', 'Thhalv10020899m.g' => 'esa', 'Thhalv10022755m.g' => 'esa', 'TPR.G23851' => 'tpr', 'TPR.G26500' => 'tpr', 'TPR.G27267' => 'tpr', 'TPR.G32001' => 'tpr', 'TPR.G6251' => 'tpr', 'TPR.G8167' => 'tpr', 'TWI12G1330' => 'twi', 'TWI18G1239' => 'twi', 'TWI34G0979' => 'twi', 'TWI36G0670' => 'twi', 'TWI36G0707' => 'twi', 'TWI56G0233' => 'twi', 'TWI75G1809' => 'twi', 'unitig_21.g20874' => 'ugi', 'unitig_26.g10343' => 'ugi', 'unitig_46.g18392' => 'ugi', 'unitig_52.g17178' => 'ugi', 'unitig_8.g2934' => 'ugi', 'vmacro01122' => 'vma', 'vmacro05875' => 'vma', 'vmacro06147' => 'vma', 'vmacro16191' => 'vma', 'vmacro18293' => 'vma', 'VMungo0251G3707' => 'vmu', 'VMungo0464G1521' => 'vmu', 'VMungo1215G0205' => 'vmu', 'VMungo1383G2484' => 'vmu', 'Zm00001eb079610' => 'zma', 'Zm00001eb135990' => 'zma', 'Zm00001eb183710' => 'zma', 'Zm00001eb246020' => 'zma' ) $gf_id = 'HOM05D001124' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001124' ) $data_identifier = 'HOM05D001124' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 6, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 7, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 21, 'bol' => (int) 10, 'bra' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 6, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 9, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 21, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 8, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 10, 'lsa' => (int) 8, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 8, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 9, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb246020' $species_info = array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ) $local_species = 'cme' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001124', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '548', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02520' => 'bna', 'A03p06630' => 'bna', 'A05p44460' => 'bna', 'A06p08710' => 'bna', 'A06p41090' => 'bna', 'A07p32320' => 'bna', 'A08p32520' => 'bna', 'A09p10360' => 'bna', 'A10p24080' => 'bna', 'Aa31LG11G15250' => 'aar', 'Aa31LG1G1800' => 'aar', 'Aa31LG2G5120' => 'aar', 'Aa31LG2G6070' => 'aar', 'Aa31LG5G10770' => 'aar', 'Aa31sc61G90' => 'aar', 'Actinidia01352' => 'ach', 'Actinidia05983' => 'ach', 'Actinidia08133' => 'ach', 'Actinidia15101' => 'ach', 'Actinidia26379' => 'ach', 'Actinidia35778' => 'ach', 'Actinidia36123' => 'ach', 'Actinidia37436' => 'ach', 'Actinidia38730' => 'ach', 'Ah.02g128210' => 'amhyb', 'Ah.03g132990' => 'amhyb', 'Ah.14g079410' => 'amhyb', 'AL1G24640' => 'aly', 'AL2G26680' => 'aly', 'AL3G10530' => 'aly', 'AL3G45230' => 'aly', 'AL5G15230' => 'aly', 'AL5G16960' => 'aly', 'AL6G25210' => 'aly', 'Aqoxy2G00441' => 'aox', 'Aqoxy3G01236' => 'aox', 'Aqoxy5G03746' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3RQ047' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C7GMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9C8JER' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MBL6KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YXCZ83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZANX40' => 'arhy', 'AT1G12990' => 'ath', 'AT1G67880' => 'ath', 'AT2G13290' => 'ath', 'AT3G01620' => 'ath', 'AT3G26445' => 'ath', 'AT3G27540' => 'ath', 'AT5G14480' => 'ath', 'ATR0824G026' => 'atr', 'ATR1098G019' => 'atr', 'Atru.chr11.2145' => 'acertr', 'Atru.chr2.3636' => 'acertr', 'Atru.chr2.3644' => 'acertr', 'Atru.chr6.2422' => 'acertr', 'Atru.chr7.1112' => 'acertr', 'AUR62005469' => 'cqu', 'AUR62011166' => 'cqu', 'AUR62013319' => 'cqu', 'AUR62024273' => 'cqu', 'AUR62028420' => 'cqu', 'AUR62041942' => 'cqu', 'BcaB01g04969' => 'bca', 'BcaB01g06371' => 'bca', 'BcaB02g11494' => 'bca', 'BcaB03g15382' => 'bca', 'BcaB08g36994' => 'bca', 'BcaC03g13477' => 'bca', 'BcaC03g13478' => 'bca', 'BcaC03g13480' => 'bca', 'BcaC03g13481' => 'bca', 'BcaC03g13486' => 'bca', 'BcaC04g19031' => 'bca', 'BcaC04g23085' => 'bca', 'BcaC05g25094' => 'bca', 'BcaC05g25096' => 'bca', 'BcaC05g25138' => 'bca', 'BcaC05g30416' => 'bca', 'BcaC05g30455' => 'bca', 'BcaC06g30979' => 'bca', 'BcaC06g33805' => 'bca', 'BcaC08g46021' => 'bca', 'BcaNung03154' => 'bca', 'BolC2t06623H' => 'bol', 'BolC2t06632H' => 'bol', 'BolC2t06635H' => 'bol', 'BolC2t06638H' => 'bol', 'BolC3t13266H' => 'bol', 'BolC5t29776H' => 'bol', 'BolC6t38912H' => 'bol', 'BolC7t44183H' => 'bol', 'BolC9t54123H' => 'bol', 'BolC9t59107H' => 'bol', 'BraA02t05221Z' => 'bra', 'BraA03t09996Z' => 'bra', 'BraA05t23210Z' => 'bra', 'BraA06t24068Z' => 'bra', 'BraA06t27032Z' => 'bra', 'BraA08t35176Z' => 'bra', 'BraA09t36680Z' => 'bra', 'BraA10t44471Z' => 'bra', 'C02p06760' => 'bna', 'C02p06890' => 'bna', 'C02p07010' => 'bna', 'C03p07660' => 'bna', 'C05p10300' => 'bna', 'C06p38150' => 'bna', 'C07p36650' => 'bna', 'C08p15770' => 'bna', 'C09p12300' => 'bna', 'C09p62700' => 'bna', 'C09p75040' => 'bna', 'CAN.G13.1' => 'can', 'CAN.G138.4' => 'can', 'CAN.G44.6' => 'can', 'CAN.G473.19' => 'can', 'CANSAT01G0835' => 'cansat', 'CANSAT11G0246' => 'cansat', 'CANSAT11G1766' => 'cansat', 'CANSAT64G1954' => 'cansat', 'CARHR013330' => 'chi', 'CARHR060530' => 'chi', 'CARHR075300' => 'chi', 'CARHR105120' => 'chi', 'CARHR148910' => 'chi', 'CARHR198830' => 'chi', 'Carub.0001s1275' => 'cru', 'Carub.0002s1437' => 'cru', 'Carub.0003s0044' => 'cru', 'Carub.0003s2787' => 'cru', 'Carub.0005s0597' => 'cru', 'Carub.0006s1266' => 'cru', 'Ca_06935_v3' => 'car', 'Ca_13559_v3' => 'car', 'Ca_16941_v3' => 'car', 'Ca_16960_v3' => 'car', 'Ca_17775_v3' => 'car', 'Ca_30464_v3' => 'car', 'Cc06_g08160' => 'ccan', 'Cc07_g01520' => 'ccan', 'Cc11_g15810' => 'ccan', 'CDE02G2840' => 'cde', 'CDE03G0093' => 'cde', 'CDE04G2127' => 'cde', 'CDE07G1857' => 'cde', 'CDE09G1246' => 'cde', 'Cfa003412' => 'cfa', 'Cfa007341' => 'cfa', 'Cfa009220' => 'cfa', 'Ciclev10008737m.g' => 'ccl', 'Ciclev10015565m.g' => 'ccl', 'Ciclev10031761m.g' => 'ccl', 'CiPaw.03G045300' => 'cil', 'CiPaw.03G247200' => 'cil', 'CiPaw.04G029500' => 'cil', 'CiPaw.04G174000' => 'cil', 'CiPaw.05G181200' => 'cil', 'CiPaw.06G067100' => 'cil', 'ClCG05G025800' => 'cla', 'ClCG06G011400' => 'cla', 'ClCG09G019360' => 'cla', 'COL.COLO4_04827' => 'col', 'COL.COLO4_29170' => 'col', 'COL.COLO4_35131' => 'col', 'COL.COLO4_35132' => 'col', 'Cpa.g.sc33.32' => 'cpa', 'Cpa.g.sc46.29' => 'cpa', 'Cpa.g.sc796.1' => 'cpa', 'CsaV3_1G030420' => 'csa', 'CsaV3_5G027050' => 'csa', 'CsaV3_5G031040' => 'csa', 'CsaV3_UNG023130' => 'csa', 'CSS0007726' => 'camsi', 'CSS0016433' => 'camsi', 'CSS0017656' => 'camsi', 'CSS0025364' => 'camsi', 'CSS0027582' => 'camsi', 'CSS0047288' => 'camsi', 'CSS0049950' => 'camsi', 'DCAR_003843' => 'dca', 'DCAR_007052' => 'dca', 'DCAR_020884' => 'dca', 'DCAR_021730' => 'dca', 'DCAR_024423' => 'dca', 'DCAR_026509' => 'dca', 'DCAR_031158' => 'dca', 'Dinv14728' => 'din', 'Dinv15219' => 'din', 'Dinv25728' => 'din', 'Dinv33428' => 'din', 'Dinv36489' => 'din', 'Dinv41486' => 'din', 'Duzib147G0469' => 'dzi', 'Duzib168G0060' => 'dzi', 'Duzib187G1215' => 'dzi', 'Duzib248G0692' => 'dzi', 'Duzib251G0767' => 'dzi', 'Duzib264G0446' => 'dzi', 'Duzib268G0691' => 'dzi', 'ECA232G4767' => 'eca', 'ECA233G2838' => 'eca', 'ECA234G0391' => 'eca', 'ECA234G0857' => 'eca', 'ECA236G1593' => 'eca', 'ECA238G0565' => 'eca', 'ECA246G1027' => 'eca', 'ECA246G3223' => 'eca', 'ECA246G3470' => 'eca', 'EL10Ac6g13829' => 'bvu', 'EL10Ac6g14093' => 'bvu', 'EL10Ac8g18707' => 'bvu', 'Eucgr.C01369' => 'egr', 'Eucgr.H02492' => 'egr', 'Eucgr.I01733' => 'egr', 'Eucgr.J02255' => 'egr', 'Eucgr.J02257' => 'egr', 'Eucgr.J02258' => 'egr', 'FAN02G1601' => 'fan', 'FAN03G1586' => 'fan', 'FAN03G2986' => 'fan', 'FAN05G4837' => 'fan', 'FAN06G0146' => 'fan', 'FAN07G0858' => 'fan', 'FAN09G3179' => 'fan', 'FAN10G0669' => 'fan', 'FAN12G2358' => 'fan', 'FAN14G4198' => 'fan', 'FAN14G5112' => 'fan', 'FAN17G0342' => 'fan', 'FAN19G0342' => 'fan', 'FAN19G0962' => 'fan', 'FAN19G1101' => 'fan', 'FAN19G1872' => 'fan', 'FAN22G0356' => 'fan', 'FAN23G0744' => 'fan', 'FAN23G1914' => 'fan', 'FAN26G0032' => 'fan', 'FAN28G0625' => 'fan', 'FvH4_1g02710' => 'fve', 'FvH4_1g02720' => 'fve', 'FvH4_4g25670' => 'fve', 'FvH4_6g51700' => 'fve', 'FvH4_7g20170' => 'fve', 'Glyma.05G175000' => 'gma', 'Glyma.08G132300' => 'gma', 'Glyma.11G243000' => 'gma', 'Glyma.13G158900' => 'gma', 'Glyma.17G112400' => 'gma', 'Glyma.18G014100' => 'gma', 'Glyma.19G003100' => 'gma', 'Glyma.19G056500' => 'gma', 'Gohir.A01G158900' => 'ghi', 'Gohir.A05G312600' => 'ghi', 'Gohir.A05G354900' => 'ghi', 'Gohir.A07G037200' => 'ghi', 'Gohir.A09G030000' => 'ghi', 'Gohir.A12G145200' => 'ghi', 'Gohir.D01G151500' => 'ghi', 'Gohir.D04G058300' => 'ghi', 'Gohir.D05G314100' => 'ghi', 'Gohir.D07G041400' => 'ghi', 'Gohir.D09G029700' => 'ghi', 'Gohir.D12G149700' => 'ghi', 'Gorai.001G043800' => 'gra', 'Gorai.002G187800' => 'gra', 'Gorai.006G034700' => 'gra', 'Gorai.008G161200' => 'gra', 'Gorai.009G335700' => 'gra', 'Gorai.012G065000' => 'gra', 'GSVIVG01000535001' => 'vvi', 'GSVIVG01015572001' => 'vvi', 'GSVIVG01032386001' => 'vvi', 'HanXRQChr05g0138531' => 'han', 'HanXRQChr06g0174391' => 'han', 'HanXRQChr07g0199021' => 'han', 'HanXRQChr08g0208211' => 'han', 'HanXRQChr09g0255471' => 'han', 'HanXRQChr10g0315791' => 'han', 'HanXRQChr12g0371991' => 'han', 'HanXRQChr15g0475251' => 'han', 'HanXRQChr17g0540001' => 'han', 'HanXRQChr17g0548631' => 'han', 'HanXRQChr17g0569561' => 'han', 'Haze_12256' => 'cav', 'Haze_14756' => 'cav', 'Haze_25528' => 'cav', 'Hma1.2p1_0079F.1_g041020' => 'hma', 'Hma1.2p1_0818F.1_g223260' => 'hma', 'Hma1.2p1_1747F.1_g300530' => 'hma', 'HPP92_004607' => 'vpl', 'HPP92_004608' => 'vpl', 'HPP92_006181' => 'vpl', 'HPP92_012192' => 'vpl', 'HPP92_015680' => 'vpl', 'HPP92_020249' => 'vpl', 'HPP92_021376' => 'vpl', 'HPP92_024275' => 'vpl', 'Hund06031' => 'sun', 'Hund25391' => 'sun', 'Lalb_Chr07g0185371' => 'lal', 'Lalb_Chr07g0185381' => 'lal', 'Lalb_Chr12g0204011' => 'lal', 'Lalb_Chr13g0301671' => 'lal', 'Lalb_Chr14g0362851' => 'lal', 'Lalb_Chr24g0403581' => 'lal', 'Lj1g0000233' => 'lja', 'Lj2g0018120' => 'lja', 'Lj3C621T0' => 'lonja', 'Lj3P1059T14' => 'lonja', 'Lj3P611T9' => 'lonja', 'Lj3P614T13' => 'lonja', 'Lj3P615T5' => 'lonja', 'Lj4g0012315' => 'lja', 'Lj4g0026182' => 'lja', 'Lj6P813T16' => 'lonja', 'Lj7C427T7' => 'lonja', 'Lj7C427T8' => 'lonja', 'Lj7P600T41' => 'lonja', 'Lju41C42G17' => 'lonja', 'Lsat_1_v5_gn_0_47300' => 'lsa', 'Lsat_1_v5_gn_2_91280' => 'lsa', 'Lsat_1_v5_gn_3_30561' => 'lsa', 'Lsat_1_v5_gn_4_184321' => 'lsa', 'Lsat_1_v5_gn_4_4041' => 'lsa', 'Lsat_1_v5_gn_5_92000' => 'lsa', 'Lsat_1_v5_gn_8_152940' => 'lsa', 'Lsat_1_v5_gn_8_62401' => 'lsa', 'Manes.06G055900' => 'mes', 'Manes.12G022200' => 'mes', 'Manes.13G023300' => 'mes', 'Manes.14G115000' => 'mes', 'Manes.15G151700' => 'mes', 'Manes.17G111300' => 'mes', 'Mapoly0226s0009' => 'mpo', 'MBI02_g25363_MAGBIO' => 'mbi', 'MBI06_g00027_MAGBIO' => 'mbi', 'MBI10_g13034_MAGBIO' => 'mbi', 'MD09G1023400' => 'mdo', 'MD13G1100100' => 'mdo', 'MD15G1169200' => 'mdo', 'MD16G1101100' => 'mdo', 'MD17G1022900' => 'mdo', 'Medtr3g096150' => 'mtr', 'Medtr4g115070' => 'mtr', 'Medtr7g033325' => 'mtr', 'Medtr8g089840' => 'mtr', 'MELO3C010319.2' => 'cme', 'MELO3C011944.2' => 'cme', 'MELO3C021589.2' => 'cme', 'Migut.E00207' => 'egut', 'Migut.H00067' => 'egut', 'Migut.K00433' => 'egut', 'Migut.K00606' => 'egut', 'Migut.K01410' => 'egut', 'MSTRG.13347' => 'ama', 'MSTRG.24045' => 'ama', 'MSTRG.2428' => 'ama', 'MSTRG.26410' => 'ama', 'MSTRG.3139' => 'ama', 'MSTRG.3286' => 'ama', 'MSTRG.563' => 'ama', 'MSTRG.7941' => 'ama', 'Nitab4.5_0000028g0060' => 'nta', 'Nitab4.5_0000065g0260' => 'nta', 'Nitab4.5_0000112g0060' => 'nta', 'Nitab4.5_0000489g0120' => 'nta', 'Nitab4.5_0001776g0050' => 'nta', 'Nitab4.5_0001854g0010' => 'nta', 'Nitab4.5_0001860g0020' => 'nta', 'Nitab4.5_0004352g0010' => 'nta', 'Nitab4.5_0008716g0020' => 'nta', 'Nitab4.5_0008922g0010' => 'nta', 'Nn3g16693' => 'nnu', 'Nn4g22596' => 'nnu', 'Nn7g37639' => 'nnu', 'Oeu001701.1' => 'oeu', 'Oeu018149.1' => 'oeu', 'Oeu026220.1' => 'oeu', 'Oeu038635.1' => 'oeu', 'Oeu049176.1' => 'oeu', 'Oeu056706.1' => 'oeu', 'Oeu056937.1' => 'oeu', 'Oeu057540.1' => 'oeu', 'Os02g0594900' => 'osa', 'Os02g0595100' => 'osa', 'Os04g0477500' => 'osa', 'Os12g0611900' => 'osa', 'Peaxi162Scf00076g00020' => 'pax', 'Peaxi162Scf00128g00217' => 'pax', 'Peaxi162Scf00129g01640' => 'pax', 'Peaxi162Scf00669g00007' => 'pax', 'Peaxi162Scf00700g00421' => 'pax', 'Peaxi162Scf00801g00038' => 'pax', 'Peaxi162Scf00891g00025' => 'pax', 'PGR083G0909' => 'pgr', 'PGR119G1005' => 'pgr', 'PGR142G2236' => 'pgr', 'PGR142G3388' => 'pgr', 'PGSC0003DMG400004514' => 'stu', 'PGSC0003DMG400012635' => 'stu', 'PGSC0003DMG400015730' => 'stu', 'PGSC0003DMG400018611' => 'stu', 'PGSC0003DMG400030897' => 'stu', 'Phvul.001G254800' => 'pvu', 'Phvul.002G260100' => 'pvu', 'Phvul.003G167600' => 'pvu', 'Phvul.004G005100' => 'pvu', 'Potri.001G343600' => 'ptr', 'Potri.006G066700' => 'ptr', 'Potri.008G186000' => 'ptr', 'Potri.010G046900' => 'ptr', 'Potri.018G127900' => 'ptr', 'Pp3c20_17750' => 'ppa', 'Pp3c24_4380' => 'ppa', 'Prupe.1G245800' => 'ppe', 'Prupe.3G293400' => 'ppe', 'Prupe.7G247400' => 'ppe', 'Psat0s145g0120' => 'psa', 'Psat0s595g0040' => 'psa', 'Psat0s595g0120' => 'psa', 'Psat3g175040' => 'psa', 'Psat7g058120' => 'psa', 'PSO017G0428' => 'pso', 'PSO063G7510' => 'pso', 'PSO067G0046' => 'pso', 'PSO478G1073' => 'pso', 'PSO675G3677' => 'pso', 'PSO675G6558' => 'pso', 'PSO675G7520' => 'pso', 'PSO675G8959' => 'pso', 'QL02p074089' => 'qlo', 'QL02p089614' => 'qlo', 'QL03p057736' => 'qlo', 'RcHm_v2.0_Chr1g0364131' => 'rch', 'RcHm_v2.0_Chr2g0087801' => 'rch', 'RcHm_v2.0_Chr2g0087821' => 'rch', 'RcHm_v2.0_Chr2g0173231' => 'rch', 'RcHm_v2.0_Chr4g0433111' => 'rch', 'Rhsim03G0250300' => 'rsi', 'Rhsim08G0048400' => 'rsi', 'Rhsim10G0014800' => 'rsi', 'Rhsim12G0040100' => 'rsi', 'Rhsim12G0109700' => 'rsi', 'Sabra06G0049600' => 'sbr', 'Sabra08G0141000' => 'sbr', 'Sabra10G0021400' => 'sbr', 'Sabra16G0222900' => 'sbr', 'Sabra18G0108600' => 'sbr', 'SalBow1G0433' => 'sbo', 'SalBow1G2038' => 'sbo', 'SalBow1G5003' => 'sbo', 'SalBow7G1197' => 'sbo', 'SalBow8G3506' => 'sbo', 'Sc03g0007300' => 'sci', 'Sc11g0000950' => 'sci', 'Sc14g0008750' => 'sci', 'Sc18g0000420' => 'sci', 'Sed0006754' => 'sed', 'Sed0008741' => 'sed', 'Sed0017172' => 'sed', 'Sed0018925' => 'sed', 'Sed0023326' => 'sed', 'Sed0025909' => 'sed', 'SEGI_05333' => 'sgi', 'SEGI_10362' => 'sgi', 'SEGI_13380' => 'sgi', 'SEGI_24306' => 'sgi', 'SEGI_29077' => 'sgi', 'SEGI_29095' => 'sgi', 'SEGI_36534' => 'sgi', 'SEGI_37506' => 'sgi', 'SEGI_38321' => 'sgi', 'SGA_v2.0_scaffold307G48031' => 'sas', 'SGA_v2.0_scaffold47G17507' => 'sas', 'SGA_v2.0_scaffold63G21736' => 'sas', 'SGA_v2.0_scaffold87G27070' => 'sas', 'SHI17794' => 'shi', 'SHI28851' => 'shi', 'SMO165G0155' => 'smo', 'SMO340G0217' => 'smo', 'SMO367G1210' => 'smo', 'Solyc02g093430.3' => 'sly', 'Solyc05g013580.4' => 'sly', 'Solyc07g008030.3' => 'sly', 'Solyc12g035470.2' => 'sly', 'Sopen02g038020' => 'spe', 'Sopen05g008490' => 'spe', 'Sopen07g003910' => 'spe', 'Sopen12g015240' => 'spe', 'Sp1g11550' => 'spa', 'Sp2g16710' => 'spa', 'Sp3g00430' => 'spa', 'Sp3g26780' => 'spa', 'Sp5g22900' => 'spa', 'Sp6g29530' => 'spa', 'TAR371G0794' => 'tar', 'TAR374G0164' => 'tar', 'TAR622G0165' => 'tar', 'TAR626G0929' => 'tar', 'TAR629G2155' => 'tar', 'THA.LOC104805282' => 'tha', 'THA.LOC104805363' => 'tha', 'THA.LOC104808968' => 'tha', 'THA.LOC104821093' => 'tha', 'THA.LOC104823953' => 'tha', 'THA.LOC104825562' => 'tha', 'THA.LOC104825665' => 'tha', 'Thecc.02G261400' => 'tca', 'Thecc.04G019200' => 'tca', 'Thecc.09G130400' => 'tca', 'Thhalv10004374m.g' => 'esa', 'Thhalv10007850m.g' => 'esa', 'Thhalv10013782m.g' => 'esa', 'Thhalv10018686m.g' => 'esa', 'Thhalv10020899m.g' => 'esa', 'Thhalv10022755m.g' => 'esa', 'TPR.G23851' => 'tpr', 'TPR.G26500' => 'tpr', 'TPR.G27267' => 'tpr', 'TPR.G32001' => 'tpr', 'TPR.G6251' => 'tpr', 'TPR.G8167' => 'tpr', 'TWI12G1330' => 'twi', 'TWI18G1239' => 'twi', 'TWI34G0979' => 'twi', 'TWI36G0670' => 'twi', 'TWI36G0707' => 'twi', 'TWI56G0233' => 'twi', 'TWI75G1809' => 'twi', 'unitig_21.g20874' => 'ugi', 'unitig_26.g10343' => 'ugi', 'unitig_46.g18392' => 'ugi', 'unitig_52.g17178' => 'ugi', 'unitig_8.g2934' => 'ugi', 'vmacro01122' => 'vma', 'vmacro05875' => 'vma', 'vmacro06147' => 'vma', 'vmacro16191' => 'vma', 'vmacro18293' => 'vma', 'VMungo0251G3707' => 'vmu', 'VMungo0464G1521' => 'vmu', 'VMungo1215G0205' => 'vmu', 'VMungo1383G2484' => 'vmu', 'Zm00001eb079610' => 'zma', 'Zm00001eb135990' => 'zma', 'Zm00001eb183710' => 'zma', 'Zm00001eb246020' => 'zma' ), 'gf_id' => 'HOM05D001124', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001124' ), 'data_identifier' => 'HOM05D001124', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001124', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '548', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02520' => 'bna', 'A03p06630' => 'bna', 'A05p44460' => 'bna', 'A06p08710' => 'bna', 'A06p41090' => 'bna', 'A07p32320' => 'bna', 'A08p32520' => 'bna', 'A09p10360' => 'bna', 'A10p24080' => 'bna', 'Aa31LG11G15250' => 'aar', 'Aa31LG1G1800' => 'aar', 'Aa31LG2G5120' => 'aar', 'Aa31LG2G6070' => 'aar', 'Aa31LG5G10770' => 'aar', 'Aa31sc61G90' => 'aar', 'Actinidia01352' => 'ach', 'Actinidia05983' => 'ach', 'Actinidia08133' => 'ach', 'Actinidia15101' => 'ach', 'Actinidia26379' => 'ach', 'Actinidia35778' => 'ach', 'Actinidia36123' => 'ach', 'Actinidia37436' => 'ach', 'Actinidia38730' => 'ach', 'Ah.02g128210' => 'amhyb', 'Ah.03g132990' => 'amhyb', 'Ah.14g079410' => 'amhyb', 'AL1G24640' => 'aly', 'AL2G26680' => 'aly', 'AL3G10530' => 'aly', 'AL3G45230' => 'aly', 'AL5G15230' => 'aly', 'AL5G16960' => 'aly', 'AL6G25210' => 'aly', 'Aqoxy2G00441' => 'aox', 'Aqoxy3G01236' => 'aox', 'Aqoxy5G03746' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3RQ047' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C7GMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9C8JER' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MBL6KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YXCZ83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZANX40' => 'arhy', 'AT1G12990' => 'ath', 'AT1G67880' => 'ath', 'AT2G13290' => 'ath', 'AT3G01620' => 'ath', 'AT3G26445' => 'ath', 'AT3G27540' => 'ath', 'AT5G14480' => 'ath', 'ATR0824G026' => 'atr', 'ATR1098G019' => 'atr', 'Atru.chr11.2145' => 'acertr', 'Atru.chr2.3636' => 'acertr', 'Atru.chr2.3644' => 'acertr', 'Atru.chr6.2422' => 'acertr', 'Atru.chr7.1112' => 'acertr', 'AUR62005469' => 'cqu', 'AUR62011166' => 'cqu', 'AUR62013319' => 'cqu', 'AUR62024273' => 'cqu', 'AUR62028420' => 'cqu', 'AUR62041942' => 'cqu', 'BcaB01g04969' => 'bca', 'BcaB01g06371' => 'bca', 'BcaB02g11494' => 'bca', 'BcaB03g15382' => 'bca', 'BcaB08g36994' => 'bca', 'BcaC03g13477' => 'bca', 'BcaC03g13478' => 'bca', 'BcaC03g13480' => 'bca', 'BcaC03g13481' => 'bca', 'BcaC03g13486' => 'bca', 'BcaC04g19031' => 'bca', 'BcaC04g23085' => 'bca', 'BcaC05g25094' => 'bca', 'BcaC05g25096' => 'bca', 'BcaC05g25138' => 'bca', 'BcaC05g30416' => 'bca', 'BcaC05g30455' => 'bca', 'BcaC06g30979' => 'bca', 'BcaC06g33805' => 'bca', 'BcaC08g46021' => 'bca', 'BcaNung03154' => 'bca', 'BolC2t06623H' => 'bol', 'BolC2t06632H' => 'bol', 'BolC2t06635H' => 'bol', 'BolC2t06638H' => 'bol', 'BolC3t13266H' => 'bol', 'BolC5t29776H' => 'bol', 'BolC6t38912H' => 'bol', 'BolC7t44183H' => 'bol', 'BolC9t54123H' => 'bol', 'BolC9t59107H' => 'bol', 'BraA02t05221Z' => 'bra', 'BraA03t09996Z' => 'bra', 'BraA05t23210Z' => 'bra', 'BraA06t24068Z' => 'bra', 'BraA06t27032Z' => 'bra', 'BraA08t35176Z' => 'bra', 'BraA09t36680Z' => 'bra', 'BraA10t44471Z' => 'bra', 'C02p06760' => 'bna', 'C02p06890' => 'bna', 'C02p07010' => 'bna', 'C03p07660' => 'bna', 'C05p10300' => 'bna', 'C06p38150' => 'bna', 'C07p36650' => 'bna', 'C08p15770' => 'bna', 'C09p12300' => 'bna', 'C09p62700' => 'bna', 'C09p75040' => 'bna', 'CAN.G13.1' => 'can', 'CAN.G138.4' => 'can', 'CAN.G44.6' => 'can', 'CAN.G473.19' => 'can', 'CANSAT01G0835' => 'cansat', 'CANSAT11G0246' => 'cansat', 'CANSAT11G1766' => 'cansat', 'CANSAT64G1954' => 'cansat', 'CARHR013330' => 'chi', 'CARHR060530' => 'chi', 'CARHR075300' => 'chi', 'CARHR105120' => 'chi', 'CARHR148910' => 'chi', 'CARHR198830' => 'chi', 'Carub.0001s1275' => 'cru', 'Carub.0002s1437' => 'cru', 'Carub.0003s0044' => 'cru', 'Carub.0003s2787' => 'cru', 'Carub.0005s0597' => 'cru', 'Carub.0006s1266' => 'cru', 'Ca_06935_v3' => 'car', 'Ca_13559_v3' => 'car', 'Ca_16941_v3' => 'car', 'Ca_16960_v3' => 'car', 'Ca_17775_v3' => 'car', 'Ca_30464_v3' => 'car', 'Cc06_g08160' => 'ccan', 'Cc07_g01520' => 'ccan', 'Cc11_g15810' => 'ccan', 'CDE02G2840' => 'cde', 'CDE03G0093' => 'cde', 'CDE04G2127' => 'cde', 'CDE07G1857' => 'cde', 'CDE09G1246' => 'cde', 'Cfa003412' => 'cfa', 'Cfa007341' => 'cfa', 'Cfa009220' => 'cfa', 'Ciclev10008737m.g' => 'ccl', 'Ciclev10015565m.g' => 'ccl', 'Ciclev10031761m.g' => 'ccl', 'CiPaw.03G045300' => 'cil', 'CiPaw.03G247200' => 'cil', 'CiPaw.04G029500' => 'cil', 'CiPaw.04G174000' => 'cil', 'CiPaw.05G181200' => 'cil', 'CiPaw.06G067100' => 'cil', 'ClCG05G025800' => 'cla', 'ClCG06G011400' => 'cla', 'ClCG09G019360' => 'cla', 'COL.COLO4_04827' => 'col', 'COL.COLO4_29170' => 'col', 'COL.COLO4_35131' => 'col', 'COL.COLO4_35132' => 'col', 'Cpa.g.sc33.32' => 'cpa', 'Cpa.g.sc46.29' => 'cpa', 'Cpa.g.sc796.1' => 'cpa', 'CsaV3_1G030420' => 'csa', 'CsaV3_5G027050' => 'csa', 'CsaV3_5G031040' => 'csa', 'CsaV3_UNG023130' => 'csa', 'CSS0007726' => 'camsi', 'CSS0016433' => 'camsi', 'CSS0017656' => 'camsi', 'CSS0025364' => 'camsi', 'CSS0027582' => 'camsi', 'CSS0047288' => 'camsi', 'CSS0049950' => 'camsi', 'DCAR_003843' => 'dca', 'DCAR_007052' => 'dca', 'DCAR_020884' => 'dca', 'DCAR_021730' => 'dca', 'DCAR_024423' => 'dca', 'DCAR_026509' => 'dca', 'DCAR_031158' => 'dca', 'Dinv14728' => 'din', 'Dinv15219' => 'din', 'Dinv25728' => 'din', 'Dinv33428' => 'din', 'Dinv36489' => 'din', 'Dinv41486' => 'din', 'Duzib147G0469' => 'dzi', 'Duzib168G0060' => 'dzi', 'Duzib187G1215' => 'dzi', 'Duzib248G0692' => 'dzi', 'Duzib251G0767' => 'dzi', 'Duzib264G0446' => 'dzi', 'Duzib268G0691' => 'dzi', 'ECA232G4767' => 'eca', 'ECA233G2838' => 'eca', 'ECA234G0391' => 'eca', 'ECA234G0857' => 'eca', 'ECA236G1593' => 'eca', 'ECA238G0565' => 'eca', 'ECA246G1027' => 'eca', 'ECA246G3223' => 'eca', 'ECA246G3470' => 'eca', 'EL10Ac6g13829' => 'bvu', 'EL10Ac6g14093' => 'bvu', 'EL10Ac8g18707' => 'bvu', 'Eucgr.C01369' => 'egr', 'Eucgr.H02492' => 'egr', 'Eucgr.I01733' => 'egr', 'Eucgr.J02255' => 'egr', 'Eucgr.J02257' => 'egr', 'Eucgr.J02258' => 'egr', 'FAN02G1601' => 'fan', 'FAN03G1586' => 'fan', 'FAN03G2986' => 'fan', 'FAN05G4837' => 'fan', 'FAN06G0146' => 'fan', 'FAN07G0858' => 'fan', 'FAN09G3179' => 'fan', 'FAN10G0669' => 'fan', 'FAN12G2358' => 'fan', 'FAN14G4198' => 'fan', 'FAN14G5112' => 'fan', 'FAN17G0342' => 'fan', 'FAN19G0342' => 'fan', 'FAN19G0962' => 'fan', 'FAN19G1101' => 'fan', 'FAN19G1872' => 'fan', 'FAN22G0356' => 'fan', 'FAN23G0744' => 'fan', 'FAN23G1914' => 'fan', 'FAN26G0032' => 'fan', 'FAN28G0625' => 'fan', 'FvH4_1g02710' => 'fve', 'FvH4_1g02720' => 'fve', 'FvH4_4g25670' => 'fve', 'FvH4_6g51700' => 'fve', 'FvH4_7g20170' => 'fve', 'Glyma.05G175000' => 'gma', 'Glyma.08G132300' => 'gma', 'Glyma.11G243000' => 'gma', 'Glyma.13G158900' => 'gma', 'Glyma.17G112400' => 'gma', 'Glyma.18G014100' => 'gma', 'Glyma.19G003100' => 'gma', 'Glyma.19G056500' => 'gma', 'Gohir.A01G158900' => 'ghi', 'Gohir.A05G312600' => 'ghi', 'Gohir.A05G354900' => 'ghi', 'Gohir.A07G037200' => 'ghi', 'Gohir.A09G030000' => 'ghi', 'Gohir.A12G145200' => 'ghi', 'Gohir.D01G151500' => 'ghi', 'Gohir.D04G058300' => 'ghi', 'Gohir.D05G314100' => 'ghi', 'Gohir.D07G041400' => 'ghi', 'Gohir.D09G029700' => 'ghi', 'Gohir.D12G149700' => 'ghi', 'Gorai.001G043800' => 'gra', 'Gorai.002G187800' => 'gra', 'Gorai.006G034700' => 'gra', 'Gorai.008G161200' => 'gra', 'Gorai.009G335700' => 'gra', 'Gorai.012G065000' => 'gra', 'GSVIVG01000535001' => 'vvi', 'GSVIVG01015572001' => 'vvi', 'GSVIVG01032386001' => 'vvi', 'HanXRQChr05g0138531' => 'han', 'HanXRQChr06g0174391' => 'han', 'HanXRQChr07g0199021' => 'han', 'HanXRQChr08g0208211' => 'han', 'HanXRQChr09g0255471' => 'han', 'HanXRQChr10g0315791' => 'han', 'HanXRQChr12g0371991' => 'han', 'HanXRQChr15g0475251' => 'han', 'HanXRQChr17g0540001' => 'han', 'HanXRQChr17g0548631' => 'han', 'HanXRQChr17g0569561' => 'han', 'Haze_12256' => 'cav', 'Haze_14756' => 'cav', 'Haze_25528' => 'cav', 'Hma1.2p1_0079F.1_g041020' => 'hma', 'Hma1.2p1_0818F.1_g223260' => 'hma', 'Hma1.2p1_1747F.1_g300530' => 'hma', 'HPP92_004607' => 'vpl', 'HPP92_004608' => 'vpl', 'HPP92_006181' => 'vpl', 'HPP92_012192' => 'vpl', 'HPP92_015680' => 'vpl', 'HPP92_020249' => 'vpl', 'HPP92_021376' => 'vpl', 'HPP92_024275' => 'vpl', 'Hund06031' => 'sun', 'Hund25391' => 'sun', 'Lalb_Chr07g0185371' => 'lal', 'Lalb_Chr07g0185381' => 'lal', 'Lalb_Chr12g0204011' => 'lal', 'Lalb_Chr13g0301671' => 'lal', 'Lalb_Chr14g0362851' => 'lal', 'Lalb_Chr24g0403581' => 'lal', 'Lj1g0000233' => 'lja', 'Lj2g0018120' => 'lja', 'Lj3C621T0' => 'lonja', 'Lj3P1059T14' => 'lonja', 'Lj3P611T9' => 'lonja', 'Lj3P614T13' => 'lonja', 'Lj3P615T5' => 'lonja', 'Lj4g0012315' => 'lja', 'Lj4g0026182' => 'lja', 'Lj6P813T16' => 'lonja', 'Lj7C427T7' => 'lonja', 'Lj7C427T8' => 'lonja', 'Lj7P600T41' => 'lonja', 'Lju41C42G17' => 'lonja', 'Lsat_1_v5_gn_0_47300' => 'lsa', 'Lsat_1_v5_gn_2_91280' => 'lsa', 'Lsat_1_v5_gn_3_30561' => 'lsa', 'Lsat_1_v5_gn_4_184321' => 'lsa', 'Lsat_1_v5_gn_4_4041' => 'lsa', 'Lsat_1_v5_gn_5_92000' => 'lsa', 'Lsat_1_v5_gn_8_152940' => 'lsa', 'Lsat_1_v5_gn_8_62401' => 'lsa', 'Manes.06G055900' => 'mes', 'Manes.12G022200' => 'mes', 'Manes.13G023300' => 'mes', 'Manes.14G115000' => 'mes', 'Manes.15G151700' => 'mes', 'Manes.17G111300' => 'mes', 'Mapoly0226s0009' => 'mpo', 'MBI02_g25363_MAGBIO' => 'mbi', 'MBI06_g00027_MAGBIO' => 'mbi', 'MBI10_g13034_MAGBIO' => 'mbi', 'MD09G1023400' => 'mdo', 'MD13G1100100' => 'mdo', 'MD15G1169200' => 'mdo', 'MD16G1101100' => 'mdo', 'MD17G1022900' => 'mdo', 'Medtr3g096150' => 'mtr', 'Medtr4g115070' => 'mtr', 'Medtr7g033325' => 'mtr', 'Medtr8g089840' => 'mtr', 'MELO3C010319.2' => 'cme', 'MELO3C011944.2' => 'cme', 'MELO3C021589.2' => 'cme', 'Migut.E00207' => 'egut', 'Migut.H00067' => 'egut', 'Migut.K00433' => 'egut', 'Migut.K00606' => 'egut', 'Migut.K01410' => 'egut', 'MSTRG.13347' => 'ama', 'MSTRG.24045' => 'ama', 'MSTRG.2428' => 'ama', 'MSTRG.26410' => 'ama', 'MSTRG.3139' => 'ama', 'MSTRG.3286' => 'ama', 'MSTRG.563' => 'ama', 'MSTRG.7941' => 'ama', 'Nitab4.5_0000028g0060' => 'nta', 'Nitab4.5_0000065g0260' => 'nta', 'Nitab4.5_0000112g0060' => 'nta', 'Nitab4.5_0000489g0120' => 'nta', 'Nitab4.5_0001776g0050' => 'nta', 'Nitab4.5_0001854g0010' => 'nta', 'Nitab4.5_0001860g0020' => 'nta', 'Nitab4.5_0004352g0010' => 'nta', 'Nitab4.5_0008716g0020' => 'nta', 'Nitab4.5_0008922g0010' => 'nta', 'Nn3g16693' => 'nnu', 'Nn4g22596' => 'nnu', 'Nn7g37639' => 'nnu', 'Oeu001701.1' => 'oeu', 'Oeu018149.1' => 'oeu', 'Oeu026220.1' => 'oeu', 'Oeu038635.1' => 'oeu', 'Oeu049176.1' => 'oeu', 'Oeu056706.1' => 'oeu', 'Oeu056937.1' => 'oeu', 'Oeu057540.1' => 'oeu', 'Os02g0594900' => 'osa', 'Os02g0595100' => 'osa', 'Os04g0477500' => 'osa', 'Os12g0611900' => 'osa', 'Peaxi162Scf00076g00020' => 'pax', 'Peaxi162Scf00128g00217' => 'pax', 'Peaxi162Scf00129g01640' => 'pax', 'Peaxi162Scf00669g00007' => 'pax', 'Peaxi162Scf00700g00421' => 'pax', 'Peaxi162Scf00801g00038' => 'pax', 'Peaxi162Scf00891g00025' => 'pax', 'PGR083G0909' => 'pgr', 'PGR119G1005' => 'pgr', 'PGR142G2236' => 'pgr', 'PGR142G3388' => 'pgr', 'PGSC0003DMG400004514' => 'stu', 'PGSC0003DMG400012635' => 'stu', 'PGSC0003DMG400015730' => 'stu', 'PGSC0003DMG400018611' => 'stu', 'PGSC0003DMG400030897' => 'stu', 'Phvul.001G254800' => 'pvu', 'Phvul.002G260100' => 'pvu', 'Phvul.003G167600' => 'pvu', 'Phvul.004G005100' => 'pvu', 'Potri.001G343600' => 'ptr', 'Potri.006G066700' => 'ptr', 'Potri.008G186000' => 'ptr', 'Potri.010G046900' => 'ptr', 'Potri.018G127900' => 'ptr', 'Pp3c20_17750' => 'ppa', 'Pp3c24_4380' => 'ppa', 'Prupe.1G245800' => 'ppe', 'Prupe.3G293400' => 'ppe', 'Prupe.7G247400' => 'ppe', 'Psat0s145g0120' => 'psa', 'Psat0s595g0040' => 'psa', 'Psat0s595g0120' => 'psa', 'Psat3g175040' => 'psa', 'Psat7g058120' => 'psa', 'PSO017G0428' => 'pso', 'PSO063G7510' => 'pso', 'PSO067G0046' => 'pso', 'PSO478G1073' => 'pso', 'PSO675G3677' => 'pso', 'PSO675G6558' => 'pso', 'PSO675G7520' => 'pso', 'PSO675G8959' => 'pso', 'QL02p074089' => 'qlo', 'QL02p089614' => 'qlo', 'QL03p057736' => 'qlo', 'RcHm_v2.0_Chr1g0364131' => 'rch', 'RcHm_v2.0_Chr2g0087801' => 'rch', 'RcHm_v2.0_Chr2g0087821' => 'rch', 'RcHm_v2.0_Chr2g0173231' => 'rch', 'RcHm_v2.0_Chr4g0433111' => 'rch', 'Rhsim03G0250300' => 'rsi', 'Rhsim08G0048400' => 'rsi', 'Rhsim10G0014800' => 'rsi', 'Rhsim12G0040100' => 'rsi', 'Rhsim12G0109700' => 'rsi', 'Sabra06G0049600' => 'sbr', 'Sabra08G0141000' => 'sbr', 'Sabra10G0021400' => 'sbr', 'Sabra16G0222900' => 'sbr', 'Sabra18G0108600' => 'sbr', 'SalBow1G0433' => 'sbo', 'SalBow1G2038' => 'sbo', 'SalBow1G5003' => 'sbo', 'SalBow7G1197' => 'sbo', 'SalBow8G3506' => 'sbo', 'Sc03g0007300' => 'sci', 'Sc11g0000950' => 'sci', 'Sc14g0008750' => 'sci', 'Sc18g0000420' => 'sci', 'Sed0006754' => 'sed', 'Sed0008741' => 'sed', 'Sed0017172' => 'sed', 'Sed0018925' => 'sed', 'Sed0023326' => 'sed', 'Sed0025909' => 'sed', 'SEGI_05333' => 'sgi', 'SEGI_10362' => 'sgi', 'SEGI_13380' => 'sgi', 'SEGI_24306' => 'sgi', 'SEGI_29077' => 'sgi', 'SEGI_29095' => 'sgi', 'SEGI_36534' => 'sgi', 'SEGI_37506' => 'sgi', 'SEGI_38321' => 'sgi', 'SGA_v2.0_scaffold307G48031' => 'sas', 'SGA_v2.0_scaffold47G17507' => 'sas', 'SGA_v2.0_scaffold63G21736' => 'sas', 'SGA_v2.0_scaffold87G27070' => 'sas', 'SHI17794' => 'shi', 'SHI28851' => 'shi', 'SMO165G0155' => 'smo', 'SMO340G0217' => 'smo', 'SMO367G1210' => 'smo', 'Solyc02g093430.3' => 'sly', 'Solyc05g013580.4' => 'sly', 'Solyc07g008030.3' => 'sly', 'Solyc12g035470.2' => 'sly', 'Sopen02g038020' => 'spe', 'Sopen05g008490' => 'spe', 'Sopen07g003910' => 'spe', 'Sopen12g015240' => 'spe', 'Sp1g11550' => 'spa', 'Sp2g16710' => 'spa', 'Sp3g00430' => 'spa', 'Sp3g26780' => 'spa', 'Sp5g22900' => 'spa', 'Sp6g29530' => 'spa', 'TAR371G0794' => 'tar', 'TAR374G0164' => 'tar', 'TAR622G0165' => 'tar', 'TAR626G0929' => 'tar', 'TAR629G2155' => 'tar', 'THA.LOC104805282' => 'tha', 'THA.LOC104805363' => 'tha', 'THA.LOC104808968' => 'tha', 'THA.LOC104821093' => 'tha', 'THA.LOC104823953' => 'tha', 'THA.LOC104825562' => 'tha', 'THA.LOC104825665' => 'tha', 'Thecc.02G261400' => 'tca', 'Thecc.04G019200' => 'tca', 'Thecc.09G130400' => 'tca', 'Thhalv10004374m.g' => 'esa', 'Thhalv10007850m.g' => 'esa', 'Thhalv10013782m.g' => 'esa', 'Thhalv10018686m.g' => 'esa', 'Thhalv10020899m.g' => 'esa', 'Thhalv10022755m.g' => 'esa', 'TPR.G23851' => 'tpr', 'TPR.G26500' => 'tpr', 'TPR.G27267' => 'tpr', 'TPR.G32001' => 'tpr', 'TPR.G6251' => 'tpr', 'TPR.G8167' => 'tpr', 'TWI12G1330' => 'twi', 'TWI18G1239' => 'twi', 'TWI34G0979' => 'twi', 'TWI36G0670' => 'twi', 'TWI36G0707' => 'twi', 'TWI56G0233' => 'twi', 'TWI75G1809' => 'twi', 'unitig_21.g20874' => 'ugi', 'unitig_26.g10343' => 'ugi', 'unitig_46.g18392' => 'ugi', 'unitig_52.g17178' => 'ugi', 'unitig_8.g2934' => 'ugi', 'vmacro01122' => 'vma', 'vmacro05875' => 'vma', 'vmacro06147' => 'vma', 'vmacro16191' => 'vma', 'vmacro18293' => 'vma', 'VMungo0251G3707' => 'vmu', 'VMungo0464G1521' => 'vmu', 'VMungo1215G0205' => 'vmu', 'VMungo1383G2484' => 'vmu', 'Zm00001eb079610' => 'zma', 'Zm00001eb135990' => 'zma', 'Zm00001eb183710' => 'zma', 'Zm00001eb246020' => 'zma' ) $gf_id = 'HOM05D001124' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001124' ) $data_identifier = 'HOM05D001124' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 6, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 7, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 21, 'bol' => (int) 10, 'bra' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 6, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 9, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 21, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 8, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 10, 'lsa' => (int) 8, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 8, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 9, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb246020' $species_info = array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ) $local_species = 'cme' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001124', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '548', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02520' => 'bna', 'A03p06630' => 'bna', 'A05p44460' => 'bna', 'A06p08710' => 'bna', 'A06p41090' => 'bna', 'A07p32320' => 'bna', 'A08p32520' => 'bna', 'A09p10360' => 'bna', 'A10p24080' => 'bna', 'Aa31LG11G15250' => 'aar', 'Aa31LG1G1800' => 'aar', 'Aa31LG2G5120' => 'aar', 'Aa31LG2G6070' => 'aar', 'Aa31LG5G10770' => 'aar', 'Aa31sc61G90' => 'aar', 'Actinidia01352' => 'ach', 'Actinidia05983' => 'ach', 'Actinidia08133' => 'ach', 'Actinidia15101' => 'ach', 'Actinidia26379' => 'ach', 'Actinidia35778' => 'ach', 'Actinidia36123' => 'ach', 'Actinidia37436' => 'ach', 'Actinidia38730' => 'ach', 'Ah.02g128210' => 'amhyb', 'Ah.03g132990' => 'amhyb', 'Ah.14g079410' => 'amhyb', 'AL1G24640' => 'aly', 'AL2G26680' => 'aly', 'AL3G10530' => 'aly', 'AL3G45230' => 'aly', 'AL5G15230' => 'aly', 'AL5G16960' => 'aly', 'AL6G25210' => 'aly', 'Aqoxy2G00441' => 'aox', 'Aqoxy3G01236' => 'aox', 'Aqoxy5G03746' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3RQ047' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C7GMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9C8JER' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MBL6KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YXCZ83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZANX40' => 'arhy', 'AT1G12990' => 'ath', 'AT1G67880' => 'ath', 'AT2G13290' => 'ath', 'AT3G01620' => 'ath', 'AT3G26445' => 'ath', 'AT3G27540' => 'ath', 'AT5G14480' => 'ath', 'ATR0824G026' => 'atr', 'ATR1098G019' => 'atr', 'Atru.chr11.2145' => 'acertr', 'Atru.chr2.3636' => 'acertr', 'Atru.chr2.3644' => 'acertr', 'Atru.chr6.2422' => 'acertr', 'Atru.chr7.1112' => 'acertr', 'AUR62005469' => 'cqu', 'AUR62011166' => 'cqu', 'AUR62013319' => 'cqu', 'AUR62024273' => 'cqu', 'AUR62028420' => 'cqu', 'AUR62041942' => 'cqu', 'BcaB01g04969' => 'bca', 'BcaB01g06371' => 'bca', 'BcaB02g11494' => 'bca', 'BcaB03g15382' => 'bca', 'BcaB08g36994' => 'bca', 'BcaC03g13477' => 'bca', 'BcaC03g13478' => 'bca', 'BcaC03g13480' => 'bca', 'BcaC03g13481' => 'bca', 'BcaC03g13486' => 'bca', 'BcaC04g19031' => 'bca', 'BcaC04g23085' => 'bca', 'BcaC05g25094' => 'bca', 'BcaC05g25096' => 'bca', 'BcaC05g25138' => 'bca', 'BcaC05g30416' => 'bca', 'BcaC05g30455' => 'bca', 'BcaC06g30979' => 'bca', 'BcaC06g33805' => 'bca', 'BcaC08g46021' => 'bca', 'BcaNung03154' => 'bca', 'BolC2t06623H' => 'bol', 'BolC2t06632H' => 'bol', 'BolC2t06635H' => 'bol', 'BolC2t06638H' => 'bol', 'BolC3t13266H' => 'bol', 'BolC5t29776H' => 'bol', 'BolC6t38912H' => 'bol', 'BolC7t44183H' => 'bol', 'BolC9t54123H' => 'bol', 'BolC9t59107H' => 'bol', 'BraA02t05221Z' => 'bra', 'BraA03t09996Z' => 'bra', 'BraA05t23210Z' => 'bra', 'BraA06t24068Z' => 'bra', 'BraA06t27032Z' => 'bra', 'BraA08t35176Z' => 'bra', 'BraA09t36680Z' => 'bra', 'BraA10t44471Z' => 'bra', 'C02p06760' => 'bna', 'C02p06890' => 'bna', 'C02p07010' => 'bna', 'C03p07660' => 'bna', 'C05p10300' => 'bna', 'C06p38150' => 'bna', 'C07p36650' => 'bna', 'C08p15770' => 'bna', 'C09p12300' => 'bna', 'C09p62700' => 'bna', 'C09p75040' => 'bna', 'CAN.G13.1' => 'can', 'CAN.G138.4' => 'can', 'CAN.G44.6' => 'can', 'CAN.G473.19' => 'can', 'CANSAT01G0835' => 'cansat', 'CANSAT11G0246' => 'cansat', 'CANSAT11G1766' => 'cansat', 'CANSAT64G1954' => 'cansat', 'CARHR013330' => 'chi', 'CARHR060530' => 'chi', 'CARHR075300' => 'chi', 'CARHR105120' => 'chi', 'CARHR148910' => 'chi', 'CARHR198830' => 'chi', 'Carub.0001s1275' => 'cru', 'Carub.0002s1437' => 'cru', 'Carub.0003s0044' => 'cru', 'Carub.0003s2787' => 'cru', 'Carub.0005s0597' => 'cru', 'Carub.0006s1266' => 'cru', 'Ca_06935_v3' => 'car', 'Ca_13559_v3' => 'car', 'Ca_16941_v3' => 'car', 'Ca_16960_v3' => 'car', 'Ca_17775_v3' => 'car', 'Ca_30464_v3' => 'car', 'Cc06_g08160' => 'ccan', 'Cc07_g01520' => 'ccan', 'Cc11_g15810' => 'ccan', 'CDE02G2840' => 'cde', 'CDE03G0093' => 'cde', 'CDE04G2127' => 'cde', 'CDE07G1857' => 'cde', 'CDE09G1246' => 'cde', 'Cfa003412' => 'cfa', 'Cfa007341' => 'cfa', 'Cfa009220' => 'cfa', 'Ciclev10008737m.g' => 'ccl', 'Ciclev10015565m.g' => 'ccl', 'Ciclev10031761m.g' => 'ccl', 'CiPaw.03G045300' => 'cil', 'CiPaw.03G247200' => 'cil', 'CiPaw.04G029500' => 'cil', 'CiPaw.04G174000' => 'cil', 'CiPaw.05G181200' => 'cil', 'CiPaw.06G067100' => 'cil', 'ClCG05G025800' => 'cla', 'ClCG06G011400' => 'cla', 'ClCG09G019360' => 'cla', 'COL.COLO4_04827' => 'col', 'COL.COLO4_29170' => 'col', 'COL.COLO4_35131' => 'col', 'COL.COLO4_35132' => 'col', 'Cpa.g.sc33.32' => 'cpa', 'Cpa.g.sc46.29' => 'cpa', 'Cpa.g.sc796.1' => 'cpa', 'CsaV3_1G030420' => 'csa', 'CsaV3_5G027050' => 'csa', 'CsaV3_5G031040' => 'csa', 'CsaV3_UNG023130' => 'csa', 'CSS0007726' => 'camsi', 'CSS0016433' => 'camsi', 'CSS0017656' => 'camsi', 'CSS0025364' => 'camsi', 'CSS0027582' => 'camsi', 'CSS0047288' => 'camsi', 'CSS0049950' => 'camsi', 'DCAR_003843' => 'dca', 'DCAR_007052' => 'dca', 'DCAR_020884' => 'dca', 'DCAR_021730' => 'dca', 'DCAR_024423' => 'dca', 'DCAR_026509' => 'dca', 'DCAR_031158' => 'dca', 'Dinv14728' => 'din', 'Dinv15219' => 'din', 'Dinv25728' => 'din', 'Dinv33428' => 'din', 'Dinv36489' => 'din', 'Dinv41486' => 'din', 'Duzib147G0469' => 'dzi', 'Duzib168G0060' => 'dzi', 'Duzib187G1215' => 'dzi', 'Duzib248G0692' => 'dzi', 'Duzib251G0767' => 'dzi', 'Duzib264G0446' => 'dzi', 'Duzib268G0691' => 'dzi', 'ECA232G4767' => 'eca', 'ECA233G2838' => 'eca', 'ECA234G0391' => 'eca', 'ECA234G0857' => 'eca', 'ECA236G1593' => 'eca', 'ECA238G0565' => 'eca', 'ECA246G1027' => 'eca', 'ECA246G3223' => 'eca', 'ECA246G3470' => 'eca', 'EL10Ac6g13829' => 'bvu', 'EL10Ac6g14093' => 'bvu', 'EL10Ac8g18707' => 'bvu', 'Eucgr.C01369' => 'egr', 'Eucgr.H02492' => 'egr', 'Eucgr.I01733' => 'egr', 'Eucgr.J02255' => 'egr', 'Eucgr.J02257' => 'egr', 'Eucgr.J02258' => 'egr', 'FAN02G1601' => 'fan', 'FAN03G1586' => 'fan', 'FAN03G2986' => 'fan', 'FAN05G4837' => 'fan', 'FAN06G0146' => 'fan', 'FAN07G0858' => 'fan', 'FAN09G3179' => 'fan', 'FAN10G0669' => 'fan', 'FAN12G2358' => 'fan', 'FAN14G4198' => 'fan', 'FAN14G5112' => 'fan', 'FAN17G0342' => 'fan', 'FAN19G0342' => 'fan', 'FAN19G0962' => 'fan', 'FAN19G1101' => 'fan', 'FAN19G1872' => 'fan', 'FAN22G0356' => 'fan', 'FAN23G0744' => 'fan', 'FAN23G1914' => 'fan', 'FAN26G0032' => 'fan', 'FAN28G0625' => 'fan', 'FvH4_1g02710' => 'fve', 'FvH4_1g02720' => 'fve', 'FvH4_4g25670' => 'fve', 'FvH4_6g51700' => 'fve', 'FvH4_7g20170' => 'fve', 'Glyma.05G175000' => 'gma', 'Glyma.08G132300' => 'gma', 'Glyma.11G243000' => 'gma', 'Glyma.13G158900' => 'gma', 'Glyma.17G112400' => 'gma', 'Glyma.18G014100' => 'gma', 'Glyma.19G003100' => 'gma', 'Glyma.19G056500' => 'gma', 'Gohir.A01G158900' => 'ghi', 'Gohir.A05G312600' => 'ghi', 'Gohir.A05G354900' => 'ghi', 'Gohir.A07G037200' => 'ghi', 'Gohir.A09G030000' => 'ghi', 'Gohir.A12G145200' => 'ghi', 'Gohir.D01G151500' => 'ghi', 'Gohir.D04G058300' => 'ghi', 'Gohir.D05G314100' => 'ghi', 'Gohir.D07G041400' => 'ghi', 'Gohir.D09G029700' => 'ghi', 'Gohir.D12G149700' => 'ghi', 'Gorai.001G043800' => 'gra', 'Gorai.002G187800' => 'gra', 'Gorai.006G034700' => 'gra', 'Gorai.008G161200' => 'gra', 'Gorai.009G335700' => 'gra', 'Gorai.012G065000' => 'gra', 'GSVIVG01000535001' => 'vvi', 'GSVIVG01015572001' => 'vvi', 'GSVIVG01032386001' => 'vvi', 'HanXRQChr05g0138531' => 'han', 'HanXRQChr06g0174391' => 'han', 'HanXRQChr07g0199021' => 'han', 'HanXRQChr08g0208211' => 'han', 'HanXRQChr09g0255471' => 'han', 'HanXRQChr10g0315791' => 'han', 'HanXRQChr12g0371991' => 'han', 'HanXRQChr15g0475251' => 'han', 'HanXRQChr17g0540001' => 'han', 'HanXRQChr17g0548631' => 'han', 'HanXRQChr17g0569561' => 'han', 'Haze_12256' => 'cav', 'Haze_14756' => 'cav', 'Haze_25528' => 'cav', 'Hma1.2p1_0079F.1_g041020' => 'hma', 'Hma1.2p1_0818F.1_g223260' => 'hma', 'Hma1.2p1_1747F.1_g300530' => 'hma', 'HPP92_004607' => 'vpl', 'HPP92_004608' => 'vpl', 'HPP92_006181' => 'vpl', 'HPP92_012192' => 'vpl', 'HPP92_015680' => 'vpl', 'HPP92_020249' => 'vpl', 'HPP92_021376' => 'vpl', 'HPP92_024275' => 'vpl', 'Hund06031' => 'sun', 'Hund25391' => 'sun', 'Lalb_Chr07g0185371' => 'lal', 'Lalb_Chr07g0185381' => 'lal', 'Lalb_Chr12g0204011' => 'lal', 'Lalb_Chr13g0301671' => 'lal', 'Lalb_Chr14g0362851' => 'lal', 'Lalb_Chr24g0403581' => 'lal', 'Lj1g0000233' => 'lja', 'Lj2g0018120' => 'lja', 'Lj3C621T0' => 'lonja', 'Lj3P1059T14' => 'lonja', 'Lj3P611T9' => 'lonja', 'Lj3P614T13' => 'lonja', 'Lj3P615T5' => 'lonja', 'Lj4g0012315' => 'lja', 'Lj4g0026182' => 'lja', 'Lj6P813T16' => 'lonja', 'Lj7C427T7' => 'lonja', 'Lj7C427T8' => 'lonja', 'Lj7P600T41' => 'lonja', 'Lju41C42G17' => 'lonja', 'Lsat_1_v5_gn_0_47300' => 'lsa', 'Lsat_1_v5_gn_2_91280' => 'lsa', 'Lsat_1_v5_gn_3_30561' => 'lsa', 'Lsat_1_v5_gn_4_184321' => 'lsa', 'Lsat_1_v5_gn_4_4041' => 'lsa', 'Lsat_1_v5_gn_5_92000' => 'lsa', 'Lsat_1_v5_gn_8_152940' => 'lsa', 'Lsat_1_v5_gn_8_62401' => 'lsa', 'Manes.06G055900' => 'mes', 'Manes.12G022200' => 'mes', 'Manes.13G023300' => 'mes', 'Manes.14G115000' => 'mes', 'Manes.15G151700' => 'mes', 'Manes.17G111300' => 'mes', 'Mapoly0226s0009' => 'mpo', 'MBI02_g25363_MAGBIO' => 'mbi', 'MBI06_g00027_MAGBIO' => 'mbi', 'MBI10_g13034_MAGBIO' => 'mbi', 'MD09G1023400' => 'mdo', 'MD13G1100100' => 'mdo', 'MD15G1169200' => 'mdo', 'MD16G1101100' => 'mdo', 'MD17G1022900' => 'mdo', 'Medtr3g096150' => 'mtr', 'Medtr4g115070' => 'mtr', 'Medtr7g033325' => 'mtr', 'Medtr8g089840' => 'mtr', 'MELO3C010319.2' => 'cme', 'MELO3C011944.2' => 'cme', 'MELO3C021589.2' => 'cme', 'Migut.E00207' => 'egut', 'Migut.H00067' => 'egut', 'Migut.K00433' => 'egut', 'Migut.K00606' => 'egut', 'Migut.K01410' => 'egut', 'MSTRG.13347' => 'ama', 'MSTRG.24045' => 'ama', 'MSTRG.2428' => 'ama', 'MSTRG.26410' => 'ama', 'MSTRG.3139' => 'ama', 'MSTRG.3286' => 'ama', 'MSTRG.563' => 'ama', 'MSTRG.7941' => 'ama', 'Nitab4.5_0000028g0060' => 'nta', 'Nitab4.5_0000065g0260' => 'nta', 'Nitab4.5_0000112g0060' => 'nta', 'Nitab4.5_0000489g0120' => 'nta', 'Nitab4.5_0001776g0050' => 'nta', 'Nitab4.5_0001854g0010' => 'nta', 'Nitab4.5_0001860g0020' => 'nta', 'Nitab4.5_0004352g0010' => 'nta', 'Nitab4.5_0008716g0020' => 'nta', 'Nitab4.5_0008922g0010' => 'nta', 'Nn3g16693' => 'nnu', 'Nn4g22596' => 'nnu', 'Nn7g37639' => 'nnu', 'Oeu001701.1' => 'oeu', 'Oeu018149.1' => 'oeu', 'Oeu026220.1' => 'oeu', 'Oeu038635.1' => 'oeu', 'Oeu049176.1' => 'oeu', 'Oeu056706.1' => 'oeu', 'Oeu056937.1' => 'oeu', 'Oeu057540.1' => 'oeu', 'Os02g0594900' => 'osa', 'Os02g0595100' => 'osa', 'Os04g0477500' => 'osa', 'Os12g0611900' => 'osa', 'Peaxi162Scf00076g00020' => 'pax', 'Peaxi162Scf00128g00217' => 'pax', 'Peaxi162Scf00129g01640' => 'pax', 'Peaxi162Scf00669g00007' => 'pax', 'Peaxi162Scf00700g00421' => 'pax', 'Peaxi162Scf00801g00038' => 'pax', 'Peaxi162Scf00891g00025' => 'pax', 'PGR083G0909' => 'pgr', 'PGR119G1005' => 'pgr', 'PGR142G2236' => 'pgr', 'PGR142G3388' => 'pgr', 'PGSC0003DMG400004514' => 'stu', 'PGSC0003DMG400012635' => 'stu', 'PGSC0003DMG400015730' => 'stu', 'PGSC0003DMG400018611' => 'stu', 'PGSC0003DMG400030897' => 'stu', 'Phvul.001G254800' => 'pvu', 'Phvul.002G260100' => 'pvu', 'Phvul.003G167600' => 'pvu', 'Phvul.004G005100' => 'pvu', 'Potri.001G343600' => 'ptr', 'Potri.006G066700' => 'ptr', 'Potri.008G186000' => 'ptr', 'Potri.010G046900' => 'ptr', 'Potri.018G127900' => 'ptr', 'Pp3c20_17750' => 'ppa', 'Pp3c24_4380' => 'ppa', 'Prupe.1G245800' => 'ppe', 'Prupe.3G293400' => 'ppe', 'Prupe.7G247400' => 'ppe', 'Psat0s145g0120' => 'psa', 'Psat0s595g0040' => 'psa', 'Psat0s595g0120' => 'psa', 'Psat3g175040' => 'psa', 'Psat7g058120' => 'psa', 'PSO017G0428' => 'pso', 'PSO063G7510' => 'pso', 'PSO067G0046' => 'pso', 'PSO478G1073' => 'pso', 'PSO675G3677' => 'pso', 'PSO675G6558' => 'pso', 'PSO675G7520' => 'pso', 'PSO675G8959' => 'pso', 'QL02p074089' => 'qlo', 'QL02p089614' => 'qlo', 'QL03p057736' => 'qlo', 'RcHm_v2.0_Chr1g0364131' => 'rch', 'RcHm_v2.0_Chr2g0087801' => 'rch', 'RcHm_v2.0_Chr2g0087821' => 'rch', 'RcHm_v2.0_Chr2g0173231' => 'rch', 'RcHm_v2.0_Chr4g0433111' => 'rch', 'Rhsim03G0250300' => 'rsi', 'Rhsim08G0048400' => 'rsi', 'Rhsim10G0014800' => 'rsi', 'Rhsim12G0040100' => 'rsi', 'Rhsim12G0109700' => 'rsi', 'Sabra06G0049600' => 'sbr', 'Sabra08G0141000' => 'sbr', 'Sabra10G0021400' => 'sbr', 'Sabra16G0222900' => 'sbr', 'Sabra18G0108600' => 'sbr', 'SalBow1G0433' => 'sbo', 'SalBow1G2038' => 'sbo', 'SalBow1G5003' => 'sbo', 'SalBow7G1197' => 'sbo', 'SalBow8G3506' => 'sbo', 'Sc03g0007300' => 'sci', 'Sc11g0000950' => 'sci', 'Sc14g0008750' => 'sci', 'Sc18g0000420' => 'sci', 'Sed0006754' => 'sed', 'Sed0008741' => 'sed', 'Sed0017172' => 'sed', 'Sed0018925' => 'sed', 'Sed0023326' => 'sed', 'Sed0025909' => 'sed', 'SEGI_05333' => 'sgi', 'SEGI_10362' => 'sgi', 'SEGI_13380' => 'sgi', 'SEGI_24306' => 'sgi', 'SEGI_29077' => 'sgi', 'SEGI_29095' => 'sgi', 'SEGI_36534' => 'sgi', 'SEGI_37506' => 'sgi', 'SEGI_38321' => 'sgi', 'SGA_v2.0_scaffold307G48031' => 'sas', 'SGA_v2.0_scaffold47G17507' => 'sas', 'SGA_v2.0_scaffold63G21736' => 'sas', 'SGA_v2.0_scaffold87G27070' => 'sas', 'SHI17794' => 'shi', 'SHI28851' => 'shi', 'SMO165G0155' => 'smo', 'SMO340G0217' => 'smo', 'SMO367G1210' => 'smo', 'Solyc02g093430.3' => 'sly', 'Solyc05g013580.4' => 'sly', 'Solyc07g008030.3' => 'sly', 'Solyc12g035470.2' => 'sly', 'Sopen02g038020' => 'spe', 'Sopen05g008490' => 'spe', 'Sopen07g003910' => 'spe', 'Sopen12g015240' => 'spe', 'Sp1g11550' => 'spa', 'Sp2g16710' => 'spa', 'Sp3g00430' => 'spa', 'Sp3g26780' => 'spa', 'Sp5g22900' => 'spa', 'Sp6g29530' => 'spa', 'TAR371G0794' => 'tar', 'TAR374G0164' => 'tar', 'TAR622G0165' => 'tar', 'TAR626G0929' => 'tar', 'TAR629G2155' => 'tar', 'THA.LOC104805282' => 'tha', 'THA.LOC104805363' => 'tha', 'THA.LOC104808968' => 'tha', 'THA.LOC104821093' => 'tha', 'THA.LOC104823953' => 'tha', 'THA.LOC104825562' => 'tha', 'THA.LOC104825665' => 'tha', 'Thecc.02G261400' => 'tca', 'Thecc.04G019200' => 'tca', 'Thecc.09G130400' => 'tca', 'Thhalv10004374m.g' => 'esa', 'Thhalv10007850m.g' => 'esa', 'Thhalv10013782m.g' => 'esa', 'Thhalv10018686m.g' => 'esa', 'Thhalv10020899m.g' => 'esa', 'Thhalv10022755m.g' => 'esa', 'TPR.G23851' => 'tpr', 'TPR.G26500' => 'tpr', 'TPR.G27267' => 'tpr', 'TPR.G32001' => 'tpr', 'TPR.G6251' => 'tpr', 'TPR.G8167' => 'tpr', 'TWI12G1330' => 'twi', 'TWI18G1239' => 'twi', 'TWI34G0979' => 'twi', 'TWI36G0670' => 'twi', 'TWI36G0707' => 'twi', 'TWI56G0233' => 'twi', 'TWI75G1809' => 'twi', 'unitig_21.g20874' => 'ugi', 'unitig_26.g10343' => 'ugi', 'unitig_46.g18392' => 'ugi', 'unitig_52.g17178' => 'ugi', 'unitig_8.g2934' => 'ugi', 'vmacro01122' => 'vma', 'vmacro05875' => 'vma', 'vmacro06147' => 'vma', 'vmacro16191' => 'vma', 'vmacro18293' => 'vma', 'VMungo0251G3707' => 'vmu', 'VMungo0464G1521' => 'vmu', 'VMungo1215G0205' => 'vmu', 'VMungo1383G2484' => 'vmu', 'Zm00001eb079610' => 'zma', 'Zm00001eb135990' => 'zma', 'Zm00001eb183710' => 'zma', 'Zm00001eb246020' => 'zma' ), 'gf_id' => 'HOM05D001124', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001124' ), 'data_identifier' => 'HOM05D001124', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001124', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '548', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02520' => 'bna', 'A03p06630' => 'bna', 'A05p44460' => 'bna', 'A06p08710' => 'bna', 'A06p41090' => 'bna', 'A07p32320' => 'bna', 'A08p32520' => 'bna', 'A09p10360' => 'bna', 'A10p24080' => 'bna', 'Aa31LG11G15250' => 'aar', 'Aa31LG1G1800' => 'aar', 'Aa31LG2G5120' => 'aar', 'Aa31LG2G6070' => 'aar', 'Aa31LG5G10770' => 'aar', 'Aa31sc61G90' => 'aar', 'Actinidia01352' => 'ach', 'Actinidia05983' => 'ach', 'Actinidia08133' => 'ach', 'Actinidia15101' => 'ach', 'Actinidia26379' => 'ach', 'Actinidia35778' => 'ach', 'Actinidia36123' => 'ach', 'Actinidia37436' => 'ach', 'Actinidia38730' => 'ach', 'Ah.02g128210' => 'amhyb', 'Ah.03g132990' => 'amhyb', 'Ah.14g079410' => 'amhyb', 'AL1G24640' => 'aly', 'AL2G26680' => 'aly', 'AL3G10530' => 'aly', 'AL3G45230' => 'aly', 'AL5G15230' => 'aly', 'AL5G16960' => 'aly', 'AL6G25210' => 'aly', 'Aqoxy2G00441' => 'aox', 'Aqoxy3G01236' => 'aox', 'Aqoxy5G03746' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3RQ047' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C7GMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9C8JER' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MBL6KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YXCZ83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZANX40' => 'arhy', 'AT1G12990' => 'ath', 'AT1G67880' => 'ath', 'AT2G13290' => 'ath', 'AT3G01620' => 'ath', 'AT3G26445' => 'ath', 'AT3G27540' => 'ath', 'AT5G14480' => 'ath', 'ATR0824G026' => 'atr', 'ATR1098G019' => 'atr', 'Atru.chr11.2145' => 'acertr', 'Atru.chr2.3636' => 'acertr', 'Atru.chr2.3644' => 'acertr', 'Atru.chr6.2422' => 'acertr', 'Atru.chr7.1112' => 'acertr', 'AUR62005469' => 'cqu', 'AUR62011166' => 'cqu', 'AUR62013319' => 'cqu', 'AUR62024273' => 'cqu', 'AUR62028420' => 'cqu', 'AUR62041942' => 'cqu', 'BcaB01g04969' => 'bca', 'BcaB01g06371' => 'bca', 'BcaB02g11494' => 'bca', 'BcaB03g15382' => 'bca', 'BcaB08g36994' => 'bca', 'BcaC03g13477' => 'bca', 'BcaC03g13478' => 'bca', 'BcaC03g13480' => 'bca', 'BcaC03g13481' => 'bca', 'BcaC03g13486' => 'bca', 'BcaC04g19031' => 'bca', 'BcaC04g23085' => 'bca', 'BcaC05g25094' => 'bca', 'BcaC05g25096' => 'bca', 'BcaC05g25138' => 'bca', 'BcaC05g30416' => 'bca', 'BcaC05g30455' => 'bca', 'BcaC06g30979' => 'bca', 'BcaC06g33805' => 'bca', 'BcaC08g46021' => 'bca', 'BcaNung03154' => 'bca', 'BolC2t06623H' => 'bol', 'BolC2t06632H' => 'bol', 'BolC2t06635H' => 'bol', 'BolC2t06638H' => 'bol', 'BolC3t13266H' => 'bol', 'BolC5t29776H' => 'bol', 'BolC6t38912H' => 'bol', 'BolC7t44183H' => 'bol', 'BolC9t54123H' => 'bol', 'BolC9t59107H' => 'bol', 'BraA02t05221Z' => 'bra', 'BraA03t09996Z' => 'bra', 'BraA05t23210Z' => 'bra', 'BraA06t24068Z' => 'bra', 'BraA06t27032Z' => 'bra', 'BraA08t35176Z' => 'bra', 'BraA09t36680Z' => 'bra', 'BraA10t44471Z' => 'bra', 'C02p06760' => 'bna', 'C02p06890' => 'bna', 'C02p07010' => 'bna', 'C03p07660' => 'bna', 'C05p10300' => 'bna', 'C06p38150' => 'bna', 'C07p36650' => 'bna', 'C08p15770' => 'bna', 'C09p12300' => 'bna', 'C09p62700' => 'bna', 'C09p75040' => 'bna', 'CAN.G13.1' => 'can', 'CAN.G138.4' => 'can', 'CAN.G44.6' => 'can', 'CAN.G473.19' => 'can', 'CANSAT01G0835' => 'cansat', 'CANSAT11G0246' => 'cansat', 'CANSAT11G1766' => 'cansat', 'CANSAT64G1954' => 'cansat', 'CARHR013330' => 'chi', 'CARHR060530' => 'chi', 'CARHR075300' => 'chi', 'CARHR105120' => 'chi', 'CARHR148910' => 'chi', 'CARHR198830' => 'chi', 'Carub.0001s1275' => 'cru', 'Carub.0002s1437' => 'cru', 'Carub.0003s0044' => 'cru', 'Carub.0003s2787' => 'cru', 'Carub.0005s0597' => 'cru', 'Carub.0006s1266' => 'cru', 'Ca_06935_v3' => 'car', 'Ca_13559_v3' => 'car', 'Ca_16941_v3' => 'car', 'Ca_16960_v3' => 'car', 'Ca_17775_v3' => 'car', 'Ca_30464_v3' => 'car', 'Cc06_g08160' => 'ccan', 'Cc07_g01520' => 'ccan', 'Cc11_g15810' => 'ccan', 'CDE02G2840' => 'cde', 'CDE03G0093' => 'cde', 'CDE04G2127' => 'cde', 'CDE07G1857' => 'cde', 'CDE09G1246' => 'cde', 'Cfa003412' => 'cfa', 'Cfa007341' => 'cfa', 'Cfa009220' => 'cfa', 'Ciclev10008737m.g' => 'ccl', 'Ciclev10015565m.g' => 'ccl', 'Ciclev10031761m.g' => 'ccl', 'CiPaw.03G045300' => 'cil', 'CiPaw.03G247200' => 'cil', 'CiPaw.04G029500' => 'cil', 'CiPaw.04G174000' => 'cil', 'CiPaw.05G181200' => 'cil', 'CiPaw.06G067100' => 'cil', 'ClCG05G025800' => 'cla', 'ClCG06G011400' => 'cla', 'ClCG09G019360' => 'cla', 'COL.COLO4_04827' => 'col', 'COL.COLO4_29170' => 'col', 'COL.COLO4_35131' => 'col', 'COL.COLO4_35132' => 'col', 'Cpa.g.sc33.32' => 'cpa', 'Cpa.g.sc46.29' => 'cpa', 'Cpa.g.sc796.1' => 'cpa', 'CsaV3_1G030420' => 'csa', 'CsaV3_5G027050' => 'csa', 'CsaV3_5G031040' => 'csa', 'CsaV3_UNG023130' => 'csa', 'CSS0007726' => 'camsi', 'CSS0016433' => 'camsi', 'CSS0017656' => 'camsi', 'CSS0025364' => 'camsi', 'CSS0027582' => 'camsi', 'CSS0047288' => 'camsi', 'CSS0049950' => 'camsi', 'DCAR_003843' => 'dca', 'DCAR_007052' => 'dca', 'DCAR_020884' => 'dca', 'DCAR_021730' => 'dca', 'DCAR_024423' => 'dca', 'DCAR_026509' => 'dca', 'DCAR_031158' => 'dca', 'Dinv14728' => 'din', 'Dinv15219' => 'din', 'Dinv25728' => 'din', 'Dinv33428' => 'din', 'Dinv36489' => 'din', 'Dinv41486' => 'din', 'Duzib147G0469' => 'dzi', 'Duzib168G0060' => 'dzi', 'Duzib187G1215' => 'dzi', 'Duzib248G0692' => 'dzi', 'Duzib251G0767' => 'dzi', 'Duzib264G0446' => 'dzi', 'Duzib268G0691' => 'dzi', 'ECA232G4767' => 'eca', 'ECA233G2838' => 'eca', 'ECA234G0391' => 'eca', 'ECA234G0857' => 'eca', 'ECA236G1593' => 'eca', 'ECA238G0565' => 'eca', 'ECA246G1027' => 'eca', 'ECA246G3223' => 'eca', 'ECA246G3470' => 'eca', 'EL10Ac6g13829' => 'bvu', 'EL10Ac6g14093' => 'bvu', 'EL10Ac8g18707' => 'bvu', 'Eucgr.C01369' => 'egr', 'Eucgr.H02492' => 'egr', 'Eucgr.I01733' => 'egr', 'Eucgr.J02255' => 'egr', 'Eucgr.J02257' => 'egr', 'Eucgr.J02258' => 'egr', 'FAN02G1601' => 'fan', 'FAN03G1586' => 'fan', 'FAN03G2986' => 'fan', 'FAN05G4837' => 'fan', 'FAN06G0146' => 'fan', 'FAN07G0858' => 'fan', 'FAN09G3179' => 'fan', 'FAN10G0669' => 'fan', 'FAN12G2358' => 'fan', 'FAN14G4198' => 'fan', 'FAN14G5112' => 'fan', 'FAN17G0342' => 'fan', 'FAN19G0342' => 'fan', 'FAN19G0962' => 'fan', 'FAN19G1101' => 'fan', 'FAN19G1872' => 'fan', 'FAN22G0356' => 'fan', 'FAN23G0744' => 'fan', 'FAN23G1914' => 'fan', 'FAN26G0032' => 'fan', 'FAN28G0625' => 'fan', 'FvH4_1g02710' => 'fve', 'FvH4_1g02720' => 'fve', 'FvH4_4g25670' => 'fve', 'FvH4_6g51700' => 'fve', 'FvH4_7g20170' => 'fve', 'Glyma.05G175000' => 'gma', 'Glyma.08G132300' => 'gma', 'Glyma.11G243000' => 'gma', 'Glyma.13G158900' => 'gma', 'Glyma.17G112400' => 'gma', 'Glyma.18G014100' => 'gma', 'Glyma.19G003100' => 'gma', 'Glyma.19G056500' => 'gma', 'Gohir.A01G158900' => 'ghi', 'Gohir.A05G312600' => 'ghi', 'Gohir.A05G354900' => 'ghi', 'Gohir.A07G037200' => 'ghi', 'Gohir.A09G030000' => 'ghi', 'Gohir.A12G145200' => 'ghi', 'Gohir.D01G151500' => 'ghi', 'Gohir.D04G058300' => 'ghi', 'Gohir.D05G314100' => 'ghi', 'Gohir.D07G041400' => 'ghi', 'Gohir.D09G029700' => 'ghi', 'Gohir.D12G149700' => 'ghi', 'Gorai.001G043800' => 'gra', 'Gorai.002G187800' => 'gra', 'Gorai.006G034700' => 'gra', 'Gorai.008G161200' => 'gra', 'Gorai.009G335700' => 'gra', 'Gorai.012G065000' => 'gra', 'GSVIVG01000535001' => 'vvi', 'GSVIVG01015572001' => 'vvi', 'GSVIVG01032386001' => 'vvi', 'HanXRQChr05g0138531' => 'han', 'HanXRQChr06g0174391' => 'han', 'HanXRQChr07g0199021' => 'han', 'HanXRQChr08g0208211' => 'han', 'HanXRQChr09g0255471' => 'han', 'HanXRQChr10g0315791' => 'han', 'HanXRQChr12g0371991' => 'han', 'HanXRQChr15g0475251' => 'han', 'HanXRQChr17g0540001' => 'han', 'HanXRQChr17g0548631' => 'han', 'HanXRQChr17g0569561' => 'han', 'Haze_12256' => 'cav', 'Haze_14756' => 'cav', 'Haze_25528' => 'cav', 'Hma1.2p1_0079F.1_g041020' => 'hma', 'Hma1.2p1_0818F.1_g223260' => 'hma', 'Hma1.2p1_1747F.1_g300530' => 'hma', 'HPP92_004607' => 'vpl', 'HPP92_004608' => 'vpl', 'HPP92_006181' => 'vpl', 'HPP92_012192' => 'vpl', 'HPP92_015680' => 'vpl', 'HPP92_020249' => 'vpl', 'HPP92_021376' => 'vpl', 'HPP92_024275' => 'vpl', 'Hund06031' => 'sun', 'Hund25391' => 'sun', 'Lalb_Chr07g0185371' => 'lal', 'Lalb_Chr07g0185381' => 'lal', 'Lalb_Chr12g0204011' => 'lal', 'Lalb_Chr13g0301671' => 'lal', 'Lalb_Chr14g0362851' => 'lal', 'Lalb_Chr24g0403581' => 'lal', 'Lj1g0000233' => 'lja', 'Lj2g0018120' => 'lja', 'Lj3C621T0' => 'lonja', 'Lj3P1059T14' => 'lonja', 'Lj3P611T9' => 'lonja', 'Lj3P614T13' => 'lonja', 'Lj3P615T5' => 'lonja', 'Lj4g0012315' => 'lja', 'Lj4g0026182' => 'lja', 'Lj6P813T16' => 'lonja', 'Lj7C427T7' => 'lonja', 'Lj7C427T8' => 'lonja', 'Lj7P600T41' => 'lonja', 'Lju41C42G17' => 'lonja', 'Lsat_1_v5_gn_0_47300' => 'lsa', 'Lsat_1_v5_gn_2_91280' => 'lsa', 'Lsat_1_v5_gn_3_30561' => 'lsa', 'Lsat_1_v5_gn_4_184321' => 'lsa', 'Lsat_1_v5_gn_4_4041' => 'lsa', 'Lsat_1_v5_gn_5_92000' => 'lsa', 'Lsat_1_v5_gn_8_152940' => 'lsa', 'Lsat_1_v5_gn_8_62401' => 'lsa', 'Manes.06G055900' => 'mes', 'Manes.12G022200' => 'mes', 'Manes.13G023300' => 'mes', 'Manes.14G115000' => 'mes', 'Manes.15G151700' => 'mes', 'Manes.17G111300' => 'mes', 'Mapoly0226s0009' => 'mpo', 'MBI02_g25363_MAGBIO' => 'mbi', 'MBI06_g00027_MAGBIO' => 'mbi', 'MBI10_g13034_MAGBIO' => 'mbi', 'MD09G1023400' => 'mdo', 'MD13G1100100' => 'mdo', 'MD15G1169200' => 'mdo', 'MD16G1101100' => 'mdo', 'MD17G1022900' => 'mdo', 'Medtr3g096150' => 'mtr', 'Medtr4g115070' => 'mtr', 'Medtr7g033325' => 'mtr', 'Medtr8g089840' => 'mtr', 'MELO3C010319.2' => 'cme', 'MELO3C011944.2' => 'cme', 'MELO3C021589.2' => 'cme', 'Migut.E00207' => 'egut', 'Migut.H00067' => 'egut', 'Migut.K00433' => 'egut', 'Migut.K00606' => 'egut', 'Migut.K01410' => 'egut', 'MSTRG.13347' => 'ama', 'MSTRG.24045' => 'ama', 'MSTRG.2428' => 'ama', 'MSTRG.26410' => 'ama', 'MSTRG.3139' => 'ama', 'MSTRG.3286' => 'ama', 'MSTRG.563' => 'ama', 'MSTRG.7941' => 'ama', 'Nitab4.5_0000028g0060' => 'nta', 'Nitab4.5_0000065g0260' => 'nta', 'Nitab4.5_0000112g0060' => 'nta', 'Nitab4.5_0000489g0120' => 'nta', 'Nitab4.5_0001776g0050' => 'nta', 'Nitab4.5_0001854g0010' => 'nta', 'Nitab4.5_0001860g0020' => 'nta', 'Nitab4.5_0004352g0010' => 'nta', 'Nitab4.5_0008716g0020' => 'nta', 'Nitab4.5_0008922g0010' => 'nta', 'Nn3g16693' => 'nnu', 'Nn4g22596' => 'nnu', 'Nn7g37639' => 'nnu', 'Oeu001701.1' => 'oeu', 'Oeu018149.1' => 'oeu', 'Oeu026220.1' => 'oeu', 'Oeu038635.1' => 'oeu', 'Oeu049176.1' => 'oeu', 'Oeu056706.1' => 'oeu', 'Oeu056937.1' => 'oeu', 'Oeu057540.1' => 'oeu', 'Os02g0594900' => 'osa', 'Os02g0595100' => 'osa', 'Os04g0477500' => 'osa', 'Os12g0611900' => 'osa', 'Peaxi162Scf00076g00020' => 'pax', 'Peaxi162Scf00128g00217' => 'pax', 'Peaxi162Scf00129g01640' => 'pax', 'Peaxi162Scf00669g00007' => 'pax', 'Peaxi162Scf00700g00421' => 'pax', 'Peaxi162Scf00801g00038' => 'pax', 'Peaxi162Scf00891g00025' => 'pax', 'PGR083G0909' => 'pgr', 'PGR119G1005' => 'pgr', 'PGR142G2236' => 'pgr', 'PGR142G3388' => 'pgr', 'PGSC0003DMG400004514' => 'stu', 'PGSC0003DMG400012635' => 'stu', 'PGSC0003DMG400015730' => 'stu', 'PGSC0003DMG400018611' => 'stu', 'PGSC0003DMG400030897' => 'stu', 'Phvul.001G254800' => 'pvu', 'Phvul.002G260100' => 'pvu', 'Phvul.003G167600' => 'pvu', 'Phvul.004G005100' => 'pvu', 'Potri.001G343600' => 'ptr', 'Potri.006G066700' => 'ptr', 'Potri.008G186000' => 'ptr', 'Potri.010G046900' => 'ptr', 'Potri.018G127900' => 'ptr', 'Pp3c20_17750' => 'ppa', 'Pp3c24_4380' => 'ppa', 'Prupe.1G245800' => 'ppe', 'Prupe.3G293400' => 'ppe', 'Prupe.7G247400' => 'ppe', 'Psat0s145g0120' => 'psa', 'Psat0s595g0040' => 'psa', 'Psat0s595g0120' => 'psa', 'Psat3g175040' => 'psa', 'Psat7g058120' => 'psa', 'PSO017G0428' => 'pso', 'PSO063G7510' => 'pso', 'PSO067G0046' => 'pso', 'PSO478G1073' => 'pso', 'PSO675G3677' => 'pso', 'PSO675G6558' => 'pso', 'PSO675G7520' => 'pso', 'PSO675G8959' => 'pso', 'QL02p074089' => 'qlo', 'QL02p089614' => 'qlo', 'QL03p057736' => 'qlo', 'RcHm_v2.0_Chr1g0364131' => 'rch', 'RcHm_v2.0_Chr2g0087801' => 'rch', 'RcHm_v2.0_Chr2g0087821' => 'rch', 'RcHm_v2.0_Chr2g0173231' => 'rch', 'RcHm_v2.0_Chr4g0433111' => 'rch', 'Rhsim03G0250300' => 'rsi', 'Rhsim08G0048400' => 'rsi', 'Rhsim10G0014800' => 'rsi', 'Rhsim12G0040100' => 'rsi', 'Rhsim12G0109700' => 'rsi', 'Sabra06G0049600' => 'sbr', 'Sabra08G0141000' => 'sbr', 'Sabra10G0021400' => 'sbr', 'Sabra16G0222900' => 'sbr', 'Sabra18G0108600' => 'sbr', 'SalBow1G0433' => 'sbo', 'SalBow1G2038' => 'sbo', 'SalBow1G5003' => 'sbo', 'SalBow7G1197' => 'sbo', 'SalBow8G3506' => 'sbo', 'Sc03g0007300' => 'sci', 'Sc11g0000950' => 'sci', 'Sc14g0008750' => 'sci', 'Sc18g0000420' => 'sci', 'Sed0006754' => 'sed', 'Sed0008741' => 'sed', 'Sed0017172' => 'sed', 'Sed0018925' => 'sed', 'Sed0023326' => 'sed', 'Sed0025909' => 'sed', 'SEGI_05333' => 'sgi', 'SEGI_10362' => 'sgi', 'SEGI_13380' => 'sgi', 'SEGI_24306' => 'sgi', 'SEGI_29077' => 'sgi', 'SEGI_29095' => 'sgi', 'SEGI_36534' => 'sgi', 'SEGI_37506' => 'sgi', 'SEGI_38321' => 'sgi', 'SGA_v2.0_scaffold307G48031' => 'sas', 'SGA_v2.0_scaffold47G17507' => 'sas', 'SGA_v2.0_scaffold63G21736' => 'sas', 'SGA_v2.0_scaffold87G27070' => 'sas', 'SHI17794' => 'shi', 'SHI28851' => 'shi', 'SMO165G0155' => 'smo', 'SMO340G0217' => 'smo', 'SMO367G1210' => 'smo', 'Solyc02g093430.3' => 'sly', 'Solyc05g013580.4' => 'sly', 'Solyc07g008030.3' => 'sly', 'Solyc12g035470.2' => 'sly', 'Sopen02g038020' => 'spe', 'Sopen05g008490' => 'spe', 'Sopen07g003910' => 'spe', 'Sopen12g015240' => 'spe', 'Sp1g11550' => 'spa', 'Sp2g16710' => 'spa', 'Sp3g00430' => 'spa', 'Sp3g26780' => 'spa', 'Sp5g22900' => 'spa', 'Sp6g29530' => 'spa', 'TAR371G0794' => 'tar', 'TAR374G0164' => 'tar', 'TAR622G0165' => 'tar', 'TAR626G0929' => 'tar', 'TAR629G2155' => 'tar', 'THA.LOC104805282' => 'tha', 'THA.LOC104805363' => 'tha', 'THA.LOC104808968' => 'tha', 'THA.LOC104821093' => 'tha', 'THA.LOC104823953' => 'tha', 'THA.LOC104825562' => 'tha', 'THA.LOC104825665' => 'tha', 'Thecc.02G261400' => 'tca', 'Thecc.04G019200' => 'tca', 'Thecc.09G130400' => 'tca', 'Thhalv10004374m.g' => 'esa', 'Thhalv10007850m.g' => 'esa', 'Thhalv10013782m.g' => 'esa', 'Thhalv10018686m.g' => 'esa', 'Thhalv10020899m.g' => 'esa', 'Thhalv10022755m.g' => 'esa', 'TPR.G23851' => 'tpr', 'TPR.G26500' => 'tpr', 'TPR.G27267' => 'tpr', 'TPR.G32001' => 'tpr', 'TPR.G6251' => 'tpr', 'TPR.G8167' => 'tpr', 'TWI12G1330' => 'twi', 'TWI18G1239' => 'twi', 'TWI34G0979' => 'twi', 'TWI36G0670' => 'twi', 'TWI36G0707' => 'twi', 'TWI56G0233' => 'twi', 'TWI75G1809' => 'twi', 'unitig_21.g20874' => 'ugi', 'unitig_26.g10343' => 'ugi', 'unitig_46.g18392' => 'ugi', 'unitig_52.g17178' => 'ugi', 'unitig_8.g2934' => 'ugi', 'vmacro01122' => 'vma', 'vmacro05875' => 'vma', 'vmacro06147' => 'vma', 'vmacro16191' => 'vma', 'vmacro18293' => 'vma', 'VMungo0251G3707' => 'vmu', 'VMungo0464G1521' => 'vmu', 'VMungo1215G0205' => 'vmu', 'VMungo1383G2484' => 'vmu', 'Zm00001eb079610' => 'zma', 'Zm00001eb135990' => 'zma', 'Zm00001eb183710' => 'zma', 'Zm00001eb246020' => 'zma' ) $gf_id = 'HOM05D001124' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001124' ) $data_identifier = 'HOM05D001124' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 6, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 7, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 21, 'bol' => (int) 10, 'bra' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 6, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 9, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 21, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 8, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 10, 'lsa' => (int) 8, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 8, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 9, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb246020' $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' => 'HOM05D001124', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '548', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02520' => 'bna', 'A03p06630' => 'bna', 'A05p44460' => 'bna', 'A06p08710' => 'bna', 'A06p41090' => 'bna', 'A07p32320' => 'bna', 'A08p32520' => 'bna', 'A09p10360' => 'bna', 'A10p24080' => 'bna', 'Aa31LG11G15250' => 'aar', 'Aa31LG1G1800' => 'aar', 'Aa31LG2G5120' => 'aar', 'Aa31LG2G6070' => 'aar', 'Aa31LG5G10770' => 'aar', 'Aa31sc61G90' => 'aar', 'Actinidia01352' => 'ach', 'Actinidia05983' => 'ach', 'Actinidia08133' => 'ach', 'Actinidia15101' => 'ach', 'Actinidia26379' => 'ach', 'Actinidia35778' => 'ach', 'Actinidia36123' => 'ach', 'Actinidia37436' => 'ach', 'Actinidia38730' => 'ach', 'Ah.02g128210' => 'amhyb', 'Ah.03g132990' => 'amhyb', 'Ah.14g079410' => 'amhyb', 'AL1G24640' => 'aly', 'AL2G26680' => 'aly', 'AL3G10530' => 'aly', 'AL3G45230' => 'aly', 'AL5G15230' => 'aly', 'AL5G16960' => 'aly', 'AL6G25210' => 'aly', 'Aqoxy2G00441' => 'aox', 'Aqoxy3G01236' => 'aox', 'Aqoxy5G03746' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3RQ047' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C7GMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9C8JER' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MBL6KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YXCZ83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZANX40' => 'arhy', 'AT1G12990' => 'ath', 'AT1G67880' => 'ath', 'AT2G13290' => 'ath', 'AT3G01620' => 'ath', 'AT3G26445' => 'ath', 'AT3G27540' => 'ath', 'AT5G14480' => 'ath', 'ATR0824G026' => 'atr', 'ATR1098G019' => 'atr', 'Atru.chr11.2145' => 'acertr', 'Atru.chr2.3636' => 'acertr', 'Atru.chr2.3644' => 'acertr', 'Atru.chr6.2422' => 'acertr', 'Atru.chr7.1112' => 'acertr', 'AUR62005469' => 'cqu', 'AUR62011166' => 'cqu', 'AUR62013319' => 'cqu', 'AUR62024273' => 'cqu', 'AUR62028420' => 'cqu', 'AUR62041942' => 'cqu', 'BcaB01g04969' => 'bca', 'BcaB01g06371' => 'bca', 'BcaB02g11494' => 'bca', 'BcaB03g15382' => 'bca', 'BcaB08g36994' => 'bca', 'BcaC03g13477' => 'bca', 'BcaC03g13478' => 'bca', 'BcaC03g13480' => 'bca', 'BcaC03g13481' => 'bca', 'BcaC03g13486' => 'bca', 'BcaC04g19031' => 'bca', 'BcaC04g23085' => 'bca', 'BcaC05g25094' => 'bca', 'BcaC05g25096' => 'bca', 'BcaC05g25138' => 'bca', 'BcaC05g30416' => 'bca', 'BcaC05g30455' => 'bca', 'BcaC06g30979' => 'bca', 'BcaC06g33805' => 'bca', 'BcaC08g46021' => 'bca', 'BcaNung03154' => 'bca', 'BolC2t06623H' => 'bol', 'BolC2t06632H' => 'bol', 'BolC2t06635H' => 'bol', 'BolC2t06638H' => 'bol', 'BolC3t13266H' => 'bol', 'BolC5t29776H' => 'bol', 'BolC6t38912H' => 'bol', 'BolC7t44183H' => 'bol', 'BolC9t54123H' => 'bol', 'BolC9t59107H' => 'bol', 'BraA02t05221Z' => 'bra', 'BraA03t09996Z' => 'bra', 'BraA05t23210Z' => 'bra', 'BraA06t24068Z' => 'bra', 'BraA06t27032Z' => 'bra', 'BraA08t35176Z' => 'bra', 'BraA09t36680Z' => 'bra', 'BraA10t44471Z' => 'bra', 'C02p06760' => 'bna', 'C02p06890' => 'bna', 'C02p07010' => 'bna', 'C03p07660' => 'bna', 'C05p10300' => 'bna', 'C06p38150' => 'bna', 'C07p36650' => 'bna', 'C08p15770' => 'bna', 'C09p12300' => 'bna', 'C09p62700' => 'bna', 'C09p75040' => 'bna', 'CAN.G13.1' => 'can', 'CAN.G138.4' => 'can', 'CAN.G44.6' => 'can', 'CAN.G473.19' => 'can', 'CANSAT01G0835' => 'cansat', 'CANSAT11G0246' => 'cansat', 'CANSAT11G1766' => 'cansat', 'CANSAT64G1954' => 'cansat', 'CARHR013330' => 'chi', 'CARHR060530' => 'chi', 'CARHR075300' => 'chi', 'CARHR105120' => 'chi', 'CARHR148910' => 'chi', 'CARHR198830' => 'chi', 'Carub.0001s1275' => 'cru', 'Carub.0002s1437' => 'cru', 'Carub.0003s0044' => 'cru', 'Carub.0003s2787' => 'cru', 'Carub.0005s0597' => 'cru', 'Carub.0006s1266' => 'cru', 'Ca_06935_v3' => 'car', 'Ca_13559_v3' => 'car', 'Ca_16941_v3' => 'car', 'Ca_16960_v3' => 'car', 'Ca_17775_v3' => 'car', 'Ca_30464_v3' => 'car', 'Cc06_g08160' => 'ccan', 'Cc07_g01520' => 'ccan', 'Cc11_g15810' => 'ccan', 'CDE02G2840' => 'cde', 'CDE03G0093' => 'cde', 'CDE04G2127' => 'cde', 'CDE07G1857' => 'cde', 'CDE09G1246' => 'cde', 'Cfa003412' => 'cfa', 'Cfa007341' => 'cfa', 'Cfa009220' => 'cfa', 'Ciclev10008737m.g' => 'ccl', 'Ciclev10015565m.g' => 'ccl', 'Ciclev10031761m.g' => 'ccl', 'CiPaw.03G045300' => 'cil', 'CiPaw.03G247200' => 'cil', 'CiPaw.04G029500' => 'cil', 'CiPaw.04G174000' => 'cil', 'CiPaw.05G181200' => 'cil', 'CiPaw.06G067100' => 'cil', 'ClCG05G025800' => 'cla', 'ClCG06G011400' => 'cla', 'ClCG09G019360' => 'cla', 'COL.COLO4_04827' => 'col', 'COL.COLO4_29170' => 'col', 'COL.COLO4_35131' => 'col', 'COL.COLO4_35132' => 'col', 'Cpa.g.sc33.32' => 'cpa', 'Cpa.g.sc46.29' => 'cpa', 'Cpa.g.sc796.1' => 'cpa', 'CsaV3_1G030420' => 'csa', 'CsaV3_5G027050' => 'csa', 'CsaV3_5G031040' => 'csa', 'CsaV3_UNG023130' => 'csa', 'CSS0007726' => 'camsi', 'CSS0016433' => 'camsi', 'CSS0017656' => 'camsi', 'CSS0025364' => 'camsi', 'CSS0027582' => 'camsi', 'CSS0047288' => 'camsi', 'CSS0049950' => 'camsi', 'DCAR_003843' => 'dca', 'DCAR_007052' => 'dca', 'DCAR_020884' => 'dca', 'DCAR_021730' => 'dca', 'DCAR_024423' => 'dca', 'DCAR_026509' => 'dca', 'DCAR_031158' => 'dca', 'Dinv14728' => 'din', 'Dinv15219' => 'din', 'Dinv25728' => 'din', 'Dinv33428' => 'din', 'Dinv36489' => 'din', 'Dinv41486' => 'din', 'Duzib147G0469' => 'dzi', 'Duzib168G0060' => 'dzi', 'Duzib187G1215' => 'dzi', 'Duzib248G0692' => 'dzi', 'Duzib251G0767' => 'dzi', 'Duzib264G0446' => 'dzi', 'Duzib268G0691' => 'dzi', 'ECA232G4767' => 'eca', 'ECA233G2838' => 'eca', 'ECA234G0391' => 'eca', 'ECA234G0857' => 'eca', 'ECA236G1593' => 'eca', 'ECA238G0565' => 'eca', 'ECA246G1027' => 'eca', 'ECA246G3223' => 'eca', 'ECA246G3470' => 'eca', 'EL10Ac6g13829' => 'bvu', 'EL10Ac6g14093' => 'bvu', 'EL10Ac8g18707' => 'bvu', 'Eucgr.C01369' => 'egr', 'Eucgr.H02492' => 'egr', 'Eucgr.I01733' => 'egr', 'Eucgr.J02255' => 'egr', 'Eucgr.J02257' => 'egr', 'Eucgr.J02258' => 'egr', 'FAN02G1601' => 'fan', 'FAN03G1586' => 'fan', 'FAN03G2986' => 'fan', 'FAN05G4837' => 'fan', 'FAN06G0146' => 'fan', 'FAN07G0858' => 'fan', 'FAN09G3179' => 'fan', 'FAN10G0669' => 'fan', 'FAN12G2358' => 'fan', 'FAN14G4198' => 'fan', 'FAN14G5112' => 'fan', 'FAN17G0342' => 'fan', 'FAN19G0342' => 'fan', 'FAN19G0962' => 'fan', 'FAN19G1101' => 'fan', 'FAN19G1872' => 'fan', 'FAN22G0356' => 'fan', 'FAN23G0744' => 'fan', 'FAN23G1914' => 'fan', 'FAN26G0032' => 'fan', 'FAN28G0625' => 'fan', 'FvH4_1g02710' => 'fve', 'FvH4_1g02720' => 'fve', 'FvH4_4g25670' => 'fve', 'FvH4_6g51700' => 'fve', 'FvH4_7g20170' => 'fve', 'Glyma.05G175000' => 'gma', 'Glyma.08G132300' => 'gma', 'Glyma.11G243000' => 'gma', 'Glyma.13G158900' => 'gma', 'Glyma.17G112400' => 'gma', 'Glyma.18G014100' => 'gma', 'Glyma.19G003100' => 'gma', 'Glyma.19G056500' => 'gma', 'Gohir.A01G158900' => 'ghi', 'Gohir.A05G312600' => 'ghi', 'Gohir.A05G354900' => 'ghi', 'Gohir.A07G037200' => 'ghi', 'Gohir.A09G030000' => 'ghi', 'Gohir.A12G145200' => 'ghi', 'Gohir.D01G151500' => 'ghi', 'Gohir.D04G058300' => 'ghi', 'Gohir.D05G314100' => 'ghi', 'Gohir.D07G041400' => 'ghi', 'Gohir.D09G029700' => 'ghi', 'Gohir.D12G149700' => 'ghi', 'Gorai.001G043800' => 'gra', 'Gorai.002G187800' => 'gra', 'Gorai.006G034700' => 'gra', 'Gorai.008G161200' => 'gra', 'Gorai.009G335700' => 'gra', 'Gorai.012G065000' => 'gra', 'GSVIVG01000535001' => 'vvi', 'GSVIVG01015572001' => 'vvi', 'GSVIVG01032386001' => 'vvi', 'HanXRQChr05g0138531' => 'han', 'HanXRQChr06g0174391' => 'han', 'HanXRQChr07g0199021' => 'han', 'HanXRQChr08g0208211' => 'han', 'HanXRQChr09g0255471' => 'han', 'HanXRQChr10g0315791' => 'han', 'HanXRQChr12g0371991' => 'han', 'HanXRQChr15g0475251' => 'han', 'HanXRQChr17g0540001' => 'han', 'HanXRQChr17g0548631' => 'han', 'HanXRQChr17g0569561' => 'han', 'Haze_12256' => 'cav', 'Haze_14756' => 'cav', 'Haze_25528' => 'cav', 'Hma1.2p1_0079F.1_g041020' => 'hma', 'Hma1.2p1_0818F.1_g223260' => 'hma', 'Hma1.2p1_1747F.1_g300530' => 'hma', 'HPP92_004607' => 'vpl', 'HPP92_004608' => 'vpl', 'HPP92_006181' => 'vpl', 'HPP92_012192' => 'vpl', 'HPP92_015680' => 'vpl', 'HPP92_020249' => 'vpl', 'HPP92_021376' => 'vpl', 'HPP92_024275' => 'vpl', 'Hund06031' => 'sun', 'Hund25391' => 'sun', 'Lalb_Chr07g0185371' => 'lal', 'Lalb_Chr07g0185381' => 'lal', 'Lalb_Chr12g0204011' => 'lal', 'Lalb_Chr13g0301671' => 'lal', 'Lalb_Chr14g0362851' => 'lal', 'Lalb_Chr24g0403581' => 'lal', 'Lj1g0000233' => 'lja', 'Lj2g0018120' => 'lja', 'Lj3C621T0' => 'lonja', 'Lj3P1059T14' => 'lonja', 'Lj3P611T9' => 'lonja', 'Lj3P614T13' => 'lonja', 'Lj3P615T5' => 'lonja', 'Lj4g0012315' => 'lja', 'Lj4g0026182' => 'lja', 'Lj6P813T16' => 'lonja', 'Lj7C427T7' => 'lonja', 'Lj7C427T8' => 'lonja', 'Lj7P600T41' => 'lonja', 'Lju41C42G17' => 'lonja', 'Lsat_1_v5_gn_0_47300' => 'lsa', 'Lsat_1_v5_gn_2_91280' => 'lsa', 'Lsat_1_v5_gn_3_30561' => 'lsa', 'Lsat_1_v5_gn_4_184321' => 'lsa', 'Lsat_1_v5_gn_4_4041' => 'lsa', 'Lsat_1_v5_gn_5_92000' => 'lsa', 'Lsat_1_v5_gn_8_152940' => 'lsa', 'Lsat_1_v5_gn_8_62401' => 'lsa', 'Manes.06G055900' => 'mes', 'Manes.12G022200' => 'mes', 'Manes.13G023300' => 'mes', 'Manes.14G115000' => 'mes', 'Manes.15G151700' => 'mes', 'Manes.17G111300' => 'mes', 'Mapoly0226s0009' => 'mpo', 'MBI02_g25363_MAGBIO' => 'mbi', 'MBI06_g00027_MAGBIO' => 'mbi', 'MBI10_g13034_MAGBIO' => 'mbi', 'MD09G1023400' => 'mdo', 'MD13G1100100' => 'mdo', 'MD15G1169200' => 'mdo', 'MD16G1101100' => 'mdo', 'MD17G1022900' => 'mdo', 'Medtr3g096150' => 'mtr', 'Medtr4g115070' => 'mtr', 'Medtr7g033325' => 'mtr', 'Medtr8g089840' => 'mtr', 'MELO3C010319.2' => 'cme', 'MELO3C011944.2' => 'cme', 'MELO3C021589.2' => 'cme', 'Migut.E00207' => 'egut', 'Migut.H00067' => 'egut', 'Migut.K00433' => 'egut', 'Migut.K00606' => 'egut', 'Migut.K01410' => 'egut', 'MSTRG.13347' => 'ama', 'MSTRG.24045' => 'ama', 'MSTRG.2428' => 'ama', 'MSTRG.26410' => 'ama', 'MSTRG.3139' => 'ama', 'MSTRG.3286' => 'ama', 'MSTRG.563' => 'ama', 'MSTRG.7941' => 'ama', 'Nitab4.5_0000028g0060' => 'nta', 'Nitab4.5_0000065g0260' => 'nta', 'Nitab4.5_0000112g0060' => 'nta', 'Nitab4.5_0000489g0120' => 'nta', 'Nitab4.5_0001776g0050' => 'nta', 'Nitab4.5_0001854g0010' => 'nta', 'Nitab4.5_0001860g0020' => 'nta', 'Nitab4.5_0004352g0010' => 'nta', 'Nitab4.5_0008716g0020' => 'nta', 'Nitab4.5_0008922g0010' => 'nta', 'Nn3g16693' => 'nnu', 'Nn4g22596' => 'nnu', 'Nn7g37639' => 'nnu', 'Oeu001701.1' => 'oeu', 'Oeu018149.1' => 'oeu', 'Oeu026220.1' => 'oeu', 'Oeu038635.1' => 'oeu', 'Oeu049176.1' => 'oeu', 'Oeu056706.1' => 'oeu', 'Oeu056937.1' => 'oeu', 'Oeu057540.1' => 'oeu', 'Os02g0594900' => 'osa', 'Os02g0595100' => 'osa', 'Os04g0477500' => 'osa', 'Os12g0611900' => 'osa', 'Peaxi162Scf00076g00020' => 'pax', 'Peaxi162Scf00128g00217' => 'pax', 'Peaxi162Scf00129g01640' => 'pax', 'Peaxi162Scf00669g00007' => 'pax', 'Peaxi162Scf00700g00421' => 'pax', 'Peaxi162Scf00801g00038' => 'pax', 'Peaxi162Scf00891g00025' => 'pax', 'PGR083G0909' => 'pgr', 'PGR119G1005' => 'pgr', 'PGR142G2236' => 'pgr', 'PGR142G3388' => 'pgr', 'PGSC0003DMG400004514' => 'stu', 'PGSC0003DMG400012635' => 'stu', 'PGSC0003DMG400015730' => 'stu', 'PGSC0003DMG400018611' => 'stu', 'PGSC0003DMG400030897' => 'stu', 'Phvul.001G254800' => 'pvu', 'Phvul.002G260100' => 'pvu', 'Phvul.003G167600' => 'pvu', 'Phvul.004G005100' => 'pvu', 'Potri.001G343600' => 'ptr', 'Potri.006G066700' => 'ptr', 'Potri.008G186000' => 'ptr', 'Potri.010G046900' => 'ptr', 'Potri.018G127900' => 'ptr', 'Pp3c20_17750' => 'ppa', 'Pp3c24_4380' => 'ppa', 'Prupe.1G245800' => 'ppe', 'Prupe.3G293400' => 'ppe', 'Prupe.7G247400' => 'ppe', 'Psat0s145g0120' => 'psa', 'Psat0s595g0040' => 'psa', 'Psat0s595g0120' => 'psa', 'Psat3g175040' => 'psa', 'Psat7g058120' => 'psa', 'PSO017G0428' => 'pso', 'PSO063G7510' => 'pso', 'PSO067G0046' => 'pso', 'PSO478G1073' => 'pso', 'PSO675G3677' => 'pso', 'PSO675G6558' => 'pso', 'PSO675G7520' => 'pso', 'PSO675G8959' => 'pso', 'QL02p074089' => 'qlo', 'QL02p089614' => 'qlo', 'QL03p057736' => 'qlo', 'RcHm_v2.0_Chr1g0364131' => 'rch', 'RcHm_v2.0_Chr2g0087801' => 'rch', 'RcHm_v2.0_Chr2g0087821' => 'rch', 'RcHm_v2.0_Chr2g0173231' => 'rch', 'RcHm_v2.0_Chr4g0433111' => 'rch', 'Rhsim03G0250300' => 'rsi', 'Rhsim08G0048400' => 'rsi', 'Rhsim10G0014800' => 'rsi', 'Rhsim12G0040100' => 'rsi', 'Rhsim12G0109700' => 'rsi', 'Sabra06G0049600' => 'sbr', 'Sabra08G0141000' => 'sbr', 'Sabra10G0021400' => 'sbr', 'Sabra16G0222900' => 'sbr', 'Sabra18G0108600' => 'sbr', 'SalBow1G0433' => 'sbo', 'SalBow1G2038' => 'sbo', 'SalBow1G5003' => 'sbo', 'SalBow7G1197' => 'sbo', 'SalBow8G3506' => 'sbo', 'Sc03g0007300' => 'sci', 'Sc11g0000950' => 'sci', 'Sc14g0008750' => 'sci', 'Sc18g0000420' => 'sci', 'Sed0006754' => 'sed', 'Sed0008741' => 'sed', 'Sed0017172' => 'sed', 'Sed0018925' => 'sed', 'Sed0023326' => 'sed', 'Sed0025909' => 'sed', 'SEGI_05333' => 'sgi', 'SEGI_10362' => 'sgi', 'SEGI_13380' => 'sgi', 'SEGI_24306' => 'sgi', 'SEGI_29077' => 'sgi', 'SEGI_29095' => 'sgi', 'SEGI_36534' => 'sgi', 'SEGI_37506' => 'sgi', 'SEGI_38321' => 'sgi', 'SGA_v2.0_scaffold307G48031' => 'sas', 'SGA_v2.0_scaffold47G17507' => 'sas', 'SGA_v2.0_scaffold63G21736' => 'sas', 'SGA_v2.0_scaffold87G27070' => 'sas', 'SHI17794' => 'shi', 'SHI28851' => 'shi', 'SMO165G0155' => 'smo', 'SMO340G0217' => 'smo', 'SMO367G1210' => 'smo', 'Solyc02g093430.3' => 'sly', 'Solyc05g013580.4' => 'sly', 'Solyc07g008030.3' => 'sly', 'Solyc12g035470.2' => 'sly', 'Sopen02g038020' => 'spe', 'Sopen05g008490' => 'spe', 'Sopen07g003910' => 'spe', 'Sopen12g015240' => 'spe', 'Sp1g11550' => 'spa', 'Sp2g16710' => 'spa', 'Sp3g00430' => 'spa', 'Sp3g26780' => 'spa', 'Sp5g22900' => 'spa', 'Sp6g29530' => 'spa', 'TAR371G0794' => 'tar', 'TAR374G0164' => 'tar', 'TAR622G0165' => 'tar', 'TAR626G0929' => 'tar', 'TAR629G2155' => 'tar', 'THA.LOC104805282' => 'tha', 'THA.LOC104805363' => 'tha', 'THA.LOC104808968' => 'tha', 'THA.LOC104821093' => 'tha', 'THA.LOC104823953' => 'tha', 'THA.LOC104825562' => 'tha', 'THA.LOC104825665' => 'tha', 'Thecc.02G261400' => 'tca', 'Thecc.04G019200' => 'tca', 'Thecc.09G130400' => 'tca', 'Thhalv10004374m.g' => 'esa', 'Thhalv10007850m.g' => 'esa', 'Thhalv10013782m.g' => 'esa', 'Thhalv10018686m.g' => 'esa', 'Thhalv10020899m.g' => 'esa', 'Thhalv10022755m.g' => 'esa', 'TPR.G23851' => 'tpr', 'TPR.G26500' => 'tpr', 'TPR.G27267' => 'tpr', 'TPR.G32001' => 'tpr', 'TPR.G6251' => 'tpr', 'TPR.G8167' => 'tpr', 'TWI12G1330' => 'twi', 'TWI18G1239' => 'twi', 'TWI34G0979' => 'twi', 'TWI36G0670' => 'twi', 'TWI36G0707' => 'twi', 'TWI56G0233' => 'twi', 'TWI75G1809' => 'twi', 'unitig_21.g20874' => 'ugi', 'unitig_26.g10343' => 'ugi', 'unitig_46.g18392' => 'ugi', 'unitig_52.g17178' => 'ugi', 'unitig_8.g2934' => 'ugi', 'vmacro01122' => 'vma', 'vmacro05875' => 'vma', 'vmacro06147' => 'vma', 'vmacro16191' => 'vma', 'vmacro18293' => 'vma', 'VMungo0251G3707' => 'vmu', 'VMungo0464G1521' => 'vmu', 'VMungo1215G0205' => 'vmu', 'VMungo1383G2484' => 'vmu', 'Zm00001eb079610' => 'zma', 'Zm00001eb135990' => 'zma', 'Zm00001eb183710' => 'zma', 'Zm00001eb246020' => 'zma' ), 'gf_id' => 'HOM05D001124', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001124' ), 'data_identifier' => 'HOM05D001124', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001124', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '548', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02520' => 'bna', 'A03p06630' => 'bna', 'A05p44460' => 'bna', 'A06p08710' => 'bna', 'A06p41090' => 'bna', 'A07p32320' => 'bna', 'A08p32520' => 'bna', 'A09p10360' => 'bna', 'A10p24080' => 'bna', 'Aa31LG11G15250' => 'aar', 'Aa31LG1G1800' => 'aar', 'Aa31LG2G5120' => 'aar', 'Aa31LG2G6070' => 'aar', 'Aa31LG5G10770' => 'aar', 'Aa31sc61G90' => 'aar', 'Actinidia01352' => 'ach', 'Actinidia05983' => 'ach', 'Actinidia08133' => 'ach', 'Actinidia15101' => 'ach', 'Actinidia26379' => 'ach', 'Actinidia35778' => 'ach', 'Actinidia36123' => 'ach', 'Actinidia37436' => 'ach', 'Actinidia38730' => 'ach', 'Ah.02g128210' => 'amhyb', 'Ah.03g132990' => 'amhyb', 'Ah.14g079410' => 'amhyb', 'AL1G24640' => 'aly', 'AL2G26680' => 'aly', 'AL3G10530' => 'aly', 'AL3G45230' => 'aly', 'AL5G15230' => 'aly', 'AL5G16960' => 'aly', 'AL6G25210' => 'aly', 'Aqoxy2G00441' => 'aox', 'Aqoxy3G01236' => 'aox', 'Aqoxy5G03746' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3RQ047' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C7GMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9C8JER' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MBL6KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YXCZ83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZANX40' => 'arhy', 'AT1G12990' => 'ath', 'AT1G67880' => 'ath', 'AT2G13290' => 'ath', 'AT3G01620' => 'ath', 'AT3G26445' => 'ath', 'AT3G27540' => 'ath', 'AT5G14480' => 'ath', 'ATR0824G026' => 'atr', 'ATR1098G019' => 'atr', 'Atru.chr11.2145' => 'acertr', 'Atru.chr2.3636' => 'acertr', 'Atru.chr2.3644' => 'acertr', 'Atru.chr6.2422' => 'acertr', 'Atru.chr7.1112' => 'acertr', 'AUR62005469' => 'cqu', 'AUR62011166' => 'cqu', 'AUR62013319' => 'cqu', 'AUR62024273' => 'cqu', 'AUR62028420' => 'cqu', 'AUR62041942' => 'cqu', 'BcaB01g04969' => 'bca', 'BcaB01g06371' => 'bca', 'BcaB02g11494' => 'bca', 'BcaB03g15382' => 'bca', 'BcaB08g36994' => 'bca', 'BcaC03g13477' => 'bca', 'BcaC03g13478' => 'bca', 'BcaC03g13480' => 'bca', 'BcaC03g13481' => 'bca', 'BcaC03g13486' => 'bca', 'BcaC04g19031' => 'bca', 'BcaC04g23085' => 'bca', 'BcaC05g25094' => 'bca', 'BcaC05g25096' => 'bca', 'BcaC05g25138' => 'bca', 'BcaC05g30416' => 'bca', 'BcaC05g30455' => 'bca', 'BcaC06g30979' => 'bca', 'BcaC06g33805' => 'bca', 'BcaC08g46021' => 'bca', 'BcaNung03154' => 'bca', 'BolC2t06623H' => 'bol', 'BolC2t06632H' => 'bol', 'BolC2t06635H' => 'bol', 'BolC2t06638H' => 'bol', 'BolC3t13266H' => 'bol', 'BolC5t29776H' => 'bol', 'BolC6t38912H' => 'bol', 'BolC7t44183H' => 'bol', 'BolC9t54123H' => 'bol', 'BolC9t59107H' => 'bol', 'BraA02t05221Z' => 'bra', 'BraA03t09996Z' => 'bra', 'BraA05t23210Z' => 'bra', 'BraA06t24068Z' => 'bra', 'BraA06t27032Z' => 'bra', 'BraA08t35176Z' => 'bra', 'BraA09t36680Z' => 'bra', 'BraA10t44471Z' => 'bra', 'C02p06760' => 'bna', 'C02p06890' => 'bna', 'C02p07010' => 'bna', 'C03p07660' => 'bna', 'C05p10300' => 'bna', 'C06p38150' => 'bna', 'C07p36650' => 'bna', 'C08p15770' => 'bna', 'C09p12300' => 'bna', 'C09p62700' => 'bna', 'C09p75040' => 'bna', 'CAN.G13.1' => 'can', 'CAN.G138.4' => 'can', 'CAN.G44.6' => 'can', 'CAN.G473.19' => 'can', 'CANSAT01G0835' => 'cansat', 'CANSAT11G0246' => 'cansat', 'CANSAT11G1766' => 'cansat', 'CANSAT64G1954' => 'cansat', 'CARHR013330' => 'chi', 'CARHR060530' => 'chi', 'CARHR075300' => 'chi', 'CARHR105120' => 'chi', 'CARHR148910' => 'chi', 'CARHR198830' => 'chi', 'Carub.0001s1275' => 'cru', 'Carub.0002s1437' => 'cru', 'Carub.0003s0044' => 'cru', 'Carub.0003s2787' => 'cru', 'Carub.0005s0597' => 'cru', 'Carub.0006s1266' => 'cru', 'Ca_06935_v3' => 'car', 'Ca_13559_v3' => 'car', 'Ca_16941_v3' => 'car', 'Ca_16960_v3' => 'car', 'Ca_17775_v3' => 'car', 'Ca_30464_v3' => 'car', 'Cc06_g08160' => 'ccan', 'Cc07_g01520' => 'ccan', 'Cc11_g15810' => 'ccan', 'CDE02G2840' => 'cde', 'CDE03G0093' => 'cde', 'CDE04G2127' => 'cde', 'CDE07G1857' => 'cde', 'CDE09G1246' => 'cde', 'Cfa003412' => 'cfa', 'Cfa007341' => 'cfa', 'Cfa009220' => 'cfa', 'Ciclev10008737m.g' => 'ccl', 'Ciclev10015565m.g' => 'ccl', 'Ciclev10031761m.g' => 'ccl', 'CiPaw.03G045300' => 'cil', 'CiPaw.03G247200' => 'cil', 'CiPaw.04G029500' => 'cil', 'CiPaw.04G174000' => 'cil', 'CiPaw.05G181200' => 'cil', 'CiPaw.06G067100' => 'cil', 'ClCG05G025800' => 'cla', 'ClCG06G011400' => 'cla', 'ClCG09G019360' => 'cla', 'COL.COLO4_04827' => 'col', 'COL.COLO4_29170' => 'col', 'COL.COLO4_35131' => 'col', 'COL.COLO4_35132' => 'col', 'Cpa.g.sc33.32' => 'cpa', 'Cpa.g.sc46.29' => 'cpa', 'Cpa.g.sc796.1' => 'cpa', 'CsaV3_1G030420' => 'csa', 'CsaV3_5G027050' => 'csa', 'CsaV3_5G031040' => 'csa', 'CsaV3_UNG023130' => 'csa', 'CSS0007726' => 'camsi', 'CSS0016433' => 'camsi', 'CSS0017656' => 'camsi', 'CSS0025364' => 'camsi', 'CSS0027582' => 'camsi', 'CSS0047288' => 'camsi', 'CSS0049950' => 'camsi', 'DCAR_003843' => 'dca', 'DCAR_007052' => 'dca', 'DCAR_020884' => 'dca', 'DCAR_021730' => 'dca', 'DCAR_024423' => 'dca', 'DCAR_026509' => 'dca', 'DCAR_031158' => 'dca', 'Dinv14728' => 'din', 'Dinv15219' => 'din', 'Dinv25728' => 'din', 'Dinv33428' => 'din', 'Dinv36489' => 'din', 'Dinv41486' => 'din', 'Duzib147G0469' => 'dzi', 'Duzib168G0060' => 'dzi', 'Duzib187G1215' => 'dzi', 'Duzib248G0692' => 'dzi', 'Duzib251G0767' => 'dzi', 'Duzib264G0446' => 'dzi', 'Duzib268G0691' => 'dzi', 'ECA232G4767' => 'eca', 'ECA233G2838' => 'eca', 'ECA234G0391' => 'eca', 'ECA234G0857' => 'eca', 'ECA236G1593' => 'eca', 'ECA238G0565' => 'eca', 'ECA246G1027' => 'eca', 'ECA246G3223' => 'eca', 'ECA246G3470' => 'eca', 'EL10Ac6g13829' => 'bvu', 'EL10Ac6g14093' => 'bvu', 'EL10Ac8g18707' => 'bvu', 'Eucgr.C01369' => 'egr', 'Eucgr.H02492' => 'egr', 'Eucgr.I01733' => 'egr', 'Eucgr.J02255' => 'egr', 'Eucgr.J02257' => 'egr', 'Eucgr.J02258' => 'egr', 'FAN02G1601' => 'fan', 'FAN03G1586' => 'fan', 'FAN03G2986' => 'fan', 'FAN05G4837' => 'fan', 'FAN06G0146' => 'fan', 'FAN07G0858' => 'fan', 'FAN09G3179' => 'fan', 'FAN10G0669' => 'fan', 'FAN12G2358' => 'fan', 'FAN14G4198' => 'fan', 'FAN14G5112' => 'fan', 'FAN17G0342' => 'fan', 'FAN19G0342' => 'fan', 'FAN19G0962' => 'fan', 'FAN19G1101' => 'fan', 'FAN19G1872' => 'fan', 'FAN22G0356' => 'fan', 'FAN23G0744' => 'fan', 'FAN23G1914' => 'fan', 'FAN26G0032' => 'fan', 'FAN28G0625' => 'fan', 'FvH4_1g02710' => 'fve', 'FvH4_1g02720' => 'fve', 'FvH4_4g25670' => 'fve', 'FvH4_6g51700' => 'fve', 'FvH4_7g20170' => 'fve', 'Glyma.05G175000' => 'gma', 'Glyma.08G132300' => 'gma', 'Glyma.11G243000' => 'gma', 'Glyma.13G158900' => 'gma', 'Glyma.17G112400' => 'gma', 'Glyma.18G014100' => 'gma', 'Glyma.19G003100' => 'gma', 'Glyma.19G056500' => 'gma', 'Gohir.A01G158900' => 'ghi', 'Gohir.A05G312600' => 'ghi', 'Gohir.A05G354900' => 'ghi', 'Gohir.A07G037200' => 'ghi', 'Gohir.A09G030000' => 'ghi', 'Gohir.A12G145200' => 'ghi', 'Gohir.D01G151500' => 'ghi', 'Gohir.D04G058300' => 'ghi', 'Gohir.D05G314100' => 'ghi', 'Gohir.D07G041400' => 'ghi', 'Gohir.D09G029700' => 'ghi', 'Gohir.D12G149700' => 'ghi', 'Gorai.001G043800' => 'gra', 'Gorai.002G187800' => 'gra', 'Gorai.006G034700' => 'gra', 'Gorai.008G161200' => 'gra', 'Gorai.009G335700' => 'gra', 'Gorai.012G065000' => 'gra', 'GSVIVG01000535001' => 'vvi', 'GSVIVG01015572001' => 'vvi', 'GSVIVG01032386001' => 'vvi', 'HanXRQChr05g0138531' => 'han', 'HanXRQChr06g0174391' => 'han', 'HanXRQChr07g0199021' => 'han', 'HanXRQChr08g0208211' => 'han', 'HanXRQChr09g0255471' => 'han', 'HanXRQChr10g0315791' => 'han', 'HanXRQChr12g0371991' => 'han', 'HanXRQChr15g0475251' => 'han', 'HanXRQChr17g0540001' => 'han', 'HanXRQChr17g0548631' => 'han', 'HanXRQChr17g0569561' => 'han', 'Haze_12256' => 'cav', 'Haze_14756' => 'cav', 'Haze_25528' => 'cav', 'Hma1.2p1_0079F.1_g041020' => 'hma', 'Hma1.2p1_0818F.1_g223260' => 'hma', 'Hma1.2p1_1747F.1_g300530' => 'hma', 'HPP92_004607' => 'vpl', 'HPP92_004608' => 'vpl', 'HPP92_006181' => 'vpl', 'HPP92_012192' => 'vpl', 'HPP92_015680' => 'vpl', 'HPP92_020249' => 'vpl', 'HPP92_021376' => 'vpl', 'HPP92_024275' => 'vpl', 'Hund06031' => 'sun', 'Hund25391' => 'sun', 'Lalb_Chr07g0185371' => 'lal', 'Lalb_Chr07g0185381' => 'lal', 'Lalb_Chr12g0204011' => 'lal', 'Lalb_Chr13g0301671' => 'lal', 'Lalb_Chr14g0362851' => 'lal', 'Lalb_Chr24g0403581' => 'lal', 'Lj1g0000233' => 'lja', 'Lj2g0018120' => 'lja', 'Lj3C621T0' => 'lonja', 'Lj3P1059T14' => 'lonja', 'Lj3P611T9' => 'lonja', 'Lj3P614T13' => 'lonja', 'Lj3P615T5' => 'lonja', 'Lj4g0012315' => 'lja', 'Lj4g0026182' => 'lja', 'Lj6P813T16' => 'lonja', 'Lj7C427T7' => 'lonja', 'Lj7C427T8' => 'lonja', 'Lj7P600T41' => 'lonja', 'Lju41C42G17' => 'lonja', 'Lsat_1_v5_gn_0_47300' => 'lsa', 'Lsat_1_v5_gn_2_91280' => 'lsa', 'Lsat_1_v5_gn_3_30561' => 'lsa', 'Lsat_1_v5_gn_4_184321' => 'lsa', 'Lsat_1_v5_gn_4_4041' => 'lsa', 'Lsat_1_v5_gn_5_92000' => 'lsa', 'Lsat_1_v5_gn_8_152940' => 'lsa', 'Lsat_1_v5_gn_8_62401' => 'lsa', 'Manes.06G055900' => 'mes', 'Manes.12G022200' => 'mes', 'Manes.13G023300' => 'mes', 'Manes.14G115000' => 'mes', 'Manes.15G151700' => 'mes', 'Manes.17G111300' => 'mes', 'Mapoly0226s0009' => 'mpo', 'MBI02_g25363_MAGBIO' => 'mbi', 'MBI06_g00027_MAGBIO' => 'mbi', 'MBI10_g13034_MAGBIO' => 'mbi', 'MD09G1023400' => 'mdo', 'MD13G1100100' => 'mdo', 'MD15G1169200' => 'mdo', 'MD16G1101100' => 'mdo', 'MD17G1022900' => 'mdo', 'Medtr3g096150' => 'mtr', 'Medtr4g115070' => 'mtr', 'Medtr7g033325' => 'mtr', 'Medtr8g089840' => 'mtr', 'MELO3C010319.2' => 'cme', 'MELO3C011944.2' => 'cme', 'MELO3C021589.2' => 'cme', 'Migut.E00207' => 'egut', 'Migut.H00067' => 'egut', 'Migut.K00433' => 'egut', 'Migut.K00606' => 'egut', 'Migut.K01410' => 'egut', 'MSTRG.13347' => 'ama', 'MSTRG.24045' => 'ama', 'MSTRG.2428' => 'ama', 'MSTRG.26410' => 'ama', 'MSTRG.3139' => 'ama', 'MSTRG.3286' => 'ama', 'MSTRG.563' => 'ama', 'MSTRG.7941' => 'ama', 'Nitab4.5_0000028g0060' => 'nta', 'Nitab4.5_0000065g0260' => 'nta', 'Nitab4.5_0000112g0060' => 'nta', 'Nitab4.5_0000489g0120' => 'nta', 'Nitab4.5_0001776g0050' => 'nta', 'Nitab4.5_0001854g0010' => 'nta', 'Nitab4.5_0001860g0020' => 'nta', 'Nitab4.5_0004352g0010' => 'nta', 'Nitab4.5_0008716g0020' => 'nta', 'Nitab4.5_0008922g0010' => 'nta', 'Nn3g16693' => 'nnu', 'Nn4g22596' => 'nnu', 'Nn7g37639' => 'nnu', 'Oeu001701.1' => 'oeu', 'Oeu018149.1' => 'oeu', 'Oeu026220.1' => 'oeu', 'Oeu038635.1' => 'oeu', 'Oeu049176.1' => 'oeu', 'Oeu056706.1' => 'oeu', 'Oeu056937.1' => 'oeu', 'Oeu057540.1' => 'oeu', 'Os02g0594900' => 'osa', 'Os02g0595100' => 'osa', 'Os04g0477500' => 'osa', 'Os12g0611900' => 'osa', 'Peaxi162Scf00076g00020' => 'pax', 'Peaxi162Scf00128g00217' => 'pax', 'Peaxi162Scf00129g01640' => 'pax', 'Peaxi162Scf00669g00007' => 'pax', 'Peaxi162Scf00700g00421' => 'pax', 'Peaxi162Scf00801g00038' => 'pax', 'Peaxi162Scf00891g00025' => 'pax', 'PGR083G0909' => 'pgr', 'PGR119G1005' => 'pgr', 'PGR142G2236' => 'pgr', 'PGR142G3388' => 'pgr', 'PGSC0003DMG400004514' => 'stu', 'PGSC0003DMG400012635' => 'stu', 'PGSC0003DMG400015730' => 'stu', 'PGSC0003DMG400018611' => 'stu', 'PGSC0003DMG400030897' => 'stu', 'Phvul.001G254800' => 'pvu', 'Phvul.002G260100' => 'pvu', 'Phvul.003G167600' => 'pvu', 'Phvul.004G005100' => 'pvu', 'Potri.001G343600' => 'ptr', 'Potri.006G066700' => 'ptr', 'Potri.008G186000' => 'ptr', 'Potri.010G046900' => 'ptr', 'Potri.018G127900' => 'ptr', 'Pp3c20_17750' => 'ppa', 'Pp3c24_4380' => 'ppa', 'Prupe.1G245800' => 'ppe', 'Prupe.3G293400' => 'ppe', 'Prupe.7G247400' => 'ppe', 'Psat0s145g0120' => 'psa', 'Psat0s595g0040' => 'psa', 'Psat0s595g0120' => 'psa', 'Psat3g175040' => 'psa', 'Psat7g058120' => 'psa', 'PSO017G0428' => 'pso', 'PSO063G7510' => 'pso', 'PSO067G0046' => 'pso', 'PSO478G1073' => 'pso', 'PSO675G3677' => 'pso', 'PSO675G6558' => 'pso', 'PSO675G7520' => 'pso', 'PSO675G8959' => 'pso', 'QL02p074089' => 'qlo', 'QL02p089614' => 'qlo', 'QL03p057736' => 'qlo', 'RcHm_v2.0_Chr1g0364131' => 'rch', 'RcHm_v2.0_Chr2g0087801' => 'rch', 'RcHm_v2.0_Chr2g0087821' => 'rch', 'RcHm_v2.0_Chr2g0173231' => 'rch', 'RcHm_v2.0_Chr4g0433111' => 'rch', 'Rhsim03G0250300' => 'rsi', 'Rhsim08G0048400' => 'rsi', 'Rhsim10G0014800' => 'rsi', 'Rhsim12G0040100' => 'rsi', 'Rhsim12G0109700' => 'rsi', 'Sabra06G0049600' => 'sbr', 'Sabra08G0141000' => 'sbr', 'Sabra10G0021400' => 'sbr', 'Sabra16G0222900' => 'sbr', 'Sabra18G0108600' => 'sbr', 'SalBow1G0433' => 'sbo', 'SalBow1G2038' => 'sbo', 'SalBow1G5003' => 'sbo', 'SalBow7G1197' => 'sbo', 'SalBow8G3506' => 'sbo', 'Sc03g0007300' => 'sci', 'Sc11g0000950' => 'sci', 'Sc14g0008750' => 'sci', 'Sc18g0000420' => 'sci', 'Sed0006754' => 'sed', 'Sed0008741' => 'sed', 'Sed0017172' => 'sed', 'Sed0018925' => 'sed', 'Sed0023326' => 'sed', 'Sed0025909' => 'sed', 'SEGI_05333' => 'sgi', 'SEGI_10362' => 'sgi', 'SEGI_13380' => 'sgi', 'SEGI_24306' => 'sgi', 'SEGI_29077' => 'sgi', 'SEGI_29095' => 'sgi', 'SEGI_36534' => 'sgi', 'SEGI_37506' => 'sgi', 'SEGI_38321' => 'sgi', 'SGA_v2.0_scaffold307G48031' => 'sas', 'SGA_v2.0_scaffold47G17507' => 'sas', 'SGA_v2.0_scaffold63G21736' => 'sas', 'SGA_v2.0_scaffold87G27070' => 'sas', 'SHI17794' => 'shi', 'SHI28851' => 'shi', 'SMO165G0155' => 'smo', 'SMO340G0217' => 'smo', 'SMO367G1210' => 'smo', 'Solyc02g093430.3' => 'sly', 'Solyc05g013580.4' => 'sly', 'Solyc07g008030.3' => 'sly', 'Solyc12g035470.2' => 'sly', 'Sopen02g038020' => 'spe', 'Sopen05g008490' => 'spe', 'Sopen07g003910' => 'spe', 'Sopen12g015240' => 'spe', 'Sp1g11550' => 'spa', 'Sp2g16710' => 'spa', 'Sp3g00430' => 'spa', 'Sp3g26780' => 'spa', 'Sp5g22900' => 'spa', 'Sp6g29530' => 'spa', 'TAR371G0794' => 'tar', 'TAR374G0164' => 'tar', 'TAR622G0165' => 'tar', 'TAR626G0929' => 'tar', 'TAR629G2155' => 'tar', 'THA.LOC104805282' => 'tha', 'THA.LOC104805363' => 'tha', 'THA.LOC104808968' => 'tha', 'THA.LOC104821093' => 'tha', 'THA.LOC104823953' => 'tha', 'THA.LOC104825562' => 'tha', 'THA.LOC104825665' => 'tha', 'Thecc.02G261400' => 'tca', 'Thecc.04G019200' => 'tca', 'Thecc.09G130400' => 'tca', 'Thhalv10004374m.g' => 'esa', 'Thhalv10007850m.g' => 'esa', 'Thhalv10013782m.g' => 'esa', 'Thhalv10018686m.g' => 'esa', 'Thhalv10020899m.g' => 'esa', 'Thhalv10022755m.g' => 'esa', 'TPR.G23851' => 'tpr', 'TPR.G26500' => 'tpr', 'TPR.G27267' => 'tpr', 'TPR.G32001' => 'tpr', 'TPR.G6251' => 'tpr', 'TPR.G8167' => 'tpr', 'TWI12G1330' => 'twi', 'TWI18G1239' => 'twi', 'TWI34G0979' => 'twi', 'TWI36G0670' => 'twi', 'TWI36G0707' => 'twi', 'TWI56G0233' => 'twi', 'TWI75G1809' => 'twi', 'unitig_21.g20874' => 'ugi', 'unitig_26.g10343' => 'ugi', 'unitig_46.g18392' => 'ugi', 'unitig_52.g17178' => 'ugi', 'unitig_8.g2934' => 'ugi', 'vmacro01122' => 'vma', 'vmacro05875' => 'vma', 'vmacro06147' => 'vma', 'vmacro16191' => 'vma', 'vmacro18293' => 'vma', 'VMungo0251G3707' => 'vmu', 'VMungo0464G1521' => 'vmu', 'VMungo1215G0205' => 'vmu', 'VMungo1383G2484' => 'vmu', 'Zm00001eb079610' => 'zma', 'Zm00001eb135990' => 'zma', 'Zm00001eb183710' => 'zma', 'Zm00001eb246020' => 'zma' ) $gf_id = 'HOM05D001124' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001124' ) $data_identifier = 'HOM05D001124' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 6, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 7, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 21, 'bol' => (int) 10, 'bra' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 6, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 9, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 21, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 8, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 10, 'lsa' => (int) 8, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 8, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 9, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb246020' $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' => 'HOM05D001124', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '548', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02520' => 'bna', 'A03p06630' => 'bna', 'A05p44460' => 'bna', 'A06p08710' => 'bna', 'A06p41090' => 'bna', 'A07p32320' => 'bna', 'A08p32520' => 'bna', 'A09p10360' => 'bna', 'A10p24080' => 'bna', 'Aa31LG11G15250' => 'aar', 'Aa31LG1G1800' => 'aar', 'Aa31LG2G5120' => 'aar', 'Aa31LG2G6070' => 'aar', 'Aa31LG5G10770' => 'aar', 'Aa31sc61G90' => 'aar', 'Actinidia01352' => 'ach', 'Actinidia05983' => 'ach', 'Actinidia08133' => 'ach', 'Actinidia15101' => 'ach', 'Actinidia26379' => 'ach', 'Actinidia35778' => 'ach', 'Actinidia36123' => 'ach', 'Actinidia37436' => 'ach', 'Actinidia38730' => 'ach', 'Ah.02g128210' => 'amhyb', 'Ah.03g132990' => 'amhyb', 'Ah.14g079410' => 'amhyb', 'AL1G24640' => 'aly', 'AL2G26680' => 'aly', 'AL3G10530' => 'aly', 'AL3G45230' => 'aly', 'AL5G15230' => 'aly', 'AL5G16960' => 'aly', 'AL6G25210' => 'aly', 'Aqoxy2G00441' => 'aox', 'Aqoxy3G01236' => 'aox', 'Aqoxy5G03746' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3RQ047' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C7GMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9C8JER' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MBL6KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YXCZ83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZANX40' => 'arhy', 'AT1G12990' => 'ath', 'AT1G67880' => 'ath', 'AT2G13290' => 'ath', 'AT3G01620' => 'ath', 'AT3G26445' => 'ath', 'AT3G27540' => 'ath', 'AT5G14480' => 'ath', 'ATR0824G026' => 'atr', 'ATR1098G019' => 'atr', 'Atru.chr11.2145' => 'acertr', 'Atru.chr2.3636' => 'acertr', 'Atru.chr2.3644' => 'acertr', 'Atru.chr6.2422' => 'acertr', 'Atru.chr7.1112' => 'acertr', 'AUR62005469' => 'cqu', 'AUR62011166' => 'cqu', 'AUR62013319' => 'cqu', 'AUR62024273' => 'cqu', 'AUR62028420' => 'cqu', 'AUR62041942' => 'cqu', 'BcaB01g04969' => 'bca', 'BcaB01g06371' => 'bca', 'BcaB02g11494' => 'bca', 'BcaB03g15382' => 'bca', 'BcaB08g36994' => 'bca', 'BcaC03g13477' => 'bca', 'BcaC03g13478' => 'bca', 'BcaC03g13480' => 'bca', 'BcaC03g13481' => 'bca', 'BcaC03g13486' => 'bca', 'BcaC04g19031' => 'bca', 'BcaC04g23085' => 'bca', 'BcaC05g25094' => 'bca', 'BcaC05g25096' => 'bca', 'BcaC05g25138' => 'bca', 'BcaC05g30416' => 'bca', 'BcaC05g30455' => 'bca', 'BcaC06g30979' => 'bca', 'BcaC06g33805' => 'bca', 'BcaC08g46021' => 'bca', 'BcaNung03154' => 'bca', 'BolC2t06623H' => 'bol', 'BolC2t06632H' => 'bol', 'BolC2t06635H' => 'bol', 'BolC2t06638H' => 'bol', 'BolC3t13266H' => 'bol', 'BolC5t29776H' => 'bol', 'BolC6t38912H' => 'bol', 'BolC7t44183H' => 'bol', 'BolC9t54123H' => 'bol', 'BolC9t59107H' => 'bol', 'BraA02t05221Z' => 'bra', 'BraA03t09996Z' => 'bra', 'BraA05t23210Z' => 'bra', 'BraA06t24068Z' => 'bra', 'BraA06t27032Z' => 'bra', 'BraA08t35176Z' => 'bra', 'BraA09t36680Z' => 'bra', 'BraA10t44471Z' => 'bra', 'C02p06760' => 'bna', 'C02p06890' => 'bna', 'C02p07010' => 'bna', 'C03p07660' => 'bna', 'C05p10300' => 'bna', 'C06p38150' => 'bna', 'C07p36650' => 'bna', 'C08p15770' => 'bna', 'C09p12300' => 'bna', 'C09p62700' => 'bna', 'C09p75040' => 'bna', 'CAN.G13.1' => 'can', 'CAN.G138.4' => 'can', 'CAN.G44.6' => 'can', 'CAN.G473.19' => 'can', 'CANSAT01G0835' => 'cansat', 'CANSAT11G0246' => 'cansat', 'CANSAT11G1766' => 'cansat', 'CANSAT64G1954' => 'cansat', 'CARHR013330' => 'chi', 'CARHR060530' => 'chi', 'CARHR075300' => 'chi', 'CARHR105120' => 'chi', 'CARHR148910' => 'chi', 'CARHR198830' => 'chi', 'Carub.0001s1275' => 'cru', 'Carub.0002s1437' => 'cru', 'Carub.0003s0044' => 'cru', 'Carub.0003s2787' => 'cru', 'Carub.0005s0597' => 'cru', 'Carub.0006s1266' => 'cru', 'Ca_06935_v3' => 'car', 'Ca_13559_v3' => 'car', 'Ca_16941_v3' => 'car', 'Ca_16960_v3' => 'car', 'Ca_17775_v3' => 'car', 'Ca_30464_v3' => 'car', 'Cc06_g08160' => 'ccan', 'Cc07_g01520' => 'ccan', 'Cc11_g15810' => 'ccan', 'CDE02G2840' => 'cde', 'CDE03G0093' => 'cde', 'CDE04G2127' => 'cde', 'CDE07G1857' => 'cde', 'CDE09G1246' => 'cde', 'Cfa003412' => 'cfa', 'Cfa007341' => 'cfa', 'Cfa009220' => 'cfa', 'Ciclev10008737m.g' => 'ccl', 'Ciclev10015565m.g' => 'ccl', 'Ciclev10031761m.g' => 'ccl', 'CiPaw.03G045300' => 'cil', 'CiPaw.03G247200' => 'cil', 'CiPaw.04G029500' => 'cil', 'CiPaw.04G174000' => 'cil', 'CiPaw.05G181200' => 'cil', 'CiPaw.06G067100' => 'cil', 'ClCG05G025800' => 'cla', 'ClCG06G011400' => 'cla', 'ClCG09G019360' => 'cla', 'COL.COLO4_04827' => 'col', 'COL.COLO4_29170' => 'col', 'COL.COLO4_35131' => 'col', 'COL.COLO4_35132' => 'col', 'Cpa.g.sc33.32' => 'cpa', 'Cpa.g.sc46.29' => 'cpa', 'Cpa.g.sc796.1' => 'cpa', 'CsaV3_1G030420' => 'csa', 'CsaV3_5G027050' => 'csa', 'CsaV3_5G031040' => 'csa', 'CsaV3_UNG023130' => 'csa', 'CSS0007726' => 'camsi', 'CSS0016433' => 'camsi', 'CSS0017656' => 'camsi', 'CSS0025364' => 'camsi', 'CSS0027582' => 'camsi', 'CSS0047288' => 'camsi', 'CSS0049950' => 'camsi', 'DCAR_003843' => 'dca', 'DCAR_007052' => 'dca', 'DCAR_020884' => 'dca', 'DCAR_021730' => 'dca', 'DCAR_024423' => 'dca', 'DCAR_026509' => 'dca', 'DCAR_031158' => 'dca', 'Dinv14728' => 'din', 'Dinv15219' => 'din', 'Dinv25728' => 'din', 'Dinv33428' => 'din', 'Dinv36489' => 'din', 'Dinv41486' => 'din', 'Duzib147G0469' => 'dzi', 'Duzib168G0060' => 'dzi', 'Duzib187G1215' => 'dzi', 'Duzib248G0692' => 'dzi', 'Duzib251G0767' => 'dzi', 'Duzib264G0446' => 'dzi', 'Duzib268G0691' => 'dzi', 'ECA232G4767' => 'eca', 'ECA233G2838' => 'eca', 'ECA234G0391' => 'eca', 'ECA234G0857' => 'eca', 'ECA236G1593' => 'eca', 'ECA238G0565' => 'eca', 'ECA246G1027' => 'eca', 'ECA246G3223' => 'eca', 'ECA246G3470' => 'eca', 'EL10Ac6g13829' => 'bvu', 'EL10Ac6g14093' => 'bvu', 'EL10Ac8g18707' => 'bvu', 'Eucgr.C01369' => 'egr', 'Eucgr.H02492' => 'egr', 'Eucgr.I01733' => 'egr', 'Eucgr.J02255' => 'egr', 'Eucgr.J02257' => 'egr', 'Eucgr.J02258' => 'egr', 'FAN02G1601' => 'fan', 'FAN03G1586' => 'fan', 'FAN03G2986' => 'fan', 'FAN05G4837' => 'fan', 'FAN06G0146' => 'fan', 'FAN07G0858' => 'fan', 'FAN09G3179' => 'fan', 'FAN10G0669' => 'fan', 'FAN12G2358' => 'fan', 'FAN14G4198' => 'fan', 'FAN14G5112' => 'fan', 'FAN17G0342' => 'fan', 'FAN19G0342' => 'fan', 'FAN19G0962' => 'fan', 'FAN19G1101' => 'fan', 'FAN19G1872' => 'fan', 'FAN22G0356' => 'fan', 'FAN23G0744' => 'fan', 'FAN23G1914' => 'fan', 'FAN26G0032' => 'fan', 'FAN28G0625' => 'fan', 'FvH4_1g02710' => 'fve', 'FvH4_1g02720' => 'fve', 'FvH4_4g25670' => 'fve', 'FvH4_6g51700' => 'fve', 'FvH4_7g20170' => 'fve', 'Glyma.05G175000' => 'gma', 'Glyma.08G132300' => 'gma', 'Glyma.11G243000' => 'gma', 'Glyma.13G158900' => 'gma', 'Glyma.17G112400' => 'gma', 'Glyma.18G014100' => 'gma', 'Glyma.19G003100' => 'gma', 'Glyma.19G056500' => 'gma', 'Gohir.A01G158900' => 'ghi', 'Gohir.A05G312600' => 'ghi', 'Gohir.A05G354900' => 'ghi', 'Gohir.A07G037200' => 'ghi', 'Gohir.A09G030000' => 'ghi', 'Gohir.A12G145200' => 'ghi', 'Gohir.D01G151500' => 'ghi', 'Gohir.D04G058300' => 'ghi', 'Gohir.D05G314100' => 'ghi', 'Gohir.D07G041400' => 'ghi', 'Gohir.D09G029700' => 'ghi', 'Gohir.D12G149700' => 'ghi', 'Gorai.001G043800' => 'gra', 'Gorai.002G187800' => 'gra', 'Gorai.006G034700' => 'gra', 'Gorai.008G161200' => 'gra', 'Gorai.009G335700' => 'gra', 'Gorai.012G065000' => 'gra', 'GSVIVG01000535001' => 'vvi', 'GSVIVG01015572001' => 'vvi', 'GSVIVG01032386001' => 'vvi', 'HanXRQChr05g0138531' => 'han', 'HanXRQChr06g0174391' => 'han', 'HanXRQChr07g0199021' => 'han', 'HanXRQChr08g0208211' => 'han', 'HanXRQChr09g0255471' => 'han', 'HanXRQChr10g0315791' => 'han', 'HanXRQChr12g0371991' => 'han', 'HanXRQChr15g0475251' => 'han', 'HanXRQChr17g0540001' => 'han', 'HanXRQChr17g0548631' => 'han', 'HanXRQChr17g0569561' => 'han', 'Haze_12256' => 'cav', 'Haze_14756' => 'cav', 'Haze_25528' => 'cav', 'Hma1.2p1_0079F.1_g041020' => 'hma', 'Hma1.2p1_0818F.1_g223260' => 'hma', 'Hma1.2p1_1747F.1_g300530' => 'hma', 'HPP92_004607' => 'vpl', 'HPP92_004608' => 'vpl', 'HPP92_006181' => 'vpl', 'HPP92_012192' => 'vpl', 'HPP92_015680' => 'vpl', 'HPP92_020249' => 'vpl', 'HPP92_021376' => 'vpl', 'HPP92_024275' => 'vpl', 'Hund06031' => 'sun', 'Hund25391' => 'sun', 'Lalb_Chr07g0185371' => 'lal', 'Lalb_Chr07g0185381' => 'lal', 'Lalb_Chr12g0204011' => 'lal', 'Lalb_Chr13g0301671' => 'lal', 'Lalb_Chr14g0362851' => 'lal', 'Lalb_Chr24g0403581' => 'lal', 'Lj1g0000233' => 'lja', 'Lj2g0018120' => 'lja', 'Lj3C621T0' => 'lonja', 'Lj3P1059T14' => 'lonja', 'Lj3P611T9' => 'lonja', 'Lj3P614T13' => 'lonja', 'Lj3P615T5' => 'lonja', 'Lj4g0012315' => 'lja', 'Lj4g0026182' => 'lja', 'Lj6P813T16' => 'lonja', 'Lj7C427T7' => 'lonja', 'Lj7C427T8' => 'lonja', 'Lj7P600T41' => 'lonja', 'Lju41C42G17' => 'lonja', 'Lsat_1_v5_gn_0_47300' => 'lsa', 'Lsat_1_v5_gn_2_91280' => 'lsa', 'Lsat_1_v5_gn_3_30561' => 'lsa', 'Lsat_1_v5_gn_4_184321' => 'lsa', 'Lsat_1_v5_gn_4_4041' => 'lsa', 'Lsat_1_v5_gn_5_92000' => 'lsa', 'Lsat_1_v5_gn_8_152940' => 'lsa', 'Lsat_1_v5_gn_8_62401' => 'lsa', 'Manes.06G055900' => 'mes', 'Manes.12G022200' => 'mes', 'Manes.13G023300' => 'mes', 'Manes.14G115000' => 'mes', 'Manes.15G151700' => 'mes', 'Manes.17G111300' => 'mes', 'Mapoly0226s0009' => 'mpo', 'MBI02_g25363_MAGBIO' => 'mbi', 'MBI06_g00027_MAGBIO' => 'mbi', 'MBI10_g13034_MAGBIO' => 'mbi', 'MD09G1023400' => 'mdo', 'MD13G1100100' => 'mdo', 'MD15G1169200' => 'mdo', 'MD16G1101100' => 'mdo', 'MD17G1022900' => 'mdo', 'Medtr3g096150' => 'mtr', 'Medtr4g115070' => 'mtr', 'Medtr7g033325' => 'mtr', 'Medtr8g089840' => 'mtr', 'MELO3C010319.2' => 'cme', 'MELO3C011944.2' => 'cme', 'MELO3C021589.2' => 'cme', 'Migut.E00207' => 'egut', 'Migut.H00067' => 'egut', 'Migut.K00433' => 'egut', 'Migut.K00606' => 'egut', 'Migut.K01410' => 'egut', 'MSTRG.13347' => 'ama', 'MSTRG.24045' => 'ama', 'MSTRG.2428' => 'ama', 'MSTRG.26410' => 'ama', 'MSTRG.3139' => 'ama', 'MSTRG.3286' => 'ama', 'MSTRG.563' => 'ama', 'MSTRG.7941' => 'ama', 'Nitab4.5_0000028g0060' => 'nta', 'Nitab4.5_0000065g0260' => 'nta', 'Nitab4.5_0000112g0060' => 'nta', 'Nitab4.5_0000489g0120' => 'nta', 'Nitab4.5_0001776g0050' => 'nta', 'Nitab4.5_0001854g0010' => 'nta', 'Nitab4.5_0001860g0020' => 'nta', 'Nitab4.5_0004352g0010' => 'nta', 'Nitab4.5_0008716g0020' => 'nta', 'Nitab4.5_0008922g0010' => 'nta', 'Nn3g16693' => 'nnu', 'Nn4g22596' => 'nnu', 'Nn7g37639' => 'nnu', 'Oeu001701.1' => 'oeu', 'Oeu018149.1' => 'oeu', 'Oeu026220.1' => 'oeu', 'Oeu038635.1' => 'oeu', 'Oeu049176.1' => 'oeu', 'Oeu056706.1' => 'oeu', 'Oeu056937.1' => 'oeu', 'Oeu057540.1' => 'oeu', 'Os02g0594900' => 'osa', 'Os02g0595100' => 'osa', 'Os04g0477500' => 'osa', 'Os12g0611900' => 'osa', 'Peaxi162Scf00076g00020' => 'pax', 'Peaxi162Scf00128g00217' => 'pax', 'Peaxi162Scf00129g01640' => 'pax', 'Peaxi162Scf00669g00007' => 'pax', 'Peaxi162Scf00700g00421' => 'pax', 'Peaxi162Scf00801g00038' => 'pax', 'Peaxi162Scf00891g00025' => 'pax', 'PGR083G0909' => 'pgr', 'PGR119G1005' => 'pgr', 'PGR142G2236' => 'pgr', 'PGR142G3388' => 'pgr', 'PGSC0003DMG400004514' => 'stu', 'PGSC0003DMG400012635' => 'stu', 'PGSC0003DMG400015730' => 'stu', 'PGSC0003DMG400018611' => 'stu', 'PGSC0003DMG400030897' => 'stu', 'Phvul.001G254800' => 'pvu', 'Phvul.002G260100' => 'pvu', 'Phvul.003G167600' => 'pvu', 'Phvul.004G005100' => 'pvu', 'Potri.001G343600' => 'ptr', 'Potri.006G066700' => 'ptr', 'Potri.008G186000' => 'ptr', 'Potri.010G046900' => 'ptr', 'Potri.018G127900' => 'ptr', 'Pp3c20_17750' => 'ppa', 'Pp3c24_4380' => 'ppa', 'Prupe.1G245800' => 'ppe', 'Prupe.3G293400' => 'ppe', 'Prupe.7G247400' => 'ppe', 'Psat0s145g0120' => 'psa', 'Psat0s595g0040' => 'psa', 'Psat0s595g0120' => 'psa', 'Psat3g175040' => 'psa', 'Psat7g058120' => 'psa', 'PSO017G0428' => 'pso', 'PSO063G7510' => 'pso', 'PSO067G0046' => 'pso', 'PSO478G1073' => 'pso', 'PSO675G3677' => 'pso', 'PSO675G6558' => 'pso', 'PSO675G7520' => 'pso', 'PSO675G8959' => 'pso', 'QL02p074089' => 'qlo', 'QL02p089614' => 'qlo', 'QL03p057736' => 'qlo', 'RcHm_v2.0_Chr1g0364131' => 'rch', 'RcHm_v2.0_Chr2g0087801' => 'rch', 'RcHm_v2.0_Chr2g0087821' => 'rch', 'RcHm_v2.0_Chr2g0173231' => 'rch', 'RcHm_v2.0_Chr4g0433111' => 'rch', 'Rhsim03G0250300' => 'rsi', 'Rhsim08G0048400' => 'rsi', 'Rhsim10G0014800' => 'rsi', 'Rhsim12G0040100' => 'rsi', 'Rhsim12G0109700' => 'rsi', 'Sabra06G0049600' => 'sbr', 'Sabra08G0141000' => 'sbr', 'Sabra10G0021400' => 'sbr', 'Sabra16G0222900' => 'sbr', 'Sabra18G0108600' => 'sbr', 'SalBow1G0433' => 'sbo', 'SalBow1G2038' => 'sbo', 'SalBow1G5003' => 'sbo', 'SalBow7G1197' => 'sbo', 'SalBow8G3506' => 'sbo', 'Sc03g0007300' => 'sci', 'Sc11g0000950' => 'sci', 'Sc14g0008750' => 'sci', 'Sc18g0000420' => 'sci', 'Sed0006754' => 'sed', 'Sed0008741' => 'sed', 'Sed0017172' => 'sed', 'Sed0018925' => 'sed', 'Sed0023326' => 'sed', 'Sed0025909' => 'sed', 'SEGI_05333' => 'sgi', 'SEGI_10362' => 'sgi', 'SEGI_13380' => 'sgi', 'SEGI_24306' => 'sgi', 'SEGI_29077' => 'sgi', 'SEGI_29095' => 'sgi', 'SEGI_36534' => 'sgi', 'SEGI_37506' => 'sgi', 'SEGI_38321' => 'sgi', 'SGA_v2.0_scaffold307G48031' => 'sas', 'SGA_v2.0_scaffold47G17507' => 'sas', 'SGA_v2.0_scaffold63G21736' => 'sas', 'SGA_v2.0_scaffold87G27070' => 'sas', 'SHI17794' => 'shi', 'SHI28851' => 'shi', 'SMO165G0155' => 'smo', 'SMO340G0217' => 'smo', 'SMO367G1210' => 'smo', 'Solyc02g093430.3' => 'sly', 'Solyc05g013580.4' => 'sly', 'Solyc07g008030.3' => 'sly', 'Solyc12g035470.2' => 'sly', 'Sopen02g038020' => 'spe', 'Sopen05g008490' => 'spe', 'Sopen07g003910' => 'spe', 'Sopen12g015240' => 'spe', 'Sp1g11550' => 'spa', 'Sp2g16710' => 'spa', 'Sp3g00430' => 'spa', 'Sp3g26780' => 'spa', 'Sp5g22900' => 'spa', 'Sp6g29530' => 'spa', 'TAR371G0794' => 'tar', 'TAR374G0164' => 'tar', 'TAR622G0165' => 'tar', 'TAR626G0929' => 'tar', 'TAR629G2155' => 'tar', 'THA.LOC104805282' => 'tha', 'THA.LOC104805363' => 'tha', 'THA.LOC104808968' => 'tha', 'THA.LOC104821093' => 'tha', 'THA.LOC104823953' => 'tha', 'THA.LOC104825562' => 'tha', 'THA.LOC104825665' => 'tha', 'Thecc.02G261400' => 'tca', 'Thecc.04G019200' => 'tca', 'Thecc.09G130400' => 'tca', 'Thhalv10004374m.g' => 'esa', 'Thhalv10007850m.g' => 'esa', 'Thhalv10013782m.g' => 'esa', 'Thhalv10018686m.g' => 'esa', 'Thhalv10020899m.g' => 'esa', 'Thhalv10022755m.g' => 'esa', 'TPR.G23851' => 'tpr', 'TPR.G26500' => 'tpr', 'TPR.G27267' => 'tpr', 'TPR.G32001' => 'tpr', 'TPR.G6251' => 'tpr', 'TPR.G8167' => 'tpr', 'TWI12G1330' => 'twi', 'TWI18G1239' => 'twi', 'TWI34G0979' => 'twi', 'TWI36G0670' => 'twi', 'TWI36G0707' => 'twi', 'TWI56G0233' => 'twi', 'TWI75G1809' => 'twi', 'unitig_21.g20874' => 'ugi', 'unitig_26.g10343' => 'ugi', 'unitig_46.g18392' => 'ugi', 'unitig_52.g17178' => 'ugi', 'unitig_8.g2934' => 'ugi', 'vmacro01122' => 'vma', 'vmacro05875' => 'vma', 'vmacro06147' => 'vma', 'vmacro16191' => 'vma', 'vmacro18293' => 'vma', 'VMungo0251G3707' => 'vmu', 'VMungo0464G1521' => 'vmu', 'VMungo1215G0205' => 'vmu', 'VMungo1383G2484' => 'vmu', 'Zm00001eb079610' => 'zma', 'Zm00001eb135990' => 'zma', 'Zm00001eb183710' => 'zma', 'Zm00001eb246020' => 'zma' ), 'gf_id' => 'HOM05D001124', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001124' ), 'data_identifier' => 'HOM05D001124', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001124', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '548', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02520' => 'bna', 'A03p06630' => 'bna', 'A05p44460' => 'bna', 'A06p08710' => 'bna', 'A06p41090' => 'bna', 'A07p32320' => 'bna', 'A08p32520' => 'bna', 'A09p10360' => 'bna', 'A10p24080' => 'bna', 'Aa31LG11G15250' => 'aar', 'Aa31LG1G1800' => 'aar', 'Aa31LG2G5120' => 'aar', 'Aa31LG2G6070' => 'aar', 'Aa31LG5G10770' => 'aar', 'Aa31sc61G90' => 'aar', 'Actinidia01352' => 'ach', 'Actinidia05983' => 'ach', 'Actinidia08133' => 'ach', 'Actinidia15101' => 'ach', 'Actinidia26379' => 'ach', 'Actinidia35778' => 'ach', 'Actinidia36123' => 'ach', 'Actinidia37436' => 'ach', 'Actinidia38730' => 'ach', 'Ah.02g128210' => 'amhyb', 'Ah.03g132990' => 'amhyb', 'Ah.14g079410' => 'amhyb', 'AL1G24640' => 'aly', 'AL2G26680' => 'aly', 'AL3G10530' => 'aly', 'AL3G45230' => 'aly', 'AL5G15230' => 'aly', 'AL5G16960' => 'aly', 'AL6G25210' => 'aly', 'Aqoxy2G00441' => 'aox', 'Aqoxy3G01236' => 'aox', 'Aqoxy5G03746' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3RQ047' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C7GMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9C8JER' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MBL6KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YXCZ83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZANX40' => 'arhy', 'AT1G12990' => 'ath', 'AT1G67880' => 'ath', 'AT2G13290' => 'ath', 'AT3G01620' => 'ath', 'AT3G26445' => 'ath', 'AT3G27540' => 'ath', 'AT5G14480' => 'ath', 'ATR0824G026' => 'atr', 'ATR1098G019' => 'atr', 'Atru.chr11.2145' => 'acertr', 'Atru.chr2.3636' => 'acertr', 'Atru.chr2.3644' => 'acertr', 'Atru.chr6.2422' => 'acertr', 'Atru.chr7.1112' => 'acertr', 'AUR62005469' => 'cqu', 'AUR62011166' => 'cqu', 'AUR62013319' => 'cqu', 'AUR62024273' => 'cqu', 'AUR62028420' => 'cqu', 'AUR62041942' => 'cqu', 'BcaB01g04969' => 'bca', 'BcaB01g06371' => 'bca', 'BcaB02g11494' => 'bca', 'BcaB03g15382' => 'bca', 'BcaB08g36994' => 'bca', 'BcaC03g13477' => 'bca', 'BcaC03g13478' => 'bca', 'BcaC03g13480' => 'bca', 'BcaC03g13481' => 'bca', 'BcaC03g13486' => 'bca', 'BcaC04g19031' => 'bca', 'BcaC04g23085' => 'bca', 'BcaC05g25094' => 'bca', 'BcaC05g25096' => 'bca', 'BcaC05g25138' => 'bca', 'BcaC05g30416' => 'bca', 'BcaC05g30455' => 'bca', 'BcaC06g30979' => 'bca', 'BcaC06g33805' => 'bca', 'BcaC08g46021' => 'bca', 'BcaNung03154' => 'bca', 'BolC2t06623H' => 'bol', 'BolC2t06632H' => 'bol', 'BolC2t06635H' => 'bol', 'BolC2t06638H' => 'bol', 'BolC3t13266H' => 'bol', 'BolC5t29776H' => 'bol', 'BolC6t38912H' => 'bol', 'BolC7t44183H' => 'bol', 'BolC9t54123H' => 'bol', 'BolC9t59107H' => 'bol', 'BraA02t05221Z' => 'bra', 'BraA03t09996Z' => 'bra', 'BraA05t23210Z' => 'bra', 'BraA06t24068Z' => 'bra', 'BraA06t27032Z' => 'bra', 'BraA08t35176Z' => 'bra', 'BraA09t36680Z' => 'bra', 'BraA10t44471Z' => 'bra', 'C02p06760' => 'bna', 'C02p06890' => 'bna', 'C02p07010' => 'bna', 'C03p07660' => 'bna', 'C05p10300' => 'bna', 'C06p38150' => 'bna', 'C07p36650' => 'bna', 'C08p15770' => 'bna', 'C09p12300' => 'bna', 'C09p62700' => 'bna', 'C09p75040' => 'bna', 'CAN.G13.1' => 'can', 'CAN.G138.4' => 'can', 'CAN.G44.6' => 'can', 'CAN.G473.19' => 'can', 'CANSAT01G0835' => 'cansat', 'CANSAT11G0246' => 'cansat', 'CANSAT11G1766' => 'cansat', 'CANSAT64G1954' => 'cansat', 'CARHR013330' => 'chi', 'CARHR060530' => 'chi', 'CARHR075300' => 'chi', 'CARHR105120' => 'chi', 'CARHR148910' => 'chi', 'CARHR198830' => 'chi', 'Carub.0001s1275' => 'cru', 'Carub.0002s1437' => 'cru', 'Carub.0003s0044' => 'cru', 'Carub.0003s2787' => 'cru', 'Carub.0005s0597' => 'cru', 'Carub.0006s1266' => 'cru', 'Ca_06935_v3' => 'car', 'Ca_13559_v3' => 'car', 'Ca_16941_v3' => 'car', 'Ca_16960_v3' => 'car', 'Ca_17775_v3' => 'car', 'Ca_30464_v3' => 'car', 'Cc06_g08160' => 'ccan', 'Cc07_g01520' => 'ccan', 'Cc11_g15810' => 'ccan', 'CDE02G2840' => 'cde', 'CDE03G0093' => 'cde', 'CDE04G2127' => 'cde', 'CDE07G1857' => 'cde', 'CDE09G1246' => 'cde', 'Cfa003412' => 'cfa', 'Cfa007341' => 'cfa', 'Cfa009220' => 'cfa', 'Ciclev10008737m.g' => 'ccl', 'Ciclev10015565m.g' => 'ccl', 'Ciclev10031761m.g' => 'ccl', 'CiPaw.03G045300' => 'cil', 'CiPaw.03G247200' => 'cil', 'CiPaw.04G029500' => 'cil', 'CiPaw.04G174000' => 'cil', 'CiPaw.05G181200' => 'cil', 'CiPaw.06G067100' => 'cil', 'ClCG05G025800' => 'cla', 'ClCG06G011400' => 'cla', 'ClCG09G019360' => 'cla', 'COL.COLO4_04827' => 'col', 'COL.COLO4_29170' => 'col', 'COL.COLO4_35131' => 'col', 'COL.COLO4_35132' => 'col', 'Cpa.g.sc33.32' => 'cpa', 'Cpa.g.sc46.29' => 'cpa', 'Cpa.g.sc796.1' => 'cpa', 'CsaV3_1G030420' => 'csa', 'CsaV3_5G027050' => 'csa', 'CsaV3_5G031040' => 'csa', 'CsaV3_UNG023130' => 'csa', 'CSS0007726' => 'camsi', 'CSS0016433' => 'camsi', 'CSS0017656' => 'camsi', 'CSS0025364' => 'camsi', 'CSS0027582' => 'camsi', 'CSS0047288' => 'camsi', 'CSS0049950' => 'camsi', 'DCAR_003843' => 'dca', 'DCAR_007052' => 'dca', 'DCAR_020884' => 'dca', 'DCAR_021730' => 'dca', 'DCAR_024423' => 'dca', 'DCAR_026509' => 'dca', 'DCAR_031158' => 'dca', 'Dinv14728' => 'din', 'Dinv15219' => 'din', 'Dinv25728' => 'din', 'Dinv33428' => 'din', 'Dinv36489' => 'din', 'Dinv41486' => 'din', 'Duzib147G0469' => 'dzi', 'Duzib168G0060' => 'dzi', 'Duzib187G1215' => 'dzi', 'Duzib248G0692' => 'dzi', 'Duzib251G0767' => 'dzi', 'Duzib264G0446' => 'dzi', 'Duzib268G0691' => 'dzi', 'ECA232G4767' => 'eca', 'ECA233G2838' => 'eca', 'ECA234G0391' => 'eca', 'ECA234G0857' => 'eca', 'ECA236G1593' => 'eca', 'ECA238G0565' => 'eca', 'ECA246G1027' => 'eca', 'ECA246G3223' => 'eca', 'ECA246G3470' => 'eca', 'EL10Ac6g13829' => 'bvu', 'EL10Ac6g14093' => 'bvu', 'EL10Ac8g18707' => 'bvu', 'Eucgr.C01369' => 'egr', 'Eucgr.H02492' => 'egr', 'Eucgr.I01733' => 'egr', 'Eucgr.J02255' => 'egr', 'Eucgr.J02257' => 'egr', 'Eucgr.J02258' => 'egr', 'FAN02G1601' => 'fan', 'FAN03G1586' => 'fan', 'FAN03G2986' => 'fan', 'FAN05G4837' => 'fan', 'FAN06G0146' => 'fan', 'FAN07G0858' => 'fan', 'FAN09G3179' => 'fan', 'FAN10G0669' => 'fan', 'FAN12G2358' => 'fan', 'FAN14G4198' => 'fan', 'FAN14G5112' => 'fan', 'FAN17G0342' => 'fan', 'FAN19G0342' => 'fan', 'FAN19G0962' => 'fan', 'FAN19G1101' => 'fan', 'FAN19G1872' => 'fan', 'FAN22G0356' => 'fan', 'FAN23G0744' => 'fan', 'FAN23G1914' => 'fan', 'FAN26G0032' => 'fan', 'FAN28G0625' => 'fan', 'FvH4_1g02710' => 'fve', 'FvH4_1g02720' => 'fve', 'FvH4_4g25670' => 'fve', 'FvH4_6g51700' => 'fve', 'FvH4_7g20170' => 'fve', 'Glyma.05G175000' => 'gma', 'Glyma.08G132300' => 'gma', 'Glyma.11G243000' => 'gma', 'Glyma.13G158900' => 'gma', 'Glyma.17G112400' => 'gma', 'Glyma.18G014100' => 'gma', 'Glyma.19G003100' => 'gma', 'Glyma.19G056500' => 'gma', 'Gohir.A01G158900' => 'ghi', 'Gohir.A05G312600' => 'ghi', 'Gohir.A05G354900' => 'ghi', 'Gohir.A07G037200' => 'ghi', 'Gohir.A09G030000' => 'ghi', 'Gohir.A12G145200' => 'ghi', 'Gohir.D01G151500' => 'ghi', 'Gohir.D04G058300' => 'ghi', 'Gohir.D05G314100' => 'ghi', 'Gohir.D07G041400' => 'ghi', 'Gohir.D09G029700' => 'ghi', 'Gohir.D12G149700' => 'ghi', 'Gorai.001G043800' => 'gra', 'Gorai.002G187800' => 'gra', 'Gorai.006G034700' => 'gra', 'Gorai.008G161200' => 'gra', 'Gorai.009G335700' => 'gra', 'Gorai.012G065000' => 'gra', 'GSVIVG01000535001' => 'vvi', 'GSVIVG01015572001' => 'vvi', 'GSVIVG01032386001' => 'vvi', 'HanXRQChr05g0138531' => 'han', 'HanXRQChr06g0174391' => 'han', 'HanXRQChr07g0199021' => 'han', 'HanXRQChr08g0208211' => 'han', 'HanXRQChr09g0255471' => 'han', 'HanXRQChr10g0315791' => 'han', 'HanXRQChr12g0371991' => 'han', 'HanXRQChr15g0475251' => 'han', 'HanXRQChr17g0540001' => 'han', 'HanXRQChr17g0548631' => 'han', 'HanXRQChr17g0569561' => 'han', 'Haze_12256' => 'cav', 'Haze_14756' => 'cav', 'Haze_25528' => 'cav', 'Hma1.2p1_0079F.1_g041020' => 'hma', 'Hma1.2p1_0818F.1_g223260' => 'hma', 'Hma1.2p1_1747F.1_g300530' => 'hma', 'HPP92_004607' => 'vpl', 'HPP92_004608' => 'vpl', 'HPP92_006181' => 'vpl', 'HPP92_012192' => 'vpl', 'HPP92_015680' => 'vpl', 'HPP92_020249' => 'vpl', 'HPP92_021376' => 'vpl', 'HPP92_024275' => 'vpl', 'Hund06031' => 'sun', 'Hund25391' => 'sun', 'Lalb_Chr07g0185371' => 'lal', 'Lalb_Chr07g0185381' => 'lal', 'Lalb_Chr12g0204011' => 'lal', 'Lalb_Chr13g0301671' => 'lal', 'Lalb_Chr14g0362851' => 'lal', 'Lalb_Chr24g0403581' => 'lal', 'Lj1g0000233' => 'lja', 'Lj2g0018120' => 'lja', 'Lj3C621T0' => 'lonja', 'Lj3P1059T14' => 'lonja', 'Lj3P611T9' => 'lonja', 'Lj3P614T13' => 'lonja', 'Lj3P615T5' => 'lonja', 'Lj4g0012315' => 'lja', 'Lj4g0026182' => 'lja', 'Lj6P813T16' => 'lonja', 'Lj7C427T7' => 'lonja', 'Lj7C427T8' => 'lonja', 'Lj7P600T41' => 'lonja', 'Lju41C42G17' => 'lonja', 'Lsat_1_v5_gn_0_47300' => 'lsa', 'Lsat_1_v5_gn_2_91280' => 'lsa', 'Lsat_1_v5_gn_3_30561' => 'lsa', 'Lsat_1_v5_gn_4_184321' => 'lsa', 'Lsat_1_v5_gn_4_4041' => 'lsa', 'Lsat_1_v5_gn_5_92000' => 'lsa', 'Lsat_1_v5_gn_8_152940' => 'lsa', 'Lsat_1_v5_gn_8_62401' => 'lsa', 'Manes.06G055900' => 'mes', 'Manes.12G022200' => 'mes', 'Manes.13G023300' => 'mes', 'Manes.14G115000' => 'mes', 'Manes.15G151700' => 'mes', 'Manes.17G111300' => 'mes', 'Mapoly0226s0009' => 'mpo', 'MBI02_g25363_MAGBIO' => 'mbi', 'MBI06_g00027_MAGBIO' => 'mbi', 'MBI10_g13034_MAGBIO' => 'mbi', 'MD09G1023400' => 'mdo', 'MD13G1100100' => 'mdo', 'MD15G1169200' => 'mdo', 'MD16G1101100' => 'mdo', 'MD17G1022900' => 'mdo', 'Medtr3g096150' => 'mtr', 'Medtr4g115070' => 'mtr', 'Medtr7g033325' => 'mtr', 'Medtr8g089840' => 'mtr', 'MELO3C010319.2' => 'cme', 'MELO3C011944.2' => 'cme', 'MELO3C021589.2' => 'cme', 'Migut.E00207' => 'egut', 'Migut.H00067' => 'egut', 'Migut.K00433' => 'egut', 'Migut.K00606' => 'egut', 'Migut.K01410' => 'egut', 'MSTRG.13347' => 'ama', 'MSTRG.24045' => 'ama', 'MSTRG.2428' => 'ama', 'MSTRG.26410' => 'ama', 'MSTRG.3139' => 'ama', 'MSTRG.3286' => 'ama', 'MSTRG.563' => 'ama', 'MSTRG.7941' => 'ama', 'Nitab4.5_0000028g0060' => 'nta', 'Nitab4.5_0000065g0260' => 'nta', 'Nitab4.5_0000112g0060' => 'nta', 'Nitab4.5_0000489g0120' => 'nta', 'Nitab4.5_0001776g0050' => 'nta', 'Nitab4.5_0001854g0010' => 'nta', 'Nitab4.5_0001860g0020' => 'nta', 'Nitab4.5_0004352g0010' => 'nta', 'Nitab4.5_0008716g0020' => 'nta', 'Nitab4.5_0008922g0010' => 'nta', 'Nn3g16693' => 'nnu', 'Nn4g22596' => 'nnu', 'Nn7g37639' => 'nnu', 'Oeu001701.1' => 'oeu', 'Oeu018149.1' => 'oeu', 'Oeu026220.1' => 'oeu', 'Oeu038635.1' => 'oeu', 'Oeu049176.1' => 'oeu', 'Oeu056706.1' => 'oeu', 'Oeu056937.1' => 'oeu', 'Oeu057540.1' => 'oeu', 'Os02g0594900' => 'osa', 'Os02g0595100' => 'osa', 'Os04g0477500' => 'osa', 'Os12g0611900' => 'osa', 'Peaxi162Scf00076g00020' => 'pax', 'Peaxi162Scf00128g00217' => 'pax', 'Peaxi162Scf00129g01640' => 'pax', 'Peaxi162Scf00669g00007' => 'pax', 'Peaxi162Scf00700g00421' => 'pax', 'Peaxi162Scf00801g00038' => 'pax', 'Peaxi162Scf00891g00025' => 'pax', 'PGR083G0909' => 'pgr', 'PGR119G1005' => 'pgr', 'PGR142G2236' => 'pgr', 'PGR142G3388' => 'pgr', 'PGSC0003DMG400004514' => 'stu', 'PGSC0003DMG400012635' => 'stu', 'PGSC0003DMG400015730' => 'stu', 'PGSC0003DMG400018611' => 'stu', 'PGSC0003DMG400030897' => 'stu', 'Phvul.001G254800' => 'pvu', 'Phvul.002G260100' => 'pvu', 'Phvul.003G167600' => 'pvu', 'Phvul.004G005100' => 'pvu', 'Potri.001G343600' => 'ptr', 'Potri.006G066700' => 'ptr', 'Potri.008G186000' => 'ptr', 'Potri.010G046900' => 'ptr', 'Potri.018G127900' => 'ptr', 'Pp3c20_17750' => 'ppa', 'Pp3c24_4380' => 'ppa', 'Prupe.1G245800' => 'ppe', 'Prupe.3G293400' => 'ppe', 'Prupe.7G247400' => 'ppe', 'Psat0s145g0120' => 'psa', 'Psat0s595g0040' => 'psa', 'Psat0s595g0120' => 'psa', 'Psat3g175040' => 'psa', 'Psat7g058120' => 'psa', 'PSO017G0428' => 'pso', 'PSO063G7510' => 'pso', 'PSO067G0046' => 'pso', 'PSO478G1073' => 'pso', 'PSO675G3677' => 'pso', 'PSO675G6558' => 'pso', 'PSO675G7520' => 'pso', 'PSO675G8959' => 'pso', 'QL02p074089' => 'qlo', 'QL02p089614' => 'qlo', 'QL03p057736' => 'qlo', 'RcHm_v2.0_Chr1g0364131' => 'rch', 'RcHm_v2.0_Chr2g0087801' => 'rch', 'RcHm_v2.0_Chr2g0087821' => 'rch', 'RcHm_v2.0_Chr2g0173231' => 'rch', 'RcHm_v2.0_Chr4g0433111' => 'rch', 'Rhsim03G0250300' => 'rsi', 'Rhsim08G0048400' => 'rsi', 'Rhsim10G0014800' => 'rsi', 'Rhsim12G0040100' => 'rsi', 'Rhsim12G0109700' => 'rsi', 'Sabra06G0049600' => 'sbr', 'Sabra08G0141000' => 'sbr', 'Sabra10G0021400' => 'sbr', 'Sabra16G0222900' => 'sbr', 'Sabra18G0108600' => 'sbr', 'SalBow1G0433' => 'sbo', 'SalBow1G2038' => 'sbo', 'SalBow1G5003' => 'sbo', 'SalBow7G1197' => 'sbo', 'SalBow8G3506' => 'sbo', 'Sc03g0007300' => 'sci', 'Sc11g0000950' => 'sci', 'Sc14g0008750' => 'sci', 'Sc18g0000420' => 'sci', 'Sed0006754' => 'sed', 'Sed0008741' => 'sed', 'Sed0017172' => 'sed', 'Sed0018925' => 'sed', 'Sed0023326' => 'sed', 'Sed0025909' => 'sed', 'SEGI_05333' => 'sgi', 'SEGI_10362' => 'sgi', 'SEGI_13380' => 'sgi', 'SEGI_24306' => 'sgi', 'SEGI_29077' => 'sgi', 'SEGI_29095' => 'sgi', 'SEGI_36534' => 'sgi', 'SEGI_37506' => 'sgi', 'SEGI_38321' => 'sgi', 'SGA_v2.0_scaffold307G48031' => 'sas', 'SGA_v2.0_scaffold47G17507' => 'sas', 'SGA_v2.0_scaffold63G21736' => 'sas', 'SGA_v2.0_scaffold87G27070' => 'sas', 'SHI17794' => 'shi', 'SHI28851' => 'shi', 'SMO165G0155' => 'smo', 'SMO340G0217' => 'smo', 'SMO367G1210' => 'smo', 'Solyc02g093430.3' => 'sly', 'Solyc05g013580.4' => 'sly', 'Solyc07g008030.3' => 'sly', 'Solyc12g035470.2' => 'sly', 'Sopen02g038020' => 'spe', 'Sopen05g008490' => 'spe', 'Sopen07g003910' => 'spe', 'Sopen12g015240' => 'spe', 'Sp1g11550' => 'spa', 'Sp2g16710' => 'spa', 'Sp3g00430' => 'spa', 'Sp3g26780' => 'spa', 'Sp5g22900' => 'spa', 'Sp6g29530' => 'spa', 'TAR371G0794' => 'tar', 'TAR374G0164' => 'tar', 'TAR622G0165' => 'tar', 'TAR626G0929' => 'tar', 'TAR629G2155' => 'tar', 'THA.LOC104805282' => 'tha', 'THA.LOC104805363' => 'tha', 'THA.LOC104808968' => 'tha', 'THA.LOC104821093' => 'tha', 'THA.LOC104823953' => 'tha', 'THA.LOC104825562' => 'tha', 'THA.LOC104825665' => 'tha', 'Thecc.02G261400' => 'tca', 'Thecc.04G019200' => 'tca', 'Thecc.09G130400' => 'tca', 'Thhalv10004374m.g' => 'esa', 'Thhalv10007850m.g' => 'esa', 'Thhalv10013782m.g' => 'esa', 'Thhalv10018686m.g' => 'esa', 'Thhalv10020899m.g' => 'esa', 'Thhalv10022755m.g' => 'esa', 'TPR.G23851' => 'tpr', 'TPR.G26500' => 'tpr', 'TPR.G27267' => 'tpr', 'TPR.G32001' => 'tpr', 'TPR.G6251' => 'tpr', 'TPR.G8167' => 'tpr', 'TWI12G1330' => 'twi', 'TWI18G1239' => 'twi', 'TWI34G0979' => 'twi', 'TWI36G0670' => 'twi', 'TWI36G0707' => 'twi', 'TWI56G0233' => 'twi', 'TWI75G1809' => 'twi', 'unitig_21.g20874' => 'ugi', 'unitig_26.g10343' => 'ugi', 'unitig_46.g18392' => 'ugi', 'unitig_52.g17178' => 'ugi', 'unitig_8.g2934' => 'ugi', 'vmacro01122' => 'vma', 'vmacro05875' => 'vma', 'vmacro06147' => 'vma', 'vmacro16191' => 'vma', 'vmacro18293' => 'vma', 'VMungo0251G3707' => 'vmu', 'VMungo0464G1521' => 'vmu', 'VMungo1215G0205' => 'vmu', 'VMungo1383G2484' => 'vmu', 'Zm00001eb079610' => 'zma', 'Zm00001eb135990' => 'zma', 'Zm00001eb183710' => 'zma', 'Zm00001eb246020' => 'zma' ) $gf_id = 'HOM05D001124' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001124' ) $data_identifier = 'HOM05D001124' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 6, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 7, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 21, 'bol' => (int) 10, 'bra' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 6, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 9, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 21, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 8, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 10, 'lsa' => (int) 8, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 8, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 9, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb246020' $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' => 'HOM05D001124', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '548', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02520' => 'bna', 'A03p06630' => 'bna', 'A05p44460' => 'bna', 'A06p08710' => 'bna', 'A06p41090' => 'bna', 'A07p32320' => 'bna', 'A08p32520' => 'bna', 'A09p10360' => 'bna', 'A10p24080' => 'bna', 'Aa31LG11G15250' => 'aar', 'Aa31LG1G1800' => 'aar', 'Aa31LG2G5120' => 'aar', 'Aa31LG2G6070' => 'aar', 'Aa31LG5G10770' => 'aar', 'Aa31sc61G90' => 'aar', 'Actinidia01352' => 'ach', 'Actinidia05983' => 'ach', 'Actinidia08133' => 'ach', 'Actinidia15101' => 'ach', 'Actinidia26379' => 'ach', 'Actinidia35778' => 'ach', 'Actinidia36123' => 'ach', 'Actinidia37436' => 'ach', 'Actinidia38730' => 'ach', 'Ah.02g128210' => 'amhyb', 'Ah.03g132990' => 'amhyb', 'Ah.14g079410' => 'amhyb', 'AL1G24640' => 'aly', 'AL2G26680' => 'aly', 'AL3G10530' => 'aly', 'AL3G45230' => 'aly', 'AL5G15230' => 'aly', 'AL5G16960' => 'aly', 'AL6G25210' => 'aly', 'Aqoxy2G00441' => 'aox', 'Aqoxy3G01236' => 'aox', 'Aqoxy5G03746' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3RQ047' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C7GMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9C8JER' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MBL6KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YXCZ83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZANX40' => 'arhy', 'AT1G12990' => 'ath', 'AT1G67880' => 'ath', 'AT2G13290' => 'ath', 'AT3G01620' => 'ath', 'AT3G26445' => 'ath', 'AT3G27540' => 'ath', 'AT5G14480' => 'ath', 'ATR0824G026' => 'atr', 'ATR1098G019' => 'atr', 'Atru.chr11.2145' => 'acertr', 'Atru.chr2.3636' => 'acertr', 'Atru.chr2.3644' => 'acertr', 'Atru.chr6.2422' => 'acertr', 'Atru.chr7.1112' => 'acertr', 'AUR62005469' => 'cqu', 'AUR62011166' => 'cqu', 'AUR62013319' => 'cqu', 'AUR62024273' => 'cqu', 'AUR62028420' => 'cqu', 'AUR62041942' => 'cqu', 'BcaB01g04969' => 'bca', 'BcaB01g06371' => 'bca', 'BcaB02g11494' => 'bca', 'BcaB03g15382' => 'bca', 'BcaB08g36994' => 'bca', 'BcaC03g13477' => 'bca', 'BcaC03g13478' => 'bca', 'BcaC03g13480' => 'bca', 'BcaC03g13481' => 'bca', 'BcaC03g13486' => 'bca', 'BcaC04g19031' => 'bca', 'BcaC04g23085' => 'bca', 'BcaC05g25094' => 'bca', 'BcaC05g25096' => 'bca', 'BcaC05g25138' => 'bca', 'BcaC05g30416' => 'bca', 'BcaC05g30455' => 'bca', 'BcaC06g30979' => 'bca', 'BcaC06g33805' => 'bca', 'BcaC08g46021' => 'bca', 'BcaNung03154' => 'bca', 'BolC2t06623H' => 'bol', 'BolC2t06632H' => 'bol', 'BolC2t06635H' => 'bol', 'BolC2t06638H' => 'bol', 'BolC3t13266H' => 'bol', 'BolC5t29776H' => 'bol', 'BolC6t38912H' => 'bol', 'BolC7t44183H' => 'bol', 'BolC9t54123H' => 'bol', 'BolC9t59107H' => 'bol', 'BraA02t05221Z' => 'bra', 'BraA03t09996Z' => 'bra', 'BraA05t23210Z' => 'bra', 'BraA06t24068Z' => 'bra', 'BraA06t27032Z' => 'bra', 'BraA08t35176Z' => 'bra', 'BraA09t36680Z' => 'bra', 'BraA10t44471Z' => 'bra', 'C02p06760' => 'bna', 'C02p06890' => 'bna', 'C02p07010' => 'bna', 'C03p07660' => 'bna', 'C05p10300' => 'bna', 'C06p38150' => 'bna', 'C07p36650' => 'bna', 'C08p15770' => 'bna', 'C09p12300' => 'bna', 'C09p62700' => 'bna', 'C09p75040' => 'bna', 'CAN.G13.1' => 'can', 'CAN.G138.4' => 'can', 'CAN.G44.6' => 'can', 'CAN.G473.19' => 'can', 'CANSAT01G0835' => 'cansat', 'CANSAT11G0246' => 'cansat', 'CANSAT11G1766' => 'cansat', 'CANSAT64G1954' => 'cansat', 'CARHR013330' => 'chi', 'CARHR060530' => 'chi', 'CARHR075300' => 'chi', 'CARHR105120' => 'chi', 'CARHR148910' => 'chi', 'CARHR198830' => 'chi', 'Carub.0001s1275' => 'cru', 'Carub.0002s1437' => 'cru', 'Carub.0003s0044' => 'cru', 'Carub.0003s2787' => 'cru', 'Carub.0005s0597' => 'cru', 'Carub.0006s1266' => 'cru', 'Ca_06935_v3' => 'car', 'Ca_13559_v3' => 'car', 'Ca_16941_v3' => 'car', 'Ca_16960_v3' => 'car', 'Ca_17775_v3' => 'car', 'Ca_30464_v3' => 'car', 'Cc06_g08160' => 'ccan', 'Cc07_g01520' => 'ccan', 'Cc11_g15810' => 'ccan', 'CDE02G2840' => 'cde', 'CDE03G0093' => 'cde', 'CDE04G2127' => 'cde', 'CDE07G1857' => 'cde', 'CDE09G1246' => 'cde', 'Cfa003412' => 'cfa', 'Cfa007341' => 'cfa', 'Cfa009220' => 'cfa', 'Ciclev10008737m.g' => 'ccl', 'Ciclev10015565m.g' => 'ccl', 'Ciclev10031761m.g' => 'ccl', 'CiPaw.03G045300' => 'cil', 'CiPaw.03G247200' => 'cil', 'CiPaw.04G029500' => 'cil', 'CiPaw.04G174000' => 'cil', 'CiPaw.05G181200' => 'cil', 'CiPaw.06G067100' => 'cil', 'ClCG05G025800' => 'cla', 'ClCG06G011400' => 'cla', 'ClCG09G019360' => 'cla', 'COL.COLO4_04827' => 'col', 'COL.COLO4_29170' => 'col', 'COL.COLO4_35131' => 'col', 'COL.COLO4_35132' => 'col', 'Cpa.g.sc33.32' => 'cpa', 'Cpa.g.sc46.29' => 'cpa', 'Cpa.g.sc796.1' => 'cpa', 'CsaV3_1G030420' => 'csa', 'CsaV3_5G027050' => 'csa', 'CsaV3_5G031040' => 'csa', 'CsaV3_UNG023130' => 'csa', 'CSS0007726' => 'camsi', 'CSS0016433' => 'camsi', 'CSS0017656' => 'camsi', 'CSS0025364' => 'camsi', 'CSS0027582' => 'camsi', 'CSS0047288' => 'camsi', 'CSS0049950' => 'camsi', 'DCAR_003843' => 'dca', 'DCAR_007052' => 'dca', 'DCAR_020884' => 'dca', 'DCAR_021730' => 'dca', 'DCAR_024423' => 'dca', 'DCAR_026509' => 'dca', 'DCAR_031158' => 'dca', 'Dinv14728' => 'din', 'Dinv15219' => 'din', 'Dinv25728' => 'din', 'Dinv33428' => 'din', 'Dinv36489' => 'din', 'Dinv41486' => 'din', 'Duzib147G0469' => 'dzi', 'Duzib168G0060' => 'dzi', 'Duzib187G1215' => 'dzi', 'Duzib248G0692' => 'dzi', 'Duzib251G0767' => 'dzi', 'Duzib264G0446' => 'dzi', 'Duzib268G0691' => 'dzi', 'ECA232G4767' => 'eca', 'ECA233G2838' => 'eca', 'ECA234G0391' => 'eca', 'ECA234G0857' => 'eca', 'ECA236G1593' => 'eca', 'ECA238G0565' => 'eca', 'ECA246G1027' => 'eca', 'ECA246G3223' => 'eca', 'ECA246G3470' => 'eca', 'EL10Ac6g13829' => 'bvu', 'EL10Ac6g14093' => 'bvu', 'EL10Ac8g18707' => 'bvu', 'Eucgr.C01369' => 'egr', 'Eucgr.H02492' => 'egr', 'Eucgr.I01733' => 'egr', 'Eucgr.J02255' => 'egr', 'Eucgr.J02257' => 'egr', 'Eucgr.J02258' => 'egr', 'FAN02G1601' => 'fan', 'FAN03G1586' => 'fan', 'FAN03G2986' => 'fan', 'FAN05G4837' => 'fan', 'FAN06G0146' => 'fan', 'FAN07G0858' => 'fan', 'FAN09G3179' => 'fan', 'FAN10G0669' => 'fan', 'FAN12G2358' => 'fan', 'FAN14G4198' => 'fan', 'FAN14G5112' => 'fan', 'FAN17G0342' => 'fan', 'FAN19G0342' => 'fan', 'FAN19G0962' => 'fan', 'FAN19G1101' => 'fan', 'FAN19G1872' => 'fan', 'FAN22G0356' => 'fan', 'FAN23G0744' => 'fan', 'FAN23G1914' => 'fan', 'FAN26G0032' => 'fan', 'FAN28G0625' => 'fan', 'FvH4_1g02710' => 'fve', 'FvH4_1g02720' => 'fve', 'FvH4_4g25670' => 'fve', 'FvH4_6g51700' => 'fve', 'FvH4_7g20170' => 'fve', 'Glyma.05G175000' => 'gma', 'Glyma.08G132300' => 'gma', 'Glyma.11G243000' => 'gma', 'Glyma.13G158900' => 'gma', 'Glyma.17G112400' => 'gma', 'Glyma.18G014100' => 'gma', 'Glyma.19G003100' => 'gma', 'Glyma.19G056500' => 'gma', 'Gohir.A01G158900' => 'ghi', 'Gohir.A05G312600' => 'ghi', 'Gohir.A05G354900' => 'ghi', 'Gohir.A07G037200' => 'ghi', 'Gohir.A09G030000' => 'ghi', 'Gohir.A12G145200' => 'ghi', 'Gohir.D01G151500' => 'ghi', 'Gohir.D04G058300' => 'ghi', 'Gohir.D05G314100' => 'ghi', 'Gohir.D07G041400' => 'ghi', 'Gohir.D09G029700' => 'ghi', 'Gohir.D12G149700' => 'ghi', 'Gorai.001G043800' => 'gra', 'Gorai.002G187800' => 'gra', 'Gorai.006G034700' => 'gra', 'Gorai.008G161200' => 'gra', 'Gorai.009G335700' => 'gra', 'Gorai.012G065000' => 'gra', 'GSVIVG01000535001' => 'vvi', 'GSVIVG01015572001' => 'vvi', 'GSVIVG01032386001' => 'vvi', 'HanXRQChr05g0138531' => 'han', 'HanXRQChr06g0174391' => 'han', 'HanXRQChr07g0199021' => 'han', 'HanXRQChr08g0208211' => 'han', 'HanXRQChr09g0255471' => 'han', 'HanXRQChr10g0315791' => 'han', 'HanXRQChr12g0371991' => 'han', 'HanXRQChr15g0475251' => 'han', 'HanXRQChr17g0540001' => 'han', 'HanXRQChr17g0548631' => 'han', 'HanXRQChr17g0569561' => 'han', 'Haze_12256' => 'cav', 'Haze_14756' => 'cav', 'Haze_25528' => 'cav', 'Hma1.2p1_0079F.1_g041020' => 'hma', 'Hma1.2p1_0818F.1_g223260' => 'hma', 'Hma1.2p1_1747F.1_g300530' => 'hma', 'HPP92_004607' => 'vpl', 'HPP92_004608' => 'vpl', 'HPP92_006181' => 'vpl', 'HPP92_012192' => 'vpl', 'HPP92_015680' => 'vpl', 'HPP92_020249' => 'vpl', 'HPP92_021376' => 'vpl', 'HPP92_024275' => 'vpl', 'Hund06031' => 'sun', 'Hund25391' => 'sun', 'Lalb_Chr07g0185371' => 'lal', 'Lalb_Chr07g0185381' => 'lal', 'Lalb_Chr12g0204011' => 'lal', 'Lalb_Chr13g0301671' => 'lal', 'Lalb_Chr14g0362851' => 'lal', 'Lalb_Chr24g0403581' => 'lal', 'Lj1g0000233' => 'lja', 'Lj2g0018120' => 'lja', 'Lj3C621T0' => 'lonja', 'Lj3P1059T14' => 'lonja', 'Lj3P611T9' => 'lonja', 'Lj3P614T13' => 'lonja', 'Lj3P615T5' => 'lonja', 'Lj4g0012315' => 'lja', 'Lj4g0026182' => 'lja', 'Lj6P813T16' => 'lonja', 'Lj7C427T7' => 'lonja', 'Lj7C427T8' => 'lonja', 'Lj7P600T41' => 'lonja', 'Lju41C42G17' => 'lonja', 'Lsat_1_v5_gn_0_47300' => 'lsa', 'Lsat_1_v5_gn_2_91280' => 'lsa', 'Lsat_1_v5_gn_3_30561' => 'lsa', 'Lsat_1_v5_gn_4_184321' => 'lsa', 'Lsat_1_v5_gn_4_4041' => 'lsa', 'Lsat_1_v5_gn_5_92000' => 'lsa', 'Lsat_1_v5_gn_8_152940' => 'lsa', 'Lsat_1_v5_gn_8_62401' => 'lsa', 'Manes.06G055900' => 'mes', 'Manes.12G022200' => 'mes', 'Manes.13G023300' => 'mes', 'Manes.14G115000' => 'mes', 'Manes.15G151700' => 'mes', 'Manes.17G111300' => 'mes', 'Mapoly0226s0009' => 'mpo', 'MBI02_g25363_MAGBIO' => 'mbi', 'MBI06_g00027_MAGBIO' => 'mbi', 'MBI10_g13034_MAGBIO' => 'mbi', 'MD09G1023400' => 'mdo', 'MD13G1100100' => 'mdo', 'MD15G1169200' => 'mdo', 'MD16G1101100' => 'mdo', 'MD17G1022900' => 'mdo', 'Medtr3g096150' => 'mtr', 'Medtr4g115070' => 'mtr', 'Medtr7g033325' => 'mtr', 'Medtr8g089840' => 'mtr', 'MELO3C010319.2' => 'cme', 'MELO3C011944.2' => 'cme', 'MELO3C021589.2' => 'cme', 'Migut.E00207' => 'egut', 'Migut.H00067' => 'egut', 'Migut.K00433' => 'egut', 'Migut.K00606' => 'egut', 'Migut.K01410' => 'egut', 'MSTRG.13347' => 'ama', 'MSTRG.24045' => 'ama', 'MSTRG.2428' => 'ama', 'MSTRG.26410' => 'ama', 'MSTRG.3139' => 'ama', 'MSTRG.3286' => 'ama', 'MSTRG.563' => 'ama', 'MSTRG.7941' => 'ama', 'Nitab4.5_0000028g0060' => 'nta', 'Nitab4.5_0000065g0260' => 'nta', 'Nitab4.5_0000112g0060' => 'nta', 'Nitab4.5_0000489g0120' => 'nta', 'Nitab4.5_0001776g0050' => 'nta', 'Nitab4.5_0001854g0010' => 'nta', 'Nitab4.5_0001860g0020' => 'nta', 'Nitab4.5_0004352g0010' => 'nta', 'Nitab4.5_0008716g0020' => 'nta', 'Nitab4.5_0008922g0010' => 'nta', 'Nn3g16693' => 'nnu', 'Nn4g22596' => 'nnu', 'Nn7g37639' => 'nnu', 'Oeu001701.1' => 'oeu', 'Oeu018149.1' => 'oeu', 'Oeu026220.1' => 'oeu', 'Oeu038635.1' => 'oeu', 'Oeu049176.1' => 'oeu', 'Oeu056706.1' => 'oeu', 'Oeu056937.1' => 'oeu', 'Oeu057540.1' => 'oeu', 'Os02g0594900' => 'osa', 'Os02g0595100' => 'osa', 'Os04g0477500' => 'osa', 'Os12g0611900' => 'osa', 'Peaxi162Scf00076g00020' => 'pax', 'Peaxi162Scf00128g00217' => 'pax', 'Peaxi162Scf00129g01640' => 'pax', 'Peaxi162Scf00669g00007' => 'pax', 'Peaxi162Scf00700g00421' => 'pax', 'Peaxi162Scf00801g00038' => 'pax', 'Peaxi162Scf00891g00025' => 'pax', 'PGR083G0909' => 'pgr', 'PGR119G1005' => 'pgr', 'PGR142G2236' => 'pgr', 'PGR142G3388' => 'pgr', 'PGSC0003DMG400004514' => 'stu', 'PGSC0003DMG400012635' => 'stu', 'PGSC0003DMG400015730' => 'stu', 'PGSC0003DMG400018611' => 'stu', 'PGSC0003DMG400030897' => 'stu', 'Phvul.001G254800' => 'pvu', 'Phvul.002G260100' => 'pvu', 'Phvul.003G167600' => 'pvu', 'Phvul.004G005100' => 'pvu', 'Potri.001G343600' => 'ptr', 'Potri.006G066700' => 'ptr', 'Potri.008G186000' => 'ptr', 'Potri.010G046900' => 'ptr', 'Potri.018G127900' => 'ptr', 'Pp3c20_17750' => 'ppa', 'Pp3c24_4380' => 'ppa', 'Prupe.1G245800' => 'ppe', 'Prupe.3G293400' => 'ppe', 'Prupe.7G247400' => 'ppe', 'Psat0s145g0120' => 'psa', 'Psat0s595g0040' => 'psa', 'Psat0s595g0120' => 'psa', 'Psat3g175040' => 'psa', 'Psat7g058120' => 'psa', 'PSO017G0428' => 'pso', 'PSO063G7510' => 'pso', 'PSO067G0046' => 'pso', 'PSO478G1073' => 'pso', 'PSO675G3677' => 'pso', 'PSO675G6558' => 'pso', 'PSO675G7520' => 'pso', 'PSO675G8959' => 'pso', 'QL02p074089' => 'qlo', 'QL02p089614' => 'qlo', 'QL03p057736' => 'qlo', 'RcHm_v2.0_Chr1g0364131' => 'rch', 'RcHm_v2.0_Chr2g0087801' => 'rch', 'RcHm_v2.0_Chr2g0087821' => 'rch', 'RcHm_v2.0_Chr2g0173231' => 'rch', 'RcHm_v2.0_Chr4g0433111' => 'rch', 'Rhsim03G0250300' => 'rsi', 'Rhsim08G0048400' => 'rsi', 'Rhsim10G0014800' => 'rsi', 'Rhsim12G0040100' => 'rsi', 'Rhsim12G0109700' => 'rsi', 'Sabra06G0049600' => 'sbr', 'Sabra08G0141000' => 'sbr', 'Sabra10G0021400' => 'sbr', 'Sabra16G0222900' => 'sbr', 'Sabra18G0108600' => 'sbr', 'SalBow1G0433' => 'sbo', 'SalBow1G2038' => 'sbo', 'SalBow1G5003' => 'sbo', 'SalBow7G1197' => 'sbo', 'SalBow8G3506' => 'sbo', 'Sc03g0007300' => 'sci', 'Sc11g0000950' => 'sci', 'Sc14g0008750' => 'sci', 'Sc18g0000420' => 'sci', 'Sed0006754' => 'sed', 'Sed0008741' => 'sed', 'Sed0017172' => 'sed', 'Sed0018925' => 'sed', 'Sed0023326' => 'sed', 'Sed0025909' => 'sed', 'SEGI_05333' => 'sgi', 'SEGI_10362' => 'sgi', 'SEGI_13380' => 'sgi', 'SEGI_24306' => 'sgi', 'SEGI_29077' => 'sgi', 'SEGI_29095' => 'sgi', 'SEGI_36534' => 'sgi', 'SEGI_37506' => 'sgi', 'SEGI_38321' => 'sgi', 'SGA_v2.0_scaffold307G48031' => 'sas', 'SGA_v2.0_scaffold47G17507' => 'sas', 'SGA_v2.0_scaffold63G21736' => 'sas', 'SGA_v2.0_scaffold87G27070' => 'sas', 'SHI17794' => 'shi', 'SHI28851' => 'shi', 'SMO165G0155' => 'smo', 'SMO340G0217' => 'smo', 'SMO367G1210' => 'smo', 'Solyc02g093430.3' => 'sly', 'Solyc05g013580.4' => 'sly', 'Solyc07g008030.3' => 'sly', 'Solyc12g035470.2' => 'sly', 'Sopen02g038020' => 'spe', 'Sopen05g008490' => 'spe', 'Sopen07g003910' => 'spe', 'Sopen12g015240' => 'spe', 'Sp1g11550' => 'spa', 'Sp2g16710' => 'spa', 'Sp3g00430' => 'spa', 'Sp3g26780' => 'spa', 'Sp5g22900' => 'spa', 'Sp6g29530' => 'spa', 'TAR371G0794' => 'tar', 'TAR374G0164' => 'tar', 'TAR622G0165' => 'tar', 'TAR626G0929' => 'tar', 'TAR629G2155' => 'tar', 'THA.LOC104805282' => 'tha', 'THA.LOC104805363' => 'tha', 'THA.LOC104808968' => 'tha', 'THA.LOC104821093' => 'tha', 'THA.LOC104823953' => 'tha', 'THA.LOC104825562' => 'tha', 'THA.LOC104825665' => 'tha', 'Thecc.02G261400' => 'tca', 'Thecc.04G019200' => 'tca', 'Thecc.09G130400' => 'tca', 'Thhalv10004374m.g' => 'esa', 'Thhalv10007850m.g' => 'esa', 'Thhalv10013782m.g' => 'esa', 'Thhalv10018686m.g' => 'esa', 'Thhalv10020899m.g' => 'esa', 'Thhalv10022755m.g' => 'esa', 'TPR.G23851' => 'tpr', 'TPR.G26500' => 'tpr', 'TPR.G27267' => 'tpr', 'TPR.G32001' => 'tpr', 'TPR.G6251' => 'tpr', 'TPR.G8167' => 'tpr', 'TWI12G1330' => 'twi', 'TWI18G1239' => 'twi', 'TWI34G0979' => 'twi', 'TWI36G0670' => 'twi', 'TWI36G0707' => 'twi', 'TWI56G0233' => 'twi', 'TWI75G1809' => 'twi', 'unitig_21.g20874' => 'ugi', 'unitig_26.g10343' => 'ugi', 'unitig_46.g18392' => 'ugi', 'unitig_52.g17178' => 'ugi', 'unitig_8.g2934' => 'ugi', 'vmacro01122' => 'vma', 'vmacro05875' => 'vma', 'vmacro06147' => 'vma', 'vmacro16191' => 'vma', 'vmacro18293' => 'vma', 'VMungo0251G3707' => 'vmu', 'VMungo0464G1521' => 'vmu', 'VMungo1215G0205' => 'vmu', 'VMungo1383G2484' => 'vmu', 'Zm00001eb079610' => 'zma', 'Zm00001eb135990' => 'zma', 'Zm00001eb183710' => 'zma', 'Zm00001eb246020' => 'zma' ), 'gf_id' => 'HOM05D001124', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001124' ), 'data_identifier' => 'HOM05D001124', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001124', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '548', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02520' => 'bna', 'A03p06630' => 'bna', 'A05p44460' => 'bna', 'A06p08710' => 'bna', 'A06p41090' => 'bna', 'A07p32320' => 'bna', 'A08p32520' => 'bna', 'A09p10360' => 'bna', 'A10p24080' => 'bna', 'Aa31LG11G15250' => 'aar', 'Aa31LG1G1800' => 'aar', 'Aa31LG2G5120' => 'aar', 'Aa31LG2G6070' => 'aar', 'Aa31LG5G10770' => 'aar', 'Aa31sc61G90' => 'aar', 'Actinidia01352' => 'ach', 'Actinidia05983' => 'ach', 'Actinidia08133' => 'ach', 'Actinidia15101' => 'ach', 'Actinidia26379' => 'ach', 'Actinidia35778' => 'ach', 'Actinidia36123' => 'ach', 'Actinidia37436' => 'ach', 'Actinidia38730' => 'ach', 'Ah.02g128210' => 'amhyb', 'Ah.03g132990' => 'amhyb', 'Ah.14g079410' => 'amhyb', 'AL1G24640' => 'aly', 'AL2G26680' => 'aly', 'AL3G10530' => 'aly', 'AL3G45230' => 'aly', 'AL5G15230' => 'aly', 'AL5G16960' => 'aly', 'AL6G25210' => 'aly', 'Aqoxy2G00441' => 'aox', 'Aqoxy3G01236' => 'aox', 'Aqoxy5G03746' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3RQ047' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C7GMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9C8JER' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MBL6KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YXCZ83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZANX40' => 'arhy', 'AT1G12990' => 'ath', 'AT1G67880' => 'ath', 'AT2G13290' => 'ath', 'AT3G01620' => 'ath', 'AT3G26445' => 'ath', 'AT3G27540' => 'ath', 'AT5G14480' => 'ath', 'ATR0824G026' => 'atr', 'ATR1098G019' => 'atr', 'Atru.chr11.2145' => 'acertr', 'Atru.chr2.3636' => 'acertr', 'Atru.chr2.3644' => 'acertr', 'Atru.chr6.2422' => 'acertr', 'Atru.chr7.1112' => 'acertr', 'AUR62005469' => 'cqu', 'AUR62011166' => 'cqu', 'AUR62013319' => 'cqu', 'AUR62024273' => 'cqu', 'AUR62028420' => 'cqu', 'AUR62041942' => 'cqu', 'BcaB01g04969' => 'bca', 'BcaB01g06371' => 'bca', 'BcaB02g11494' => 'bca', 'BcaB03g15382' => 'bca', 'BcaB08g36994' => 'bca', 'BcaC03g13477' => 'bca', 'BcaC03g13478' => 'bca', 'BcaC03g13480' => 'bca', 'BcaC03g13481' => 'bca', 'BcaC03g13486' => 'bca', 'BcaC04g19031' => 'bca', 'BcaC04g23085' => 'bca', 'BcaC05g25094' => 'bca', 'BcaC05g25096' => 'bca', 'BcaC05g25138' => 'bca', 'BcaC05g30416' => 'bca', 'BcaC05g30455' => 'bca', 'BcaC06g30979' => 'bca', 'BcaC06g33805' => 'bca', 'BcaC08g46021' => 'bca', 'BcaNung03154' => 'bca', 'BolC2t06623H' => 'bol', 'BolC2t06632H' => 'bol', 'BolC2t06635H' => 'bol', 'BolC2t06638H' => 'bol', 'BolC3t13266H' => 'bol', 'BolC5t29776H' => 'bol', 'BolC6t38912H' => 'bol', 'BolC7t44183H' => 'bol', 'BolC9t54123H' => 'bol', 'BolC9t59107H' => 'bol', 'BraA02t05221Z' => 'bra', 'BraA03t09996Z' => 'bra', 'BraA05t23210Z' => 'bra', 'BraA06t24068Z' => 'bra', 'BraA06t27032Z' => 'bra', 'BraA08t35176Z' => 'bra', 'BraA09t36680Z' => 'bra', 'BraA10t44471Z' => 'bra', 'C02p06760' => 'bna', 'C02p06890' => 'bna', 'C02p07010' => 'bna', 'C03p07660' => 'bna', 'C05p10300' => 'bna', 'C06p38150' => 'bna', 'C07p36650' => 'bna', 'C08p15770' => 'bna', 'C09p12300' => 'bna', 'C09p62700' => 'bna', 'C09p75040' => 'bna', 'CAN.G13.1' => 'can', 'CAN.G138.4' => 'can', 'CAN.G44.6' => 'can', 'CAN.G473.19' => 'can', 'CANSAT01G0835' => 'cansat', 'CANSAT11G0246' => 'cansat', 'CANSAT11G1766' => 'cansat', 'CANSAT64G1954' => 'cansat', 'CARHR013330' => 'chi', 'CARHR060530' => 'chi', 'CARHR075300' => 'chi', 'CARHR105120' => 'chi', 'CARHR148910' => 'chi', 'CARHR198830' => 'chi', 'Carub.0001s1275' => 'cru', 'Carub.0002s1437' => 'cru', 'Carub.0003s0044' => 'cru', 'Carub.0003s2787' => 'cru', 'Carub.0005s0597' => 'cru', 'Carub.0006s1266' => 'cru', 'Ca_06935_v3' => 'car', 'Ca_13559_v3' => 'car', 'Ca_16941_v3' => 'car', 'Ca_16960_v3' => 'car', 'Ca_17775_v3' => 'car', 'Ca_30464_v3' => 'car', 'Cc06_g08160' => 'ccan', 'Cc07_g01520' => 'ccan', 'Cc11_g15810' => 'ccan', 'CDE02G2840' => 'cde', 'CDE03G0093' => 'cde', 'CDE04G2127' => 'cde', 'CDE07G1857' => 'cde', 'CDE09G1246' => 'cde', 'Cfa003412' => 'cfa', 'Cfa007341' => 'cfa', 'Cfa009220' => 'cfa', 'Ciclev10008737m.g' => 'ccl', 'Ciclev10015565m.g' => 'ccl', 'Ciclev10031761m.g' => 'ccl', 'CiPaw.03G045300' => 'cil', 'CiPaw.03G247200' => 'cil', 'CiPaw.04G029500' => 'cil', 'CiPaw.04G174000' => 'cil', 'CiPaw.05G181200' => 'cil', 'CiPaw.06G067100' => 'cil', 'ClCG05G025800' => 'cla', 'ClCG06G011400' => 'cla', 'ClCG09G019360' => 'cla', 'COL.COLO4_04827' => 'col', 'COL.COLO4_29170' => 'col', 'COL.COLO4_35131' => 'col', 'COL.COLO4_35132' => 'col', 'Cpa.g.sc33.32' => 'cpa', 'Cpa.g.sc46.29' => 'cpa', 'Cpa.g.sc796.1' => 'cpa', 'CsaV3_1G030420' => 'csa', 'CsaV3_5G027050' => 'csa', 'CsaV3_5G031040' => 'csa', 'CsaV3_UNG023130' => 'csa', 'CSS0007726' => 'camsi', 'CSS0016433' => 'camsi', 'CSS0017656' => 'camsi', 'CSS0025364' => 'camsi', 'CSS0027582' => 'camsi', 'CSS0047288' => 'camsi', 'CSS0049950' => 'camsi', 'DCAR_003843' => 'dca', 'DCAR_007052' => 'dca', 'DCAR_020884' => 'dca', 'DCAR_021730' => 'dca', 'DCAR_024423' => 'dca', 'DCAR_026509' => 'dca', 'DCAR_031158' => 'dca', 'Dinv14728' => 'din', 'Dinv15219' => 'din', 'Dinv25728' => 'din', 'Dinv33428' => 'din', 'Dinv36489' => 'din', 'Dinv41486' => 'din', 'Duzib147G0469' => 'dzi', 'Duzib168G0060' => 'dzi', 'Duzib187G1215' => 'dzi', 'Duzib248G0692' => 'dzi', 'Duzib251G0767' => 'dzi', 'Duzib264G0446' => 'dzi', 'Duzib268G0691' => 'dzi', 'ECA232G4767' => 'eca', 'ECA233G2838' => 'eca', 'ECA234G0391' => 'eca', 'ECA234G0857' => 'eca', 'ECA236G1593' => 'eca', 'ECA238G0565' => 'eca', 'ECA246G1027' => 'eca', 'ECA246G3223' => 'eca', 'ECA246G3470' => 'eca', 'EL10Ac6g13829' => 'bvu', 'EL10Ac6g14093' => 'bvu', 'EL10Ac8g18707' => 'bvu', 'Eucgr.C01369' => 'egr', 'Eucgr.H02492' => 'egr', 'Eucgr.I01733' => 'egr', 'Eucgr.J02255' => 'egr', 'Eucgr.J02257' => 'egr', 'Eucgr.J02258' => 'egr', 'FAN02G1601' => 'fan', 'FAN03G1586' => 'fan', 'FAN03G2986' => 'fan', 'FAN05G4837' => 'fan', 'FAN06G0146' => 'fan', 'FAN07G0858' => 'fan', 'FAN09G3179' => 'fan', 'FAN10G0669' => 'fan', 'FAN12G2358' => 'fan', 'FAN14G4198' => 'fan', 'FAN14G5112' => 'fan', 'FAN17G0342' => 'fan', 'FAN19G0342' => 'fan', 'FAN19G0962' => 'fan', 'FAN19G1101' => 'fan', 'FAN19G1872' => 'fan', 'FAN22G0356' => 'fan', 'FAN23G0744' => 'fan', 'FAN23G1914' => 'fan', 'FAN26G0032' => 'fan', 'FAN28G0625' => 'fan', 'FvH4_1g02710' => 'fve', 'FvH4_1g02720' => 'fve', 'FvH4_4g25670' => 'fve', 'FvH4_6g51700' => 'fve', 'FvH4_7g20170' => 'fve', 'Glyma.05G175000' => 'gma', 'Glyma.08G132300' => 'gma', 'Glyma.11G243000' => 'gma', 'Glyma.13G158900' => 'gma', 'Glyma.17G112400' => 'gma', 'Glyma.18G014100' => 'gma', 'Glyma.19G003100' => 'gma', 'Glyma.19G056500' => 'gma', 'Gohir.A01G158900' => 'ghi', 'Gohir.A05G312600' => 'ghi', 'Gohir.A05G354900' => 'ghi', 'Gohir.A07G037200' => 'ghi', 'Gohir.A09G030000' => 'ghi', 'Gohir.A12G145200' => 'ghi', 'Gohir.D01G151500' => 'ghi', 'Gohir.D04G058300' => 'ghi', 'Gohir.D05G314100' => 'ghi', 'Gohir.D07G041400' => 'ghi', 'Gohir.D09G029700' => 'ghi', 'Gohir.D12G149700' => 'ghi', 'Gorai.001G043800' => 'gra', 'Gorai.002G187800' => 'gra', 'Gorai.006G034700' => 'gra', 'Gorai.008G161200' => 'gra', 'Gorai.009G335700' => 'gra', 'Gorai.012G065000' => 'gra', 'GSVIVG01000535001' => 'vvi', 'GSVIVG01015572001' => 'vvi', 'GSVIVG01032386001' => 'vvi', 'HanXRQChr05g0138531' => 'han', 'HanXRQChr06g0174391' => 'han', 'HanXRQChr07g0199021' => 'han', 'HanXRQChr08g0208211' => 'han', 'HanXRQChr09g0255471' => 'han', 'HanXRQChr10g0315791' => 'han', 'HanXRQChr12g0371991' => 'han', 'HanXRQChr15g0475251' => 'han', 'HanXRQChr17g0540001' => 'han', 'HanXRQChr17g0548631' => 'han', 'HanXRQChr17g0569561' => 'han', 'Haze_12256' => 'cav', 'Haze_14756' => 'cav', 'Haze_25528' => 'cav', 'Hma1.2p1_0079F.1_g041020' => 'hma', 'Hma1.2p1_0818F.1_g223260' => 'hma', 'Hma1.2p1_1747F.1_g300530' => 'hma', 'HPP92_004607' => 'vpl', 'HPP92_004608' => 'vpl', 'HPP92_006181' => 'vpl', 'HPP92_012192' => 'vpl', 'HPP92_015680' => 'vpl', 'HPP92_020249' => 'vpl', 'HPP92_021376' => 'vpl', 'HPP92_024275' => 'vpl', 'Hund06031' => 'sun', 'Hund25391' => 'sun', 'Lalb_Chr07g0185371' => 'lal', 'Lalb_Chr07g0185381' => 'lal', 'Lalb_Chr12g0204011' => 'lal', 'Lalb_Chr13g0301671' => 'lal', 'Lalb_Chr14g0362851' => 'lal', 'Lalb_Chr24g0403581' => 'lal', 'Lj1g0000233' => 'lja', 'Lj2g0018120' => 'lja', 'Lj3C621T0' => 'lonja', 'Lj3P1059T14' => 'lonja', 'Lj3P611T9' => 'lonja', 'Lj3P614T13' => 'lonja', 'Lj3P615T5' => 'lonja', 'Lj4g0012315' => 'lja', 'Lj4g0026182' => 'lja', 'Lj6P813T16' => 'lonja', 'Lj7C427T7' => 'lonja', 'Lj7C427T8' => 'lonja', 'Lj7P600T41' => 'lonja', 'Lju41C42G17' => 'lonja', 'Lsat_1_v5_gn_0_47300' => 'lsa', 'Lsat_1_v5_gn_2_91280' => 'lsa', 'Lsat_1_v5_gn_3_30561' => 'lsa', 'Lsat_1_v5_gn_4_184321' => 'lsa', 'Lsat_1_v5_gn_4_4041' => 'lsa', 'Lsat_1_v5_gn_5_92000' => 'lsa', 'Lsat_1_v5_gn_8_152940' => 'lsa', 'Lsat_1_v5_gn_8_62401' => 'lsa', 'Manes.06G055900' => 'mes', 'Manes.12G022200' => 'mes', 'Manes.13G023300' => 'mes', 'Manes.14G115000' => 'mes', 'Manes.15G151700' => 'mes', 'Manes.17G111300' => 'mes', 'Mapoly0226s0009' => 'mpo', 'MBI02_g25363_MAGBIO' => 'mbi', 'MBI06_g00027_MAGBIO' => 'mbi', 'MBI10_g13034_MAGBIO' => 'mbi', 'MD09G1023400' => 'mdo', 'MD13G1100100' => 'mdo', 'MD15G1169200' => 'mdo', 'MD16G1101100' => 'mdo', 'MD17G1022900' => 'mdo', 'Medtr3g096150' => 'mtr', 'Medtr4g115070' => 'mtr', 'Medtr7g033325' => 'mtr', 'Medtr8g089840' => 'mtr', 'MELO3C010319.2' => 'cme', 'MELO3C011944.2' => 'cme', 'MELO3C021589.2' => 'cme', 'Migut.E00207' => 'egut', 'Migut.H00067' => 'egut', 'Migut.K00433' => 'egut', 'Migut.K00606' => 'egut', 'Migut.K01410' => 'egut', 'MSTRG.13347' => 'ama', 'MSTRG.24045' => 'ama', 'MSTRG.2428' => 'ama', 'MSTRG.26410' => 'ama', 'MSTRG.3139' => 'ama', 'MSTRG.3286' => 'ama', 'MSTRG.563' => 'ama', 'MSTRG.7941' => 'ama', 'Nitab4.5_0000028g0060' => 'nta', 'Nitab4.5_0000065g0260' => 'nta', 'Nitab4.5_0000112g0060' => 'nta', 'Nitab4.5_0000489g0120' => 'nta', 'Nitab4.5_0001776g0050' => 'nta', 'Nitab4.5_0001854g0010' => 'nta', 'Nitab4.5_0001860g0020' => 'nta', 'Nitab4.5_0004352g0010' => 'nta', 'Nitab4.5_0008716g0020' => 'nta', 'Nitab4.5_0008922g0010' => 'nta', 'Nn3g16693' => 'nnu', 'Nn4g22596' => 'nnu', 'Nn7g37639' => 'nnu', 'Oeu001701.1' => 'oeu', 'Oeu018149.1' => 'oeu', 'Oeu026220.1' => 'oeu', 'Oeu038635.1' => 'oeu', 'Oeu049176.1' => 'oeu', 'Oeu056706.1' => 'oeu', 'Oeu056937.1' => 'oeu', 'Oeu057540.1' => 'oeu', 'Os02g0594900' => 'osa', 'Os02g0595100' => 'osa', 'Os04g0477500' => 'osa', 'Os12g0611900' => 'osa', 'Peaxi162Scf00076g00020' => 'pax', 'Peaxi162Scf00128g00217' => 'pax', 'Peaxi162Scf00129g01640' => 'pax', 'Peaxi162Scf00669g00007' => 'pax', 'Peaxi162Scf00700g00421' => 'pax', 'Peaxi162Scf00801g00038' => 'pax', 'Peaxi162Scf00891g00025' => 'pax', 'PGR083G0909' => 'pgr', 'PGR119G1005' => 'pgr', 'PGR142G2236' => 'pgr', 'PGR142G3388' => 'pgr', 'PGSC0003DMG400004514' => 'stu', 'PGSC0003DMG400012635' => 'stu', 'PGSC0003DMG400015730' => 'stu', 'PGSC0003DMG400018611' => 'stu', 'PGSC0003DMG400030897' => 'stu', 'Phvul.001G254800' => 'pvu', 'Phvul.002G260100' => 'pvu', 'Phvul.003G167600' => 'pvu', 'Phvul.004G005100' => 'pvu', 'Potri.001G343600' => 'ptr', 'Potri.006G066700' => 'ptr', 'Potri.008G186000' => 'ptr', 'Potri.010G046900' => 'ptr', 'Potri.018G127900' => 'ptr', 'Pp3c20_17750' => 'ppa', 'Pp3c24_4380' => 'ppa', 'Prupe.1G245800' => 'ppe', 'Prupe.3G293400' => 'ppe', 'Prupe.7G247400' => 'ppe', 'Psat0s145g0120' => 'psa', 'Psat0s595g0040' => 'psa', 'Psat0s595g0120' => 'psa', 'Psat3g175040' => 'psa', 'Psat7g058120' => 'psa', 'PSO017G0428' => 'pso', 'PSO063G7510' => 'pso', 'PSO067G0046' => 'pso', 'PSO478G1073' => 'pso', 'PSO675G3677' => 'pso', 'PSO675G6558' => 'pso', 'PSO675G7520' => 'pso', 'PSO675G8959' => 'pso', 'QL02p074089' => 'qlo', 'QL02p089614' => 'qlo', 'QL03p057736' => 'qlo', 'RcHm_v2.0_Chr1g0364131' => 'rch', 'RcHm_v2.0_Chr2g0087801' => 'rch', 'RcHm_v2.0_Chr2g0087821' => 'rch', 'RcHm_v2.0_Chr2g0173231' => 'rch', 'RcHm_v2.0_Chr4g0433111' => 'rch', 'Rhsim03G0250300' => 'rsi', 'Rhsim08G0048400' => 'rsi', 'Rhsim10G0014800' => 'rsi', 'Rhsim12G0040100' => 'rsi', 'Rhsim12G0109700' => 'rsi', 'Sabra06G0049600' => 'sbr', 'Sabra08G0141000' => 'sbr', 'Sabra10G0021400' => 'sbr', 'Sabra16G0222900' => 'sbr', 'Sabra18G0108600' => 'sbr', 'SalBow1G0433' => 'sbo', 'SalBow1G2038' => 'sbo', 'SalBow1G5003' => 'sbo', 'SalBow7G1197' => 'sbo', 'SalBow8G3506' => 'sbo', 'Sc03g0007300' => 'sci', 'Sc11g0000950' => 'sci', 'Sc14g0008750' => 'sci', 'Sc18g0000420' => 'sci', 'Sed0006754' => 'sed', 'Sed0008741' => 'sed', 'Sed0017172' => 'sed', 'Sed0018925' => 'sed', 'Sed0023326' => 'sed', 'Sed0025909' => 'sed', 'SEGI_05333' => 'sgi', 'SEGI_10362' => 'sgi', 'SEGI_13380' => 'sgi', 'SEGI_24306' => 'sgi', 'SEGI_29077' => 'sgi', 'SEGI_29095' => 'sgi', 'SEGI_36534' => 'sgi', 'SEGI_37506' => 'sgi', 'SEGI_38321' => 'sgi', 'SGA_v2.0_scaffold307G48031' => 'sas', 'SGA_v2.0_scaffold47G17507' => 'sas', 'SGA_v2.0_scaffold63G21736' => 'sas', 'SGA_v2.0_scaffold87G27070' => 'sas', 'SHI17794' => 'shi', 'SHI28851' => 'shi', 'SMO165G0155' => 'smo', 'SMO340G0217' => 'smo', 'SMO367G1210' => 'smo', 'Solyc02g093430.3' => 'sly', 'Solyc05g013580.4' => 'sly', 'Solyc07g008030.3' => 'sly', 'Solyc12g035470.2' => 'sly', 'Sopen02g038020' => 'spe', 'Sopen05g008490' => 'spe', 'Sopen07g003910' => 'spe', 'Sopen12g015240' => 'spe', 'Sp1g11550' => 'spa', 'Sp2g16710' => 'spa', 'Sp3g00430' => 'spa', 'Sp3g26780' => 'spa', 'Sp5g22900' => 'spa', 'Sp6g29530' => 'spa', 'TAR371G0794' => 'tar', 'TAR374G0164' => 'tar', 'TAR622G0165' => 'tar', 'TAR626G0929' => 'tar', 'TAR629G2155' => 'tar', 'THA.LOC104805282' => 'tha', 'THA.LOC104805363' => 'tha', 'THA.LOC104808968' => 'tha', 'THA.LOC104821093' => 'tha', 'THA.LOC104823953' => 'tha', 'THA.LOC104825562' => 'tha', 'THA.LOC104825665' => 'tha', 'Thecc.02G261400' => 'tca', 'Thecc.04G019200' => 'tca', 'Thecc.09G130400' => 'tca', 'Thhalv10004374m.g' => 'esa', 'Thhalv10007850m.g' => 'esa', 'Thhalv10013782m.g' => 'esa', 'Thhalv10018686m.g' => 'esa', 'Thhalv10020899m.g' => 'esa', 'Thhalv10022755m.g' => 'esa', 'TPR.G23851' => 'tpr', 'TPR.G26500' => 'tpr', 'TPR.G27267' => 'tpr', 'TPR.G32001' => 'tpr', 'TPR.G6251' => 'tpr', 'TPR.G8167' => 'tpr', 'TWI12G1330' => 'twi', 'TWI18G1239' => 'twi', 'TWI34G0979' => 'twi', 'TWI36G0670' => 'twi', 'TWI36G0707' => 'twi', 'TWI56G0233' => 'twi', 'TWI75G1809' => 'twi', 'unitig_21.g20874' => 'ugi', 'unitig_26.g10343' => 'ugi', 'unitig_46.g18392' => 'ugi', 'unitig_52.g17178' => 'ugi', 'unitig_8.g2934' => 'ugi', 'vmacro01122' => 'vma', 'vmacro05875' => 'vma', 'vmacro06147' => 'vma', 'vmacro16191' => 'vma', 'vmacro18293' => 'vma', 'VMungo0251G3707' => 'vmu', 'VMungo0464G1521' => 'vmu', 'VMungo1215G0205' => 'vmu', 'VMungo1383G2484' => 'vmu', 'Zm00001eb079610' => 'zma', 'Zm00001eb135990' => 'zma', 'Zm00001eb183710' => 'zma', 'Zm00001eb246020' => 'zma' ) $gf_id = 'HOM05D001124' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001124' ) $data_identifier = 'HOM05D001124' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 6, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 7, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 21, 'bol' => (int) 10, 'bra' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 6, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 9, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 21, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 8, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 10, 'lsa' => (int) 8, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 8, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 9, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb246020' $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' => 'HOM05D001124', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '548', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02520' => 'bna', 'A03p06630' => 'bna', 'A05p44460' => 'bna', 'A06p08710' => 'bna', 'A06p41090' => 'bna', 'A07p32320' => 'bna', 'A08p32520' => 'bna', 'A09p10360' => 'bna', 'A10p24080' => 'bna', 'Aa31LG11G15250' => 'aar', 'Aa31LG1G1800' => 'aar', 'Aa31LG2G5120' => 'aar', 'Aa31LG2G6070' => 'aar', 'Aa31LG5G10770' => 'aar', 'Aa31sc61G90' => 'aar', 'Actinidia01352' => 'ach', 'Actinidia05983' => 'ach', 'Actinidia08133' => 'ach', 'Actinidia15101' => 'ach', 'Actinidia26379' => 'ach', 'Actinidia35778' => 'ach', 'Actinidia36123' => 'ach', 'Actinidia37436' => 'ach', 'Actinidia38730' => 'ach', 'Ah.02g128210' => 'amhyb', 'Ah.03g132990' => 'amhyb', 'Ah.14g079410' => 'amhyb', 'AL1G24640' => 'aly', 'AL2G26680' => 'aly', 'AL3G10530' => 'aly', 'AL3G45230' => 'aly', 'AL5G15230' => 'aly', 'AL5G16960' => 'aly', 'AL6G25210' => 'aly', 'Aqoxy2G00441' => 'aox', 'Aqoxy3G01236' => 'aox', 'Aqoxy5G03746' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3RQ047' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C7GMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9C8JER' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MBL6KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YXCZ83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZANX40' => 'arhy', 'AT1G12990' => 'ath', 'AT1G67880' => 'ath', 'AT2G13290' => 'ath', 'AT3G01620' => 'ath', 'AT3G26445' => 'ath', 'AT3G27540' => 'ath', 'AT5G14480' => 'ath', 'ATR0824G026' => 'atr', 'ATR1098G019' => 'atr', 'Atru.chr11.2145' => 'acertr', 'Atru.chr2.3636' => 'acertr', 'Atru.chr2.3644' => 'acertr', 'Atru.chr6.2422' => 'acertr', 'Atru.chr7.1112' => 'acertr', 'AUR62005469' => 'cqu', 'AUR62011166' => 'cqu', 'AUR62013319' => 'cqu', 'AUR62024273' => 'cqu', 'AUR62028420' => 'cqu', 'AUR62041942' => 'cqu', 'BcaB01g04969' => 'bca', 'BcaB01g06371' => 'bca', 'BcaB02g11494' => 'bca', 'BcaB03g15382' => 'bca', 'BcaB08g36994' => 'bca', 'BcaC03g13477' => 'bca', 'BcaC03g13478' => 'bca', 'BcaC03g13480' => 'bca', 'BcaC03g13481' => 'bca', 'BcaC03g13486' => 'bca', 'BcaC04g19031' => 'bca', 'BcaC04g23085' => 'bca', 'BcaC05g25094' => 'bca', 'BcaC05g25096' => 'bca', 'BcaC05g25138' => 'bca', 'BcaC05g30416' => 'bca', 'BcaC05g30455' => 'bca', 'BcaC06g30979' => 'bca', 'BcaC06g33805' => 'bca', 'BcaC08g46021' => 'bca', 'BcaNung03154' => 'bca', 'BolC2t06623H' => 'bol', 'BolC2t06632H' => 'bol', 'BolC2t06635H' => 'bol', 'BolC2t06638H' => 'bol', 'BolC3t13266H' => 'bol', 'BolC5t29776H' => 'bol', 'BolC6t38912H' => 'bol', 'BolC7t44183H' => 'bol', 'BolC9t54123H' => 'bol', 'BolC9t59107H' => 'bol', 'BraA02t05221Z' => 'bra', 'BraA03t09996Z' => 'bra', 'BraA05t23210Z' => 'bra', 'BraA06t24068Z' => 'bra', 'BraA06t27032Z' => 'bra', 'BraA08t35176Z' => 'bra', 'BraA09t36680Z' => 'bra', 'BraA10t44471Z' => 'bra', 'C02p06760' => 'bna', 'C02p06890' => 'bna', 'C02p07010' => 'bna', 'C03p07660' => 'bna', 'C05p10300' => 'bna', 'C06p38150' => 'bna', 'C07p36650' => 'bna', 'C08p15770' => 'bna', 'C09p12300' => 'bna', 'C09p62700' => 'bna', 'C09p75040' => 'bna', 'CAN.G13.1' => 'can', 'CAN.G138.4' => 'can', 'CAN.G44.6' => 'can', 'CAN.G473.19' => 'can', 'CANSAT01G0835' => 'cansat', 'CANSAT11G0246' => 'cansat', 'CANSAT11G1766' => 'cansat', 'CANSAT64G1954' => 'cansat', 'CARHR013330' => 'chi', 'CARHR060530' => 'chi', 'CARHR075300' => 'chi', 'CARHR105120' => 'chi', 'CARHR148910' => 'chi', 'CARHR198830' => 'chi', 'Carub.0001s1275' => 'cru', 'Carub.0002s1437' => 'cru', 'Carub.0003s0044' => 'cru', 'Carub.0003s2787' => 'cru', 'Carub.0005s0597' => 'cru', 'Carub.0006s1266' => 'cru', 'Ca_06935_v3' => 'car', 'Ca_13559_v3' => 'car', 'Ca_16941_v3' => 'car', 'Ca_16960_v3' => 'car', 'Ca_17775_v3' => 'car', 'Ca_30464_v3' => 'car', 'Cc06_g08160' => 'ccan', 'Cc07_g01520' => 'ccan', 'Cc11_g15810' => 'ccan', 'CDE02G2840' => 'cde', 'CDE03G0093' => 'cde', 'CDE04G2127' => 'cde', 'CDE07G1857' => 'cde', 'CDE09G1246' => 'cde', 'Cfa003412' => 'cfa', 'Cfa007341' => 'cfa', 'Cfa009220' => 'cfa', 'Ciclev10008737m.g' => 'ccl', 'Ciclev10015565m.g' => 'ccl', 'Ciclev10031761m.g' => 'ccl', 'CiPaw.03G045300' => 'cil', 'CiPaw.03G247200' => 'cil', 'CiPaw.04G029500' => 'cil', 'CiPaw.04G174000' => 'cil', 'CiPaw.05G181200' => 'cil', 'CiPaw.06G067100' => 'cil', 'ClCG05G025800' => 'cla', 'ClCG06G011400' => 'cla', 'ClCG09G019360' => 'cla', 'COL.COLO4_04827' => 'col', 'COL.COLO4_29170' => 'col', 'COL.COLO4_35131' => 'col', 'COL.COLO4_35132' => 'col', 'Cpa.g.sc33.32' => 'cpa', 'Cpa.g.sc46.29' => 'cpa', 'Cpa.g.sc796.1' => 'cpa', 'CsaV3_1G030420' => 'csa', 'CsaV3_5G027050' => 'csa', 'CsaV3_5G031040' => 'csa', 'CsaV3_UNG023130' => 'csa', 'CSS0007726' => 'camsi', 'CSS0016433' => 'camsi', 'CSS0017656' => 'camsi', 'CSS0025364' => 'camsi', 'CSS0027582' => 'camsi', 'CSS0047288' => 'camsi', 'CSS0049950' => 'camsi', 'DCAR_003843' => 'dca', 'DCAR_007052' => 'dca', 'DCAR_020884' => 'dca', 'DCAR_021730' => 'dca', 'DCAR_024423' => 'dca', 'DCAR_026509' => 'dca', 'DCAR_031158' => 'dca', 'Dinv14728' => 'din', 'Dinv15219' => 'din', 'Dinv25728' => 'din', 'Dinv33428' => 'din', 'Dinv36489' => 'din', 'Dinv41486' => 'din', 'Duzib147G0469' => 'dzi', 'Duzib168G0060' => 'dzi', 'Duzib187G1215' => 'dzi', 'Duzib248G0692' => 'dzi', 'Duzib251G0767' => 'dzi', 'Duzib264G0446' => 'dzi', 'Duzib268G0691' => 'dzi', 'ECA232G4767' => 'eca', 'ECA233G2838' => 'eca', 'ECA234G0391' => 'eca', 'ECA234G0857' => 'eca', 'ECA236G1593' => 'eca', 'ECA238G0565' => 'eca', 'ECA246G1027' => 'eca', 'ECA246G3223' => 'eca', 'ECA246G3470' => 'eca', 'EL10Ac6g13829' => 'bvu', 'EL10Ac6g14093' => 'bvu', 'EL10Ac8g18707' => 'bvu', 'Eucgr.C01369' => 'egr', 'Eucgr.H02492' => 'egr', 'Eucgr.I01733' => 'egr', 'Eucgr.J02255' => 'egr', 'Eucgr.J02257' => 'egr', 'Eucgr.J02258' => 'egr', 'FAN02G1601' => 'fan', 'FAN03G1586' => 'fan', 'FAN03G2986' => 'fan', 'FAN05G4837' => 'fan', 'FAN06G0146' => 'fan', 'FAN07G0858' => 'fan', 'FAN09G3179' => 'fan', 'FAN10G0669' => 'fan', 'FAN12G2358' => 'fan', 'FAN14G4198' => 'fan', 'FAN14G5112' => 'fan', 'FAN17G0342' => 'fan', 'FAN19G0342' => 'fan', 'FAN19G0962' => 'fan', 'FAN19G1101' => 'fan', 'FAN19G1872' => 'fan', 'FAN22G0356' => 'fan', 'FAN23G0744' => 'fan', 'FAN23G1914' => 'fan', 'FAN26G0032' => 'fan', 'FAN28G0625' => 'fan', 'FvH4_1g02710' => 'fve', 'FvH4_1g02720' => 'fve', 'FvH4_4g25670' => 'fve', 'FvH4_6g51700' => 'fve', 'FvH4_7g20170' => 'fve', 'Glyma.05G175000' => 'gma', 'Glyma.08G132300' => 'gma', 'Glyma.11G243000' => 'gma', 'Glyma.13G158900' => 'gma', 'Glyma.17G112400' => 'gma', 'Glyma.18G014100' => 'gma', 'Glyma.19G003100' => 'gma', 'Glyma.19G056500' => 'gma', 'Gohir.A01G158900' => 'ghi', 'Gohir.A05G312600' => 'ghi', 'Gohir.A05G354900' => 'ghi', 'Gohir.A07G037200' => 'ghi', 'Gohir.A09G030000' => 'ghi', 'Gohir.A12G145200' => 'ghi', 'Gohir.D01G151500' => 'ghi', 'Gohir.D04G058300' => 'ghi', 'Gohir.D05G314100' => 'ghi', 'Gohir.D07G041400' => 'ghi', 'Gohir.D09G029700' => 'ghi', 'Gohir.D12G149700' => 'ghi', 'Gorai.001G043800' => 'gra', 'Gorai.002G187800' => 'gra', 'Gorai.006G034700' => 'gra', 'Gorai.008G161200' => 'gra', 'Gorai.009G335700' => 'gra', 'Gorai.012G065000' => 'gra', 'GSVIVG01000535001' => 'vvi', 'GSVIVG01015572001' => 'vvi', 'GSVIVG01032386001' => 'vvi', 'HanXRQChr05g0138531' => 'han', 'HanXRQChr06g0174391' => 'han', 'HanXRQChr07g0199021' => 'han', 'HanXRQChr08g0208211' => 'han', 'HanXRQChr09g0255471' => 'han', 'HanXRQChr10g0315791' => 'han', 'HanXRQChr12g0371991' => 'han', 'HanXRQChr15g0475251' => 'han', 'HanXRQChr17g0540001' => 'han', 'HanXRQChr17g0548631' => 'han', 'HanXRQChr17g0569561' => 'han', 'Haze_12256' => 'cav', 'Haze_14756' => 'cav', 'Haze_25528' => 'cav', 'Hma1.2p1_0079F.1_g041020' => 'hma', 'Hma1.2p1_0818F.1_g223260' => 'hma', 'Hma1.2p1_1747F.1_g300530' => 'hma', 'HPP92_004607' => 'vpl', 'HPP92_004608' => 'vpl', 'HPP92_006181' => 'vpl', 'HPP92_012192' => 'vpl', 'HPP92_015680' => 'vpl', 'HPP92_020249' => 'vpl', 'HPP92_021376' => 'vpl', 'HPP92_024275' => 'vpl', 'Hund06031' => 'sun', 'Hund25391' => 'sun', 'Lalb_Chr07g0185371' => 'lal', 'Lalb_Chr07g0185381' => 'lal', 'Lalb_Chr12g0204011' => 'lal', 'Lalb_Chr13g0301671' => 'lal', 'Lalb_Chr14g0362851' => 'lal', 'Lalb_Chr24g0403581' => 'lal', 'Lj1g0000233' => 'lja', 'Lj2g0018120' => 'lja', 'Lj3C621T0' => 'lonja', 'Lj3P1059T14' => 'lonja', 'Lj3P611T9' => 'lonja', 'Lj3P614T13' => 'lonja', 'Lj3P615T5' => 'lonja', 'Lj4g0012315' => 'lja', 'Lj4g0026182' => 'lja', 'Lj6P813T16' => 'lonja', 'Lj7C427T7' => 'lonja', 'Lj7C427T8' => 'lonja', 'Lj7P600T41' => 'lonja', 'Lju41C42G17' => 'lonja', 'Lsat_1_v5_gn_0_47300' => 'lsa', 'Lsat_1_v5_gn_2_91280' => 'lsa', 'Lsat_1_v5_gn_3_30561' => 'lsa', 'Lsat_1_v5_gn_4_184321' => 'lsa', 'Lsat_1_v5_gn_4_4041' => 'lsa', 'Lsat_1_v5_gn_5_92000' => 'lsa', 'Lsat_1_v5_gn_8_152940' => 'lsa', 'Lsat_1_v5_gn_8_62401' => 'lsa', 'Manes.06G055900' => 'mes', 'Manes.12G022200' => 'mes', 'Manes.13G023300' => 'mes', 'Manes.14G115000' => 'mes', 'Manes.15G151700' => 'mes', 'Manes.17G111300' => 'mes', 'Mapoly0226s0009' => 'mpo', 'MBI02_g25363_MAGBIO' => 'mbi', 'MBI06_g00027_MAGBIO' => 'mbi', 'MBI10_g13034_MAGBIO' => 'mbi', 'MD09G1023400' => 'mdo', 'MD13G1100100' => 'mdo', 'MD15G1169200' => 'mdo', 'MD16G1101100' => 'mdo', 'MD17G1022900' => 'mdo', 'Medtr3g096150' => 'mtr', 'Medtr4g115070' => 'mtr', 'Medtr7g033325' => 'mtr', 'Medtr8g089840' => 'mtr', 'MELO3C010319.2' => 'cme', 'MELO3C011944.2' => 'cme', 'MELO3C021589.2' => 'cme', 'Migut.E00207' => 'egut', 'Migut.H00067' => 'egut', 'Migut.K00433' => 'egut', 'Migut.K00606' => 'egut', 'Migut.K01410' => 'egut', 'MSTRG.13347' => 'ama', 'MSTRG.24045' => 'ama', 'MSTRG.2428' => 'ama', 'MSTRG.26410' => 'ama', 'MSTRG.3139' => 'ama', 'MSTRG.3286' => 'ama', 'MSTRG.563' => 'ama', 'MSTRG.7941' => 'ama', 'Nitab4.5_0000028g0060' => 'nta', 'Nitab4.5_0000065g0260' => 'nta', 'Nitab4.5_0000112g0060' => 'nta', 'Nitab4.5_0000489g0120' => 'nta', 'Nitab4.5_0001776g0050' => 'nta', 'Nitab4.5_0001854g0010' => 'nta', 'Nitab4.5_0001860g0020' => 'nta', 'Nitab4.5_0004352g0010' => 'nta', 'Nitab4.5_0008716g0020' => 'nta', 'Nitab4.5_0008922g0010' => 'nta', 'Nn3g16693' => 'nnu', 'Nn4g22596' => 'nnu', 'Nn7g37639' => 'nnu', 'Oeu001701.1' => 'oeu', 'Oeu018149.1' => 'oeu', 'Oeu026220.1' => 'oeu', 'Oeu038635.1' => 'oeu', 'Oeu049176.1' => 'oeu', 'Oeu056706.1' => 'oeu', 'Oeu056937.1' => 'oeu', 'Oeu057540.1' => 'oeu', 'Os02g0594900' => 'osa', 'Os02g0595100' => 'osa', 'Os04g0477500' => 'osa', 'Os12g0611900' => 'osa', 'Peaxi162Scf00076g00020' => 'pax', 'Peaxi162Scf00128g00217' => 'pax', 'Peaxi162Scf00129g01640' => 'pax', 'Peaxi162Scf00669g00007' => 'pax', 'Peaxi162Scf00700g00421' => 'pax', 'Peaxi162Scf00801g00038' => 'pax', 'Peaxi162Scf00891g00025' => 'pax', 'PGR083G0909' => 'pgr', 'PGR119G1005' => 'pgr', 'PGR142G2236' => 'pgr', 'PGR142G3388' => 'pgr', 'PGSC0003DMG400004514' => 'stu', 'PGSC0003DMG400012635' => 'stu', 'PGSC0003DMG400015730' => 'stu', 'PGSC0003DMG400018611' => 'stu', 'PGSC0003DMG400030897' => 'stu', 'Phvul.001G254800' => 'pvu', 'Phvul.002G260100' => 'pvu', 'Phvul.003G167600' => 'pvu', 'Phvul.004G005100' => 'pvu', 'Potri.001G343600' => 'ptr', 'Potri.006G066700' => 'ptr', 'Potri.008G186000' => 'ptr', 'Potri.010G046900' => 'ptr', 'Potri.018G127900' => 'ptr', 'Pp3c20_17750' => 'ppa', 'Pp3c24_4380' => 'ppa', 'Prupe.1G245800' => 'ppe', 'Prupe.3G293400' => 'ppe', 'Prupe.7G247400' => 'ppe', 'Psat0s145g0120' => 'psa', 'Psat0s595g0040' => 'psa', 'Psat0s595g0120' => 'psa', 'Psat3g175040' => 'psa', 'Psat7g058120' => 'psa', 'PSO017G0428' => 'pso', 'PSO063G7510' => 'pso', 'PSO067G0046' => 'pso', 'PSO478G1073' => 'pso', 'PSO675G3677' => 'pso', 'PSO675G6558' => 'pso', 'PSO675G7520' => 'pso', 'PSO675G8959' => 'pso', 'QL02p074089' => 'qlo', 'QL02p089614' => 'qlo', 'QL03p057736' => 'qlo', 'RcHm_v2.0_Chr1g0364131' => 'rch', 'RcHm_v2.0_Chr2g0087801' => 'rch', 'RcHm_v2.0_Chr2g0087821' => 'rch', 'RcHm_v2.0_Chr2g0173231' => 'rch', 'RcHm_v2.0_Chr4g0433111' => 'rch', 'Rhsim03G0250300' => 'rsi', 'Rhsim08G0048400' => 'rsi', 'Rhsim10G0014800' => 'rsi', 'Rhsim12G0040100' => 'rsi', 'Rhsim12G0109700' => 'rsi', 'Sabra06G0049600' => 'sbr', 'Sabra08G0141000' => 'sbr', 'Sabra10G0021400' => 'sbr', 'Sabra16G0222900' => 'sbr', 'Sabra18G0108600' => 'sbr', 'SalBow1G0433' => 'sbo', 'SalBow1G2038' => 'sbo', 'SalBow1G5003' => 'sbo', 'SalBow7G1197' => 'sbo', 'SalBow8G3506' => 'sbo', 'Sc03g0007300' => 'sci', 'Sc11g0000950' => 'sci', 'Sc14g0008750' => 'sci', 'Sc18g0000420' => 'sci', 'Sed0006754' => 'sed', 'Sed0008741' => 'sed', 'Sed0017172' => 'sed', 'Sed0018925' => 'sed', 'Sed0023326' => 'sed', 'Sed0025909' => 'sed', 'SEGI_05333' => 'sgi', 'SEGI_10362' => 'sgi', 'SEGI_13380' => 'sgi', 'SEGI_24306' => 'sgi', 'SEGI_29077' => 'sgi', 'SEGI_29095' => 'sgi', 'SEGI_36534' => 'sgi', 'SEGI_37506' => 'sgi', 'SEGI_38321' => 'sgi', 'SGA_v2.0_scaffold307G48031' => 'sas', 'SGA_v2.0_scaffold47G17507' => 'sas', 'SGA_v2.0_scaffold63G21736' => 'sas', 'SGA_v2.0_scaffold87G27070' => 'sas', 'SHI17794' => 'shi', 'SHI28851' => 'shi', 'SMO165G0155' => 'smo', 'SMO340G0217' => 'smo', 'SMO367G1210' => 'smo', 'Solyc02g093430.3' => 'sly', 'Solyc05g013580.4' => 'sly', 'Solyc07g008030.3' => 'sly', 'Solyc12g035470.2' => 'sly', 'Sopen02g038020' => 'spe', 'Sopen05g008490' => 'spe', 'Sopen07g003910' => 'spe', 'Sopen12g015240' => 'spe', 'Sp1g11550' => 'spa', 'Sp2g16710' => 'spa', 'Sp3g00430' => 'spa', 'Sp3g26780' => 'spa', 'Sp5g22900' => 'spa', 'Sp6g29530' => 'spa', 'TAR371G0794' => 'tar', 'TAR374G0164' => 'tar', 'TAR622G0165' => 'tar', 'TAR626G0929' => 'tar', 'TAR629G2155' => 'tar', 'THA.LOC104805282' => 'tha', 'THA.LOC104805363' => 'tha', 'THA.LOC104808968' => 'tha', 'THA.LOC104821093' => 'tha', 'THA.LOC104823953' => 'tha', 'THA.LOC104825562' => 'tha', 'THA.LOC104825665' => 'tha', 'Thecc.02G261400' => 'tca', 'Thecc.04G019200' => 'tca', 'Thecc.09G130400' => 'tca', 'Thhalv10004374m.g' => 'esa', 'Thhalv10007850m.g' => 'esa', 'Thhalv10013782m.g' => 'esa', 'Thhalv10018686m.g' => 'esa', 'Thhalv10020899m.g' => 'esa', 'Thhalv10022755m.g' => 'esa', 'TPR.G23851' => 'tpr', 'TPR.G26500' => 'tpr', 'TPR.G27267' => 'tpr', 'TPR.G32001' => 'tpr', 'TPR.G6251' => 'tpr', 'TPR.G8167' => 'tpr', 'TWI12G1330' => 'twi', 'TWI18G1239' => 'twi', 'TWI34G0979' => 'twi', 'TWI36G0670' => 'twi', 'TWI36G0707' => 'twi', 'TWI56G0233' => 'twi', 'TWI75G1809' => 'twi', 'unitig_21.g20874' => 'ugi', 'unitig_26.g10343' => 'ugi', 'unitig_46.g18392' => 'ugi', 'unitig_52.g17178' => 'ugi', 'unitig_8.g2934' => 'ugi', 'vmacro01122' => 'vma', 'vmacro05875' => 'vma', 'vmacro06147' => 'vma', 'vmacro16191' => 'vma', 'vmacro18293' => 'vma', 'VMungo0251G3707' => 'vmu', 'VMungo0464G1521' => 'vmu', 'VMungo1215G0205' => 'vmu', 'VMungo1383G2484' => 'vmu', 'Zm00001eb079610' => 'zma', 'Zm00001eb135990' => 'zma', 'Zm00001eb183710' => 'zma', 'Zm00001eb246020' => 'zma' ), 'gf_id' => 'HOM05D001124', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001124' ), 'data_identifier' => 'HOM05D001124', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001124', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '548', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02520' => 'bna', 'A03p06630' => 'bna', 'A05p44460' => 'bna', 'A06p08710' => 'bna', 'A06p41090' => 'bna', 'A07p32320' => 'bna', 'A08p32520' => 'bna', 'A09p10360' => 'bna', 'A10p24080' => 'bna', 'Aa31LG11G15250' => 'aar', 'Aa31LG1G1800' => 'aar', 'Aa31LG2G5120' => 'aar', 'Aa31LG2G6070' => 'aar', 'Aa31LG5G10770' => 'aar', 'Aa31sc61G90' => 'aar', 'Actinidia01352' => 'ach', 'Actinidia05983' => 'ach', 'Actinidia08133' => 'ach', 'Actinidia15101' => 'ach', 'Actinidia26379' => 'ach', 'Actinidia35778' => 'ach', 'Actinidia36123' => 'ach', 'Actinidia37436' => 'ach', 'Actinidia38730' => 'ach', 'Ah.02g128210' => 'amhyb', 'Ah.03g132990' => 'amhyb', 'Ah.14g079410' => 'amhyb', 'AL1G24640' => 'aly', 'AL2G26680' => 'aly', 'AL3G10530' => 'aly', 'AL3G45230' => 'aly', 'AL5G15230' => 'aly', 'AL5G16960' => 'aly', 'AL6G25210' => 'aly', 'Aqoxy2G00441' => 'aox', 'Aqoxy3G01236' => 'aox', 'Aqoxy5G03746' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3RQ047' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C7GMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9C8JER' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MBL6KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YXCZ83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZANX40' => 'arhy', 'AT1G12990' => 'ath', 'AT1G67880' => 'ath', 'AT2G13290' => 'ath', 'AT3G01620' => 'ath', 'AT3G26445' => 'ath', 'AT3G27540' => 'ath', 'AT5G14480' => 'ath', 'ATR0824G026' => 'atr', 'ATR1098G019' => 'atr', 'Atru.chr11.2145' => 'acertr', 'Atru.chr2.3636' => 'acertr', 'Atru.chr2.3644' => 'acertr', 'Atru.chr6.2422' => 'acertr', 'Atru.chr7.1112' => 'acertr', 'AUR62005469' => 'cqu', 'AUR62011166' => 'cqu', 'AUR62013319' => 'cqu', 'AUR62024273' => 'cqu', 'AUR62028420' => 'cqu', 'AUR62041942' => 'cqu', 'BcaB01g04969' => 'bca', 'BcaB01g06371' => 'bca', 'BcaB02g11494' => 'bca', 'BcaB03g15382' => 'bca', 'BcaB08g36994' => 'bca', 'BcaC03g13477' => 'bca', 'BcaC03g13478' => 'bca', 'BcaC03g13480' => 'bca', 'BcaC03g13481' => 'bca', 'BcaC03g13486' => 'bca', 'BcaC04g19031' => 'bca', 'BcaC04g23085' => 'bca', 'BcaC05g25094' => 'bca', 'BcaC05g25096' => 'bca', 'BcaC05g25138' => 'bca', 'BcaC05g30416' => 'bca', 'BcaC05g30455' => 'bca', 'BcaC06g30979' => 'bca', 'BcaC06g33805' => 'bca', 'BcaC08g46021' => 'bca', 'BcaNung03154' => 'bca', 'BolC2t06623H' => 'bol', 'BolC2t06632H' => 'bol', 'BolC2t06635H' => 'bol', 'BolC2t06638H' => 'bol', 'BolC3t13266H' => 'bol', 'BolC5t29776H' => 'bol', 'BolC6t38912H' => 'bol', 'BolC7t44183H' => 'bol', 'BolC9t54123H' => 'bol', 'BolC9t59107H' => 'bol', 'BraA02t05221Z' => 'bra', 'BraA03t09996Z' => 'bra', 'BraA05t23210Z' => 'bra', 'BraA06t24068Z' => 'bra', 'BraA06t27032Z' => 'bra', 'BraA08t35176Z' => 'bra', 'BraA09t36680Z' => 'bra', 'BraA10t44471Z' => 'bra', 'C02p06760' => 'bna', 'C02p06890' => 'bna', 'C02p07010' => 'bna', 'C03p07660' => 'bna', 'C05p10300' => 'bna', 'C06p38150' => 'bna', 'C07p36650' => 'bna', 'C08p15770' => 'bna', 'C09p12300' => 'bna', 'C09p62700' => 'bna', 'C09p75040' => 'bna', 'CAN.G13.1' => 'can', 'CAN.G138.4' => 'can', 'CAN.G44.6' => 'can', 'CAN.G473.19' => 'can', 'CANSAT01G0835' => 'cansat', 'CANSAT11G0246' => 'cansat', 'CANSAT11G1766' => 'cansat', 'CANSAT64G1954' => 'cansat', 'CARHR013330' => 'chi', 'CARHR060530' => 'chi', 'CARHR075300' => 'chi', 'CARHR105120' => 'chi', 'CARHR148910' => 'chi', 'CARHR198830' => 'chi', 'Carub.0001s1275' => 'cru', 'Carub.0002s1437' => 'cru', 'Carub.0003s0044' => 'cru', 'Carub.0003s2787' => 'cru', 'Carub.0005s0597' => 'cru', 'Carub.0006s1266' => 'cru', 'Ca_06935_v3' => 'car', 'Ca_13559_v3' => 'car', 'Ca_16941_v3' => 'car', 'Ca_16960_v3' => 'car', 'Ca_17775_v3' => 'car', 'Ca_30464_v3' => 'car', 'Cc06_g08160' => 'ccan', 'Cc07_g01520' => 'ccan', 'Cc11_g15810' => 'ccan', 'CDE02G2840' => 'cde', 'CDE03G0093' => 'cde', 'CDE04G2127' => 'cde', 'CDE07G1857' => 'cde', 'CDE09G1246' => 'cde', 'Cfa003412' => 'cfa', 'Cfa007341' => 'cfa', 'Cfa009220' => 'cfa', 'Ciclev10008737m.g' => 'ccl', 'Ciclev10015565m.g' => 'ccl', 'Ciclev10031761m.g' => 'ccl', 'CiPaw.03G045300' => 'cil', 'CiPaw.03G247200' => 'cil', 'CiPaw.04G029500' => 'cil', 'CiPaw.04G174000' => 'cil', 'CiPaw.05G181200' => 'cil', 'CiPaw.06G067100' => 'cil', 'ClCG05G025800' => 'cla', 'ClCG06G011400' => 'cla', 'ClCG09G019360' => 'cla', 'COL.COLO4_04827' => 'col', 'COL.COLO4_29170' => 'col', 'COL.COLO4_35131' => 'col', 'COL.COLO4_35132' => 'col', 'Cpa.g.sc33.32' => 'cpa', 'Cpa.g.sc46.29' => 'cpa', 'Cpa.g.sc796.1' => 'cpa', 'CsaV3_1G030420' => 'csa', 'CsaV3_5G027050' => 'csa', 'CsaV3_5G031040' => 'csa', 'CsaV3_UNG023130' => 'csa', 'CSS0007726' => 'camsi', 'CSS0016433' => 'camsi', 'CSS0017656' => 'camsi', 'CSS0025364' => 'camsi', 'CSS0027582' => 'camsi', 'CSS0047288' => 'camsi', 'CSS0049950' => 'camsi', 'DCAR_003843' => 'dca', 'DCAR_007052' => 'dca', 'DCAR_020884' => 'dca', 'DCAR_021730' => 'dca', 'DCAR_024423' => 'dca', 'DCAR_026509' => 'dca', 'DCAR_031158' => 'dca', 'Dinv14728' => 'din', 'Dinv15219' => 'din', 'Dinv25728' => 'din', 'Dinv33428' => 'din', 'Dinv36489' => 'din', 'Dinv41486' => 'din', 'Duzib147G0469' => 'dzi', 'Duzib168G0060' => 'dzi', 'Duzib187G1215' => 'dzi', 'Duzib248G0692' => 'dzi', 'Duzib251G0767' => 'dzi', 'Duzib264G0446' => 'dzi', 'Duzib268G0691' => 'dzi', 'ECA232G4767' => 'eca', 'ECA233G2838' => 'eca', 'ECA234G0391' => 'eca', 'ECA234G0857' => 'eca', 'ECA236G1593' => 'eca', 'ECA238G0565' => 'eca', 'ECA246G1027' => 'eca', 'ECA246G3223' => 'eca', 'ECA246G3470' => 'eca', 'EL10Ac6g13829' => 'bvu', 'EL10Ac6g14093' => 'bvu', 'EL10Ac8g18707' => 'bvu', 'Eucgr.C01369' => 'egr', 'Eucgr.H02492' => 'egr', 'Eucgr.I01733' => 'egr', 'Eucgr.J02255' => 'egr', 'Eucgr.J02257' => 'egr', 'Eucgr.J02258' => 'egr', 'FAN02G1601' => 'fan', 'FAN03G1586' => 'fan', 'FAN03G2986' => 'fan', 'FAN05G4837' => 'fan', 'FAN06G0146' => 'fan', 'FAN07G0858' => 'fan', 'FAN09G3179' => 'fan', 'FAN10G0669' => 'fan', 'FAN12G2358' => 'fan', 'FAN14G4198' => 'fan', 'FAN14G5112' => 'fan', 'FAN17G0342' => 'fan', 'FAN19G0342' => 'fan', 'FAN19G0962' => 'fan', 'FAN19G1101' => 'fan', 'FAN19G1872' => 'fan', 'FAN22G0356' => 'fan', 'FAN23G0744' => 'fan', 'FAN23G1914' => 'fan', 'FAN26G0032' => 'fan', 'FAN28G0625' => 'fan', 'FvH4_1g02710' => 'fve', 'FvH4_1g02720' => 'fve', 'FvH4_4g25670' => 'fve', 'FvH4_6g51700' => 'fve', 'FvH4_7g20170' => 'fve', 'Glyma.05G175000' => 'gma', 'Glyma.08G132300' => 'gma', 'Glyma.11G243000' => 'gma', 'Glyma.13G158900' => 'gma', 'Glyma.17G112400' => 'gma', 'Glyma.18G014100' => 'gma', 'Glyma.19G003100' => 'gma', 'Glyma.19G056500' => 'gma', 'Gohir.A01G158900' => 'ghi', 'Gohir.A05G312600' => 'ghi', 'Gohir.A05G354900' => 'ghi', 'Gohir.A07G037200' => 'ghi', 'Gohir.A09G030000' => 'ghi', 'Gohir.A12G145200' => 'ghi', 'Gohir.D01G151500' => 'ghi', 'Gohir.D04G058300' => 'ghi', 'Gohir.D05G314100' => 'ghi', 'Gohir.D07G041400' => 'ghi', 'Gohir.D09G029700' => 'ghi', 'Gohir.D12G149700' => 'ghi', 'Gorai.001G043800' => 'gra', 'Gorai.002G187800' => 'gra', 'Gorai.006G034700' => 'gra', 'Gorai.008G161200' => 'gra', 'Gorai.009G335700' => 'gra', 'Gorai.012G065000' => 'gra', 'GSVIVG01000535001' => 'vvi', 'GSVIVG01015572001' => 'vvi', 'GSVIVG01032386001' => 'vvi', 'HanXRQChr05g0138531' => 'han', 'HanXRQChr06g0174391' => 'han', 'HanXRQChr07g0199021' => 'han', 'HanXRQChr08g0208211' => 'han', 'HanXRQChr09g0255471' => 'han', 'HanXRQChr10g0315791' => 'han', 'HanXRQChr12g0371991' => 'han', 'HanXRQChr15g0475251' => 'han', 'HanXRQChr17g0540001' => 'han', 'HanXRQChr17g0548631' => 'han', 'HanXRQChr17g0569561' => 'han', 'Haze_12256' => 'cav', 'Haze_14756' => 'cav', 'Haze_25528' => 'cav', 'Hma1.2p1_0079F.1_g041020' => 'hma', 'Hma1.2p1_0818F.1_g223260' => 'hma', 'Hma1.2p1_1747F.1_g300530' => 'hma', 'HPP92_004607' => 'vpl', 'HPP92_004608' => 'vpl', 'HPP92_006181' => 'vpl', 'HPP92_012192' => 'vpl', 'HPP92_015680' => 'vpl', 'HPP92_020249' => 'vpl', 'HPP92_021376' => 'vpl', 'HPP92_024275' => 'vpl', 'Hund06031' => 'sun', 'Hund25391' => 'sun', 'Lalb_Chr07g0185371' => 'lal', 'Lalb_Chr07g0185381' => 'lal', 'Lalb_Chr12g0204011' => 'lal', 'Lalb_Chr13g0301671' => 'lal', 'Lalb_Chr14g0362851' => 'lal', 'Lalb_Chr24g0403581' => 'lal', 'Lj1g0000233' => 'lja', 'Lj2g0018120' => 'lja', 'Lj3C621T0' => 'lonja', 'Lj3P1059T14' => 'lonja', 'Lj3P611T9' => 'lonja', 'Lj3P614T13' => 'lonja', 'Lj3P615T5' => 'lonja', 'Lj4g0012315' => 'lja', 'Lj4g0026182' => 'lja', 'Lj6P813T16' => 'lonja', 'Lj7C427T7' => 'lonja', 'Lj7C427T8' => 'lonja', 'Lj7P600T41' => 'lonja', 'Lju41C42G17' => 'lonja', 'Lsat_1_v5_gn_0_47300' => 'lsa', 'Lsat_1_v5_gn_2_91280' => 'lsa', 'Lsat_1_v5_gn_3_30561' => 'lsa', 'Lsat_1_v5_gn_4_184321' => 'lsa', 'Lsat_1_v5_gn_4_4041' => 'lsa', 'Lsat_1_v5_gn_5_92000' => 'lsa', 'Lsat_1_v5_gn_8_152940' => 'lsa', 'Lsat_1_v5_gn_8_62401' => 'lsa', 'Manes.06G055900' => 'mes', 'Manes.12G022200' => 'mes', 'Manes.13G023300' => 'mes', 'Manes.14G115000' => 'mes', 'Manes.15G151700' => 'mes', 'Manes.17G111300' => 'mes', 'Mapoly0226s0009' => 'mpo', 'MBI02_g25363_MAGBIO' => 'mbi', 'MBI06_g00027_MAGBIO' => 'mbi', 'MBI10_g13034_MAGBIO' => 'mbi', 'MD09G1023400' => 'mdo', 'MD13G1100100' => 'mdo', 'MD15G1169200' => 'mdo', 'MD16G1101100' => 'mdo', 'MD17G1022900' => 'mdo', 'Medtr3g096150' => 'mtr', 'Medtr4g115070' => 'mtr', 'Medtr7g033325' => 'mtr', 'Medtr8g089840' => 'mtr', 'MELO3C010319.2' => 'cme', 'MELO3C011944.2' => 'cme', 'MELO3C021589.2' => 'cme', 'Migut.E00207' => 'egut', 'Migut.H00067' => 'egut', 'Migut.K00433' => 'egut', 'Migut.K00606' => 'egut', 'Migut.K01410' => 'egut', 'MSTRG.13347' => 'ama', 'MSTRG.24045' => 'ama', 'MSTRG.2428' => 'ama', 'MSTRG.26410' => 'ama', 'MSTRG.3139' => 'ama', 'MSTRG.3286' => 'ama', 'MSTRG.563' => 'ama', 'MSTRG.7941' => 'ama', 'Nitab4.5_0000028g0060' => 'nta', 'Nitab4.5_0000065g0260' => 'nta', 'Nitab4.5_0000112g0060' => 'nta', 'Nitab4.5_0000489g0120' => 'nta', 'Nitab4.5_0001776g0050' => 'nta', 'Nitab4.5_0001854g0010' => 'nta', 'Nitab4.5_0001860g0020' => 'nta', 'Nitab4.5_0004352g0010' => 'nta', 'Nitab4.5_0008716g0020' => 'nta', 'Nitab4.5_0008922g0010' => 'nta', 'Nn3g16693' => 'nnu', 'Nn4g22596' => 'nnu', 'Nn7g37639' => 'nnu', 'Oeu001701.1' => 'oeu', 'Oeu018149.1' => 'oeu', 'Oeu026220.1' => 'oeu', 'Oeu038635.1' => 'oeu', 'Oeu049176.1' => 'oeu', 'Oeu056706.1' => 'oeu', 'Oeu056937.1' => 'oeu', 'Oeu057540.1' => 'oeu', 'Os02g0594900' => 'osa', 'Os02g0595100' => 'osa', 'Os04g0477500' => 'osa', 'Os12g0611900' => 'osa', 'Peaxi162Scf00076g00020' => 'pax', 'Peaxi162Scf00128g00217' => 'pax', 'Peaxi162Scf00129g01640' => 'pax', 'Peaxi162Scf00669g00007' => 'pax', 'Peaxi162Scf00700g00421' => 'pax', 'Peaxi162Scf00801g00038' => 'pax', 'Peaxi162Scf00891g00025' => 'pax', 'PGR083G0909' => 'pgr', 'PGR119G1005' => 'pgr', 'PGR142G2236' => 'pgr', 'PGR142G3388' => 'pgr', 'PGSC0003DMG400004514' => 'stu', 'PGSC0003DMG400012635' => 'stu', 'PGSC0003DMG400015730' => 'stu', 'PGSC0003DMG400018611' => 'stu', 'PGSC0003DMG400030897' => 'stu', 'Phvul.001G254800' => 'pvu', 'Phvul.002G260100' => 'pvu', 'Phvul.003G167600' => 'pvu', 'Phvul.004G005100' => 'pvu', 'Potri.001G343600' => 'ptr', 'Potri.006G066700' => 'ptr', 'Potri.008G186000' => 'ptr', 'Potri.010G046900' => 'ptr', 'Potri.018G127900' => 'ptr', 'Pp3c20_17750' => 'ppa', 'Pp3c24_4380' => 'ppa', 'Prupe.1G245800' => 'ppe', 'Prupe.3G293400' => 'ppe', 'Prupe.7G247400' => 'ppe', 'Psat0s145g0120' => 'psa', 'Psat0s595g0040' => 'psa', 'Psat0s595g0120' => 'psa', 'Psat3g175040' => 'psa', 'Psat7g058120' => 'psa', 'PSO017G0428' => 'pso', 'PSO063G7510' => 'pso', 'PSO067G0046' => 'pso', 'PSO478G1073' => 'pso', 'PSO675G3677' => 'pso', 'PSO675G6558' => 'pso', 'PSO675G7520' => 'pso', 'PSO675G8959' => 'pso', 'QL02p074089' => 'qlo', 'QL02p089614' => 'qlo', 'QL03p057736' => 'qlo', 'RcHm_v2.0_Chr1g0364131' => 'rch', 'RcHm_v2.0_Chr2g0087801' => 'rch', 'RcHm_v2.0_Chr2g0087821' => 'rch', 'RcHm_v2.0_Chr2g0173231' => 'rch', 'RcHm_v2.0_Chr4g0433111' => 'rch', 'Rhsim03G0250300' => 'rsi', 'Rhsim08G0048400' => 'rsi', 'Rhsim10G0014800' => 'rsi', 'Rhsim12G0040100' => 'rsi', 'Rhsim12G0109700' => 'rsi', 'Sabra06G0049600' => 'sbr', 'Sabra08G0141000' => 'sbr', 'Sabra10G0021400' => 'sbr', 'Sabra16G0222900' => 'sbr', 'Sabra18G0108600' => 'sbr', 'SalBow1G0433' => 'sbo', 'SalBow1G2038' => 'sbo', 'SalBow1G5003' => 'sbo', 'SalBow7G1197' => 'sbo', 'SalBow8G3506' => 'sbo', 'Sc03g0007300' => 'sci', 'Sc11g0000950' => 'sci', 'Sc14g0008750' => 'sci', 'Sc18g0000420' => 'sci', 'Sed0006754' => 'sed', 'Sed0008741' => 'sed', 'Sed0017172' => 'sed', 'Sed0018925' => 'sed', 'Sed0023326' => 'sed', 'Sed0025909' => 'sed', 'SEGI_05333' => 'sgi', 'SEGI_10362' => 'sgi', 'SEGI_13380' => 'sgi', 'SEGI_24306' => 'sgi', 'SEGI_29077' => 'sgi', 'SEGI_29095' => 'sgi', 'SEGI_36534' => 'sgi', 'SEGI_37506' => 'sgi', 'SEGI_38321' => 'sgi', 'SGA_v2.0_scaffold307G48031' => 'sas', 'SGA_v2.0_scaffold47G17507' => 'sas', 'SGA_v2.0_scaffold63G21736' => 'sas', 'SGA_v2.0_scaffold87G27070' => 'sas', 'SHI17794' => 'shi', 'SHI28851' => 'shi', 'SMO165G0155' => 'smo', 'SMO340G0217' => 'smo', 'SMO367G1210' => 'smo', 'Solyc02g093430.3' => 'sly', 'Solyc05g013580.4' => 'sly', 'Solyc07g008030.3' => 'sly', 'Solyc12g035470.2' => 'sly', 'Sopen02g038020' => 'spe', 'Sopen05g008490' => 'spe', 'Sopen07g003910' => 'spe', 'Sopen12g015240' => 'spe', 'Sp1g11550' => 'spa', 'Sp2g16710' => 'spa', 'Sp3g00430' => 'spa', 'Sp3g26780' => 'spa', 'Sp5g22900' => 'spa', 'Sp6g29530' => 'spa', 'TAR371G0794' => 'tar', 'TAR374G0164' => 'tar', 'TAR622G0165' => 'tar', 'TAR626G0929' => 'tar', 'TAR629G2155' => 'tar', 'THA.LOC104805282' => 'tha', 'THA.LOC104805363' => 'tha', 'THA.LOC104808968' => 'tha', 'THA.LOC104821093' => 'tha', 'THA.LOC104823953' => 'tha', 'THA.LOC104825562' => 'tha', 'THA.LOC104825665' => 'tha', 'Thecc.02G261400' => 'tca', 'Thecc.04G019200' => 'tca', 'Thecc.09G130400' => 'tca', 'Thhalv10004374m.g' => 'esa', 'Thhalv10007850m.g' => 'esa', 'Thhalv10013782m.g' => 'esa', 'Thhalv10018686m.g' => 'esa', 'Thhalv10020899m.g' => 'esa', 'Thhalv10022755m.g' => 'esa', 'TPR.G23851' => 'tpr', 'TPR.G26500' => 'tpr', 'TPR.G27267' => 'tpr', 'TPR.G32001' => 'tpr', 'TPR.G6251' => 'tpr', 'TPR.G8167' => 'tpr', 'TWI12G1330' => 'twi', 'TWI18G1239' => 'twi', 'TWI34G0979' => 'twi', 'TWI36G0670' => 'twi', 'TWI36G0707' => 'twi', 'TWI56G0233' => 'twi', 'TWI75G1809' => 'twi', 'unitig_21.g20874' => 'ugi', 'unitig_26.g10343' => 'ugi', 'unitig_46.g18392' => 'ugi', 'unitig_52.g17178' => 'ugi', 'unitig_8.g2934' => 'ugi', 'vmacro01122' => 'vma', 'vmacro05875' => 'vma', 'vmacro06147' => 'vma', 'vmacro16191' => 'vma', 'vmacro18293' => 'vma', 'VMungo0251G3707' => 'vmu', 'VMungo0464G1521' => 'vmu', 'VMungo1215G0205' => 'vmu', 'VMungo1383G2484' => 'vmu', 'Zm00001eb079610' => 'zma', 'Zm00001eb135990' => 'zma', 'Zm00001eb183710' => 'zma', 'Zm00001eb246020' => 'zma' ) $gf_id = 'HOM05D001124' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001124' ) $data_identifier = 'HOM05D001124' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 6, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 7, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 21, 'bol' => (int) 10, 'bra' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 6, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 9, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 21, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 8, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 10, 'lsa' => (int) 8, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 8, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 9, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb246020' $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' => 'HOM05D001124', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '548', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02520' => 'bna', 'A03p06630' => 'bna', 'A05p44460' => 'bna', 'A06p08710' => 'bna', 'A06p41090' => 'bna', 'A07p32320' => 'bna', 'A08p32520' => 'bna', 'A09p10360' => 'bna', 'A10p24080' => 'bna', 'Aa31LG11G15250' => 'aar', 'Aa31LG1G1800' => 'aar', 'Aa31LG2G5120' => 'aar', 'Aa31LG2G6070' => 'aar', 'Aa31LG5G10770' => 'aar', 'Aa31sc61G90' => 'aar', 'Actinidia01352' => 'ach', 'Actinidia05983' => 'ach', 'Actinidia08133' => 'ach', 'Actinidia15101' => 'ach', 'Actinidia26379' => 'ach', 'Actinidia35778' => 'ach', 'Actinidia36123' => 'ach', 'Actinidia37436' => 'ach', 'Actinidia38730' => 'ach', 'Ah.02g128210' => 'amhyb', 'Ah.03g132990' => 'amhyb', 'Ah.14g079410' => 'amhyb', 'AL1G24640' => 'aly', 'AL2G26680' => 'aly', 'AL3G10530' => 'aly', 'AL3G45230' => 'aly', 'AL5G15230' => 'aly', 'AL5G16960' => 'aly', 'AL6G25210' => 'aly', 'Aqoxy2G00441' => 'aox', 'Aqoxy3G01236' => 'aox', 'Aqoxy5G03746' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3RQ047' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C7GMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9C8JER' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MBL6KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YXCZ83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZANX40' => 'arhy', 'AT1G12990' => 'ath', 'AT1G67880' => 'ath', 'AT2G13290' => 'ath', 'AT3G01620' => 'ath', 'AT3G26445' => 'ath', 'AT3G27540' => 'ath', 'AT5G14480' => 'ath', 'ATR0824G026' => 'atr', 'ATR1098G019' => 'atr', 'Atru.chr11.2145' => 'acertr', 'Atru.chr2.3636' => 'acertr', 'Atru.chr2.3644' => 'acertr', 'Atru.chr6.2422' => 'acertr', 'Atru.chr7.1112' => 'acertr', 'AUR62005469' => 'cqu', 'AUR62011166' => 'cqu', 'AUR62013319' => 'cqu', 'AUR62024273' => 'cqu', 'AUR62028420' => 'cqu', 'AUR62041942' => 'cqu', 'BcaB01g04969' => 'bca', 'BcaB01g06371' => 'bca', 'BcaB02g11494' => 'bca', 'BcaB03g15382' => 'bca', 'BcaB08g36994' => 'bca', 'BcaC03g13477' => 'bca', 'BcaC03g13478' => 'bca', 'BcaC03g13480' => 'bca', 'BcaC03g13481' => 'bca', 'BcaC03g13486' => 'bca', 'BcaC04g19031' => 'bca', 'BcaC04g23085' => 'bca', 'BcaC05g25094' => 'bca', 'BcaC05g25096' => 'bca', 'BcaC05g25138' => 'bca', 'BcaC05g30416' => 'bca', 'BcaC05g30455' => 'bca', 'BcaC06g30979' => 'bca', 'BcaC06g33805' => 'bca', 'BcaC08g46021' => 'bca', 'BcaNung03154' => 'bca', 'BolC2t06623H' => 'bol', 'BolC2t06632H' => 'bol', 'BolC2t06635H' => 'bol', 'BolC2t06638H' => 'bol', 'BolC3t13266H' => 'bol', 'BolC5t29776H' => 'bol', 'BolC6t38912H' => 'bol', 'BolC7t44183H' => 'bol', 'BolC9t54123H' => 'bol', 'BolC9t59107H' => 'bol', 'BraA02t05221Z' => 'bra', 'BraA03t09996Z' => 'bra', 'BraA05t23210Z' => 'bra', 'BraA06t24068Z' => 'bra', 'BraA06t27032Z' => 'bra', 'BraA08t35176Z' => 'bra', 'BraA09t36680Z' => 'bra', 'BraA10t44471Z' => 'bra', 'C02p06760' => 'bna', 'C02p06890' => 'bna', 'C02p07010' => 'bna', 'C03p07660' => 'bna', 'C05p10300' => 'bna', 'C06p38150' => 'bna', 'C07p36650' => 'bna', 'C08p15770' => 'bna', 'C09p12300' => 'bna', 'C09p62700' => 'bna', 'C09p75040' => 'bna', 'CAN.G13.1' => 'can', 'CAN.G138.4' => 'can', 'CAN.G44.6' => 'can', 'CAN.G473.19' => 'can', 'CANSAT01G0835' => 'cansat', 'CANSAT11G0246' => 'cansat', 'CANSAT11G1766' => 'cansat', 'CANSAT64G1954' => 'cansat', 'CARHR013330' => 'chi', 'CARHR060530' => 'chi', 'CARHR075300' => 'chi', 'CARHR105120' => 'chi', 'CARHR148910' => 'chi', 'CARHR198830' => 'chi', 'Carub.0001s1275' => 'cru', 'Carub.0002s1437' => 'cru', 'Carub.0003s0044' => 'cru', 'Carub.0003s2787' => 'cru', 'Carub.0005s0597' => 'cru', 'Carub.0006s1266' => 'cru', 'Ca_06935_v3' => 'car', 'Ca_13559_v3' => 'car', 'Ca_16941_v3' => 'car', 'Ca_16960_v3' => 'car', 'Ca_17775_v3' => 'car', 'Ca_30464_v3' => 'car', 'Cc06_g08160' => 'ccan', 'Cc07_g01520' => 'ccan', 'Cc11_g15810' => 'ccan', 'CDE02G2840' => 'cde', 'CDE03G0093' => 'cde', 'CDE04G2127' => 'cde', 'CDE07G1857' => 'cde', 'CDE09G1246' => 'cde', 'Cfa003412' => 'cfa', 'Cfa007341' => 'cfa', 'Cfa009220' => 'cfa', 'Ciclev10008737m.g' => 'ccl', 'Ciclev10015565m.g' => 'ccl', 'Ciclev10031761m.g' => 'ccl', 'CiPaw.03G045300' => 'cil', 'CiPaw.03G247200' => 'cil', 'CiPaw.04G029500' => 'cil', 'CiPaw.04G174000' => 'cil', 'CiPaw.05G181200' => 'cil', 'CiPaw.06G067100' => 'cil', 'ClCG05G025800' => 'cla', 'ClCG06G011400' => 'cla', 'ClCG09G019360' => 'cla', 'COL.COLO4_04827' => 'col', 'COL.COLO4_29170' => 'col', 'COL.COLO4_35131' => 'col', 'COL.COLO4_35132' => 'col', 'Cpa.g.sc33.32' => 'cpa', 'Cpa.g.sc46.29' => 'cpa', 'Cpa.g.sc796.1' => 'cpa', 'CsaV3_1G030420' => 'csa', 'CsaV3_5G027050' => 'csa', 'CsaV3_5G031040' => 'csa', 'CsaV3_UNG023130' => 'csa', 'CSS0007726' => 'camsi', 'CSS0016433' => 'camsi', 'CSS0017656' => 'camsi', 'CSS0025364' => 'camsi', 'CSS0027582' => 'camsi', 'CSS0047288' => 'camsi', 'CSS0049950' => 'camsi', 'DCAR_003843' => 'dca', 'DCAR_007052' => 'dca', 'DCAR_020884' => 'dca', 'DCAR_021730' => 'dca', 'DCAR_024423' => 'dca', 'DCAR_026509' => 'dca', 'DCAR_031158' => 'dca', 'Dinv14728' => 'din', 'Dinv15219' => 'din', 'Dinv25728' => 'din', 'Dinv33428' => 'din', 'Dinv36489' => 'din', 'Dinv41486' => 'din', 'Duzib147G0469' => 'dzi', 'Duzib168G0060' => 'dzi', 'Duzib187G1215' => 'dzi', 'Duzib248G0692' => 'dzi', 'Duzib251G0767' => 'dzi', 'Duzib264G0446' => 'dzi', 'Duzib268G0691' => 'dzi', 'ECA232G4767' => 'eca', 'ECA233G2838' => 'eca', 'ECA234G0391' => 'eca', 'ECA234G0857' => 'eca', 'ECA236G1593' => 'eca', 'ECA238G0565' => 'eca', 'ECA246G1027' => 'eca', 'ECA246G3223' => 'eca', 'ECA246G3470' => 'eca', 'EL10Ac6g13829' => 'bvu', 'EL10Ac6g14093' => 'bvu', 'EL10Ac8g18707' => 'bvu', 'Eucgr.C01369' => 'egr', 'Eucgr.H02492' => 'egr', 'Eucgr.I01733' => 'egr', 'Eucgr.J02255' => 'egr', 'Eucgr.J02257' => 'egr', 'Eucgr.J02258' => 'egr', 'FAN02G1601' => 'fan', 'FAN03G1586' => 'fan', 'FAN03G2986' => 'fan', 'FAN05G4837' => 'fan', 'FAN06G0146' => 'fan', 'FAN07G0858' => 'fan', 'FAN09G3179' => 'fan', 'FAN10G0669' => 'fan', 'FAN12G2358' => 'fan', 'FAN14G4198' => 'fan', 'FAN14G5112' => 'fan', 'FAN17G0342' => 'fan', 'FAN19G0342' => 'fan', 'FAN19G0962' => 'fan', 'FAN19G1101' => 'fan', 'FAN19G1872' => 'fan', 'FAN22G0356' => 'fan', 'FAN23G0744' => 'fan', 'FAN23G1914' => 'fan', 'FAN26G0032' => 'fan', 'FAN28G0625' => 'fan', 'FvH4_1g02710' => 'fve', 'FvH4_1g02720' => 'fve', 'FvH4_4g25670' => 'fve', 'FvH4_6g51700' => 'fve', 'FvH4_7g20170' => 'fve', 'Glyma.05G175000' => 'gma', 'Glyma.08G132300' => 'gma', 'Glyma.11G243000' => 'gma', 'Glyma.13G158900' => 'gma', 'Glyma.17G112400' => 'gma', 'Glyma.18G014100' => 'gma', 'Glyma.19G003100' => 'gma', 'Glyma.19G056500' => 'gma', 'Gohir.A01G158900' => 'ghi', 'Gohir.A05G312600' => 'ghi', 'Gohir.A05G354900' => 'ghi', 'Gohir.A07G037200' => 'ghi', 'Gohir.A09G030000' => 'ghi', 'Gohir.A12G145200' => 'ghi', 'Gohir.D01G151500' => 'ghi', 'Gohir.D04G058300' => 'ghi', 'Gohir.D05G314100' => 'ghi', 'Gohir.D07G041400' => 'ghi', 'Gohir.D09G029700' => 'ghi', 'Gohir.D12G149700' => 'ghi', 'Gorai.001G043800' => 'gra', 'Gorai.002G187800' => 'gra', 'Gorai.006G034700' => 'gra', 'Gorai.008G161200' => 'gra', 'Gorai.009G335700' => 'gra', 'Gorai.012G065000' => 'gra', 'GSVIVG01000535001' => 'vvi', 'GSVIVG01015572001' => 'vvi', 'GSVIVG01032386001' => 'vvi', 'HanXRQChr05g0138531' => 'han', 'HanXRQChr06g0174391' => 'han', 'HanXRQChr07g0199021' => 'han', 'HanXRQChr08g0208211' => 'han', 'HanXRQChr09g0255471' => 'han', 'HanXRQChr10g0315791' => 'han', 'HanXRQChr12g0371991' => 'han', 'HanXRQChr15g0475251' => 'han', 'HanXRQChr17g0540001' => 'han', 'HanXRQChr17g0548631' => 'han', 'HanXRQChr17g0569561' => 'han', 'Haze_12256' => 'cav', 'Haze_14756' => 'cav', 'Haze_25528' => 'cav', 'Hma1.2p1_0079F.1_g041020' => 'hma', 'Hma1.2p1_0818F.1_g223260' => 'hma', 'Hma1.2p1_1747F.1_g300530' => 'hma', 'HPP92_004607' => 'vpl', 'HPP92_004608' => 'vpl', 'HPP92_006181' => 'vpl', 'HPP92_012192' => 'vpl', 'HPP92_015680' => 'vpl', 'HPP92_020249' => 'vpl', 'HPP92_021376' => 'vpl', 'HPP92_024275' => 'vpl', 'Hund06031' => 'sun', 'Hund25391' => 'sun', 'Lalb_Chr07g0185371' => 'lal', 'Lalb_Chr07g0185381' => 'lal', 'Lalb_Chr12g0204011' => 'lal', 'Lalb_Chr13g0301671' => 'lal', 'Lalb_Chr14g0362851' => 'lal', 'Lalb_Chr24g0403581' => 'lal', 'Lj1g0000233' => 'lja', 'Lj2g0018120' => 'lja', 'Lj3C621T0' => 'lonja', 'Lj3P1059T14' => 'lonja', 'Lj3P611T9' => 'lonja', 'Lj3P614T13' => 'lonja', 'Lj3P615T5' => 'lonja', 'Lj4g0012315' => 'lja', 'Lj4g0026182' => 'lja', 'Lj6P813T16' => 'lonja', 'Lj7C427T7' => 'lonja', 'Lj7C427T8' => 'lonja', 'Lj7P600T41' => 'lonja', 'Lju41C42G17' => 'lonja', 'Lsat_1_v5_gn_0_47300' => 'lsa', 'Lsat_1_v5_gn_2_91280' => 'lsa', 'Lsat_1_v5_gn_3_30561' => 'lsa', 'Lsat_1_v5_gn_4_184321' => 'lsa', 'Lsat_1_v5_gn_4_4041' => 'lsa', 'Lsat_1_v5_gn_5_92000' => 'lsa', 'Lsat_1_v5_gn_8_152940' => 'lsa', 'Lsat_1_v5_gn_8_62401' => 'lsa', 'Manes.06G055900' => 'mes', 'Manes.12G022200' => 'mes', 'Manes.13G023300' => 'mes', 'Manes.14G115000' => 'mes', 'Manes.15G151700' => 'mes', 'Manes.17G111300' => 'mes', 'Mapoly0226s0009' => 'mpo', 'MBI02_g25363_MAGBIO' => 'mbi', 'MBI06_g00027_MAGBIO' => 'mbi', 'MBI10_g13034_MAGBIO' => 'mbi', 'MD09G1023400' => 'mdo', 'MD13G1100100' => 'mdo', 'MD15G1169200' => 'mdo', 'MD16G1101100' => 'mdo', 'MD17G1022900' => 'mdo', 'Medtr3g096150' => 'mtr', 'Medtr4g115070' => 'mtr', 'Medtr7g033325' => 'mtr', 'Medtr8g089840' => 'mtr', 'MELO3C010319.2' => 'cme', 'MELO3C011944.2' => 'cme', 'MELO3C021589.2' => 'cme', 'Migut.E00207' => 'egut', 'Migut.H00067' => 'egut', 'Migut.K00433' => 'egut', 'Migut.K00606' => 'egut', 'Migut.K01410' => 'egut', 'MSTRG.13347' => 'ama', 'MSTRG.24045' => 'ama', 'MSTRG.2428' => 'ama', 'MSTRG.26410' => 'ama', 'MSTRG.3139' => 'ama', 'MSTRG.3286' => 'ama', 'MSTRG.563' => 'ama', 'MSTRG.7941' => 'ama', 'Nitab4.5_0000028g0060' => 'nta', 'Nitab4.5_0000065g0260' => 'nta', 'Nitab4.5_0000112g0060' => 'nta', 'Nitab4.5_0000489g0120' => 'nta', 'Nitab4.5_0001776g0050' => 'nta', 'Nitab4.5_0001854g0010' => 'nta', 'Nitab4.5_0001860g0020' => 'nta', 'Nitab4.5_0004352g0010' => 'nta', 'Nitab4.5_0008716g0020' => 'nta', 'Nitab4.5_0008922g0010' => 'nta', 'Nn3g16693' => 'nnu', 'Nn4g22596' => 'nnu', 'Nn7g37639' => 'nnu', 'Oeu001701.1' => 'oeu', 'Oeu018149.1' => 'oeu', 'Oeu026220.1' => 'oeu', 'Oeu038635.1' => 'oeu', 'Oeu049176.1' => 'oeu', 'Oeu056706.1' => 'oeu', 'Oeu056937.1' => 'oeu', 'Oeu057540.1' => 'oeu', 'Os02g0594900' => 'osa', 'Os02g0595100' => 'osa', 'Os04g0477500' => 'osa', 'Os12g0611900' => 'osa', 'Peaxi162Scf00076g00020' => 'pax', 'Peaxi162Scf00128g00217' => 'pax', 'Peaxi162Scf00129g01640' => 'pax', 'Peaxi162Scf00669g00007' => 'pax', 'Peaxi162Scf00700g00421' => 'pax', 'Peaxi162Scf00801g00038' => 'pax', 'Peaxi162Scf00891g00025' => 'pax', 'PGR083G0909' => 'pgr', 'PGR119G1005' => 'pgr', 'PGR142G2236' => 'pgr', 'PGR142G3388' => 'pgr', 'PGSC0003DMG400004514' => 'stu', 'PGSC0003DMG400012635' => 'stu', 'PGSC0003DMG400015730' => 'stu', 'PGSC0003DMG400018611' => 'stu', 'PGSC0003DMG400030897' => 'stu', 'Phvul.001G254800' => 'pvu', 'Phvul.002G260100' => 'pvu', 'Phvul.003G167600' => 'pvu', 'Phvul.004G005100' => 'pvu', 'Potri.001G343600' => 'ptr', 'Potri.006G066700' => 'ptr', 'Potri.008G186000' => 'ptr', 'Potri.010G046900' => 'ptr', 'Potri.018G127900' => 'ptr', 'Pp3c20_17750' => 'ppa', 'Pp3c24_4380' => 'ppa', 'Prupe.1G245800' => 'ppe', 'Prupe.3G293400' => 'ppe', 'Prupe.7G247400' => 'ppe', 'Psat0s145g0120' => 'psa', 'Psat0s595g0040' => 'psa', 'Psat0s595g0120' => 'psa', 'Psat3g175040' => 'psa', 'Psat7g058120' => 'psa', 'PSO017G0428' => 'pso', 'PSO063G7510' => 'pso', 'PSO067G0046' => 'pso', 'PSO478G1073' => 'pso', 'PSO675G3677' => 'pso', 'PSO675G6558' => 'pso', 'PSO675G7520' => 'pso', 'PSO675G8959' => 'pso', 'QL02p074089' => 'qlo', 'QL02p089614' => 'qlo', 'QL03p057736' => 'qlo', 'RcHm_v2.0_Chr1g0364131' => 'rch', 'RcHm_v2.0_Chr2g0087801' => 'rch', 'RcHm_v2.0_Chr2g0087821' => 'rch', 'RcHm_v2.0_Chr2g0173231' => 'rch', 'RcHm_v2.0_Chr4g0433111' => 'rch', 'Rhsim03G0250300' => 'rsi', 'Rhsim08G0048400' => 'rsi', 'Rhsim10G0014800' => 'rsi', 'Rhsim12G0040100' => 'rsi', 'Rhsim12G0109700' => 'rsi', 'Sabra06G0049600' => 'sbr', 'Sabra08G0141000' => 'sbr', 'Sabra10G0021400' => 'sbr', 'Sabra16G0222900' => 'sbr', 'Sabra18G0108600' => 'sbr', 'SalBow1G0433' => 'sbo', 'SalBow1G2038' => 'sbo', 'SalBow1G5003' => 'sbo', 'SalBow7G1197' => 'sbo', 'SalBow8G3506' => 'sbo', 'Sc03g0007300' => 'sci', 'Sc11g0000950' => 'sci', 'Sc14g0008750' => 'sci', 'Sc18g0000420' => 'sci', 'Sed0006754' => 'sed', 'Sed0008741' => 'sed', 'Sed0017172' => 'sed', 'Sed0018925' => 'sed', 'Sed0023326' => 'sed', 'Sed0025909' => 'sed', 'SEGI_05333' => 'sgi', 'SEGI_10362' => 'sgi', 'SEGI_13380' => 'sgi', 'SEGI_24306' => 'sgi', 'SEGI_29077' => 'sgi', 'SEGI_29095' => 'sgi', 'SEGI_36534' => 'sgi', 'SEGI_37506' => 'sgi', 'SEGI_38321' => 'sgi', 'SGA_v2.0_scaffold307G48031' => 'sas', 'SGA_v2.0_scaffold47G17507' => 'sas', 'SGA_v2.0_scaffold63G21736' => 'sas', 'SGA_v2.0_scaffold87G27070' => 'sas', 'SHI17794' => 'shi', 'SHI28851' => 'shi', 'SMO165G0155' => 'smo', 'SMO340G0217' => 'smo', 'SMO367G1210' => 'smo', 'Solyc02g093430.3' => 'sly', 'Solyc05g013580.4' => 'sly', 'Solyc07g008030.3' => 'sly', 'Solyc12g035470.2' => 'sly', 'Sopen02g038020' => 'spe', 'Sopen05g008490' => 'spe', 'Sopen07g003910' => 'spe', 'Sopen12g015240' => 'spe', 'Sp1g11550' => 'spa', 'Sp2g16710' => 'spa', 'Sp3g00430' => 'spa', 'Sp3g26780' => 'spa', 'Sp5g22900' => 'spa', 'Sp6g29530' => 'spa', 'TAR371G0794' => 'tar', 'TAR374G0164' => 'tar', 'TAR622G0165' => 'tar', 'TAR626G0929' => 'tar', 'TAR629G2155' => 'tar', 'THA.LOC104805282' => 'tha', 'THA.LOC104805363' => 'tha', 'THA.LOC104808968' => 'tha', 'THA.LOC104821093' => 'tha', 'THA.LOC104823953' => 'tha', 'THA.LOC104825562' => 'tha', 'THA.LOC104825665' => 'tha', 'Thecc.02G261400' => 'tca', 'Thecc.04G019200' => 'tca', 'Thecc.09G130400' => 'tca', 'Thhalv10004374m.g' => 'esa', 'Thhalv10007850m.g' => 'esa', 'Thhalv10013782m.g' => 'esa', 'Thhalv10018686m.g' => 'esa', 'Thhalv10020899m.g' => 'esa', 'Thhalv10022755m.g' => 'esa', 'TPR.G23851' => 'tpr', 'TPR.G26500' => 'tpr', 'TPR.G27267' => 'tpr', 'TPR.G32001' => 'tpr', 'TPR.G6251' => 'tpr', 'TPR.G8167' => 'tpr', 'TWI12G1330' => 'twi', 'TWI18G1239' => 'twi', 'TWI34G0979' => 'twi', 'TWI36G0670' => 'twi', 'TWI36G0707' => 'twi', 'TWI56G0233' => 'twi', 'TWI75G1809' => 'twi', 'unitig_21.g20874' => 'ugi', 'unitig_26.g10343' => 'ugi', 'unitig_46.g18392' => 'ugi', 'unitig_52.g17178' => 'ugi', 'unitig_8.g2934' => 'ugi', 'vmacro01122' => 'vma', 'vmacro05875' => 'vma', 'vmacro06147' => 'vma', 'vmacro16191' => 'vma', 'vmacro18293' => 'vma', 'VMungo0251G3707' => 'vmu', 'VMungo0464G1521' => 'vmu', 'VMungo1215G0205' => 'vmu', 'VMungo1383G2484' => 'vmu', 'Zm00001eb079610' => 'zma', 'Zm00001eb135990' => 'zma', 'Zm00001eb183710' => 'zma', 'Zm00001eb246020' => 'zma' ), 'gf_id' => 'HOM05D001124', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001124' ), 'data_identifier' => 'HOM05D001124', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001124', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '548', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02520' => 'bna', 'A03p06630' => 'bna', 'A05p44460' => 'bna', 'A06p08710' => 'bna', 'A06p41090' => 'bna', 'A07p32320' => 'bna', 'A08p32520' => 'bna', 'A09p10360' => 'bna', 'A10p24080' => 'bna', 'Aa31LG11G15250' => 'aar', 'Aa31LG1G1800' => 'aar', 'Aa31LG2G5120' => 'aar', 'Aa31LG2G6070' => 'aar', 'Aa31LG5G10770' => 'aar', 'Aa31sc61G90' => 'aar', 'Actinidia01352' => 'ach', 'Actinidia05983' => 'ach', 'Actinidia08133' => 'ach', 'Actinidia15101' => 'ach', 'Actinidia26379' => 'ach', 'Actinidia35778' => 'ach', 'Actinidia36123' => 'ach', 'Actinidia37436' => 'ach', 'Actinidia38730' => 'ach', 'Ah.02g128210' => 'amhyb', 'Ah.03g132990' => 'amhyb', 'Ah.14g079410' => 'amhyb', 'AL1G24640' => 'aly', 'AL2G26680' => 'aly', 'AL3G10530' => 'aly', 'AL3G45230' => 'aly', 'AL5G15230' => 'aly', 'AL5G16960' => 'aly', 'AL6G25210' => 'aly', 'Aqoxy2G00441' => 'aox', 'Aqoxy3G01236' => 'aox', 'Aqoxy5G03746' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3RQ047' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C7GMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9C8JER' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MBL6KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YXCZ83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZANX40' => 'arhy', 'AT1G12990' => 'ath', 'AT1G67880' => 'ath', 'AT2G13290' => 'ath', 'AT3G01620' => 'ath', 'AT3G26445' => 'ath', 'AT3G27540' => 'ath', 'AT5G14480' => 'ath', 'ATR0824G026' => 'atr', 'ATR1098G019' => 'atr', 'Atru.chr11.2145' => 'acertr', 'Atru.chr2.3636' => 'acertr', 'Atru.chr2.3644' => 'acertr', 'Atru.chr6.2422' => 'acertr', 'Atru.chr7.1112' => 'acertr', 'AUR62005469' => 'cqu', 'AUR62011166' => 'cqu', 'AUR62013319' => 'cqu', 'AUR62024273' => 'cqu', 'AUR62028420' => 'cqu', 'AUR62041942' => 'cqu', 'BcaB01g04969' => 'bca', 'BcaB01g06371' => 'bca', 'BcaB02g11494' => 'bca', 'BcaB03g15382' => 'bca', 'BcaB08g36994' => 'bca', 'BcaC03g13477' => 'bca', 'BcaC03g13478' => 'bca', 'BcaC03g13480' => 'bca', 'BcaC03g13481' => 'bca', 'BcaC03g13486' => 'bca', 'BcaC04g19031' => 'bca', 'BcaC04g23085' => 'bca', 'BcaC05g25094' => 'bca', 'BcaC05g25096' => 'bca', 'BcaC05g25138' => 'bca', 'BcaC05g30416' => 'bca', 'BcaC05g30455' => 'bca', 'BcaC06g30979' => 'bca', 'BcaC06g33805' => 'bca', 'BcaC08g46021' => 'bca', 'BcaNung03154' => 'bca', 'BolC2t06623H' => 'bol', 'BolC2t06632H' => 'bol', 'BolC2t06635H' => 'bol', 'BolC2t06638H' => 'bol', 'BolC3t13266H' => 'bol', 'BolC5t29776H' => 'bol', 'BolC6t38912H' => 'bol', 'BolC7t44183H' => 'bol', 'BolC9t54123H' => 'bol', 'BolC9t59107H' => 'bol', 'BraA02t05221Z' => 'bra', 'BraA03t09996Z' => 'bra', 'BraA05t23210Z' => 'bra', 'BraA06t24068Z' => 'bra', 'BraA06t27032Z' => 'bra', 'BraA08t35176Z' => 'bra', 'BraA09t36680Z' => 'bra', 'BraA10t44471Z' => 'bra', 'C02p06760' => 'bna', 'C02p06890' => 'bna', 'C02p07010' => 'bna', 'C03p07660' => 'bna', 'C05p10300' => 'bna', 'C06p38150' => 'bna', 'C07p36650' => 'bna', 'C08p15770' => 'bna', 'C09p12300' => 'bna', 'C09p62700' => 'bna', 'C09p75040' => 'bna', 'CAN.G13.1' => 'can', 'CAN.G138.4' => 'can', 'CAN.G44.6' => 'can', 'CAN.G473.19' => 'can', 'CANSAT01G0835' => 'cansat', 'CANSAT11G0246' => 'cansat', 'CANSAT11G1766' => 'cansat', 'CANSAT64G1954' => 'cansat', 'CARHR013330' => 'chi', 'CARHR060530' => 'chi', 'CARHR075300' => 'chi', 'CARHR105120' => 'chi', 'CARHR148910' => 'chi', 'CARHR198830' => 'chi', 'Carub.0001s1275' => 'cru', 'Carub.0002s1437' => 'cru', 'Carub.0003s0044' => 'cru', 'Carub.0003s2787' => 'cru', 'Carub.0005s0597' => 'cru', 'Carub.0006s1266' => 'cru', 'Ca_06935_v3' => 'car', 'Ca_13559_v3' => 'car', 'Ca_16941_v3' => 'car', 'Ca_16960_v3' => 'car', 'Ca_17775_v3' => 'car', 'Ca_30464_v3' => 'car', 'Cc06_g08160' => 'ccan', 'Cc07_g01520' => 'ccan', 'Cc11_g15810' => 'ccan', 'CDE02G2840' => 'cde', 'CDE03G0093' => 'cde', 'CDE04G2127' => 'cde', 'CDE07G1857' => 'cde', 'CDE09G1246' => 'cde', 'Cfa003412' => 'cfa', 'Cfa007341' => 'cfa', 'Cfa009220' => 'cfa', 'Ciclev10008737m.g' => 'ccl', 'Ciclev10015565m.g' => 'ccl', 'Ciclev10031761m.g' => 'ccl', 'CiPaw.03G045300' => 'cil', 'CiPaw.03G247200' => 'cil', 'CiPaw.04G029500' => 'cil', 'CiPaw.04G174000' => 'cil', 'CiPaw.05G181200' => 'cil', 'CiPaw.06G067100' => 'cil', 'ClCG05G025800' => 'cla', 'ClCG06G011400' => 'cla', 'ClCG09G019360' => 'cla', 'COL.COLO4_04827' => 'col', 'COL.COLO4_29170' => 'col', 'COL.COLO4_35131' => 'col', 'COL.COLO4_35132' => 'col', 'Cpa.g.sc33.32' => 'cpa', 'Cpa.g.sc46.29' => 'cpa', 'Cpa.g.sc796.1' => 'cpa', 'CsaV3_1G030420' => 'csa', 'CsaV3_5G027050' => 'csa', 'CsaV3_5G031040' => 'csa', 'CsaV3_UNG023130' => 'csa', 'CSS0007726' => 'camsi', 'CSS0016433' => 'camsi', 'CSS0017656' => 'camsi', 'CSS0025364' => 'camsi', 'CSS0027582' => 'camsi', 'CSS0047288' => 'camsi', 'CSS0049950' => 'camsi', 'DCAR_003843' => 'dca', 'DCAR_007052' => 'dca', 'DCAR_020884' => 'dca', 'DCAR_021730' => 'dca', 'DCAR_024423' => 'dca', 'DCAR_026509' => 'dca', 'DCAR_031158' => 'dca', 'Dinv14728' => 'din', 'Dinv15219' => 'din', 'Dinv25728' => 'din', 'Dinv33428' => 'din', 'Dinv36489' => 'din', 'Dinv41486' => 'din', 'Duzib147G0469' => 'dzi', 'Duzib168G0060' => 'dzi', 'Duzib187G1215' => 'dzi', 'Duzib248G0692' => 'dzi', 'Duzib251G0767' => 'dzi', 'Duzib264G0446' => 'dzi', 'Duzib268G0691' => 'dzi', 'ECA232G4767' => 'eca', 'ECA233G2838' => 'eca', 'ECA234G0391' => 'eca', 'ECA234G0857' => 'eca', 'ECA236G1593' => 'eca', 'ECA238G0565' => 'eca', 'ECA246G1027' => 'eca', 'ECA246G3223' => 'eca', 'ECA246G3470' => 'eca', 'EL10Ac6g13829' => 'bvu', 'EL10Ac6g14093' => 'bvu', 'EL10Ac8g18707' => 'bvu', 'Eucgr.C01369' => 'egr', 'Eucgr.H02492' => 'egr', 'Eucgr.I01733' => 'egr', 'Eucgr.J02255' => 'egr', 'Eucgr.J02257' => 'egr', 'Eucgr.J02258' => 'egr', 'FAN02G1601' => 'fan', 'FAN03G1586' => 'fan', 'FAN03G2986' => 'fan', 'FAN05G4837' => 'fan', 'FAN06G0146' => 'fan', 'FAN07G0858' => 'fan', 'FAN09G3179' => 'fan', 'FAN10G0669' => 'fan', 'FAN12G2358' => 'fan', 'FAN14G4198' => 'fan', 'FAN14G5112' => 'fan', 'FAN17G0342' => 'fan', 'FAN19G0342' => 'fan', 'FAN19G0962' => 'fan', 'FAN19G1101' => 'fan', 'FAN19G1872' => 'fan', 'FAN22G0356' => 'fan', 'FAN23G0744' => 'fan', 'FAN23G1914' => 'fan', 'FAN26G0032' => 'fan', 'FAN28G0625' => 'fan', 'FvH4_1g02710' => 'fve', 'FvH4_1g02720' => 'fve', 'FvH4_4g25670' => 'fve', 'FvH4_6g51700' => 'fve', 'FvH4_7g20170' => 'fve', 'Glyma.05G175000' => 'gma', 'Glyma.08G132300' => 'gma', 'Glyma.11G243000' => 'gma', 'Glyma.13G158900' => 'gma', 'Glyma.17G112400' => 'gma', 'Glyma.18G014100' => 'gma', 'Glyma.19G003100' => 'gma', 'Glyma.19G056500' => 'gma', 'Gohir.A01G158900' => 'ghi', 'Gohir.A05G312600' => 'ghi', 'Gohir.A05G354900' => 'ghi', 'Gohir.A07G037200' => 'ghi', 'Gohir.A09G030000' => 'ghi', 'Gohir.A12G145200' => 'ghi', 'Gohir.D01G151500' => 'ghi', 'Gohir.D04G058300' => 'ghi', 'Gohir.D05G314100' => 'ghi', 'Gohir.D07G041400' => 'ghi', 'Gohir.D09G029700' => 'ghi', 'Gohir.D12G149700' => 'ghi', 'Gorai.001G043800' => 'gra', 'Gorai.002G187800' => 'gra', 'Gorai.006G034700' => 'gra', 'Gorai.008G161200' => 'gra', 'Gorai.009G335700' => 'gra', 'Gorai.012G065000' => 'gra', 'GSVIVG01000535001' => 'vvi', 'GSVIVG01015572001' => 'vvi', 'GSVIVG01032386001' => 'vvi', 'HanXRQChr05g0138531' => 'han', 'HanXRQChr06g0174391' => 'han', 'HanXRQChr07g0199021' => 'han', 'HanXRQChr08g0208211' => 'han', 'HanXRQChr09g0255471' => 'han', 'HanXRQChr10g0315791' => 'han', 'HanXRQChr12g0371991' => 'han', 'HanXRQChr15g0475251' => 'han', 'HanXRQChr17g0540001' => 'han', 'HanXRQChr17g0548631' => 'han', 'HanXRQChr17g0569561' => 'han', 'Haze_12256' => 'cav', 'Haze_14756' => 'cav', 'Haze_25528' => 'cav', 'Hma1.2p1_0079F.1_g041020' => 'hma', 'Hma1.2p1_0818F.1_g223260' => 'hma', 'Hma1.2p1_1747F.1_g300530' => 'hma', 'HPP92_004607' => 'vpl', 'HPP92_004608' => 'vpl', 'HPP92_006181' => 'vpl', 'HPP92_012192' => 'vpl', 'HPP92_015680' => 'vpl', 'HPP92_020249' => 'vpl', 'HPP92_021376' => 'vpl', 'HPP92_024275' => 'vpl', 'Hund06031' => 'sun', 'Hund25391' => 'sun', 'Lalb_Chr07g0185371' => 'lal', 'Lalb_Chr07g0185381' => 'lal', 'Lalb_Chr12g0204011' => 'lal', 'Lalb_Chr13g0301671' => 'lal', 'Lalb_Chr14g0362851' => 'lal', 'Lalb_Chr24g0403581' => 'lal', 'Lj1g0000233' => 'lja', 'Lj2g0018120' => 'lja', 'Lj3C621T0' => 'lonja', 'Lj3P1059T14' => 'lonja', 'Lj3P611T9' => 'lonja', 'Lj3P614T13' => 'lonja', 'Lj3P615T5' => 'lonja', 'Lj4g0012315' => 'lja', 'Lj4g0026182' => 'lja', 'Lj6P813T16' => 'lonja', 'Lj7C427T7' => 'lonja', 'Lj7C427T8' => 'lonja', 'Lj7P600T41' => 'lonja', 'Lju41C42G17' => 'lonja', 'Lsat_1_v5_gn_0_47300' => 'lsa', 'Lsat_1_v5_gn_2_91280' => 'lsa', 'Lsat_1_v5_gn_3_30561' => 'lsa', 'Lsat_1_v5_gn_4_184321' => 'lsa', 'Lsat_1_v5_gn_4_4041' => 'lsa', 'Lsat_1_v5_gn_5_92000' => 'lsa', 'Lsat_1_v5_gn_8_152940' => 'lsa', 'Lsat_1_v5_gn_8_62401' => 'lsa', 'Manes.06G055900' => 'mes', 'Manes.12G022200' => 'mes', 'Manes.13G023300' => 'mes', 'Manes.14G115000' => 'mes', 'Manes.15G151700' => 'mes', 'Manes.17G111300' => 'mes', 'Mapoly0226s0009' => 'mpo', 'MBI02_g25363_MAGBIO' => 'mbi', 'MBI06_g00027_MAGBIO' => 'mbi', 'MBI10_g13034_MAGBIO' => 'mbi', 'MD09G1023400' => 'mdo', 'MD13G1100100' => 'mdo', 'MD15G1169200' => 'mdo', 'MD16G1101100' => 'mdo', 'MD17G1022900' => 'mdo', 'Medtr3g096150' => 'mtr', 'Medtr4g115070' => 'mtr', 'Medtr7g033325' => 'mtr', 'Medtr8g089840' => 'mtr', 'MELO3C010319.2' => 'cme', 'MELO3C011944.2' => 'cme', 'MELO3C021589.2' => 'cme', 'Migut.E00207' => 'egut', 'Migut.H00067' => 'egut', 'Migut.K00433' => 'egut', 'Migut.K00606' => 'egut', 'Migut.K01410' => 'egut', 'MSTRG.13347' => 'ama', 'MSTRG.24045' => 'ama', 'MSTRG.2428' => 'ama', 'MSTRG.26410' => 'ama', 'MSTRG.3139' => 'ama', 'MSTRG.3286' => 'ama', 'MSTRG.563' => 'ama', 'MSTRG.7941' => 'ama', 'Nitab4.5_0000028g0060' => 'nta', 'Nitab4.5_0000065g0260' => 'nta', 'Nitab4.5_0000112g0060' => 'nta', 'Nitab4.5_0000489g0120' => 'nta', 'Nitab4.5_0001776g0050' => 'nta', 'Nitab4.5_0001854g0010' => 'nta', 'Nitab4.5_0001860g0020' => 'nta', 'Nitab4.5_0004352g0010' => 'nta', 'Nitab4.5_0008716g0020' => 'nta', 'Nitab4.5_0008922g0010' => 'nta', 'Nn3g16693' => 'nnu', 'Nn4g22596' => 'nnu', 'Nn7g37639' => 'nnu', 'Oeu001701.1' => 'oeu', 'Oeu018149.1' => 'oeu', 'Oeu026220.1' => 'oeu', 'Oeu038635.1' => 'oeu', 'Oeu049176.1' => 'oeu', 'Oeu056706.1' => 'oeu', 'Oeu056937.1' => 'oeu', 'Oeu057540.1' => 'oeu', 'Os02g0594900' => 'osa', 'Os02g0595100' => 'osa', 'Os04g0477500' => 'osa', 'Os12g0611900' => 'osa', 'Peaxi162Scf00076g00020' => 'pax', 'Peaxi162Scf00128g00217' => 'pax', 'Peaxi162Scf00129g01640' => 'pax', 'Peaxi162Scf00669g00007' => 'pax', 'Peaxi162Scf00700g00421' => 'pax', 'Peaxi162Scf00801g00038' => 'pax', 'Peaxi162Scf00891g00025' => 'pax', 'PGR083G0909' => 'pgr', 'PGR119G1005' => 'pgr', 'PGR142G2236' => 'pgr', 'PGR142G3388' => 'pgr', 'PGSC0003DMG400004514' => 'stu', 'PGSC0003DMG400012635' => 'stu', 'PGSC0003DMG400015730' => 'stu', 'PGSC0003DMG400018611' => 'stu', 'PGSC0003DMG400030897' => 'stu', 'Phvul.001G254800' => 'pvu', 'Phvul.002G260100' => 'pvu', 'Phvul.003G167600' => 'pvu', 'Phvul.004G005100' => 'pvu', 'Potri.001G343600' => 'ptr', 'Potri.006G066700' => 'ptr', 'Potri.008G186000' => 'ptr', 'Potri.010G046900' => 'ptr', 'Potri.018G127900' => 'ptr', 'Pp3c20_17750' => 'ppa', 'Pp3c24_4380' => 'ppa', 'Prupe.1G245800' => 'ppe', 'Prupe.3G293400' => 'ppe', 'Prupe.7G247400' => 'ppe', 'Psat0s145g0120' => 'psa', 'Psat0s595g0040' => 'psa', 'Psat0s595g0120' => 'psa', 'Psat3g175040' => 'psa', 'Psat7g058120' => 'psa', 'PSO017G0428' => 'pso', 'PSO063G7510' => 'pso', 'PSO067G0046' => 'pso', 'PSO478G1073' => 'pso', 'PSO675G3677' => 'pso', 'PSO675G6558' => 'pso', 'PSO675G7520' => 'pso', 'PSO675G8959' => 'pso', 'QL02p074089' => 'qlo', 'QL02p089614' => 'qlo', 'QL03p057736' => 'qlo', 'RcHm_v2.0_Chr1g0364131' => 'rch', 'RcHm_v2.0_Chr2g0087801' => 'rch', 'RcHm_v2.0_Chr2g0087821' => 'rch', 'RcHm_v2.0_Chr2g0173231' => 'rch', 'RcHm_v2.0_Chr4g0433111' => 'rch', 'Rhsim03G0250300' => 'rsi', 'Rhsim08G0048400' => 'rsi', 'Rhsim10G0014800' => 'rsi', 'Rhsim12G0040100' => 'rsi', 'Rhsim12G0109700' => 'rsi', 'Sabra06G0049600' => 'sbr', 'Sabra08G0141000' => 'sbr', 'Sabra10G0021400' => 'sbr', 'Sabra16G0222900' => 'sbr', 'Sabra18G0108600' => 'sbr', 'SalBow1G0433' => 'sbo', 'SalBow1G2038' => 'sbo', 'SalBow1G5003' => 'sbo', 'SalBow7G1197' => 'sbo', 'SalBow8G3506' => 'sbo', 'Sc03g0007300' => 'sci', 'Sc11g0000950' => 'sci', 'Sc14g0008750' => 'sci', 'Sc18g0000420' => 'sci', 'Sed0006754' => 'sed', 'Sed0008741' => 'sed', 'Sed0017172' => 'sed', 'Sed0018925' => 'sed', 'Sed0023326' => 'sed', 'Sed0025909' => 'sed', 'SEGI_05333' => 'sgi', 'SEGI_10362' => 'sgi', 'SEGI_13380' => 'sgi', 'SEGI_24306' => 'sgi', 'SEGI_29077' => 'sgi', 'SEGI_29095' => 'sgi', 'SEGI_36534' => 'sgi', 'SEGI_37506' => 'sgi', 'SEGI_38321' => 'sgi', 'SGA_v2.0_scaffold307G48031' => 'sas', 'SGA_v2.0_scaffold47G17507' => 'sas', 'SGA_v2.0_scaffold63G21736' => 'sas', 'SGA_v2.0_scaffold87G27070' => 'sas', 'SHI17794' => 'shi', 'SHI28851' => 'shi', 'SMO165G0155' => 'smo', 'SMO340G0217' => 'smo', 'SMO367G1210' => 'smo', 'Solyc02g093430.3' => 'sly', 'Solyc05g013580.4' => 'sly', 'Solyc07g008030.3' => 'sly', 'Solyc12g035470.2' => 'sly', 'Sopen02g038020' => 'spe', 'Sopen05g008490' => 'spe', 'Sopen07g003910' => 'spe', 'Sopen12g015240' => 'spe', 'Sp1g11550' => 'spa', 'Sp2g16710' => 'spa', 'Sp3g00430' => 'spa', 'Sp3g26780' => 'spa', 'Sp5g22900' => 'spa', 'Sp6g29530' => 'spa', 'TAR371G0794' => 'tar', 'TAR374G0164' => 'tar', 'TAR622G0165' => 'tar', 'TAR626G0929' => 'tar', 'TAR629G2155' => 'tar', 'THA.LOC104805282' => 'tha', 'THA.LOC104805363' => 'tha', 'THA.LOC104808968' => 'tha', 'THA.LOC104821093' => 'tha', 'THA.LOC104823953' => 'tha', 'THA.LOC104825562' => 'tha', 'THA.LOC104825665' => 'tha', 'Thecc.02G261400' => 'tca', 'Thecc.04G019200' => 'tca', 'Thecc.09G130400' => 'tca', 'Thhalv10004374m.g' => 'esa', 'Thhalv10007850m.g' => 'esa', 'Thhalv10013782m.g' => 'esa', 'Thhalv10018686m.g' => 'esa', 'Thhalv10020899m.g' => 'esa', 'Thhalv10022755m.g' => 'esa', 'TPR.G23851' => 'tpr', 'TPR.G26500' => 'tpr', 'TPR.G27267' => 'tpr', 'TPR.G32001' => 'tpr', 'TPR.G6251' => 'tpr', 'TPR.G8167' => 'tpr', 'TWI12G1330' => 'twi', 'TWI18G1239' => 'twi', 'TWI34G0979' => 'twi', 'TWI36G0670' => 'twi', 'TWI36G0707' => 'twi', 'TWI56G0233' => 'twi', 'TWI75G1809' => 'twi', 'unitig_21.g20874' => 'ugi', 'unitig_26.g10343' => 'ugi', 'unitig_46.g18392' => 'ugi', 'unitig_52.g17178' => 'ugi', 'unitig_8.g2934' => 'ugi', 'vmacro01122' => 'vma', 'vmacro05875' => 'vma', 'vmacro06147' => 'vma', 'vmacro16191' => 'vma', 'vmacro18293' => 'vma', 'VMungo0251G3707' => 'vmu', 'VMungo0464G1521' => 'vmu', 'VMungo1215G0205' => 'vmu', 'VMungo1383G2484' => 'vmu', 'Zm00001eb079610' => 'zma', 'Zm00001eb135990' => 'zma', 'Zm00001eb183710' => 'zma', 'Zm00001eb246020' => 'zma' ) $gf_id = 'HOM05D001124' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001124' ) $data_identifier = 'HOM05D001124' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 6, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 7, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 21, 'bol' => (int) 10, 'bra' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 6, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 9, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 21, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 8, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 10, 'lsa' => (int) 8, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 8, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 9, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb246020' $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' => 'HOM05D001124', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '548', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02520' => 'bna', 'A03p06630' => 'bna', 'A05p44460' => 'bna', 'A06p08710' => 'bna', 'A06p41090' => 'bna', 'A07p32320' => 'bna', 'A08p32520' => 'bna', 'A09p10360' => 'bna', 'A10p24080' => 'bna', 'Aa31LG11G15250' => 'aar', 'Aa31LG1G1800' => 'aar', 'Aa31LG2G5120' => 'aar', 'Aa31LG2G6070' => 'aar', 'Aa31LG5G10770' => 'aar', 'Aa31sc61G90' => 'aar', 'Actinidia01352' => 'ach', 'Actinidia05983' => 'ach', 'Actinidia08133' => 'ach', 'Actinidia15101' => 'ach', 'Actinidia26379' => 'ach', 'Actinidia35778' => 'ach', 'Actinidia36123' => 'ach', 'Actinidia37436' => 'ach', 'Actinidia38730' => 'ach', 'Ah.02g128210' => 'amhyb', 'Ah.03g132990' => 'amhyb', 'Ah.14g079410' => 'amhyb', 'AL1G24640' => 'aly', 'AL2G26680' => 'aly', 'AL3G10530' => 'aly', 'AL3G45230' => 'aly', 'AL5G15230' => 'aly', 'AL5G16960' => 'aly', 'AL6G25210' => 'aly', 'Aqoxy2G00441' => 'aox', 'Aqoxy3G01236' => 'aox', 'Aqoxy5G03746' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3RQ047' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C7GMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9C8JER' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MBL6KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YXCZ83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZANX40' => 'arhy', 'AT1G12990' => 'ath', 'AT1G67880' => 'ath', 'AT2G13290' => 'ath', 'AT3G01620' => 'ath', 'AT3G26445' => 'ath', 'AT3G27540' => 'ath', 'AT5G14480' => 'ath', 'ATR0824G026' => 'atr', 'ATR1098G019' => 'atr', 'Atru.chr11.2145' => 'acertr', 'Atru.chr2.3636' => 'acertr', 'Atru.chr2.3644' => 'acertr', 'Atru.chr6.2422' => 'acertr', 'Atru.chr7.1112' => 'acertr', 'AUR62005469' => 'cqu', 'AUR62011166' => 'cqu', 'AUR62013319' => 'cqu', 'AUR62024273' => 'cqu', 'AUR62028420' => 'cqu', 'AUR62041942' => 'cqu', 'BcaB01g04969' => 'bca', 'BcaB01g06371' => 'bca', 'BcaB02g11494' => 'bca', 'BcaB03g15382' => 'bca', 'BcaB08g36994' => 'bca', 'BcaC03g13477' => 'bca', 'BcaC03g13478' => 'bca', 'BcaC03g13480' => 'bca', 'BcaC03g13481' => 'bca', 'BcaC03g13486' => 'bca', 'BcaC04g19031' => 'bca', 'BcaC04g23085' => 'bca', 'BcaC05g25094' => 'bca', 'BcaC05g25096' => 'bca', 'BcaC05g25138' => 'bca', 'BcaC05g30416' => 'bca', 'BcaC05g30455' => 'bca', 'BcaC06g30979' => 'bca', 'BcaC06g33805' => 'bca', 'BcaC08g46021' => 'bca', 'BcaNung03154' => 'bca', 'BolC2t06623H' => 'bol', 'BolC2t06632H' => 'bol', 'BolC2t06635H' => 'bol', 'BolC2t06638H' => 'bol', 'BolC3t13266H' => 'bol', 'BolC5t29776H' => 'bol', 'BolC6t38912H' => 'bol', 'BolC7t44183H' => 'bol', 'BolC9t54123H' => 'bol', 'BolC9t59107H' => 'bol', 'BraA02t05221Z' => 'bra', 'BraA03t09996Z' => 'bra', 'BraA05t23210Z' => 'bra', 'BraA06t24068Z' => 'bra', 'BraA06t27032Z' => 'bra', 'BraA08t35176Z' => 'bra', 'BraA09t36680Z' => 'bra', 'BraA10t44471Z' => 'bra', 'C02p06760' => 'bna', 'C02p06890' => 'bna', 'C02p07010' => 'bna', 'C03p07660' => 'bna', 'C05p10300' => 'bna', 'C06p38150' => 'bna', 'C07p36650' => 'bna', 'C08p15770' => 'bna', 'C09p12300' => 'bna', 'C09p62700' => 'bna', 'C09p75040' => 'bna', 'CAN.G13.1' => 'can', 'CAN.G138.4' => 'can', 'CAN.G44.6' => 'can', 'CAN.G473.19' => 'can', 'CANSAT01G0835' => 'cansat', 'CANSAT11G0246' => 'cansat', 'CANSAT11G1766' => 'cansat', 'CANSAT64G1954' => 'cansat', 'CARHR013330' => 'chi', 'CARHR060530' => 'chi', 'CARHR075300' => 'chi', 'CARHR105120' => 'chi', 'CARHR148910' => 'chi', 'CARHR198830' => 'chi', 'Carub.0001s1275' => 'cru', 'Carub.0002s1437' => 'cru', 'Carub.0003s0044' => 'cru', 'Carub.0003s2787' => 'cru', 'Carub.0005s0597' => 'cru', 'Carub.0006s1266' => 'cru', 'Ca_06935_v3' => 'car', 'Ca_13559_v3' => 'car', 'Ca_16941_v3' => 'car', 'Ca_16960_v3' => 'car', 'Ca_17775_v3' => 'car', 'Ca_30464_v3' => 'car', 'Cc06_g08160' => 'ccan', 'Cc07_g01520' => 'ccan', 'Cc11_g15810' => 'ccan', 'CDE02G2840' => 'cde', 'CDE03G0093' => 'cde', 'CDE04G2127' => 'cde', 'CDE07G1857' => 'cde', 'CDE09G1246' => 'cde', 'Cfa003412' => 'cfa', 'Cfa007341' => 'cfa', 'Cfa009220' => 'cfa', 'Ciclev10008737m.g' => 'ccl', 'Ciclev10015565m.g' => 'ccl', 'Ciclev10031761m.g' => 'ccl', 'CiPaw.03G045300' => 'cil', 'CiPaw.03G247200' => 'cil', 'CiPaw.04G029500' => 'cil', 'CiPaw.04G174000' => 'cil', 'CiPaw.05G181200' => 'cil', 'CiPaw.06G067100' => 'cil', 'ClCG05G025800' => 'cla', 'ClCG06G011400' => 'cla', 'ClCG09G019360' => 'cla', 'COL.COLO4_04827' => 'col', 'COL.COLO4_29170' => 'col', 'COL.COLO4_35131' => 'col', 'COL.COLO4_35132' => 'col', 'Cpa.g.sc33.32' => 'cpa', 'Cpa.g.sc46.29' => 'cpa', 'Cpa.g.sc796.1' => 'cpa', 'CsaV3_1G030420' => 'csa', 'CsaV3_5G027050' => 'csa', 'CsaV3_5G031040' => 'csa', 'CsaV3_UNG023130' => 'csa', 'CSS0007726' => 'camsi', 'CSS0016433' => 'camsi', 'CSS0017656' => 'camsi', 'CSS0025364' => 'camsi', 'CSS0027582' => 'camsi', 'CSS0047288' => 'camsi', 'CSS0049950' => 'camsi', 'DCAR_003843' => 'dca', 'DCAR_007052' => 'dca', 'DCAR_020884' => 'dca', 'DCAR_021730' => 'dca', 'DCAR_024423' => 'dca', 'DCAR_026509' => 'dca', 'DCAR_031158' => 'dca', 'Dinv14728' => 'din', 'Dinv15219' => 'din', 'Dinv25728' => 'din', 'Dinv33428' => 'din', 'Dinv36489' => 'din', 'Dinv41486' => 'din', 'Duzib147G0469' => 'dzi', 'Duzib168G0060' => 'dzi', 'Duzib187G1215' => 'dzi', 'Duzib248G0692' => 'dzi', 'Duzib251G0767' => 'dzi', 'Duzib264G0446' => 'dzi', 'Duzib268G0691' => 'dzi', 'ECA232G4767' => 'eca', 'ECA233G2838' => 'eca', 'ECA234G0391' => 'eca', 'ECA234G0857' => 'eca', 'ECA236G1593' => 'eca', 'ECA238G0565' => 'eca', 'ECA246G1027' => 'eca', 'ECA246G3223' => 'eca', 'ECA246G3470' => 'eca', 'EL10Ac6g13829' => 'bvu', 'EL10Ac6g14093' => 'bvu', 'EL10Ac8g18707' => 'bvu', 'Eucgr.C01369' => 'egr', 'Eucgr.H02492' => 'egr', 'Eucgr.I01733' => 'egr', 'Eucgr.J02255' => 'egr', 'Eucgr.J02257' => 'egr', 'Eucgr.J02258' => 'egr', 'FAN02G1601' => 'fan', 'FAN03G1586' => 'fan', 'FAN03G2986' => 'fan', 'FAN05G4837' => 'fan', 'FAN06G0146' => 'fan', 'FAN07G0858' => 'fan', 'FAN09G3179' => 'fan', 'FAN10G0669' => 'fan', 'FAN12G2358' => 'fan', 'FAN14G4198' => 'fan', 'FAN14G5112' => 'fan', 'FAN17G0342' => 'fan', 'FAN19G0342' => 'fan', 'FAN19G0962' => 'fan', 'FAN19G1101' => 'fan', 'FAN19G1872' => 'fan', 'FAN22G0356' => 'fan', 'FAN23G0744' => 'fan', 'FAN23G1914' => 'fan', 'FAN26G0032' => 'fan', 'FAN28G0625' => 'fan', 'FvH4_1g02710' => 'fve', 'FvH4_1g02720' => 'fve', 'FvH4_4g25670' => 'fve', 'FvH4_6g51700' => 'fve', 'FvH4_7g20170' => 'fve', 'Glyma.05G175000' => 'gma', 'Glyma.08G132300' => 'gma', 'Glyma.11G243000' => 'gma', 'Glyma.13G158900' => 'gma', 'Glyma.17G112400' => 'gma', 'Glyma.18G014100' => 'gma', 'Glyma.19G003100' => 'gma', 'Glyma.19G056500' => 'gma', 'Gohir.A01G158900' => 'ghi', 'Gohir.A05G312600' => 'ghi', 'Gohir.A05G354900' => 'ghi', 'Gohir.A07G037200' => 'ghi', 'Gohir.A09G030000' => 'ghi', 'Gohir.A12G145200' => 'ghi', 'Gohir.D01G151500' => 'ghi', 'Gohir.D04G058300' => 'ghi', 'Gohir.D05G314100' => 'ghi', 'Gohir.D07G041400' => 'ghi', 'Gohir.D09G029700' => 'ghi', 'Gohir.D12G149700' => 'ghi', 'Gorai.001G043800' => 'gra', 'Gorai.002G187800' => 'gra', 'Gorai.006G034700' => 'gra', 'Gorai.008G161200' => 'gra', 'Gorai.009G335700' => 'gra', 'Gorai.012G065000' => 'gra', 'GSVIVG01000535001' => 'vvi', 'GSVIVG01015572001' => 'vvi', 'GSVIVG01032386001' => 'vvi', 'HanXRQChr05g0138531' => 'han', 'HanXRQChr06g0174391' => 'han', 'HanXRQChr07g0199021' => 'han', 'HanXRQChr08g0208211' => 'han', 'HanXRQChr09g0255471' => 'han', 'HanXRQChr10g0315791' => 'han', 'HanXRQChr12g0371991' => 'han', 'HanXRQChr15g0475251' => 'han', 'HanXRQChr17g0540001' => 'han', 'HanXRQChr17g0548631' => 'han', 'HanXRQChr17g0569561' => 'han', 'Haze_12256' => 'cav', 'Haze_14756' => 'cav', 'Haze_25528' => 'cav', 'Hma1.2p1_0079F.1_g041020' => 'hma', 'Hma1.2p1_0818F.1_g223260' => 'hma', 'Hma1.2p1_1747F.1_g300530' => 'hma', 'HPP92_004607' => 'vpl', 'HPP92_004608' => 'vpl', 'HPP92_006181' => 'vpl', 'HPP92_012192' => 'vpl', 'HPP92_015680' => 'vpl', 'HPP92_020249' => 'vpl', 'HPP92_021376' => 'vpl', 'HPP92_024275' => 'vpl', 'Hund06031' => 'sun', 'Hund25391' => 'sun', 'Lalb_Chr07g0185371' => 'lal', 'Lalb_Chr07g0185381' => 'lal', 'Lalb_Chr12g0204011' => 'lal', 'Lalb_Chr13g0301671' => 'lal', 'Lalb_Chr14g0362851' => 'lal', 'Lalb_Chr24g0403581' => 'lal', 'Lj1g0000233' => 'lja', 'Lj2g0018120' => 'lja', 'Lj3C621T0' => 'lonja', 'Lj3P1059T14' => 'lonja', 'Lj3P611T9' => 'lonja', 'Lj3P614T13' => 'lonja', 'Lj3P615T5' => 'lonja', 'Lj4g0012315' => 'lja', 'Lj4g0026182' => 'lja', 'Lj6P813T16' => 'lonja', 'Lj7C427T7' => 'lonja', 'Lj7C427T8' => 'lonja', 'Lj7P600T41' => 'lonja', 'Lju41C42G17' => 'lonja', 'Lsat_1_v5_gn_0_47300' => 'lsa', 'Lsat_1_v5_gn_2_91280' => 'lsa', 'Lsat_1_v5_gn_3_30561' => 'lsa', 'Lsat_1_v5_gn_4_184321' => 'lsa', 'Lsat_1_v5_gn_4_4041' => 'lsa', 'Lsat_1_v5_gn_5_92000' => 'lsa', 'Lsat_1_v5_gn_8_152940' => 'lsa', 'Lsat_1_v5_gn_8_62401' => 'lsa', 'Manes.06G055900' => 'mes', 'Manes.12G022200' => 'mes', 'Manes.13G023300' => 'mes', 'Manes.14G115000' => 'mes', 'Manes.15G151700' => 'mes', 'Manes.17G111300' => 'mes', 'Mapoly0226s0009' => 'mpo', 'MBI02_g25363_MAGBIO' => 'mbi', 'MBI06_g00027_MAGBIO' => 'mbi', 'MBI10_g13034_MAGBIO' => 'mbi', 'MD09G1023400' => 'mdo', 'MD13G1100100' => 'mdo', 'MD15G1169200' => 'mdo', 'MD16G1101100' => 'mdo', 'MD17G1022900' => 'mdo', 'Medtr3g096150' => 'mtr', 'Medtr4g115070' => 'mtr', 'Medtr7g033325' => 'mtr', 'Medtr8g089840' => 'mtr', 'MELO3C010319.2' => 'cme', 'MELO3C011944.2' => 'cme', 'MELO3C021589.2' => 'cme', 'Migut.E00207' => 'egut', 'Migut.H00067' => 'egut', 'Migut.K00433' => 'egut', 'Migut.K00606' => 'egut', 'Migut.K01410' => 'egut', 'MSTRG.13347' => 'ama', 'MSTRG.24045' => 'ama', 'MSTRG.2428' => 'ama', 'MSTRG.26410' => 'ama', 'MSTRG.3139' => 'ama', 'MSTRG.3286' => 'ama', 'MSTRG.563' => 'ama', 'MSTRG.7941' => 'ama', 'Nitab4.5_0000028g0060' => 'nta', 'Nitab4.5_0000065g0260' => 'nta', 'Nitab4.5_0000112g0060' => 'nta', 'Nitab4.5_0000489g0120' => 'nta', 'Nitab4.5_0001776g0050' => 'nta', 'Nitab4.5_0001854g0010' => 'nta', 'Nitab4.5_0001860g0020' => 'nta', 'Nitab4.5_0004352g0010' => 'nta', 'Nitab4.5_0008716g0020' => 'nta', 'Nitab4.5_0008922g0010' => 'nta', 'Nn3g16693' => 'nnu', 'Nn4g22596' => 'nnu', 'Nn7g37639' => 'nnu', 'Oeu001701.1' => 'oeu', 'Oeu018149.1' => 'oeu', 'Oeu026220.1' => 'oeu', 'Oeu038635.1' => 'oeu', 'Oeu049176.1' => 'oeu', 'Oeu056706.1' => 'oeu', 'Oeu056937.1' => 'oeu', 'Oeu057540.1' => 'oeu', 'Os02g0594900' => 'osa', 'Os02g0595100' => 'osa', 'Os04g0477500' => 'osa', 'Os12g0611900' => 'osa', 'Peaxi162Scf00076g00020' => 'pax', 'Peaxi162Scf00128g00217' => 'pax', 'Peaxi162Scf00129g01640' => 'pax', 'Peaxi162Scf00669g00007' => 'pax', 'Peaxi162Scf00700g00421' => 'pax', 'Peaxi162Scf00801g00038' => 'pax', 'Peaxi162Scf00891g00025' => 'pax', 'PGR083G0909' => 'pgr', 'PGR119G1005' => 'pgr', 'PGR142G2236' => 'pgr', 'PGR142G3388' => 'pgr', 'PGSC0003DMG400004514' => 'stu', 'PGSC0003DMG400012635' => 'stu', 'PGSC0003DMG400015730' => 'stu', 'PGSC0003DMG400018611' => 'stu', 'PGSC0003DMG400030897' => 'stu', 'Phvul.001G254800' => 'pvu', 'Phvul.002G260100' => 'pvu', 'Phvul.003G167600' => 'pvu', 'Phvul.004G005100' => 'pvu', 'Potri.001G343600' => 'ptr', 'Potri.006G066700' => 'ptr', 'Potri.008G186000' => 'ptr', 'Potri.010G046900' => 'ptr', 'Potri.018G127900' => 'ptr', 'Pp3c20_17750' => 'ppa', 'Pp3c24_4380' => 'ppa', 'Prupe.1G245800' => 'ppe', 'Prupe.3G293400' => 'ppe', 'Prupe.7G247400' => 'ppe', 'Psat0s145g0120' => 'psa', 'Psat0s595g0040' => 'psa', 'Psat0s595g0120' => 'psa', 'Psat3g175040' => 'psa', 'Psat7g058120' => 'psa', 'PSO017G0428' => 'pso', 'PSO063G7510' => 'pso', 'PSO067G0046' => 'pso', 'PSO478G1073' => 'pso', 'PSO675G3677' => 'pso', 'PSO675G6558' => 'pso', 'PSO675G7520' => 'pso', 'PSO675G8959' => 'pso', 'QL02p074089' => 'qlo', 'QL02p089614' => 'qlo', 'QL03p057736' => 'qlo', 'RcHm_v2.0_Chr1g0364131' => 'rch', 'RcHm_v2.0_Chr2g0087801' => 'rch', 'RcHm_v2.0_Chr2g0087821' => 'rch', 'RcHm_v2.0_Chr2g0173231' => 'rch', 'RcHm_v2.0_Chr4g0433111' => 'rch', 'Rhsim03G0250300' => 'rsi', 'Rhsim08G0048400' => 'rsi', 'Rhsim10G0014800' => 'rsi', 'Rhsim12G0040100' => 'rsi', 'Rhsim12G0109700' => 'rsi', 'Sabra06G0049600' => 'sbr', 'Sabra08G0141000' => 'sbr', 'Sabra10G0021400' => 'sbr', 'Sabra16G0222900' => 'sbr', 'Sabra18G0108600' => 'sbr', 'SalBow1G0433' => 'sbo', 'SalBow1G2038' => 'sbo', 'SalBow1G5003' => 'sbo', 'SalBow7G1197' => 'sbo', 'SalBow8G3506' => 'sbo', 'Sc03g0007300' => 'sci', 'Sc11g0000950' => 'sci', 'Sc14g0008750' => 'sci', 'Sc18g0000420' => 'sci', 'Sed0006754' => 'sed', 'Sed0008741' => 'sed', 'Sed0017172' => 'sed', 'Sed0018925' => 'sed', 'Sed0023326' => 'sed', 'Sed0025909' => 'sed', 'SEGI_05333' => 'sgi', 'SEGI_10362' => 'sgi', 'SEGI_13380' => 'sgi', 'SEGI_24306' => 'sgi', 'SEGI_29077' => 'sgi', 'SEGI_29095' => 'sgi', 'SEGI_36534' => 'sgi', 'SEGI_37506' => 'sgi', 'SEGI_38321' => 'sgi', 'SGA_v2.0_scaffold307G48031' => 'sas', 'SGA_v2.0_scaffold47G17507' => 'sas', 'SGA_v2.0_scaffold63G21736' => 'sas', 'SGA_v2.0_scaffold87G27070' => 'sas', 'SHI17794' => 'shi', 'SHI28851' => 'shi', 'SMO165G0155' => 'smo', 'SMO340G0217' => 'smo', 'SMO367G1210' => 'smo', 'Solyc02g093430.3' => 'sly', 'Solyc05g013580.4' => 'sly', 'Solyc07g008030.3' => 'sly', 'Solyc12g035470.2' => 'sly', 'Sopen02g038020' => 'spe', 'Sopen05g008490' => 'spe', 'Sopen07g003910' => 'spe', 'Sopen12g015240' => 'spe', 'Sp1g11550' => 'spa', 'Sp2g16710' => 'spa', 'Sp3g00430' => 'spa', 'Sp3g26780' => 'spa', 'Sp5g22900' => 'spa', 'Sp6g29530' => 'spa', 'TAR371G0794' => 'tar', 'TAR374G0164' => 'tar', 'TAR622G0165' => 'tar', 'TAR626G0929' => 'tar', 'TAR629G2155' => 'tar', 'THA.LOC104805282' => 'tha', 'THA.LOC104805363' => 'tha', 'THA.LOC104808968' => 'tha', 'THA.LOC104821093' => 'tha', 'THA.LOC104823953' => 'tha', 'THA.LOC104825562' => 'tha', 'THA.LOC104825665' => 'tha', 'Thecc.02G261400' => 'tca', 'Thecc.04G019200' => 'tca', 'Thecc.09G130400' => 'tca', 'Thhalv10004374m.g' => 'esa', 'Thhalv10007850m.g' => 'esa', 'Thhalv10013782m.g' => 'esa', 'Thhalv10018686m.g' => 'esa', 'Thhalv10020899m.g' => 'esa', 'Thhalv10022755m.g' => 'esa', 'TPR.G23851' => 'tpr', 'TPR.G26500' => 'tpr', 'TPR.G27267' => 'tpr', 'TPR.G32001' => 'tpr', 'TPR.G6251' => 'tpr', 'TPR.G8167' => 'tpr', 'TWI12G1330' => 'twi', 'TWI18G1239' => 'twi', 'TWI34G0979' => 'twi', 'TWI36G0670' => 'twi', 'TWI36G0707' => 'twi', 'TWI56G0233' => 'twi', 'TWI75G1809' => 'twi', 'unitig_21.g20874' => 'ugi', 'unitig_26.g10343' => 'ugi', 'unitig_46.g18392' => 'ugi', 'unitig_52.g17178' => 'ugi', 'unitig_8.g2934' => 'ugi', 'vmacro01122' => 'vma', 'vmacro05875' => 'vma', 'vmacro06147' => 'vma', 'vmacro16191' => 'vma', 'vmacro18293' => 'vma', 'VMungo0251G3707' => 'vmu', 'VMungo0464G1521' => 'vmu', 'VMungo1215G0205' => 'vmu', 'VMungo1383G2484' => 'vmu', 'Zm00001eb079610' => 'zma', 'Zm00001eb135990' => 'zma', 'Zm00001eb183710' => 'zma', 'Zm00001eb246020' => 'zma' ), 'gf_id' => 'HOM05D001124', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001124' ), 'data_identifier' => 'HOM05D001124', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001124', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '548', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02520' => 'bna', 'A03p06630' => 'bna', 'A05p44460' => 'bna', 'A06p08710' => 'bna', 'A06p41090' => 'bna', 'A07p32320' => 'bna', 'A08p32520' => 'bna', 'A09p10360' => 'bna', 'A10p24080' => 'bna', 'Aa31LG11G15250' => 'aar', 'Aa31LG1G1800' => 'aar', 'Aa31LG2G5120' => 'aar', 'Aa31LG2G6070' => 'aar', 'Aa31LG5G10770' => 'aar', 'Aa31sc61G90' => 'aar', 'Actinidia01352' => 'ach', 'Actinidia05983' => 'ach', 'Actinidia08133' => 'ach', 'Actinidia15101' => 'ach', 'Actinidia26379' => 'ach', 'Actinidia35778' => 'ach', 'Actinidia36123' => 'ach', 'Actinidia37436' => 'ach', 'Actinidia38730' => 'ach', 'Ah.02g128210' => 'amhyb', 'Ah.03g132990' => 'amhyb', 'Ah.14g079410' => 'amhyb', 'AL1G24640' => 'aly', 'AL2G26680' => 'aly', 'AL3G10530' => 'aly', 'AL3G45230' => 'aly', 'AL5G15230' => 'aly', 'AL5G16960' => 'aly', 'AL6G25210' => 'aly', 'Aqoxy2G00441' => 'aox', 'Aqoxy3G01236' => 'aox', 'Aqoxy5G03746' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3RQ047' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C7GMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9C8JER' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MBL6KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YXCZ83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZANX40' => 'arhy', 'AT1G12990' => 'ath', 'AT1G67880' => 'ath', 'AT2G13290' => 'ath', 'AT3G01620' => 'ath', 'AT3G26445' => 'ath', 'AT3G27540' => 'ath', 'AT5G14480' => 'ath', 'ATR0824G026' => 'atr', 'ATR1098G019' => 'atr', 'Atru.chr11.2145' => 'acertr', 'Atru.chr2.3636' => 'acertr', 'Atru.chr2.3644' => 'acertr', 'Atru.chr6.2422' => 'acertr', 'Atru.chr7.1112' => 'acertr', 'AUR62005469' => 'cqu', 'AUR62011166' => 'cqu', 'AUR62013319' => 'cqu', 'AUR62024273' => 'cqu', 'AUR62028420' => 'cqu', 'AUR62041942' => 'cqu', 'BcaB01g04969' => 'bca', 'BcaB01g06371' => 'bca', 'BcaB02g11494' => 'bca', 'BcaB03g15382' => 'bca', 'BcaB08g36994' => 'bca', 'BcaC03g13477' => 'bca', 'BcaC03g13478' => 'bca', 'BcaC03g13480' => 'bca', 'BcaC03g13481' => 'bca', 'BcaC03g13486' => 'bca', 'BcaC04g19031' => 'bca', 'BcaC04g23085' => 'bca', 'BcaC05g25094' => 'bca', 'BcaC05g25096' => 'bca', 'BcaC05g25138' => 'bca', 'BcaC05g30416' => 'bca', 'BcaC05g30455' => 'bca', 'BcaC06g30979' => 'bca', 'BcaC06g33805' => 'bca', 'BcaC08g46021' => 'bca', 'BcaNung03154' => 'bca', 'BolC2t06623H' => 'bol', 'BolC2t06632H' => 'bol', 'BolC2t06635H' => 'bol', 'BolC2t06638H' => 'bol', 'BolC3t13266H' => 'bol', 'BolC5t29776H' => 'bol', 'BolC6t38912H' => 'bol', 'BolC7t44183H' => 'bol', 'BolC9t54123H' => 'bol', 'BolC9t59107H' => 'bol', 'BraA02t05221Z' => 'bra', 'BraA03t09996Z' => 'bra', 'BraA05t23210Z' => 'bra', 'BraA06t24068Z' => 'bra', 'BraA06t27032Z' => 'bra', 'BraA08t35176Z' => 'bra', 'BraA09t36680Z' => 'bra', 'BraA10t44471Z' => 'bra', 'C02p06760' => 'bna', 'C02p06890' => 'bna', 'C02p07010' => 'bna', 'C03p07660' => 'bna', 'C05p10300' => 'bna', 'C06p38150' => 'bna', 'C07p36650' => 'bna', 'C08p15770' => 'bna', 'C09p12300' => 'bna', 'C09p62700' => 'bna', 'C09p75040' => 'bna', 'CAN.G13.1' => 'can', 'CAN.G138.4' => 'can', 'CAN.G44.6' => 'can', 'CAN.G473.19' => 'can', 'CANSAT01G0835' => 'cansat', 'CANSAT11G0246' => 'cansat', 'CANSAT11G1766' => 'cansat', 'CANSAT64G1954' => 'cansat', 'CARHR013330' => 'chi', 'CARHR060530' => 'chi', 'CARHR075300' => 'chi', 'CARHR105120' => 'chi', 'CARHR148910' => 'chi', 'CARHR198830' => 'chi', 'Carub.0001s1275' => 'cru', 'Carub.0002s1437' => 'cru', 'Carub.0003s0044' => 'cru', 'Carub.0003s2787' => 'cru', 'Carub.0005s0597' => 'cru', 'Carub.0006s1266' => 'cru', 'Ca_06935_v3' => 'car', 'Ca_13559_v3' => 'car', 'Ca_16941_v3' => 'car', 'Ca_16960_v3' => 'car', 'Ca_17775_v3' => 'car', 'Ca_30464_v3' => 'car', 'Cc06_g08160' => 'ccan', 'Cc07_g01520' => 'ccan', 'Cc11_g15810' => 'ccan', 'CDE02G2840' => 'cde', 'CDE03G0093' => 'cde', 'CDE04G2127' => 'cde', 'CDE07G1857' => 'cde', 'CDE09G1246' => 'cde', 'Cfa003412' => 'cfa', 'Cfa007341' => 'cfa', 'Cfa009220' => 'cfa', 'Ciclev10008737m.g' => 'ccl', 'Ciclev10015565m.g' => 'ccl', 'Ciclev10031761m.g' => 'ccl', 'CiPaw.03G045300' => 'cil', 'CiPaw.03G247200' => 'cil', 'CiPaw.04G029500' => 'cil', 'CiPaw.04G174000' => 'cil', 'CiPaw.05G181200' => 'cil', 'CiPaw.06G067100' => 'cil', 'ClCG05G025800' => 'cla', 'ClCG06G011400' => 'cla', 'ClCG09G019360' => 'cla', 'COL.COLO4_04827' => 'col', 'COL.COLO4_29170' => 'col', 'COL.COLO4_35131' => 'col', 'COL.COLO4_35132' => 'col', 'Cpa.g.sc33.32' => 'cpa', 'Cpa.g.sc46.29' => 'cpa', 'Cpa.g.sc796.1' => 'cpa', 'CsaV3_1G030420' => 'csa', 'CsaV3_5G027050' => 'csa', 'CsaV3_5G031040' => 'csa', 'CsaV3_UNG023130' => 'csa', 'CSS0007726' => 'camsi', 'CSS0016433' => 'camsi', 'CSS0017656' => 'camsi', 'CSS0025364' => 'camsi', 'CSS0027582' => 'camsi', 'CSS0047288' => 'camsi', 'CSS0049950' => 'camsi', 'DCAR_003843' => 'dca', 'DCAR_007052' => 'dca', 'DCAR_020884' => 'dca', 'DCAR_021730' => 'dca', 'DCAR_024423' => 'dca', 'DCAR_026509' => 'dca', 'DCAR_031158' => 'dca', 'Dinv14728' => 'din', 'Dinv15219' => 'din', 'Dinv25728' => 'din', 'Dinv33428' => 'din', 'Dinv36489' => 'din', 'Dinv41486' => 'din', 'Duzib147G0469' => 'dzi', 'Duzib168G0060' => 'dzi', 'Duzib187G1215' => 'dzi', 'Duzib248G0692' => 'dzi', 'Duzib251G0767' => 'dzi', 'Duzib264G0446' => 'dzi', 'Duzib268G0691' => 'dzi', 'ECA232G4767' => 'eca', 'ECA233G2838' => 'eca', 'ECA234G0391' => 'eca', 'ECA234G0857' => 'eca', 'ECA236G1593' => 'eca', 'ECA238G0565' => 'eca', 'ECA246G1027' => 'eca', 'ECA246G3223' => 'eca', 'ECA246G3470' => 'eca', 'EL10Ac6g13829' => 'bvu', 'EL10Ac6g14093' => 'bvu', 'EL10Ac8g18707' => 'bvu', 'Eucgr.C01369' => 'egr', 'Eucgr.H02492' => 'egr', 'Eucgr.I01733' => 'egr', 'Eucgr.J02255' => 'egr', 'Eucgr.J02257' => 'egr', 'Eucgr.J02258' => 'egr', 'FAN02G1601' => 'fan', 'FAN03G1586' => 'fan', 'FAN03G2986' => 'fan', 'FAN05G4837' => 'fan', 'FAN06G0146' => 'fan', 'FAN07G0858' => 'fan', 'FAN09G3179' => 'fan', 'FAN10G0669' => 'fan', 'FAN12G2358' => 'fan', 'FAN14G4198' => 'fan', 'FAN14G5112' => 'fan', 'FAN17G0342' => 'fan', 'FAN19G0342' => 'fan', 'FAN19G0962' => 'fan', 'FAN19G1101' => 'fan', 'FAN19G1872' => 'fan', 'FAN22G0356' => 'fan', 'FAN23G0744' => 'fan', 'FAN23G1914' => 'fan', 'FAN26G0032' => 'fan', 'FAN28G0625' => 'fan', 'FvH4_1g02710' => 'fve', 'FvH4_1g02720' => 'fve', 'FvH4_4g25670' => 'fve', 'FvH4_6g51700' => 'fve', 'FvH4_7g20170' => 'fve', 'Glyma.05G175000' => 'gma', 'Glyma.08G132300' => 'gma', 'Glyma.11G243000' => 'gma', 'Glyma.13G158900' => 'gma', 'Glyma.17G112400' => 'gma', 'Glyma.18G014100' => 'gma', 'Glyma.19G003100' => 'gma', 'Glyma.19G056500' => 'gma', 'Gohir.A01G158900' => 'ghi', 'Gohir.A05G312600' => 'ghi', 'Gohir.A05G354900' => 'ghi', 'Gohir.A07G037200' => 'ghi', 'Gohir.A09G030000' => 'ghi', 'Gohir.A12G145200' => 'ghi', 'Gohir.D01G151500' => 'ghi', 'Gohir.D04G058300' => 'ghi', 'Gohir.D05G314100' => 'ghi', 'Gohir.D07G041400' => 'ghi', 'Gohir.D09G029700' => 'ghi', 'Gohir.D12G149700' => 'ghi', 'Gorai.001G043800' => 'gra', 'Gorai.002G187800' => 'gra', 'Gorai.006G034700' => 'gra', 'Gorai.008G161200' => 'gra', 'Gorai.009G335700' => 'gra', 'Gorai.012G065000' => 'gra', 'GSVIVG01000535001' => 'vvi', 'GSVIVG01015572001' => 'vvi', 'GSVIVG01032386001' => 'vvi', 'HanXRQChr05g0138531' => 'han', 'HanXRQChr06g0174391' => 'han', 'HanXRQChr07g0199021' => 'han', 'HanXRQChr08g0208211' => 'han', 'HanXRQChr09g0255471' => 'han', 'HanXRQChr10g0315791' => 'han', 'HanXRQChr12g0371991' => 'han', 'HanXRQChr15g0475251' => 'han', 'HanXRQChr17g0540001' => 'han', 'HanXRQChr17g0548631' => 'han', 'HanXRQChr17g0569561' => 'han', 'Haze_12256' => 'cav', 'Haze_14756' => 'cav', 'Haze_25528' => 'cav', 'Hma1.2p1_0079F.1_g041020' => 'hma', 'Hma1.2p1_0818F.1_g223260' => 'hma', 'Hma1.2p1_1747F.1_g300530' => 'hma', 'HPP92_004607' => 'vpl', 'HPP92_004608' => 'vpl', 'HPP92_006181' => 'vpl', 'HPP92_012192' => 'vpl', 'HPP92_015680' => 'vpl', 'HPP92_020249' => 'vpl', 'HPP92_021376' => 'vpl', 'HPP92_024275' => 'vpl', 'Hund06031' => 'sun', 'Hund25391' => 'sun', 'Lalb_Chr07g0185371' => 'lal', 'Lalb_Chr07g0185381' => 'lal', 'Lalb_Chr12g0204011' => 'lal', 'Lalb_Chr13g0301671' => 'lal', 'Lalb_Chr14g0362851' => 'lal', 'Lalb_Chr24g0403581' => 'lal', 'Lj1g0000233' => 'lja', 'Lj2g0018120' => 'lja', 'Lj3C621T0' => 'lonja', 'Lj3P1059T14' => 'lonja', 'Lj3P611T9' => 'lonja', 'Lj3P614T13' => 'lonja', 'Lj3P615T5' => 'lonja', 'Lj4g0012315' => 'lja', 'Lj4g0026182' => 'lja', 'Lj6P813T16' => 'lonja', 'Lj7C427T7' => 'lonja', 'Lj7C427T8' => 'lonja', 'Lj7P600T41' => 'lonja', 'Lju41C42G17' => 'lonja', 'Lsat_1_v5_gn_0_47300' => 'lsa', 'Lsat_1_v5_gn_2_91280' => 'lsa', 'Lsat_1_v5_gn_3_30561' => 'lsa', 'Lsat_1_v5_gn_4_184321' => 'lsa', 'Lsat_1_v5_gn_4_4041' => 'lsa', 'Lsat_1_v5_gn_5_92000' => 'lsa', 'Lsat_1_v5_gn_8_152940' => 'lsa', 'Lsat_1_v5_gn_8_62401' => 'lsa', 'Manes.06G055900' => 'mes', 'Manes.12G022200' => 'mes', 'Manes.13G023300' => 'mes', 'Manes.14G115000' => 'mes', 'Manes.15G151700' => 'mes', 'Manes.17G111300' => 'mes', 'Mapoly0226s0009' => 'mpo', 'MBI02_g25363_MAGBIO' => 'mbi', 'MBI06_g00027_MAGBIO' => 'mbi', 'MBI10_g13034_MAGBIO' => 'mbi', 'MD09G1023400' => 'mdo', 'MD13G1100100' => 'mdo', 'MD15G1169200' => 'mdo', 'MD16G1101100' => 'mdo', 'MD17G1022900' => 'mdo', 'Medtr3g096150' => 'mtr', 'Medtr4g115070' => 'mtr', 'Medtr7g033325' => 'mtr', 'Medtr8g089840' => 'mtr', 'MELO3C010319.2' => 'cme', 'MELO3C011944.2' => 'cme', 'MELO3C021589.2' => 'cme', 'Migut.E00207' => 'egut', 'Migut.H00067' => 'egut', 'Migut.K00433' => 'egut', 'Migut.K00606' => 'egut', 'Migut.K01410' => 'egut', 'MSTRG.13347' => 'ama', 'MSTRG.24045' => 'ama', 'MSTRG.2428' => 'ama', 'MSTRG.26410' => 'ama', 'MSTRG.3139' => 'ama', 'MSTRG.3286' => 'ama', 'MSTRG.563' => 'ama', 'MSTRG.7941' => 'ama', 'Nitab4.5_0000028g0060' => 'nta', 'Nitab4.5_0000065g0260' => 'nta', 'Nitab4.5_0000112g0060' => 'nta', 'Nitab4.5_0000489g0120' => 'nta', 'Nitab4.5_0001776g0050' => 'nta', 'Nitab4.5_0001854g0010' => 'nta', 'Nitab4.5_0001860g0020' => 'nta', 'Nitab4.5_0004352g0010' => 'nta', 'Nitab4.5_0008716g0020' => 'nta', 'Nitab4.5_0008922g0010' => 'nta', 'Nn3g16693' => 'nnu', 'Nn4g22596' => 'nnu', 'Nn7g37639' => 'nnu', 'Oeu001701.1' => 'oeu', 'Oeu018149.1' => 'oeu', 'Oeu026220.1' => 'oeu', 'Oeu038635.1' => 'oeu', 'Oeu049176.1' => 'oeu', 'Oeu056706.1' => 'oeu', 'Oeu056937.1' => 'oeu', 'Oeu057540.1' => 'oeu', 'Os02g0594900' => 'osa', 'Os02g0595100' => 'osa', 'Os04g0477500' => 'osa', 'Os12g0611900' => 'osa', 'Peaxi162Scf00076g00020' => 'pax', 'Peaxi162Scf00128g00217' => 'pax', 'Peaxi162Scf00129g01640' => 'pax', 'Peaxi162Scf00669g00007' => 'pax', 'Peaxi162Scf00700g00421' => 'pax', 'Peaxi162Scf00801g00038' => 'pax', 'Peaxi162Scf00891g00025' => 'pax', 'PGR083G0909' => 'pgr', 'PGR119G1005' => 'pgr', 'PGR142G2236' => 'pgr', 'PGR142G3388' => 'pgr', 'PGSC0003DMG400004514' => 'stu', 'PGSC0003DMG400012635' => 'stu', 'PGSC0003DMG400015730' => 'stu', 'PGSC0003DMG400018611' => 'stu', 'PGSC0003DMG400030897' => 'stu', 'Phvul.001G254800' => 'pvu', 'Phvul.002G260100' => 'pvu', 'Phvul.003G167600' => 'pvu', 'Phvul.004G005100' => 'pvu', 'Potri.001G343600' => 'ptr', 'Potri.006G066700' => 'ptr', 'Potri.008G186000' => 'ptr', 'Potri.010G046900' => 'ptr', 'Potri.018G127900' => 'ptr', 'Pp3c20_17750' => 'ppa', 'Pp3c24_4380' => 'ppa', 'Prupe.1G245800' => 'ppe', 'Prupe.3G293400' => 'ppe', 'Prupe.7G247400' => 'ppe', 'Psat0s145g0120' => 'psa', 'Psat0s595g0040' => 'psa', 'Psat0s595g0120' => 'psa', 'Psat3g175040' => 'psa', 'Psat7g058120' => 'psa', 'PSO017G0428' => 'pso', 'PSO063G7510' => 'pso', 'PSO067G0046' => 'pso', 'PSO478G1073' => 'pso', 'PSO675G3677' => 'pso', 'PSO675G6558' => 'pso', 'PSO675G7520' => 'pso', 'PSO675G8959' => 'pso', 'QL02p074089' => 'qlo', 'QL02p089614' => 'qlo', 'QL03p057736' => 'qlo', 'RcHm_v2.0_Chr1g0364131' => 'rch', 'RcHm_v2.0_Chr2g0087801' => 'rch', 'RcHm_v2.0_Chr2g0087821' => 'rch', 'RcHm_v2.0_Chr2g0173231' => 'rch', 'RcHm_v2.0_Chr4g0433111' => 'rch', 'Rhsim03G0250300' => 'rsi', 'Rhsim08G0048400' => 'rsi', 'Rhsim10G0014800' => 'rsi', 'Rhsim12G0040100' => 'rsi', 'Rhsim12G0109700' => 'rsi', 'Sabra06G0049600' => 'sbr', 'Sabra08G0141000' => 'sbr', 'Sabra10G0021400' => 'sbr', 'Sabra16G0222900' => 'sbr', 'Sabra18G0108600' => 'sbr', 'SalBow1G0433' => 'sbo', 'SalBow1G2038' => 'sbo', 'SalBow1G5003' => 'sbo', 'SalBow7G1197' => 'sbo', 'SalBow8G3506' => 'sbo', 'Sc03g0007300' => 'sci', 'Sc11g0000950' => 'sci', 'Sc14g0008750' => 'sci', 'Sc18g0000420' => 'sci', 'Sed0006754' => 'sed', 'Sed0008741' => 'sed', 'Sed0017172' => 'sed', 'Sed0018925' => 'sed', 'Sed0023326' => 'sed', 'Sed0025909' => 'sed', 'SEGI_05333' => 'sgi', 'SEGI_10362' => 'sgi', 'SEGI_13380' => 'sgi', 'SEGI_24306' => 'sgi', 'SEGI_29077' => 'sgi', 'SEGI_29095' => 'sgi', 'SEGI_36534' => 'sgi', 'SEGI_37506' => 'sgi', 'SEGI_38321' => 'sgi', 'SGA_v2.0_scaffold307G48031' => 'sas', 'SGA_v2.0_scaffold47G17507' => 'sas', 'SGA_v2.0_scaffold63G21736' => 'sas', 'SGA_v2.0_scaffold87G27070' => 'sas', 'SHI17794' => 'shi', 'SHI28851' => 'shi', 'SMO165G0155' => 'smo', 'SMO340G0217' => 'smo', 'SMO367G1210' => 'smo', 'Solyc02g093430.3' => 'sly', 'Solyc05g013580.4' => 'sly', 'Solyc07g008030.3' => 'sly', 'Solyc12g035470.2' => 'sly', 'Sopen02g038020' => 'spe', 'Sopen05g008490' => 'spe', 'Sopen07g003910' => 'spe', 'Sopen12g015240' => 'spe', 'Sp1g11550' => 'spa', 'Sp2g16710' => 'spa', 'Sp3g00430' => 'spa', 'Sp3g26780' => 'spa', 'Sp5g22900' => 'spa', 'Sp6g29530' => 'spa', 'TAR371G0794' => 'tar', 'TAR374G0164' => 'tar', 'TAR622G0165' => 'tar', 'TAR626G0929' => 'tar', 'TAR629G2155' => 'tar', 'THA.LOC104805282' => 'tha', 'THA.LOC104805363' => 'tha', 'THA.LOC104808968' => 'tha', 'THA.LOC104821093' => 'tha', 'THA.LOC104823953' => 'tha', 'THA.LOC104825562' => 'tha', 'THA.LOC104825665' => 'tha', 'Thecc.02G261400' => 'tca', 'Thecc.04G019200' => 'tca', 'Thecc.09G130400' => 'tca', 'Thhalv10004374m.g' => 'esa', 'Thhalv10007850m.g' => 'esa', 'Thhalv10013782m.g' => 'esa', 'Thhalv10018686m.g' => 'esa', 'Thhalv10020899m.g' => 'esa', 'Thhalv10022755m.g' => 'esa', 'TPR.G23851' => 'tpr', 'TPR.G26500' => 'tpr', 'TPR.G27267' => 'tpr', 'TPR.G32001' => 'tpr', 'TPR.G6251' => 'tpr', 'TPR.G8167' => 'tpr', 'TWI12G1330' => 'twi', 'TWI18G1239' => 'twi', 'TWI34G0979' => 'twi', 'TWI36G0670' => 'twi', 'TWI36G0707' => 'twi', 'TWI56G0233' => 'twi', 'TWI75G1809' => 'twi', 'unitig_21.g20874' => 'ugi', 'unitig_26.g10343' => 'ugi', 'unitig_46.g18392' => 'ugi', 'unitig_52.g17178' => 'ugi', 'unitig_8.g2934' => 'ugi', 'vmacro01122' => 'vma', 'vmacro05875' => 'vma', 'vmacro06147' => 'vma', 'vmacro16191' => 'vma', 'vmacro18293' => 'vma', 'VMungo0251G3707' => 'vmu', 'VMungo0464G1521' => 'vmu', 'VMungo1215G0205' => 'vmu', 'VMungo1383G2484' => 'vmu', 'Zm00001eb079610' => 'zma', 'Zm00001eb135990' => 'zma', 'Zm00001eb183710' => 'zma', 'Zm00001eb246020' => 'zma' ) $gf_id = 'HOM05D001124' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001124' ) $data_identifier = 'HOM05D001124' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 6, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 7, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 21, 'bol' => (int) 10, 'bra' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 6, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 9, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 21, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 8, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 10, 'lsa' => (int) 8, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 8, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 9, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb246020' $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' => 'HOM05D001124', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '548', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02520' => 'bna', 'A03p06630' => 'bna', 'A05p44460' => 'bna', 'A06p08710' => 'bna', 'A06p41090' => 'bna', 'A07p32320' => 'bna', 'A08p32520' => 'bna', 'A09p10360' => 'bna', 'A10p24080' => 'bna', 'Aa31LG11G15250' => 'aar', 'Aa31LG1G1800' => 'aar', 'Aa31LG2G5120' => 'aar', 'Aa31LG2G6070' => 'aar', 'Aa31LG5G10770' => 'aar', 'Aa31sc61G90' => 'aar', 'Actinidia01352' => 'ach', 'Actinidia05983' => 'ach', 'Actinidia08133' => 'ach', 'Actinidia15101' => 'ach', 'Actinidia26379' => 'ach', 'Actinidia35778' => 'ach', 'Actinidia36123' => 'ach', 'Actinidia37436' => 'ach', 'Actinidia38730' => 'ach', 'Ah.02g128210' => 'amhyb', 'Ah.03g132990' => 'amhyb', 'Ah.14g079410' => 'amhyb', 'AL1G24640' => 'aly', 'AL2G26680' => 'aly', 'AL3G10530' => 'aly', 'AL3G45230' => 'aly', 'AL5G15230' => 'aly', 'AL5G16960' => 'aly', 'AL6G25210' => 'aly', 'Aqoxy2G00441' => 'aox', 'Aqoxy3G01236' => 'aox', 'Aqoxy5G03746' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3RQ047' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C7GMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9C8JER' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MBL6KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YXCZ83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZANX40' => 'arhy', 'AT1G12990' => 'ath', 'AT1G67880' => 'ath', 'AT2G13290' => 'ath', 'AT3G01620' => 'ath', 'AT3G26445' => 'ath', 'AT3G27540' => 'ath', 'AT5G14480' => 'ath', 'ATR0824G026' => 'atr', 'ATR1098G019' => 'atr', 'Atru.chr11.2145' => 'acertr', 'Atru.chr2.3636' => 'acertr', 'Atru.chr2.3644' => 'acertr', 'Atru.chr6.2422' => 'acertr', 'Atru.chr7.1112' => 'acertr', 'AUR62005469' => 'cqu', 'AUR62011166' => 'cqu', 'AUR62013319' => 'cqu', 'AUR62024273' => 'cqu', 'AUR62028420' => 'cqu', 'AUR62041942' => 'cqu', 'BcaB01g04969' => 'bca', 'BcaB01g06371' => 'bca', 'BcaB02g11494' => 'bca', 'BcaB03g15382' => 'bca', 'BcaB08g36994' => 'bca', 'BcaC03g13477' => 'bca', 'BcaC03g13478' => 'bca', 'BcaC03g13480' => 'bca', 'BcaC03g13481' => 'bca', 'BcaC03g13486' => 'bca', 'BcaC04g19031' => 'bca', 'BcaC04g23085' => 'bca', 'BcaC05g25094' => 'bca', 'BcaC05g25096' => 'bca', 'BcaC05g25138' => 'bca', 'BcaC05g30416' => 'bca', 'BcaC05g30455' => 'bca', 'BcaC06g30979' => 'bca', 'BcaC06g33805' => 'bca', 'BcaC08g46021' => 'bca', 'BcaNung03154' => 'bca', 'BolC2t06623H' => 'bol', 'BolC2t06632H' => 'bol', 'BolC2t06635H' => 'bol', 'BolC2t06638H' => 'bol', 'BolC3t13266H' => 'bol', 'BolC5t29776H' => 'bol', 'BolC6t38912H' => 'bol', 'BolC7t44183H' => 'bol', 'BolC9t54123H' => 'bol', 'BolC9t59107H' => 'bol', 'BraA02t05221Z' => 'bra', 'BraA03t09996Z' => 'bra', 'BraA05t23210Z' => 'bra', 'BraA06t24068Z' => 'bra', 'BraA06t27032Z' => 'bra', 'BraA08t35176Z' => 'bra', 'BraA09t36680Z' => 'bra', 'BraA10t44471Z' => 'bra', 'C02p06760' => 'bna', 'C02p06890' => 'bna', 'C02p07010' => 'bna', 'C03p07660' => 'bna', 'C05p10300' => 'bna', 'C06p38150' => 'bna', 'C07p36650' => 'bna', 'C08p15770' => 'bna', 'C09p12300' => 'bna', 'C09p62700' => 'bna', 'C09p75040' => 'bna', 'CAN.G13.1' => 'can', 'CAN.G138.4' => 'can', 'CAN.G44.6' => 'can', 'CAN.G473.19' => 'can', 'CANSAT01G0835' => 'cansat', 'CANSAT11G0246' => 'cansat', 'CANSAT11G1766' => 'cansat', 'CANSAT64G1954' => 'cansat', 'CARHR013330' => 'chi', 'CARHR060530' => 'chi', 'CARHR075300' => 'chi', 'CARHR105120' => 'chi', 'CARHR148910' => 'chi', 'CARHR198830' => 'chi', 'Carub.0001s1275' => 'cru', 'Carub.0002s1437' => 'cru', 'Carub.0003s0044' => 'cru', 'Carub.0003s2787' => 'cru', 'Carub.0005s0597' => 'cru', 'Carub.0006s1266' => 'cru', 'Ca_06935_v3' => 'car', 'Ca_13559_v3' => 'car', 'Ca_16941_v3' => 'car', 'Ca_16960_v3' => 'car', 'Ca_17775_v3' => 'car', 'Ca_30464_v3' => 'car', 'Cc06_g08160' => 'ccan', 'Cc07_g01520' => 'ccan', 'Cc11_g15810' => 'ccan', 'CDE02G2840' => 'cde', 'CDE03G0093' => 'cde', 'CDE04G2127' => 'cde', 'CDE07G1857' => 'cde', 'CDE09G1246' => 'cde', 'Cfa003412' => 'cfa', 'Cfa007341' => 'cfa', 'Cfa009220' => 'cfa', 'Ciclev10008737m.g' => 'ccl', 'Ciclev10015565m.g' => 'ccl', 'Ciclev10031761m.g' => 'ccl', 'CiPaw.03G045300' => 'cil', 'CiPaw.03G247200' => 'cil', 'CiPaw.04G029500' => 'cil', 'CiPaw.04G174000' => 'cil', 'CiPaw.05G181200' => 'cil', 'CiPaw.06G067100' => 'cil', 'ClCG05G025800' => 'cla', 'ClCG06G011400' => 'cla', 'ClCG09G019360' => 'cla', 'COL.COLO4_04827' => 'col', 'COL.COLO4_29170' => 'col', 'COL.COLO4_35131' => 'col', 'COL.COLO4_35132' => 'col', 'Cpa.g.sc33.32' => 'cpa', 'Cpa.g.sc46.29' => 'cpa', 'Cpa.g.sc796.1' => 'cpa', 'CsaV3_1G030420' => 'csa', 'CsaV3_5G027050' => 'csa', 'CsaV3_5G031040' => 'csa', 'CsaV3_UNG023130' => 'csa', 'CSS0007726' => 'camsi', 'CSS0016433' => 'camsi', 'CSS0017656' => 'camsi', 'CSS0025364' => 'camsi', 'CSS0027582' => 'camsi', 'CSS0047288' => 'camsi', 'CSS0049950' => 'camsi', 'DCAR_003843' => 'dca', 'DCAR_007052' => 'dca', 'DCAR_020884' => 'dca', 'DCAR_021730' => 'dca', 'DCAR_024423' => 'dca', 'DCAR_026509' => 'dca', 'DCAR_031158' => 'dca', 'Dinv14728' => 'din', 'Dinv15219' => 'din', 'Dinv25728' => 'din', 'Dinv33428' => 'din', 'Dinv36489' => 'din', 'Dinv41486' => 'din', 'Duzib147G0469' => 'dzi', 'Duzib168G0060' => 'dzi', 'Duzib187G1215' => 'dzi', 'Duzib248G0692' => 'dzi', 'Duzib251G0767' => 'dzi', 'Duzib264G0446' => 'dzi', 'Duzib268G0691' => 'dzi', 'ECA232G4767' => 'eca', 'ECA233G2838' => 'eca', 'ECA234G0391' => 'eca', 'ECA234G0857' => 'eca', 'ECA236G1593' => 'eca', 'ECA238G0565' => 'eca', 'ECA246G1027' => 'eca', 'ECA246G3223' => 'eca', 'ECA246G3470' => 'eca', 'EL10Ac6g13829' => 'bvu', 'EL10Ac6g14093' => 'bvu', 'EL10Ac8g18707' => 'bvu', 'Eucgr.C01369' => 'egr', 'Eucgr.H02492' => 'egr', 'Eucgr.I01733' => 'egr', 'Eucgr.J02255' => 'egr', 'Eucgr.J02257' => 'egr', 'Eucgr.J02258' => 'egr', 'FAN02G1601' => 'fan', 'FAN03G1586' => 'fan', 'FAN03G2986' => 'fan', 'FAN05G4837' => 'fan', 'FAN06G0146' => 'fan', 'FAN07G0858' => 'fan', 'FAN09G3179' => 'fan', 'FAN10G0669' => 'fan', 'FAN12G2358' => 'fan', 'FAN14G4198' => 'fan', 'FAN14G5112' => 'fan', 'FAN17G0342' => 'fan', 'FAN19G0342' => 'fan', 'FAN19G0962' => 'fan', 'FAN19G1101' => 'fan', 'FAN19G1872' => 'fan', 'FAN22G0356' => 'fan', 'FAN23G0744' => 'fan', 'FAN23G1914' => 'fan', 'FAN26G0032' => 'fan', 'FAN28G0625' => 'fan', 'FvH4_1g02710' => 'fve', 'FvH4_1g02720' => 'fve', 'FvH4_4g25670' => 'fve', 'FvH4_6g51700' => 'fve', 'FvH4_7g20170' => 'fve', 'Glyma.05G175000' => 'gma', 'Glyma.08G132300' => 'gma', 'Glyma.11G243000' => 'gma', 'Glyma.13G158900' => 'gma', 'Glyma.17G112400' => 'gma', 'Glyma.18G014100' => 'gma', 'Glyma.19G003100' => 'gma', 'Glyma.19G056500' => 'gma', 'Gohir.A01G158900' => 'ghi', 'Gohir.A05G312600' => 'ghi', 'Gohir.A05G354900' => 'ghi', 'Gohir.A07G037200' => 'ghi', 'Gohir.A09G030000' => 'ghi', 'Gohir.A12G145200' => 'ghi', 'Gohir.D01G151500' => 'ghi', 'Gohir.D04G058300' => 'ghi', 'Gohir.D05G314100' => 'ghi', 'Gohir.D07G041400' => 'ghi', 'Gohir.D09G029700' => 'ghi', 'Gohir.D12G149700' => 'ghi', 'Gorai.001G043800' => 'gra', 'Gorai.002G187800' => 'gra', 'Gorai.006G034700' => 'gra', 'Gorai.008G161200' => 'gra', 'Gorai.009G335700' => 'gra', 'Gorai.012G065000' => 'gra', 'GSVIVG01000535001' => 'vvi', 'GSVIVG01015572001' => 'vvi', 'GSVIVG01032386001' => 'vvi', 'HanXRQChr05g0138531' => 'han', 'HanXRQChr06g0174391' => 'han', 'HanXRQChr07g0199021' => 'han', 'HanXRQChr08g0208211' => 'han', 'HanXRQChr09g0255471' => 'han', 'HanXRQChr10g0315791' => 'han', 'HanXRQChr12g0371991' => 'han', 'HanXRQChr15g0475251' => 'han', 'HanXRQChr17g0540001' => 'han', 'HanXRQChr17g0548631' => 'han', 'HanXRQChr17g0569561' => 'han', 'Haze_12256' => 'cav', 'Haze_14756' => 'cav', 'Haze_25528' => 'cav', 'Hma1.2p1_0079F.1_g041020' => 'hma', 'Hma1.2p1_0818F.1_g223260' => 'hma', 'Hma1.2p1_1747F.1_g300530' => 'hma', 'HPP92_004607' => 'vpl', 'HPP92_004608' => 'vpl', 'HPP92_006181' => 'vpl', 'HPP92_012192' => 'vpl', 'HPP92_015680' => 'vpl', 'HPP92_020249' => 'vpl', 'HPP92_021376' => 'vpl', 'HPP92_024275' => 'vpl', 'Hund06031' => 'sun', 'Hund25391' => 'sun', 'Lalb_Chr07g0185371' => 'lal', 'Lalb_Chr07g0185381' => 'lal', 'Lalb_Chr12g0204011' => 'lal', 'Lalb_Chr13g0301671' => 'lal', 'Lalb_Chr14g0362851' => 'lal', 'Lalb_Chr24g0403581' => 'lal', 'Lj1g0000233' => 'lja', 'Lj2g0018120' => 'lja', 'Lj3C621T0' => 'lonja', 'Lj3P1059T14' => 'lonja', 'Lj3P611T9' => 'lonja', 'Lj3P614T13' => 'lonja', 'Lj3P615T5' => 'lonja', 'Lj4g0012315' => 'lja', 'Lj4g0026182' => 'lja', 'Lj6P813T16' => 'lonja', 'Lj7C427T7' => 'lonja', 'Lj7C427T8' => 'lonja', 'Lj7P600T41' => 'lonja', 'Lju41C42G17' => 'lonja', 'Lsat_1_v5_gn_0_47300' => 'lsa', 'Lsat_1_v5_gn_2_91280' => 'lsa', 'Lsat_1_v5_gn_3_30561' => 'lsa', 'Lsat_1_v5_gn_4_184321' => 'lsa', 'Lsat_1_v5_gn_4_4041' => 'lsa', 'Lsat_1_v5_gn_5_92000' => 'lsa', 'Lsat_1_v5_gn_8_152940' => 'lsa', 'Lsat_1_v5_gn_8_62401' => 'lsa', 'Manes.06G055900' => 'mes', 'Manes.12G022200' => 'mes', 'Manes.13G023300' => 'mes', 'Manes.14G115000' => 'mes', 'Manes.15G151700' => 'mes', 'Manes.17G111300' => 'mes', 'Mapoly0226s0009' => 'mpo', 'MBI02_g25363_MAGBIO' => 'mbi', 'MBI06_g00027_MAGBIO' => 'mbi', 'MBI10_g13034_MAGBIO' => 'mbi', 'MD09G1023400' => 'mdo', 'MD13G1100100' => 'mdo', 'MD15G1169200' => 'mdo', 'MD16G1101100' => 'mdo', 'MD17G1022900' => 'mdo', 'Medtr3g096150' => 'mtr', 'Medtr4g115070' => 'mtr', 'Medtr7g033325' => 'mtr', 'Medtr8g089840' => 'mtr', 'MELO3C010319.2' => 'cme', 'MELO3C011944.2' => 'cme', 'MELO3C021589.2' => 'cme', 'Migut.E00207' => 'egut', 'Migut.H00067' => 'egut', 'Migut.K00433' => 'egut', 'Migut.K00606' => 'egut', 'Migut.K01410' => 'egut', 'MSTRG.13347' => 'ama', 'MSTRG.24045' => 'ama', 'MSTRG.2428' => 'ama', 'MSTRG.26410' => 'ama', 'MSTRG.3139' => 'ama', 'MSTRG.3286' => 'ama', 'MSTRG.563' => 'ama', 'MSTRG.7941' => 'ama', 'Nitab4.5_0000028g0060' => 'nta', 'Nitab4.5_0000065g0260' => 'nta', 'Nitab4.5_0000112g0060' => 'nta', 'Nitab4.5_0000489g0120' => 'nta', 'Nitab4.5_0001776g0050' => 'nta', 'Nitab4.5_0001854g0010' => 'nta', 'Nitab4.5_0001860g0020' => 'nta', 'Nitab4.5_0004352g0010' => 'nta', 'Nitab4.5_0008716g0020' => 'nta', 'Nitab4.5_0008922g0010' => 'nta', 'Nn3g16693' => 'nnu', 'Nn4g22596' => 'nnu', 'Nn7g37639' => 'nnu', 'Oeu001701.1' => 'oeu', 'Oeu018149.1' => 'oeu', 'Oeu026220.1' => 'oeu', 'Oeu038635.1' => 'oeu', 'Oeu049176.1' => 'oeu', 'Oeu056706.1' => 'oeu', 'Oeu056937.1' => 'oeu', 'Oeu057540.1' => 'oeu', 'Os02g0594900' => 'osa', 'Os02g0595100' => 'osa', 'Os04g0477500' => 'osa', 'Os12g0611900' => 'osa', 'Peaxi162Scf00076g00020' => 'pax', 'Peaxi162Scf00128g00217' => 'pax', 'Peaxi162Scf00129g01640' => 'pax', 'Peaxi162Scf00669g00007' => 'pax', 'Peaxi162Scf00700g00421' => 'pax', 'Peaxi162Scf00801g00038' => 'pax', 'Peaxi162Scf00891g00025' => 'pax', 'PGR083G0909' => 'pgr', 'PGR119G1005' => 'pgr', 'PGR142G2236' => 'pgr', 'PGR142G3388' => 'pgr', 'PGSC0003DMG400004514' => 'stu', 'PGSC0003DMG400012635' => 'stu', 'PGSC0003DMG400015730' => 'stu', 'PGSC0003DMG400018611' => 'stu', 'PGSC0003DMG400030897' => 'stu', 'Phvul.001G254800' => 'pvu', 'Phvul.002G260100' => 'pvu', 'Phvul.003G167600' => 'pvu', 'Phvul.004G005100' => 'pvu', 'Potri.001G343600' => 'ptr', 'Potri.006G066700' => 'ptr', 'Potri.008G186000' => 'ptr', 'Potri.010G046900' => 'ptr', 'Potri.018G127900' => 'ptr', 'Pp3c20_17750' => 'ppa', 'Pp3c24_4380' => 'ppa', 'Prupe.1G245800' => 'ppe', 'Prupe.3G293400' => 'ppe', 'Prupe.7G247400' => 'ppe', 'Psat0s145g0120' => 'psa', 'Psat0s595g0040' => 'psa', 'Psat0s595g0120' => 'psa', 'Psat3g175040' => 'psa', 'Psat7g058120' => 'psa', 'PSO017G0428' => 'pso', 'PSO063G7510' => 'pso', 'PSO067G0046' => 'pso', 'PSO478G1073' => 'pso', 'PSO675G3677' => 'pso', 'PSO675G6558' => 'pso', 'PSO675G7520' => 'pso', 'PSO675G8959' => 'pso', 'QL02p074089' => 'qlo', 'QL02p089614' => 'qlo', 'QL03p057736' => 'qlo', 'RcHm_v2.0_Chr1g0364131' => 'rch', 'RcHm_v2.0_Chr2g0087801' => 'rch', 'RcHm_v2.0_Chr2g0087821' => 'rch', 'RcHm_v2.0_Chr2g0173231' => 'rch', 'RcHm_v2.0_Chr4g0433111' => 'rch', 'Rhsim03G0250300' => 'rsi', 'Rhsim08G0048400' => 'rsi', 'Rhsim10G0014800' => 'rsi', 'Rhsim12G0040100' => 'rsi', 'Rhsim12G0109700' => 'rsi', 'Sabra06G0049600' => 'sbr', 'Sabra08G0141000' => 'sbr', 'Sabra10G0021400' => 'sbr', 'Sabra16G0222900' => 'sbr', 'Sabra18G0108600' => 'sbr', 'SalBow1G0433' => 'sbo', 'SalBow1G2038' => 'sbo', 'SalBow1G5003' => 'sbo', 'SalBow7G1197' => 'sbo', 'SalBow8G3506' => 'sbo', 'Sc03g0007300' => 'sci', 'Sc11g0000950' => 'sci', 'Sc14g0008750' => 'sci', 'Sc18g0000420' => 'sci', 'Sed0006754' => 'sed', 'Sed0008741' => 'sed', 'Sed0017172' => 'sed', 'Sed0018925' => 'sed', 'Sed0023326' => 'sed', 'Sed0025909' => 'sed', 'SEGI_05333' => 'sgi', 'SEGI_10362' => 'sgi', 'SEGI_13380' => 'sgi', 'SEGI_24306' => 'sgi', 'SEGI_29077' => 'sgi', 'SEGI_29095' => 'sgi', 'SEGI_36534' => 'sgi', 'SEGI_37506' => 'sgi', 'SEGI_38321' => 'sgi', 'SGA_v2.0_scaffold307G48031' => 'sas', 'SGA_v2.0_scaffold47G17507' => 'sas', 'SGA_v2.0_scaffold63G21736' => 'sas', 'SGA_v2.0_scaffold87G27070' => 'sas', 'SHI17794' => 'shi', 'SHI28851' => 'shi', 'SMO165G0155' => 'smo', 'SMO340G0217' => 'smo', 'SMO367G1210' => 'smo', 'Solyc02g093430.3' => 'sly', 'Solyc05g013580.4' => 'sly', 'Solyc07g008030.3' => 'sly', 'Solyc12g035470.2' => 'sly', 'Sopen02g038020' => 'spe', 'Sopen05g008490' => 'spe', 'Sopen07g003910' => 'spe', 'Sopen12g015240' => 'spe', 'Sp1g11550' => 'spa', 'Sp2g16710' => 'spa', 'Sp3g00430' => 'spa', 'Sp3g26780' => 'spa', 'Sp5g22900' => 'spa', 'Sp6g29530' => 'spa', 'TAR371G0794' => 'tar', 'TAR374G0164' => 'tar', 'TAR622G0165' => 'tar', 'TAR626G0929' => 'tar', 'TAR629G2155' => 'tar', 'THA.LOC104805282' => 'tha', 'THA.LOC104805363' => 'tha', 'THA.LOC104808968' => 'tha', 'THA.LOC104821093' => 'tha', 'THA.LOC104823953' => 'tha', 'THA.LOC104825562' => 'tha', 'THA.LOC104825665' => 'tha', 'Thecc.02G261400' => 'tca', 'Thecc.04G019200' => 'tca', 'Thecc.09G130400' => 'tca', 'Thhalv10004374m.g' => 'esa', 'Thhalv10007850m.g' => 'esa', 'Thhalv10013782m.g' => 'esa', 'Thhalv10018686m.g' => 'esa', 'Thhalv10020899m.g' => 'esa', 'Thhalv10022755m.g' => 'esa', 'TPR.G23851' => 'tpr', 'TPR.G26500' => 'tpr', 'TPR.G27267' => 'tpr', 'TPR.G32001' => 'tpr', 'TPR.G6251' => 'tpr', 'TPR.G8167' => 'tpr', 'TWI12G1330' => 'twi', 'TWI18G1239' => 'twi', 'TWI34G0979' => 'twi', 'TWI36G0670' => 'twi', 'TWI36G0707' => 'twi', 'TWI56G0233' => 'twi', 'TWI75G1809' => 'twi', 'unitig_21.g20874' => 'ugi', 'unitig_26.g10343' => 'ugi', 'unitig_46.g18392' => 'ugi', 'unitig_52.g17178' => 'ugi', 'unitig_8.g2934' => 'ugi', 'vmacro01122' => 'vma', 'vmacro05875' => 'vma', 'vmacro06147' => 'vma', 'vmacro16191' => 'vma', 'vmacro18293' => 'vma', 'VMungo0251G3707' => 'vmu', 'VMungo0464G1521' => 'vmu', 'VMungo1215G0205' => 'vmu', 'VMungo1383G2484' => 'vmu', 'Zm00001eb079610' => 'zma', 'Zm00001eb135990' => 'zma', 'Zm00001eb183710' => 'zma', 'Zm00001eb246020' => 'zma' ), 'gf_id' => 'HOM05D001124', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001124' ), 'data_identifier' => 'HOM05D001124', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001124', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '548', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02520' => 'bna', 'A03p06630' => 'bna', 'A05p44460' => 'bna', 'A06p08710' => 'bna', 'A06p41090' => 'bna', 'A07p32320' => 'bna', 'A08p32520' => 'bna', 'A09p10360' => 'bna', 'A10p24080' => 'bna', 'Aa31LG11G15250' => 'aar', 'Aa31LG1G1800' => 'aar', 'Aa31LG2G5120' => 'aar', 'Aa31LG2G6070' => 'aar', 'Aa31LG5G10770' => 'aar', 'Aa31sc61G90' => 'aar', 'Actinidia01352' => 'ach', 'Actinidia05983' => 'ach', 'Actinidia08133' => 'ach', 'Actinidia15101' => 'ach', 'Actinidia26379' => 'ach', 'Actinidia35778' => 'ach', 'Actinidia36123' => 'ach', 'Actinidia37436' => 'ach', 'Actinidia38730' => 'ach', 'Ah.02g128210' => 'amhyb', 'Ah.03g132990' => 'amhyb', 'Ah.14g079410' => 'amhyb', 'AL1G24640' => 'aly', 'AL2G26680' => 'aly', 'AL3G10530' => 'aly', 'AL3G45230' => 'aly', 'AL5G15230' => 'aly', 'AL5G16960' => 'aly', 'AL6G25210' => 'aly', 'Aqoxy2G00441' => 'aox', 'Aqoxy3G01236' => 'aox', 'Aqoxy5G03746' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3RQ047' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C7GMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9C8JER' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MBL6KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YXCZ83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZANX40' => 'arhy', 'AT1G12990' => 'ath', 'AT1G67880' => 'ath', 'AT2G13290' => 'ath', 'AT3G01620' => 'ath', 'AT3G26445' => 'ath', 'AT3G27540' => 'ath', 'AT5G14480' => 'ath', 'ATR0824G026' => 'atr', 'ATR1098G019' => 'atr', 'Atru.chr11.2145' => 'acertr', 'Atru.chr2.3636' => 'acertr', 'Atru.chr2.3644' => 'acertr', 'Atru.chr6.2422' => 'acertr', 'Atru.chr7.1112' => 'acertr', 'AUR62005469' => 'cqu', 'AUR62011166' => 'cqu', 'AUR62013319' => 'cqu', 'AUR62024273' => 'cqu', 'AUR62028420' => 'cqu', 'AUR62041942' => 'cqu', 'BcaB01g04969' => 'bca', 'BcaB01g06371' => 'bca', 'BcaB02g11494' => 'bca', 'BcaB03g15382' => 'bca', 'BcaB08g36994' => 'bca', 'BcaC03g13477' => 'bca', 'BcaC03g13478' => 'bca', 'BcaC03g13480' => 'bca', 'BcaC03g13481' => 'bca', 'BcaC03g13486' => 'bca', 'BcaC04g19031' => 'bca', 'BcaC04g23085' => 'bca', 'BcaC05g25094' => 'bca', 'BcaC05g25096' => 'bca', 'BcaC05g25138' => 'bca', 'BcaC05g30416' => 'bca', 'BcaC05g30455' => 'bca', 'BcaC06g30979' => 'bca', 'BcaC06g33805' => 'bca', 'BcaC08g46021' => 'bca', 'BcaNung03154' => 'bca', 'BolC2t06623H' => 'bol', 'BolC2t06632H' => 'bol', 'BolC2t06635H' => 'bol', 'BolC2t06638H' => 'bol', 'BolC3t13266H' => 'bol', 'BolC5t29776H' => 'bol', 'BolC6t38912H' => 'bol', 'BolC7t44183H' => 'bol', 'BolC9t54123H' => 'bol', 'BolC9t59107H' => 'bol', 'BraA02t05221Z' => 'bra', 'BraA03t09996Z' => 'bra', 'BraA05t23210Z' => 'bra', 'BraA06t24068Z' => 'bra', 'BraA06t27032Z' => 'bra', 'BraA08t35176Z' => 'bra', 'BraA09t36680Z' => 'bra', 'BraA10t44471Z' => 'bra', 'C02p06760' => 'bna', 'C02p06890' => 'bna', 'C02p07010' => 'bna', 'C03p07660' => 'bna', 'C05p10300' => 'bna', 'C06p38150' => 'bna', 'C07p36650' => 'bna', 'C08p15770' => 'bna', 'C09p12300' => 'bna', 'C09p62700' => 'bna', 'C09p75040' => 'bna', 'CAN.G13.1' => 'can', 'CAN.G138.4' => 'can', 'CAN.G44.6' => 'can', 'CAN.G473.19' => 'can', 'CANSAT01G0835' => 'cansat', 'CANSAT11G0246' => 'cansat', 'CANSAT11G1766' => 'cansat', 'CANSAT64G1954' => 'cansat', 'CARHR013330' => 'chi', 'CARHR060530' => 'chi', 'CARHR075300' => 'chi', 'CARHR105120' => 'chi', 'CARHR148910' => 'chi', 'CARHR198830' => 'chi', 'Carub.0001s1275' => 'cru', 'Carub.0002s1437' => 'cru', 'Carub.0003s0044' => 'cru', 'Carub.0003s2787' => 'cru', 'Carub.0005s0597' => 'cru', 'Carub.0006s1266' => 'cru', 'Ca_06935_v3' => 'car', 'Ca_13559_v3' => 'car', 'Ca_16941_v3' => 'car', 'Ca_16960_v3' => 'car', 'Ca_17775_v3' => 'car', 'Ca_30464_v3' => 'car', 'Cc06_g08160' => 'ccan', 'Cc07_g01520' => 'ccan', 'Cc11_g15810' => 'ccan', 'CDE02G2840' => 'cde', 'CDE03G0093' => 'cde', 'CDE04G2127' => 'cde', 'CDE07G1857' => 'cde', 'CDE09G1246' => 'cde', 'Cfa003412' => 'cfa', 'Cfa007341' => 'cfa', 'Cfa009220' => 'cfa', 'Ciclev10008737m.g' => 'ccl', 'Ciclev10015565m.g' => 'ccl', 'Ciclev10031761m.g' => 'ccl', 'CiPaw.03G045300' => 'cil', 'CiPaw.03G247200' => 'cil', 'CiPaw.04G029500' => 'cil', 'CiPaw.04G174000' => 'cil', 'CiPaw.05G181200' => 'cil', 'CiPaw.06G067100' => 'cil', 'ClCG05G025800' => 'cla', 'ClCG06G011400' => 'cla', 'ClCG09G019360' => 'cla', 'COL.COLO4_04827' => 'col', 'COL.COLO4_29170' => 'col', 'COL.COLO4_35131' => 'col', 'COL.COLO4_35132' => 'col', 'Cpa.g.sc33.32' => 'cpa', 'Cpa.g.sc46.29' => 'cpa', 'Cpa.g.sc796.1' => 'cpa', 'CsaV3_1G030420' => 'csa', 'CsaV3_5G027050' => 'csa', 'CsaV3_5G031040' => 'csa', 'CsaV3_UNG023130' => 'csa', 'CSS0007726' => 'camsi', 'CSS0016433' => 'camsi', 'CSS0017656' => 'camsi', 'CSS0025364' => 'camsi', 'CSS0027582' => 'camsi', 'CSS0047288' => 'camsi', 'CSS0049950' => 'camsi', 'DCAR_003843' => 'dca', 'DCAR_007052' => 'dca', 'DCAR_020884' => 'dca', 'DCAR_021730' => 'dca', 'DCAR_024423' => 'dca', 'DCAR_026509' => 'dca', 'DCAR_031158' => 'dca', 'Dinv14728' => 'din', 'Dinv15219' => 'din', 'Dinv25728' => 'din', 'Dinv33428' => 'din', 'Dinv36489' => 'din', 'Dinv41486' => 'din', 'Duzib147G0469' => 'dzi', 'Duzib168G0060' => 'dzi', 'Duzib187G1215' => 'dzi', 'Duzib248G0692' => 'dzi', 'Duzib251G0767' => 'dzi', 'Duzib264G0446' => 'dzi', 'Duzib268G0691' => 'dzi', 'ECA232G4767' => 'eca', 'ECA233G2838' => 'eca', 'ECA234G0391' => 'eca', 'ECA234G0857' => 'eca', 'ECA236G1593' => 'eca', 'ECA238G0565' => 'eca', 'ECA246G1027' => 'eca', 'ECA246G3223' => 'eca', 'ECA246G3470' => 'eca', 'EL10Ac6g13829' => 'bvu', 'EL10Ac6g14093' => 'bvu', 'EL10Ac8g18707' => 'bvu', 'Eucgr.C01369' => 'egr', 'Eucgr.H02492' => 'egr', 'Eucgr.I01733' => 'egr', 'Eucgr.J02255' => 'egr', 'Eucgr.J02257' => 'egr', 'Eucgr.J02258' => 'egr', 'FAN02G1601' => 'fan', 'FAN03G1586' => 'fan', 'FAN03G2986' => 'fan', 'FAN05G4837' => 'fan', 'FAN06G0146' => 'fan', 'FAN07G0858' => 'fan', 'FAN09G3179' => 'fan', 'FAN10G0669' => 'fan', 'FAN12G2358' => 'fan', 'FAN14G4198' => 'fan', 'FAN14G5112' => 'fan', 'FAN17G0342' => 'fan', 'FAN19G0342' => 'fan', 'FAN19G0962' => 'fan', 'FAN19G1101' => 'fan', 'FAN19G1872' => 'fan', 'FAN22G0356' => 'fan', 'FAN23G0744' => 'fan', 'FAN23G1914' => 'fan', 'FAN26G0032' => 'fan', 'FAN28G0625' => 'fan', 'FvH4_1g02710' => 'fve', 'FvH4_1g02720' => 'fve', 'FvH4_4g25670' => 'fve', 'FvH4_6g51700' => 'fve', 'FvH4_7g20170' => 'fve', 'Glyma.05G175000' => 'gma', 'Glyma.08G132300' => 'gma', 'Glyma.11G243000' => 'gma', 'Glyma.13G158900' => 'gma', 'Glyma.17G112400' => 'gma', 'Glyma.18G014100' => 'gma', 'Glyma.19G003100' => 'gma', 'Glyma.19G056500' => 'gma', 'Gohir.A01G158900' => 'ghi', 'Gohir.A05G312600' => 'ghi', 'Gohir.A05G354900' => 'ghi', 'Gohir.A07G037200' => 'ghi', 'Gohir.A09G030000' => 'ghi', 'Gohir.A12G145200' => 'ghi', 'Gohir.D01G151500' => 'ghi', 'Gohir.D04G058300' => 'ghi', 'Gohir.D05G314100' => 'ghi', 'Gohir.D07G041400' => 'ghi', 'Gohir.D09G029700' => 'ghi', 'Gohir.D12G149700' => 'ghi', 'Gorai.001G043800' => 'gra', 'Gorai.002G187800' => 'gra', 'Gorai.006G034700' => 'gra', 'Gorai.008G161200' => 'gra', 'Gorai.009G335700' => 'gra', 'Gorai.012G065000' => 'gra', 'GSVIVG01000535001' => 'vvi', 'GSVIVG01015572001' => 'vvi', 'GSVIVG01032386001' => 'vvi', 'HanXRQChr05g0138531' => 'han', 'HanXRQChr06g0174391' => 'han', 'HanXRQChr07g0199021' => 'han', 'HanXRQChr08g0208211' => 'han', 'HanXRQChr09g0255471' => 'han', 'HanXRQChr10g0315791' => 'han', 'HanXRQChr12g0371991' => 'han', 'HanXRQChr15g0475251' => 'han', 'HanXRQChr17g0540001' => 'han', 'HanXRQChr17g0548631' => 'han', 'HanXRQChr17g0569561' => 'han', 'Haze_12256' => 'cav', 'Haze_14756' => 'cav', 'Haze_25528' => 'cav', 'Hma1.2p1_0079F.1_g041020' => 'hma', 'Hma1.2p1_0818F.1_g223260' => 'hma', 'Hma1.2p1_1747F.1_g300530' => 'hma', 'HPP92_004607' => 'vpl', 'HPP92_004608' => 'vpl', 'HPP92_006181' => 'vpl', 'HPP92_012192' => 'vpl', 'HPP92_015680' => 'vpl', 'HPP92_020249' => 'vpl', 'HPP92_021376' => 'vpl', 'HPP92_024275' => 'vpl', 'Hund06031' => 'sun', 'Hund25391' => 'sun', 'Lalb_Chr07g0185371' => 'lal', 'Lalb_Chr07g0185381' => 'lal', 'Lalb_Chr12g0204011' => 'lal', 'Lalb_Chr13g0301671' => 'lal', 'Lalb_Chr14g0362851' => 'lal', 'Lalb_Chr24g0403581' => 'lal', 'Lj1g0000233' => 'lja', 'Lj2g0018120' => 'lja', 'Lj3C621T0' => 'lonja', 'Lj3P1059T14' => 'lonja', 'Lj3P611T9' => 'lonja', 'Lj3P614T13' => 'lonja', 'Lj3P615T5' => 'lonja', 'Lj4g0012315' => 'lja', 'Lj4g0026182' => 'lja', 'Lj6P813T16' => 'lonja', 'Lj7C427T7' => 'lonja', 'Lj7C427T8' => 'lonja', 'Lj7P600T41' => 'lonja', 'Lju41C42G17' => 'lonja', 'Lsat_1_v5_gn_0_47300' => 'lsa', 'Lsat_1_v5_gn_2_91280' => 'lsa', 'Lsat_1_v5_gn_3_30561' => 'lsa', 'Lsat_1_v5_gn_4_184321' => 'lsa', 'Lsat_1_v5_gn_4_4041' => 'lsa', 'Lsat_1_v5_gn_5_92000' => 'lsa', 'Lsat_1_v5_gn_8_152940' => 'lsa', 'Lsat_1_v5_gn_8_62401' => 'lsa', 'Manes.06G055900' => 'mes', 'Manes.12G022200' => 'mes', 'Manes.13G023300' => 'mes', 'Manes.14G115000' => 'mes', 'Manes.15G151700' => 'mes', 'Manes.17G111300' => 'mes', 'Mapoly0226s0009' => 'mpo', 'MBI02_g25363_MAGBIO' => 'mbi', 'MBI06_g00027_MAGBIO' => 'mbi', 'MBI10_g13034_MAGBIO' => 'mbi', 'MD09G1023400' => 'mdo', 'MD13G1100100' => 'mdo', 'MD15G1169200' => 'mdo', 'MD16G1101100' => 'mdo', 'MD17G1022900' => 'mdo', 'Medtr3g096150' => 'mtr', 'Medtr4g115070' => 'mtr', 'Medtr7g033325' => 'mtr', 'Medtr8g089840' => 'mtr', 'MELO3C010319.2' => 'cme', 'MELO3C011944.2' => 'cme', 'MELO3C021589.2' => 'cme', 'Migut.E00207' => 'egut', 'Migut.H00067' => 'egut', 'Migut.K00433' => 'egut', 'Migut.K00606' => 'egut', 'Migut.K01410' => 'egut', 'MSTRG.13347' => 'ama', 'MSTRG.24045' => 'ama', 'MSTRG.2428' => 'ama', 'MSTRG.26410' => 'ama', 'MSTRG.3139' => 'ama', 'MSTRG.3286' => 'ama', 'MSTRG.563' => 'ama', 'MSTRG.7941' => 'ama', 'Nitab4.5_0000028g0060' => 'nta', 'Nitab4.5_0000065g0260' => 'nta', 'Nitab4.5_0000112g0060' => 'nta', 'Nitab4.5_0000489g0120' => 'nta', 'Nitab4.5_0001776g0050' => 'nta', 'Nitab4.5_0001854g0010' => 'nta', 'Nitab4.5_0001860g0020' => 'nta', 'Nitab4.5_0004352g0010' => 'nta', 'Nitab4.5_0008716g0020' => 'nta', 'Nitab4.5_0008922g0010' => 'nta', 'Nn3g16693' => 'nnu', 'Nn4g22596' => 'nnu', 'Nn7g37639' => 'nnu', 'Oeu001701.1' => 'oeu', 'Oeu018149.1' => 'oeu', 'Oeu026220.1' => 'oeu', 'Oeu038635.1' => 'oeu', 'Oeu049176.1' => 'oeu', 'Oeu056706.1' => 'oeu', 'Oeu056937.1' => 'oeu', 'Oeu057540.1' => 'oeu', 'Os02g0594900' => 'osa', 'Os02g0595100' => 'osa', 'Os04g0477500' => 'osa', 'Os12g0611900' => 'osa', 'Peaxi162Scf00076g00020' => 'pax', 'Peaxi162Scf00128g00217' => 'pax', 'Peaxi162Scf00129g01640' => 'pax', 'Peaxi162Scf00669g00007' => 'pax', 'Peaxi162Scf00700g00421' => 'pax', 'Peaxi162Scf00801g00038' => 'pax', 'Peaxi162Scf00891g00025' => 'pax', 'PGR083G0909' => 'pgr', 'PGR119G1005' => 'pgr', 'PGR142G2236' => 'pgr', 'PGR142G3388' => 'pgr', 'PGSC0003DMG400004514' => 'stu', 'PGSC0003DMG400012635' => 'stu', 'PGSC0003DMG400015730' => 'stu', 'PGSC0003DMG400018611' => 'stu', 'PGSC0003DMG400030897' => 'stu', 'Phvul.001G254800' => 'pvu', 'Phvul.002G260100' => 'pvu', 'Phvul.003G167600' => 'pvu', 'Phvul.004G005100' => 'pvu', 'Potri.001G343600' => 'ptr', 'Potri.006G066700' => 'ptr', 'Potri.008G186000' => 'ptr', 'Potri.010G046900' => 'ptr', 'Potri.018G127900' => 'ptr', 'Pp3c20_17750' => 'ppa', 'Pp3c24_4380' => 'ppa', 'Prupe.1G245800' => 'ppe', 'Prupe.3G293400' => 'ppe', 'Prupe.7G247400' => 'ppe', 'Psat0s145g0120' => 'psa', 'Psat0s595g0040' => 'psa', 'Psat0s595g0120' => 'psa', 'Psat3g175040' => 'psa', 'Psat7g058120' => 'psa', 'PSO017G0428' => 'pso', 'PSO063G7510' => 'pso', 'PSO067G0046' => 'pso', 'PSO478G1073' => 'pso', 'PSO675G3677' => 'pso', 'PSO675G6558' => 'pso', 'PSO675G7520' => 'pso', 'PSO675G8959' => 'pso', 'QL02p074089' => 'qlo', 'QL02p089614' => 'qlo', 'QL03p057736' => 'qlo', 'RcHm_v2.0_Chr1g0364131' => 'rch', 'RcHm_v2.0_Chr2g0087801' => 'rch', 'RcHm_v2.0_Chr2g0087821' => 'rch', 'RcHm_v2.0_Chr2g0173231' => 'rch', 'RcHm_v2.0_Chr4g0433111' => 'rch', 'Rhsim03G0250300' => 'rsi', 'Rhsim08G0048400' => 'rsi', 'Rhsim10G0014800' => 'rsi', 'Rhsim12G0040100' => 'rsi', 'Rhsim12G0109700' => 'rsi', 'Sabra06G0049600' => 'sbr', 'Sabra08G0141000' => 'sbr', 'Sabra10G0021400' => 'sbr', 'Sabra16G0222900' => 'sbr', 'Sabra18G0108600' => 'sbr', 'SalBow1G0433' => 'sbo', 'SalBow1G2038' => 'sbo', 'SalBow1G5003' => 'sbo', 'SalBow7G1197' => 'sbo', 'SalBow8G3506' => 'sbo', 'Sc03g0007300' => 'sci', 'Sc11g0000950' => 'sci', 'Sc14g0008750' => 'sci', 'Sc18g0000420' => 'sci', 'Sed0006754' => 'sed', 'Sed0008741' => 'sed', 'Sed0017172' => 'sed', 'Sed0018925' => 'sed', 'Sed0023326' => 'sed', 'Sed0025909' => 'sed', 'SEGI_05333' => 'sgi', 'SEGI_10362' => 'sgi', 'SEGI_13380' => 'sgi', 'SEGI_24306' => 'sgi', 'SEGI_29077' => 'sgi', 'SEGI_29095' => 'sgi', 'SEGI_36534' => 'sgi', 'SEGI_37506' => 'sgi', 'SEGI_38321' => 'sgi', 'SGA_v2.0_scaffold307G48031' => 'sas', 'SGA_v2.0_scaffold47G17507' => 'sas', 'SGA_v2.0_scaffold63G21736' => 'sas', 'SGA_v2.0_scaffold87G27070' => 'sas', 'SHI17794' => 'shi', 'SHI28851' => 'shi', 'SMO165G0155' => 'smo', 'SMO340G0217' => 'smo', 'SMO367G1210' => 'smo', 'Solyc02g093430.3' => 'sly', 'Solyc05g013580.4' => 'sly', 'Solyc07g008030.3' => 'sly', 'Solyc12g035470.2' => 'sly', 'Sopen02g038020' => 'spe', 'Sopen05g008490' => 'spe', 'Sopen07g003910' => 'spe', 'Sopen12g015240' => 'spe', 'Sp1g11550' => 'spa', 'Sp2g16710' => 'spa', 'Sp3g00430' => 'spa', 'Sp3g26780' => 'spa', 'Sp5g22900' => 'spa', 'Sp6g29530' => 'spa', 'TAR371G0794' => 'tar', 'TAR374G0164' => 'tar', 'TAR622G0165' => 'tar', 'TAR626G0929' => 'tar', 'TAR629G2155' => 'tar', 'THA.LOC104805282' => 'tha', 'THA.LOC104805363' => 'tha', 'THA.LOC104808968' => 'tha', 'THA.LOC104821093' => 'tha', 'THA.LOC104823953' => 'tha', 'THA.LOC104825562' => 'tha', 'THA.LOC104825665' => 'tha', 'Thecc.02G261400' => 'tca', 'Thecc.04G019200' => 'tca', 'Thecc.09G130400' => 'tca', 'Thhalv10004374m.g' => 'esa', 'Thhalv10007850m.g' => 'esa', 'Thhalv10013782m.g' => 'esa', 'Thhalv10018686m.g' => 'esa', 'Thhalv10020899m.g' => 'esa', 'Thhalv10022755m.g' => 'esa', 'TPR.G23851' => 'tpr', 'TPR.G26500' => 'tpr', 'TPR.G27267' => 'tpr', 'TPR.G32001' => 'tpr', 'TPR.G6251' => 'tpr', 'TPR.G8167' => 'tpr', 'TWI12G1330' => 'twi', 'TWI18G1239' => 'twi', 'TWI34G0979' => 'twi', 'TWI36G0670' => 'twi', 'TWI36G0707' => 'twi', 'TWI56G0233' => 'twi', 'TWI75G1809' => 'twi', 'unitig_21.g20874' => 'ugi', 'unitig_26.g10343' => 'ugi', 'unitig_46.g18392' => 'ugi', 'unitig_52.g17178' => 'ugi', 'unitig_8.g2934' => 'ugi', 'vmacro01122' => 'vma', 'vmacro05875' => 'vma', 'vmacro06147' => 'vma', 'vmacro16191' => 'vma', 'vmacro18293' => 'vma', 'VMungo0251G3707' => 'vmu', 'VMungo0464G1521' => 'vmu', 'VMungo1215G0205' => 'vmu', 'VMungo1383G2484' => 'vmu', 'Zm00001eb079610' => 'zma', 'Zm00001eb135990' => 'zma', 'Zm00001eb183710' => 'zma', 'Zm00001eb246020' => 'zma' ) $gf_id = 'HOM05D001124' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001124' ) $data_identifier = 'HOM05D001124' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 6, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 7, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 21, 'bol' => (int) 10, 'bra' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 6, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 9, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 21, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 8, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 10, 'lsa' => (int) 8, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 8, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 9, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb246020' $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' => 'HOM05D001124', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '548', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02520' => 'bna', 'A03p06630' => 'bna', 'A05p44460' => 'bna', 'A06p08710' => 'bna', 'A06p41090' => 'bna', 'A07p32320' => 'bna', 'A08p32520' => 'bna', 'A09p10360' => 'bna', 'A10p24080' => 'bna', 'Aa31LG11G15250' => 'aar', 'Aa31LG1G1800' => 'aar', 'Aa31LG2G5120' => 'aar', 'Aa31LG2G6070' => 'aar', 'Aa31LG5G10770' => 'aar', 'Aa31sc61G90' => 'aar', 'Actinidia01352' => 'ach', 'Actinidia05983' => 'ach', 'Actinidia08133' => 'ach', 'Actinidia15101' => 'ach', 'Actinidia26379' => 'ach', 'Actinidia35778' => 'ach', 'Actinidia36123' => 'ach', 'Actinidia37436' => 'ach', 'Actinidia38730' => 'ach', 'Ah.02g128210' => 'amhyb', 'Ah.03g132990' => 'amhyb', 'Ah.14g079410' => 'amhyb', 'AL1G24640' => 'aly', 'AL2G26680' => 'aly', 'AL3G10530' => 'aly', 'AL3G45230' => 'aly', 'AL5G15230' => 'aly', 'AL5G16960' => 'aly', 'AL6G25210' => 'aly', 'Aqoxy2G00441' => 'aox', 'Aqoxy3G01236' => 'aox', 'Aqoxy5G03746' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3RQ047' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C7GMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9C8JER' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MBL6KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YXCZ83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZANX40' => 'arhy', 'AT1G12990' => 'ath', 'AT1G67880' => 'ath', 'AT2G13290' => 'ath', 'AT3G01620' => 'ath', 'AT3G26445' => 'ath', 'AT3G27540' => 'ath', 'AT5G14480' => 'ath', 'ATR0824G026' => 'atr', 'ATR1098G019' => 'atr', 'Atru.chr11.2145' => 'acertr', 'Atru.chr2.3636' => 'acertr', 'Atru.chr2.3644' => 'acertr', 'Atru.chr6.2422' => 'acertr', 'Atru.chr7.1112' => 'acertr', 'AUR62005469' => 'cqu', 'AUR62011166' => 'cqu', 'AUR62013319' => 'cqu', 'AUR62024273' => 'cqu', 'AUR62028420' => 'cqu', 'AUR62041942' => 'cqu', 'BcaB01g04969' => 'bca', 'BcaB01g06371' => 'bca', 'BcaB02g11494' => 'bca', 'BcaB03g15382' => 'bca', 'BcaB08g36994' => 'bca', 'BcaC03g13477' => 'bca', 'BcaC03g13478' => 'bca', 'BcaC03g13480' => 'bca', 'BcaC03g13481' => 'bca', 'BcaC03g13486' => 'bca', 'BcaC04g19031' => 'bca', 'BcaC04g23085' => 'bca', 'BcaC05g25094' => 'bca', 'BcaC05g25096' => 'bca', 'BcaC05g25138' => 'bca', 'BcaC05g30416' => 'bca', 'BcaC05g30455' => 'bca', 'BcaC06g30979' => 'bca', 'BcaC06g33805' => 'bca', 'BcaC08g46021' => 'bca', 'BcaNung03154' => 'bca', 'BolC2t06623H' => 'bol', 'BolC2t06632H' => 'bol', 'BolC2t06635H' => 'bol', 'BolC2t06638H' => 'bol', 'BolC3t13266H' => 'bol', 'BolC5t29776H' => 'bol', 'BolC6t38912H' => 'bol', 'BolC7t44183H' => 'bol', 'BolC9t54123H' => 'bol', 'BolC9t59107H' => 'bol', 'BraA02t05221Z' => 'bra', 'BraA03t09996Z' => 'bra', 'BraA05t23210Z' => 'bra', 'BraA06t24068Z' => 'bra', 'BraA06t27032Z' => 'bra', 'BraA08t35176Z' => 'bra', 'BraA09t36680Z' => 'bra', 'BraA10t44471Z' => 'bra', 'C02p06760' => 'bna', 'C02p06890' => 'bna', 'C02p07010' => 'bna', 'C03p07660' => 'bna', 'C05p10300' => 'bna', 'C06p38150' => 'bna', 'C07p36650' => 'bna', 'C08p15770' => 'bna', 'C09p12300' => 'bna', 'C09p62700' => 'bna', 'C09p75040' => 'bna', 'CAN.G13.1' => 'can', 'CAN.G138.4' => 'can', 'CAN.G44.6' => 'can', 'CAN.G473.19' => 'can', 'CANSAT01G0835' => 'cansat', 'CANSAT11G0246' => 'cansat', 'CANSAT11G1766' => 'cansat', 'CANSAT64G1954' => 'cansat', 'CARHR013330' => 'chi', 'CARHR060530' => 'chi', 'CARHR075300' => 'chi', 'CARHR105120' => 'chi', 'CARHR148910' => 'chi', 'CARHR198830' => 'chi', 'Carub.0001s1275' => 'cru', 'Carub.0002s1437' => 'cru', 'Carub.0003s0044' => 'cru', 'Carub.0003s2787' => 'cru', 'Carub.0005s0597' => 'cru', 'Carub.0006s1266' => 'cru', 'Ca_06935_v3' => 'car', 'Ca_13559_v3' => 'car', 'Ca_16941_v3' => 'car', 'Ca_16960_v3' => 'car', 'Ca_17775_v3' => 'car', 'Ca_30464_v3' => 'car', 'Cc06_g08160' => 'ccan', 'Cc07_g01520' => 'ccan', 'Cc11_g15810' => 'ccan', 'CDE02G2840' => 'cde', 'CDE03G0093' => 'cde', 'CDE04G2127' => 'cde', 'CDE07G1857' => 'cde', 'CDE09G1246' => 'cde', 'Cfa003412' => 'cfa', 'Cfa007341' => 'cfa', 'Cfa009220' => 'cfa', 'Ciclev10008737m.g' => 'ccl', 'Ciclev10015565m.g' => 'ccl', 'Ciclev10031761m.g' => 'ccl', 'CiPaw.03G045300' => 'cil', 'CiPaw.03G247200' => 'cil', 'CiPaw.04G029500' => 'cil', 'CiPaw.04G174000' => 'cil', 'CiPaw.05G181200' => 'cil', 'CiPaw.06G067100' => 'cil', 'ClCG05G025800' => 'cla', 'ClCG06G011400' => 'cla', 'ClCG09G019360' => 'cla', 'COL.COLO4_04827' => 'col', 'COL.COLO4_29170' => 'col', 'COL.COLO4_35131' => 'col', 'COL.COLO4_35132' => 'col', 'Cpa.g.sc33.32' => 'cpa', 'Cpa.g.sc46.29' => 'cpa', 'Cpa.g.sc796.1' => 'cpa', 'CsaV3_1G030420' => 'csa', 'CsaV3_5G027050' => 'csa', 'CsaV3_5G031040' => 'csa', 'CsaV3_UNG023130' => 'csa', 'CSS0007726' => 'camsi', 'CSS0016433' => 'camsi', 'CSS0017656' => 'camsi', 'CSS0025364' => 'camsi', 'CSS0027582' => 'camsi', 'CSS0047288' => 'camsi', 'CSS0049950' => 'camsi', 'DCAR_003843' => 'dca', 'DCAR_007052' => 'dca', 'DCAR_020884' => 'dca', 'DCAR_021730' => 'dca', 'DCAR_024423' => 'dca', 'DCAR_026509' => 'dca', 'DCAR_031158' => 'dca', 'Dinv14728' => 'din', 'Dinv15219' => 'din', 'Dinv25728' => 'din', 'Dinv33428' => 'din', 'Dinv36489' => 'din', 'Dinv41486' => 'din', 'Duzib147G0469' => 'dzi', 'Duzib168G0060' => 'dzi', 'Duzib187G1215' => 'dzi', 'Duzib248G0692' => 'dzi', 'Duzib251G0767' => 'dzi', 'Duzib264G0446' => 'dzi', 'Duzib268G0691' => 'dzi', 'ECA232G4767' => 'eca', 'ECA233G2838' => 'eca', 'ECA234G0391' => 'eca', 'ECA234G0857' => 'eca', 'ECA236G1593' => 'eca', 'ECA238G0565' => 'eca', 'ECA246G1027' => 'eca', 'ECA246G3223' => 'eca', 'ECA246G3470' => 'eca', 'EL10Ac6g13829' => 'bvu', 'EL10Ac6g14093' => 'bvu', 'EL10Ac8g18707' => 'bvu', 'Eucgr.C01369' => 'egr', 'Eucgr.H02492' => 'egr', 'Eucgr.I01733' => 'egr', 'Eucgr.J02255' => 'egr', 'Eucgr.J02257' => 'egr', 'Eucgr.J02258' => 'egr', 'FAN02G1601' => 'fan', 'FAN03G1586' => 'fan', 'FAN03G2986' => 'fan', 'FAN05G4837' => 'fan', 'FAN06G0146' => 'fan', 'FAN07G0858' => 'fan', 'FAN09G3179' => 'fan', 'FAN10G0669' => 'fan', 'FAN12G2358' => 'fan', 'FAN14G4198' => 'fan', 'FAN14G5112' => 'fan', 'FAN17G0342' => 'fan', 'FAN19G0342' => 'fan', 'FAN19G0962' => 'fan', 'FAN19G1101' => 'fan', 'FAN19G1872' => 'fan', 'FAN22G0356' => 'fan', 'FAN23G0744' => 'fan', 'FAN23G1914' => 'fan', 'FAN26G0032' => 'fan', 'FAN28G0625' => 'fan', 'FvH4_1g02710' => 'fve', 'FvH4_1g02720' => 'fve', 'FvH4_4g25670' => 'fve', 'FvH4_6g51700' => 'fve', 'FvH4_7g20170' => 'fve', 'Glyma.05G175000' => 'gma', 'Glyma.08G132300' => 'gma', 'Glyma.11G243000' => 'gma', 'Glyma.13G158900' => 'gma', 'Glyma.17G112400' => 'gma', 'Glyma.18G014100' => 'gma', 'Glyma.19G003100' => 'gma', 'Glyma.19G056500' => 'gma', 'Gohir.A01G158900' => 'ghi', 'Gohir.A05G312600' => 'ghi', 'Gohir.A05G354900' => 'ghi', 'Gohir.A07G037200' => 'ghi', 'Gohir.A09G030000' => 'ghi', 'Gohir.A12G145200' => 'ghi', 'Gohir.D01G151500' => 'ghi', 'Gohir.D04G058300' => 'ghi', 'Gohir.D05G314100' => 'ghi', 'Gohir.D07G041400' => 'ghi', 'Gohir.D09G029700' => 'ghi', 'Gohir.D12G149700' => 'ghi', 'Gorai.001G043800' => 'gra', 'Gorai.002G187800' => 'gra', 'Gorai.006G034700' => 'gra', 'Gorai.008G161200' => 'gra', 'Gorai.009G335700' => 'gra', 'Gorai.012G065000' => 'gra', 'GSVIVG01000535001' => 'vvi', 'GSVIVG01015572001' => 'vvi', 'GSVIVG01032386001' => 'vvi', 'HanXRQChr05g0138531' => 'han', 'HanXRQChr06g0174391' => 'han', 'HanXRQChr07g0199021' => 'han', 'HanXRQChr08g0208211' => 'han', 'HanXRQChr09g0255471' => 'han', 'HanXRQChr10g0315791' => 'han', 'HanXRQChr12g0371991' => 'han', 'HanXRQChr15g0475251' => 'han', 'HanXRQChr17g0540001' => 'han', 'HanXRQChr17g0548631' => 'han', 'HanXRQChr17g0569561' => 'han', 'Haze_12256' => 'cav', 'Haze_14756' => 'cav', 'Haze_25528' => 'cav', 'Hma1.2p1_0079F.1_g041020' => 'hma', 'Hma1.2p1_0818F.1_g223260' => 'hma', 'Hma1.2p1_1747F.1_g300530' => 'hma', 'HPP92_004607' => 'vpl', 'HPP92_004608' => 'vpl', 'HPP92_006181' => 'vpl', 'HPP92_012192' => 'vpl', 'HPP92_015680' => 'vpl', 'HPP92_020249' => 'vpl', 'HPP92_021376' => 'vpl', 'HPP92_024275' => 'vpl', 'Hund06031' => 'sun', 'Hund25391' => 'sun', 'Lalb_Chr07g0185371' => 'lal', 'Lalb_Chr07g0185381' => 'lal', 'Lalb_Chr12g0204011' => 'lal', 'Lalb_Chr13g0301671' => 'lal', 'Lalb_Chr14g0362851' => 'lal', 'Lalb_Chr24g0403581' => 'lal', 'Lj1g0000233' => 'lja', 'Lj2g0018120' => 'lja', 'Lj3C621T0' => 'lonja', 'Lj3P1059T14' => 'lonja', 'Lj3P611T9' => 'lonja', 'Lj3P614T13' => 'lonja', 'Lj3P615T5' => 'lonja', 'Lj4g0012315' => 'lja', 'Lj4g0026182' => 'lja', 'Lj6P813T16' => 'lonja', 'Lj7C427T7' => 'lonja', 'Lj7C427T8' => 'lonja', 'Lj7P600T41' => 'lonja', 'Lju41C42G17' => 'lonja', 'Lsat_1_v5_gn_0_47300' => 'lsa', 'Lsat_1_v5_gn_2_91280' => 'lsa', 'Lsat_1_v5_gn_3_30561' => 'lsa', 'Lsat_1_v5_gn_4_184321' => 'lsa', 'Lsat_1_v5_gn_4_4041' => 'lsa', 'Lsat_1_v5_gn_5_92000' => 'lsa', 'Lsat_1_v5_gn_8_152940' => 'lsa', 'Lsat_1_v5_gn_8_62401' => 'lsa', 'Manes.06G055900' => 'mes', 'Manes.12G022200' => 'mes', 'Manes.13G023300' => 'mes', 'Manes.14G115000' => 'mes', 'Manes.15G151700' => 'mes', 'Manes.17G111300' => 'mes', 'Mapoly0226s0009' => 'mpo', 'MBI02_g25363_MAGBIO' => 'mbi', 'MBI06_g00027_MAGBIO' => 'mbi', 'MBI10_g13034_MAGBIO' => 'mbi', 'MD09G1023400' => 'mdo', 'MD13G1100100' => 'mdo', 'MD15G1169200' => 'mdo', 'MD16G1101100' => 'mdo', 'MD17G1022900' => 'mdo', 'Medtr3g096150' => 'mtr', 'Medtr4g115070' => 'mtr', 'Medtr7g033325' => 'mtr', 'Medtr8g089840' => 'mtr', 'MELO3C010319.2' => 'cme', 'MELO3C011944.2' => 'cme', 'MELO3C021589.2' => 'cme', 'Migut.E00207' => 'egut', 'Migut.H00067' => 'egut', 'Migut.K00433' => 'egut', 'Migut.K00606' => 'egut', 'Migut.K01410' => 'egut', 'MSTRG.13347' => 'ama', 'MSTRG.24045' => 'ama', 'MSTRG.2428' => 'ama', 'MSTRG.26410' => 'ama', 'MSTRG.3139' => 'ama', 'MSTRG.3286' => 'ama', 'MSTRG.563' => 'ama', 'MSTRG.7941' => 'ama', 'Nitab4.5_0000028g0060' => 'nta', 'Nitab4.5_0000065g0260' => 'nta', 'Nitab4.5_0000112g0060' => 'nta', 'Nitab4.5_0000489g0120' => 'nta', 'Nitab4.5_0001776g0050' => 'nta', 'Nitab4.5_0001854g0010' => 'nta', 'Nitab4.5_0001860g0020' => 'nta', 'Nitab4.5_0004352g0010' => 'nta', 'Nitab4.5_0008716g0020' => 'nta', 'Nitab4.5_0008922g0010' => 'nta', 'Nn3g16693' => 'nnu', 'Nn4g22596' => 'nnu', 'Nn7g37639' => 'nnu', 'Oeu001701.1' => 'oeu', 'Oeu018149.1' => 'oeu', 'Oeu026220.1' => 'oeu', 'Oeu038635.1' => 'oeu', 'Oeu049176.1' => 'oeu', 'Oeu056706.1' => 'oeu', 'Oeu056937.1' => 'oeu', 'Oeu057540.1' => 'oeu', 'Os02g0594900' => 'osa', 'Os02g0595100' => 'osa', 'Os04g0477500' => 'osa', 'Os12g0611900' => 'osa', 'Peaxi162Scf00076g00020' => 'pax', 'Peaxi162Scf00128g00217' => 'pax', 'Peaxi162Scf00129g01640' => 'pax', 'Peaxi162Scf00669g00007' => 'pax', 'Peaxi162Scf00700g00421' => 'pax', 'Peaxi162Scf00801g00038' => 'pax', 'Peaxi162Scf00891g00025' => 'pax', 'PGR083G0909' => 'pgr', 'PGR119G1005' => 'pgr', 'PGR142G2236' => 'pgr', 'PGR142G3388' => 'pgr', 'PGSC0003DMG400004514' => 'stu', 'PGSC0003DMG400012635' => 'stu', 'PGSC0003DMG400015730' => 'stu', 'PGSC0003DMG400018611' => 'stu', 'PGSC0003DMG400030897' => 'stu', 'Phvul.001G254800' => 'pvu', 'Phvul.002G260100' => 'pvu', 'Phvul.003G167600' => 'pvu', 'Phvul.004G005100' => 'pvu', 'Potri.001G343600' => 'ptr', 'Potri.006G066700' => 'ptr', 'Potri.008G186000' => 'ptr', 'Potri.010G046900' => 'ptr', 'Potri.018G127900' => 'ptr', 'Pp3c20_17750' => 'ppa', 'Pp3c24_4380' => 'ppa', 'Prupe.1G245800' => 'ppe', 'Prupe.3G293400' => 'ppe', 'Prupe.7G247400' => 'ppe', 'Psat0s145g0120' => 'psa', 'Psat0s595g0040' => 'psa', 'Psat0s595g0120' => 'psa', 'Psat3g175040' => 'psa', 'Psat7g058120' => 'psa', 'PSO017G0428' => 'pso', 'PSO063G7510' => 'pso', 'PSO067G0046' => 'pso', 'PSO478G1073' => 'pso', 'PSO675G3677' => 'pso', 'PSO675G6558' => 'pso', 'PSO675G7520' => 'pso', 'PSO675G8959' => 'pso', 'QL02p074089' => 'qlo', 'QL02p089614' => 'qlo', 'QL03p057736' => 'qlo', 'RcHm_v2.0_Chr1g0364131' => 'rch', 'RcHm_v2.0_Chr2g0087801' => 'rch', 'RcHm_v2.0_Chr2g0087821' => 'rch', 'RcHm_v2.0_Chr2g0173231' => 'rch', 'RcHm_v2.0_Chr4g0433111' => 'rch', 'Rhsim03G0250300' => 'rsi', 'Rhsim08G0048400' => 'rsi', 'Rhsim10G0014800' => 'rsi', 'Rhsim12G0040100' => 'rsi', 'Rhsim12G0109700' => 'rsi', 'Sabra06G0049600' => 'sbr', 'Sabra08G0141000' => 'sbr', 'Sabra10G0021400' => 'sbr', 'Sabra16G0222900' => 'sbr', 'Sabra18G0108600' => 'sbr', 'SalBow1G0433' => 'sbo', 'SalBow1G2038' => 'sbo', 'SalBow1G5003' => 'sbo', 'SalBow7G1197' => 'sbo', 'SalBow8G3506' => 'sbo', 'Sc03g0007300' => 'sci', 'Sc11g0000950' => 'sci', 'Sc14g0008750' => 'sci', 'Sc18g0000420' => 'sci', 'Sed0006754' => 'sed', 'Sed0008741' => 'sed', 'Sed0017172' => 'sed', 'Sed0018925' => 'sed', 'Sed0023326' => 'sed', 'Sed0025909' => 'sed', 'SEGI_05333' => 'sgi', 'SEGI_10362' => 'sgi', 'SEGI_13380' => 'sgi', 'SEGI_24306' => 'sgi', 'SEGI_29077' => 'sgi', 'SEGI_29095' => 'sgi', 'SEGI_36534' => 'sgi', 'SEGI_37506' => 'sgi', 'SEGI_38321' => 'sgi', 'SGA_v2.0_scaffold307G48031' => 'sas', 'SGA_v2.0_scaffold47G17507' => 'sas', 'SGA_v2.0_scaffold63G21736' => 'sas', 'SGA_v2.0_scaffold87G27070' => 'sas', 'SHI17794' => 'shi', 'SHI28851' => 'shi', 'SMO165G0155' => 'smo', 'SMO340G0217' => 'smo', 'SMO367G1210' => 'smo', 'Solyc02g093430.3' => 'sly', 'Solyc05g013580.4' => 'sly', 'Solyc07g008030.3' => 'sly', 'Solyc12g035470.2' => 'sly', 'Sopen02g038020' => 'spe', 'Sopen05g008490' => 'spe', 'Sopen07g003910' => 'spe', 'Sopen12g015240' => 'spe', 'Sp1g11550' => 'spa', 'Sp2g16710' => 'spa', 'Sp3g00430' => 'spa', 'Sp3g26780' => 'spa', 'Sp5g22900' => 'spa', 'Sp6g29530' => 'spa', 'TAR371G0794' => 'tar', 'TAR374G0164' => 'tar', 'TAR622G0165' => 'tar', 'TAR626G0929' => 'tar', 'TAR629G2155' => 'tar', 'THA.LOC104805282' => 'tha', 'THA.LOC104805363' => 'tha', 'THA.LOC104808968' => 'tha', 'THA.LOC104821093' => 'tha', 'THA.LOC104823953' => 'tha', 'THA.LOC104825562' => 'tha', 'THA.LOC104825665' => 'tha', 'Thecc.02G261400' => 'tca', 'Thecc.04G019200' => 'tca', 'Thecc.09G130400' => 'tca', 'Thhalv10004374m.g' => 'esa', 'Thhalv10007850m.g' => 'esa', 'Thhalv10013782m.g' => 'esa', 'Thhalv10018686m.g' => 'esa', 'Thhalv10020899m.g' => 'esa', 'Thhalv10022755m.g' => 'esa', 'TPR.G23851' => 'tpr', 'TPR.G26500' => 'tpr', 'TPR.G27267' => 'tpr', 'TPR.G32001' => 'tpr', 'TPR.G6251' => 'tpr', 'TPR.G8167' => 'tpr', 'TWI12G1330' => 'twi', 'TWI18G1239' => 'twi', 'TWI34G0979' => 'twi', 'TWI36G0670' => 'twi', 'TWI36G0707' => 'twi', 'TWI56G0233' => 'twi', 'TWI75G1809' => 'twi', 'unitig_21.g20874' => 'ugi', 'unitig_26.g10343' => 'ugi', 'unitig_46.g18392' => 'ugi', 'unitig_52.g17178' => 'ugi', 'unitig_8.g2934' => 'ugi', 'vmacro01122' => 'vma', 'vmacro05875' => 'vma', 'vmacro06147' => 'vma', 'vmacro16191' => 'vma', 'vmacro18293' => 'vma', 'VMungo0251G3707' => 'vmu', 'VMungo0464G1521' => 'vmu', 'VMungo1215G0205' => 'vmu', 'VMungo1383G2484' => 'vmu', 'Zm00001eb079610' => 'zma', 'Zm00001eb135990' => 'zma', 'Zm00001eb183710' => 'zma', 'Zm00001eb246020' => 'zma' ), 'gf_id' => 'HOM05D001124', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001124' ), 'data_identifier' => 'HOM05D001124', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001124', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '548', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02520' => 'bna', 'A03p06630' => 'bna', 'A05p44460' => 'bna', 'A06p08710' => 'bna', 'A06p41090' => 'bna', 'A07p32320' => 'bna', 'A08p32520' => 'bna', 'A09p10360' => 'bna', 'A10p24080' => 'bna', 'Aa31LG11G15250' => 'aar', 'Aa31LG1G1800' => 'aar', 'Aa31LG2G5120' => 'aar', 'Aa31LG2G6070' => 'aar', 'Aa31LG5G10770' => 'aar', 'Aa31sc61G90' => 'aar', 'Actinidia01352' => 'ach', 'Actinidia05983' => 'ach', 'Actinidia08133' => 'ach', 'Actinidia15101' => 'ach', 'Actinidia26379' => 'ach', 'Actinidia35778' => 'ach', 'Actinidia36123' => 'ach', 'Actinidia37436' => 'ach', 'Actinidia38730' => 'ach', 'Ah.02g128210' => 'amhyb', 'Ah.03g132990' => 'amhyb', 'Ah.14g079410' => 'amhyb', 'AL1G24640' => 'aly', 'AL2G26680' => 'aly', 'AL3G10530' => 'aly', 'AL3G45230' => 'aly', 'AL5G15230' => 'aly', 'AL5G16960' => 'aly', 'AL6G25210' => 'aly', 'Aqoxy2G00441' => 'aox', 'Aqoxy3G01236' => 'aox', 'Aqoxy5G03746' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3RQ047' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C7GMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9C8JER' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MBL6KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YXCZ83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZANX40' => 'arhy', 'AT1G12990' => 'ath', 'AT1G67880' => 'ath', 'AT2G13290' => 'ath', 'AT3G01620' => 'ath', 'AT3G26445' => 'ath', 'AT3G27540' => 'ath', 'AT5G14480' => 'ath', 'ATR0824G026' => 'atr', 'ATR1098G019' => 'atr', 'Atru.chr11.2145' => 'acertr', 'Atru.chr2.3636' => 'acertr', 'Atru.chr2.3644' => 'acertr', 'Atru.chr6.2422' => 'acertr', 'Atru.chr7.1112' => 'acertr', 'AUR62005469' => 'cqu', 'AUR62011166' => 'cqu', 'AUR62013319' => 'cqu', 'AUR62024273' => 'cqu', 'AUR62028420' => 'cqu', 'AUR62041942' => 'cqu', 'BcaB01g04969' => 'bca', 'BcaB01g06371' => 'bca', 'BcaB02g11494' => 'bca', 'BcaB03g15382' => 'bca', 'BcaB08g36994' => 'bca', 'BcaC03g13477' => 'bca', 'BcaC03g13478' => 'bca', 'BcaC03g13480' => 'bca', 'BcaC03g13481' => 'bca', 'BcaC03g13486' => 'bca', 'BcaC04g19031' => 'bca', 'BcaC04g23085' => 'bca', 'BcaC05g25094' => 'bca', 'BcaC05g25096' => 'bca', 'BcaC05g25138' => 'bca', 'BcaC05g30416' => 'bca', 'BcaC05g30455' => 'bca', 'BcaC06g30979' => 'bca', 'BcaC06g33805' => 'bca', 'BcaC08g46021' => 'bca', 'BcaNung03154' => 'bca', 'BolC2t06623H' => 'bol', 'BolC2t06632H' => 'bol', 'BolC2t06635H' => 'bol', 'BolC2t06638H' => 'bol', 'BolC3t13266H' => 'bol', 'BolC5t29776H' => 'bol', 'BolC6t38912H' => 'bol', 'BolC7t44183H' => 'bol', 'BolC9t54123H' => 'bol', 'BolC9t59107H' => 'bol', 'BraA02t05221Z' => 'bra', 'BraA03t09996Z' => 'bra', 'BraA05t23210Z' => 'bra', 'BraA06t24068Z' => 'bra', 'BraA06t27032Z' => 'bra', 'BraA08t35176Z' => 'bra', 'BraA09t36680Z' => 'bra', 'BraA10t44471Z' => 'bra', 'C02p06760' => 'bna', 'C02p06890' => 'bna', 'C02p07010' => 'bna', 'C03p07660' => 'bna', 'C05p10300' => 'bna', 'C06p38150' => 'bna', 'C07p36650' => 'bna', 'C08p15770' => 'bna', 'C09p12300' => 'bna', 'C09p62700' => 'bna', 'C09p75040' => 'bna', 'CAN.G13.1' => 'can', 'CAN.G138.4' => 'can', 'CAN.G44.6' => 'can', 'CAN.G473.19' => 'can', 'CANSAT01G0835' => 'cansat', 'CANSAT11G0246' => 'cansat', 'CANSAT11G1766' => 'cansat', 'CANSAT64G1954' => 'cansat', 'CARHR013330' => 'chi', 'CARHR060530' => 'chi', 'CARHR075300' => 'chi', 'CARHR105120' => 'chi', 'CARHR148910' => 'chi', 'CARHR198830' => 'chi', 'Carub.0001s1275' => 'cru', 'Carub.0002s1437' => 'cru', 'Carub.0003s0044' => 'cru', 'Carub.0003s2787' => 'cru', 'Carub.0005s0597' => 'cru', 'Carub.0006s1266' => 'cru', 'Ca_06935_v3' => 'car', 'Ca_13559_v3' => 'car', 'Ca_16941_v3' => 'car', 'Ca_16960_v3' => 'car', 'Ca_17775_v3' => 'car', 'Ca_30464_v3' => 'car', 'Cc06_g08160' => 'ccan', 'Cc07_g01520' => 'ccan', 'Cc11_g15810' => 'ccan', 'CDE02G2840' => 'cde', 'CDE03G0093' => 'cde', 'CDE04G2127' => 'cde', 'CDE07G1857' => 'cde', 'CDE09G1246' => 'cde', 'Cfa003412' => 'cfa', 'Cfa007341' => 'cfa', 'Cfa009220' => 'cfa', 'Ciclev10008737m.g' => 'ccl', 'Ciclev10015565m.g' => 'ccl', 'Ciclev10031761m.g' => 'ccl', 'CiPaw.03G045300' => 'cil', 'CiPaw.03G247200' => 'cil', 'CiPaw.04G029500' => 'cil', 'CiPaw.04G174000' => 'cil', 'CiPaw.05G181200' => 'cil', 'CiPaw.06G067100' => 'cil', 'ClCG05G025800' => 'cla', 'ClCG06G011400' => 'cla', 'ClCG09G019360' => 'cla', 'COL.COLO4_04827' => 'col', 'COL.COLO4_29170' => 'col', 'COL.COLO4_35131' => 'col', 'COL.COLO4_35132' => 'col', 'Cpa.g.sc33.32' => 'cpa', 'Cpa.g.sc46.29' => 'cpa', 'Cpa.g.sc796.1' => 'cpa', 'CsaV3_1G030420' => 'csa', 'CsaV3_5G027050' => 'csa', 'CsaV3_5G031040' => 'csa', 'CsaV3_UNG023130' => 'csa', 'CSS0007726' => 'camsi', 'CSS0016433' => 'camsi', 'CSS0017656' => 'camsi', 'CSS0025364' => 'camsi', 'CSS0027582' => 'camsi', 'CSS0047288' => 'camsi', 'CSS0049950' => 'camsi', 'DCAR_003843' => 'dca', 'DCAR_007052' => 'dca', 'DCAR_020884' => 'dca', 'DCAR_021730' => 'dca', 'DCAR_024423' => 'dca', 'DCAR_026509' => 'dca', 'DCAR_031158' => 'dca', 'Dinv14728' => 'din', 'Dinv15219' => 'din', 'Dinv25728' => 'din', 'Dinv33428' => 'din', 'Dinv36489' => 'din', 'Dinv41486' => 'din', 'Duzib147G0469' => 'dzi', 'Duzib168G0060' => 'dzi', 'Duzib187G1215' => 'dzi', 'Duzib248G0692' => 'dzi', 'Duzib251G0767' => 'dzi', 'Duzib264G0446' => 'dzi', 'Duzib268G0691' => 'dzi', 'ECA232G4767' => 'eca', 'ECA233G2838' => 'eca', 'ECA234G0391' => 'eca', 'ECA234G0857' => 'eca', 'ECA236G1593' => 'eca', 'ECA238G0565' => 'eca', 'ECA246G1027' => 'eca', 'ECA246G3223' => 'eca', 'ECA246G3470' => 'eca', 'EL10Ac6g13829' => 'bvu', 'EL10Ac6g14093' => 'bvu', 'EL10Ac8g18707' => 'bvu', 'Eucgr.C01369' => 'egr', 'Eucgr.H02492' => 'egr', 'Eucgr.I01733' => 'egr', 'Eucgr.J02255' => 'egr', 'Eucgr.J02257' => 'egr', 'Eucgr.J02258' => 'egr', 'FAN02G1601' => 'fan', 'FAN03G1586' => 'fan', 'FAN03G2986' => 'fan', 'FAN05G4837' => 'fan', 'FAN06G0146' => 'fan', 'FAN07G0858' => 'fan', 'FAN09G3179' => 'fan', 'FAN10G0669' => 'fan', 'FAN12G2358' => 'fan', 'FAN14G4198' => 'fan', 'FAN14G5112' => 'fan', 'FAN17G0342' => 'fan', 'FAN19G0342' => 'fan', 'FAN19G0962' => 'fan', 'FAN19G1101' => 'fan', 'FAN19G1872' => 'fan', 'FAN22G0356' => 'fan', 'FAN23G0744' => 'fan', 'FAN23G1914' => 'fan', 'FAN26G0032' => 'fan', 'FAN28G0625' => 'fan', 'FvH4_1g02710' => 'fve', 'FvH4_1g02720' => 'fve', 'FvH4_4g25670' => 'fve', 'FvH4_6g51700' => 'fve', 'FvH4_7g20170' => 'fve', 'Glyma.05G175000' => 'gma', 'Glyma.08G132300' => 'gma', 'Glyma.11G243000' => 'gma', 'Glyma.13G158900' => 'gma', 'Glyma.17G112400' => 'gma', 'Glyma.18G014100' => 'gma', 'Glyma.19G003100' => 'gma', 'Glyma.19G056500' => 'gma', 'Gohir.A01G158900' => 'ghi', 'Gohir.A05G312600' => 'ghi', 'Gohir.A05G354900' => 'ghi', 'Gohir.A07G037200' => 'ghi', 'Gohir.A09G030000' => 'ghi', 'Gohir.A12G145200' => 'ghi', 'Gohir.D01G151500' => 'ghi', 'Gohir.D04G058300' => 'ghi', 'Gohir.D05G314100' => 'ghi', 'Gohir.D07G041400' => 'ghi', 'Gohir.D09G029700' => 'ghi', 'Gohir.D12G149700' => 'ghi', 'Gorai.001G043800' => 'gra', 'Gorai.002G187800' => 'gra', 'Gorai.006G034700' => 'gra', 'Gorai.008G161200' => 'gra', 'Gorai.009G335700' => 'gra', 'Gorai.012G065000' => 'gra', 'GSVIVG01000535001' => 'vvi', 'GSVIVG01015572001' => 'vvi', 'GSVIVG01032386001' => 'vvi', 'HanXRQChr05g0138531' => 'han', 'HanXRQChr06g0174391' => 'han', 'HanXRQChr07g0199021' => 'han', 'HanXRQChr08g0208211' => 'han', 'HanXRQChr09g0255471' => 'han', 'HanXRQChr10g0315791' => 'han', 'HanXRQChr12g0371991' => 'han', 'HanXRQChr15g0475251' => 'han', 'HanXRQChr17g0540001' => 'han', 'HanXRQChr17g0548631' => 'han', 'HanXRQChr17g0569561' => 'han', 'Haze_12256' => 'cav', 'Haze_14756' => 'cav', 'Haze_25528' => 'cav', 'Hma1.2p1_0079F.1_g041020' => 'hma', 'Hma1.2p1_0818F.1_g223260' => 'hma', 'Hma1.2p1_1747F.1_g300530' => 'hma', 'HPP92_004607' => 'vpl', 'HPP92_004608' => 'vpl', 'HPP92_006181' => 'vpl', 'HPP92_012192' => 'vpl', 'HPP92_015680' => 'vpl', 'HPP92_020249' => 'vpl', 'HPP92_021376' => 'vpl', 'HPP92_024275' => 'vpl', 'Hund06031' => 'sun', 'Hund25391' => 'sun', 'Lalb_Chr07g0185371' => 'lal', 'Lalb_Chr07g0185381' => 'lal', 'Lalb_Chr12g0204011' => 'lal', 'Lalb_Chr13g0301671' => 'lal', 'Lalb_Chr14g0362851' => 'lal', 'Lalb_Chr24g0403581' => 'lal', 'Lj1g0000233' => 'lja', 'Lj2g0018120' => 'lja', 'Lj3C621T0' => 'lonja', 'Lj3P1059T14' => 'lonja', 'Lj3P611T9' => 'lonja', 'Lj3P614T13' => 'lonja', 'Lj3P615T5' => 'lonja', 'Lj4g0012315' => 'lja', 'Lj4g0026182' => 'lja', 'Lj6P813T16' => 'lonja', 'Lj7C427T7' => 'lonja', 'Lj7C427T8' => 'lonja', 'Lj7P600T41' => 'lonja', 'Lju41C42G17' => 'lonja', 'Lsat_1_v5_gn_0_47300' => 'lsa', 'Lsat_1_v5_gn_2_91280' => 'lsa', 'Lsat_1_v5_gn_3_30561' => 'lsa', 'Lsat_1_v5_gn_4_184321' => 'lsa', 'Lsat_1_v5_gn_4_4041' => 'lsa', 'Lsat_1_v5_gn_5_92000' => 'lsa', 'Lsat_1_v5_gn_8_152940' => 'lsa', 'Lsat_1_v5_gn_8_62401' => 'lsa', 'Manes.06G055900' => 'mes', 'Manes.12G022200' => 'mes', 'Manes.13G023300' => 'mes', 'Manes.14G115000' => 'mes', 'Manes.15G151700' => 'mes', 'Manes.17G111300' => 'mes', 'Mapoly0226s0009' => 'mpo', 'MBI02_g25363_MAGBIO' => 'mbi', 'MBI06_g00027_MAGBIO' => 'mbi', 'MBI10_g13034_MAGBIO' => 'mbi', 'MD09G1023400' => 'mdo', 'MD13G1100100' => 'mdo', 'MD15G1169200' => 'mdo', 'MD16G1101100' => 'mdo', 'MD17G1022900' => 'mdo', 'Medtr3g096150' => 'mtr', 'Medtr4g115070' => 'mtr', 'Medtr7g033325' => 'mtr', 'Medtr8g089840' => 'mtr', 'MELO3C010319.2' => 'cme', 'MELO3C011944.2' => 'cme', 'MELO3C021589.2' => 'cme', 'Migut.E00207' => 'egut', 'Migut.H00067' => 'egut', 'Migut.K00433' => 'egut', 'Migut.K00606' => 'egut', 'Migut.K01410' => 'egut', 'MSTRG.13347' => 'ama', 'MSTRG.24045' => 'ama', 'MSTRG.2428' => 'ama', 'MSTRG.26410' => 'ama', 'MSTRG.3139' => 'ama', 'MSTRG.3286' => 'ama', 'MSTRG.563' => 'ama', 'MSTRG.7941' => 'ama', 'Nitab4.5_0000028g0060' => 'nta', 'Nitab4.5_0000065g0260' => 'nta', 'Nitab4.5_0000112g0060' => 'nta', 'Nitab4.5_0000489g0120' => 'nta', 'Nitab4.5_0001776g0050' => 'nta', 'Nitab4.5_0001854g0010' => 'nta', 'Nitab4.5_0001860g0020' => 'nta', 'Nitab4.5_0004352g0010' => 'nta', 'Nitab4.5_0008716g0020' => 'nta', 'Nitab4.5_0008922g0010' => 'nta', 'Nn3g16693' => 'nnu', 'Nn4g22596' => 'nnu', 'Nn7g37639' => 'nnu', 'Oeu001701.1' => 'oeu', 'Oeu018149.1' => 'oeu', 'Oeu026220.1' => 'oeu', 'Oeu038635.1' => 'oeu', 'Oeu049176.1' => 'oeu', 'Oeu056706.1' => 'oeu', 'Oeu056937.1' => 'oeu', 'Oeu057540.1' => 'oeu', 'Os02g0594900' => 'osa', 'Os02g0595100' => 'osa', 'Os04g0477500' => 'osa', 'Os12g0611900' => 'osa', 'Peaxi162Scf00076g00020' => 'pax', 'Peaxi162Scf00128g00217' => 'pax', 'Peaxi162Scf00129g01640' => 'pax', 'Peaxi162Scf00669g00007' => 'pax', 'Peaxi162Scf00700g00421' => 'pax', 'Peaxi162Scf00801g00038' => 'pax', 'Peaxi162Scf00891g00025' => 'pax', 'PGR083G0909' => 'pgr', 'PGR119G1005' => 'pgr', 'PGR142G2236' => 'pgr', 'PGR142G3388' => 'pgr', 'PGSC0003DMG400004514' => 'stu', 'PGSC0003DMG400012635' => 'stu', 'PGSC0003DMG400015730' => 'stu', 'PGSC0003DMG400018611' => 'stu', 'PGSC0003DMG400030897' => 'stu', 'Phvul.001G254800' => 'pvu', 'Phvul.002G260100' => 'pvu', 'Phvul.003G167600' => 'pvu', 'Phvul.004G005100' => 'pvu', 'Potri.001G343600' => 'ptr', 'Potri.006G066700' => 'ptr', 'Potri.008G186000' => 'ptr', 'Potri.010G046900' => 'ptr', 'Potri.018G127900' => 'ptr', 'Pp3c20_17750' => 'ppa', 'Pp3c24_4380' => 'ppa', 'Prupe.1G245800' => 'ppe', 'Prupe.3G293400' => 'ppe', 'Prupe.7G247400' => 'ppe', 'Psat0s145g0120' => 'psa', 'Psat0s595g0040' => 'psa', 'Psat0s595g0120' => 'psa', 'Psat3g175040' => 'psa', 'Psat7g058120' => 'psa', 'PSO017G0428' => 'pso', 'PSO063G7510' => 'pso', 'PSO067G0046' => 'pso', 'PSO478G1073' => 'pso', 'PSO675G3677' => 'pso', 'PSO675G6558' => 'pso', 'PSO675G7520' => 'pso', 'PSO675G8959' => 'pso', 'QL02p074089' => 'qlo', 'QL02p089614' => 'qlo', 'QL03p057736' => 'qlo', 'RcHm_v2.0_Chr1g0364131' => 'rch', 'RcHm_v2.0_Chr2g0087801' => 'rch', 'RcHm_v2.0_Chr2g0087821' => 'rch', 'RcHm_v2.0_Chr2g0173231' => 'rch', 'RcHm_v2.0_Chr4g0433111' => 'rch', 'Rhsim03G0250300' => 'rsi', 'Rhsim08G0048400' => 'rsi', 'Rhsim10G0014800' => 'rsi', 'Rhsim12G0040100' => 'rsi', 'Rhsim12G0109700' => 'rsi', 'Sabra06G0049600' => 'sbr', 'Sabra08G0141000' => 'sbr', 'Sabra10G0021400' => 'sbr', 'Sabra16G0222900' => 'sbr', 'Sabra18G0108600' => 'sbr', 'SalBow1G0433' => 'sbo', 'SalBow1G2038' => 'sbo', 'SalBow1G5003' => 'sbo', 'SalBow7G1197' => 'sbo', 'SalBow8G3506' => 'sbo', 'Sc03g0007300' => 'sci', 'Sc11g0000950' => 'sci', 'Sc14g0008750' => 'sci', 'Sc18g0000420' => 'sci', 'Sed0006754' => 'sed', 'Sed0008741' => 'sed', 'Sed0017172' => 'sed', 'Sed0018925' => 'sed', 'Sed0023326' => 'sed', 'Sed0025909' => 'sed', 'SEGI_05333' => 'sgi', 'SEGI_10362' => 'sgi', 'SEGI_13380' => 'sgi', 'SEGI_24306' => 'sgi', 'SEGI_29077' => 'sgi', 'SEGI_29095' => 'sgi', 'SEGI_36534' => 'sgi', 'SEGI_37506' => 'sgi', 'SEGI_38321' => 'sgi', 'SGA_v2.0_scaffold307G48031' => 'sas', 'SGA_v2.0_scaffold47G17507' => 'sas', 'SGA_v2.0_scaffold63G21736' => 'sas', 'SGA_v2.0_scaffold87G27070' => 'sas', 'SHI17794' => 'shi', 'SHI28851' => 'shi', 'SMO165G0155' => 'smo', 'SMO340G0217' => 'smo', 'SMO367G1210' => 'smo', 'Solyc02g093430.3' => 'sly', 'Solyc05g013580.4' => 'sly', 'Solyc07g008030.3' => 'sly', 'Solyc12g035470.2' => 'sly', 'Sopen02g038020' => 'spe', 'Sopen05g008490' => 'spe', 'Sopen07g003910' => 'spe', 'Sopen12g015240' => 'spe', 'Sp1g11550' => 'spa', 'Sp2g16710' => 'spa', 'Sp3g00430' => 'spa', 'Sp3g26780' => 'spa', 'Sp5g22900' => 'spa', 'Sp6g29530' => 'spa', 'TAR371G0794' => 'tar', 'TAR374G0164' => 'tar', 'TAR622G0165' => 'tar', 'TAR626G0929' => 'tar', 'TAR629G2155' => 'tar', 'THA.LOC104805282' => 'tha', 'THA.LOC104805363' => 'tha', 'THA.LOC104808968' => 'tha', 'THA.LOC104821093' => 'tha', 'THA.LOC104823953' => 'tha', 'THA.LOC104825562' => 'tha', 'THA.LOC104825665' => 'tha', 'Thecc.02G261400' => 'tca', 'Thecc.04G019200' => 'tca', 'Thecc.09G130400' => 'tca', 'Thhalv10004374m.g' => 'esa', 'Thhalv10007850m.g' => 'esa', 'Thhalv10013782m.g' => 'esa', 'Thhalv10018686m.g' => 'esa', 'Thhalv10020899m.g' => 'esa', 'Thhalv10022755m.g' => 'esa', 'TPR.G23851' => 'tpr', 'TPR.G26500' => 'tpr', 'TPR.G27267' => 'tpr', 'TPR.G32001' => 'tpr', 'TPR.G6251' => 'tpr', 'TPR.G8167' => 'tpr', 'TWI12G1330' => 'twi', 'TWI18G1239' => 'twi', 'TWI34G0979' => 'twi', 'TWI36G0670' => 'twi', 'TWI36G0707' => 'twi', 'TWI56G0233' => 'twi', 'TWI75G1809' => 'twi', 'unitig_21.g20874' => 'ugi', 'unitig_26.g10343' => 'ugi', 'unitig_46.g18392' => 'ugi', 'unitig_52.g17178' => 'ugi', 'unitig_8.g2934' => 'ugi', 'vmacro01122' => 'vma', 'vmacro05875' => 'vma', 'vmacro06147' => 'vma', 'vmacro16191' => 'vma', 'vmacro18293' => 'vma', 'VMungo0251G3707' => 'vmu', 'VMungo0464G1521' => 'vmu', 'VMungo1215G0205' => 'vmu', 'VMungo1383G2484' => 'vmu', 'Zm00001eb079610' => 'zma', 'Zm00001eb135990' => 'zma', 'Zm00001eb183710' => 'zma', 'Zm00001eb246020' => 'zma' ) $gf_id = 'HOM05D001124' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001124' ) $data_identifier = 'HOM05D001124' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 6, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 7, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 21, 'bol' => (int) 10, 'bra' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 6, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 9, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 21, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 8, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 10, 'lsa' => (int) 8, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 8, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 9, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb246020' $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' => 'HOM05D001124', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '548', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02520' => 'bna', 'A03p06630' => 'bna', 'A05p44460' => 'bna', 'A06p08710' => 'bna', 'A06p41090' => 'bna', 'A07p32320' => 'bna', 'A08p32520' => 'bna', 'A09p10360' => 'bna', 'A10p24080' => 'bna', 'Aa31LG11G15250' => 'aar', 'Aa31LG1G1800' => 'aar', 'Aa31LG2G5120' => 'aar', 'Aa31LG2G6070' => 'aar', 'Aa31LG5G10770' => 'aar', 'Aa31sc61G90' => 'aar', 'Actinidia01352' => 'ach', 'Actinidia05983' => 'ach', 'Actinidia08133' => 'ach', 'Actinidia15101' => 'ach', 'Actinidia26379' => 'ach', 'Actinidia35778' => 'ach', 'Actinidia36123' => 'ach', 'Actinidia37436' => 'ach', 'Actinidia38730' => 'ach', 'Ah.02g128210' => 'amhyb', 'Ah.03g132990' => 'amhyb', 'Ah.14g079410' => 'amhyb', 'AL1G24640' => 'aly', 'AL2G26680' => 'aly', 'AL3G10530' => 'aly', 'AL3G45230' => 'aly', 'AL5G15230' => 'aly', 'AL5G16960' => 'aly', 'AL6G25210' => 'aly', 'Aqoxy2G00441' => 'aox', 'Aqoxy3G01236' => 'aox', 'Aqoxy5G03746' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3RQ047' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C7GMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9C8JER' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MBL6KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YXCZ83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZANX40' => 'arhy', 'AT1G12990' => 'ath', 'AT1G67880' => 'ath', 'AT2G13290' => 'ath', 'AT3G01620' => 'ath', 'AT3G26445' => 'ath', 'AT3G27540' => 'ath', 'AT5G14480' => 'ath', 'ATR0824G026' => 'atr', 'ATR1098G019' => 'atr', 'Atru.chr11.2145' => 'acertr', 'Atru.chr2.3636' => 'acertr', 'Atru.chr2.3644' => 'acertr', 'Atru.chr6.2422' => 'acertr', 'Atru.chr7.1112' => 'acertr', 'AUR62005469' => 'cqu', 'AUR62011166' => 'cqu', 'AUR62013319' => 'cqu', 'AUR62024273' => 'cqu', 'AUR62028420' => 'cqu', 'AUR62041942' => 'cqu', 'BcaB01g04969' => 'bca', 'BcaB01g06371' => 'bca', 'BcaB02g11494' => 'bca', 'BcaB03g15382' => 'bca', 'BcaB08g36994' => 'bca', 'BcaC03g13477' => 'bca', 'BcaC03g13478' => 'bca', 'BcaC03g13480' => 'bca', 'BcaC03g13481' => 'bca', 'BcaC03g13486' => 'bca', 'BcaC04g19031' => 'bca', 'BcaC04g23085' => 'bca', 'BcaC05g25094' => 'bca', 'BcaC05g25096' => 'bca', 'BcaC05g25138' => 'bca', 'BcaC05g30416' => 'bca', 'BcaC05g30455' => 'bca', 'BcaC06g30979' => 'bca', 'BcaC06g33805' => 'bca', 'BcaC08g46021' => 'bca', 'BcaNung03154' => 'bca', 'BolC2t06623H' => 'bol', 'BolC2t06632H' => 'bol', 'BolC2t06635H' => 'bol', 'BolC2t06638H' => 'bol', 'BolC3t13266H' => 'bol', 'BolC5t29776H' => 'bol', 'BolC6t38912H' => 'bol', 'BolC7t44183H' => 'bol', 'BolC9t54123H' => 'bol', 'BolC9t59107H' => 'bol', 'BraA02t05221Z' => 'bra', 'BraA03t09996Z' => 'bra', 'BraA05t23210Z' => 'bra', 'BraA06t24068Z' => 'bra', 'BraA06t27032Z' => 'bra', 'BraA08t35176Z' => 'bra', 'BraA09t36680Z' => 'bra', 'BraA10t44471Z' => 'bra', 'C02p06760' => 'bna', 'C02p06890' => 'bna', 'C02p07010' => 'bna', 'C03p07660' => 'bna', 'C05p10300' => 'bna', 'C06p38150' => 'bna', 'C07p36650' => 'bna', 'C08p15770' => 'bna', 'C09p12300' => 'bna', 'C09p62700' => 'bna', 'C09p75040' => 'bna', 'CAN.G13.1' => 'can', 'CAN.G138.4' => 'can', 'CAN.G44.6' => 'can', 'CAN.G473.19' => 'can', 'CANSAT01G0835' => 'cansat', 'CANSAT11G0246' => 'cansat', 'CANSAT11G1766' => 'cansat', 'CANSAT64G1954' => 'cansat', 'CARHR013330' => 'chi', 'CARHR060530' => 'chi', 'CARHR075300' => 'chi', 'CARHR105120' => 'chi', 'CARHR148910' => 'chi', 'CARHR198830' => 'chi', 'Carub.0001s1275' => 'cru', 'Carub.0002s1437' => 'cru', 'Carub.0003s0044' => 'cru', 'Carub.0003s2787' => 'cru', 'Carub.0005s0597' => 'cru', 'Carub.0006s1266' => 'cru', 'Ca_06935_v3' => 'car', 'Ca_13559_v3' => 'car', 'Ca_16941_v3' => 'car', 'Ca_16960_v3' => 'car', 'Ca_17775_v3' => 'car', 'Ca_30464_v3' => 'car', 'Cc06_g08160' => 'ccan', 'Cc07_g01520' => 'ccan', 'Cc11_g15810' => 'ccan', 'CDE02G2840' => 'cde', 'CDE03G0093' => 'cde', 'CDE04G2127' => 'cde', 'CDE07G1857' => 'cde', 'CDE09G1246' => 'cde', 'Cfa003412' => 'cfa', 'Cfa007341' => 'cfa', 'Cfa009220' => 'cfa', 'Ciclev10008737m.g' => 'ccl', 'Ciclev10015565m.g' => 'ccl', 'Ciclev10031761m.g' => 'ccl', 'CiPaw.03G045300' => 'cil', 'CiPaw.03G247200' => 'cil', 'CiPaw.04G029500' => 'cil', 'CiPaw.04G174000' => 'cil', 'CiPaw.05G181200' => 'cil', 'CiPaw.06G067100' => 'cil', 'ClCG05G025800' => 'cla', 'ClCG06G011400' => 'cla', 'ClCG09G019360' => 'cla', 'COL.COLO4_04827' => 'col', 'COL.COLO4_29170' => 'col', 'COL.COLO4_35131' => 'col', 'COL.COLO4_35132' => 'col', 'Cpa.g.sc33.32' => 'cpa', 'Cpa.g.sc46.29' => 'cpa', 'Cpa.g.sc796.1' => 'cpa', 'CsaV3_1G030420' => 'csa', 'CsaV3_5G027050' => 'csa', 'CsaV3_5G031040' => 'csa', 'CsaV3_UNG023130' => 'csa', 'CSS0007726' => 'camsi', 'CSS0016433' => 'camsi', 'CSS0017656' => 'camsi', 'CSS0025364' => 'camsi', 'CSS0027582' => 'camsi', 'CSS0047288' => 'camsi', 'CSS0049950' => 'camsi', 'DCAR_003843' => 'dca', 'DCAR_007052' => 'dca', 'DCAR_020884' => 'dca', 'DCAR_021730' => 'dca', 'DCAR_024423' => 'dca', 'DCAR_026509' => 'dca', 'DCAR_031158' => 'dca', 'Dinv14728' => 'din', 'Dinv15219' => 'din', 'Dinv25728' => 'din', 'Dinv33428' => 'din', 'Dinv36489' => 'din', 'Dinv41486' => 'din', 'Duzib147G0469' => 'dzi', 'Duzib168G0060' => 'dzi', 'Duzib187G1215' => 'dzi', 'Duzib248G0692' => 'dzi', 'Duzib251G0767' => 'dzi', 'Duzib264G0446' => 'dzi', 'Duzib268G0691' => 'dzi', 'ECA232G4767' => 'eca', 'ECA233G2838' => 'eca', 'ECA234G0391' => 'eca', 'ECA234G0857' => 'eca', 'ECA236G1593' => 'eca', 'ECA238G0565' => 'eca', 'ECA246G1027' => 'eca', 'ECA246G3223' => 'eca', 'ECA246G3470' => 'eca', 'EL10Ac6g13829' => 'bvu', 'EL10Ac6g14093' => 'bvu', 'EL10Ac8g18707' => 'bvu', 'Eucgr.C01369' => 'egr', 'Eucgr.H02492' => 'egr', 'Eucgr.I01733' => 'egr', 'Eucgr.J02255' => 'egr', 'Eucgr.J02257' => 'egr', 'Eucgr.J02258' => 'egr', 'FAN02G1601' => 'fan', 'FAN03G1586' => 'fan', 'FAN03G2986' => 'fan', 'FAN05G4837' => 'fan', 'FAN06G0146' => 'fan', 'FAN07G0858' => 'fan', 'FAN09G3179' => 'fan', 'FAN10G0669' => 'fan', 'FAN12G2358' => 'fan', 'FAN14G4198' => 'fan', 'FAN14G5112' => 'fan', 'FAN17G0342' => 'fan', 'FAN19G0342' => 'fan', 'FAN19G0962' => 'fan', 'FAN19G1101' => 'fan', 'FAN19G1872' => 'fan', 'FAN22G0356' => 'fan', 'FAN23G0744' => 'fan', 'FAN23G1914' => 'fan', 'FAN26G0032' => 'fan', 'FAN28G0625' => 'fan', 'FvH4_1g02710' => 'fve', 'FvH4_1g02720' => 'fve', 'FvH4_4g25670' => 'fve', 'FvH4_6g51700' => 'fve', 'FvH4_7g20170' => 'fve', 'Glyma.05G175000' => 'gma', 'Glyma.08G132300' => 'gma', 'Glyma.11G243000' => 'gma', 'Glyma.13G158900' => 'gma', 'Glyma.17G112400' => 'gma', 'Glyma.18G014100' => 'gma', 'Glyma.19G003100' => 'gma', 'Glyma.19G056500' => 'gma', 'Gohir.A01G158900' => 'ghi', 'Gohir.A05G312600' => 'ghi', 'Gohir.A05G354900' => 'ghi', 'Gohir.A07G037200' => 'ghi', 'Gohir.A09G030000' => 'ghi', 'Gohir.A12G145200' => 'ghi', 'Gohir.D01G151500' => 'ghi', 'Gohir.D04G058300' => 'ghi', 'Gohir.D05G314100' => 'ghi', 'Gohir.D07G041400' => 'ghi', 'Gohir.D09G029700' => 'ghi', 'Gohir.D12G149700' => 'ghi', 'Gorai.001G043800' => 'gra', 'Gorai.002G187800' => 'gra', 'Gorai.006G034700' => 'gra', 'Gorai.008G161200' => 'gra', 'Gorai.009G335700' => 'gra', 'Gorai.012G065000' => 'gra', 'GSVIVG01000535001' => 'vvi', 'GSVIVG01015572001' => 'vvi', 'GSVIVG01032386001' => 'vvi', 'HanXRQChr05g0138531' => 'han', 'HanXRQChr06g0174391' => 'han', 'HanXRQChr07g0199021' => 'han', 'HanXRQChr08g0208211' => 'han', 'HanXRQChr09g0255471' => 'han', 'HanXRQChr10g0315791' => 'han', 'HanXRQChr12g0371991' => 'han', 'HanXRQChr15g0475251' => 'han', 'HanXRQChr17g0540001' => 'han', 'HanXRQChr17g0548631' => 'han', 'HanXRQChr17g0569561' => 'han', 'Haze_12256' => 'cav', 'Haze_14756' => 'cav', 'Haze_25528' => 'cav', 'Hma1.2p1_0079F.1_g041020' => 'hma', 'Hma1.2p1_0818F.1_g223260' => 'hma', 'Hma1.2p1_1747F.1_g300530' => 'hma', 'HPP92_004607' => 'vpl', 'HPP92_004608' => 'vpl', 'HPP92_006181' => 'vpl', 'HPP92_012192' => 'vpl', 'HPP92_015680' => 'vpl', 'HPP92_020249' => 'vpl', 'HPP92_021376' => 'vpl', 'HPP92_024275' => 'vpl', 'Hund06031' => 'sun', 'Hund25391' => 'sun', 'Lalb_Chr07g0185371' => 'lal', 'Lalb_Chr07g0185381' => 'lal', 'Lalb_Chr12g0204011' => 'lal', 'Lalb_Chr13g0301671' => 'lal', 'Lalb_Chr14g0362851' => 'lal', 'Lalb_Chr24g0403581' => 'lal', 'Lj1g0000233' => 'lja', 'Lj2g0018120' => 'lja', 'Lj3C621T0' => 'lonja', 'Lj3P1059T14' => 'lonja', 'Lj3P611T9' => 'lonja', 'Lj3P614T13' => 'lonja', 'Lj3P615T5' => 'lonja', 'Lj4g0012315' => 'lja', 'Lj4g0026182' => 'lja', 'Lj6P813T16' => 'lonja', 'Lj7C427T7' => 'lonja', 'Lj7C427T8' => 'lonja', 'Lj7P600T41' => 'lonja', 'Lju41C42G17' => 'lonja', 'Lsat_1_v5_gn_0_47300' => 'lsa', 'Lsat_1_v5_gn_2_91280' => 'lsa', 'Lsat_1_v5_gn_3_30561' => 'lsa', 'Lsat_1_v5_gn_4_184321' => 'lsa', 'Lsat_1_v5_gn_4_4041' => 'lsa', 'Lsat_1_v5_gn_5_92000' => 'lsa', 'Lsat_1_v5_gn_8_152940' => 'lsa', 'Lsat_1_v5_gn_8_62401' => 'lsa', 'Manes.06G055900' => 'mes', 'Manes.12G022200' => 'mes', 'Manes.13G023300' => 'mes', 'Manes.14G115000' => 'mes', 'Manes.15G151700' => 'mes', 'Manes.17G111300' => 'mes', 'Mapoly0226s0009' => 'mpo', 'MBI02_g25363_MAGBIO' => 'mbi', 'MBI06_g00027_MAGBIO' => 'mbi', 'MBI10_g13034_MAGBIO' => 'mbi', 'MD09G1023400' => 'mdo', 'MD13G1100100' => 'mdo', 'MD15G1169200' => 'mdo', 'MD16G1101100' => 'mdo', 'MD17G1022900' => 'mdo', 'Medtr3g096150' => 'mtr', 'Medtr4g115070' => 'mtr', 'Medtr7g033325' => 'mtr', 'Medtr8g089840' => 'mtr', 'MELO3C010319.2' => 'cme', 'MELO3C011944.2' => 'cme', 'MELO3C021589.2' => 'cme', 'Migut.E00207' => 'egut', 'Migut.H00067' => 'egut', 'Migut.K00433' => 'egut', 'Migut.K00606' => 'egut', 'Migut.K01410' => 'egut', 'MSTRG.13347' => 'ama', 'MSTRG.24045' => 'ama', 'MSTRG.2428' => 'ama', 'MSTRG.26410' => 'ama', 'MSTRG.3139' => 'ama', 'MSTRG.3286' => 'ama', 'MSTRG.563' => 'ama', 'MSTRG.7941' => 'ama', 'Nitab4.5_0000028g0060' => 'nta', 'Nitab4.5_0000065g0260' => 'nta', 'Nitab4.5_0000112g0060' => 'nta', 'Nitab4.5_0000489g0120' => 'nta', 'Nitab4.5_0001776g0050' => 'nta', 'Nitab4.5_0001854g0010' => 'nta', 'Nitab4.5_0001860g0020' => 'nta', 'Nitab4.5_0004352g0010' => 'nta', 'Nitab4.5_0008716g0020' => 'nta', 'Nitab4.5_0008922g0010' => 'nta', 'Nn3g16693' => 'nnu', 'Nn4g22596' => 'nnu', 'Nn7g37639' => 'nnu', 'Oeu001701.1' => 'oeu', 'Oeu018149.1' => 'oeu', 'Oeu026220.1' => 'oeu', 'Oeu038635.1' => 'oeu', 'Oeu049176.1' => 'oeu', 'Oeu056706.1' => 'oeu', 'Oeu056937.1' => 'oeu', 'Oeu057540.1' => 'oeu', 'Os02g0594900' => 'osa', 'Os02g0595100' => 'osa', 'Os04g0477500' => 'osa', 'Os12g0611900' => 'osa', 'Peaxi162Scf00076g00020' => 'pax', 'Peaxi162Scf00128g00217' => 'pax', 'Peaxi162Scf00129g01640' => 'pax', 'Peaxi162Scf00669g00007' => 'pax', 'Peaxi162Scf00700g00421' => 'pax', 'Peaxi162Scf00801g00038' => 'pax', 'Peaxi162Scf00891g00025' => 'pax', 'PGR083G0909' => 'pgr', 'PGR119G1005' => 'pgr', 'PGR142G2236' => 'pgr', 'PGR142G3388' => 'pgr', 'PGSC0003DMG400004514' => 'stu', 'PGSC0003DMG400012635' => 'stu', 'PGSC0003DMG400015730' => 'stu', 'PGSC0003DMG400018611' => 'stu', 'PGSC0003DMG400030897' => 'stu', 'Phvul.001G254800' => 'pvu', 'Phvul.002G260100' => 'pvu', 'Phvul.003G167600' => 'pvu', 'Phvul.004G005100' => 'pvu', 'Potri.001G343600' => 'ptr', 'Potri.006G066700' => 'ptr', 'Potri.008G186000' => 'ptr', 'Potri.010G046900' => 'ptr', 'Potri.018G127900' => 'ptr', 'Pp3c20_17750' => 'ppa', 'Pp3c24_4380' => 'ppa', 'Prupe.1G245800' => 'ppe', 'Prupe.3G293400' => 'ppe', 'Prupe.7G247400' => 'ppe', 'Psat0s145g0120' => 'psa', 'Psat0s595g0040' => 'psa', 'Psat0s595g0120' => 'psa', 'Psat3g175040' => 'psa', 'Psat7g058120' => 'psa', 'PSO017G0428' => 'pso', 'PSO063G7510' => 'pso', 'PSO067G0046' => 'pso', 'PSO478G1073' => 'pso', 'PSO675G3677' => 'pso', 'PSO675G6558' => 'pso', 'PSO675G7520' => 'pso', 'PSO675G8959' => 'pso', 'QL02p074089' => 'qlo', 'QL02p089614' => 'qlo', 'QL03p057736' => 'qlo', 'RcHm_v2.0_Chr1g0364131' => 'rch', 'RcHm_v2.0_Chr2g0087801' => 'rch', 'RcHm_v2.0_Chr2g0087821' => 'rch', 'RcHm_v2.0_Chr2g0173231' => 'rch', 'RcHm_v2.0_Chr4g0433111' => 'rch', 'Rhsim03G0250300' => 'rsi', 'Rhsim08G0048400' => 'rsi', 'Rhsim10G0014800' => 'rsi', 'Rhsim12G0040100' => 'rsi', 'Rhsim12G0109700' => 'rsi', 'Sabra06G0049600' => 'sbr', 'Sabra08G0141000' => 'sbr', 'Sabra10G0021400' => 'sbr', 'Sabra16G0222900' => 'sbr', 'Sabra18G0108600' => 'sbr', 'SalBow1G0433' => 'sbo', 'SalBow1G2038' => 'sbo', 'SalBow1G5003' => 'sbo', 'SalBow7G1197' => 'sbo', 'SalBow8G3506' => 'sbo', 'Sc03g0007300' => 'sci', 'Sc11g0000950' => 'sci', 'Sc14g0008750' => 'sci', 'Sc18g0000420' => 'sci', 'Sed0006754' => 'sed', 'Sed0008741' => 'sed', 'Sed0017172' => 'sed', 'Sed0018925' => 'sed', 'Sed0023326' => 'sed', 'Sed0025909' => 'sed', 'SEGI_05333' => 'sgi', 'SEGI_10362' => 'sgi', 'SEGI_13380' => 'sgi', 'SEGI_24306' => 'sgi', 'SEGI_29077' => 'sgi', 'SEGI_29095' => 'sgi', 'SEGI_36534' => 'sgi', 'SEGI_37506' => 'sgi', 'SEGI_38321' => 'sgi', 'SGA_v2.0_scaffold307G48031' => 'sas', 'SGA_v2.0_scaffold47G17507' => 'sas', 'SGA_v2.0_scaffold63G21736' => 'sas', 'SGA_v2.0_scaffold87G27070' => 'sas', 'SHI17794' => 'shi', 'SHI28851' => 'shi', 'SMO165G0155' => 'smo', 'SMO340G0217' => 'smo', 'SMO367G1210' => 'smo', 'Solyc02g093430.3' => 'sly', 'Solyc05g013580.4' => 'sly', 'Solyc07g008030.3' => 'sly', 'Solyc12g035470.2' => 'sly', 'Sopen02g038020' => 'spe', 'Sopen05g008490' => 'spe', 'Sopen07g003910' => 'spe', 'Sopen12g015240' => 'spe', 'Sp1g11550' => 'spa', 'Sp2g16710' => 'spa', 'Sp3g00430' => 'spa', 'Sp3g26780' => 'spa', 'Sp5g22900' => 'spa', 'Sp6g29530' => 'spa', 'TAR371G0794' => 'tar', 'TAR374G0164' => 'tar', 'TAR622G0165' => 'tar', 'TAR626G0929' => 'tar', 'TAR629G2155' => 'tar', 'THA.LOC104805282' => 'tha', 'THA.LOC104805363' => 'tha', 'THA.LOC104808968' => 'tha', 'THA.LOC104821093' => 'tha', 'THA.LOC104823953' => 'tha', 'THA.LOC104825562' => 'tha', 'THA.LOC104825665' => 'tha', 'Thecc.02G261400' => 'tca', 'Thecc.04G019200' => 'tca', 'Thecc.09G130400' => 'tca', 'Thhalv10004374m.g' => 'esa', 'Thhalv10007850m.g' => 'esa', 'Thhalv10013782m.g' => 'esa', 'Thhalv10018686m.g' => 'esa', 'Thhalv10020899m.g' => 'esa', 'Thhalv10022755m.g' => 'esa', 'TPR.G23851' => 'tpr', 'TPR.G26500' => 'tpr', 'TPR.G27267' => 'tpr', 'TPR.G32001' => 'tpr', 'TPR.G6251' => 'tpr', 'TPR.G8167' => 'tpr', 'TWI12G1330' => 'twi', 'TWI18G1239' => 'twi', 'TWI34G0979' => 'twi', 'TWI36G0670' => 'twi', 'TWI36G0707' => 'twi', 'TWI56G0233' => 'twi', 'TWI75G1809' => 'twi', 'unitig_21.g20874' => 'ugi', 'unitig_26.g10343' => 'ugi', 'unitig_46.g18392' => 'ugi', 'unitig_52.g17178' => 'ugi', 'unitig_8.g2934' => 'ugi', 'vmacro01122' => 'vma', 'vmacro05875' => 'vma', 'vmacro06147' => 'vma', 'vmacro16191' => 'vma', 'vmacro18293' => 'vma', 'VMungo0251G3707' => 'vmu', 'VMungo0464G1521' => 'vmu', 'VMungo1215G0205' => 'vmu', 'VMungo1383G2484' => 'vmu', 'Zm00001eb079610' => 'zma', 'Zm00001eb135990' => 'zma', 'Zm00001eb183710' => 'zma', 'Zm00001eb246020' => 'zma' ), 'gf_id' => 'HOM05D001124', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001124' ), 'data_identifier' => 'HOM05D001124', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001124', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '548', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02520' => 'bna', 'A03p06630' => 'bna', 'A05p44460' => 'bna', 'A06p08710' => 'bna', 'A06p41090' => 'bna', 'A07p32320' => 'bna', 'A08p32520' => 'bna', 'A09p10360' => 'bna', 'A10p24080' => 'bna', 'Aa31LG11G15250' => 'aar', 'Aa31LG1G1800' => 'aar', 'Aa31LG2G5120' => 'aar', 'Aa31LG2G6070' => 'aar', 'Aa31LG5G10770' => 'aar', 'Aa31sc61G90' => 'aar', 'Actinidia01352' => 'ach', 'Actinidia05983' => 'ach', 'Actinidia08133' => 'ach', 'Actinidia15101' => 'ach', 'Actinidia26379' => 'ach', 'Actinidia35778' => 'ach', 'Actinidia36123' => 'ach', 'Actinidia37436' => 'ach', 'Actinidia38730' => 'ach', 'Ah.02g128210' => 'amhyb', 'Ah.03g132990' => 'amhyb', 'Ah.14g079410' => 'amhyb', 'AL1G24640' => 'aly', 'AL2G26680' => 'aly', 'AL3G10530' => 'aly', 'AL3G45230' => 'aly', 'AL5G15230' => 'aly', 'AL5G16960' => 'aly', 'AL6G25210' => 'aly', 'Aqoxy2G00441' => 'aox', 'Aqoxy3G01236' => 'aox', 'Aqoxy5G03746' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3RQ047' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C7GMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9C8JER' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MBL6KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YXCZ83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZANX40' => 'arhy', 'AT1G12990' => 'ath', 'AT1G67880' => 'ath', 'AT2G13290' => 'ath', 'AT3G01620' => 'ath', 'AT3G26445' => 'ath', 'AT3G27540' => 'ath', 'AT5G14480' => 'ath', 'ATR0824G026' => 'atr', 'ATR1098G019' => 'atr', 'Atru.chr11.2145' => 'acertr', 'Atru.chr2.3636' => 'acertr', 'Atru.chr2.3644' => 'acertr', 'Atru.chr6.2422' => 'acertr', 'Atru.chr7.1112' => 'acertr', 'AUR62005469' => 'cqu', 'AUR62011166' => 'cqu', 'AUR62013319' => 'cqu', 'AUR62024273' => 'cqu', 'AUR62028420' => 'cqu', 'AUR62041942' => 'cqu', 'BcaB01g04969' => 'bca', 'BcaB01g06371' => 'bca', 'BcaB02g11494' => 'bca', 'BcaB03g15382' => 'bca', 'BcaB08g36994' => 'bca', 'BcaC03g13477' => 'bca', 'BcaC03g13478' => 'bca', 'BcaC03g13480' => 'bca', 'BcaC03g13481' => 'bca', 'BcaC03g13486' => 'bca', 'BcaC04g19031' => 'bca', 'BcaC04g23085' => 'bca', 'BcaC05g25094' => 'bca', 'BcaC05g25096' => 'bca', 'BcaC05g25138' => 'bca', 'BcaC05g30416' => 'bca', 'BcaC05g30455' => 'bca', 'BcaC06g30979' => 'bca', 'BcaC06g33805' => 'bca', 'BcaC08g46021' => 'bca', 'BcaNung03154' => 'bca', 'BolC2t06623H' => 'bol', 'BolC2t06632H' => 'bol', 'BolC2t06635H' => 'bol', 'BolC2t06638H' => 'bol', 'BolC3t13266H' => 'bol', 'BolC5t29776H' => 'bol', 'BolC6t38912H' => 'bol', 'BolC7t44183H' => 'bol', 'BolC9t54123H' => 'bol', 'BolC9t59107H' => 'bol', 'BraA02t05221Z' => 'bra', 'BraA03t09996Z' => 'bra', 'BraA05t23210Z' => 'bra', 'BraA06t24068Z' => 'bra', 'BraA06t27032Z' => 'bra', 'BraA08t35176Z' => 'bra', 'BraA09t36680Z' => 'bra', 'BraA10t44471Z' => 'bra', 'C02p06760' => 'bna', 'C02p06890' => 'bna', 'C02p07010' => 'bna', 'C03p07660' => 'bna', 'C05p10300' => 'bna', 'C06p38150' => 'bna', 'C07p36650' => 'bna', 'C08p15770' => 'bna', 'C09p12300' => 'bna', 'C09p62700' => 'bna', 'C09p75040' => 'bna', 'CAN.G13.1' => 'can', 'CAN.G138.4' => 'can', 'CAN.G44.6' => 'can', 'CAN.G473.19' => 'can', 'CANSAT01G0835' => 'cansat', 'CANSAT11G0246' => 'cansat', 'CANSAT11G1766' => 'cansat', 'CANSAT64G1954' => 'cansat', 'CARHR013330' => 'chi', 'CARHR060530' => 'chi', 'CARHR075300' => 'chi', 'CARHR105120' => 'chi', 'CARHR148910' => 'chi', 'CARHR198830' => 'chi', 'Carub.0001s1275' => 'cru', 'Carub.0002s1437' => 'cru', 'Carub.0003s0044' => 'cru', 'Carub.0003s2787' => 'cru', 'Carub.0005s0597' => 'cru', 'Carub.0006s1266' => 'cru', 'Ca_06935_v3' => 'car', 'Ca_13559_v3' => 'car', 'Ca_16941_v3' => 'car', 'Ca_16960_v3' => 'car', 'Ca_17775_v3' => 'car', 'Ca_30464_v3' => 'car', 'Cc06_g08160' => 'ccan', 'Cc07_g01520' => 'ccan', 'Cc11_g15810' => 'ccan', 'CDE02G2840' => 'cde', 'CDE03G0093' => 'cde', 'CDE04G2127' => 'cde', 'CDE07G1857' => 'cde', 'CDE09G1246' => 'cde', 'Cfa003412' => 'cfa', 'Cfa007341' => 'cfa', 'Cfa009220' => 'cfa', 'Ciclev10008737m.g' => 'ccl', 'Ciclev10015565m.g' => 'ccl', 'Ciclev10031761m.g' => 'ccl', 'CiPaw.03G045300' => 'cil', 'CiPaw.03G247200' => 'cil', 'CiPaw.04G029500' => 'cil', 'CiPaw.04G174000' => 'cil', 'CiPaw.05G181200' => 'cil', 'CiPaw.06G067100' => 'cil', 'ClCG05G025800' => 'cla', 'ClCG06G011400' => 'cla', 'ClCG09G019360' => 'cla', 'COL.COLO4_04827' => 'col', 'COL.COLO4_29170' => 'col', 'COL.COLO4_35131' => 'col', 'COL.COLO4_35132' => 'col', 'Cpa.g.sc33.32' => 'cpa', 'Cpa.g.sc46.29' => 'cpa', 'Cpa.g.sc796.1' => 'cpa', 'CsaV3_1G030420' => 'csa', 'CsaV3_5G027050' => 'csa', 'CsaV3_5G031040' => 'csa', 'CsaV3_UNG023130' => 'csa', 'CSS0007726' => 'camsi', 'CSS0016433' => 'camsi', 'CSS0017656' => 'camsi', 'CSS0025364' => 'camsi', 'CSS0027582' => 'camsi', 'CSS0047288' => 'camsi', 'CSS0049950' => 'camsi', 'DCAR_003843' => 'dca', 'DCAR_007052' => 'dca', 'DCAR_020884' => 'dca', 'DCAR_021730' => 'dca', 'DCAR_024423' => 'dca', 'DCAR_026509' => 'dca', 'DCAR_031158' => 'dca', 'Dinv14728' => 'din', 'Dinv15219' => 'din', 'Dinv25728' => 'din', 'Dinv33428' => 'din', 'Dinv36489' => 'din', 'Dinv41486' => 'din', 'Duzib147G0469' => 'dzi', 'Duzib168G0060' => 'dzi', 'Duzib187G1215' => 'dzi', 'Duzib248G0692' => 'dzi', 'Duzib251G0767' => 'dzi', 'Duzib264G0446' => 'dzi', 'Duzib268G0691' => 'dzi', 'ECA232G4767' => 'eca', 'ECA233G2838' => 'eca', 'ECA234G0391' => 'eca', 'ECA234G0857' => 'eca', 'ECA236G1593' => 'eca', 'ECA238G0565' => 'eca', 'ECA246G1027' => 'eca', 'ECA246G3223' => 'eca', 'ECA246G3470' => 'eca', 'EL10Ac6g13829' => 'bvu', 'EL10Ac6g14093' => 'bvu', 'EL10Ac8g18707' => 'bvu', 'Eucgr.C01369' => 'egr', 'Eucgr.H02492' => 'egr', 'Eucgr.I01733' => 'egr', 'Eucgr.J02255' => 'egr', 'Eucgr.J02257' => 'egr', 'Eucgr.J02258' => 'egr', 'FAN02G1601' => 'fan', 'FAN03G1586' => 'fan', 'FAN03G2986' => 'fan', 'FAN05G4837' => 'fan', 'FAN06G0146' => 'fan', 'FAN07G0858' => 'fan', 'FAN09G3179' => 'fan', 'FAN10G0669' => 'fan', 'FAN12G2358' => 'fan', 'FAN14G4198' => 'fan', 'FAN14G5112' => 'fan', 'FAN17G0342' => 'fan', 'FAN19G0342' => 'fan', 'FAN19G0962' => 'fan', 'FAN19G1101' => 'fan', 'FAN19G1872' => 'fan', 'FAN22G0356' => 'fan', 'FAN23G0744' => 'fan', 'FAN23G1914' => 'fan', 'FAN26G0032' => 'fan', 'FAN28G0625' => 'fan', 'FvH4_1g02710' => 'fve', 'FvH4_1g02720' => 'fve', 'FvH4_4g25670' => 'fve', 'FvH4_6g51700' => 'fve', 'FvH4_7g20170' => 'fve', 'Glyma.05G175000' => 'gma', 'Glyma.08G132300' => 'gma', 'Glyma.11G243000' => 'gma', 'Glyma.13G158900' => 'gma', 'Glyma.17G112400' => 'gma', 'Glyma.18G014100' => 'gma', 'Glyma.19G003100' => 'gma', 'Glyma.19G056500' => 'gma', 'Gohir.A01G158900' => 'ghi', 'Gohir.A05G312600' => 'ghi', 'Gohir.A05G354900' => 'ghi', 'Gohir.A07G037200' => 'ghi', 'Gohir.A09G030000' => 'ghi', 'Gohir.A12G145200' => 'ghi', 'Gohir.D01G151500' => 'ghi', 'Gohir.D04G058300' => 'ghi', 'Gohir.D05G314100' => 'ghi', 'Gohir.D07G041400' => 'ghi', 'Gohir.D09G029700' => 'ghi', 'Gohir.D12G149700' => 'ghi', 'Gorai.001G043800' => 'gra', 'Gorai.002G187800' => 'gra', 'Gorai.006G034700' => 'gra', 'Gorai.008G161200' => 'gra', 'Gorai.009G335700' => 'gra', 'Gorai.012G065000' => 'gra', 'GSVIVG01000535001' => 'vvi', 'GSVIVG01015572001' => 'vvi', 'GSVIVG01032386001' => 'vvi', 'HanXRQChr05g0138531' => 'han', 'HanXRQChr06g0174391' => 'han', 'HanXRQChr07g0199021' => 'han', 'HanXRQChr08g0208211' => 'han', 'HanXRQChr09g0255471' => 'han', 'HanXRQChr10g0315791' => 'han', 'HanXRQChr12g0371991' => 'han', 'HanXRQChr15g0475251' => 'han', 'HanXRQChr17g0540001' => 'han', 'HanXRQChr17g0548631' => 'han', 'HanXRQChr17g0569561' => 'han', 'Haze_12256' => 'cav', 'Haze_14756' => 'cav', 'Haze_25528' => 'cav', 'Hma1.2p1_0079F.1_g041020' => 'hma', 'Hma1.2p1_0818F.1_g223260' => 'hma', 'Hma1.2p1_1747F.1_g300530' => 'hma', 'HPP92_004607' => 'vpl', 'HPP92_004608' => 'vpl', 'HPP92_006181' => 'vpl', 'HPP92_012192' => 'vpl', 'HPP92_015680' => 'vpl', 'HPP92_020249' => 'vpl', 'HPP92_021376' => 'vpl', 'HPP92_024275' => 'vpl', 'Hund06031' => 'sun', 'Hund25391' => 'sun', 'Lalb_Chr07g0185371' => 'lal', 'Lalb_Chr07g0185381' => 'lal', 'Lalb_Chr12g0204011' => 'lal', 'Lalb_Chr13g0301671' => 'lal', 'Lalb_Chr14g0362851' => 'lal', 'Lalb_Chr24g0403581' => 'lal', 'Lj1g0000233' => 'lja', 'Lj2g0018120' => 'lja', 'Lj3C621T0' => 'lonja', 'Lj3P1059T14' => 'lonja', 'Lj3P611T9' => 'lonja', 'Lj3P614T13' => 'lonja', 'Lj3P615T5' => 'lonja', 'Lj4g0012315' => 'lja', 'Lj4g0026182' => 'lja', 'Lj6P813T16' => 'lonja', 'Lj7C427T7' => 'lonja', 'Lj7C427T8' => 'lonja', 'Lj7P600T41' => 'lonja', 'Lju41C42G17' => 'lonja', 'Lsat_1_v5_gn_0_47300' => 'lsa', 'Lsat_1_v5_gn_2_91280' => 'lsa', 'Lsat_1_v5_gn_3_30561' => 'lsa', 'Lsat_1_v5_gn_4_184321' => 'lsa', 'Lsat_1_v5_gn_4_4041' => 'lsa', 'Lsat_1_v5_gn_5_92000' => 'lsa', 'Lsat_1_v5_gn_8_152940' => 'lsa', 'Lsat_1_v5_gn_8_62401' => 'lsa', 'Manes.06G055900' => 'mes', 'Manes.12G022200' => 'mes', 'Manes.13G023300' => 'mes', 'Manes.14G115000' => 'mes', 'Manes.15G151700' => 'mes', 'Manes.17G111300' => 'mes', 'Mapoly0226s0009' => 'mpo', 'MBI02_g25363_MAGBIO' => 'mbi', 'MBI06_g00027_MAGBIO' => 'mbi', 'MBI10_g13034_MAGBIO' => 'mbi', 'MD09G1023400' => 'mdo', 'MD13G1100100' => 'mdo', 'MD15G1169200' => 'mdo', 'MD16G1101100' => 'mdo', 'MD17G1022900' => 'mdo', 'Medtr3g096150' => 'mtr', 'Medtr4g115070' => 'mtr', 'Medtr7g033325' => 'mtr', 'Medtr8g089840' => 'mtr', 'MELO3C010319.2' => 'cme', 'MELO3C011944.2' => 'cme', 'MELO3C021589.2' => 'cme', 'Migut.E00207' => 'egut', 'Migut.H00067' => 'egut', 'Migut.K00433' => 'egut', 'Migut.K00606' => 'egut', 'Migut.K01410' => 'egut', 'MSTRG.13347' => 'ama', 'MSTRG.24045' => 'ama', 'MSTRG.2428' => 'ama', 'MSTRG.26410' => 'ama', 'MSTRG.3139' => 'ama', 'MSTRG.3286' => 'ama', 'MSTRG.563' => 'ama', 'MSTRG.7941' => 'ama', 'Nitab4.5_0000028g0060' => 'nta', 'Nitab4.5_0000065g0260' => 'nta', 'Nitab4.5_0000112g0060' => 'nta', 'Nitab4.5_0000489g0120' => 'nta', 'Nitab4.5_0001776g0050' => 'nta', 'Nitab4.5_0001854g0010' => 'nta', 'Nitab4.5_0001860g0020' => 'nta', 'Nitab4.5_0004352g0010' => 'nta', 'Nitab4.5_0008716g0020' => 'nta', 'Nitab4.5_0008922g0010' => 'nta', 'Nn3g16693' => 'nnu', 'Nn4g22596' => 'nnu', 'Nn7g37639' => 'nnu', 'Oeu001701.1' => 'oeu', 'Oeu018149.1' => 'oeu', 'Oeu026220.1' => 'oeu', 'Oeu038635.1' => 'oeu', 'Oeu049176.1' => 'oeu', 'Oeu056706.1' => 'oeu', 'Oeu056937.1' => 'oeu', 'Oeu057540.1' => 'oeu', 'Os02g0594900' => 'osa', 'Os02g0595100' => 'osa', 'Os04g0477500' => 'osa', 'Os12g0611900' => 'osa', 'Peaxi162Scf00076g00020' => 'pax', 'Peaxi162Scf00128g00217' => 'pax', 'Peaxi162Scf00129g01640' => 'pax', 'Peaxi162Scf00669g00007' => 'pax', 'Peaxi162Scf00700g00421' => 'pax', 'Peaxi162Scf00801g00038' => 'pax', 'Peaxi162Scf00891g00025' => 'pax', 'PGR083G0909' => 'pgr', 'PGR119G1005' => 'pgr', 'PGR142G2236' => 'pgr', 'PGR142G3388' => 'pgr', 'PGSC0003DMG400004514' => 'stu', 'PGSC0003DMG400012635' => 'stu', 'PGSC0003DMG400015730' => 'stu', 'PGSC0003DMG400018611' => 'stu', 'PGSC0003DMG400030897' => 'stu', 'Phvul.001G254800' => 'pvu', 'Phvul.002G260100' => 'pvu', 'Phvul.003G167600' => 'pvu', 'Phvul.004G005100' => 'pvu', 'Potri.001G343600' => 'ptr', 'Potri.006G066700' => 'ptr', 'Potri.008G186000' => 'ptr', 'Potri.010G046900' => 'ptr', 'Potri.018G127900' => 'ptr', 'Pp3c20_17750' => 'ppa', 'Pp3c24_4380' => 'ppa', 'Prupe.1G245800' => 'ppe', 'Prupe.3G293400' => 'ppe', 'Prupe.7G247400' => 'ppe', 'Psat0s145g0120' => 'psa', 'Psat0s595g0040' => 'psa', 'Psat0s595g0120' => 'psa', 'Psat3g175040' => 'psa', 'Psat7g058120' => 'psa', 'PSO017G0428' => 'pso', 'PSO063G7510' => 'pso', 'PSO067G0046' => 'pso', 'PSO478G1073' => 'pso', 'PSO675G3677' => 'pso', 'PSO675G6558' => 'pso', 'PSO675G7520' => 'pso', 'PSO675G8959' => 'pso', 'QL02p074089' => 'qlo', 'QL02p089614' => 'qlo', 'QL03p057736' => 'qlo', 'RcHm_v2.0_Chr1g0364131' => 'rch', 'RcHm_v2.0_Chr2g0087801' => 'rch', 'RcHm_v2.0_Chr2g0087821' => 'rch', 'RcHm_v2.0_Chr2g0173231' => 'rch', 'RcHm_v2.0_Chr4g0433111' => 'rch', 'Rhsim03G0250300' => 'rsi', 'Rhsim08G0048400' => 'rsi', 'Rhsim10G0014800' => 'rsi', 'Rhsim12G0040100' => 'rsi', 'Rhsim12G0109700' => 'rsi', 'Sabra06G0049600' => 'sbr', 'Sabra08G0141000' => 'sbr', 'Sabra10G0021400' => 'sbr', 'Sabra16G0222900' => 'sbr', 'Sabra18G0108600' => 'sbr', 'SalBow1G0433' => 'sbo', 'SalBow1G2038' => 'sbo', 'SalBow1G5003' => 'sbo', 'SalBow7G1197' => 'sbo', 'SalBow8G3506' => 'sbo', 'Sc03g0007300' => 'sci', 'Sc11g0000950' => 'sci', 'Sc14g0008750' => 'sci', 'Sc18g0000420' => 'sci', 'Sed0006754' => 'sed', 'Sed0008741' => 'sed', 'Sed0017172' => 'sed', 'Sed0018925' => 'sed', 'Sed0023326' => 'sed', 'Sed0025909' => 'sed', 'SEGI_05333' => 'sgi', 'SEGI_10362' => 'sgi', 'SEGI_13380' => 'sgi', 'SEGI_24306' => 'sgi', 'SEGI_29077' => 'sgi', 'SEGI_29095' => 'sgi', 'SEGI_36534' => 'sgi', 'SEGI_37506' => 'sgi', 'SEGI_38321' => 'sgi', 'SGA_v2.0_scaffold307G48031' => 'sas', 'SGA_v2.0_scaffold47G17507' => 'sas', 'SGA_v2.0_scaffold63G21736' => 'sas', 'SGA_v2.0_scaffold87G27070' => 'sas', 'SHI17794' => 'shi', 'SHI28851' => 'shi', 'SMO165G0155' => 'smo', 'SMO340G0217' => 'smo', 'SMO367G1210' => 'smo', 'Solyc02g093430.3' => 'sly', 'Solyc05g013580.4' => 'sly', 'Solyc07g008030.3' => 'sly', 'Solyc12g035470.2' => 'sly', 'Sopen02g038020' => 'spe', 'Sopen05g008490' => 'spe', 'Sopen07g003910' => 'spe', 'Sopen12g015240' => 'spe', 'Sp1g11550' => 'spa', 'Sp2g16710' => 'spa', 'Sp3g00430' => 'spa', 'Sp3g26780' => 'spa', 'Sp5g22900' => 'spa', 'Sp6g29530' => 'spa', 'TAR371G0794' => 'tar', 'TAR374G0164' => 'tar', 'TAR622G0165' => 'tar', 'TAR626G0929' => 'tar', 'TAR629G2155' => 'tar', 'THA.LOC104805282' => 'tha', 'THA.LOC104805363' => 'tha', 'THA.LOC104808968' => 'tha', 'THA.LOC104821093' => 'tha', 'THA.LOC104823953' => 'tha', 'THA.LOC104825562' => 'tha', 'THA.LOC104825665' => 'tha', 'Thecc.02G261400' => 'tca', 'Thecc.04G019200' => 'tca', 'Thecc.09G130400' => 'tca', 'Thhalv10004374m.g' => 'esa', 'Thhalv10007850m.g' => 'esa', 'Thhalv10013782m.g' => 'esa', 'Thhalv10018686m.g' => 'esa', 'Thhalv10020899m.g' => 'esa', 'Thhalv10022755m.g' => 'esa', 'TPR.G23851' => 'tpr', 'TPR.G26500' => 'tpr', 'TPR.G27267' => 'tpr', 'TPR.G32001' => 'tpr', 'TPR.G6251' => 'tpr', 'TPR.G8167' => 'tpr', 'TWI12G1330' => 'twi', 'TWI18G1239' => 'twi', 'TWI34G0979' => 'twi', 'TWI36G0670' => 'twi', 'TWI36G0707' => 'twi', 'TWI56G0233' => 'twi', 'TWI75G1809' => 'twi', 'unitig_21.g20874' => 'ugi', 'unitig_26.g10343' => 'ugi', 'unitig_46.g18392' => 'ugi', 'unitig_52.g17178' => 'ugi', 'unitig_8.g2934' => 'ugi', 'vmacro01122' => 'vma', 'vmacro05875' => 'vma', 'vmacro06147' => 'vma', 'vmacro16191' => 'vma', 'vmacro18293' => 'vma', 'VMungo0251G3707' => 'vmu', 'VMungo0464G1521' => 'vmu', 'VMungo1215G0205' => 'vmu', 'VMungo1383G2484' => 'vmu', 'Zm00001eb079610' => 'zma', 'Zm00001eb135990' => 'zma', 'Zm00001eb183710' => 'zma', 'Zm00001eb246020' => 'zma' ) $gf_id = 'HOM05D001124' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001124' ) $data_identifier = 'HOM05D001124' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 6, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 7, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 21, 'bol' => (int) 10, 'bra' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 6, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 9, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 21, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 8, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 10, 'lsa' => (int) 8, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 8, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 9, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb246020' $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' => 'HOM05D001124', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '548', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02520' => 'bna', 'A03p06630' => 'bna', 'A05p44460' => 'bna', 'A06p08710' => 'bna', 'A06p41090' => 'bna', 'A07p32320' => 'bna', 'A08p32520' => 'bna', 'A09p10360' => 'bna', 'A10p24080' => 'bna', 'Aa31LG11G15250' => 'aar', 'Aa31LG1G1800' => 'aar', 'Aa31LG2G5120' => 'aar', 'Aa31LG2G6070' => 'aar', 'Aa31LG5G10770' => 'aar', 'Aa31sc61G90' => 'aar', 'Actinidia01352' => 'ach', 'Actinidia05983' => 'ach', 'Actinidia08133' => 'ach', 'Actinidia15101' => 'ach', 'Actinidia26379' => 'ach', 'Actinidia35778' => 'ach', 'Actinidia36123' => 'ach', 'Actinidia37436' => 'ach', 'Actinidia38730' => 'ach', 'Ah.02g128210' => 'amhyb', 'Ah.03g132990' => 'amhyb', 'Ah.14g079410' => 'amhyb', 'AL1G24640' => 'aly', 'AL2G26680' => 'aly', 'AL3G10530' => 'aly', 'AL3G45230' => 'aly', 'AL5G15230' => 'aly', 'AL5G16960' => 'aly', 'AL6G25210' => 'aly', 'Aqoxy2G00441' => 'aox', 'Aqoxy3G01236' => 'aox', 'Aqoxy5G03746' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3RQ047' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C7GMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9C8JER' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MBL6KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YXCZ83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZANX40' => 'arhy', 'AT1G12990' => 'ath', 'AT1G67880' => 'ath', 'AT2G13290' => 'ath', 'AT3G01620' => 'ath', 'AT3G26445' => 'ath', 'AT3G27540' => 'ath', 'AT5G14480' => 'ath', 'ATR0824G026' => 'atr', 'ATR1098G019' => 'atr', 'Atru.chr11.2145' => 'acertr', 'Atru.chr2.3636' => 'acertr', 'Atru.chr2.3644' => 'acertr', 'Atru.chr6.2422' => 'acertr', 'Atru.chr7.1112' => 'acertr', 'AUR62005469' => 'cqu', 'AUR62011166' => 'cqu', 'AUR62013319' => 'cqu', 'AUR62024273' => 'cqu', 'AUR62028420' => 'cqu', 'AUR62041942' => 'cqu', 'BcaB01g04969' => 'bca', 'BcaB01g06371' => 'bca', 'BcaB02g11494' => 'bca', 'BcaB03g15382' => 'bca', 'BcaB08g36994' => 'bca', 'BcaC03g13477' => 'bca', 'BcaC03g13478' => 'bca', 'BcaC03g13480' => 'bca', 'BcaC03g13481' => 'bca', 'BcaC03g13486' => 'bca', 'BcaC04g19031' => 'bca', 'BcaC04g23085' => 'bca', 'BcaC05g25094' => 'bca', 'BcaC05g25096' => 'bca', 'BcaC05g25138' => 'bca', 'BcaC05g30416' => 'bca', 'BcaC05g30455' => 'bca', 'BcaC06g30979' => 'bca', 'BcaC06g33805' => 'bca', 'BcaC08g46021' => 'bca', 'BcaNung03154' => 'bca', 'BolC2t06623H' => 'bol', 'BolC2t06632H' => 'bol', 'BolC2t06635H' => 'bol', 'BolC2t06638H' => 'bol', 'BolC3t13266H' => 'bol', 'BolC5t29776H' => 'bol', 'BolC6t38912H' => 'bol', 'BolC7t44183H' => 'bol', 'BolC9t54123H' => 'bol', 'BolC9t59107H' => 'bol', 'BraA02t05221Z' => 'bra', 'BraA03t09996Z' => 'bra', 'BraA05t23210Z' => 'bra', 'BraA06t24068Z' => 'bra', 'BraA06t27032Z' => 'bra', 'BraA08t35176Z' => 'bra', 'BraA09t36680Z' => 'bra', 'BraA10t44471Z' => 'bra', 'C02p06760' => 'bna', 'C02p06890' => 'bna', 'C02p07010' => 'bna', 'C03p07660' => 'bna', 'C05p10300' => 'bna', 'C06p38150' => 'bna', 'C07p36650' => 'bna', 'C08p15770' => 'bna', 'C09p12300' => 'bna', 'C09p62700' => 'bna', 'C09p75040' => 'bna', 'CAN.G13.1' => 'can', 'CAN.G138.4' => 'can', 'CAN.G44.6' => 'can', 'CAN.G473.19' => 'can', 'CANSAT01G0835' => 'cansat', 'CANSAT11G0246' => 'cansat', 'CANSAT11G1766' => 'cansat', 'CANSAT64G1954' => 'cansat', 'CARHR013330' => 'chi', 'CARHR060530' => 'chi', 'CARHR075300' => 'chi', 'CARHR105120' => 'chi', 'CARHR148910' => 'chi', 'CARHR198830' => 'chi', 'Carub.0001s1275' => 'cru', 'Carub.0002s1437' => 'cru', 'Carub.0003s0044' => 'cru', 'Carub.0003s2787' => 'cru', 'Carub.0005s0597' => 'cru', 'Carub.0006s1266' => 'cru', 'Ca_06935_v3' => 'car', 'Ca_13559_v3' => 'car', 'Ca_16941_v3' => 'car', 'Ca_16960_v3' => 'car', 'Ca_17775_v3' => 'car', 'Ca_30464_v3' => 'car', 'Cc06_g08160' => 'ccan', 'Cc07_g01520' => 'ccan', 'Cc11_g15810' => 'ccan', 'CDE02G2840' => 'cde', 'CDE03G0093' => 'cde', 'CDE04G2127' => 'cde', 'CDE07G1857' => 'cde', 'CDE09G1246' => 'cde', 'Cfa003412' => 'cfa', 'Cfa007341' => 'cfa', 'Cfa009220' => 'cfa', 'Ciclev10008737m.g' => 'ccl', 'Ciclev10015565m.g' => 'ccl', 'Ciclev10031761m.g' => 'ccl', 'CiPaw.03G045300' => 'cil', 'CiPaw.03G247200' => 'cil', 'CiPaw.04G029500' => 'cil', 'CiPaw.04G174000' => 'cil', 'CiPaw.05G181200' => 'cil', 'CiPaw.06G067100' => 'cil', 'ClCG05G025800' => 'cla', 'ClCG06G011400' => 'cla', 'ClCG09G019360' => 'cla', 'COL.COLO4_04827' => 'col', 'COL.COLO4_29170' => 'col', 'COL.COLO4_35131' => 'col', 'COL.COLO4_35132' => 'col', 'Cpa.g.sc33.32' => 'cpa', 'Cpa.g.sc46.29' => 'cpa', 'Cpa.g.sc796.1' => 'cpa', 'CsaV3_1G030420' => 'csa', 'CsaV3_5G027050' => 'csa', 'CsaV3_5G031040' => 'csa', 'CsaV3_UNG023130' => 'csa', 'CSS0007726' => 'camsi', 'CSS0016433' => 'camsi', 'CSS0017656' => 'camsi', 'CSS0025364' => 'camsi', 'CSS0027582' => 'camsi', 'CSS0047288' => 'camsi', 'CSS0049950' => 'camsi', 'DCAR_003843' => 'dca', 'DCAR_007052' => 'dca', 'DCAR_020884' => 'dca', 'DCAR_021730' => 'dca', 'DCAR_024423' => 'dca', 'DCAR_026509' => 'dca', 'DCAR_031158' => 'dca', 'Dinv14728' => 'din', 'Dinv15219' => 'din', 'Dinv25728' => 'din', 'Dinv33428' => 'din', 'Dinv36489' => 'din', 'Dinv41486' => 'din', 'Duzib147G0469' => 'dzi', 'Duzib168G0060' => 'dzi', 'Duzib187G1215' => 'dzi', 'Duzib248G0692' => 'dzi', 'Duzib251G0767' => 'dzi', 'Duzib264G0446' => 'dzi', 'Duzib268G0691' => 'dzi', 'ECA232G4767' => 'eca', 'ECA233G2838' => 'eca', 'ECA234G0391' => 'eca', 'ECA234G0857' => 'eca', 'ECA236G1593' => 'eca', 'ECA238G0565' => 'eca', 'ECA246G1027' => 'eca', 'ECA246G3223' => 'eca', 'ECA246G3470' => 'eca', 'EL10Ac6g13829' => 'bvu', 'EL10Ac6g14093' => 'bvu', 'EL10Ac8g18707' => 'bvu', 'Eucgr.C01369' => 'egr', 'Eucgr.H02492' => 'egr', 'Eucgr.I01733' => 'egr', 'Eucgr.J02255' => 'egr', 'Eucgr.J02257' => 'egr', 'Eucgr.J02258' => 'egr', 'FAN02G1601' => 'fan', 'FAN03G1586' => 'fan', 'FAN03G2986' => 'fan', 'FAN05G4837' => 'fan', 'FAN06G0146' => 'fan', 'FAN07G0858' => 'fan', 'FAN09G3179' => 'fan', 'FAN10G0669' => 'fan', 'FAN12G2358' => 'fan', 'FAN14G4198' => 'fan', 'FAN14G5112' => 'fan', 'FAN17G0342' => 'fan', 'FAN19G0342' => 'fan', 'FAN19G0962' => 'fan', 'FAN19G1101' => 'fan', 'FAN19G1872' => 'fan', 'FAN22G0356' => 'fan', 'FAN23G0744' => 'fan', 'FAN23G1914' => 'fan', 'FAN26G0032' => 'fan', 'FAN28G0625' => 'fan', 'FvH4_1g02710' => 'fve', 'FvH4_1g02720' => 'fve', 'FvH4_4g25670' => 'fve', 'FvH4_6g51700' => 'fve', 'FvH4_7g20170' => 'fve', 'Glyma.05G175000' => 'gma', 'Glyma.08G132300' => 'gma', 'Glyma.11G243000' => 'gma', 'Glyma.13G158900' => 'gma', 'Glyma.17G112400' => 'gma', 'Glyma.18G014100' => 'gma', 'Glyma.19G003100' => 'gma', 'Glyma.19G056500' => 'gma', 'Gohir.A01G158900' => 'ghi', 'Gohir.A05G312600' => 'ghi', 'Gohir.A05G354900' => 'ghi', 'Gohir.A07G037200' => 'ghi', 'Gohir.A09G030000' => 'ghi', 'Gohir.A12G145200' => 'ghi', 'Gohir.D01G151500' => 'ghi', 'Gohir.D04G058300' => 'ghi', 'Gohir.D05G314100' => 'ghi', 'Gohir.D07G041400' => 'ghi', 'Gohir.D09G029700' => 'ghi', 'Gohir.D12G149700' => 'ghi', 'Gorai.001G043800' => 'gra', 'Gorai.002G187800' => 'gra', 'Gorai.006G034700' => 'gra', 'Gorai.008G161200' => 'gra', 'Gorai.009G335700' => 'gra', 'Gorai.012G065000' => 'gra', 'GSVIVG01000535001' => 'vvi', 'GSVIVG01015572001' => 'vvi', 'GSVIVG01032386001' => 'vvi', 'HanXRQChr05g0138531' => 'han', 'HanXRQChr06g0174391' => 'han', 'HanXRQChr07g0199021' => 'han', 'HanXRQChr08g0208211' => 'han', 'HanXRQChr09g0255471' => 'han', 'HanXRQChr10g0315791' => 'han', 'HanXRQChr12g0371991' => 'han', 'HanXRQChr15g0475251' => 'han', 'HanXRQChr17g0540001' => 'han', 'HanXRQChr17g0548631' => 'han', 'HanXRQChr17g0569561' => 'han', 'Haze_12256' => 'cav', 'Haze_14756' => 'cav', 'Haze_25528' => 'cav', 'Hma1.2p1_0079F.1_g041020' => 'hma', 'Hma1.2p1_0818F.1_g223260' => 'hma', 'Hma1.2p1_1747F.1_g300530' => 'hma', 'HPP92_004607' => 'vpl', 'HPP92_004608' => 'vpl', 'HPP92_006181' => 'vpl', 'HPP92_012192' => 'vpl', 'HPP92_015680' => 'vpl', 'HPP92_020249' => 'vpl', 'HPP92_021376' => 'vpl', 'HPP92_024275' => 'vpl', 'Hund06031' => 'sun', 'Hund25391' => 'sun', 'Lalb_Chr07g0185371' => 'lal', 'Lalb_Chr07g0185381' => 'lal', 'Lalb_Chr12g0204011' => 'lal', 'Lalb_Chr13g0301671' => 'lal', 'Lalb_Chr14g0362851' => 'lal', 'Lalb_Chr24g0403581' => 'lal', 'Lj1g0000233' => 'lja', 'Lj2g0018120' => 'lja', 'Lj3C621T0' => 'lonja', 'Lj3P1059T14' => 'lonja', 'Lj3P611T9' => 'lonja', 'Lj3P614T13' => 'lonja', 'Lj3P615T5' => 'lonja', 'Lj4g0012315' => 'lja', 'Lj4g0026182' => 'lja', 'Lj6P813T16' => 'lonja', 'Lj7C427T7' => 'lonja', 'Lj7C427T8' => 'lonja', 'Lj7P600T41' => 'lonja', 'Lju41C42G17' => 'lonja', 'Lsat_1_v5_gn_0_47300' => 'lsa', 'Lsat_1_v5_gn_2_91280' => 'lsa', 'Lsat_1_v5_gn_3_30561' => 'lsa', 'Lsat_1_v5_gn_4_184321' => 'lsa', 'Lsat_1_v5_gn_4_4041' => 'lsa', 'Lsat_1_v5_gn_5_92000' => 'lsa', 'Lsat_1_v5_gn_8_152940' => 'lsa', 'Lsat_1_v5_gn_8_62401' => 'lsa', 'Manes.06G055900' => 'mes', 'Manes.12G022200' => 'mes', 'Manes.13G023300' => 'mes', 'Manes.14G115000' => 'mes', 'Manes.15G151700' => 'mes', 'Manes.17G111300' => 'mes', 'Mapoly0226s0009' => 'mpo', 'MBI02_g25363_MAGBIO' => 'mbi', 'MBI06_g00027_MAGBIO' => 'mbi', 'MBI10_g13034_MAGBIO' => 'mbi', 'MD09G1023400' => 'mdo', 'MD13G1100100' => 'mdo', 'MD15G1169200' => 'mdo', 'MD16G1101100' => 'mdo', 'MD17G1022900' => 'mdo', 'Medtr3g096150' => 'mtr', 'Medtr4g115070' => 'mtr', 'Medtr7g033325' => 'mtr', 'Medtr8g089840' => 'mtr', 'MELO3C010319.2' => 'cme', 'MELO3C011944.2' => 'cme', 'MELO3C021589.2' => 'cme', 'Migut.E00207' => 'egut', 'Migut.H00067' => 'egut', 'Migut.K00433' => 'egut', 'Migut.K00606' => 'egut', 'Migut.K01410' => 'egut', 'MSTRG.13347' => 'ama', 'MSTRG.24045' => 'ama', 'MSTRG.2428' => 'ama', 'MSTRG.26410' => 'ama', 'MSTRG.3139' => 'ama', 'MSTRG.3286' => 'ama', 'MSTRG.563' => 'ama', 'MSTRG.7941' => 'ama', 'Nitab4.5_0000028g0060' => 'nta', 'Nitab4.5_0000065g0260' => 'nta', 'Nitab4.5_0000112g0060' => 'nta', 'Nitab4.5_0000489g0120' => 'nta', 'Nitab4.5_0001776g0050' => 'nta', 'Nitab4.5_0001854g0010' => 'nta', 'Nitab4.5_0001860g0020' => 'nta', 'Nitab4.5_0004352g0010' => 'nta', 'Nitab4.5_0008716g0020' => 'nta', 'Nitab4.5_0008922g0010' => 'nta', 'Nn3g16693' => 'nnu', 'Nn4g22596' => 'nnu', 'Nn7g37639' => 'nnu', 'Oeu001701.1' => 'oeu', 'Oeu018149.1' => 'oeu', 'Oeu026220.1' => 'oeu', 'Oeu038635.1' => 'oeu', 'Oeu049176.1' => 'oeu', 'Oeu056706.1' => 'oeu', 'Oeu056937.1' => 'oeu', 'Oeu057540.1' => 'oeu', 'Os02g0594900' => 'osa', 'Os02g0595100' => 'osa', 'Os04g0477500' => 'osa', 'Os12g0611900' => 'osa', 'Peaxi162Scf00076g00020' => 'pax', 'Peaxi162Scf00128g00217' => 'pax', 'Peaxi162Scf00129g01640' => 'pax', 'Peaxi162Scf00669g00007' => 'pax', 'Peaxi162Scf00700g00421' => 'pax', 'Peaxi162Scf00801g00038' => 'pax', 'Peaxi162Scf00891g00025' => 'pax', 'PGR083G0909' => 'pgr', 'PGR119G1005' => 'pgr', 'PGR142G2236' => 'pgr', 'PGR142G3388' => 'pgr', 'PGSC0003DMG400004514' => 'stu', 'PGSC0003DMG400012635' => 'stu', 'PGSC0003DMG400015730' => 'stu', 'PGSC0003DMG400018611' => 'stu', 'PGSC0003DMG400030897' => 'stu', 'Phvul.001G254800' => 'pvu', 'Phvul.002G260100' => 'pvu', 'Phvul.003G167600' => 'pvu', 'Phvul.004G005100' => 'pvu', 'Potri.001G343600' => 'ptr', 'Potri.006G066700' => 'ptr', 'Potri.008G186000' => 'ptr', 'Potri.010G046900' => 'ptr', 'Potri.018G127900' => 'ptr', 'Pp3c20_17750' => 'ppa', 'Pp3c24_4380' => 'ppa', 'Prupe.1G245800' => 'ppe', 'Prupe.3G293400' => 'ppe', 'Prupe.7G247400' => 'ppe', 'Psat0s145g0120' => 'psa', 'Psat0s595g0040' => 'psa', 'Psat0s595g0120' => 'psa', 'Psat3g175040' => 'psa', 'Psat7g058120' => 'psa', 'PSO017G0428' => 'pso', 'PSO063G7510' => 'pso', 'PSO067G0046' => 'pso', 'PSO478G1073' => 'pso', 'PSO675G3677' => 'pso', 'PSO675G6558' => 'pso', 'PSO675G7520' => 'pso', 'PSO675G8959' => 'pso', 'QL02p074089' => 'qlo', 'QL02p089614' => 'qlo', 'QL03p057736' => 'qlo', 'RcHm_v2.0_Chr1g0364131' => 'rch', 'RcHm_v2.0_Chr2g0087801' => 'rch', 'RcHm_v2.0_Chr2g0087821' => 'rch', 'RcHm_v2.0_Chr2g0173231' => 'rch', 'RcHm_v2.0_Chr4g0433111' => 'rch', 'Rhsim03G0250300' => 'rsi', 'Rhsim08G0048400' => 'rsi', 'Rhsim10G0014800' => 'rsi', 'Rhsim12G0040100' => 'rsi', 'Rhsim12G0109700' => 'rsi', 'Sabra06G0049600' => 'sbr', 'Sabra08G0141000' => 'sbr', 'Sabra10G0021400' => 'sbr', 'Sabra16G0222900' => 'sbr', 'Sabra18G0108600' => 'sbr', 'SalBow1G0433' => 'sbo', 'SalBow1G2038' => 'sbo', 'SalBow1G5003' => 'sbo', 'SalBow7G1197' => 'sbo', 'SalBow8G3506' => 'sbo', 'Sc03g0007300' => 'sci', 'Sc11g0000950' => 'sci', 'Sc14g0008750' => 'sci', 'Sc18g0000420' => 'sci', 'Sed0006754' => 'sed', 'Sed0008741' => 'sed', 'Sed0017172' => 'sed', 'Sed0018925' => 'sed', 'Sed0023326' => 'sed', 'Sed0025909' => 'sed', 'SEGI_05333' => 'sgi', 'SEGI_10362' => 'sgi', 'SEGI_13380' => 'sgi', 'SEGI_24306' => 'sgi', 'SEGI_29077' => 'sgi', 'SEGI_29095' => 'sgi', 'SEGI_36534' => 'sgi', 'SEGI_37506' => 'sgi', 'SEGI_38321' => 'sgi', 'SGA_v2.0_scaffold307G48031' => 'sas', 'SGA_v2.0_scaffold47G17507' => 'sas', 'SGA_v2.0_scaffold63G21736' => 'sas', 'SGA_v2.0_scaffold87G27070' => 'sas', 'SHI17794' => 'shi', 'SHI28851' => 'shi', 'SMO165G0155' => 'smo', 'SMO340G0217' => 'smo', 'SMO367G1210' => 'smo', 'Solyc02g093430.3' => 'sly', 'Solyc05g013580.4' => 'sly', 'Solyc07g008030.3' => 'sly', 'Solyc12g035470.2' => 'sly', 'Sopen02g038020' => 'spe', 'Sopen05g008490' => 'spe', 'Sopen07g003910' => 'spe', 'Sopen12g015240' => 'spe', 'Sp1g11550' => 'spa', 'Sp2g16710' => 'spa', 'Sp3g00430' => 'spa', 'Sp3g26780' => 'spa', 'Sp5g22900' => 'spa', 'Sp6g29530' => 'spa', 'TAR371G0794' => 'tar', 'TAR374G0164' => 'tar', 'TAR622G0165' => 'tar', 'TAR626G0929' => 'tar', 'TAR629G2155' => 'tar', 'THA.LOC104805282' => 'tha', 'THA.LOC104805363' => 'tha', 'THA.LOC104808968' => 'tha', 'THA.LOC104821093' => 'tha', 'THA.LOC104823953' => 'tha', 'THA.LOC104825562' => 'tha', 'THA.LOC104825665' => 'tha', 'Thecc.02G261400' => 'tca', 'Thecc.04G019200' => 'tca', 'Thecc.09G130400' => 'tca', 'Thhalv10004374m.g' => 'esa', 'Thhalv10007850m.g' => 'esa', 'Thhalv10013782m.g' => 'esa', 'Thhalv10018686m.g' => 'esa', 'Thhalv10020899m.g' => 'esa', 'Thhalv10022755m.g' => 'esa', 'TPR.G23851' => 'tpr', 'TPR.G26500' => 'tpr', 'TPR.G27267' => 'tpr', 'TPR.G32001' => 'tpr', 'TPR.G6251' => 'tpr', 'TPR.G8167' => 'tpr', 'TWI12G1330' => 'twi', 'TWI18G1239' => 'twi', 'TWI34G0979' => 'twi', 'TWI36G0670' => 'twi', 'TWI36G0707' => 'twi', 'TWI56G0233' => 'twi', 'TWI75G1809' => 'twi', 'unitig_21.g20874' => 'ugi', 'unitig_26.g10343' => 'ugi', 'unitig_46.g18392' => 'ugi', 'unitig_52.g17178' => 'ugi', 'unitig_8.g2934' => 'ugi', 'vmacro01122' => 'vma', 'vmacro05875' => 'vma', 'vmacro06147' => 'vma', 'vmacro16191' => 'vma', 'vmacro18293' => 'vma', 'VMungo0251G3707' => 'vmu', 'VMungo0464G1521' => 'vmu', 'VMungo1215G0205' => 'vmu', 'VMungo1383G2484' => 'vmu', 'Zm00001eb079610' => 'zma', 'Zm00001eb135990' => 'zma', 'Zm00001eb183710' => 'zma', 'Zm00001eb246020' => 'zma' ), 'gf_id' => 'HOM05D001124', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001124' ), 'data_identifier' => 'HOM05D001124', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001124', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '548', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02520' => 'bna', 'A03p06630' => 'bna', 'A05p44460' => 'bna', 'A06p08710' => 'bna', 'A06p41090' => 'bna', 'A07p32320' => 'bna', 'A08p32520' => 'bna', 'A09p10360' => 'bna', 'A10p24080' => 'bna', 'Aa31LG11G15250' => 'aar', 'Aa31LG1G1800' => 'aar', 'Aa31LG2G5120' => 'aar', 'Aa31LG2G6070' => 'aar', 'Aa31LG5G10770' => 'aar', 'Aa31sc61G90' => 'aar', 'Actinidia01352' => 'ach', 'Actinidia05983' => 'ach', 'Actinidia08133' => 'ach', 'Actinidia15101' => 'ach', 'Actinidia26379' => 'ach', 'Actinidia35778' => 'ach', 'Actinidia36123' => 'ach', 'Actinidia37436' => 'ach', 'Actinidia38730' => 'ach', 'Ah.02g128210' => 'amhyb', 'Ah.03g132990' => 'amhyb', 'Ah.14g079410' => 'amhyb', 'AL1G24640' => 'aly', 'AL2G26680' => 'aly', 'AL3G10530' => 'aly', 'AL3G45230' => 'aly', 'AL5G15230' => 'aly', 'AL5G16960' => 'aly', 'AL6G25210' => 'aly', 'Aqoxy2G00441' => 'aox', 'Aqoxy3G01236' => 'aox', 'Aqoxy5G03746' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3RQ047' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C7GMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9C8JER' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MBL6KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YXCZ83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZANX40' => 'arhy', 'AT1G12990' => 'ath', 'AT1G67880' => 'ath', 'AT2G13290' => 'ath', 'AT3G01620' => 'ath', 'AT3G26445' => 'ath', 'AT3G27540' => 'ath', 'AT5G14480' => 'ath', 'ATR0824G026' => 'atr', 'ATR1098G019' => 'atr', 'Atru.chr11.2145' => 'acertr', 'Atru.chr2.3636' => 'acertr', 'Atru.chr2.3644' => 'acertr', 'Atru.chr6.2422' => 'acertr', 'Atru.chr7.1112' => 'acertr', 'AUR62005469' => 'cqu', 'AUR62011166' => 'cqu', 'AUR62013319' => 'cqu', 'AUR62024273' => 'cqu', 'AUR62028420' => 'cqu', 'AUR62041942' => 'cqu', 'BcaB01g04969' => 'bca', 'BcaB01g06371' => 'bca', 'BcaB02g11494' => 'bca', 'BcaB03g15382' => 'bca', 'BcaB08g36994' => 'bca', 'BcaC03g13477' => 'bca', 'BcaC03g13478' => 'bca', 'BcaC03g13480' => 'bca', 'BcaC03g13481' => 'bca', 'BcaC03g13486' => 'bca', 'BcaC04g19031' => 'bca', 'BcaC04g23085' => 'bca', 'BcaC05g25094' => 'bca', 'BcaC05g25096' => 'bca', 'BcaC05g25138' => 'bca', 'BcaC05g30416' => 'bca', 'BcaC05g30455' => 'bca', 'BcaC06g30979' => 'bca', 'BcaC06g33805' => 'bca', 'BcaC08g46021' => 'bca', 'BcaNung03154' => 'bca', 'BolC2t06623H' => 'bol', 'BolC2t06632H' => 'bol', 'BolC2t06635H' => 'bol', 'BolC2t06638H' => 'bol', 'BolC3t13266H' => 'bol', 'BolC5t29776H' => 'bol', 'BolC6t38912H' => 'bol', 'BolC7t44183H' => 'bol', 'BolC9t54123H' => 'bol', 'BolC9t59107H' => 'bol', 'BraA02t05221Z' => 'bra', 'BraA03t09996Z' => 'bra', 'BraA05t23210Z' => 'bra', 'BraA06t24068Z' => 'bra', 'BraA06t27032Z' => 'bra', 'BraA08t35176Z' => 'bra', 'BraA09t36680Z' => 'bra', 'BraA10t44471Z' => 'bra', 'C02p06760' => 'bna', 'C02p06890' => 'bna', 'C02p07010' => 'bna', 'C03p07660' => 'bna', 'C05p10300' => 'bna', 'C06p38150' => 'bna', 'C07p36650' => 'bna', 'C08p15770' => 'bna', 'C09p12300' => 'bna', 'C09p62700' => 'bna', 'C09p75040' => 'bna', 'CAN.G13.1' => 'can', 'CAN.G138.4' => 'can', 'CAN.G44.6' => 'can', 'CAN.G473.19' => 'can', 'CANSAT01G0835' => 'cansat', 'CANSAT11G0246' => 'cansat', 'CANSAT11G1766' => 'cansat', 'CANSAT64G1954' => 'cansat', 'CARHR013330' => 'chi', 'CARHR060530' => 'chi', 'CARHR075300' => 'chi', 'CARHR105120' => 'chi', 'CARHR148910' => 'chi', 'CARHR198830' => 'chi', 'Carub.0001s1275' => 'cru', 'Carub.0002s1437' => 'cru', 'Carub.0003s0044' => 'cru', 'Carub.0003s2787' => 'cru', 'Carub.0005s0597' => 'cru', 'Carub.0006s1266' => 'cru', 'Ca_06935_v3' => 'car', 'Ca_13559_v3' => 'car', 'Ca_16941_v3' => 'car', 'Ca_16960_v3' => 'car', 'Ca_17775_v3' => 'car', 'Ca_30464_v3' => 'car', 'Cc06_g08160' => 'ccan', 'Cc07_g01520' => 'ccan', 'Cc11_g15810' => 'ccan', 'CDE02G2840' => 'cde', 'CDE03G0093' => 'cde', 'CDE04G2127' => 'cde', 'CDE07G1857' => 'cde', 'CDE09G1246' => 'cde', 'Cfa003412' => 'cfa', 'Cfa007341' => 'cfa', 'Cfa009220' => 'cfa', 'Ciclev10008737m.g' => 'ccl', 'Ciclev10015565m.g' => 'ccl', 'Ciclev10031761m.g' => 'ccl', 'CiPaw.03G045300' => 'cil', 'CiPaw.03G247200' => 'cil', 'CiPaw.04G029500' => 'cil', 'CiPaw.04G174000' => 'cil', 'CiPaw.05G181200' => 'cil', 'CiPaw.06G067100' => 'cil', 'ClCG05G025800' => 'cla', 'ClCG06G011400' => 'cla', 'ClCG09G019360' => 'cla', 'COL.COLO4_04827' => 'col', 'COL.COLO4_29170' => 'col', 'COL.COLO4_35131' => 'col', 'COL.COLO4_35132' => 'col', 'Cpa.g.sc33.32' => 'cpa', 'Cpa.g.sc46.29' => 'cpa', 'Cpa.g.sc796.1' => 'cpa', 'CsaV3_1G030420' => 'csa', 'CsaV3_5G027050' => 'csa', 'CsaV3_5G031040' => 'csa', 'CsaV3_UNG023130' => 'csa', 'CSS0007726' => 'camsi', 'CSS0016433' => 'camsi', 'CSS0017656' => 'camsi', 'CSS0025364' => 'camsi', 'CSS0027582' => 'camsi', 'CSS0047288' => 'camsi', 'CSS0049950' => 'camsi', 'DCAR_003843' => 'dca', 'DCAR_007052' => 'dca', 'DCAR_020884' => 'dca', 'DCAR_021730' => 'dca', 'DCAR_024423' => 'dca', 'DCAR_026509' => 'dca', 'DCAR_031158' => 'dca', 'Dinv14728' => 'din', 'Dinv15219' => 'din', 'Dinv25728' => 'din', 'Dinv33428' => 'din', 'Dinv36489' => 'din', 'Dinv41486' => 'din', 'Duzib147G0469' => 'dzi', 'Duzib168G0060' => 'dzi', 'Duzib187G1215' => 'dzi', 'Duzib248G0692' => 'dzi', 'Duzib251G0767' => 'dzi', 'Duzib264G0446' => 'dzi', 'Duzib268G0691' => 'dzi', 'ECA232G4767' => 'eca', 'ECA233G2838' => 'eca', 'ECA234G0391' => 'eca', 'ECA234G0857' => 'eca', 'ECA236G1593' => 'eca', 'ECA238G0565' => 'eca', 'ECA246G1027' => 'eca', 'ECA246G3223' => 'eca', 'ECA246G3470' => 'eca', 'EL10Ac6g13829' => 'bvu', 'EL10Ac6g14093' => 'bvu', 'EL10Ac8g18707' => 'bvu', 'Eucgr.C01369' => 'egr', 'Eucgr.H02492' => 'egr', 'Eucgr.I01733' => 'egr', 'Eucgr.J02255' => 'egr', 'Eucgr.J02257' => 'egr', 'Eucgr.J02258' => 'egr', 'FAN02G1601' => 'fan', 'FAN03G1586' => 'fan', 'FAN03G2986' => 'fan', 'FAN05G4837' => 'fan', 'FAN06G0146' => 'fan', 'FAN07G0858' => 'fan', 'FAN09G3179' => 'fan', 'FAN10G0669' => 'fan', 'FAN12G2358' => 'fan', 'FAN14G4198' => 'fan', 'FAN14G5112' => 'fan', 'FAN17G0342' => 'fan', 'FAN19G0342' => 'fan', 'FAN19G0962' => 'fan', 'FAN19G1101' => 'fan', 'FAN19G1872' => 'fan', 'FAN22G0356' => 'fan', 'FAN23G0744' => 'fan', 'FAN23G1914' => 'fan', 'FAN26G0032' => 'fan', 'FAN28G0625' => 'fan', 'FvH4_1g02710' => 'fve', 'FvH4_1g02720' => 'fve', 'FvH4_4g25670' => 'fve', 'FvH4_6g51700' => 'fve', 'FvH4_7g20170' => 'fve', 'Glyma.05G175000' => 'gma', 'Glyma.08G132300' => 'gma', 'Glyma.11G243000' => 'gma', 'Glyma.13G158900' => 'gma', 'Glyma.17G112400' => 'gma', 'Glyma.18G014100' => 'gma', 'Glyma.19G003100' => 'gma', 'Glyma.19G056500' => 'gma', 'Gohir.A01G158900' => 'ghi', 'Gohir.A05G312600' => 'ghi', 'Gohir.A05G354900' => 'ghi', 'Gohir.A07G037200' => 'ghi', 'Gohir.A09G030000' => 'ghi', 'Gohir.A12G145200' => 'ghi', 'Gohir.D01G151500' => 'ghi', 'Gohir.D04G058300' => 'ghi', 'Gohir.D05G314100' => 'ghi', 'Gohir.D07G041400' => 'ghi', 'Gohir.D09G029700' => 'ghi', 'Gohir.D12G149700' => 'ghi', 'Gorai.001G043800' => 'gra', 'Gorai.002G187800' => 'gra', 'Gorai.006G034700' => 'gra', 'Gorai.008G161200' => 'gra', 'Gorai.009G335700' => 'gra', 'Gorai.012G065000' => 'gra', 'GSVIVG01000535001' => 'vvi', 'GSVIVG01015572001' => 'vvi', 'GSVIVG01032386001' => 'vvi', 'HanXRQChr05g0138531' => 'han', 'HanXRQChr06g0174391' => 'han', 'HanXRQChr07g0199021' => 'han', 'HanXRQChr08g0208211' => 'han', 'HanXRQChr09g0255471' => 'han', 'HanXRQChr10g0315791' => 'han', 'HanXRQChr12g0371991' => 'han', 'HanXRQChr15g0475251' => 'han', 'HanXRQChr17g0540001' => 'han', 'HanXRQChr17g0548631' => 'han', 'HanXRQChr17g0569561' => 'han', 'Haze_12256' => 'cav', 'Haze_14756' => 'cav', 'Haze_25528' => 'cav', 'Hma1.2p1_0079F.1_g041020' => 'hma', 'Hma1.2p1_0818F.1_g223260' => 'hma', 'Hma1.2p1_1747F.1_g300530' => 'hma', 'HPP92_004607' => 'vpl', 'HPP92_004608' => 'vpl', 'HPP92_006181' => 'vpl', 'HPP92_012192' => 'vpl', 'HPP92_015680' => 'vpl', 'HPP92_020249' => 'vpl', 'HPP92_021376' => 'vpl', 'HPP92_024275' => 'vpl', 'Hund06031' => 'sun', 'Hund25391' => 'sun', 'Lalb_Chr07g0185371' => 'lal', 'Lalb_Chr07g0185381' => 'lal', 'Lalb_Chr12g0204011' => 'lal', 'Lalb_Chr13g0301671' => 'lal', 'Lalb_Chr14g0362851' => 'lal', 'Lalb_Chr24g0403581' => 'lal', 'Lj1g0000233' => 'lja', 'Lj2g0018120' => 'lja', 'Lj3C621T0' => 'lonja', 'Lj3P1059T14' => 'lonja', 'Lj3P611T9' => 'lonja', 'Lj3P614T13' => 'lonja', 'Lj3P615T5' => 'lonja', 'Lj4g0012315' => 'lja', 'Lj4g0026182' => 'lja', 'Lj6P813T16' => 'lonja', 'Lj7C427T7' => 'lonja', 'Lj7C427T8' => 'lonja', 'Lj7P600T41' => 'lonja', 'Lju41C42G17' => 'lonja', 'Lsat_1_v5_gn_0_47300' => 'lsa', 'Lsat_1_v5_gn_2_91280' => 'lsa', 'Lsat_1_v5_gn_3_30561' => 'lsa', 'Lsat_1_v5_gn_4_184321' => 'lsa', 'Lsat_1_v5_gn_4_4041' => 'lsa', 'Lsat_1_v5_gn_5_92000' => 'lsa', 'Lsat_1_v5_gn_8_152940' => 'lsa', 'Lsat_1_v5_gn_8_62401' => 'lsa', 'Manes.06G055900' => 'mes', 'Manes.12G022200' => 'mes', 'Manes.13G023300' => 'mes', 'Manes.14G115000' => 'mes', 'Manes.15G151700' => 'mes', 'Manes.17G111300' => 'mes', 'Mapoly0226s0009' => 'mpo', 'MBI02_g25363_MAGBIO' => 'mbi', 'MBI06_g00027_MAGBIO' => 'mbi', 'MBI10_g13034_MAGBIO' => 'mbi', 'MD09G1023400' => 'mdo', 'MD13G1100100' => 'mdo', 'MD15G1169200' => 'mdo', 'MD16G1101100' => 'mdo', 'MD17G1022900' => 'mdo', 'Medtr3g096150' => 'mtr', 'Medtr4g115070' => 'mtr', 'Medtr7g033325' => 'mtr', 'Medtr8g089840' => 'mtr', 'MELO3C010319.2' => 'cme', 'MELO3C011944.2' => 'cme', 'MELO3C021589.2' => 'cme', 'Migut.E00207' => 'egut', 'Migut.H00067' => 'egut', 'Migut.K00433' => 'egut', 'Migut.K00606' => 'egut', 'Migut.K01410' => 'egut', 'MSTRG.13347' => 'ama', 'MSTRG.24045' => 'ama', 'MSTRG.2428' => 'ama', 'MSTRG.26410' => 'ama', 'MSTRG.3139' => 'ama', 'MSTRG.3286' => 'ama', 'MSTRG.563' => 'ama', 'MSTRG.7941' => 'ama', 'Nitab4.5_0000028g0060' => 'nta', 'Nitab4.5_0000065g0260' => 'nta', 'Nitab4.5_0000112g0060' => 'nta', 'Nitab4.5_0000489g0120' => 'nta', 'Nitab4.5_0001776g0050' => 'nta', 'Nitab4.5_0001854g0010' => 'nta', 'Nitab4.5_0001860g0020' => 'nta', 'Nitab4.5_0004352g0010' => 'nta', 'Nitab4.5_0008716g0020' => 'nta', 'Nitab4.5_0008922g0010' => 'nta', 'Nn3g16693' => 'nnu', 'Nn4g22596' => 'nnu', 'Nn7g37639' => 'nnu', 'Oeu001701.1' => 'oeu', 'Oeu018149.1' => 'oeu', 'Oeu026220.1' => 'oeu', 'Oeu038635.1' => 'oeu', 'Oeu049176.1' => 'oeu', 'Oeu056706.1' => 'oeu', 'Oeu056937.1' => 'oeu', 'Oeu057540.1' => 'oeu', 'Os02g0594900' => 'osa', 'Os02g0595100' => 'osa', 'Os04g0477500' => 'osa', 'Os12g0611900' => 'osa', 'Peaxi162Scf00076g00020' => 'pax', 'Peaxi162Scf00128g00217' => 'pax', 'Peaxi162Scf00129g01640' => 'pax', 'Peaxi162Scf00669g00007' => 'pax', 'Peaxi162Scf00700g00421' => 'pax', 'Peaxi162Scf00801g00038' => 'pax', 'Peaxi162Scf00891g00025' => 'pax', 'PGR083G0909' => 'pgr', 'PGR119G1005' => 'pgr', 'PGR142G2236' => 'pgr', 'PGR142G3388' => 'pgr', 'PGSC0003DMG400004514' => 'stu', 'PGSC0003DMG400012635' => 'stu', 'PGSC0003DMG400015730' => 'stu', 'PGSC0003DMG400018611' => 'stu', 'PGSC0003DMG400030897' => 'stu', 'Phvul.001G254800' => 'pvu', 'Phvul.002G260100' => 'pvu', 'Phvul.003G167600' => 'pvu', 'Phvul.004G005100' => 'pvu', 'Potri.001G343600' => 'ptr', 'Potri.006G066700' => 'ptr', 'Potri.008G186000' => 'ptr', 'Potri.010G046900' => 'ptr', 'Potri.018G127900' => 'ptr', 'Pp3c20_17750' => 'ppa', 'Pp3c24_4380' => 'ppa', 'Prupe.1G245800' => 'ppe', 'Prupe.3G293400' => 'ppe', 'Prupe.7G247400' => 'ppe', 'Psat0s145g0120' => 'psa', 'Psat0s595g0040' => 'psa', 'Psat0s595g0120' => 'psa', 'Psat3g175040' => 'psa', 'Psat7g058120' => 'psa', 'PSO017G0428' => 'pso', 'PSO063G7510' => 'pso', 'PSO067G0046' => 'pso', 'PSO478G1073' => 'pso', 'PSO675G3677' => 'pso', 'PSO675G6558' => 'pso', 'PSO675G7520' => 'pso', 'PSO675G8959' => 'pso', 'QL02p074089' => 'qlo', 'QL02p089614' => 'qlo', 'QL03p057736' => 'qlo', 'RcHm_v2.0_Chr1g0364131' => 'rch', 'RcHm_v2.0_Chr2g0087801' => 'rch', 'RcHm_v2.0_Chr2g0087821' => 'rch', 'RcHm_v2.0_Chr2g0173231' => 'rch', 'RcHm_v2.0_Chr4g0433111' => 'rch', 'Rhsim03G0250300' => 'rsi', 'Rhsim08G0048400' => 'rsi', 'Rhsim10G0014800' => 'rsi', 'Rhsim12G0040100' => 'rsi', 'Rhsim12G0109700' => 'rsi', 'Sabra06G0049600' => 'sbr', 'Sabra08G0141000' => 'sbr', 'Sabra10G0021400' => 'sbr', 'Sabra16G0222900' => 'sbr', 'Sabra18G0108600' => 'sbr', 'SalBow1G0433' => 'sbo', 'SalBow1G2038' => 'sbo', 'SalBow1G5003' => 'sbo', 'SalBow7G1197' => 'sbo', 'SalBow8G3506' => 'sbo', 'Sc03g0007300' => 'sci', 'Sc11g0000950' => 'sci', 'Sc14g0008750' => 'sci', 'Sc18g0000420' => 'sci', 'Sed0006754' => 'sed', 'Sed0008741' => 'sed', 'Sed0017172' => 'sed', 'Sed0018925' => 'sed', 'Sed0023326' => 'sed', 'Sed0025909' => 'sed', 'SEGI_05333' => 'sgi', 'SEGI_10362' => 'sgi', 'SEGI_13380' => 'sgi', 'SEGI_24306' => 'sgi', 'SEGI_29077' => 'sgi', 'SEGI_29095' => 'sgi', 'SEGI_36534' => 'sgi', 'SEGI_37506' => 'sgi', 'SEGI_38321' => 'sgi', 'SGA_v2.0_scaffold307G48031' => 'sas', 'SGA_v2.0_scaffold47G17507' => 'sas', 'SGA_v2.0_scaffold63G21736' => 'sas', 'SGA_v2.0_scaffold87G27070' => 'sas', 'SHI17794' => 'shi', 'SHI28851' => 'shi', 'SMO165G0155' => 'smo', 'SMO340G0217' => 'smo', 'SMO367G1210' => 'smo', 'Solyc02g093430.3' => 'sly', 'Solyc05g013580.4' => 'sly', 'Solyc07g008030.3' => 'sly', 'Solyc12g035470.2' => 'sly', 'Sopen02g038020' => 'spe', 'Sopen05g008490' => 'spe', 'Sopen07g003910' => 'spe', 'Sopen12g015240' => 'spe', 'Sp1g11550' => 'spa', 'Sp2g16710' => 'spa', 'Sp3g00430' => 'spa', 'Sp3g26780' => 'spa', 'Sp5g22900' => 'spa', 'Sp6g29530' => 'spa', 'TAR371G0794' => 'tar', 'TAR374G0164' => 'tar', 'TAR622G0165' => 'tar', 'TAR626G0929' => 'tar', 'TAR629G2155' => 'tar', 'THA.LOC104805282' => 'tha', 'THA.LOC104805363' => 'tha', 'THA.LOC104808968' => 'tha', 'THA.LOC104821093' => 'tha', 'THA.LOC104823953' => 'tha', 'THA.LOC104825562' => 'tha', 'THA.LOC104825665' => 'tha', 'Thecc.02G261400' => 'tca', 'Thecc.04G019200' => 'tca', 'Thecc.09G130400' => 'tca', 'Thhalv10004374m.g' => 'esa', 'Thhalv10007850m.g' => 'esa', 'Thhalv10013782m.g' => 'esa', 'Thhalv10018686m.g' => 'esa', 'Thhalv10020899m.g' => 'esa', 'Thhalv10022755m.g' => 'esa', 'TPR.G23851' => 'tpr', 'TPR.G26500' => 'tpr', 'TPR.G27267' => 'tpr', 'TPR.G32001' => 'tpr', 'TPR.G6251' => 'tpr', 'TPR.G8167' => 'tpr', 'TWI12G1330' => 'twi', 'TWI18G1239' => 'twi', 'TWI34G0979' => 'twi', 'TWI36G0670' => 'twi', 'TWI36G0707' => 'twi', 'TWI56G0233' => 'twi', 'TWI75G1809' => 'twi', 'unitig_21.g20874' => 'ugi', 'unitig_26.g10343' => 'ugi', 'unitig_46.g18392' => 'ugi', 'unitig_52.g17178' => 'ugi', 'unitig_8.g2934' => 'ugi', 'vmacro01122' => 'vma', 'vmacro05875' => 'vma', 'vmacro06147' => 'vma', 'vmacro16191' => 'vma', 'vmacro18293' => 'vma', 'VMungo0251G3707' => 'vmu', 'VMungo0464G1521' => 'vmu', 'VMungo1215G0205' => 'vmu', 'VMungo1383G2484' => 'vmu', 'Zm00001eb079610' => 'zma', 'Zm00001eb135990' => 'zma', 'Zm00001eb183710' => 'zma', 'Zm00001eb246020' => 'zma' ) $gf_id = 'HOM05D001124' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001124' ) $data_identifier = 'HOM05D001124' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 6, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 7, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 21, 'bol' => (int) 10, 'bra' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 6, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 9, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 21, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 8, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 10, 'lsa' => (int) 8, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 8, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 9, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb246020' $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' => 'HOM05D001124', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '548', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02520' => 'bna', 'A03p06630' => 'bna', 'A05p44460' => 'bna', 'A06p08710' => 'bna', 'A06p41090' => 'bna', 'A07p32320' => 'bna', 'A08p32520' => 'bna', 'A09p10360' => 'bna', 'A10p24080' => 'bna', 'Aa31LG11G15250' => 'aar', 'Aa31LG1G1800' => 'aar', 'Aa31LG2G5120' => 'aar', 'Aa31LG2G6070' => 'aar', 'Aa31LG5G10770' => 'aar', 'Aa31sc61G90' => 'aar', 'Actinidia01352' => 'ach', 'Actinidia05983' => 'ach', 'Actinidia08133' => 'ach', 'Actinidia15101' => 'ach', 'Actinidia26379' => 'ach', 'Actinidia35778' => 'ach', 'Actinidia36123' => 'ach', 'Actinidia37436' => 'ach', 'Actinidia38730' => 'ach', 'Ah.02g128210' => 'amhyb', 'Ah.03g132990' => 'amhyb', 'Ah.14g079410' => 'amhyb', 'AL1G24640' => 'aly', 'AL2G26680' => 'aly', 'AL3G10530' => 'aly', 'AL3G45230' => 'aly', 'AL5G15230' => 'aly', 'AL5G16960' => 'aly', 'AL6G25210' => 'aly', 'Aqoxy2G00441' => 'aox', 'Aqoxy3G01236' => 'aox', 'Aqoxy5G03746' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3RQ047' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C7GMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9C8JER' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MBL6KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YXCZ83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZANX40' => 'arhy', 'AT1G12990' => 'ath', 'AT1G67880' => 'ath', 'AT2G13290' => 'ath', 'AT3G01620' => 'ath', 'AT3G26445' => 'ath', 'AT3G27540' => 'ath', 'AT5G14480' => 'ath', 'ATR0824G026' => 'atr', 'ATR1098G019' => 'atr', 'Atru.chr11.2145' => 'acertr', 'Atru.chr2.3636' => 'acertr', 'Atru.chr2.3644' => 'acertr', 'Atru.chr6.2422' => 'acertr', 'Atru.chr7.1112' => 'acertr', 'AUR62005469' => 'cqu', 'AUR62011166' => 'cqu', 'AUR62013319' => 'cqu', 'AUR62024273' => 'cqu', 'AUR62028420' => 'cqu', 'AUR62041942' => 'cqu', 'BcaB01g04969' => 'bca', 'BcaB01g06371' => 'bca', 'BcaB02g11494' => 'bca', 'BcaB03g15382' => 'bca', 'BcaB08g36994' => 'bca', 'BcaC03g13477' => 'bca', 'BcaC03g13478' => 'bca', 'BcaC03g13480' => 'bca', 'BcaC03g13481' => 'bca', 'BcaC03g13486' => 'bca', 'BcaC04g19031' => 'bca', 'BcaC04g23085' => 'bca', 'BcaC05g25094' => 'bca', 'BcaC05g25096' => 'bca', 'BcaC05g25138' => 'bca', 'BcaC05g30416' => 'bca', 'BcaC05g30455' => 'bca', 'BcaC06g30979' => 'bca', 'BcaC06g33805' => 'bca', 'BcaC08g46021' => 'bca', 'BcaNung03154' => 'bca', 'BolC2t06623H' => 'bol', 'BolC2t06632H' => 'bol', 'BolC2t06635H' => 'bol', 'BolC2t06638H' => 'bol', 'BolC3t13266H' => 'bol', 'BolC5t29776H' => 'bol', 'BolC6t38912H' => 'bol', 'BolC7t44183H' => 'bol', 'BolC9t54123H' => 'bol', 'BolC9t59107H' => 'bol', 'BraA02t05221Z' => 'bra', 'BraA03t09996Z' => 'bra', 'BraA05t23210Z' => 'bra', 'BraA06t24068Z' => 'bra', 'BraA06t27032Z' => 'bra', 'BraA08t35176Z' => 'bra', 'BraA09t36680Z' => 'bra', 'BraA10t44471Z' => 'bra', 'C02p06760' => 'bna', 'C02p06890' => 'bna', 'C02p07010' => 'bna', 'C03p07660' => 'bna', 'C05p10300' => 'bna', 'C06p38150' => 'bna', 'C07p36650' => 'bna', 'C08p15770' => 'bna', 'C09p12300' => 'bna', 'C09p62700' => 'bna', 'C09p75040' => 'bna', 'CAN.G13.1' => 'can', 'CAN.G138.4' => 'can', 'CAN.G44.6' => 'can', 'CAN.G473.19' => 'can', 'CANSAT01G0835' => 'cansat', 'CANSAT11G0246' => 'cansat', 'CANSAT11G1766' => 'cansat', 'CANSAT64G1954' => 'cansat', 'CARHR013330' => 'chi', 'CARHR060530' => 'chi', 'CARHR075300' => 'chi', 'CARHR105120' => 'chi', 'CARHR148910' => 'chi', 'CARHR198830' => 'chi', 'Carub.0001s1275' => 'cru', 'Carub.0002s1437' => 'cru', 'Carub.0003s0044' => 'cru', 'Carub.0003s2787' => 'cru', 'Carub.0005s0597' => 'cru', 'Carub.0006s1266' => 'cru', 'Ca_06935_v3' => 'car', 'Ca_13559_v3' => 'car', 'Ca_16941_v3' => 'car', 'Ca_16960_v3' => 'car', 'Ca_17775_v3' => 'car', 'Ca_30464_v3' => 'car', 'Cc06_g08160' => 'ccan', 'Cc07_g01520' => 'ccan', 'Cc11_g15810' => 'ccan', 'CDE02G2840' => 'cde', 'CDE03G0093' => 'cde', 'CDE04G2127' => 'cde', 'CDE07G1857' => 'cde', 'CDE09G1246' => 'cde', 'Cfa003412' => 'cfa', 'Cfa007341' => 'cfa', 'Cfa009220' => 'cfa', 'Ciclev10008737m.g' => 'ccl', 'Ciclev10015565m.g' => 'ccl', 'Ciclev10031761m.g' => 'ccl', 'CiPaw.03G045300' => 'cil', 'CiPaw.03G247200' => 'cil', 'CiPaw.04G029500' => 'cil', 'CiPaw.04G174000' => 'cil', 'CiPaw.05G181200' => 'cil', 'CiPaw.06G067100' => 'cil', 'ClCG05G025800' => 'cla', 'ClCG06G011400' => 'cla', 'ClCG09G019360' => 'cla', 'COL.COLO4_04827' => 'col', 'COL.COLO4_29170' => 'col', 'COL.COLO4_35131' => 'col', 'COL.COLO4_35132' => 'col', 'Cpa.g.sc33.32' => 'cpa', 'Cpa.g.sc46.29' => 'cpa', 'Cpa.g.sc796.1' => 'cpa', 'CsaV3_1G030420' => 'csa', 'CsaV3_5G027050' => 'csa', 'CsaV3_5G031040' => 'csa', 'CsaV3_UNG023130' => 'csa', 'CSS0007726' => 'camsi', 'CSS0016433' => 'camsi', 'CSS0017656' => 'camsi', 'CSS0025364' => 'camsi', 'CSS0027582' => 'camsi', 'CSS0047288' => 'camsi', 'CSS0049950' => 'camsi', 'DCAR_003843' => 'dca', 'DCAR_007052' => 'dca', 'DCAR_020884' => 'dca', 'DCAR_021730' => 'dca', 'DCAR_024423' => 'dca', 'DCAR_026509' => 'dca', 'DCAR_031158' => 'dca', 'Dinv14728' => 'din', 'Dinv15219' => 'din', 'Dinv25728' => 'din', 'Dinv33428' => 'din', 'Dinv36489' => 'din', 'Dinv41486' => 'din', 'Duzib147G0469' => 'dzi', 'Duzib168G0060' => 'dzi', 'Duzib187G1215' => 'dzi', 'Duzib248G0692' => 'dzi', 'Duzib251G0767' => 'dzi', 'Duzib264G0446' => 'dzi', 'Duzib268G0691' => 'dzi', 'ECA232G4767' => 'eca', 'ECA233G2838' => 'eca', 'ECA234G0391' => 'eca', 'ECA234G0857' => 'eca', 'ECA236G1593' => 'eca', 'ECA238G0565' => 'eca', 'ECA246G1027' => 'eca', 'ECA246G3223' => 'eca', 'ECA246G3470' => 'eca', 'EL10Ac6g13829' => 'bvu', 'EL10Ac6g14093' => 'bvu', 'EL10Ac8g18707' => 'bvu', 'Eucgr.C01369' => 'egr', 'Eucgr.H02492' => 'egr', 'Eucgr.I01733' => 'egr', 'Eucgr.J02255' => 'egr', 'Eucgr.J02257' => 'egr', 'Eucgr.J02258' => 'egr', 'FAN02G1601' => 'fan', 'FAN03G1586' => 'fan', 'FAN03G2986' => 'fan', 'FAN05G4837' => 'fan', 'FAN06G0146' => 'fan', 'FAN07G0858' => 'fan', 'FAN09G3179' => 'fan', 'FAN10G0669' => 'fan', 'FAN12G2358' => 'fan', 'FAN14G4198' => 'fan', 'FAN14G5112' => 'fan', 'FAN17G0342' => 'fan', 'FAN19G0342' => 'fan', 'FAN19G0962' => 'fan', 'FAN19G1101' => 'fan', 'FAN19G1872' => 'fan', 'FAN22G0356' => 'fan', 'FAN23G0744' => 'fan', 'FAN23G1914' => 'fan', 'FAN26G0032' => 'fan', 'FAN28G0625' => 'fan', 'FvH4_1g02710' => 'fve', 'FvH4_1g02720' => 'fve', 'FvH4_4g25670' => 'fve', 'FvH4_6g51700' => 'fve', 'FvH4_7g20170' => 'fve', 'Glyma.05G175000' => 'gma', 'Glyma.08G132300' => 'gma', 'Glyma.11G243000' => 'gma', 'Glyma.13G158900' => 'gma', 'Glyma.17G112400' => 'gma', 'Glyma.18G014100' => 'gma', 'Glyma.19G003100' => 'gma', 'Glyma.19G056500' => 'gma', 'Gohir.A01G158900' => 'ghi', 'Gohir.A05G312600' => 'ghi', 'Gohir.A05G354900' => 'ghi', 'Gohir.A07G037200' => 'ghi', 'Gohir.A09G030000' => 'ghi', 'Gohir.A12G145200' => 'ghi', 'Gohir.D01G151500' => 'ghi', 'Gohir.D04G058300' => 'ghi', 'Gohir.D05G314100' => 'ghi', 'Gohir.D07G041400' => 'ghi', 'Gohir.D09G029700' => 'ghi', 'Gohir.D12G149700' => 'ghi', 'Gorai.001G043800' => 'gra', 'Gorai.002G187800' => 'gra', 'Gorai.006G034700' => 'gra', 'Gorai.008G161200' => 'gra', 'Gorai.009G335700' => 'gra', 'Gorai.012G065000' => 'gra', 'GSVIVG01000535001' => 'vvi', 'GSVIVG01015572001' => 'vvi', 'GSVIVG01032386001' => 'vvi', 'HanXRQChr05g0138531' => 'han', 'HanXRQChr06g0174391' => 'han', 'HanXRQChr07g0199021' => 'han', 'HanXRQChr08g0208211' => 'han', 'HanXRQChr09g0255471' => 'han', 'HanXRQChr10g0315791' => 'han', 'HanXRQChr12g0371991' => 'han', 'HanXRQChr15g0475251' => 'han', 'HanXRQChr17g0540001' => 'han', 'HanXRQChr17g0548631' => 'han', 'HanXRQChr17g0569561' => 'han', 'Haze_12256' => 'cav', 'Haze_14756' => 'cav', 'Haze_25528' => 'cav', 'Hma1.2p1_0079F.1_g041020' => 'hma', 'Hma1.2p1_0818F.1_g223260' => 'hma', 'Hma1.2p1_1747F.1_g300530' => 'hma', 'HPP92_004607' => 'vpl', 'HPP92_004608' => 'vpl', 'HPP92_006181' => 'vpl', 'HPP92_012192' => 'vpl', 'HPP92_015680' => 'vpl', 'HPP92_020249' => 'vpl', 'HPP92_021376' => 'vpl', 'HPP92_024275' => 'vpl', 'Hund06031' => 'sun', 'Hund25391' => 'sun', 'Lalb_Chr07g0185371' => 'lal', 'Lalb_Chr07g0185381' => 'lal', 'Lalb_Chr12g0204011' => 'lal', 'Lalb_Chr13g0301671' => 'lal', 'Lalb_Chr14g0362851' => 'lal', 'Lalb_Chr24g0403581' => 'lal', 'Lj1g0000233' => 'lja', 'Lj2g0018120' => 'lja', 'Lj3C621T0' => 'lonja', 'Lj3P1059T14' => 'lonja', 'Lj3P611T9' => 'lonja', 'Lj3P614T13' => 'lonja', 'Lj3P615T5' => 'lonja', 'Lj4g0012315' => 'lja', 'Lj4g0026182' => 'lja', 'Lj6P813T16' => 'lonja', 'Lj7C427T7' => 'lonja', 'Lj7C427T8' => 'lonja', 'Lj7P600T41' => 'lonja', 'Lju41C42G17' => 'lonja', 'Lsat_1_v5_gn_0_47300' => 'lsa', 'Lsat_1_v5_gn_2_91280' => 'lsa', 'Lsat_1_v5_gn_3_30561' => 'lsa', 'Lsat_1_v5_gn_4_184321' => 'lsa', 'Lsat_1_v5_gn_4_4041' => 'lsa', 'Lsat_1_v5_gn_5_92000' => 'lsa', 'Lsat_1_v5_gn_8_152940' => 'lsa', 'Lsat_1_v5_gn_8_62401' => 'lsa', 'Manes.06G055900' => 'mes', 'Manes.12G022200' => 'mes', 'Manes.13G023300' => 'mes', 'Manes.14G115000' => 'mes', 'Manes.15G151700' => 'mes', 'Manes.17G111300' => 'mes', 'Mapoly0226s0009' => 'mpo', 'MBI02_g25363_MAGBIO' => 'mbi', 'MBI06_g00027_MAGBIO' => 'mbi', 'MBI10_g13034_MAGBIO' => 'mbi', 'MD09G1023400' => 'mdo', 'MD13G1100100' => 'mdo', 'MD15G1169200' => 'mdo', 'MD16G1101100' => 'mdo', 'MD17G1022900' => 'mdo', 'Medtr3g096150' => 'mtr', 'Medtr4g115070' => 'mtr', 'Medtr7g033325' => 'mtr', 'Medtr8g089840' => 'mtr', 'MELO3C010319.2' => 'cme', 'MELO3C011944.2' => 'cme', 'MELO3C021589.2' => 'cme', 'Migut.E00207' => 'egut', 'Migut.H00067' => 'egut', 'Migut.K00433' => 'egut', 'Migut.K00606' => 'egut', 'Migut.K01410' => 'egut', 'MSTRG.13347' => 'ama', 'MSTRG.24045' => 'ama', 'MSTRG.2428' => 'ama', 'MSTRG.26410' => 'ama', 'MSTRG.3139' => 'ama', 'MSTRG.3286' => 'ama', 'MSTRG.563' => 'ama', 'MSTRG.7941' => 'ama', 'Nitab4.5_0000028g0060' => 'nta', 'Nitab4.5_0000065g0260' => 'nta', 'Nitab4.5_0000112g0060' => 'nta', 'Nitab4.5_0000489g0120' => 'nta', 'Nitab4.5_0001776g0050' => 'nta', 'Nitab4.5_0001854g0010' => 'nta', 'Nitab4.5_0001860g0020' => 'nta', 'Nitab4.5_0004352g0010' => 'nta', 'Nitab4.5_0008716g0020' => 'nta', 'Nitab4.5_0008922g0010' => 'nta', 'Nn3g16693' => 'nnu', 'Nn4g22596' => 'nnu', 'Nn7g37639' => 'nnu', 'Oeu001701.1' => 'oeu', 'Oeu018149.1' => 'oeu', 'Oeu026220.1' => 'oeu', 'Oeu038635.1' => 'oeu', 'Oeu049176.1' => 'oeu', 'Oeu056706.1' => 'oeu', 'Oeu056937.1' => 'oeu', 'Oeu057540.1' => 'oeu', 'Os02g0594900' => 'osa', 'Os02g0595100' => 'osa', 'Os04g0477500' => 'osa', 'Os12g0611900' => 'osa', 'Peaxi162Scf00076g00020' => 'pax', 'Peaxi162Scf00128g00217' => 'pax', 'Peaxi162Scf00129g01640' => 'pax', 'Peaxi162Scf00669g00007' => 'pax', 'Peaxi162Scf00700g00421' => 'pax', 'Peaxi162Scf00801g00038' => 'pax', 'Peaxi162Scf00891g00025' => 'pax', 'PGR083G0909' => 'pgr', 'PGR119G1005' => 'pgr', 'PGR142G2236' => 'pgr', 'PGR142G3388' => 'pgr', 'PGSC0003DMG400004514' => 'stu', 'PGSC0003DMG400012635' => 'stu', 'PGSC0003DMG400015730' => 'stu', 'PGSC0003DMG400018611' => 'stu', 'PGSC0003DMG400030897' => 'stu', 'Phvul.001G254800' => 'pvu', 'Phvul.002G260100' => 'pvu', 'Phvul.003G167600' => 'pvu', 'Phvul.004G005100' => 'pvu', 'Potri.001G343600' => 'ptr', 'Potri.006G066700' => 'ptr', 'Potri.008G186000' => 'ptr', 'Potri.010G046900' => 'ptr', 'Potri.018G127900' => 'ptr', 'Pp3c20_17750' => 'ppa', 'Pp3c24_4380' => 'ppa', 'Prupe.1G245800' => 'ppe', 'Prupe.3G293400' => 'ppe', 'Prupe.7G247400' => 'ppe', 'Psat0s145g0120' => 'psa', 'Psat0s595g0040' => 'psa', 'Psat0s595g0120' => 'psa', 'Psat3g175040' => 'psa', 'Psat7g058120' => 'psa', 'PSO017G0428' => 'pso', 'PSO063G7510' => 'pso', 'PSO067G0046' => 'pso', 'PSO478G1073' => 'pso', 'PSO675G3677' => 'pso', 'PSO675G6558' => 'pso', 'PSO675G7520' => 'pso', 'PSO675G8959' => 'pso', 'QL02p074089' => 'qlo', 'QL02p089614' => 'qlo', 'QL03p057736' => 'qlo', 'RcHm_v2.0_Chr1g0364131' => 'rch', 'RcHm_v2.0_Chr2g0087801' => 'rch', 'RcHm_v2.0_Chr2g0087821' => 'rch', 'RcHm_v2.0_Chr2g0173231' => 'rch', 'RcHm_v2.0_Chr4g0433111' => 'rch', 'Rhsim03G0250300' => 'rsi', 'Rhsim08G0048400' => 'rsi', 'Rhsim10G0014800' => 'rsi', 'Rhsim12G0040100' => 'rsi', 'Rhsim12G0109700' => 'rsi', 'Sabra06G0049600' => 'sbr', 'Sabra08G0141000' => 'sbr', 'Sabra10G0021400' => 'sbr', 'Sabra16G0222900' => 'sbr', 'Sabra18G0108600' => 'sbr', 'SalBow1G0433' => 'sbo', 'SalBow1G2038' => 'sbo', 'SalBow1G5003' => 'sbo', 'SalBow7G1197' => 'sbo', 'SalBow8G3506' => 'sbo', 'Sc03g0007300' => 'sci', 'Sc11g0000950' => 'sci', 'Sc14g0008750' => 'sci', 'Sc18g0000420' => 'sci', 'Sed0006754' => 'sed', 'Sed0008741' => 'sed', 'Sed0017172' => 'sed', 'Sed0018925' => 'sed', 'Sed0023326' => 'sed', 'Sed0025909' => 'sed', 'SEGI_05333' => 'sgi', 'SEGI_10362' => 'sgi', 'SEGI_13380' => 'sgi', 'SEGI_24306' => 'sgi', 'SEGI_29077' => 'sgi', 'SEGI_29095' => 'sgi', 'SEGI_36534' => 'sgi', 'SEGI_37506' => 'sgi', 'SEGI_38321' => 'sgi', 'SGA_v2.0_scaffold307G48031' => 'sas', 'SGA_v2.0_scaffold47G17507' => 'sas', 'SGA_v2.0_scaffold63G21736' => 'sas', 'SGA_v2.0_scaffold87G27070' => 'sas', 'SHI17794' => 'shi', 'SHI28851' => 'shi', 'SMO165G0155' => 'smo', 'SMO340G0217' => 'smo', 'SMO367G1210' => 'smo', 'Solyc02g093430.3' => 'sly', 'Solyc05g013580.4' => 'sly', 'Solyc07g008030.3' => 'sly', 'Solyc12g035470.2' => 'sly', 'Sopen02g038020' => 'spe', 'Sopen05g008490' => 'spe', 'Sopen07g003910' => 'spe', 'Sopen12g015240' => 'spe', 'Sp1g11550' => 'spa', 'Sp2g16710' => 'spa', 'Sp3g00430' => 'spa', 'Sp3g26780' => 'spa', 'Sp5g22900' => 'spa', 'Sp6g29530' => 'spa', 'TAR371G0794' => 'tar', 'TAR374G0164' => 'tar', 'TAR622G0165' => 'tar', 'TAR626G0929' => 'tar', 'TAR629G2155' => 'tar', 'THA.LOC104805282' => 'tha', 'THA.LOC104805363' => 'tha', 'THA.LOC104808968' => 'tha', 'THA.LOC104821093' => 'tha', 'THA.LOC104823953' => 'tha', 'THA.LOC104825562' => 'tha', 'THA.LOC104825665' => 'tha', 'Thecc.02G261400' => 'tca', 'Thecc.04G019200' => 'tca', 'Thecc.09G130400' => 'tca', 'Thhalv10004374m.g' => 'esa', 'Thhalv10007850m.g' => 'esa', 'Thhalv10013782m.g' => 'esa', 'Thhalv10018686m.g' => 'esa', 'Thhalv10020899m.g' => 'esa', 'Thhalv10022755m.g' => 'esa', 'TPR.G23851' => 'tpr', 'TPR.G26500' => 'tpr', 'TPR.G27267' => 'tpr', 'TPR.G32001' => 'tpr', 'TPR.G6251' => 'tpr', 'TPR.G8167' => 'tpr', 'TWI12G1330' => 'twi', 'TWI18G1239' => 'twi', 'TWI34G0979' => 'twi', 'TWI36G0670' => 'twi', 'TWI36G0707' => 'twi', 'TWI56G0233' => 'twi', 'TWI75G1809' => 'twi', 'unitig_21.g20874' => 'ugi', 'unitig_26.g10343' => 'ugi', 'unitig_46.g18392' => 'ugi', 'unitig_52.g17178' => 'ugi', 'unitig_8.g2934' => 'ugi', 'vmacro01122' => 'vma', 'vmacro05875' => 'vma', 'vmacro06147' => 'vma', 'vmacro16191' => 'vma', 'vmacro18293' => 'vma', 'VMungo0251G3707' => 'vmu', 'VMungo0464G1521' => 'vmu', 'VMungo1215G0205' => 'vmu', 'VMungo1383G2484' => 'vmu', 'Zm00001eb079610' => 'zma', 'Zm00001eb135990' => 'zma', 'Zm00001eb183710' => 'zma', 'Zm00001eb246020' => 'zma' ), 'gf_id' => 'HOM05D001124', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001124' ), 'data_identifier' => 'HOM05D001124', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001124', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '548', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02520' => 'bna', 'A03p06630' => 'bna', 'A05p44460' => 'bna', 'A06p08710' => 'bna', 'A06p41090' => 'bna', 'A07p32320' => 'bna', 'A08p32520' => 'bna', 'A09p10360' => 'bna', 'A10p24080' => 'bna', 'Aa31LG11G15250' => 'aar', 'Aa31LG1G1800' => 'aar', 'Aa31LG2G5120' => 'aar', 'Aa31LG2G6070' => 'aar', 'Aa31LG5G10770' => 'aar', 'Aa31sc61G90' => 'aar', 'Actinidia01352' => 'ach', 'Actinidia05983' => 'ach', 'Actinidia08133' => 'ach', 'Actinidia15101' => 'ach', 'Actinidia26379' => 'ach', 'Actinidia35778' => 'ach', 'Actinidia36123' => 'ach', 'Actinidia37436' => 'ach', 'Actinidia38730' => 'ach', 'Ah.02g128210' => 'amhyb', 'Ah.03g132990' => 'amhyb', 'Ah.14g079410' => 'amhyb', 'AL1G24640' => 'aly', 'AL2G26680' => 'aly', 'AL3G10530' => 'aly', 'AL3G45230' => 'aly', 'AL5G15230' => 'aly', 'AL5G16960' => 'aly', 'AL6G25210' => 'aly', 'Aqoxy2G00441' => 'aox', 'Aqoxy3G01236' => 'aox', 'Aqoxy5G03746' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3RQ047' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C7GMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9C8JER' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MBL6KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YXCZ83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZANX40' => 'arhy', 'AT1G12990' => 'ath', 'AT1G67880' => 'ath', 'AT2G13290' => 'ath', 'AT3G01620' => 'ath', 'AT3G26445' => 'ath', 'AT3G27540' => 'ath', 'AT5G14480' => 'ath', 'ATR0824G026' => 'atr', 'ATR1098G019' => 'atr', 'Atru.chr11.2145' => 'acertr', 'Atru.chr2.3636' => 'acertr', 'Atru.chr2.3644' => 'acertr', 'Atru.chr6.2422' => 'acertr', 'Atru.chr7.1112' => 'acertr', 'AUR62005469' => 'cqu', 'AUR62011166' => 'cqu', 'AUR62013319' => 'cqu', 'AUR62024273' => 'cqu', 'AUR62028420' => 'cqu', 'AUR62041942' => 'cqu', 'BcaB01g04969' => 'bca', 'BcaB01g06371' => 'bca', 'BcaB02g11494' => 'bca', 'BcaB03g15382' => 'bca', 'BcaB08g36994' => 'bca', 'BcaC03g13477' => 'bca', 'BcaC03g13478' => 'bca', 'BcaC03g13480' => 'bca', 'BcaC03g13481' => 'bca', 'BcaC03g13486' => 'bca', 'BcaC04g19031' => 'bca', 'BcaC04g23085' => 'bca', 'BcaC05g25094' => 'bca', 'BcaC05g25096' => 'bca', 'BcaC05g25138' => 'bca', 'BcaC05g30416' => 'bca', 'BcaC05g30455' => 'bca', 'BcaC06g30979' => 'bca', 'BcaC06g33805' => 'bca', 'BcaC08g46021' => 'bca', 'BcaNung03154' => 'bca', 'BolC2t06623H' => 'bol', 'BolC2t06632H' => 'bol', 'BolC2t06635H' => 'bol', 'BolC2t06638H' => 'bol', 'BolC3t13266H' => 'bol', 'BolC5t29776H' => 'bol', 'BolC6t38912H' => 'bol', 'BolC7t44183H' => 'bol', 'BolC9t54123H' => 'bol', 'BolC9t59107H' => 'bol', 'BraA02t05221Z' => 'bra', 'BraA03t09996Z' => 'bra', 'BraA05t23210Z' => 'bra', 'BraA06t24068Z' => 'bra', 'BraA06t27032Z' => 'bra', 'BraA08t35176Z' => 'bra', 'BraA09t36680Z' => 'bra', 'BraA10t44471Z' => 'bra', 'C02p06760' => 'bna', 'C02p06890' => 'bna', 'C02p07010' => 'bna', 'C03p07660' => 'bna', 'C05p10300' => 'bna', 'C06p38150' => 'bna', 'C07p36650' => 'bna', 'C08p15770' => 'bna', 'C09p12300' => 'bna', 'C09p62700' => 'bna', 'C09p75040' => 'bna', 'CAN.G13.1' => 'can', 'CAN.G138.4' => 'can', 'CAN.G44.6' => 'can', 'CAN.G473.19' => 'can', 'CANSAT01G0835' => 'cansat', 'CANSAT11G0246' => 'cansat', 'CANSAT11G1766' => 'cansat', 'CANSAT64G1954' => 'cansat', 'CARHR013330' => 'chi', 'CARHR060530' => 'chi', 'CARHR075300' => 'chi', 'CARHR105120' => 'chi', 'CARHR148910' => 'chi', 'CARHR198830' => 'chi', 'Carub.0001s1275' => 'cru', 'Carub.0002s1437' => 'cru', 'Carub.0003s0044' => 'cru', 'Carub.0003s2787' => 'cru', 'Carub.0005s0597' => 'cru', 'Carub.0006s1266' => 'cru', 'Ca_06935_v3' => 'car', 'Ca_13559_v3' => 'car', 'Ca_16941_v3' => 'car', 'Ca_16960_v3' => 'car', 'Ca_17775_v3' => 'car', 'Ca_30464_v3' => 'car', 'Cc06_g08160' => 'ccan', 'Cc07_g01520' => 'ccan', 'Cc11_g15810' => 'ccan', 'CDE02G2840' => 'cde', 'CDE03G0093' => 'cde', 'CDE04G2127' => 'cde', 'CDE07G1857' => 'cde', 'CDE09G1246' => 'cde', 'Cfa003412' => 'cfa', 'Cfa007341' => 'cfa', 'Cfa009220' => 'cfa', 'Ciclev10008737m.g' => 'ccl', 'Ciclev10015565m.g' => 'ccl', 'Ciclev10031761m.g' => 'ccl', 'CiPaw.03G045300' => 'cil', 'CiPaw.03G247200' => 'cil', 'CiPaw.04G029500' => 'cil', 'CiPaw.04G174000' => 'cil', 'CiPaw.05G181200' => 'cil', 'CiPaw.06G067100' => 'cil', 'ClCG05G025800' => 'cla', 'ClCG06G011400' => 'cla', 'ClCG09G019360' => 'cla', 'COL.COLO4_04827' => 'col', 'COL.COLO4_29170' => 'col', 'COL.COLO4_35131' => 'col', 'COL.COLO4_35132' => 'col', 'Cpa.g.sc33.32' => 'cpa', 'Cpa.g.sc46.29' => 'cpa', 'Cpa.g.sc796.1' => 'cpa', 'CsaV3_1G030420' => 'csa', 'CsaV3_5G027050' => 'csa', 'CsaV3_5G031040' => 'csa', 'CsaV3_UNG023130' => 'csa', 'CSS0007726' => 'camsi', 'CSS0016433' => 'camsi', 'CSS0017656' => 'camsi', 'CSS0025364' => 'camsi', 'CSS0027582' => 'camsi', 'CSS0047288' => 'camsi', 'CSS0049950' => 'camsi', 'DCAR_003843' => 'dca', 'DCAR_007052' => 'dca', 'DCAR_020884' => 'dca', 'DCAR_021730' => 'dca', 'DCAR_024423' => 'dca', 'DCAR_026509' => 'dca', 'DCAR_031158' => 'dca', 'Dinv14728' => 'din', 'Dinv15219' => 'din', 'Dinv25728' => 'din', 'Dinv33428' => 'din', 'Dinv36489' => 'din', 'Dinv41486' => 'din', 'Duzib147G0469' => 'dzi', 'Duzib168G0060' => 'dzi', 'Duzib187G1215' => 'dzi', 'Duzib248G0692' => 'dzi', 'Duzib251G0767' => 'dzi', 'Duzib264G0446' => 'dzi', 'Duzib268G0691' => 'dzi', 'ECA232G4767' => 'eca', 'ECA233G2838' => 'eca', 'ECA234G0391' => 'eca', 'ECA234G0857' => 'eca', 'ECA236G1593' => 'eca', 'ECA238G0565' => 'eca', 'ECA246G1027' => 'eca', 'ECA246G3223' => 'eca', 'ECA246G3470' => 'eca', 'EL10Ac6g13829' => 'bvu', 'EL10Ac6g14093' => 'bvu', 'EL10Ac8g18707' => 'bvu', 'Eucgr.C01369' => 'egr', 'Eucgr.H02492' => 'egr', 'Eucgr.I01733' => 'egr', 'Eucgr.J02255' => 'egr', 'Eucgr.J02257' => 'egr', 'Eucgr.J02258' => 'egr', 'FAN02G1601' => 'fan', 'FAN03G1586' => 'fan', 'FAN03G2986' => 'fan', 'FAN05G4837' => 'fan', 'FAN06G0146' => 'fan', 'FAN07G0858' => 'fan', 'FAN09G3179' => 'fan', 'FAN10G0669' => 'fan', 'FAN12G2358' => 'fan', 'FAN14G4198' => 'fan', 'FAN14G5112' => 'fan', 'FAN17G0342' => 'fan', 'FAN19G0342' => 'fan', 'FAN19G0962' => 'fan', 'FAN19G1101' => 'fan', 'FAN19G1872' => 'fan', 'FAN22G0356' => 'fan', 'FAN23G0744' => 'fan', 'FAN23G1914' => 'fan', 'FAN26G0032' => 'fan', 'FAN28G0625' => 'fan', 'FvH4_1g02710' => 'fve', 'FvH4_1g02720' => 'fve', 'FvH4_4g25670' => 'fve', 'FvH4_6g51700' => 'fve', 'FvH4_7g20170' => 'fve', 'Glyma.05G175000' => 'gma', 'Glyma.08G132300' => 'gma', 'Glyma.11G243000' => 'gma', 'Glyma.13G158900' => 'gma', 'Glyma.17G112400' => 'gma', 'Glyma.18G014100' => 'gma', 'Glyma.19G003100' => 'gma', 'Glyma.19G056500' => 'gma', 'Gohir.A01G158900' => 'ghi', 'Gohir.A05G312600' => 'ghi', 'Gohir.A05G354900' => 'ghi', 'Gohir.A07G037200' => 'ghi', 'Gohir.A09G030000' => 'ghi', 'Gohir.A12G145200' => 'ghi', 'Gohir.D01G151500' => 'ghi', 'Gohir.D04G058300' => 'ghi', 'Gohir.D05G314100' => 'ghi', 'Gohir.D07G041400' => 'ghi', 'Gohir.D09G029700' => 'ghi', 'Gohir.D12G149700' => 'ghi', 'Gorai.001G043800' => 'gra', 'Gorai.002G187800' => 'gra', 'Gorai.006G034700' => 'gra', 'Gorai.008G161200' => 'gra', 'Gorai.009G335700' => 'gra', 'Gorai.012G065000' => 'gra', 'GSVIVG01000535001' => 'vvi', 'GSVIVG01015572001' => 'vvi', 'GSVIVG01032386001' => 'vvi', 'HanXRQChr05g0138531' => 'han', 'HanXRQChr06g0174391' => 'han', 'HanXRQChr07g0199021' => 'han', 'HanXRQChr08g0208211' => 'han', 'HanXRQChr09g0255471' => 'han', 'HanXRQChr10g0315791' => 'han', 'HanXRQChr12g0371991' => 'han', 'HanXRQChr15g0475251' => 'han', 'HanXRQChr17g0540001' => 'han', 'HanXRQChr17g0548631' => 'han', 'HanXRQChr17g0569561' => 'han', 'Haze_12256' => 'cav', 'Haze_14756' => 'cav', 'Haze_25528' => 'cav', 'Hma1.2p1_0079F.1_g041020' => 'hma', 'Hma1.2p1_0818F.1_g223260' => 'hma', 'Hma1.2p1_1747F.1_g300530' => 'hma', 'HPP92_004607' => 'vpl', 'HPP92_004608' => 'vpl', 'HPP92_006181' => 'vpl', 'HPP92_012192' => 'vpl', 'HPP92_015680' => 'vpl', 'HPP92_020249' => 'vpl', 'HPP92_021376' => 'vpl', 'HPP92_024275' => 'vpl', 'Hund06031' => 'sun', 'Hund25391' => 'sun', 'Lalb_Chr07g0185371' => 'lal', 'Lalb_Chr07g0185381' => 'lal', 'Lalb_Chr12g0204011' => 'lal', 'Lalb_Chr13g0301671' => 'lal', 'Lalb_Chr14g0362851' => 'lal', 'Lalb_Chr24g0403581' => 'lal', 'Lj1g0000233' => 'lja', 'Lj2g0018120' => 'lja', 'Lj3C621T0' => 'lonja', 'Lj3P1059T14' => 'lonja', 'Lj3P611T9' => 'lonja', 'Lj3P614T13' => 'lonja', 'Lj3P615T5' => 'lonja', 'Lj4g0012315' => 'lja', 'Lj4g0026182' => 'lja', 'Lj6P813T16' => 'lonja', 'Lj7C427T7' => 'lonja', 'Lj7C427T8' => 'lonja', 'Lj7P600T41' => 'lonja', 'Lju41C42G17' => 'lonja', 'Lsat_1_v5_gn_0_47300' => 'lsa', 'Lsat_1_v5_gn_2_91280' => 'lsa', 'Lsat_1_v5_gn_3_30561' => 'lsa', 'Lsat_1_v5_gn_4_184321' => 'lsa', 'Lsat_1_v5_gn_4_4041' => 'lsa', 'Lsat_1_v5_gn_5_92000' => 'lsa', 'Lsat_1_v5_gn_8_152940' => 'lsa', 'Lsat_1_v5_gn_8_62401' => 'lsa', 'Manes.06G055900' => 'mes', 'Manes.12G022200' => 'mes', 'Manes.13G023300' => 'mes', 'Manes.14G115000' => 'mes', 'Manes.15G151700' => 'mes', 'Manes.17G111300' => 'mes', 'Mapoly0226s0009' => 'mpo', 'MBI02_g25363_MAGBIO' => 'mbi', 'MBI06_g00027_MAGBIO' => 'mbi', 'MBI10_g13034_MAGBIO' => 'mbi', 'MD09G1023400' => 'mdo', 'MD13G1100100' => 'mdo', 'MD15G1169200' => 'mdo', 'MD16G1101100' => 'mdo', 'MD17G1022900' => 'mdo', 'Medtr3g096150' => 'mtr', 'Medtr4g115070' => 'mtr', 'Medtr7g033325' => 'mtr', 'Medtr8g089840' => 'mtr', 'MELO3C010319.2' => 'cme', 'MELO3C011944.2' => 'cme', 'MELO3C021589.2' => 'cme', 'Migut.E00207' => 'egut', 'Migut.H00067' => 'egut', 'Migut.K00433' => 'egut', 'Migut.K00606' => 'egut', 'Migut.K01410' => 'egut', 'MSTRG.13347' => 'ama', 'MSTRG.24045' => 'ama', 'MSTRG.2428' => 'ama', 'MSTRG.26410' => 'ama', 'MSTRG.3139' => 'ama', 'MSTRG.3286' => 'ama', 'MSTRG.563' => 'ama', 'MSTRG.7941' => 'ama', 'Nitab4.5_0000028g0060' => 'nta', 'Nitab4.5_0000065g0260' => 'nta', 'Nitab4.5_0000112g0060' => 'nta', 'Nitab4.5_0000489g0120' => 'nta', 'Nitab4.5_0001776g0050' => 'nta', 'Nitab4.5_0001854g0010' => 'nta', 'Nitab4.5_0001860g0020' => 'nta', 'Nitab4.5_0004352g0010' => 'nta', 'Nitab4.5_0008716g0020' => 'nta', 'Nitab4.5_0008922g0010' => 'nta', 'Nn3g16693' => 'nnu', 'Nn4g22596' => 'nnu', 'Nn7g37639' => 'nnu', 'Oeu001701.1' => 'oeu', 'Oeu018149.1' => 'oeu', 'Oeu026220.1' => 'oeu', 'Oeu038635.1' => 'oeu', 'Oeu049176.1' => 'oeu', 'Oeu056706.1' => 'oeu', 'Oeu056937.1' => 'oeu', 'Oeu057540.1' => 'oeu', 'Os02g0594900' => 'osa', 'Os02g0595100' => 'osa', 'Os04g0477500' => 'osa', 'Os12g0611900' => 'osa', 'Peaxi162Scf00076g00020' => 'pax', 'Peaxi162Scf00128g00217' => 'pax', 'Peaxi162Scf00129g01640' => 'pax', 'Peaxi162Scf00669g00007' => 'pax', 'Peaxi162Scf00700g00421' => 'pax', 'Peaxi162Scf00801g00038' => 'pax', 'Peaxi162Scf00891g00025' => 'pax', 'PGR083G0909' => 'pgr', 'PGR119G1005' => 'pgr', 'PGR142G2236' => 'pgr', 'PGR142G3388' => 'pgr', 'PGSC0003DMG400004514' => 'stu', 'PGSC0003DMG400012635' => 'stu', 'PGSC0003DMG400015730' => 'stu', 'PGSC0003DMG400018611' => 'stu', 'PGSC0003DMG400030897' => 'stu', 'Phvul.001G254800' => 'pvu', 'Phvul.002G260100' => 'pvu', 'Phvul.003G167600' => 'pvu', 'Phvul.004G005100' => 'pvu', 'Potri.001G343600' => 'ptr', 'Potri.006G066700' => 'ptr', 'Potri.008G186000' => 'ptr', 'Potri.010G046900' => 'ptr', 'Potri.018G127900' => 'ptr', 'Pp3c20_17750' => 'ppa', 'Pp3c24_4380' => 'ppa', 'Prupe.1G245800' => 'ppe', 'Prupe.3G293400' => 'ppe', 'Prupe.7G247400' => 'ppe', 'Psat0s145g0120' => 'psa', 'Psat0s595g0040' => 'psa', 'Psat0s595g0120' => 'psa', 'Psat3g175040' => 'psa', 'Psat7g058120' => 'psa', 'PSO017G0428' => 'pso', 'PSO063G7510' => 'pso', 'PSO067G0046' => 'pso', 'PSO478G1073' => 'pso', 'PSO675G3677' => 'pso', 'PSO675G6558' => 'pso', 'PSO675G7520' => 'pso', 'PSO675G8959' => 'pso', 'QL02p074089' => 'qlo', 'QL02p089614' => 'qlo', 'QL03p057736' => 'qlo', 'RcHm_v2.0_Chr1g0364131' => 'rch', 'RcHm_v2.0_Chr2g0087801' => 'rch', 'RcHm_v2.0_Chr2g0087821' => 'rch', 'RcHm_v2.0_Chr2g0173231' => 'rch', 'RcHm_v2.0_Chr4g0433111' => 'rch', 'Rhsim03G0250300' => 'rsi', 'Rhsim08G0048400' => 'rsi', 'Rhsim10G0014800' => 'rsi', 'Rhsim12G0040100' => 'rsi', 'Rhsim12G0109700' => 'rsi', 'Sabra06G0049600' => 'sbr', 'Sabra08G0141000' => 'sbr', 'Sabra10G0021400' => 'sbr', 'Sabra16G0222900' => 'sbr', 'Sabra18G0108600' => 'sbr', 'SalBow1G0433' => 'sbo', 'SalBow1G2038' => 'sbo', 'SalBow1G5003' => 'sbo', 'SalBow7G1197' => 'sbo', 'SalBow8G3506' => 'sbo', 'Sc03g0007300' => 'sci', 'Sc11g0000950' => 'sci', 'Sc14g0008750' => 'sci', 'Sc18g0000420' => 'sci', 'Sed0006754' => 'sed', 'Sed0008741' => 'sed', 'Sed0017172' => 'sed', 'Sed0018925' => 'sed', 'Sed0023326' => 'sed', 'Sed0025909' => 'sed', 'SEGI_05333' => 'sgi', 'SEGI_10362' => 'sgi', 'SEGI_13380' => 'sgi', 'SEGI_24306' => 'sgi', 'SEGI_29077' => 'sgi', 'SEGI_29095' => 'sgi', 'SEGI_36534' => 'sgi', 'SEGI_37506' => 'sgi', 'SEGI_38321' => 'sgi', 'SGA_v2.0_scaffold307G48031' => 'sas', 'SGA_v2.0_scaffold47G17507' => 'sas', 'SGA_v2.0_scaffold63G21736' => 'sas', 'SGA_v2.0_scaffold87G27070' => 'sas', 'SHI17794' => 'shi', 'SHI28851' => 'shi', 'SMO165G0155' => 'smo', 'SMO340G0217' => 'smo', 'SMO367G1210' => 'smo', 'Solyc02g093430.3' => 'sly', 'Solyc05g013580.4' => 'sly', 'Solyc07g008030.3' => 'sly', 'Solyc12g035470.2' => 'sly', 'Sopen02g038020' => 'spe', 'Sopen05g008490' => 'spe', 'Sopen07g003910' => 'spe', 'Sopen12g015240' => 'spe', 'Sp1g11550' => 'spa', 'Sp2g16710' => 'spa', 'Sp3g00430' => 'spa', 'Sp3g26780' => 'spa', 'Sp5g22900' => 'spa', 'Sp6g29530' => 'spa', 'TAR371G0794' => 'tar', 'TAR374G0164' => 'tar', 'TAR622G0165' => 'tar', 'TAR626G0929' => 'tar', 'TAR629G2155' => 'tar', 'THA.LOC104805282' => 'tha', 'THA.LOC104805363' => 'tha', 'THA.LOC104808968' => 'tha', 'THA.LOC104821093' => 'tha', 'THA.LOC104823953' => 'tha', 'THA.LOC104825562' => 'tha', 'THA.LOC104825665' => 'tha', 'Thecc.02G261400' => 'tca', 'Thecc.04G019200' => 'tca', 'Thecc.09G130400' => 'tca', 'Thhalv10004374m.g' => 'esa', 'Thhalv10007850m.g' => 'esa', 'Thhalv10013782m.g' => 'esa', 'Thhalv10018686m.g' => 'esa', 'Thhalv10020899m.g' => 'esa', 'Thhalv10022755m.g' => 'esa', 'TPR.G23851' => 'tpr', 'TPR.G26500' => 'tpr', 'TPR.G27267' => 'tpr', 'TPR.G32001' => 'tpr', 'TPR.G6251' => 'tpr', 'TPR.G8167' => 'tpr', 'TWI12G1330' => 'twi', 'TWI18G1239' => 'twi', 'TWI34G0979' => 'twi', 'TWI36G0670' => 'twi', 'TWI36G0707' => 'twi', 'TWI56G0233' => 'twi', 'TWI75G1809' => 'twi', 'unitig_21.g20874' => 'ugi', 'unitig_26.g10343' => 'ugi', 'unitig_46.g18392' => 'ugi', 'unitig_52.g17178' => 'ugi', 'unitig_8.g2934' => 'ugi', 'vmacro01122' => 'vma', 'vmacro05875' => 'vma', 'vmacro06147' => 'vma', 'vmacro16191' => 'vma', 'vmacro18293' => 'vma', 'VMungo0251G3707' => 'vmu', 'VMungo0464G1521' => 'vmu', 'VMungo1215G0205' => 'vmu', 'VMungo1383G2484' => 'vmu', 'Zm00001eb079610' => 'zma', 'Zm00001eb135990' => 'zma', 'Zm00001eb183710' => 'zma', 'Zm00001eb246020' => 'zma' ) $gf_id = 'HOM05D001124' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001124' ) $data_identifier = 'HOM05D001124' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 6, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 7, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 21, 'bol' => (int) 10, 'bra' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 6, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 9, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 21, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 8, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 10, 'lsa' => (int) 8, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 8, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 9, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb246020' $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' => 'HOM05D001124', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '548', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02520' => 'bna', 'A03p06630' => 'bna', 'A05p44460' => 'bna', 'A06p08710' => 'bna', 'A06p41090' => 'bna', 'A07p32320' => 'bna', 'A08p32520' => 'bna', 'A09p10360' => 'bna', 'A10p24080' => 'bna', 'Aa31LG11G15250' => 'aar', 'Aa31LG1G1800' => 'aar', 'Aa31LG2G5120' => 'aar', 'Aa31LG2G6070' => 'aar', 'Aa31LG5G10770' => 'aar', 'Aa31sc61G90' => 'aar', 'Actinidia01352' => 'ach', 'Actinidia05983' => 'ach', 'Actinidia08133' => 'ach', 'Actinidia15101' => 'ach', 'Actinidia26379' => 'ach', 'Actinidia35778' => 'ach', 'Actinidia36123' => 'ach', 'Actinidia37436' => 'ach', 'Actinidia38730' => 'ach', 'Ah.02g128210' => 'amhyb', 'Ah.03g132990' => 'amhyb', 'Ah.14g079410' => 'amhyb', 'AL1G24640' => 'aly', 'AL2G26680' => 'aly', 'AL3G10530' => 'aly', 'AL3G45230' => 'aly', 'AL5G15230' => 'aly', 'AL5G16960' => 'aly', 'AL6G25210' => 'aly', 'Aqoxy2G00441' => 'aox', 'Aqoxy3G01236' => 'aox', 'Aqoxy5G03746' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3RQ047' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C7GMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9C8JER' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MBL6KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YXCZ83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZANX40' => 'arhy', 'AT1G12990' => 'ath', 'AT1G67880' => 'ath', 'AT2G13290' => 'ath', 'AT3G01620' => 'ath', 'AT3G26445' => 'ath', 'AT3G27540' => 'ath', 'AT5G14480' => 'ath', 'ATR0824G026' => 'atr', 'ATR1098G019' => 'atr', 'Atru.chr11.2145' => 'acertr', 'Atru.chr2.3636' => 'acertr', 'Atru.chr2.3644' => 'acertr', 'Atru.chr6.2422' => 'acertr', 'Atru.chr7.1112' => 'acertr', 'AUR62005469' => 'cqu', 'AUR62011166' => 'cqu', 'AUR62013319' => 'cqu', 'AUR62024273' => 'cqu', 'AUR62028420' => 'cqu', 'AUR62041942' => 'cqu', 'BcaB01g04969' => 'bca', 'BcaB01g06371' => 'bca', 'BcaB02g11494' => 'bca', 'BcaB03g15382' => 'bca', 'BcaB08g36994' => 'bca', 'BcaC03g13477' => 'bca', 'BcaC03g13478' => 'bca', 'BcaC03g13480' => 'bca', 'BcaC03g13481' => 'bca', 'BcaC03g13486' => 'bca', 'BcaC04g19031' => 'bca', 'BcaC04g23085' => 'bca', 'BcaC05g25094' => 'bca', 'BcaC05g25096' => 'bca', 'BcaC05g25138' => 'bca', 'BcaC05g30416' => 'bca', 'BcaC05g30455' => 'bca', 'BcaC06g30979' => 'bca', 'BcaC06g33805' => 'bca', 'BcaC08g46021' => 'bca', 'BcaNung03154' => 'bca', 'BolC2t06623H' => 'bol', 'BolC2t06632H' => 'bol', 'BolC2t06635H' => 'bol', 'BolC2t06638H' => 'bol', 'BolC3t13266H' => 'bol', 'BolC5t29776H' => 'bol', 'BolC6t38912H' => 'bol', 'BolC7t44183H' => 'bol', 'BolC9t54123H' => 'bol', 'BolC9t59107H' => 'bol', 'BraA02t05221Z' => 'bra', 'BraA03t09996Z' => 'bra', 'BraA05t23210Z' => 'bra', 'BraA06t24068Z' => 'bra', 'BraA06t27032Z' => 'bra', 'BraA08t35176Z' => 'bra', 'BraA09t36680Z' => 'bra', 'BraA10t44471Z' => 'bra', 'C02p06760' => 'bna', 'C02p06890' => 'bna', 'C02p07010' => 'bna', 'C03p07660' => 'bna', 'C05p10300' => 'bna', 'C06p38150' => 'bna', 'C07p36650' => 'bna', 'C08p15770' => 'bna', 'C09p12300' => 'bna', 'C09p62700' => 'bna', 'C09p75040' => 'bna', 'CAN.G13.1' => 'can', 'CAN.G138.4' => 'can', 'CAN.G44.6' => 'can', 'CAN.G473.19' => 'can', 'CANSAT01G0835' => 'cansat', 'CANSAT11G0246' => 'cansat', 'CANSAT11G1766' => 'cansat', 'CANSAT64G1954' => 'cansat', 'CARHR013330' => 'chi', 'CARHR060530' => 'chi', 'CARHR075300' => 'chi', 'CARHR105120' => 'chi', 'CARHR148910' => 'chi', 'CARHR198830' => 'chi', 'Carub.0001s1275' => 'cru', 'Carub.0002s1437' => 'cru', 'Carub.0003s0044' => 'cru', 'Carub.0003s2787' => 'cru', 'Carub.0005s0597' => 'cru', 'Carub.0006s1266' => 'cru', 'Ca_06935_v3' => 'car', 'Ca_13559_v3' => 'car', 'Ca_16941_v3' => 'car', 'Ca_16960_v3' => 'car', 'Ca_17775_v3' => 'car', 'Ca_30464_v3' => 'car', 'Cc06_g08160' => 'ccan', 'Cc07_g01520' => 'ccan', 'Cc11_g15810' => 'ccan', 'CDE02G2840' => 'cde', 'CDE03G0093' => 'cde', 'CDE04G2127' => 'cde', 'CDE07G1857' => 'cde', 'CDE09G1246' => 'cde', 'Cfa003412' => 'cfa', 'Cfa007341' => 'cfa', 'Cfa009220' => 'cfa', 'Ciclev10008737m.g' => 'ccl', 'Ciclev10015565m.g' => 'ccl', 'Ciclev10031761m.g' => 'ccl', 'CiPaw.03G045300' => 'cil', 'CiPaw.03G247200' => 'cil', 'CiPaw.04G029500' => 'cil', 'CiPaw.04G174000' => 'cil', 'CiPaw.05G181200' => 'cil', 'CiPaw.06G067100' => 'cil', 'ClCG05G025800' => 'cla', 'ClCG06G011400' => 'cla', 'ClCG09G019360' => 'cla', 'COL.COLO4_04827' => 'col', 'COL.COLO4_29170' => 'col', 'COL.COLO4_35131' => 'col', 'COL.COLO4_35132' => 'col', 'Cpa.g.sc33.32' => 'cpa', 'Cpa.g.sc46.29' => 'cpa', 'Cpa.g.sc796.1' => 'cpa', 'CsaV3_1G030420' => 'csa', 'CsaV3_5G027050' => 'csa', 'CsaV3_5G031040' => 'csa', 'CsaV3_UNG023130' => 'csa', 'CSS0007726' => 'camsi', 'CSS0016433' => 'camsi', 'CSS0017656' => 'camsi', 'CSS0025364' => 'camsi', 'CSS0027582' => 'camsi', 'CSS0047288' => 'camsi', 'CSS0049950' => 'camsi', 'DCAR_003843' => 'dca', 'DCAR_007052' => 'dca', 'DCAR_020884' => 'dca', 'DCAR_021730' => 'dca', 'DCAR_024423' => 'dca', 'DCAR_026509' => 'dca', 'DCAR_031158' => 'dca', 'Dinv14728' => 'din', 'Dinv15219' => 'din', 'Dinv25728' => 'din', 'Dinv33428' => 'din', 'Dinv36489' => 'din', 'Dinv41486' => 'din', 'Duzib147G0469' => 'dzi', 'Duzib168G0060' => 'dzi', 'Duzib187G1215' => 'dzi', 'Duzib248G0692' => 'dzi', 'Duzib251G0767' => 'dzi', 'Duzib264G0446' => 'dzi', 'Duzib268G0691' => 'dzi', 'ECA232G4767' => 'eca', 'ECA233G2838' => 'eca', 'ECA234G0391' => 'eca', 'ECA234G0857' => 'eca', 'ECA236G1593' => 'eca', 'ECA238G0565' => 'eca', 'ECA246G1027' => 'eca', 'ECA246G3223' => 'eca', 'ECA246G3470' => 'eca', 'EL10Ac6g13829' => 'bvu', 'EL10Ac6g14093' => 'bvu', 'EL10Ac8g18707' => 'bvu', 'Eucgr.C01369' => 'egr', 'Eucgr.H02492' => 'egr', 'Eucgr.I01733' => 'egr', 'Eucgr.J02255' => 'egr', 'Eucgr.J02257' => 'egr', 'Eucgr.J02258' => 'egr', 'FAN02G1601' => 'fan', 'FAN03G1586' => 'fan', 'FAN03G2986' => 'fan', 'FAN05G4837' => 'fan', 'FAN06G0146' => 'fan', 'FAN07G0858' => 'fan', 'FAN09G3179' => 'fan', 'FAN10G0669' => 'fan', 'FAN12G2358' => 'fan', 'FAN14G4198' => 'fan', 'FAN14G5112' => 'fan', 'FAN17G0342' => 'fan', 'FAN19G0342' => 'fan', 'FAN19G0962' => 'fan', 'FAN19G1101' => 'fan', 'FAN19G1872' => 'fan', 'FAN22G0356' => 'fan', 'FAN23G0744' => 'fan', 'FAN23G1914' => 'fan', 'FAN26G0032' => 'fan', 'FAN28G0625' => 'fan', 'FvH4_1g02710' => 'fve', 'FvH4_1g02720' => 'fve', 'FvH4_4g25670' => 'fve', 'FvH4_6g51700' => 'fve', 'FvH4_7g20170' => 'fve', 'Glyma.05G175000' => 'gma', 'Glyma.08G132300' => 'gma', 'Glyma.11G243000' => 'gma', 'Glyma.13G158900' => 'gma', 'Glyma.17G112400' => 'gma', 'Glyma.18G014100' => 'gma', 'Glyma.19G003100' => 'gma', 'Glyma.19G056500' => 'gma', 'Gohir.A01G158900' => 'ghi', 'Gohir.A05G312600' => 'ghi', 'Gohir.A05G354900' => 'ghi', 'Gohir.A07G037200' => 'ghi', 'Gohir.A09G030000' => 'ghi', 'Gohir.A12G145200' => 'ghi', 'Gohir.D01G151500' => 'ghi', 'Gohir.D04G058300' => 'ghi', 'Gohir.D05G314100' => 'ghi', 'Gohir.D07G041400' => 'ghi', 'Gohir.D09G029700' => 'ghi', 'Gohir.D12G149700' => 'ghi', 'Gorai.001G043800' => 'gra', 'Gorai.002G187800' => 'gra', 'Gorai.006G034700' => 'gra', 'Gorai.008G161200' => 'gra', 'Gorai.009G335700' => 'gra', 'Gorai.012G065000' => 'gra', 'GSVIVG01000535001' => 'vvi', 'GSVIVG01015572001' => 'vvi', 'GSVIVG01032386001' => 'vvi', 'HanXRQChr05g0138531' => 'han', 'HanXRQChr06g0174391' => 'han', 'HanXRQChr07g0199021' => 'han', 'HanXRQChr08g0208211' => 'han', 'HanXRQChr09g0255471' => 'han', 'HanXRQChr10g0315791' => 'han', 'HanXRQChr12g0371991' => 'han', 'HanXRQChr15g0475251' => 'han', 'HanXRQChr17g0540001' => 'han', 'HanXRQChr17g0548631' => 'han', 'HanXRQChr17g0569561' => 'han', 'Haze_12256' => 'cav', 'Haze_14756' => 'cav', 'Haze_25528' => 'cav', 'Hma1.2p1_0079F.1_g041020' => 'hma', 'Hma1.2p1_0818F.1_g223260' => 'hma', 'Hma1.2p1_1747F.1_g300530' => 'hma', 'HPP92_004607' => 'vpl', 'HPP92_004608' => 'vpl', 'HPP92_006181' => 'vpl', 'HPP92_012192' => 'vpl', 'HPP92_015680' => 'vpl', 'HPP92_020249' => 'vpl', 'HPP92_021376' => 'vpl', 'HPP92_024275' => 'vpl', 'Hund06031' => 'sun', 'Hund25391' => 'sun', 'Lalb_Chr07g0185371' => 'lal', 'Lalb_Chr07g0185381' => 'lal', 'Lalb_Chr12g0204011' => 'lal', 'Lalb_Chr13g0301671' => 'lal', 'Lalb_Chr14g0362851' => 'lal', 'Lalb_Chr24g0403581' => 'lal', 'Lj1g0000233' => 'lja', 'Lj2g0018120' => 'lja', 'Lj3C621T0' => 'lonja', 'Lj3P1059T14' => 'lonja', 'Lj3P611T9' => 'lonja', 'Lj3P614T13' => 'lonja', 'Lj3P615T5' => 'lonja', 'Lj4g0012315' => 'lja', 'Lj4g0026182' => 'lja', 'Lj6P813T16' => 'lonja', 'Lj7C427T7' => 'lonja', 'Lj7C427T8' => 'lonja', 'Lj7P600T41' => 'lonja', 'Lju41C42G17' => 'lonja', 'Lsat_1_v5_gn_0_47300' => 'lsa', 'Lsat_1_v5_gn_2_91280' => 'lsa', 'Lsat_1_v5_gn_3_30561' => 'lsa', 'Lsat_1_v5_gn_4_184321' => 'lsa', 'Lsat_1_v5_gn_4_4041' => 'lsa', 'Lsat_1_v5_gn_5_92000' => 'lsa', 'Lsat_1_v5_gn_8_152940' => 'lsa', 'Lsat_1_v5_gn_8_62401' => 'lsa', 'Manes.06G055900' => 'mes', 'Manes.12G022200' => 'mes', 'Manes.13G023300' => 'mes', 'Manes.14G115000' => 'mes', 'Manes.15G151700' => 'mes', 'Manes.17G111300' => 'mes', 'Mapoly0226s0009' => 'mpo', 'MBI02_g25363_MAGBIO' => 'mbi', 'MBI06_g00027_MAGBIO' => 'mbi', 'MBI10_g13034_MAGBIO' => 'mbi', 'MD09G1023400' => 'mdo', 'MD13G1100100' => 'mdo', 'MD15G1169200' => 'mdo', 'MD16G1101100' => 'mdo', 'MD17G1022900' => 'mdo', 'Medtr3g096150' => 'mtr', 'Medtr4g115070' => 'mtr', 'Medtr7g033325' => 'mtr', 'Medtr8g089840' => 'mtr', 'MELO3C010319.2' => 'cme', 'MELO3C011944.2' => 'cme', 'MELO3C021589.2' => 'cme', 'Migut.E00207' => 'egut', 'Migut.H00067' => 'egut', 'Migut.K00433' => 'egut', 'Migut.K00606' => 'egut', 'Migut.K01410' => 'egut', 'MSTRG.13347' => 'ama', 'MSTRG.24045' => 'ama', 'MSTRG.2428' => 'ama', 'MSTRG.26410' => 'ama', 'MSTRG.3139' => 'ama', 'MSTRG.3286' => 'ama', 'MSTRG.563' => 'ama', 'MSTRG.7941' => 'ama', 'Nitab4.5_0000028g0060' => 'nta', 'Nitab4.5_0000065g0260' => 'nta', 'Nitab4.5_0000112g0060' => 'nta', 'Nitab4.5_0000489g0120' => 'nta', 'Nitab4.5_0001776g0050' => 'nta', 'Nitab4.5_0001854g0010' => 'nta', 'Nitab4.5_0001860g0020' => 'nta', 'Nitab4.5_0004352g0010' => 'nta', 'Nitab4.5_0008716g0020' => 'nta', 'Nitab4.5_0008922g0010' => 'nta', 'Nn3g16693' => 'nnu', 'Nn4g22596' => 'nnu', 'Nn7g37639' => 'nnu', 'Oeu001701.1' => 'oeu', 'Oeu018149.1' => 'oeu', 'Oeu026220.1' => 'oeu', 'Oeu038635.1' => 'oeu', 'Oeu049176.1' => 'oeu', 'Oeu056706.1' => 'oeu', 'Oeu056937.1' => 'oeu', 'Oeu057540.1' => 'oeu', 'Os02g0594900' => 'osa', 'Os02g0595100' => 'osa', 'Os04g0477500' => 'osa', 'Os12g0611900' => 'osa', 'Peaxi162Scf00076g00020' => 'pax', 'Peaxi162Scf00128g00217' => 'pax', 'Peaxi162Scf00129g01640' => 'pax', 'Peaxi162Scf00669g00007' => 'pax', 'Peaxi162Scf00700g00421' => 'pax', 'Peaxi162Scf00801g00038' => 'pax', 'Peaxi162Scf00891g00025' => 'pax', 'PGR083G0909' => 'pgr', 'PGR119G1005' => 'pgr', 'PGR142G2236' => 'pgr', 'PGR142G3388' => 'pgr', 'PGSC0003DMG400004514' => 'stu', 'PGSC0003DMG400012635' => 'stu', 'PGSC0003DMG400015730' => 'stu', 'PGSC0003DMG400018611' => 'stu', 'PGSC0003DMG400030897' => 'stu', 'Phvul.001G254800' => 'pvu', 'Phvul.002G260100' => 'pvu', 'Phvul.003G167600' => 'pvu', 'Phvul.004G005100' => 'pvu', 'Potri.001G343600' => 'ptr', 'Potri.006G066700' => 'ptr', 'Potri.008G186000' => 'ptr', 'Potri.010G046900' => 'ptr', 'Potri.018G127900' => 'ptr', 'Pp3c20_17750' => 'ppa', 'Pp3c24_4380' => 'ppa', 'Prupe.1G245800' => 'ppe', 'Prupe.3G293400' => 'ppe', 'Prupe.7G247400' => 'ppe', 'Psat0s145g0120' => 'psa', 'Psat0s595g0040' => 'psa', 'Psat0s595g0120' => 'psa', 'Psat3g175040' => 'psa', 'Psat7g058120' => 'psa', 'PSO017G0428' => 'pso', 'PSO063G7510' => 'pso', 'PSO067G0046' => 'pso', 'PSO478G1073' => 'pso', 'PSO675G3677' => 'pso', 'PSO675G6558' => 'pso', 'PSO675G7520' => 'pso', 'PSO675G8959' => 'pso', 'QL02p074089' => 'qlo', 'QL02p089614' => 'qlo', 'QL03p057736' => 'qlo', 'RcHm_v2.0_Chr1g0364131' => 'rch', 'RcHm_v2.0_Chr2g0087801' => 'rch', 'RcHm_v2.0_Chr2g0087821' => 'rch', 'RcHm_v2.0_Chr2g0173231' => 'rch', 'RcHm_v2.0_Chr4g0433111' => 'rch', 'Rhsim03G0250300' => 'rsi', 'Rhsim08G0048400' => 'rsi', 'Rhsim10G0014800' => 'rsi', 'Rhsim12G0040100' => 'rsi', 'Rhsim12G0109700' => 'rsi', 'Sabra06G0049600' => 'sbr', 'Sabra08G0141000' => 'sbr', 'Sabra10G0021400' => 'sbr', 'Sabra16G0222900' => 'sbr', 'Sabra18G0108600' => 'sbr', 'SalBow1G0433' => 'sbo', 'SalBow1G2038' => 'sbo', 'SalBow1G5003' => 'sbo', 'SalBow7G1197' => 'sbo', 'SalBow8G3506' => 'sbo', 'Sc03g0007300' => 'sci', 'Sc11g0000950' => 'sci', 'Sc14g0008750' => 'sci', 'Sc18g0000420' => 'sci', 'Sed0006754' => 'sed', 'Sed0008741' => 'sed', 'Sed0017172' => 'sed', 'Sed0018925' => 'sed', 'Sed0023326' => 'sed', 'Sed0025909' => 'sed', 'SEGI_05333' => 'sgi', 'SEGI_10362' => 'sgi', 'SEGI_13380' => 'sgi', 'SEGI_24306' => 'sgi', 'SEGI_29077' => 'sgi', 'SEGI_29095' => 'sgi', 'SEGI_36534' => 'sgi', 'SEGI_37506' => 'sgi', 'SEGI_38321' => 'sgi', 'SGA_v2.0_scaffold307G48031' => 'sas', 'SGA_v2.0_scaffold47G17507' => 'sas', 'SGA_v2.0_scaffold63G21736' => 'sas', 'SGA_v2.0_scaffold87G27070' => 'sas', 'SHI17794' => 'shi', 'SHI28851' => 'shi', 'SMO165G0155' => 'smo', 'SMO340G0217' => 'smo', 'SMO367G1210' => 'smo', 'Solyc02g093430.3' => 'sly', 'Solyc05g013580.4' => 'sly', 'Solyc07g008030.3' => 'sly', 'Solyc12g035470.2' => 'sly', 'Sopen02g038020' => 'spe', 'Sopen05g008490' => 'spe', 'Sopen07g003910' => 'spe', 'Sopen12g015240' => 'spe', 'Sp1g11550' => 'spa', 'Sp2g16710' => 'spa', 'Sp3g00430' => 'spa', 'Sp3g26780' => 'spa', 'Sp5g22900' => 'spa', 'Sp6g29530' => 'spa', 'TAR371G0794' => 'tar', 'TAR374G0164' => 'tar', 'TAR622G0165' => 'tar', 'TAR626G0929' => 'tar', 'TAR629G2155' => 'tar', 'THA.LOC104805282' => 'tha', 'THA.LOC104805363' => 'tha', 'THA.LOC104808968' => 'tha', 'THA.LOC104821093' => 'tha', 'THA.LOC104823953' => 'tha', 'THA.LOC104825562' => 'tha', 'THA.LOC104825665' => 'tha', 'Thecc.02G261400' => 'tca', 'Thecc.04G019200' => 'tca', 'Thecc.09G130400' => 'tca', 'Thhalv10004374m.g' => 'esa', 'Thhalv10007850m.g' => 'esa', 'Thhalv10013782m.g' => 'esa', 'Thhalv10018686m.g' => 'esa', 'Thhalv10020899m.g' => 'esa', 'Thhalv10022755m.g' => 'esa', 'TPR.G23851' => 'tpr', 'TPR.G26500' => 'tpr', 'TPR.G27267' => 'tpr', 'TPR.G32001' => 'tpr', 'TPR.G6251' => 'tpr', 'TPR.G8167' => 'tpr', 'TWI12G1330' => 'twi', 'TWI18G1239' => 'twi', 'TWI34G0979' => 'twi', 'TWI36G0670' => 'twi', 'TWI36G0707' => 'twi', 'TWI56G0233' => 'twi', 'TWI75G1809' => 'twi', 'unitig_21.g20874' => 'ugi', 'unitig_26.g10343' => 'ugi', 'unitig_46.g18392' => 'ugi', 'unitig_52.g17178' => 'ugi', 'unitig_8.g2934' => 'ugi', 'vmacro01122' => 'vma', 'vmacro05875' => 'vma', 'vmacro06147' => 'vma', 'vmacro16191' => 'vma', 'vmacro18293' => 'vma', 'VMungo0251G3707' => 'vmu', 'VMungo0464G1521' => 'vmu', 'VMungo1215G0205' => 'vmu', 'VMungo1383G2484' => 'vmu', 'Zm00001eb079610' => 'zma', 'Zm00001eb135990' => 'zma', 'Zm00001eb183710' => 'zma', 'Zm00001eb246020' => 'zma' ), 'gf_id' => 'HOM05D001124', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001124' ), 'data_identifier' => 'HOM05D001124', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001124', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '548', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02520' => 'bna', 'A03p06630' => 'bna', 'A05p44460' => 'bna', 'A06p08710' => 'bna', 'A06p41090' => 'bna', 'A07p32320' => 'bna', 'A08p32520' => 'bna', 'A09p10360' => 'bna', 'A10p24080' => 'bna', 'Aa31LG11G15250' => 'aar', 'Aa31LG1G1800' => 'aar', 'Aa31LG2G5120' => 'aar', 'Aa31LG2G6070' => 'aar', 'Aa31LG5G10770' => 'aar', 'Aa31sc61G90' => 'aar', 'Actinidia01352' => 'ach', 'Actinidia05983' => 'ach', 'Actinidia08133' => 'ach', 'Actinidia15101' => 'ach', 'Actinidia26379' => 'ach', 'Actinidia35778' => 'ach', 'Actinidia36123' => 'ach', 'Actinidia37436' => 'ach', 'Actinidia38730' => 'ach', 'Ah.02g128210' => 'amhyb', 'Ah.03g132990' => 'amhyb', 'Ah.14g079410' => 'amhyb', 'AL1G24640' => 'aly', 'AL2G26680' => 'aly', 'AL3G10530' => 'aly', 'AL3G45230' => 'aly', 'AL5G15230' => 'aly', 'AL5G16960' => 'aly', 'AL6G25210' => 'aly', 'Aqoxy2G00441' => 'aox', 'Aqoxy3G01236' => 'aox', 'Aqoxy5G03746' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3RQ047' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C7GMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9C8JER' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MBL6KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YXCZ83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZANX40' => 'arhy', 'AT1G12990' => 'ath', 'AT1G67880' => 'ath', 'AT2G13290' => 'ath', 'AT3G01620' => 'ath', 'AT3G26445' => 'ath', 'AT3G27540' => 'ath', 'AT5G14480' => 'ath', 'ATR0824G026' => 'atr', 'ATR1098G019' => 'atr', 'Atru.chr11.2145' => 'acertr', 'Atru.chr2.3636' => 'acertr', 'Atru.chr2.3644' => 'acertr', 'Atru.chr6.2422' => 'acertr', 'Atru.chr7.1112' => 'acertr', 'AUR62005469' => 'cqu', 'AUR62011166' => 'cqu', 'AUR62013319' => 'cqu', 'AUR62024273' => 'cqu', 'AUR62028420' => 'cqu', 'AUR62041942' => 'cqu', 'BcaB01g04969' => 'bca', 'BcaB01g06371' => 'bca', 'BcaB02g11494' => 'bca', 'BcaB03g15382' => 'bca', 'BcaB08g36994' => 'bca', 'BcaC03g13477' => 'bca', 'BcaC03g13478' => 'bca', 'BcaC03g13480' => 'bca', 'BcaC03g13481' => 'bca', 'BcaC03g13486' => 'bca', 'BcaC04g19031' => 'bca', 'BcaC04g23085' => 'bca', 'BcaC05g25094' => 'bca', 'BcaC05g25096' => 'bca', 'BcaC05g25138' => 'bca', 'BcaC05g30416' => 'bca', 'BcaC05g30455' => 'bca', 'BcaC06g30979' => 'bca', 'BcaC06g33805' => 'bca', 'BcaC08g46021' => 'bca', 'BcaNung03154' => 'bca', 'BolC2t06623H' => 'bol', 'BolC2t06632H' => 'bol', 'BolC2t06635H' => 'bol', 'BolC2t06638H' => 'bol', 'BolC3t13266H' => 'bol', 'BolC5t29776H' => 'bol', 'BolC6t38912H' => 'bol', 'BolC7t44183H' => 'bol', 'BolC9t54123H' => 'bol', 'BolC9t59107H' => 'bol', 'BraA02t05221Z' => 'bra', 'BraA03t09996Z' => 'bra', 'BraA05t23210Z' => 'bra', 'BraA06t24068Z' => 'bra', 'BraA06t27032Z' => 'bra', 'BraA08t35176Z' => 'bra', 'BraA09t36680Z' => 'bra', 'BraA10t44471Z' => 'bra', 'C02p06760' => 'bna', 'C02p06890' => 'bna', 'C02p07010' => 'bna', 'C03p07660' => 'bna', 'C05p10300' => 'bna', 'C06p38150' => 'bna', 'C07p36650' => 'bna', 'C08p15770' => 'bna', 'C09p12300' => 'bna', 'C09p62700' => 'bna', 'C09p75040' => 'bna', 'CAN.G13.1' => 'can', 'CAN.G138.4' => 'can', 'CAN.G44.6' => 'can', 'CAN.G473.19' => 'can', 'CANSAT01G0835' => 'cansat', 'CANSAT11G0246' => 'cansat', 'CANSAT11G1766' => 'cansat', 'CANSAT64G1954' => 'cansat', 'CARHR013330' => 'chi', 'CARHR060530' => 'chi', 'CARHR075300' => 'chi', 'CARHR105120' => 'chi', 'CARHR148910' => 'chi', 'CARHR198830' => 'chi', 'Carub.0001s1275' => 'cru', 'Carub.0002s1437' => 'cru', 'Carub.0003s0044' => 'cru', 'Carub.0003s2787' => 'cru', 'Carub.0005s0597' => 'cru', 'Carub.0006s1266' => 'cru', 'Ca_06935_v3' => 'car', 'Ca_13559_v3' => 'car', 'Ca_16941_v3' => 'car', 'Ca_16960_v3' => 'car', 'Ca_17775_v3' => 'car', 'Ca_30464_v3' => 'car', 'Cc06_g08160' => 'ccan', 'Cc07_g01520' => 'ccan', 'Cc11_g15810' => 'ccan', 'CDE02G2840' => 'cde', 'CDE03G0093' => 'cde', 'CDE04G2127' => 'cde', 'CDE07G1857' => 'cde', 'CDE09G1246' => 'cde', 'Cfa003412' => 'cfa', 'Cfa007341' => 'cfa', 'Cfa009220' => 'cfa', 'Ciclev10008737m.g' => 'ccl', 'Ciclev10015565m.g' => 'ccl', 'Ciclev10031761m.g' => 'ccl', 'CiPaw.03G045300' => 'cil', 'CiPaw.03G247200' => 'cil', 'CiPaw.04G029500' => 'cil', 'CiPaw.04G174000' => 'cil', 'CiPaw.05G181200' => 'cil', 'CiPaw.06G067100' => 'cil', 'ClCG05G025800' => 'cla', 'ClCG06G011400' => 'cla', 'ClCG09G019360' => 'cla', 'COL.COLO4_04827' => 'col', 'COL.COLO4_29170' => 'col', 'COL.COLO4_35131' => 'col', 'COL.COLO4_35132' => 'col', 'Cpa.g.sc33.32' => 'cpa', 'Cpa.g.sc46.29' => 'cpa', 'Cpa.g.sc796.1' => 'cpa', 'CsaV3_1G030420' => 'csa', 'CsaV3_5G027050' => 'csa', 'CsaV3_5G031040' => 'csa', 'CsaV3_UNG023130' => 'csa', 'CSS0007726' => 'camsi', 'CSS0016433' => 'camsi', 'CSS0017656' => 'camsi', 'CSS0025364' => 'camsi', 'CSS0027582' => 'camsi', 'CSS0047288' => 'camsi', 'CSS0049950' => 'camsi', 'DCAR_003843' => 'dca', 'DCAR_007052' => 'dca', 'DCAR_020884' => 'dca', 'DCAR_021730' => 'dca', 'DCAR_024423' => 'dca', 'DCAR_026509' => 'dca', 'DCAR_031158' => 'dca', 'Dinv14728' => 'din', 'Dinv15219' => 'din', 'Dinv25728' => 'din', 'Dinv33428' => 'din', 'Dinv36489' => 'din', 'Dinv41486' => 'din', 'Duzib147G0469' => 'dzi', 'Duzib168G0060' => 'dzi', 'Duzib187G1215' => 'dzi', 'Duzib248G0692' => 'dzi', 'Duzib251G0767' => 'dzi', 'Duzib264G0446' => 'dzi', 'Duzib268G0691' => 'dzi', 'ECA232G4767' => 'eca', 'ECA233G2838' => 'eca', 'ECA234G0391' => 'eca', 'ECA234G0857' => 'eca', 'ECA236G1593' => 'eca', 'ECA238G0565' => 'eca', 'ECA246G1027' => 'eca', 'ECA246G3223' => 'eca', 'ECA246G3470' => 'eca', 'EL10Ac6g13829' => 'bvu', 'EL10Ac6g14093' => 'bvu', 'EL10Ac8g18707' => 'bvu', 'Eucgr.C01369' => 'egr', 'Eucgr.H02492' => 'egr', 'Eucgr.I01733' => 'egr', 'Eucgr.J02255' => 'egr', 'Eucgr.J02257' => 'egr', 'Eucgr.J02258' => 'egr', 'FAN02G1601' => 'fan', 'FAN03G1586' => 'fan', 'FAN03G2986' => 'fan', 'FAN05G4837' => 'fan', 'FAN06G0146' => 'fan', 'FAN07G0858' => 'fan', 'FAN09G3179' => 'fan', 'FAN10G0669' => 'fan', 'FAN12G2358' => 'fan', 'FAN14G4198' => 'fan', 'FAN14G5112' => 'fan', 'FAN17G0342' => 'fan', 'FAN19G0342' => 'fan', 'FAN19G0962' => 'fan', 'FAN19G1101' => 'fan', 'FAN19G1872' => 'fan', 'FAN22G0356' => 'fan', 'FAN23G0744' => 'fan', 'FAN23G1914' => 'fan', 'FAN26G0032' => 'fan', 'FAN28G0625' => 'fan', 'FvH4_1g02710' => 'fve', 'FvH4_1g02720' => 'fve', 'FvH4_4g25670' => 'fve', 'FvH4_6g51700' => 'fve', 'FvH4_7g20170' => 'fve', 'Glyma.05G175000' => 'gma', 'Glyma.08G132300' => 'gma', 'Glyma.11G243000' => 'gma', 'Glyma.13G158900' => 'gma', 'Glyma.17G112400' => 'gma', 'Glyma.18G014100' => 'gma', 'Glyma.19G003100' => 'gma', 'Glyma.19G056500' => 'gma', 'Gohir.A01G158900' => 'ghi', 'Gohir.A05G312600' => 'ghi', 'Gohir.A05G354900' => 'ghi', 'Gohir.A07G037200' => 'ghi', 'Gohir.A09G030000' => 'ghi', 'Gohir.A12G145200' => 'ghi', 'Gohir.D01G151500' => 'ghi', 'Gohir.D04G058300' => 'ghi', 'Gohir.D05G314100' => 'ghi', 'Gohir.D07G041400' => 'ghi', 'Gohir.D09G029700' => 'ghi', 'Gohir.D12G149700' => 'ghi', 'Gorai.001G043800' => 'gra', 'Gorai.002G187800' => 'gra', 'Gorai.006G034700' => 'gra', 'Gorai.008G161200' => 'gra', 'Gorai.009G335700' => 'gra', 'Gorai.012G065000' => 'gra', 'GSVIVG01000535001' => 'vvi', 'GSVIVG01015572001' => 'vvi', 'GSVIVG01032386001' => 'vvi', 'HanXRQChr05g0138531' => 'han', 'HanXRQChr06g0174391' => 'han', 'HanXRQChr07g0199021' => 'han', 'HanXRQChr08g0208211' => 'han', 'HanXRQChr09g0255471' => 'han', 'HanXRQChr10g0315791' => 'han', 'HanXRQChr12g0371991' => 'han', 'HanXRQChr15g0475251' => 'han', 'HanXRQChr17g0540001' => 'han', 'HanXRQChr17g0548631' => 'han', 'HanXRQChr17g0569561' => 'han', 'Haze_12256' => 'cav', 'Haze_14756' => 'cav', 'Haze_25528' => 'cav', 'Hma1.2p1_0079F.1_g041020' => 'hma', 'Hma1.2p1_0818F.1_g223260' => 'hma', 'Hma1.2p1_1747F.1_g300530' => 'hma', 'HPP92_004607' => 'vpl', 'HPP92_004608' => 'vpl', 'HPP92_006181' => 'vpl', 'HPP92_012192' => 'vpl', 'HPP92_015680' => 'vpl', 'HPP92_020249' => 'vpl', 'HPP92_021376' => 'vpl', 'HPP92_024275' => 'vpl', 'Hund06031' => 'sun', 'Hund25391' => 'sun', 'Lalb_Chr07g0185371' => 'lal', 'Lalb_Chr07g0185381' => 'lal', 'Lalb_Chr12g0204011' => 'lal', 'Lalb_Chr13g0301671' => 'lal', 'Lalb_Chr14g0362851' => 'lal', 'Lalb_Chr24g0403581' => 'lal', 'Lj1g0000233' => 'lja', 'Lj2g0018120' => 'lja', 'Lj3C621T0' => 'lonja', 'Lj3P1059T14' => 'lonja', 'Lj3P611T9' => 'lonja', 'Lj3P614T13' => 'lonja', 'Lj3P615T5' => 'lonja', 'Lj4g0012315' => 'lja', 'Lj4g0026182' => 'lja', 'Lj6P813T16' => 'lonja', 'Lj7C427T7' => 'lonja', 'Lj7C427T8' => 'lonja', 'Lj7P600T41' => 'lonja', 'Lju41C42G17' => 'lonja', 'Lsat_1_v5_gn_0_47300' => 'lsa', 'Lsat_1_v5_gn_2_91280' => 'lsa', 'Lsat_1_v5_gn_3_30561' => 'lsa', 'Lsat_1_v5_gn_4_184321' => 'lsa', 'Lsat_1_v5_gn_4_4041' => 'lsa', 'Lsat_1_v5_gn_5_92000' => 'lsa', 'Lsat_1_v5_gn_8_152940' => 'lsa', 'Lsat_1_v5_gn_8_62401' => 'lsa', 'Manes.06G055900' => 'mes', 'Manes.12G022200' => 'mes', 'Manes.13G023300' => 'mes', 'Manes.14G115000' => 'mes', 'Manes.15G151700' => 'mes', 'Manes.17G111300' => 'mes', 'Mapoly0226s0009' => 'mpo', 'MBI02_g25363_MAGBIO' => 'mbi', 'MBI06_g00027_MAGBIO' => 'mbi', 'MBI10_g13034_MAGBIO' => 'mbi', 'MD09G1023400' => 'mdo', 'MD13G1100100' => 'mdo', 'MD15G1169200' => 'mdo', 'MD16G1101100' => 'mdo', 'MD17G1022900' => 'mdo', 'Medtr3g096150' => 'mtr', 'Medtr4g115070' => 'mtr', 'Medtr7g033325' => 'mtr', 'Medtr8g089840' => 'mtr', 'MELO3C010319.2' => 'cme', 'MELO3C011944.2' => 'cme', 'MELO3C021589.2' => 'cme', 'Migut.E00207' => 'egut', 'Migut.H00067' => 'egut', 'Migut.K00433' => 'egut', 'Migut.K00606' => 'egut', 'Migut.K01410' => 'egut', 'MSTRG.13347' => 'ama', 'MSTRG.24045' => 'ama', 'MSTRG.2428' => 'ama', 'MSTRG.26410' => 'ama', 'MSTRG.3139' => 'ama', 'MSTRG.3286' => 'ama', 'MSTRG.563' => 'ama', 'MSTRG.7941' => 'ama', 'Nitab4.5_0000028g0060' => 'nta', 'Nitab4.5_0000065g0260' => 'nta', 'Nitab4.5_0000112g0060' => 'nta', 'Nitab4.5_0000489g0120' => 'nta', 'Nitab4.5_0001776g0050' => 'nta', 'Nitab4.5_0001854g0010' => 'nta', 'Nitab4.5_0001860g0020' => 'nta', 'Nitab4.5_0004352g0010' => 'nta', 'Nitab4.5_0008716g0020' => 'nta', 'Nitab4.5_0008922g0010' => 'nta', 'Nn3g16693' => 'nnu', 'Nn4g22596' => 'nnu', 'Nn7g37639' => 'nnu', 'Oeu001701.1' => 'oeu', 'Oeu018149.1' => 'oeu', 'Oeu026220.1' => 'oeu', 'Oeu038635.1' => 'oeu', 'Oeu049176.1' => 'oeu', 'Oeu056706.1' => 'oeu', 'Oeu056937.1' => 'oeu', 'Oeu057540.1' => 'oeu', 'Os02g0594900' => 'osa', 'Os02g0595100' => 'osa', 'Os04g0477500' => 'osa', 'Os12g0611900' => 'osa', 'Peaxi162Scf00076g00020' => 'pax', 'Peaxi162Scf00128g00217' => 'pax', 'Peaxi162Scf00129g01640' => 'pax', 'Peaxi162Scf00669g00007' => 'pax', 'Peaxi162Scf00700g00421' => 'pax', 'Peaxi162Scf00801g00038' => 'pax', 'Peaxi162Scf00891g00025' => 'pax', 'PGR083G0909' => 'pgr', 'PGR119G1005' => 'pgr', 'PGR142G2236' => 'pgr', 'PGR142G3388' => 'pgr', 'PGSC0003DMG400004514' => 'stu', 'PGSC0003DMG400012635' => 'stu', 'PGSC0003DMG400015730' => 'stu', 'PGSC0003DMG400018611' => 'stu', 'PGSC0003DMG400030897' => 'stu', 'Phvul.001G254800' => 'pvu', 'Phvul.002G260100' => 'pvu', 'Phvul.003G167600' => 'pvu', 'Phvul.004G005100' => 'pvu', 'Potri.001G343600' => 'ptr', 'Potri.006G066700' => 'ptr', 'Potri.008G186000' => 'ptr', 'Potri.010G046900' => 'ptr', 'Potri.018G127900' => 'ptr', 'Pp3c20_17750' => 'ppa', 'Pp3c24_4380' => 'ppa', 'Prupe.1G245800' => 'ppe', 'Prupe.3G293400' => 'ppe', 'Prupe.7G247400' => 'ppe', 'Psat0s145g0120' => 'psa', 'Psat0s595g0040' => 'psa', 'Psat0s595g0120' => 'psa', 'Psat3g175040' => 'psa', 'Psat7g058120' => 'psa', 'PSO017G0428' => 'pso', 'PSO063G7510' => 'pso', 'PSO067G0046' => 'pso', 'PSO478G1073' => 'pso', 'PSO675G3677' => 'pso', 'PSO675G6558' => 'pso', 'PSO675G7520' => 'pso', 'PSO675G8959' => 'pso', 'QL02p074089' => 'qlo', 'QL02p089614' => 'qlo', 'QL03p057736' => 'qlo', 'RcHm_v2.0_Chr1g0364131' => 'rch', 'RcHm_v2.0_Chr2g0087801' => 'rch', 'RcHm_v2.0_Chr2g0087821' => 'rch', 'RcHm_v2.0_Chr2g0173231' => 'rch', 'RcHm_v2.0_Chr4g0433111' => 'rch', 'Rhsim03G0250300' => 'rsi', 'Rhsim08G0048400' => 'rsi', 'Rhsim10G0014800' => 'rsi', 'Rhsim12G0040100' => 'rsi', 'Rhsim12G0109700' => 'rsi', 'Sabra06G0049600' => 'sbr', 'Sabra08G0141000' => 'sbr', 'Sabra10G0021400' => 'sbr', 'Sabra16G0222900' => 'sbr', 'Sabra18G0108600' => 'sbr', 'SalBow1G0433' => 'sbo', 'SalBow1G2038' => 'sbo', 'SalBow1G5003' => 'sbo', 'SalBow7G1197' => 'sbo', 'SalBow8G3506' => 'sbo', 'Sc03g0007300' => 'sci', 'Sc11g0000950' => 'sci', 'Sc14g0008750' => 'sci', 'Sc18g0000420' => 'sci', 'Sed0006754' => 'sed', 'Sed0008741' => 'sed', 'Sed0017172' => 'sed', 'Sed0018925' => 'sed', 'Sed0023326' => 'sed', 'Sed0025909' => 'sed', 'SEGI_05333' => 'sgi', 'SEGI_10362' => 'sgi', 'SEGI_13380' => 'sgi', 'SEGI_24306' => 'sgi', 'SEGI_29077' => 'sgi', 'SEGI_29095' => 'sgi', 'SEGI_36534' => 'sgi', 'SEGI_37506' => 'sgi', 'SEGI_38321' => 'sgi', 'SGA_v2.0_scaffold307G48031' => 'sas', 'SGA_v2.0_scaffold47G17507' => 'sas', 'SGA_v2.0_scaffold63G21736' => 'sas', 'SGA_v2.0_scaffold87G27070' => 'sas', 'SHI17794' => 'shi', 'SHI28851' => 'shi', 'SMO165G0155' => 'smo', 'SMO340G0217' => 'smo', 'SMO367G1210' => 'smo', 'Solyc02g093430.3' => 'sly', 'Solyc05g013580.4' => 'sly', 'Solyc07g008030.3' => 'sly', 'Solyc12g035470.2' => 'sly', 'Sopen02g038020' => 'spe', 'Sopen05g008490' => 'spe', 'Sopen07g003910' => 'spe', 'Sopen12g015240' => 'spe', 'Sp1g11550' => 'spa', 'Sp2g16710' => 'spa', 'Sp3g00430' => 'spa', 'Sp3g26780' => 'spa', 'Sp5g22900' => 'spa', 'Sp6g29530' => 'spa', 'TAR371G0794' => 'tar', 'TAR374G0164' => 'tar', 'TAR622G0165' => 'tar', 'TAR626G0929' => 'tar', 'TAR629G2155' => 'tar', 'THA.LOC104805282' => 'tha', 'THA.LOC104805363' => 'tha', 'THA.LOC104808968' => 'tha', 'THA.LOC104821093' => 'tha', 'THA.LOC104823953' => 'tha', 'THA.LOC104825562' => 'tha', 'THA.LOC104825665' => 'tha', 'Thecc.02G261400' => 'tca', 'Thecc.04G019200' => 'tca', 'Thecc.09G130400' => 'tca', 'Thhalv10004374m.g' => 'esa', 'Thhalv10007850m.g' => 'esa', 'Thhalv10013782m.g' => 'esa', 'Thhalv10018686m.g' => 'esa', 'Thhalv10020899m.g' => 'esa', 'Thhalv10022755m.g' => 'esa', 'TPR.G23851' => 'tpr', 'TPR.G26500' => 'tpr', 'TPR.G27267' => 'tpr', 'TPR.G32001' => 'tpr', 'TPR.G6251' => 'tpr', 'TPR.G8167' => 'tpr', 'TWI12G1330' => 'twi', 'TWI18G1239' => 'twi', 'TWI34G0979' => 'twi', 'TWI36G0670' => 'twi', 'TWI36G0707' => 'twi', 'TWI56G0233' => 'twi', 'TWI75G1809' => 'twi', 'unitig_21.g20874' => 'ugi', 'unitig_26.g10343' => 'ugi', 'unitig_46.g18392' => 'ugi', 'unitig_52.g17178' => 'ugi', 'unitig_8.g2934' => 'ugi', 'vmacro01122' => 'vma', 'vmacro05875' => 'vma', 'vmacro06147' => 'vma', 'vmacro16191' => 'vma', 'vmacro18293' => 'vma', 'VMungo0251G3707' => 'vmu', 'VMungo0464G1521' => 'vmu', 'VMungo1215G0205' => 'vmu', 'VMungo1383G2484' => 'vmu', 'Zm00001eb079610' => 'zma', 'Zm00001eb135990' => 'zma', 'Zm00001eb183710' => 'zma', 'Zm00001eb246020' => 'zma' ) $gf_id = 'HOM05D001124' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001124' ) $data_identifier = 'HOM05D001124' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 6, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 7, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 21, 'bol' => (int) 10, 'bra' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 6, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 9, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 21, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 8, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 10, 'lsa' => (int) 8, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 8, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 9, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb246020' $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' => 'HOM05D001124', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '548', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02520' => 'bna', 'A03p06630' => 'bna', 'A05p44460' => 'bna', 'A06p08710' => 'bna', 'A06p41090' => 'bna', 'A07p32320' => 'bna', 'A08p32520' => 'bna', 'A09p10360' => 'bna', 'A10p24080' => 'bna', 'Aa31LG11G15250' => 'aar', 'Aa31LG1G1800' => 'aar', 'Aa31LG2G5120' => 'aar', 'Aa31LG2G6070' => 'aar', 'Aa31LG5G10770' => 'aar', 'Aa31sc61G90' => 'aar', 'Actinidia01352' => 'ach', 'Actinidia05983' => 'ach', 'Actinidia08133' => 'ach', 'Actinidia15101' => 'ach', 'Actinidia26379' => 'ach', 'Actinidia35778' => 'ach', 'Actinidia36123' => 'ach', 'Actinidia37436' => 'ach', 'Actinidia38730' => 'ach', 'Ah.02g128210' => 'amhyb', 'Ah.03g132990' => 'amhyb', 'Ah.14g079410' => 'amhyb', 'AL1G24640' => 'aly', 'AL2G26680' => 'aly', 'AL3G10530' => 'aly', 'AL3G45230' => 'aly', 'AL5G15230' => 'aly', 'AL5G16960' => 'aly', 'AL6G25210' => 'aly', 'Aqoxy2G00441' => 'aox', 'Aqoxy3G01236' => 'aox', 'Aqoxy5G03746' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3RQ047' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C7GMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9C8JER' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MBL6KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YXCZ83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZANX40' => 'arhy', 'AT1G12990' => 'ath', 'AT1G67880' => 'ath', 'AT2G13290' => 'ath', 'AT3G01620' => 'ath', 'AT3G26445' => 'ath', 'AT3G27540' => 'ath', 'AT5G14480' => 'ath', 'ATR0824G026' => 'atr', 'ATR1098G019' => 'atr', 'Atru.chr11.2145' => 'acertr', 'Atru.chr2.3636' => 'acertr', 'Atru.chr2.3644' => 'acertr', 'Atru.chr6.2422' => 'acertr', 'Atru.chr7.1112' => 'acertr', 'AUR62005469' => 'cqu', 'AUR62011166' => 'cqu', 'AUR62013319' => 'cqu', 'AUR62024273' => 'cqu', 'AUR62028420' => 'cqu', 'AUR62041942' => 'cqu', 'BcaB01g04969' => 'bca', 'BcaB01g06371' => 'bca', 'BcaB02g11494' => 'bca', 'BcaB03g15382' => 'bca', 'BcaB08g36994' => 'bca', 'BcaC03g13477' => 'bca', 'BcaC03g13478' => 'bca', 'BcaC03g13480' => 'bca', 'BcaC03g13481' => 'bca', 'BcaC03g13486' => 'bca', 'BcaC04g19031' => 'bca', 'BcaC04g23085' => 'bca', 'BcaC05g25094' => 'bca', 'BcaC05g25096' => 'bca', 'BcaC05g25138' => 'bca', 'BcaC05g30416' => 'bca', 'BcaC05g30455' => 'bca', 'BcaC06g30979' => 'bca', 'BcaC06g33805' => 'bca', 'BcaC08g46021' => 'bca', 'BcaNung03154' => 'bca', 'BolC2t06623H' => 'bol', 'BolC2t06632H' => 'bol', 'BolC2t06635H' => 'bol', 'BolC2t06638H' => 'bol', 'BolC3t13266H' => 'bol', 'BolC5t29776H' => 'bol', 'BolC6t38912H' => 'bol', 'BolC7t44183H' => 'bol', 'BolC9t54123H' => 'bol', 'BolC9t59107H' => 'bol', 'BraA02t05221Z' => 'bra', 'BraA03t09996Z' => 'bra', 'BraA05t23210Z' => 'bra', 'BraA06t24068Z' => 'bra', 'BraA06t27032Z' => 'bra', 'BraA08t35176Z' => 'bra', 'BraA09t36680Z' => 'bra', 'BraA10t44471Z' => 'bra', 'C02p06760' => 'bna', 'C02p06890' => 'bna', 'C02p07010' => 'bna', 'C03p07660' => 'bna', 'C05p10300' => 'bna', 'C06p38150' => 'bna', 'C07p36650' => 'bna', 'C08p15770' => 'bna', 'C09p12300' => 'bna', 'C09p62700' => 'bna', 'C09p75040' => 'bna', 'CAN.G13.1' => 'can', 'CAN.G138.4' => 'can', 'CAN.G44.6' => 'can', 'CAN.G473.19' => 'can', 'CANSAT01G0835' => 'cansat', 'CANSAT11G0246' => 'cansat', 'CANSAT11G1766' => 'cansat', 'CANSAT64G1954' => 'cansat', 'CARHR013330' => 'chi', 'CARHR060530' => 'chi', 'CARHR075300' => 'chi', 'CARHR105120' => 'chi', 'CARHR148910' => 'chi', 'CARHR198830' => 'chi', 'Carub.0001s1275' => 'cru', 'Carub.0002s1437' => 'cru', 'Carub.0003s0044' => 'cru', 'Carub.0003s2787' => 'cru', 'Carub.0005s0597' => 'cru', 'Carub.0006s1266' => 'cru', 'Ca_06935_v3' => 'car', 'Ca_13559_v3' => 'car', 'Ca_16941_v3' => 'car', 'Ca_16960_v3' => 'car', 'Ca_17775_v3' => 'car', 'Ca_30464_v3' => 'car', 'Cc06_g08160' => 'ccan', 'Cc07_g01520' => 'ccan', 'Cc11_g15810' => 'ccan', 'CDE02G2840' => 'cde', 'CDE03G0093' => 'cde', 'CDE04G2127' => 'cde', 'CDE07G1857' => 'cde', 'CDE09G1246' => 'cde', 'Cfa003412' => 'cfa', 'Cfa007341' => 'cfa', 'Cfa009220' => 'cfa', 'Ciclev10008737m.g' => 'ccl', 'Ciclev10015565m.g' => 'ccl', 'Ciclev10031761m.g' => 'ccl', 'CiPaw.03G045300' => 'cil', 'CiPaw.03G247200' => 'cil', 'CiPaw.04G029500' => 'cil', 'CiPaw.04G174000' => 'cil', 'CiPaw.05G181200' => 'cil', 'CiPaw.06G067100' => 'cil', 'ClCG05G025800' => 'cla', 'ClCG06G011400' => 'cla', 'ClCG09G019360' => 'cla', 'COL.COLO4_04827' => 'col', 'COL.COLO4_29170' => 'col', 'COL.COLO4_35131' => 'col', 'COL.COLO4_35132' => 'col', 'Cpa.g.sc33.32' => 'cpa', 'Cpa.g.sc46.29' => 'cpa', 'Cpa.g.sc796.1' => 'cpa', 'CsaV3_1G030420' => 'csa', 'CsaV3_5G027050' => 'csa', 'CsaV3_5G031040' => 'csa', 'CsaV3_UNG023130' => 'csa', 'CSS0007726' => 'camsi', 'CSS0016433' => 'camsi', 'CSS0017656' => 'camsi', 'CSS0025364' => 'camsi', 'CSS0027582' => 'camsi', 'CSS0047288' => 'camsi', 'CSS0049950' => 'camsi', 'DCAR_003843' => 'dca', 'DCAR_007052' => 'dca', 'DCAR_020884' => 'dca', 'DCAR_021730' => 'dca', 'DCAR_024423' => 'dca', 'DCAR_026509' => 'dca', 'DCAR_031158' => 'dca', 'Dinv14728' => 'din', 'Dinv15219' => 'din', 'Dinv25728' => 'din', 'Dinv33428' => 'din', 'Dinv36489' => 'din', 'Dinv41486' => 'din', 'Duzib147G0469' => 'dzi', 'Duzib168G0060' => 'dzi', 'Duzib187G1215' => 'dzi', 'Duzib248G0692' => 'dzi', 'Duzib251G0767' => 'dzi', 'Duzib264G0446' => 'dzi', 'Duzib268G0691' => 'dzi', 'ECA232G4767' => 'eca', 'ECA233G2838' => 'eca', 'ECA234G0391' => 'eca', 'ECA234G0857' => 'eca', 'ECA236G1593' => 'eca', 'ECA238G0565' => 'eca', 'ECA246G1027' => 'eca', 'ECA246G3223' => 'eca', 'ECA246G3470' => 'eca', 'EL10Ac6g13829' => 'bvu', 'EL10Ac6g14093' => 'bvu', 'EL10Ac8g18707' => 'bvu', 'Eucgr.C01369' => 'egr', 'Eucgr.H02492' => 'egr', 'Eucgr.I01733' => 'egr', 'Eucgr.J02255' => 'egr', 'Eucgr.J02257' => 'egr', 'Eucgr.J02258' => 'egr', 'FAN02G1601' => 'fan', 'FAN03G1586' => 'fan', 'FAN03G2986' => 'fan', 'FAN05G4837' => 'fan', 'FAN06G0146' => 'fan', 'FAN07G0858' => 'fan', 'FAN09G3179' => 'fan', 'FAN10G0669' => 'fan', 'FAN12G2358' => 'fan', 'FAN14G4198' => 'fan', 'FAN14G5112' => 'fan', 'FAN17G0342' => 'fan', 'FAN19G0342' => 'fan', 'FAN19G0962' => 'fan', 'FAN19G1101' => 'fan', 'FAN19G1872' => 'fan', 'FAN22G0356' => 'fan', 'FAN23G0744' => 'fan', 'FAN23G1914' => 'fan', 'FAN26G0032' => 'fan', 'FAN28G0625' => 'fan', 'FvH4_1g02710' => 'fve', 'FvH4_1g02720' => 'fve', 'FvH4_4g25670' => 'fve', 'FvH4_6g51700' => 'fve', 'FvH4_7g20170' => 'fve', 'Glyma.05G175000' => 'gma', 'Glyma.08G132300' => 'gma', 'Glyma.11G243000' => 'gma', 'Glyma.13G158900' => 'gma', 'Glyma.17G112400' => 'gma', 'Glyma.18G014100' => 'gma', 'Glyma.19G003100' => 'gma', 'Glyma.19G056500' => 'gma', 'Gohir.A01G158900' => 'ghi', 'Gohir.A05G312600' => 'ghi', 'Gohir.A05G354900' => 'ghi', 'Gohir.A07G037200' => 'ghi', 'Gohir.A09G030000' => 'ghi', 'Gohir.A12G145200' => 'ghi', 'Gohir.D01G151500' => 'ghi', 'Gohir.D04G058300' => 'ghi', 'Gohir.D05G314100' => 'ghi', 'Gohir.D07G041400' => 'ghi', 'Gohir.D09G029700' => 'ghi', 'Gohir.D12G149700' => 'ghi', 'Gorai.001G043800' => 'gra', 'Gorai.002G187800' => 'gra', 'Gorai.006G034700' => 'gra', 'Gorai.008G161200' => 'gra', 'Gorai.009G335700' => 'gra', 'Gorai.012G065000' => 'gra', 'GSVIVG01000535001' => 'vvi', 'GSVIVG01015572001' => 'vvi', 'GSVIVG01032386001' => 'vvi', 'HanXRQChr05g0138531' => 'han', 'HanXRQChr06g0174391' => 'han', 'HanXRQChr07g0199021' => 'han', 'HanXRQChr08g0208211' => 'han', 'HanXRQChr09g0255471' => 'han', 'HanXRQChr10g0315791' => 'han', 'HanXRQChr12g0371991' => 'han', 'HanXRQChr15g0475251' => 'han', 'HanXRQChr17g0540001' => 'han', 'HanXRQChr17g0548631' => 'han', 'HanXRQChr17g0569561' => 'han', 'Haze_12256' => 'cav', 'Haze_14756' => 'cav', 'Haze_25528' => 'cav', 'Hma1.2p1_0079F.1_g041020' => 'hma', 'Hma1.2p1_0818F.1_g223260' => 'hma', 'Hma1.2p1_1747F.1_g300530' => 'hma', 'HPP92_004607' => 'vpl', 'HPP92_004608' => 'vpl', 'HPP92_006181' => 'vpl', 'HPP92_012192' => 'vpl', 'HPP92_015680' => 'vpl', 'HPP92_020249' => 'vpl', 'HPP92_021376' => 'vpl', 'HPP92_024275' => 'vpl', 'Hund06031' => 'sun', 'Hund25391' => 'sun', 'Lalb_Chr07g0185371' => 'lal', 'Lalb_Chr07g0185381' => 'lal', 'Lalb_Chr12g0204011' => 'lal', 'Lalb_Chr13g0301671' => 'lal', 'Lalb_Chr14g0362851' => 'lal', 'Lalb_Chr24g0403581' => 'lal', 'Lj1g0000233' => 'lja', 'Lj2g0018120' => 'lja', 'Lj3C621T0' => 'lonja', 'Lj3P1059T14' => 'lonja', 'Lj3P611T9' => 'lonja', 'Lj3P614T13' => 'lonja', 'Lj3P615T5' => 'lonja', 'Lj4g0012315' => 'lja', 'Lj4g0026182' => 'lja', 'Lj6P813T16' => 'lonja', 'Lj7C427T7' => 'lonja', 'Lj7C427T8' => 'lonja', 'Lj7P600T41' => 'lonja', 'Lju41C42G17' => 'lonja', 'Lsat_1_v5_gn_0_47300' => 'lsa', 'Lsat_1_v5_gn_2_91280' => 'lsa', 'Lsat_1_v5_gn_3_30561' => 'lsa', 'Lsat_1_v5_gn_4_184321' => 'lsa', 'Lsat_1_v5_gn_4_4041' => 'lsa', 'Lsat_1_v5_gn_5_92000' => 'lsa', 'Lsat_1_v5_gn_8_152940' => 'lsa', 'Lsat_1_v5_gn_8_62401' => 'lsa', 'Manes.06G055900' => 'mes', 'Manes.12G022200' => 'mes', 'Manes.13G023300' => 'mes', 'Manes.14G115000' => 'mes', 'Manes.15G151700' => 'mes', 'Manes.17G111300' => 'mes', 'Mapoly0226s0009' => 'mpo', 'MBI02_g25363_MAGBIO' => 'mbi', 'MBI06_g00027_MAGBIO' => 'mbi', 'MBI10_g13034_MAGBIO' => 'mbi', 'MD09G1023400' => 'mdo', 'MD13G1100100' => 'mdo', 'MD15G1169200' => 'mdo', 'MD16G1101100' => 'mdo', 'MD17G1022900' => 'mdo', 'Medtr3g096150' => 'mtr', 'Medtr4g115070' => 'mtr', 'Medtr7g033325' => 'mtr', 'Medtr8g089840' => 'mtr', 'MELO3C010319.2' => 'cme', 'MELO3C011944.2' => 'cme', 'MELO3C021589.2' => 'cme', 'Migut.E00207' => 'egut', 'Migut.H00067' => 'egut', 'Migut.K00433' => 'egut', 'Migut.K00606' => 'egut', 'Migut.K01410' => 'egut', 'MSTRG.13347' => 'ama', 'MSTRG.24045' => 'ama', 'MSTRG.2428' => 'ama', 'MSTRG.26410' => 'ama', 'MSTRG.3139' => 'ama', 'MSTRG.3286' => 'ama', 'MSTRG.563' => 'ama', 'MSTRG.7941' => 'ama', 'Nitab4.5_0000028g0060' => 'nta', 'Nitab4.5_0000065g0260' => 'nta', 'Nitab4.5_0000112g0060' => 'nta', 'Nitab4.5_0000489g0120' => 'nta', 'Nitab4.5_0001776g0050' => 'nta', 'Nitab4.5_0001854g0010' => 'nta', 'Nitab4.5_0001860g0020' => 'nta', 'Nitab4.5_0004352g0010' => 'nta', 'Nitab4.5_0008716g0020' => 'nta', 'Nitab4.5_0008922g0010' => 'nta', 'Nn3g16693' => 'nnu', 'Nn4g22596' => 'nnu', 'Nn7g37639' => 'nnu', 'Oeu001701.1' => 'oeu', 'Oeu018149.1' => 'oeu', 'Oeu026220.1' => 'oeu', 'Oeu038635.1' => 'oeu', 'Oeu049176.1' => 'oeu', 'Oeu056706.1' => 'oeu', 'Oeu056937.1' => 'oeu', 'Oeu057540.1' => 'oeu', 'Os02g0594900' => 'osa', 'Os02g0595100' => 'osa', 'Os04g0477500' => 'osa', 'Os12g0611900' => 'osa', 'Peaxi162Scf00076g00020' => 'pax', 'Peaxi162Scf00128g00217' => 'pax', 'Peaxi162Scf00129g01640' => 'pax', 'Peaxi162Scf00669g00007' => 'pax', 'Peaxi162Scf00700g00421' => 'pax', 'Peaxi162Scf00801g00038' => 'pax', 'Peaxi162Scf00891g00025' => 'pax', 'PGR083G0909' => 'pgr', 'PGR119G1005' => 'pgr', 'PGR142G2236' => 'pgr', 'PGR142G3388' => 'pgr', 'PGSC0003DMG400004514' => 'stu', 'PGSC0003DMG400012635' => 'stu', 'PGSC0003DMG400015730' => 'stu', 'PGSC0003DMG400018611' => 'stu', 'PGSC0003DMG400030897' => 'stu', 'Phvul.001G254800' => 'pvu', 'Phvul.002G260100' => 'pvu', 'Phvul.003G167600' => 'pvu', 'Phvul.004G005100' => 'pvu', 'Potri.001G343600' => 'ptr', 'Potri.006G066700' => 'ptr', 'Potri.008G186000' => 'ptr', 'Potri.010G046900' => 'ptr', 'Potri.018G127900' => 'ptr', 'Pp3c20_17750' => 'ppa', 'Pp3c24_4380' => 'ppa', 'Prupe.1G245800' => 'ppe', 'Prupe.3G293400' => 'ppe', 'Prupe.7G247400' => 'ppe', 'Psat0s145g0120' => 'psa', 'Psat0s595g0040' => 'psa', 'Psat0s595g0120' => 'psa', 'Psat3g175040' => 'psa', 'Psat7g058120' => 'psa', 'PSO017G0428' => 'pso', 'PSO063G7510' => 'pso', 'PSO067G0046' => 'pso', 'PSO478G1073' => 'pso', 'PSO675G3677' => 'pso', 'PSO675G6558' => 'pso', 'PSO675G7520' => 'pso', 'PSO675G8959' => 'pso', 'QL02p074089' => 'qlo', 'QL02p089614' => 'qlo', 'QL03p057736' => 'qlo', 'RcHm_v2.0_Chr1g0364131' => 'rch', 'RcHm_v2.0_Chr2g0087801' => 'rch', 'RcHm_v2.0_Chr2g0087821' => 'rch', 'RcHm_v2.0_Chr2g0173231' => 'rch', 'RcHm_v2.0_Chr4g0433111' => 'rch', 'Rhsim03G0250300' => 'rsi', 'Rhsim08G0048400' => 'rsi', 'Rhsim10G0014800' => 'rsi', 'Rhsim12G0040100' => 'rsi', 'Rhsim12G0109700' => 'rsi', 'Sabra06G0049600' => 'sbr', 'Sabra08G0141000' => 'sbr', 'Sabra10G0021400' => 'sbr', 'Sabra16G0222900' => 'sbr', 'Sabra18G0108600' => 'sbr', 'SalBow1G0433' => 'sbo', 'SalBow1G2038' => 'sbo', 'SalBow1G5003' => 'sbo', 'SalBow7G1197' => 'sbo', 'SalBow8G3506' => 'sbo', 'Sc03g0007300' => 'sci', 'Sc11g0000950' => 'sci', 'Sc14g0008750' => 'sci', 'Sc18g0000420' => 'sci', 'Sed0006754' => 'sed', 'Sed0008741' => 'sed', 'Sed0017172' => 'sed', 'Sed0018925' => 'sed', 'Sed0023326' => 'sed', 'Sed0025909' => 'sed', 'SEGI_05333' => 'sgi', 'SEGI_10362' => 'sgi', 'SEGI_13380' => 'sgi', 'SEGI_24306' => 'sgi', 'SEGI_29077' => 'sgi', 'SEGI_29095' => 'sgi', 'SEGI_36534' => 'sgi', 'SEGI_37506' => 'sgi', 'SEGI_38321' => 'sgi', 'SGA_v2.0_scaffold307G48031' => 'sas', 'SGA_v2.0_scaffold47G17507' => 'sas', 'SGA_v2.0_scaffold63G21736' => 'sas', 'SGA_v2.0_scaffold87G27070' => 'sas', 'SHI17794' => 'shi', 'SHI28851' => 'shi', 'SMO165G0155' => 'smo', 'SMO340G0217' => 'smo', 'SMO367G1210' => 'smo', 'Solyc02g093430.3' => 'sly', 'Solyc05g013580.4' => 'sly', 'Solyc07g008030.3' => 'sly', 'Solyc12g035470.2' => 'sly', 'Sopen02g038020' => 'spe', 'Sopen05g008490' => 'spe', 'Sopen07g003910' => 'spe', 'Sopen12g015240' => 'spe', 'Sp1g11550' => 'spa', 'Sp2g16710' => 'spa', 'Sp3g00430' => 'spa', 'Sp3g26780' => 'spa', 'Sp5g22900' => 'spa', 'Sp6g29530' => 'spa', 'TAR371G0794' => 'tar', 'TAR374G0164' => 'tar', 'TAR622G0165' => 'tar', 'TAR626G0929' => 'tar', 'TAR629G2155' => 'tar', 'THA.LOC104805282' => 'tha', 'THA.LOC104805363' => 'tha', 'THA.LOC104808968' => 'tha', 'THA.LOC104821093' => 'tha', 'THA.LOC104823953' => 'tha', 'THA.LOC104825562' => 'tha', 'THA.LOC104825665' => 'tha', 'Thecc.02G261400' => 'tca', 'Thecc.04G019200' => 'tca', 'Thecc.09G130400' => 'tca', 'Thhalv10004374m.g' => 'esa', 'Thhalv10007850m.g' => 'esa', 'Thhalv10013782m.g' => 'esa', 'Thhalv10018686m.g' => 'esa', 'Thhalv10020899m.g' => 'esa', 'Thhalv10022755m.g' => 'esa', 'TPR.G23851' => 'tpr', 'TPR.G26500' => 'tpr', 'TPR.G27267' => 'tpr', 'TPR.G32001' => 'tpr', 'TPR.G6251' => 'tpr', 'TPR.G8167' => 'tpr', 'TWI12G1330' => 'twi', 'TWI18G1239' => 'twi', 'TWI34G0979' => 'twi', 'TWI36G0670' => 'twi', 'TWI36G0707' => 'twi', 'TWI56G0233' => 'twi', 'TWI75G1809' => 'twi', 'unitig_21.g20874' => 'ugi', 'unitig_26.g10343' => 'ugi', 'unitig_46.g18392' => 'ugi', 'unitig_52.g17178' => 'ugi', 'unitig_8.g2934' => 'ugi', 'vmacro01122' => 'vma', 'vmacro05875' => 'vma', 'vmacro06147' => 'vma', 'vmacro16191' => 'vma', 'vmacro18293' => 'vma', 'VMungo0251G3707' => 'vmu', 'VMungo0464G1521' => 'vmu', 'VMungo1215G0205' => 'vmu', 'VMungo1383G2484' => 'vmu', 'Zm00001eb079610' => 'zma', 'Zm00001eb135990' => 'zma', 'Zm00001eb183710' => 'zma', 'Zm00001eb246020' => 'zma' ), 'gf_id' => 'HOM05D001124', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001124' ), 'data_identifier' => 'HOM05D001124', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001124', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '548', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02520' => 'bna', 'A03p06630' => 'bna', 'A05p44460' => 'bna', 'A06p08710' => 'bna', 'A06p41090' => 'bna', 'A07p32320' => 'bna', 'A08p32520' => 'bna', 'A09p10360' => 'bna', 'A10p24080' => 'bna', 'Aa31LG11G15250' => 'aar', 'Aa31LG1G1800' => 'aar', 'Aa31LG2G5120' => 'aar', 'Aa31LG2G6070' => 'aar', 'Aa31LG5G10770' => 'aar', 'Aa31sc61G90' => 'aar', 'Actinidia01352' => 'ach', 'Actinidia05983' => 'ach', 'Actinidia08133' => 'ach', 'Actinidia15101' => 'ach', 'Actinidia26379' => 'ach', 'Actinidia35778' => 'ach', 'Actinidia36123' => 'ach', 'Actinidia37436' => 'ach', 'Actinidia38730' => 'ach', 'Ah.02g128210' => 'amhyb', 'Ah.03g132990' => 'amhyb', 'Ah.14g079410' => 'amhyb', 'AL1G24640' => 'aly', 'AL2G26680' => 'aly', 'AL3G10530' => 'aly', 'AL3G45230' => 'aly', 'AL5G15230' => 'aly', 'AL5G16960' => 'aly', 'AL6G25210' => 'aly', 'Aqoxy2G00441' => 'aox', 'Aqoxy3G01236' => 'aox', 'Aqoxy5G03746' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3RQ047' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C7GMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9C8JER' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MBL6KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YXCZ83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZANX40' => 'arhy', 'AT1G12990' => 'ath', 'AT1G67880' => 'ath', 'AT2G13290' => 'ath', 'AT3G01620' => 'ath', 'AT3G26445' => 'ath', 'AT3G27540' => 'ath', 'AT5G14480' => 'ath', 'ATR0824G026' => 'atr', 'ATR1098G019' => 'atr', 'Atru.chr11.2145' => 'acertr', 'Atru.chr2.3636' => 'acertr', 'Atru.chr2.3644' => 'acertr', 'Atru.chr6.2422' => 'acertr', 'Atru.chr7.1112' => 'acertr', 'AUR62005469' => 'cqu', 'AUR62011166' => 'cqu', 'AUR62013319' => 'cqu', 'AUR62024273' => 'cqu', 'AUR62028420' => 'cqu', 'AUR62041942' => 'cqu', 'BcaB01g04969' => 'bca', 'BcaB01g06371' => 'bca', 'BcaB02g11494' => 'bca', 'BcaB03g15382' => 'bca', 'BcaB08g36994' => 'bca', 'BcaC03g13477' => 'bca', 'BcaC03g13478' => 'bca', 'BcaC03g13480' => 'bca', 'BcaC03g13481' => 'bca', 'BcaC03g13486' => 'bca', 'BcaC04g19031' => 'bca', 'BcaC04g23085' => 'bca', 'BcaC05g25094' => 'bca', 'BcaC05g25096' => 'bca', 'BcaC05g25138' => 'bca', 'BcaC05g30416' => 'bca', 'BcaC05g30455' => 'bca', 'BcaC06g30979' => 'bca', 'BcaC06g33805' => 'bca', 'BcaC08g46021' => 'bca', 'BcaNung03154' => 'bca', 'BolC2t06623H' => 'bol', 'BolC2t06632H' => 'bol', 'BolC2t06635H' => 'bol', 'BolC2t06638H' => 'bol', 'BolC3t13266H' => 'bol', 'BolC5t29776H' => 'bol', 'BolC6t38912H' => 'bol', 'BolC7t44183H' => 'bol', 'BolC9t54123H' => 'bol', 'BolC9t59107H' => 'bol', 'BraA02t05221Z' => 'bra', 'BraA03t09996Z' => 'bra', 'BraA05t23210Z' => 'bra', 'BraA06t24068Z' => 'bra', 'BraA06t27032Z' => 'bra', 'BraA08t35176Z' => 'bra', 'BraA09t36680Z' => 'bra', 'BraA10t44471Z' => 'bra', 'C02p06760' => 'bna', 'C02p06890' => 'bna', 'C02p07010' => 'bna', 'C03p07660' => 'bna', 'C05p10300' => 'bna', 'C06p38150' => 'bna', 'C07p36650' => 'bna', 'C08p15770' => 'bna', 'C09p12300' => 'bna', 'C09p62700' => 'bna', 'C09p75040' => 'bna', 'CAN.G13.1' => 'can', 'CAN.G138.4' => 'can', 'CAN.G44.6' => 'can', 'CAN.G473.19' => 'can', 'CANSAT01G0835' => 'cansat', 'CANSAT11G0246' => 'cansat', 'CANSAT11G1766' => 'cansat', 'CANSAT64G1954' => 'cansat', 'CARHR013330' => 'chi', 'CARHR060530' => 'chi', 'CARHR075300' => 'chi', 'CARHR105120' => 'chi', 'CARHR148910' => 'chi', 'CARHR198830' => 'chi', 'Carub.0001s1275' => 'cru', 'Carub.0002s1437' => 'cru', 'Carub.0003s0044' => 'cru', 'Carub.0003s2787' => 'cru', 'Carub.0005s0597' => 'cru', 'Carub.0006s1266' => 'cru', 'Ca_06935_v3' => 'car', 'Ca_13559_v3' => 'car', 'Ca_16941_v3' => 'car', 'Ca_16960_v3' => 'car', 'Ca_17775_v3' => 'car', 'Ca_30464_v3' => 'car', 'Cc06_g08160' => 'ccan', 'Cc07_g01520' => 'ccan', 'Cc11_g15810' => 'ccan', 'CDE02G2840' => 'cde', 'CDE03G0093' => 'cde', 'CDE04G2127' => 'cde', 'CDE07G1857' => 'cde', 'CDE09G1246' => 'cde', 'Cfa003412' => 'cfa', 'Cfa007341' => 'cfa', 'Cfa009220' => 'cfa', 'Ciclev10008737m.g' => 'ccl', 'Ciclev10015565m.g' => 'ccl', 'Ciclev10031761m.g' => 'ccl', 'CiPaw.03G045300' => 'cil', 'CiPaw.03G247200' => 'cil', 'CiPaw.04G029500' => 'cil', 'CiPaw.04G174000' => 'cil', 'CiPaw.05G181200' => 'cil', 'CiPaw.06G067100' => 'cil', 'ClCG05G025800' => 'cla', 'ClCG06G011400' => 'cla', 'ClCG09G019360' => 'cla', 'COL.COLO4_04827' => 'col', 'COL.COLO4_29170' => 'col', 'COL.COLO4_35131' => 'col', 'COL.COLO4_35132' => 'col', 'Cpa.g.sc33.32' => 'cpa', 'Cpa.g.sc46.29' => 'cpa', 'Cpa.g.sc796.1' => 'cpa', 'CsaV3_1G030420' => 'csa', 'CsaV3_5G027050' => 'csa', 'CsaV3_5G031040' => 'csa', 'CsaV3_UNG023130' => 'csa', 'CSS0007726' => 'camsi', 'CSS0016433' => 'camsi', 'CSS0017656' => 'camsi', 'CSS0025364' => 'camsi', 'CSS0027582' => 'camsi', 'CSS0047288' => 'camsi', 'CSS0049950' => 'camsi', 'DCAR_003843' => 'dca', 'DCAR_007052' => 'dca', 'DCAR_020884' => 'dca', 'DCAR_021730' => 'dca', 'DCAR_024423' => 'dca', 'DCAR_026509' => 'dca', 'DCAR_031158' => 'dca', 'Dinv14728' => 'din', 'Dinv15219' => 'din', 'Dinv25728' => 'din', 'Dinv33428' => 'din', 'Dinv36489' => 'din', 'Dinv41486' => 'din', 'Duzib147G0469' => 'dzi', 'Duzib168G0060' => 'dzi', 'Duzib187G1215' => 'dzi', 'Duzib248G0692' => 'dzi', 'Duzib251G0767' => 'dzi', 'Duzib264G0446' => 'dzi', 'Duzib268G0691' => 'dzi', 'ECA232G4767' => 'eca', 'ECA233G2838' => 'eca', 'ECA234G0391' => 'eca', 'ECA234G0857' => 'eca', 'ECA236G1593' => 'eca', 'ECA238G0565' => 'eca', 'ECA246G1027' => 'eca', 'ECA246G3223' => 'eca', 'ECA246G3470' => 'eca', 'EL10Ac6g13829' => 'bvu', 'EL10Ac6g14093' => 'bvu', 'EL10Ac8g18707' => 'bvu', 'Eucgr.C01369' => 'egr', 'Eucgr.H02492' => 'egr', 'Eucgr.I01733' => 'egr', 'Eucgr.J02255' => 'egr', 'Eucgr.J02257' => 'egr', 'Eucgr.J02258' => 'egr', 'FAN02G1601' => 'fan', 'FAN03G1586' => 'fan', 'FAN03G2986' => 'fan', 'FAN05G4837' => 'fan', 'FAN06G0146' => 'fan', 'FAN07G0858' => 'fan', 'FAN09G3179' => 'fan', 'FAN10G0669' => 'fan', 'FAN12G2358' => 'fan', 'FAN14G4198' => 'fan', 'FAN14G5112' => 'fan', 'FAN17G0342' => 'fan', 'FAN19G0342' => 'fan', 'FAN19G0962' => 'fan', 'FAN19G1101' => 'fan', 'FAN19G1872' => 'fan', 'FAN22G0356' => 'fan', 'FAN23G0744' => 'fan', 'FAN23G1914' => 'fan', 'FAN26G0032' => 'fan', 'FAN28G0625' => 'fan', 'FvH4_1g02710' => 'fve', 'FvH4_1g02720' => 'fve', 'FvH4_4g25670' => 'fve', 'FvH4_6g51700' => 'fve', 'FvH4_7g20170' => 'fve', 'Glyma.05G175000' => 'gma', 'Glyma.08G132300' => 'gma', 'Glyma.11G243000' => 'gma', 'Glyma.13G158900' => 'gma', 'Glyma.17G112400' => 'gma', 'Glyma.18G014100' => 'gma', 'Glyma.19G003100' => 'gma', 'Glyma.19G056500' => 'gma', 'Gohir.A01G158900' => 'ghi', 'Gohir.A05G312600' => 'ghi', 'Gohir.A05G354900' => 'ghi', 'Gohir.A07G037200' => 'ghi', 'Gohir.A09G030000' => 'ghi', 'Gohir.A12G145200' => 'ghi', 'Gohir.D01G151500' => 'ghi', 'Gohir.D04G058300' => 'ghi', 'Gohir.D05G314100' => 'ghi', 'Gohir.D07G041400' => 'ghi', 'Gohir.D09G029700' => 'ghi', 'Gohir.D12G149700' => 'ghi', 'Gorai.001G043800' => 'gra', 'Gorai.002G187800' => 'gra', 'Gorai.006G034700' => 'gra', 'Gorai.008G161200' => 'gra', 'Gorai.009G335700' => 'gra', 'Gorai.012G065000' => 'gra', 'GSVIVG01000535001' => 'vvi', 'GSVIVG01015572001' => 'vvi', 'GSVIVG01032386001' => 'vvi', 'HanXRQChr05g0138531' => 'han', 'HanXRQChr06g0174391' => 'han', 'HanXRQChr07g0199021' => 'han', 'HanXRQChr08g0208211' => 'han', 'HanXRQChr09g0255471' => 'han', 'HanXRQChr10g0315791' => 'han', 'HanXRQChr12g0371991' => 'han', 'HanXRQChr15g0475251' => 'han', 'HanXRQChr17g0540001' => 'han', 'HanXRQChr17g0548631' => 'han', 'HanXRQChr17g0569561' => 'han', 'Haze_12256' => 'cav', 'Haze_14756' => 'cav', 'Haze_25528' => 'cav', 'Hma1.2p1_0079F.1_g041020' => 'hma', 'Hma1.2p1_0818F.1_g223260' => 'hma', 'Hma1.2p1_1747F.1_g300530' => 'hma', 'HPP92_004607' => 'vpl', 'HPP92_004608' => 'vpl', 'HPP92_006181' => 'vpl', 'HPP92_012192' => 'vpl', 'HPP92_015680' => 'vpl', 'HPP92_020249' => 'vpl', 'HPP92_021376' => 'vpl', 'HPP92_024275' => 'vpl', 'Hund06031' => 'sun', 'Hund25391' => 'sun', 'Lalb_Chr07g0185371' => 'lal', 'Lalb_Chr07g0185381' => 'lal', 'Lalb_Chr12g0204011' => 'lal', 'Lalb_Chr13g0301671' => 'lal', 'Lalb_Chr14g0362851' => 'lal', 'Lalb_Chr24g0403581' => 'lal', 'Lj1g0000233' => 'lja', 'Lj2g0018120' => 'lja', 'Lj3C621T0' => 'lonja', 'Lj3P1059T14' => 'lonja', 'Lj3P611T9' => 'lonja', 'Lj3P614T13' => 'lonja', 'Lj3P615T5' => 'lonja', 'Lj4g0012315' => 'lja', 'Lj4g0026182' => 'lja', 'Lj6P813T16' => 'lonja', 'Lj7C427T7' => 'lonja', 'Lj7C427T8' => 'lonja', 'Lj7P600T41' => 'lonja', 'Lju41C42G17' => 'lonja', 'Lsat_1_v5_gn_0_47300' => 'lsa', 'Lsat_1_v5_gn_2_91280' => 'lsa', 'Lsat_1_v5_gn_3_30561' => 'lsa', 'Lsat_1_v5_gn_4_184321' => 'lsa', 'Lsat_1_v5_gn_4_4041' => 'lsa', 'Lsat_1_v5_gn_5_92000' => 'lsa', 'Lsat_1_v5_gn_8_152940' => 'lsa', 'Lsat_1_v5_gn_8_62401' => 'lsa', 'Manes.06G055900' => 'mes', 'Manes.12G022200' => 'mes', 'Manes.13G023300' => 'mes', 'Manes.14G115000' => 'mes', 'Manes.15G151700' => 'mes', 'Manes.17G111300' => 'mes', 'Mapoly0226s0009' => 'mpo', 'MBI02_g25363_MAGBIO' => 'mbi', 'MBI06_g00027_MAGBIO' => 'mbi', 'MBI10_g13034_MAGBIO' => 'mbi', 'MD09G1023400' => 'mdo', 'MD13G1100100' => 'mdo', 'MD15G1169200' => 'mdo', 'MD16G1101100' => 'mdo', 'MD17G1022900' => 'mdo', 'Medtr3g096150' => 'mtr', 'Medtr4g115070' => 'mtr', 'Medtr7g033325' => 'mtr', 'Medtr8g089840' => 'mtr', 'MELO3C010319.2' => 'cme', 'MELO3C011944.2' => 'cme', 'MELO3C021589.2' => 'cme', 'Migut.E00207' => 'egut', 'Migut.H00067' => 'egut', 'Migut.K00433' => 'egut', 'Migut.K00606' => 'egut', 'Migut.K01410' => 'egut', 'MSTRG.13347' => 'ama', 'MSTRG.24045' => 'ama', 'MSTRG.2428' => 'ama', 'MSTRG.26410' => 'ama', 'MSTRG.3139' => 'ama', 'MSTRG.3286' => 'ama', 'MSTRG.563' => 'ama', 'MSTRG.7941' => 'ama', 'Nitab4.5_0000028g0060' => 'nta', 'Nitab4.5_0000065g0260' => 'nta', 'Nitab4.5_0000112g0060' => 'nta', 'Nitab4.5_0000489g0120' => 'nta', 'Nitab4.5_0001776g0050' => 'nta', 'Nitab4.5_0001854g0010' => 'nta', 'Nitab4.5_0001860g0020' => 'nta', 'Nitab4.5_0004352g0010' => 'nta', 'Nitab4.5_0008716g0020' => 'nta', 'Nitab4.5_0008922g0010' => 'nta', 'Nn3g16693' => 'nnu', 'Nn4g22596' => 'nnu', 'Nn7g37639' => 'nnu', 'Oeu001701.1' => 'oeu', 'Oeu018149.1' => 'oeu', 'Oeu026220.1' => 'oeu', 'Oeu038635.1' => 'oeu', 'Oeu049176.1' => 'oeu', 'Oeu056706.1' => 'oeu', 'Oeu056937.1' => 'oeu', 'Oeu057540.1' => 'oeu', 'Os02g0594900' => 'osa', 'Os02g0595100' => 'osa', 'Os04g0477500' => 'osa', 'Os12g0611900' => 'osa', 'Peaxi162Scf00076g00020' => 'pax', 'Peaxi162Scf00128g00217' => 'pax', 'Peaxi162Scf00129g01640' => 'pax', 'Peaxi162Scf00669g00007' => 'pax', 'Peaxi162Scf00700g00421' => 'pax', 'Peaxi162Scf00801g00038' => 'pax', 'Peaxi162Scf00891g00025' => 'pax', 'PGR083G0909' => 'pgr', 'PGR119G1005' => 'pgr', 'PGR142G2236' => 'pgr', 'PGR142G3388' => 'pgr', 'PGSC0003DMG400004514' => 'stu', 'PGSC0003DMG400012635' => 'stu', 'PGSC0003DMG400015730' => 'stu', 'PGSC0003DMG400018611' => 'stu', 'PGSC0003DMG400030897' => 'stu', 'Phvul.001G254800' => 'pvu', 'Phvul.002G260100' => 'pvu', 'Phvul.003G167600' => 'pvu', 'Phvul.004G005100' => 'pvu', 'Potri.001G343600' => 'ptr', 'Potri.006G066700' => 'ptr', 'Potri.008G186000' => 'ptr', 'Potri.010G046900' => 'ptr', 'Potri.018G127900' => 'ptr', 'Pp3c20_17750' => 'ppa', 'Pp3c24_4380' => 'ppa', 'Prupe.1G245800' => 'ppe', 'Prupe.3G293400' => 'ppe', 'Prupe.7G247400' => 'ppe', 'Psat0s145g0120' => 'psa', 'Psat0s595g0040' => 'psa', 'Psat0s595g0120' => 'psa', 'Psat3g175040' => 'psa', 'Psat7g058120' => 'psa', 'PSO017G0428' => 'pso', 'PSO063G7510' => 'pso', 'PSO067G0046' => 'pso', 'PSO478G1073' => 'pso', 'PSO675G3677' => 'pso', 'PSO675G6558' => 'pso', 'PSO675G7520' => 'pso', 'PSO675G8959' => 'pso', 'QL02p074089' => 'qlo', 'QL02p089614' => 'qlo', 'QL03p057736' => 'qlo', 'RcHm_v2.0_Chr1g0364131' => 'rch', 'RcHm_v2.0_Chr2g0087801' => 'rch', 'RcHm_v2.0_Chr2g0087821' => 'rch', 'RcHm_v2.0_Chr2g0173231' => 'rch', 'RcHm_v2.0_Chr4g0433111' => 'rch', 'Rhsim03G0250300' => 'rsi', 'Rhsim08G0048400' => 'rsi', 'Rhsim10G0014800' => 'rsi', 'Rhsim12G0040100' => 'rsi', 'Rhsim12G0109700' => 'rsi', 'Sabra06G0049600' => 'sbr', 'Sabra08G0141000' => 'sbr', 'Sabra10G0021400' => 'sbr', 'Sabra16G0222900' => 'sbr', 'Sabra18G0108600' => 'sbr', 'SalBow1G0433' => 'sbo', 'SalBow1G2038' => 'sbo', 'SalBow1G5003' => 'sbo', 'SalBow7G1197' => 'sbo', 'SalBow8G3506' => 'sbo', 'Sc03g0007300' => 'sci', 'Sc11g0000950' => 'sci', 'Sc14g0008750' => 'sci', 'Sc18g0000420' => 'sci', 'Sed0006754' => 'sed', 'Sed0008741' => 'sed', 'Sed0017172' => 'sed', 'Sed0018925' => 'sed', 'Sed0023326' => 'sed', 'Sed0025909' => 'sed', 'SEGI_05333' => 'sgi', 'SEGI_10362' => 'sgi', 'SEGI_13380' => 'sgi', 'SEGI_24306' => 'sgi', 'SEGI_29077' => 'sgi', 'SEGI_29095' => 'sgi', 'SEGI_36534' => 'sgi', 'SEGI_37506' => 'sgi', 'SEGI_38321' => 'sgi', 'SGA_v2.0_scaffold307G48031' => 'sas', 'SGA_v2.0_scaffold47G17507' => 'sas', 'SGA_v2.0_scaffold63G21736' => 'sas', 'SGA_v2.0_scaffold87G27070' => 'sas', 'SHI17794' => 'shi', 'SHI28851' => 'shi', 'SMO165G0155' => 'smo', 'SMO340G0217' => 'smo', 'SMO367G1210' => 'smo', 'Solyc02g093430.3' => 'sly', 'Solyc05g013580.4' => 'sly', 'Solyc07g008030.3' => 'sly', 'Solyc12g035470.2' => 'sly', 'Sopen02g038020' => 'spe', 'Sopen05g008490' => 'spe', 'Sopen07g003910' => 'spe', 'Sopen12g015240' => 'spe', 'Sp1g11550' => 'spa', 'Sp2g16710' => 'spa', 'Sp3g00430' => 'spa', 'Sp3g26780' => 'spa', 'Sp5g22900' => 'spa', 'Sp6g29530' => 'spa', 'TAR371G0794' => 'tar', 'TAR374G0164' => 'tar', 'TAR622G0165' => 'tar', 'TAR626G0929' => 'tar', 'TAR629G2155' => 'tar', 'THA.LOC104805282' => 'tha', 'THA.LOC104805363' => 'tha', 'THA.LOC104808968' => 'tha', 'THA.LOC104821093' => 'tha', 'THA.LOC104823953' => 'tha', 'THA.LOC104825562' => 'tha', 'THA.LOC104825665' => 'tha', 'Thecc.02G261400' => 'tca', 'Thecc.04G019200' => 'tca', 'Thecc.09G130400' => 'tca', 'Thhalv10004374m.g' => 'esa', 'Thhalv10007850m.g' => 'esa', 'Thhalv10013782m.g' => 'esa', 'Thhalv10018686m.g' => 'esa', 'Thhalv10020899m.g' => 'esa', 'Thhalv10022755m.g' => 'esa', 'TPR.G23851' => 'tpr', 'TPR.G26500' => 'tpr', 'TPR.G27267' => 'tpr', 'TPR.G32001' => 'tpr', 'TPR.G6251' => 'tpr', 'TPR.G8167' => 'tpr', 'TWI12G1330' => 'twi', 'TWI18G1239' => 'twi', 'TWI34G0979' => 'twi', 'TWI36G0670' => 'twi', 'TWI36G0707' => 'twi', 'TWI56G0233' => 'twi', 'TWI75G1809' => 'twi', 'unitig_21.g20874' => 'ugi', 'unitig_26.g10343' => 'ugi', 'unitig_46.g18392' => 'ugi', 'unitig_52.g17178' => 'ugi', 'unitig_8.g2934' => 'ugi', 'vmacro01122' => 'vma', 'vmacro05875' => 'vma', 'vmacro06147' => 'vma', 'vmacro16191' => 'vma', 'vmacro18293' => 'vma', 'VMungo0251G3707' => 'vmu', 'VMungo0464G1521' => 'vmu', 'VMungo1215G0205' => 'vmu', 'VMungo1383G2484' => 'vmu', 'Zm00001eb079610' => 'zma', 'Zm00001eb135990' => 'zma', 'Zm00001eb183710' => 'zma', 'Zm00001eb246020' => 'zma' ) $gf_id = 'HOM05D001124' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001124' ) $data_identifier = 'HOM05D001124' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 6, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 7, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 21, 'bol' => (int) 10, 'bra' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 6, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 9, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 21, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 8, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 10, 'lsa' => (int) 8, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 8, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 9, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb246020' $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' => 'HOM05D001124', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '548', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02520' => 'bna', 'A03p06630' => 'bna', 'A05p44460' => 'bna', 'A06p08710' => 'bna', 'A06p41090' => 'bna', 'A07p32320' => 'bna', 'A08p32520' => 'bna', 'A09p10360' => 'bna', 'A10p24080' => 'bna', 'Aa31LG11G15250' => 'aar', 'Aa31LG1G1800' => 'aar', 'Aa31LG2G5120' => 'aar', 'Aa31LG2G6070' => 'aar', 'Aa31LG5G10770' => 'aar', 'Aa31sc61G90' => 'aar', 'Actinidia01352' => 'ach', 'Actinidia05983' => 'ach', 'Actinidia08133' => 'ach', 'Actinidia15101' => 'ach', 'Actinidia26379' => 'ach', 'Actinidia35778' => 'ach', 'Actinidia36123' => 'ach', 'Actinidia37436' => 'ach', 'Actinidia38730' => 'ach', 'Ah.02g128210' => 'amhyb', 'Ah.03g132990' => 'amhyb', 'Ah.14g079410' => 'amhyb', 'AL1G24640' => 'aly', 'AL2G26680' => 'aly', 'AL3G10530' => 'aly', 'AL3G45230' => 'aly', 'AL5G15230' => 'aly', 'AL5G16960' => 'aly', 'AL6G25210' => 'aly', 'Aqoxy2G00441' => 'aox', 'Aqoxy3G01236' => 'aox', 'Aqoxy5G03746' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3RQ047' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C7GMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9C8JER' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MBL6KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YXCZ83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZANX40' => 'arhy', 'AT1G12990' => 'ath', 'AT1G67880' => 'ath', 'AT2G13290' => 'ath', 'AT3G01620' => 'ath', 'AT3G26445' => 'ath', 'AT3G27540' => 'ath', 'AT5G14480' => 'ath', 'ATR0824G026' => 'atr', 'ATR1098G019' => 'atr', 'Atru.chr11.2145' => 'acertr', 'Atru.chr2.3636' => 'acertr', 'Atru.chr2.3644' => 'acertr', 'Atru.chr6.2422' => 'acertr', 'Atru.chr7.1112' => 'acertr', 'AUR62005469' => 'cqu', 'AUR62011166' => 'cqu', 'AUR62013319' => 'cqu', 'AUR62024273' => 'cqu', 'AUR62028420' => 'cqu', 'AUR62041942' => 'cqu', 'BcaB01g04969' => 'bca', 'BcaB01g06371' => 'bca', 'BcaB02g11494' => 'bca', 'BcaB03g15382' => 'bca', 'BcaB08g36994' => 'bca', 'BcaC03g13477' => 'bca', 'BcaC03g13478' => 'bca', 'BcaC03g13480' => 'bca', 'BcaC03g13481' => 'bca', 'BcaC03g13486' => 'bca', 'BcaC04g19031' => 'bca', 'BcaC04g23085' => 'bca', 'BcaC05g25094' => 'bca', 'BcaC05g25096' => 'bca', 'BcaC05g25138' => 'bca', 'BcaC05g30416' => 'bca', 'BcaC05g30455' => 'bca', 'BcaC06g30979' => 'bca', 'BcaC06g33805' => 'bca', 'BcaC08g46021' => 'bca', 'BcaNung03154' => 'bca', 'BolC2t06623H' => 'bol', 'BolC2t06632H' => 'bol', 'BolC2t06635H' => 'bol', 'BolC2t06638H' => 'bol', 'BolC3t13266H' => 'bol', 'BolC5t29776H' => 'bol', 'BolC6t38912H' => 'bol', 'BolC7t44183H' => 'bol', 'BolC9t54123H' => 'bol', 'BolC9t59107H' => 'bol', 'BraA02t05221Z' => 'bra', 'BraA03t09996Z' => 'bra', 'BraA05t23210Z' => 'bra', 'BraA06t24068Z' => 'bra', 'BraA06t27032Z' => 'bra', 'BraA08t35176Z' => 'bra', 'BraA09t36680Z' => 'bra', 'BraA10t44471Z' => 'bra', 'C02p06760' => 'bna', 'C02p06890' => 'bna', 'C02p07010' => 'bna', 'C03p07660' => 'bna', 'C05p10300' => 'bna', 'C06p38150' => 'bna', 'C07p36650' => 'bna', 'C08p15770' => 'bna', 'C09p12300' => 'bna', 'C09p62700' => 'bna', 'C09p75040' => 'bna', 'CAN.G13.1' => 'can', 'CAN.G138.4' => 'can', 'CAN.G44.6' => 'can', 'CAN.G473.19' => 'can', 'CANSAT01G0835' => 'cansat', 'CANSAT11G0246' => 'cansat', 'CANSAT11G1766' => 'cansat', 'CANSAT64G1954' => 'cansat', 'CARHR013330' => 'chi', 'CARHR060530' => 'chi', 'CARHR075300' => 'chi', 'CARHR105120' => 'chi', 'CARHR148910' => 'chi', 'CARHR198830' => 'chi', 'Carub.0001s1275' => 'cru', 'Carub.0002s1437' => 'cru', 'Carub.0003s0044' => 'cru', 'Carub.0003s2787' => 'cru', 'Carub.0005s0597' => 'cru', 'Carub.0006s1266' => 'cru', 'Ca_06935_v3' => 'car', 'Ca_13559_v3' => 'car', 'Ca_16941_v3' => 'car', 'Ca_16960_v3' => 'car', 'Ca_17775_v3' => 'car', 'Ca_30464_v3' => 'car', 'Cc06_g08160' => 'ccan', 'Cc07_g01520' => 'ccan', 'Cc11_g15810' => 'ccan', 'CDE02G2840' => 'cde', 'CDE03G0093' => 'cde', 'CDE04G2127' => 'cde', 'CDE07G1857' => 'cde', 'CDE09G1246' => 'cde', 'Cfa003412' => 'cfa', 'Cfa007341' => 'cfa', 'Cfa009220' => 'cfa', 'Ciclev10008737m.g' => 'ccl', 'Ciclev10015565m.g' => 'ccl', 'Ciclev10031761m.g' => 'ccl', 'CiPaw.03G045300' => 'cil', 'CiPaw.03G247200' => 'cil', 'CiPaw.04G029500' => 'cil', 'CiPaw.04G174000' => 'cil', 'CiPaw.05G181200' => 'cil', 'CiPaw.06G067100' => 'cil', 'ClCG05G025800' => 'cla', 'ClCG06G011400' => 'cla', 'ClCG09G019360' => 'cla', 'COL.COLO4_04827' => 'col', 'COL.COLO4_29170' => 'col', 'COL.COLO4_35131' => 'col', 'COL.COLO4_35132' => 'col', 'Cpa.g.sc33.32' => 'cpa', 'Cpa.g.sc46.29' => 'cpa', 'Cpa.g.sc796.1' => 'cpa', 'CsaV3_1G030420' => 'csa', 'CsaV3_5G027050' => 'csa', 'CsaV3_5G031040' => 'csa', 'CsaV3_UNG023130' => 'csa', 'CSS0007726' => 'camsi', 'CSS0016433' => 'camsi', 'CSS0017656' => 'camsi', 'CSS0025364' => 'camsi', 'CSS0027582' => 'camsi', 'CSS0047288' => 'camsi', 'CSS0049950' => 'camsi', 'DCAR_003843' => 'dca', 'DCAR_007052' => 'dca', 'DCAR_020884' => 'dca', 'DCAR_021730' => 'dca', 'DCAR_024423' => 'dca', 'DCAR_026509' => 'dca', 'DCAR_031158' => 'dca', 'Dinv14728' => 'din', 'Dinv15219' => 'din', 'Dinv25728' => 'din', 'Dinv33428' => 'din', 'Dinv36489' => 'din', 'Dinv41486' => 'din', 'Duzib147G0469' => 'dzi', 'Duzib168G0060' => 'dzi', 'Duzib187G1215' => 'dzi', 'Duzib248G0692' => 'dzi', 'Duzib251G0767' => 'dzi', 'Duzib264G0446' => 'dzi', 'Duzib268G0691' => 'dzi', 'ECA232G4767' => 'eca', 'ECA233G2838' => 'eca', 'ECA234G0391' => 'eca', 'ECA234G0857' => 'eca', 'ECA236G1593' => 'eca', 'ECA238G0565' => 'eca', 'ECA246G1027' => 'eca', 'ECA246G3223' => 'eca', 'ECA246G3470' => 'eca', 'EL10Ac6g13829' => 'bvu', 'EL10Ac6g14093' => 'bvu', 'EL10Ac8g18707' => 'bvu', 'Eucgr.C01369' => 'egr', 'Eucgr.H02492' => 'egr', 'Eucgr.I01733' => 'egr', 'Eucgr.J02255' => 'egr', 'Eucgr.J02257' => 'egr', 'Eucgr.J02258' => 'egr', 'FAN02G1601' => 'fan', 'FAN03G1586' => 'fan', 'FAN03G2986' => 'fan', 'FAN05G4837' => 'fan', 'FAN06G0146' => 'fan', 'FAN07G0858' => 'fan', 'FAN09G3179' => 'fan', 'FAN10G0669' => 'fan', 'FAN12G2358' => 'fan', 'FAN14G4198' => 'fan', 'FAN14G5112' => 'fan', 'FAN17G0342' => 'fan', 'FAN19G0342' => 'fan', 'FAN19G0962' => 'fan', 'FAN19G1101' => 'fan', 'FAN19G1872' => 'fan', 'FAN22G0356' => 'fan', 'FAN23G0744' => 'fan', 'FAN23G1914' => 'fan', 'FAN26G0032' => 'fan', 'FAN28G0625' => 'fan', 'FvH4_1g02710' => 'fve', 'FvH4_1g02720' => 'fve', 'FvH4_4g25670' => 'fve', 'FvH4_6g51700' => 'fve', 'FvH4_7g20170' => 'fve', 'Glyma.05G175000' => 'gma', 'Glyma.08G132300' => 'gma', 'Glyma.11G243000' => 'gma', 'Glyma.13G158900' => 'gma', 'Glyma.17G112400' => 'gma', 'Glyma.18G014100' => 'gma', 'Glyma.19G003100' => 'gma', 'Glyma.19G056500' => 'gma', 'Gohir.A01G158900' => 'ghi', 'Gohir.A05G312600' => 'ghi', 'Gohir.A05G354900' => 'ghi', 'Gohir.A07G037200' => 'ghi', 'Gohir.A09G030000' => 'ghi', 'Gohir.A12G145200' => 'ghi', 'Gohir.D01G151500' => 'ghi', 'Gohir.D04G058300' => 'ghi', 'Gohir.D05G314100' => 'ghi', 'Gohir.D07G041400' => 'ghi', 'Gohir.D09G029700' => 'ghi', 'Gohir.D12G149700' => 'ghi', 'Gorai.001G043800' => 'gra', 'Gorai.002G187800' => 'gra', 'Gorai.006G034700' => 'gra', 'Gorai.008G161200' => 'gra', 'Gorai.009G335700' => 'gra', 'Gorai.012G065000' => 'gra', 'GSVIVG01000535001' => 'vvi', 'GSVIVG01015572001' => 'vvi', 'GSVIVG01032386001' => 'vvi', 'HanXRQChr05g0138531' => 'han', 'HanXRQChr06g0174391' => 'han', 'HanXRQChr07g0199021' => 'han', 'HanXRQChr08g0208211' => 'han', 'HanXRQChr09g0255471' => 'han', 'HanXRQChr10g0315791' => 'han', 'HanXRQChr12g0371991' => 'han', 'HanXRQChr15g0475251' => 'han', 'HanXRQChr17g0540001' => 'han', 'HanXRQChr17g0548631' => 'han', 'HanXRQChr17g0569561' => 'han', 'Haze_12256' => 'cav', 'Haze_14756' => 'cav', 'Haze_25528' => 'cav', 'Hma1.2p1_0079F.1_g041020' => 'hma', 'Hma1.2p1_0818F.1_g223260' => 'hma', 'Hma1.2p1_1747F.1_g300530' => 'hma', 'HPP92_004607' => 'vpl', 'HPP92_004608' => 'vpl', 'HPP92_006181' => 'vpl', 'HPP92_012192' => 'vpl', 'HPP92_015680' => 'vpl', 'HPP92_020249' => 'vpl', 'HPP92_021376' => 'vpl', 'HPP92_024275' => 'vpl', 'Hund06031' => 'sun', 'Hund25391' => 'sun', 'Lalb_Chr07g0185371' => 'lal', 'Lalb_Chr07g0185381' => 'lal', 'Lalb_Chr12g0204011' => 'lal', 'Lalb_Chr13g0301671' => 'lal', 'Lalb_Chr14g0362851' => 'lal', 'Lalb_Chr24g0403581' => 'lal', 'Lj1g0000233' => 'lja', 'Lj2g0018120' => 'lja', 'Lj3C621T0' => 'lonja', 'Lj3P1059T14' => 'lonja', 'Lj3P611T9' => 'lonja', 'Lj3P614T13' => 'lonja', 'Lj3P615T5' => 'lonja', 'Lj4g0012315' => 'lja', 'Lj4g0026182' => 'lja', 'Lj6P813T16' => 'lonja', 'Lj7C427T7' => 'lonja', 'Lj7C427T8' => 'lonja', 'Lj7P600T41' => 'lonja', 'Lju41C42G17' => 'lonja', 'Lsat_1_v5_gn_0_47300' => 'lsa', 'Lsat_1_v5_gn_2_91280' => 'lsa', 'Lsat_1_v5_gn_3_30561' => 'lsa', 'Lsat_1_v5_gn_4_184321' => 'lsa', 'Lsat_1_v5_gn_4_4041' => 'lsa', 'Lsat_1_v5_gn_5_92000' => 'lsa', 'Lsat_1_v5_gn_8_152940' => 'lsa', 'Lsat_1_v5_gn_8_62401' => 'lsa', 'Manes.06G055900' => 'mes', 'Manes.12G022200' => 'mes', 'Manes.13G023300' => 'mes', 'Manes.14G115000' => 'mes', 'Manes.15G151700' => 'mes', 'Manes.17G111300' => 'mes', 'Mapoly0226s0009' => 'mpo', 'MBI02_g25363_MAGBIO' => 'mbi', 'MBI06_g00027_MAGBIO' => 'mbi', 'MBI10_g13034_MAGBIO' => 'mbi', 'MD09G1023400' => 'mdo', 'MD13G1100100' => 'mdo', 'MD15G1169200' => 'mdo', 'MD16G1101100' => 'mdo', 'MD17G1022900' => 'mdo', 'Medtr3g096150' => 'mtr', 'Medtr4g115070' => 'mtr', 'Medtr7g033325' => 'mtr', 'Medtr8g089840' => 'mtr', 'MELO3C010319.2' => 'cme', 'MELO3C011944.2' => 'cme', 'MELO3C021589.2' => 'cme', 'Migut.E00207' => 'egut', 'Migut.H00067' => 'egut', 'Migut.K00433' => 'egut', 'Migut.K00606' => 'egut', 'Migut.K01410' => 'egut', 'MSTRG.13347' => 'ama', 'MSTRG.24045' => 'ama', 'MSTRG.2428' => 'ama', 'MSTRG.26410' => 'ama', 'MSTRG.3139' => 'ama', 'MSTRG.3286' => 'ama', 'MSTRG.563' => 'ama', 'MSTRG.7941' => 'ama', 'Nitab4.5_0000028g0060' => 'nta', 'Nitab4.5_0000065g0260' => 'nta', 'Nitab4.5_0000112g0060' => 'nta', 'Nitab4.5_0000489g0120' => 'nta', 'Nitab4.5_0001776g0050' => 'nta', 'Nitab4.5_0001854g0010' => 'nta', 'Nitab4.5_0001860g0020' => 'nta', 'Nitab4.5_0004352g0010' => 'nta', 'Nitab4.5_0008716g0020' => 'nta', 'Nitab4.5_0008922g0010' => 'nta', 'Nn3g16693' => 'nnu', 'Nn4g22596' => 'nnu', 'Nn7g37639' => 'nnu', 'Oeu001701.1' => 'oeu', 'Oeu018149.1' => 'oeu', 'Oeu026220.1' => 'oeu', 'Oeu038635.1' => 'oeu', 'Oeu049176.1' => 'oeu', 'Oeu056706.1' => 'oeu', 'Oeu056937.1' => 'oeu', 'Oeu057540.1' => 'oeu', 'Os02g0594900' => 'osa', 'Os02g0595100' => 'osa', 'Os04g0477500' => 'osa', 'Os12g0611900' => 'osa', 'Peaxi162Scf00076g00020' => 'pax', 'Peaxi162Scf00128g00217' => 'pax', 'Peaxi162Scf00129g01640' => 'pax', 'Peaxi162Scf00669g00007' => 'pax', 'Peaxi162Scf00700g00421' => 'pax', 'Peaxi162Scf00801g00038' => 'pax', 'Peaxi162Scf00891g00025' => 'pax', 'PGR083G0909' => 'pgr', 'PGR119G1005' => 'pgr', 'PGR142G2236' => 'pgr', 'PGR142G3388' => 'pgr', 'PGSC0003DMG400004514' => 'stu', 'PGSC0003DMG400012635' => 'stu', 'PGSC0003DMG400015730' => 'stu', 'PGSC0003DMG400018611' => 'stu', 'PGSC0003DMG400030897' => 'stu', 'Phvul.001G254800' => 'pvu', 'Phvul.002G260100' => 'pvu', 'Phvul.003G167600' => 'pvu', 'Phvul.004G005100' => 'pvu', 'Potri.001G343600' => 'ptr', 'Potri.006G066700' => 'ptr', 'Potri.008G186000' => 'ptr', 'Potri.010G046900' => 'ptr', 'Potri.018G127900' => 'ptr', 'Pp3c20_17750' => 'ppa', 'Pp3c24_4380' => 'ppa', 'Prupe.1G245800' => 'ppe', 'Prupe.3G293400' => 'ppe', 'Prupe.7G247400' => 'ppe', 'Psat0s145g0120' => 'psa', 'Psat0s595g0040' => 'psa', 'Psat0s595g0120' => 'psa', 'Psat3g175040' => 'psa', 'Psat7g058120' => 'psa', 'PSO017G0428' => 'pso', 'PSO063G7510' => 'pso', 'PSO067G0046' => 'pso', 'PSO478G1073' => 'pso', 'PSO675G3677' => 'pso', 'PSO675G6558' => 'pso', 'PSO675G7520' => 'pso', 'PSO675G8959' => 'pso', 'QL02p074089' => 'qlo', 'QL02p089614' => 'qlo', 'QL03p057736' => 'qlo', 'RcHm_v2.0_Chr1g0364131' => 'rch', 'RcHm_v2.0_Chr2g0087801' => 'rch', 'RcHm_v2.0_Chr2g0087821' => 'rch', 'RcHm_v2.0_Chr2g0173231' => 'rch', 'RcHm_v2.0_Chr4g0433111' => 'rch', 'Rhsim03G0250300' => 'rsi', 'Rhsim08G0048400' => 'rsi', 'Rhsim10G0014800' => 'rsi', 'Rhsim12G0040100' => 'rsi', 'Rhsim12G0109700' => 'rsi', 'Sabra06G0049600' => 'sbr', 'Sabra08G0141000' => 'sbr', 'Sabra10G0021400' => 'sbr', 'Sabra16G0222900' => 'sbr', 'Sabra18G0108600' => 'sbr', 'SalBow1G0433' => 'sbo', 'SalBow1G2038' => 'sbo', 'SalBow1G5003' => 'sbo', 'SalBow7G1197' => 'sbo', 'SalBow8G3506' => 'sbo', 'Sc03g0007300' => 'sci', 'Sc11g0000950' => 'sci', 'Sc14g0008750' => 'sci', 'Sc18g0000420' => 'sci', 'Sed0006754' => 'sed', 'Sed0008741' => 'sed', 'Sed0017172' => 'sed', 'Sed0018925' => 'sed', 'Sed0023326' => 'sed', 'Sed0025909' => 'sed', 'SEGI_05333' => 'sgi', 'SEGI_10362' => 'sgi', 'SEGI_13380' => 'sgi', 'SEGI_24306' => 'sgi', 'SEGI_29077' => 'sgi', 'SEGI_29095' => 'sgi', 'SEGI_36534' => 'sgi', 'SEGI_37506' => 'sgi', 'SEGI_38321' => 'sgi', 'SGA_v2.0_scaffold307G48031' => 'sas', 'SGA_v2.0_scaffold47G17507' => 'sas', 'SGA_v2.0_scaffold63G21736' => 'sas', 'SGA_v2.0_scaffold87G27070' => 'sas', 'SHI17794' => 'shi', 'SHI28851' => 'shi', 'SMO165G0155' => 'smo', 'SMO340G0217' => 'smo', 'SMO367G1210' => 'smo', 'Solyc02g093430.3' => 'sly', 'Solyc05g013580.4' => 'sly', 'Solyc07g008030.3' => 'sly', 'Solyc12g035470.2' => 'sly', 'Sopen02g038020' => 'spe', 'Sopen05g008490' => 'spe', 'Sopen07g003910' => 'spe', 'Sopen12g015240' => 'spe', 'Sp1g11550' => 'spa', 'Sp2g16710' => 'spa', 'Sp3g00430' => 'spa', 'Sp3g26780' => 'spa', 'Sp5g22900' => 'spa', 'Sp6g29530' => 'spa', 'TAR371G0794' => 'tar', 'TAR374G0164' => 'tar', 'TAR622G0165' => 'tar', 'TAR626G0929' => 'tar', 'TAR629G2155' => 'tar', 'THA.LOC104805282' => 'tha', 'THA.LOC104805363' => 'tha', 'THA.LOC104808968' => 'tha', 'THA.LOC104821093' => 'tha', 'THA.LOC104823953' => 'tha', 'THA.LOC104825562' => 'tha', 'THA.LOC104825665' => 'tha', 'Thecc.02G261400' => 'tca', 'Thecc.04G019200' => 'tca', 'Thecc.09G130400' => 'tca', 'Thhalv10004374m.g' => 'esa', 'Thhalv10007850m.g' => 'esa', 'Thhalv10013782m.g' => 'esa', 'Thhalv10018686m.g' => 'esa', 'Thhalv10020899m.g' => 'esa', 'Thhalv10022755m.g' => 'esa', 'TPR.G23851' => 'tpr', 'TPR.G26500' => 'tpr', 'TPR.G27267' => 'tpr', 'TPR.G32001' => 'tpr', 'TPR.G6251' => 'tpr', 'TPR.G8167' => 'tpr', 'TWI12G1330' => 'twi', 'TWI18G1239' => 'twi', 'TWI34G0979' => 'twi', 'TWI36G0670' => 'twi', 'TWI36G0707' => 'twi', 'TWI56G0233' => 'twi', 'TWI75G1809' => 'twi', 'unitig_21.g20874' => 'ugi', 'unitig_26.g10343' => 'ugi', 'unitig_46.g18392' => 'ugi', 'unitig_52.g17178' => 'ugi', 'unitig_8.g2934' => 'ugi', 'vmacro01122' => 'vma', 'vmacro05875' => 'vma', 'vmacro06147' => 'vma', 'vmacro16191' => 'vma', 'vmacro18293' => 'vma', 'VMungo0251G3707' => 'vmu', 'VMungo0464G1521' => 'vmu', 'VMungo1215G0205' => 'vmu', 'VMungo1383G2484' => 'vmu', 'Zm00001eb079610' => 'zma', 'Zm00001eb135990' => 'zma', 'Zm00001eb183710' => 'zma', 'Zm00001eb246020' => 'zma' ), 'gf_id' => 'HOM05D001124', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001124' ), 'data_identifier' => 'HOM05D001124', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001124', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '548', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02520' => 'bna', 'A03p06630' => 'bna', 'A05p44460' => 'bna', 'A06p08710' => 'bna', 'A06p41090' => 'bna', 'A07p32320' => 'bna', 'A08p32520' => 'bna', 'A09p10360' => 'bna', 'A10p24080' => 'bna', 'Aa31LG11G15250' => 'aar', 'Aa31LG1G1800' => 'aar', 'Aa31LG2G5120' => 'aar', 'Aa31LG2G6070' => 'aar', 'Aa31LG5G10770' => 'aar', 'Aa31sc61G90' => 'aar', 'Actinidia01352' => 'ach', 'Actinidia05983' => 'ach', 'Actinidia08133' => 'ach', 'Actinidia15101' => 'ach', 'Actinidia26379' => 'ach', 'Actinidia35778' => 'ach', 'Actinidia36123' => 'ach', 'Actinidia37436' => 'ach', 'Actinidia38730' => 'ach', 'Ah.02g128210' => 'amhyb', 'Ah.03g132990' => 'amhyb', 'Ah.14g079410' => 'amhyb', 'AL1G24640' => 'aly', 'AL2G26680' => 'aly', 'AL3G10530' => 'aly', 'AL3G45230' => 'aly', 'AL5G15230' => 'aly', 'AL5G16960' => 'aly', 'AL6G25210' => 'aly', 'Aqoxy2G00441' => 'aox', 'Aqoxy3G01236' => 'aox', 'Aqoxy5G03746' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3RQ047' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C7GMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9C8JER' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MBL6KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YXCZ83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZANX40' => 'arhy', 'AT1G12990' => 'ath', 'AT1G67880' => 'ath', 'AT2G13290' => 'ath', 'AT3G01620' => 'ath', 'AT3G26445' => 'ath', 'AT3G27540' => 'ath', 'AT5G14480' => 'ath', 'ATR0824G026' => 'atr', 'ATR1098G019' => 'atr', 'Atru.chr11.2145' => 'acertr', 'Atru.chr2.3636' => 'acertr', 'Atru.chr2.3644' => 'acertr', 'Atru.chr6.2422' => 'acertr', 'Atru.chr7.1112' => 'acertr', 'AUR62005469' => 'cqu', 'AUR62011166' => 'cqu', 'AUR62013319' => 'cqu', 'AUR62024273' => 'cqu', 'AUR62028420' => 'cqu', 'AUR62041942' => 'cqu', 'BcaB01g04969' => 'bca', 'BcaB01g06371' => 'bca', 'BcaB02g11494' => 'bca', 'BcaB03g15382' => 'bca', 'BcaB08g36994' => 'bca', 'BcaC03g13477' => 'bca', 'BcaC03g13478' => 'bca', 'BcaC03g13480' => 'bca', 'BcaC03g13481' => 'bca', 'BcaC03g13486' => 'bca', 'BcaC04g19031' => 'bca', 'BcaC04g23085' => 'bca', 'BcaC05g25094' => 'bca', 'BcaC05g25096' => 'bca', 'BcaC05g25138' => 'bca', 'BcaC05g30416' => 'bca', 'BcaC05g30455' => 'bca', 'BcaC06g30979' => 'bca', 'BcaC06g33805' => 'bca', 'BcaC08g46021' => 'bca', 'BcaNung03154' => 'bca', 'BolC2t06623H' => 'bol', 'BolC2t06632H' => 'bol', 'BolC2t06635H' => 'bol', 'BolC2t06638H' => 'bol', 'BolC3t13266H' => 'bol', 'BolC5t29776H' => 'bol', 'BolC6t38912H' => 'bol', 'BolC7t44183H' => 'bol', 'BolC9t54123H' => 'bol', 'BolC9t59107H' => 'bol', 'BraA02t05221Z' => 'bra', 'BraA03t09996Z' => 'bra', 'BraA05t23210Z' => 'bra', 'BraA06t24068Z' => 'bra', 'BraA06t27032Z' => 'bra', 'BraA08t35176Z' => 'bra', 'BraA09t36680Z' => 'bra', 'BraA10t44471Z' => 'bra', 'C02p06760' => 'bna', 'C02p06890' => 'bna', 'C02p07010' => 'bna', 'C03p07660' => 'bna', 'C05p10300' => 'bna', 'C06p38150' => 'bna', 'C07p36650' => 'bna', 'C08p15770' => 'bna', 'C09p12300' => 'bna', 'C09p62700' => 'bna', 'C09p75040' => 'bna', 'CAN.G13.1' => 'can', 'CAN.G138.4' => 'can', 'CAN.G44.6' => 'can', 'CAN.G473.19' => 'can', 'CANSAT01G0835' => 'cansat', 'CANSAT11G0246' => 'cansat', 'CANSAT11G1766' => 'cansat', 'CANSAT64G1954' => 'cansat', 'CARHR013330' => 'chi', 'CARHR060530' => 'chi', 'CARHR075300' => 'chi', 'CARHR105120' => 'chi', 'CARHR148910' => 'chi', 'CARHR198830' => 'chi', 'Carub.0001s1275' => 'cru', 'Carub.0002s1437' => 'cru', 'Carub.0003s0044' => 'cru', 'Carub.0003s2787' => 'cru', 'Carub.0005s0597' => 'cru', 'Carub.0006s1266' => 'cru', 'Ca_06935_v3' => 'car', 'Ca_13559_v3' => 'car', 'Ca_16941_v3' => 'car', 'Ca_16960_v3' => 'car', 'Ca_17775_v3' => 'car', 'Ca_30464_v3' => 'car', 'Cc06_g08160' => 'ccan', 'Cc07_g01520' => 'ccan', 'Cc11_g15810' => 'ccan', 'CDE02G2840' => 'cde', 'CDE03G0093' => 'cde', 'CDE04G2127' => 'cde', 'CDE07G1857' => 'cde', 'CDE09G1246' => 'cde', 'Cfa003412' => 'cfa', 'Cfa007341' => 'cfa', 'Cfa009220' => 'cfa', 'Ciclev10008737m.g' => 'ccl', 'Ciclev10015565m.g' => 'ccl', 'Ciclev10031761m.g' => 'ccl', 'CiPaw.03G045300' => 'cil', 'CiPaw.03G247200' => 'cil', 'CiPaw.04G029500' => 'cil', 'CiPaw.04G174000' => 'cil', 'CiPaw.05G181200' => 'cil', 'CiPaw.06G067100' => 'cil', 'ClCG05G025800' => 'cla', 'ClCG06G011400' => 'cla', 'ClCG09G019360' => 'cla', 'COL.COLO4_04827' => 'col', 'COL.COLO4_29170' => 'col', 'COL.COLO4_35131' => 'col', 'COL.COLO4_35132' => 'col', 'Cpa.g.sc33.32' => 'cpa', 'Cpa.g.sc46.29' => 'cpa', 'Cpa.g.sc796.1' => 'cpa', 'CsaV3_1G030420' => 'csa', 'CsaV3_5G027050' => 'csa', 'CsaV3_5G031040' => 'csa', 'CsaV3_UNG023130' => 'csa', 'CSS0007726' => 'camsi', 'CSS0016433' => 'camsi', 'CSS0017656' => 'camsi', 'CSS0025364' => 'camsi', 'CSS0027582' => 'camsi', 'CSS0047288' => 'camsi', 'CSS0049950' => 'camsi', 'DCAR_003843' => 'dca', 'DCAR_007052' => 'dca', 'DCAR_020884' => 'dca', 'DCAR_021730' => 'dca', 'DCAR_024423' => 'dca', 'DCAR_026509' => 'dca', 'DCAR_031158' => 'dca', 'Dinv14728' => 'din', 'Dinv15219' => 'din', 'Dinv25728' => 'din', 'Dinv33428' => 'din', 'Dinv36489' => 'din', 'Dinv41486' => 'din', 'Duzib147G0469' => 'dzi', 'Duzib168G0060' => 'dzi', 'Duzib187G1215' => 'dzi', 'Duzib248G0692' => 'dzi', 'Duzib251G0767' => 'dzi', 'Duzib264G0446' => 'dzi', 'Duzib268G0691' => 'dzi', 'ECA232G4767' => 'eca', 'ECA233G2838' => 'eca', 'ECA234G0391' => 'eca', 'ECA234G0857' => 'eca', 'ECA236G1593' => 'eca', 'ECA238G0565' => 'eca', 'ECA246G1027' => 'eca', 'ECA246G3223' => 'eca', 'ECA246G3470' => 'eca', 'EL10Ac6g13829' => 'bvu', 'EL10Ac6g14093' => 'bvu', 'EL10Ac8g18707' => 'bvu', 'Eucgr.C01369' => 'egr', 'Eucgr.H02492' => 'egr', 'Eucgr.I01733' => 'egr', 'Eucgr.J02255' => 'egr', 'Eucgr.J02257' => 'egr', 'Eucgr.J02258' => 'egr', 'FAN02G1601' => 'fan', 'FAN03G1586' => 'fan', 'FAN03G2986' => 'fan', 'FAN05G4837' => 'fan', 'FAN06G0146' => 'fan', 'FAN07G0858' => 'fan', 'FAN09G3179' => 'fan', 'FAN10G0669' => 'fan', 'FAN12G2358' => 'fan', 'FAN14G4198' => 'fan', 'FAN14G5112' => 'fan', 'FAN17G0342' => 'fan', 'FAN19G0342' => 'fan', 'FAN19G0962' => 'fan', 'FAN19G1101' => 'fan', 'FAN19G1872' => 'fan', 'FAN22G0356' => 'fan', 'FAN23G0744' => 'fan', 'FAN23G1914' => 'fan', 'FAN26G0032' => 'fan', 'FAN28G0625' => 'fan', 'FvH4_1g02710' => 'fve', 'FvH4_1g02720' => 'fve', 'FvH4_4g25670' => 'fve', 'FvH4_6g51700' => 'fve', 'FvH4_7g20170' => 'fve', 'Glyma.05G175000' => 'gma', 'Glyma.08G132300' => 'gma', 'Glyma.11G243000' => 'gma', 'Glyma.13G158900' => 'gma', 'Glyma.17G112400' => 'gma', 'Glyma.18G014100' => 'gma', 'Glyma.19G003100' => 'gma', 'Glyma.19G056500' => 'gma', 'Gohir.A01G158900' => 'ghi', 'Gohir.A05G312600' => 'ghi', 'Gohir.A05G354900' => 'ghi', 'Gohir.A07G037200' => 'ghi', 'Gohir.A09G030000' => 'ghi', 'Gohir.A12G145200' => 'ghi', 'Gohir.D01G151500' => 'ghi', 'Gohir.D04G058300' => 'ghi', 'Gohir.D05G314100' => 'ghi', 'Gohir.D07G041400' => 'ghi', 'Gohir.D09G029700' => 'ghi', 'Gohir.D12G149700' => 'ghi', 'Gorai.001G043800' => 'gra', 'Gorai.002G187800' => 'gra', 'Gorai.006G034700' => 'gra', 'Gorai.008G161200' => 'gra', 'Gorai.009G335700' => 'gra', 'Gorai.012G065000' => 'gra', 'GSVIVG01000535001' => 'vvi', 'GSVIVG01015572001' => 'vvi', 'GSVIVG01032386001' => 'vvi', 'HanXRQChr05g0138531' => 'han', 'HanXRQChr06g0174391' => 'han', 'HanXRQChr07g0199021' => 'han', 'HanXRQChr08g0208211' => 'han', 'HanXRQChr09g0255471' => 'han', 'HanXRQChr10g0315791' => 'han', 'HanXRQChr12g0371991' => 'han', 'HanXRQChr15g0475251' => 'han', 'HanXRQChr17g0540001' => 'han', 'HanXRQChr17g0548631' => 'han', 'HanXRQChr17g0569561' => 'han', 'Haze_12256' => 'cav', 'Haze_14756' => 'cav', 'Haze_25528' => 'cav', 'Hma1.2p1_0079F.1_g041020' => 'hma', 'Hma1.2p1_0818F.1_g223260' => 'hma', 'Hma1.2p1_1747F.1_g300530' => 'hma', 'HPP92_004607' => 'vpl', 'HPP92_004608' => 'vpl', 'HPP92_006181' => 'vpl', 'HPP92_012192' => 'vpl', 'HPP92_015680' => 'vpl', 'HPP92_020249' => 'vpl', 'HPP92_021376' => 'vpl', 'HPP92_024275' => 'vpl', 'Hund06031' => 'sun', 'Hund25391' => 'sun', 'Lalb_Chr07g0185371' => 'lal', 'Lalb_Chr07g0185381' => 'lal', 'Lalb_Chr12g0204011' => 'lal', 'Lalb_Chr13g0301671' => 'lal', 'Lalb_Chr14g0362851' => 'lal', 'Lalb_Chr24g0403581' => 'lal', 'Lj1g0000233' => 'lja', 'Lj2g0018120' => 'lja', 'Lj3C621T0' => 'lonja', 'Lj3P1059T14' => 'lonja', 'Lj3P611T9' => 'lonja', 'Lj3P614T13' => 'lonja', 'Lj3P615T5' => 'lonja', 'Lj4g0012315' => 'lja', 'Lj4g0026182' => 'lja', 'Lj6P813T16' => 'lonja', 'Lj7C427T7' => 'lonja', 'Lj7C427T8' => 'lonja', 'Lj7P600T41' => 'lonja', 'Lju41C42G17' => 'lonja', 'Lsat_1_v5_gn_0_47300' => 'lsa', 'Lsat_1_v5_gn_2_91280' => 'lsa', 'Lsat_1_v5_gn_3_30561' => 'lsa', 'Lsat_1_v5_gn_4_184321' => 'lsa', 'Lsat_1_v5_gn_4_4041' => 'lsa', 'Lsat_1_v5_gn_5_92000' => 'lsa', 'Lsat_1_v5_gn_8_152940' => 'lsa', 'Lsat_1_v5_gn_8_62401' => 'lsa', 'Manes.06G055900' => 'mes', 'Manes.12G022200' => 'mes', 'Manes.13G023300' => 'mes', 'Manes.14G115000' => 'mes', 'Manes.15G151700' => 'mes', 'Manes.17G111300' => 'mes', 'Mapoly0226s0009' => 'mpo', 'MBI02_g25363_MAGBIO' => 'mbi', 'MBI06_g00027_MAGBIO' => 'mbi', 'MBI10_g13034_MAGBIO' => 'mbi', 'MD09G1023400' => 'mdo', 'MD13G1100100' => 'mdo', 'MD15G1169200' => 'mdo', 'MD16G1101100' => 'mdo', 'MD17G1022900' => 'mdo', 'Medtr3g096150' => 'mtr', 'Medtr4g115070' => 'mtr', 'Medtr7g033325' => 'mtr', 'Medtr8g089840' => 'mtr', 'MELO3C010319.2' => 'cme', 'MELO3C011944.2' => 'cme', 'MELO3C021589.2' => 'cme', 'Migut.E00207' => 'egut', 'Migut.H00067' => 'egut', 'Migut.K00433' => 'egut', 'Migut.K00606' => 'egut', 'Migut.K01410' => 'egut', 'MSTRG.13347' => 'ama', 'MSTRG.24045' => 'ama', 'MSTRG.2428' => 'ama', 'MSTRG.26410' => 'ama', 'MSTRG.3139' => 'ama', 'MSTRG.3286' => 'ama', 'MSTRG.563' => 'ama', 'MSTRG.7941' => 'ama', 'Nitab4.5_0000028g0060' => 'nta', 'Nitab4.5_0000065g0260' => 'nta', 'Nitab4.5_0000112g0060' => 'nta', 'Nitab4.5_0000489g0120' => 'nta', 'Nitab4.5_0001776g0050' => 'nta', 'Nitab4.5_0001854g0010' => 'nta', 'Nitab4.5_0001860g0020' => 'nta', 'Nitab4.5_0004352g0010' => 'nta', 'Nitab4.5_0008716g0020' => 'nta', 'Nitab4.5_0008922g0010' => 'nta', 'Nn3g16693' => 'nnu', 'Nn4g22596' => 'nnu', 'Nn7g37639' => 'nnu', 'Oeu001701.1' => 'oeu', 'Oeu018149.1' => 'oeu', 'Oeu026220.1' => 'oeu', 'Oeu038635.1' => 'oeu', 'Oeu049176.1' => 'oeu', 'Oeu056706.1' => 'oeu', 'Oeu056937.1' => 'oeu', 'Oeu057540.1' => 'oeu', 'Os02g0594900' => 'osa', 'Os02g0595100' => 'osa', 'Os04g0477500' => 'osa', 'Os12g0611900' => 'osa', 'Peaxi162Scf00076g00020' => 'pax', 'Peaxi162Scf00128g00217' => 'pax', 'Peaxi162Scf00129g01640' => 'pax', 'Peaxi162Scf00669g00007' => 'pax', 'Peaxi162Scf00700g00421' => 'pax', 'Peaxi162Scf00801g00038' => 'pax', 'Peaxi162Scf00891g00025' => 'pax', 'PGR083G0909' => 'pgr', 'PGR119G1005' => 'pgr', 'PGR142G2236' => 'pgr', 'PGR142G3388' => 'pgr', 'PGSC0003DMG400004514' => 'stu', 'PGSC0003DMG400012635' => 'stu', 'PGSC0003DMG400015730' => 'stu', 'PGSC0003DMG400018611' => 'stu', 'PGSC0003DMG400030897' => 'stu', 'Phvul.001G254800' => 'pvu', 'Phvul.002G260100' => 'pvu', 'Phvul.003G167600' => 'pvu', 'Phvul.004G005100' => 'pvu', 'Potri.001G343600' => 'ptr', 'Potri.006G066700' => 'ptr', 'Potri.008G186000' => 'ptr', 'Potri.010G046900' => 'ptr', 'Potri.018G127900' => 'ptr', 'Pp3c20_17750' => 'ppa', 'Pp3c24_4380' => 'ppa', 'Prupe.1G245800' => 'ppe', 'Prupe.3G293400' => 'ppe', 'Prupe.7G247400' => 'ppe', 'Psat0s145g0120' => 'psa', 'Psat0s595g0040' => 'psa', 'Psat0s595g0120' => 'psa', 'Psat3g175040' => 'psa', 'Psat7g058120' => 'psa', 'PSO017G0428' => 'pso', 'PSO063G7510' => 'pso', 'PSO067G0046' => 'pso', 'PSO478G1073' => 'pso', 'PSO675G3677' => 'pso', 'PSO675G6558' => 'pso', 'PSO675G7520' => 'pso', 'PSO675G8959' => 'pso', 'QL02p074089' => 'qlo', 'QL02p089614' => 'qlo', 'QL03p057736' => 'qlo', 'RcHm_v2.0_Chr1g0364131' => 'rch', 'RcHm_v2.0_Chr2g0087801' => 'rch', 'RcHm_v2.0_Chr2g0087821' => 'rch', 'RcHm_v2.0_Chr2g0173231' => 'rch', 'RcHm_v2.0_Chr4g0433111' => 'rch', 'Rhsim03G0250300' => 'rsi', 'Rhsim08G0048400' => 'rsi', 'Rhsim10G0014800' => 'rsi', 'Rhsim12G0040100' => 'rsi', 'Rhsim12G0109700' => 'rsi', 'Sabra06G0049600' => 'sbr', 'Sabra08G0141000' => 'sbr', 'Sabra10G0021400' => 'sbr', 'Sabra16G0222900' => 'sbr', 'Sabra18G0108600' => 'sbr', 'SalBow1G0433' => 'sbo', 'SalBow1G2038' => 'sbo', 'SalBow1G5003' => 'sbo', 'SalBow7G1197' => 'sbo', 'SalBow8G3506' => 'sbo', 'Sc03g0007300' => 'sci', 'Sc11g0000950' => 'sci', 'Sc14g0008750' => 'sci', 'Sc18g0000420' => 'sci', 'Sed0006754' => 'sed', 'Sed0008741' => 'sed', 'Sed0017172' => 'sed', 'Sed0018925' => 'sed', 'Sed0023326' => 'sed', 'Sed0025909' => 'sed', 'SEGI_05333' => 'sgi', 'SEGI_10362' => 'sgi', 'SEGI_13380' => 'sgi', 'SEGI_24306' => 'sgi', 'SEGI_29077' => 'sgi', 'SEGI_29095' => 'sgi', 'SEGI_36534' => 'sgi', 'SEGI_37506' => 'sgi', 'SEGI_38321' => 'sgi', 'SGA_v2.0_scaffold307G48031' => 'sas', 'SGA_v2.0_scaffold47G17507' => 'sas', 'SGA_v2.0_scaffold63G21736' => 'sas', 'SGA_v2.0_scaffold87G27070' => 'sas', 'SHI17794' => 'shi', 'SHI28851' => 'shi', 'SMO165G0155' => 'smo', 'SMO340G0217' => 'smo', 'SMO367G1210' => 'smo', 'Solyc02g093430.3' => 'sly', 'Solyc05g013580.4' => 'sly', 'Solyc07g008030.3' => 'sly', 'Solyc12g035470.2' => 'sly', 'Sopen02g038020' => 'spe', 'Sopen05g008490' => 'spe', 'Sopen07g003910' => 'spe', 'Sopen12g015240' => 'spe', 'Sp1g11550' => 'spa', 'Sp2g16710' => 'spa', 'Sp3g00430' => 'spa', 'Sp3g26780' => 'spa', 'Sp5g22900' => 'spa', 'Sp6g29530' => 'spa', 'TAR371G0794' => 'tar', 'TAR374G0164' => 'tar', 'TAR622G0165' => 'tar', 'TAR626G0929' => 'tar', 'TAR629G2155' => 'tar', 'THA.LOC104805282' => 'tha', 'THA.LOC104805363' => 'tha', 'THA.LOC104808968' => 'tha', 'THA.LOC104821093' => 'tha', 'THA.LOC104823953' => 'tha', 'THA.LOC104825562' => 'tha', 'THA.LOC104825665' => 'tha', 'Thecc.02G261400' => 'tca', 'Thecc.04G019200' => 'tca', 'Thecc.09G130400' => 'tca', 'Thhalv10004374m.g' => 'esa', 'Thhalv10007850m.g' => 'esa', 'Thhalv10013782m.g' => 'esa', 'Thhalv10018686m.g' => 'esa', 'Thhalv10020899m.g' => 'esa', 'Thhalv10022755m.g' => 'esa', 'TPR.G23851' => 'tpr', 'TPR.G26500' => 'tpr', 'TPR.G27267' => 'tpr', 'TPR.G32001' => 'tpr', 'TPR.G6251' => 'tpr', 'TPR.G8167' => 'tpr', 'TWI12G1330' => 'twi', 'TWI18G1239' => 'twi', 'TWI34G0979' => 'twi', 'TWI36G0670' => 'twi', 'TWI36G0707' => 'twi', 'TWI56G0233' => 'twi', 'TWI75G1809' => 'twi', 'unitig_21.g20874' => 'ugi', 'unitig_26.g10343' => 'ugi', 'unitig_46.g18392' => 'ugi', 'unitig_52.g17178' => 'ugi', 'unitig_8.g2934' => 'ugi', 'vmacro01122' => 'vma', 'vmacro05875' => 'vma', 'vmacro06147' => 'vma', 'vmacro16191' => 'vma', 'vmacro18293' => 'vma', 'VMungo0251G3707' => 'vmu', 'VMungo0464G1521' => 'vmu', 'VMungo1215G0205' => 'vmu', 'VMungo1383G2484' => 'vmu', 'Zm00001eb079610' => 'zma', 'Zm00001eb135990' => 'zma', 'Zm00001eb183710' => 'zma', 'Zm00001eb246020' => 'zma' ) $gf_id = 'HOM05D001124' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001124' ) $data_identifier = 'HOM05D001124' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 6, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 7, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 21, 'bol' => (int) 10, 'bra' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 6, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 9, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 21, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 8, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 10, 'lsa' => (int) 8, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 8, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 9, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb246020' $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' => 'HOM05D001124', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '548', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02520' => 'bna', 'A03p06630' => 'bna', 'A05p44460' => 'bna', 'A06p08710' => 'bna', 'A06p41090' => 'bna', 'A07p32320' => 'bna', 'A08p32520' => 'bna', 'A09p10360' => 'bna', 'A10p24080' => 'bna', 'Aa31LG11G15250' => 'aar', 'Aa31LG1G1800' => 'aar', 'Aa31LG2G5120' => 'aar', 'Aa31LG2G6070' => 'aar', 'Aa31LG5G10770' => 'aar', 'Aa31sc61G90' => 'aar', 'Actinidia01352' => 'ach', 'Actinidia05983' => 'ach', 'Actinidia08133' => 'ach', 'Actinidia15101' => 'ach', 'Actinidia26379' => 'ach', 'Actinidia35778' => 'ach', 'Actinidia36123' => 'ach', 'Actinidia37436' => 'ach', 'Actinidia38730' => 'ach', 'Ah.02g128210' => 'amhyb', 'Ah.03g132990' => 'amhyb', 'Ah.14g079410' => 'amhyb', 'AL1G24640' => 'aly', 'AL2G26680' => 'aly', 'AL3G10530' => 'aly', 'AL3G45230' => 'aly', 'AL5G15230' => 'aly', 'AL5G16960' => 'aly', 'AL6G25210' => 'aly', 'Aqoxy2G00441' => 'aox', 'Aqoxy3G01236' => 'aox', 'Aqoxy5G03746' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3RQ047' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C7GMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9C8JER' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MBL6KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YXCZ83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZANX40' => 'arhy', 'AT1G12990' => 'ath', 'AT1G67880' => 'ath', 'AT2G13290' => 'ath', 'AT3G01620' => 'ath', 'AT3G26445' => 'ath', 'AT3G27540' => 'ath', 'AT5G14480' => 'ath', 'ATR0824G026' => 'atr', 'ATR1098G019' => 'atr', 'Atru.chr11.2145' => 'acertr', 'Atru.chr2.3636' => 'acertr', 'Atru.chr2.3644' => 'acertr', 'Atru.chr6.2422' => 'acertr', 'Atru.chr7.1112' => 'acertr', 'AUR62005469' => 'cqu', 'AUR62011166' => 'cqu', 'AUR62013319' => 'cqu', 'AUR62024273' => 'cqu', 'AUR62028420' => 'cqu', 'AUR62041942' => 'cqu', 'BcaB01g04969' => 'bca', 'BcaB01g06371' => 'bca', 'BcaB02g11494' => 'bca', 'BcaB03g15382' => 'bca', 'BcaB08g36994' => 'bca', 'BcaC03g13477' => 'bca', 'BcaC03g13478' => 'bca', 'BcaC03g13480' => 'bca', 'BcaC03g13481' => 'bca', 'BcaC03g13486' => 'bca', 'BcaC04g19031' => 'bca', 'BcaC04g23085' => 'bca', 'BcaC05g25094' => 'bca', 'BcaC05g25096' => 'bca', 'BcaC05g25138' => 'bca', 'BcaC05g30416' => 'bca', 'BcaC05g30455' => 'bca', 'BcaC06g30979' => 'bca', 'BcaC06g33805' => 'bca', 'BcaC08g46021' => 'bca', 'BcaNung03154' => 'bca', 'BolC2t06623H' => 'bol', 'BolC2t06632H' => 'bol', 'BolC2t06635H' => 'bol', 'BolC2t06638H' => 'bol', 'BolC3t13266H' => 'bol', 'BolC5t29776H' => 'bol', 'BolC6t38912H' => 'bol', 'BolC7t44183H' => 'bol', 'BolC9t54123H' => 'bol', 'BolC9t59107H' => 'bol', 'BraA02t05221Z' => 'bra', 'BraA03t09996Z' => 'bra', 'BraA05t23210Z' => 'bra', 'BraA06t24068Z' => 'bra', 'BraA06t27032Z' => 'bra', 'BraA08t35176Z' => 'bra', 'BraA09t36680Z' => 'bra', 'BraA10t44471Z' => 'bra', 'C02p06760' => 'bna', 'C02p06890' => 'bna', 'C02p07010' => 'bna', 'C03p07660' => 'bna', 'C05p10300' => 'bna', 'C06p38150' => 'bna', 'C07p36650' => 'bna', 'C08p15770' => 'bna', 'C09p12300' => 'bna', 'C09p62700' => 'bna', 'C09p75040' => 'bna', 'CAN.G13.1' => 'can', 'CAN.G138.4' => 'can', 'CAN.G44.6' => 'can', 'CAN.G473.19' => 'can', 'CANSAT01G0835' => 'cansat', 'CANSAT11G0246' => 'cansat', 'CANSAT11G1766' => 'cansat', 'CANSAT64G1954' => 'cansat', 'CARHR013330' => 'chi', 'CARHR060530' => 'chi', 'CARHR075300' => 'chi', 'CARHR105120' => 'chi', 'CARHR148910' => 'chi', 'CARHR198830' => 'chi', 'Carub.0001s1275' => 'cru', 'Carub.0002s1437' => 'cru', 'Carub.0003s0044' => 'cru', 'Carub.0003s2787' => 'cru', 'Carub.0005s0597' => 'cru', 'Carub.0006s1266' => 'cru', 'Ca_06935_v3' => 'car', 'Ca_13559_v3' => 'car', 'Ca_16941_v3' => 'car', 'Ca_16960_v3' => 'car', 'Ca_17775_v3' => 'car', 'Ca_30464_v3' => 'car', 'Cc06_g08160' => 'ccan', 'Cc07_g01520' => 'ccan', 'Cc11_g15810' => 'ccan', 'CDE02G2840' => 'cde', 'CDE03G0093' => 'cde', 'CDE04G2127' => 'cde', 'CDE07G1857' => 'cde', 'CDE09G1246' => 'cde', 'Cfa003412' => 'cfa', 'Cfa007341' => 'cfa', 'Cfa009220' => 'cfa', 'Ciclev10008737m.g' => 'ccl', 'Ciclev10015565m.g' => 'ccl', 'Ciclev10031761m.g' => 'ccl', 'CiPaw.03G045300' => 'cil', 'CiPaw.03G247200' => 'cil', 'CiPaw.04G029500' => 'cil', 'CiPaw.04G174000' => 'cil', 'CiPaw.05G181200' => 'cil', 'CiPaw.06G067100' => 'cil', 'ClCG05G025800' => 'cla', 'ClCG06G011400' => 'cla', 'ClCG09G019360' => 'cla', 'COL.COLO4_04827' => 'col', 'COL.COLO4_29170' => 'col', 'COL.COLO4_35131' => 'col', 'COL.COLO4_35132' => 'col', 'Cpa.g.sc33.32' => 'cpa', 'Cpa.g.sc46.29' => 'cpa', 'Cpa.g.sc796.1' => 'cpa', 'CsaV3_1G030420' => 'csa', 'CsaV3_5G027050' => 'csa', 'CsaV3_5G031040' => 'csa', 'CsaV3_UNG023130' => 'csa', 'CSS0007726' => 'camsi', 'CSS0016433' => 'camsi', 'CSS0017656' => 'camsi', 'CSS0025364' => 'camsi', 'CSS0027582' => 'camsi', 'CSS0047288' => 'camsi', 'CSS0049950' => 'camsi', 'DCAR_003843' => 'dca', 'DCAR_007052' => 'dca', 'DCAR_020884' => 'dca', 'DCAR_021730' => 'dca', 'DCAR_024423' => 'dca', 'DCAR_026509' => 'dca', 'DCAR_031158' => 'dca', 'Dinv14728' => 'din', 'Dinv15219' => 'din', 'Dinv25728' => 'din', 'Dinv33428' => 'din', 'Dinv36489' => 'din', 'Dinv41486' => 'din', 'Duzib147G0469' => 'dzi', 'Duzib168G0060' => 'dzi', 'Duzib187G1215' => 'dzi', 'Duzib248G0692' => 'dzi', 'Duzib251G0767' => 'dzi', 'Duzib264G0446' => 'dzi', 'Duzib268G0691' => 'dzi', 'ECA232G4767' => 'eca', 'ECA233G2838' => 'eca', 'ECA234G0391' => 'eca', 'ECA234G0857' => 'eca', 'ECA236G1593' => 'eca', 'ECA238G0565' => 'eca', 'ECA246G1027' => 'eca', 'ECA246G3223' => 'eca', 'ECA246G3470' => 'eca', 'EL10Ac6g13829' => 'bvu', 'EL10Ac6g14093' => 'bvu', 'EL10Ac8g18707' => 'bvu', 'Eucgr.C01369' => 'egr', 'Eucgr.H02492' => 'egr', 'Eucgr.I01733' => 'egr', 'Eucgr.J02255' => 'egr', 'Eucgr.J02257' => 'egr', 'Eucgr.J02258' => 'egr', 'FAN02G1601' => 'fan', 'FAN03G1586' => 'fan', 'FAN03G2986' => 'fan', 'FAN05G4837' => 'fan', 'FAN06G0146' => 'fan', 'FAN07G0858' => 'fan', 'FAN09G3179' => 'fan', 'FAN10G0669' => 'fan', 'FAN12G2358' => 'fan', 'FAN14G4198' => 'fan', 'FAN14G5112' => 'fan', 'FAN17G0342' => 'fan', 'FAN19G0342' => 'fan', 'FAN19G0962' => 'fan', 'FAN19G1101' => 'fan', 'FAN19G1872' => 'fan', 'FAN22G0356' => 'fan', 'FAN23G0744' => 'fan', 'FAN23G1914' => 'fan', 'FAN26G0032' => 'fan', 'FAN28G0625' => 'fan', 'FvH4_1g02710' => 'fve', 'FvH4_1g02720' => 'fve', 'FvH4_4g25670' => 'fve', 'FvH4_6g51700' => 'fve', 'FvH4_7g20170' => 'fve', 'Glyma.05G175000' => 'gma', 'Glyma.08G132300' => 'gma', 'Glyma.11G243000' => 'gma', 'Glyma.13G158900' => 'gma', 'Glyma.17G112400' => 'gma', 'Glyma.18G014100' => 'gma', 'Glyma.19G003100' => 'gma', 'Glyma.19G056500' => 'gma', 'Gohir.A01G158900' => 'ghi', 'Gohir.A05G312600' => 'ghi', 'Gohir.A05G354900' => 'ghi', 'Gohir.A07G037200' => 'ghi', 'Gohir.A09G030000' => 'ghi', 'Gohir.A12G145200' => 'ghi', 'Gohir.D01G151500' => 'ghi', 'Gohir.D04G058300' => 'ghi', 'Gohir.D05G314100' => 'ghi', 'Gohir.D07G041400' => 'ghi', 'Gohir.D09G029700' => 'ghi', 'Gohir.D12G149700' => 'ghi', 'Gorai.001G043800' => 'gra', 'Gorai.002G187800' => 'gra', 'Gorai.006G034700' => 'gra', 'Gorai.008G161200' => 'gra', 'Gorai.009G335700' => 'gra', 'Gorai.012G065000' => 'gra', 'GSVIVG01000535001' => 'vvi', 'GSVIVG01015572001' => 'vvi', 'GSVIVG01032386001' => 'vvi', 'HanXRQChr05g0138531' => 'han', 'HanXRQChr06g0174391' => 'han', 'HanXRQChr07g0199021' => 'han', 'HanXRQChr08g0208211' => 'han', 'HanXRQChr09g0255471' => 'han', 'HanXRQChr10g0315791' => 'han', 'HanXRQChr12g0371991' => 'han', 'HanXRQChr15g0475251' => 'han', 'HanXRQChr17g0540001' => 'han', 'HanXRQChr17g0548631' => 'han', 'HanXRQChr17g0569561' => 'han', 'Haze_12256' => 'cav', 'Haze_14756' => 'cav', 'Haze_25528' => 'cav', 'Hma1.2p1_0079F.1_g041020' => 'hma', 'Hma1.2p1_0818F.1_g223260' => 'hma', 'Hma1.2p1_1747F.1_g300530' => 'hma', 'HPP92_004607' => 'vpl', 'HPP92_004608' => 'vpl', 'HPP92_006181' => 'vpl', 'HPP92_012192' => 'vpl', 'HPP92_015680' => 'vpl', 'HPP92_020249' => 'vpl', 'HPP92_021376' => 'vpl', 'HPP92_024275' => 'vpl', 'Hund06031' => 'sun', 'Hund25391' => 'sun', 'Lalb_Chr07g0185371' => 'lal', 'Lalb_Chr07g0185381' => 'lal', 'Lalb_Chr12g0204011' => 'lal', 'Lalb_Chr13g0301671' => 'lal', 'Lalb_Chr14g0362851' => 'lal', 'Lalb_Chr24g0403581' => 'lal', 'Lj1g0000233' => 'lja', 'Lj2g0018120' => 'lja', 'Lj3C621T0' => 'lonja', 'Lj3P1059T14' => 'lonja', 'Lj3P611T9' => 'lonja', 'Lj3P614T13' => 'lonja', 'Lj3P615T5' => 'lonja', 'Lj4g0012315' => 'lja', 'Lj4g0026182' => 'lja', 'Lj6P813T16' => 'lonja', 'Lj7C427T7' => 'lonja', 'Lj7C427T8' => 'lonja', 'Lj7P600T41' => 'lonja', 'Lju41C42G17' => 'lonja', 'Lsat_1_v5_gn_0_47300' => 'lsa', 'Lsat_1_v5_gn_2_91280' => 'lsa', 'Lsat_1_v5_gn_3_30561' => 'lsa', 'Lsat_1_v5_gn_4_184321' => 'lsa', 'Lsat_1_v5_gn_4_4041' => 'lsa', 'Lsat_1_v5_gn_5_92000' => 'lsa', 'Lsat_1_v5_gn_8_152940' => 'lsa', 'Lsat_1_v5_gn_8_62401' => 'lsa', 'Manes.06G055900' => 'mes', 'Manes.12G022200' => 'mes', 'Manes.13G023300' => 'mes', 'Manes.14G115000' => 'mes', 'Manes.15G151700' => 'mes', 'Manes.17G111300' => 'mes', 'Mapoly0226s0009' => 'mpo', 'MBI02_g25363_MAGBIO' => 'mbi', 'MBI06_g00027_MAGBIO' => 'mbi', 'MBI10_g13034_MAGBIO' => 'mbi', 'MD09G1023400' => 'mdo', 'MD13G1100100' => 'mdo', 'MD15G1169200' => 'mdo', 'MD16G1101100' => 'mdo', 'MD17G1022900' => 'mdo', 'Medtr3g096150' => 'mtr', 'Medtr4g115070' => 'mtr', 'Medtr7g033325' => 'mtr', 'Medtr8g089840' => 'mtr', 'MELO3C010319.2' => 'cme', 'MELO3C011944.2' => 'cme', 'MELO3C021589.2' => 'cme', 'Migut.E00207' => 'egut', 'Migut.H00067' => 'egut', 'Migut.K00433' => 'egut', 'Migut.K00606' => 'egut', 'Migut.K01410' => 'egut', 'MSTRG.13347' => 'ama', 'MSTRG.24045' => 'ama', 'MSTRG.2428' => 'ama', 'MSTRG.26410' => 'ama', 'MSTRG.3139' => 'ama', 'MSTRG.3286' => 'ama', 'MSTRG.563' => 'ama', 'MSTRG.7941' => 'ama', 'Nitab4.5_0000028g0060' => 'nta', 'Nitab4.5_0000065g0260' => 'nta', 'Nitab4.5_0000112g0060' => 'nta', 'Nitab4.5_0000489g0120' => 'nta', 'Nitab4.5_0001776g0050' => 'nta', 'Nitab4.5_0001854g0010' => 'nta', 'Nitab4.5_0001860g0020' => 'nta', 'Nitab4.5_0004352g0010' => 'nta', 'Nitab4.5_0008716g0020' => 'nta', 'Nitab4.5_0008922g0010' => 'nta', 'Nn3g16693' => 'nnu', 'Nn4g22596' => 'nnu', 'Nn7g37639' => 'nnu', 'Oeu001701.1' => 'oeu', 'Oeu018149.1' => 'oeu', 'Oeu026220.1' => 'oeu', 'Oeu038635.1' => 'oeu', 'Oeu049176.1' => 'oeu', 'Oeu056706.1' => 'oeu', 'Oeu056937.1' => 'oeu', 'Oeu057540.1' => 'oeu', 'Os02g0594900' => 'osa', 'Os02g0595100' => 'osa', 'Os04g0477500' => 'osa', 'Os12g0611900' => 'osa', 'Peaxi162Scf00076g00020' => 'pax', 'Peaxi162Scf00128g00217' => 'pax', 'Peaxi162Scf00129g01640' => 'pax', 'Peaxi162Scf00669g00007' => 'pax', 'Peaxi162Scf00700g00421' => 'pax', 'Peaxi162Scf00801g00038' => 'pax', 'Peaxi162Scf00891g00025' => 'pax', 'PGR083G0909' => 'pgr', 'PGR119G1005' => 'pgr', 'PGR142G2236' => 'pgr', 'PGR142G3388' => 'pgr', 'PGSC0003DMG400004514' => 'stu', 'PGSC0003DMG400012635' => 'stu', 'PGSC0003DMG400015730' => 'stu', 'PGSC0003DMG400018611' => 'stu', 'PGSC0003DMG400030897' => 'stu', 'Phvul.001G254800' => 'pvu', 'Phvul.002G260100' => 'pvu', 'Phvul.003G167600' => 'pvu', 'Phvul.004G005100' => 'pvu', 'Potri.001G343600' => 'ptr', 'Potri.006G066700' => 'ptr', 'Potri.008G186000' => 'ptr', 'Potri.010G046900' => 'ptr', 'Potri.018G127900' => 'ptr', 'Pp3c20_17750' => 'ppa', 'Pp3c24_4380' => 'ppa', 'Prupe.1G245800' => 'ppe', 'Prupe.3G293400' => 'ppe', 'Prupe.7G247400' => 'ppe', 'Psat0s145g0120' => 'psa', 'Psat0s595g0040' => 'psa', 'Psat0s595g0120' => 'psa', 'Psat3g175040' => 'psa', 'Psat7g058120' => 'psa', 'PSO017G0428' => 'pso', 'PSO063G7510' => 'pso', 'PSO067G0046' => 'pso', 'PSO478G1073' => 'pso', 'PSO675G3677' => 'pso', 'PSO675G6558' => 'pso', 'PSO675G7520' => 'pso', 'PSO675G8959' => 'pso', 'QL02p074089' => 'qlo', 'QL02p089614' => 'qlo', 'QL03p057736' => 'qlo', 'RcHm_v2.0_Chr1g0364131' => 'rch', 'RcHm_v2.0_Chr2g0087801' => 'rch', 'RcHm_v2.0_Chr2g0087821' => 'rch', 'RcHm_v2.0_Chr2g0173231' => 'rch', 'RcHm_v2.0_Chr4g0433111' => 'rch', 'Rhsim03G0250300' => 'rsi', 'Rhsim08G0048400' => 'rsi', 'Rhsim10G0014800' => 'rsi', 'Rhsim12G0040100' => 'rsi', 'Rhsim12G0109700' => 'rsi', 'Sabra06G0049600' => 'sbr', 'Sabra08G0141000' => 'sbr', 'Sabra10G0021400' => 'sbr', 'Sabra16G0222900' => 'sbr', 'Sabra18G0108600' => 'sbr', 'SalBow1G0433' => 'sbo', 'SalBow1G2038' => 'sbo', 'SalBow1G5003' => 'sbo', 'SalBow7G1197' => 'sbo', 'SalBow8G3506' => 'sbo', 'Sc03g0007300' => 'sci', 'Sc11g0000950' => 'sci', 'Sc14g0008750' => 'sci', 'Sc18g0000420' => 'sci', 'Sed0006754' => 'sed', 'Sed0008741' => 'sed', 'Sed0017172' => 'sed', 'Sed0018925' => 'sed', 'Sed0023326' => 'sed', 'Sed0025909' => 'sed', 'SEGI_05333' => 'sgi', 'SEGI_10362' => 'sgi', 'SEGI_13380' => 'sgi', 'SEGI_24306' => 'sgi', 'SEGI_29077' => 'sgi', 'SEGI_29095' => 'sgi', 'SEGI_36534' => 'sgi', 'SEGI_37506' => 'sgi', 'SEGI_38321' => 'sgi', 'SGA_v2.0_scaffold307G48031' => 'sas', 'SGA_v2.0_scaffold47G17507' => 'sas', 'SGA_v2.0_scaffold63G21736' => 'sas', 'SGA_v2.0_scaffold87G27070' => 'sas', 'SHI17794' => 'shi', 'SHI28851' => 'shi', 'SMO165G0155' => 'smo', 'SMO340G0217' => 'smo', 'SMO367G1210' => 'smo', 'Solyc02g093430.3' => 'sly', 'Solyc05g013580.4' => 'sly', 'Solyc07g008030.3' => 'sly', 'Solyc12g035470.2' => 'sly', 'Sopen02g038020' => 'spe', 'Sopen05g008490' => 'spe', 'Sopen07g003910' => 'spe', 'Sopen12g015240' => 'spe', 'Sp1g11550' => 'spa', 'Sp2g16710' => 'spa', 'Sp3g00430' => 'spa', 'Sp3g26780' => 'spa', 'Sp5g22900' => 'spa', 'Sp6g29530' => 'spa', 'TAR371G0794' => 'tar', 'TAR374G0164' => 'tar', 'TAR622G0165' => 'tar', 'TAR626G0929' => 'tar', 'TAR629G2155' => 'tar', 'THA.LOC104805282' => 'tha', 'THA.LOC104805363' => 'tha', 'THA.LOC104808968' => 'tha', 'THA.LOC104821093' => 'tha', 'THA.LOC104823953' => 'tha', 'THA.LOC104825562' => 'tha', 'THA.LOC104825665' => 'tha', 'Thecc.02G261400' => 'tca', 'Thecc.04G019200' => 'tca', 'Thecc.09G130400' => 'tca', 'Thhalv10004374m.g' => 'esa', 'Thhalv10007850m.g' => 'esa', 'Thhalv10013782m.g' => 'esa', 'Thhalv10018686m.g' => 'esa', 'Thhalv10020899m.g' => 'esa', 'Thhalv10022755m.g' => 'esa', 'TPR.G23851' => 'tpr', 'TPR.G26500' => 'tpr', 'TPR.G27267' => 'tpr', 'TPR.G32001' => 'tpr', 'TPR.G6251' => 'tpr', 'TPR.G8167' => 'tpr', 'TWI12G1330' => 'twi', 'TWI18G1239' => 'twi', 'TWI34G0979' => 'twi', 'TWI36G0670' => 'twi', 'TWI36G0707' => 'twi', 'TWI56G0233' => 'twi', 'TWI75G1809' => 'twi', 'unitig_21.g20874' => 'ugi', 'unitig_26.g10343' => 'ugi', 'unitig_46.g18392' => 'ugi', 'unitig_52.g17178' => 'ugi', 'unitig_8.g2934' => 'ugi', 'vmacro01122' => 'vma', 'vmacro05875' => 'vma', 'vmacro06147' => 'vma', 'vmacro16191' => 'vma', 'vmacro18293' => 'vma', 'VMungo0251G3707' => 'vmu', 'VMungo0464G1521' => 'vmu', 'VMungo1215G0205' => 'vmu', 'VMungo1383G2484' => 'vmu', 'Zm00001eb079610' => 'zma', 'Zm00001eb135990' => 'zma', 'Zm00001eb183710' => 'zma', 'Zm00001eb246020' => 'zma' ), 'gf_id' => 'HOM05D001124', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001124' ), 'data_identifier' => 'HOM05D001124', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001124', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '548', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02520' => 'bna', 'A03p06630' => 'bna', 'A05p44460' => 'bna', 'A06p08710' => 'bna', 'A06p41090' => 'bna', 'A07p32320' => 'bna', 'A08p32520' => 'bna', 'A09p10360' => 'bna', 'A10p24080' => 'bna', 'Aa31LG11G15250' => 'aar', 'Aa31LG1G1800' => 'aar', 'Aa31LG2G5120' => 'aar', 'Aa31LG2G6070' => 'aar', 'Aa31LG5G10770' => 'aar', 'Aa31sc61G90' => 'aar', 'Actinidia01352' => 'ach', 'Actinidia05983' => 'ach', 'Actinidia08133' => 'ach', 'Actinidia15101' => 'ach', 'Actinidia26379' => 'ach', 'Actinidia35778' => 'ach', 'Actinidia36123' => 'ach', 'Actinidia37436' => 'ach', 'Actinidia38730' => 'ach', 'Ah.02g128210' => 'amhyb', 'Ah.03g132990' => 'amhyb', 'Ah.14g079410' => 'amhyb', 'AL1G24640' => 'aly', 'AL2G26680' => 'aly', 'AL3G10530' => 'aly', 'AL3G45230' => 'aly', 'AL5G15230' => 'aly', 'AL5G16960' => 'aly', 'AL6G25210' => 'aly', 'Aqoxy2G00441' => 'aox', 'Aqoxy3G01236' => 'aox', 'Aqoxy5G03746' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3RQ047' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C7GMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9C8JER' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MBL6KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YXCZ83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZANX40' => 'arhy', 'AT1G12990' => 'ath', 'AT1G67880' => 'ath', 'AT2G13290' => 'ath', 'AT3G01620' => 'ath', 'AT3G26445' => 'ath', 'AT3G27540' => 'ath', 'AT5G14480' => 'ath', 'ATR0824G026' => 'atr', 'ATR1098G019' => 'atr', 'Atru.chr11.2145' => 'acertr', 'Atru.chr2.3636' => 'acertr', 'Atru.chr2.3644' => 'acertr', 'Atru.chr6.2422' => 'acertr', 'Atru.chr7.1112' => 'acertr', 'AUR62005469' => 'cqu', 'AUR62011166' => 'cqu', 'AUR62013319' => 'cqu', 'AUR62024273' => 'cqu', 'AUR62028420' => 'cqu', 'AUR62041942' => 'cqu', 'BcaB01g04969' => 'bca', 'BcaB01g06371' => 'bca', 'BcaB02g11494' => 'bca', 'BcaB03g15382' => 'bca', 'BcaB08g36994' => 'bca', 'BcaC03g13477' => 'bca', 'BcaC03g13478' => 'bca', 'BcaC03g13480' => 'bca', 'BcaC03g13481' => 'bca', 'BcaC03g13486' => 'bca', 'BcaC04g19031' => 'bca', 'BcaC04g23085' => 'bca', 'BcaC05g25094' => 'bca', 'BcaC05g25096' => 'bca', 'BcaC05g25138' => 'bca', 'BcaC05g30416' => 'bca', 'BcaC05g30455' => 'bca', 'BcaC06g30979' => 'bca', 'BcaC06g33805' => 'bca', 'BcaC08g46021' => 'bca', 'BcaNung03154' => 'bca', 'BolC2t06623H' => 'bol', 'BolC2t06632H' => 'bol', 'BolC2t06635H' => 'bol', 'BolC2t06638H' => 'bol', 'BolC3t13266H' => 'bol', 'BolC5t29776H' => 'bol', 'BolC6t38912H' => 'bol', 'BolC7t44183H' => 'bol', 'BolC9t54123H' => 'bol', 'BolC9t59107H' => 'bol', 'BraA02t05221Z' => 'bra', 'BraA03t09996Z' => 'bra', 'BraA05t23210Z' => 'bra', 'BraA06t24068Z' => 'bra', 'BraA06t27032Z' => 'bra', 'BraA08t35176Z' => 'bra', 'BraA09t36680Z' => 'bra', 'BraA10t44471Z' => 'bra', 'C02p06760' => 'bna', 'C02p06890' => 'bna', 'C02p07010' => 'bna', 'C03p07660' => 'bna', 'C05p10300' => 'bna', 'C06p38150' => 'bna', 'C07p36650' => 'bna', 'C08p15770' => 'bna', 'C09p12300' => 'bna', 'C09p62700' => 'bna', 'C09p75040' => 'bna', 'CAN.G13.1' => 'can', 'CAN.G138.4' => 'can', 'CAN.G44.6' => 'can', 'CAN.G473.19' => 'can', 'CANSAT01G0835' => 'cansat', 'CANSAT11G0246' => 'cansat', 'CANSAT11G1766' => 'cansat', 'CANSAT64G1954' => 'cansat', 'CARHR013330' => 'chi', 'CARHR060530' => 'chi', 'CARHR075300' => 'chi', 'CARHR105120' => 'chi', 'CARHR148910' => 'chi', 'CARHR198830' => 'chi', 'Carub.0001s1275' => 'cru', 'Carub.0002s1437' => 'cru', 'Carub.0003s0044' => 'cru', 'Carub.0003s2787' => 'cru', 'Carub.0005s0597' => 'cru', 'Carub.0006s1266' => 'cru', 'Ca_06935_v3' => 'car', 'Ca_13559_v3' => 'car', 'Ca_16941_v3' => 'car', 'Ca_16960_v3' => 'car', 'Ca_17775_v3' => 'car', 'Ca_30464_v3' => 'car', 'Cc06_g08160' => 'ccan', 'Cc07_g01520' => 'ccan', 'Cc11_g15810' => 'ccan', 'CDE02G2840' => 'cde', 'CDE03G0093' => 'cde', 'CDE04G2127' => 'cde', 'CDE07G1857' => 'cde', 'CDE09G1246' => 'cde', 'Cfa003412' => 'cfa', 'Cfa007341' => 'cfa', 'Cfa009220' => 'cfa', 'Ciclev10008737m.g' => 'ccl', 'Ciclev10015565m.g' => 'ccl', 'Ciclev10031761m.g' => 'ccl', 'CiPaw.03G045300' => 'cil', 'CiPaw.03G247200' => 'cil', 'CiPaw.04G029500' => 'cil', 'CiPaw.04G174000' => 'cil', 'CiPaw.05G181200' => 'cil', 'CiPaw.06G067100' => 'cil', 'ClCG05G025800' => 'cla', 'ClCG06G011400' => 'cla', 'ClCG09G019360' => 'cla', 'COL.COLO4_04827' => 'col', 'COL.COLO4_29170' => 'col', 'COL.COLO4_35131' => 'col', 'COL.COLO4_35132' => 'col', 'Cpa.g.sc33.32' => 'cpa', 'Cpa.g.sc46.29' => 'cpa', 'Cpa.g.sc796.1' => 'cpa', 'CsaV3_1G030420' => 'csa', 'CsaV3_5G027050' => 'csa', 'CsaV3_5G031040' => 'csa', 'CsaV3_UNG023130' => 'csa', 'CSS0007726' => 'camsi', 'CSS0016433' => 'camsi', 'CSS0017656' => 'camsi', 'CSS0025364' => 'camsi', 'CSS0027582' => 'camsi', 'CSS0047288' => 'camsi', 'CSS0049950' => 'camsi', 'DCAR_003843' => 'dca', 'DCAR_007052' => 'dca', 'DCAR_020884' => 'dca', 'DCAR_021730' => 'dca', 'DCAR_024423' => 'dca', 'DCAR_026509' => 'dca', 'DCAR_031158' => 'dca', 'Dinv14728' => 'din', 'Dinv15219' => 'din', 'Dinv25728' => 'din', 'Dinv33428' => 'din', 'Dinv36489' => 'din', 'Dinv41486' => 'din', 'Duzib147G0469' => 'dzi', 'Duzib168G0060' => 'dzi', 'Duzib187G1215' => 'dzi', 'Duzib248G0692' => 'dzi', 'Duzib251G0767' => 'dzi', 'Duzib264G0446' => 'dzi', 'Duzib268G0691' => 'dzi', 'ECA232G4767' => 'eca', 'ECA233G2838' => 'eca', 'ECA234G0391' => 'eca', 'ECA234G0857' => 'eca', 'ECA236G1593' => 'eca', 'ECA238G0565' => 'eca', 'ECA246G1027' => 'eca', 'ECA246G3223' => 'eca', 'ECA246G3470' => 'eca', 'EL10Ac6g13829' => 'bvu', 'EL10Ac6g14093' => 'bvu', 'EL10Ac8g18707' => 'bvu', 'Eucgr.C01369' => 'egr', 'Eucgr.H02492' => 'egr', 'Eucgr.I01733' => 'egr', 'Eucgr.J02255' => 'egr', 'Eucgr.J02257' => 'egr', 'Eucgr.J02258' => 'egr', 'FAN02G1601' => 'fan', 'FAN03G1586' => 'fan', 'FAN03G2986' => 'fan', 'FAN05G4837' => 'fan', 'FAN06G0146' => 'fan', 'FAN07G0858' => 'fan', 'FAN09G3179' => 'fan', 'FAN10G0669' => 'fan', 'FAN12G2358' => 'fan', 'FAN14G4198' => 'fan', 'FAN14G5112' => 'fan', 'FAN17G0342' => 'fan', 'FAN19G0342' => 'fan', 'FAN19G0962' => 'fan', 'FAN19G1101' => 'fan', 'FAN19G1872' => 'fan', 'FAN22G0356' => 'fan', 'FAN23G0744' => 'fan', 'FAN23G1914' => 'fan', 'FAN26G0032' => 'fan', 'FAN28G0625' => 'fan', 'FvH4_1g02710' => 'fve', 'FvH4_1g02720' => 'fve', 'FvH4_4g25670' => 'fve', 'FvH4_6g51700' => 'fve', 'FvH4_7g20170' => 'fve', 'Glyma.05G175000' => 'gma', 'Glyma.08G132300' => 'gma', 'Glyma.11G243000' => 'gma', 'Glyma.13G158900' => 'gma', 'Glyma.17G112400' => 'gma', 'Glyma.18G014100' => 'gma', 'Glyma.19G003100' => 'gma', 'Glyma.19G056500' => 'gma', 'Gohir.A01G158900' => 'ghi', 'Gohir.A05G312600' => 'ghi', 'Gohir.A05G354900' => 'ghi', 'Gohir.A07G037200' => 'ghi', 'Gohir.A09G030000' => 'ghi', 'Gohir.A12G145200' => 'ghi', 'Gohir.D01G151500' => 'ghi', 'Gohir.D04G058300' => 'ghi', 'Gohir.D05G314100' => 'ghi', 'Gohir.D07G041400' => 'ghi', 'Gohir.D09G029700' => 'ghi', 'Gohir.D12G149700' => 'ghi', 'Gorai.001G043800' => 'gra', 'Gorai.002G187800' => 'gra', 'Gorai.006G034700' => 'gra', 'Gorai.008G161200' => 'gra', 'Gorai.009G335700' => 'gra', 'Gorai.012G065000' => 'gra', 'GSVIVG01000535001' => 'vvi', 'GSVIVG01015572001' => 'vvi', 'GSVIVG01032386001' => 'vvi', 'HanXRQChr05g0138531' => 'han', 'HanXRQChr06g0174391' => 'han', 'HanXRQChr07g0199021' => 'han', 'HanXRQChr08g0208211' => 'han', 'HanXRQChr09g0255471' => 'han', 'HanXRQChr10g0315791' => 'han', 'HanXRQChr12g0371991' => 'han', 'HanXRQChr15g0475251' => 'han', 'HanXRQChr17g0540001' => 'han', 'HanXRQChr17g0548631' => 'han', 'HanXRQChr17g0569561' => 'han', 'Haze_12256' => 'cav', 'Haze_14756' => 'cav', 'Haze_25528' => 'cav', 'Hma1.2p1_0079F.1_g041020' => 'hma', 'Hma1.2p1_0818F.1_g223260' => 'hma', 'Hma1.2p1_1747F.1_g300530' => 'hma', 'HPP92_004607' => 'vpl', 'HPP92_004608' => 'vpl', 'HPP92_006181' => 'vpl', 'HPP92_012192' => 'vpl', 'HPP92_015680' => 'vpl', 'HPP92_020249' => 'vpl', 'HPP92_021376' => 'vpl', 'HPP92_024275' => 'vpl', 'Hund06031' => 'sun', 'Hund25391' => 'sun', 'Lalb_Chr07g0185371' => 'lal', 'Lalb_Chr07g0185381' => 'lal', 'Lalb_Chr12g0204011' => 'lal', 'Lalb_Chr13g0301671' => 'lal', 'Lalb_Chr14g0362851' => 'lal', 'Lalb_Chr24g0403581' => 'lal', 'Lj1g0000233' => 'lja', 'Lj2g0018120' => 'lja', 'Lj3C621T0' => 'lonja', 'Lj3P1059T14' => 'lonja', 'Lj3P611T9' => 'lonja', 'Lj3P614T13' => 'lonja', 'Lj3P615T5' => 'lonja', 'Lj4g0012315' => 'lja', 'Lj4g0026182' => 'lja', 'Lj6P813T16' => 'lonja', 'Lj7C427T7' => 'lonja', 'Lj7C427T8' => 'lonja', 'Lj7P600T41' => 'lonja', 'Lju41C42G17' => 'lonja', 'Lsat_1_v5_gn_0_47300' => 'lsa', 'Lsat_1_v5_gn_2_91280' => 'lsa', 'Lsat_1_v5_gn_3_30561' => 'lsa', 'Lsat_1_v5_gn_4_184321' => 'lsa', 'Lsat_1_v5_gn_4_4041' => 'lsa', 'Lsat_1_v5_gn_5_92000' => 'lsa', 'Lsat_1_v5_gn_8_152940' => 'lsa', 'Lsat_1_v5_gn_8_62401' => 'lsa', 'Manes.06G055900' => 'mes', 'Manes.12G022200' => 'mes', 'Manes.13G023300' => 'mes', 'Manes.14G115000' => 'mes', 'Manes.15G151700' => 'mes', 'Manes.17G111300' => 'mes', 'Mapoly0226s0009' => 'mpo', 'MBI02_g25363_MAGBIO' => 'mbi', 'MBI06_g00027_MAGBIO' => 'mbi', 'MBI10_g13034_MAGBIO' => 'mbi', 'MD09G1023400' => 'mdo', 'MD13G1100100' => 'mdo', 'MD15G1169200' => 'mdo', 'MD16G1101100' => 'mdo', 'MD17G1022900' => 'mdo', 'Medtr3g096150' => 'mtr', 'Medtr4g115070' => 'mtr', 'Medtr7g033325' => 'mtr', 'Medtr8g089840' => 'mtr', 'MELO3C010319.2' => 'cme', 'MELO3C011944.2' => 'cme', 'MELO3C021589.2' => 'cme', 'Migut.E00207' => 'egut', 'Migut.H00067' => 'egut', 'Migut.K00433' => 'egut', 'Migut.K00606' => 'egut', 'Migut.K01410' => 'egut', 'MSTRG.13347' => 'ama', 'MSTRG.24045' => 'ama', 'MSTRG.2428' => 'ama', 'MSTRG.26410' => 'ama', 'MSTRG.3139' => 'ama', 'MSTRG.3286' => 'ama', 'MSTRG.563' => 'ama', 'MSTRG.7941' => 'ama', 'Nitab4.5_0000028g0060' => 'nta', 'Nitab4.5_0000065g0260' => 'nta', 'Nitab4.5_0000112g0060' => 'nta', 'Nitab4.5_0000489g0120' => 'nta', 'Nitab4.5_0001776g0050' => 'nta', 'Nitab4.5_0001854g0010' => 'nta', 'Nitab4.5_0001860g0020' => 'nta', 'Nitab4.5_0004352g0010' => 'nta', 'Nitab4.5_0008716g0020' => 'nta', 'Nitab4.5_0008922g0010' => 'nta', 'Nn3g16693' => 'nnu', 'Nn4g22596' => 'nnu', 'Nn7g37639' => 'nnu', 'Oeu001701.1' => 'oeu', 'Oeu018149.1' => 'oeu', 'Oeu026220.1' => 'oeu', 'Oeu038635.1' => 'oeu', 'Oeu049176.1' => 'oeu', 'Oeu056706.1' => 'oeu', 'Oeu056937.1' => 'oeu', 'Oeu057540.1' => 'oeu', 'Os02g0594900' => 'osa', 'Os02g0595100' => 'osa', 'Os04g0477500' => 'osa', 'Os12g0611900' => 'osa', 'Peaxi162Scf00076g00020' => 'pax', 'Peaxi162Scf00128g00217' => 'pax', 'Peaxi162Scf00129g01640' => 'pax', 'Peaxi162Scf00669g00007' => 'pax', 'Peaxi162Scf00700g00421' => 'pax', 'Peaxi162Scf00801g00038' => 'pax', 'Peaxi162Scf00891g00025' => 'pax', 'PGR083G0909' => 'pgr', 'PGR119G1005' => 'pgr', 'PGR142G2236' => 'pgr', 'PGR142G3388' => 'pgr', 'PGSC0003DMG400004514' => 'stu', 'PGSC0003DMG400012635' => 'stu', 'PGSC0003DMG400015730' => 'stu', 'PGSC0003DMG400018611' => 'stu', 'PGSC0003DMG400030897' => 'stu', 'Phvul.001G254800' => 'pvu', 'Phvul.002G260100' => 'pvu', 'Phvul.003G167600' => 'pvu', 'Phvul.004G005100' => 'pvu', 'Potri.001G343600' => 'ptr', 'Potri.006G066700' => 'ptr', 'Potri.008G186000' => 'ptr', 'Potri.010G046900' => 'ptr', 'Potri.018G127900' => 'ptr', 'Pp3c20_17750' => 'ppa', 'Pp3c24_4380' => 'ppa', 'Prupe.1G245800' => 'ppe', 'Prupe.3G293400' => 'ppe', 'Prupe.7G247400' => 'ppe', 'Psat0s145g0120' => 'psa', 'Psat0s595g0040' => 'psa', 'Psat0s595g0120' => 'psa', 'Psat3g175040' => 'psa', 'Psat7g058120' => 'psa', 'PSO017G0428' => 'pso', 'PSO063G7510' => 'pso', 'PSO067G0046' => 'pso', 'PSO478G1073' => 'pso', 'PSO675G3677' => 'pso', 'PSO675G6558' => 'pso', 'PSO675G7520' => 'pso', 'PSO675G8959' => 'pso', 'QL02p074089' => 'qlo', 'QL02p089614' => 'qlo', 'QL03p057736' => 'qlo', 'RcHm_v2.0_Chr1g0364131' => 'rch', 'RcHm_v2.0_Chr2g0087801' => 'rch', 'RcHm_v2.0_Chr2g0087821' => 'rch', 'RcHm_v2.0_Chr2g0173231' => 'rch', 'RcHm_v2.0_Chr4g0433111' => 'rch', 'Rhsim03G0250300' => 'rsi', 'Rhsim08G0048400' => 'rsi', 'Rhsim10G0014800' => 'rsi', 'Rhsim12G0040100' => 'rsi', 'Rhsim12G0109700' => 'rsi', 'Sabra06G0049600' => 'sbr', 'Sabra08G0141000' => 'sbr', 'Sabra10G0021400' => 'sbr', 'Sabra16G0222900' => 'sbr', 'Sabra18G0108600' => 'sbr', 'SalBow1G0433' => 'sbo', 'SalBow1G2038' => 'sbo', 'SalBow1G5003' => 'sbo', 'SalBow7G1197' => 'sbo', 'SalBow8G3506' => 'sbo', 'Sc03g0007300' => 'sci', 'Sc11g0000950' => 'sci', 'Sc14g0008750' => 'sci', 'Sc18g0000420' => 'sci', 'Sed0006754' => 'sed', 'Sed0008741' => 'sed', 'Sed0017172' => 'sed', 'Sed0018925' => 'sed', 'Sed0023326' => 'sed', 'Sed0025909' => 'sed', 'SEGI_05333' => 'sgi', 'SEGI_10362' => 'sgi', 'SEGI_13380' => 'sgi', 'SEGI_24306' => 'sgi', 'SEGI_29077' => 'sgi', 'SEGI_29095' => 'sgi', 'SEGI_36534' => 'sgi', 'SEGI_37506' => 'sgi', 'SEGI_38321' => 'sgi', 'SGA_v2.0_scaffold307G48031' => 'sas', 'SGA_v2.0_scaffold47G17507' => 'sas', 'SGA_v2.0_scaffold63G21736' => 'sas', 'SGA_v2.0_scaffold87G27070' => 'sas', 'SHI17794' => 'shi', 'SHI28851' => 'shi', 'SMO165G0155' => 'smo', 'SMO340G0217' => 'smo', 'SMO367G1210' => 'smo', 'Solyc02g093430.3' => 'sly', 'Solyc05g013580.4' => 'sly', 'Solyc07g008030.3' => 'sly', 'Solyc12g035470.2' => 'sly', 'Sopen02g038020' => 'spe', 'Sopen05g008490' => 'spe', 'Sopen07g003910' => 'spe', 'Sopen12g015240' => 'spe', 'Sp1g11550' => 'spa', 'Sp2g16710' => 'spa', 'Sp3g00430' => 'spa', 'Sp3g26780' => 'spa', 'Sp5g22900' => 'spa', 'Sp6g29530' => 'spa', 'TAR371G0794' => 'tar', 'TAR374G0164' => 'tar', 'TAR622G0165' => 'tar', 'TAR626G0929' => 'tar', 'TAR629G2155' => 'tar', 'THA.LOC104805282' => 'tha', 'THA.LOC104805363' => 'tha', 'THA.LOC104808968' => 'tha', 'THA.LOC104821093' => 'tha', 'THA.LOC104823953' => 'tha', 'THA.LOC104825562' => 'tha', 'THA.LOC104825665' => 'tha', 'Thecc.02G261400' => 'tca', 'Thecc.04G019200' => 'tca', 'Thecc.09G130400' => 'tca', 'Thhalv10004374m.g' => 'esa', 'Thhalv10007850m.g' => 'esa', 'Thhalv10013782m.g' => 'esa', 'Thhalv10018686m.g' => 'esa', 'Thhalv10020899m.g' => 'esa', 'Thhalv10022755m.g' => 'esa', 'TPR.G23851' => 'tpr', 'TPR.G26500' => 'tpr', 'TPR.G27267' => 'tpr', 'TPR.G32001' => 'tpr', 'TPR.G6251' => 'tpr', 'TPR.G8167' => 'tpr', 'TWI12G1330' => 'twi', 'TWI18G1239' => 'twi', 'TWI34G0979' => 'twi', 'TWI36G0670' => 'twi', 'TWI36G0707' => 'twi', 'TWI56G0233' => 'twi', 'TWI75G1809' => 'twi', 'unitig_21.g20874' => 'ugi', 'unitig_26.g10343' => 'ugi', 'unitig_46.g18392' => 'ugi', 'unitig_52.g17178' => 'ugi', 'unitig_8.g2934' => 'ugi', 'vmacro01122' => 'vma', 'vmacro05875' => 'vma', 'vmacro06147' => 'vma', 'vmacro16191' => 'vma', 'vmacro18293' => 'vma', 'VMungo0251G3707' => 'vmu', 'VMungo0464G1521' => 'vmu', 'VMungo1215G0205' => 'vmu', 'VMungo1383G2484' => 'vmu', 'Zm00001eb079610' => 'zma', 'Zm00001eb135990' => 'zma', 'Zm00001eb183710' => 'zma', 'Zm00001eb246020' => 'zma' ) $gf_id = 'HOM05D001124' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001124' ) $data_identifier = 'HOM05D001124' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 6, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 7, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 21, 'bol' => (int) 10, 'bra' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 6, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 9, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 21, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 8, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 10, 'lsa' => (int) 8, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 8, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 9, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb246020' $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' => 'HOM05D001124', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '548', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02520' => 'bna', 'A03p06630' => 'bna', 'A05p44460' => 'bna', 'A06p08710' => 'bna', 'A06p41090' => 'bna', 'A07p32320' => 'bna', 'A08p32520' => 'bna', 'A09p10360' => 'bna', 'A10p24080' => 'bna', 'Aa31LG11G15250' => 'aar', 'Aa31LG1G1800' => 'aar', 'Aa31LG2G5120' => 'aar', 'Aa31LG2G6070' => 'aar', 'Aa31LG5G10770' => 'aar', 'Aa31sc61G90' => 'aar', 'Actinidia01352' => 'ach', 'Actinidia05983' => 'ach', 'Actinidia08133' => 'ach', 'Actinidia15101' => 'ach', 'Actinidia26379' => 'ach', 'Actinidia35778' => 'ach', 'Actinidia36123' => 'ach', 'Actinidia37436' => 'ach', 'Actinidia38730' => 'ach', 'Ah.02g128210' => 'amhyb', 'Ah.03g132990' => 'amhyb', 'Ah.14g079410' => 'amhyb', 'AL1G24640' => 'aly', 'AL2G26680' => 'aly', 'AL3G10530' => 'aly', 'AL3G45230' => 'aly', 'AL5G15230' => 'aly', 'AL5G16960' => 'aly', 'AL6G25210' => 'aly', 'Aqoxy2G00441' => 'aox', 'Aqoxy3G01236' => 'aox', 'Aqoxy5G03746' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3RQ047' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C7GMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9C8JER' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MBL6KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YXCZ83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZANX40' => 'arhy', 'AT1G12990' => 'ath', 'AT1G67880' => 'ath', 'AT2G13290' => 'ath', 'AT3G01620' => 'ath', 'AT3G26445' => 'ath', 'AT3G27540' => 'ath', 'AT5G14480' => 'ath', 'ATR0824G026' => 'atr', 'ATR1098G019' => 'atr', 'Atru.chr11.2145' => 'acertr', 'Atru.chr2.3636' => 'acertr', 'Atru.chr2.3644' => 'acertr', 'Atru.chr6.2422' => 'acertr', 'Atru.chr7.1112' => 'acertr', 'AUR62005469' => 'cqu', 'AUR62011166' => 'cqu', 'AUR62013319' => 'cqu', 'AUR62024273' => 'cqu', 'AUR62028420' => 'cqu', 'AUR62041942' => 'cqu', 'BcaB01g04969' => 'bca', 'BcaB01g06371' => 'bca', 'BcaB02g11494' => 'bca', 'BcaB03g15382' => 'bca', 'BcaB08g36994' => 'bca', 'BcaC03g13477' => 'bca', 'BcaC03g13478' => 'bca', 'BcaC03g13480' => 'bca', 'BcaC03g13481' => 'bca', 'BcaC03g13486' => 'bca', 'BcaC04g19031' => 'bca', 'BcaC04g23085' => 'bca', 'BcaC05g25094' => 'bca', 'BcaC05g25096' => 'bca', 'BcaC05g25138' => 'bca', 'BcaC05g30416' => 'bca', 'BcaC05g30455' => 'bca', 'BcaC06g30979' => 'bca', 'BcaC06g33805' => 'bca', 'BcaC08g46021' => 'bca', 'BcaNung03154' => 'bca', 'BolC2t06623H' => 'bol', 'BolC2t06632H' => 'bol', 'BolC2t06635H' => 'bol', 'BolC2t06638H' => 'bol', 'BolC3t13266H' => 'bol', 'BolC5t29776H' => 'bol', 'BolC6t38912H' => 'bol', 'BolC7t44183H' => 'bol', 'BolC9t54123H' => 'bol', 'BolC9t59107H' => 'bol', 'BraA02t05221Z' => 'bra', 'BraA03t09996Z' => 'bra', 'BraA05t23210Z' => 'bra', 'BraA06t24068Z' => 'bra', 'BraA06t27032Z' => 'bra', 'BraA08t35176Z' => 'bra', 'BraA09t36680Z' => 'bra', 'BraA10t44471Z' => 'bra', 'C02p06760' => 'bna', 'C02p06890' => 'bna', 'C02p07010' => 'bna', 'C03p07660' => 'bna', 'C05p10300' => 'bna', 'C06p38150' => 'bna', 'C07p36650' => 'bna', 'C08p15770' => 'bna', 'C09p12300' => 'bna', 'C09p62700' => 'bna', 'C09p75040' => 'bna', 'CAN.G13.1' => 'can', 'CAN.G138.4' => 'can', 'CAN.G44.6' => 'can', 'CAN.G473.19' => 'can', 'CANSAT01G0835' => 'cansat', 'CANSAT11G0246' => 'cansat', 'CANSAT11G1766' => 'cansat', 'CANSAT64G1954' => 'cansat', 'CARHR013330' => 'chi', 'CARHR060530' => 'chi', 'CARHR075300' => 'chi', 'CARHR105120' => 'chi', 'CARHR148910' => 'chi', 'CARHR198830' => 'chi', 'Carub.0001s1275' => 'cru', 'Carub.0002s1437' => 'cru', 'Carub.0003s0044' => 'cru', 'Carub.0003s2787' => 'cru', 'Carub.0005s0597' => 'cru', 'Carub.0006s1266' => 'cru', 'Ca_06935_v3' => 'car', 'Ca_13559_v3' => 'car', 'Ca_16941_v3' => 'car', 'Ca_16960_v3' => 'car', 'Ca_17775_v3' => 'car', 'Ca_30464_v3' => 'car', 'Cc06_g08160' => 'ccan', 'Cc07_g01520' => 'ccan', 'Cc11_g15810' => 'ccan', 'CDE02G2840' => 'cde', 'CDE03G0093' => 'cde', 'CDE04G2127' => 'cde', 'CDE07G1857' => 'cde', 'CDE09G1246' => 'cde', 'Cfa003412' => 'cfa', 'Cfa007341' => 'cfa', 'Cfa009220' => 'cfa', 'Ciclev10008737m.g' => 'ccl', 'Ciclev10015565m.g' => 'ccl', 'Ciclev10031761m.g' => 'ccl', 'CiPaw.03G045300' => 'cil', 'CiPaw.03G247200' => 'cil', 'CiPaw.04G029500' => 'cil', 'CiPaw.04G174000' => 'cil', 'CiPaw.05G181200' => 'cil', 'CiPaw.06G067100' => 'cil', 'ClCG05G025800' => 'cla', 'ClCG06G011400' => 'cla', 'ClCG09G019360' => 'cla', 'COL.COLO4_04827' => 'col', 'COL.COLO4_29170' => 'col', 'COL.COLO4_35131' => 'col', 'COL.COLO4_35132' => 'col', 'Cpa.g.sc33.32' => 'cpa', 'Cpa.g.sc46.29' => 'cpa', 'Cpa.g.sc796.1' => 'cpa', 'CsaV3_1G030420' => 'csa', 'CsaV3_5G027050' => 'csa', 'CsaV3_5G031040' => 'csa', 'CsaV3_UNG023130' => 'csa', 'CSS0007726' => 'camsi', 'CSS0016433' => 'camsi', 'CSS0017656' => 'camsi', 'CSS0025364' => 'camsi', 'CSS0027582' => 'camsi', 'CSS0047288' => 'camsi', 'CSS0049950' => 'camsi', 'DCAR_003843' => 'dca', 'DCAR_007052' => 'dca', 'DCAR_020884' => 'dca', 'DCAR_021730' => 'dca', 'DCAR_024423' => 'dca', 'DCAR_026509' => 'dca', 'DCAR_031158' => 'dca', 'Dinv14728' => 'din', 'Dinv15219' => 'din', 'Dinv25728' => 'din', 'Dinv33428' => 'din', 'Dinv36489' => 'din', 'Dinv41486' => 'din', 'Duzib147G0469' => 'dzi', 'Duzib168G0060' => 'dzi', 'Duzib187G1215' => 'dzi', 'Duzib248G0692' => 'dzi', 'Duzib251G0767' => 'dzi', 'Duzib264G0446' => 'dzi', 'Duzib268G0691' => 'dzi', 'ECA232G4767' => 'eca', 'ECA233G2838' => 'eca', 'ECA234G0391' => 'eca', 'ECA234G0857' => 'eca', 'ECA236G1593' => 'eca', 'ECA238G0565' => 'eca', 'ECA246G1027' => 'eca', 'ECA246G3223' => 'eca', 'ECA246G3470' => 'eca', 'EL10Ac6g13829' => 'bvu', 'EL10Ac6g14093' => 'bvu', 'EL10Ac8g18707' => 'bvu', 'Eucgr.C01369' => 'egr', 'Eucgr.H02492' => 'egr', 'Eucgr.I01733' => 'egr', 'Eucgr.J02255' => 'egr', 'Eucgr.J02257' => 'egr', 'Eucgr.J02258' => 'egr', 'FAN02G1601' => 'fan', 'FAN03G1586' => 'fan', 'FAN03G2986' => 'fan', 'FAN05G4837' => 'fan', 'FAN06G0146' => 'fan', 'FAN07G0858' => 'fan', 'FAN09G3179' => 'fan', 'FAN10G0669' => 'fan', 'FAN12G2358' => 'fan', 'FAN14G4198' => 'fan', 'FAN14G5112' => 'fan', 'FAN17G0342' => 'fan', 'FAN19G0342' => 'fan', 'FAN19G0962' => 'fan', 'FAN19G1101' => 'fan', 'FAN19G1872' => 'fan', 'FAN22G0356' => 'fan', 'FAN23G0744' => 'fan', 'FAN23G1914' => 'fan', 'FAN26G0032' => 'fan', 'FAN28G0625' => 'fan', 'FvH4_1g02710' => 'fve', 'FvH4_1g02720' => 'fve', 'FvH4_4g25670' => 'fve', 'FvH4_6g51700' => 'fve', 'FvH4_7g20170' => 'fve', 'Glyma.05G175000' => 'gma', 'Glyma.08G132300' => 'gma', 'Glyma.11G243000' => 'gma', 'Glyma.13G158900' => 'gma', 'Glyma.17G112400' => 'gma', 'Glyma.18G014100' => 'gma', 'Glyma.19G003100' => 'gma', 'Glyma.19G056500' => 'gma', 'Gohir.A01G158900' => 'ghi', 'Gohir.A05G312600' => 'ghi', 'Gohir.A05G354900' => 'ghi', 'Gohir.A07G037200' => 'ghi', 'Gohir.A09G030000' => 'ghi', 'Gohir.A12G145200' => 'ghi', 'Gohir.D01G151500' => 'ghi', 'Gohir.D04G058300' => 'ghi', 'Gohir.D05G314100' => 'ghi', 'Gohir.D07G041400' => 'ghi', 'Gohir.D09G029700' => 'ghi', 'Gohir.D12G149700' => 'ghi', 'Gorai.001G043800' => 'gra', 'Gorai.002G187800' => 'gra', 'Gorai.006G034700' => 'gra', 'Gorai.008G161200' => 'gra', 'Gorai.009G335700' => 'gra', 'Gorai.012G065000' => 'gra', 'GSVIVG01000535001' => 'vvi', 'GSVIVG01015572001' => 'vvi', 'GSVIVG01032386001' => 'vvi', 'HanXRQChr05g0138531' => 'han', 'HanXRQChr06g0174391' => 'han', 'HanXRQChr07g0199021' => 'han', 'HanXRQChr08g0208211' => 'han', 'HanXRQChr09g0255471' => 'han', 'HanXRQChr10g0315791' => 'han', 'HanXRQChr12g0371991' => 'han', 'HanXRQChr15g0475251' => 'han', 'HanXRQChr17g0540001' => 'han', 'HanXRQChr17g0548631' => 'han', 'HanXRQChr17g0569561' => 'han', 'Haze_12256' => 'cav', 'Haze_14756' => 'cav', 'Haze_25528' => 'cav', 'Hma1.2p1_0079F.1_g041020' => 'hma', 'Hma1.2p1_0818F.1_g223260' => 'hma', 'Hma1.2p1_1747F.1_g300530' => 'hma', 'HPP92_004607' => 'vpl', 'HPP92_004608' => 'vpl', 'HPP92_006181' => 'vpl', 'HPP92_012192' => 'vpl', 'HPP92_015680' => 'vpl', 'HPP92_020249' => 'vpl', 'HPP92_021376' => 'vpl', 'HPP92_024275' => 'vpl', 'Hund06031' => 'sun', 'Hund25391' => 'sun', 'Lalb_Chr07g0185371' => 'lal', 'Lalb_Chr07g0185381' => 'lal', 'Lalb_Chr12g0204011' => 'lal', 'Lalb_Chr13g0301671' => 'lal', 'Lalb_Chr14g0362851' => 'lal', 'Lalb_Chr24g0403581' => 'lal', 'Lj1g0000233' => 'lja', 'Lj2g0018120' => 'lja', 'Lj3C621T0' => 'lonja', 'Lj3P1059T14' => 'lonja', 'Lj3P611T9' => 'lonja', 'Lj3P614T13' => 'lonja', 'Lj3P615T5' => 'lonja', 'Lj4g0012315' => 'lja', 'Lj4g0026182' => 'lja', 'Lj6P813T16' => 'lonja', 'Lj7C427T7' => 'lonja', 'Lj7C427T8' => 'lonja', 'Lj7P600T41' => 'lonja', 'Lju41C42G17' => 'lonja', 'Lsat_1_v5_gn_0_47300' => 'lsa', 'Lsat_1_v5_gn_2_91280' => 'lsa', 'Lsat_1_v5_gn_3_30561' => 'lsa', 'Lsat_1_v5_gn_4_184321' => 'lsa', 'Lsat_1_v5_gn_4_4041' => 'lsa', 'Lsat_1_v5_gn_5_92000' => 'lsa', 'Lsat_1_v5_gn_8_152940' => 'lsa', 'Lsat_1_v5_gn_8_62401' => 'lsa', 'Manes.06G055900' => 'mes', 'Manes.12G022200' => 'mes', 'Manes.13G023300' => 'mes', 'Manes.14G115000' => 'mes', 'Manes.15G151700' => 'mes', 'Manes.17G111300' => 'mes', 'Mapoly0226s0009' => 'mpo', 'MBI02_g25363_MAGBIO' => 'mbi', 'MBI06_g00027_MAGBIO' => 'mbi', 'MBI10_g13034_MAGBIO' => 'mbi', 'MD09G1023400' => 'mdo', 'MD13G1100100' => 'mdo', 'MD15G1169200' => 'mdo', 'MD16G1101100' => 'mdo', 'MD17G1022900' => 'mdo', 'Medtr3g096150' => 'mtr', 'Medtr4g115070' => 'mtr', 'Medtr7g033325' => 'mtr', 'Medtr8g089840' => 'mtr', 'MELO3C010319.2' => 'cme', 'MELO3C011944.2' => 'cme', 'MELO3C021589.2' => 'cme', 'Migut.E00207' => 'egut', 'Migut.H00067' => 'egut', 'Migut.K00433' => 'egut', 'Migut.K00606' => 'egut', 'Migut.K01410' => 'egut', 'MSTRG.13347' => 'ama', 'MSTRG.24045' => 'ama', 'MSTRG.2428' => 'ama', 'MSTRG.26410' => 'ama', 'MSTRG.3139' => 'ama', 'MSTRG.3286' => 'ama', 'MSTRG.563' => 'ama', 'MSTRG.7941' => 'ama', 'Nitab4.5_0000028g0060' => 'nta', 'Nitab4.5_0000065g0260' => 'nta', 'Nitab4.5_0000112g0060' => 'nta', 'Nitab4.5_0000489g0120' => 'nta', 'Nitab4.5_0001776g0050' => 'nta', 'Nitab4.5_0001854g0010' => 'nta', 'Nitab4.5_0001860g0020' => 'nta', 'Nitab4.5_0004352g0010' => 'nta', 'Nitab4.5_0008716g0020' => 'nta', 'Nitab4.5_0008922g0010' => 'nta', 'Nn3g16693' => 'nnu', 'Nn4g22596' => 'nnu', 'Nn7g37639' => 'nnu', 'Oeu001701.1' => 'oeu', 'Oeu018149.1' => 'oeu', 'Oeu026220.1' => 'oeu', 'Oeu038635.1' => 'oeu', 'Oeu049176.1' => 'oeu', 'Oeu056706.1' => 'oeu', 'Oeu056937.1' => 'oeu', 'Oeu057540.1' => 'oeu', 'Os02g0594900' => 'osa', 'Os02g0595100' => 'osa', 'Os04g0477500' => 'osa', 'Os12g0611900' => 'osa', 'Peaxi162Scf00076g00020' => 'pax', 'Peaxi162Scf00128g00217' => 'pax', 'Peaxi162Scf00129g01640' => 'pax', 'Peaxi162Scf00669g00007' => 'pax', 'Peaxi162Scf00700g00421' => 'pax', 'Peaxi162Scf00801g00038' => 'pax', 'Peaxi162Scf00891g00025' => 'pax', 'PGR083G0909' => 'pgr', 'PGR119G1005' => 'pgr', 'PGR142G2236' => 'pgr', 'PGR142G3388' => 'pgr', 'PGSC0003DMG400004514' => 'stu', 'PGSC0003DMG400012635' => 'stu', 'PGSC0003DMG400015730' => 'stu', 'PGSC0003DMG400018611' => 'stu', 'PGSC0003DMG400030897' => 'stu', 'Phvul.001G254800' => 'pvu', 'Phvul.002G260100' => 'pvu', 'Phvul.003G167600' => 'pvu', 'Phvul.004G005100' => 'pvu', 'Potri.001G343600' => 'ptr', 'Potri.006G066700' => 'ptr', 'Potri.008G186000' => 'ptr', 'Potri.010G046900' => 'ptr', 'Potri.018G127900' => 'ptr', 'Pp3c20_17750' => 'ppa', 'Pp3c24_4380' => 'ppa', 'Prupe.1G245800' => 'ppe', 'Prupe.3G293400' => 'ppe', 'Prupe.7G247400' => 'ppe', 'Psat0s145g0120' => 'psa', 'Psat0s595g0040' => 'psa', 'Psat0s595g0120' => 'psa', 'Psat3g175040' => 'psa', 'Psat7g058120' => 'psa', 'PSO017G0428' => 'pso', 'PSO063G7510' => 'pso', 'PSO067G0046' => 'pso', 'PSO478G1073' => 'pso', 'PSO675G3677' => 'pso', 'PSO675G6558' => 'pso', 'PSO675G7520' => 'pso', 'PSO675G8959' => 'pso', 'QL02p074089' => 'qlo', 'QL02p089614' => 'qlo', 'QL03p057736' => 'qlo', 'RcHm_v2.0_Chr1g0364131' => 'rch', 'RcHm_v2.0_Chr2g0087801' => 'rch', 'RcHm_v2.0_Chr2g0087821' => 'rch', 'RcHm_v2.0_Chr2g0173231' => 'rch', 'RcHm_v2.0_Chr4g0433111' => 'rch', 'Rhsim03G0250300' => 'rsi', 'Rhsim08G0048400' => 'rsi', 'Rhsim10G0014800' => 'rsi', 'Rhsim12G0040100' => 'rsi', 'Rhsim12G0109700' => 'rsi', 'Sabra06G0049600' => 'sbr', 'Sabra08G0141000' => 'sbr', 'Sabra10G0021400' => 'sbr', 'Sabra16G0222900' => 'sbr', 'Sabra18G0108600' => 'sbr', 'SalBow1G0433' => 'sbo', 'SalBow1G2038' => 'sbo', 'SalBow1G5003' => 'sbo', 'SalBow7G1197' => 'sbo', 'SalBow8G3506' => 'sbo', 'Sc03g0007300' => 'sci', 'Sc11g0000950' => 'sci', 'Sc14g0008750' => 'sci', 'Sc18g0000420' => 'sci', 'Sed0006754' => 'sed', 'Sed0008741' => 'sed', 'Sed0017172' => 'sed', 'Sed0018925' => 'sed', 'Sed0023326' => 'sed', 'Sed0025909' => 'sed', 'SEGI_05333' => 'sgi', 'SEGI_10362' => 'sgi', 'SEGI_13380' => 'sgi', 'SEGI_24306' => 'sgi', 'SEGI_29077' => 'sgi', 'SEGI_29095' => 'sgi', 'SEGI_36534' => 'sgi', 'SEGI_37506' => 'sgi', 'SEGI_38321' => 'sgi', 'SGA_v2.0_scaffold307G48031' => 'sas', 'SGA_v2.0_scaffold47G17507' => 'sas', 'SGA_v2.0_scaffold63G21736' => 'sas', 'SGA_v2.0_scaffold87G27070' => 'sas', 'SHI17794' => 'shi', 'SHI28851' => 'shi', 'SMO165G0155' => 'smo', 'SMO340G0217' => 'smo', 'SMO367G1210' => 'smo', 'Solyc02g093430.3' => 'sly', 'Solyc05g013580.4' => 'sly', 'Solyc07g008030.3' => 'sly', 'Solyc12g035470.2' => 'sly', 'Sopen02g038020' => 'spe', 'Sopen05g008490' => 'spe', 'Sopen07g003910' => 'spe', 'Sopen12g015240' => 'spe', 'Sp1g11550' => 'spa', 'Sp2g16710' => 'spa', 'Sp3g00430' => 'spa', 'Sp3g26780' => 'spa', 'Sp5g22900' => 'spa', 'Sp6g29530' => 'spa', 'TAR371G0794' => 'tar', 'TAR374G0164' => 'tar', 'TAR622G0165' => 'tar', 'TAR626G0929' => 'tar', 'TAR629G2155' => 'tar', 'THA.LOC104805282' => 'tha', 'THA.LOC104805363' => 'tha', 'THA.LOC104808968' => 'tha', 'THA.LOC104821093' => 'tha', 'THA.LOC104823953' => 'tha', 'THA.LOC104825562' => 'tha', 'THA.LOC104825665' => 'tha', 'Thecc.02G261400' => 'tca', 'Thecc.04G019200' => 'tca', 'Thecc.09G130400' => 'tca', 'Thhalv10004374m.g' => 'esa', 'Thhalv10007850m.g' => 'esa', 'Thhalv10013782m.g' => 'esa', 'Thhalv10018686m.g' => 'esa', 'Thhalv10020899m.g' => 'esa', 'Thhalv10022755m.g' => 'esa', 'TPR.G23851' => 'tpr', 'TPR.G26500' => 'tpr', 'TPR.G27267' => 'tpr', 'TPR.G32001' => 'tpr', 'TPR.G6251' => 'tpr', 'TPR.G8167' => 'tpr', 'TWI12G1330' => 'twi', 'TWI18G1239' => 'twi', 'TWI34G0979' => 'twi', 'TWI36G0670' => 'twi', 'TWI36G0707' => 'twi', 'TWI56G0233' => 'twi', 'TWI75G1809' => 'twi', 'unitig_21.g20874' => 'ugi', 'unitig_26.g10343' => 'ugi', 'unitig_46.g18392' => 'ugi', 'unitig_52.g17178' => 'ugi', 'unitig_8.g2934' => 'ugi', 'vmacro01122' => 'vma', 'vmacro05875' => 'vma', 'vmacro06147' => 'vma', 'vmacro16191' => 'vma', 'vmacro18293' => 'vma', 'VMungo0251G3707' => 'vmu', 'VMungo0464G1521' => 'vmu', 'VMungo1215G0205' => 'vmu', 'VMungo1383G2484' => 'vmu', 'Zm00001eb079610' => 'zma', 'Zm00001eb135990' => 'zma', 'Zm00001eb183710' => 'zma', 'Zm00001eb246020' => 'zma' ), 'gf_id' => 'HOM05D001124', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001124' ), 'data_identifier' => 'HOM05D001124', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001124', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '548', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02520' => 'bna', 'A03p06630' => 'bna', 'A05p44460' => 'bna', 'A06p08710' => 'bna', 'A06p41090' => 'bna', 'A07p32320' => 'bna', 'A08p32520' => 'bna', 'A09p10360' => 'bna', 'A10p24080' => 'bna', 'Aa31LG11G15250' => 'aar', 'Aa31LG1G1800' => 'aar', 'Aa31LG2G5120' => 'aar', 'Aa31LG2G6070' => 'aar', 'Aa31LG5G10770' => 'aar', 'Aa31sc61G90' => 'aar', 'Actinidia01352' => 'ach', 'Actinidia05983' => 'ach', 'Actinidia08133' => 'ach', 'Actinidia15101' => 'ach', 'Actinidia26379' => 'ach', 'Actinidia35778' => 'ach', 'Actinidia36123' => 'ach', 'Actinidia37436' => 'ach', 'Actinidia38730' => 'ach', 'Ah.02g128210' => 'amhyb', 'Ah.03g132990' => 'amhyb', 'Ah.14g079410' => 'amhyb', 'AL1G24640' => 'aly', 'AL2G26680' => 'aly', 'AL3G10530' => 'aly', 'AL3G45230' => 'aly', 'AL5G15230' => 'aly', 'AL5G16960' => 'aly', 'AL6G25210' => 'aly', 'Aqoxy2G00441' => 'aox', 'Aqoxy3G01236' => 'aox', 'Aqoxy5G03746' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3RQ047' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C7GMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9C8JER' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MBL6KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YXCZ83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZANX40' => 'arhy', 'AT1G12990' => 'ath', 'AT1G67880' => 'ath', 'AT2G13290' => 'ath', 'AT3G01620' => 'ath', 'AT3G26445' => 'ath', 'AT3G27540' => 'ath', 'AT5G14480' => 'ath', 'ATR0824G026' => 'atr', 'ATR1098G019' => 'atr', 'Atru.chr11.2145' => 'acertr', 'Atru.chr2.3636' => 'acertr', 'Atru.chr2.3644' => 'acertr', 'Atru.chr6.2422' => 'acertr', 'Atru.chr7.1112' => 'acertr', 'AUR62005469' => 'cqu', 'AUR62011166' => 'cqu', 'AUR62013319' => 'cqu', 'AUR62024273' => 'cqu', 'AUR62028420' => 'cqu', 'AUR62041942' => 'cqu', 'BcaB01g04969' => 'bca', 'BcaB01g06371' => 'bca', 'BcaB02g11494' => 'bca', 'BcaB03g15382' => 'bca', 'BcaB08g36994' => 'bca', 'BcaC03g13477' => 'bca', 'BcaC03g13478' => 'bca', 'BcaC03g13480' => 'bca', 'BcaC03g13481' => 'bca', 'BcaC03g13486' => 'bca', 'BcaC04g19031' => 'bca', 'BcaC04g23085' => 'bca', 'BcaC05g25094' => 'bca', 'BcaC05g25096' => 'bca', 'BcaC05g25138' => 'bca', 'BcaC05g30416' => 'bca', 'BcaC05g30455' => 'bca', 'BcaC06g30979' => 'bca', 'BcaC06g33805' => 'bca', 'BcaC08g46021' => 'bca', 'BcaNung03154' => 'bca', 'BolC2t06623H' => 'bol', 'BolC2t06632H' => 'bol', 'BolC2t06635H' => 'bol', 'BolC2t06638H' => 'bol', 'BolC3t13266H' => 'bol', 'BolC5t29776H' => 'bol', 'BolC6t38912H' => 'bol', 'BolC7t44183H' => 'bol', 'BolC9t54123H' => 'bol', 'BolC9t59107H' => 'bol', 'BraA02t05221Z' => 'bra', 'BraA03t09996Z' => 'bra', 'BraA05t23210Z' => 'bra', 'BraA06t24068Z' => 'bra', 'BraA06t27032Z' => 'bra', 'BraA08t35176Z' => 'bra', 'BraA09t36680Z' => 'bra', 'BraA10t44471Z' => 'bra', 'C02p06760' => 'bna', 'C02p06890' => 'bna', 'C02p07010' => 'bna', 'C03p07660' => 'bna', 'C05p10300' => 'bna', 'C06p38150' => 'bna', 'C07p36650' => 'bna', 'C08p15770' => 'bna', 'C09p12300' => 'bna', 'C09p62700' => 'bna', 'C09p75040' => 'bna', 'CAN.G13.1' => 'can', 'CAN.G138.4' => 'can', 'CAN.G44.6' => 'can', 'CAN.G473.19' => 'can', 'CANSAT01G0835' => 'cansat', 'CANSAT11G0246' => 'cansat', 'CANSAT11G1766' => 'cansat', 'CANSAT64G1954' => 'cansat', 'CARHR013330' => 'chi', 'CARHR060530' => 'chi', 'CARHR075300' => 'chi', 'CARHR105120' => 'chi', 'CARHR148910' => 'chi', 'CARHR198830' => 'chi', 'Carub.0001s1275' => 'cru', 'Carub.0002s1437' => 'cru', 'Carub.0003s0044' => 'cru', 'Carub.0003s2787' => 'cru', 'Carub.0005s0597' => 'cru', 'Carub.0006s1266' => 'cru', 'Ca_06935_v3' => 'car', 'Ca_13559_v3' => 'car', 'Ca_16941_v3' => 'car', 'Ca_16960_v3' => 'car', 'Ca_17775_v3' => 'car', 'Ca_30464_v3' => 'car', 'Cc06_g08160' => 'ccan', 'Cc07_g01520' => 'ccan', 'Cc11_g15810' => 'ccan', 'CDE02G2840' => 'cde', 'CDE03G0093' => 'cde', 'CDE04G2127' => 'cde', 'CDE07G1857' => 'cde', 'CDE09G1246' => 'cde', 'Cfa003412' => 'cfa', 'Cfa007341' => 'cfa', 'Cfa009220' => 'cfa', 'Ciclev10008737m.g' => 'ccl', 'Ciclev10015565m.g' => 'ccl', 'Ciclev10031761m.g' => 'ccl', 'CiPaw.03G045300' => 'cil', 'CiPaw.03G247200' => 'cil', 'CiPaw.04G029500' => 'cil', 'CiPaw.04G174000' => 'cil', 'CiPaw.05G181200' => 'cil', 'CiPaw.06G067100' => 'cil', 'ClCG05G025800' => 'cla', 'ClCG06G011400' => 'cla', 'ClCG09G019360' => 'cla', 'COL.COLO4_04827' => 'col', 'COL.COLO4_29170' => 'col', 'COL.COLO4_35131' => 'col', 'COL.COLO4_35132' => 'col', 'Cpa.g.sc33.32' => 'cpa', 'Cpa.g.sc46.29' => 'cpa', 'Cpa.g.sc796.1' => 'cpa', 'CsaV3_1G030420' => 'csa', 'CsaV3_5G027050' => 'csa', 'CsaV3_5G031040' => 'csa', 'CsaV3_UNG023130' => 'csa', 'CSS0007726' => 'camsi', 'CSS0016433' => 'camsi', 'CSS0017656' => 'camsi', 'CSS0025364' => 'camsi', 'CSS0027582' => 'camsi', 'CSS0047288' => 'camsi', 'CSS0049950' => 'camsi', 'DCAR_003843' => 'dca', 'DCAR_007052' => 'dca', 'DCAR_020884' => 'dca', 'DCAR_021730' => 'dca', 'DCAR_024423' => 'dca', 'DCAR_026509' => 'dca', 'DCAR_031158' => 'dca', 'Dinv14728' => 'din', 'Dinv15219' => 'din', 'Dinv25728' => 'din', 'Dinv33428' => 'din', 'Dinv36489' => 'din', 'Dinv41486' => 'din', 'Duzib147G0469' => 'dzi', 'Duzib168G0060' => 'dzi', 'Duzib187G1215' => 'dzi', 'Duzib248G0692' => 'dzi', 'Duzib251G0767' => 'dzi', 'Duzib264G0446' => 'dzi', 'Duzib268G0691' => 'dzi', 'ECA232G4767' => 'eca', 'ECA233G2838' => 'eca', 'ECA234G0391' => 'eca', 'ECA234G0857' => 'eca', 'ECA236G1593' => 'eca', 'ECA238G0565' => 'eca', 'ECA246G1027' => 'eca', 'ECA246G3223' => 'eca', 'ECA246G3470' => 'eca', 'EL10Ac6g13829' => 'bvu', 'EL10Ac6g14093' => 'bvu', 'EL10Ac8g18707' => 'bvu', 'Eucgr.C01369' => 'egr', 'Eucgr.H02492' => 'egr', 'Eucgr.I01733' => 'egr', 'Eucgr.J02255' => 'egr', 'Eucgr.J02257' => 'egr', 'Eucgr.J02258' => 'egr', 'FAN02G1601' => 'fan', 'FAN03G1586' => 'fan', 'FAN03G2986' => 'fan', 'FAN05G4837' => 'fan', 'FAN06G0146' => 'fan', 'FAN07G0858' => 'fan', 'FAN09G3179' => 'fan', 'FAN10G0669' => 'fan', 'FAN12G2358' => 'fan', 'FAN14G4198' => 'fan', 'FAN14G5112' => 'fan', 'FAN17G0342' => 'fan', 'FAN19G0342' => 'fan', 'FAN19G0962' => 'fan', 'FAN19G1101' => 'fan', 'FAN19G1872' => 'fan', 'FAN22G0356' => 'fan', 'FAN23G0744' => 'fan', 'FAN23G1914' => 'fan', 'FAN26G0032' => 'fan', 'FAN28G0625' => 'fan', 'FvH4_1g02710' => 'fve', 'FvH4_1g02720' => 'fve', 'FvH4_4g25670' => 'fve', 'FvH4_6g51700' => 'fve', 'FvH4_7g20170' => 'fve', 'Glyma.05G175000' => 'gma', 'Glyma.08G132300' => 'gma', 'Glyma.11G243000' => 'gma', 'Glyma.13G158900' => 'gma', 'Glyma.17G112400' => 'gma', 'Glyma.18G014100' => 'gma', 'Glyma.19G003100' => 'gma', 'Glyma.19G056500' => 'gma', 'Gohir.A01G158900' => 'ghi', 'Gohir.A05G312600' => 'ghi', 'Gohir.A05G354900' => 'ghi', 'Gohir.A07G037200' => 'ghi', 'Gohir.A09G030000' => 'ghi', 'Gohir.A12G145200' => 'ghi', 'Gohir.D01G151500' => 'ghi', 'Gohir.D04G058300' => 'ghi', 'Gohir.D05G314100' => 'ghi', 'Gohir.D07G041400' => 'ghi', 'Gohir.D09G029700' => 'ghi', 'Gohir.D12G149700' => 'ghi', 'Gorai.001G043800' => 'gra', 'Gorai.002G187800' => 'gra', 'Gorai.006G034700' => 'gra', 'Gorai.008G161200' => 'gra', 'Gorai.009G335700' => 'gra', 'Gorai.012G065000' => 'gra', 'GSVIVG01000535001' => 'vvi', 'GSVIVG01015572001' => 'vvi', 'GSVIVG01032386001' => 'vvi', 'HanXRQChr05g0138531' => 'han', 'HanXRQChr06g0174391' => 'han', 'HanXRQChr07g0199021' => 'han', 'HanXRQChr08g0208211' => 'han', 'HanXRQChr09g0255471' => 'han', 'HanXRQChr10g0315791' => 'han', 'HanXRQChr12g0371991' => 'han', 'HanXRQChr15g0475251' => 'han', 'HanXRQChr17g0540001' => 'han', 'HanXRQChr17g0548631' => 'han', 'HanXRQChr17g0569561' => 'han', 'Haze_12256' => 'cav', 'Haze_14756' => 'cav', 'Haze_25528' => 'cav', 'Hma1.2p1_0079F.1_g041020' => 'hma', 'Hma1.2p1_0818F.1_g223260' => 'hma', 'Hma1.2p1_1747F.1_g300530' => 'hma', 'HPP92_004607' => 'vpl', 'HPP92_004608' => 'vpl', 'HPP92_006181' => 'vpl', 'HPP92_012192' => 'vpl', 'HPP92_015680' => 'vpl', 'HPP92_020249' => 'vpl', 'HPP92_021376' => 'vpl', 'HPP92_024275' => 'vpl', 'Hund06031' => 'sun', 'Hund25391' => 'sun', 'Lalb_Chr07g0185371' => 'lal', 'Lalb_Chr07g0185381' => 'lal', 'Lalb_Chr12g0204011' => 'lal', 'Lalb_Chr13g0301671' => 'lal', 'Lalb_Chr14g0362851' => 'lal', 'Lalb_Chr24g0403581' => 'lal', 'Lj1g0000233' => 'lja', 'Lj2g0018120' => 'lja', 'Lj3C621T0' => 'lonja', 'Lj3P1059T14' => 'lonja', 'Lj3P611T9' => 'lonja', 'Lj3P614T13' => 'lonja', 'Lj3P615T5' => 'lonja', 'Lj4g0012315' => 'lja', 'Lj4g0026182' => 'lja', 'Lj6P813T16' => 'lonja', 'Lj7C427T7' => 'lonja', 'Lj7C427T8' => 'lonja', 'Lj7P600T41' => 'lonja', 'Lju41C42G17' => 'lonja', 'Lsat_1_v5_gn_0_47300' => 'lsa', 'Lsat_1_v5_gn_2_91280' => 'lsa', 'Lsat_1_v5_gn_3_30561' => 'lsa', 'Lsat_1_v5_gn_4_184321' => 'lsa', 'Lsat_1_v5_gn_4_4041' => 'lsa', 'Lsat_1_v5_gn_5_92000' => 'lsa', 'Lsat_1_v5_gn_8_152940' => 'lsa', 'Lsat_1_v5_gn_8_62401' => 'lsa', 'Manes.06G055900' => 'mes', 'Manes.12G022200' => 'mes', 'Manes.13G023300' => 'mes', 'Manes.14G115000' => 'mes', 'Manes.15G151700' => 'mes', 'Manes.17G111300' => 'mes', 'Mapoly0226s0009' => 'mpo', 'MBI02_g25363_MAGBIO' => 'mbi', 'MBI06_g00027_MAGBIO' => 'mbi', 'MBI10_g13034_MAGBIO' => 'mbi', 'MD09G1023400' => 'mdo', 'MD13G1100100' => 'mdo', 'MD15G1169200' => 'mdo', 'MD16G1101100' => 'mdo', 'MD17G1022900' => 'mdo', 'Medtr3g096150' => 'mtr', 'Medtr4g115070' => 'mtr', 'Medtr7g033325' => 'mtr', 'Medtr8g089840' => 'mtr', 'MELO3C010319.2' => 'cme', 'MELO3C011944.2' => 'cme', 'MELO3C021589.2' => 'cme', 'Migut.E00207' => 'egut', 'Migut.H00067' => 'egut', 'Migut.K00433' => 'egut', 'Migut.K00606' => 'egut', 'Migut.K01410' => 'egut', 'MSTRG.13347' => 'ama', 'MSTRG.24045' => 'ama', 'MSTRG.2428' => 'ama', 'MSTRG.26410' => 'ama', 'MSTRG.3139' => 'ama', 'MSTRG.3286' => 'ama', 'MSTRG.563' => 'ama', 'MSTRG.7941' => 'ama', 'Nitab4.5_0000028g0060' => 'nta', 'Nitab4.5_0000065g0260' => 'nta', 'Nitab4.5_0000112g0060' => 'nta', 'Nitab4.5_0000489g0120' => 'nta', 'Nitab4.5_0001776g0050' => 'nta', 'Nitab4.5_0001854g0010' => 'nta', 'Nitab4.5_0001860g0020' => 'nta', 'Nitab4.5_0004352g0010' => 'nta', 'Nitab4.5_0008716g0020' => 'nta', 'Nitab4.5_0008922g0010' => 'nta', 'Nn3g16693' => 'nnu', 'Nn4g22596' => 'nnu', 'Nn7g37639' => 'nnu', 'Oeu001701.1' => 'oeu', 'Oeu018149.1' => 'oeu', 'Oeu026220.1' => 'oeu', 'Oeu038635.1' => 'oeu', 'Oeu049176.1' => 'oeu', 'Oeu056706.1' => 'oeu', 'Oeu056937.1' => 'oeu', 'Oeu057540.1' => 'oeu', 'Os02g0594900' => 'osa', 'Os02g0595100' => 'osa', 'Os04g0477500' => 'osa', 'Os12g0611900' => 'osa', 'Peaxi162Scf00076g00020' => 'pax', 'Peaxi162Scf00128g00217' => 'pax', 'Peaxi162Scf00129g01640' => 'pax', 'Peaxi162Scf00669g00007' => 'pax', 'Peaxi162Scf00700g00421' => 'pax', 'Peaxi162Scf00801g00038' => 'pax', 'Peaxi162Scf00891g00025' => 'pax', 'PGR083G0909' => 'pgr', 'PGR119G1005' => 'pgr', 'PGR142G2236' => 'pgr', 'PGR142G3388' => 'pgr', 'PGSC0003DMG400004514' => 'stu', 'PGSC0003DMG400012635' => 'stu', 'PGSC0003DMG400015730' => 'stu', 'PGSC0003DMG400018611' => 'stu', 'PGSC0003DMG400030897' => 'stu', 'Phvul.001G254800' => 'pvu', 'Phvul.002G260100' => 'pvu', 'Phvul.003G167600' => 'pvu', 'Phvul.004G005100' => 'pvu', 'Potri.001G343600' => 'ptr', 'Potri.006G066700' => 'ptr', 'Potri.008G186000' => 'ptr', 'Potri.010G046900' => 'ptr', 'Potri.018G127900' => 'ptr', 'Pp3c20_17750' => 'ppa', 'Pp3c24_4380' => 'ppa', 'Prupe.1G245800' => 'ppe', 'Prupe.3G293400' => 'ppe', 'Prupe.7G247400' => 'ppe', 'Psat0s145g0120' => 'psa', 'Psat0s595g0040' => 'psa', 'Psat0s595g0120' => 'psa', 'Psat3g175040' => 'psa', 'Psat7g058120' => 'psa', 'PSO017G0428' => 'pso', 'PSO063G7510' => 'pso', 'PSO067G0046' => 'pso', 'PSO478G1073' => 'pso', 'PSO675G3677' => 'pso', 'PSO675G6558' => 'pso', 'PSO675G7520' => 'pso', 'PSO675G8959' => 'pso', 'QL02p074089' => 'qlo', 'QL02p089614' => 'qlo', 'QL03p057736' => 'qlo', 'RcHm_v2.0_Chr1g0364131' => 'rch', 'RcHm_v2.0_Chr2g0087801' => 'rch', 'RcHm_v2.0_Chr2g0087821' => 'rch', 'RcHm_v2.0_Chr2g0173231' => 'rch', 'RcHm_v2.0_Chr4g0433111' => 'rch', 'Rhsim03G0250300' => 'rsi', 'Rhsim08G0048400' => 'rsi', 'Rhsim10G0014800' => 'rsi', 'Rhsim12G0040100' => 'rsi', 'Rhsim12G0109700' => 'rsi', 'Sabra06G0049600' => 'sbr', 'Sabra08G0141000' => 'sbr', 'Sabra10G0021400' => 'sbr', 'Sabra16G0222900' => 'sbr', 'Sabra18G0108600' => 'sbr', 'SalBow1G0433' => 'sbo', 'SalBow1G2038' => 'sbo', 'SalBow1G5003' => 'sbo', 'SalBow7G1197' => 'sbo', 'SalBow8G3506' => 'sbo', 'Sc03g0007300' => 'sci', 'Sc11g0000950' => 'sci', 'Sc14g0008750' => 'sci', 'Sc18g0000420' => 'sci', 'Sed0006754' => 'sed', 'Sed0008741' => 'sed', 'Sed0017172' => 'sed', 'Sed0018925' => 'sed', 'Sed0023326' => 'sed', 'Sed0025909' => 'sed', 'SEGI_05333' => 'sgi', 'SEGI_10362' => 'sgi', 'SEGI_13380' => 'sgi', 'SEGI_24306' => 'sgi', 'SEGI_29077' => 'sgi', 'SEGI_29095' => 'sgi', 'SEGI_36534' => 'sgi', 'SEGI_37506' => 'sgi', 'SEGI_38321' => 'sgi', 'SGA_v2.0_scaffold307G48031' => 'sas', 'SGA_v2.0_scaffold47G17507' => 'sas', 'SGA_v2.0_scaffold63G21736' => 'sas', 'SGA_v2.0_scaffold87G27070' => 'sas', 'SHI17794' => 'shi', 'SHI28851' => 'shi', 'SMO165G0155' => 'smo', 'SMO340G0217' => 'smo', 'SMO367G1210' => 'smo', 'Solyc02g093430.3' => 'sly', 'Solyc05g013580.4' => 'sly', 'Solyc07g008030.3' => 'sly', 'Solyc12g035470.2' => 'sly', 'Sopen02g038020' => 'spe', 'Sopen05g008490' => 'spe', 'Sopen07g003910' => 'spe', 'Sopen12g015240' => 'spe', 'Sp1g11550' => 'spa', 'Sp2g16710' => 'spa', 'Sp3g00430' => 'spa', 'Sp3g26780' => 'spa', 'Sp5g22900' => 'spa', 'Sp6g29530' => 'spa', 'TAR371G0794' => 'tar', 'TAR374G0164' => 'tar', 'TAR622G0165' => 'tar', 'TAR626G0929' => 'tar', 'TAR629G2155' => 'tar', 'THA.LOC104805282' => 'tha', 'THA.LOC104805363' => 'tha', 'THA.LOC104808968' => 'tha', 'THA.LOC104821093' => 'tha', 'THA.LOC104823953' => 'tha', 'THA.LOC104825562' => 'tha', 'THA.LOC104825665' => 'tha', 'Thecc.02G261400' => 'tca', 'Thecc.04G019200' => 'tca', 'Thecc.09G130400' => 'tca', 'Thhalv10004374m.g' => 'esa', 'Thhalv10007850m.g' => 'esa', 'Thhalv10013782m.g' => 'esa', 'Thhalv10018686m.g' => 'esa', 'Thhalv10020899m.g' => 'esa', 'Thhalv10022755m.g' => 'esa', 'TPR.G23851' => 'tpr', 'TPR.G26500' => 'tpr', 'TPR.G27267' => 'tpr', 'TPR.G32001' => 'tpr', 'TPR.G6251' => 'tpr', 'TPR.G8167' => 'tpr', 'TWI12G1330' => 'twi', 'TWI18G1239' => 'twi', 'TWI34G0979' => 'twi', 'TWI36G0670' => 'twi', 'TWI36G0707' => 'twi', 'TWI56G0233' => 'twi', 'TWI75G1809' => 'twi', 'unitig_21.g20874' => 'ugi', 'unitig_26.g10343' => 'ugi', 'unitig_46.g18392' => 'ugi', 'unitig_52.g17178' => 'ugi', 'unitig_8.g2934' => 'ugi', 'vmacro01122' => 'vma', 'vmacro05875' => 'vma', 'vmacro06147' => 'vma', 'vmacro16191' => 'vma', 'vmacro18293' => 'vma', 'VMungo0251G3707' => 'vmu', 'VMungo0464G1521' => 'vmu', 'VMungo1215G0205' => 'vmu', 'VMungo1383G2484' => 'vmu', 'Zm00001eb079610' => 'zma', 'Zm00001eb135990' => 'zma', 'Zm00001eb183710' => 'zma', 'Zm00001eb246020' => 'zma' ) $gf_id = 'HOM05D001124' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001124' ) $data_identifier = 'HOM05D001124' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 6, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 7, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 21, 'bol' => (int) 10, 'bra' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 6, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 9, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 21, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 8, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 10, 'lsa' => (int) 8, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 8, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 9, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb246020' $species_info = array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ) $local_species = 'fve' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001124', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '548', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02520' => 'bna', 'A03p06630' => 'bna', 'A05p44460' => 'bna', 'A06p08710' => 'bna', 'A06p41090' => 'bna', 'A07p32320' => 'bna', 'A08p32520' => 'bna', 'A09p10360' => 'bna', 'A10p24080' => 'bna', 'Aa31LG11G15250' => 'aar', 'Aa31LG1G1800' => 'aar', 'Aa31LG2G5120' => 'aar', 'Aa31LG2G6070' => 'aar', 'Aa31LG5G10770' => 'aar', 'Aa31sc61G90' => 'aar', 'Actinidia01352' => 'ach', 'Actinidia05983' => 'ach', 'Actinidia08133' => 'ach', 'Actinidia15101' => 'ach', 'Actinidia26379' => 'ach', 'Actinidia35778' => 'ach', 'Actinidia36123' => 'ach', 'Actinidia37436' => 'ach', 'Actinidia38730' => 'ach', 'Ah.02g128210' => 'amhyb', 'Ah.03g132990' => 'amhyb', 'Ah.14g079410' => 'amhyb', 'AL1G24640' => 'aly', 'AL2G26680' => 'aly', 'AL3G10530' => 'aly', 'AL3G45230' => 'aly', 'AL5G15230' => 'aly', 'AL5G16960' => 'aly', 'AL6G25210' => 'aly', 'Aqoxy2G00441' => 'aox', 'Aqoxy3G01236' => 'aox', 'Aqoxy5G03746' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3RQ047' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C7GMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9C8JER' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MBL6KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YXCZ83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZANX40' => 'arhy', 'AT1G12990' => 'ath', 'AT1G67880' => 'ath', 'AT2G13290' => 'ath', 'AT3G01620' => 'ath', 'AT3G26445' => 'ath', 'AT3G27540' => 'ath', 'AT5G14480' => 'ath', 'ATR0824G026' => 'atr', 'ATR1098G019' => 'atr', 'Atru.chr11.2145' => 'acertr', 'Atru.chr2.3636' => 'acertr', 'Atru.chr2.3644' => 'acertr', 'Atru.chr6.2422' => 'acertr', 'Atru.chr7.1112' => 'acertr', 'AUR62005469' => 'cqu', 'AUR62011166' => 'cqu', 'AUR62013319' => 'cqu', 'AUR62024273' => 'cqu', 'AUR62028420' => 'cqu', 'AUR62041942' => 'cqu', 'BcaB01g04969' => 'bca', 'BcaB01g06371' => 'bca', 'BcaB02g11494' => 'bca', 'BcaB03g15382' => 'bca', 'BcaB08g36994' => 'bca', 'BcaC03g13477' => 'bca', 'BcaC03g13478' => 'bca', 'BcaC03g13480' => 'bca', 'BcaC03g13481' => 'bca', 'BcaC03g13486' => 'bca', 'BcaC04g19031' => 'bca', 'BcaC04g23085' => 'bca', 'BcaC05g25094' => 'bca', 'BcaC05g25096' => 'bca', 'BcaC05g25138' => 'bca', 'BcaC05g30416' => 'bca', 'BcaC05g30455' => 'bca', 'BcaC06g30979' => 'bca', 'BcaC06g33805' => 'bca', 'BcaC08g46021' => 'bca', 'BcaNung03154' => 'bca', 'BolC2t06623H' => 'bol', 'BolC2t06632H' => 'bol', 'BolC2t06635H' => 'bol', 'BolC2t06638H' => 'bol', 'BolC3t13266H' => 'bol', 'BolC5t29776H' => 'bol', 'BolC6t38912H' => 'bol', 'BolC7t44183H' => 'bol', 'BolC9t54123H' => 'bol', 'BolC9t59107H' => 'bol', 'BraA02t05221Z' => 'bra', 'BraA03t09996Z' => 'bra', 'BraA05t23210Z' => 'bra', 'BraA06t24068Z' => 'bra', 'BraA06t27032Z' => 'bra', 'BraA08t35176Z' => 'bra', 'BraA09t36680Z' => 'bra', 'BraA10t44471Z' => 'bra', 'C02p06760' => 'bna', 'C02p06890' => 'bna', 'C02p07010' => 'bna', 'C03p07660' => 'bna', 'C05p10300' => 'bna', 'C06p38150' => 'bna', 'C07p36650' => 'bna', 'C08p15770' => 'bna', 'C09p12300' => 'bna', 'C09p62700' => 'bna', 'C09p75040' => 'bna', 'CAN.G13.1' => 'can', 'CAN.G138.4' => 'can', 'CAN.G44.6' => 'can', 'CAN.G473.19' => 'can', 'CANSAT01G0835' => 'cansat', 'CANSAT11G0246' => 'cansat', 'CANSAT11G1766' => 'cansat', 'CANSAT64G1954' => 'cansat', 'CARHR013330' => 'chi', 'CARHR060530' => 'chi', 'CARHR075300' => 'chi', 'CARHR105120' => 'chi', 'CARHR148910' => 'chi', 'CARHR198830' => 'chi', 'Carub.0001s1275' => 'cru', 'Carub.0002s1437' => 'cru', 'Carub.0003s0044' => 'cru', 'Carub.0003s2787' => 'cru', 'Carub.0005s0597' => 'cru', 'Carub.0006s1266' => 'cru', 'Ca_06935_v3' => 'car', 'Ca_13559_v3' => 'car', 'Ca_16941_v3' => 'car', 'Ca_16960_v3' => 'car', 'Ca_17775_v3' => 'car', 'Ca_30464_v3' => 'car', 'Cc06_g08160' => 'ccan', 'Cc07_g01520' => 'ccan', 'Cc11_g15810' => 'ccan', 'CDE02G2840' => 'cde', 'CDE03G0093' => 'cde', 'CDE04G2127' => 'cde', 'CDE07G1857' => 'cde', 'CDE09G1246' => 'cde', 'Cfa003412' => 'cfa', 'Cfa007341' => 'cfa', 'Cfa009220' => 'cfa', 'Ciclev10008737m.g' => 'ccl', 'Ciclev10015565m.g' => 'ccl', 'Ciclev10031761m.g' => 'ccl', 'CiPaw.03G045300' => 'cil', 'CiPaw.03G247200' => 'cil', 'CiPaw.04G029500' => 'cil', 'CiPaw.04G174000' => 'cil', 'CiPaw.05G181200' => 'cil', 'CiPaw.06G067100' => 'cil', 'ClCG05G025800' => 'cla', 'ClCG06G011400' => 'cla', 'ClCG09G019360' => 'cla', 'COL.COLO4_04827' => 'col', 'COL.COLO4_29170' => 'col', 'COL.COLO4_35131' => 'col', 'COL.COLO4_35132' => 'col', 'Cpa.g.sc33.32' => 'cpa', 'Cpa.g.sc46.29' => 'cpa', 'Cpa.g.sc796.1' => 'cpa', 'CsaV3_1G030420' => 'csa', 'CsaV3_5G027050' => 'csa', 'CsaV3_5G031040' => 'csa', 'CsaV3_UNG023130' => 'csa', 'CSS0007726' => 'camsi', 'CSS0016433' => 'camsi', 'CSS0017656' => 'camsi', 'CSS0025364' => 'camsi', 'CSS0027582' => 'camsi', 'CSS0047288' => 'camsi', 'CSS0049950' => 'camsi', 'DCAR_003843' => 'dca', 'DCAR_007052' => 'dca', 'DCAR_020884' => 'dca', 'DCAR_021730' => 'dca', 'DCAR_024423' => 'dca', 'DCAR_026509' => 'dca', 'DCAR_031158' => 'dca', 'Dinv14728' => 'din', 'Dinv15219' => 'din', 'Dinv25728' => 'din', 'Dinv33428' => 'din', 'Dinv36489' => 'din', 'Dinv41486' => 'din', 'Duzib147G0469' => 'dzi', 'Duzib168G0060' => 'dzi', 'Duzib187G1215' => 'dzi', 'Duzib248G0692' => 'dzi', 'Duzib251G0767' => 'dzi', 'Duzib264G0446' => 'dzi', 'Duzib268G0691' => 'dzi', 'ECA232G4767' => 'eca', 'ECA233G2838' => 'eca', 'ECA234G0391' => 'eca', 'ECA234G0857' => 'eca', 'ECA236G1593' => 'eca', 'ECA238G0565' => 'eca', 'ECA246G1027' => 'eca', 'ECA246G3223' => 'eca', 'ECA246G3470' => 'eca', 'EL10Ac6g13829' => 'bvu', 'EL10Ac6g14093' => 'bvu', 'EL10Ac8g18707' => 'bvu', 'Eucgr.C01369' => 'egr', 'Eucgr.H02492' => 'egr', 'Eucgr.I01733' => 'egr', 'Eucgr.J02255' => 'egr', 'Eucgr.J02257' => 'egr', 'Eucgr.J02258' => 'egr', 'FAN02G1601' => 'fan', 'FAN03G1586' => 'fan', 'FAN03G2986' => 'fan', 'FAN05G4837' => 'fan', 'FAN06G0146' => 'fan', 'FAN07G0858' => 'fan', 'FAN09G3179' => 'fan', 'FAN10G0669' => 'fan', 'FAN12G2358' => 'fan', 'FAN14G4198' => 'fan', 'FAN14G5112' => 'fan', 'FAN17G0342' => 'fan', 'FAN19G0342' => 'fan', 'FAN19G0962' => 'fan', 'FAN19G1101' => 'fan', 'FAN19G1872' => 'fan', 'FAN22G0356' => 'fan', 'FAN23G0744' => 'fan', 'FAN23G1914' => 'fan', 'FAN26G0032' => 'fan', 'FAN28G0625' => 'fan', 'FvH4_1g02710' => 'fve', 'FvH4_1g02720' => 'fve', 'FvH4_4g25670' => 'fve', 'FvH4_6g51700' => 'fve', 'FvH4_7g20170' => 'fve', 'Glyma.05G175000' => 'gma', 'Glyma.08G132300' => 'gma', 'Glyma.11G243000' => 'gma', 'Glyma.13G158900' => 'gma', 'Glyma.17G112400' => 'gma', 'Glyma.18G014100' => 'gma', 'Glyma.19G003100' => 'gma', 'Glyma.19G056500' => 'gma', 'Gohir.A01G158900' => 'ghi', 'Gohir.A05G312600' => 'ghi', 'Gohir.A05G354900' => 'ghi', 'Gohir.A07G037200' => 'ghi', 'Gohir.A09G030000' => 'ghi', 'Gohir.A12G145200' => 'ghi', 'Gohir.D01G151500' => 'ghi', 'Gohir.D04G058300' => 'ghi', 'Gohir.D05G314100' => 'ghi', 'Gohir.D07G041400' => 'ghi', 'Gohir.D09G029700' => 'ghi', 'Gohir.D12G149700' => 'ghi', 'Gorai.001G043800' => 'gra', 'Gorai.002G187800' => 'gra', 'Gorai.006G034700' => 'gra', 'Gorai.008G161200' => 'gra', 'Gorai.009G335700' => 'gra', 'Gorai.012G065000' => 'gra', 'GSVIVG01000535001' => 'vvi', 'GSVIVG01015572001' => 'vvi', 'GSVIVG01032386001' => 'vvi', 'HanXRQChr05g0138531' => 'han', 'HanXRQChr06g0174391' => 'han', 'HanXRQChr07g0199021' => 'han', 'HanXRQChr08g0208211' => 'han', 'HanXRQChr09g0255471' => 'han', 'HanXRQChr10g0315791' => 'han', 'HanXRQChr12g0371991' => 'han', 'HanXRQChr15g0475251' => 'han', 'HanXRQChr17g0540001' => 'han', 'HanXRQChr17g0548631' => 'han', 'HanXRQChr17g0569561' => 'han', 'Haze_12256' => 'cav', 'Haze_14756' => 'cav', 'Haze_25528' => 'cav', 'Hma1.2p1_0079F.1_g041020' => 'hma', 'Hma1.2p1_0818F.1_g223260' => 'hma', 'Hma1.2p1_1747F.1_g300530' => 'hma', 'HPP92_004607' => 'vpl', 'HPP92_004608' => 'vpl', 'HPP92_006181' => 'vpl', 'HPP92_012192' => 'vpl', 'HPP92_015680' => 'vpl', 'HPP92_020249' => 'vpl', 'HPP92_021376' => 'vpl', 'HPP92_024275' => 'vpl', 'Hund06031' => 'sun', 'Hund25391' => 'sun', 'Lalb_Chr07g0185371' => 'lal', 'Lalb_Chr07g0185381' => 'lal', 'Lalb_Chr12g0204011' => 'lal', 'Lalb_Chr13g0301671' => 'lal', 'Lalb_Chr14g0362851' => 'lal', 'Lalb_Chr24g0403581' => 'lal', 'Lj1g0000233' => 'lja', 'Lj2g0018120' => 'lja', 'Lj3C621T0' => 'lonja', 'Lj3P1059T14' => 'lonja', 'Lj3P611T9' => 'lonja', 'Lj3P614T13' => 'lonja', 'Lj3P615T5' => 'lonja', 'Lj4g0012315' => 'lja', 'Lj4g0026182' => 'lja', 'Lj6P813T16' => 'lonja', 'Lj7C427T7' => 'lonja', 'Lj7C427T8' => 'lonja', 'Lj7P600T41' => 'lonja', 'Lju41C42G17' => 'lonja', 'Lsat_1_v5_gn_0_47300' => 'lsa', 'Lsat_1_v5_gn_2_91280' => 'lsa', 'Lsat_1_v5_gn_3_30561' => 'lsa', 'Lsat_1_v5_gn_4_184321' => 'lsa', 'Lsat_1_v5_gn_4_4041' => 'lsa', 'Lsat_1_v5_gn_5_92000' => 'lsa', 'Lsat_1_v5_gn_8_152940' => 'lsa', 'Lsat_1_v5_gn_8_62401' => 'lsa', 'Manes.06G055900' => 'mes', 'Manes.12G022200' => 'mes', 'Manes.13G023300' => 'mes', 'Manes.14G115000' => 'mes', 'Manes.15G151700' => 'mes', 'Manes.17G111300' => 'mes', 'Mapoly0226s0009' => 'mpo', 'MBI02_g25363_MAGBIO' => 'mbi', 'MBI06_g00027_MAGBIO' => 'mbi', 'MBI10_g13034_MAGBIO' => 'mbi', 'MD09G1023400' => 'mdo', 'MD13G1100100' => 'mdo', 'MD15G1169200' => 'mdo', 'MD16G1101100' => 'mdo', 'MD17G1022900' => 'mdo', 'Medtr3g096150' => 'mtr', 'Medtr4g115070' => 'mtr', 'Medtr7g033325' => 'mtr', 'Medtr8g089840' => 'mtr', 'MELO3C010319.2' => 'cme', 'MELO3C011944.2' => 'cme', 'MELO3C021589.2' => 'cme', 'Migut.E00207' => 'egut', 'Migut.H00067' => 'egut', 'Migut.K00433' => 'egut', 'Migut.K00606' => 'egut', 'Migut.K01410' => 'egut', 'MSTRG.13347' => 'ama', 'MSTRG.24045' => 'ama', 'MSTRG.2428' => 'ama', 'MSTRG.26410' => 'ama', 'MSTRG.3139' => 'ama', 'MSTRG.3286' => 'ama', 'MSTRG.563' => 'ama', 'MSTRG.7941' => 'ama', 'Nitab4.5_0000028g0060' => 'nta', 'Nitab4.5_0000065g0260' => 'nta', 'Nitab4.5_0000112g0060' => 'nta', 'Nitab4.5_0000489g0120' => 'nta', 'Nitab4.5_0001776g0050' => 'nta', 'Nitab4.5_0001854g0010' => 'nta', 'Nitab4.5_0001860g0020' => 'nta', 'Nitab4.5_0004352g0010' => 'nta', 'Nitab4.5_0008716g0020' => 'nta', 'Nitab4.5_0008922g0010' => 'nta', 'Nn3g16693' => 'nnu', 'Nn4g22596' => 'nnu', 'Nn7g37639' => 'nnu', 'Oeu001701.1' => 'oeu', 'Oeu018149.1' => 'oeu', 'Oeu026220.1' => 'oeu', 'Oeu038635.1' => 'oeu', 'Oeu049176.1' => 'oeu', 'Oeu056706.1' => 'oeu', 'Oeu056937.1' => 'oeu', 'Oeu057540.1' => 'oeu', 'Os02g0594900' => 'osa', 'Os02g0595100' => 'osa', 'Os04g0477500' => 'osa', 'Os12g0611900' => 'osa', 'Peaxi162Scf00076g00020' => 'pax', 'Peaxi162Scf00128g00217' => 'pax', 'Peaxi162Scf00129g01640' => 'pax', 'Peaxi162Scf00669g00007' => 'pax', 'Peaxi162Scf00700g00421' => 'pax', 'Peaxi162Scf00801g00038' => 'pax', 'Peaxi162Scf00891g00025' => 'pax', 'PGR083G0909' => 'pgr', 'PGR119G1005' => 'pgr', 'PGR142G2236' => 'pgr', 'PGR142G3388' => 'pgr', 'PGSC0003DMG400004514' => 'stu', 'PGSC0003DMG400012635' => 'stu', 'PGSC0003DMG400015730' => 'stu', 'PGSC0003DMG400018611' => 'stu', 'PGSC0003DMG400030897' => 'stu', 'Phvul.001G254800' => 'pvu', 'Phvul.002G260100' => 'pvu', 'Phvul.003G167600' => 'pvu', 'Phvul.004G005100' => 'pvu', 'Potri.001G343600' => 'ptr', 'Potri.006G066700' => 'ptr', 'Potri.008G186000' => 'ptr', 'Potri.010G046900' => 'ptr', 'Potri.018G127900' => 'ptr', 'Pp3c20_17750' => 'ppa', 'Pp3c24_4380' => 'ppa', 'Prupe.1G245800' => 'ppe', 'Prupe.3G293400' => 'ppe', 'Prupe.7G247400' => 'ppe', 'Psat0s145g0120' => 'psa', 'Psat0s595g0040' => 'psa', 'Psat0s595g0120' => 'psa', 'Psat3g175040' => 'psa', 'Psat7g058120' => 'psa', 'PSO017G0428' => 'pso', 'PSO063G7510' => 'pso', 'PSO067G0046' => 'pso', 'PSO478G1073' => 'pso', 'PSO675G3677' => 'pso', 'PSO675G6558' => 'pso', 'PSO675G7520' => 'pso', 'PSO675G8959' => 'pso', 'QL02p074089' => 'qlo', 'QL02p089614' => 'qlo', 'QL03p057736' => 'qlo', 'RcHm_v2.0_Chr1g0364131' => 'rch', 'RcHm_v2.0_Chr2g0087801' => 'rch', 'RcHm_v2.0_Chr2g0087821' => 'rch', 'RcHm_v2.0_Chr2g0173231' => 'rch', 'RcHm_v2.0_Chr4g0433111' => 'rch', 'Rhsim03G0250300' => 'rsi', 'Rhsim08G0048400' => 'rsi', 'Rhsim10G0014800' => 'rsi', 'Rhsim12G0040100' => 'rsi', 'Rhsim12G0109700' => 'rsi', 'Sabra06G0049600' => 'sbr', 'Sabra08G0141000' => 'sbr', 'Sabra10G0021400' => 'sbr', 'Sabra16G0222900' => 'sbr', 'Sabra18G0108600' => 'sbr', 'SalBow1G0433' => 'sbo', 'SalBow1G2038' => 'sbo', 'SalBow1G5003' => 'sbo', 'SalBow7G1197' => 'sbo', 'SalBow8G3506' => 'sbo', 'Sc03g0007300' => 'sci', 'Sc11g0000950' => 'sci', 'Sc14g0008750' => 'sci', 'Sc18g0000420' => 'sci', 'Sed0006754' => 'sed', 'Sed0008741' => 'sed', 'Sed0017172' => 'sed', 'Sed0018925' => 'sed', 'Sed0023326' => 'sed', 'Sed0025909' => 'sed', 'SEGI_05333' => 'sgi', 'SEGI_10362' => 'sgi', 'SEGI_13380' => 'sgi', 'SEGI_24306' => 'sgi', 'SEGI_29077' => 'sgi', 'SEGI_29095' => 'sgi', 'SEGI_36534' => 'sgi', 'SEGI_37506' => 'sgi', 'SEGI_38321' => 'sgi', 'SGA_v2.0_scaffold307G48031' => 'sas', 'SGA_v2.0_scaffold47G17507' => 'sas', 'SGA_v2.0_scaffold63G21736' => 'sas', 'SGA_v2.0_scaffold87G27070' => 'sas', 'SHI17794' => 'shi', 'SHI28851' => 'shi', 'SMO165G0155' => 'smo', 'SMO340G0217' => 'smo', 'SMO367G1210' => 'smo', 'Solyc02g093430.3' => 'sly', 'Solyc05g013580.4' => 'sly', 'Solyc07g008030.3' => 'sly', 'Solyc12g035470.2' => 'sly', 'Sopen02g038020' => 'spe', 'Sopen05g008490' => 'spe', 'Sopen07g003910' => 'spe', 'Sopen12g015240' => 'spe', 'Sp1g11550' => 'spa', 'Sp2g16710' => 'spa', 'Sp3g00430' => 'spa', 'Sp3g26780' => 'spa', 'Sp5g22900' => 'spa', 'Sp6g29530' => 'spa', 'TAR371G0794' => 'tar', 'TAR374G0164' => 'tar', 'TAR622G0165' => 'tar', 'TAR626G0929' => 'tar', 'TAR629G2155' => 'tar', 'THA.LOC104805282' => 'tha', 'THA.LOC104805363' => 'tha', 'THA.LOC104808968' => 'tha', 'THA.LOC104821093' => 'tha', 'THA.LOC104823953' => 'tha', 'THA.LOC104825562' => 'tha', 'THA.LOC104825665' => 'tha', 'Thecc.02G261400' => 'tca', 'Thecc.04G019200' => 'tca', 'Thecc.09G130400' => 'tca', 'Thhalv10004374m.g' => 'esa', 'Thhalv10007850m.g' => 'esa', 'Thhalv10013782m.g' => 'esa', 'Thhalv10018686m.g' => 'esa', 'Thhalv10020899m.g' => 'esa', 'Thhalv10022755m.g' => 'esa', 'TPR.G23851' => 'tpr', 'TPR.G26500' => 'tpr', 'TPR.G27267' => 'tpr', 'TPR.G32001' => 'tpr', 'TPR.G6251' => 'tpr', 'TPR.G8167' => 'tpr', 'TWI12G1330' => 'twi', 'TWI18G1239' => 'twi', 'TWI34G0979' => 'twi', 'TWI36G0670' => 'twi', 'TWI36G0707' => 'twi', 'TWI56G0233' => 'twi', 'TWI75G1809' => 'twi', 'unitig_21.g20874' => 'ugi', 'unitig_26.g10343' => 'ugi', 'unitig_46.g18392' => 'ugi', 'unitig_52.g17178' => 'ugi', 'unitig_8.g2934' => 'ugi', 'vmacro01122' => 'vma', 'vmacro05875' => 'vma', 'vmacro06147' => 'vma', 'vmacro16191' => 'vma', 'vmacro18293' => 'vma', 'VMungo0251G3707' => 'vmu', 'VMungo0464G1521' => 'vmu', 'VMungo1215G0205' => 'vmu', 'VMungo1383G2484' => 'vmu', 'Zm00001eb079610' => 'zma', 'Zm00001eb135990' => 'zma', 'Zm00001eb183710' => 'zma', 'Zm00001eb246020' => 'zma' ), 'gf_id' => 'HOM05D001124', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001124' ), 'data_identifier' => 'HOM05D001124', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001124', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '548', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02520' => 'bna', 'A03p06630' => 'bna', 'A05p44460' => 'bna', 'A06p08710' => 'bna', 'A06p41090' => 'bna', 'A07p32320' => 'bna', 'A08p32520' => 'bna', 'A09p10360' => 'bna', 'A10p24080' => 'bna', 'Aa31LG11G15250' => 'aar', 'Aa31LG1G1800' => 'aar', 'Aa31LG2G5120' => 'aar', 'Aa31LG2G6070' => 'aar', 'Aa31LG5G10770' => 'aar', 'Aa31sc61G90' => 'aar', 'Actinidia01352' => 'ach', 'Actinidia05983' => 'ach', 'Actinidia08133' => 'ach', 'Actinidia15101' => 'ach', 'Actinidia26379' => 'ach', 'Actinidia35778' => 'ach', 'Actinidia36123' => 'ach', 'Actinidia37436' => 'ach', 'Actinidia38730' => 'ach', 'Ah.02g128210' => 'amhyb', 'Ah.03g132990' => 'amhyb', 'Ah.14g079410' => 'amhyb', 'AL1G24640' => 'aly', 'AL2G26680' => 'aly', 'AL3G10530' => 'aly', 'AL3G45230' => 'aly', 'AL5G15230' => 'aly', 'AL5G16960' => 'aly', 'AL6G25210' => 'aly', 'Aqoxy2G00441' => 'aox', 'Aqoxy3G01236' => 'aox', 'Aqoxy5G03746' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3RQ047' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C7GMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9C8JER' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MBL6KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YXCZ83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZANX40' => 'arhy', 'AT1G12990' => 'ath', 'AT1G67880' => 'ath', 'AT2G13290' => 'ath', 'AT3G01620' => 'ath', 'AT3G26445' => 'ath', 'AT3G27540' => 'ath', 'AT5G14480' => 'ath', 'ATR0824G026' => 'atr', 'ATR1098G019' => 'atr', 'Atru.chr11.2145' => 'acertr', 'Atru.chr2.3636' => 'acertr', 'Atru.chr2.3644' => 'acertr', 'Atru.chr6.2422' => 'acertr', 'Atru.chr7.1112' => 'acertr', 'AUR62005469' => 'cqu', 'AUR62011166' => 'cqu', 'AUR62013319' => 'cqu', 'AUR62024273' => 'cqu', 'AUR62028420' => 'cqu', 'AUR62041942' => 'cqu', 'BcaB01g04969' => 'bca', 'BcaB01g06371' => 'bca', 'BcaB02g11494' => 'bca', 'BcaB03g15382' => 'bca', 'BcaB08g36994' => 'bca', 'BcaC03g13477' => 'bca', 'BcaC03g13478' => 'bca', 'BcaC03g13480' => 'bca', 'BcaC03g13481' => 'bca', 'BcaC03g13486' => 'bca', 'BcaC04g19031' => 'bca', 'BcaC04g23085' => 'bca', 'BcaC05g25094' => 'bca', 'BcaC05g25096' => 'bca', 'BcaC05g25138' => 'bca', 'BcaC05g30416' => 'bca', 'BcaC05g30455' => 'bca', 'BcaC06g30979' => 'bca', 'BcaC06g33805' => 'bca', 'BcaC08g46021' => 'bca', 'BcaNung03154' => 'bca', 'BolC2t06623H' => 'bol', 'BolC2t06632H' => 'bol', 'BolC2t06635H' => 'bol', 'BolC2t06638H' => 'bol', 'BolC3t13266H' => 'bol', 'BolC5t29776H' => 'bol', 'BolC6t38912H' => 'bol', 'BolC7t44183H' => 'bol', 'BolC9t54123H' => 'bol', 'BolC9t59107H' => 'bol', 'BraA02t05221Z' => 'bra', 'BraA03t09996Z' => 'bra', 'BraA05t23210Z' => 'bra', 'BraA06t24068Z' => 'bra', 'BraA06t27032Z' => 'bra', 'BraA08t35176Z' => 'bra', 'BraA09t36680Z' => 'bra', 'BraA10t44471Z' => 'bra', 'C02p06760' => 'bna', 'C02p06890' => 'bna', 'C02p07010' => 'bna', 'C03p07660' => 'bna', 'C05p10300' => 'bna', 'C06p38150' => 'bna', 'C07p36650' => 'bna', 'C08p15770' => 'bna', 'C09p12300' => 'bna', 'C09p62700' => 'bna', 'C09p75040' => 'bna', 'CAN.G13.1' => 'can', 'CAN.G138.4' => 'can', 'CAN.G44.6' => 'can', 'CAN.G473.19' => 'can', 'CANSAT01G0835' => 'cansat', 'CANSAT11G0246' => 'cansat', 'CANSAT11G1766' => 'cansat', 'CANSAT64G1954' => 'cansat', 'CARHR013330' => 'chi', 'CARHR060530' => 'chi', 'CARHR075300' => 'chi', 'CARHR105120' => 'chi', 'CARHR148910' => 'chi', 'CARHR198830' => 'chi', 'Carub.0001s1275' => 'cru', 'Carub.0002s1437' => 'cru', 'Carub.0003s0044' => 'cru', 'Carub.0003s2787' => 'cru', 'Carub.0005s0597' => 'cru', 'Carub.0006s1266' => 'cru', 'Ca_06935_v3' => 'car', 'Ca_13559_v3' => 'car', 'Ca_16941_v3' => 'car', 'Ca_16960_v3' => 'car', 'Ca_17775_v3' => 'car', 'Ca_30464_v3' => 'car', 'Cc06_g08160' => 'ccan', 'Cc07_g01520' => 'ccan', 'Cc11_g15810' => 'ccan', 'CDE02G2840' => 'cde', 'CDE03G0093' => 'cde', 'CDE04G2127' => 'cde', 'CDE07G1857' => 'cde', 'CDE09G1246' => 'cde', 'Cfa003412' => 'cfa', 'Cfa007341' => 'cfa', 'Cfa009220' => 'cfa', 'Ciclev10008737m.g' => 'ccl', 'Ciclev10015565m.g' => 'ccl', 'Ciclev10031761m.g' => 'ccl', 'CiPaw.03G045300' => 'cil', 'CiPaw.03G247200' => 'cil', 'CiPaw.04G029500' => 'cil', 'CiPaw.04G174000' => 'cil', 'CiPaw.05G181200' => 'cil', 'CiPaw.06G067100' => 'cil', 'ClCG05G025800' => 'cla', 'ClCG06G011400' => 'cla', 'ClCG09G019360' => 'cla', 'COL.COLO4_04827' => 'col', 'COL.COLO4_29170' => 'col', 'COL.COLO4_35131' => 'col', 'COL.COLO4_35132' => 'col', 'Cpa.g.sc33.32' => 'cpa', 'Cpa.g.sc46.29' => 'cpa', 'Cpa.g.sc796.1' => 'cpa', 'CsaV3_1G030420' => 'csa', 'CsaV3_5G027050' => 'csa', 'CsaV3_5G031040' => 'csa', 'CsaV3_UNG023130' => 'csa', 'CSS0007726' => 'camsi', 'CSS0016433' => 'camsi', 'CSS0017656' => 'camsi', 'CSS0025364' => 'camsi', 'CSS0027582' => 'camsi', 'CSS0047288' => 'camsi', 'CSS0049950' => 'camsi', 'DCAR_003843' => 'dca', 'DCAR_007052' => 'dca', 'DCAR_020884' => 'dca', 'DCAR_021730' => 'dca', 'DCAR_024423' => 'dca', 'DCAR_026509' => 'dca', 'DCAR_031158' => 'dca', 'Dinv14728' => 'din', 'Dinv15219' => 'din', 'Dinv25728' => 'din', 'Dinv33428' => 'din', 'Dinv36489' => 'din', 'Dinv41486' => 'din', 'Duzib147G0469' => 'dzi', 'Duzib168G0060' => 'dzi', 'Duzib187G1215' => 'dzi', 'Duzib248G0692' => 'dzi', 'Duzib251G0767' => 'dzi', 'Duzib264G0446' => 'dzi', 'Duzib268G0691' => 'dzi', 'ECA232G4767' => 'eca', 'ECA233G2838' => 'eca', 'ECA234G0391' => 'eca', 'ECA234G0857' => 'eca', 'ECA236G1593' => 'eca', 'ECA238G0565' => 'eca', 'ECA246G1027' => 'eca', 'ECA246G3223' => 'eca', 'ECA246G3470' => 'eca', 'EL10Ac6g13829' => 'bvu', 'EL10Ac6g14093' => 'bvu', 'EL10Ac8g18707' => 'bvu', 'Eucgr.C01369' => 'egr', 'Eucgr.H02492' => 'egr', 'Eucgr.I01733' => 'egr', 'Eucgr.J02255' => 'egr', 'Eucgr.J02257' => 'egr', 'Eucgr.J02258' => 'egr', 'FAN02G1601' => 'fan', 'FAN03G1586' => 'fan', 'FAN03G2986' => 'fan', 'FAN05G4837' => 'fan', 'FAN06G0146' => 'fan', 'FAN07G0858' => 'fan', 'FAN09G3179' => 'fan', 'FAN10G0669' => 'fan', 'FAN12G2358' => 'fan', 'FAN14G4198' => 'fan', 'FAN14G5112' => 'fan', 'FAN17G0342' => 'fan', 'FAN19G0342' => 'fan', 'FAN19G0962' => 'fan', 'FAN19G1101' => 'fan', 'FAN19G1872' => 'fan', 'FAN22G0356' => 'fan', 'FAN23G0744' => 'fan', 'FAN23G1914' => 'fan', 'FAN26G0032' => 'fan', 'FAN28G0625' => 'fan', 'FvH4_1g02710' => 'fve', 'FvH4_1g02720' => 'fve', 'FvH4_4g25670' => 'fve', 'FvH4_6g51700' => 'fve', 'FvH4_7g20170' => 'fve', 'Glyma.05G175000' => 'gma', 'Glyma.08G132300' => 'gma', 'Glyma.11G243000' => 'gma', 'Glyma.13G158900' => 'gma', 'Glyma.17G112400' => 'gma', 'Glyma.18G014100' => 'gma', 'Glyma.19G003100' => 'gma', 'Glyma.19G056500' => 'gma', 'Gohir.A01G158900' => 'ghi', 'Gohir.A05G312600' => 'ghi', 'Gohir.A05G354900' => 'ghi', 'Gohir.A07G037200' => 'ghi', 'Gohir.A09G030000' => 'ghi', 'Gohir.A12G145200' => 'ghi', 'Gohir.D01G151500' => 'ghi', 'Gohir.D04G058300' => 'ghi', 'Gohir.D05G314100' => 'ghi', 'Gohir.D07G041400' => 'ghi', 'Gohir.D09G029700' => 'ghi', 'Gohir.D12G149700' => 'ghi', 'Gorai.001G043800' => 'gra', 'Gorai.002G187800' => 'gra', 'Gorai.006G034700' => 'gra', 'Gorai.008G161200' => 'gra', 'Gorai.009G335700' => 'gra', 'Gorai.012G065000' => 'gra', 'GSVIVG01000535001' => 'vvi', 'GSVIVG01015572001' => 'vvi', 'GSVIVG01032386001' => 'vvi', 'HanXRQChr05g0138531' => 'han', 'HanXRQChr06g0174391' => 'han', 'HanXRQChr07g0199021' => 'han', 'HanXRQChr08g0208211' => 'han', 'HanXRQChr09g0255471' => 'han', 'HanXRQChr10g0315791' => 'han', 'HanXRQChr12g0371991' => 'han', 'HanXRQChr15g0475251' => 'han', 'HanXRQChr17g0540001' => 'han', 'HanXRQChr17g0548631' => 'han', 'HanXRQChr17g0569561' => 'han', 'Haze_12256' => 'cav', 'Haze_14756' => 'cav', 'Haze_25528' => 'cav', 'Hma1.2p1_0079F.1_g041020' => 'hma', 'Hma1.2p1_0818F.1_g223260' => 'hma', 'Hma1.2p1_1747F.1_g300530' => 'hma', 'HPP92_004607' => 'vpl', 'HPP92_004608' => 'vpl', 'HPP92_006181' => 'vpl', 'HPP92_012192' => 'vpl', 'HPP92_015680' => 'vpl', 'HPP92_020249' => 'vpl', 'HPP92_021376' => 'vpl', 'HPP92_024275' => 'vpl', 'Hund06031' => 'sun', 'Hund25391' => 'sun', 'Lalb_Chr07g0185371' => 'lal', 'Lalb_Chr07g0185381' => 'lal', 'Lalb_Chr12g0204011' => 'lal', 'Lalb_Chr13g0301671' => 'lal', 'Lalb_Chr14g0362851' => 'lal', 'Lalb_Chr24g0403581' => 'lal', 'Lj1g0000233' => 'lja', 'Lj2g0018120' => 'lja', 'Lj3C621T0' => 'lonja', 'Lj3P1059T14' => 'lonja', 'Lj3P611T9' => 'lonja', 'Lj3P614T13' => 'lonja', 'Lj3P615T5' => 'lonja', 'Lj4g0012315' => 'lja', 'Lj4g0026182' => 'lja', 'Lj6P813T16' => 'lonja', 'Lj7C427T7' => 'lonja', 'Lj7C427T8' => 'lonja', 'Lj7P600T41' => 'lonja', 'Lju41C42G17' => 'lonja', 'Lsat_1_v5_gn_0_47300' => 'lsa', 'Lsat_1_v5_gn_2_91280' => 'lsa', 'Lsat_1_v5_gn_3_30561' => 'lsa', 'Lsat_1_v5_gn_4_184321' => 'lsa', 'Lsat_1_v5_gn_4_4041' => 'lsa', 'Lsat_1_v5_gn_5_92000' => 'lsa', 'Lsat_1_v5_gn_8_152940' => 'lsa', 'Lsat_1_v5_gn_8_62401' => 'lsa', 'Manes.06G055900' => 'mes', 'Manes.12G022200' => 'mes', 'Manes.13G023300' => 'mes', 'Manes.14G115000' => 'mes', 'Manes.15G151700' => 'mes', 'Manes.17G111300' => 'mes', 'Mapoly0226s0009' => 'mpo', 'MBI02_g25363_MAGBIO' => 'mbi', 'MBI06_g00027_MAGBIO' => 'mbi', 'MBI10_g13034_MAGBIO' => 'mbi', 'MD09G1023400' => 'mdo', 'MD13G1100100' => 'mdo', 'MD15G1169200' => 'mdo', 'MD16G1101100' => 'mdo', 'MD17G1022900' => 'mdo', 'Medtr3g096150' => 'mtr', 'Medtr4g115070' => 'mtr', 'Medtr7g033325' => 'mtr', 'Medtr8g089840' => 'mtr', 'MELO3C010319.2' => 'cme', 'MELO3C011944.2' => 'cme', 'MELO3C021589.2' => 'cme', 'Migut.E00207' => 'egut', 'Migut.H00067' => 'egut', 'Migut.K00433' => 'egut', 'Migut.K00606' => 'egut', 'Migut.K01410' => 'egut', 'MSTRG.13347' => 'ama', 'MSTRG.24045' => 'ama', 'MSTRG.2428' => 'ama', 'MSTRG.26410' => 'ama', 'MSTRG.3139' => 'ama', 'MSTRG.3286' => 'ama', 'MSTRG.563' => 'ama', 'MSTRG.7941' => 'ama', 'Nitab4.5_0000028g0060' => 'nta', 'Nitab4.5_0000065g0260' => 'nta', 'Nitab4.5_0000112g0060' => 'nta', 'Nitab4.5_0000489g0120' => 'nta', 'Nitab4.5_0001776g0050' => 'nta', 'Nitab4.5_0001854g0010' => 'nta', 'Nitab4.5_0001860g0020' => 'nta', 'Nitab4.5_0004352g0010' => 'nta', 'Nitab4.5_0008716g0020' => 'nta', 'Nitab4.5_0008922g0010' => 'nta', 'Nn3g16693' => 'nnu', 'Nn4g22596' => 'nnu', 'Nn7g37639' => 'nnu', 'Oeu001701.1' => 'oeu', 'Oeu018149.1' => 'oeu', 'Oeu026220.1' => 'oeu', 'Oeu038635.1' => 'oeu', 'Oeu049176.1' => 'oeu', 'Oeu056706.1' => 'oeu', 'Oeu056937.1' => 'oeu', 'Oeu057540.1' => 'oeu', 'Os02g0594900' => 'osa', 'Os02g0595100' => 'osa', 'Os04g0477500' => 'osa', 'Os12g0611900' => 'osa', 'Peaxi162Scf00076g00020' => 'pax', 'Peaxi162Scf00128g00217' => 'pax', 'Peaxi162Scf00129g01640' => 'pax', 'Peaxi162Scf00669g00007' => 'pax', 'Peaxi162Scf00700g00421' => 'pax', 'Peaxi162Scf00801g00038' => 'pax', 'Peaxi162Scf00891g00025' => 'pax', 'PGR083G0909' => 'pgr', 'PGR119G1005' => 'pgr', 'PGR142G2236' => 'pgr', 'PGR142G3388' => 'pgr', 'PGSC0003DMG400004514' => 'stu', 'PGSC0003DMG400012635' => 'stu', 'PGSC0003DMG400015730' => 'stu', 'PGSC0003DMG400018611' => 'stu', 'PGSC0003DMG400030897' => 'stu', 'Phvul.001G254800' => 'pvu', 'Phvul.002G260100' => 'pvu', 'Phvul.003G167600' => 'pvu', 'Phvul.004G005100' => 'pvu', 'Potri.001G343600' => 'ptr', 'Potri.006G066700' => 'ptr', 'Potri.008G186000' => 'ptr', 'Potri.010G046900' => 'ptr', 'Potri.018G127900' => 'ptr', 'Pp3c20_17750' => 'ppa', 'Pp3c24_4380' => 'ppa', 'Prupe.1G245800' => 'ppe', 'Prupe.3G293400' => 'ppe', 'Prupe.7G247400' => 'ppe', 'Psat0s145g0120' => 'psa', 'Psat0s595g0040' => 'psa', 'Psat0s595g0120' => 'psa', 'Psat3g175040' => 'psa', 'Psat7g058120' => 'psa', 'PSO017G0428' => 'pso', 'PSO063G7510' => 'pso', 'PSO067G0046' => 'pso', 'PSO478G1073' => 'pso', 'PSO675G3677' => 'pso', 'PSO675G6558' => 'pso', 'PSO675G7520' => 'pso', 'PSO675G8959' => 'pso', 'QL02p074089' => 'qlo', 'QL02p089614' => 'qlo', 'QL03p057736' => 'qlo', 'RcHm_v2.0_Chr1g0364131' => 'rch', 'RcHm_v2.0_Chr2g0087801' => 'rch', 'RcHm_v2.0_Chr2g0087821' => 'rch', 'RcHm_v2.0_Chr2g0173231' => 'rch', 'RcHm_v2.0_Chr4g0433111' => 'rch', 'Rhsim03G0250300' => 'rsi', 'Rhsim08G0048400' => 'rsi', 'Rhsim10G0014800' => 'rsi', 'Rhsim12G0040100' => 'rsi', 'Rhsim12G0109700' => 'rsi', 'Sabra06G0049600' => 'sbr', 'Sabra08G0141000' => 'sbr', 'Sabra10G0021400' => 'sbr', 'Sabra16G0222900' => 'sbr', 'Sabra18G0108600' => 'sbr', 'SalBow1G0433' => 'sbo', 'SalBow1G2038' => 'sbo', 'SalBow1G5003' => 'sbo', 'SalBow7G1197' => 'sbo', 'SalBow8G3506' => 'sbo', 'Sc03g0007300' => 'sci', 'Sc11g0000950' => 'sci', 'Sc14g0008750' => 'sci', 'Sc18g0000420' => 'sci', 'Sed0006754' => 'sed', 'Sed0008741' => 'sed', 'Sed0017172' => 'sed', 'Sed0018925' => 'sed', 'Sed0023326' => 'sed', 'Sed0025909' => 'sed', 'SEGI_05333' => 'sgi', 'SEGI_10362' => 'sgi', 'SEGI_13380' => 'sgi', 'SEGI_24306' => 'sgi', 'SEGI_29077' => 'sgi', 'SEGI_29095' => 'sgi', 'SEGI_36534' => 'sgi', 'SEGI_37506' => 'sgi', 'SEGI_38321' => 'sgi', 'SGA_v2.0_scaffold307G48031' => 'sas', 'SGA_v2.0_scaffold47G17507' => 'sas', 'SGA_v2.0_scaffold63G21736' => 'sas', 'SGA_v2.0_scaffold87G27070' => 'sas', 'SHI17794' => 'shi', 'SHI28851' => 'shi', 'SMO165G0155' => 'smo', 'SMO340G0217' => 'smo', 'SMO367G1210' => 'smo', 'Solyc02g093430.3' => 'sly', 'Solyc05g013580.4' => 'sly', 'Solyc07g008030.3' => 'sly', 'Solyc12g035470.2' => 'sly', 'Sopen02g038020' => 'spe', 'Sopen05g008490' => 'spe', 'Sopen07g003910' => 'spe', 'Sopen12g015240' => 'spe', 'Sp1g11550' => 'spa', 'Sp2g16710' => 'spa', 'Sp3g00430' => 'spa', 'Sp3g26780' => 'spa', 'Sp5g22900' => 'spa', 'Sp6g29530' => 'spa', 'TAR371G0794' => 'tar', 'TAR374G0164' => 'tar', 'TAR622G0165' => 'tar', 'TAR626G0929' => 'tar', 'TAR629G2155' => 'tar', 'THA.LOC104805282' => 'tha', 'THA.LOC104805363' => 'tha', 'THA.LOC104808968' => 'tha', 'THA.LOC104821093' => 'tha', 'THA.LOC104823953' => 'tha', 'THA.LOC104825562' => 'tha', 'THA.LOC104825665' => 'tha', 'Thecc.02G261400' => 'tca', 'Thecc.04G019200' => 'tca', 'Thecc.09G130400' => 'tca', 'Thhalv10004374m.g' => 'esa', 'Thhalv10007850m.g' => 'esa', 'Thhalv10013782m.g' => 'esa', 'Thhalv10018686m.g' => 'esa', 'Thhalv10020899m.g' => 'esa', 'Thhalv10022755m.g' => 'esa', 'TPR.G23851' => 'tpr', 'TPR.G26500' => 'tpr', 'TPR.G27267' => 'tpr', 'TPR.G32001' => 'tpr', 'TPR.G6251' => 'tpr', 'TPR.G8167' => 'tpr', 'TWI12G1330' => 'twi', 'TWI18G1239' => 'twi', 'TWI34G0979' => 'twi', 'TWI36G0670' => 'twi', 'TWI36G0707' => 'twi', 'TWI56G0233' => 'twi', 'TWI75G1809' => 'twi', 'unitig_21.g20874' => 'ugi', 'unitig_26.g10343' => 'ugi', 'unitig_46.g18392' => 'ugi', 'unitig_52.g17178' => 'ugi', 'unitig_8.g2934' => 'ugi', 'vmacro01122' => 'vma', 'vmacro05875' => 'vma', 'vmacro06147' => 'vma', 'vmacro16191' => 'vma', 'vmacro18293' => 'vma', 'VMungo0251G3707' => 'vmu', 'VMungo0464G1521' => 'vmu', 'VMungo1215G0205' => 'vmu', 'VMungo1383G2484' => 'vmu', 'Zm00001eb079610' => 'zma', 'Zm00001eb135990' => 'zma', 'Zm00001eb183710' => 'zma', 'Zm00001eb246020' => 'zma' ) $gf_id = 'HOM05D001124' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001124' ) $data_identifier = 'HOM05D001124' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 6, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 7, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 21, 'bol' => (int) 10, 'bra' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 6, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 9, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 21, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 8, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 10, 'lsa' => (int) 8, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 8, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 9, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb246020' $species_info = array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ) $local_species = 'fve' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001124', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '548', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02520' => 'bna', 'A03p06630' => 'bna', 'A05p44460' => 'bna', 'A06p08710' => 'bna', 'A06p41090' => 'bna', 'A07p32320' => 'bna', 'A08p32520' => 'bna', 'A09p10360' => 'bna', 'A10p24080' => 'bna', 'Aa31LG11G15250' => 'aar', 'Aa31LG1G1800' => 'aar', 'Aa31LG2G5120' => 'aar', 'Aa31LG2G6070' => 'aar', 'Aa31LG5G10770' => 'aar', 'Aa31sc61G90' => 'aar', 'Actinidia01352' => 'ach', 'Actinidia05983' => 'ach', 'Actinidia08133' => 'ach', 'Actinidia15101' => 'ach', 'Actinidia26379' => 'ach', 'Actinidia35778' => 'ach', 'Actinidia36123' => 'ach', 'Actinidia37436' => 'ach', 'Actinidia38730' => 'ach', 'Ah.02g128210' => 'amhyb', 'Ah.03g132990' => 'amhyb', 'Ah.14g079410' => 'amhyb', 'AL1G24640' => 'aly', 'AL2G26680' => 'aly', 'AL3G10530' => 'aly', 'AL3G45230' => 'aly', 'AL5G15230' => 'aly', 'AL5G16960' => 'aly', 'AL6G25210' => 'aly', 'Aqoxy2G00441' => 'aox', 'Aqoxy3G01236' => 'aox', 'Aqoxy5G03746' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3RQ047' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C7GMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9C8JER' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MBL6KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YXCZ83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZANX40' => 'arhy', 'AT1G12990' => 'ath', 'AT1G67880' => 'ath', 'AT2G13290' => 'ath', 'AT3G01620' => 'ath', 'AT3G26445' => 'ath', 'AT3G27540' => 'ath', 'AT5G14480' => 'ath', 'ATR0824G026' => 'atr', 'ATR1098G019' => 'atr', 'Atru.chr11.2145' => 'acertr', 'Atru.chr2.3636' => 'acertr', 'Atru.chr2.3644' => 'acertr', 'Atru.chr6.2422' => 'acertr', 'Atru.chr7.1112' => 'acertr', 'AUR62005469' => 'cqu', 'AUR62011166' => 'cqu', 'AUR62013319' => 'cqu', 'AUR62024273' => 'cqu', 'AUR62028420' => 'cqu', 'AUR62041942' => 'cqu', 'BcaB01g04969' => 'bca', 'BcaB01g06371' => 'bca', 'BcaB02g11494' => 'bca', 'BcaB03g15382' => 'bca', 'BcaB08g36994' => 'bca', 'BcaC03g13477' => 'bca', 'BcaC03g13478' => 'bca', 'BcaC03g13480' => 'bca', 'BcaC03g13481' => 'bca', 'BcaC03g13486' => 'bca', 'BcaC04g19031' => 'bca', 'BcaC04g23085' => 'bca', 'BcaC05g25094' => 'bca', 'BcaC05g25096' => 'bca', 'BcaC05g25138' => 'bca', 'BcaC05g30416' => 'bca', 'BcaC05g30455' => 'bca', 'BcaC06g30979' => 'bca', 'BcaC06g33805' => 'bca', 'BcaC08g46021' => 'bca', 'BcaNung03154' => 'bca', 'BolC2t06623H' => 'bol', 'BolC2t06632H' => 'bol', 'BolC2t06635H' => 'bol', 'BolC2t06638H' => 'bol', 'BolC3t13266H' => 'bol', 'BolC5t29776H' => 'bol', 'BolC6t38912H' => 'bol', 'BolC7t44183H' => 'bol', 'BolC9t54123H' => 'bol', 'BolC9t59107H' => 'bol', 'BraA02t05221Z' => 'bra', 'BraA03t09996Z' => 'bra', 'BraA05t23210Z' => 'bra', 'BraA06t24068Z' => 'bra', 'BraA06t27032Z' => 'bra', 'BraA08t35176Z' => 'bra', 'BraA09t36680Z' => 'bra', 'BraA10t44471Z' => 'bra', 'C02p06760' => 'bna', 'C02p06890' => 'bna', 'C02p07010' => 'bna', 'C03p07660' => 'bna', 'C05p10300' => 'bna', 'C06p38150' => 'bna', 'C07p36650' => 'bna', 'C08p15770' => 'bna', 'C09p12300' => 'bna', 'C09p62700' => 'bna', 'C09p75040' => 'bna', 'CAN.G13.1' => 'can', 'CAN.G138.4' => 'can', 'CAN.G44.6' => 'can', 'CAN.G473.19' => 'can', 'CANSAT01G0835' => 'cansat', 'CANSAT11G0246' => 'cansat', 'CANSAT11G1766' => 'cansat', 'CANSAT64G1954' => 'cansat', 'CARHR013330' => 'chi', 'CARHR060530' => 'chi', 'CARHR075300' => 'chi', 'CARHR105120' => 'chi', 'CARHR148910' => 'chi', 'CARHR198830' => 'chi', 'Carub.0001s1275' => 'cru', 'Carub.0002s1437' => 'cru', 'Carub.0003s0044' => 'cru', 'Carub.0003s2787' => 'cru', 'Carub.0005s0597' => 'cru', 'Carub.0006s1266' => 'cru', 'Ca_06935_v3' => 'car', 'Ca_13559_v3' => 'car', 'Ca_16941_v3' => 'car', 'Ca_16960_v3' => 'car', 'Ca_17775_v3' => 'car', 'Ca_30464_v3' => 'car', 'Cc06_g08160' => 'ccan', 'Cc07_g01520' => 'ccan', 'Cc11_g15810' => 'ccan', 'CDE02G2840' => 'cde', 'CDE03G0093' => 'cde', 'CDE04G2127' => 'cde', 'CDE07G1857' => 'cde', 'CDE09G1246' => 'cde', 'Cfa003412' => 'cfa', 'Cfa007341' => 'cfa', 'Cfa009220' => 'cfa', 'Ciclev10008737m.g' => 'ccl', 'Ciclev10015565m.g' => 'ccl', 'Ciclev10031761m.g' => 'ccl', 'CiPaw.03G045300' => 'cil', 'CiPaw.03G247200' => 'cil', 'CiPaw.04G029500' => 'cil', 'CiPaw.04G174000' => 'cil', 'CiPaw.05G181200' => 'cil', 'CiPaw.06G067100' => 'cil', 'ClCG05G025800' => 'cla', 'ClCG06G011400' => 'cla', 'ClCG09G019360' => 'cla', 'COL.COLO4_04827' => 'col', 'COL.COLO4_29170' => 'col', 'COL.COLO4_35131' => 'col', 'COL.COLO4_35132' => 'col', 'Cpa.g.sc33.32' => 'cpa', 'Cpa.g.sc46.29' => 'cpa', 'Cpa.g.sc796.1' => 'cpa', 'CsaV3_1G030420' => 'csa', 'CsaV3_5G027050' => 'csa', 'CsaV3_5G031040' => 'csa', 'CsaV3_UNG023130' => 'csa', 'CSS0007726' => 'camsi', 'CSS0016433' => 'camsi', 'CSS0017656' => 'camsi', 'CSS0025364' => 'camsi', 'CSS0027582' => 'camsi', 'CSS0047288' => 'camsi', 'CSS0049950' => 'camsi', 'DCAR_003843' => 'dca', 'DCAR_007052' => 'dca', 'DCAR_020884' => 'dca', 'DCAR_021730' => 'dca', 'DCAR_024423' => 'dca', 'DCAR_026509' => 'dca', 'DCAR_031158' => 'dca', 'Dinv14728' => 'din', 'Dinv15219' => 'din', 'Dinv25728' => 'din', 'Dinv33428' => 'din', 'Dinv36489' => 'din', 'Dinv41486' => 'din', 'Duzib147G0469' => 'dzi', 'Duzib168G0060' => 'dzi', 'Duzib187G1215' => 'dzi', 'Duzib248G0692' => 'dzi', 'Duzib251G0767' => 'dzi', 'Duzib264G0446' => 'dzi', 'Duzib268G0691' => 'dzi', 'ECA232G4767' => 'eca', 'ECA233G2838' => 'eca', 'ECA234G0391' => 'eca', 'ECA234G0857' => 'eca', 'ECA236G1593' => 'eca', 'ECA238G0565' => 'eca', 'ECA246G1027' => 'eca', 'ECA246G3223' => 'eca', 'ECA246G3470' => 'eca', 'EL10Ac6g13829' => 'bvu', 'EL10Ac6g14093' => 'bvu', 'EL10Ac8g18707' => 'bvu', 'Eucgr.C01369' => 'egr', 'Eucgr.H02492' => 'egr', 'Eucgr.I01733' => 'egr', 'Eucgr.J02255' => 'egr', 'Eucgr.J02257' => 'egr', 'Eucgr.J02258' => 'egr', 'FAN02G1601' => 'fan', 'FAN03G1586' => 'fan', 'FAN03G2986' => 'fan', 'FAN05G4837' => 'fan', 'FAN06G0146' => 'fan', 'FAN07G0858' => 'fan', 'FAN09G3179' => 'fan', 'FAN10G0669' => 'fan', 'FAN12G2358' => 'fan', 'FAN14G4198' => 'fan', 'FAN14G5112' => 'fan', 'FAN17G0342' => 'fan', 'FAN19G0342' => 'fan', 'FAN19G0962' => 'fan', 'FAN19G1101' => 'fan', 'FAN19G1872' => 'fan', 'FAN22G0356' => 'fan', 'FAN23G0744' => 'fan', 'FAN23G1914' => 'fan', 'FAN26G0032' => 'fan', 'FAN28G0625' => 'fan', 'FvH4_1g02710' => 'fve', 'FvH4_1g02720' => 'fve', 'FvH4_4g25670' => 'fve', 'FvH4_6g51700' => 'fve', 'FvH4_7g20170' => 'fve', 'Glyma.05G175000' => 'gma', 'Glyma.08G132300' => 'gma', 'Glyma.11G243000' => 'gma', 'Glyma.13G158900' => 'gma', 'Glyma.17G112400' => 'gma', 'Glyma.18G014100' => 'gma', 'Glyma.19G003100' => 'gma', 'Glyma.19G056500' => 'gma', 'Gohir.A01G158900' => 'ghi', 'Gohir.A05G312600' => 'ghi', 'Gohir.A05G354900' => 'ghi', 'Gohir.A07G037200' => 'ghi', 'Gohir.A09G030000' => 'ghi', 'Gohir.A12G145200' => 'ghi', 'Gohir.D01G151500' => 'ghi', 'Gohir.D04G058300' => 'ghi', 'Gohir.D05G314100' => 'ghi', 'Gohir.D07G041400' => 'ghi', 'Gohir.D09G029700' => 'ghi', 'Gohir.D12G149700' => 'ghi', 'Gorai.001G043800' => 'gra', 'Gorai.002G187800' => 'gra', 'Gorai.006G034700' => 'gra', 'Gorai.008G161200' => 'gra', 'Gorai.009G335700' => 'gra', 'Gorai.012G065000' => 'gra', 'GSVIVG01000535001' => 'vvi', 'GSVIVG01015572001' => 'vvi', 'GSVIVG01032386001' => 'vvi', 'HanXRQChr05g0138531' => 'han', 'HanXRQChr06g0174391' => 'han', 'HanXRQChr07g0199021' => 'han', 'HanXRQChr08g0208211' => 'han', 'HanXRQChr09g0255471' => 'han', 'HanXRQChr10g0315791' => 'han', 'HanXRQChr12g0371991' => 'han', 'HanXRQChr15g0475251' => 'han', 'HanXRQChr17g0540001' => 'han', 'HanXRQChr17g0548631' => 'han', 'HanXRQChr17g0569561' => 'han', 'Haze_12256' => 'cav', 'Haze_14756' => 'cav', 'Haze_25528' => 'cav', 'Hma1.2p1_0079F.1_g041020' => 'hma', 'Hma1.2p1_0818F.1_g223260' => 'hma', 'Hma1.2p1_1747F.1_g300530' => 'hma', 'HPP92_004607' => 'vpl', 'HPP92_004608' => 'vpl', 'HPP92_006181' => 'vpl', 'HPP92_012192' => 'vpl', 'HPP92_015680' => 'vpl', 'HPP92_020249' => 'vpl', 'HPP92_021376' => 'vpl', 'HPP92_024275' => 'vpl', 'Hund06031' => 'sun', 'Hund25391' => 'sun', 'Lalb_Chr07g0185371' => 'lal', 'Lalb_Chr07g0185381' => 'lal', 'Lalb_Chr12g0204011' => 'lal', 'Lalb_Chr13g0301671' => 'lal', 'Lalb_Chr14g0362851' => 'lal', 'Lalb_Chr24g0403581' => 'lal', 'Lj1g0000233' => 'lja', 'Lj2g0018120' => 'lja', 'Lj3C621T0' => 'lonja', 'Lj3P1059T14' => 'lonja', 'Lj3P611T9' => 'lonja', 'Lj3P614T13' => 'lonja', 'Lj3P615T5' => 'lonja', 'Lj4g0012315' => 'lja', 'Lj4g0026182' => 'lja', 'Lj6P813T16' => 'lonja', 'Lj7C427T7' => 'lonja', 'Lj7C427T8' => 'lonja', 'Lj7P600T41' => 'lonja', 'Lju41C42G17' => 'lonja', 'Lsat_1_v5_gn_0_47300' => 'lsa', 'Lsat_1_v5_gn_2_91280' => 'lsa', 'Lsat_1_v5_gn_3_30561' => 'lsa', 'Lsat_1_v5_gn_4_184321' => 'lsa', 'Lsat_1_v5_gn_4_4041' => 'lsa', 'Lsat_1_v5_gn_5_92000' => 'lsa', 'Lsat_1_v5_gn_8_152940' => 'lsa', 'Lsat_1_v5_gn_8_62401' => 'lsa', 'Manes.06G055900' => 'mes', 'Manes.12G022200' => 'mes', 'Manes.13G023300' => 'mes', 'Manes.14G115000' => 'mes', 'Manes.15G151700' => 'mes', 'Manes.17G111300' => 'mes', 'Mapoly0226s0009' => 'mpo', 'MBI02_g25363_MAGBIO' => 'mbi', 'MBI06_g00027_MAGBIO' => 'mbi', 'MBI10_g13034_MAGBIO' => 'mbi', 'MD09G1023400' => 'mdo', 'MD13G1100100' => 'mdo', 'MD15G1169200' => 'mdo', 'MD16G1101100' => 'mdo', 'MD17G1022900' => 'mdo', 'Medtr3g096150' => 'mtr', 'Medtr4g115070' => 'mtr', 'Medtr7g033325' => 'mtr', 'Medtr8g089840' => 'mtr', 'MELO3C010319.2' => 'cme', 'MELO3C011944.2' => 'cme', 'MELO3C021589.2' => 'cme', 'Migut.E00207' => 'egut', 'Migut.H00067' => 'egut', 'Migut.K00433' => 'egut', 'Migut.K00606' => 'egut', 'Migut.K01410' => 'egut', 'MSTRG.13347' => 'ama', 'MSTRG.24045' => 'ama', 'MSTRG.2428' => 'ama', 'MSTRG.26410' => 'ama', 'MSTRG.3139' => 'ama', 'MSTRG.3286' => 'ama', 'MSTRG.563' => 'ama', 'MSTRG.7941' => 'ama', 'Nitab4.5_0000028g0060' => 'nta', 'Nitab4.5_0000065g0260' => 'nta', 'Nitab4.5_0000112g0060' => 'nta', 'Nitab4.5_0000489g0120' => 'nta', 'Nitab4.5_0001776g0050' => 'nta', 'Nitab4.5_0001854g0010' => 'nta', 'Nitab4.5_0001860g0020' => 'nta', 'Nitab4.5_0004352g0010' => 'nta', 'Nitab4.5_0008716g0020' => 'nta', 'Nitab4.5_0008922g0010' => 'nta', 'Nn3g16693' => 'nnu', 'Nn4g22596' => 'nnu', 'Nn7g37639' => 'nnu', 'Oeu001701.1' => 'oeu', 'Oeu018149.1' => 'oeu', 'Oeu026220.1' => 'oeu', 'Oeu038635.1' => 'oeu', 'Oeu049176.1' => 'oeu', 'Oeu056706.1' => 'oeu', 'Oeu056937.1' => 'oeu', 'Oeu057540.1' => 'oeu', 'Os02g0594900' => 'osa', 'Os02g0595100' => 'osa', 'Os04g0477500' => 'osa', 'Os12g0611900' => 'osa', 'Peaxi162Scf00076g00020' => 'pax', 'Peaxi162Scf00128g00217' => 'pax', 'Peaxi162Scf00129g01640' => 'pax', 'Peaxi162Scf00669g00007' => 'pax', 'Peaxi162Scf00700g00421' => 'pax', 'Peaxi162Scf00801g00038' => 'pax', 'Peaxi162Scf00891g00025' => 'pax', 'PGR083G0909' => 'pgr', 'PGR119G1005' => 'pgr', 'PGR142G2236' => 'pgr', 'PGR142G3388' => 'pgr', 'PGSC0003DMG400004514' => 'stu', 'PGSC0003DMG400012635' => 'stu', 'PGSC0003DMG400015730' => 'stu', 'PGSC0003DMG400018611' => 'stu', 'PGSC0003DMG400030897' => 'stu', 'Phvul.001G254800' => 'pvu', 'Phvul.002G260100' => 'pvu', 'Phvul.003G167600' => 'pvu', 'Phvul.004G005100' => 'pvu', 'Potri.001G343600' => 'ptr', 'Potri.006G066700' => 'ptr', 'Potri.008G186000' => 'ptr', 'Potri.010G046900' => 'ptr', 'Potri.018G127900' => 'ptr', 'Pp3c20_17750' => 'ppa', 'Pp3c24_4380' => 'ppa', 'Prupe.1G245800' => 'ppe', 'Prupe.3G293400' => 'ppe', 'Prupe.7G247400' => 'ppe', 'Psat0s145g0120' => 'psa', 'Psat0s595g0040' => 'psa', 'Psat0s595g0120' => 'psa', 'Psat3g175040' => 'psa', 'Psat7g058120' => 'psa', 'PSO017G0428' => 'pso', 'PSO063G7510' => 'pso', 'PSO067G0046' => 'pso', 'PSO478G1073' => 'pso', 'PSO675G3677' => 'pso', 'PSO675G6558' => 'pso', 'PSO675G7520' => 'pso', 'PSO675G8959' => 'pso', 'QL02p074089' => 'qlo', 'QL02p089614' => 'qlo', 'QL03p057736' => 'qlo', 'RcHm_v2.0_Chr1g0364131' => 'rch', 'RcHm_v2.0_Chr2g0087801' => 'rch', 'RcHm_v2.0_Chr2g0087821' => 'rch', 'RcHm_v2.0_Chr2g0173231' => 'rch', 'RcHm_v2.0_Chr4g0433111' => 'rch', 'Rhsim03G0250300' => 'rsi', 'Rhsim08G0048400' => 'rsi', 'Rhsim10G0014800' => 'rsi', 'Rhsim12G0040100' => 'rsi', 'Rhsim12G0109700' => 'rsi', 'Sabra06G0049600' => 'sbr', 'Sabra08G0141000' => 'sbr', 'Sabra10G0021400' => 'sbr', 'Sabra16G0222900' => 'sbr', 'Sabra18G0108600' => 'sbr', 'SalBow1G0433' => 'sbo', 'SalBow1G2038' => 'sbo', 'SalBow1G5003' => 'sbo', 'SalBow7G1197' => 'sbo', 'SalBow8G3506' => 'sbo', 'Sc03g0007300' => 'sci', 'Sc11g0000950' => 'sci', 'Sc14g0008750' => 'sci', 'Sc18g0000420' => 'sci', 'Sed0006754' => 'sed', 'Sed0008741' => 'sed', 'Sed0017172' => 'sed', 'Sed0018925' => 'sed', 'Sed0023326' => 'sed', 'Sed0025909' => 'sed', 'SEGI_05333' => 'sgi', 'SEGI_10362' => 'sgi', 'SEGI_13380' => 'sgi', 'SEGI_24306' => 'sgi', 'SEGI_29077' => 'sgi', 'SEGI_29095' => 'sgi', 'SEGI_36534' => 'sgi', 'SEGI_37506' => 'sgi', 'SEGI_38321' => 'sgi', 'SGA_v2.0_scaffold307G48031' => 'sas', 'SGA_v2.0_scaffold47G17507' => 'sas', 'SGA_v2.0_scaffold63G21736' => 'sas', 'SGA_v2.0_scaffold87G27070' => 'sas', 'SHI17794' => 'shi', 'SHI28851' => 'shi', 'SMO165G0155' => 'smo', 'SMO340G0217' => 'smo', 'SMO367G1210' => 'smo', 'Solyc02g093430.3' => 'sly', 'Solyc05g013580.4' => 'sly', 'Solyc07g008030.3' => 'sly', 'Solyc12g035470.2' => 'sly', 'Sopen02g038020' => 'spe', 'Sopen05g008490' => 'spe', 'Sopen07g003910' => 'spe', 'Sopen12g015240' => 'spe', 'Sp1g11550' => 'spa', 'Sp2g16710' => 'spa', 'Sp3g00430' => 'spa', 'Sp3g26780' => 'spa', 'Sp5g22900' => 'spa', 'Sp6g29530' => 'spa', 'TAR371G0794' => 'tar', 'TAR374G0164' => 'tar', 'TAR622G0165' => 'tar', 'TAR626G0929' => 'tar', 'TAR629G2155' => 'tar', 'THA.LOC104805282' => 'tha', 'THA.LOC104805363' => 'tha', 'THA.LOC104808968' => 'tha', 'THA.LOC104821093' => 'tha', 'THA.LOC104823953' => 'tha', 'THA.LOC104825562' => 'tha', 'THA.LOC104825665' => 'tha', 'Thecc.02G261400' => 'tca', 'Thecc.04G019200' => 'tca', 'Thecc.09G130400' => 'tca', 'Thhalv10004374m.g' => 'esa', 'Thhalv10007850m.g' => 'esa', 'Thhalv10013782m.g' => 'esa', 'Thhalv10018686m.g' => 'esa', 'Thhalv10020899m.g' => 'esa', 'Thhalv10022755m.g' => 'esa', 'TPR.G23851' => 'tpr', 'TPR.G26500' => 'tpr', 'TPR.G27267' => 'tpr', 'TPR.G32001' => 'tpr', 'TPR.G6251' => 'tpr', 'TPR.G8167' => 'tpr', 'TWI12G1330' => 'twi', 'TWI18G1239' => 'twi', 'TWI34G0979' => 'twi', 'TWI36G0670' => 'twi', 'TWI36G0707' => 'twi', 'TWI56G0233' => 'twi', 'TWI75G1809' => 'twi', 'unitig_21.g20874' => 'ugi', 'unitig_26.g10343' => 'ugi', 'unitig_46.g18392' => 'ugi', 'unitig_52.g17178' => 'ugi', 'unitig_8.g2934' => 'ugi', 'vmacro01122' => 'vma', 'vmacro05875' => 'vma', 'vmacro06147' => 'vma', 'vmacro16191' => 'vma', 'vmacro18293' => 'vma', 'VMungo0251G3707' => 'vmu', 'VMungo0464G1521' => 'vmu', 'VMungo1215G0205' => 'vmu', 'VMungo1383G2484' => 'vmu', 'Zm00001eb079610' => 'zma', 'Zm00001eb135990' => 'zma', 'Zm00001eb183710' => 'zma', 'Zm00001eb246020' => 'zma' ), 'gf_id' => 'HOM05D001124', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001124' ), 'data_identifier' => 'HOM05D001124', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001124', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '548', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02520' => 'bna', 'A03p06630' => 'bna', 'A05p44460' => 'bna', 'A06p08710' => 'bna', 'A06p41090' => 'bna', 'A07p32320' => 'bna', 'A08p32520' => 'bna', 'A09p10360' => 'bna', 'A10p24080' => 'bna', 'Aa31LG11G15250' => 'aar', 'Aa31LG1G1800' => 'aar', 'Aa31LG2G5120' => 'aar', 'Aa31LG2G6070' => 'aar', 'Aa31LG5G10770' => 'aar', 'Aa31sc61G90' => 'aar', 'Actinidia01352' => 'ach', 'Actinidia05983' => 'ach', 'Actinidia08133' => 'ach', 'Actinidia15101' => 'ach', 'Actinidia26379' => 'ach', 'Actinidia35778' => 'ach', 'Actinidia36123' => 'ach', 'Actinidia37436' => 'ach', 'Actinidia38730' => 'ach', 'Ah.02g128210' => 'amhyb', 'Ah.03g132990' => 'amhyb', 'Ah.14g079410' => 'amhyb', 'AL1G24640' => 'aly', 'AL2G26680' => 'aly', 'AL3G10530' => 'aly', 'AL3G45230' => 'aly', 'AL5G15230' => 'aly', 'AL5G16960' => 'aly', 'AL6G25210' => 'aly', 'Aqoxy2G00441' => 'aox', 'Aqoxy3G01236' => 'aox', 'Aqoxy5G03746' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3RQ047' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C7GMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9C8JER' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MBL6KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YXCZ83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZANX40' => 'arhy', 'AT1G12990' => 'ath', 'AT1G67880' => 'ath', 'AT2G13290' => 'ath', 'AT3G01620' => 'ath', 'AT3G26445' => 'ath', 'AT3G27540' => 'ath', 'AT5G14480' => 'ath', 'ATR0824G026' => 'atr', 'ATR1098G019' => 'atr', 'Atru.chr11.2145' => 'acertr', 'Atru.chr2.3636' => 'acertr', 'Atru.chr2.3644' => 'acertr', 'Atru.chr6.2422' => 'acertr', 'Atru.chr7.1112' => 'acertr', 'AUR62005469' => 'cqu', 'AUR62011166' => 'cqu', 'AUR62013319' => 'cqu', 'AUR62024273' => 'cqu', 'AUR62028420' => 'cqu', 'AUR62041942' => 'cqu', 'BcaB01g04969' => 'bca', 'BcaB01g06371' => 'bca', 'BcaB02g11494' => 'bca', 'BcaB03g15382' => 'bca', 'BcaB08g36994' => 'bca', 'BcaC03g13477' => 'bca', 'BcaC03g13478' => 'bca', 'BcaC03g13480' => 'bca', 'BcaC03g13481' => 'bca', 'BcaC03g13486' => 'bca', 'BcaC04g19031' => 'bca', 'BcaC04g23085' => 'bca', 'BcaC05g25094' => 'bca', 'BcaC05g25096' => 'bca', 'BcaC05g25138' => 'bca', 'BcaC05g30416' => 'bca', 'BcaC05g30455' => 'bca', 'BcaC06g30979' => 'bca', 'BcaC06g33805' => 'bca', 'BcaC08g46021' => 'bca', 'BcaNung03154' => 'bca', 'BolC2t06623H' => 'bol', 'BolC2t06632H' => 'bol', 'BolC2t06635H' => 'bol', 'BolC2t06638H' => 'bol', 'BolC3t13266H' => 'bol', 'BolC5t29776H' => 'bol', 'BolC6t38912H' => 'bol', 'BolC7t44183H' => 'bol', 'BolC9t54123H' => 'bol', 'BolC9t59107H' => 'bol', 'BraA02t05221Z' => 'bra', 'BraA03t09996Z' => 'bra', 'BraA05t23210Z' => 'bra', 'BraA06t24068Z' => 'bra', 'BraA06t27032Z' => 'bra', 'BraA08t35176Z' => 'bra', 'BraA09t36680Z' => 'bra', 'BraA10t44471Z' => 'bra', 'C02p06760' => 'bna', 'C02p06890' => 'bna', 'C02p07010' => 'bna', 'C03p07660' => 'bna', 'C05p10300' => 'bna', 'C06p38150' => 'bna', 'C07p36650' => 'bna', 'C08p15770' => 'bna', 'C09p12300' => 'bna', 'C09p62700' => 'bna', 'C09p75040' => 'bna', 'CAN.G13.1' => 'can', 'CAN.G138.4' => 'can', 'CAN.G44.6' => 'can', 'CAN.G473.19' => 'can', 'CANSAT01G0835' => 'cansat', 'CANSAT11G0246' => 'cansat', 'CANSAT11G1766' => 'cansat', 'CANSAT64G1954' => 'cansat', 'CARHR013330' => 'chi', 'CARHR060530' => 'chi', 'CARHR075300' => 'chi', 'CARHR105120' => 'chi', 'CARHR148910' => 'chi', 'CARHR198830' => 'chi', 'Carub.0001s1275' => 'cru', 'Carub.0002s1437' => 'cru', 'Carub.0003s0044' => 'cru', 'Carub.0003s2787' => 'cru', 'Carub.0005s0597' => 'cru', 'Carub.0006s1266' => 'cru', 'Ca_06935_v3' => 'car', 'Ca_13559_v3' => 'car', 'Ca_16941_v3' => 'car', 'Ca_16960_v3' => 'car', 'Ca_17775_v3' => 'car', 'Ca_30464_v3' => 'car', 'Cc06_g08160' => 'ccan', 'Cc07_g01520' => 'ccan', 'Cc11_g15810' => 'ccan', 'CDE02G2840' => 'cde', 'CDE03G0093' => 'cde', 'CDE04G2127' => 'cde', 'CDE07G1857' => 'cde', 'CDE09G1246' => 'cde', 'Cfa003412' => 'cfa', 'Cfa007341' => 'cfa', 'Cfa009220' => 'cfa', 'Ciclev10008737m.g' => 'ccl', 'Ciclev10015565m.g' => 'ccl', 'Ciclev10031761m.g' => 'ccl', 'CiPaw.03G045300' => 'cil', 'CiPaw.03G247200' => 'cil', 'CiPaw.04G029500' => 'cil', 'CiPaw.04G174000' => 'cil', 'CiPaw.05G181200' => 'cil', 'CiPaw.06G067100' => 'cil', 'ClCG05G025800' => 'cla', 'ClCG06G011400' => 'cla', 'ClCG09G019360' => 'cla', 'COL.COLO4_04827' => 'col', 'COL.COLO4_29170' => 'col', 'COL.COLO4_35131' => 'col', 'COL.COLO4_35132' => 'col', 'Cpa.g.sc33.32' => 'cpa', 'Cpa.g.sc46.29' => 'cpa', 'Cpa.g.sc796.1' => 'cpa', 'CsaV3_1G030420' => 'csa', 'CsaV3_5G027050' => 'csa', 'CsaV3_5G031040' => 'csa', 'CsaV3_UNG023130' => 'csa', 'CSS0007726' => 'camsi', 'CSS0016433' => 'camsi', 'CSS0017656' => 'camsi', 'CSS0025364' => 'camsi', 'CSS0027582' => 'camsi', 'CSS0047288' => 'camsi', 'CSS0049950' => 'camsi', 'DCAR_003843' => 'dca', 'DCAR_007052' => 'dca', 'DCAR_020884' => 'dca', 'DCAR_021730' => 'dca', 'DCAR_024423' => 'dca', 'DCAR_026509' => 'dca', 'DCAR_031158' => 'dca', 'Dinv14728' => 'din', 'Dinv15219' => 'din', 'Dinv25728' => 'din', 'Dinv33428' => 'din', 'Dinv36489' => 'din', 'Dinv41486' => 'din', 'Duzib147G0469' => 'dzi', 'Duzib168G0060' => 'dzi', 'Duzib187G1215' => 'dzi', 'Duzib248G0692' => 'dzi', 'Duzib251G0767' => 'dzi', 'Duzib264G0446' => 'dzi', 'Duzib268G0691' => 'dzi', 'ECA232G4767' => 'eca', 'ECA233G2838' => 'eca', 'ECA234G0391' => 'eca', 'ECA234G0857' => 'eca', 'ECA236G1593' => 'eca', 'ECA238G0565' => 'eca', 'ECA246G1027' => 'eca', 'ECA246G3223' => 'eca', 'ECA246G3470' => 'eca', 'EL10Ac6g13829' => 'bvu', 'EL10Ac6g14093' => 'bvu', 'EL10Ac8g18707' => 'bvu', 'Eucgr.C01369' => 'egr', 'Eucgr.H02492' => 'egr', 'Eucgr.I01733' => 'egr', 'Eucgr.J02255' => 'egr', 'Eucgr.J02257' => 'egr', 'Eucgr.J02258' => 'egr', 'FAN02G1601' => 'fan', 'FAN03G1586' => 'fan', 'FAN03G2986' => 'fan', 'FAN05G4837' => 'fan', 'FAN06G0146' => 'fan', 'FAN07G0858' => 'fan', 'FAN09G3179' => 'fan', 'FAN10G0669' => 'fan', 'FAN12G2358' => 'fan', 'FAN14G4198' => 'fan', 'FAN14G5112' => 'fan', 'FAN17G0342' => 'fan', 'FAN19G0342' => 'fan', 'FAN19G0962' => 'fan', 'FAN19G1101' => 'fan', 'FAN19G1872' => 'fan', 'FAN22G0356' => 'fan', 'FAN23G0744' => 'fan', 'FAN23G1914' => 'fan', 'FAN26G0032' => 'fan', 'FAN28G0625' => 'fan', 'FvH4_1g02710' => 'fve', 'FvH4_1g02720' => 'fve', 'FvH4_4g25670' => 'fve', 'FvH4_6g51700' => 'fve', 'FvH4_7g20170' => 'fve', 'Glyma.05G175000' => 'gma', 'Glyma.08G132300' => 'gma', 'Glyma.11G243000' => 'gma', 'Glyma.13G158900' => 'gma', 'Glyma.17G112400' => 'gma', 'Glyma.18G014100' => 'gma', 'Glyma.19G003100' => 'gma', 'Glyma.19G056500' => 'gma', 'Gohir.A01G158900' => 'ghi', 'Gohir.A05G312600' => 'ghi', 'Gohir.A05G354900' => 'ghi', 'Gohir.A07G037200' => 'ghi', 'Gohir.A09G030000' => 'ghi', 'Gohir.A12G145200' => 'ghi', 'Gohir.D01G151500' => 'ghi', 'Gohir.D04G058300' => 'ghi', 'Gohir.D05G314100' => 'ghi', 'Gohir.D07G041400' => 'ghi', 'Gohir.D09G029700' => 'ghi', 'Gohir.D12G149700' => 'ghi', 'Gorai.001G043800' => 'gra', 'Gorai.002G187800' => 'gra', 'Gorai.006G034700' => 'gra', 'Gorai.008G161200' => 'gra', 'Gorai.009G335700' => 'gra', 'Gorai.012G065000' => 'gra', 'GSVIVG01000535001' => 'vvi', 'GSVIVG01015572001' => 'vvi', 'GSVIVG01032386001' => 'vvi', 'HanXRQChr05g0138531' => 'han', 'HanXRQChr06g0174391' => 'han', 'HanXRQChr07g0199021' => 'han', 'HanXRQChr08g0208211' => 'han', 'HanXRQChr09g0255471' => 'han', 'HanXRQChr10g0315791' => 'han', 'HanXRQChr12g0371991' => 'han', 'HanXRQChr15g0475251' => 'han', 'HanXRQChr17g0540001' => 'han', 'HanXRQChr17g0548631' => 'han', 'HanXRQChr17g0569561' => 'han', 'Haze_12256' => 'cav', 'Haze_14756' => 'cav', 'Haze_25528' => 'cav', 'Hma1.2p1_0079F.1_g041020' => 'hma', 'Hma1.2p1_0818F.1_g223260' => 'hma', 'Hma1.2p1_1747F.1_g300530' => 'hma', 'HPP92_004607' => 'vpl', 'HPP92_004608' => 'vpl', 'HPP92_006181' => 'vpl', 'HPP92_012192' => 'vpl', 'HPP92_015680' => 'vpl', 'HPP92_020249' => 'vpl', 'HPP92_021376' => 'vpl', 'HPP92_024275' => 'vpl', 'Hund06031' => 'sun', 'Hund25391' => 'sun', 'Lalb_Chr07g0185371' => 'lal', 'Lalb_Chr07g0185381' => 'lal', 'Lalb_Chr12g0204011' => 'lal', 'Lalb_Chr13g0301671' => 'lal', 'Lalb_Chr14g0362851' => 'lal', 'Lalb_Chr24g0403581' => 'lal', 'Lj1g0000233' => 'lja', 'Lj2g0018120' => 'lja', 'Lj3C621T0' => 'lonja', 'Lj3P1059T14' => 'lonja', 'Lj3P611T9' => 'lonja', 'Lj3P614T13' => 'lonja', 'Lj3P615T5' => 'lonja', 'Lj4g0012315' => 'lja', 'Lj4g0026182' => 'lja', 'Lj6P813T16' => 'lonja', 'Lj7C427T7' => 'lonja', 'Lj7C427T8' => 'lonja', 'Lj7P600T41' => 'lonja', 'Lju41C42G17' => 'lonja', 'Lsat_1_v5_gn_0_47300' => 'lsa', 'Lsat_1_v5_gn_2_91280' => 'lsa', 'Lsat_1_v5_gn_3_30561' => 'lsa', 'Lsat_1_v5_gn_4_184321' => 'lsa', 'Lsat_1_v5_gn_4_4041' => 'lsa', 'Lsat_1_v5_gn_5_92000' => 'lsa', 'Lsat_1_v5_gn_8_152940' => 'lsa', 'Lsat_1_v5_gn_8_62401' => 'lsa', 'Manes.06G055900' => 'mes', 'Manes.12G022200' => 'mes', 'Manes.13G023300' => 'mes', 'Manes.14G115000' => 'mes', 'Manes.15G151700' => 'mes', 'Manes.17G111300' => 'mes', 'Mapoly0226s0009' => 'mpo', 'MBI02_g25363_MAGBIO' => 'mbi', 'MBI06_g00027_MAGBIO' => 'mbi', 'MBI10_g13034_MAGBIO' => 'mbi', 'MD09G1023400' => 'mdo', 'MD13G1100100' => 'mdo', 'MD15G1169200' => 'mdo', 'MD16G1101100' => 'mdo', 'MD17G1022900' => 'mdo', 'Medtr3g096150' => 'mtr', 'Medtr4g115070' => 'mtr', 'Medtr7g033325' => 'mtr', 'Medtr8g089840' => 'mtr', 'MELO3C010319.2' => 'cme', 'MELO3C011944.2' => 'cme', 'MELO3C021589.2' => 'cme', 'Migut.E00207' => 'egut', 'Migut.H00067' => 'egut', 'Migut.K00433' => 'egut', 'Migut.K00606' => 'egut', 'Migut.K01410' => 'egut', 'MSTRG.13347' => 'ama', 'MSTRG.24045' => 'ama', 'MSTRG.2428' => 'ama', 'MSTRG.26410' => 'ama', 'MSTRG.3139' => 'ama', 'MSTRG.3286' => 'ama', 'MSTRG.563' => 'ama', 'MSTRG.7941' => 'ama', 'Nitab4.5_0000028g0060' => 'nta', 'Nitab4.5_0000065g0260' => 'nta', 'Nitab4.5_0000112g0060' => 'nta', 'Nitab4.5_0000489g0120' => 'nta', 'Nitab4.5_0001776g0050' => 'nta', 'Nitab4.5_0001854g0010' => 'nta', 'Nitab4.5_0001860g0020' => 'nta', 'Nitab4.5_0004352g0010' => 'nta', 'Nitab4.5_0008716g0020' => 'nta', 'Nitab4.5_0008922g0010' => 'nta', 'Nn3g16693' => 'nnu', 'Nn4g22596' => 'nnu', 'Nn7g37639' => 'nnu', 'Oeu001701.1' => 'oeu', 'Oeu018149.1' => 'oeu', 'Oeu026220.1' => 'oeu', 'Oeu038635.1' => 'oeu', 'Oeu049176.1' => 'oeu', 'Oeu056706.1' => 'oeu', 'Oeu056937.1' => 'oeu', 'Oeu057540.1' => 'oeu', 'Os02g0594900' => 'osa', 'Os02g0595100' => 'osa', 'Os04g0477500' => 'osa', 'Os12g0611900' => 'osa', 'Peaxi162Scf00076g00020' => 'pax', 'Peaxi162Scf00128g00217' => 'pax', 'Peaxi162Scf00129g01640' => 'pax', 'Peaxi162Scf00669g00007' => 'pax', 'Peaxi162Scf00700g00421' => 'pax', 'Peaxi162Scf00801g00038' => 'pax', 'Peaxi162Scf00891g00025' => 'pax', 'PGR083G0909' => 'pgr', 'PGR119G1005' => 'pgr', 'PGR142G2236' => 'pgr', 'PGR142G3388' => 'pgr', 'PGSC0003DMG400004514' => 'stu', 'PGSC0003DMG400012635' => 'stu', 'PGSC0003DMG400015730' => 'stu', 'PGSC0003DMG400018611' => 'stu', 'PGSC0003DMG400030897' => 'stu', 'Phvul.001G254800' => 'pvu', 'Phvul.002G260100' => 'pvu', 'Phvul.003G167600' => 'pvu', 'Phvul.004G005100' => 'pvu', 'Potri.001G343600' => 'ptr', 'Potri.006G066700' => 'ptr', 'Potri.008G186000' => 'ptr', 'Potri.010G046900' => 'ptr', 'Potri.018G127900' => 'ptr', 'Pp3c20_17750' => 'ppa', 'Pp3c24_4380' => 'ppa', 'Prupe.1G245800' => 'ppe', 'Prupe.3G293400' => 'ppe', 'Prupe.7G247400' => 'ppe', 'Psat0s145g0120' => 'psa', 'Psat0s595g0040' => 'psa', 'Psat0s595g0120' => 'psa', 'Psat3g175040' => 'psa', 'Psat7g058120' => 'psa', 'PSO017G0428' => 'pso', 'PSO063G7510' => 'pso', 'PSO067G0046' => 'pso', 'PSO478G1073' => 'pso', 'PSO675G3677' => 'pso', 'PSO675G6558' => 'pso', 'PSO675G7520' => 'pso', 'PSO675G8959' => 'pso', 'QL02p074089' => 'qlo', 'QL02p089614' => 'qlo', 'QL03p057736' => 'qlo', 'RcHm_v2.0_Chr1g0364131' => 'rch', 'RcHm_v2.0_Chr2g0087801' => 'rch', 'RcHm_v2.0_Chr2g0087821' => 'rch', 'RcHm_v2.0_Chr2g0173231' => 'rch', 'RcHm_v2.0_Chr4g0433111' => 'rch', 'Rhsim03G0250300' => 'rsi', 'Rhsim08G0048400' => 'rsi', 'Rhsim10G0014800' => 'rsi', 'Rhsim12G0040100' => 'rsi', 'Rhsim12G0109700' => 'rsi', 'Sabra06G0049600' => 'sbr', 'Sabra08G0141000' => 'sbr', 'Sabra10G0021400' => 'sbr', 'Sabra16G0222900' => 'sbr', 'Sabra18G0108600' => 'sbr', 'SalBow1G0433' => 'sbo', 'SalBow1G2038' => 'sbo', 'SalBow1G5003' => 'sbo', 'SalBow7G1197' => 'sbo', 'SalBow8G3506' => 'sbo', 'Sc03g0007300' => 'sci', 'Sc11g0000950' => 'sci', 'Sc14g0008750' => 'sci', 'Sc18g0000420' => 'sci', 'Sed0006754' => 'sed', 'Sed0008741' => 'sed', 'Sed0017172' => 'sed', 'Sed0018925' => 'sed', 'Sed0023326' => 'sed', 'Sed0025909' => 'sed', 'SEGI_05333' => 'sgi', 'SEGI_10362' => 'sgi', 'SEGI_13380' => 'sgi', 'SEGI_24306' => 'sgi', 'SEGI_29077' => 'sgi', 'SEGI_29095' => 'sgi', 'SEGI_36534' => 'sgi', 'SEGI_37506' => 'sgi', 'SEGI_38321' => 'sgi', 'SGA_v2.0_scaffold307G48031' => 'sas', 'SGA_v2.0_scaffold47G17507' => 'sas', 'SGA_v2.0_scaffold63G21736' => 'sas', 'SGA_v2.0_scaffold87G27070' => 'sas', 'SHI17794' => 'shi', 'SHI28851' => 'shi', 'SMO165G0155' => 'smo', 'SMO340G0217' => 'smo', 'SMO367G1210' => 'smo', 'Solyc02g093430.3' => 'sly', 'Solyc05g013580.4' => 'sly', 'Solyc07g008030.3' => 'sly', 'Solyc12g035470.2' => 'sly', 'Sopen02g038020' => 'spe', 'Sopen05g008490' => 'spe', 'Sopen07g003910' => 'spe', 'Sopen12g015240' => 'spe', 'Sp1g11550' => 'spa', 'Sp2g16710' => 'spa', 'Sp3g00430' => 'spa', 'Sp3g26780' => 'spa', 'Sp5g22900' => 'spa', 'Sp6g29530' => 'spa', 'TAR371G0794' => 'tar', 'TAR374G0164' => 'tar', 'TAR622G0165' => 'tar', 'TAR626G0929' => 'tar', 'TAR629G2155' => 'tar', 'THA.LOC104805282' => 'tha', 'THA.LOC104805363' => 'tha', 'THA.LOC104808968' => 'tha', 'THA.LOC104821093' => 'tha', 'THA.LOC104823953' => 'tha', 'THA.LOC104825562' => 'tha', 'THA.LOC104825665' => 'tha', 'Thecc.02G261400' => 'tca', 'Thecc.04G019200' => 'tca', 'Thecc.09G130400' => 'tca', 'Thhalv10004374m.g' => 'esa', 'Thhalv10007850m.g' => 'esa', 'Thhalv10013782m.g' => 'esa', 'Thhalv10018686m.g' => 'esa', 'Thhalv10020899m.g' => 'esa', 'Thhalv10022755m.g' => 'esa', 'TPR.G23851' => 'tpr', 'TPR.G26500' => 'tpr', 'TPR.G27267' => 'tpr', 'TPR.G32001' => 'tpr', 'TPR.G6251' => 'tpr', 'TPR.G8167' => 'tpr', 'TWI12G1330' => 'twi', 'TWI18G1239' => 'twi', 'TWI34G0979' => 'twi', 'TWI36G0670' => 'twi', 'TWI36G0707' => 'twi', 'TWI56G0233' => 'twi', 'TWI75G1809' => 'twi', 'unitig_21.g20874' => 'ugi', 'unitig_26.g10343' => 'ugi', 'unitig_46.g18392' => 'ugi', 'unitig_52.g17178' => 'ugi', 'unitig_8.g2934' => 'ugi', 'vmacro01122' => 'vma', 'vmacro05875' => 'vma', 'vmacro06147' => 'vma', 'vmacro16191' => 'vma', 'vmacro18293' => 'vma', 'VMungo0251G3707' => 'vmu', 'VMungo0464G1521' => 'vmu', 'VMungo1215G0205' => 'vmu', 'VMungo1383G2484' => 'vmu', 'Zm00001eb079610' => 'zma', 'Zm00001eb135990' => 'zma', 'Zm00001eb183710' => 'zma', 'Zm00001eb246020' => 'zma' ) $gf_id = 'HOM05D001124' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001124' ) $data_identifier = 'HOM05D001124' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 6, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 7, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 21, 'bol' => (int) 10, 'bra' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 6, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 9, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 21, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 8, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 10, 'lsa' => (int) 8, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 8, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 9, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb246020' $species_info = array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ) $local_species = 'fan' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001124', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '548', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02520' => 'bna', 'A03p06630' => 'bna', 'A05p44460' => 'bna', 'A06p08710' => 'bna', 'A06p41090' => 'bna', 'A07p32320' => 'bna', 'A08p32520' => 'bna', 'A09p10360' => 'bna', 'A10p24080' => 'bna', 'Aa31LG11G15250' => 'aar', 'Aa31LG1G1800' => 'aar', 'Aa31LG2G5120' => 'aar', 'Aa31LG2G6070' => 'aar', 'Aa31LG5G10770' => 'aar', 'Aa31sc61G90' => 'aar', 'Actinidia01352' => 'ach', 'Actinidia05983' => 'ach', 'Actinidia08133' => 'ach', 'Actinidia15101' => 'ach', 'Actinidia26379' => 'ach', 'Actinidia35778' => 'ach', 'Actinidia36123' => 'ach', 'Actinidia37436' => 'ach', 'Actinidia38730' => 'ach', 'Ah.02g128210' => 'amhyb', 'Ah.03g132990' => 'amhyb', 'Ah.14g079410' => 'amhyb', 'AL1G24640' => 'aly', 'AL2G26680' => 'aly', 'AL3G10530' => 'aly', 'AL3G45230' => 'aly', 'AL5G15230' => 'aly', 'AL5G16960' => 'aly', 'AL6G25210' => 'aly', 'Aqoxy2G00441' => 'aox', 'Aqoxy3G01236' => 'aox', 'Aqoxy5G03746' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3RQ047' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C7GMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9C8JER' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MBL6KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YXCZ83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZANX40' => 'arhy', 'AT1G12990' => 'ath', 'AT1G67880' => 'ath', 'AT2G13290' => 'ath', 'AT3G01620' => 'ath', 'AT3G26445' => 'ath', 'AT3G27540' => 'ath', 'AT5G14480' => 'ath', 'ATR0824G026' => 'atr', 'ATR1098G019' => 'atr', 'Atru.chr11.2145' => 'acertr', 'Atru.chr2.3636' => 'acertr', 'Atru.chr2.3644' => 'acertr', 'Atru.chr6.2422' => 'acertr', 'Atru.chr7.1112' => 'acertr', 'AUR62005469' => 'cqu', 'AUR62011166' => 'cqu', 'AUR62013319' => 'cqu', 'AUR62024273' => 'cqu', 'AUR62028420' => 'cqu', 'AUR62041942' => 'cqu', 'BcaB01g04969' => 'bca', 'BcaB01g06371' => 'bca', 'BcaB02g11494' => 'bca', 'BcaB03g15382' => 'bca', 'BcaB08g36994' => 'bca', 'BcaC03g13477' => 'bca', 'BcaC03g13478' => 'bca', 'BcaC03g13480' => 'bca', 'BcaC03g13481' => 'bca', 'BcaC03g13486' => 'bca', 'BcaC04g19031' => 'bca', 'BcaC04g23085' => 'bca', 'BcaC05g25094' => 'bca', 'BcaC05g25096' => 'bca', 'BcaC05g25138' => 'bca', 'BcaC05g30416' => 'bca', 'BcaC05g30455' => 'bca', 'BcaC06g30979' => 'bca', 'BcaC06g33805' => 'bca', 'BcaC08g46021' => 'bca', 'BcaNung03154' => 'bca', 'BolC2t06623H' => 'bol', 'BolC2t06632H' => 'bol', 'BolC2t06635H' => 'bol', 'BolC2t06638H' => 'bol', 'BolC3t13266H' => 'bol', 'BolC5t29776H' => 'bol', 'BolC6t38912H' => 'bol', 'BolC7t44183H' => 'bol', 'BolC9t54123H' => 'bol', 'BolC9t59107H' => 'bol', 'BraA02t05221Z' => 'bra', 'BraA03t09996Z' => 'bra', 'BraA05t23210Z' => 'bra', 'BraA06t24068Z' => 'bra', 'BraA06t27032Z' => 'bra', 'BraA08t35176Z' => 'bra', 'BraA09t36680Z' => 'bra', 'BraA10t44471Z' => 'bra', 'C02p06760' => 'bna', 'C02p06890' => 'bna', 'C02p07010' => 'bna', 'C03p07660' => 'bna', 'C05p10300' => 'bna', 'C06p38150' => 'bna', 'C07p36650' => 'bna', 'C08p15770' => 'bna', 'C09p12300' => 'bna', 'C09p62700' => 'bna', 'C09p75040' => 'bna', 'CAN.G13.1' => 'can', 'CAN.G138.4' => 'can', 'CAN.G44.6' => 'can', 'CAN.G473.19' => 'can', 'CANSAT01G0835' => 'cansat', 'CANSAT11G0246' => 'cansat', 'CANSAT11G1766' => 'cansat', 'CANSAT64G1954' => 'cansat', 'CARHR013330' => 'chi', 'CARHR060530' => 'chi', 'CARHR075300' => 'chi', 'CARHR105120' => 'chi', 'CARHR148910' => 'chi', 'CARHR198830' => 'chi', 'Carub.0001s1275' => 'cru', 'Carub.0002s1437' => 'cru', 'Carub.0003s0044' => 'cru', 'Carub.0003s2787' => 'cru', 'Carub.0005s0597' => 'cru', 'Carub.0006s1266' => 'cru', 'Ca_06935_v3' => 'car', 'Ca_13559_v3' => 'car', 'Ca_16941_v3' => 'car', 'Ca_16960_v3' => 'car', 'Ca_17775_v3' => 'car', 'Ca_30464_v3' => 'car', 'Cc06_g08160' => 'ccan', 'Cc07_g01520' => 'ccan', 'Cc11_g15810' => 'ccan', 'CDE02G2840' => 'cde', 'CDE03G0093' => 'cde', 'CDE04G2127' => 'cde', 'CDE07G1857' => 'cde', 'CDE09G1246' => 'cde', 'Cfa003412' => 'cfa', 'Cfa007341' => 'cfa', 'Cfa009220' => 'cfa', 'Ciclev10008737m.g' => 'ccl', 'Ciclev10015565m.g' => 'ccl', 'Ciclev10031761m.g' => 'ccl', 'CiPaw.03G045300' => 'cil', 'CiPaw.03G247200' => 'cil', 'CiPaw.04G029500' => 'cil', 'CiPaw.04G174000' => 'cil', 'CiPaw.05G181200' => 'cil', 'CiPaw.06G067100' => 'cil', 'ClCG05G025800' => 'cla', 'ClCG06G011400' => 'cla', 'ClCG09G019360' => 'cla', 'COL.COLO4_04827' => 'col', 'COL.COLO4_29170' => 'col', 'COL.COLO4_35131' => 'col', 'COL.COLO4_35132' => 'col', 'Cpa.g.sc33.32' => 'cpa', 'Cpa.g.sc46.29' => 'cpa', 'Cpa.g.sc796.1' => 'cpa', 'CsaV3_1G030420' => 'csa', 'CsaV3_5G027050' => 'csa', 'CsaV3_5G031040' => 'csa', 'CsaV3_UNG023130' => 'csa', 'CSS0007726' => 'camsi', 'CSS0016433' => 'camsi', 'CSS0017656' => 'camsi', 'CSS0025364' => 'camsi', 'CSS0027582' => 'camsi', 'CSS0047288' => 'camsi', 'CSS0049950' => 'camsi', 'DCAR_003843' => 'dca', 'DCAR_007052' => 'dca', 'DCAR_020884' => 'dca', 'DCAR_021730' => 'dca', 'DCAR_024423' => 'dca', 'DCAR_026509' => 'dca', 'DCAR_031158' => 'dca', 'Dinv14728' => 'din', 'Dinv15219' => 'din', 'Dinv25728' => 'din', 'Dinv33428' => 'din', 'Dinv36489' => 'din', 'Dinv41486' => 'din', 'Duzib147G0469' => 'dzi', 'Duzib168G0060' => 'dzi', 'Duzib187G1215' => 'dzi', 'Duzib248G0692' => 'dzi', 'Duzib251G0767' => 'dzi', 'Duzib264G0446' => 'dzi', 'Duzib268G0691' => 'dzi', 'ECA232G4767' => 'eca', 'ECA233G2838' => 'eca', 'ECA234G0391' => 'eca', 'ECA234G0857' => 'eca', 'ECA236G1593' => 'eca', 'ECA238G0565' => 'eca', 'ECA246G1027' => 'eca', 'ECA246G3223' => 'eca', 'ECA246G3470' => 'eca', 'EL10Ac6g13829' => 'bvu', 'EL10Ac6g14093' => 'bvu', 'EL10Ac8g18707' => 'bvu', 'Eucgr.C01369' => 'egr', 'Eucgr.H02492' => 'egr', 'Eucgr.I01733' => 'egr', 'Eucgr.J02255' => 'egr', 'Eucgr.J02257' => 'egr', 'Eucgr.J02258' => 'egr', 'FAN02G1601' => 'fan', 'FAN03G1586' => 'fan', 'FAN03G2986' => 'fan', 'FAN05G4837' => 'fan', 'FAN06G0146' => 'fan', 'FAN07G0858' => 'fan', 'FAN09G3179' => 'fan', 'FAN10G0669' => 'fan', 'FAN12G2358' => 'fan', 'FAN14G4198' => 'fan', 'FAN14G5112' => 'fan', 'FAN17G0342' => 'fan', 'FAN19G0342' => 'fan', 'FAN19G0962' => 'fan', 'FAN19G1101' => 'fan', 'FAN19G1872' => 'fan', 'FAN22G0356' => 'fan', 'FAN23G0744' => 'fan', 'FAN23G1914' => 'fan', 'FAN26G0032' => 'fan', 'FAN28G0625' => 'fan', 'FvH4_1g02710' => 'fve', 'FvH4_1g02720' => 'fve', 'FvH4_4g25670' => 'fve', 'FvH4_6g51700' => 'fve', 'FvH4_7g20170' => 'fve', 'Glyma.05G175000' => 'gma', 'Glyma.08G132300' => 'gma', 'Glyma.11G243000' => 'gma', 'Glyma.13G158900' => 'gma', 'Glyma.17G112400' => 'gma', 'Glyma.18G014100' => 'gma', 'Glyma.19G003100' => 'gma', 'Glyma.19G056500' => 'gma', 'Gohir.A01G158900' => 'ghi', 'Gohir.A05G312600' => 'ghi', 'Gohir.A05G354900' => 'ghi', 'Gohir.A07G037200' => 'ghi', 'Gohir.A09G030000' => 'ghi', 'Gohir.A12G145200' => 'ghi', 'Gohir.D01G151500' => 'ghi', 'Gohir.D04G058300' => 'ghi', 'Gohir.D05G314100' => 'ghi', 'Gohir.D07G041400' => 'ghi', 'Gohir.D09G029700' => 'ghi', 'Gohir.D12G149700' => 'ghi', 'Gorai.001G043800' => 'gra', 'Gorai.002G187800' => 'gra', 'Gorai.006G034700' => 'gra', 'Gorai.008G161200' => 'gra', 'Gorai.009G335700' => 'gra', 'Gorai.012G065000' => 'gra', 'GSVIVG01000535001' => 'vvi', 'GSVIVG01015572001' => 'vvi', 'GSVIVG01032386001' => 'vvi', 'HanXRQChr05g0138531' => 'han', 'HanXRQChr06g0174391' => 'han', 'HanXRQChr07g0199021' => 'han', 'HanXRQChr08g0208211' => 'han', 'HanXRQChr09g0255471' => 'han', 'HanXRQChr10g0315791' => 'han', 'HanXRQChr12g0371991' => 'han', 'HanXRQChr15g0475251' => 'han', 'HanXRQChr17g0540001' => 'han', 'HanXRQChr17g0548631' => 'han', 'HanXRQChr17g0569561' => 'han', 'Haze_12256' => 'cav', 'Haze_14756' => 'cav', 'Haze_25528' => 'cav', 'Hma1.2p1_0079F.1_g041020' => 'hma', 'Hma1.2p1_0818F.1_g223260' => 'hma', 'Hma1.2p1_1747F.1_g300530' => 'hma', 'HPP92_004607' => 'vpl', 'HPP92_004608' => 'vpl', 'HPP92_006181' => 'vpl', 'HPP92_012192' => 'vpl', 'HPP92_015680' => 'vpl', 'HPP92_020249' => 'vpl', 'HPP92_021376' => 'vpl', 'HPP92_024275' => 'vpl', 'Hund06031' => 'sun', 'Hund25391' => 'sun', 'Lalb_Chr07g0185371' => 'lal', 'Lalb_Chr07g0185381' => 'lal', 'Lalb_Chr12g0204011' => 'lal', 'Lalb_Chr13g0301671' => 'lal', 'Lalb_Chr14g0362851' => 'lal', 'Lalb_Chr24g0403581' => 'lal', 'Lj1g0000233' => 'lja', 'Lj2g0018120' => 'lja', 'Lj3C621T0' => 'lonja', 'Lj3P1059T14' => 'lonja', 'Lj3P611T9' => 'lonja', 'Lj3P614T13' => 'lonja', 'Lj3P615T5' => 'lonja', 'Lj4g0012315' => 'lja', 'Lj4g0026182' => 'lja', 'Lj6P813T16' => 'lonja', 'Lj7C427T7' => 'lonja', 'Lj7C427T8' => 'lonja', 'Lj7P600T41' => 'lonja', 'Lju41C42G17' => 'lonja', 'Lsat_1_v5_gn_0_47300' => 'lsa', 'Lsat_1_v5_gn_2_91280' => 'lsa', 'Lsat_1_v5_gn_3_30561' => 'lsa', 'Lsat_1_v5_gn_4_184321' => 'lsa', 'Lsat_1_v5_gn_4_4041' => 'lsa', 'Lsat_1_v5_gn_5_92000' => 'lsa', 'Lsat_1_v5_gn_8_152940' => 'lsa', 'Lsat_1_v5_gn_8_62401' => 'lsa', 'Manes.06G055900' => 'mes', 'Manes.12G022200' => 'mes', 'Manes.13G023300' => 'mes', 'Manes.14G115000' => 'mes', 'Manes.15G151700' => 'mes', 'Manes.17G111300' => 'mes', 'Mapoly0226s0009' => 'mpo', 'MBI02_g25363_MAGBIO' => 'mbi', 'MBI06_g00027_MAGBIO' => 'mbi', 'MBI10_g13034_MAGBIO' => 'mbi', 'MD09G1023400' => 'mdo', 'MD13G1100100' => 'mdo', 'MD15G1169200' => 'mdo', 'MD16G1101100' => 'mdo', 'MD17G1022900' => 'mdo', 'Medtr3g096150' => 'mtr', 'Medtr4g115070' => 'mtr', 'Medtr7g033325' => 'mtr', 'Medtr8g089840' => 'mtr', 'MELO3C010319.2' => 'cme', 'MELO3C011944.2' => 'cme', 'MELO3C021589.2' => 'cme', 'Migut.E00207' => 'egut', 'Migut.H00067' => 'egut', 'Migut.K00433' => 'egut', 'Migut.K00606' => 'egut', 'Migut.K01410' => 'egut', 'MSTRG.13347' => 'ama', 'MSTRG.24045' => 'ama', 'MSTRG.2428' => 'ama', 'MSTRG.26410' => 'ama', 'MSTRG.3139' => 'ama', 'MSTRG.3286' => 'ama', 'MSTRG.563' => 'ama', 'MSTRG.7941' => 'ama', 'Nitab4.5_0000028g0060' => 'nta', 'Nitab4.5_0000065g0260' => 'nta', 'Nitab4.5_0000112g0060' => 'nta', 'Nitab4.5_0000489g0120' => 'nta', 'Nitab4.5_0001776g0050' => 'nta', 'Nitab4.5_0001854g0010' => 'nta', 'Nitab4.5_0001860g0020' => 'nta', 'Nitab4.5_0004352g0010' => 'nta', 'Nitab4.5_0008716g0020' => 'nta', 'Nitab4.5_0008922g0010' => 'nta', 'Nn3g16693' => 'nnu', 'Nn4g22596' => 'nnu', 'Nn7g37639' => 'nnu', 'Oeu001701.1' => 'oeu', 'Oeu018149.1' => 'oeu', 'Oeu026220.1' => 'oeu', 'Oeu038635.1' => 'oeu', 'Oeu049176.1' => 'oeu', 'Oeu056706.1' => 'oeu', 'Oeu056937.1' => 'oeu', 'Oeu057540.1' => 'oeu', 'Os02g0594900' => 'osa', 'Os02g0595100' => 'osa', 'Os04g0477500' => 'osa', 'Os12g0611900' => 'osa', 'Peaxi162Scf00076g00020' => 'pax', 'Peaxi162Scf00128g00217' => 'pax', 'Peaxi162Scf00129g01640' => 'pax', 'Peaxi162Scf00669g00007' => 'pax', 'Peaxi162Scf00700g00421' => 'pax', 'Peaxi162Scf00801g00038' => 'pax', 'Peaxi162Scf00891g00025' => 'pax', 'PGR083G0909' => 'pgr', 'PGR119G1005' => 'pgr', 'PGR142G2236' => 'pgr', 'PGR142G3388' => 'pgr', 'PGSC0003DMG400004514' => 'stu', 'PGSC0003DMG400012635' => 'stu', 'PGSC0003DMG400015730' => 'stu', 'PGSC0003DMG400018611' => 'stu', 'PGSC0003DMG400030897' => 'stu', 'Phvul.001G254800' => 'pvu', 'Phvul.002G260100' => 'pvu', 'Phvul.003G167600' => 'pvu', 'Phvul.004G005100' => 'pvu', 'Potri.001G343600' => 'ptr', 'Potri.006G066700' => 'ptr', 'Potri.008G186000' => 'ptr', 'Potri.010G046900' => 'ptr', 'Potri.018G127900' => 'ptr', 'Pp3c20_17750' => 'ppa', 'Pp3c24_4380' => 'ppa', 'Prupe.1G245800' => 'ppe', 'Prupe.3G293400' => 'ppe', 'Prupe.7G247400' => 'ppe', 'Psat0s145g0120' => 'psa', 'Psat0s595g0040' => 'psa', 'Psat0s595g0120' => 'psa', 'Psat3g175040' => 'psa', 'Psat7g058120' => 'psa', 'PSO017G0428' => 'pso', 'PSO063G7510' => 'pso', 'PSO067G0046' => 'pso', 'PSO478G1073' => 'pso', 'PSO675G3677' => 'pso', 'PSO675G6558' => 'pso', 'PSO675G7520' => 'pso', 'PSO675G8959' => 'pso', 'QL02p074089' => 'qlo', 'QL02p089614' => 'qlo', 'QL03p057736' => 'qlo', 'RcHm_v2.0_Chr1g0364131' => 'rch', 'RcHm_v2.0_Chr2g0087801' => 'rch', 'RcHm_v2.0_Chr2g0087821' => 'rch', 'RcHm_v2.0_Chr2g0173231' => 'rch', 'RcHm_v2.0_Chr4g0433111' => 'rch', 'Rhsim03G0250300' => 'rsi', 'Rhsim08G0048400' => 'rsi', 'Rhsim10G0014800' => 'rsi', 'Rhsim12G0040100' => 'rsi', 'Rhsim12G0109700' => 'rsi', 'Sabra06G0049600' => 'sbr', 'Sabra08G0141000' => 'sbr', 'Sabra10G0021400' => 'sbr', 'Sabra16G0222900' => 'sbr', 'Sabra18G0108600' => 'sbr', 'SalBow1G0433' => 'sbo', 'SalBow1G2038' => 'sbo', 'SalBow1G5003' => 'sbo', 'SalBow7G1197' => 'sbo', 'SalBow8G3506' => 'sbo', 'Sc03g0007300' => 'sci', 'Sc11g0000950' => 'sci', 'Sc14g0008750' => 'sci', 'Sc18g0000420' => 'sci', 'Sed0006754' => 'sed', 'Sed0008741' => 'sed', 'Sed0017172' => 'sed', 'Sed0018925' => 'sed', 'Sed0023326' => 'sed', 'Sed0025909' => 'sed', 'SEGI_05333' => 'sgi', 'SEGI_10362' => 'sgi', 'SEGI_13380' => 'sgi', 'SEGI_24306' => 'sgi', 'SEGI_29077' => 'sgi', 'SEGI_29095' => 'sgi', 'SEGI_36534' => 'sgi', 'SEGI_37506' => 'sgi', 'SEGI_38321' => 'sgi', 'SGA_v2.0_scaffold307G48031' => 'sas', 'SGA_v2.0_scaffold47G17507' => 'sas', 'SGA_v2.0_scaffold63G21736' => 'sas', 'SGA_v2.0_scaffold87G27070' => 'sas', 'SHI17794' => 'shi', 'SHI28851' => 'shi', 'SMO165G0155' => 'smo', 'SMO340G0217' => 'smo', 'SMO367G1210' => 'smo', 'Solyc02g093430.3' => 'sly', 'Solyc05g013580.4' => 'sly', 'Solyc07g008030.3' => 'sly', 'Solyc12g035470.2' => 'sly', 'Sopen02g038020' => 'spe', 'Sopen05g008490' => 'spe', 'Sopen07g003910' => 'spe', 'Sopen12g015240' => 'spe', 'Sp1g11550' => 'spa', 'Sp2g16710' => 'spa', 'Sp3g00430' => 'spa', 'Sp3g26780' => 'spa', 'Sp5g22900' => 'spa', 'Sp6g29530' => 'spa', 'TAR371G0794' => 'tar', 'TAR374G0164' => 'tar', 'TAR622G0165' => 'tar', 'TAR626G0929' => 'tar', 'TAR629G2155' => 'tar', 'THA.LOC104805282' => 'tha', 'THA.LOC104805363' => 'tha', 'THA.LOC104808968' => 'tha', 'THA.LOC104821093' => 'tha', 'THA.LOC104823953' => 'tha', 'THA.LOC104825562' => 'tha', 'THA.LOC104825665' => 'tha', 'Thecc.02G261400' => 'tca', 'Thecc.04G019200' => 'tca', 'Thecc.09G130400' => 'tca', 'Thhalv10004374m.g' => 'esa', 'Thhalv10007850m.g' => 'esa', 'Thhalv10013782m.g' => 'esa', 'Thhalv10018686m.g' => 'esa', 'Thhalv10020899m.g' => 'esa', 'Thhalv10022755m.g' => 'esa', 'TPR.G23851' => 'tpr', 'TPR.G26500' => 'tpr', 'TPR.G27267' => 'tpr', 'TPR.G32001' => 'tpr', 'TPR.G6251' => 'tpr', 'TPR.G8167' => 'tpr', 'TWI12G1330' => 'twi', 'TWI18G1239' => 'twi', 'TWI34G0979' => 'twi', 'TWI36G0670' => 'twi', 'TWI36G0707' => 'twi', 'TWI56G0233' => 'twi', 'TWI75G1809' => 'twi', 'unitig_21.g20874' => 'ugi', 'unitig_26.g10343' => 'ugi', 'unitig_46.g18392' => 'ugi', 'unitig_52.g17178' => 'ugi', 'unitig_8.g2934' => 'ugi', 'vmacro01122' => 'vma', 'vmacro05875' => 'vma', 'vmacro06147' => 'vma', 'vmacro16191' => 'vma', 'vmacro18293' => 'vma', 'VMungo0251G3707' => 'vmu', 'VMungo0464G1521' => 'vmu', 'VMungo1215G0205' => 'vmu', 'VMungo1383G2484' => 'vmu', 'Zm00001eb079610' => 'zma', 'Zm00001eb135990' => 'zma', 'Zm00001eb183710' => 'zma', 'Zm00001eb246020' => 'zma' ), 'gf_id' => 'HOM05D001124', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001124' ), 'data_identifier' => 'HOM05D001124', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001124', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '548', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02520' => 'bna', 'A03p06630' => 'bna', 'A05p44460' => 'bna', 'A06p08710' => 'bna', 'A06p41090' => 'bna', 'A07p32320' => 'bna', 'A08p32520' => 'bna', 'A09p10360' => 'bna', 'A10p24080' => 'bna', 'Aa31LG11G15250' => 'aar', 'Aa31LG1G1800' => 'aar', 'Aa31LG2G5120' => 'aar', 'Aa31LG2G6070' => 'aar', 'Aa31LG5G10770' => 'aar', 'Aa31sc61G90' => 'aar', 'Actinidia01352' => 'ach', 'Actinidia05983' => 'ach', 'Actinidia08133' => 'ach', 'Actinidia15101' => 'ach', 'Actinidia26379' => 'ach', 'Actinidia35778' => 'ach', 'Actinidia36123' => 'ach', 'Actinidia37436' => 'ach', 'Actinidia38730' => 'ach', 'Ah.02g128210' => 'amhyb', 'Ah.03g132990' => 'amhyb', 'Ah.14g079410' => 'amhyb', 'AL1G24640' => 'aly', 'AL2G26680' => 'aly', 'AL3G10530' => 'aly', 'AL3G45230' => 'aly', 'AL5G15230' => 'aly', 'AL5G16960' => 'aly', 'AL6G25210' => 'aly', 'Aqoxy2G00441' => 'aox', 'Aqoxy3G01236' => 'aox', 'Aqoxy5G03746' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3RQ047' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C7GMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9C8JER' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MBL6KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YXCZ83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZANX40' => 'arhy', 'AT1G12990' => 'ath', 'AT1G67880' => 'ath', 'AT2G13290' => 'ath', 'AT3G01620' => 'ath', 'AT3G26445' => 'ath', 'AT3G27540' => 'ath', 'AT5G14480' => 'ath', 'ATR0824G026' => 'atr', 'ATR1098G019' => 'atr', 'Atru.chr11.2145' => 'acertr', 'Atru.chr2.3636' => 'acertr', 'Atru.chr2.3644' => 'acertr', 'Atru.chr6.2422' => 'acertr', 'Atru.chr7.1112' => 'acertr', 'AUR62005469' => 'cqu', 'AUR62011166' => 'cqu', 'AUR62013319' => 'cqu', 'AUR62024273' => 'cqu', 'AUR62028420' => 'cqu', 'AUR62041942' => 'cqu', 'BcaB01g04969' => 'bca', 'BcaB01g06371' => 'bca', 'BcaB02g11494' => 'bca', 'BcaB03g15382' => 'bca', 'BcaB08g36994' => 'bca', 'BcaC03g13477' => 'bca', 'BcaC03g13478' => 'bca', 'BcaC03g13480' => 'bca', 'BcaC03g13481' => 'bca', 'BcaC03g13486' => 'bca', 'BcaC04g19031' => 'bca', 'BcaC04g23085' => 'bca', 'BcaC05g25094' => 'bca', 'BcaC05g25096' => 'bca', 'BcaC05g25138' => 'bca', 'BcaC05g30416' => 'bca', 'BcaC05g30455' => 'bca', 'BcaC06g30979' => 'bca', 'BcaC06g33805' => 'bca', 'BcaC08g46021' => 'bca', 'BcaNung03154' => 'bca', 'BolC2t06623H' => 'bol', 'BolC2t06632H' => 'bol', 'BolC2t06635H' => 'bol', 'BolC2t06638H' => 'bol', 'BolC3t13266H' => 'bol', 'BolC5t29776H' => 'bol', 'BolC6t38912H' => 'bol', 'BolC7t44183H' => 'bol', 'BolC9t54123H' => 'bol', 'BolC9t59107H' => 'bol', 'BraA02t05221Z' => 'bra', 'BraA03t09996Z' => 'bra', 'BraA05t23210Z' => 'bra', 'BraA06t24068Z' => 'bra', 'BraA06t27032Z' => 'bra', 'BraA08t35176Z' => 'bra', 'BraA09t36680Z' => 'bra', 'BraA10t44471Z' => 'bra', 'C02p06760' => 'bna', 'C02p06890' => 'bna', 'C02p07010' => 'bna', 'C03p07660' => 'bna', 'C05p10300' => 'bna', 'C06p38150' => 'bna', 'C07p36650' => 'bna', 'C08p15770' => 'bna', 'C09p12300' => 'bna', 'C09p62700' => 'bna', 'C09p75040' => 'bna', 'CAN.G13.1' => 'can', 'CAN.G138.4' => 'can', 'CAN.G44.6' => 'can', 'CAN.G473.19' => 'can', 'CANSAT01G0835' => 'cansat', 'CANSAT11G0246' => 'cansat', 'CANSAT11G1766' => 'cansat', 'CANSAT64G1954' => 'cansat', 'CARHR013330' => 'chi', 'CARHR060530' => 'chi', 'CARHR075300' => 'chi', 'CARHR105120' => 'chi', 'CARHR148910' => 'chi', 'CARHR198830' => 'chi', 'Carub.0001s1275' => 'cru', 'Carub.0002s1437' => 'cru', 'Carub.0003s0044' => 'cru', 'Carub.0003s2787' => 'cru', 'Carub.0005s0597' => 'cru', 'Carub.0006s1266' => 'cru', 'Ca_06935_v3' => 'car', 'Ca_13559_v3' => 'car', 'Ca_16941_v3' => 'car', 'Ca_16960_v3' => 'car', 'Ca_17775_v3' => 'car', 'Ca_30464_v3' => 'car', 'Cc06_g08160' => 'ccan', 'Cc07_g01520' => 'ccan', 'Cc11_g15810' => 'ccan', 'CDE02G2840' => 'cde', 'CDE03G0093' => 'cde', 'CDE04G2127' => 'cde', 'CDE07G1857' => 'cde', 'CDE09G1246' => 'cde', 'Cfa003412' => 'cfa', 'Cfa007341' => 'cfa', 'Cfa009220' => 'cfa', 'Ciclev10008737m.g' => 'ccl', 'Ciclev10015565m.g' => 'ccl', 'Ciclev10031761m.g' => 'ccl', 'CiPaw.03G045300' => 'cil', 'CiPaw.03G247200' => 'cil', 'CiPaw.04G029500' => 'cil', 'CiPaw.04G174000' => 'cil', 'CiPaw.05G181200' => 'cil', 'CiPaw.06G067100' => 'cil', 'ClCG05G025800' => 'cla', 'ClCG06G011400' => 'cla', 'ClCG09G019360' => 'cla', 'COL.COLO4_04827' => 'col', 'COL.COLO4_29170' => 'col', 'COL.COLO4_35131' => 'col', 'COL.COLO4_35132' => 'col', 'Cpa.g.sc33.32' => 'cpa', 'Cpa.g.sc46.29' => 'cpa', 'Cpa.g.sc796.1' => 'cpa', 'CsaV3_1G030420' => 'csa', 'CsaV3_5G027050' => 'csa', 'CsaV3_5G031040' => 'csa', 'CsaV3_UNG023130' => 'csa', 'CSS0007726' => 'camsi', 'CSS0016433' => 'camsi', 'CSS0017656' => 'camsi', 'CSS0025364' => 'camsi', 'CSS0027582' => 'camsi', 'CSS0047288' => 'camsi', 'CSS0049950' => 'camsi', 'DCAR_003843' => 'dca', 'DCAR_007052' => 'dca', 'DCAR_020884' => 'dca', 'DCAR_021730' => 'dca', 'DCAR_024423' => 'dca', 'DCAR_026509' => 'dca', 'DCAR_031158' => 'dca', 'Dinv14728' => 'din', 'Dinv15219' => 'din', 'Dinv25728' => 'din', 'Dinv33428' => 'din', 'Dinv36489' => 'din', 'Dinv41486' => 'din', 'Duzib147G0469' => 'dzi', 'Duzib168G0060' => 'dzi', 'Duzib187G1215' => 'dzi', 'Duzib248G0692' => 'dzi', 'Duzib251G0767' => 'dzi', 'Duzib264G0446' => 'dzi', 'Duzib268G0691' => 'dzi', 'ECA232G4767' => 'eca', 'ECA233G2838' => 'eca', 'ECA234G0391' => 'eca', 'ECA234G0857' => 'eca', 'ECA236G1593' => 'eca', 'ECA238G0565' => 'eca', 'ECA246G1027' => 'eca', 'ECA246G3223' => 'eca', 'ECA246G3470' => 'eca', 'EL10Ac6g13829' => 'bvu', 'EL10Ac6g14093' => 'bvu', 'EL10Ac8g18707' => 'bvu', 'Eucgr.C01369' => 'egr', 'Eucgr.H02492' => 'egr', 'Eucgr.I01733' => 'egr', 'Eucgr.J02255' => 'egr', 'Eucgr.J02257' => 'egr', 'Eucgr.J02258' => 'egr', 'FAN02G1601' => 'fan', 'FAN03G1586' => 'fan', 'FAN03G2986' => 'fan', 'FAN05G4837' => 'fan', 'FAN06G0146' => 'fan', 'FAN07G0858' => 'fan', 'FAN09G3179' => 'fan', 'FAN10G0669' => 'fan', 'FAN12G2358' => 'fan', 'FAN14G4198' => 'fan', 'FAN14G5112' => 'fan', 'FAN17G0342' => 'fan', 'FAN19G0342' => 'fan', 'FAN19G0962' => 'fan', 'FAN19G1101' => 'fan', 'FAN19G1872' => 'fan', 'FAN22G0356' => 'fan', 'FAN23G0744' => 'fan', 'FAN23G1914' => 'fan', 'FAN26G0032' => 'fan', 'FAN28G0625' => 'fan', 'FvH4_1g02710' => 'fve', 'FvH4_1g02720' => 'fve', 'FvH4_4g25670' => 'fve', 'FvH4_6g51700' => 'fve', 'FvH4_7g20170' => 'fve', 'Glyma.05G175000' => 'gma', 'Glyma.08G132300' => 'gma', 'Glyma.11G243000' => 'gma', 'Glyma.13G158900' => 'gma', 'Glyma.17G112400' => 'gma', 'Glyma.18G014100' => 'gma', 'Glyma.19G003100' => 'gma', 'Glyma.19G056500' => 'gma', 'Gohir.A01G158900' => 'ghi', 'Gohir.A05G312600' => 'ghi', 'Gohir.A05G354900' => 'ghi', 'Gohir.A07G037200' => 'ghi', 'Gohir.A09G030000' => 'ghi', 'Gohir.A12G145200' => 'ghi', 'Gohir.D01G151500' => 'ghi', 'Gohir.D04G058300' => 'ghi', 'Gohir.D05G314100' => 'ghi', 'Gohir.D07G041400' => 'ghi', 'Gohir.D09G029700' => 'ghi', 'Gohir.D12G149700' => 'ghi', 'Gorai.001G043800' => 'gra', 'Gorai.002G187800' => 'gra', 'Gorai.006G034700' => 'gra', 'Gorai.008G161200' => 'gra', 'Gorai.009G335700' => 'gra', 'Gorai.012G065000' => 'gra', 'GSVIVG01000535001' => 'vvi', 'GSVIVG01015572001' => 'vvi', 'GSVIVG01032386001' => 'vvi', 'HanXRQChr05g0138531' => 'han', 'HanXRQChr06g0174391' => 'han', 'HanXRQChr07g0199021' => 'han', 'HanXRQChr08g0208211' => 'han', 'HanXRQChr09g0255471' => 'han', 'HanXRQChr10g0315791' => 'han', 'HanXRQChr12g0371991' => 'han', 'HanXRQChr15g0475251' => 'han', 'HanXRQChr17g0540001' => 'han', 'HanXRQChr17g0548631' => 'han', 'HanXRQChr17g0569561' => 'han', 'Haze_12256' => 'cav', 'Haze_14756' => 'cav', 'Haze_25528' => 'cav', 'Hma1.2p1_0079F.1_g041020' => 'hma', 'Hma1.2p1_0818F.1_g223260' => 'hma', 'Hma1.2p1_1747F.1_g300530' => 'hma', 'HPP92_004607' => 'vpl', 'HPP92_004608' => 'vpl', 'HPP92_006181' => 'vpl', 'HPP92_012192' => 'vpl', 'HPP92_015680' => 'vpl', 'HPP92_020249' => 'vpl', 'HPP92_021376' => 'vpl', 'HPP92_024275' => 'vpl', 'Hund06031' => 'sun', 'Hund25391' => 'sun', 'Lalb_Chr07g0185371' => 'lal', 'Lalb_Chr07g0185381' => 'lal', 'Lalb_Chr12g0204011' => 'lal', 'Lalb_Chr13g0301671' => 'lal', 'Lalb_Chr14g0362851' => 'lal', 'Lalb_Chr24g0403581' => 'lal', 'Lj1g0000233' => 'lja', 'Lj2g0018120' => 'lja', 'Lj3C621T0' => 'lonja', 'Lj3P1059T14' => 'lonja', 'Lj3P611T9' => 'lonja', 'Lj3P614T13' => 'lonja', 'Lj3P615T5' => 'lonja', 'Lj4g0012315' => 'lja', 'Lj4g0026182' => 'lja', 'Lj6P813T16' => 'lonja', 'Lj7C427T7' => 'lonja', 'Lj7C427T8' => 'lonja', 'Lj7P600T41' => 'lonja', 'Lju41C42G17' => 'lonja', 'Lsat_1_v5_gn_0_47300' => 'lsa', 'Lsat_1_v5_gn_2_91280' => 'lsa', 'Lsat_1_v5_gn_3_30561' => 'lsa', 'Lsat_1_v5_gn_4_184321' => 'lsa', 'Lsat_1_v5_gn_4_4041' => 'lsa', 'Lsat_1_v5_gn_5_92000' => 'lsa', 'Lsat_1_v5_gn_8_152940' => 'lsa', 'Lsat_1_v5_gn_8_62401' => 'lsa', 'Manes.06G055900' => 'mes', 'Manes.12G022200' => 'mes', 'Manes.13G023300' => 'mes', 'Manes.14G115000' => 'mes', 'Manes.15G151700' => 'mes', 'Manes.17G111300' => 'mes', 'Mapoly0226s0009' => 'mpo', 'MBI02_g25363_MAGBIO' => 'mbi', 'MBI06_g00027_MAGBIO' => 'mbi', 'MBI10_g13034_MAGBIO' => 'mbi', 'MD09G1023400' => 'mdo', 'MD13G1100100' => 'mdo', 'MD15G1169200' => 'mdo', 'MD16G1101100' => 'mdo', 'MD17G1022900' => 'mdo', 'Medtr3g096150' => 'mtr', 'Medtr4g115070' => 'mtr', 'Medtr7g033325' => 'mtr', 'Medtr8g089840' => 'mtr', 'MELO3C010319.2' => 'cme', 'MELO3C011944.2' => 'cme', 'MELO3C021589.2' => 'cme', 'Migut.E00207' => 'egut', 'Migut.H00067' => 'egut', 'Migut.K00433' => 'egut', 'Migut.K00606' => 'egut', 'Migut.K01410' => 'egut', 'MSTRG.13347' => 'ama', 'MSTRG.24045' => 'ama', 'MSTRG.2428' => 'ama', 'MSTRG.26410' => 'ama', 'MSTRG.3139' => 'ama', 'MSTRG.3286' => 'ama', 'MSTRG.563' => 'ama', 'MSTRG.7941' => 'ama', 'Nitab4.5_0000028g0060' => 'nta', 'Nitab4.5_0000065g0260' => 'nta', 'Nitab4.5_0000112g0060' => 'nta', 'Nitab4.5_0000489g0120' => 'nta', 'Nitab4.5_0001776g0050' => 'nta', 'Nitab4.5_0001854g0010' => 'nta', 'Nitab4.5_0001860g0020' => 'nta', 'Nitab4.5_0004352g0010' => 'nta', 'Nitab4.5_0008716g0020' => 'nta', 'Nitab4.5_0008922g0010' => 'nta', 'Nn3g16693' => 'nnu', 'Nn4g22596' => 'nnu', 'Nn7g37639' => 'nnu', 'Oeu001701.1' => 'oeu', 'Oeu018149.1' => 'oeu', 'Oeu026220.1' => 'oeu', 'Oeu038635.1' => 'oeu', 'Oeu049176.1' => 'oeu', 'Oeu056706.1' => 'oeu', 'Oeu056937.1' => 'oeu', 'Oeu057540.1' => 'oeu', 'Os02g0594900' => 'osa', 'Os02g0595100' => 'osa', 'Os04g0477500' => 'osa', 'Os12g0611900' => 'osa', 'Peaxi162Scf00076g00020' => 'pax', 'Peaxi162Scf00128g00217' => 'pax', 'Peaxi162Scf00129g01640' => 'pax', 'Peaxi162Scf00669g00007' => 'pax', 'Peaxi162Scf00700g00421' => 'pax', 'Peaxi162Scf00801g00038' => 'pax', 'Peaxi162Scf00891g00025' => 'pax', 'PGR083G0909' => 'pgr', 'PGR119G1005' => 'pgr', 'PGR142G2236' => 'pgr', 'PGR142G3388' => 'pgr', 'PGSC0003DMG400004514' => 'stu', 'PGSC0003DMG400012635' => 'stu', 'PGSC0003DMG400015730' => 'stu', 'PGSC0003DMG400018611' => 'stu', 'PGSC0003DMG400030897' => 'stu', 'Phvul.001G254800' => 'pvu', 'Phvul.002G260100' => 'pvu', 'Phvul.003G167600' => 'pvu', 'Phvul.004G005100' => 'pvu', 'Potri.001G343600' => 'ptr', 'Potri.006G066700' => 'ptr', 'Potri.008G186000' => 'ptr', 'Potri.010G046900' => 'ptr', 'Potri.018G127900' => 'ptr', 'Pp3c20_17750' => 'ppa', 'Pp3c24_4380' => 'ppa', 'Prupe.1G245800' => 'ppe', 'Prupe.3G293400' => 'ppe', 'Prupe.7G247400' => 'ppe', 'Psat0s145g0120' => 'psa', 'Psat0s595g0040' => 'psa', 'Psat0s595g0120' => 'psa', 'Psat3g175040' => 'psa', 'Psat7g058120' => 'psa', 'PSO017G0428' => 'pso', 'PSO063G7510' => 'pso', 'PSO067G0046' => 'pso', 'PSO478G1073' => 'pso', 'PSO675G3677' => 'pso', 'PSO675G6558' => 'pso', 'PSO675G7520' => 'pso', 'PSO675G8959' => 'pso', 'QL02p074089' => 'qlo', 'QL02p089614' => 'qlo', 'QL03p057736' => 'qlo', 'RcHm_v2.0_Chr1g0364131' => 'rch', 'RcHm_v2.0_Chr2g0087801' => 'rch', 'RcHm_v2.0_Chr2g0087821' => 'rch', 'RcHm_v2.0_Chr2g0173231' => 'rch', 'RcHm_v2.0_Chr4g0433111' => 'rch', 'Rhsim03G0250300' => 'rsi', 'Rhsim08G0048400' => 'rsi', 'Rhsim10G0014800' => 'rsi', 'Rhsim12G0040100' => 'rsi', 'Rhsim12G0109700' => 'rsi', 'Sabra06G0049600' => 'sbr', 'Sabra08G0141000' => 'sbr', 'Sabra10G0021400' => 'sbr', 'Sabra16G0222900' => 'sbr', 'Sabra18G0108600' => 'sbr', 'SalBow1G0433' => 'sbo', 'SalBow1G2038' => 'sbo', 'SalBow1G5003' => 'sbo', 'SalBow7G1197' => 'sbo', 'SalBow8G3506' => 'sbo', 'Sc03g0007300' => 'sci', 'Sc11g0000950' => 'sci', 'Sc14g0008750' => 'sci', 'Sc18g0000420' => 'sci', 'Sed0006754' => 'sed', 'Sed0008741' => 'sed', 'Sed0017172' => 'sed', 'Sed0018925' => 'sed', 'Sed0023326' => 'sed', 'Sed0025909' => 'sed', 'SEGI_05333' => 'sgi', 'SEGI_10362' => 'sgi', 'SEGI_13380' => 'sgi', 'SEGI_24306' => 'sgi', 'SEGI_29077' => 'sgi', 'SEGI_29095' => 'sgi', 'SEGI_36534' => 'sgi', 'SEGI_37506' => 'sgi', 'SEGI_38321' => 'sgi', 'SGA_v2.0_scaffold307G48031' => 'sas', 'SGA_v2.0_scaffold47G17507' => 'sas', 'SGA_v2.0_scaffold63G21736' => 'sas', 'SGA_v2.0_scaffold87G27070' => 'sas', 'SHI17794' => 'shi', 'SHI28851' => 'shi', 'SMO165G0155' => 'smo', 'SMO340G0217' => 'smo', 'SMO367G1210' => 'smo', 'Solyc02g093430.3' => 'sly', 'Solyc05g013580.4' => 'sly', 'Solyc07g008030.3' => 'sly', 'Solyc12g035470.2' => 'sly', 'Sopen02g038020' => 'spe', 'Sopen05g008490' => 'spe', 'Sopen07g003910' => 'spe', 'Sopen12g015240' => 'spe', 'Sp1g11550' => 'spa', 'Sp2g16710' => 'spa', 'Sp3g00430' => 'spa', 'Sp3g26780' => 'spa', 'Sp5g22900' => 'spa', 'Sp6g29530' => 'spa', 'TAR371G0794' => 'tar', 'TAR374G0164' => 'tar', 'TAR622G0165' => 'tar', 'TAR626G0929' => 'tar', 'TAR629G2155' => 'tar', 'THA.LOC104805282' => 'tha', 'THA.LOC104805363' => 'tha', 'THA.LOC104808968' => 'tha', 'THA.LOC104821093' => 'tha', 'THA.LOC104823953' => 'tha', 'THA.LOC104825562' => 'tha', 'THA.LOC104825665' => 'tha', 'Thecc.02G261400' => 'tca', 'Thecc.04G019200' => 'tca', 'Thecc.09G130400' => 'tca', 'Thhalv10004374m.g' => 'esa', 'Thhalv10007850m.g' => 'esa', 'Thhalv10013782m.g' => 'esa', 'Thhalv10018686m.g' => 'esa', 'Thhalv10020899m.g' => 'esa', 'Thhalv10022755m.g' => 'esa', 'TPR.G23851' => 'tpr', 'TPR.G26500' => 'tpr', 'TPR.G27267' => 'tpr', 'TPR.G32001' => 'tpr', 'TPR.G6251' => 'tpr', 'TPR.G8167' => 'tpr', 'TWI12G1330' => 'twi', 'TWI18G1239' => 'twi', 'TWI34G0979' => 'twi', 'TWI36G0670' => 'twi', 'TWI36G0707' => 'twi', 'TWI56G0233' => 'twi', 'TWI75G1809' => 'twi', 'unitig_21.g20874' => 'ugi', 'unitig_26.g10343' => 'ugi', 'unitig_46.g18392' => 'ugi', 'unitig_52.g17178' => 'ugi', 'unitig_8.g2934' => 'ugi', 'vmacro01122' => 'vma', 'vmacro05875' => 'vma', 'vmacro06147' => 'vma', 'vmacro16191' => 'vma', 'vmacro18293' => 'vma', 'VMungo0251G3707' => 'vmu', 'VMungo0464G1521' => 'vmu', 'VMungo1215G0205' => 'vmu', 'VMungo1383G2484' => 'vmu', 'Zm00001eb079610' => 'zma', 'Zm00001eb135990' => 'zma', 'Zm00001eb183710' => 'zma', 'Zm00001eb246020' => 'zma' ) $gf_id = 'HOM05D001124' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001124' ) $data_identifier = 'HOM05D001124' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 6, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 7, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 21, 'bol' => (int) 10, 'bra' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 6, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 9, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 21, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 8, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 10, 'lsa' => (int) 8, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 8, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 9, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb246020' $species_info = array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ) $local_species = 'fan' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001124', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '548', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02520' => 'bna', 'A03p06630' => 'bna', 'A05p44460' => 'bna', 'A06p08710' => 'bna', 'A06p41090' => 'bna', 'A07p32320' => 'bna', 'A08p32520' => 'bna', 'A09p10360' => 'bna', 'A10p24080' => 'bna', 'Aa31LG11G15250' => 'aar', 'Aa31LG1G1800' => 'aar', 'Aa31LG2G5120' => 'aar', 'Aa31LG2G6070' => 'aar', 'Aa31LG5G10770' => 'aar', 'Aa31sc61G90' => 'aar', 'Actinidia01352' => 'ach', 'Actinidia05983' => 'ach', 'Actinidia08133' => 'ach', 'Actinidia15101' => 'ach', 'Actinidia26379' => 'ach', 'Actinidia35778' => 'ach', 'Actinidia36123' => 'ach', 'Actinidia37436' => 'ach', 'Actinidia38730' => 'ach', 'Ah.02g128210' => 'amhyb', 'Ah.03g132990' => 'amhyb', 'Ah.14g079410' => 'amhyb', 'AL1G24640' => 'aly', 'AL2G26680' => 'aly', 'AL3G10530' => 'aly', 'AL3G45230' => 'aly', 'AL5G15230' => 'aly', 'AL5G16960' => 'aly', 'AL6G25210' => 'aly', 'Aqoxy2G00441' => 'aox', 'Aqoxy3G01236' => 'aox', 'Aqoxy5G03746' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3RQ047' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C7GMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9C8JER' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MBL6KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YXCZ83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZANX40' => 'arhy', 'AT1G12990' => 'ath', 'AT1G67880' => 'ath', 'AT2G13290' => 'ath', 'AT3G01620' => 'ath', 'AT3G26445' => 'ath', 'AT3G27540' => 'ath', 'AT5G14480' => 'ath', 'ATR0824G026' => 'atr', 'ATR1098G019' => 'atr', 'Atru.chr11.2145' => 'acertr', 'Atru.chr2.3636' => 'acertr', 'Atru.chr2.3644' => 'acertr', 'Atru.chr6.2422' => 'acertr', 'Atru.chr7.1112' => 'acertr', 'AUR62005469' => 'cqu', 'AUR62011166' => 'cqu', 'AUR62013319' => 'cqu', 'AUR62024273' => 'cqu', 'AUR62028420' => 'cqu', 'AUR62041942' => 'cqu', 'BcaB01g04969' => 'bca', 'BcaB01g06371' => 'bca', 'BcaB02g11494' => 'bca', 'BcaB03g15382' => 'bca', 'BcaB08g36994' => 'bca', 'BcaC03g13477' => 'bca', 'BcaC03g13478' => 'bca', 'BcaC03g13480' => 'bca', 'BcaC03g13481' => 'bca', 'BcaC03g13486' => 'bca', 'BcaC04g19031' => 'bca', 'BcaC04g23085' => 'bca', 'BcaC05g25094' => 'bca', 'BcaC05g25096' => 'bca', 'BcaC05g25138' => 'bca', 'BcaC05g30416' => 'bca', 'BcaC05g30455' => 'bca', 'BcaC06g30979' => 'bca', 'BcaC06g33805' => 'bca', 'BcaC08g46021' => 'bca', 'BcaNung03154' => 'bca', 'BolC2t06623H' => 'bol', 'BolC2t06632H' => 'bol', 'BolC2t06635H' => 'bol', 'BolC2t06638H' => 'bol', 'BolC3t13266H' => 'bol', 'BolC5t29776H' => 'bol', 'BolC6t38912H' => 'bol', 'BolC7t44183H' => 'bol', 'BolC9t54123H' => 'bol', 'BolC9t59107H' => 'bol', 'BraA02t05221Z' => 'bra', 'BraA03t09996Z' => 'bra', 'BraA05t23210Z' => 'bra', 'BraA06t24068Z' => 'bra', 'BraA06t27032Z' => 'bra', 'BraA08t35176Z' => 'bra', 'BraA09t36680Z' => 'bra', 'BraA10t44471Z' => 'bra', 'C02p06760' => 'bna', 'C02p06890' => 'bna', 'C02p07010' => 'bna', 'C03p07660' => 'bna', 'C05p10300' => 'bna', 'C06p38150' => 'bna', 'C07p36650' => 'bna', 'C08p15770' => 'bna', 'C09p12300' => 'bna', 'C09p62700' => 'bna', 'C09p75040' => 'bna', 'CAN.G13.1' => 'can', 'CAN.G138.4' => 'can', 'CAN.G44.6' => 'can', 'CAN.G473.19' => 'can', 'CANSAT01G0835' => 'cansat', 'CANSAT11G0246' => 'cansat', 'CANSAT11G1766' => 'cansat', 'CANSAT64G1954' => 'cansat', 'CARHR013330' => 'chi', 'CARHR060530' => 'chi', 'CARHR075300' => 'chi', 'CARHR105120' => 'chi', 'CARHR148910' => 'chi', 'CARHR198830' => 'chi', 'Carub.0001s1275' => 'cru', 'Carub.0002s1437' => 'cru', 'Carub.0003s0044' => 'cru', 'Carub.0003s2787' => 'cru', 'Carub.0005s0597' => 'cru', 'Carub.0006s1266' => 'cru', 'Ca_06935_v3' => 'car', 'Ca_13559_v3' => 'car', 'Ca_16941_v3' => 'car', 'Ca_16960_v3' => 'car', 'Ca_17775_v3' => 'car', 'Ca_30464_v3' => 'car', 'Cc06_g08160' => 'ccan', 'Cc07_g01520' => 'ccan', 'Cc11_g15810' => 'ccan', 'CDE02G2840' => 'cde', 'CDE03G0093' => 'cde', 'CDE04G2127' => 'cde', 'CDE07G1857' => 'cde', 'CDE09G1246' => 'cde', 'Cfa003412' => 'cfa', 'Cfa007341' => 'cfa', 'Cfa009220' => 'cfa', 'Ciclev10008737m.g' => 'ccl', 'Ciclev10015565m.g' => 'ccl', 'Ciclev10031761m.g' => 'ccl', 'CiPaw.03G045300' => 'cil', 'CiPaw.03G247200' => 'cil', 'CiPaw.04G029500' => 'cil', 'CiPaw.04G174000' => 'cil', 'CiPaw.05G181200' => 'cil', 'CiPaw.06G067100' => 'cil', 'ClCG05G025800' => 'cla', 'ClCG06G011400' => 'cla', 'ClCG09G019360' => 'cla', 'COL.COLO4_04827' => 'col', 'COL.COLO4_29170' => 'col', 'COL.COLO4_35131' => 'col', 'COL.COLO4_35132' => 'col', 'Cpa.g.sc33.32' => 'cpa', 'Cpa.g.sc46.29' => 'cpa', 'Cpa.g.sc796.1' => 'cpa', 'CsaV3_1G030420' => 'csa', 'CsaV3_5G027050' => 'csa', 'CsaV3_5G031040' => 'csa', 'CsaV3_UNG023130' => 'csa', 'CSS0007726' => 'camsi', 'CSS0016433' => 'camsi', 'CSS0017656' => 'camsi', 'CSS0025364' => 'camsi', 'CSS0027582' => 'camsi', 'CSS0047288' => 'camsi', 'CSS0049950' => 'camsi', 'DCAR_003843' => 'dca', 'DCAR_007052' => 'dca', 'DCAR_020884' => 'dca', 'DCAR_021730' => 'dca', 'DCAR_024423' => 'dca', 'DCAR_026509' => 'dca', 'DCAR_031158' => 'dca', 'Dinv14728' => 'din', 'Dinv15219' => 'din', 'Dinv25728' => 'din', 'Dinv33428' => 'din', 'Dinv36489' => 'din', 'Dinv41486' => 'din', 'Duzib147G0469' => 'dzi', 'Duzib168G0060' => 'dzi', 'Duzib187G1215' => 'dzi', 'Duzib248G0692' => 'dzi', 'Duzib251G0767' => 'dzi', 'Duzib264G0446' => 'dzi', 'Duzib268G0691' => 'dzi', 'ECA232G4767' => 'eca', 'ECA233G2838' => 'eca', 'ECA234G0391' => 'eca', 'ECA234G0857' => 'eca', 'ECA236G1593' => 'eca', 'ECA238G0565' => 'eca', 'ECA246G1027' => 'eca', 'ECA246G3223' => 'eca', 'ECA246G3470' => 'eca', 'EL10Ac6g13829' => 'bvu', 'EL10Ac6g14093' => 'bvu', 'EL10Ac8g18707' => 'bvu', 'Eucgr.C01369' => 'egr', 'Eucgr.H02492' => 'egr', 'Eucgr.I01733' => 'egr', 'Eucgr.J02255' => 'egr', 'Eucgr.J02257' => 'egr', 'Eucgr.J02258' => 'egr', 'FAN02G1601' => 'fan', 'FAN03G1586' => 'fan', 'FAN03G2986' => 'fan', 'FAN05G4837' => 'fan', 'FAN06G0146' => 'fan', 'FAN07G0858' => 'fan', 'FAN09G3179' => 'fan', 'FAN10G0669' => 'fan', 'FAN12G2358' => 'fan', 'FAN14G4198' => 'fan', 'FAN14G5112' => 'fan', 'FAN17G0342' => 'fan', 'FAN19G0342' => 'fan', 'FAN19G0962' => 'fan', 'FAN19G1101' => 'fan', 'FAN19G1872' => 'fan', 'FAN22G0356' => 'fan', 'FAN23G0744' => 'fan', 'FAN23G1914' => 'fan', 'FAN26G0032' => 'fan', 'FAN28G0625' => 'fan', 'FvH4_1g02710' => 'fve', 'FvH4_1g02720' => 'fve', 'FvH4_4g25670' => 'fve', 'FvH4_6g51700' => 'fve', 'FvH4_7g20170' => 'fve', 'Glyma.05G175000' => 'gma', 'Glyma.08G132300' => 'gma', 'Glyma.11G243000' => 'gma', 'Glyma.13G158900' => 'gma', 'Glyma.17G112400' => 'gma', 'Glyma.18G014100' => 'gma', 'Glyma.19G003100' => 'gma', 'Glyma.19G056500' => 'gma', 'Gohir.A01G158900' => 'ghi', 'Gohir.A05G312600' => 'ghi', 'Gohir.A05G354900' => 'ghi', 'Gohir.A07G037200' => 'ghi', 'Gohir.A09G030000' => 'ghi', 'Gohir.A12G145200' => 'ghi', 'Gohir.D01G151500' => 'ghi', 'Gohir.D04G058300' => 'ghi', 'Gohir.D05G314100' => 'ghi', 'Gohir.D07G041400' => 'ghi', 'Gohir.D09G029700' => 'ghi', 'Gohir.D12G149700' => 'ghi', 'Gorai.001G043800' => 'gra', 'Gorai.002G187800' => 'gra', 'Gorai.006G034700' => 'gra', 'Gorai.008G161200' => 'gra', 'Gorai.009G335700' => 'gra', 'Gorai.012G065000' => 'gra', 'GSVIVG01000535001' => 'vvi', 'GSVIVG01015572001' => 'vvi', 'GSVIVG01032386001' => 'vvi', 'HanXRQChr05g0138531' => 'han', 'HanXRQChr06g0174391' => 'han', 'HanXRQChr07g0199021' => 'han', 'HanXRQChr08g0208211' => 'han', 'HanXRQChr09g0255471' => 'han', 'HanXRQChr10g0315791' => 'han', 'HanXRQChr12g0371991' => 'han', 'HanXRQChr15g0475251' => 'han', 'HanXRQChr17g0540001' => 'han', 'HanXRQChr17g0548631' => 'han', 'HanXRQChr17g0569561' => 'han', 'Haze_12256' => 'cav', 'Haze_14756' => 'cav', 'Haze_25528' => 'cav', 'Hma1.2p1_0079F.1_g041020' => 'hma', 'Hma1.2p1_0818F.1_g223260' => 'hma', 'Hma1.2p1_1747F.1_g300530' => 'hma', 'HPP92_004607' => 'vpl', 'HPP92_004608' => 'vpl', 'HPP92_006181' => 'vpl', 'HPP92_012192' => 'vpl', 'HPP92_015680' => 'vpl', 'HPP92_020249' => 'vpl', 'HPP92_021376' => 'vpl', 'HPP92_024275' => 'vpl', 'Hund06031' => 'sun', 'Hund25391' => 'sun', 'Lalb_Chr07g0185371' => 'lal', 'Lalb_Chr07g0185381' => 'lal', 'Lalb_Chr12g0204011' => 'lal', 'Lalb_Chr13g0301671' => 'lal', 'Lalb_Chr14g0362851' => 'lal', 'Lalb_Chr24g0403581' => 'lal', 'Lj1g0000233' => 'lja', 'Lj2g0018120' => 'lja', 'Lj3C621T0' => 'lonja', 'Lj3P1059T14' => 'lonja', 'Lj3P611T9' => 'lonja', 'Lj3P614T13' => 'lonja', 'Lj3P615T5' => 'lonja', 'Lj4g0012315' => 'lja', 'Lj4g0026182' => 'lja', 'Lj6P813T16' => 'lonja', 'Lj7C427T7' => 'lonja', 'Lj7C427T8' => 'lonja', 'Lj7P600T41' => 'lonja', 'Lju41C42G17' => 'lonja', 'Lsat_1_v5_gn_0_47300' => 'lsa', 'Lsat_1_v5_gn_2_91280' => 'lsa', 'Lsat_1_v5_gn_3_30561' => 'lsa', 'Lsat_1_v5_gn_4_184321' => 'lsa', 'Lsat_1_v5_gn_4_4041' => 'lsa', 'Lsat_1_v5_gn_5_92000' => 'lsa', 'Lsat_1_v5_gn_8_152940' => 'lsa', 'Lsat_1_v5_gn_8_62401' => 'lsa', 'Manes.06G055900' => 'mes', 'Manes.12G022200' => 'mes', 'Manes.13G023300' => 'mes', 'Manes.14G115000' => 'mes', 'Manes.15G151700' => 'mes', 'Manes.17G111300' => 'mes', 'Mapoly0226s0009' => 'mpo', 'MBI02_g25363_MAGBIO' => 'mbi', 'MBI06_g00027_MAGBIO' => 'mbi', 'MBI10_g13034_MAGBIO' => 'mbi', 'MD09G1023400' => 'mdo', 'MD13G1100100' => 'mdo', 'MD15G1169200' => 'mdo', 'MD16G1101100' => 'mdo', 'MD17G1022900' => 'mdo', 'Medtr3g096150' => 'mtr', 'Medtr4g115070' => 'mtr', 'Medtr7g033325' => 'mtr', 'Medtr8g089840' => 'mtr', 'MELO3C010319.2' => 'cme', 'MELO3C011944.2' => 'cme', 'MELO3C021589.2' => 'cme', 'Migut.E00207' => 'egut', 'Migut.H00067' => 'egut', 'Migut.K00433' => 'egut', 'Migut.K00606' => 'egut', 'Migut.K01410' => 'egut', 'MSTRG.13347' => 'ama', 'MSTRG.24045' => 'ama', 'MSTRG.2428' => 'ama', 'MSTRG.26410' => 'ama', 'MSTRG.3139' => 'ama', 'MSTRG.3286' => 'ama', 'MSTRG.563' => 'ama', 'MSTRG.7941' => 'ama', 'Nitab4.5_0000028g0060' => 'nta', 'Nitab4.5_0000065g0260' => 'nta', 'Nitab4.5_0000112g0060' => 'nta', 'Nitab4.5_0000489g0120' => 'nta', 'Nitab4.5_0001776g0050' => 'nta', 'Nitab4.5_0001854g0010' => 'nta', 'Nitab4.5_0001860g0020' => 'nta', 'Nitab4.5_0004352g0010' => 'nta', 'Nitab4.5_0008716g0020' => 'nta', 'Nitab4.5_0008922g0010' => 'nta', 'Nn3g16693' => 'nnu', 'Nn4g22596' => 'nnu', 'Nn7g37639' => 'nnu', 'Oeu001701.1' => 'oeu', 'Oeu018149.1' => 'oeu', 'Oeu026220.1' => 'oeu', 'Oeu038635.1' => 'oeu', 'Oeu049176.1' => 'oeu', 'Oeu056706.1' => 'oeu', 'Oeu056937.1' => 'oeu', 'Oeu057540.1' => 'oeu', 'Os02g0594900' => 'osa', 'Os02g0595100' => 'osa', 'Os04g0477500' => 'osa', 'Os12g0611900' => 'osa', 'Peaxi162Scf00076g00020' => 'pax', 'Peaxi162Scf00128g00217' => 'pax', 'Peaxi162Scf00129g01640' => 'pax', 'Peaxi162Scf00669g00007' => 'pax', 'Peaxi162Scf00700g00421' => 'pax', 'Peaxi162Scf00801g00038' => 'pax', 'Peaxi162Scf00891g00025' => 'pax', 'PGR083G0909' => 'pgr', 'PGR119G1005' => 'pgr', 'PGR142G2236' => 'pgr', 'PGR142G3388' => 'pgr', 'PGSC0003DMG400004514' => 'stu', 'PGSC0003DMG400012635' => 'stu', 'PGSC0003DMG400015730' => 'stu', 'PGSC0003DMG400018611' => 'stu', 'PGSC0003DMG400030897' => 'stu', 'Phvul.001G254800' => 'pvu', 'Phvul.002G260100' => 'pvu', 'Phvul.003G167600' => 'pvu', 'Phvul.004G005100' => 'pvu', 'Potri.001G343600' => 'ptr', 'Potri.006G066700' => 'ptr', 'Potri.008G186000' => 'ptr', 'Potri.010G046900' => 'ptr', 'Potri.018G127900' => 'ptr', 'Pp3c20_17750' => 'ppa', 'Pp3c24_4380' => 'ppa', 'Prupe.1G245800' => 'ppe', 'Prupe.3G293400' => 'ppe', 'Prupe.7G247400' => 'ppe', 'Psat0s145g0120' => 'psa', 'Psat0s595g0040' => 'psa', 'Psat0s595g0120' => 'psa', 'Psat3g175040' => 'psa', 'Psat7g058120' => 'psa', 'PSO017G0428' => 'pso', 'PSO063G7510' => 'pso', 'PSO067G0046' => 'pso', 'PSO478G1073' => 'pso', 'PSO675G3677' => 'pso', 'PSO675G6558' => 'pso', 'PSO675G7520' => 'pso', 'PSO675G8959' => 'pso', 'QL02p074089' => 'qlo', 'QL02p089614' => 'qlo', 'QL03p057736' => 'qlo', 'RcHm_v2.0_Chr1g0364131' => 'rch', 'RcHm_v2.0_Chr2g0087801' => 'rch', 'RcHm_v2.0_Chr2g0087821' => 'rch', 'RcHm_v2.0_Chr2g0173231' => 'rch', 'RcHm_v2.0_Chr4g0433111' => 'rch', 'Rhsim03G0250300' => 'rsi', 'Rhsim08G0048400' => 'rsi', 'Rhsim10G0014800' => 'rsi', 'Rhsim12G0040100' => 'rsi', 'Rhsim12G0109700' => 'rsi', 'Sabra06G0049600' => 'sbr', 'Sabra08G0141000' => 'sbr', 'Sabra10G0021400' => 'sbr', 'Sabra16G0222900' => 'sbr', 'Sabra18G0108600' => 'sbr', 'SalBow1G0433' => 'sbo', 'SalBow1G2038' => 'sbo', 'SalBow1G5003' => 'sbo', 'SalBow7G1197' => 'sbo', 'SalBow8G3506' => 'sbo', 'Sc03g0007300' => 'sci', 'Sc11g0000950' => 'sci', 'Sc14g0008750' => 'sci', 'Sc18g0000420' => 'sci', 'Sed0006754' => 'sed', 'Sed0008741' => 'sed', 'Sed0017172' => 'sed', 'Sed0018925' => 'sed', 'Sed0023326' => 'sed', 'Sed0025909' => 'sed', 'SEGI_05333' => 'sgi', 'SEGI_10362' => 'sgi', 'SEGI_13380' => 'sgi', 'SEGI_24306' => 'sgi', 'SEGI_29077' => 'sgi', 'SEGI_29095' => 'sgi', 'SEGI_36534' => 'sgi', 'SEGI_37506' => 'sgi', 'SEGI_38321' => 'sgi', 'SGA_v2.0_scaffold307G48031' => 'sas', 'SGA_v2.0_scaffold47G17507' => 'sas', 'SGA_v2.0_scaffold63G21736' => 'sas', 'SGA_v2.0_scaffold87G27070' => 'sas', 'SHI17794' => 'shi', 'SHI28851' => 'shi', 'SMO165G0155' => 'smo', 'SMO340G0217' => 'smo', 'SMO367G1210' => 'smo', 'Solyc02g093430.3' => 'sly', 'Solyc05g013580.4' => 'sly', 'Solyc07g008030.3' => 'sly', 'Solyc12g035470.2' => 'sly', 'Sopen02g038020' => 'spe', 'Sopen05g008490' => 'spe', 'Sopen07g003910' => 'spe', 'Sopen12g015240' => 'spe', 'Sp1g11550' => 'spa', 'Sp2g16710' => 'spa', 'Sp3g00430' => 'spa', 'Sp3g26780' => 'spa', 'Sp5g22900' => 'spa', 'Sp6g29530' => 'spa', 'TAR371G0794' => 'tar', 'TAR374G0164' => 'tar', 'TAR622G0165' => 'tar', 'TAR626G0929' => 'tar', 'TAR629G2155' => 'tar', 'THA.LOC104805282' => 'tha', 'THA.LOC104805363' => 'tha', 'THA.LOC104808968' => 'tha', 'THA.LOC104821093' => 'tha', 'THA.LOC104823953' => 'tha', 'THA.LOC104825562' => 'tha', 'THA.LOC104825665' => 'tha', 'Thecc.02G261400' => 'tca', 'Thecc.04G019200' => 'tca', 'Thecc.09G130400' => 'tca', 'Thhalv10004374m.g' => 'esa', 'Thhalv10007850m.g' => 'esa', 'Thhalv10013782m.g' => 'esa', 'Thhalv10018686m.g' => 'esa', 'Thhalv10020899m.g' => 'esa', 'Thhalv10022755m.g' => 'esa', 'TPR.G23851' => 'tpr', 'TPR.G26500' => 'tpr', 'TPR.G27267' => 'tpr', 'TPR.G32001' => 'tpr', 'TPR.G6251' => 'tpr', 'TPR.G8167' => 'tpr', 'TWI12G1330' => 'twi', 'TWI18G1239' => 'twi', 'TWI34G0979' => 'twi', 'TWI36G0670' => 'twi', 'TWI36G0707' => 'twi', 'TWI56G0233' => 'twi', 'TWI75G1809' => 'twi', 'unitig_21.g20874' => 'ugi', 'unitig_26.g10343' => 'ugi', 'unitig_46.g18392' => 'ugi', 'unitig_52.g17178' => 'ugi', 'unitig_8.g2934' => 'ugi', 'vmacro01122' => 'vma', 'vmacro05875' => 'vma', 'vmacro06147' => 'vma', 'vmacro16191' => 'vma', 'vmacro18293' => 'vma', 'VMungo0251G3707' => 'vmu', 'VMungo0464G1521' => 'vmu', 'VMungo1215G0205' => 'vmu', 'VMungo1383G2484' => 'vmu', 'Zm00001eb079610' => 'zma', 'Zm00001eb135990' => 'zma', 'Zm00001eb183710' => 'zma', 'Zm00001eb246020' => 'zma' ), 'gf_id' => 'HOM05D001124', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001124' ), 'data_identifier' => 'HOM05D001124', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001124', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '548', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02520' => 'bna', 'A03p06630' => 'bna', 'A05p44460' => 'bna', 'A06p08710' => 'bna', 'A06p41090' => 'bna', 'A07p32320' => 'bna', 'A08p32520' => 'bna', 'A09p10360' => 'bna', 'A10p24080' => 'bna', 'Aa31LG11G15250' => 'aar', 'Aa31LG1G1800' => 'aar', 'Aa31LG2G5120' => 'aar', 'Aa31LG2G6070' => 'aar', 'Aa31LG5G10770' => 'aar', 'Aa31sc61G90' => 'aar', 'Actinidia01352' => 'ach', 'Actinidia05983' => 'ach', 'Actinidia08133' => 'ach', 'Actinidia15101' => 'ach', 'Actinidia26379' => 'ach', 'Actinidia35778' => 'ach', 'Actinidia36123' => 'ach', 'Actinidia37436' => 'ach', 'Actinidia38730' => 'ach', 'Ah.02g128210' => 'amhyb', 'Ah.03g132990' => 'amhyb', 'Ah.14g079410' => 'amhyb', 'AL1G24640' => 'aly', 'AL2G26680' => 'aly', 'AL3G10530' => 'aly', 'AL3G45230' => 'aly', 'AL5G15230' => 'aly', 'AL5G16960' => 'aly', 'AL6G25210' => 'aly', 'Aqoxy2G00441' => 'aox', 'Aqoxy3G01236' => 'aox', 'Aqoxy5G03746' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3RQ047' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C7GMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9C8JER' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MBL6KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YXCZ83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZANX40' => 'arhy', 'AT1G12990' => 'ath', 'AT1G67880' => 'ath', 'AT2G13290' => 'ath', 'AT3G01620' => 'ath', 'AT3G26445' => 'ath', 'AT3G27540' => 'ath', 'AT5G14480' => 'ath', 'ATR0824G026' => 'atr', 'ATR1098G019' => 'atr', 'Atru.chr11.2145' => 'acertr', 'Atru.chr2.3636' => 'acertr', 'Atru.chr2.3644' => 'acertr', 'Atru.chr6.2422' => 'acertr', 'Atru.chr7.1112' => 'acertr', 'AUR62005469' => 'cqu', 'AUR62011166' => 'cqu', 'AUR62013319' => 'cqu', 'AUR62024273' => 'cqu', 'AUR62028420' => 'cqu', 'AUR62041942' => 'cqu', 'BcaB01g04969' => 'bca', 'BcaB01g06371' => 'bca', 'BcaB02g11494' => 'bca', 'BcaB03g15382' => 'bca', 'BcaB08g36994' => 'bca', 'BcaC03g13477' => 'bca', 'BcaC03g13478' => 'bca', 'BcaC03g13480' => 'bca', 'BcaC03g13481' => 'bca', 'BcaC03g13486' => 'bca', 'BcaC04g19031' => 'bca', 'BcaC04g23085' => 'bca', 'BcaC05g25094' => 'bca', 'BcaC05g25096' => 'bca', 'BcaC05g25138' => 'bca', 'BcaC05g30416' => 'bca', 'BcaC05g30455' => 'bca', 'BcaC06g30979' => 'bca', 'BcaC06g33805' => 'bca', 'BcaC08g46021' => 'bca', 'BcaNung03154' => 'bca', 'BolC2t06623H' => 'bol', 'BolC2t06632H' => 'bol', 'BolC2t06635H' => 'bol', 'BolC2t06638H' => 'bol', 'BolC3t13266H' => 'bol', 'BolC5t29776H' => 'bol', 'BolC6t38912H' => 'bol', 'BolC7t44183H' => 'bol', 'BolC9t54123H' => 'bol', 'BolC9t59107H' => 'bol', 'BraA02t05221Z' => 'bra', 'BraA03t09996Z' => 'bra', 'BraA05t23210Z' => 'bra', 'BraA06t24068Z' => 'bra', 'BraA06t27032Z' => 'bra', 'BraA08t35176Z' => 'bra', 'BraA09t36680Z' => 'bra', 'BraA10t44471Z' => 'bra', 'C02p06760' => 'bna', 'C02p06890' => 'bna', 'C02p07010' => 'bna', 'C03p07660' => 'bna', 'C05p10300' => 'bna', 'C06p38150' => 'bna', 'C07p36650' => 'bna', 'C08p15770' => 'bna', 'C09p12300' => 'bna', 'C09p62700' => 'bna', 'C09p75040' => 'bna', 'CAN.G13.1' => 'can', 'CAN.G138.4' => 'can', 'CAN.G44.6' => 'can', 'CAN.G473.19' => 'can', 'CANSAT01G0835' => 'cansat', 'CANSAT11G0246' => 'cansat', 'CANSAT11G1766' => 'cansat', 'CANSAT64G1954' => 'cansat', 'CARHR013330' => 'chi', 'CARHR060530' => 'chi', 'CARHR075300' => 'chi', 'CARHR105120' => 'chi', 'CARHR148910' => 'chi', 'CARHR198830' => 'chi', 'Carub.0001s1275' => 'cru', 'Carub.0002s1437' => 'cru', 'Carub.0003s0044' => 'cru', 'Carub.0003s2787' => 'cru', 'Carub.0005s0597' => 'cru', 'Carub.0006s1266' => 'cru', 'Ca_06935_v3' => 'car', 'Ca_13559_v3' => 'car', 'Ca_16941_v3' => 'car', 'Ca_16960_v3' => 'car', 'Ca_17775_v3' => 'car', 'Ca_30464_v3' => 'car', 'Cc06_g08160' => 'ccan', 'Cc07_g01520' => 'ccan', 'Cc11_g15810' => 'ccan', 'CDE02G2840' => 'cde', 'CDE03G0093' => 'cde', 'CDE04G2127' => 'cde', 'CDE07G1857' => 'cde', 'CDE09G1246' => 'cde', 'Cfa003412' => 'cfa', 'Cfa007341' => 'cfa', 'Cfa009220' => 'cfa', 'Ciclev10008737m.g' => 'ccl', 'Ciclev10015565m.g' => 'ccl', 'Ciclev10031761m.g' => 'ccl', 'CiPaw.03G045300' => 'cil', 'CiPaw.03G247200' => 'cil', 'CiPaw.04G029500' => 'cil', 'CiPaw.04G174000' => 'cil', 'CiPaw.05G181200' => 'cil', 'CiPaw.06G067100' => 'cil', 'ClCG05G025800' => 'cla', 'ClCG06G011400' => 'cla', 'ClCG09G019360' => 'cla', 'COL.COLO4_04827' => 'col', 'COL.COLO4_29170' => 'col', 'COL.COLO4_35131' => 'col', 'COL.COLO4_35132' => 'col', 'Cpa.g.sc33.32' => 'cpa', 'Cpa.g.sc46.29' => 'cpa', 'Cpa.g.sc796.1' => 'cpa', 'CsaV3_1G030420' => 'csa', 'CsaV3_5G027050' => 'csa', 'CsaV3_5G031040' => 'csa', 'CsaV3_UNG023130' => 'csa', 'CSS0007726' => 'camsi', 'CSS0016433' => 'camsi', 'CSS0017656' => 'camsi', 'CSS0025364' => 'camsi', 'CSS0027582' => 'camsi', 'CSS0047288' => 'camsi', 'CSS0049950' => 'camsi', 'DCAR_003843' => 'dca', 'DCAR_007052' => 'dca', 'DCAR_020884' => 'dca', 'DCAR_021730' => 'dca', 'DCAR_024423' => 'dca', 'DCAR_026509' => 'dca', 'DCAR_031158' => 'dca', 'Dinv14728' => 'din', 'Dinv15219' => 'din', 'Dinv25728' => 'din', 'Dinv33428' => 'din', 'Dinv36489' => 'din', 'Dinv41486' => 'din', 'Duzib147G0469' => 'dzi', 'Duzib168G0060' => 'dzi', 'Duzib187G1215' => 'dzi', 'Duzib248G0692' => 'dzi', 'Duzib251G0767' => 'dzi', 'Duzib264G0446' => 'dzi', 'Duzib268G0691' => 'dzi', 'ECA232G4767' => 'eca', 'ECA233G2838' => 'eca', 'ECA234G0391' => 'eca', 'ECA234G0857' => 'eca', 'ECA236G1593' => 'eca', 'ECA238G0565' => 'eca', 'ECA246G1027' => 'eca', 'ECA246G3223' => 'eca', 'ECA246G3470' => 'eca', 'EL10Ac6g13829' => 'bvu', 'EL10Ac6g14093' => 'bvu', 'EL10Ac8g18707' => 'bvu', 'Eucgr.C01369' => 'egr', 'Eucgr.H02492' => 'egr', 'Eucgr.I01733' => 'egr', 'Eucgr.J02255' => 'egr', 'Eucgr.J02257' => 'egr', 'Eucgr.J02258' => 'egr', 'FAN02G1601' => 'fan', 'FAN03G1586' => 'fan', 'FAN03G2986' => 'fan', 'FAN05G4837' => 'fan', 'FAN06G0146' => 'fan', 'FAN07G0858' => 'fan', 'FAN09G3179' => 'fan', 'FAN10G0669' => 'fan', 'FAN12G2358' => 'fan', 'FAN14G4198' => 'fan', 'FAN14G5112' => 'fan', 'FAN17G0342' => 'fan', 'FAN19G0342' => 'fan', 'FAN19G0962' => 'fan', 'FAN19G1101' => 'fan', 'FAN19G1872' => 'fan', 'FAN22G0356' => 'fan', 'FAN23G0744' => 'fan', 'FAN23G1914' => 'fan', 'FAN26G0032' => 'fan', 'FAN28G0625' => 'fan', 'FvH4_1g02710' => 'fve', 'FvH4_1g02720' => 'fve', 'FvH4_4g25670' => 'fve', 'FvH4_6g51700' => 'fve', 'FvH4_7g20170' => 'fve', 'Glyma.05G175000' => 'gma', 'Glyma.08G132300' => 'gma', 'Glyma.11G243000' => 'gma', 'Glyma.13G158900' => 'gma', 'Glyma.17G112400' => 'gma', 'Glyma.18G014100' => 'gma', 'Glyma.19G003100' => 'gma', 'Glyma.19G056500' => 'gma', 'Gohir.A01G158900' => 'ghi', 'Gohir.A05G312600' => 'ghi', 'Gohir.A05G354900' => 'ghi', 'Gohir.A07G037200' => 'ghi', 'Gohir.A09G030000' => 'ghi', 'Gohir.A12G145200' => 'ghi', 'Gohir.D01G151500' => 'ghi', 'Gohir.D04G058300' => 'ghi', 'Gohir.D05G314100' => 'ghi', 'Gohir.D07G041400' => 'ghi', 'Gohir.D09G029700' => 'ghi', 'Gohir.D12G149700' => 'ghi', 'Gorai.001G043800' => 'gra', 'Gorai.002G187800' => 'gra', 'Gorai.006G034700' => 'gra', 'Gorai.008G161200' => 'gra', 'Gorai.009G335700' => 'gra', 'Gorai.012G065000' => 'gra', 'GSVIVG01000535001' => 'vvi', 'GSVIVG01015572001' => 'vvi', 'GSVIVG01032386001' => 'vvi', 'HanXRQChr05g0138531' => 'han', 'HanXRQChr06g0174391' => 'han', 'HanXRQChr07g0199021' => 'han', 'HanXRQChr08g0208211' => 'han', 'HanXRQChr09g0255471' => 'han', 'HanXRQChr10g0315791' => 'han', 'HanXRQChr12g0371991' => 'han', 'HanXRQChr15g0475251' => 'han', 'HanXRQChr17g0540001' => 'han', 'HanXRQChr17g0548631' => 'han', 'HanXRQChr17g0569561' => 'han', 'Haze_12256' => 'cav', 'Haze_14756' => 'cav', 'Haze_25528' => 'cav', 'Hma1.2p1_0079F.1_g041020' => 'hma', 'Hma1.2p1_0818F.1_g223260' => 'hma', 'Hma1.2p1_1747F.1_g300530' => 'hma', 'HPP92_004607' => 'vpl', 'HPP92_004608' => 'vpl', 'HPP92_006181' => 'vpl', 'HPP92_012192' => 'vpl', 'HPP92_015680' => 'vpl', 'HPP92_020249' => 'vpl', 'HPP92_021376' => 'vpl', 'HPP92_024275' => 'vpl', 'Hund06031' => 'sun', 'Hund25391' => 'sun', 'Lalb_Chr07g0185371' => 'lal', 'Lalb_Chr07g0185381' => 'lal', 'Lalb_Chr12g0204011' => 'lal', 'Lalb_Chr13g0301671' => 'lal', 'Lalb_Chr14g0362851' => 'lal', 'Lalb_Chr24g0403581' => 'lal', 'Lj1g0000233' => 'lja', 'Lj2g0018120' => 'lja', 'Lj3C621T0' => 'lonja', 'Lj3P1059T14' => 'lonja', 'Lj3P611T9' => 'lonja', 'Lj3P614T13' => 'lonja', 'Lj3P615T5' => 'lonja', 'Lj4g0012315' => 'lja', 'Lj4g0026182' => 'lja', 'Lj6P813T16' => 'lonja', 'Lj7C427T7' => 'lonja', 'Lj7C427T8' => 'lonja', 'Lj7P600T41' => 'lonja', 'Lju41C42G17' => 'lonja', 'Lsat_1_v5_gn_0_47300' => 'lsa', 'Lsat_1_v5_gn_2_91280' => 'lsa', 'Lsat_1_v5_gn_3_30561' => 'lsa', 'Lsat_1_v5_gn_4_184321' => 'lsa', 'Lsat_1_v5_gn_4_4041' => 'lsa', 'Lsat_1_v5_gn_5_92000' => 'lsa', 'Lsat_1_v5_gn_8_152940' => 'lsa', 'Lsat_1_v5_gn_8_62401' => 'lsa', 'Manes.06G055900' => 'mes', 'Manes.12G022200' => 'mes', 'Manes.13G023300' => 'mes', 'Manes.14G115000' => 'mes', 'Manes.15G151700' => 'mes', 'Manes.17G111300' => 'mes', 'Mapoly0226s0009' => 'mpo', 'MBI02_g25363_MAGBIO' => 'mbi', 'MBI06_g00027_MAGBIO' => 'mbi', 'MBI10_g13034_MAGBIO' => 'mbi', 'MD09G1023400' => 'mdo', 'MD13G1100100' => 'mdo', 'MD15G1169200' => 'mdo', 'MD16G1101100' => 'mdo', 'MD17G1022900' => 'mdo', 'Medtr3g096150' => 'mtr', 'Medtr4g115070' => 'mtr', 'Medtr7g033325' => 'mtr', 'Medtr8g089840' => 'mtr', 'MELO3C010319.2' => 'cme', 'MELO3C011944.2' => 'cme', 'MELO3C021589.2' => 'cme', 'Migut.E00207' => 'egut', 'Migut.H00067' => 'egut', 'Migut.K00433' => 'egut', 'Migut.K00606' => 'egut', 'Migut.K01410' => 'egut', 'MSTRG.13347' => 'ama', 'MSTRG.24045' => 'ama', 'MSTRG.2428' => 'ama', 'MSTRG.26410' => 'ama', 'MSTRG.3139' => 'ama', 'MSTRG.3286' => 'ama', 'MSTRG.563' => 'ama', 'MSTRG.7941' => 'ama', 'Nitab4.5_0000028g0060' => 'nta', 'Nitab4.5_0000065g0260' => 'nta', 'Nitab4.5_0000112g0060' => 'nta', 'Nitab4.5_0000489g0120' => 'nta', 'Nitab4.5_0001776g0050' => 'nta', 'Nitab4.5_0001854g0010' => 'nta', 'Nitab4.5_0001860g0020' => 'nta', 'Nitab4.5_0004352g0010' => 'nta', 'Nitab4.5_0008716g0020' => 'nta', 'Nitab4.5_0008922g0010' => 'nta', 'Nn3g16693' => 'nnu', 'Nn4g22596' => 'nnu', 'Nn7g37639' => 'nnu', 'Oeu001701.1' => 'oeu', 'Oeu018149.1' => 'oeu', 'Oeu026220.1' => 'oeu', 'Oeu038635.1' => 'oeu', 'Oeu049176.1' => 'oeu', 'Oeu056706.1' => 'oeu', 'Oeu056937.1' => 'oeu', 'Oeu057540.1' => 'oeu', 'Os02g0594900' => 'osa', 'Os02g0595100' => 'osa', 'Os04g0477500' => 'osa', 'Os12g0611900' => 'osa', 'Peaxi162Scf00076g00020' => 'pax', 'Peaxi162Scf00128g00217' => 'pax', 'Peaxi162Scf00129g01640' => 'pax', 'Peaxi162Scf00669g00007' => 'pax', 'Peaxi162Scf00700g00421' => 'pax', 'Peaxi162Scf00801g00038' => 'pax', 'Peaxi162Scf00891g00025' => 'pax', 'PGR083G0909' => 'pgr', 'PGR119G1005' => 'pgr', 'PGR142G2236' => 'pgr', 'PGR142G3388' => 'pgr', 'PGSC0003DMG400004514' => 'stu', 'PGSC0003DMG400012635' => 'stu', 'PGSC0003DMG400015730' => 'stu', 'PGSC0003DMG400018611' => 'stu', 'PGSC0003DMG400030897' => 'stu', 'Phvul.001G254800' => 'pvu', 'Phvul.002G260100' => 'pvu', 'Phvul.003G167600' => 'pvu', 'Phvul.004G005100' => 'pvu', 'Potri.001G343600' => 'ptr', 'Potri.006G066700' => 'ptr', 'Potri.008G186000' => 'ptr', 'Potri.010G046900' => 'ptr', 'Potri.018G127900' => 'ptr', 'Pp3c20_17750' => 'ppa', 'Pp3c24_4380' => 'ppa', 'Prupe.1G245800' => 'ppe', 'Prupe.3G293400' => 'ppe', 'Prupe.7G247400' => 'ppe', 'Psat0s145g0120' => 'psa', 'Psat0s595g0040' => 'psa', 'Psat0s595g0120' => 'psa', 'Psat3g175040' => 'psa', 'Psat7g058120' => 'psa', 'PSO017G0428' => 'pso', 'PSO063G7510' => 'pso', 'PSO067G0046' => 'pso', 'PSO478G1073' => 'pso', 'PSO675G3677' => 'pso', 'PSO675G6558' => 'pso', 'PSO675G7520' => 'pso', 'PSO675G8959' => 'pso', 'QL02p074089' => 'qlo', 'QL02p089614' => 'qlo', 'QL03p057736' => 'qlo', 'RcHm_v2.0_Chr1g0364131' => 'rch', 'RcHm_v2.0_Chr2g0087801' => 'rch', 'RcHm_v2.0_Chr2g0087821' => 'rch', 'RcHm_v2.0_Chr2g0173231' => 'rch', 'RcHm_v2.0_Chr4g0433111' => 'rch', 'Rhsim03G0250300' => 'rsi', 'Rhsim08G0048400' => 'rsi', 'Rhsim10G0014800' => 'rsi', 'Rhsim12G0040100' => 'rsi', 'Rhsim12G0109700' => 'rsi', 'Sabra06G0049600' => 'sbr', 'Sabra08G0141000' => 'sbr', 'Sabra10G0021400' => 'sbr', 'Sabra16G0222900' => 'sbr', 'Sabra18G0108600' => 'sbr', 'SalBow1G0433' => 'sbo', 'SalBow1G2038' => 'sbo', 'SalBow1G5003' => 'sbo', 'SalBow7G1197' => 'sbo', 'SalBow8G3506' => 'sbo', 'Sc03g0007300' => 'sci', 'Sc11g0000950' => 'sci', 'Sc14g0008750' => 'sci', 'Sc18g0000420' => 'sci', 'Sed0006754' => 'sed', 'Sed0008741' => 'sed', 'Sed0017172' => 'sed', 'Sed0018925' => 'sed', 'Sed0023326' => 'sed', 'Sed0025909' => 'sed', 'SEGI_05333' => 'sgi', 'SEGI_10362' => 'sgi', 'SEGI_13380' => 'sgi', 'SEGI_24306' => 'sgi', 'SEGI_29077' => 'sgi', 'SEGI_29095' => 'sgi', 'SEGI_36534' => 'sgi', 'SEGI_37506' => 'sgi', 'SEGI_38321' => 'sgi', 'SGA_v2.0_scaffold307G48031' => 'sas', 'SGA_v2.0_scaffold47G17507' => 'sas', 'SGA_v2.0_scaffold63G21736' => 'sas', 'SGA_v2.0_scaffold87G27070' => 'sas', 'SHI17794' => 'shi', 'SHI28851' => 'shi', 'SMO165G0155' => 'smo', 'SMO340G0217' => 'smo', 'SMO367G1210' => 'smo', 'Solyc02g093430.3' => 'sly', 'Solyc05g013580.4' => 'sly', 'Solyc07g008030.3' => 'sly', 'Solyc12g035470.2' => 'sly', 'Sopen02g038020' => 'spe', 'Sopen05g008490' => 'spe', 'Sopen07g003910' => 'spe', 'Sopen12g015240' => 'spe', 'Sp1g11550' => 'spa', 'Sp2g16710' => 'spa', 'Sp3g00430' => 'spa', 'Sp3g26780' => 'spa', 'Sp5g22900' => 'spa', 'Sp6g29530' => 'spa', 'TAR371G0794' => 'tar', 'TAR374G0164' => 'tar', 'TAR622G0165' => 'tar', 'TAR626G0929' => 'tar', 'TAR629G2155' => 'tar', 'THA.LOC104805282' => 'tha', 'THA.LOC104805363' => 'tha', 'THA.LOC104808968' => 'tha', 'THA.LOC104821093' => 'tha', 'THA.LOC104823953' => 'tha', 'THA.LOC104825562' => 'tha', 'THA.LOC104825665' => 'tha', 'Thecc.02G261400' => 'tca', 'Thecc.04G019200' => 'tca', 'Thecc.09G130400' => 'tca', 'Thhalv10004374m.g' => 'esa', 'Thhalv10007850m.g' => 'esa', 'Thhalv10013782m.g' => 'esa', 'Thhalv10018686m.g' => 'esa', 'Thhalv10020899m.g' => 'esa', 'Thhalv10022755m.g' => 'esa', 'TPR.G23851' => 'tpr', 'TPR.G26500' => 'tpr', 'TPR.G27267' => 'tpr', 'TPR.G32001' => 'tpr', 'TPR.G6251' => 'tpr', 'TPR.G8167' => 'tpr', 'TWI12G1330' => 'twi', 'TWI18G1239' => 'twi', 'TWI34G0979' => 'twi', 'TWI36G0670' => 'twi', 'TWI36G0707' => 'twi', 'TWI56G0233' => 'twi', 'TWI75G1809' => 'twi', 'unitig_21.g20874' => 'ugi', 'unitig_26.g10343' => 'ugi', 'unitig_46.g18392' => 'ugi', 'unitig_52.g17178' => 'ugi', 'unitig_8.g2934' => 'ugi', 'vmacro01122' => 'vma', 'vmacro05875' => 'vma', 'vmacro06147' => 'vma', 'vmacro16191' => 'vma', 'vmacro18293' => 'vma', 'VMungo0251G3707' => 'vmu', 'VMungo0464G1521' => 'vmu', 'VMungo1215G0205' => 'vmu', 'VMungo1383G2484' => 'vmu', 'Zm00001eb079610' => 'zma', 'Zm00001eb135990' => 'zma', 'Zm00001eb183710' => 'zma', 'Zm00001eb246020' => 'zma' ) $gf_id = 'HOM05D001124' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001124' ) $data_identifier = 'HOM05D001124' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 6, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 7, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 21, 'bol' => (int) 10, 'bra' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 6, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 9, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 21, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 8, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 10, 'lsa' => (int) 8, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 8, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 9, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb246020' $species_info = array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ) $local_species = 'gma' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001124', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '548', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02520' => 'bna', 'A03p06630' => 'bna', 'A05p44460' => 'bna', 'A06p08710' => 'bna', 'A06p41090' => 'bna', 'A07p32320' => 'bna', 'A08p32520' => 'bna', 'A09p10360' => 'bna', 'A10p24080' => 'bna', 'Aa31LG11G15250' => 'aar', 'Aa31LG1G1800' => 'aar', 'Aa31LG2G5120' => 'aar', 'Aa31LG2G6070' => 'aar', 'Aa31LG5G10770' => 'aar', 'Aa31sc61G90' => 'aar', 'Actinidia01352' => 'ach', 'Actinidia05983' => 'ach', 'Actinidia08133' => 'ach', 'Actinidia15101' => 'ach', 'Actinidia26379' => 'ach', 'Actinidia35778' => 'ach', 'Actinidia36123' => 'ach', 'Actinidia37436' => 'ach', 'Actinidia38730' => 'ach', 'Ah.02g128210' => 'amhyb', 'Ah.03g132990' => 'amhyb', 'Ah.14g079410' => 'amhyb', 'AL1G24640' => 'aly', 'AL2G26680' => 'aly', 'AL3G10530' => 'aly', 'AL3G45230' => 'aly', 'AL5G15230' => 'aly', 'AL5G16960' => 'aly', 'AL6G25210' => 'aly', 'Aqoxy2G00441' => 'aox', 'Aqoxy3G01236' => 'aox', 'Aqoxy5G03746' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3RQ047' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C7GMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9C8JER' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MBL6KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YXCZ83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZANX40' => 'arhy', 'AT1G12990' => 'ath', 'AT1G67880' => 'ath', 'AT2G13290' => 'ath', 'AT3G01620' => 'ath', 'AT3G26445' => 'ath', 'AT3G27540' => 'ath', 'AT5G14480' => 'ath', 'ATR0824G026' => 'atr', 'ATR1098G019' => 'atr', 'Atru.chr11.2145' => 'acertr', 'Atru.chr2.3636' => 'acertr', 'Atru.chr2.3644' => 'acertr', 'Atru.chr6.2422' => 'acertr', 'Atru.chr7.1112' => 'acertr', 'AUR62005469' => 'cqu', 'AUR62011166' => 'cqu', 'AUR62013319' => 'cqu', 'AUR62024273' => 'cqu', 'AUR62028420' => 'cqu', 'AUR62041942' => 'cqu', 'BcaB01g04969' => 'bca', 'BcaB01g06371' => 'bca', 'BcaB02g11494' => 'bca', 'BcaB03g15382' => 'bca', 'BcaB08g36994' => 'bca', 'BcaC03g13477' => 'bca', 'BcaC03g13478' => 'bca', 'BcaC03g13480' => 'bca', 'BcaC03g13481' => 'bca', 'BcaC03g13486' => 'bca', 'BcaC04g19031' => 'bca', 'BcaC04g23085' => 'bca', 'BcaC05g25094' => 'bca', 'BcaC05g25096' => 'bca', 'BcaC05g25138' => 'bca', 'BcaC05g30416' => 'bca', 'BcaC05g30455' => 'bca', 'BcaC06g30979' => 'bca', 'BcaC06g33805' => 'bca', 'BcaC08g46021' => 'bca', 'BcaNung03154' => 'bca', 'BolC2t06623H' => 'bol', 'BolC2t06632H' => 'bol', 'BolC2t06635H' => 'bol', 'BolC2t06638H' => 'bol', 'BolC3t13266H' => 'bol', 'BolC5t29776H' => 'bol', 'BolC6t38912H' => 'bol', 'BolC7t44183H' => 'bol', 'BolC9t54123H' => 'bol', 'BolC9t59107H' => 'bol', 'BraA02t05221Z' => 'bra', 'BraA03t09996Z' => 'bra', 'BraA05t23210Z' => 'bra', 'BraA06t24068Z' => 'bra', 'BraA06t27032Z' => 'bra', 'BraA08t35176Z' => 'bra', 'BraA09t36680Z' => 'bra', 'BraA10t44471Z' => 'bra', 'C02p06760' => 'bna', 'C02p06890' => 'bna', 'C02p07010' => 'bna', 'C03p07660' => 'bna', 'C05p10300' => 'bna', 'C06p38150' => 'bna', 'C07p36650' => 'bna', 'C08p15770' => 'bna', 'C09p12300' => 'bna', 'C09p62700' => 'bna', 'C09p75040' => 'bna', 'CAN.G13.1' => 'can', 'CAN.G138.4' => 'can', 'CAN.G44.6' => 'can', 'CAN.G473.19' => 'can', 'CANSAT01G0835' => 'cansat', 'CANSAT11G0246' => 'cansat', 'CANSAT11G1766' => 'cansat', 'CANSAT64G1954' => 'cansat', 'CARHR013330' => 'chi', 'CARHR060530' => 'chi', 'CARHR075300' => 'chi', 'CARHR105120' => 'chi', 'CARHR148910' => 'chi', 'CARHR198830' => 'chi', 'Carub.0001s1275' => 'cru', 'Carub.0002s1437' => 'cru', 'Carub.0003s0044' => 'cru', 'Carub.0003s2787' => 'cru', 'Carub.0005s0597' => 'cru', 'Carub.0006s1266' => 'cru', 'Ca_06935_v3' => 'car', 'Ca_13559_v3' => 'car', 'Ca_16941_v3' => 'car', 'Ca_16960_v3' => 'car', 'Ca_17775_v3' => 'car', 'Ca_30464_v3' => 'car', 'Cc06_g08160' => 'ccan', 'Cc07_g01520' => 'ccan', 'Cc11_g15810' => 'ccan', 'CDE02G2840' => 'cde', 'CDE03G0093' => 'cde', 'CDE04G2127' => 'cde', 'CDE07G1857' => 'cde', 'CDE09G1246' => 'cde', 'Cfa003412' => 'cfa', 'Cfa007341' => 'cfa', 'Cfa009220' => 'cfa', 'Ciclev10008737m.g' => 'ccl', 'Ciclev10015565m.g' => 'ccl', 'Ciclev10031761m.g' => 'ccl', 'CiPaw.03G045300' => 'cil', 'CiPaw.03G247200' => 'cil', 'CiPaw.04G029500' => 'cil', 'CiPaw.04G174000' => 'cil', 'CiPaw.05G181200' => 'cil', 'CiPaw.06G067100' => 'cil', 'ClCG05G025800' => 'cla', 'ClCG06G011400' => 'cla', 'ClCG09G019360' => 'cla', 'COL.COLO4_04827' => 'col', 'COL.COLO4_29170' => 'col', 'COL.COLO4_35131' => 'col', 'COL.COLO4_35132' => 'col', 'Cpa.g.sc33.32' => 'cpa', 'Cpa.g.sc46.29' => 'cpa', 'Cpa.g.sc796.1' => 'cpa', 'CsaV3_1G030420' => 'csa', 'CsaV3_5G027050' => 'csa', 'CsaV3_5G031040' => 'csa', 'CsaV3_UNG023130' => 'csa', 'CSS0007726' => 'camsi', 'CSS0016433' => 'camsi', 'CSS0017656' => 'camsi', 'CSS0025364' => 'camsi', 'CSS0027582' => 'camsi', 'CSS0047288' => 'camsi', 'CSS0049950' => 'camsi', 'DCAR_003843' => 'dca', 'DCAR_007052' => 'dca', 'DCAR_020884' => 'dca', 'DCAR_021730' => 'dca', 'DCAR_024423' => 'dca', 'DCAR_026509' => 'dca', 'DCAR_031158' => 'dca', 'Dinv14728' => 'din', 'Dinv15219' => 'din', 'Dinv25728' => 'din', 'Dinv33428' => 'din', 'Dinv36489' => 'din', 'Dinv41486' => 'din', 'Duzib147G0469' => 'dzi', 'Duzib168G0060' => 'dzi', 'Duzib187G1215' => 'dzi', 'Duzib248G0692' => 'dzi', 'Duzib251G0767' => 'dzi', 'Duzib264G0446' => 'dzi', 'Duzib268G0691' => 'dzi', 'ECA232G4767' => 'eca', 'ECA233G2838' => 'eca', 'ECA234G0391' => 'eca', 'ECA234G0857' => 'eca', 'ECA236G1593' => 'eca', 'ECA238G0565' => 'eca', 'ECA246G1027' => 'eca', 'ECA246G3223' => 'eca', 'ECA246G3470' => 'eca', 'EL10Ac6g13829' => 'bvu', 'EL10Ac6g14093' => 'bvu', 'EL10Ac8g18707' => 'bvu', 'Eucgr.C01369' => 'egr', 'Eucgr.H02492' => 'egr', 'Eucgr.I01733' => 'egr', 'Eucgr.J02255' => 'egr', 'Eucgr.J02257' => 'egr', 'Eucgr.J02258' => 'egr', 'FAN02G1601' => 'fan', 'FAN03G1586' => 'fan', 'FAN03G2986' => 'fan', 'FAN05G4837' => 'fan', 'FAN06G0146' => 'fan', 'FAN07G0858' => 'fan', 'FAN09G3179' => 'fan', 'FAN10G0669' => 'fan', 'FAN12G2358' => 'fan', 'FAN14G4198' => 'fan', 'FAN14G5112' => 'fan', 'FAN17G0342' => 'fan', 'FAN19G0342' => 'fan', 'FAN19G0962' => 'fan', 'FAN19G1101' => 'fan', 'FAN19G1872' => 'fan', 'FAN22G0356' => 'fan', 'FAN23G0744' => 'fan', 'FAN23G1914' => 'fan', 'FAN26G0032' => 'fan', 'FAN28G0625' => 'fan', 'FvH4_1g02710' => 'fve', 'FvH4_1g02720' => 'fve', 'FvH4_4g25670' => 'fve', 'FvH4_6g51700' => 'fve', 'FvH4_7g20170' => 'fve', 'Glyma.05G175000' => 'gma', 'Glyma.08G132300' => 'gma', 'Glyma.11G243000' => 'gma', 'Glyma.13G158900' => 'gma', 'Glyma.17G112400' => 'gma', 'Glyma.18G014100' => 'gma', 'Glyma.19G003100' => 'gma', 'Glyma.19G056500' => 'gma', 'Gohir.A01G158900' => 'ghi', 'Gohir.A05G312600' => 'ghi', 'Gohir.A05G354900' => 'ghi', 'Gohir.A07G037200' => 'ghi', 'Gohir.A09G030000' => 'ghi', 'Gohir.A12G145200' => 'ghi', 'Gohir.D01G151500' => 'ghi', 'Gohir.D04G058300' => 'ghi', 'Gohir.D05G314100' => 'ghi', 'Gohir.D07G041400' => 'ghi', 'Gohir.D09G029700' => 'ghi', 'Gohir.D12G149700' => 'ghi', 'Gorai.001G043800' => 'gra', 'Gorai.002G187800' => 'gra', 'Gorai.006G034700' => 'gra', 'Gorai.008G161200' => 'gra', 'Gorai.009G335700' => 'gra', 'Gorai.012G065000' => 'gra', 'GSVIVG01000535001' => 'vvi', 'GSVIVG01015572001' => 'vvi', 'GSVIVG01032386001' => 'vvi', 'HanXRQChr05g0138531' => 'han', 'HanXRQChr06g0174391' => 'han', 'HanXRQChr07g0199021' => 'han', 'HanXRQChr08g0208211' => 'han', 'HanXRQChr09g0255471' => 'han', 'HanXRQChr10g0315791' => 'han', 'HanXRQChr12g0371991' => 'han', 'HanXRQChr15g0475251' => 'han', 'HanXRQChr17g0540001' => 'han', 'HanXRQChr17g0548631' => 'han', 'HanXRQChr17g0569561' => 'han', 'Haze_12256' => 'cav', 'Haze_14756' => 'cav', 'Haze_25528' => 'cav', 'Hma1.2p1_0079F.1_g041020' => 'hma', 'Hma1.2p1_0818F.1_g223260' => 'hma', 'Hma1.2p1_1747F.1_g300530' => 'hma', 'HPP92_004607' => 'vpl', 'HPP92_004608' => 'vpl', 'HPP92_006181' => 'vpl', 'HPP92_012192' => 'vpl', 'HPP92_015680' => 'vpl', 'HPP92_020249' => 'vpl', 'HPP92_021376' => 'vpl', 'HPP92_024275' => 'vpl', 'Hund06031' => 'sun', 'Hund25391' => 'sun', 'Lalb_Chr07g0185371' => 'lal', 'Lalb_Chr07g0185381' => 'lal', 'Lalb_Chr12g0204011' => 'lal', 'Lalb_Chr13g0301671' => 'lal', 'Lalb_Chr14g0362851' => 'lal', 'Lalb_Chr24g0403581' => 'lal', 'Lj1g0000233' => 'lja', 'Lj2g0018120' => 'lja', 'Lj3C621T0' => 'lonja', 'Lj3P1059T14' => 'lonja', 'Lj3P611T9' => 'lonja', 'Lj3P614T13' => 'lonja', 'Lj3P615T5' => 'lonja', 'Lj4g0012315' => 'lja', 'Lj4g0026182' => 'lja', 'Lj6P813T16' => 'lonja', 'Lj7C427T7' => 'lonja', 'Lj7C427T8' => 'lonja', 'Lj7P600T41' => 'lonja', 'Lju41C42G17' => 'lonja', 'Lsat_1_v5_gn_0_47300' => 'lsa', 'Lsat_1_v5_gn_2_91280' => 'lsa', 'Lsat_1_v5_gn_3_30561' => 'lsa', 'Lsat_1_v5_gn_4_184321' => 'lsa', 'Lsat_1_v5_gn_4_4041' => 'lsa', 'Lsat_1_v5_gn_5_92000' => 'lsa', 'Lsat_1_v5_gn_8_152940' => 'lsa', 'Lsat_1_v5_gn_8_62401' => 'lsa', 'Manes.06G055900' => 'mes', 'Manes.12G022200' => 'mes', 'Manes.13G023300' => 'mes', 'Manes.14G115000' => 'mes', 'Manes.15G151700' => 'mes', 'Manes.17G111300' => 'mes', 'Mapoly0226s0009' => 'mpo', 'MBI02_g25363_MAGBIO' => 'mbi', 'MBI06_g00027_MAGBIO' => 'mbi', 'MBI10_g13034_MAGBIO' => 'mbi', 'MD09G1023400' => 'mdo', 'MD13G1100100' => 'mdo', 'MD15G1169200' => 'mdo', 'MD16G1101100' => 'mdo', 'MD17G1022900' => 'mdo', 'Medtr3g096150' => 'mtr', 'Medtr4g115070' => 'mtr', 'Medtr7g033325' => 'mtr', 'Medtr8g089840' => 'mtr', 'MELO3C010319.2' => 'cme', 'MELO3C011944.2' => 'cme', 'MELO3C021589.2' => 'cme', 'Migut.E00207' => 'egut', 'Migut.H00067' => 'egut', 'Migut.K00433' => 'egut', 'Migut.K00606' => 'egut', 'Migut.K01410' => 'egut', 'MSTRG.13347' => 'ama', 'MSTRG.24045' => 'ama', 'MSTRG.2428' => 'ama', 'MSTRG.26410' => 'ama', 'MSTRG.3139' => 'ama', 'MSTRG.3286' => 'ama', 'MSTRG.563' => 'ama', 'MSTRG.7941' => 'ama', 'Nitab4.5_0000028g0060' => 'nta', 'Nitab4.5_0000065g0260' => 'nta', 'Nitab4.5_0000112g0060' => 'nta', 'Nitab4.5_0000489g0120' => 'nta', 'Nitab4.5_0001776g0050' => 'nta', 'Nitab4.5_0001854g0010' => 'nta', 'Nitab4.5_0001860g0020' => 'nta', 'Nitab4.5_0004352g0010' => 'nta', 'Nitab4.5_0008716g0020' => 'nta', 'Nitab4.5_0008922g0010' => 'nta', 'Nn3g16693' => 'nnu', 'Nn4g22596' => 'nnu', 'Nn7g37639' => 'nnu', 'Oeu001701.1' => 'oeu', 'Oeu018149.1' => 'oeu', 'Oeu026220.1' => 'oeu', 'Oeu038635.1' => 'oeu', 'Oeu049176.1' => 'oeu', 'Oeu056706.1' => 'oeu', 'Oeu056937.1' => 'oeu', 'Oeu057540.1' => 'oeu', 'Os02g0594900' => 'osa', 'Os02g0595100' => 'osa', 'Os04g0477500' => 'osa', 'Os12g0611900' => 'osa', 'Peaxi162Scf00076g00020' => 'pax', 'Peaxi162Scf00128g00217' => 'pax', 'Peaxi162Scf00129g01640' => 'pax', 'Peaxi162Scf00669g00007' => 'pax', 'Peaxi162Scf00700g00421' => 'pax', 'Peaxi162Scf00801g00038' => 'pax', 'Peaxi162Scf00891g00025' => 'pax', 'PGR083G0909' => 'pgr', 'PGR119G1005' => 'pgr', 'PGR142G2236' => 'pgr', 'PGR142G3388' => 'pgr', 'PGSC0003DMG400004514' => 'stu', 'PGSC0003DMG400012635' => 'stu', 'PGSC0003DMG400015730' => 'stu', 'PGSC0003DMG400018611' => 'stu', 'PGSC0003DMG400030897' => 'stu', 'Phvul.001G254800' => 'pvu', 'Phvul.002G260100' => 'pvu', 'Phvul.003G167600' => 'pvu', 'Phvul.004G005100' => 'pvu', 'Potri.001G343600' => 'ptr', 'Potri.006G066700' => 'ptr', 'Potri.008G186000' => 'ptr', 'Potri.010G046900' => 'ptr', 'Potri.018G127900' => 'ptr', 'Pp3c20_17750' => 'ppa', 'Pp3c24_4380' => 'ppa', 'Prupe.1G245800' => 'ppe', 'Prupe.3G293400' => 'ppe', 'Prupe.7G247400' => 'ppe', 'Psat0s145g0120' => 'psa', 'Psat0s595g0040' => 'psa', 'Psat0s595g0120' => 'psa', 'Psat3g175040' => 'psa', 'Psat7g058120' => 'psa', 'PSO017G0428' => 'pso', 'PSO063G7510' => 'pso', 'PSO067G0046' => 'pso', 'PSO478G1073' => 'pso', 'PSO675G3677' => 'pso', 'PSO675G6558' => 'pso', 'PSO675G7520' => 'pso', 'PSO675G8959' => 'pso', 'QL02p074089' => 'qlo', 'QL02p089614' => 'qlo', 'QL03p057736' => 'qlo', 'RcHm_v2.0_Chr1g0364131' => 'rch', 'RcHm_v2.0_Chr2g0087801' => 'rch', 'RcHm_v2.0_Chr2g0087821' => 'rch', 'RcHm_v2.0_Chr2g0173231' => 'rch', 'RcHm_v2.0_Chr4g0433111' => 'rch', 'Rhsim03G0250300' => 'rsi', 'Rhsim08G0048400' => 'rsi', 'Rhsim10G0014800' => 'rsi', 'Rhsim12G0040100' => 'rsi', 'Rhsim12G0109700' => 'rsi', 'Sabra06G0049600' => 'sbr', 'Sabra08G0141000' => 'sbr', 'Sabra10G0021400' => 'sbr', 'Sabra16G0222900' => 'sbr', 'Sabra18G0108600' => 'sbr', 'SalBow1G0433' => 'sbo', 'SalBow1G2038' => 'sbo', 'SalBow1G5003' => 'sbo', 'SalBow7G1197' => 'sbo', 'SalBow8G3506' => 'sbo', 'Sc03g0007300' => 'sci', 'Sc11g0000950' => 'sci', 'Sc14g0008750' => 'sci', 'Sc18g0000420' => 'sci', 'Sed0006754' => 'sed', 'Sed0008741' => 'sed', 'Sed0017172' => 'sed', 'Sed0018925' => 'sed', 'Sed0023326' => 'sed', 'Sed0025909' => 'sed', 'SEGI_05333' => 'sgi', 'SEGI_10362' => 'sgi', 'SEGI_13380' => 'sgi', 'SEGI_24306' => 'sgi', 'SEGI_29077' => 'sgi', 'SEGI_29095' => 'sgi', 'SEGI_36534' => 'sgi', 'SEGI_37506' => 'sgi', 'SEGI_38321' => 'sgi', 'SGA_v2.0_scaffold307G48031' => 'sas', 'SGA_v2.0_scaffold47G17507' => 'sas', 'SGA_v2.0_scaffold63G21736' => 'sas', 'SGA_v2.0_scaffold87G27070' => 'sas', 'SHI17794' => 'shi', 'SHI28851' => 'shi', 'SMO165G0155' => 'smo', 'SMO340G0217' => 'smo', 'SMO367G1210' => 'smo', 'Solyc02g093430.3' => 'sly', 'Solyc05g013580.4' => 'sly', 'Solyc07g008030.3' => 'sly', 'Solyc12g035470.2' => 'sly', 'Sopen02g038020' => 'spe', 'Sopen05g008490' => 'spe', 'Sopen07g003910' => 'spe', 'Sopen12g015240' => 'spe', 'Sp1g11550' => 'spa', 'Sp2g16710' => 'spa', 'Sp3g00430' => 'spa', 'Sp3g26780' => 'spa', 'Sp5g22900' => 'spa', 'Sp6g29530' => 'spa', 'TAR371G0794' => 'tar', 'TAR374G0164' => 'tar', 'TAR622G0165' => 'tar', 'TAR626G0929' => 'tar', 'TAR629G2155' => 'tar', 'THA.LOC104805282' => 'tha', 'THA.LOC104805363' => 'tha', 'THA.LOC104808968' => 'tha', 'THA.LOC104821093' => 'tha', 'THA.LOC104823953' => 'tha', 'THA.LOC104825562' => 'tha', 'THA.LOC104825665' => 'tha', 'Thecc.02G261400' => 'tca', 'Thecc.04G019200' => 'tca', 'Thecc.09G130400' => 'tca', 'Thhalv10004374m.g' => 'esa', 'Thhalv10007850m.g' => 'esa', 'Thhalv10013782m.g' => 'esa', 'Thhalv10018686m.g' => 'esa', 'Thhalv10020899m.g' => 'esa', 'Thhalv10022755m.g' => 'esa', 'TPR.G23851' => 'tpr', 'TPR.G26500' => 'tpr', 'TPR.G27267' => 'tpr', 'TPR.G32001' => 'tpr', 'TPR.G6251' => 'tpr', 'TPR.G8167' => 'tpr', 'TWI12G1330' => 'twi', 'TWI18G1239' => 'twi', 'TWI34G0979' => 'twi', 'TWI36G0670' => 'twi', 'TWI36G0707' => 'twi', 'TWI56G0233' => 'twi', 'TWI75G1809' => 'twi', 'unitig_21.g20874' => 'ugi', 'unitig_26.g10343' => 'ugi', 'unitig_46.g18392' => 'ugi', 'unitig_52.g17178' => 'ugi', 'unitig_8.g2934' => 'ugi', 'vmacro01122' => 'vma', 'vmacro05875' => 'vma', 'vmacro06147' => 'vma', 'vmacro16191' => 'vma', 'vmacro18293' => 'vma', 'VMungo0251G3707' => 'vmu', 'VMungo0464G1521' => 'vmu', 'VMungo1215G0205' => 'vmu', 'VMungo1383G2484' => 'vmu', 'Zm00001eb079610' => 'zma', 'Zm00001eb135990' => 'zma', 'Zm00001eb183710' => 'zma', 'Zm00001eb246020' => 'zma' ), 'gf_id' => 'HOM05D001124', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001124' ), 'data_identifier' => 'HOM05D001124', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001124', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '548', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02520' => 'bna', 'A03p06630' => 'bna', 'A05p44460' => 'bna', 'A06p08710' => 'bna', 'A06p41090' => 'bna', 'A07p32320' => 'bna', 'A08p32520' => 'bna', 'A09p10360' => 'bna', 'A10p24080' => 'bna', 'Aa31LG11G15250' => 'aar', 'Aa31LG1G1800' => 'aar', 'Aa31LG2G5120' => 'aar', 'Aa31LG2G6070' => 'aar', 'Aa31LG5G10770' => 'aar', 'Aa31sc61G90' => 'aar', 'Actinidia01352' => 'ach', 'Actinidia05983' => 'ach', 'Actinidia08133' => 'ach', 'Actinidia15101' => 'ach', 'Actinidia26379' => 'ach', 'Actinidia35778' => 'ach', 'Actinidia36123' => 'ach', 'Actinidia37436' => 'ach', 'Actinidia38730' => 'ach', 'Ah.02g128210' => 'amhyb', 'Ah.03g132990' => 'amhyb', 'Ah.14g079410' => 'amhyb', 'AL1G24640' => 'aly', 'AL2G26680' => 'aly', 'AL3G10530' => 'aly', 'AL3G45230' => 'aly', 'AL5G15230' => 'aly', 'AL5G16960' => 'aly', 'AL6G25210' => 'aly', 'Aqoxy2G00441' => 'aox', 'Aqoxy3G01236' => 'aox', 'Aqoxy5G03746' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3RQ047' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C7GMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9C8JER' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MBL6KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YXCZ83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZANX40' => 'arhy', 'AT1G12990' => 'ath', 'AT1G67880' => 'ath', 'AT2G13290' => 'ath', 'AT3G01620' => 'ath', 'AT3G26445' => 'ath', 'AT3G27540' => 'ath', 'AT5G14480' => 'ath', 'ATR0824G026' => 'atr', 'ATR1098G019' => 'atr', 'Atru.chr11.2145' => 'acertr', 'Atru.chr2.3636' => 'acertr', 'Atru.chr2.3644' => 'acertr', 'Atru.chr6.2422' => 'acertr', 'Atru.chr7.1112' => 'acertr', 'AUR62005469' => 'cqu', 'AUR62011166' => 'cqu', 'AUR62013319' => 'cqu', 'AUR62024273' => 'cqu', 'AUR62028420' => 'cqu', 'AUR62041942' => 'cqu', 'BcaB01g04969' => 'bca', 'BcaB01g06371' => 'bca', 'BcaB02g11494' => 'bca', 'BcaB03g15382' => 'bca', 'BcaB08g36994' => 'bca', 'BcaC03g13477' => 'bca', 'BcaC03g13478' => 'bca', 'BcaC03g13480' => 'bca', 'BcaC03g13481' => 'bca', 'BcaC03g13486' => 'bca', 'BcaC04g19031' => 'bca', 'BcaC04g23085' => 'bca', 'BcaC05g25094' => 'bca', 'BcaC05g25096' => 'bca', 'BcaC05g25138' => 'bca', 'BcaC05g30416' => 'bca', 'BcaC05g30455' => 'bca', 'BcaC06g30979' => 'bca', 'BcaC06g33805' => 'bca', 'BcaC08g46021' => 'bca', 'BcaNung03154' => 'bca', 'BolC2t06623H' => 'bol', 'BolC2t06632H' => 'bol', 'BolC2t06635H' => 'bol', 'BolC2t06638H' => 'bol', 'BolC3t13266H' => 'bol', 'BolC5t29776H' => 'bol', 'BolC6t38912H' => 'bol', 'BolC7t44183H' => 'bol', 'BolC9t54123H' => 'bol', 'BolC9t59107H' => 'bol', 'BraA02t05221Z' => 'bra', 'BraA03t09996Z' => 'bra', 'BraA05t23210Z' => 'bra', 'BraA06t24068Z' => 'bra', 'BraA06t27032Z' => 'bra', 'BraA08t35176Z' => 'bra', 'BraA09t36680Z' => 'bra', 'BraA10t44471Z' => 'bra', 'C02p06760' => 'bna', 'C02p06890' => 'bna', 'C02p07010' => 'bna', 'C03p07660' => 'bna', 'C05p10300' => 'bna', 'C06p38150' => 'bna', 'C07p36650' => 'bna', 'C08p15770' => 'bna', 'C09p12300' => 'bna', 'C09p62700' => 'bna', 'C09p75040' => 'bna', 'CAN.G13.1' => 'can', 'CAN.G138.4' => 'can', 'CAN.G44.6' => 'can', 'CAN.G473.19' => 'can', 'CANSAT01G0835' => 'cansat', 'CANSAT11G0246' => 'cansat', 'CANSAT11G1766' => 'cansat', 'CANSAT64G1954' => 'cansat', 'CARHR013330' => 'chi', 'CARHR060530' => 'chi', 'CARHR075300' => 'chi', 'CARHR105120' => 'chi', 'CARHR148910' => 'chi', 'CARHR198830' => 'chi', 'Carub.0001s1275' => 'cru', 'Carub.0002s1437' => 'cru', 'Carub.0003s0044' => 'cru', 'Carub.0003s2787' => 'cru', 'Carub.0005s0597' => 'cru', 'Carub.0006s1266' => 'cru', 'Ca_06935_v3' => 'car', 'Ca_13559_v3' => 'car', 'Ca_16941_v3' => 'car', 'Ca_16960_v3' => 'car', 'Ca_17775_v3' => 'car', 'Ca_30464_v3' => 'car', 'Cc06_g08160' => 'ccan', 'Cc07_g01520' => 'ccan', 'Cc11_g15810' => 'ccan', 'CDE02G2840' => 'cde', 'CDE03G0093' => 'cde', 'CDE04G2127' => 'cde', 'CDE07G1857' => 'cde', 'CDE09G1246' => 'cde', 'Cfa003412' => 'cfa', 'Cfa007341' => 'cfa', 'Cfa009220' => 'cfa', 'Ciclev10008737m.g' => 'ccl', 'Ciclev10015565m.g' => 'ccl', 'Ciclev10031761m.g' => 'ccl', 'CiPaw.03G045300' => 'cil', 'CiPaw.03G247200' => 'cil', 'CiPaw.04G029500' => 'cil', 'CiPaw.04G174000' => 'cil', 'CiPaw.05G181200' => 'cil', 'CiPaw.06G067100' => 'cil', 'ClCG05G025800' => 'cla', 'ClCG06G011400' => 'cla', 'ClCG09G019360' => 'cla', 'COL.COLO4_04827' => 'col', 'COL.COLO4_29170' => 'col', 'COL.COLO4_35131' => 'col', 'COL.COLO4_35132' => 'col', 'Cpa.g.sc33.32' => 'cpa', 'Cpa.g.sc46.29' => 'cpa', 'Cpa.g.sc796.1' => 'cpa', 'CsaV3_1G030420' => 'csa', 'CsaV3_5G027050' => 'csa', 'CsaV3_5G031040' => 'csa', 'CsaV3_UNG023130' => 'csa', 'CSS0007726' => 'camsi', 'CSS0016433' => 'camsi', 'CSS0017656' => 'camsi', 'CSS0025364' => 'camsi', 'CSS0027582' => 'camsi', 'CSS0047288' => 'camsi', 'CSS0049950' => 'camsi', 'DCAR_003843' => 'dca', 'DCAR_007052' => 'dca', 'DCAR_020884' => 'dca', 'DCAR_021730' => 'dca', 'DCAR_024423' => 'dca', 'DCAR_026509' => 'dca', 'DCAR_031158' => 'dca', 'Dinv14728' => 'din', 'Dinv15219' => 'din', 'Dinv25728' => 'din', 'Dinv33428' => 'din', 'Dinv36489' => 'din', 'Dinv41486' => 'din', 'Duzib147G0469' => 'dzi', 'Duzib168G0060' => 'dzi', 'Duzib187G1215' => 'dzi', 'Duzib248G0692' => 'dzi', 'Duzib251G0767' => 'dzi', 'Duzib264G0446' => 'dzi', 'Duzib268G0691' => 'dzi', 'ECA232G4767' => 'eca', 'ECA233G2838' => 'eca', 'ECA234G0391' => 'eca', 'ECA234G0857' => 'eca', 'ECA236G1593' => 'eca', 'ECA238G0565' => 'eca', 'ECA246G1027' => 'eca', 'ECA246G3223' => 'eca', 'ECA246G3470' => 'eca', 'EL10Ac6g13829' => 'bvu', 'EL10Ac6g14093' => 'bvu', 'EL10Ac8g18707' => 'bvu', 'Eucgr.C01369' => 'egr', 'Eucgr.H02492' => 'egr', 'Eucgr.I01733' => 'egr', 'Eucgr.J02255' => 'egr', 'Eucgr.J02257' => 'egr', 'Eucgr.J02258' => 'egr', 'FAN02G1601' => 'fan', 'FAN03G1586' => 'fan', 'FAN03G2986' => 'fan', 'FAN05G4837' => 'fan', 'FAN06G0146' => 'fan', 'FAN07G0858' => 'fan', 'FAN09G3179' => 'fan', 'FAN10G0669' => 'fan', 'FAN12G2358' => 'fan', 'FAN14G4198' => 'fan', 'FAN14G5112' => 'fan', 'FAN17G0342' => 'fan', 'FAN19G0342' => 'fan', 'FAN19G0962' => 'fan', 'FAN19G1101' => 'fan', 'FAN19G1872' => 'fan', 'FAN22G0356' => 'fan', 'FAN23G0744' => 'fan', 'FAN23G1914' => 'fan', 'FAN26G0032' => 'fan', 'FAN28G0625' => 'fan', 'FvH4_1g02710' => 'fve', 'FvH4_1g02720' => 'fve', 'FvH4_4g25670' => 'fve', 'FvH4_6g51700' => 'fve', 'FvH4_7g20170' => 'fve', 'Glyma.05G175000' => 'gma', 'Glyma.08G132300' => 'gma', 'Glyma.11G243000' => 'gma', 'Glyma.13G158900' => 'gma', 'Glyma.17G112400' => 'gma', 'Glyma.18G014100' => 'gma', 'Glyma.19G003100' => 'gma', 'Glyma.19G056500' => 'gma', 'Gohir.A01G158900' => 'ghi', 'Gohir.A05G312600' => 'ghi', 'Gohir.A05G354900' => 'ghi', 'Gohir.A07G037200' => 'ghi', 'Gohir.A09G030000' => 'ghi', 'Gohir.A12G145200' => 'ghi', 'Gohir.D01G151500' => 'ghi', 'Gohir.D04G058300' => 'ghi', 'Gohir.D05G314100' => 'ghi', 'Gohir.D07G041400' => 'ghi', 'Gohir.D09G029700' => 'ghi', 'Gohir.D12G149700' => 'ghi', 'Gorai.001G043800' => 'gra', 'Gorai.002G187800' => 'gra', 'Gorai.006G034700' => 'gra', 'Gorai.008G161200' => 'gra', 'Gorai.009G335700' => 'gra', 'Gorai.012G065000' => 'gra', 'GSVIVG01000535001' => 'vvi', 'GSVIVG01015572001' => 'vvi', 'GSVIVG01032386001' => 'vvi', 'HanXRQChr05g0138531' => 'han', 'HanXRQChr06g0174391' => 'han', 'HanXRQChr07g0199021' => 'han', 'HanXRQChr08g0208211' => 'han', 'HanXRQChr09g0255471' => 'han', 'HanXRQChr10g0315791' => 'han', 'HanXRQChr12g0371991' => 'han', 'HanXRQChr15g0475251' => 'han', 'HanXRQChr17g0540001' => 'han', 'HanXRQChr17g0548631' => 'han', 'HanXRQChr17g0569561' => 'han', 'Haze_12256' => 'cav', 'Haze_14756' => 'cav', 'Haze_25528' => 'cav', 'Hma1.2p1_0079F.1_g041020' => 'hma', 'Hma1.2p1_0818F.1_g223260' => 'hma', 'Hma1.2p1_1747F.1_g300530' => 'hma', 'HPP92_004607' => 'vpl', 'HPP92_004608' => 'vpl', 'HPP92_006181' => 'vpl', 'HPP92_012192' => 'vpl', 'HPP92_015680' => 'vpl', 'HPP92_020249' => 'vpl', 'HPP92_021376' => 'vpl', 'HPP92_024275' => 'vpl', 'Hund06031' => 'sun', 'Hund25391' => 'sun', 'Lalb_Chr07g0185371' => 'lal', 'Lalb_Chr07g0185381' => 'lal', 'Lalb_Chr12g0204011' => 'lal', 'Lalb_Chr13g0301671' => 'lal', 'Lalb_Chr14g0362851' => 'lal', 'Lalb_Chr24g0403581' => 'lal', 'Lj1g0000233' => 'lja', 'Lj2g0018120' => 'lja', 'Lj3C621T0' => 'lonja', 'Lj3P1059T14' => 'lonja', 'Lj3P611T9' => 'lonja', 'Lj3P614T13' => 'lonja', 'Lj3P615T5' => 'lonja', 'Lj4g0012315' => 'lja', 'Lj4g0026182' => 'lja', 'Lj6P813T16' => 'lonja', 'Lj7C427T7' => 'lonja', 'Lj7C427T8' => 'lonja', 'Lj7P600T41' => 'lonja', 'Lju41C42G17' => 'lonja', 'Lsat_1_v5_gn_0_47300' => 'lsa', 'Lsat_1_v5_gn_2_91280' => 'lsa', 'Lsat_1_v5_gn_3_30561' => 'lsa', 'Lsat_1_v5_gn_4_184321' => 'lsa', 'Lsat_1_v5_gn_4_4041' => 'lsa', 'Lsat_1_v5_gn_5_92000' => 'lsa', 'Lsat_1_v5_gn_8_152940' => 'lsa', 'Lsat_1_v5_gn_8_62401' => 'lsa', 'Manes.06G055900' => 'mes', 'Manes.12G022200' => 'mes', 'Manes.13G023300' => 'mes', 'Manes.14G115000' => 'mes', 'Manes.15G151700' => 'mes', 'Manes.17G111300' => 'mes', 'Mapoly0226s0009' => 'mpo', 'MBI02_g25363_MAGBIO' => 'mbi', 'MBI06_g00027_MAGBIO' => 'mbi', 'MBI10_g13034_MAGBIO' => 'mbi', 'MD09G1023400' => 'mdo', 'MD13G1100100' => 'mdo', 'MD15G1169200' => 'mdo', 'MD16G1101100' => 'mdo', 'MD17G1022900' => 'mdo', 'Medtr3g096150' => 'mtr', 'Medtr4g115070' => 'mtr', 'Medtr7g033325' => 'mtr', 'Medtr8g089840' => 'mtr', 'MELO3C010319.2' => 'cme', 'MELO3C011944.2' => 'cme', 'MELO3C021589.2' => 'cme', 'Migut.E00207' => 'egut', 'Migut.H00067' => 'egut', 'Migut.K00433' => 'egut', 'Migut.K00606' => 'egut', 'Migut.K01410' => 'egut', 'MSTRG.13347' => 'ama', 'MSTRG.24045' => 'ama', 'MSTRG.2428' => 'ama', 'MSTRG.26410' => 'ama', 'MSTRG.3139' => 'ama', 'MSTRG.3286' => 'ama', 'MSTRG.563' => 'ama', 'MSTRG.7941' => 'ama', 'Nitab4.5_0000028g0060' => 'nta', 'Nitab4.5_0000065g0260' => 'nta', 'Nitab4.5_0000112g0060' => 'nta', 'Nitab4.5_0000489g0120' => 'nta', 'Nitab4.5_0001776g0050' => 'nta', 'Nitab4.5_0001854g0010' => 'nta', 'Nitab4.5_0001860g0020' => 'nta', 'Nitab4.5_0004352g0010' => 'nta', 'Nitab4.5_0008716g0020' => 'nta', 'Nitab4.5_0008922g0010' => 'nta', 'Nn3g16693' => 'nnu', 'Nn4g22596' => 'nnu', 'Nn7g37639' => 'nnu', 'Oeu001701.1' => 'oeu', 'Oeu018149.1' => 'oeu', 'Oeu026220.1' => 'oeu', 'Oeu038635.1' => 'oeu', 'Oeu049176.1' => 'oeu', 'Oeu056706.1' => 'oeu', 'Oeu056937.1' => 'oeu', 'Oeu057540.1' => 'oeu', 'Os02g0594900' => 'osa', 'Os02g0595100' => 'osa', 'Os04g0477500' => 'osa', 'Os12g0611900' => 'osa', 'Peaxi162Scf00076g00020' => 'pax', 'Peaxi162Scf00128g00217' => 'pax', 'Peaxi162Scf00129g01640' => 'pax', 'Peaxi162Scf00669g00007' => 'pax', 'Peaxi162Scf00700g00421' => 'pax', 'Peaxi162Scf00801g00038' => 'pax', 'Peaxi162Scf00891g00025' => 'pax', 'PGR083G0909' => 'pgr', 'PGR119G1005' => 'pgr', 'PGR142G2236' => 'pgr', 'PGR142G3388' => 'pgr', 'PGSC0003DMG400004514' => 'stu', 'PGSC0003DMG400012635' => 'stu', 'PGSC0003DMG400015730' => 'stu', 'PGSC0003DMG400018611' => 'stu', 'PGSC0003DMG400030897' => 'stu', 'Phvul.001G254800' => 'pvu', 'Phvul.002G260100' => 'pvu', 'Phvul.003G167600' => 'pvu', 'Phvul.004G005100' => 'pvu', 'Potri.001G343600' => 'ptr', 'Potri.006G066700' => 'ptr', 'Potri.008G186000' => 'ptr', 'Potri.010G046900' => 'ptr', 'Potri.018G127900' => 'ptr', 'Pp3c20_17750' => 'ppa', 'Pp3c24_4380' => 'ppa', 'Prupe.1G245800' => 'ppe', 'Prupe.3G293400' => 'ppe', 'Prupe.7G247400' => 'ppe', 'Psat0s145g0120' => 'psa', 'Psat0s595g0040' => 'psa', 'Psat0s595g0120' => 'psa', 'Psat3g175040' => 'psa', 'Psat7g058120' => 'psa', 'PSO017G0428' => 'pso', 'PSO063G7510' => 'pso', 'PSO067G0046' => 'pso', 'PSO478G1073' => 'pso', 'PSO675G3677' => 'pso', 'PSO675G6558' => 'pso', 'PSO675G7520' => 'pso', 'PSO675G8959' => 'pso', 'QL02p074089' => 'qlo', 'QL02p089614' => 'qlo', 'QL03p057736' => 'qlo', 'RcHm_v2.0_Chr1g0364131' => 'rch', 'RcHm_v2.0_Chr2g0087801' => 'rch', 'RcHm_v2.0_Chr2g0087821' => 'rch', 'RcHm_v2.0_Chr2g0173231' => 'rch', 'RcHm_v2.0_Chr4g0433111' => 'rch', 'Rhsim03G0250300' => 'rsi', 'Rhsim08G0048400' => 'rsi', 'Rhsim10G0014800' => 'rsi', 'Rhsim12G0040100' => 'rsi', 'Rhsim12G0109700' => 'rsi', 'Sabra06G0049600' => 'sbr', 'Sabra08G0141000' => 'sbr', 'Sabra10G0021400' => 'sbr', 'Sabra16G0222900' => 'sbr', 'Sabra18G0108600' => 'sbr', 'SalBow1G0433' => 'sbo', 'SalBow1G2038' => 'sbo', 'SalBow1G5003' => 'sbo', 'SalBow7G1197' => 'sbo', 'SalBow8G3506' => 'sbo', 'Sc03g0007300' => 'sci', 'Sc11g0000950' => 'sci', 'Sc14g0008750' => 'sci', 'Sc18g0000420' => 'sci', 'Sed0006754' => 'sed', 'Sed0008741' => 'sed', 'Sed0017172' => 'sed', 'Sed0018925' => 'sed', 'Sed0023326' => 'sed', 'Sed0025909' => 'sed', 'SEGI_05333' => 'sgi', 'SEGI_10362' => 'sgi', 'SEGI_13380' => 'sgi', 'SEGI_24306' => 'sgi', 'SEGI_29077' => 'sgi', 'SEGI_29095' => 'sgi', 'SEGI_36534' => 'sgi', 'SEGI_37506' => 'sgi', 'SEGI_38321' => 'sgi', 'SGA_v2.0_scaffold307G48031' => 'sas', 'SGA_v2.0_scaffold47G17507' => 'sas', 'SGA_v2.0_scaffold63G21736' => 'sas', 'SGA_v2.0_scaffold87G27070' => 'sas', 'SHI17794' => 'shi', 'SHI28851' => 'shi', 'SMO165G0155' => 'smo', 'SMO340G0217' => 'smo', 'SMO367G1210' => 'smo', 'Solyc02g093430.3' => 'sly', 'Solyc05g013580.4' => 'sly', 'Solyc07g008030.3' => 'sly', 'Solyc12g035470.2' => 'sly', 'Sopen02g038020' => 'spe', 'Sopen05g008490' => 'spe', 'Sopen07g003910' => 'spe', 'Sopen12g015240' => 'spe', 'Sp1g11550' => 'spa', 'Sp2g16710' => 'spa', 'Sp3g00430' => 'spa', 'Sp3g26780' => 'spa', 'Sp5g22900' => 'spa', 'Sp6g29530' => 'spa', 'TAR371G0794' => 'tar', 'TAR374G0164' => 'tar', 'TAR622G0165' => 'tar', 'TAR626G0929' => 'tar', 'TAR629G2155' => 'tar', 'THA.LOC104805282' => 'tha', 'THA.LOC104805363' => 'tha', 'THA.LOC104808968' => 'tha', 'THA.LOC104821093' => 'tha', 'THA.LOC104823953' => 'tha', 'THA.LOC104825562' => 'tha', 'THA.LOC104825665' => 'tha', 'Thecc.02G261400' => 'tca', 'Thecc.04G019200' => 'tca', 'Thecc.09G130400' => 'tca', 'Thhalv10004374m.g' => 'esa', 'Thhalv10007850m.g' => 'esa', 'Thhalv10013782m.g' => 'esa', 'Thhalv10018686m.g' => 'esa', 'Thhalv10020899m.g' => 'esa', 'Thhalv10022755m.g' => 'esa', 'TPR.G23851' => 'tpr', 'TPR.G26500' => 'tpr', 'TPR.G27267' => 'tpr', 'TPR.G32001' => 'tpr', 'TPR.G6251' => 'tpr', 'TPR.G8167' => 'tpr', 'TWI12G1330' => 'twi', 'TWI18G1239' => 'twi', 'TWI34G0979' => 'twi', 'TWI36G0670' => 'twi', 'TWI36G0707' => 'twi', 'TWI56G0233' => 'twi', 'TWI75G1809' => 'twi', 'unitig_21.g20874' => 'ugi', 'unitig_26.g10343' => 'ugi', 'unitig_46.g18392' => 'ugi', 'unitig_52.g17178' => 'ugi', 'unitig_8.g2934' => 'ugi', 'vmacro01122' => 'vma', 'vmacro05875' => 'vma', 'vmacro06147' => 'vma', 'vmacro16191' => 'vma', 'vmacro18293' => 'vma', 'VMungo0251G3707' => 'vmu', 'VMungo0464G1521' => 'vmu', 'VMungo1215G0205' => 'vmu', 'VMungo1383G2484' => 'vmu', 'Zm00001eb079610' => 'zma', 'Zm00001eb135990' => 'zma', 'Zm00001eb183710' => 'zma', 'Zm00001eb246020' => 'zma' ) $gf_id = 'HOM05D001124' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001124' ) $data_identifier = 'HOM05D001124' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 6, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 7, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 21, 'bol' => (int) 10, 'bra' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 6, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 9, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 21, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 8, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 10, 'lsa' => (int) 8, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 8, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 9, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb246020' $species_info = array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ) $local_species = 'gma' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001124', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '548', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02520' => 'bna', 'A03p06630' => 'bna', 'A05p44460' => 'bna', 'A06p08710' => 'bna', 'A06p41090' => 'bna', 'A07p32320' => 'bna', 'A08p32520' => 'bna', 'A09p10360' => 'bna', 'A10p24080' => 'bna', 'Aa31LG11G15250' => 'aar', 'Aa31LG1G1800' => 'aar', 'Aa31LG2G5120' => 'aar', 'Aa31LG2G6070' => 'aar', 'Aa31LG5G10770' => 'aar', 'Aa31sc61G90' => 'aar', 'Actinidia01352' => 'ach', 'Actinidia05983' => 'ach', 'Actinidia08133' => 'ach', 'Actinidia15101' => 'ach', 'Actinidia26379' => 'ach', 'Actinidia35778' => 'ach', 'Actinidia36123' => 'ach', 'Actinidia37436' => 'ach', 'Actinidia38730' => 'ach', 'Ah.02g128210' => 'amhyb', 'Ah.03g132990' => 'amhyb', 'Ah.14g079410' => 'amhyb', 'AL1G24640' => 'aly', 'AL2G26680' => 'aly', 'AL3G10530' => 'aly', 'AL3G45230' => 'aly', 'AL5G15230' => 'aly', 'AL5G16960' => 'aly', 'AL6G25210' => 'aly', 'Aqoxy2G00441' => 'aox', 'Aqoxy3G01236' => 'aox', 'Aqoxy5G03746' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3RQ047' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C7GMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9C8JER' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MBL6KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YXCZ83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZANX40' => 'arhy', 'AT1G12990' => 'ath', 'AT1G67880' => 'ath', 'AT2G13290' => 'ath', 'AT3G01620' => 'ath', 'AT3G26445' => 'ath', 'AT3G27540' => 'ath', 'AT5G14480' => 'ath', 'ATR0824G026' => 'atr', 'ATR1098G019' => 'atr', 'Atru.chr11.2145' => 'acertr', 'Atru.chr2.3636' => 'acertr', 'Atru.chr2.3644' => 'acertr', 'Atru.chr6.2422' => 'acertr', 'Atru.chr7.1112' => 'acertr', 'AUR62005469' => 'cqu', 'AUR62011166' => 'cqu', 'AUR62013319' => 'cqu', 'AUR62024273' => 'cqu', 'AUR62028420' => 'cqu', 'AUR62041942' => 'cqu', 'BcaB01g04969' => 'bca', 'BcaB01g06371' => 'bca', 'BcaB02g11494' => 'bca', 'BcaB03g15382' => 'bca', 'BcaB08g36994' => 'bca', 'BcaC03g13477' => 'bca', 'BcaC03g13478' => 'bca', 'BcaC03g13480' => 'bca', 'BcaC03g13481' => 'bca', 'BcaC03g13486' => 'bca', 'BcaC04g19031' => 'bca', 'BcaC04g23085' => 'bca', 'BcaC05g25094' => 'bca', 'BcaC05g25096' => 'bca', 'BcaC05g25138' => 'bca', 'BcaC05g30416' => 'bca', 'BcaC05g30455' => 'bca', 'BcaC06g30979' => 'bca', 'BcaC06g33805' => 'bca', 'BcaC08g46021' => 'bca', 'BcaNung03154' => 'bca', 'BolC2t06623H' => 'bol', 'BolC2t06632H' => 'bol', 'BolC2t06635H' => 'bol', 'BolC2t06638H' => 'bol', 'BolC3t13266H' => 'bol', 'BolC5t29776H' => 'bol', 'BolC6t38912H' => 'bol', 'BolC7t44183H' => 'bol', 'BolC9t54123H' => 'bol', 'BolC9t59107H' => 'bol', 'BraA02t05221Z' => 'bra', 'BraA03t09996Z' => 'bra', 'BraA05t23210Z' => 'bra', 'BraA06t24068Z' => 'bra', 'BraA06t27032Z' => 'bra', 'BraA08t35176Z' => 'bra', 'BraA09t36680Z' => 'bra', 'BraA10t44471Z' => 'bra', 'C02p06760' => 'bna', 'C02p06890' => 'bna', 'C02p07010' => 'bna', 'C03p07660' => 'bna', 'C05p10300' => 'bna', 'C06p38150' => 'bna', 'C07p36650' => 'bna', 'C08p15770' => 'bna', 'C09p12300' => 'bna', 'C09p62700' => 'bna', 'C09p75040' => 'bna', 'CAN.G13.1' => 'can', 'CAN.G138.4' => 'can', 'CAN.G44.6' => 'can', 'CAN.G473.19' => 'can', 'CANSAT01G0835' => 'cansat', 'CANSAT11G0246' => 'cansat', 'CANSAT11G1766' => 'cansat', 'CANSAT64G1954' => 'cansat', 'CARHR013330' => 'chi', 'CARHR060530' => 'chi', 'CARHR075300' => 'chi', 'CARHR105120' => 'chi', 'CARHR148910' => 'chi', 'CARHR198830' => 'chi', 'Carub.0001s1275' => 'cru', 'Carub.0002s1437' => 'cru', 'Carub.0003s0044' => 'cru', 'Carub.0003s2787' => 'cru', 'Carub.0005s0597' => 'cru', 'Carub.0006s1266' => 'cru', 'Ca_06935_v3' => 'car', 'Ca_13559_v3' => 'car', 'Ca_16941_v3' => 'car', 'Ca_16960_v3' => 'car', 'Ca_17775_v3' => 'car', 'Ca_30464_v3' => 'car', 'Cc06_g08160' => 'ccan', 'Cc07_g01520' => 'ccan', 'Cc11_g15810' => 'ccan', 'CDE02G2840' => 'cde', 'CDE03G0093' => 'cde', 'CDE04G2127' => 'cde', 'CDE07G1857' => 'cde', 'CDE09G1246' => 'cde', 'Cfa003412' => 'cfa', 'Cfa007341' => 'cfa', 'Cfa009220' => 'cfa', 'Ciclev10008737m.g' => 'ccl', 'Ciclev10015565m.g' => 'ccl', 'Ciclev10031761m.g' => 'ccl', 'CiPaw.03G045300' => 'cil', 'CiPaw.03G247200' => 'cil', 'CiPaw.04G029500' => 'cil', 'CiPaw.04G174000' => 'cil', 'CiPaw.05G181200' => 'cil', 'CiPaw.06G067100' => 'cil', 'ClCG05G025800' => 'cla', 'ClCG06G011400' => 'cla', 'ClCG09G019360' => 'cla', 'COL.COLO4_04827' => 'col', 'COL.COLO4_29170' => 'col', 'COL.COLO4_35131' => 'col', 'COL.COLO4_35132' => 'col', 'Cpa.g.sc33.32' => 'cpa', 'Cpa.g.sc46.29' => 'cpa', 'Cpa.g.sc796.1' => 'cpa', 'CsaV3_1G030420' => 'csa', 'CsaV3_5G027050' => 'csa', 'CsaV3_5G031040' => 'csa', 'CsaV3_UNG023130' => 'csa', 'CSS0007726' => 'camsi', 'CSS0016433' => 'camsi', 'CSS0017656' => 'camsi', 'CSS0025364' => 'camsi', 'CSS0027582' => 'camsi', 'CSS0047288' => 'camsi', 'CSS0049950' => 'camsi', 'DCAR_003843' => 'dca', 'DCAR_007052' => 'dca', 'DCAR_020884' => 'dca', 'DCAR_021730' => 'dca', 'DCAR_024423' => 'dca', 'DCAR_026509' => 'dca', 'DCAR_031158' => 'dca', 'Dinv14728' => 'din', 'Dinv15219' => 'din', 'Dinv25728' => 'din', 'Dinv33428' => 'din', 'Dinv36489' => 'din', 'Dinv41486' => 'din', 'Duzib147G0469' => 'dzi', 'Duzib168G0060' => 'dzi', 'Duzib187G1215' => 'dzi', 'Duzib248G0692' => 'dzi', 'Duzib251G0767' => 'dzi', 'Duzib264G0446' => 'dzi', 'Duzib268G0691' => 'dzi', 'ECA232G4767' => 'eca', 'ECA233G2838' => 'eca', 'ECA234G0391' => 'eca', 'ECA234G0857' => 'eca', 'ECA236G1593' => 'eca', 'ECA238G0565' => 'eca', 'ECA246G1027' => 'eca', 'ECA246G3223' => 'eca', 'ECA246G3470' => 'eca', 'EL10Ac6g13829' => 'bvu', 'EL10Ac6g14093' => 'bvu', 'EL10Ac8g18707' => 'bvu', 'Eucgr.C01369' => 'egr', 'Eucgr.H02492' => 'egr', 'Eucgr.I01733' => 'egr', 'Eucgr.J02255' => 'egr', 'Eucgr.J02257' => 'egr', 'Eucgr.J02258' => 'egr', 'FAN02G1601' => 'fan', 'FAN03G1586' => 'fan', 'FAN03G2986' => 'fan', 'FAN05G4837' => 'fan', 'FAN06G0146' => 'fan', 'FAN07G0858' => 'fan', 'FAN09G3179' => 'fan', 'FAN10G0669' => 'fan', 'FAN12G2358' => 'fan', 'FAN14G4198' => 'fan', 'FAN14G5112' => 'fan', 'FAN17G0342' => 'fan', 'FAN19G0342' => 'fan', 'FAN19G0962' => 'fan', 'FAN19G1101' => 'fan', 'FAN19G1872' => 'fan', 'FAN22G0356' => 'fan', 'FAN23G0744' => 'fan', 'FAN23G1914' => 'fan', 'FAN26G0032' => 'fan', 'FAN28G0625' => 'fan', 'FvH4_1g02710' => 'fve', 'FvH4_1g02720' => 'fve', 'FvH4_4g25670' => 'fve', 'FvH4_6g51700' => 'fve', 'FvH4_7g20170' => 'fve', 'Glyma.05G175000' => 'gma', 'Glyma.08G132300' => 'gma', 'Glyma.11G243000' => 'gma', 'Glyma.13G158900' => 'gma', 'Glyma.17G112400' => 'gma', 'Glyma.18G014100' => 'gma', 'Glyma.19G003100' => 'gma', 'Glyma.19G056500' => 'gma', 'Gohir.A01G158900' => 'ghi', 'Gohir.A05G312600' => 'ghi', 'Gohir.A05G354900' => 'ghi', 'Gohir.A07G037200' => 'ghi', 'Gohir.A09G030000' => 'ghi', 'Gohir.A12G145200' => 'ghi', 'Gohir.D01G151500' => 'ghi', 'Gohir.D04G058300' => 'ghi', 'Gohir.D05G314100' => 'ghi', 'Gohir.D07G041400' => 'ghi', 'Gohir.D09G029700' => 'ghi', 'Gohir.D12G149700' => 'ghi', 'Gorai.001G043800' => 'gra', 'Gorai.002G187800' => 'gra', 'Gorai.006G034700' => 'gra', 'Gorai.008G161200' => 'gra', 'Gorai.009G335700' => 'gra', 'Gorai.012G065000' => 'gra', 'GSVIVG01000535001' => 'vvi', 'GSVIVG01015572001' => 'vvi', 'GSVIVG01032386001' => 'vvi', 'HanXRQChr05g0138531' => 'han', 'HanXRQChr06g0174391' => 'han', 'HanXRQChr07g0199021' => 'han', 'HanXRQChr08g0208211' => 'han', 'HanXRQChr09g0255471' => 'han', 'HanXRQChr10g0315791' => 'han', 'HanXRQChr12g0371991' => 'han', 'HanXRQChr15g0475251' => 'han', 'HanXRQChr17g0540001' => 'han', 'HanXRQChr17g0548631' => 'han', 'HanXRQChr17g0569561' => 'han', 'Haze_12256' => 'cav', 'Haze_14756' => 'cav', 'Haze_25528' => 'cav', 'Hma1.2p1_0079F.1_g041020' => 'hma', 'Hma1.2p1_0818F.1_g223260' => 'hma', 'Hma1.2p1_1747F.1_g300530' => 'hma', 'HPP92_004607' => 'vpl', 'HPP92_004608' => 'vpl', 'HPP92_006181' => 'vpl', 'HPP92_012192' => 'vpl', 'HPP92_015680' => 'vpl', 'HPP92_020249' => 'vpl', 'HPP92_021376' => 'vpl', 'HPP92_024275' => 'vpl', 'Hund06031' => 'sun', 'Hund25391' => 'sun', 'Lalb_Chr07g0185371' => 'lal', 'Lalb_Chr07g0185381' => 'lal', 'Lalb_Chr12g0204011' => 'lal', 'Lalb_Chr13g0301671' => 'lal', 'Lalb_Chr14g0362851' => 'lal', 'Lalb_Chr24g0403581' => 'lal', 'Lj1g0000233' => 'lja', 'Lj2g0018120' => 'lja', 'Lj3C621T0' => 'lonja', 'Lj3P1059T14' => 'lonja', 'Lj3P611T9' => 'lonja', 'Lj3P614T13' => 'lonja', 'Lj3P615T5' => 'lonja', 'Lj4g0012315' => 'lja', 'Lj4g0026182' => 'lja', 'Lj6P813T16' => 'lonja', 'Lj7C427T7' => 'lonja', 'Lj7C427T8' => 'lonja', 'Lj7P600T41' => 'lonja', 'Lju41C42G17' => 'lonja', 'Lsat_1_v5_gn_0_47300' => 'lsa', 'Lsat_1_v5_gn_2_91280' => 'lsa', 'Lsat_1_v5_gn_3_30561' => 'lsa', 'Lsat_1_v5_gn_4_184321' => 'lsa', 'Lsat_1_v5_gn_4_4041' => 'lsa', 'Lsat_1_v5_gn_5_92000' => 'lsa', 'Lsat_1_v5_gn_8_152940' => 'lsa', 'Lsat_1_v5_gn_8_62401' => 'lsa', 'Manes.06G055900' => 'mes', 'Manes.12G022200' => 'mes', 'Manes.13G023300' => 'mes', 'Manes.14G115000' => 'mes', 'Manes.15G151700' => 'mes', 'Manes.17G111300' => 'mes', 'Mapoly0226s0009' => 'mpo', 'MBI02_g25363_MAGBIO' => 'mbi', 'MBI06_g00027_MAGBIO' => 'mbi', 'MBI10_g13034_MAGBIO' => 'mbi', 'MD09G1023400' => 'mdo', 'MD13G1100100' => 'mdo', 'MD15G1169200' => 'mdo', 'MD16G1101100' => 'mdo', 'MD17G1022900' => 'mdo', 'Medtr3g096150' => 'mtr', 'Medtr4g115070' => 'mtr', 'Medtr7g033325' => 'mtr', 'Medtr8g089840' => 'mtr', 'MELO3C010319.2' => 'cme', 'MELO3C011944.2' => 'cme', 'MELO3C021589.2' => 'cme', 'Migut.E00207' => 'egut', 'Migut.H00067' => 'egut', 'Migut.K00433' => 'egut', 'Migut.K00606' => 'egut', 'Migut.K01410' => 'egut', 'MSTRG.13347' => 'ama', 'MSTRG.24045' => 'ama', 'MSTRG.2428' => 'ama', 'MSTRG.26410' => 'ama', 'MSTRG.3139' => 'ama', 'MSTRG.3286' => 'ama', 'MSTRG.563' => 'ama', 'MSTRG.7941' => 'ama', 'Nitab4.5_0000028g0060' => 'nta', 'Nitab4.5_0000065g0260' => 'nta', 'Nitab4.5_0000112g0060' => 'nta', 'Nitab4.5_0000489g0120' => 'nta', 'Nitab4.5_0001776g0050' => 'nta', 'Nitab4.5_0001854g0010' => 'nta', 'Nitab4.5_0001860g0020' => 'nta', 'Nitab4.5_0004352g0010' => 'nta', 'Nitab4.5_0008716g0020' => 'nta', 'Nitab4.5_0008922g0010' => 'nta', 'Nn3g16693' => 'nnu', 'Nn4g22596' => 'nnu', 'Nn7g37639' => 'nnu', 'Oeu001701.1' => 'oeu', 'Oeu018149.1' => 'oeu', 'Oeu026220.1' => 'oeu', 'Oeu038635.1' => 'oeu', 'Oeu049176.1' => 'oeu', 'Oeu056706.1' => 'oeu', 'Oeu056937.1' => 'oeu', 'Oeu057540.1' => 'oeu', 'Os02g0594900' => 'osa', 'Os02g0595100' => 'osa', 'Os04g0477500' => 'osa', 'Os12g0611900' => 'osa', 'Peaxi162Scf00076g00020' => 'pax', 'Peaxi162Scf00128g00217' => 'pax', 'Peaxi162Scf00129g01640' => 'pax', 'Peaxi162Scf00669g00007' => 'pax', 'Peaxi162Scf00700g00421' => 'pax', 'Peaxi162Scf00801g00038' => 'pax', 'Peaxi162Scf00891g00025' => 'pax', 'PGR083G0909' => 'pgr', 'PGR119G1005' => 'pgr', 'PGR142G2236' => 'pgr', 'PGR142G3388' => 'pgr', 'PGSC0003DMG400004514' => 'stu', 'PGSC0003DMG400012635' => 'stu', 'PGSC0003DMG400015730' => 'stu', 'PGSC0003DMG400018611' => 'stu', 'PGSC0003DMG400030897' => 'stu', 'Phvul.001G254800' => 'pvu', 'Phvul.002G260100' => 'pvu', 'Phvul.003G167600' => 'pvu', 'Phvul.004G005100' => 'pvu', 'Potri.001G343600' => 'ptr', 'Potri.006G066700' => 'ptr', 'Potri.008G186000' => 'ptr', 'Potri.010G046900' => 'ptr', 'Potri.018G127900' => 'ptr', 'Pp3c20_17750' => 'ppa', 'Pp3c24_4380' => 'ppa', 'Prupe.1G245800' => 'ppe', 'Prupe.3G293400' => 'ppe', 'Prupe.7G247400' => 'ppe', 'Psat0s145g0120' => 'psa', 'Psat0s595g0040' => 'psa', 'Psat0s595g0120' => 'psa', 'Psat3g175040' => 'psa', 'Psat7g058120' => 'psa', 'PSO017G0428' => 'pso', 'PSO063G7510' => 'pso', 'PSO067G0046' => 'pso', 'PSO478G1073' => 'pso', 'PSO675G3677' => 'pso', 'PSO675G6558' => 'pso', 'PSO675G7520' => 'pso', 'PSO675G8959' => 'pso', 'QL02p074089' => 'qlo', 'QL02p089614' => 'qlo', 'QL03p057736' => 'qlo', 'RcHm_v2.0_Chr1g0364131' => 'rch', 'RcHm_v2.0_Chr2g0087801' => 'rch', 'RcHm_v2.0_Chr2g0087821' => 'rch', 'RcHm_v2.0_Chr2g0173231' => 'rch', 'RcHm_v2.0_Chr4g0433111' => 'rch', 'Rhsim03G0250300' => 'rsi', 'Rhsim08G0048400' => 'rsi', 'Rhsim10G0014800' => 'rsi', 'Rhsim12G0040100' => 'rsi', 'Rhsim12G0109700' => 'rsi', 'Sabra06G0049600' => 'sbr', 'Sabra08G0141000' => 'sbr', 'Sabra10G0021400' => 'sbr', 'Sabra16G0222900' => 'sbr', 'Sabra18G0108600' => 'sbr', 'SalBow1G0433' => 'sbo', 'SalBow1G2038' => 'sbo', 'SalBow1G5003' => 'sbo', 'SalBow7G1197' => 'sbo', 'SalBow8G3506' => 'sbo', 'Sc03g0007300' => 'sci', 'Sc11g0000950' => 'sci', 'Sc14g0008750' => 'sci', 'Sc18g0000420' => 'sci', 'Sed0006754' => 'sed', 'Sed0008741' => 'sed', 'Sed0017172' => 'sed', 'Sed0018925' => 'sed', 'Sed0023326' => 'sed', 'Sed0025909' => 'sed', 'SEGI_05333' => 'sgi', 'SEGI_10362' => 'sgi', 'SEGI_13380' => 'sgi', 'SEGI_24306' => 'sgi', 'SEGI_29077' => 'sgi', 'SEGI_29095' => 'sgi', 'SEGI_36534' => 'sgi', 'SEGI_37506' => 'sgi', 'SEGI_38321' => 'sgi', 'SGA_v2.0_scaffold307G48031' => 'sas', 'SGA_v2.0_scaffold47G17507' => 'sas', 'SGA_v2.0_scaffold63G21736' => 'sas', 'SGA_v2.0_scaffold87G27070' => 'sas', 'SHI17794' => 'shi', 'SHI28851' => 'shi', 'SMO165G0155' => 'smo', 'SMO340G0217' => 'smo', 'SMO367G1210' => 'smo', 'Solyc02g093430.3' => 'sly', 'Solyc05g013580.4' => 'sly', 'Solyc07g008030.3' => 'sly', 'Solyc12g035470.2' => 'sly', 'Sopen02g038020' => 'spe', 'Sopen05g008490' => 'spe', 'Sopen07g003910' => 'spe', 'Sopen12g015240' => 'spe', 'Sp1g11550' => 'spa', 'Sp2g16710' => 'spa', 'Sp3g00430' => 'spa', 'Sp3g26780' => 'spa', 'Sp5g22900' => 'spa', 'Sp6g29530' => 'spa', 'TAR371G0794' => 'tar', 'TAR374G0164' => 'tar', 'TAR622G0165' => 'tar', 'TAR626G0929' => 'tar', 'TAR629G2155' => 'tar', 'THA.LOC104805282' => 'tha', 'THA.LOC104805363' => 'tha', 'THA.LOC104808968' => 'tha', 'THA.LOC104821093' => 'tha', 'THA.LOC104823953' => 'tha', 'THA.LOC104825562' => 'tha', 'THA.LOC104825665' => 'tha', 'Thecc.02G261400' => 'tca', 'Thecc.04G019200' => 'tca', 'Thecc.09G130400' => 'tca', 'Thhalv10004374m.g' => 'esa', 'Thhalv10007850m.g' => 'esa', 'Thhalv10013782m.g' => 'esa', 'Thhalv10018686m.g' => 'esa', 'Thhalv10020899m.g' => 'esa', 'Thhalv10022755m.g' => 'esa', 'TPR.G23851' => 'tpr', 'TPR.G26500' => 'tpr', 'TPR.G27267' => 'tpr', 'TPR.G32001' => 'tpr', 'TPR.G6251' => 'tpr', 'TPR.G8167' => 'tpr', 'TWI12G1330' => 'twi', 'TWI18G1239' => 'twi', 'TWI34G0979' => 'twi', 'TWI36G0670' => 'twi', 'TWI36G0707' => 'twi', 'TWI56G0233' => 'twi', 'TWI75G1809' => 'twi', 'unitig_21.g20874' => 'ugi', 'unitig_26.g10343' => 'ugi', 'unitig_46.g18392' => 'ugi', 'unitig_52.g17178' => 'ugi', 'unitig_8.g2934' => 'ugi', 'vmacro01122' => 'vma', 'vmacro05875' => 'vma', 'vmacro06147' => 'vma', 'vmacro16191' => 'vma', 'vmacro18293' => 'vma', 'VMungo0251G3707' => 'vmu', 'VMungo0464G1521' => 'vmu', 'VMungo1215G0205' => 'vmu', 'VMungo1383G2484' => 'vmu', 'Zm00001eb079610' => 'zma', 'Zm00001eb135990' => 'zma', 'Zm00001eb183710' => 'zma', 'Zm00001eb246020' => 'zma' ), 'gf_id' => 'HOM05D001124', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001124' ), 'data_identifier' => 'HOM05D001124', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001124', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '548', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02520' => 'bna', 'A03p06630' => 'bna', 'A05p44460' => 'bna', 'A06p08710' => 'bna', 'A06p41090' => 'bna', 'A07p32320' => 'bna', 'A08p32520' => 'bna', 'A09p10360' => 'bna', 'A10p24080' => 'bna', 'Aa31LG11G15250' => 'aar', 'Aa31LG1G1800' => 'aar', 'Aa31LG2G5120' => 'aar', 'Aa31LG2G6070' => 'aar', 'Aa31LG5G10770' => 'aar', 'Aa31sc61G90' => 'aar', 'Actinidia01352' => 'ach', 'Actinidia05983' => 'ach', 'Actinidia08133' => 'ach', 'Actinidia15101' => 'ach', 'Actinidia26379' => 'ach', 'Actinidia35778' => 'ach', 'Actinidia36123' => 'ach', 'Actinidia37436' => 'ach', 'Actinidia38730' => 'ach', 'Ah.02g128210' => 'amhyb', 'Ah.03g132990' => 'amhyb', 'Ah.14g079410' => 'amhyb', 'AL1G24640' => 'aly', 'AL2G26680' => 'aly', 'AL3G10530' => 'aly', 'AL3G45230' => 'aly', 'AL5G15230' => 'aly', 'AL5G16960' => 'aly', 'AL6G25210' => 'aly', 'Aqoxy2G00441' => 'aox', 'Aqoxy3G01236' => 'aox', 'Aqoxy5G03746' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3RQ047' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C7GMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9C8JER' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MBL6KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YXCZ83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZANX40' => 'arhy', 'AT1G12990' => 'ath', 'AT1G67880' => 'ath', 'AT2G13290' => 'ath', 'AT3G01620' => 'ath', 'AT3G26445' => 'ath', 'AT3G27540' => 'ath', 'AT5G14480' => 'ath', 'ATR0824G026' => 'atr', 'ATR1098G019' => 'atr', 'Atru.chr11.2145' => 'acertr', 'Atru.chr2.3636' => 'acertr', 'Atru.chr2.3644' => 'acertr', 'Atru.chr6.2422' => 'acertr', 'Atru.chr7.1112' => 'acertr', 'AUR62005469' => 'cqu', 'AUR62011166' => 'cqu', 'AUR62013319' => 'cqu', 'AUR62024273' => 'cqu', 'AUR62028420' => 'cqu', 'AUR62041942' => 'cqu', 'BcaB01g04969' => 'bca', 'BcaB01g06371' => 'bca', 'BcaB02g11494' => 'bca', 'BcaB03g15382' => 'bca', 'BcaB08g36994' => 'bca', 'BcaC03g13477' => 'bca', 'BcaC03g13478' => 'bca', 'BcaC03g13480' => 'bca', 'BcaC03g13481' => 'bca', 'BcaC03g13486' => 'bca', 'BcaC04g19031' => 'bca', 'BcaC04g23085' => 'bca', 'BcaC05g25094' => 'bca', 'BcaC05g25096' => 'bca', 'BcaC05g25138' => 'bca', 'BcaC05g30416' => 'bca', 'BcaC05g30455' => 'bca', 'BcaC06g30979' => 'bca', 'BcaC06g33805' => 'bca', 'BcaC08g46021' => 'bca', 'BcaNung03154' => 'bca', 'BolC2t06623H' => 'bol', 'BolC2t06632H' => 'bol', 'BolC2t06635H' => 'bol', 'BolC2t06638H' => 'bol', 'BolC3t13266H' => 'bol', 'BolC5t29776H' => 'bol', 'BolC6t38912H' => 'bol', 'BolC7t44183H' => 'bol', 'BolC9t54123H' => 'bol', 'BolC9t59107H' => 'bol', 'BraA02t05221Z' => 'bra', 'BraA03t09996Z' => 'bra', 'BraA05t23210Z' => 'bra', 'BraA06t24068Z' => 'bra', 'BraA06t27032Z' => 'bra', 'BraA08t35176Z' => 'bra', 'BraA09t36680Z' => 'bra', 'BraA10t44471Z' => 'bra', 'C02p06760' => 'bna', 'C02p06890' => 'bna', 'C02p07010' => 'bna', 'C03p07660' => 'bna', 'C05p10300' => 'bna', 'C06p38150' => 'bna', 'C07p36650' => 'bna', 'C08p15770' => 'bna', 'C09p12300' => 'bna', 'C09p62700' => 'bna', 'C09p75040' => 'bna', 'CAN.G13.1' => 'can', 'CAN.G138.4' => 'can', 'CAN.G44.6' => 'can', 'CAN.G473.19' => 'can', 'CANSAT01G0835' => 'cansat', 'CANSAT11G0246' => 'cansat', 'CANSAT11G1766' => 'cansat', 'CANSAT64G1954' => 'cansat', 'CARHR013330' => 'chi', 'CARHR060530' => 'chi', 'CARHR075300' => 'chi', 'CARHR105120' => 'chi', 'CARHR148910' => 'chi', 'CARHR198830' => 'chi', 'Carub.0001s1275' => 'cru', 'Carub.0002s1437' => 'cru', 'Carub.0003s0044' => 'cru', 'Carub.0003s2787' => 'cru', 'Carub.0005s0597' => 'cru', 'Carub.0006s1266' => 'cru', 'Ca_06935_v3' => 'car', 'Ca_13559_v3' => 'car', 'Ca_16941_v3' => 'car', 'Ca_16960_v3' => 'car', 'Ca_17775_v3' => 'car', 'Ca_30464_v3' => 'car', 'Cc06_g08160' => 'ccan', 'Cc07_g01520' => 'ccan', 'Cc11_g15810' => 'ccan', 'CDE02G2840' => 'cde', 'CDE03G0093' => 'cde', 'CDE04G2127' => 'cde', 'CDE07G1857' => 'cde', 'CDE09G1246' => 'cde', 'Cfa003412' => 'cfa', 'Cfa007341' => 'cfa', 'Cfa009220' => 'cfa', 'Ciclev10008737m.g' => 'ccl', 'Ciclev10015565m.g' => 'ccl', 'Ciclev10031761m.g' => 'ccl', 'CiPaw.03G045300' => 'cil', 'CiPaw.03G247200' => 'cil', 'CiPaw.04G029500' => 'cil', 'CiPaw.04G174000' => 'cil', 'CiPaw.05G181200' => 'cil', 'CiPaw.06G067100' => 'cil', 'ClCG05G025800' => 'cla', 'ClCG06G011400' => 'cla', 'ClCG09G019360' => 'cla', 'COL.COLO4_04827' => 'col', 'COL.COLO4_29170' => 'col', 'COL.COLO4_35131' => 'col', 'COL.COLO4_35132' => 'col', 'Cpa.g.sc33.32' => 'cpa', 'Cpa.g.sc46.29' => 'cpa', 'Cpa.g.sc796.1' => 'cpa', 'CsaV3_1G030420' => 'csa', 'CsaV3_5G027050' => 'csa', 'CsaV3_5G031040' => 'csa', 'CsaV3_UNG023130' => 'csa', 'CSS0007726' => 'camsi', 'CSS0016433' => 'camsi', 'CSS0017656' => 'camsi', 'CSS0025364' => 'camsi', 'CSS0027582' => 'camsi', 'CSS0047288' => 'camsi', 'CSS0049950' => 'camsi', 'DCAR_003843' => 'dca', 'DCAR_007052' => 'dca', 'DCAR_020884' => 'dca', 'DCAR_021730' => 'dca', 'DCAR_024423' => 'dca', 'DCAR_026509' => 'dca', 'DCAR_031158' => 'dca', 'Dinv14728' => 'din', 'Dinv15219' => 'din', 'Dinv25728' => 'din', 'Dinv33428' => 'din', 'Dinv36489' => 'din', 'Dinv41486' => 'din', 'Duzib147G0469' => 'dzi', 'Duzib168G0060' => 'dzi', 'Duzib187G1215' => 'dzi', 'Duzib248G0692' => 'dzi', 'Duzib251G0767' => 'dzi', 'Duzib264G0446' => 'dzi', 'Duzib268G0691' => 'dzi', 'ECA232G4767' => 'eca', 'ECA233G2838' => 'eca', 'ECA234G0391' => 'eca', 'ECA234G0857' => 'eca', 'ECA236G1593' => 'eca', 'ECA238G0565' => 'eca', 'ECA246G1027' => 'eca', 'ECA246G3223' => 'eca', 'ECA246G3470' => 'eca', 'EL10Ac6g13829' => 'bvu', 'EL10Ac6g14093' => 'bvu', 'EL10Ac8g18707' => 'bvu', 'Eucgr.C01369' => 'egr', 'Eucgr.H02492' => 'egr', 'Eucgr.I01733' => 'egr', 'Eucgr.J02255' => 'egr', 'Eucgr.J02257' => 'egr', 'Eucgr.J02258' => 'egr', 'FAN02G1601' => 'fan', 'FAN03G1586' => 'fan', 'FAN03G2986' => 'fan', 'FAN05G4837' => 'fan', 'FAN06G0146' => 'fan', 'FAN07G0858' => 'fan', 'FAN09G3179' => 'fan', 'FAN10G0669' => 'fan', 'FAN12G2358' => 'fan', 'FAN14G4198' => 'fan', 'FAN14G5112' => 'fan', 'FAN17G0342' => 'fan', 'FAN19G0342' => 'fan', 'FAN19G0962' => 'fan', 'FAN19G1101' => 'fan', 'FAN19G1872' => 'fan', 'FAN22G0356' => 'fan', 'FAN23G0744' => 'fan', 'FAN23G1914' => 'fan', 'FAN26G0032' => 'fan', 'FAN28G0625' => 'fan', 'FvH4_1g02710' => 'fve', 'FvH4_1g02720' => 'fve', 'FvH4_4g25670' => 'fve', 'FvH4_6g51700' => 'fve', 'FvH4_7g20170' => 'fve', 'Glyma.05G175000' => 'gma', 'Glyma.08G132300' => 'gma', 'Glyma.11G243000' => 'gma', 'Glyma.13G158900' => 'gma', 'Glyma.17G112400' => 'gma', 'Glyma.18G014100' => 'gma', 'Glyma.19G003100' => 'gma', 'Glyma.19G056500' => 'gma', 'Gohir.A01G158900' => 'ghi', 'Gohir.A05G312600' => 'ghi', 'Gohir.A05G354900' => 'ghi', 'Gohir.A07G037200' => 'ghi', 'Gohir.A09G030000' => 'ghi', 'Gohir.A12G145200' => 'ghi', 'Gohir.D01G151500' => 'ghi', 'Gohir.D04G058300' => 'ghi', 'Gohir.D05G314100' => 'ghi', 'Gohir.D07G041400' => 'ghi', 'Gohir.D09G029700' => 'ghi', 'Gohir.D12G149700' => 'ghi', 'Gorai.001G043800' => 'gra', 'Gorai.002G187800' => 'gra', 'Gorai.006G034700' => 'gra', 'Gorai.008G161200' => 'gra', 'Gorai.009G335700' => 'gra', 'Gorai.012G065000' => 'gra', 'GSVIVG01000535001' => 'vvi', 'GSVIVG01015572001' => 'vvi', 'GSVIVG01032386001' => 'vvi', 'HanXRQChr05g0138531' => 'han', 'HanXRQChr06g0174391' => 'han', 'HanXRQChr07g0199021' => 'han', 'HanXRQChr08g0208211' => 'han', 'HanXRQChr09g0255471' => 'han', 'HanXRQChr10g0315791' => 'han', 'HanXRQChr12g0371991' => 'han', 'HanXRQChr15g0475251' => 'han', 'HanXRQChr17g0540001' => 'han', 'HanXRQChr17g0548631' => 'han', 'HanXRQChr17g0569561' => 'han', 'Haze_12256' => 'cav', 'Haze_14756' => 'cav', 'Haze_25528' => 'cav', 'Hma1.2p1_0079F.1_g041020' => 'hma', 'Hma1.2p1_0818F.1_g223260' => 'hma', 'Hma1.2p1_1747F.1_g300530' => 'hma', 'HPP92_004607' => 'vpl', 'HPP92_004608' => 'vpl', 'HPP92_006181' => 'vpl', 'HPP92_012192' => 'vpl', 'HPP92_015680' => 'vpl', 'HPP92_020249' => 'vpl', 'HPP92_021376' => 'vpl', 'HPP92_024275' => 'vpl', 'Hund06031' => 'sun', 'Hund25391' => 'sun', 'Lalb_Chr07g0185371' => 'lal', 'Lalb_Chr07g0185381' => 'lal', 'Lalb_Chr12g0204011' => 'lal', 'Lalb_Chr13g0301671' => 'lal', 'Lalb_Chr14g0362851' => 'lal', 'Lalb_Chr24g0403581' => 'lal', 'Lj1g0000233' => 'lja', 'Lj2g0018120' => 'lja', 'Lj3C621T0' => 'lonja', 'Lj3P1059T14' => 'lonja', 'Lj3P611T9' => 'lonja', 'Lj3P614T13' => 'lonja', 'Lj3P615T5' => 'lonja', 'Lj4g0012315' => 'lja', 'Lj4g0026182' => 'lja', 'Lj6P813T16' => 'lonja', 'Lj7C427T7' => 'lonja', 'Lj7C427T8' => 'lonja', 'Lj7P600T41' => 'lonja', 'Lju41C42G17' => 'lonja', 'Lsat_1_v5_gn_0_47300' => 'lsa', 'Lsat_1_v5_gn_2_91280' => 'lsa', 'Lsat_1_v5_gn_3_30561' => 'lsa', 'Lsat_1_v5_gn_4_184321' => 'lsa', 'Lsat_1_v5_gn_4_4041' => 'lsa', 'Lsat_1_v5_gn_5_92000' => 'lsa', 'Lsat_1_v5_gn_8_152940' => 'lsa', 'Lsat_1_v5_gn_8_62401' => 'lsa', 'Manes.06G055900' => 'mes', 'Manes.12G022200' => 'mes', 'Manes.13G023300' => 'mes', 'Manes.14G115000' => 'mes', 'Manes.15G151700' => 'mes', 'Manes.17G111300' => 'mes', 'Mapoly0226s0009' => 'mpo', 'MBI02_g25363_MAGBIO' => 'mbi', 'MBI06_g00027_MAGBIO' => 'mbi', 'MBI10_g13034_MAGBIO' => 'mbi', 'MD09G1023400' => 'mdo', 'MD13G1100100' => 'mdo', 'MD15G1169200' => 'mdo', 'MD16G1101100' => 'mdo', 'MD17G1022900' => 'mdo', 'Medtr3g096150' => 'mtr', 'Medtr4g115070' => 'mtr', 'Medtr7g033325' => 'mtr', 'Medtr8g089840' => 'mtr', 'MELO3C010319.2' => 'cme', 'MELO3C011944.2' => 'cme', 'MELO3C021589.2' => 'cme', 'Migut.E00207' => 'egut', 'Migut.H00067' => 'egut', 'Migut.K00433' => 'egut', 'Migut.K00606' => 'egut', 'Migut.K01410' => 'egut', 'MSTRG.13347' => 'ama', 'MSTRG.24045' => 'ama', 'MSTRG.2428' => 'ama', 'MSTRG.26410' => 'ama', 'MSTRG.3139' => 'ama', 'MSTRG.3286' => 'ama', 'MSTRG.563' => 'ama', 'MSTRG.7941' => 'ama', 'Nitab4.5_0000028g0060' => 'nta', 'Nitab4.5_0000065g0260' => 'nta', 'Nitab4.5_0000112g0060' => 'nta', 'Nitab4.5_0000489g0120' => 'nta', 'Nitab4.5_0001776g0050' => 'nta', 'Nitab4.5_0001854g0010' => 'nta', 'Nitab4.5_0001860g0020' => 'nta', 'Nitab4.5_0004352g0010' => 'nta', 'Nitab4.5_0008716g0020' => 'nta', 'Nitab4.5_0008922g0010' => 'nta', 'Nn3g16693' => 'nnu', 'Nn4g22596' => 'nnu', 'Nn7g37639' => 'nnu', 'Oeu001701.1' => 'oeu', 'Oeu018149.1' => 'oeu', 'Oeu026220.1' => 'oeu', 'Oeu038635.1' => 'oeu', 'Oeu049176.1' => 'oeu', 'Oeu056706.1' => 'oeu', 'Oeu056937.1' => 'oeu', 'Oeu057540.1' => 'oeu', 'Os02g0594900' => 'osa', 'Os02g0595100' => 'osa', 'Os04g0477500' => 'osa', 'Os12g0611900' => 'osa', 'Peaxi162Scf00076g00020' => 'pax', 'Peaxi162Scf00128g00217' => 'pax', 'Peaxi162Scf00129g01640' => 'pax', 'Peaxi162Scf00669g00007' => 'pax', 'Peaxi162Scf00700g00421' => 'pax', 'Peaxi162Scf00801g00038' => 'pax', 'Peaxi162Scf00891g00025' => 'pax', 'PGR083G0909' => 'pgr', 'PGR119G1005' => 'pgr', 'PGR142G2236' => 'pgr', 'PGR142G3388' => 'pgr', 'PGSC0003DMG400004514' => 'stu', 'PGSC0003DMG400012635' => 'stu', 'PGSC0003DMG400015730' => 'stu', 'PGSC0003DMG400018611' => 'stu', 'PGSC0003DMG400030897' => 'stu', 'Phvul.001G254800' => 'pvu', 'Phvul.002G260100' => 'pvu', 'Phvul.003G167600' => 'pvu', 'Phvul.004G005100' => 'pvu', 'Potri.001G343600' => 'ptr', 'Potri.006G066700' => 'ptr', 'Potri.008G186000' => 'ptr', 'Potri.010G046900' => 'ptr', 'Potri.018G127900' => 'ptr', 'Pp3c20_17750' => 'ppa', 'Pp3c24_4380' => 'ppa', 'Prupe.1G245800' => 'ppe', 'Prupe.3G293400' => 'ppe', 'Prupe.7G247400' => 'ppe', 'Psat0s145g0120' => 'psa', 'Psat0s595g0040' => 'psa', 'Psat0s595g0120' => 'psa', 'Psat3g175040' => 'psa', 'Psat7g058120' => 'psa', 'PSO017G0428' => 'pso', 'PSO063G7510' => 'pso', 'PSO067G0046' => 'pso', 'PSO478G1073' => 'pso', 'PSO675G3677' => 'pso', 'PSO675G6558' => 'pso', 'PSO675G7520' => 'pso', 'PSO675G8959' => 'pso', 'QL02p074089' => 'qlo', 'QL02p089614' => 'qlo', 'QL03p057736' => 'qlo', 'RcHm_v2.0_Chr1g0364131' => 'rch', 'RcHm_v2.0_Chr2g0087801' => 'rch', 'RcHm_v2.0_Chr2g0087821' => 'rch', 'RcHm_v2.0_Chr2g0173231' => 'rch', 'RcHm_v2.0_Chr4g0433111' => 'rch', 'Rhsim03G0250300' => 'rsi', 'Rhsim08G0048400' => 'rsi', 'Rhsim10G0014800' => 'rsi', 'Rhsim12G0040100' => 'rsi', 'Rhsim12G0109700' => 'rsi', 'Sabra06G0049600' => 'sbr', 'Sabra08G0141000' => 'sbr', 'Sabra10G0021400' => 'sbr', 'Sabra16G0222900' => 'sbr', 'Sabra18G0108600' => 'sbr', 'SalBow1G0433' => 'sbo', 'SalBow1G2038' => 'sbo', 'SalBow1G5003' => 'sbo', 'SalBow7G1197' => 'sbo', 'SalBow8G3506' => 'sbo', 'Sc03g0007300' => 'sci', 'Sc11g0000950' => 'sci', 'Sc14g0008750' => 'sci', 'Sc18g0000420' => 'sci', 'Sed0006754' => 'sed', 'Sed0008741' => 'sed', 'Sed0017172' => 'sed', 'Sed0018925' => 'sed', 'Sed0023326' => 'sed', 'Sed0025909' => 'sed', 'SEGI_05333' => 'sgi', 'SEGI_10362' => 'sgi', 'SEGI_13380' => 'sgi', 'SEGI_24306' => 'sgi', 'SEGI_29077' => 'sgi', 'SEGI_29095' => 'sgi', 'SEGI_36534' => 'sgi', 'SEGI_37506' => 'sgi', 'SEGI_38321' => 'sgi', 'SGA_v2.0_scaffold307G48031' => 'sas', 'SGA_v2.0_scaffold47G17507' => 'sas', 'SGA_v2.0_scaffold63G21736' => 'sas', 'SGA_v2.0_scaffold87G27070' => 'sas', 'SHI17794' => 'shi', 'SHI28851' => 'shi', 'SMO165G0155' => 'smo', 'SMO340G0217' => 'smo', 'SMO367G1210' => 'smo', 'Solyc02g093430.3' => 'sly', 'Solyc05g013580.4' => 'sly', 'Solyc07g008030.3' => 'sly', 'Solyc12g035470.2' => 'sly', 'Sopen02g038020' => 'spe', 'Sopen05g008490' => 'spe', 'Sopen07g003910' => 'spe', 'Sopen12g015240' => 'spe', 'Sp1g11550' => 'spa', 'Sp2g16710' => 'spa', 'Sp3g00430' => 'spa', 'Sp3g26780' => 'spa', 'Sp5g22900' => 'spa', 'Sp6g29530' => 'spa', 'TAR371G0794' => 'tar', 'TAR374G0164' => 'tar', 'TAR622G0165' => 'tar', 'TAR626G0929' => 'tar', 'TAR629G2155' => 'tar', 'THA.LOC104805282' => 'tha', 'THA.LOC104805363' => 'tha', 'THA.LOC104808968' => 'tha', 'THA.LOC104821093' => 'tha', 'THA.LOC104823953' => 'tha', 'THA.LOC104825562' => 'tha', 'THA.LOC104825665' => 'tha', 'Thecc.02G261400' => 'tca', 'Thecc.04G019200' => 'tca', 'Thecc.09G130400' => 'tca', 'Thhalv10004374m.g' => 'esa', 'Thhalv10007850m.g' => 'esa', 'Thhalv10013782m.g' => 'esa', 'Thhalv10018686m.g' => 'esa', 'Thhalv10020899m.g' => 'esa', 'Thhalv10022755m.g' => 'esa', 'TPR.G23851' => 'tpr', 'TPR.G26500' => 'tpr', 'TPR.G27267' => 'tpr', 'TPR.G32001' => 'tpr', 'TPR.G6251' => 'tpr', 'TPR.G8167' => 'tpr', 'TWI12G1330' => 'twi', 'TWI18G1239' => 'twi', 'TWI34G0979' => 'twi', 'TWI36G0670' => 'twi', 'TWI36G0707' => 'twi', 'TWI56G0233' => 'twi', 'TWI75G1809' => 'twi', 'unitig_21.g20874' => 'ugi', 'unitig_26.g10343' => 'ugi', 'unitig_46.g18392' => 'ugi', 'unitig_52.g17178' => 'ugi', 'unitig_8.g2934' => 'ugi', 'vmacro01122' => 'vma', 'vmacro05875' => 'vma', 'vmacro06147' => 'vma', 'vmacro16191' => 'vma', 'vmacro18293' => 'vma', 'VMungo0251G3707' => 'vmu', 'VMungo0464G1521' => 'vmu', 'VMungo1215G0205' => 'vmu', 'VMungo1383G2484' => 'vmu', 'Zm00001eb079610' => 'zma', 'Zm00001eb135990' => 'zma', 'Zm00001eb183710' => 'zma', 'Zm00001eb246020' => 'zma' ) $gf_id = 'HOM05D001124' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001124' ) $data_identifier = 'HOM05D001124' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 6, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 7, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 21, 'bol' => (int) 10, 'bra' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 6, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 9, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 21, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 8, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 10, 'lsa' => (int) 8, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 8, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 9, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb246020' $species_info = array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ) $local_species = 'ghi' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001124', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '548', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02520' => 'bna', 'A03p06630' => 'bna', 'A05p44460' => 'bna', 'A06p08710' => 'bna', 'A06p41090' => 'bna', 'A07p32320' => 'bna', 'A08p32520' => 'bna', 'A09p10360' => 'bna', 'A10p24080' => 'bna', 'Aa31LG11G15250' => 'aar', 'Aa31LG1G1800' => 'aar', 'Aa31LG2G5120' => 'aar', 'Aa31LG2G6070' => 'aar', 'Aa31LG5G10770' => 'aar', 'Aa31sc61G90' => 'aar', 'Actinidia01352' => 'ach', 'Actinidia05983' => 'ach', 'Actinidia08133' => 'ach', 'Actinidia15101' => 'ach', 'Actinidia26379' => 'ach', 'Actinidia35778' => 'ach', 'Actinidia36123' => 'ach', 'Actinidia37436' => 'ach', 'Actinidia38730' => 'ach', 'Ah.02g128210' => 'amhyb', 'Ah.03g132990' => 'amhyb', 'Ah.14g079410' => 'amhyb', 'AL1G24640' => 'aly', 'AL2G26680' => 'aly', 'AL3G10530' => 'aly', 'AL3G45230' => 'aly', 'AL5G15230' => 'aly', 'AL5G16960' => 'aly', 'AL6G25210' => 'aly', 'Aqoxy2G00441' => 'aox', 'Aqoxy3G01236' => 'aox', 'Aqoxy5G03746' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3RQ047' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C7GMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9C8JER' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MBL6KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YXCZ83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZANX40' => 'arhy', 'AT1G12990' => 'ath', 'AT1G67880' => 'ath', 'AT2G13290' => 'ath', 'AT3G01620' => 'ath', 'AT3G26445' => 'ath', 'AT3G27540' => 'ath', 'AT5G14480' => 'ath', 'ATR0824G026' => 'atr', 'ATR1098G019' => 'atr', 'Atru.chr11.2145' => 'acertr', 'Atru.chr2.3636' => 'acertr', 'Atru.chr2.3644' => 'acertr', 'Atru.chr6.2422' => 'acertr', 'Atru.chr7.1112' => 'acertr', 'AUR62005469' => 'cqu', 'AUR62011166' => 'cqu', 'AUR62013319' => 'cqu', 'AUR62024273' => 'cqu', 'AUR62028420' => 'cqu', 'AUR62041942' => 'cqu', 'BcaB01g04969' => 'bca', 'BcaB01g06371' => 'bca', 'BcaB02g11494' => 'bca', 'BcaB03g15382' => 'bca', 'BcaB08g36994' => 'bca', 'BcaC03g13477' => 'bca', 'BcaC03g13478' => 'bca', 'BcaC03g13480' => 'bca', 'BcaC03g13481' => 'bca', 'BcaC03g13486' => 'bca', 'BcaC04g19031' => 'bca', 'BcaC04g23085' => 'bca', 'BcaC05g25094' => 'bca', 'BcaC05g25096' => 'bca', 'BcaC05g25138' => 'bca', 'BcaC05g30416' => 'bca', 'BcaC05g30455' => 'bca', 'BcaC06g30979' => 'bca', 'BcaC06g33805' => 'bca', 'BcaC08g46021' => 'bca', 'BcaNung03154' => 'bca', 'BolC2t06623H' => 'bol', 'BolC2t06632H' => 'bol', 'BolC2t06635H' => 'bol', 'BolC2t06638H' => 'bol', 'BolC3t13266H' => 'bol', 'BolC5t29776H' => 'bol', 'BolC6t38912H' => 'bol', 'BolC7t44183H' => 'bol', 'BolC9t54123H' => 'bol', 'BolC9t59107H' => 'bol', 'BraA02t05221Z' => 'bra', 'BraA03t09996Z' => 'bra', 'BraA05t23210Z' => 'bra', 'BraA06t24068Z' => 'bra', 'BraA06t27032Z' => 'bra', 'BraA08t35176Z' => 'bra', 'BraA09t36680Z' => 'bra', 'BraA10t44471Z' => 'bra', 'C02p06760' => 'bna', 'C02p06890' => 'bna', 'C02p07010' => 'bna', 'C03p07660' => 'bna', 'C05p10300' => 'bna', 'C06p38150' => 'bna', 'C07p36650' => 'bna', 'C08p15770' => 'bna', 'C09p12300' => 'bna', 'C09p62700' => 'bna', 'C09p75040' => 'bna', 'CAN.G13.1' => 'can', 'CAN.G138.4' => 'can', 'CAN.G44.6' => 'can', 'CAN.G473.19' => 'can', 'CANSAT01G0835' => 'cansat', 'CANSAT11G0246' => 'cansat', 'CANSAT11G1766' => 'cansat', 'CANSAT64G1954' => 'cansat', 'CARHR013330' => 'chi', 'CARHR060530' => 'chi', 'CARHR075300' => 'chi', 'CARHR105120' => 'chi', 'CARHR148910' => 'chi', 'CARHR198830' => 'chi', 'Carub.0001s1275' => 'cru', 'Carub.0002s1437' => 'cru', 'Carub.0003s0044' => 'cru', 'Carub.0003s2787' => 'cru', 'Carub.0005s0597' => 'cru', 'Carub.0006s1266' => 'cru', 'Ca_06935_v3' => 'car', 'Ca_13559_v3' => 'car', 'Ca_16941_v3' => 'car', 'Ca_16960_v3' => 'car', 'Ca_17775_v3' => 'car', 'Ca_30464_v3' => 'car', 'Cc06_g08160' => 'ccan', 'Cc07_g01520' => 'ccan', 'Cc11_g15810' => 'ccan', 'CDE02G2840' => 'cde', 'CDE03G0093' => 'cde', 'CDE04G2127' => 'cde', 'CDE07G1857' => 'cde', 'CDE09G1246' => 'cde', 'Cfa003412' => 'cfa', 'Cfa007341' => 'cfa', 'Cfa009220' => 'cfa', 'Ciclev10008737m.g' => 'ccl', 'Ciclev10015565m.g' => 'ccl', 'Ciclev10031761m.g' => 'ccl', 'CiPaw.03G045300' => 'cil', 'CiPaw.03G247200' => 'cil', 'CiPaw.04G029500' => 'cil', 'CiPaw.04G174000' => 'cil', 'CiPaw.05G181200' => 'cil', 'CiPaw.06G067100' => 'cil', 'ClCG05G025800' => 'cla', 'ClCG06G011400' => 'cla', 'ClCG09G019360' => 'cla', 'COL.COLO4_04827' => 'col', 'COL.COLO4_29170' => 'col', 'COL.COLO4_35131' => 'col', 'COL.COLO4_35132' => 'col', 'Cpa.g.sc33.32' => 'cpa', 'Cpa.g.sc46.29' => 'cpa', 'Cpa.g.sc796.1' => 'cpa', 'CsaV3_1G030420' => 'csa', 'CsaV3_5G027050' => 'csa', 'CsaV3_5G031040' => 'csa', 'CsaV3_UNG023130' => 'csa', 'CSS0007726' => 'camsi', 'CSS0016433' => 'camsi', 'CSS0017656' => 'camsi', 'CSS0025364' => 'camsi', 'CSS0027582' => 'camsi', 'CSS0047288' => 'camsi', 'CSS0049950' => 'camsi', 'DCAR_003843' => 'dca', 'DCAR_007052' => 'dca', 'DCAR_020884' => 'dca', 'DCAR_021730' => 'dca', 'DCAR_024423' => 'dca', 'DCAR_026509' => 'dca', 'DCAR_031158' => 'dca', 'Dinv14728' => 'din', 'Dinv15219' => 'din', 'Dinv25728' => 'din', 'Dinv33428' => 'din', 'Dinv36489' => 'din', 'Dinv41486' => 'din', 'Duzib147G0469' => 'dzi', 'Duzib168G0060' => 'dzi', 'Duzib187G1215' => 'dzi', 'Duzib248G0692' => 'dzi', 'Duzib251G0767' => 'dzi', 'Duzib264G0446' => 'dzi', 'Duzib268G0691' => 'dzi', 'ECA232G4767' => 'eca', 'ECA233G2838' => 'eca', 'ECA234G0391' => 'eca', 'ECA234G0857' => 'eca', 'ECA236G1593' => 'eca', 'ECA238G0565' => 'eca', 'ECA246G1027' => 'eca', 'ECA246G3223' => 'eca', 'ECA246G3470' => 'eca', 'EL10Ac6g13829' => 'bvu', 'EL10Ac6g14093' => 'bvu', 'EL10Ac8g18707' => 'bvu', 'Eucgr.C01369' => 'egr', 'Eucgr.H02492' => 'egr', 'Eucgr.I01733' => 'egr', 'Eucgr.J02255' => 'egr', 'Eucgr.J02257' => 'egr', 'Eucgr.J02258' => 'egr', 'FAN02G1601' => 'fan', 'FAN03G1586' => 'fan', 'FAN03G2986' => 'fan', 'FAN05G4837' => 'fan', 'FAN06G0146' => 'fan', 'FAN07G0858' => 'fan', 'FAN09G3179' => 'fan', 'FAN10G0669' => 'fan', 'FAN12G2358' => 'fan', 'FAN14G4198' => 'fan', 'FAN14G5112' => 'fan', 'FAN17G0342' => 'fan', 'FAN19G0342' => 'fan', 'FAN19G0962' => 'fan', 'FAN19G1101' => 'fan', 'FAN19G1872' => 'fan', 'FAN22G0356' => 'fan', 'FAN23G0744' => 'fan', 'FAN23G1914' => 'fan', 'FAN26G0032' => 'fan', 'FAN28G0625' => 'fan', 'FvH4_1g02710' => 'fve', 'FvH4_1g02720' => 'fve', 'FvH4_4g25670' => 'fve', 'FvH4_6g51700' => 'fve', 'FvH4_7g20170' => 'fve', 'Glyma.05G175000' => 'gma', 'Glyma.08G132300' => 'gma', 'Glyma.11G243000' => 'gma', 'Glyma.13G158900' => 'gma', 'Glyma.17G112400' => 'gma', 'Glyma.18G014100' => 'gma', 'Glyma.19G003100' => 'gma', 'Glyma.19G056500' => 'gma', 'Gohir.A01G158900' => 'ghi', 'Gohir.A05G312600' => 'ghi', 'Gohir.A05G354900' => 'ghi', 'Gohir.A07G037200' => 'ghi', 'Gohir.A09G030000' => 'ghi', 'Gohir.A12G145200' => 'ghi', 'Gohir.D01G151500' => 'ghi', 'Gohir.D04G058300' => 'ghi', 'Gohir.D05G314100' => 'ghi', 'Gohir.D07G041400' => 'ghi', 'Gohir.D09G029700' => 'ghi', 'Gohir.D12G149700' => 'ghi', 'Gorai.001G043800' => 'gra', 'Gorai.002G187800' => 'gra', 'Gorai.006G034700' => 'gra', 'Gorai.008G161200' => 'gra', 'Gorai.009G335700' => 'gra', 'Gorai.012G065000' => 'gra', 'GSVIVG01000535001' => 'vvi', 'GSVIVG01015572001' => 'vvi', 'GSVIVG01032386001' => 'vvi', 'HanXRQChr05g0138531' => 'han', 'HanXRQChr06g0174391' => 'han', 'HanXRQChr07g0199021' => 'han', 'HanXRQChr08g0208211' => 'han', 'HanXRQChr09g0255471' => 'han', 'HanXRQChr10g0315791' => 'han', 'HanXRQChr12g0371991' => 'han', 'HanXRQChr15g0475251' => 'han', 'HanXRQChr17g0540001' => 'han', 'HanXRQChr17g0548631' => 'han', 'HanXRQChr17g0569561' => 'han', 'Haze_12256' => 'cav', 'Haze_14756' => 'cav', 'Haze_25528' => 'cav', 'Hma1.2p1_0079F.1_g041020' => 'hma', 'Hma1.2p1_0818F.1_g223260' => 'hma', 'Hma1.2p1_1747F.1_g300530' => 'hma', 'HPP92_004607' => 'vpl', 'HPP92_004608' => 'vpl', 'HPP92_006181' => 'vpl', 'HPP92_012192' => 'vpl', 'HPP92_015680' => 'vpl', 'HPP92_020249' => 'vpl', 'HPP92_021376' => 'vpl', 'HPP92_024275' => 'vpl', 'Hund06031' => 'sun', 'Hund25391' => 'sun', 'Lalb_Chr07g0185371' => 'lal', 'Lalb_Chr07g0185381' => 'lal', 'Lalb_Chr12g0204011' => 'lal', 'Lalb_Chr13g0301671' => 'lal', 'Lalb_Chr14g0362851' => 'lal', 'Lalb_Chr24g0403581' => 'lal', 'Lj1g0000233' => 'lja', 'Lj2g0018120' => 'lja', 'Lj3C621T0' => 'lonja', 'Lj3P1059T14' => 'lonja', 'Lj3P611T9' => 'lonja', 'Lj3P614T13' => 'lonja', 'Lj3P615T5' => 'lonja', 'Lj4g0012315' => 'lja', 'Lj4g0026182' => 'lja', 'Lj6P813T16' => 'lonja', 'Lj7C427T7' => 'lonja', 'Lj7C427T8' => 'lonja', 'Lj7P600T41' => 'lonja', 'Lju41C42G17' => 'lonja', 'Lsat_1_v5_gn_0_47300' => 'lsa', 'Lsat_1_v5_gn_2_91280' => 'lsa', 'Lsat_1_v5_gn_3_30561' => 'lsa', 'Lsat_1_v5_gn_4_184321' => 'lsa', 'Lsat_1_v5_gn_4_4041' => 'lsa', 'Lsat_1_v5_gn_5_92000' => 'lsa', 'Lsat_1_v5_gn_8_152940' => 'lsa', 'Lsat_1_v5_gn_8_62401' => 'lsa', 'Manes.06G055900' => 'mes', 'Manes.12G022200' => 'mes', 'Manes.13G023300' => 'mes', 'Manes.14G115000' => 'mes', 'Manes.15G151700' => 'mes', 'Manes.17G111300' => 'mes', 'Mapoly0226s0009' => 'mpo', 'MBI02_g25363_MAGBIO' => 'mbi', 'MBI06_g00027_MAGBIO' => 'mbi', 'MBI10_g13034_MAGBIO' => 'mbi', 'MD09G1023400' => 'mdo', 'MD13G1100100' => 'mdo', 'MD15G1169200' => 'mdo', 'MD16G1101100' => 'mdo', 'MD17G1022900' => 'mdo', 'Medtr3g096150' => 'mtr', 'Medtr4g115070' => 'mtr', 'Medtr7g033325' => 'mtr', 'Medtr8g089840' => 'mtr', 'MELO3C010319.2' => 'cme', 'MELO3C011944.2' => 'cme', 'MELO3C021589.2' => 'cme', 'Migut.E00207' => 'egut', 'Migut.H00067' => 'egut', 'Migut.K00433' => 'egut', 'Migut.K00606' => 'egut', 'Migut.K01410' => 'egut', 'MSTRG.13347' => 'ama', 'MSTRG.24045' => 'ama', 'MSTRG.2428' => 'ama', 'MSTRG.26410' => 'ama', 'MSTRG.3139' => 'ama', 'MSTRG.3286' => 'ama', 'MSTRG.563' => 'ama', 'MSTRG.7941' => 'ama', 'Nitab4.5_0000028g0060' => 'nta', 'Nitab4.5_0000065g0260' => 'nta', 'Nitab4.5_0000112g0060' => 'nta', 'Nitab4.5_0000489g0120' => 'nta', 'Nitab4.5_0001776g0050' => 'nta', 'Nitab4.5_0001854g0010' => 'nta', 'Nitab4.5_0001860g0020' => 'nta', 'Nitab4.5_0004352g0010' => 'nta', 'Nitab4.5_0008716g0020' => 'nta', 'Nitab4.5_0008922g0010' => 'nta', 'Nn3g16693' => 'nnu', 'Nn4g22596' => 'nnu', 'Nn7g37639' => 'nnu', 'Oeu001701.1' => 'oeu', 'Oeu018149.1' => 'oeu', 'Oeu026220.1' => 'oeu', 'Oeu038635.1' => 'oeu', 'Oeu049176.1' => 'oeu', 'Oeu056706.1' => 'oeu', 'Oeu056937.1' => 'oeu', 'Oeu057540.1' => 'oeu', 'Os02g0594900' => 'osa', 'Os02g0595100' => 'osa', 'Os04g0477500' => 'osa', 'Os12g0611900' => 'osa', 'Peaxi162Scf00076g00020' => 'pax', 'Peaxi162Scf00128g00217' => 'pax', 'Peaxi162Scf00129g01640' => 'pax', 'Peaxi162Scf00669g00007' => 'pax', 'Peaxi162Scf00700g00421' => 'pax', 'Peaxi162Scf00801g00038' => 'pax', 'Peaxi162Scf00891g00025' => 'pax', 'PGR083G0909' => 'pgr', 'PGR119G1005' => 'pgr', 'PGR142G2236' => 'pgr', 'PGR142G3388' => 'pgr', 'PGSC0003DMG400004514' => 'stu', 'PGSC0003DMG400012635' => 'stu', 'PGSC0003DMG400015730' => 'stu', 'PGSC0003DMG400018611' => 'stu', 'PGSC0003DMG400030897' => 'stu', 'Phvul.001G254800' => 'pvu', 'Phvul.002G260100' => 'pvu', 'Phvul.003G167600' => 'pvu', 'Phvul.004G005100' => 'pvu', 'Potri.001G343600' => 'ptr', 'Potri.006G066700' => 'ptr', 'Potri.008G186000' => 'ptr', 'Potri.010G046900' => 'ptr', 'Potri.018G127900' => 'ptr', 'Pp3c20_17750' => 'ppa', 'Pp3c24_4380' => 'ppa', 'Prupe.1G245800' => 'ppe', 'Prupe.3G293400' => 'ppe', 'Prupe.7G247400' => 'ppe', 'Psat0s145g0120' => 'psa', 'Psat0s595g0040' => 'psa', 'Psat0s595g0120' => 'psa', 'Psat3g175040' => 'psa', 'Psat7g058120' => 'psa', 'PSO017G0428' => 'pso', 'PSO063G7510' => 'pso', 'PSO067G0046' => 'pso', 'PSO478G1073' => 'pso', 'PSO675G3677' => 'pso', 'PSO675G6558' => 'pso', 'PSO675G7520' => 'pso', 'PSO675G8959' => 'pso', 'QL02p074089' => 'qlo', 'QL02p089614' => 'qlo', 'QL03p057736' => 'qlo', 'RcHm_v2.0_Chr1g0364131' => 'rch', 'RcHm_v2.0_Chr2g0087801' => 'rch', 'RcHm_v2.0_Chr2g0087821' => 'rch', 'RcHm_v2.0_Chr2g0173231' => 'rch', 'RcHm_v2.0_Chr4g0433111' => 'rch', 'Rhsim03G0250300' => 'rsi', 'Rhsim08G0048400' => 'rsi', 'Rhsim10G0014800' => 'rsi', 'Rhsim12G0040100' => 'rsi', 'Rhsim12G0109700' => 'rsi', 'Sabra06G0049600' => 'sbr', 'Sabra08G0141000' => 'sbr', 'Sabra10G0021400' => 'sbr', 'Sabra16G0222900' => 'sbr', 'Sabra18G0108600' => 'sbr', 'SalBow1G0433' => 'sbo', 'SalBow1G2038' => 'sbo', 'SalBow1G5003' => 'sbo', 'SalBow7G1197' => 'sbo', 'SalBow8G3506' => 'sbo', 'Sc03g0007300' => 'sci', 'Sc11g0000950' => 'sci', 'Sc14g0008750' => 'sci', 'Sc18g0000420' => 'sci', 'Sed0006754' => 'sed', 'Sed0008741' => 'sed', 'Sed0017172' => 'sed', 'Sed0018925' => 'sed', 'Sed0023326' => 'sed', 'Sed0025909' => 'sed', 'SEGI_05333' => 'sgi', 'SEGI_10362' => 'sgi', 'SEGI_13380' => 'sgi', 'SEGI_24306' => 'sgi', 'SEGI_29077' => 'sgi', 'SEGI_29095' => 'sgi', 'SEGI_36534' => 'sgi', 'SEGI_37506' => 'sgi', 'SEGI_38321' => 'sgi', 'SGA_v2.0_scaffold307G48031' => 'sas', 'SGA_v2.0_scaffold47G17507' => 'sas', 'SGA_v2.0_scaffold63G21736' => 'sas', 'SGA_v2.0_scaffold87G27070' => 'sas', 'SHI17794' => 'shi', 'SHI28851' => 'shi', 'SMO165G0155' => 'smo', 'SMO340G0217' => 'smo', 'SMO367G1210' => 'smo', 'Solyc02g093430.3' => 'sly', 'Solyc05g013580.4' => 'sly', 'Solyc07g008030.3' => 'sly', 'Solyc12g035470.2' => 'sly', 'Sopen02g038020' => 'spe', 'Sopen05g008490' => 'spe', 'Sopen07g003910' => 'spe', 'Sopen12g015240' => 'spe', 'Sp1g11550' => 'spa', 'Sp2g16710' => 'spa', 'Sp3g00430' => 'spa', 'Sp3g26780' => 'spa', 'Sp5g22900' => 'spa', 'Sp6g29530' => 'spa', 'TAR371G0794' => 'tar', 'TAR374G0164' => 'tar', 'TAR622G0165' => 'tar', 'TAR626G0929' => 'tar', 'TAR629G2155' => 'tar', 'THA.LOC104805282' => 'tha', 'THA.LOC104805363' => 'tha', 'THA.LOC104808968' => 'tha', 'THA.LOC104821093' => 'tha', 'THA.LOC104823953' => 'tha', 'THA.LOC104825562' => 'tha', 'THA.LOC104825665' => 'tha', 'Thecc.02G261400' => 'tca', 'Thecc.04G019200' => 'tca', 'Thecc.09G130400' => 'tca', 'Thhalv10004374m.g' => 'esa', 'Thhalv10007850m.g' => 'esa', 'Thhalv10013782m.g' => 'esa', 'Thhalv10018686m.g' => 'esa', 'Thhalv10020899m.g' => 'esa', 'Thhalv10022755m.g' => 'esa', 'TPR.G23851' => 'tpr', 'TPR.G26500' => 'tpr', 'TPR.G27267' => 'tpr', 'TPR.G32001' => 'tpr', 'TPR.G6251' => 'tpr', 'TPR.G8167' => 'tpr', 'TWI12G1330' => 'twi', 'TWI18G1239' => 'twi', 'TWI34G0979' => 'twi', 'TWI36G0670' => 'twi', 'TWI36G0707' => 'twi', 'TWI56G0233' => 'twi', 'TWI75G1809' => 'twi', 'unitig_21.g20874' => 'ugi', 'unitig_26.g10343' => 'ugi', 'unitig_46.g18392' => 'ugi', 'unitig_52.g17178' => 'ugi', 'unitig_8.g2934' => 'ugi', 'vmacro01122' => 'vma', 'vmacro05875' => 'vma', 'vmacro06147' => 'vma', 'vmacro16191' => 'vma', 'vmacro18293' => 'vma', 'VMungo0251G3707' => 'vmu', 'VMungo0464G1521' => 'vmu', 'VMungo1215G0205' => 'vmu', 'VMungo1383G2484' => 'vmu', 'Zm00001eb079610' => 'zma', 'Zm00001eb135990' => 'zma', 'Zm00001eb183710' => 'zma', 'Zm00001eb246020' => 'zma' ), 'gf_id' => 'HOM05D001124', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001124' ), 'data_identifier' => 'HOM05D001124', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001124', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '548', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02520' => 'bna', 'A03p06630' => 'bna', 'A05p44460' => 'bna', 'A06p08710' => 'bna', 'A06p41090' => 'bna', 'A07p32320' => 'bna', 'A08p32520' => 'bna', 'A09p10360' => 'bna', 'A10p24080' => 'bna', 'Aa31LG11G15250' => 'aar', 'Aa31LG1G1800' => 'aar', 'Aa31LG2G5120' => 'aar', 'Aa31LG2G6070' => 'aar', 'Aa31LG5G10770' => 'aar', 'Aa31sc61G90' => 'aar', 'Actinidia01352' => 'ach', 'Actinidia05983' => 'ach', 'Actinidia08133' => 'ach', 'Actinidia15101' => 'ach', 'Actinidia26379' => 'ach', 'Actinidia35778' => 'ach', 'Actinidia36123' => 'ach', 'Actinidia37436' => 'ach', 'Actinidia38730' => 'ach', 'Ah.02g128210' => 'amhyb', 'Ah.03g132990' => 'amhyb', 'Ah.14g079410' => 'amhyb', 'AL1G24640' => 'aly', 'AL2G26680' => 'aly', 'AL3G10530' => 'aly', 'AL3G45230' => 'aly', 'AL5G15230' => 'aly', 'AL5G16960' => 'aly', 'AL6G25210' => 'aly', 'Aqoxy2G00441' => 'aox', 'Aqoxy3G01236' => 'aox', 'Aqoxy5G03746' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3RQ047' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C7GMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9C8JER' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MBL6KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YXCZ83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZANX40' => 'arhy', 'AT1G12990' => 'ath', 'AT1G67880' => 'ath', 'AT2G13290' => 'ath', 'AT3G01620' => 'ath', 'AT3G26445' => 'ath', 'AT3G27540' => 'ath', 'AT5G14480' => 'ath', 'ATR0824G026' => 'atr', 'ATR1098G019' => 'atr', 'Atru.chr11.2145' => 'acertr', 'Atru.chr2.3636' => 'acertr', 'Atru.chr2.3644' => 'acertr', 'Atru.chr6.2422' => 'acertr', 'Atru.chr7.1112' => 'acertr', 'AUR62005469' => 'cqu', 'AUR62011166' => 'cqu', 'AUR62013319' => 'cqu', 'AUR62024273' => 'cqu', 'AUR62028420' => 'cqu', 'AUR62041942' => 'cqu', 'BcaB01g04969' => 'bca', 'BcaB01g06371' => 'bca', 'BcaB02g11494' => 'bca', 'BcaB03g15382' => 'bca', 'BcaB08g36994' => 'bca', 'BcaC03g13477' => 'bca', 'BcaC03g13478' => 'bca', 'BcaC03g13480' => 'bca', 'BcaC03g13481' => 'bca', 'BcaC03g13486' => 'bca', 'BcaC04g19031' => 'bca', 'BcaC04g23085' => 'bca', 'BcaC05g25094' => 'bca', 'BcaC05g25096' => 'bca', 'BcaC05g25138' => 'bca', 'BcaC05g30416' => 'bca', 'BcaC05g30455' => 'bca', 'BcaC06g30979' => 'bca', 'BcaC06g33805' => 'bca', 'BcaC08g46021' => 'bca', 'BcaNung03154' => 'bca', 'BolC2t06623H' => 'bol', 'BolC2t06632H' => 'bol', 'BolC2t06635H' => 'bol', 'BolC2t06638H' => 'bol', 'BolC3t13266H' => 'bol', 'BolC5t29776H' => 'bol', 'BolC6t38912H' => 'bol', 'BolC7t44183H' => 'bol', 'BolC9t54123H' => 'bol', 'BolC9t59107H' => 'bol', 'BraA02t05221Z' => 'bra', 'BraA03t09996Z' => 'bra', 'BraA05t23210Z' => 'bra', 'BraA06t24068Z' => 'bra', 'BraA06t27032Z' => 'bra', 'BraA08t35176Z' => 'bra', 'BraA09t36680Z' => 'bra', 'BraA10t44471Z' => 'bra', 'C02p06760' => 'bna', 'C02p06890' => 'bna', 'C02p07010' => 'bna', 'C03p07660' => 'bna', 'C05p10300' => 'bna', 'C06p38150' => 'bna', 'C07p36650' => 'bna', 'C08p15770' => 'bna', 'C09p12300' => 'bna', 'C09p62700' => 'bna', 'C09p75040' => 'bna', 'CAN.G13.1' => 'can', 'CAN.G138.4' => 'can', 'CAN.G44.6' => 'can', 'CAN.G473.19' => 'can', 'CANSAT01G0835' => 'cansat', 'CANSAT11G0246' => 'cansat', 'CANSAT11G1766' => 'cansat', 'CANSAT64G1954' => 'cansat', 'CARHR013330' => 'chi', 'CARHR060530' => 'chi', 'CARHR075300' => 'chi', 'CARHR105120' => 'chi', 'CARHR148910' => 'chi', 'CARHR198830' => 'chi', 'Carub.0001s1275' => 'cru', 'Carub.0002s1437' => 'cru', 'Carub.0003s0044' => 'cru', 'Carub.0003s2787' => 'cru', 'Carub.0005s0597' => 'cru', 'Carub.0006s1266' => 'cru', 'Ca_06935_v3' => 'car', 'Ca_13559_v3' => 'car', 'Ca_16941_v3' => 'car', 'Ca_16960_v3' => 'car', 'Ca_17775_v3' => 'car', 'Ca_30464_v3' => 'car', 'Cc06_g08160' => 'ccan', 'Cc07_g01520' => 'ccan', 'Cc11_g15810' => 'ccan', 'CDE02G2840' => 'cde', 'CDE03G0093' => 'cde', 'CDE04G2127' => 'cde', 'CDE07G1857' => 'cde', 'CDE09G1246' => 'cde', 'Cfa003412' => 'cfa', 'Cfa007341' => 'cfa', 'Cfa009220' => 'cfa', 'Ciclev10008737m.g' => 'ccl', 'Ciclev10015565m.g' => 'ccl', 'Ciclev10031761m.g' => 'ccl', 'CiPaw.03G045300' => 'cil', 'CiPaw.03G247200' => 'cil', 'CiPaw.04G029500' => 'cil', 'CiPaw.04G174000' => 'cil', 'CiPaw.05G181200' => 'cil', 'CiPaw.06G067100' => 'cil', 'ClCG05G025800' => 'cla', 'ClCG06G011400' => 'cla', 'ClCG09G019360' => 'cla', 'COL.COLO4_04827' => 'col', 'COL.COLO4_29170' => 'col', 'COL.COLO4_35131' => 'col', 'COL.COLO4_35132' => 'col', 'Cpa.g.sc33.32' => 'cpa', 'Cpa.g.sc46.29' => 'cpa', 'Cpa.g.sc796.1' => 'cpa', 'CsaV3_1G030420' => 'csa', 'CsaV3_5G027050' => 'csa', 'CsaV3_5G031040' => 'csa', 'CsaV3_UNG023130' => 'csa', 'CSS0007726' => 'camsi', 'CSS0016433' => 'camsi', 'CSS0017656' => 'camsi', 'CSS0025364' => 'camsi', 'CSS0027582' => 'camsi', 'CSS0047288' => 'camsi', 'CSS0049950' => 'camsi', 'DCAR_003843' => 'dca', 'DCAR_007052' => 'dca', 'DCAR_020884' => 'dca', 'DCAR_021730' => 'dca', 'DCAR_024423' => 'dca', 'DCAR_026509' => 'dca', 'DCAR_031158' => 'dca', 'Dinv14728' => 'din', 'Dinv15219' => 'din', 'Dinv25728' => 'din', 'Dinv33428' => 'din', 'Dinv36489' => 'din', 'Dinv41486' => 'din', 'Duzib147G0469' => 'dzi', 'Duzib168G0060' => 'dzi', 'Duzib187G1215' => 'dzi', 'Duzib248G0692' => 'dzi', 'Duzib251G0767' => 'dzi', 'Duzib264G0446' => 'dzi', 'Duzib268G0691' => 'dzi', 'ECA232G4767' => 'eca', 'ECA233G2838' => 'eca', 'ECA234G0391' => 'eca', 'ECA234G0857' => 'eca', 'ECA236G1593' => 'eca', 'ECA238G0565' => 'eca', 'ECA246G1027' => 'eca', 'ECA246G3223' => 'eca', 'ECA246G3470' => 'eca', 'EL10Ac6g13829' => 'bvu', 'EL10Ac6g14093' => 'bvu', 'EL10Ac8g18707' => 'bvu', 'Eucgr.C01369' => 'egr', 'Eucgr.H02492' => 'egr', 'Eucgr.I01733' => 'egr', 'Eucgr.J02255' => 'egr', 'Eucgr.J02257' => 'egr', 'Eucgr.J02258' => 'egr', 'FAN02G1601' => 'fan', 'FAN03G1586' => 'fan', 'FAN03G2986' => 'fan', 'FAN05G4837' => 'fan', 'FAN06G0146' => 'fan', 'FAN07G0858' => 'fan', 'FAN09G3179' => 'fan', 'FAN10G0669' => 'fan', 'FAN12G2358' => 'fan', 'FAN14G4198' => 'fan', 'FAN14G5112' => 'fan', 'FAN17G0342' => 'fan', 'FAN19G0342' => 'fan', 'FAN19G0962' => 'fan', 'FAN19G1101' => 'fan', 'FAN19G1872' => 'fan', 'FAN22G0356' => 'fan', 'FAN23G0744' => 'fan', 'FAN23G1914' => 'fan', 'FAN26G0032' => 'fan', 'FAN28G0625' => 'fan', 'FvH4_1g02710' => 'fve', 'FvH4_1g02720' => 'fve', 'FvH4_4g25670' => 'fve', 'FvH4_6g51700' => 'fve', 'FvH4_7g20170' => 'fve', 'Glyma.05G175000' => 'gma', 'Glyma.08G132300' => 'gma', 'Glyma.11G243000' => 'gma', 'Glyma.13G158900' => 'gma', 'Glyma.17G112400' => 'gma', 'Glyma.18G014100' => 'gma', 'Glyma.19G003100' => 'gma', 'Glyma.19G056500' => 'gma', 'Gohir.A01G158900' => 'ghi', 'Gohir.A05G312600' => 'ghi', 'Gohir.A05G354900' => 'ghi', 'Gohir.A07G037200' => 'ghi', 'Gohir.A09G030000' => 'ghi', 'Gohir.A12G145200' => 'ghi', 'Gohir.D01G151500' => 'ghi', 'Gohir.D04G058300' => 'ghi', 'Gohir.D05G314100' => 'ghi', 'Gohir.D07G041400' => 'ghi', 'Gohir.D09G029700' => 'ghi', 'Gohir.D12G149700' => 'ghi', 'Gorai.001G043800' => 'gra', 'Gorai.002G187800' => 'gra', 'Gorai.006G034700' => 'gra', 'Gorai.008G161200' => 'gra', 'Gorai.009G335700' => 'gra', 'Gorai.012G065000' => 'gra', 'GSVIVG01000535001' => 'vvi', 'GSVIVG01015572001' => 'vvi', 'GSVIVG01032386001' => 'vvi', 'HanXRQChr05g0138531' => 'han', 'HanXRQChr06g0174391' => 'han', 'HanXRQChr07g0199021' => 'han', 'HanXRQChr08g0208211' => 'han', 'HanXRQChr09g0255471' => 'han', 'HanXRQChr10g0315791' => 'han', 'HanXRQChr12g0371991' => 'han', 'HanXRQChr15g0475251' => 'han', 'HanXRQChr17g0540001' => 'han', 'HanXRQChr17g0548631' => 'han', 'HanXRQChr17g0569561' => 'han', 'Haze_12256' => 'cav', 'Haze_14756' => 'cav', 'Haze_25528' => 'cav', 'Hma1.2p1_0079F.1_g041020' => 'hma', 'Hma1.2p1_0818F.1_g223260' => 'hma', 'Hma1.2p1_1747F.1_g300530' => 'hma', 'HPP92_004607' => 'vpl', 'HPP92_004608' => 'vpl', 'HPP92_006181' => 'vpl', 'HPP92_012192' => 'vpl', 'HPP92_015680' => 'vpl', 'HPP92_020249' => 'vpl', 'HPP92_021376' => 'vpl', 'HPP92_024275' => 'vpl', 'Hund06031' => 'sun', 'Hund25391' => 'sun', 'Lalb_Chr07g0185371' => 'lal', 'Lalb_Chr07g0185381' => 'lal', 'Lalb_Chr12g0204011' => 'lal', 'Lalb_Chr13g0301671' => 'lal', 'Lalb_Chr14g0362851' => 'lal', 'Lalb_Chr24g0403581' => 'lal', 'Lj1g0000233' => 'lja', 'Lj2g0018120' => 'lja', 'Lj3C621T0' => 'lonja', 'Lj3P1059T14' => 'lonja', 'Lj3P611T9' => 'lonja', 'Lj3P614T13' => 'lonja', 'Lj3P615T5' => 'lonja', 'Lj4g0012315' => 'lja', 'Lj4g0026182' => 'lja', 'Lj6P813T16' => 'lonja', 'Lj7C427T7' => 'lonja', 'Lj7C427T8' => 'lonja', 'Lj7P600T41' => 'lonja', 'Lju41C42G17' => 'lonja', 'Lsat_1_v5_gn_0_47300' => 'lsa', 'Lsat_1_v5_gn_2_91280' => 'lsa', 'Lsat_1_v5_gn_3_30561' => 'lsa', 'Lsat_1_v5_gn_4_184321' => 'lsa', 'Lsat_1_v5_gn_4_4041' => 'lsa', 'Lsat_1_v5_gn_5_92000' => 'lsa', 'Lsat_1_v5_gn_8_152940' => 'lsa', 'Lsat_1_v5_gn_8_62401' => 'lsa', 'Manes.06G055900' => 'mes', 'Manes.12G022200' => 'mes', 'Manes.13G023300' => 'mes', 'Manes.14G115000' => 'mes', 'Manes.15G151700' => 'mes', 'Manes.17G111300' => 'mes', 'Mapoly0226s0009' => 'mpo', 'MBI02_g25363_MAGBIO' => 'mbi', 'MBI06_g00027_MAGBIO' => 'mbi', 'MBI10_g13034_MAGBIO' => 'mbi', 'MD09G1023400' => 'mdo', 'MD13G1100100' => 'mdo', 'MD15G1169200' => 'mdo', 'MD16G1101100' => 'mdo', 'MD17G1022900' => 'mdo', 'Medtr3g096150' => 'mtr', 'Medtr4g115070' => 'mtr', 'Medtr7g033325' => 'mtr', 'Medtr8g089840' => 'mtr', 'MELO3C010319.2' => 'cme', 'MELO3C011944.2' => 'cme', 'MELO3C021589.2' => 'cme', 'Migut.E00207' => 'egut', 'Migut.H00067' => 'egut', 'Migut.K00433' => 'egut', 'Migut.K00606' => 'egut', 'Migut.K01410' => 'egut', 'MSTRG.13347' => 'ama', 'MSTRG.24045' => 'ama', 'MSTRG.2428' => 'ama', 'MSTRG.26410' => 'ama', 'MSTRG.3139' => 'ama', 'MSTRG.3286' => 'ama', 'MSTRG.563' => 'ama', 'MSTRG.7941' => 'ama', 'Nitab4.5_0000028g0060' => 'nta', 'Nitab4.5_0000065g0260' => 'nta', 'Nitab4.5_0000112g0060' => 'nta', 'Nitab4.5_0000489g0120' => 'nta', 'Nitab4.5_0001776g0050' => 'nta', 'Nitab4.5_0001854g0010' => 'nta', 'Nitab4.5_0001860g0020' => 'nta', 'Nitab4.5_0004352g0010' => 'nta', 'Nitab4.5_0008716g0020' => 'nta', 'Nitab4.5_0008922g0010' => 'nta', 'Nn3g16693' => 'nnu', 'Nn4g22596' => 'nnu', 'Nn7g37639' => 'nnu', 'Oeu001701.1' => 'oeu', 'Oeu018149.1' => 'oeu', 'Oeu026220.1' => 'oeu', 'Oeu038635.1' => 'oeu', 'Oeu049176.1' => 'oeu', 'Oeu056706.1' => 'oeu', 'Oeu056937.1' => 'oeu', 'Oeu057540.1' => 'oeu', 'Os02g0594900' => 'osa', 'Os02g0595100' => 'osa', 'Os04g0477500' => 'osa', 'Os12g0611900' => 'osa', 'Peaxi162Scf00076g00020' => 'pax', 'Peaxi162Scf00128g00217' => 'pax', 'Peaxi162Scf00129g01640' => 'pax', 'Peaxi162Scf00669g00007' => 'pax', 'Peaxi162Scf00700g00421' => 'pax', 'Peaxi162Scf00801g00038' => 'pax', 'Peaxi162Scf00891g00025' => 'pax', 'PGR083G0909' => 'pgr', 'PGR119G1005' => 'pgr', 'PGR142G2236' => 'pgr', 'PGR142G3388' => 'pgr', 'PGSC0003DMG400004514' => 'stu', 'PGSC0003DMG400012635' => 'stu', 'PGSC0003DMG400015730' => 'stu', 'PGSC0003DMG400018611' => 'stu', 'PGSC0003DMG400030897' => 'stu', 'Phvul.001G254800' => 'pvu', 'Phvul.002G260100' => 'pvu', 'Phvul.003G167600' => 'pvu', 'Phvul.004G005100' => 'pvu', 'Potri.001G343600' => 'ptr', 'Potri.006G066700' => 'ptr', 'Potri.008G186000' => 'ptr', 'Potri.010G046900' => 'ptr', 'Potri.018G127900' => 'ptr', 'Pp3c20_17750' => 'ppa', 'Pp3c24_4380' => 'ppa', 'Prupe.1G245800' => 'ppe', 'Prupe.3G293400' => 'ppe', 'Prupe.7G247400' => 'ppe', 'Psat0s145g0120' => 'psa', 'Psat0s595g0040' => 'psa', 'Psat0s595g0120' => 'psa', 'Psat3g175040' => 'psa', 'Psat7g058120' => 'psa', 'PSO017G0428' => 'pso', 'PSO063G7510' => 'pso', 'PSO067G0046' => 'pso', 'PSO478G1073' => 'pso', 'PSO675G3677' => 'pso', 'PSO675G6558' => 'pso', 'PSO675G7520' => 'pso', 'PSO675G8959' => 'pso', 'QL02p074089' => 'qlo', 'QL02p089614' => 'qlo', 'QL03p057736' => 'qlo', 'RcHm_v2.0_Chr1g0364131' => 'rch', 'RcHm_v2.0_Chr2g0087801' => 'rch', 'RcHm_v2.0_Chr2g0087821' => 'rch', 'RcHm_v2.0_Chr2g0173231' => 'rch', 'RcHm_v2.0_Chr4g0433111' => 'rch', 'Rhsim03G0250300' => 'rsi', 'Rhsim08G0048400' => 'rsi', 'Rhsim10G0014800' => 'rsi', 'Rhsim12G0040100' => 'rsi', 'Rhsim12G0109700' => 'rsi', 'Sabra06G0049600' => 'sbr', 'Sabra08G0141000' => 'sbr', 'Sabra10G0021400' => 'sbr', 'Sabra16G0222900' => 'sbr', 'Sabra18G0108600' => 'sbr', 'SalBow1G0433' => 'sbo', 'SalBow1G2038' => 'sbo', 'SalBow1G5003' => 'sbo', 'SalBow7G1197' => 'sbo', 'SalBow8G3506' => 'sbo', 'Sc03g0007300' => 'sci', 'Sc11g0000950' => 'sci', 'Sc14g0008750' => 'sci', 'Sc18g0000420' => 'sci', 'Sed0006754' => 'sed', 'Sed0008741' => 'sed', 'Sed0017172' => 'sed', 'Sed0018925' => 'sed', 'Sed0023326' => 'sed', 'Sed0025909' => 'sed', 'SEGI_05333' => 'sgi', 'SEGI_10362' => 'sgi', 'SEGI_13380' => 'sgi', 'SEGI_24306' => 'sgi', 'SEGI_29077' => 'sgi', 'SEGI_29095' => 'sgi', 'SEGI_36534' => 'sgi', 'SEGI_37506' => 'sgi', 'SEGI_38321' => 'sgi', 'SGA_v2.0_scaffold307G48031' => 'sas', 'SGA_v2.0_scaffold47G17507' => 'sas', 'SGA_v2.0_scaffold63G21736' => 'sas', 'SGA_v2.0_scaffold87G27070' => 'sas', 'SHI17794' => 'shi', 'SHI28851' => 'shi', 'SMO165G0155' => 'smo', 'SMO340G0217' => 'smo', 'SMO367G1210' => 'smo', 'Solyc02g093430.3' => 'sly', 'Solyc05g013580.4' => 'sly', 'Solyc07g008030.3' => 'sly', 'Solyc12g035470.2' => 'sly', 'Sopen02g038020' => 'spe', 'Sopen05g008490' => 'spe', 'Sopen07g003910' => 'spe', 'Sopen12g015240' => 'spe', 'Sp1g11550' => 'spa', 'Sp2g16710' => 'spa', 'Sp3g00430' => 'spa', 'Sp3g26780' => 'spa', 'Sp5g22900' => 'spa', 'Sp6g29530' => 'spa', 'TAR371G0794' => 'tar', 'TAR374G0164' => 'tar', 'TAR622G0165' => 'tar', 'TAR626G0929' => 'tar', 'TAR629G2155' => 'tar', 'THA.LOC104805282' => 'tha', 'THA.LOC104805363' => 'tha', 'THA.LOC104808968' => 'tha', 'THA.LOC104821093' => 'tha', 'THA.LOC104823953' => 'tha', 'THA.LOC104825562' => 'tha', 'THA.LOC104825665' => 'tha', 'Thecc.02G261400' => 'tca', 'Thecc.04G019200' => 'tca', 'Thecc.09G130400' => 'tca', 'Thhalv10004374m.g' => 'esa', 'Thhalv10007850m.g' => 'esa', 'Thhalv10013782m.g' => 'esa', 'Thhalv10018686m.g' => 'esa', 'Thhalv10020899m.g' => 'esa', 'Thhalv10022755m.g' => 'esa', 'TPR.G23851' => 'tpr', 'TPR.G26500' => 'tpr', 'TPR.G27267' => 'tpr', 'TPR.G32001' => 'tpr', 'TPR.G6251' => 'tpr', 'TPR.G8167' => 'tpr', 'TWI12G1330' => 'twi', 'TWI18G1239' => 'twi', 'TWI34G0979' => 'twi', 'TWI36G0670' => 'twi', 'TWI36G0707' => 'twi', 'TWI56G0233' => 'twi', 'TWI75G1809' => 'twi', 'unitig_21.g20874' => 'ugi', 'unitig_26.g10343' => 'ugi', 'unitig_46.g18392' => 'ugi', 'unitig_52.g17178' => 'ugi', 'unitig_8.g2934' => 'ugi', 'vmacro01122' => 'vma', 'vmacro05875' => 'vma', 'vmacro06147' => 'vma', 'vmacro16191' => 'vma', 'vmacro18293' => 'vma', 'VMungo0251G3707' => 'vmu', 'VMungo0464G1521' => 'vmu', 'VMungo1215G0205' => 'vmu', 'VMungo1383G2484' => 'vmu', 'Zm00001eb079610' => 'zma', 'Zm00001eb135990' => 'zma', 'Zm00001eb183710' => 'zma', 'Zm00001eb246020' => 'zma' ) $gf_id = 'HOM05D001124' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001124' ) $data_identifier = 'HOM05D001124' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 6, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 7, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 21, 'bol' => (int) 10, 'bra' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 6, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 9, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 21, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 8, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 10, 'lsa' => (int) 8, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 8, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 9, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb246020' $species_info = array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ) $local_species = 'ghi' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001124', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '548', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02520' => 'bna', 'A03p06630' => 'bna', 'A05p44460' => 'bna', 'A06p08710' => 'bna', 'A06p41090' => 'bna', 'A07p32320' => 'bna', 'A08p32520' => 'bna', 'A09p10360' => 'bna', 'A10p24080' => 'bna', 'Aa31LG11G15250' => 'aar', 'Aa31LG1G1800' => 'aar', 'Aa31LG2G5120' => 'aar', 'Aa31LG2G6070' => 'aar', 'Aa31LG5G10770' => 'aar', 'Aa31sc61G90' => 'aar', 'Actinidia01352' => 'ach', 'Actinidia05983' => 'ach', 'Actinidia08133' => 'ach', 'Actinidia15101' => 'ach', 'Actinidia26379' => 'ach', 'Actinidia35778' => 'ach', 'Actinidia36123' => 'ach', 'Actinidia37436' => 'ach', 'Actinidia38730' => 'ach', 'Ah.02g128210' => 'amhyb', 'Ah.03g132990' => 'amhyb', 'Ah.14g079410' => 'amhyb', 'AL1G24640' => 'aly', 'AL2G26680' => 'aly', 'AL3G10530' => 'aly', 'AL3G45230' => 'aly', 'AL5G15230' => 'aly', 'AL5G16960' => 'aly', 'AL6G25210' => 'aly', 'Aqoxy2G00441' => 'aox', 'Aqoxy3G01236' => 'aox', 'Aqoxy5G03746' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3RQ047' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C7GMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9C8JER' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MBL6KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YXCZ83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZANX40' => 'arhy', 'AT1G12990' => 'ath', 'AT1G67880' => 'ath', 'AT2G13290' => 'ath', 'AT3G01620' => 'ath', 'AT3G26445' => 'ath', 'AT3G27540' => 'ath', 'AT5G14480' => 'ath', 'ATR0824G026' => 'atr', 'ATR1098G019' => 'atr', 'Atru.chr11.2145' => 'acertr', 'Atru.chr2.3636' => 'acertr', 'Atru.chr2.3644' => 'acertr', 'Atru.chr6.2422' => 'acertr', 'Atru.chr7.1112' => 'acertr', 'AUR62005469' => 'cqu', 'AUR62011166' => 'cqu', 'AUR62013319' => 'cqu', 'AUR62024273' => 'cqu', 'AUR62028420' => 'cqu', 'AUR62041942' => 'cqu', 'BcaB01g04969' => 'bca', 'BcaB01g06371' => 'bca', 'BcaB02g11494' => 'bca', 'BcaB03g15382' => 'bca', 'BcaB08g36994' => 'bca', 'BcaC03g13477' => 'bca', 'BcaC03g13478' => 'bca', 'BcaC03g13480' => 'bca', 'BcaC03g13481' => 'bca', 'BcaC03g13486' => 'bca', 'BcaC04g19031' => 'bca', 'BcaC04g23085' => 'bca', 'BcaC05g25094' => 'bca', 'BcaC05g25096' => 'bca', 'BcaC05g25138' => 'bca', 'BcaC05g30416' => 'bca', 'BcaC05g30455' => 'bca', 'BcaC06g30979' => 'bca', 'BcaC06g33805' => 'bca', 'BcaC08g46021' => 'bca', 'BcaNung03154' => 'bca', 'BolC2t06623H' => 'bol', 'BolC2t06632H' => 'bol', 'BolC2t06635H' => 'bol', 'BolC2t06638H' => 'bol', 'BolC3t13266H' => 'bol', 'BolC5t29776H' => 'bol', 'BolC6t38912H' => 'bol', 'BolC7t44183H' => 'bol', 'BolC9t54123H' => 'bol', 'BolC9t59107H' => 'bol', 'BraA02t05221Z' => 'bra', 'BraA03t09996Z' => 'bra', 'BraA05t23210Z' => 'bra', 'BraA06t24068Z' => 'bra', 'BraA06t27032Z' => 'bra', 'BraA08t35176Z' => 'bra', 'BraA09t36680Z' => 'bra', 'BraA10t44471Z' => 'bra', 'C02p06760' => 'bna', 'C02p06890' => 'bna', 'C02p07010' => 'bna', 'C03p07660' => 'bna', 'C05p10300' => 'bna', 'C06p38150' => 'bna', 'C07p36650' => 'bna', 'C08p15770' => 'bna', 'C09p12300' => 'bna', 'C09p62700' => 'bna', 'C09p75040' => 'bna', 'CAN.G13.1' => 'can', 'CAN.G138.4' => 'can', 'CAN.G44.6' => 'can', 'CAN.G473.19' => 'can', 'CANSAT01G0835' => 'cansat', 'CANSAT11G0246' => 'cansat', 'CANSAT11G1766' => 'cansat', 'CANSAT64G1954' => 'cansat', 'CARHR013330' => 'chi', 'CARHR060530' => 'chi', 'CARHR075300' => 'chi', 'CARHR105120' => 'chi', 'CARHR148910' => 'chi', 'CARHR198830' => 'chi', 'Carub.0001s1275' => 'cru', 'Carub.0002s1437' => 'cru', 'Carub.0003s0044' => 'cru', 'Carub.0003s2787' => 'cru', 'Carub.0005s0597' => 'cru', 'Carub.0006s1266' => 'cru', 'Ca_06935_v3' => 'car', 'Ca_13559_v3' => 'car', 'Ca_16941_v3' => 'car', 'Ca_16960_v3' => 'car', 'Ca_17775_v3' => 'car', 'Ca_30464_v3' => 'car', 'Cc06_g08160' => 'ccan', 'Cc07_g01520' => 'ccan', 'Cc11_g15810' => 'ccan', 'CDE02G2840' => 'cde', 'CDE03G0093' => 'cde', 'CDE04G2127' => 'cde', 'CDE07G1857' => 'cde', 'CDE09G1246' => 'cde', 'Cfa003412' => 'cfa', 'Cfa007341' => 'cfa', 'Cfa009220' => 'cfa', 'Ciclev10008737m.g' => 'ccl', 'Ciclev10015565m.g' => 'ccl', 'Ciclev10031761m.g' => 'ccl', 'CiPaw.03G045300' => 'cil', 'CiPaw.03G247200' => 'cil', 'CiPaw.04G029500' => 'cil', 'CiPaw.04G174000' => 'cil', 'CiPaw.05G181200' => 'cil', 'CiPaw.06G067100' => 'cil', 'ClCG05G025800' => 'cla', 'ClCG06G011400' => 'cla', 'ClCG09G019360' => 'cla', 'COL.COLO4_04827' => 'col', 'COL.COLO4_29170' => 'col', 'COL.COLO4_35131' => 'col', 'COL.COLO4_35132' => 'col', 'Cpa.g.sc33.32' => 'cpa', 'Cpa.g.sc46.29' => 'cpa', 'Cpa.g.sc796.1' => 'cpa', 'CsaV3_1G030420' => 'csa', 'CsaV3_5G027050' => 'csa', 'CsaV3_5G031040' => 'csa', 'CsaV3_UNG023130' => 'csa', 'CSS0007726' => 'camsi', 'CSS0016433' => 'camsi', 'CSS0017656' => 'camsi', 'CSS0025364' => 'camsi', 'CSS0027582' => 'camsi', 'CSS0047288' => 'camsi', 'CSS0049950' => 'camsi', 'DCAR_003843' => 'dca', 'DCAR_007052' => 'dca', 'DCAR_020884' => 'dca', 'DCAR_021730' => 'dca', 'DCAR_024423' => 'dca', 'DCAR_026509' => 'dca', 'DCAR_031158' => 'dca', 'Dinv14728' => 'din', 'Dinv15219' => 'din', 'Dinv25728' => 'din', 'Dinv33428' => 'din', 'Dinv36489' => 'din', 'Dinv41486' => 'din', 'Duzib147G0469' => 'dzi', 'Duzib168G0060' => 'dzi', 'Duzib187G1215' => 'dzi', 'Duzib248G0692' => 'dzi', 'Duzib251G0767' => 'dzi', 'Duzib264G0446' => 'dzi', 'Duzib268G0691' => 'dzi', 'ECA232G4767' => 'eca', 'ECA233G2838' => 'eca', 'ECA234G0391' => 'eca', 'ECA234G0857' => 'eca', 'ECA236G1593' => 'eca', 'ECA238G0565' => 'eca', 'ECA246G1027' => 'eca', 'ECA246G3223' => 'eca', 'ECA246G3470' => 'eca', 'EL10Ac6g13829' => 'bvu', 'EL10Ac6g14093' => 'bvu', 'EL10Ac8g18707' => 'bvu', 'Eucgr.C01369' => 'egr', 'Eucgr.H02492' => 'egr', 'Eucgr.I01733' => 'egr', 'Eucgr.J02255' => 'egr', 'Eucgr.J02257' => 'egr', 'Eucgr.J02258' => 'egr', 'FAN02G1601' => 'fan', 'FAN03G1586' => 'fan', 'FAN03G2986' => 'fan', 'FAN05G4837' => 'fan', 'FAN06G0146' => 'fan', 'FAN07G0858' => 'fan', 'FAN09G3179' => 'fan', 'FAN10G0669' => 'fan', 'FAN12G2358' => 'fan', 'FAN14G4198' => 'fan', 'FAN14G5112' => 'fan', 'FAN17G0342' => 'fan', 'FAN19G0342' => 'fan', 'FAN19G0962' => 'fan', 'FAN19G1101' => 'fan', 'FAN19G1872' => 'fan', 'FAN22G0356' => 'fan', 'FAN23G0744' => 'fan', 'FAN23G1914' => 'fan', 'FAN26G0032' => 'fan', 'FAN28G0625' => 'fan', 'FvH4_1g02710' => 'fve', 'FvH4_1g02720' => 'fve', 'FvH4_4g25670' => 'fve', 'FvH4_6g51700' => 'fve', 'FvH4_7g20170' => 'fve', 'Glyma.05G175000' => 'gma', 'Glyma.08G132300' => 'gma', 'Glyma.11G243000' => 'gma', 'Glyma.13G158900' => 'gma', 'Glyma.17G112400' => 'gma', 'Glyma.18G014100' => 'gma', 'Glyma.19G003100' => 'gma', 'Glyma.19G056500' => 'gma', 'Gohir.A01G158900' => 'ghi', 'Gohir.A05G312600' => 'ghi', 'Gohir.A05G354900' => 'ghi', 'Gohir.A07G037200' => 'ghi', 'Gohir.A09G030000' => 'ghi', 'Gohir.A12G145200' => 'ghi', 'Gohir.D01G151500' => 'ghi', 'Gohir.D04G058300' => 'ghi', 'Gohir.D05G314100' => 'ghi', 'Gohir.D07G041400' => 'ghi', 'Gohir.D09G029700' => 'ghi', 'Gohir.D12G149700' => 'ghi', 'Gorai.001G043800' => 'gra', 'Gorai.002G187800' => 'gra', 'Gorai.006G034700' => 'gra', 'Gorai.008G161200' => 'gra', 'Gorai.009G335700' => 'gra', 'Gorai.012G065000' => 'gra', 'GSVIVG01000535001' => 'vvi', 'GSVIVG01015572001' => 'vvi', 'GSVIVG01032386001' => 'vvi', 'HanXRQChr05g0138531' => 'han', 'HanXRQChr06g0174391' => 'han', 'HanXRQChr07g0199021' => 'han', 'HanXRQChr08g0208211' => 'han', 'HanXRQChr09g0255471' => 'han', 'HanXRQChr10g0315791' => 'han', 'HanXRQChr12g0371991' => 'han', 'HanXRQChr15g0475251' => 'han', 'HanXRQChr17g0540001' => 'han', 'HanXRQChr17g0548631' => 'han', 'HanXRQChr17g0569561' => 'han', 'Haze_12256' => 'cav', 'Haze_14756' => 'cav', 'Haze_25528' => 'cav', 'Hma1.2p1_0079F.1_g041020' => 'hma', 'Hma1.2p1_0818F.1_g223260' => 'hma', 'Hma1.2p1_1747F.1_g300530' => 'hma', 'HPP92_004607' => 'vpl', 'HPP92_004608' => 'vpl', 'HPP92_006181' => 'vpl', 'HPP92_012192' => 'vpl', 'HPP92_015680' => 'vpl', 'HPP92_020249' => 'vpl', 'HPP92_021376' => 'vpl', 'HPP92_024275' => 'vpl', 'Hund06031' => 'sun', 'Hund25391' => 'sun', 'Lalb_Chr07g0185371' => 'lal', 'Lalb_Chr07g0185381' => 'lal', 'Lalb_Chr12g0204011' => 'lal', 'Lalb_Chr13g0301671' => 'lal', 'Lalb_Chr14g0362851' => 'lal', 'Lalb_Chr24g0403581' => 'lal', 'Lj1g0000233' => 'lja', 'Lj2g0018120' => 'lja', 'Lj3C621T0' => 'lonja', 'Lj3P1059T14' => 'lonja', 'Lj3P611T9' => 'lonja', 'Lj3P614T13' => 'lonja', 'Lj3P615T5' => 'lonja', 'Lj4g0012315' => 'lja', 'Lj4g0026182' => 'lja', 'Lj6P813T16' => 'lonja', 'Lj7C427T7' => 'lonja', 'Lj7C427T8' => 'lonja', 'Lj7P600T41' => 'lonja', 'Lju41C42G17' => 'lonja', 'Lsat_1_v5_gn_0_47300' => 'lsa', 'Lsat_1_v5_gn_2_91280' => 'lsa', 'Lsat_1_v5_gn_3_30561' => 'lsa', 'Lsat_1_v5_gn_4_184321' => 'lsa', 'Lsat_1_v5_gn_4_4041' => 'lsa', 'Lsat_1_v5_gn_5_92000' => 'lsa', 'Lsat_1_v5_gn_8_152940' => 'lsa', 'Lsat_1_v5_gn_8_62401' => 'lsa', 'Manes.06G055900' => 'mes', 'Manes.12G022200' => 'mes', 'Manes.13G023300' => 'mes', 'Manes.14G115000' => 'mes', 'Manes.15G151700' => 'mes', 'Manes.17G111300' => 'mes', 'Mapoly0226s0009' => 'mpo', 'MBI02_g25363_MAGBIO' => 'mbi', 'MBI06_g00027_MAGBIO' => 'mbi', 'MBI10_g13034_MAGBIO' => 'mbi', 'MD09G1023400' => 'mdo', 'MD13G1100100' => 'mdo', 'MD15G1169200' => 'mdo', 'MD16G1101100' => 'mdo', 'MD17G1022900' => 'mdo', 'Medtr3g096150' => 'mtr', 'Medtr4g115070' => 'mtr', 'Medtr7g033325' => 'mtr', 'Medtr8g089840' => 'mtr', 'MELO3C010319.2' => 'cme', 'MELO3C011944.2' => 'cme', 'MELO3C021589.2' => 'cme', 'Migut.E00207' => 'egut', 'Migut.H00067' => 'egut', 'Migut.K00433' => 'egut', 'Migut.K00606' => 'egut', 'Migut.K01410' => 'egut', 'MSTRG.13347' => 'ama', 'MSTRG.24045' => 'ama', 'MSTRG.2428' => 'ama', 'MSTRG.26410' => 'ama', 'MSTRG.3139' => 'ama', 'MSTRG.3286' => 'ama', 'MSTRG.563' => 'ama', 'MSTRG.7941' => 'ama', 'Nitab4.5_0000028g0060' => 'nta', 'Nitab4.5_0000065g0260' => 'nta', 'Nitab4.5_0000112g0060' => 'nta', 'Nitab4.5_0000489g0120' => 'nta', 'Nitab4.5_0001776g0050' => 'nta', 'Nitab4.5_0001854g0010' => 'nta', 'Nitab4.5_0001860g0020' => 'nta', 'Nitab4.5_0004352g0010' => 'nta', 'Nitab4.5_0008716g0020' => 'nta', 'Nitab4.5_0008922g0010' => 'nta', 'Nn3g16693' => 'nnu', 'Nn4g22596' => 'nnu', 'Nn7g37639' => 'nnu', 'Oeu001701.1' => 'oeu', 'Oeu018149.1' => 'oeu', 'Oeu026220.1' => 'oeu', 'Oeu038635.1' => 'oeu', 'Oeu049176.1' => 'oeu', 'Oeu056706.1' => 'oeu', 'Oeu056937.1' => 'oeu', 'Oeu057540.1' => 'oeu', 'Os02g0594900' => 'osa', 'Os02g0595100' => 'osa', 'Os04g0477500' => 'osa', 'Os12g0611900' => 'osa', 'Peaxi162Scf00076g00020' => 'pax', 'Peaxi162Scf00128g00217' => 'pax', 'Peaxi162Scf00129g01640' => 'pax', 'Peaxi162Scf00669g00007' => 'pax', 'Peaxi162Scf00700g00421' => 'pax', 'Peaxi162Scf00801g00038' => 'pax', 'Peaxi162Scf00891g00025' => 'pax', 'PGR083G0909' => 'pgr', 'PGR119G1005' => 'pgr', 'PGR142G2236' => 'pgr', 'PGR142G3388' => 'pgr', 'PGSC0003DMG400004514' => 'stu', 'PGSC0003DMG400012635' => 'stu', 'PGSC0003DMG400015730' => 'stu', 'PGSC0003DMG400018611' => 'stu', 'PGSC0003DMG400030897' => 'stu', 'Phvul.001G254800' => 'pvu', 'Phvul.002G260100' => 'pvu', 'Phvul.003G167600' => 'pvu', 'Phvul.004G005100' => 'pvu', 'Potri.001G343600' => 'ptr', 'Potri.006G066700' => 'ptr', 'Potri.008G186000' => 'ptr', 'Potri.010G046900' => 'ptr', 'Potri.018G127900' => 'ptr', 'Pp3c20_17750' => 'ppa', 'Pp3c24_4380' => 'ppa', 'Prupe.1G245800' => 'ppe', 'Prupe.3G293400' => 'ppe', 'Prupe.7G247400' => 'ppe', 'Psat0s145g0120' => 'psa', 'Psat0s595g0040' => 'psa', 'Psat0s595g0120' => 'psa', 'Psat3g175040' => 'psa', 'Psat7g058120' => 'psa', 'PSO017G0428' => 'pso', 'PSO063G7510' => 'pso', 'PSO067G0046' => 'pso', 'PSO478G1073' => 'pso', 'PSO675G3677' => 'pso', 'PSO675G6558' => 'pso', 'PSO675G7520' => 'pso', 'PSO675G8959' => 'pso', 'QL02p074089' => 'qlo', 'QL02p089614' => 'qlo', 'QL03p057736' => 'qlo', 'RcHm_v2.0_Chr1g0364131' => 'rch', 'RcHm_v2.0_Chr2g0087801' => 'rch', 'RcHm_v2.0_Chr2g0087821' => 'rch', 'RcHm_v2.0_Chr2g0173231' => 'rch', 'RcHm_v2.0_Chr4g0433111' => 'rch', 'Rhsim03G0250300' => 'rsi', 'Rhsim08G0048400' => 'rsi', 'Rhsim10G0014800' => 'rsi', 'Rhsim12G0040100' => 'rsi', 'Rhsim12G0109700' => 'rsi', 'Sabra06G0049600' => 'sbr', 'Sabra08G0141000' => 'sbr', 'Sabra10G0021400' => 'sbr', 'Sabra16G0222900' => 'sbr', 'Sabra18G0108600' => 'sbr', 'SalBow1G0433' => 'sbo', 'SalBow1G2038' => 'sbo', 'SalBow1G5003' => 'sbo', 'SalBow7G1197' => 'sbo', 'SalBow8G3506' => 'sbo', 'Sc03g0007300' => 'sci', 'Sc11g0000950' => 'sci', 'Sc14g0008750' => 'sci', 'Sc18g0000420' => 'sci', 'Sed0006754' => 'sed', 'Sed0008741' => 'sed', 'Sed0017172' => 'sed', 'Sed0018925' => 'sed', 'Sed0023326' => 'sed', 'Sed0025909' => 'sed', 'SEGI_05333' => 'sgi', 'SEGI_10362' => 'sgi', 'SEGI_13380' => 'sgi', 'SEGI_24306' => 'sgi', 'SEGI_29077' => 'sgi', 'SEGI_29095' => 'sgi', 'SEGI_36534' => 'sgi', 'SEGI_37506' => 'sgi', 'SEGI_38321' => 'sgi', 'SGA_v2.0_scaffold307G48031' => 'sas', 'SGA_v2.0_scaffold47G17507' => 'sas', 'SGA_v2.0_scaffold63G21736' => 'sas', 'SGA_v2.0_scaffold87G27070' => 'sas', 'SHI17794' => 'shi', 'SHI28851' => 'shi', 'SMO165G0155' => 'smo', 'SMO340G0217' => 'smo', 'SMO367G1210' => 'smo', 'Solyc02g093430.3' => 'sly', 'Solyc05g013580.4' => 'sly', 'Solyc07g008030.3' => 'sly', 'Solyc12g035470.2' => 'sly', 'Sopen02g038020' => 'spe', 'Sopen05g008490' => 'spe', 'Sopen07g003910' => 'spe', 'Sopen12g015240' => 'spe', 'Sp1g11550' => 'spa', 'Sp2g16710' => 'spa', 'Sp3g00430' => 'spa', 'Sp3g26780' => 'spa', 'Sp5g22900' => 'spa', 'Sp6g29530' => 'spa', 'TAR371G0794' => 'tar', 'TAR374G0164' => 'tar', 'TAR622G0165' => 'tar', 'TAR626G0929' => 'tar', 'TAR629G2155' => 'tar', 'THA.LOC104805282' => 'tha', 'THA.LOC104805363' => 'tha', 'THA.LOC104808968' => 'tha', 'THA.LOC104821093' => 'tha', 'THA.LOC104823953' => 'tha', 'THA.LOC104825562' => 'tha', 'THA.LOC104825665' => 'tha', 'Thecc.02G261400' => 'tca', 'Thecc.04G019200' => 'tca', 'Thecc.09G130400' => 'tca', 'Thhalv10004374m.g' => 'esa', 'Thhalv10007850m.g' => 'esa', 'Thhalv10013782m.g' => 'esa', 'Thhalv10018686m.g' => 'esa', 'Thhalv10020899m.g' => 'esa', 'Thhalv10022755m.g' => 'esa', 'TPR.G23851' => 'tpr', 'TPR.G26500' => 'tpr', 'TPR.G27267' => 'tpr', 'TPR.G32001' => 'tpr', 'TPR.G6251' => 'tpr', 'TPR.G8167' => 'tpr', 'TWI12G1330' => 'twi', 'TWI18G1239' => 'twi', 'TWI34G0979' => 'twi', 'TWI36G0670' => 'twi', 'TWI36G0707' => 'twi', 'TWI56G0233' => 'twi', 'TWI75G1809' => 'twi', 'unitig_21.g20874' => 'ugi', 'unitig_26.g10343' => 'ugi', 'unitig_46.g18392' => 'ugi', 'unitig_52.g17178' => 'ugi', 'unitig_8.g2934' => 'ugi', 'vmacro01122' => 'vma', 'vmacro05875' => 'vma', 'vmacro06147' => 'vma', 'vmacro16191' => 'vma', 'vmacro18293' => 'vma', 'VMungo0251G3707' => 'vmu', 'VMungo0464G1521' => 'vmu', 'VMungo1215G0205' => 'vmu', 'VMungo1383G2484' => 'vmu', 'Zm00001eb079610' => 'zma', 'Zm00001eb135990' => 'zma', 'Zm00001eb183710' => 'zma', 'Zm00001eb246020' => 'zma' ), 'gf_id' => 'HOM05D001124', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001124' ), 'data_identifier' => 'HOM05D001124', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001124', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '548', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02520' => 'bna', 'A03p06630' => 'bna', 'A05p44460' => 'bna', 'A06p08710' => 'bna', 'A06p41090' => 'bna', 'A07p32320' => 'bna', 'A08p32520' => 'bna', 'A09p10360' => 'bna', 'A10p24080' => 'bna', 'Aa31LG11G15250' => 'aar', 'Aa31LG1G1800' => 'aar', 'Aa31LG2G5120' => 'aar', 'Aa31LG2G6070' => 'aar', 'Aa31LG5G10770' => 'aar', 'Aa31sc61G90' => 'aar', 'Actinidia01352' => 'ach', 'Actinidia05983' => 'ach', 'Actinidia08133' => 'ach', 'Actinidia15101' => 'ach', 'Actinidia26379' => 'ach', 'Actinidia35778' => 'ach', 'Actinidia36123' => 'ach', 'Actinidia37436' => 'ach', 'Actinidia38730' => 'ach', 'Ah.02g128210' => 'amhyb', 'Ah.03g132990' => 'amhyb', 'Ah.14g079410' => 'amhyb', 'AL1G24640' => 'aly', 'AL2G26680' => 'aly', 'AL3G10530' => 'aly', 'AL3G45230' => 'aly', 'AL5G15230' => 'aly', 'AL5G16960' => 'aly', 'AL6G25210' => 'aly', 'Aqoxy2G00441' => 'aox', 'Aqoxy3G01236' => 'aox', 'Aqoxy5G03746' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3RQ047' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C7GMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9C8JER' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MBL6KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YXCZ83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZANX40' => 'arhy', 'AT1G12990' => 'ath', 'AT1G67880' => 'ath', 'AT2G13290' => 'ath', 'AT3G01620' => 'ath', 'AT3G26445' => 'ath', 'AT3G27540' => 'ath', 'AT5G14480' => 'ath', 'ATR0824G026' => 'atr', 'ATR1098G019' => 'atr', 'Atru.chr11.2145' => 'acertr', 'Atru.chr2.3636' => 'acertr', 'Atru.chr2.3644' => 'acertr', 'Atru.chr6.2422' => 'acertr', 'Atru.chr7.1112' => 'acertr', 'AUR62005469' => 'cqu', 'AUR62011166' => 'cqu', 'AUR62013319' => 'cqu', 'AUR62024273' => 'cqu', 'AUR62028420' => 'cqu', 'AUR62041942' => 'cqu', 'BcaB01g04969' => 'bca', 'BcaB01g06371' => 'bca', 'BcaB02g11494' => 'bca', 'BcaB03g15382' => 'bca', 'BcaB08g36994' => 'bca', 'BcaC03g13477' => 'bca', 'BcaC03g13478' => 'bca', 'BcaC03g13480' => 'bca', 'BcaC03g13481' => 'bca', 'BcaC03g13486' => 'bca', 'BcaC04g19031' => 'bca', 'BcaC04g23085' => 'bca', 'BcaC05g25094' => 'bca', 'BcaC05g25096' => 'bca', 'BcaC05g25138' => 'bca', 'BcaC05g30416' => 'bca', 'BcaC05g30455' => 'bca', 'BcaC06g30979' => 'bca', 'BcaC06g33805' => 'bca', 'BcaC08g46021' => 'bca', 'BcaNung03154' => 'bca', 'BolC2t06623H' => 'bol', 'BolC2t06632H' => 'bol', 'BolC2t06635H' => 'bol', 'BolC2t06638H' => 'bol', 'BolC3t13266H' => 'bol', 'BolC5t29776H' => 'bol', 'BolC6t38912H' => 'bol', 'BolC7t44183H' => 'bol', 'BolC9t54123H' => 'bol', 'BolC9t59107H' => 'bol', 'BraA02t05221Z' => 'bra', 'BraA03t09996Z' => 'bra', 'BraA05t23210Z' => 'bra', 'BraA06t24068Z' => 'bra', 'BraA06t27032Z' => 'bra', 'BraA08t35176Z' => 'bra', 'BraA09t36680Z' => 'bra', 'BraA10t44471Z' => 'bra', 'C02p06760' => 'bna', 'C02p06890' => 'bna', 'C02p07010' => 'bna', 'C03p07660' => 'bna', 'C05p10300' => 'bna', 'C06p38150' => 'bna', 'C07p36650' => 'bna', 'C08p15770' => 'bna', 'C09p12300' => 'bna', 'C09p62700' => 'bna', 'C09p75040' => 'bna', 'CAN.G13.1' => 'can', 'CAN.G138.4' => 'can', 'CAN.G44.6' => 'can', 'CAN.G473.19' => 'can', 'CANSAT01G0835' => 'cansat', 'CANSAT11G0246' => 'cansat', 'CANSAT11G1766' => 'cansat', 'CANSAT64G1954' => 'cansat', 'CARHR013330' => 'chi', 'CARHR060530' => 'chi', 'CARHR075300' => 'chi', 'CARHR105120' => 'chi', 'CARHR148910' => 'chi', 'CARHR198830' => 'chi', 'Carub.0001s1275' => 'cru', 'Carub.0002s1437' => 'cru', 'Carub.0003s0044' => 'cru', 'Carub.0003s2787' => 'cru', 'Carub.0005s0597' => 'cru', 'Carub.0006s1266' => 'cru', 'Ca_06935_v3' => 'car', 'Ca_13559_v3' => 'car', 'Ca_16941_v3' => 'car', 'Ca_16960_v3' => 'car', 'Ca_17775_v3' => 'car', 'Ca_30464_v3' => 'car', 'Cc06_g08160' => 'ccan', 'Cc07_g01520' => 'ccan', 'Cc11_g15810' => 'ccan', 'CDE02G2840' => 'cde', 'CDE03G0093' => 'cde', 'CDE04G2127' => 'cde', 'CDE07G1857' => 'cde', 'CDE09G1246' => 'cde', 'Cfa003412' => 'cfa', 'Cfa007341' => 'cfa', 'Cfa009220' => 'cfa', 'Ciclev10008737m.g' => 'ccl', 'Ciclev10015565m.g' => 'ccl', 'Ciclev10031761m.g' => 'ccl', 'CiPaw.03G045300' => 'cil', 'CiPaw.03G247200' => 'cil', 'CiPaw.04G029500' => 'cil', 'CiPaw.04G174000' => 'cil', 'CiPaw.05G181200' => 'cil', 'CiPaw.06G067100' => 'cil', 'ClCG05G025800' => 'cla', 'ClCG06G011400' => 'cla', 'ClCG09G019360' => 'cla', 'COL.COLO4_04827' => 'col', 'COL.COLO4_29170' => 'col', 'COL.COLO4_35131' => 'col', 'COL.COLO4_35132' => 'col', 'Cpa.g.sc33.32' => 'cpa', 'Cpa.g.sc46.29' => 'cpa', 'Cpa.g.sc796.1' => 'cpa', 'CsaV3_1G030420' => 'csa', 'CsaV3_5G027050' => 'csa', 'CsaV3_5G031040' => 'csa', 'CsaV3_UNG023130' => 'csa', 'CSS0007726' => 'camsi', 'CSS0016433' => 'camsi', 'CSS0017656' => 'camsi', 'CSS0025364' => 'camsi', 'CSS0027582' => 'camsi', 'CSS0047288' => 'camsi', 'CSS0049950' => 'camsi', 'DCAR_003843' => 'dca', 'DCAR_007052' => 'dca', 'DCAR_020884' => 'dca', 'DCAR_021730' => 'dca', 'DCAR_024423' => 'dca', 'DCAR_026509' => 'dca', 'DCAR_031158' => 'dca', 'Dinv14728' => 'din', 'Dinv15219' => 'din', 'Dinv25728' => 'din', 'Dinv33428' => 'din', 'Dinv36489' => 'din', 'Dinv41486' => 'din', 'Duzib147G0469' => 'dzi', 'Duzib168G0060' => 'dzi', 'Duzib187G1215' => 'dzi', 'Duzib248G0692' => 'dzi', 'Duzib251G0767' => 'dzi', 'Duzib264G0446' => 'dzi', 'Duzib268G0691' => 'dzi', 'ECA232G4767' => 'eca', 'ECA233G2838' => 'eca', 'ECA234G0391' => 'eca', 'ECA234G0857' => 'eca', 'ECA236G1593' => 'eca', 'ECA238G0565' => 'eca', 'ECA246G1027' => 'eca', 'ECA246G3223' => 'eca', 'ECA246G3470' => 'eca', 'EL10Ac6g13829' => 'bvu', 'EL10Ac6g14093' => 'bvu', 'EL10Ac8g18707' => 'bvu', 'Eucgr.C01369' => 'egr', 'Eucgr.H02492' => 'egr', 'Eucgr.I01733' => 'egr', 'Eucgr.J02255' => 'egr', 'Eucgr.J02257' => 'egr', 'Eucgr.J02258' => 'egr', 'FAN02G1601' => 'fan', 'FAN03G1586' => 'fan', 'FAN03G2986' => 'fan', 'FAN05G4837' => 'fan', 'FAN06G0146' => 'fan', 'FAN07G0858' => 'fan', 'FAN09G3179' => 'fan', 'FAN10G0669' => 'fan', 'FAN12G2358' => 'fan', 'FAN14G4198' => 'fan', 'FAN14G5112' => 'fan', 'FAN17G0342' => 'fan', 'FAN19G0342' => 'fan', 'FAN19G0962' => 'fan', 'FAN19G1101' => 'fan', 'FAN19G1872' => 'fan', 'FAN22G0356' => 'fan', 'FAN23G0744' => 'fan', 'FAN23G1914' => 'fan', 'FAN26G0032' => 'fan', 'FAN28G0625' => 'fan', 'FvH4_1g02710' => 'fve', 'FvH4_1g02720' => 'fve', 'FvH4_4g25670' => 'fve', 'FvH4_6g51700' => 'fve', 'FvH4_7g20170' => 'fve', 'Glyma.05G175000' => 'gma', 'Glyma.08G132300' => 'gma', 'Glyma.11G243000' => 'gma', 'Glyma.13G158900' => 'gma', 'Glyma.17G112400' => 'gma', 'Glyma.18G014100' => 'gma', 'Glyma.19G003100' => 'gma', 'Glyma.19G056500' => 'gma', 'Gohir.A01G158900' => 'ghi', 'Gohir.A05G312600' => 'ghi', 'Gohir.A05G354900' => 'ghi', 'Gohir.A07G037200' => 'ghi', 'Gohir.A09G030000' => 'ghi', 'Gohir.A12G145200' => 'ghi', 'Gohir.D01G151500' => 'ghi', 'Gohir.D04G058300' => 'ghi', 'Gohir.D05G314100' => 'ghi', 'Gohir.D07G041400' => 'ghi', 'Gohir.D09G029700' => 'ghi', 'Gohir.D12G149700' => 'ghi', 'Gorai.001G043800' => 'gra', 'Gorai.002G187800' => 'gra', 'Gorai.006G034700' => 'gra', 'Gorai.008G161200' => 'gra', 'Gorai.009G335700' => 'gra', 'Gorai.012G065000' => 'gra', 'GSVIVG01000535001' => 'vvi', 'GSVIVG01015572001' => 'vvi', 'GSVIVG01032386001' => 'vvi', 'HanXRQChr05g0138531' => 'han', 'HanXRQChr06g0174391' => 'han', 'HanXRQChr07g0199021' => 'han', 'HanXRQChr08g0208211' => 'han', 'HanXRQChr09g0255471' => 'han', 'HanXRQChr10g0315791' => 'han', 'HanXRQChr12g0371991' => 'han', 'HanXRQChr15g0475251' => 'han', 'HanXRQChr17g0540001' => 'han', 'HanXRQChr17g0548631' => 'han', 'HanXRQChr17g0569561' => 'han', 'Haze_12256' => 'cav', 'Haze_14756' => 'cav', 'Haze_25528' => 'cav', 'Hma1.2p1_0079F.1_g041020' => 'hma', 'Hma1.2p1_0818F.1_g223260' => 'hma', 'Hma1.2p1_1747F.1_g300530' => 'hma', 'HPP92_004607' => 'vpl', 'HPP92_004608' => 'vpl', 'HPP92_006181' => 'vpl', 'HPP92_012192' => 'vpl', 'HPP92_015680' => 'vpl', 'HPP92_020249' => 'vpl', 'HPP92_021376' => 'vpl', 'HPP92_024275' => 'vpl', 'Hund06031' => 'sun', 'Hund25391' => 'sun', 'Lalb_Chr07g0185371' => 'lal', 'Lalb_Chr07g0185381' => 'lal', 'Lalb_Chr12g0204011' => 'lal', 'Lalb_Chr13g0301671' => 'lal', 'Lalb_Chr14g0362851' => 'lal', 'Lalb_Chr24g0403581' => 'lal', 'Lj1g0000233' => 'lja', 'Lj2g0018120' => 'lja', 'Lj3C621T0' => 'lonja', 'Lj3P1059T14' => 'lonja', 'Lj3P611T9' => 'lonja', 'Lj3P614T13' => 'lonja', 'Lj3P615T5' => 'lonja', 'Lj4g0012315' => 'lja', 'Lj4g0026182' => 'lja', 'Lj6P813T16' => 'lonja', 'Lj7C427T7' => 'lonja', 'Lj7C427T8' => 'lonja', 'Lj7P600T41' => 'lonja', 'Lju41C42G17' => 'lonja', 'Lsat_1_v5_gn_0_47300' => 'lsa', 'Lsat_1_v5_gn_2_91280' => 'lsa', 'Lsat_1_v5_gn_3_30561' => 'lsa', 'Lsat_1_v5_gn_4_184321' => 'lsa', 'Lsat_1_v5_gn_4_4041' => 'lsa', 'Lsat_1_v5_gn_5_92000' => 'lsa', 'Lsat_1_v5_gn_8_152940' => 'lsa', 'Lsat_1_v5_gn_8_62401' => 'lsa', 'Manes.06G055900' => 'mes', 'Manes.12G022200' => 'mes', 'Manes.13G023300' => 'mes', 'Manes.14G115000' => 'mes', 'Manes.15G151700' => 'mes', 'Manes.17G111300' => 'mes', 'Mapoly0226s0009' => 'mpo', 'MBI02_g25363_MAGBIO' => 'mbi', 'MBI06_g00027_MAGBIO' => 'mbi', 'MBI10_g13034_MAGBIO' => 'mbi', 'MD09G1023400' => 'mdo', 'MD13G1100100' => 'mdo', 'MD15G1169200' => 'mdo', 'MD16G1101100' => 'mdo', 'MD17G1022900' => 'mdo', 'Medtr3g096150' => 'mtr', 'Medtr4g115070' => 'mtr', 'Medtr7g033325' => 'mtr', 'Medtr8g089840' => 'mtr', 'MELO3C010319.2' => 'cme', 'MELO3C011944.2' => 'cme', 'MELO3C021589.2' => 'cme', 'Migut.E00207' => 'egut', 'Migut.H00067' => 'egut', 'Migut.K00433' => 'egut', 'Migut.K00606' => 'egut', 'Migut.K01410' => 'egut', 'MSTRG.13347' => 'ama', 'MSTRG.24045' => 'ama', 'MSTRG.2428' => 'ama', 'MSTRG.26410' => 'ama', 'MSTRG.3139' => 'ama', 'MSTRG.3286' => 'ama', 'MSTRG.563' => 'ama', 'MSTRG.7941' => 'ama', 'Nitab4.5_0000028g0060' => 'nta', 'Nitab4.5_0000065g0260' => 'nta', 'Nitab4.5_0000112g0060' => 'nta', 'Nitab4.5_0000489g0120' => 'nta', 'Nitab4.5_0001776g0050' => 'nta', 'Nitab4.5_0001854g0010' => 'nta', 'Nitab4.5_0001860g0020' => 'nta', 'Nitab4.5_0004352g0010' => 'nta', 'Nitab4.5_0008716g0020' => 'nta', 'Nitab4.5_0008922g0010' => 'nta', 'Nn3g16693' => 'nnu', 'Nn4g22596' => 'nnu', 'Nn7g37639' => 'nnu', 'Oeu001701.1' => 'oeu', 'Oeu018149.1' => 'oeu', 'Oeu026220.1' => 'oeu', 'Oeu038635.1' => 'oeu', 'Oeu049176.1' => 'oeu', 'Oeu056706.1' => 'oeu', 'Oeu056937.1' => 'oeu', 'Oeu057540.1' => 'oeu', 'Os02g0594900' => 'osa', 'Os02g0595100' => 'osa', 'Os04g0477500' => 'osa', 'Os12g0611900' => 'osa', 'Peaxi162Scf00076g00020' => 'pax', 'Peaxi162Scf00128g00217' => 'pax', 'Peaxi162Scf00129g01640' => 'pax', 'Peaxi162Scf00669g00007' => 'pax', 'Peaxi162Scf00700g00421' => 'pax', 'Peaxi162Scf00801g00038' => 'pax', 'Peaxi162Scf00891g00025' => 'pax', 'PGR083G0909' => 'pgr', 'PGR119G1005' => 'pgr', 'PGR142G2236' => 'pgr', 'PGR142G3388' => 'pgr', 'PGSC0003DMG400004514' => 'stu', 'PGSC0003DMG400012635' => 'stu', 'PGSC0003DMG400015730' => 'stu', 'PGSC0003DMG400018611' => 'stu', 'PGSC0003DMG400030897' => 'stu', 'Phvul.001G254800' => 'pvu', 'Phvul.002G260100' => 'pvu', 'Phvul.003G167600' => 'pvu', 'Phvul.004G005100' => 'pvu', 'Potri.001G343600' => 'ptr', 'Potri.006G066700' => 'ptr', 'Potri.008G186000' => 'ptr', 'Potri.010G046900' => 'ptr', 'Potri.018G127900' => 'ptr', 'Pp3c20_17750' => 'ppa', 'Pp3c24_4380' => 'ppa', 'Prupe.1G245800' => 'ppe', 'Prupe.3G293400' => 'ppe', 'Prupe.7G247400' => 'ppe', 'Psat0s145g0120' => 'psa', 'Psat0s595g0040' => 'psa', 'Psat0s595g0120' => 'psa', 'Psat3g175040' => 'psa', 'Psat7g058120' => 'psa', 'PSO017G0428' => 'pso', 'PSO063G7510' => 'pso', 'PSO067G0046' => 'pso', 'PSO478G1073' => 'pso', 'PSO675G3677' => 'pso', 'PSO675G6558' => 'pso', 'PSO675G7520' => 'pso', 'PSO675G8959' => 'pso', 'QL02p074089' => 'qlo', 'QL02p089614' => 'qlo', 'QL03p057736' => 'qlo', 'RcHm_v2.0_Chr1g0364131' => 'rch', 'RcHm_v2.0_Chr2g0087801' => 'rch', 'RcHm_v2.0_Chr2g0087821' => 'rch', 'RcHm_v2.0_Chr2g0173231' => 'rch', 'RcHm_v2.0_Chr4g0433111' => 'rch', 'Rhsim03G0250300' => 'rsi', 'Rhsim08G0048400' => 'rsi', 'Rhsim10G0014800' => 'rsi', 'Rhsim12G0040100' => 'rsi', 'Rhsim12G0109700' => 'rsi', 'Sabra06G0049600' => 'sbr', 'Sabra08G0141000' => 'sbr', 'Sabra10G0021400' => 'sbr', 'Sabra16G0222900' => 'sbr', 'Sabra18G0108600' => 'sbr', 'SalBow1G0433' => 'sbo', 'SalBow1G2038' => 'sbo', 'SalBow1G5003' => 'sbo', 'SalBow7G1197' => 'sbo', 'SalBow8G3506' => 'sbo', 'Sc03g0007300' => 'sci', 'Sc11g0000950' => 'sci', 'Sc14g0008750' => 'sci', 'Sc18g0000420' => 'sci', 'Sed0006754' => 'sed', 'Sed0008741' => 'sed', 'Sed0017172' => 'sed', 'Sed0018925' => 'sed', 'Sed0023326' => 'sed', 'Sed0025909' => 'sed', 'SEGI_05333' => 'sgi', 'SEGI_10362' => 'sgi', 'SEGI_13380' => 'sgi', 'SEGI_24306' => 'sgi', 'SEGI_29077' => 'sgi', 'SEGI_29095' => 'sgi', 'SEGI_36534' => 'sgi', 'SEGI_37506' => 'sgi', 'SEGI_38321' => 'sgi', 'SGA_v2.0_scaffold307G48031' => 'sas', 'SGA_v2.0_scaffold47G17507' => 'sas', 'SGA_v2.0_scaffold63G21736' => 'sas', 'SGA_v2.0_scaffold87G27070' => 'sas', 'SHI17794' => 'shi', 'SHI28851' => 'shi', 'SMO165G0155' => 'smo', 'SMO340G0217' => 'smo', 'SMO367G1210' => 'smo', 'Solyc02g093430.3' => 'sly', 'Solyc05g013580.4' => 'sly', 'Solyc07g008030.3' => 'sly', 'Solyc12g035470.2' => 'sly', 'Sopen02g038020' => 'spe', 'Sopen05g008490' => 'spe', 'Sopen07g003910' => 'spe', 'Sopen12g015240' => 'spe', 'Sp1g11550' => 'spa', 'Sp2g16710' => 'spa', 'Sp3g00430' => 'spa', 'Sp3g26780' => 'spa', 'Sp5g22900' => 'spa', 'Sp6g29530' => 'spa', 'TAR371G0794' => 'tar', 'TAR374G0164' => 'tar', 'TAR622G0165' => 'tar', 'TAR626G0929' => 'tar', 'TAR629G2155' => 'tar', 'THA.LOC104805282' => 'tha', 'THA.LOC104805363' => 'tha', 'THA.LOC104808968' => 'tha', 'THA.LOC104821093' => 'tha', 'THA.LOC104823953' => 'tha', 'THA.LOC104825562' => 'tha', 'THA.LOC104825665' => 'tha', 'Thecc.02G261400' => 'tca', 'Thecc.04G019200' => 'tca', 'Thecc.09G130400' => 'tca', 'Thhalv10004374m.g' => 'esa', 'Thhalv10007850m.g' => 'esa', 'Thhalv10013782m.g' => 'esa', 'Thhalv10018686m.g' => 'esa', 'Thhalv10020899m.g' => 'esa', 'Thhalv10022755m.g' => 'esa', 'TPR.G23851' => 'tpr', 'TPR.G26500' => 'tpr', 'TPR.G27267' => 'tpr', 'TPR.G32001' => 'tpr', 'TPR.G6251' => 'tpr', 'TPR.G8167' => 'tpr', 'TWI12G1330' => 'twi', 'TWI18G1239' => 'twi', 'TWI34G0979' => 'twi', 'TWI36G0670' => 'twi', 'TWI36G0707' => 'twi', 'TWI56G0233' => 'twi', 'TWI75G1809' => 'twi', 'unitig_21.g20874' => 'ugi', 'unitig_26.g10343' => 'ugi', 'unitig_46.g18392' => 'ugi', 'unitig_52.g17178' => 'ugi', 'unitig_8.g2934' => 'ugi', 'vmacro01122' => 'vma', 'vmacro05875' => 'vma', 'vmacro06147' => 'vma', 'vmacro16191' => 'vma', 'vmacro18293' => 'vma', 'VMungo0251G3707' => 'vmu', 'VMungo0464G1521' => 'vmu', 'VMungo1215G0205' => 'vmu', 'VMungo1383G2484' => 'vmu', 'Zm00001eb079610' => 'zma', 'Zm00001eb135990' => 'zma', 'Zm00001eb183710' => 'zma', 'Zm00001eb246020' => 'zma' ) $gf_id = 'HOM05D001124' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001124' ) $data_identifier = 'HOM05D001124' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 6, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 7, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 21, 'bol' => (int) 10, 'bra' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 6, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 9, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 21, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 8, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 10, 'lsa' => (int) 8, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 8, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 9, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb246020' $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' => 'HOM05D001124', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '548', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02520' => 'bna', 'A03p06630' => 'bna', 'A05p44460' => 'bna', 'A06p08710' => 'bna', 'A06p41090' => 'bna', 'A07p32320' => 'bna', 'A08p32520' => 'bna', 'A09p10360' => 'bna', 'A10p24080' => 'bna', 'Aa31LG11G15250' => 'aar', 'Aa31LG1G1800' => 'aar', 'Aa31LG2G5120' => 'aar', 'Aa31LG2G6070' => 'aar', 'Aa31LG5G10770' => 'aar', 'Aa31sc61G90' => 'aar', 'Actinidia01352' => 'ach', 'Actinidia05983' => 'ach', 'Actinidia08133' => 'ach', 'Actinidia15101' => 'ach', 'Actinidia26379' => 'ach', 'Actinidia35778' => 'ach', 'Actinidia36123' => 'ach', 'Actinidia37436' => 'ach', 'Actinidia38730' => 'ach', 'Ah.02g128210' => 'amhyb', 'Ah.03g132990' => 'amhyb', 'Ah.14g079410' => 'amhyb', 'AL1G24640' => 'aly', 'AL2G26680' => 'aly', 'AL3G10530' => 'aly', 'AL3G45230' => 'aly', 'AL5G15230' => 'aly', 'AL5G16960' => 'aly', 'AL6G25210' => 'aly', 'Aqoxy2G00441' => 'aox', 'Aqoxy3G01236' => 'aox', 'Aqoxy5G03746' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3RQ047' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C7GMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9C8JER' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MBL6KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YXCZ83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZANX40' => 'arhy', 'AT1G12990' => 'ath', 'AT1G67880' => 'ath', 'AT2G13290' => 'ath', 'AT3G01620' => 'ath', 'AT3G26445' => 'ath', 'AT3G27540' => 'ath', 'AT5G14480' => 'ath', 'ATR0824G026' => 'atr', 'ATR1098G019' => 'atr', 'Atru.chr11.2145' => 'acertr', 'Atru.chr2.3636' => 'acertr', 'Atru.chr2.3644' => 'acertr', 'Atru.chr6.2422' => 'acertr', 'Atru.chr7.1112' => 'acertr', 'AUR62005469' => 'cqu', 'AUR62011166' => 'cqu', 'AUR62013319' => 'cqu', 'AUR62024273' => 'cqu', 'AUR62028420' => 'cqu', 'AUR62041942' => 'cqu', 'BcaB01g04969' => 'bca', 'BcaB01g06371' => 'bca', 'BcaB02g11494' => 'bca', 'BcaB03g15382' => 'bca', 'BcaB08g36994' => 'bca', 'BcaC03g13477' => 'bca', 'BcaC03g13478' => 'bca', 'BcaC03g13480' => 'bca', 'BcaC03g13481' => 'bca', 'BcaC03g13486' => 'bca', 'BcaC04g19031' => 'bca', 'BcaC04g23085' => 'bca', 'BcaC05g25094' => 'bca', 'BcaC05g25096' => 'bca', 'BcaC05g25138' => 'bca', 'BcaC05g30416' => 'bca', 'BcaC05g30455' => 'bca', 'BcaC06g30979' => 'bca', 'BcaC06g33805' => 'bca', 'BcaC08g46021' => 'bca', 'BcaNung03154' => 'bca', 'BolC2t06623H' => 'bol', 'BolC2t06632H' => 'bol', 'BolC2t06635H' => 'bol', 'BolC2t06638H' => 'bol', 'BolC3t13266H' => 'bol', 'BolC5t29776H' => 'bol', 'BolC6t38912H' => 'bol', 'BolC7t44183H' => 'bol', 'BolC9t54123H' => 'bol', 'BolC9t59107H' => 'bol', 'BraA02t05221Z' => 'bra', 'BraA03t09996Z' => 'bra', 'BraA05t23210Z' => 'bra', 'BraA06t24068Z' => 'bra', 'BraA06t27032Z' => 'bra', 'BraA08t35176Z' => 'bra', 'BraA09t36680Z' => 'bra', 'BraA10t44471Z' => 'bra', 'C02p06760' => 'bna', 'C02p06890' => 'bna', 'C02p07010' => 'bna', 'C03p07660' => 'bna', 'C05p10300' => 'bna', 'C06p38150' => 'bna', 'C07p36650' => 'bna', 'C08p15770' => 'bna', 'C09p12300' => 'bna', 'C09p62700' => 'bna', 'C09p75040' => 'bna', 'CAN.G13.1' => 'can', 'CAN.G138.4' => 'can', 'CAN.G44.6' => 'can', 'CAN.G473.19' => 'can', 'CANSAT01G0835' => 'cansat', 'CANSAT11G0246' => 'cansat', 'CANSAT11G1766' => 'cansat', 'CANSAT64G1954' => 'cansat', 'CARHR013330' => 'chi', 'CARHR060530' => 'chi', 'CARHR075300' => 'chi', 'CARHR105120' => 'chi', 'CARHR148910' => 'chi', 'CARHR198830' => 'chi', 'Carub.0001s1275' => 'cru', 'Carub.0002s1437' => 'cru', 'Carub.0003s0044' => 'cru', 'Carub.0003s2787' => 'cru', 'Carub.0005s0597' => 'cru', 'Carub.0006s1266' => 'cru', 'Ca_06935_v3' => 'car', 'Ca_13559_v3' => 'car', 'Ca_16941_v3' => 'car', 'Ca_16960_v3' => 'car', 'Ca_17775_v3' => 'car', 'Ca_30464_v3' => 'car', 'Cc06_g08160' => 'ccan', 'Cc07_g01520' => 'ccan', 'Cc11_g15810' => 'ccan', 'CDE02G2840' => 'cde', 'CDE03G0093' => 'cde', 'CDE04G2127' => 'cde', 'CDE07G1857' => 'cde', 'CDE09G1246' => 'cde', 'Cfa003412' => 'cfa', 'Cfa007341' => 'cfa', 'Cfa009220' => 'cfa', 'Ciclev10008737m.g' => 'ccl', 'Ciclev10015565m.g' => 'ccl', 'Ciclev10031761m.g' => 'ccl', 'CiPaw.03G045300' => 'cil', 'CiPaw.03G247200' => 'cil', 'CiPaw.04G029500' => 'cil', 'CiPaw.04G174000' => 'cil', 'CiPaw.05G181200' => 'cil', 'CiPaw.06G067100' => 'cil', 'ClCG05G025800' => 'cla', 'ClCG06G011400' => 'cla', 'ClCG09G019360' => 'cla', 'COL.COLO4_04827' => 'col', 'COL.COLO4_29170' => 'col', 'COL.COLO4_35131' => 'col', 'COL.COLO4_35132' => 'col', 'Cpa.g.sc33.32' => 'cpa', 'Cpa.g.sc46.29' => 'cpa', 'Cpa.g.sc796.1' => 'cpa', 'CsaV3_1G030420' => 'csa', 'CsaV3_5G027050' => 'csa', 'CsaV3_5G031040' => 'csa', 'CsaV3_UNG023130' => 'csa', 'CSS0007726' => 'camsi', 'CSS0016433' => 'camsi', 'CSS0017656' => 'camsi', 'CSS0025364' => 'camsi', 'CSS0027582' => 'camsi', 'CSS0047288' => 'camsi', 'CSS0049950' => 'camsi', 'DCAR_003843' => 'dca', 'DCAR_007052' => 'dca', 'DCAR_020884' => 'dca', 'DCAR_021730' => 'dca', 'DCAR_024423' => 'dca', 'DCAR_026509' => 'dca', 'DCAR_031158' => 'dca', 'Dinv14728' => 'din', 'Dinv15219' => 'din', 'Dinv25728' => 'din', 'Dinv33428' => 'din', 'Dinv36489' => 'din', 'Dinv41486' => 'din', 'Duzib147G0469' => 'dzi', 'Duzib168G0060' => 'dzi', 'Duzib187G1215' => 'dzi', 'Duzib248G0692' => 'dzi', 'Duzib251G0767' => 'dzi', 'Duzib264G0446' => 'dzi', 'Duzib268G0691' => 'dzi', 'ECA232G4767' => 'eca', 'ECA233G2838' => 'eca', 'ECA234G0391' => 'eca', 'ECA234G0857' => 'eca', 'ECA236G1593' => 'eca', 'ECA238G0565' => 'eca', 'ECA246G1027' => 'eca', 'ECA246G3223' => 'eca', 'ECA246G3470' => 'eca', 'EL10Ac6g13829' => 'bvu', 'EL10Ac6g14093' => 'bvu', 'EL10Ac8g18707' => 'bvu', 'Eucgr.C01369' => 'egr', 'Eucgr.H02492' => 'egr', 'Eucgr.I01733' => 'egr', 'Eucgr.J02255' => 'egr', 'Eucgr.J02257' => 'egr', 'Eucgr.J02258' => 'egr', 'FAN02G1601' => 'fan', 'FAN03G1586' => 'fan', 'FAN03G2986' => 'fan', 'FAN05G4837' => 'fan', 'FAN06G0146' => 'fan', 'FAN07G0858' => 'fan', 'FAN09G3179' => 'fan', 'FAN10G0669' => 'fan', 'FAN12G2358' => 'fan', 'FAN14G4198' => 'fan', 'FAN14G5112' => 'fan', 'FAN17G0342' => 'fan', 'FAN19G0342' => 'fan', 'FAN19G0962' => 'fan', 'FAN19G1101' => 'fan', 'FAN19G1872' => 'fan', 'FAN22G0356' => 'fan', 'FAN23G0744' => 'fan', 'FAN23G1914' => 'fan', 'FAN26G0032' => 'fan', 'FAN28G0625' => 'fan', 'FvH4_1g02710' => 'fve', 'FvH4_1g02720' => 'fve', 'FvH4_4g25670' => 'fve', 'FvH4_6g51700' => 'fve', 'FvH4_7g20170' => 'fve', 'Glyma.05G175000' => 'gma', 'Glyma.08G132300' => 'gma', 'Glyma.11G243000' => 'gma', 'Glyma.13G158900' => 'gma', 'Glyma.17G112400' => 'gma', 'Glyma.18G014100' => 'gma', 'Glyma.19G003100' => 'gma', 'Glyma.19G056500' => 'gma', 'Gohir.A01G158900' => 'ghi', 'Gohir.A05G312600' => 'ghi', 'Gohir.A05G354900' => 'ghi', 'Gohir.A07G037200' => 'ghi', 'Gohir.A09G030000' => 'ghi', 'Gohir.A12G145200' => 'ghi', 'Gohir.D01G151500' => 'ghi', 'Gohir.D04G058300' => 'ghi', 'Gohir.D05G314100' => 'ghi', 'Gohir.D07G041400' => 'ghi', 'Gohir.D09G029700' => 'ghi', 'Gohir.D12G149700' => 'ghi', 'Gorai.001G043800' => 'gra', 'Gorai.002G187800' => 'gra', 'Gorai.006G034700' => 'gra', 'Gorai.008G161200' => 'gra', 'Gorai.009G335700' => 'gra', 'Gorai.012G065000' => 'gra', 'GSVIVG01000535001' => 'vvi', 'GSVIVG01015572001' => 'vvi', 'GSVIVG01032386001' => 'vvi', 'HanXRQChr05g0138531' => 'han', 'HanXRQChr06g0174391' => 'han', 'HanXRQChr07g0199021' => 'han', 'HanXRQChr08g0208211' => 'han', 'HanXRQChr09g0255471' => 'han', 'HanXRQChr10g0315791' => 'han', 'HanXRQChr12g0371991' => 'han', 'HanXRQChr15g0475251' => 'han', 'HanXRQChr17g0540001' => 'han', 'HanXRQChr17g0548631' => 'han', 'HanXRQChr17g0569561' => 'han', 'Haze_12256' => 'cav', 'Haze_14756' => 'cav', 'Haze_25528' => 'cav', 'Hma1.2p1_0079F.1_g041020' => 'hma', 'Hma1.2p1_0818F.1_g223260' => 'hma', 'Hma1.2p1_1747F.1_g300530' => 'hma', 'HPP92_004607' => 'vpl', 'HPP92_004608' => 'vpl', 'HPP92_006181' => 'vpl', 'HPP92_012192' => 'vpl', 'HPP92_015680' => 'vpl', 'HPP92_020249' => 'vpl', 'HPP92_021376' => 'vpl', 'HPP92_024275' => 'vpl', 'Hund06031' => 'sun', 'Hund25391' => 'sun', 'Lalb_Chr07g0185371' => 'lal', 'Lalb_Chr07g0185381' => 'lal', 'Lalb_Chr12g0204011' => 'lal', 'Lalb_Chr13g0301671' => 'lal', 'Lalb_Chr14g0362851' => 'lal', 'Lalb_Chr24g0403581' => 'lal', 'Lj1g0000233' => 'lja', 'Lj2g0018120' => 'lja', 'Lj3C621T0' => 'lonja', 'Lj3P1059T14' => 'lonja', 'Lj3P611T9' => 'lonja', 'Lj3P614T13' => 'lonja', 'Lj3P615T5' => 'lonja', 'Lj4g0012315' => 'lja', 'Lj4g0026182' => 'lja', 'Lj6P813T16' => 'lonja', 'Lj7C427T7' => 'lonja', 'Lj7C427T8' => 'lonja', 'Lj7P600T41' => 'lonja', 'Lju41C42G17' => 'lonja', 'Lsat_1_v5_gn_0_47300' => 'lsa', 'Lsat_1_v5_gn_2_91280' => 'lsa', 'Lsat_1_v5_gn_3_30561' => 'lsa', 'Lsat_1_v5_gn_4_184321' => 'lsa', 'Lsat_1_v5_gn_4_4041' => 'lsa', 'Lsat_1_v5_gn_5_92000' => 'lsa', 'Lsat_1_v5_gn_8_152940' => 'lsa', 'Lsat_1_v5_gn_8_62401' => 'lsa', 'Manes.06G055900' => 'mes', 'Manes.12G022200' => 'mes', 'Manes.13G023300' => 'mes', 'Manes.14G115000' => 'mes', 'Manes.15G151700' => 'mes', 'Manes.17G111300' => 'mes', 'Mapoly0226s0009' => 'mpo', 'MBI02_g25363_MAGBIO' => 'mbi', 'MBI06_g00027_MAGBIO' => 'mbi', 'MBI10_g13034_MAGBIO' => 'mbi', 'MD09G1023400' => 'mdo', 'MD13G1100100' => 'mdo', 'MD15G1169200' => 'mdo', 'MD16G1101100' => 'mdo', 'MD17G1022900' => 'mdo', 'Medtr3g096150' => 'mtr', 'Medtr4g115070' => 'mtr', 'Medtr7g033325' => 'mtr', 'Medtr8g089840' => 'mtr', 'MELO3C010319.2' => 'cme', 'MELO3C011944.2' => 'cme', 'MELO3C021589.2' => 'cme', 'Migut.E00207' => 'egut', 'Migut.H00067' => 'egut', 'Migut.K00433' => 'egut', 'Migut.K00606' => 'egut', 'Migut.K01410' => 'egut', 'MSTRG.13347' => 'ama', 'MSTRG.24045' => 'ama', 'MSTRG.2428' => 'ama', 'MSTRG.26410' => 'ama', 'MSTRG.3139' => 'ama', 'MSTRG.3286' => 'ama', 'MSTRG.563' => 'ama', 'MSTRG.7941' => 'ama', 'Nitab4.5_0000028g0060' => 'nta', 'Nitab4.5_0000065g0260' => 'nta', 'Nitab4.5_0000112g0060' => 'nta', 'Nitab4.5_0000489g0120' => 'nta', 'Nitab4.5_0001776g0050' => 'nta', 'Nitab4.5_0001854g0010' => 'nta', 'Nitab4.5_0001860g0020' => 'nta', 'Nitab4.5_0004352g0010' => 'nta', 'Nitab4.5_0008716g0020' => 'nta', 'Nitab4.5_0008922g0010' => 'nta', 'Nn3g16693' => 'nnu', 'Nn4g22596' => 'nnu', 'Nn7g37639' => 'nnu', 'Oeu001701.1' => 'oeu', 'Oeu018149.1' => 'oeu', 'Oeu026220.1' => 'oeu', 'Oeu038635.1' => 'oeu', 'Oeu049176.1' => 'oeu', 'Oeu056706.1' => 'oeu', 'Oeu056937.1' => 'oeu', 'Oeu057540.1' => 'oeu', 'Os02g0594900' => 'osa', 'Os02g0595100' => 'osa', 'Os04g0477500' => 'osa', 'Os12g0611900' => 'osa', 'Peaxi162Scf00076g00020' => 'pax', 'Peaxi162Scf00128g00217' => 'pax', 'Peaxi162Scf00129g01640' => 'pax', 'Peaxi162Scf00669g00007' => 'pax', 'Peaxi162Scf00700g00421' => 'pax', 'Peaxi162Scf00801g00038' => 'pax', 'Peaxi162Scf00891g00025' => 'pax', 'PGR083G0909' => 'pgr', 'PGR119G1005' => 'pgr', 'PGR142G2236' => 'pgr', 'PGR142G3388' => 'pgr', 'PGSC0003DMG400004514' => 'stu', 'PGSC0003DMG400012635' => 'stu', 'PGSC0003DMG400015730' => 'stu', 'PGSC0003DMG400018611' => 'stu', 'PGSC0003DMG400030897' => 'stu', 'Phvul.001G254800' => 'pvu', 'Phvul.002G260100' => 'pvu', 'Phvul.003G167600' => 'pvu', 'Phvul.004G005100' => 'pvu', 'Potri.001G343600' => 'ptr', 'Potri.006G066700' => 'ptr', 'Potri.008G186000' => 'ptr', 'Potri.010G046900' => 'ptr', 'Potri.018G127900' => 'ptr', 'Pp3c20_17750' => 'ppa', 'Pp3c24_4380' => 'ppa', 'Prupe.1G245800' => 'ppe', 'Prupe.3G293400' => 'ppe', 'Prupe.7G247400' => 'ppe', 'Psat0s145g0120' => 'psa', 'Psat0s595g0040' => 'psa', 'Psat0s595g0120' => 'psa', 'Psat3g175040' => 'psa', 'Psat7g058120' => 'psa', 'PSO017G0428' => 'pso', 'PSO063G7510' => 'pso', 'PSO067G0046' => 'pso', 'PSO478G1073' => 'pso', 'PSO675G3677' => 'pso', 'PSO675G6558' => 'pso', 'PSO675G7520' => 'pso', 'PSO675G8959' => 'pso', 'QL02p074089' => 'qlo', 'QL02p089614' => 'qlo', 'QL03p057736' => 'qlo', 'RcHm_v2.0_Chr1g0364131' => 'rch', 'RcHm_v2.0_Chr2g0087801' => 'rch', 'RcHm_v2.0_Chr2g0087821' => 'rch', 'RcHm_v2.0_Chr2g0173231' => 'rch', 'RcHm_v2.0_Chr4g0433111' => 'rch', 'Rhsim03G0250300' => 'rsi', 'Rhsim08G0048400' => 'rsi', 'Rhsim10G0014800' => 'rsi', 'Rhsim12G0040100' => 'rsi', 'Rhsim12G0109700' => 'rsi', 'Sabra06G0049600' => 'sbr', 'Sabra08G0141000' => 'sbr', 'Sabra10G0021400' => 'sbr', 'Sabra16G0222900' => 'sbr', 'Sabra18G0108600' => 'sbr', 'SalBow1G0433' => 'sbo', 'SalBow1G2038' => 'sbo', 'SalBow1G5003' => 'sbo', 'SalBow7G1197' => 'sbo', 'SalBow8G3506' => 'sbo', 'Sc03g0007300' => 'sci', 'Sc11g0000950' => 'sci', 'Sc14g0008750' => 'sci', 'Sc18g0000420' => 'sci', 'Sed0006754' => 'sed', 'Sed0008741' => 'sed', 'Sed0017172' => 'sed', 'Sed0018925' => 'sed', 'Sed0023326' => 'sed', 'Sed0025909' => 'sed', 'SEGI_05333' => 'sgi', 'SEGI_10362' => 'sgi', 'SEGI_13380' => 'sgi', 'SEGI_24306' => 'sgi', 'SEGI_29077' => 'sgi', 'SEGI_29095' => 'sgi', 'SEGI_36534' => 'sgi', 'SEGI_37506' => 'sgi', 'SEGI_38321' => 'sgi', 'SGA_v2.0_scaffold307G48031' => 'sas', 'SGA_v2.0_scaffold47G17507' => 'sas', 'SGA_v2.0_scaffold63G21736' => 'sas', 'SGA_v2.0_scaffold87G27070' => 'sas', 'SHI17794' => 'shi', 'SHI28851' => 'shi', 'SMO165G0155' => 'smo', 'SMO340G0217' => 'smo', 'SMO367G1210' => 'smo', 'Solyc02g093430.3' => 'sly', 'Solyc05g013580.4' => 'sly', 'Solyc07g008030.3' => 'sly', 'Solyc12g035470.2' => 'sly', 'Sopen02g038020' => 'spe', 'Sopen05g008490' => 'spe', 'Sopen07g003910' => 'spe', 'Sopen12g015240' => 'spe', 'Sp1g11550' => 'spa', 'Sp2g16710' => 'spa', 'Sp3g00430' => 'spa', 'Sp3g26780' => 'spa', 'Sp5g22900' => 'spa', 'Sp6g29530' => 'spa', 'TAR371G0794' => 'tar', 'TAR374G0164' => 'tar', 'TAR622G0165' => 'tar', 'TAR626G0929' => 'tar', 'TAR629G2155' => 'tar', 'THA.LOC104805282' => 'tha', 'THA.LOC104805363' => 'tha', 'THA.LOC104808968' => 'tha', 'THA.LOC104821093' => 'tha', 'THA.LOC104823953' => 'tha', 'THA.LOC104825562' => 'tha', 'THA.LOC104825665' => 'tha', 'Thecc.02G261400' => 'tca', 'Thecc.04G019200' => 'tca', 'Thecc.09G130400' => 'tca', 'Thhalv10004374m.g' => 'esa', 'Thhalv10007850m.g' => 'esa', 'Thhalv10013782m.g' => 'esa', 'Thhalv10018686m.g' => 'esa', 'Thhalv10020899m.g' => 'esa', 'Thhalv10022755m.g' => 'esa', 'TPR.G23851' => 'tpr', 'TPR.G26500' => 'tpr', 'TPR.G27267' => 'tpr', 'TPR.G32001' => 'tpr', 'TPR.G6251' => 'tpr', 'TPR.G8167' => 'tpr', 'TWI12G1330' => 'twi', 'TWI18G1239' => 'twi', 'TWI34G0979' => 'twi', 'TWI36G0670' => 'twi', 'TWI36G0707' => 'twi', 'TWI56G0233' => 'twi', 'TWI75G1809' => 'twi', 'unitig_21.g20874' => 'ugi', 'unitig_26.g10343' => 'ugi', 'unitig_46.g18392' => 'ugi', 'unitig_52.g17178' => 'ugi', 'unitig_8.g2934' => 'ugi', 'vmacro01122' => 'vma', 'vmacro05875' => 'vma', 'vmacro06147' => 'vma', 'vmacro16191' => 'vma', 'vmacro18293' => 'vma', 'VMungo0251G3707' => 'vmu', 'VMungo0464G1521' => 'vmu', 'VMungo1215G0205' => 'vmu', 'VMungo1383G2484' => 'vmu', 'Zm00001eb079610' => 'zma', 'Zm00001eb135990' => 'zma', 'Zm00001eb183710' => 'zma', 'Zm00001eb246020' => 'zma' ), 'gf_id' => 'HOM05D001124', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001124' ), 'data_identifier' => 'HOM05D001124', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001124', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '548', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02520' => 'bna', 'A03p06630' => 'bna', 'A05p44460' => 'bna', 'A06p08710' => 'bna', 'A06p41090' => 'bna', 'A07p32320' => 'bna', 'A08p32520' => 'bna', 'A09p10360' => 'bna', 'A10p24080' => 'bna', 'Aa31LG11G15250' => 'aar', 'Aa31LG1G1800' => 'aar', 'Aa31LG2G5120' => 'aar', 'Aa31LG2G6070' => 'aar', 'Aa31LG5G10770' => 'aar', 'Aa31sc61G90' => 'aar', 'Actinidia01352' => 'ach', 'Actinidia05983' => 'ach', 'Actinidia08133' => 'ach', 'Actinidia15101' => 'ach', 'Actinidia26379' => 'ach', 'Actinidia35778' => 'ach', 'Actinidia36123' => 'ach', 'Actinidia37436' => 'ach', 'Actinidia38730' => 'ach', 'Ah.02g128210' => 'amhyb', 'Ah.03g132990' => 'amhyb', 'Ah.14g079410' => 'amhyb', 'AL1G24640' => 'aly', 'AL2G26680' => 'aly', 'AL3G10530' => 'aly', 'AL3G45230' => 'aly', 'AL5G15230' => 'aly', 'AL5G16960' => 'aly', 'AL6G25210' => 'aly', 'Aqoxy2G00441' => 'aox', 'Aqoxy3G01236' => 'aox', 'Aqoxy5G03746' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3RQ047' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C7GMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9C8JER' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MBL6KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YXCZ83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZANX40' => 'arhy', 'AT1G12990' => 'ath', 'AT1G67880' => 'ath', 'AT2G13290' => 'ath', 'AT3G01620' => 'ath', 'AT3G26445' => 'ath', 'AT3G27540' => 'ath', 'AT5G14480' => 'ath', 'ATR0824G026' => 'atr', 'ATR1098G019' => 'atr', 'Atru.chr11.2145' => 'acertr', 'Atru.chr2.3636' => 'acertr', 'Atru.chr2.3644' => 'acertr', 'Atru.chr6.2422' => 'acertr', 'Atru.chr7.1112' => 'acertr', 'AUR62005469' => 'cqu', 'AUR62011166' => 'cqu', 'AUR62013319' => 'cqu', 'AUR62024273' => 'cqu', 'AUR62028420' => 'cqu', 'AUR62041942' => 'cqu', 'BcaB01g04969' => 'bca', 'BcaB01g06371' => 'bca', 'BcaB02g11494' => 'bca', 'BcaB03g15382' => 'bca', 'BcaB08g36994' => 'bca', 'BcaC03g13477' => 'bca', 'BcaC03g13478' => 'bca', 'BcaC03g13480' => 'bca', 'BcaC03g13481' => 'bca', 'BcaC03g13486' => 'bca', 'BcaC04g19031' => 'bca', 'BcaC04g23085' => 'bca', 'BcaC05g25094' => 'bca', 'BcaC05g25096' => 'bca', 'BcaC05g25138' => 'bca', 'BcaC05g30416' => 'bca', 'BcaC05g30455' => 'bca', 'BcaC06g30979' => 'bca', 'BcaC06g33805' => 'bca', 'BcaC08g46021' => 'bca', 'BcaNung03154' => 'bca', 'BolC2t06623H' => 'bol', 'BolC2t06632H' => 'bol', 'BolC2t06635H' => 'bol', 'BolC2t06638H' => 'bol', 'BolC3t13266H' => 'bol', 'BolC5t29776H' => 'bol', 'BolC6t38912H' => 'bol', 'BolC7t44183H' => 'bol', 'BolC9t54123H' => 'bol', 'BolC9t59107H' => 'bol', 'BraA02t05221Z' => 'bra', 'BraA03t09996Z' => 'bra', 'BraA05t23210Z' => 'bra', 'BraA06t24068Z' => 'bra', 'BraA06t27032Z' => 'bra', 'BraA08t35176Z' => 'bra', 'BraA09t36680Z' => 'bra', 'BraA10t44471Z' => 'bra', 'C02p06760' => 'bna', 'C02p06890' => 'bna', 'C02p07010' => 'bna', 'C03p07660' => 'bna', 'C05p10300' => 'bna', 'C06p38150' => 'bna', 'C07p36650' => 'bna', 'C08p15770' => 'bna', 'C09p12300' => 'bna', 'C09p62700' => 'bna', 'C09p75040' => 'bna', 'CAN.G13.1' => 'can', 'CAN.G138.4' => 'can', 'CAN.G44.6' => 'can', 'CAN.G473.19' => 'can', 'CANSAT01G0835' => 'cansat', 'CANSAT11G0246' => 'cansat', 'CANSAT11G1766' => 'cansat', 'CANSAT64G1954' => 'cansat', 'CARHR013330' => 'chi', 'CARHR060530' => 'chi', 'CARHR075300' => 'chi', 'CARHR105120' => 'chi', 'CARHR148910' => 'chi', 'CARHR198830' => 'chi', 'Carub.0001s1275' => 'cru', 'Carub.0002s1437' => 'cru', 'Carub.0003s0044' => 'cru', 'Carub.0003s2787' => 'cru', 'Carub.0005s0597' => 'cru', 'Carub.0006s1266' => 'cru', 'Ca_06935_v3' => 'car', 'Ca_13559_v3' => 'car', 'Ca_16941_v3' => 'car', 'Ca_16960_v3' => 'car', 'Ca_17775_v3' => 'car', 'Ca_30464_v3' => 'car', 'Cc06_g08160' => 'ccan', 'Cc07_g01520' => 'ccan', 'Cc11_g15810' => 'ccan', 'CDE02G2840' => 'cde', 'CDE03G0093' => 'cde', 'CDE04G2127' => 'cde', 'CDE07G1857' => 'cde', 'CDE09G1246' => 'cde', 'Cfa003412' => 'cfa', 'Cfa007341' => 'cfa', 'Cfa009220' => 'cfa', 'Ciclev10008737m.g' => 'ccl', 'Ciclev10015565m.g' => 'ccl', 'Ciclev10031761m.g' => 'ccl', 'CiPaw.03G045300' => 'cil', 'CiPaw.03G247200' => 'cil', 'CiPaw.04G029500' => 'cil', 'CiPaw.04G174000' => 'cil', 'CiPaw.05G181200' => 'cil', 'CiPaw.06G067100' => 'cil', 'ClCG05G025800' => 'cla', 'ClCG06G011400' => 'cla', 'ClCG09G019360' => 'cla', 'COL.COLO4_04827' => 'col', 'COL.COLO4_29170' => 'col', 'COL.COLO4_35131' => 'col', 'COL.COLO4_35132' => 'col', 'Cpa.g.sc33.32' => 'cpa', 'Cpa.g.sc46.29' => 'cpa', 'Cpa.g.sc796.1' => 'cpa', 'CsaV3_1G030420' => 'csa', 'CsaV3_5G027050' => 'csa', 'CsaV3_5G031040' => 'csa', 'CsaV3_UNG023130' => 'csa', 'CSS0007726' => 'camsi', 'CSS0016433' => 'camsi', 'CSS0017656' => 'camsi', 'CSS0025364' => 'camsi', 'CSS0027582' => 'camsi', 'CSS0047288' => 'camsi', 'CSS0049950' => 'camsi', 'DCAR_003843' => 'dca', 'DCAR_007052' => 'dca', 'DCAR_020884' => 'dca', 'DCAR_021730' => 'dca', 'DCAR_024423' => 'dca', 'DCAR_026509' => 'dca', 'DCAR_031158' => 'dca', 'Dinv14728' => 'din', 'Dinv15219' => 'din', 'Dinv25728' => 'din', 'Dinv33428' => 'din', 'Dinv36489' => 'din', 'Dinv41486' => 'din', 'Duzib147G0469' => 'dzi', 'Duzib168G0060' => 'dzi', 'Duzib187G1215' => 'dzi', 'Duzib248G0692' => 'dzi', 'Duzib251G0767' => 'dzi', 'Duzib264G0446' => 'dzi', 'Duzib268G0691' => 'dzi', 'ECA232G4767' => 'eca', 'ECA233G2838' => 'eca', 'ECA234G0391' => 'eca', 'ECA234G0857' => 'eca', 'ECA236G1593' => 'eca', 'ECA238G0565' => 'eca', 'ECA246G1027' => 'eca', 'ECA246G3223' => 'eca', 'ECA246G3470' => 'eca', 'EL10Ac6g13829' => 'bvu', 'EL10Ac6g14093' => 'bvu', 'EL10Ac8g18707' => 'bvu', 'Eucgr.C01369' => 'egr', 'Eucgr.H02492' => 'egr', 'Eucgr.I01733' => 'egr', 'Eucgr.J02255' => 'egr', 'Eucgr.J02257' => 'egr', 'Eucgr.J02258' => 'egr', 'FAN02G1601' => 'fan', 'FAN03G1586' => 'fan', 'FAN03G2986' => 'fan', 'FAN05G4837' => 'fan', 'FAN06G0146' => 'fan', 'FAN07G0858' => 'fan', 'FAN09G3179' => 'fan', 'FAN10G0669' => 'fan', 'FAN12G2358' => 'fan', 'FAN14G4198' => 'fan', 'FAN14G5112' => 'fan', 'FAN17G0342' => 'fan', 'FAN19G0342' => 'fan', 'FAN19G0962' => 'fan', 'FAN19G1101' => 'fan', 'FAN19G1872' => 'fan', 'FAN22G0356' => 'fan', 'FAN23G0744' => 'fan', 'FAN23G1914' => 'fan', 'FAN26G0032' => 'fan', 'FAN28G0625' => 'fan', 'FvH4_1g02710' => 'fve', 'FvH4_1g02720' => 'fve', 'FvH4_4g25670' => 'fve', 'FvH4_6g51700' => 'fve', 'FvH4_7g20170' => 'fve', 'Glyma.05G175000' => 'gma', 'Glyma.08G132300' => 'gma', 'Glyma.11G243000' => 'gma', 'Glyma.13G158900' => 'gma', 'Glyma.17G112400' => 'gma', 'Glyma.18G014100' => 'gma', 'Glyma.19G003100' => 'gma', 'Glyma.19G056500' => 'gma', 'Gohir.A01G158900' => 'ghi', 'Gohir.A05G312600' => 'ghi', 'Gohir.A05G354900' => 'ghi', 'Gohir.A07G037200' => 'ghi', 'Gohir.A09G030000' => 'ghi', 'Gohir.A12G145200' => 'ghi', 'Gohir.D01G151500' => 'ghi', 'Gohir.D04G058300' => 'ghi', 'Gohir.D05G314100' => 'ghi', 'Gohir.D07G041400' => 'ghi', 'Gohir.D09G029700' => 'ghi', 'Gohir.D12G149700' => 'ghi', 'Gorai.001G043800' => 'gra', 'Gorai.002G187800' => 'gra', 'Gorai.006G034700' => 'gra', 'Gorai.008G161200' => 'gra', 'Gorai.009G335700' => 'gra', 'Gorai.012G065000' => 'gra', 'GSVIVG01000535001' => 'vvi', 'GSVIVG01015572001' => 'vvi', 'GSVIVG01032386001' => 'vvi', 'HanXRQChr05g0138531' => 'han', 'HanXRQChr06g0174391' => 'han', 'HanXRQChr07g0199021' => 'han', 'HanXRQChr08g0208211' => 'han', 'HanXRQChr09g0255471' => 'han', 'HanXRQChr10g0315791' => 'han', 'HanXRQChr12g0371991' => 'han', 'HanXRQChr15g0475251' => 'han', 'HanXRQChr17g0540001' => 'han', 'HanXRQChr17g0548631' => 'han', 'HanXRQChr17g0569561' => 'han', 'Haze_12256' => 'cav', 'Haze_14756' => 'cav', 'Haze_25528' => 'cav', 'Hma1.2p1_0079F.1_g041020' => 'hma', 'Hma1.2p1_0818F.1_g223260' => 'hma', 'Hma1.2p1_1747F.1_g300530' => 'hma', 'HPP92_004607' => 'vpl', 'HPP92_004608' => 'vpl', 'HPP92_006181' => 'vpl', 'HPP92_012192' => 'vpl', 'HPP92_015680' => 'vpl', 'HPP92_020249' => 'vpl', 'HPP92_021376' => 'vpl', 'HPP92_024275' => 'vpl', 'Hund06031' => 'sun', 'Hund25391' => 'sun', 'Lalb_Chr07g0185371' => 'lal', 'Lalb_Chr07g0185381' => 'lal', 'Lalb_Chr12g0204011' => 'lal', 'Lalb_Chr13g0301671' => 'lal', 'Lalb_Chr14g0362851' => 'lal', 'Lalb_Chr24g0403581' => 'lal', 'Lj1g0000233' => 'lja', 'Lj2g0018120' => 'lja', 'Lj3C621T0' => 'lonja', 'Lj3P1059T14' => 'lonja', 'Lj3P611T9' => 'lonja', 'Lj3P614T13' => 'lonja', 'Lj3P615T5' => 'lonja', 'Lj4g0012315' => 'lja', 'Lj4g0026182' => 'lja', 'Lj6P813T16' => 'lonja', 'Lj7C427T7' => 'lonja', 'Lj7C427T8' => 'lonja', 'Lj7P600T41' => 'lonja', 'Lju41C42G17' => 'lonja', 'Lsat_1_v5_gn_0_47300' => 'lsa', 'Lsat_1_v5_gn_2_91280' => 'lsa', 'Lsat_1_v5_gn_3_30561' => 'lsa', 'Lsat_1_v5_gn_4_184321' => 'lsa', 'Lsat_1_v5_gn_4_4041' => 'lsa', 'Lsat_1_v5_gn_5_92000' => 'lsa', 'Lsat_1_v5_gn_8_152940' => 'lsa', 'Lsat_1_v5_gn_8_62401' => 'lsa', 'Manes.06G055900' => 'mes', 'Manes.12G022200' => 'mes', 'Manes.13G023300' => 'mes', 'Manes.14G115000' => 'mes', 'Manes.15G151700' => 'mes', 'Manes.17G111300' => 'mes', 'Mapoly0226s0009' => 'mpo', 'MBI02_g25363_MAGBIO' => 'mbi', 'MBI06_g00027_MAGBIO' => 'mbi', 'MBI10_g13034_MAGBIO' => 'mbi', 'MD09G1023400' => 'mdo', 'MD13G1100100' => 'mdo', 'MD15G1169200' => 'mdo', 'MD16G1101100' => 'mdo', 'MD17G1022900' => 'mdo', 'Medtr3g096150' => 'mtr', 'Medtr4g115070' => 'mtr', 'Medtr7g033325' => 'mtr', 'Medtr8g089840' => 'mtr', 'MELO3C010319.2' => 'cme', 'MELO3C011944.2' => 'cme', 'MELO3C021589.2' => 'cme', 'Migut.E00207' => 'egut', 'Migut.H00067' => 'egut', 'Migut.K00433' => 'egut', 'Migut.K00606' => 'egut', 'Migut.K01410' => 'egut', 'MSTRG.13347' => 'ama', 'MSTRG.24045' => 'ama', 'MSTRG.2428' => 'ama', 'MSTRG.26410' => 'ama', 'MSTRG.3139' => 'ama', 'MSTRG.3286' => 'ama', 'MSTRG.563' => 'ama', 'MSTRG.7941' => 'ama', 'Nitab4.5_0000028g0060' => 'nta', 'Nitab4.5_0000065g0260' => 'nta', 'Nitab4.5_0000112g0060' => 'nta', 'Nitab4.5_0000489g0120' => 'nta', 'Nitab4.5_0001776g0050' => 'nta', 'Nitab4.5_0001854g0010' => 'nta', 'Nitab4.5_0001860g0020' => 'nta', 'Nitab4.5_0004352g0010' => 'nta', 'Nitab4.5_0008716g0020' => 'nta', 'Nitab4.5_0008922g0010' => 'nta', 'Nn3g16693' => 'nnu', 'Nn4g22596' => 'nnu', 'Nn7g37639' => 'nnu', 'Oeu001701.1' => 'oeu', 'Oeu018149.1' => 'oeu', 'Oeu026220.1' => 'oeu', 'Oeu038635.1' => 'oeu', 'Oeu049176.1' => 'oeu', 'Oeu056706.1' => 'oeu', 'Oeu056937.1' => 'oeu', 'Oeu057540.1' => 'oeu', 'Os02g0594900' => 'osa', 'Os02g0595100' => 'osa', 'Os04g0477500' => 'osa', 'Os12g0611900' => 'osa', 'Peaxi162Scf00076g00020' => 'pax', 'Peaxi162Scf00128g00217' => 'pax', 'Peaxi162Scf00129g01640' => 'pax', 'Peaxi162Scf00669g00007' => 'pax', 'Peaxi162Scf00700g00421' => 'pax', 'Peaxi162Scf00801g00038' => 'pax', 'Peaxi162Scf00891g00025' => 'pax', 'PGR083G0909' => 'pgr', 'PGR119G1005' => 'pgr', 'PGR142G2236' => 'pgr', 'PGR142G3388' => 'pgr', 'PGSC0003DMG400004514' => 'stu', 'PGSC0003DMG400012635' => 'stu', 'PGSC0003DMG400015730' => 'stu', 'PGSC0003DMG400018611' => 'stu', 'PGSC0003DMG400030897' => 'stu', 'Phvul.001G254800' => 'pvu', 'Phvul.002G260100' => 'pvu', 'Phvul.003G167600' => 'pvu', 'Phvul.004G005100' => 'pvu', 'Potri.001G343600' => 'ptr', 'Potri.006G066700' => 'ptr', 'Potri.008G186000' => 'ptr', 'Potri.010G046900' => 'ptr', 'Potri.018G127900' => 'ptr', 'Pp3c20_17750' => 'ppa', 'Pp3c24_4380' => 'ppa', 'Prupe.1G245800' => 'ppe', 'Prupe.3G293400' => 'ppe', 'Prupe.7G247400' => 'ppe', 'Psat0s145g0120' => 'psa', 'Psat0s595g0040' => 'psa', 'Psat0s595g0120' => 'psa', 'Psat3g175040' => 'psa', 'Psat7g058120' => 'psa', 'PSO017G0428' => 'pso', 'PSO063G7510' => 'pso', 'PSO067G0046' => 'pso', 'PSO478G1073' => 'pso', 'PSO675G3677' => 'pso', 'PSO675G6558' => 'pso', 'PSO675G7520' => 'pso', 'PSO675G8959' => 'pso', 'QL02p074089' => 'qlo', 'QL02p089614' => 'qlo', 'QL03p057736' => 'qlo', 'RcHm_v2.0_Chr1g0364131' => 'rch', 'RcHm_v2.0_Chr2g0087801' => 'rch', 'RcHm_v2.0_Chr2g0087821' => 'rch', 'RcHm_v2.0_Chr2g0173231' => 'rch', 'RcHm_v2.0_Chr4g0433111' => 'rch', 'Rhsim03G0250300' => 'rsi', 'Rhsim08G0048400' => 'rsi', 'Rhsim10G0014800' => 'rsi', 'Rhsim12G0040100' => 'rsi', 'Rhsim12G0109700' => 'rsi', 'Sabra06G0049600' => 'sbr', 'Sabra08G0141000' => 'sbr', 'Sabra10G0021400' => 'sbr', 'Sabra16G0222900' => 'sbr', 'Sabra18G0108600' => 'sbr', 'SalBow1G0433' => 'sbo', 'SalBow1G2038' => 'sbo', 'SalBow1G5003' => 'sbo', 'SalBow7G1197' => 'sbo', 'SalBow8G3506' => 'sbo', 'Sc03g0007300' => 'sci', 'Sc11g0000950' => 'sci', 'Sc14g0008750' => 'sci', 'Sc18g0000420' => 'sci', 'Sed0006754' => 'sed', 'Sed0008741' => 'sed', 'Sed0017172' => 'sed', 'Sed0018925' => 'sed', 'Sed0023326' => 'sed', 'Sed0025909' => 'sed', 'SEGI_05333' => 'sgi', 'SEGI_10362' => 'sgi', 'SEGI_13380' => 'sgi', 'SEGI_24306' => 'sgi', 'SEGI_29077' => 'sgi', 'SEGI_29095' => 'sgi', 'SEGI_36534' => 'sgi', 'SEGI_37506' => 'sgi', 'SEGI_38321' => 'sgi', 'SGA_v2.0_scaffold307G48031' => 'sas', 'SGA_v2.0_scaffold47G17507' => 'sas', 'SGA_v2.0_scaffold63G21736' => 'sas', 'SGA_v2.0_scaffold87G27070' => 'sas', 'SHI17794' => 'shi', 'SHI28851' => 'shi', 'SMO165G0155' => 'smo', 'SMO340G0217' => 'smo', 'SMO367G1210' => 'smo', 'Solyc02g093430.3' => 'sly', 'Solyc05g013580.4' => 'sly', 'Solyc07g008030.3' => 'sly', 'Solyc12g035470.2' => 'sly', 'Sopen02g038020' => 'spe', 'Sopen05g008490' => 'spe', 'Sopen07g003910' => 'spe', 'Sopen12g015240' => 'spe', 'Sp1g11550' => 'spa', 'Sp2g16710' => 'spa', 'Sp3g00430' => 'spa', 'Sp3g26780' => 'spa', 'Sp5g22900' => 'spa', 'Sp6g29530' => 'spa', 'TAR371G0794' => 'tar', 'TAR374G0164' => 'tar', 'TAR622G0165' => 'tar', 'TAR626G0929' => 'tar', 'TAR629G2155' => 'tar', 'THA.LOC104805282' => 'tha', 'THA.LOC104805363' => 'tha', 'THA.LOC104808968' => 'tha', 'THA.LOC104821093' => 'tha', 'THA.LOC104823953' => 'tha', 'THA.LOC104825562' => 'tha', 'THA.LOC104825665' => 'tha', 'Thecc.02G261400' => 'tca', 'Thecc.04G019200' => 'tca', 'Thecc.09G130400' => 'tca', 'Thhalv10004374m.g' => 'esa', 'Thhalv10007850m.g' => 'esa', 'Thhalv10013782m.g' => 'esa', 'Thhalv10018686m.g' => 'esa', 'Thhalv10020899m.g' => 'esa', 'Thhalv10022755m.g' => 'esa', 'TPR.G23851' => 'tpr', 'TPR.G26500' => 'tpr', 'TPR.G27267' => 'tpr', 'TPR.G32001' => 'tpr', 'TPR.G6251' => 'tpr', 'TPR.G8167' => 'tpr', 'TWI12G1330' => 'twi', 'TWI18G1239' => 'twi', 'TWI34G0979' => 'twi', 'TWI36G0670' => 'twi', 'TWI36G0707' => 'twi', 'TWI56G0233' => 'twi', 'TWI75G1809' => 'twi', 'unitig_21.g20874' => 'ugi', 'unitig_26.g10343' => 'ugi', 'unitig_46.g18392' => 'ugi', 'unitig_52.g17178' => 'ugi', 'unitig_8.g2934' => 'ugi', 'vmacro01122' => 'vma', 'vmacro05875' => 'vma', 'vmacro06147' => 'vma', 'vmacro16191' => 'vma', 'vmacro18293' => 'vma', 'VMungo0251G3707' => 'vmu', 'VMungo0464G1521' => 'vmu', 'VMungo1215G0205' => 'vmu', 'VMungo1383G2484' => 'vmu', 'Zm00001eb079610' => 'zma', 'Zm00001eb135990' => 'zma', 'Zm00001eb183710' => 'zma', 'Zm00001eb246020' => 'zma' ) $gf_id = 'HOM05D001124' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001124' ) $data_identifier = 'HOM05D001124' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 6, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 7, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 21, 'bol' => (int) 10, 'bra' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 6, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 9, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 21, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 8, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 10, 'lsa' => (int) 8, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 8, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 9, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb246020' $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' => 'HOM05D001124', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '548', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02520' => 'bna', 'A03p06630' => 'bna', 'A05p44460' => 'bna', 'A06p08710' => 'bna', 'A06p41090' => 'bna', 'A07p32320' => 'bna', 'A08p32520' => 'bna', 'A09p10360' => 'bna', 'A10p24080' => 'bna', 'Aa31LG11G15250' => 'aar', 'Aa31LG1G1800' => 'aar', 'Aa31LG2G5120' => 'aar', 'Aa31LG2G6070' => 'aar', 'Aa31LG5G10770' => 'aar', 'Aa31sc61G90' => 'aar', 'Actinidia01352' => 'ach', 'Actinidia05983' => 'ach', 'Actinidia08133' => 'ach', 'Actinidia15101' => 'ach', 'Actinidia26379' => 'ach', 'Actinidia35778' => 'ach', 'Actinidia36123' => 'ach', 'Actinidia37436' => 'ach', 'Actinidia38730' => 'ach', 'Ah.02g128210' => 'amhyb', 'Ah.03g132990' => 'amhyb', 'Ah.14g079410' => 'amhyb', 'AL1G24640' => 'aly', 'AL2G26680' => 'aly', 'AL3G10530' => 'aly', 'AL3G45230' => 'aly', 'AL5G15230' => 'aly', 'AL5G16960' => 'aly', 'AL6G25210' => 'aly', 'Aqoxy2G00441' => 'aox', 'Aqoxy3G01236' => 'aox', 'Aqoxy5G03746' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3RQ047' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C7GMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9C8JER' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MBL6KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YXCZ83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZANX40' => 'arhy', 'AT1G12990' => 'ath', 'AT1G67880' => 'ath', 'AT2G13290' => 'ath', 'AT3G01620' => 'ath', 'AT3G26445' => 'ath', 'AT3G27540' => 'ath', 'AT5G14480' => 'ath', 'ATR0824G026' => 'atr', 'ATR1098G019' => 'atr', 'Atru.chr11.2145' => 'acertr', 'Atru.chr2.3636' => 'acertr', 'Atru.chr2.3644' => 'acertr', 'Atru.chr6.2422' => 'acertr', 'Atru.chr7.1112' => 'acertr', 'AUR62005469' => 'cqu', 'AUR62011166' => 'cqu', 'AUR62013319' => 'cqu', 'AUR62024273' => 'cqu', 'AUR62028420' => 'cqu', 'AUR62041942' => 'cqu', 'BcaB01g04969' => 'bca', 'BcaB01g06371' => 'bca', 'BcaB02g11494' => 'bca', 'BcaB03g15382' => 'bca', 'BcaB08g36994' => 'bca', 'BcaC03g13477' => 'bca', 'BcaC03g13478' => 'bca', 'BcaC03g13480' => 'bca', 'BcaC03g13481' => 'bca', 'BcaC03g13486' => 'bca', 'BcaC04g19031' => 'bca', 'BcaC04g23085' => 'bca', 'BcaC05g25094' => 'bca', 'BcaC05g25096' => 'bca', 'BcaC05g25138' => 'bca', 'BcaC05g30416' => 'bca', 'BcaC05g30455' => 'bca', 'BcaC06g30979' => 'bca', 'BcaC06g33805' => 'bca', 'BcaC08g46021' => 'bca', 'BcaNung03154' => 'bca', 'BolC2t06623H' => 'bol', 'BolC2t06632H' => 'bol', 'BolC2t06635H' => 'bol', 'BolC2t06638H' => 'bol', 'BolC3t13266H' => 'bol', 'BolC5t29776H' => 'bol', 'BolC6t38912H' => 'bol', 'BolC7t44183H' => 'bol', 'BolC9t54123H' => 'bol', 'BolC9t59107H' => 'bol', 'BraA02t05221Z' => 'bra', 'BraA03t09996Z' => 'bra', 'BraA05t23210Z' => 'bra', 'BraA06t24068Z' => 'bra', 'BraA06t27032Z' => 'bra', 'BraA08t35176Z' => 'bra', 'BraA09t36680Z' => 'bra', 'BraA10t44471Z' => 'bra', 'C02p06760' => 'bna', 'C02p06890' => 'bna', 'C02p07010' => 'bna', 'C03p07660' => 'bna', 'C05p10300' => 'bna', 'C06p38150' => 'bna', 'C07p36650' => 'bna', 'C08p15770' => 'bna', 'C09p12300' => 'bna', 'C09p62700' => 'bna', 'C09p75040' => 'bna', 'CAN.G13.1' => 'can', 'CAN.G138.4' => 'can', 'CAN.G44.6' => 'can', 'CAN.G473.19' => 'can', 'CANSAT01G0835' => 'cansat', 'CANSAT11G0246' => 'cansat', 'CANSAT11G1766' => 'cansat', 'CANSAT64G1954' => 'cansat', 'CARHR013330' => 'chi', 'CARHR060530' => 'chi', 'CARHR075300' => 'chi', 'CARHR105120' => 'chi', 'CARHR148910' => 'chi', 'CARHR198830' => 'chi', 'Carub.0001s1275' => 'cru', 'Carub.0002s1437' => 'cru', 'Carub.0003s0044' => 'cru', 'Carub.0003s2787' => 'cru', 'Carub.0005s0597' => 'cru', 'Carub.0006s1266' => 'cru', 'Ca_06935_v3' => 'car', 'Ca_13559_v3' => 'car', 'Ca_16941_v3' => 'car', 'Ca_16960_v3' => 'car', 'Ca_17775_v3' => 'car', 'Ca_30464_v3' => 'car', 'Cc06_g08160' => 'ccan', 'Cc07_g01520' => 'ccan', 'Cc11_g15810' => 'ccan', 'CDE02G2840' => 'cde', 'CDE03G0093' => 'cde', 'CDE04G2127' => 'cde', 'CDE07G1857' => 'cde', 'CDE09G1246' => 'cde', 'Cfa003412' => 'cfa', 'Cfa007341' => 'cfa', 'Cfa009220' => 'cfa', 'Ciclev10008737m.g' => 'ccl', 'Ciclev10015565m.g' => 'ccl', 'Ciclev10031761m.g' => 'ccl', 'CiPaw.03G045300' => 'cil', 'CiPaw.03G247200' => 'cil', 'CiPaw.04G029500' => 'cil', 'CiPaw.04G174000' => 'cil', 'CiPaw.05G181200' => 'cil', 'CiPaw.06G067100' => 'cil', 'ClCG05G025800' => 'cla', 'ClCG06G011400' => 'cla', 'ClCG09G019360' => 'cla', 'COL.COLO4_04827' => 'col', 'COL.COLO4_29170' => 'col', 'COL.COLO4_35131' => 'col', 'COL.COLO4_35132' => 'col', 'Cpa.g.sc33.32' => 'cpa', 'Cpa.g.sc46.29' => 'cpa', 'Cpa.g.sc796.1' => 'cpa', 'CsaV3_1G030420' => 'csa', 'CsaV3_5G027050' => 'csa', 'CsaV3_5G031040' => 'csa', 'CsaV3_UNG023130' => 'csa', 'CSS0007726' => 'camsi', 'CSS0016433' => 'camsi', 'CSS0017656' => 'camsi', 'CSS0025364' => 'camsi', 'CSS0027582' => 'camsi', 'CSS0047288' => 'camsi', 'CSS0049950' => 'camsi', 'DCAR_003843' => 'dca', 'DCAR_007052' => 'dca', 'DCAR_020884' => 'dca', 'DCAR_021730' => 'dca', 'DCAR_024423' => 'dca', 'DCAR_026509' => 'dca', 'DCAR_031158' => 'dca', 'Dinv14728' => 'din', 'Dinv15219' => 'din', 'Dinv25728' => 'din', 'Dinv33428' => 'din', 'Dinv36489' => 'din', 'Dinv41486' => 'din', 'Duzib147G0469' => 'dzi', 'Duzib168G0060' => 'dzi', 'Duzib187G1215' => 'dzi', 'Duzib248G0692' => 'dzi', 'Duzib251G0767' => 'dzi', 'Duzib264G0446' => 'dzi', 'Duzib268G0691' => 'dzi', 'ECA232G4767' => 'eca', 'ECA233G2838' => 'eca', 'ECA234G0391' => 'eca', 'ECA234G0857' => 'eca', 'ECA236G1593' => 'eca', 'ECA238G0565' => 'eca', 'ECA246G1027' => 'eca', 'ECA246G3223' => 'eca', 'ECA246G3470' => 'eca', 'EL10Ac6g13829' => 'bvu', 'EL10Ac6g14093' => 'bvu', 'EL10Ac8g18707' => 'bvu', 'Eucgr.C01369' => 'egr', 'Eucgr.H02492' => 'egr', 'Eucgr.I01733' => 'egr', 'Eucgr.J02255' => 'egr', 'Eucgr.J02257' => 'egr', 'Eucgr.J02258' => 'egr', 'FAN02G1601' => 'fan', 'FAN03G1586' => 'fan', 'FAN03G2986' => 'fan', 'FAN05G4837' => 'fan', 'FAN06G0146' => 'fan', 'FAN07G0858' => 'fan', 'FAN09G3179' => 'fan', 'FAN10G0669' => 'fan', 'FAN12G2358' => 'fan', 'FAN14G4198' => 'fan', 'FAN14G5112' => 'fan', 'FAN17G0342' => 'fan', 'FAN19G0342' => 'fan', 'FAN19G0962' => 'fan', 'FAN19G1101' => 'fan', 'FAN19G1872' => 'fan', 'FAN22G0356' => 'fan', 'FAN23G0744' => 'fan', 'FAN23G1914' => 'fan', 'FAN26G0032' => 'fan', 'FAN28G0625' => 'fan', 'FvH4_1g02710' => 'fve', 'FvH4_1g02720' => 'fve', 'FvH4_4g25670' => 'fve', 'FvH4_6g51700' => 'fve', 'FvH4_7g20170' => 'fve', 'Glyma.05G175000' => 'gma', 'Glyma.08G132300' => 'gma', 'Glyma.11G243000' => 'gma', 'Glyma.13G158900' => 'gma', 'Glyma.17G112400' => 'gma', 'Glyma.18G014100' => 'gma', 'Glyma.19G003100' => 'gma', 'Glyma.19G056500' => 'gma', 'Gohir.A01G158900' => 'ghi', 'Gohir.A05G312600' => 'ghi', 'Gohir.A05G354900' => 'ghi', 'Gohir.A07G037200' => 'ghi', 'Gohir.A09G030000' => 'ghi', 'Gohir.A12G145200' => 'ghi', 'Gohir.D01G151500' => 'ghi', 'Gohir.D04G058300' => 'ghi', 'Gohir.D05G314100' => 'ghi', 'Gohir.D07G041400' => 'ghi', 'Gohir.D09G029700' => 'ghi', 'Gohir.D12G149700' => 'ghi', 'Gorai.001G043800' => 'gra', 'Gorai.002G187800' => 'gra', 'Gorai.006G034700' => 'gra', 'Gorai.008G161200' => 'gra', 'Gorai.009G335700' => 'gra', 'Gorai.012G065000' => 'gra', 'GSVIVG01000535001' => 'vvi', 'GSVIVG01015572001' => 'vvi', 'GSVIVG01032386001' => 'vvi', 'HanXRQChr05g0138531' => 'han', 'HanXRQChr06g0174391' => 'han', 'HanXRQChr07g0199021' => 'han', 'HanXRQChr08g0208211' => 'han', 'HanXRQChr09g0255471' => 'han', 'HanXRQChr10g0315791' => 'han', 'HanXRQChr12g0371991' => 'han', 'HanXRQChr15g0475251' => 'han', 'HanXRQChr17g0540001' => 'han', 'HanXRQChr17g0548631' => 'han', 'HanXRQChr17g0569561' => 'han', 'Haze_12256' => 'cav', 'Haze_14756' => 'cav', 'Haze_25528' => 'cav', 'Hma1.2p1_0079F.1_g041020' => 'hma', 'Hma1.2p1_0818F.1_g223260' => 'hma', 'Hma1.2p1_1747F.1_g300530' => 'hma', 'HPP92_004607' => 'vpl', 'HPP92_004608' => 'vpl', 'HPP92_006181' => 'vpl', 'HPP92_012192' => 'vpl', 'HPP92_015680' => 'vpl', 'HPP92_020249' => 'vpl', 'HPP92_021376' => 'vpl', 'HPP92_024275' => 'vpl', 'Hund06031' => 'sun', 'Hund25391' => 'sun', 'Lalb_Chr07g0185371' => 'lal', 'Lalb_Chr07g0185381' => 'lal', 'Lalb_Chr12g0204011' => 'lal', 'Lalb_Chr13g0301671' => 'lal', 'Lalb_Chr14g0362851' => 'lal', 'Lalb_Chr24g0403581' => 'lal', 'Lj1g0000233' => 'lja', 'Lj2g0018120' => 'lja', 'Lj3C621T0' => 'lonja', 'Lj3P1059T14' => 'lonja', 'Lj3P611T9' => 'lonja', 'Lj3P614T13' => 'lonja', 'Lj3P615T5' => 'lonja', 'Lj4g0012315' => 'lja', 'Lj4g0026182' => 'lja', 'Lj6P813T16' => 'lonja', 'Lj7C427T7' => 'lonja', 'Lj7C427T8' => 'lonja', 'Lj7P600T41' => 'lonja', 'Lju41C42G17' => 'lonja', 'Lsat_1_v5_gn_0_47300' => 'lsa', 'Lsat_1_v5_gn_2_91280' => 'lsa', 'Lsat_1_v5_gn_3_30561' => 'lsa', 'Lsat_1_v5_gn_4_184321' => 'lsa', 'Lsat_1_v5_gn_4_4041' => 'lsa', 'Lsat_1_v5_gn_5_92000' => 'lsa', 'Lsat_1_v5_gn_8_152940' => 'lsa', 'Lsat_1_v5_gn_8_62401' => 'lsa', 'Manes.06G055900' => 'mes', 'Manes.12G022200' => 'mes', 'Manes.13G023300' => 'mes', 'Manes.14G115000' => 'mes', 'Manes.15G151700' => 'mes', 'Manes.17G111300' => 'mes', 'Mapoly0226s0009' => 'mpo', 'MBI02_g25363_MAGBIO' => 'mbi', 'MBI06_g00027_MAGBIO' => 'mbi', 'MBI10_g13034_MAGBIO' => 'mbi', 'MD09G1023400' => 'mdo', 'MD13G1100100' => 'mdo', 'MD15G1169200' => 'mdo', 'MD16G1101100' => 'mdo', 'MD17G1022900' => 'mdo', 'Medtr3g096150' => 'mtr', 'Medtr4g115070' => 'mtr', 'Medtr7g033325' => 'mtr', 'Medtr8g089840' => 'mtr', 'MELO3C010319.2' => 'cme', 'MELO3C011944.2' => 'cme', 'MELO3C021589.2' => 'cme', 'Migut.E00207' => 'egut', 'Migut.H00067' => 'egut', 'Migut.K00433' => 'egut', 'Migut.K00606' => 'egut', 'Migut.K01410' => 'egut', 'MSTRG.13347' => 'ama', 'MSTRG.24045' => 'ama', 'MSTRG.2428' => 'ama', 'MSTRG.26410' => 'ama', 'MSTRG.3139' => 'ama', 'MSTRG.3286' => 'ama', 'MSTRG.563' => 'ama', 'MSTRG.7941' => 'ama', 'Nitab4.5_0000028g0060' => 'nta', 'Nitab4.5_0000065g0260' => 'nta', 'Nitab4.5_0000112g0060' => 'nta', 'Nitab4.5_0000489g0120' => 'nta', 'Nitab4.5_0001776g0050' => 'nta', 'Nitab4.5_0001854g0010' => 'nta', 'Nitab4.5_0001860g0020' => 'nta', 'Nitab4.5_0004352g0010' => 'nta', 'Nitab4.5_0008716g0020' => 'nta', 'Nitab4.5_0008922g0010' => 'nta', 'Nn3g16693' => 'nnu', 'Nn4g22596' => 'nnu', 'Nn7g37639' => 'nnu', 'Oeu001701.1' => 'oeu', 'Oeu018149.1' => 'oeu', 'Oeu026220.1' => 'oeu', 'Oeu038635.1' => 'oeu', 'Oeu049176.1' => 'oeu', 'Oeu056706.1' => 'oeu', 'Oeu056937.1' => 'oeu', 'Oeu057540.1' => 'oeu', 'Os02g0594900' => 'osa', 'Os02g0595100' => 'osa', 'Os04g0477500' => 'osa', 'Os12g0611900' => 'osa', 'Peaxi162Scf00076g00020' => 'pax', 'Peaxi162Scf00128g00217' => 'pax', 'Peaxi162Scf00129g01640' => 'pax', 'Peaxi162Scf00669g00007' => 'pax', 'Peaxi162Scf00700g00421' => 'pax', 'Peaxi162Scf00801g00038' => 'pax', 'Peaxi162Scf00891g00025' => 'pax', 'PGR083G0909' => 'pgr', 'PGR119G1005' => 'pgr', 'PGR142G2236' => 'pgr', 'PGR142G3388' => 'pgr', 'PGSC0003DMG400004514' => 'stu', 'PGSC0003DMG400012635' => 'stu', 'PGSC0003DMG400015730' => 'stu', 'PGSC0003DMG400018611' => 'stu', 'PGSC0003DMG400030897' => 'stu', 'Phvul.001G254800' => 'pvu', 'Phvul.002G260100' => 'pvu', 'Phvul.003G167600' => 'pvu', 'Phvul.004G005100' => 'pvu', 'Potri.001G343600' => 'ptr', 'Potri.006G066700' => 'ptr', 'Potri.008G186000' => 'ptr', 'Potri.010G046900' => 'ptr', 'Potri.018G127900' => 'ptr', 'Pp3c20_17750' => 'ppa', 'Pp3c24_4380' => 'ppa', 'Prupe.1G245800' => 'ppe', 'Prupe.3G293400' => 'ppe', 'Prupe.7G247400' => 'ppe', 'Psat0s145g0120' => 'psa', 'Psat0s595g0040' => 'psa', 'Psat0s595g0120' => 'psa', 'Psat3g175040' => 'psa', 'Psat7g058120' => 'psa', 'PSO017G0428' => 'pso', 'PSO063G7510' => 'pso', 'PSO067G0046' => 'pso', 'PSO478G1073' => 'pso', 'PSO675G3677' => 'pso', 'PSO675G6558' => 'pso', 'PSO675G7520' => 'pso', 'PSO675G8959' => 'pso', 'QL02p074089' => 'qlo', 'QL02p089614' => 'qlo', 'QL03p057736' => 'qlo', 'RcHm_v2.0_Chr1g0364131' => 'rch', 'RcHm_v2.0_Chr2g0087801' => 'rch', 'RcHm_v2.0_Chr2g0087821' => 'rch', 'RcHm_v2.0_Chr2g0173231' => 'rch', 'RcHm_v2.0_Chr4g0433111' => 'rch', 'Rhsim03G0250300' => 'rsi', 'Rhsim08G0048400' => 'rsi', 'Rhsim10G0014800' => 'rsi', 'Rhsim12G0040100' => 'rsi', 'Rhsim12G0109700' => 'rsi', 'Sabra06G0049600' => 'sbr', 'Sabra08G0141000' => 'sbr', 'Sabra10G0021400' => 'sbr', 'Sabra16G0222900' => 'sbr', 'Sabra18G0108600' => 'sbr', 'SalBow1G0433' => 'sbo', 'SalBow1G2038' => 'sbo', 'SalBow1G5003' => 'sbo', 'SalBow7G1197' => 'sbo', 'SalBow8G3506' => 'sbo', 'Sc03g0007300' => 'sci', 'Sc11g0000950' => 'sci', 'Sc14g0008750' => 'sci', 'Sc18g0000420' => 'sci', 'Sed0006754' => 'sed', 'Sed0008741' => 'sed', 'Sed0017172' => 'sed', 'Sed0018925' => 'sed', 'Sed0023326' => 'sed', 'Sed0025909' => 'sed', 'SEGI_05333' => 'sgi', 'SEGI_10362' => 'sgi', 'SEGI_13380' => 'sgi', 'SEGI_24306' => 'sgi', 'SEGI_29077' => 'sgi', 'SEGI_29095' => 'sgi', 'SEGI_36534' => 'sgi', 'SEGI_37506' => 'sgi', 'SEGI_38321' => 'sgi', 'SGA_v2.0_scaffold307G48031' => 'sas', 'SGA_v2.0_scaffold47G17507' => 'sas', 'SGA_v2.0_scaffold63G21736' => 'sas', 'SGA_v2.0_scaffold87G27070' => 'sas', 'SHI17794' => 'shi', 'SHI28851' => 'shi', 'SMO165G0155' => 'smo', 'SMO340G0217' => 'smo', 'SMO367G1210' => 'smo', 'Solyc02g093430.3' => 'sly', 'Solyc05g013580.4' => 'sly', 'Solyc07g008030.3' => 'sly', 'Solyc12g035470.2' => 'sly', 'Sopen02g038020' => 'spe', 'Sopen05g008490' => 'spe', 'Sopen07g003910' => 'spe', 'Sopen12g015240' => 'spe', 'Sp1g11550' => 'spa', 'Sp2g16710' => 'spa', 'Sp3g00430' => 'spa', 'Sp3g26780' => 'spa', 'Sp5g22900' => 'spa', 'Sp6g29530' => 'spa', 'TAR371G0794' => 'tar', 'TAR374G0164' => 'tar', 'TAR622G0165' => 'tar', 'TAR626G0929' => 'tar', 'TAR629G2155' => 'tar', 'THA.LOC104805282' => 'tha', 'THA.LOC104805363' => 'tha', 'THA.LOC104808968' => 'tha', 'THA.LOC104821093' => 'tha', 'THA.LOC104823953' => 'tha', 'THA.LOC104825562' => 'tha', 'THA.LOC104825665' => 'tha', 'Thecc.02G261400' => 'tca', 'Thecc.04G019200' => 'tca', 'Thecc.09G130400' => 'tca', 'Thhalv10004374m.g' => 'esa', 'Thhalv10007850m.g' => 'esa', 'Thhalv10013782m.g' => 'esa', 'Thhalv10018686m.g' => 'esa', 'Thhalv10020899m.g' => 'esa', 'Thhalv10022755m.g' => 'esa', 'TPR.G23851' => 'tpr', 'TPR.G26500' => 'tpr', 'TPR.G27267' => 'tpr', 'TPR.G32001' => 'tpr', 'TPR.G6251' => 'tpr', 'TPR.G8167' => 'tpr', 'TWI12G1330' => 'twi', 'TWI18G1239' => 'twi', 'TWI34G0979' => 'twi', 'TWI36G0670' => 'twi', 'TWI36G0707' => 'twi', 'TWI56G0233' => 'twi', 'TWI75G1809' => 'twi', 'unitig_21.g20874' => 'ugi', 'unitig_26.g10343' => 'ugi', 'unitig_46.g18392' => 'ugi', 'unitig_52.g17178' => 'ugi', 'unitig_8.g2934' => 'ugi', 'vmacro01122' => 'vma', 'vmacro05875' => 'vma', 'vmacro06147' => 'vma', 'vmacro16191' => 'vma', 'vmacro18293' => 'vma', 'VMungo0251G3707' => 'vmu', 'VMungo0464G1521' => 'vmu', 'VMungo1215G0205' => 'vmu', 'VMungo1383G2484' => 'vmu', 'Zm00001eb079610' => 'zma', 'Zm00001eb135990' => 'zma', 'Zm00001eb183710' => 'zma', 'Zm00001eb246020' => 'zma' ), 'gf_id' => 'HOM05D001124', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001124' ), 'data_identifier' => 'HOM05D001124', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001124', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '548', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02520' => 'bna', 'A03p06630' => 'bna', 'A05p44460' => 'bna', 'A06p08710' => 'bna', 'A06p41090' => 'bna', 'A07p32320' => 'bna', 'A08p32520' => 'bna', 'A09p10360' => 'bna', 'A10p24080' => 'bna', 'Aa31LG11G15250' => 'aar', 'Aa31LG1G1800' => 'aar', 'Aa31LG2G5120' => 'aar', 'Aa31LG2G6070' => 'aar', 'Aa31LG5G10770' => 'aar', 'Aa31sc61G90' => 'aar', 'Actinidia01352' => 'ach', 'Actinidia05983' => 'ach', 'Actinidia08133' => 'ach', 'Actinidia15101' => 'ach', 'Actinidia26379' => 'ach', 'Actinidia35778' => 'ach', 'Actinidia36123' => 'ach', 'Actinidia37436' => 'ach', 'Actinidia38730' => 'ach', 'Ah.02g128210' => 'amhyb', 'Ah.03g132990' => 'amhyb', 'Ah.14g079410' => 'amhyb', 'AL1G24640' => 'aly', 'AL2G26680' => 'aly', 'AL3G10530' => 'aly', 'AL3G45230' => 'aly', 'AL5G15230' => 'aly', 'AL5G16960' => 'aly', 'AL6G25210' => 'aly', 'Aqoxy2G00441' => 'aox', 'Aqoxy3G01236' => 'aox', 'Aqoxy5G03746' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3RQ047' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C7GMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9C8JER' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MBL6KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YXCZ83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZANX40' => 'arhy', 'AT1G12990' => 'ath', 'AT1G67880' => 'ath', 'AT2G13290' => 'ath', 'AT3G01620' => 'ath', 'AT3G26445' => 'ath', 'AT3G27540' => 'ath', 'AT5G14480' => 'ath', 'ATR0824G026' => 'atr', 'ATR1098G019' => 'atr', 'Atru.chr11.2145' => 'acertr', 'Atru.chr2.3636' => 'acertr', 'Atru.chr2.3644' => 'acertr', 'Atru.chr6.2422' => 'acertr', 'Atru.chr7.1112' => 'acertr', 'AUR62005469' => 'cqu', 'AUR62011166' => 'cqu', 'AUR62013319' => 'cqu', 'AUR62024273' => 'cqu', 'AUR62028420' => 'cqu', 'AUR62041942' => 'cqu', 'BcaB01g04969' => 'bca', 'BcaB01g06371' => 'bca', 'BcaB02g11494' => 'bca', 'BcaB03g15382' => 'bca', 'BcaB08g36994' => 'bca', 'BcaC03g13477' => 'bca', 'BcaC03g13478' => 'bca', 'BcaC03g13480' => 'bca', 'BcaC03g13481' => 'bca', 'BcaC03g13486' => 'bca', 'BcaC04g19031' => 'bca', 'BcaC04g23085' => 'bca', 'BcaC05g25094' => 'bca', 'BcaC05g25096' => 'bca', 'BcaC05g25138' => 'bca', 'BcaC05g30416' => 'bca', 'BcaC05g30455' => 'bca', 'BcaC06g30979' => 'bca', 'BcaC06g33805' => 'bca', 'BcaC08g46021' => 'bca', 'BcaNung03154' => 'bca', 'BolC2t06623H' => 'bol', 'BolC2t06632H' => 'bol', 'BolC2t06635H' => 'bol', 'BolC2t06638H' => 'bol', 'BolC3t13266H' => 'bol', 'BolC5t29776H' => 'bol', 'BolC6t38912H' => 'bol', 'BolC7t44183H' => 'bol', 'BolC9t54123H' => 'bol', 'BolC9t59107H' => 'bol', 'BraA02t05221Z' => 'bra', 'BraA03t09996Z' => 'bra', 'BraA05t23210Z' => 'bra', 'BraA06t24068Z' => 'bra', 'BraA06t27032Z' => 'bra', 'BraA08t35176Z' => 'bra', 'BraA09t36680Z' => 'bra', 'BraA10t44471Z' => 'bra', 'C02p06760' => 'bna', 'C02p06890' => 'bna', 'C02p07010' => 'bna', 'C03p07660' => 'bna', 'C05p10300' => 'bna', 'C06p38150' => 'bna', 'C07p36650' => 'bna', 'C08p15770' => 'bna', 'C09p12300' => 'bna', 'C09p62700' => 'bna', 'C09p75040' => 'bna', 'CAN.G13.1' => 'can', 'CAN.G138.4' => 'can', 'CAN.G44.6' => 'can', 'CAN.G473.19' => 'can', 'CANSAT01G0835' => 'cansat', 'CANSAT11G0246' => 'cansat', 'CANSAT11G1766' => 'cansat', 'CANSAT64G1954' => 'cansat', 'CARHR013330' => 'chi', 'CARHR060530' => 'chi', 'CARHR075300' => 'chi', 'CARHR105120' => 'chi', 'CARHR148910' => 'chi', 'CARHR198830' => 'chi', 'Carub.0001s1275' => 'cru', 'Carub.0002s1437' => 'cru', 'Carub.0003s0044' => 'cru', 'Carub.0003s2787' => 'cru', 'Carub.0005s0597' => 'cru', 'Carub.0006s1266' => 'cru', 'Ca_06935_v3' => 'car', 'Ca_13559_v3' => 'car', 'Ca_16941_v3' => 'car', 'Ca_16960_v3' => 'car', 'Ca_17775_v3' => 'car', 'Ca_30464_v3' => 'car', 'Cc06_g08160' => 'ccan', 'Cc07_g01520' => 'ccan', 'Cc11_g15810' => 'ccan', 'CDE02G2840' => 'cde', 'CDE03G0093' => 'cde', 'CDE04G2127' => 'cde', 'CDE07G1857' => 'cde', 'CDE09G1246' => 'cde', 'Cfa003412' => 'cfa', 'Cfa007341' => 'cfa', 'Cfa009220' => 'cfa', 'Ciclev10008737m.g' => 'ccl', 'Ciclev10015565m.g' => 'ccl', 'Ciclev10031761m.g' => 'ccl', 'CiPaw.03G045300' => 'cil', 'CiPaw.03G247200' => 'cil', 'CiPaw.04G029500' => 'cil', 'CiPaw.04G174000' => 'cil', 'CiPaw.05G181200' => 'cil', 'CiPaw.06G067100' => 'cil', 'ClCG05G025800' => 'cla', 'ClCG06G011400' => 'cla', 'ClCG09G019360' => 'cla', 'COL.COLO4_04827' => 'col', 'COL.COLO4_29170' => 'col', 'COL.COLO4_35131' => 'col', 'COL.COLO4_35132' => 'col', 'Cpa.g.sc33.32' => 'cpa', 'Cpa.g.sc46.29' => 'cpa', 'Cpa.g.sc796.1' => 'cpa', 'CsaV3_1G030420' => 'csa', 'CsaV3_5G027050' => 'csa', 'CsaV3_5G031040' => 'csa', 'CsaV3_UNG023130' => 'csa', 'CSS0007726' => 'camsi', 'CSS0016433' => 'camsi', 'CSS0017656' => 'camsi', 'CSS0025364' => 'camsi', 'CSS0027582' => 'camsi', 'CSS0047288' => 'camsi', 'CSS0049950' => 'camsi', 'DCAR_003843' => 'dca', 'DCAR_007052' => 'dca', 'DCAR_020884' => 'dca', 'DCAR_021730' => 'dca', 'DCAR_024423' => 'dca', 'DCAR_026509' => 'dca', 'DCAR_031158' => 'dca', 'Dinv14728' => 'din', 'Dinv15219' => 'din', 'Dinv25728' => 'din', 'Dinv33428' => 'din', 'Dinv36489' => 'din', 'Dinv41486' => 'din', 'Duzib147G0469' => 'dzi', 'Duzib168G0060' => 'dzi', 'Duzib187G1215' => 'dzi', 'Duzib248G0692' => 'dzi', 'Duzib251G0767' => 'dzi', 'Duzib264G0446' => 'dzi', 'Duzib268G0691' => 'dzi', 'ECA232G4767' => 'eca', 'ECA233G2838' => 'eca', 'ECA234G0391' => 'eca', 'ECA234G0857' => 'eca', 'ECA236G1593' => 'eca', 'ECA238G0565' => 'eca', 'ECA246G1027' => 'eca', 'ECA246G3223' => 'eca', 'ECA246G3470' => 'eca', 'EL10Ac6g13829' => 'bvu', 'EL10Ac6g14093' => 'bvu', 'EL10Ac8g18707' => 'bvu', 'Eucgr.C01369' => 'egr', 'Eucgr.H02492' => 'egr', 'Eucgr.I01733' => 'egr', 'Eucgr.J02255' => 'egr', 'Eucgr.J02257' => 'egr', 'Eucgr.J02258' => 'egr', 'FAN02G1601' => 'fan', 'FAN03G1586' => 'fan', 'FAN03G2986' => 'fan', 'FAN05G4837' => 'fan', 'FAN06G0146' => 'fan', 'FAN07G0858' => 'fan', 'FAN09G3179' => 'fan', 'FAN10G0669' => 'fan', 'FAN12G2358' => 'fan', 'FAN14G4198' => 'fan', 'FAN14G5112' => 'fan', 'FAN17G0342' => 'fan', 'FAN19G0342' => 'fan', 'FAN19G0962' => 'fan', 'FAN19G1101' => 'fan', 'FAN19G1872' => 'fan', 'FAN22G0356' => 'fan', 'FAN23G0744' => 'fan', 'FAN23G1914' => 'fan', 'FAN26G0032' => 'fan', 'FAN28G0625' => 'fan', 'FvH4_1g02710' => 'fve', 'FvH4_1g02720' => 'fve', 'FvH4_4g25670' => 'fve', 'FvH4_6g51700' => 'fve', 'FvH4_7g20170' => 'fve', 'Glyma.05G175000' => 'gma', 'Glyma.08G132300' => 'gma', 'Glyma.11G243000' => 'gma', 'Glyma.13G158900' => 'gma', 'Glyma.17G112400' => 'gma', 'Glyma.18G014100' => 'gma', 'Glyma.19G003100' => 'gma', 'Glyma.19G056500' => 'gma', 'Gohir.A01G158900' => 'ghi', 'Gohir.A05G312600' => 'ghi', 'Gohir.A05G354900' => 'ghi', 'Gohir.A07G037200' => 'ghi', 'Gohir.A09G030000' => 'ghi', 'Gohir.A12G145200' => 'ghi', 'Gohir.D01G151500' => 'ghi', 'Gohir.D04G058300' => 'ghi', 'Gohir.D05G314100' => 'ghi', 'Gohir.D07G041400' => 'ghi', 'Gohir.D09G029700' => 'ghi', 'Gohir.D12G149700' => 'ghi', 'Gorai.001G043800' => 'gra', 'Gorai.002G187800' => 'gra', 'Gorai.006G034700' => 'gra', 'Gorai.008G161200' => 'gra', 'Gorai.009G335700' => 'gra', 'Gorai.012G065000' => 'gra', 'GSVIVG01000535001' => 'vvi', 'GSVIVG01015572001' => 'vvi', 'GSVIVG01032386001' => 'vvi', 'HanXRQChr05g0138531' => 'han', 'HanXRQChr06g0174391' => 'han', 'HanXRQChr07g0199021' => 'han', 'HanXRQChr08g0208211' => 'han', 'HanXRQChr09g0255471' => 'han', 'HanXRQChr10g0315791' => 'han', 'HanXRQChr12g0371991' => 'han', 'HanXRQChr15g0475251' => 'han', 'HanXRQChr17g0540001' => 'han', 'HanXRQChr17g0548631' => 'han', 'HanXRQChr17g0569561' => 'han', 'Haze_12256' => 'cav', 'Haze_14756' => 'cav', 'Haze_25528' => 'cav', 'Hma1.2p1_0079F.1_g041020' => 'hma', 'Hma1.2p1_0818F.1_g223260' => 'hma', 'Hma1.2p1_1747F.1_g300530' => 'hma', 'HPP92_004607' => 'vpl', 'HPP92_004608' => 'vpl', 'HPP92_006181' => 'vpl', 'HPP92_012192' => 'vpl', 'HPP92_015680' => 'vpl', 'HPP92_020249' => 'vpl', 'HPP92_021376' => 'vpl', 'HPP92_024275' => 'vpl', 'Hund06031' => 'sun', 'Hund25391' => 'sun', 'Lalb_Chr07g0185371' => 'lal', 'Lalb_Chr07g0185381' => 'lal', 'Lalb_Chr12g0204011' => 'lal', 'Lalb_Chr13g0301671' => 'lal', 'Lalb_Chr14g0362851' => 'lal', 'Lalb_Chr24g0403581' => 'lal', 'Lj1g0000233' => 'lja', 'Lj2g0018120' => 'lja', 'Lj3C621T0' => 'lonja', 'Lj3P1059T14' => 'lonja', 'Lj3P611T9' => 'lonja', 'Lj3P614T13' => 'lonja', 'Lj3P615T5' => 'lonja', 'Lj4g0012315' => 'lja', 'Lj4g0026182' => 'lja', 'Lj6P813T16' => 'lonja', 'Lj7C427T7' => 'lonja', 'Lj7C427T8' => 'lonja', 'Lj7P600T41' => 'lonja', 'Lju41C42G17' => 'lonja', 'Lsat_1_v5_gn_0_47300' => 'lsa', 'Lsat_1_v5_gn_2_91280' => 'lsa', 'Lsat_1_v5_gn_3_30561' => 'lsa', 'Lsat_1_v5_gn_4_184321' => 'lsa', 'Lsat_1_v5_gn_4_4041' => 'lsa', 'Lsat_1_v5_gn_5_92000' => 'lsa', 'Lsat_1_v5_gn_8_152940' => 'lsa', 'Lsat_1_v5_gn_8_62401' => 'lsa', 'Manes.06G055900' => 'mes', 'Manes.12G022200' => 'mes', 'Manes.13G023300' => 'mes', 'Manes.14G115000' => 'mes', 'Manes.15G151700' => 'mes', 'Manes.17G111300' => 'mes', 'Mapoly0226s0009' => 'mpo', 'MBI02_g25363_MAGBIO' => 'mbi', 'MBI06_g00027_MAGBIO' => 'mbi', 'MBI10_g13034_MAGBIO' => 'mbi', 'MD09G1023400' => 'mdo', 'MD13G1100100' => 'mdo', 'MD15G1169200' => 'mdo', 'MD16G1101100' => 'mdo', 'MD17G1022900' => 'mdo', 'Medtr3g096150' => 'mtr', 'Medtr4g115070' => 'mtr', 'Medtr7g033325' => 'mtr', 'Medtr8g089840' => 'mtr', 'MELO3C010319.2' => 'cme', 'MELO3C011944.2' => 'cme', 'MELO3C021589.2' => 'cme', 'Migut.E00207' => 'egut', 'Migut.H00067' => 'egut', 'Migut.K00433' => 'egut', 'Migut.K00606' => 'egut', 'Migut.K01410' => 'egut', 'MSTRG.13347' => 'ama', 'MSTRG.24045' => 'ama', 'MSTRG.2428' => 'ama', 'MSTRG.26410' => 'ama', 'MSTRG.3139' => 'ama', 'MSTRG.3286' => 'ama', 'MSTRG.563' => 'ama', 'MSTRG.7941' => 'ama', 'Nitab4.5_0000028g0060' => 'nta', 'Nitab4.5_0000065g0260' => 'nta', 'Nitab4.5_0000112g0060' => 'nta', 'Nitab4.5_0000489g0120' => 'nta', 'Nitab4.5_0001776g0050' => 'nta', 'Nitab4.5_0001854g0010' => 'nta', 'Nitab4.5_0001860g0020' => 'nta', 'Nitab4.5_0004352g0010' => 'nta', 'Nitab4.5_0008716g0020' => 'nta', 'Nitab4.5_0008922g0010' => 'nta', 'Nn3g16693' => 'nnu', 'Nn4g22596' => 'nnu', 'Nn7g37639' => 'nnu', 'Oeu001701.1' => 'oeu', 'Oeu018149.1' => 'oeu', 'Oeu026220.1' => 'oeu', 'Oeu038635.1' => 'oeu', 'Oeu049176.1' => 'oeu', 'Oeu056706.1' => 'oeu', 'Oeu056937.1' => 'oeu', 'Oeu057540.1' => 'oeu', 'Os02g0594900' => 'osa', 'Os02g0595100' => 'osa', 'Os04g0477500' => 'osa', 'Os12g0611900' => 'osa', 'Peaxi162Scf00076g00020' => 'pax', 'Peaxi162Scf00128g00217' => 'pax', 'Peaxi162Scf00129g01640' => 'pax', 'Peaxi162Scf00669g00007' => 'pax', 'Peaxi162Scf00700g00421' => 'pax', 'Peaxi162Scf00801g00038' => 'pax', 'Peaxi162Scf00891g00025' => 'pax', 'PGR083G0909' => 'pgr', 'PGR119G1005' => 'pgr', 'PGR142G2236' => 'pgr', 'PGR142G3388' => 'pgr', 'PGSC0003DMG400004514' => 'stu', 'PGSC0003DMG400012635' => 'stu', 'PGSC0003DMG400015730' => 'stu', 'PGSC0003DMG400018611' => 'stu', 'PGSC0003DMG400030897' => 'stu', 'Phvul.001G254800' => 'pvu', 'Phvul.002G260100' => 'pvu', 'Phvul.003G167600' => 'pvu', 'Phvul.004G005100' => 'pvu', 'Potri.001G343600' => 'ptr', 'Potri.006G066700' => 'ptr', 'Potri.008G186000' => 'ptr', 'Potri.010G046900' => 'ptr', 'Potri.018G127900' => 'ptr', 'Pp3c20_17750' => 'ppa', 'Pp3c24_4380' => 'ppa', 'Prupe.1G245800' => 'ppe', 'Prupe.3G293400' => 'ppe', 'Prupe.7G247400' => 'ppe', 'Psat0s145g0120' => 'psa', 'Psat0s595g0040' => 'psa', 'Psat0s595g0120' => 'psa', 'Psat3g175040' => 'psa', 'Psat7g058120' => 'psa', 'PSO017G0428' => 'pso', 'PSO063G7510' => 'pso', 'PSO067G0046' => 'pso', 'PSO478G1073' => 'pso', 'PSO675G3677' => 'pso', 'PSO675G6558' => 'pso', 'PSO675G7520' => 'pso', 'PSO675G8959' => 'pso', 'QL02p074089' => 'qlo', 'QL02p089614' => 'qlo', 'QL03p057736' => 'qlo', 'RcHm_v2.0_Chr1g0364131' => 'rch', 'RcHm_v2.0_Chr2g0087801' => 'rch', 'RcHm_v2.0_Chr2g0087821' => 'rch', 'RcHm_v2.0_Chr2g0173231' => 'rch', 'RcHm_v2.0_Chr4g0433111' => 'rch', 'Rhsim03G0250300' => 'rsi', 'Rhsim08G0048400' => 'rsi', 'Rhsim10G0014800' => 'rsi', 'Rhsim12G0040100' => 'rsi', 'Rhsim12G0109700' => 'rsi', 'Sabra06G0049600' => 'sbr', 'Sabra08G0141000' => 'sbr', 'Sabra10G0021400' => 'sbr', 'Sabra16G0222900' => 'sbr', 'Sabra18G0108600' => 'sbr', 'SalBow1G0433' => 'sbo', 'SalBow1G2038' => 'sbo', 'SalBow1G5003' => 'sbo', 'SalBow7G1197' => 'sbo', 'SalBow8G3506' => 'sbo', 'Sc03g0007300' => 'sci', 'Sc11g0000950' => 'sci', 'Sc14g0008750' => 'sci', 'Sc18g0000420' => 'sci', 'Sed0006754' => 'sed', 'Sed0008741' => 'sed', 'Sed0017172' => 'sed', 'Sed0018925' => 'sed', 'Sed0023326' => 'sed', 'Sed0025909' => 'sed', 'SEGI_05333' => 'sgi', 'SEGI_10362' => 'sgi', 'SEGI_13380' => 'sgi', 'SEGI_24306' => 'sgi', 'SEGI_29077' => 'sgi', 'SEGI_29095' => 'sgi', 'SEGI_36534' => 'sgi', 'SEGI_37506' => 'sgi', 'SEGI_38321' => 'sgi', 'SGA_v2.0_scaffold307G48031' => 'sas', 'SGA_v2.0_scaffold47G17507' => 'sas', 'SGA_v2.0_scaffold63G21736' => 'sas', 'SGA_v2.0_scaffold87G27070' => 'sas', 'SHI17794' => 'shi', 'SHI28851' => 'shi', 'SMO165G0155' => 'smo', 'SMO340G0217' => 'smo', 'SMO367G1210' => 'smo', 'Solyc02g093430.3' => 'sly', 'Solyc05g013580.4' => 'sly', 'Solyc07g008030.3' => 'sly', 'Solyc12g035470.2' => 'sly', 'Sopen02g038020' => 'spe', 'Sopen05g008490' => 'spe', 'Sopen07g003910' => 'spe', 'Sopen12g015240' => 'spe', 'Sp1g11550' => 'spa', 'Sp2g16710' => 'spa', 'Sp3g00430' => 'spa', 'Sp3g26780' => 'spa', 'Sp5g22900' => 'spa', 'Sp6g29530' => 'spa', 'TAR371G0794' => 'tar', 'TAR374G0164' => 'tar', 'TAR622G0165' => 'tar', 'TAR626G0929' => 'tar', 'TAR629G2155' => 'tar', 'THA.LOC104805282' => 'tha', 'THA.LOC104805363' => 'tha', 'THA.LOC104808968' => 'tha', 'THA.LOC104821093' => 'tha', 'THA.LOC104823953' => 'tha', 'THA.LOC104825562' => 'tha', 'THA.LOC104825665' => 'tha', 'Thecc.02G261400' => 'tca', 'Thecc.04G019200' => 'tca', 'Thecc.09G130400' => 'tca', 'Thhalv10004374m.g' => 'esa', 'Thhalv10007850m.g' => 'esa', 'Thhalv10013782m.g' => 'esa', 'Thhalv10018686m.g' => 'esa', 'Thhalv10020899m.g' => 'esa', 'Thhalv10022755m.g' => 'esa', 'TPR.G23851' => 'tpr', 'TPR.G26500' => 'tpr', 'TPR.G27267' => 'tpr', 'TPR.G32001' => 'tpr', 'TPR.G6251' => 'tpr', 'TPR.G8167' => 'tpr', 'TWI12G1330' => 'twi', 'TWI18G1239' => 'twi', 'TWI34G0979' => 'twi', 'TWI36G0670' => 'twi', 'TWI36G0707' => 'twi', 'TWI56G0233' => 'twi', 'TWI75G1809' => 'twi', 'unitig_21.g20874' => 'ugi', 'unitig_26.g10343' => 'ugi', 'unitig_46.g18392' => 'ugi', 'unitig_52.g17178' => 'ugi', 'unitig_8.g2934' => 'ugi', 'vmacro01122' => 'vma', 'vmacro05875' => 'vma', 'vmacro06147' => 'vma', 'vmacro16191' => 'vma', 'vmacro18293' => 'vma', 'VMungo0251G3707' => 'vmu', 'VMungo0464G1521' => 'vmu', 'VMungo1215G0205' => 'vmu', 'VMungo1383G2484' => 'vmu', 'Zm00001eb079610' => 'zma', 'Zm00001eb135990' => 'zma', 'Zm00001eb183710' => 'zma', 'Zm00001eb246020' => 'zma' ) $gf_id = 'HOM05D001124' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001124' ) $data_identifier = 'HOM05D001124' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 6, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 7, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 21, 'bol' => (int) 10, 'bra' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 6, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 9, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 21, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 8, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 10, 'lsa' => (int) 8, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 8, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 9, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb246020' $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' => 'HOM05D001124', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '548', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02520' => 'bna', 'A03p06630' => 'bna', 'A05p44460' => 'bna', 'A06p08710' => 'bna', 'A06p41090' => 'bna', 'A07p32320' => 'bna', 'A08p32520' => 'bna', 'A09p10360' => 'bna', 'A10p24080' => 'bna', 'Aa31LG11G15250' => 'aar', 'Aa31LG1G1800' => 'aar', 'Aa31LG2G5120' => 'aar', 'Aa31LG2G6070' => 'aar', 'Aa31LG5G10770' => 'aar', 'Aa31sc61G90' => 'aar', 'Actinidia01352' => 'ach', 'Actinidia05983' => 'ach', 'Actinidia08133' => 'ach', 'Actinidia15101' => 'ach', 'Actinidia26379' => 'ach', 'Actinidia35778' => 'ach', 'Actinidia36123' => 'ach', 'Actinidia37436' => 'ach', 'Actinidia38730' => 'ach', 'Ah.02g128210' => 'amhyb', 'Ah.03g132990' => 'amhyb', 'Ah.14g079410' => 'amhyb', 'AL1G24640' => 'aly', 'AL2G26680' => 'aly', 'AL3G10530' => 'aly', 'AL3G45230' => 'aly', 'AL5G15230' => 'aly', 'AL5G16960' => 'aly', 'AL6G25210' => 'aly', 'Aqoxy2G00441' => 'aox', 'Aqoxy3G01236' => 'aox', 'Aqoxy5G03746' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3RQ047' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C7GMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9C8JER' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MBL6KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YXCZ83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZANX40' => 'arhy', 'AT1G12990' => 'ath', 'AT1G67880' => 'ath', 'AT2G13290' => 'ath', 'AT3G01620' => 'ath', 'AT3G26445' => 'ath', 'AT3G27540' => 'ath', 'AT5G14480' => 'ath', 'ATR0824G026' => 'atr', 'ATR1098G019' => 'atr', 'Atru.chr11.2145' => 'acertr', 'Atru.chr2.3636' => 'acertr', 'Atru.chr2.3644' => 'acertr', 'Atru.chr6.2422' => 'acertr', 'Atru.chr7.1112' => 'acertr', 'AUR62005469' => 'cqu', 'AUR62011166' => 'cqu', 'AUR62013319' => 'cqu', 'AUR62024273' => 'cqu', 'AUR62028420' => 'cqu', 'AUR62041942' => 'cqu', 'BcaB01g04969' => 'bca', 'BcaB01g06371' => 'bca', 'BcaB02g11494' => 'bca', 'BcaB03g15382' => 'bca', 'BcaB08g36994' => 'bca', 'BcaC03g13477' => 'bca', 'BcaC03g13478' => 'bca', 'BcaC03g13480' => 'bca', 'BcaC03g13481' => 'bca', 'BcaC03g13486' => 'bca', 'BcaC04g19031' => 'bca', 'BcaC04g23085' => 'bca', 'BcaC05g25094' => 'bca', 'BcaC05g25096' => 'bca', 'BcaC05g25138' => 'bca', 'BcaC05g30416' => 'bca', 'BcaC05g30455' => 'bca', 'BcaC06g30979' => 'bca', 'BcaC06g33805' => 'bca', 'BcaC08g46021' => 'bca', 'BcaNung03154' => 'bca', 'BolC2t06623H' => 'bol', 'BolC2t06632H' => 'bol', 'BolC2t06635H' => 'bol', 'BolC2t06638H' => 'bol', 'BolC3t13266H' => 'bol', 'BolC5t29776H' => 'bol', 'BolC6t38912H' => 'bol', 'BolC7t44183H' => 'bol', 'BolC9t54123H' => 'bol', 'BolC9t59107H' => 'bol', 'BraA02t05221Z' => 'bra', 'BraA03t09996Z' => 'bra', 'BraA05t23210Z' => 'bra', 'BraA06t24068Z' => 'bra', 'BraA06t27032Z' => 'bra', 'BraA08t35176Z' => 'bra', 'BraA09t36680Z' => 'bra', 'BraA10t44471Z' => 'bra', 'C02p06760' => 'bna', 'C02p06890' => 'bna', 'C02p07010' => 'bna', 'C03p07660' => 'bna', 'C05p10300' => 'bna', 'C06p38150' => 'bna', 'C07p36650' => 'bna', 'C08p15770' => 'bna', 'C09p12300' => 'bna', 'C09p62700' => 'bna', 'C09p75040' => 'bna', 'CAN.G13.1' => 'can', 'CAN.G138.4' => 'can', 'CAN.G44.6' => 'can', 'CAN.G473.19' => 'can', 'CANSAT01G0835' => 'cansat', 'CANSAT11G0246' => 'cansat', 'CANSAT11G1766' => 'cansat', 'CANSAT64G1954' => 'cansat', 'CARHR013330' => 'chi', 'CARHR060530' => 'chi', 'CARHR075300' => 'chi', 'CARHR105120' => 'chi', 'CARHR148910' => 'chi', 'CARHR198830' => 'chi', 'Carub.0001s1275' => 'cru', 'Carub.0002s1437' => 'cru', 'Carub.0003s0044' => 'cru', 'Carub.0003s2787' => 'cru', 'Carub.0005s0597' => 'cru', 'Carub.0006s1266' => 'cru', 'Ca_06935_v3' => 'car', 'Ca_13559_v3' => 'car', 'Ca_16941_v3' => 'car', 'Ca_16960_v3' => 'car', 'Ca_17775_v3' => 'car', 'Ca_30464_v3' => 'car', 'Cc06_g08160' => 'ccan', 'Cc07_g01520' => 'ccan', 'Cc11_g15810' => 'ccan', 'CDE02G2840' => 'cde', 'CDE03G0093' => 'cde', 'CDE04G2127' => 'cde', 'CDE07G1857' => 'cde', 'CDE09G1246' => 'cde', 'Cfa003412' => 'cfa', 'Cfa007341' => 'cfa', 'Cfa009220' => 'cfa', 'Ciclev10008737m.g' => 'ccl', 'Ciclev10015565m.g' => 'ccl', 'Ciclev10031761m.g' => 'ccl', 'CiPaw.03G045300' => 'cil', 'CiPaw.03G247200' => 'cil', 'CiPaw.04G029500' => 'cil', 'CiPaw.04G174000' => 'cil', 'CiPaw.05G181200' => 'cil', 'CiPaw.06G067100' => 'cil', 'ClCG05G025800' => 'cla', 'ClCG06G011400' => 'cla', 'ClCG09G019360' => 'cla', 'COL.COLO4_04827' => 'col', 'COL.COLO4_29170' => 'col', 'COL.COLO4_35131' => 'col', 'COL.COLO4_35132' => 'col', 'Cpa.g.sc33.32' => 'cpa', 'Cpa.g.sc46.29' => 'cpa', 'Cpa.g.sc796.1' => 'cpa', 'CsaV3_1G030420' => 'csa', 'CsaV3_5G027050' => 'csa', 'CsaV3_5G031040' => 'csa', 'CsaV3_UNG023130' => 'csa', 'CSS0007726' => 'camsi', 'CSS0016433' => 'camsi', 'CSS0017656' => 'camsi', 'CSS0025364' => 'camsi', 'CSS0027582' => 'camsi', 'CSS0047288' => 'camsi', 'CSS0049950' => 'camsi', 'DCAR_003843' => 'dca', 'DCAR_007052' => 'dca', 'DCAR_020884' => 'dca', 'DCAR_021730' => 'dca', 'DCAR_024423' => 'dca', 'DCAR_026509' => 'dca', 'DCAR_031158' => 'dca', 'Dinv14728' => 'din', 'Dinv15219' => 'din', 'Dinv25728' => 'din', 'Dinv33428' => 'din', 'Dinv36489' => 'din', 'Dinv41486' => 'din', 'Duzib147G0469' => 'dzi', 'Duzib168G0060' => 'dzi', 'Duzib187G1215' => 'dzi', 'Duzib248G0692' => 'dzi', 'Duzib251G0767' => 'dzi', 'Duzib264G0446' => 'dzi', 'Duzib268G0691' => 'dzi', 'ECA232G4767' => 'eca', 'ECA233G2838' => 'eca', 'ECA234G0391' => 'eca', 'ECA234G0857' => 'eca', 'ECA236G1593' => 'eca', 'ECA238G0565' => 'eca', 'ECA246G1027' => 'eca', 'ECA246G3223' => 'eca', 'ECA246G3470' => 'eca', 'EL10Ac6g13829' => 'bvu', 'EL10Ac6g14093' => 'bvu', 'EL10Ac8g18707' => 'bvu', 'Eucgr.C01369' => 'egr', 'Eucgr.H02492' => 'egr', 'Eucgr.I01733' => 'egr', 'Eucgr.J02255' => 'egr', 'Eucgr.J02257' => 'egr', 'Eucgr.J02258' => 'egr', 'FAN02G1601' => 'fan', 'FAN03G1586' => 'fan', 'FAN03G2986' => 'fan', 'FAN05G4837' => 'fan', 'FAN06G0146' => 'fan', 'FAN07G0858' => 'fan', 'FAN09G3179' => 'fan', 'FAN10G0669' => 'fan', 'FAN12G2358' => 'fan', 'FAN14G4198' => 'fan', 'FAN14G5112' => 'fan', 'FAN17G0342' => 'fan', 'FAN19G0342' => 'fan', 'FAN19G0962' => 'fan', 'FAN19G1101' => 'fan', 'FAN19G1872' => 'fan', 'FAN22G0356' => 'fan', 'FAN23G0744' => 'fan', 'FAN23G1914' => 'fan', 'FAN26G0032' => 'fan', 'FAN28G0625' => 'fan', 'FvH4_1g02710' => 'fve', 'FvH4_1g02720' => 'fve', 'FvH4_4g25670' => 'fve', 'FvH4_6g51700' => 'fve', 'FvH4_7g20170' => 'fve', 'Glyma.05G175000' => 'gma', 'Glyma.08G132300' => 'gma', 'Glyma.11G243000' => 'gma', 'Glyma.13G158900' => 'gma', 'Glyma.17G112400' => 'gma', 'Glyma.18G014100' => 'gma', 'Glyma.19G003100' => 'gma', 'Glyma.19G056500' => 'gma', 'Gohir.A01G158900' => 'ghi', 'Gohir.A05G312600' => 'ghi', 'Gohir.A05G354900' => 'ghi', 'Gohir.A07G037200' => 'ghi', 'Gohir.A09G030000' => 'ghi', 'Gohir.A12G145200' => 'ghi', 'Gohir.D01G151500' => 'ghi', 'Gohir.D04G058300' => 'ghi', 'Gohir.D05G314100' => 'ghi', 'Gohir.D07G041400' => 'ghi', 'Gohir.D09G029700' => 'ghi', 'Gohir.D12G149700' => 'ghi', 'Gorai.001G043800' => 'gra', 'Gorai.002G187800' => 'gra', 'Gorai.006G034700' => 'gra', 'Gorai.008G161200' => 'gra', 'Gorai.009G335700' => 'gra', 'Gorai.012G065000' => 'gra', 'GSVIVG01000535001' => 'vvi', 'GSVIVG01015572001' => 'vvi', 'GSVIVG01032386001' => 'vvi', 'HanXRQChr05g0138531' => 'han', 'HanXRQChr06g0174391' => 'han', 'HanXRQChr07g0199021' => 'han', 'HanXRQChr08g0208211' => 'han', 'HanXRQChr09g0255471' => 'han', 'HanXRQChr10g0315791' => 'han', 'HanXRQChr12g0371991' => 'han', 'HanXRQChr15g0475251' => 'han', 'HanXRQChr17g0540001' => 'han', 'HanXRQChr17g0548631' => 'han', 'HanXRQChr17g0569561' => 'han', 'Haze_12256' => 'cav', 'Haze_14756' => 'cav', 'Haze_25528' => 'cav', 'Hma1.2p1_0079F.1_g041020' => 'hma', 'Hma1.2p1_0818F.1_g223260' => 'hma', 'Hma1.2p1_1747F.1_g300530' => 'hma', 'HPP92_004607' => 'vpl', 'HPP92_004608' => 'vpl', 'HPP92_006181' => 'vpl', 'HPP92_012192' => 'vpl', 'HPP92_015680' => 'vpl', 'HPP92_020249' => 'vpl', 'HPP92_021376' => 'vpl', 'HPP92_024275' => 'vpl', 'Hund06031' => 'sun', 'Hund25391' => 'sun', 'Lalb_Chr07g0185371' => 'lal', 'Lalb_Chr07g0185381' => 'lal', 'Lalb_Chr12g0204011' => 'lal', 'Lalb_Chr13g0301671' => 'lal', 'Lalb_Chr14g0362851' => 'lal', 'Lalb_Chr24g0403581' => 'lal', 'Lj1g0000233' => 'lja', 'Lj2g0018120' => 'lja', 'Lj3C621T0' => 'lonja', 'Lj3P1059T14' => 'lonja', 'Lj3P611T9' => 'lonja', 'Lj3P614T13' => 'lonja', 'Lj3P615T5' => 'lonja', 'Lj4g0012315' => 'lja', 'Lj4g0026182' => 'lja', 'Lj6P813T16' => 'lonja', 'Lj7C427T7' => 'lonja', 'Lj7C427T8' => 'lonja', 'Lj7P600T41' => 'lonja', 'Lju41C42G17' => 'lonja', 'Lsat_1_v5_gn_0_47300' => 'lsa', 'Lsat_1_v5_gn_2_91280' => 'lsa', 'Lsat_1_v5_gn_3_30561' => 'lsa', 'Lsat_1_v5_gn_4_184321' => 'lsa', 'Lsat_1_v5_gn_4_4041' => 'lsa', 'Lsat_1_v5_gn_5_92000' => 'lsa', 'Lsat_1_v5_gn_8_152940' => 'lsa', 'Lsat_1_v5_gn_8_62401' => 'lsa', 'Manes.06G055900' => 'mes', 'Manes.12G022200' => 'mes', 'Manes.13G023300' => 'mes', 'Manes.14G115000' => 'mes', 'Manes.15G151700' => 'mes', 'Manes.17G111300' => 'mes', 'Mapoly0226s0009' => 'mpo', 'MBI02_g25363_MAGBIO' => 'mbi', 'MBI06_g00027_MAGBIO' => 'mbi', 'MBI10_g13034_MAGBIO' => 'mbi', 'MD09G1023400' => 'mdo', 'MD13G1100100' => 'mdo', 'MD15G1169200' => 'mdo', 'MD16G1101100' => 'mdo', 'MD17G1022900' => 'mdo', 'Medtr3g096150' => 'mtr', 'Medtr4g115070' => 'mtr', 'Medtr7g033325' => 'mtr', 'Medtr8g089840' => 'mtr', 'MELO3C010319.2' => 'cme', 'MELO3C011944.2' => 'cme', 'MELO3C021589.2' => 'cme', 'Migut.E00207' => 'egut', 'Migut.H00067' => 'egut', 'Migut.K00433' => 'egut', 'Migut.K00606' => 'egut', 'Migut.K01410' => 'egut', 'MSTRG.13347' => 'ama', 'MSTRG.24045' => 'ama', 'MSTRG.2428' => 'ama', 'MSTRG.26410' => 'ama', 'MSTRG.3139' => 'ama', 'MSTRG.3286' => 'ama', 'MSTRG.563' => 'ama', 'MSTRG.7941' => 'ama', 'Nitab4.5_0000028g0060' => 'nta', 'Nitab4.5_0000065g0260' => 'nta', 'Nitab4.5_0000112g0060' => 'nta', 'Nitab4.5_0000489g0120' => 'nta', 'Nitab4.5_0001776g0050' => 'nta', 'Nitab4.5_0001854g0010' => 'nta', 'Nitab4.5_0001860g0020' => 'nta', 'Nitab4.5_0004352g0010' => 'nta', 'Nitab4.5_0008716g0020' => 'nta', 'Nitab4.5_0008922g0010' => 'nta', 'Nn3g16693' => 'nnu', 'Nn4g22596' => 'nnu', 'Nn7g37639' => 'nnu', 'Oeu001701.1' => 'oeu', 'Oeu018149.1' => 'oeu', 'Oeu026220.1' => 'oeu', 'Oeu038635.1' => 'oeu', 'Oeu049176.1' => 'oeu', 'Oeu056706.1' => 'oeu', 'Oeu056937.1' => 'oeu', 'Oeu057540.1' => 'oeu', 'Os02g0594900' => 'osa', 'Os02g0595100' => 'osa', 'Os04g0477500' => 'osa', 'Os12g0611900' => 'osa', 'Peaxi162Scf00076g00020' => 'pax', 'Peaxi162Scf00128g00217' => 'pax', 'Peaxi162Scf00129g01640' => 'pax', 'Peaxi162Scf00669g00007' => 'pax', 'Peaxi162Scf00700g00421' => 'pax', 'Peaxi162Scf00801g00038' => 'pax', 'Peaxi162Scf00891g00025' => 'pax', 'PGR083G0909' => 'pgr', 'PGR119G1005' => 'pgr', 'PGR142G2236' => 'pgr', 'PGR142G3388' => 'pgr', 'PGSC0003DMG400004514' => 'stu', 'PGSC0003DMG400012635' => 'stu', 'PGSC0003DMG400015730' => 'stu', 'PGSC0003DMG400018611' => 'stu', 'PGSC0003DMG400030897' => 'stu', 'Phvul.001G254800' => 'pvu', 'Phvul.002G260100' => 'pvu', 'Phvul.003G167600' => 'pvu', 'Phvul.004G005100' => 'pvu', 'Potri.001G343600' => 'ptr', 'Potri.006G066700' => 'ptr', 'Potri.008G186000' => 'ptr', 'Potri.010G046900' => 'ptr', 'Potri.018G127900' => 'ptr', 'Pp3c20_17750' => 'ppa', 'Pp3c24_4380' => 'ppa', 'Prupe.1G245800' => 'ppe', 'Prupe.3G293400' => 'ppe', 'Prupe.7G247400' => 'ppe', 'Psat0s145g0120' => 'psa', 'Psat0s595g0040' => 'psa', 'Psat0s595g0120' => 'psa', 'Psat3g175040' => 'psa', 'Psat7g058120' => 'psa', 'PSO017G0428' => 'pso', 'PSO063G7510' => 'pso', 'PSO067G0046' => 'pso', 'PSO478G1073' => 'pso', 'PSO675G3677' => 'pso', 'PSO675G6558' => 'pso', 'PSO675G7520' => 'pso', 'PSO675G8959' => 'pso', 'QL02p074089' => 'qlo', 'QL02p089614' => 'qlo', 'QL03p057736' => 'qlo', 'RcHm_v2.0_Chr1g0364131' => 'rch', 'RcHm_v2.0_Chr2g0087801' => 'rch', 'RcHm_v2.0_Chr2g0087821' => 'rch', 'RcHm_v2.0_Chr2g0173231' => 'rch', 'RcHm_v2.0_Chr4g0433111' => 'rch', 'Rhsim03G0250300' => 'rsi', 'Rhsim08G0048400' => 'rsi', 'Rhsim10G0014800' => 'rsi', 'Rhsim12G0040100' => 'rsi', 'Rhsim12G0109700' => 'rsi', 'Sabra06G0049600' => 'sbr', 'Sabra08G0141000' => 'sbr', 'Sabra10G0021400' => 'sbr', 'Sabra16G0222900' => 'sbr', 'Sabra18G0108600' => 'sbr', 'SalBow1G0433' => 'sbo', 'SalBow1G2038' => 'sbo', 'SalBow1G5003' => 'sbo', 'SalBow7G1197' => 'sbo', 'SalBow8G3506' => 'sbo', 'Sc03g0007300' => 'sci', 'Sc11g0000950' => 'sci', 'Sc14g0008750' => 'sci', 'Sc18g0000420' => 'sci', 'Sed0006754' => 'sed', 'Sed0008741' => 'sed', 'Sed0017172' => 'sed', 'Sed0018925' => 'sed', 'Sed0023326' => 'sed', 'Sed0025909' => 'sed', 'SEGI_05333' => 'sgi', 'SEGI_10362' => 'sgi', 'SEGI_13380' => 'sgi', 'SEGI_24306' => 'sgi', 'SEGI_29077' => 'sgi', 'SEGI_29095' => 'sgi', 'SEGI_36534' => 'sgi', 'SEGI_37506' => 'sgi', 'SEGI_38321' => 'sgi', 'SGA_v2.0_scaffold307G48031' => 'sas', 'SGA_v2.0_scaffold47G17507' => 'sas', 'SGA_v2.0_scaffold63G21736' => 'sas', 'SGA_v2.0_scaffold87G27070' => 'sas', 'SHI17794' => 'shi', 'SHI28851' => 'shi', 'SMO165G0155' => 'smo', 'SMO340G0217' => 'smo', 'SMO367G1210' => 'smo', 'Solyc02g093430.3' => 'sly', 'Solyc05g013580.4' => 'sly', 'Solyc07g008030.3' => 'sly', 'Solyc12g035470.2' => 'sly', 'Sopen02g038020' => 'spe', 'Sopen05g008490' => 'spe', 'Sopen07g003910' => 'spe', 'Sopen12g015240' => 'spe', 'Sp1g11550' => 'spa', 'Sp2g16710' => 'spa', 'Sp3g00430' => 'spa', 'Sp3g26780' => 'spa', 'Sp5g22900' => 'spa', 'Sp6g29530' => 'spa', 'TAR371G0794' => 'tar', 'TAR374G0164' => 'tar', 'TAR622G0165' => 'tar', 'TAR626G0929' => 'tar', 'TAR629G2155' => 'tar', 'THA.LOC104805282' => 'tha', 'THA.LOC104805363' => 'tha', 'THA.LOC104808968' => 'tha', 'THA.LOC104821093' => 'tha', 'THA.LOC104823953' => 'tha', 'THA.LOC104825562' => 'tha', 'THA.LOC104825665' => 'tha', 'Thecc.02G261400' => 'tca', 'Thecc.04G019200' => 'tca', 'Thecc.09G130400' => 'tca', 'Thhalv10004374m.g' => 'esa', 'Thhalv10007850m.g' => 'esa', 'Thhalv10013782m.g' => 'esa', 'Thhalv10018686m.g' => 'esa', 'Thhalv10020899m.g' => 'esa', 'Thhalv10022755m.g' => 'esa', 'TPR.G23851' => 'tpr', 'TPR.G26500' => 'tpr', 'TPR.G27267' => 'tpr', 'TPR.G32001' => 'tpr', 'TPR.G6251' => 'tpr', 'TPR.G8167' => 'tpr', 'TWI12G1330' => 'twi', 'TWI18G1239' => 'twi', 'TWI34G0979' => 'twi', 'TWI36G0670' => 'twi', 'TWI36G0707' => 'twi', 'TWI56G0233' => 'twi', 'TWI75G1809' => 'twi', 'unitig_21.g20874' => 'ugi', 'unitig_26.g10343' => 'ugi', 'unitig_46.g18392' => 'ugi', 'unitig_52.g17178' => 'ugi', 'unitig_8.g2934' => 'ugi', 'vmacro01122' => 'vma', 'vmacro05875' => 'vma', 'vmacro06147' => 'vma', 'vmacro16191' => 'vma', 'vmacro18293' => 'vma', 'VMungo0251G3707' => 'vmu', 'VMungo0464G1521' => 'vmu', 'VMungo1215G0205' => 'vmu', 'VMungo1383G2484' => 'vmu', 'Zm00001eb079610' => 'zma', 'Zm00001eb135990' => 'zma', 'Zm00001eb183710' => 'zma', 'Zm00001eb246020' => 'zma' ), 'gf_id' => 'HOM05D001124', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001124' ), 'data_identifier' => 'HOM05D001124', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001124', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '548', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02520' => 'bna', 'A03p06630' => 'bna', 'A05p44460' => 'bna', 'A06p08710' => 'bna', 'A06p41090' => 'bna', 'A07p32320' => 'bna', 'A08p32520' => 'bna', 'A09p10360' => 'bna', 'A10p24080' => 'bna', 'Aa31LG11G15250' => 'aar', 'Aa31LG1G1800' => 'aar', 'Aa31LG2G5120' => 'aar', 'Aa31LG2G6070' => 'aar', 'Aa31LG5G10770' => 'aar', 'Aa31sc61G90' => 'aar', 'Actinidia01352' => 'ach', 'Actinidia05983' => 'ach', 'Actinidia08133' => 'ach', 'Actinidia15101' => 'ach', 'Actinidia26379' => 'ach', 'Actinidia35778' => 'ach', 'Actinidia36123' => 'ach', 'Actinidia37436' => 'ach', 'Actinidia38730' => 'ach', 'Ah.02g128210' => 'amhyb', 'Ah.03g132990' => 'amhyb', 'Ah.14g079410' => 'amhyb', 'AL1G24640' => 'aly', 'AL2G26680' => 'aly', 'AL3G10530' => 'aly', 'AL3G45230' => 'aly', 'AL5G15230' => 'aly', 'AL5G16960' => 'aly', 'AL6G25210' => 'aly', 'Aqoxy2G00441' => 'aox', 'Aqoxy3G01236' => 'aox', 'Aqoxy5G03746' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3RQ047' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C7GMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9C8JER' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MBL6KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YXCZ83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZANX40' => 'arhy', 'AT1G12990' => 'ath', 'AT1G67880' => 'ath', 'AT2G13290' => 'ath', 'AT3G01620' => 'ath', 'AT3G26445' => 'ath', 'AT3G27540' => 'ath', 'AT5G14480' => 'ath', 'ATR0824G026' => 'atr', 'ATR1098G019' => 'atr', 'Atru.chr11.2145' => 'acertr', 'Atru.chr2.3636' => 'acertr', 'Atru.chr2.3644' => 'acertr', 'Atru.chr6.2422' => 'acertr', 'Atru.chr7.1112' => 'acertr', 'AUR62005469' => 'cqu', 'AUR62011166' => 'cqu', 'AUR62013319' => 'cqu', 'AUR62024273' => 'cqu', 'AUR62028420' => 'cqu', 'AUR62041942' => 'cqu', 'BcaB01g04969' => 'bca', 'BcaB01g06371' => 'bca', 'BcaB02g11494' => 'bca', 'BcaB03g15382' => 'bca', 'BcaB08g36994' => 'bca', 'BcaC03g13477' => 'bca', 'BcaC03g13478' => 'bca', 'BcaC03g13480' => 'bca', 'BcaC03g13481' => 'bca', 'BcaC03g13486' => 'bca', 'BcaC04g19031' => 'bca', 'BcaC04g23085' => 'bca', 'BcaC05g25094' => 'bca', 'BcaC05g25096' => 'bca', 'BcaC05g25138' => 'bca', 'BcaC05g30416' => 'bca', 'BcaC05g30455' => 'bca', 'BcaC06g30979' => 'bca', 'BcaC06g33805' => 'bca', 'BcaC08g46021' => 'bca', 'BcaNung03154' => 'bca', 'BolC2t06623H' => 'bol', 'BolC2t06632H' => 'bol', 'BolC2t06635H' => 'bol', 'BolC2t06638H' => 'bol', 'BolC3t13266H' => 'bol', 'BolC5t29776H' => 'bol', 'BolC6t38912H' => 'bol', 'BolC7t44183H' => 'bol', 'BolC9t54123H' => 'bol', 'BolC9t59107H' => 'bol', 'BraA02t05221Z' => 'bra', 'BraA03t09996Z' => 'bra', 'BraA05t23210Z' => 'bra', 'BraA06t24068Z' => 'bra', 'BraA06t27032Z' => 'bra', 'BraA08t35176Z' => 'bra', 'BraA09t36680Z' => 'bra', 'BraA10t44471Z' => 'bra', 'C02p06760' => 'bna', 'C02p06890' => 'bna', 'C02p07010' => 'bna', 'C03p07660' => 'bna', 'C05p10300' => 'bna', 'C06p38150' => 'bna', 'C07p36650' => 'bna', 'C08p15770' => 'bna', 'C09p12300' => 'bna', 'C09p62700' => 'bna', 'C09p75040' => 'bna', 'CAN.G13.1' => 'can', 'CAN.G138.4' => 'can', 'CAN.G44.6' => 'can', 'CAN.G473.19' => 'can', 'CANSAT01G0835' => 'cansat', 'CANSAT11G0246' => 'cansat', 'CANSAT11G1766' => 'cansat', 'CANSAT64G1954' => 'cansat', 'CARHR013330' => 'chi', 'CARHR060530' => 'chi', 'CARHR075300' => 'chi', 'CARHR105120' => 'chi', 'CARHR148910' => 'chi', 'CARHR198830' => 'chi', 'Carub.0001s1275' => 'cru', 'Carub.0002s1437' => 'cru', 'Carub.0003s0044' => 'cru', 'Carub.0003s2787' => 'cru', 'Carub.0005s0597' => 'cru', 'Carub.0006s1266' => 'cru', 'Ca_06935_v3' => 'car', 'Ca_13559_v3' => 'car', 'Ca_16941_v3' => 'car', 'Ca_16960_v3' => 'car', 'Ca_17775_v3' => 'car', 'Ca_30464_v3' => 'car', 'Cc06_g08160' => 'ccan', 'Cc07_g01520' => 'ccan', 'Cc11_g15810' => 'ccan', 'CDE02G2840' => 'cde', 'CDE03G0093' => 'cde', 'CDE04G2127' => 'cde', 'CDE07G1857' => 'cde', 'CDE09G1246' => 'cde', 'Cfa003412' => 'cfa', 'Cfa007341' => 'cfa', 'Cfa009220' => 'cfa', 'Ciclev10008737m.g' => 'ccl', 'Ciclev10015565m.g' => 'ccl', 'Ciclev10031761m.g' => 'ccl', 'CiPaw.03G045300' => 'cil', 'CiPaw.03G247200' => 'cil', 'CiPaw.04G029500' => 'cil', 'CiPaw.04G174000' => 'cil', 'CiPaw.05G181200' => 'cil', 'CiPaw.06G067100' => 'cil', 'ClCG05G025800' => 'cla', 'ClCG06G011400' => 'cla', 'ClCG09G019360' => 'cla', 'COL.COLO4_04827' => 'col', 'COL.COLO4_29170' => 'col', 'COL.COLO4_35131' => 'col', 'COL.COLO4_35132' => 'col', 'Cpa.g.sc33.32' => 'cpa', 'Cpa.g.sc46.29' => 'cpa', 'Cpa.g.sc796.1' => 'cpa', 'CsaV3_1G030420' => 'csa', 'CsaV3_5G027050' => 'csa', 'CsaV3_5G031040' => 'csa', 'CsaV3_UNG023130' => 'csa', 'CSS0007726' => 'camsi', 'CSS0016433' => 'camsi', 'CSS0017656' => 'camsi', 'CSS0025364' => 'camsi', 'CSS0027582' => 'camsi', 'CSS0047288' => 'camsi', 'CSS0049950' => 'camsi', 'DCAR_003843' => 'dca', 'DCAR_007052' => 'dca', 'DCAR_020884' => 'dca', 'DCAR_021730' => 'dca', 'DCAR_024423' => 'dca', 'DCAR_026509' => 'dca', 'DCAR_031158' => 'dca', 'Dinv14728' => 'din', 'Dinv15219' => 'din', 'Dinv25728' => 'din', 'Dinv33428' => 'din', 'Dinv36489' => 'din', 'Dinv41486' => 'din', 'Duzib147G0469' => 'dzi', 'Duzib168G0060' => 'dzi', 'Duzib187G1215' => 'dzi', 'Duzib248G0692' => 'dzi', 'Duzib251G0767' => 'dzi', 'Duzib264G0446' => 'dzi', 'Duzib268G0691' => 'dzi', 'ECA232G4767' => 'eca', 'ECA233G2838' => 'eca', 'ECA234G0391' => 'eca', 'ECA234G0857' => 'eca', 'ECA236G1593' => 'eca', 'ECA238G0565' => 'eca', 'ECA246G1027' => 'eca', 'ECA246G3223' => 'eca', 'ECA246G3470' => 'eca', 'EL10Ac6g13829' => 'bvu', 'EL10Ac6g14093' => 'bvu', 'EL10Ac8g18707' => 'bvu', 'Eucgr.C01369' => 'egr', 'Eucgr.H02492' => 'egr', 'Eucgr.I01733' => 'egr', 'Eucgr.J02255' => 'egr', 'Eucgr.J02257' => 'egr', 'Eucgr.J02258' => 'egr', 'FAN02G1601' => 'fan', 'FAN03G1586' => 'fan', 'FAN03G2986' => 'fan', 'FAN05G4837' => 'fan', 'FAN06G0146' => 'fan', 'FAN07G0858' => 'fan', 'FAN09G3179' => 'fan', 'FAN10G0669' => 'fan', 'FAN12G2358' => 'fan', 'FAN14G4198' => 'fan', 'FAN14G5112' => 'fan', 'FAN17G0342' => 'fan', 'FAN19G0342' => 'fan', 'FAN19G0962' => 'fan', 'FAN19G1101' => 'fan', 'FAN19G1872' => 'fan', 'FAN22G0356' => 'fan', 'FAN23G0744' => 'fan', 'FAN23G1914' => 'fan', 'FAN26G0032' => 'fan', 'FAN28G0625' => 'fan', 'FvH4_1g02710' => 'fve', 'FvH4_1g02720' => 'fve', 'FvH4_4g25670' => 'fve', 'FvH4_6g51700' => 'fve', 'FvH4_7g20170' => 'fve', 'Glyma.05G175000' => 'gma', 'Glyma.08G132300' => 'gma', 'Glyma.11G243000' => 'gma', 'Glyma.13G158900' => 'gma', 'Glyma.17G112400' => 'gma', 'Glyma.18G014100' => 'gma', 'Glyma.19G003100' => 'gma', 'Glyma.19G056500' => 'gma', 'Gohir.A01G158900' => 'ghi', 'Gohir.A05G312600' => 'ghi', 'Gohir.A05G354900' => 'ghi', 'Gohir.A07G037200' => 'ghi', 'Gohir.A09G030000' => 'ghi', 'Gohir.A12G145200' => 'ghi', 'Gohir.D01G151500' => 'ghi', 'Gohir.D04G058300' => 'ghi', 'Gohir.D05G314100' => 'ghi', 'Gohir.D07G041400' => 'ghi', 'Gohir.D09G029700' => 'ghi', 'Gohir.D12G149700' => 'ghi', 'Gorai.001G043800' => 'gra', 'Gorai.002G187800' => 'gra', 'Gorai.006G034700' => 'gra', 'Gorai.008G161200' => 'gra', 'Gorai.009G335700' => 'gra', 'Gorai.012G065000' => 'gra', 'GSVIVG01000535001' => 'vvi', 'GSVIVG01015572001' => 'vvi', 'GSVIVG01032386001' => 'vvi', 'HanXRQChr05g0138531' => 'han', 'HanXRQChr06g0174391' => 'han', 'HanXRQChr07g0199021' => 'han', 'HanXRQChr08g0208211' => 'han', 'HanXRQChr09g0255471' => 'han', 'HanXRQChr10g0315791' => 'han', 'HanXRQChr12g0371991' => 'han', 'HanXRQChr15g0475251' => 'han', 'HanXRQChr17g0540001' => 'han', 'HanXRQChr17g0548631' => 'han', 'HanXRQChr17g0569561' => 'han', 'Haze_12256' => 'cav', 'Haze_14756' => 'cav', 'Haze_25528' => 'cav', 'Hma1.2p1_0079F.1_g041020' => 'hma', 'Hma1.2p1_0818F.1_g223260' => 'hma', 'Hma1.2p1_1747F.1_g300530' => 'hma', 'HPP92_004607' => 'vpl', 'HPP92_004608' => 'vpl', 'HPP92_006181' => 'vpl', 'HPP92_012192' => 'vpl', 'HPP92_015680' => 'vpl', 'HPP92_020249' => 'vpl', 'HPP92_021376' => 'vpl', 'HPP92_024275' => 'vpl', 'Hund06031' => 'sun', 'Hund25391' => 'sun', 'Lalb_Chr07g0185371' => 'lal', 'Lalb_Chr07g0185381' => 'lal', 'Lalb_Chr12g0204011' => 'lal', 'Lalb_Chr13g0301671' => 'lal', 'Lalb_Chr14g0362851' => 'lal', 'Lalb_Chr24g0403581' => 'lal', 'Lj1g0000233' => 'lja', 'Lj2g0018120' => 'lja', 'Lj3C621T0' => 'lonja', 'Lj3P1059T14' => 'lonja', 'Lj3P611T9' => 'lonja', 'Lj3P614T13' => 'lonja', 'Lj3P615T5' => 'lonja', 'Lj4g0012315' => 'lja', 'Lj4g0026182' => 'lja', 'Lj6P813T16' => 'lonja', 'Lj7C427T7' => 'lonja', 'Lj7C427T8' => 'lonja', 'Lj7P600T41' => 'lonja', 'Lju41C42G17' => 'lonja', 'Lsat_1_v5_gn_0_47300' => 'lsa', 'Lsat_1_v5_gn_2_91280' => 'lsa', 'Lsat_1_v5_gn_3_30561' => 'lsa', 'Lsat_1_v5_gn_4_184321' => 'lsa', 'Lsat_1_v5_gn_4_4041' => 'lsa', 'Lsat_1_v5_gn_5_92000' => 'lsa', 'Lsat_1_v5_gn_8_152940' => 'lsa', 'Lsat_1_v5_gn_8_62401' => 'lsa', 'Manes.06G055900' => 'mes', 'Manes.12G022200' => 'mes', 'Manes.13G023300' => 'mes', 'Manes.14G115000' => 'mes', 'Manes.15G151700' => 'mes', 'Manes.17G111300' => 'mes', 'Mapoly0226s0009' => 'mpo', 'MBI02_g25363_MAGBIO' => 'mbi', 'MBI06_g00027_MAGBIO' => 'mbi', 'MBI10_g13034_MAGBIO' => 'mbi', 'MD09G1023400' => 'mdo', 'MD13G1100100' => 'mdo', 'MD15G1169200' => 'mdo', 'MD16G1101100' => 'mdo', 'MD17G1022900' => 'mdo', 'Medtr3g096150' => 'mtr', 'Medtr4g115070' => 'mtr', 'Medtr7g033325' => 'mtr', 'Medtr8g089840' => 'mtr', 'MELO3C010319.2' => 'cme', 'MELO3C011944.2' => 'cme', 'MELO3C021589.2' => 'cme', 'Migut.E00207' => 'egut', 'Migut.H00067' => 'egut', 'Migut.K00433' => 'egut', 'Migut.K00606' => 'egut', 'Migut.K01410' => 'egut', 'MSTRG.13347' => 'ama', 'MSTRG.24045' => 'ama', 'MSTRG.2428' => 'ama', 'MSTRG.26410' => 'ama', 'MSTRG.3139' => 'ama', 'MSTRG.3286' => 'ama', 'MSTRG.563' => 'ama', 'MSTRG.7941' => 'ama', 'Nitab4.5_0000028g0060' => 'nta', 'Nitab4.5_0000065g0260' => 'nta', 'Nitab4.5_0000112g0060' => 'nta', 'Nitab4.5_0000489g0120' => 'nta', 'Nitab4.5_0001776g0050' => 'nta', 'Nitab4.5_0001854g0010' => 'nta', 'Nitab4.5_0001860g0020' => 'nta', 'Nitab4.5_0004352g0010' => 'nta', 'Nitab4.5_0008716g0020' => 'nta', 'Nitab4.5_0008922g0010' => 'nta', 'Nn3g16693' => 'nnu', 'Nn4g22596' => 'nnu', 'Nn7g37639' => 'nnu', 'Oeu001701.1' => 'oeu', 'Oeu018149.1' => 'oeu', 'Oeu026220.1' => 'oeu', 'Oeu038635.1' => 'oeu', 'Oeu049176.1' => 'oeu', 'Oeu056706.1' => 'oeu', 'Oeu056937.1' => 'oeu', 'Oeu057540.1' => 'oeu', 'Os02g0594900' => 'osa', 'Os02g0595100' => 'osa', 'Os04g0477500' => 'osa', 'Os12g0611900' => 'osa', 'Peaxi162Scf00076g00020' => 'pax', 'Peaxi162Scf00128g00217' => 'pax', 'Peaxi162Scf00129g01640' => 'pax', 'Peaxi162Scf00669g00007' => 'pax', 'Peaxi162Scf00700g00421' => 'pax', 'Peaxi162Scf00801g00038' => 'pax', 'Peaxi162Scf00891g00025' => 'pax', 'PGR083G0909' => 'pgr', 'PGR119G1005' => 'pgr', 'PGR142G2236' => 'pgr', 'PGR142G3388' => 'pgr', 'PGSC0003DMG400004514' => 'stu', 'PGSC0003DMG400012635' => 'stu', 'PGSC0003DMG400015730' => 'stu', 'PGSC0003DMG400018611' => 'stu', 'PGSC0003DMG400030897' => 'stu', 'Phvul.001G254800' => 'pvu', 'Phvul.002G260100' => 'pvu', 'Phvul.003G167600' => 'pvu', 'Phvul.004G005100' => 'pvu', 'Potri.001G343600' => 'ptr', 'Potri.006G066700' => 'ptr', 'Potri.008G186000' => 'ptr', 'Potri.010G046900' => 'ptr', 'Potri.018G127900' => 'ptr', 'Pp3c20_17750' => 'ppa', 'Pp3c24_4380' => 'ppa', 'Prupe.1G245800' => 'ppe', 'Prupe.3G293400' => 'ppe', 'Prupe.7G247400' => 'ppe', 'Psat0s145g0120' => 'psa', 'Psat0s595g0040' => 'psa', 'Psat0s595g0120' => 'psa', 'Psat3g175040' => 'psa', 'Psat7g058120' => 'psa', 'PSO017G0428' => 'pso', 'PSO063G7510' => 'pso', 'PSO067G0046' => 'pso', 'PSO478G1073' => 'pso', 'PSO675G3677' => 'pso', 'PSO675G6558' => 'pso', 'PSO675G7520' => 'pso', 'PSO675G8959' => 'pso', 'QL02p074089' => 'qlo', 'QL02p089614' => 'qlo', 'QL03p057736' => 'qlo', 'RcHm_v2.0_Chr1g0364131' => 'rch', 'RcHm_v2.0_Chr2g0087801' => 'rch', 'RcHm_v2.0_Chr2g0087821' => 'rch', 'RcHm_v2.0_Chr2g0173231' => 'rch', 'RcHm_v2.0_Chr4g0433111' => 'rch', 'Rhsim03G0250300' => 'rsi', 'Rhsim08G0048400' => 'rsi', 'Rhsim10G0014800' => 'rsi', 'Rhsim12G0040100' => 'rsi', 'Rhsim12G0109700' => 'rsi', 'Sabra06G0049600' => 'sbr', 'Sabra08G0141000' => 'sbr', 'Sabra10G0021400' => 'sbr', 'Sabra16G0222900' => 'sbr', 'Sabra18G0108600' => 'sbr', 'SalBow1G0433' => 'sbo', 'SalBow1G2038' => 'sbo', 'SalBow1G5003' => 'sbo', 'SalBow7G1197' => 'sbo', 'SalBow8G3506' => 'sbo', 'Sc03g0007300' => 'sci', 'Sc11g0000950' => 'sci', 'Sc14g0008750' => 'sci', 'Sc18g0000420' => 'sci', 'Sed0006754' => 'sed', 'Sed0008741' => 'sed', 'Sed0017172' => 'sed', 'Sed0018925' => 'sed', 'Sed0023326' => 'sed', 'Sed0025909' => 'sed', 'SEGI_05333' => 'sgi', 'SEGI_10362' => 'sgi', 'SEGI_13380' => 'sgi', 'SEGI_24306' => 'sgi', 'SEGI_29077' => 'sgi', 'SEGI_29095' => 'sgi', 'SEGI_36534' => 'sgi', 'SEGI_37506' => 'sgi', 'SEGI_38321' => 'sgi', 'SGA_v2.0_scaffold307G48031' => 'sas', 'SGA_v2.0_scaffold47G17507' => 'sas', 'SGA_v2.0_scaffold63G21736' => 'sas', 'SGA_v2.0_scaffold87G27070' => 'sas', 'SHI17794' => 'shi', 'SHI28851' => 'shi', 'SMO165G0155' => 'smo', 'SMO340G0217' => 'smo', 'SMO367G1210' => 'smo', 'Solyc02g093430.3' => 'sly', 'Solyc05g013580.4' => 'sly', 'Solyc07g008030.3' => 'sly', 'Solyc12g035470.2' => 'sly', 'Sopen02g038020' => 'spe', 'Sopen05g008490' => 'spe', 'Sopen07g003910' => 'spe', 'Sopen12g015240' => 'spe', 'Sp1g11550' => 'spa', 'Sp2g16710' => 'spa', 'Sp3g00430' => 'spa', 'Sp3g26780' => 'spa', 'Sp5g22900' => 'spa', 'Sp6g29530' => 'spa', 'TAR371G0794' => 'tar', 'TAR374G0164' => 'tar', 'TAR622G0165' => 'tar', 'TAR626G0929' => 'tar', 'TAR629G2155' => 'tar', 'THA.LOC104805282' => 'tha', 'THA.LOC104805363' => 'tha', 'THA.LOC104808968' => 'tha', 'THA.LOC104821093' => 'tha', 'THA.LOC104823953' => 'tha', 'THA.LOC104825562' => 'tha', 'THA.LOC104825665' => 'tha', 'Thecc.02G261400' => 'tca', 'Thecc.04G019200' => 'tca', 'Thecc.09G130400' => 'tca', 'Thhalv10004374m.g' => 'esa', 'Thhalv10007850m.g' => 'esa', 'Thhalv10013782m.g' => 'esa', 'Thhalv10018686m.g' => 'esa', 'Thhalv10020899m.g' => 'esa', 'Thhalv10022755m.g' => 'esa', 'TPR.G23851' => 'tpr', 'TPR.G26500' => 'tpr', 'TPR.G27267' => 'tpr', 'TPR.G32001' => 'tpr', 'TPR.G6251' => 'tpr', 'TPR.G8167' => 'tpr', 'TWI12G1330' => 'twi', 'TWI18G1239' => 'twi', 'TWI34G0979' => 'twi', 'TWI36G0670' => 'twi', 'TWI36G0707' => 'twi', 'TWI56G0233' => 'twi', 'TWI75G1809' => 'twi', 'unitig_21.g20874' => 'ugi', 'unitig_26.g10343' => 'ugi', 'unitig_46.g18392' => 'ugi', 'unitig_52.g17178' => 'ugi', 'unitig_8.g2934' => 'ugi', 'vmacro01122' => 'vma', 'vmacro05875' => 'vma', 'vmacro06147' => 'vma', 'vmacro16191' => 'vma', 'vmacro18293' => 'vma', 'VMungo0251G3707' => 'vmu', 'VMungo0464G1521' => 'vmu', 'VMungo1215G0205' => 'vmu', 'VMungo1383G2484' => 'vmu', 'Zm00001eb079610' => 'zma', 'Zm00001eb135990' => 'zma', 'Zm00001eb183710' => 'zma', 'Zm00001eb246020' => 'zma' ) $gf_id = 'HOM05D001124' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001124' ) $data_identifier = 'HOM05D001124' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 6, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 7, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 21, 'bol' => (int) 10, 'bra' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 6, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 9, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 21, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 8, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 10, 'lsa' => (int) 8, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 8, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 9, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb246020' $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' => 'HOM05D001124', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '548', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02520' => 'bna', 'A03p06630' => 'bna', 'A05p44460' => 'bna', 'A06p08710' => 'bna', 'A06p41090' => 'bna', 'A07p32320' => 'bna', 'A08p32520' => 'bna', 'A09p10360' => 'bna', 'A10p24080' => 'bna', 'Aa31LG11G15250' => 'aar', 'Aa31LG1G1800' => 'aar', 'Aa31LG2G5120' => 'aar', 'Aa31LG2G6070' => 'aar', 'Aa31LG5G10770' => 'aar', 'Aa31sc61G90' => 'aar', 'Actinidia01352' => 'ach', 'Actinidia05983' => 'ach', 'Actinidia08133' => 'ach', 'Actinidia15101' => 'ach', 'Actinidia26379' => 'ach', 'Actinidia35778' => 'ach', 'Actinidia36123' => 'ach', 'Actinidia37436' => 'ach', 'Actinidia38730' => 'ach', 'Ah.02g128210' => 'amhyb', 'Ah.03g132990' => 'amhyb', 'Ah.14g079410' => 'amhyb', 'AL1G24640' => 'aly', 'AL2G26680' => 'aly', 'AL3G10530' => 'aly', 'AL3G45230' => 'aly', 'AL5G15230' => 'aly', 'AL5G16960' => 'aly', 'AL6G25210' => 'aly', 'Aqoxy2G00441' => 'aox', 'Aqoxy3G01236' => 'aox', 'Aqoxy5G03746' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3RQ047' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C7GMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9C8JER' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MBL6KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YXCZ83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZANX40' => 'arhy', 'AT1G12990' => 'ath', 'AT1G67880' => 'ath', 'AT2G13290' => 'ath', 'AT3G01620' => 'ath', 'AT3G26445' => 'ath', 'AT3G27540' => 'ath', 'AT5G14480' => 'ath', 'ATR0824G026' => 'atr', 'ATR1098G019' => 'atr', 'Atru.chr11.2145' => 'acertr', 'Atru.chr2.3636' => 'acertr', 'Atru.chr2.3644' => 'acertr', 'Atru.chr6.2422' => 'acertr', 'Atru.chr7.1112' => 'acertr', 'AUR62005469' => 'cqu', 'AUR62011166' => 'cqu', 'AUR62013319' => 'cqu', 'AUR62024273' => 'cqu', 'AUR62028420' => 'cqu', 'AUR62041942' => 'cqu', 'BcaB01g04969' => 'bca', 'BcaB01g06371' => 'bca', 'BcaB02g11494' => 'bca', 'BcaB03g15382' => 'bca', 'BcaB08g36994' => 'bca', 'BcaC03g13477' => 'bca', 'BcaC03g13478' => 'bca', 'BcaC03g13480' => 'bca', 'BcaC03g13481' => 'bca', 'BcaC03g13486' => 'bca', 'BcaC04g19031' => 'bca', 'BcaC04g23085' => 'bca', 'BcaC05g25094' => 'bca', 'BcaC05g25096' => 'bca', 'BcaC05g25138' => 'bca', 'BcaC05g30416' => 'bca', 'BcaC05g30455' => 'bca', 'BcaC06g30979' => 'bca', 'BcaC06g33805' => 'bca', 'BcaC08g46021' => 'bca', 'BcaNung03154' => 'bca', 'BolC2t06623H' => 'bol', 'BolC2t06632H' => 'bol', 'BolC2t06635H' => 'bol', 'BolC2t06638H' => 'bol', 'BolC3t13266H' => 'bol', 'BolC5t29776H' => 'bol', 'BolC6t38912H' => 'bol', 'BolC7t44183H' => 'bol', 'BolC9t54123H' => 'bol', 'BolC9t59107H' => 'bol', 'BraA02t05221Z' => 'bra', 'BraA03t09996Z' => 'bra', 'BraA05t23210Z' => 'bra', 'BraA06t24068Z' => 'bra', 'BraA06t27032Z' => 'bra', 'BraA08t35176Z' => 'bra', 'BraA09t36680Z' => 'bra', 'BraA10t44471Z' => 'bra', 'C02p06760' => 'bna', 'C02p06890' => 'bna', 'C02p07010' => 'bna', 'C03p07660' => 'bna', 'C05p10300' => 'bna', 'C06p38150' => 'bna', 'C07p36650' => 'bna', 'C08p15770' => 'bna', 'C09p12300' => 'bna', 'C09p62700' => 'bna', 'C09p75040' => 'bna', 'CAN.G13.1' => 'can', 'CAN.G138.4' => 'can', 'CAN.G44.6' => 'can', 'CAN.G473.19' => 'can', 'CANSAT01G0835' => 'cansat', 'CANSAT11G0246' => 'cansat', 'CANSAT11G1766' => 'cansat', 'CANSAT64G1954' => 'cansat', 'CARHR013330' => 'chi', 'CARHR060530' => 'chi', 'CARHR075300' => 'chi', 'CARHR105120' => 'chi', 'CARHR148910' => 'chi', 'CARHR198830' => 'chi', 'Carub.0001s1275' => 'cru', 'Carub.0002s1437' => 'cru', 'Carub.0003s0044' => 'cru', 'Carub.0003s2787' => 'cru', 'Carub.0005s0597' => 'cru', 'Carub.0006s1266' => 'cru', 'Ca_06935_v3' => 'car', 'Ca_13559_v3' => 'car', 'Ca_16941_v3' => 'car', 'Ca_16960_v3' => 'car', 'Ca_17775_v3' => 'car', 'Ca_30464_v3' => 'car', 'Cc06_g08160' => 'ccan', 'Cc07_g01520' => 'ccan', 'Cc11_g15810' => 'ccan', 'CDE02G2840' => 'cde', 'CDE03G0093' => 'cde', 'CDE04G2127' => 'cde', 'CDE07G1857' => 'cde', 'CDE09G1246' => 'cde', 'Cfa003412' => 'cfa', 'Cfa007341' => 'cfa', 'Cfa009220' => 'cfa', 'Ciclev10008737m.g' => 'ccl', 'Ciclev10015565m.g' => 'ccl', 'Ciclev10031761m.g' => 'ccl', 'CiPaw.03G045300' => 'cil', 'CiPaw.03G247200' => 'cil', 'CiPaw.04G029500' => 'cil', 'CiPaw.04G174000' => 'cil', 'CiPaw.05G181200' => 'cil', 'CiPaw.06G067100' => 'cil', 'ClCG05G025800' => 'cla', 'ClCG06G011400' => 'cla', 'ClCG09G019360' => 'cla', 'COL.COLO4_04827' => 'col', 'COL.COLO4_29170' => 'col', 'COL.COLO4_35131' => 'col', 'COL.COLO4_35132' => 'col', 'Cpa.g.sc33.32' => 'cpa', 'Cpa.g.sc46.29' => 'cpa', 'Cpa.g.sc796.1' => 'cpa', 'CsaV3_1G030420' => 'csa', 'CsaV3_5G027050' => 'csa', 'CsaV3_5G031040' => 'csa', 'CsaV3_UNG023130' => 'csa', 'CSS0007726' => 'camsi', 'CSS0016433' => 'camsi', 'CSS0017656' => 'camsi', 'CSS0025364' => 'camsi', 'CSS0027582' => 'camsi', 'CSS0047288' => 'camsi', 'CSS0049950' => 'camsi', 'DCAR_003843' => 'dca', 'DCAR_007052' => 'dca', 'DCAR_020884' => 'dca', 'DCAR_021730' => 'dca', 'DCAR_024423' => 'dca', 'DCAR_026509' => 'dca', 'DCAR_031158' => 'dca', 'Dinv14728' => 'din', 'Dinv15219' => 'din', 'Dinv25728' => 'din', 'Dinv33428' => 'din', 'Dinv36489' => 'din', 'Dinv41486' => 'din', 'Duzib147G0469' => 'dzi', 'Duzib168G0060' => 'dzi', 'Duzib187G1215' => 'dzi', 'Duzib248G0692' => 'dzi', 'Duzib251G0767' => 'dzi', 'Duzib264G0446' => 'dzi', 'Duzib268G0691' => 'dzi', 'ECA232G4767' => 'eca', 'ECA233G2838' => 'eca', 'ECA234G0391' => 'eca', 'ECA234G0857' => 'eca', 'ECA236G1593' => 'eca', 'ECA238G0565' => 'eca', 'ECA246G1027' => 'eca', 'ECA246G3223' => 'eca', 'ECA246G3470' => 'eca', 'EL10Ac6g13829' => 'bvu', 'EL10Ac6g14093' => 'bvu', 'EL10Ac8g18707' => 'bvu', 'Eucgr.C01369' => 'egr', 'Eucgr.H02492' => 'egr', 'Eucgr.I01733' => 'egr', 'Eucgr.J02255' => 'egr', 'Eucgr.J02257' => 'egr', 'Eucgr.J02258' => 'egr', 'FAN02G1601' => 'fan', 'FAN03G1586' => 'fan', 'FAN03G2986' => 'fan', 'FAN05G4837' => 'fan', 'FAN06G0146' => 'fan', 'FAN07G0858' => 'fan', 'FAN09G3179' => 'fan', 'FAN10G0669' => 'fan', 'FAN12G2358' => 'fan', 'FAN14G4198' => 'fan', 'FAN14G5112' => 'fan', 'FAN17G0342' => 'fan', 'FAN19G0342' => 'fan', 'FAN19G0962' => 'fan', 'FAN19G1101' => 'fan', 'FAN19G1872' => 'fan', 'FAN22G0356' => 'fan', 'FAN23G0744' => 'fan', 'FAN23G1914' => 'fan', 'FAN26G0032' => 'fan', 'FAN28G0625' => 'fan', 'FvH4_1g02710' => 'fve', 'FvH4_1g02720' => 'fve', 'FvH4_4g25670' => 'fve', 'FvH4_6g51700' => 'fve', 'FvH4_7g20170' => 'fve', 'Glyma.05G175000' => 'gma', 'Glyma.08G132300' => 'gma', 'Glyma.11G243000' => 'gma', 'Glyma.13G158900' => 'gma', 'Glyma.17G112400' => 'gma', 'Glyma.18G014100' => 'gma', 'Glyma.19G003100' => 'gma', 'Glyma.19G056500' => 'gma', 'Gohir.A01G158900' => 'ghi', 'Gohir.A05G312600' => 'ghi', 'Gohir.A05G354900' => 'ghi', 'Gohir.A07G037200' => 'ghi', 'Gohir.A09G030000' => 'ghi', 'Gohir.A12G145200' => 'ghi', 'Gohir.D01G151500' => 'ghi', 'Gohir.D04G058300' => 'ghi', 'Gohir.D05G314100' => 'ghi', 'Gohir.D07G041400' => 'ghi', 'Gohir.D09G029700' => 'ghi', 'Gohir.D12G149700' => 'ghi', 'Gorai.001G043800' => 'gra', 'Gorai.002G187800' => 'gra', 'Gorai.006G034700' => 'gra', 'Gorai.008G161200' => 'gra', 'Gorai.009G335700' => 'gra', 'Gorai.012G065000' => 'gra', 'GSVIVG01000535001' => 'vvi', 'GSVIVG01015572001' => 'vvi', 'GSVIVG01032386001' => 'vvi', 'HanXRQChr05g0138531' => 'han', 'HanXRQChr06g0174391' => 'han', 'HanXRQChr07g0199021' => 'han', 'HanXRQChr08g0208211' => 'han', 'HanXRQChr09g0255471' => 'han', 'HanXRQChr10g0315791' => 'han', 'HanXRQChr12g0371991' => 'han', 'HanXRQChr15g0475251' => 'han', 'HanXRQChr17g0540001' => 'han', 'HanXRQChr17g0548631' => 'han', 'HanXRQChr17g0569561' => 'han', 'Haze_12256' => 'cav', 'Haze_14756' => 'cav', 'Haze_25528' => 'cav', 'Hma1.2p1_0079F.1_g041020' => 'hma', 'Hma1.2p1_0818F.1_g223260' => 'hma', 'Hma1.2p1_1747F.1_g300530' => 'hma', 'HPP92_004607' => 'vpl', 'HPP92_004608' => 'vpl', 'HPP92_006181' => 'vpl', 'HPP92_012192' => 'vpl', 'HPP92_015680' => 'vpl', 'HPP92_020249' => 'vpl', 'HPP92_021376' => 'vpl', 'HPP92_024275' => 'vpl', 'Hund06031' => 'sun', 'Hund25391' => 'sun', 'Lalb_Chr07g0185371' => 'lal', 'Lalb_Chr07g0185381' => 'lal', 'Lalb_Chr12g0204011' => 'lal', 'Lalb_Chr13g0301671' => 'lal', 'Lalb_Chr14g0362851' => 'lal', 'Lalb_Chr24g0403581' => 'lal', 'Lj1g0000233' => 'lja', 'Lj2g0018120' => 'lja', 'Lj3C621T0' => 'lonja', 'Lj3P1059T14' => 'lonja', 'Lj3P611T9' => 'lonja', 'Lj3P614T13' => 'lonja', 'Lj3P615T5' => 'lonja', 'Lj4g0012315' => 'lja', 'Lj4g0026182' => 'lja', 'Lj6P813T16' => 'lonja', 'Lj7C427T7' => 'lonja', 'Lj7C427T8' => 'lonja', 'Lj7P600T41' => 'lonja', 'Lju41C42G17' => 'lonja', 'Lsat_1_v5_gn_0_47300' => 'lsa', 'Lsat_1_v5_gn_2_91280' => 'lsa', 'Lsat_1_v5_gn_3_30561' => 'lsa', 'Lsat_1_v5_gn_4_184321' => 'lsa', 'Lsat_1_v5_gn_4_4041' => 'lsa', 'Lsat_1_v5_gn_5_92000' => 'lsa', 'Lsat_1_v5_gn_8_152940' => 'lsa', 'Lsat_1_v5_gn_8_62401' => 'lsa', 'Manes.06G055900' => 'mes', 'Manes.12G022200' => 'mes', 'Manes.13G023300' => 'mes', 'Manes.14G115000' => 'mes', 'Manes.15G151700' => 'mes', 'Manes.17G111300' => 'mes', 'Mapoly0226s0009' => 'mpo', 'MBI02_g25363_MAGBIO' => 'mbi', 'MBI06_g00027_MAGBIO' => 'mbi', 'MBI10_g13034_MAGBIO' => 'mbi', 'MD09G1023400' => 'mdo', 'MD13G1100100' => 'mdo', 'MD15G1169200' => 'mdo', 'MD16G1101100' => 'mdo', 'MD17G1022900' => 'mdo', 'Medtr3g096150' => 'mtr', 'Medtr4g115070' => 'mtr', 'Medtr7g033325' => 'mtr', 'Medtr8g089840' => 'mtr', 'MELO3C010319.2' => 'cme', 'MELO3C011944.2' => 'cme', 'MELO3C021589.2' => 'cme', 'Migut.E00207' => 'egut', 'Migut.H00067' => 'egut', 'Migut.K00433' => 'egut', 'Migut.K00606' => 'egut', 'Migut.K01410' => 'egut', 'MSTRG.13347' => 'ama', 'MSTRG.24045' => 'ama', 'MSTRG.2428' => 'ama', 'MSTRG.26410' => 'ama', 'MSTRG.3139' => 'ama', 'MSTRG.3286' => 'ama', 'MSTRG.563' => 'ama', 'MSTRG.7941' => 'ama', 'Nitab4.5_0000028g0060' => 'nta', 'Nitab4.5_0000065g0260' => 'nta', 'Nitab4.5_0000112g0060' => 'nta', 'Nitab4.5_0000489g0120' => 'nta', 'Nitab4.5_0001776g0050' => 'nta', 'Nitab4.5_0001854g0010' => 'nta', 'Nitab4.5_0001860g0020' => 'nta', 'Nitab4.5_0004352g0010' => 'nta', 'Nitab4.5_0008716g0020' => 'nta', 'Nitab4.5_0008922g0010' => 'nta', 'Nn3g16693' => 'nnu', 'Nn4g22596' => 'nnu', 'Nn7g37639' => 'nnu', 'Oeu001701.1' => 'oeu', 'Oeu018149.1' => 'oeu', 'Oeu026220.1' => 'oeu', 'Oeu038635.1' => 'oeu', 'Oeu049176.1' => 'oeu', 'Oeu056706.1' => 'oeu', 'Oeu056937.1' => 'oeu', 'Oeu057540.1' => 'oeu', 'Os02g0594900' => 'osa', 'Os02g0595100' => 'osa', 'Os04g0477500' => 'osa', 'Os12g0611900' => 'osa', 'Peaxi162Scf00076g00020' => 'pax', 'Peaxi162Scf00128g00217' => 'pax', 'Peaxi162Scf00129g01640' => 'pax', 'Peaxi162Scf00669g00007' => 'pax', 'Peaxi162Scf00700g00421' => 'pax', 'Peaxi162Scf00801g00038' => 'pax', 'Peaxi162Scf00891g00025' => 'pax', 'PGR083G0909' => 'pgr', 'PGR119G1005' => 'pgr', 'PGR142G2236' => 'pgr', 'PGR142G3388' => 'pgr', 'PGSC0003DMG400004514' => 'stu', 'PGSC0003DMG400012635' => 'stu', 'PGSC0003DMG400015730' => 'stu', 'PGSC0003DMG400018611' => 'stu', 'PGSC0003DMG400030897' => 'stu', 'Phvul.001G254800' => 'pvu', 'Phvul.002G260100' => 'pvu', 'Phvul.003G167600' => 'pvu', 'Phvul.004G005100' => 'pvu', 'Potri.001G343600' => 'ptr', 'Potri.006G066700' => 'ptr', 'Potri.008G186000' => 'ptr', 'Potri.010G046900' => 'ptr', 'Potri.018G127900' => 'ptr', 'Pp3c20_17750' => 'ppa', 'Pp3c24_4380' => 'ppa', 'Prupe.1G245800' => 'ppe', 'Prupe.3G293400' => 'ppe', 'Prupe.7G247400' => 'ppe', 'Psat0s145g0120' => 'psa', 'Psat0s595g0040' => 'psa', 'Psat0s595g0120' => 'psa', 'Psat3g175040' => 'psa', 'Psat7g058120' => 'psa', 'PSO017G0428' => 'pso', 'PSO063G7510' => 'pso', 'PSO067G0046' => 'pso', 'PSO478G1073' => 'pso', 'PSO675G3677' => 'pso', 'PSO675G6558' => 'pso', 'PSO675G7520' => 'pso', 'PSO675G8959' => 'pso', 'QL02p074089' => 'qlo', 'QL02p089614' => 'qlo', 'QL03p057736' => 'qlo', 'RcHm_v2.0_Chr1g0364131' => 'rch', 'RcHm_v2.0_Chr2g0087801' => 'rch', 'RcHm_v2.0_Chr2g0087821' => 'rch', 'RcHm_v2.0_Chr2g0173231' => 'rch', 'RcHm_v2.0_Chr4g0433111' => 'rch', 'Rhsim03G0250300' => 'rsi', 'Rhsim08G0048400' => 'rsi', 'Rhsim10G0014800' => 'rsi', 'Rhsim12G0040100' => 'rsi', 'Rhsim12G0109700' => 'rsi', 'Sabra06G0049600' => 'sbr', 'Sabra08G0141000' => 'sbr', 'Sabra10G0021400' => 'sbr', 'Sabra16G0222900' => 'sbr', 'Sabra18G0108600' => 'sbr', 'SalBow1G0433' => 'sbo', 'SalBow1G2038' => 'sbo', 'SalBow1G5003' => 'sbo', 'SalBow7G1197' => 'sbo', 'SalBow8G3506' => 'sbo', 'Sc03g0007300' => 'sci', 'Sc11g0000950' => 'sci', 'Sc14g0008750' => 'sci', 'Sc18g0000420' => 'sci', 'Sed0006754' => 'sed', 'Sed0008741' => 'sed', 'Sed0017172' => 'sed', 'Sed0018925' => 'sed', 'Sed0023326' => 'sed', 'Sed0025909' => 'sed', 'SEGI_05333' => 'sgi', 'SEGI_10362' => 'sgi', 'SEGI_13380' => 'sgi', 'SEGI_24306' => 'sgi', 'SEGI_29077' => 'sgi', 'SEGI_29095' => 'sgi', 'SEGI_36534' => 'sgi', 'SEGI_37506' => 'sgi', 'SEGI_38321' => 'sgi', 'SGA_v2.0_scaffold307G48031' => 'sas', 'SGA_v2.0_scaffold47G17507' => 'sas', 'SGA_v2.0_scaffold63G21736' => 'sas', 'SGA_v2.0_scaffold87G27070' => 'sas', 'SHI17794' => 'shi', 'SHI28851' => 'shi', 'SMO165G0155' => 'smo', 'SMO340G0217' => 'smo', 'SMO367G1210' => 'smo', 'Solyc02g093430.3' => 'sly', 'Solyc05g013580.4' => 'sly', 'Solyc07g008030.3' => 'sly', 'Solyc12g035470.2' => 'sly', 'Sopen02g038020' => 'spe', 'Sopen05g008490' => 'spe', 'Sopen07g003910' => 'spe', 'Sopen12g015240' => 'spe', 'Sp1g11550' => 'spa', 'Sp2g16710' => 'spa', 'Sp3g00430' => 'spa', 'Sp3g26780' => 'spa', 'Sp5g22900' => 'spa', 'Sp6g29530' => 'spa', 'TAR371G0794' => 'tar', 'TAR374G0164' => 'tar', 'TAR622G0165' => 'tar', 'TAR626G0929' => 'tar', 'TAR629G2155' => 'tar', 'THA.LOC104805282' => 'tha', 'THA.LOC104805363' => 'tha', 'THA.LOC104808968' => 'tha', 'THA.LOC104821093' => 'tha', 'THA.LOC104823953' => 'tha', 'THA.LOC104825562' => 'tha', 'THA.LOC104825665' => 'tha', 'Thecc.02G261400' => 'tca', 'Thecc.04G019200' => 'tca', 'Thecc.09G130400' => 'tca', 'Thhalv10004374m.g' => 'esa', 'Thhalv10007850m.g' => 'esa', 'Thhalv10013782m.g' => 'esa', 'Thhalv10018686m.g' => 'esa', 'Thhalv10020899m.g' => 'esa', 'Thhalv10022755m.g' => 'esa', 'TPR.G23851' => 'tpr', 'TPR.G26500' => 'tpr', 'TPR.G27267' => 'tpr', 'TPR.G32001' => 'tpr', 'TPR.G6251' => 'tpr', 'TPR.G8167' => 'tpr', 'TWI12G1330' => 'twi', 'TWI18G1239' => 'twi', 'TWI34G0979' => 'twi', 'TWI36G0670' => 'twi', 'TWI36G0707' => 'twi', 'TWI56G0233' => 'twi', 'TWI75G1809' => 'twi', 'unitig_21.g20874' => 'ugi', 'unitig_26.g10343' => 'ugi', 'unitig_46.g18392' => 'ugi', 'unitig_52.g17178' => 'ugi', 'unitig_8.g2934' => 'ugi', 'vmacro01122' => 'vma', 'vmacro05875' => 'vma', 'vmacro06147' => 'vma', 'vmacro16191' => 'vma', 'vmacro18293' => 'vma', 'VMungo0251G3707' => 'vmu', 'VMungo0464G1521' => 'vmu', 'VMungo1215G0205' => 'vmu', 'VMungo1383G2484' => 'vmu', 'Zm00001eb079610' => 'zma', 'Zm00001eb135990' => 'zma', 'Zm00001eb183710' => 'zma', 'Zm00001eb246020' => 'zma' ), 'gf_id' => 'HOM05D001124', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001124' ), 'data_identifier' => 'HOM05D001124', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001124', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '548', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02520' => 'bna', 'A03p06630' => 'bna', 'A05p44460' => 'bna', 'A06p08710' => 'bna', 'A06p41090' => 'bna', 'A07p32320' => 'bna', 'A08p32520' => 'bna', 'A09p10360' => 'bna', 'A10p24080' => 'bna', 'Aa31LG11G15250' => 'aar', 'Aa31LG1G1800' => 'aar', 'Aa31LG2G5120' => 'aar', 'Aa31LG2G6070' => 'aar', 'Aa31LG5G10770' => 'aar', 'Aa31sc61G90' => 'aar', 'Actinidia01352' => 'ach', 'Actinidia05983' => 'ach', 'Actinidia08133' => 'ach', 'Actinidia15101' => 'ach', 'Actinidia26379' => 'ach', 'Actinidia35778' => 'ach', 'Actinidia36123' => 'ach', 'Actinidia37436' => 'ach', 'Actinidia38730' => 'ach', 'Ah.02g128210' => 'amhyb', 'Ah.03g132990' => 'amhyb', 'Ah.14g079410' => 'amhyb', 'AL1G24640' => 'aly', 'AL2G26680' => 'aly', 'AL3G10530' => 'aly', 'AL3G45230' => 'aly', 'AL5G15230' => 'aly', 'AL5G16960' => 'aly', 'AL6G25210' => 'aly', 'Aqoxy2G00441' => 'aox', 'Aqoxy3G01236' => 'aox', 'Aqoxy5G03746' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3RQ047' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C7GMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9C8JER' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MBL6KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YXCZ83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZANX40' => 'arhy', 'AT1G12990' => 'ath', 'AT1G67880' => 'ath', 'AT2G13290' => 'ath', 'AT3G01620' => 'ath', 'AT3G26445' => 'ath', 'AT3G27540' => 'ath', 'AT5G14480' => 'ath', 'ATR0824G026' => 'atr', 'ATR1098G019' => 'atr', 'Atru.chr11.2145' => 'acertr', 'Atru.chr2.3636' => 'acertr', 'Atru.chr2.3644' => 'acertr', 'Atru.chr6.2422' => 'acertr', 'Atru.chr7.1112' => 'acertr', 'AUR62005469' => 'cqu', 'AUR62011166' => 'cqu', 'AUR62013319' => 'cqu', 'AUR62024273' => 'cqu', 'AUR62028420' => 'cqu', 'AUR62041942' => 'cqu', 'BcaB01g04969' => 'bca', 'BcaB01g06371' => 'bca', 'BcaB02g11494' => 'bca', 'BcaB03g15382' => 'bca', 'BcaB08g36994' => 'bca', 'BcaC03g13477' => 'bca', 'BcaC03g13478' => 'bca', 'BcaC03g13480' => 'bca', 'BcaC03g13481' => 'bca', 'BcaC03g13486' => 'bca', 'BcaC04g19031' => 'bca', 'BcaC04g23085' => 'bca', 'BcaC05g25094' => 'bca', 'BcaC05g25096' => 'bca', 'BcaC05g25138' => 'bca', 'BcaC05g30416' => 'bca', 'BcaC05g30455' => 'bca', 'BcaC06g30979' => 'bca', 'BcaC06g33805' => 'bca', 'BcaC08g46021' => 'bca', 'BcaNung03154' => 'bca', 'BolC2t06623H' => 'bol', 'BolC2t06632H' => 'bol', 'BolC2t06635H' => 'bol', 'BolC2t06638H' => 'bol', 'BolC3t13266H' => 'bol', 'BolC5t29776H' => 'bol', 'BolC6t38912H' => 'bol', 'BolC7t44183H' => 'bol', 'BolC9t54123H' => 'bol', 'BolC9t59107H' => 'bol', 'BraA02t05221Z' => 'bra', 'BraA03t09996Z' => 'bra', 'BraA05t23210Z' => 'bra', 'BraA06t24068Z' => 'bra', 'BraA06t27032Z' => 'bra', 'BraA08t35176Z' => 'bra', 'BraA09t36680Z' => 'bra', 'BraA10t44471Z' => 'bra', 'C02p06760' => 'bna', 'C02p06890' => 'bna', 'C02p07010' => 'bna', 'C03p07660' => 'bna', 'C05p10300' => 'bna', 'C06p38150' => 'bna', 'C07p36650' => 'bna', 'C08p15770' => 'bna', 'C09p12300' => 'bna', 'C09p62700' => 'bna', 'C09p75040' => 'bna', 'CAN.G13.1' => 'can', 'CAN.G138.4' => 'can', 'CAN.G44.6' => 'can', 'CAN.G473.19' => 'can', 'CANSAT01G0835' => 'cansat', 'CANSAT11G0246' => 'cansat', 'CANSAT11G1766' => 'cansat', 'CANSAT64G1954' => 'cansat', 'CARHR013330' => 'chi', 'CARHR060530' => 'chi', 'CARHR075300' => 'chi', 'CARHR105120' => 'chi', 'CARHR148910' => 'chi', 'CARHR198830' => 'chi', 'Carub.0001s1275' => 'cru', 'Carub.0002s1437' => 'cru', 'Carub.0003s0044' => 'cru', 'Carub.0003s2787' => 'cru', 'Carub.0005s0597' => 'cru', 'Carub.0006s1266' => 'cru', 'Ca_06935_v3' => 'car', 'Ca_13559_v3' => 'car', 'Ca_16941_v3' => 'car', 'Ca_16960_v3' => 'car', 'Ca_17775_v3' => 'car', 'Ca_30464_v3' => 'car', 'Cc06_g08160' => 'ccan', 'Cc07_g01520' => 'ccan', 'Cc11_g15810' => 'ccan', 'CDE02G2840' => 'cde', 'CDE03G0093' => 'cde', 'CDE04G2127' => 'cde', 'CDE07G1857' => 'cde', 'CDE09G1246' => 'cde', 'Cfa003412' => 'cfa', 'Cfa007341' => 'cfa', 'Cfa009220' => 'cfa', 'Ciclev10008737m.g' => 'ccl', 'Ciclev10015565m.g' => 'ccl', 'Ciclev10031761m.g' => 'ccl', 'CiPaw.03G045300' => 'cil', 'CiPaw.03G247200' => 'cil', 'CiPaw.04G029500' => 'cil', 'CiPaw.04G174000' => 'cil', 'CiPaw.05G181200' => 'cil', 'CiPaw.06G067100' => 'cil', 'ClCG05G025800' => 'cla', 'ClCG06G011400' => 'cla', 'ClCG09G019360' => 'cla', 'COL.COLO4_04827' => 'col', 'COL.COLO4_29170' => 'col', 'COL.COLO4_35131' => 'col', 'COL.COLO4_35132' => 'col', 'Cpa.g.sc33.32' => 'cpa', 'Cpa.g.sc46.29' => 'cpa', 'Cpa.g.sc796.1' => 'cpa', 'CsaV3_1G030420' => 'csa', 'CsaV3_5G027050' => 'csa', 'CsaV3_5G031040' => 'csa', 'CsaV3_UNG023130' => 'csa', 'CSS0007726' => 'camsi', 'CSS0016433' => 'camsi', 'CSS0017656' => 'camsi', 'CSS0025364' => 'camsi', 'CSS0027582' => 'camsi', 'CSS0047288' => 'camsi', 'CSS0049950' => 'camsi', 'DCAR_003843' => 'dca', 'DCAR_007052' => 'dca', 'DCAR_020884' => 'dca', 'DCAR_021730' => 'dca', 'DCAR_024423' => 'dca', 'DCAR_026509' => 'dca', 'DCAR_031158' => 'dca', 'Dinv14728' => 'din', 'Dinv15219' => 'din', 'Dinv25728' => 'din', 'Dinv33428' => 'din', 'Dinv36489' => 'din', 'Dinv41486' => 'din', 'Duzib147G0469' => 'dzi', 'Duzib168G0060' => 'dzi', 'Duzib187G1215' => 'dzi', 'Duzib248G0692' => 'dzi', 'Duzib251G0767' => 'dzi', 'Duzib264G0446' => 'dzi', 'Duzib268G0691' => 'dzi', 'ECA232G4767' => 'eca', 'ECA233G2838' => 'eca', 'ECA234G0391' => 'eca', 'ECA234G0857' => 'eca', 'ECA236G1593' => 'eca', 'ECA238G0565' => 'eca', 'ECA246G1027' => 'eca', 'ECA246G3223' => 'eca', 'ECA246G3470' => 'eca', 'EL10Ac6g13829' => 'bvu', 'EL10Ac6g14093' => 'bvu', 'EL10Ac8g18707' => 'bvu', 'Eucgr.C01369' => 'egr', 'Eucgr.H02492' => 'egr', 'Eucgr.I01733' => 'egr', 'Eucgr.J02255' => 'egr', 'Eucgr.J02257' => 'egr', 'Eucgr.J02258' => 'egr', 'FAN02G1601' => 'fan', 'FAN03G1586' => 'fan', 'FAN03G2986' => 'fan', 'FAN05G4837' => 'fan', 'FAN06G0146' => 'fan', 'FAN07G0858' => 'fan', 'FAN09G3179' => 'fan', 'FAN10G0669' => 'fan', 'FAN12G2358' => 'fan', 'FAN14G4198' => 'fan', 'FAN14G5112' => 'fan', 'FAN17G0342' => 'fan', 'FAN19G0342' => 'fan', 'FAN19G0962' => 'fan', 'FAN19G1101' => 'fan', 'FAN19G1872' => 'fan', 'FAN22G0356' => 'fan', 'FAN23G0744' => 'fan', 'FAN23G1914' => 'fan', 'FAN26G0032' => 'fan', 'FAN28G0625' => 'fan', 'FvH4_1g02710' => 'fve', 'FvH4_1g02720' => 'fve', 'FvH4_4g25670' => 'fve', 'FvH4_6g51700' => 'fve', 'FvH4_7g20170' => 'fve', 'Glyma.05G175000' => 'gma', 'Glyma.08G132300' => 'gma', 'Glyma.11G243000' => 'gma', 'Glyma.13G158900' => 'gma', 'Glyma.17G112400' => 'gma', 'Glyma.18G014100' => 'gma', 'Glyma.19G003100' => 'gma', 'Glyma.19G056500' => 'gma', 'Gohir.A01G158900' => 'ghi', 'Gohir.A05G312600' => 'ghi', 'Gohir.A05G354900' => 'ghi', 'Gohir.A07G037200' => 'ghi', 'Gohir.A09G030000' => 'ghi', 'Gohir.A12G145200' => 'ghi', 'Gohir.D01G151500' => 'ghi', 'Gohir.D04G058300' => 'ghi', 'Gohir.D05G314100' => 'ghi', 'Gohir.D07G041400' => 'ghi', 'Gohir.D09G029700' => 'ghi', 'Gohir.D12G149700' => 'ghi', 'Gorai.001G043800' => 'gra', 'Gorai.002G187800' => 'gra', 'Gorai.006G034700' => 'gra', 'Gorai.008G161200' => 'gra', 'Gorai.009G335700' => 'gra', 'Gorai.012G065000' => 'gra', 'GSVIVG01000535001' => 'vvi', 'GSVIVG01015572001' => 'vvi', 'GSVIVG01032386001' => 'vvi', 'HanXRQChr05g0138531' => 'han', 'HanXRQChr06g0174391' => 'han', 'HanXRQChr07g0199021' => 'han', 'HanXRQChr08g0208211' => 'han', 'HanXRQChr09g0255471' => 'han', 'HanXRQChr10g0315791' => 'han', 'HanXRQChr12g0371991' => 'han', 'HanXRQChr15g0475251' => 'han', 'HanXRQChr17g0540001' => 'han', 'HanXRQChr17g0548631' => 'han', 'HanXRQChr17g0569561' => 'han', 'Haze_12256' => 'cav', 'Haze_14756' => 'cav', 'Haze_25528' => 'cav', 'Hma1.2p1_0079F.1_g041020' => 'hma', 'Hma1.2p1_0818F.1_g223260' => 'hma', 'Hma1.2p1_1747F.1_g300530' => 'hma', 'HPP92_004607' => 'vpl', 'HPP92_004608' => 'vpl', 'HPP92_006181' => 'vpl', 'HPP92_012192' => 'vpl', 'HPP92_015680' => 'vpl', 'HPP92_020249' => 'vpl', 'HPP92_021376' => 'vpl', 'HPP92_024275' => 'vpl', 'Hund06031' => 'sun', 'Hund25391' => 'sun', 'Lalb_Chr07g0185371' => 'lal', 'Lalb_Chr07g0185381' => 'lal', 'Lalb_Chr12g0204011' => 'lal', 'Lalb_Chr13g0301671' => 'lal', 'Lalb_Chr14g0362851' => 'lal', 'Lalb_Chr24g0403581' => 'lal', 'Lj1g0000233' => 'lja', 'Lj2g0018120' => 'lja', 'Lj3C621T0' => 'lonja', 'Lj3P1059T14' => 'lonja', 'Lj3P611T9' => 'lonja', 'Lj3P614T13' => 'lonja', 'Lj3P615T5' => 'lonja', 'Lj4g0012315' => 'lja', 'Lj4g0026182' => 'lja', 'Lj6P813T16' => 'lonja', 'Lj7C427T7' => 'lonja', 'Lj7C427T8' => 'lonja', 'Lj7P600T41' => 'lonja', 'Lju41C42G17' => 'lonja', 'Lsat_1_v5_gn_0_47300' => 'lsa', 'Lsat_1_v5_gn_2_91280' => 'lsa', 'Lsat_1_v5_gn_3_30561' => 'lsa', 'Lsat_1_v5_gn_4_184321' => 'lsa', 'Lsat_1_v5_gn_4_4041' => 'lsa', 'Lsat_1_v5_gn_5_92000' => 'lsa', 'Lsat_1_v5_gn_8_152940' => 'lsa', 'Lsat_1_v5_gn_8_62401' => 'lsa', 'Manes.06G055900' => 'mes', 'Manes.12G022200' => 'mes', 'Manes.13G023300' => 'mes', 'Manes.14G115000' => 'mes', 'Manes.15G151700' => 'mes', 'Manes.17G111300' => 'mes', 'Mapoly0226s0009' => 'mpo', 'MBI02_g25363_MAGBIO' => 'mbi', 'MBI06_g00027_MAGBIO' => 'mbi', 'MBI10_g13034_MAGBIO' => 'mbi', 'MD09G1023400' => 'mdo', 'MD13G1100100' => 'mdo', 'MD15G1169200' => 'mdo', 'MD16G1101100' => 'mdo', 'MD17G1022900' => 'mdo', 'Medtr3g096150' => 'mtr', 'Medtr4g115070' => 'mtr', 'Medtr7g033325' => 'mtr', 'Medtr8g089840' => 'mtr', 'MELO3C010319.2' => 'cme', 'MELO3C011944.2' => 'cme', 'MELO3C021589.2' => 'cme', 'Migut.E00207' => 'egut', 'Migut.H00067' => 'egut', 'Migut.K00433' => 'egut', 'Migut.K00606' => 'egut', 'Migut.K01410' => 'egut', 'MSTRG.13347' => 'ama', 'MSTRG.24045' => 'ama', 'MSTRG.2428' => 'ama', 'MSTRG.26410' => 'ama', 'MSTRG.3139' => 'ama', 'MSTRG.3286' => 'ama', 'MSTRG.563' => 'ama', 'MSTRG.7941' => 'ama', 'Nitab4.5_0000028g0060' => 'nta', 'Nitab4.5_0000065g0260' => 'nta', 'Nitab4.5_0000112g0060' => 'nta', 'Nitab4.5_0000489g0120' => 'nta', 'Nitab4.5_0001776g0050' => 'nta', 'Nitab4.5_0001854g0010' => 'nta', 'Nitab4.5_0001860g0020' => 'nta', 'Nitab4.5_0004352g0010' => 'nta', 'Nitab4.5_0008716g0020' => 'nta', 'Nitab4.5_0008922g0010' => 'nta', 'Nn3g16693' => 'nnu', 'Nn4g22596' => 'nnu', 'Nn7g37639' => 'nnu', 'Oeu001701.1' => 'oeu', 'Oeu018149.1' => 'oeu', 'Oeu026220.1' => 'oeu', 'Oeu038635.1' => 'oeu', 'Oeu049176.1' => 'oeu', 'Oeu056706.1' => 'oeu', 'Oeu056937.1' => 'oeu', 'Oeu057540.1' => 'oeu', 'Os02g0594900' => 'osa', 'Os02g0595100' => 'osa', 'Os04g0477500' => 'osa', 'Os12g0611900' => 'osa', 'Peaxi162Scf00076g00020' => 'pax', 'Peaxi162Scf00128g00217' => 'pax', 'Peaxi162Scf00129g01640' => 'pax', 'Peaxi162Scf00669g00007' => 'pax', 'Peaxi162Scf00700g00421' => 'pax', 'Peaxi162Scf00801g00038' => 'pax', 'Peaxi162Scf00891g00025' => 'pax', 'PGR083G0909' => 'pgr', 'PGR119G1005' => 'pgr', 'PGR142G2236' => 'pgr', 'PGR142G3388' => 'pgr', 'PGSC0003DMG400004514' => 'stu', 'PGSC0003DMG400012635' => 'stu', 'PGSC0003DMG400015730' => 'stu', 'PGSC0003DMG400018611' => 'stu', 'PGSC0003DMG400030897' => 'stu', 'Phvul.001G254800' => 'pvu', 'Phvul.002G260100' => 'pvu', 'Phvul.003G167600' => 'pvu', 'Phvul.004G005100' => 'pvu', 'Potri.001G343600' => 'ptr', 'Potri.006G066700' => 'ptr', 'Potri.008G186000' => 'ptr', 'Potri.010G046900' => 'ptr', 'Potri.018G127900' => 'ptr', 'Pp3c20_17750' => 'ppa', 'Pp3c24_4380' => 'ppa', 'Prupe.1G245800' => 'ppe', 'Prupe.3G293400' => 'ppe', 'Prupe.7G247400' => 'ppe', 'Psat0s145g0120' => 'psa', 'Psat0s595g0040' => 'psa', 'Psat0s595g0120' => 'psa', 'Psat3g175040' => 'psa', 'Psat7g058120' => 'psa', 'PSO017G0428' => 'pso', 'PSO063G7510' => 'pso', 'PSO067G0046' => 'pso', 'PSO478G1073' => 'pso', 'PSO675G3677' => 'pso', 'PSO675G6558' => 'pso', 'PSO675G7520' => 'pso', 'PSO675G8959' => 'pso', 'QL02p074089' => 'qlo', 'QL02p089614' => 'qlo', 'QL03p057736' => 'qlo', 'RcHm_v2.0_Chr1g0364131' => 'rch', 'RcHm_v2.0_Chr2g0087801' => 'rch', 'RcHm_v2.0_Chr2g0087821' => 'rch', 'RcHm_v2.0_Chr2g0173231' => 'rch', 'RcHm_v2.0_Chr4g0433111' => 'rch', 'Rhsim03G0250300' => 'rsi', 'Rhsim08G0048400' => 'rsi', 'Rhsim10G0014800' => 'rsi', 'Rhsim12G0040100' => 'rsi', 'Rhsim12G0109700' => 'rsi', 'Sabra06G0049600' => 'sbr', 'Sabra08G0141000' => 'sbr', 'Sabra10G0021400' => 'sbr', 'Sabra16G0222900' => 'sbr', 'Sabra18G0108600' => 'sbr', 'SalBow1G0433' => 'sbo', 'SalBow1G2038' => 'sbo', 'SalBow1G5003' => 'sbo', 'SalBow7G1197' => 'sbo', 'SalBow8G3506' => 'sbo', 'Sc03g0007300' => 'sci', 'Sc11g0000950' => 'sci', 'Sc14g0008750' => 'sci', 'Sc18g0000420' => 'sci', 'Sed0006754' => 'sed', 'Sed0008741' => 'sed', 'Sed0017172' => 'sed', 'Sed0018925' => 'sed', 'Sed0023326' => 'sed', 'Sed0025909' => 'sed', 'SEGI_05333' => 'sgi', 'SEGI_10362' => 'sgi', 'SEGI_13380' => 'sgi', 'SEGI_24306' => 'sgi', 'SEGI_29077' => 'sgi', 'SEGI_29095' => 'sgi', 'SEGI_36534' => 'sgi', 'SEGI_37506' => 'sgi', 'SEGI_38321' => 'sgi', 'SGA_v2.0_scaffold307G48031' => 'sas', 'SGA_v2.0_scaffold47G17507' => 'sas', 'SGA_v2.0_scaffold63G21736' => 'sas', 'SGA_v2.0_scaffold87G27070' => 'sas', 'SHI17794' => 'shi', 'SHI28851' => 'shi', 'SMO165G0155' => 'smo', 'SMO340G0217' => 'smo', 'SMO367G1210' => 'smo', 'Solyc02g093430.3' => 'sly', 'Solyc05g013580.4' => 'sly', 'Solyc07g008030.3' => 'sly', 'Solyc12g035470.2' => 'sly', 'Sopen02g038020' => 'spe', 'Sopen05g008490' => 'spe', 'Sopen07g003910' => 'spe', 'Sopen12g015240' => 'spe', 'Sp1g11550' => 'spa', 'Sp2g16710' => 'spa', 'Sp3g00430' => 'spa', 'Sp3g26780' => 'spa', 'Sp5g22900' => 'spa', 'Sp6g29530' => 'spa', 'TAR371G0794' => 'tar', 'TAR374G0164' => 'tar', 'TAR622G0165' => 'tar', 'TAR626G0929' => 'tar', 'TAR629G2155' => 'tar', 'THA.LOC104805282' => 'tha', 'THA.LOC104805363' => 'tha', 'THA.LOC104808968' => 'tha', 'THA.LOC104821093' => 'tha', 'THA.LOC104823953' => 'tha', 'THA.LOC104825562' => 'tha', 'THA.LOC104825665' => 'tha', 'Thecc.02G261400' => 'tca', 'Thecc.04G019200' => 'tca', 'Thecc.09G130400' => 'tca', 'Thhalv10004374m.g' => 'esa', 'Thhalv10007850m.g' => 'esa', 'Thhalv10013782m.g' => 'esa', 'Thhalv10018686m.g' => 'esa', 'Thhalv10020899m.g' => 'esa', 'Thhalv10022755m.g' => 'esa', 'TPR.G23851' => 'tpr', 'TPR.G26500' => 'tpr', 'TPR.G27267' => 'tpr', 'TPR.G32001' => 'tpr', 'TPR.G6251' => 'tpr', 'TPR.G8167' => 'tpr', 'TWI12G1330' => 'twi', 'TWI18G1239' => 'twi', 'TWI34G0979' => 'twi', 'TWI36G0670' => 'twi', 'TWI36G0707' => 'twi', 'TWI56G0233' => 'twi', 'TWI75G1809' => 'twi', 'unitig_21.g20874' => 'ugi', 'unitig_26.g10343' => 'ugi', 'unitig_46.g18392' => 'ugi', 'unitig_52.g17178' => 'ugi', 'unitig_8.g2934' => 'ugi', 'vmacro01122' => 'vma', 'vmacro05875' => 'vma', 'vmacro06147' => 'vma', 'vmacro16191' => 'vma', 'vmacro18293' => 'vma', 'VMungo0251G3707' => 'vmu', 'VMungo0464G1521' => 'vmu', 'VMungo1215G0205' => 'vmu', 'VMungo1383G2484' => 'vmu', 'Zm00001eb079610' => 'zma', 'Zm00001eb135990' => 'zma', 'Zm00001eb183710' => 'zma', 'Zm00001eb246020' => 'zma' ) $gf_id = 'HOM05D001124' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001124' ) $data_identifier = 'HOM05D001124' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 6, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 7, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 21, 'bol' => (int) 10, 'bra' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 6, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 9, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 21, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 8, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 10, 'lsa' => (int) 8, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 8, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 9, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb246020' $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' => 'HOM05D001124', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '548', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02520' => 'bna', 'A03p06630' => 'bna', 'A05p44460' => 'bna', 'A06p08710' => 'bna', 'A06p41090' => 'bna', 'A07p32320' => 'bna', 'A08p32520' => 'bna', 'A09p10360' => 'bna', 'A10p24080' => 'bna', 'Aa31LG11G15250' => 'aar', 'Aa31LG1G1800' => 'aar', 'Aa31LG2G5120' => 'aar', 'Aa31LG2G6070' => 'aar', 'Aa31LG5G10770' => 'aar', 'Aa31sc61G90' => 'aar', 'Actinidia01352' => 'ach', 'Actinidia05983' => 'ach', 'Actinidia08133' => 'ach', 'Actinidia15101' => 'ach', 'Actinidia26379' => 'ach', 'Actinidia35778' => 'ach', 'Actinidia36123' => 'ach', 'Actinidia37436' => 'ach', 'Actinidia38730' => 'ach', 'Ah.02g128210' => 'amhyb', 'Ah.03g132990' => 'amhyb', 'Ah.14g079410' => 'amhyb', 'AL1G24640' => 'aly', 'AL2G26680' => 'aly', 'AL3G10530' => 'aly', 'AL3G45230' => 'aly', 'AL5G15230' => 'aly', 'AL5G16960' => 'aly', 'AL6G25210' => 'aly', 'Aqoxy2G00441' => 'aox', 'Aqoxy3G01236' => 'aox', 'Aqoxy5G03746' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3RQ047' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C7GMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9C8JER' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MBL6KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YXCZ83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZANX40' => 'arhy', 'AT1G12990' => 'ath', 'AT1G67880' => 'ath', 'AT2G13290' => 'ath', 'AT3G01620' => 'ath', 'AT3G26445' => 'ath', 'AT3G27540' => 'ath', 'AT5G14480' => 'ath', 'ATR0824G026' => 'atr', 'ATR1098G019' => 'atr', 'Atru.chr11.2145' => 'acertr', 'Atru.chr2.3636' => 'acertr', 'Atru.chr2.3644' => 'acertr', 'Atru.chr6.2422' => 'acertr', 'Atru.chr7.1112' => 'acertr', 'AUR62005469' => 'cqu', 'AUR62011166' => 'cqu', 'AUR62013319' => 'cqu', 'AUR62024273' => 'cqu', 'AUR62028420' => 'cqu', 'AUR62041942' => 'cqu', 'BcaB01g04969' => 'bca', 'BcaB01g06371' => 'bca', 'BcaB02g11494' => 'bca', 'BcaB03g15382' => 'bca', 'BcaB08g36994' => 'bca', 'BcaC03g13477' => 'bca', 'BcaC03g13478' => 'bca', 'BcaC03g13480' => 'bca', 'BcaC03g13481' => 'bca', 'BcaC03g13486' => 'bca', 'BcaC04g19031' => 'bca', 'BcaC04g23085' => 'bca', 'BcaC05g25094' => 'bca', 'BcaC05g25096' => 'bca', 'BcaC05g25138' => 'bca', 'BcaC05g30416' => 'bca', 'BcaC05g30455' => 'bca', 'BcaC06g30979' => 'bca', 'BcaC06g33805' => 'bca', 'BcaC08g46021' => 'bca', 'BcaNung03154' => 'bca', 'BolC2t06623H' => 'bol', 'BolC2t06632H' => 'bol', 'BolC2t06635H' => 'bol', 'BolC2t06638H' => 'bol', 'BolC3t13266H' => 'bol', 'BolC5t29776H' => 'bol', 'BolC6t38912H' => 'bol', 'BolC7t44183H' => 'bol', 'BolC9t54123H' => 'bol', 'BolC9t59107H' => 'bol', 'BraA02t05221Z' => 'bra', 'BraA03t09996Z' => 'bra', 'BraA05t23210Z' => 'bra', 'BraA06t24068Z' => 'bra', 'BraA06t27032Z' => 'bra', 'BraA08t35176Z' => 'bra', 'BraA09t36680Z' => 'bra', 'BraA10t44471Z' => 'bra', 'C02p06760' => 'bna', 'C02p06890' => 'bna', 'C02p07010' => 'bna', 'C03p07660' => 'bna', 'C05p10300' => 'bna', 'C06p38150' => 'bna', 'C07p36650' => 'bna', 'C08p15770' => 'bna', 'C09p12300' => 'bna', 'C09p62700' => 'bna', 'C09p75040' => 'bna', 'CAN.G13.1' => 'can', 'CAN.G138.4' => 'can', 'CAN.G44.6' => 'can', 'CAN.G473.19' => 'can', 'CANSAT01G0835' => 'cansat', 'CANSAT11G0246' => 'cansat', 'CANSAT11G1766' => 'cansat', 'CANSAT64G1954' => 'cansat', 'CARHR013330' => 'chi', 'CARHR060530' => 'chi', 'CARHR075300' => 'chi', 'CARHR105120' => 'chi', 'CARHR148910' => 'chi', 'CARHR198830' => 'chi', 'Carub.0001s1275' => 'cru', 'Carub.0002s1437' => 'cru', 'Carub.0003s0044' => 'cru', 'Carub.0003s2787' => 'cru', 'Carub.0005s0597' => 'cru', 'Carub.0006s1266' => 'cru', 'Ca_06935_v3' => 'car', 'Ca_13559_v3' => 'car', 'Ca_16941_v3' => 'car', 'Ca_16960_v3' => 'car', 'Ca_17775_v3' => 'car', 'Ca_30464_v3' => 'car', 'Cc06_g08160' => 'ccan', 'Cc07_g01520' => 'ccan', 'Cc11_g15810' => 'ccan', 'CDE02G2840' => 'cde', 'CDE03G0093' => 'cde', 'CDE04G2127' => 'cde', 'CDE07G1857' => 'cde', 'CDE09G1246' => 'cde', 'Cfa003412' => 'cfa', 'Cfa007341' => 'cfa', 'Cfa009220' => 'cfa', 'Ciclev10008737m.g' => 'ccl', 'Ciclev10015565m.g' => 'ccl', 'Ciclev10031761m.g' => 'ccl', 'CiPaw.03G045300' => 'cil', 'CiPaw.03G247200' => 'cil', 'CiPaw.04G029500' => 'cil', 'CiPaw.04G174000' => 'cil', 'CiPaw.05G181200' => 'cil', 'CiPaw.06G067100' => 'cil', 'ClCG05G025800' => 'cla', 'ClCG06G011400' => 'cla', 'ClCG09G019360' => 'cla', 'COL.COLO4_04827' => 'col', 'COL.COLO4_29170' => 'col', 'COL.COLO4_35131' => 'col', 'COL.COLO4_35132' => 'col', 'Cpa.g.sc33.32' => 'cpa', 'Cpa.g.sc46.29' => 'cpa', 'Cpa.g.sc796.1' => 'cpa', 'CsaV3_1G030420' => 'csa', 'CsaV3_5G027050' => 'csa', 'CsaV3_5G031040' => 'csa', 'CsaV3_UNG023130' => 'csa', 'CSS0007726' => 'camsi', 'CSS0016433' => 'camsi', 'CSS0017656' => 'camsi', 'CSS0025364' => 'camsi', 'CSS0027582' => 'camsi', 'CSS0047288' => 'camsi', 'CSS0049950' => 'camsi', 'DCAR_003843' => 'dca', 'DCAR_007052' => 'dca', 'DCAR_020884' => 'dca', 'DCAR_021730' => 'dca', 'DCAR_024423' => 'dca', 'DCAR_026509' => 'dca', 'DCAR_031158' => 'dca', 'Dinv14728' => 'din', 'Dinv15219' => 'din', 'Dinv25728' => 'din', 'Dinv33428' => 'din', 'Dinv36489' => 'din', 'Dinv41486' => 'din', 'Duzib147G0469' => 'dzi', 'Duzib168G0060' => 'dzi', 'Duzib187G1215' => 'dzi', 'Duzib248G0692' => 'dzi', 'Duzib251G0767' => 'dzi', 'Duzib264G0446' => 'dzi', 'Duzib268G0691' => 'dzi', 'ECA232G4767' => 'eca', 'ECA233G2838' => 'eca', 'ECA234G0391' => 'eca', 'ECA234G0857' => 'eca', 'ECA236G1593' => 'eca', 'ECA238G0565' => 'eca', 'ECA246G1027' => 'eca', 'ECA246G3223' => 'eca', 'ECA246G3470' => 'eca', 'EL10Ac6g13829' => 'bvu', 'EL10Ac6g14093' => 'bvu', 'EL10Ac8g18707' => 'bvu', 'Eucgr.C01369' => 'egr', 'Eucgr.H02492' => 'egr', 'Eucgr.I01733' => 'egr', 'Eucgr.J02255' => 'egr', 'Eucgr.J02257' => 'egr', 'Eucgr.J02258' => 'egr', 'FAN02G1601' => 'fan', 'FAN03G1586' => 'fan', 'FAN03G2986' => 'fan', 'FAN05G4837' => 'fan', 'FAN06G0146' => 'fan', 'FAN07G0858' => 'fan', 'FAN09G3179' => 'fan', 'FAN10G0669' => 'fan', 'FAN12G2358' => 'fan', 'FAN14G4198' => 'fan', 'FAN14G5112' => 'fan', 'FAN17G0342' => 'fan', 'FAN19G0342' => 'fan', 'FAN19G0962' => 'fan', 'FAN19G1101' => 'fan', 'FAN19G1872' => 'fan', 'FAN22G0356' => 'fan', 'FAN23G0744' => 'fan', 'FAN23G1914' => 'fan', 'FAN26G0032' => 'fan', 'FAN28G0625' => 'fan', 'FvH4_1g02710' => 'fve', 'FvH4_1g02720' => 'fve', 'FvH4_4g25670' => 'fve', 'FvH4_6g51700' => 'fve', 'FvH4_7g20170' => 'fve', 'Glyma.05G175000' => 'gma', 'Glyma.08G132300' => 'gma', 'Glyma.11G243000' => 'gma', 'Glyma.13G158900' => 'gma', 'Glyma.17G112400' => 'gma', 'Glyma.18G014100' => 'gma', 'Glyma.19G003100' => 'gma', 'Glyma.19G056500' => 'gma', 'Gohir.A01G158900' => 'ghi', 'Gohir.A05G312600' => 'ghi', 'Gohir.A05G354900' => 'ghi', 'Gohir.A07G037200' => 'ghi', 'Gohir.A09G030000' => 'ghi', 'Gohir.A12G145200' => 'ghi', 'Gohir.D01G151500' => 'ghi', 'Gohir.D04G058300' => 'ghi', 'Gohir.D05G314100' => 'ghi', 'Gohir.D07G041400' => 'ghi', 'Gohir.D09G029700' => 'ghi', 'Gohir.D12G149700' => 'ghi', 'Gorai.001G043800' => 'gra', 'Gorai.002G187800' => 'gra', 'Gorai.006G034700' => 'gra', 'Gorai.008G161200' => 'gra', 'Gorai.009G335700' => 'gra', 'Gorai.012G065000' => 'gra', 'GSVIVG01000535001' => 'vvi', 'GSVIVG01015572001' => 'vvi', 'GSVIVG01032386001' => 'vvi', 'HanXRQChr05g0138531' => 'han', 'HanXRQChr06g0174391' => 'han', 'HanXRQChr07g0199021' => 'han', 'HanXRQChr08g0208211' => 'han', 'HanXRQChr09g0255471' => 'han', 'HanXRQChr10g0315791' => 'han', 'HanXRQChr12g0371991' => 'han', 'HanXRQChr15g0475251' => 'han', 'HanXRQChr17g0540001' => 'han', 'HanXRQChr17g0548631' => 'han', 'HanXRQChr17g0569561' => 'han', 'Haze_12256' => 'cav', 'Haze_14756' => 'cav', 'Haze_25528' => 'cav', 'Hma1.2p1_0079F.1_g041020' => 'hma', 'Hma1.2p1_0818F.1_g223260' => 'hma', 'Hma1.2p1_1747F.1_g300530' => 'hma', 'HPP92_004607' => 'vpl', 'HPP92_004608' => 'vpl', 'HPP92_006181' => 'vpl', 'HPP92_012192' => 'vpl', 'HPP92_015680' => 'vpl', 'HPP92_020249' => 'vpl', 'HPP92_021376' => 'vpl', 'HPP92_024275' => 'vpl', 'Hund06031' => 'sun', 'Hund25391' => 'sun', 'Lalb_Chr07g0185371' => 'lal', 'Lalb_Chr07g0185381' => 'lal', 'Lalb_Chr12g0204011' => 'lal', 'Lalb_Chr13g0301671' => 'lal', 'Lalb_Chr14g0362851' => 'lal', 'Lalb_Chr24g0403581' => 'lal', 'Lj1g0000233' => 'lja', 'Lj2g0018120' => 'lja', 'Lj3C621T0' => 'lonja', 'Lj3P1059T14' => 'lonja', 'Lj3P611T9' => 'lonja', 'Lj3P614T13' => 'lonja', 'Lj3P615T5' => 'lonja', 'Lj4g0012315' => 'lja', 'Lj4g0026182' => 'lja', 'Lj6P813T16' => 'lonja', 'Lj7C427T7' => 'lonja', 'Lj7C427T8' => 'lonja', 'Lj7P600T41' => 'lonja', 'Lju41C42G17' => 'lonja', 'Lsat_1_v5_gn_0_47300' => 'lsa', 'Lsat_1_v5_gn_2_91280' => 'lsa', 'Lsat_1_v5_gn_3_30561' => 'lsa', 'Lsat_1_v5_gn_4_184321' => 'lsa', 'Lsat_1_v5_gn_4_4041' => 'lsa', 'Lsat_1_v5_gn_5_92000' => 'lsa', 'Lsat_1_v5_gn_8_152940' => 'lsa', 'Lsat_1_v5_gn_8_62401' => 'lsa', 'Manes.06G055900' => 'mes', 'Manes.12G022200' => 'mes', 'Manes.13G023300' => 'mes', 'Manes.14G115000' => 'mes', 'Manes.15G151700' => 'mes', 'Manes.17G111300' => 'mes', 'Mapoly0226s0009' => 'mpo', 'MBI02_g25363_MAGBIO' => 'mbi', 'MBI06_g00027_MAGBIO' => 'mbi', 'MBI10_g13034_MAGBIO' => 'mbi', 'MD09G1023400' => 'mdo', 'MD13G1100100' => 'mdo', 'MD15G1169200' => 'mdo', 'MD16G1101100' => 'mdo', 'MD17G1022900' => 'mdo', 'Medtr3g096150' => 'mtr', 'Medtr4g115070' => 'mtr', 'Medtr7g033325' => 'mtr', 'Medtr8g089840' => 'mtr', 'MELO3C010319.2' => 'cme', 'MELO3C011944.2' => 'cme', 'MELO3C021589.2' => 'cme', 'Migut.E00207' => 'egut', 'Migut.H00067' => 'egut', 'Migut.K00433' => 'egut', 'Migut.K00606' => 'egut', 'Migut.K01410' => 'egut', 'MSTRG.13347' => 'ama', 'MSTRG.24045' => 'ama', 'MSTRG.2428' => 'ama', 'MSTRG.26410' => 'ama', 'MSTRG.3139' => 'ama', 'MSTRG.3286' => 'ama', 'MSTRG.563' => 'ama', 'MSTRG.7941' => 'ama', 'Nitab4.5_0000028g0060' => 'nta', 'Nitab4.5_0000065g0260' => 'nta', 'Nitab4.5_0000112g0060' => 'nta', 'Nitab4.5_0000489g0120' => 'nta', 'Nitab4.5_0001776g0050' => 'nta', 'Nitab4.5_0001854g0010' => 'nta', 'Nitab4.5_0001860g0020' => 'nta', 'Nitab4.5_0004352g0010' => 'nta', 'Nitab4.5_0008716g0020' => 'nta', 'Nitab4.5_0008922g0010' => 'nta', 'Nn3g16693' => 'nnu', 'Nn4g22596' => 'nnu', 'Nn7g37639' => 'nnu', 'Oeu001701.1' => 'oeu', 'Oeu018149.1' => 'oeu', 'Oeu026220.1' => 'oeu', 'Oeu038635.1' => 'oeu', 'Oeu049176.1' => 'oeu', 'Oeu056706.1' => 'oeu', 'Oeu056937.1' => 'oeu', 'Oeu057540.1' => 'oeu', 'Os02g0594900' => 'osa', 'Os02g0595100' => 'osa', 'Os04g0477500' => 'osa', 'Os12g0611900' => 'osa', 'Peaxi162Scf00076g00020' => 'pax', 'Peaxi162Scf00128g00217' => 'pax', 'Peaxi162Scf00129g01640' => 'pax', 'Peaxi162Scf00669g00007' => 'pax', 'Peaxi162Scf00700g00421' => 'pax', 'Peaxi162Scf00801g00038' => 'pax', 'Peaxi162Scf00891g00025' => 'pax', 'PGR083G0909' => 'pgr', 'PGR119G1005' => 'pgr', 'PGR142G2236' => 'pgr', 'PGR142G3388' => 'pgr', 'PGSC0003DMG400004514' => 'stu', 'PGSC0003DMG400012635' => 'stu', 'PGSC0003DMG400015730' => 'stu', 'PGSC0003DMG400018611' => 'stu', 'PGSC0003DMG400030897' => 'stu', 'Phvul.001G254800' => 'pvu', 'Phvul.002G260100' => 'pvu', 'Phvul.003G167600' => 'pvu', 'Phvul.004G005100' => 'pvu', 'Potri.001G343600' => 'ptr', 'Potri.006G066700' => 'ptr', 'Potri.008G186000' => 'ptr', 'Potri.010G046900' => 'ptr', 'Potri.018G127900' => 'ptr', 'Pp3c20_17750' => 'ppa', 'Pp3c24_4380' => 'ppa', 'Prupe.1G245800' => 'ppe', 'Prupe.3G293400' => 'ppe', 'Prupe.7G247400' => 'ppe', 'Psat0s145g0120' => 'psa', 'Psat0s595g0040' => 'psa', 'Psat0s595g0120' => 'psa', 'Psat3g175040' => 'psa', 'Psat7g058120' => 'psa', 'PSO017G0428' => 'pso', 'PSO063G7510' => 'pso', 'PSO067G0046' => 'pso', 'PSO478G1073' => 'pso', 'PSO675G3677' => 'pso', 'PSO675G6558' => 'pso', 'PSO675G7520' => 'pso', 'PSO675G8959' => 'pso', 'QL02p074089' => 'qlo', 'QL02p089614' => 'qlo', 'QL03p057736' => 'qlo', 'RcHm_v2.0_Chr1g0364131' => 'rch', 'RcHm_v2.0_Chr2g0087801' => 'rch', 'RcHm_v2.0_Chr2g0087821' => 'rch', 'RcHm_v2.0_Chr2g0173231' => 'rch', 'RcHm_v2.0_Chr4g0433111' => 'rch', 'Rhsim03G0250300' => 'rsi', 'Rhsim08G0048400' => 'rsi', 'Rhsim10G0014800' => 'rsi', 'Rhsim12G0040100' => 'rsi', 'Rhsim12G0109700' => 'rsi', 'Sabra06G0049600' => 'sbr', 'Sabra08G0141000' => 'sbr', 'Sabra10G0021400' => 'sbr', 'Sabra16G0222900' => 'sbr', 'Sabra18G0108600' => 'sbr', 'SalBow1G0433' => 'sbo', 'SalBow1G2038' => 'sbo', 'SalBow1G5003' => 'sbo', 'SalBow7G1197' => 'sbo', 'SalBow8G3506' => 'sbo', 'Sc03g0007300' => 'sci', 'Sc11g0000950' => 'sci', 'Sc14g0008750' => 'sci', 'Sc18g0000420' => 'sci', 'Sed0006754' => 'sed', 'Sed0008741' => 'sed', 'Sed0017172' => 'sed', 'Sed0018925' => 'sed', 'Sed0023326' => 'sed', 'Sed0025909' => 'sed', 'SEGI_05333' => 'sgi', 'SEGI_10362' => 'sgi', 'SEGI_13380' => 'sgi', 'SEGI_24306' => 'sgi', 'SEGI_29077' => 'sgi', 'SEGI_29095' => 'sgi', 'SEGI_36534' => 'sgi', 'SEGI_37506' => 'sgi', 'SEGI_38321' => 'sgi', 'SGA_v2.0_scaffold307G48031' => 'sas', 'SGA_v2.0_scaffold47G17507' => 'sas', 'SGA_v2.0_scaffold63G21736' => 'sas', 'SGA_v2.0_scaffold87G27070' => 'sas', 'SHI17794' => 'shi', 'SHI28851' => 'shi', 'SMO165G0155' => 'smo', 'SMO340G0217' => 'smo', 'SMO367G1210' => 'smo', 'Solyc02g093430.3' => 'sly', 'Solyc05g013580.4' => 'sly', 'Solyc07g008030.3' => 'sly', 'Solyc12g035470.2' => 'sly', 'Sopen02g038020' => 'spe', 'Sopen05g008490' => 'spe', 'Sopen07g003910' => 'spe', 'Sopen12g015240' => 'spe', 'Sp1g11550' => 'spa', 'Sp2g16710' => 'spa', 'Sp3g00430' => 'spa', 'Sp3g26780' => 'spa', 'Sp5g22900' => 'spa', 'Sp6g29530' => 'spa', 'TAR371G0794' => 'tar', 'TAR374G0164' => 'tar', 'TAR622G0165' => 'tar', 'TAR626G0929' => 'tar', 'TAR629G2155' => 'tar', 'THA.LOC104805282' => 'tha', 'THA.LOC104805363' => 'tha', 'THA.LOC104808968' => 'tha', 'THA.LOC104821093' => 'tha', 'THA.LOC104823953' => 'tha', 'THA.LOC104825562' => 'tha', 'THA.LOC104825665' => 'tha', 'Thecc.02G261400' => 'tca', 'Thecc.04G019200' => 'tca', 'Thecc.09G130400' => 'tca', 'Thhalv10004374m.g' => 'esa', 'Thhalv10007850m.g' => 'esa', 'Thhalv10013782m.g' => 'esa', 'Thhalv10018686m.g' => 'esa', 'Thhalv10020899m.g' => 'esa', 'Thhalv10022755m.g' => 'esa', 'TPR.G23851' => 'tpr', 'TPR.G26500' => 'tpr', 'TPR.G27267' => 'tpr', 'TPR.G32001' => 'tpr', 'TPR.G6251' => 'tpr', 'TPR.G8167' => 'tpr', 'TWI12G1330' => 'twi', 'TWI18G1239' => 'twi', 'TWI34G0979' => 'twi', 'TWI36G0670' => 'twi', 'TWI36G0707' => 'twi', 'TWI56G0233' => 'twi', 'TWI75G1809' => 'twi', 'unitig_21.g20874' => 'ugi', 'unitig_26.g10343' => 'ugi', 'unitig_46.g18392' => 'ugi', 'unitig_52.g17178' => 'ugi', 'unitig_8.g2934' => 'ugi', 'vmacro01122' => 'vma', 'vmacro05875' => 'vma', 'vmacro06147' => 'vma', 'vmacro16191' => 'vma', 'vmacro18293' => 'vma', 'VMungo0251G3707' => 'vmu', 'VMungo0464G1521' => 'vmu', 'VMungo1215G0205' => 'vmu', 'VMungo1383G2484' => 'vmu', 'Zm00001eb079610' => 'zma', 'Zm00001eb135990' => 'zma', 'Zm00001eb183710' => 'zma', 'Zm00001eb246020' => 'zma' ), 'gf_id' => 'HOM05D001124', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001124' ), 'data_identifier' => 'HOM05D001124', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001124', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '548', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02520' => 'bna', 'A03p06630' => 'bna', 'A05p44460' => 'bna', 'A06p08710' => 'bna', 'A06p41090' => 'bna', 'A07p32320' => 'bna', 'A08p32520' => 'bna', 'A09p10360' => 'bna', 'A10p24080' => 'bna', 'Aa31LG11G15250' => 'aar', 'Aa31LG1G1800' => 'aar', 'Aa31LG2G5120' => 'aar', 'Aa31LG2G6070' => 'aar', 'Aa31LG5G10770' => 'aar', 'Aa31sc61G90' => 'aar', 'Actinidia01352' => 'ach', 'Actinidia05983' => 'ach', 'Actinidia08133' => 'ach', 'Actinidia15101' => 'ach', 'Actinidia26379' => 'ach', 'Actinidia35778' => 'ach', 'Actinidia36123' => 'ach', 'Actinidia37436' => 'ach', 'Actinidia38730' => 'ach', 'Ah.02g128210' => 'amhyb', 'Ah.03g132990' => 'amhyb', 'Ah.14g079410' => 'amhyb', 'AL1G24640' => 'aly', 'AL2G26680' => 'aly', 'AL3G10530' => 'aly', 'AL3G45230' => 'aly', 'AL5G15230' => 'aly', 'AL5G16960' => 'aly', 'AL6G25210' => 'aly', 'Aqoxy2G00441' => 'aox', 'Aqoxy3G01236' => 'aox', 'Aqoxy5G03746' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3RQ047' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C7GMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9C8JER' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MBL6KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YXCZ83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZANX40' => 'arhy', 'AT1G12990' => 'ath', 'AT1G67880' => 'ath', 'AT2G13290' => 'ath', 'AT3G01620' => 'ath', 'AT3G26445' => 'ath', 'AT3G27540' => 'ath', 'AT5G14480' => 'ath', 'ATR0824G026' => 'atr', 'ATR1098G019' => 'atr', 'Atru.chr11.2145' => 'acertr', 'Atru.chr2.3636' => 'acertr', 'Atru.chr2.3644' => 'acertr', 'Atru.chr6.2422' => 'acertr', 'Atru.chr7.1112' => 'acertr', 'AUR62005469' => 'cqu', 'AUR62011166' => 'cqu', 'AUR62013319' => 'cqu', 'AUR62024273' => 'cqu', 'AUR62028420' => 'cqu', 'AUR62041942' => 'cqu', 'BcaB01g04969' => 'bca', 'BcaB01g06371' => 'bca', 'BcaB02g11494' => 'bca', 'BcaB03g15382' => 'bca', 'BcaB08g36994' => 'bca', 'BcaC03g13477' => 'bca', 'BcaC03g13478' => 'bca', 'BcaC03g13480' => 'bca', 'BcaC03g13481' => 'bca', 'BcaC03g13486' => 'bca', 'BcaC04g19031' => 'bca', 'BcaC04g23085' => 'bca', 'BcaC05g25094' => 'bca', 'BcaC05g25096' => 'bca', 'BcaC05g25138' => 'bca', 'BcaC05g30416' => 'bca', 'BcaC05g30455' => 'bca', 'BcaC06g30979' => 'bca', 'BcaC06g33805' => 'bca', 'BcaC08g46021' => 'bca', 'BcaNung03154' => 'bca', 'BolC2t06623H' => 'bol', 'BolC2t06632H' => 'bol', 'BolC2t06635H' => 'bol', 'BolC2t06638H' => 'bol', 'BolC3t13266H' => 'bol', 'BolC5t29776H' => 'bol', 'BolC6t38912H' => 'bol', 'BolC7t44183H' => 'bol', 'BolC9t54123H' => 'bol', 'BolC9t59107H' => 'bol', 'BraA02t05221Z' => 'bra', 'BraA03t09996Z' => 'bra', 'BraA05t23210Z' => 'bra', 'BraA06t24068Z' => 'bra', 'BraA06t27032Z' => 'bra', 'BraA08t35176Z' => 'bra', 'BraA09t36680Z' => 'bra', 'BraA10t44471Z' => 'bra', 'C02p06760' => 'bna', 'C02p06890' => 'bna', 'C02p07010' => 'bna', 'C03p07660' => 'bna', 'C05p10300' => 'bna', 'C06p38150' => 'bna', 'C07p36650' => 'bna', 'C08p15770' => 'bna', 'C09p12300' => 'bna', 'C09p62700' => 'bna', 'C09p75040' => 'bna', 'CAN.G13.1' => 'can', 'CAN.G138.4' => 'can', 'CAN.G44.6' => 'can', 'CAN.G473.19' => 'can', 'CANSAT01G0835' => 'cansat', 'CANSAT11G0246' => 'cansat', 'CANSAT11G1766' => 'cansat', 'CANSAT64G1954' => 'cansat', 'CARHR013330' => 'chi', 'CARHR060530' => 'chi', 'CARHR075300' => 'chi', 'CARHR105120' => 'chi', 'CARHR148910' => 'chi', 'CARHR198830' => 'chi', 'Carub.0001s1275' => 'cru', 'Carub.0002s1437' => 'cru', 'Carub.0003s0044' => 'cru', 'Carub.0003s2787' => 'cru', 'Carub.0005s0597' => 'cru', 'Carub.0006s1266' => 'cru', 'Ca_06935_v3' => 'car', 'Ca_13559_v3' => 'car', 'Ca_16941_v3' => 'car', 'Ca_16960_v3' => 'car', 'Ca_17775_v3' => 'car', 'Ca_30464_v3' => 'car', 'Cc06_g08160' => 'ccan', 'Cc07_g01520' => 'ccan', 'Cc11_g15810' => 'ccan', 'CDE02G2840' => 'cde', 'CDE03G0093' => 'cde', 'CDE04G2127' => 'cde', 'CDE07G1857' => 'cde', 'CDE09G1246' => 'cde', 'Cfa003412' => 'cfa', 'Cfa007341' => 'cfa', 'Cfa009220' => 'cfa', 'Ciclev10008737m.g' => 'ccl', 'Ciclev10015565m.g' => 'ccl', 'Ciclev10031761m.g' => 'ccl', 'CiPaw.03G045300' => 'cil', 'CiPaw.03G247200' => 'cil', 'CiPaw.04G029500' => 'cil', 'CiPaw.04G174000' => 'cil', 'CiPaw.05G181200' => 'cil', 'CiPaw.06G067100' => 'cil', 'ClCG05G025800' => 'cla', 'ClCG06G011400' => 'cla', 'ClCG09G019360' => 'cla', 'COL.COLO4_04827' => 'col', 'COL.COLO4_29170' => 'col', 'COL.COLO4_35131' => 'col', 'COL.COLO4_35132' => 'col', 'Cpa.g.sc33.32' => 'cpa', 'Cpa.g.sc46.29' => 'cpa', 'Cpa.g.sc796.1' => 'cpa', 'CsaV3_1G030420' => 'csa', 'CsaV3_5G027050' => 'csa', 'CsaV3_5G031040' => 'csa', 'CsaV3_UNG023130' => 'csa', 'CSS0007726' => 'camsi', 'CSS0016433' => 'camsi', 'CSS0017656' => 'camsi', 'CSS0025364' => 'camsi', 'CSS0027582' => 'camsi', 'CSS0047288' => 'camsi', 'CSS0049950' => 'camsi', 'DCAR_003843' => 'dca', 'DCAR_007052' => 'dca', 'DCAR_020884' => 'dca', 'DCAR_021730' => 'dca', 'DCAR_024423' => 'dca', 'DCAR_026509' => 'dca', 'DCAR_031158' => 'dca', 'Dinv14728' => 'din', 'Dinv15219' => 'din', 'Dinv25728' => 'din', 'Dinv33428' => 'din', 'Dinv36489' => 'din', 'Dinv41486' => 'din', 'Duzib147G0469' => 'dzi', 'Duzib168G0060' => 'dzi', 'Duzib187G1215' => 'dzi', 'Duzib248G0692' => 'dzi', 'Duzib251G0767' => 'dzi', 'Duzib264G0446' => 'dzi', 'Duzib268G0691' => 'dzi', 'ECA232G4767' => 'eca', 'ECA233G2838' => 'eca', 'ECA234G0391' => 'eca', 'ECA234G0857' => 'eca', 'ECA236G1593' => 'eca', 'ECA238G0565' => 'eca', 'ECA246G1027' => 'eca', 'ECA246G3223' => 'eca', 'ECA246G3470' => 'eca', 'EL10Ac6g13829' => 'bvu', 'EL10Ac6g14093' => 'bvu', 'EL10Ac8g18707' => 'bvu', 'Eucgr.C01369' => 'egr', 'Eucgr.H02492' => 'egr', 'Eucgr.I01733' => 'egr', 'Eucgr.J02255' => 'egr', 'Eucgr.J02257' => 'egr', 'Eucgr.J02258' => 'egr', 'FAN02G1601' => 'fan', 'FAN03G1586' => 'fan', 'FAN03G2986' => 'fan', 'FAN05G4837' => 'fan', 'FAN06G0146' => 'fan', 'FAN07G0858' => 'fan', 'FAN09G3179' => 'fan', 'FAN10G0669' => 'fan', 'FAN12G2358' => 'fan', 'FAN14G4198' => 'fan', 'FAN14G5112' => 'fan', 'FAN17G0342' => 'fan', 'FAN19G0342' => 'fan', 'FAN19G0962' => 'fan', 'FAN19G1101' => 'fan', 'FAN19G1872' => 'fan', 'FAN22G0356' => 'fan', 'FAN23G0744' => 'fan', 'FAN23G1914' => 'fan', 'FAN26G0032' => 'fan', 'FAN28G0625' => 'fan', 'FvH4_1g02710' => 'fve', 'FvH4_1g02720' => 'fve', 'FvH4_4g25670' => 'fve', 'FvH4_6g51700' => 'fve', 'FvH4_7g20170' => 'fve', 'Glyma.05G175000' => 'gma', 'Glyma.08G132300' => 'gma', 'Glyma.11G243000' => 'gma', 'Glyma.13G158900' => 'gma', 'Glyma.17G112400' => 'gma', 'Glyma.18G014100' => 'gma', 'Glyma.19G003100' => 'gma', 'Glyma.19G056500' => 'gma', 'Gohir.A01G158900' => 'ghi', 'Gohir.A05G312600' => 'ghi', 'Gohir.A05G354900' => 'ghi', 'Gohir.A07G037200' => 'ghi', 'Gohir.A09G030000' => 'ghi', 'Gohir.A12G145200' => 'ghi', 'Gohir.D01G151500' => 'ghi', 'Gohir.D04G058300' => 'ghi', 'Gohir.D05G314100' => 'ghi', 'Gohir.D07G041400' => 'ghi', 'Gohir.D09G029700' => 'ghi', 'Gohir.D12G149700' => 'ghi', 'Gorai.001G043800' => 'gra', 'Gorai.002G187800' => 'gra', 'Gorai.006G034700' => 'gra', 'Gorai.008G161200' => 'gra', 'Gorai.009G335700' => 'gra', 'Gorai.012G065000' => 'gra', 'GSVIVG01000535001' => 'vvi', 'GSVIVG01015572001' => 'vvi', 'GSVIVG01032386001' => 'vvi', 'HanXRQChr05g0138531' => 'han', 'HanXRQChr06g0174391' => 'han', 'HanXRQChr07g0199021' => 'han', 'HanXRQChr08g0208211' => 'han', 'HanXRQChr09g0255471' => 'han', 'HanXRQChr10g0315791' => 'han', 'HanXRQChr12g0371991' => 'han', 'HanXRQChr15g0475251' => 'han', 'HanXRQChr17g0540001' => 'han', 'HanXRQChr17g0548631' => 'han', 'HanXRQChr17g0569561' => 'han', 'Haze_12256' => 'cav', 'Haze_14756' => 'cav', 'Haze_25528' => 'cav', 'Hma1.2p1_0079F.1_g041020' => 'hma', 'Hma1.2p1_0818F.1_g223260' => 'hma', 'Hma1.2p1_1747F.1_g300530' => 'hma', 'HPP92_004607' => 'vpl', 'HPP92_004608' => 'vpl', 'HPP92_006181' => 'vpl', 'HPP92_012192' => 'vpl', 'HPP92_015680' => 'vpl', 'HPP92_020249' => 'vpl', 'HPP92_021376' => 'vpl', 'HPP92_024275' => 'vpl', 'Hund06031' => 'sun', 'Hund25391' => 'sun', 'Lalb_Chr07g0185371' => 'lal', 'Lalb_Chr07g0185381' => 'lal', 'Lalb_Chr12g0204011' => 'lal', 'Lalb_Chr13g0301671' => 'lal', 'Lalb_Chr14g0362851' => 'lal', 'Lalb_Chr24g0403581' => 'lal', 'Lj1g0000233' => 'lja', 'Lj2g0018120' => 'lja', 'Lj3C621T0' => 'lonja', 'Lj3P1059T14' => 'lonja', 'Lj3P611T9' => 'lonja', 'Lj3P614T13' => 'lonja', 'Lj3P615T5' => 'lonja', 'Lj4g0012315' => 'lja', 'Lj4g0026182' => 'lja', 'Lj6P813T16' => 'lonja', 'Lj7C427T7' => 'lonja', 'Lj7C427T8' => 'lonja', 'Lj7P600T41' => 'lonja', 'Lju41C42G17' => 'lonja', 'Lsat_1_v5_gn_0_47300' => 'lsa', 'Lsat_1_v5_gn_2_91280' => 'lsa', 'Lsat_1_v5_gn_3_30561' => 'lsa', 'Lsat_1_v5_gn_4_184321' => 'lsa', 'Lsat_1_v5_gn_4_4041' => 'lsa', 'Lsat_1_v5_gn_5_92000' => 'lsa', 'Lsat_1_v5_gn_8_152940' => 'lsa', 'Lsat_1_v5_gn_8_62401' => 'lsa', 'Manes.06G055900' => 'mes', 'Manes.12G022200' => 'mes', 'Manes.13G023300' => 'mes', 'Manes.14G115000' => 'mes', 'Manes.15G151700' => 'mes', 'Manes.17G111300' => 'mes', 'Mapoly0226s0009' => 'mpo', 'MBI02_g25363_MAGBIO' => 'mbi', 'MBI06_g00027_MAGBIO' => 'mbi', 'MBI10_g13034_MAGBIO' => 'mbi', 'MD09G1023400' => 'mdo', 'MD13G1100100' => 'mdo', 'MD15G1169200' => 'mdo', 'MD16G1101100' => 'mdo', 'MD17G1022900' => 'mdo', 'Medtr3g096150' => 'mtr', 'Medtr4g115070' => 'mtr', 'Medtr7g033325' => 'mtr', 'Medtr8g089840' => 'mtr', 'MELO3C010319.2' => 'cme', 'MELO3C011944.2' => 'cme', 'MELO3C021589.2' => 'cme', 'Migut.E00207' => 'egut', 'Migut.H00067' => 'egut', 'Migut.K00433' => 'egut', 'Migut.K00606' => 'egut', 'Migut.K01410' => 'egut', 'MSTRG.13347' => 'ama', 'MSTRG.24045' => 'ama', 'MSTRG.2428' => 'ama', 'MSTRG.26410' => 'ama', 'MSTRG.3139' => 'ama', 'MSTRG.3286' => 'ama', 'MSTRG.563' => 'ama', 'MSTRG.7941' => 'ama', 'Nitab4.5_0000028g0060' => 'nta', 'Nitab4.5_0000065g0260' => 'nta', 'Nitab4.5_0000112g0060' => 'nta', 'Nitab4.5_0000489g0120' => 'nta', 'Nitab4.5_0001776g0050' => 'nta', 'Nitab4.5_0001854g0010' => 'nta', 'Nitab4.5_0001860g0020' => 'nta', 'Nitab4.5_0004352g0010' => 'nta', 'Nitab4.5_0008716g0020' => 'nta', 'Nitab4.5_0008922g0010' => 'nta', 'Nn3g16693' => 'nnu', 'Nn4g22596' => 'nnu', 'Nn7g37639' => 'nnu', 'Oeu001701.1' => 'oeu', 'Oeu018149.1' => 'oeu', 'Oeu026220.1' => 'oeu', 'Oeu038635.1' => 'oeu', 'Oeu049176.1' => 'oeu', 'Oeu056706.1' => 'oeu', 'Oeu056937.1' => 'oeu', 'Oeu057540.1' => 'oeu', 'Os02g0594900' => 'osa', 'Os02g0595100' => 'osa', 'Os04g0477500' => 'osa', 'Os12g0611900' => 'osa', 'Peaxi162Scf00076g00020' => 'pax', 'Peaxi162Scf00128g00217' => 'pax', 'Peaxi162Scf00129g01640' => 'pax', 'Peaxi162Scf00669g00007' => 'pax', 'Peaxi162Scf00700g00421' => 'pax', 'Peaxi162Scf00801g00038' => 'pax', 'Peaxi162Scf00891g00025' => 'pax', 'PGR083G0909' => 'pgr', 'PGR119G1005' => 'pgr', 'PGR142G2236' => 'pgr', 'PGR142G3388' => 'pgr', 'PGSC0003DMG400004514' => 'stu', 'PGSC0003DMG400012635' => 'stu', 'PGSC0003DMG400015730' => 'stu', 'PGSC0003DMG400018611' => 'stu', 'PGSC0003DMG400030897' => 'stu', 'Phvul.001G254800' => 'pvu', 'Phvul.002G260100' => 'pvu', 'Phvul.003G167600' => 'pvu', 'Phvul.004G005100' => 'pvu', 'Potri.001G343600' => 'ptr', 'Potri.006G066700' => 'ptr', 'Potri.008G186000' => 'ptr', 'Potri.010G046900' => 'ptr', 'Potri.018G127900' => 'ptr', 'Pp3c20_17750' => 'ppa', 'Pp3c24_4380' => 'ppa', 'Prupe.1G245800' => 'ppe', 'Prupe.3G293400' => 'ppe', 'Prupe.7G247400' => 'ppe', 'Psat0s145g0120' => 'psa', 'Psat0s595g0040' => 'psa', 'Psat0s595g0120' => 'psa', 'Psat3g175040' => 'psa', 'Psat7g058120' => 'psa', 'PSO017G0428' => 'pso', 'PSO063G7510' => 'pso', 'PSO067G0046' => 'pso', 'PSO478G1073' => 'pso', 'PSO675G3677' => 'pso', 'PSO675G6558' => 'pso', 'PSO675G7520' => 'pso', 'PSO675G8959' => 'pso', 'QL02p074089' => 'qlo', 'QL02p089614' => 'qlo', 'QL03p057736' => 'qlo', 'RcHm_v2.0_Chr1g0364131' => 'rch', 'RcHm_v2.0_Chr2g0087801' => 'rch', 'RcHm_v2.0_Chr2g0087821' => 'rch', 'RcHm_v2.0_Chr2g0173231' => 'rch', 'RcHm_v2.0_Chr4g0433111' => 'rch', 'Rhsim03G0250300' => 'rsi', 'Rhsim08G0048400' => 'rsi', 'Rhsim10G0014800' => 'rsi', 'Rhsim12G0040100' => 'rsi', 'Rhsim12G0109700' => 'rsi', 'Sabra06G0049600' => 'sbr', 'Sabra08G0141000' => 'sbr', 'Sabra10G0021400' => 'sbr', 'Sabra16G0222900' => 'sbr', 'Sabra18G0108600' => 'sbr', 'SalBow1G0433' => 'sbo', 'SalBow1G2038' => 'sbo', 'SalBow1G5003' => 'sbo', 'SalBow7G1197' => 'sbo', 'SalBow8G3506' => 'sbo', 'Sc03g0007300' => 'sci', 'Sc11g0000950' => 'sci', 'Sc14g0008750' => 'sci', 'Sc18g0000420' => 'sci', 'Sed0006754' => 'sed', 'Sed0008741' => 'sed', 'Sed0017172' => 'sed', 'Sed0018925' => 'sed', 'Sed0023326' => 'sed', 'Sed0025909' => 'sed', 'SEGI_05333' => 'sgi', 'SEGI_10362' => 'sgi', 'SEGI_13380' => 'sgi', 'SEGI_24306' => 'sgi', 'SEGI_29077' => 'sgi', 'SEGI_29095' => 'sgi', 'SEGI_36534' => 'sgi', 'SEGI_37506' => 'sgi', 'SEGI_38321' => 'sgi', 'SGA_v2.0_scaffold307G48031' => 'sas', 'SGA_v2.0_scaffold47G17507' => 'sas', 'SGA_v2.0_scaffold63G21736' => 'sas', 'SGA_v2.0_scaffold87G27070' => 'sas', 'SHI17794' => 'shi', 'SHI28851' => 'shi', 'SMO165G0155' => 'smo', 'SMO340G0217' => 'smo', 'SMO367G1210' => 'smo', 'Solyc02g093430.3' => 'sly', 'Solyc05g013580.4' => 'sly', 'Solyc07g008030.3' => 'sly', 'Solyc12g035470.2' => 'sly', 'Sopen02g038020' => 'spe', 'Sopen05g008490' => 'spe', 'Sopen07g003910' => 'spe', 'Sopen12g015240' => 'spe', 'Sp1g11550' => 'spa', 'Sp2g16710' => 'spa', 'Sp3g00430' => 'spa', 'Sp3g26780' => 'spa', 'Sp5g22900' => 'spa', 'Sp6g29530' => 'spa', 'TAR371G0794' => 'tar', 'TAR374G0164' => 'tar', 'TAR622G0165' => 'tar', 'TAR626G0929' => 'tar', 'TAR629G2155' => 'tar', 'THA.LOC104805282' => 'tha', 'THA.LOC104805363' => 'tha', 'THA.LOC104808968' => 'tha', 'THA.LOC104821093' => 'tha', 'THA.LOC104823953' => 'tha', 'THA.LOC104825562' => 'tha', 'THA.LOC104825665' => 'tha', 'Thecc.02G261400' => 'tca', 'Thecc.04G019200' => 'tca', 'Thecc.09G130400' => 'tca', 'Thhalv10004374m.g' => 'esa', 'Thhalv10007850m.g' => 'esa', 'Thhalv10013782m.g' => 'esa', 'Thhalv10018686m.g' => 'esa', 'Thhalv10020899m.g' => 'esa', 'Thhalv10022755m.g' => 'esa', 'TPR.G23851' => 'tpr', 'TPR.G26500' => 'tpr', 'TPR.G27267' => 'tpr', 'TPR.G32001' => 'tpr', 'TPR.G6251' => 'tpr', 'TPR.G8167' => 'tpr', 'TWI12G1330' => 'twi', 'TWI18G1239' => 'twi', 'TWI34G0979' => 'twi', 'TWI36G0670' => 'twi', 'TWI36G0707' => 'twi', 'TWI56G0233' => 'twi', 'TWI75G1809' => 'twi', 'unitig_21.g20874' => 'ugi', 'unitig_26.g10343' => 'ugi', 'unitig_46.g18392' => 'ugi', 'unitig_52.g17178' => 'ugi', 'unitig_8.g2934' => 'ugi', 'vmacro01122' => 'vma', 'vmacro05875' => 'vma', 'vmacro06147' => 'vma', 'vmacro16191' => 'vma', 'vmacro18293' => 'vma', 'VMungo0251G3707' => 'vmu', 'VMungo0464G1521' => 'vmu', 'VMungo1215G0205' => 'vmu', 'VMungo1383G2484' => 'vmu', 'Zm00001eb079610' => 'zma', 'Zm00001eb135990' => 'zma', 'Zm00001eb183710' => 'zma', 'Zm00001eb246020' => 'zma' ) $gf_id = 'HOM05D001124' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001124' ) $data_identifier = 'HOM05D001124' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 6, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 7, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 21, 'bol' => (int) 10, 'bra' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 6, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 9, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 21, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 8, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 10, 'lsa' => (int) 8, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 8, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 9, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb246020' $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' => 'HOM05D001124', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '548', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02520' => 'bna', 'A03p06630' => 'bna', 'A05p44460' => 'bna', 'A06p08710' => 'bna', 'A06p41090' => 'bna', 'A07p32320' => 'bna', 'A08p32520' => 'bna', 'A09p10360' => 'bna', 'A10p24080' => 'bna', 'Aa31LG11G15250' => 'aar', 'Aa31LG1G1800' => 'aar', 'Aa31LG2G5120' => 'aar', 'Aa31LG2G6070' => 'aar', 'Aa31LG5G10770' => 'aar', 'Aa31sc61G90' => 'aar', 'Actinidia01352' => 'ach', 'Actinidia05983' => 'ach', 'Actinidia08133' => 'ach', 'Actinidia15101' => 'ach', 'Actinidia26379' => 'ach', 'Actinidia35778' => 'ach', 'Actinidia36123' => 'ach', 'Actinidia37436' => 'ach', 'Actinidia38730' => 'ach', 'Ah.02g128210' => 'amhyb', 'Ah.03g132990' => 'amhyb', 'Ah.14g079410' => 'amhyb', 'AL1G24640' => 'aly', 'AL2G26680' => 'aly', 'AL3G10530' => 'aly', 'AL3G45230' => 'aly', 'AL5G15230' => 'aly', 'AL5G16960' => 'aly', 'AL6G25210' => 'aly', 'Aqoxy2G00441' => 'aox', 'Aqoxy3G01236' => 'aox', 'Aqoxy5G03746' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3RQ047' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C7GMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9C8JER' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MBL6KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YXCZ83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZANX40' => 'arhy', 'AT1G12990' => 'ath', 'AT1G67880' => 'ath', 'AT2G13290' => 'ath', 'AT3G01620' => 'ath', 'AT3G26445' => 'ath', 'AT3G27540' => 'ath', 'AT5G14480' => 'ath', 'ATR0824G026' => 'atr', 'ATR1098G019' => 'atr', 'Atru.chr11.2145' => 'acertr', 'Atru.chr2.3636' => 'acertr', 'Atru.chr2.3644' => 'acertr', 'Atru.chr6.2422' => 'acertr', 'Atru.chr7.1112' => 'acertr', 'AUR62005469' => 'cqu', 'AUR62011166' => 'cqu', 'AUR62013319' => 'cqu', 'AUR62024273' => 'cqu', 'AUR62028420' => 'cqu', 'AUR62041942' => 'cqu', 'BcaB01g04969' => 'bca', 'BcaB01g06371' => 'bca', 'BcaB02g11494' => 'bca', 'BcaB03g15382' => 'bca', 'BcaB08g36994' => 'bca', 'BcaC03g13477' => 'bca', 'BcaC03g13478' => 'bca', 'BcaC03g13480' => 'bca', 'BcaC03g13481' => 'bca', 'BcaC03g13486' => 'bca', 'BcaC04g19031' => 'bca', 'BcaC04g23085' => 'bca', 'BcaC05g25094' => 'bca', 'BcaC05g25096' => 'bca', 'BcaC05g25138' => 'bca', 'BcaC05g30416' => 'bca', 'BcaC05g30455' => 'bca', 'BcaC06g30979' => 'bca', 'BcaC06g33805' => 'bca', 'BcaC08g46021' => 'bca', 'BcaNung03154' => 'bca', 'BolC2t06623H' => 'bol', 'BolC2t06632H' => 'bol', 'BolC2t06635H' => 'bol', 'BolC2t06638H' => 'bol', 'BolC3t13266H' => 'bol', 'BolC5t29776H' => 'bol', 'BolC6t38912H' => 'bol', 'BolC7t44183H' => 'bol', 'BolC9t54123H' => 'bol', 'BolC9t59107H' => 'bol', 'BraA02t05221Z' => 'bra', 'BraA03t09996Z' => 'bra', 'BraA05t23210Z' => 'bra', 'BraA06t24068Z' => 'bra', 'BraA06t27032Z' => 'bra', 'BraA08t35176Z' => 'bra', 'BraA09t36680Z' => 'bra', 'BraA10t44471Z' => 'bra', 'C02p06760' => 'bna', 'C02p06890' => 'bna', 'C02p07010' => 'bna', 'C03p07660' => 'bna', 'C05p10300' => 'bna', 'C06p38150' => 'bna', 'C07p36650' => 'bna', 'C08p15770' => 'bna', 'C09p12300' => 'bna', 'C09p62700' => 'bna', 'C09p75040' => 'bna', 'CAN.G13.1' => 'can', 'CAN.G138.4' => 'can', 'CAN.G44.6' => 'can', 'CAN.G473.19' => 'can', 'CANSAT01G0835' => 'cansat', 'CANSAT11G0246' => 'cansat', 'CANSAT11G1766' => 'cansat', 'CANSAT64G1954' => 'cansat', 'CARHR013330' => 'chi', 'CARHR060530' => 'chi', 'CARHR075300' => 'chi', 'CARHR105120' => 'chi', 'CARHR148910' => 'chi', 'CARHR198830' => 'chi', 'Carub.0001s1275' => 'cru', 'Carub.0002s1437' => 'cru', 'Carub.0003s0044' => 'cru', 'Carub.0003s2787' => 'cru', 'Carub.0005s0597' => 'cru', 'Carub.0006s1266' => 'cru', 'Ca_06935_v3' => 'car', 'Ca_13559_v3' => 'car', 'Ca_16941_v3' => 'car', 'Ca_16960_v3' => 'car', 'Ca_17775_v3' => 'car', 'Ca_30464_v3' => 'car', 'Cc06_g08160' => 'ccan', 'Cc07_g01520' => 'ccan', 'Cc11_g15810' => 'ccan', 'CDE02G2840' => 'cde', 'CDE03G0093' => 'cde', 'CDE04G2127' => 'cde', 'CDE07G1857' => 'cde', 'CDE09G1246' => 'cde', 'Cfa003412' => 'cfa', 'Cfa007341' => 'cfa', 'Cfa009220' => 'cfa', 'Ciclev10008737m.g' => 'ccl', 'Ciclev10015565m.g' => 'ccl', 'Ciclev10031761m.g' => 'ccl', 'CiPaw.03G045300' => 'cil', 'CiPaw.03G247200' => 'cil', 'CiPaw.04G029500' => 'cil', 'CiPaw.04G174000' => 'cil', 'CiPaw.05G181200' => 'cil', 'CiPaw.06G067100' => 'cil', 'ClCG05G025800' => 'cla', 'ClCG06G011400' => 'cla', 'ClCG09G019360' => 'cla', 'COL.COLO4_04827' => 'col', 'COL.COLO4_29170' => 'col', 'COL.COLO4_35131' => 'col', 'COL.COLO4_35132' => 'col', 'Cpa.g.sc33.32' => 'cpa', 'Cpa.g.sc46.29' => 'cpa', 'Cpa.g.sc796.1' => 'cpa', 'CsaV3_1G030420' => 'csa', 'CsaV3_5G027050' => 'csa', 'CsaV3_5G031040' => 'csa', 'CsaV3_UNG023130' => 'csa', 'CSS0007726' => 'camsi', 'CSS0016433' => 'camsi', 'CSS0017656' => 'camsi', 'CSS0025364' => 'camsi', 'CSS0027582' => 'camsi', 'CSS0047288' => 'camsi', 'CSS0049950' => 'camsi', 'DCAR_003843' => 'dca', 'DCAR_007052' => 'dca', 'DCAR_020884' => 'dca', 'DCAR_021730' => 'dca', 'DCAR_024423' => 'dca', 'DCAR_026509' => 'dca', 'DCAR_031158' => 'dca', 'Dinv14728' => 'din', 'Dinv15219' => 'din', 'Dinv25728' => 'din', 'Dinv33428' => 'din', 'Dinv36489' => 'din', 'Dinv41486' => 'din', 'Duzib147G0469' => 'dzi', 'Duzib168G0060' => 'dzi', 'Duzib187G1215' => 'dzi', 'Duzib248G0692' => 'dzi', 'Duzib251G0767' => 'dzi', 'Duzib264G0446' => 'dzi', 'Duzib268G0691' => 'dzi', 'ECA232G4767' => 'eca', 'ECA233G2838' => 'eca', 'ECA234G0391' => 'eca', 'ECA234G0857' => 'eca', 'ECA236G1593' => 'eca', 'ECA238G0565' => 'eca', 'ECA246G1027' => 'eca', 'ECA246G3223' => 'eca', 'ECA246G3470' => 'eca', 'EL10Ac6g13829' => 'bvu', 'EL10Ac6g14093' => 'bvu', 'EL10Ac8g18707' => 'bvu', 'Eucgr.C01369' => 'egr', 'Eucgr.H02492' => 'egr', 'Eucgr.I01733' => 'egr', 'Eucgr.J02255' => 'egr', 'Eucgr.J02257' => 'egr', 'Eucgr.J02258' => 'egr', 'FAN02G1601' => 'fan', 'FAN03G1586' => 'fan', 'FAN03G2986' => 'fan', 'FAN05G4837' => 'fan', 'FAN06G0146' => 'fan', 'FAN07G0858' => 'fan', 'FAN09G3179' => 'fan', 'FAN10G0669' => 'fan', 'FAN12G2358' => 'fan', 'FAN14G4198' => 'fan', 'FAN14G5112' => 'fan', 'FAN17G0342' => 'fan', 'FAN19G0342' => 'fan', 'FAN19G0962' => 'fan', 'FAN19G1101' => 'fan', 'FAN19G1872' => 'fan', 'FAN22G0356' => 'fan', 'FAN23G0744' => 'fan', 'FAN23G1914' => 'fan', 'FAN26G0032' => 'fan', 'FAN28G0625' => 'fan', 'FvH4_1g02710' => 'fve', 'FvH4_1g02720' => 'fve', 'FvH4_4g25670' => 'fve', 'FvH4_6g51700' => 'fve', 'FvH4_7g20170' => 'fve', 'Glyma.05G175000' => 'gma', 'Glyma.08G132300' => 'gma', 'Glyma.11G243000' => 'gma', 'Glyma.13G158900' => 'gma', 'Glyma.17G112400' => 'gma', 'Glyma.18G014100' => 'gma', 'Glyma.19G003100' => 'gma', 'Glyma.19G056500' => 'gma', 'Gohir.A01G158900' => 'ghi', 'Gohir.A05G312600' => 'ghi', 'Gohir.A05G354900' => 'ghi', 'Gohir.A07G037200' => 'ghi', 'Gohir.A09G030000' => 'ghi', 'Gohir.A12G145200' => 'ghi', 'Gohir.D01G151500' => 'ghi', 'Gohir.D04G058300' => 'ghi', 'Gohir.D05G314100' => 'ghi', 'Gohir.D07G041400' => 'ghi', 'Gohir.D09G029700' => 'ghi', 'Gohir.D12G149700' => 'ghi', 'Gorai.001G043800' => 'gra', 'Gorai.002G187800' => 'gra', 'Gorai.006G034700' => 'gra', 'Gorai.008G161200' => 'gra', 'Gorai.009G335700' => 'gra', 'Gorai.012G065000' => 'gra', 'GSVIVG01000535001' => 'vvi', 'GSVIVG01015572001' => 'vvi', 'GSVIVG01032386001' => 'vvi', 'HanXRQChr05g0138531' => 'han', 'HanXRQChr06g0174391' => 'han', 'HanXRQChr07g0199021' => 'han', 'HanXRQChr08g0208211' => 'han', 'HanXRQChr09g0255471' => 'han', 'HanXRQChr10g0315791' => 'han', 'HanXRQChr12g0371991' => 'han', 'HanXRQChr15g0475251' => 'han', 'HanXRQChr17g0540001' => 'han', 'HanXRQChr17g0548631' => 'han', 'HanXRQChr17g0569561' => 'han', 'Haze_12256' => 'cav', 'Haze_14756' => 'cav', 'Haze_25528' => 'cav', 'Hma1.2p1_0079F.1_g041020' => 'hma', 'Hma1.2p1_0818F.1_g223260' => 'hma', 'Hma1.2p1_1747F.1_g300530' => 'hma', 'HPP92_004607' => 'vpl', 'HPP92_004608' => 'vpl', 'HPP92_006181' => 'vpl', 'HPP92_012192' => 'vpl', 'HPP92_015680' => 'vpl', 'HPP92_020249' => 'vpl', 'HPP92_021376' => 'vpl', 'HPP92_024275' => 'vpl', 'Hund06031' => 'sun', 'Hund25391' => 'sun', 'Lalb_Chr07g0185371' => 'lal', 'Lalb_Chr07g0185381' => 'lal', 'Lalb_Chr12g0204011' => 'lal', 'Lalb_Chr13g0301671' => 'lal', 'Lalb_Chr14g0362851' => 'lal', 'Lalb_Chr24g0403581' => 'lal', 'Lj1g0000233' => 'lja', 'Lj2g0018120' => 'lja', 'Lj3C621T0' => 'lonja', 'Lj3P1059T14' => 'lonja', 'Lj3P611T9' => 'lonja', 'Lj3P614T13' => 'lonja', 'Lj3P615T5' => 'lonja', 'Lj4g0012315' => 'lja', 'Lj4g0026182' => 'lja', 'Lj6P813T16' => 'lonja', 'Lj7C427T7' => 'lonja', 'Lj7C427T8' => 'lonja', 'Lj7P600T41' => 'lonja', 'Lju41C42G17' => 'lonja', 'Lsat_1_v5_gn_0_47300' => 'lsa', 'Lsat_1_v5_gn_2_91280' => 'lsa', 'Lsat_1_v5_gn_3_30561' => 'lsa', 'Lsat_1_v5_gn_4_184321' => 'lsa', 'Lsat_1_v5_gn_4_4041' => 'lsa', 'Lsat_1_v5_gn_5_92000' => 'lsa', 'Lsat_1_v5_gn_8_152940' => 'lsa', 'Lsat_1_v5_gn_8_62401' => 'lsa', 'Manes.06G055900' => 'mes', 'Manes.12G022200' => 'mes', 'Manes.13G023300' => 'mes', 'Manes.14G115000' => 'mes', 'Manes.15G151700' => 'mes', 'Manes.17G111300' => 'mes', 'Mapoly0226s0009' => 'mpo', 'MBI02_g25363_MAGBIO' => 'mbi', 'MBI06_g00027_MAGBIO' => 'mbi', 'MBI10_g13034_MAGBIO' => 'mbi', 'MD09G1023400' => 'mdo', 'MD13G1100100' => 'mdo', 'MD15G1169200' => 'mdo', 'MD16G1101100' => 'mdo', 'MD17G1022900' => 'mdo', 'Medtr3g096150' => 'mtr', 'Medtr4g115070' => 'mtr', 'Medtr7g033325' => 'mtr', 'Medtr8g089840' => 'mtr', 'MELO3C010319.2' => 'cme', 'MELO3C011944.2' => 'cme', 'MELO3C021589.2' => 'cme', 'Migut.E00207' => 'egut', 'Migut.H00067' => 'egut', 'Migut.K00433' => 'egut', 'Migut.K00606' => 'egut', 'Migut.K01410' => 'egut', 'MSTRG.13347' => 'ama', 'MSTRG.24045' => 'ama', 'MSTRG.2428' => 'ama', 'MSTRG.26410' => 'ama', 'MSTRG.3139' => 'ama', 'MSTRG.3286' => 'ama', 'MSTRG.563' => 'ama', 'MSTRG.7941' => 'ama', 'Nitab4.5_0000028g0060' => 'nta', 'Nitab4.5_0000065g0260' => 'nta', 'Nitab4.5_0000112g0060' => 'nta', 'Nitab4.5_0000489g0120' => 'nta', 'Nitab4.5_0001776g0050' => 'nta', 'Nitab4.5_0001854g0010' => 'nta', 'Nitab4.5_0001860g0020' => 'nta', 'Nitab4.5_0004352g0010' => 'nta', 'Nitab4.5_0008716g0020' => 'nta', 'Nitab4.5_0008922g0010' => 'nta', 'Nn3g16693' => 'nnu', 'Nn4g22596' => 'nnu', 'Nn7g37639' => 'nnu', 'Oeu001701.1' => 'oeu', 'Oeu018149.1' => 'oeu', 'Oeu026220.1' => 'oeu', 'Oeu038635.1' => 'oeu', 'Oeu049176.1' => 'oeu', 'Oeu056706.1' => 'oeu', 'Oeu056937.1' => 'oeu', 'Oeu057540.1' => 'oeu', 'Os02g0594900' => 'osa', 'Os02g0595100' => 'osa', 'Os04g0477500' => 'osa', 'Os12g0611900' => 'osa', 'Peaxi162Scf00076g00020' => 'pax', 'Peaxi162Scf00128g00217' => 'pax', 'Peaxi162Scf00129g01640' => 'pax', 'Peaxi162Scf00669g00007' => 'pax', 'Peaxi162Scf00700g00421' => 'pax', 'Peaxi162Scf00801g00038' => 'pax', 'Peaxi162Scf00891g00025' => 'pax', 'PGR083G0909' => 'pgr', 'PGR119G1005' => 'pgr', 'PGR142G2236' => 'pgr', 'PGR142G3388' => 'pgr', 'PGSC0003DMG400004514' => 'stu', 'PGSC0003DMG400012635' => 'stu', 'PGSC0003DMG400015730' => 'stu', 'PGSC0003DMG400018611' => 'stu', 'PGSC0003DMG400030897' => 'stu', 'Phvul.001G254800' => 'pvu', 'Phvul.002G260100' => 'pvu', 'Phvul.003G167600' => 'pvu', 'Phvul.004G005100' => 'pvu', 'Potri.001G343600' => 'ptr', 'Potri.006G066700' => 'ptr', 'Potri.008G186000' => 'ptr', 'Potri.010G046900' => 'ptr', 'Potri.018G127900' => 'ptr', 'Pp3c20_17750' => 'ppa', 'Pp3c24_4380' => 'ppa', 'Prupe.1G245800' => 'ppe', 'Prupe.3G293400' => 'ppe', 'Prupe.7G247400' => 'ppe', 'Psat0s145g0120' => 'psa', 'Psat0s595g0040' => 'psa', 'Psat0s595g0120' => 'psa', 'Psat3g175040' => 'psa', 'Psat7g058120' => 'psa', 'PSO017G0428' => 'pso', 'PSO063G7510' => 'pso', 'PSO067G0046' => 'pso', 'PSO478G1073' => 'pso', 'PSO675G3677' => 'pso', 'PSO675G6558' => 'pso', 'PSO675G7520' => 'pso', 'PSO675G8959' => 'pso', 'QL02p074089' => 'qlo', 'QL02p089614' => 'qlo', 'QL03p057736' => 'qlo', 'RcHm_v2.0_Chr1g0364131' => 'rch', 'RcHm_v2.0_Chr2g0087801' => 'rch', 'RcHm_v2.0_Chr2g0087821' => 'rch', 'RcHm_v2.0_Chr2g0173231' => 'rch', 'RcHm_v2.0_Chr4g0433111' => 'rch', 'Rhsim03G0250300' => 'rsi', 'Rhsim08G0048400' => 'rsi', 'Rhsim10G0014800' => 'rsi', 'Rhsim12G0040100' => 'rsi', 'Rhsim12G0109700' => 'rsi', 'Sabra06G0049600' => 'sbr', 'Sabra08G0141000' => 'sbr', 'Sabra10G0021400' => 'sbr', 'Sabra16G0222900' => 'sbr', 'Sabra18G0108600' => 'sbr', 'SalBow1G0433' => 'sbo', 'SalBow1G2038' => 'sbo', 'SalBow1G5003' => 'sbo', 'SalBow7G1197' => 'sbo', 'SalBow8G3506' => 'sbo', 'Sc03g0007300' => 'sci', 'Sc11g0000950' => 'sci', 'Sc14g0008750' => 'sci', 'Sc18g0000420' => 'sci', 'Sed0006754' => 'sed', 'Sed0008741' => 'sed', 'Sed0017172' => 'sed', 'Sed0018925' => 'sed', 'Sed0023326' => 'sed', 'Sed0025909' => 'sed', 'SEGI_05333' => 'sgi', 'SEGI_10362' => 'sgi', 'SEGI_13380' => 'sgi', 'SEGI_24306' => 'sgi', 'SEGI_29077' => 'sgi', 'SEGI_29095' => 'sgi', 'SEGI_36534' => 'sgi', 'SEGI_37506' => 'sgi', 'SEGI_38321' => 'sgi', 'SGA_v2.0_scaffold307G48031' => 'sas', 'SGA_v2.0_scaffold47G17507' => 'sas', 'SGA_v2.0_scaffold63G21736' => 'sas', 'SGA_v2.0_scaffold87G27070' => 'sas', 'SHI17794' => 'shi', 'SHI28851' => 'shi', 'SMO165G0155' => 'smo', 'SMO340G0217' => 'smo', 'SMO367G1210' => 'smo', 'Solyc02g093430.3' => 'sly', 'Solyc05g013580.4' => 'sly', 'Solyc07g008030.3' => 'sly', 'Solyc12g035470.2' => 'sly', 'Sopen02g038020' => 'spe', 'Sopen05g008490' => 'spe', 'Sopen07g003910' => 'spe', 'Sopen12g015240' => 'spe', 'Sp1g11550' => 'spa', 'Sp2g16710' => 'spa', 'Sp3g00430' => 'spa', 'Sp3g26780' => 'spa', 'Sp5g22900' => 'spa', 'Sp6g29530' => 'spa', 'TAR371G0794' => 'tar', 'TAR374G0164' => 'tar', 'TAR622G0165' => 'tar', 'TAR626G0929' => 'tar', 'TAR629G2155' => 'tar', 'THA.LOC104805282' => 'tha', 'THA.LOC104805363' => 'tha', 'THA.LOC104808968' => 'tha', 'THA.LOC104821093' => 'tha', 'THA.LOC104823953' => 'tha', 'THA.LOC104825562' => 'tha', 'THA.LOC104825665' => 'tha', 'Thecc.02G261400' => 'tca', 'Thecc.04G019200' => 'tca', 'Thecc.09G130400' => 'tca', 'Thhalv10004374m.g' => 'esa', 'Thhalv10007850m.g' => 'esa', 'Thhalv10013782m.g' => 'esa', 'Thhalv10018686m.g' => 'esa', 'Thhalv10020899m.g' => 'esa', 'Thhalv10022755m.g' => 'esa', 'TPR.G23851' => 'tpr', 'TPR.G26500' => 'tpr', 'TPR.G27267' => 'tpr', 'TPR.G32001' => 'tpr', 'TPR.G6251' => 'tpr', 'TPR.G8167' => 'tpr', 'TWI12G1330' => 'twi', 'TWI18G1239' => 'twi', 'TWI34G0979' => 'twi', 'TWI36G0670' => 'twi', 'TWI36G0707' => 'twi', 'TWI56G0233' => 'twi', 'TWI75G1809' => 'twi', 'unitig_21.g20874' => 'ugi', 'unitig_26.g10343' => 'ugi', 'unitig_46.g18392' => 'ugi', 'unitig_52.g17178' => 'ugi', 'unitig_8.g2934' => 'ugi', 'vmacro01122' => 'vma', 'vmacro05875' => 'vma', 'vmacro06147' => 'vma', 'vmacro16191' => 'vma', 'vmacro18293' => 'vma', 'VMungo0251G3707' => 'vmu', 'VMungo0464G1521' => 'vmu', 'VMungo1215G0205' => 'vmu', 'VMungo1383G2484' => 'vmu', 'Zm00001eb079610' => 'zma', 'Zm00001eb135990' => 'zma', 'Zm00001eb183710' => 'zma', 'Zm00001eb246020' => 'zma' ), 'gf_id' => 'HOM05D001124', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001124' ), 'data_identifier' => 'HOM05D001124', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001124', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '548', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02520' => 'bna', 'A03p06630' => 'bna', 'A05p44460' => 'bna', 'A06p08710' => 'bna', 'A06p41090' => 'bna', 'A07p32320' => 'bna', 'A08p32520' => 'bna', 'A09p10360' => 'bna', 'A10p24080' => 'bna', 'Aa31LG11G15250' => 'aar', 'Aa31LG1G1800' => 'aar', 'Aa31LG2G5120' => 'aar', 'Aa31LG2G6070' => 'aar', 'Aa31LG5G10770' => 'aar', 'Aa31sc61G90' => 'aar', 'Actinidia01352' => 'ach', 'Actinidia05983' => 'ach', 'Actinidia08133' => 'ach', 'Actinidia15101' => 'ach', 'Actinidia26379' => 'ach', 'Actinidia35778' => 'ach', 'Actinidia36123' => 'ach', 'Actinidia37436' => 'ach', 'Actinidia38730' => 'ach', 'Ah.02g128210' => 'amhyb', 'Ah.03g132990' => 'amhyb', 'Ah.14g079410' => 'amhyb', 'AL1G24640' => 'aly', 'AL2G26680' => 'aly', 'AL3G10530' => 'aly', 'AL3G45230' => 'aly', 'AL5G15230' => 'aly', 'AL5G16960' => 'aly', 'AL6G25210' => 'aly', 'Aqoxy2G00441' => 'aox', 'Aqoxy3G01236' => 'aox', 'Aqoxy5G03746' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3RQ047' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C7GMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9C8JER' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MBL6KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YXCZ83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZANX40' => 'arhy', 'AT1G12990' => 'ath', 'AT1G67880' => 'ath', 'AT2G13290' => 'ath', 'AT3G01620' => 'ath', 'AT3G26445' => 'ath', 'AT3G27540' => 'ath', 'AT5G14480' => 'ath', 'ATR0824G026' => 'atr', 'ATR1098G019' => 'atr', 'Atru.chr11.2145' => 'acertr', 'Atru.chr2.3636' => 'acertr', 'Atru.chr2.3644' => 'acertr', 'Atru.chr6.2422' => 'acertr', 'Atru.chr7.1112' => 'acertr', 'AUR62005469' => 'cqu', 'AUR62011166' => 'cqu', 'AUR62013319' => 'cqu', 'AUR62024273' => 'cqu', 'AUR62028420' => 'cqu', 'AUR62041942' => 'cqu', 'BcaB01g04969' => 'bca', 'BcaB01g06371' => 'bca', 'BcaB02g11494' => 'bca', 'BcaB03g15382' => 'bca', 'BcaB08g36994' => 'bca', 'BcaC03g13477' => 'bca', 'BcaC03g13478' => 'bca', 'BcaC03g13480' => 'bca', 'BcaC03g13481' => 'bca', 'BcaC03g13486' => 'bca', 'BcaC04g19031' => 'bca', 'BcaC04g23085' => 'bca', 'BcaC05g25094' => 'bca', 'BcaC05g25096' => 'bca', 'BcaC05g25138' => 'bca', 'BcaC05g30416' => 'bca', 'BcaC05g30455' => 'bca', 'BcaC06g30979' => 'bca', 'BcaC06g33805' => 'bca', 'BcaC08g46021' => 'bca', 'BcaNung03154' => 'bca', 'BolC2t06623H' => 'bol', 'BolC2t06632H' => 'bol', 'BolC2t06635H' => 'bol', 'BolC2t06638H' => 'bol', 'BolC3t13266H' => 'bol', 'BolC5t29776H' => 'bol', 'BolC6t38912H' => 'bol', 'BolC7t44183H' => 'bol', 'BolC9t54123H' => 'bol', 'BolC9t59107H' => 'bol', 'BraA02t05221Z' => 'bra', 'BraA03t09996Z' => 'bra', 'BraA05t23210Z' => 'bra', 'BraA06t24068Z' => 'bra', 'BraA06t27032Z' => 'bra', 'BraA08t35176Z' => 'bra', 'BraA09t36680Z' => 'bra', 'BraA10t44471Z' => 'bra', 'C02p06760' => 'bna', 'C02p06890' => 'bna', 'C02p07010' => 'bna', 'C03p07660' => 'bna', 'C05p10300' => 'bna', 'C06p38150' => 'bna', 'C07p36650' => 'bna', 'C08p15770' => 'bna', 'C09p12300' => 'bna', 'C09p62700' => 'bna', 'C09p75040' => 'bna', 'CAN.G13.1' => 'can', 'CAN.G138.4' => 'can', 'CAN.G44.6' => 'can', 'CAN.G473.19' => 'can', 'CANSAT01G0835' => 'cansat', 'CANSAT11G0246' => 'cansat', 'CANSAT11G1766' => 'cansat', 'CANSAT64G1954' => 'cansat', 'CARHR013330' => 'chi', 'CARHR060530' => 'chi', 'CARHR075300' => 'chi', 'CARHR105120' => 'chi', 'CARHR148910' => 'chi', 'CARHR198830' => 'chi', 'Carub.0001s1275' => 'cru', 'Carub.0002s1437' => 'cru', 'Carub.0003s0044' => 'cru', 'Carub.0003s2787' => 'cru', 'Carub.0005s0597' => 'cru', 'Carub.0006s1266' => 'cru', 'Ca_06935_v3' => 'car', 'Ca_13559_v3' => 'car', 'Ca_16941_v3' => 'car', 'Ca_16960_v3' => 'car', 'Ca_17775_v3' => 'car', 'Ca_30464_v3' => 'car', 'Cc06_g08160' => 'ccan', 'Cc07_g01520' => 'ccan', 'Cc11_g15810' => 'ccan', 'CDE02G2840' => 'cde', 'CDE03G0093' => 'cde', 'CDE04G2127' => 'cde', 'CDE07G1857' => 'cde', 'CDE09G1246' => 'cde', 'Cfa003412' => 'cfa', 'Cfa007341' => 'cfa', 'Cfa009220' => 'cfa', 'Ciclev10008737m.g' => 'ccl', 'Ciclev10015565m.g' => 'ccl', 'Ciclev10031761m.g' => 'ccl', 'CiPaw.03G045300' => 'cil', 'CiPaw.03G247200' => 'cil', 'CiPaw.04G029500' => 'cil', 'CiPaw.04G174000' => 'cil', 'CiPaw.05G181200' => 'cil', 'CiPaw.06G067100' => 'cil', 'ClCG05G025800' => 'cla', 'ClCG06G011400' => 'cla', 'ClCG09G019360' => 'cla', 'COL.COLO4_04827' => 'col', 'COL.COLO4_29170' => 'col', 'COL.COLO4_35131' => 'col', 'COL.COLO4_35132' => 'col', 'Cpa.g.sc33.32' => 'cpa', 'Cpa.g.sc46.29' => 'cpa', 'Cpa.g.sc796.1' => 'cpa', 'CsaV3_1G030420' => 'csa', 'CsaV3_5G027050' => 'csa', 'CsaV3_5G031040' => 'csa', 'CsaV3_UNG023130' => 'csa', 'CSS0007726' => 'camsi', 'CSS0016433' => 'camsi', 'CSS0017656' => 'camsi', 'CSS0025364' => 'camsi', 'CSS0027582' => 'camsi', 'CSS0047288' => 'camsi', 'CSS0049950' => 'camsi', 'DCAR_003843' => 'dca', 'DCAR_007052' => 'dca', 'DCAR_020884' => 'dca', 'DCAR_021730' => 'dca', 'DCAR_024423' => 'dca', 'DCAR_026509' => 'dca', 'DCAR_031158' => 'dca', 'Dinv14728' => 'din', 'Dinv15219' => 'din', 'Dinv25728' => 'din', 'Dinv33428' => 'din', 'Dinv36489' => 'din', 'Dinv41486' => 'din', 'Duzib147G0469' => 'dzi', 'Duzib168G0060' => 'dzi', 'Duzib187G1215' => 'dzi', 'Duzib248G0692' => 'dzi', 'Duzib251G0767' => 'dzi', 'Duzib264G0446' => 'dzi', 'Duzib268G0691' => 'dzi', 'ECA232G4767' => 'eca', 'ECA233G2838' => 'eca', 'ECA234G0391' => 'eca', 'ECA234G0857' => 'eca', 'ECA236G1593' => 'eca', 'ECA238G0565' => 'eca', 'ECA246G1027' => 'eca', 'ECA246G3223' => 'eca', 'ECA246G3470' => 'eca', 'EL10Ac6g13829' => 'bvu', 'EL10Ac6g14093' => 'bvu', 'EL10Ac8g18707' => 'bvu', 'Eucgr.C01369' => 'egr', 'Eucgr.H02492' => 'egr', 'Eucgr.I01733' => 'egr', 'Eucgr.J02255' => 'egr', 'Eucgr.J02257' => 'egr', 'Eucgr.J02258' => 'egr', 'FAN02G1601' => 'fan', 'FAN03G1586' => 'fan', 'FAN03G2986' => 'fan', 'FAN05G4837' => 'fan', 'FAN06G0146' => 'fan', 'FAN07G0858' => 'fan', 'FAN09G3179' => 'fan', 'FAN10G0669' => 'fan', 'FAN12G2358' => 'fan', 'FAN14G4198' => 'fan', 'FAN14G5112' => 'fan', 'FAN17G0342' => 'fan', 'FAN19G0342' => 'fan', 'FAN19G0962' => 'fan', 'FAN19G1101' => 'fan', 'FAN19G1872' => 'fan', 'FAN22G0356' => 'fan', 'FAN23G0744' => 'fan', 'FAN23G1914' => 'fan', 'FAN26G0032' => 'fan', 'FAN28G0625' => 'fan', 'FvH4_1g02710' => 'fve', 'FvH4_1g02720' => 'fve', 'FvH4_4g25670' => 'fve', 'FvH4_6g51700' => 'fve', 'FvH4_7g20170' => 'fve', 'Glyma.05G175000' => 'gma', 'Glyma.08G132300' => 'gma', 'Glyma.11G243000' => 'gma', 'Glyma.13G158900' => 'gma', 'Glyma.17G112400' => 'gma', 'Glyma.18G014100' => 'gma', 'Glyma.19G003100' => 'gma', 'Glyma.19G056500' => 'gma', 'Gohir.A01G158900' => 'ghi', 'Gohir.A05G312600' => 'ghi', 'Gohir.A05G354900' => 'ghi', 'Gohir.A07G037200' => 'ghi', 'Gohir.A09G030000' => 'ghi', 'Gohir.A12G145200' => 'ghi', 'Gohir.D01G151500' => 'ghi', 'Gohir.D04G058300' => 'ghi', 'Gohir.D05G314100' => 'ghi', 'Gohir.D07G041400' => 'ghi', 'Gohir.D09G029700' => 'ghi', 'Gohir.D12G149700' => 'ghi', 'Gorai.001G043800' => 'gra', 'Gorai.002G187800' => 'gra', 'Gorai.006G034700' => 'gra', 'Gorai.008G161200' => 'gra', 'Gorai.009G335700' => 'gra', 'Gorai.012G065000' => 'gra', 'GSVIVG01000535001' => 'vvi', 'GSVIVG01015572001' => 'vvi', 'GSVIVG01032386001' => 'vvi', 'HanXRQChr05g0138531' => 'han', 'HanXRQChr06g0174391' => 'han', 'HanXRQChr07g0199021' => 'han', 'HanXRQChr08g0208211' => 'han', 'HanXRQChr09g0255471' => 'han', 'HanXRQChr10g0315791' => 'han', 'HanXRQChr12g0371991' => 'han', 'HanXRQChr15g0475251' => 'han', 'HanXRQChr17g0540001' => 'han', 'HanXRQChr17g0548631' => 'han', 'HanXRQChr17g0569561' => 'han', 'Haze_12256' => 'cav', 'Haze_14756' => 'cav', 'Haze_25528' => 'cav', 'Hma1.2p1_0079F.1_g041020' => 'hma', 'Hma1.2p1_0818F.1_g223260' => 'hma', 'Hma1.2p1_1747F.1_g300530' => 'hma', 'HPP92_004607' => 'vpl', 'HPP92_004608' => 'vpl', 'HPP92_006181' => 'vpl', 'HPP92_012192' => 'vpl', 'HPP92_015680' => 'vpl', 'HPP92_020249' => 'vpl', 'HPP92_021376' => 'vpl', 'HPP92_024275' => 'vpl', 'Hund06031' => 'sun', 'Hund25391' => 'sun', 'Lalb_Chr07g0185371' => 'lal', 'Lalb_Chr07g0185381' => 'lal', 'Lalb_Chr12g0204011' => 'lal', 'Lalb_Chr13g0301671' => 'lal', 'Lalb_Chr14g0362851' => 'lal', 'Lalb_Chr24g0403581' => 'lal', 'Lj1g0000233' => 'lja', 'Lj2g0018120' => 'lja', 'Lj3C621T0' => 'lonja', 'Lj3P1059T14' => 'lonja', 'Lj3P611T9' => 'lonja', 'Lj3P614T13' => 'lonja', 'Lj3P615T5' => 'lonja', 'Lj4g0012315' => 'lja', 'Lj4g0026182' => 'lja', 'Lj6P813T16' => 'lonja', 'Lj7C427T7' => 'lonja', 'Lj7C427T8' => 'lonja', 'Lj7P600T41' => 'lonja', 'Lju41C42G17' => 'lonja', 'Lsat_1_v5_gn_0_47300' => 'lsa', 'Lsat_1_v5_gn_2_91280' => 'lsa', 'Lsat_1_v5_gn_3_30561' => 'lsa', 'Lsat_1_v5_gn_4_184321' => 'lsa', 'Lsat_1_v5_gn_4_4041' => 'lsa', 'Lsat_1_v5_gn_5_92000' => 'lsa', 'Lsat_1_v5_gn_8_152940' => 'lsa', 'Lsat_1_v5_gn_8_62401' => 'lsa', 'Manes.06G055900' => 'mes', 'Manes.12G022200' => 'mes', 'Manes.13G023300' => 'mes', 'Manes.14G115000' => 'mes', 'Manes.15G151700' => 'mes', 'Manes.17G111300' => 'mes', 'Mapoly0226s0009' => 'mpo', 'MBI02_g25363_MAGBIO' => 'mbi', 'MBI06_g00027_MAGBIO' => 'mbi', 'MBI10_g13034_MAGBIO' => 'mbi', 'MD09G1023400' => 'mdo', 'MD13G1100100' => 'mdo', 'MD15G1169200' => 'mdo', 'MD16G1101100' => 'mdo', 'MD17G1022900' => 'mdo', 'Medtr3g096150' => 'mtr', 'Medtr4g115070' => 'mtr', 'Medtr7g033325' => 'mtr', 'Medtr8g089840' => 'mtr', 'MELO3C010319.2' => 'cme', 'MELO3C011944.2' => 'cme', 'MELO3C021589.2' => 'cme', 'Migut.E00207' => 'egut', 'Migut.H00067' => 'egut', 'Migut.K00433' => 'egut', 'Migut.K00606' => 'egut', 'Migut.K01410' => 'egut', 'MSTRG.13347' => 'ama', 'MSTRG.24045' => 'ama', 'MSTRG.2428' => 'ama', 'MSTRG.26410' => 'ama', 'MSTRG.3139' => 'ama', 'MSTRG.3286' => 'ama', 'MSTRG.563' => 'ama', 'MSTRG.7941' => 'ama', 'Nitab4.5_0000028g0060' => 'nta', 'Nitab4.5_0000065g0260' => 'nta', 'Nitab4.5_0000112g0060' => 'nta', 'Nitab4.5_0000489g0120' => 'nta', 'Nitab4.5_0001776g0050' => 'nta', 'Nitab4.5_0001854g0010' => 'nta', 'Nitab4.5_0001860g0020' => 'nta', 'Nitab4.5_0004352g0010' => 'nta', 'Nitab4.5_0008716g0020' => 'nta', 'Nitab4.5_0008922g0010' => 'nta', 'Nn3g16693' => 'nnu', 'Nn4g22596' => 'nnu', 'Nn7g37639' => 'nnu', 'Oeu001701.1' => 'oeu', 'Oeu018149.1' => 'oeu', 'Oeu026220.1' => 'oeu', 'Oeu038635.1' => 'oeu', 'Oeu049176.1' => 'oeu', 'Oeu056706.1' => 'oeu', 'Oeu056937.1' => 'oeu', 'Oeu057540.1' => 'oeu', 'Os02g0594900' => 'osa', 'Os02g0595100' => 'osa', 'Os04g0477500' => 'osa', 'Os12g0611900' => 'osa', 'Peaxi162Scf00076g00020' => 'pax', 'Peaxi162Scf00128g00217' => 'pax', 'Peaxi162Scf00129g01640' => 'pax', 'Peaxi162Scf00669g00007' => 'pax', 'Peaxi162Scf00700g00421' => 'pax', 'Peaxi162Scf00801g00038' => 'pax', 'Peaxi162Scf00891g00025' => 'pax', 'PGR083G0909' => 'pgr', 'PGR119G1005' => 'pgr', 'PGR142G2236' => 'pgr', 'PGR142G3388' => 'pgr', 'PGSC0003DMG400004514' => 'stu', 'PGSC0003DMG400012635' => 'stu', 'PGSC0003DMG400015730' => 'stu', 'PGSC0003DMG400018611' => 'stu', 'PGSC0003DMG400030897' => 'stu', 'Phvul.001G254800' => 'pvu', 'Phvul.002G260100' => 'pvu', 'Phvul.003G167600' => 'pvu', 'Phvul.004G005100' => 'pvu', 'Potri.001G343600' => 'ptr', 'Potri.006G066700' => 'ptr', 'Potri.008G186000' => 'ptr', 'Potri.010G046900' => 'ptr', 'Potri.018G127900' => 'ptr', 'Pp3c20_17750' => 'ppa', 'Pp3c24_4380' => 'ppa', 'Prupe.1G245800' => 'ppe', 'Prupe.3G293400' => 'ppe', 'Prupe.7G247400' => 'ppe', 'Psat0s145g0120' => 'psa', 'Psat0s595g0040' => 'psa', 'Psat0s595g0120' => 'psa', 'Psat3g175040' => 'psa', 'Psat7g058120' => 'psa', 'PSO017G0428' => 'pso', 'PSO063G7510' => 'pso', 'PSO067G0046' => 'pso', 'PSO478G1073' => 'pso', 'PSO675G3677' => 'pso', 'PSO675G6558' => 'pso', 'PSO675G7520' => 'pso', 'PSO675G8959' => 'pso', 'QL02p074089' => 'qlo', 'QL02p089614' => 'qlo', 'QL03p057736' => 'qlo', 'RcHm_v2.0_Chr1g0364131' => 'rch', 'RcHm_v2.0_Chr2g0087801' => 'rch', 'RcHm_v2.0_Chr2g0087821' => 'rch', 'RcHm_v2.0_Chr2g0173231' => 'rch', 'RcHm_v2.0_Chr4g0433111' => 'rch', 'Rhsim03G0250300' => 'rsi', 'Rhsim08G0048400' => 'rsi', 'Rhsim10G0014800' => 'rsi', 'Rhsim12G0040100' => 'rsi', 'Rhsim12G0109700' => 'rsi', 'Sabra06G0049600' => 'sbr', 'Sabra08G0141000' => 'sbr', 'Sabra10G0021400' => 'sbr', 'Sabra16G0222900' => 'sbr', 'Sabra18G0108600' => 'sbr', 'SalBow1G0433' => 'sbo', 'SalBow1G2038' => 'sbo', 'SalBow1G5003' => 'sbo', 'SalBow7G1197' => 'sbo', 'SalBow8G3506' => 'sbo', 'Sc03g0007300' => 'sci', 'Sc11g0000950' => 'sci', 'Sc14g0008750' => 'sci', 'Sc18g0000420' => 'sci', 'Sed0006754' => 'sed', 'Sed0008741' => 'sed', 'Sed0017172' => 'sed', 'Sed0018925' => 'sed', 'Sed0023326' => 'sed', 'Sed0025909' => 'sed', 'SEGI_05333' => 'sgi', 'SEGI_10362' => 'sgi', 'SEGI_13380' => 'sgi', 'SEGI_24306' => 'sgi', 'SEGI_29077' => 'sgi', 'SEGI_29095' => 'sgi', 'SEGI_36534' => 'sgi', 'SEGI_37506' => 'sgi', 'SEGI_38321' => 'sgi', 'SGA_v2.0_scaffold307G48031' => 'sas', 'SGA_v2.0_scaffold47G17507' => 'sas', 'SGA_v2.0_scaffold63G21736' => 'sas', 'SGA_v2.0_scaffold87G27070' => 'sas', 'SHI17794' => 'shi', 'SHI28851' => 'shi', 'SMO165G0155' => 'smo', 'SMO340G0217' => 'smo', 'SMO367G1210' => 'smo', 'Solyc02g093430.3' => 'sly', 'Solyc05g013580.4' => 'sly', 'Solyc07g008030.3' => 'sly', 'Solyc12g035470.2' => 'sly', 'Sopen02g038020' => 'spe', 'Sopen05g008490' => 'spe', 'Sopen07g003910' => 'spe', 'Sopen12g015240' => 'spe', 'Sp1g11550' => 'spa', 'Sp2g16710' => 'spa', 'Sp3g00430' => 'spa', 'Sp3g26780' => 'spa', 'Sp5g22900' => 'spa', 'Sp6g29530' => 'spa', 'TAR371G0794' => 'tar', 'TAR374G0164' => 'tar', 'TAR622G0165' => 'tar', 'TAR626G0929' => 'tar', 'TAR629G2155' => 'tar', 'THA.LOC104805282' => 'tha', 'THA.LOC104805363' => 'tha', 'THA.LOC104808968' => 'tha', 'THA.LOC104821093' => 'tha', 'THA.LOC104823953' => 'tha', 'THA.LOC104825562' => 'tha', 'THA.LOC104825665' => 'tha', 'Thecc.02G261400' => 'tca', 'Thecc.04G019200' => 'tca', 'Thecc.09G130400' => 'tca', 'Thhalv10004374m.g' => 'esa', 'Thhalv10007850m.g' => 'esa', 'Thhalv10013782m.g' => 'esa', 'Thhalv10018686m.g' => 'esa', 'Thhalv10020899m.g' => 'esa', 'Thhalv10022755m.g' => 'esa', 'TPR.G23851' => 'tpr', 'TPR.G26500' => 'tpr', 'TPR.G27267' => 'tpr', 'TPR.G32001' => 'tpr', 'TPR.G6251' => 'tpr', 'TPR.G8167' => 'tpr', 'TWI12G1330' => 'twi', 'TWI18G1239' => 'twi', 'TWI34G0979' => 'twi', 'TWI36G0670' => 'twi', 'TWI36G0707' => 'twi', 'TWI56G0233' => 'twi', 'TWI75G1809' => 'twi', 'unitig_21.g20874' => 'ugi', 'unitig_26.g10343' => 'ugi', 'unitig_46.g18392' => 'ugi', 'unitig_52.g17178' => 'ugi', 'unitig_8.g2934' => 'ugi', 'vmacro01122' => 'vma', 'vmacro05875' => 'vma', 'vmacro06147' => 'vma', 'vmacro16191' => 'vma', 'vmacro18293' => 'vma', 'VMungo0251G3707' => 'vmu', 'VMungo0464G1521' => 'vmu', 'VMungo1215G0205' => 'vmu', 'VMungo1383G2484' => 'vmu', 'Zm00001eb079610' => 'zma', 'Zm00001eb135990' => 'zma', 'Zm00001eb183710' => 'zma', 'Zm00001eb246020' => 'zma' ) $gf_id = 'HOM05D001124' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001124' ) $data_identifier = 'HOM05D001124' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 6, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 7, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 21, 'bol' => (int) 10, 'bra' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 6, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 9, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 21, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 8, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 10, 'lsa' => (int) 8, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 8, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 9, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb246020' $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' => 'HOM05D001124', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '548', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02520' => 'bna', 'A03p06630' => 'bna', 'A05p44460' => 'bna', 'A06p08710' => 'bna', 'A06p41090' => 'bna', 'A07p32320' => 'bna', 'A08p32520' => 'bna', 'A09p10360' => 'bna', 'A10p24080' => 'bna', 'Aa31LG11G15250' => 'aar', 'Aa31LG1G1800' => 'aar', 'Aa31LG2G5120' => 'aar', 'Aa31LG2G6070' => 'aar', 'Aa31LG5G10770' => 'aar', 'Aa31sc61G90' => 'aar', 'Actinidia01352' => 'ach', 'Actinidia05983' => 'ach', 'Actinidia08133' => 'ach', 'Actinidia15101' => 'ach', 'Actinidia26379' => 'ach', 'Actinidia35778' => 'ach', 'Actinidia36123' => 'ach', 'Actinidia37436' => 'ach', 'Actinidia38730' => 'ach', 'Ah.02g128210' => 'amhyb', 'Ah.03g132990' => 'amhyb', 'Ah.14g079410' => 'amhyb', 'AL1G24640' => 'aly', 'AL2G26680' => 'aly', 'AL3G10530' => 'aly', 'AL3G45230' => 'aly', 'AL5G15230' => 'aly', 'AL5G16960' => 'aly', 'AL6G25210' => 'aly', 'Aqoxy2G00441' => 'aox', 'Aqoxy3G01236' => 'aox', 'Aqoxy5G03746' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3RQ047' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C7GMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9C8JER' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MBL6KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YXCZ83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZANX40' => 'arhy', 'AT1G12990' => 'ath', 'AT1G67880' => 'ath', 'AT2G13290' => 'ath', 'AT3G01620' => 'ath', 'AT3G26445' => 'ath', 'AT3G27540' => 'ath', 'AT5G14480' => 'ath', 'ATR0824G026' => 'atr', 'ATR1098G019' => 'atr', 'Atru.chr11.2145' => 'acertr', 'Atru.chr2.3636' => 'acertr', 'Atru.chr2.3644' => 'acertr', 'Atru.chr6.2422' => 'acertr', 'Atru.chr7.1112' => 'acertr', 'AUR62005469' => 'cqu', 'AUR62011166' => 'cqu', 'AUR62013319' => 'cqu', 'AUR62024273' => 'cqu', 'AUR62028420' => 'cqu', 'AUR62041942' => 'cqu', 'BcaB01g04969' => 'bca', 'BcaB01g06371' => 'bca', 'BcaB02g11494' => 'bca', 'BcaB03g15382' => 'bca', 'BcaB08g36994' => 'bca', 'BcaC03g13477' => 'bca', 'BcaC03g13478' => 'bca', 'BcaC03g13480' => 'bca', 'BcaC03g13481' => 'bca', 'BcaC03g13486' => 'bca', 'BcaC04g19031' => 'bca', 'BcaC04g23085' => 'bca', 'BcaC05g25094' => 'bca', 'BcaC05g25096' => 'bca', 'BcaC05g25138' => 'bca', 'BcaC05g30416' => 'bca', 'BcaC05g30455' => 'bca', 'BcaC06g30979' => 'bca', 'BcaC06g33805' => 'bca', 'BcaC08g46021' => 'bca', 'BcaNung03154' => 'bca', 'BolC2t06623H' => 'bol', 'BolC2t06632H' => 'bol', 'BolC2t06635H' => 'bol', 'BolC2t06638H' => 'bol', 'BolC3t13266H' => 'bol', 'BolC5t29776H' => 'bol', 'BolC6t38912H' => 'bol', 'BolC7t44183H' => 'bol', 'BolC9t54123H' => 'bol', 'BolC9t59107H' => 'bol', 'BraA02t05221Z' => 'bra', 'BraA03t09996Z' => 'bra', 'BraA05t23210Z' => 'bra', 'BraA06t24068Z' => 'bra', 'BraA06t27032Z' => 'bra', 'BraA08t35176Z' => 'bra', 'BraA09t36680Z' => 'bra', 'BraA10t44471Z' => 'bra', 'C02p06760' => 'bna', 'C02p06890' => 'bna', 'C02p07010' => 'bna', 'C03p07660' => 'bna', 'C05p10300' => 'bna', 'C06p38150' => 'bna', 'C07p36650' => 'bna', 'C08p15770' => 'bna', 'C09p12300' => 'bna', 'C09p62700' => 'bna', 'C09p75040' => 'bna', 'CAN.G13.1' => 'can', 'CAN.G138.4' => 'can', 'CAN.G44.6' => 'can', 'CAN.G473.19' => 'can', 'CANSAT01G0835' => 'cansat', 'CANSAT11G0246' => 'cansat', 'CANSAT11G1766' => 'cansat', 'CANSAT64G1954' => 'cansat', 'CARHR013330' => 'chi', 'CARHR060530' => 'chi', 'CARHR075300' => 'chi', 'CARHR105120' => 'chi', 'CARHR148910' => 'chi', 'CARHR198830' => 'chi', 'Carub.0001s1275' => 'cru', 'Carub.0002s1437' => 'cru', 'Carub.0003s0044' => 'cru', 'Carub.0003s2787' => 'cru', 'Carub.0005s0597' => 'cru', 'Carub.0006s1266' => 'cru', 'Ca_06935_v3' => 'car', 'Ca_13559_v3' => 'car', 'Ca_16941_v3' => 'car', 'Ca_16960_v3' => 'car', 'Ca_17775_v3' => 'car', 'Ca_30464_v3' => 'car', 'Cc06_g08160' => 'ccan', 'Cc07_g01520' => 'ccan', 'Cc11_g15810' => 'ccan', 'CDE02G2840' => 'cde', 'CDE03G0093' => 'cde', 'CDE04G2127' => 'cde', 'CDE07G1857' => 'cde', 'CDE09G1246' => 'cde', 'Cfa003412' => 'cfa', 'Cfa007341' => 'cfa', 'Cfa009220' => 'cfa', 'Ciclev10008737m.g' => 'ccl', 'Ciclev10015565m.g' => 'ccl', 'Ciclev10031761m.g' => 'ccl', 'CiPaw.03G045300' => 'cil', 'CiPaw.03G247200' => 'cil', 'CiPaw.04G029500' => 'cil', 'CiPaw.04G174000' => 'cil', 'CiPaw.05G181200' => 'cil', 'CiPaw.06G067100' => 'cil', 'ClCG05G025800' => 'cla', 'ClCG06G011400' => 'cla', 'ClCG09G019360' => 'cla', 'COL.COLO4_04827' => 'col', 'COL.COLO4_29170' => 'col', 'COL.COLO4_35131' => 'col', 'COL.COLO4_35132' => 'col', 'Cpa.g.sc33.32' => 'cpa', 'Cpa.g.sc46.29' => 'cpa', 'Cpa.g.sc796.1' => 'cpa', 'CsaV3_1G030420' => 'csa', 'CsaV3_5G027050' => 'csa', 'CsaV3_5G031040' => 'csa', 'CsaV3_UNG023130' => 'csa', 'CSS0007726' => 'camsi', 'CSS0016433' => 'camsi', 'CSS0017656' => 'camsi', 'CSS0025364' => 'camsi', 'CSS0027582' => 'camsi', 'CSS0047288' => 'camsi', 'CSS0049950' => 'camsi', 'DCAR_003843' => 'dca', 'DCAR_007052' => 'dca', 'DCAR_020884' => 'dca', 'DCAR_021730' => 'dca', 'DCAR_024423' => 'dca', 'DCAR_026509' => 'dca', 'DCAR_031158' => 'dca', 'Dinv14728' => 'din', 'Dinv15219' => 'din', 'Dinv25728' => 'din', 'Dinv33428' => 'din', 'Dinv36489' => 'din', 'Dinv41486' => 'din', 'Duzib147G0469' => 'dzi', 'Duzib168G0060' => 'dzi', 'Duzib187G1215' => 'dzi', 'Duzib248G0692' => 'dzi', 'Duzib251G0767' => 'dzi', 'Duzib264G0446' => 'dzi', 'Duzib268G0691' => 'dzi', 'ECA232G4767' => 'eca', 'ECA233G2838' => 'eca', 'ECA234G0391' => 'eca', 'ECA234G0857' => 'eca', 'ECA236G1593' => 'eca', 'ECA238G0565' => 'eca', 'ECA246G1027' => 'eca', 'ECA246G3223' => 'eca', 'ECA246G3470' => 'eca', 'EL10Ac6g13829' => 'bvu', 'EL10Ac6g14093' => 'bvu', 'EL10Ac8g18707' => 'bvu', 'Eucgr.C01369' => 'egr', 'Eucgr.H02492' => 'egr', 'Eucgr.I01733' => 'egr', 'Eucgr.J02255' => 'egr', 'Eucgr.J02257' => 'egr', 'Eucgr.J02258' => 'egr', 'FAN02G1601' => 'fan', 'FAN03G1586' => 'fan', 'FAN03G2986' => 'fan', 'FAN05G4837' => 'fan', 'FAN06G0146' => 'fan', 'FAN07G0858' => 'fan', 'FAN09G3179' => 'fan', 'FAN10G0669' => 'fan', 'FAN12G2358' => 'fan', 'FAN14G4198' => 'fan', 'FAN14G5112' => 'fan', 'FAN17G0342' => 'fan', 'FAN19G0342' => 'fan', 'FAN19G0962' => 'fan', 'FAN19G1101' => 'fan', 'FAN19G1872' => 'fan', 'FAN22G0356' => 'fan', 'FAN23G0744' => 'fan', 'FAN23G1914' => 'fan', 'FAN26G0032' => 'fan', 'FAN28G0625' => 'fan', 'FvH4_1g02710' => 'fve', 'FvH4_1g02720' => 'fve', 'FvH4_4g25670' => 'fve', 'FvH4_6g51700' => 'fve', 'FvH4_7g20170' => 'fve', 'Glyma.05G175000' => 'gma', 'Glyma.08G132300' => 'gma', 'Glyma.11G243000' => 'gma', 'Glyma.13G158900' => 'gma', 'Glyma.17G112400' => 'gma', 'Glyma.18G014100' => 'gma', 'Glyma.19G003100' => 'gma', 'Glyma.19G056500' => 'gma', 'Gohir.A01G158900' => 'ghi', 'Gohir.A05G312600' => 'ghi', 'Gohir.A05G354900' => 'ghi', 'Gohir.A07G037200' => 'ghi', 'Gohir.A09G030000' => 'ghi', 'Gohir.A12G145200' => 'ghi', 'Gohir.D01G151500' => 'ghi', 'Gohir.D04G058300' => 'ghi', 'Gohir.D05G314100' => 'ghi', 'Gohir.D07G041400' => 'ghi', 'Gohir.D09G029700' => 'ghi', 'Gohir.D12G149700' => 'ghi', 'Gorai.001G043800' => 'gra', 'Gorai.002G187800' => 'gra', 'Gorai.006G034700' => 'gra', 'Gorai.008G161200' => 'gra', 'Gorai.009G335700' => 'gra', 'Gorai.012G065000' => 'gra', 'GSVIVG01000535001' => 'vvi', 'GSVIVG01015572001' => 'vvi', 'GSVIVG01032386001' => 'vvi', 'HanXRQChr05g0138531' => 'han', 'HanXRQChr06g0174391' => 'han', 'HanXRQChr07g0199021' => 'han', 'HanXRQChr08g0208211' => 'han', 'HanXRQChr09g0255471' => 'han', 'HanXRQChr10g0315791' => 'han', 'HanXRQChr12g0371991' => 'han', 'HanXRQChr15g0475251' => 'han', 'HanXRQChr17g0540001' => 'han', 'HanXRQChr17g0548631' => 'han', 'HanXRQChr17g0569561' => 'han', 'Haze_12256' => 'cav', 'Haze_14756' => 'cav', 'Haze_25528' => 'cav', 'Hma1.2p1_0079F.1_g041020' => 'hma', 'Hma1.2p1_0818F.1_g223260' => 'hma', 'Hma1.2p1_1747F.1_g300530' => 'hma', 'HPP92_004607' => 'vpl', 'HPP92_004608' => 'vpl', 'HPP92_006181' => 'vpl', 'HPP92_012192' => 'vpl', 'HPP92_015680' => 'vpl', 'HPP92_020249' => 'vpl', 'HPP92_021376' => 'vpl', 'HPP92_024275' => 'vpl', 'Hund06031' => 'sun', 'Hund25391' => 'sun', 'Lalb_Chr07g0185371' => 'lal', 'Lalb_Chr07g0185381' => 'lal', 'Lalb_Chr12g0204011' => 'lal', 'Lalb_Chr13g0301671' => 'lal', 'Lalb_Chr14g0362851' => 'lal', 'Lalb_Chr24g0403581' => 'lal', 'Lj1g0000233' => 'lja', 'Lj2g0018120' => 'lja', 'Lj3C621T0' => 'lonja', 'Lj3P1059T14' => 'lonja', 'Lj3P611T9' => 'lonja', 'Lj3P614T13' => 'lonja', 'Lj3P615T5' => 'lonja', 'Lj4g0012315' => 'lja', 'Lj4g0026182' => 'lja', 'Lj6P813T16' => 'lonja', 'Lj7C427T7' => 'lonja', 'Lj7C427T8' => 'lonja', 'Lj7P600T41' => 'lonja', 'Lju41C42G17' => 'lonja', 'Lsat_1_v5_gn_0_47300' => 'lsa', 'Lsat_1_v5_gn_2_91280' => 'lsa', 'Lsat_1_v5_gn_3_30561' => 'lsa', 'Lsat_1_v5_gn_4_184321' => 'lsa', 'Lsat_1_v5_gn_4_4041' => 'lsa', 'Lsat_1_v5_gn_5_92000' => 'lsa', 'Lsat_1_v5_gn_8_152940' => 'lsa', 'Lsat_1_v5_gn_8_62401' => 'lsa', 'Manes.06G055900' => 'mes', 'Manes.12G022200' => 'mes', 'Manes.13G023300' => 'mes', 'Manes.14G115000' => 'mes', 'Manes.15G151700' => 'mes', 'Manes.17G111300' => 'mes', 'Mapoly0226s0009' => 'mpo', 'MBI02_g25363_MAGBIO' => 'mbi', 'MBI06_g00027_MAGBIO' => 'mbi', 'MBI10_g13034_MAGBIO' => 'mbi', 'MD09G1023400' => 'mdo', 'MD13G1100100' => 'mdo', 'MD15G1169200' => 'mdo', 'MD16G1101100' => 'mdo', 'MD17G1022900' => 'mdo', 'Medtr3g096150' => 'mtr', 'Medtr4g115070' => 'mtr', 'Medtr7g033325' => 'mtr', 'Medtr8g089840' => 'mtr', 'MELO3C010319.2' => 'cme', 'MELO3C011944.2' => 'cme', 'MELO3C021589.2' => 'cme', 'Migut.E00207' => 'egut', 'Migut.H00067' => 'egut', 'Migut.K00433' => 'egut', 'Migut.K00606' => 'egut', 'Migut.K01410' => 'egut', 'MSTRG.13347' => 'ama', 'MSTRG.24045' => 'ama', 'MSTRG.2428' => 'ama', 'MSTRG.26410' => 'ama', 'MSTRG.3139' => 'ama', 'MSTRG.3286' => 'ama', 'MSTRG.563' => 'ama', 'MSTRG.7941' => 'ama', 'Nitab4.5_0000028g0060' => 'nta', 'Nitab4.5_0000065g0260' => 'nta', 'Nitab4.5_0000112g0060' => 'nta', 'Nitab4.5_0000489g0120' => 'nta', 'Nitab4.5_0001776g0050' => 'nta', 'Nitab4.5_0001854g0010' => 'nta', 'Nitab4.5_0001860g0020' => 'nta', 'Nitab4.5_0004352g0010' => 'nta', 'Nitab4.5_0008716g0020' => 'nta', 'Nitab4.5_0008922g0010' => 'nta', 'Nn3g16693' => 'nnu', 'Nn4g22596' => 'nnu', 'Nn7g37639' => 'nnu', 'Oeu001701.1' => 'oeu', 'Oeu018149.1' => 'oeu', 'Oeu026220.1' => 'oeu', 'Oeu038635.1' => 'oeu', 'Oeu049176.1' => 'oeu', 'Oeu056706.1' => 'oeu', 'Oeu056937.1' => 'oeu', 'Oeu057540.1' => 'oeu', 'Os02g0594900' => 'osa', 'Os02g0595100' => 'osa', 'Os04g0477500' => 'osa', 'Os12g0611900' => 'osa', 'Peaxi162Scf00076g00020' => 'pax', 'Peaxi162Scf00128g00217' => 'pax', 'Peaxi162Scf00129g01640' => 'pax', 'Peaxi162Scf00669g00007' => 'pax', 'Peaxi162Scf00700g00421' => 'pax', 'Peaxi162Scf00801g00038' => 'pax', 'Peaxi162Scf00891g00025' => 'pax', 'PGR083G0909' => 'pgr', 'PGR119G1005' => 'pgr', 'PGR142G2236' => 'pgr', 'PGR142G3388' => 'pgr', 'PGSC0003DMG400004514' => 'stu', 'PGSC0003DMG400012635' => 'stu', 'PGSC0003DMG400015730' => 'stu', 'PGSC0003DMG400018611' => 'stu', 'PGSC0003DMG400030897' => 'stu', 'Phvul.001G254800' => 'pvu', 'Phvul.002G260100' => 'pvu', 'Phvul.003G167600' => 'pvu', 'Phvul.004G005100' => 'pvu', 'Potri.001G343600' => 'ptr', 'Potri.006G066700' => 'ptr', 'Potri.008G186000' => 'ptr', 'Potri.010G046900' => 'ptr', 'Potri.018G127900' => 'ptr', 'Pp3c20_17750' => 'ppa', 'Pp3c24_4380' => 'ppa', 'Prupe.1G245800' => 'ppe', 'Prupe.3G293400' => 'ppe', 'Prupe.7G247400' => 'ppe', 'Psat0s145g0120' => 'psa', 'Psat0s595g0040' => 'psa', 'Psat0s595g0120' => 'psa', 'Psat3g175040' => 'psa', 'Psat7g058120' => 'psa', 'PSO017G0428' => 'pso', 'PSO063G7510' => 'pso', 'PSO067G0046' => 'pso', 'PSO478G1073' => 'pso', 'PSO675G3677' => 'pso', 'PSO675G6558' => 'pso', 'PSO675G7520' => 'pso', 'PSO675G8959' => 'pso', 'QL02p074089' => 'qlo', 'QL02p089614' => 'qlo', 'QL03p057736' => 'qlo', 'RcHm_v2.0_Chr1g0364131' => 'rch', 'RcHm_v2.0_Chr2g0087801' => 'rch', 'RcHm_v2.0_Chr2g0087821' => 'rch', 'RcHm_v2.0_Chr2g0173231' => 'rch', 'RcHm_v2.0_Chr4g0433111' => 'rch', 'Rhsim03G0250300' => 'rsi', 'Rhsim08G0048400' => 'rsi', 'Rhsim10G0014800' => 'rsi', 'Rhsim12G0040100' => 'rsi', 'Rhsim12G0109700' => 'rsi', 'Sabra06G0049600' => 'sbr', 'Sabra08G0141000' => 'sbr', 'Sabra10G0021400' => 'sbr', 'Sabra16G0222900' => 'sbr', 'Sabra18G0108600' => 'sbr', 'SalBow1G0433' => 'sbo', 'SalBow1G2038' => 'sbo', 'SalBow1G5003' => 'sbo', 'SalBow7G1197' => 'sbo', 'SalBow8G3506' => 'sbo', 'Sc03g0007300' => 'sci', 'Sc11g0000950' => 'sci', 'Sc14g0008750' => 'sci', 'Sc18g0000420' => 'sci', 'Sed0006754' => 'sed', 'Sed0008741' => 'sed', 'Sed0017172' => 'sed', 'Sed0018925' => 'sed', 'Sed0023326' => 'sed', 'Sed0025909' => 'sed', 'SEGI_05333' => 'sgi', 'SEGI_10362' => 'sgi', 'SEGI_13380' => 'sgi', 'SEGI_24306' => 'sgi', 'SEGI_29077' => 'sgi', 'SEGI_29095' => 'sgi', 'SEGI_36534' => 'sgi', 'SEGI_37506' => 'sgi', 'SEGI_38321' => 'sgi', 'SGA_v2.0_scaffold307G48031' => 'sas', 'SGA_v2.0_scaffold47G17507' => 'sas', 'SGA_v2.0_scaffold63G21736' => 'sas', 'SGA_v2.0_scaffold87G27070' => 'sas', 'SHI17794' => 'shi', 'SHI28851' => 'shi', 'SMO165G0155' => 'smo', 'SMO340G0217' => 'smo', 'SMO367G1210' => 'smo', 'Solyc02g093430.3' => 'sly', 'Solyc05g013580.4' => 'sly', 'Solyc07g008030.3' => 'sly', 'Solyc12g035470.2' => 'sly', 'Sopen02g038020' => 'spe', 'Sopen05g008490' => 'spe', 'Sopen07g003910' => 'spe', 'Sopen12g015240' => 'spe', 'Sp1g11550' => 'spa', 'Sp2g16710' => 'spa', 'Sp3g00430' => 'spa', 'Sp3g26780' => 'spa', 'Sp5g22900' => 'spa', 'Sp6g29530' => 'spa', 'TAR371G0794' => 'tar', 'TAR374G0164' => 'tar', 'TAR622G0165' => 'tar', 'TAR626G0929' => 'tar', 'TAR629G2155' => 'tar', 'THA.LOC104805282' => 'tha', 'THA.LOC104805363' => 'tha', 'THA.LOC104808968' => 'tha', 'THA.LOC104821093' => 'tha', 'THA.LOC104823953' => 'tha', 'THA.LOC104825562' => 'tha', 'THA.LOC104825665' => 'tha', 'Thecc.02G261400' => 'tca', 'Thecc.04G019200' => 'tca', 'Thecc.09G130400' => 'tca', 'Thhalv10004374m.g' => 'esa', 'Thhalv10007850m.g' => 'esa', 'Thhalv10013782m.g' => 'esa', 'Thhalv10018686m.g' => 'esa', 'Thhalv10020899m.g' => 'esa', 'Thhalv10022755m.g' => 'esa', 'TPR.G23851' => 'tpr', 'TPR.G26500' => 'tpr', 'TPR.G27267' => 'tpr', 'TPR.G32001' => 'tpr', 'TPR.G6251' => 'tpr', 'TPR.G8167' => 'tpr', 'TWI12G1330' => 'twi', 'TWI18G1239' => 'twi', 'TWI34G0979' => 'twi', 'TWI36G0670' => 'twi', 'TWI36G0707' => 'twi', 'TWI56G0233' => 'twi', 'TWI75G1809' => 'twi', 'unitig_21.g20874' => 'ugi', 'unitig_26.g10343' => 'ugi', 'unitig_46.g18392' => 'ugi', 'unitig_52.g17178' => 'ugi', 'unitig_8.g2934' => 'ugi', 'vmacro01122' => 'vma', 'vmacro05875' => 'vma', 'vmacro06147' => 'vma', 'vmacro16191' => 'vma', 'vmacro18293' => 'vma', 'VMungo0251G3707' => 'vmu', 'VMungo0464G1521' => 'vmu', 'VMungo1215G0205' => 'vmu', 'VMungo1383G2484' => 'vmu', 'Zm00001eb079610' => 'zma', 'Zm00001eb135990' => 'zma', 'Zm00001eb183710' => 'zma', 'Zm00001eb246020' => 'zma' ), 'gf_id' => 'HOM05D001124', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001124' ), 'data_identifier' => 'HOM05D001124', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001124', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '548', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02520' => 'bna', 'A03p06630' => 'bna', 'A05p44460' => 'bna', 'A06p08710' => 'bna', 'A06p41090' => 'bna', 'A07p32320' => 'bna', 'A08p32520' => 'bna', 'A09p10360' => 'bna', 'A10p24080' => 'bna', 'Aa31LG11G15250' => 'aar', 'Aa31LG1G1800' => 'aar', 'Aa31LG2G5120' => 'aar', 'Aa31LG2G6070' => 'aar', 'Aa31LG5G10770' => 'aar', 'Aa31sc61G90' => 'aar', 'Actinidia01352' => 'ach', 'Actinidia05983' => 'ach', 'Actinidia08133' => 'ach', 'Actinidia15101' => 'ach', 'Actinidia26379' => 'ach', 'Actinidia35778' => 'ach', 'Actinidia36123' => 'ach', 'Actinidia37436' => 'ach', 'Actinidia38730' => 'ach', 'Ah.02g128210' => 'amhyb', 'Ah.03g132990' => 'amhyb', 'Ah.14g079410' => 'amhyb', 'AL1G24640' => 'aly', 'AL2G26680' => 'aly', 'AL3G10530' => 'aly', 'AL3G45230' => 'aly', 'AL5G15230' => 'aly', 'AL5G16960' => 'aly', 'AL6G25210' => 'aly', 'Aqoxy2G00441' => 'aox', 'Aqoxy3G01236' => 'aox', 'Aqoxy5G03746' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3RQ047' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C7GMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9C8JER' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MBL6KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YXCZ83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZANX40' => 'arhy', 'AT1G12990' => 'ath', 'AT1G67880' => 'ath', 'AT2G13290' => 'ath', 'AT3G01620' => 'ath', 'AT3G26445' => 'ath', 'AT3G27540' => 'ath', 'AT5G14480' => 'ath', 'ATR0824G026' => 'atr', 'ATR1098G019' => 'atr', 'Atru.chr11.2145' => 'acertr', 'Atru.chr2.3636' => 'acertr', 'Atru.chr2.3644' => 'acertr', 'Atru.chr6.2422' => 'acertr', 'Atru.chr7.1112' => 'acertr', 'AUR62005469' => 'cqu', 'AUR62011166' => 'cqu', 'AUR62013319' => 'cqu', 'AUR62024273' => 'cqu', 'AUR62028420' => 'cqu', 'AUR62041942' => 'cqu', 'BcaB01g04969' => 'bca', 'BcaB01g06371' => 'bca', 'BcaB02g11494' => 'bca', 'BcaB03g15382' => 'bca', 'BcaB08g36994' => 'bca', 'BcaC03g13477' => 'bca', 'BcaC03g13478' => 'bca', 'BcaC03g13480' => 'bca', 'BcaC03g13481' => 'bca', 'BcaC03g13486' => 'bca', 'BcaC04g19031' => 'bca', 'BcaC04g23085' => 'bca', 'BcaC05g25094' => 'bca', 'BcaC05g25096' => 'bca', 'BcaC05g25138' => 'bca', 'BcaC05g30416' => 'bca', 'BcaC05g30455' => 'bca', 'BcaC06g30979' => 'bca', 'BcaC06g33805' => 'bca', 'BcaC08g46021' => 'bca', 'BcaNung03154' => 'bca', 'BolC2t06623H' => 'bol', 'BolC2t06632H' => 'bol', 'BolC2t06635H' => 'bol', 'BolC2t06638H' => 'bol', 'BolC3t13266H' => 'bol', 'BolC5t29776H' => 'bol', 'BolC6t38912H' => 'bol', 'BolC7t44183H' => 'bol', 'BolC9t54123H' => 'bol', 'BolC9t59107H' => 'bol', 'BraA02t05221Z' => 'bra', 'BraA03t09996Z' => 'bra', 'BraA05t23210Z' => 'bra', 'BraA06t24068Z' => 'bra', 'BraA06t27032Z' => 'bra', 'BraA08t35176Z' => 'bra', 'BraA09t36680Z' => 'bra', 'BraA10t44471Z' => 'bra', 'C02p06760' => 'bna', 'C02p06890' => 'bna', 'C02p07010' => 'bna', 'C03p07660' => 'bna', 'C05p10300' => 'bna', 'C06p38150' => 'bna', 'C07p36650' => 'bna', 'C08p15770' => 'bna', 'C09p12300' => 'bna', 'C09p62700' => 'bna', 'C09p75040' => 'bna', 'CAN.G13.1' => 'can', 'CAN.G138.4' => 'can', 'CAN.G44.6' => 'can', 'CAN.G473.19' => 'can', 'CANSAT01G0835' => 'cansat', 'CANSAT11G0246' => 'cansat', 'CANSAT11G1766' => 'cansat', 'CANSAT64G1954' => 'cansat', 'CARHR013330' => 'chi', 'CARHR060530' => 'chi', 'CARHR075300' => 'chi', 'CARHR105120' => 'chi', 'CARHR148910' => 'chi', 'CARHR198830' => 'chi', 'Carub.0001s1275' => 'cru', 'Carub.0002s1437' => 'cru', 'Carub.0003s0044' => 'cru', 'Carub.0003s2787' => 'cru', 'Carub.0005s0597' => 'cru', 'Carub.0006s1266' => 'cru', 'Ca_06935_v3' => 'car', 'Ca_13559_v3' => 'car', 'Ca_16941_v3' => 'car', 'Ca_16960_v3' => 'car', 'Ca_17775_v3' => 'car', 'Ca_30464_v3' => 'car', 'Cc06_g08160' => 'ccan', 'Cc07_g01520' => 'ccan', 'Cc11_g15810' => 'ccan', 'CDE02G2840' => 'cde', 'CDE03G0093' => 'cde', 'CDE04G2127' => 'cde', 'CDE07G1857' => 'cde', 'CDE09G1246' => 'cde', 'Cfa003412' => 'cfa', 'Cfa007341' => 'cfa', 'Cfa009220' => 'cfa', 'Ciclev10008737m.g' => 'ccl', 'Ciclev10015565m.g' => 'ccl', 'Ciclev10031761m.g' => 'ccl', 'CiPaw.03G045300' => 'cil', 'CiPaw.03G247200' => 'cil', 'CiPaw.04G029500' => 'cil', 'CiPaw.04G174000' => 'cil', 'CiPaw.05G181200' => 'cil', 'CiPaw.06G067100' => 'cil', 'ClCG05G025800' => 'cla', 'ClCG06G011400' => 'cla', 'ClCG09G019360' => 'cla', 'COL.COLO4_04827' => 'col', 'COL.COLO4_29170' => 'col', 'COL.COLO4_35131' => 'col', 'COL.COLO4_35132' => 'col', 'Cpa.g.sc33.32' => 'cpa', 'Cpa.g.sc46.29' => 'cpa', 'Cpa.g.sc796.1' => 'cpa', 'CsaV3_1G030420' => 'csa', 'CsaV3_5G027050' => 'csa', 'CsaV3_5G031040' => 'csa', 'CsaV3_UNG023130' => 'csa', 'CSS0007726' => 'camsi', 'CSS0016433' => 'camsi', 'CSS0017656' => 'camsi', 'CSS0025364' => 'camsi', 'CSS0027582' => 'camsi', 'CSS0047288' => 'camsi', 'CSS0049950' => 'camsi', 'DCAR_003843' => 'dca', 'DCAR_007052' => 'dca', 'DCAR_020884' => 'dca', 'DCAR_021730' => 'dca', 'DCAR_024423' => 'dca', 'DCAR_026509' => 'dca', 'DCAR_031158' => 'dca', 'Dinv14728' => 'din', 'Dinv15219' => 'din', 'Dinv25728' => 'din', 'Dinv33428' => 'din', 'Dinv36489' => 'din', 'Dinv41486' => 'din', 'Duzib147G0469' => 'dzi', 'Duzib168G0060' => 'dzi', 'Duzib187G1215' => 'dzi', 'Duzib248G0692' => 'dzi', 'Duzib251G0767' => 'dzi', 'Duzib264G0446' => 'dzi', 'Duzib268G0691' => 'dzi', 'ECA232G4767' => 'eca', 'ECA233G2838' => 'eca', 'ECA234G0391' => 'eca', 'ECA234G0857' => 'eca', 'ECA236G1593' => 'eca', 'ECA238G0565' => 'eca', 'ECA246G1027' => 'eca', 'ECA246G3223' => 'eca', 'ECA246G3470' => 'eca', 'EL10Ac6g13829' => 'bvu', 'EL10Ac6g14093' => 'bvu', 'EL10Ac8g18707' => 'bvu', 'Eucgr.C01369' => 'egr', 'Eucgr.H02492' => 'egr', 'Eucgr.I01733' => 'egr', 'Eucgr.J02255' => 'egr', 'Eucgr.J02257' => 'egr', 'Eucgr.J02258' => 'egr', 'FAN02G1601' => 'fan', 'FAN03G1586' => 'fan', 'FAN03G2986' => 'fan', 'FAN05G4837' => 'fan', 'FAN06G0146' => 'fan', 'FAN07G0858' => 'fan', 'FAN09G3179' => 'fan', 'FAN10G0669' => 'fan', 'FAN12G2358' => 'fan', 'FAN14G4198' => 'fan', 'FAN14G5112' => 'fan', 'FAN17G0342' => 'fan', 'FAN19G0342' => 'fan', 'FAN19G0962' => 'fan', 'FAN19G1101' => 'fan', 'FAN19G1872' => 'fan', 'FAN22G0356' => 'fan', 'FAN23G0744' => 'fan', 'FAN23G1914' => 'fan', 'FAN26G0032' => 'fan', 'FAN28G0625' => 'fan', 'FvH4_1g02710' => 'fve', 'FvH4_1g02720' => 'fve', 'FvH4_4g25670' => 'fve', 'FvH4_6g51700' => 'fve', 'FvH4_7g20170' => 'fve', 'Glyma.05G175000' => 'gma', 'Glyma.08G132300' => 'gma', 'Glyma.11G243000' => 'gma', 'Glyma.13G158900' => 'gma', 'Glyma.17G112400' => 'gma', 'Glyma.18G014100' => 'gma', 'Glyma.19G003100' => 'gma', 'Glyma.19G056500' => 'gma', 'Gohir.A01G158900' => 'ghi', 'Gohir.A05G312600' => 'ghi', 'Gohir.A05G354900' => 'ghi', 'Gohir.A07G037200' => 'ghi', 'Gohir.A09G030000' => 'ghi', 'Gohir.A12G145200' => 'ghi', 'Gohir.D01G151500' => 'ghi', 'Gohir.D04G058300' => 'ghi', 'Gohir.D05G314100' => 'ghi', 'Gohir.D07G041400' => 'ghi', 'Gohir.D09G029700' => 'ghi', 'Gohir.D12G149700' => 'ghi', 'Gorai.001G043800' => 'gra', 'Gorai.002G187800' => 'gra', 'Gorai.006G034700' => 'gra', 'Gorai.008G161200' => 'gra', 'Gorai.009G335700' => 'gra', 'Gorai.012G065000' => 'gra', 'GSVIVG01000535001' => 'vvi', 'GSVIVG01015572001' => 'vvi', 'GSVIVG01032386001' => 'vvi', 'HanXRQChr05g0138531' => 'han', 'HanXRQChr06g0174391' => 'han', 'HanXRQChr07g0199021' => 'han', 'HanXRQChr08g0208211' => 'han', 'HanXRQChr09g0255471' => 'han', 'HanXRQChr10g0315791' => 'han', 'HanXRQChr12g0371991' => 'han', 'HanXRQChr15g0475251' => 'han', 'HanXRQChr17g0540001' => 'han', 'HanXRQChr17g0548631' => 'han', 'HanXRQChr17g0569561' => 'han', 'Haze_12256' => 'cav', 'Haze_14756' => 'cav', 'Haze_25528' => 'cav', 'Hma1.2p1_0079F.1_g041020' => 'hma', 'Hma1.2p1_0818F.1_g223260' => 'hma', 'Hma1.2p1_1747F.1_g300530' => 'hma', 'HPP92_004607' => 'vpl', 'HPP92_004608' => 'vpl', 'HPP92_006181' => 'vpl', 'HPP92_012192' => 'vpl', 'HPP92_015680' => 'vpl', 'HPP92_020249' => 'vpl', 'HPP92_021376' => 'vpl', 'HPP92_024275' => 'vpl', 'Hund06031' => 'sun', 'Hund25391' => 'sun', 'Lalb_Chr07g0185371' => 'lal', 'Lalb_Chr07g0185381' => 'lal', 'Lalb_Chr12g0204011' => 'lal', 'Lalb_Chr13g0301671' => 'lal', 'Lalb_Chr14g0362851' => 'lal', 'Lalb_Chr24g0403581' => 'lal', 'Lj1g0000233' => 'lja', 'Lj2g0018120' => 'lja', 'Lj3C621T0' => 'lonja', 'Lj3P1059T14' => 'lonja', 'Lj3P611T9' => 'lonja', 'Lj3P614T13' => 'lonja', 'Lj3P615T5' => 'lonja', 'Lj4g0012315' => 'lja', 'Lj4g0026182' => 'lja', 'Lj6P813T16' => 'lonja', 'Lj7C427T7' => 'lonja', 'Lj7C427T8' => 'lonja', 'Lj7P600T41' => 'lonja', 'Lju41C42G17' => 'lonja', 'Lsat_1_v5_gn_0_47300' => 'lsa', 'Lsat_1_v5_gn_2_91280' => 'lsa', 'Lsat_1_v5_gn_3_30561' => 'lsa', 'Lsat_1_v5_gn_4_184321' => 'lsa', 'Lsat_1_v5_gn_4_4041' => 'lsa', 'Lsat_1_v5_gn_5_92000' => 'lsa', 'Lsat_1_v5_gn_8_152940' => 'lsa', 'Lsat_1_v5_gn_8_62401' => 'lsa', 'Manes.06G055900' => 'mes', 'Manes.12G022200' => 'mes', 'Manes.13G023300' => 'mes', 'Manes.14G115000' => 'mes', 'Manes.15G151700' => 'mes', 'Manes.17G111300' => 'mes', 'Mapoly0226s0009' => 'mpo', 'MBI02_g25363_MAGBIO' => 'mbi', 'MBI06_g00027_MAGBIO' => 'mbi', 'MBI10_g13034_MAGBIO' => 'mbi', 'MD09G1023400' => 'mdo', 'MD13G1100100' => 'mdo', 'MD15G1169200' => 'mdo', 'MD16G1101100' => 'mdo', 'MD17G1022900' => 'mdo', 'Medtr3g096150' => 'mtr', 'Medtr4g115070' => 'mtr', 'Medtr7g033325' => 'mtr', 'Medtr8g089840' => 'mtr', 'MELO3C010319.2' => 'cme', 'MELO3C011944.2' => 'cme', 'MELO3C021589.2' => 'cme', 'Migut.E00207' => 'egut', 'Migut.H00067' => 'egut', 'Migut.K00433' => 'egut', 'Migut.K00606' => 'egut', 'Migut.K01410' => 'egut', 'MSTRG.13347' => 'ama', 'MSTRG.24045' => 'ama', 'MSTRG.2428' => 'ama', 'MSTRG.26410' => 'ama', 'MSTRG.3139' => 'ama', 'MSTRG.3286' => 'ama', 'MSTRG.563' => 'ama', 'MSTRG.7941' => 'ama', 'Nitab4.5_0000028g0060' => 'nta', 'Nitab4.5_0000065g0260' => 'nta', 'Nitab4.5_0000112g0060' => 'nta', 'Nitab4.5_0000489g0120' => 'nta', 'Nitab4.5_0001776g0050' => 'nta', 'Nitab4.5_0001854g0010' => 'nta', 'Nitab4.5_0001860g0020' => 'nta', 'Nitab4.5_0004352g0010' => 'nta', 'Nitab4.5_0008716g0020' => 'nta', 'Nitab4.5_0008922g0010' => 'nta', 'Nn3g16693' => 'nnu', 'Nn4g22596' => 'nnu', 'Nn7g37639' => 'nnu', 'Oeu001701.1' => 'oeu', 'Oeu018149.1' => 'oeu', 'Oeu026220.1' => 'oeu', 'Oeu038635.1' => 'oeu', 'Oeu049176.1' => 'oeu', 'Oeu056706.1' => 'oeu', 'Oeu056937.1' => 'oeu', 'Oeu057540.1' => 'oeu', 'Os02g0594900' => 'osa', 'Os02g0595100' => 'osa', 'Os04g0477500' => 'osa', 'Os12g0611900' => 'osa', 'Peaxi162Scf00076g00020' => 'pax', 'Peaxi162Scf00128g00217' => 'pax', 'Peaxi162Scf00129g01640' => 'pax', 'Peaxi162Scf00669g00007' => 'pax', 'Peaxi162Scf00700g00421' => 'pax', 'Peaxi162Scf00801g00038' => 'pax', 'Peaxi162Scf00891g00025' => 'pax', 'PGR083G0909' => 'pgr', 'PGR119G1005' => 'pgr', 'PGR142G2236' => 'pgr', 'PGR142G3388' => 'pgr', 'PGSC0003DMG400004514' => 'stu', 'PGSC0003DMG400012635' => 'stu', 'PGSC0003DMG400015730' => 'stu', 'PGSC0003DMG400018611' => 'stu', 'PGSC0003DMG400030897' => 'stu', 'Phvul.001G254800' => 'pvu', 'Phvul.002G260100' => 'pvu', 'Phvul.003G167600' => 'pvu', 'Phvul.004G005100' => 'pvu', 'Potri.001G343600' => 'ptr', 'Potri.006G066700' => 'ptr', 'Potri.008G186000' => 'ptr', 'Potri.010G046900' => 'ptr', 'Potri.018G127900' => 'ptr', 'Pp3c20_17750' => 'ppa', 'Pp3c24_4380' => 'ppa', 'Prupe.1G245800' => 'ppe', 'Prupe.3G293400' => 'ppe', 'Prupe.7G247400' => 'ppe', 'Psat0s145g0120' => 'psa', 'Psat0s595g0040' => 'psa', 'Psat0s595g0120' => 'psa', 'Psat3g175040' => 'psa', 'Psat7g058120' => 'psa', 'PSO017G0428' => 'pso', 'PSO063G7510' => 'pso', 'PSO067G0046' => 'pso', 'PSO478G1073' => 'pso', 'PSO675G3677' => 'pso', 'PSO675G6558' => 'pso', 'PSO675G7520' => 'pso', 'PSO675G8959' => 'pso', 'QL02p074089' => 'qlo', 'QL02p089614' => 'qlo', 'QL03p057736' => 'qlo', 'RcHm_v2.0_Chr1g0364131' => 'rch', 'RcHm_v2.0_Chr2g0087801' => 'rch', 'RcHm_v2.0_Chr2g0087821' => 'rch', 'RcHm_v2.0_Chr2g0173231' => 'rch', 'RcHm_v2.0_Chr4g0433111' => 'rch', 'Rhsim03G0250300' => 'rsi', 'Rhsim08G0048400' => 'rsi', 'Rhsim10G0014800' => 'rsi', 'Rhsim12G0040100' => 'rsi', 'Rhsim12G0109700' => 'rsi', 'Sabra06G0049600' => 'sbr', 'Sabra08G0141000' => 'sbr', 'Sabra10G0021400' => 'sbr', 'Sabra16G0222900' => 'sbr', 'Sabra18G0108600' => 'sbr', 'SalBow1G0433' => 'sbo', 'SalBow1G2038' => 'sbo', 'SalBow1G5003' => 'sbo', 'SalBow7G1197' => 'sbo', 'SalBow8G3506' => 'sbo', 'Sc03g0007300' => 'sci', 'Sc11g0000950' => 'sci', 'Sc14g0008750' => 'sci', 'Sc18g0000420' => 'sci', 'Sed0006754' => 'sed', 'Sed0008741' => 'sed', 'Sed0017172' => 'sed', 'Sed0018925' => 'sed', 'Sed0023326' => 'sed', 'Sed0025909' => 'sed', 'SEGI_05333' => 'sgi', 'SEGI_10362' => 'sgi', 'SEGI_13380' => 'sgi', 'SEGI_24306' => 'sgi', 'SEGI_29077' => 'sgi', 'SEGI_29095' => 'sgi', 'SEGI_36534' => 'sgi', 'SEGI_37506' => 'sgi', 'SEGI_38321' => 'sgi', 'SGA_v2.0_scaffold307G48031' => 'sas', 'SGA_v2.0_scaffold47G17507' => 'sas', 'SGA_v2.0_scaffold63G21736' => 'sas', 'SGA_v2.0_scaffold87G27070' => 'sas', 'SHI17794' => 'shi', 'SHI28851' => 'shi', 'SMO165G0155' => 'smo', 'SMO340G0217' => 'smo', 'SMO367G1210' => 'smo', 'Solyc02g093430.3' => 'sly', 'Solyc05g013580.4' => 'sly', 'Solyc07g008030.3' => 'sly', 'Solyc12g035470.2' => 'sly', 'Sopen02g038020' => 'spe', 'Sopen05g008490' => 'spe', 'Sopen07g003910' => 'spe', 'Sopen12g015240' => 'spe', 'Sp1g11550' => 'spa', 'Sp2g16710' => 'spa', 'Sp3g00430' => 'spa', 'Sp3g26780' => 'spa', 'Sp5g22900' => 'spa', 'Sp6g29530' => 'spa', 'TAR371G0794' => 'tar', 'TAR374G0164' => 'tar', 'TAR622G0165' => 'tar', 'TAR626G0929' => 'tar', 'TAR629G2155' => 'tar', 'THA.LOC104805282' => 'tha', 'THA.LOC104805363' => 'tha', 'THA.LOC104808968' => 'tha', 'THA.LOC104821093' => 'tha', 'THA.LOC104823953' => 'tha', 'THA.LOC104825562' => 'tha', 'THA.LOC104825665' => 'tha', 'Thecc.02G261400' => 'tca', 'Thecc.04G019200' => 'tca', 'Thecc.09G130400' => 'tca', 'Thhalv10004374m.g' => 'esa', 'Thhalv10007850m.g' => 'esa', 'Thhalv10013782m.g' => 'esa', 'Thhalv10018686m.g' => 'esa', 'Thhalv10020899m.g' => 'esa', 'Thhalv10022755m.g' => 'esa', 'TPR.G23851' => 'tpr', 'TPR.G26500' => 'tpr', 'TPR.G27267' => 'tpr', 'TPR.G32001' => 'tpr', 'TPR.G6251' => 'tpr', 'TPR.G8167' => 'tpr', 'TWI12G1330' => 'twi', 'TWI18G1239' => 'twi', 'TWI34G0979' => 'twi', 'TWI36G0670' => 'twi', 'TWI36G0707' => 'twi', 'TWI56G0233' => 'twi', 'TWI75G1809' => 'twi', 'unitig_21.g20874' => 'ugi', 'unitig_26.g10343' => 'ugi', 'unitig_46.g18392' => 'ugi', 'unitig_52.g17178' => 'ugi', 'unitig_8.g2934' => 'ugi', 'vmacro01122' => 'vma', 'vmacro05875' => 'vma', 'vmacro06147' => 'vma', 'vmacro16191' => 'vma', 'vmacro18293' => 'vma', 'VMungo0251G3707' => 'vmu', 'VMungo0464G1521' => 'vmu', 'VMungo1215G0205' => 'vmu', 'VMungo1383G2484' => 'vmu', 'Zm00001eb079610' => 'zma', 'Zm00001eb135990' => 'zma', 'Zm00001eb183710' => 'zma', 'Zm00001eb246020' => 'zma' ) $gf_id = 'HOM05D001124' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001124' ) $data_identifier = 'HOM05D001124' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 6, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 7, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 21, 'bol' => (int) 10, 'bra' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 6, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 9, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 21, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 8, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 10, 'lsa' => (int) 8, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 8, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 9, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb246020' $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' => 'HOM05D001124', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '548', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02520' => 'bna', 'A03p06630' => 'bna', 'A05p44460' => 'bna', 'A06p08710' => 'bna', 'A06p41090' => 'bna', 'A07p32320' => 'bna', 'A08p32520' => 'bna', 'A09p10360' => 'bna', 'A10p24080' => 'bna', 'Aa31LG11G15250' => 'aar', 'Aa31LG1G1800' => 'aar', 'Aa31LG2G5120' => 'aar', 'Aa31LG2G6070' => 'aar', 'Aa31LG5G10770' => 'aar', 'Aa31sc61G90' => 'aar', 'Actinidia01352' => 'ach', 'Actinidia05983' => 'ach', 'Actinidia08133' => 'ach', 'Actinidia15101' => 'ach', 'Actinidia26379' => 'ach', 'Actinidia35778' => 'ach', 'Actinidia36123' => 'ach', 'Actinidia37436' => 'ach', 'Actinidia38730' => 'ach', 'Ah.02g128210' => 'amhyb', 'Ah.03g132990' => 'amhyb', 'Ah.14g079410' => 'amhyb', 'AL1G24640' => 'aly', 'AL2G26680' => 'aly', 'AL3G10530' => 'aly', 'AL3G45230' => 'aly', 'AL5G15230' => 'aly', 'AL5G16960' => 'aly', 'AL6G25210' => 'aly', 'Aqoxy2G00441' => 'aox', 'Aqoxy3G01236' => 'aox', 'Aqoxy5G03746' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3RQ047' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C7GMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9C8JER' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MBL6KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YXCZ83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZANX40' => 'arhy', 'AT1G12990' => 'ath', 'AT1G67880' => 'ath', 'AT2G13290' => 'ath', 'AT3G01620' => 'ath', 'AT3G26445' => 'ath', 'AT3G27540' => 'ath', 'AT5G14480' => 'ath', 'ATR0824G026' => 'atr', 'ATR1098G019' => 'atr', 'Atru.chr11.2145' => 'acertr', 'Atru.chr2.3636' => 'acertr', 'Atru.chr2.3644' => 'acertr', 'Atru.chr6.2422' => 'acertr', 'Atru.chr7.1112' => 'acertr', 'AUR62005469' => 'cqu', 'AUR62011166' => 'cqu', 'AUR62013319' => 'cqu', 'AUR62024273' => 'cqu', 'AUR62028420' => 'cqu', 'AUR62041942' => 'cqu', 'BcaB01g04969' => 'bca', 'BcaB01g06371' => 'bca', 'BcaB02g11494' => 'bca', 'BcaB03g15382' => 'bca', 'BcaB08g36994' => 'bca', 'BcaC03g13477' => 'bca', 'BcaC03g13478' => 'bca', 'BcaC03g13480' => 'bca', 'BcaC03g13481' => 'bca', 'BcaC03g13486' => 'bca', 'BcaC04g19031' => 'bca', 'BcaC04g23085' => 'bca', 'BcaC05g25094' => 'bca', 'BcaC05g25096' => 'bca', 'BcaC05g25138' => 'bca', 'BcaC05g30416' => 'bca', 'BcaC05g30455' => 'bca', 'BcaC06g30979' => 'bca', 'BcaC06g33805' => 'bca', 'BcaC08g46021' => 'bca', 'BcaNung03154' => 'bca', 'BolC2t06623H' => 'bol', 'BolC2t06632H' => 'bol', 'BolC2t06635H' => 'bol', 'BolC2t06638H' => 'bol', 'BolC3t13266H' => 'bol', 'BolC5t29776H' => 'bol', 'BolC6t38912H' => 'bol', 'BolC7t44183H' => 'bol', 'BolC9t54123H' => 'bol', 'BolC9t59107H' => 'bol', 'BraA02t05221Z' => 'bra', 'BraA03t09996Z' => 'bra', 'BraA05t23210Z' => 'bra', 'BraA06t24068Z' => 'bra', 'BraA06t27032Z' => 'bra', 'BraA08t35176Z' => 'bra', 'BraA09t36680Z' => 'bra', 'BraA10t44471Z' => 'bra', 'C02p06760' => 'bna', 'C02p06890' => 'bna', 'C02p07010' => 'bna', 'C03p07660' => 'bna', 'C05p10300' => 'bna', 'C06p38150' => 'bna', 'C07p36650' => 'bna', 'C08p15770' => 'bna', 'C09p12300' => 'bna', 'C09p62700' => 'bna', 'C09p75040' => 'bna', 'CAN.G13.1' => 'can', 'CAN.G138.4' => 'can', 'CAN.G44.6' => 'can', 'CAN.G473.19' => 'can', 'CANSAT01G0835' => 'cansat', 'CANSAT11G0246' => 'cansat', 'CANSAT11G1766' => 'cansat', 'CANSAT64G1954' => 'cansat', 'CARHR013330' => 'chi', 'CARHR060530' => 'chi', 'CARHR075300' => 'chi', 'CARHR105120' => 'chi', 'CARHR148910' => 'chi', 'CARHR198830' => 'chi', 'Carub.0001s1275' => 'cru', 'Carub.0002s1437' => 'cru', 'Carub.0003s0044' => 'cru', 'Carub.0003s2787' => 'cru', 'Carub.0005s0597' => 'cru', 'Carub.0006s1266' => 'cru', 'Ca_06935_v3' => 'car', 'Ca_13559_v3' => 'car', 'Ca_16941_v3' => 'car', 'Ca_16960_v3' => 'car', 'Ca_17775_v3' => 'car', 'Ca_30464_v3' => 'car', 'Cc06_g08160' => 'ccan', 'Cc07_g01520' => 'ccan', 'Cc11_g15810' => 'ccan', 'CDE02G2840' => 'cde', 'CDE03G0093' => 'cde', 'CDE04G2127' => 'cde', 'CDE07G1857' => 'cde', 'CDE09G1246' => 'cde', 'Cfa003412' => 'cfa', 'Cfa007341' => 'cfa', 'Cfa009220' => 'cfa', 'Ciclev10008737m.g' => 'ccl', 'Ciclev10015565m.g' => 'ccl', 'Ciclev10031761m.g' => 'ccl', 'CiPaw.03G045300' => 'cil', 'CiPaw.03G247200' => 'cil', 'CiPaw.04G029500' => 'cil', 'CiPaw.04G174000' => 'cil', 'CiPaw.05G181200' => 'cil', 'CiPaw.06G067100' => 'cil', 'ClCG05G025800' => 'cla', 'ClCG06G011400' => 'cla', 'ClCG09G019360' => 'cla', 'COL.COLO4_04827' => 'col', 'COL.COLO4_29170' => 'col', 'COL.COLO4_35131' => 'col', 'COL.COLO4_35132' => 'col', 'Cpa.g.sc33.32' => 'cpa', 'Cpa.g.sc46.29' => 'cpa', 'Cpa.g.sc796.1' => 'cpa', 'CsaV3_1G030420' => 'csa', 'CsaV3_5G027050' => 'csa', 'CsaV3_5G031040' => 'csa', 'CsaV3_UNG023130' => 'csa', 'CSS0007726' => 'camsi', 'CSS0016433' => 'camsi', 'CSS0017656' => 'camsi', 'CSS0025364' => 'camsi', 'CSS0027582' => 'camsi', 'CSS0047288' => 'camsi', 'CSS0049950' => 'camsi', 'DCAR_003843' => 'dca', 'DCAR_007052' => 'dca', 'DCAR_020884' => 'dca', 'DCAR_021730' => 'dca', 'DCAR_024423' => 'dca', 'DCAR_026509' => 'dca', 'DCAR_031158' => 'dca', 'Dinv14728' => 'din', 'Dinv15219' => 'din', 'Dinv25728' => 'din', 'Dinv33428' => 'din', 'Dinv36489' => 'din', 'Dinv41486' => 'din', 'Duzib147G0469' => 'dzi', 'Duzib168G0060' => 'dzi', 'Duzib187G1215' => 'dzi', 'Duzib248G0692' => 'dzi', 'Duzib251G0767' => 'dzi', 'Duzib264G0446' => 'dzi', 'Duzib268G0691' => 'dzi', 'ECA232G4767' => 'eca', 'ECA233G2838' => 'eca', 'ECA234G0391' => 'eca', 'ECA234G0857' => 'eca', 'ECA236G1593' => 'eca', 'ECA238G0565' => 'eca', 'ECA246G1027' => 'eca', 'ECA246G3223' => 'eca', 'ECA246G3470' => 'eca', 'EL10Ac6g13829' => 'bvu', 'EL10Ac6g14093' => 'bvu', 'EL10Ac8g18707' => 'bvu', 'Eucgr.C01369' => 'egr', 'Eucgr.H02492' => 'egr', 'Eucgr.I01733' => 'egr', 'Eucgr.J02255' => 'egr', 'Eucgr.J02257' => 'egr', 'Eucgr.J02258' => 'egr', 'FAN02G1601' => 'fan', 'FAN03G1586' => 'fan', 'FAN03G2986' => 'fan', 'FAN05G4837' => 'fan', 'FAN06G0146' => 'fan', 'FAN07G0858' => 'fan', 'FAN09G3179' => 'fan', 'FAN10G0669' => 'fan', 'FAN12G2358' => 'fan', 'FAN14G4198' => 'fan', 'FAN14G5112' => 'fan', 'FAN17G0342' => 'fan', 'FAN19G0342' => 'fan', 'FAN19G0962' => 'fan', 'FAN19G1101' => 'fan', 'FAN19G1872' => 'fan', 'FAN22G0356' => 'fan', 'FAN23G0744' => 'fan', 'FAN23G1914' => 'fan', 'FAN26G0032' => 'fan', 'FAN28G0625' => 'fan', 'FvH4_1g02710' => 'fve', 'FvH4_1g02720' => 'fve', 'FvH4_4g25670' => 'fve', 'FvH4_6g51700' => 'fve', 'FvH4_7g20170' => 'fve', 'Glyma.05G175000' => 'gma', 'Glyma.08G132300' => 'gma', 'Glyma.11G243000' => 'gma', 'Glyma.13G158900' => 'gma', 'Glyma.17G112400' => 'gma', 'Glyma.18G014100' => 'gma', 'Glyma.19G003100' => 'gma', 'Glyma.19G056500' => 'gma', 'Gohir.A01G158900' => 'ghi', 'Gohir.A05G312600' => 'ghi', 'Gohir.A05G354900' => 'ghi', 'Gohir.A07G037200' => 'ghi', 'Gohir.A09G030000' => 'ghi', 'Gohir.A12G145200' => 'ghi', 'Gohir.D01G151500' => 'ghi', 'Gohir.D04G058300' => 'ghi', 'Gohir.D05G314100' => 'ghi', 'Gohir.D07G041400' => 'ghi', 'Gohir.D09G029700' => 'ghi', 'Gohir.D12G149700' => 'ghi', 'Gorai.001G043800' => 'gra', 'Gorai.002G187800' => 'gra', 'Gorai.006G034700' => 'gra', 'Gorai.008G161200' => 'gra', 'Gorai.009G335700' => 'gra', 'Gorai.012G065000' => 'gra', 'GSVIVG01000535001' => 'vvi', 'GSVIVG01015572001' => 'vvi', 'GSVIVG01032386001' => 'vvi', 'HanXRQChr05g0138531' => 'han', 'HanXRQChr06g0174391' => 'han', 'HanXRQChr07g0199021' => 'han', 'HanXRQChr08g0208211' => 'han', 'HanXRQChr09g0255471' => 'han', 'HanXRQChr10g0315791' => 'han', 'HanXRQChr12g0371991' => 'han', 'HanXRQChr15g0475251' => 'han', 'HanXRQChr17g0540001' => 'han', 'HanXRQChr17g0548631' => 'han', 'HanXRQChr17g0569561' => 'han', 'Haze_12256' => 'cav', 'Haze_14756' => 'cav', 'Haze_25528' => 'cav', 'Hma1.2p1_0079F.1_g041020' => 'hma', 'Hma1.2p1_0818F.1_g223260' => 'hma', 'Hma1.2p1_1747F.1_g300530' => 'hma', 'HPP92_004607' => 'vpl', 'HPP92_004608' => 'vpl', 'HPP92_006181' => 'vpl', 'HPP92_012192' => 'vpl', 'HPP92_015680' => 'vpl', 'HPP92_020249' => 'vpl', 'HPP92_021376' => 'vpl', 'HPP92_024275' => 'vpl', 'Hund06031' => 'sun', 'Hund25391' => 'sun', 'Lalb_Chr07g0185371' => 'lal', 'Lalb_Chr07g0185381' => 'lal', 'Lalb_Chr12g0204011' => 'lal', 'Lalb_Chr13g0301671' => 'lal', 'Lalb_Chr14g0362851' => 'lal', 'Lalb_Chr24g0403581' => 'lal', 'Lj1g0000233' => 'lja', 'Lj2g0018120' => 'lja', 'Lj3C621T0' => 'lonja', 'Lj3P1059T14' => 'lonja', 'Lj3P611T9' => 'lonja', 'Lj3P614T13' => 'lonja', 'Lj3P615T5' => 'lonja', 'Lj4g0012315' => 'lja', 'Lj4g0026182' => 'lja', 'Lj6P813T16' => 'lonja', 'Lj7C427T7' => 'lonja', 'Lj7C427T8' => 'lonja', 'Lj7P600T41' => 'lonja', 'Lju41C42G17' => 'lonja', 'Lsat_1_v5_gn_0_47300' => 'lsa', 'Lsat_1_v5_gn_2_91280' => 'lsa', 'Lsat_1_v5_gn_3_30561' => 'lsa', 'Lsat_1_v5_gn_4_184321' => 'lsa', 'Lsat_1_v5_gn_4_4041' => 'lsa', 'Lsat_1_v5_gn_5_92000' => 'lsa', 'Lsat_1_v5_gn_8_152940' => 'lsa', 'Lsat_1_v5_gn_8_62401' => 'lsa', 'Manes.06G055900' => 'mes', 'Manes.12G022200' => 'mes', 'Manes.13G023300' => 'mes', 'Manes.14G115000' => 'mes', 'Manes.15G151700' => 'mes', 'Manes.17G111300' => 'mes', 'Mapoly0226s0009' => 'mpo', 'MBI02_g25363_MAGBIO' => 'mbi', 'MBI06_g00027_MAGBIO' => 'mbi', 'MBI10_g13034_MAGBIO' => 'mbi', 'MD09G1023400' => 'mdo', 'MD13G1100100' => 'mdo', 'MD15G1169200' => 'mdo', 'MD16G1101100' => 'mdo', 'MD17G1022900' => 'mdo', 'Medtr3g096150' => 'mtr', 'Medtr4g115070' => 'mtr', 'Medtr7g033325' => 'mtr', 'Medtr8g089840' => 'mtr', 'MELO3C010319.2' => 'cme', 'MELO3C011944.2' => 'cme', 'MELO3C021589.2' => 'cme', 'Migut.E00207' => 'egut', 'Migut.H00067' => 'egut', 'Migut.K00433' => 'egut', 'Migut.K00606' => 'egut', 'Migut.K01410' => 'egut', 'MSTRG.13347' => 'ama', 'MSTRG.24045' => 'ama', 'MSTRG.2428' => 'ama', 'MSTRG.26410' => 'ama', 'MSTRG.3139' => 'ama', 'MSTRG.3286' => 'ama', 'MSTRG.563' => 'ama', 'MSTRG.7941' => 'ama', 'Nitab4.5_0000028g0060' => 'nta', 'Nitab4.5_0000065g0260' => 'nta', 'Nitab4.5_0000112g0060' => 'nta', 'Nitab4.5_0000489g0120' => 'nta', 'Nitab4.5_0001776g0050' => 'nta', 'Nitab4.5_0001854g0010' => 'nta', 'Nitab4.5_0001860g0020' => 'nta', 'Nitab4.5_0004352g0010' => 'nta', 'Nitab4.5_0008716g0020' => 'nta', 'Nitab4.5_0008922g0010' => 'nta', 'Nn3g16693' => 'nnu', 'Nn4g22596' => 'nnu', 'Nn7g37639' => 'nnu', 'Oeu001701.1' => 'oeu', 'Oeu018149.1' => 'oeu', 'Oeu026220.1' => 'oeu', 'Oeu038635.1' => 'oeu', 'Oeu049176.1' => 'oeu', 'Oeu056706.1' => 'oeu', 'Oeu056937.1' => 'oeu', 'Oeu057540.1' => 'oeu', 'Os02g0594900' => 'osa', 'Os02g0595100' => 'osa', 'Os04g0477500' => 'osa', 'Os12g0611900' => 'osa', 'Peaxi162Scf00076g00020' => 'pax', 'Peaxi162Scf00128g00217' => 'pax', 'Peaxi162Scf00129g01640' => 'pax', 'Peaxi162Scf00669g00007' => 'pax', 'Peaxi162Scf00700g00421' => 'pax', 'Peaxi162Scf00801g00038' => 'pax', 'Peaxi162Scf00891g00025' => 'pax', 'PGR083G0909' => 'pgr', 'PGR119G1005' => 'pgr', 'PGR142G2236' => 'pgr', 'PGR142G3388' => 'pgr', 'PGSC0003DMG400004514' => 'stu', 'PGSC0003DMG400012635' => 'stu', 'PGSC0003DMG400015730' => 'stu', 'PGSC0003DMG400018611' => 'stu', 'PGSC0003DMG400030897' => 'stu', 'Phvul.001G254800' => 'pvu', 'Phvul.002G260100' => 'pvu', 'Phvul.003G167600' => 'pvu', 'Phvul.004G005100' => 'pvu', 'Potri.001G343600' => 'ptr', 'Potri.006G066700' => 'ptr', 'Potri.008G186000' => 'ptr', 'Potri.010G046900' => 'ptr', 'Potri.018G127900' => 'ptr', 'Pp3c20_17750' => 'ppa', 'Pp3c24_4380' => 'ppa', 'Prupe.1G245800' => 'ppe', 'Prupe.3G293400' => 'ppe', 'Prupe.7G247400' => 'ppe', 'Psat0s145g0120' => 'psa', 'Psat0s595g0040' => 'psa', 'Psat0s595g0120' => 'psa', 'Psat3g175040' => 'psa', 'Psat7g058120' => 'psa', 'PSO017G0428' => 'pso', 'PSO063G7510' => 'pso', 'PSO067G0046' => 'pso', 'PSO478G1073' => 'pso', 'PSO675G3677' => 'pso', 'PSO675G6558' => 'pso', 'PSO675G7520' => 'pso', 'PSO675G8959' => 'pso', 'QL02p074089' => 'qlo', 'QL02p089614' => 'qlo', 'QL03p057736' => 'qlo', 'RcHm_v2.0_Chr1g0364131' => 'rch', 'RcHm_v2.0_Chr2g0087801' => 'rch', 'RcHm_v2.0_Chr2g0087821' => 'rch', 'RcHm_v2.0_Chr2g0173231' => 'rch', 'RcHm_v2.0_Chr4g0433111' => 'rch', 'Rhsim03G0250300' => 'rsi', 'Rhsim08G0048400' => 'rsi', 'Rhsim10G0014800' => 'rsi', 'Rhsim12G0040100' => 'rsi', 'Rhsim12G0109700' => 'rsi', 'Sabra06G0049600' => 'sbr', 'Sabra08G0141000' => 'sbr', 'Sabra10G0021400' => 'sbr', 'Sabra16G0222900' => 'sbr', 'Sabra18G0108600' => 'sbr', 'SalBow1G0433' => 'sbo', 'SalBow1G2038' => 'sbo', 'SalBow1G5003' => 'sbo', 'SalBow7G1197' => 'sbo', 'SalBow8G3506' => 'sbo', 'Sc03g0007300' => 'sci', 'Sc11g0000950' => 'sci', 'Sc14g0008750' => 'sci', 'Sc18g0000420' => 'sci', 'Sed0006754' => 'sed', 'Sed0008741' => 'sed', 'Sed0017172' => 'sed', 'Sed0018925' => 'sed', 'Sed0023326' => 'sed', 'Sed0025909' => 'sed', 'SEGI_05333' => 'sgi', 'SEGI_10362' => 'sgi', 'SEGI_13380' => 'sgi', 'SEGI_24306' => 'sgi', 'SEGI_29077' => 'sgi', 'SEGI_29095' => 'sgi', 'SEGI_36534' => 'sgi', 'SEGI_37506' => 'sgi', 'SEGI_38321' => 'sgi', 'SGA_v2.0_scaffold307G48031' => 'sas', 'SGA_v2.0_scaffold47G17507' => 'sas', 'SGA_v2.0_scaffold63G21736' => 'sas', 'SGA_v2.0_scaffold87G27070' => 'sas', 'SHI17794' => 'shi', 'SHI28851' => 'shi', 'SMO165G0155' => 'smo', 'SMO340G0217' => 'smo', 'SMO367G1210' => 'smo', 'Solyc02g093430.3' => 'sly', 'Solyc05g013580.4' => 'sly', 'Solyc07g008030.3' => 'sly', 'Solyc12g035470.2' => 'sly', 'Sopen02g038020' => 'spe', 'Sopen05g008490' => 'spe', 'Sopen07g003910' => 'spe', 'Sopen12g015240' => 'spe', 'Sp1g11550' => 'spa', 'Sp2g16710' => 'spa', 'Sp3g00430' => 'spa', 'Sp3g26780' => 'spa', 'Sp5g22900' => 'spa', 'Sp6g29530' => 'spa', 'TAR371G0794' => 'tar', 'TAR374G0164' => 'tar', 'TAR622G0165' => 'tar', 'TAR626G0929' => 'tar', 'TAR629G2155' => 'tar', 'THA.LOC104805282' => 'tha', 'THA.LOC104805363' => 'tha', 'THA.LOC104808968' => 'tha', 'THA.LOC104821093' => 'tha', 'THA.LOC104823953' => 'tha', 'THA.LOC104825562' => 'tha', 'THA.LOC104825665' => 'tha', 'Thecc.02G261400' => 'tca', 'Thecc.04G019200' => 'tca', 'Thecc.09G130400' => 'tca', 'Thhalv10004374m.g' => 'esa', 'Thhalv10007850m.g' => 'esa', 'Thhalv10013782m.g' => 'esa', 'Thhalv10018686m.g' => 'esa', 'Thhalv10020899m.g' => 'esa', 'Thhalv10022755m.g' => 'esa', 'TPR.G23851' => 'tpr', 'TPR.G26500' => 'tpr', 'TPR.G27267' => 'tpr', 'TPR.G32001' => 'tpr', 'TPR.G6251' => 'tpr', 'TPR.G8167' => 'tpr', 'TWI12G1330' => 'twi', 'TWI18G1239' => 'twi', 'TWI34G0979' => 'twi', 'TWI36G0670' => 'twi', 'TWI36G0707' => 'twi', 'TWI56G0233' => 'twi', 'TWI75G1809' => 'twi', 'unitig_21.g20874' => 'ugi', 'unitig_26.g10343' => 'ugi', 'unitig_46.g18392' => 'ugi', 'unitig_52.g17178' => 'ugi', 'unitig_8.g2934' => 'ugi', 'vmacro01122' => 'vma', 'vmacro05875' => 'vma', 'vmacro06147' => 'vma', 'vmacro16191' => 'vma', 'vmacro18293' => 'vma', 'VMungo0251G3707' => 'vmu', 'VMungo0464G1521' => 'vmu', 'VMungo1215G0205' => 'vmu', 'VMungo1383G2484' => 'vmu', 'Zm00001eb079610' => 'zma', 'Zm00001eb135990' => 'zma', 'Zm00001eb183710' => 'zma', 'Zm00001eb246020' => 'zma' ), 'gf_id' => 'HOM05D001124', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001124' ), 'data_identifier' => 'HOM05D001124', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001124', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '548', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02520' => 'bna', 'A03p06630' => 'bna', 'A05p44460' => 'bna', 'A06p08710' => 'bna', 'A06p41090' => 'bna', 'A07p32320' => 'bna', 'A08p32520' => 'bna', 'A09p10360' => 'bna', 'A10p24080' => 'bna', 'Aa31LG11G15250' => 'aar', 'Aa31LG1G1800' => 'aar', 'Aa31LG2G5120' => 'aar', 'Aa31LG2G6070' => 'aar', 'Aa31LG5G10770' => 'aar', 'Aa31sc61G90' => 'aar', 'Actinidia01352' => 'ach', 'Actinidia05983' => 'ach', 'Actinidia08133' => 'ach', 'Actinidia15101' => 'ach', 'Actinidia26379' => 'ach', 'Actinidia35778' => 'ach', 'Actinidia36123' => 'ach', 'Actinidia37436' => 'ach', 'Actinidia38730' => 'ach', 'Ah.02g128210' => 'amhyb', 'Ah.03g132990' => 'amhyb', 'Ah.14g079410' => 'amhyb', 'AL1G24640' => 'aly', 'AL2G26680' => 'aly', 'AL3G10530' => 'aly', 'AL3G45230' => 'aly', 'AL5G15230' => 'aly', 'AL5G16960' => 'aly', 'AL6G25210' => 'aly', 'Aqoxy2G00441' => 'aox', 'Aqoxy3G01236' => 'aox', 'Aqoxy5G03746' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3RQ047' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C7GMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9C8JER' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MBL6KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YXCZ83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZANX40' => 'arhy', 'AT1G12990' => 'ath', 'AT1G67880' => 'ath', 'AT2G13290' => 'ath', 'AT3G01620' => 'ath', 'AT3G26445' => 'ath', 'AT3G27540' => 'ath', 'AT5G14480' => 'ath', 'ATR0824G026' => 'atr', 'ATR1098G019' => 'atr', 'Atru.chr11.2145' => 'acertr', 'Atru.chr2.3636' => 'acertr', 'Atru.chr2.3644' => 'acertr', 'Atru.chr6.2422' => 'acertr', 'Atru.chr7.1112' => 'acertr', 'AUR62005469' => 'cqu', 'AUR62011166' => 'cqu', 'AUR62013319' => 'cqu', 'AUR62024273' => 'cqu', 'AUR62028420' => 'cqu', 'AUR62041942' => 'cqu', 'BcaB01g04969' => 'bca', 'BcaB01g06371' => 'bca', 'BcaB02g11494' => 'bca', 'BcaB03g15382' => 'bca', 'BcaB08g36994' => 'bca', 'BcaC03g13477' => 'bca', 'BcaC03g13478' => 'bca', 'BcaC03g13480' => 'bca', 'BcaC03g13481' => 'bca', 'BcaC03g13486' => 'bca', 'BcaC04g19031' => 'bca', 'BcaC04g23085' => 'bca', 'BcaC05g25094' => 'bca', 'BcaC05g25096' => 'bca', 'BcaC05g25138' => 'bca', 'BcaC05g30416' => 'bca', 'BcaC05g30455' => 'bca', 'BcaC06g30979' => 'bca', 'BcaC06g33805' => 'bca', 'BcaC08g46021' => 'bca', 'BcaNung03154' => 'bca', 'BolC2t06623H' => 'bol', 'BolC2t06632H' => 'bol', 'BolC2t06635H' => 'bol', 'BolC2t06638H' => 'bol', 'BolC3t13266H' => 'bol', 'BolC5t29776H' => 'bol', 'BolC6t38912H' => 'bol', 'BolC7t44183H' => 'bol', 'BolC9t54123H' => 'bol', 'BolC9t59107H' => 'bol', 'BraA02t05221Z' => 'bra', 'BraA03t09996Z' => 'bra', 'BraA05t23210Z' => 'bra', 'BraA06t24068Z' => 'bra', 'BraA06t27032Z' => 'bra', 'BraA08t35176Z' => 'bra', 'BraA09t36680Z' => 'bra', 'BraA10t44471Z' => 'bra', 'C02p06760' => 'bna', 'C02p06890' => 'bna', 'C02p07010' => 'bna', 'C03p07660' => 'bna', 'C05p10300' => 'bna', 'C06p38150' => 'bna', 'C07p36650' => 'bna', 'C08p15770' => 'bna', 'C09p12300' => 'bna', 'C09p62700' => 'bna', 'C09p75040' => 'bna', 'CAN.G13.1' => 'can', 'CAN.G138.4' => 'can', 'CAN.G44.6' => 'can', 'CAN.G473.19' => 'can', 'CANSAT01G0835' => 'cansat', 'CANSAT11G0246' => 'cansat', 'CANSAT11G1766' => 'cansat', 'CANSAT64G1954' => 'cansat', 'CARHR013330' => 'chi', 'CARHR060530' => 'chi', 'CARHR075300' => 'chi', 'CARHR105120' => 'chi', 'CARHR148910' => 'chi', 'CARHR198830' => 'chi', 'Carub.0001s1275' => 'cru', 'Carub.0002s1437' => 'cru', 'Carub.0003s0044' => 'cru', 'Carub.0003s2787' => 'cru', 'Carub.0005s0597' => 'cru', 'Carub.0006s1266' => 'cru', 'Ca_06935_v3' => 'car', 'Ca_13559_v3' => 'car', 'Ca_16941_v3' => 'car', 'Ca_16960_v3' => 'car', 'Ca_17775_v3' => 'car', 'Ca_30464_v3' => 'car', 'Cc06_g08160' => 'ccan', 'Cc07_g01520' => 'ccan', 'Cc11_g15810' => 'ccan', 'CDE02G2840' => 'cde', 'CDE03G0093' => 'cde', 'CDE04G2127' => 'cde', 'CDE07G1857' => 'cde', 'CDE09G1246' => 'cde', 'Cfa003412' => 'cfa', 'Cfa007341' => 'cfa', 'Cfa009220' => 'cfa', 'Ciclev10008737m.g' => 'ccl', 'Ciclev10015565m.g' => 'ccl', 'Ciclev10031761m.g' => 'ccl', 'CiPaw.03G045300' => 'cil', 'CiPaw.03G247200' => 'cil', 'CiPaw.04G029500' => 'cil', 'CiPaw.04G174000' => 'cil', 'CiPaw.05G181200' => 'cil', 'CiPaw.06G067100' => 'cil', 'ClCG05G025800' => 'cla', 'ClCG06G011400' => 'cla', 'ClCG09G019360' => 'cla', 'COL.COLO4_04827' => 'col', 'COL.COLO4_29170' => 'col', 'COL.COLO4_35131' => 'col', 'COL.COLO4_35132' => 'col', 'Cpa.g.sc33.32' => 'cpa', 'Cpa.g.sc46.29' => 'cpa', 'Cpa.g.sc796.1' => 'cpa', 'CsaV3_1G030420' => 'csa', 'CsaV3_5G027050' => 'csa', 'CsaV3_5G031040' => 'csa', 'CsaV3_UNG023130' => 'csa', 'CSS0007726' => 'camsi', 'CSS0016433' => 'camsi', 'CSS0017656' => 'camsi', 'CSS0025364' => 'camsi', 'CSS0027582' => 'camsi', 'CSS0047288' => 'camsi', 'CSS0049950' => 'camsi', 'DCAR_003843' => 'dca', 'DCAR_007052' => 'dca', 'DCAR_020884' => 'dca', 'DCAR_021730' => 'dca', 'DCAR_024423' => 'dca', 'DCAR_026509' => 'dca', 'DCAR_031158' => 'dca', 'Dinv14728' => 'din', 'Dinv15219' => 'din', 'Dinv25728' => 'din', 'Dinv33428' => 'din', 'Dinv36489' => 'din', 'Dinv41486' => 'din', 'Duzib147G0469' => 'dzi', 'Duzib168G0060' => 'dzi', 'Duzib187G1215' => 'dzi', 'Duzib248G0692' => 'dzi', 'Duzib251G0767' => 'dzi', 'Duzib264G0446' => 'dzi', 'Duzib268G0691' => 'dzi', 'ECA232G4767' => 'eca', 'ECA233G2838' => 'eca', 'ECA234G0391' => 'eca', 'ECA234G0857' => 'eca', 'ECA236G1593' => 'eca', 'ECA238G0565' => 'eca', 'ECA246G1027' => 'eca', 'ECA246G3223' => 'eca', 'ECA246G3470' => 'eca', 'EL10Ac6g13829' => 'bvu', 'EL10Ac6g14093' => 'bvu', 'EL10Ac8g18707' => 'bvu', 'Eucgr.C01369' => 'egr', 'Eucgr.H02492' => 'egr', 'Eucgr.I01733' => 'egr', 'Eucgr.J02255' => 'egr', 'Eucgr.J02257' => 'egr', 'Eucgr.J02258' => 'egr', 'FAN02G1601' => 'fan', 'FAN03G1586' => 'fan', 'FAN03G2986' => 'fan', 'FAN05G4837' => 'fan', 'FAN06G0146' => 'fan', 'FAN07G0858' => 'fan', 'FAN09G3179' => 'fan', 'FAN10G0669' => 'fan', 'FAN12G2358' => 'fan', 'FAN14G4198' => 'fan', 'FAN14G5112' => 'fan', 'FAN17G0342' => 'fan', 'FAN19G0342' => 'fan', 'FAN19G0962' => 'fan', 'FAN19G1101' => 'fan', 'FAN19G1872' => 'fan', 'FAN22G0356' => 'fan', 'FAN23G0744' => 'fan', 'FAN23G1914' => 'fan', 'FAN26G0032' => 'fan', 'FAN28G0625' => 'fan', 'FvH4_1g02710' => 'fve', 'FvH4_1g02720' => 'fve', 'FvH4_4g25670' => 'fve', 'FvH4_6g51700' => 'fve', 'FvH4_7g20170' => 'fve', 'Glyma.05G175000' => 'gma', 'Glyma.08G132300' => 'gma', 'Glyma.11G243000' => 'gma', 'Glyma.13G158900' => 'gma', 'Glyma.17G112400' => 'gma', 'Glyma.18G014100' => 'gma', 'Glyma.19G003100' => 'gma', 'Glyma.19G056500' => 'gma', 'Gohir.A01G158900' => 'ghi', 'Gohir.A05G312600' => 'ghi', 'Gohir.A05G354900' => 'ghi', 'Gohir.A07G037200' => 'ghi', 'Gohir.A09G030000' => 'ghi', 'Gohir.A12G145200' => 'ghi', 'Gohir.D01G151500' => 'ghi', 'Gohir.D04G058300' => 'ghi', 'Gohir.D05G314100' => 'ghi', 'Gohir.D07G041400' => 'ghi', 'Gohir.D09G029700' => 'ghi', 'Gohir.D12G149700' => 'ghi', 'Gorai.001G043800' => 'gra', 'Gorai.002G187800' => 'gra', 'Gorai.006G034700' => 'gra', 'Gorai.008G161200' => 'gra', 'Gorai.009G335700' => 'gra', 'Gorai.012G065000' => 'gra', 'GSVIVG01000535001' => 'vvi', 'GSVIVG01015572001' => 'vvi', 'GSVIVG01032386001' => 'vvi', 'HanXRQChr05g0138531' => 'han', 'HanXRQChr06g0174391' => 'han', 'HanXRQChr07g0199021' => 'han', 'HanXRQChr08g0208211' => 'han', 'HanXRQChr09g0255471' => 'han', 'HanXRQChr10g0315791' => 'han', 'HanXRQChr12g0371991' => 'han', 'HanXRQChr15g0475251' => 'han', 'HanXRQChr17g0540001' => 'han', 'HanXRQChr17g0548631' => 'han', 'HanXRQChr17g0569561' => 'han', 'Haze_12256' => 'cav', 'Haze_14756' => 'cav', 'Haze_25528' => 'cav', 'Hma1.2p1_0079F.1_g041020' => 'hma', 'Hma1.2p1_0818F.1_g223260' => 'hma', 'Hma1.2p1_1747F.1_g300530' => 'hma', 'HPP92_004607' => 'vpl', 'HPP92_004608' => 'vpl', 'HPP92_006181' => 'vpl', 'HPP92_012192' => 'vpl', 'HPP92_015680' => 'vpl', 'HPP92_020249' => 'vpl', 'HPP92_021376' => 'vpl', 'HPP92_024275' => 'vpl', 'Hund06031' => 'sun', 'Hund25391' => 'sun', 'Lalb_Chr07g0185371' => 'lal', 'Lalb_Chr07g0185381' => 'lal', 'Lalb_Chr12g0204011' => 'lal', 'Lalb_Chr13g0301671' => 'lal', 'Lalb_Chr14g0362851' => 'lal', 'Lalb_Chr24g0403581' => 'lal', 'Lj1g0000233' => 'lja', 'Lj2g0018120' => 'lja', 'Lj3C621T0' => 'lonja', 'Lj3P1059T14' => 'lonja', 'Lj3P611T9' => 'lonja', 'Lj3P614T13' => 'lonja', 'Lj3P615T5' => 'lonja', 'Lj4g0012315' => 'lja', 'Lj4g0026182' => 'lja', 'Lj6P813T16' => 'lonja', 'Lj7C427T7' => 'lonja', 'Lj7C427T8' => 'lonja', 'Lj7P600T41' => 'lonja', 'Lju41C42G17' => 'lonja', 'Lsat_1_v5_gn_0_47300' => 'lsa', 'Lsat_1_v5_gn_2_91280' => 'lsa', 'Lsat_1_v5_gn_3_30561' => 'lsa', 'Lsat_1_v5_gn_4_184321' => 'lsa', 'Lsat_1_v5_gn_4_4041' => 'lsa', 'Lsat_1_v5_gn_5_92000' => 'lsa', 'Lsat_1_v5_gn_8_152940' => 'lsa', 'Lsat_1_v5_gn_8_62401' => 'lsa', 'Manes.06G055900' => 'mes', 'Manes.12G022200' => 'mes', 'Manes.13G023300' => 'mes', 'Manes.14G115000' => 'mes', 'Manes.15G151700' => 'mes', 'Manes.17G111300' => 'mes', 'Mapoly0226s0009' => 'mpo', 'MBI02_g25363_MAGBIO' => 'mbi', 'MBI06_g00027_MAGBIO' => 'mbi', 'MBI10_g13034_MAGBIO' => 'mbi', 'MD09G1023400' => 'mdo', 'MD13G1100100' => 'mdo', 'MD15G1169200' => 'mdo', 'MD16G1101100' => 'mdo', 'MD17G1022900' => 'mdo', 'Medtr3g096150' => 'mtr', 'Medtr4g115070' => 'mtr', 'Medtr7g033325' => 'mtr', 'Medtr8g089840' => 'mtr', 'MELO3C010319.2' => 'cme', 'MELO3C011944.2' => 'cme', 'MELO3C021589.2' => 'cme', 'Migut.E00207' => 'egut', 'Migut.H00067' => 'egut', 'Migut.K00433' => 'egut', 'Migut.K00606' => 'egut', 'Migut.K01410' => 'egut', 'MSTRG.13347' => 'ama', 'MSTRG.24045' => 'ama', 'MSTRG.2428' => 'ama', 'MSTRG.26410' => 'ama', 'MSTRG.3139' => 'ama', 'MSTRG.3286' => 'ama', 'MSTRG.563' => 'ama', 'MSTRG.7941' => 'ama', 'Nitab4.5_0000028g0060' => 'nta', 'Nitab4.5_0000065g0260' => 'nta', 'Nitab4.5_0000112g0060' => 'nta', 'Nitab4.5_0000489g0120' => 'nta', 'Nitab4.5_0001776g0050' => 'nta', 'Nitab4.5_0001854g0010' => 'nta', 'Nitab4.5_0001860g0020' => 'nta', 'Nitab4.5_0004352g0010' => 'nta', 'Nitab4.5_0008716g0020' => 'nta', 'Nitab4.5_0008922g0010' => 'nta', 'Nn3g16693' => 'nnu', 'Nn4g22596' => 'nnu', 'Nn7g37639' => 'nnu', 'Oeu001701.1' => 'oeu', 'Oeu018149.1' => 'oeu', 'Oeu026220.1' => 'oeu', 'Oeu038635.1' => 'oeu', 'Oeu049176.1' => 'oeu', 'Oeu056706.1' => 'oeu', 'Oeu056937.1' => 'oeu', 'Oeu057540.1' => 'oeu', 'Os02g0594900' => 'osa', 'Os02g0595100' => 'osa', 'Os04g0477500' => 'osa', 'Os12g0611900' => 'osa', 'Peaxi162Scf00076g00020' => 'pax', 'Peaxi162Scf00128g00217' => 'pax', 'Peaxi162Scf00129g01640' => 'pax', 'Peaxi162Scf00669g00007' => 'pax', 'Peaxi162Scf00700g00421' => 'pax', 'Peaxi162Scf00801g00038' => 'pax', 'Peaxi162Scf00891g00025' => 'pax', 'PGR083G0909' => 'pgr', 'PGR119G1005' => 'pgr', 'PGR142G2236' => 'pgr', 'PGR142G3388' => 'pgr', 'PGSC0003DMG400004514' => 'stu', 'PGSC0003DMG400012635' => 'stu', 'PGSC0003DMG400015730' => 'stu', 'PGSC0003DMG400018611' => 'stu', 'PGSC0003DMG400030897' => 'stu', 'Phvul.001G254800' => 'pvu', 'Phvul.002G260100' => 'pvu', 'Phvul.003G167600' => 'pvu', 'Phvul.004G005100' => 'pvu', 'Potri.001G343600' => 'ptr', 'Potri.006G066700' => 'ptr', 'Potri.008G186000' => 'ptr', 'Potri.010G046900' => 'ptr', 'Potri.018G127900' => 'ptr', 'Pp3c20_17750' => 'ppa', 'Pp3c24_4380' => 'ppa', 'Prupe.1G245800' => 'ppe', 'Prupe.3G293400' => 'ppe', 'Prupe.7G247400' => 'ppe', 'Psat0s145g0120' => 'psa', 'Psat0s595g0040' => 'psa', 'Psat0s595g0120' => 'psa', 'Psat3g175040' => 'psa', 'Psat7g058120' => 'psa', 'PSO017G0428' => 'pso', 'PSO063G7510' => 'pso', 'PSO067G0046' => 'pso', 'PSO478G1073' => 'pso', 'PSO675G3677' => 'pso', 'PSO675G6558' => 'pso', 'PSO675G7520' => 'pso', 'PSO675G8959' => 'pso', 'QL02p074089' => 'qlo', 'QL02p089614' => 'qlo', 'QL03p057736' => 'qlo', 'RcHm_v2.0_Chr1g0364131' => 'rch', 'RcHm_v2.0_Chr2g0087801' => 'rch', 'RcHm_v2.0_Chr2g0087821' => 'rch', 'RcHm_v2.0_Chr2g0173231' => 'rch', 'RcHm_v2.0_Chr4g0433111' => 'rch', 'Rhsim03G0250300' => 'rsi', 'Rhsim08G0048400' => 'rsi', 'Rhsim10G0014800' => 'rsi', 'Rhsim12G0040100' => 'rsi', 'Rhsim12G0109700' => 'rsi', 'Sabra06G0049600' => 'sbr', 'Sabra08G0141000' => 'sbr', 'Sabra10G0021400' => 'sbr', 'Sabra16G0222900' => 'sbr', 'Sabra18G0108600' => 'sbr', 'SalBow1G0433' => 'sbo', 'SalBow1G2038' => 'sbo', 'SalBow1G5003' => 'sbo', 'SalBow7G1197' => 'sbo', 'SalBow8G3506' => 'sbo', 'Sc03g0007300' => 'sci', 'Sc11g0000950' => 'sci', 'Sc14g0008750' => 'sci', 'Sc18g0000420' => 'sci', 'Sed0006754' => 'sed', 'Sed0008741' => 'sed', 'Sed0017172' => 'sed', 'Sed0018925' => 'sed', 'Sed0023326' => 'sed', 'Sed0025909' => 'sed', 'SEGI_05333' => 'sgi', 'SEGI_10362' => 'sgi', 'SEGI_13380' => 'sgi', 'SEGI_24306' => 'sgi', 'SEGI_29077' => 'sgi', 'SEGI_29095' => 'sgi', 'SEGI_36534' => 'sgi', 'SEGI_37506' => 'sgi', 'SEGI_38321' => 'sgi', 'SGA_v2.0_scaffold307G48031' => 'sas', 'SGA_v2.0_scaffold47G17507' => 'sas', 'SGA_v2.0_scaffold63G21736' => 'sas', 'SGA_v2.0_scaffold87G27070' => 'sas', 'SHI17794' => 'shi', 'SHI28851' => 'shi', 'SMO165G0155' => 'smo', 'SMO340G0217' => 'smo', 'SMO367G1210' => 'smo', 'Solyc02g093430.3' => 'sly', 'Solyc05g013580.4' => 'sly', 'Solyc07g008030.3' => 'sly', 'Solyc12g035470.2' => 'sly', 'Sopen02g038020' => 'spe', 'Sopen05g008490' => 'spe', 'Sopen07g003910' => 'spe', 'Sopen12g015240' => 'spe', 'Sp1g11550' => 'spa', 'Sp2g16710' => 'spa', 'Sp3g00430' => 'spa', 'Sp3g26780' => 'spa', 'Sp5g22900' => 'spa', 'Sp6g29530' => 'spa', 'TAR371G0794' => 'tar', 'TAR374G0164' => 'tar', 'TAR622G0165' => 'tar', 'TAR626G0929' => 'tar', 'TAR629G2155' => 'tar', 'THA.LOC104805282' => 'tha', 'THA.LOC104805363' => 'tha', 'THA.LOC104808968' => 'tha', 'THA.LOC104821093' => 'tha', 'THA.LOC104823953' => 'tha', 'THA.LOC104825562' => 'tha', 'THA.LOC104825665' => 'tha', 'Thecc.02G261400' => 'tca', 'Thecc.04G019200' => 'tca', 'Thecc.09G130400' => 'tca', 'Thhalv10004374m.g' => 'esa', 'Thhalv10007850m.g' => 'esa', 'Thhalv10013782m.g' => 'esa', 'Thhalv10018686m.g' => 'esa', 'Thhalv10020899m.g' => 'esa', 'Thhalv10022755m.g' => 'esa', 'TPR.G23851' => 'tpr', 'TPR.G26500' => 'tpr', 'TPR.G27267' => 'tpr', 'TPR.G32001' => 'tpr', 'TPR.G6251' => 'tpr', 'TPR.G8167' => 'tpr', 'TWI12G1330' => 'twi', 'TWI18G1239' => 'twi', 'TWI34G0979' => 'twi', 'TWI36G0670' => 'twi', 'TWI36G0707' => 'twi', 'TWI56G0233' => 'twi', 'TWI75G1809' => 'twi', 'unitig_21.g20874' => 'ugi', 'unitig_26.g10343' => 'ugi', 'unitig_46.g18392' => 'ugi', 'unitig_52.g17178' => 'ugi', 'unitig_8.g2934' => 'ugi', 'vmacro01122' => 'vma', 'vmacro05875' => 'vma', 'vmacro06147' => 'vma', 'vmacro16191' => 'vma', 'vmacro18293' => 'vma', 'VMungo0251G3707' => 'vmu', 'VMungo0464G1521' => 'vmu', 'VMungo1215G0205' => 'vmu', 'VMungo1383G2484' => 'vmu', 'Zm00001eb079610' => 'zma', 'Zm00001eb135990' => 'zma', 'Zm00001eb183710' => 'zma', 'Zm00001eb246020' => 'zma' ) $gf_id = 'HOM05D001124' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001124' ) $data_identifier = 'HOM05D001124' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 6, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 7, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 21, 'bol' => (int) 10, 'bra' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 6, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 9, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 21, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 8, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 10, 'lsa' => (int) 8, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 8, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 9, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb246020' $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' => 'HOM05D001124', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '548', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02520' => 'bna', 'A03p06630' => 'bna', 'A05p44460' => 'bna', 'A06p08710' => 'bna', 'A06p41090' => 'bna', 'A07p32320' => 'bna', 'A08p32520' => 'bna', 'A09p10360' => 'bna', 'A10p24080' => 'bna', 'Aa31LG11G15250' => 'aar', 'Aa31LG1G1800' => 'aar', 'Aa31LG2G5120' => 'aar', 'Aa31LG2G6070' => 'aar', 'Aa31LG5G10770' => 'aar', 'Aa31sc61G90' => 'aar', 'Actinidia01352' => 'ach', 'Actinidia05983' => 'ach', 'Actinidia08133' => 'ach', 'Actinidia15101' => 'ach', 'Actinidia26379' => 'ach', 'Actinidia35778' => 'ach', 'Actinidia36123' => 'ach', 'Actinidia37436' => 'ach', 'Actinidia38730' => 'ach', 'Ah.02g128210' => 'amhyb', 'Ah.03g132990' => 'amhyb', 'Ah.14g079410' => 'amhyb', 'AL1G24640' => 'aly', 'AL2G26680' => 'aly', 'AL3G10530' => 'aly', 'AL3G45230' => 'aly', 'AL5G15230' => 'aly', 'AL5G16960' => 'aly', 'AL6G25210' => 'aly', 'Aqoxy2G00441' => 'aox', 'Aqoxy3G01236' => 'aox', 'Aqoxy5G03746' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3RQ047' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C7GMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9C8JER' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MBL6KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YXCZ83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZANX40' => 'arhy', 'AT1G12990' => 'ath', 'AT1G67880' => 'ath', 'AT2G13290' => 'ath', 'AT3G01620' => 'ath', 'AT3G26445' => 'ath', 'AT3G27540' => 'ath', 'AT5G14480' => 'ath', 'ATR0824G026' => 'atr', 'ATR1098G019' => 'atr', 'Atru.chr11.2145' => 'acertr', 'Atru.chr2.3636' => 'acertr', 'Atru.chr2.3644' => 'acertr', 'Atru.chr6.2422' => 'acertr', 'Atru.chr7.1112' => 'acertr', 'AUR62005469' => 'cqu', 'AUR62011166' => 'cqu', 'AUR62013319' => 'cqu', 'AUR62024273' => 'cqu', 'AUR62028420' => 'cqu', 'AUR62041942' => 'cqu', 'BcaB01g04969' => 'bca', 'BcaB01g06371' => 'bca', 'BcaB02g11494' => 'bca', 'BcaB03g15382' => 'bca', 'BcaB08g36994' => 'bca', 'BcaC03g13477' => 'bca', 'BcaC03g13478' => 'bca', 'BcaC03g13480' => 'bca', 'BcaC03g13481' => 'bca', 'BcaC03g13486' => 'bca', 'BcaC04g19031' => 'bca', 'BcaC04g23085' => 'bca', 'BcaC05g25094' => 'bca', 'BcaC05g25096' => 'bca', 'BcaC05g25138' => 'bca', 'BcaC05g30416' => 'bca', 'BcaC05g30455' => 'bca', 'BcaC06g30979' => 'bca', 'BcaC06g33805' => 'bca', 'BcaC08g46021' => 'bca', 'BcaNung03154' => 'bca', 'BolC2t06623H' => 'bol', 'BolC2t06632H' => 'bol', 'BolC2t06635H' => 'bol', 'BolC2t06638H' => 'bol', 'BolC3t13266H' => 'bol', 'BolC5t29776H' => 'bol', 'BolC6t38912H' => 'bol', 'BolC7t44183H' => 'bol', 'BolC9t54123H' => 'bol', 'BolC9t59107H' => 'bol', 'BraA02t05221Z' => 'bra', 'BraA03t09996Z' => 'bra', 'BraA05t23210Z' => 'bra', 'BraA06t24068Z' => 'bra', 'BraA06t27032Z' => 'bra', 'BraA08t35176Z' => 'bra', 'BraA09t36680Z' => 'bra', 'BraA10t44471Z' => 'bra', 'C02p06760' => 'bna', 'C02p06890' => 'bna', 'C02p07010' => 'bna', 'C03p07660' => 'bna', 'C05p10300' => 'bna', 'C06p38150' => 'bna', 'C07p36650' => 'bna', 'C08p15770' => 'bna', 'C09p12300' => 'bna', 'C09p62700' => 'bna', 'C09p75040' => 'bna', 'CAN.G13.1' => 'can', 'CAN.G138.4' => 'can', 'CAN.G44.6' => 'can', 'CAN.G473.19' => 'can', 'CANSAT01G0835' => 'cansat', 'CANSAT11G0246' => 'cansat', 'CANSAT11G1766' => 'cansat', 'CANSAT64G1954' => 'cansat', 'CARHR013330' => 'chi', 'CARHR060530' => 'chi', 'CARHR075300' => 'chi', 'CARHR105120' => 'chi', 'CARHR148910' => 'chi', 'CARHR198830' => 'chi', 'Carub.0001s1275' => 'cru', 'Carub.0002s1437' => 'cru', 'Carub.0003s0044' => 'cru', 'Carub.0003s2787' => 'cru', 'Carub.0005s0597' => 'cru', 'Carub.0006s1266' => 'cru', 'Ca_06935_v3' => 'car', 'Ca_13559_v3' => 'car', 'Ca_16941_v3' => 'car', 'Ca_16960_v3' => 'car', 'Ca_17775_v3' => 'car', 'Ca_30464_v3' => 'car', 'Cc06_g08160' => 'ccan', 'Cc07_g01520' => 'ccan', 'Cc11_g15810' => 'ccan', 'CDE02G2840' => 'cde', 'CDE03G0093' => 'cde', 'CDE04G2127' => 'cde', 'CDE07G1857' => 'cde', 'CDE09G1246' => 'cde', 'Cfa003412' => 'cfa', 'Cfa007341' => 'cfa', 'Cfa009220' => 'cfa', 'Ciclev10008737m.g' => 'ccl', 'Ciclev10015565m.g' => 'ccl', 'Ciclev10031761m.g' => 'ccl', 'CiPaw.03G045300' => 'cil', 'CiPaw.03G247200' => 'cil', 'CiPaw.04G029500' => 'cil', 'CiPaw.04G174000' => 'cil', 'CiPaw.05G181200' => 'cil', 'CiPaw.06G067100' => 'cil', 'ClCG05G025800' => 'cla', 'ClCG06G011400' => 'cla', 'ClCG09G019360' => 'cla', 'COL.COLO4_04827' => 'col', 'COL.COLO4_29170' => 'col', 'COL.COLO4_35131' => 'col', 'COL.COLO4_35132' => 'col', 'Cpa.g.sc33.32' => 'cpa', 'Cpa.g.sc46.29' => 'cpa', 'Cpa.g.sc796.1' => 'cpa', 'CsaV3_1G030420' => 'csa', 'CsaV3_5G027050' => 'csa', 'CsaV3_5G031040' => 'csa', 'CsaV3_UNG023130' => 'csa', 'CSS0007726' => 'camsi', 'CSS0016433' => 'camsi', 'CSS0017656' => 'camsi', 'CSS0025364' => 'camsi', 'CSS0027582' => 'camsi', 'CSS0047288' => 'camsi', 'CSS0049950' => 'camsi', 'DCAR_003843' => 'dca', 'DCAR_007052' => 'dca', 'DCAR_020884' => 'dca', 'DCAR_021730' => 'dca', 'DCAR_024423' => 'dca', 'DCAR_026509' => 'dca', 'DCAR_031158' => 'dca', 'Dinv14728' => 'din', 'Dinv15219' => 'din', 'Dinv25728' => 'din', 'Dinv33428' => 'din', 'Dinv36489' => 'din', 'Dinv41486' => 'din', 'Duzib147G0469' => 'dzi', 'Duzib168G0060' => 'dzi', 'Duzib187G1215' => 'dzi', 'Duzib248G0692' => 'dzi', 'Duzib251G0767' => 'dzi', 'Duzib264G0446' => 'dzi', 'Duzib268G0691' => 'dzi', 'ECA232G4767' => 'eca', 'ECA233G2838' => 'eca', 'ECA234G0391' => 'eca', 'ECA234G0857' => 'eca', 'ECA236G1593' => 'eca', 'ECA238G0565' => 'eca', 'ECA246G1027' => 'eca', 'ECA246G3223' => 'eca', 'ECA246G3470' => 'eca', 'EL10Ac6g13829' => 'bvu', 'EL10Ac6g14093' => 'bvu', 'EL10Ac8g18707' => 'bvu', 'Eucgr.C01369' => 'egr', 'Eucgr.H02492' => 'egr', 'Eucgr.I01733' => 'egr', 'Eucgr.J02255' => 'egr', 'Eucgr.J02257' => 'egr', 'Eucgr.J02258' => 'egr', 'FAN02G1601' => 'fan', 'FAN03G1586' => 'fan', 'FAN03G2986' => 'fan', 'FAN05G4837' => 'fan', 'FAN06G0146' => 'fan', 'FAN07G0858' => 'fan', 'FAN09G3179' => 'fan', 'FAN10G0669' => 'fan', 'FAN12G2358' => 'fan', 'FAN14G4198' => 'fan', 'FAN14G5112' => 'fan', 'FAN17G0342' => 'fan', 'FAN19G0342' => 'fan', 'FAN19G0962' => 'fan', 'FAN19G1101' => 'fan', 'FAN19G1872' => 'fan', 'FAN22G0356' => 'fan', 'FAN23G0744' => 'fan', 'FAN23G1914' => 'fan', 'FAN26G0032' => 'fan', 'FAN28G0625' => 'fan', 'FvH4_1g02710' => 'fve', 'FvH4_1g02720' => 'fve', 'FvH4_4g25670' => 'fve', 'FvH4_6g51700' => 'fve', 'FvH4_7g20170' => 'fve', 'Glyma.05G175000' => 'gma', 'Glyma.08G132300' => 'gma', 'Glyma.11G243000' => 'gma', 'Glyma.13G158900' => 'gma', 'Glyma.17G112400' => 'gma', 'Glyma.18G014100' => 'gma', 'Glyma.19G003100' => 'gma', 'Glyma.19G056500' => 'gma', 'Gohir.A01G158900' => 'ghi', 'Gohir.A05G312600' => 'ghi', 'Gohir.A05G354900' => 'ghi', 'Gohir.A07G037200' => 'ghi', 'Gohir.A09G030000' => 'ghi', 'Gohir.A12G145200' => 'ghi', 'Gohir.D01G151500' => 'ghi', 'Gohir.D04G058300' => 'ghi', 'Gohir.D05G314100' => 'ghi', 'Gohir.D07G041400' => 'ghi', 'Gohir.D09G029700' => 'ghi', 'Gohir.D12G149700' => 'ghi', 'Gorai.001G043800' => 'gra', 'Gorai.002G187800' => 'gra', 'Gorai.006G034700' => 'gra', 'Gorai.008G161200' => 'gra', 'Gorai.009G335700' => 'gra', 'Gorai.012G065000' => 'gra', 'GSVIVG01000535001' => 'vvi', 'GSVIVG01015572001' => 'vvi', 'GSVIVG01032386001' => 'vvi', 'HanXRQChr05g0138531' => 'han', 'HanXRQChr06g0174391' => 'han', 'HanXRQChr07g0199021' => 'han', 'HanXRQChr08g0208211' => 'han', 'HanXRQChr09g0255471' => 'han', 'HanXRQChr10g0315791' => 'han', 'HanXRQChr12g0371991' => 'han', 'HanXRQChr15g0475251' => 'han', 'HanXRQChr17g0540001' => 'han', 'HanXRQChr17g0548631' => 'han', 'HanXRQChr17g0569561' => 'han', 'Haze_12256' => 'cav', 'Haze_14756' => 'cav', 'Haze_25528' => 'cav', 'Hma1.2p1_0079F.1_g041020' => 'hma', 'Hma1.2p1_0818F.1_g223260' => 'hma', 'Hma1.2p1_1747F.1_g300530' => 'hma', 'HPP92_004607' => 'vpl', 'HPP92_004608' => 'vpl', 'HPP92_006181' => 'vpl', 'HPP92_012192' => 'vpl', 'HPP92_015680' => 'vpl', 'HPP92_020249' => 'vpl', 'HPP92_021376' => 'vpl', 'HPP92_024275' => 'vpl', 'Hund06031' => 'sun', 'Hund25391' => 'sun', 'Lalb_Chr07g0185371' => 'lal', 'Lalb_Chr07g0185381' => 'lal', 'Lalb_Chr12g0204011' => 'lal', 'Lalb_Chr13g0301671' => 'lal', 'Lalb_Chr14g0362851' => 'lal', 'Lalb_Chr24g0403581' => 'lal', 'Lj1g0000233' => 'lja', 'Lj2g0018120' => 'lja', 'Lj3C621T0' => 'lonja', 'Lj3P1059T14' => 'lonja', 'Lj3P611T9' => 'lonja', 'Lj3P614T13' => 'lonja', 'Lj3P615T5' => 'lonja', 'Lj4g0012315' => 'lja', 'Lj4g0026182' => 'lja', 'Lj6P813T16' => 'lonja', 'Lj7C427T7' => 'lonja', 'Lj7C427T8' => 'lonja', 'Lj7P600T41' => 'lonja', 'Lju41C42G17' => 'lonja', 'Lsat_1_v5_gn_0_47300' => 'lsa', 'Lsat_1_v5_gn_2_91280' => 'lsa', 'Lsat_1_v5_gn_3_30561' => 'lsa', 'Lsat_1_v5_gn_4_184321' => 'lsa', 'Lsat_1_v5_gn_4_4041' => 'lsa', 'Lsat_1_v5_gn_5_92000' => 'lsa', 'Lsat_1_v5_gn_8_152940' => 'lsa', 'Lsat_1_v5_gn_8_62401' => 'lsa', 'Manes.06G055900' => 'mes', 'Manes.12G022200' => 'mes', 'Manes.13G023300' => 'mes', 'Manes.14G115000' => 'mes', 'Manes.15G151700' => 'mes', 'Manes.17G111300' => 'mes', 'Mapoly0226s0009' => 'mpo', 'MBI02_g25363_MAGBIO' => 'mbi', 'MBI06_g00027_MAGBIO' => 'mbi', 'MBI10_g13034_MAGBIO' => 'mbi', 'MD09G1023400' => 'mdo', 'MD13G1100100' => 'mdo', 'MD15G1169200' => 'mdo', 'MD16G1101100' => 'mdo', 'MD17G1022900' => 'mdo', 'Medtr3g096150' => 'mtr', 'Medtr4g115070' => 'mtr', 'Medtr7g033325' => 'mtr', 'Medtr8g089840' => 'mtr', 'MELO3C010319.2' => 'cme', 'MELO3C011944.2' => 'cme', 'MELO3C021589.2' => 'cme', 'Migut.E00207' => 'egut', 'Migut.H00067' => 'egut', 'Migut.K00433' => 'egut', 'Migut.K00606' => 'egut', 'Migut.K01410' => 'egut', 'MSTRG.13347' => 'ama', 'MSTRG.24045' => 'ama', 'MSTRG.2428' => 'ama', 'MSTRG.26410' => 'ama', 'MSTRG.3139' => 'ama', 'MSTRG.3286' => 'ama', 'MSTRG.563' => 'ama', 'MSTRG.7941' => 'ama', 'Nitab4.5_0000028g0060' => 'nta', 'Nitab4.5_0000065g0260' => 'nta', 'Nitab4.5_0000112g0060' => 'nta', 'Nitab4.5_0000489g0120' => 'nta', 'Nitab4.5_0001776g0050' => 'nta', 'Nitab4.5_0001854g0010' => 'nta', 'Nitab4.5_0001860g0020' => 'nta', 'Nitab4.5_0004352g0010' => 'nta', 'Nitab4.5_0008716g0020' => 'nta', 'Nitab4.5_0008922g0010' => 'nta', 'Nn3g16693' => 'nnu', 'Nn4g22596' => 'nnu', 'Nn7g37639' => 'nnu', 'Oeu001701.1' => 'oeu', 'Oeu018149.1' => 'oeu', 'Oeu026220.1' => 'oeu', 'Oeu038635.1' => 'oeu', 'Oeu049176.1' => 'oeu', 'Oeu056706.1' => 'oeu', 'Oeu056937.1' => 'oeu', 'Oeu057540.1' => 'oeu', 'Os02g0594900' => 'osa', 'Os02g0595100' => 'osa', 'Os04g0477500' => 'osa', 'Os12g0611900' => 'osa', 'Peaxi162Scf00076g00020' => 'pax', 'Peaxi162Scf00128g00217' => 'pax', 'Peaxi162Scf00129g01640' => 'pax', 'Peaxi162Scf00669g00007' => 'pax', 'Peaxi162Scf00700g00421' => 'pax', 'Peaxi162Scf00801g00038' => 'pax', 'Peaxi162Scf00891g00025' => 'pax', 'PGR083G0909' => 'pgr', 'PGR119G1005' => 'pgr', 'PGR142G2236' => 'pgr', 'PGR142G3388' => 'pgr', 'PGSC0003DMG400004514' => 'stu', 'PGSC0003DMG400012635' => 'stu', 'PGSC0003DMG400015730' => 'stu', 'PGSC0003DMG400018611' => 'stu', 'PGSC0003DMG400030897' => 'stu', 'Phvul.001G254800' => 'pvu', 'Phvul.002G260100' => 'pvu', 'Phvul.003G167600' => 'pvu', 'Phvul.004G005100' => 'pvu', 'Potri.001G343600' => 'ptr', 'Potri.006G066700' => 'ptr', 'Potri.008G186000' => 'ptr', 'Potri.010G046900' => 'ptr', 'Potri.018G127900' => 'ptr', 'Pp3c20_17750' => 'ppa', 'Pp3c24_4380' => 'ppa', 'Prupe.1G245800' => 'ppe', 'Prupe.3G293400' => 'ppe', 'Prupe.7G247400' => 'ppe', 'Psat0s145g0120' => 'psa', 'Psat0s595g0040' => 'psa', 'Psat0s595g0120' => 'psa', 'Psat3g175040' => 'psa', 'Psat7g058120' => 'psa', 'PSO017G0428' => 'pso', 'PSO063G7510' => 'pso', 'PSO067G0046' => 'pso', 'PSO478G1073' => 'pso', 'PSO675G3677' => 'pso', 'PSO675G6558' => 'pso', 'PSO675G7520' => 'pso', 'PSO675G8959' => 'pso', 'QL02p074089' => 'qlo', 'QL02p089614' => 'qlo', 'QL03p057736' => 'qlo', 'RcHm_v2.0_Chr1g0364131' => 'rch', 'RcHm_v2.0_Chr2g0087801' => 'rch', 'RcHm_v2.0_Chr2g0087821' => 'rch', 'RcHm_v2.0_Chr2g0173231' => 'rch', 'RcHm_v2.0_Chr4g0433111' => 'rch', 'Rhsim03G0250300' => 'rsi', 'Rhsim08G0048400' => 'rsi', 'Rhsim10G0014800' => 'rsi', 'Rhsim12G0040100' => 'rsi', 'Rhsim12G0109700' => 'rsi', 'Sabra06G0049600' => 'sbr', 'Sabra08G0141000' => 'sbr', 'Sabra10G0021400' => 'sbr', 'Sabra16G0222900' => 'sbr', 'Sabra18G0108600' => 'sbr', 'SalBow1G0433' => 'sbo', 'SalBow1G2038' => 'sbo', 'SalBow1G5003' => 'sbo', 'SalBow7G1197' => 'sbo', 'SalBow8G3506' => 'sbo', 'Sc03g0007300' => 'sci', 'Sc11g0000950' => 'sci', 'Sc14g0008750' => 'sci', 'Sc18g0000420' => 'sci', 'Sed0006754' => 'sed', 'Sed0008741' => 'sed', 'Sed0017172' => 'sed', 'Sed0018925' => 'sed', 'Sed0023326' => 'sed', 'Sed0025909' => 'sed', 'SEGI_05333' => 'sgi', 'SEGI_10362' => 'sgi', 'SEGI_13380' => 'sgi', 'SEGI_24306' => 'sgi', 'SEGI_29077' => 'sgi', 'SEGI_29095' => 'sgi', 'SEGI_36534' => 'sgi', 'SEGI_37506' => 'sgi', 'SEGI_38321' => 'sgi', 'SGA_v2.0_scaffold307G48031' => 'sas', 'SGA_v2.0_scaffold47G17507' => 'sas', 'SGA_v2.0_scaffold63G21736' => 'sas', 'SGA_v2.0_scaffold87G27070' => 'sas', 'SHI17794' => 'shi', 'SHI28851' => 'shi', 'SMO165G0155' => 'smo', 'SMO340G0217' => 'smo', 'SMO367G1210' => 'smo', 'Solyc02g093430.3' => 'sly', 'Solyc05g013580.4' => 'sly', 'Solyc07g008030.3' => 'sly', 'Solyc12g035470.2' => 'sly', 'Sopen02g038020' => 'spe', 'Sopen05g008490' => 'spe', 'Sopen07g003910' => 'spe', 'Sopen12g015240' => 'spe', 'Sp1g11550' => 'spa', 'Sp2g16710' => 'spa', 'Sp3g00430' => 'spa', 'Sp3g26780' => 'spa', 'Sp5g22900' => 'spa', 'Sp6g29530' => 'spa', 'TAR371G0794' => 'tar', 'TAR374G0164' => 'tar', 'TAR622G0165' => 'tar', 'TAR626G0929' => 'tar', 'TAR629G2155' => 'tar', 'THA.LOC104805282' => 'tha', 'THA.LOC104805363' => 'tha', 'THA.LOC104808968' => 'tha', 'THA.LOC104821093' => 'tha', 'THA.LOC104823953' => 'tha', 'THA.LOC104825562' => 'tha', 'THA.LOC104825665' => 'tha', 'Thecc.02G261400' => 'tca', 'Thecc.04G019200' => 'tca', 'Thecc.09G130400' => 'tca', 'Thhalv10004374m.g' => 'esa', 'Thhalv10007850m.g' => 'esa', 'Thhalv10013782m.g' => 'esa', 'Thhalv10018686m.g' => 'esa', 'Thhalv10020899m.g' => 'esa', 'Thhalv10022755m.g' => 'esa', 'TPR.G23851' => 'tpr', 'TPR.G26500' => 'tpr', 'TPR.G27267' => 'tpr', 'TPR.G32001' => 'tpr', 'TPR.G6251' => 'tpr', 'TPR.G8167' => 'tpr', 'TWI12G1330' => 'twi', 'TWI18G1239' => 'twi', 'TWI34G0979' => 'twi', 'TWI36G0670' => 'twi', 'TWI36G0707' => 'twi', 'TWI56G0233' => 'twi', 'TWI75G1809' => 'twi', 'unitig_21.g20874' => 'ugi', 'unitig_26.g10343' => 'ugi', 'unitig_46.g18392' => 'ugi', 'unitig_52.g17178' => 'ugi', 'unitig_8.g2934' => 'ugi', 'vmacro01122' => 'vma', 'vmacro05875' => 'vma', 'vmacro06147' => 'vma', 'vmacro16191' => 'vma', 'vmacro18293' => 'vma', 'VMungo0251G3707' => 'vmu', 'VMungo0464G1521' => 'vmu', 'VMungo1215G0205' => 'vmu', 'VMungo1383G2484' => 'vmu', 'Zm00001eb079610' => 'zma', 'Zm00001eb135990' => 'zma', 'Zm00001eb183710' => 'zma', 'Zm00001eb246020' => 'zma' ), 'gf_id' => 'HOM05D001124', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001124' ), 'data_identifier' => 'HOM05D001124', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001124', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '548', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02520' => 'bna', 'A03p06630' => 'bna', 'A05p44460' => 'bna', 'A06p08710' => 'bna', 'A06p41090' => 'bna', 'A07p32320' => 'bna', 'A08p32520' => 'bna', 'A09p10360' => 'bna', 'A10p24080' => 'bna', 'Aa31LG11G15250' => 'aar', 'Aa31LG1G1800' => 'aar', 'Aa31LG2G5120' => 'aar', 'Aa31LG2G6070' => 'aar', 'Aa31LG5G10770' => 'aar', 'Aa31sc61G90' => 'aar', 'Actinidia01352' => 'ach', 'Actinidia05983' => 'ach', 'Actinidia08133' => 'ach', 'Actinidia15101' => 'ach', 'Actinidia26379' => 'ach', 'Actinidia35778' => 'ach', 'Actinidia36123' => 'ach', 'Actinidia37436' => 'ach', 'Actinidia38730' => 'ach', 'Ah.02g128210' => 'amhyb', 'Ah.03g132990' => 'amhyb', 'Ah.14g079410' => 'amhyb', 'AL1G24640' => 'aly', 'AL2G26680' => 'aly', 'AL3G10530' => 'aly', 'AL3G45230' => 'aly', 'AL5G15230' => 'aly', 'AL5G16960' => 'aly', 'AL6G25210' => 'aly', 'Aqoxy2G00441' => 'aox', 'Aqoxy3G01236' => 'aox', 'Aqoxy5G03746' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3RQ047' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C7GMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9C8JER' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MBL6KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YXCZ83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZANX40' => 'arhy', 'AT1G12990' => 'ath', 'AT1G67880' => 'ath', 'AT2G13290' => 'ath', 'AT3G01620' => 'ath', 'AT3G26445' => 'ath', 'AT3G27540' => 'ath', 'AT5G14480' => 'ath', 'ATR0824G026' => 'atr', 'ATR1098G019' => 'atr', 'Atru.chr11.2145' => 'acertr', 'Atru.chr2.3636' => 'acertr', 'Atru.chr2.3644' => 'acertr', 'Atru.chr6.2422' => 'acertr', 'Atru.chr7.1112' => 'acertr', 'AUR62005469' => 'cqu', 'AUR62011166' => 'cqu', 'AUR62013319' => 'cqu', 'AUR62024273' => 'cqu', 'AUR62028420' => 'cqu', 'AUR62041942' => 'cqu', 'BcaB01g04969' => 'bca', 'BcaB01g06371' => 'bca', 'BcaB02g11494' => 'bca', 'BcaB03g15382' => 'bca', 'BcaB08g36994' => 'bca', 'BcaC03g13477' => 'bca', 'BcaC03g13478' => 'bca', 'BcaC03g13480' => 'bca', 'BcaC03g13481' => 'bca', 'BcaC03g13486' => 'bca', 'BcaC04g19031' => 'bca', 'BcaC04g23085' => 'bca', 'BcaC05g25094' => 'bca', 'BcaC05g25096' => 'bca', 'BcaC05g25138' => 'bca', 'BcaC05g30416' => 'bca', 'BcaC05g30455' => 'bca', 'BcaC06g30979' => 'bca', 'BcaC06g33805' => 'bca', 'BcaC08g46021' => 'bca', 'BcaNung03154' => 'bca', 'BolC2t06623H' => 'bol', 'BolC2t06632H' => 'bol', 'BolC2t06635H' => 'bol', 'BolC2t06638H' => 'bol', 'BolC3t13266H' => 'bol', 'BolC5t29776H' => 'bol', 'BolC6t38912H' => 'bol', 'BolC7t44183H' => 'bol', 'BolC9t54123H' => 'bol', 'BolC9t59107H' => 'bol', 'BraA02t05221Z' => 'bra', 'BraA03t09996Z' => 'bra', 'BraA05t23210Z' => 'bra', 'BraA06t24068Z' => 'bra', 'BraA06t27032Z' => 'bra', 'BraA08t35176Z' => 'bra', 'BraA09t36680Z' => 'bra', 'BraA10t44471Z' => 'bra', 'C02p06760' => 'bna', 'C02p06890' => 'bna', 'C02p07010' => 'bna', 'C03p07660' => 'bna', 'C05p10300' => 'bna', 'C06p38150' => 'bna', 'C07p36650' => 'bna', 'C08p15770' => 'bna', 'C09p12300' => 'bna', 'C09p62700' => 'bna', 'C09p75040' => 'bna', 'CAN.G13.1' => 'can', 'CAN.G138.4' => 'can', 'CAN.G44.6' => 'can', 'CAN.G473.19' => 'can', 'CANSAT01G0835' => 'cansat', 'CANSAT11G0246' => 'cansat', 'CANSAT11G1766' => 'cansat', 'CANSAT64G1954' => 'cansat', 'CARHR013330' => 'chi', 'CARHR060530' => 'chi', 'CARHR075300' => 'chi', 'CARHR105120' => 'chi', 'CARHR148910' => 'chi', 'CARHR198830' => 'chi', 'Carub.0001s1275' => 'cru', 'Carub.0002s1437' => 'cru', 'Carub.0003s0044' => 'cru', 'Carub.0003s2787' => 'cru', 'Carub.0005s0597' => 'cru', 'Carub.0006s1266' => 'cru', 'Ca_06935_v3' => 'car', 'Ca_13559_v3' => 'car', 'Ca_16941_v3' => 'car', 'Ca_16960_v3' => 'car', 'Ca_17775_v3' => 'car', 'Ca_30464_v3' => 'car', 'Cc06_g08160' => 'ccan', 'Cc07_g01520' => 'ccan', 'Cc11_g15810' => 'ccan', 'CDE02G2840' => 'cde', 'CDE03G0093' => 'cde', 'CDE04G2127' => 'cde', 'CDE07G1857' => 'cde', 'CDE09G1246' => 'cde', 'Cfa003412' => 'cfa', 'Cfa007341' => 'cfa', 'Cfa009220' => 'cfa', 'Ciclev10008737m.g' => 'ccl', 'Ciclev10015565m.g' => 'ccl', 'Ciclev10031761m.g' => 'ccl', 'CiPaw.03G045300' => 'cil', 'CiPaw.03G247200' => 'cil', 'CiPaw.04G029500' => 'cil', 'CiPaw.04G174000' => 'cil', 'CiPaw.05G181200' => 'cil', 'CiPaw.06G067100' => 'cil', 'ClCG05G025800' => 'cla', 'ClCG06G011400' => 'cla', 'ClCG09G019360' => 'cla', 'COL.COLO4_04827' => 'col', 'COL.COLO4_29170' => 'col', 'COL.COLO4_35131' => 'col', 'COL.COLO4_35132' => 'col', 'Cpa.g.sc33.32' => 'cpa', 'Cpa.g.sc46.29' => 'cpa', 'Cpa.g.sc796.1' => 'cpa', 'CsaV3_1G030420' => 'csa', 'CsaV3_5G027050' => 'csa', 'CsaV3_5G031040' => 'csa', 'CsaV3_UNG023130' => 'csa', 'CSS0007726' => 'camsi', 'CSS0016433' => 'camsi', 'CSS0017656' => 'camsi', 'CSS0025364' => 'camsi', 'CSS0027582' => 'camsi', 'CSS0047288' => 'camsi', 'CSS0049950' => 'camsi', 'DCAR_003843' => 'dca', 'DCAR_007052' => 'dca', 'DCAR_020884' => 'dca', 'DCAR_021730' => 'dca', 'DCAR_024423' => 'dca', 'DCAR_026509' => 'dca', 'DCAR_031158' => 'dca', 'Dinv14728' => 'din', 'Dinv15219' => 'din', 'Dinv25728' => 'din', 'Dinv33428' => 'din', 'Dinv36489' => 'din', 'Dinv41486' => 'din', 'Duzib147G0469' => 'dzi', 'Duzib168G0060' => 'dzi', 'Duzib187G1215' => 'dzi', 'Duzib248G0692' => 'dzi', 'Duzib251G0767' => 'dzi', 'Duzib264G0446' => 'dzi', 'Duzib268G0691' => 'dzi', 'ECA232G4767' => 'eca', 'ECA233G2838' => 'eca', 'ECA234G0391' => 'eca', 'ECA234G0857' => 'eca', 'ECA236G1593' => 'eca', 'ECA238G0565' => 'eca', 'ECA246G1027' => 'eca', 'ECA246G3223' => 'eca', 'ECA246G3470' => 'eca', 'EL10Ac6g13829' => 'bvu', 'EL10Ac6g14093' => 'bvu', 'EL10Ac8g18707' => 'bvu', 'Eucgr.C01369' => 'egr', 'Eucgr.H02492' => 'egr', 'Eucgr.I01733' => 'egr', 'Eucgr.J02255' => 'egr', 'Eucgr.J02257' => 'egr', 'Eucgr.J02258' => 'egr', 'FAN02G1601' => 'fan', 'FAN03G1586' => 'fan', 'FAN03G2986' => 'fan', 'FAN05G4837' => 'fan', 'FAN06G0146' => 'fan', 'FAN07G0858' => 'fan', 'FAN09G3179' => 'fan', 'FAN10G0669' => 'fan', 'FAN12G2358' => 'fan', 'FAN14G4198' => 'fan', 'FAN14G5112' => 'fan', 'FAN17G0342' => 'fan', 'FAN19G0342' => 'fan', 'FAN19G0962' => 'fan', 'FAN19G1101' => 'fan', 'FAN19G1872' => 'fan', 'FAN22G0356' => 'fan', 'FAN23G0744' => 'fan', 'FAN23G1914' => 'fan', 'FAN26G0032' => 'fan', 'FAN28G0625' => 'fan', 'FvH4_1g02710' => 'fve', 'FvH4_1g02720' => 'fve', 'FvH4_4g25670' => 'fve', 'FvH4_6g51700' => 'fve', 'FvH4_7g20170' => 'fve', 'Glyma.05G175000' => 'gma', 'Glyma.08G132300' => 'gma', 'Glyma.11G243000' => 'gma', 'Glyma.13G158900' => 'gma', 'Glyma.17G112400' => 'gma', 'Glyma.18G014100' => 'gma', 'Glyma.19G003100' => 'gma', 'Glyma.19G056500' => 'gma', 'Gohir.A01G158900' => 'ghi', 'Gohir.A05G312600' => 'ghi', 'Gohir.A05G354900' => 'ghi', 'Gohir.A07G037200' => 'ghi', 'Gohir.A09G030000' => 'ghi', 'Gohir.A12G145200' => 'ghi', 'Gohir.D01G151500' => 'ghi', 'Gohir.D04G058300' => 'ghi', 'Gohir.D05G314100' => 'ghi', 'Gohir.D07G041400' => 'ghi', 'Gohir.D09G029700' => 'ghi', 'Gohir.D12G149700' => 'ghi', 'Gorai.001G043800' => 'gra', 'Gorai.002G187800' => 'gra', 'Gorai.006G034700' => 'gra', 'Gorai.008G161200' => 'gra', 'Gorai.009G335700' => 'gra', 'Gorai.012G065000' => 'gra', 'GSVIVG01000535001' => 'vvi', 'GSVIVG01015572001' => 'vvi', 'GSVIVG01032386001' => 'vvi', 'HanXRQChr05g0138531' => 'han', 'HanXRQChr06g0174391' => 'han', 'HanXRQChr07g0199021' => 'han', 'HanXRQChr08g0208211' => 'han', 'HanXRQChr09g0255471' => 'han', 'HanXRQChr10g0315791' => 'han', 'HanXRQChr12g0371991' => 'han', 'HanXRQChr15g0475251' => 'han', 'HanXRQChr17g0540001' => 'han', 'HanXRQChr17g0548631' => 'han', 'HanXRQChr17g0569561' => 'han', 'Haze_12256' => 'cav', 'Haze_14756' => 'cav', 'Haze_25528' => 'cav', 'Hma1.2p1_0079F.1_g041020' => 'hma', 'Hma1.2p1_0818F.1_g223260' => 'hma', 'Hma1.2p1_1747F.1_g300530' => 'hma', 'HPP92_004607' => 'vpl', 'HPP92_004608' => 'vpl', 'HPP92_006181' => 'vpl', 'HPP92_012192' => 'vpl', 'HPP92_015680' => 'vpl', 'HPP92_020249' => 'vpl', 'HPP92_021376' => 'vpl', 'HPP92_024275' => 'vpl', 'Hund06031' => 'sun', 'Hund25391' => 'sun', 'Lalb_Chr07g0185371' => 'lal', 'Lalb_Chr07g0185381' => 'lal', 'Lalb_Chr12g0204011' => 'lal', 'Lalb_Chr13g0301671' => 'lal', 'Lalb_Chr14g0362851' => 'lal', 'Lalb_Chr24g0403581' => 'lal', 'Lj1g0000233' => 'lja', 'Lj2g0018120' => 'lja', 'Lj3C621T0' => 'lonja', 'Lj3P1059T14' => 'lonja', 'Lj3P611T9' => 'lonja', 'Lj3P614T13' => 'lonja', 'Lj3P615T5' => 'lonja', 'Lj4g0012315' => 'lja', 'Lj4g0026182' => 'lja', 'Lj6P813T16' => 'lonja', 'Lj7C427T7' => 'lonja', 'Lj7C427T8' => 'lonja', 'Lj7P600T41' => 'lonja', 'Lju41C42G17' => 'lonja', 'Lsat_1_v5_gn_0_47300' => 'lsa', 'Lsat_1_v5_gn_2_91280' => 'lsa', 'Lsat_1_v5_gn_3_30561' => 'lsa', 'Lsat_1_v5_gn_4_184321' => 'lsa', 'Lsat_1_v5_gn_4_4041' => 'lsa', 'Lsat_1_v5_gn_5_92000' => 'lsa', 'Lsat_1_v5_gn_8_152940' => 'lsa', 'Lsat_1_v5_gn_8_62401' => 'lsa', 'Manes.06G055900' => 'mes', 'Manes.12G022200' => 'mes', 'Manes.13G023300' => 'mes', 'Manes.14G115000' => 'mes', 'Manes.15G151700' => 'mes', 'Manes.17G111300' => 'mes', 'Mapoly0226s0009' => 'mpo', 'MBI02_g25363_MAGBIO' => 'mbi', 'MBI06_g00027_MAGBIO' => 'mbi', 'MBI10_g13034_MAGBIO' => 'mbi', 'MD09G1023400' => 'mdo', 'MD13G1100100' => 'mdo', 'MD15G1169200' => 'mdo', 'MD16G1101100' => 'mdo', 'MD17G1022900' => 'mdo', 'Medtr3g096150' => 'mtr', 'Medtr4g115070' => 'mtr', 'Medtr7g033325' => 'mtr', 'Medtr8g089840' => 'mtr', 'MELO3C010319.2' => 'cme', 'MELO3C011944.2' => 'cme', 'MELO3C021589.2' => 'cme', 'Migut.E00207' => 'egut', 'Migut.H00067' => 'egut', 'Migut.K00433' => 'egut', 'Migut.K00606' => 'egut', 'Migut.K01410' => 'egut', 'MSTRG.13347' => 'ama', 'MSTRG.24045' => 'ama', 'MSTRG.2428' => 'ama', 'MSTRG.26410' => 'ama', 'MSTRG.3139' => 'ama', 'MSTRG.3286' => 'ama', 'MSTRG.563' => 'ama', 'MSTRG.7941' => 'ama', 'Nitab4.5_0000028g0060' => 'nta', 'Nitab4.5_0000065g0260' => 'nta', 'Nitab4.5_0000112g0060' => 'nta', 'Nitab4.5_0000489g0120' => 'nta', 'Nitab4.5_0001776g0050' => 'nta', 'Nitab4.5_0001854g0010' => 'nta', 'Nitab4.5_0001860g0020' => 'nta', 'Nitab4.5_0004352g0010' => 'nta', 'Nitab4.5_0008716g0020' => 'nta', 'Nitab4.5_0008922g0010' => 'nta', 'Nn3g16693' => 'nnu', 'Nn4g22596' => 'nnu', 'Nn7g37639' => 'nnu', 'Oeu001701.1' => 'oeu', 'Oeu018149.1' => 'oeu', 'Oeu026220.1' => 'oeu', 'Oeu038635.1' => 'oeu', 'Oeu049176.1' => 'oeu', 'Oeu056706.1' => 'oeu', 'Oeu056937.1' => 'oeu', 'Oeu057540.1' => 'oeu', 'Os02g0594900' => 'osa', 'Os02g0595100' => 'osa', 'Os04g0477500' => 'osa', 'Os12g0611900' => 'osa', 'Peaxi162Scf00076g00020' => 'pax', 'Peaxi162Scf00128g00217' => 'pax', 'Peaxi162Scf00129g01640' => 'pax', 'Peaxi162Scf00669g00007' => 'pax', 'Peaxi162Scf00700g00421' => 'pax', 'Peaxi162Scf00801g00038' => 'pax', 'Peaxi162Scf00891g00025' => 'pax', 'PGR083G0909' => 'pgr', 'PGR119G1005' => 'pgr', 'PGR142G2236' => 'pgr', 'PGR142G3388' => 'pgr', 'PGSC0003DMG400004514' => 'stu', 'PGSC0003DMG400012635' => 'stu', 'PGSC0003DMG400015730' => 'stu', 'PGSC0003DMG400018611' => 'stu', 'PGSC0003DMG400030897' => 'stu', 'Phvul.001G254800' => 'pvu', 'Phvul.002G260100' => 'pvu', 'Phvul.003G167600' => 'pvu', 'Phvul.004G005100' => 'pvu', 'Potri.001G343600' => 'ptr', 'Potri.006G066700' => 'ptr', 'Potri.008G186000' => 'ptr', 'Potri.010G046900' => 'ptr', 'Potri.018G127900' => 'ptr', 'Pp3c20_17750' => 'ppa', 'Pp3c24_4380' => 'ppa', 'Prupe.1G245800' => 'ppe', 'Prupe.3G293400' => 'ppe', 'Prupe.7G247400' => 'ppe', 'Psat0s145g0120' => 'psa', 'Psat0s595g0040' => 'psa', 'Psat0s595g0120' => 'psa', 'Psat3g175040' => 'psa', 'Psat7g058120' => 'psa', 'PSO017G0428' => 'pso', 'PSO063G7510' => 'pso', 'PSO067G0046' => 'pso', 'PSO478G1073' => 'pso', 'PSO675G3677' => 'pso', 'PSO675G6558' => 'pso', 'PSO675G7520' => 'pso', 'PSO675G8959' => 'pso', 'QL02p074089' => 'qlo', 'QL02p089614' => 'qlo', 'QL03p057736' => 'qlo', 'RcHm_v2.0_Chr1g0364131' => 'rch', 'RcHm_v2.0_Chr2g0087801' => 'rch', 'RcHm_v2.0_Chr2g0087821' => 'rch', 'RcHm_v2.0_Chr2g0173231' => 'rch', 'RcHm_v2.0_Chr4g0433111' => 'rch', 'Rhsim03G0250300' => 'rsi', 'Rhsim08G0048400' => 'rsi', 'Rhsim10G0014800' => 'rsi', 'Rhsim12G0040100' => 'rsi', 'Rhsim12G0109700' => 'rsi', 'Sabra06G0049600' => 'sbr', 'Sabra08G0141000' => 'sbr', 'Sabra10G0021400' => 'sbr', 'Sabra16G0222900' => 'sbr', 'Sabra18G0108600' => 'sbr', 'SalBow1G0433' => 'sbo', 'SalBow1G2038' => 'sbo', 'SalBow1G5003' => 'sbo', 'SalBow7G1197' => 'sbo', 'SalBow8G3506' => 'sbo', 'Sc03g0007300' => 'sci', 'Sc11g0000950' => 'sci', 'Sc14g0008750' => 'sci', 'Sc18g0000420' => 'sci', 'Sed0006754' => 'sed', 'Sed0008741' => 'sed', 'Sed0017172' => 'sed', 'Sed0018925' => 'sed', 'Sed0023326' => 'sed', 'Sed0025909' => 'sed', 'SEGI_05333' => 'sgi', 'SEGI_10362' => 'sgi', 'SEGI_13380' => 'sgi', 'SEGI_24306' => 'sgi', 'SEGI_29077' => 'sgi', 'SEGI_29095' => 'sgi', 'SEGI_36534' => 'sgi', 'SEGI_37506' => 'sgi', 'SEGI_38321' => 'sgi', 'SGA_v2.0_scaffold307G48031' => 'sas', 'SGA_v2.0_scaffold47G17507' => 'sas', 'SGA_v2.0_scaffold63G21736' => 'sas', 'SGA_v2.0_scaffold87G27070' => 'sas', 'SHI17794' => 'shi', 'SHI28851' => 'shi', 'SMO165G0155' => 'smo', 'SMO340G0217' => 'smo', 'SMO367G1210' => 'smo', 'Solyc02g093430.3' => 'sly', 'Solyc05g013580.4' => 'sly', 'Solyc07g008030.3' => 'sly', 'Solyc12g035470.2' => 'sly', 'Sopen02g038020' => 'spe', 'Sopen05g008490' => 'spe', 'Sopen07g003910' => 'spe', 'Sopen12g015240' => 'spe', 'Sp1g11550' => 'spa', 'Sp2g16710' => 'spa', 'Sp3g00430' => 'spa', 'Sp3g26780' => 'spa', 'Sp5g22900' => 'spa', 'Sp6g29530' => 'spa', 'TAR371G0794' => 'tar', 'TAR374G0164' => 'tar', 'TAR622G0165' => 'tar', 'TAR626G0929' => 'tar', 'TAR629G2155' => 'tar', 'THA.LOC104805282' => 'tha', 'THA.LOC104805363' => 'tha', 'THA.LOC104808968' => 'tha', 'THA.LOC104821093' => 'tha', 'THA.LOC104823953' => 'tha', 'THA.LOC104825562' => 'tha', 'THA.LOC104825665' => 'tha', 'Thecc.02G261400' => 'tca', 'Thecc.04G019200' => 'tca', 'Thecc.09G130400' => 'tca', 'Thhalv10004374m.g' => 'esa', 'Thhalv10007850m.g' => 'esa', 'Thhalv10013782m.g' => 'esa', 'Thhalv10018686m.g' => 'esa', 'Thhalv10020899m.g' => 'esa', 'Thhalv10022755m.g' => 'esa', 'TPR.G23851' => 'tpr', 'TPR.G26500' => 'tpr', 'TPR.G27267' => 'tpr', 'TPR.G32001' => 'tpr', 'TPR.G6251' => 'tpr', 'TPR.G8167' => 'tpr', 'TWI12G1330' => 'twi', 'TWI18G1239' => 'twi', 'TWI34G0979' => 'twi', 'TWI36G0670' => 'twi', 'TWI36G0707' => 'twi', 'TWI56G0233' => 'twi', 'TWI75G1809' => 'twi', 'unitig_21.g20874' => 'ugi', 'unitig_26.g10343' => 'ugi', 'unitig_46.g18392' => 'ugi', 'unitig_52.g17178' => 'ugi', 'unitig_8.g2934' => 'ugi', 'vmacro01122' => 'vma', 'vmacro05875' => 'vma', 'vmacro06147' => 'vma', 'vmacro16191' => 'vma', 'vmacro18293' => 'vma', 'VMungo0251G3707' => 'vmu', 'VMungo0464G1521' => 'vmu', 'VMungo1215G0205' => 'vmu', 'VMungo1383G2484' => 'vmu', 'Zm00001eb079610' => 'zma', 'Zm00001eb135990' => 'zma', 'Zm00001eb183710' => 'zma', 'Zm00001eb246020' => 'zma' ) $gf_id = 'HOM05D001124' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001124' ) $data_identifier = 'HOM05D001124' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 6, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 7, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 21, 'bol' => (int) 10, 'bra' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 6, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 9, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 21, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 8, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 10, 'lsa' => (int) 8, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 8, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 9, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb246020' $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' => 'HOM05D001124', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '548', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02520' => 'bna', 'A03p06630' => 'bna', 'A05p44460' => 'bna', 'A06p08710' => 'bna', 'A06p41090' => 'bna', 'A07p32320' => 'bna', 'A08p32520' => 'bna', 'A09p10360' => 'bna', 'A10p24080' => 'bna', 'Aa31LG11G15250' => 'aar', 'Aa31LG1G1800' => 'aar', 'Aa31LG2G5120' => 'aar', 'Aa31LG2G6070' => 'aar', 'Aa31LG5G10770' => 'aar', 'Aa31sc61G90' => 'aar', 'Actinidia01352' => 'ach', 'Actinidia05983' => 'ach', 'Actinidia08133' => 'ach', 'Actinidia15101' => 'ach', 'Actinidia26379' => 'ach', 'Actinidia35778' => 'ach', 'Actinidia36123' => 'ach', 'Actinidia37436' => 'ach', 'Actinidia38730' => 'ach', 'Ah.02g128210' => 'amhyb', 'Ah.03g132990' => 'amhyb', 'Ah.14g079410' => 'amhyb', 'AL1G24640' => 'aly', 'AL2G26680' => 'aly', 'AL3G10530' => 'aly', 'AL3G45230' => 'aly', 'AL5G15230' => 'aly', 'AL5G16960' => 'aly', 'AL6G25210' => 'aly', 'Aqoxy2G00441' => 'aox', 'Aqoxy3G01236' => 'aox', 'Aqoxy5G03746' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3RQ047' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C7GMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9C8JER' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MBL6KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YXCZ83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZANX40' => 'arhy', 'AT1G12990' => 'ath', 'AT1G67880' => 'ath', 'AT2G13290' => 'ath', 'AT3G01620' => 'ath', 'AT3G26445' => 'ath', 'AT3G27540' => 'ath', 'AT5G14480' => 'ath', 'ATR0824G026' => 'atr', 'ATR1098G019' => 'atr', 'Atru.chr11.2145' => 'acertr', 'Atru.chr2.3636' => 'acertr', 'Atru.chr2.3644' => 'acertr', 'Atru.chr6.2422' => 'acertr', 'Atru.chr7.1112' => 'acertr', 'AUR62005469' => 'cqu', 'AUR62011166' => 'cqu', 'AUR62013319' => 'cqu', 'AUR62024273' => 'cqu', 'AUR62028420' => 'cqu', 'AUR62041942' => 'cqu', 'BcaB01g04969' => 'bca', 'BcaB01g06371' => 'bca', 'BcaB02g11494' => 'bca', 'BcaB03g15382' => 'bca', 'BcaB08g36994' => 'bca', 'BcaC03g13477' => 'bca', 'BcaC03g13478' => 'bca', 'BcaC03g13480' => 'bca', 'BcaC03g13481' => 'bca', 'BcaC03g13486' => 'bca', 'BcaC04g19031' => 'bca', 'BcaC04g23085' => 'bca', 'BcaC05g25094' => 'bca', 'BcaC05g25096' => 'bca', 'BcaC05g25138' => 'bca', 'BcaC05g30416' => 'bca', 'BcaC05g30455' => 'bca', 'BcaC06g30979' => 'bca', 'BcaC06g33805' => 'bca', 'BcaC08g46021' => 'bca', 'BcaNung03154' => 'bca', 'BolC2t06623H' => 'bol', 'BolC2t06632H' => 'bol', 'BolC2t06635H' => 'bol', 'BolC2t06638H' => 'bol', 'BolC3t13266H' => 'bol', 'BolC5t29776H' => 'bol', 'BolC6t38912H' => 'bol', 'BolC7t44183H' => 'bol', 'BolC9t54123H' => 'bol', 'BolC9t59107H' => 'bol', 'BraA02t05221Z' => 'bra', 'BraA03t09996Z' => 'bra', 'BraA05t23210Z' => 'bra', 'BraA06t24068Z' => 'bra', 'BraA06t27032Z' => 'bra', 'BraA08t35176Z' => 'bra', 'BraA09t36680Z' => 'bra', 'BraA10t44471Z' => 'bra', 'C02p06760' => 'bna', 'C02p06890' => 'bna', 'C02p07010' => 'bna', 'C03p07660' => 'bna', 'C05p10300' => 'bna', 'C06p38150' => 'bna', 'C07p36650' => 'bna', 'C08p15770' => 'bna', 'C09p12300' => 'bna', 'C09p62700' => 'bna', 'C09p75040' => 'bna', 'CAN.G13.1' => 'can', 'CAN.G138.4' => 'can', 'CAN.G44.6' => 'can', 'CAN.G473.19' => 'can', 'CANSAT01G0835' => 'cansat', 'CANSAT11G0246' => 'cansat', 'CANSAT11G1766' => 'cansat', 'CANSAT64G1954' => 'cansat', 'CARHR013330' => 'chi', 'CARHR060530' => 'chi', 'CARHR075300' => 'chi', 'CARHR105120' => 'chi', 'CARHR148910' => 'chi', 'CARHR198830' => 'chi', 'Carub.0001s1275' => 'cru', 'Carub.0002s1437' => 'cru', 'Carub.0003s0044' => 'cru', 'Carub.0003s2787' => 'cru', 'Carub.0005s0597' => 'cru', 'Carub.0006s1266' => 'cru', 'Ca_06935_v3' => 'car', 'Ca_13559_v3' => 'car', 'Ca_16941_v3' => 'car', 'Ca_16960_v3' => 'car', 'Ca_17775_v3' => 'car', 'Ca_30464_v3' => 'car', 'Cc06_g08160' => 'ccan', 'Cc07_g01520' => 'ccan', 'Cc11_g15810' => 'ccan', 'CDE02G2840' => 'cde', 'CDE03G0093' => 'cde', 'CDE04G2127' => 'cde', 'CDE07G1857' => 'cde', 'CDE09G1246' => 'cde', 'Cfa003412' => 'cfa', 'Cfa007341' => 'cfa', 'Cfa009220' => 'cfa', 'Ciclev10008737m.g' => 'ccl', 'Ciclev10015565m.g' => 'ccl', 'Ciclev10031761m.g' => 'ccl', 'CiPaw.03G045300' => 'cil', 'CiPaw.03G247200' => 'cil', 'CiPaw.04G029500' => 'cil', 'CiPaw.04G174000' => 'cil', 'CiPaw.05G181200' => 'cil', 'CiPaw.06G067100' => 'cil', 'ClCG05G025800' => 'cla', 'ClCG06G011400' => 'cla', 'ClCG09G019360' => 'cla', 'COL.COLO4_04827' => 'col', 'COL.COLO4_29170' => 'col', 'COL.COLO4_35131' => 'col', 'COL.COLO4_35132' => 'col', 'Cpa.g.sc33.32' => 'cpa', 'Cpa.g.sc46.29' => 'cpa', 'Cpa.g.sc796.1' => 'cpa', 'CsaV3_1G030420' => 'csa', 'CsaV3_5G027050' => 'csa', 'CsaV3_5G031040' => 'csa', 'CsaV3_UNG023130' => 'csa', 'CSS0007726' => 'camsi', 'CSS0016433' => 'camsi', 'CSS0017656' => 'camsi', 'CSS0025364' => 'camsi', 'CSS0027582' => 'camsi', 'CSS0047288' => 'camsi', 'CSS0049950' => 'camsi', 'DCAR_003843' => 'dca', 'DCAR_007052' => 'dca', 'DCAR_020884' => 'dca', 'DCAR_021730' => 'dca', 'DCAR_024423' => 'dca', 'DCAR_026509' => 'dca', 'DCAR_031158' => 'dca', 'Dinv14728' => 'din', 'Dinv15219' => 'din', 'Dinv25728' => 'din', 'Dinv33428' => 'din', 'Dinv36489' => 'din', 'Dinv41486' => 'din', 'Duzib147G0469' => 'dzi', 'Duzib168G0060' => 'dzi', 'Duzib187G1215' => 'dzi', 'Duzib248G0692' => 'dzi', 'Duzib251G0767' => 'dzi', 'Duzib264G0446' => 'dzi', 'Duzib268G0691' => 'dzi', 'ECA232G4767' => 'eca', 'ECA233G2838' => 'eca', 'ECA234G0391' => 'eca', 'ECA234G0857' => 'eca', 'ECA236G1593' => 'eca', 'ECA238G0565' => 'eca', 'ECA246G1027' => 'eca', 'ECA246G3223' => 'eca', 'ECA246G3470' => 'eca', 'EL10Ac6g13829' => 'bvu', 'EL10Ac6g14093' => 'bvu', 'EL10Ac8g18707' => 'bvu', 'Eucgr.C01369' => 'egr', 'Eucgr.H02492' => 'egr', 'Eucgr.I01733' => 'egr', 'Eucgr.J02255' => 'egr', 'Eucgr.J02257' => 'egr', 'Eucgr.J02258' => 'egr', 'FAN02G1601' => 'fan', 'FAN03G1586' => 'fan', 'FAN03G2986' => 'fan', 'FAN05G4837' => 'fan', 'FAN06G0146' => 'fan', 'FAN07G0858' => 'fan', 'FAN09G3179' => 'fan', 'FAN10G0669' => 'fan', 'FAN12G2358' => 'fan', 'FAN14G4198' => 'fan', 'FAN14G5112' => 'fan', 'FAN17G0342' => 'fan', 'FAN19G0342' => 'fan', 'FAN19G0962' => 'fan', 'FAN19G1101' => 'fan', 'FAN19G1872' => 'fan', 'FAN22G0356' => 'fan', 'FAN23G0744' => 'fan', 'FAN23G1914' => 'fan', 'FAN26G0032' => 'fan', 'FAN28G0625' => 'fan', 'FvH4_1g02710' => 'fve', 'FvH4_1g02720' => 'fve', 'FvH4_4g25670' => 'fve', 'FvH4_6g51700' => 'fve', 'FvH4_7g20170' => 'fve', 'Glyma.05G175000' => 'gma', 'Glyma.08G132300' => 'gma', 'Glyma.11G243000' => 'gma', 'Glyma.13G158900' => 'gma', 'Glyma.17G112400' => 'gma', 'Glyma.18G014100' => 'gma', 'Glyma.19G003100' => 'gma', 'Glyma.19G056500' => 'gma', 'Gohir.A01G158900' => 'ghi', 'Gohir.A05G312600' => 'ghi', 'Gohir.A05G354900' => 'ghi', 'Gohir.A07G037200' => 'ghi', 'Gohir.A09G030000' => 'ghi', 'Gohir.A12G145200' => 'ghi', 'Gohir.D01G151500' => 'ghi', 'Gohir.D04G058300' => 'ghi', 'Gohir.D05G314100' => 'ghi', 'Gohir.D07G041400' => 'ghi', 'Gohir.D09G029700' => 'ghi', 'Gohir.D12G149700' => 'ghi', 'Gorai.001G043800' => 'gra', 'Gorai.002G187800' => 'gra', 'Gorai.006G034700' => 'gra', 'Gorai.008G161200' => 'gra', 'Gorai.009G335700' => 'gra', 'Gorai.012G065000' => 'gra', 'GSVIVG01000535001' => 'vvi', 'GSVIVG01015572001' => 'vvi', 'GSVIVG01032386001' => 'vvi', 'HanXRQChr05g0138531' => 'han', 'HanXRQChr06g0174391' => 'han', 'HanXRQChr07g0199021' => 'han', 'HanXRQChr08g0208211' => 'han', 'HanXRQChr09g0255471' => 'han', 'HanXRQChr10g0315791' => 'han', 'HanXRQChr12g0371991' => 'han', 'HanXRQChr15g0475251' => 'han', 'HanXRQChr17g0540001' => 'han', 'HanXRQChr17g0548631' => 'han', 'HanXRQChr17g0569561' => 'han', 'Haze_12256' => 'cav', 'Haze_14756' => 'cav', 'Haze_25528' => 'cav', 'Hma1.2p1_0079F.1_g041020' => 'hma', 'Hma1.2p1_0818F.1_g223260' => 'hma', 'Hma1.2p1_1747F.1_g300530' => 'hma', 'HPP92_004607' => 'vpl', 'HPP92_004608' => 'vpl', 'HPP92_006181' => 'vpl', 'HPP92_012192' => 'vpl', 'HPP92_015680' => 'vpl', 'HPP92_020249' => 'vpl', 'HPP92_021376' => 'vpl', 'HPP92_024275' => 'vpl', 'Hund06031' => 'sun', 'Hund25391' => 'sun', 'Lalb_Chr07g0185371' => 'lal', 'Lalb_Chr07g0185381' => 'lal', 'Lalb_Chr12g0204011' => 'lal', 'Lalb_Chr13g0301671' => 'lal', 'Lalb_Chr14g0362851' => 'lal', 'Lalb_Chr24g0403581' => 'lal', 'Lj1g0000233' => 'lja', 'Lj2g0018120' => 'lja', 'Lj3C621T0' => 'lonja', 'Lj3P1059T14' => 'lonja', 'Lj3P611T9' => 'lonja', 'Lj3P614T13' => 'lonja', 'Lj3P615T5' => 'lonja', 'Lj4g0012315' => 'lja', 'Lj4g0026182' => 'lja', 'Lj6P813T16' => 'lonja', 'Lj7C427T7' => 'lonja', 'Lj7C427T8' => 'lonja', 'Lj7P600T41' => 'lonja', 'Lju41C42G17' => 'lonja', 'Lsat_1_v5_gn_0_47300' => 'lsa', 'Lsat_1_v5_gn_2_91280' => 'lsa', 'Lsat_1_v5_gn_3_30561' => 'lsa', 'Lsat_1_v5_gn_4_184321' => 'lsa', 'Lsat_1_v5_gn_4_4041' => 'lsa', 'Lsat_1_v5_gn_5_92000' => 'lsa', 'Lsat_1_v5_gn_8_152940' => 'lsa', 'Lsat_1_v5_gn_8_62401' => 'lsa', 'Manes.06G055900' => 'mes', 'Manes.12G022200' => 'mes', 'Manes.13G023300' => 'mes', 'Manes.14G115000' => 'mes', 'Manes.15G151700' => 'mes', 'Manes.17G111300' => 'mes', 'Mapoly0226s0009' => 'mpo', 'MBI02_g25363_MAGBIO' => 'mbi', 'MBI06_g00027_MAGBIO' => 'mbi', 'MBI10_g13034_MAGBIO' => 'mbi', 'MD09G1023400' => 'mdo', 'MD13G1100100' => 'mdo', 'MD15G1169200' => 'mdo', 'MD16G1101100' => 'mdo', 'MD17G1022900' => 'mdo', 'Medtr3g096150' => 'mtr', 'Medtr4g115070' => 'mtr', 'Medtr7g033325' => 'mtr', 'Medtr8g089840' => 'mtr', 'MELO3C010319.2' => 'cme', 'MELO3C011944.2' => 'cme', 'MELO3C021589.2' => 'cme', 'Migut.E00207' => 'egut', 'Migut.H00067' => 'egut', 'Migut.K00433' => 'egut', 'Migut.K00606' => 'egut', 'Migut.K01410' => 'egut', 'MSTRG.13347' => 'ama', 'MSTRG.24045' => 'ama', 'MSTRG.2428' => 'ama', 'MSTRG.26410' => 'ama', 'MSTRG.3139' => 'ama', 'MSTRG.3286' => 'ama', 'MSTRG.563' => 'ama', 'MSTRG.7941' => 'ama', 'Nitab4.5_0000028g0060' => 'nta', 'Nitab4.5_0000065g0260' => 'nta', 'Nitab4.5_0000112g0060' => 'nta', 'Nitab4.5_0000489g0120' => 'nta', 'Nitab4.5_0001776g0050' => 'nta', 'Nitab4.5_0001854g0010' => 'nta', 'Nitab4.5_0001860g0020' => 'nta', 'Nitab4.5_0004352g0010' => 'nta', 'Nitab4.5_0008716g0020' => 'nta', 'Nitab4.5_0008922g0010' => 'nta', 'Nn3g16693' => 'nnu', 'Nn4g22596' => 'nnu', 'Nn7g37639' => 'nnu', 'Oeu001701.1' => 'oeu', 'Oeu018149.1' => 'oeu', 'Oeu026220.1' => 'oeu', 'Oeu038635.1' => 'oeu', 'Oeu049176.1' => 'oeu', 'Oeu056706.1' => 'oeu', 'Oeu056937.1' => 'oeu', 'Oeu057540.1' => 'oeu', 'Os02g0594900' => 'osa', 'Os02g0595100' => 'osa', 'Os04g0477500' => 'osa', 'Os12g0611900' => 'osa', 'Peaxi162Scf00076g00020' => 'pax', 'Peaxi162Scf00128g00217' => 'pax', 'Peaxi162Scf00129g01640' => 'pax', 'Peaxi162Scf00669g00007' => 'pax', 'Peaxi162Scf00700g00421' => 'pax', 'Peaxi162Scf00801g00038' => 'pax', 'Peaxi162Scf00891g00025' => 'pax', 'PGR083G0909' => 'pgr', 'PGR119G1005' => 'pgr', 'PGR142G2236' => 'pgr', 'PGR142G3388' => 'pgr', 'PGSC0003DMG400004514' => 'stu', 'PGSC0003DMG400012635' => 'stu', 'PGSC0003DMG400015730' => 'stu', 'PGSC0003DMG400018611' => 'stu', 'PGSC0003DMG400030897' => 'stu', 'Phvul.001G254800' => 'pvu', 'Phvul.002G260100' => 'pvu', 'Phvul.003G167600' => 'pvu', 'Phvul.004G005100' => 'pvu', 'Potri.001G343600' => 'ptr', 'Potri.006G066700' => 'ptr', 'Potri.008G186000' => 'ptr', 'Potri.010G046900' => 'ptr', 'Potri.018G127900' => 'ptr', 'Pp3c20_17750' => 'ppa', 'Pp3c24_4380' => 'ppa', 'Prupe.1G245800' => 'ppe', 'Prupe.3G293400' => 'ppe', 'Prupe.7G247400' => 'ppe', 'Psat0s145g0120' => 'psa', 'Psat0s595g0040' => 'psa', 'Psat0s595g0120' => 'psa', 'Psat3g175040' => 'psa', 'Psat7g058120' => 'psa', 'PSO017G0428' => 'pso', 'PSO063G7510' => 'pso', 'PSO067G0046' => 'pso', 'PSO478G1073' => 'pso', 'PSO675G3677' => 'pso', 'PSO675G6558' => 'pso', 'PSO675G7520' => 'pso', 'PSO675G8959' => 'pso', 'QL02p074089' => 'qlo', 'QL02p089614' => 'qlo', 'QL03p057736' => 'qlo', 'RcHm_v2.0_Chr1g0364131' => 'rch', 'RcHm_v2.0_Chr2g0087801' => 'rch', 'RcHm_v2.0_Chr2g0087821' => 'rch', 'RcHm_v2.0_Chr2g0173231' => 'rch', 'RcHm_v2.0_Chr4g0433111' => 'rch', 'Rhsim03G0250300' => 'rsi', 'Rhsim08G0048400' => 'rsi', 'Rhsim10G0014800' => 'rsi', 'Rhsim12G0040100' => 'rsi', 'Rhsim12G0109700' => 'rsi', 'Sabra06G0049600' => 'sbr', 'Sabra08G0141000' => 'sbr', 'Sabra10G0021400' => 'sbr', 'Sabra16G0222900' => 'sbr', 'Sabra18G0108600' => 'sbr', 'SalBow1G0433' => 'sbo', 'SalBow1G2038' => 'sbo', 'SalBow1G5003' => 'sbo', 'SalBow7G1197' => 'sbo', 'SalBow8G3506' => 'sbo', 'Sc03g0007300' => 'sci', 'Sc11g0000950' => 'sci', 'Sc14g0008750' => 'sci', 'Sc18g0000420' => 'sci', 'Sed0006754' => 'sed', 'Sed0008741' => 'sed', 'Sed0017172' => 'sed', 'Sed0018925' => 'sed', 'Sed0023326' => 'sed', 'Sed0025909' => 'sed', 'SEGI_05333' => 'sgi', 'SEGI_10362' => 'sgi', 'SEGI_13380' => 'sgi', 'SEGI_24306' => 'sgi', 'SEGI_29077' => 'sgi', 'SEGI_29095' => 'sgi', 'SEGI_36534' => 'sgi', 'SEGI_37506' => 'sgi', 'SEGI_38321' => 'sgi', 'SGA_v2.0_scaffold307G48031' => 'sas', 'SGA_v2.0_scaffold47G17507' => 'sas', 'SGA_v2.0_scaffold63G21736' => 'sas', 'SGA_v2.0_scaffold87G27070' => 'sas', 'SHI17794' => 'shi', 'SHI28851' => 'shi', 'SMO165G0155' => 'smo', 'SMO340G0217' => 'smo', 'SMO367G1210' => 'smo', 'Solyc02g093430.3' => 'sly', 'Solyc05g013580.4' => 'sly', 'Solyc07g008030.3' => 'sly', 'Solyc12g035470.2' => 'sly', 'Sopen02g038020' => 'spe', 'Sopen05g008490' => 'spe', 'Sopen07g003910' => 'spe', 'Sopen12g015240' => 'spe', 'Sp1g11550' => 'spa', 'Sp2g16710' => 'spa', 'Sp3g00430' => 'spa', 'Sp3g26780' => 'spa', 'Sp5g22900' => 'spa', 'Sp6g29530' => 'spa', 'TAR371G0794' => 'tar', 'TAR374G0164' => 'tar', 'TAR622G0165' => 'tar', 'TAR626G0929' => 'tar', 'TAR629G2155' => 'tar', 'THA.LOC104805282' => 'tha', 'THA.LOC104805363' => 'tha', 'THA.LOC104808968' => 'tha', 'THA.LOC104821093' => 'tha', 'THA.LOC104823953' => 'tha', 'THA.LOC104825562' => 'tha', 'THA.LOC104825665' => 'tha', 'Thecc.02G261400' => 'tca', 'Thecc.04G019200' => 'tca', 'Thecc.09G130400' => 'tca', 'Thhalv10004374m.g' => 'esa', 'Thhalv10007850m.g' => 'esa', 'Thhalv10013782m.g' => 'esa', 'Thhalv10018686m.g' => 'esa', 'Thhalv10020899m.g' => 'esa', 'Thhalv10022755m.g' => 'esa', 'TPR.G23851' => 'tpr', 'TPR.G26500' => 'tpr', 'TPR.G27267' => 'tpr', 'TPR.G32001' => 'tpr', 'TPR.G6251' => 'tpr', 'TPR.G8167' => 'tpr', 'TWI12G1330' => 'twi', 'TWI18G1239' => 'twi', 'TWI34G0979' => 'twi', 'TWI36G0670' => 'twi', 'TWI36G0707' => 'twi', 'TWI56G0233' => 'twi', 'TWI75G1809' => 'twi', 'unitig_21.g20874' => 'ugi', 'unitig_26.g10343' => 'ugi', 'unitig_46.g18392' => 'ugi', 'unitig_52.g17178' => 'ugi', 'unitig_8.g2934' => 'ugi', 'vmacro01122' => 'vma', 'vmacro05875' => 'vma', 'vmacro06147' => 'vma', 'vmacro16191' => 'vma', 'vmacro18293' => 'vma', 'VMungo0251G3707' => 'vmu', 'VMungo0464G1521' => 'vmu', 'VMungo1215G0205' => 'vmu', 'VMungo1383G2484' => 'vmu', 'Zm00001eb079610' => 'zma', 'Zm00001eb135990' => 'zma', 'Zm00001eb183710' => 'zma', 'Zm00001eb246020' => 'zma' ), 'gf_id' => 'HOM05D001124', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001124' ), 'data_identifier' => 'HOM05D001124', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001124', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '548', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02520' => 'bna', 'A03p06630' => 'bna', 'A05p44460' => 'bna', 'A06p08710' => 'bna', 'A06p41090' => 'bna', 'A07p32320' => 'bna', 'A08p32520' => 'bna', 'A09p10360' => 'bna', 'A10p24080' => 'bna', 'Aa31LG11G15250' => 'aar', 'Aa31LG1G1800' => 'aar', 'Aa31LG2G5120' => 'aar', 'Aa31LG2G6070' => 'aar', 'Aa31LG5G10770' => 'aar', 'Aa31sc61G90' => 'aar', 'Actinidia01352' => 'ach', 'Actinidia05983' => 'ach', 'Actinidia08133' => 'ach', 'Actinidia15101' => 'ach', 'Actinidia26379' => 'ach', 'Actinidia35778' => 'ach', 'Actinidia36123' => 'ach', 'Actinidia37436' => 'ach', 'Actinidia38730' => 'ach', 'Ah.02g128210' => 'amhyb', 'Ah.03g132990' => 'amhyb', 'Ah.14g079410' => 'amhyb', 'AL1G24640' => 'aly', 'AL2G26680' => 'aly', 'AL3G10530' => 'aly', 'AL3G45230' => 'aly', 'AL5G15230' => 'aly', 'AL5G16960' => 'aly', 'AL6G25210' => 'aly', 'Aqoxy2G00441' => 'aox', 'Aqoxy3G01236' => 'aox', 'Aqoxy5G03746' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3RQ047' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C7GMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9C8JER' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MBL6KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YXCZ83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZANX40' => 'arhy', 'AT1G12990' => 'ath', 'AT1G67880' => 'ath', 'AT2G13290' => 'ath', 'AT3G01620' => 'ath', 'AT3G26445' => 'ath', 'AT3G27540' => 'ath', 'AT5G14480' => 'ath', 'ATR0824G026' => 'atr', 'ATR1098G019' => 'atr', 'Atru.chr11.2145' => 'acertr', 'Atru.chr2.3636' => 'acertr', 'Atru.chr2.3644' => 'acertr', 'Atru.chr6.2422' => 'acertr', 'Atru.chr7.1112' => 'acertr', 'AUR62005469' => 'cqu', 'AUR62011166' => 'cqu', 'AUR62013319' => 'cqu', 'AUR62024273' => 'cqu', 'AUR62028420' => 'cqu', 'AUR62041942' => 'cqu', 'BcaB01g04969' => 'bca', 'BcaB01g06371' => 'bca', 'BcaB02g11494' => 'bca', 'BcaB03g15382' => 'bca', 'BcaB08g36994' => 'bca', 'BcaC03g13477' => 'bca', 'BcaC03g13478' => 'bca', 'BcaC03g13480' => 'bca', 'BcaC03g13481' => 'bca', 'BcaC03g13486' => 'bca', 'BcaC04g19031' => 'bca', 'BcaC04g23085' => 'bca', 'BcaC05g25094' => 'bca', 'BcaC05g25096' => 'bca', 'BcaC05g25138' => 'bca', 'BcaC05g30416' => 'bca', 'BcaC05g30455' => 'bca', 'BcaC06g30979' => 'bca', 'BcaC06g33805' => 'bca', 'BcaC08g46021' => 'bca', 'BcaNung03154' => 'bca', 'BolC2t06623H' => 'bol', 'BolC2t06632H' => 'bol', 'BolC2t06635H' => 'bol', 'BolC2t06638H' => 'bol', 'BolC3t13266H' => 'bol', 'BolC5t29776H' => 'bol', 'BolC6t38912H' => 'bol', 'BolC7t44183H' => 'bol', 'BolC9t54123H' => 'bol', 'BolC9t59107H' => 'bol', 'BraA02t05221Z' => 'bra', 'BraA03t09996Z' => 'bra', 'BraA05t23210Z' => 'bra', 'BraA06t24068Z' => 'bra', 'BraA06t27032Z' => 'bra', 'BraA08t35176Z' => 'bra', 'BraA09t36680Z' => 'bra', 'BraA10t44471Z' => 'bra', 'C02p06760' => 'bna', 'C02p06890' => 'bna', 'C02p07010' => 'bna', 'C03p07660' => 'bna', 'C05p10300' => 'bna', 'C06p38150' => 'bna', 'C07p36650' => 'bna', 'C08p15770' => 'bna', 'C09p12300' => 'bna', 'C09p62700' => 'bna', 'C09p75040' => 'bna', 'CAN.G13.1' => 'can', 'CAN.G138.4' => 'can', 'CAN.G44.6' => 'can', 'CAN.G473.19' => 'can', 'CANSAT01G0835' => 'cansat', 'CANSAT11G0246' => 'cansat', 'CANSAT11G1766' => 'cansat', 'CANSAT64G1954' => 'cansat', 'CARHR013330' => 'chi', 'CARHR060530' => 'chi', 'CARHR075300' => 'chi', 'CARHR105120' => 'chi', 'CARHR148910' => 'chi', 'CARHR198830' => 'chi', 'Carub.0001s1275' => 'cru', 'Carub.0002s1437' => 'cru', 'Carub.0003s0044' => 'cru', 'Carub.0003s2787' => 'cru', 'Carub.0005s0597' => 'cru', 'Carub.0006s1266' => 'cru', 'Ca_06935_v3' => 'car', 'Ca_13559_v3' => 'car', 'Ca_16941_v3' => 'car', 'Ca_16960_v3' => 'car', 'Ca_17775_v3' => 'car', 'Ca_30464_v3' => 'car', 'Cc06_g08160' => 'ccan', 'Cc07_g01520' => 'ccan', 'Cc11_g15810' => 'ccan', 'CDE02G2840' => 'cde', 'CDE03G0093' => 'cde', 'CDE04G2127' => 'cde', 'CDE07G1857' => 'cde', 'CDE09G1246' => 'cde', 'Cfa003412' => 'cfa', 'Cfa007341' => 'cfa', 'Cfa009220' => 'cfa', 'Ciclev10008737m.g' => 'ccl', 'Ciclev10015565m.g' => 'ccl', 'Ciclev10031761m.g' => 'ccl', 'CiPaw.03G045300' => 'cil', 'CiPaw.03G247200' => 'cil', 'CiPaw.04G029500' => 'cil', 'CiPaw.04G174000' => 'cil', 'CiPaw.05G181200' => 'cil', 'CiPaw.06G067100' => 'cil', 'ClCG05G025800' => 'cla', 'ClCG06G011400' => 'cla', 'ClCG09G019360' => 'cla', 'COL.COLO4_04827' => 'col', 'COL.COLO4_29170' => 'col', 'COL.COLO4_35131' => 'col', 'COL.COLO4_35132' => 'col', 'Cpa.g.sc33.32' => 'cpa', 'Cpa.g.sc46.29' => 'cpa', 'Cpa.g.sc796.1' => 'cpa', 'CsaV3_1G030420' => 'csa', 'CsaV3_5G027050' => 'csa', 'CsaV3_5G031040' => 'csa', 'CsaV3_UNG023130' => 'csa', 'CSS0007726' => 'camsi', 'CSS0016433' => 'camsi', 'CSS0017656' => 'camsi', 'CSS0025364' => 'camsi', 'CSS0027582' => 'camsi', 'CSS0047288' => 'camsi', 'CSS0049950' => 'camsi', 'DCAR_003843' => 'dca', 'DCAR_007052' => 'dca', 'DCAR_020884' => 'dca', 'DCAR_021730' => 'dca', 'DCAR_024423' => 'dca', 'DCAR_026509' => 'dca', 'DCAR_031158' => 'dca', 'Dinv14728' => 'din', 'Dinv15219' => 'din', 'Dinv25728' => 'din', 'Dinv33428' => 'din', 'Dinv36489' => 'din', 'Dinv41486' => 'din', 'Duzib147G0469' => 'dzi', 'Duzib168G0060' => 'dzi', 'Duzib187G1215' => 'dzi', 'Duzib248G0692' => 'dzi', 'Duzib251G0767' => 'dzi', 'Duzib264G0446' => 'dzi', 'Duzib268G0691' => 'dzi', 'ECA232G4767' => 'eca', 'ECA233G2838' => 'eca', 'ECA234G0391' => 'eca', 'ECA234G0857' => 'eca', 'ECA236G1593' => 'eca', 'ECA238G0565' => 'eca', 'ECA246G1027' => 'eca', 'ECA246G3223' => 'eca', 'ECA246G3470' => 'eca', 'EL10Ac6g13829' => 'bvu', 'EL10Ac6g14093' => 'bvu', 'EL10Ac8g18707' => 'bvu', 'Eucgr.C01369' => 'egr', 'Eucgr.H02492' => 'egr', 'Eucgr.I01733' => 'egr', 'Eucgr.J02255' => 'egr', 'Eucgr.J02257' => 'egr', 'Eucgr.J02258' => 'egr', 'FAN02G1601' => 'fan', 'FAN03G1586' => 'fan', 'FAN03G2986' => 'fan', 'FAN05G4837' => 'fan', 'FAN06G0146' => 'fan', 'FAN07G0858' => 'fan', 'FAN09G3179' => 'fan', 'FAN10G0669' => 'fan', 'FAN12G2358' => 'fan', 'FAN14G4198' => 'fan', 'FAN14G5112' => 'fan', 'FAN17G0342' => 'fan', 'FAN19G0342' => 'fan', 'FAN19G0962' => 'fan', 'FAN19G1101' => 'fan', 'FAN19G1872' => 'fan', 'FAN22G0356' => 'fan', 'FAN23G0744' => 'fan', 'FAN23G1914' => 'fan', 'FAN26G0032' => 'fan', 'FAN28G0625' => 'fan', 'FvH4_1g02710' => 'fve', 'FvH4_1g02720' => 'fve', 'FvH4_4g25670' => 'fve', 'FvH4_6g51700' => 'fve', 'FvH4_7g20170' => 'fve', 'Glyma.05G175000' => 'gma', 'Glyma.08G132300' => 'gma', 'Glyma.11G243000' => 'gma', 'Glyma.13G158900' => 'gma', 'Glyma.17G112400' => 'gma', 'Glyma.18G014100' => 'gma', 'Glyma.19G003100' => 'gma', 'Glyma.19G056500' => 'gma', 'Gohir.A01G158900' => 'ghi', 'Gohir.A05G312600' => 'ghi', 'Gohir.A05G354900' => 'ghi', 'Gohir.A07G037200' => 'ghi', 'Gohir.A09G030000' => 'ghi', 'Gohir.A12G145200' => 'ghi', 'Gohir.D01G151500' => 'ghi', 'Gohir.D04G058300' => 'ghi', 'Gohir.D05G314100' => 'ghi', 'Gohir.D07G041400' => 'ghi', 'Gohir.D09G029700' => 'ghi', 'Gohir.D12G149700' => 'ghi', 'Gorai.001G043800' => 'gra', 'Gorai.002G187800' => 'gra', 'Gorai.006G034700' => 'gra', 'Gorai.008G161200' => 'gra', 'Gorai.009G335700' => 'gra', 'Gorai.012G065000' => 'gra', 'GSVIVG01000535001' => 'vvi', 'GSVIVG01015572001' => 'vvi', 'GSVIVG01032386001' => 'vvi', 'HanXRQChr05g0138531' => 'han', 'HanXRQChr06g0174391' => 'han', 'HanXRQChr07g0199021' => 'han', 'HanXRQChr08g0208211' => 'han', 'HanXRQChr09g0255471' => 'han', 'HanXRQChr10g0315791' => 'han', 'HanXRQChr12g0371991' => 'han', 'HanXRQChr15g0475251' => 'han', 'HanXRQChr17g0540001' => 'han', 'HanXRQChr17g0548631' => 'han', 'HanXRQChr17g0569561' => 'han', 'Haze_12256' => 'cav', 'Haze_14756' => 'cav', 'Haze_25528' => 'cav', 'Hma1.2p1_0079F.1_g041020' => 'hma', 'Hma1.2p1_0818F.1_g223260' => 'hma', 'Hma1.2p1_1747F.1_g300530' => 'hma', 'HPP92_004607' => 'vpl', 'HPP92_004608' => 'vpl', 'HPP92_006181' => 'vpl', 'HPP92_012192' => 'vpl', 'HPP92_015680' => 'vpl', 'HPP92_020249' => 'vpl', 'HPP92_021376' => 'vpl', 'HPP92_024275' => 'vpl', 'Hund06031' => 'sun', 'Hund25391' => 'sun', 'Lalb_Chr07g0185371' => 'lal', 'Lalb_Chr07g0185381' => 'lal', 'Lalb_Chr12g0204011' => 'lal', 'Lalb_Chr13g0301671' => 'lal', 'Lalb_Chr14g0362851' => 'lal', 'Lalb_Chr24g0403581' => 'lal', 'Lj1g0000233' => 'lja', 'Lj2g0018120' => 'lja', 'Lj3C621T0' => 'lonja', 'Lj3P1059T14' => 'lonja', 'Lj3P611T9' => 'lonja', 'Lj3P614T13' => 'lonja', 'Lj3P615T5' => 'lonja', 'Lj4g0012315' => 'lja', 'Lj4g0026182' => 'lja', 'Lj6P813T16' => 'lonja', 'Lj7C427T7' => 'lonja', 'Lj7C427T8' => 'lonja', 'Lj7P600T41' => 'lonja', 'Lju41C42G17' => 'lonja', 'Lsat_1_v5_gn_0_47300' => 'lsa', 'Lsat_1_v5_gn_2_91280' => 'lsa', 'Lsat_1_v5_gn_3_30561' => 'lsa', 'Lsat_1_v5_gn_4_184321' => 'lsa', 'Lsat_1_v5_gn_4_4041' => 'lsa', 'Lsat_1_v5_gn_5_92000' => 'lsa', 'Lsat_1_v5_gn_8_152940' => 'lsa', 'Lsat_1_v5_gn_8_62401' => 'lsa', 'Manes.06G055900' => 'mes', 'Manes.12G022200' => 'mes', 'Manes.13G023300' => 'mes', 'Manes.14G115000' => 'mes', 'Manes.15G151700' => 'mes', 'Manes.17G111300' => 'mes', 'Mapoly0226s0009' => 'mpo', 'MBI02_g25363_MAGBIO' => 'mbi', 'MBI06_g00027_MAGBIO' => 'mbi', 'MBI10_g13034_MAGBIO' => 'mbi', 'MD09G1023400' => 'mdo', 'MD13G1100100' => 'mdo', 'MD15G1169200' => 'mdo', 'MD16G1101100' => 'mdo', 'MD17G1022900' => 'mdo', 'Medtr3g096150' => 'mtr', 'Medtr4g115070' => 'mtr', 'Medtr7g033325' => 'mtr', 'Medtr8g089840' => 'mtr', 'MELO3C010319.2' => 'cme', 'MELO3C011944.2' => 'cme', 'MELO3C021589.2' => 'cme', 'Migut.E00207' => 'egut', 'Migut.H00067' => 'egut', 'Migut.K00433' => 'egut', 'Migut.K00606' => 'egut', 'Migut.K01410' => 'egut', 'MSTRG.13347' => 'ama', 'MSTRG.24045' => 'ama', 'MSTRG.2428' => 'ama', 'MSTRG.26410' => 'ama', 'MSTRG.3139' => 'ama', 'MSTRG.3286' => 'ama', 'MSTRG.563' => 'ama', 'MSTRG.7941' => 'ama', 'Nitab4.5_0000028g0060' => 'nta', 'Nitab4.5_0000065g0260' => 'nta', 'Nitab4.5_0000112g0060' => 'nta', 'Nitab4.5_0000489g0120' => 'nta', 'Nitab4.5_0001776g0050' => 'nta', 'Nitab4.5_0001854g0010' => 'nta', 'Nitab4.5_0001860g0020' => 'nta', 'Nitab4.5_0004352g0010' => 'nta', 'Nitab4.5_0008716g0020' => 'nta', 'Nitab4.5_0008922g0010' => 'nta', 'Nn3g16693' => 'nnu', 'Nn4g22596' => 'nnu', 'Nn7g37639' => 'nnu', 'Oeu001701.1' => 'oeu', 'Oeu018149.1' => 'oeu', 'Oeu026220.1' => 'oeu', 'Oeu038635.1' => 'oeu', 'Oeu049176.1' => 'oeu', 'Oeu056706.1' => 'oeu', 'Oeu056937.1' => 'oeu', 'Oeu057540.1' => 'oeu', 'Os02g0594900' => 'osa', 'Os02g0595100' => 'osa', 'Os04g0477500' => 'osa', 'Os12g0611900' => 'osa', 'Peaxi162Scf00076g00020' => 'pax', 'Peaxi162Scf00128g00217' => 'pax', 'Peaxi162Scf00129g01640' => 'pax', 'Peaxi162Scf00669g00007' => 'pax', 'Peaxi162Scf00700g00421' => 'pax', 'Peaxi162Scf00801g00038' => 'pax', 'Peaxi162Scf00891g00025' => 'pax', 'PGR083G0909' => 'pgr', 'PGR119G1005' => 'pgr', 'PGR142G2236' => 'pgr', 'PGR142G3388' => 'pgr', 'PGSC0003DMG400004514' => 'stu', 'PGSC0003DMG400012635' => 'stu', 'PGSC0003DMG400015730' => 'stu', 'PGSC0003DMG400018611' => 'stu', 'PGSC0003DMG400030897' => 'stu', 'Phvul.001G254800' => 'pvu', 'Phvul.002G260100' => 'pvu', 'Phvul.003G167600' => 'pvu', 'Phvul.004G005100' => 'pvu', 'Potri.001G343600' => 'ptr', 'Potri.006G066700' => 'ptr', 'Potri.008G186000' => 'ptr', 'Potri.010G046900' => 'ptr', 'Potri.018G127900' => 'ptr', 'Pp3c20_17750' => 'ppa', 'Pp3c24_4380' => 'ppa', 'Prupe.1G245800' => 'ppe', 'Prupe.3G293400' => 'ppe', 'Prupe.7G247400' => 'ppe', 'Psat0s145g0120' => 'psa', 'Psat0s595g0040' => 'psa', 'Psat0s595g0120' => 'psa', 'Psat3g175040' => 'psa', 'Psat7g058120' => 'psa', 'PSO017G0428' => 'pso', 'PSO063G7510' => 'pso', 'PSO067G0046' => 'pso', 'PSO478G1073' => 'pso', 'PSO675G3677' => 'pso', 'PSO675G6558' => 'pso', 'PSO675G7520' => 'pso', 'PSO675G8959' => 'pso', 'QL02p074089' => 'qlo', 'QL02p089614' => 'qlo', 'QL03p057736' => 'qlo', 'RcHm_v2.0_Chr1g0364131' => 'rch', 'RcHm_v2.0_Chr2g0087801' => 'rch', 'RcHm_v2.0_Chr2g0087821' => 'rch', 'RcHm_v2.0_Chr2g0173231' => 'rch', 'RcHm_v2.0_Chr4g0433111' => 'rch', 'Rhsim03G0250300' => 'rsi', 'Rhsim08G0048400' => 'rsi', 'Rhsim10G0014800' => 'rsi', 'Rhsim12G0040100' => 'rsi', 'Rhsim12G0109700' => 'rsi', 'Sabra06G0049600' => 'sbr', 'Sabra08G0141000' => 'sbr', 'Sabra10G0021400' => 'sbr', 'Sabra16G0222900' => 'sbr', 'Sabra18G0108600' => 'sbr', 'SalBow1G0433' => 'sbo', 'SalBow1G2038' => 'sbo', 'SalBow1G5003' => 'sbo', 'SalBow7G1197' => 'sbo', 'SalBow8G3506' => 'sbo', 'Sc03g0007300' => 'sci', 'Sc11g0000950' => 'sci', 'Sc14g0008750' => 'sci', 'Sc18g0000420' => 'sci', 'Sed0006754' => 'sed', 'Sed0008741' => 'sed', 'Sed0017172' => 'sed', 'Sed0018925' => 'sed', 'Sed0023326' => 'sed', 'Sed0025909' => 'sed', 'SEGI_05333' => 'sgi', 'SEGI_10362' => 'sgi', 'SEGI_13380' => 'sgi', 'SEGI_24306' => 'sgi', 'SEGI_29077' => 'sgi', 'SEGI_29095' => 'sgi', 'SEGI_36534' => 'sgi', 'SEGI_37506' => 'sgi', 'SEGI_38321' => 'sgi', 'SGA_v2.0_scaffold307G48031' => 'sas', 'SGA_v2.0_scaffold47G17507' => 'sas', 'SGA_v2.0_scaffold63G21736' => 'sas', 'SGA_v2.0_scaffold87G27070' => 'sas', 'SHI17794' => 'shi', 'SHI28851' => 'shi', 'SMO165G0155' => 'smo', 'SMO340G0217' => 'smo', 'SMO367G1210' => 'smo', 'Solyc02g093430.3' => 'sly', 'Solyc05g013580.4' => 'sly', 'Solyc07g008030.3' => 'sly', 'Solyc12g035470.2' => 'sly', 'Sopen02g038020' => 'spe', 'Sopen05g008490' => 'spe', 'Sopen07g003910' => 'spe', 'Sopen12g015240' => 'spe', 'Sp1g11550' => 'spa', 'Sp2g16710' => 'spa', 'Sp3g00430' => 'spa', 'Sp3g26780' => 'spa', 'Sp5g22900' => 'spa', 'Sp6g29530' => 'spa', 'TAR371G0794' => 'tar', 'TAR374G0164' => 'tar', 'TAR622G0165' => 'tar', 'TAR626G0929' => 'tar', 'TAR629G2155' => 'tar', 'THA.LOC104805282' => 'tha', 'THA.LOC104805363' => 'tha', 'THA.LOC104808968' => 'tha', 'THA.LOC104821093' => 'tha', 'THA.LOC104823953' => 'tha', 'THA.LOC104825562' => 'tha', 'THA.LOC104825665' => 'tha', 'Thecc.02G261400' => 'tca', 'Thecc.04G019200' => 'tca', 'Thecc.09G130400' => 'tca', 'Thhalv10004374m.g' => 'esa', 'Thhalv10007850m.g' => 'esa', 'Thhalv10013782m.g' => 'esa', 'Thhalv10018686m.g' => 'esa', 'Thhalv10020899m.g' => 'esa', 'Thhalv10022755m.g' => 'esa', 'TPR.G23851' => 'tpr', 'TPR.G26500' => 'tpr', 'TPR.G27267' => 'tpr', 'TPR.G32001' => 'tpr', 'TPR.G6251' => 'tpr', 'TPR.G8167' => 'tpr', 'TWI12G1330' => 'twi', 'TWI18G1239' => 'twi', 'TWI34G0979' => 'twi', 'TWI36G0670' => 'twi', 'TWI36G0707' => 'twi', 'TWI56G0233' => 'twi', 'TWI75G1809' => 'twi', 'unitig_21.g20874' => 'ugi', 'unitig_26.g10343' => 'ugi', 'unitig_46.g18392' => 'ugi', 'unitig_52.g17178' => 'ugi', 'unitig_8.g2934' => 'ugi', 'vmacro01122' => 'vma', 'vmacro05875' => 'vma', 'vmacro06147' => 'vma', 'vmacro16191' => 'vma', 'vmacro18293' => 'vma', 'VMungo0251G3707' => 'vmu', 'VMungo0464G1521' => 'vmu', 'VMungo1215G0205' => 'vmu', 'VMungo1383G2484' => 'vmu', 'Zm00001eb079610' => 'zma', 'Zm00001eb135990' => 'zma', 'Zm00001eb183710' => 'zma', 'Zm00001eb246020' => 'zma' ) $gf_id = 'HOM05D001124' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001124' ) $data_identifier = 'HOM05D001124' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 6, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 7, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 21, 'bol' => (int) 10, 'bra' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 6, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 9, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 21, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 8, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 10, 'lsa' => (int) 8, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 8, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 9, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb246020' $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' => 'HOM05D001124', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '548', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02520' => 'bna', 'A03p06630' => 'bna', 'A05p44460' => 'bna', 'A06p08710' => 'bna', 'A06p41090' => 'bna', 'A07p32320' => 'bna', 'A08p32520' => 'bna', 'A09p10360' => 'bna', 'A10p24080' => 'bna', 'Aa31LG11G15250' => 'aar', 'Aa31LG1G1800' => 'aar', 'Aa31LG2G5120' => 'aar', 'Aa31LG2G6070' => 'aar', 'Aa31LG5G10770' => 'aar', 'Aa31sc61G90' => 'aar', 'Actinidia01352' => 'ach', 'Actinidia05983' => 'ach', 'Actinidia08133' => 'ach', 'Actinidia15101' => 'ach', 'Actinidia26379' => 'ach', 'Actinidia35778' => 'ach', 'Actinidia36123' => 'ach', 'Actinidia37436' => 'ach', 'Actinidia38730' => 'ach', 'Ah.02g128210' => 'amhyb', 'Ah.03g132990' => 'amhyb', 'Ah.14g079410' => 'amhyb', 'AL1G24640' => 'aly', 'AL2G26680' => 'aly', 'AL3G10530' => 'aly', 'AL3G45230' => 'aly', 'AL5G15230' => 'aly', 'AL5G16960' => 'aly', 'AL6G25210' => 'aly', 'Aqoxy2G00441' => 'aox', 'Aqoxy3G01236' => 'aox', 'Aqoxy5G03746' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3RQ047' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C7GMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9C8JER' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MBL6KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YXCZ83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZANX40' => 'arhy', 'AT1G12990' => 'ath', 'AT1G67880' => 'ath', 'AT2G13290' => 'ath', 'AT3G01620' => 'ath', 'AT3G26445' => 'ath', 'AT3G27540' => 'ath', 'AT5G14480' => 'ath', 'ATR0824G026' => 'atr', 'ATR1098G019' => 'atr', 'Atru.chr11.2145' => 'acertr', 'Atru.chr2.3636' => 'acertr', 'Atru.chr2.3644' => 'acertr', 'Atru.chr6.2422' => 'acertr', 'Atru.chr7.1112' => 'acertr', 'AUR62005469' => 'cqu', 'AUR62011166' => 'cqu', 'AUR62013319' => 'cqu', 'AUR62024273' => 'cqu', 'AUR62028420' => 'cqu', 'AUR62041942' => 'cqu', 'BcaB01g04969' => 'bca', 'BcaB01g06371' => 'bca', 'BcaB02g11494' => 'bca', 'BcaB03g15382' => 'bca', 'BcaB08g36994' => 'bca', 'BcaC03g13477' => 'bca', 'BcaC03g13478' => 'bca', 'BcaC03g13480' => 'bca', 'BcaC03g13481' => 'bca', 'BcaC03g13486' => 'bca', 'BcaC04g19031' => 'bca', 'BcaC04g23085' => 'bca', 'BcaC05g25094' => 'bca', 'BcaC05g25096' => 'bca', 'BcaC05g25138' => 'bca', 'BcaC05g30416' => 'bca', 'BcaC05g30455' => 'bca', 'BcaC06g30979' => 'bca', 'BcaC06g33805' => 'bca', 'BcaC08g46021' => 'bca', 'BcaNung03154' => 'bca', 'BolC2t06623H' => 'bol', 'BolC2t06632H' => 'bol', 'BolC2t06635H' => 'bol', 'BolC2t06638H' => 'bol', 'BolC3t13266H' => 'bol', 'BolC5t29776H' => 'bol', 'BolC6t38912H' => 'bol', 'BolC7t44183H' => 'bol', 'BolC9t54123H' => 'bol', 'BolC9t59107H' => 'bol', 'BraA02t05221Z' => 'bra', 'BraA03t09996Z' => 'bra', 'BraA05t23210Z' => 'bra', 'BraA06t24068Z' => 'bra', 'BraA06t27032Z' => 'bra', 'BraA08t35176Z' => 'bra', 'BraA09t36680Z' => 'bra', 'BraA10t44471Z' => 'bra', 'C02p06760' => 'bna', 'C02p06890' => 'bna', 'C02p07010' => 'bna', 'C03p07660' => 'bna', 'C05p10300' => 'bna', 'C06p38150' => 'bna', 'C07p36650' => 'bna', 'C08p15770' => 'bna', 'C09p12300' => 'bna', 'C09p62700' => 'bna', 'C09p75040' => 'bna', 'CAN.G13.1' => 'can', 'CAN.G138.4' => 'can', 'CAN.G44.6' => 'can', 'CAN.G473.19' => 'can', 'CANSAT01G0835' => 'cansat', 'CANSAT11G0246' => 'cansat', 'CANSAT11G1766' => 'cansat', 'CANSAT64G1954' => 'cansat', 'CARHR013330' => 'chi', 'CARHR060530' => 'chi', 'CARHR075300' => 'chi', 'CARHR105120' => 'chi', 'CARHR148910' => 'chi', 'CARHR198830' => 'chi', 'Carub.0001s1275' => 'cru', 'Carub.0002s1437' => 'cru', 'Carub.0003s0044' => 'cru', 'Carub.0003s2787' => 'cru', 'Carub.0005s0597' => 'cru', 'Carub.0006s1266' => 'cru', 'Ca_06935_v3' => 'car', 'Ca_13559_v3' => 'car', 'Ca_16941_v3' => 'car', 'Ca_16960_v3' => 'car', 'Ca_17775_v3' => 'car', 'Ca_30464_v3' => 'car', 'Cc06_g08160' => 'ccan', 'Cc07_g01520' => 'ccan', 'Cc11_g15810' => 'ccan', 'CDE02G2840' => 'cde', 'CDE03G0093' => 'cde', 'CDE04G2127' => 'cde', 'CDE07G1857' => 'cde', 'CDE09G1246' => 'cde', 'Cfa003412' => 'cfa', 'Cfa007341' => 'cfa', 'Cfa009220' => 'cfa', 'Ciclev10008737m.g' => 'ccl', 'Ciclev10015565m.g' => 'ccl', 'Ciclev10031761m.g' => 'ccl', 'CiPaw.03G045300' => 'cil', 'CiPaw.03G247200' => 'cil', 'CiPaw.04G029500' => 'cil', 'CiPaw.04G174000' => 'cil', 'CiPaw.05G181200' => 'cil', 'CiPaw.06G067100' => 'cil', 'ClCG05G025800' => 'cla', 'ClCG06G011400' => 'cla', 'ClCG09G019360' => 'cla', 'COL.COLO4_04827' => 'col', 'COL.COLO4_29170' => 'col', 'COL.COLO4_35131' => 'col', 'COL.COLO4_35132' => 'col', 'Cpa.g.sc33.32' => 'cpa', 'Cpa.g.sc46.29' => 'cpa', 'Cpa.g.sc796.1' => 'cpa', 'CsaV3_1G030420' => 'csa', 'CsaV3_5G027050' => 'csa', 'CsaV3_5G031040' => 'csa', 'CsaV3_UNG023130' => 'csa', 'CSS0007726' => 'camsi', 'CSS0016433' => 'camsi', 'CSS0017656' => 'camsi', 'CSS0025364' => 'camsi', 'CSS0027582' => 'camsi', 'CSS0047288' => 'camsi', 'CSS0049950' => 'camsi', 'DCAR_003843' => 'dca', 'DCAR_007052' => 'dca', 'DCAR_020884' => 'dca', 'DCAR_021730' => 'dca', 'DCAR_024423' => 'dca', 'DCAR_026509' => 'dca', 'DCAR_031158' => 'dca', 'Dinv14728' => 'din', 'Dinv15219' => 'din', 'Dinv25728' => 'din', 'Dinv33428' => 'din', 'Dinv36489' => 'din', 'Dinv41486' => 'din', 'Duzib147G0469' => 'dzi', 'Duzib168G0060' => 'dzi', 'Duzib187G1215' => 'dzi', 'Duzib248G0692' => 'dzi', 'Duzib251G0767' => 'dzi', 'Duzib264G0446' => 'dzi', 'Duzib268G0691' => 'dzi', 'ECA232G4767' => 'eca', 'ECA233G2838' => 'eca', 'ECA234G0391' => 'eca', 'ECA234G0857' => 'eca', 'ECA236G1593' => 'eca', 'ECA238G0565' => 'eca', 'ECA246G1027' => 'eca', 'ECA246G3223' => 'eca', 'ECA246G3470' => 'eca', 'EL10Ac6g13829' => 'bvu', 'EL10Ac6g14093' => 'bvu', 'EL10Ac8g18707' => 'bvu', 'Eucgr.C01369' => 'egr', 'Eucgr.H02492' => 'egr', 'Eucgr.I01733' => 'egr', 'Eucgr.J02255' => 'egr', 'Eucgr.J02257' => 'egr', 'Eucgr.J02258' => 'egr', 'FAN02G1601' => 'fan', 'FAN03G1586' => 'fan', 'FAN03G2986' => 'fan', 'FAN05G4837' => 'fan', 'FAN06G0146' => 'fan', 'FAN07G0858' => 'fan', 'FAN09G3179' => 'fan', 'FAN10G0669' => 'fan', 'FAN12G2358' => 'fan', 'FAN14G4198' => 'fan', 'FAN14G5112' => 'fan', 'FAN17G0342' => 'fan', 'FAN19G0342' => 'fan', 'FAN19G0962' => 'fan', 'FAN19G1101' => 'fan', 'FAN19G1872' => 'fan', 'FAN22G0356' => 'fan', 'FAN23G0744' => 'fan', 'FAN23G1914' => 'fan', 'FAN26G0032' => 'fan', 'FAN28G0625' => 'fan', 'FvH4_1g02710' => 'fve', 'FvH4_1g02720' => 'fve', 'FvH4_4g25670' => 'fve', 'FvH4_6g51700' => 'fve', 'FvH4_7g20170' => 'fve', 'Glyma.05G175000' => 'gma', 'Glyma.08G132300' => 'gma', 'Glyma.11G243000' => 'gma', 'Glyma.13G158900' => 'gma', 'Glyma.17G112400' => 'gma', 'Glyma.18G014100' => 'gma', 'Glyma.19G003100' => 'gma', 'Glyma.19G056500' => 'gma', 'Gohir.A01G158900' => 'ghi', 'Gohir.A05G312600' => 'ghi', 'Gohir.A05G354900' => 'ghi', 'Gohir.A07G037200' => 'ghi', 'Gohir.A09G030000' => 'ghi', 'Gohir.A12G145200' => 'ghi', 'Gohir.D01G151500' => 'ghi', 'Gohir.D04G058300' => 'ghi', 'Gohir.D05G314100' => 'ghi', 'Gohir.D07G041400' => 'ghi', 'Gohir.D09G029700' => 'ghi', 'Gohir.D12G149700' => 'ghi', 'Gorai.001G043800' => 'gra', 'Gorai.002G187800' => 'gra', 'Gorai.006G034700' => 'gra', 'Gorai.008G161200' => 'gra', 'Gorai.009G335700' => 'gra', 'Gorai.012G065000' => 'gra', 'GSVIVG01000535001' => 'vvi', 'GSVIVG01015572001' => 'vvi', 'GSVIVG01032386001' => 'vvi', 'HanXRQChr05g0138531' => 'han', 'HanXRQChr06g0174391' => 'han', 'HanXRQChr07g0199021' => 'han', 'HanXRQChr08g0208211' => 'han', 'HanXRQChr09g0255471' => 'han', 'HanXRQChr10g0315791' => 'han', 'HanXRQChr12g0371991' => 'han', 'HanXRQChr15g0475251' => 'han', 'HanXRQChr17g0540001' => 'han', 'HanXRQChr17g0548631' => 'han', 'HanXRQChr17g0569561' => 'han', 'Haze_12256' => 'cav', 'Haze_14756' => 'cav', 'Haze_25528' => 'cav', 'Hma1.2p1_0079F.1_g041020' => 'hma', 'Hma1.2p1_0818F.1_g223260' => 'hma', 'Hma1.2p1_1747F.1_g300530' => 'hma', 'HPP92_004607' => 'vpl', 'HPP92_004608' => 'vpl', 'HPP92_006181' => 'vpl', 'HPP92_012192' => 'vpl', 'HPP92_015680' => 'vpl', 'HPP92_020249' => 'vpl', 'HPP92_021376' => 'vpl', 'HPP92_024275' => 'vpl', 'Hund06031' => 'sun', 'Hund25391' => 'sun', 'Lalb_Chr07g0185371' => 'lal', 'Lalb_Chr07g0185381' => 'lal', 'Lalb_Chr12g0204011' => 'lal', 'Lalb_Chr13g0301671' => 'lal', 'Lalb_Chr14g0362851' => 'lal', 'Lalb_Chr24g0403581' => 'lal', 'Lj1g0000233' => 'lja', 'Lj2g0018120' => 'lja', 'Lj3C621T0' => 'lonja', 'Lj3P1059T14' => 'lonja', 'Lj3P611T9' => 'lonja', 'Lj3P614T13' => 'lonja', 'Lj3P615T5' => 'lonja', 'Lj4g0012315' => 'lja', 'Lj4g0026182' => 'lja', 'Lj6P813T16' => 'lonja', 'Lj7C427T7' => 'lonja', 'Lj7C427T8' => 'lonja', 'Lj7P600T41' => 'lonja', 'Lju41C42G17' => 'lonja', 'Lsat_1_v5_gn_0_47300' => 'lsa', 'Lsat_1_v5_gn_2_91280' => 'lsa', 'Lsat_1_v5_gn_3_30561' => 'lsa', 'Lsat_1_v5_gn_4_184321' => 'lsa', 'Lsat_1_v5_gn_4_4041' => 'lsa', 'Lsat_1_v5_gn_5_92000' => 'lsa', 'Lsat_1_v5_gn_8_152940' => 'lsa', 'Lsat_1_v5_gn_8_62401' => 'lsa', 'Manes.06G055900' => 'mes', 'Manes.12G022200' => 'mes', 'Manes.13G023300' => 'mes', 'Manes.14G115000' => 'mes', 'Manes.15G151700' => 'mes', 'Manes.17G111300' => 'mes', 'Mapoly0226s0009' => 'mpo', 'MBI02_g25363_MAGBIO' => 'mbi', 'MBI06_g00027_MAGBIO' => 'mbi', 'MBI10_g13034_MAGBIO' => 'mbi', 'MD09G1023400' => 'mdo', 'MD13G1100100' => 'mdo', 'MD15G1169200' => 'mdo', 'MD16G1101100' => 'mdo', 'MD17G1022900' => 'mdo', 'Medtr3g096150' => 'mtr', 'Medtr4g115070' => 'mtr', 'Medtr7g033325' => 'mtr', 'Medtr8g089840' => 'mtr', 'MELO3C010319.2' => 'cme', 'MELO3C011944.2' => 'cme', 'MELO3C021589.2' => 'cme', 'Migut.E00207' => 'egut', 'Migut.H00067' => 'egut', 'Migut.K00433' => 'egut', 'Migut.K00606' => 'egut', 'Migut.K01410' => 'egut', 'MSTRG.13347' => 'ama', 'MSTRG.24045' => 'ama', 'MSTRG.2428' => 'ama', 'MSTRG.26410' => 'ama', 'MSTRG.3139' => 'ama', 'MSTRG.3286' => 'ama', 'MSTRG.563' => 'ama', 'MSTRG.7941' => 'ama', 'Nitab4.5_0000028g0060' => 'nta', 'Nitab4.5_0000065g0260' => 'nta', 'Nitab4.5_0000112g0060' => 'nta', 'Nitab4.5_0000489g0120' => 'nta', 'Nitab4.5_0001776g0050' => 'nta', 'Nitab4.5_0001854g0010' => 'nta', 'Nitab4.5_0001860g0020' => 'nta', 'Nitab4.5_0004352g0010' => 'nta', 'Nitab4.5_0008716g0020' => 'nta', 'Nitab4.5_0008922g0010' => 'nta', 'Nn3g16693' => 'nnu', 'Nn4g22596' => 'nnu', 'Nn7g37639' => 'nnu', 'Oeu001701.1' => 'oeu', 'Oeu018149.1' => 'oeu', 'Oeu026220.1' => 'oeu', 'Oeu038635.1' => 'oeu', 'Oeu049176.1' => 'oeu', 'Oeu056706.1' => 'oeu', 'Oeu056937.1' => 'oeu', 'Oeu057540.1' => 'oeu', 'Os02g0594900' => 'osa', 'Os02g0595100' => 'osa', 'Os04g0477500' => 'osa', 'Os12g0611900' => 'osa', 'Peaxi162Scf00076g00020' => 'pax', 'Peaxi162Scf00128g00217' => 'pax', 'Peaxi162Scf00129g01640' => 'pax', 'Peaxi162Scf00669g00007' => 'pax', 'Peaxi162Scf00700g00421' => 'pax', 'Peaxi162Scf00801g00038' => 'pax', 'Peaxi162Scf00891g00025' => 'pax', 'PGR083G0909' => 'pgr', 'PGR119G1005' => 'pgr', 'PGR142G2236' => 'pgr', 'PGR142G3388' => 'pgr', 'PGSC0003DMG400004514' => 'stu', 'PGSC0003DMG400012635' => 'stu', 'PGSC0003DMG400015730' => 'stu', 'PGSC0003DMG400018611' => 'stu', 'PGSC0003DMG400030897' => 'stu', 'Phvul.001G254800' => 'pvu', 'Phvul.002G260100' => 'pvu', 'Phvul.003G167600' => 'pvu', 'Phvul.004G005100' => 'pvu', 'Potri.001G343600' => 'ptr', 'Potri.006G066700' => 'ptr', 'Potri.008G186000' => 'ptr', 'Potri.010G046900' => 'ptr', 'Potri.018G127900' => 'ptr', 'Pp3c20_17750' => 'ppa', 'Pp3c24_4380' => 'ppa', 'Prupe.1G245800' => 'ppe', 'Prupe.3G293400' => 'ppe', 'Prupe.7G247400' => 'ppe', 'Psat0s145g0120' => 'psa', 'Psat0s595g0040' => 'psa', 'Psat0s595g0120' => 'psa', 'Psat3g175040' => 'psa', 'Psat7g058120' => 'psa', 'PSO017G0428' => 'pso', 'PSO063G7510' => 'pso', 'PSO067G0046' => 'pso', 'PSO478G1073' => 'pso', 'PSO675G3677' => 'pso', 'PSO675G6558' => 'pso', 'PSO675G7520' => 'pso', 'PSO675G8959' => 'pso', 'QL02p074089' => 'qlo', 'QL02p089614' => 'qlo', 'QL03p057736' => 'qlo', 'RcHm_v2.0_Chr1g0364131' => 'rch', 'RcHm_v2.0_Chr2g0087801' => 'rch', 'RcHm_v2.0_Chr2g0087821' => 'rch', 'RcHm_v2.0_Chr2g0173231' => 'rch', 'RcHm_v2.0_Chr4g0433111' => 'rch', 'Rhsim03G0250300' => 'rsi', 'Rhsim08G0048400' => 'rsi', 'Rhsim10G0014800' => 'rsi', 'Rhsim12G0040100' => 'rsi', 'Rhsim12G0109700' => 'rsi', 'Sabra06G0049600' => 'sbr', 'Sabra08G0141000' => 'sbr', 'Sabra10G0021400' => 'sbr', 'Sabra16G0222900' => 'sbr', 'Sabra18G0108600' => 'sbr', 'SalBow1G0433' => 'sbo', 'SalBow1G2038' => 'sbo', 'SalBow1G5003' => 'sbo', 'SalBow7G1197' => 'sbo', 'SalBow8G3506' => 'sbo', 'Sc03g0007300' => 'sci', 'Sc11g0000950' => 'sci', 'Sc14g0008750' => 'sci', 'Sc18g0000420' => 'sci', 'Sed0006754' => 'sed', 'Sed0008741' => 'sed', 'Sed0017172' => 'sed', 'Sed0018925' => 'sed', 'Sed0023326' => 'sed', 'Sed0025909' => 'sed', 'SEGI_05333' => 'sgi', 'SEGI_10362' => 'sgi', 'SEGI_13380' => 'sgi', 'SEGI_24306' => 'sgi', 'SEGI_29077' => 'sgi', 'SEGI_29095' => 'sgi', 'SEGI_36534' => 'sgi', 'SEGI_37506' => 'sgi', 'SEGI_38321' => 'sgi', 'SGA_v2.0_scaffold307G48031' => 'sas', 'SGA_v2.0_scaffold47G17507' => 'sas', 'SGA_v2.0_scaffold63G21736' => 'sas', 'SGA_v2.0_scaffold87G27070' => 'sas', 'SHI17794' => 'shi', 'SHI28851' => 'shi', 'SMO165G0155' => 'smo', 'SMO340G0217' => 'smo', 'SMO367G1210' => 'smo', 'Solyc02g093430.3' => 'sly', 'Solyc05g013580.4' => 'sly', 'Solyc07g008030.3' => 'sly', 'Solyc12g035470.2' => 'sly', 'Sopen02g038020' => 'spe', 'Sopen05g008490' => 'spe', 'Sopen07g003910' => 'spe', 'Sopen12g015240' => 'spe', 'Sp1g11550' => 'spa', 'Sp2g16710' => 'spa', 'Sp3g00430' => 'spa', 'Sp3g26780' => 'spa', 'Sp5g22900' => 'spa', 'Sp6g29530' => 'spa', 'TAR371G0794' => 'tar', 'TAR374G0164' => 'tar', 'TAR622G0165' => 'tar', 'TAR626G0929' => 'tar', 'TAR629G2155' => 'tar', 'THA.LOC104805282' => 'tha', 'THA.LOC104805363' => 'tha', 'THA.LOC104808968' => 'tha', 'THA.LOC104821093' => 'tha', 'THA.LOC104823953' => 'tha', 'THA.LOC104825562' => 'tha', 'THA.LOC104825665' => 'tha', 'Thecc.02G261400' => 'tca', 'Thecc.04G019200' => 'tca', 'Thecc.09G130400' => 'tca', 'Thhalv10004374m.g' => 'esa', 'Thhalv10007850m.g' => 'esa', 'Thhalv10013782m.g' => 'esa', 'Thhalv10018686m.g' => 'esa', 'Thhalv10020899m.g' => 'esa', 'Thhalv10022755m.g' => 'esa', 'TPR.G23851' => 'tpr', 'TPR.G26500' => 'tpr', 'TPR.G27267' => 'tpr', 'TPR.G32001' => 'tpr', 'TPR.G6251' => 'tpr', 'TPR.G8167' => 'tpr', 'TWI12G1330' => 'twi', 'TWI18G1239' => 'twi', 'TWI34G0979' => 'twi', 'TWI36G0670' => 'twi', 'TWI36G0707' => 'twi', 'TWI56G0233' => 'twi', 'TWI75G1809' => 'twi', 'unitig_21.g20874' => 'ugi', 'unitig_26.g10343' => 'ugi', 'unitig_46.g18392' => 'ugi', 'unitig_52.g17178' => 'ugi', 'unitig_8.g2934' => 'ugi', 'vmacro01122' => 'vma', 'vmacro05875' => 'vma', 'vmacro06147' => 'vma', 'vmacro16191' => 'vma', 'vmacro18293' => 'vma', 'VMungo0251G3707' => 'vmu', 'VMungo0464G1521' => 'vmu', 'VMungo1215G0205' => 'vmu', 'VMungo1383G2484' => 'vmu', 'Zm00001eb079610' => 'zma', 'Zm00001eb135990' => 'zma', 'Zm00001eb183710' => 'zma', 'Zm00001eb246020' => 'zma' ), 'gf_id' => 'HOM05D001124', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001124' ), 'data_identifier' => 'HOM05D001124', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001124', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '548', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02520' => 'bna', 'A03p06630' => 'bna', 'A05p44460' => 'bna', 'A06p08710' => 'bna', 'A06p41090' => 'bna', 'A07p32320' => 'bna', 'A08p32520' => 'bna', 'A09p10360' => 'bna', 'A10p24080' => 'bna', 'Aa31LG11G15250' => 'aar', 'Aa31LG1G1800' => 'aar', 'Aa31LG2G5120' => 'aar', 'Aa31LG2G6070' => 'aar', 'Aa31LG5G10770' => 'aar', 'Aa31sc61G90' => 'aar', 'Actinidia01352' => 'ach', 'Actinidia05983' => 'ach', 'Actinidia08133' => 'ach', 'Actinidia15101' => 'ach', 'Actinidia26379' => 'ach', 'Actinidia35778' => 'ach', 'Actinidia36123' => 'ach', 'Actinidia37436' => 'ach', 'Actinidia38730' => 'ach', 'Ah.02g128210' => 'amhyb', 'Ah.03g132990' => 'amhyb', 'Ah.14g079410' => 'amhyb', 'AL1G24640' => 'aly', 'AL2G26680' => 'aly', 'AL3G10530' => 'aly', 'AL3G45230' => 'aly', 'AL5G15230' => 'aly', 'AL5G16960' => 'aly', 'AL6G25210' => 'aly', 'Aqoxy2G00441' => 'aox', 'Aqoxy3G01236' => 'aox', 'Aqoxy5G03746' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3RQ047' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C7GMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9C8JER' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MBL6KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YXCZ83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZANX40' => 'arhy', 'AT1G12990' => 'ath', 'AT1G67880' => 'ath', 'AT2G13290' => 'ath', 'AT3G01620' => 'ath', 'AT3G26445' => 'ath', 'AT3G27540' => 'ath', 'AT5G14480' => 'ath', 'ATR0824G026' => 'atr', 'ATR1098G019' => 'atr', 'Atru.chr11.2145' => 'acertr', 'Atru.chr2.3636' => 'acertr', 'Atru.chr2.3644' => 'acertr', 'Atru.chr6.2422' => 'acertr', 'Atru.chr7.1112' => 'acertr', 'AUR62005469' => 'cqu', 'AUR62011166' => 'cqu', 'AUR62013319' => 'cqu', 'AUR62024273' => 'cqu', 'AUR62028420' => 'cqu', 'AUR62041942' => 'cqu', 'BcaB01g04969' => 'bca', 'BcaB01g06371' => 'bca', 'BcaB02g11494' => 'bca', 'BcaB03g15382' => 'bca', 'BcaB08g36994' => 'bca', 'BcaC03g13477' => 'bca', 'BcaC03g13478' => 'bca', 'BcaC03g13480' => 'bca', 'BcaC03g13481' => 'bca', 'BcaC03g13486' => 'bca', 'BcaC04g19031' => 'bca', 'BcaC04g23085' => 'bca', 'BcaC05g25094' => 'bca', 'BcaC05g25096' => 'bca', 'BcaC05g25138' => 'bca', 'BcaC05g30416' => 'bca', 'BcaC05g30455' => 'bca', 'BcaC06g30979' => 'bca', 'BcaC06g33805' => 'bca', 'BcaC08g46021' => 'bca', 'BcaNung03154' => 'bca', 'BolC2t06623H' => 'bol', 'BolC2t06632H' => 'bol', 'BolC2t06635H' => 'bol', 'BolC2t06638H' => 'bol', 'BolC3t13266H' => 'bol', 'BolC5t29776H' => 'bol', 'BolC6t38912H' => 'bol', 'BolC7t44183H' => 'bol', 'BolC9t54123H' => 'bol', 'BolC9t59107H' => 'bol', 'BraA02t05221Z' => 'bra', 'BraA03t09996Z' => 'bra', 'BraA05t23210Z' => 'bra', 'BraA06t24068Z' => 'bra', 'BraA06t27032Z' => 'bra', 'BraA08t35176Z' => 'bra', 'BraA09t36680Z' => 'bra', 'BraA10t44471Z' => 'bra', 'C02p06760' => 'bna', 'C02p06890' => 'bna', 'C02p07010' => 'bna', 'C03p07660' => 'bna', 'C05p10300' => 'bna', 'C06p38150' => 'bna', 'C07p36650' => 'bna', 'C08p15770' => 'bna', 'C09p12300' => 'bna', 'C09p62700' => 'bna', 'C09p75040' => 'bna', 'CAN.G13.1' => 'can', 'CAN.G138.4' => 'can', 'CAN.G44.6' => 'can', 'CAN.G473.19' => 'can', 'CANSAT01G0835' => 'cansat', 'CANSAT11G0246' => 'cansat', 'CANSAT11G1766' => 'cansat', 'CANSAT64G1954' => 'cansat', 'CARHR013330' => 'chi', 'CARHR060530' => 'chi', 'CARHR075300' => 'chi', 'CARHR105120' => 'chi', 'CARHR148910' => 'chi', 'CARHR198830' => 'chi', 'Carub.0001s1275' => 'cru', 'Carub.0002s1437' => 'cru', 'Carub.0003s0044' => 'cru', 'Carub.0003s2787' => 'cru', 'Carub.0005s0597' => 'cru', 'Carub.0006s1266' => 'cru', 'Ca_06935_v3' => 'car', 'Ca_13559_v3' => 'car', 'Ca_16941_v3' => 'car', 'Ca_16960_v3' => 'car', 'Ca_17775_v3' => 'car', 'Ca_30464_v3' => 'car', 'Cc06_g08160' => 'ccan', 'Cc07_g01520' => 'ccan', 'Cc11_g15810' => 'ccan', 'CDE02G2840' => 'cde', 'CDE03G0093' => 'cde', 'CDE04G2127' => 'cde', 'CDE07G1857' => 'cde', 'CDE09G1246' => 'cde', 'Cfa003412' => 'cfa', 'Cfa007341' => 'cfa', 'Cfa009220' => 'cfa', 'Ciclev10008737m.g' => 'ccl', 'Ciclev10015565m.g' => 'ccl', 'Ciclev10031761m.g' => 'ccl', 'CiPaw.03G045300' => 'cil', 'CiPaw.03G247200' => 'cil', 'CiPaw.04G029500' => 'cil', 'CiPaw.04G174000' => 'cil', 'CiPaw.05G181200' => 'cil', 'CiPaw.06G067100' => 'cil', 'ClCG05G025800' => 'cla', 'ClCG06G011400' => 'cla', 'ClCG09G019360' => 'cla', 'COL.COLO4_04827' => 'col', 'COL.COLO4_29170' => 'col', 'COL.COLO4_35131' => 'col', 'COL.COLO4_35132' => 'col', 'Cpa.g.sc33.32' => 'cpa', 'Cpa.g.sc46.29' => 'cpa', 'Cpa.g.sc796.1' => 'cpa', 'CsaV3_1G030420' => 'csa', 'CsaV3_5G027050' => 'csa', 'CsaV3_5G031040' => 'csa', 'CsaV3_UNG023130' => 'csa', 'CSS0007726' => 'camsi', 'CSS0016433' => 'camsi', 'CSS0017656' => 'camsi', 'CSS0025364' => 'camsi', 'CSS0027582' => 'camsi', 'CSS0047288' => 'camsi', 'CSS0049950' => 'camsi', 'DCAR_003843' => 'dca', 'DCAR_007052' => 'dca', 'DCAR_020884' => 'dca', 'DCAR_021730' => 'dca', 'DCAR_024423' => 'dca', 'DCAR_026509' => 'dca', 'DCAR_031158' => 'dca', 'Dinv14728' => 'din', 'Dinv15219' => 'din', 'Dinv25728' => 'din', 'Dinv33428' => 'din', 'Dinv36489' => 'din', 'Dinv41486' => 'din', 'Duzib147G0469' => 'dzi', 'Duzib168G0060' => 'dzi', 'Duzib187G1215' => 'dzi', 'Duzib248G0692' => 'dzi', 'Duzib251G0767' => 'dzi', 'Duzib264G0446' => 'dzi', 'Duzib268G0691' => 'dzi', 'ECA232G4767' => 'eca', 'ECA233G2838' => 'eca', 'ECA234G0391' => 'eca', 'ECA234G0857' => 'eca', 'ECA236G1593' => 'eca', 'ECA238G0565' => 'eca', 'ECA246G1027' => 'eca', 'ECA246G3223' => 'eca', 'ECA246G3470' => 'eca', 'EL10Ac6g13829' => 'bvu', 'EL10Ac6g14093' => 'bvu', 'EL10Ac8g18707' => 'bvu', 'Eucgr.C01369' => 'egr', 'Eucgr.H02492' => 'egr', 'Eucgr.I01733' => 'egr', 'Eucgr.J02255' => 'egr', 'Eucgr.J02257' => 'egr', 'Eucgr.J02258' => 'egr', 'FAN02G1601' => 'fan', 'FAN03G1586' => 'fan', 'FAN03G2986' => 'fan', 'FAN05G4837' => 'fan', 'FAN06G0146' => 'fan', 'FAN07G0858' => 'fan', 'FAN09G3179' => 'fan', 'FAN10G0669' => 'fan', 'FAN12G2358' => 'fan', 'FAN14G4198' => 'fan', 'FAN14G5112' => 'fan', 'FAN17G0342' => 'fan', 'FAN19G0342' => 'fan', 'FAN19G0962' => 'fan', 'FAN19G1101' => 'fan', 'FAN19G1872' => 'fan', 'FAN22G0356' => 'fan', 'FAN23G0744' => 'fan', 'FAN23G1914' => 'fan', 'FAN26G0032' => 'fan', 'FAN28G0625' => 'fan', 'FvH4_1g02710' => 'fve', 'FvH4_1g02720' => 'fve', 'FvH4_4g25670' => 'fve', 'FvH4_6g51700' => 'fve', 'FvH4_7g20170' => 'fve', 'Glyma.05G175000' => 'gma', 'Glyma.08G132300' => 'gma', 'Glyma.11G243000' => 'gma', 'Glyma.13G158900' => 'gma', 'Glyma.17G112400' => 'gma', 'Glyma.18G014100' => 'gma', 'Glyma.19G003100' => 'gma', 'Glyma.19G056500' => 'gma', 'Gohir.A01G158900' => 'ghi', 'Gohir.A05G312600' => 'ghi', 'Gohir.A05G354900' => 'ghi', 'Gohir.A07G037200' => 'ghi', 'Gohir.A09G030000' => 'ghi', 'Gohir.A12G145200' => 'ghi', 'Gohir.D01G151500' => 'ghi', 'Gohir.D04G058300' => 'ghi', 'Gohir.D05G314100' => 'ghi', 'Gohir.D07G041400' => 'ghi', 'Gohir.D09G029700' => 'ghi', 'Gohir.D12G149700' => 'ghi', 'Gorai.001G043800' => 'gra', 'Gorai.002G187800' => 'gra', 'Gorai.006G034700' => 'gra', 'Gorai.008G161200' => 'gra', 'Gorai.009G335700' => 'gra', 'Gorai.012G065000' => 'gra', 'GSVIVG01000535001' => 'vvi', 'GSVIVG01015572001' => 'vvi', 'GSVIVG01032386001' => 'vvi', 'HanXRQChr05g0138531' => 'han', 'HanXRQChr06g0174391' => 'han', 'HanXRQChr07g0199021' => 'han', 'HanXRQChr08g0208211' => 'han', 'HanXRQChr09g0255471' => 'han', 'HanXRQChr10g0315791' => 'han', 'HanXRQChr12g0371991' => 'han', 'HanXRQChr15g0475251' => 'han', 'HanXRQChr17g0540001' => 'han', 'HanXRQChr17g0548631' => 'han', 'HanXRQChr17g0569561' => 'han', 'Haze_12256' => 'cav', 'Haze_14756' => 'cav', 'Haze_25528' => 'cav', 'Hma1.2p1_0079F.1_g041020' => 'hma', 'Hma1.2p1_0818F.1_g223260' => 'hma', 'Hma1.2p1_1747F.1_g300530' => 'hma', 'HPP92_004607' => 'vpl', 'HPP92_004608' => 'vpl', 'HPP92_006181' => 'vpl', 'HPP92_012192' => 'vpl', 'HPP92_015680' => 'vpl', 'HPP92_020249' => 'vpl', 'HPP92_021376' => 'vpl', 'HPP92_024275' => 'vpl', 'Hund06031' => 'sun', 'Hund25391' => 'sun', 'Lalb_Chr07g0185371' => 'lal', 'Lalb_Chr07g0185381' => 'lal', 'Lalb_Chr12g0204011' => 'lal', 'Lalb_Chr13g0301671' => 'lal', 'Lalb_Chr14g0362851' => 'lal', 'Lalb_Chr24g0403581' => 'lal', 'Lj1g0000233' => 'lja', 'Lj2g0018120' => 'lja', 'Lj3C621T0' => 'lonja', 'Lj3P1059T14' => 'lonja', 'Lj3P611T9' => 'lonja', 'Lj3P614T13' => 'lonja', 'Lj3P615T5' => 'lonja', 'Lj4g0012315' => 'lja', 'Lj4g0026182' => 'lja', 'Lj6P813T16' => 'lonja', 'Lj7C427T7' => 'lonja', 'Lj7C427T8' => 'lonja', 'Lj7P600T41' => 'lonja', 'Lju41C42G17' => 'lonja', 'Lsat_1_v5_gn_0_47300' => 'lsa', 'Lsat_1_v5_gn_2_91280' => 'lsa', 'Lsat_1_v5_gn_3_30561' => 'lsa', 'Lsat_1_v5_gn_4_184321' => 'lsa', 'Lsat_1_v5_gn_4_4041' => 'lsa', 'Lsat_1_v5_gn_5_92000' => 'lsa', 'Lsat_1_v5_gn_8_152940' => 'lsa', 'Lsat_1_v5_gn_8_62401' => 'lsa', 'Manes.06G055900' => 'mes', 'Manes.12G022200' => 'mes', 'Manes.13G023300' => 'mes', 'Manes.14G115000' => 'mes', 'Manes.15G151700' => 'mes', 'Manes.17G111300' => 'mes', 'Mapoly0226s0009' => 'mpo', 'MBI02_g25363_MAGBIO' => 'mbi', 'MBI06_g00027_MAGBIO' => 'mbi', 'MBI10_g13034_MAGBIO' => 'mbi', 'MD09G1023400' => 'mdo', 'MD13G1100100' => 'mdo', 'MD15G1169200' => 'mdo', 'MD16G1101100' => 'mdo', 'MD17G1022900' => 'mdo', 'Medtr3g096150' => 'mtr', 'Medtr4g115070' => 'mtr', 'Medtr7g033325' => 'mtr', 'Medtr8g089840' => 'mtr', 'MELO3C010319.2' => 'cme', 'MELO3C011944.2' => 'cme', 'MELO3C021589.2' => 'cme', 'Migut.E00207' => 'egut', 'Migut.H00067' => 'egut', 'Migut.K00433' => 'egut', 'Migut.K00606' => 'egut', 'Migut.K01410' => 'egut', 'MSTRG.13347' => 'ama', 'MSTRG.24045' => 'ama', 'MSTRG.2428' => 'ama', 'MSTRG.26410' => 'ama', 'MSTRG.3139' => 'ama', 'MSTRG.3286' => 'ama', 'MSTRG.563' => 'ama', 'MSTRG.7941' => 'ama', 'Nitab4.5_0000028g0060' => 'nta', 'Nitab4.5_0000065g0260' => 'nta', 'Nitab4.5_0000112g0060' => 'nta', 'Nitab4.5_0000489g0120' => 'nta', 'Nitab4.5_0001776g0050' => 'nta', 'Nitab4.5_0001854g0010' => 'nta', 'Nitab4.5_0001860g0020' => 'nta', 'Nitab4.5_0004352g0010' => 'nta', 'Nitab4.5_0008716g0020' => 'nta', 'Nitab4.5_0008922g0010' => 'nta', 'Nn3g16693' => 'nnu', 'Nn4g22596' => 'nnu', 'Nn7g37639' => 'nnu', 'Oeu001701.1' => 'oeu', 'Oeu018149.1' => 'oeu', 'Oeu026220.1' => 'oeu', 'Oeu038635.1' => 'oeu', 'Oeu049176.1' => 'oeu', 'Oeu056706.1' => 'oeu', 'Oeu056937.1' => 'oeu', 'Oeu057540.1' => 'oeu', 'Os02g0594900' => 'osa', 'Os02g0595100' => 'osa', 'Os04g0477500' => 'osa', 'Os12g0611900' => 'osa', 'Peaxi162Scf00076g00020' => 'pax', 'Peaxi162Scf00128g00217' => 'pax', 'Peaxi162Scf00129g01640' => 'pax', 'Peaxi162Scf00669g00007' => 'pax', 'Peaxi162Scf00700g00421' => 'pax', 'Peaxi162Scf00801g00038' => 'pax', 'Peaxi162Scf00891g00025' => 'pax', 'PGR083G0909' => 'pgr', 'PGR119G1005' => 'pgr', 'PGR142G2236' => 'pgr', 'PGR142G3388' => 'pgr', 'PGSC0003DMG400004514' => 'stu', 'PGSC0003DMG400012635' => 'stu', 'PGSC0003DMG400015730' => 'stu', 'PGSC0003DMG400018611' => 'stu', 'PGSC0003DMG400030897' => 'stu', 'Phvul.001G254800' => 'pvu', 'Phvul.002G260100' => 'pvu', 'Phvul.003G167600' => 'pvu', 'Phvul.004G005100' => 'pvu', 'Potri.001G343600' => 'ptr', 'Potri.006G066700' => 'ptr', 'Potri.008G186000' => 'ptr', 'Potri.010G046900' => 'ptr', 'Potri.018G127900' => 'ptr', 'Pp3c20_17750' => 'ppa', 'Pp3c24_4380' => 'ppa', 'Prupe.1G245800' => 'ppe', 'Prupe.3G293400' => 'ppe', 'Prupe.7G247400' => 'ppe', 'Psat0s145g0120' => 'psa', 'Psat0s595g0040' => 'psa', 'Psat0s595g0120' => 'psa', 'Psat3g175040' => 'psa', 'Psat7g058120' => 'psa', 'PSO017G0428' => 'pso', 'PSO063G7510' => 'pso', 'PSO067G0046' => 'pso', 'PSO478G1073' => 'pso', 'PSO675G3677' => 'pso', 'PSO675G6558' => 'pso', 'PSO675G7520' => 'pso', 'PSO675G8959' => 'pso', 'QL02p074089' => 'qlo', 'QL02p089614' => 'qlo', 'QL03p057736' => 'qlo', 'RcHm_v2.0_Chr1g0364131' => 'rch', 'RcHm_v2.0_Chr2g0087801' => 'rch', 'RcHm_v2.0_Chr2g0087821' => 'rch', 'RcHm_v2.0_Chr2g0173231' => 'rch', 'RcHm_v2.0_Chr4g0433111' => 'rch', 'Rhsim03G0250300' => 'rsi', 'Rhsim08G0048400' => 'rsi', 'Rhsim10G0014800' => 'rsi', 'Rhsim12G0040100' => 'rsi', 'Rhsim12G0109700' => 'rsi', 'Sabra06G0049600' => 'sbr', 'Sabra08G0141000' => 'sbr', 'Sabra10G0021400' => 'sbr', 'Sabra16G0222900' => 'sbr', 'Sabra18G0108600' => 'sbr', 'SalBow1G0433' => 'sbo', 'SalBow1G2038' => 'sbo', 'SalBow1G5003' => 'sbo', 'SalBow7G1197' => 'sbo', 'SalBow8G3506' => 'sbo', 'Sc03g0007300' => 'sci', 'Sc11g0000950' => 'sci', 'Sc14g0008750' => 'sci', 'Sc18g0000420' => 'sci', 'Sed0006754' => 'sed', 'Sed0008741' => 'sed', 'Sed0017172' => 'sed', 'Sed0018925' => 'sed', 'Sed0023326' => 'sed', 'Sed0025909' => 'sed', 'SEGI_05333' => 'sgi', 'SEGI_10362' => 'sgi', 'SEGI_13380' => 'sgi', 'SEGI_24306' => 'sgi', 'SEGI_29077' => 'sgi', 'SEGI_29095' => 'sgi', 'SEGI_36534' => 'sgi', 'SEGI_37506' => 'sgi', 'SEGI_38321' => 'sgi', 'SGA_v2.0_scaffold307G48031' => 'sas', 'SGA_v2.0_scaffold47G17507' => 'sas', 'SGA_v2.0_scaffold63G21736' => 'sas', 'SGA_v2.0_scaffold87G27070' => 'sas', 'SHI17794' => 'shi', 'SHI28851' => 'shi', 'SMO165G0155' => 'smo', 'SMO340G0217' => 'smo', 'SMO367G1210' => 'smo', 'Solyc02g093430.3' => 'sly', 'Solyc05g013580.4' => 'sly', 'Solyc07g008030.3' => 'sly', 'Solyc12g035470.2' => 'sly', 'Sopen02g038020' => 'spe', 'Sopen05g008490' => 'spe', 'Sopen07g003910' => 'spe', 'Sopen12g015240' => 'spe', 'Sp1g11550' => 'spa', 'Sp2g16710' => 'spa', 'Sp3g00430' => 'spa', 'Sp3g26780' => 'spa', 'Sp5g22900' => 'spa', 'Sp6g29530' => 'spa', 'TAR371G0794' => 'tar', 'TAR374G0164' => 'tar', 'TAR622G0165' => 'tar', 'TAR626G0929' => 'tar', 'TAR629G2155' => 'tar', 'THA.LOC104805282' => 'tha', 'THA.LOC104805363' => 'tha', 'THA.LOC104808968' => 'tha', 'THA.LOC104821093' => 'tha', 'THA.LOC104823953' => 'tha', 'THA.LOC104825562' => 'tha', 'THA.LOC104825665' => 'tha', 'Thecc.02G261400' => 'tca', 'Thecc.04G019200' => 'tca', 'Thecc.09G130400' => 'tca', 'Thhalv10004374m.g' => 'esa', 'Thhalv10007850m.g' => 'esa', 'Thhalv10013782m.g' => 'esa', 'Thhalv10018686m.g' => 'esa', 'Thhalv10020899m.g' => 'esa', 'Thhalv10022755m.g' => 'esa', 'TPR.G23851' => 'tpr', 'TPR.G26500' => 'tpr', 'TPR.G27267' => 'tpr', 'TPR.G32001' => 'tpr', 'TPR.G6251' => 'tpr', 'TPR.G8167' => 'tpr', 'TWI12G1330' => 'twi', 'TWI18G1239' => 'twi', 'TWI34G0979' => 'twi', 'TWI36G0670' => 'twi', 'TWI36G0707' => 'twi', 'TWI56G0233' => 'twi', 'TWI75G1809' => 'twi', 'unitig_21.g20874' => 'ugi', 'unitig_26.g10343' => 'ugi', 'unitig_46.g18392' => 'ugi', 'unitig_52.g17178' => 'ugi', 'unitig_8.g2934' => 'ugi', 'vmacro01122' => 'vma', 'vmacro05875' => 'vma', 'vmacro06147' => 'vma', 'vmacro16191' => 'vma', 'vmacro18293' => 'vma', 'VMungo0251G3707' => 'vmu', 'VMungo0464G1521' => 'vmu', 'VMungo1215G0205' => 'vmu', 'VMungo1383G2484' => 'vmu', 'Zm00001eb079610' => 'zma', 'Zm00001eb135990' => 'zma', 'Zm00001eb183710' => 'zma', 'Zm00001eb246020' => 'zma' ) $gf_id = 'HOM05D001124' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001124' ) $data_identifier = 'HOM05D001124' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 6, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 7, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 21, 'bol' => (int) 10, 'bra' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 6, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 9, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 21, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 8, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 10, 'lsa' => (int) 8, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 8, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 9, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb246020' $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' => 'HOM05D001124', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '548', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02520' => 'bna', 'A03p06630' => 'bna', 'A05p44460' => 'bna', 'A06p08710' => 'bna', 'A06p41090' => 'bna', 'A07p32320' => 'bna', 'A08p32520' => 'bna', 'A09p10360' => 'bna', 'A10p24080' => 'bna', 'Aa31LG11G15250' => 'aar', 'Aa31LG1G1800' => 'aar', 'Aa31LG2G5120' => 'aar', 'Aa31LG2G6070' => 'aar', 'Aa31LG5G10770' => 'aar', 'Aa31sc61G90' => 'aar', 'Actinidia01352' => 'ach', 'Actinidia05983' => 'ach', 'Actinidia08133' => 'ach', 'Actinidia15101' => 'ach', 'Actinidia26379' => 'ach', 'Actinidia35778' => 'ach', 'Actinidia36123' => 'ach', 'Actinidia37436' => 'ach', 'Actinidia38730' => 'ach', 'Ah.02g128210' => 'amhyb', 'Ah.03g132990' => 'amhyb', 'Ah.14g079410' => 'amhyb', 'AL1G24640' => 'aly', 'AL2G26680' => 'aly', 'AL3G10530' => 'aly', 'AL3G45230' => 'aly', 'AL5G15230' => 'aly', 'AL5G16960' => 'aly', 'AL6G25210' => 'aly', 'Aqoxy2G00441' => 'aox', 'Aqoxy3G01236' => 'aox', 'Aqoxy5G03746' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3RQ047' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C7GMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9C8JER' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MBL6KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YXCZ83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZANX40' => 'arhy', 'AT1G12990' => 'ath', 'AT1G67880' => 'ath', 'AT2G13290' => 'ath', 'AT3G01620' => 'ath', 'AT3G26445' => 'ath', 'AT3G27540' => 'ath', 'AT5G14480' => 'ath', 'ATR0824G026' => 'atr', 'ATR1098G019' => 'atr', 'Atru.chr11.2145' => 'acertr', 'Atru.chr2.3636' => 'acertr', 'Atru.chr2.3644' => 'acertr', 'Atru.chr6.2422' => 'acertr', 'Atru.chr7.1112' => 'acertr', 'AUR62005469' => 'cqu', 'AUR62011166' => 'cqu', 'AUR62013319' => 'cqu', 'AUR62024273' => 'cqu', 'AUR62028420' => 'cqu', 'AUR62041942' => 'cqu', 'BcaB01g04969' => 'bca', 'BcaB01g06371' => 'bca', 'BcaB02g11494' => 'bca', 'BcaB03g15382' => 'bca', 'BcaB08g36994' => 'bca', 'BcaC03g13477' => 'bca', 'BcaC03g13478' => 'bca', 'BcaC03g13480' => 'bca', 'BcaC03g13481' => 'bca', 'BcaC03g13486' => 'bca', 'BcaC04g19031' => 'bca', 'BcaC04g23085' => 'bca', 'BcaC05g25094' => 'bca', 'BcaC05g25096' => 'bca', 'BcaC05g25138' => 'bca', 'BcaC05g30416' => 'bca', 'BcaC05g30455' => 'bca', 'BcaC06g30979' => 'bca', 'BcaC06g33805' => 'bca', 'BcaC08g46021' => 'bca', 'BcaNung03154' => 'bca', 'BolC2t06623H' => 'bol', 'BolC2t06632H' => 'bol', 'BolC2t06635H' => 'bol', 'BolC2t06638H' => 'bol', 'BolC3t13266H' => 'bol', 'BolC5t29776H' => 'bol', 'BolC6t38912H' => 'bol', 'BolC7t44183H' => 'bol', 'BolC9t54123H' => 'bol', 'BolC9t59107H' => 'bol', 'BraA02t05221Z' => 'bra', 'BraA03t09996Z' => 'bra', 'BraA05t23210Z' => 'bra', 'BraA06t24068Z' => 'bra', 'BraA06t27032Z' => 'bra', 'BraA08t35176Z' => 'bra', 'BraA09t36680Z' => 'bra', 'BraA10t44471Z' => 'bra', 'C02p06760' => 'bna', 'C02p06890' => 'bna', 'C02p07010' => 'bna', 'C03p07660' => 'bna', 'C05p10300' => 'bna', 'C06p38150' => 'bna', 'C07p36650' => 'bna', 'C08p15770' => 'bna', 'C09p12300' => 'bna', 'C09p62700' => 'bna', 'C09p75040' => 'bna', 'CAN.G13.1' => 'can', 'CAN.G138.4' => 'can', 'CAN.G44.6' => 'can', 'CAN.G473.19' => 'can', 'CANSAT01G0835' => 'cansat', 'CANSAT11G0246' => 'cansat', 'CANSAT11G1766' => 'cansat', 'CANSAT64G1954' => 'cansat', 'CARHR013330' => 'chi', 'CARHR060530' => 'chi', 'CARHR075300' => 'chi', 'CARHR105120' => 'chi', 'CARHR148910' => 'chi', 'CARHR198830' => 'chi', 'Carub.0001s1275' => 'cru', 'Carub.0002s1437' => 'cru', 'Carub.0003s0044' => 'cru', 'Carub.0003s2787' => 'cru', 'Carub.0005s0597' => 'cru', 'Carub.0006s1266' => 'cru', 'Ca_06935_v3' => 'car', 'Ca_13559_v3' => 'car', 'Ca_16941_v3' => 'car', 'Ca_16960_v3' => 'car', 'Ca_17775_v3' => 'car', 'Ca_30464_v3' => 'car', 'Cc06_g08160' => 'ccan', 'Cc07_g01520' => 'ccan', 'Cc11_g15810' => 'ccan', 'CDE02G2840' => 'cde', 'CDE03G0093' => 'cde', 'CDE04G2127' => 'cde', 'CDE07G1857' => 'cde', 'CDE09G1246' => 'cde', 'Cfa003412' => 'cfa', 'Cfa007341' => 'cfa', 'Cfa009220' => 'cfa', 'Ciclev10008737m.g' => 'ccl', 'Ciclev10015565m.g' => 'ccl', 'Ciclev10031761m.g' => 'ccl', 'CiPaw.03G045300' => 'cil', 'CiPaw.03G247200' => 'cil', 'CiPaw.04G029500' => 'cil', 'CiPaw.04G174000' => 'cil', 'CiPaw.05G181200' => 'cil', 'CiPaw.06G067100' => 'cil', 'ClCG05G025800' => 'cla', 'ClCG06G011400' => 'cla', 'ClCG09G019360' => 'cla', 'COL.COLO4_04827' => 'col', 'COL.COLO4_29170' => 'col', 'COL.COLO4_35131' => 'col', 'COL.COLO4_35132' => 'col', 'Cpa.g.sc33.32' => 'cpa', 'Cpa.g.sc46.29' => 'cpa', 'Cpa.g.sc796.1' => 'cpa', 'CsaV3_1G030420' => 'csa', 'CsaV3_5G027050' => 'csa', 'CsaV3_5G031040' => 'csa', 'CsaV3_UNG023130' => 'csa', 'CSS0007726' => 'camsi', 'CSS0016433' => 'camsi', 'CSS0017656' => 'camsi', 'CSS0025364' => 'camsi', 'CSS0027582' => 'camsi', 'CSS0047288' => 'camsi', 'CSS0049950' => 'camsi', 'DCAR_003843' => 'dca', 'DCAR_007052' => 'dca', 'DCAR_020884' => 'dca', 'DCAR_021730' => 'dca', 'DCAR_024423' => 'dca', 'DCAR_026509' => 'dca', 'DCAR_031158' => 'dca', 'Dinv14728' => 'din', 'Dinv15219' => 'din', 'Dinv25728' => 'din', 'Dinv33428' => 'din', 'Dinv36489' => 'din', 'Dinv41486' => 'din', 'Duzib147G0469' => 'dzi', 'Duzib168G0060' => 'dzi', 'Duzib187G1215' => 'dzi', 'Duzib248G0692' => 'dzi', 'Duzib251G0767' => 'dzi', 'Duzib264G0446' => 'dzi', 'Duzib268G0691' => 'dzi', 'ECA232G4767' => 'eca', 'ECA233G2838' => 'eca', 'ECA234G0391' => 'eca', 'ECA234G0857' => 'eca', 'ECA236G1593' => 'eca', 'ECA238G0565' => 'eca', 'ECA246G1027' => 'eca', 'ECA246G3223' => 'eca', 'ECA246G3470' => 'eca', 'EL10Ac6g13829' => 'bvu', 'EL10Ac6g14093' => 'bvu', 'EL10Ac8g18707' => 'bvu', 'Eucgr.C01369' => 'egr', 'Eucgr.H02492' => 'egr', 'Eucgr.I01733' => 'egr', 'Eucgr.J02255' => 'egr', 'Eucgr.J02257' => 'egr', 'Eucgr.J02258' => 'egr', 'FAN02G1601' => 'fan', 'FAN03G1586' => 'fan', 'FAN03G2986' => 'fan', 'FAN05G4837' => 'fan', 'FAN06G0146' => 'fan', 'FAN07G0858' => 'fan', 'FAN09G3179' => 'fan', 'FAN10G0669' => 'fan', 'FAN12G2358' => 'fan', 'FAN14G4198' => 'fan', 'FAN14G5112' => 'fan', 'FAN17G0342' => 'fan', 'FAN19G0342' => 'fan', 'FAN19G0962' => 'fan', 'FAN19G1101' => 'fan', 'FAN19G1872' => 'fan', 'FAN22G0356' => 'fan', 'FAN23G0744' => 'fan', 'FAN23G1914' => 'fan', 'FAN26G0032' => 'fan', 'FAN28G0625' => 'fan', 'FvH4_1g02710' => 'fve', 'FvH4_1g02720' => 'fve', 'FvH4_4g25670' => 'fve', 'FvH4_6g51700' => 'fve', 'FvH4_7g20170' => 'fve', 'Glyma.05G175000' => 'gma', 'Glyma.08G132300' => 'gma', 'Glyma.11G243000' => 'gma', 'Glyma.13G158900' => 'gma', 'Glyma.17G112400' => 'gma', 'Glyma.18G014100' => 'gma', 'Glyma.19G003100' => 'gma', 'Glyma.19G056500' => 'gma', 'Gohir.A01G158900' => 'ghi', 'Gohir.A05G312600' => 'ghi', 'Gohir.A05G354900' => 'ghi', 'Gohir.A07G037200' => 'ghi', 'Gohir.A09G030000' => 'ghi', 'Gohir.A12G145200' => 'ghi', 'Gohir.D01G151500' => 'ghi', 'Gohir.D04G058300' => 'ghi', 'Gohir.D05G314100' => 'ghi', 'Gohir.D07G041400' => 'ghi', 'Gohir.D09G029700' => 'ghi', 'Gohir.D12G149700' => 'ghi', 'Gorai.001G043800' => 'gra', 'Gorai.002G187800' => 'gra', 'Gorai.006G034700' => 'gra', 'Gorai.008G161200' => 'gra', 'Gorai.009G335700' => 'gra', 'Gorai.012G065000' => 'gra', 'GSVIVG01000535001' => 'vvi', 'GSVIVG01015572001' => 'vvi', 'GSVIVG01032386001' => 'vvi', 'HanXRQChr05g0138531' => 'han', 'HanXRQChr06g0174391' => 'han', 'HanXRQChr07g0199021' => 'han', 'HanXRQChr08g0208211' => 'han', 'HanXRQChr09g0255471' => 'han', 'HanXRQChr10g0315791' => 'han', 'HanXRQChr12g0371991' => 'han', 'HanXRQChr15g0475251' => 'han', 'HanXRQChr17g0540001' => 'han', 'HanXRQChr17g0548631' => 'han', 'HanXRQChr17g0569561' => 'han', 'Haze_12256' => 'cav', 'Haze_14756' => 'cav', 'Haze_25528' => 'cav', 'Hma1.2p1_0079F.1_g041020' => 'hma', 'Hma1.2p1_0818F.1_g223260' => 'hma', 'Hma1.2p1_1747F.1_g300530' => 'hma', 'HPP92_004607' => 'vpl', 'HPP92_004608' => 'vpl', 'HPP92_006181' => 'vpl', 'HPP92_012192' => 'vpl', 'HPP92_015680' => 'vpl', 'HPP92_020249' => 'vpl', 'HPP92_021376' => 'vpl', 'HPP92_024275' => 'vpl', 'Hund06031' => 'sun', 'Hund25391' => 'sun', 'Lalb_Chr07g0185371' => 'lal', 'Lalb_Chr07g0185381' => 'lal', 'Lalb_Chr12g0204011' => 'lal', 'Lalb_Chr13g0301671' => 'lal', 'Lalb_Chr14g0362851' => 'lal', 'Lalb_Chr24g0403581' => 'lal', 'Lj1g0000233' => 'lja', 'Lj2g0018120' => 'lja', 'Lj3C621T0' => 'lonja', 'Lj3P1059T14' => 'lonja', 'Lj3P611T9' => 'lonja', 'Lj3P614T13' => 'lonja', 'Lj3P615T5' => 'lonja', 'Lj4g0012315' => 'lja', 'Lj4g0026182' => 'lja', 'Lj6P813T16' => 'lonja', 'Lj7C427T7' => 'lonja', 'Lj7C427T8' => 'lonja', 'Lj7P600T41' => 'lonja', 'Lju41C42G17' => 'lonja', 'Lsat_1_v5_gn_0_47300' => 'lsa', 'Lsat_1_v5_gn_2_91280' => 'lsa', 'Lsat_1_v5_gn_3_30561' => 'lsa', 'Lsat_1_v5_gn_4_184321' => 'lsa', 'Lsat_1_v5_gn_4_4041' => 'lsa', 'Lsat_1_v5_gn_5_92000' => 'lsa', 'Lsat_1_v5_gn_8_152940' => 'lsa', 'Lsat_1_v5_gn_8_62401' => 'lsa', 'Manes.06G055900' => 'mes', 'Manes.12G022200' => 'mes', 'Manes.13G023300' => 'mes', 'Manes.14G115000' => 'mes', 'Manes.15G151700' => 'mes', 'Manes.17G111300' => 'mes', 'Mapoly0226s0009' => 'mpo', 'MBI02_g25363_MAGBIO' => 'mbi', 'MBI06_g00027_MAGBIO' => 'mbi', 'MBI10_g13034_MAGBIO' => 'mbi', 'MD09G1023400' => 'mdo', 'MD13G1100100' => 'mdo', 'MD15G1169200' => 'mdo', 'MD16G1101100' => 'mdo', 'MD17G1022900' => 'mdo', 'Medtr3g096150' => 'mtr', 'Medtr4g115070' => 'mtr', 'Medtr7g033325' => 'mtr', 'Medtr8g089840' => 'mtr', 'MELO3C010319.2' => 'cme', 'MELO3C011944.2' => 'cme', 'MELO3C021589.2' => 'cme', 'Migut.E00207' => 'egut', 'Migut.H00067' => 'egut', 'Migut.K00433' => 'egut', 'Migut.K00606' => 'egut', 'Migut.K01410' => 'egut', 'MSTRG.13347' => 'ama', 'MSTRG.24045' => 'ama', 'MSTRG.2428' => 'ama', 'MSTRG.26410' => 'ama', 'MSTRG.3139' => 'ama', 'MSTRG.3286' => 'ama', 'MSTRG.563' => 'ama', 'MSTRG.7941' => 'ama', 'Nitab4.5_0000028g0060' => 'nta', 'Nitab4.5_0000065g0260' => 'nta', 'Nitab4.5_0000112g0060' => 'nta', 'Nitab4.5_0000489g0120' => 'nta', 'Nitab4.5_0001776g0050' => 'nta', 'Nitab4.5_0001854g0010' => 'nta', 'Nitab4.5_0001860g0020' => 'nta', 'Nitab4.5_0004352g0010' => 'nta', 'Nitab4.5_0008716g0020' => 'nta', 'Nitab4.5_0008922g0010' => 'nta', 'Nn3g16693' => 'nnu', 'Nn4g22596' => 'nnu', 'Nn7g37639' => 'nnu', 'Oeu001701.1' => 'oeu', 'Oeu018149.1' => 'oeu', 'Oeu026220.1' => 'oeu', 'Oeu038635.1' => 'oeu', 'Oeu049176.1' => 'oeu', 'Oeu056706.1' => 'oeu', 'Oeu056937.1' => 'oeu', 'Oeu057540.1' => 'oeu', 'Os02g0594900' => 'osa', 'Os02g0595100' => 'osa', 'Os04g0477500' => 'osa', 'Os12g0611900' => 'osa', 'Peaxi162Scf00076g00020' => 'pax', 'Peaxi162Scf00128g00217' => 'pax', 'Peaxi162Scf00129g01640' => 'pax', 'Peaxi162Scf00669g00007' => 'pax', 'Peaxi162Scf00700g00421' => 'pax', 'Peaxi162Scf00801g00038' => 'pax', 'Peaxi162Scf00891g00025' => 'pax', 'PGR083G0909' => 'pgr', 'PGR119G1005' => 'pgr', 'PGR142G2236' => 'pgr', 'PGR142G3388' => 'pgr', 'PGSC0003DMG400004514' => 'stu', 'PGSC0003DMG400012635' => 'stu', 'PGSC0003DMG400015730' => 'stu', 'PGSC0003DMG400018611' => 'stu', 'PGSC0003DMG400030897' => 'stu', 'Phvul.001G254800' => 'pvu', 'Phvul.002G260100' => 'pvu', 'Phvul.003G167600' => 'pvu', 'Phvul.004G005100' => 'pvu', 'Potri.001G343600' => 'ptr', 'Potri.006G066700' => 'ptr', 'Potri.008G186000' => 'ptr', 'Potri.010G046900' => 'ptr', 'Potri.018G127900' => 'ptr', 'Pp3c20_17750' => 'ppa', 'Pp3c24_4380' => 'ppa', 'Prupe.1G245800' => 'ppe', 'Prupe.3G293400' => 'ppe', 'Prupe.7G247400' => 'ppe', 'Psat0s145g0120' => 'psa', 'Psat0s595g0040' => 'psa', 'Psat0s595g0120' => 'psa', 'Psat3g175040' => 'psa', 'Psat7g058120' => 'psa', 'PSO017G0428' => 'pso', 'PSO063G7510' => 'pso', 'PSO067G0046' => 'pso', 'PSO478G1073' => 'pso', 'PSO675G3677' => 'pso', 'PSO675G6558' => 'pso', 'PSO675G7520' => 'pso', 'PSO675G8959' => 'pso', 'QL02p074089' => 'qlo', 'QL02p089614' => 'qlo', 'QL03p057736' => 'qlo', 'RcHm_v2.0_Chr1g0364131' => 'rch', 'RcHm_v2.0_Chr2g0087801' => 'rch', 'RcHm_v2.0_Chr2g0087821' => 'rch', 'RcHm_v2.0_Chr2g0173231' => 'rch', 'RcHm_v2.0_Chr4g0433111' => 'rch', 'Rhsim03G0250300' => 'rsi', 'Rhsim08G0048400' => 'rsi', 'Rhsim10G0014800' => 'rsi', 'Rhsim12G0040100' => 'rsi', 'Rhsim12G0109700' => 'rsi', 'Sabra06G0049600' => 'sbr', 'Sabra08G0141000' => 'sbr', 'Sabra10G0021400' => 'sbr', 'Sabra16G0222900' => 'sbr', 'Sabra18G0108600' => 'sbr', 'SalBow1G0433' => 'sbo', 'SalBow1G2038' => 'sbo', 'SalBow1G5003' => 'sbo', 'SalBow7G1197' => 'sbo', 'SalBow8G3506' => 'sbo', 'Sc03g0007300' => 'sci', 'Sc11g0000950' => 'sci', 'Sc14g0008750' => 'sci', 'Sc18g0000420' => 'sci', 'Sed0006754' => 'sed', 'Sed0008741' => 'sed', 'Sed0017172' => 'sed', 'Sed0018925' => 'sed', 'Sed0023326' => 'sed', 'Sed0025909' => 'sed', 'SEGI_05333' => 'sgi', 'SEGI_10362' => 'sgi', 'SEGI_13380' => 'sgi', 'SEGI_24306' => 'sgi', 'SEGI_29077' => 'sgi', 'SEGI_29095' => 'sgi', 'SEGI_36534' => 'sgi', 'SEGI_37506' => 'sgi', 'SEGI_38321' => 'sgi', 'SGA_v2.0_scaffold307G48031' => 'sas', 'SGA_v2.0_scaffold47G17507' => 'sas', 'SGA_v2.0_scaffold63G21736' => 'sas', 'SGA_v2.0_scaffold87G27070' => 'sas', 'SHI17794' => 'shi', 'SHI28851' => 'shi', 'SMO165G0155' => 'smo', 'SMO340G0217' => 'smo', 'SMO367G1210' => 'smo', 'Solyc02g093430.3' => 'sly', 'Solyc05g013580.4' => 'sly', 'Solyc07g008030.3' => 'sly', 'Solyc12g035470.2' => 'sly', 'Sopen02g038020' => 'spe', 'Sopen05g008490' => 'spe', 'Sopen07g003910' => 'spe', 'Sopen12g015240' => 'spe', 'Sp1g11550' => 'spa', 'Sp2g16710' => 'spa', 'Sp3g00430' => 'spa', 'Sp3g26780' => 'spa', 'Sp5g22900' => 'spa', 'Sp6g29530' => 'spa', 'TAR371G0794' => 'tar', 'TAR374G0164' => 'tar', 'TAR622G0165' => 'tar', 'TAR626G0929' => 'tar', 'TAR629G2155' => 'tar', 'THA.LOC104805282' => 'tha', 'THA.LOC104805363' => 'tha', 'THA.LOC104808968' => 'tha', 'THA.LOC104821093' => 'tha', 'THA.LOC104823953' => 'tha', 'THA.LOC104825562' => 'tha', 'THA.LOC104825665' => 'tha', 'Thecc.02G261400' => 'tca', 'Thecc.04G019200' => 'tca', 'Thecc.09G130400' => 'tca', 'Thhalv10004374m.g' => 'esa', 'Thhalv10007850m.g' => 'esa', 'Thhalv10013782m.g' => 'esa', 'Thhalv10018686m.g' => 'esa', 'Thhalv10020899m.g' => 'esa', 'Thhalv10022755m.g' => 'esa', 'TPR.G23851' => 'tpr', 'TPR.G26500' => 'tpr', 'TPR.G27267' => 'tpr', 'TPR.G32001' => 'tpr', 'TPR.G6251' => 'tpr', 'TPR.G8167' => 'tpr', 'TWI12G1330' => 'twi', 'TWI18G1239' => 'twi', 'TWI34G0979' => 'twi', 'TWI36G0670' => 'twi', 'TWI36G0707' => 'twi', 'TWI56G0233' => 'twi', 'TWI75G1809' => 'twi', 'unitig_21.g20874' => 'ugi', 'unitig_26.g10343' => 'ugi', 'unitig_46.g18392' => 'ugi', 'unitig_52.g17178' => 'ugi', 'unitig_8.g2934' => 'ugi', 'vmacro01122' => 'vma', 'vmacro05875' => 'vma', 'vmacro06147' => 'vma', 'vmacro16191' => 'vma', 'vmacro18293' => 'vma', 'VMungo0251G3707' => 'vmu', 'VMungo0464G1521' => 'vmu', 'VMungo1215G0205' => 'vmu', 'VMungo1383G2484' => 'vmu', 'Zm00001eb079610' => 'zma', 'Zm00001eb135990' => 'zma', 'Zm00001eb183710' => 'zma', 'Zm00001eb246020' => 'zma' ), 'gf_id' => 'HOM05D001124', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001124' ), 'data_identifier' => 'HOM05D001124', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001124', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '548', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02520' => 'bna', 'A03p06630' => 'bna', 'A05p44460' => 'bna', 'A06p08710' => 'bna', 'A06p41090' => 'bna', 'A07p32320' => 'bna', 'A08p32520' => 'bna', 'A09p10360' => 'bna', 'A10p24080' => 'bna', 'Aa31LG11G15250' => 'aar', 'Aa31LG1G1800' => 'aar', 'Aa31LG2G5120' => 'aar', 'Aa31LG2G6070' => 'aar', 'Aa31LG5G10770' => 'aar', 'Aa31sc61G90' => 'aar', 'Actinidia01352' => 'ach', 'Actinidia05983' => 'ach', 'Actinidia08133' => 'ach', 'Actinidia15101' => 'ach', 'Actinidia26379' => 'ach', 'Actinidia35778' => 'ach', 'Actinidia36123' => 'ach', 'Actinidia37436' => 'ach', 'Actinidia38730' => 'ach', 'Ah.02g128210' => 'amhyb', 'Ah.03g132990' => 'amhyb', 'Ah.14g079410' => 'amhyb', 'AL1G24640' => 'aly', 'AL2G26680' => 'aly', 'AL3G10530' => 'aly', 'AL3G45230' => 'aly', 'AL5G15230' => 'aly', 'AL5G16960' => 'aly', 'AL6G25210' => 'aly', 'Aqoxy2G00441' => 'aox', 'Aqoxy3G01236' => 'aox', 'Aqoxy5G03746' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3RQ047' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C7GMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9C8JER' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MBL6KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YXCZ83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZANX40' => 'arhy', 'AT1G12990' => 'ath', 'AT1G67880' => 'ath', 'AT2G13290' => 'ath', 'AT3G01620' => 'ath', 'AT3G26445' => 'ath', 'AT3G27540' => 'ath', 'AT5G14480' => 'ath', 'ATR0824G026' => 'atr', 'ATR1098G019' => 'atr', 'Atru.chr11.2145' => 'acertr', 'Atru.chr2.3636' => 'acertr', 'Atru.chr2.3644' => 'acertr', 'Atru.chr6.2422' => 'acertr', 'Atru.chr7.1112' => 'acertr', 'AUR62005469' => 'cqu', 'AUR62011166' => 'cqu', 'AUR62013319' => 'cqu', 'AUR62024273' => 'cqu', 'AUR62028420' => 'cqu', 'AUR62041942' => 'cqu', 'BcaB01g04969' => 'bca', 'BcaB01g06371' => 'bca', 'BcaB02g11494' => 'bca', 'BcaB03g15382' => 'bca', 'BcaB08g36994' => 'bca', 'BcaC03g13477' => 'bca', 'BcaC03g13478' => 'bca', 'BcaC03g13480' => 'bca', 'BcaC03g13481' => 'bca', 'BcaC03g13486' => 'bca', 'BcaC04g19031' => 'bca', 'BcaC04g23085' => 'bca', 'BcaC05g25094' => 'bca', 'BcaC05g25096' => 'bca', 'BcaC05g25138' => 'bca', 'BcaC05g30416' => 'bca', 'BcaC05g30455' => 'bca', 'BcaC06g30979' => 'bca', 'BcaC06g33805' => 'bca', 'BcaC08g46021' => 'bca', 'BcaNung03154' => 'bca', 'BolC2t06623H' => 'bol', 'BolC2t06632H' => 'bol', 'BolC2t06635H' => 'bol', 'BolC2t06638H' => 'bol', 'BolC3t13266H' => 'bol', 'BolC5t29776H' => 'bol', 'BolC6t38912H' => 'bol', 'BolC7t44183H' => 'bol', 'BolC9t54123H' => 'bol', 'BolC9t59107H' => 'bol', 'BraA02t05221Z' => 'bra', 'BraA03t09996Z' => 'bra', 'BraA05t23210Z' => 'bra', 'BraA06t24068Z' => 'bra', 'BraA06t27032Z' => 'bra', 'BraA08t35176Z' => 'bra', 'BraA09t36680Z' => 'bra', 'BraA10t44471Z' => 'bra', 'C02p06760' => 'bna', 'C02p06890' => 'bna', 'C02p07010' => 'bna', 'C03p07660' => 'bna', 'C05p10300' => 'bna', 'C06p38150' => 'bna', 'C07p36650' => 'bna', 'C08p15770' => 'bna', 'C09p12300' => 'bna', 'C09p62700' => 'bna', 'C09p75040' => 'bna', 'CAN.G13.1' => 'can', 'CAN.G138.4' => 'can', 'CAN.G44.6' => 'can', 'CAN.G473.19' => 'can', 'CANSAT01G0835' => 'cansat', 'CANSAT11G0246' => 'cansat', 'CANSAT11G1766' => 'cansat', 'CANSAT64G1954' => 'cansat', 'CARHR013330' => 'chi', 'CARHR060530' => 'chi', 'CARHR075300' => 'chi', 'CARHR105120' => 'chi', 'CARHR148910' => 'chi', 'CARHR198830' => 'chi', 'Carub.0001s1275' => 'cru', 'Carub.0002s1437' => 'cru', 'Carub.0003s0044' => 'cru', 'Carub.0003s2787' => 'cru', 'Carub.0005s0597' => 'cru', 'Carub.0006s1266' => 'cru', 'Ca_06935_v3' => 'car', 'Ca_13559_v3' => 'car', 'Ca_16941_v3' => 'car', 'Ca_16960_v3' => 'car', 'Ca_17775_v3' => 'car', 'Ca_30464_v3' => 'car', 'Cc06_g08160' => 'ccan', 'Cc07_g01520' => 'ccan', 'Cc11_g15810' => 'ccan', 'CDE02G2840' => 'cde', 'CDE03G0093' => 'cde', 'CDE04G2127' => 'cde', 'CDE07G1857' => 'cde', 'CDE09G1246' => 'cde', 'Cfa003412' => 'cfa', 'Cfa007341' => 'cfa', 'Cfa009220' => 'cfa', 'Ciclev10008737m.g' => 'ccl', 'Ciclev10015565m.g' => 'ccl', 'Ciclev10031761m.g' => 'ccl', 'CiPaw.03G045300' => 'cil', 'CiPaw.03G247200' => 'cil', 'CiPaw.04G029500' => 'cil', 'CiPaw.04G174000' => 'cil', 'CiPaw.05G181200' => 'cil', 'CiPaw.06G067100' => 'cil', 'ClCG05G025800' => 'cla', 'ClCG06G011400' => 'cla', 'ClCG09G019360' => 'cla', 'COL.COLO4_04827' => 'col', 'COL.COLO4_29170' => 'col', 'COL.COLO4_35131' => 'col', 'COL.COLO4_35132' => 'col', 'Cpa.g.sc33.32' => 'cpa', 'Cpa.g.sc46.29' => 'cpa', 'Cpa.g.sc796.1' => 'cpa', 'CsaV3_1G030420' => 'csa', 'CsaV3_5G027050' => 'csa', 'CsaV3_5G031040' => 'csa', 'CsaV3_UNG023130' => 'csa', 'CSS0007726' => 'camsi', 'CSS0016433' => 'camsi', 'CSS0017656' => 'camsi', 'CSS0025364' => 'camsi', 'CSS0027582' => 'camsi', 'CSS0047288' => 'camsi', 'CSS0049950' => 'camsi', 'DCAR_003843' => 'dca', 'DCAR_007052' => 'dca', 'DCAR_020884' => 'dca', 'DCAR_021730' => 'dca', 'DCAR_024423' => 'dca', 'DCAR_026509' => 'dca', 'DCAR_031158' => 'dca', 'Dinv14728' => 'din', 'Dinv15219' => 'din', 'Dinv25728' => 'din', 'Dinv33428' => 'din', 'Dinv36489' => 'din', 'Dinv41486' => 'din', 'Duzib147G0469' => 'dzi', 'Duzib168G0060' => 'dzi', 'Duzib187G1215' => 'dzi', 'Duzib248G0692' => 'dzi', 'Duzib251G0767' => 'dzi', 'Duzib264G0446' => 'dzi', 'Duzib268G0691' => 'dzi', 'ECA232G4767' => 'eca', 'ECA233G2838' => 'eca', 'ECA234G0391' => 'eca', 'ECA234G0857' => 'eca', 'ECA236G1593' => 'eca', 'ECA238G0565' => 'eca', 'ECA246G1027' => 'eca', 'ECA246G3223' => 'eca', 'ECA246G3470' => 'eca', 'EL10Ac6g13829' => 'bvu', 'EL10Ac6g14093' => 'bvu', 'EL10Ac8g18707' => 'bvu', 'Eucgr.C01369' => 'egr', 'Eucgr.H02492' => 'egr', 'Eucgr.I01733' => 'egr', 'Eucgr.J02255' => 'egr', 'Eucgr.J02257' => 'egr', 'Eucgr.J02258' => 'egr', 'FAN02G1601' => 'fan', 'FAN03G1586' => 'fan', 'FAN03G2986' => 'fan', 'FAN05G4837' => 'fan', 'FAN06G0146' => 'fan', 'FAN07G0858' => 'fan', 'FAN09G3179' => 'fan', 'FAN10G0669' => 'fan', 'FAN12G2358' => 'fan', 'FAN14G4198' => 'fan', 'FAN14G5112' => 'fan', 'FAN17G0342' => 'fan', 'FAN19G0342' => 'fan', 'FAN19G0962' => 'fan', 'FAN19G1101' => 'fan', 'FAN19G1872' => 'fan', 'FAN22G0356' => 'fan', 'FAN23G0744' => 'fan', 'FAN23G1914' => 'fan', 'FAN26G0032' => 'fan', 'FAN28G0625' => 'fan', 'FvH4_1g02710' => 'fve', 'FvH4_1g02720' => 'fve', 'FvH4_4g25670' => 'fve', 'FvH4_6g51700' => 'fve', 'FvH4_7g20170' => 'fve', 'Glyma.05G175000' => 'gma', 'Glyma.08G132300' => 'gma', 'Glyma.11G243000' => 'gma', 'Glyma.13G158900' => 'gma', 'Glyma.17G112400' => 'gma', 'Glyma.18G014100' => 'gma', 'Glyma.19G003100' => 'gma', 'Glyma.19G056500' => 'gma', 'Gohir.A01G158900' => 'ghi', 'Gohir.A05G312600' => 'ghi', 'Gohir.A05G354900' => 'ghi', 'Gohir.A07G037200' => 'ghi', 'Gohir.A09G030000' => 'ghi', 'Gohir.A12G145200' => 'ghi', 'Gohir.D01G151500' => 'ghi', 'Gohir.D04G058300' => 'ghi', 'Gohir.D05G314100' => 'ghi', 'Gohir.D07G041400' => 'ghi', 'Gohir.D09G029700' => 'ghi', 'Gohir.D12G149700' => 'ghi', 'Gorai.001G043800' => 'gra', 'Gorai.002G187800' => 'gra', 'Gorai.006G034700' => 'gra', 'Gorai.008G161200' => 'gra', 'Gorai.009G335700' => 'gra', 'Gorai.012G065000' => 'gra', 'GSVIVG01000535001' => 'vvi', 'GSVIVG01015572001' => 'vvi', 'GSVIVG01032386001' => 'vvi', 'HanXRQChr05g0138531' => 'han', 'HanXRQChr06g0174391' => 'han', 'HanXRQChr07g0199021' => 'han', 'HanXRQChr08g0208211' => 'han', 'HanXRQChr09g0255471' => 'han', 'HanXRQChr10g0315791' => 'han', 'HanXRQChr12g0371991' => 'han', 'HanXRQChr15g0475251' => 'han', 'HanXRQChr17g0540001' => 'han', 'HanXRQChr17g0548631' => 'han', 'HanXRQChr17g0569561' => 'han', 'Haze_12256' => 'cav', 'Haze_14756' => 'cav', 'Haze_25528' => 'cav', 'Hma1.2p1_0079F.1_g041020' => 'hma', 'Hma1.2p1_0818F.1_g223260' => 'hma', 'Hma1.2p1_1747F.1_g300530' => 'hma', 'HPP92_004607' => 'vpl', 'HPP92_004608' => 'vpl', 'HPP92_006181' => 'vpl', 'HPP92_012192' => 'vpl', 'HPP92_015680' => 'vpl', 'HPP92_020249' => 'vpl', 'HPP92_021376' => 'vpl', 'HPP92_024275' => 'vpl', 'Hund06031' => 'sun', 'Hund25391' => 'sun', 'Lalb_Chr07g0185371' => 'lal', 'Lalb_Chr07g0185381' => 'lal', 'Lalb_Chr12g0204011' => 'lal', 'Lalb_Chr13g0301671' => 'lal', 'Lalb_Chr14g0362851' => 'lal', 'Lalb_Chr24g0403581' => 'lal', 'Lj1g0000233' => 'lja', 'Lj2g0018120' => 'lja', 'Lj3C621T0' => 'lonja', 'Lj3P1059T14' => 'lonja', 'Lj3P611T9' => 'lonja', 'Lj3P614T13' => 'lonja', 'Lj3P615T5' => 'lonja', 'Lj4g0012315' => 'lja', 'Lj4g0026182' => 'lja', 'Lj6P813T16' => 'lonja', 'Lj7C427T7' => 'lonja', 'Lj7C427T8' => 'lonja', 'Lj7P600T41' => 'lonja', 'Lju41C42G17' => 'lonja', 'Lsat_1_v5_gn_0_47300' => 'lsa', 'Lsat_1_v5_gn_2_91280' => 'lsa', 'Lsat_1_v5_gn_3_30561' => 'lsa', 'Lsat_1_v5_gn_4_184321' => 'lsa', 'Lsat_1_v5_gn_4_4041' => 'lsa', 'Lsat_1_v5_gn_5_92000' => 'lsa', 'Lsat_1_v5_gn_8_152940' => 'lsa', 'Lsat_1_v5_gn_8_62401' => 'lsa', 'Manes.06G055900' => 'mes', 'Manes.12G022200' => 'mes', 'Manes.13G023300' => 'mes', 'Manes.14G115000' => 'mes', 'Manes.15G151700' => 'mes', 'Manes.17G111300' => 'mes', 'Mapoly0226s0009' => 'mpo', 'MBI02_g25363_MAGBIO' => 'mbi', 'MBI06_g00027_MAGBIO' => 'mbi', 'MBI10_g13034_MAGBIO' => 'mbi', 'MD09G1023400' => 'mdo', 'MD13G1100100' => 'mdo', 'MD15G1169200' => 'mdo', 'MD16G1101100' => 'mdo', 'MD17G1022900' => 'mdo', 'Medtr3g096150' => 'mtr', 'Medtr4g115070' => 'mtr', 'Medtr7g033325' => 'mtr', 'Medtr8g089840' => 'mtr', 'MELO3C010319.2' => 'cme', 'MELO3C011944.2' => 'cme', 'MELO3C021589.2' => 'cme', 'Migut.E00207' => 'egut', 'Migut.H00067' => 'egut', 'Migut.K00433' => 'egut', 'Migut.K00606' => 'egut', 'Migut.K01410' => 'egut', 'MSTRG.13347' => 'ama', 'MSTRG.24045' => 'ama', 'MSTRG.2428' => 'ama', 'MSTRG.26410' => 'ama', 'MSTRG.3139' => 'ama', 'MSTRG.3286' => 'ama', 'MSTRG.563' => 'ama', 'MSTRG.7941' => 'ama', 'Nitab4.5_0000028g0060' => 'nta', 'Nitab4.5_0000065g0260' => 'nta', 'Nitab4.5_0000112g0060' => 'nta', 'Nitab4.5_0000489g0120' => 'nta', 'Nitab4.5_0001776g0050' => 'nta', 'Nitab4.5_0001854g0010' => 'nta', 'Nitab4.5_0001860g0020' => 'nta', 'Nitab4.5_0004352g0010' => 'nta', 'Nitab4.5_0008716g0020' => 'nta', 'Nitab4.5_0008922g0010' => 'nta', 'Nn3g16693' => 'nnu', 'Nn4g22596' => 'nnu', 'Nn7g37639' => 'nnu', 'Oeu001701.1' => 'oeu', 'Oeu018149.1' => 'oeu', 'Oeu026220.1' => 'oeu', 'Oeu038635.1' => 'oeu', 'Oeu049176.1' => 'oeu', 'Oeu056706.1' => 'oeu', 'Oeu056937.1' => 'oeu', 'Oeu057540.1' => 'oeu', 'Os02g0594900' => 'osa', 'Os02g0595100' => 'osa', 'Os04g0477500' => 'osa', 'Os12g0611900' => 'osa', 'Peaxi162Scf00076g00020' => 'pax', 'Peaxi162Scf00128g00217' => 'pax', 'Peaxi162Scf00129g01640' => 'pax', 'Peaxi162Scf00669g00007' => 'pax', 'Peaxi162Scf00700g00421' => 'pax', 'Peaxi162Scf00801g00038' => 'pax', 'Peaxi162Scf00891g00025' => 'pax', 'PGR083G0909' => 'pgr', 'PGR119G1005' => 'pgr', 'PGR142G2236' => 'pgr', 'PGR142G3388' => 'pgr', 'PGSC0003DMG400004514' => 'stu', 'PGSC0003DMG400012635' => 'stu', 'PGSC0003DMG400015730' => 'stu', 'PGSC0003DMG400018611' => 'stu', 'PGSC0003DMG400030897' => 'stu', 'Phvul.001G254800' => 'pvu', 'Phvul.002G260100' => 'pvu', 'Phvul.003G167600' => 'pvu', 'Phvul.004G005100' => 'pvu', 'Potri.001G343600' => 'ptr', 'Potri.006G066700' => 'ptr', 'Potri.008G186000' => 'ptr', 'Potri.010G046900' => 'ptr', 'Potri.018G127900' => 'ptr', 'Pp3c20_17750' => 'ppa', 'Pp3c24_4380' => 'ppa', 'Prupe.1G245800' => 'ppe', 'Prupe.3G293400' => 'ppe', 'Prupe.7G247400' => 'ppe', 'Psat0s145g0120' => 'psa', 'Psat0s595g0040' => 'psa', 'Psat0s595g0120' => 'psa', 'Psat3g175040' => 'psa', 'Psat7g058120' => 'psa', 'PSO017G0428' => 'pso', 'PSO063G7510' => 'pso', 'PSO067G0046' => 'pso', 'PSO478G1073' => 'pso', 'PSO675G3677' => 'pso', 'PSO675G6558' => 'pso', 'PSO675G7520' => 'pso', 'PSO675G8959' => 'pso', 'QL02p074089' => 'qlo', 'QL02p089614' => 'qlo', 'QL03p057736' => 'qlo', 'RcHm_v2.0_Chr1g0364131' => 'rch', 'RcHm_v2.0_Chr2g0087801' => 'rch', 'RcHm_v2.0_Chr2g0087821' => 'rch', 'RcHm_v2.0_Chr2g0173231' => 'rch', 'RcHm_v2.0_Chr4g0433111' => 'rch', 'Rhsim03G0250300' => 'rsi', 'Rhsim08G0048400' => 'rsi', 'Rhsim10G0014800' => 'rsi', 'Rhsim12G0040100' => 'rsi', 'Rhsim12G0109700' => 'rsi', 'Sabra06G0049600' => 'sbr', 'Sabra08G0141000' => 'sbr', 'Sabra10G0021400' => 'sbr', 'Sabra16G0222900' => 'sbr', 'Sabra18G0108600' => 'sbr', 'SalBow1G0433' => 'sbo', 'SalBow1G2038' => 'sbo', 'SalBow1G5003' => 'sbo', 'SalBow7G1197' => 'sbo', 'SalBow8G3506' => 'sbo', 'Sc03g0007300' => 'sci', 'Sc11g0000950' => 'sci', 'Sc14g0008750' => 'sci', 'Sc18g0000420' => 'sci', 'Sed0006754' => 'sed', 'Sed0008741' => 'sed', 'Sed0017172' => 'sed', 'Sed0018925' => 'sed', 'Sed0023326' => 'sed', 'Sed0025909' => 'sed', 'SEGI_05333' => 'sgi', 'SEGI_10362' => 'sgi', 'SEGI_13380' => 'sgi', 'SEGI_24306' => 'sgi', 'SEGI_29077' => 'sgi', 'SEGI_29095' => 'sgi', 'SEGI_36534' => 'sgi', 'SEGI_37506' => 'sgi', 'SEGI_38321' => 'sgi', 'SGA_v2.0_scaffold307G48031' => 'sas', 'SGA_v2.0_scaffold47G17507' => 'sas', 'SGA_v2.0_scaffold63G21736' => 'sas', 'SGA_v2.0_scaffold87G27070' => 'sas', 'SHI17794' => 'shi', 'SHI28851' => 'shi', 'SMO165G0155' => 'smo', 'SMO340G0217' => 'smo', 'SMO367G1210' => 'smo', 'Solyc02g093430.3' => 'sly', 'Solyc05g013580.4' => 'sly', 'Solyc07g008030.3' => 'sly', 'Solyc12g035470.2' => 'sly', 'Sopen02g038020' => 'spe', 'Sopen05g008490' => 'spe', 'Sopen07g003910' => 'spe', 'Sopen12g015240' => 'spe', 'Sp1g11550' => 'spa', 'Sp2g16710' => 'spa', 'Sp3g00430' => 'spa', 'Sp3g26780' => 'spa', 'Sp5g22900' => 'spa', 'Sp6g29530' => 'spa', 'TAR371G0794' => 'tar', 'TAR374G0164' => 'tar', 'TAR622G0165' => 'tar', 'TAR626G0929' => 'tar', 'TAR629G2155' => 'tar', 'THA.LOC104805282' => 'tha', 'THA.LOC104805363' => 'tha', 'THA.LOC104808968' => 'tha', 'THA.LOC104821093' => 'tha', 'THA.LOC104823953' => 'tha', 'THA.LOC104825562' => 'tha', 'THA.LOC104825665' => 'tha', 'Thecc.02G261400' => 'tca', 'Thecc.04G019200' => 'tca', 'Thecc.09G130400' => 'tca', 'Thhalv10004374m.g' => 'esa', 'Thhalv10007850m.g' => 'esa', 'Thhalv10013782m.g' => 'esa', 'Thhalv10018686m.g' => 'esa', 'Thhalv10020899m.g' => 'esa', 'Thhalv10022755m.g' => 'esa', 'TPR.G23851' => 'tpr', 'TPR.G26500' => 'tpr', 'TPR.G27267' => 'tpr', 'TPR.G32001' => 'tpr', 'TPR.G6251' => 'tpr', 'TPR.G8167' => 'tpr', 'TWI12G1330' => 'twi', 'TWI18G1239' => 'twi', 'TWI34G0979' => 'twi', 'TWI36G0670' => 'twi', 'TWI36G0707' => 'twi', 'TWI56G0233' => 'twi', 'TWI75G1809' => 'twi', 'unitig_21.g20874' => 'ugi', 'unitig_26.g10343' => 'ugi', 'unitig_46.g18392' => 'ugi', 'unitig_52.g17178' => 'ugi', 'unitig_8.g2934' => 'ugi', 'vmacro01122' => 'vma', 'vmacro05875' => 'vma', 'vmacro06147' => 'vma', 'vmacro16191' => 'vma', 'vmacro18293' => 'vma', 'VMungo0251G3707' => 'vmu', 'VMungo0464G1521' => 'vmu', 'VMungo1215G0205' => 'vmu', 'VMungo1383G2484' => 'vmu', 'Zm00001eb079610' => 'zma', 'Zm00001eb135990' => 'zma', 'Zm00001eb183710' => 'zma', 'Zm00001eb246020' => 'zma' ) $gf_id = 'HOM05D001124' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001124' ) $data_identifier = 'HOM05D001124' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 6, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 7, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 21, 'bol' => (int) 10, 'bra' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 6, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 9, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 21, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 8, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 10, 'lsa' => (int) 8, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 8, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 9, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb246020' $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' => 'HOM05D001124', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '548', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02520' => 'bna', 'A03p06630' => 'bna', 'A05p44460' => 'bna', 'A06p08710' => 'bna', 'A06p41090' => 'bna', 'A07p32320' => 'bna', 'A08p32520' => 'bna', 'A09p10360' => 'bna', 'A10p24080' => 'bna', 'Aa31LG11G15250' => 'aar', 'Aa31LG1G1800' => 'aar', 'Aa31LG2G5120' => 'aar', 'Aa31LG2G6070' => 'aar', 'Aa31LG5G10770' => 'aar', 'Aa31sc61G90' => 'aar', 'Actinidia01352' => 'ach', 'Actinidia05983' => 'ach', 'Actinidia08133' => 'ach', 'Actinidia15101' => 'ach', 'Actinidia26379' => 'ach', 'Actinidia35778' => 'ach', 'Actinidia36123' => 'ach', 'Actinidia37436' => 'ach', 'Actinidia38730' => 'ach', 'Ah.02g128210' => 'amhyb', 'Ah.03g132990' => 'amhyb', 'Ah.14g079410' => 'amhyb', 'AL1G24640' => 'aly', 'AL2G26680' => 'aly', 'AL3G10530' => 'aly', 'AL3G45230' => 'aly', 'AL5G15230' => 'aly', 'AL5G16960' => 'aly', 'AL6G25210' => 'aly', 'Aqoxy2G00441' => 'aox', 'Aqoxy3G01236' => 'aox', 'Aqoxy5G03746' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3RQ047' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C7GMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9C8JER' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MBL6KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YXCZ83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZANX40' => 'arhy', 'AT1G12990' => 'ath', 'AT1G67880' => 'ath', 'AT2G13290' => 'ath', 'AT3G01620' => 'ath', 'AT3G26445' => 'ath', 'AT3G27540' => 'ath', 'AT5G14480' => 'ath', 'ATR0824G026' => 'atr', 'ATR1098G019' => 'atr', 'Atru.chr11.2145' => 'acertr', 'Atru.chr2.3636' => 'acertr', 'Atru.chr2.3644' => 'acertr', 'Atru.chr6.2422' => 'acertr', 'Atru.chr7.1112' => 'acertr', 'AUR62005469' => 'cqu', 'AUR62011166' => 'cqu', 'AUR62013319' => 'cqu', 'AUR62024273' => 'cqu', 'AUR62028420' => 'cqu', 'AUR62041942' => 'cqu', 'BcaB01g04969' => 'bca', 'BcaB01g06371' => 'bca', 'BcaB02g11494' => 'bca', 'BcaB03g15382' => 'bca', 'BcaB08g36994' => 'bca', 'BcaC03g13477' => 'bca', 'BcaC03g13478' => 'bca', 'BcaC03g13480' => 'bca', 'BcaC03g13481' => 'bca', 'BcaC03g13486' => 'bca', 'BcaC04g19031' => 'bca', 'BcaC04g23085' => 'bca', 'BcaC05g25094' => 'bca', 'BcaC05g25096' => 'bca', 'BcaC05g25138' => 'bca', 'BcaC05g30416' => 'bca', 'BcaC05g30455' => 'bca', 'BcaC06g30979' => 'bca', 'BcaC06g33805' => 'bca', 'BcaC08g46021' => 'bca', 'BcaNung03154' => 'bca', 'BolC2t06623H' => 'bol', 'BolC2t06632H' => 'bol', 'BolC2t06635H' => 'bol', 'BolC2t06638H' => 'bol', 'BolC3t13266H' => 'bol', 'BolC5t29776H' => 'bol', 'BolC6t38912H' => 'bol', 'BolC7t44183H' => 'bol', 'BolC9t54123H' => 'bol', 'BolC9t59107H' => 'bol', 'BraA02t05221Z' => 'bra', 'BraA03t09996Z' => 'bra', 'BraA05t23210Z' => 'bra', 'BraA06t24068Z' => 'bra', 'BraA06t27032Z' => 'bra', 'BraA08t35176Z' => 'bra', 'BraA09t36680Z' => 'bra', 'BraA10t44471Z' => 'bra', 'C02p06760' => 'bna', 'C02p06890' => 'bna', 'C02p07010' => 'bna', 'C03p07660' => 'bna', 'C05p10300' => 'bna', 'C06p38150' => 'bna', 'C07p36650' => 'bna', 'C08p15770' => 'bna', 'C09p12300' => 'bna', 'C09p62700' => 'bna', 'C09p75040' => 'bna', 'CAN.G13.1' => 'can', 'CAN.G138.4' => 'can', 'CAN.G44.6' => 'can', 'CAN.G473.19' => 'can', 'CANSAT01G0835' => 'cansat', 'CANSAT11G0246' => 'cansat', 'CANSAT11G1766' => 'cansat', 'CANSAT64G1954' => 'cansat', 'CARHR013330' => 'chi', 'CARHR060530' => 'chi', 'CARHR075300' => 'chi', 'CARHR105120' => 'chi', 'CARHR148910' => 'chi', 'CARHR198830' => 'chi', 'Carub.0001s1275' => 'cru', 'Carub.0002s1437' => 'cru', 'Carub.0003s0044' => 'cru', 'Carub.0003s2787' => 'cru', 'Carub.0005s0597' => 'cru', 'Carub.0006s1266' => 'cru', 'Ca_06935_v3' => 'car', 'Ca_13559_v3' => 'car', 'Ca_16941_v3' => 'car', 'Ca_16960_v3' => 'car', 'Ca_17775_v3' => 'car', 'Ca_30464_v3' => 'car', 'Cc06_g08160' => 'ccan', 'Cc07_g01520' => 'ccan', 'Cc11_g15810' => 'ccan', 'CDE02G2840' => 'cde', 'CDE03G0093' => 'cde', 'CDE04G2127' => 'cde', 'CDE07G1857' => 'cde', 'CDE09G1246' => 'cde', 'Cfa003412' => 'cfa', 'Cfa007341' => 'cfa', 'Cfa009220' => 'cfa', 'Ciclev10008737m.g' => 'ccl', 'Ciclev10015565m.g' => 'ccl', 'Ciclev10031761m.g' => 'ccl', 'CiPaw.03G045300' => 'cil', 'CiPaw.03G247200' => 'cil', 'CiPaw.04G029500' => 'cil', 'CiPaw.04G174000' => 'cil', 'CiPaw.05G181200' => 'cil', 'CiPaw.06G067100' => 'cil', 'ClCG05G025800' => 'cla', 'ClCG06G011400' => 'cla', 'ClCG09G019360' => 'cla', 'COL.COLO4_04827' => 'col', 'COL.COLO4_29170' => 'col', 'COL.COLO4_35131' => 'col', 'COL.COLO4_35132' => 'col', 'Cpa.g.sc33.32' => 'cpa', 'Cpa.g.sc46.29' => 'cpa', 'Cpa.g.sc796.1' => 'cpa', 'CsaV3_1G030420' => 'csa', 'CsaV3_5G027050' => 'csa', 'CsaV3_5G031040' => 'csa', 'CsaV3_UNG023130' => 'csa', 'CSS0007726' => 'camsi', 'CSS0016433' => 'camsi', 'CSS0017656' => 'camsi', 'CSS0025364' => 'camsi', 'CSS0027582' => 'camsi', 'CSS0047288' => 'camsi', 'CSS0049950' => 'camsi', 'DCAR_003843' => 'dca', 'DCAR_007052' => 'dca', 'DCAR_020884' => 'dca', 'DCAR_021730' => 'dca', 'DCAR_024423' => 'dca', 'DCAR_026509' => 'dca', 'DCAR_031158' => 'dca', 'Dinv14728' => 'din', 'Dinv15219' => 'din', 'Dinv25728' => 'din', 'Dinv33428' => 'din', 'Dinv36489' => 'din', 'Dinv41486' => 'din', 'Duzib147G0469' => 'dzi', 'Duzib168G0060' => 'dzi', 'Duzib187G1215' => 'dzi', 'Duzib248G0692' => 'dzi', 'Duzib251G0767' => 'dzi', 'Duzib264G0446' => 'dzi', 'Duzib268G0691' => 'dzi', 'ECA232G4767' => 'eca', 'ECA233G2838' => 'eca', 'ECA234G0391' => 'eca', 'ECA234G0857' => 'eca', 'ECA236G1593' => 'eca', 'ECA238G0565' => 'eca', 'ECA246G1027' => 'eca', 'ECA246G3223' => 'eca', 'ECA246G3470' => 'eca', 'EL10Ac6g13829' => 'bvu', 'EL10Ac6g14093' => 'bvu', 'EL10Ac8g18707' => 'bvu', 'Eucgr.C01369' => 'egr', 'Eucgr.H02492' => 'egr', 'Eucgr.I01733' => 'egr', 'Eucgr.J02255' => 'egr', 'Eucgr.J02257' => 'egr', 'Eucgr.J02258' => 'egr', 'FAN02G1601' => 'fan', 'FAN03G1586' => 'fan', 'FAN03G2986' => 'fan', 'FAN05G4837' => 'fan', 'FAN06G0146' => 'fan', 'FAN07G0858' => 'fan', 'FAN09G3179' => 'fan', 'FAN10G0669' => 'fan', 'FAN12G2358' => 'fan', 'FAN14G4198' => 'fan', 'FAN14G5112' => 'fan', 'FAN17G0342' => 'fan', 'FAN19G0342' => 'fan', 'FAN19G0962' => 'fan', 'FAN19G1101' => 'fan', 'FAN19G1872' => 'fan', 'FAN22G0356' => 'fan', 'FAN23G0744' => 'fan', 'FAN23G1914' => 'fan', 'FAN26G0032' => 'fan', 'FAN28G0625' => 'fan', 'FvH4_1g02710' => 'fve', 'FvH4_1g02720' => 'fve', 'FvH4_4g25670' => 'fve', 'FvH4_6g51700' => 'fve', 'FvH4_7g20170' => 'fve', 'Glyma.05G175000' => 'gma', 'Glyma.08G132300' => 'gma', 'Glyma.11G243000' => 'gma', 'Glyma.13G158900' => 'gma', 'Glyma.17G112400' => 'gma', 'Glyma.18G014100' => 'gma', 'Glyma.19G003100' => 'gma', 'Glyma.19G056500' => 'gma', 'Gohir.A01G158900' => 'ghi', 'Gohir.A05G312600' => 'ghi', 'Gohir.A05G354900' => 'ghi', 'Gohir.A07G037200' => 'ghi', 'Gohir.A09G030000' => 'ghi', 'Gohir.A12G145200' => 'ghi', 'Gohir.D01G151500' => 'ghi', 'Gohir.D04G058300' => 'ghi', 'Gohir.D05G314100' => 'ghi', 'Gohir.D07G041400' => 'ghi', 'Gohir.D09G029700' => 'ghi', 'Gohir.D12G149700' => 'ghi', 'Gorai.001G043800' => 'gra', 'Gorai.002G187800' => 'gra', 'Gorai.006G034700' => 'gra', 'Gorai.008G161200' => 'gra', 'Gorai.009G335700' => 'gra', 'Gorai.012G065000' => 'gra', 'GSVIVG01000535001' => 'vvi', 'GSVIVG01015572001' => 'vvi', 'GSVIVG01032386001' => 'vvi', 'HanXRQChr05g0138531' => 'han', 'HanXRQChr06g0174391' => 'han', 'HanXRQChr07g0199021' => 'han', 'HanXRQChr08g0208211' => 'han', 'HanXRQChr09g0255471' => 'han', 'HanXRQChr10g0315791' => 'han', 'HanXRQChr12g0371991' => 'han', 'HanXRQChr15g0475251' => 'han', 'HanXRQChr17g0540001' => 'han', 'HanXRQChr17g0548631' => 'han', 'HanXRQChr17g0569561' => 'han', 'Haze_12256' => 'cav', 'Haze_14756' => 'cav', 'Haze_25528' => 'cav', 'Hma1.2p1_0079F.1_g041020' => 'hma', 'Hma1.2p1_0818F.1_g223260' => 'hma', 'Hma1.2p1_1747F.1_g300530' => 'hma', 'HPP92_004607' => 'vpl', 'HPP92_004608' => 'vpl', 'HPP92_006181' => 'vpl', 'HPP92_012192' => 'vpl', 'HPP92_015680' => 'vpl', 'HPP92_020249' => 'vpl', 'HPP92_021376' => 'vpl', 'HPP92_024275' => 'vpl', 'Hund06031' => 'sun', 'Hund25391' => 'sun', 'Lalb_Chr07g0185371' => 'lal', 'Lalb_Chr07g0185381' => 'lal', 'Lalb_Chr12g0204011' => 'lal', 'Lalb_Chr13g0301671' => 'lal', 'Lalb_Chr14g0362851' => 'lal', 'Lalb_Chr24g0403581' => 'lal', 'Lj1g0000233' => 'lja', 'Lj2g0018120' => 'lja', 'Lj3C621T0' => 'lonja', 'Lj3P1059T14' => 'lonja', 'Lj3P611T9' => 'lonja', 'Lj3P614T13' => 'lonja', 'Lj3P615T5' => 'lonja', 'Lj4g0012315' => 'lja', 'Lj4g0026182' => 'lja', 'Lj6P813T16' => 'lonja', 'Lj7C427T7' => 'lonja', 'Lj7C427T8' => 'lonja', 'Lj7P600T41' => 'lonja', 'Lju41C42G17' => 'lonja', 'Lsat_1_v5_gn_0_47300' => 'lsa', 'Lsat_1_v5_gn_2_91280' => 'lsa', 'Lsat_1_v5_gn_3_30561' => 'lsa', 'Lsat_1_v5_gn_4_184321' => 'lsa', 'Lsat_1_v5_gn_4_4041' => 'lsa', 'Lsat_1_v5_gn_5_92000' => 'lsa', 'Lsat_1_v5_gn_8_152940' => 'lsa', 'Lsat_1_v5_gn_8_62401' => 'lsa', 'Manes.06G055900' => 'mes', 'Manes.12G022200' => 'mes', 'Manes.13G023300' => 'mes', 'Manes.14G115000' => 'mes', 'Manes.15G151700' => 'mes', 'Manes.17G111300' => 'mes', 'Mapoly0226s0009' => 'mpo', 'MBI02_g25363_MAGBIO' => 'mbi', 'MBI06_g00027_MAGBIO' => 'mbi', 'MBI10_g13034_MAGBIO' => 'mbi', 'MD09G1023400' => 'mdo', 'MD13G1100100' => 'mdo', 'MD15G1169200' => 'mdo', 'MD16G1101100' => 'mdo', 'MD17G1022900' => 'mdo', 'Medtr3g096150' => 'mtr', 'Medtr4g115070' => 'mtr', 'Medtr7g033325' => 'mtr', 'Medtr8g089840' => 'mtr', 'MELO3C010319.2' => 'cme', 'MELO3C011944.2' => 'cme', 'MELO3C021589.2' => 'cme', 'Migut.E00207' => 'egut', 'Migut.H00067' => 'egut', 'Migut.K00433' => 'egut', 'Migut.K00606' => 'egut', 'Migut.K01410' => 'egut', 'MSTRG.13347' => 'ama', 'MSTRG.24045' => 'ama', 'MSTRG.2428' => 'ama', 'MSTRG.26410' => 'ama', 'MSTRG.3139' => 'ama', 'MSTRG.3286' => 'ama', 'MSTRG.563' => 'ama', 'MSTRG.7941' => 'ama', 'Nitab4.5_0000028g0060' => 'nta', 'Nitab4.5_0000065g0260' => 'nta', 'Nitab4.5_0000112g0060' => 'nta', 'Nitab4.5_0000489g0120' => 'nta', 'Nitab4.5_0001776g0050' => 'nta', 'Nitab4.5_0001854g0010' => 'nta', 'Nitab4.5_0001860g0020' => 'nta', 'Nitab4.5_0004352g0010' => 'nta', 'Nitab4.5_0008716g0020' => 'nta', 'Nitab4.5_0008922g0010' => 'nta', 'Nn3g16693' => 'nnu', 'Nn4g22596' => 'nnu', 'Nn7g37639' => 'nnu', 'Oeu001701.1' => 'oeu', 'Oeu018149.1' => 'oeu', 'Oeu026220.1' => 'oeu', 'Oeu038635.1' => 'oeu', 'Oeu049176.1' => 'oeu', 'Oeu056706.1' => 'oeu', 'Oeu056937.1' => 'oeu', 'Oeu057540.1' => 'oeu', 'Os02g0594900' => 'osa', 'Os02g0595100' => 'osa', 'Os04g0477500' => 'osa', 'Os12g0611900' => 'osa', 'Peaxi162Scf00076g00020' => 'pax', 'Peaxi162Scf00128g00217' => 'pax', 'Peaxi162Scf00129g01640' => 'pax', 'Peaxi162Scf00669g00007' => 'pax', 'Peaxi162Scf00700g00421' => 'pax', 'Peaxi162Scf00801g00038' => 'pax', 'Peaxi162Scf00891g00025' => 'pax', 'PGR083G0909' => 'pgr', 'PGR119G1005' => 'pgr', 'PGR142G2236' => 'pgr', 'PGR142G3388' => 'pgr', 'PGSC0003DMG400004514' => 'stu', 'PGSC0003DMG400012635' => 'stu', 'PGSC0003DMG400015730' => 'stu', 'PGSC0003DMG400018611' => 'stu', 'PGSC0003DMG400030897' => 'stu', 'Phvul.001G254800' => 'pvu', 'Phvul.002G260100' => 'pvu', 'Phvul.003G167600' => 'pvu', 'Phvul.004G005100' => 'pvu', 'Potri.001G343600' => 'ptr', 'Potri.006G066700' => 'ptr', 'Potri.008G186000' => 'ptr', 'Potri.010G046900' => 'ptr', 'Potri.018G127900' => 'ptr', 'Pp3c20_17750' => 'ppa', 'Pp3c24_4380' => 'ppa', 'Prupe.1G245800' => 'ppe', 'Prupe.3G293400' => 'ppe', 'Prupe.7G247400' => 'ppe', 'Psat0s145g0120' => 'psa', 'Psat0s595g0040' => 'psa', 'Psat0s595g0120' => 'psa', 'Psat3g175040' => 'psa', 'Psat7g058120' => 'psa', 'PSO017G0428' => 'pso', 'PSO063G7510' => 'pso', 'PSO067G0046' => 'pso', 'PSO478G1073' => 'pso', 'PSO675G3677' => 'pso', 'PSO675G6558' => 'pso', 'PSO675G7520' => 'pso', 'PSO675G8959' => 'pso', 'QL02p074089' => 'qlo', 'QL02p089614' => 'qlo', 'QL03p057736' => 'qlo', 'RcHm_v2.0_Chr1g0364131' => 'rch', 'RcHm_v2.0_Chr2g0087801' => 'rch', 'RcHm_v2.0_Chr2g0087821' => 'rch', 'RcHm_v2.0_Chr2g0173231' => 'rch', 'RcHm_v2.0_Chr4g0433111' => 'rch', 'Rhsim03G0250300' => 'rsi', 'Rhsim08G0048400' => 'rsi', 'Rhsim10G0014800' => 'rsi', 'Rhsim12G0040100' => 'rsi', 'Rhsim12G0109700' => 'rsi', 'Sabra06G0049600' => 'sbr', 'Sabra08G0141000' => 'sbr', 'Sabra10G0021400' => 'sbr', 'Sabra16G0222900' => 'sbr', 'Sabra18G0108600' => 'sbr', 'SalBow1G0433' => 'sbo', 'SalBow1G2038' => 'sbo', 'SalBow1G5003' => 'sbo', 'SalBow7G1197' => 'sbo', 'SalBow8G3506' => 'sbo', 'Sc03g0007300' => 'sci', 'Sc11g0000950' => 'sci', 'Sc14g0008750' => 'sci', 'Sc18g0000420' => 'sci', 'Sed0006754' => 'sed', 'Sed0008741' => 'sed', 'Sed0017172' => 'sed', 'Sed0018925' => 'sed', 'Sed0023326' => 'sed', 'Sed0025909' => 'sed', 'SEGI_05333' => 'sgi', 'SEGI_10362' => 'sgi', 'SEGI_13380' => 'sgi', 'SEGI_24306' => 'sgi', 'SEGI_29077' => 'sgi', 'SEGI_29095' => 'sgi', 'SEGI_36534' => 'sgi', 'SEGI_37506' => 'sgi', 'SEGI_38321' => 'sgi', 'SGA_v2.0_scaffold307G48031' => 'sas', 'SGA_v2.0_scaffold47G17507' => 'sas', 'SGA_v2.0_scaffold63G21736' => 'sas', 'SGA_v2.0_scaffold87G27070' => 'sas', 'SHI17794' => 'shi', 'SHI28851' => 'shi', 'SMO165G0155' => 'smo', 'SMO340G0217' => 'smo', 'SMO367G1210' => 'smo', 'Solyc02g093430.3' => 'sly', 'Solyc05g013580.4' => 'sly', 'Solyc07g008030.3' => 'sly', 'Solyc12g035470.2' => 'sly', 'Sopen02g038020' => 'spe', 'Sopen05g008490' => 'spe', 'Sopen07g003910' => 'spe', 'Sopen12g015240' => 'spe', 'Sp1g11550' => 'spa', 'Sp2g16710' => 'spa', 'Sp3g00430' => 'spa', 'Sp3g26780' => 'spa', 'Sp5g22900' => 'spa', 'Sp6g29530' => 'spa', 'TAR371G0794' => 'tar', 'TAR374G0164' => 'tar', 'TAR622G0165' => 'tar', 'TAR626G0929' => 'tar', 'TAR629G2155' => 'tar', 'THA.LOC104805282' => 'tha', 'THA.LOC104805363' => 'tha', 'THA.LOC104808968' => 'tha', 'THA.LOC104821093' => 'tha', 'THA.LOC104823953' => 'tha', 'THA.LOC104825562' => 'tha', 'THA.LOC104825665' => 'tha', 'Thecc.02G261400' => 'tca', 'Thecc.04G019200' => 'tca', 'Thecc.09G130400' => 'tca', 'Thhalv10004374m.g' => 'esa', 'Thhalv10007850m.g' => 'esa', 'Thhalv10013782m.g' => 'esa', 'Thhalv10018686m.g' => 'esa', 'Thhalv10020899m.g' => 'esa', 'Thhalv10022755m.g' => 'esa', 'TPR.G23851' => 'tpr', 'TPR.G26500' => 'tpr', 'TPR.G27267' => 'tpr', 'TPR.G32001' => 'tpr', 'TPR.G6251' => 'tpr', 'TPR.G8167' => 'tpr', 'TWI12G1330' => 'twi', 'TWI18G1239' => 'twi', 'TWI34G0979' => 'twi', 'TWI36G0670' => 'twi', 'TWI36G0707' => 'twi', 'TWI56G0233' => 'twi', 'TWI75G1809' => 'twi', 'unitig_21.g20874' => 'ugi', 'unitig_26.g10343' => 'ugi', 'unitig_46.g18392' => 'ugi', 'unitig_52.g17178' => 'ugi', 'unitig_8.g2934' => 'ugi', 'vmacro01122' => 'vma', 'vmacro05875' => 'vma', 'vmacro06147' => 'vma', 'vmacro16191' => 'vma', 'vmacro18293' => 'vma', 'VMungo0251G3707' => 'vmu', 'VMungo0464G1521' => 'vmu', 'VMungo1215G0205' => 'vmu', 'VMungo1383G2484' => 'vmu', 'Zm00001eb079610' => 'zma', 'Zm00001eb135990' => 'zma', 'Zm00001eb183710' => 'zma', 'Zm00001eb246020' => 'zma' ), 'gf_id' => 'HOM05D001124', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001124' ), 'data_identifier' => 'HOM05D001124', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001124', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '548', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02520' => 'bna', 'A03p06630' => 'bna', 'A05p44460' => 'bna', 'A06p08710' => 'bna', 'A06p41090' => 'bna', 'A07p32320' => 'bna', 'A08p32520' => 'bna', 'A09p10360' => 'bna', 'A10p24080' => 'bna', 'Aa31LG11G15250' => 'aar', 'Aa31LG1G1800' => 'aar', 'Aa31LG2G5120' => 'aar', 'Aa31LG2G6070' => 'aar', 'Aa31LG5G10770' => 'aar', 'Aa31sc61G90' => 'aar', 'Actinidia01352' => 'ach', 'Actinidia05983' => 'ach', 'Actinidia08133' => 'ach', 'Actinidia15101' => 'ach', 'Actinidia26379' => 'ach', 'Actinidia35778' => 'ach', 'Actinidia36123' => 'ach', 'Actinidia37436' => 'ach', 'Actinidia38730' => 'ach', 'Ah.02g128210' => 'amhyb', 'Ah.03g132990' => 'amhyb', 'Ah.14g079410' => 'amhyb', 'AL1G24640' => 'aly', 'AL2G26680' => 'aly', 'AL3G10530' => 'aly', 'AL3G45230' => 'aly', 'AL5G15230' => 'aly', 'AL5G16960' => 'aly', 'AL6G25210' => 'aly', 'Aqoxy2G00441' => 'aox', 'Aqoxy3G01236' => 'aox', 'Aqoxy5G03746' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3RQ047' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C7GMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9C8JER' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MBL6KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YXCZ83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZANX40' => 'arhy', 'AT1G12990' => 'ath', 'AT1G67880' => 'ath', 'AT2G13290' => 'ath', 'AT3G01620' => 'ath', 'AT3G26445' => 'ath', 'AT3G27540' => 'ath', 'AT5G14480' => 'ath', 'ATR0824G026' => 'atr', 'ATR1098G019' => 'atr', 'Atru.chr11.2145' => 'acertr', 'Atru.chr2.3636' => 'acertr', 'Atru.chr2.3644' => 'acertr', 'Atru.chr6.2422' => 'acertr', 'Atru.chr7.1112' => 'acertr', 'AUR62005469' => 'cqu', 'AUR62011166' => 'cqu', 'AUR62013319' => 'cqu', 'AUR62024273' => 'cqu', 'AUR62028420' => 'cqu', 'AUR62041942' => 'cqu', 'BcaB01g04969' => 'bca', 'BcaB01g06371' => 'bca', 'BcaB02g11494' => 'bca', 'BcaB03g15382' => 'bca', 'BcaB08g36994' => 'bca', 'BcaC03g13477' => 'bca', 'BcaC03g13478' => 'bca', 'BcaC03g13480' => 'bca', 'BcaC03g13481' => 'bca', 'BcaC03g13486' => 'bca', 'BcaC04g19031' => 'bca', 'BcaC04g23085' => 'bca', 'BcaC05g25094' => 'bca', 'BcaC05g25096' => 'bca', 'BcaC05g25138' => 'bca', 'BcaC05g30416' => 'bca', 'BcaC05g30455' => 'bca', 'BcaC06g30979' => 'bca', 'BcaC06g33805' => 'bca', 'BcaC08g46021' => 'bca', 'BcaNung03154' => 'bca', 'BolC2t06623H' => 'bol', 'BolC2t06632H' => 'bol', 'BolC2t06635H' => 'bol', 'BolC2t06638H' => 'bol', 'BolC3t13266H' => 'bol', 'BolC5t29776H' => 'bol', 'BolC6t38912H' => 'bol', 'BolC7t44183H' => 'bol', 'BolC9t54123H' => 'bol', 'BolC9t59107H' => 'bol', 'BraA02t05221Z' => 'bra', 'BraA03t09996Z' => 'bra', 'BraA05t23210Z' => 'bra', 'BraA06t24068Z' => 'bra', 'BraA06t27032Z' => 'bra', 'BraA08t35176Z' => 'bra', 'BraA09t36680Z' => 'bra', 'BraA10t44471Z' => 'bra', 'C02p06760' => 'bna', 'C02p06890' => 'bna', 'C02p07010' => 'bna', 'C03p07660' => 'bna', 'C05p10300' => 'bna', 'C06p38150' => 'bna', 'C07p36650' => 'bna', 'C08p15770' => 'bna', 'C09p12300' => 'bna', 'C09p62700' => 'bna', 'C09p75040' => 'bna', 'CAN.G13.1' => 'can', 'CAN.G138.4' => 'can', 'CAN.G44.6' => 'can', 'CAN.G473.19' => 'can', 'CANSAT01G0835' => 'cansat', 'CANSAT11G0246' => 'cansat', 'CANSAT11G1766' => 'cansat', 'CANSAT64G1954' => 'cansat', 'CARHR013330' => 'chi', 'CARHR060530' => 'chi', 'CARHR075300' => 'chi', 'CARHR105120' => 'chi', 'CARHR148910' => 'chi', 'CARHR198830' => 'chi', 'Carub.0001s1275' => 'cru', 'Carub.0002s1437' => 'cru', 'Carub.0003s0044' => 'cru', 'Carub.0003s2787' => 'cru', 'Carub.0005s0597' => 'cru', 'Carub.0006s1266' => 'cru', 'Ca_06935_v3' => 'car', 'Ca_13559_v3' => 'car', 'Ca_16941_v3' => 'car', 'Ca_16960_v3' => 'car', 'Ca_17775_v3' => 'car', 'Ca_30464_v3' => 'car', 'Cc06_g08160' => 'ccan', 'Cc07_g01520' => 'ccan', 'Cc11_g15810' => 'ccan', 'CDE02G2840' => 'cde', 'CDE03G0093' => 'cde', 'CDE04G2127' => 'cde', 'CDE07G1857' => 'cde', 'CDE09G1246' => 'cde', 'Cfa003412' => 'cfa', 'Cfa007341' => 'cfa', 'Cfa009220' => 'cfa', 'Ciclev10008737m.g' => 'ccl', 'Ciclev10015565m.g' => 'ccl', 'Ciclev10031761m.g' => 'ccl', 'CiPaw.03G045300' => 'cil', 'CiPaw.03G247200' => 'cil', 'CiPaw.04G029500' => 'cil', 'CiPaw.04G174000' => 'cil', 'CiPaw.05G181200' => 'cil', 'CiPaw.06G067100' => 'cil', 'ClCG05G025800' => 'cla', 'ClCG06G011400' => 'cla', 'ClCG09G019360' => 'cla', 'COL.COLO4_04827' => 'col', 'COL.COLO4_29170' => 'col', 'COL.COLO4_35131' => 'col', 'COL.COLO4_35132' => 'col', 'Cpa.g.sc33.32' => 'cpa', 'Cpa.g.sc46.29' => 'cpa', 'Cpa.g.sc796.1' => 'cpa', 'CsaV3_1G030420' => 'csa', 'CsaV3_5G027050' => 'csa', 'CsaV3_5G031040' => 'csa', 'CsaV3_UNG023130' => 'csa', 'CSS0007726' => 'camsi', 'CSS0016433' => 'camsi', 'CSS0017656' => 'camsi', 'CSS0025364' => 'camsi', 'CSS0027582' => 'camsi', 'CSS0047288' => 'camsi', 'CSS0049950' => 'camsi', 'DCAR_003843' => 'dca', 'DCAR_007052' => 'dca', 'DCAR_020884' => 'dca', 'DCAR_021730' => 'dca', 'DCAR_024423' => 'dca', 'DCAR_026509' => 'dca', 'DCAR_031158' => 'dca', 'Dinv14728' => 'din', 'Dinv15219' => 'din', 'Dinv25728' => 'din', 'Dinv33428' => 'din', 'Dinv36489' => 'din', 'Dinv41486' => 'din', 'Duzib147G0469' => 'dzi', 'Duzib168G0060' => 'dzi', 'Duzib187G1215' => 'dzi', 'Duzib248G0692' => 'dzi', 'Duzib251G0767' => 'dzi', 'Duzib264G0446' => 'dzi', 'Duzib268G0691' => 'dzi', 'ECA232G4767' => 'eca', 'ECA233G2838' => 'eca', 'ECA234G0391' => 'eca', 'ECA234G0857' => 'eca', 'ECA236G1593' => 'eca', 'ECA238G0565' => 'eca', 'ECA246G1027' => 'eca', 'ECA246G3223' => 'eca', 'ECA246G3470' => 'eca', 'EL10Ac6g13829' => 'bvu', 'EL10Ac6g14093' => 'bvu', 'EL10Ac8g18707' => 'bvu', 'Eucgr.C01369' => 'egr', 'Eucgr.H02492' => 'egr', 'Eucgr.I01733' => 'egr', 'Eucgr.J02255' => 'egr', 'Eucgr.J02257' => 'egr', 'Eucgr.J02258' => 'egr', 'FAN02G1601' => 'fan', 'FAN03G1586' => 'fan', 'FAN03G2986' => 'fan', 'FAN05G4837' => 'fan', 'FAN06G0146' => 'fan', 'FAN07G0858' => 'fan', 'FAN09G3179' => 'fan', 'FAN10G0669' => 'fan', 'FAN12G2358' => 'fan', 'FAN14G4198' => 'fan', 'FAN14G5112' => 'fan', 'FAN17G0342' => 'fan', 'FAN19G0342' => 'fan', 'FAN19G0962' => 'fan', 'FAN19G1101' => 'fan', 'FAN19G1872' => 'fan', 'FAN22G0356' => 'fan', 'FAN23G0744' => 'fan', 'FAN23G1914' => 'fan', 'FAN26G0032' => 'fan', 'FAN28G0625' => 'fan', 'FvH4_1g02710' => 'fve', 'FvH4_1g02720' => 'fve', 'FvH4_4g25670' => 'fve', 'FvH4_6g51700' => 'fve', 'FvH4_7g20170' => 'fve', 'Glyma.05G175000' => 'gma', 'Glyma.08G132300' => 'gma', 'Glyma.11G243000' => 'gma', 'Glyma.13G158900' => 'gma', 'Glyma.17G112400' => 'gma', 'Glyma.18G014100' => 'gma', 'Glyma.19G003100' => 'gma', 'Glyma.19G056500' => 'gma', 'Gohir.A01G158900' => 'ghi', 'Gohir.A05G312600' => 'ghi', 'Gohir.A05G354900' => 'ghi', 'Gohir.A07G037200' => 'ghi', 'Gohir.A09G030000' => 'ghi', 'Gohir.A12G145200' => 'ghi', 'Gohir.D01G151500' => 'ghi', 'Gohir.D04G058300' => 'ghi', 'Gohir.D05G314100' => 'ghi', 'Gohir.D07G041400' => 'ghi', 'Gohir.D09G029700' => 'ghi', 'Gohir.D12G149700' => 'ghi', 'Gorai.001G043800' => 'gra', 'Gorai.002G187800' => 'gra', 'Gorai.006G034700' => 'gra', 'Gorai.008G161200' => 'gra', 'Gorai.009G335700' => 'gra', 'Gorai.012G065000' => 'gra', 'GSVIVG01000535001' => 'vvi', 'GSVIVG01015572001' => 'vvi', 'GSVIVG01032386001' => 'vvi', 'HanXRQChr05g0138531' => 'han', 'HanXRQChr06g0174391' => 'han', 'HanXRQChr07g0199021' => 'han', 'HanXRQChr08g0208211' => 'han', 'HanXRQChr09g0255471' => 'han', 'HanXRQChr10g0315791' => 'han', 'HanXRQChr12g0371991' => 'han', 'HanXRQChr15g0475251' => 'han', 'HanXRQChr17g0540001' => 'han', 'HanXRQChr17g0548631' => 'han', 'HanXRQChr17g0569561' => 'han', 'Haze_12256' => 'cav', 'Haze_14756' => 'cav', 'Haze_25528' => 'cav', 'Hma1.2p1_0079F.1_g041020' => 'hma', 'Hma1.2p1_0818F.1_g223260' => 'hma', 'Hma1.2p1_1747F.1_g300530' => 'hma', 'HPP92_004607' => 'vpl', 'HPP92_004608' => 'vpl', 'HPP92_006181' => 'vpl', 'HPP92_012192' => 'vpl', 'HPP92_015680' => 'vpl', 'HPP92_020249' => 'vpl', 'HPP92_021376' => 'vpl', 'HPP92_024275' => 'vpl', 'Hund06031' => 'sun', 'Hund25391' => 'sun', 'Lalb_Chr07g0185371' => 'lal', 'Lalb_Chr07g0185381' => 'lal', 'Lalb_Chr12g0204011' => 'lal', 'Lalb_Chr13g0301671' => 'lal', 'Lalb_Chr14g0362851' => 'lal', 'Lalb_Chr24g0403581' => 'lal', 'Lj1g0000233' => 'lja', 'Lj2g0018120' => 'lja', 'Lj3C621T0' => 'lonja', 'Lj3P1059T14' => 'lonja', 'Lj3P611T9' => 'lonja', 'Lj3P614T13' => 'lonja', 'Lj3P615T5' => 'lonja', 'Lj4g0012315' => 'lja', 'Lj4g0026182' => 'lja', 'Lj6P813T16' => 'lonja', 'Lj7C427T7' => 'lonja', 'Lj7C427T8' => 'lonja', 'Lj7P600T41' => 'lonja', 'Lju41C42G17' => 'lonja', 'Lsat_1_v5_gn_0_47300' => 'lsa', 'Lsat_1_v5_gn_2_91280' => 'lsa', 'Lsat_1_v5_gn_3_30561' => 'lsa', 'Lsat_1_v5_gn_4_184321' => 'lsa', 'Lsat_1_v5_gn_4_4041' => 'lsa', 'Lsat_1_v5_gn_5_92000' => 'lsa', 'Lsat_1_v5_gn_8_152940' => 'lsa', 'Lsat_1_v5_gn_8_62401' => 'lsa', 'Manes.06G055900' => 'mes', 'Manes.12G022200' => 'mes', 'Manes.13G023300' => 'mes', 'Manes.14G115000' => 'mes', 'Manes.15G151700' => 'mes', 'Manes.17G111300' => 'mes', 'Mapoly0226s0009' => 'mpo', 'MBI02_g25363_MAGBIO' => 'mbi', 'MBI06_g00027_MAGBIO' => 'mbi', 'MBI10_g13034_MAGBIO' => 'mbi', 'MD09G1023400' => 'mdo', 'MD13G1100100' => 'mdo', 'MD15G1169200' => 'mdo', 'MD16G1101100' => 'mdo', 'MD17G1022900' => 'mdo', 'Medtr3g096150' => 'mtr', 'Medtr4g115070' => 'mtr', 'Medtr7g033325' => 'mtr', 'Medtr8g089840' => 'mtr', 'MELO3C010319.2' => 'cme', 'MELO3C011944.2' => 'cme', 'MELO3C021589.2' => 'cme', 'Migut.E00207' => 'egut', 'Migut.H00067' => 'egut', 'Migut.K00433' => 'egut', 'Migut.K00606' => 'egut', 'Migut.K01410' => 'egut', 'MSTRG.13347' => 'ama', 'MSTRG.24045' => 'ama', 'MSTRG.2428' => 'ama', 'MSTRG.26410' => 'ama', 'MSTRG.3139' => 'ama', 'MSTRG.3286' => 'ama', 'MSTRG.563' => 'ama', 'MSTRG.7941' => 'ama', 'Nitab4.5_0000028g0060' => 'nta', 'Nitab4.5_0000065g0260' => 'nta', 'Nitab4.5_0000112g0060' => 'nta', 'Nitab4.5_0000489g0120' => 'nta', 'Nitab4.5_0001776g0050' => 'nta', 'Nitab4.5_0001854g0010' => 'nta', 'Nitab4.5_0001860g0020' => 'nta', 'Nitab4.5_0004352g0010' => 'nta', 'Nitab4.5_0008716g0020' => 'nta', 'Nitab4.5_0008922g0010' => 'nta', 'Nn3g16693' => 'nnu', 'Nn4g22596' => 'nnu', 'Nn7g37639' => 'nnu', 'Oeu001701.1' => 'oeu', 'Oeu018149.1' => 'oeu', 'Oeu026220.1' => 'oeu', 'Oeu038635.1' => 'oeu', 'Oeu049176.1' => 'oeu', 'Oeu056706.1' => 'oeu', 'Oeu056937.1' => 'oeu', 'Oeu057540.1' => 'oeu', 'Os02g0594900' => 'osa', 'Os02g0595100' => 'osa', 'Os04g0477500' => 'osa', 'Os12g0611900' => 'osa', 'Peaxi162Scf00076g00020' => 'pax', 'Peaxi162Scf00128g00217' => 'pax', 'Peaxi162Scf00129g01640' => 'pax', 'Peaxi162Scf00669g00007' => 'pax', 'Peaxi162Scf00700g00421' => 'pax', 'Peaxi162Scf00801g00038' => 'pax', 'Peaxi162Scf00891g00025' => 'pax', 'PGR083G0909' => 'pgr', 'PGR119G1005' => 'pgr', 'PGR142G2236' => 'pgr', 'PGR142G3388' => 'pgr', 'PGSC0003DMG400004514' => 'stu', 'PGSC0003DMG400012635' => 'stu', 'PGSC0003DMG400015730' => 'stu', 'PGSC0003DMG400018611' => 'stu', 'PGSC0003DMG400030897' => 'stu', 'Phvul.001G254800' => 'pvu', 'Phvul.002G260100' => 'pvu', 'Phvul.003G167600' => 'pvu', 'Phvul.004G005100' => 'pvu', 'Potri.001G343600' => 'ptr', 'Potri.006G066700' => 'ptr', 'Potri.008G186000' => 'ptr', 'Potri.010G046900' => 'ptr', 'Potri.018G127900' => 'ptr', 'Pp3c20_17750' => 'ppa', 'Pp3c24_4380' => 'ppa', 'Prupe.1G245800' => 'ppe', 'Prupe.3G293400' => 'ppe', 'Prupe.7G247400' => 'ppe', 'Psat0s145g0120' => 'psa', 'Psat0s595g0040' => 'psa', 'Psat0s595g0120' => 'psa', 'Psat3g175040' => 'psa', 'Psat7g058120' => 'psa', 'PSO017G0428' => 'pso', 'PSO063G7510' => 'pso', 'PSO067G0046' => 'pso', 'PSO478G1073' => 'pso', 'PSO675G3677' => 'pso', 'PSO675G6558' => 'pso', 'PSO675G7520' => 'pso', 'PSO675G8959' => 'pso', 'QL02p074089' => 'qlo', 'QL02p089614' => 'qlo', 'QL03p057736' => 'qlo', 'RcHm_v2.0_Chr1g0364131' => 'rch', 'RcHm_v2.0_Chr2g0087801' => 'rch', 'RcHm_v2.0_Chr2g0087821' => 'rch', 'RcHm_v2.0_Chr2g0173231' => 'rch', 'RcHm_v2.0_Chr4g0433111' => 'rch', 'Rhsim03G0250300' => 'rsi', 'Rhsim08G0048400' => 'rsi', 'Rhsim10G0014800' => 'rsi', 'Rhsim12G0040100' => 'rsi', 'Rhsim12G0109700' => 'rsi', 'Sabra06G0049600' => 'sbr', 'Sabra08G0141000' => 'sbr', 'Sabra10G0021400' => 'sbr', 'Sabra16G0222900' => 'sbr', 'Sabra18G0108600' => 'sbr', 'SalBow1G0433' => 'sbo', 'SalBow1G2038' => 'sbo', 'SalBow1G5003' => 'sbo', 'SalBow7G1197' => 'sbo', 'SalBow8G3506' => 'sbo', 'Sc03g0007300' => 'sci', 'Sc11g0000950' => 'sci', 'Sc14g0008750' => 'sci', 'Sc18g0000420' => 'sci', 'Sed0006754' => 'sed', 'Sed0008741' => 'sed', 'Sed0017172' => 'sed', 'Sed0018925' => 'sed', 'Sed0023326' => 'sed', 'Sed0025909' => 'sed', 'SEGI_05333' => 'sgi', 'SEGI_10362' => 'sgi', 'SEGI_13380' => 'sgi', 'SEGI_24306' => 'sgi', 'SEGI_29077' => 'sgi', 'SEGI_29095' => 'sgi', 'SEGI_36534' => 'sgi', 'SEGI_37506' => 'sgi', 'SEGI_38321' => 'sgi', 'SGA_v2.0_scaffold307G48031' => 'sas', 'SGA_v2.0_scaffold47G17507' => 'sas', 'SGA_v2.0_scaffold63G21736' => 'sas', 'SGA_v2.0_scaffold87G27070' => 'sas', 'SHI17794' => 'shi', 'SHI28851' => 'shi', 'SMO165G0155' => 'smo', 'SMO340G0217' => 'smo', 'SMO367G1210' => 'smo', 'Solyc02g093430.3' => 'sly', 'Solyc05g013580.4' => 'sly', 'Solyc07g008030.3' => 'sly', 'Solyc12g035470.2' => 'sly', 'Sopen02g038020' => 'spe', 'Sopen05g008490' => 'spe', 'Sopen07g003910' => 'spe', 'Sopen12g015240' => 'spe', 'Sp1g11550' => 'spa', 'Sp2g16710' => 'spa', 'Sp3g00430' => 'spa', 'Sp3g26780' => 'spa', 'Sp5g22900' => 'spa', 'Sp6g29530' => 'spa', 'TAR371G0794' => 'tar', 'TAR374G0164' => 'tar', 'TAR622G0165' => 'tar', 'TAR626G0929' => 'tar', 'TAR629G2155' => 'tar', 'THA.LOC104805282' => 'tha', 'THA.LOC104805363' => 'tha', 'THA.LOC104808968' => 'tha', 'THA.LOC104821093' => 'tha', 'THA.LOC104823953' => 'tha', 'THA.LOC104825562' => 'tha', 'THA.LOC104825665' => 'tha', 'Thecc.02G261400' => 'tca', 'Thecc.04G019200' => 'tca', 'Thecc.09G130400' => 'tca', 'Thhalv10004374m.g' => 'esa', 'Thhalv10007850m.g' => 'esa', 'Thhalv10013782m.g' => 'esa', 'Thhalv10018686m.g' => 'esa', 'Thhalv10020899m.g' => 'esa', 'Thhalv10022755m.g' => 'esa', 'TPR.G23851' => 'tpr', 'TPR.G26500' => 'tpr', 'TPR.G27267' => 'tpr', 'TPR.G32001' => 'tpr', 'TPR.G6251' => 'tpr', 'TPR.G8167' => 'tpr', 'TWI12G1330' => 'twi', 'TWI18G1239' => 'twi', 'TWI34G0979' => 'twi', 'TWI36G0670' => 'twi', 'TWI36G0707' => 'twi', 'TWI56G0233' => 'twi', 'TWI75G1809' => 'twi', 'unitig_21.g20874' => 'ugi', 'unitig_26.g10343' => 'ugi', 'unitig_46.g18392' => 'ugi', 'unitig_52.g17178' => 'ugi', 'unitig_8.g2934' => 'ugi', 'vmacro01122' => 'vma', 'vmacro05875' => 'vma', 'vmacro06147' => 'vma', 'vmacro16191' => 'vma', 'vmacro18293' => 'vma', 'VMungo0251G3707' => 'vmu', 'VMungo0464G1521' => 'vmu', 'VMungo1215G0205' => 'vmu', 'VMungo1383G2484' => 'vmu', 'Zm00001eb079610' => 'zma', 'Zm00001eb135990' => 'zma', 'Zm00001eb183710' => 'zma', 'Zm00001eb246020' => 'zma' ) $gf_id = 'HOM05D001124' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001124' ) $data_identifier = 'HOM05D001124' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 6, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 7, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 21, 'bol' => (int) 10, 'bra' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 6, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 9, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 21, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 8, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 10, 'lsa' => (int) 8, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 8, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 9, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb246020' $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' => 'HOM05D001124', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '548', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02520' => 'bna', 'A03p06630' => 'bna', 'A05p44460' => 'bna', 'A06p08710' => 'bna', 'A06p41090' => 'bna', 'A07p32320' => 'bna', 'A08p32520' => 'bna', 'A09p10360' => 'bna', 'A10p24080' => 'bna', 'Aa31LG11G15250' => 'aar', 'Aa31LG1G1800' => 'aar', 'Aa31LG2G5120' => 'aar', 'Aa31LG2G6070' => 'aar', 'Aa31LG5G10770' => 'aar', 'Aa31sc61G90' => 'aar', 'Actinidia01352' => 'ach', 'Actinidia05983' => 'ach', 'Actinidia08133' => 'ach', 'Actinidia15101' => 'ach', 'Actinidia26379' => 'ach', 'Actinidia35778' => 'ach', 'Actinidia36123' => 'ach', 'Actinidia37436' => 'ach', 'Actinidia38730' => 'ach', 'Ah.02g128210' => 'amhyb', 'Ah.03g132990' => 'amhyb', 'Ah.14g079410' => 'amhyb', 'AL1G24640' => 'aly', 'AL2G26680' => 'aly', 'AL3G10530' => 'aly', 'AL3G45230' => 'aly', 'AL5G15230' => 'aly', 'AL5G16960' => 'aly', 'AL6G25210' => 'aly', 'Aqoxy2G00441' => 'aox', 'Aqoxy3G01236' => 'aox', 'Aqoxy5G03746' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3RQ047' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C7GMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9C8JER' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MBL6KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YXCZ83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZANX40' => 'arhy', 'AT1G12990' => 'ath', 'AT1G67880' => 'ath', 'AT2G13290' => 'ath', 'AT3G01620' => 'ath', 'AT3G26445' => 'ath', 'AT3G27540' => 'ath', 'AT5G14480' => 'ath', 'ATR0824G026' => 'atr', 'ATR1098G019' => 'atr', 'Atru.chr11.2145' => 'acertr', 'Atru.chr2.3636' => 'acertr', 'Atru.chr2.3644' => 'acertr', 'Atru.chr6.2422' => 'acertr', 'Atru.chr7.1112' => 'acertr', 'AUR62005469' => 'cqu', 'AUR62011166' => 'cqu', 'AUR62013319' => 'cqu', 'AUR62024273' => 'cqu', 'AUR62028420' => 'cqu', 'AUR62041942' => 'cqu', 'BcaB01g04969' => 'bca', 'BcaB01g06371' => 'bca', 'BcaB02g11494' => 'bca', 'BcaB03g15382' => 'bca', 'BcaB08g36994' => 'bca', 'BcaC03g13477' => 'bca', 'BcaC03g13478' => 'bca', 'BcaC03g13480' => 'bca', 'BcaC03g13481' => 'bca', 'BcaC03g13486' => 'bca', 'BcaC04g19031' => 'bca', 'BcaC04g23085' => 'bca', 'BcaC05g25094' => 'bca', 'BcaC05g25096' => 'bca', 'BcaC05g25138' => 'bca', 'BcaC05g30416' => 'bca', 'BcaC05g30455' => 'bca', 'BcaC06g30979' => 'bca', 'BcaC06g33805' => 'bca', 'BcaC08g46021' => 'bca', 'BcaNung03154' => 'bca', 'BolC2t06623H' => 'bol', 'BolC2t06632H' => 'bol', 'BolC2t06635H' => 'bol', 'BolC2t06638H' => 'bol', 'BolC3t13266H' => 'bol', 'BolC5t29776H' => 'bol', 'BolC6t38912H' => 'bol', 'BolC7t44183H' => 'bol', 'BolC9t54123H' => 'bol', 'BolC9t59107H' => 'bol', 'BraA02t05221Z' => 'bra', 'BraA03t09996Z' => 'bra', 'BraA05t23210Z' => 'bra', 'BraA06t24068Z' => 'bra', 'BraA06t27032Z' => 'bra', 'BraA08t35176Z' => 'bra', 'BraA09t36680Z' => 'bra', 'BraA10t44471Z' => 'bra', 'C02p06760' => 'bna', 'C02p06890' => 'bna', 'C02p07010' => 'bna', 'C03p07660' => 'bna', 'C05p10300' => 'bna', 'C06p38150' => 'bna', 'C07p36650' => 'bna', 'C08p15770' => 'bna', 'C09p12300' => 'bna', 'C09p62700' => 'bna', 'C09p75040' => 'bna', 'CAN.G13.1' => 'can', 'CAN.G138.4' => 'can', 'CAN.G44.6' => 'can', 'CAN.G473.19' => 'can', 'CANSAT01G0835' => 'cansat', 'CANSAT11G0246' => 'cansat', 'CANSAT11G1766' => 'cansat', 'CANSAT64G1954' => 'cansat', 'CARHR013330' => 'chi', 'CARHR060530' => 'chi', 'CARHR075300' => 'chi', 'CARHR105120' => 'chi', 'CARHR148910' => 'chi', 'CARHR198830' => 'chi', 'Carub.0001s1275' => 'cru', 'Carub.0002s1437' => 'cru', 'Carub.0003s0044' => 'cru', 'Carub.0003s2787' => 'cru', 'Carub.0005s0597' => 'cru', 'Carub.0006s1266' => 'cru', 'Ca_06935_v3' => 'car', 'Ca_13559_v3' => 'car', 'Ca_16941_v3' => 'car', 'Ca_16960_v3' => 'car', 'Ca_17775_v3' => 'car', 'Ca_30464_v3' => 'car', 'Cc06_g08160' => 'ccan', 'Cc07_g01520' => 'ccan', 'Cc11_g15810' => 'ccan', 'CDE02G2840' => 'cde', 'CDE03G0093' => 'cde', 'CDE04G2127' => 'cde', 'CDE07G1857' => 'cde', 'CDE09G1246' => 'cde', 'Cfa003412' => 'cfa', 'Cfa007341' => 'cfa', 'Cfa009220' => 'cfa', 'Ciclev10008737m.g' => 'ccl', 'Ciclev10015565m.g' => 'ccl', 'Ciclev10031761m.g' => 'ccl', 'CiPaw.03G045300' => 'cil', 'CiPaw.03G247200' => 'cil', 'CiPaw.04G029500' => 'cil', 'CiPaw.04G174000' => 'cil', 'CiPaw.05G181200' => 'cil', 'CiPaw.06G067100' => 'cil', 'ClCG05G025800' => 'cla', 'ClCG06G011400' => 'cla', 'ClCG09G019360' => 'cla', 'COL.COLO4_04827' => 'col', 'COL.COLO4_29170' => 'col', 'COL.COLO4_35131' => 'col', 'COL.COLO4_35132' => 'col', 'Cpa.g.sc33.32' => 'cpa', 'Cpa.g.sc46.29' => 'cpa', 'Cpa.g.sc796.1' => 'cpa', 'CsaV3_1G030420' => 'csa', 'CsaV3_5G027050' => 'csa', 'CsaV3_5G031040' => 'csa', 'CsaV3_UNG023130' => 'csa', 'CSS0007726' => 'camsi', 'CSS0016433' => 'camsi', 'CSS0017656' => 'camsi', 'CSS0025364' => 'camsi', 'CSS0027582' => 'camsi', 'CSS0047288' => 'camsi', 'CSS0049950' => 'camsi', 'DCAR_003843' => 'dca', 'DCAR_007052' => 'dca', 'DCAR_020884' => 'dca', 'DCAR_021730' => 'dca', 'DCAR_024423' => 'dca', 'DCAR_026509' => 'dca', 'DCAR_031158' => 'dca', 'Dinv14728' => 'din', 'Dinv15219' => 'din', 'Dinv25728' => 'din', 'Dinv33428' => 'din', 'Dinv36489' => 'din', 'Dinv41486' => 'din', 'Duzib147G0469' => 'dzi', 'Duzib168G0060' => 'dzi', 'Duzib187G1215' => 'dzi', 'Duzib248G0692' => 'dzi', 'Duzib251G0767' => 'dzi', 'Duzib264G0446' => 'dzi', 'Duzib268G0691' => 'dzi', 'ECA232G4767' => 'eca', 'ECA233G2838' => 'eca', 'ECA234G0391' => 'eca', 'ECA234G0857' => 'eca', 'ECA236G1593' => 'eca', 'ECA238G0565' => 'eca', 'ECA246G1027' => 'eca', 'ECA246G3223' => 'eca', 'ECA246G3470' => 'eca', 'EL10Ac6g13829' => 'bvu', 'EL10Ac6g14093' => 'bvu', 'EL10Ac8g18707' => 'bvu', 'Eucgr.C01369' => 'egr', 'Eucgr.H02492' => 'egr', 'Eucgr.I01733' => 'egr', 'Eucgr.J02255' => 'egr', 'Eucgr.J02257' => 'egr', 'Eucgr.J02258' => 'egr', 'FAN02G1601' => 'fan', 'FAN03G1586' => 'fan', 'FAN03G2986' => 'fan', 'FAN05G4837' => 'fan', 'FAN06G0146' => 'fan', 'FAN07G0858' => 'fan', 'FAN09G3179' => 'fan', 'FAN10G0669' => 'fan', 'FAN12G2358' => 'fan', 'FAN14G4198' => 'fan', 'FAN14G5112' => 'fan', 'FAN17G0342' => 'fan', 'FAN19G0342' => 'fan', 'FAN19G0962' => 'fan', 'FAN19G1101' => 'fan', 'FAN19G1872' => 'fan', 'FAN22G0356' => 'fan', 'FAN23G0744' => 'fan', 'FAN23G1914' => 'fan', 'FAN26G0032' => 'fan', 'FAN28G0625' => 'fan', 'FvH4_1g02710' => 'fve', 'FvH4_1g02720' => 'fve', 'FvH4_4g25670' => 'fve', 'FvH4_6g51700' => 'fve', 'FvH4_7g20170' => 'fve', 'Glyma.05G175000' => 'gma', 'Glyma.08G132300' => 'gma', 'Glyma.11G243000' => 'gma', 'Glyma.13G158900' => 'gma', 'Glyma.17G112400' => 'gma', 'Glyma.18G014100' => 'gma', 'Glyma.19G003100' => 'gma', 'Glyma.19G056500' => 'gma', 'Gohir.A01G158900' => 'ghi', 'Gohir.A05G312600' => 'ghi', 'Gohir.A05G354900' => 'ghi', 'Gohir.A07G037200' => 'ghi', 'Gohir.A09G030000' => 'ghi', 'Gohir.A12G145200' => 'ghi', 'Gohir.D01G151500' => 'ghi', 'Gohir.D04G058300' => 'ghi', 'Gohir.D05G314100' => 'ghi', 'Gohir.D07G041400' => 'ghi', 'Gohir.D09G029700' => 'ghi', 'Gohir.D12G149700' => 'ghi', 'Gorai.001G043800' => 'gra', 'Gorai.002G187800' => 'gra', 'Gorai.006G034700' => 'gra', 'Gorai.008G161200' => 'gra', 'Gorai.009G335700' => 'gra', 'Gorai.012G065000' => 'gra', 'GSVIVG01000535001' => 'vvi', 'GSVIVG01015572001' => 'vvi', 'GSVIVG01032386001' => 'vvi', 'HanXRQChr05g0138531' => 'han', 'HanXRQChr06g0174391' => 'han', 'HanXRQChr07g0199021' => 'han', 'HanXRQChr08g0208211' => 'han', 'HanXRQChr09g0255471' => 'han', 'HanXRQChr10g0315791' => 'han', 'HanXRQChr12g0371991' => 'han', 'HanXRQChr15g0475251' => 'han', 'HanXRQChr17g0540001' => 'han', 'HanXRQChr17g0548631' => 'han', 'HanXRQChr17g0569561' => 'han', 'Haze_12256' => 'cav', 'Haze_14756' => 'cav', 'Haze_25528' => 'cav', 'Hma1.2p1_0079F.1_g041020' => 'hma', 'Hma1.2p1_0818F.1_g223260' => 'hma', 'Hma1.2p1_1747F.1_g300530' => 'hma', 'HPP92_004607' => 'vpl', 'HPP92_004608' => 'vpl', 'HPP92_006181' => 'vpl', 'HPP92_012192' => 'vpl', 'HPP92_015680' => 'vpl', 'HPP92_020249' => 'vpl', 'HPP92_021376' => 'vpl', 'HPP92_024275' => 'vpl', 'Hund06031' => 'sun', 'Hund25391' => 'sun', 'Lalb_Chr07g0185371' => 'lal', 'Lalb_Chr07g0185381' => 'lal', 'Lalb_Chr12g0204011' => 'lal', 'Lalb_Chr13g0301671' => 'lal', 'Lalb_Chr14g0362851' => 'lal', 'Lalb_Chr24g0403581' => 'lal', 'Lj1g0000233' => 'lja', 'Lj2g0018120' => 'lja', 'Lj3C621T0' => 'lonja', 'Lj3P1059T14' => 'lonja', 'Lj3P611T9' => 'lonja', 'Lj3P614T13' => 'lonja', 'Lj3P615T5' => 'lonja', 'Lj4g0012315' => 'lja', 'Lj4g0026182' => 'lja', 'Lj6P813T16' => 'lonja', 'Lj7C427T7' => 'lonja', 'Lj7C427T8' => 'lonja', 'Lj7P600T41' => 'lonja', 'Lju41C42G17' => 'lonja', 'Lsat_1_v5_gn_0_47300' => 'lsa', 'Lsat_1_v5_gn_2_91280' => 'lsa', 'Lsat_1_v5_gn_3_30561' => 'lsa', 'Lsat_1_v5_gn_4_184321' => 'lsa', 'Lsat_1_v5_gn_4_4041' => 'lsa', 'Lsat_1_v5_gn_5_92000' => 'lsa', 'Lsat_1_v5_gn_8_152940' => 'lsa', 'Lsat_1_v5_gn_8_62401' => 'lsa', 'Manes.06G055900' => 'mes', 'Manes.12G022200' => 'mes', 'Manes.13G023300' => 'mes', 'Manes.14G115000' => 'mes', 'Manes.15G151700' => 'mes', 'Manes.17G111300' => 'mes', 'Mapoly0226s0009' => 'mpo', 'MBI02_g25363_MAGBIO' => 'mbi', 'MBI06_g00027_MAGBIO' => 'mbi', 'MBI10_g13034_MAGBIO' => 'mbi', 'MD09G1023400' => 'mdo', 'MD13G1100100' => 'mdo', 'MD15G1169200' => 'mdo', 'MD16G1101100' => 'mdo', 'MD17G1022900' => 'mdo', 'Medtr3g096150' => 'mtr', 'Medtr4g115070' => 'mtr', 'Medtr7g033325' => 'mtr', 'Medtr8g089840' => 'mtr', 'MELO3C010319.2' => 'cme', 'MELO3C011944.2' => 'cme', 'MELO3C021589.2' => 'cme', 'Migut.E00207' => 'egut', 'Migut.H00067' => 'egut', 'Migut.K00433' => 'egut', 'Migut.K00606' => 'egut', 'Migut.K01410' => 'egut', 'MSTRG.13347' => 'ama', 'MSTRG.24045' => 'ama', 'MSTRG.2428' => 'ama', 'MSTRG.26410' => 'ama', 'MSTRG.3139' => 'ama', 'MSTRG.3286' => 'ama', 'MSTRG.563' => 'ama', 'MSTRG.7941' => 'ama', 'Nitab4.5_0000028g0060' => 'nta', 'Nitab4.5_0000065g0260' => 'nta', 'Nitab4.5_0000112g0060' => 'nta', 'Nitab4.5_0000489g0120' => 'nta', 'Nitab4.5_0001776g0050' => 'nta', 'Nitab4.5_0001854g0010' => 'nta', 'Nitab4.5_0001860g0020' => 'nta', 'Nitab4.5_0004352g0010' => 'nta', 'Nitab4.5_0008716g0020' => 'nta', 'Nitab4.5_0008922g0010' => 'nta', 'Nn3g16693' => 'nnu', 'Nn4g22596' => 'nnu', 'Nn7g37639' => 'nnu', 'Oeu001701.1' => 'oeu', 'Oeu018149.1' => 'oeu', 'Oeu026220.1' => 'oeu', 'Oeu038635.1' => 'oeu', 'Oeu049176.1' => 'oeu', 'Oeu056706.1' => 'oeu', 'Oeu056937.1' => 'oeu', 'Oeu057540.1' => 'oeu', 'Os02g0594900' => 'osa', 'Os02g0595100' => 'osa', 'Os04g0477500' => 'osa', 'Os12g0611900' => 'osa', 'Peaxi162Scf00076g00020' => 'pax', 'Peaxi162Scf00128g00217' => 'pax', 'Peaxi162Scf00129g01640' => 'pax', 'Peaxi162Scf00669g00007' => 'pax', 'Peaxi162Scf00700g00421' => 'pax', 'Peaxi162Scf00801g00038' => 'pax', 'Peaxi162Scf00891g00025' => 'pax', 'PGR083G0909' => 'pgr', 'PGR119G1005' => 'pgr', 'PGR142G2236' => 'pgr', 'PGR142G3388' => 'pgr', 'PGSC0003DMG400004514' => 'stu', 'PGSC0003DMG400012635' => 'stu', 'PGSC0003DMG400015730' => 'stu', 'PGSC0003DMG400018611' => 'stu', 'PGSC0003DMG400030897' => 'stu', 'Phvul.001G254800' => 'pvu', 'Phvul.002G260100' => 'pvu', 'Phvul.003G167600' => 'pvu', 'Phvul.004G005100' => 'pvu', 'Potri.001G343600' => 'ptr', 'Potri.006G066700' => 'ptr', 'Potri.008G186000' => 'ptr', 'Potri.010G046900' => 'ptr', 'Potri.018G127900' => 'ptr', 'Pp3c20_17750' => 'ppa', 'Pp3c24_4380' => 'ppa', 'Prupe.1G245800' => 'ppe', 'Prupe.3G293400' => 'ppe', 'Prupe.7G247400' => 'ppe', 'Psat0s145g0120' => 'psa', 'Psat0s595g0040' => 'psa', 'Psat0s595g0120' => 'psa', 'Psat3g175040' => 'psa', 'Psat7g058120' => 'psa', 'PSO017G0428' => 'pso', 'PSO063G7510' => 'pso', 'PSO067G0046' => 'pso', 'PSO478G1073' => 'pso', 'PSO675G3677' => 'pso', 'PSO675G6558' => 'pso', 'PSO675G7520' => 'pso', 'PSO675G8959' => 'pso', 'QL02p074089' => 'qlo', 'QL02p089614' => 'qlo', 'QL03p057736' => 'qlo', 'RcHm_v2.0_Chr1g0364131' => 'rch', 'RcHm_v2.0_Chr2g0087801' => 'rch', 'RcHm_v2.0_Chr2g0087821' => 'rch', 'RcHm_v2.0_Chr2g0173231' => 'rch', 'RcHm_v2.0_Chr4g0433111' => 'rch', 'Rhsim03G0250300' => 'rsi', 'Rhsim08G0048400' => 'rsi', 'Rhsim10G0014800' => 'rsi', 'Rhsim12G0040100' => 'rsi', 'Rhsim12G0109700' => 'rsi', 'Sabra06G0049600' => 'sbr', 'Sabra08G0141000' => 'sbr', 'Sabra10G0021400' => 'sbr', 'Sabra16G0222900' => 'sbr', 'Sabra18G0108600' => 'sbr', 'SalBow1G0433' => 'sbo', 'SalBow1G2038' => 'sbo', 'SalBow1G5003' => 'sbo', 'SalBow7G1197' => 'sbo', 'SalBow8G3506' => 'sbo', 'Sc03g0007300' => 'sci', 'Sc11g0000950' => 'sci', 'Sc14g0008750' => 'sci', 'Sc18g0000420' => 'sci', 'Sed0006754' => 'sed', 'Sed0008741' => 'sed', 'Sed0017172' => 'sed', 'Sed0018925' => 'sed', 'Sed0023326' => 'sed', 'Sed0025909' => 'sed', 'SEGI_05333' => 'sgi', 'SEGI_10362' => 'sgi', 'SEGI_13380' => 'sgi', 'SEGI_24306' => 'sgi', 'SEGI_29077' => 'sgi', 'SEGI_29095' => 'sgi', 'SEGI_36534' => 'sgi', 'SEGI_37506' => 'sgi', 'SEGI_38321' => 'sgi', 'SGA_v2.0_scaffold307G48031' => 'sas', 'SGA_v2.0_scaffold47G17507' => 'sas', 'SGA_v2.0_scaffold63G21736' => 'sas', 'SGA_v2.0_scaffold87G27070' => 'sas', 'SHI17794' => 'shi', 'SHI28851' => 'shi', 'SMO165G0155' => 'smo', 'SMO340G0217' => 'smo', 'SMO367G1210' => 'smo', 'Solyc02g093430.3' => 'sly', 'Solyc05g013580.4' => 'sly', 'Solyc07g008030.3' => 'sly', 'Solyc12g035470.2' => 'sly', 'Sopen02g038020' => 'spe', 'Sopen05g008490' => 'spe', 'Sopen07g003910' => 'spe', 'Sopen12g015240' => 'spe', 'Sp1g11550' => 'spa', 'Sp2g16710' => 'spa', 'Sp3g00430' => 'spa', 'Sp3g26780' => 'spa', 'Sp5g22900' => 'spa', 'Sp6g29530' => 'spa', 'TAR371G0794' => 'tar', 'TAR374G0164' => 'tar', 'TAR622G0165' => 'tar', 'TAR626G0929' => 'tar', 'TAR629G2155' => 'tar', 'THA.LOC104805282' => 'tha', 'THA.LOC104805363' => 'tha', 'THA.LOC104808968' => 'tha', 'THA.LOC104821093' => 'tha', 'THA.LOC104823953' => 'tha', 'THA.LOC104825562' => 'tha', 'THA.LOC104825665' => 'tha', 'Thecc.02G261400' => 'tca', 'Thecc.04G019200' => 'tca', 'Thecc.09G130400' => 'tca', 'Thhalv10004374m.g' => 'esa', 'Thhalv10007850m.g' => 'esa', 'Thhalv10013782m.g' => 'esa', 'Thhalv10018686m.g' => 'esa', 'Thhalv10020899m.g' => 'esa', 'Thhalv10022755m.g' => 'esa', 'TPR.G23851' => 'tpr', 'TPR.G26500' => 'tpr', 'TPR.G27267' => 'tpr', 'TPR.G32001' => 'tpr', 'TPR.G6251' => 'tpr', 'TPR.G8167' => 'tpr', 'TWI12G1330' => 'twi', 'TWI18G1239' => 'twi', 'TWI34G0979' => 'twi', 'TWI36G0670' => 'twi', 'TWI36G0707' => 'twi', 'TWI56G0233' => 'twi', 'TWI75G1809' => 'twi', 'unitig_21.g20874' => 'ugi', 'unitig_26.g10343' => 'ugi', 'unitig_46.g18392' => 'ugi', 'unitig_52.g17178' => 'ugi', 'unitig_8.g2934' => 'ugi', 'vmacro01122' => 'vma', 'vmacro05875' => 'vma', 'vmacro06147' => 'vma', 'vmacro16191' => 'vma', 'vmacro18293' => 'vma', 'VMungo0251G3707' => 'vmu', 'VMungo0464G1521' => 'vmu', 'VMungo1215G0205' => 'vmu', 'VMungo1383G2484' => 'vmu', 'Zm00001eb079610' => 'zma', 'Zm00001eb135990' => 'zma', 'Zm00001eb183710' => 'zma', 'Zm00001eb246020' => 'zma' ), 'gf_id' => 'HOM05D001124', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001124' ), 'data_identifier' => 'HOM05D001124', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001124', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '548', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02520' => 'bna', 'A03p06630' => 'bna', 'A05p44460' => 'bna', 'A06p08710' => 'bna', 'A06p41090' => 'bna', 'A07p32320' => 'bna', 'A08p32520' => 'bna', 'A09p10360' => 'bna', 'A10p24080' => 'bna', 'Aa31LG11G15250' => 'aar', 'Aa31LG1G1800' => 'aar', 'Aa31LG2G5120' => 'aar', 'Aa31LG2G6070' => 'aar', 'Aa31LG5G10770' => 'aar', 'Aa31sc61G90' => 'aar', 'Actinidia01352' => 'ach', 'Actinidia05983' => 'ach', 'Actinidia08133' => 'ach', 'Actinidia15101' => 'ach', 'Actinidia26379' => 'ach', 'Actinidia35778' => 'ach', 'Actinidia36123' => 'ach', 'Actinidia37436' => 'ach', 'Actinidia38730' => 'ach', 'Ah.02g128210' => 'amhyb', 'Ah.03g132990' => 'amhyb', 'Ah.14g079410' => 'amhyb', 'AL1G24640' => 'aly', 'AL2G26680' => 'aly', 'AL3G10530' => 'aly', 'AL3G45230' => 'aly', 'AL5G15230' => 'aly', 'AL5G16960' => 'aly', 'AL6G25210' => 'aly', 'Aqoxy2G00441' => 'aox', 'Aqoxy3G01236' => 'aox', 'Aqoxy5G03746' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3RQ047' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C7GMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9C8JER' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MBL6KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YXCZ83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZANX40' => 'arhy', 'AT1G12990' => 'ath', 'AT1G67880' => 'ath', 'AT2G13290' => 'ath', 'AT3G01620' => 'ath', 'AT3G26445' => 'ath', 'AT3G27540' => 'ath', 'AT5G14480' => 'ath', 'ATR0824G026' => 'atr', 'ATR1098G019' => 'atr', 'Atru.chr11.2145' => 'acertr', 'Atru.chr2.3636' => 'acertr', 'Atru.chr2.3644' => 'acertr', 'Atru.chr6.2422' => 'acertr', 'Atru.chr7.1112' => 'acertr', 'AUR62005469' => 'cqu', 'AUR62011166' => 'cqu', 'AUR62013319' => 'cqu', 'AUR62024273' => 'cqu', 'AUR62028420' => 'cqu', 'AUR62041942' => 'cqu', 'BcaB01g04969' => 'bca', 'BcaB01g06371' => 'bca', 'BcaB02g11494' => 'bca', 'BcaB03g15382' => 'bca', 'BcaB08g36994' => 'bca', 'BcaC03g13477' => 'bca', 'BcaC03g13478' => 'bca', 'BcaC03g13480' => 'bca', 'BcaC03g13481' => 'bca', 'BcaC03g13486' => 'bca', 'BcaC04g19031' => 'bca', 'BcaC04g23085' => 'bca', 'BcaC05g25094' => 'bca', 'BcaC05g25096' => 'bca', 'BcaC05g25138' => 'bca', 'BcaC05g30416' => 'bca', 'BcaC05g30455' => 'bca', 'BcaC06g30979' => 'bca', 'BcaC06g33805' => 'bca', 'BcaC08g46021' => 'bca', 'BcaNung03154' => 'bca', 'BolC2t06623H' => 'bol', 'BolC2t06632H' => 'bol', 'BolC2t06635H' => 'bol', 'BolC2t06638H' => 'bol', 'BolC3t13266H' => 'bol', 'BolC5t29776H' => 'bol', 'BolC6t38912H' => 'bol', 'BolC7t44183H' => 'bol', 'BolC9t54123H' => 'bol', 'BolC9t59107H' => 'bol', 'BraA02t05221Z' => 'bra', 'BraA03t09996Z' => 'bra', 'BraA05t23210Z' => 'bra', 'BraA06t24068Z' => 'bra', 'BraA06t27032Z' => 'bra', 'BraA08t35176Z' => 'bra', 'BraA09t36680Z' => 'bra', 'BraA10t44471Z' => 'bra', 'C02p06760' => 'bna', 'C02p06890' => 'bna', 'C02p07010' => 'bna', 'C03p07660' => 'bna', 'C05p10300' => 'bna', 'C06p38150' => 'bna', 'C07p36650' => 'bna', 'C08p15770' => 'bna', 'C09p12300' => 'bna', 'C09p62700' => 'bna', 'C09p75040' => 'bna', 'CAN.G13.1' => 'can', 'CAN.G138.4' => 'can', 'CAN.G44.6' => 'can', 'CAN.G473.19' => 'can', 'CANSAT01G0835' => 'cansat', 'CANSAT11G0246' => 'cansat', 'CANSAT11G1766' => 'cansat', 'CANSAT64G1954' => 'cansat', 'CARHR013330' => 'chi', 'CARHR060530' => 'chi', 'CARHR075300' => 'chi', 'CARHR105120' => 'chi', 'CARHR148910' => 'chi', 'CARHR198830' => 'chi', 'Carub.0001s1275' => 'cru', 'Carub.0002s1437' => 'cru', 'Carub.0003s0044' => 'cru', 'Carub.0003s2787' => 'cru', 'Carub.0005s0597' => 'cru', 'Carub.0006s1266' => 'cru', 'Ca_06935_v3' => 'car', 'Ca_13559_v3' => 'car', 'Ca_16941_v3' => 'car', 'Ca_16960_v3' => 'car', 'Ca_17775_v3' => 'car', 'Ca_30464_v3' => 'car', 'Cc06_g08160' => 'ccan', 'Cc07_g01520' => 'ccan', 'Cc11_g15810' => 'ccan', 'CDE02G2840' => 'cde', 'CDE03G0093' => 'cde', 'CDE04G2127' => 'cde', 'CDE07G1857' => 'cde', 'CDE09G1246' => 'cde', 'Cfa003412' => 'cfa', 'Cfa007341' => 'cfa', 'Cfa009220' => 'cfa', 'Ciclev10008737m.g' => 'ccl', 'Ciclev10015565m.g' => 'ccl', 'Ciclev10031761m.g' => 'ccl', 'CiPaw.03G045300' => 'cil', 'CiPaw.03G247200' => 'cil', 'CiPaw.04G029500' => 'cil', 'CiPaw.04G174000' => 'cil', 'CiPaw.05G181200' => 'cil', 'CiPaw.06G067100' => 'cil', 'ClCG05G025800' => 'cla', 'ClCG06G011400' => 'cla', 'ClCG09G019360' => 'cla', 'COL.COLO4_04827' => 'col', 'COL.COLO4_29170' => 'col', 'COL.COLO4_35131' => 'col', 'COL.COLO4_35132' => 'col', 'Cpa.g.sc33.32' => 'cpa', 'Cpa.g.sc46.29' => 'cpa', 'Cpa.g.sc796.1' => 'cpa', 'CsaV3_1G030420' => 'csa', 'CsaV3_5G027050' => 'csa', 'CsaV3_5G031040' => 'csa', 'CsaV3_UNG023130' => 'csa', 'CSS0007726' => 'camsi', 'CSS0016433' => 'camsi', 'CSS0017656' => 'camsi', 'CSS0025364' => 'camsi', 'CSS0027582' => 'camsi', 'CSS0047288' => 'camsi', 'CSS0049950' => 'camsi', 'DCAR_003843' => 'dca', 'DCAR_007052' => 'dca', 'DCAR_020884' => 'dca', 'DCAR_021730' => 'dca', 'DCAR_024423' => 'dca', 'DCAR_026509' => 'dca', 'DCAR_031158' => 'dca', 'Dinv14728' => 'din', 'Dinv15219' => 'din', 'Dinv25728' => 'din', 'Dinv33428' => 'din', 'Dinv36489' => 'din', 'Dinv41486' => 'din', 'Duzib147G0469' => 'dzi', 'Duzib168G0060' => 'dzi', 'Duzib187G1215' => 'dzi', 'Duzib248G0692' => 'dzi', 'Duzib251G0767' => 'dzi', 'Duzib264G0446' => 'dzi', 'Duzib268G0691' => 'dzi', 'ECA232G4767' => 'eca', 'ECA233G2838' => 'eca', 'ECA234G0391' => 'eca', 'ECA234G0857' => 'eca', 'ECA236G1593' => 'eca', 'ECA238G0565' => 'eca', 'ECA246G1027' => 'eca', 'ECA246G3223' => 'eca', 'ECA246G3470' => 'eca', 'EL10Ac6g13829' => 'bvu', 'EL10Ac6g14093' => 'bvu', 'EL10Ac8g18707' => 'bvu', 'Eucgr.C01369' => 'egr', 'Eucgr.H02492' => 'egr', 'Eucgr.I01733' => 'egr', 'Eucgr.J02255' => 'egr', 'Eucgr.J02257' => 'egr', 'Eucgr.J02258' => 'egr', 'FAN02G1601' => 'fan', 'FAN03G1586' => 'fan', 'FAN03G2986' => 'fan', 'FAN05G4837' => 'fan', 'FAN06G0146' => 'fan', 'FAN07G0858' => 'fan', 'FAN09G3179' => 'fan', 'FAN10G0669' => 'fan', 'FAN12G2358' => 'fan', 'FAN14G4198' => 'fan', 'FAN14G5112' => 'fan', 'FAN17G0342' => 'fan', 'FAN19G0342' => 'fan', 'FAN19G0962' => 'fan', 'FAN19G1101' => 'fan', 'FAN19G1872' => 'fan', 'FAN22G0356' => 'fan', 'FAN23G0744' => 'fan', 'FAN23G1914' => 'fan', 'FAN26G0032' => 'fan', 'FAN28G0625' => 'fan', 'FvH4_1g02710' => 'fve', 'FvH4_1g02720' => 'fve', 'FvH4_4g25670' => 'fve', 'FvH4_6g51700' => 'fve', 'FvH4_7g20170' => 'fve', 'Glyma.05G175000' => 'gma', 'Glyma.08G132300' => 'gma', 'Glyma.11G243000' => 'gma', 'Glyma.13G158900' => 'gma', 'Glyma.17G112400' => 'gma', 'Glyma.18G014100' => 'gma', 'Glyma.19G003100' => 'gma', 'Glyma.19G056500' => 'gma', 'Gohir.A01G158900' => 'ghi', 'Gohir.A05G312600' => 'ghi', 'Gohir.A05G354900' => 'ghi', 'Gohir.A07G037200' => 'ghi', 'Gohir.A09G030000' => 'ghi', 'Gohir.A12G145200' => 'ghi', 'Gohir.D01G151500' => 'ghi', 'Gohir.D04G058300' => 'ghi', 'Gohir.D05G314100' => 'ghi', 'Gohir.D07G041400' => 'ghi', 'Gohir.D09G029700' => 'ghi', 'Gohir.D12G149700' => 'ghi', 'Gorai.001G043800' => 'gra', 'Gorai.002G187800' => 'gra', 'Gorai.006G034700' => 'gra', 'Gorai.008G161200' => 'gra', 'Gorai.009G335700' => 'gra', 'Gorai.012G065000' => 'gra', 'GSVIVG01000535001' => 'vvi', 'GSVIVG01015572001' => 'vvi', 'GSVIVG01032386001' => 'vvi', 'HanXRQChr05g0138531' => 'han', 'HanXRQChr06g0174391' => 'han', 'HanXRQChr07g0199021' => 'han', 'HanXRQChr08g0208211' => 'han', 'HanXRQChr09g0255471' => 'han', 'HanXRQChr10g0315791' => 'han', 'HanXRQChr12g0371991' => 'han', 'HanXRQChr15g0475251' => 'han', 'HanXRQChr17g0540001' => 'han', 'HanXRQChr17g0548631' => 'han', 'HanXRQChr17g0569561' => 'han', 'Haze_12256' => 'cav', 'Haze_14756' => 'cav', 'Haze_25528' => 'cav', 'Hma1.2p1_0079F.1_g041020' => 'hma', 'Hma1.2p1_0818F.1_g223260' => 'hma', 'Hma1.2p1_1747F.1_g300530' => 'hma', 'HPP92_004607' => 'vpl', 'HPP92_004608' => 'vpl', 'HPP92_006181' => 'vpl', 'HPP92_012192' => 'vpl', 'HPP92_015680' => 'vpl', 'HPP92_020249' => 'vpl', 'HPP92_021376' => 'vpl', 'HPP92_024275' => 'vpl', 'Hund06031' => 'sun', 'Hund25391' => 'sun', 'Lalb_Chr07g0185371' => 'lal', 'Lalb_Chr07g0185381' => 'lal', 'Lalb_Chr12g0204011' => 'lal', 'Lalb_Chr13g0301671' => 'lal', 'Lalb_Chr14g0362851' => 'lal', 'Lalb_Chr24g0403581' => 'lal', 'Lj1g0000233' => 'lja', 'Lj2g0018120' => 'lja', 'Lj3C621T0' => 'lonja', 'Lj3P1059T14' => 'lonja', 'Lj3P611T9' => 'lonja', 'Lj3P614T13' => 'lonja', 'Lj3P615T5' => 'lonja', 'Lj4g0012315' => 'lja', 'Lj4g0026182' => 'lja', 'Lj6P813T16' => 'lonja', 'Lj7C427T7' => 'lonja', 'Lj7C427T8' => 'lonja', 'Lj7P600T41' => 'lonja', 'Lju41C42G17' => 'lonja', 'Lsat_1_v5_gn_0_47300' => 'lsa', 'Lsat_1_v5_gn_2_91280' => 'lsa', 'Lsat_1_v5_gn_3_30561' => 'lsa', 'Lsat_1_v5_gn_4_184321' => 'lsa', 'Lsat_1_v5_gn_4_4041' => 'lsa', 'Lsat_1_v5_gn_5_92000' => 'lsa', 'Lsat_1_v5_gn_8_152940' => 'lsa', 'Lsat_1_v5_gn_8_62401' => 'lsa', 'Manes.06G055900' => 'mes', 'Manes.12G022200' => 'mes', 'Manes.13G023300' => 'mes', 'Manes.14G115000' => 'mes', 'Manes.15G151700' => 'mes', 'Manes.17G111300' => 'mes', 'Mapoly0226s0009' => 'mpo', 'MBI02_g25363_MAGBIO' => 'mbi', 'MBI06_g00027_MAGBIO' => 'mbi', 'MBI10_g13034_MAGBIO' => 'mbi', 'MD09G1023400' => 'mdo', 'MD13G1100100' => 'mdo', 'MD15G1169200' => 'mdo', 'MD16G1101100' => 'mdo', 'MD17G1022900' => 'mdo', 'Medtr3g096150' => 'mtr', 'Medtr4g115070' => 'mtr', 'Medtr7g033325' => 'mtr', 'Medtr8g089840' => 'mtr', 'MELO3C010319.2' => 'cme', 'MELO3C011944.2' => 'cme', 'MELO3C021589.2' => 'cme', 'Migut.E00207' => 'egut', 'Migut.H00067' => 'egut', 'Migut.K00433' => 'egut', 'Migut.K00606' => 'egut', 'Migut.K01410' => 'egut', 'MSTRG.13347' => 'ama', 'MSTRG.24045' => 'ama', 'MSTRG.2428' => 'ama', 'MSTRG.26410' => 'ama', 'MSTRG.3139' => 'ama', 'MSTRG.3286' => 'ama', 'MSTRG.563' => 'ama', 'MSTRG.7941' => 'ama', 'Nitab4.5_0000028g0060' => 'nta', 'Nitab4.5_0000065g0260' => 'nta', 'Nitab4.5_0000112g0060' => 'nta', 'Nitab4.5_0000489g0120' => 'nta', 'Nitab4.5_0001776g0050' => 'nta', 'Nitab4.5_0001854g0010' => 'nta', 'Nitab4.5_0001860g0020' => 'nta', 'Nitab4.5_0004352g0010' => 'nta', 'Nitab4.5_0008716g0020' => 'nta', 'Nitab4.5_0008922g0010' => 'nta', 'Nn3g16693' => 'nnu', 'Nn4g22596' => 'nnu', 'Nn7g37639' => 'nnu', 'Oeu001701.1' => 'oeu', 'Oeu018149.1' => 'oeu', 'Oeu026220.1' => 'oeu', 'Oeu038635.1' => 'oeu', 'Oeu049176.1' => 'oeu', 'Oeu056706.1' => 'oeu', 'Oeu056937.1' => 'oeu', 'Oeu057540.1' => 'oeu', 'Os02g0594900' => 'osa', 'Os02g0595100' => 'osa', 'Os04g0477500' => 'osa', 'Os12g0611900' => 'osa', 'Peaxi162Scf00076g00020' => 'pax', 'Peaxi162Scf00128g00217' => 'pax', 'Peaxi162Scf00129g01640' => 'pax', 'Peaxi162Scf00669g00007' => 'pax', 'Peaxi162Scf00700g00421' => 'pax', 'Peaxi162Scf00801g00038' => 'pax', 'Peaxi162Scf00891g00025' => 'pax', 'PGR083G0909' => 'pgr', 'PGR119G1005' => 'pgr', 'PGR142G2236' => 'pgr', 'PGR142G3388' => 'pgr', 'PGSC0003DMG400004514' => 'stu', 'PGSC0003DMG400012635' => 'stu', 'PGSC0003DMG400015730' => 'stu', 'PGSC0003DMG400018611' => 'stu', 'PGSC0003DMG400030897' => 'stu', 'Phvul.001G254800' => 'pvu', 'Phvul.002G260100' => 'pvu', 'Phvul.003G167600' => 'pvu', 'Phvul.004G005100' => 'pvu', 'Potri.001G343600' => 'ptr', 'Potri.006G066700' => 'ptr', 'Potri.008G186000' => 'ptr', 'Potri.010G046900' => 'ptr', 'Potri.018G127900' => 'ptr', 'Pp3c20_17750' => 'ppa', 'Pp3c24_4380' => 'ppa', 'Prupe.1G245800' => 'ppe', 'Prupe.3G293400' => 'ppe', 'Prupe.7G247400' => 'ppe', 'Psat0s145g0120' => 'psa', 'Psat0s595g0040' => 'psa', 'Psat0s595g0120' => 'psa', 'Psat3g175040' => 'psa', 'Psat7g058120' => 'psa', 'PSO017G0428' => 'pso', 'PSO063G7510' => 'pso', 'PSO067G0046' => 'pso', 'PSO478G1073' => 'pso', 'PSO675G3677' => 'pso', 'PSO675G6558' => 'pso', 'PSO675G7520' => 'pso', 'PSO675G8959' => 'pso', 'QL02p074089' => 'qlo', 'QL02p089614' => 'qlo', 'QL03p057736' => 'qlo', 'RcHm_v2.0_Chr1g0364131' => 'rch', 'RcHm_v2.0_Chr2g0087801' => 'rch', 'RcHm_v2.0_Chr2g0087821' => 'rch', 'RcHm_v2.0_Chr2g0173231' => 'rch', 'RcHm_v2.0_Chr4g0433111' => 'rch', 'Rhsim03G0250300' => 'rsi', 'Rhsim08G0048400' => 'rsi', 'Rhsim10G0014800' => 'rsi', 'Rhsim12G0040100' => 'rsi', 'Rhsim12G0109700' => 'rsi', 'Sabra06G0049600' => 'sbr', 'Sabra08G0141000' => 'sbr', 'Sabra10G0021400' => 'sbr', 'Sabra16G0222900' => 'sbr', 'Sabra18G0108600' => 'sbr', 'SalBow1G0433' => 'sbo', 'SalBow1G2038' => 'sbo', 'SalBow1G5003' => 'sbo', 'SalBow7G1197' => 'sbo', 'SalBow8G3506' => 'sbo', 'Sc03g0007300' => 'sci', 'Sc11g0000950' => 'sci', 'Sc14g0008750' => 'sci', 'Sc18g0000420' => 'sci', 'Sed0006754' => 'sed', 'Sed0008741' => 'sed', 'Sed0017172' => 'sed', 'Sed0018925' => 'sed', 'Sed0023326' => 'sed', 'Sed0025909' => 'sed', 'SEGI_05333' => 'sgi', 'SEGI_10362' => 'sgi', 'SEGI_13380' => 'sgi', 'SEGI_24306' => 'sgi', 'SEGI_29077' => 'sgi', 'SEGI_29095' => 'sgi', 'SEGI_36534' => 'sgi', 'SEGI_37506' => 'sgi', 'SEGI_38321' => 'sgi', 'SGA_v2.0_scaffold307G48031' => 'sas', 'SGA_v2.0_scaffold47G17507' => 'sas', 'SGA_v2.0_scaffold63G21736' => 'sas', 'SGA_v2.0_scaffold87G27070' => 'sas', 'SHI17794' => 'shi', 'SHI28851' => 'shi', 'SMO165G0155' => 'smo', 'SMO340G0217' => 'smo', 'SMO367G1210' => 'smo', 'Solyc02g093430.3' => 'sly', 'Solyc05g013580.4' => 'sly', 'Solyc07g008030.3' => 'sly', 'Solyc12g035470.2' => 'sly', 'Sopen02g038020' => 'spe', 'Sopen05g008490' => 'spe', 'Sopen07g003910' => 'spe', 'Sopen12g015240' => 'spe', 'Sp1g11550' => 'spa', 'Sp2g16710' => 'spa', 'Sp3g00430' => 'spa', 'Sp3g26780' => 'spa', 'Sp5g22900' => 'spa', 'Sp6g29530' => 'spa', 'TAR371G0794' => 'tar', 'TAR374G0164' => 'tar', 'TAR622G0165' => 'tar', 'TAR626G0929' => 'tar', 'TAR629G2155' => 'tar', 'THA.LOC104805282' => 'tha', 'THA.LOC104805363' => 'tha', 'THA.LOC104808968' => 'tha', 'THA.LOC104821093' => 'tha', 'THA.LOC104823953' => 'tha', 'THA.LOC104825562' => 'tha', 'THA.LOC104825665' => 'tha', 'Thecc.02G261400' => 'tca', 'Thecc.04G019200' => 'tca', 'Thecc.09G130400' => 'tca', 'Thhalv10004374m.g' => 'esa', 'Thhalv10007850m.g' => 'esa', 'Thhalv10013782m.g' => 'esa', 'Thhalv10018686m.g' => 'esa', 'Thhalv10020899m.g' => 'esa', 'Thhalv10022755m.g' => 'esa', 'TPR.G23851' => 'tpr', 'TPR.G26500' => 'tpr', 'TPR.G27267' => 'tpr', 'TPR.G32001' => 'tpr', 'TPR.G6251' => 'tpr', 'TPR.G8167' => 'tpr', 'TWI12G1330' => 'twi', 'TWI18G1239' => 'twi', 'TWI34G0979' => 'twi', 'TWI36G0670' => 'twi', 'TWI36G0707' => 'twi', 'TWI56G0233' => 'twi', 'TWI75G1809' => 'twi', 'unitig_21.g20874' => 'ugi', 'unitig_26.g10343' => 'ugi', 'unitig_46.g18392' => 'ugi', 'unitig_52.g17178' => 'ugi', 'unitig_8.g2934' => 'ugi', 'vmacro01122' => 'vma', 'vmacro05875' => 'vma', 'vmacro06147' => 'vma', 'vmacro16191' => 'vma', 'vmacro18293' => 'vma', 'VMungo0251G3707' => 'vmu', 'VMungo0464G1521' => 'vmu', 'VMungo1215G0205' => 'vmu', 'VMungo1383G2484' => 'vmu', 'Zm00001eb079610' => 'zma', 'Zm00001eb135990' => 'zma', 'Zm00001eb183710' => 'zma', 'Zm00001eb246020' => 'zma' ) $gf_id = 'HOM05D001124' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001124' ) $data_identifier = 'HOM05D001124' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 6, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 7, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 21, 'bol' => (int) 10, 'bra' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 6, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 9, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 21, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 8, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 10, 'lsa' => (int) 8, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 8, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 9, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb246020' $species_info = array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ) $local_species = 'mbi' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001124', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '548', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02520' => 'bna', 'A03p06630' => 'bna', 'A05p44460' => 'bna', 'A06p08710' => 'bna', 'A06p41090' => 'bna', 'A07p32320' => 'bna', 'A08p32520' => 'bna', 'A09p10360' => 'bna', 'A10p24080' => 'bna', 'Aa31LG11G15250' => 'aar', 'Aa31LG1G1800' => 'aar', 'Aa31LG2G5120' => 'aar', 'Aa31LG2G6070' => 'aar', 'Aa31LG5G10770' => 'aar', 'Aa31sc61G90' => 'aar', 'Actinidia01352' => 'ach', 'Actinidia05983' => 'ach', 'Actinidia08133' => 'ach', 'Actinidia15101' => 'ach', 'Actinidia26379' => 'ach', 'Actinidia35778' => 'ach', 'Actinidia36123' => 'ach', 'Actinidia37436' => 'ach', 'Actinidia38730' => 'ach', 'Ah.02g128210' => 'amhyb', 'Ah.03g132990' => 'amhyb', 'Ah.14g079410' => 'amhyb', 'AL1G24640' => 'aly', 'AL2G26680' => 'aly', 'AL3G10530' => 'aly', 'AL3G45230' => 'aly', 'AL5G15230' => 'aly', 'AL5G16960' => 'aly', 'AL6G25210' => 'aly', 'Aqoxy2G00441' => 'aox', 'Aqoxy3G01236' => 'aox', 'Aqoxy5G03746' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3RQ047' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C7GMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9C8JER' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MBL6KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YXCZ83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZANX40' => 'arhy', 'AT1G12990' => 'ath', 'AT1G67880' => 'ath', 'AT2G13290' => 'ath', 'AT3G01620' => 'ath', 'AT3G26445' => 'ath', 'AT3G27540' => 'ath', 'AT5G14480' => 'ath', 'ATR0824G026' => 'atr', 'ATR1098G019' => 'atr', 'Atru.chr11.2145' => 'acertr', 'Atru.chr2.3636' => 'acertr', 'Atru.chr2.3644' => 'acertr', 'Atru.chr6.2422' => 'acertr', 'Atru.chr7.1112' => 'acertr', 'AUR62005469' => 'cqu', 'AUR62011166' => 'cqu', 'AUR62013319' => 'cqu', 'AUR62024273' => 'cqu', 'AUR62028420' => 'cqu', 'AUR62041942' => 'cqu', 'BcaB01g04969' => 'bca', 'BcaB01g06371' => 'bca', 'BcaB02g11494' => 'bca', 'BcaB03g15382' => 'bca', 'BcaB08g36994' => 'bca', 'BcaC03g13477' => 'bca', 'BcaC03g13478' => 'bca', 'BcaC03g13480' => 'bca', 'BcaC03g13481' => 'bca', 'BcaC03g13486' => 'bca', 'BcaC04g19031' => 'bca', 'BcaC04g23085' => 'bca', 'BcaC05g25094' => 'bca', 'BcaC05g25096' => 'bca', 'BcaC05g25138' => 'bca', 'BcaC05g30416' => 'bca', 'BcaC05g30455' => 'bca', 'BcaC06g30979' => 'bca', 'BcaC06g33805' => 'bca', 'BcaC08g46021' => 'bca', 'BcaNung03154' => 'bca', 'BolC2t06623H' => 'bol', 'BolC2t06632H' => 'bol', 'BolC2t06635H' => 'bol', 'BolC2t06638H' => 'bol', 'BolC3t13266H' => 'bol', 'BolC5t29776H' => 'bol', 'BolC6t38912H' => 'bol', 'BolC7t44183H' => 'bol', 'BolC9t54123H' => 'bol', 'BolC9t59107H' => 'bol', 'BraA02t05221Z' => 'bra', 'BraA03t09996Z' => 'bra', 'BraA05t23210Z' => 'bra', 'BraA06t24068Z' => 'bra', 'BraA06t27032Z' => 'bra', 'BraA08t35176Z' => 'bra', 'BraA09t36680Z' => 'bra', 'BraA10t44471Z' => 'bra', 'C02p06760' => 'bna', 'C02p06890' => 'bna', 'C02p07010' => 'bna', 'C03p07660' => 'bna', 'C05p10300' => 'bna', 'C06p38150' => 'bna', 'C07p36650' => 'bna', 'C08p15770' => 'bna', 'C09p12300' => 'bna', 'C09p62700' => 'bna', 'C09p75040' => 'bna', 'CAN.G13.1' => 'can', 'CAN.G138.4' => 'can', 'CAN.G44.6' => 'can', 'CAN.G473.19' => 'can', 'CANSAT01G0835' => 'cansat', 'CANSAT11G0246' => 'cansat', 'CANSAT11G1766' => 'cansat', 'CANSAT64G1954' => 'cansat', 'CARHR013330' => 'chi', 'CARHR060530' => 'chi', 'CARHR075300' => 'chi', 'CARHR105120' => 'chi', 'CARHR148910' => 'chi', 'CARHR198830' => 'chi', 'Carub.0001s1275' => 'cru', 'Carub.0002s1437' => 'cru', 'Carub.0003s0044' => 'cru', 'Carub.0003s2787' => 'cru', 'Carub.0005s0597' => 'cru', 'Carub.0006s1266' => 'cru', 'Ca_06935_v3' => 'car', 'Ca_13559_v3' => 'car', 'Ca_16941_v3' => 'car', 'Ca_16960_v3' => 'car', 'Ca_17775_v3' => 'car', 'Ca_30464_v3' => 'car', 'Cc06_g08160' => 'ccan', 'Cc07_g01520' => 'ccan', 'Cc11_g15810' => 'ccan', 'CDE02G2840' => 'cde', 'CDE03G0093' => 'cde', 'CDE04G2127' => 'cde', 'CDE07G1857' => 'cde', 'CDE09G1246' => 'cde', 'Cfa003412' => 'cfa', 'Cfa007341' => 'cfa', 'Cfa009220' => 'cfa', 'Ciclev10008737m.g' => 'ccl', 'Ciclev10015565m.g' => 'ccl', 'Ciclev10031761m.g' => 'ccl', 'CiPaw.03G045300' => 'cil', 'CiPaw.03G247200' => 'cil', 'CiPaw.04G029500' => 'cil', 'CiPaw.04G174000' => 'cil', 'CiPaw.05G181200' => 'cil', 'CiPaw.06G067100' => 'cil', 'ClCG05G025800' => 'cla', 'ClCG06G011400' => 'cla', 'ClCG09G019360' => 'cla', 'COL.COLO4_04827' => 'col', 'COL.COLO4_29170' => 'col', 'COL.COLO4_35131' => 'col', 'COL.COLO4_35132' => 'col', 'Cpa.g.sc33.32' => 'cpa', 'Cpa.g.sc46.29' => 'cpa', 'Cpa.g.sc796.1' => 'cpa', 'CsaV3_1G030420' => 'csa', 'CsaV3_5G027050' => 'csa', 'CsaV3_5G031040' => 'csa', 'CsaV3_UNG023130' => 'csa', 'CSS0007726' => 'camsi', 'CSS0016433' => 'camsi', 'CSS0017656' => 'camsi', 'CSS0025364' => 'camsi', 'CSS0027582' => 'camsi', 'CSS0047288' => 'camsi', 'CSS0049950' => 'camsi', 'DCAR_003843' => 'dca', 'DCAR_007052' => 'dca', 'DCAR_020884' => 'dca', 'DCAR_021730' => 'dca', 'DCAR_024423' => 'dca', 'DCAR_026509' => 'dca', 'DCAR_031158' => 'dca', 'Dinv14728' => 'din', 'Dinv15219' => 'din', 'Dinv25728' => 'din', 'Dinv33428' => 'din', 'Dinv36489' => 'din', 'Dinv41486' => 'din', 'Duzib147G0469' => 'dzi', 'Duzib168G0060' => 'dzi', 'Duzib187G1215' => 'dzi', 'Duzib248G0692' => 'dzi', 'Duzib251G0767' => 'dzi', 'Duzib264G0446' => 'dzi', 'Duzib268G0691' => 'dzi', 'ECA232G4767' => 'eca', 'ECA233G2838' => 'eca', 'ECA234G0391' => 'eca', 'ECA234G0857' => 'eca', 'ECA236G1593' => 'eca', 'ECA238G0565' => 'eca', 'ECA246G1027' => 'eca', 'ECA246G3223' => 'eca', 'ECA246G3470' => 'eca', 'EL10Ac6g13829' => 'bvu', 'EL10Ac6g14093' => 'bvu', 'EL10Ac8g18707' => 'bvu', 'Eucgr.C01369' => 'egr', 'Eucgr.H02492' => 'egr', 'Eucgr.I01733' => 'egr', 'Eucgr.J02255' => 'egr', 'Eucgr.J02257' => 'egr', 'Eucgr.J02258' => 'egr', 'FAN02G1601' => 'fan', 'FAN03G1586' => 'fan', 'FAN03G2986' => 'fan', 'FAN05G4837' => 'fan', 'FAN06G0146' => 'fan', 'FAN07G0858' => 'fan', 'FAN09G3179' => 'fan', 'FAN10G0669' => 'fan', 'FAN12G2358' => 'fan', 'FAN14G4198' => 'fan', 'FAN14G5112' => 'fan', 'FAN17G0342' => 'fan', 'FAN19G0342' => 'fan', 'FAN19G0962' => 'fan', 'FAN19G1101' => 'fan', 'FAN19G1872' => 'fan', 'FAN22G0356' => 'fan', 'FAN23G0744' => 'fan', 'FAN23G1914' => 'fan', 'FAN26G0032' => 'fan', 'FAN28G0625' => 'fan', 'FvH4_1g02710' => 'fve', 'FvH4_1g02720' => 'fve', 'FvH4_4g25670' => 'fve', 'FvH4_6g51700' => 'fve', 'FvH4_7g20170' => 'fve', 'Glyma.05G175000' => 'gma', 'Glyma.08G132300' => 'gma', 'Glyma.11G243000' => 'gma', 'Glyma.13G158900' => 'gma', 'Glyma.17G112400' => 'gma', 'Glyma.18G014100' => 'gma', 'Glyma.19G003100' => 'gma', 'Glyma.19G056500' => 'gma', 'Gohir.A01G158900' => 'ghi', 'Gohir.A05G312600' => 'ghi', 'Gohir.A05G354900' => 'ghi', 'Gohir.A07G037200' => 'ghi', 'Gohir.A09G030000' => 'ghi', 'Gohir.A12G145200' => 'ghi', 'Gohir.D01G151500' => 'ghi', 'Gohir.D04G058300' => 'ghi', 'Gohir.D05G314100' => 'ghi', 'Gohir.D07G041400' => 'ghi', 'Gohir.D09G029700' => 'ghi', 'Gohir.D12G149700' => 'ghi', 'Gorai.001G043800' => 'gra', 'Gorai.002G187800' => 'gra', 'Gorai.006G034700' => 'gra', 'Gorai.008G161200' => 'gra', 'Gorai.009G335700' => 'gra', 'Gorai.012G065000' => 'gra', 'GSVIVG01000535001' => 'vvi', 'GSVIVG01015572001' => 'vvi', 'GSVIVG01032386001' => 'vvi', 'HanXRQChr05g0138531' => 'han', 'HanXRQChr06g0174391' => 'han', 'HanXRQChr07g0199021' => 'han', 'HanXRQChr08g0208211' => 'han', 'HanXRQChr09g0255471' => 'han', 'HanXRQChr10g0315791' => 'han', 'HanXRQChr12g0371991' => 'han', 'HanXRQChr15g0475251' => 'han', 'HanXRQChr17g0540001' => 'han', 'HanXRQChr17g0548631' => 'han', 'HanXRQChr17g0569561' => 'han', 'Haze_12256' => 'cav', 'Haze_14756' => 'cav', 'Haze_25528' => 'cav', 'Hma1.2p1_0079F.1_g041020' => 'hma', 'Hma1.2p1_0818F.1_g223260' => 'hma', 'Hma1.2p1_1747F.1_g300530' => 'hma', 'HPP92_004607' => 'vpl', 'HPP92_004608' => 'vpl', 'HPP92_006181' => 'vpl', 'HPP92_012192' => 'vpl', 'HPP92_015680' => 'vpl', 'HPP92_020249' => 'vpl', 'HPP92_021376' => 'vpl', 'HPP92_024275' => 'vpl', 'Hund06031' => 'sun', 'Hund25391' => 'sun', 'Lalb_Chr07g0185371' => 'lal', 'Lalb_Chr07g0185381' => 'lal', 'Lalb_Chr12g0204011' => 'lal', 'Lalb_Chr13g0301671' => 'lal', 'Lalb_Chr14g0362851' => 'lal', 'Lalb_Chr24g0403581' => 'lal', 'Lj1g0000233' => 'lja', 'Lj2g0018120' => 'lja', 'Lj3C621T0' => 'lonja', 'Lj3P1059T14' => 'lonja', 'Lj3P611T9' => 'lonja', 'Lj3P614T13' => 'lonja', 'Lj3P615T5' => 'lonja', 'Lj4g0012315' => 'lja', 'Lj4g0026182' => 'lja', 'Lj6P813T16' => 'lonja', 'Lj7C427T7' => 'lonja', 'Lj7C427T8' => 'lonja', 'Lj7P600T41' => 'lonja', 'Lju41C42G17' => 'lonja', 'Lsat_1_v5_gn_0_47300' => 'lsa', 'Lsat_1_v5_gn_2_91280' => 'lsa', 'Lsat_1_v5_gn_3_30561' => 'lsa', 'Lsat_1_v5_gn_4_184321' => 'lsa', 'Lsat_1_v5_gn_4_4041' => 'lsa', 'Lsat_1_v5_gn_5_92000' => 'lsa', 'Lsat_1_v5_gn_8_152940' => 'lsa', 'Lsat_1_v5_gn_8_62401' => 'lsa', 'Manes.06G055900' => 'mes', 'Manes.12G022200' => 'mes', 'Manes.13G023300' => 'mes', 'Manes.14G115000' => 'mes', 'Manes.15G151700' => 'mes', 'Manes.17G111300' => 'mes', 'Mapoly0226s0009' => 'mpo', 'MBI02_g25363_MAGBIO' => 'mbi', 'MBI06_g00027_MAGBIO' => 'mbi', 'MBI10_g13034_MAGBIO' => 'mbi', 'MD09G1023400' => 'mdo', 'MD13G1100100' => 'mdo', 'MD15G1169200' => 'mdo', 'MD16G1101100' => 'mdo', 'MD17G1022900' => 'mdo', 'Medtr3g096150' => 'mtr', 'Medtr4g115070' => 'mtr', 'Medtr7g033325' => 'mtr', 'Medtr8g089840' => 'mtr', 'MELO3C010319.2' => 'cme', 'MELO3C011944.2' => 'cme', 'MELO3C021589.2' => 'cme', 'Migut.E00207' => 'egut', 'Migut.H00067' => 'egut', 'Migut.K00433' => 'egut', 'Migut.K00606' => 'egut', 'Migut.K01410' => 'egut', 'MSTRG.13347' => 'ama', 'MSTRG.24045' => 'ama', 'MSTRG.2428' => 'ama', 'MSTRG.26410' => 'ama', 'MSTRG.3139' => 'ama', 'MSTRG.3286' => 'ama', 'MSTRG.563' => 'ama', 'MSTRG.7941' => 'ama', 'Nitab4.5_0000028g0060' => 'nta', 'Nitab4.5_0000065g0260' => 'nta', 'Nitab4.5_0000112g0060' => 'nta', 'Nitab4.5_0000489g0120' => 'nta', 'Nitab4.5_0001776g0050' => 'nta', 'Nitab4.5_0001854g0010' => 'nta', 'Nitab4.5_0001860g0020' => 'nta', 'Nitab4.5_0004352g0010' => 'nta', 'Nitab4.5_0008716g0020' => 'nta', 'Nitab4.5_0008922g0010' => 'nta', 'Nn3g16693' => 'nnu', 'Nn4g22596' => 'nnu', 'Nn7g37639' => 'nnu', 'Oeu001701.1' => 'oeu', 'Oeu018149.1' => 'oeu', 'Oeu026220.1' => 'oeu', 'Oeu038635.1' => 'oeu', 'Oeu049176.1' => 'oeu', 'Oeu056706.1' => 'oeu', 'Oeu056937.1' => 'oeu', 'Oeu057540.1' => 'oeu', 'Os02g0594900' => 'osa', 'Os02g0595100' => 'osa', 'Os04g0477500' => 'osa', 'Os12g0611900' => 'osa', 'Peaxi162Scf00076g00020' => 'pax', 'Peaxi162Scf00128g00217' => 'pax', 'Peaxi162Scf00129g01640' => 'pax', 'Peaxi162Scf00669g00007' => 'pax', 'Peaxi162Scf00700g00421' => 'pax', 'Peaxi162Scf00801g00038' => 'pax', 'Peaxi162Scf00891g00025' => 'pax', 'PGR083G0909' => 'pgr', 'PGR119G1005' => 'pgr', 'PGR142G2236' => 'pgr', 'PGR142G3388' => 'pgr', 'PGSC0003DMG400004514' => 'stu', 'PGSC0003DMG400012635' => 'stu', 'PGSC0003DMG400015730' => 'stu', 'PGSC0003DMG400018611' => 'stu', 'PGSC0003DMG400030897' => 'stu', 'Phvul.001G254800' => 'pvu', 'Phvul.002G260100' => 'pvu', 'Phvul.003G167600' => 'pvu', 'Phvul.004G005100' => 'pvu', 'Potri.001G343600' => 'ptr', 'Potri.006G066700' => 'ptr', 'Potri.008G186000' => 'ptr', 'Potri.010G046900' => 'ptr', 'Potri.018G127900' => 'ptr', 'Pp3c20_17750' => 'ppa', 'Pp3c24_4380' => 'ppa', 'Prupe.1G245800' => 'ppe', 'Prupe.3G293400' => 'ppe', 'Prupe.7G247400' => 'ppe', 'Psat0s145g0120' => 'psa', 'Psat0s595g0040' => 'psa', 'Psat0s595g0120' => 'psa', 'Psat3g175040' => 'psa', 'Psat7g058120' => 'psa', 'PSO017G0428' => 'pso', 'PSO063G7510' => 'pso', 'PSO067G0046' => 'pso', 'PSO478G1073' => 'pso', 'PSO675G3677' => 'pso', 'PSO675G6558' => 'pso', 'PSO675G7520' => 'pso', 'PSO675G8959' => 'pso', 'QL02p074089' => 'qlo', 'QL02p089614' => 'qlo', 'QL03p057736' => 'qlo', 'RcHm_v2.0_Chr1g0364131' => 'rch', 'RcHm_v2.0_Chr2g0087801' => 'rch', 'RcHm_v2.0_Chr2g0087821' => 'rch', 'RcHm_v2.0_Chr2g0173231' => 'rch', 'RcHm_v2.0_Chr4g0433111' => 'rch', 'Rhsim03G0250300' => 'rsi', 'Rhsim08G0048400' => 'rsi', 'Rhsim10G0014800' => 'rsi', 'Rhsim12G0040100' => 'rsi', 'Rhsim12G0109700' => 'rsi', 'Sabra06G0049600' => 'sbr', 'Sabra08G0141000' => 'sbr', 'Sabra10G0021400' => 'sbr', 'Sabra16G0222900' => 'sbr', 'Sabra18G0108600' => 'sbr', 'SalBow1G0433' => 'sbo', 'SalBow1G2038' => 'sbo', 'SalBow1G5003' => 'sbo', 'SalBow7G1197' => 'sbo', 'SalBow8G3506' => 'sbo', 'Sc03g0007300' => 'sci', 'Sc11g0000950' => 'sci', 'Sc14g0008750' => 'sci', 'Sc18g0000420' => 'sci', 'Sed0006754' => 'sed', 'Sed0008741' => 'sed', 'Sed0017172' => 'sed', 'Sed0018925' => 'sed', 'Sed0023326' => 'sed', 'Sed0025909' => 'sed', 'SEGI_05333' => 'sgi', 'SEGI_10362' => 'sgi', 'SEGI_13380' => 'sgi', 'SEGI_24306' => 'sgi', 'SEGI_29077' => 'sgi', 'SEGI_29095' => 'sgi', 'SEGI_36534' => 'sgi', 'SEGI_37506' => 'sgi', 'SEGI_38321' => 'sgi', 'SGA_v2.0_scaffold307G48031' => 'sas', 'SGA_v2.0_scaffold47G17507' => 'sas', 'SGA_v2.0_scaffold63G21736' => 'sas', 'SGA_v2.0_scaffold87G27070' => 'sas', 'SHI17794' => 'shi', 'SHI28851' => 'shi', 'SMO165G0155' => 'smo', 'SMO340G0217' => 'smo', 'SMO367G1210' => 'smo', 'Solyc02g093430.3' => 'sly', 'Solyc05g013580.4' => 'sly', 'Solyc07g008030.3' => 'sly', 'Solyc12g035470.2' => 'sly', 'Sopen02g038020' => 'spe', 'Sopen05g008490' => 'spe', 'Sopen07g003910' => 'spe', 'Sopen12g015240' => 'spe', 'Sp1g11550' => 'spa', 'Sp2g16710' => 'spa', 'Sp3g00430' => 'spa', 'Sp3g26780' => 'spa', 'Sp5g22900' => 'spa', 'Sp6g29530' => 'spa', 'TAR371G0794' => 'tar', 'TAR374G0164' => 'tar', 'TAR622G0165' => 'tar', 'TAR626G0929' => 'tar', 'TAR629G2155' => 'tar', 'THA.LOC104805282' => 'tha', 'THA.LOC104805363' => 'tha', 'THA.LOC104808968' => 'tha', 'THA.LOC104821093' => 'tha', 'THA.LOC104823953' => 'tha', 'THA.LOC104825562' => 'tha', 'THA.LOC104825665' => 'tha', 'Thecc.02G261400' => 'tca', 'Thecc.04G019200' => 'tca', 'Thecc.09G130400' => 'tca', 'Thhalv10004374m.g' => 'esa', 'Thhalv10007850m.g' => 'esa', 'Thhalv10013782m.g' => 'esa', 'Thhalv10018686m.g' => 'esa', 'Thhalv10020899m.g' => 'esa', 'Thhalv10022755m.g' => 'esa', 'TPR.G23851' => 'tpr', 'TPR.G26500' => 'tpr', 'TPR.G27267' => 'tpr', 'TPR.G32001' => 'tpr', 'TPR.G6251' => 'tpr', 'TPR.G8167' => 'tpr', 'TWI12G1330' => 'twi', 'TWI18G1239' => 'twi', 'TWI34G0979' => 'twi', 'TWI36G0670' => 'twi', 'TWI36G0707' => 'twi', 'TWI56G0233' => 'twi', 'TWI75G1809' => 'twi', 'unitig_21.g20874' => 'ugi', 'unitig_26.g10343' => 'ugi', 'unitig_46.g18392' => 'ugi', 'unitig_52.g17178' => 'ugi', 'unitig_8.g2934' => 'ugi', 'vmacro01122' => 'vma', 'vmacro05875' => 'vma', 'vmacro06147' => 'vma', 'vmacro16191' => 'vma', 'vmacro18293' => 'vma', 'VMungo0251G3707' => 'vmu', 'VMungo0464G1521' => 'vmu', 'VMungo1215G0205' => 'vmu', 'VMungo1383G2484' => 'vmu', 'Zm00001eb079610' => 'zma', 'Zm00001eb135990' => 'zma', 'Zm00001eb183710' => 'zma', 'Zm00001eb246020' => 'zma' ), 'gf_id' => 'HOM05D001124', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001124' ), 'data_identifier' => 'HOM05D001124', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001124', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '548', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02520' => 'bna', 'A03p06630' => 'bna', 'A05p44460' => 'bna', 'A06p08710' => 'bna', 'A06p41090' => 'bna', 'A07p32320' => 'bna', 'A08p32520' => 'bna', 'A09p10360' => 'bna', 'A10p24080' => 'bna', 'Aa31LG11G15250' => 'aar', 'Aa31LG1G1800' => 'aar', 'Aa31LG2G5120' => 'aar', 'Aa31LG2G6070' => 'aar', 'Aa31LG5G10770' => 'aar', 'Aa31sc61G90' => 'aar', 'Actinidia01352' => 'ach', 'Actinidia05983' => 'ach', 'Actinidia08133' => 'ach', 'Actinidia15101' => 'ach', 'Actinidia26379' => 'ach', 'Actinidia35778' => 'ach', 'Actinidia36123' => 'ach', 'Actinidia37436' => 'ach', 'Actinidia38730' => 'ach', 'Ah.02g128210' => 'amhyb', 'Ah.03g132990' => 'amhyb', 'Ah.14g079410' => 'amhyb', 'AL1G24640' => 'aly', 'AL2G26680' => 'aly', 'AL3G10530' => 'aly', 'AL3G45230' => 'aly', 'AL5G15230' => 'aly', 'AL5G16960' => 'aly', 'AL6G25210' => 'aly', 'Aqoxy2G00441' => 'aox', 'Aqoxy3G01236' => 'aox', 'Aqoxy5G03746' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3RQ047' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C7GMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9C8JER' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MBL6KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YXCZ83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZANX40' => 'arhy', 'AT1G12990' => 'ath', 'AT1G67880' => 'ath', 'AT2G13290' => 'ath', 'AT3G01620' => 'ath', 'AT3G26445' => 'ath', 'AT3G27540' => 'ath', 'AT5G14480' => 'ath', 'ATR0824G026' => 'atr', 'ATR1098G019' => 'atr', 'Atru.chr11.2145' => 'acertr', 'Atru.chr2.3636' => 'acertr', 'Atru.chr2.3644' => 'acertr', 'Atru.chr6.2422' => 'acertr', 'Atru.chr7.1112' => 'acertr', 'AUR62005469' => 'cqu', 'AUR62011166' => 'cqu', 'AUR62013319' => 'cqu', 'AUR62024273' => 'cqu', 'AUR62028420' => 'cqu', 'AUR62041942' => 'cqu', 'BcaB01g04969' => 'bca', 'BcaB01g06371' => 'bca', 'BcaB02g11494' => 'bca', 'BcaB03g15382' => 'bca', 'BcaB08g36994' => 'bca', 'BcaC03g13477' => 'bca', 'BcaC03g13478' => 'bca', 'BcaC03g13480' => 'bca', 'BcaC03g13481' => 'bca', 'BcaC03g13486' => 'bca', 'BcaC04g19031' => 'bca', 'BcaC04g23085' => 'bca', 'BcaC05g25094' => 'bca', 'BcaC05g25096' => 'bca', 'BcaC05g25138' => 'bca', 'BcaC05g30416' => 'bca', 'BcaC05g30455' => 'bca', 'BcaC06g30979' => 'bca', 'BcaC06g33805' => 'bca', 'BcaC08g46021' => 'bca', 'BcaNung03154' => 'bca', 'BolC2t06623H' => 'bol', 'BolC2t06632H' => 'bol', 'BolC2t06635H' => 'bol', 'BolC2t06638H' => 'bol', 'BolC3t13266H' => 'bol', 'BolC5t29776H' => 'bol', 'BolC6t38912H' => 'bol', 'BolC7t44183H' => 'bol', 'BolC9t54123H' => 'bol', 'BolC9t59107H' => 'bol', 'BraA02t05221Z' => 'bra', 'BraA03t09996Z' => 'bra', 'BraA05t23210Z' => 'bra', 'BraA06t24068Z' => 'bra', 'BraA06t27032Z' => 'bra', 'BraA08t35176Z' => 'bra', 'BraA09t36680Z' => 'bra', 'BraA10t44471Z' => 'bra', 'C02p06760' => 'bna', 'C02p06890' => 'bna', 'C02p07010' => 'bna', 'C03p07660' => 'bna', 'C05p10300' => 'bna', 'C06p38150' => 'bna', 'C07p36650' => 'bna', 'C08p15770' => 'bna', 'C09p12300' => 'bna', 'C09p62700' => 'bna', 'C09p75040' => 'bna', 'CAN.G13.1' => 'can', 'CAN.G138.4' => 'can', 'CAN.G44.6' => 'can', 'CAN.G473.19' => 'can', 'CANSAT01G0835' => 'cansat', 'CANSAT11G0246' => 'cansat', 'CANSAT11G1766' => 'cansat', 'CANSAT64G1954' => 'cansat', 'CARHR013330' => 'chi', 'CARHR060530' => 'chi', 'CARHR075300' => 'chi', 'CARHR105120' => 'chi', 'CARHR148910' => 'chi', 'CARHR198830' => 'chi', 'Carub.0001s1275' => 'cru', 'Carub.0002s1437' => 'cru', 'Carub.0003s0044' => 'cru', 'Carub.0003s2787' => 'cru', 'Carub.0005s0597' => 'cru', 'Carub.0006s1266' => 'cru', 'Ca_06935_v3' => 'car', 'Ca_13559_v3' => 'car', 'Ca_16941_v3' => 'car', 'Ca_16960_v3' => 'car', 'Ca_17775_v3' => 'car', 'Ca_30464_v3' => 'car', 'Cc06_g08160' => 'ccan', 'Cc07_g01520' => 'ccan', 'Cc11_g15810' => 'ccan', 'CDE02G2840' => 'cde', 'CDE03G0093' => 'cde', 'CDE04G2127' => 'cde', 'CDE07G1857' => 'cde', 'CDE09G1246' => 'cde', 'Cfa003412' => 'cfa', 'Cfa007341' => 'cfa', 'Cfa009220' => 'cfa', 'Ciclev10008737m.g' => 'ccl', 'Ciclev10015565m.g' => 'ccl', 'Ciclev10031761m.g' => 'ccl', 'CiPaw.03G045300' => 'cil', 'CiPaw.03G247200' => 'cil', 'CiPaw.04G029500' => 'cil', 'CiPaw.04G174000' => 'cil', 'CiPaw.05G181200' => 'cil', 'CiPaw.06G067100' => 'cil', 'ClCG05G025800' => 'cla', 'ClCG06G011400' => 'cla', 'ClCG09G019360' => 'cla', 'COL.COLO4_04827' => 'col', 'COL.COLO4_29170' => 'col', 'COL.COLO4_35131' => 'col', 'COL.COLO4_35132' => 'col', 'Cpa.g.sc33.32' => 'cpa', 'Cpa.g.sc46.29' => 'cpa', 'Cpa.g.sc796.1' => 'cpa', 'CsaV3_1G030420' => 'csa', 'CsaV3_5G027050' => 'csa', 'CsaV3_5G031040' => 'csa', 'CsaV3_UNG023130' => 'csa', 'CSS0007726' => 'camsi', 'CSS0016433' => 'camsi', 'CSS0017656' => 'camsi', 'CSS0025364' => 'camsi', 'CSS0027582' => 'camsi', 'CSS0047288' => 'camsi', 'CSS0049950' => 'camsi', 'DCAR_003843' => 'dca', 'DCAR_007052' => 'dca', 'DCAR_020884' => 'dca', 'DCAR_021730' => 'dca', 'DCAR_024423' => 'dca', 'DCAR_026509' => 'dca', 'DCAR_031158' => 'dca', 'Dinv14728' => 'din', 'Dinv15219' => 'din', 'Dinv25728' => 'din', 'Dinv33428' => 'din', 'Dinv36489' => 'din', 'Dinv41486' => 'din', 'Duzib147G0469' => 'dzi', 'Duzib168G0060' => 'dzi', 'Duzib187G1215' => 'dzi', 'Duzib248G0692' => 'dzi', 'Duzib251G0767' => 'dzi', 'Duzib264G0446' => 'dzi', 'Duzib268G0691' => 'dzi', 'ECA232G4767' => 'eca', 'ECA233G2838' => 'eca', 'ECA234G0391' => 'eca', 'ECA234G0857' => 'eca', 'ECA236G1593' => 'eca', 'ECA238G0565' => 'eca', 'ECA246G1027' => 'eca', 'ECA246G3223' => 'eca', 'ECA246G3470' => 'eca', 'EL10Ac6g13829' => 'bvu', 'EL10Ac6g14093' => 'bvu', 'EL10Ac8g18707' => 'bvu', 'Eucgr.C01369' => 'egr', 'Eucgr.H02492' => 'egr', 'Eucgr.I01733' => 'egr', 'Eucgr.J02255' => 'egr', 'Eucgr.J02257' => 'egr', 'Eucgr.J02258' => 'egr', 'FAN02G1601' => 'fan', 'FAN03G1586' => 'fan', 'FAN03G2986' => 'fan', 'FAN05G4837' => 'fan', 'FAN06G0146' => 'fan', 'FAN07G0858' => 'fan', 'FAN09G3179' => 'fan', 'FAN10G0669' => 'fan', 'FAN12G2358' => 'fan', 'FAN14G4198' => 'fan', 'FAN14G5112' => 'fan', 'FAN17G0342' => 'fan', 'FAN19G0342' => 'fan', 'FAN19G0962' => 'fan', 'FAN19G1101' => 'fan', 'FAN19G1872' => 'fan', 'FAN22G0356' => 'fan', 'FAN23G0744' => 'fan', 'FAN23G1914' => 'fan', 'FAN26G0032' => 'fan', 'FAN28G0625' => 'fan', 'FvH4_1g02710' => 'fve', 'FvH4_1g02720' => 'fve', 'FvH4_4g25670' => 'fve', 'FvH4_6g51700' => 'fve', 'FvH4_7g20170' => 'fve', 'Glyma.05G175000' => 'gma', 'Glyma.08G132300' => 'gma', 'Glyma.11G243000' => 'gma', 'Glyma.13G158900' => 'gma', 'Glyma.17G112400' => 'gma', 'Glyma.18G014100' => 'gma', 'Glyma.19G003100' => 'gma', 'Glyma.19G056500' => 'gma', 'Gohir.A01G158900' => 'ghi', 'Gohir.A05G312600' => 'ghi', 'Gohir.A05G354900' => 'ghi', 'Gohir.A07G037200' => 'ghi', 'Gohir.A09G030000' => 'ghi', 'Gohir.A12G145200' => 'ghi', 'Gohir.D01G151500' => 'ghi', 'Gohir.D04G058300' => 'ghi', 'Gohir.D05G314100' => 'ghi', 'Gohir.D07G041400' => 'ghi', 'Gohir.D09G029700' => 'ghi', 'Gohir.D12G149700' => 'ghi', 'Gorai.001G043800' => 'gra', 'Gorai.002G187800' => 'gra', 'Gorai.006G034700' => 'gra', 'Gorai.008G161200' => 'gra', 'Gorai.009G335700' => 'gra', 'Gorai.012G065000' => 'gra', 'GSVIVG01000535001' => 'vvi', 'GSVIVG01015572001' => 'vvi', 'GSVIVG01032386001' => 'vvi', 'HanXRQChr05g0138531' => 'han', 'HanXRQChr06g0174391' => 'han', 'HanXRQChr07g0199021' => 'han', 'HanXRQChr08g0208211' => 'han', 'HanXRQChr09g0255471' => 'han', 'HanXRQChr10g0315791' => 'han', 'HanXRQChr12g0371991' => 'han', 'HanXRQChr15g0475251' => 'han', 'HanXRQChr17g0540001' => 'han', 'HanXRQChr17g0548631' => 'han', 'HanXRQChr17g0569561' => 'han', 'Haze_12256' => 'cav', 'Haze_14756' => 'cav', 'Haze_25528' => 'cav', 'Hma1.2p1_0079F.1_g041020' => 'hma', 'Hma1.2p1_0818F.1_g223260' => 'hma', 'Hma1.2p1_1747F.1_g300530' => 'hma', 'HPP92_004607' => 'vpl', 'HPP92_004608' => 'vpl', 'HPP92_006181' => 'vpl', 'HPP92_012192' => 'vpl', 'HPP92_015680' => 'vpl', 'HPP92_020249' => 'vpl', 'HPP92_021376' => 'vpl', 'HPP92_024275' => 'vpl', 'Hund06031' => 'sun', 'Hund25391' => 'sun', 'Lalb_Chr07g0185371' => 'lal', 'Lalb_Chr07g0185381' => 'lal', 'Lalb_Chr12g0204011' => 'lal', 'Lalb_Chr13g0301671' => 'lal', 'Lalb_Chr14g0362851' => 'lal', 'Lalb_Chr24g0403581' => 'lal', 'Lj1g0000233' => 'lja', 'Lj2g0018120' => 'lja', 'Lj3C621T0' => 'lonja', 'Lj3P1059T14' => 'lonja', 'Lj3P611T9' => 'lonja', 'Lj3P614T13' => 'lonja', 'Lj3P615T5' => 'lonja', 'Lj4g0012315' => 'lja', 'Lj4g0026182' => 'lja', 'Lj6P813T16' => 'lonja', 'Lj7C427T7' => 'lonja', 'Lj7C427T8' => 'lonja', 'Lj7P600T41' => 'lonja', 'Lju41C42G17' => 'lonja', 'Lsat_1_v5_gn_0_47300' => 'lsa', 'Lsat_1_v5_gn_2_91280' => 'lsa', 'Lsat_1_v5_gn_3_30561' => 'lsa', 'Lsat_1_v5_gn_4_184321' => 'lsa', 'Lsat_1_v5_gn_4_4041' => 'lsa', 'Lsat_1_v5_gn_5_92000' => 'lsa', 'Lsat_1_v5_gn_8_152940' => 'lsa', 'Lsat_1_v5_gn_8_62401' => 'lsa', 'Manes.06G055900' => 'mes', 'Manes.12G022200' => 'mes', 'Manes.13G023300' => 'mes', 'Manes.14G115000' => 'mes', 'Manes.15G151700' => 'mes', 'Manes.17G111300' => 'mes', 'Mapoly0226s0009' => 'mpo', 'MBI02_g25363_MAGBIO' => 'mbi', 'MBI06_g00027_MAGBIO' => 'mbi', 'MBI10_g13034_MAGBIO' => 'mbi', 'MD09G1023400' => 'mdo', 'MD13G1100100' => 'mdo', 'MD15G1169200' => 'mdo', 'MD16G1101100' => 'mdo', 'MD17G1022900' => 'mdo', 'Medtr3g096150' => 'mtr', 'Medtr4g115070' => 'mtr', 'Medtr7g033325' => 'mtr', 'Medtr8g089840' => 'mtr', 'MELO3C010319.2' => 'cme', 'MELO3C011944.2' => 'cme', 'MELO3C021589.2' => 'cme', 'Migut.E00207' => 'egut', 'Migut.H00067' => 'egut', 'Migut.K00433' => 'egut', 'Migut.K00606' => 'egut', 'Migut.K01410' => 'egut', 'MSTRG.13347' => 'ama', 'MSTRG.24045' => 'ama', 'MSTRG.2428' => 'ama', 'MSTRG.26410' => 'ama', 'MSTRG.3139' => 'ama', 'MSTRG.3286' => 'ama', 'MSTRG.563' => 'ama', 'MSTRG.7941' => 'ama', 'Nitab4.5_0000028g0060' => 'nta', 'Nitab4.5_0000065g0260' => 'nta', 'Nitab4.5_0000112g0060' => 'nta', 'Nitab4.5_0000489g0120' => 'nta', 'Nitab4.5_0001776g0050' => 'nta', 'Nitab4.5_0001854g0010' => 'nta', 'Nitab4.5_0001860g0020' => 'nta', 'Nitab4.5_0004352g0010' => 'nta', 'Nitab4.5_0008716g0020' => 'nta', 'Nitab4.5_0008922g0010' => 'nta', 'Nn3g16693' => 'nnu', 'Nn4g22596' => 'nnu', 'Nn7g37639' => 'nnu', 'Oeu001701.1' => 'oeu', 'Oeu018149.1' => 'oeu', 'Oeu026220.1' => 'oeu', 'Oeu038635.1' => 'oeu', 'Oeu049176.1' => 'oeu', 'Oeu056706.1' => 'oeu', 'Oeu056937.1' => 'oeu', 'Oeu057540.1' => 'oeu', 'Os02g0594900' => 'osa', 'Os02g0595100' => 'osa', 'Os04g0477500' => 'osa', 'Os12g0611900' => 'osa', 'Peaxi162Scf00076g00020' => 'pax', 'Peaxi162Scf00128g00217' => 'pax', 'Peaxi162Scf00129g01640' => 'pax', 'Peaxi162Scf00669g00007' => 'pax', 'Peaxi162Scf00700g00421' => 'pax', 'Peaxi162Scf00801g00038' => 'pax', 'Peaxi162Scf00891g00025' => 'pax', 'PGR083G0909' => 'pgr', 'PGR119G1005' => 'pgr', 'PGR142G2236' => 'pgr', 'PGR142G3388' => 'pgr', 'PGSC0003DMG400004514' => 'stu', 'PGSC0003DMG400012635' => 'stu', 'PGSC0003DMG400015730' => 'stu', 'PGSC0003DMG400018611' => 'stu', 'PGSC0003DMG400030897' => 'stu', 'Phvul.001G254800' => 'pvu', 'Phvul.002G260100' => 'pvu', 'Phvul.003G167600' => 'pvu', 'Phvul.004G005100' => 'pvu', 'Potri.001G343600' => 'ptr', 'Potri.006G066700' => 'ptr', 'Potri.008G186000' => 'ptr', 'Potri.010G046900' => 'ptr', 'Potri.018G127900' => 'ptr', 'Pp3c20_17750' => 'ppa', 'Pp3c24_4380' => 'ppa', 'Prupe.1G245800' => 'ppe', 'Prupe.3G293400' => 'ppe', 'Prupe.7G247400' => 'ppe', 'Psat0s145g0120' => 'psa', 'Psat0s595g0040' => 'psa', 'Psat0s595g0120' => 'psa', 'Psat3g175040' => 'psa', 'Psat7g058120' => 'psa', 'PSO017G0428' => 'pso', 'PSO063G7510' => 'pso', 'PSO067G0046' => 'pso', 'PSO478G1073' => 'pso', 'PSO675G3677' => 'pso', 'PSO675G6558' => 'pso', 'PSO675G7520' => 'pso', 'PSO675G8959' => 'pso', 'QL02p074089' => 'qlo', 'QL02p089614' => 'qlo', 'QL03p057736' => 'qlo', 'RcHm_v2.0_Chr1g0364131' => 'rch', 'RcHm_v2.0_Chr2g0087801' => 'rch', 'RcHm_v2.0_Chr2g0087821' => 'rch', 'RcHm_v2.0_Chr2g0173231' => 'rch', 'RcHm_v2.0_Chr4g0433111' => 'rch', 'Rhsim03G0250300' => 'rsi', 'Rhsim08G0048400' => 'rsi', 'Rhsim10G0014800' => 'rsi', 'Rhsim12G0040100' => 'rsi', 'Rhsim12G0109700' => 'rsi', 'Sabra06G0049600' => 'sbr', 'Sabra08G0141000' => 'sbr', 'Sabra10G0021400' => 'sbr', 'Sabra16G0222900' => 'sbr', 'Sabra18G0108600' => 'sbr', 'SalBow1G0433' => 'sbo', 'SalBow1G2038' => 'sbo', 'SalBow1G5003' => 'sbo', 'SalBow7G1197' => 'sbo', 'SalBow8G3506' => 'sbo', 'Sc03g0007300' => 'sci', 'Sc11g0000950' => 'sci', 'Sc14g0008750' => 'sci', 'Sc18g0000420' => 'sci', 'Sed0006754' => 'sed', 'Sed0008741' => 'sed', 'Sed0017172' => 'sed', 'Sed0018925' => 'sed', 'Sed0023326' => 'sed', 'Sed0025909' => 'sed', 'SEGI_05333' => 'sgi', 'SEGI_10362' => 'sgi', 'SEGI_13380' => 'sgi', 'SEGI_24306' => 'sgi', 'SEGI_29077' => 'sgi', 'SEGI_29095' => 'sgi', 'SEGI_36534' => 'sgi', 'SEGI_37506' => 'sgi', 'SEGI_38321' => 'sgi', 'SGA_v2.0_scaffold307G48031' => 'sas', 'SGA_v2.0_scaffold47G17507' => 'sas', 'SGA_v2.0_scaffold63G21736' => 'sas', 'SGA_v2.0_scaffold87G27070' => 'sas', 'SHI17794' => 'shi', 'SHI28851' => 'shi', 'SMO165G0155' => 'smo', 'SMO340G0217' => 'smo', 'SMO367G1210' => 'smo', 'Solyc02g093430.3' => 'sly', 'Solyc05g013580.4' => 'sly', 'Solyc07g008030.3' => 'sly', 'Solyc12g035470.2' => 'sly', 'Sopen02g038020' => 'spe', 'Sopen05g008490' => 'spe', 'Sopen07g003910' => 'spe', 'Sopen12g015240' => 'spe', 'Sp1g11550' => 'spa', 'Sp2g16710' => 'spa', 'Sp3g00430' => 'spa', 'Sp3g26780' => 'spa', 'Sp5g22900' => 'spa', 'Sp6g29530' => 'spa', 'TAR371G0794' => 'tar', 'TAR374G0164' => 'tar', 'TAR622G0165' => 'tar', 'TAR626G0929' => 'tar', 'TAR629G2155' => 'tar', 'THA.LOC104805282' => 'tha', 'THA.LOC104805363' => 'tha', 'THA.LOC104808968' => 'tha', 'THA.LOC104821093' => 'tha', 'THA.LOC104823953' => 'tha', 'THA.LOC104825562' => 'tha', 'THA.LOC104825665' => 'tha', 'Thecc.02G261400' => 'tca', 'Thecc.04G019200' => 'tca', 'Thecc.09G130400' => 'tca', 'Thhalv10004374m.g' => 'esa', 'Thhalv10007850m.g' => 'esa', 'Thhalv10013782m.g' => 'esa', 'Thhalv10018686m.g' => 'esa', 'Thhalv10020899m.g' => 'esa', 'Thhalv10022755m.g' => 'esa', 'TPR.G23851' => 'tpr', 'TPR.G26500' => 'tpr', 'TPR.G27267' => 'tpr', 'TPR.G32001' => 'tpr', 'TPR.G6251' => 'tpr', 'TPR.G8167' => 'tpr', 'TWI12G1330' => 'twi', 'TWI18G1239' => 'twi', 'TWI34G0979' => 'twi', 'TWI36G0670' => 'twi', 'TWI36G0707' => 'twi', 'TWI56G0233' => 'twi', 'TWI75G1809' => 'twi', 'unitig_21.g20874' => 'ugi', 'unitig_26.g10343' => 'ugi', 'unitig_46.g18392' => 'ugi', 'unitig_52.g17178' => 'ugi', 'unitig_8.g2934' => 'ugi', 'vmacro01122' => 'vma', 'vmacro05875' => 'vma', 'vmacro06147' => 'vma', 'vmacro16191' => 'vma', 'vmacro18293' => 'vma', 'VMungo0251G3707' => 'vmu', 'VMungo0464G1521' => 'vmu', 'VMungo1215G0205' => 'vmu', 'VMungo1383G2484' => 'vmu', 'Zm00001eb079610' => 'zma', 'Zm00001eb135990' => 'zma', 'Zm00001eb183710' => 'zma', 'Zm00001eb246020' => 'zma' ) $gf_id = 'HOM05D001124' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001124' ) $data_identifier = 'HOM05D001124' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 6, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 7, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 21, 'bol' => (int) 10, 'bra' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 6, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 9, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 21, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 8, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 10, 'lsa' => (int) 8, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 8, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 9, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb246020' $species_info = array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ) $local_species = 'mbi' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001124', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '548', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02520' => 'bna', 'A03p06630' => 'bna', 'A05p44460' => 'bna', 'A06p08710' => 'bna', 'A06p41090' => 'bna', 'A07p32320' => 'bna', 'A08p32520' => 'bna', 'A09p10360' => 'bna', 'A10p24080' => 'bna', 'Aa31LG11G15250' => 'aar', 'Aa31LG1G1800' => 'aar', 'Aa31LG2G5120' => 'aar', 'Aa31LG2G6070' => 'aar', 'Aa31LG5G10770' => 'aar', 'Aa31sc61G90' => 'aar', 'Actinidia01352' => 'ach', 'Actinidia05983' => 'ach', 'Actinidia08133' => 'ach', 'Actinidia15101' => 'ach', 'Actinidia26379' => 'ach', 'Actinidia35778' => 'ach', 'Actinidia36123' => 'ach', 'Actinidia37436' => 'ach', 'Actinidia38730' => 'ach', 'Ah.02g128210' => 'amhyb', 'Ah.03g132990' => 'amhyb', 'Ah.14g079410' => 'amhyb', 'AL1G24640' => 'aly', 'AL2G26680' => 'aly', 'AL3G10530' => 'aly', 'AL3G45230' => 'aly', 'AL5G15230' => 'aly', 'AL5G16960' => 'aly', 'AL6G25210' => 'aly', 'Aqoxy2G00441' => 'aox', 'Aqoxy3G01236' => 'aox', 'Aqoxy5G03746' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3RQ047' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C7GMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9C8JER' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MBL6KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YXCZ83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZANX40' => 'arhy', 'AT1G12990' => 'ath', 'AT1G67880' => 'ath', 'AT2G13290' => 'ath', 'AT3G01620' => 'ath', 'AT3G26445' => 'ath', 'AT3G27540' => 'ath', 'AT5G14480' => 'ath', 'ATR0824G026' => 'atr', 'ATR1098G019' => 'atr', 'Atru.chr11.2145' => 'acertr', 'Atru.chr2.3636' => 'acertr', 'Atru.chr2.3644' => 'acertr', 'Atru.chr6.2422' => 'acertr', 'Atru.chr7.1112' => 'acertr', 'AUR62005469' => 'cqu', 'AUR62011166' => 'cqu', 'AUR62013319' => 'cqu', 'AUR62024273' => 'cqu', 'AUR62028420' => 'cqu', 'AUR62041942' => 'cqu', 'BcaB01g04969' => 'bca', 'BcaB01g06371' => 'bca', 'BcaB02g11494' => 'bca', 'BcaB03g15382' => 'bca', 'BcaB08g36994' => 'bca', 'BcaC03g13477' => 'bca', 'BcaC03g13478' => 'bca', 'BcaC03g13480' => 'bca', 'BcaC03g13481' => 'bca', 'BcaC03g13486' => 'bca', 'BcaC04g19031' => 'bca', 'BcaC04g23085' => 'bca', 'BcaC05g25094' => 'bca', 'BcaC05g25096' => 'bca', 'BcaC05g25138' => 'bca', 'BcaC05g30416' => 'bca', 'BcaC05g30455' => 'bca', 'BcaC06g30979' => 'bca', 'BcaC06g33805' => 'bca', 'BcaC08g46021' => 'bca', 'BcaNung03154' => 'bca', 'BolC2t06623H' => 'bol', 'BolC2t06632H' => 'bol', 'BolC2t06635H' => 'bol', 'BolC2t06638H' => 'bol', 'BolC3t13266H' => 'bol', 'BolC5t29776H' => 'bol', 'BolC6t38912H' => 'bol', 'BolC7t44183H' => 'bol', 'BolC9t54123H' => 'bol', 'BolC9t59107H' => 'bol', 'BraA02t05221Z' => 'bra', 'BraA03t09996Z' => 'bra', 'BraA05t23210Z' => 'bra', 'BraA06t24068Z' => 'bra', 'BraA06t27032Z' => 'bra', 'BraA08t35176Z' => 'bra', 'BraA09t36680Z' => 'bra', 'BraA10t44471Z' => 'bra', 'C02p06760' => 'bna', 'C02p06890' => 'bna', 'C02p07010' => 'bna', 'C03p07660' => 'bna', 'C05p10300' => 'bna', 'C06p38150' => 'bna', 'C07p36650' => 'bna', 'C08p15770' => 'bna', 'C09p12300' => 'bna', 'C09p62700' => 'bna', 'C09p75040' => 'bna', 'CAN.G13.1' => 'can', 'CAN.G138.4' => 'can', 'CAN.G44.6' => 'can', 'CAN.G473.19' => 'can', 'CANSAT01G0835' => 'cansat', 'CANSAT11G0246' => 'cansat', 'CANSAT11G1766' => 'cansat', 'CANSAT64G1954' => 'cansat', 'CARHR013330' => 'chi', 'CARHR060530' => 'chi', 'CARHR075300' => 'chi', 'CARHR105120' => 'chi', 'CARHR148910' => 'chi', 'CARHR198830' => 'chi', 'Carub.0001s1275' => 'cru', 'Carub.0002s1437' => 'cru', 'Carub.0003s0044' => 'cru', 'Carub.0003s2787' => 'cru', 'Carub.0005s0597' => 'cru', 'Carub.0006s1266' => 'cru', 'Ca_06935_v3' => 'car', 'Ca_13559_v3' => 'car', 'Ca_16941_v3' => 'car', 'Ca_16960_v3' => 'car', 'Ca_17775_v3' => 'car', 'Ca_30464_v3' => 'car', 'Cc06_g08160' => 'ccan', 'Cc07_g01520' => 'ccan', 'Cc11_g15810' => 'ccan', 'CDE02G2840' => 'cde', 'CDE03G0093' => 'cde', 'CDE04G2127' => 'cde', 'CDE07G1857' => 'cde', 'CDE09G1246' => 'cde', 'Cfa003412' => 'cfa', 'Cfa007341' => 'cfa', 'Cfa009220' => 'cfa', 'Ciclev10008737m.g' => 'ccl', 'Ciclev10015565m.g' => 'ccl', 'Ciclev10031761m.g' => 'ccl', 'CiPaw.03G045300' => 'cil', 'CiPaw.03G247200' => 'cil', 'CiPaw.04G029500' => 'cil', 'CiPaw.04G174000' => 'cil', 'CiPaw.05G181200' => 'cil', 'CiPaw.06G067100' => 'cil', 'ClCG05G025800' => 'cla', 'ClCG06G011400' => 'cla', 'ClCG09G019360' => 'cla', 'COL.COLO4_04827' => 'col', 'COL.COLO4_29170' => 'col', 'COL.COLO4_35131' => 'col', 'COL.COLO4_35132' => 'col', 'Cpa.g.sc33.32' => 'cpa', 'Cpa.g.sc46.29' => 'cpa', 'Cpa.g.sc796.1' => 'cpa', 'CsaV3_1G030420' => 'csa', 'CsaV3_5G027050' => 'csa', 'CsaV3_5G031040' => 'csa', 'CsaV3_UNG023130' => 'csa', 'CSS0007726' => 'camsi', 'CSS0016433' => 'camsi', 'CSS0017656' => 'camsi', 'CSS0025364' => 'camsi', 'CSS0027582' => 'camsi', 'CSS0047288' => 'camsi', 'CSS0049950' => 'camsi', 'DCAR_003843' => 'dca', 'DCAR_007052' => 'dca', 'DCAR_020884' => 'dca', 'DCAR_021730' => 'dca', 'DCAR_024423' => 'dca', 'DCAR_026509' => 'dca', 'DCAR_031158' => 'dca', 'Dinv14728' => 'din', 'Dinv15219' => 'din', 'Dinv25728' => 'din', 'Dinv33428' => 'din', 'Dinv36489' => 'din', 'Dinv41486' => 'din', 'Duzib147G0469' => 'dzi', 'Duzib168G0060' => 'dzi', 'Duzib187G1215' => 'dzi', 'Duzib248G0692' => 'dzi', 'Duzib251G0767' => 'dzi', 'Duzib264G0446' => 'dzi', 'Duzib268G0691' => 'dzi', 'ECA232G4767' => 'eca', 'ECA233G2838' => 'eca', 'ECA234G0391' => 'eca', 'ECA234G0857' => 'eca', 'ECA236G1593' => 'eca', 'ECA238G0565' => 'eca', 'ECA246G1027' => 'eca', 'ECA246G3223' => 'eca', 'ECA246G3470' => 'eca', 'EL10Ac6g13829' => 'bvu', 'EL10Ac6g14093' => 'bvu', 'EL10Ac8g18707' => 'bvu', 'Eucgr.C01369' => 'egr', 'Eucgr.H02492' => 'egr', 'Eucgr.I01733' => 'egr', 'Eucgr.J02255' => 'egr', 'Eucgr.J02257' => 'egr', 'Eucgr.J02258' => 'egr', 'FAN02G1601' => 'fan', 'FAN03G1586' => 'fan', 'FAN03G2986' => 'fan', 'FAN05G4837' => 'fan', 'FAN06G0146' => 'fan', 'FAN07G0858' => 'fan', 'FAN09G3179' => 'fan', 'FAN10G0669' => 'fan', 'FAN12G2358' => 'fan', 'FAN14G4198' => 'fan', 'FAN14G5112' => 'fan', 'FAN17G0342' => 'fan', 'FAN19G0342' => 'fan', 'FAN19G0962' => 'fan', 'FAN19G1101' => 'fan', 'FAN19G1872' => 'fan', 'FAN22G0356' => 'fan', 'FAN23G0744' => 'fan', 'FAN23G1914' => 'fan', 'FAN26G0032' => 'fan', 'FAN28G0625' => 'fan', 'FvH4_1g02710' => 'fve', 'FvH4_1g02720' => 'fve', 'FvH4_4g25670' => 'fve', 'FvH4_6g51700' => 'fve', 'FvH4_7g20170' => 'fve', 'Glyma.05G175000' => 'gma', 'Glyma.08G132300' => 'gma', 'Glyma.11G243000' => 'gma', 'Glyma.13G158900' => 'gma', 'Glyma.17G112400' => 'gma', 'Glyma.18G014100' => 'gma', 'Glyma.19G003100' => 'gma', 'Glyma.19G056500' => 'gma', 'Gohir.A01G158900' => 'ghi', 'Gohir.A05G312600' => 'ghi', 'Gohir.A05G354900' => 'ghi', 'Gohir.A07G037200' => 'ghi', 'Gohir.A09G030000' => 'ghi', 'Gohir.A12G145200' => 'ghi', 'Gohir.D01G151500' => 'ghi', 'Gohir.D04G058300' => 'ghi', 'Gohir.D05G314100' => 'ghi', 'Gohir.D07G041400' => 'ghi', 'Gohir.D09G029700' => 'ghi', 'Gohir.D12G149700' => 'ghi', 'Gorai.001G043800' => 'gra', 'Gorai.002G187800' => 'gra', 'Gorai.006G034700' => 'gra', 'Gorai.008G161200' => 'gra', 'Gorai.009G335700' => 'gra', 'Gorai.012G065000' => 'gra', 'GSVIVG01000535001' => 'vvi', 'GSVIVG01015572001' => 'vvi', 'GSVIVG01032386001' => 'vvi', 'HanXRQChr05g0138531' => 'han', 'HanXRQChr06g0174391' => 'han', 'HanXRQChr07g0199021' => 'han', 'HanXRQChr08g0208211' => 'han', 'HanXRQChr09g0255471' => 'han', 'HanXRQChr10g0315791' => 'han', 'HanXRQChr12g0371991' => 'han', 'HanXRQChr15g0475251' => 'han', 'HanXRQChr17g0540001' => 'han', 'HanXRQChr17g0548631' => 'han', 'HanXRQChr17g0569561' => 'han', 'Haze_12256' => 'cav', 'Haze_14756' => 'cav', 'Haze_25528' => 'cav', 'Hma1.2p1_0079F.1_g041020' => 'hma', 'Hma1.2p1_0818F.1_g223260' => 'hma', 'Hma1.2p1_1747F.1_g300530' => 'hma', 'HPP92_004607' => 'vpl', 'HPP92_004608' => 'vpl', 'HPP92_006181' => 'vpl', 'HPP92_012192' => 'vpl', 'HPP92_015680' => 'vpl', 'HPP92_020249' => 'vpl', 'HPP92_021376' => 'vpl', 'HPP92_024275' => 'vpl', 'Hund06031' => 'sun', 'Hund25391' => 'sun', 'Lalb_Chr07g0185371' => 'lal', 'Lalb_Chr07g0185381' => 'lal', 'Lalb_Chr12g0204011' => 'lal', 'Lalb_Chr13g0301671' => 'lal', 'Lalb_Chr14g0362851' => 'lal', 'Lalb_Chr24g0403581' => 'lal', 'Lj1g0000233' => 'lja', 'Lj2g0018120' => 'lja', 'Lj3C621T0' => 'lonja', 'Lj3P1059T14' => 'lonja', 'Lj3P611T9' => 'lonja', 'Lj3P614T13' => 'lonja', 'Lj3P615T5' => 'lonja', 'Lj4g0012315' => 'lja', 'Lj4g0026182' => 'lja', 'Lj6P813T16' => 'lonja', 'Lj7C427T7' => 'lonja', 'Lj7C427T8' => 'lonja', 'Lj7P600T41' => 'lonja', 'Lju41C42G17' => 'lonja', 'Lsat_1_v5_gn_0_47300' => 'lsa', 'Lsat_1_v5_gn_2_91280' => 'lsa', 'Lsat_1_v5_gn_3_30561' => 'lsa', 'Lsat_1_v5_gn_4_184321' => 'lsa', 'Lsat_1_v5_gn_4_4041' => 'lsa', 'Lsat_1_v5_gn_5_92000' => 'lsa', 'Lsat_1_v5_gn_8_152940' => 'lsa', 'Lsat_1_v5_gn_8_62401' => 'lsa', 'Manes.06G055900' => 'mes', 'Manes.12G022200' => 'mes', 'Manes.13G023300' => 'mes', 'Manes.14G115000' => 'mes', 'Manes.15G151700' => 'mes', 'Manes.17G111300' => 'mes', 'Mapoly0226s0009' => 'mpo', 'MBI02_g25363_MAGBIO' => 'mbi', 'MBI06_g00027_MAGBIO' => 'mbi', 'MBI10_g13034_MAGBIO' => 'mbi', 'MD09G1023400' => 'mdo', 'MD13G1100100' => 'mdo', 'MD15G1169200' => 'mdo', 'MD16G1101100' => 'mdo', 'MD17G1022900' => 'mdo', 'Medtr3g096150' => 'mtr', 'Medtr4g115070' => 'mtr', 'Medtr7g033325' => 'mtr', 'Medtr8g089840' => 'mtr', 'MELO3C010319.2' => 'cme', 'MELO3C011944.2' => 'cme', 'MELO3C021589.2' => 'cme', 'Migut.E00207' => 'egut', 'Migut.H00067' => 'egut', 'Migut.K00433' => 'egut', 'Migut.K00606' => 'egut', 'Migut.K01410' => 'egut', 'MSTRG.13347' => 'ama', 'MSTRG.24045' => 'ama', 'MSTRG.2428' => 'ama', 'MSTRG.26410' => 'ama', 'MSTRG.3139' => 'ama', 'MSTRG.3286' => 'ama', 'MSTRG.563' => 'ama', 'MSTRG.7941' => 'ama', 'Nitab4.5_0000028g0060' => 'nta', 'Nitab4.5_0000065g0260' => 'nta', 'Nitab4.5_0000112g0060' => 'nta', 'Nitab4.5_0000489g0120' => 'nta', 'Nitab4.5_0001776g0050' => 'nta', 'Nitab4.5_0001854g0010' => 'nta', 'Nitab4.5_0001860g0020' => 'nta', 'Nitab4.5_0004352g0010' => 'nta', 'Nitab4.5_0008716g0020' => 'nta', 'Nitab4.5_0008922g0010' => 'nta', 'Nn3g16693' => 'nnu', 'Nn4g22596' => 'nnu', 'Nn7g37639' => 'nnu', 'Oeu001701.1' => 'oeu', 'Oeu018149.1' => 'oeu', 'Oeu026220.1' => 'oeu', 'Oeu038635.1' => 'oeu', 'Oeu049176.1' => 'oeu', 'Oeu056706.1' => 'oeu', 'Oeu056937.1' => 'oeu', 'Oeu057540.1' => 'oeu', 'Os02g0594900' => 'osa', 'Os02g0595100' => 'osa', 'Os04g0477500' => 'osa', 'Os12g0611900' => 'osa', 'Peaxi162Scf00076g00020' => 'pax', 'Peaxi162Scf00128g00217' => 'pax', 'Peaxi162Scf00129g01640' => 'pax', 'Peaxi162Scf00669g00007' => 'pax', 'Peaxi162Scf00700g00421' => 'pax', 'Peaxi162Scf00801g00038' => 'pax', 'Peaxi162Scf00891g00025' => 'pax', 'PGR083G0909' => 'pgr', 'PGR119G1005' => 'pgr', 'PGR142G2236' => 'pgr', 'PGR142G3388' => 'pgr', 'PGSC0003DMG400004514' => 'stu', 'PGSC0003DMG400012635' => 'stu', 'PGSC0003DMG400015730' => 'stu', 'PGSC0003DMG400018611' => 'stu', 'PGSC0003DMG400030897' => 'stu', 'Phvul.001G254800' => 'pvu', 'Phvul.002G260100' => 'pvu', 'Phvul.003G167600' => 'pvu', 'Phvul.004G005100' => 'pvu', 'Potri.001G343600' => 'ptr', 'Potri.006G066700' => 'ptr', 'Potri.008G186000' => 'ptr', 'Potri.010G046900' => 'ptr', 'Potri.018G127900' => 'ptr', 'Pp3c20_17750' => 'ppa', 'Pp3c24_4380' => 'ppa', 'Prupe.1G245800' => 'ppe', 'Prupe.3G293400' => 'ppe', 'Prupe.7G247400' => 'ppe', 'Psat0s145g0120' => 'psa', 'Psat0s595g0040' => 'psa', 'Psat0s595g0120' => 'psa', 'Psat3g175040' => 'psa', 'Psat7g058120' => 'psa', 'PSO017G0428' => 'pso', 'PSO063G7510' => 'pso', 'PSO067G0046' => 'pso', 'PSO478G1073' => 'pso', 'PSO675G3677' => 'pso', 'PSO675G6558' => 'pso', 'PSO675G7520' => 'pso', 'PSO675G8959' => 'pso', 'QL02p074089' => 'qlo', 'QL02p089614' => 'qlo', 'QL03p057736' => 'qlo', 'RcHm_v2.0_Chr1g0364131' => 'rch', 'RcHm_v2.0_Chr2g0087801' => 'rch', 'RcHm_v2.0_Chr2g0087821' => 'rch', 'RcHm_v2.0_Chr2g0173231' => 'rch', 'RcHm_v2.0_Chr4g0433111' => 'rch', 'Rhsim03G0250300' => 'rsi', 'Rhsim08G0048400' => 'rsi', 'Rhsim10G0014800' => 'rsi', 'Rhsim12G0040100' => 'rsi', 'Rhsim12G0109700' => 'rsi', 'Sabra06G0049600' => 'sbr', 'Sabra08G0141000' => 'sbr', 'Sabra10G0021400' => 'sbr', 'Sabra16G0222900' => 'sbr', 'Sabra18G0108600' => 'sbr', 'SalBow1G0433' => 'sbo', 'SalBow1G2038' => 'sbo', 'SalBow1G5003' => 'sbo', 'SalBow7G1197' => 'sbo', 'SalBow8G3506' => 'sbo', 'Sc03g0007300' => 'sci', 'Sc11g0000950' => 'sci', 'Sc14g0008750' => 'sci', 'Sc18g0000420' => 'sci', 'Sed0006754' => 'sed', 'Sed0008741' => 'sed', 'Sed0017172' => 'sed', 'Sed0018925' => 'sed', 'Sed0023326' => 'sed', 'Sed0025909' => 'sed', 'SEGI_05333' => 'sgi', 'SEGI_10362' => 'sgi', 'SEGI_13380' => 'sgi', 'SEGI_24306' => 'sgi', 'SEGI_29077' => 'sgi', 'SEGI_29095' => 'sgi', 'SEGI_36534' => 'sgi', 'SEGI_37506' => 'sgi', 'SEGI_38321' => 'sgi', 'SGA_v2.0_scaffold307G48031' => 'sas', 'SGA_v2.0_scaffold47G17507' => 'sas', 'SGA_v2.0_scaffold63G21736' => 'sas', 'SGA_v2.0_scaffold87G27070' => 'sas', 'SHI17794' => 'shi', 'SHI28851' => 'shi', 'SMO165G0155' => 'smo', 'SMO340G0217' => 'smo', 'SMO367G1210' => 'smo', 'Solyc02g093430.3' => 'sly', 'Solyc05g013580.4' => 'sly', 'Solyc07g008030.3' => 'sly', 'Solyc12g035470.2' => 'sly', 'Sopen02g038020' => 'spe', 'Sopen05g008490' => 'spe', 'Sopen07g003910' => 'spe', 'Sopen12g015240' => 'spe', 'Sp1g11550' => 'spa', 'Sp2g16710' => 'spa', 'Sp3g00430' => 'spa', 'Sp3g26780' => 'spa', 'Sp5g22900' => 'spa', 'Sp6g29530' => 'spa', 'TAR371G0794' => 'tar', 'TAR374G0164' => 'tar', 'TAR622G0165' => 'tar', 'TAR626G0929' => 'tar', 'TAR629G2155' => 'tar', 'THA.LOC104805282' => 'tha', 'THA.LOC104805363' => 'tha', 'THA.LOC104808968' => 'tha', 'THA.LOC104821093' => 'tha', 'THA.LOC104823953' => 'tha', 'THA.LOC104825562' => 'tha', 'THA.LOC104825665' => 'tha', 'Thecc.02G261400' => 'tca', 'Thecc.04G019200' => 'tca', 'Thecc.09G130400' => 'tca', 'Thhalv10004374m.g' => 'esa', 'Thhalv10007850m.g' => 'esa', 'Thhalv10013782m.g' => 'esa', 'Thhalv10018686m.g' => 'esa', 'Thhalv10020899m.g' => 'esa', 'Thhalv10022755m.g' => 'esa', 'TPR.G23851' => 'tpr', 'TPR.G26500' => 'tpr', 'TPR.G27267' => 'tpr', 'TPR.G32001' => 'tpr', 'TPR.G6251' => 'tpr', 'TPR.G8167' => 'tpr', 'TWI12G1330' => 'twi', 'TWI18G1239' => 'twi', 'TWI34G0979' => 'twi', 'TWI36G0670' => 'twi', 'TWI36G0707' => 'twi', 'TWI56G0233' => 'twi', 'TWI75G1809' => 'twi', 'unitig_21.g20874' => 'ugi', 'unitig_26.g10343' => 'ugi', 'unitig_46.g18392' => 'ugi', 'unitig_52.g17178' => 'ugi', 'unitig_8.g2934' => 'ugi', 'vmacro01122' => 'vma', 'vmacro05875' => 'vma', 'vmacro06147' => 'vma', 'vmacro16191' => 'vma', 'vmacro18293' => 'vma', 'VMungo0251G3707' => 'vmu', 'VMungo0464G1521' => 'vmu', 'VMungo1215G0205' => 'vmu', 'VMungo1383G2484' => 'vmu', 'Zm00001eb079610' => 'zma', 'Zm00001eb135990' => 'zma', 'Zm00001eb183710' => 'zma', 'Zm00001eb246020' => 'zma' ), 'gf_id' => 'HOM05D001124', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001124' ), 'data_identifier' => 'HOM05D001124', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001124', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '548', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02520' => 'bna', 'A03p06630' => 'bna', 'A05p44460' => 'bna', 'A06p08710' => 'bna', 'A06p41090' => 'bna', 'A07p32320' => 'bna', 'A08p32520' => 'bna', 'A09p10360' => 'bna', 'A10p24080' => 'bna', 'Aa31LG11G15250' => 'aar', 'Aa31LG1G1800' => 'aar', 'Aa31LG2G5120' => 'aar', 'Aa31LG2G6070' => 'aar', 'Aa31LG5G10770' => 'aar', 'Aa31sc61G90' => 'aar', 'Actinidia01352' => 'ach', 'Actinidia05983' => 'ach', 'Actinidia08133' => 'ach', 'Actinidia15101' => 'ach', 'Actinidia26379' => 'ach', 'Actinidia35778' => 'ach', 'Actinidia36123' => 'ach', 'Actinidia37436' => 'ach', 'Actinidia38730' => 'ach', 'Ah.02g128210' => 'amhyb', 'Ah.03g132990' => 'amhyb', 'Ah.14g079410' => 'amhyb', 'AL1G24640' => 'aly', 'AL2G26680' => 'aly', 'AL3G10530' => 'aly', 'AL3G45230' => 'aly', 'AL5G15230' => 'aly', 'AL5G16960' => 'aly', 'AL6G25210' => 'aly', 'Aqoxy2G00441' => 'aox', 'Aqoxy3G01236' => 'aox', 'Aqoxy5G03746' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3RQ047' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C7GMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9C8JER' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MBL6KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YXCZ83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZANX40' => 'arhy', 'AT1G12990' => 'ath', 'AT1G67880' => 'ath', 'AT2G13290' => 'ath', 'AT3G01620' => 'ath', 'AT3G26445' => 'ath', 'AT3G27540' => 'ath', 'AT5G14480' => 'ath', 'ATR0824G026' => 'atr', 'ATR1098G019' => 'atr', 'Atru.chr11.2145' => 'acertr', 'Atru.chr2.3636' => 'acertr', 'Atru.chr2.3644' => 'acertr', 'Atru.chr6.2422' => 'acertr', 'Atru.chr7.1112' => 'acertr', 'AUR62005469' => 'cqu', 'AUR62011166' => 'cqu', 'AUR62013319' => 'cqu', 'AUR62024273' => 'cqu', 'AUR62028420' => 'cqu', 'AUR62041942' => 'cqu', 'BcaB01g04969' => 'bca', 'BcaB01g06371' => 'bca', 'BcaB02g11494' => 'bca', 'BcaB03g15382' => 'bca', 'BcaB08g36994' => 'bca', 'BcaC03g13477' => 'bca', 'BcaC03g13478' => 'bca', 'BcaC03g13480' => 'bca', 'BcaC03g13481' => 'bca', 'BcaC03g13486' => 'bca', 'BcaC04g19031' => 'bca', 'BcaC04g23085' => 'bca', 'BcaC05g25094' => 'bca', 'BcaC05g25096' => 'bca', 'BcaC05g25138' => 'bca', 'BcaC05g30416' => 'bca', 'BcaC05g30455' => 'bca', 'BcaC06g30979' => 'bca', 'BcaC06g33805' => 'bca', 'BcaC08g46021' => 'bca', 'BcaNung03154' => 'bca', 'BolC2t06623H' => 'bol', 'BolC2t06632H' => 'bol', 'BolC2t06635H' => 'bol', 'BolC2t06638H' => 'bol', 'BolC3t13266H' => 'bol', 'BolC5t29776H' => 'bol', 'BolC6t38912H' => 'bol', 'BolC7t44183H' => 'bol', 'BolC9t54123H' => 'bol', 'BolC9t59107H' => 'bol', 'BraA02t05221Z' => 'bra', 'BraA03t09996Z' => 'bra', 'BraA05t23210Z' => 'bra', 'BraA06t24068Z' => 'bra', 'BraA06t27032Z' => 'bra', 'BraA08t35176Z' => 'bra', 'BraA09t36680Z' => 'bra', 'BraA10t44471Z' => 'bra', 'C02p06760' => 'bna', 'C02p06890' => 'bna', 'C02p07010' => 'bna', 'C03p07660' => 'bna', 'C05p10300' => 'bna', 'C06p38150' => 'bna', 'C07p36650' => 'bna', 'C08p15770' => 'bna', 'C09p12300' => 'bna', 'C09p62700' => 'bna', 'C09p75040' => 'bna', 'CAN.G13.1' => 'can', 'CAN.G138.4' => 'can', 'CAN.G44.6' => 'can', 'CAN.G473.19' => 'can', 'CANSAT01G0835' => 'cansat', 'CANSAT11G0246' => 'cansat', 'CANSAT11G1766' => 'cansat', 'CANSAT64G1954' => 'cansat', 'CARHR013330' => 'chi', 'CARHR060530' => 'chi', 'CARHR075300' => 'chi', 'CARHR105120' => 'chi', 'CARHR148910' => 'chi', 'CARHR198830' => 'chi', 'Carub.0001s1275' => 'cru', 'Carub.0002s1437' => 'cru', 'Carub.0003s0044' => 'cru', 'Carub.0003s2787' => 'cru', 'Carub.0005s0597' => 'cru', 'Carub.0006s1266' => 'cru', 'Ca_06935_v3' => 'car', 'Ca_13559_v3' => 'car', 'Ca_16941_v3' => 'car', 'Ca_16960_v3' => 'car', 'Ca_17775_v3' => 'car', 'Ca_30464_v3' => 'car', 'Cc06_g08160' => 'ccan', 'Cc07_g01520' => 'ccan', 'Cc11_g15810' => 'ccan', 'CDE02G2840' => 'cde', 'CDE03G0093' => 'cde', 'CDE04G2127' => 'cde', 'CDE07G1857' => 'cde', 'CDE09G1246' => 'cde', 'Cfa003412' => 'cfa', 'Cfa007341' => 'cfa', 'Cfa009220' => 'cfa', 'Ciclev10008737m.g' => 'ccl', 'Ciclev10015565m.g' => 'ccl', 'Ciclev10031761m.g' => 'ccl', 'CiPaw.03G045300' => 'cil', 'CiPaw.03G247200' => 'cil', 'CiPaw.04G029500' => 'cil', 'CiPaw.04G174000' => 'cil', 'CiPaw.05G181200' => 'cil', 'CiPaw.06G067100' => 'cil', 'ClCG05G025800' => 'cla', 'ClCG06G011400' => 'cla', 'ClCG09G019360' => 'cla', 'COL.COLO4_04827' => 'col', 'COL.COLO4_29170' => 'col', 'COL.COLO4_35131' => 'col', 'COL.COLO4_35132' => 'col', 'Cpa.g.sc33.32' => 'cpa', 'Cpa.g.sc46.29' => 'cpa', 'Cpa.g.sc796.1' => 'cpa', 'CsaV3_1G030420' => 'csa', 'CsaV3_5G027050' => 'csa', 'CsaV3_5G031040' => 'csa', 'CsaV3_UNG023130' => 'csa', 'CSS0007726' => 'camsi', 'CSS0016433' => 'camsi', 'CSS0017656' => 'camsi', 'CSS0025364' => 'camsi', 'CSS0027582' => 'camsi', 'CSS0047288' => 'camsi', 'CSS0049950' => 'camsi', 'DCAR_003843' => 'dca', 'DCAR_007052' => 'dca', 'DCAR_020884' => 'dca', 'DCAR_021730' => 'dca', 'DCAR_024423' => 'dca', 'DCAR_026509' => 'dca', 'DCAR_031158' => 'dca', 'Dinv14728' => 'din', 'Dinv15219' => 'din', 'Dinv25728' => 'din', 'Dinv33428' => 'din', 'Dinv36489' => 'din', 'Dinv41486' => 'din', 'Duzib147G0469' => 'dzi', 'Duzib168G0060' => 'dzi', 'Duzib187G1215' => 'dzi', 'Duzib248G0692' => 'dzi', 'Duzib251G0767' => 'dzi', 'Duzib264G0446' => 'dzi', 'Duzib268G0691' => 'dzi', 'ECA232G4767' => 'eca', 'ECA233G2838' => 'eca', 'ECA234G0391' => 'eca', 'ECA234G0857' => 'eca', 'ECA236G1593' => 'eca', 'ECA238G0565' => 'eca', 'ECA246G1027' => 'eca', 'ECA246G3223' => 'eca', 'ECA246G3470' => 'eca', 'EL10Ac6g13829' => 'bvu', 'EL10Ac6g14093' => 'bvu', 'EL10Ac8g18707' => 'bvu', 'Eucgr.C01369' => 'egr', 'Eucgr.H02492' => 'egr', 'Eucgr.I01733' => 'egr', 'Eucgr.J02255' => 'egr', 'Eucgr.J02257' => 'egr', 'Eucgr.J02258' => 'egr', 'FAN02G1601' => 'fan', 'FAN03G1586' => 'fan', 'FAN03G2986' => 'fan', 'FAN05G4837' => 'fan', 'FAN06G0146' => 'fan', 'FAN07G0858' => 'fan', 'FAN09G3179' => 'fan', 'FAN10G0669' => 'fan', 'FAN12G2358' => 'fan', 'FAN14G4198' => 'fan', 'FAN14G5112' => 'fan', 'FAN17G0342' => 'fan', 'FAN19G0342' => 'fan', 'FAN19G0962' => 'fan', 'FAN19G1101' => 'fan', 'FAN19G1872' => 'fan', 'FAN22G0356' => 'fan', 'FAN23G0744' => 'fan', 'FAN23G1914' => 'fan', 'FAN26G0032' => 'fan', 'FAN28G0625' => 'fan', 'FvH4_1g02710' => 'fve', 'FvH4_1g02720' => 'fve', 'FvH4_4g25670' => 'fve', 'FvH4_6g51700' => 'fve', 'FvH4_7g20170' => 'fve', 'Glyma.05G175000' => 'gma', 'Glyma.08G132300' => 'gma', 'Glyma.11G243000' => 'gma', 'Glyma.13G158900' => 'gma', 'Glyma.17G112400' => 'gma', 'Glyma.18G014100' => 'gma', 'Glyma.19G003100' => 'gma', 'Glyma.19G056500' => 'gma', 'Gohir.A01G158900' => 'ghi', 'Gohir.A05G312600' => 'ghi', 'Gohir.A05G354900' => 'ghi', 'Gohir.A07G037200' => 'ghi', 'Gohir.A09G030000' => 'ghi', 'Gohir.A12G145200' => 'ghi', 'Gohir.D01G151500' => 'ghi', 'Gohir.D04G058300' => 'ghi', 'Gohir.D05G314100' => 'ghi', 'Gohir.D07G041400' => 'ghi', 'Gohir.D09G029700' => 'ghi', 'Gohir.D12G149700' => 'ghi', 'Gorai.001G043800' => 'gra', 'Gorai.002G187800' => 'gra', 'Gorai.006G034700' => 'gra', 'Gorai.008G161200' => 'gra', 'Gorai.009G335700' => 'gra', 'Gorai.012G065000' => 'gra', 'GSVIVG01000535001' => 'vvi', 'GSVIVG01015572001' => 'vvi', 'GSVIVG01032386001' => 'vvi', 'HanXRQChr05g0138531' => 'han', 'HanXRQChr06g0174391' => 'han', 'HanXRQChr07g0199021' => 'han', 'HanXRQChr08g0208211' => 'han', 'HanXRQChr09g0255471' => 'han', 'HanXRQChr10g0315791' => 'han', 'HanXRQChr12g0371991' => 'han', 'HanXRQChr15g0475251' => 'han', 'HanXRQChr17g0540001' => 'han', 'HanXRQChr17g0548631' => 'han', 'HanXRQChr17g0569561' => 'han', 'Haze_12256' => 'cav', 'Haze_14756' => 'cav', 'Haze_25528' => 'cav', 'Hma1.2p1_0079F.1_g041020' => 'hma', 'Hma1.2p1_0818F.1_g223260' => 'hma', 'Hma1.2p1_1747F.1_g300530' => 'hma', 'HPP92_004607' => 'vpl', 'HPP92_004608' => 'vpl', 'HPP92_006181' => 'vpl', 'HPP92_012192' => 'vpl', 'HPP92_015680' => 'vpl', 'HPP92_020249' => 'vpl', 'HPP92_021376' => 'vpl', 'HPP92_024275' => 'vpl', 'Hund06031' => 'sun', 'Hund25391' => 'sun', 'Lalb_Chr07g0185371' => 'lal', 'Lalb_Chr07g0185381' => 'lal', 'Lalb_Chr12g0204011' => 'lal', 'Lalb_Chr13g0301671' => 'lal', 'Lalb_Chr14g0362851' => 'lal', 'Lalb_Chr24g0403581' => 'lal', 'Lj1g0000233' => 'lja', 'Lj2g0018120' => 'lja', 'Lj3C621T0' => 'lonja', 'Lj3P1059T14' => 'lonja', 'Lj3P611T9' => 'lonja', 'Lj3P614T13' => 'lonja', 'Lj3P615T5' => 'lonja', 'Lj4g0012315' => 'lja', 'Lj4g0026182' => 'lja', 'Lj6P813T16' => 'lonja', 'Lj7C427T7' => 'lonja', 'Lj7C427T8' => 'lonja', 'Lj7P600T41' => 'lonja', 'Lju41C42G17' => 'lonja', 'Lsat_1_v5_gn_0_47300' => 'lsa', 'Lsat_1_v5_gn_2_91280' => 'lsa', 'Lsat_1_v5_gn_3_30561' => 'lsa', 'Lsat_1_v5_gn_4_184321' => 'lsa', 'Lsat_1_v5_gn_4_4041' => 'lsa', 'Lsat_1_v5_gn_5_92000' => 'lsa', 'Lsat_1_v5_gn_8_152940' => 'lsa', 'Lsat_1_v5_gn_8_62401' => 'lsa', 'Manes.06G055900' => 'mes', 'Manes.12G022200' => 'mes', 'Manes.13G023300' => 'mes', 'Manes.14G115000' => 'mes', 'Manes.15G151700' => 'mes', 'Manes.17G111300' => 'mes', 'Mapoly0226s0009' => 'mpo', 'MBI02_g25363_MAGBIO' => 'mbi', 'MBI06_g00027_MAGBIO' => 'mbi', 'MBI10_g13034_MAGBIO' => 'mbi', 'MD09G1023400' => 'mdo', 'MD13G1100100' => 'mdo', 'MD15G1169200' => 'mdo', 'MD16G1101100' => 'mdo', 'MD17G1022900' => 'mdo', 'Medtr3g096150' => 'mtr', 'Medtr4g115070' => 'mtr', 'Medtr7g033325' => 'mtr', 'Medtr8g089840' => 'mtr', 'MELO3C010319.2' => 'cme', 'MELO3C011944.2' => 'cme', 'MELO3C021589.2' => 'cme', 'Migut.E00207' => 'egut', 'Migut.H00067' => 'egut', 'Migut.K00433' => 'egut', 'Migut.K00606' => 'egut', 'Migut.K01410' => 'egut', 'MSTRG.13347' => 'ama', 'MSTRG.24045' => 'ama', 'MSTRG.2428' => 'ama', 'MSTRG.26410' => 'ama', 'MSTRG.3139' => 'ama', 'MSTRG.3286' => 'ama', 'MSTRG.563' => 'ama', 'MSTRG.7941' => 'ama', 'Nitab4.5_0000028g0060' => 'nta', 'Nitab4.5_0000065g0260' => 'nta', 'Nitab4.5_0000112g0060' => 'nta', 'Nitab4.5_0000489g0120' => 'nta', 'Nitab4.5_0001776g0050' => 'nta', 'Nitab4.5_0001854g0010' => 'nta', 'Nitab4.5_0001860g0020' => 'nta', 'Nitab4.5_0004352g0010' => 'nta', 'Nitab4.5_0008716g0020' => 'nta', 'Nitab4.5_0008922g0010' => 'nta', 'Nn3g16693' => 'nnu', 'Nn4g22596' => 'nnu', 'Nn7g37639' => 'nnu', 'Oeu001701.1' => 'oeu', 'Oeu018149.1' => 'oeu', 'Oeu026220.1' => 'oeu', 'Oeu038635.1' => 'oeu', 'Oeu049176.1' => 'oeu', 'Oeu056706.1' => 'oeu', 'Oeu056937.1' => 'oeu', 'Oeu057540.1' => 'oeu', 'Os02g0594900' => 'osa', 'Os02g0595100' => 'osa', 'Os04g0477500' => 'osa', 'Os12g0611900' => 'osa', 'Peaxi162Scf00076g00020' => 'pax', 'Peaxi162Scf00128g00217' => 'pax', 'Peaxi162Scf00129g01640' => 'pax', 'Peaxi162Scf00669g00007' => 'pax', 'Peaxi162Scf00700g00421' => 'pax', 'Peaxi162Scf00801g00038' => 'pax', 'Peaxi162Scf00891g00025' => 'pax', 'PGR083G0909' => 'pgr', 'PGR119G1005' => 'pgr', 'PGR142G2236' => 'pgr', 'PGR142G3388' => 'pgr', 'PGSC0003DMG400004514' => 'stu', 'PGSC0003DMG400012635' => 'stu', 'PGSC0003DMG400015730' => 'stu', 'PGSC0003DMG400018611' => 'stu', 'PGSC0003DMG400030897' => 'stu', 'Phvul.001G254800' => 'pvu', 'Phvul.002G260100' => 'pvu', 'Phvul.003G167600' => 'pvu', 'Phvul.004G005100' => 'pvu', 'Potri.001G343600' => 'ptr', 'Potri.006G066700' => 'ptr', 'Potri.008G186000' => 'ptr', 'Potri.010G046900' => 'ptr', 'Potri.018G127900' => 'ptr', 'Pp3c20_17750' => 'ppa', 'Pp3c24_4380' => 'ppa', 'Prupe.1G245800' => 'ppe', 'Prupe.3G293400' => 'ppe', 'Prupe.7G247400' => 'ppe', 'Psat0s145g0120' => 'psa', 'Psat0s595g0040' => 'psa', 'Psat0s595g0120' => 'psa', 'Psat3g175040' => 'psa', 'Psat7g058120' => 'psa', 'PSO017G0428' => 'pso', 'PSO063G7510' => 'pso', 'PSO067G0046' => 'pso', 'PSO478G1073' => 'pso', 'PSO675G3677' => 'pso', 'PSO675G6558' => 'pso', 'PSO675G7520' => 'pso', 'PSO675G8959' => 'pso', 'QL02p074089' => 'qlo', 'QL02p089614' => 'qlo', 'QL03p057736' => 'qlo', 'RcHm_v2.0_Chr1g0364131' => 'rch', 'RcHm_v2.0_Chr2g0087801' => 'rch', 'RcHm_v2.0_Chr2g0087821' => 'rch', 'RcHm_v2.0_Chr2g0173231' => 'rch', 'RcHm_v2.0_Chr4g0433111' => 'rch', 'Rhsim03G0250300' => 'rsi', 'Rhsim08G0048400' => 'rsi', 'Rhsim10G0014800' => 'rsi', 'Rhsim12G0040100' => 'rsi', 'Rhsim12G0109700' => 'rsi', 'Sabra06G0049600' => 'sbr', 'Sabra08G0141000' => 'sbr', 'Sabra10G0021400' => 'sbr', 'Sabra16G0222900' => 'sbr', 'Sabra18G0108600' => 'sbr', 'SalBow1G0433' => 'sbo', 'SalBow1G2038' => 'sbo', 'SalBow1G5003' => 'sbo', 'SalBow7G1197' => 'sbo', 'SalBow8G3506' => 'sbo', 'Sc03g0007300' => 'sci', 'Sc11g0000950' => 'sci', 'Sc14g0008750' => 'sci', 'Sc18g0000420' => 'sci', 'Sed0006754' => 'sed', 'Sed0008741' => 'sed', 'Sed0017172' => 'sed', 'Sed0018925' => 'sed', 'Sed0023326' => 'sed', 'Sed0025909' => 'sed', 'SEGI_05333' => 'sgi', 'SEGI_10362' => 'sgi', 'SEGI_13380' => 'sgi', 'SEGI_24306' => 'sgi', 'SEGI_29077' => 'sgi', 'SEGI_29095' => 'sgi', 'SEGI_36534' => 'sgi', 'SEGI_37506' => 'sgi', 'SEGI_38321' => 'sgi', 'SGA_v2.0_scaffold307G48031' => 'sas', 'SGA_v2.0_scaffold47G17507' => 'sas', 'SGA_v2.0_scaffold63G21736' => 'sas', 'SGA_v2.0_scaffold87G27070' => 'sas', 'SHI17794' => 'shi', 'SHI28851' => 'shi', 'SMO165G0155' => 'smo', 'SMO340G0217' => 'smo', 'SMO367G1210' => 'smo', 'Solyc02g093430.3' => 'sly', 'Solyc05g013580.4' => 'sly', 'Solyc07g008030.3' => 'sly', 'Solyc12g035470.2' => 'sly', 'Sopen02g038020' => 'spe', 'Sopen05g008490' => 'spe', 'Sopen07g003910' => 'spe', 'Sopen12g015240' => 'spe', 'Sp1g11550' => 'spa', 'Sp2g16710' => 'spa', 'Sp3g00430' => 'spa', 'Sp3g26780' => 'spa', 'Sp5g22900' => 'spa', 'Sp6g29530' => 'spa', 'TAR371G0794' => 'tar', 'TAR374G0164' => 'tar', 'TAR622G0165' => 'tar', 'TAR626G0929' => 'tar', 'TAR629G2155' => 'tar', 'THA.LOC104805282' => 'tha', 'THA.LOC104805363' => 'tha', 'THA.LOC104808968' => 'tha', 'THA.LOC104821093' => 'tha', 'THA.LOC104823953' => 'tha', 'THA.LOC104825562' => 'tha', 'THA.LOC104825665' => 'tha', 'Thecc.02G261400' => 'tca', 'Thecc.04G019200' => 'tca', 'Thecc.09G130400' => 'tca', 'Thhalv10004374m.g' => 'esa', 'Thhalv10007850m.g' => 'esa', 'Thhalv10013782m.g' => 'esa', 'Thhalv10018686m.g' => 'esa', 'Thhalv10020899m.g' => 'esa', 'Thhalv10022755m.g' => 'esa', 'TPR.G23851' => 'tpr', 'TPR.G26500' => 'tpr', 'TPR.G27267' => 'tpr', 'TPR.G32001' => 'tpr', 'TPR.G6251' => 'tpr', 'TPR.G8167' => 'tpr', 'TWI12G1330' => 'twi', 'TWI18G1239' => 'twi', 'TWI34G0979' => 'twi', 'TWI36G0670' => 'twi', 'TWI36G0707' => 'twi', 'TWI56G0233' => 'twi', 'TWI75G1809' => 'twi', 'unitig_21.g20874' => 'ugi', 'unitig_26.g10343' => 'ugi', 'unitig_46.g18392' => 'ugi', 'unitig_52.g17178' => 'ugi', 'unitig_8.g2934' => 'ugi', 'vmacro01122' => 'vma', 'vmacro05875' => 'vma', 'vmacro06147' => 'vma', 'vmacro16191' => 'vma', 'vmacro18293' => 'vma', 'VMungo0251G3707' => 'vmu', 'VMungo0464G1521' => 'vmu', 'VMungo1215G0205' => 'vmu', 'VMungo1383G2484' => 'vmu', 'Zm00001eb079610' => 'zma', 'Zm00001eb135990' => 'zma', 'Zm00001eb183710' => 'zma', 'Zm00001eb246020' => 'zma' ) $gf_id = 'HOM05D001124' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001124' ) $data_identifier = 'HOM05D001124' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 6, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 7, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 21, 'bol' => (int) 10, 'bra' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 6, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 9, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 21, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 8, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 10, 'lsa' => (int) 8, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 8, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 9, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb246020' $species_info = array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ) $local_species = 'mdo' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001124', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '548', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02520' => 'bna', 'A03p06630' => 'bna', 'A05p44460' => 'bna', 'A06p08710' => 'bna', 'A06p41090' => 'bna', 'A07p32320' => 'bna', 'A08p32520' => 'bna', 'A09p10360' => 'bna', 'A10p24080' => 'bna', 'Aa31LG11G15250' => 'aar', 'Aa31LG1G1800' => 'aar', 'Aa31LG2G5120' => 'aar', 'Aa31LG2G6070' => 'aar', 'Aa31LG5G10770' => 'aar', 'Aa31sc61G90' => 'aar', 'Actinidia01352' => 'ach', 'Actinidia05983' => 'ach', 'Actinidia08133' => 'ach', 'Actinidia15101' => 'ach', 'Actinidia26379' => 'ach', 'Actinidia35778' => 'ach', 'Actinidia36123' => 'ach', 'Actinidia37436' => 'ach', 'Actinidia38730' => 'ach', 'Ah.02g128210' => 'amhyb', 'Ah.03g132990' => 'amhyb', 'Ah.14g079410' => 'amhyb', 'AL1G24640' => 'aly', 'AL2G26680' => 'aly', 'AL3G10530' => 'aly', 'AL3G45230' => 'aly', 'AL5G15230' => 'aly', 'AL5G16960' => 'aly', 'AL6G25210' => 'aly', 'Aqoxy2G00441' => 'aox', 'Aqoxy3G01236' => 'aox', 'Aqoxy5G03746' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3RQ047' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C7GMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9C8JER' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MBL6KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YXCZ83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZANX40' => 'arhy', 'AT1G12990' => 'ath', 'AT1G67880' => 'ath', 'AT2G13290' => 'ath', 'AT3G01620' => 'ath', 'AT3G26445' => 'ath', 'AT3G27540' => 'ath', 'AT5G14480' => 'ath', 'ATR0824G026' => 'atr', 'ATR1098G019' => 'atr', 'Atru.chr11.2145' => 'acertr', 'Atru.chr2.3636' => 'acertr', 'Atru.chr2.3644' => 'acertr', 'Atru.chr6.2422' => 'acertr', 'Atru.chr7.1112' => 'acertr', 'AUR62005469' => 'cqu', 'AUR62011166' => 'cqu', 'AUR62013319' => 'cqu', 'AUR62024273' => 'cqu', 'AUR62028420' => 'cqu', 'AUR62041942' => 'cqu', 'BcaB01g04969' => 'bca', 'BcaB01g06371' => 'bca', 'BcaB02g11494' => 'bca', 'BcaB03g15382' => 'bca', 'BcaB08g36994' => 'bca', 'BcaC03g13477' => 'bca', 'BcaC03g13478' => 'bca', 'BcaC03g13480' => 'bca', 'BcaC03g13481' => 'bca', 'BcaC03g13486' => 'bca', 'BcaC04g19031' => 'bca', 'BcaC04g23085' => 'bca', 'BcaC05g25094' => 'bca', 'BcaC05g25096' => 'bca', 'BcaC05g25138' => 'bca', 'BcaC05g30416' => 'bca', 'BcaC05g30455' => 'bca', 'BcaC06g30979' => 'bca', 'BcaC06g33805' => 'bca', 'BcaC08g46021' => 'bca', 'BcaNung03154' => 'bca', 'BolC2t06623H' => 'bol', 'BolC2t06632H' => 'bol', 'BolC2t06635H' => 'bol', 'BolC2t06638H' => 'bol', 'BolC3t13266H' => 'bol', 'BolC5t29776H' => 'bol', 'BolC6t38912H' => 'bol', 'BolC7t44183H' => 'bol', 'BolC9t54123H' => 'bol', 'BolC9t59107H' => 'bol', 'BraA02t05221Z' => 'bra', 'BraA03t09996Z' => 'bra', 'BraA05t23210Z' => 'bra', 'BraA06t24068Z' => 'bra', 'BraA06t27032Z' => 'bra', 'BraA08t35176Z' => 'bra', 'BraA09t36680Z' => 'bra', 'BraA10t44471Z' => 'bra', 'C02p06760' => 'bna', 'C02p06890' => 'bna', 'C02p07010' => 'bna', 'C03p07660' => 'bna', 'C05p10300' => 'bna', 'C06p38150' => 'bna', 'C07p36650' => 'bna', 'C08p15770' => 'bna', 'C09p12300' => 'bna', 'C09p62700' => 'bna', 'C09p75040' => 'bna', 'CAN.G13.1' => 'can', 'CAN.G138.4' => 'can', 'CAN.G44.6' => 'can', 'CAN.G473.19' => 'can', 'CANSAT01G0835' => 'cansat', 'CANSAT11G0246' => 'cansat', 'CANSAT11G1766' => 'cansat', 'CANSAT64G1954' => 'cansat', 'CARHR013330' => 'chi', 'CARHR060530' => 'chi', 'CARHR075300' => 'chi', 'CARHR105120' => 'chi', 'CARHR148910' => 'chi', 'CARHR198830' => 'chi', 'Carub.0001s1275' => 'cru', 'Carub.0002s1437' => 'cru', 'Carub.0003s0044' => 'cru', 'Carub.0003s2787' => 'cru', 'Carub.0005s0597' => 'cru', 'Carub.0006s1266' => 'cru', 'Ca_06935_v3' => 'car', 'Ca_13559_v3' => 'car', 'Ca_16941_v3' => 'car', 'Ca_16960_v3' => 'car', 'Ca_17775_v3' => 'car', 'Ca_30464_v3' => 'car', 'Cc06_g08160' => 'ccan', 'Cc07_g01520' => 'ccan', 'Cc11_g15810' => 'ccan', 'CDE02G2840' => 'cde', 'CDE03G0093' => 'cde', 'CDE04G2127' => 'cde', 'CDE07G1857' => 'cde', 'CDE09G1246' => 'cde', 'Cfa003412' => 'cfa', 'Cfa007341' => 'cfa', 'Cfa009220' => 'cfa', 'Ciclev10008737m.g' => 'ccl', 'Ciclev10015565m.g' => 'ccl', 'Ciclev10031761m.g' => 'ccl', 'CiPaw.03G045300' => 'cil', 'CiPaw.03G247200' => 'cil', 'CiPaw.04G029500' => 'cil', 'CiPaw.04G174000' => 'cil', 'CiPaw.05G181200' => 'cil', 'CiPaw.06G067100' => 'cil', 'ClCG05G025800' => 'cla', 'ClCG06G011400' => 'cla', 'ClCG09G019360' => 'cla', 'COL.COLO4_04827' => 'col', 'COL.COLO4_29170' => 'col', 'COL.COLO4_35131' => 'col', 'COL.COLO4_35132' => 'col', 'Cpa.g.sc33.32' => 'cpa', 'Cpa.g.sc46.29' => 'cpa', 'Cpa.g.sc796.1' => 'cpa', 'CsaV3_1G030420' => 'csa', 'CsaV3_5G027050' => 'csa', 'CsaV3_5G031040' => 'csa', 'CsaV3_UNG023130' => 'csa', 'CSS0007726' => 'camsi', 'CSS0016433' => 'camsi', 'CSS0017656' => 'camsi', 'CSS0025364' => 'camsi', 'CSS0027582' => 'camsi', 'CSS0047288' => 'camsi', 'CSS0049950' => 'camsi', 'DCAR_003843' => 'dca', 'DCAR_007052' => 'dca', 'DCAR_020884' => 'dca', 'DCAR_021730' => 'dca', 'DCAR_024423' => 'dca', 'DCAR_026509' => 'dca', 'DCAR_031158' => 'dca', 'Dinv14728' => 'din', 'Dinv15219' => 'din', 'Dinv25728' => 'din', 'Dinv33428' => 'din', 'Dinv36489' => 'din', 'Dinv41486' => 'din', 'Duzib147G0469' => 'dzi', 'Duzib168G0060' => 'dzi', 'Duzib187G1215' => 'dzi', 'Duzib248G0692' => 'dzi', 'Duzib251G0767' => 'dzi', 'Duzib264G0446' => 'dzi', 'Duzib268G0691' => 'dzi', 'ECA232G4767' => 'eca', 'ECA233G2838' => 'eca', 'ECA234G0391' => 'eca', 'ECA234G0857' => 'eca', 'ECA236G1593' => 'eca', 'ECA238G0565' => 'eca', 'ECA246G1027' => 'eca', 'ECA246G3223' => 'eca', 'ECA246G3470' => 'eca', 'EL10Ac6g13829' => 'bvu', 'EL10Ac6g14093' => 'bvu', 'EL10Ac8g18707' => 'bvu', 'Eucgr.C01369' => 'egr', 'Eucgr.H02492' => 'egr', 'Eucgr.I01733' => 'egr', 'Eucgr.J02255' => 'egr', 'Eucgr.J02257' => 'egr', 'Eucgr.J02258' => 'egr', 'FAN02G1601' => 'fan', 'FAN03G1586' => 'fan', 'FAN03G2986' => 'fan', 'FAN05G4837' => 'fan', 'FAN06G0146' => 'fan', 'FAN07G0858' => 'fan', 'FAN09G3179' => 'fan', 'FAN10G0669' => 'fan', 'FAN12G2358' => 'fan', 'FAN14G4198' => 'fan', 'FAN14G5112' => 'fan', 'FAN17G0342' => 'fan', 'FAN19G0342' => 'fan', 'FAN19G0962' => 'fan', 'FAN19G1101' => 'fan', 'FAN19G1872' => 'fan', 'FAN22G0356' => 'fan', 'FAN23G0744' => 'fan', 'FAN23G1914' => 'fan', 'FAN26G0032' => 'fan', 'FAN28G0625' => 'fan', 'FvH4_1g02710' => 'fve', 'FvH4_1g02720' => 'fve', 'FvH4_4g25670' => 'fve', 'FvH4_6g51700' => 'fve', 'FvH4_7g20170' => 'fve', 'Glyma.05G175000' => 'gma', 'Glyma.08G132300' => 'gma', 'Glyma.11G243000' => 'gma', 'Glyma.13G158900' => 'gma', 'Glyma.17G112400' => 'gma', 'Glyma.18G014100' => 'gma', 'Glyma.19G003100' => 'gma', 'Glyma.19G056500' => 'gma', 'Gohir.A01G158900' => 'ghi', 'Gohir.A05G312600' => 'ghi', 'Gohir.A05G354900' => 'ghi', 'Gohir.A07G037200' => 'ghi', 'Gohir.A09G030000' => 'ghi', 'Gohir.A12G145200' => 'ghi', 'Gohir.D01G151500' => 'ghi', 'Gohir.D04G058300' => 'ghi', 'Gohir.D05G314100' => 'ghi', 'Gohir.D07G041400' => 'ghi', 'Gohir.D09G029700' => 'ghi', 'Gohir.D12G149700' => 'ghi', 'Gorai.001G043800' => 'gra', 'Gorai.002G187800' => 'gra', 'Gorai.006G034700' => 'gra', 'Gorai.008G161200' => 'gra', 'Gorai.009G335700' => 'gra', 'Gorai.012G065000' => 'gra', 'GSVIVG01000535001' => 'vvi', 'GSVIVG01015572001' => 'vvi', 'GSVIVG01032386001' => 'vvi', 'HanXRQChr05g0138531' => 'han', 'HanXRQChr06g0174391' => 'han', 'HanXRQChr07g0199021' => 'han', 'HanXRQChr08g0208211' => 'han', 'HanXRQChr09g0255471' => 'han', 'HanXRQChr10g0315791' => 'han', 'HanXRQChr12g0371991' => 'han', 'HanXRQChr15g0475251' => 'han', 'HanXRQChr17g0540001' => 'han', 'HanXRQChr17g0548631' => 'han', 'HanXRQChr17g0569561' => 'han', 'Haze_12256' => 'cav', 'Haze_14756' => 'cav', 'Haze_25528' => 'cav', 'Hma1.2p1_0079F.1_g041020' => 'hma', 'Hma1.2p1_0818F.1_g223260' => 'hma', 'Hma1.2p1_1747F.1_g300530' => 'hma', 'HPP92_004607' => 'vpl', 'HPP92_004608' => 'vpl', 'HPP92_006181' => 'vpl', 'HPP92_012192' => 'vpl', 'HPP92_015680' => 'vpl', 'HPP92_020249' => 'vpl', 'HPP92_021376' => 'vpl', 'HPP92_024275' => 'vpl', 'Hund06031' => 'sun', 'Hund25391' => 'sun', 'Lalb_Chr07g0185371' => 'lal', 'Lalb_Chr07g0185381' => 'lal', 'Lalb_Chr12g0204011' => 'lal', 'Lalb_Chr13g0301671' => 'lal', 'Lalb_Chr14g0362851' => 'lal', 'Lalb_Chr24g0403581' => 'lal', 'Lj1g0000233' => 'lja', 'Lj2g0018120' => 'lja', 'Lj3C621T0' => 'lonja', 'Lj3P1059T14' => 'lonja', 'Lj3P611T9' => 'lonja', 'Lj3P614T13' => 'lonja', 'Lj3P615T5' => 'lonja', 'Lj4g0012315' => 'lja', 'Lj4g0026182' => 'lja', 'Lj6P813T16' => 'lonja', 'Lj7C427T7' => 'lonja', 'Lj7C427T8' => 'lonja', 'Lj7P600T41' => 'lonja', 'Lju41C42G17' => 'lonja', 'Lsat_1_v5_gn_0_47300' => 'lsa', 'Lsat_1_v5_gn_2_91280' => 'lsa', 'Lsat_1_v5_gn_3_30561' => 'lsa', 'Lsat_1_v5_gn_4_184321' => 'lsa', 'Lsat_1_v5_gn_4_4041' => 'lsa', 'Lsat_1_v5_gn_5_92000' => 'lsa', 'Lsat_1_v5_gn_8_152940' => 'lsa', 'Lsat_1_v5_gn_8_62401' => 'lsa', 'Manes.06G055900' => 'mes', 'Manes.12G022200' => 'mes', 'Manes.13G023300' => 'mes', 'Manes.14G115000' => 'mes', 'Manes.15G151700' => 'mes', 'Manes.17G111300' => 'mes', 'Mapoly0226s0009' => 'mpo', 'MBI02_g25363_MAGBIO' => 'mbi', 'MBI06_g00027_MAGBIO' => 'mbi', 'MBI10_g13034_MAGBIO' => 'mbi', 'MD09G1023400' => 'mdo', 'MD13G1100100' => 'mdo', 'MD15G1169200' => 'mdo', 'MD16G1101100' => 'mdo', 'MD17G1022900' => 'mdo', 'Medtr3g096150' => 'mtr', 'Medtr4g115070' => 'mtr', 'Medtr7g033325' => 'mtr', 'Medtr8g089840' => 'mtr', 'MELO3C010319.2' => 'cme', 'MELO3C011944.2' => 'cme', 'MELO3C021589.2' => 'cme', 'Migut.E00207' => 'egut', 'Migut.H00067' => 'egut', 'Migut.K00433' => 'egut', 'Migut.K00606' => 'egut', 'Migut.K01410' => 'egut', 'MSTRG.13347' => 'ama', 'MSTRG.24045' => 'ama', 'MSTRG.2428' => 'ama', 'MSTRG.26410' => 'ama', 'MSTRG.3139' => 'ama', 'MSTRG.3286' => 'ama', 'MSTRG.563' => 'ama', 'MSTRG.7941' => 'ama', 'Nitab4.5_0000028g0060' => 'nta', 'Nitab4.5_0000065g0260' => 'nta', 'Nitab4.5_0000112g0060' => 'nta', 'Nitab4.5_0000489g0120' => 'nta', 'Nitab4.5_0001776g0050' => 'nta', 'Nitab4.5_0001854g0010' => 'nta', 'Nitab4.5_0001860g0020' => 'nta', 'Nitab4.5_0004352g0010' => 'nta', 'Nitab4.5_0008716g0020' => 'nta', 'Nitab4.5_0008922g0010' => 'nta', 'Nn3g16693' => 'nnu', 'Nn4g22596' => 'nnu', 'Nn7g37639' => 'nnu', 'Oeu001701.1' => 'oeu', 'Oeu018149.1' => 'oeu', 'Oeu026220.1' => 'oeu', 'Oeu038635.1' => 'oeu', 'Oeu049176.1' => 'oeu', 'Oeu056706.1' => 'oeu', 'Oeu056937.1' => 'oeu', 'Oeu057540.1' => 'oeu', 'Os02g0594900' => 'osa', 'Os02g0595100' => 'osa', 'Os04g0477500' => 'osa', 'Os12g0611900' => 'osa', 'Peaxi162Scf00076g00020' => 'pax', 'Peaxi162Scf00128g00217' => 'pax', 'Peaxi162Scf00129g01640' => 'pax', 'Peaxi162Scf00669g00007' => 'pax', 'Peaxi162Scf00700g00421' => 'pax', 'Peaxi162Scf00801g00038' => 'pax', 'Peaxi162Scf00891g00025' => 'pax', 'PGR083G0909' => 'pgr', 'PGR119G1005' => 'pgr', 'PGR142G2236' => 'pgr', 'PGR142G3388' => 'pgr', 'PGSC0003DMG400004514' => 'stu', 'PGSC0003DMG400012635' => 'stu', 'PGSC0003DMG400015730' => 'stu', 'PGSC0003DMG400018611' => 'stu', 'PGSC0003DMG400030897' => 'stu', 'Phvul.001G254800' => 'pvu', 'Phvul.002G260100' => 'pvu', 'Phvul.003G167600' => 'pvu', 'Phvul.004G005100' => 'pvu', 'Potri.001G343600' => 'ptr', 'Potri.006G066700' => 'ptr', 'Potri.008G186000' => 'ptr', 'Potri.010G046900' => 'ptr', 'Potri.018G127900' => 'ptr', 'Pp3c20_17750' => 'ppa', 'Pp3c24_4380' => 'ppa', 'Prupe.1G245800' => 'ppe', 'Prupe.3G293400' => 'ppe', 'Prupe.7G247400' => 'ppe', 'Psat0s145g0120' => 'psa', 'Psat0s595g0040' => 'psa', 'Psat0s595g0120' => 'psa', 'Psat3g175040' => 'psa', 'Psat7g058120' => 'psa', 'PSO017G0428' => 'pso', 'PSO063G7510' => 'pso', 'PSO067G0046' => 'pso', 'PSO478G1073' => 'pso', 'PSO675G3677' => 'pso', 'PSO675G6558' => 'pso', 'PSO675G7520' => 'pso', 'PSO675G8959' => 'pso', 'QL02p074089' => 'qlo', 'QL02p089614' => 'qlo', 'QL03p057736' => 'qlo', 'RcHm_v2.0_Chr1g0364131' => 'rch', 'RcHm_v2.0_Chr2g0087801' => 'rch', 'RcHm_v2.0_Chr2g0087821' => 'rch', 'RcHm_v2.0_Chr2g0173231' => 'rch', 'RcHm_v2.0_Chr4g0433111' => 'rch', 'Rhsim03G0250300' => 'rsi', 'Rhsim08G0048400' => 'rsi', 'Rhsim10G0014800' => 'rsi', 'Rhsim12G0040100' => 'rsi', 'Rhsim12G0109700' => 'rsi', 'Sabra06G0049600' => 'sbr', 'Sabra08G0141000' => 'sbr', 'Sabra10G0021400' => 'sbr', 'Sabra16G0222900' => 'sbr', 'Sabra18G0108600' => 'sbr', 'SalBow1G0433' => 'sbo', 'SalBow1G2038' => 'sbo', 'SalBow1G5003' => 'sbo', 'SalBow7G1197' => 'sbo', 'SalBow8G3506' => 'sbo', 'Sc03g0007300' => 'sci', 'Sc11g0000950' => 'sci', 'Sc14g0008750' => 'sci', 'Sc18g0000420' => 'sci', 'Sed0006754' => 'sed', 'Sed0008741' => 'sed', 'Sed0017172' => 'sed', 'Sed0018925' => 'sed', 'Sed0023326' => 'sed', 'Sed0025909' => 'sed', 'SEGI_05333' => 'sgi', 'SEGI_10362' => 'sgi', 'SEGI_13380' => 'sgi', 'SEGI_24306' => 'sgi', 'SEGI_29077' => 'sgi', 'SEGI_29095' => 'sgi', 'SEGI_36534' => 'sgi', 'SEGI_37506' => 'sgi', 'SEGI_38321' => 'sgi', 'SGA_v2.0_scaffold307G48031' => 'sas', 'SGA_v2.0_scaffold47G17507' => 'sas', 'SGA_v2.0_scaffold63G21736' => 'sas', 'SGA_v2.0_scaffold87G27070' => 'sas', 'SHI17794' => 'shi', 'SHI28851' => 'shi', 'SMO165G0155' => 'smo', 'SMO340G0217' => 'smo', 'SMO367G1210' => 'smo', 'Solyc02g093430.3' => 'sly', 'Solyc05g013580.4' => 'sly', 'Solyc07g008030.3' => 'sly', 'Solyc12g035470.2' => 'sly', 'Sopen02g038020' => 'spe', 'Sopen05g008490' => 'spe', 'Sopen07g003910' => 'spe', 'Sopen12g015240' => 'spe', 'Sp1g11550' => 'spa', 'Sp2g16710' => 'spa', 'Sp3g00430' => 'spa', 'Sp3g26780' => 'spa', 'Sp5g22900' => 'spa', 'Sp6g29530' => 'spa', 'TAR371G0794' => 'tar', 'TAR374G0164' => 'tar', 'TAR622G0165' => 'tar', 'TAR626G0929' => 'tar', 'TAR629G2155' => 'tar', 'THA.LOC104805282' => 'tha', 'THA.LOC104805363' => 'tha', 'THA.LOC104808968' => 'tha', 'THA.LOC104821093' => 'tha', 'THA.LOC104823953' => 'tha', 'THA.LOC104825562' => 'tha', 'THA.LOC104825665' => 'tha', 'Thecc.02G261400' => 'tca', 'Thecc.04G019200' => 'tca', 'Thecc.09G130400' => 'tca', 'Thhalv10004374m.g' => 'esa', 'Thhalv10007850m.g' => 'esa', 'Thhalv10013782m.g' => 'esa', 'Thhalv10018686m.g' => 'esa', 'Thhalv10020899m.g' => 'esa', 'Thhalv10022755m.g' => 'esa', 'TPR.G23851' => 'tpr', 'TPR.G26500' => 'tpr', 'TPR.G27267' => 'tpr', 'TPR.G32001' => 'tpr', 'TPR.G6251' => 'tpr', 'TPR.G8167' => 'tpr', 'TWI12G1330' => 'twi', 'TWI18G1239' => 'twi', 'TWI34G0979' => 'twi', 'TWI36G0670' => 'twi', 'TWI36G0707' => 'twi', 'TWI56G0233' => 'twi', 'TWI75G1809' => 'twi', 'unitig_21.g20874' => 'ugi', 'unitig_26.g10343' => 'ugi', 'unitig_46.g18392' => 'ugi', 'unitig_52.g17178' => 'ugi', 'unitig_8.g2934' => 'ugi', 'vmacro01122' => 'vma', 'vmacro05875' => 'vma', 'vmacro06147' => 'vma', 'vmacro16191' => 'vma', 'vmacro18293' => 'vma', 'VMungo0251G3707' => 'vmu', 'VMungo0464G1521' => 'vmu', 'VMungo1215G0205' => 'vmu', 'VMungo1383G2484' => 'vmu', 'Zm00001eb079610' => 'zma', 'Zm00001eb135990' => 'zma', 'Zm00001eb183710' => 'zma', 'Zm00001eb246020' => 'zma' ), 'gf_id' => 'HOM05D001124', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001124' ), 'data_identifier' => 'HOM05D001124', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001124', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '548', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02520' => 'bna', 'A03p06630' => 'bna', 'A05p44460' => 'bna', 'A06p08710' => 'bna', 'A06p41090' => 'bna', 'A07p32320' => 'bna', 'A08p32520' => 'bna', 'A09p10360' => 'bna', 'A10p24080' => 'bna', 'Aa31LG11G15250' => 'aar', 'Aa31LG1G1800' => 'aar', 'Aa31LG2G5120' => 'aar', 'Aa31LG2G6070' => 'aar', 'Aa31LG5G10770' => 'aar', 'Aa31sc61G90' => 'aar', 'Actinidia01352' => 'ach', 'Actinidia05983' => 'ach', 'Actinidia08133' => 'ach', 'Actinidia15101' => 'ach', 'Actinidia26379' => 'ach', 'Actinidia35778' => 'ach', 'Actinidia36123' => 'ach', 'Actinidia37436' => 'ach', 'Actinidia38730' => 'ach', 'Ah.02g128210' => 'amhyb', 'Ah.03g132990' => 'amhyb', 'Ah.14g079410' => 'amhyb', 'AL1G24640' => 'aly', 'AL2G26680' => 'aly', 'AL3G10530' => 'aly', 'AL3G45230' => 'aly', 'AL5G15230' => 'aly', 'AL5G16960' => 'aly', 'AL6G25210' => 'aly', 'Aqoxy2G00441' => 'aox', 'Aqoxy3G01236' => 'aox', 'Aqoxy5G03746' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3RQ047' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C7GMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9C8JER' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MBL6KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YXCZ83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZANX40' => 'arhy', 'AT1G12990' => 'ath', 'AT1G67880' => 'ath', 'AT2G13290' => 'ath', 'AT3G01620' => 'ath', 'AT3G26445' => 'ath', 'AT3G27540' => 'ath', 'AT5G14480' => 'ath', 'ATR0824G026' => 'atr', 'ATR1098G019' => 'atr', 'Atru.chr11.2145' => 'acertr', 'Atru.chr2.3636' => 'acertr', 'Atru.chr2.3644' => 'acertr', 'Atru.chr6.2422' => 'acertr', 'Atru.chr7.1112' => 'acertr', 'AUR62005469' => 'cqu', 'AUR62011166' => 'cqu', 'AUR62013319' => 'cqu', 'AUR62024273' => 'cqu', 'AUR62028420' => 'cqu', 'AUR62041942' => 'cqu', 'BcaB01g04969' => 'bca', 'BcaB01g06371' => 'bca', 'BcaB02g11494' => 'bca', 'BcaB03g15382' => 'bca', 'BcaB08g36994' => 'bca', 'BcaC03g13477' => 'bca', 'BcaC03g13478' => 'bca', 'BcaC03g13480' => 'bca', 'BcaC03g13481' => 'bca', 'BcaC03g13486' => 'bca', 'BcaC04g19031' => 'bca', 'BcaC04g23085' => 'bca', 'BcaC05g25094' => 'bca', 'BcaC05g25096' => 'bca', 'BcaC05g25138' => 'bca', 'BcaC05g30416' => 'bca', 'BcaC05g30455' => 'bca', 'BcaC06g30979' => 'bca', 'BcaC06g33805' => 'bca', 'BcaC08g46021' => 'bca', 'BcaNung03154' => 'bca', 'BolC2t06623H' => 'bol', 'BolC2t06632H' => 'bol', 'BolC2t06635H' => 'bol', 'BolC2t06638H' => 'bol', 'BolC3t13266H' => 'bol', 'BolC5t29776H' => 'bol', 'BolC6t38912H' => 'bol', 'BolC7t44183H' => 'bol', 'BolC9t54123H' => 'bol', 'BolC9t59107H' => 'bol', 'BraA02t05221Z' => 'bra', 'BraA03t09996Z' => 'bra', 'BraA05t23210Z' => 'bra', 'BraA06t24068Z' => 'bra', 'BraA06t27032Z' => 'bra', 'BraA08t35176Z' => 'bra', 'BraA09t36680Z' => 'bra', 'BraA10t44471Z' => 'bra', 'C02p06760' => 'bna', 'C02p06890' => 'bna', 'C02p07010' => 'bna', 'C03p07660' => 'bna', 'C05p10300' => 'bna', 'C06p38150' => 'bna', 'C07p36650' => 'bna', 'C08p15770' => 'bna', 'C09p12300' => 'bna', 'C09p62700' => 'bna', 'C09p75040' => 'bna', 'CAN.G13.1' => 'can', 'CAN.G138.4' => 'can', 'CAN.G44.6' => 'can', 'CAN.G473.19' => 'can', 'CANSAT01G0835' => 'cansat', 'CANSAT11G0246' => 'cansat', 'CANSAT11G1766' => 'cansat', 'CANSAT64G1954' => 'cansat', 'CARHR013330' => 'chi', 'CARHR060530' => 'chi', 'CARHR075300' => 'chi', 'CARHR105120' => 'chi', 'CARHR148910' => 'chi', 'CARHR198830' => 'chi', 'Carub.0001s1275' => 'cru', 'Carub.0002s1437' => 'cru', 'Carub.0003s0044' => 'cru', 'Carub.0003s2787' => 'cru', 'Carub.0005s0597' => 'cru', 'Carub.0006s1266' => 'cru', 'Ca_06935_v3' => 'car', 'Ca_13559_v3' => 'car', 'Ca_16941_v3' => 'car', 'Ca_16960_v3' => 'car', 'Ca_17775_v3' => 'car', 'Ca_30464_v3' => 'car', 'Cc06_g08160' => 'ccan', 'Cc07_g01520' => 'ccan', 'Cc11_g15810' => 'ccan', 'CDE02G2840' => 'cde', 'CDE03G0093' => 'cde', 'CDE04G2127' => 'cde', 'CDE07G1857' => 'cde', 'CDE09G1246' => 'cde', 'Cfa003412' => 'cfa', 'Cfa007341' => 'cfa', 'Cfa009220' => 'cfa', 'Ciclev10008737m.g' => 'ccl', 'Ciclev10015565m.g' => 'ccl', 'Ciclev10031761m.g' => 'ccl', 'CiPaw.03G045300' => 'cil', 'CiPaw.03G247200' => 'cil', 'CiPaw.04G029500' => 'cil', 'CiPaw.04G174000' => 'cil', 'CiPaw.05G181200' => 'cil', 'CiPaw.06G067100' => 'cil', 'ClCG05G025800' => 'cla', 'ClCG06G011400' => 'cla', 'ClCG09G019360' => 'cla', 'COL.COLO4_04827' => 'col', 'COL.COLO4_29170' => 'col', 'COL.COLO4_35131' => 'col', 'COL.COLO4_35132' => 'col', 'Cpa.g.sc33.32' => 'cpa', 'Cpa.g.sc46.29' => 'cpa', 'Cpa.g.sc796.1' => 'cpa', 'CsaV3_1G030420' => 'csa', 'CsaV3_5G027050' => 'csa', 'CsaV3_5G031040' => 'csa', 'CsaV3_UNG023130' => 'csa', 'CSS0007726' => 'camsi', 'CSS0016433' => 'camsi', 'CSS0017656' => 'camsi', 'CSS0025364' => 'camsi', 'CSS0027582' => 'camsi', 'CSS0047288' => 'camsi', 'CSS0049950' => 'camsi', 'DCAR_003843' => 'dca', 'DCAR_007052' => 'dca', 'DCAR_020884' => 'dca', 'DCAR_021730' => 'dca', 'DCAR_024423' => 'dca', 'DCAR_026509' => 'dca', 'DCAR_031158' => 'dca', 'Dinv14728' => 'din', 'Dinv15219' => 'din', 'Dinv25728' => 'din', 'Dinv33428' => 'din', 'Dinv36489' => 'din', 'Dinv41486' => 'din', 'Duzib147G0469' => 'dzi', 'Duzib168G0060' => 'dzi', 'Duzib187G1215' => 'dzi', 'Duzib248G0692' => 'dzi', 'Duzib251G0767' => 'dzi', 'Duzib264G0446' => 'dzi', 'Duzib268G0691' => 'dzi', 'ECA232G4767' => 'eca', 'ECA233G2838' => 'eca', 'ECA234G0391' => 'eca', 'ECA234G0857' => 'eca', 'ECA236G1593' => 'eca', 'ECA238G0565' => 'eca', 'ECA246G1027' => 'eca', 'ECA246G3223' => 'eca', 'ECA246G3470' => 'eca', 'EL10Ac6g13829' => 'bvu', 'EL10Ac6g14093' => 'bvu', 'EL10Ac8g18707' => 'bvu', 'Eucgr.C01369' => 'egr', 'Eucgr.H02492' => 'egr', 'Eucgr.I01733' => 'egr', 'Eucgr.J02255' => 'egr', 'Eucgr.J02257' => 'egr', 'Eucgr.J02258' => 'egr', 'FAN02G1601' => 'fan', 'FAN03G1586' => 'fan', 'FAN03G2986' => 'fan', 'FAN05G4837' => 'fan', 'FAN06G0146' => 'fan', 'FAN07G0858' => 'fan', 'FAN09G3179' => 'fan', 'FAN10G0669' => 'fan', 'FAN12G2358' => 'fan', 'FAN14G4198' => 'fan', 'FAN14G5112' => 'fan', 'FAN17G0342' => 'fan', 'FAN19G0342' => 'fan', 'FAN19G0962' => 'fan', 'FAN19G1101' => 'fan', 'FAN19G1872' => 'fan', 'FAN22G0356' => 'fan', 'FAN23G0744' => 'fan', 'FAN23G1914' => 'fan', 'FAN26G0032' => 'fan', 'FAN28G0625' => 'fan', 'FvH4_1g02710' => 'fve', 'FvH4_1g02720' => 'fve', 'FvH4_4g25670' => 'fve', 'FvH4_6g51700' => 'fve', 'FvH4_7g20170' => 'fve', 'Glyma.05G175000' => 'gma', 'Glyma.08G132300' => 'gma', 'Glyma.11G243000' => 'gma', 'Glyma.13G158900' => 'gma', 'Glyma.17G112400' => 'gma', 'Glyma.18G014100' => 'gma', 'Glyma.19G003100' => 'gma', 'Glyma.19G056500' => 'gma', 'Gohir.A01G158900' => 'ghi', 'Gohir.A05G312600' => 'ghi', 'Gohir.A05G354900' => 'ghi', 'Gohir.A07G037200' => 'ghi', 'Gohir.A09G030000' => 'ghi', 'Gohir.A12G145200' => 'ghi', 'Gohir.D01G151500' => 'ghi', 'Gohir.D04G058300' => 'ghi', 'Gohir.D05G314100' => 'ghi', 'Gohir.D07G041400' => 'ghi', 'Gohir.D09G029700' => 'ghi', 'Gohir.D12G149700' => 'ghi', 'Gorai.001G043800' => 'gra', 'Gorai.002G187800' => 'gra', 'Gorai.006G034700' => 'gra', 'Gorai.008G161200' => 'gra', 'Gorai.009G335700' => 'gra', 'Gorai.012G065000' => 'gra', 'GSVIVG01000535001' => 'vvi', 'GSVIVG01015572001' => 'vvi', 'GSVIVG01032386001' => 'vvi', 'HanXRQChr05g0138531' => 'han', 'HanXRQChr06g0174391' => 'han', 'HanXRQChr07g0199021' => 'han', 'HanXRQChr08g0208211' => 'han', 'HanXRQChr09g0255471' => 'han', 'HanXRQChr10g0315791' => 'han', 'HanXRQChr12g0371991' => 'han', 'HanXRQChr15g0475251' => 'han', 'HanXRQChr17g0540001' => 'han', 'HanXRQChr17g0548631' => 'han', 'HanXRQChr17g0569561' => 'han', 'Haze_12256' => 'cav', 'Haze_14756' => 'cav', 'Haze_25528' => 'cav', 'Hma1.2p1_0079F.1_g041020' => 'hma', 'Hma1.2p1_0818F.1_g223260' => 'hma', 'Hma1.2p1_1747F.1_g300530' => 'hma', 'HPP92_004607' => 'vpl', 'HPP92_004608' => 'vpl', 'HPP92_006181' => 'vpl', 'HPP92_012192' => 'vpl', 'HPP92_015680' => 'vpl', 'HPP92_020249' => 'vpl', 'HPP92_021376' => 'vpl', 'HPP92_024275' => 'vpl', 'Hund06031' => 'sun', 'Hund25391' => 'sun', 'Lalb_Chr07g0185371' => 'lal', 'Lalb_Chr07g0185381' => 'lal', 'Lalb_Chr12g0204011' => 'lal', 'Lalb_Chr13g0301671' => 'lal', 'Lalb_Chr14g0362851' => 'lal', 'Lalb_Chr24g0403581' => 'lal', 'Lj1g0000233' => 'lja', 'Lj2g0018120' => 'lja', 'Lj3C621T0' => 'lonja', 'Lj3P1059T14' => 'lonja', 'Lj3P611T9' => 'lonja', 'Lj3P614T13' => 'lonja', 'Lj3P615T5' => 'lonja', 'Lj4g0012315' => 'lja', 'Lj4g0026182' => 'lja', 'Lj6P813T16' => 'lonja', 'Lj7C427T7' => 'lonja', 'Lj7C427T8' => 'lonja', 'Lj7P600T41' => 'lonja', 'Lju41C42G17' => 'lonja', 'Lsat_1_v5_gn_0_47300' => 'lsa', 'Lsat_1_v5_gn_2_91280' => 'lsa', 'Lsat_1_v5_gn_3_30561' => 'lsa', 'Lsat_1_v5_gn_4_184321' => 'lsa', 'Lsat_1_v5_gn_4_4041' => 'lsa', 'Lsat_1_v5_gn_5_92000' => 'lsa', 'Lsat_1_v5_gn_8_152940' => 'lsa', 'Lsat_1_v5_gn_8_62401' => 'lsa', 'Manes.06G055900' => 'mes', 'Manes.12G022200' => 'mes', 'Manes.13G023300' => 'mes', 'Manes.14G115000' => 'mes', 'Manes.15G151700' => 'mes', 'Manes.17G111300' => 'mes', 'Mapoly0226s0009' => 'mpo', 'MBI02_g25363_MAGBIO' => 'mbi', 'MBI06_g00027_MAGBIO' => 'mbi', 'MBI10_g13034_MAGBIO' => 'mbi', 'MD09G1023400' => 'mdo', 'MD13G1100100' => 'mdo', 'MD15G1169200' => 'mdo', 'MD16G1101100' => 'mdo', 'MD17G1022900' => 'mdo', 'Medtr3g096150' => 'mtr', 'Medtr4g115070' => 'mtr', 'Medtr7g033325' => 'mtr', 'Medtr8g089840' => 'mtr', 'MELO3C010319.2' => 'cme', 'MELO3C011944.2' => 'cme', 'MELO3C021589.2' => 'cme', 'Migut.E00207' => 'egut', 'Migut.H00067' => 'egut', 'Migut.K00433' => 'egut', 'Migut.K00606' => 'egut', 'Migut.K01410' => 'egut', 'MSTRG.13347' => 'ama', 'MSTRG.24045' => 'ama', 'MSTRG.2428' => 'ama', 'MSTRG.26410' => 'ama', 'MSTRG.3139' => 'ama', 'MSTRG.3286' => 'ama', 'MSTRG.563' => 'ama', 'MSTRG.7941' => 'ama', 'Nitab4.5_0000028g0060' => 'nta', 'Nitab4.5_0000065g0260' => 'nta', 'Nitab4.5_0000112g0060' => 'nta', 'Nitab4.5_0000489g0120' => 'nta', 'Nitab4.5_0001776g0050' => 'nta', 'Nitab4.5_0001854g0010' => 'nta', 'Nitab4.5_0001860g0020' => 'nta', 'Nitab4.5_0004352g0010' => 'nta', 'Nitab4.5_0008716g0020' => 'nta', 'Nitab4.5_0008922g0010' => 'nta', 'Nn3g16693' => 'nnu', 'Nn4g22596' => 'nnu', 'Nn7g37639' => 'nnu', 'Oeu001701.1' => 'oeu', 'Oeu018149.1' => 'oeu', 'Oeu026220.1' => 'oeu', 'Oeu038635.1' => 'oeu', 'Oeu049176.1' => 'oeu', 'Oeu056706.1' => 'oeu', 'Oeu056937.1' => 'oeu', 'Oeu057540.1' => 'oeu', 'Os02g0594900' => 'osa', 'Os02g0595100' => 'osa', 'Os04g0477500' => 'osa', 'Os12g0611900' => 'osa', 'Peaxi162Scf00076g00020' => 'pax', 'Peaxi162Scf00128g00217' => 'pax', 'Peaxi162Scf00129g01640' => 'pax', 'Peaxi162Scf00669g00007' => 'pax', 'Peaxi162Scf00700g00421' => 'pax', 'Peaxi162Scf00801g00038' => 'pax', 'Peaxi162Scf00891g00025' => 'pax', 'PGR083G0909' => 'pgr', 'PGR119G1005' => 'pgr', 'PGR142G2236' => 'pgr', 'PGR142G3388' => 'pgr', 'PGSC0003DMG400004514' => 'stu', 'PGSC0003DMG400012635' => 'stu', 'PGSC0003DMG400015730' => 'stu', 'PGSC0003DMG400018611' => 'stu', 'PGSC0003DMG400030897' => 'stu', 'Phvul.001G254800' => 'pvu', 'Phvul.002G260100' => 'pvu', 'Phvul.003G167600' => 'pvu', 'Phvul.004G005100' => 'pvu', 'Potri.001G343600' => 'ptr', 'Potri.006G066700' => 'ptr', 'Potri.008G186000' => 'ptr', 'Potri.010G046900' => 'ptr', 'Potri.018G127900' => 'ptr', 'Pp3c20_17750' => 'ppa', 'Pp3c24_4380' => 'ppa', 'Prupe.1G245800' => 'ppe', 'Prupe.3G293400' => 'ppe', 'Prupe.7G247400' => 'ppe', 'Psat0s145g0120' => 'psa', 'Psat0s595g0040' => 'psa', 'Psat0s595g0120' => 'psa', 'Psat3g175040' => 'psa', 'Psat7g058120' => 'psa', 'PSO017G0428' => 'pso', 'PSO063G7510' => 'pso', 'PSO067G0046' => 'pso', 'PSO478G1073' => 'pso', 'PSO675G3677' => 'pso', 'PSO675G6558' => 'pso', 'PSO675G7520' => 'pso', 'PSO675G8959' => 'pso', 'QL02p074089' => 'qlo', 'QL02p089614' => 'qlo', 'QL03p057736' => 'qlo', 'RcHm_v2.0_Chr1g0364131' => 'rch', 'RcHm_v2.0_Chr2g0087801' => 'rch', 'RcHm_v2.0_Chr2g0087821' => 'rch', 'RcHm_v2.0_Chr2g0173231' => 'rch', 'RcHm_v2.0_Chr4g0433111' => 'rch', 'Rhsim03G0250300' => 'rsi', 'Rhsim08G0048400' => 'rsi', 'Rhsim10G0014800' => 'rsi', 'Rhsim12G0040100' => 'rsi', 'Rhsim12G0109700' => 'rsi', 'Sabra06G0049600' => 'sbr', 'Sabra08G0141000' => 'sbr', 'Sabra10G0021400' => 'sbr', 'Sabra16G0222900' => 'sbr', 'Sabra18G0108600' => 'sbr', 'SalBow1G0433' => 'sbo', 'SalBow1G2038' => 'sbo', 'SalBow1G5003' => 'sbo', 'SalBow7G1197' => 'sbo', 'SalBow8G3506' => 'sbo', 'Sc03g0007300' => 'sci', 'Sc11g0000950' => 'sci', 'Sc14g0008750' => 'sci', 'Sc18g0000420' => 'sci', 'Sed0006754' => 'sed', 'Sed0008741' => 'sed', 'Sed0017172' => 'sed', 'Sed0018925' => 'sed', 'Sed0023326' => 'sed', 'Sed0025909' => 'sed', 'SEGI_05333' => 'sgi', 'SEGI_10362' => 'sgi', 'SEGI_13380' => 'sgi', 'SEGI_24306' => 'sgi', 'SEGI_29077' => 'sgi', 'SEGI_29095' => 'sgi', 'SEGI_36534' => 'sgi', 'SEGI_37506' => 'sgi', 'SEGI_38321' => 'sgi', 'SGA_v2.0_scaffold307G48031' => 'sas', 'SGA_v2.0_scaffold47G17507' => 'sas', 'SGA_v2.0_scaffold63G21736' => 'sas', 'SGA_v2.0_scaffold87G27070' => 'sas', 'SHI17794' => 'shi', 'SHI28851' => 'shi', 'SMO165G0155' => 'smo', 'SMO340G0217' => 'smo', 'SMO367G1210' => 'smo', 'Solyc02g093430.3' => 'sly', 'Solyc05g013580.4' => 'sly', 'Solyc07g008030.3' => 'sly', 'Solyc12g035470.2' => 'sly', 'Sopen02g038020' => 'spe', 'Sopen05g008490' => 'spe', 'Sopen07g003910' => 'spe', 'Sopen12g015240' => 'spe', 'Sp1g11550' => 'spa', 'Sp2g16710' => 'spa', 'Sp3g00430' => 'spa', 'Sp3g26780' => 'spa', 'Sp5g22900' => 'spa', 'Sp6g29530' => 'spa', 'TAR371G0794' => 'tar', 'TAR374G0164' => 'tar', 'TAR622G0165' => 'tar', 'TAR626G0929' => 'tar', 'TAR629G2155' => 'tar', 'THA.LOC104805282' => 'tha', 'THA.LOC104805363' => 'tha', 'THA.LOC104808968' => 'tha', 'THA.LOC104821093' => 'tha', 'THA.LOC104823953' => 'tha', 'THA.LOC104825562' => 'tha', 'THA.LOC104825665' => 'tha', 'Thecc.02G261400' => 'tca', 'Thecc.04G019200' => 'tca', 'Thecc.09G130400' => 'tca', 'Thhalv10004374m.g' => 'esa', 'Thhalv10007850m.g' => 'esa', 'Thhalv10013782m.g' => 'esa', 'Thhalv10018686m.g' => 'esa', 'Thhalv10020899m.g' => 'esa', 'Thhalv10022755m.g' => 'esa', 'TPR.G23851' => 'tpr', 'TPR.G26500' => 'tpr', 'TPR.G27267' => 'tpr', 'TPR.G32001' => 'tpr', 'TPR.G6251' => 'tpr', 'TPR.G8167' => 'tpr', 'TWI12G1330' => 'twi', 'TWI18G1239' => 'twi', 'TWI34G0979' => 'twi', 'TWI36G0670' => 'twi', 'TWI36G0707' => 'twi', 'TWI56G0233' => 'twi', 'TWI75G1809' => 'twi', 'unitig_21.g20874' => 'ugi', 'unitig_26.g10343' => 'ugi', 'unitig_46.g18392' => 'ugi', 'unitig_52.g17178' => 'ugi', 'unitig_8.g2934' => 'ugi', 'vmacro01122' => 'vma', 'vmacro05875' => 'vma', 'vmacro06147' => 'vma', 'vmacro16191' => 'vma', 'vmacro18293' => 'vma', 'VMungo0251G3707' => 'vmu', 'VMungo0464G1521' => 'vmu', 'VMungo1215G0205' => 'vmu', 'VMungo1383G2484' => 'vmu', 'Zm00001eb079610' => 'zma', 'Zm00001eb135990' => 'zma', 'Zm00001eb183710' => 'zma', 'Zm00001eb246020' => 'zma' ) $gf_id = 'HOM05D001124' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001124' ) $data_identifier = 'HOM05D001124' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 6, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 7, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 21, 'bol' => (int) 10, 'bra' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 6, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 9, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 21, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 8, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 10, 'lsa' => (int) 8, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 8, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 9, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb246020' $species_info = array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ) $local_species = 'mdo' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001124', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '548', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02520' => 'bna', 'A03p06630' => 'bna', 'A05p44460' => 'bna', 'A06p08710' => 'bna', 'A06p41090' => 'bna', 'A07p32320' => 'bna', 'A08p32520' => 'bna', 'A09p10360' => 'bna', 'A10p24080' => 'bna', 'Aa31LG11G15250' => 'aar', 'Aa31LG1G1800' => 'aar', 'Aa31LG2G5120' => 'aar', 'Aa31LG2G6070' => 'aar', 'Aa31LG5G10770' => 'aar', 'Aa31sc61G90' => 'aar', 'Actinidia01352' => 'ach', 'Actinidia05983' => 'ach', 'Actinidia08133' => 'ach', 'Actinidia15101' => 'ach', 'Actinidia26379' => 'ach', 'Actinidia35778' => 'ach', 'Actinidia36123' => 'ach', 'Actinidia37436' => 'ach', 'Actinidia38730' => 'ach', 'Ah.02g128210' => 'amhyb', 'Ah.03g132990' => 'amhyb', 'Ah.14g079410' => 'amhyb', 'AL1G24640' => 'aly', 'AL2G26680' => 'aly', 'AL3G10530' => 'aly', 'AL3G45230' => 'aly', 'AL5G15230' => 'aly', 'AL5G16960' => 'aly', 'AL6G25210' => 'aly', 'Aqoxy2G00441' => 'aox', 'Aqoxy3G01236' => 'aox', 'Aqoxy5G03746' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3RQ047' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C7GMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9C8JER' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MBL6KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YXCZ83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZANX40' => 'arhy', 'AT1G12990' => 'ath', 'AT1G67880' => 'ath', 'AT2G13290' => 'ath', 'AT3G01620' => 'ath', 'AT3G26445' => 'ath', 'AT3G27540' => 'ath', 'AT5G14480' => 'ath', 'ATR0824G026' => 'atr', 'ATR1098G019' => 'atr', 'Atru.chr11.2145' => 'acertr', 'Atru.chr2.3636' => 'acertr', 'Atru.chr2.3644' => 'acertr', 'Atru.chr6.2422' => 'acertr', 'Atru.chr7.1112' => 'acertr', 'AUR62005469' => 'cqu', 'AUR62011166' => 'cqu', 'AUR62013319' => 'cqu', 'AUR62024273' => 'cqu', 'AUR62028420' => 'cqu', 'AUR62041942' => 'cqu', 'BcaB01g04969' => 'bca', 'BcaB01g06371' => 'bca', 'BcaB02g11494' => 'bca', 'BcaB03g15382' => 'bca', 'BcaB08g36994' => 'bca', 'BcaC03g13477' => 'bca', 'BcaC03g13478' => 'bca', 'BcaC03g13480' => 'bca', 'BcaC03g13481' => 'bca', 'BcaC03g13486' => 'bca', 'BcaC04g19031' => 'bca', 'BcaC04g23085' => 'bca', 'BcaC05g25094' => 'bca', 'BcaC05g25096' => 'bca', 'BcaC05g25138' => 'bca', 'BcaC05g30416' => 'bca', 'BcaC05g30455' => 'bca', 'BcaC06g30979' => 'bca', 'BcaC06g33805' => 'bca', 'BcaC08g46021' => 'bca', 'BcaNung03154' => 'bca', 'BolC2t06623H' => 'bol', 'BolC2t06632H' => 'bol', 'BolC2t06635H' => 'bol', 'BolC2t06638H' => 'bol', 'BolC3t13266H' => 'bol', 'BolC5t29776H' => 'bol', 'BolC6t38912H' => 'bol', 'BolC7t44183H' => 'bol', 'BolC9t54123H' => 'bol', 'BolC9t59107H' => 'bol', 'BraA02t05221Z' => 'bra', 'BraA03t09996Z' => 'bra', 'BraA05t23210Z' => 'bra', 'BraA06t24068Z' => 'bra', 'BraA06t27032Z' => 'bra', 'BraA08t35176Z' => 'bra', 'BraA09t36680Z' => 'bra', 'BraA10t44471Z' => 'bra', 'C02p06760' => 'bna', 'C02p06890' => 'bna', 'C02p07010' => 'bna', 'C03p07660' => 'bna', 'C05p10300' => 'bna', 'C06p38150' => 'bna', 'C07p36650' => 'bna', 'C08p15770' => 'bna', 'C09p12300' => 'bna', 'C09p62700' => 'bna', 'C09p75040' => 'bna', 'CAN.G13.1' => 'can', 'CAN.G138.4' => 'can', 'CAN.G44.6' => 'can', 'CAN.G473.19' => 'can', 'CANSAT01G0835' => 'cansat', 'CANSAT11G0246' => 'cansat', 'CANSAT11G1766' => 'cansat', 'CANSAT64G1954' => 'cansat', 'CARHR013330' => 'chi', 'CARHR060530' => 'chi', 'CARHR075300' => 'chi', 'CARHR105120' => 'chi', 'CARHR148910' => 'chi', 'CARHR198830' => 'chi', 'Carub.0001s1275' => 'cru', 'Carub.0002s1437' => 'cru', 'Carub.0003s0044' => 'cru', 'Carub.0003s2787' => 'cru', 'Carub.0005s0597' => 'cru', 'Carub.0006s1266' => 'cru', 'Ca_06935_v3' => 'car', 'Ca_13559_v3' => 'car', 'Ca_16941_v3' => 'car', 'Ca_16960_v3' => 'car', 'Ca_17775_v3' => 'car', 'Ca_30464_v3' => 'car', 'Cc06_g08160' => 'ccan', 'Cc07_g01520' => 'ccan', 'Cc11_g15810' => 'ccan', 'CDE02G2840' => 'cde', 'CDE03G0093' => 'cde', 'CDE04G2127' => 'cde', 'CDE07G1857' => 'cde', 'CDE09G1246' => 'cde', 'Cfa003412' => 'cfa', 'Cfa007341' => 'cfa', 'Cfa009220' => 'cfa', 'Ciclev10008737m.g' => 'ccl', 'Ciclev10015565m.g' => 'ccl', 'Ciclev10031761m.g' => 'ccl', 'CiPaw.03G045300' => 'cil', 'CiPaw.03G247200' => 'cil', 'CiPaw.04G029500' => 'cil', 'CiPaw.04G174000' => 'cil', 'CiPaw.05G181200' => 'cil', 'CiPaw.06G067100' => 'cil', 'ClCG05G025800' => 'cla', 'ClCG06G011400' => 'cla', 'ClCG09G019360' => 'cla', 'COL.COLO4_04827' => 'col', 'COL.COLO4_29170' => 'col', 'COL.COLO4_35131' => 'col', 'COL.COLO4_35132' => 'col', 'Cpa.g.sc33.32' => 'cpa', 'Cpa.g.sc46.29' => 'cpa', 'Cpa.g.sc796.1' => 'cpa', 'CsaV3_1G030420' => 'csa', 'CsaV3_5G027050' => 'csa', 'CsaV3_5G031040' => 'csa', 'CsaV3_UNG023130' => 'csa', 'CSS0007726' => 'camsi', 'CSS0016433' => 'camsi', 'CSS0017656' => 'camsi', 'CSS0025364' => 'camsi', 'CSS0027582' => 'camsi', 'CSS0047288' => 'camsi', 'CSS0049950' => 'camsi', 'DCAR_003843' => 'dca', 'DCAR_007052' => 'dca', 'DCAR_020884' => 'dca', 'DCAR_021730' => 'dca', 'DCAR_024423' => 'dca', 'DCAR_026509' => 'dca', 'DCAR_031158' => 'dca', 'Dinv14728' => 'din', 'Dinv15219' => 'din', 'Dinv25728' => 'din', 'Dinv33428' => 'din', 'Dinv36489' => 'din', 'Dinv41486' => 'din', 'Duzib147G0469' => 'dzi', 'Duzib168G0060' => 'dzi', 'Duzib187G1215' => 'dzi', 'Duzib248G0692' => 'dzi', 'Duzib251G0767' => 'dzi', 'Duzib264G0446' => 'dzi', 'Duzib268G0691' => 'dzi', 'ECA232G4767' => 'eca', 'ECA233G2838' => 'eca', 'ECA234G0391' => 'eca', 'ECA234G0857' => 'eca', 'ECA236G1593' => 'eca', 'ECA238G0565' => 'eca', 'ECA246G1027' => 'eca', 'ECA246G3223' => 'eca', 'ECA246G3470' => 'eca', 'EL10Ac6g13829' => 'bvu', 'EL10Ac6g14093' => 'bvu', 'EL10Ac8g18707' => 'bvu', 'Eucgr.C01369' => 'egr', 'Eucgr.H02492' => 'egr', 'Eucgr.I01733' => 'egr', 'Eucgr.J02255' => 'egr', 'Eucgr.J02257' => 'egr', 'Eucgr.J02258' => 'egr', 'FAN02G1601' => 'fan', 'FAN03G1586' => 'fan', 'FAN03G2986' => 'fan', 'FAN05G4837' => 'fan', 'FAN06G0146' => 'fan', 'FAN07G0858' => 'fan', 'FAN09G3179' => 'fan', 'FAN10G0669' => 'fan', 'FAN12G2358' => 'fan', 'FAN14G4198' => 'fan', 'FAN14G5112' => 'fan', 'FAN17G0342' => 'fan', 'FAN19G0342' => 'fan', 'FAN19G0962' => 'fan', 'FAN19G1101' => 'fan', 'FAN19G1872' => 'fan', 'FAN22G0356' => 'fan', 'FAN23G0744' => 'fan', 'FAN23G1914' => 'fan', 'FAN26G0032' => 'fan', 'FAN28G0625' => 'fan', 'FvH4_1g02710' => 'fve', 'FvH4_1g02720' => 'fve', 'FvH4_4g25670' => 'fve', 'FvH4_6g51700' => 'fve', 'FvH4_7g20170' => 'fve', 'Glyma.05G175000' => 'gma', 'Glyma.08G132300' => 'gma', 'Glyma.11G243000' => 'gma', 'Glyma.13G158900' => 'gma', 'Glyma.17G112400' => 'gma', 'Glyma.18G014100' => 'gma', 'Glyma.19G003100' => 'gma', 'Glyma.19G056500' => 'gma', 'Gohir.A01G158900' => 'ghi', 'Gohir.A05G312600' => 'ghi', 'Gohir.A05G354900' => 'ghi', 'Gohir.A07G037200' => 'ghi', 'Gohir.A09G030000' => 'ghi', 'Gohir.A12G145200' => 'ghi', 'Gohir.D01G151500' => 'ghi', 'Gohir.D04G058300' => 'ghi', 'Gohir.D05G314100' => 'ghi', 'Gohir.D07G041400' => 'ghi', 'Gohir.D09G029700' => 'ghi', 'Gohir.D12G149700' => 'ghi', 'Gorai.001G043800' => 'gra', 'Gorai.002G187800' => 'gra', 'Gorai.006G034700' => 'gra', 'Gorai.008G161200' => 'gra', 'Gorai.009G335700' => 'gra', 'Gorai.012G065000' => 'gra', 'GSVIVG01000535001' => 'vvi', 'GSVIVG01015572001' => 'vvi', 'GSVIVG01032386001' => 'vvi', 'HanXRQChr05g0138531' => 'han', 'HanXRQChr06g0174391' => 'han', 'HanXRQChr07g0199021' => 'han', 'HanXRQChr08g0208211' => 'han', 'HanXRQChr09g0255471' => 'han', 'HanXRQChr10g0315791' => 'han', 'HanXRQChr12g0371991' => 'han', 'HanXRQChr15g0475251' => 'han', 'HanXRQChr17g0540001' => 'han', 'HanXRQChr17g0548631' => 'han', 'HanXRQChr17g0569561' => 'han', 'Haze_12256' => 'cav', 'Haze_14756' => 'cav', 'Haze_25528' => 'cav', 'Hma1.2p1_0079F.1_g041020' => 'hma', 'Hma1.2p1_0818F.1_g223260' => 'hma', 'Hma1.2p1_1747F.1_g300530' => 'hma', 'HPP92_004607' => 'vpl', 'HPP92_004608' => 'vpl', 'HPP92_006181' => 'vpl', 'HPP92_012192' => 'vpl', 'HPP92_015680' => 'vpl', 'HPP92_020249' => 'vpl', 'HPP92_021376' => 'vpl', 'HPP92_024275' => 'vpl', 'Hund06031' => 'sun', 'Hund25391' => 'sun', 'Lalb_Chr07g0185371' => 'lal', 'Lalb_Chr07g0185381' => 'lal', 'Lalb_Chr12g0204011' => 'lal', 'Lalb_Chr13g0301671' => 'lal', 'Lalb_Chr14g0362851' => 'lal', 'Lalb_Chr24g0403581' => 'lal', 'Lj1g0000233' => 'lja', 'Lj2g0018120' => 'lja', 'Lj3C621T0' => 'lonja', 'Lj3P1059T14' => 'lonja', 'Lj3P611T9' => 'lonja', 'Lj3P614T13' => 'lonja', 'Lj3P615T5' => 'lonja', 'Lj4g0012315' => 'lja', 'Lj4g0026182' => 'lja', 'Lj6P813T16' => 'lonja', 'Lj7C427T7' => 'lonja', 'Lj7C427T8' => 'lonja', 'Lj7P600T41' => 'lonja', 'Lju41C42G17' => 'lonja', 'Lsat_1_v5_gn_0_47300' => 'lsa', 'Lsat_1_v5_gn_2_91280' => 'lsa', 'Lsat_1_v5_gn_3_30561' => 'lsa', 'Lsat_1_v5_gn_4_184321' => 'lsa', 'Lsat_1_v5_gn_4_4041' => 'lsa', 'Lsat_1_v5_gn_5_92000' => 'lsa', 'Lsat_1_v5_gn_8_152940' => 'lsa', 'Lsat_1_v5_gn_8_62401' => 'lsa', 'Manes.06G055900' => 'mes', 'Manes.12G022200' => 'mes', 'Manes.13G023300' => 'mes', 'Manes.14G115000' => 'mes', 'Manes.15G151700' => 'mes', 'Manes.17G111300' => 'mes', 'Mapoly0226s0009' => 'mpo', 'MBI02_g25363_MAGBIO' => 'mbi', 'MBI06_g00027_MAGBIO' => 'mbi', 'MBI10_g13034_MAGBIO' => 'mbi', 'MD09G1023400' => 'mdo', 'MD13G1100100' => 'mdo', 'MD15G1169200' => 'mdo', 'MD16G1101100' => 'mdo', 'MD17G1022900' => 'mdo', 'Medtr3g096150' => 'mtr', 'Medtr4g115070' => 'mtr', 'Medtr7g033325' => 'mtr', 'Medtr8g089840' => 'mtr', 'MELO3C010319.2' => 'cme', 'MELO3C011944.2' => 'cme', 'MELO3C021589.2' => 'cme', 'Migut.E00207' => 'egut', 'Migut.H00067' => 'egut', 'Migut.K00433' => 'egut', 'Migut.K00606' => 'egut', 'Migut.K01410' => 'egut', 'MSTRG.13347' => 'ama', 'MSTRG.24045' => 'ama', 'MSTRG.2428' => 'ama', 'MSTRG.26410' => 'ama', 'MSTRG.3139' => 'ama', 'MSTRG.3286' => 'ama', 'MSTRG.563' => 'ama', 'MSTRG.7941' => 'ama', 'Nitab4.5_0000028g0060' => 'nta', 'Nitab4.5_0000065g0260' => 'nta', 'Nitab4.5_0000112g0060' => 'nta', 'Nitab4.5_0000489g0120' => 'nta', 'Nitab4.5_0001776g0050' => 'nta', 'Nitab4.5_0001854g0010' => 'nta', 'Nitab4.5_0001860g0020' => 'nta', 'Nitab4.5_0004352g0010' => 'nta', 'Nitab4.5_0008716g0020' => 'nta', 'Nitab4.5_0008922g0010' => 'nta', 'Nn3g16693' => 'nnu', 'Nn4g22596' => 'nnu', 'Nn7g37639' => 'nnu', 'Oeu001701.1' => 'oeu', 'Oeu018149.1' => 'oeu', 'Oeu026220.1' => 'oeu', 'Oeu038635.1' => 'oeu', 'Oeu049176.1' => 'oeu', 'Oeu056706.1' => 'oeu', 'Oeu056937.1' => 'oeu', 'Oeu057540.1' => 'oeu', 'Os02g0594900' => 'osa', 'Os02g0595100' => 'osa', 'Os04g0477500' => 'osa', 'Os12g0611900' => 'osa', 'Peaxi162Scf00076g00020' => 'pax', 'Peaxi162Scf00128g00217' => 'pax', 'Peaxi162Scf00129g01640' => 'pax', 'Peaxi162Scf00669g00007' => 'pax', 'Peaxi162Scf00700g00421' => 'pax', 'Peaxi162Scf00801g00038' => 'pax', 'Peaxi162Scf00891g00025' => 'pax', 'PGR083G0909' => 'pgr', 'PGR119G1005' => 'pgr', 'PGR142G2236' => 'pgr', 'PGR142G3388' => 'pgr', 'PGSC0003DMG400004514' => 'stu', 'PGSC0003DMG400012635' => 'stu', 'PGSC0003DMG400015730' => 'stu', 'PGSC0003DMG400018611' => 'stu', 'PGSC0003DMG400030897' => 'stu', 'Phvul.001G254800' => 'pvu', 'Phvul.002G260100' => 'pvu', 'Phvul.003G167600' => 'pvu', 'Phvul.004G005100' => 'pvu', 'Potri.001G343600' => 'ptr', 'Potri.006G066700' => 'ptr', 'Potri.008G186000' => 'ptr', 'Potri.010G046900' => 'ptr', 'Potri.018G127900' => 'ptr', 'Pp3c20_17750' => 'ppa', 'Pp3c24_4380' => 'ppa', 'Prupe.1G245800' => 'ppe', 'Prupe.3G293400' => 'ppe', 'Prupe.7G247400' => 'ppe', 'Psat0s145g0120' => 'psa', 'Psat0s595g0040' => 'psa', 'Psat0s595g0120' => 'psa', 'Psat3g175040' => 'psa', 'Psat7g058120' => 'psa', 'PSO017G0428' => 'pso', 'PSO063G7510' => 'pso', 'PSO067G0046' => 'pso', 'PSO478G1073' => 'pso', 'PSO675G3677' => 'pso', 'PSO675G6558' => 'pso', 'PSO675G7520' => 'pso', 'PSO675G8959' => 'pso', 'QL02p074089' => 'qlo', 'QL02p089614' => 'qlo', 'QL03p057736' => 'qlo', 'RcHm_v2.0_Chr1g0364131' => 'rch', 'RcHm_v2.0_Chr2g0087801' => 'rch', 'RcHm_v2.0_Chr2g0087821' => 'rch', 'RcHm_v2.0_Chr2g0173231' => 'rch', 'RcHm_v2.0_Chr4g0433111' => 'rch', 'Rhsim03G0250300' => 'rsi', 'Rhsim08G0048400' => 'rsi', 'Rhsim10G0014800' => 'rsi', 'Rhsim12G0040100' => 'rsi', 'Rhsim12G0109700' => 'rsi', 'Sabra06G0049600' => 'sbr', 'Sabra08G0141000' => 'sbr', 'Sabra10G0021400' => 'sbr', 'Sabra16G0222900' => 'sbr', 'Sabra18G0108600' => 'sbr', 'SalBow1G0433' => 'sbo', 'SalBow1G2038' => 'sbo', 'SalBow1G5003' => 'sbo', 'SalBow7G1197' => 'sbo', 'SalBow8G3506' => 'sbo', 'Sc03g0007300' => 'sci', 'Sc11g0000950' => 'sci', 'Sc14g0008750' => 'sci', 'Sc18g0000420' => 'sci', 'Sed0006754' => 'sed', 'Sed0008741' => 'sed', 'Sed0017172' => 'sed', 'Sed0018925' => 'sed', 'Sed0023326' => 'sed', 'Sed0025909' => 'sed', 'SEGI_05333' => 'sgi', 'SEGI_10362' => 'sgi', 'SEGI_13380' => 'sgi', 'SEGI_24306' => 'sgi', 'SEGI_29077' => 'sgi', 'SEGI_29095' => 'sgi', 'SEGI_36534' => 'sgi', 'SEGI_37506' => 'sgi', 'SEGI_38321' => 'sgi', 'SGA_v2.0_scaffold307G48031' => 'sas', 'SGA_v2.0_scaffold47G17507' => 'sas', 'SGA_v2.0_scaffold63G21736' => 'sas', 'SGA_v2.0_scaffold87G27070' => 'sas', 'SHI17794' => 'shi', 'SHI28851' => 'shi', 'SMO165G0155' => 'smo', 'SMO340G0217' => 'smo', 'SMO367G1210' => 'smo', 'Solyc02g093430.3' => 'sly', 'Solyc05g013580.4' => 'sly', 'Solyc07g008030.3' => 'sly', 'Solyc12g035470.2' => 'sly', 'Sopen02g038020' => 'spe', 'Sopen05g008490' => 'spe', 'Sopen07g003910' => 'spe', 'Sopen12g015240' => 'spe', 'Sp1g11550' => 'spa', 'Sp2g16710' => 'spa', 'Sp3g00430' => 'spa', 'Sp3g26780' => 'spa', 'Sp5g22900' => 'spa', 'Sp6g29530' => 'spa', 'TAR371G0794' => 'tar', 'TAR374G0164' => 'tar', 'TAR622G0165' => 'tar', 'TAR626G0929' => 'tar', 'TAR629G2155' => 'tar', 'THA.LOC104805282' => 'tha', 'THA.LOC104805363' => 'tha', 'THA.LOC104808968' => 'tha', 'THA.LOC104821093' => 'tha', 'THA.LOC104823953' => 'tha', 'THA.LOC104825562' => 'tha', 'THA.LOC104825665' => 'tha', 'Thecc.02G261400' => 'tca', 'Thecc.04G019200' => 'tca', 'Thecc.09G130400' => 'tca', 'Thhalv10004374m.g' => 'esa', 'Thhalv10007850m.g' => 'esa', 'Thhalv10013782m.g' => 'esa', 'Thhalv10018686m.g' => 'esa', 'Thhalv10020899m.g' => 'esa', 'Thhalv10022755m.g' => 'esa', 'TPR.G23851' => 'tpr', 'TPR.G26500' => 'tpr', 'TPR.G27267' => 'tpr', 'TPR.G32001' => 'tpr', 'TPR.G6251' => 'tpr', 'TPR.G8167' => 'tpr', 'TWI12G1330' => 'twi', 'TWI18G1239' => 'twi', 'TWI34G0979' => 'twi', 'TWI36G0670' => 'twi', 'TWI36G0707' => 'twi', 'TWI56G0233' => 'twi', 'TWI75G1809' => 'twi', 'unitig_21.g20874' => 'ugi', 'unitig_26.g10343' => 'ugi', 'unitig_46.g18392' => 'ugi', 'unitig_52.g17178' => 'ugi', 'unitig_8.g2934' => 'ugi', 'vmacro01122' => 'vma', 'vmacro05875' => 'vma', 'vmacro06147' => 'vma', 'vmacro16191' => 'vma', 'vmacro18293' => 'vma', 'VMungo0251G3707' => 'vmu', 'VMungo0464G1521' => 'vmu', 'VMungo1215G0205' => 'vmu', 'VMungo1383G2484' => 'vmu', 'Zm00001eb079610' => 'zma', 'Zm00001eb135990' => 'zma', 'Zm00001eb183710' => 'zma', 'Zm00001eb246020' => 'zma' ), 'gf_id' => 'HOM05D001124', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001124' ), 'data_identifier' => 'HOM05D001124', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001124', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '548', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02520' => 'bna', 'A03p06630' => 'bna', 'A05p44460' => 'bna', 'A06p08710' => 'bna', 'A06p41090' => 'bna', 'A07p32320' => 'bna', 'A08p32520' => 'bna', 'A09p10360' => 'bna', 'A10p24080' => 'bna', 'Aa31LG11G15250' => 'aar', 'Aa31LG1G1800' => 'aar', 'Aa31LG2G5120' => 'aar', 'Aa31LG2G6070' => 'aar', 'Aa31LG5G10770' => 'aar', 'Aa31sc61G90' => 'aar', 'Actinidia01352' => 'ach', 'Actinidia05983' => 'ach', 'Actinidia08133' => 'ach', 'Actinidia15101' => 'ach', 'Actinidia26379' => 'ach', 'Actinidia35778' => 'ach', 'Actinidia36123' => 'ach', 'Actinidia37436' => 'ach', 'Actinidia38730' => 'ach', 'Ah.02g128210' => 'amhyb', 'Ah.03g132990' => 'amhyb', 'Ah.14g079410' => 'amhyb', 'AL1G24640' => 'aly', 'AL2G26680' => 'aly', 'AL3G10530' => 'aly', 'AL3G45230' => 'aly', 'AL5G15230' => 'aly', 'AL5G16960' => 'aly', 'AL6G25210' => 'aly', 'Aqoxy2G00441' => 'aox', 'Aqoxy3G01236' => 'aox', 'Aqoxy5G03746' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3RQ047' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C7GMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9C8JER' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MBL6KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YXCZ83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZANX40' => 'arhy', 'AT1G12990' => 'ath', 'AT1G67880' => 'ath', 'AT2G13290' => 'ath', 'AT3G01620' => 'ath', 'AT3G26445' => 'ath', 'AT3G27540' => 'ath', 'AT5G14480' => 'ath', 'ATR0824G026' => 'atr', 'ATR1098G019' => 'atr', 'Atru.chr11.2145' => 'acertr', 'Atru.chr2.3636' => 'acertr', 'Atru.chr2.3644' => 'acertr', 'Atru.chr6.2422' => 'acertr', 'Atru.chr7.1112' => 'acertr', 'AUR62005469' => 'cqu', 'AUR62011166' => 'cqu', 'AUR62013319' => 'cqu', 'AUR62024273' => 'cqu', 'AUR62028420' => 'cqu', 'AUR62041942' => 'cqu', 'BcaB01g04969' => 'bca', 'BcaB01g06371' => 'bca', 'BcaB02g11494' => 'bca', 'BcaB03g15382' => 'bca', 'BcaB08g36994' => 'bca', 'BcaC03g13477' => 'bca', 'BcaC03g13478' => 'bca', 'BcaC03g13480' => 'bca', 'BcaC03g13481' => 'bca', 'BcaC03g13486' => 'bca', 'BcaC04g19031' => 'bca', 'BcaC04g23085' => 'bca', 'BcaC05g25094' => 'bca', 'BcaC05g25096' => 'bca', 'BcaC05g25138' => 'bca', 'BcaC05g30416' => 'bca', 'BcaC05g30455' => 'bca', 'BcaC06g30979' => 'bca', 'BcaC06g33805' => 'bca', 'BcaC08g46021' => 'bca', 'BcaNung03154' => 'bca', 'BolC2t06623H' => 'bol', 'BolC2t06632H' => 'bol', 'BolC2t06635H' => 'bol', 'BolC2t06638H' => 'bol', 'BolC3t13266H' => 'bol', 'BolC5t29776H' => 'bol', 'BolC6t38912H' => 'bol', 'BolC7t44183H' => 'bol', 'BolC9t54123H' => 'bol', 'BolC9t59107H' => 'bol', 'BraA02t05221Z' => 'bra', 'BraA03t09996Z' => 'bra', 'BraA05t23210Z' => 'bra', 'BraA06t24068Z' => 'bra', 'BraA06t27032Z' => 'bra', 'BraA08t35176Z' => 'bra', 'BraA09t36680Z' => 'bra', 'BraA10t44471Z' => 'bra', 'C02p06760' => 'bna', 'C02p06890' => 'bna', 'C02p07010' => 'bna', 'C03p07660' => 'bna', 'C05p10300' => 'bna', 'C06p38150' => 'bna', 'C07p36650' => 'bna', 'C08p15770' => 'bna', 'C09p12300' => 'bna', 'C09p62700' => 'bna', 'C09p75040' => 'bna', 'CAN.G13.1' => 'can', 'CAN.G138.4' => 'can', 'CAN.G44.6' => 'can', 'CAN.G473.19' => 'can', 'CANSAT01G0835' => 'cansat', 'CANSAT11G0246' => 'cansat', 'CANSAT11G1766' => 'cansat', 'CANSAT64G1954' => 'cansat', 'CARHR013330' => 'chi', 'CARHR060530' => 'chi', 'CARHR075300' => 'chi', 'CARHR105120' => 'chi', 'CARHR148910' => 'chi', 'CARHR198830' => 'chi', 'Carub.0001s1275' => 'cru', 'Carub.0002s1437' => 'cru', 'Carub.0003s0044' => 'cru', 'Carub.0003s2787' => 'cru', 'Carub.0005s0597' => 'cru', 'Carub.0006s1266' => 'cru', 'Ca_06935_v3' => 'car', 'Ca_13559_v3' => 'car', 'Ca_16941_v3' => 'car', 'Ca_16960_v3' => 'car', 'Ca_17775_v3' => 'car', 'Ca_30464_v3' => 'car', 'Cc06_g08160' => 'ccan', 'Cc07_g01520' => 'ccan', 'Cc11_g15810' => 'ccan', 'CDE02G2840' => 'cde', 'CDE03G0093' => 'cde', 'CDE04G2127' => 'cde', 'CDE07G1857' => 'cde', 'CDE09G1246' => 'cde', 'Cfa003412' => 'cfa', 'Cfa007341' => 'cfa', 'Cfa009220' => 'cfa', 'Ciclev10008737m.g' => 'ccl', 'Ciclev10015565m.g' => 'ccl', 'Ciclev10031761m.g' => 'ccl', 'CiPaw.03G045300' => 'cil', 'CiPaw.03G247200' => 'cil', 'CiPaw.04G029500' => 'cil', 'CiPaw.04G174000' => 'cil', 'CiPaw.05G181200' => 'cil', 'CiPaw.06G067100' => 'cil', 'ClCG05G025800' => 'cla', 'ClCG06G011400' => 'cla', 'ClCG09G019360' => 'cla', 'COL.COLO4_04827' => 'col', 'COL.COLO4_29170' => 'col', 'COL.COLO4_35131' => 'col', 'COL.COLO4_35132' => 'col', 'Cpa.g.sc33.32' => 'cpa', 'Cpa.g.sc46.29' => 'cpa', 'Cpa.g.sc796.1' => 'cpa', 'CsaV3_1G030420' => 'csa', 'CsaV3_5G027050' => 'csa', 'CsaV3_5G031040' => 'csa', 'CsaV3_UNG023130' => 'csa', 'CSS0007726' => 'camsi', 'CSS0016433' => 'camsi', 'CSS0017656' => 'camsi', 'CSS0025364' => 'camsi', 'CSS0027582' => 'camsi', 'CSS0047288' => 'camsi', 'CSS0049950' => 'camsi', 'DCAR_003843' => 'dca', 'DCAR_007052' => 'dca', 'DCAR_020884' => 'dca', 'DCAR_021730' => 'dca', 'DCAR_024423' => 'dca', 'DCAR_026509' => 'dca', 'DCAR_031158' => 'dca', 'Dinv14728' => 'din', 'Dinv15219' => 'din', 'Dinv25728' => 'din', 'Dinv33428' => 'din', 'Dinv36489' => 'din', 'Dinv41486' => 'din', 'Duzib147G0469' => 'dzi', 'Duzib168G0060' => 'dzi', 'Duzib187G1215' => 'dzi', 'Duzib248G0692' => 'dzi', 'Duzib251G0767' => 'dzi', 'Duzib264G0446' => 'dzi', 'Duzib268G0691' => 'dzi', 'ECA232G4767' => 'eca', 'ECA233G2838' => 'eca', 'ECA234G0391' => 'eca', 'ECA234G0857' => 'eca', 'ECA236G1593' => 'eca', 'ECA238G0565' => 'eca', 'ECA246G1027' => 'eca', 'ECA246G3223' => 'eca', 'ECA246G3470' => 'eca', 'EL10Ac6g13829' => 'bvu', 'EL10Ac6g14093' => 'bvu', 'EL10Ac8g18707' => 'bvu', 'Eucgr.C01369' => 'egr', 'Eucgr.H02492' => 'egr', 'Eucgr.I01733' => 'egr', 'Eucgr.J02255' => 'egr', 'Eucgr.J02257' => 'egr', 'Eucgr.J02258' => 'egr', 'FAN02G1601' => 'fan', 'FAN03G1586' => 'fan', 'FAN03G2986' => 'fan', 'FAN05G4837' => 'fan', 'FAN06G0146' => 'fan', 'FAN07G0858' => 'fan', 'FAN09G3179' => 'fan', 'FAN10G0669' => 'fan', 'FAN12G2358' => 'fan', 'FAN14G4198' => 'fan', 'FAN14G5112' => 'fan', 'FAN17G0342' => 'fan', 'FAN19G0342' => 'fan', 'FAN19G0962' => 'fan', 'FAN19G1101' => 'fan', 'FAN19G1872' => 'fan', 'FAN22G0356' => 'fan', 'FAN23G0744' => 'fan', 'FAN23G1914' => 'fan', 'FAN26G0032' => 'fan', 'FAN28G0625' => 'fan', 'FvH4_1g02710' => 'fve', 'FvH4_1g02720' => 'fve', 'FvH4_4g25670' => 'fve', 'FvH4_6g51700' => 'fve', 'FvH4_7g20170' => 'fve', 'Glyma.05G175000' => 'gma', 'Glyma.08G132300' => 'gma', 'Glyma.11G243000' => 'gma', 'Glyma.13G158900' => 'gma', 'Glyma.17G112400' => 'gma', 'Glyma.18G014100' => 'gma', 'Glyma.19G003100' => 'gma', 'Glyma.19G056500' => 'gma', 'Gohir.A01G158900' => 'ghi', 'Gohir.A05G312600' => 'ghi', 'Gohir.A05G354900' => 'ghi', 'Gohir.A07G037200' => 'ghi', 'Gohir.A09G030000' => 'ghi', 'Gohir.A12G145200' => 'ghi', 'Gohir.D01G151500' => 'ghi', 'Gohir.D04G058300' => 'ghi', 'Gohir.D05G314100' => 'ghi', 'Gohir.D07G041400' => 'ghi', 'Gohir.D09G029700' => 'ghi', 'Gohir.D12G149700' => 'ghi', 'Gorai.001G043800' => 'gra', 'Gorai.002G187800' => 'gra', 'Gorai.006G034700' => 'gra', 'Gorai.008G161200' => 'gra', 'Gorai.009G335700' => 'gra', 'Gorai.012G065000' => 'gra', 'GSVIVG01000535001' => 'vvi', 'GSVIVG01015572001' => 'vvi', 'GSVIVG01032386001' => 'vvi', 'HanXRQChr05g0138531' => 'han', 'HanXRQChr06g0174391' => 'han', 'HanXRQChr07g0199021' => 'han', 'HanXRQChr08g0208211' => 'han', 'HanXRQChr09g0255471' => 'han', 'HanXRQChr10g0315791' => 'han', 'HanXRQChr12g0371991' => 'han', 'HanXRQChr15g0475251' => 'han', 'HanXRQChr17g0540001' => 'han', 'HanXRQChr17g0548631' => 'han', 'HanXRQChr17g0569561' => 'han', 'Haze_12256' => 'cav', 'Haze_14756' => 'cav', 'Haze_25528' => 'cav', 'Hma1.2p1_0079F.1_g041020' => 'hma', 'Hma1.2p1_0818F.1_g223260' => 'hma', 'Hma1.2p1_1747F.1_g300530' => 'hma', 'HPP92_004607' => 'vpl', 'HPP92_004608' => 'vpl', 'HPP92_006181' => 'vpl', 'HPP92_012192' => 'vpl', 'HPP92_015680' => 'vpl', 'HPP92_020249' => 'vpl', 'HPP92_021376' => 'vpl', 'HPP92_024275' => 'vpl', 'Hund06031' => 'sun', 'Hund25391' => 'sun', 'Lalb_Chr07g0185371' => 'lal', 'Lalb_Chr07g0185381' => 'lal', 'Lalb_Chr12g0204011' => 'lal', 'Lalb_Chr13g0301671' => 'lal', 'Lalb_Chr14g0362851' => 'lal', 'Lalb_Chr24g0403581' => 'lal', 'Lj1g0000233' => 'lja', 'Lj2g0018120' => 'lja', 'Lj3C621T0' => 'lonja', 'Lj3P1059T14' => 'lonja', 'Lj3P611T9' => 'lonja', 'Lj3P614T13' => 'lonja', 'Lj3P615T5' => 'lonja', 'Lj4g0012315' => 'lja', 'Lj4g0026182' => 'lja', 'Lj6P813T16' => 'lonja', 'Lj7C427T7' => 'lonja', 'Lj7C427T8' => 'lonja', 'Lj7P600T41' => 'lonja', 'Lju41C42G17' => 'lonja', 'Lsat_1_v5_gn_0_47300' => 'lsa', 'Lsat_1_v5_gn_2_91280' => 'lsa', 'Lsat_1_v5_gn_3_30561' => 'lsa', 'Lsat_1_v5_gn_4_184321' => 'lsa', 'Lsat_1_v5_gn_4_4041' => 'lsa', 'Lsat_1_v5_gn_5_92000' => 'lsa', 'Lsat_1_v5_gn_8_152940' => 'lsa', 'Lsat_1_v5_gn_8_62401' => 'lsa', 'Manes.06G055900' => 'mes', 'Manes.12G022200' => 'mes', 'Manes.13G023300' => 'mes', 'Manes.14G115000' => 'mes', 'Manes.15G151700' => 'mes', 'Manes.17G111300' => 'mes', 'Mapoly0226s0009' => 'mpo', 'MBI02_g25363_MAGBIO' => 'mbi', 'MBI06_g00027_MAGBIO' => 'mbi', 'MBI10_g13034_MAGBIO' => 'mbi', 'MD09G1023400' => 'mdo', 'MD13G1100100' => 'mdo', 'MD15G1169200' => 'mdo', 'MD16G1101100' => 'mdo', 'MD17G1022900' => 'mdo', 'Medtr3g096150' => 'mtr', 'Medtr4g115070' => 'mtr', 'Medtr7g033325' => 'mtr', 'Medtr8g089840' => 'mtr', 'MELO3C010319.2' => 'cme', 'MELO3C011944.2' => 'cme', 'MELO3C021589.2' => 'cme', 'Migut.E00207' => 'egut', 'Migut.H00067' => 'egut', 'Migut.K00433' => 'egut', 'Migut.K00606' => 'egut', 'Migut.K01410' => 'egut', 'MSTRG.13347' => 'ama', 'MSTRG.24045' => 'ama', 'MSTRG.2428' => 'ama', 'MSTRG.26410' => 'ama', 'MSTRG.3139' => 'ama', 'MSTRG.3286' => 'ama', 'MSTRG.563' => 'ama', 'MSTRG.7941' => 'ama', 'Nitab4.5_0000028g0060' => 'nta', 'Nitab4.5_0000065g0260' => 'nta', 'Nitab4.5_0000112g0060' => 'nta', 'Nitab4.5_0000489g0120' => 'nta', 'Nitab4.5_0001776g0050' => 'nta', 'Nitab4.5_0001854g0010' => 'nta', 'Nitab4.5_0001860g0020' => 'nta', 'Nitab4.5_0004352g0010' => 'nta', 'Nitab4.5_0008716g0020' => 'nta', 'Nitab4.5_0008922g0010' => 'nta', 'Nn3g16693' => 'nnu', 'Nn4g22596' => 'nnu', 'Nn7g37639' => 'nnu', 'Oeu001701.1' => 'oeu', 'Oeu018149.1' => 'oeu', 'Oeu026220.1' => 'oeu', 'Oeu038635.1' => 'oeu', 'Oeu049176.1' => 'oeu', 'Oeu056706.1' => 'oeu', 'Oeu056937.1' => 'oeu', 'Oeu057540.1' => 'oeu', 'Os02g0594900' => 'osa', 'Os02g0595100' => 'osa', 'Os04g0477500' => 'osa', 'Os12g0611900' => 'osa', 'Peaxi162Scf00076g00020' => 'pax', 'Peaxi162Scf00128g00217' => 'pax', 'Peaxi162Scf00129g01640' => 'pax', 'Peaxi162Scf00669g00007' => 'pax', 'Peaxi162Scf00700g00421' => 'pax', 'Peaxi162Scf00801g00038' => 'pax', 'Peaxi162Scf00891g00025' => 'pax', 'PGR083G0909' => 'pgr', 'PGR119G1005' => 'pgr', 'PGR142G2236' => 'pgr', 'PGR142G3388' => 'pgr', 'PGSC0003DMG400004514' => 'stu', 'PGSC0003DMG400012635' => 'stu', 'PGSC0003DMG400015730' => 'stu', 'PGSC0003DMG400018611' => 'stu', 'PGSC0003DMG400030897' => 'stu', 'Phvul.001G254800' => 'pvu', 'Phvul.002G260100' => 'pvu', 'Phvul.003G167600' => 'pvu', 'Phvul.004G005100' => 'pvu', 'Potri.001G343600' => 'ptr', 'Potri.006G066700' => 'ptr', 'Potri.008G186000' => 'ptr', 'Potri.010G046900' => 'ptr', 'Potri.018G127900' => 'ptr', 'Pp3c20_17750' => 'ppa', 'Pp3c24_4380' => 'ppa', 'Prupe.1G245800' => 'ppe', 'Prupe.3G293400' => 'ppe', 'Prupe.7G247400' => 'ppe', 'Psat0s145g0120' => 'psa', 'Psat0s595g0040' => 'psa', 'Psat0s595g0120' => 'psa', 'Psat3g175040' => 'psa', 'Psat7g058120' => 'psa', 'PSO017G0428' => 'pso', 'PSO063G7510' => 'pso', 'PSO067G0046' => 'pso', 'PSO478G1073' => 'pso', 'PSO675G3677' => 'pso', 'PSO675G6558' => 'pso', 'PSO675G7520' => 'pso', 'PSO675G8959' => 'pso', 'QL02p074089' => 'qlo', 'QL02p089614' => 'qlo', 'QL03p057736' => 'qlo', 'RcHm_v2.0_Chr1g0364131' => 'rch', 'RcHm_v2.0_Chr2g0087801' => 'rch', 'RcHm_v2.0_Chr2g0087821' => 'rch', 'RcHm_v2.0_Chr2g0173231' => 'rch', 'RcHm_v2.0_Chr4g0433111' => 'rch', 'Rhsim03G0250300' => 'rsi', 'Rhsim08G0048400' => 'rsi', 'Rhsim10G0014800' => 'rsi', 'Rhsim12G0040100' => 'rsi', 'Rhsim12G0109700' => 'rsi', 'Sabra06G0049600' => 'sbr', 'Sabra08G0141000' => 'sbr', 'Sabra10G0021400' => 'sbr', 'Sabra16G0222900' => 'sbr', 'Sabra18G0108600' => 'sbr', 'SalBow1G0433' => 'sbo', 'SalBow1G2038' => 'sbo', 'SalBow1G5003' => 'sbo', 'SalBow7G1197' => 'sbo', 'SalBow8G3506' => 'sbo', 'Sc03g0007300' => 'sci', 'Sc11g0000950' => 'sci', 'Sc14g0008750' => 'sci', 'Sc18g0000420' => 'sci', 'Sed0006754' => 'sed', 'Sed0008741' => 'sed', 'Sed0017172' => 'sed', 'Sed0018925' => 'sed', 'Sed0023326' => 'sed', 'Sed0025909' => 'sed', 'SEGI_05333' => 'sgi', 'SEGI_10362' => 'sgi', 'SEGI_13380' => 'sgi', 'SEGI_24306' => 'sgi', 'SEGI_29077' => 'sgi', 'SEGI_29095' => 'sgi', 'SEGI_36534' => 'sgi', 'SEGI_37506' => 'sgi', 'SEGI_38321' => 'sgi', 'SGA_v2.0_scaffold307G48031' => 'sas', 'SGA_v2.0_scaffold47G17507' => 'sas', 'SGA_v2.0_scaffold63G21736' => 'sas', 'SGA_v2.0_scaffold87G27070' => 'sas', 'SHI17794' => 'shi', 'SHI28851' => 'shi', 'SMO165G0155' => 'smo', 'SMO340G0217' => 'smo', 'SMO367G1210' => 'smo', 'Solyc02g093430.3' => 'sly', 'Solyc05g013580.4' => 'sly', 'Solyc07g008030.3' => 'sly', 'Solyc12g035470.2' => 'sly', 'Sopen02g038020' => 'spe', 'Sopen05g008490' => 'spe', 'Sopen07g003910' => 'spe', 'Sopen12g015240' => 'spe', 'Sp1g11550' => 'spa', 'Sp2g16710' => 'spa', 'Sp3g00430' => 'spa', 'Sp3g26780' => 'spa', 'Sp5g22900' => 'spa', 'Sp6g29530' => 'spa', 'TAR371G0794' => 'tar', 'TAR374G0164' => 'tar', 'TAR622G0165' => 'tar', 'TAR626G0929' => 'tar', 'TAR629G2155' => 'tar', 'THA.LOC104805282' => 'tha', 'THA.LOC104805363' => 'tha', 'THA.LOC104808968' => 'tha', 'THA.LOC104821093' => 'tha', 'THA.LOC104823953' => 'tha', 'THA.LOC104825562' => 'tha', 'THA.LOC104825665' => 'tha', 'Thecc.02G261400' => 'tca', 'Thecc.04G019200' => 'tca', 'Thecc.09G130400' => 'tca', 'Thhalv10004374m.g' => 'esa', 'Thhalv10007850m.g' => 'esa', 'Thhalv10013782m.g' => 'esa', 'Thhalv10018686m.g' => 'esa', 'Thhalv10020899m.g' => 'esa', 'Thhalv10022755m.g' => 'esa', 'TPR.G23851' => 'tpr', 'TPR.G26500' => 'tpr', 'TPR.G27267' => 'tpr', 'TPR.G32001' => 'tpr', 'TPR.G6251' => 'tpr', 'TPR.G8167' => 'tpr', 'TWI12G1330' => 'twi', 'TWI18G1239' => 'twi', 'TWI34G0979' => 'twi', 'TWI36G0670' => 'twi', 'TWI36G0707' => 'twi', 'TWI56G0233' => 'twi', 'TWI75G1809' => 'twi', 'unitig_21.g20874' => 'ugi', 'unitig_26.g10343' => 'ugi', 'unitig_46.g18392' => 'ugi', 'unitig_52.g17178' => 'ugi', 'unitig_8.g2934' => 'ugi', 'vmacro01122' => 'vma', 'vmacro05875' => 'vma', 'vmacro06147' => 'vma', 'vmacro16191' => 'vma', 'vmacro18293' => 'vma', 'VMungo0251G3707' => 'vmu', 'VMungo0464G1521' => 'vmu', 'VMungo1215G0205' => 'vmu', 'VMungo1383G2484' => 'vmu', 'Zm00001eb079610' => 'zma', 'Zm00001eb135990' => 'zma', 'Zm00001eb183710' => 'zma', 'Zm00001eb246020' => 'zma' ) $gf_id = 'HOM05D001124' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001124' ) $data_identifier = 'HOM05D001124' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 6, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 7, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 21, 'bol' => (int) 10, 'bra' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 6, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 9, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 21, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 8, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 10, 'lsa' => (int) 8, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 8, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 9, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb246020' $species_info = array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ) $local_species = 'mes' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001124', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '548', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02520' => 'bna', 'A03p06630' => 'bna', 'A05p44460' => 'bna', 'A06p08710' => 'bna', 'A06p41090' => 'bna', 'A07p32320' => 'bna', 'A08p32520' => 'bna', 'A09p10360' => 'bna', 'A10p24080' => 'bna', 'Aa31LG11G15250' => 'aar', 'Aa31LG1G1800' => 'aar', 'Aa31LG2G5120' => 'aar', 'Aa31LG2G6070' => 'aar', 'Aa31LG5G10770' => 'aar', 'Aa31sc61G90' => 'aar', 'Actinidia01352' => 'ach', 'Actinidia05983' => 'ach', 'Actinidia08133' => 'ach', 'Actinidia15101' => 'ach', 'Actinidia26379' => 'ach', 'Actinidia35778' => 'ach', 'Actinidia36123' => 'ach', 'Actinidia37436' => 'ach', 'Actinidia38730' => 'ach', 'Ah.02g128210' => 'amhyb', 'Ah.03g132990' => 'amhyb', 'Ah.14g079410' => 'amhyb', 'AL1G24640' => 'aly', 'AL2G26680' => 'aly', 'AL3G10530' => 'aly', 'AL3G45230' => 'aly', 'AL5G15230' => 'aly', 'AL5G16960' => 'aly', 'AL6G25210' => 'aly', 'Aqoxy2G00441' => 'aox', 'Aqoxy3G01236' => 'aox', 'Aqoxy5G03746' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3RQ047' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C7GMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9C8JER' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MBL6KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YXCZ83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZANX40' => 'arhy', 'AT1G12990' => 'ath', 'AT1G67880' => 'ath', 'AT2G13290' => 'ath', 'AT3G01620' => 'ath', 'AT3G26445' => 'ath', 'AT3G27540' => 'ath', 'AT5G14480' => 'ath', 'ATR0824G026' => 'atr', 'ATR1098G019' => 'atr', 'Atru.chr11.2145' => 'acertr', 'Atru.chr2.3636' => 'acertr', 'Atru.chr2.3644' => 'acertr', 'Atru.chr6.2422' => 'acertr', 'Atru.chr7.1112' => 'acertr', 'AUR62005469' => 'cqu', 'AUR62011166' => 'cqu', 'AUR62013319' => 'cqu', 'AUR62024273' => 'cqu', 'AUR62028420' => 'cqu', 'AUR62041942' => 'cqu', 'BcaB01g04969' => 'bca', 'BcaB01g06371' => 'bca', 'BcaB02g11494' => 'bca', 'BcaB03g15382' => 'bca', 'BcaB08g36994' => 'bca', 'BcaC03g13477' => 'bca', 'BcaC03g13478' => 'bca', 'BcaC03g13480' => 'bca', 'BcaC03g13481' => 'bca', 'BcaC03g13486' => 'bca', 'BcaC04g19031' => 'bca', 'BcaC04g23085' => 'bca', 'BcaC05g25094' => 'bca', 'BcaC05g25096' => 'bca', 'BcaC05g25138' => 'bca', 'BcaC05g30416' => 'bca', 'BcaC05g30455' => 'bca', 'BcaC06g30979' => 'bca', 'BcaC06g33805' => 'bca', 'BcaC08g46021' => 'bca', 'BcaNung03154' => 'bca', 'BolC2t06623H' => 'bol', 'BolC2t06632H' => 'bol', 'BolC2t06635H' => 'bol', 'BolC2t06638H' => 'bol', 'BolC3t13266H' => 'bol', 'BolC5t29776H' => 'bol', 'BolC6t38912H' => 'bol', 'BolC7t44183H' => 'bol', 'BolC9t54123H' => 'bol', 'BolC9t59107H' => 'bol', 'BraA02t05221Z' => 'bra', 'BraA03t09996Z' => 'bra', 'BraA05t23210Z' => 'bra', 'BraA06t24068Z' => 'bra', 'BraA06t27032Z' => 'bra', 'BraA08t35176Z' => 'bra', 'BraA09t36680Z' => 'bra', 'BraA10t44471Z' => 'bra', 'C02p06760' => 'bna', 'C02p06890' => 'bna', 'C02p07010' => 'bna', 'C03p07660' => 'bna', 'C05p10300' => 'bna', 'C06p38150' => 'bna', 'C07p36650' => 'bna', 'C08p15770' => 'bna', 'C09p12300' => 'bna', 'C09p62700' => 'bna', 'C09p75040' => 'bna', 'CAN.G13.1' => 'can', 'CAN.G138.4' => 'can', 'CAN.G44.6' => 'can', 'CAN.G473.19' => 'can', 'CANSAT01G0835' => 'cansat', 'CANSAT11G0246' => 'cansat', 'CANSAT11G1766' => 'cansat', 'CANSAT64G1954' => 'cansat', 'CARHR013330' => 'chi', 'CARHR060530' => 'chi', 'CARHR075300' => 'chi', 'CARHR105120' => 'chi', 'CARHR148910' => 'chi', 'CARHR198830' => 'chi', 'Carub.0001s1275' => 'cru', 'Carub.0002s1437' => 'cru', 'Carub.0003s0044' => 'cru', 'Carub.0003s2787' => 'cru', 'Carub.0005s0597' => 'cru', 'Carub.0006s1266' => 'cru', 'Ca_06935_v3' => 'car', 'Ca_13559_v3' => 'car', 'Ca_16941_v3' => 'car', 'Ca_16960_v3' => 'car', 'Ca_17775_v3' => 'car', 'Ca_30464_v3' => 'car', 'Cc06_g08160' => 'ccan', 'Cc07_g01520' => 'ccan', 'Cc11_g15810' => 'ccan', 'CDE02G2840' => 'cde', 'CDE03G0093' => 'cde', 'CDE04G2127' => 'cde', 'CDE07G1857' => 'cde', 'CDE09G1246' => 'cde', 'Cfa003412' => 'cfa', 'Cfa007341' => 'cfa', 'Cfa009220' => 'cfa', 'Ciclev10008737m.g' => 'ccl', 'Ciclev10015565m.g' => 'ccl', 'Ciclev10031761m.g' => 'ccl', 'CiPaw.03G045300' => 'cil', 'CiPaw.03G247200' => 'cil', 'CiPaw.04G029500' => 'cil', 'CiPaw.04G174000' => 'cil', 'CiPaw.05G181200' => 'cil', 'CiPaw.06G067100' => 'cil', 'ClCG05G025800' => 'cla', 'ClCG06G011400' => 'cla', 'ClCG09G019360' => 'cla', 'COL.COLO4_04827' => 'col', 'COL.COLO4_29170' => 'col', 'COL.COLO4_35131' => 'col', 'COL.COLO4_35132' => 'col', 'Cpa.g.sc33.32' => 'cpa', 'Cpa.g.sc46.29' => 'cpa', 'Cpa.g.sc796.1' => 'cpa', 'CsaV3_1G030420' => 'csa', 'CsaV3_5G027050' => 'csa', 'CsaV3_5G031040' => 'csa', 'CsaV3_UNG023130' => 'csa', 'CSS0007726' => 'camsi', 'CSS0016433' => 'camsi', 'CSS0017656' => 'camsi', 'CSS0025364' => 'camsi', 'CSS0027582' => 'camsi', 'CSS0047288' => 'camsi', 'CSS0049950' => 'camsi', 'DCAR_003843' => 'dca', 'DCAR_007052' => 'dca', 'DCAR_020884' => 'dca', 'DCAR_021730' => 'dca', 'DCAR_024423' => 'dca', 'DCAR_026509' => 'dca', 'DCAR_031158' => 'dca', 'Dinv14728' => 'din', 'Dinv15219' => 'din', 'Dinv25728' => 'din', 'Dinv33428' => 'din', 'Dinv36489' => 'din', 'Dinv41486' => 'din', 'Duzib147G0469' => 'dzi', 'Duzib168G0060' => 'dzi', 'Duzib187G1215' => 'dzi', 'Duzib248G0692' => 'dzi', 'Duzib251G0767' => 'dzi', 'Duzib264G0446' => 'dzi', 'Duzib268G0691' => 'dzi', 'ECA232G4767' => 'eca', 'ECA233G2838' => 'eca', 'ECA234G0391' => 'eca', 'ECA234G0857' => 'eca', 'ECA236G1593' => 'eca', 'ECA238G0565' => 'eca', 'ECA246G1027' => 'eca', 'ECA246G3223' => 'eca', 'ECA246G3470' => 'eca', 'EL10Ac6g13829' => 'bvu', 'EL10Ac6g14093' => 'bvu', 'EL10Ac8g18707' => 'bvu', 'Eucgr.C01369' => 'egr', 'Eucgr.H02492' => 'egr', 'Eucgr.I01733' => 'egr', 'Eucgr.J02255' => 'egr', 'Eucgr.J02257' => 'egr', 'Eucgr.J02258' => 'egr', 'FAN02G1601' => 'fan', 'FAN03G1586' => 'fan', 'FAN03G2986' => 'fan', 'FAN05G4837' => 'fan', 'FAN06G0146' => 'fan', 'FAN07G0858' => 'fan', 'FAN09G3179' => 'fan', 'FAN10G0669' => 'fan', 'FAN12G2358' => 'fan', 'FAN14G4198' => 'fan', 'FAN14G5112' => 'fan', 'FAN17G0342' => 'fan', 'FAN19G0342' => 'fan', 'FAN19G0962' => 'fan', 'FAN19G1101' => 'fan', 'FAN19G1872' => 'fan', 'FAN22G0356' => 'fan', 'FAN23G0744' => 'fan', 'FAN23G1914' => 'fan', 'FAN26G0032' => 'fan', 'FAN28G0625' => 'fan', 'FvH4_1g02710' => 'fve', 'FvH4_1g02720' => 'fve', 'FvH4_4g25670' => 'fve', 'FvH4_6g51700' => 'fve', 'FvH4_7g20170' => 'fve', 'Glyma.05G175000' => 'gma', 'Glyma.08G132300' => 'gma', 'Glyma.11G243000' => 'gma', 'Glyma.13G158900' => 'gma', 'Glyma.17G112400' => 'gma', 'Glyma.18G014100' => 'gma', 'Glyma.19G003100' => 'gma', 'Glyma.19G056500' => 'gma', 'Gohir.A01G158900' => 'ghi', 'Gohir.A05G312600' => 'ghi', 'Gohir.A05G354900' => 'ghi', 'Gohir.A07G037200' => 'ghi', 'Gohir.A09G030000' => 'ghi', 'Gohir.A12G145200' => 'ghi', 'Gohir.D01G151500' => 'ghi', 'Gohir.D04G058300' => 'ghi', 'Gohir.D05G314100' => 'ghi', 'Gohir.D07G041400' => 'ghi', 'Gohir.D09G029700' => 'ghi', 'Gohir.D12G149700' => 'ghi', 'Gorai.001G043800' => 'gra', 'Gorai.002G187800' => 'gra', 'Gorai.006G034700' => 'gra', 'Gorai.008G161200' => 'gra', 'Gorai.009G335700' => 'gra', 'Gorai.012G065000' => 'gra', 'GSVIVG01000535001' => 'vvi', 'GSVIVG01015572001' => 'vvi', 'GSVIVG01032386001' => 'vvi', 'HanXRQChr05g0138531' => 'han', 'HanXRQChr06g0174391' => 'han', 'HanXRQChr07g0199021' => 'han', 'HanXRQChr08g0208211' => 'han', 'HanXRQChr09g0255471' => 'han', 'HanXRQChr10g0315791' => 'han', 'HanXRQChr12g0371991' => 'han', 'HanXRQChr15g0475251' => 'han', 'HanXRQChr17g0540001' => 'han', 'HanXRQChr17g0548631' => 'han', 'HanXRQChr17g0569561' => 'han', 'Haze_12256' => 'cav', 'Haze_14756' => 'cav', 'Haze_25528' => 'cav', 'Hma1.2p1_0079F.1_g041020' => 'hma', 'Hma1.2p1_0818F.1_g223260' => 'hma', 'Hma1.2p1_1747F.1_g300530' => 'hma', 'HPP92_004607' => 'vpl', 'HPP92_004608' => 'vpl', 'HPP92_006181' => 'vpl', 'HPP92_012192' => 'vpl', 'HPP92_015680' => 'vpl', 'HPP92_020249' => 'vpl', 'HPP92_021376' => 'vpl', 'HPP92_024275' => 'vpl', 'Hund06031' => 'sun', 'Hund25391' => 'sun', 'Lalb_Chr07g0185371' => 'lal', 'Lalb_Chr07g0185381' => 'lal', 'Lalb_Chr12g0204011' => 'lal', 'Lalb_Chr13g0301671' => 'lal', 'Lalb_Chr14g0362851' => 'lal', 'Lalb_Chr24g0403581' => 'lal', 'Lj1g0000233' => 'lja', 'Lj2g0018120' => 'lja', 'Lj3C621T0' => 'lonja', 'Lj3P1059T14' => 'lonja', 'Lj3P611T9' => 'lonja', 'Lj3P614T13' => 'lonja', 'Lj3P615T5' => 'lonja', 'Lj4g0012315' => 'lja', 'Lj4g0026182' => 'lja', 'Lj6P813T16' => 'lonja', 'Lj7C427T7' => 'lonja', 'Lj7C427T8' => 'lonja', 'Lj7P600T41' => 'lonja', 'Lju41C42G17' => 'lonja', 'Lsat_1_v5_gn_0_47300' => 'lsa', 'Lsat_1_v5_gn_2_91280' => 'lsa', 'Lsat_1_v5_gn_3_30561' => 'lsa', 'Lsat_1_v5_gn_4_184321' => 'lsa', 'Lsat_1_v5_gn_4_4041' => 'lsa', 'Lsat_1_v5_gn_5_92000' => 'lsa', 'Lsat_1_v5_gn_8_152940' => 'lsa', 'Lsat_1_v5_gn_8_62401' => 'lsa', 'Manes.06G055900' => 'mes', 'Manes.12G022200' => 'mes', 'Manes.13G023300' => 'mes', 'Manes.14G115000' => 'mes', 'Manes.15G151700' => 'mes', 'Manes.17G111300' => 'mes', 'Mapoly0226s0009' => 'mpo', 'MBI02_g25363_MAGBIO' => 'mbi', 'MBI06_g00027_MAGBIO' => 'mbi', 'MBI10_g13034_MAGBIO' => 'mbi', 'MD09G1023400' => 'mdo', 'MD13G1100100' => 'mdo', 'MD15G1169200' => 'mdo', 'MD16G1101100' => 'mdo', 'MD17G1022900' => 'mdo', 'Medtr3g096150' => 'mtr', 'Medtr4g115070' => 'mtr', 'Medtr7g033325' => 'mtr', 'Medtr8g089840' => 'mtr', 'MELO3C010319.2' => 'cme', 'MELO3C011944.2' => 'cme', 'MELO3C021589.2' => 'cme', 'Migut.E00207' => 'egut', 'Migut.H00067' => 'egut', 'Migut.K00433' => 'egut', 'Migut.K00606' => 'egut', 'Migut.K01410' => 'egut', 'MSTRG.13347' => 'ama', 'MSTRG.24045' => 'ama', 'MSTRG.2428' => 'ama', 'MSTRG.26410' => 'ama', 'MSTRG.3139' => 'ama', 'MSTRG.3286' => 'ama', 'MSTRG.563' => 'ama', 'MSTRG.7941' => 'ama', 'Nitab4.5_0000028g0060' => 'nta', 'Nitab4.5_0000065g0260' => 'nta', 'Nitab4.5_0000112g0060' => 'nta', 'Nitab4.5_0000489g0120' => 'nta', 'Nitab4.5_0001776g0050' => 'nta', 'Nitab4.5_0001854g0010' => 'nta', 'Nitab4.5_0001860g0020' => 'nta', 'Nitab4.5_0004352g0010' => 'nta', 'Nitab4.5_0008716g0020' => 'nta', 'Nitab4.5_0008922g0010' => 'nta', 'Nn3g16693' => 'nnu', 'Nn4g22596' => 'nnu', 'Nn7g37639' => 'nnu', 'Oeu001701.1' => 'oeu', 'Oeu018149.1' => 'oeu', 'Oeu026220.1' => 'oeu', 'Oeu038635.1' => 'oeu', 'Oeu049176.1' => 'oeu', 'Oeu056706.1' => 'oeu', 'Oeu056937.1' => 'oeu', 'Oeu057540.1' => 'oeu', 'Os02g0594900' => 'osa', 'Os02g0595100' => 'osa', 'Os04g0477500' => 'osa', 'Os12g0611900' => 'osa', 'Peaxi162Scf00076g00020' => 'pax', 'Peaxi162Scf00128g00217' => 'pax', 'Peaxi162Scf00129g01640' => 'pax', 'Peaxi162Scf00669g00007' => 'pax', 'Peaxi162Scf00700g00421' => 'pax', 'Peaxi162Scf00801g00038' => 'pax', 'Peaxi162Scf00891g00025' => 'pax', 'PGR083G0909' => 'pgr', 'PGR119G1005' => 'pgr', 'PGR142G2236' => 'pgr', 'PGR142G3388' => 'pgr', 'PGSC0003DMG400004514' => 'stu', 'PGSC0003DMG400012635' => 'stu', 'PGSC0003DMG400015730' => 'stu', 'PGSC0003DMG400018611' => 'stu', 'PGSC0003DMG400030897' => 'stu', 'Phvul.001G254800' => 'pvu', 'Phvul.002G260100' => 'pvu', 'Phvul.003G167600' => 'pvu', 'Phvul.004G005100' => 'pvu', 'Potri.001G343600' => 'ptr', 'Potri.006G066700' => 'ptr', 'Potri.008G186000' => 'ptr', 'Potri.010G046900' => 'ptr', 'Potri.018G127900' => 'ptr', 'Pp3c20_17750' => 'ppa', 'Pp3c24_4380' => 'ppa', 'Prupe.1G245800' => 'ppe', 'Prupe.3G293400' => 'ppe', 'Prupe.7G247400' => 'ppe', 'Psat0s145g0120' => 'psa', 'Psat0s595g0040' => 'psa', 'Psat0s595g0120' => 'psa', 'Psat3g175040' => 'psa', 'Psat7g058120' => 'psa', 'PSO017G0428' => 'pso', 'PSO063G7510' => 'pso', 'PSO067G0046' => 'pso', 'PSO478G1073' => 'pso', 'PSO675G3677' => 'pso', 'PSO675G6558' => 'pso', 'PSO675G7520' => 'pso', 'PSO675G8959' => 'pso', 'QL02p074089' => 'qlo', 'QL02p089614' => 'qlo', 'QL03p057736' => 'qlo', 'RcHm_v2.0_Chr1g0364131' => 'rch', 'RcHm_v2.0_Chr2g0087801' => 'rch', 'RcHm_v2.0_Chr2g0087821' => 'rch', 'RcHm_v2.0_Chr2g0173231' => 'rch', 'RcHm_v2.0_Chr4g0433111' => 'rch', 'Rhsim03G0250300' => 'rsi', 'Rhsim08G0048400' => 'rsi', 'Rhsim10G0014800' => 'rsi', 'Rhsim12G0040100' => 'rsi', 'Rhsim12G0109700' => 'rsi', 'Sabra06G0049600' => 'sbr', 'Sabra08G0141000' => 'sbr', 'Sabra10G0021400' => 'sbr', 'Sabra16G0222900' => 'sbr', 'Sabra18G0108600' => 'sbr', 'SalBow1G0433' => 'sbo', 'SalBow1G2038' => 'sbo', 'SalBow1G5003' => 'sbo', 'SalBow7G1197' => 'sbo', 'SalBow8G3506' => 'sbo', 'Sc03g0007300' => 'sci', 'Sc11g0000950' => 'sci', 'Sc14g0008750' => 'sci', 'Sc18g0000420' => 'sci', 'Sed0006754' => 'sed', 'Sed0008741' => 'sed', 'Sed0017172' => 'sed', 'Sed0018925' => 'sed', 'Sed0023326' => 'sed', 'Sed0025909' => 'sed', 'SEGI_05333' => 'sgi', 'SEGI_10362' => 'sgi', 'SEGI_13380' => 'sgi', 'SEGI_24306' => 'sgi', 'SEGI_29077' => 'sgi', 'SEGI_29095' => 'sgi', 'SEGI_36534' => 'sgi', 'SEGI_37506' => 'sgi', 'SEGI_38321' => 'sgi', 'SGA_v2.0_scaffold307G48031' => 'sas', 'SGA_v2.0_scaffold47G17507' => 'sas', 'SGA_v2.0_scaffold63G21736' => 'sas', 'SGA_v2.0_scaffold87G27070' => 'sas', 'SHI17794' => 'shi', 'SHI28851' => 'shi', 'SMO165G0155' => 'smo', 'SMO340G0217' => 'smo', 'SMO367G1210' => 'smo', 'Solyc02g093430.3' => 'sly', 'Solyc05g013580.4' => 'sly', 'Solyc07g008030.3' => 'sly', 'Solyc12g035470.2' => 'sly', 'Sopen02g038020' => 'spe', 'Sopen05g008490' => 'spe', 'Sopen07g003910' => 'spe', 'Sopen12g015240' => 'spe', 'Sp1g11550' => 'spa', 'Sp2g16710' => 'spa', 'Sp3g00430' => 'spa', 'Sp3g26780' => 'spa', 'Sp5g22900' => 'spa', 'Sp6g29530' => 'spa', 'TAR371G0794' => 'tar', 'TAR374G0164' => 'tar', 'TAR622G0165' => 'tar', 'TAR626G0929' => 'tar', 'TAR629G2155' => 'tar', 'THA.LOC104805282' => 'tha', 'THA.LOC104805363' => 'tha', 'THA.LOC104808968' => 'tha', 'THA.LOC104821093' => 'tha', 'THA.LOC104823953' => 'tha', 'THA.LOC104825562' => 'tha', 'THA.LOC104825665' => 'tha', 'Thecc.02G261400' => 'tca', 'Thecc.04G019200' => 'tca', 'Thecc.09G130400' => 'tca', 'Thhalv10004374m.g' => 'esa', 'Thhalv10007850m.g' => 'esa', 'Thhalv10013782m.g' => 'esa', 'Thhalv10018686m.g' => 'esa', 'Thhalv10020899m.g' => 'esa', 'Thhalv10022755m.g' => 'esa', 'TPR.G23851' => 'tpr', 'TPR.G26500' => 'tpr', 'TPR.G27267' => 'tpr', 'TPR.G32001' => 'tpr', 'TPR.G6251' => 'tpr', 'TPR.G8167' => 'tpr', 'TWI12G1330' => 'twi', 'TWI18G1239' => 'twi', 'TWI34G0979' => 'twi', 'TWI36G0670' => 'twi', 'TWI36G0707' => 'twi', 'TWI56G0233' => 'twi', 'TWI75G1809' => 'twi', 'unitig_21.g20874' => 'ugi', 'unitig_26.g10343' => 'ugi', 'unitig_46.g18392' => 'ugi', 'unitig_52.g17178' => 'ugi', 'unitig_8.g2934' => 'ugi', 'vmacro01122' => 'vma', 'vmacro05875' => 'vma', 'vmacro06147' => 'vma', 'vmacro16191' => 'vma', 'vmacro18293' => 'vma', 'VMungo0251G3707' => 'vmu', 'VMungo0464G1521' => 'vmu', 'VMungo1215G0205' => 'vmu', 'VMungo1383G2484' => 'vmu', 'Zm00001eb079610' => 'zma', 'Zm00001eb135990' => 'zma', 'Zm00001eb183710' => 'zma', 'Zm00001eb246020' => 'zma' ), 'gf_id' => 'HOM05D001124', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001124' ), 'data_identifier' => 'HOM05D001124', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001124', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '548', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02520' => 'bna', 'A03p06630' => 'bna', 'A05p44460' => 'bna', 'A06p08710' => 'bna', 'A06p41090' => 'bna', 'A07p32320' => 'bna', 'A08p32520' => 'bna', 'A09p10360' => 'bna', 'A10p24080' => 'bna', 'Aa31LG11G15250' => 'aar', 'Aa31LG1G1800' => 'aar', 'Aa31LG2G5120' => 'aar', 'Aa31LG2G6070' => 'aar', 'Aa31LG5G10770' => 'aar', 'Aa31sc61G90' => 'aar', 'Actinidia01352' => 'ach', 'Actinidia05983' => 'ach', 'Actinidia08133' => 'ach', 'Actinidia15101' => 'ach', 'Actinidia26379' => 'ach', 'Actinidia35778' => 'ach', 'Actinidia36123' => 'ach', 'Actinidia37436' => 'ach', 'Actinidia38730' => 'ach', 'Ah.02g128210' => 'amhyb', 'Ah.03g132990' => 'amhyb', 'Ah.14g079410' => 'amhyb', 'AL1G24640' => 'aly', 'AL2G26680' => 'aly', 'AL3G10530' => 'aly', 'AL3G45230' => 'aly', 'AL5G15230' => 'aly', 'AL5G16960' => 'aly', 'AL6G25210' => 'aly', 'Aqoxy2G00441' => 'aox', 'Aqoxy3G01236' => 'aox', 'Aqoxy5G03746' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3RQ047' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C7GMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9C8JER' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MBL6KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YXCZ83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZANX40' => 'arhy', 'AT1G12990' => 'ath', 'AT1G67880' => 'ath', 'AT2G13290' => 'ath', 'AT3G01620' => 'ath', 'AT3G26445' => 'ath', 'AT3G27540' => 'ath', 'AT5G14480' => 'ath', 'ATR0824G026' => 'atr', 'ATR1098G019' => 'atr', 'Atru.chr11.2145' => 'acertr', 'Atru.chr2.3636' => 'acertr', 'Atru.chr2.3644' => 'acertr', 'Atru.chr6.2422' => 'acertr', 'Atru.chr7.1112' => 'acertr', 'AUR62005469' => 'cqu', 'AUR62011166' => 'cqu', 'AUR62013319' => 'cqu', 'AUR62024273' => 'cqu', 'AUR62028420' => 'cqu', 'AUR62041942' => 'cqu', 'BcaB01g04969' => 'bca', 'BcaB01g06371' => 'bca', 'BcaB02g11494' => 'bca', 'BcaB03g15382' => 'bca', 'BcaB08g36994' => 'bca', 'BcaC03g13477' => 'bca', 'BcaC03g13478' => 'bca', 'BcaC03g13480' => 'bca', 'BcaC03g13481' => 'bca', 'BcaC03g13486' => 'bca', 'BcaC04g19031' => 'bca', 'BcaC04g23085' => 'bca', 'BcaC05g25094' => 'bca', 'BcaC05g25096' => 'bca', 'BcaC05g25138' => 'bca', 'BcaC05g30416' => 'bca', 'BcaC05g30455' => 'bca', 'BcaC06g30979' => 'bca', 'BcaC06g33805' => 'bca', 'BcaC08g46021' => 'bca', 'BcaNung03154' => 'bca', 'BolC2t06623H' => 'bol', 'BolC2t06632H' => 'bol', 'BolC2t06635H' => 'bol', 'BolC2t06638H' => 'bol', 'BolC3t13266H' => 'bol', 'BolC5t29776H' => 'bol', 'BolC6t38912H' => 'bol', 'BolC7t44183H' => 'bol', 'BolC9t54123H' => 'bol', 'BolC9t59107H' => 'bol', 'BraA02t05221Z' => 'bra', 'BraA03t09996Z' => 'bra', 'BraA05t23210Z' => 'bra', 'BraA06t24068Z' => 'bra', 'BraA06t27032Z' => 'bra', 'BraA08t35176Z' => 'bra', 'BraA09t36680Z' => 'bra', 'BraA10t44471Z' => 'bra', 'C02p06760' => 'bna', 'C02p06890' => 'bna', 'C02p07010' => 'bna', 'C03p07660' => 'bna', 'C05p10300' => 'bna', 'C06p38150' => 'bna', 'C07p36650' => 'bna', 'C08p15770' => 'bna', 'C09p12300' => 'bna', 'C09p62700' => 'bna', 'C09p75040' => 'bna', 'CAN.G13.1' => 'can', 'CAN.G138.4' => 'can', 'CAN.G44.6' => 'can', 'CAN.G473.19' => 'can', 'CANSAT01G0835' => 'cansat', 'CANSAT11G0246' => 'cansat', 'CANSAT11G1766' => 'cansat', 'CANSAT64G1954' => 'cansat', 'CARHR013330' => 'chi', 'CARHR060530' => 'chi', 'CARHR075300' => 'chi', 'CARHR105120' => 'chi', 'CARHR148910' => 'chi', 'CARHR198830' => 'chi', 'Carub.0001s1275' => 'cru', 'Carub.0002s1437' => 'cru', 'Carub.0003s0044' => 'cru', 'Carub.0003s2787' => 'cru', 'Carub.0005s0597' => 'cru', 'Carub.0006s1266' => 'cru', 'Ca_06935_v3' => 'car', 'Ca_13559_v3' => 'car', 'Ca_16941_v3' => 'car', 'Ca_16960_v3' => 'car', 'Ca_17775_v3' => 'car', 'Ca_30464_v3' => 'car', 'Cc06_g08160' => 'ccan', 'Cc07_g01520' => 'ccan', 'Cc11_g15810' => 'ccan', 'CDE02G2840' => 'cde', 'CDE03G0093' => 'cde', 'CDE04G2127' => 'cde', 'CDE07G1857' => 'cde', 'CDE09G1246' => 'cde', 'Cfa003412' => 'cfa', 'Cfa007341' => 'cfa', 'Cfa009220' => 'cfa', 'Ciclev10008737m.g' => 'ccl', 'Ciclev10015565m.g' => 'ccl', 'Ciclev10031761m.g' => 'ccl', 'CiPaw.03G045300' => 'cil', 'CiPaw.03G247200' => 'cil', 'CiPaw.04G029500' => 'cil', 'CiPaw.04G174000' => 'cil', 'CiPaw.05G181200' => 'cil', 'CiPaw.06G067100' => 'cil', 'ClCG05G025800' => 'cla', 'ClCG06G011400' => 'cla', 'ClCG09G019360' => 'cla', 'COL.COLO4_04827' => 'col', 'COL.COLO4_29170' => 'col', 'COL.COLO4_35131' => 'col', 'COL.COLO4_35132' => 'col', 'Cpa.g.sc33.32' => 'cpa', 'Cpa.g.sc46.29' => 'cpa', 'Cpa.g.sc796.1' => 'cpa', 'CsaV3_1G030420' => 'csa', 'CsaV3_5G027050' => 'csa', 'CsaV3_5G031040' => 'csa', 'CsaV3_UNG023130' => 'csa', 'CSS0007726' => 'camsi', 'CSS0016433' => 'camsi', 'CSS0017656' => 'camsi', 'CSS0025364' => 'camsi', 'CSS0027582' => 'camsi', 'CSS0047288' => 'camsi', 'CSS0049950' => 'camsi', 'DCAR_003843' => 'dca', 'DCAR_007052' => 'dca', 'DCAR_020884' => 'dca', 'DCAR_021730' => 'dca', 'DCAR_024423' => 'dca', 'DCAR_026509' => 'dca', 'DCAR_031158' => 'dca', 'Dinv14728' => 'din', 'Dinv15219' => 'din', 'Dinv25728' => 'din', 'Dinv33428' => 'din', 'Dinv36489' => 'din', 'Dinv41486' => 'din', 'Duzib147G0469' => 'dzi', 'Duzib168G0060' => 'dzi', 'Duzib187G1215' => 'dzi', 'Duzib248G0692' => 'dzi', 'Duzib251G0767' => 'dzi', 'Duzib264G0446' => 'dzi', 'Duzib268G0691' => 'dzi', 'ECA232G4767' => 'eca', 'ECA233G2838' => 'eca', 'ECA234G0391' => 'eca', 'ECA234G0857' => 'eca', 'ECA236G1593' => 'eca', 'ECA238G0565' => 'eca', 'ECA246G1027' => 'eca', 'ECA246G3223' => 'eca', 'ECA246G3470' => 'eca', 'EL10Ac6g13829' => 'bvu', 'EL10Ac6g14093' => 'bvu', 'EL10Ac8g18707' => 'bvu', 'Eucgr.C01369' => 'egr', 'Eucgr.H02492' => 'egr', 'Eucgr.I01733' => 'egr', 'Eucgr.J02255' => 'egr', 'Eucgr.J02257' => 'egr', 'Eucgr.J02258' => 'egr', 'FAN02G1601' => 'fan', 'FAN03G1586' => 'fan', 'FAN03G2986' => 'fan', 'FAN05G4837' => 'fan', 'FAN06G0146' => 'fan', 'FAN07G0858' => 'fan', 'FAN09G3179' => 'fan', 'FAN10G0669' => 'fan', 'FAN12G2358' => 'fan', 'FAN14G4198' => 'fan', 'FAN14G5112' => 'fan', 'FAN17G0342' => 'fan', 'FAN19G0342' => 'fan', 'FAN19G0962' => 'fan', 'FAN19G1101' => 'fan', 'FAN19G1872' => 'fan', 'FAN22G0356' => 'fan', 'FAN23G0744' => 'fan', 'FAN23G1914' => 'fan', 'FAN26G0032' => 'fan', 'FAN28G0625' => 'fan', 'FvH4_1g02710' => 'fve', 'FvH4_1g02720' => 'fve', 'FvH4_4g25670' => 'fve', 'FvH4_6g51700' => 'fve', 'FvH4_7g20170' => 'fve', 'Glyma.05G175000' => 'gma', 'Glyma.08G132300' => 'gma', 'Glyma.11G243000' => 'gma', 'Glyma.13G158900' => 'gma', 'Glyma.17G112400' => 'gma', 'Glyma.18G014100' => 'gma', 'Glyma.19G003100' => 'gma', 'Glyma.19G056500' => 'gma', 'Gohir.A01G158900' => 'ghi', 'Gohir.A05G312600' => 'ghi', 'Gohir.A05G354900' => 'ghi', 'Gohir.A07G037200' => 'ghi', 'Gohir.A09G030000' => 'ghi', 'Gohir.A12G145200' => 'ghi', 'Gohir.D01G151500' => 'ghi', 'Gohir.D04G058300' => 'ghi', 'Gohir.D05G314100' => 'ghi', 'Gohir.D07G041400' => 'ghi', 'Gohir.D09G029700' => 'ghi', 'Gohir.D12G149700' => 'ghi', 'Gorai.001G043800' => 'gra', 'Gorai.002G187800' => 'gra', 'Gorai.006G034700' => 'gra', 'Gorai.008G161200' => 'gra', 'Gorai.009G335700' => 'gra', 'Gorai.012G065000' => 'gra', 'GSVIVG01000535001' => 'vvi', 'GSVIVG01015572001' => 'vvi', 'GSVIVG01032386001' => 'vvi', 'HanXRQChr05g0138531' => 'han', 'HanXRQChr06g0174391' => 'han', 'HanXRQChr07g0199021' => 'han', 'HanXRQChr08g0208211' => 'han', 'HanXRQChr09g0255471' => 'han', 'HanXRQChr10g0315791' => 'han', 'HanXRQChr12g0371991' => 'han', 'HanXRQChr15g0475251' => 'han', 'HanXRQChr17g0540001' => 'han', 'HanXRQChr17g0548631' => 'han', 'HanXRQChr17g0569561' => 'han', 'Haze_12256' => 'cav', 'Haze_14756' => 'cav', 'Haze_25528' => 'cav', 'Hma1.2p1_0079F.1_g041020' => 'hma', 'Hma1.2p1_0818F.1_g223260' => 'hma', 'Hma1.2p1_1747F.1_g300530' => 'hma', 'HPP92_004607' => 'vpl', 'HPP92_004608' => 'vpl', 'HPP92_006181' => 'vpl', 'HPP92_012192' => 'vpl', 'HPP92_015680' => 'vpl', 'HPP92_020249' => 'vpl', 'HPP92_021376' => 'vpl', 'HPP92_024275' => 'vpl', 'Hund06031' => 'sun', 'Hund25391' => 'sun', 'Lalb_Chr07g0185371' => 'lal', 'Lalb_Chr07g0185381' => 'lal', 'Lalb_Chr12g0204011' => 'lal', 'Lalb_Chr13g0301671' => 'lal', 'Lalb_Chr14g0362851' => 'lal', 'Lalb_Chr24g0403581' => 'lal', 'Lj1g0000233' => 'lja', 'Lj2g0018120' => 'lja', 'Lj3C621T0' => 'lonja', 'Lj3P1059T14' => 'lonja', 'Lj3P611T9' => 'lonja', 'Lj3P614T13' => 'lonja', 'Lj3P615T5' => 'lonja', 'Lj4g0012315' => 'lja', 'Lj4g0026182' => 'lja', 'Lj6P813T16' => 'lonja', 'Lj7C427T7' => 'lonja', 'Lj7C427T8' => 'lonja', 'Lj7P600T41' => 'lonja', 'Lju41C42G17' => 'lonja', 'Lsat_1_v5_gn_0_47300' => 'lsa', 'Lsat_1_v5_gn_2_91280' => 'lsa', 'Lsat_1_v5_gn_3_30561' => 'lsa', 'Lsat_1_v5_gn_4_184321' => 'lsa', 'Lsat_1_v5_gn_4_4041' => 'lsa', 'Lsat_1_v5_gn_5_92000' => 'lsa', 'Lsat_1_v5_gn_8_152940' => 'lsa', 'Lsat_1_v5_gn_8_62401' => 'lsa', 'Manes.06G055900' => 'mes', 'Manes.12G022200' => 'mes', 'Manes.13G023300' => 'mes', 'Manes.14G115000' => 'mes', 'Manes.15G151700' => 'mes', 'Manes.17G111300' => 'mes', 'Mapoly0226s0009' => 'mpo', 'MBI02_g25363_MAGBIO' => 'mbi', 'MBI06_g00027_MAGBIO' => 'mbi', 'MBI10_g13034_MAGBIO' => 'mbi', 'MD09G1023400' => 'mdo', 'MD13G1100100' => 'mdo', 'MD15G1169200' => 'mdo', 'MD16G1101100' => 'mdo', 'MD17G1022900' => 'mdo', 'Medtr3g096150' => 'mtr', 'Medtr4g115070' => 'mtr', 'Medtr7g033325' => 'mtr', 'Medtr8g089840' => 'mtr', 'MELO3C010319.2' => 'cme', 'MELO3C011944.2' => 'cme', 'MELO3C021589.2' => 'cme', 'Migut.E00207' => 'egut', 'Migut.H00067' => 'egut', 'Migut.K00433' => 'egut', 'Migut.K00606' => 'egut', 'Migut.K01410' => 'egut', 'MSTRG.13347' => 'ama', 'MSTRG.24045' => 'ama', 'MSTRG.2428' => 'ama', 'MSTRG.26410' => 'ama', 'MSTRG.3139' => 'ama', 'MSTRG.3286' => 'ama', 'MSTRG.563' => 'ama', 'MSTRG.7941' => 'ama', 'Nitab4.5_0000028g0060' => 'nta', 'Nitab4.5_0000065g0260' => 'nta', 'Nitab4.5_0000112g0060' => 'nta', 'Nitab4.5_0000489g0120' => 'nta', 'Nitab4.5_0001776g0050' => 'nta', 'Nitab4.5_0001854g0010' => 'nta', 'Nitab4.5_0001860g0020' => 'nta', 'Nitab4.5_0004352g0010' => 'nta', 'Nitab4.5_0008716g0020' => 'nta', 'Nitab4.5_0008922g0010' => 'nta', 'Nn3g16693' => 'nnu', 'Nn4g22596' => 'nnu', 'Nn7g37639' => 'nnu', 'Oeu001701.1' => 'oeu', 'Oeu018149.1' => 'oeu', 'Oeu026220.1' => 'oeu', 'Oeu038635.1' => 'oeu', 'Oeu049176.1' => 'oeu', 'Oeu056706.1' => 'oeu', 'Oeu056937.1' => 'oeu', 'Oeu057540.1' => 'oeu', 'Os02g0594900' => 'osa', 'Os02g0595100' => 'osa', 'Os04g0477500' => 'osa', 'Os12g0611900' => 'osa', 'Peaxi162Scf00076g00020' => 'pax', 'Peaxi162Scf00128g00217' => 'pax', 'Peaxi162Scf00129g01640' => 'pax', 'Peaxi162Scf00669g00007' => 'pax', 'Peaxi162Scf00700g00421' => 'pax', 'Peaxi162Scf00801g00038' => 'pax', 'Peaxi162Scf00891g00025' => 'pax', 'PGR083G0909' => 'pgr', 'PGR119G1005' => 'pgr', 'PGR142G2236' => 'pgr', 'PGR142G3388' => 'pgr', 'PGSC0003DMG400004514' => 'stu', 'PGSC0003DMG400012635' => 'stu', 'PGSC0003DMG400015730' => 'stu', 'PGSC0003DMG400018611' => 'stu', 'PGSC0003DMG400030897' => 'stu', 'Phvul.001G254800' => 'pvu', 'Phvul.002G260100' => 'pvu', 'Phvul.003G167600' => 'pvu', 'Phvul.004G005100' => 'pvu', 'Potri.001G343600' => 'ptr', 'Potri.006G066700' => 'ptr', 'Potri.008G186000' => 'ptr', 'Potri.010G046900' => 'ptr', 'Potri.018G127900' => 'ptr', 'Pp3c20_17750' => 'ppa', 'Pp3c24_4380' => 'ppa', 'Prupe.1G245800' => 'ppe', 'Prupe.3G293400' => 'ppe', 'Prupe.7G247400' => 'ppe', 'Psat0s145g0120' => 'psa', 'Psat0s595g0040' => 'psa', 'Psat0s595g0120' => 'psa', 'Psat3g175040' => 'psa', 'Psat7g058120' => 'psa', 'PSO017G0428' => 'pso', 'PSO063G7510' => 'pso', 'PSO067G0046' => 'pso', 'PSO478G1073' => 'pso', 'PSO675G3677' => 'pso', 'PSO675G6558' => 'pso', 'PSO675G7520' => 'pso', 'PSO675G8959' => 'pso', 'QL02p074089' => 'qlo', 'QL02p089614' => 'qlo', 'QL03p057736' => 'qlo', 'RcHm_v2.0_Chr1g0364131' => 'rch', 'RcHm_v2.0_Chr2g0087801' => 'rch', 'RcHm_v2.0_Chr2g0087821' => 'rch', 'RcHm_v2.0_Chr2g0173231' => 'rch', 'RcHm_v2.0_Chr4g0433111' => 'rch', 'Rhsim03G0250300' => 'rsi', 'Rhsim08G0048400' => 'rsi', 'Rhsim10G0014800' => 'rsi', 'Rhsim12G0040100' => 'rsi', 'Rhsim12G0109700' => 'rsi', 'Sabra06G0049600' => 'sbr', 'Sabra08G0141000' => 'sbr', 'Sabra10G0021400' => 'sbr', 'Sabra16G0222900' => 'sbr', 'Sabra18G0108600' => 'sbr', 'SalBow1G0433' => 'sbo', 'SalBow1G2038' => 'sbo', 'SalBow1G5003' => 'sbo', 'SalBow7G1197' => 'sbo', 'SalBow8G3506' => 'sbo', 'Sc03g0007300' => 'sci', 'Sc11g0000950' => 'sci', 'Sc14g0008750' => 'sci', 'Sc18g0000420' => 'sci', 'Sed0006754' => 'sed', 'Sed0008741' => 'sed', 'Sed0017172' => 'sed', 'Sed0018925' => 'sed', 'Sed0023326' => 'sed', 'Sed0025909' => 'sed', 'SEGI_05333' => 'sgi', 'SEGI_10362' => 'sgi', 'SEGI_13380' => 'sgi', 'SEGI_24306' => 'sgi', 'SEGI_29077' => 'sgi', 'SEGI_29095' => 'sgi', 'SEGI_36534' => 'sgi', 'SEGI_37506' => 'sgi', 'SEGI_38321' => 'sgi', 'SGA_v2.0_scaffold307G48031' => 'sas', 'SGA_v2.0_scaffold47G17507' => 'sas', 'SGA_v2.0_scaffold63G21736' => 'sas', 'SGA_v2.0_scaffold87G27070' => 'sas', 'SHI17794' => 'shi', 'SHI28851' => 'shi', 'SMO165G0155' => 'smo', 'SMO340G0217' => 'smo', 'SMO367G1210' => 'smo', 'Solyc02g093430.3' => 'sly', 'Solyc05g013580.4' => 'sly', 'Solyc07g008030.3' => 'sly', 'Solyc12g035470.2' => 'sly', 'Sopen02g038020' => 'spe', 'Sopen05g008490' => 'spe', 'Sopen07g003910' => 'spe', 'Sopen12g015240' => 'spe', 'Sp1g11550' => 'spa', 'Sp2g16710' => 'spa', 'Sp3g00430' => 'spa', 'Sp3g26780' => 'spa', 'Sp5g22900' => 'spa', 'Sp6g29530' => 'spa', 'TAR371G0794' => 'tar', 'TAR374G0164' => 'tar', 'TAR622G0165' => 'tar', 'TAR626G0929' => 'tar', 'TAR629G2155' => 'tar', 'THA.LOC104805282' => 'tha', 'THA.LOC104805363' => 'tha', 'THA.LOC104808968' => 'tha', 'THA.LOC104821093' => 'tha', 'THA.LOC104823953' => 'tha', 'THA.LOC104825562' => 'tha', 'THA.LOC104825665' => 'tha', 'Thecc.02G261400' => 'tca', 'Thecc.04G019200' => 'tca', 'Thecc.09G130400' => 'tca', 'Thhalv10004374m.g' => 'esa', 'Thhalv10007850m.g' => 'esa', 'Thhalv10013782m.g' => 'esa', 'Thhalv10018686m.g' => 'esa', 'Thhalv10020899m.g' => 'esa', 'Thhalv10022755m.g' => 'esa', 'TPR.G23851' => 'tpr', 'TPR.G26500' => 'tpr', 'TPR.G27267' => 'tpr', 'TPR.G32001' => 'tpr', 'TPR.G6251' => 'tpr', 'TPR.G8167' => 'tpr', 'TWI12G1330' => 'twi', 'TWI18G1239' => 'twi', 'TWI34G0979' => 'twi', 'TWI36G0670' => 'twi', 'TWI36G0707' => 'twi', 'TWI56G0233' => 'twi', 'TWI75G1809' => 'twi', 'unitig_21.g20874' => 'ugi', 'unitig_26.g10343' => 'ugi', 'unitig_46.g18392' => 'ugi', 'unitig_52.g17178' => 'ugi', 'unitig_8.g2934' => 'ugi', 'vmacro01122' => 'vma', 'vmacro05875' => 'vma', 'vmacro06147' => 'vma', 'vmacro16191' => 'vma', 'vmacro18293' => 'vma', 'VMungo0251G3707' => 'vmu', 'VMungo0464G1521' => 'vmu', 'VMungo1215G0205' => 'vmu', 'VMungo1383G2484' => 'vmu', 'Zm00001eb079610' => 'zma', 'Zm00001eb135990' => 'zma', 'Zm00001eb183710' => 'zma', 'Zm00001eb246020' => 'zma' ) $gf_id = 'HOM05D001124' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001124' ) $data_identifier = 'HOM05D001124' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 6, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 7, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 21, 'bol' => (int) 10, 'bra' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 6, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 9, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 21, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 8, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 10, 'lsa' => (int) 8, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 8, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 9, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb246020' $species_info = array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ) $local_species = 'mes' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001124', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '548', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02520' => 'bna', 'A03p06630' => 'bna', 'A05p44460' => 'bna', 'A06p08710' => 'bna', 'A06p41090' => 'bna', 'A07p32320' => 'bna', 'A08p32520' => 'bna', 'A09p10360' => 'bna', 'A10p24080' => 'bna', 'Aa31LG11G15250' => 'aar', 'Aa31LG1G1800' => 'aar', 'Aa31LG2G5120' => 'aar', 'Aa31LG2G6070' => 'aar', 'Aa31LG5G10770' => 'aar', 'Aa31sc61G90' => 'aar', 'Actinidia01352' => 'ach', 'Actinidia05983' => 'ach', 'Actinidia08133' => 'ach', 'Actinidia15101' => 'ach', 'Actinidia26379' => 'ach', 'Actinidia35778' => 'ach', 'Actinidia36123' => 'ach', 'Actinidia37436' => 'ach', 'Actinidia38730' => 'ach', 'Ah.02g128210' => 'amhyb', 'Ah.03g132990' => 'amhyb', 'Ah.14g079410' => 'amhyb', 'AL1G24640' => 'aly', 'AL2G26680' => 'aly', 'AL3G10530' => 'aly', 'AL3G45230' => 'aly', 'AL5G15230' => 'aly', 'AL5G16960' => 'aly', 'AL6G25210' => 'aly', 'Aqoxy2G00441' => 'aox', 'Aqoxy3G01236' => 'aox', 'Aqoxy5G03746' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3RQ047' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C7GMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9C8JER' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MBL6KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YXCZ83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZANX40' => 'arhy', 'AT1G12990' => 'ath', 'AT1G67880' => 'ath', 'AT2G13290' => 'ath', 'AT3G01620' => 'ath', 'AT3G26445' => 'ath', 'AT3G27540' => 'ath', 'AT5G14480' => 'ath', 'ATR0824G026' => 'atr', 'ATR1098G019' => 'atr', 'Atru.chr11.2145' => 'acertr', 'Atru.chr2.3636' => 'acertr', 'Atru.chr2.3644' => 'acertr', 'Atru.chr6.2422' => 'acertr', 'Atru.chr7.1112' => 'acertr', 'AUR62005469' => 'cqu', 'AUR62011166' => 'cqu', 'AUR62013319' => 'cqu', 'AUR62024273' => 'cqu', 'AUR62028420' => 'cqu', 'AUR62041942' => 'cqu', 'BcaB01g04969' => 'bca', 'BcaB01g06371' => 'bca', 'BcaB02g11494' => 'bca', 'BcaB03g15382' => 'bca', 'BcaB08g36994' => 'bca', 'BcaC03g13477' => 'bca', 'BcaC03g13478' => 'bca', 'BcaC03g13480' => 'bca', 'BcaC03g13481' => 'bca', 'BcaC03g13486' => 'bca', 'BcaC04g19031' => 'bca', 'BcaC04g23085' => 'bca', 'BcaC05g25094' => 'bca', 'BcaC05g25096' => 'bca', 'BcaC05g25138' => 'bca', 'BcaC05g30416' => 'bca', 'BcaC05g30455' => 'bca', 'BcaC06g30979' => 'bca', 'BcaC06g33805' => 'bca', 'BcaC08g46021' => 'bca', 'BcaNung03154' => 'bca', 'BolC2t06623H' => 'bol', 'BolC2t06632H' => 'bol', 'BolC2t06635H' => 'bol', 'BolC2t06638H' => 'bol', 'BolC3t13266H' => 'bol', 'BolC5t29776H' => 'bol', 'BolC6t38912H' => 'bol', 'BolC7t44183H' => 'bol', 'BolC9t54123H' => 'bol', 'BolC9t59107H' => 'bol', 'BraA02t05221Z' => 'bra', 'BraA03t09996Z' => 'bra', 'BraA05t23210Z' => 'bra', 'BraA06t24068Z' => 'bra', 'BraA06t27032Z' => 'bra', 'BraA08t35176Z' => 'bra', 'BraA09t36680Z' => 'bra', 'BraA10t44471Z' => 'bra', 'C02p06760' => 'bna', 'C02p06890' => 'bna', 'C02p07010' => 'bna', 'C03p07660' => 'bna', 'C05p10300' => 'bna', 'C06p38150' => 'bna', 'C07p36650' => 'bna', 'C08p15770' => 'bna', 'C09p12300' => 'bna', 'C09p62700' => 'bna', 'C09p75040' => 'bna', 'CAN.G13.1' => 'can', 'CAN.G138.4' => 'can', 'CAN.G44.6' => 'can', 'CAN.G473.19' => 'can', 'CANSAT01G0835' => 'cansat', 'CANSAT11G0246' => 'cansat', 'CANSAT11G1766' => 'cansat', 'CANSAT64G1954' => 'cansat', 'CARHR013330' => 'chi', 'CARHR060530' => 'chi', 'CARHR075300' => 'chi', 'CARHR105120' => 'chi', 'CARHR148910' => 'chi', 'CARHR198830' => 'chi', 'Carub.0001s1275' => 'cru', 'Carub.0002s1437' => 'cru', 'Carub.0003s0044' => 'cru', 'Carub.0003s2787' => 'cru', 'Carub.0005s0597' => 'cru', 'Carub.0006s1266' => 'cru', 'Ca_06935_v3' => 'car', 'Ca_13559_v3' => 'car', 'Ca_16941_v3' => 'car', 'Ca_16960_v3' => 'car', 'Ca_17775_v3' => 'car', 'Ca_30464_v3' => 'car', 'Cc06_g08160' => 'ccan', 'Cc07_g01520' => 'ccan', 'Cc11_g15810' => 'ccan', 'CDE02G2840' => 'cde', 'CDE03G0093' => 'cde', 'CDE04G2127' => 'cde', 'CDE07G1857' => 'cde', 'CDE09G1246' => 'cde', 'Cfa003412' => 'cfa', 'Cfa007341' => 'cfa', 'Cfa009220' => 'cfa', 'Ciclev10008737m.g' => 'ccl', 'Ciclev10015565m.g' => 'ccl', 'Ciclev10031761m.g' => 'ccl', 'CiPaw.03G045300' => 'cil', 'CiPaw.03G247200' => 'cil', 'CiPaw.04G029500' => 'cil', 'CiPaw.04G174000' => 'cil', 'CiPaw.05G181200' => 'cil', 'CiPaw.06G067100' => 'cil', 'ClCG05G025800' => 'cla', 'ClCG06G011400' => 'cla', 'ClCG09G019360' => 'cla', 'COL.COLO4_04827' => 'col', 'COL.COLO4_29170' => 'col', 'COL.COLO4_35131' => 'col', 'COL.COLO4_35132' => 'col', 'Cpa.g.sc33.32' => 'cpa', 'Cpa.g.sc46.29' => 'cpa', 'Cpa.g.sc796.1' => 'cpa', 'CsaV3_1G030420' => 'csa', 'CsaV3_5G027050' => 'csa', 'CsaV3_5G031040' => 'csa', 'CsaV3_UNG023130' => 'csa', 'CSS0007726' => 'camsi', 'CSS0016433' => 'camsi', 'CSS0017656' => 'camsi', 'CSS0025364' => 'camsi', 'CSS0027582' => 'camsi', 'CSS0047288' => 'camsi', 'CSS0049950' => 'camsi', 'DCAR_003843' => 'dca', 'DCAR_007052' => 'dca', 'DCAR_020884' => 'dca', 'DCAR_021730' => 'dca', 'DCAR_024423' => 'dca', 'DCAR_026509' => 'dca', 'DCAR_031158' => 'dca', 'Dinv14728' => 'din', 'Dinv15219' => 'din', 'Dinv25728' => 'din', 'Dinv33428' => 'din', 'Dinv36489' => 'din', 'Dinv41486' => 'din', 'Duzib147G0469' => 'dzi', 'Duzib168G0060' => 'dzi', 'Duzib187G1215' => 'dzi', 'Duzib248G0692' => 'dzi', 'Duzib251G0767' => 'dzi', 'Duzib264G0446' => 'dzi', 'Duzib268G0691' => 'dzi', 'ECA232G4767' => 'eca', 'ECA233G2838' => 'eca', 'ECA234G0391' => 'eca', 'ECA234G0857' => 'eca', 'ECA236G1593' => 'eca', 'ECA238G0565' => 'eca', 'ECA246G1027' => 'eca', 'ECA246G3223' => 'eca', 'ECA246G3470' => 'eca', 'EL10Ac6g13829' => 'bvu', 'EL10Ac6g14093' => 'bvu', 'EL10Ac8g18707' => 'bvu', 'Eucgr.C01369' => 'egr', 'Eucgr.H02492' => 'egr', 'Eucgr.I01733' => 'egr', 'Eucgr.J02255' => 'egr', 'Eucgr.J02257' => 'egr', 'Eucgr.J02258' => 'egr', 'FAN02G1601' => 'fan', 'FAN03G1586' => 'fan', 'FAN03G2986' => 'fan', 'FAN05G4837' => 'fan', 'FAN06G0146' => 'fan', 'FAN07G0858' => 'fan', 'FAN09G3179' => 'fan', 'FAN10G0669' => 'fan', 'FAN12G2358' => 'fan', 'FAN14G4198' => 'fan', 'FAN14G5112' => 'fan', 'FAN17G0342' => 'fan', 'FAN19G0342' => 'fan', 'FAN19G0962' => 'fan', 'FAN19G1101' => 'fan', 'FAN19G1872' => 'fan', 'FAN22G0356' => 'fan', 'FAN23G0744' => 'fan', 'FAN23G1914' => 'fan', 'FAN26G0032' => 'fan', 'FAN28G0625' => 'fan', 'FvH4_1g02710' => 'fve', 'FvH4_1g02720' => 'fve', 'FvH4_4g25670' => 'fve', 'FvH4_6g51700' => 'fve', 'FvH4_7g20170' => 'fve', 'Glyma.05G175000' => 'gma', 'Glyma.08G132300' => 'gma', 'Glyma.11G243000' => 'gma', 'Glyma.13G158900' => 'gma', 'Glyma.17G112400' => 'gma', 'Glyma.18G014100' => 'gma', 'Glyma.19G003100' => 'gma', 'Glyma.19G056500' => 'gma', 'Gohir.A01G158900' => 'ghi', 'Gohir.A05G312600' => 'ghi', 'Gohir.A05G354900' => 'ghi', 'Gohir.A07G037200' => 'ghi', 'Gohir.A09G030000' => 'ghi', 'Gohir.A12G145200' => 'ghi', 'Gohir.D01G151500' => 'ghi', 'Gohir.D04G058300' => 'ghi', 'Gohir.D05G314100' => 'ghi', 'Gohir.D07G041400' => 'ghi', 'Gohir.D09G029700' => 'ghi', 'Gohir.D12G149700' => 'ghi', 'Gorai.001G043800' => 'gra', 'Gorai.002G187800' => 'gra', 'Gorai.006G034700' => 'gra', 'Gorai.008G161200' => 'gra', 'Gorai.009G335700' => 'gra', 'Gorai.012G065000' => 'gra', 'GSVIVG01000535001' => 'vvi', 'GSVIVG01015572001' => 'vvi', 'GSVIVG01032386001' => 'vvi', 'HanXRQChr05g0138531' => 'han', 'HanXRQChr06g0174391' => 'han', 'HanXRQChr07g0199021' => 'han', 'HanXRQChr08g0208211' => 'han', 'HanXRQChr09g0255471' => 'han', 'HanXRQChr10g0315791' => 'han', 'HanXRQChr12g0371991' => 'han', 'HanXRQChr15g0475251' => 'han', 'HanXRQChr17g0540001' => 'han', 'HanXRQChr17g0548631' => 'han', 'HanXRQChr17g0569561' => 'han', 'Haze_12256' => 'cav', 'Haze_14756' => 'cav', 'Haze_25528' => 'cav', 'Hma1.2p1_0079F.1_g041020' => 'hma', 'Hma1.2p1_0818F.1_g223260' => 'hma', 'Hma1.2p1_1747F.1_g300530' => 'hma', 'HPP92_004607' => 'vpl', 'HPP92_004608' => 'vpl', 'HPP92_006181' => 'vpl', 'HPP92_012192' => 'vpl', 'HPP92_015680' => 'vpl', 'HPP92_020249' => 'vpl', 'HPP92_021376' => 'vpl', 'HPP92_024275' => 'vpl', 'Hund06031' => 'sun', 'Hund25391' => 'sun', 'Lalb_Chr07g0185371' => 'lal', 'Lalb_Chr07g0185381' => 'lal', 'Lalb_Chr12g0204011' => 'lal', 'Lalb_Chr13g0301671' => 'lal', 'Lalb_Chr14g0362851' => 'lal', 'Lalb_Chr24g0403581' => 'lal', 'Lj1g0000233' => 'lja', 'Lj2g0018120' => 'lja', 'Lj3C621T0' => 'lonja', 'Lj3P1059T14' => 'lonja', 'Lj3P611T9' => 'lonja', 'Lj3P614T13' => 'lonja', 'Lj3P615T5' => 'lonja', 'Lj4g0012315' => 'lja', 'Lj4g0026182' => 'lja', 'Lj6P813T16' => 'lonja', 'Lj7C427T7' => 'lonja', 'Lj7C427T8' => 'lonja', 'Lj7P600T41' => 'lonja', 'Lju41C42G17' => 'lonja', 'Lsat_1_v5_gn_0_47300' => 'lsa', 'Lsat_1_v5_gn_2_91280' => 'lsa', 'Lsat_1_v5_gn_3_30561' => 'lsa', 'Lsat_1_v5_gn_4_184321' => 'lsa', 'Lsat_1_v5_gn_4_4041' => 'lsa', 'Lsat_1_v5_gn_5_92000' => 'lsa', 'Lsat_1_v5_gn_8_152940' => 'lsa', 'Lsat_1_v5_gn_8_62401' => 'lsa', 'Manes.06G055900' => 'mes', 'Manes.12G022200' => 'mes', 'Manes.13G023300' => 'mes', 'Manes.14G115000' => 'mes', 'Manes.15G151700' => 'mes', 'Manes.17G111300' => 'mes', 'Mapoly0226s0009' => 'mpo', 'MBI02_g25363_MAGBIO' => 'mbi', 'MBI06_g00027_MAGBIO' => 'mbi', 'MBI10_g13034_MAGBIO' => 'mbi', 'MD09G1023400' => 'mdo', 'MD13G1100100' => 'mdo', 'MD15G1169200' => 'mdo', 'MD16G1101100' => 'mdo', 'MD17G1022900' => 'mdo', 'Medtr3g096150' => 'mtr', 'Medtr4g115070' => 'mtr', 'Medtr7g033325' => 'mtr', 'Medtr8g089840' => 'mtr', 'MELO3C010319.2' => 'cme', 'MELO3C011944.2' => 'cme', 'MELO3C021589.2' => 'cme', 'Migut.E00207' => 'egut', 'Migut.H00067' => 'egut', 'Migut.K00433' => 'egut', 'Migut.K00606' => 'egut', 'Migut.K01410' => 'egut', 'MSTRG.13347' => 'ama', 'MSTRG.24045' => 'ama', 'MSTRG.2428' => 'ama', 'MSTRG.26410' => 'ama', 'MSTRG.3139' => 'ama', 'MSTRG.3286' => 'ama', 'MSTRG.563' => 'ama', 'MSTRG.7941' => 'ama', 'Nitab4.5_0000028g0060' => 'nta', 'Nitab4.5_0000065g0260' => 'nta', 'Nitab4.5_0000112g0060' => 'nta', 'Nitab4.5_0000489g0120' => 'nta', 'Nitab4.5_0001776g0050' => 'nta', 'Nitab4.5_0001854g0010' => 'nta', 'Nitab4.5_0001860g0020' => 'nta', 'Nitab4.5_0004352g0010' => 'nta', 'Nitab4.5_0008716g0020' => 'nta', 'Nitab4.5_0008922g0010' => 'nta', 'Nn3g16693' => 'nnu', 'Nn4g22596' => 'nnu', 'Nn7g37639' => 'nnu', 'Oeu001701.1' => 'oeu', 'Oeu018149.1' => 'oeu', 'Oeu026220.1' => 'oeu', 'Oeu038635.1' => 'oeu', 'Oeu049176.1' => 'oeu', 'Oeu056706.1' => 'oeu', 'Oeu056937.1' => 'oeu', 'Oeu057540.1' => 'oeu', 'Os02g0594900' => 'osa', 'Os02g0595100' => 'osa', 'Os04g0477500' => 'osa', 'Os12g0611900' => 'osa', 'Peaxi162Scf00076g00020' => 'pax', 'Peaxi162Scf00128g00217' => 'pax', 'Peaxi162Scf00129g01640' => 'pax', 'Peaxi162Scf00669g00007' => 'pax', 'Peaxi162Scf00700g00421' => 'pax', 'Peaxi162Scf00801g00038' => 'pax', 'Peaxi162Scf00891g00025' => 'pax', 'PGR083G0909' => 'pgr', 'PGR119G1005' => 'pgr', 'PGR142G2236' => 'pgr', 'PGR142G3388' => 'pgr', 'PGSC0003DMG400004514' => 'stu', 'PGSC0003DMG400012635' => 'stu', 'PGSC0003DMG400015730' => 'stu', 'PGSC0003DMG400018611' => 'stu', 'PGSC0003DMG400030897' => 'stu', 'Phvul.001G254800' => 'pvu', 'Phvul.002G260100' => 'pvu', 'Phvul.003G167600' => 'pvu', 'Phvul.004G005100' => 'pvu', 'Potri.001G343600' => 'ptr', 'Potri.006G066700' => 'ptr', 'Potri.008G186000' => 'ptr', 'Potri.010G046900' => 'ptr', 'Potri.018G127900' => 'ptr', 'Pp3c20_17750' => 'ppa', 'Pp3c24_4380' => 'ppa', 'Prupe.1G245800' => 'ppe', 'Prupe.3G293400' => 'ppe', 'Prupe.7G247400' => 'ppe', 'Psat0s145g0120' => 'psa', 'Psat0s595g0040' => 'psa', 'Psat0s595g0120' => 'psa', 'Psat3g175040' => 'psa', 'Psat7g058120' => 'psa', 'PSO017G0428' => 'pso', 'PSO063G7510' => 'pso', 'PSO067G0046' => 'pso', 'PSO478G1073' => 'pso', 'PSO675G3677' => 'pso', 'PSO675G6558' => 'pso', 'PSO675G7520' => 'pso', 'PSO675G8959' => 'pso', 'QL02p074089' => 'qlo', 'QL02p089614' => 'qlo', 'QL03p057736' => 'qlo', 'RcHm_v2.0_Chr1g0364131' => 'rch', 'RcHm_v2.0_Chr2g0087801' => 'rch', 'RcHm_v2.0_Chr2g0087821' => 'rch', 'RcHm_v2.0_Chr2g0173231' => 'rch', 'RcHm_v2.0_Chr4g0433111' => 'rch', 'Rhsim03G0250300' => 'rsi', 'Rhsim08G0048400' => 'rsi', 'Rhsim10G0014800' => 'rsi', 'Rhsim12G0040100' => 'rsi', 'Rhsim12G0109700' => 'rsi', 'Sabra06G0049600' => 'sbr', 'Sabra08G0141000' => 'sbr', 'Sabra10G0021400' => 'sbr', 'Sabra16G0222900' => 'sbr', 'Sabra18G0108600' => 'sbr', 'SalBow1G0433' => 'sbo', 'SalBow1G2038' => 'sbo', 'SalBow1G5003' => 'sbo', 'SalBow7G1197' => 'sbo', 'SalBow8G3506' => 'sbo', 'Sc03g0007300' => 'sci', 'Sc11g0000950' => 'sci', 'Sc14g0008750' => 'sci', 'Sc18g0000420' => 'sci', 'Sed0006754' => 'sed', 'Sed0008741' => 'sed', 'Sed0017172' => 'sed', 'Sed0018925' => 'sed', 'Sed0023326' => 'sed', 'Sed0025909' => 'sed', 'SEGI_05333' => 'sgi', 'SEGI_10362' => 'sgi', 'SEGI_13380' => 'sgi', 'SEGI_24306' => 'sgi', 'SEGI_29077' => 'sgi', 'SEGI_29095' => 'sgi', 'SEGI_36534' => 'sgi', 'SEGI_37506' => 'sgi', 'SEGI_38321' => 'sgi', 'SGA_v2.0_scaffold307G48031' => 'sas', 'SGA_v2.0_scaffold47G17507' => 'sas', 'SGA_v2.0_scaffold63G21736' => 'sas', 'SGA_v2.0_scaffold87G27070' => 'sas', 'SHI17794' => 'shi', 'SHI28851' => 'shi', 'SMO165G0155' => 'smo', 'SMO340G0217' => 'smo', 'SMO367G1210' => 'smo', 'Solyc02g093430.3' => 'sly', 'Solyc05g013580.4' => 'sly', 'Solyc07g008030.3' => 'sly', 'Solyc12g035470.2' => 'sly', 'Sopen02g038020' => 'spe', 'Sopen05g008490' => 'spe', 'Sopen07g003910' => 'spe', 'Sopen12g015240' => 'spe', 'Sp1g11550' => 'spa', 'Sp2g16710' => 'spa', 'Sp3g00430' => 'spa', 'Sp3g26780' => 'spa', 'Sp5g22900' => 'spa', 'Sp6g29530' => 'spa', 'TAR371G0794' => 'tar', 'TAR374G0164' => 'tar', 'TAR622G0165' => 'tar', 'TAR626G0929' => 'tar', 'TAR629G2155' => 'tar', 'THA.LOC104805282' => 'tha', 'THA.LOC104805363' => 'tha', 'THA.LOC104808968' => 'tha', 'THA.LOC104821093' => 'tha', 'THA.LOC104823953' => 'tha', 'THA.LOC104825562' => 'tha', 'THA.LOC104825665' => 'tha', 'Thecc.02G261400' => 'tca', 'Thecc.04G019200' => 'tca', 'Thecc.09G130400' => 'tca', 'Thhalv10004374m.g' => 'esa', 'Thhalv10007850m.g' => 'esa', 'Thhalv10013782m.g' => 'esa', 'Thhalv10018686m.g' => 'esa', 'Thhalv10020899m.g' => 'esa', 'Thhalv10022755m.g' => 'esa', 'TPR.G23851' => 'tpr', 'TPR.G26500' => 'tpr', 'TPR.G27267' => 'tpr', 'TPR.G32001' => 'tpr', 'TPR.G6251' => 'tpr', 'TPR.G8167' => 'tpr', 'TWI12G1330' => 'twi', 'TWI18G1239' => 'twi', 'TWI34G0979' => 'twi', 'TWI36G0670' => 'twi', 'TWI36G0707' => 'twi', 'TWI56G0233' => 'twi', 'TWI75G1809' => 'twi', 'unitig_21.g20874' => 'ugi', 'unitig_26.g10343' => 'ugi', 'unitig_46.g18392' => 'ugi', 'unitig_52.g17178' => 'ugi', 'unitig_8.g2934' => 'ugi', 'vmacro01122' => 'vma', 'vmacro05875' => 'vma', 'vmacro06147' => 'vma', 'vmacro16191' => 'vma', 'vmacro18293' => 'vma', 'VMungo0251G3707' => 'vmu', 'VMungo0464G1521' => 'vmu', 'VMungo1215G0205' => 'vmu', 'VMungo1383G2484' => 'vmu', 'Zm00001eb079610' => 'zma', 'Zm00001eb135990' => 'zma', 'Zm00001eb183710' => 'zma', 'Zm00001eb246020' => 'zma' ), 'gf_id' => 'HOM05D001124', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001124' ), 'data_identifier' => 'HOM05D001124', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001124', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '548', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02520' => 'bna', 'A03p06630' => 'bna', 'A05p44460' => 'bna', 'A06p08710' => 'bna', 'A06p41090' => 'bna', 'A07p32320' => 'bna', 'A08p32520' => 'bna', 'A09p10360' => 'bna', 'A10p24080' => 'bna', 'Aa31LG11G15250' => 'aar', 'Aa31LG1G1800' => 'aar', 'Aa31LG2G5120' => 'aar', 'Aa31LG2G6070' => 'aar', 'Aa31LG5G10770' => 'aar', 'Aa31sc61G90' => 'aar', 'Actinidia01352' => 'ach', 'Actinidia05983' => 'ach', 'Actinidia08133' => 'ach', 'Actinidia15101' => 'ach', 'Actinidia26379' => 'ach', 'Actinidia35778' => 'ach', 'Actinidia36123' => 'ach', 'Actinidia37436' => 'ach', 'Actinidia38730' => 'ach', 'Ah.02g128210' => 'amhyb', 'Ah.03g132990' => 'amhyb', 'Ah.14g079410' => 'amhyb', 'AL1G24640' => 'aly', 'AL2G26680' => 'aly', 'AL3G10530' => 'aly', 'AL3G45230' => 'aly', 'AL5G15230' => 'aly', 'AL5G16960' => 'aly', 'AL6G25210' => 'aly', 'Aqoxy2G00441' => 'aox', 'Aqoxy3G01236' => 'aox', 'Aqoxy5G03746' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3RQ047' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C7GMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9C8JER' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MBL6KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YXCZ83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZANX40' => 'arhy', 'AT1G12990' => 'ath', 'AT1G67880' => 'ath', 'AT2G13290' => 'ath', 'AT3G01620' => 'ath', 'AT3G26445' => 'ath', 'AT3G27540' => 'ath', 'AT5G14480' => 'ath', 'ATR0824G026' => 'atr', 'ATR1098G019' => 'atr', 'Atru.chr11.2145' => 'acertr', 'Atru.chr2.3636' => 'acertr', 'Atru.chr2.3644' => 'acertr', 'Atru.chr6.2422' => 'acertr', 'Atru.chr7.1112' => 'acertr', 'AUR62005469' => 'cqu', 'AUR62011166' => 'cqu', 'AUR62013319' => 'cqu', 'AUR62024273' => 'cqu', 'AUR62028420' => 'cqu', 'AUR62041942' => 'cqu', 'BcaB01g04969' => 'bca', 'BcaB01g06371' => 'bca', 'BcaB02g11494' => 'bca', 'BcaB03g15382' => 'bca', 'BcaB08g36994' => 'bca', 'BcaC03g13477' => 'bca', 'BcaC03g13478' => 'bca', 'BcaC03g13480' => 'bca', 'BcaC03g13481' => 'bca', 'BcaC03g13486' => 'bca', 'BcaC04g19031' => 'bca', 'BcaC04g23085' => 'bca', 'BcaC05g25094' => 'bca', 'BcaC05g25096' => 'bca', 'BcaC05g25138' => 'bca', 'BcaC05g30416' => 'bca', 'BcaC05g30455' => 'bca', 'BcaC06g30979' => 'bca', 'BcaC06g33805' => 'bca', 'BcaC08g46021' => 'bca', 'BcaNung03154' => 'bca', 'BolC2t06623H' => 'bol', 'BolC2t06632H' => 'bol', 'BolC2t06635H' => 'bol', 'BolC2t06638H' => 'bol', 'BolC3t13266H' => 'bol', 'BolC5t29776H' => 'bol', 'BolC6t38912H' => 'bol', 'BolC7t44183H' => 'bol', 'BolC9t54123H' => 'bol', 'BolC9t59107H' => 'bol', 'BraA02t05221Z' => 'bra', 'BraA03t09996Z' => 'bra', 'BraA05t23210Z' => 'bra', 'BraA06t24068Z' => 'bra', 'BraA06t27032Z' => 'bra', 'BraA08t35176Z' => 'bra', 'BraA09t36680Z' => 'bra', 'BraA10t44471Z' => 'bra', 'C02p06760' => 'bna', 'C02p06890' => 'bna', 'C02p07010' => 'bna', 'C03p07660' => 'bna', 'C05p10300' => 'bna', 'C06p38150' => 'bna', 'C07p36650' => 'bna', 'C08p15770' => 'bna', 'C09p12300' => 'bna', 'C09p62700' => 'bna', 'C09p75040' => 'bna', 'CAN.G13.1' => 'can', 'CAN.G138.4' => 'can', 'CAN.G44.6' => 'can', 'CAN.G473.19' => 'can', 'CANSAT01G0835' => 'cansat', 'CANSAT11G0246' => 'cansat', 'CANSAT11G1766' => 'cansat', 'CANSAT64G1954' => 'cansat', 'CARHR013330' => 'chi', 'CARHR060530' => 'chi', 'CARHR075300' => 'chi', 'CARHR105120' => 'chi', 'CARHR148910' => 'chi', 'CARHR198830' => 'chi', 'Carub.0001s1275' => 'cru', 'Carub.0002s1437' => 'cru', 'Carub.0003s0044' => 'cru', 'Carub.0003s2787' => 'cru', 'Carub.0005s0597' => 'cru', 'Carub.0006s1266' => 'cru', 'Ca_06935_v3' => 'car', 'Ca_13559_v3' => 'car', 'Ca_16941_v3' => 'car', 'Ca_16960_v3' => 'car', 'Ca_17775_v3' => 'car', 'Ca_30464_v3' => 'car', 'Cc06_g08160' => 'ccan', 'Cc07_g01520' => 'ccan', 'Cc11_g15810' => 'ccan', 'CDE02G2840' => 'cde', 'CDE03G0093' => 'cde', 'CDE04G2127' => 'cde', 'CDE07G1857' => 'cde', 'CDE09G1246' => 'cde', 'Cfa003412' => 'cfa', 'Cfa007341' => 'cfa', 'Cfa009220' => 'cfa', 'Ciclev10008737m.g' => 'ccl', 'Ciclev10015565m.g' => 'ccl', 'Ciclev10031761m.g' => 'ccl', 'CiPaw.03G045300' => 'cil', 'CiPaw.03G247200' => 'cil', 'CiPaw.04G029500' => 'cil', 'CiPaw.04G174000' => 'cil', 'CiPaw.05G181200' => 'cil', 'CiPaw.06G067100' => 'cil', 'ClCG05G025800' => 'cla', 'ClCG06G011400' => 'cla', 'ClCG09G019360' => 'cla', 'COL.COLO4_04827' => 'col', 'COL.COLO4_29170' => 'col', 'COL.COLO4_35131' => 'col', 'COL.COLO4_35132' => 'col', 'Cpa.g.sc33.32' => 'cpa', 'Cpa.g.sc46.29' => 'cpa', 'Cpa.g.sc796.1' => 'cpa', 'CsaV3_1G030420' => 'csa', 'CsaV3_5G027050' => 'csa', 'CsaV3_5G031040' => 'csa', 'CsaV3_UNG023130' => 'csa', 'CSS0007726' => 'camsi', 'CSS0016433' => 'camsi', 'CSS0017656' => 'camsi', 'CSS0025364' => 'camsi', 'CSS0027582' => 'camsi', 'CSS0047288' => 'camsi', 'CSS0049950' => 'camsi', 'DCAR_003843' => 'dca', 'DCAR_007052' => 'dca', 'DCAR_020884' => 'dca', 'DCAR_021730' => 'dca', 'DCAR_024423' => 'dca', 'DCAR_026509' => 'dca', 'DCAR_031158' => 'dca', 'Dinv14728' => 'din', 'Dinv15219' => 'din', 'Dinv25728' => 'din', 'Dinv33428' => 'din', 'Dinv36489' => 'din', 'Dinv41486' => 'din', 'Duzib147G0469' => 'dzi', 'Duzib168G0060' => 'dzi', 'Duzib187G1215' => 'dzi', 'Duzib248G0692' => 'dzi', 'Duzib251G0767' => 'dzi', 'Duzib264G0446' => 'dzi', 'Duzib268G0691' => 'dzi', 'ECA232G4767' => 'eca', 'ECA233G2838' => 'eca', 'ECA234G0391' => 'eca', 'ECA234G0857' => 'eca', 'ECA236G1593' => 'eca', 'ECA238G0565' => 'eca', 'ECA246G1027' => 'eca', 'ECA246G3223' => 'eca', 'ECA246G3470' => 'eca', 'EL10Ac6g13829' => 'bvu', 'EL10Ac6g14093' => 'bvu', 'EL10Ac8g18707' => 'bvu', 'Eucgr.C01369' => 'egr', 'Eucgr.H02492' => 'egr', 'Eucgr.I01733' => 'egr', 'Eucgr.J02255' => 'egr', 'Eucgr.J02257' => 'egr', 'Eucgr.J02258' => 'egr', 'FAN02G1601' => 'fan', 'FAN03G1586' => 'fan', 'FAN03G2986' => 'fan', 'FAN05G4837' => 'fan', 'FAN06G0146' => 'fan', 'FAN07G0858' => 'fan', 'FAN09G3179' => 'fan', 'FAN10G0669' => 'fan', 'FAN12G2358' => 'fan', 'FAN14G4198' => 'fan', 'FAN14G5112' => 'fan', 'FAN17G0342' => 'fan', 'FAN19G0342' => 'fan', 'FAN19G0962' => 'fan', 'FAN19G1101' => 'fan', 'FAN19G1872' => 'fan', 'FAN22G0356' => 'fan', 'FAN23G0744' => 'fan', 'FAN23G1914' => 'fan', 'FAN26G0032' => 'fan', 'FAN28G0625' => 'fan', 'FvH4_1g02710' => 'fve', 'FvH4_1g02720' => 'fve', 'FvH4_4g25670' => 'fve', 'FvH4_6g51700' => 'fve', 'FvH4_7g20170' => 'fve', 'Glyma.05G175000' => 'gma', 'Glyma.08G132300' => 'gma', 'Glyma.11G243000' => 'gma', 'Glyma.13G158900' => 'gma', 'Glyma.17G112400' => 'gma', 'Glyma.18G014100' => 'gma', 'Glyma.19G003100' => 'gma', 'Glyma.19G056500' => 'gma', 'Gohir.A01G158900' => 'ghi', 'Gohir.A05G312600' => 'ghi', 'Gohir.A05G354900' => 'ghi', 'Gohir.A07G037200' => 'ghi', 'Gohir.A09G030000' => 'ghi', 'Gohir.A12G145200' => 'ghi', 'Gohir.D01G151500' => 'ghi', 'Gohir.D04G058300' => 'ghi', 'Gohir.D05G314100' => 'ghi', 'Gohir.D07G041400' => 'ghi', 'Gohir.D09G029700' => 'ghi', 'Gohir.D12G149700' => 'ghi', 'Gorai.001G043800' => 'gra', 'Gorai.002G187800' => 'gra', 'Gorai.006G034700' => 'gra', 'Gorai.008G161200' => 'gra', 'Gorai.009G335700' => 'gra', 'Gorai.012G065000' => 'gra', 'GSVIVG01000535001' => 'vvi', 'GSVIVG01015572001' => 'vvi', 'GSVIVG01032386001' => 'vvi', 'HanXRQChr05g0138531' => 'han', 'HanXRQChr06g0174391' => 'han', 'HanXRQChr07g0199021' => 'han', 'HanXRQChr08g0208211' => 'han', 'HanXRQChr09g0255471' => 'han', 'HanXRQChr10g0315791' => 'han', 'HanXRQChr12g0371991' => 'han', 'HanXRQChr15g0475251' => 'han', 'HanXRQChr17g0540001' => 'han', 'HanXRQChr17g0548631' => 'han', 'HanXRQChr17g0569561' => 'han', 'Haze_12256' => 'cav', 'Haze_14756' => 'cav', 'Haze_25528' => 'cav', 'Hma1.2p1_0079F.1_g041020' => 'hma', 'Hma1.2p1_0818F.1_g223260' => 'hma', 'Hma1.2p1_1747F.1_g300530' => 'hma', 'HPP92_004607' => 'vpl', 'HPP92_004608' => 'vpl', 'HPP92_006181' => 'vpl', 'HPP92_012192' => 'vpl', 'HPP92_015680' => 'vpl', 'HPP92_020249' => 'vpl', 'HPP92_021376' => 'vpl', 'HPP92_024275' => 'vpl', 'Hund06031' => 'sun', 'Hund25391' => 'sun', 'Lalb_Chr07g0185371' => 'lal', 'Lalb_Chr07g0185381' => 'lal', 'Lalb_Chr12g0204011' => 'lal', 'Lalb_Chr13g0301671' => 'lal', 'Lalb_Chr14g0362851' => 'lal', 'Lalb_Chr24g0403581' => 'lal', 'Lj1g0000233' => 'lja', 'Lj2g0018120' => 'lja', 'Lj3C621T0' => 'lonja', 'Lj3P1059T14' => 'lonja', 'Lj3P611T9' => 'lonja', 'Lj3P614T13' => 'lonja', 'Lj3P615T5' => 'lonja', 'Lj4g0012315' => 'lja', 'Lj4g0026182' => 'lja', 'Lj6P813T16' => 'lonja', 'Lj7C427T7' => 'lonja', 'Lj7C427T8' => 'lonja', 'Lj7P600T41' => 'lonja', 'Lju41C42G17' => 'lonja', 'Lsat_1_v5_gn_0_47300' => 'lsa', 'Lsat_1_v5_gn_2_91280' => 'lsa', 'Lsat_1_v5_gn_3_30561' => 'lsa', 'Lsat_1_v5_gn_4_184321' => 'lsa', 'Lsat_1_v5_gn_4_4041' => 'lsa', 'Lsat_1_v5_gn_5_92000' => 'lsa', 'Lsat_1_v5_gn_8_152940' => 'lsa', 'Lsat_1_v5_gn_8_62401' => 'lsa', 'Manes.06G055900' => 'mes', 'Manes.12G022200' => 'mes', 'Manes.13G023300' => 'mes', 'Manes.14G115000' => 'mes', 'Manes.15G151700' => 'mes', 'Manes.17G111300' => 'mes', 'Mapoly0226s0009' => 'mpo', 'MBI02_g25363_MAGBIO' => 'mbi', 'MBI06_g00027_MAGBIO' => 'mbi', 'MBI10_g13034_MAGBIO' => 'mbi', 'MD09G1023400' => 'mdo', 'MD13G1100100' => 'mdo', 'MD15G1169200' => 'mdo', 'MD16G1101100' => 'mdo', 'MD17G1022900' => 'mdo', 'Medtr3g096150' => 'mtr', 'Medtr4g115070' => 'mtr', 'Medtr7g033325' => 'mtr', 'Medtr8g089840' => 'mtr', 'MELO3C010319.2' => 'cme', 'MELO3C011944.2' => 'cme', 'MELO3C021589.2' => 'cme', 'Migut.E00207' => 'egut', 'Migut.H00067' => 'egut', 'Migut.K00433' => 'egut', 'Migut.K00606' => 'egut', 'Migut.K01410' => 'egut', 'MSTRG.13347' => 'ama', 'MSTRG.24045' => 'ama', 'MSTRG.2428' => 'ama', 'MSTRG.26410' => 'ama', 'MSTRG.3139' => 'ama', 'MSTRG.3286' => 'ama', 'MSTRG.563' => 'ama', 'MSTRG.7941' => 'ama', 'Nitab4.5_0000028g0060' => 'nta', 'Nitab4.5_0000065g0260' => 'nta', 'Nitab4.5_0000112g0060' => 'nta', 'Nitab4.5_0000489g0120' => 'nta', 'Nitab4.5_0001776g0050' => 'nta', 'Nitab4.5_0001854g0010' => 'nta', 'Nitab4.5_0001860g0020' => 'nta', 'Nitab4.5_0004352g0010' => 'nta', 'Nitab4.5_0008716g0020' => 'nta', 'Nitab4.5_0008922g0010' => 'nta', 'Nn3g16693' => 'nnu', 'Nn4g22596' => 'nnu', 'Nn7g37639' => 'nnu', 'Oeu001701.1' => 'oeu', 'Oeu018149.1' => 'oeu', 'Oeu026220.1' => 'oeu', 'Oeu038635.1' => 'oeu', 'Oeu049176.1' => 'oeu', 'Oeu056706.1' => 'oeu', 'Oeu056937.1' => 'oeu', 'Oeu057540.1' => 'oeu', 'Os02g0594900' => 'osa', 'Os02g0595100' => 'osa', 'Os04g0477500' => 'osa', 'Os12g0611900' => 'osa', 'Peaxi162Scf00076g00020' => 'pax', 'Peaxi162Scf00128g00217' => 'pax', 'Peaxi162Scf00129g01640' => 'pax', 'Peaxi162Scf00669g00007' => 'pax', 'Peaxi162Scf00700g00421' => 'pax', 'Peaxi162Scf00801g00038' => 'pax', 'Peaxi162Scf00891g00025' => 'pax', 'PGR083G0909' => 'pgr', 'PGR119G1005' => 'pgr', 'PGR142G2236' => 'pgr', 'PGR142G3388' => 'pgr', 'PGSC0003DMG400004514' => 'stu', 'PGSC0003DMG400012635' => 'stu', 'PGSC0003DMG400015730' => 'stu', 'PGSC0003DMG400018611' => 'stu', 'PGSC0003DMG400030897' => 'stu', 'Phvul.001G254800' => 'pvu', 'Phvul.002G260100' => 'pvu', 'Phvul.003G167600' => 'pvu', 'Phvul.004G005100' => 'pvu', 'Potri.001G343600' => 'ptr', 'Potri.006G066700' => 'ptr', 'Potri.008G186000' => 'ptr', 'Potri.010G046900' => 'ptr', 'Potri.018G127900' => 'ptr', 'Pp3c20_17750' => 'ppa', 'Pp3c24_4380' => 'ppa', 'Prupe.1G245800' => 'ppe', 'Prupe.3G293400' => 'ppe', 'Prupe.7G247400' => 'ppe', 'Psat0s145g0120' => 'psa', 'Psat0s595g0040' => 'psa', 'Psat0s595g0120' => 'psa', 'Psat3g175040' => 'psa', 'Psat7g058120' => 'psa', 'PSO017G0428' => 'pso', 'PSO063G7510' => 'pso', 'PSO067G0046' => 'pso', 'PSO478G1073' => 'pso', 'PSO675G3677' => 'pso', 'PSO675G6558' => 'pso', 'PSO675G7520' => 'pso', 'PSO675G8959' => 'pso', 'QL02p074089' => 'qlo', 'QL02p089614' => 'qlo', 'QL03p057736' => 'qlo', 'RcHm_v2.0_Chr1g0364131' => 'rch', 'RcHm_v2.0_Chr2g0087801' => 'rch', 'RcHm_v2.0_Chr2g0087821' => 'rch', 'RcHm_v2.0_Chr2g0173231' => 'rch', 'RcHm_v2.0_Chr4g0433111' => 'rch', 'Rhsim03G0250300' => 'rsi', 'Rhsim08G0048400' => 'rsi', 'Rhsim10G0014800' => 'rsi', 'Rhsim12G0040100' => 'rsi', 'Rhsim12G0109700' => 'rsi', 'Sabra06G0049600' => 'sbr', 'Sabra08G0141000' => 'sbr', 'Sabra10G0021400' => 'sbr', 'Sabra16G0222900' => 'sbr', 'Sabra18G0108600' => 'sbr', 'SalBow1G0433' => 'sbo', 'SalBow1G2038' => 'sbo', 'SalBow1G5003' => 'sbo', 'SalBow7G1197' => 'sbo', 'SalBow8G3506' => 'sbo', 'Sc03g0007300' => 'sci', 'Sc11g0000950' => 'sci', 'Sc14g0008750' => 'sci', 'Sc18g0000420' => 'sci', 'Sed0006754' => 'sed', 'Sed0008741' => 'sed', 'Sed0017172' => 'sed', 'Sed0018925' => 'sed', 'Sed0023326' => 'sed', 'Sed0025909' => 'sed', 'SEGI_05333' => 'sgi', 'SEGI_10362' => 'sgi', 'SEGI_13380' => 'sgi', 'SEGI_24306' => 'sgi', 'SEGI_29077' => 'sgi', 'SEGI_29095' => 'sgi', 'SEGI_36534' => 'sgi', 'SEGI_37506' => 'sgi', 'SEGI_38321' => 'sgi', 'SGA_v2.0_scaffold307G48031' => 'sas', 'SGA_v2.0_scaffold47G17507' => 'sas', 'SGA_v2.0_scaffold63G21736' => 'sas', 'SGA_v2.0_scaffold87G27070' => 'sas', 'SHI17794' => 'shi', 'SHI28851' => 'shi', 'SMO165G0155' => 'smo', 'SMO340G0217' => 'smo', 'SMO367G1210' => 'smo', 'Solyc02g093430.3' => 'sly', 'Solyc05g013580.4' => 'sly', 'Solyc07g008030.3' => 'sly', 'Solyc12g035470.2' => 'sly', 'Sopen02g038020' => 'spe', 'Sopen05g008490' => 'spe', 'Sopen07g003910' => 'spe', 'Sopen12g015240' => 'spe', 'Sp1g11550' => 'spa', 'Sp2g16710' => 'spa', 'Sp3g00430' => 'spa', 'Sp3g26780' => 'spa', 'Sp5g22900' => 'spa', 'Sp6g29530' => 'spa', 'TAR371G0794' => 'tar', 'TAR374G0164' => 'tar', 'TAR622G0165' => 'tar', 'TAR626G0929' => 'tar', 'TAR629G2155' => 'tar', 'THA.LOC104805282' => 'tha', 'THA.LOC104805363' => 'tha', 'THA.LOC104808968' => 'tha', 'THA.LOC104821093' => 'tha', 'THA.LOC104823953' => 'tha', 'THA.LOC104825562' => 'tha', 'THA.LOC104825665' => 'tha', 'Thecc.02G261400' => 'tca', 'Thecc.04G019200' => 'tca', 'Thecc.09G130400' => 'tca', 'Thhalv10004374m.g' => 'esa', 'Thhalv10007850m.g' => 'esa', 'Thhalv10013782m.g' => 'esa', 'Thhalv10018686m.g' => 'esa', 'Thhalv10020899m.g' => 'esa', 'Thhalv10022755m.g' => 'esa', 'TPR.G23851' => 'tpr', 'TPR.G26500' => 'tpr', 'TPR.G27267' => 'tpr', 'TPR.G32001' => 'tpr', 'TPR.G6251' => 'tpr', 'TPR.G8167' => 'tpr', 'TWI12G1330' => 'twi', 'TWI18G1239' => 'twi', 'TWI34G0979' => 'twi', 'TWI36G0670' => 'twi', 'TWI36G0707' => 'twi', 'TWI56G0233' => 'twi', 'TWI75G1809' => 'twi', 'unitig_21.g20874' => 'ugi', 'unitig_26.g10343' => 'ugi', 'unitig_46.g18392' => 'ugi', 'unitig_52.g17178' => 'ugi', 'unitig_8.g2934' => 'ugi', 'vmacro01122' => 'vma', 'vmacro05875' => 'vma', 'vmacro06147' => 'vma', 'vmacro16191' => 'vma', 'vmacro18293' => 'vma', 'VMungo0251G3707' => 'vmu', 'VMungo0464G1521' => 'vmu', 'VMungo1215G0205' => 'vmu', 'VMungo1383G2484' => 'vmu', 'Zm00001eb079610' => 'zma', 'Zm00001eb135990' => 'zma', 'Zm00001eb183710' => 'zma', 'Zm00001eb246020' => 'zma' ) $gf_id = 'HOM05D001124' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001124' ) $data_identifier = 'HOM05D001124' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 6, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 7, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 21, 'bol' => (int) 10, 'bra' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 6, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 9, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 21, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 8, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 10, 'lsa' => (int) 8, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 8, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 9, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb246020' $species_info = array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ) $local_species = 'mpo' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001124', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '548', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02520' => 'bna', 'A03p06630' => 'bna', 'A05p44460' => 'bna', 'A06p08710' => 'bna', 'A06p41090' => 'bna', 'A07p32320' => 'bna', 'A08p32520' => 'bna', 'A09p10360' => 'bna', 'A10p24080' => 'bna', 'Aa31LG11G15250' => 'aar', 'Aa31LG1G1800' => 'aar', 'Aa31LG2G5120' => 'aar', 'Aa31LG2G6070' => 'aar', 'Aa31LG5G10770' => 'aar', 'Aa31sc61G90' => 'aar', 'Actinidia01352' => 'ach', 'Actinidia05983' => 'ach', 'Actinidia08133' => 'ach', 'Actinidia15101' => 'ach', 'Actinidia26379' => 'ach', 'Actinidia35778' => 'ach', 'Actinidia36123' => 'ach', 'Actinidia37436' => 'ach', 'Actinidia38730' => 'ach', 'Ah.02g128210' => 'amhyb', 'Ah.03g132990' => 'amhyb', 'Ah.14g079410' => 'amhyb', 'AL1G24640' => 'aly', 'AL2G26680' => 'aly', 'AL3G10530' => 'aly', 'AL3G45230' => 'aly', 'AL5G15230' => 'aly', 'AL5G16960' => 'aly', 'AL6G25210' => 'aly', 'Aqoxy2G00441' => 'aox', 'Aqoxy3G01236' => 'aox', 'Aqoxy5G03746' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3RQ047' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C7GMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9C8JER' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MBL6KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YXCZ83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZANX40' => 'arhy', 'AT1G12990' => 'ath', 'AT1G67880' => 'ath', 'AT2G13290' => 'ath', 'AT3G01620' => 'ath', 'AT3G26445' => 'ath', 'AT3G27540' => 'ath', 'AT5G14480' => 'ath', 'ATR0824G026' => 'atr', 'ATR1098G019' => 'atr', 'Atru.chr11.2145' => 'acertr', 'Atru.chr2.3636' => 'acertr', 'Atru.chr2.3644' => 'acertr', 'Atru.chr6.2422' => 'acertr', 'Atru.chr7.1112' => 'acertr', 'AUR62005469' => 'cqu', 'AUR62011166' => 'cqu', 'AUR62013319' => 'cqu', 'AUR62024273' => 'cqu', 'AUR62028420' => 'cqu', 'AUR62041942' => 'cqu', 'BcaB01g04969' => 'bca', 'BcaB01g06371' => 'bca', 'BcaB02g11494' => 'bca', 'BcaB03g15382' => 'bca', 'BcaB08g36994' => 'bca', 'BcaC03g13477' => 'bca', 'BcaC03g13478' => 'bca', 'BcaC03g13480' => 'bca', 'BcaC03g13481' => 'bca', 'BcaC03g13486' => 'bca', 'BcaC04g19031' => 'bca', 'BcaC04g23085' => 'bca', 'BcaC05g25094' => 'bca', 'BcaC05g25096' => 'bca', 'BcaC05g25138' => 'bca', 'BcaC05g30416' => 'bca', 'BcaC05g30455' => 'bca', 'BcaC06g30979' => 'bca', 'BcaC06g33805' => 'bca', 'BcaC08g46021' => 'bca', 'BcaNung03154' => 'bca', 'BolC2t06623H' => 'bol', 'BolC2t06632H' => 'bol', 'BolC2t06635H' => 'bol', 'BolC2t06638H' => 'bol', 'BolC3t13266H' => 'bol', 'BolC5t29776H' => 'bol', 'BolC6t38912H' => 'bol', 'BolC7t44183H' => 'bol', 'BolC9t54123H' => 'bol', 'BolC9t59107H' => 'bol', 'BraA02t05221Z' => 'bra', 'BraA03t09996Z' => 'bra', 'BraA05t23210Z' => 'bra', 'BraA06t24068Z' => 'bra', 'BraA06t27032Z' => 'bra', 'BraA08t35176Z' => 'bra', 'BraA09t36680Z' => 'bra', 'BraA10t44471Z' => 'bra', 'C02p06760' => 'bna', 'C02p06890' => 'bna', 'C02p07010' => 'bna', 'C03p07660' => 'bna', 'C05p10300' => 'bna', 'C06p38150' => 'bna', 'C07p36650' => 'bna', 'C08p15770' => 'bna', 'C09p12300' => 'bna', 'C09p62700' => 'bna', 'C09p75040' => 'bna', 'CAN.G13.1' => 'can', 'CAN.G138.4' => 'can', 'CAN.G44.6' => 'can', 'CAN.G473.19' => 'can', 'CANSAT01G0835' => 'cansat', 'CANSAT11G0246' => 'cansat', 'CANSAT11G1766' => 'cansat', 'CANSAT64G1954' => 'cansat', 'CARHR013330' => 'chi', 'CARHR060530' => 'chi', 'CARHR075300' => 'chi', 'CARHR105120' => 'chi', 'CARHR148910' => 'chi', 'CARHR198830' => 'chi', 'Carub.0001s1275' => 'cru', 'Carub.0002s1437' => 'cru', 'Carub.0003s0044' => 'cru', 'Carub.0003s2787' => 'cru', 'Carub.0005s0597' => 'cru', 'Carub.0006s1266' => 'cru', 'Ca_06935_v3' => 'car', 'Ca_13559_v3' => 'car', 'Ca_16941_v3' => 'car', 'Ca_16960_v3' => 'car', 'Ca_17775_v3' => 'car', 'Ca_30464_v3' => 'car', 'Cc06_g08160' => 'ccan', 'Cc07_g01520' => 'ccan', 'Cc11_g15810' => 'ccan', 'CDE02G2840' => 'cde', 'CDE03G0093' => 'cde', 'CDE04G2127' => 'cde', 'CDE07G1857' => 'cde', 'CDE09G1246' => 'cde', 'Cfa003412' => 'cfa', 'Cfa007341' => 'cfa', 'Cfa009220' => 'cfa', 'Ciclev10008737m.g' => 'ccl', 'Ciclev10015565m.g' => 'ccl', 'Ciclev10031761m.g' => 'ccl', 'CiPaw.03G045300' => 'cil', 'CiPaw.03G247200' => 'cil', 'CiPaw.04G029500' => 'cil', 'CiPaw.04G174000' => 'cil', 'CiPaw.05G181200' => 'cil', 'CiPaw.06G067100' => 'cil', 'ClCG05G025800' => 'cla', 'ClCG06G011400' => 'cla', 'ClCG09G019360' => 'cla', 'COL.COLO4_04827' => 'col', 'COL.COLO4_29170' => 'col', 'COL.COLO4_35131' => 'col', 'COL.COLO4_35132' => 'col', 'Cpa.g.sc33.32' => 'cpa', 'Cpa.g.sc46.29' => 'cpa', 'Cpa.g.sc796.1' => 'cpa', 'CsaV3_1G030420' => 'csa', 'CsaV3_5G027050' => 'csa', 'CsaV3_5G031040' => 'csa', 'CsaV3_UNG023130' => 'csa', 'CSS0007726' => 'camsi', 'CSS0016433' => 'camsi', 'CSS0017656' => 'camsi', 'CSS0025364' => 'camsi', 'CSS0027582' => 'camsi', 'CSS0047288' => 'camsi', 'CSS0049950' => 'camsi', 'DCAR_003843' => 'dca', 'DCAR_007052' => 'dca', 'DCAR_020884' => 'dca', 'DCAR_021730' => 'dca', 'DCAR_024423' => 'dca', 'DCAR_026509' => 'dca', 'DCAR_031158' => 'dca', 'Dinv14728' => 'din', 'Dinv15219' => 'din', 'Dinv25728' => 'din', 'Dinv33428' => 'din', 'Dinv36489' => 'din', 'Dinv41486' => 'din', 'Duzib147G0469' => 'dzi', 'Duzib168G0060' => 'dzi', 'Duzib187G1215' => 'dzi', 'Duzib248G0692' => 'dzi', 'Duzib251G0767' => 'dzi', 'Duzib264G0446' => 'dzi', 'Duzib268G0691' => 'dzi', 'ECA232G4767' => 'eca', 'ECA233G2838' => 'eca', 'ECA234G0391' => 'eca', 'ECA234G0857' => 'eca', 'ECA236G1593' => 'eca', 'ECA238G0565' => 'eca', 'ECA246G1027' => 'eca', 'ECA246G3223' => 'eca', 'ECA246G3470' => 'eca', 'EL10Ac6g13829' => 'bvu', 'EL10Ac6g14093' => 'bvu', 'EL10Ac8g18707' => 'bvu', 'Eucgr.C01369' => 'egr', 'Eucgr.H02492' => 'egr', 'Eucgr.I01733' => 'egr', 'Eucgr.J02255' => 'egr', 'Eucgr.J02257' => 'egr', 'Eucgr.J02258' => 'egr', 'FAN02G1601' => 'fan', 'FAN03G1586' => 'fan', 'FAN03G2986' => 'fan', 'FAN05G4837' => 'fan', 'FAN06G0146' => 'fan', 'FAN07G0858' => 'fan', 'FAN09G3179' => 'fan', 'FAN10G0669' => 'fan', 'FAN12G2358' => 'fan', 'FAN14G4198' => 'fan', 'FAN14G5112' => 'fan', 'FAN17G0342' => 'fan', 'FAN19G0342' => 'fan', 'FAN19G0962' => 'fan', 'FAN19G1101' => 'fan', 'FAN19G1872' => 'fan', 'FAN22G0356' => 'fan', 'FAN23G0744' => 'fan', 'FAN23G1914' => 'fan', 'FAN26G0032' => 'fan', 'FAN28G0625' => 'fan', 'FvH4_1g02710' => 'fve', 'FvH4_1g02720' => 'fve', 'FvH4_4g25670' => 'fve', 'FvH4_6g51700' => 'fve', 'FvH4_7g20170' => 'fve', 'Glyma.05G175000' => 'gma', 'Glyma.08G132300' => 'gma', 'Glyma.11G243000' => 'gma', 'Glyma.13G158900' => 'gma', 'Glyma.17G112400' => 'gma', 'Glyma.18G014100' => 'gma', 'Glyma.19G003100' => 'gma', 'Glyma.19G056500' => 'gma', 'Gohir.A01G158900' => 'ghi', 'Gohir.A05G312600' => 'ghi', 'Gohir.A05G354900' => 'ghi', 'Gohir.A07G037200' => 'ghi', 'Gohir.A09G030000' => 'ghi', 'Gohir.A12G145200' => 'ghi', 'Gohir.D01G151500' => 'ghi', 'Gohir.D04G058300' => 'ghi', 'Gohir.D05G314100' => 'ghi', 'Gohir.D07G041400' => 'ghi', 'Gohir.D09G029700' => 'ghi', 'Gohir.D12G149700' => 'ghi', 'Gorai.001G043800' => 'gra', 'Gorai.002G187800' => 'gra', 'Gorai.006G034700' => 'gra', 'Gorai.008G161200' => 'gra', 'Gorai.009G335700' => 'gra', 'Gorai.012G065000' => 'gra', 'GSVIVG01000535001' => 'vvi', 'GSVIVG01015572001' => 'vvi', 'GSVIVG01032386001' => 'vvi', 'HanXRQChr05g0138531' => 'han', 'HanXRQChr06g0174391' => 'han', 'HanXRQChr07g0199021' => 'han', 'HanXRQChr08g0208211' => 'han', 'HanXRQChr09g0255471' => 'han', 'HanXRQChr10g0315791' => 'han', 'HanXRQChr12g0371991' => 'han', 'HanXRQChr15g0475251' => 'han', 'HanXRQChr17g0540001' => 'han', 'HanXRQChr17g0548631' => 'han', 'HanXRQChr17g0569561' => 'han', 'Haze_12256' => 'cav', 'Haze_14756' => 'cav', 'Haze_25528' => 'cav', 'Hma1.2p1_0079F.1_g041020' => 'hma', 'Hma1.2p1_0818F.1_g223260' => 'hma', 'Hma1.2p1_1747F.1_g300530' => 'hma', 'HPP92_004607' => 'vpl', 'HPP92_004608' => 'vpl', 'HPP92_006181' => 'vpl', 'HPP92_012192' => 'vpl', 'HPP92_015680' => 'vpl', 'HPP92_020249' => 'vpl', 'HPP92_021376' => 'vpl', 'HPP92_024275' => 'vpl', 'Hund06031' => 'sun', 'Hund25391' => 'sun', 'Lalb_Chr07g0185371' => 'lal', 'Lalb_Chr07g0185381' => 'lal', 'Lalb_Chr12g0204011' => 'lal', 'Lalb_Chr13g0301671' => 'lal', 'Lalb_Chr14g0362851' => 'lal', 'Lalb_Chr24g0403581' => 'lal', 'Lj1g0000233' => 'lja', 'Lj2g0018120' => 'lja', 'Lj3C621T0' => 'lonja', 'Lj3P1059T14' => 'lonja', 'Lj3P611T9' => 'lonja', 'Lj3P614T13' => 'lonja', 'Lj3P615T5' => 'lonja', 'Lj4g0012315' => 'lja', 'Lj4g0026182' => 'lja', 'Lj6P813T16' => 'lonja', 'Lj7C427T7' => 'lonja', 'Lj7C427T8' => 'lonja', 'Lj7P600T41' => 'lonja', 'Lju41C42G17' => 'lonja', 'Lsat_1_v5_gn_0_47300' => 'lsa', 'Lsat_1_v5_gn_2_91280' => 'lsa', 'Lsat_1_v5_gn_3_30561' => 'lsa', 'Lsat_1_v5_gn_4_184321' => 'lsa', 'Lsat_1_v5_gn_4_4041' => 'lsa', 'Lsat_1_v5_gn_5_92000' => 'lsa', 'Lsat_1_v5_gn_8_152940' => 'lsa', 'Lsat_1_v5_gn_8_62401' => 'lsa', 'Manes.06G055900' => 'mes', 'Manes.12G022200' => 'mes', 'Manes.13G023300' => 'mes', 'Manes.14G115000' => 'mes', 'Manes.15G151700' => 'mes', 'Manes.17G111300' => 'mes', 'Mapoly0226s0009' => 'mpo', 'MBI02_g25363_MAGBIO' => 'mbi', 'MBI06_g00027_MAGBIO' => 'mbi', 'MBI10_g13034_MAGBIO' => 'mbi', 'MD09G1023400' => 'mdo', 'MD13G1100100' => 'mdo', 'MD15G1169200' => 'mdo', 'MD16G1101100' => 'mdo', 'MD17G1022900' => 'mdo', 'Medtr3g096150' => 'mtr', 'Medtr4g115070' => 'mtr', 'Medtr7g033325' => 'mtr', 'Medtr8g089840' => 'mtr', 'MELO3C010319.2' => 'cme', 'MELO3C011944.2' => 'cme', 'MELO3C021589.2' => 'cme', 'Migut.E00207' => 'egut', 'Migut.H00067' => 'egut', 'Migut.K00433' => 'egut', 'Migut.K00606' => 'egut', 'Migut.K01410' => 'egut', 'MSTRG.13347' => 'ama', 'MSTRG.24045' => 'ama', 'MSTRG.2428' => 'ama', 'MSTRG.26410' => 'ama', 'MSTRG.3139' => 'ama', 'MSTRG.3286' => 'ama', 'MSTRG.563' => 'ama', 'MSTRG.7941' => 'ama', 'Nitab4.5_0000028g0060' => 'nta', 'Nitab4.5_0000065g0260' => 'nta', 'Nitab4.5_0000112g0060' => 'nta', 'Nitab4.5_0000489g0120' => 'nta', 'Nitab4.5_0001776g0050' => 'nta', 'Nitab4.5_0001854g0010' => 'nta', 'Nitab4.5_0001860g0020' => 'nta', 'Nitab4.5_0004352g0010' => 'nta', 'Nitab4.5_0008716g0020' => 'nta', 'Nitab4.5_0008922g0010' => 'nta', 'Nn3g16693' => 'nnu', 'Nn4g22596' => 'nnu', 'Nn7g37639' => 'nnu', 'Oeu001701.1' => 'oeu', 'Oeu018149.1' => 'oeu', 'Oeu026220.1' => 'oeu', 'Oeu038635.1' => 'oeu', 'Oeu049176.1' => 'oeu', 'Oeu056706.1' => 'oeu', 'Oeu056937.1' => 'oeu', 'Oeu057540.1' => 'oeu', 'Os02g0594900' => 'osa', 'Os02g0595100' => 'osa', 'Os04g0477500' => 'osa', 'Os12g0611900' => 'osa', 'Peaxi162Scf00076g00020' => 'pax', 'Peaxi162Scf00128g00217' => 'pax', 'Peaxi162Scf00129g01640' => 'pax', 'Peaxi162Scf00669g00007' => 'pax', 'Peaxi162Scf00700g00421' => 'pax', 'Peaxi162Scf00801g00038' => 'pax', 'Peaxi162Scf00891g00025' => 'pax', 'PGR083G0909' => 'pgr', 'PGR119G1005' => 'pgr', 'PGR142G2236' => 'pgr', 'PGR142G3388' => 'pgr', 'PGSC0003DMG400004514' => 'stu', 'PGSC0003DMG400012635' => 'stu', 'PGSC0003DMG400015730' => 'stu', 'PGSC0003DMG400018611' => 'stu', 'PGSC0003DMG400030897' => 'stu', 'Phvul.001G254800' => 'pvu', 'Phvul.002G260100' => 'pvu', 'Phvul.003G167600' => 'pvu', 'Phvul.004G005100' => 'pvu', 'Potri.001G343600' => 'ptr', 'Potri.006G066700' => 'ptr', 'Potri.008G186000' => 'ptr', 'Potri.010G046900' => 'ptr', 'Potri.018G127900' => 'ptr', 'Pp3c20_17750' => 'ppa', 'Pp3c24_4380' => 'ppa', 'Prupe.1G245800' => 'ppe', 'Prupe.3G293400' => 'ppe', 'Prupe.7G247400' => 'ppe', 'Psat0s145g0120' => 'psa', 'Psat0s595g0040' => 'psa', 'Psat0s595g0120' => 'psa', 'Psat3g175040' => 'psa', 'Psat7g058120' => 'psa', 'PSO017G0428' => 'pso', 'PSO063G7510' => 'pso', 'PSO067G0046' => 'pso', 'PSO478G1073' => 'pso', 'PSO675G3677' => 'pso', 'PSO675G6558' => 'pso', 'PSO675G7520' => 'pso', 'PSO675G8959' => 'pso', 'QL02p074089' => 'qlo', 'QL02p089614' => 'qlo', 'QL03p057736' => 'qlo', 'RcHm_v2.0_Chr1g0364131' => 'rch', 'RcHm_v2.0_Chr2g0087801' => 'rch', 'RcHm_v2.0_Chr2g0087821' => 'rch', 'RcHm_v2.0_Chr2g0173231' => 'rch', 'RcHm_v2.0_Chr4g0433111' => 'rch', 'Rhsim03G0250300' => 'rsi', 'Rhsim08G0048400' => 'rsi', 'Rhsim10G0014800' => 'rsi', 'Rhsim12G0040100' => 'rsi', 'Rhsim12G0109700' => 'rsi', 'Sabra06G0049600' => 'sbr', 'Sabra08G0141000' => 'sbr', 'Sabra10G0021400' => 'sbr', 'Sabra16G0222900' => 'sbr', 'Sabra18G0108600' => 'sbr', 'SalBow1G0433' => 'sbo', 'SalBow1G2038' => 'sbo', 'SalBow1G5003' => 'sbo', 'SalBow7G1197' => 'sbo', 'SalBow8G3506' => 'sbo', 'Sc03g0007300' => 'sci', 'Sc11g0000950' => 'sci', 'Sc14g0008750' => 'sci', 'Sc18g0000420' => 'sci', 'Sed0006754' => 'sed', 'Sed0008741' => 'sed', 'Sed0017172' => 'sed', 'Sed0018925' => 'sed', 'Sed0023326' => 'sed', 'Sed0025909' => 'sed', 'SEGI_05333' => 'sgi', 'SEGI_10362' => 'sgi', 'SEGI_13380' => 'sgi', 'SEGI_24306' => 'sgi', 'SEGI_29077' => 'sgi', 'SEGI_29095' => 'sgi', 'SEGI_36534' => 'sgi', 'SEGI_37506' => 'sgi', 'SEGI_38321' => 'sgi', 'SGA_v2.0_scaffold307G48031' => 'sas', 'SGA_v2.0_scaffold47G17507' => 'sas', 'SGA_v2.0_scaffold63G21736' => 'sas', 'SGA_v2.0_scaffold87G27070' => 'sas', 'SHI17794' => 'shi', 'SHI28851' => 'shi', 'SMO165G0155' => 'smo', 'SMO340G0217' => 'smo', 'SMO367G1210' => 'smo', 'Solyc02g093430.3' => 'sly', 'Solyc05g013580.4' => 'sly', 'Solyc07g008030.3' => 'sly', 'Solyc12g035470.2' => 'sly', 'Sopen02g038020' => 'spe', 'Sopen05g008490' => 'spe', 'Sopen07g003910' => 'spe', 'Sopen12g015240' => 'spe', 'Sp1g11550' => 'spa', 'Sp2g16710' => 'spa', 'Sp3g00430' => 'spa', 'Sp3g26780' => 'spa', 'Sp5g22900' => 'spa', 'Sp6g29530' => 'spa', 'TAR371G0794' => 'tar', 'TAR374G0164' => 'tar', 'TAR622G0165' => 'tar', 'TAR626G0929' => 'tar', 'TAR629G2155' => 'tar', 'THA.LOC104805282' => 'tha', 'THA.LOC104805363' => 'tha', 'THA.LOC104808968' => 'tha', 'THA.LOC104821093' => 'tha', 'THA.LOC104823953' => 'tha', 'THA.LOC104825562' => 'tha', 'THA.LOC104825665' => 'tha', 'Thecc.02G261400' => 'tca', 'Thecc.04G019200' => 'tca', 'Thecc.09G130400' => 'tca', 'Thhalv10004374m.g' => 'esa', 'Thhalv10007850m.g' => 'esa', 'Thhalv10013782m.g' => 'esa', 'Thhalv10018686m.g' => 'esa', 'Thhalv10020899m.g' => 'esa', 'Thhalv10022755m.g' => 'esa', 'TPR.G23851' => 'tpr', 'TPR.G26500' => 'tpr', 'TPR.G27267' => 'tpr', 'TPR.G32001' => 'tpr', 'TPR.G6251' => 'tpr', 'TPR.G8167' => 'tpr', 'TWI12G1330' => 'twi', 'TWI18G1239' => 'twi', 'TWI34G0979' => 'twi', 'TWI36G0670' => 'twi', 'TWI36G0707' => 'twi', 'TWI56G0233' => 'twi', 'TWI75G1809' => 'twi', 'unitig_21.g20874' => 'ugi', 'unitig_26.g10343' => 'ugi', 'unitig_46.g18392' => 'ugi', 'unitig_52.g17178' => 'ugi', 'unitig_8.g2934' => 'ugi', 'vmacro01122' => 'vma', 'vmacro05875' => 'vma', 'vmacro06147' => 'vma', 'vmacro16191' => 'vma', 'vmacro18293' => 'vma', 'VMungo0251G3707' => 'vmu', 'VMungo0464G1521' => 'vmu', 'VMungo1215G0205' => 'vmu', 'VMungo1383G2484' => 'vmu', 'Zm00001eb079610' => 'zma', 'Zm00001eb135990' => 'zma', 'Zm00001eb183710' => 'zma', 'Zm00001eb246020' => 'zma' ), 'gf_id' => 'HOM05D001124', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001124' ), 'data_identifier' => 'HOM05D001124', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001124', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '548', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02520' => 'bna', 'A03p06630' => 'bna', 'A05p44460' => 'bna', 'A06p08710' => 'bna', 'A06p41090' => 'bna', 'A07p32320' => 'bna', 'A08p32520' => 'bna', 'A09p10360' => 'bna', 'A10p24080' => 'bna', 'Aa31LG11G15250' => 'aar', 'Aa31LG1G1800' => 'aar', 'Aa31LG2G5120' => 'aar', 'Aa31LG2G6070' => 'aar', 'Aa31LG5G10770' => 'aar', 'Aa31sc61G90' => 'aar', 'Actinidia01352' => 'ach', 'Actinidia05983' => 'ach', 'Actinidia08133' => 'ach', 'Actinidia15101' => 'ach', 'Actinidia26379' => 'ach', 'Actinidia35778' => 'ach', 'Actinidia36123' => 'ach', 'Actinidia37436' => 'ach', 'Actinidia38730' => 'ach', 'Ah.02g128210' => 'amhyb', 'Ah.03g132990' => 'amhyb', 'Ah.14g079410' => 'amhyb', 'AL1G24640' => 'aly', 'AL2G26680' => 'aly', 'AL3G10530' => 'aly', 'AL3G45230' => 'aly', 'AL5G15230' => 'aly', 'AL5G16960' => 'aly', 'AL6G25210' => 'aly', 'Aqoxy2G00441' => 'aox', 'Aqoxy3G01236' => 'aox', 'Aqoxy5G03746' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3RQ047' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C7GMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9C8JER' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MBL6KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YXCZ83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZANX40' => 'arhy', 'AT1G12990' => 'ath', 'AT1G67880' => 'ath', 'AT2G13290' => 'ath', 'AT3G01620' => 'ath', 'AT3G26445' => 'ath', 'AT3G27540' => 'ath', 'AT5G14480' => 'ath', 'ATR0824G026' => 'atr', 'ATR1098G019' => 'atr', 'Atru.chr11.2145' => 'acertr', 'Atru.chr2.3636' => 'acertr', 'Atru.chr2.3644' => 'acertr', 'Atru.chr6.2422' => 'acertr', 'Atru.chr7.1112' => 'acertr', 'AUR62005469' => 'cqu', 'AUR62011166' => 'cqu', 'AUR62013319' => 'cqu', 'AUR62024273' => 'cqu', 'AUR62028420' => 'cqu', 'AUR62041942' => 'cqu', 'BcaB01g04969' => 'bca', 'BcaB01g06371' => 'bca', 'BcaB02g11494' => 'bca', 'BcaB03g15382' => 'bca', 'BcaB08g36994' => 'bca', 'BcaC03g13477' => 'bca', 'BcaC03g13478' => 'bca', 'BcaC03g13480' => 'bca', 'BcaC03g13481' => 'bca', 'BcaC03g13486' => 'bca', 'BcaC04g19031' => 'bca', 'BcaC04g23085' => 'bca', 'BcaC05g25094' => 'bca', 'BcaC05g25096' => 'bca', 'BcaC05g25138' => 'bca', 'BcaC05g30416' => 'bca', 'BcaC05g30455' => 'bca', 'BcaC06g30979' => 'bca', 'BcaC06g33805' => 'bca', 'BcaC08g46021' => 'bca', 'BcaNung03154' => 'bca', 'BolC2t06623H' => 'bol', 'BolC2t06632H' => 'bol', 'BolC2t06635H' => 'bol', 'BolC2t06638H' => 'bol', 'BolC3t13266H' => 'bol', 'BolC5t29776H' => 'bol', 'BolC6t38912H' => 'bol', 'BolC7t44183H' => 'bol', 'BolC9t54123H' => 'bol', 'BolC9t59107H' => 'bol', 'BraA02t05221Z' => 'bra', 'BraA03t09996Z' => 'bra', 'BraA05t23210Z' => 'bra', 'BraA06t24068Z' => 'bra', 'BraA06t27032Z' => 'bra', 'BraA08t35176Z' => 'bra', 'BraA09t36680Z' => 'bra', 'BraA10t44471Z' => 'bra', 'C02p06760' => 'bna', 'C02p06890' => 'bna', 'C02p07010' => 'bna', 'C03p07660' => 'bna', 'C05p10300' => 'bna', 'C06p38150' => 'bna', 'C07p36650' => 'bna', 'C08p15770' => 'bna', 'C09p12300' => 'bna', 'C09p62700' => 'bna', 'C09p75040' => 'bna', 'CAN.G13.1' => 'can', 'CAN.G138.4' => 'can', 'CAN.G44.6' => 'can', 'CAN.G473.19' => 'can', 'CANSAT01G0835' => 'cansat', 'CANSAT11G0246' => 'cansat', 'CANSAT11G1766' => 'cansat', 'CANSAT64G1954' => 'cansat', 'CARHR013330' => 'chi', 'CARHR060530' => 'chi', 'CARHR075300' => 'chi', 'CARHR105120' => 'chi', 'CARHR148910' => 'chi', 'CARHR198830' => 'chi', 'Carub.0001s1275' => 'cru', 'Carub.0002s1437' => 'cru', 'Carub.0003s0044' => 'cru', 'Carub.0003s2787' => 'cru', 'Carub.0005s0597' => 'cru', 'Carub.0006s1266' => 'cru', 'Ca_06935_v3' => 'car', 'Ca_13559_v3' => 'car', 'Ca_16941_v3' => 'car', 'Ca_16960_v3' => 'car', 'Ca_17775_v3' => 'car', 'Ca_30464_v3' => 'car', 'Cc06_g08160' => 'ccan', 'Cc07_g01520' => 'ccan', 'Cc11_g15810' => 'ccan', 'CDE02G2840' => 'cde', 'CDE03G0093' => 'cde', 'CDE04G2127' => 'cde', 'CDE07G1857' => 'cde', 'CDE09G1246' => 'cde', 'Cfa003412' => 'cfa', 'Cfa007341' => 'cfa', 'Cfa009220' => 'cfa', 'Ciclev10008737m.g' => 'ccl', 'Ciclev10015565m.g' => 'ccl', 'Ciclev10031761m.g' => 'ccl', 'CiPaw.03G045300' => 'cil', 'CiPaw.03G247200' => 'cil', 'CiPaw.04G029500' => 'cil', 'CiPaw.04G174000' => 'cil', 'CiPaw.05G181200' => 'cil', 'CiPaw.06G067100' => 'cil', 'ClCG05G025800' => 'cla', 'ClCG06G011400' => 'cla', 'ClCG09G019360' => 'cla', 'COL.COLO4_04827' => 'col', 'COL.COLO4_29170' => 'col', 'COL.COLO4_35131' => 'col', 'COL.COLO4_35132' => 'col', 'Cpa.g.sc33.32' => 'cpa', 'Cpa.g.sc46.29' => 'cpa', 'Cpa.g.sc796.1' => 'cpa', 'CsaV3_1G030420' => 'csa', 'CsaV3_5G027050' => 'csa', 'CsaV3_5G031040' => 'csa', 'CsaV3_UNG023130' => 'csa', 'CSS0007726' => 'camsi', 'CSS0016433' => 'camsi', 'CSS0017656' => 'camsi', 'CSS0025364' => 'camsi', 'CSS0027582' => 'camsi', 'CSS0047288' => 'camsi', 'CSS0049950' => 'camsi', 'DCAR_003843' => 'dca', 'DCAR_007052' => 'dca', 'DCAR_020884' => 'dca', 'DCAR_021730' => 'dca', 'DCAR_024423' => 'dca', 'DCAR_026509' => 'dca', 'DCAR_031158' => 'dca', 'Dinv14728' => 'din', 'Dinv15219' => 'din', 'Dinv25728' => 'din', 'Dinv33428' => 'din', 'Dinv36489' => 'din', 'Dinv41486' => 'din', 'Duzib147G0469' => 'dzi', 'Duzib168G0060' => 'dzi', 'Duzib187G1215' => 'dzi', 'Duzib248G0692' => 'dzi', 'Duzib251G0767' => 'dzi', 'Duzib264G0446' => 'dzi', 'Duzib268G0691' => 'dzi', 'ECA232G4767' => 'eca', 'ECA233G2838' => 'eca', 'ECA234G0391' => 'eca', 'ECA234G0857' => 'eca', 'ECA236G1593' => 'eca', 'ECA238G0565' => 'eca', 'ECA246G1027' => 'eca', 'ECA246G3223' => 'eca', 'ECA246G3470' => 'eca', 'EL10Ac6g13829' => 'bvu', 'EL10Ac6g14093' => 'bvu', 'EL10Ac8g18707' => 'bvu', 'Eucgr.C01369' => 'egr', 'Eucgr.H02492' => 'egr', 'Eucgr.I01733' => 'egr', 'Eucgr.J02255' => 'egr', 'Eucgr.J02257' => 'egr', 'Eucgr.J02258' => 'egr', 'FAN02G1601' => 'fan', 'FAN03G1586' => 'fan', 'FAN03G2986' => 'fan', 'FAN05G4837' => 'fan', 'FAN06G0146' => 'fan', 'FAN07G0858' => 'fan', 'FAN09G3179' => 'fan', 'FAN10G0669' => 'fan', 'FAN12G2358' => 'fan', 'FAN14G4198' => 'fan', 'FAN14G5112' => 'fan', 'FAN17G0342' => 'fan', 'FAN19G0342' => 'fan', 'FAN19G0962' => 'fan', 'FAN19G1101' => 'fan', 'FAN19G1872' => 'fan', 'FAN22G0356' => 'fan', 'FAN23G0744' => 'fan', 'FAN23G1914' => 'fan', 'FAN26G0032' => 'fan', 'FAN28G0625' => 'fan', 'FvH4_1g02710' => 'fve', 'FvH4_1g02720' => 'fve', 'FvH4_4g25670' => 'fve', 'FvH4_6g51700' => 'fve', 'FvH4_7g20170' => 'fve', 'Glyma.05G175000' => 'gma', 'Glyma.08G132300' => 'gma', 'Glyma.11G243000' => 'gma', 'Glyma.13G158900' => 'gma', 'Glyma.17G112400' => 'gma', 'Glyma.18G014100' => 'gma', 'Glyma.19G003100' => 'gma', 'Glyma.19G056500' => 'gma', 'Gohir.A01G158900' => 'ghi', 'Gohir.A05G312600' => 'ghi', 'Gohir.A05G354900' => 'ghi', 'Gohir.A07G037200' => 'ghi', 'Gohir.A09G030000' => 'ghi', 'Gohir.A12G145200' => 'ghi', 'Gohir.D01G151500' => 'ghi', 'Gohir.D04G058300' => 'ghi', 'Gohir.D05G314100' => 'ghi', 'Gohir.D07G041400' => 'ghi', 'Gohir.D09G029700' => 'ghi', 'Gohir.D12G149700' => 'ghi', 'Gorai.001G043800' => 'gra', 'Gorai.002G187800' => 'gra', 'Gorai.006G034700' => 'gra', 'Gorai.008G161200' => 'gra', 'Gorai.009G335700' => 'gra', 'Gorai.012G065000' => 'gra', 'GSVIVG01000535001' => 'vvi', 'GSVIVG01015572001' => 'vvi', 'GSVIVG01032386001' => 'vvi', 'HanXRQChr05g0138531' => 'han', 'HanXRQChr06g0174391' => 'han', 'HanXRQChr07g0199021' => 'han', 'HanXRQChr08g0208211' => 'han', 'HanXRQChr09g0255471' => 'han', 'HanXRQChr10g0315791' => 'han', 'HanXRQChr12g0371991' => 'han', 'HanXRQChr15g0475251' => 'han', 'HanXRQChr17g0540001' => 'han', 'HanXRQChr17g0548631' => 'han', 'HanXRQChr17g0569561' => 'han', 'Haze_12256' => 'cav', 'Haze_14756' => 'cav', 'Haze_25528' => 'cav', 'Hma1.2p1_0079F.1_g041020' => 'hma', 'Hma1.2p1_0818F.1_g223260' => 'hma', 'Hma1.2p1_1747F.1_g300530' => 'hma', 'HPP92_004607' => 'vpl', 'HPP92_004608' => 'vpl', 'HPP92_006181' => 'vpl', 'HPP92_012192' => 'vpl', 'HPP92_015680' => 'vpl', 'HPP92_020249' => 'vpl', 'HPP92_021376' => 'vpl', 'HPP92_024275' => 'vpl', 'Hund06031' => 'sun', 'Hund25391' => 'sun', 'Lalb_Chr07g0185371' => 'lal', 'Lalb_Chr07g0185381' => 'lal', 'Lalb_Chr12g0204011' => 'lal', 'Lalb_Chr13g0301671' => 'lal', 'Lalb_Chr14g0362851' => 'lal', 'Lalb_Chr24g0403581' => 'lal', 'Lj1g0000233' => 'lja', 'Lj2g0018120' => 'lja', 'Lj3C621T0' => 'lonja', 'Lj3P1059T14' => 'lonja', 'Lj3P611T9' => 'lonja', 'Lj3P614T13' => 'lonja', 'Lj3P615T5' => 'lonja', 'Lj4g0012315' => 'lja', 'Lj4g0026182' => 'lja', 'Lj6P813T16' => 'lonja', 'Lj7C427T7' => 'lonja', 'Lj7C427T8' => 'lonja', 'Lj7P600T41' => 'lonja', 'Lju41C42G17' => 'lonja', 'Lsat_1_v5_gn_0_47300' => 'lsa', 'Lsat_1_v5_gn_2_91280' => 'lsa', 'Lsat_1_v5_gn_3_30561' => 'lsa', 'Lsat_1_v5_gn_4_184321' => 'lsa', 'Lsat_1_v5_gn_4_4041' => 'lsa', 'Lsat_1_v5_gn_5_92000' => 'lsa', 'Lsat_1_v5_gn_8_152940' => 'lsa', 'Lsat_1_v5_gn_8_62401' => 'lsa', 'Manes.06G055900' => 'mes', 'Manes.12G022200' => 'mes', 'Manes.13G023300' => 'mes', 'Manes.14G115000' => 'mes', 'Manes.15G151700' => 'mes', 'Manes.17G111300' => 'mes', 'Mapoly0226s0009' => 'mpo', 'MBI02_g25363_MAGBIO' => 'mbi', 'MBI06_g00027_MAGBIO' => 'mbi', 'MBI10_g13034_MAGBIO' => 'mbi', 'MD09G1023400' => 'mdo', 'MD13G1100100' => 'mdo', 'MD15G1169200' => 'mdo', 'MD16G1101100' => 'mdo', 'MD17G1022900' => 'mdo', 'Medtr3g096150' => 'mtr', 'Medtr4g115070' => 'mtr', 'Medtr7g033325' => 'mtr', 'Medtr8g089840' => 'mtr', 'MELO3C010319.2' => 'cme', 'MELO3C011944.2' => 'cme', 'MELO3C021589.2' => 'cme', 'Migut.E00207' => 'egut', 'Migut.H00067' => 'egut', 'Migut.K00433' => 'egut', 'Migut.K00606' => 'egut', 'Migut.K01410' => 'egut', 'MSTRG.13347' => 'ama', 'MSTRG.24045' => 'ama', 'MSTRG.2428' => 'ama', 'MSTRG.26410' => 'ama', 'MSTRG.3139' => 'ama', 'MSTRG.3286' => 'ama', 'MSTRG.563' => 'ama', 'MSTRG.7941' => 'ama', 'Nitab4.5_0000028g0060' => 'nta', 'Nitab4.5_0000065g0260' => 'nta', 'Nitab4.5_0000112g0060' => 'nta', 'Nitab4.5_0000489g0120' => 'nta', 'Nitab4.5_0001776g0050' => 'nta', 'Nitab4.5_0001854g0010' => 'nta', 'Nitab4.5_0001860g0020' => 'nta', 'Nitab4.5_0004352g0010' => 'nta', 'Nitab4.5_0008716g0020' => 'nta', 'Nitab4.5_0008922g0010' => 'nta', 'Nn3g16693' => 'nnu', 'Nn4g22596' => 'nnu', 'Nn7g37639' => 'nnu', 'Oeu001701.1' => 'oeu', 'Oeu018149.1' => 'oeu', 'Oeu026220.1' => 'oeu', 'Oeu038635.1' => 'oeu', 'Oeu049176.1' => 'oeu', 'Oeu056706.1' => 'oeu', 'Oeu056937.1' => 'oeu', 'Oeu057540.1' => 'oeu', 'Os02g0594900' => 'osa', 'Os02g0595100' => 'osa', 'Os04g0477500' => 'osa', 'Os12g0611900' => 'osa', 'Peaxi162Scf00076g00020' => 'pax', 'Peaxi162Scf00128g00217' => 'pax', 'Peaxi162Scf00129g01640' => 'pax', 'Peaxi162Scf00669g00007' => 'pax', 'Peaxi162Scf00700g00421' => 'pax', 'Peaxi162Scf00801g00038' => 'pax', 'Peaxi162Scf00891g00025' => 'pax', 'PGR083G0909' => 'pgr', 'PGR119G1005' => 'pgr', 'PGR142G2236' => 'pgr', 'PGR142G3388' => 'pgr', 'PGSC0003DMG400004514' => 'stu', 'PGSC0003DMG400012635' => 'stu', 'PGSC0003DMG400015730' => 'stu', 'PGSC0003DMG400018611' => 'stu', 'PGSC0003DMG400030897' => 'stu', 'Phvul.001G254800' => 'pvu', 'Phvul.002G260100' => 'pvu', 'Phvul.003G167600' => 'pvu', 'Phvul.004G005100' => 'pvu', 'Potri.001G343600' => 'ptr', 'Potri.006G066700' => 'ptr', 'Potri.008G186000' => 'ptr', 'Potri.010G046900' => 'ptr', 'Potri.018G127900' => 'ptr', 'Pp3c20_17750' => 'ppa', 'Pp3c24_4380' => 'ppa', 'Prupe.1G245800' => 'ppe', 'Prupe.3G293400' => 'ppe', 'Prupe.7G247400' => 'ppe', 'Psat0s145g0120' => 'psa', 'Psat0s595g0040' => 'psa', 'Psat0s595g0120' => 'psa', 'Psat3g175040' => 'psa', 'Psat7g058120' => 'psa', 'PSO017G0428' => 'pso', 'PSO063G7510' => 'pso', 'PSO067G0046' => 'pso', 'PSO478G1073' => 'pso', 'PSO675G3677' => 'pso', 'PSO675G6558' => 'pso', 'PSO675G7520' => 'pso', 'PSO675G8959' => 'pso', 'QL02p074089' => 'qlo', 'QL02p089614' => 'qlo', 'QL03p057736' => 'qlo', 'RcHm_v2.0_Chr1g0364131' => 'rch', 'RcHm_v2.0_Chr2g0087801' => 'rch', 'RcHm_v2.0_Chr2g0087821' => 'rch', 'RcHm_v2.0_Chr2g0173231' => 'rch', 'RcHm_v2.0_Chr4g0433111' => 'rch', 'Rhsim03G0250300' => 'rsi', 'Rhsim08G0048400' => 'rsi', 'Rhsim10G0014800' => 'rsi', 'Rhsim12G0040100' => 'rsi', 'Rhsim12G0109700' => 'rsi', 'Sabra06G0049600' => 'sbr', 'Sabra08G0141000' => 'sbr', 'Sabra10G0021400' => 'sbr', 'Sabra16G0222900' => 'sbr', 'Sabra18G0108600' => 'sbr', 'SalBow1G0433' => 'sbo', 'SalBow1G2038' => 'sbo', 'SalBow1G5003' => 'sbo', 'SalBow7G1197' => 'sbo', 'SalBow8G3506' => 'sbo', 'Sc03g0007300' => 'sci', 'Sc11g0000950' => 'sci', 'Sc14g0008750' => 'sci', 'Sc18g0000420' => 'sci', 'Sed0006754' => 'sed', 'Sed0008741' => 'sed', 'Sed0017172' => 'sed', 'Sed0018925' => 'sed', 'Sed0023326' => 'sed', 'Sed0025909' => 'sed', 'SEGI_05333' => 'sgi', 'SEGI_10362' => 'sgi', 'SEGI_13380' => 'sgi', 'SEGI_24306' => 'sgi', 'SEGI_29077' => 'sgi', 'SEGI_29095' => 'sgi', 'SEGI_36534' => 'sgi', 'SEGI_37506' => 'sgi', 'SEGI_38321' => 'sgi', 'SGA_v2.0_scaffold307G48031' => 'sas', 'SGA_v2.0_scaffold47G17507' => 'sas', 'SGA_v2.0_scaffold63G21736' => 'sas', 'SGA_v2.0_scaffold87G27070' => 'sas', 'SHI17794' => 'shi', 'SHI28851' => 'shi', 'SMO165G0155' => 'smo', 'SMO340G0217' => 'smo', 'SMO367G1210' => 'smo', 'Solyc02g093430.3' => 'sly', 'Solyc05g013580.4' => 'sly', 'Solyc07g008030.3' => 'sly', 'Solyc12g035470.2' => 'sly', 'Sopen02g038020' => 'spe', 'Sopen05g008490' => 'spe', 'Sopen07g003910' => 'spe', 'Sopen12g015240' => 'spe', 'Sp1g11550' => 'spa', 'Sp2g16710' => 'spa', 'Sp3g00430' => 'spa', 'Sp3g26780' => 'spa', 'Sp5g22900' => 'spa', 'Sp6g29530' => 'spa', 'TAR371G0794' => 'tar', 'TAR374G0164' => 'tar', 'TAR622G0165' => 'tar', 'TAR626G0929' => 'tar', 'TAR629G2155' => 'tar', 'THA.LOC104805282' => 'tha', 'THA.LOC104805363' => 'tha', 'THA.LOC104808968' => 'tha', 'THA.LOC104821093' => 'tha', 'THA.LOC104823953' => 'tha', 'THA.LOC104825562' => 'tha', 'THA.LOC104825665' => 'tha', 'Thecc.02G261400' => 'tca', 'Thecc.04G019200' => 'tca', 'Thecc.09G130400' => 'tca', 'Thhalv10004374m.g' => 'esa', 'Thhalv10007850m.g' => 'esa', 'Thhalv10013782m.g' => 'esa', 'Thhalv10018686m.g' => 'esa', 'Thhalv10020899m.g' => 'esa', 'Thhalv10022755m.g' => 'esa', 'TPR.G23851' => 'tpr', 'TPR.G26500' => 'tpr', 'TPR.G27267' => 'tpr', 'TPR.G32001' => 'tpr', 'TPR.G6251' => 'tpr', 'TPR.G8167' => 'tpr', 'TWI12G1330' => 'twi', 'TWI18G1239' => 'twi', 'TWI34G0979' => 'twi', 'TWI36G0670' => 'twi', 'TWI36G0707' => 'twi', 'TWI56G0233' => 'twi', 'TWI75G1809' => 'twi', 'unitig_21.g20874' => 'ugi', 'unitig_26.g10343' => 'ugi', 'unitig_46.g18392' => 'ugi', 'unitig_52.g17178' => 'ugi', 'unitig_8.g2934' => 'ugi', 'vmacro01122' => 'vma', 'vmacro05875' => 'vma', 'vmacro06147' => 'vma', 'vmacro16191' => 'vma', 'vmacro18293' => 'vma', 'VMungo0251G3707' => 'vmu', 'VMungo0464G1521' => 'vmu', 'VMungo1215G0205' => 'vmu', 'VMungo1383G2484' => 'vmu', 'Zm00001eb079610' => 'zma', 'Zm00001eb135990' => 'zma', 'Zm00001eb183710' => 'zma', 'Zm00001eb246020' => 'zma' ) $gf_id = 'HOM05D001124' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001124' ) $data_identifier = 'HOM05D001124' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 6, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 7, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 21, 'bol' => (int) 10, 'bra' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 6, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 9, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 21, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 8, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 10, 'lsa' => (int) 8, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 8, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 9, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb246020' $species_info = array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ) $local_species = 'mpo' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001124', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '548', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02520' => 'bna', 'A03p06630' => 'bna', 'A05p44460' => 'bna', 'A06p08710' => 'bna', 'A06p41090' => 'bna', 'A07p32320' => 'bna', 'A08p32520' => 'bna', 'A09p10360' => 'bna', 'A10p24080' => 'bna', 'Aa31LG11G15250' => 'aar', 'Aa31LG1G1800' => 'aar', 'Aa31LG2G5120' => 'aar', 'Aa31LG2G6070' => 'aar', 'Aa31LG5G10770' => 'aar', 'Aa31sc61G90' => 'aar', 'Actinidia01352' => 'ach', 'Actinidia05983' => 'ach', 'Actinidia08133' => 'ach', 'Actinidia15101' => 'ach', 'Actinidia26379' => 'ach', 'Actinidia35778' => 'ach', 'Actinidia36123' => 'ach', 'Actinidia37436' => 'ach', 'Actinidia38730' => 'ach', 'Ah.02g128210' => 'amhyb', 'Ah.03g132990' => 'amhyb', 'Ah.14g079410' => 'amhyb', 'AL1G24640' => 'aly', 'AL2G26680' => 'aly', 'AL3G10530' => 'aly', 'AL3G45230' => 'aly', 'AL5G15230' => 'aly', 'AL5G16960' => 'aly', 'AL6G25210' => 'aly', 'Aqoxy2G00441' => 'aox', 'Aqoxy3G01236' => 'aox', 'Aqoxy5G03746' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3RQ047' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C7GMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9C8JER' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MBL6KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YXCZ83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZANX40' => 'arhy', 'AT1G12990' => 'ath', 'AT1G67880' => 'ath', 'AT2G13290' => 'ath', 'AT3G01620' => 'ath', 'AT3G26445' => 'ath', 'AT3G27540' => 'ath', 'AT5G14480' => 'ath', 'ATR0824G026' => 'atr', 'ATR1098G019' => 'atr', 'Atru.chr11.2145' => 'acertr', 'Atru.chr2.3636' => 'acertr', 'Atru.chr2.3644' => 'acertr', 'Atru.chr6.2422' => 'acertr', 'Atru.chr7.1112' => 'acertr', 'AUR62005469' => 'cqu', 'AUR62011166' => 'cqu', 'AUR62013319' => 'cqu', 'AUR62024273' => 'cqu', 'AUR62028420' => 'cqu', 'AUR62041942' => 'cqu', 'BcaB01g04969' => 'bca', 'BcaB01g06371' => 'bca', 'BcaB02g11494' => 'bca', 'BcaB03g15382' => 'bca', 'BcaB08g36994' => 'bca', 'BcaC03g13477' => 'bca', 'BcaC03g13478' => 'bca', 'BcaC03g13480' => 'bca', 'BcaC03g13481' => 'bca', 'BcaC03g13486' => 'bca', 'BcaC04g19031' => 'bca', 'BcaC04g23085' => 'bca', 'BcaC05g25094' => 'bca', 'BcaC05g25096' => 'bca', 'BcaC05g25138' => 'bca', 'BcaC05g30416' => 'bca', 'BcaC05g30455' => 'bca', 'BcaC06g30979' => 'bca', 'BcaC06g33805' => 'bca', 'BcaC08g46021' => 'bca', 'BcaNung03154' => 'bca', 'BolC2t06623H' => 'bol', 'BolC2t06632H' => 'bol', 'BolC2t06635H' => 'bol', 'BolC2t06638H' => 'bol', 'BolC3t13266H' => 'bol', 'BolC5t29776H' => 'bol', 'BolC6t38912H' => 'bol', 'BolC7t44183H' => 'bol', 'BolC9t54123H' => 'bol', 'BolC9t59107H' => 'bol', 'BraA02t05221Z' => 'bra', 'BraA03t09996Z' => 'bra', 'BraA05t23210Z' => 'bra', 'BraA06t24068Z' => 'bra', 'BraA06t27032Z' => 'bra', 'BraA08t35176Z' => 'bra', 'BraA09t36680Z' => 'bra', 'BraA10t44471Z' => 'bra', 'C02p06760' => 'bna', 'C02p06890' => 'bna', 'C02p07010' => 'bna', 'C03p07660' => 'bna', 'C05p10300' => 'bna', 'C06p38150' => 'bna', 'C07p36650' => 'bna', 'C08p15770' => 'bna', 'C09p12300' => 'bna', 'C09p62700' => 'bna', 'C09p75040' => 'bna', 'CAN.G13.1' => 'can', 'CAN.G138.4' => 'can', 'CAN.G44.6' => 'can', 'CAN.G473.19' => 'can', 'CANSAT01G0835' => 'cansat', 'CANSAT11G0246' => 'cansat', 'CANSAT11G1766' => 'cansat', 'CANSAT64G1954' => 'cansat', 'CARHR013330' => 'chi', 'CARHR060530' => 'chi', 'CARHR075300' => 'chi', 'CARHR105120' => 'chi', 'CARHR148910' => 'chi', 'CARHR198830' => 'chi', 'Carub.0001s1275' => 'cru', 'Carub.0002s1437' => 'cru', 'Carub.0003s0044' => 'cru', 'Carub.0003s2787' => 'cru', 'Carub.0005s0597' => 'cru', 'Carub.0006s1266' => 'cru', 'Ca_06935_v3' => 'car', 'Ca_13559_v3' => 'car', 'Ca_16941_v3' => 'car', 'Ca_16960_v3' => 'car', 'Ca_17775_v3' => 'car', 'Ca_30464_v3' => 'car', 'Cc06_g08160' => 'ccan', 'Cc07_g01520' => 'ccan', 'Cc11_g15810' => 'ccan', 'CDE02G2840' => 'cde', 'CDE03G0093' => 'cde', 'CDE04G2127' => 'cde', 'CDE07G1857' => 'cde', 'CDE09G1246' => 'cde', 'Cfa003412' => 'cfa', 'Cfa007341' => 'cfa', 'Cfa009220' => 'cfa', 'Ciclev10008737m.g' => 'ccl', 'Ciclev10015565m.g' => 'ccl', 'Ciclev10031761m.g' => 'ccl', 'CiPaw.03G045300' => 'cil', 'CiPaw.03G247200' => 'cil', 'CiPaw.04G029500' => 'cil', 'CiPaw.04G174000' => 'cil', 'CiPaw.05G181200' => 'cil', 'CiPaw.06G067100' => 'cil', 'ClCG05G025800' => 'cla', 'ClCG06G011400' => 'cla', 'ClCG09G019360' => 'cla', 'COL.COLO4_04827' => 'col', 'COL.COLO4_29170' => 'col', 'COL.COLO4_35131' => 'col', 'COL.COLO4_35132' => 'col', 'Cpa.g.sc33.32' => 'cpa', 'Cpa.g.sc46.29' => 'cpa', 'Cpa.g.sc796.1' => 'cpa', 'CsaV3_1G030420' => 'csa', 'CsaV3_5G027050' => 'csa', 'CsaV3_5G031040' => 'csa', 'CsaV3_UNG023130' => 'csa', 'CSS0007726' => 'camsi', 'CSS0016433' => 'camsi', 'CSS0017656' => 'camsi', 'CSS0025364' => 'camsi', 'CSS0027582' => 'camsi', 'CSS0047288' => 'camsi', 'CSS0049950' => 'camsi', 'DCAR_003843' => 'dca', 'DCAR_007052' => 'dca', 'DCAR_020884' => 'dca', 'DCAR_021730' => 'dca', 'DCAR_024423' => 'dca', 'DCAR_026509' => 'dca', 'DCAR_031158' => 'dca', 'Dinv14728' => 'din', 'Dinv15219' => 'din', 'Dinv25728' => 'din', 'Dinv33428' => 'din', 'Dinv36489' => 'din', 'Dinv41486' => 'din', 'Duzib147G0469' => 'dzi', 'Duzib168G0060' => 'dzi', 'Duzib187G1215' => 'dzi', 'Duzib248G0692' => 'dzi', 'Duzib251G0767' => 'dzi', 'Duzib264G0446' => 'dzi', 'Duzib268G0691' => 'dzi', 'ECA232G4767' => 'eca', 'ECA233G2838' => 'eca', 'ECA234G0391' => 'eca', 'ECA234G0857' => 'eca', 'ECA236G1593' => 'eca', 'ECA238G0565' => 'eca', 'ECA246G1027' => 'eca', 'ECA246G3223' => 'eca', 'ECA246G3470' => 'eca', 'EL10Ac6g13829' => 'bvu', 'EL10Ac6g14093' => 'bvu', 'EL10Ac8g18707' => 'bvu', 'Eucgr.C01369' => 'egr', 'Eucgr.H02492' => 'egr', 'Eucgr.I01733' => 'egr', 'Eucgr.J02255' => 'egr', 'Eucgr.J02257' => 'egr', 'Eucgr.J02258' => 'egr', 'FAN02G1601' => 'fan', 'FAN03G1586' => 'fan', 'FAN03G2986' => 'fan', 'FAN05G4837' => 'fan', 'FAN06G0146' => 'fan', 'FAN07G0858' => 'fan', 'FAN09G3179' => 'fan', 'FAN10G0669' => 'fan', 'FAN12G2358' => 'fan', 'FAN14G4198' => 'fan', 'FAN14G5112' => 'fan', 'FAN17G0342' => 'fan', 'FAN19G0342' => 'fan', 'FAN19G0962' => 'fan', 'FAN19G1101' => 'fan', 'FAN19G1872' => 'fan', 'FAN22G0356' => 'fan', 'FAN23G0744' => 'fan', 'FAN23G1914' => 'fan', 'FAN26G0032' => 'fan', 'FAN28G0625' => 'fan', 'FvH4_1g02710' => 'fve', 'FvH4_1g02720' => 'fve', 'FvH4_4g25670' => 'fve', 'FvH4_6g51700' => 'fve', 'FvH4_7g20170' => 'fve', 'Glyma.05G175000' => 'gma', 'Glyma.08G132300' => 'gma', 'Glyma.11G243000' => 'gma', 'Glyma.13G158900' => 'gma', 'Glyma.17G112400' => 'gma', 'Glyma.18G014100' => 'gma', 'Glyma.19G003100' => 'gma', 'Glyma.19G056500' => 'gma', 'Gohir.A01G158900' => 'ghi', 'Gohir.A05G312600' => 'ghi', 'Gohir.A05G354900' => 'ghi', 'Gohir.A07G037200' => 'ghi', 'Gohir.A09G030000' => 'ghi', 'Gohir.A12G145200' => 'ghi', 'Gohir.D01G151500' => 'ghi', 'Gohir.D04G058300' => 'ghi', 'Gohir.D05G314100' => 'ghi', 'Gohir.D07G041400' => 'ghi', 'Gohir.D09G029700' => 'ghi', 'Gohir.D12G149700' => 'ghi', 'Gorai.001G043800' => 'gra', 'Gorai.002G187800' => 'gra', 'Gorai.006G034700' => 'gra', 'Gorai.008G161200' => 'gra', 'Gorai.009G335700' => 'gra', 'Gorai.012G065000' => 'gra', 'GSVIVG01000535001' => 'vvi', 'GSVIVG01015572001' => 'vvi', 'GSVIVG01032386001' => 'vvi', 'HanXRQChr05g0138531' => 'han', 'HanXRQChr06g0174391' => 'han', 'HanXRQChr07g0199021' => 'han', 'HanXRQChr08g0208211' => 'han', 'HanXRQChr09g0255471' => 'han', 'HanXRQChr10g0315791' => 'han', 'HanXRQChr12g0371991' => 'han', 'HanXRQChr15g0475251' => 'han', 'HanXRQChr17g0540001' => 'han', 'HanXRQChr17g0548631' => 'han', 'HanXRQChr17g0569561' => 'han', 'Haze_12256' => 'cav', 'Haze_14756' => 'cav', 'Haze_25528' => 'cav', 'Hma1.2p1_0079F.1_g041020' => 'hma', 'Hma1.2p1_0818F.1_g223260' => 'hma', 'Hma1.2p1_1747F.1_g300530' => 'hma', 'HPP92_004607' => 'vpl', 'HPP92_004608' => 'vpl', 'HPP92_006181' => 'vpl', 'HPP92_012192' => 'vpl', 'HPP92_015680' => 'vpl', 'HPP92_020249' => 'vpl', 'HPP92_021376' => 'vpl', 'HPP92_024275' => 'vpl', 'Hund06031' => 'sun', 'Hund25391' => 'sun', 'Lalb_Chr07g0185371' => 'lal', 'Lalb_Chr07g0185381' => 'lal', 'Lalb_Chr12g0204011' => 'lal', 'Lalb_Chr13g0301671' => 'lal', 'Lalb_Chr14g0362851' => 'lal', 'Lalb_Chr24g0403581' => 'lal', 'Lj1g0000233' => 'lja', 'Lj2g0018120' => 'lja', 'Lj3C621T0' => 'lonja', 'Lj3P1059T14' => 'lonja', 'Lj3P611T9' => 'lonja', 'Lj3P614T13' => 'lonja', 'Lj3P615T5' => 'lonja', 'Lj4g0012315' => 'lja', 'Lj4g0026182' => 'lja', 'Lj6P813T16' => 'lonja', 'Lj7C427T7' => 'lonja', 'Lj7C427T8' => 'lonja', 'Lj7P600T41' => 'lonja', 'Lju41C42G17' => 'lonja', 'Lsat_1_v5_gn_0_47300' => 'lsa', 'Lsat_1_v5_gn_2_91280' => 'lsa', 'Lsat_1_v5_gn_3_30561' => 'lsa', 'Lsat_1_v5_gn_4_184321' => 'lsa', 'Lsat_1_v5_gn_4_4041' => 'lsa', 'Lsat_1_v5_gn_5_92000' => 'lsa', 'Lsat_1_v5_gn_8_152940' => 'lsa', 'Lsat_1_v5_gn_8_62401' => 'lsa', 'Manes.06G055900' => 'mes', 'Manes.12G022200' => 'mes', 'Manes.13G023300' => 'mes', 'Manes.14G115000' => 'mes', 'Manes.15G151700' => 'mes', 'Manes.17G111300' => 'mes', 'Mapoly0226s0009' => 'mpo', 'MBI02_g25363_MAGBIO' => 'mbi', 'MBI06_g00027_MAGBIO' => 'mbi', 'MBI10_g13034_MAGBIO' => 'mbi', 'MD09G1023400' => 'mdo', 'MD13G1100100' => 'mdo', 'MD15G1169200' => 'mdo', 'MD16G1101100' => 'mdo', 'MD17G1022900' => 'mdo', 'Medtr3g096150' => 'mtr', 'Medtr4g115070' => 'mtr', 'Medtr7g033325' => 'mtr', 'Medtr8g089840' => 'mtr', 'MELO3C010319.2' => 'cme', 'MELO3C011944.2' => 'cme', 'MELO3C021589.2' => 'cme', 'Migut.E00207' => 'egut', 'Migut.H00067' => 'egut', 'Migut.K00433' => 'egut', 'Migut.K00606' => 'egut', 'Migut.K01410' => 'egut', 'MSTRG.13347' => 'ama', 'MSTRG.24045' => 'ama', 'MSTRG.2428' => 'ama', 'MSTRG.26410' => 'ama', 'MSTRG.3139' => 'ama', 'MSTRG.3286' => 'ama', 'MSTRG.563' => 'ama', 'MSTRG.7941' => 'ama', 'Nitab4.5_0000028g0060' => 'nta', 'Nitab4.5_0000065g0260' => 'nta', 'Nitab4.5_0000112g0060' => 'nta', 'Nitab4.5_0000489g0120' => 'nta', 'Nitab4.5_0001776g0050' => 'nta', 'Nitab4.5_0001854g0010' => 'nta', 'Nitab4.5_0001860g0020' => 'nta', 'Nitab4.5_0004352g0010' => 'nta', 'Nitab4.5_0008716g0020' => 'nta', 'Nitab4.5_0008922g0010' => 'nta', 'Nn3g16693' => 'nnu', 'Nn4g22596' => 'nnu', 'Nn7g37639' => 'nnu', 'Oeu001701.1' => 'oeu', 'Oeu018149.1' => 'oeu', 'Oeu026220.1' => 'oeu', 'Oeu038635.1' => 'oeu', 'Oeu049176.1' => 'oeu', 'Oeu056706.1' => 'oeu', 'Oeu056937.1' => 'oeu', 'Oeu057540.1' => 'oeu', 'Os02g0594900' => 'osa', 'Os02g0595100' => 'osa', 'Os04g0477500' => 'osa', 'Os12g0611900' => 'osa', 'Peaxi162Scf00076g00020' => 'pax', 'Peaxi162Scf00128g00217' => 'pax', 'Peaxi162Scf00129g01640' => 'pax', 'Peaxi162Scf00669g00007' => 'pax', 'Peaxi162Scf00700g00421' => 'pax', 'Peaxi162Scf00801g00038' => 'pax', 'Peaxi162Scf00891g00025' => 'pax', 'PGR083G0909' => 'pgr', 'PGR119G1005' => 'pgr', 'PGR142G2236' => 'pgr', 'PGR142G3388' => 'pgr', 'PGSC0003DMG400004514' => 'stu', 'PGSC0003DMG400012635' => 'stu', 'PGSC0003DMG400015730' => 'stu', 'PGSC0003DMG400018611' => 'stu', 'PGSC0003DMG400030897' => 'stu', 'Phvul.001G254800' => 'pvu', 'Phvul.002G260100' => 'pvu', 'Phvul.003G167600' => 'pvu', 'Phvul.004G005100' => 'pvu', 'Potri.001G343600' => 'ptr', 'Potri.006G066700' => 'ptr', 'Potri.008G186000' => 'ptr', 'Potri.010G046900' => 'ptr', 'Potri.018G127900' => 'ptr', 'Pp3c20_17750' => 'ppa', 'Pp3c24_4380' => 'ppa', 'Prupe.1G245800' => 'ppe', 'Prupe.3G293400' => 'ppe', 'Prupe.7G247400' => 'ppe', 'Psat0s145g0120' => 'psa', 'Psat0s595g0040' => 'psa', 'Psat0s595g0120' => 'psa', 'Psat3g175040' => 'psa', 'Psat7g058120' => 'psa', 'PSO017G0428' => 'pso', 'PSO063G7510' => 'pso', 'PSO067G0046' => 'pso', 'PSO478G1073' => 'pso', 'PSO675G3677' => 'pso', 'PSO675G6558' => 'pso', 'PSO675G7520' => 'pso', 'PSO675G8959' => 'pso', 'QL02p074089' => 'qlo', 'QL02p089614' => 'qlo', 'QL03p057736' => 'qlo', 'RcHm_v2.0_Chr1g0364131' => 'rch', 'RcHm_v2.0_Chr2g0087801' => 'rch', 'RcHm_v2.0_Chr2g0087821' => 'rch', 'RcHm_v2.0_Chr2g0173231' => 'rch', 'RcHm_v2.0_Chr4g0433111' => 'rch', 'Rhsim03G0250300' => 'rsi', 'Rhsim08G0048400' => 'rsi', 'Rhsim10G0014800' => 'rsi', 'Rhsim12G0040100' => 'rsi', 'Rhsim12G0109700' => 'rsi', 'Sabra06G0049600' => 'sbr', 'Sabra08G0141000' => 'sbr', 'Sabra10G0021400' => 'sbr', 'Sabra16G0222900' => 'sbr', 'Sabra18G0108600' => 'sbr', 'SalBow1G0433' => 'sbo', 'SalBow1G2038' => 'sbo', 'SalBow1G5003' => 'sbo', 'SalBow7G1197' => 'sbo', 'SalBow8G3506' => 'sbo', 'Sc03g0007300' => 'sci', 'Sc11g0000950' => 'sci', 'Sc14g0008750' => 'sci', 'Sc18g0000420' => 'sci', 'Sed0006754' => 'sed', 'Sed0008741' => 'sed', 'Sed0017172' => 'sed', 'Sed0018925' => 'sed', 'Sed0023326' => 'sed', 'Sed0025909' => 'sed', 'SEGI_05333' => 'sgi', 'SEGI_10362' => 'sgi', 'SEGI_13380' => 'sgi', 'SEGI_24306' => 'sgi', 'SEGI_29077' => 'sgi', 'SEGI_29095' => 'sgi', 'SEGI_36534' => 'sgi', 'SEGI_37506' => 'sgi', 'SEGI_38321' => 'sgi', 'SGA_v2.0_scaffold307G48031' => 'sas', 'SGA_v2.0_scaffold47G17507' => 'sas', 'SGA_v2.0_scaffold63G21736' => 'sas', 'SGA_v2.0_scaffold87G27070' => 'sas', 'SHI17794' => 'shi', 'SHI28851' => 'shi', 'SMO165G0155' => 'smo', 'SMO340G0217' => 'smo', 'SMO367G1210' => 'smo', 'Solyc02g093430.3' => 'sly', 'Solyc05g013580.4' => 'sly', 'Solyc07g008030.3' => 'sly', 'Solyc12g035470.2' => 'sly', 'Sopen02g038020' => 'spe', 'Sopen05g008490' => 'spe', 'Sopen07g003910' => 'spe', 'Sopen12g015240' => 'spe', 'Sp1g11550' => 'spa', 'Sp2g16710' => 'spa', 'Sp3g00430' => 'spa', 'Sp3g26780' => 'spa', 'Sp5g22900' => 'spa', 'Sp6g29530' => 'spa', 'TAR371G0794' => 'tar', 'TAR374G0164' => 'tar', 'TAR622G0165' => 'tar', 'TAR626G0929' => 'tar', 'TAR629G2155' => 'tar', 'THA.LOC104805282' => 'tha', 'THA.LOC104805363' => 'tha', 'THA.LOC104808968' => 'tha', 'THA.LOC104821093' => 'tha', 'THA.LOC104823953' => 'tha', 'THA.LOC104825562' => 'tha', 'THA.LOC104825665' => 'tha', 'Thecc.02G261400' => 'tca', 'Thecc.04G019200' => 'tca', 'Thecc.09G130400' => 'tca', 'Thhalv10004374m.g' => 'esa', 'Thhalv10007850m.g' => 'esa', 'Thhalv10013782m.g' => 'esa', 'Thhalv10018686m.g' => 'esa', 'Thhalv10020899m.g' => 'esa', 'Thhalv10022755m.g' => 'esa', 'TPR.G23851' => 'tpr', 'TPR.G26500' => 'tpr', 'TPR.G27267' => 'tpr', 'TPR.G32001' => 'tpr', 'TPR.G6251' => 'tpr', 'TPR.G8167' => 'tpr', 'TWI12G1330' => 'twi', 'TWI18G1239' => 'twi', 'TWI34G0979' => 'twi', 'TWI36G0670' => 'twi', 'TWI36G0707' => 'twi', 'TWI56G0233' => 'twi', 'TWI75G1809' => 'twi', 'unitig_21.g20874' => 'ugi', 'unitig_26.g10343' => 'ugi', 'unitig_46.g18392' => 'ugi', 'unitig_52.g17178' => 'ugi', 'unitig_8.g2934' => 'ugi', 'vmacro01122' => 'vma', 'vmacro05875' => 'vma', 'vmacro06147' => 'vma', 'vmacro16191' => 'vma', 'vmacro18293' => 'vma', 'VMungo0251G3707' => 'vmu', 'VMungo0464G1521' => 'vmu', 'VMungo1215G0205' => 'vmu', 'VMungo1383G2484' => 'vmu', 'Zm00001eb079610' => 'zma', 'Zm00001eb135990' => 'zma', 'Zm00001eb183710' => 'zma', 'Zm00001eb246020' => 'zma' ), 'gf_id' => 'HOM05D001124', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001124' ), 'data_identifier' => 'HOM05D001124', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001124', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '548', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02520' => 'bna', 'A03p06630' => 'bna', 'A05p44460' => 'bna', 'A06p08710' => 'bna', 'A06p41090' => 'bna', 'A07p32320' => 'bna', 'A08p32520' => 'bna', 'A09p10360' => 'bna', 'A10p24080' => 'bna', 'Aa31LG11G15250' => 'aar', 'Aa31LG1G1800' => 'aar', 'Aa31LG2G5120' => 'aar', 'Aa31LG2G6070' => 'aar', 'Aa31LG5G10770' => 'aar', 'Aa31sc61G90' => 'aar', 'Actinidia01352' => 'ach', 'Actinidia05983' => 'ach', 'Actinidia08133' => 'ach', 'Actinidia15101' => 'ach', 'Actinidia26379' => 'ach', 'Actinidia35778' => 'ach', 'Actinidia36123' => 'ach', 'Actinidia37436' => 'ach', 'Actinidia38730' => 'ach', 'Ah.02g128210' => 'amhyb', 'Ah.03g132990' => 'amhyb', 'Ah.14g079410' => 'amhyb', 'AL1G24640' => 'aly', 'AL2G26680' => 'aly', 'AL3G10530' => 'aly', 'AL3G45230' => 'aly', 'AL5G15230' => 'aly', 'AL5G16960' => 'aly', 'AL6G25210' => 'aly', 'Aqoxy2G00441' => 'aox', 'Aqoxy3G01236' => 'aox', 'Aqoxy5G03746' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3RQ047' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C7GMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9C8JER' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MBL6KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YXCZ83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZANX40' => 'arhy', 'AT1G12990' => 'ath', 'AT1G67880' => 'ath', 'AT2G13290' => 'ath', 'AT3G01620' => 'ath', 'AT3G26445' => 'ath', 'AT3G27540' => 'ath', 'AT5G14480' => 'ath', 'ATR0824G026' => 'atr', 'ATR1098G019' => 'atr', 'Atru.chr11.2145' => 'acertr', 'Atru.chr2.3636' => 'acertr', 'Atru.chr2.3644' => 'acertr', 'Atru.chr6.2422' => 'acertr', 'Atru.chr7.1112' => 'acertr', 'AUR62005469' => 'cqu', 'AUR62011166' => 'cqu', 'AUR62013319' => 'cqu', 'AUR62024273' => 'cqu', 'AUR62028420' => 'cqu', 'AUR62041942' => 'cqu', 'BcaB01g04969' => 'bca', 'BcaB01g06371' => 'bca', 'BcaB02g11494' => 'bca', 'BcaB03g15382' => 'bca', 'BcaB08g36994' => 'bca', 'BcaC03g13477' => 'bca', 'BcaC03g13478' => 'bca', 'BcaC03g13480' => 'bca', 'BcaC03g13481' => 'bca', 'BcaC03g13486' => 'bca', 'BcaC04g19031' => 'bca', 'BcaC04g23085' => 'bca', 'BcaC05g25094' => 'bca', 'BcaC05g25096' => 'bca', 'BcaC05g25138' => 'bca', 'BcaC05g30416' => 'bca', 'BcaC05g30455' => 'bca', 'BcaC06g30979' => 'bca', 'BcaC06g33805' => 'bca', 'BcaC08g46021' => 'bca', 'BcaNung03154' => 'bca', 'BolC2t06623H' => 'bol', 'BolC2t06632H' => 'bol', 'BolC2t06635H' => 'bol', 'BolC2t06638H' => 'bol', 'BolC3t13266H' => 'bol', 'BolC5t29776H' => 'bol', 'BolC6t38912H' => 'bol', 'BolC7t44183H' => 'bol', 'BolC9t54123H' => 'bol', 'BolC9t59107H' => 'bol', 'BraA02t05221Z' => 'bra', 'BraA03t09996Z' => 'bra', 'BraA05t23210Z' => 'bra', 'BraA06t24068Z' => 'bra', 'BraA06t27032Z' => 'bra', 'BraA08t35176Z' => 'bra', 'BraA09t36680Z' => 'bra', 'BraA10t44471Z' => 'bra', 'C02p06760' => 'bna', 'C02p06890' => 'bna', 'C02p07010' => 'bna', 'C03p07660' => 'bna', 'C05p10300' => 'bna', 'C06p38150' => 'bna', 'C07p36650' => 'bna', 'C08p15770' => 'bna', 'C09p12300' => 'bna', 'C09p62700' => 'bna', 'C09p75040' => 'bna', 'CAN.G13.1' => 'can', 'CAN.G138.4' => 'can', 'CAN.G44.6' => 'can', 'CAN.G473.19' => 'can', 'CANSAT01G0835' => 'cansat', 'CANSAT11G0246' => 'cansat', 'CANSAT11G1766' => 'cansat', 'CANSAT64G1954' => 'cansat', 'CARHR013330' => 'chi', 'CARHR060530' => 'chi', 'CARHR075300' => 'chi', 'CARHR105120' => 'chi', 'CARHR148910' => 'chi', 'CARHR198830' => 'chi', 'Carub.0001s1275' => 'cru', 'Carub.0002s1437' => 'cru', 'Carub.0003s0044' => 'cru', 'Carub.0003s2787' => 'cru', 'Carub.0005s0597' => 'cru', 'Carub.0006s1266' => 'cru', 'Ca_06935_v3' => 'car', 'Ca_13559_v3' => 'car', 'Ca_16941_v3' => 'car', 'Ca_16960_v3' => 'car', 'Ca_17775_v3' => 'car', 'Ca_30464_v3' => 'car', 'Cc06_g08160' => 'ccan', 'Cc07_g01520' => 'ccan', 'Cc11_g15810' => 'ccan', 'CDE02G2840' => 'cde', 'CDE03G0093' => 'cde', 'CDE04G2127' => 'cde', 'CDE07G1857' => 'cde', 'CDE09G1246' => 'cde', 'Cfa003412' => 'cfa', 'Cfa007341' => 'cfa', 'Cfa009220' => 'cfa', 'Ciclev10008737m.g' => 'ccl', 'Ciclev10015565m.g' => 'ccl', 'Ciclev10031761m.g' => 'ccl', 'CiPaw.03G045300' => 'cil', 'CiPaw.03G247200' => 'cil', 'CiPaw.04G029500' => 'cil', 'CiPaw.04G174000' => 'cil', 'CiPaw.05G181200' => 'cil', 'CiPaw.06G067100' => 'cil', 'ClCG05G025800' => 'cla', 'ClCG06G011400' => 'cla', 'ClCG09G019360' => 'cla', 'COL.COLO4_04827' => 'col', 'COL.COLO4_29170' => 'col', 'COL.COLO4_35131' => 'col', 'COL.COLO4_35132' => 'col', 'Cpa.g.sc33.32' => 'cpa', 'Cpa.g.sc46.29' => 'cpa', 'Cpa.g.sc796.1' => 'cpa', 'CsaV3_1G030420' => 'csa', 'CsaV3_5G027050' => 'csa', 'CsaV3_5G031040' => 'csa', 'CsaV3_UNG023130' => 'csa', 'CSS0007726' => 'camsi', 'CSS0016433' => 'camsi', 'CSS0017656' => 'camsi', 'CSS0025364' => 'camsi', 'CSS0027582' => 'camsi', 'CSS0047288' => 'camsi', 'CSS0049950' => 'camsi', 'DCAR_003843' => 'dca', 'DCAR_007052' => 'dca', 'DCAR_020884' => 'dca', 'DCAR_021730' => 'dca', 'DCAR_024423' => 'dca', 'DCAR_026509' => 'dca', 'DCAR_031158' => 'dca', 'Dinv14728' => 'din', 'Dinv15219' => 'din', 'Dinv25728' => 'din', 'Dinv33428' => 'din', 'Dinv36489' => 'din', 'Dinv41486' => 'din', 'Duzib147G0469' => 'dzi', 'Duzib168G0060' => 'dzi', 'Duzib187G1215' => 'dzi', 'Duzib248G0692' => 'dzi', 'Duzib251G0767' => 'dzi', 'Duzib264G0446' => 'dzi', 'Duzib268G0691' => 'dzi', 'ECA232G4767' => 'eca', 'ECA233G2838' => 'eca', 'ECA234G0391' => 'eca', 'ECA234G0857' => 'eca', 'ECA236G1593' => 'eca', 'ECA238G0565' => 'eca', 'ECA246G1027' => 'eca', 'ECA246G3223' => 'eca', 'ECA246G3470' => 'eca', 'EL10Ac6g13829' => 'bvu', 'EL10Ac6g14093' => 'bvu', 'EL10Ac8g18707' => 'bvu', 'Eucgr.C01369' => 'egr', 'Eucgr.H02492' => 'egr', 'Eucgr.I01733' => 'egr', 'Eucgr.J02255' => 'egr', 'Eucgr.J02257' => 'egr', 'Eucgr.J02258' => 'egr', 'FAN02G1601' => 'fan', 'FAN03G1586' => 'fan', 'FAN03G2986' => 'fan', 'FAN05G4837' => 'fan', 'FAN06G0146' => 'fan', 'FAN07G0858' => 'fan', 'FAN09G3179' => 'fan', 'FAN10G0669' => 'fan', 'FAN12G2358' => 'fan', 'FAN14G4198' => 'fan', 'FAN14G5112' => 'fan', 'FAN17G0342' => 'fan', 'FAN19G0342' => 'fan', 'FAN19G0962' => 'fan', 'FAN19G1101' => 'fan', 'FAN19G1872' => 'fan', 'FAN22G0356' => 'fan', 'FAN23G0744' => 'fan', 'FAN23G1914' => 'fan', 'FAN26G0032' => 'fan', 'FAN28G0625' => 'fan', 'FvH4_1g02710' => 'fve', 'FvH4_1g02720' => 'fve', 'FvH4_4g25670' => 'fve', 'FvH4_6g51700' => 'fve', 'FvH4_7g20170' => 'fve', 'Glyma.05G175000' => 'gma', 'Glyma.08G132300' => 'gma', 'Glyma.11G243000' => 'gma', 'Glyma.13G158900' => 'gma', 'Glyma.17G112400' => 'gma', 'Glyma.18G014100' => 'gma', 'Glyma.19G003100' => 'gma', 'Glyma.19G056500' => 'gma', 'Gohir.A01G158900' => 'ghi', 'Gohir.A05G312600' => 'ghi', 'Gohir.A05G354900' => 'ghi', 'Gohir.A07G037200' => 'ghi', 'Gohir.A09G030000' => 'ghi', 'Gohir.A12G145200' => 'ghi', 'Gohir.D01G151500' => 'ghi', 'Gohir.D04G058300' => 'ghi', 'Gohir.D05G314100' => 'ghi', 'Gohir.D07G041400' => 'ghi', 'Gohir.D09G029700' => 'ghi', 'Gohir.D12G149700' => 'ghi', 'Gorai.001G043800' => 'gra', 'Gorai.002G187800' => 'gra', 'Gorai.006G034700' => 'gra', 'Gorai.008G161200' => 'gra', 'Gorai.009G335700' => 'gra', 'Gorai.012G065000' => 'gra', 'GSVIVG01000535001' => 'vvi', 'GSVIVG01015572001' => 'vvi', 'GSVIVG01032386001' => 'vvi', 'HanXRQChr05g0138531' => 'han', 'HanXRQChr06g0174391' => 'han', 'HanXRQChr07g0199021' => 'han', 'HanXRQChr08g0208211' => 'han', 'HanXRQChr09g0255471' => 'han', 'HanXRQChr10g0315791' => 'han', 'HanXRQChr12g0371991' => 'han', 'HanXRQChr15g0475251' => 'han', 'HanXRQChr17g0540001' => 'han', 'HanXRQChr17g0548631' => 'han', 'HanXRQChr17g0569561' => 'han', 'Haze_12256' => 'cav', 'Haze_14756' => 'cav', 'Haze_25528' => 'cav', 'Hma1.2p1_0079F.1_g041020' => 'hma', 'Hma1.2p1_0818F.1_g223260' => 'hma', 'Hma1.2p1_1747F.1_g300530' => 'hma', 'HPP92_004607' => 'vpl', 'HPP92_004608' => 'vpl', 'HPP92_006181' => 'vpl', 'HPP92_012192' => 'vpl', 'HPP92_015680' => 'vpl', 'HPP92_020249' => 'vpl', 'HPP92_021376' => 'vpl', 'HPP92_024275' => 'vpl', 'Hund06031' => 'sun', 'Hund25391' => 'sun', 'Lalb_Chr07g0185371' => 'lal', 'Lalb_Chr07g0185381' => 'lal', 'Lalb_Chr12g0204011' => 'lal', 'Lalb_Chr13g0301671' => 'lal', 'Lalb_Chr14g0362851' => 'lal', 'Lalb_Chr24g0403581' => 'lal', 'Lj1g0000233' => 'lja', 'Lj2g0018120' => 'lja', 'Lj3C621T0' => 'lonja', 'Lj3P1059T14' => 'lonja', 'Lj3P611T9' => 'lonja', 'Lj3P614T13' => 'lonja', 'Lj3P615T5' => 'lonja', 'Lj4g0012315' => 'lja', 'Lj4g0026182' => 'lja', 'Lj6P813T16' => 'lonja', 'Lj7C427T7' => 'lonja', 'Lj7C427T8' => 'lonja', 'Lj7P600T41' => 'lonja', 'Lju41C42G17' => 'lonja', 'Lsat_1_v5_gn_0_47300' => 'lsa', 'Lsat_1_v5_gn_2_91280' => 'lsa', 'Lsat_1_v5_gn_3_30561' => 'lsa', 'Lsat_1_v5_gn_4_184321' => 'lsa', 'Lsat_1_v5_gn_4_4041' => 'lsa', 'Lsat_1_v5_gn_5_92000' => 'lsa', 'Lsat_1_v5_gn_8_152940' => 'lsa', 'Lsat_1_v5_gn_8_62401' => 'lsa', 'Manes.06G055900' => 'mes', 'Manes.12G022200' => 'mes', 'Manes.13G023300' => 'mes', 'Manes.14G115000' => 'mes', 'Manes.15G151700' => 'mes', 'Manes.17G111300' => 'mes', 'Mapoly0226s0009' => 'mpo', 'MBI02_g25363_MAGBIO' => 'mbi', 'MBI06_g00027_MAGBIO' => 'mbi', 'MBI10_g13034_MAGBIO' => 'mbi', 'MD09G1023400' => 'mdo', 'MD13G1100100' => 'mdo', 'MD15G1169200' => 'mdo', 'MD16G1101100' => 'mdo', 'MD17G1022900' => 'mdo', 'Medtr3g096150' => 'mtr', 'Medtr4g115070' => 'mtr', 'Medtr7g033325' => 'mtr', 'Medtr8g089840' => 'mtr', 'MELO3C010319.2' => 'cme', 'MELO3C011944.2' => 'cme', 'MELO3C021589.2' => 'cme', 'Migut.E00207' => 'egut', 'Migut.H00067' => 'egut', 'Migut.K00433' => 'egut', 'Migut.K00606' => 'egut', 'Migut.K01410' => 'egut', 'MSTRG.13347' => 'ama', 'MSTRG.24045' => 'ama', 'MSTRG.2428' => 'ama', 'MSTRG.26410' => 'ama', 'MSTRG.3139' => 'ama', 'MSTRG.3286' => 'ama', 'MSTRG.563' => 'ama', 'MSTRG.7941' => 'ama', 'Nitab4.5_0000028g0060' => 'nta', 'Nitab4.5_0000065g0260' => 'nta', 'Nitab4.5_0000112g0060' => 'nta', 'Nitab4.5_0000489g0120' => 'nta', 'Nitab4.5_0001776g0050' => 'nta', 'Nitab4.5_0001854g0010' => 'nta', 'Nitab4.5_0001860g0020' => 'nta', 'Nitab4.5_0004352g0010' => 'nta', 'Nitab4.5_0008716g0020' => 'nta', 'Nitab4.5_0008922g0010' => 'nta', 'Nn3g16693' => 'nnu', 'Nn4g22596' => 'nnu', 'Nn7g37639' => 'nnu', 'Oeu001701.1' => 'oeu', 'Oeu018149.1' => 'oeu', 'Oeu026220.1' => 'oeu', 'Oeu038635.1' => 'oeu', 'Oeu049176.1' => 'oeu', 'Oeu056706.1' => 'oeu', 'Oeu056937.1' => 'oeu', 'Oeu057540.1' => 'oeu', 'Os02g0594900' => 'osa', 'Os02g0595100' => 'osa', 'Os04g0477500' => 'osa', 'Os12g0611900' => 'osa', 'Peaxi162Scf00076g00020' => 'pax', 'Peaxi162Scf00128g00217' => 'pax', 'Peaxi162Scf00129g01640' => 'pax', 'Peaxi162Scf00669g00007' => 'pax', 'Peaxi162Scf00700g00421' => 'pax', 'Peaxi162Scf00801g00038' => 'pax', 'Peaxi162Scf00891g00025' => 'pax', 'PGR083G0909' => 'pgr', 'PGR119G1005' => 'pgr', 'PGR142G2236' => 'pgr', 'PGR142G3388' => 'pgr', 'PGSC0003DMG400004514' => 'stu', 'PGSC0003DMG400012635' => 'stu', 'PGSC0003DMG400015730' => 'stu', 'PGSC0003DMG400018611' => 'stu', 'PGSC0003DMG400030897' => 'stu', 'Phvul.001G254800' => 'pvu', 'Phvul.002G260100' => 'pvu', 'Phvul.003G167600' => 'pvu', 'Phvul.004G005100' => 'pvu', 'Potri.001G343600' => 'ptr', 'Potri.006G066700' => 'ptr', 'Potri.008G186000' => 'ptr', 'Potri.010G046900' => 'ptr', 'Potri.018G127900' => 'ptr', 'Pp3c20_17750' => 'ppa', 'Pp3c24_4380' => 'ppa', 'Prupe.1G245800' => 'ppe', 'Prupe.3G293400' => 'ppe', 'Prupe.7G247400' => 'ppe', 'Psat0s145g0120' => 'psa', 'Psat0s595g0040' => 'psa', 'Psat0s595g0120' => 'psa', 'Psat3g175040' => 'psa', 'Psat7g058120' => 'psa', 'PSO017G0428' => 'pso', 'PSO063G7510' => 'pso', 'PSO067G0046' => 'pso', 'PSO478G1073' => 'pso', 'PSO675G3677' => 'pso', 'PSO675G6558' => 'pso', 'PSO675G7520' => 'pso', 'PSO675G8959' => 'pso', 'QL02p074089' => 'qlo', 'QL02p089614' => 'qlo', 'QL03p057736' => 'qlo', 'RcHm_v2.0_Chr1g0364131' => 'rch', 'RcHm_v2.0_Chr2g0087801' => 'rch', 'RcHm_v2.0_Chr2g0087821' => 'rch', 'RcHm_v2.0_Chr2g0173231' => 'rch', 'RcHm_v2.0_Chr4g0433111' => 'rch', 'Rhsim03G0250300' => 'rsi', 'Rhsim08G0048400' => 'rsi', 'Rhsim10G0014800' => 'rsi', 'Rhsim12G0040100' => 'rsi', 'Rhsim12G0109700' => 'rsi', 'Sabra06G0049600' => 'sbr', 'Sabra08G0141000' => 'sbr', 'Sabra10G0021400' => 'sbr', 'Sabra16G0222900' => 'sbr', 'Sabra18G0108600' => 'sbr', 'SalBow1G0433' => 'sbo', 'SalBow1G2038' => 'sbo', 'SalBow1G5003' => 'sbo', 'SalBow7G1197' => 'sbo', 'SalBow8G3506' => 'sbo', 'Sc03g0007300' => 'sci', 'Sc11g0000950' => 'sci', 'Sc14g0008750' => 'sci', 'Sc18g0000420' => 'sci', 'Sed0006754' => 'sed', 'Sed0008741' => 'sed', 'Sed0017172' => 'sed', 'Sed0018925' => 'sed', 'Sed0023326' => 'sed', 'Sed0025909' => 'sed', 'SEGI_05333' => 'sgi', 'SEGI_10362' => 'sgi', 'SEGI_13380' => 'sgi', 'SEGI_24306' => 'sgi', 'SEGI_29077' => 'sgi', 'SEGI_29095' => 'sgi', 'SEGI_36534' => 'sgi', 'SEGI_37506' => 'sgi', 'SEGI_38321' => 'sgi', 'SGA_v2.0_scaffold307G48031' => 'sas', 'SGA_v2.0_scaffold47G17507' => 'sas', 'SGA_v2.0_scaffold63G21736' => 'sas', 'SGA_v2.0_scaffold87G27070' => 'sas', 'SHI17794' => 'shi', 'SHI28851' => 'shi', 'SMO165G0155' => 'smo', 'SMO340G0217' => 'smo', 'SMO367G1210' => 'smo', 'Solyc02g093430.3' => 'sly', 'Solyc05g013580.4' => 'sly', 'Solyc07g008030.3' => 'sly', 'Solyc12g035470.2' => 'sly', 'Sopen02g038020' => 'spe', 'Sopen05g008490' => 'spe', 'Sopen07g003910' => 'spe', 'Sopen12g015240' => 'spe', 'Sp1g11550' => 'spa', 'Sp2g16710' => 'spa', 'Sp3g00430' => 'spa', 'Sp3g26780' => 'spa', 'Sp5g22900' => 'spa', 'Sp6g29530' => 'spa', 'TAR371G0794' => 'tar', 'TAR374G0164' => 'tar', 'TAR622G0165' => 'tar', 'TAR626G0929' => 'tar', 'TAR629G2155' => 'tar', 'THA.LOC104805282' => 'tha', 'THA.LOC104805363' => 'tha', 'THA.LOC104808968' => 'tha', 'THA.LOC104821093' => 'tha', 'THA.LOC104823953' => 'tha', 'THA.LOC104825562' => 'tha', 'THA.LOC104825665' => 'tha', 'Thecc.02G261400' => 'tca', 'Thecc.04G019200' => 'tca', 'Thecc.09G130400' => 'tca', 'Thhalv10004374m.g' => 'esa', 'Thhalv10007850m.g' => 'esa', 'Thhalv10013782m.g' => 'esa', 'Thhalv10018686m.g' => 'esa', 'Thhalv10020899m.g' => 'esa', 'Thhalv10022755m.g' => 'esa', 'TPR.G23851' => 'tpr', 'TPR.G26500' => 'tpr', 'TPR.G27267' => 'tpr', 'TPR.G32001' => 'tpr', 'TPR.G6251' => 'tpr', 'TPR.G8167' => 'tpr', 'TWI12G1330' => 'twi', 'TWI18G1239' => 'twi', 'TWI34G0979' => 'twi', 'TWI36G0670' => 'twi', 'TWI36G0707' => 'twi', 'TWI56G0233' => 'twi', 'TWI75G1809' => 'twi', 'unitig_21.g20874' => 'ugi', 'unitig_26.g10343' => 'ugi', 'unitig_46.g18392' => 'ugi', 'unitig_52.g17178' => 'ugi', 'unitig_8.g2934' => 'ugi', 'vmacro01122' => 'vma', 'vmacro05875' => 'vma', 'vmacro06147' => 'vma', 'vmacro16191' => 'vma', 'vmacro18293' => 'vma', 'VMungo0251G3707' => 'vmu', 'VMungo0464G1521' => 'vmu', 'VMungo1215G0205' => 'vmu', 'VMungo1383G2484' => 'vmu', 'Zm00001eb079610' => 'zma', 'Zm00001eb135990' => 'zma', 'Zm00001eb183710' => 'zma', 'Zm00001eb246020' => 'zma' ) $gf_id = 'HOM05D001124' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001124' ) $data_identifier = 'HOM05D001124' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 6, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 7, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 21, 'bol' => (int) 10, 'bra' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 6, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 9, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 21, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 8, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 10, 'lsa' => (int) 8, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 8, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 9, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb246020' $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' => 'HOM05D001124', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '548', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02520' => 'bna', 'A03p06630' => 'bna', 'A05p44460' => 'bna', 'A06p08710' => 'bna', 'A06p41090' => 'bna', 'A07p32320' => 'bna', 'A08p32520' => 'bna', 'A09p10360' => 'bna', 'A10p24080' => 'bna', 'Aa31LG11G15250' => 'aar', 'Aa31LG1G1800' => 'aar', 'Aa31LG2G5120' => 'aar', 'Aa31LG2G6070' => 'aar', 'Aa31LG5G10770' => 'aar', 'Aa31sc61G90' => 'aar', 'Actinidia01352' => 'ach', 'Actinidia05983' => 'ach', 'Actinidia08133' => 'ach', 'Actinidia15101' => 'ach', 'Actinidia26379' => 'ach', 'Actinidia35778' => 'ach', 'Actinidia36123' => 'ach', 'Actinidia37436' => 'ach', 'Actinidia38730' => 'ach', 'Ah.02g128210' => 'amhyb', 'Ah.03g132990' => 'amhyb', 'Ah.14g079410' => 'amhyb', 'AL1G24640' => 'aly', 'AL2G26680' => 'aly', 'AL3G10530' => 'aly', 'AL3G45230' => 'aly', 'AL5G15230' => 'aly', 'AL5G16960' => 'aly', 'AL6G25210' => 'aly', 'Aqoxy2G00441' => 'aox', 'Aqoxy3G01236' => 'aox', 'Aqoxy5G03746' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3RQ047' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C7GMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9C8JER' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MBL6KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YXCZ83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZANX40' => 'arhy', 'AT1G12990' => 'ath', 'AT1G67880' => 'ath', 'AT2G13290' => 'ath', 'AT3G01620' => 'ath', 'AT3G26445' => 'ath', 'AT3G27540' => 'ath', 'AT5G14480' => 'ath', 'ATR0824G026' => 'atr', 'ATR1098G019' => 'atr', 'Atru.chr11.2145' => 'acertr', 'Atru.chr2.3636' => 'acertr', 'Atru.chr2.3644' => 'acertr', 'Atru.chr6.2422' => 'acertr', 'Atru.chr7.1112' => 'acertr', 'AUR62005469' => 'cqu', 'AUR62011166' => 'cqu', 'AUR62013319' => 'cqu', 'AUR62024273' => 'cqu', 'AUR62028420' => 'cqu', 'AUR62041942' => 'cqu', 'BcaB01g04969' => 'bca', 'BcaB01g06371' => 'bca', 'BcaB02g11494' => 'bca', 'BcaB03g15382' => 'bca', 'BcaB08g36994' => 'bca', 'BcaC03g13477' => 'bca', 'BcaC03g13478' => 'bca', 'BcaC03g13480' => 'bca', 'BcaC03g13481' => 'bca', 'BcaC03g13486' => 'bca', 'BcaC04g19031' => 'bca', 'BcaC04g23085' => 'bca', 'BcaC05g25094' => 'bca', 'BcaC05g25096' => 'bca', 'BcaC05g25138' => 'bca', 'BcaC05g30416' => 'bca', 'BcaC05g30455' => 'bca', 'BcaC06g30979' => 'bca', 'BcaC06g33805' => 'bca', 'BcaC08g46021' => 'bca', 'BcaNung03154' => 'bca', 'BolC2t06623H' => 'bol', 'BolC2t06632H' => 'bol', 'BolC2t06635H' => 'bol', 'BolC2t06638H' => 'bol', 'BolC3t13266H' => 'bol', 'BolC5t29776H' => 'bol', 'BolC6t38912H' => 'bol', 'BolC7t44183H' => 'bol', 'BolC9t54123H' => 'bol', 'BolC9t59107H' => 'bol', 'BraA02t05221Z' => 'bra', 'BraA03t09996Z' => 'bra', 'BraA05t23210Z' => 'bra', 'BraA06t24068Z' => 'bra', 'BraA06t27032Z' => 'bra', 'BraA08t35176Z' => 'bra', 'BraA09t36680Z' => 'bra', 'BraA10t44471Z' => 'bra', 'C02p06760' => 'bna', 'C02p06890' => 'bna', 'C02p07010' => 'bna', 'C03p07660' => 'bna', 'C05p10300' => 'bna', 'C06p38150' => 'bna', 'C07p36650' => 'bna', 'C08p15770' => 'bna', 'C09p12300' => 'bna', 'C09p62700' => 'bna', 'C09p75040' => 'bna', 'CAN.G13.1' => 'can', 'CAN.G138.4' => 'can', 'CAN.G44.6' => 'can', 'CAN.G473.19' => 'can', 'CANSAT01G0835' => 'cansat', 'CANSAT11G0246' => 'cansat', 'CANSAT11G1766' => 'cansat', 'CANSAT64G1954' => 'cansat', 'CARHR013330' => 'chi', 'CARHR060530' => 'chi', 'CARHR075300' => 'chi', 'CARHR105120' => 'chi', 'CARHR148910' => 'chi', 'CARHR198830' => 'chi', 'Carub.0001s1275' => 'cru', 'Carub.0002s1437' => 'cru', 'Carub.0003s0044' => 'cru', 'Carub.0003s2787' => 'cru', 'Carub.0005s0597' => 'cru', 'Carub.0006s1266' => 'cru', 'Ca_06935_v3' => 'car', 'Ca_13559_v3' => 'car', 'Ca_16941_v3' => 'car', 'Ca_16960_v3' => 'car', 'Ca_17775_v3' => 'car', 'Ca_30464_v3' => 'car', 'Cc06_g08160' => 'ccan', 'Cc07_g01520' => 'ccan', 'Cc11_g15810' => 'ccan', 'CDE02G2840' => 'cde', 'CDE03G0093' => 'cde', 'CDE04G2127' => 'cde', 'CDE07G1857' => 'cde', 'CDE09G1246' => 'cde', 'Cfa003412' => 'cfa', 'Cfa007341' => 'cfa', 'Cfa009220' => 'cfa', 'Ciclev10008737m.g' => 'ccl', 'Ciclev10015565m.g' => 'ccl', 'Ciclev10031761m.g' => 'ccl', 'CiPaw.03G045300' => 'cil', 'CiPaw.03G247200' => 'cil', 'CiPaw.04G029500' => 'cil', 'CiPaw.04G174000' => 'cil', 'CiPaw.05G181200' => 'cil', 'CiPaw.06G067100' => 'cil', 'ClCG05G025800' => 'cla', 'ClCG06G011400' => 'cla', 'ClCG09G019360' => 'cla', 'COL.COLO4_04827' => 'col', 'COL.COLO4_29170' => 'col', 'COL.COLO4_35131' => 'col', 'COL.COLO4_35132' => 'col', 'Cpa.g.sc33.32' => 'cpa', 'Cpa.g.sc46.29' => 'cpa', 'Cpa.g.sc796.1' => 'cpa', 'CsaV3_1G030420' => 'csa', 'CsaV3_5G027050' => 'csa', 'CsaV3_5G031040' => 'csa', 'CsaV3_UNG023130' => 'csa', 'CSS0007726' => 'camsi', 'CSS0016433' => 'camsi', 'CSS0017656' => 'camsi', 'CSS0025364' => 'camsi', 'CSS0027582' => 'camsi', 'CSS0047288' => 'camsi', 'CSS0049950' => 'camsi', 'DCAR_003843' => 'dca', 'DCAR_007052' => 'dca', 'DCAR_020884' => 'dca', 'DCAR_021730' => 'dca', 'DCAR_024423' => 'dca', 'DCAR_026509' => 'dca', 'DCAR_031158' => 'dca', 'Dinv14728' => 'din', 'Dinv15219' => 'din', 'Dinv25728' => 'din', 'Dinv33428' => 'din', 'Dinv36489' => 'din', 'Dinv41486' => 'din', 'Duzib147G0469' => 'dzi', 'Duzib168G0060' => 'dzi', 'Duzib187G1215' => 'dzi', 'Duzib248G0692' => 'dzi', 'Duzib251G0767' => 'dzi', 'Duzib264G0446' => 'dzi', 'Duzib268G0691' => 'dzi', 'ECA232G4767' => 'eca', 'ECA233G2838' => 'eca', 'ECA234G0391' => 'eca', 'ECA234G0857' => 'eca', 'ECA236G1593' => 'eca', 'ECA238G0565' => 'eca', 'ECA246G1027' => 'eca', 'ECA246G3223' => 'eca', 'ECA246G3470' => 'eca', 'EL10Ac6g13829' => 'bvu', 'EL10Ac6g14093' => 'bvu', 'EL10Ac8g18707' => 'bvu', 'Eucgr.C01369' => 'egr', 'Eucgr.H02492' => 'egr', 'Eucgr.I01733' => 'egr', 'Eucgr.J02255' => 'egr', 'Eucgr.J02257' => 'egr', 'Eucgr.J02258' => 'egr', 'FAN02G1601' => 'fan', 'FAN03G1586' => 'fan', 'FAN03G2986' => 'fan', 'FAN05G4837' => 'fan', 'FAN06G0146' => 'fan', 'FAN07G0858' => 'fan', 'FAN09G3179' => 'fan', 'FAN10G0669' => 'fan', 'FAN12G2358' => 'fan', 'FAN14G4198' => 'fan', 'FAN14G5112' => 'fan', 'FAN17G0342' => 'fan', 'FAN19G0342' => 'fan', 'FAN19G0962' => 'fan', 'FAN19G1101' => 'fan', 'FAN19G1872' => 'fan', 'FAN22G0356' => 'fan', 'FAN23G0744' => 'fan', 'FAN23G1914' => 'fan', 'FAN26G0032' => 'fan', 'FAN28G0625' => 'fan', 'FvH4_1g02710' => 'fve', 'FvH4_1g02720' => 'fve', 'FvH4_4g25670' => 'fve', 'FvH4_6g51700' => 'fve', 'FvH4_7g20170' => 'fve', 'Glyma.05G175000' => 'gma', 'Glyma.08G132300' => 'gma', 'Glyma.11G243000' => 'gma', 'Glyma.13G158900' => 'gma', 'Glyma.17G112400' => 'gma', 'Glyma.18G014100' => 'gma', 'Glyma.19G003100' => 'gma', 'Glyma.19G056500' => 'gma', 'Gohir.A01G158900' => 'ghi', 'Gohir.A05G312600' => 'ghi', 'Gohir.A05G354900' => 'ghi', 'Gohir.A07G037200' => 'ghi', 'Gohir.A09G030000' => 'ghi', 'Gohir.A12G145200' => 'ghi', 'Gohir.D01G151500' => 'ghi', 'Gohir.D04G058300' => 'ghi', 'Gohir.D05G314100' => 'ghi', 'Gohir.D07G041400' => 'ghi', 'Gohir.D09G029700' => 'ghi', 'Gohir.D12G149700' => 'ghi', 'Gorai.001G043800' => 'gra', 'Gorai.002G187800' => 'gra', 'Gorai.006G034700' => 'gra', 'Gorai.008G161200' => 'gra', 'Gorai.009G335700' => 'gra', 'Gorai.012G065000' => 'gra', 'GSVIVG01000535001' => 'vvi', 'GSVIVG01015572001' => 'vvi', 'GSVIVG01032386001' => 'vvi', 'HanXRQChr05g0138531' => 'han', 'HanXRQChr06g0174391' => 'han', 'HanXRQChr07g0199021' => 'han', 'HanXRQChr08g0208211' => 'han', 'HanXRQChr09g0255471' => 'han', 'HanXRQChr10g0315791' => 'han', 'HanXRQChr12g0371991' => 'han', 'HanXRQChr15g0475251' => 'han', 'HanXRQChr17g0540001' => 'han', 'HanXRQChr17g0548631' => 'han', 'HanXRQChr17g0569561' => 'han', 'Haze_12256' => 'cav', 'Haze_14756' => 'cav', 'Haze_25528' => 'cav', 'Hma1.2p1_0079F.1_g041020' => 'hma', 'Hma1.2p1_0818F.1_g223260' => 'hma', 'Hma1.2p1_1747F.1_g300530' => 'hma', 'HPP92_004607' => 'vpl', 'HPP92_004608' => 'vpl', 'HPP92_006181' => 'vpl', 'HPP92_012192' => 'vpl', 'HPP92_015680' => 'vpl', 'HPP92_020249' => 'vpl', 'HPP92_021376' => 'vpl', 'HPP92_024275' => 'vpl', 'Hund06031' => 'sun', 'Hund25391' => 'sun', 'Lalb_Chr07g0185371' => 'lal', 'Lalb_Chr07g0185381' => 'lal', 'Lalb_Chr12g0204011' => 'lal', 'Lalb_Chr13g0301671' => 'lal', 'Lalb_Chr14g0362851' => 'lal', 'Lalb_Chr24g0403581' => 'lal', 'Lj1g0000233' => 'lja', 'Lj2g0018120' => 'lja', 'Lj3C621T0' => 'lonja', 'Lj3P1059T14' => 'lonja', 'Lj3P611T9' => 'lonja', 'Lj3P614T13' => 'lonja', 'Lj3P615T5' => 'lonja', 'Lj4g0012315' => 'lja', 'Lj4g0026182' => 'lja', 'Lj6P813T16' => 'lonja', 'Lj7C427T7' => 'lonja', 'Lj7C427T8' => 'lonja', 'Lj7P600T41' => 'lonja', 'Lju41C42G17' => 'lonja', 'Lsat_1_v5_gn_0_47300' => 'lsa', 'Lsat_1_v5_gn_2_91280' => 'lsa', 'Lsat_1_v5_gn_3_30561' => 'lsa', 'Lsat_1_v5_gn_4_184321' => 'lsa', 'Lsat_1_v5_gn_4_4041' => 'lsa', 'Lsat_1_v5_gn_5_92000' => 'lsa', 'Lsat_1_v5_gn_8_152940' => 'lsa', 'Lsat_1_v5_gn_8_62401' => 'lsa', 'Manes.06G055900' => 'mes', 'Manes.12G022200' => 'mes', 'Manes.13G023300' => 'mes', 'Manes.14G115000' => 'mes', 'Manes.15G151700' => 'mes', 'Manes.17G111300' => 'mes', 'Mapoly0226s0009' => 'mpo', 'MBI02_g25363_MAGBIO' => 'mbi', 'MBI06_g00027_MAGBIO' => 'mbi', 'MBI10_g13034_MAGBIO' => 'mbi', 'MD09G1023400' => 'mdo', 'MD13G1100100' => 'mdo', 'MD15G1169200' => 'mdo', 'MD16G1101100' => 'mdo', 'MD17G1022900' => 'mdo', 'Medtr3g096150' => 'mtr', 'Medtr4g115070' => 'mtr', 'Medtr7g033325' => 'mtr', 'Medtr8g089840' => 'mtr', 'MELO3C010319.2' => 'cme', 'MELO3C011944.2' => 'cme', 'MELO3C021589.2' => 'cme', 'Migut.E00207' => 'egut', 'Migut.H00067' => 'egut', 'Migut.K00433' => 'egut', 'Migut.K00606' => 'egut', 'Migut.K01410' => 'egut', 'MSTRG.13347' => 'ama', 'MSTRG.24045' => 'ama', 'MSTRG.2428' => 'ama', 'MSTRG.26410' => 'ama', 'MSTRG.3139' => 'ama', 'MSTRG.3286' => 'ama', 'MSTRG.563' => 'ama', 'MSTRG.7941' => 'ama', 'Nitab4.5_0000028g0060' => 'nta', 'Nitab4.5_0000065g0260' => 'nta', 'Nitab4.5_0000112g0060' => 'nta', 'Nitab4.5_0000489g0120' => 'nta', 'Nitab4.5_0001776g0050' => 'nta', 'Nitab4.5_0001854g0010' => 'nta', 'Nitab4.5_0001860g0020' => 'nta', 'Nitab4.5_0004352g0010' => 'nta', 'Nitab4.5_0008716g0020' => 'nta', 'Nitab4.5_0008922g0010' => 'nta', 'Nn3g16693' => 'nnu', 'Nn4g22596' => 'nnu', 'Nn7g37639' => 'nnu', 'Oeu001701.1' => 'oeu', 'Oeu018149.1' => 'oeu', 'Oeu026220.1' => 'oeu', 'Oeu038635.1' => 'oeu', 'Oeu049176.1' => 'oeu', 'Oeu056706.1' => 'oeu', 'Oeu056937.1' => 'oeu', 'Oeu057540.1' => 'oeu', 'Os02g0594900' => 'osa', 'Os02g0595100' => 'osa', 'Os04g0477500' => 'osa', 'Os12g0611900' => 'osa', 'Peaxi162Scf00076g00020' => 'pax', 'Peaxi162Scf00128g00217' => 'pax', 'Peaxi162Scf00129g01640' => 'pax', 'Peaxi162Scf00669g00007' => 'pax', 'Peaxi162Scf00700g00421' => 'pax', 'Peaxi162Scf00801g00038' => 'pax', 'Peaxi162Scf00891g00025' => 'pax', 'PGR083G0909' => 'pgr', 'PGR119G1005' => 'pgr', 'PGR142G2236' => 'pgr', 'PGR142G3388' => 'pgr', 'PGSC0003DMG400004514' => 'stu', 'PGSC0003DMG400012635' => 'stu', 'PGSC0003DMG400015730' => 'stu', 'PGSC0003DMG400018611' => 'stu', 'PGSC0003DMG400030897' => 'stu', 'Phvul.001G254800' => 'pvu', 'Phvul.002G260100' => 'pvu', 'Phvul.003G167600' => 'pvu', 'Phvul.004G005100' => 'pvu', 'Potri.001G343600' => 'ptr', 'Potri.006G066700' => 'ptr', 'Potri.008G186000' => 'ptr', 'Potri.010G046900' => 'ptr', 'Potri.018G127900' => 'ptr', 'Pp3c20_17750' => 'ppa', 'Pp3c24_4380' => 'ppa', 'Prupe.1G245800' => 'ppe', 'Prupe.3G293400' => 'ppe', 'Prupe.7G247400' => 'ppe', 'Psat0s145g0120' => 'psa', 'Psat0s595g0040' => 'psa', 'Psat0s595g0120' => 'psa', 'Psat3g175040' => 'psa', 'Psat7g058120' => 'psa', 'PSO017G0428' => 'pso', 'PSO063G7510' => 'pso', 'PSO067G0046' => 'pso', 'PSO478G1073' => 'pso', 'PSO675G3677' => 'pso', 'PSO675G6558' => 'pso', 'PSO675G7520' => 'pso', 'PSO675G8959' => 'pso', 'QL02p074089' => 'qlo', 'QL02p089614' => 'qlo', 'QL03p057736' => 'qlo', 'RcHm_v2.0_Chr1g0364131' => 'rch', 'RcHm_v2.0_Chr2g0087801' => 'rch', 'RcHm_v2.0_Chr2g0087821' => 'rch', 'RcHm_v2.0_Chr2g0173231' => 'rch', 'RcHm_v2.0_Chr4g0433111' => 'rch', 'Rhsim03G0250300' => 'rsi', 'Rhsim08G0048400' => 'rsi', 'Rhsim10G0014800' => 'rsi', 'Rhsim12G0040100' => 'rsi', 'Rhsim12G0109700' => 'rsi', 'Sabra06G0049600' => 'sbr', 'Sabra08G0141000' => 'sbr', 'Sabra10G0021400' => 'sbr', 'Sabra16G0222900' => 'sbr', 'Sabra18G0108600' => 'sbr', 'SalBow1G0433' => 'sbo', 'SalBow1G2038' => 'sbo', 'SalBow1G5003' => 'sbo', 'SalBow7G1197' => 'sbo', 'SalBow8G3506' => 'sbo', 'Sc03g0007300' => 'sci', 'Sc11g0000950' => 'sci', 'Sc14g0008750' => 'sci', 'Sc18g0000420' => 'sci', 'Sed0006754' => 'sed', 'Sed0008741' => 'sed', 'Sed0017172' => 'sed', 'Sed0018925' => 'sed', 'Sed0023326' => 'sed', 'Sed0025909' => 'sed', 'SEGI_05333' => 'sgi', 'SEGI_10362' => 'sgi', 'SEGI_13380' => 'sgi', 'SEGI_24306' => 'sgi', 'SEGI_29077' => 'sgi', 'SEGI_29095' => 'sgi', 'SEGI_36534' => 'sgi', 'SEGI_37506' => 'sgi', 'SEGI_38321' => 'sgi', 'SGA_v2.0_scaffold307G48031' => 'sas', 'SGA_v2.0_scaffold47G17507' => 'sas', 'SGA_v2.0_scaffold63G21736' => 'sas', 'SGA_v2.0_scaffold87G27070' => 'sas', 'SHI17794' => 'shi', 'SHI28851' => 'shi', 'SMO165G0155' => 'smo', 'SMO340G0217' => 'smo', 'SMO367G1210' => 'smo', 'Solyc02g093430.3' => 'sly', 'Solyc05g013580.4' => 'sly', 'Solyc07g008030.3' => 'sly', 'Solyc12g035470.2' => 'sly', 'Sopen02g038020' => 'spe', 'Sopen05g008490' => 'spe', 'Sopen07g003910' => 'spe', 'Sopen12g015240' => 'spe', 'Sp1g11550' => 'spa', 'Sp2g16710' => 'spa', 'Sp3g00430' => 'spa', 'Sp3g26780' => 'spa', 'Sp5g22900' => 'spa', 'Sp6g29530' => 'spa', 'TAR371G0794' => 'tar', 'TAR374G0164' => 'tar', 'TAR622G0165' => 'tar', 'TAR626G0929' => 'tar', 'TAR629G2155' => 'tar', 'THA.LOC104805282' => 'tha', 'THA.LOC104805363' => 'tha', 'THA.LOC104808968' => 'tha', 'THA.LOC104821093' => 'tha', 'THA.LOC104823953' => 'tha', 'THA.LOC104825562' => 'tha', 'THA.LOC104825665' => 'tha', 'Thecc.02G261400' => 'tca', 'Thecc.04G019200' => 'tca', 'Thecc.09G130400' => 'tca', 'Thhalv10004374m.g' => 'esa', 'Thhalv10007850m.g' => 'esa', 'Thhalv10013782m.g' => 'esa', 'Thhalv10018686m.g' => 'esa', 'Thhalv10020899m.g' => 'esa', 'Thhalv10022755m.g' => 'esa', 'TPR.G23851' => 'tpr', 'TPR.G26500' => 'tpr', 'TPR.G27267' => 'tpr', 'TPR.G32001' => 'tpr', 'TPR.G6251' => 'tpr', 'TPR.G8167' => 'tpr', 'TWI12G1330' => 'twi', 'TWI18G1239' => 'twi', 'TWI34G0979' => 'twi', 'TWI36G0670' => 'twi', 'TWI36G0707' => 'twi', 'TWI56G0233' => 'twi', 'TWI75G1809' => 'twi', 'unitig_21.g20874' => 'ugi', 'unitig_26.g10343' => 'ugi', 'unitig_46.g18392' => 'ugi', 'unitig_52.g17178' => 'ugi', 'unitig_8.g2934' => 'ugi', 'vmacro01122' => 'vma', 'vmacro05875' => 'vma', 'vmacro06147' => 'vma', 'vmacro16191' => 'vma', 'vmacro18293' => 'vma', 'VMungo0251G3707' => 'vmu', 'VMungo0464G1521' => 'vmu', 'VMungo1215G0205' => 'vmu', 'VMungo1383G2484' => 'vmu', 'Zm00001eb079610' => 'zma', 'Zm00001eb135990' => 'zma', 'Zm00001eb183710' => 'zma', 'Zm00001eb246020' => 'zma' ), 'gf_id' => 'HOM05D001124', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001124' ), 'data_identifier' => 'HOM05D001124', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001124', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '548', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02520' => 'bna', 'A03p06630' => 'bna', 'A05p44460' => 'bna', 'A06p08710' => 'bna', 'A06p41090' => 'bna', 'A07p32320' => 'bna', 'A08p32520' => 'bna', 'A09p10360' => 'bna', 'A10p24080' => 'bna', 'Aa31LG11G15250' => 'aar', 'Aa31LG1G1800' => 'aar', 'Aa31LG2G5120' => 'aar', 'Aa31LG2G6070' => 'aar', 'Aa31LG5G10770' => 'aar', 'Aa31sc61G90' => 'aar', 'Actinidia01352' => 'ach', 'Actinidia05983' => 'ach', 'Actinidia08133' => 'ach', 'Actinidia15101' => 'ach', 'Actinidia26379' => 'ach', 'Actinidia35778' => 'ach', 'Actinidia36123' => 'ach', 'Actinidia37436' => 'ach', 'Actinidia38730' => 'ach', 'Ah.02g128210' => 'amhyb', 'Ah.03g132990' => 'amhyb', 'Ah.14g079410' => 'amhyb', 'AL1G24640' => 'aly', 'AL2G26680' => 'aly', 'AL3G10530' => 'aly', 'AL3G45230' => 'aly', 'AL5G15230' => 'aly', 'AL5G16960' => 'aly', 'AL6G25210' => 'aly', 'Aqoxy2G00441' => 'aox', 'Aqoxy3G01236' => 'aox', 'Aqoxy5G03746' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3RQ047' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C7GMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9C8JER' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MBL6KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YXCZ83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZANX40' => 'arhy', 'AT1G12990' => 'ath', 'AT1G67880' => 'ath', 'AT2G13290' => 'ath', 'AT3G01620' => 'ath', 'AT3G26445' => 'ath', 'AT3G27540' => 'ath', 'AT5G14480' => 'ath', 'ATR0824G026' => 'atr', 'ATR1098G019' => 'atr', 'Atru.chr11.2145' => 'acertr', 'Atru.chr2.3636' => 'acertr', 'Atru.chr2.3644' => 'acertr', 'Atru.chr6.2422' => 'acertr', 'Atru.chr7.1112' => 'acertr', 'AUR62005469' => 'cqu', 'AUR62011166' => 'cqu', 'AUR62013319' => 'cqu', 'AUR62024273' => 'cqu', 'AUR62028420' => 'cqu', 'AUR62041942' => 'cqu', 'BcaB01g04969' => 'bca', 'BcaB01g06371' => 'bca', 'BcaB02g11494' => 'bca', 'BcaB03g15382' => 'bca', 'BcaB08g36994' => 'bca', 'BcaC03g13477' => 'bca', 'BcaC03g13478' => 'bca', 'BcaC03g13480' => 'bca', 'BcaC03g13481' => 'bca', 'BcaC03g13486' => 'bca', 'BcaC04g19031' => 'bca', 'BcaC04g23085' => 'bca', 'BcaC05g25094' => 'bca', 'BcaC05g25096' => 'bca', 'BcaC05g25138' => 'bca', 'BcaC05g30416' => 'bca', 'BcaC05g30455' => 'bca', 'BcaC06g30979' => 'bca', 'BcaC06g33805' => 'bca', 'BcaC08g46021' => 'bca', 'BcaNung03154' => 'bca', 'BolC2t06623H' => 'bol', 'BolC2t06632H' => 'bol', 'BolC2t06635H' => 'bol', 'BolC2t06638H' => 'bol', 'BolC3t13266H' => 'bol', 'BolC5t29776H' => 'bol', 'BolC6t38912H' => 'bol', 'BolC7t44183H' => 'bol', 'BolC9t54123H' => 'bol', 'BolC9t59107H' => 'bol', 'BraA02t05221Z' => 'bra', 'BraA03t09996Z' => 'bra', 'BraA05t23210Z' => 'bra', 'BraA06t24068Z' => 'bra', 'BraA06t27032Z' => 'bra', 'BraA08t35176Z' => 'bra', 'BraA09t36680Z' => 'bra', 'BraA10t44471Z' => 'bra', 'C02p06760' => 'bna', 'C02p06890' => 'bna', 'C02p07010' => 'bna', 'C03p07660' => 'bna', 'C05p10300' => 'bna', 'C06p38150' => 'bna', 'C07p36650' => 'bna', 'C08p15770' => 'bna', 'C09p12300' => 'bna', 'C09p62700' => 'bna', 'C09p75040' => 'bna', 'CAN.G13.1' => 'can', 'CAN.G138.4' => 'can', 'CAN.G44.6' => 'can', 'CAN.G473.19' => 'can', 'CANSAT01G0835' => 'cansat', 'CANSAT11G0246' => 'cansat', 'CANSAT11G1766' => 'cansat', 'CANSAT64G1954' => 'cansat', 'CARHR013330' => 'chi', 'CARHR060530' => 'chi', 'CARHR075300' => 'chi', 'CARHR105120' => 'chi', 'CARHR148910' => 'chi', 'CARHR198830' => 'chi', 'Carub.0001s1275' => 'cru', 'Carub.0002s1437' => 'cru', 'Carub.0003s0044' => 'cru', 'Carub.0003s2787' => 'cru', 'Carub.0005s0597' => 'cru', 'Carub.0006s1266' => 'cru', 'Ca_06935_v3' => 'car', 'Ca_13559_v3' => 'car', 'Ca_16941_v3' => 'car', 'Ca_16960_v3' => 'car', 'Ca_17775_v3' => 'car', 'Ca_30464_v3' => 'car', 'Cc06_g08160' => 'ccan', 'Cc07_g01520' => 'ccan', 'Cc11_g15810' => 'ccan', 'CDE02G2840' => 'cde', 'CDE03G0093' => 'cde', 'CDE04G2127' => 'cde', 'CDE07G1857' => 'cde', 'CDE09G1246' => 'cde', 'Cfa003412' => 'cfa', 'Cfa007341' => 'cfa', 'Cfa009220' => 'cfa', 'Ciclev10008737m.g' => 'ccl', 'Ciclev10015565m.g' => 'ccl', 'Ciclev10031761m.g' => 'ccl', 'CiPaw.03G045300' => 'cil', 'CiPaw.03G247200' => 'cil', 'CiPaw.04G029500' => 'cil', 'CiPaw.04G174000' => 'cil', 'CiPaw.05G181200' => 'cil', 'CiPaw.06G067100' => 'cil', 'ClCG05G025800' => 'cla', 'ClCG06G011400' => 'cla', 'ClCG09G019360' => 'cla', 'COL.COLO4_04827' => 'col', 'COL.COLO4_29170' => 'col', 'COL.COLO4_35131' => 'col', 'COL.COLO4_35132' => 'col', 'Cpa.g.sc33.32' => 'cpa', 'Cpa.g.sc46.29' => 'cpa', 'Cpa.g.sc796.1' => 'cpa', 'CsaV3_1G030420' => 'csa', 'CsaV3_5G027050' => 'csa', 'CsaV3_5G031040' => 'csa', 'CsaV3_UNG023130' => 'csa', 'CSS0007726' => 'camsi', 'CSS0016433' => 'camsi', 'CSS0017656' => 'camsi', 'CSS0025364' => 'camsi', 'CSS0027582' => 'camsi', 'CSS0047288' => 'camsi', 'CSS0049950' => 'camsi', 'DCAR_003843' => 'dca', 'DCAR_007052' => 'dca', 'DCAR_020884' => 'dca', 'DCAR_021730' => 'dca', 'DCAR_024423' => 'dca', 'DCAR_026509' => 'dca', 'DCAR_031158' => 'dca', 'Dinv14728' => 'din', 'Dinv15219' => 'din', 'Dinv25728' => 'din', 'Dinv33428' => 'din', 'Dinv36489' => 'din', 'Dinv41486' => 'din', 'Duzib147G0469' => 'dzi', 'Duzib168G0060' => 'dzi', 'Duzib187G1215' => 'dzi', 'Duzib248G0692' => 'dzi', 'Duzib251G0767' => 'dzi', 'Duzib264G0446' => 'dzi', 'Duzib268G0691' => 'dzi', 'ECA232G4767' => 'eca', 'ECA233G2838' => 'eca', 'ECA234G0391' => 'eca', 'ECA234G0857' => 'eca', 'ECA236G1593' => 'eca', 'ECA238G0565' => 'eca', 'ECA246G1027' => 'eca', 'ECA246G3223' => 'eca', 'ECA246G3470' => 'eca', 'EL10Ac6g13829' => 'bvu', 'EL10Ac6g14093' => 'bvu', 'EL10Ac8g18707' => 'bvu', 'Eucgr.C01369' => 'egr', 'Eucgr.H02492' => 'egr', 'Eucgr.I01733' => 'egr', 'Eucgr.J02255' => 'egr', 'Eucgr.J02257' => 'egr', 'Eucgr.J02258' => 'egr', 'FAN02G1601' => 'fan', 'FAN03G1586' => 'fan', 'FAN03G2986' => 'fan', 'FAN05G4837' => 'fan', 'FAN06G0146' => 'fan', 'FAN07G0858' => 'fan', 'FAN09G3179' => 'fan', 'FAN10G0669' => 'fan', 'FAN12G2358' => 'fan', 'FAN14G4198' => 'fan', 'FAN14G5112' => 'fan', 'FAN17G0342' => 'fan', 'FAN19G0342' => 'fan', 'FAN19G0962' => 'fan', 'FAN19G1101' => 'fan', 'FAN19G1872' => 'fan', 'FAN22G0356' => 'fan', 'FAN23G0744' => 'fan', 'FAN23G1914' => 'fan', 'FAN26G0032' => 'fan', 'FAN28G0625' => 'fan', 'FvH4_1g02710' => 'fve', 'FvH4_1g02720' => 'fve', 'FvH4_4g25670' => 'fve', 'FvH4_6g51700' => 'fve', 'FvH4_7g20170' => 'fve', 'Glyma.05G175000' => 'gma', 'Glyma.08G132300' => 'gma', 'Glyma.11G243000' => 'gma', 'Glyma.13G158900' => 'gma', 'Glyma.17G112400' => 'gma', 'Glyma.18G014100' => 'gma', 'Glyma.19G003100' => 'gma', 'Glyma.19G056500' => 'gma', 'Gohir.A01G158900' => 'ghi', 'Gohir.A05G312600' => 'ghi', 'Gohir.A05G354900' => 'ghi', 'Gohir.A07G037200' => 'ghi', 'Gohir.A09G030000' => 'ghi', 'Gohir.A12G145200' => 'ghi', 'Gohir.D01G151500' => 'ghi', 'Gohir.D04G058300' => 'ghi', 'Gohir.D05G314100' => 'ghi', 'Gohir.D07G041400' => 'ghi', 'Gohir.D09G029700' => 'ghi', 'Gohir.D12G149700' => 'ghi', 'Gorai.001G043800' => 'gra', 'Gorai.002G187800' => 'gra', 'Gorai.006G034700' => 'gra', 'Gorai.008G161200' => 'gra', 'Gorai.009G335700' => 'gra', 'Gorai.012G065000' => 'gra', 'GSVIVG01000535001' => 'vvi', 'GSVIVG01015572001' => 'vvi', 'GSVIVG01032386001' => 'vvi', 'HanXRQChr05g0138531' => 'han', 'HanXRQChr06g0174391' => 'han', 'HanXRQChr07g0199021' => 'han', 'HanXRQChr08g0208211' => 'han', 'HanXRQChr09g0255471' => 'han', 'HanXRQChr10g0315791' => 'han', 'HanXRQChr12g0371991' => 'han', 'HanXRQChr15g0475251' => 'han', 'HanXRQChr17g0540001' => 'han', 'HanXRQChr17g0548631' => 'han', 'HanXRQChr17g0569561' => 'han', 'Haze_12256' => 'cav', 'Haze_14756' => 'cav', 'Haze_25528' => 'cav', 'Hma1.2p1_0079F.1_g041020' => 'hma', 'Hma1.2p1_0818F.1_g223260' => 'hma', 'Hma1.2p1_1747F.1_g300530' => 'hma', 'HPP92_004607' => 'vpl', 'HPP92_004608' => 'vpl', 'HPP92_006181' => 'vpl', 'HPP92_012192' => 'vpl', 'HPP92_015680' => 'vpl', 'HPP92_020249' => 'vpl', 'HPP92_021376' => 'vpl', 'HPP92_024275' => 'vpl', 'Hund06031' => 'sun', 'Hund25391' => 'sun', 'Lalb_Chr07g0185371' => 'lal', 'Lalb_Chr07g0185381' => 'lal', 'Lalb_Chr12g0204011' => 'lal', 'Lalb_Chr13g0301671' => 'lal', 'Lalb_Chr14g0362851' => 'lal', 'Lalb_Chr24g0403581' => 'lal', 'Lj1g0000233' => 'lja', 'Lj2g0018120' => 'lja', 'Lj3C621T0' => 'lonja', 'Lj3P1059T14' => 'lonja', 'Lj3P611T9' => 'lonja', 'Lj3P614T13' => 'lonja', 'Lj3P615T5' => 'lonja', 'Lj4g0012315' => 'lja', 'Lj4g0026182' => 'lja', 'Lj6P813T16' => 'lonja', 'Lj7C427T7' => 'lonja', 'Lj7C427T8' => 'lonja', 'Lj7P600T41' => 'lonja', 'Lju41C42G17' => 'lonja', 'Lsat_1_v5_gn_0_47300' => 'lsa', 'Lsat_1_v5_gn_2_91280' => 'lsa', 'Lsat_1_v5_gn_3_30561' => 'lsa', 'Lsat_1_v5_gn_4_184321' => 'lsa', 'Lsat_1_v5_gn_4_4041' => 'lsa', 'Lsat_1_v5_gn_5_92000' => 'lsa', 'Lsat_1_v5_gn_8_152940' => 'lsa', 'Lsat_1_v5_gn_8_62401' => 'lsa', 'Manes.06G055900' => 'mes', 'Manes.12G022200' => 'mes', 'Manes.13G023300' => 'mes', 'Manes.14G115000' => 'mes', 'Manes.15G151700' => 'mes', 'Manes.17G111300' => 'mes', 'Mapoly0226s0009' => 'mpo', 'MBI02_g25363_MAGBIO' => 'mbi', 'MBI06_g00027_MAGBIO' => 'mbi', 'MBI10_g13034_MAGBIO' => 'mbi', 'MD09G1023400' => 'mdo', 'MD13G1100100' => 'mdo', 'MD15G1169200' => 'mdo', 'MD16G1101100' => 'mdo', 'MD17G1022900' => 'mdo', 'Medtr3g096150' => 'mtr', 'Medtr4g115070' => 'mtr', 'Medtr7g033325' => 'mtr', 'Medtr8g089840' => 'mtr', 'MELO3C010319.2' => 'cme', 'MELO3C011944.2' => 'cme', 'MELO3C021589.2' => 'cme', 'Migut.E00207' => 'egut', 'Migut.H00067' => 'egut', 'Migut.K00433' => 'egut', 'Migut.K00606' => 'egut', 'Migut.K01410' => 'egut', 'MSTRG.13347' => 'ama', 'MSTRG.24045' => 'ama', 'MSTRG.2428' => 'ama', 'MSTRG.26410' => 'ama', 'MSTRG.3139' => 'ama', 'MSTRG.3286' => 'ama', 'MSTRG.563' => 'ama', 'MSTRG.7941' => 'ama', 'Nitab4.5_0000028g0060' => 'nta', 'Nitab4.5_0000065g0260' => 'nta', 'Nitab4.5_0000112g0060' => 'nta', 'Nitab4.5_0000489g0120' => 'nta', 'Nitab4.5_0001776g0050' => 'nta', 'Nitab4.5_0001854g0010' => 'nta', 'Nitab4.5_0001860g0020' => 'nta', 'Nitab4.5_0004352g0010' => 'nta', 'Nitab4.5_0008716g0020' => 'nta', 'Nitab4.5_0008922g0010' => 'nta', 'Nn3g16693' => 'nnu', 'Nn4g22596' => 'nnu', 'Nn7g37639' => 'nnu', 'Oeu001701.1' => 'oeu', 'Oeu018149.1' => 'oeu', 'Oeu026220.1' => 'oeu', 'Oeu038635.1' => 'oeu', 'Oeu049176.1' => 'oeu', 'Oeu056706.1' => 'oeu', 'Oeu056937.1' => 'oeu', 'Oeu057540.1' => 'oeu', 'Os02g0594900' => 'osa', 'Os02g0595100' => 'osa', 'Os04g0477500' => 'osa', 'Os12g0611900' => 'osa', 'Peaxi162Scf00076g00020' => 'pax', 'Peaxi162Scf00128g00217' => 'pax', 'Peaxi162Scf00129g01640' => 'pax', 'Peaxi162Scf00669g00007' => 'pax', 'Peaxi162Scf00700g00421' => 'pax', 'Peaxi162Scf00801g00038' => 'pax', 'Peaxi162Scf00891g00025' => 'pax', 'PGR083G0909' => 'pgr', 'PGR119G1005' => 'pgr', 'PGR142G2236' => 'pgr', 'PGR142G3388' => 'pgr', 'PGSC0003DMG400004514' => 'stu', 'PGSC0003DMG400012635' => 'stu', 'PGSC0003DMG400015730' => 'stu', 'PGSC0003DMG400018611' => 'stu', 'PGSC0003DMG400030897' => 'stu', 'Phvul.001G254800' => 'pvu', 'Phvul.002G260100' => 'pvu', 'Phvul.003G167600' => 'pvu', 'Phvul.004G005100' => 'pvu', 'Potri.001G343600' => 'ptr', 'Potri.006G066700' => 'ptr', 'Potri.008G186000' => 'ptr', 'Potri.010G046900' => 'ptr', 'Potri.018G127900' => 'ptr', 'Pp3c20_17750' => 'ppa', 'Pp3c24_4380' => 'ppa', 'Prupe.1G245800' => 'ppe', 'Prupe.3G293400' => 'ppe', 'Prupe.7G247400' => 'ppe', 'Psat0s145g0120' => 'psa', 'Psat0s595g0040' => 'psa', 'Psat0s595g0120' => 'psa', 'Psat3g175040' => 'psa', 'Psat7g058120' => 'psa', 'PSO017G0428' => 'pso', 'PSO063G7510' => 'pso', 'PSO067G0046' => 'pso', 'PSO478G1073' => 'pso', 'PSO675G3677' => 'pso', 'PSO675G6558' => 'pso', 'PSO675G7520' => 'pso', 'PSO675G8959' => 'pso', 'QL02p074089' => 'qlo', 'QL02p089614' => 'qlo', 'QL03p057736' => 'qlo', 'RcHm_v2.0_Chr1g0364131' => 'rch', 'RcHm_v2.0_Chr2g0087801' => 'rch', 'RcHm_v2.0_Chr2g0087821' => 'rch', 'RcHm_v2.0_Chr2g0173231' => 'rch', 'RcHm_v2.0_Chr4g0433111' => 'rch', 'Rhsim03G0250300' => 'rsi', 'Rhsim08G0048400' => 'rsi', 'Rhsim10G0014800' => 'rsi', 'Rhsim12G0040100' => 'rsi', 'Rhsim12G0109700' => 'rsi', 'Sabra06G0049600' => 'sbr', 'Sabra08G0141000' => 'sbr', 'Sabra10G0021400' => 'sbr', 'Sabra16G0222900' => 'sbr', 'Sabra18G0108600' => 'sbr', 'SalBow1G0433' => 'sbo', 'SalBow1G2038' => 'sbo', 'SalBow1G5003' => 'sbo', 'SalBow7G1197' => 'sbo', 'SalBow8G3506' => 'sbo', 'Sc03g0007300' => 'sci', 'Sc11g0000950' => 'sci', 'Sc14g0008750' => 'sci', 'Sc18g0000420' => 'sci', 'Sed0006754' => 'sed', 'Sed0008741' => 'sed', 'Sed0017172' => 'sed', 'Sed0018925' => 'sed', 'Sed0023326' => 'sed', 'Sed0025909' => 'sed', 'SEGI_05333' => 'sgi', 'SEGI_10362' => 'sgi', 'SEGI_13380' => 'sgi', 'SEGI_24306' => 'sgi', 'SEGI_29077' => 'sgi', 'SEGI_29095' => 'sgi', 'SEGI_36534' => 'sgi', 'SEGI_37506' => 'sgi', 'SEGI_38321' => 'sgi', 'SGA_v2.0_scaffold307G48031' => 'sas', 'SGA_v2.0_scaffold47G17507' => 'sas', 'SGA_v2.0_scaffold63G21736' => 'sas', 'SGA_v2.0_scaffold87G27070' => 'sas', 'SHI17794' => 'shi', 'SHI28851' => 'shi', 'SMO165G0155' => 'smo', 'SMO340G0217' => 'smo', 'SMO367G1210' => 'smo', 'Solyc02g093430.3' => 'sly', 'Solyc05g013580.4' => 'sly', 'Solyc07g008030.3' => 'sly', 'Solyc12g035470.2' => 'sly', 'Sopen02g038020' => 'spe', 'Sopen05g008490' => 'spe', 'Sopen07g003910' => 'spe', 'Sopen12g015240' => 'spe', 'Sp1g11550' => 'spa', 'Sp2g16710' => 'spa', 'Sp3g00430' => 'spa', 'Sp3g26780' => 'spa', 'Sp5g22900' => 'spa', 'Sp6g29530' => 'spa', 'TAR371G0794' => 'tar', 'TAR374G0164' => 'tar', 'TAR622G0165' => 'tar', 'TAR626G0929' => 'tar', 'TAR629G2155' => 'tar', 'THA.LOC104805282' => 'tha', 'THA.LOC104805363' => 'tha', 'THA.LOC104808968' => 'tha', 'THA.LOC104821093' => 'tha', 'THA.LOC104823953' => 'tha', 'THA.LOC104825562' => 'tha', 'THA.LOC104825665' => 'tha', 'Thecc.02G261400' => 'tca', 'Thecc.04G019200' => 'tca', 'Thecc.09G130400' => 'tca', 'Thhalv10004374m.g' => 'esa', 'Thhalv10007850m.g' => 'esa', 'Thhalv10013782m.g' => 'esa', 'Thhalv10018686m.g' => 'esa', 'Thhalv10020899m.g' => 'esa', 'Thhalv10022755m.g' => 'esa', 'TPR.G23851' => 'tpr', 'TPR.G26500' => 'tpr', 'TPR.G27267' => 'tpr', 'TPR.G32001' => 'tpr', 'TPR.G6251' => 'tpr', 'TPR.G8167' => 'tpr', 'TWI12G1330' => 'twi', 'TWI18G1239' => 'twi', 'TWI34G0979' => 'twi', 'TWI36G0670' => 'twi', 'TWI36G0707' => 'twi', 'TWI56G0233' => 'twi', 'TWI75G1809' => 'twi', 'unitig_21.g20874' => 'ugi', 'unitig_26.g10343' => 'ugi', 'unitig_46.g18392' => 'ugi', 'unitig_52.g17178' => 'ugi', 'unitig_8.g2934' => 'ugi', 'vmacro01122' => 'vma', 'vmacro05875' => 'vma', 'vmacro06147' => 'vma', 'vmacro16191' => 'vma', 'vmacro18293' => 'vma', 'VMungo0251G3707' => 'vmu', 'VMungo0464G1521' => 'vmu', 'VMungo1215G0205' => 'vmu', 'VMungo1383G2484' => 'vmu', 'Zm00001eb079610' => 'zma', 'Zm00001eb135990' => 'zma', 'Zm00001eb183710' => 'zma', 'Zm00001eb246020' => 'zma' ) $gf_id = 'HOM05D001124' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001124' ) $data_identifier = 'HOM05D001124' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 6, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 7, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 21, 'bol' => (int) 10, 'bra' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 6, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 9, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 21, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 8, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 10, 'lsa' => (int) 8, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 8, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 9, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb246020' $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' => 'HOM05D001124', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '548', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02520' => 'bna', 'A03p06630' => 'bna', 'A05p44460' => 'bna', 'A06p08710' => 'bna', 'A06p41090' => 'bna', 'A07p32320' => 'bna', 'A08p32520' => 'bna', 'A09p10360' => 'bna', 'A10p24080' => 'bna', 'Aa31LG11G15250' => 'aar', 'Aa31LG1G1800' => 'aar', 'Aa31LG2G5120' => 'aar', 'Aa31LG2G6070' => 'aar', 'Aa31LG5G10770' => 'aar', 'Aa31sc61G90' => 'aar', 'Actinidia01352' => 'ach', 'Actinidia05983' => 'ach', 'Actinidia08133' => 'ach', 'Actinidia15101' => 'ach', 'Actinidia26379' => 'ach', 'Actinidia35778' => 'ach', 'Actinidia36123' => 'ach', 'Actinidia37436' => 'ach', 'Actinidia38730' => 'ach', 'Ah.02g128210' => 'amhyb', 'Ah.03g132990' => 'amhyb', 'Ah.14g079410' => 'amhyb', 'AL1G24640' => 'aly', 'AL2G26680' => 'aly', 'AL3G10530' => 'aly', 'AL3G45230' => 'aly', 'AL5G15230' => 'aly', 'AL5G16960' => 'aly', 'AL6G25210' => 'aly', 'Aqoxy2G00441' => 'aox', 'Aqoxy3G01236' => 'aox', 'Aqoxy5G03746' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3RQ047' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C7GMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9C8JER' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MBL6KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YXCZ83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZANX40' => 'arhy', 'AT1G12990' => 'ath', 'AT1G67880' => 'ath', 'AT2G13290' => 'ath', 'AT3G01620' => 'ath', 'AT3G26445' => 'ath', 'AT3G27540' => 'ath', 'AT5G14480' => 'ath', 'ATR0824G026' => 'atr', 'ATR1098G019' => 'atr', 'Atru.chr11.2145' => 'acertr', 'Atru.chr2.3636' => 'acertr', 'Atru.chr2.3644' => 'acertr', 'Atru.chr6.2422' => 'acertr', 'Atru.chr7.1112' => 'acertr', 'AUR62005469' => 'cqu', 'AUR62011166' => 'cqu', 'AUR62013319' => 'cqu', 'AUR62024273' => 'cqu', 'AUR62028420' => 'cqu', 'AUR62041942' => 'cqu', 'BcaB01g04969' => 'bca', 'BcaB01g06371' => 'bca', 'BcaB02g11494' => 'bca', 'BcaB03g15382' => 'bca', 'BcaB08g36994' => 'bca', 'BcaC03g13477' => 'bca', 'BcaC03g13478' => 'bca', 'BcaC03g13480' => 'bca', 'BcaC03g13481' => 'bca', 'BcaC03g13486' => 'bca', 'BcaC04g19031' => 'bca', 'BcaC04g23085' => 'bca', 'BcaC05g25094' => 'bca', 'BcaC05g25096' => 'bca', 'BcaC05g25138' => 'bca', 'BcaC05g30416' => 'bca', 'BcaC05g30455' => 'bca', 'BcaC06g30979' => 'bca', 'BcaC06g33805' => 'bca', 'BcaC08g46021' => 'bca', 'BcaNung03154' => 'bca', 'BolC2t06623H' => 'bol', 'BolC2t06632H' => 'bol', 'BolC2t06635H' => 'bol', 'BolC2t06638H' => 'bol', 'BolC3t13266H' => 'bol', 'BolC5t29776H' => 'bol', 'BolC6t38912H' => 'bol', 'BolC7t44183H' => 'bol', 'BolC9t54123H' => 'bol', 'BolC9t59107H' => 'bol', 'BraA02t05221Z' => 'bra', 'BraA03t09996Z' => 'bra', 'BraA05t23210Z' => 'bra', 'BraA06t24068Z' => 'bra', 'BraA06t27032Z' => 'bra', 'BraA08t35176Z' => 'bra', 'BraA09t36680Z' => 'bra', 'BraA10t44471Z' => 'bra', 'C02p06760' => 'bna', 'C02p06890' => 'bna', 'C02p07010' => 'bna', 'C03p07660' => 'bna', 'C05p10300' => 'bna', 'C06p38150' => 'bna', 'C07p36650' => 'bna', 'C08p15770' => 'bna', 'C09p12300' => 'bna', 'C09p62700' => 'bna', 'C09p75040' => 'bna', 'CAN.G13.1' => 'can', 'CAN.G138.4' => 'can', 'CAN.G44.6' => 'can', 'CAN.G473.19' => 'can', 'CANSAT01G0835' => 'cansat', 'CANSAT11G0246' => 'cansat', 'CANSAT11G1766' => 'cansat', 'CANSAT64G1954' => 'cansat', 'CARHR013330' => 'chi', 'CARHR060530' => 'chi', 'CARHR075300' => 'chi', 'CARHR105120' => 'chi', 'CARHR148910' => 'chi', 'CARHR198830' => 'chi', 'Carub.0001s1275' => 'cru', 'Carub.0002s1437' => 'cru', 'Carub.0003s0044' => 'cru', 'Carub.0003s2787' => 'cru', 'Carub.0005s0597' => 'cru', 'Carub.0006s1266' => 'cru', 'Ca_06935_v3' => 'car', 'Ca_13559_v3' => 'car', 'Ca_16941_v3' => 'car', 'Ca_16960_v3' => 'car', 'Ca_17775_v3' => 'car', 'Ca_30464_v3' => 'car', 'Cc06_g08160' => 'ccan', 'Cc07_g01520' => 'ccan', 'Cc11_g15810' => 'ccan', 'CDE02G2840' => 'cde', 'CDE03G0093' => 'cde', 'CDE04G2127' => 'cde', 'CDE07G1857' => 'cde', 'CDE09G1246' => 'cde', 'Cfa003412' => 'cfa', 'Cfa007341' => 'cfa', 'Cfa009220' => 'cfa', 'Ciclev10008737m.g' => 'ccl', 'Ciclev10015565m.g' => 'ccl', 'Ciclev10031761m.g' => 'ccl', 'CiPaw.03G045300' => 'cil', 'CiPaw.03G247200' => 'cil', 'CiPaw.04G029500' => 'cil', 'CiPaw.04G174000' => 'cil', 'CiPaw.05G181200' => 'cil', 'CiPaw.06G067100' => 'cil', 'ClCG05G025800' => 'cla', 'ClCG06G011400' => 'cla', 'ClCG09G019360' => 'cla', 'COL.COLO4_04827' => 'col', 'COL.COLO4_29170' => 'col', 'COL.COLO4_35131' => 'col', 'COL.COLO4_35132' => 'col', 'Cpa.g.sc33.32' => 'cpa', 'Cpa.g.sc46.29' => 'cpa', 'Cpa.g.sc796.1' => 'cpa', 'CsaV3_1G030420' => 'csa', 'CsaV3_5G027050' => 'csa', 'CsaV3_5G031040' => 'csa', 'CsaV3_UNG023130' => 'csa', 'CSS0007726' => 'camsi', 'CSS0016433' => 'camsi', 'CSS0017656' => 'camsi', 'CSS0025364' => 'camsi', 'CSS0027582' => 'camsi', 'CSS0047288' => 'camsi', 'CSS0049950' => 'camsi', 'DCAR_003843' => 'dca', 'DCAR_007052' => 'dca', 'DCAR_020884' => 'dca', 'DCAR_021730' => 'dca', 'DCAR_024423' => 'dca', 'DCAR_026509' => 'dca', 'DCAR_031158' => 'dca', 'Dinv14728' => 'din', 'Dinv15219' => 'din', 'Dinv25728' => 'din', 'Dinv33428' => 'din', 'Dinv36489' => 'din', 'Dinv41486' => 'din', 'Duzib147G0469' => 'dzi', 'Duzib168G0060' => 'dzi', 'Duzib187G1215' => 'dzi', 'Duzib248G0692' => 'dzi', 'Duzib251G0767' => 'dzi', 'Duzib264G0446' => 'dzi', 'Duzib268G0691' => 'dzi', 'ECA232G4767' => 'eca', 'ECA233G2838' => 'eca', 'ECA234G0391' => 'eca', 'ECA234G0857' => 'eca', 'ECA236G1593' => 'eca', 'ECA238G0565' => 'eca', 'ECA246G1027' => 'eca', 'ECA246G3223' => 'eca', 'ECA246G3470' => 'eca', 'EL10Ac6g13829' => 'bvu', 'EL10Ac6g14093' => 'bvu', 'EL10Ac8g18707' => 'bvu', 'Eucgr.C01369' => 'egr', 'Eucgr.H02492' => 'egr', 'Eucgr.I01733' => 'egr', 'Eucgr.J02255' => 'egr', 'Eucgr.J02257' => 'egr', 'Eucgr.J02258' => 'egr', 'FAN02G1601' => 'fan', 'FAN03G1586' => 'fan', 'FAN03G2986' => 'fan', 'FAN05G4837' => 'fan', 'FAN06G0146' => 'fan', 'FAN07G0858' => 'fan', 'FAN09G3179' => 'fan', 'FAN10G0669' => 'fan', 'FAN12G2358' => 'fan', 'FAN14G4198' => 'fan', 'FAN14G5112' => 'fan', 'FAN17G0342' => 'fan', 'FAN19G0342' => 'fan', 'FAN19G0962' => 'fan', 'FAN19G1101' => 'fan', 'FAN19G1872' => 'fan', 'FAN22G0356' => 'fan', 'FAN23G0744' => 'fan', 'FAN23G1914' => 'fan', 'FAN26G0032' => 'fan', 'FAN28G0625' => 'fan', 'FvH4_1g02710' => 'fve', 'FvH4_1g02720' => 'fve', 'FvH4_4g25670' => 'fve', 'FvH4_6g51700' => 'fve', 'FvH4_7g20170' => 'fve', 'Glyma.05G175000' => 'gma', 'Glyma.08G132300' => 'gma', 'Glyma.11G243000' => 'gma', 'Glyma.13G158900' => 'gma', 'Glyma.17G112400' => 'gma', 'Glyma.18G014100' => 'gma', 'Glyma.19G003100' => 'gma', 'Glyma.19G056500' => 'gma', 'Gohir.A01G158900' => 'ghi', 'Gohir.A05G312600' => 'ghi', 'Gohir.A05G354900' => 'ghi', 'Gohir.A07G037200' => 'ghi', 'Gohir.A09G030000' => 'ghi', 'Gohir.A12G145200' => 'ghi', 'Gohir.D01G151500' => 'ghi', 'Gohir.D04G058300' => 'ghi', 'Gohir.D05G314100' => 'ghi', 'Gohir.D07G041400' => 'ghi', 'Gohir.D09G029700' => 'ghi', 'Gohir.D12G149700' => 'ghi', 'Gorai.001G043800' => 'gra', 'Gorai.002G187800' => 'gra', 'Gorai.006G034700' => 'gra', 'Gorai.008G161200' => 'gra', 'Gorai.009G335700' => 'gra', 'Gorai.012G065000' => 'gra', 'GSVIVG01000535001' => 'vvi', 'GSVIVG01015572001' => 'vvi', 'GSVIVG01032386001' => 'vvi', 'HanXRQChr05g0138531' => 'han', 'HanXRQChr06g0174391' => 'han', 'HanXRQChr07g0199021' => 'han', 'HanXRQChr08g0208211' => 'han', 'HanXRQChr09g0255471' => 'han', 'HanXRQChr10g0315791' => 'han', 'HanXRQChr12g0371991' => 'han', 'HanXRQChr15g0475251' => 'han', 'HanXRQChr17g0540001' => 'han', 'HanXRQChr17g0548631' => 'han', 'HanXRQChr17g0569561' => 'han', 'Haze_12256' => 'cav', 'Haze_14756' => 'cav', 'Haze_25528' => 'cav', 'Hma1.2p1_0079F.1_g041020' => 'hma', 'Hma1.2p1_0818F.1_g223260' => 'hma', 'Hma1.2p1_1747F.1_g300530' => 'hma', 'HPP92_004607' => 'vpl', 'HPP92_004608' => 'vpl', 'HPP92_006181' => 'vpl', 'HPP92_012192' => 'vpl', 'HPP92_015680' => 'vpl', 'HPP92_020249' => 'vpl', 'HPP92_021376' => 'vpl', 'HPP92_024275' => 'vpl', 'Hund06031' => 'sun', 'Hund25391' => 'sun', 'Lalb_Chr07g0185371' => 'lal', 'Lalb_Chr07g0185381' => 'lal', 'Lalb_Chr12g0204011' => 'lal', 'Lalb_Chr13g0301671' => 'lal', 'Lalb_Chr14g0362851' => 'lal', 'Lalb_Chr24g0403581' => 'lal', 'Lj1g0000233' => 'lja', 'Lj2g0018120' => 'lja', 'Lj3C621T0' => 'lonja', 'Lj3P1059T14' => 'lonja', 'Lj3P611T9' => 'lonja', 'Lj3P614T13' => 'lonja', 'Lj3P615T5' => 'lonja', 'Lj4g0012315' => 'lja', 'Lj4g0026182' => 'lja', 'Lj6P813T16' => 'lonja', 'Lj7C427T7' => 'lonja', 'Lj7C427T8' => 'lonja', 'Lj7P600T41' => 'lonja', 'Lju41C42G17' => 'lonja', 'Lsat_1_v5_gn_0_47300' => 'lsa', 'Lsat_1_v5_gn_2_91280' => 'lsa', 'Lsat_1_v5_gn_3_30561' => 'lsa', 'Lsat_1_v5_gn_4_184321' => 'lsa', 'Lsat_1_v5_gn_4_4041' => 'lsa', 'Lsat_1_v5_gn_5_92000' => 'lsa', 'Lsat_1_v5_gn_8_152940' => 'lsa', 'Lsat_1_v5_gn_8_62401' => 'lsa', 'Manes.06G055900' => 'mes', 'Manes.12G022200' => 'mes', 'Manes.13G023300' => 'mes', 'Manes.14G115000' => 'mes', 'Manes.15G151700' => 'mes', 'Manes.17G111300' => 'mes', 'Mapoly0226s0009' => 'mpo', 'MBI02_g25363_MAGBIO' => 'mbi', 'MBI06_g00027_MAGBIO' => 'mbi', 'MBI10_g13034_MAGBIO' => 'mbi', 'MD09G1023400' => 'mdo', 'MD13G1100100' => 'mdo', 'MD15G1169200' => 'mdo', 'MD16G1101100' => 'mdo', 'MD17G1022900' => 'mdo', 'Medtr3g096150' => 'mtr', 'Medtr4g115070' => 'mtr', 'Medtr7g033325' => 'mtr', 'Medtr8g089840' => 'mtr', 'MELO3C010319.2' => 'cme', 'MELO3C011944.2' => 'cme', 'MELO3C021589.2' => 'cme', 'Migut.E00207' => 'egut', 'Migut.H00067' => 'egut', 'Migut.K00433' => 'egut', 'Migut.K00606' => 'egut', 'Migut.K01410' => 'egut', 'MSTRG.13347' => 'ama', 'MSTRG.24045' => 'ama', 'MSTRG.2428' => 'ama', 'MSTRG.26410' => 'ama', 'MSTRG.3139' => 'ama', 'MSTRG.3286' => 'ama', 'MSTRG.563' => 'ama', 'MSTRG.7941' => 'ama', 'Nitab4.5_0000028g0060' => 'nta', 'Nitab4.5_0000065g0260' => 'nta', 'Nitab4.5_0000112g0060' => 'nta', 'Nitab4.5_0000489g0120' => 'nta', 'Nitab4.5_0001776g0050' => 'nta', 'Nitab4.5_0001854g0010' => 'nta', 'Nitab4.5_0001860g0020' => 'nta', 'Nitab4.5_0004352g0010' => 'nta', 'Nitab4.5_0008716g0020' => 'nta', 'Nitab4.5_0008922g0010' => 'nta', 'Nn3g16693' => 'nnu', 'Nn4g22596' => 'nnu', 'Nn7g37639' => 'nnu', 'Oeu001701.1' => 'oeu', 'Oeu018149.1' => 'oeu', 'Oeu026220.1' => 'oeu', 'Oeu038635.1' => 'oeu', 'Oeu049176.1' => 'oeu', 'Oeu056706.1' => 'oeu', 'Oeu056937.1' => 'oeu', 'Oeu057540.1' => 'oeu', 'Os02g0594900' => 'osa', 'Os02g0595100' => 'osa', 'Os04g0477500' => 'osa', 'Os12g0611900' => 'osa', 'Peaxi162Scf00076g00020' => 'pax', 'Peaxi162Scf00128g00217' => 'pax', 'Peaxi162Scf00129g01640' => 'pax', 'Peaxi162Scf00669g00007' => 'pax', 'Peaxi162Scf00700g00421' => 'pax', 'Peaxi162Scf00801g00038' => 'pax', 'Peaxi162Scf00891g00025' => 'pax', 'PGR083G0909' => 'pgr', 'PGR119G1005' => 'pgr', 'PGR142G2236' => 'pgr', 'PGR142G3388' => 'pgr', 'PGSC0003DMG400004514' => 'stu', 'PGSC0003DMG400012635' => 'stu', 'PGSC0003DMG400015730' => 'stu', 'PGSC0003DMG400018611' => 'stu', 'PGSC0003DMG400030897' => 'stu', 'Phvul.001G254800' => 'pvu', 'Phvul.002G260100' => 'pvu', 'Phvul.003G167600' => 'pvu', 'Phvul.004G005100' => 'pvu', 'Potri.001G343600' => 'ptr', 'Potri.006G066700' => 'ptr', 'Potri.008G186000' => 'ptr', 'Potri.010G046900' => 'ptr', 'Potri.018G127900' => 'ptr', 'Pp3c20_17750' => 'ppa', 'Pp3c24_4380' => 'ppa', 'Prupe.1G245800' => 'ppe', 'Prupe.3G293400' => 'ppe', 'Prupe.7G247400' => 'ppe', 'Psat0s145g0120' => 'psa', 'Psat0s595g0040' => 'psa', 'Psat0s595g0120' => 'psa', 'Psat3g175040' => 'psa', 'Psat7g058120' => 'psa', 'PSO017G0428' => 'pso', 'PSO063G7510' => 'pso', 'PSO067G0046' => 'pso', 'PSO478G1073' => 'pso', 'PSO675G3677' => 'pso', 'PSO675G6558' => 'pso', 'PSO675G7520' => 'pso', 'PSO675G8959' => 'pso', 'QL02p074089' => 'qlo', 'QL02p089614' => 'qlo', 'QL03p057736' => 'qlo', 'RcHm_v2.0_Chr1g0364131' => 'rch', 'RcHm_v2.0_Chr2g0087801' => 'rch', 'RcHm_v2.0_Chr2g0087821' => 'rch', 'RcHm_v2.0_Chr2g0173231' => 'rch', 'RcHm_v2.0_Chr4g0433111' => 'rch', 'Rhsim03G0250300' => 'rsi', 'Rhsim08G0048400' => 'rsi', 'Rhsim10G0014800' => 'rsi', 'Rhsim12G0040100' => 'rsi', 'Rhsim12G0109700' => 'rsi', 'Sabra06G0049600' => 'sbr', 'Sabra08G0141000' => 'sbr', 'Sabra10G0021400' => 'sbr', 'Sabra16G0222900' => 'sbr', 'Sabra18G0108600' => 'sbr', 'SalBow1G0433' => 'sbo', 'SalBow1G2038' => 'sbo', 'SalBow1G5003' => 'sbo', 'SalBow7G1197' => 'sbo', 'SalBow8G3506' => 'sbo', 'Sc03g0007300' => 'sci', 'Sc11g0000950' => 'sci', 'Sc14g0008750' => 'sci', 'Sc18g0000420' => 'sci', 'Sed0006754' => 'sed', 'Sed0008741' => 'sed', 'Sed0017172' => 'sed', 'Sed0018925' => 'sed', 'Sed0023326' => 'sed', 'Sed0025909' => 'sed', 'SEGI_05333' => 'sgi', 'SEGI_10362' => 'sgi', 'SEGI_13380' => 'sgi', 'SEGI_24306' => 'sgi', 'SEGI_29077' => 'sgi', 'SEGI_29095' => 'sgi', 'SEGI_36534' => 'sgi', 'SEGI_37506' => 'sgi', 'SEGI_38321' => 'sgi', 'SGA_v2.0_scaffold307G48031' => 'sas', 'SGA_v2.0_scaffold47G17507' => 'sas', 'SGA_v2.0_scaffold63G21736' => 'sas', 'SGA_v2.0_scaffold87G27070' => 'sas', 'SHI17794' => 'shi', 'SHI28851' => 'shi', 'SMO165G0155' => 'smo', 'SMO340G0217' => 'smo', 'SMO367G1210' => 'smo', 'Solyc02g093430.3' => 'sly', 'Solyc05g013580.4' => 'sly', 'Solyc07g008030.3' => 'sly', 'Solyc12g035470.2' => 'sly', 'Sopen02g038020' => 'spe', 'Sopen05g008490' => 'spe', 'Sopen07g003910' => 'spe', 'Sopen12g015240' => 'spe', 'Sp1g11550' => 'spa', 'Sp2g16710' => 'spa', 'Sp3g00430' => 'spa', 'Sp3g26780' => 'spa', 'Sp5g22900' => 'spa', 'Sp6g29530' => 'spa', 'TAR371G0794' => 'tar', 'TAR374G0164' => 'tar', 'TAR622G0165' => 'tar', 'TAR626G0929' => 'tar', 'TAR629G2155' => 'tar', 'THA.LOC104805282' => 'tha', 'THA.LOC104805363' => 'tha', 'THA.LOC104808968' => 'tha', 'THA.LOC104821093' => 'tha', 'THA.LOC104823953' => 'tha', 'THA.LOC104825562' => 'tha', 'THA.LOC104825665' => 'tha', 'Thecc.02G261400' => 'tca', 'Thecc.04G019200' => 'tca', 'Thecc.09G130400' => 'tca', 'Thhalv10004374m.g' => 'esa', 'Thhalv10007850m.g' => 'esa', 'Thhalv10013782m.g' => 'esa', 'Thhalv10018686m.g' => 'esa', 'Thhalv10020899m.g' => 'esa', 'Thhalv10022755m.g' => 'esa', 'TPR.G23851' => 'tpr', 'TPR.G26500' => 'tpr', 'TPR.G27267' => 'tpr', 'TPR.G32001' => 'tpr', 'TPR.G6251' => 'tpr', 'TPR.G8167' => 'tpr', 'TWI12G1330' => 'twi', 'TWI18G1239' => 'twi', 'TWI34G0979' => 'twi', 'TWI36G0670' => 'twi', 'TWI36G0707' => 'twi', 'TWI56G0233' => 'twi', 'TWI75G1809' => 'twi', 'unitig_21.g20874' => 'ugi', 'unitig_26.g10343' => 'ugi', 'unitig_46.g18392' => 'ugi', 'unitig_52.g17178' => 'ugi', 'unitig_8.g2934' => 'ugi', 'vmacro01122' => 'vma', 'vmacro05875' => 'vma', 'vmacro06147' => 'vma', 'vmacro16191' => 'vma', 'vmacro18293' => 'vma', 'VMungo0251G3707' => 'vmu', 'VMungo0464G1521' => 'vmu', 'VMungo1215G0205' => 'vmu', 'VMungo1383G2484' => 'vmu', 'Zm00001eb079610' => 'zma', 'Zm00001eb135990' => 'zma', 'Zm00001eb183710' => 'zma', 'Zm00001eb246020' => 'zma' ), 'gf_id' => 'HOM05D001124', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001124' ), 'data_identifier' => 'HOM05D001124', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001124', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '548', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02520' => 'bna', 'A03p06630' => 'bna', 'A05p44460' => 'bna', 'A06p08710' => 'bna', 'A06p41090' => 'bna', 'A07p32320' => 'bna', 'A08p32520' => 'bna', 'A09p10360' => 'bna', 'A10p24080' => 'bna', 'Aa31LG11G15250' => 'aar', 'Aa31LG1G1800' => 'aar', 'Aa31LG2G5120' => 'aar', 'Aa31LG2G6070' => 'aar', 'Aa31LG5G10770' => 'aar', 'Aa31sc61G90' => 'aar', 'Actinidia01352' => 'ach', 'Actinidia05983' => 'ach', 'Actinidia08133' => 'ach', 'Actinidia15101' => 'ach', 'Actinidia26379' => 'ach', 'Actinidia35778' => 'ach', 'Actinidia36123' => 'ach', 'Actinidia37436' => 'ach', 'Actinidia38730' => 'ach', 'Ah.02g128210' => 'amhyb', 'Ah.03g132990' => 'amhyb', 'Ah.14g079410' => 'amhyb', 'AL1G24640' => 'aly', 'AL2G26680' => 'aly', 'AL3G10530' => 'aly', 'AL3G45230' => 'aly', 'AL5G15230' => 'aly', 'AL5G16960' => 'aly', 'AL6G25210' => 'aly', 'Aqoxy2G00441' => 'aox', 'Aqoxy3G01236' => 'aox', 'Aqoxy5G03746' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3RQ047' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C7GMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9C8JER' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MBL6KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YXCZ83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZANX40' => 'arhy', 'AT1G12990' => 'ath', 'AT1G67880' => 'ath', 'AT2G13290' => 'ath', 'AT3G01620' => 'ath', 'AT3G26445' => 'ath', 'AT3G27540' => 'ath', 'AT5G14480' => 'ath', 'ATR0824G026' => 'atr', 'ATR1098G019' => 'atr', 'Atru.chr11.2145' => 'acertr', 'Atru.chr2.3636' => 'acertr', 'Atru.chr2.3644' => 'acertr', 'Atru.chr6.2422' => 'acertr', 'Atru.chr7.1112' => 'acertr', 'AUR62005469' => 'cqu', 'AUR62011166' => 'cqu', 'AUR62013319' => 'cqu', 'AUR62024273' => 'cqu', 'AUR62028420' => 'cqu', 'AUR62041942' => 'cqu', 'BcaB01g04969' => 'bca', 'BcaB01g06371' => 'bca', 'BcaB02g11494' => 'bca', 'BcaB03g15382' => 'bca', 'BcaB08g36994' => 'bca', 'BcaC03g13477' => 'bca', 'BcaC03g13478' => 'bca', 'BcaC03g13480' => 'bca', 'BcaC03g13481' => 'bca', 'BcaC03g13486' => 'bca', 'BcaC04g19031' => 'bca', 'BcaC04g23085' => 'bca', 'BcaC05g25094' => 'bca', 'BcaC05g25096' => 'bca', 'BcaC05g25138' => 'bca', 'BcaC05g30416' => 'bca', 'BcaC05g30455' => 'bca', 'BcaC06g30979' => 'bca', 'BcaC06g33805' => 'bca', 'BcaC08g46021' => 'bca', 'BcaNung03154' => 'bca', 'BolC2t06623H' => 'bol', 'BolC2t06632H' => 'bol', 'BolC2t06635H' => 'bol', 'BolC2t06638H' => 'bol', 'BolC3t13266H' => 'bol', 'BolC5t29776H' => 'bol', 'BolC6t38912H' => 'bol', 'BolC7t44183H' => 'bol', 'BolC9t54123H' => 'bol', 'BolC9t59107H' => 'bol', 'BraA02t05221Z' => 'bra', 'BraA03t09996Z' => 'bra', 'BraA05t23210Z' => 'bra', 'BraA06t24068Z' => 'bra', 'BraA06t27032Z' => 'bra', 'BraA08t35176Z' => 'bra', 'BraA09t36680Z' => 'bra', 'BraA10t44471Z' => 'bra', 'C02p06760' => 'bna', 'C02p06890' => 'bna', 'C02p07010' => 'bna', 'C03p07660' => 'bna', 'C05p10300' => 'bna', 'C06p38150' => 'bna', 'C07p36650' => 'bna', 'C08p15770' => 'bna', 'C09p12300' => 'bna', 'C09p62700' => 'bna', 'C09p75040' => 'bna', 'CAN.G13.1' => 'can', 'CAN.G138.4' => 'can', 'CAN.G44.6' => 'can', 'CAN.G473.19' => 'can', 'CANSAT01G0835' => 'cansat', 'CANSAT11G0246' => 'cansat', 'CANSAT11G1766' => 'cansat', 'CANSAT64G1954' => 'cansat', 'CARHR013330' => 'chi', 'CARHR060530' => 'chi', 'CARHR075300' => 'chi', 'CARHR105120' => 'chi', 'CARHR148910' => 'chi', 'CARHR198830' => 'chi', 'Carub.0001s1275' => 'cru', 'Carub.0002s1437' => 'cru', 'Carub.0003s0044' => 'cru', 'Carub.0003s2787' => 'cru', 'Carub.0005s0597' => 'cru', 'Carub.0006s1266' => 'cru', 'Ca_06935_v3' => 'car', 'Ca_13559_v3' => 'car', 'Ca_16941_v3' => 'car', 'Ca_16960_v3' => 'car', 'Ca_17775_v3' => 'car', 'Ca_30464_v3' => 'car', 'Cc06_g08160' => 'ccan', 'Cc07_g01520' => 'ccan', 'Cc11_g15810' => 'ccan', 'CDE02G2840' => 'cde', 'CDE03G0093' => 'cde', 'CDE04G2127' => 'cde', 'CDE07G1857' => 'cde', 'CDE09G1246' => 'cde', 'Cfa003412' => 'cfa', 'Cfa007341' => 'cfa', 'Cfa009220' => 'cfa', 'Ciclev10008737m.g' => 'ccl', 'Ciclev10015565m.g' => 'ccl', 'Ciclev10031761m.g' => 'ccl', 'CiPaw.03G045300' => 'cil', 'CiPaw.03G247200' => 'cil', 'CiPaw.04G029500' => 'cil', 'CiPaw.04G174000' => 'cil', 'CiPaw.05G181200' => 'cil', 'CiPaw.06G067100' => 'cil', 'ClCG05G025800' => 'cla', 'ClCG06G011400' => 'cla', 'ClCG09G019360' => 'cla', 'COL.COLO4_04827' => 'col', 'COL.COLO4_29170' => 'col', 'COL.COLO4_35131' => 'col', 'COL.COLO4_35132' => 'col', 'Cpa.g.sc33.32' => 'cpa', 'Cpa.g.sc46.29' => 'cpa', 'Cpa.g.sc796.1' => 'cpa', 'CsaV3_1G030420' => 'csa', 'CsaV3_5G027050' => 'csa', 'CsaV3_5G031040' => 'csa', 'CsaV3_UNG023130' => 'csa', 'CSS0007726' => 'camsi', 'CSS0016433' => 'camsi', 'CSS0017656' => 'camsi', 'CSS0025364' => 'camsi', 'CSS0027582' => 'camsi', 'CSS0047288' => 'camsi', 'CSS0049950' => 'camsi', 'DCAR_003843' => 'dca', 'DCAR_007052' => 'dca', 'DCAR_020884' => 'dca', 'DCAR_021730' => 'dca', 'DCAR_024423' => 'dca', 'DCAR_026509' => 'dca', 'DCAR_031158' => 'dca', 'Dinv14728' => 'din', 'Dinv15219' => 'din', 'Dinv25728' => 'din', 'Dinv33428' => 'din', 'Dinv36489' => 'din', 'Dinv41486' => 'din', 'Duzib147G0469' => 'dzi', 'Duzib168G0060' => 'dzi', 'Duzib187G1215' => 'dzi', 'Duzib248G0692' => 'dzi', 'Duzib251G0767' => 'dzi', 'Duzib264G0446' => 'dzi', 'Duzib268G0691' => 'dzi', 'ECA232G4767' => 'eca', 'ECA233G2838' => 'eca', 'ECA234G0391' => 'eca', 'ECA234G0857' => 'eca', 'ECA236G1593' => 'eca', 'ECA238G0565' => 'eca', 'ECA246G1027' => 'eca', 'ECA246G3223' => 'eca', 'ECA246G3470' => 'eca', 'EL10Ac6g13829' => 'bvu', 'EL10Ac6g14093' => 'bvu', 'EL10Ac8g18707' => 'bvu', 'Eucgr.C01369' => 'egr', 'Eucgr.H02492' => 'egr', 'Eucgr.I01733' => 'egr', 'Eucgr.J02255' => 'egr', 'Eucgr.J02257' => 'egr', 'Eucgr.J02258' => 'egr', 'FAN02G1601' => 'fan', 'FAN03G1586' => 'fan', 'FAN03G2986' => 'fan', 'FAN05G4837' => 'fan', 'FAN06G0146' => 'fan', 'FAN07G0858' => 'fan', 'FAN09G3179' => 'fan', 'FAN10G0669' => 'fan', 'FAN12G2358' => 'fan', 'FAN14G4198' => 'fan', 'FAN14G5112' => 'fan', 'FAN17G0342' => 'fan', 'FAN19G0342' => 'fan', 'FAN19G0962' => 'fan', 'FAN19G1101' => 'fan', 'FAN19G1872' => 'fan', 'FAN22G0356' => 'fan', 'FAN23G0744' => 'fan', 'FAN23G1914' => 'fan', 'FAN26G0032' => 'fan', 'FAN28G0625' => 'fan', 'FvH4_1g02710' => 'fve', 'FvH4_1g02720' => 'fve', 'FvH4_4g25670' => 'fve', 'FvH4_6g51700' => 'fve', 'FvH4_7g20170' => 'fve', 'Glyma.05G175000' => 'gma', 'Glyma.08G132300' => 'gma', 'Glyma.11G243000' => 'gma', 'Glyma.13G158900' => 'gma', 'Glyma.17G112400' => 'gma', 'Glyma.18G014100' => 'gma', 'Glyma.19G003100' => 'gma', 'Glyma.19G056500' => 'gma', 'Gohir.A01G158900' => 'ghi', 'Gohir.A05G312600' => 'ghi', 'Gohir.A05G354900' => 'ghi', 'Gohir.A07G037200' => 'ghi', 'Gohir.A09G030000' => 'ghi', 'Gohir.A12G145200' => 'ghi', 'Gohir.D01G151500' => 'ghi', 'Gohir.D04G058300' => 'ghi', 'Gohir.D05G314100' => 'ghi', 'Gohir.D07G041400' => 'ghi', 'Gohir.D09G029700' => 'ghi', 'Gohir.D12G149700' => 'ghi', 'Gorai.001G043800' => 'gra', 'Gorai.002G187800' => 'gra', 'Gorai.006G034700' => 'gra', 'Gorai.008G161200' => 'gra', 'Gorai.009G335700' => 'gra', 'Gorai.012G065000' => 'gra', 'GSVIVG01000535001' => 'vvi', 'GSVIVG01015572001' => 'vvi', 'GSVIVG01032386001' => 'vvi', 'HanXRQChr05g0138531' => 'han', 'HanXRQChr06g0174391' => 'han', 'HanXRQChr07g0199021' => 'han', 'HanXRQChr08g0208211' => 'han', 'HanXRQChr09g0255471' => 'han', 'HanXRQChr10g0315791' => 'han', 'HanXRQChr12g0371991' => 'han', 'HanXRQChr15g0475251' => 'han', 'HanXRQChr17g0540001' => 'han', 'HanXRQChr17g0548631' => 'han', 'HanXRQChr17g0569561' => 'han', 'Haze_12256' => 'cav', 'Haze_14756' => 'cav', 'Haze_25528' => 'cav', 'Hma1.2p1_0079F.1_g041020' => 'hma', 'Hma1.2p1_0818F.1_g223260' => 'hma', 'Hma1.2p1_1747F.1_g300530' => 'hma', 'HPP92_004607' => 'vpl', 'HPP92_004608' => 'vpl', 'HPP92_006181' => 'vpl', 'HPP92_012192' => 'vpl', 'HPP92_015680' => 'vpl', 'HPP92_020249' => 'vpl', 'HPP92_021376' => 'vpl', 'HPP92_024275' => 'vpl', 'Hund06031' => 'sun', 'Hund25391' => 'sun', 'Lalb_Chr07g0185371' => 'lal', 'Lalb_Chr07g0185381' => 'lal', 'Lalb_Chr12g0204011' => 'lal', 'Lalb_Chr13g0301671' => 'lal', 'Lalb_Chr14g0362851' => 'lal', 'Lalb_Chr24g0403581' => 'lal', 'Lj1g0000233' => 'lja', 'Lj2g0018120' => 'lja', 'Lj3C621T0' => 'lonja', 'Lj3P1059T14' => 'lonja', 'Lj3P611T9' => 'lonja', 'Lj3P614T13' => 'lonja', 'Lj3P615T5' => 'lonja', 'Lj4g0012315' => 'lja', 'Lj4g0026182' => 'lja', 'Lj6P813T16' => 'lonja', 'Lj7C427T7' => 'lonja', 'Lj7C427T8' => 'lonja', 'Lj7P600T41' => 'lonja', 'Lju41C42G17' => 'lonja', 'Lsat_1_v5_gn_0_47300' => 'lsa', 'Lsat_1_v5_gn_2_91280' => 'lsa', 'Lsat_1_v5_gn_3_30561' => 'lsa', 'Lsat_1_v5_gn_4_184321' => 'lsa', 'Lsat_1_v5_gn_4_4041' => 'lsa', 'Lsat_1_v5_gn_5_92000' => 'lsa', 'Lsat_1_v5_gn_8_152940' => 'lsa', 'Lsat_1_v5_gn_8_62401' => 'lsa', 'Manes.06G055900' => 'mes', 'Manes.12G022200' => 'mes', 'Manes.13G023300' => 'mes', 'Manes.14G115000' => 'mes', 'Manes.15G151700' => 'mes', 'Manes.17G111300' => 'mes', 'Mapoly0226s0009' => 'mpo', 'MBI02_g25363_MAGBIO' => 'mbi', 'MBI06_g00027_MAGBIO' => 'mbi', 'MBI10_g13034_MAGBIO' => 'mbi', 'MD09G1023400' => 'mdo', 'MD13G1100100' => 'mdo', 'MD15G1169200' => 'mdo', 'MD16G1101100' => 'mdo', 'MD17G1022900' => 'mdo', 'Medtr3g096150' => 'mtr', 'Medtr4g115070' => 'mtr', 'Medtr7g033325' => 'mtr', 'Medtr8g089840' => 'mtr', 'MELO3C010319.2' => 'cme', 'MELO3C011944.2' => 'cme', 'MELO3C021589.2' => 'cme', 'Migut.E00207' => 'egut', 'Migut.H00067' => 'egut', 'Migut.K00433' => 'egut', 'Migut.K00606' => 'egut', 'Migut.K01410' => 'egut', 'MSTRG.13347' => 'ama', 'MSTRG.24045' => 'ama', 'MSTRG.2428' => 'ama', 'MSTRG.26410' => 'ama', 'MSTRG.3139' => 'ama', 'MSTRG.3286' => 'ama', 'MSTRG.563' => 'ama', 'MSTRG.7941' => 'ama', 'Nitab4.5_0000028g0060' => 'nta', 'Nitab4.5_0000065g0260' => 'nta', 'Nitab4.5_0000112g0060' => 'nta', 'Nitab4.5_0000489g0120' => 'nta', 'Nitab4.5_0001776g0050' => 'nta', 'Nitab4.5_0001854g0010' => 'nta', 'Nitab4.5_0001860g0020' => 'nta', 'Nitab4.5_0004352g0010' => 'nta', 'Nitab4.5_0008716g0020' => 'nta', 'Nitab4.5_0008922g0010' => 'nta', 'Nn3g16693' => 'nnu', 'Nn4g22596' => 'nnu', 'Nn7g37639' => 'nnu', 'Oeu001701.1' => 'oeu', 'Oeu018149.1' => 'oeu', 'Oeu026220.1' => 'oeu', 'Oeu038635.1' => 'oeu', 'Oeu049176.1' => 'oeu', 'Oeu056706.1' => 'oeu', 'Oeu056937.1' => 'oeu', 'Oeu057540.1' => 'oeu', 'Os02g0594900' => 'osa', 'Os02g0595100' => 'osa', 'Os04g0477500' => 'osa', 'Os12g0611900' => 'osa', 'Peaxi162Scf00076g00020' => 'pax', 'Peaxi162Scf00128g00217' => 'pax', 'Peaxi162Scf00129g01640' => 'pax', 'Peaxi162Scf00669g00007' => 'pax', 'Peaxi162Scf00700g00421' => 'pax', 'Peaxi162Scf00801g00038' => 'pax', 'Peaxi162Scf00891g00025' => 'pax', 'PGR083G0909' => 'pgr', 'PGR119G1005' => 'pgr', 'PGR142G2236' => 'pgr', 'PGR142G3388' => 'pgr', 'PGSC0003DMG400004514' => 'stu', 'PGSC0003DMG400012635' => 'stu', 'PGSC0003DMG400015730' => 'stu', 'PGSC0003DMG400018611' => 'stu', 'PGSC0003DMG400030897' => 'stu', 'Phvul.001G254800' => 'pvu', 'Phvul.002G260100' => 'pvu', 'Phvul.003G167600' => 'pvu', 'Phvul.004G005100' => 'pvu', 'Potri.001G343600' => 'ptr', 'Potri.006G066700' => 'ptr', 'Potri.008G186000' => 'ptr', 'Potri.010G046900' => 'ptr', 'Potri.018G127900' => 'ptr', 'Pp3c20_17750' => 'ppa', 'Pp3c24_4380' => 'ppa', 'Prupe.1G245800' => 'ppe', 'Prupe.3G293400' => 'ppe', 'Prupe.7G247400' => 'ppe', 'Psat0s145g0120' => 'psa', 'Psat0s595g0040' => 'psa', 'Psat0s595g0120' => 'psa', 'Psat3g175040' => 'psa', 'Psat7g058120' => 'psa', 'PSO017G0428' => 'pso', 'PSO063G7510' => 'pso', 'PSO067G0046' => 'pso', 'PSO478G1073' => 'pso', 'PSO675G3677' => 'pso', 'PSO675G6558' => 'pso', 'PSO675G7520' => 'pso', 'PSO675G8959' => 'pso', 'QL02p074089' => 'qlo', 'QL02p089614' => 'qlo', 'QL03p057736' => 'qlo', 'RcHm_v2.0_Chr1g0364131' => 'rch', 'RcHm_v2.0_Chr2g0087801' => 'rch', 'RcHm_v2.0_Chr2g0087821' => 'rch', 'RcHm_v2.0_Chr2g0173231' => 'rch', 'RcHm_v2.0_Chr4g0433111' => 'rch', 'Rhsim03G0250300' => 'rsi', 'Rhsim08G0048400' => 'rsi', 'Rhsim10G0014800' => 'rsi', 'Rhsim12G0040100' => 'rsi', 'Rhsim12G0109700' => 'rsi', 'Sabra06G0049600' => 'sbr', 'Sabra08G0141000' => 'sbr', 'Sabra10G0021400' => 'sbr', 'Sabra16G0222900' => 'sbr', 'Sabra18G0108600' => 'sbr', 'SalBow1G0433' => 'sbo', 'SalBow1G2038' => 'sbo', 'SalBow1G5003' => 'sbo', 'SalBow7G1197' => 'sbo', 'SalBow8G3506' => 'sbo', 'Sc03g0007300' => 'sci', 'Sc11g0000950' => 'sci', 'Sc14g0008750' => 'sci', 'Sc18g0000420' => 'sci', 'Sed0006754' => 'sed', 'Sed0008741' => 'sed', 'Sed0017172' => 'sed', 'Sed0018925' => 'sed', 'Sed0023326' => 'sed', 'Sed0025909' => 'sed', 'SEGI_05333' => 'sgi', 'SEGI_10362' => 'sgi', 'SEGI_13380' => 'sgi', 'SEGI_24306' => 'sgi', 'SEGI_29077' => 'sgi', 'SEGI_29095' => 'sgi', 'SEGI_36534' => 'sgi', 'SEGI_37506' => 'sgi', 'SEGI_38321' => 'sgi', 'SGA_v2.0_scaffold307G48031' => 'sas', 'SGA_v2.0_scaffold47G17507' => 'sas', 'SGA_v2.0_scaffold63G21736' => 'sas', 'SGA_v2.0_scaffold87G27070' => 'sas', 'SHI17794' => 'shi', 'SHI28851' => 'shi', 'SMO165G0155' => 'smo', 'SMO340G0217' => 'smo', 'SMO367G1210' => 'smo', 'Solyc02g093430.3' => 'sly', 'Solyc05g013580.4' => 'sly', 'Solyc07g008030.3' => 'sly', 'Solyc12g035470.2' => 'sly', 'Sopen02g038020' => 'spe', 'Sopen05g008490' => 'spe', 'Sopen07g003910' => 'spe', 'Sopen12g015240' => 'spe', 'Sp1g11550' => 'spa', 'Sp2g16710' => 'spa', 'Sp3g00430' => 'spa', 'Sp3g26780' => 'spa', 'Sp5g22900' => 'spa', 'Sp6g29530' => 'spa', 'TAR371G0794' => 'tar', 'TAR374G0164' => 'tar', 'TAR622G0165' => 'tar', 'TAR626G0929' => 'tar', 'TAR629G2155' => 'tar', 'THA.LOC104805282' => 'tha', 'THA.LOC104805363' => 'tha', 'THA.LOC104808968' => 'tha', 'THA.LOC104821093' => 'tha', 'THA.LOC104823953' => 'tha', 'THA.LOC104825562' => 'tha', 'THA.LOC104825665' => 'tha', 'Thecc.02G261400' => 'tca', 'Thecc.04G019200' => 'tca', 'Thecc.09G130400' => 'tca', 'Thhalv10004374m.g' => 'esa', 'Thhalv10007850m.g' => 'esa', 'Thhalv10013782m.g' => 'esa', 'Thhalv10018686m.g' => 'esa', 'Thhalv10020899m.g' => 'esa', 'Thhalv10022755m.g' => 'esa', 'TPR.G23851' => 'tpr', 'TPR.G26500' => 'tpr', 'TPR.G27267' => 'tpr', 'TPR.G32001' => 'tpr', 'TPR.G6251' => 'tpr', 'TPR.G8167' => 'tpr', 'TWI12G1330' => 'twi', 'TWI18G1239' => 'twi', 'TWI34G0979' => 'twi', 'TWI36G0670' => 'twi', 'TWI36G0707' => 'twi', 'TWI56G0233' => 'twi', 'TWI75G1809' => 'twi', 'unitig_21.g20874' => 'ugi', 'unitig_26.g10343' => 'ugi', 'unitig_46.g18392' => 'ugi', 'unitig_52.g17178' => 'ugi', 'unitig_8.g2934' => 'ugi', 'vmacro01122' => 'vma', 'vmacro05875' => 'vma', 'vmacro06147' => 'vma', 'vmacro16191' => 'vma', 'vmacro18293' => 'vma', 'VMungo0251G3707' => 'vmu', 'VMungo0464G1521' => 'vmu', 'VMungo1215G0205' => 'vmu', 'VMungo1383G2484' => 'vmu', 'Zm00001eb079610' => 'zma', 'Zm00001eb135990' => 'zma', 'Zm00001eb183710' => 'zma', 'Zm00001eb246020' => 'zma' ) $gf_id = 'HOM05D001124' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001124' ) $data_identifier = 'HOM05D001124' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 6, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 7, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 21, 'bol' => (int) 10, 'bra' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 6, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 9, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 21, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 8, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 10, 'lsa' => (int) 8, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 8, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 9, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb246020' $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' => 'HOM05D001124', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '548', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02520' => 'bna', 'A03p06630' => 'bna', 'A05p44460' => 'bna', 'A06p08710' => 'bna', 'A06p41090' => 'bna', 'A07p32320' => 'bna', 'A08p32520' => 'bna', 'A09p10360' => 'bna', 'A10p24080' => 'bna', 'Aa31LG11G15250' => 'aar', 'Aa31LG1G1800' => 'aar', 'Aa31LG2G5120' => 'aar', 'Aa31LG2G6070' => 'aar', 'Aa31LG5G10770' => 'aar', 'Aa31sc61G90' => 'aar', 'Actinidia01352' => 'ach', 'Actinidia05983' => 'ach', 'Actinidia08133' => 'ach', 'Actinidia15101' => 'ach', 'Actinidia26379' => 'ach', 'Actinidia35778' => 'ach', 'Actinidia36123' => 'ach', 'Actinidia37436' => 'ach', 'Actinidia38730' => 'ach', 'Ah.02g128210' => 'amhyb', 'Ah.03g132990' => 'amhyb', 'Ah.14g079410' => 'amhyb', 'AL1G24640' => 'aly', 'AL2G26680' => 'aly', 'AL3G10530' => 'aly', 'AL3G45230' => 'aly', 'AL5G15230' => 'aly', 'AL5G16960' => 'aly', 'AL6G25210' => 'aly', 'Aqoxy2G00441' => 'aox', 'Aqoxy3G01236' => 'aox', 'Aqoxy5G03746' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3RQ047' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C7GMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9C8JER' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MBL6KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YXCZ83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZANX40' => 'arhy', 'AT1G12990' => 'ath', 'AT1G67880' => 'ath', 'AT2G13290' => 'ath', 'AT3G01620' => 'ath', 'AT3G26445' => 'ath', 'AT3G27540' => 'ath', 'AT5G14480' => 'ath', 'ATR0824G026' => 'atr', 'ATR1098G019' => 'atr', 'Atru.chr11.2145' => 'acertr', 'Atru.chr2.3636' => 'acertr', 'Atru.chr2.3644' => 'acertr', 'Atru.chr6.2422' => 'acertr', 'Atru.chr7.1112' => 'acertr', 'AUR62005469' => 'cqu', 'AUR62011166' => 'cqu', 'AUR62013319' => 'cqu', 'AUR62024273' => 'cqu', 'AUR62028420' => 'cqu', 'AUR62041942' => 'cqu', 'BcaB01g04969' => 'bca', 'BcaB01g06371' => 'bca', 'BcaB02g11494' => 'bca', 'BcaB03g15382' => 'bca', 'BcaB08g36994' => 'bca', 'BcaC03g13477' => 'bca', 'BcaC03g13478' => 'bca', 'BcaC03g13480' => 'bca', 'BcaC03g13481' => 'bca', 'BcaC03g13486' => 'bca', 'BcaC04g19031' => 'bca', 'BcaC04g23085' => 'bca', 'BcaC05g25094' => 'bca', 'BcaC05g25096' => 'bca', 'BcaC05g25138' => 'bca', 'BcaC05g30416' => 'bca', 'BcaC05g30455' => 'bca', 'BcaC06g30979' => 'bca', 'BcaC06g33805' => 'bca', 'BcaC08g46021' => 'bca', 'BcaNung03154' => 'bca', 'BolC2t06623H' => 'bol', 'BolC2t06632H' => 'bol', 'BolC2t06635H' => 'bol', 'BolC2t06638H' => 'bol', 'BolC3t13266H' => 'bol', 'BolC5t29776H' => 'bol', 'BolC6t38912H' => 'bol', 'BolC7t44183H' => 'bol', 'BolC9t54123H' => 'bol', 'BolC9t59107H' => 'bol', 'BraA02t05221Z' => 'bra', 'BraA03t09996Z' => 'bra', 'BraA05t23210Z' => 'bra', 'BraA06t24068Z' => 'bra', 'BraA06t27032Z' => 'bra', 'BraA08t35176Z' => 'bra', 'BraA09t36680Z' => 'bra', 'BraA10t44471Z' => 'bra', 'C02p06760' => 'bna', 'C02p06890' => 'bna', 'C02p07010' => 'bna', 'C03p07660' => 'bna', 'C05p10300' => 'bna', 'C06p38150' => 'bna', 'C07p36650' => 'bna', 'C08p15770' => 'bna', 'C09p12300' => 'bna', 'C09p62700' => 'bna', 'C09p75040' => 'bna', 'CAN.G13.1' => 'can', 'CAN.G138.4' => 'can', 'CAN.G44.6' => 'can', 'CAN.G473.19' => 'can', 'CANSAT01G0835' => 'cansat', 'CANSAT11G0246' => 'cansat', 'CANSAT11G1766' => 'cansat', 'CANSAT64G1954' => 'cansat', 'CARHR013330' => 'chi', 'CARHR060530' => 'chi', 'CARHR075300' => 'chi', 'CARHR105120' => 'chi', 'CARHR148910' => 'chi', 'CARHR198830' => 'chi', 'Carub.0001s1275' => 'cru', 'Carub.0002s1437' => 'cru', 'Carub.0003s0044' => 'cru', 'Carub.0003s2787' => 'cru', 'Carub.0005s0597' => 'cru', 'Carub.0006s1266' => 'cru', 'Ca_06935_v3' => 'car', 'Ca_13559_v3' => 'car', 'Ca_16941_v3' => 'car', 'Ca_16960_v3' => 'car', 'Ca_17775_v3' => 'car', 'Ca_30464_v3' => 'car', 'Cc06_g08160' => 'ccan', 'Cc07_g01520' => 'ccan', 'Cc11_g15810' => 'ccan', 'CDE02G2840' => 'cde', 'CDE03G0093' => 'cde', 'CDE04G2127' => 'cde', 'CDE07G1857' => 'cde', 'CDE09G1246' => 'cde', 'Cfa003412' => 'cfa', 'Cfa007341' => 'cfa', 'Cfa009220' => 'cfa', 'Ciclev10008737m.g' => 'ccl', 'Ciclev10015565m.g' => 'ccl', 'Ciclev10031761m.g' => 'ccl', 'CiPaw.03G045300' => 'cil', 'CiPaw.03G247200' => 'cil', 'CiPaw.04G029500' => 'cil', 'CiPaw.04G174000' => 'cil', 'CiPaw.05G181200' => 'cil', 'CiPaw.06G067100' => 'cil', 'ClCG05G025800' => 'cla', 'ClCG06G011400' => 'cla', 'ClCG09G019360' => 'cla', 'COL.COLO4_04827' => 'col', 'COL.COLO4_29170' => 'col', 'COL.COLO4_35131' => 'col', 'COL.COLO4_35132' => 'col', 'Cpa.g.sc33.32' => 'cpa', 'Cpa.g.sc46.29' => 'cpa', 'Cpa.g.sc796.1' => 'cpa', 'CsaV3_1G030420' => 'csa', 'CsaV3_5G027050' => 'csa', 'CsaV3_5G031040' => 'csa', 'CsaV3_UNG023130' => 'csa', 'CSS0007726' => 'camsi', 'CSS0016433' => 'camsi', 'CSS0017656' => 'camsi', 'CSS0025364' => 'camsi', 'CSS0027582' => 'camsi', 'CSS0047288' => 'camsi', 'CSS0049950' => 'camsi', 'DCAR_003843' => 'dca', 'DCAR_007052' => 'dca', 'DCAR_020884' => 'dca', 'DCAR_021730' => 'dca', 'DCAR_024423' => 'dca', 'DCAR_026509' => 'dca', 'DCAR_031158' => 'dca', 'Dinv14728' => 'din', 'Dinv15219' => 'din', 'Dinv25728' => 'din', 'Dinv33428' => 'din', 'Dinv36489' => 'din', 'Dinv41486' => 'din', 'Duzib147G0469' => 'dzi', 'Duzib168G0060' => 'dzi', 'Duzib187G1215' => 'dzi', 'Duzib248G0692' => 'dzi', 'Duzib251G0767' => 'dzi', 'Duzib264G0446' => 'dzi', 'Duzib268G0691' => 'dzi', 'ECA232G4767' => 'eca', 'ECA233G2838' => 'eca', 'ECA234G0391' => 'eca', 'ECA234G0857' => 'eca', 'ECA236G1593' => 'eca', 'ECA238G0565' => 'eca', 'ECA246G1027' => 'eca', 'ECA246G3223' => 'eca', 'ECA246G3470' => 'eca', 'EL10Ac6g13829' => 'bvu', 'EL10Ac6g14093' => 'bvu', 'EL10Ac8g18707' => 'bvu', 'Eucgr.C01369' => 'egr', 'Eucgr.H02492' => 'egr', 'Eucgr.I01733' => 'egr', 'Eucgr.J02255' => 'egr', 'Eucgr.J02257' => 'egr', 'Eucgr.J02258' => 'egr', 'FAN02G1601' => 'fan', 'FAN03G1586' => 'fan', 'FAN03G2986' => 'fan', 'FAN05G4837' => 'fan', 'FAN06G0146' => 'fan', 'FAN07G0858' => 'fan', 'FAN09G3179' => 'fan', 'FAN10G0669' => 'fan', 'FAN12G2358' => 'fan', 'FAN14G4198' => 'fan', 'FAN14G5112' => 'fan', 'FAN17G0342' => 'fan', 'FAN19G0342' => 'fan', 'FAN19G0962' => 'fan', 'FAN19G1101' => 'fan', 'FAN19G1872' => 'fan', 'FAN22G0356' => 'fan', 'FAN23G0744' => 'fan', 'FAN23G1914' => 'fan', 'FAN26G0032' => 'fan', 'FAN28G0625' => 'fan', 'FvH4_1g02710' => 'fve', 'FvH4_1g02720' => 'fve', 'FvH4_4g25670' => 'fve', 'FvH4_6g51700' => 'fve', 'FvH4_7g20170' => 'fve', 'Glyma.05G175000' => 'gma', 'Glyma.08G132300' => 'gma', 'Glyma.11G243000' => 'gma', 'Glyma.13G158900' => 'gma', 'Glyma.17G112400' => 'gma', 'Glyma.18G014100' => 'gma', 'Glyma.19G003100' => 'gma', 'Glyma.19G056500' => 'gma', 'Gohir.A01G158900' => 'ghi', 'Gohir.A05G312600' => 'ghi', 'Gohir.A05G354900' => 'ghi', 'Gohir.A07G037200' => 'ghi', 'Gohir.A09G030000' => 'ghi', 'Gohir.A12G145200' => 'ghi', 'Gohir.D01G151500' => 'ghi', 'Gohir.D04G058300' => 'ghi', 'Gohir.D05G314100' => 'ghi', 'Gohir.D07G041400' => 'ghi', 'Gohir.D09G029700' => 'ghi', 'Gohir.D12G149700' => 'ghi', 'Gorai.001G043800' => 'gra', 'Gorai.002G187800' => 'gra', 'Gorai.006G034700' => 'gra', 'Gorai.008G161200' => 'gra', 'Gorai.009G335700' => 'gra', 'Gorai.012G065000' => 'gra', 'GSVIVG01000535001' => 'vvi', 'GSVIVG01015572001' => 'vvi', 'GSVIVG01032386001' => 'vvi', 'HanXRQChr05g0138531' => 'han', 'HanXRQChr06g0174391' => 'han', 'HanXRQChr07g0199021' => 'han', 'HanXRQChr08g0208211' => 'han', 'HanXRQChr09g0255471' => 'han', 'HanXRQChr10g0315791' => 'han', 'HanXRQChr12g0371991' => 'han', 'HanXRQChr15g0475251' => 'han', 'HanXRQChr17g0540001' => 'han', 'HanXRQChr17g0548631' => 'han', 'HanXRQChr17g0569561' => 'han', 'Haze_12256' => 'cav', 'Haze_14756' => 'cav', 'Haze_25528' => 'cav', 'Hma1.2p1_0079F.1_g041020' => 'hma', 'Hma1.2p1_0818F.1_g223260' => 'hma', 'Hma1.2p1_1747F.1_g300530' => 'hma', 'HPP92_004607' => 'vpl', 'HPP92_004608' => 'vpl', 'HPP92_006181' => 'vpl', 'HPP92_012192' => 'vpl', 'HPP92_015680' => 'vpl', 'HPP92_020249' => 'vpl', 'HPP92_021376' => 'vpl', 'HPP92_024275' => 'vpl', 'Hund06031' => 'sun', 'Hund25391' => 'sun', 'Lalb_Chr07g0185371' => 'lal', 'Lalb_Chr07g0185381' => 'lal', 'Lalb_Chr12g0204011' => 'lal', 'Lalb_Chr13g0301671' => 'lal', 'Lalb_Chr14g0362851' => 'lal', 'Lalb_Chr24g0403581' => 'lal', 'Lj1g0000233' => 'lja', 'Lj2g0018120' => 'lja', 'Lj3C621T0' => 'lonja', 'Lj3P1059T14' => 'lonja', 'Lj3P611T9' => 'lonja', 'Lj3P614T13' => 'lonja', 'Lj3P615T5' => 'lonja', 'Lj4g0012315' => 'lja', 'Lj4g0026182' => 'lja', 'Lj6P813T16' => 'lonja', 'Lj7C427T7' => 'lonja', 'Lj7C427T8' => 'lonja', 'Lj7P600T41' => 'lonja', 'Lju41C42G17' => 'lonja', 'Lsat_1_v5_gn_0_47300' => 'lsa', 'Lsat_1_v5_gn_2_91280' => 'lsa', 'Lsat_1_v5_gn_3_30561' => 'lsa', 'Lsat_1_v5_gn_4_184321' => 'lsa', 'Lsat_1_v5_gn_4_4041' => 'lsa', 'Lsat_1_v5_gn_5_92000' => 'lsa', 'Lsat_1_v5_gn_8_152940' => 'lsa', 'Lsat_1_v5_gn_8_62401' => 'lsa', 'Manes.06G055900' => 'mes', 'Manes.12G022200' => 'mes', 'Manes.13G023300' => 'mes', 'Manes.14G115000' => 'mes', 'Manes.15G151700' => 'mes', 'Manes.17G111300' => 'mes', 'Mapoly0226s0009' => 'mpo', 'MBI02_g25363_MAGBIO' => 'mbi', 'MBI06_g00027_MAGBIO' => 'mbi', 'MBI10_g13034_MAGBIO' => 'mbi', 'MD09G1023400' => 'mdo', 'MD13G1100100' => 'mdo', 'MD15G1169200' => 'mdo', 'MD16G1101100' => 'mdo', 'MD17G1022900' => 'mdo', 'Medtr3g096150' => 'mtr', 'Medtr4g115070' => 'mtr', 'Medtr7g033325' => 'mtr', 'Medtr8g089840' => 'mtr', 'MELO3C010319.2' => 'cme', 'MELO3C011944.2' => 'cme', 'MELO3C021589.2' => 'cme', 'Migut.E00207' => 'egut', 'Migut.H00067' => 'egut', 'Migut.K00433' => 'egut', 'Migut.K00606' => 'egut', 'Migut.K01410' => 'egut', 'MSTRG.13347' => 'ama', 'MSTRG.24045' => 'ama', 'MSTRG.2428' => 'ama', 'MSTRG.26410' => 'ama', 'MSTRG.3139' => 'ama', 'MSTRG.3286' => 'ama', 'MSTRG.563' => 'ama', 'MSTRG.7941' => 'ama', 'Nitab4.5_0000028g0060' => 'nta', 'Nitab4.5_0000065g0260' => 'nta', 'Nitab4.5_0000112g0060' => 'nta', 'Nitab4.5_0000489g0120' => 'nta', 'Nitab4.5_0001776g0050' => 'nta', 'Nitab4.5_0001854g0010' => 'nta', 'Nitab4.5_0001860g0020' => 'nta', 'Nitab4.5_0004352g0010' => 'nta', 'Nitab4.5_0008716g0020' => 'nta', 'Nitab4.5_0008922g0010' => 'nta', 'Nn3g16693' => 'nnu', 'Nn4g22596' => 'nnu', 'Nn7g37639' => 'nnu', 'Oeu001701.1' => 'oeu', 'Oeu018149.1' => 'oeu', 'Oeu026220.1' => 'oeu', 'Oeu038635.1' => 'oeu', 'Oeu049176.1' => 'oeu', 'Oeu056706.1' => 'oeu', 'Oeu056937.1' => 'oeu', 'Oeu057540.1' => 'oeu', 'Os02g0594900' => 'osa', 'Os02g0595100' => 'osa', 'Os04g0477500' => 'osa', 'Os12g0611900' => 'osa', 'Peaxi162Scf00076g00020' => 'pax', 'Peaxi162Scf00128g00217' => 'pax', 'Peaxi162Scf00129g01640' => 'pax', 'Peaxi162Scf00669g00007' => 'pax', 'Peaxi162Scf00700g00421' => 'pax', 'Peaxi162Scf00801g00038' => 'pax', 'Peaxi162Scf00891g00025' => 'pax', 'PGR083G0909' => 'pgr', 'PGR119G1005' => 'pgr', 'PGR142G2236' => 'pgr', 'PGR142G3388' => 'pgr', 'PGSC0003DMG400004514' => 'stu', 'PGSC0003DMG400012635' => 'stu', 'PGSC0003DMG400015730' => 'stu', 'PGSC0003DMG400018611' => 'stu', 'PGSC0003DMG400030897' => 'stu', 'Phvul.001G254800' => 'pvu', 'Phvul.002G260100' => 'pvu', 'Phvul.003G167600' => 'pvu', 'Phvul.004G005100' => 'pvu', 'Potri.001G343600' => 'ptr', 'Potri.006G066700' => 'ptr', 'Potri.008G186000' => 'ptr', 'Potri.010G046900' => 'ptr', 'Potri.018G127900' => 'ptr', 'Pp3c20_17750' => 'ppa', 'Pp3c24_4380' => 'ppa', 'Prupe.1G245800' => 'ppe', 'Prupe.3G293400' => 'ppe', 'Prupe.7G247400' => 'ppe', 'Psat0s145g0120' => 'psa', 'Psat0s595g0040' => 'psa', 'Psat0s595g0120' => 'psa', 'Psat3g175040' => 'psa', 'Psat7g058120' => 'psa', 'PSO017G0428' => 'pso', 'PSO063G7510' => 'pso', 'PSO067G0046' => 'pso', 'PSO478G1073' => 'pso', 'PSO675G3677' => 'pso', 'PSO675G6558' => 'pso', 'PSO675G7520' => 'pso', 'PSO675G8959' => 'pso', 'QL02p074089' => 'qlo', 'QL02p089614' => 'qlo', 'QL03p057736' => 'qlo', 'RcHm_v2.0_Chr1g0364131' => 'rch', 'RcHm_v2.0_Chr2g0087801' => 'rch', 'RcHm_v2.0_Chr2g0087821' => 'rch', 'RcHm_v2.0_Chr2g0173231' => 'rch', 'RcHm_v2.0_Chr4g0433111' => 'rch', 'Rhsim03G0250300' => 'rsi', 'Rhsim08G0048400' => 'rsi', 'Rhsim10G0014800' => 'rsi', 'Rhsim12G0040100' => 'rsi', 'Rhsim12G0109700' => 'rsi', 'Sabra06G0049600' => 'sbr', 'Sabra08G0141000' => 'sbr', 'Sabra10G0021400' => 'sbr', 'Sabra16G0222900' => 'sbr', 'Sabra18G0108600' => 'sbr', 'SalBow1G0433' => 'sbo', 'SalBow1G2038' => 'sbo', 'SalBow1G5003' => 'sbo', 'SalBow7G1197' => 'sbo', 'SalBow8G3506' => 'sbo', 'Sc03g0007300' => 'sci', 'Sc11g0000950' => 'sci', 'Sc14g0008750' => 'sci', 'Sc18g0000420' => 'sci', 'Sed0006754' => 'sed', 'Sed0008741' => 'sed', 'Sed0017172' => 'sed', 'Sed0018925' => 'sed', 'Sed0023326' => 'sed', 'Sed0025909' => 'sed', 'SEGI_05333' => 'sgi', 'SEGI_10362' => 'sgi', 'SEGI_13380' => 'sgi', 'SEGI_24306' => 'sgi', 'SEGI_29077' => 'sgi', 'SEGI_29095' => 'sgi', 'SEGI_36534' => 'sgi', 'SEGI_37506' => 'sgi', 'SEGI_38321' => 'sgi', 'SGA_v2.0_scaffold307G48031' => 'sas', 'SGA_v2.0_scaffold47G17507' => 'sas', 'SGA_v2.0_scaffold63G21736' => 'sas', 'SGA_v2.0_scaffold87G27070' => 'sas', 'SHI17794' => 'shi', 'SHI28851' => 'shi', 'SMO165G0155' => 'smo', 'SMO340G0217' => 'smo', 'SMO367G1210' => 'smo', 'Solyc02g093430.3' => 'sly', 'Solyc05g013580.4' => 'sly', 'Solyc07g008030.3' => 'sly', 'Solyc12g035470.2' => 'sly', 'Sopen02g038020' => 'spe', 'Sopen05g008490' => 'spe', 'Sopen07g003910' => 'spe', 'Sopen12g015240' => 'spe', 'Sp1g11550' => 'spa', 'Sp2g16710' => 'spa', 'Sp3g00430' => 'spa', 'Sp3g26780' => 'spa', 'Sp5g22900' => 'spa', 'Sp6g29530' => 'spa', 'TAR371G0794' => 'tar', 'TAR374G0164' => 'tar', 'TAR622G0165' => 'tar', 'TAR626G0929' => 'tar', 'TAR629G2155' => 'tar', 'THA.LOC104805282' => 'tha', 'THA.LOC104805363' => 'tha', 'THA.LOC104808968' => 'tha', 'THA.LOC104821093' => 'tha', 'THA.LOC104823953' => 'tha', 'THA.LOC104825562' => 'tha', 'THA.LOC104825665' => 'tha', 'Thecc.02G261400' => 'tca', 'Thecc.04G019200' => 'tca', 'Thecc.09G130400' => 'tca', 'Thhalv10004374m.g' => 'esa', 'Thhalv10007850m.g' => 'esa', 'Thhalv10013782m.g' => 'esa', 'Thhalv10018686m.g' => 'esa', 'Thhalv10020899m.g' => 'esa', 'Thhalv10022755m.g' => 'esa', 'TPR.G23851' => 'tpr', 'TPR.G26500' => 'tpr', 'TPR.G27267' => 'tpr', 'TPR.G32001' => 'tpr', 'TPR.G6251' => 'tpr', 'TPR.G8167' => 'tpr', 'TWI12G1330' => 'twi', 'TWI18G1239' => 'twi', 'TWI34G0979' => 'twi', 'TWI36G0670' => 'twi', 'TWI36G0707' => 'twi', 'TWI56G0233' => 'twi', 'TWI75G1809' => 'twi', 'unitig_21.g20874' => 'ugi', 'unitig_26.g10343' => 'ugi', 'unitig_46.g18392' => 'ugi', 'unitig_52.g17178' => 'ugi', 'unitig_8.g2934' => 'ugi', 'vmacro01122' => 'vma', 'vmacro05875' => 'vma', 'vmacro06147' => 'vma', 'vmacro16191' => 'vma', 'vmacro18293' => 'vma', 'VMungo0251G3707' => 'vmu', 'VMungo0464G1521' => 'vmu', 'VMungo1215G0205' => 'vmu', 'VMungo1383G2484' => 'vmu', 'Zm00001eb079610' => 'zma', 'Zm00001eb135990' => 'zma', 'Zm00001eb183710' => 'zma', 'Zm00001eb246020' => 'zma' ), 'gf_id' => 'HOM05D001124', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001124' ), 'data_identifier' => 'HOM05D001124', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001124', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '548', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02520' => 'bna', 'A03p06630' => 'bna', 'A05p44460' => 'bna', 'A06p08710' => 'bna', 'A06p41090' => 'bna', 'A07p32320' => 'bna', 'A08p32520' => 'bna', 'A09p10360' => 'bna', 'A10p24080' => 'bna', 'Aa31LG11G15250' => 'aar', 'Aa31LG1G1800' => 'aar', 'Aa31LG2G5120' => 'aar', 'Aa31LG2G6070' => 'aar', 'Aa31LG5G10770' => 'aar', 'Aa31sc61G90' => 'aar', 'Actinidia01352' => 'ach', 'Actinidia05983' => 'ach', 'Actinidia08133' => 'ach', 'Actinidia15101' => 'ach', 'Actinidia26379' => 'ach', 'Actinidia35778' => 'ach', 'Actinidia36123' => 'ach', 'Actinidia37436' => 'ach', 'Actinidia38730' => 'ach', 'Ah.02g128210' => 'amhyb', 'Ah.03g132990' => 'amhyb', 'Ah.14g079410' => 'amhyb', 'AL1G24640' => 'aly', 'AL2G26680' => 'aly', 'AL3G10530' => 'aly', 'AL3G45230' => 'aly', 'AL5G15230' => 'aly', 'AL5G16960' => 'aly', 'AL6G25210' => 'aly', 'Aqoxy2G00441' => 'aox', 'Aqoxy3G01236' => 'aox', 'Aqoxy5G03746' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3RQ047' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C7GMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9C8JER' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MBL6KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YXCZ83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZANX40' => 'arhy', 'AT1G12990' => 'ath', 'AT1G67880' => 'ath', 'AT2G13290' => 'ath', 'AT3G01620' => 'ath', 'AT3G26445' => 'ath', 'AT3G27540' => 'ath', 'AT5G14480' => 'ath', 'ATR0824G026' => 'atr', 'ATR1098G019' => 'atr', 'Atru.chr11.2145' => 'acertr', 'Atru.chr2.3636' => 'acertr', 'Atru.chr2.3644' => 'acertr', 'Atru.chr6.2422' => 'acertr', 'Atru.chr7.1112' => 'acertr', 'AUR62005469' => 'cqu', 'AUR62011166' => 'cqu', 'AUR62013319' => 'cqu', 'AUR62024273' => 'cqu', 'AUR62028420' => 'cqu', 'AUR62041942' => 'cqu', 'BcaB01g04969' => 'bca', 'BcaB01g06371' => 'bca', 'BcaB02g11494' => 'bca', 'BcaB03g15382' => 'bca', 'BcaB08g36994' => 'bca', 'BcaC03g13477' => 'bca', 'BcaC03g13478' => 'bca', 'BcaC03g13480' => 'bca', 'BcaC03g13481' => 'bca', 'BcaC03g13486' => 'bca', 'BcaC04g19031' => 'bca', 'BcaC04g23085' => 'bca', 'BcaC05g25094' => 'bca', 'BcaC05g25096' => 'bca', 'BcaC05g25138' => 'bca', 'BcaC05g30416' => 'bca', 'BcaC05g30455' => 'bca', 'BcaC06g30979' => 'bca', 'BcaC06g33805' => 'bca', 'BcaC08g46021' => 'bca', 'BcaNung03154' => 'bca', 'BolC2t06623H' => 'bol', 'BolC2t06632H' => 'bol', 'BolC2t06635H' => 'bol', 'BolC2t06638H' => 'bol', 'BolC3t13266H' => 'bol', 'BolC5t29776H' => 'bol', 'BolC6t38912H' => 'bol', 'BolC7t44183H' => 'bol', 'BolC9t54123H' => 'bol', 'BolC9t59107H' => 'bol', 'BraA02t05221Z' => 'bra', 'BraA03t09996Z' => 'bra', 'BraA05t23210Z' => 'bra', 'BraA06t24068Z' => 'bra', 'BraA06t27032Z' => 'bra', 'BraA08t35176Z' => 'bra', 'BraA09t36680Z' => 'bra', 'BraA10t44471Z' => 'bra', 'C02p06760' => 'bna', 'C02p06890' => 'bna', 'C02p07010' => 'bna', 'C03p07660' => 'bna', 'C05p10300' => 'bna', 'C06p38150' => 'bna', 'C07p36650' => 'bna', 'C08p15770' => 'bna', 'C09p12300' => 'bna', 'C09p62700' => 'bna', 'C09p75040' => 'bna', 'CAN.G13.1' => 'can', 'CAN.G138.4' => 'can', 'CAN.G44.6' => 'can', 'CAN.G473.19' => 'can', 'CANSAT01G0835' => 'cansat', 'CANSAT11G0246' => 'cansat', 'CANSAT11G1766' => 'cansat', 'CANSAT64G1954' => 'cansat', 'CARHR013330' => 'chi', 'CARHR060530' => 'chi', 'CARHR075300' => 'chi', 'CARHR105120' => 'chi', 'CARHR148910' => 'chi', 'CARHR198830' => 'chi', 'Carub.0001s1275' => 'cru', 'Carub.0002s1437' => 'cru', 'Carub.0003s0044' => 'cru', 'Carub.0003s2787' => 'cru', 'Carub.0005s0597' => 'cru', 'Carub.0006s1266' => 'cru', 'Ca_06935_v3' => 'car', 'Ca_13559_v3' => 'car', 'Ca_16941_v3' => 'car', 'Ca_16960_v3' => 'car', 'Ca_17775_v3' => 'car', 'Ca_30464_v3' => 'car', 'Cc06_g08160' => 'ccan', 'Cc07_g01520' => 'ccan', 'Cc11_g15810' => 'ccan', 'CDE02G2840' => 'cde', 'CDE03G0093' => 'cde', 'CDE04G2127' => 'cde', 'CDE07G1857' => 'cde', 'CDE09G1246' => 'cde', 'Cfa003412' => 'cfa', 'Cfa007341' => 'cfa', 'Cfa009220' => 'cfa', 'Ciclev10008737m.g' => 'ccl', 'Ciclev10015565m.g' => 'ccl', 'Ciclev10031761m.g' => 'ccl', 'CiPaw.03G045300' => 'cil', 'CiPaw.03G247200' => 'cil', 'CiPaw.04G029500' => 'cil', 'CiPaw.04G174000' => 'cil', 'CiPaw.05G181200' => 'cil', 'CiPaw.06G067100' => 'cil', 'ClCG05G025800' => 'cla', 'ClCG06G011400' => 'cla', 'ClCG09G019360' => 'cla', 'COL.COLO4_04827' => 'col', 'COL.COLO4_29170' => 'col', 'COL.COLO4_35131' => 'col', 'COL.COLO4_35132' => 'col', 'Cpa.g.sc33.32' => 'cpa', 'Cpa.g.sc46.29' => 'cpa', 'Cpa.g.sc796.1' => 'cpa', 'CsaV3_1G030420' => 'csa', 'CsaV3_5G027050' => 'csa', 'CsaV3_5G031040' => 'csa', 'CsaV3_UNG023130' => 'csa', 'CSS0007726' => 'camsi', 'CSS0016433' => 'camsi', 'CSS0017656' => 'camsi', 'CSS0025364' => 'camsi', 'CSS0027582' => 'camsi', 'CSS0047288' => 'camsi', 'CSS0049950' => 'camsi', 'DCAR_003843' => 'dca', 'DCAR_007052' => 'dca', 'DCAR_020884' => 'dca', 'DCAR_021730' => 'dca', 'DCAR_024423' => 'dca', 'DCAR_026509' => 'dca', 'DCAR_031158' => 'dca', 'Dinv14728' => 'din', 'Dinv15219' => 'din', 'Dinv25728' => 'din', 'Dinv33428' => 'din', 'Dinv36489' => 'din', 'Dinv41486' => 'din', 'Duzib147G0469' => 'dzi', 'Duzib168G0060' => 'dzi', 'Duzib187G1215' => 'dzi', 'Duzib248G0692' => 'dzi', 'Duzib251G0767' => 'dzi', 'Duzib264G0446' => 'dzi', 'Duzib268G0691' => 'dzi', 'ECA232G4767' => 'eca', 'ECA233G2838' => 'eca', 'ECA234G0391' => 'eca', 'ECA234G0857' => 'eca', 'ECA236G1593' => 'eca', 'ECA238G0565' => 'eca', 'ECA246G1027' => 'eca', 'ECA246G3223' => 'eca', 'ECA246G3470' => 'eca', 'EL10Ac6g13829' => 'bvu', 'EL10Ac6g14093' => 'bvu', 'EL10Ac8g18707' => 'bvu', 'Eucgr.C01369' => 'egr', 'Eucgr.H02492' => 'egr', 'Eucgr.I01733' => 'egr', 'Eucgr.J02255' => 'egr', 'Eucgr.J02257' => 'egr', 'Eucgr.J02258' => 'egr', 'FAN02G1601' => 'fan', 'FAN03G1586' => 'fan', 'FAN03G2986' => 'fan', 'FAN05G4837' => 'fan', 'FAN06G0146' => 'fan', 'FAN07G0858' => 'fan', 'FAN09G3179' => 'fan', 'FAN10G0669' => 'fan', 'FAN12G2358' => 'fan', 'FAN14G4198' => 'fan', 'FAN14G5112' => 'fan', 'FAN17G0342' => 'fan', 'FAN19G0342' => 'fan', 'FAN19G0962' => 'fan', 'FAN19G1101' => 'fan', 'FAN19G1872' => 'fan', 'FAN22G0356' => 'fan', 'FAN23G0744' => 'fan', 'FAN23G1914' => 'fan', 'FAN26G0032' => 'fan', 'FAN28G0625' => 'fan', 'FvH4_1g02710' => 'fve', 'FvH4_1g02720' => 'fve', 'FvH4_4g25670' => 'fve', 'FvH4_6g51700' => 'fve', 'FvH4_7g20170' => 'fve', 'Glyma.05G175000' => 'gma', 'Glyma.08G132300' => 'gma', 'Glyma.11G243000' => 'gma', 'Glyma.13G158900' => 'gma', 'Glyma.17G112400' => 'gma', 'Glyma.18G014100' => 'gma', 'Glyma.19G003100' => 'gma', 'Glyma.19G056500' => 'gma', 'Gohir.A01G158900' => 'ghi', 'Gohir.A05G312600' => 'ghi', 'Gohir.A05G354900' => 'ghi', 'Gohir.A07G037200' => 'ghi', 'Gohir.A09G030000' => 'ghi', 'Gohir.A12G145200' => 'ghi', 'Gohir.D01G151500' => 'ghi', 'Gohir.D04G058300' => 'ghi', 'Gohir.D05G314100' => 'ghi', 'Gohir.D07G041400' => 'ghi', 'Gohir.D09G029700' => 'ghi', 'Gohir.D12G149700' => 'ghi', 'Gorai.001G043800' => 'gra', 'Gorai.002G187800' => 'gra', 'Gorai.006G034700' => 'gra', 'Gorai.008G161200' => 'gra', 'Gorai.009G335700' => 'gra', 'Gorai.012G065000' => 'gra', 'GSVIVG01000535001' => 'vvi', 'GSVIVG01015572001' => 'vvi', 'GSVIVG01032386001' => 'vvi', 'HanXRQChr05g0138531' => 'han', 'HanXRQChr06g0174391' => 'han', 'HanXRQChr07g0199021' => 'han', 'HanXRQChr08g0208211' => 'han', 'HanXRQChr09g0255471' => 'han', 'HanXRQChr10g0315791' => 'han', 'HanXRQChr12g0371991' => 'han', 'HanXRQChr15g0475251' => 'han', 'HanXRQChr17g0540001' => 'han', 'HanXRQChr17g0548631' => 'han', 'HanXRQChr17g0569561' => 'han', 'Haze_12256' => 'cav', 'Haze_14756' => 'cav', 'Haze_25528' => 'cav', 'Hma1.2p1_0079F.1_g041020' => 'hma', 'Hma1.2p1_0818F.1_g223260' => 'hma', 'Hma1.2p1_1747F.1_g300530' => 'hma', 'HPP92_004607' => 'vpl', 'HPP92_004608' => 'vpl', 'HPP92_006181' => 'vpl', 'HPP92_012192' => 'vpl', 'HPP92_015680' => 'vpl', 'HPP92_020249' => 'vpl', 'HPP92_021376' => 'vpl', 'HPP92_024275' => 'vpl', 'Hund06031' => 'sun', 'Hund25391' => 'sun', 'Lalb_Chr07g0185371' => 'lal', 'Lalb_Chr07g0185381' => 'lal', 'Lalb_Chr12g0204011' => 'lal', 'Lalb_Chr13g0301671' => 'lal', 'Lalb_Chr14g0362851' => 'lal', 'Lalb_Chr24g0403581' => 'lal', 'Lj1g0000233' => 'lja', 'Lj2g0018120' => 'lja', 'Lj3C621T0' => 'lonja', 'Lj3P1059T14' => 'lonja', 'Lj3P611T9' => 'lonja', 'Lj3P614T13' => 'lonja', 'Lj3P615T5' => 'lonja', 'Lj4g0012315' => 'lja', 'Lj4g0026182' => 'lja', 'Lj6P813T16' => 'lonja', 'Lj7C427T7' => 'lonja', 'Lj7C427T8' => 'lonja', 'Lj7P600T41' => 'lonja', 'Lju41C42G17' => 'lonja', 'Lsat_1_v5_gn_0_47300' => 'lsa', 'Lsat_1_v5_gn_2_91280' => 'lsa', 'Lsat_1_v5_gn_3_30561' => 'lsa', 'Lsat_1_v5_gn_4_184321' => 'lsa', 'Lsat_1_v5_gn_4_4041' => 'lsa', 'Lsat_1_v5_gn_5_92000' => 'lsa', 'Lsat_1_v5_gn_8_152940' => 'lsa', 'Lsat_1_v5_gn_8_62401' => 'lsa', 'Manes.06G055900' => 'mes', 'Manes.12G022200' => 'mes', 'Manes.13G023300' => 'mes', 'Manes.14G115000' => 'mes', 'Manes.15G151700' => 'mes', 'Manes.17G111300' => 'mes', 'Mapoly0226s0009' => 'mpo', 'MBI02_g25363_MAGBIO' => 'mbi', 'MBI06_g00027_MAGBIO' => 'mbi', 'MBI10_g13034_MAGBIO' => 'mbi', 'MD09G1023400' => 'mdo', 'MD13G1100100' => 'mdo', 'MD15G1169200' => 'mdo', 'MD16G1101100' => 'mdo', 'MD17G1022900' => 'mdo', 'Medtr3g096150' => 'mtr', 'Medtr4g115070' => 'mtr', 'Medtr7g033325' => 'mtr', 'Medtr8g089840' => 'mtr', 'MELO3C010319.2' => 'cme', 'MELO3C011944.2' => 'cme', 'MELO3C021589.2' => 'cme', 'Migut.E00207' => 'egut', 'Migut.H00067' => 'egut', 'Migut.K00433' => 'egut', 'Migut.K00606' => 'egut', 'Migut.K01410' => 'egut', 'MSTRG.13347' => 'ama', 'MSTRG.24045' => 'ama', 'MSTRG.2428' => 'ama', 'MSTRG.26410' => 'ama', 'MSTRG.3139' => 'ama', 'MSTRG.3286' => 'ama', 'MSTRG.563' => 'ama', 'MSTRG.7941' => 'ama', 'Nitab4.5_0000028g0060' => 'nta', 'Nitab4.5_0000065g0260' => 'nta', 'Nitab4.5_0000112g0060' => 'nta', 'Nitab4.5_0000489g0120' => 'nta', 'Nitab4.5_0001776g0050' => 'nta', 'Nitab4.5_0001854g0010' => 'nta', 'Nitab4.5_0001860g0020' => 'nta', 'Nitab4.5_0004352g0010' => 'nta', 'Nitab4.5_0008716g0020' => 'nta', 'Nitab4.5_0008922g0010' => 'nta', 'Nn3g16693' => 'nnu', 'Nn4g22596' => 'nnu', 'Nn7g37639' => 'nnu', 'Oeu001701.1' => 'oeu', 'Oeu018149.1' => 'oeu', 'Oeu026220.1' => 'oeu', 'Oeu038635.1' => 'oeu', 'Oeu049176.1' => 'oeu', 'Oeu056706.1' => 'oeu', 'Oeu056937.1' => 'oeu', 'Oeu057540.1' => 'oeu', 'Os02g0594900' => 'osa', 'Os02g0595100' => 'osa', 'Os04g0477500' => 'osa', 'Os12g0611900' => 'osa', 'Peaxi162Scf00076g00020' => 'pax', 'Peaxi162Scf00128g00217' => 'pax', 'Peaxi162Scf00129g01640' => 'pax', 'Peaxi162Scf00669g00007' => 'pax', 'Peaxi162Scf00700g00421' => 'pax', 'Peaxi162Scf00801g00038' => 'pax', 'Peaxi162Scf00891g00025' => 'pax', 'PGR083G0909' => 'pgr', 'PGR119G1005' => 'pgr', 'PGR142G2236' => 'pgr', 'PGR142G3388' => 'pgr', 'PGSC0003DMG400004514' => 'stu', 'PGSC0003DMG400012635' => 'stu', 'PGSC0003DMG400015730' => 'stu', 'PGSC0003DMG400018611' => 'stu', 'PGSC0003DMG400030897' => 'stu', 'Phvul.001G254800' => 'pvu', 'Phvul.002G260100' => 'pvu', 'Phvul.003G167600' => 'pvu', 'Phvul.004G005100' => 'pvu', 'Potri.001G343600' => 'ptr', 'Potri.006G066700' => 'ptr', 'Potri.008G186000' => 'ptr', 'Potri.010G046900' => 'ptr', 'Potri.018G127900' => 'ptr', 'Pp3c20_17750' => 'ppa', 'Pp3c24_4380' => 'ppa', 'Prupe.1G245800' => 'ppe', 'Prupe.3G293400' => 'ppe', 'Prupe.7G247400' => 'ppe', 'Psat0s145g0120' => 'psa', 'Psat0s595g0040' => 'psa', 'Psat0s595g0120' => 'psa', 'Psat3g175040' => 'psa', 'Psat7g058120' => 'psa', 'PSO017G0428' => 'pso', 'PSO063G7510' => 'pso', 'PSO067G0046' => 'pso', 'PSO478G1073' => 'pso', 'PSO675G3677' => 'pso', 'PSO675G6558' => 'pso', 'PSO675G7520' => 'pso', 'PSO675G8959' => 'pso', 'QL02p074089' => 'qlo', 'QL02p089614' => 'qlo', 'QL03p057736' => 'qlo', 'RcHm_v2.0_Chr1g0364131' => 'rch', 'RcHm_v2.0_Chr2g0087801' => 'rch', 'RcHm_v2.0_Chr2g0087821' => 'rch', 'RcHm_v2.0_Chr2g0173231' => 'rch', 'RcHm_v2.0_Chr4g0433111' => 'rch', 'Rhsim03G0250300' => 'rsi', 'Rhsim08G0048400' => 'rsi', 'Rhsim10G0014800' => 'rsi', 'Rhsim12G0040100' => 'rsi', 'Rhsim12G0109700' => 'rsi', 'Sabra06G0049600' => 'sbr', 'Sabra08G0141000' => 'sbr', 'Sabra10G0021400' => 'sbr', 'Sabra16G0222900' => 'sbr', 'Sabra18G0108600' => 'sbr', 'SalBow1G0433' => 'sbo', 'SalBow1G2038' => 'sbo', 'SalBow1G5003' => 'sbo', 'SalBow7G1197' => 'sbo', 'SalBow8G3506' => 'sbo', 'Sc03g0007300' => 'sci', 'Sc11g0000950' => 'sci', 'Sc14g0008750' => 'sci', 'Sc18g0000420' => 'sci', 'Sed0006754' => 'sed', 'Sed0008741' => 'sed', 'Sed0017172' => 'sed', 'Sed0018925' => 'sed', 'Sed0023326' => 'sed', 'Sed0025909' => 'sed', 'SEGI_05333' => 'sgi', 'SEGI_10362' => 'sgi', 'SEGI_13380' => 'sgi', 'SEGI_24306' => 'sgi', 'SEGI_29077' => 'sgi', 'SEGI_29095' => 'sgi', 'SEGI_36534' => 'sgi', 'SEGI_37506' => 'sgi', 'SEGI_38321' => 'sgi', 'SGA_v2.0_scaffold307G48031' => 'sas', 'SGA_v2.0_scaffold47G17507' => 'sas', 'SGA_v2.0_scaffold63G21736' => 'sas', 'SGA_v2.0_scaffold87G27070' => 'sas', 'SHI17794' => 'shi', 'SHI28851' => 'shi', 'SMO165G0155' => 'smo', 'SMO340G0217' => 'smo', 'SMO367G1210' => 'smo', 'Solyc02g093430.3' => 'sly', 'Solyc05g013580.4' => 'sly', 'Solyc07g008030.3' => 'sly', 'Solyc12g035470.2' => 'sly', 'Sopen02g038020' => 'spe', 'Sopen05g008490' => 'spe', 'Sopen07g003910' => 'spe', 'Sopen12g015240' => 'spe', 'Sp1g11550' => 'spa', 'Sp2g16710' => 'spa', 'Sp3g00430' => 'spa', 'Sp3g26780' => 'spa', 'Sp5g22900' => 'spa', 'Sp6g29530' => 'spa', 'TAR371G0794' => 'tar', 'TAR374G0164' => 'tar', 'TAR622G0165' => 'tar', 'TAR626G0929' => 'tar', 'TAR629G2155' => 'tar', 'THA.LOC104805282' => 'tha', 'THA.LOC104805363' => 'tha', 'THA.LOC104808968' => 'tha', 'THA.LOC104821093' => 'tha', 'THA.LOC104823953' => 'tha', 'THA.LOC104825562' => 'tha', 'THA.LOC104825665' => 'tha', 'Thecc.02G261400' => 'tca', 'Thecc.04G019200' => 'tca', 'Thecc.09G130400' => 'tca', 'Thhalv10004374m.g' => 'esa', 'Thhalv10007850m.g' => 'esa', 'Thhalv10013782m.g' => 'esa', 'Thhalv10018686m.g' => 'esa', 'Thhalv10020899m.g' => 'esa', 'Thhalv10022755m.g' => 'esa', 'TPR.G23851' => 'tpr', 'TPR.G26500' => 'tpr', 'TPR.G27267' => 'tpr', 'TPR.G32001' => 'tpr', 'TPR.G6251' => 'tpr', 'TPR.G8167' => 'tpr', 'TWI12G1330' => 'twi', 'TWI18G1239' => 'twi', 'TWI34G0979' => 'twi', 'TWI36G0670' => 'twi', 'TWI36G0707' => 'twi', 'TWI56G0233' => 'twi', 'TWI75G1809' => 'twi', 'unitig_21.g20874' => 'ugi', 'unitig_26.g10343' => 'ugi', 'unitig_46.g18392' => 'ugi', 'unitig_52.g17178' => 'ugi', 'unitig_8.g2934' => 'ugi', 'vmacro01122' => 'vma', 'vmacro05875' => 'vma', 'vmacro06147' => 'vma', 'vmacro16191' => 'vma', 'vmacro18293' => 'vma', 'VMungo0251G3707' => 'vmu', 'VMungo0464G1521' => 'vmu', 'VMungo1215G0205' => 'vmu', 'VMungo1383G2484' => 'vmu', 'Zm00001eb079610' => 'zma', 'Zm00001eb135990' => 'zma', 'Zm00001eb183710' => 'zma', 'Zm00001eb246020' => 'zma' ) $gf_id = 'HOM05D001124' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001124' ) $data_identifier = 'HOM05D001124' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 6, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 7, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 21, 'bol' => (int) 10, 'bra' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 6, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 9, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 21, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 8, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 10, 'lsa' => (int) 8, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 8, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 9, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb246020' $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' => 'HOM05D001124', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '548', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02520' => 'bna', 'A03p06630' => 'bna', 'A05p44460' => 'bna', 'A06p08710' => 'bna', 'A06p41090' => 'bna', 'A07p32320' => 'bna', 'A08p32520' => 'bna', 'A09p10360' => 'bna', 'A10p24080' => 'bna', 'Aa31LG11G15250' => 'aar', 'Aa31LG1G1800' => 'aar', 'Aa31LG2G5120' => 'aar', 'Aa31LG2G6070' => 'aar', 'Aa31LG5G10770' => 'aar', 'Aa31sc61G90' => 'aar', 'Actinidia01352' => 'ach', 'Actinidia05983' => 'ach', 'Actinidia08133' => 'ach', 'Actinidia15101' => 'ach', 'Actinidia26379' => 'ach', 'Actinidia35778' => 'ach', 'Actinidia36123' => 'ach', 'Actinidia37436' => 'ach', 'Actinidia38730' => 'ach', 'Ah.02g128210' => 'amhyb', 'Ah.03g132990' => 'amhyb', 'Ah.14g079410' => 'amhyb', 'AL1G24640' => 'aly', 'AL2G26680' => 'aly', 'AL3G10530' => 'aly', 'AL3G45230' => 'aly', 'AL5G15230' => 'aly', 'AL5G16960' => 'aly', 'AL6G25210' => 'aly', 'Aqoxy2G00441' => 'aox', 'Aqoxy3G01236' => 'aox', 'Aqoxy5G03746' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3RQ047' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C7GMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9C8JER' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MBL6KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YXCZ83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZANX40' => 'arhy', 'AT1G12990' => 'ath', 'AT1G67880' => 'ath', 'AT2G13290' => 'ath', 'AT3G01620' => 'ath', 'AT3G26445' => 'ath', 'AT3G27540' => 'ath', 'AT5G14480' => 'ath', 'ATR0824G026' => 'atr', 'ATR1098G019' => 'atr', 'Atru.chr11.2145' => 'acertr', 'Atru.chr2.3636' => 'acertr', 'Atru.chr2.3644' => 'acertr', 'Atru.chr6.2422' => 'acertr', 'Atru.chr7.1112' => 'acertr', 'AUR62005469' => 'cqu', 'AUR62011166' => 'cqu', 'AUR62013319' => 'cqu', 'AUR62024273' => 'cqu', 'AUR62028420' => 'cqu', 'AUR62041942' => 'cqu', 'BcaB01g04969' => 'bca', 'BcaB01g06371' => 'bca', 'BcaB02g11494' => 'bca', 'BcaB03g15382' => 'bca', 'BcaB08g36994' => 'bca', 'BcaC03g13477' => 'bca', 'BcaC03g13478' => 'bca', 'BcaC03g13480' => 'bca', 'BcaC03g13481' => 'bca', 'BcaC03g13486' => 'bca', 'BcaC04g19031' => 'bca', 'BcaC04g23085' => 'bca', 'BcaC05g25094' => 'bca', 'BcaC05g25096' => 'bca', 'BcaC05g25138' => 'bca', 'BcaC05g30416' => 'bca', 'BcaC05g30455' => 'bca', 'BcaC06g30979' => 'bca', 'BcaC06g33805' => 'bca', 'BcaC08g46021' => 'bca', 'BcaNung03154' => 'bca', 'BolC2t06623H' => 'bol', 'BolC2t06632H' => 'bol', 'BolC2t06635H' => 'bol', 'BolC2t06638H' => 'bol', 'BolC3t13266H' => 'bol', 'BolC5t29776H' => 'bol', 'BolC6t38912H' => 'bol', 'BolC7t44183H' => 'bol', 'BolC9t54123H' => 'bol', 'BolC9t59107H' => 'bol', 'BraA02t05221Z' => 'bra', 'BraA03t09996Z' => 'bra', 'BraA05t23210Z' => 'bra', 'BraA06t24068Z' => 'bra', 'BraA06t27032Z' => 'bra', 'BraA08t35176Z' => 'bra', 'BraA09t36680Z' => 'bra', 'BraA10t44471Z' => 'bra', 'C02p06760' => 'bna', 'C02p06890' => 'bna', 'C02p07010' => 'bna', 'C03p07660' => 'bna', 'C05p10300' => 'bna', 'C06p38150' => 'bna', 'C07p36650' => 'bna', 'C08p15770' => 'bna', 'C09p12300' => 'bna', 'C09p62700' => 'bna', 'C09p75040' => 'bna', 'CAN.G13.1' => 'can', 'CAN.G138.4' => 'can', 'CAN.G44.6' => 'can', 'CAN.G473.19' => 'can', 'CANSAT01G0835' => 'cansat', 'CANSAT11G0246' => 'cansat', 'CANSAT11G1766' => 'cansat', 'CANSAT64G1954' => 'cansat', 'CARHR013330' => 'chi', 'CARHR060530' => 'chi', 'CARHR075300' => 'chi', 'CARHR105120' => 'chi', 'CARHR148910' => 'chi', 'CARHR198830' => 'chi', 'Carub.0001s1275' => 'cru', 'Carub.0002s1437' => 'cru', 'Carub.0003s0044' => 'cru', 'Carub.0003s2787' => 'cru', 'Carub.0005s0597' => 'cru', 'Carub.0006s1266' => 'cru', 'Ca_06935_v3' => 'car', 'Ca_13559_v3' => 'car', 'Ca_16941_v3' => 'car', 'Ca_16960_v3' => 'car', 'Ca_17775_v3' => 'car', 'Ca_30464_v3' => 'car', 'Cc06_g08160' => 'ccan', 'Cc07_g01520' => 'ccan', 'Cc11_g15810' => 'ccan', 'CDE02G2840' => 'cde', 'CDE03G0093' => 'cde', 'CDE04G2127' => 'cde', 'CDE07G1857' => 'cde', 'CDE09G1246' => 'cde', 'Cfa003412' => 'cfa', 'Cfa007341' => 'cfa', 'Cfa009220' => 'cfa', 'Ciclev10008737m.g' => 'ccl', 'Ciclev10015565m.g' => 'ccl', 'Ciclev10031761m.g' => 'ccl', 'CiPaw.03G045300' => 'cil', 'CiPaw.03G247200' => 'cil', 'CiPaw.04G029500' => 'cil', 'CiPaw.04G174000' => 'cil', 'CiPaw.05G181200' => 'cil', 'CiPaw.06G067100' => 'cil', 'ClCG05G025800' => 'cla', 'ClCG06G011400' => 'cla', 'ClCG09G019360' => 'cla', 'COL.COLO4_04827' => 'col', 'COL.COLO4_29170' => 'col', 'COL.COLO4_35131' => 'col', 'COL.COLO4_35132' => 'col', 'Cpa.g.sc33.32' => 'cpa', 'Cpa.g.sc46.29' => 'cpa', 'Cpa.g.sc796.1' => 'cpa', 'CsaV3_1G030420' => 'csa', 'CsaV3_5G027050' => 'csa', 'CsaV3_5G031040' => 'csa', 'CsaV3_UNG023130' => 'csa', 'CSS0007726' => 'camsi', 'CSS0016433' => 'camsi', 'CSS0017656' => 'camsi', 'CSS0025364' => 'camsi', 'CSS0027582' => 'camsi', 'CSS0047288' => 'camsi', 'CSS0049950' => 'camsi', 'DCAR_003843' => 'dca', 'DCAR_007052' => 'dca', 'DCAR_020884' => 'dca', 'DCAR_021730' => 'dca', 'DCAR_024423' => 'dca', 'DCAR_026509' => 'dca', 'DCAR_031158' => 'dca', 'Dinv14728' => 'din', 'Dinv15219' => 'din', 'Dinv25728' => 'din', 'Dinv33428' => 'din', 'Dinv36489' => 'din', 'Dinv41486' => 'din', 'Duzib147G0469' => 'dzi', 'Duzib168G0060' => 'dzi', 'Duzib187G1215' => 'dzi', 'Duzib248G0692' => 'dzi', 'Duzib251G0767' => 'dzi', 'Duzib264G0446' => 'dzi', 'Duzib268G0691' => 'dzi', 'ECA232G4767' => 'eca', 'ECA233G2838' => 'eca', 'ECA234G0391' => 'eca', 'ECA234G0857' => 'eca', 'ECA236G1593' => 'eca', 'ECA238G0565' => 'eca', 'ECA246G1027' => 'eca', 'ECA246G3223' => 'eca', 'ECA246G3470' => 'eca', 'EL10Ac6g13829' => 'bvu', 'EL10Ac6g14093' => 'bvu', 'EL10Ac8g18707' => 'bvu', 'Eucgr.C01369' => 'egr', 'Eucgr.H02492' => 'egr', 'Eucgr.I01733' => 'egr', 'Eucgr.J02255' => 'egr', 'Eucgr.J02257' => 'egr', 'Eucgr.J02258' => 'egr', 'FAN02G1601' => 'fan', 'FAN03G1586' => 'fan', 'FAN03G2986' => 'fan', 'FAN05G4837' => 'fan', 'FAN06G0146' => 'fan', 'FAN07G0858' => 'fan', 'FAN09G3179' => 'fan', 'FAN10G0669' => 'fan', 'FAN12G2358' => 'fan', 'FAN14G4198' => 'fan', 'FAN14G5112' => 'fan', 'FAN17G0342' => 'fan', 'FAN19G0342' => 'fan', 'FAN19G0962' => 'fan', 'FAN19G1101' => 'fan', 'FAN19G1872' => 'fan', 'FAN22G0356' => 'fan', 'FAN23G0744' => 'fan', 'FAN23G1914' => 'fan', 'FAN26G0032' => 'fan', 'FAN28G0625' => 'fan', 'FvH4_1g02710' => 'fve', 'FvH4_1g02720' => 'fve', 'FvH4_4g25670' => 'fve', 'FvH4_6g51700' => 'fve', 'FvH4_7g20170' => 'fve', 'Glyma.05G175000' => 'gma', 'Glyma.08G132300' => 'gma', 'Glyma.11G243000' => 'gma', 'Glyma.13G158900' => 'gma', 'Glyma.17G112400' => 'gma', 'Glyma.18G014100' => 'gma', 'Glyma.19G003100' => 'gma', 'Glyma.19G056500' => 'gma', 'Gohir.A01G158900' => 'ghi', 'Gohir.A05G312600' => 'ghi', 'Gohir.A05G354900' => 'ghi', 'Gohir.A07G037200' => 'ghi', 'Gohir.A09G030000' => 'ghi', 'Gohir.A12G145200' => 'ghi', 'Gohir.D01G151500' => 'ghi', 'Gohir.D04G058300' => 'ghi', 'Gohir.D05G314100' => 'ghi', 'Gohir.D07G041400' => 'ghi', 'Gohir.D09G029700' => 'ghi', 'Gohir.D12G149700' => 'ghi', 'Gorai.001G043800' => 'gra', 'Gorai.002G187800' => 'gra', 'Gorai.006G034700' => 'gra', 'Gorai.008G161200' => 'gra', 'Gorai.009G335700' => 'gra', 'Gorai.012G065000' => 'gra', 'GSVIVG01000535001' => 'vvi', 'GSVIVG01015572001' => 'vvi', 'GSVIVG01032386001' => 'vvi', 'HanXRQChr05g0138531' => 'han', 'HanXRQChr06g0174391' => 'han', 'HanXRQChr07g0199021' => 'han', 'HanXRQChr08g0208211' => 'han', 'HanXRQChr09g0255471' => 'han', 'HanXRQChr10g0315791' => 'han', 'HanXRQChr12g0371991' => 'han', 'HanXRQChr15g0475251' => 'han', 'HanXRQChr17g0540001' => 'han', 'HanXRQChr17g0548631' => 'han', 'HanXRQChr17g0569561' => 'han', 'Haze_12256' => 'cav', 'Haze_14756' => 'cav', 'Haze_25528' => 'cav', 'Hma1.2p1_0079F.1_g041020' => 'hma', 'Hma1.2p1_0818F.1_g223260' => 'hma', 'Hma1.2p1_1747F.1_g300530' => 'hma', 'HPP92_004607' => 'vpl', 'HPP92_004608' => 'vpl', 'HPP92_006181' => 'vpl', 'HPP92_012192' => 'vpl', 'HPP92_015680' => 'vpl', 'HPP92_020249' => 'vpl', 'HPP92_021376' => 'vpl', 'HPP92_024275' => 'vpl', 'Hund06031' => 'sun', 'Hund25391' => 'sun', 'Lalb_Chr07g0185371' => 'lal', 'Lalb_Chr07g0185381' => 'lal', 'Lalb_Chr12g0204011' => 'lal', 'Lalb_Chr13g0301671' => 'lal', 'Lalb_Chr14g0362851' => 'lal', 'Lalb_Chr24g0403581' => 'lal', 'Lj1g0000233' => 'lja', 'Lj2g0018120' => 'lja', 'Lj3C621T0' => 'lonja', 'Lj3P1059T14' => 'lonja', 'Lj3P611T9' => 'lonja', 'Lj3P614T13' => 'lonja', 'Lj3P615T5' => 'lonja', 'Lj4g0012315' => 'lja', 'Lj4g0026182' => 'lja', 'Lj6P813T16' => 'lonja', 'Lj7C427T7' => 'lonja', 'Lj7C427T8' => 'lonja', 'Lj7P600T41' => 'lonja', 'Lju41C42G17' => 'lonja', 'Lsat_1_v5_gn_0_47300' => 'lsa', 'Lsat_1_v5_gn_2_91280' => 'lsa', 'Lsat_1_v5_gn_3_30561' => 'lsa', 'Lsat_1_v5_gn_4_184321' => 'lsa', 'Lsat_1_v5_gn_4_4041' => 'lsa', 'Lsat_1_v5_gn_5_92000' => 'lsa', 'Lsat_1_v5_gn_8_152940' => 'lsa', 'Lsat_1_v5_gn_8_62401' => 'lsa', 'Manes.06G055900' => 'mes', 'Manes.12G022200' => 'mes', 'Manes.13G023300' => 'mes', 'Manes.14G115000' => 'mes', 'Manes.15G151700' => 'mes', 'Manes.17G111300' => 'mes', 'Mapoly0226s0009' => 'mpo', 'MBI02_g25363_MAGBIO' => 'mbi', 'MBI06_g00027_MAGBIO' => 'mbi', 'MBI10_g13034_MAGBIO' => 'mbi', 'MD09G1023400' => 'mdo', 'MD13G1100100' => 'mdo', 'MD15G1169200' => 'mdo', 'MD16G1101100' => 'mdo', 'MD17G1022900' => 'mdo', 'Medtr3g096150' => 'mtr', 'Medtr4g115070' => 'mtr', 'Medtr7g033325' => 'mtr', 'Medtr8g089840' => 'mtr', 'MELO3C010319.2' => 'cme', 'MELO3C011944.2' => 'cme', 'MELO3C021589.2' => 'cme', 'Migut.E00207' => 'egut', 'Migut.H00067' => 'egut', 'Migut.K00433' => 'egut', 'Migut.K00606' => 'egut', 'Migut.K01410' => 'egut', 'MSTRG.13347' => 'ama', 'MSTRG.24045' => 'ama', 'MSTRG.2428' => 'ama', 'MSTRG.26410' => 'ama', 'MSTRG.3139' => 'ama', 'MSTRG.3286' => 'ama', 'MSTRG.563' => 'ama', 'MSTRG.7941' => 'ama', 'Nitab4.5_0000028g0060' => 'nta', 'Nitab4.5_0000065g0260' => 'nta', 'Nitab4.5_0000112g0060' => 'nta', 'Nitab4.5_0000489g0120' => 'nta', 'Nitab4.5_0001776g0050' => 'nta', 'Nitab4.5_0001854g0010' => 'nta', 'Nitab4.5_0001860g0020' => 'nta', 'Nitab4.5_0004352g0010' => 'nta', 'Nitab4.5_0008716g0020' => 'nta', 'Nitab4.5_0008922g0010' => 'nta', 'Nn3g16693' => 'nnu', 'Nn4g22596' => 'nnu', 'Nn7g37639' => 'nnu', 'Oeu001701.1' => 'oeu', 'Oeu018149.1' => 'oeu', 'Oeu026220.1' => 'oeu', 'Oeu038635.1' => 'oeu', 'Oeu049176.1' => 'oeu', 'Oeu056706.1' => 'oeu', 'Oeu056937.1' => 'oeu', 'Oeu057540.1' => 'oeu', 'Os02g0594900' => 'osa', 'Os02g0595100' => 'osa', 'Os04g0477500' => 'osa', 'Os12g0611900' => 'osa', 'Peaxi162Scf00076g00020' => 'pax', 'Peaxi162Scf00128g00217' => 'pax', 'Peaxi162Scf00129g01640' => 'pax', 'Peaxi162Scf00669g00007' => 'pax', 'Peaxi162Scf00700g00421' => 'pax', 'Peaxi162Scf00801g00038' => 'pax', 'Peaxi162Scf00891g00025' => 'pax', 'PGR083G0909' => 'pgr', 'PGR119G1005' => 'pgr', 'PGR142G2236' => 'pgr', 'PGR142G3388' => 'pgr', 'PGSC0003DMG400004514' => 'stu', 'PGSC0003DMG400012635' => 'stu', 'PGSC0003DMG400015730' => 'stu', 'PGSC0003DMG400018611' => 'stu', 'PGSC0003DMG400030897' => 'stu', 'Phvul.001G254800' => 'pvu', 'Phvul.002G260100' => 'pvu', 'Phvul.003G167600' => 'pvu', 'Phvul.004G005100' => 'pvu', 'Potri.001G343600' => 'ptr', 'Potri.006G066700' => 'ptr', 'Potri.008G186000' => 'ptr', 'Potri.010G046900' => 'ptr', 'Potri.018G127900' => 'ptr', 'Pp3c20_17750' => 'ppa', 'Pp3c24_4380' => 'ppa', 'Prupe.1G245800' => 'ppe', 'Prupe.3G293400' => 'ppe', 'Prupe.7G247400' => 'ppe', 'Psat0s145g0120' => 'psa', 'Psat0s595g0040' => 'psa', 'Psat0s595g0120' => 'psa', 'Psat3g175040' => 'psa', 'Psat7g058120' => 'psa', 'PSO017G0428' => 'pso', 'PSO063G7510' => 'pso', 'PSO067G0046' => 'pso', 'PSO478G1073' => 'pso', 'PSO675G3677' => 'pso', 'PSO675G6558' => 'pso', 'PSO675G7520' => 'pso', 'PSO675G8959' => 'pso', 'QL02p074089' => 'qlo', 'QL02p089614' => 'qlo', 'QL03p057736' => 'qlo', 'RcHm_v2.0_Chr1g0364131' => 'rch', 'RcHm_v2.0_Chr2g0087801' => 'rch', 'RcHm_v2.0_Chr2g0087821' => 'rch', 'RcHm_v2.0_Chr2g0173231' => 'rch', 'RcHm_v2.0_Chr4g0433111' => 'rch', 'Rhsim03G0250300' => 'rsi', 'Rhsim08G0048400' => 'rsi', 'Rhsim10G0014800' => 'rsi', 'Rhsim12G0040100' => 'rsi', 'Rhsim12G0109700' => 'rsi', 'Sabra06G0049600' => 'sbr', 'Sabra08G0141000' => 'sbr', 'Sabra10G0021400' => 'sbr', 'Sabra16G0222900' => 'sbr', 'Sabra18G0108600' => 'sbr', 'SalBow1G0433' => 'sbo', 'SalBow1G2038' => 'sbo', 'SalBow1G5003' => 'sbo', 'SalBow7G1197' => 'sbo', 'SalBow8G3506' => 'sbo', 'Sc03g0007300' => 'sci', 'Sc11g0000950' => 'sci', 'Sc14g0008750' => 'sci', 'Sc18g0000420' => 'sci', 'Sed0006754' => 'sed', 'Sed0008741' => 'sed', 'Sed0017172' => 'sed', 'Sed0018925' => 'sed', 'Sed0023326' => 'sed', 'Sed0025909' => 'sed', 'SEGI_05333' => 'sgi', 'SEGI_10362' => 'sgi', 'SEGI_13380' => 'sgi', 'SEGI_24306' => 'sgi', 'SEGI_29077' => 'sgi', 'SEGI_29095' => 'sgi', 'SEGI_36534' => 'sgi', 'SEGI_37506' => 'sgi', 'SEGI_38321' => 'sgi', 'SGA_v2.0_scaffold307G48031' => 'sas', 'SGA_v2.0_scaffold47G17507' => 'sas', 'SGA_v2.0_scaffold63G21736' => 'sas', 'SGA_v2.0_scaffold87G27070' => 'sas', 'SHI17794' => 'shi', 'SHI28851' => 'shi', 'SMO165G0155' => 'smo', 'SMO340G0217' => 'smo', 'SMO367G1210' => 'smo', 'Solyc02g093430.3' => 'sly', 'Solyc05g013580.4' => 'sly', 'Solyc07g008030.3' => 'sly', 'Solyc12g035470.2' => 'sly', 'Sopen02g038020' => 'spe', 'Sopen05g008490' => 'spe', 'Sopen07g003910' => 'spe', 'Sopen12g015240' => 'spe', 'Sp1g11550' => 'spa', 'Sp2g16710' => 'spa', 'Sp3g00430' => 'spa', 'Sp3g26780' => 'spa', 'Sp5g22900' => 'spa', 'Sp6g29530' => 'spa', 'TAR371G0794' => 'tar', 'TAR374G0164' => 'tar', 'TAR622G0165' => 'tar', 'TAR626G0929' => 'tar', 'TAR629G2155' => 'tar', 'THA.LOC104805282' => 'tha', 'THA.LOC104805363' => 'tha', 'THA.LOC104808968' => 'tha', 'THA.LOC104821093' => 'tha', 'THA.LOC104823953' => 'tha', 'THA.LOC104825562' => 'tha', 'THA.LOC104825665' => 'tha', 'Thecc.02G261400' => 'tca', 'Thecc.04G019200' => 'tca', 'Thecc.09G130400' => 'tca', 'Thhalv10004374m.g' => 'esa', 'Thhalv10007850m.g' => 'esa', 'Thhalv10013782m.g' => 'esa', 'Thhalv10018686m.g' => 'esa', 'Thhalv10020899m.g' => 'esa', 'Thhalv10022755m.g' => 'esa', 'TPR.G23851' => 'tpr', 'TPR.G26500' => 'tpr', 'TPR.G27267' => 'tpr', 'TPR.G32001' => 'tpr', 'TPR.G6251' => 'tpr', 'TPR.G8167' => 'tpr', 'TWI12G1330' => 'twi', 'TWI18G1239' => 'twi', 'TWI34G0979' => 'twi', 'TWI36G0670' => 'twi', 'TWI36G0707' => 'twi', 'TWI56G0233' => 'twi', 'TWI75G1809' => 'twi', 'unitig_21.g20874' => 'ugi', 'unitig_26.g10343' => 'ugi', 'unitig_46.g18392' => 'ugi', 'unitig_52.g17178' => 'ugi', 'unitig_8.g2934' => 'ugi', 'vmacro01122' => 'vma', 'vmacro05875' => 'vma', 'vmacro06147' => 'vma', 'vmacro16191' => 'vma', 'vmacro18293' => 'vma', 'VMungo0251G3707' => 'vmu', 'VMungo0464G1521' => 'vmu', 'VMungo1215G0205' => 'vmu', 'VMungo1383G2484' => 'vmu', 'Zm00001eb079610' => 'zma', 'Zm00001eb135990' => 'zma', 'Zm00001eb183710' => 'zma', 'Zm00001eb246020' => 'zma' ), 'gf_id' => 'HOM05D001124', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001124' ), 'data_identifier' => 'HOM05D001124', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001124', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '548', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02520' => 'bna', 'A03p06630' => 'bna', 'A05p44460' => 'bna', 'A06p08710' => 'bna', 'A06p41090' => 'bna', 'A07p32320' => 'bna', 'A08p32520' => 'bna', 'A09p10360' => 'bna', 'A10p24080' => 'bna', 'Aa31LG11G15250' => 'aar', 'Aa31LG1G1800' => 'aar', 'Aa31LG2G5120' => 'aar', 'Aa31LG2G6070' => 'aar', 'Aa31LG5G10770' => 'aar', 'Aa31sc61G90' => 'aar', 'Actinidia01352' => 'ach', 'Actinidia05983' => 'ach', 'Actinidia08133' => 'ach', 'Actinidia15101' => 'ach', 'Actinidia26379' => 'ach', 'Actinidia35778' => 'ach', 'Actinidia36123' => 'ach', 'Actinidia37436' => 'ach', 'Actinidia38730' => 'ach', 'Ah.02g128210' => 'amhyb', 'Ah.03g132990' => 'amhyb', 'Ah.14g079410' => 'amhyb', 'AL1G24640' => 'aly', 'AL2G26680' => 'aly', 'AL3G10530' => 'aly', 'AL3G45230' => 'aly', 'AL5G15230' => 'aly', 'AL5G16960' => 'aly', 'AL6G25210' => 'aly', 'Aqoxy2G00441' => 'aox', 'Aqoxy3G01236' => 'aox', 'Aqoxy5G03746' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3RQ047' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C7GMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9C8JER' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MBL6KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YXCZ83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZANX40' => 'arhy', 'AT1G12990' => 'ath', 'AT1G67880' => 'ath', 'AT2G13290' => 'ath', 'AT3G01620' => 'ath', 'AT3G26445' => 'ath', 'AT3G27540' => 'ath', 'AT5G14480' => 'ath', 'ATR0824G026' => 'atr', 'ATR1098G019' => 'atr', 'Atru.chr11.2145' => 'acertr', 'Atru.chr2.3636' => 'acertr', 'Atru.chr2.3644' => 'acertr', 'Atru.chr6.2422' => 'acertr', 'Atru.chr7.1112' => 'acertr', 'AUR62005469' => 'cqu', 'AUR62011166' => 'cqu', 'AUR62013319' => 'cqu', 'AUR62024273' => 'cqu', 'AUR62028420' => 'cqu', 'AUR62041942' => 'cqu', 'BcaB01g04969' => 'bca', 'BcaB01g06371' => 'bca', 'BcaB02g11494' => 'bca', 'BcaB03g15382' => 'bca', 'BcaB08g36994' => 'bca', 'BcaC03g13477' => 'bca', 'BcaC03g13478' => 'bca', 'BcaC03g13480' => 'bca', 'BcaC03g13481' => 'bca', 'BcaC03g13486' => 'bca', 'BcaC04g19031' => 'bca', 'BcaC04g23085' => 'bca', 'BcaC05g25094' => 'bca', 'BcaC05g25096' => 'bca', 'BcaC05g25138' => 'bca', 'BcaC05g30416' => 'bca', 'BcaC05g30455' => 'bca', 'BcaC06g30979' => 'bca', 'BcaC06g33805' => 'bca', 'BcaC08g46021' => 'bca', 'BcaNung03154' => 'bca', 'BolC2t06623H' => 'bol', 'BolC2t06632H' => 'bol', 'BolC2t06635H' => 'bol', 'BolC2t06638H' => 'bol', 'BolC3t13266H' => 'bol', 'BolC5t29776H' => 'bol', 'BolC6t38912H' => 'bol', 'BolC7t44183H' => 'bol', 'BolC9t54123H' => 'bol', 'BolC9t59107H' => 'bol', 'BraA02t05221Z' => 'bra', 'BraA03t09996Z' => 'bra', 'BraA05t23210Z' => 'bra', 'BraA06t24068Z' => 'bra', 'BraA06t27032Z' => 'bra', 'BraA08t35176Z' => 'bra', 'BraA09t36680Z' => 'bra', 'BraA10t44471Z' => 'bra', 'C02p06760' => 'bna', 'C02p06890' => 'bna', 'C02p07010' => 'bna', 'C03p07660' => 'bna', 'C05p10300' => 'bna', 'C06p38150' => 'bna', 'C07p36650' => 'bna', 'C08p15770' => 'bna', 'C09p12300' => 'bna', 'C09p62700' => 'bna', 'C09p75040' => 'bna', 'CAN.G13.1' => 'can', 'CAN.G138.4' => 'can', 'CAN.G44.6' => 'can', 'CAN.G473.19' => 'can', 'CANSAT01G0835' => 'cansat', 'CANSAT11G0246' => 'cansat', 'CANSAT11G1766' => 'cansat', 'CANSAT64G1954' => 'cansat', 'CARHR013330' => 'chi', 'CARHR060530' => 'chi', 'CARHR075300' => 'chi', 'CARHR105120' => 'chi', 'CARHR148910' => 'chi', 'CARHR198830' => 'chi', 'Carub.0001s1275' => 'cru', 'Carub.0002s1437' => 'cru', 'Carub.0003s0044' => 'cru', 'Carub.0003s2787' => 'cru', 'Carub.0005s0597' => 'cru', 'Carub.0006s1266' => 'cru', 'Ca_06935_v3' => 'car', 'Ca_13559_v3' => 'car', 'Ca_16941_v3' => 'car', 'Ca_16960_v3' => 'car', 'Ca_17775_v3' => 'car', 'Ca_30464_v3' => 'car', 'Cc06_g08160' => 'ccan', 'Cc07_g01520' => 'ccan', 'Cc11_g15810' => 'ccan', 'CDE02G2840' => 'cde', 'CDE03G0093' => 'cde', 'CDE04G2127' => 'cde', 'CDE07G1857' => 'cde', 'CDE09G1246' => 'cde', 'Cfa003412' => 'cfa', 'Cfa007341' => 'cfa', 'Cfa009220' => 'cfa', 'Ciclev10008737m.g' => 'ccl', 'Ciclev10015565m.g' => 'ccl', 'Ciclev10031761m.g' => 'ccl', 'CiPaw.03G045300' => 'cil', 'CiPaw.03G247200' => 'cil', 'CiPaw.04G029500' => 'cil', 'CiPaw.04G174000' => 'cil', 'CiPaw.05G181200' => 'cil', 'CiPaw.06G067100' => 'cil', 'ClCG05G025800' => 'cla', 'ClCG06G011400' => 'cla', 'ClCG09G019360' => 'cla', 'COL.COLO4_04827' => 'col', 'COL.COLO4_29170' => 'col', 'COL.COLO4_35131' => 'col', 'COL.COLO4_35132' => 'col', 'Cpa.g.sc33.32' => 'cpa', 'Cpa.g.sc46.29' => 'cpa', 'Cpa.g.sc796.1' => 'cpa', 'CsaV3_1G030420' => 'csa', 'CsaV3_5G027050' => 'csa', 'CsaV3_5G031040' => 'csa', 'CsaV3_UNG023130' => 'csa', 'CSS0007726' => 'camsi', 'CSS0016433' => 'camsi', 'CSS0017656' => 'camsi', 'CSS0025364' => 'camsi', 'CSS0027582' => 'camsi', 'CSS0047288' => 'camsi', 'CSS0049950' => 'camsi', 'DCAR_003843' => 'dca', 'DCAR_007052' => 'dca', 'DCAR_020884' => 'dca', 'DCAR_021730' => 'dca', 'DCAR_024423' => 'dca', 'DCAR_026509' => 'dca', 'DCAR_031158' => 'dca', 'Dinv14728' => 'din', 'Dinv15219' => 'din', 'Dinv25728' => 'din', 'Dinv33428' => 'din', 'Dinv36489' => 'din', 'Dinv41486' => 'din', 'Duzib147G0469' => 'dzi', 'Duzib168G0060' => 'dzi', 'Duzib187G1215' => 'dzi', 'Duzib248G0692' => 'dzi', 'Duzib251G0767' => 'dzi', 'Duzib264G0446' => 'dzi', 'Duzib268G0691' => 'dzi', 'ECA232G4767' => 'eca', 'ECA233G2838' => 'eca', 'ECA234G0391' => 'eca', 'ECA234G0857' => 'eca', 'ECA236G1593' => 'eca', 'ECA238G0565' => 'eca', 'ECA246G1027' => 'eca', 'ECA246G3223' => 'eca', 'ECA246G3470' => 'eca', 'EL10Ac6g13829' => 'bvu', 'EL10Ac6g14093' => 'bvu', 'EL10Ac8g18707' => 'bvu', 'Eucgr.C01369' => 'egr', 'Eucgr.H02492' => 'egr', 'Eucgr.I01733' => 'egr', 'Eucgr.J02255' => 'egr', 'Eucgr.J02257' => 'egr', 'Eucgr.J02258' => 'egr', 'FAN02G1601' => 'fan', 'FAN03G1586' => 'fan', 'FAN03G2986' => 'fan', 'FAN05G4837' => 'fan', 'FAN06G0146' => 'fan', 'FAN07G0858' => 'fan', 'FAN09G3179' => 'fan', 'FAN10G0669' => 'fan', 'FAN12G2358' => 'fan', 'FAN14G4198' => 'fan', 'FAN14G5112' => 'fan', 'FAN17G0342' => 'fan', 'FAN19G0342' => 'fan', 'FAN19G0962' => 'fan', 'FAN19G1101' => 'fan', 'FAN19G1872' => 'fan', 'FAN22G0356' => 'fan', 'FAN23G0744' => 'fan', 'FAN23G1914' => 'fan', 'FAN26G0032' => 'fan', 'FAN28G0625' => 'fan', 'FvH4_1g02710' => 'fve', 'FvH4_1g02720' => 'fve', 'FvH4_4g25670' => 'fve', 'FvH4_6g51700' => 'fve', 'FvH4_7g20170' => 'fve', 'Glyma.05G175000' => 'gma', 'Glyma.08G132300' => 'gma', 'Glyma.11G243000' => 'gma', 'Glyma.13G158900' => 'gma', 'Glyma.17G112400' => 'gma', 'Glyma.18G014100' => 'gma', 'Glyma.19G003100' => 'gma', 'Glyma.19G056500' => 'gma', 'Gohir.A01G158900' => 'ghi', 'Gohir.A05G312600' => 'ghi', 'Gohir.A05G354900' => 'ghi', 'Gohir.A07G037200' => 'ghi', 'Gohir.A09G030000' => 'ghi', 'Gohir.A12G145200' => 'ghi', 'Gohir.D01G151500' => 'ghi', 'Gohir.D04G058300' => 'ghi', 'Gohir.D05G314100' => 'ghi', 'Gohir.D07G041400' => 'ghi', 'Gohir.D09G029700' => 'ghi', 'Gohir.D12G149700' => 'ghi', 'Gorai.001G043800' => 'gra', 'Gorai.002G187800' => 'gra', 'Gorai.006G034700' => 'gra', 'Gorai.008G161200' => 'gra', 'Gorai.009G335700' => 'gra', 'Gorai.012G065000' => 'gra', 'GSVIVG01000535001' => 'vvi', 'GSVIVG01015572001' => 'vvi', 'GSVIVG01032386001' => 'vvi', 'HanXRQChr05g0138531' => 'han', 'HanXRQChr06g0174391' => 'han', 'HanXRQChr07g0199021' => 'han', 'HanXRQChr08g0208211' => 'han', 'HanXRQChr09g0255471' => 'han', 'HanXRQChr10g0315791' => 'han', 'HanXRQChr12g0371991' => 'han', 'HanXRQChr15g0475251' => 'han', 'HanXRQChr17g0540001' => 'han', 'HanXRQChr17g0548631' => 'han', 'HanXRQChr17g0569561' => 'han', 'Haze_12256' => 'cav', 'Haze_14756' => 'cav', 'Haze_25528' => 'cav', 'Hma1.2p1_0079F.1_g041020' => 'hma', 'Hma1.2p1_0818F.1_g223260' => 'hma', 'Hma1.2p1_1747F.1_g300530' => 'hma', 'HPP92_004607' => 'vpl', 'HPP92_004608' => 'vpl', 'HPP92_006181' => 'vpl', 'HPP92_012192' => 'vpl', 'HPP92_015680' => 'vpl', 'HPP92_020249' => 'vpl', 'HPP92_021376' => 'vpl', 'HPP92_024275' => 'vpl', 'Hund06031' => 'sun', 'Hund25391' => 'sun', 'Lalb_Chr07g0185371' => 'lal', 'Lalb_Chr07g0185381' => 'lal', 'Lalb_Chr12g0204011' => 'lal', 'Lalb_Chr13g0301671' => 'lal', 'Lalb_Chr14g0362851' => 'lal', 'Lalb_Chr24g0403581' => 'lal', 'Lj1g0000233' => 'lja', 'Lj2g0018120' => 'lja', 'Lj3C621T0' => 'lonja', 'Lj3P1059T14' => 'lonja', 'Lj3P611T9' => 'lonja', 'Lj3P614T13' => 'lonja', 'Lj3P615T5' => 'lonja', 'Lj4g0012315' => 'lja', 'Lj4g0026182' => 'lja', 'Lj6P813T16' => 'lonja', 'Lj7C427T7' => 'lonja', 'Lj7C427T8' => 'lonja', 'Lj7P600T41' => 'lonja', 'Lju41C42G17' => 'lonja', 'Lsat_1_v5_gn_0_47300' => 'lsa', 'Lsat_1_v5_gn_2_91280' => 'lsa', 'Lsat_1_v5_gn_3_30561' => 'lsa', 'Lsat_1_v5_gn_4_184321' => 'lsa', 'Lsat_1_v5_gn_4_4041' => 'lsa', 'Lsat_1_v5_gn_5_92000' => 'lsa', 'Lsat_1_v5_gn_8_152940' => 'lsa', 'Lsat_1_v5_gn_8_62401' => 'lsa', 'Manes.06G055900' => 'mes', 'Manes.12G022200' => 'mes', 'Manes.13G023300' => 'mes', 'Manes.14G115000' => 'mes', 'Manes.15G151700' => 'mes', 'Manes.17G111300' => 'mes', 'Mapoly0226s0009' => 'mpo', 'MBI02_g25363_MAGBIO' => 'mbi', 'MBI06_g00027_MAGBIO' => 'mbi', 'MBI10_g13034_MAGBIO' => 'mbi', 'MD09G1023400' => 'mdo', 'MD13G1100100' => 'mdo', 'MD15G1169200' => 'mdo', 'MD16G1101100' => 'mdo', 'MD17G1022900' => 'mdo', 'Medtr3g096150' => 'mtr', 'Medtr4g115070' => 'mtr', 'Medtr7g033325' => 'mtr', 'Medtr8g089840' => 'mtr', 'MELO3C010319.2' => 'cme', 'MELO3C011944.2' => 'cme', 'MELO3C021589.2' => 'cme', 'Migut.E00207' => 'egut', 'Migut.H00067' => 'egut', 'Migut.K00433' => 'egut', 'Migut.K00606' => 'egut', 'Migut.K01410' => 'egut', 'MSTRG.13347' => 'ama', 'MSTRG.24045' => 'ama', 'MSTRG.2428' => 'ama', 'MSTRG.26410' => 'ama', 'MSTRG.3139' => 'ama', 'MSTRG.3286' => 'ama', 'MSTRG.563' => 'ama', 'MSTRG.7941' => 'ama', 'Nitab4.5_0000028g0060' => 'nta', 'Nitab4.5_0000065g0260' => 'nta', 'Nitab4.5_0000112g0060' => 'nta', 'Nitab4.5_0000489g0120' => 'nta', 'Nitab4.5_0001776g0050' => 'nta', 'Nitab4.5_0001854g0010' => 'nta', 'Nitab4.5_0001860g0020' => 'nta', 'Nitab4.5_0004352g0010' => 'nta', 'Nitab4.5_0008716g0020' => 'nta', 'Nitab4.5_0008922g0010' => 'nta', 'Nn3g16693' => 'nnu', 'Nn4g22596' => 'nnu', 'Nn7g37639' => 'nnu', 'Oeu001701.1' => 'oeu', 'Oeu018149.1' => 'oeu', 'Oeu026220.1' => 'oeu', 'Oeu038635.1' => 'oeu', 'Oeu049176.1' => 'oeu', 'Oeu056706.1' => 'oeu', 'Oeu056937.1' => 'oeu', 'Oeu057540.1' => 'oeu', 'Os02g0594900' => 'osa', 'Os02g0595100' => 'osa', 'Os04g0477500' => 'osa', 'Os12g0611900' => 'osa', 'Peaxi162Scf00076g00020' => 'pax', 'Peaxi162Scf00128g00217' => 'pax', 'Peaxi162Scf00129g01640' => 'pax', 'Peaxi162Scf00669g00007' => 'pax', 'Peaxi162Scf00700g00421' => 'pax', 'Peaxi162Scf00801g00038' => 'pax', 'Peaxi162Scf00891g00025' => 'pax', 'PGR083G0909' => 'pgr', 'PGR119G1005' => 'pgr', 'PGR142G2236' => 'pgr', 'PGR142G3388' => 'pgr', 'PGSC0003DMG400004514' => 'stu', 'PGSC0003DMG400012635' => 'stu', 'PGSC0003DMG400015730' => 'stu', 'PGSC0003DMG400018611' => 'stu', 'PGSC0003DMG400030897' => 'stu', 'Phvul.001G254800' => 'pvu', 'Phvul.002G260100' => 'pvu', 'Phvul.003G167600' => 'pvu', 'Phvul.004G005100' => 'pvu', 'Potri.001G343600' => 'ptr', 'Potri.006G066700' => 'ptr', 'Potri.008G186000' => 'ptr', 'Potri.010G046900' => 'ptr', 'Potri.018G127900' => 'ptr', 'Pp3c20_17750' => 'ppa', 'Pp3c24_4380' => 'ppa', 'Prupe.1G245800' => 'ppe', 'Prupe.3G293400' => 'ppe', 'Prupe.7G247400' => 'ppe', 'Psat0s145g0120' => 'psa', 'Psat0s595g0040' => 'psa', 'Psat0s595g0120' => 'psa', 'Psat3g175040' => 'psa', 'Psat7g058120' => 'psa', 'PSO017G0428' => 'pso', 'PSO063G7510' => 'pso', 'PSO067G0046' => 'pso', 'PSO478G1073' => 'pso', 'PSO675G3677' => 'pso', 'PSO675G6558' => 'pso', 'PSO675G7520' => 'pso', 'PSO675G8959' => 'pso', 'QL02p074089' => 'qlo', 'QL02p089614' => 'qlo', 'QL03p057736' => 'qlo', 'RcHm_v2.0_Chr1g0364131' => 'rch', 'RcHm_v2.0_Chr2g0087801' => 'rch', 'RcHm_v2.0_Chr2g0087821' => 'rch', 'RcHm_v2.0_Chr2g0173231' => 'rch', 'RcHm_v2.0_Chr4g0433111' => 'rch', 'Rhsim03G0250300' => 'rsi', 'Rhsim08G0048400' => 'rsi', 'Rhsim10G0014800' => 'rsi', 'Rhsim12G0040100' => 'rsi', 'Rhsim12G0109700' => 'rsi', 'Sabra06G0049600' => 'sbr', 'Sabra08G0141000' => 'sbr', 'Sabra10G0021400' => 'sbr', 'Sabra16G0222900' => 'sbr', 'Sabra18G0108600' => 'sbr', 'SalBow1G0433' => 'sbo', 'SalBow1G2038' => 'sbo', 'SalBow1G5003' => 'sbo', 'SalBow7G1197' => 'sbo', 'SalBow8G3506' => 'sbo', 'Sc03g0007300' => 'sci', 'Sc11g0000950' => 'sci', 'Sc14g0008750' => 'sci', 'Sc18g0000420' => 'sci', 'Sed0006754' => 'sed', 'Sed0008741' => 'sed', 'Sed0017172' => 'sed', 'Sed0018925' => 'sed', 'Sed0023326' => 'sed', 'Sed0025909' => 'sed', 'SEGI_05333' => 'sgi', 'SEGI_10362' => 'sgi', 'SEGI_13380' => 'sgi', 'SEGI_24306' => 'sgi', 'SEGI_29077' => 'sgi', 'SEGI_29095' => 'sgi', 'SEGI_36534' => 'sgi', 'SEGI_37506' => 'sgi', 'SEGI_38321' => 'sgi', 'SGA_v2.0_scaffold307G48031' => 'sas', 'SGA_v2.0_scaffold47G17507' => 'sas', 'SGA_v2.0_scaffold63G21736' => 'sas', 'SGA_v2.0_scaffold87G27070' => 'sas', 'SHI17794' => 'shi', 'SHI28851' => 'shi', 'SMO165G0155' => 'smo', 'SMO340G0217' => 'smo', 'SMO367G1210' => 'smo', 'Solyc02g093430.3' => 'sly', 'Solyc05g013580.4' => 'sly', 'Solyc07g008030.3' => 'sly', 'Solyc12g035470.2' => 'sly', 'Sopen02g038020' => 'spe', 'Sopen05g008490' => 'spe', 'Sopen07g003910' => 'spe', 'Sopen12g015240' => 'spe', 'Sp1g11550' => 'spa', 'Sp2g16710' => 'spa', 'Sp3g00430' => 'spa', 'Sp3g26780' => 'spa', 'Sp5g22900' => 'spa', 'Sp6g29530' => 'spa', 'TAR371G0794' => 'tar', 'TAR374G0164' => 'tar', 'TAR622G0165' => 'tar', 'TAR626G0929' => 'tar', 'TAR629G2155' => 'tar', 'THA.LOC104805282' => 'tha', 'THA.LOC104805363' => 'tha', 'THA.LOC104808968' => 'tha', 'THA.LOC104821093' => 'tha', 'THA.LOC104823953' => 'tha', 'THA.LOC104825562' => 'tha', 'THA.LOC104825665' => 'tha', 'Thecc.02G261400' => 'tca', 'Thecc.04G019200' => 'tca', 'Thecc.09G130400' => 'tca', 'Thhalv10004374m.g' => 'esa', 'Thhalv10007850m.g' => 'esa', 'Thhalv10013782m.g' => 'esa', 'Thhalv10018686m.g' => 'esa', 'Thhalv10020899m.g' => 'esa', 'Thhalv10022755m.g' => 'esa', 'TPR.G23851' => 'tpr', 'TPR.G26500' => 'tpr', 'TPR.G27267' => 'tpr', 'TPR.G32001' => 'tpr', 'TPR.G6251' => 'tpr', 'TPR.G8167' => 'tpr', 'TWI12G1330' => 'twi', 'TWI18G1239' => 'twi', 'TWI34G0979' => 'twi', 'TWI36G0670' => 'twi', 'TWI36G0707' => 'twi', 'TWI56G0233' => 'twi', 'TWI75G1809' => 'twi', 'unitig_21.g20874' => 'ugi', 'unitig_26.g10343' => 'ugi', 'unitig_46.g18392' => 'ugi', 'unitig_52.g17178' => 'ugi', 'unitig_8.g2934' => 'ugi', 'vmacro01122' => 'vma', 'vmacro05875' => 'vma', 'vmacro06147' => 'vma', 'vmacro16191' => 'vma', 'vmacro18293' => 'vma', 'VMungo0251G3707' => 'vmu', 'VMungo0464G1521' => 'vmu', 'VMungo1215G0205' => 'vmu', 'VMungo1383G2484' => 'vmu', 'Zm00001eb079610' => 'zma', 'Zm00001eb135990' => 'zma', 'Zm00001eb183710' => 'zma', 'Zm00001eb246020' => 'zma' ) $gf_id = 'HOM05D001124' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001124' ) $data_identifier = 'HOM05D001124' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 6, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 7, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 21, 'bol' => (int) 10, 'bra' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 6, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 9, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 21, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 8, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 10, 'lsa' => (int) 8, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 8, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 9, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb246020' $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' => 'HOM05D001124', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '548', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02520' => 'bna', 'A03p06630' => 'bna', 'A05p44460' => 'bna', 'A06p08710' => 'bna', 'A06p41090' => 'bna', 'A07p32320' => 'bna', 'A08p32520' => 'bna', 'A09p10360' => 'bna', 'A10p24080' => 'bna', 'Aa31LG11G15250' => 'aar', 'Aa31LG1G1800' => 'aar', 'Aa31LG2G5120' => 'aar', 'Aa31LG2G6070' => 'aar', 'Aa31LG5G10770' => 'aar', 'Aa31sc61G90' => 'aar', 'Actinidia01352' => 'ach', 'Actinidia05983' => 'ach', 'Actinidia08133' => 'ach', 'Actinidia15101' => 'ach', 'Actinidia26379' => 'ach', 'Actinidia35778' => 'ach', 'Actinidia36123' => 'ach', 'Actinidia37436' => 'ach', 'Actinidia38730' => 'ach', 'Ah.02g128210' => 'amhyb', 'Ah.03g132990' => 'amhyb', 'Ah.14g079410' => 'amhyb', 'AL1G24640' => 'aly', 'AL2G26680' => 'aly', 'AL3G10530' => 'aly', 'AL3G45230' => 'aly', 'AL5G15230' => 'aly', 'AL5G16960' => 'aly', 'AL6G25210' => 'aly', 'Aqoxy2G00441' => 'aox', 'Aqoxy3G01236' => 'aox', 'Aqoxy5G03746' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3RQ047' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C7GMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9C8JER' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MBL6KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YXCZ83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZANX40' => 'arhy', 'AT1G12990' => 'ath', 'AT1G67880' => 'ath', 'AT2G13290' => 'ath', 'AT3G01620' => 'ath', 'AT3G26445' => 'ath', 'AT3G27540' => 'ath', 'AT5G14480' => 'ath', 'ATR0824G026' => 'atr', 'ATR1098G019' => 'atr', 'Atru.chr11.2145' => 'acertr', 'Atru.chr2.3636' => 'acertr', 'Atru.chr2.3644' => 'acertr', 'Atru.chr6.2422' => 'acertr', 'Atru.chr7.1112' => 'acertr', 'AUR62005469' => 'cqu', 'AUR62011166' => 'cqu', 'AUR62013319' => 'cqu', 'AUR62024273' => 'cqu', 'AUR62028420' => 'cqu', 'AUR62041942' => 'cqu', 'BcaB01g04969' => 'bca', 'BcaB01g06371' => 'bca', 'BcaB02g11494' => 'bca', 'BcaB03g15382' => 'bca', 'BcaB08g36994' => 'bca', 'BcaC03g13477' => 'bca', 'BcaC03g13478' => 'bca', 'BcaC03g13480' => 'bca', 'BcaC03g13481' => 'bca', 'BcaC03g13486' => 'bca', 'BcaC04g19031' => 'bca', 'BcaC04g23085' => 'bca', 'BcaC05g25094' => 'bca', 'BcaC05g25096' => 'bca', 'BcaC05g25138' => 'bca', 'BcaC05g30416' => 'bca', 'BcaC05g30455' => 'bca', 'BcaC06g30979' => 'bca', 'BcaC06g33805' => 'bca', 'BcaC08g46021' => 'bca', 'BcaNung03154' => 'bca', 'BolC2t06623H' => 'bol', 'BolC2t06632H' => 'bol', 'BolC2t06635H' => 'bol', 'BolC2t06638H' => 'bol', 'BolC3t13266H' => 'bol', 'BolC5t29776H' => 'bol', 'BolC6t38912H' => 'bol', 'BolC7t44183H' => 'bol', 'BolC9t54123H' => 'bol', 'BolC9t59107H' => 'bol', 'BraA02t05221Z' => 'bra', 'BraA03t09996Z' => 'bra', 'BraA05t23210Z' => 'bra', 'BraA06t24068Z' => 'bra', 'BraA06t27032Z' => 'bra', 'BraA08t35176Z' => 'bra', 'BraA09t36680Z' => 'bra', 'BraA10t44471Z' => 'bra', 'C02p06760' => 'bna', 'C02p06890' => 'bna', 'C02p07010' => 'bna', 'C03p07660' => 'bna', 'C05p10300' => 'bna', 'C06p38150' => 'bna', 'C07p36650' => 'bna', 'C08p15770' => 'bna', 'C09p12300' => 'bna', 'C09p62700' => 'bna', 'C09p75040' => 'bna', 'CAN.G13.1' => 'can', 'CAN.G138.4' => 'can', 'CAN.G44.6' => 'can', 'CAN.G473.19' => 'can', 'CANSAT01G0835' => 'cansat', 'CANSAT11G0246' => 'cansat', 'CANSAT11G1766' => 'cansat', 'CANSAT64G1954' => 'cansat', 'CARHR013330' => 'chi', 'CARHR060530' => 'chi', 'CARHR075300' => 'chi', 'CARHR105120' => 'chi', 'CARHR148910' => 'chi', 'CARHR198830' => 'chi', 'Carub.0001s1275' => 'cru', 'Carub.0002s1437' => 'cru', 'Carub.0003s0044' => 'cru', 'Carub.0003s2787' => 'cru', 'Carub.0005s0597' => 'cru', 'Carub.0006s1266' => 'cru', 'Ca_06935_v3' => 'car', 'Ca_13559_v3' => 'car', 'Ca_16941_v3' => 'car', 'Ca_16960_v3' => 'car', 'Ca_17775_v3' => 'car', 'Ca_30464_v3' => 'car', 'Cc06_g08160' => 'ccan', 'Cc07_g01520' => 'ccan', 'Cc11_g15810' => 'ccan', 'CDE02G2840' => 'cde', 'CDE03G0093' => 'cde', 'CDE04G2127' => 'cde', 'CDE07G1857' => 'cde', 'CDE09G1246' => 'cde', 'Cfa003412' => 'cfa', 'Cfa007341' => 'cfa', 'Cfa009220' => 'cfa', 'Ciclev10008737m.g' => 'ccl', 'Ciclev10015565m.g' => 'ccl', 'Ciclev10031761m.g' => 'ccl', 'CiPaw.03G045300' => 'cil', 'CiPaw.03G247200' => 'cil', 'CiPaw.04G029500' => 'cil', 'CiPaw.04G174000' => 'cil', 'CiPaw.05G181200' => 'cil', 'CiPaw.06G067100' => 'cil', 'ClCG05G025800' => 'cla', 'ClCG06G011400' => 'cla', 'ClCG09G019360' => 'cla', 'COL.COLO4_04827' => 'col', 'COL.COLO4_29170' => 'col', 'COL.COLO4_35131' => 'col', 'COL.COLO4_35132' => 'col', 'Cpa.g.sc33.32' => 'cpa', 'Cpa.g.sc46.29' => 'cpa', 'Cpa.g.sc796.1' => 'cpa', 'CsaV3_1G030420' => 'csa', 'CsaV3_5G027050' => 'csa', 'CsaV3_5G031040' => 'csa', 'CsaV3_UNG023130' => 'csa', 'CSS0007726' => 'camsi', 'CSS0016433' => 'camsi', 'CSS0017656' => 'camsi', 'CSS0025364' => 'camsi', 'CSS0027582' => 'camsi', 'CSS0047288' => 'camsi', 'CSS0049950' => 'camsi', 'DCAR_003843' => 'dca', 'DCAR_007052' => 'dca', 'DCAR_020884' => 'dca', 'DCAR_021730' => 'dca', 'DCAR_024423' => 'dca', 'DCAR_026509' => 'dca', 'DCAR_031158' => 'dca', 'Dinv14728' => 'din', 'Dinv15219' => 'din', 'Dinv25728' => 'din', 'Dinv33428' => 'din', 'Dinv36489' => 'din', 'Dinv41486' => 'din', 'Duzib147G0469' => 'dzi', 'Duzib168G0060' => 'dzi', 'Duzib187G1215' => 'dzi', 'Duzib248G0692' => 'dzi', 'Duzib251G0767' => 'dzi', 'Duzib264G0446' => 'dzi', 'Duzib268G0691' => 'dzi', 'ECA232G4767' => 'eca', 'ECA233G2838' => 'eca', 'ECA234G0391' => 'eca', 'ECA234G0857' => 'eca', 'ECA236G1593' => 'eca', 'ECA238G0565' => 'eca', 'ECA246G1027' => 'eca', 'ECA246G3223' => 'eca', 'ECA246G3470' => 'eca', 'EL10Ac6g13829' => 'bvu', 'EL10Ac6g14093' => 'bvu', 'EL10Ac8g18707' => 'bvu', 'Eucgr.C01369' => 'egr', 'Eucgr.H02492' => 'egr', 'Eucgr.I01733' => 'egr', 'Eucgr.J02255' => 'egr', 'Eucgr.J02257' => 'egr', 'Eucgr.J02258' => 'egr', 'FAN02G1601' => 'fan', 'FAN03G1586' => 'fan', 'FAN03G2986' => 'fan', 'FAN05G4837' => 'fan', 'FAN06G0146' => 'fan', 'FAN07G0858' => 'fan', 'FAN09G3179' => 'fan', 'FAN10G0669' => 'fan', 'FAN12G2358' => 'fan', 'FAN14G4198' => 'fan', 'FAN14G5112' => 'fan', 'FAN17G0342' => 'fan', 'FAN19G0342' => 'fan', 'FAN19G0962' => 'fan', 'FAN19G1101' => 'fan', 'FAN19G1872' => 'fan', 'FAN22G0356' => 'fan', 'FAN23G0744' => 'fan', 'FAN23G1914' => 'fan', 'FAN26G0032' => 'fan', 'FAN28G0625' => 'fan', 'FvH4_1g02710' => 'fve', 'FvH4_1g02720' => 'fve', 'FvH4_4g25670' => 'fve', 'FvH4_6g51700' => 'fve', 'FvH4_7g20170' => 'fve', 'Glyma.05G175000' => 'gma', 'Glyma.08G132300' => 'gma', 'Glyma.11G243000' => 'gma', 'Glyma.13G158900' => 'gma', 'Glyma.17G112400' => 'gma', 'Glyma.18G014100' => 'gma', 'Glyma.19G003100' => 'gma', 'Glyma.19G056500' => 'gma', 'Gohir.A01G158900' => 'ghi', 'Gohir.A05G312600' => 'ghi', 'Gohir.A05G354900' => 'ghi', 'Gohir.A07G037200' => 'ghi', 'Gohir.A09G030000' => 'ghi', 'Gohir.A12G145200' => 'ghi', 'Gohir.D01G151500' => 'ghi', 'Gohir.D04G058300' => 'ghi', 'Gohir.D05G314100' => 'ghi', 'Gohir.D07G041400' => 'ghi', 'Gohir.D09G029700' => 'ghi', 'Gohir.D12G149700' => 'ghi', 'Gorai.001G043800' => 'gra', 'Gorai.002G187800' => 'gra', 'Gorai.006G034700' => 'gra', 'Gorai.008G161200' => 'gra', 'Gorai.009G335700' => 'gra', 'Gorai.012G065000' => 'gra', 'GSVIVG01000535001' => 'vvi', 'GSVIVG01015572001' => 'vvi', 'GSVIVG01032386001' => 'vvi', 'HanXRQChr05g0138531' => 'han', 'HanXRQChr06g0174391' => 'han', 'HanXRQChr07g0199021' => 'han', 'HanXRQChr08g0208211' => 'han', 'HanXRQChr09g0255471' => 'han', 'HanXRQChr10g0315791' => 'han', 'HanXRQChr12g0371991' => 'han', 'HanXRQChr15g0475251' => 'han', 'HanXRQChr17g0540001' => 'han', 'HanXRQChr17g0548631' => 'han', 'HanXRQChr17g0569561' => 'han', 'Haze_12256' => 'cav', 'Haze_14756' => 'cav', 'Haze_25528' => 'cav', 'Hma1.2p1_0079F.1_g041020' => 'hma', 'Hma1.2p1_0818F.1_g223260' => 'hma', 'Hma1.2p1_1747F.1_g300530' => 'hma', 'HPP92_004607' => 'vpl', 'HPP92_004608' => 'vpl', 'HPP92_006181' => 'vpl', 'HPP92_012192' => 'vpl', 'HPP92_015680' => 'vpl', 'HPP92_020249' => 'vpl', 'HPP92_021376' => 'vpl', 'HPP92_024275' => 'vpl', 'Hund06031' => 'sun', 'Hund25391' => 'sun', 'Lalb_Chr07g0185371' => 'lal', 'Lalb_Chr07g0185381' => 'lal', 'Lalb_Chr12g0204011' => 'lal', 'Lalb_Chr13g0301671' => 'lal', 'Lalb_Chr14g0362851' => 'lal', 'Lalb_Chr24g0403581' => 'lal', 'Lj1g0000233' => 'lja', 'Lj2g0018120' => 'lja', 'Lj3C621T0' => 'lonja', 'Lj3P1059T14' => 'lonja', 'Lj3P611T9' => 'lonja', 'Lj3P614T13' => 'lonja', 'Lj3P615T5' => 'lonja', 'Lj4g0012315' => 'lja', 'Lj4g0026182' => 'lja', 'Lj6P813T16' => 'lonja', 'Lj7C427T7' => 'lonja', 'Lj7C427T8' => 'lonja', 'Lj7P600T41' => 'lonja', 'Lju41C42G17' => 'lonja', 'Lsat_1_v5_gn_0_47300' => 'lsa', 'Lsat_1_v5_gn_2_91280' => 'lsa', 'Lsat_1_v5_gn_3_30561' => 'lsa', 'Lsat_1_v5_gn_4_184321' => 'lsa', 'Lsat_1_v5_gn_4_4041' => 'lsa', 'Lsat_1_v5_gn_5_92000' => 'lsa', 'Lsat_1_v5_gn_8_152940' => 'lsa', 'Lsat_1_v5_gn_8_62401' => 'lsa', 'Manes.06G055900' => 'mes', 'Manes.12G022200' => 'mes', 'Manes.13G023300' => 'mes', 'Manes.14G115000' => 'mes', 'Manes.15G151700' => 'mes', 'Manes.17G111300' => 'mes', 'Mapoly0226s0009' => 'mpo', 'MBI02_g25363_MAGBIO' => 'mbi', 'MBI06_g00027_MAGBIO' => 'mbi', 'MBI10_g13034_MAGBIO' => 'mbi', 'MD09G1023400' => 'mdo', 'MD13G1100100' => 'mdo', 'MD15G1169200' => 'mdo', 'MD16G1101100' => 'mdo', 'MD17G1022900' => 'mdo', 'Medtr3g096150' => 'mtr', 'Medtr4g115070' => 'mtr', 'Medtr7g033325' => 'mtr', 'Medtr8g089840' => 'mtr', 'MELO3C010319.2' => 'cme', 'MELO3C011944.2' => 'cme', 'MELO3C021589.2' => 'cme', 'Migut.E00207' => 'egut', 'Migut.H00067' => 'egut', 'Migut.K00433' => 'egut', 'Migut.K00606' => 'egut', 'Migut.K01410' => 'egut', 'MSTRG.13347' => 'ama', 'MSTRG.24045' => 'ama', 'MSTRG.2428' => 'ama', 'MSTRG.26410' => 'ama', 'MSTRG.3139' => 'ama', 'MSTRG.3286' => 'ama', 'MSTRG.563' => 'ama', 'MSTRG.7941' => 'ama', 'Nitab4.5_0000028g0060' => 'nta', 'Nitab4.5_0000065g0260' => 'nta', 'Nitab4.5_0000112g0060' => 'nta', 'Nitab4.5_0000489g0120' => 'nta', 'Nitab4.5_0001776g0050' => 'nta', 'Nitab4.5_0001854g0010' => 'nta', 'Nitab4.5_0001860g0020' => 'nta', 'Nitab4.5_0004352g0010' => 'nta', 'Nitab4.5_0008716g0020' => 'nta', 'Nitab4.5_0008922g0010' => 'nta', 'Nn3g16693' => 'nnu', 'Nn4g22596' => 'nnu', 'Nn7g37639' => 'nnu', 'Oeu001701.1' => 'oeu', 'Oeu018149.1' => 'oeu', 'Oeu026220.1' => 'oeu', 'Oeu038635.1' => 'oeu', 'Oeu049176.1' => 'oeu', 'Oeu056706.1' => 'oeu', 'Oeu056937.1' => 'oeu', 'Oeu057540.1' => 'oeu', 'Os02g0594900' => 'osa', 'Os02g0595100' => 'osa', 'Os04g0477500' => 'osa', 'Os12g0611900' => 'osa', 'Peaxi162Scf00076g00020' => 'pax', 'Peaxi162Scf00128g00217' => 'pax', 'Peaxi162Scf00129g01640' => 'pax', 'Peaxi162Scf00669g00007' => 'pax', 'Peaxi162Scf00700g00421' => 'pax', 'Peaxi162Scf00801g00038' => 'pax', 'Peaxi162Scf00891g00025' => 'pax', 'PGR083G0909' => 'pgr', 'PGR119G1005' => 'pgr', 'PGR142G2236' => 'pgr', 'PGR142G3388' => 'pgr', 'PGSC0003DMG400004514' => 'stu', 'PGSC0003DMG400012635' => 'stu', 'PGSC0003DMG400015730' => 'stu', 'PGSC0003DMG400018611' => 'stu', 'PGSC0003DMG400030897' => 'stu', 'Phvul.001G254800' => 'pvu', 'Phvul.002G260100' => 'pvu', 'Phvul.003G167600' => 'pvu', 'Phvul.004G005100' => 'pvu', 'Potri.001G343600' => 'ptr', 'Potri.006G066700' => 'ptr', 'Potri.008G186000' => 'ptr', 'Potri.010G046900' => 'ptr', 'Potri.018G127900' => 'ptr', 'Pp3c20_17750' => 'ppa', 'Pp3c24_4380' => 'ppa', 'Prupe.1G245800' => 'ppe', 'Prupe.3G293400' => 'ppe', 'Prupe.7G247400' => 'ppe', 'Psat0s145g0120' => 'psa', 'Psat0s595g0040' => 'psa', 'Psat0s595g0120' => 'psa', 'Psat3g175040' => 'psa', 'Psat7g058120' => 'psa', 'PSO017G0428' => 'pso', 'PSO063G7510' => 'pso', 'PSO067G0046' => 'pso', 'PSO478G1073' => 'pso', 'PSO675G3677' => 'pso', 'PSO675G6558' => 'pso', 'PSO675G7520' => 'pso', 'PSO675G8959' => 'pso', 'QL02p074089' => 'qlo', 'QL02p089614' => 'qlo', 'QL03p057736' => 'qlo', 'RcHm_v2.0_Chr1g0364131' => 'rch', 'RcHm_v2.0_Chr2g0087801' => 'rch', 'RcHm_v2.0_Chr2g0087821' => 'rch', 'RcHm_v2.0_Chr2g0173231' => 'rch', 'RcHm_v2.0_Chr4g0433111' => 'rch', 'Rhsim03G0250300' => 'rsi', 'Rhsim08G0048400' => 'rsi', 'Rhsim10G0014800' => 'rsi', 'Rhsim12G0040100' => 'rsi', 'Rhsim12G0109700' => 'rsi', 'Sabra06G0049600' => 'sbr', 'Sabra08G0141000' => 'sbr', 'Sabra10G0021400' => 'sbr', 'Sabra16G0222900' => 'sbr', 'Sabra18G0108600' => 'sbr', 'SalBow1G0433' => 'sbo', 'SalBow1G2038' => 'sbo', 'SalBow1G5003' => 'sbo', 'SalBow7G1197' => 'sbo', 'SalBow8G3506' => 'sbo', 'Sc03g0007300' => 'sci', 'Sc11g0000950' => 'sci', 'Sc14g0008750' => 'sci', 'Sc18g0000420' => 'sci', 'Sed0006754' => 'sed', 'Sed0008741' => 'sed', 'Sed0017172' => 'sed', 'Sed0018925' => 'sed', 'Sed0023326' => 'sed', 'Sed0025909' => 'sed', 'SEGI_05333' => 'sgi', 'SEGI_10362' => 'sgi', 'SEGI_13380' => 'sgi', 'SEGI_24306' => 'sgi', 'SEGI_29077' => 'sgi', 'SEGI_29095' => 'sgi', 'SEGI_36534' => 'sgi', 'SEGI_37506' => 'sgi', 'SEGI_38321' => 'sgi', 'SGA_v2.0_scaffold307G48031' => 'sas', 'SGA_v2.0_scaffold47G17507' => 'sas', 'SGA_v2.0_scaffold63G21736' => 'sas', 'SGA_v2.0_scaffold87G27070' => 'sas', 'SHI17794' => 'shi', 'SHI28851' => 'shi', 'SMO165G0155' => 'smo', 'SMO340G0217' => 'smo', 'SMO367G1210' => 'smo', 'Solyc02g093430.3' => 'sly', 'Solyc05g013580.4' => 'sly', 'Solyc07g008030.3' => 'sly', 'Solyc12g035470.2' => 'sly', 'Sopen02g038020' => 'spe', 'Sopen05g008490' => 'spe', 'Sopen07g003910' => 'spe', 'Sopen12g015240' => 'spe', 'Sp1g11550' => 'spa', 'Sp2g16710' => 'spa', 'Sp3g00430' => 'spa', 'Sp3g26780' => 'spa', 'Sp5g22900' => 'spa', 'Sp6g29530' => 'spa', 'TAR371G0794' => 'tar', 'TAR374G0164' => 'tar', 'TAR622G0165' => 'tar', 'TAR626G0929' => 'tar', 'TAR629G2155' => 'tar', 'THA.LOC104805282' => 'tha', 'THA.LOC104805363' => 'tha', 'THA.LOC104808968' => 'tha', 'THA.LOC104821093' => 'tha', 'THA.LOC104823953' => 'tha', 'THA.LOC104825562' => 'tha', 'THA.LOC104825665' => 'tha', 'Thecc.02G261400' => 'tca', 'Thecc.04G019200' => 'tca', 'Thecc.09G130400' => 'tca', 'Thhalv10004374m.g' => 'esa', 'Thhalv10007850m.g' => 'esa', 'Thhalv10013782m.g' => 'esa', 'Thhalv10018686m.g' => 'esa', 'Thhalv10020899m.g' => 'esa', 'Thhalv10022755m.g' => 'esa', 'TPR.G23851' => 'tpr', 'TPR.G26500' => 'tpr', 'TPR.G27267' => 'tpr', 'TPR.G32001' => 'tpr', 'TPR.G6251' => 'tpr', 'TPR.G8167' => 'tpr', 'TWI12G1330' => 'twi', 'TWI18G1239' => 'twi', 'TWI34G0979' => 'twi', 'TWI36G0670' => 'twi', 'TWI36G0707' => 'twi', 'TWI56G0233' => 'twi', 'TWI75G1809' => 'twi', 'unitig_21.g20874' => 'ugi', 'unitig_26.g10343' => 'ugi', 'unitig_46.g18392' => 'ugi', 'unitig_52.g17178' => 'ugi', 'unitig_8.g2934' => 'ugi', 'vmacro01122' => 'vma', 'vmacro05875' => 'vma', 'vmacro06147' => 'vma', 'vmacro16191' => 'vma', 'vmacro18293' => 'vma', 'VMungo0251G3707' => 'vmu', 'VMungo0464G1521' => 'vmu', 'VMungo1215G0205' => 'vmu', 'VMungo1383G2484' => 'vmu', 'Zm00001eb079610' => 'zma', 'Zm00001eb135990' => 'zma', 'Zm00001eb183710' => 'zma', 'Zm00001eb246020' => 'zma' ), 'gf_id' => 'HOM05D001124', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001124' ), 'data_identifier' => 'HOM05D001124', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001124', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '548', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02520' => 'bna', 'A03p06630' => 'bna', 'A05p44460' => 'bna', 'A06p08710' => 'bna', 'A06p41090' => 'bna', 'A07p32320' => 'bna', 'A08p32520' => 'bna', 'A09p10360' => 'bna', 'A10p24080' => 'bna', 'Aa31LG11G15250' => 'aar', 'Aa31LG1G1800' => 'aar', 'Aa31LG2G5120' => 'aar', 'Aa31LG2G6070' => 'aar', 'Aa31LG5G10770' => 'aar', 'Aa31sc61G90' => 'aar', 'Actinidia01352' => 'ach', 'Actinidia05983' => 'ach', 'Actinidia08133' => 'ach', 'Actinidia15101' => 'ach', 'Actinidia26379' => 'ach', 'Actinidia35778' => 'ach', 'Actinidia36123' => 'ach', 'Actinidia37436' => 'ach', 'Actinidia38730' => 'ach', 'Ah.02g128210' => 'amhyb', 'Ah.03g132990' => 'amhyb', 'Ah.14g079410' => 'amhyb', 'AL1G24640' => 'aly', 'AL2G26680' => 'aly', 'AL3G10530' => 'aly', 'AL3G45230' => 'aly', 'AL5G15230' => 'aly', 'AL5G16960' => 'aly', 'AL6G25210' => 'aly', 'Aqoxy2G00441' => 'aox', 'Aqoxy3G01236' => 'aox', 'Aqoxy5G03746' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3RQ047' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C7GMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9C8JER' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MBL6KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YXCZ83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZANX40' => 'arhy', 'AT1G12990' => 'ath', 'AT1G67880' => 'ath', 'AT2G13290' => 'ath', 'AT3G01620' => 'ath', 'AT3G26445' => 'ath', 'AT3G27540' => 'ath', 'AT5G14480' => 'ath', 'ATR0824G026' => 'atr', 'ATR1098G019' => 'atr', 'Atru.chr11.2145' => 'acertr', 'Atru.chr2.3636' => 'acertr', 'Atru.chr2.3644' => 'acertr', 'Atru.chr6.2422' => 'acertr', 'Atru.chr7.1112' => 'acertr', 'AUR62005469' => 'cqu', 'AUR62011166' => 'cqu', 'AUR62013319' => 'cqu', 'AUR62024273' => 'cqu', 'AUR62028420' => 'cqu', 'AUR62041942' => 'cqu', 'BcaB01g04969' => 'bca', 'BcaB01g06371' => 'bca', 'BcaB02g11494' => 'bca', 'BcaB03g15382' => 'bca', 'BcaB08g36994' => 'bca', 'BcaC03g13477' => 'bca', 'BcaC03g13478' => 'bca', 'BcaC03g13480' => 'bca', 'BcaC03g13481' => 'bca', 'BcaC03g13486' => 'bca', 'BcaC04g19031' => 'bca', 'BcaC04g23085' => 'bca', 'BcaC05g25094' => 'bca', 'BcaC05g25096' => 'bca', 'BcaC05g25138' => 'bca', 'BcaC05g30416' => 'bca', 'BcaC05g30455' => 'bca', 'BcaC06g30979' => 'bca', 'BcaC06g33805' => 'bca', 'BcaC08g46021' => 'bca', 'BcaNung03154' => 'bca', 'BolC2t06623H' => 'bol', 'BolC2t06632H' => 'bol', 'BolC2t06635H' => 'bol', 'BolC2t06638H' => 'bol', 'BolC3t13266H' => 'bol', 'BolC5t29776H' => 'bol', 'BolC6t38912H' => 'bol', 'BolC7t44183H' => 'bol', 'BolC9t54123H' => 'bol', 'BolC9t59107H' => 'bol', 'BraA02t05221Z' => 'bra', 'BraA03t09996Z' => 'bra', 'BraA05t23210Z' => 'bra', 'BraA06t24068Z' => 'bra', 'BraA06t27032Z' => 'bra', 'BraA08t35176Z' => 'bra', 'BraA09t36680Z' => 'bra', 'BraA10t44471Z' => 'bra', 'C02p06760' => 'bna', 'C02p06890' => 'bna', 'C02p07010' => 'bna', 'C03p07660' => 'bna', 'C05p10300' => 'bna', 'C06p38150' => 'bna', 'C07p36650' => 'bna', 'C08p15770' => 'bna', 'C09p12300' => 'bna', 'C09p62700' => 'bna', 'C09p75040' => 'bna', 'CAN.G13.1' => 'can', 'CAN.G138.4' => 'can', 'CAN.G44.6' => 'can', 'CAN.G473.19' => 'can', 'CANSAT01G0835' => 'cansat', 'CANSAT11G0246' => 'cansat', 'CANSAT11G1766' => 'cansat', 'CANSAT64G1954' => 'cansat', 'CARHR013330' => 'chi', 'CARHR060530' => 'chi', 'CARHR075300' => 'chi', 'CARHR105120' => 'chi', 'CARHR148910' => 'chi', 'CARHR198830' => 'chi', 'Carub.0001s1275' => 'cru', 'Carub.0002s1437' => 'cru', 'Carub.0003s0044' => 'cru', 'Carub.0003s2787' => 'cru', 'Carub.0005s0597' => 'cru', 'Carub.0006s1266' => 'cru', 'Ca_06935_v3' => 'car', 'Ca_13559_v3' => 'car', 'Ca_16941_v3' => 'car', 'Ca_16960_v3' => 'car', 'Ca_17775_v3' => 'car', 'Ca_30464_v3' => 'car', 'Cc06_g08160' => 'ccan', 'Cc07_g01520' => 'ccan', 'Cc11_g15810' => 'ccan', 'CDE02G2840' => 'cde', 'CDE03G0093' => 'cde', 'CDE04G2127' => 'cde', 'CDE07G1857' => 'cde', 'CDE09G1246' => 'cde', 'Cfa003412' => 'cfa', 'Cfa007341' => 'cfa', 'Cfa009220' => 'cfa', 'Ciclev10008737m.g' => 'ccl', 'Ciclev10015565m.g' => 'ccl', 'Ciclev10031761m.g' => 'ccl', 'CiPaw.03G045300' => 'cil', 'CiPaw.03G247200' => 'cil', 'CiPaw.04G029500' => 'cil', 'CiPaw.04G174000' => 'cil', 'CiPaw.05G181200' => 'cil', 'CiPaw.06G067100' => 'cil', 'ClCG05G025800' => 'cla', 'ClCG06G011400' => 'cla', 'ClCG09G019360' => 'cla', 'COL.COLO4_04827' => 'col', 'COL.COLO4_29170' => 'col', 'COL.COLO4_35131' => 'col', 'COL.COLO4_35132' => 'col', 'Cpa.g.sc33.32' => 'cpa', 'Cpa.g.sc46.29' => 'cpa', 'Cpa.g.sc796.1' => 'cpa', 'CsaV3_1G030420' => 'csa', 'CsaV3_5G027050' => 'csa', 'CsaV3_5G031040' => 'csa', 'CsaV3_UNG023130' => 'csa', 'CSS0007726' => 'camsi', 'CSS0016433' => 'camsi', 'CSS0017656' => 'camsi', 'CSS0025364' => 'camsi', 'CSS0027582' => 'camsi', 'CSS0047288' => 'camsi', 'CSS0049950' => 'camsi', 'DCAR_003843' => 'dca', 'DCAR_007052' => 'dca', 'DCAR_020884' => 'dca', 'DCAR_021730' => 'dca', 'DCAR_024423' => 'dca', 'DCAR_026509' => 'dca', 'DCAR_031158' => 'dca', 'Dinv14728' => 'din', 'Dinv15219' => 'din', 'Dinv25728' => 'din', 'Dinv33428' => 'din', 'Dinv36489' => 'din', 'Dinv41486' => 'din', 'Duzib147G0469' => 'dzi', 'Duzib168G0060' => 'dzi', 'Duzib187G1215' => 'dzi', 'Duzib248G0692' => 'dzi', 'Duzib251G0767' => 'dzi', 'Duzib264G0446' => 'dzi', 'Duzib268G0691' => 'dzi', 'ECA232G4767' => 'eca', 'ECA233G2838' => 'eca', 'ECA234G0391' => 'eca', 'ECA234G0857' => 'eca', 'ECA236G1593' => 'eca', 'ECA238G0565' => 'eca', 'ECA246G1027' => 'eca', 'ECA246G3223' => 'eca', 'ECA246G3470' => 'eca', 'EL10Ac6g13829' => 'bvu', 'EL10Ac6g14093' => 'bvu', 'EL10Ac8g18707' => 'bvu', 'Eucgr.C01369' => 'egr', 'Eucgr.H02492' => 'egr', 'Eucgr.I01733' => 'egr', 'Eucgr.J02255' => 'egr', 'Eucgr.J02257' => 'egr', 'Eucgr.J02258' => 'egr', 'FAN02G1601' => 'fan', 'FAN03G1586' => 'fan', 'FAN03G2986' => 'fan', 'FAN05G4837' => 'fan', 'FAN06G0146' => 'fan', 'FAN07G0858' => 'fan', 'FAN09G3179' => 'fan', 'FAN10G0669' => 'fan', 'FAN12G2358' => 'fan', 'FAN14G4198' => 'fan', 'FAN14G5112' => 'fan', 'FAN17G0342' => 'fan', 'FAN19G0342' => 'fan', 'FAN19G0962' => 'fan', 'FAN19G1101' => 'fan', 'FAN19G1872' => 'fan', 'FAN22G0356' => 'fan', 'FAN23G0744' => 'fan', 'FAN23G1914' => 'fan', 'FAN26G0032' => 'fan', 'FAN28G0625' => 'fan', 'FvH4_1g02710' => 'fve', 'FvH4_1g02720' => 'fve', 'FvH4_4g25670' => 'fve', 'FvH4_6g51700' => 'fve', 'FvH4_7g20170' => 'fve', 'Glyma.05G175000' => 'gma', 'Glyma.08G132300' => 'gma', 'Glyma.11G243000' => 'gma', 'Glyma.13G158900' => 'gma', 'Glyma.17G112400' => 'gma', 'Glyma.18G014100' => 'gma', 'Glyma.19G003100' => 'gma', 'Glyma.19G056500' => 'gma', 'Gohir.A01G158900' => 'ghi', 'Gohir.A05G312600' => 'ghi', 'Gohir.A05G354900' => 'ghi', 'Gohir.A07G037200' => 'ghi', 'Gohir.A09G030000' => 'ghi', 'Gohir.A12G145200' => 'ghi', 'Gohir.D01G151500' => 'ghi', 'Gohir.D04G058300' => 'ghi', 'Gohir.D05G314100' => 'ghi', 'Gohir.D07G041400' => 'ghi', 'Gohir.D09G029700' => 'ghi', 'Gohir.D12G149700' => 'ghi', 'Gorai.001G043800' => 'gra', 'Gorai.002G187800' => 'gra', 'Gorai.006G034700' => 'gra', 'Gorai.008G161200' => 'gra', 'Gorai.009G335700' => 'gra', 'Gorai.012G065000' => 'gra', 'GSVIVG01000535001' => 'vvi', 'GSVIVG01015572001' => 'vvi', 'GSVIVG01032386001' => 'vvi', 'HanXRQChr05g0138531' => 'han', 'HanXRQChr06g0174391' => 'han', 'HanXRQChr07g0199021' => 'han', 'HanXRQChr08g0208211' => 'han', 'HanXRQChr09g0255471' => 'han', 'HanXRQChr10g0315791' => 'han', 'HanXRQChr12g0371991' => 'han', 'HanXRQChr15g0475251' => 'han', 'HanXRQChr17g0540001' => 'han', 'HanXRQChr17g0548631' => 'han', 'HanXRQChr17g0569561' => 'han', 'Haze_12256' => 'cav', 'Haze_14756' => 'cav', 'Haze_25528' => 'cav', 'Hma1.2p1_0079F.1_g041020' => 'hma', 'Hma1.2p1_0818F.1_g223260' => 'hma', 'Hma1.2p1_1747F.1_g300530' => 'hma', 'HPP92_004607' => 'vpl', 'HPP92_004608' => 'vpl', 'HPP92_006181' => 'vpl', 'HPP92_012192' => 'vpl', 'HPP92_015680' => 'vpl', 'HPP92_020249' => 'vpl', 'HPP92_021376' => 'vpl', 'HPP92_024275' => 'vpl', 'Hund06031' => 'sun', 'Hund25391' => 'sun', 'Lalb_Chr07g0185371' => 'lal', 'Lalb_Chr07g0185381' => 'lal', 'Lalb_Chr12g0204011' => 'lal', 'Lalb_Chr13g0301671' => 'lal', 'Lalb_Chr14g0362851' => 'lal', 'Lalb_Chr24g0403581' => 'lal', 'Lj1g0000233' => 'lja', 'Lj2g0018120' => 'lja', 'Lj3C621T0' => 'lonja', 'Lj3P1059T14' => 'lonja', 'Lj3P611T9' => 'lonja', 'Lj3P614T13' => 'lonja', 'Lj3P615T5' => 'lonja', 'Lj4g0012315' => 'lja', 'Lj4g0026182' => 'lja', 'Lj6P813T16' => 'lonja', 'Lj7C427T7' => 'lonja', 'Lj7C427T8' => 'lonja', 'Lj7P600T41' => 'lonja', 'Lju41C42G17' => 'lonja', 'Lsat_1_v5_gn_0_47300' => 'lsa', 'Lsat_1_v5_gn_2_91280' => 'lsa', 'Lsat_1_v5_gn_3_30561' => 'lsa', 'Lsat_1_v5_gn_4_184321' => 'lsa', 'Lsat_1_v5_gn_4_4041' => 'lsa', 'Lsat_1_v5_gn_5_92000' => 'lsa', 'Lsat_1_v5_gn_8_152940' => 'lsa', 'Lsat_1_v5_gn_8_62401' => 'lsa', 'Manes.06G055900' => 'mes', 'Manes.12G022200' => 'mes', 'Manes.13G023300' => 'mes', 'Manes.14G115000' => 'mes', 'Manes.15G151700' => 'mes', 'Manes.17G111300' => 'mes', 'Mapoly0226s0009' => 'mpo', 'MBI02_g25363_MAGBIO' => 'mbi', 'MBI06_g00027_MAGBIO' => 'mbi', 'MBI10_g13034_MAGBIO' => 'mbi', 'MD09G1023400' => 'mdo', 'MD13G1100100' => 'mdo', 'MD15G1169200' => 'mdo', 'MD16G1101100' => 'mdo', 'MD17G1022900' => 'mdo', 'Medtr3g096150' => 'mtr', 'Medtr4g115070' => 'mtr', 'Medtr7g033325' => 'mtr', 'Medtr8g089840' => 'mtr', 'MELO3C010319.2' => 'cme', 'MELO3C011944.2' => 'cme', 'MELO3C021589.2' => 'cme', 'Migut.E00207' => 'egut', 'Migut.H00067' => 'egut', 'Migut.K00433' => 'egut', 'Migut.K00606' => 'egut', 'Migut.K01410' => 'egut', 'MSTRG.13347' => 'ama', 'MSTRG.24045' => 'ama', 'MSTRG.2428' => 'ama', 'MSTRG.26410' => 'ama', 'MSTRG.3139' => 'ama', 'MSTRG.3286' => 'ama', 'MSTRG.563' => 'ama', 'MSTRG.7941' => 'ama', 'Nitab4.5_0000028g0060' => 'nta', 'Nitab4.5_0000065g0260' => 'nta', 'Nitab4.5_0000112g0060' => 'nta', 'Nitab4.5_0000489g0120' => 'nta', 'Nitab4.5_0001776g0050' => 'nta', 'Nitab4.5_0001854g0010' => 'nta', 'Nitab4.5_0001860g0020' => 'nta', 'Nitab4.5_0004352g0010' => 'nta', 'Nitab4.5_0008716g0020' => 'nta', 'Nitab4.5_0008922g0010' => 'nta', 'Nn3g16693' => 'nnu', 'Nn4g22596' => 'nnu', 'Nn7g37639' => 'nnu', 'Oeu001701.1' => 'oeu', 'Oeu018149.1' => 'oeu', 'Oeu026220.1' => 'oeu', 'Oeu038635.1' => 'oeu', 'Oeu049176.1' => 'oeu', 'Oeu056706.1' => 'oeu', 'Oeu056937.1' => 'oeu', 'Oeu057540.1' => 'oeu', 'Os02g0594900' => 'osa', 'Os02g0595100' => 'osa', 'Os04g0477500' => 'osa', 'Os12g0611900' => 'osa', 'Peaxi162Scf00076g00020' => 'pax', 'Peaxi162Scf00128g00217' => 'pax', 'Peaxi162Scf00129g01640' => 'pax', 'Peaxi162Scf00669g00007' => 'pax', 'Peaxi162Scf00700g00421' => 'pax', 'Peaxi162Scf00801g00038' => 'pax', 'Peaxi162Scf00891g00025' => 'pax', 'PGR083G0909' => 'pgr', 'PGR119G1005' => 'pgr', 'PGR142G2236' => 'pgr', 'PGR142G3388' => 'pgr', 'PGSC0003DMG400004514' => 'stu', 'PGSC0003DMG400012635' => 'stu', 'PGSC0003DMG400015730' => 'stu', 'PGSC0003DMG400018611' => 'stu', 'PGSC0003DMG400030897' => 'stu', 'Phvul.001G254800' => 'pvu', 'Phvul.002G260100' => 'pvu', 'Phvul.003G167600' => 'pvu', 'Phvul.004G005100' => 'pvu', 'Potri.001G343600' => 'ptr', 'Potri.006G066700' => 'ptr', 'Potri.008G186000' => 'ptr', 'Potri.010G046900' => 'ptr', 'Potri.018G127900' => 'ptr', 'Pp3c20_17750' => 'ppa', 'Pp3c24_4380' => 'ppa', 'Prupe.1G245800' => 'ppe', 'Prupe.3G293400' => 'ppe', 'Prupe.7G247400' => 'ppe', 'Psat0s145g0120' => 'psa', 'Psat0s595g0040' => 'psa', 'Psat0s595g0120' => 'psa', 'Psat3g175040' => 'psa', 'Psat7g058120' => 'psa', 'PSO017G0428' => 'pso', 'PSO063G7510' => 'pso', 'PSO067G0046' => 'pso', 'PSO478G1073' => 'pso', 'PSO675G3677' => 'pso', 'PSO675G6558' => 'pso', 'PSO675G7520' => 'pso', 'PSO675G8959' => 'pso', 'QL02p074089' => 'qlo', 'QL02p089614' => 'qlo', 'QL03p057736' => 'qlo', 'RcHm_v2.0_Chr1g0364131' => 'rch', 'RcHm_v2.0_Chr2g0087801' => 'rch', 'RcHm_v2.0_Chr2g0087821' => 'rch', 'RcHm_v2.0_Chr2g0173231' => 'rch', 'RcHm_v2.0_Chr4g0433111' => 'rch', 'Rhsim03G0250300' => 'rsi', 'Rhsim08G0048400' => 'rsi', 'Rhsim10G0014800' => 'rsi', 'Rhsim12G0040100' => 'rsi', 'Rhsim12G0109700' => 'rsi', 'Sabra06G0049600' => 'sbr', 'Sabra08G0141000' => 'sbr', 'Sabra10G0021400' => 'sbr', 'Sabra16G0222900' => 'sbr', 'Sabra18G0108600' => 'sbr', 'SalBow1G0433' => 'sbo', 'SalBow1G2038' => 'sbo', 'SalBow1G5003' => 'sbo', 'SalBow7G1197' => 'sbo', 'SalBow8G3506' => 'sbo', 'Sc03g0007300' => 'sci', 'Sc11g0000950' => 'sci', 'Sc14g0008750' => 'sci', 'Sc18g0000420' => 'sci', 'Sed0006754' => 'sed', 'Sed0008741' => 'sed', 'Sed0017172' => 'sed', 'Sed0018925' => 'sed', 'Sed0023326' => 'sed', 'Sed0025909' => 'sed', 'SEGI_05333' => 'sgi', 'SEGI_10362' => 'sgi', 'SEGI_13380' => 'sgi', 'SEGI_24306' => 'sgi', 'SEGI_29077' => 'sgi', 'SEGI_29095' => 'sgi', 'SEGI_36534' => 'sgi', 'SEGI_37506' => 'sgi', 'SEGI_38321' => 'sgi', 'SGA_v2.0_scaffold307G48031' => 'sas', 'SGA_v2.0_scaffold47G17507' => 'sas', 'SGA_v2.0_scaffold63G21736' => 'sas', 'SGA_v2.0_scaffold87G27070' => 'sas', 'SHI17794' => 'shi', 'SHI28851' => 'shi', 'SMO165G0155' => 'smo', 'SMO340G0217' => 'smo', 'SMO367G1210' => 'smo', 'Solyc02g093430.3' => 'sly', 'Solyc05g013580.4' => 'sly', 'Solyc07g008030.3' => 'sly', 'Solyc12g035470.2' => 'sly', 'Sopen02g038020' => 'spe', 'Sopen05g008490' => 'spe', 'Sopen07g003910' => 'spe', 'Sopen12g015240' => 'spe', 'Sp1g11550' => 'spa', 'Sp2g16710' => 'spa', 'Sp3g00430' => 'spa', 'Sp3g26780' => 'spa', 'Sp5g22900' => 'spa', 'Sp6g29530' => 'spa', 'TAR371G0794' => 'tar', 'TAR374G0164' => 'tar', 'TAR622G0165' => 'tar', 'TAR626G0929' => 'tar', 'TAR629G2155' => 'tar', 'THA.LOC104805282' => 'tha', 'THA.LOC104805363' => 'tha', 'THA.LOC104808968' => 'tha', 'THA.LOC104821093' => 'tha', 'THA.LOC104823953' => 'tha', 'THA.LOC104825562' => 'tha', 'THA.LOC104825665' => 'tha', 'Thecc.02G261400' => 'tca', 'Thecc.04G019200' => 'tca', 'Thecc.09G130400' => 'tca', 'Thhalv10004374m.g' => 'esa', 'Thhalv10007850m.g' => 'esa', 'Thhalv10013782m.g' => 'esa', 'Thhalv10018686m.g' => 'esa', 'Thhalv10020899m.g' => 'esa', 'Thhalv10022755m.g' => 'esa', 'TPR.G23851' => 'tpr', 'TPR.G26500' => 'tpr', 'TPR.G27267' => 'tpr', 'TPR.G32001' => 'tpr', 'TPR.G6251' => 'tpr', 'TPR.G8167' => 'tpr', 'TWI12G1330' => 'twi', 'TWI18G1239' => 'twi', 'TWI34G0979' => 'twi', 'TWI36G0670' => 'twi', 'TWI36G0707' => 'twi', 'TWI56G0233' => 'twi', 'TWI75G1809' => 'twi', 'unitig_21.g20874' => 'ugi', 'unitig_26.g10343' => 'ugi', 'unitig_46.g18392' => 'ugi', 'unitig_52.g17178' => 'ugi', 'unitig_8.g2934' => 'ugi', 'vmacro01122' => 'vma', 'vmacro05875' => 'vma', 'vmacro06147' => 'vma', 'vmacro16191' => 'vma', 'vmacro18293' => 'vma', 'VMungo0251G3707' => 'vmu', 'VMungo0464G1521' => 'vmu', 'VMungo1215G0205' => 'vmu', 'VMungo1383G2484' => 'vmu', 'Zm00001eb079610' => 'zma', 'Zm00001eb135990' => 'zma', 'Zm00001eb183710' => 'zma', 'Zm00001eb246020' => 'zma' ) $gf_id = 'HOM05D001124' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001124' ) $data_identifier = 'HOM05D001124' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 6, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 7, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 21, 'bol' => (int) 10, 'bra' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 6, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 9, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 21, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 8, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 10, 'lsa' => (int) 8, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 8, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 9, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb246020' $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' => 'HOM05D001124', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '548', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02520' => 'bna', 'A03p06630' => 'bna', 'A05p44460' => 'bna', 'A06p08710' => 'bna', 'A06p41090' => 'bna', 'A07p32320' => 'bna', 'A08p32520' => 'bna', 'A09p10360' => 'bna', 'A10p24080' => 'bna', 'Aa31LG11G15250' => 'aar', 'Aa31LG1G1800' => 'aar', 'Aa31LG2G5120' => 'aar', 'Aa31LG2G6070' => 'aar', 'Aa31LG5G10770' => 'aar', 'Aa31sc61G90' => 'aar', 'Actinidia01352' => 'ach', 'Actinidia05983' => 'ach', 'Actinidia08133' => 'ach', 'Actinidia15101' => 'ach', 'Actinidia26379' => 'ach', 'Actinidia35778' => 'ach', 'Actinidia36123' => 'ach', 'Actinidia37436' => 'ach', 'Actinidia38730' => 'ach', 'Ah.02g128210' => 'amhyb', 'Ah.03g132990' => 'amhyb', 'Ah.14g079410' => 'amhyb', 'AL1G24640' => 'aly', 'AL2G26680' => 'aly', 'AL3G10530' => 'aly', 'AL3G45230' => 'aly', 'AL5G15230' => 'aly', 'AL5G16960' => 'aly', 'AL6G25210' => 'aly', 'Aqoxy2G00441' => 'aox', 'Aqoxy3G01236' => 'aox', 'Aqoxy5G03746' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3RQ047' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C7GMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9C8JER' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MBL6KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YXCZ83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZANX40' => 'arhy', 'AT1G12990' => 'ath', 'AT1G67880' => 'ath', 'AT2G13290' => 'ath', 'AT3G01620' => 'ath', 'AT3G26445' => 'ath', 'AT3G27540' => 'ath', 'AT5G14480' => 'ath', 'ATR0824G026' => 'atr', 'ATR1098G019' => 'atr', 'Atru.chr11.2145' => 'acertr', 'Atru.chr2.3636' => 'acertr', 'Atru.chr2.3644' => 'acertr', 'Atru.chr6.2422' => 'acertr', 'Atru.chr7.1112' => 'acertr', 'AUR62005469' => 'cqu', 'AUR62011166' => 'cqu', 'AUR62013319' => 'cqu', 'AUR62024273' => 'cqu', 'AUR62028420' => 'cqu', 'AUR62041942' => 'cqu', 'BcaB01g04969' => 'bca', 'BcaB01g06371' => 'bca', 'BcaB02g11494' => 'bca', 'BcaB03g15382' => 'bca', 'BcaB08g36994' => 'bca', 'BcaC03g13477' => 'bca', 'BcaC03g13478' => 'bca', 'BcaC03g13480' => 'bca', 'BcaC03g13481' => 'bca', 'BcaC03g13486' => 'bca', 'BcaC04g19031' => 'bca', 'BcaC04g23085' => 'bca', 'BcaC05g25094' => 'bca', 'BcaC05g25096' => 'bca', 'BcaC05g25138' => 'bca', 'BcaC05g30416' => 'bca', 'BcaC05g30455' => 'bca', 'BcaC06g30979' => 'bca', 'BcaC06g33805' => 'bca', 'BcaC08g46021' => 'bca', 'BcaNung03154' => 'bca', 'BolC2t06623H' => 'bol', 'BolC2t06632H' => 'bol', 'BolC2t06635H' => 'bol', 'BolC2t06638H' => 'bol', 'BolC3t13266H' => 'bol', 'BolC5t29776H' => 'bol', 'BolC6t38912H' => 'bol', 'BolC7t44183H' => 'bol', 'BolC9t54123H' => 'bol', 'BolC9t59107H' => 'bol', 'BraA02t05221Z' => 'bra', 'BraA03t09996Z' => 'bra', 'BraA05t23210Z' => 'bra', 'BraA06t24068Z' => 'bra', 'BraA06t27032Z' => 'bra', 'BraA08t35176Z' => 'bra', 'BraA09t36680Z' => 'bra', 'BraA10t44471Z' => 'bra', 'C02p06760' => 'bna', 'C02p06890' => 'bna', 'C02p07010' => 'bna', 'C03p07660' => 'bna', 'C05p10300' => 'bna', 'C06p38150' => 'bna', 'C07p36650' => 'bna', 'C08p15770' => 'bna', 'C09p12300' => 'bna', 'C09p62700' => 'bna', 'C09p75040' => 'bna', 'CAN.G13.1' => 'can', 'CAN.G138.4' => 'can', 'CAN.G44.6' => 'can', 'CAN.G473.19' => 'can', 'CANSAT01G0835' => 'cansat', 'CANSAT11G0246' => 'cansat', 'CANSAT11G1766' => 'cansat', 'CANSAT64G1954' => 'cansat', 'CARHR013330' => 'chi', 'CARHR060530' => 'chi', 'CARHR075300' => 'chi', 'CARHR105120' => 'chi', 'CARHR148910' => 'chi', 'CARHR198830' => 'chi', 'Carub.0001s1275' => 'cru', 'Carub.0002s1437' => 'cru', 'Carub.0003s0044' => 'cru', 'Carub.0003s2787' => 'cru', 'Carub.0005s0597' => 'cru', 'Carub.0006s1266' => 'cru', 'Ca_06935_v3' => 'car', 'Ca_13559_v3' => 'car', 'Ca_16941_v3' => 'car', 'Ca_16960_v3' => 'car', 'Ca_17775_v3' => 'car', 'Ca_30464_v3' => 'car', 'Cc06_g08160' => 'ccan', 'Cc07_g01520' => 'ccan', 'Cc11_g15810' => 'ccan', 'CDE02G2840' => 'cde', 'CDE03G0093' => 'cde', 'CDE04G2127' => 'cde', 'CDE07G1857' => 'cde', 'CDE09G1246' => 'cde', 'Cfa003412' => 'cfa', 'Cfa007341' => 'cfa', 'Cfa009220' => 'cfa', 'Ciclev10008737m.g' => 'ccl', 'Ciclev10015565m.g' => 'ccl', 'Ciclev10031761m.g' => 'ccl', 'CiPaw.03G045300' => 'cil', 'CiPaw.03G247200' => 'cil', 'CiPaw.04G029500' => 'cil', 'CiPaw.04G174000' => 'cil', 'CiPaw.05G181200' => 'cil', 'CiPaw.06G067100' => 'cil', 'ClCG05G025800' => 'cla', 'ClCG06G011400' => 'cla', 'ClCG09G019360' => 'cla', 'COL.COLO4_04827' => 'col', 'COL.COLO4_29170' => 'col', 'COL.COLO4_35131' => 'col', 'COL.COLO4_35132' => 'col', 'Cpa.g.sc33.32' => 'cpa', 'Cpa.g.sc46.29' => 'cpa', 'Cpa.g.sc796.1' => 'cpa', 'CsaV3_1G030420' => 'csa', 'CsaV3_5G027050' => 'csa', 'CsaV3_5G031040' => 'csa', 'CsaV3_UNG023130' => 'csa', 'CSS0007726' => 'camsi', 'CSS0016433' => 'camsi', 'CSS0017656' => 'camsi', 'CSS0025364' => 'camsi', 'CSS0027582' => 'camsi', 'CSS0047288' => 'camsi', 'CSS0049950' => 'camsi', 'DCAR_003843' => 'dca', 'DCAR_007052' => 'dca', 'DCAR_020884' => 'dca', 'DCAR_021730' => 'dca', 'DCAR_024423' => 'dca', 'DCAR_026509' => 'dca', 'DCAR_031158' => 'dca', 'Dinv14728' => 'din', 'Dinv15219' => 'din', 'Dinv25728' => 'din', 'Dinv33428' => 'din', 'Dinv36489' => 'din', 'Dinv41486' => 'din', 'Duzib147G0469' => 'dzi', 'Duzib168G0060' => 'dzi', 'Duzib187G1215' => 'dzi', 'Duzib248G0692' => 'dzi', 'Duzib251G0767' => 'dzi', 'Duzib264G0446' => 'dzi', 'Duzib268G0691' => 'dzi', 'ECA232G4767' => 'eca', 'ECA233G2838' => 'eca', 'ECA234G0391' => 'eca', 'ECA234G0857' => 'eca', 'ECA236G1593' => 'eca', 'ECA238G0565' => 'eca', 'ECA246G1027' => 'eca', 'ECA246G3223' => 'eca', 'ECA246G3470' => 'eca', 'EL10Ac6g13829' => 'bvu', 'EL10Ac6g14093' => 'bvu', 'EL10Ac8g18707' => 'bvu', 'Eucgr.C01369' => 'egr', 'Eucgr.H02492' => 'egr', 'Eucgr.I01733' => 'egr', 'Eucgr.J02255' => 'egr', 'Eucgr.J02257' => 'egr', 'Eucgr.J02258' => 'egr', 'FAN02G1601' => 'fan', 'FAN03G1586' => 'fan', 'FAN03G2986' => 'fan', 'FAN05G4837' => 'fan', 'FAN06G0146' => 'fan', 'FAN07G0858' => 'fan', 'FAN09G3179' => 'fan', 'FAN10G0669' => 'fan', 'FAN12G2358' => 'fan', 'FAN14G4198' => 'fan', 'FAN14G5112' => 'fan', 'FAN17G0342' => 'fan', 'FAN19G0342' => 'fan', 'FAN19G0962' => 'fan', 'FAN19G1101' => 'fan', 'FAN19G1872' => 'fan', 'FAN22G0356' => 'fan', 'FAN23G0744' => 'fan', 'FAN23G1914' => 'fan', 'FAN26G0032' => 'fan', 'FAN28G0625' => 'fan', 'FvH4_1g02710' => 'fve', 'FvH4_1g02720' => 'fve', 'FvH4_4g25670' => 'fve', 'FvH4_6g51700' => 'fve', 'FvH4_7g20170' => 'fve', 'Glyma.05G175000' => 'gma', 'Glyma.08G132300' => 'gma', 'Glyma.11G243000' => 'gma', 'Glyma.13G158900' => 'gma', 'Glyma.17G112400' => 'gma', 'Glyma.18G014100' => 'gma', 'Glyma.19G003100' => 'gma', 'Glyma.19G056500' => 'gma', 'Gohir.A01G158900' => 'ghi', 'Gohir.A05G312600' => 'ghi', 'Gohir.A05G354900' => 'ghi', 'Gohir.A07G037200' => 'ghi', 'Gohir.A09G030000' => 'ghi', 'Gohir.A12G145200' => 'ghi', 'Gohir.D01G151500' => 'ghi', 'Gohir.D04G058300' => 'ghi', 'Gohir.D05G314100' => 'ghi', 'Gohir.D07G041400' => 'ghi', 'Gohir.D09G029700' => 'ghi', 'Gohir.D12G149700' => 'ghi', 'Gorai.001G043800' => 'gra', 'Gorai.002G187800' => 'gra', 'Gorai.006G034700' => 'gra', 'Gorai.008G161200' => 'gra', 'Gorai.009G335700' => 'gra', 'Gorai.012G065000' => 'gra', 'GSVIVG01000535001' => 'vvi', 'GSVIVG01015572001' => 'vvi', 'GSVIVG01032386001' => 'vvi', 'HanXRQChr05g0138531' => 'han', 'HanXRQChr06g0174391' => 'han', 'HanXRQChr07g0199021' => 'han', 'HanXRQChr08g0208211' => 'han', 'HanXRQChr09g0255471' => 'han', 'HanXRQChr10g0315791' => 'han', 'HanXRQChr12g0371991' => 'han', 'HanXRQChr15g0475251' => 'han', 'HanXRQChr17g0540001' => 'han', 'HanXRQChr17g0548631' => 'han', 'HanXRQChr17g0569561' => 'han', 'Haze_12256' => 'cav', 'Haze_14756' => 'cav', 'Haze_25528' => 'cav', 'Hma1.2p1_0079F.1_g041020' => 'hma', 'Hma1.2p1_0818F.1_g223260' => 'hma', 'Hma1.2p1_1747F.1_g300530' => 'hma', 'HPP92_004607' => 'vpl', 'HPP92_004608' => 'vpl', 'HPP92_006181' => 'vpl', 'HPP92_012192' => 'vpl', 'HPP92_015680' => 'vpl', 'HPP92_020249' => 'vpl', 'HPP92_021376' => 'vpl', 'HPP92_024275' => 'vpl', 'Hund06031' => 'sun', 'Hund25391' => 'sun', 'Lalb_Chr07g0185371' => 'lal', 'Lalb_Chr07g0185381' => 'lal', 'Lalb_Chr12g0204011' => 'lal', 'Lalb_Chr13g0301671' => 'lal', 'Lalb_Chr14g0362851' => 'lal', 'Lalb_Chr24g0403581' => 'lal', 'Lj1g0000233' => 'lja', 'Lj2g0018120' => 'lja', 'Lj3C621T0' => 'lonja', 'Lj3P1059T14' => 'lonja', 'Lj3P611T9' => 'lonja', 'Lj3P614T13' => 'lonja', 'Lj3P615T5' => 'lonja', 'Lj4g0012315' => 'lja', 'Lj4g0026182' => 'lja', 'Lj6P813T16' => 'lonja', 'Lj7C427T7' => 'lonja', 'Lj7C427T8' => 'lonja', 'Lj7P600T41' => 'lonja', 'Lju41C42G17' => 'lonja', 'Lsat_1_v5_gn_0_47300' => 'lsa', 'Lsat_1_v5_gn_2_91280' => 'lsa', 'Lsat_1_v5_gn_3_30561' => 'lsa', 'Lsat_1_v5_gn_4_184321' => 'lsa', 'Lsat_1_v5_gn_4_4041' => 'lsa', 'Lsat_1_v5_gn_5_92000' => 'lsa', 'Lsat_1_v5_gn_8_152940' => 'lsa', 'Lsat_1_v5_gn_8_62401' => 'lsa', 'Manes.06G055900' => 'mes', 'Manes.12G022200' => 'mes', 'Manes.13G023300' => 'mes', 'Manes.14G115000' => 'mes', 'Manes.15G151700' => 'mes', 'Manes.17G111300' => 'mes', 'Mapoly0226s0009' => 'mpo', 'MBI02_g25363_MAGBIO' => 'mbi', 'MBI06_g00027_MAGBIO' => 'mbi', 'MBI10_g13034_MAGBIO' => 'mbi', 'MD09G1023400' => 'mdo', 'MD13G1100100' => 'mdo', 'MD15G1169200' => 'mdo', 'MD16G1101100' => 'mdo', 'MD17G1022900' => 'mdo', 'Medtr3g096150' => 'mtr', 'Medtr4g115070' => 'mtr', 'Medtr7g033325' => 'mtr', 'Medtr8g089840' => 'mtr', 'MELO3C010319.2' => 'cme', 'MELO3C011944.2' => 'cme', 'MELO3C021589.2' => 'cme', 'Migut.E00207' => 'egut', 'Migut.H00067' => 'egut', 'Migut.K00433' => 'egut', 'Migut.K00606' => 'egut', 'Migut.K01410' => 'egut', 'MSTRG.13347' => 'ama', 'MSTRG.24045' => 'ama', 'MSTRG.2428' => 'ama', 'MSTRG.26410' => 'ama', 'MSTRG.3139' => 'ama', 'MSTRG.3286' => 'ama', 'MSTRG.563' => 'ama', 'MSTRG.7941' => 'ama', 'Nitab4.5_0000028g0060' => 'nta', 'Nitab4.5_0000065g0260' => 'nta', 'Nitab4.5_0000112g0060' => 'nta', 'Nitab4.5_0000489g0120' => 'nta', 'Nitab4.5_0001776g0050' => 'nta', 'Nitab4.5_0001854g0010' => 'nta', 'Nitab4.5_0001860g0020' => 'nta', 'Nitab4.5_0004352g0010' => 'nta', 'Nitab4.5_0008716g0020' => 'nta', 'Nitab4.5_0008922g0010' => 'nta', 'Nn3g16693' => 'nnu', 'Nn4g22596' => 'nnu', 'Nn7g37639' => 'nnu', 'Oeu001701.1' => 'oeu', 'Oeu018149.1' => 'oeu', 'Oeu026220.1' => 'oeu', 'Oeu038635.1' => 'oeu', 'Oeu049176.1' => 'oeu', 'Oeu056706.1' => 'oeu', 'Oeu056937.1' => 'oeu', 'Oeu057540.1' => 'oeu', 'Os02g0594900' => 'osa', 'Os02g0595100' => 'osa', 'Os04g0477500' => 'osa', 'Os12g0611900' => 'osa', 'Peaxi162Scf00076g00020' => 'pax', 'Peaxi162Scf00128g00217' => 'pax', 'Peaxi162Scf00129g01640' => 'pax', 'Peaxi162Scf00669g00007' => 'pax', 'Peaxi162Scf00700g00421' => 'pax', 'Peaxi162Scf00801g00038' => 'pax', 'Peaxi162Scf00891g00025' => 'pax', 'PGR083G0909' => 'pgr', 'PGR119G1005' => 'pgr', 'PGR142G2236' => 'pgr', 'PGR142G3388' => 'pgr', 'PGSC0003DMG400004514' => 'stu', 'PGSC0003DMG400012635' => 'stu', 'PGSC0003DMG400015730' => 'stu', 'PGSC0003DMG400018611' => 'stu', 'PGSC0003DMG400030897' => 'stu', 'Phvul.001G254800' => 'pvu', 'Phvul.002G260100' => 'pvu', 'Phvul.003G167600' => 'pvu', 'Phvul.004G005100' => 'pvu', 'Potri.001G343600' => 'ptr', 'Potri.006G066700' => 'ptr', 'Potri.008G186000' => 'ptr', 'Potri.010G046900' => 'ptr', 'Potri.018G127900' => 'ptr', 'Pp3c20_17750' => 'ppa', 'Pp3c24_4380' => 'ppa', 'Prupe.1G245800' => 'ppe', 'Prupe.3G293400' => 'ppe', 'Prupe.7G247400' => 'ppe', 'Psat0s145g0120' => 'psa', 'Psat0s595g0040' => 'psa', 'Psat0s595g0120' => 'psa', 'Psat3g175040' => 'psa', 'Psat7g058120' => 'psa', 'PSO017G0428' => 'pso', 'PSO063G7510' => 'pso', 'PSO067G0046' => 'pso', 'PSO478G1073' => 'pso', 'PSO675G3677' => 'pso', 'PSO675G6558' => 'pso', 'PSO675G7520' => 'pso', 'PSO675G8959' => 'pso', 'QL02p074089' => 'qlo', 'QL02p089614' => 'qlo', 'QL03p057736' => 'qlo', 'RcHm_v2.0_Chr1g0364131' => 'rch', 'RcHm_v2.0_Chr2g0087801' => 'rch', 'RcHm_v2.0_Chr2g0087821' => 'rch', 'RcHm_v2.0_Chr2g0173231' => 'rch', 'RcHm_v2.0_Chr4g0433111' => 'rch', 'Rhsim03G0250300' => 'rsi', 'Rhsim08G0048400' => 'rsi', 'Rhsim10G0014800' => 'rsi', 'Rhsim12G0040100' => 'rsi', 'Rhsim12G0109700' => 'rsi', 'Sabra06G0049600' => 'sbr', 'Sabra08G0141000' => 'sbr', 'Sabra10G0021400' => 'sbr', 'Sabra16G0222900' => 'sbr', 'Sabra18G0108600' => 'sbr', 'SalBow1G0433' => 'sbo', 'SalBow1G2038' => 'sbo', 'SalBow1G5003' => 'sbo', 'SalBow7G1197' => 'sbo', 'SalBow8G3506' => 'sbo', 'Sc03g0007300' => 'sci', 'Sc11g0000950' => 'sci', 'Sc14g0008750' => 'sci', 'Sc18g0000420' => 'sci', 'Sed0006754' => 'sed', 'Sed0008741' => 'sed', 'Sed0017172' => 'sed', 'Sed0018925' => 'sed', 'Sed0023326' => 'sed', 'Sed0025909' => 'sed', 'SEGI_05333' => 'sgi', 'SEGI_10362' => 'sgi', 'SEGI_13380' => 'sgi', 'SEGI_24306' => 'sgi', 'SEGI_29077' => 'sgi', 'SEGI_29095' => 'sgi', 'SEGI_36534' => 'sgi', 'SEGI_37506' => 'sgi', 'SEGI_38321' => 'sgi', 'SGA_v2.0_scaffold307G48031' => 'sas', 'SGA_v2.0_scaffold47G17507' => 'sas', 'SGA_v2.0_scaffold63G21736' => 'sas', 'SGA_v2.0_scaffold87G27070' => 'sas', 'SHI17794' => 'shi', 'SHI28851' => 'shi', 'SMO165G0155' => 'smo', 'SMO340G0217' => 'smo', 'SMO367G1210' => 'smo', 'Solyc02g093430.3' => 'sly', 'Solyc05g013580.4' => 'sly', 'Solyc07g008030.3' => 'sly', 'Solyc12g035470.2' => 'sly', 'Sopen02g038020' => 'spe', 'Sopen05g008490' => 'spe', 'Sopen07g003910' => 'spe', 'Sopen12g015240' => 'spe', 'Sp1g11550' => 'spa', 'Sp2g16710' => 'spa', 'Sp3g00430' => 'spa', 'Sp3g26780' => 'spa', 'Sp5g22900' => 'spa', 'Sp6g29530' => 'spa', 'TAR371G0794' => 'tar', 'TAR374G0164' => 'tar', 'TAR622G0165' => 'tar', 'TAR626G0929' => 'tar', 'TAR629G2155' => 'tar', 'THA.LOC104805282' => 'tha', 'THA.LOC104805363' => 'tha', 'THA.LOC104808968' => 'tha', 'THA.LOC104821093' => 'tha', 'THA.LOC104823953' => 'tha', 'THA.LOC104825562' => 'tha', 'THA.LOC104825665' => 'tha', 'Thecc.02G261400' => 'tca', 'Thecc.04G019200' => 'tca', 'Thecc.09G130400' => 'tca', 'Thhalv10004374m.g' => 'esa', 'Thhalv10007850m.g' => 'esa', 'Thhalv10013782m.g' => 'esa', 'Thhalv10018686m.g' => 'esa', 'Thhalv10020899m.g' => 'esa', 'Thhalv10022755m.g' => 'esa', 'TPR.G23851' => 'tpr', 'TPR.G26500' => 'tpr', 'TPR.G27267' => 'tpr', 'TPR.G32001' => 'tpr', 'TPR.G6251' => 'tpr', 'TPR.G8167' => 'tpr', 'TWI12G1330' => 'twi', 'TWI18G1239' => 'twi', 'TWI34G0979' => 'twi', 'TWI36G0670' => 'twi', 'TWI36G0707' => 'twi', 'TWI56G0233' => 'twi', 'TWI75G1809' => 'twi', 'unitig_21.g20874' => 'ugi', 'unitig_26.g10343' => 'ugi', 'unitig_46.g18392' => 'ugi', 'unitig_52.g17178' => 'ugi', 'unitig_8.g2934' => 'ugi', 'vmacro01122' => 'vma', 'vmacro05875' => 'vma', 'vmacro06147' => 'vma', 'vmacro16191' => 'vma', 'vmacro18293' => 'vma', 'VMungo0251G3707' => 'vmu', 'VMungo0464G1521' => 'vmu', 'VMungo1215G0205' => 'vmu', 'VMungo1383G2484' => 'vmu', 'Zm00001eb079610' => 'zma', 'Zm00001eb135990' => 'zma', 'Zm00001eb183710' => 'zma', 'Zm00001eb246020' => 'zma' ), 'gf_id' => 'HOM05D001124', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001124' ), 'data_identifier' => 'HOM05D001124', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001124', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '548', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02520' => 'bna', 'A03p06630' => 'bna', 'A05p44460' => 'bna', 'A06p08710' => 'bna', 'A06p41090' => 'bna', 'A07p32320' => 'bna', 'A08p32520' => 'bna', 'A09p10360' => 'bna', 'A10p24080' => 'bna', 'Aa31LG11G15250' => 'aar', 'Aa31LG1G1800' => 'aar', 'Aa31LG2G5120' => 'aar', 'Aa31LG2G6070' => 'aar', 'Aa31LG5G10770' => 'aar', 'Aa31sc61G90' => 'aar', 'Actinidia01352' => 'ach', 'Actinidia05983' => 'ach', 'Actinidia08133' => 'ach', 'Actinidia15101' => 'ach', 'Actinidia26379' => 'ach', 'Actinidia35778' => 'ach', 'Actinidia36123' => 'ach', 'Actinidia37436' => 'ach', 'Actinidia38730' => 'ach', 'Ah.02g128210' => 'amhyb', 'Ah.03g132990' => 'amhyb', 'Ah.14g079410' => 'amhyb', 'AL1G24640' => 'aly', 'AL2G26680' => 'aly', 'AL3G10530' => 'aly', 'AL3G45230' => 'aly', 'AL5G15230' => 'aly', 'AL5G16960' => 'aly', 'AL6G25210' => 'aly', 'Aqoxy2G00441' => 'aox', 'Aqoxy3G01236' => 'aox', 'Aqoxy5G03746' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3RQ047' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C7GMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9C8JER' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MBL6KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YXCZ83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZANX40' => 'arhy', 'AT1G12990' => 'ath', 'AT1G67880' => 'ath', 'AT2G13290' => 'ath', 'AT3G01620' => 'ath', 'AT3G26445' => 'ath', 'AT3G27540' => 'ath', 'AT5G14480' => 'ath', 'ATR0824G026' => 'atr', 'ATR1098G019' => 'atr', 'Atru.chr11.2145' => 'acertr', 'Atru.chr2.3636' => 'acertr', 'Atru.chr2.3644' => 'acertr', 'Atru.chr6.2422' => 'acertr', 'Atru.chr7.1112' => 'acertr', 'AUR62005469' => 'cqu', 'AUR62011166' => 'cqu', 'AUR62013319' => 'cqu', 'AUR62024273' => 'cqu', 'AUR62028420' => 'cqu', 'AUR62041942' => 'cqu', 'BcaB01g04969' => 'bca', 'BcaB01g06371' => 'bca', 'BcaB02g11494' => 'bca', 'BcaB03g15382' => 'bca', 'BcaB08g36994' => 'bca', 'BcaC03g13477' => 'bca', 'BcaC03g13478' => 'bca', 'BcaC03g13480' => 'bca', 'BcaC03g13481' => 'bca', 'BcaC03g13486' => 'bca', 'BcaC04g19031' => 'bca', 'BcaC04g23085' => 'bca', 'BcaC05g25094' => 'bca', 'BcaC05g25096' => 'bca', 'BcaC05g25138' => 'bca', 'BcaC05g30416' => 'bca', 'BcaC05g30455' => 'bca', 'BcaC06g30979' => 'bca', 'BcaC06g33805' => 'bca', 'BcaC08g46021' => 'bca', 'BcaNung03154' => 'bca', 'BolC2t06623H' => 'bol', 'BolC2t06632H' => 'bol', 'BolC2t06635H' => 'bol', 'BolC2t06638H' => 'bol', 'BolC3t13266H' => 'bol', 'BolC5t29776H' => 'bol', 'BolC6t38912H' => 'bol', 'BolC7t44183H' => 'bol', 'BolC9t54123H' => 'bol', 'BolC9t59107H' => 'bol', 'BraA02t05221Z' => 'bra', 'BraA03t09996Z' => 'bra', 'BraA05t23210Z' => 'bra', 'BraA06t24068Z' => 'bra', 'BraA06t27032Z' => 'bra', 'BraA08t35176Z' => 'bra', 'BraA09t36680Z' => 'bra', 'BraA10t44471Z' => 'bra', 'C02p06760' => 'bna', 'C02p06890' => 'bna', 'C02p07010' => 'bna', 'C03p07660' => 'bna', 'C05p10300' => 'bna', 'C06p38150' => 'bna', 'C07p36650' => 'bna', 'C08p15770' => 'bna', 'C09p12300' => 'bna', 'C09p62700' => 'bna', 'C09p75040' => 'bna', 'CAN.G13.1' => 'can', 'CAN.G138.4' => 'can', 'CAN.G44.6' => 'can', 'CAN.G473.19' => 'can', 'CANSAT01G0835' => 'cansat', 'CANSAT11G0246' => 'cansat', 'CANSAT11G1766' => 'cansat', 'CANSAT64G1954' => 'cansat', 'CARHR013330' => 'chi', 'CARHR060530' => 'chi', 'CARHR075300' => 'chi', 'CARHR105120' => 'chi', 'CARHR148910' => 'chi', 'CARHR198830' => 'chi', 'Carub.0001s1275' => 'cru', 'Carub.0002s1437' => 'cru', 'Carub.0003s0044' => 'cru', 'Carub.0003s2787' => 'cru', 'Carub.0005s0597' => 'cru', 'Carub.0006s1266' => 'cru', 'Ca_06935_v3' => 'car', 'Ca_13559_v3' => 'car', 'Ca_16941_v3' => 'car', 'Ca_16960_v3' => 'car', 'Ca_17775_v3' => 'car', 'Ca_30464_v3' => 'car', 'Cc06_g08160' => 'ccan', 'Cc07_g01520' => 'ccan', 'Cc11_g15810' => 'ccan', 'CDE02G2840' => 'cde', 'CDE03G0093' => 'cde', 'CDE04G2127' => 'cde', 'CDE07G1857' => 'cde', 'CDE09G1246' => 'cde', 'Cfa003412' => 'cfa', 'Cfa007341' => 'cfa', 'Cfa009220' => 'cfa', 'Ciclev10008737m.g' => 'ccl', 'Ciclev10015565m.g' => 'ccl', 'Ciclev10031761m.g' => 'ccl', 'CiPaw.03G045300' => 'cil', 'CiPaw.03G247200' => 'cil', 'CiPaw.04G029500' => 'cil', 'CiPaw.04G174000' => 'cil', 'CiPaw.05G181200' => 'cil', 'CiPaw.06G067100' => 'cil', 'ClCG05G025800' => 'cla', 'ClCG06G011400' => 'cla', 'ClCG09G019360' => 'cla', 'COL.COLO4_04827' => 'col', 'COL.COLO4_29170' => 'col', 'COL.COLO4_35131' => 'col', 'COL.COLO4_35132' => 'col', 'Cpa.g.sc33.32' => 'cpa', 'Cpa.g.sc46.29' => 'cpa', 'Cpa.g.sc796.1' => 'cpa', 'CsaV3_1G030420' => 'csa', 'CsaV3_5G027050' => 'csa', 'CsaV3_5G031040' => 'csa', 'CsaV3_UNG023130' => 'csa', 'CSS0007726' => 'camsi', 'CSS0016433' => 'camsi', 'CSS0017656' => 'camsi', 'CSS0025364' => 'camsi', 'CSS0027582' => 'camsi', 'CSS0047288' => 'camsi', 'CSS0049950' => 'camsi', 'DCAR_003843' => 'dca', 'DCAR_007052' => 'dca', 'DCAR_020884' => 'dca', 'DCAR_021730' => 'dca', 'DCAR_024423' => 'dca', 'DCAR_026509' => 'dca', 'DCAR_031158' => 'dca', 'Dinv14728' => 'din', 'Dinv15219' => 'din', 'Dinv25728' => 'din', 'Dinv33428' => 'din', 'Dinv36489' => 'din', 'Dinv41486' => 'din', 'Duzib147G0469' => 'dzi', 'Duzib168G0060' => 'dzi', 'Duzib187G1215' => 'dzi', 'Duzib248G0692' => 'dzi', 'Duzib251G0767' => 'dzi', 'Duzib264G0446' => 'dzi', 'Duzib268G0691' => 'dzi', 'ECA232G4767' => 'eca', 'ECA233G2838' => 'eca', 'ECA234G0391' => 'eca', 'ECA234G0857' => 'eca', 'ECA236G1593' => 'eca', 'ECA238G0565' => 'eca', 'ECA246G1027' => 'eca', 'ECA246G3223' => 'eca', 'ECA246G3470' => 'eca', 'EL10Ac6g13829' => 'bvu', 'EL10Ac6g14093' => 'bvu', 'EL10Ac8g18707' => 'bvu', 'Eucgr.C01369' => 'egr', 'Eucgr.H02492' => 'egr', 'Eucgr.I01733' => 'egr', 'Eucgr.J02255' => 'egr', 'Eucgr.J02257' => 'egr', 'Eucgr.J02258' => 'egr', 'FAN02G1601' => 'fan', 'FAN03G1586' => 'fan', 'FAN03G2986' => 'fan', 'FAN05G4837' => 'fan', 'FAN06G0146' => 'fan', 'FAN07G0858' => 'fan', 'FAN09G3179' => 'fan', 'FAN10G0669' => 'fan', 'FAN12G2358' => 'fan', 'FAN14G4198' => 'fan', 'FAN14G5112' => 'fan', 'FAN17G0342' => 'fan', 'FAN19G0342' => 'fan', 'FAN19G0962' => 'fan', 'FAN19G1101' => 'fan', 'FAN19G1872' => 'fan', 'FAN22G0356' => 'fan', 'FAN23G0744' => 'fan', 'FAN23G1914' => 'fan', 'FAN26G0032' => 'fan', 'FAN28G0625' => 'fan', 'FvH4_1g02710' => 'fve', 'FvH4_1g02720' => 'fve', 'FvH4_4g25670' => 'fve', 'FvH4_6g51700' => 'fve', 'FvH4_7g20170' => 'fve', 'Glyma.05G175000' => 'gma', 'Glyma.08G132300' => 'gma', 'Glyma.11G243000' => 'gma', 'Glyma.13G158900' => 'gma', 'Glyma.17G112400' => 'gma', 'Glyma.18G014100' => 'gma', 'Glyma.19G003100' => 'gma', 'Glyma.19G056500' => 'gma', 'Gohir.A01G158900' => 'ghi', 'Gohir.A05G312600' => 'ghi', 'Gohir.A05G354900' => 'ghi', 'Gohir.A07G037200' => 'ghi', 'Gohir.A09G030000' => 'ghi', 'Gohir.A12G145200' => 'ghi', 'Gohir.D01G151500' => 'ghi', 'Gohir.D04G058300' => 'ghi', 'Gohir.D05G314100' => 'ghi', 'Gohir.D07G041400' => 'ghi', 'Gohir.D09G029700' => 'ghi', 'Gohir.D12G149700' => 'ghi', 'Gorai.001G043800' => 'gra', 'Gorai.002G187800' => 'gra', 'Gorai.006G034700' => 'gra', 'Gorai.008G161200' => 'gra', 'Gorai.009G335700' => 'gra', 'Gorai.012G065000' => 'gra', 'GSVIVG01000535001' => 'vvi', 'GSVIVG01015572001' => 'vvi', 'GSVIVG01032386001' => 'vvi', 'HanXRQChr05g0138531' => 'han', 'HanXRQChr06g0174391' => 'han', 'HanXRQChr07g0199021' => 'han', 'HanXRQChr08g0208211' => 'han', 'HanXRQChr09g0255471' => 'han', 'HanXRQChr10g0315791' => 'han', 'HanXRQChr12g0371991' => 'han', 'HanXRQChr15g0475251' => 'han', 'HanXRQChr17g0540001' => 'han', 'HanXRQChr17g0548631' => 'han', 'HanXRQChr17g0569561' => 'han', 'Haze_12256' => 'cav', 'Haze_14756' => 'cav', 'Haze_25528' => 'cav', 'Hma1.2p1_0079F.1_g041020' => 'hma', 'Hma1.2p1_0818F.1_g223260' => 'hma', 'Hma1.2p1_1747F.1_g300530' => 'hma', 'HPP92_004607' => 'vpl', 'HPP92_004608' => 'vpl', 'HPP92_006181' => 'vpl', 'HPP92_012192' => 'vpl', 'HPP92_015680' => 'vpl', 'HPP92_020249' => 'vpl', 'HPP92_021376' => 'vpl', 'HPP92_024275' => 'vpl', 'Hund06031' => 'sun', 'Hund25391' => 'sun', 'Lalb_Chr07g0185371' => 'lal', 'Lalb_Chr07g0185381' => 'lal', 'Lalb_Chr12g0204011' => 'lal', 'Lalb_Chr13g0301671' => 'lal', 'Lalb_Chr14g0362851' => 'lal', 'Lalb_Chr24g0403581' => 'lal', 'Lj1g0000233' => 'lja', 'Lj2g0018120' => 'lja', 'Lj3C621T0' => 'lonja', 'Lj3P1059T14' => 'lonja', 'Lj3P611T9' => 'lonja', 'Lj3P614T13' => 'lonja', 'Lj3P615T5' => 'lonja', 'Lj4g0012315' => 'lja', 'Lj4g0026182' => 'lja', 'Lj6P813T16' => 'lonja', 'Lj7C427T7' => 'lonja', 'Lj7C427T8' => 'lonja', 'Lj7P600T41' => 'lonja', 'Lju41C42G17' => 'lonja', 'Lsat_1_v5_gn_0_47300' => 'lsa', 'Lsat_1_v5_gn_2_91280' => 'lsa', 'Lsat_1_v5_gn_3_30561' => 'lsa', 'Lsat_1_v5_gn_4_184321' => 'lsa', 'Lsat_1_v5_gn_4_4041' => 'lsa', 'Lsat_1_v5_gn_5_92000' => 'lsa', 'Lsat_1_v5_gn_8_152940' => 'lsa', 'Lsat_1_v5_gn_8_62401' => 'lsa', 'Manes.06G055900' => 'mes', 'Manes.12G022200' => 'mes', 'Manes.13G023300' => 'mes', 'Manes.14G115000' => 'mes', 'Manes.15G151700' => 'mes', 'Manes.17G111300' => 'mes', 'Mapoly0226s0009' => 'mpo', 'MBI02_g25363_MAGBIO' => 'mbi', 'MBI06_g00027_MAGBIO' => 'mbi', 'MBI10_g13034_MAGBIO' => 'mbi', 'MD09G1023400' => 'mdo', 'MD13G1100100' => 'mdo', 'MD15G1169200' => 'mdo', 'MD16G1101100' => 'mdo', 'MD17G1022900' => 'mdo', 'Medtr3g096150' => 'mtr', 'Medtr4g115070' => 'mtr', 'Medtr7g033325' => 'mtr', 'Medtr8g089840' => 'mtr', 'MELO3C010319.2' => 'cme', 'MELO3C011944.2' => 'cme', 'MELO3C021589.2' => 'cme', 'Migut.E00207' => 'egut', 'Migut.H00067' => 'egut', 'Migut.K00433' => 'egut', 'Migut.K00606' => 'egut', 'Migut.K01410' => 'egut', 'MSTRG.13347' => 'ama', 'MSTRG.24045' => 'ama', 'MSTRG.2428' => 'ama', 'MSTRG.26410' => 'ama', 'MSTRG.3139' => 'ama', 'MSTRG.3286' => 'ama', 'MSTRG.563' => 'ama', 'MSTRG.7941' => 'ama', 'Nitab4.5_0000028g0060' => 'nta', 'Nitab4.5_0000065g0260' => 'nta', 'Nitab4.5_0000112g0060' => 'nta', 'Nitab4.5_0000489g0120' => 'nta', 'Nitab4.5_0001776g0050' => 'nta', 'Nitab4.5_0001854g0010' => 'nta', 'Nitab4.5_0001860g0020' => 'nta', 'Nitab4.5_0004352g0010' => 'nta', 'Nitab4.5_0008716g0020' => 'nta', 'Nitab4.5_0008922g0010' => 'nta', 'Nn3g16693' => 'nnu', 'Nn4g22596' => 'nnu', 'Nn7g37639' => 'nnu', 'Oeu001701.1' => 'oeu', 'Oeu018149.1' => 'oeu', 'Oeu026220.1' => 'oeu', 'Oeu038635.1' => 'oeu', 'Oeu049176.1' => 'oeu', 'Oeu056706.1' => 'oeu', 'Oeu056937.1' => 'oeu', 'Oeu057540.1' => 'oeu', 'Os02g0594900' => 'osa', 'Os02g0595100' => 'osa', 'Os04g0477500' => 'osa', 'Os12g0611900' => 'osa', 'Peaxi162Scf00076g00020' => 'pax', 'Peaxi162Scf00128g00217' => 'pax', 'Peaxi162Scf00129g01640' => 'pax', 'Peaxi162Scf00669g00007' => 'pax', 'Peaxi162Scf00700g00421' => 'pax', 'Peaxi162Scf00801g00038' => 'pax', 'Peaxi162Scf00891g00025' => 'pax', 'PGR083G0909' => 'pgr', 'PGR119G1005' => 'pgr', 'PGR142G2236' => 'pgr', 'PGR142G3388' => 'pgr', 'PGSC0003DMG400004514' => 'stu', 'PGSC0003DMG400012635' => 'stu', 'PGSC0003DMG400015730' => 'stu', 'PGSC0003DMG400018611' => 'stu', 'PGSC0003DMG400030897' => 'stu', 'Phvul.001G254800' => 'pvu', 'Phvul.002G260100' => 'pvu', 'Phvul.003G167600' => 'pvu', 'Phvul.004G005100' => 'pvu', 'Potri.001G343600' => 'ptr', 'Potri.006G066700' => 'ptr', 'Potri.008G186000' => 'ptr', 'Potri.010G046900' => 'ptr', 'Potri.018G127900' => 'ptr', 'Pp3c20_17750' => 'ppa', 'Pp3c24_4380' => 'ppa', 'Prupe.1G245800' => 'ppe', 'Prupe.3G293400' => 'ppe', 'Prupe.7G247400' => 'ppe', 'Psat0s145g0120' => 'psa', 'Psat0s595g0040' => 'psa', 'Psat0s595g0120' => 'psa', 'Psat3g175040' => 'psa', 'Psat7g058120' => 'psa', 'PSO017G0428' => 'pso', 'PSO063G7510' => 'pso', 'PSO067G0046' => 'pso', 'PSO478G1073' => 'pso', 'PSO675G3677' => 'pso', 'PSO675G6558' => 'pso', 'PSO675G7520' => 'pso', 'PSO675G8959' => 'pso', 'QL02p074089' => 'qlo', 'QL02p089614' => 'qlo', 'QL03p057736' => 'qlo', 'RcHm_v2.0_Chr1g0364131' => 'rch', 'RcHm_v2.0_Chr2g0087801' => 'rch', 'RcHm_v2.0_Chr2g0087821' => 'rch', 'RcHm_v2.0_Chr2g0173231' => 'rch', 'RcHm_v2.0_Chr4g0433111' => 'rch', 'Rhsim03G0250300' => 'rsi', 'Rhsim08G0048400' => 'rsi', 'Rhsim10G0014800' => 'rsi', 'Rhsim12G0040100' => 'rsi', 'Rhsim12G0109700' => 'rsi', 'Sabra06G0049600' => 'sbr', 'Sabra08G0141000' => 'sbr', 'Sabra10G0021400' => 'sbr', 'Sabra16G0222900' => 'sbr', 'Sabra18G0108600' => 'sbr', 'SalBow1G0433' => 'sbo', 'SalBow1G2038' => 'sbo', 'SalBow1G5003' => 'sbo', 'SalBow7G1197' => 'sbo', 'SalBow8G3506' => 'sbo', 'Sc03g0007300' => 'sci', 'Sc11g0000950' => 'sci', 'Sc14g0008750' => 'sci', 'Sc18g0000420' => 'sci', 'Sed0006754' => 'sed', 'Sed0008741' => 'sed', 'Sed0017172' => 'sed', 'Sed0018925' => 'sed', 'Sed0023326' => 'sed', 'Sed0025909' => 'sed', 'SEGI_05333' => 'sgi', 'SEGI_10362' => 'sgi', 'SEGI_13380' => 'sgi', 'SEGI_24306' => 'sgi', 'SEGI_29077' => 'sgi', 'SEGI_29095' => 'sgi', 'SEGI_36534' => 'sgi', 'SEGI_37506' => 'sgi', 'SEGI_38321' => 'sgi', 'SGA_v2.0_scaffold307G48031' => 'sas', 'SGA_v2.0_scaffold47G17507' => 'sas', 'SGA_v2.0_scaffold63G21736' => 'sas', 'SGA_v2.0_scaffold87G27070' => 'sas', 'SHI17794' => 'shi', 'SHI28851' => 'shi', 'SMO165G0155' => 'smo', 'SMO340G0217' => 'smo', 'SMO367G1210' => 'smo', 'Solyc02g093430.3' => 'sly', 'Solyc05g013580.4' => 'sly', 'Solyc07g008030.3' => 'sly', 'Solyc12g035470.2' => 'sly', 'Sopen02g038020' => 'spe', 'Sopen05g008490' => 'spe', 'Sopen07g003910' => 'spe', 'Sopen12g015240' => 'spe', 'Sp1g11550' => 'spa', 'Sp2g16710' => 'spa', 'Sp3g00430' => 'spa', 'Sp3g26780' => 'spa', 'Sp5g22900' => 'spa', 'Sp6g29530' => 'spa', 'TAR371G0794' => 'tar', 'TAR374G0164' => 'tar', 'TAR622G0165' => 'tar', 'TAR626G0929' => 'tar', 'TAR629G2155' => 'tar', 'THA.LOC104805282' => 'tha', 'THA.LOC104805363' => 'tha', 'THA.LOC104808968' => 'tha', 'THA.LOC104821093' => 'tha', 'THA.LOC104823953' => 'tha', 'THA.LOC104825562' => 'tha', 'THA.LOC104825665' => 'tha', 'Thecc.02G261400' => 'tca', 'Thecc.04G019200' => 'tca', 'Thecc.09G130400' => 'tca', 'Thhalv10004374m.g' => 'esa', 'Thhalv10007850m.g' => 'esa', 'Thhalv10013782m.g' => 'esa', 'Thhalv10018686m.g' => 'esa', 'Thhalv10020899m.g' => 'esa', 'Thhalv10022755m.g' => 'esa', 'TPR.G23851' => 'tpr', 'TPR.G26500' => 'tpr', 'TPR.G27267' => 'tpr', 'TPR.G32001' => 'tpr', 'TPR.G6251' => 'tpr', 'TPR.G8167' => 'tpr', 'TWI12G1330' => 'twi', 'TWI18G1239' => 'twi', 'TWI34G0979' => 'twi', 'TWI36G0670' => 'twi', 'TWI36G0707' => 'twi', 'TWI56G0233' => 'twi', 'TWI75G1809' => 'twi', 'unitig_21.g20874' => 'ugi', 'unitig_26.g10343' => 'ugi', 'unitig_46.g18392' => 'ugi', 'unitig_52.g17178' => 'ugi', 'unitig_8.g2934' => 'ugi', 'vmacro01122' => 'vma', 'vmacro05875' => 'vma', 'vmacro06147' => 'vma', 'vmacro16191' => 'vma', 'vmacro18293' => 'vma', 'VMungo0251G3707' => 'vmu', 'VMungo0464G1521' => 'vmu', 'VMungo1215G0205' => 'vmu', 'VMungo1383G2484' => 'vmu', 'Zm00001eb079610' => 'zma', 'Zm00001eb135990' => 'zma', 'Zm00001eb183710' => 'zma', 'Zm00001eb246020' => 'zma' ) $gf_id = 'HOM05D001124' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001124' ) $data_identifier = 'HOM05D001124' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 6, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 7, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 21, 'bol' => (int) 10, 'bra' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 6, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 9, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 21, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 8, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 10, 'lsa' => (int) 8, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 8, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 9, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb246020' $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' => 'HOM05D001124', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '548', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02520' => 'bna', 'A03p06630' => 'bna', 'A05p44460' => 'bna', 'A06p08710' => 'bna', 'A06p41090' => 'bna', 'A07p32320' => 'bna', 'A08p32520' => 'bna', 'A09p10360' => 'bna', 'A10p24080' => 'bna', 'Aa31LG11G15250' => 'aar', 'Aa31LG1G1800' => 'aar', 'Aa31LG2G5120' => 'aar', 'Aa31LG2G6070' => 'aar', 'Aa31LG5G10770' => 'aar', 'Aa31sc61G90' => 'aar', 'Actinidia01352' => 'ach', 'Actinidia05983' => 'ach', 'Actinidia08133' => 'ach', 'Actinidia15101' => 'ach', 'Actinidia26379' => 'ach', 'Actinidia35778' => 'ach', 'Actinidia36123' => 'ach', 'Actinidia37436' => 'ach', 'Actinidia38730' => 'ach', 'Ah.02g128210' => 'amhyb', 'Ah.03g132990' => 'amhyb', 'Ah.14g079410' => 'amhyb', 'AL1G24640' => 'aly', 'AL2G26680' => 'aly', 'AL3G10530' => 'aly', 'AL3G45230' => 'aly', 'AL5G15230' => 'aly', 'AL5G16960' => 'aly', 'AL6G25210' => 'aly', 'Aqoxy2G00441' => 'aox', 'Aqoxy3G01236' => 'aox', 'Aqoxy5G03746' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3RQ047' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C7GMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9C8JER' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MBL6KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YXCZ83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZANX40' => 'arhy', 'AT1G12990' => 'ath', 'AT1G67880' => 'ath', 'AT2G13290' => 'ath', 'AT3G01620' => 'ath', 'AT3G26445' => 'ath', 'AT3G27540' => 'ath', 'AT5G14480' => 'ath', 'ATR0824G026' => 'atr', 'ATR1098G019' => 'atr', 'Atru.chr11.2145' => 'acertr', 'Atru.chr2.3636' => 'acertr', 'Atru.chr2.3644' => 'acertr', 'Atru.chr6.2422' => 'acertr', 'Atru.chr7.1112' => 'acertr', 'AUR62005469' => 'cqu', 'AUR62011166' => 'cqu', 'AUR62013319' => 'cqu', 'AUR62024273' => 'cqu', 'AUR62028420' => 'cqu', 'AUR62041942' => 'cqu', 'BcaB01g04969' => 'bca', 'BcaB01g06371' => 'bca', 'BcaB02g11494' => 'bca', 'BcaB03g15382' => 'bca', 'BcaB08g36994' => 'bca', 'BcaC03g13477' => 'bca', 'BcaC03g13478' => 'bca', 'BcaC03g13480' => 'bca', 'BcaC03g13481' => 'bca', 'BcaC03g13486' => 'bca', 'BcaC04g19031' => 'bca', 'BcaC04g23085' => 'bca', 'BcaC05g25094' => 'bca', 'BcaC05g25096' => 'bca', 'BcaC05g25138' => 'bca', 'BcaC05g30416' => 'bca', 'BcaC05g30455' => 'bca', 'BcaC06g30979' => 'bca', 'BcaC06g33805' => 'bca', 'BcaC08g46021' => 'bca', 'BcaNung03154' => 'bca', 'BolC2t06623H' => 'bol', 'BolC2t06632H' => 'bol', 'BolC2t06635H' => 'bol', 'BolC2t06638H' => 'bol', 'BolC3t13266H' => 'bol', 'BolC5t29776H' => 'bol', 'BolC6t38912H' => 'bol', 'BolC7t44183H' => 'bol', 'BolC9t54123H' => 'bol', 'BolC9t59107H' => 'bol', 'BraA02t05221Z' => 'bra', 'BraA03t09996Z' => 'bra', 'BraA05t23210Z' => 'bra', 'BraA06t24068Z' => 'bra', 'BraA06t27032Z' => 'bra', 'BraA08t35176Z' => 'bra', 'BraA09t36680Z' => 'bra', 'BraA10t44471Z' => 'bra', 'C02p06760' => 'bna', 'C02p06890' => 'bna', 'C02p07010' => 'bna', 'C03p07660' => 'bna', 'C05p10300' => 'bna', 'C06p38150' => 'bna', 'C07p36650' => 'bna', 'C08p15770' => 'bna', 'C09p12300' => 'bna', 'C09p62700' => 'bna', 'C09p75040' => 'bna', 'CAN.G13.1' => 'can', 'CAN.G138.4' => 'can', 'CAN.G44.6' => 'can', 'CAN.G473.19' => 'can', 'CANSAT01G0835' => 'cansat', 'CANSAT11G0246' => 'cansat', 'CANSAT11G1766' => 'cansat', 'CANSAT64G1954' => 'cansat', 'CARHR013330' => 'chi', 'CARHR060530' => 'chi', 'CARHR075300' => 'chi', 'CARHR105120' => 'chi', 'CARHR148910' => 'chi', 'CARHR198830' => 'chi', 'Carub.0001s1275' => 'cru', 'Carub.0002s1437' => 'cru', 'Carub.0003s0044' => 'cru', 'Carub.0003s2787' => 'cru', 'Carub.0005s0597' => 'cru', 'Carub.0006s1266' => 'cru', 'Ca_06935_v3' => 'car', 'Ca_13559_v3' => 'car', 'Ca_16941_v3' => 'car', 'Ca_16960_v3' => 'car', 'Ca_17775_v3' => 'car', 'Ca_30464_v3' => 'car', 'Cc06_g08160' => 'ccan', 'Cc07_g01520' => 'ccan', 'Cc11_g15810' => 'ccan', 'CDE02G2840' => 'cde', 'CDE03G0093' => 'cde', 'CDE04G2127' => 'cde', 'CDE07G1857' => 'cde', 'CDE09G1246' => 'cde', 'Cfa003412' => 'cfa', 'Cfa007341' => 'cfa', 'Cfa009220' => 'cfa', 'Ciclev10008737m.g' => 'ccl', 'Ciclev10015565m.g' => 'ccl', 'Ciclev10031761m.g' => 'ccl', 'CiPaw.03G045300' => 'cil', 'CiPaw.03G247200' => 'cil', 'CiPaw.04G029500' => 'cil', 'CiPaw.04G174000' => 'cil', 'CiPaw.05G181200' => 'cil', 'CiPaw.06G067100' => 'cil', 'ClCG05G025800' => 'cla', 'ClCG06G011400' => 'cla', 'ClCG09G019360' => 'cla', 'COL.COLO4_04827' => 'col', 'COL.COLO4_29170' => 'col', 'COL.COLO4_35131' => 'col', 'COL.COLO4_35132' => 'col', 'Cpa.g.sc33.32' => 'cpa', 'Cpa.g.sc46.29' => 'cpa', 'Cpa.g.sc796.1' => 'cpa', 'CsaV3_1G030420' => 'csa', 'CsaV3_5G027050' => 'csa', 'CsaV3_5G031040' => 'csa', 'CsaV3_UNG023130' => 'csa', 'CSS0007726' => 'camsi', 'CSS0016433' => 'camsi', 'CSS0017656' => 'camsi', 'CSS0025364' => 'camsi', 'CSS0027582' => 'camsi', 'CSS0047288' => 'camsi', 'CSS0049950' => 'camsi', 'DCAR_003843' => 'dca', 'DCAR_007052' => 'dca', 'DCAR_020884' => 'dca', 'DCAR_021730' => 'dca', 'DCAR_024423' => 'dca', 'DCAR_026509' => 'dca', 'DCAR_031158' => 'dca', 'Dinv14728' => 'din', 'Dinv15219' => 'din', 'Dinv25728' => 'din', 'Dinv33428' => 'din', 'Dinv36489' => 'din', 'Dinv41486' => 'din', 'Duzib147G0469' => 'dzi', 'Duzib168G0060' => 'dzi', 'Duzib187G1215' => 'dzi', 'Duzib248G0692' => 'dzi', 'Duzib251G0767' => 'dzi', 'Duzib264G0446' => 'dzi', 'Duzib268G0691' => 'dzi', 'ECA232G4767' => 'eca', 'ECA233G2838' => 'eca', 'ECA234G0391' => 'eca', 'ECA234G0857' => 'eca', 'ECA236G1593' => 'eca', 'ECA238G0565' => 'eca', 'ECA246G1027' => 'eca', 'ECA246G3223' => 'eca', 'ECA246G3470' => 'eca', 'EL10Ac6g13829' => 'bvu', 'EL10Ac6g14093' => 'bvu', 'EL10Ac8g18707' => 'bvu', 'Eucgr.C01369' => 'egr', 'Eucgr.H02492' => 'egr', 'Eucgr.I01733' => 'egr', 'Eucgr.J02255' => 'egr', 'Eucgr.J02257' => 'egr', 'Eucgr.J02258' => 'egr', 'FAN02G1601' => 'fan', 'FAN03G1586' => 'fan', 'FAN03G2986' => 'fan', 'FAN05G4837' => 'fan', 'FAN06G0146' => 'fan', 'FAN07G0858' => 'fan', 'FAN09G3179' => 'fan', 'FAN10G0669' => 'fan', 'FAN12G2358' => 'fan', 'FAN14G4198' => 'fan', 'FAN14G5112' => 'fan', 'FAN17G0342' => 'fan', 'FAN19G0342' => 'fan', 'FAN19G0962' => 'fan', 'FAN19G1101' => 'fan', 'FAN19G1872' => 'fan', 'FAN22G0356' => 'fan', 'FAN23G0744' => 'fan', 'FAN23G1914' => 'fan', 'FAN26G0032' => 'fan', 'FAN28G0625' => 'fan', 'FvH4_1g02710' => 'fve', 'FvH4_1g02720' => 'fve', 'FvH4_4g25670' => 'fve', 'FvH4_6g51700' => 'fve', 'FvH4_7g20170' => 'fve', 'Glyma.05G175000' => 'gma', 'Glyma.08G132300' => 'gma', 'Glyma.11G243000' => 'gma', 'Glyma.13G158900' => 'gma', 'Glyma.17G112400' => 'gma', 'Glyma.18G014100' => 'gma', 'Glyma.19G003100' => 'gma', 'Glyma.19G056500' => 'gma', 'Gohir.A01G158900' => 'ghi', 'Gohir.A05G312600' => 'ghi', 'Gohir.A05G354900' => 'ghi', 'Gohir.A07G037200' => 'ghi', 'Gohir.A09G030000' => 'ghi', 'Gohir.A12G145200' => 'ghi', 'Gohir.D01G151500' => 'ghi', 'Gohir.D04G058300' => 'ghi', 'Gohir.D05G314100' => 'ghi', 'Gohir.D07G041400' => 'ghi', 'Gohir.D09G029700' => 'ghi', 'Gohir.D12G149700' => 'ghi', 'Gorai.001G043800' => 'gra', 'Gorai.002G187800' => 'gra', 'Gorai.006G034700' => 'gra', 'Gorai.008G161200' => 'gra', 'Gorai.009G335700' => 'gra', 'Gorai.012G065000' => 'gra', 'GSVIVG01000535001' => 'vvi', 'GSVIVG01015572001' => 'vvi', 'GSVIVG01032386001' => 'vvi', 'HanXRQChr05g0138531' => 'han', 'HanXRQChr06g0174391' => 'han', 'HanXRQChr07g0199021' => 'han', 'HanXRQChr08g0208211' => 'han', 'HanXRQChr09g0255471' => 'han', 'HanXRQChr10g0315791' => 'han', 'HanXRQChr12g0371991' => 'han', 'HanXRQChr15g0475251' => 'han', 'HanXRQChr17g0540001' => 'han', 'HanXRQChr17g0548631' => 'han', 'HanXRQChr17g0569561' => 'han', 'Haze_12256' => 'cav', 'Haze_14756' => 'cav', 'Haze_25528' => 'cav', 'Hma1.2p1_0079F.1_g041020' => 'hma', 'Hma1.2p1_0818F.1_g223260' => 'hma', 'Hma1.2p1_1747F.1_g300530' => 'hma', 'HPP92_004607' => 'vpl', 'HPP92_004608' => 'vpl', 'HPP92_006181' => 'vpl', 'HPP92_012192' => 'vpl', 'HPP92_015680' => 'vpl', 'HPP92_020249' => 'vpl', 'HPP92_021376' => 'vpl', 'HPP92_024275' => 'vpl', 'Hund06031' => 'sun', 'Hund25391' => 'sun', 'Lalb_Chr07g0185371' => 'lal', 'Lalb_Chr07g0185381' => 'lal', 'Lalb_Chr12g0204011' => 'lal', 'Lalb_Chr13g0301671' => 'lal', 'Lalb_Chr14g0362851' => 'lal', 'Lalb_Chr24g0403581' => 'lal', 'Lj1g0000233' => 'lja', 'Lj2g0018120' => 'lja', 'Lj3C621T0' => 'lonja', 'Lj3P1059T14' => 'lonja', 'Lj3P611T9' => 'lonja', 'Lj3P614T13' => 'lonja', 'Lj3P615T5' => 'lonja', 'Lj4g0012315' => 'lja', 'Lj4g0026182' => 'lja', 'Lj6P813T16' => 'lonja', 'Lj7C427T7' => 'lonja', 'Lj7C427T8' => 'lonja', 'Lj7P600T41' => 'lonja', 'Lju41C42G17' => 'lonja', 'Lsat_1_v5_gn_0_47300' => 'lsa', 'Lsat_1_v5_gn_2_91280' => 'lsa', 'Lsat_1_v5_gn_3_30561' => 'lsa', 'Lsat_1_v5_gn_4_184321' => 'lsa', 'Lsat_1_v5_gn_4_4041' => 'lsa', 'Lsat_1_v5_gn_5_92000' => 'lsa', 'Lsat_1_v5_gn_8_152940' => 'lsa', 'Lsat_1_v5_gn_8_62401' => 'lsa', 'Manes.06G055900' => 'mes', 'Manes.12G022200' => 'mes', 'Manes.13G023300' => 'mes', 'Manes.14G115000' => 'mes', 'Manes.15G151700' => 'mes', 'Manes.17G111300' => 'mes', 'Mapoly0226s0009' => 'mpo', 'MBI02_g25363_MAGBIO' => 'mbi', 'MBI06_g00027_MAGBIO' => 'mbi', 'MBI10_g13034_MAGBIO' => 'mbi', 'MD09G1023400' => 'mdo', 'MD13G1100100' => 'mdo', 'MD15G1169200' => 'mdo', 'MD16G1101100' => 'mdo', 'MD17G1022900' => 'mdo', 'Medtr3g096150' => 'mtr', 'Medtr4g115070' => 'mtr', 'Medtr7g033325' => 'mtr', 'Medtr8g089840' => 'mtr', 'MELO3C010319.2' => 'cme', 'MELO3C011944.2' => 'cme', 'MELO3C021589.2' => 'cme', 'Migut.E00207' => 'egut', 'Migut.H00067' => 'egut', 'Migut.K00433' => 'egut', 'Migut.K00606' => 'egut', 'Migut.K01410' => 'egut', 'MSTRG.13347' => 'ama', 'MSTRG.24045' => 'ama', 'MSTRG.2428' => 'ama', 'MSTRG.26410' => 'ama', 'MSTRG.3139' => 'ama', 'MSTRG.3286' => 'ama', 'MSTRG.563' => 'ama', 'MSTRG.7941' => 'ama', 'Nitab4.5_0000028g0060' => 'nta', 'Nitab4.5_0000065g0260' => 'nta', 'Nitab4.5_0000112g0060' => 'nta', 'Nitab4.5_0000489g0120' => 'nta', 'Nitab4.5_0001776g0050' => 'nta', 'Nitab4.5_0001854g0010' => 'nta', 'Nitab4.5_0001860g0020' => 'nta', 'Nitab4.5_0004352g0010' => 'nta', 'Nitab4.5_0008716g0020' => 'nta', 'Nitab4.5_0008922g0010' => 'nta', 'Nn3g16693' => 'nnu', 'Nn4g22596' => 'nnu', 'Nn7g37639' => 'nnu', 'Oeu001701.1' => 'oeu', 'Oeu018149.1' => 'oeu', 'Oeu026220.1' => 'oeu', 'Oeu038635.1' => 'oeu', 'Oeu049176.1' => 'oeu', 'Oeu056706.1' => 'oeu', 'Oeu056937.1' => 'oeu', 'Oeu057540.1' => 'oeu', 'Os02g0594900' => 'osa', 'Os02g0595100' => 'osa', 'Os04g0477500' => 'osa', 'Os12g0611900' => 'osa', 'Peaxi162Scf00076g00020' => 'pax', 'Peaxi162Scf00128g00217' => 'pax', 'Peaxi162Scf00129g01640' => 'pax', 'Peaxi162Scf00669g00007' => 'pax', 'Peaxi162Scf00700g00421' => 'pax', 'Peaxi162Scf00801g00038' => 'pax', 'Peaxi162Scf00891g00025' => 'pax', 'PGR083G0909' => 'pgr', 'PGR119G1005' => 'pgr', 'PGR142G2236' => 'pgr', 'PGR142G3388' => 'pgr', 'PGSC0003DMG400004514' => 'stu', 'PGSC0003DMG400012635' => 'stu', 'PGSC0003DMG400015730' => 'stu', 'PGSC0003DMG400018611' => 'stu', 'PGSC0003DMG400030897' => 'stu', 'Phvul.001G254800' => 'pvu', 'Phvul.002G260100' => 'pvu', 'Phvul.003G167600' => 'pvu', 'Phvul.004G005100' => 'pvu', 'Potri.001G343600' => 'ptr', 'Potri.006G066700' => 'ptr', 'Potri.008G186000' => 'ptr', 'Potri.010G046900' => 'ptr', 'Potri.018G127900' => 'ptr', 'Pp3c20_17750' => 'ppa', 'Pp3c24_4380' => 'ppa', 'Prupe.1G245800' => 'ppe', 'Prupe.3G293400' => 'ppe', 'Prupe.7G247400' => 'ppe', 'Psat0s145g0120' => 'psa', 'Psat0s595g0040' => 'psa', 'Psat0s595g0120' => 'psa', 'Psat3g175040' => 'psa', 'Psat7g058120' => 'psa', 'PSO017G0428' => 'pso', 'PSO063G7510' => 'pso', 'PSO067G0046' => 'pso', 'PSO478G1073' => 'pso', 'PSO675G3677' => 'pso', 'PSO675G6558' => 'pso', 'PSO675G7520' => 'pso', 'PSO675G8959' => 'pso', 'QL02p074089' => 'qlo', 'QL02p089614' => 'qlo', 'QL03p057736' => 'qlo', 'RcHm_v2.0_Chr1g0364131' => 'rch', 'RcHm_v2.0_Chr2g0087801' => 'rch', 'RcHm_v2.0_Chr2g0087821' => 'rch', 'RcHm_v2.0_Chr2g0173231' => 'rch', 'RcHm_v2.0_Chr4g0433111' => 'rch', 'Rhsim03G0250300' => 'rsi', 'Rhsim08G0048400' => 'rsi', 'Rhsim10G0014800' => 'rsi', 'Rhsim12G0040100' => 'rsi', 'Rhsim12G0109700' => 'rsi', 'Sabra06G0049600' => 'sbr', 'Sabra08G0141000' => 'sbr', 'Sabra10G0021400' => 'sbr', 'Sabra16G0222900' => 'sbr', 'Sabra18G0108600' => 'sbr', 'SalBow1G0433' => 'sbo', 'SalBow1G2038' => 'sbo', 'SalBow1G5003' => 'sbo', 'SalBow7G1197' => 'sbo', 'SalBow8G3506' => 'sbo', 'Sc03g0007300' => 'sci', 'Sc11g0000950' => 'sci', 'Sc14g0008750' => 'sci', 'Sc18g0000420' => 'sci', 'Sed0006754' => 'sed', 'Sed0008741' => 'sed', 'Sed0017172' => 'sed', 'Sed0018925' => 'sed', 'Sed0023326' => 'sed', 'Sed0025909' => 'sed', 'SEGI_05333' => 'sgi', 'SEGI_10362' => 'sgi', 'SEGI_13380' => 'sgi', 'SEGI_24306' => 'sgi', 'SEGI_29077' => 'sgi', 'SEGI_29095' => 'sgi', 'SEGI_36534' => 'sgi', 'SEGI_37506' => 'sgi', 'SEGI_38321' => 'sgi', 'SGA_v2.0_scaffold307G48031' => 'sas', 'SGA_v2.0_scaffold47G17507' => 'sas', 'SGA_v2.0_scaffold63G21736' => 'sas', 'SGA_v2.0_scaffold87G27070' => 'sas', 'SHI17794' => 'shi', 'SHI28851' => 'shi', 'SMO165G0155' => 'smo', 'SMO340G0217' => 'smo', 'SMO367G1210' => 'smo', 'Solyc02g093430.3' => 'sly', 'Solyc05g013580.4' => 'sly', 'Solyc07g008030.3' => 'sly', 'Solyc12g035470.2' => 'sly', 'Sopen02g038020' => 'spe', 'Sopen05g008490' => 'spe', 'Sopen07g003910' => 'spe', 'Sopen12g015240' => 'spe', 'Sp1g11550' => 'spa', 'Sp2g16710' => 'spa', 'Sp3g00430' => 'spa', 'Sp3g26780' => 'spa', 'Sp5g22900' => 'spa', 'Sp6g29530' => 'spa', 'TAR371G0794' => 'tar', 'TAR374G0164' => 'tar', 'TAR622G0165' => 'tar', 'TAR626G0929' => 'tar', 'TAR629G2155' => 'tar', 'THA.LOC104805282' => 'tha', 'THA.LOC104805363' => 'tha', 'THA.LOC104808968' => 'tha', 'THA.LOC104821093' => 'tha', 'THA.LOC104823953' => 'tha', 'THA.LOC104825562' => 'tha', 'THA.LOC104825665' => 'tha', 'Thecc.02G261400' => 'tca', 'Thecc.04G019200' => 'tca', 'Thecc.09G130400' => 'tca', 'Thhalv10004374m.g' => 'esa', 'Thhalv10007850m.g' => 'esa', 'Thhalv10013782m.g' => 'esa', 'Thhalv10018686m.g' => 'esa', 'Thhalv10020899m.g' => 'esa', 'Thhalv10022755m.g' => 'esa', 'TPR.G23851' => 'tpr', 'TPR.G26500' => 'tpr', 'TPR.G27267' => 'tpr', 'TPR.G32001' => 'tpr', 'TPR.G6251' => 'tpr', 'TPR.G8167' => 'tpr', 'TWI12G1330' => 'twi', 'TWI18G1239' => 'twi', 'TWI34G0979' => 'twi', 'TWI36G0670' => 'twi', 'TWI36G0707' => 'twi', 'TWI56G0233' => 'twi', 'TWI75G1809' => 'twi', 'unitig_21.g20874' => 'ugi', 'unitig_26.g10343' => 'ugi', 'unitig_46.g18392' => 'ugi', 'unitig_52.g17178' => 'ugi', 'unitig_8.g2934' => 'ugi', 'vmacro01122' => 'vma', 'vmacro05875' => 'vma', 'vmacro06147' => 'vma', 'vmacro16191' => 'vma', 'vmacro18293' => 'vma', 'VMungo0251G3707' => 'vmu', 'VMungo0464G1521' => 'vmu', 'VMungo1215G0205' => 'vmu', 'VMungo1383G2484' => 'vmu', 'Zm00001eb079610' => 'zma', 'Zm00001eb135990' => 'zma', 'Zm00001eb183710' => 'zma', 'Zm00001eb246020' => 'zma' ), 'gf_id' => 'HOM05D001124', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001124' ), 'data_identifier' => 'HOM05D001124', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001124', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '548', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02520' => 'bna', 'A03p06630' => 'bna', 'A05p44460' => 'bna', 'A06p08710' => 'bna', 'A06p41090' => 'bna', 'A07p32320' => 'bna', 'A08p32520' => 'bna', 'A09p10360' => 'bna', 'A10p24080' => 'bna', 'Aa31LG11G15250' => 'aar', 'Aa31LG1G1800' => 'aar', 'Aa31LG2G5120' => 'aar', 'Aa31LG2G6070' => 'aar', 'Aa31LG5G10770' => 'aar', 'Aa31sc61G90' => 'aar', 'Actinidia01352' => 'ach', 'Actinidia05983' => 'ach', 'Actinidia08133' => 'ach', 'Actinidia15101' => 'ach', 'Actinidia26379' => 'ach', 'Actinidia35778' => 'ach', 'Actinidia36123' => 'ach', 'Actinidia37436' => 'ach', 'Actinidia38730' => 'ach', 'Ah.02g128210' => 'amhyb', 'Ah.03g132990' => 'amhyb', 'Ah.14g079410' => 'amhyb', 'AL1G24640' => 'aly', 'AL2G26680' => 'aly', 'AL3G10530' => 'aly', 'AL3G45230' => 'aly', 'AL5G15230' => 'aly', 'AL5G16960' => 'aly', 'AL6G25210' => 'aly', 'Aqoxy2G00441' => 'aox', 'Aqoxy3G01236' => 'aox', 'Aqoxy5G03746' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3RQ047' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C7GMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9C8JER' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MBL6KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YXCZ83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZANX40' => 'arhy', 'AT1G12990' => 'ath', 'AT1G67880' => 'ath', 'AT2G13290' => 'ath', 'AT3G01620' => 'ath', 'AT3G26445' => 'ath', 'AT3G27540' => 'ath', 'AT5G14480' => 'ath', 'ATR0824G026' => 'atr', 'ATR1098G019' => 'atr', 'Atru.chr11.2145' => 'acertr', 'Atru.chr2.3636' => 'acertr', 'Atru.chr2.3644' => 'acertr', 'Atru.chr6.2422' => 'acertr', 'Atru.chr7.1112' => 'acertr', 'AUR62005469' => 'cqu', 'AUR62011166' => 'cqu', 'AUR62013319' => 'cqu', 'AUR62024273' => 'cqu', 'AUR62028420' => 'cqu', 'AUR62041942' => 'cqu', 'BcaB01g04969' => 'bca', 'BcaB01g06371' => 'bca', 'BcaB02g11494' => 'bca', 'BcaB03g15382' => 'bca', 'BcaB08g36994' => 'bca', 'BcaC03g13477' => 'bca', 'BcaC03g13478' => 'bca', 'BcaC03g13480' => 'bca', 'BcaC03g13481' => 'bca', 'BcaC03g13486' => 'bca', 'BcaC04g19031' => 'bca', 'BcaC04g23085' => 'bca', 'BcaC05g25094' => 'bca', 'BcaC05g25096' => 'bca', 'BcaC05g25138' => 'bca', 'BcaC05g30416' => 'bca', 'BcaC05g30455' => 'bca', 'BcaC06g30979' => 'bca', 'BcaC06g33805' => 'bca', 'BcaC08g46021' => 'bca', 'BcaNung03154' => 'bca', 'BolC2t06623H' => 'bol', 'BolC2t06632H' => 'bol', 'BolC2t06635H' => 'bol', 'BolC2t06638H' => 'bol', 'BolC3t13266H' => 'bol', 'BolC5t29776H' => 'bol', 'BolC6t38912H' => 'bol', 'BolC7t44183H' => 'bol', 'BolC9t54123H' => 'bol', 'BolC9t59107H' => 'bol', 'BraA02t05221Z' => 'bra', 'BraA03t09996Z' => 'bra', 'BraA05t23210Z' => 'bra', 'BraA06t24068Z' => 'bra', 'BraA06t27032Z' => 'bra', 'BraA08t35176Z' => 'bra', 'BraA09t36680Z' => 'bra', 'BraA10t44471Z' => 'bra', 'C02p06760' => 'bna', 'C02p06890' => 'bna', 'C02p07010' => 'bna', 'C03p07660' => 'bna', 'C05p10300' => 'bna', 'C06p38150' => 'bna', 'C07p36650' => 'bna', 'C08p15770' => 'bna', 'C09p12300' => 'bna', 'C09p62700' => 'bna', 'C09p75040' => 'bna', 'CAN.G13.1' => 'can', 'CAN.G138.4' => 'can', 'CAN.G44.6' => 'can', 'CAN.G473.19' => 'can', 'CANSAT01G0835' => 'cansat', 'CANSAT11G0246' => 'cansat', 'CANSAT11G1766' => 'cansat', 'CANSAT64G1954' => 'cansat', 'CARHR013330' => 'chi', 'CARHR060530' => 'chi', 'CARHR075300' => 'chi', 'CARHR105120' => 'chi', 'CARHR148910' => 'chi', 'CARHR198830' => 'chi', 'Carub.0001s1275' => 'cru', 'Carub.0002s1437' => 'cru', 'Carub.0003s0044' => 'cru', 'Carub.0003s2787' => 'cru', 'Carub.0005s0597' => 'cru', 'Carub.0006s1266' => 'cru', 'Ca_06935_v3' => 'car', 'Ca_13559_v3' => 'car', 'Ca_16941_v3' => 'car', 'Ca_16960_v3' => 'car', 'Ca_17775_v3' => 'car', 'Ca_30464_v3' => 'car', 'Cc06_g08160' => 'ccan', 'Cc07_g01520' => 'ccan', 'Cc11_g15810' => 'ccan', 'CDE02G2840' => 'cde', 'CDE03G0093' => 'cde', 'CDE04G2127' => 'cde', 'CDE07G1857' => 'cde', 'CDE09G1246' => 'cde', 'Cfa003412' => 'cfa', 'Cfa007341' => 'cfa', 'Cfa009220' => 'cfa', 'Ciclev10008737m.g' => 'ccl', 'Ciclev10015565m.g' => 'ccl', 'Ciclev10031761m.g' => 'ccl', 'CiPaw.03G045300' => 'cil', 'CiPaw.03G247200' => 'cil', 'CiPaw.04G029500' => 'cil', 'CiPaw.04G174000' => 'cil', 'CiPaw.05G181200' => 'cil', 'CiPaw.06G067100' => 'cil', 'ClCG05G025800' => 'cla', 'ClCG06G011400' => 'cla', 'ClCG09G019360' => 'cla', 'COL.COLO4_04827' => 'col', 'COL.COLO4_29170' => 'col', 'COL.COLO4_35131' => 'col', 'COL.COLO4_35132' => 'col', 'Cpa.g.sc33.32' => 'cpa', 'Cpa.g.sc46.29' => 'cpa', 'Cpa.g.sc796.1' => 'cpa', 'CsaV3_1G030420' => 'csa', 'CsaV3_5G027050' => 'csa', 'CsaV3_5G031040' => 'csa', 'CsaV3_UNG023130' => 'csa', 'CSS0007726' => 'camsi', 'CSS0016433' => 'camsi', 'CSS0017656' => 'camsi', 'CSS0025364' => 'camsi', 'CSS0027582' => 'camsi', 'CSS0047288' => 'camsi', 'CSS0049950' => 'camsi', 'DCAR_003843' => 'dca', 'DCAR_007052' => 'dca', 'DCAR_020884' => 'dca', 'DCAR_021730' => 'dca', 'DCAR_024423' => 'dca', 'DCAR_026509' => 'dca', 'DCAR_031158' => 'dca', 'Dinv14728' => 'din', 'Dinv15219' => 'din', 'Dinv25728' => 'din', 'Dinv33428' => 'din', 'Dinv36489' => 'din', 'Dinv41486' => 'din', 'Duzib147G0469' => 'dzi', 'Duzib168G0060' => 'dzi', 'Duzib187G1215' => 'dzi', 'Duzib248G0692' => 'dzi', 'Duzib251G0767' => 'dzi', 'Duzib264G0446' => 'dzi', 'Duzib268G0691' => 'dzi', 'ECA232G4767' => 'eca', 'ECA233G2838' => 'eca', 'ECA234G0391' => 'eca', 'ECA234G0857' => 'eca', 'ECA236G1593' => 'eca', 'ECA238G0565' => 'eca', 'ECA246G1027' => 'eca', 'ECA246G3223' => 'eca', 'ECA246G3470' => 'eca', 'EL10Ac6g13829' => 'bvu', 'EL10Ac6g14093' => 'bvu', 'EL10Ac8g18707' => 'bvu', 'Eucgr.C01369' => 'egr', 'Eucgr.H02492' => 'egr', 'Eucgr.I01733' => 'egr', 'Eucgr.J02255' => 'egr', 'Eucgr.J02257' => 'egr', 'Eucgr.J02258' => 'egr', 'FAN02G1601' => 'fan', 'FAN03G1586' => 'fan', 'FAN03G2986' => 'fan', 'FAN05G4837' => 'fan', 'FAN06G0146' => 'fan', 'FAN07G0858' => 'fan', 'FAN09G3179' => 'fan', 'FAN10G0669' => 'fan', 'FAN12G2358' => 'fan', 'FAN14G4198' => 'fan', 'FAN14G5112' => 'fan', 'FAN17G0342' => 'fan', 'FAN19G0342' => 'fan', 'FAN19G0962' => 'fan', 'FAN19G1101' => 'fan', 'FAN19G1872' => 'fan', 'FAN22G0356' => 'fan', 'FAN23G0744' => 'fan', 'FAN23G1914' => 'fan', 'FAN26G0032' => 'fan', 'FAN28G0625' => 'fan', 'FvH4_1g02710' => 'fve', 'FvH4_1g02720' => 'fve', 'FvH4_4g25670' => 'fve', 'FvH4_6g51700' => 'fve', 'FvH4_7g20170' => 'fve', 'Glyma.05G175000' => 'gma', 'Glyma.08G132300' => 'gma', 'Glyma.11G243000' => 'gma', 'Glyma.13G158900' => 'gma', 'Glyma.17G112400' => 'gma', 'Glyma.18G014100' => 'gma', 'Glyma.19G003100' => 'gma', 'Glyma.19G056500' => 'gma', 'Gohir.A01G158900' => 'ghi', 'Gohir.A05G312600' => 'ghi', 'Gohir.A05G354900' => 'ghi', 'Gohir.A07G037200' => 'ghi', 'Gohir.A09G030000' => 'ghi', 'Gohir.A12G145200' => 'ghi', 'Gohir.D01G151500' => 'ghi', 'Gohir.D04G058300' => 'ghi', 'Gohir.D05G314100' => 'ghi', 'Gohir.D07G041400' => 'ghi', 'Gohir.D09G029700' => 'ghi', 'Gohir.D12G149700' => 'ghi', 'Gorai.001G043800' => 'gra', 'Gorai.002G187800' => 'gra', 'Gorai.006G034700' => 'gra', 'Gorai.008G161200' => 'gra', 'Gorai.009G335700' => 'gra', 'Gorai.012G065000' => 'gra', 'GSVIVG01000535001' => 'vvi', 'GSVIVG01015572001' => 'vvi', 'GSVIVG01032386001' => 'vvi', 'HanXRQChr05g0138531' => 'han', 'HanXRQChr06g0174391' => 'han', 'HanXRQChr07g0199021' => 'han', 'HanXRQChr08g0208211' => 'han', 'HanXRQChr09g0255471' => 'han', 'HanXRQChr10g0315791' => 'han', 'HanXRQChr12g0371991' => 'han', 'HanXRQChr15g0475251' => 'han', 'HanXRQChr17g0540001' => 'han', 'HanXRQChr17g0548631' => 'han', 'HanXRQChr17g0569561' => 'han', 'Haze_12256' => 'cav', 'Haze_14756' => 'cav', 'Haze_25528' => 'cav', 'Hma1.2p1_0079F.1_g041020' => 'hma', 'Hma1.2p1_0818F.1_g223260' => 'hma', 'Hma1.2p1_1747F.1_g300530' => 'hma', 'HPP92_004607' => 'vpl', 'HPP92_004608' => 'vpl', 'HPP92_006181' => 'vpl', 'HPP92_012192' => 'vpl', 'HPP92_015680' => 'vpl', 'HPP92_020249' => 'vpl', 'HPP92_021376' => 'vpl', 'HPP92_024275' => 'vpl', 'Hund06031' => 'sun', 'Hund25391' => 'sun', 'Lalb_Chr07g0185371' => 'lal', 'Lalb_Chr07g0185381' => 'lal', 'Lalb_Chr12g0204011' => 'lal', 'Lalb_Chr13g0301671' => 'lal', 'Lalb_Chr14g0362851' => 'lal', 'Lalb_Chr24g0403581' => 'lal', 'Lj1g0000233' => 'lja', 'Lj2g0018120' => 'lja', 'Lj3C621T0' => 'lonja', 'Lj3P1059T14' => 'lonja', 'Lj3P611T9' => 'lonja', 'Lj3P614T13' => 'lonja', 'Lj3P615T5' => 'lonja', 'Lj4g0012315' => 'lja', 'Lj4g0026182' => 'lja', 'Lj6P813T16' => 'lonja', 'Lj7C427T7' => 'lonja', 'Lj7C427T8' => 'lonja', 'Lj7P600T41' => 'lonja', 'Lju41C42G17' => 'lonja', 'Lsat_1_v5_gn_0_47300' => 'lsa', 'Lsat_1_v5_gn_2_91280' => 'lsa', 'Lsat_1_v5_gn_3_30561' => 'lsa', 'Lsat_1_v5_gn_4_184321' => 'lsa', 'Lsat_1_v5_gn_4_4041' => 'lsa', 'Lsat_1_v5_gn_5_92000' => 'lsa', 'Lsat_1_v5_gn_8_152940' => 'lsa', 'Lsat_1_v5_gn_8_62401' => 'lsa', 'Manes.06G055900' => 'mes', 'Manes.12G022200' => 'mes', 'Manes.13G023300' => 'mes', 'Manes.14G115000' => 'mes', 'Manes.15G151700' => 'mes', 'Manes.17G111300' => 'mes', 'Mapoly0226s0009' => 'mpo', 'MBI02_g25363_MAGBIO' => 'mbi', 'MBI06_g00027_MAGBIO' => 'mbi', 'MBI10_g13034_MAGBIO' => 'mbi', 'MD09G1023400' => 'mdo', 'MD13G1100100' => 'mdo', 'MD15G1169200' => 'mdo', 'MD16G1101100' => 'mdo', 'MD17G1022900' => 'mdo', 'Medtr3g096150' => 'mtr', 'Medtr4g115070' => 'mtr', 'Medtr7g033325' => 'mtr', 'Medtr8g089840' => 'mtr', 'MELO3C010319.2' => 'cme', 'MELO3C011944.2' => 'cme', 'MELO3C021589.2' => 'cme', 'Migut.E00207' => 'egut', 'Migut.H00067' => 'egut', 'Migut.K00433' => 'egut', 'Migut.K00606' => 'egut', 'Migut.K01410' => 'egut', 'MSTRG.13347' => 'ama', 'MSTRG.24045' => 'ama', 'MSTRG.2428' => 'ama', 'MSTRG.26410' => 'ama', 'MSTRG.3139' => 'ama', 'MSTRG.3286' => 'ama', 'MSTRG.563' => 'ama', 'MSTRG.7941' => 'ama', 'Nitab4.5_0000028g0060' => 'nta', 'Nitab4.5_0000065g0260' => 'nta', 'Nitab4.5_0000112g0060' => 'nta', 'Nitab4.5_0000489g0120' => 'nta', 'Nitab4.5_0001776g0050' => 'nta', 'Nitab4.5_0001854g0010' => 'nta', 'Nitab4.5_0001860g0020' => 'nta', 'Nitab4.5_0004352g0010' => 'nta', 'Nitab4.5_0008716g0020' => 'nta', 'Nitab4.5_0008922g0010' => 'nta', 'Nn3g16693' => 'nnu', 'Nn4g22596' => 'nnu', 'Nn7g37639' => 'nnu', 'Oeu001701.1' => 'oeu', 'Oeu018149.1' => 'oeu', 'Oeu026220.1' => 'oeu', 'Oeu038635.1' => 'oeu', 'Oeu049176.1' => 'oeu', 'Oeu056706.1' => 'oeu', 'Oeu056937.1' => 'oeu', 'Oeu057540.1' => 'oeu', 'Os02g0594900' => 'osa', 'Os02g0595100' => 'osa', 'Os04g0477500' => 'osa', 'Os12g0611900' => 'osa', 'Peaxi162Scf00076g00020' => 'pax', 'Peaxi162Scf00128g00217' => 'pax', 'Peaxi162Scf00129g01640' => 'pax', 'Peaxi162Scf00669g00007' => 'pax', 'Peaxi162Scf00700g00421' => 'pax', 'Peaxi162Scf00801g00038' => 'pax', 'Peaxi162Scf00891g00025' => 'pax', 'PGR083G0909' => 'pgr', 'PGR119G1005' => 'pgr', 'PGR142G2236' => 'pgr', 'PGR142G3388' => 'pgr', 'PGSC0003DMG400004514' => 'stu', 'PGSC0003DMG400012635' => 'stu', 'PGSC0003DMG400015730' => 'stu', 'PGSC0003DMG400018611' => 'stu', 'PGSC0003DMG400030897' => 'stu', 'Phvul.001G254800' => 'pvu', 'Phvul.002G260100' => 'pvu', 'Phvul.003G167600' => 'pvu', 'Phvul.004G005100' => 'pvu', 'Potri.001G343600' => 'ptr', 'Potri.006G066700' => 'ptr', 'Potri.008G186000' => 'ptr', 'Potri.010G046900' => 'ptr', 'Potri.018G127900' => 'ptr', 'Pp3c20_17750' => 'ppa', 'Pp3c24_4380' => 'ppa', 'Prupe.1G245800' => 'ppe', 'Prupe.3G293400' => 'ppe', 'Prupe.7G247400' => 'ppe', 'Psat0s145g0120' => 'psa', 'Psat0s595g0040' => 'psa', 'Psat0s595g0120' => 'psa', 'Psat3g175040' => 'psa', 'Psat7g058120' => 'psa', 'PSO017G0428' => 'pso', 'PSO063G7510' => 'pso', 'PSO067G0046' => 'pso', 'PSO478G1073' => 'pso', 'PSO675G3677' => 'pso', 'PSO675G6558' => 'pso', 'PSO675G7520' => 'pso', 'PSO675G8959' => 'pso', 'QL02p074089' => 'qlo', 'QL02p089614' => 'qlo', 'QL03p057736' => 'qlo', 'RcHm_v2.0_Chr1g0364131' => 'rch', 'RcHm_v2.0_Chr2g0087801' => 'rch', 'RcHm_v2.0_Chr2g0087821' => 'rch', 'RcHm_v2.0_Chr2g0173231' => 'rch', 'RcHm_v2.0_Chr4g0433111' => 'rch', 'Rhsim03G0250300' => 'rsi', 'Rhsim08G0048400' => 'rsi', 'Rhsim10G0014800' => 'rsi', 'Rhsim12G0040100' => 'rsi', 'Rhsim12G0109700' => 'rsi', 'Sabra06G0049600' => 'sbr', 'Sabra08G0141000' => 'sbr', 'Sabra10G0021400' => 'sbr', 'Sabra16G0222900' => 'sbr', 'Sabra18G0108600' => 'sbr', 'SalBow1G0433' => 'sbo', 'SalBow1G2038' => 'sbo', 'SalBow1G5003' => 'sbo', 'SalBow7G1197' => 'sbo', 'SalBow8G3506' => 'sbo', 'Sc03g0007300' => 'sci', 'Sc11g0000950' => 'sci', 'Sc14g0008750' => 'sci', 'Sc18g0000420' => 'sci', 'Sed0006754' => 'sed', 'Sed0008741' => 'sed', 'Sed0017172' => 'sed', 'Sed0018925' => 'sed', 'Sed0023326' => 'sed', 'Sed0025909' => 'sed', 'SEGI_05333' => 'sgi', 'SEGI_10362' => 'sgi', 'SEGI_13380' => 'sgi', 'SEGI_24306' => 'sgi', 'SEGI_29077' => 'sgi', 'SEGI_29095' => 'sgi', 'SEGI_36534' => 'sgi', 'SEGI_37506' => 'sgi', 'SEGI_38321' => 'sgi', 'SGA_v2.0_scaffold307G48031' => 'sas', 'SGA_v2.0_scaffold47G17507' => 'sas', 'SGA_v2.0_scaffold63G21736' => 'sas', 'SGA_v2.0_scaffold87G27070' => 'sas', 'SHI17794' => 'shi', 'SHI28851' => 'shi', 'SMO165G0155' => 'smo', 'SMO340G0217' => 'smo', 'SMO367G1210' => 'smo', 'Solyc02g093430.3' => 'sly', 'Solyc05g013580.4' => 'sly', 'Solyc07g008030.3' => 'sly', 'Solyc12g035470.2' => 'sly', 'Sopen02g038020' => 'spe', 'Sopen05g008490' => 'spe', 'Sopen07g003910' => 'spe', 'Sopen12g015240' => 'spe', 'Sp1g11550' => 'spa', 'Sp2g16710' => 'spa', 'Sp3g00430' => 'spa', 'Sp3g26780' => 'spa', 'Sp5g22900' => 'spa', 'Sp6g29530' => 'spa', 'TAR371G0794' => 'tar', 'TAR374G0164' => 'tar', 'TAR622G0165' => 'tar', 'TAR626G0929' => 'tar', 'TAR629G2155' => 'tar', 'THA.LOC104805282' => 'tha', 'THA.LOC104805363' => 'tha', 'THA.LOC104808968' => 'tha', 'THA.LOC104821093' => 'tha', 'THA.LOC104823953' => 'tha', 'THA.LOC104825562' => 'tha', 'THA.LOC104825665' => 'tha', 'Thecc.02G261400' => 'tca', 'Thecc.04G019200' => 'tca', 'Thecc.09G130400' => 'tca', 'Thhalv10004374m.g' => 'esa', 'Thhalv10007850m.g' => 'esa', 'Thhalv10013782m.g' => 'esa', 'Thhalv10018686m.g' => 'esa', 'Thhalv10020899m.g' => 'esa', 'Thhalv10022755m.g' => 'esa', 'TPR.G23851' => 'tpr', 'TPR.G26500' => 'tpr', 'TPR.G27267' => 'tpr', 'TPR.G32001' => 'tpr', 'TPR.G6251' => 'tpr', 'TPR.G8167' => 'tpr', 'TWI12G1330' => 'twi', 'TWI18G1239' => 'twi', 'TWI34G0979' => 'twi', 'TWI36G0670' => 'twi', 'TWI36G0707' => 'twi', 'TWI56G0233' => 'twi', 'TWI75G1809' => 'twi', 'unitig_21.g20874' => 'ugi', 'unitig_26.g10343' => 'ugi', 'unitig_46.g18392' => 'ugi', 'unitig_52.g17178' => 'ugi', 'unitig_8.g2934' => 'ugi', 'vmacro01122' => 'vma', 'vmacro05875' => 'vma', 'vmacro06147' => 'vma', 'vmacro16191' => 'vma', 'vmacro18293' => 'vma', 'VMungo0251G3707' => 'vmu', 'VMungo0464G1521' => 'vmu', 'VMungo1215G0205' => 'vmu', 'VMungo1383G2484' => 'vmu', 'Zm00001eb079610' => 'zma', 'Zm00001eb135990' => 'zma', 'Zm00001eb183710' => 'zma', 'Zm00001eb246020' => 'zma' ) $gf_id = 'HOM05D001124' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001124' ) $data_identifier = 'HOM05D001124' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 6, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 7, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 21, 'bol' => (int) 10, 'bra' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 6, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 9, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 21, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 8, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 10, 'lsa' => (int) 8, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 8, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 9, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb246020' $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' => 'HOM05D001124', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '548', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02520' => 'bna', 'A03p06630' => 'bna', 'A05p44460' => 'bna', 'A06p08710' => 'bna', 'A06p41090' => 'bna', 'A07p32320' => 'bna', 'A08p32520' => 'bna', 'A09p10360' => 'bna', 'A10p24080' => 'bna', 'Aa31LG11G15250' => 'aar', 'Aa31LG1G1800' => 'aar', 'Aa31LG2G5120' => 'aar', 'Aa31LG2G6070' => 'aar', 'Aa31LG5G10770' => 'aar', 'Aa31sc61G90' => 'aar', 'Actinidia01352' => 'ach', 'Actinidia05983' => 'ach', 'Actinidia08133' => 'ach', 'Actinidia15101' => 'ach', 'Actinidia26379' => 'ach', 'Actinidia35778' => 'ach', 'Actinidia36123' => 'ach', 'Actinidia37436' => 'ach', 'Actinidia38730' => 'ach', 'Ah.02g128210' => 'amhyb', 'Ah.03g132990' => 'amhyb', 'Ah.14g079410' => 'amhyb', 'AL1G24640' => 'aly', 'AL2G26680' => 'aly', 'AL3G10530' => 'aly', 'AL3G45230' => 'aly', 'AL5G15230' => 'aly', 'AL5G16960' => 'aly', 'AL6G25210' => 'aly', 'Aqoxy2G00441' => 'aox', 'Aqoxy3G01236' => 'aox', 'Aqoxy5G03746' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3RQ047' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C7GMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9C8JER' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MBL6KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YXCZ83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZANX40' => 'arhy', 'AT1G12990' => 'ath', 'AT1G67880' => 'ath', 'AT2G13290' => 'ath', 'AT3G01620' => 'ath', 'AT3G26445' => 'ath', 'AT3G27540' => 'ath', 'AT5G14480' => 'ath', 'ATR0824G026' => 'atr', 'ATR1098G019' => 'atr', 'Atru.chr11.2145' => 'acertr', 'Atru.chr2.3636' => 'acertr', 'Atru.chr2.3644' => 'acertr', 'Atru.chr6.2422' => 'acertr', 'Atru.chr7.1112' => 'acertr', 'AUR62005469' => 'cqu', 'AUR62011166' => 'cqu', 'AUR62013319' => 'cqu', 'AUR62024273' => 'cqu', 'AUR62028420' => 'cqu', 'AUR62041942' => 'cqu', 'BcaB01g04969' => 'bca', 'BcaB01g06371' => 'bca', 'BcaB02g11494' => 'bca', 'BcaB03g15382' => 'bca', 'BcaB08g36994' => 'bca', 'BcaC03g13477' => 'bca', 'BcaC03g13478' => 'bca', 'BcaC03g13480' => 'bca', 'BcaC03g13481' => 'bca', 'BcaC03g13486' => 'bca', 'BcaC04g19031' => 'bca', 'BcaC04g23085' => 'bca', 'BcaC05g25094' => 'bca', 'BcaC05g25096' => 'bca', 'BcaC05g25138' => 'bca', 'BcaC05g30416' => 'bca', 'BcaC05g30455' => 'bca', 'BcaC06g30979' => 'bca', 'BcaC06g33805' => 'bca', 'BcaC08g46021' => 'bca', 'BcaNung03154' => 'bca', 'BolC2t06623H' => 'bol', 'BolC2t06632H' => 'bol', 'BolC2t06635H' => 'bol', 'BolC2t06638H' => 'bol', 'BolC3t13266H' => 'bol', 'BolC5t29776H' => 'bol', 'BolC6t38912H' => 'bol', 'BolC7t44183H' => 'bol', 'BolC9t54123H' => 'bol', 'BolC9t59107H' => 'bol', 'BraA02t05221Z' => 'bra', 'BraA03t09996Z' => 'bra', 'BraA05t23210Z' => 'bra', 'BraA06t24068Z' => 'bra', 'BraA06t27032Z' => 'bra', 'BraA08t35176Z' => 'bra', 'BraA09t36680Z' => 'bra', 'BraA10t44471Z' => 'bra', 'C02p06760' => 'bna', 'C02p06890' => 'bna', 'C02p07010' => 'bna', 'C03p07660' => 'bna', 'C05p10300' => 'bna', 'C06p38150' => 'bna', 'C07p36650' => 'bna', 'C08p15770' => 'bna', 'C09p12300' => 'bna', 'C09p62700' => 'bna', 'C09p75040' => 'bna', 'CAN.G13.1' => 'can', 'CAN.G138.4' => 'can', 'CAN.G44.6' => 'can', 'CAN.G473.19' => 'can', 'CANSAT01G0835' => 'cansat', 'CANSAT11G0246' => 'cansat', 'CANSAT11G1766' => 'cansat', 'CANSAT64G1954' => 'cansat', 'CARHR013330' => 'chi', 'CARHR060530' => 'chi', 'CARHR075300' => 'chi', 'CARHR105120' => 'chi', 'CARHR148910' => 'chi', 'CARHR198830' => 'chi', 'Carub.0001s1275' => 'cru', 'Carub.0002s1437' => 'cru', 'Carub.0003s0044' => 'cru', 'Carub.0003s2787' => 'cru', 'Carub.0005s0597' => 'cru', 'Carub.0006s1266' => 'cru', 'Ca_06935_v3' => 'car', 'Ca_13559_v3' => 'car', 'Ca_16941_v3' => 'car', 'Ca_16960_v3' => 'car', 'Ca_17775_v3' => 'car', 'Ca_30464_v3' => 'car', 'Cc06_g08160' => 'ccan', 'Cc07_g01520' => 'ccan', 'Cc11_g15810' => 'ccan', 'CDE02G2840' => 'cde', 'CDE03G0093' => 'cde', 'CDE04G2127' => 'cde', 'CDE07G1857' => 'cde', 'CDE09G1246' => 'cde', 'Cfa003412' => 'cfa', 'Cfa007341' => 'cfa', 'Cfa009220' => 'cfa', 'Ciclev10008737m.g' => 'ccl', 'Ciclev10015565m.g' => 'ccl', 'Ciclev10031761m.g' => 'ccl', 'CiPaw.03G045300' => 'cil', 'CiPaw.03G247200' => 'cil', 'CiPaw.04G029500' => 'cil', 'CiPaw.04G174000' => 'cil', 'CiPaw.05G181200' => 'cil', 'CiPaw.06G067100' => 'cil', 'ClCG05G025800' => 'cla', 'ClCG06G011400' => 'cla', 'ClCG09G019360' => 'cla', 'COL.COLO4_04827' => 'col', 'COL.COLO4_29170' => 'col', 'COL.COLO4_35131' => 'col', 'COL.COLO4_35132' => 'col', 'Cpa.g.sc33.32' => 'cpa', 'Cpa.g.sc46.29' => 'cpa', 'Cpa.g.sc796.1' => 'cpa', 'CsaV3_1G030420' => 'csa', 'CsaV3_5G027050' => 'csa', 'CsaV3_5G031040' => 'csa', 'CsaV3_UNG023130' => 'csa', 'CSS0007726' => 'camsi', 'CSS0016433' => 'camsi', 'CSS0017656' => 'camsi', 'CSS0025364' => 'camsi', 'CSS0027582' => 'camsi', 'CSS0047288' => 'camsi', 'CSS0049950' => 'camsi', 'DCAR_003843' => 'dca', 'DCAR_007052' => 'dca', 'DCAR_020884' => 'dca', 'DCAR_021730' => 'dca', 'DCAR_024423' => 'dca', 'DCAR_026509' => 'dca', 'DCAR_031158' => 'dca', 'Dinv14728' => 'din', 'Dinv15219' => 'din', 'Dinv25728' => 'din', 'Dinv33428' => 'din', 'Dinv36489' => 'din', 'Dinv41486' => 'din', 'Duzib147G0469' => 'dzi', 'Duzib168G0060' => 'dzi', 'Duzib187G1215' => 'dzi', 'Duzib248G0692' => 'dzi', 'Duzib251G0767' => 'dzi', 'Duzib264G0446' => 'dzi', 'Duzib268G0691' => 'dzi', 'ECA232G4767' => 'eca', 'ECA233G2838' => 'eca', 'ECA234G0391' => 'eca', 'ECA234G0857' => 'eca', 'ECA236G1593' => 'eca', 'ECA238G0565' => 'eca', 'ECA246G1027' => 'eca', 'ECA246G3223' => 'eca', 'ECA246G3470' => 'eca', 'EL10Ac6g13829' => 'bvu', 'EL10Ac6g14093' => 'bvu', 'EL10Ac8g18707' => 'bvu', 'Eucgr.C01369' => 'egr', 'Eucgr.H02492' => 'egr', 'Eucgr.I01733' => 'egr', 'Eucgr.J02255' => 'egr', 'Eucgr.J02257' => 'egr', 'Eucgr.J02258' => 'egr', 'FAN02G1601' => 'fan', 'FAN03G1586' => 'fan', 'FAN03G2986' => 'fan', 'FAN05G4837' => 'fan', 'FAN06G0146' => 'fan', 'FAN07G0858' => 'fan', 'FAN09G3179' => 'fan', 'FAN10G0669' => 'fan', 'FAN12G2358' => 'fan', 'FAN14G4198' => 'fan', 'FAN14G5112' => 'fan', 'FAN17G0342' => 'fan', 'FAN19G0342' => 'fan', 'FAN19G0962' => 'fan', 'FAN19G1101' => 'fan', 'FAN19G1872' => 'fan', 'FAN22G0356' => 'fan', 'FAN23G0744' => 'fan', 'FAN23G1914' => 'fan', 'FAN26G0032' => 'fan', 'FAN28G0625' => 'fan', 'FvH4_1g02710' => 'fve', 'FvH4_1g02720' => 'fve', 'FvH4_4g25670' => 'fve', 'FvH4_6g51700' => 'fve', 'FvH4_7g20170' => 'fve', 'Glyma.05G175000' => 'gma', 'Glyma.08G132300' => 'gma', 'Glyma.11G243000' => 'gma', 'Glyma.13G158900' => 'gma', 'Glyma.17G112400' => 'gma', 'Glyma.18G014100' => 'gma', 'Glyma.19G003100' => 'gma', 'Glyma.19G056500' => 'gma', 'Gohir.A01G158900' => 'ghi', 'Gohir.A05G312600' => 'ghi', 'Gohir.A05G354900' => 'ghi', 'Gohir.A07G037200' => 'ghi', 'Gohir.A09G030000' => 'ghi', 'Gohir.A12G145200' => 'ghi', 'Gohir.D01G151500' => 'ghi', 'Gohir.D04G058300' => 'ghi', 'Gohir.D05G314100' => 'ghi', 'Gohir.D07G041400' => 'ghi', 'Gohir.D09G029700' => 'ghi', 'Gohir.D12G149700' => 'ghi', 'Gorai.001G043800' => 'gra', 'Gorai.002G187800' => 'gra', 'Gorai.006G034700' => 'gra', 'Gorai.008G161200' => 'gra', 'Gorai.009G335700' => 'gra', 'Gorai.012G065000' => 'gra', 'GSVIVG01000535001' => 'vvi', 'GSVIVG01015572001' => 'vvi', 'GSVIVG01032386001' => 'vvi', 'HanXRQChr05g0138531' => 'han', 'HanXRQChr06g0174391' => 'han', 'HanXRQChr07g0199021' => 'han', 'HanXRQChr08g0208211' => 'han', 'HanXRQChr09g0255471' => 'han', 'HanXRQChr10g0315791' => 'han', 'HanXRQChr12g0371991' => 'han', 'HanXRQChr15g0475251' => 'han', 'HanXRQChr17g0540001' => 'han', 'HanXRQChr17g0548631' => 'han', 'HanXRQChr17g0569561' => 'han', 'Haze_12256' => 'cav', 'Haze_14756' => 'cav', 'Haze_25528' => 'cav', 'Hma1.2p1_0079F.1_g041020' => 'hma', 'Hma1.2p1_0818F.1_g223260' => 'hma', 'Hma1.2p1_1747F.1_g300530' => 'hma', 'HPP92_004607' => 'vpl', 'HPP92_004608' => 'vpl', 'HPP92_006181' => 'vpl', 'HPP92_012192' => 'vpl', 'HPP92_015680' => 'vpl', 'HPP92_020249' => 'vpl', 'HPP92_021376' => 'vpl', 'HPP92_024275' => 'vpl', 'Hund06031' => 'sun', 'Hund25391' => 'sun', 'Lalb_Chr07g0185371' => 'lal', 'Lalb_Chr07g0185381' => 'lal', 'Lalb_Chr12g0204011' => 'lal', 'Lalb_Chr13g0301671' => 'lal', 'Lalb_Chr14g0362851' => 'lal', 'Lalb_Chr24g0403581' => 'lal', 'Lj1g0000233' => 'lja', 'Lj2g0018120' => 'lja', 'Lj3C621T0' => 'lonja', 'Lj3P1059T14' => 'lonja', 'Lj3P611T9' => 'lonja', 'Lj3P614T13' => 'lonja', 'Lj3P615T5' => 'lonja', 'Lj4g0012315' => 'lja', 'Lj4g0026182' => 'lja', 'Lj6P813T16' => 'lonja', 'Lj7C427T7' => 'lonja', 'Lj7C427T8' => 'lonja', 'Lj7P600T41' => 'lonja', 'Lju41C42G17' => 'lonja', 'Lsat_1_v5_gn_0_47300' => 'lsa', 'Lsat_1_v5_gn_2_91280' => 'lsa', 'Lsat_1_v5_gn_3_30561' => 'lsa', 'Lsat_1_v5_gn_4_184321' => 'lsa', 'Lsat_1_v5_gn_4_4041' => 'lsa', 'Lsat_1_v5_gn_5_92000' => 'lsa', 'Lsat_1_v5_gn_8_152940' => 'lsa', 'Lsat_1_v5_gn_8_62401' => 'lsa', 'Manes.06G055900' => 'mes', 'Manes.12G022200' => 'mes', 'Manes.13G023300' => 'mes', 'Manes.14G115000' => 'mes', 'Manes.15G151700' => 'mes', 'Manes.17G111300' => 'mes', 'Mapoly0226s0009' => 'mpo', 'MBI02_g25363_MAGBIO' => 'mbi', 'MBI06_g00027_MAGBIO' => 'mbi', 'MBI10_g13034_MAGBIO' => 'mbi', 'MD09G1023400' => 'mdo', 'MD13G1100100' => 'mdo', 'MD15G1169200' => 'mdo', 'MD16G1101100' => 'mdo', 'MD17G1022900' => 'mdo', 'Medtr3g096150' => 'mtr', 'Medtr4g115070' => 'mtr', 'Medtr7g033325' => 'mtr', 'Medtr8g089840' => 'mtr', 'MELO3C010319.2' => 'cme', 'MELO3C011944.2' => 'cme', 'MELO3C021589.2' => 'cme', 'Migut.E00207' => 'egut', 'Migut.H00067' => 'egut', 'Migut.K00433' => 'egut', 'Migut.K00606' => 'egut', 'Migut.K01410' => 'egut', 'MSTRG.13347' => 'ama', 'MSTRG.24045' => 'ama', 'MSTRG.2428' => 'ama', 'MSTRG.26410' => 'ama', 'MSTRG.3139' => 'ama', 'MSTRG.3286' => 'ama', 'MSTRG.563' => 'ama', 'MSTRG.7941' => 'ama', 'Nitab4.5_0000028g0060' => 'nta', 'Nitab4.5_0000065g0260' => 'nta', 'Nitab4.5_0000112g0060' => 'nta', 'Nitab4.5_0000489g0120' => 'nta', 'Nitab4.5_0001776g0050' => 'nta', 'Nitab4.5_0001854g0010' => 'nta', 'Nitab4.5_0001860g0020' => 'nta', 'Nitab4.5_0004352g0010' => 'nta', 'Nitab4.5_0008716g0020' => 'nta', 'Nitab4.5_0008922g0010' => 'nta', 'Nn3g16693' => 'nnu', 'Nn4g22596' => 'nnu', 'Nn7g37639' => 'nnu', 'Oeu001701.1' => 'oeu', 'Oeu018149.1' => 'oeu', 'Oeu026220.1' => 'oeu', 'Oeu038635.1' => 'oeu', 'Oeu049176.1' => 'oeu', 'Oeu056706.1' => 'oeu', 'Oeu056937.1' => 'oeu', 'Oeu057540.1' => 'oeu', 'Os02g0594900' => 'osa', 'Os02g0595100' => 'osa', 'Os04g0477500' => 'osa', 'Os12g0611900' => 'osa', 'Peaxi162Scf00076g00020' => 'pax', 'Peaxi162Scf00128g00217' => 'pax', 'Peaxi162Scf00129g01640' => 'pax', 'Peaxi162Scf00669g00007' => 'pax', 'Peaxi162Scf00700g00421' => 'pax', 'Peaxi162Scf00801g00038' => 'pax', 'Peaxi162Scf00891g00025' => 'pax', 'PGR083G0909' => 'pgr', 'PGR119G1005' => 'pgr', 'PGR142G2236' => 'pgr', 'PGR142G3388' => 'pgr', 'PGSC0003DMG400004514' => 'stu', 'PGSC0003DMG400012635' => 'stu', 'PGSC0003DMG400015730' => 'stu', 'PGSC0003DMG400018611' => 'stu', 'PGSC0003DMG400030897' => 'stu', 'Phvul.001G254800' => 'pvu', 'Phvul.002G260100' => 'pvu', 'Phvul.003G167600' => 'pvu', 'Phvul.004G005100' => 'pvu', 'Potri.001G343600' => 'ptr', 'Potri.006G066700' => 'ptr', 'Potri.008G186000' => 'ptr', 'Potri.010G046900' => 'ptr', 'Potri.018G127900' => 'ptr', 'Pp3c20_17750' => 'ppa', 'Pp3c24_4380' => 'ppa', 'Prupe.1G245800' => 'ppe', 'Prupe.3G293400' => 'ppe', 'Prupe.7G247400' => 'ppe', 'Psat0s145g0120' => 'psa', 'Psat0s595g0040' => 'psa', 'Psat0s595g0120' => 'psa', 'Psat3g175040' => 'psa', 'Psat7g058120' => 'psa', 'PSO017G0428' => 'pso', 'PSO063G7510' => 'pso', 'PSO067G0046' => 'pso', 'PSO478G1073' => 'pso', 'PSO675G3677' => 'pso', 'PSO675G6558' => 'pso', 'PSO675G7520' => 'pso', 'PSO675G8959' => 'pso', 'QL02p074089' => 'qlo', 'QL02p089614' => 'qlo', 'QL03p057736' => 'qlo', 'RcHm_v2.0_Chr1g0364131' => 'rch', 'RcHm_v2.0_Chr2g0087801' => 'rch', 'RcHm_v2.0_Chr2g0087821' => 'rch', 'RcHm_v2.0_Chr2g0173231' => 'rch', 'RcHm_v2.0_Chr4g0433111' => 'rch', 'Rhsim03G0250300' => 'rsi', 'Rhsim08G0048400' => 'rsi', 'Rhsim10G0014800' => 'rsi', 'Rhsim12G0040100' => 'rsi', 'Rhsim12G0109700' => 'rsi', 'Sabra06G0049600' => 'sbr', 'Sabra08G0141000' => 'sbr', 'Sabra10G0021400' => 'sbr', 'Sabra16G0222900' => 'sbr', 'Sabra18G0108600' => 'sbr', 'SalBow1G0433' => 'sbo', 'SalBow1G2038' => 'sbo', 'SalBow1G5003' => 'sbo', 'SalBow7G1197' => 'sbo', 'SalBow8G3506' => 'sbo', 'Sc03g0007300' => 'sci', 'Sc11g0000950' => 'sci', 'Sc14g0008750' => 'sci', 'Sc18g0000420' => 'sci', 'Sed0006754' => 'sed', 'Sed0008741' => 'sed', 'Sed0017172' => 'sed', 'Sed0018925' => 'sed', 'Sed0023326' => 'sed', 'Sed0025909' => 'sed', 'SEGI_05333' => 'sgi', 'SEGI_10362' => 'sgi', 'SEGI_13380' => 'sgi', 'SEGI_24306' => 'sgi', 'SEGI_29077' => 'sgi', 'SEGI_29095' => 'sgi', 'SEGI_36534' => 'sgi', 'SEGI_37506' => 'sgi', 'SEGI_38321' => 'sgi', 'SGA_v2.0_scaffold307G48031' => 'sas', 'SGA_v2.0_scaffold47G17507' => 'sas', 'SGA_v2.0_scaffold63G21736' => 'sas', 'SGA_v2.0_scaffold87G27070' => 'sas', 'SHI17794' => 'shi', 'SHI28851' => 'shi', 'SMO165G0155' => 'smo', 'SMO340G0217' => 'smo', 'SMO367G1210' => 'smo', 'Solyc02g093430.3' => 'sly', 'Solyc05g013580.4' => 'sly', 'Solyc07g008030.3' => 'sly', 'Solyc12g035470.2' => 'sly', 'Sopen02g038020' => 'spe', 'Sopen05g008490' => 'spe', 'Sopen07g003910' => 'spe', 'Sopen12g015240' => 'spe', 'Sp1g11550' => 'spa', 'Sp2g16710' => 'spa', 'Sp3g00430' => 'spa', 'Sp3g26780' => 'spa', 'Sp5g22900' => 'spa', 'Sp6g29530' => 'spa', 'TAR371G0794' => 'tar', 'TAR374G0164' => 'tar', 'TAR622G0165' => 'tar', 'TAR626G0929' => 'tar', 'TAR629G2155' => 'tar', 'THA.LOC104805282' => 'tha', 'THA.LOC104805363' => 'tha', 'THA.LOC104808968' => 'tha', 'THA.LOC104821093' => 'tha', 'THA.LOC104823953' => 'tha', 'THA.LOC104825562' => 'tha', 'THA.LOC104825665' => 'tha', 'Thecc.02G261400' => 'tca', 'Thecc.04G019200' => 'tca', 'Thecc.09G130400' => 'tca', 'Thhalv10004374m.g' => 'esa', 'Thhalv10007850m.g' => 'esa', 'Thhalv10013782m.g' => 'esa', 'Thhalv10018686m.g' => 'esa', 'Thhalv10020899m.g' => 'esa', 'Thhalv10022755m.g' => 'esa', 'TPR.G23851' => 'tpr', 'TPR.G26500' => 'tpr', 'TPR.G27267' => 'tpr', 'TPR.G32001' => 'tpr', 'TPR.G6251' => 'tpr', 'TPR.G8167' => 'tpr', 'TWI12G1330' => 'twi', 'TWI18G1239' => 'twi', 'TWI34G0979' => 'twi', 'TWI36G0670' => 'twi', 'TWI36G0707' => 'twi', 'TWI56G0233' => 'twi', 'TWI75G1809' => 'twi', 'unitig_21.g20874' => 'ugi', 'unitig_26.g10343' => 'ugi', 'unitig_46.g18392' => 'ugi', 'unitig_52.g17178' => 'ugi', 'unitig_8.g2934' => 'ugi', 'vmacro01122' => 'vma', 'vmacro05875' => 'vma', 'vmacro06147' => 'vma', 'vmacro16191' => 'vma', 'vmacro18293' => 'vma', 'VMungo0251G3707' => 'vmu', 'VMungo0464G1521' => 'vmu', 'VMungo1215G0205' => 'vmu', 'VMungo1383G2484' => 'vmu', 'Zm00001eb079610' => 'zma', 'Zm00001eb135990' => 'zma', 'Zm00001eb183710' => 'zma', 'Zm00001eb246020' => 'zma' ), 'gf_id' => 'HOM05D001124', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001124' ), 'data_identifier' => 'HOM05D001124', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001124', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '548', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02520' => 'bna', 'A03p06630' => 'bna', 'A05p44460' => 'bna', 'A06p08710' => 'bna', 'A06p41090' => 'bna', 'A07p32320' => 'bna', 'A08p32520' => 'bna', 'A09p10360' => 'bna', 'A10p24080' => 'bna', 'Aa31LG11G15250' => 'aar', 'Aa31LG1G1800' => 'aar', 'Aa31LG2G5120' => 'aar', 'Aa31LG2G6070' => 'aar', 'Aa31LG5G10770' => 'aar', 'Aa31sc61G90' => 'aar', 'Actinidia01352' => 'ach', 'Actinidia05983' => 'ach', 'Actinidia08133' => 'ach', 'Actinidia15101' => 'ach', 'Actinidia26379' => 'ach', 'Actinidia35778' => 'ach', 'Actinidia36123' => 'ach', 'Actinidia37436' => 'ach', 'Actinidia38730' => 'ach', 'Ah.02g128210' => 'amhyb', 'Ah.03g132990' => 'amhyb', 'Ah.14g079410' => 'amhyb', 'AL1G24640' => 'aly', 'AL2G26680' => 'aly', 'AL3G10530' => 'aly', 'AL3G45230' => 'aly', 'AL5G15230' => 'aly', 'AL5G16960' => 'aly', 'AL6G25210' => 'aly', 'Aqoxy2G00441' => 'aox', 'Aqoxy3G01236' => 'aox', 'Aqoxy5G03746' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3RQ047' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C7GMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9C8JER' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MBL6KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YXCZ83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZANX40' => 'arhy', 'AT1G12990' => 'ath', 'AT1G67880' => 'ath', 'AT2G13290' => 'ath', 'AT3G01620' => 'ath', 'AT3G26445' => 'ath', 'AT3G27540' => 'ath', 'AT5G14480' => 'ath', 'ATR0824G026' => 'atr', 'ATR1098G019' => 'atr', 'Atru.chr11.2145' => 'acertr', 'Atru.chr2.3636' => 'acertr', 'Atru.chr2.3644' => 'acertr', 'Atru.chr6.2422' => 'acertr', 'Atru.chr7.1112' => 'acertr', 'AUR62005469' => 'cqu', 'AUR62011166' => 'cqu', 'AUR62013319' => 'cqu', 'AUR62024273' => 'cqu', 'AUR62028420' => 'cqu', 'AUR62041942' => 'cqu', 'BcaB01g04969' => 'bca', 'BcaB01g06371' => 'bca', 'BcaB02g11494' => 'bca', 'BcaB03g15382' => 'bca', 'BcaB08g36994' => 'bca', 'BcaC03g13477' => 'bca', 'BcaC03g13478' => 'bca', 'BcaC03g13480' => 'bca', 'BcaC03g13481' => 'bca', 'BcaC03g13486' => 'bca', 'BcaC04g19031' => 'bca', 'BcaC04g23085' => 'bca', 'BcaC05g25094' => 'bca', 'BcaC05g25096' => 'bca', 'BcaC05g25138' => 'bca', 'BcaC05g30416' => 'bca', 'BcaC05g30455' => 'bca', 'BcaC06g30979' => 'bca', 'BcaC06g33805' => 'bca', 'BcaC08g46021' => 'bca', 'BcaNung03154' => 'bca', 'BolC2t06623H' => 'bol', 'BolC2t06632H' => 'bol', 'BolC2t06635H' => 'bol', 'BolC2t06638H' => 'bol', 'BolC3t13266H' => 'bol', 'BolC5t29776H' => 'bol', 'BolC6t38912H' => 'bol', 'BolC7t44183H' => 'bol', 'BolC9t54123H' => 'bol', 'BolC9t59107H' => 'bol', 'BraA02t05221Z' => 'bra', 'BraA03t09996Z' => 'bra', 'BraA05t23210Z' => 'bra', 'BraA06t24068Z' => 'bra', 'BraA06t27032Z' => 'bra', 'BraA08t35176Z' => 'bra', 'BraA09t36680Z' => 'bra', 'BraA10t44471Z' => 'bra', 'C02p06760' => 'bna', 'C02p06890' => 'bna', 'C02p07010' => 'bna', 'C03p07660' => 'bna', 'C05p10300' => 'bna', 'C06p38150' => 'bna', 'C07p36650' => 'bna', 'C08p15770' => 'bna', 'C09p12300' => 'bna', 'C09p62700' => 'bna', 'C09p75040' => 'bna', 'CAN.G13.1' => 'can', 'CAN.G138.4' => 'can', 'CAN.G44.6' => 'can', 'CAN.G473.19' => 'can', 'CANSAT01G0835' => 'cansat', 'CANSAT11G0246' => 'cansat', 'CANSAT11G1766' => 'cansat', 'CANSAT64G1954' => 'cansat', 'CARHR013330' => 'chi', 'CARHR060530' => 'chi', 'CARHR075300' => 'chi', 'CARHR105120' => 'chi', 'CARHR148910' => 'chi', 'CARHR198830' => 'chi', 'Carub.0001s1275' => 'cru', 'Carub.0002s1437' => 'cru', 'Carub.0003s0044' => 'cru', 'Carub.0003s2787' => 'cru', 'Carub.0005s0597' => 'cru', 'Carub.0006s1266' => 'cru', 'Ca_06935_v3' => 'car', 'Ca_13559_v3' => 'car', 'Ca_16941_v3' => 'car', 'Ca_16960_v3' => 'car', 'Ca_17775_v3' => 'car', 'Ca_30464_v3' => 'car', 'Cc06_g08160' => 'ccan', 'Cc07_g01520' => 'ccan', 'Cc11_g15810' => 'ccan', 'CDE02G2840' => 'cde', 'CDE03G0093' => 'cde', 'CDE04G2127' => 'cde', 'CDE07G1857' => 'cde', 'CDE09G1246' => 'cde', 'Cfa003412' => 'cfa', 'Cfa007341' => 'cfa', 'Cfa009220' => 'cfa', 'Ciclev10008737m.g' => 'ccl', 'Ciclev10015565m.g' => 'ccl', 'Ciclev10031761m.g' => 'ccl', 'CiPaw.03G045300' => 'cil', 'CiPaw.03G247200' => 'cil', 'CiPaw.04G029500' => 'cil', 'CiPaw.04G174000' => 'cil', 'CiPaw.05G181200' => 'cil', 'CiPaw.06G067100' => 'cil', 'ClCG05G025800' => 'cla', 'ClCG06G011400' => 'cla', 'ClCG09G019360' => 'cla', 'COL.COLO4_04827' => 'col', 'COL.COLO4_29170' => 'col', 'COL.COLO4_35131' => 'col', 'COL.COLO4_35132' => 'col', 'Cpa.g.sc33.32' => 'cpa', 'Cpa.g.sc46.29' => 'cpa', 'Cpa.g.sc796.1' => 'cpa', 'CsaV3_1G030420' => 'csa', 'CsaV3_5G027050' => 'csa', 'CsaV3_5G031040' => 'csa', 'CsaV3_UNG023130' => 'csa', 'CSS0007726' => 'camsi', 'CSS0016433' => 'camsi', 'CSS0017656' => 'camsi', 'CSS0025364' => 'camsi', 'CSS0027582' => 'camsi', 'CSS0047288' => 'camsi', 'CSS0049950' => 'camsi', 'DCAR_003843' => 'dca', 'DCAR_007052' => 'dca', 'DCAR_020884' => 'dca', 'DCAR_021730' => 'dca', 'DCAR_024423' => 'dca', 'DCAR_026509' => 'dca', 'DCAR_031158' => 'dca', 'Dinv14728' => 'din', 'Dinv15219' => 'din', 'Dinv25728' => 'din', 'Dinv33428' => 'din', 'Dinv36489' => 'din', 'Dinv41486' => 'din', 'Duzib147G0469' => 'dzi', 'Duzib168G0060' => 'dzi', 'Duzib187G1215' => 'dzi', 'Duzib248G0692' => 'dzi', 'Duzib251G0767' => 'dzi', 'Duzib264G0446' => 'dzi', 'Duzib268G0691' => 'dzi', 'ECA232G4767' => 'eca', 'ECA233G2838' => 'eca', 'ECA234G0391' => 'eca', 'ECA234G0857' => 'eca', 'ECA236G1593' => 'eca', 'ECA238G0565' => 'eca', 'ECA246G1027' => 'eca', 'ECA246G3223' => 'eca', 'ECA246G3470' => 'eca', 'EL10Ac6g13829' => 'bvu', 'EL10Ac6g14093' => 'bvu', 'EL10Ac8g18707' => 'bvu', 'Eucgr.C01369' => 'egr', 'Eucgr.H02492' => 'egr', 'Eucgr.I01733' => 'egr', 'Eucgr.J02255' => 'egr', 'Eucgr.J02257' => 'egr', 'Eucgr.J02258' => 'egr', 'FAN02G1601' => 'fan', 'FAN03G1586' => 'fan', 'FAN03G2986' => 'fan', 'FAN05G4837' => 'fan', 'FAN06G0146' => 'fan', 'FAN07G0858' => 'fan', 'FAN09G3179' => 'fan', 'FAN10G0669' => 'fan', 'FAN12G2358' => 'fan', 'FAN14G4198' => 'fan', 'FAN14G5112' => 'fan', 'FAN17G0342' => 'fan', 'FAN19G0342' => 'fan', 'FAN19G0962' => 'fan', 'FAN19G1101' => 'fan', 'FAN19G1872' => 'fan', 'FAN22G0356' => 'fan', 'FAN23G0744' => 'fan', 'FAN23G1914' => 'fan', 'FAN26G0032' => 'fan', 'FAN28G0625' => 'fan', 'FvH4_1g02710' => 'fve', 'FvH4_1g02720' => 'fve', 'FvH4_4g25670' => 'fve', 'FvH4_6g51700' => 'fve', 'FvH4_7g20170' => 'fve', 'Glyma.05G175000' => 'gma', 'Glyma.08G132300' => 'gma', 'Glyma.11G243000' => 'gma', 'Glyma.13G158900' => 'gma', 'Glyma.17G112400' => 'gma', 'Glyma.18G014100' => 'gma', 'Glyma.19G003100' => 'gma', 'Glyma.19G056500' => 'gma', 'Gohir.A01G158900' => 'ghi', 'Gohir.A05G312600' => 'ghi', 'Gohir.A05G354900' => 'ghi', 'Gohir.A07G037200' => 'ghi', 'Gohir.A09G030000' => 'ghi', 'Gohir.A12G145200' => 'ghi', 'Gohir.D01G151500' => 'ghi', 'Gohir.D04G058300' => 'ghi', 'Gohir.D05G314100' => 'ghi', 'Gohir.D07G041400' => 'ghi', 'Gohir.D09G029700' => 'ghi', 'Gohir.D12G149700' => 'ghi', 'Gorai.001G043800' => 'gra', 'Gorai.002G187800' => 'gra', 'Gorai.006G034700' => 'gra', 'Gorai.008G161200' => 'gra', 'Gorai.009G335700' => 'gra', 'Gorai.012G065000' => 'gra', 'GSVIVG01000535001' => 'vvi', 'GSVIVG01015572001' => 'vvi', 'GSVIVG01032386001' => 'vvi', 'HanXRQChr05g0138531' => 'han', 'HanXRQChr06g0174391' => 'han', 'HanXRQChr07g0199021' => 'han', 'HanXRQChr08g0208211' => 'han', 'HanXRQChr09g0255471' => 'han', 'HanXRQChr10g0315791' => 'han', 'HanXRQChr12g0371991' => 'han', 'HanXRQChr15g0475251' => 'han', 'HanXRQChr17g0540001' => 'han', 'HanXRQChr17g0548631' => 'han', 'HanXRQChr17g0569561' => 'han', 'Haze_12256' => 'cav', 'Haze_14756' => 'cav', 'Haze_25528' => 'cav', 'Hma1.2p1_0079F.1_g041020' => 'hma', 'Hma1.2p1_0818F.1_g223260' => 'hma', 'Hma1.2p1_1747F.1_g300530' => 'hma', 'HPP92_004607' => 'vpl', 'HPP92_004608' => 'vpl', 'HPP92_006181' => 'vpl', 'HPP92_012192' => 'vpl', 'HPP92_015680' => 'vpl', 'HPP92_020249' => 'vpl', 'HPP92_021376' => 'vpl', 'HPP92_024275' => 'vpl', 'Hund06031' => 'sun', 'Hund25391' => 'sun', 'Lalb_Chr07g0185371' => 'lal', 'Lalb_Chr07g0185381' => 'lal', 'Lalb_Chr12g0204011' => 'lal', 'Lalb_Chr13g0301671' => 'lal', 'Lalb_Chr14g0362851' => 'lal', 'Lalb_Chr24g0403581' => 'lal', 'Lj1g0000233' => 'lja', 'Lj2g0018120' => 'lja', 'Lj3C621T0' => 'lonja', 'Lj3P1059T14' => 'lonja', 'Lj3P611T9' => 'lonja', 'Lj3P614T13' => 'lonja', 'Lj3P615T5' => 'lonja', 'Lj4g0012315' => 'lja', 'Lj4g0026182' => 'lja', 'Lj6P813T16' => 'lonja', 'Lj7C427T7' => 'lonja', 'Lj7C427T8' => 'lonja', 'Lj7P600T41' => 'lonja', 'Lju41C42G17' => 'lonja', 'Lsat_1_v5_gn_0_47300' => 'lsa', 'Lsat_1_v5_gn_2_91280' => 'lsa', 'Lsat_1_v5_gn_3_30561' => 'lsa', 'Lsat_1_v5_gn_4_184321' => 'lsa', 'Lsat_1_v5_gn_4_4041' => 'lsa', 'Lsat_1_v5_gn_5_92000' => 'lsa', 'Lsat_1_v5_gn_8_152940' => 'lsa', 'Lsat_1_v5_gn_8_62401' => 'lsa', 'Manes.06G055900' => 'mes', 'Manes.12G022200' => 'mes', 'Manes.13G023300' => 'mes', 'Manes.14G115000' => 'mes', 'Manes.15G151700' => 'mes', 'Manes.17G111300' => 'mes', 'Mapoly0226s0009' => 'mpo', 'MBI02_g25363_MAGBIO' => 'mbi', 'MBI06_g00027_MAGBIO' => 'mbi', 'MBI10_g13034_MAGBIO' => 'mbi', 'MD09G1023400' => 'mdo', 'MD13G1100100' => 'mdo', 'MD15G1169200' => 'mdo', 'MD16G1101100' => 'mdo', 'MD17G1022900' => 'mdo', 'Medtr3g096150' => 'mtr', 'Medtr4g115070' => 'mtr', 'Medtr7g033325' => 'mtr', 'Medtr8g089840' => 'mtr', 'MELO3C010319.2' => 'cme', 'MELO3C011944.2' => 'cme', 'MELO3C021589.2' => 'cme', 'Migut.E00207' => 'egut', 'Migut.H00067' => 'egut', 'Migut.K00433' => 'egut', 'Migut.K00606' => 'egut', 'Migut.K01410' => 'egut', 'MSTRG.13347' => 'ama', 'MSTRG.24045' => 'ama', 'MSTRG.2428' => 'ama', 'MSTRG.26410' => 'ama', 'MSTRG.3139' => 'ama', 'MSTRG.3286' => 'ama', 'MSTRG.563' => 'ama', 'MSTRG.7941' => 'ama', 'Nitab4.5_0000028g0060' => 'nta', 'Nitab4.5_0000065g0260' => 'nta', 'Nitab4.5_0000112g0060' => 'nta', 'Nitab4.5_0000489g0120' => 'nta', 'Nitab4.5_0001776g0050' => 'nta', 'Nitab4.5_0001854g0010' => 'nta', 'Nitab4.5_0001860g0020' => 'nta', 'Nitab4.5_0004352g0010' => 'nta', 'Nitab4.5_0008716g0020' => 'nta', 'Nitab4.5_0008922g0010' => 'nta', 'Nn3g16693' => 'nnu', 'Nn4g22596' => 'nnu', 'Nn7g37639' => 'nnu', 'Oeu001701.1' => 'oeu', 'Oeu018149.1' => 'oeu', 'Oeu026220.1' => 'oeu', 'Oeu038635.1' => 'oeu', 'Oeu049176.1' => 'oeu', 'Oeu056706.1' => 'oeu', 'Oeu056937.1' => 'oeu', 'Oeu057540.1' => 'oeu', 'Os02g0594900' => 'osa', 'Os02g0595100' => 'osa', 'Os04g0477500' => 'osa', 'Os12g0611900' => 'osa', 'Peaxi162Scf00076g00020' => 'pax', 'Peaxi162Scf00128g00217' => 'pax', 'Peaxi162Scf00129g01640' => 'pax', 'Peaxi162Scf00669g00007' => 'pax', 'Peaxi162Scf00700g00421' => 'pax', 'Peaxi162Scf00801g00038' => 'pax', 'Peaxi162Scf00891g00025' => 'pax', 'PGR083G0909' => 'pgr', 'PGR119G1005' => 'pgr', 'PGR142G2236' => 'pgr', 'PGR142G3388' => 'pgr', 'PGSC0003DMG400004514' => 'stu', 'PGSC0003DMG400012635' => 'stu', 'PGSC0003DMG400015730' => 'stu', 'PGSC0003DMG400018611' => 'stu', 'PGSC0003DMG400030897' => 'stu', 'Phvul.001G254800' => 'pvu', 'Phvul.002G260100' => 'pvu', 'Phvul.003G167600' => 'pvu', 'Phvul.004G005100' => 'pvu', 'Potri.001G343600' => 'ptr', 'Potri.006G066700' => 'ptr', 'Potri.008G186000' => 'ptr', 'Potri.010G046900' => 'ptr', 'Potri.018G127900' => 'ptr', 'Pp3c20_17750' => 'ppa', 'Pp3c24_4380' => 'ppa', 'Prupe.1G245800' => 'ppe', 'Prupe.3G293400' => 'ppe', 'Prupe.7G247400' => 'ppe', 'Psat0s145g0120' => 'psa', 'Psat0s595g0040' => 'psa', 'Psat0s595g0120' => 'psa', 'Psat3g175040' => 'psa', 'Psat7g058120' => 'psa', 'PSO017G0428' => 'pso', 'PSO063G7510' => 'pso', 'PSO067G0046' => 'pso', 'PSO478G1073' => 'pso', 'PSO675G3677' => 'pso', 'PSO675G6558' => 'pso', 'PSO675G7520' => 'pso', 'PSO675G8959' => 'pso', 'QL02p074089' => 'qlo', 'QL02p089614' => 'qlo', 'QL03p057736' => 'qlo', 'RcHm_v2.0_Chr1g0364131' => 'rch', 'RcHm_v2.0_Chr2g0087801' => 'rch', 'RcHm_v2.0_Chr2g0087821' => 'rch', 'RcHm_v2.0_Chr2g0173231' => 'rch', 'RcHm_v2.0_Chr4g0433111' => 'rch', 'Rhsim03G0250300' => 'rsi', 'Rhsim08G0048400' => 'rsi', 'Rhsim10G0014800' => 'rsi', 'Rhsim12G0040100' => 'rsi', 'Rhsim12G0109700' => 'rsi', 'Sabra06G0049600' => 'sbr', 'Sabra08G0141000' => 'sbr', 'Sabra10G0021400' => 'sbr', 'Sabra16G0222900' => 'sbr', 'Sabra18G0108600' => 'sbr', 'SalBow1G0433' => 'sbo', 'SalBow1G2038' => 'sbo', 'SalBow1G5003' => 'sbo', 'SalBow7G1197' => 'sbo', 'SalBow8G3506' => 'sbo', 'Sc03g0007300' => 'sci', 'Sc11g0000950' => 'sci', 'Sc14g0008750' => 'sci', 'Sc18g0000420' => 'sci', 'Sed0006754' => 'sed', 'Sed0008741' => 'sed', 'Sed0017172' => 'sed', 'Sed0018925' => 'sed', 'Sed0023326' => 'sed', 'Sed0025909' => 'sed', 'SEGI_05333' => 'sgi', 'SEGI_10362' => 'sgi', 'SEGI_13380' => 'sgi', 'SEGI_24306' => 'sgi', 'SEGI_29077' => 'sgi', 'SEGI_29095' => 'sgi', 'SEGI_36534' => 'sgi', 'SEGI_37506' => 'sgi', 'SEGI_38321' => 'sgi', 'SGA_v2.0_scaffold307G48031' => 'sas', 'SGA_v2.0_scaffold47G17507' => 'sas', 'SGA_v2.0_scaffold63G21736' => 'sas', 'SGA_v2.0_scaffold87G27070' => 'sas', 'SHI17794' => 'shi', 'SHI28851' => 'shi', 'SMO165G0155' => 'smo', 'SMO340G0217' => 'smo', 'SMO367G1210' => 'smo', 'Solyc02g093430.3' => 'sly', 'Solyc05g013580.4' => 'sly', 'Solyc07g008030.3' => 'sly', 'Solyc12g035470.2' => 'sly', 'Sopen02g038020' => 'spe', 'Sopen05g008490' => 'spe', 'Sopen07g003910' => 'spe', 'Sopen12g015240' => 'spe', 'Sp1g11550' => 'spa', 'Sp2g16710' => 'spa', 'Sp3g00430' => 'spa', 'Sp3g26780' => 'spa', 'Sp5g22900' => 'spa', 'Sp6g29530' => 'spa', 'TAR371G0794' => 'tar', 'TAR374G0164' => 'tar', 'TAR622G0165' => 'tar', 'TAR626G0929' => 'tar', 'TAR629G2155' => 'tar', 'THA.LOC104805282' => 'tha', 'THA.LOC104805363' => 'tha', 'THA.LOC104808968' => 'tha', 'THA.LOC104821093' => 'tha', 'THA.LOC104823953' => 'tha', 'THA.LOC104825562' => 'tha', 'THA.LOC104825665' => 'tha', 'Thecc.02G261400' => 'tca', 'Thecc.04G019200' => 'tca', 'Thecc.09G130400' => 'tca', 'Thhalv10004374m.g' => 'esa', 'Thhalv10007850m.g' => 'esa', 'Thhalv10013782m.g' => 'esa', 'Thhalv10018686m.g' => 'esa', 'Thhalv10020899m.g' => 'esa', 'Thhalv10022755m.g' => 'esa', 'TPR.G23851' => 'tpr', 'TPR.G26500' => 'tpr', 'TPR.G27267' => 'tpr', 'TPR.G32001' => 'tpr', 'TPR.G6251' => 'tpr', 'TPR.G8167' => 'tpr', 'TWI12G1330' => 'twi', 'TWI18G1239' => 'twi', 'TWI34G0979' => 'twi', 'TWI36G0670' => 'twi', 'TWI36G0707' => 'twi', 'TWI56G0233' => 'twi', 'TWI75G1809' => 'twi', 'unitig_21.g20874' => 'ugi', 'unitig_26.g10343' => 'ugi', 'unitig_46.g18392' => 'ugi', 'unitig_52.g17178' => 'ugi', 'unitig_8.g2934' => 'ugi', 'vmacro01122' => 'vma', 'vmacro05875' => 'vma', 'vmacro06147' => 'vma', 'vmacro16191' => 'vma', 'vmacro18293' => 'vma', 'VMungo0251G3707' => 'vmu', 'VMungo0464G1521' => 'vmu', 'VMungo1215G0205' => 'vmu', 'VMungo1383G2484' => 'vmu', 'Zm00001eb079610' => 'zma', 'Zm00001eb135990' => 'zma', 'Zm00001eb183710' => 'zma', 'Zm00001eb246020' => 'zma' ) $gf_id = 'HOM05D001124' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001124' ) $data_identifier = 'HOM05D001124' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 6, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 7, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 21, 'bol' => (int) 10, 'bra' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 6, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 9, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 21, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 8, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 10, 'lsa' => (int) 8, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 8, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 9, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb246020' $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' => 'HOM05D001124', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '548', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02520' => 'bna', 'A03p06630' => 'bna', 'A05p44460' => 'bna', 'A06p08710' => 'bna', 'A06p41090' => 'bna', 'A07p32320' => 'bna', 'A08p32520' => 'bna', 'A09p10360' => 'bna', 'A10p24080' => 'bna', 'Aa31LG11G15250' => 'aar', 'Aa31LG1G1800' => 'aar', 'Aa31LG2G5120' => 'aar', 'Aa31LG2G6070' => 'aar', 'Aa31LG5G10770' => 'aar', 'Aa31sc61G90' => 'aar', 'Actinidia01352' => 'ach', 'Actinidia05983' => 'ach', 'Actinidia08133' => 'ach', 'Actinidia15101' => 'ach', 'Actinidia26379' => 'ach', 'Actinidia35778' => 'ach', 'Actinidia36123' => 'ach', 'Actinidia37436' => 'ach', 'Actinidia38730' => 'ach', 'Ah.02g128210' => 'amhyb', 'Ah.03g132990' => 'amhyb', 'Ah.14g079410' => 'amhyb', 'AL1G24640' => 'aly', 'AL2G26680' => 'aly', 'AL3G10530' => 'aly', 'AL3G45230' => 'aly', 'AL5G15230' => 'aly', 'AL5G16960' => 'aly', 'AL6G25210' => 'aly', 'Aqoxy2G00441' => 'aox', 'Aqoxy3G01236' => 'aox', 'Aqoxy5G03746' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3RQ047' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C7GMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9C8JER' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MBL6KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YXCZ83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZANX40' => 'arhy', 'AT1G12990' => 'ath', 'AT1G67880' => 'ath', 'AT2G13290' => 'ath', 'AT3G01620' => 'ath', 'AT3G26445' => 'ath', 'AT3G27540' => 'ath', 'AT5G14480' => 'ath', 'ATR0824G026' => 'atr', 'ATR1098G019' => 'atr', 'Atru.chr11.2145' => 'acertr', 'Atru.chr2.3636' => 'acertr', 'Atru.chr2.3644' => 'acertr', 'Atru.chr6.2422' => 'acertr', 'Atru.chr7.1112' => 'acertr', 'AUR62005469' => 'cqu', 'AUR62011166' => 'cqu', 'AUR62013319' => 'cqu', 'AUR62024273' => 'cqu', 'AUR62028420' => 'cqu', 'AUR62041942' => 'cqu', 'BcaB01g04969' => 'bca', 'BcaB01g06371' => 'bca', 'BcaB02g11494' => 'bca', 'BcaB03g15382' => 'bca', 'BcaB08g36994' => 'bca', 'BcaC03g13477' => 'bca', 'BcaC03g13478' => 'bca', 'BcaC03g13480' => 'bca', 'BcaC03g13481' => 'bca', 'BcaC03g13486' => 'bca', 'BcaC04g19031' => 'bca', 'BcaC04g23085' => 'bca', 'BcaC05g25094' => 'bca', 'BcaC05g25096' => 'bca', 'BcaC05g25138' => 'bca', 'BcaC05g30416' => 'bca', 'BcaC05g30455' => 'bca', 'BcaC06g30979' => 'bca', 'BcaC06g33805' => 'bca', 'BcaC08g46021' => 'bca', 'BcaNung03154' => 'bca', 'BolC2t06623H' => 'bol', 'BolC2t06632H' => 'bol', 'BolC2t06635H' => 'bol', 'BolC2t06638H' => 'bol', 'BolC3t13266H' => 'bol', 'BolC5t29776H' => 'bol', 'BolC6t38912H' => 'bol', 'BolC7t44183H' => 'bol', 'BolC9t54123H' => 'bol', 'BolC9t59107H' => 'bol', 'BraA02t05221Z' => 'bra', 'BraA03t09996Z' => 'bra', 'BraA05t23210Z' => 'bra', 'BraA06t24068Z' => 'bra', 'BraA06t27032Z' => 'bra', 'BraA08t35176Z' => 'bra', 'BraA09t36680Z' => 'bra', 'BraA10t44471Z' => 'bra', 'C02p06760' => 'bna', 'C02p06890' => 'bna', 'C02p07010' => 'bna', 'C03p07660' => 'bna', 'C05p10300' => 'bna', 'C06p38150' => 'bna', 'C07p36650' => 'bna', 'C08p15770' => 'bna', 'C09p12300' => 'bna', 'C09p62700' => 'bna', 'C09p75040' => 'bna', 'CAN.G13.1' => 'can', 'CAN.G138.4' => 'can', 'CAN.G44.6' => 'can', 'CAN.G473.19' => 'can', 'CANSAT01G0835' => 'cansat', 'CANSAT11G0246' => 'cansat', 'CANSAT11G1766' => 'cansat', 'CANSAT64G1954' => 'cansat', 'CARHR013330' => 'chi', 'CARHR060530' => 'chi', 'CARHR075300' => 'chi', 'CARHR105120' => 'chi', 'CARHR148910' => 'chi', 'CARHR198830' => 'chi', 'Carub.0001s1275' => 'cru', 'Carub.0002s1437' => 'cru', 'Carub.0003s0044' => 'cru', 'Carub.0003s2787' => 'cru', 'Carub.0005s0597' => 'cru', 'Carub.0006s1266' => 'cru', 'Ca_06935_v3' => 'car', 'Ca_13559_v3' => 'car', 'Ca_16941_v3' => 'car', 'Ca_16960_v3' => 'car', 'Ca_17775_v3' => 'car', 'Ca_30464_v3' => 'car', 'Cc06_g08160' => 'ccan', 'Cc07_g01520' => 'ccan', 'Cc11_g15810' => 'ccan', 'CDE02G2840' => 'cde', 'CDE03G0093' => 'cde', 'CDE04G2127' => 'cde', 'CDE07G1857' => 'cde', 'CDE09G1246' => 'cde', 'Cfa003412' => 'cfa', 'Cfa007341' => 'cfa', 'Cfa009220' => 'cfa', 'Ciclev10008737m.g' => 'ccl', 'Ciclev10015565m.g' => 'ccl', 'Ciclev10031761m.g' => 'ccl', 'CiPaw.03G045300' => 'cil', 'CiPaw.03G247200' => 'cil', 'CiPaw.04G029500' => 'cil', 'CiPaw.04G174000' => 'cil', 'CiPaw.05G181200' => 'cil', 'CiPaw.06G067100' => 'cil', 'ClCG05G025800' => 'cla', 'ClCG06G011400' => 'cla', 'ClCG09G019360' => 'cla', 'COL.COLO4_04827' => 'col', 'COL.COLO4_29170' => 'col', 'COL.COLO4_35131' => 'col', 'COL.COLO4_35132' => 'col', 'Cpa.g.sc33.32' => 'cpa', 'Cpa.g.sc46.29' => 'cpa', 'Cpa.g.sc796.1' => 'cpa', 'CsaV3_1G030420' => 'csa', 'CsaV3_5G027050' => 'csa', 'CsaV3_5G031040' => 'csa', 'CsaV3_UNG023130' => 'csa', 'CSS0007726' => 'camsi', 'CSS0016433' => 'camsi', 'CSS0017656' => 'camsi', 'CSS0025364' => 'camsi', 'CSS0027582' => 'camsi', 'CSS0047288' => 'camsi', 'CSS0049950' => 'camsi', 'DCAR_003843' => 'dca', 'DCAR_007052' => 'dca', 'DCAR_020884' => 'dca', 'DCAR_021730' => 'dca', 'DCAR_024423' => 'dca', 'DCAR_026509' => 'dca', 'DCAR_031158' => 'dca', 'Dinv14728' => 'din', 'Dinv15219' => 'din', 'Dinv25728' => 'din', 'Dinv33428' => 'din', 'Dinv36489' => 'din', 'Dinv41486' => 'din', 'Duzib147G0469' => 'dzi', 'Duzib168G0060' => 'dzi', 'Duzib187G1215' => 'dzi', 'Duzib248G0692' => 'dzi', 'Duzib251G0767' => 'dzi', 'Duzib264G0446' => 'dzi', 'Duzib268G0691' => 'dzi', 'ECA232G4767' => 'eca', 'ECA233G2838' => 'eca', 'ECA234G0391' => 'eca', 'ECA234G0857' => 'eca', 'ECA236G1593' => 'eca', 'ECA238G0565' => 'eca', 'ECA246G1027' => 'eca', 'ECA246G3223' => 'eca', 'ECA246G3470' => 'eca', 'EL10Ac6g13829' => 'bvu', 'EL10Ac6g14093' => 'bvu', 'EL10Ac8g18707' => 'bvu', 'Eucgr.C01369' => 'egr', 'Eucgr.H02492' => 'egr', 'Eucgr.I01733' => 'egr', 'Eucgr.J02255' => 'egr', 'Eucgr.J02257' => 'egr', 'Eucgr.J02258' => 'egr', 'FAN02G1601' => 'fan', 'FAN03G1586' => 'fan', 'FAN03G2986' => 'fan', 'FAN05G4837' => 'fan', 'FAN06G0146' => 'fan', 'FAN07G0858' => 'fan', 'FAN09G3179' => 'fan', 'FAN10G0669' => 'fan', 'FAN12G2358' => 'fan', 'FAN14G4198' => 'fan', 'FAN14G5112' => 'fan', 'FAN17G0342' => 'fan', 'FAN19G0342' => 'fan', 'FAN19G0962' => 'fan', 'FAN19G1101' => 'fan', 'FAN19G1872' => 'fan', 'FAN22G0356' => 'fan', 'FAN23G0744' => 'fan', 'FAN23G1914' => 'fan', 'FAN26G0032' => 'fan', 'FAN28G0625' => 'fan', 'FvH4_1g02710' => 'fve', 'FvH4_1g02720' => 'fve', 'FvH4_4g25670' => 'fve', 'FvH4_6g51700' => 'fve', 'FvH4_7g20170' => 'fve', 'Glyma.05G175000' => 'gma', 'Glyma.08G132300' => 'gma', 'Glyma.11G243000' => 'gma', 'Glyma.13G158900' => 'gma', 'Glyma.17G112400' => 'gma', 'Glyma.18G014100' => 'gma', 'Glyma.19G003100' => 'gma', 'Glyma.19G056500' => 'gma', 'Gohir.A01G158900' => 'ghi', 'Gohir.A05G312600' => 'ghi', 'Gohir.A05G354900' => 'ghi', 'Gohir.A07G037200' => 'ghi', 'Gohir.A09G030000' => 'ghi', 'Gohir.A12G145200' => 'ghi', 'Gohir.D01G151500' => 'ghi', 'Gohir.D04G058300' => 'ghi', 'Gohir.D05G314100' => 'ghi', 'Gohir.D07G041400' => 'ghi', 'Gohir.D09G029700' => 'ghi', 'Gohir.D12G149700' => 'ghi', 'Gorai.001G043800' => 'gra', 'Gorai.002G187800' => 'gra', 'Gorai.006G034700' => 'gra', 'Gorai.008G161200' => 'gra', 'Gorai.009G335700' => 'gra', 'Gorai.012G065000' => 'gra', 'GSVIVG01000535001' => 'vvi', 'GSVIVG01015572001' => 'vvi', 'GSVIVG01032386001' => 'vvi', 'HanXRQChr05g0138531' => 'han', 'HanXRQChr06g0174391' => 'han', 'HanXRQChr07g0199021' => 'han', 'HanXRQChr08g0208211' => 'han', 'HanXRQChr09g0255471' => 'han', 'HanXRQChr10g0315791' => 'han', 'HanXRQChr12g0371991' => 'han', 'HanXRQChr15g0475251' => 'han', 'HanXRQChr17g0540001' => 'han', 'HanXRQChr17g0548631' => 'han', 'HanXRQChr17g0569561' => 'han', 'Haze_12256' => 'cav', 'Haze_14756' => 'cav', 'Haze_25528' => 'cav', 'Hma1.2p1_0079F.1_g041020' => 'hma', 'Hma1.2p1_0818F.1_g223260' => 'hma', 'Hma1.2p1_1747F.1_g300530' => 'hma', 'HPP92_004607' => 'vpl', 'HPP92_004608' => 'vpl', 'HPP92_006181' => 'vpl', 'HPP92_012192' => 'vpl', 'HPP92_015680' => 'vpl', 'HPP92_020249' => 'vpl', 'HPP92_021376' => 'vpl', 'HPP92_024275' => 'vpl', 'Hund06031' => 'sun', 'Hund25391' => 'sun', 'Lalb_Chr07g0185371' => 'lal', 'Lalb_Chr07g0185381' => 'lal', 'Lalb_Chr12g0204011' => 'lal', 'Lalb_Chr13g0301671' => 'lal', 'Lalb_Chr14g0362851' => 'lal', 'Lalb_Chr24g0403581' => 'lal', 'Lj1g0000233' => 'lja', 'Lj2g0018120' => 'lja', 'Lj3C621T0' => 'lonja', 'Lj3P1059T14' => 'lonja', 'Lj3P611T9' => 'lonja', 'Lj3P614T13' => 'lonja', 'Lj3P615T5' => 'lonja', 'Lj4g0012315' => 'lja', 'Lj4g0026182' => 'lja', 'Lj6P813T16' => 'lonja', 'Lj7C427T7' => 'lonja', 'Lj7C427T8' => 'lonja', 'Lj7P600T41' => 'lonja', 'Lju41C42G17' => 'lonja', 'Lsat_1_v5_gn_0_47300' => 'lsa', 'Lsat_1_v5_gn_2_91280' => 'lsa', 'Lsat_1_v5_gn_3_30561' => 'lsa', 'Lsat_1_v5_gn_4_184321' => 'lsa', 'Lsat_1_v5_gn_4_4041' => 'lsa', 'Lsat_1_v5_gn_5_92000' => 'lsa', 'Lsat_1_v5_gn_8_152940' => 'lsa', 'Lsat_1_v5_gn_8_62401' => 'lsa', 'Manes.06G055900' => 'mes', 'Manes.12G022200' => 'mes', 'Manes.13G023300' => 'mes', 'Manes.14G115000' => 'mes', 'Manes.15G151700' => 'mes', 'Manes.17G111300' => 'mes', 'Mapoly0226s0009' => 'mpo', 'MBI02_g25363_MAGBIO' => 'mbi', 'MBI06_g00027_MAGBIO' => 'mbi', 'MBI10_g13034_MAGBIO' => 'mbi', 'MD09G1023400' => 'mdo', 'MD13G1100100' => 'mdo', 'MD15G1169200' => 'mdo', 'MD16G1101100' => 'mdo', 'MD17G1022900' => 'mdo', 'Medtr3g096150' => 'mtr', 'Medtr4g115070' => 'mtr', 'Medtr7g033325' => 'mtr', 'Medtr8g089840' => 'mtr', 'MELO3C010319.2' => 'cme', 'MELO3C011944.2' => 'cme', 'MELO3C021589.2' => 'cme', 'Migut.E00207' => 'egut', 'Migut.H00067' => 'egut', 'Migut.K00433' => 'egut', 'Migut.K00606' => 'egut', 'Migut.K01410' => 'egut', 'MSTRG.13347' => 'ama', 'MSTRG.24045' => 'ama', 'MSTRG.2428' => 'ama', 'MSTRG.26410' => 'ama', 'MSTRG.3139' => 'ama', 'MSTRG.3286' => 'ama', 'MSTRG.563' => 'ama', 'MSTRG.7941' => 'ama', 'Nitab4.5_0000028g0060' => 'nta', 'Nitab4.5_0000065g0260' => 'nta', 'Nitab4.5_0000112g0060' => 'nta', 'Nitab4.5_0000489g0120' => 'nta', 'Nitab4.5_0001776g0050' => 'nta', 'Nitab4.5_0001854g0010' => 'nta', 'Nitab4.5_0001860g0020' => 'nta', 'Nitab4.5_0004352g0010' => 'nta', 'Nitab4.5_0008716g0020' => 'nta', 'Nitab4.5_0008922g0010' => 'nta', 'Nn3g16693' => 'nnu', 'Nn4g22596' => 'nnu', 'Nn7g37639' => 'nnu', 'Oeu001701.1' => 'oeu', 'Oeu018149.1' => 'oeu', 'Oeu026220.1' => 'oeu', 'Oeu038635.1' => 'oeu', 'Oeu049176.1' => 'oeu', 'Oeu056706.1' => 'oeu', 'Oeu056937.1' => 'oeu', 'Oeu057540.1' => 'oeu', 'Os02g0594900' => 'osa', 'Os02g0595100' => 'osa', 'Os04g0477500' => 'osa', 'Os12g0611900' => 'osa', 'Peaxi162Scf00076g00020' => 'pax', 'Peaxi162Scf00128g00217' => 'pax', 'Peaxi162Scf00129g01640' => 'pax', 'Peaxi162Scf00669g00007' => 'pax', 'Peaxi162Scf00700g00421' => 'pax', 'Peaxi162Scf00801g00038' => 'pax', 'Peaxi162Scf00891g00025' => 'pax', 'PGR083G0909' => 'pgr', 'PGR119G1005' => 'pgr', 'PGR142G2236' => 'pgr', 'PGR142G3388' => 'pgr', 'PGSC0003DMG400004514' => 'stu', 'PGSC0003DMG400012635' => 'stu', 'PGSC0003DMG400015730' => 'stu', 'PGSC0003DMG400018611' => 'stu', 'PGSC0003DMG400030897' => 'stu', 'Phvul.001G254800' => 'pvu', 'Phvul.002G260100' => 'pvu', 'Phvul.003G167600' => 'pvu', 'Phvul.004G005100' => 'pvu', 'Potri.001G343600' => 'ptr', 'Potri.006G066700' => 'ptr', 'Potri.008G186000' => 'ptr', 'Potri.010G046900' => 'ptr', 'Potri.018G127900' => 'ptr', 'Pp3c20_17750' => 'ppa', 'Pp3c24_4380' => 'ppa', 'Prupe.1G245800' => 'ppe', 'Prupe.3G293400' => 'ppe', 'Prupe.7G247400' => 'ppe', 'Psat0s145g0120' => 'psa', 'Psat0s595g0040' => 'psa', 'Psat0s595g0120' => 'psa', 'Psat3g175040' => 'psa', 'Psat7g058120' => 'psa', 'PSO017G0428' => 'pso', 'PSO063G7510' => 'pso', 'PSO067G0046' => 'pso', 'PSO478G1073' => 'pso', 'PSO675G3677' => 'pso', 'PSO675G6558' => 'pso', 'PSO675G7520' => 'pso', 'PSO675G8959' => 'pso', 'QL02p074089' => 'qlo', 'QL02p089614' => 'qlo', 'QL03p057736' => 'qlo', 'RcHm_v2.0_Chr1g0364131' => 'rch', 'RcHm_v2.0_Chr2g0087801' => 'rch', 'RcHm_v2.0_Chr2g0087821' => 'rch', 'RcHm_v2.0_Chr2g0173231' => 'rch', 'RcHm_v2.0_Chr4g0433111' => 'rch', 'Rhsim03G0250300' => 'rsi', 'Rhsim08G0048400' => 'rsi', 'Rhsim10G0014800' => 'rsi', 'Rhsim12G0040100' => 'rsi', 'Rhsim12G0109700' => 'rsi', 'Sabra06G0049600' => 'sbr', 'Sabra08G0141000' => 'sbr', 'Sabra10G0021400' => 'sbr', 'Sabra16G0222900' => 'sbr', 'Sabra18G0108600' => 'sbr', 'SalBow1G0433' => 'sbo', 'SalBow1G2038' => 'sbo', 'SalBow1G5003' => 'sbo', 'SalBow7G1197' => 'sbo', 'SalBow8G3506' => 'sbo', 'Sc03g0007300' => 'sci', 'Sc11g0000950' => 'sci', 'Sc14g0008750' => 'sci', 'Sc18g0000420' => 'sci', 'Sed0006754' => 'sed', 'Sed0008741' => 'sed', 'Sed0017172' => 'sed', 'Sed0018925' => 'sed', 'Sed0023326' => 'sed', 'Sed0025909' => 'sed', 'SEGI_05333' => 'sgi', 'SEGI_10362' => 'sgi', 'SEGI_13380' => 'sgi', 'SEGI_24306' => 'sgi', 'SEGI_29077' => 'sgi', 'SEGI_29095' => 'sgi', 'SEGI_36534' => 'sgi', 'SEGI_37506' => 'sgi', 'SEGI_38321' => 'sgi', 'SGA_v2.0_scaffold307G48031' => 'sas', 'SGA_v2.0_scaffold47G17507' => 'sas', 'SGA_v2.0_scaffold63G21736' => 'sas', 'SGA_v2.0_scaffold87G27070' => 'sas', 'SHI17794' => 'shi', 'SHI28851' => 'shi', 'SMO165G0155' => 'smo', 'SMO340G0217' => 'smo', 'SMO367G1210' => 'smo', 'Solyc02g093430.3' => 'sly', 'Solyc05g013580.4' => 'sly', 'Solyc07g008030.3' => 'sly', 'Solyc12g035470.2' => 'sly', 'Sopen02g038020' => 'spe', 'Sopen05g008490' => 'spe', 'Sopen07g003910' => 'spe', 'Sopen12g015240' => 'spe', 'Sp1g11550' => 'spa', 'Sp2g16710' => 'spa', 'Sp3g00430' => 'spa', 'Sp3g26780' => 'spa', 'Sp5g22900' => 'spa', 'Sp6g29530' => 'spa', 'TAR371G0794' => 'tar', 'TAR374G0164' => 'tar', 'TAR622G0165' => 'tar', 'TAR626G0929' => 'tar', 'TAR629G2155' => 'tar', 'THA.LOC104805282' => 'tha', 'THA.LOC104805363' => 'tha', 'THA.LOC104808968' => 'tha', 'THA.LOC104821093' => 'tha', 'THA.LOC104823953' => 'tha', 'THA.LOC104825562' => 'tha', 'THA.LOC104825665' => 'tha', 'Thecc.02G261400' => 'tca', 'Thecc.04G019200' => 'tca', 'Thecc.09G130400' => 'tca', 'Thhalv10004374m.g' => 'esa', 'Thhalv10007850m.g' => 'esa', 'Thhalv10013782m.g' => 'esa', 'Thhalv10018686m.g' => 'esa', 'Thhalv10020899m.g' => 'esa', 'Thhalv10022755m.g' => 'esa', 'TPR.G23851' => 'tpr', 'TPR.G26500' => 'tpr', 'TPR.G27267' => 'tpr', 'TPR.G32001' => 'tpr', 'TPR.G6251' => 'tpr', 'TPR.G8167' => 'tpr', 'TWI12G1330' => 'twi', 'TWI18G1239' => 'twi', 'TWI34G0979' => 'twi', 'TWI36G0670' => 'twi', 'TWI36G0707' => 'twi', 'TWI56G0233' => 'twi', 'TWI75G1809' => 'twi', 'unitig_21.g20874' => 'ugi', 'unitig_26.g10343' => 'ugi', 'unitig_46.g18392' => 'ugi', 'unitig_52.g17178' => 'ugi', 'unitig_8.g2934' => 'ugi', 'vmacro01122' => 'vma', 'vmacro05875' => 'vma', 'vmacro06147' => 'vma', 'vmacro16191' => 'vma', 'vmacro18293' => 'vma', 'VMungo0251G3707' => 'vmu', 'VMungo0464G1521' => 'vmu', 'VMungo1215G0205' => 'vmu', 'VMungo1383G2484' => 'vmu', 'Zm00001eb079610' => 'zma', 'Zm00001eb135990' => 'zma', 'Zm00001eb183710' => 'zma', 'Zm00001eb246020' => 'zma' ), 'gf_id' => 'HOM05D001124', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001124' ), 'data_identifier' => 'HOM05D001124', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001124', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '548', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02520' => 'bna', 'A03p06630' => 'bna', 'A05p44460' => 'bna', 'A06p08710' => 'bna', 'A06p41090' => 'bna', 'A07p32320' => 'bna', 'A08p32520' => 'bna', 'A09p10360' => 'bna', 'A10p24080' => 'bna', 'Aa31LG11G15250' => 'aar', 'Aa31LG1G1800' => 'aar', 'Aa31LG2G5120' => 'aar', 'Aa31LG2G6070' => 'aar', 'Aa31LG5G10770' => 'aar', 'Aa31sc61G90' => 'aar', 'Actinidia01352' => 'ach', 'Actinidia05983' => 'ach', 'Actinidia08133' => 'ach', 'Actinidia15101' => 'ach', 'Actinidia26379' => 'ach', 'Actinidia35778' => 'ach', 'Actinidia36123' => 'ach', 'Actinidia37436' => 'ach', 'Actinidia38730' => 'ach', 'Ah.02g128210' => 'amhyb', 'Ah.03g132990' => 'amhyb', 'Ah.14g079410' => 'amhyb', 'AL1G24640' => 'aly', 'AL2G26680' => 'aly', 'AL3G10530' => 'aly', 'AL3G45230' => 'aly', 'AL5G15230' => 'aly', 'AL5G16960' => 'aly', 'AL6G25210' => 'aly', 'Aqoxy2G00441' => 'aox', 'Aqoxy3G01236' => 'aox', 'Aqoxy5G03746' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3RQ047' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C7GMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9C8JER' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MBL6KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YXCZ83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZANX40' => 'arhy', 'AT1G12990' => 'ath', 'AT1G67880' => 'ath', 'AT2G13290' => 'ath', 'AT3G01620' => 'ath', 'AT3G26445' => 'ath', 'AT3G27540' => 'ath', 'AT5G14480' => 'ath', 'ATR0824G026' => 'atr', 'ATR1098G019' => 'atr', 'Atru.chr11.2145' => 'acertr', 'Atru.chr2.3636' => 'acertr', 'Atru.chr2.3644' => 'acertr', 'Atru.chr6.2422' => 'acertr', 'Atru.chr7.1112' => 'acertr', 'AUR62005469' => 'cqu', 'AUR62011166' => 'cqu', 'AUR62013319' => 'cqu', 'AUR62024273' => 'cqu', 'AUR62028420' => 'cqu', 'AUR62041942' => 'cqu', 'BcaB01g04969' => 'bca', 'BcaB01g06371' => 'bca', 'BcaB02g11494' => 'bca', 'BcaB03g15382' => 'bca', 'BcaB08g36994' => 'bca', 'BcaC03g13477' => 'bca', 'BcaC03g13478' => 'bca', 'BcaC03g13480' => 'bca', 'BcaC03g13481' => 'bca', 'BcaC03g13486' => 'bca', 'BcaC04g19031' => 'bca', 'BcaC04g23085' => 'bca', 'BcaC05g25094' => 'bca', 'BcaC05g25096' => 'bca', 'BcaC05g25138' => 'bca', 'BcaC05g30416' => 'bca', 'BcaC05g30455' => 'bca', 'BcaC06g30979' => 'bca', 'BcaC06g33805' => 'bca', 'BcaC08g46021' => 'bca', 'BcaNung03154' => 'bca', 'BolC2t06623H' => 'bol', 'BolC2t06632H' => 'bol', 'BolC2t06635H' => 'bol', 'BolC2t06638H' => 'bol', 'BolC3t13266H' => 'bol', 'BolC5t29776H' => 'bol', 'BolC6t38912H' => 'bol', 'BolC7t44183H' => 'bol', 'BolC9t54123H' => 'bol', 'BolC9t59107H' => 'bol', 'BraA02t05221Z' => 'bra', 'BraA03t09996Z' => 'bra', 'BraA05t23210Z' => 'bra', 'BraA06t24068Z' => 'bra', 'BraA06t27032Z' => 'bra', 'BraA08t35176Z' => 'bra', 'BraA09t36680Z' => 'bra', 'BraA10t44471Z' => 'bra', 'C02p06760' => 'bna', 'C02p06890' => 'bna', 'C02p07010' => 'bna', 'C03p07660' => 'bna', 'C05p10300' => 'bna', 'C06p38150' => 'bna', 'C07p36650' => 'bna', 'C08p15770' => 'bna', 'C09p12300' => 'bna', 'C09p62700' => 'bna', 'C09p75040' => 'bna', 'CAN.G13.1' => 'can', 'CAN.G138.4' => 'can', 'CAN.G44.6' => 'can', 'CAN.G473.19' => 'can', 'CANSAT01G0835' => 'cansat', 'CANSAT11G0246' => 'cansat', 'CANSAT11G1766' => 'cansat', 'CANSAT64G1954' => 'cansat', 'CARHR013330' => 'chi', 'CARHR060530' => 'chi', 'CARHR075300' => 'chi', 'CARHR105120' => 'chi', 'CARHR148910' => 'chi', 'CARHR198830' => 'chi', 'Carub.0001s1275' => 'cru', 'Carub.0002s1437' => 'cru', 'Carub.0003s0044' => 'cru', 'Carub.0003s2787' => 'cru', 'Carub.0005s0597' => 'cru', 'Carub.0006s1266' => 'cru', 'Ca_06935_v3' => 'car', 'Ca_13559_v3' => 'car', 'Ca_16941_v3' => 'car', 'Ca_16960_v3' => 'car', 'Ca_17775_v3' => 'car', 'Ca_30464_v3' => 'car', 'Cc06_g08160' => 'ccan', 'Cc07_g01520' => 'ccan', 'Cc11_g15810' => 'ccan', 'CDE02G2840' => 'cde', 'CDE03G0093' => 'cde', 'CDE04G2127' => 'cde', 'CDE07G1857' => 'cde', 'CDE09G1246' => 'cde', 'Cfa003412' => 'cfa', 'Cfa007341' => 'cfa', 'Cfa009220' => 'cfa', 'Ciclev10008737m.g' => 'ccl', 'Ciclev10015565m.g' => 'ccl', 'Ciclev10031761m.g' => 'ccl', 'CiPaw.03G045300' => 'cil', 'CiPaw.03G247200' => 'cil', 'CiPaw.04G029500' => 'cil', 'CiPaw.04G174000' => 'cil', 'CiPaw.05G181200' => 'cil', 'CiPaw.06G067100' => 'cil', 'ClCG05G025800' => 'cla', 'ClCG06G011400' => 'cla', 'ClCG09G019360' => 'cla', 'COL.COLO4_04827' => 'col', 'COL.COLO4_29170' => 'col', 'COL.COLO4_35131' => 'col', 'COL.COLO4_35132' => 'col', 'Cpa.g.sc33.32' => 'cpa', 'Cpa.g.sc46.29' => 'cpa', 'Cpa.g.sc796.1' => 'cpa', 'CsaV3_1G030420' => 'csa', 'CsaV3_5G027050' => 'csa', 'CsaV3_5G031040' => 'csa', 'CsaV3_UNG023130' => 'csa', 'CSS0007726' => 'camsi', 'CSS0016433' => 'camsi', 'CSS0017656' => 'camsi', 'CSS0025364' => 'camsi', 'CSS0027582' => 'camsi', 'CSS0047288' => 'camsi', 'CSS0049950' => 'camsi', 'DCAR_003843' => 'dca', 'DCAR_007052' => 'dca', 'DCAR_020884' => 'dca', 'DCAR_021730' => 'dca', 'DCAR_024423' => 'dca', 'DCAR_026509' => 'dca', 'DCAR_031158' => 'dca', 'Dinv14728' => 'din', 'Dinv15219' => 'din', 'Dinv25728' => 'din', 'Dinv33428' => 'din', 'Dinv36489' => 'din', 'Dinv41486' => 'din', 'Duzib147G0469' => 'dzi', 'Duzib168G0060' => 'dzi', 'Duzib187G1215' => 'dzi', 'Duzib248G0692' => 'dzi', 'Duzib251G0767' => 'dzi', 'Duzib264G0446' => 'dzi', 'Duzib268G0691' => 'dzi', 'ECA232G4767' => 'eca', 'ECA233G2838' => 'eca', 'ECA234G0391' => 'eca', 'ECA234G0857' => 'eca', 'ECA236G1593' => 'eca', 'ECA238G0565' => 'eca', 'ECA246G1027' => 'eca', 'ECA246G3223' => 'eca', 'ECA246G3470' => 'eca', 'EL10Ac6g13829' => 'bvu', 'EL10Ac6g14093' => 'bvu', 'EL10Ac8g18707' => 'bvu', 'Eucgr.C01369' => 'egr', 'Eucgr.H02492' => 'egr', 'Eucgr.I01733' => 'egr', 'Eucgr.J02255' => 'egr', 'Eucgr.J02257' => 'egr', 'Eucgr.J02258' => 'egr', 'FAN02G1601' => 'fan', 'FAN03G1586' => 'fan', 'FAN03G2986' => 'fan', 'FAN05G4837' => 'fan', 'FAN06G0146' => 'fan', 'FAN07G0858' => 'fan', 'FAN09G3179' => 'fan', 'FAN10G0669' => 'fan', 'FAN12G2358' => 'fan', 'FAN14G4198' => 'fan', 'FAN14G5112' => 'fan', 'FAN17G0342' => 'fan', 'FAN19G0342' => 'fan', 'FAN19G0962' => 'fan', 'FAN19G1101' => 'fan', 'FAN19G1872' => 'fan', 'FAN22G0356' => 'fan', 'FAN23G0744' => 'fan', 'FAN23G1914' => 'fan', 'FAN26G0032' => 'fan', 'FAN28G0625' => 'fan', 'FvH4_1g02710' => 'fve', 'FvH4_1g02720' => 'fve', 'FvH4_4g25670' => 'fve', 'FvH4_6g51700' => 'fve', 'FvH4_7g20170' => 'fve', 'Glyma.05G175000' => 'gma', 'Glyma.08G132300' => 'gma', 'Glyma.11G243000' => 'gma', 'Glyma.13G158900' => 'gma', 'Glyma.17G112400' => 'gma', 'Glyma.18G014100' => 'gma', 'Glyma.19G003100' => 'gma', 'Glyma.19G056500' => 'gma', 'Gohir.A01G158900' => 'ghi', 'Gohir.A05G312600' => 'ghi', 'Gohir.A05G354900' => 'ghi', 'Gohir.A07G037200' => 'ghi', 'Gohir.A09G030000' => 'ghi', 'Gohir.A12G145200' => 'ghi', 'Gohir.D01G151500' => 'ghi', 'Gohir.D04G058300' => 'ghi', 'Gohir.D05G314100' => 'ghi', 'Gohir.D07G041400' => 'ghi', 'Gohir.D09G029700' => 'ghi', 'Gohir.D12G149700' => 'ghi', 'Gorai.001G043800' => 'gra', 'Gorai.002G187800' => 'gra', 'Gorai.006G034700' => 'gra', 'Gorai.008G161200' => 'gra', 'Gorai.009G335700' => 'gra', 'Gorai.012G065000' => 'gra', 'GSVIVG01000535001' => 'vvi', 'GSVIVG01015572001' => 'vvi', 'GSVIVG01032386001' => 'vvi', 'HanXRQChr05g0138531' => 'han', 'HanXRQChr06g0174391' => 'han', 'HanXRQChr07g0199021' => 'han', 'HanXRQChr08g0208211' => 'han', 'HanXRQChr09g0255471' => 'han', 'HanXRQChr10g0315791' => 'han', 'HanXRQChr12g0371991' => 'han', 'HanXRQChr15g0475251' => 'han', 'HanXRQChr17g0540001' => 'han', 'HanXRQChr17g0548631' => 'han', 'HanXRQChr17g0569561' => 'han', 'Haze_12256' => 'cav', 'Haze_14756' => 'cav', 'Haze_25528' => 'cav', 'Hma1.2p1_0079F.1_g041020' => 'hma', 'Hma1.2p1_0818F.1_g223260' => 'hma', 'Hma1.2p1_1747F.1_g300530' => 'hma', 'HPP92_004607' => 'vpl', 'HPP92_004608' => 'vpl', 'HPP92_006181' => 'vpl', 'HPP92_012192' => 'vpl', 'HPP92_015680' => 'vpl', 'HPP92_020249' => 'vpl', 'HPP92_021376' => 'vpl', 'HPP92_024275' => 'vpl', 'Hund06031' => 'sun', 'Hund25391' => 'sun', 'Lalb_Chr07g0185371' => 'lal', 'Lalb_Chr07g0185381' => 'lal', 'Lalb_Chr12g0204011' => 'lal', 'Lalb_Chr13g0301671' => 'lal', 'Lalb_Chr14g0362851' => 'lal', 'Lalb_Chr24g0403581' => 'lal', 'Lj1g0000233' => 'lja', 'Lj2g0018120' => 'lja', 'Lj3C621T0' => 'lonja', 'Lj3P1059T14' => 'lonja', 'Lj3P611T9' => 'lonja', 'Lj3P614T13' => 'lonja', 'Lj3P615T5' => 'lonja', 'Lj4g0012315' => 'lja', 'Lj4g0026182' => 'lja', 'Lj6P813T16' => 'lonja', 'Lj7C427T7' => 'lonja', 'Lj7C427T8' => 'lonja', 'Lj7P600T41' => 'lonja', 'Lju41C42G17' => 'lonja', 'Lsat_1_v5_gn_0_47300' => 'lsa', 'Lsat_1_v5_gn_2_91280' => 'lsa', 'Lsat_1_v5_gn_3_30561' => 'lsa', 'Lsat_1_v5_gn_4_184321' => 'lsa', 'Lsat_1_v5_gn_4_4041' => 'lsa', 'Lsat_1_v5_gn_5_92000' => 'lsa', 'Lsat_1_v5_gn_8_152940' => 'lsa', 'Lsat_1_v5_gn_8_62401' => 'lsa', 'Manes.06G055900' => 'mes', 'Manes.12G022200' => 'mes', 'Manes.13G023300' => 'mes', 'Manes.14G115000' => 'mes', 'Manes.15G151700' => 'mes', 'Manes.17G111300' => 'mes', 'Mapoly0226s0009' => 'mpo', 'MBI02_g25363_MAGBIO' => 'mbi', 'MBI06_g00027_MAGBIO' => 'mbi', 'MBI10_g13034_MAGBIO' => 'mbi', 'MD09G1023400' => 'mdo', 'MD13G1100100' => 'mdo', 'MD15G1169200' => 'mdo', 'MD16G1101100' => 'mdo', 'MD17G1022900' => 'mdo', 'Medtr3g096150' => 'mtr', 'Medtr4g115070' => 'mtr', 'Medtr7g033325' => 'mtr', 'Medtr8g089840' => 'mtr', 'MELO3C010319.2' => 'cme', 'MELO3C011944.2' => 'cme', 'MELO3C021589.2' => 'cme', 'Migut.E00207' => 'egut', 'Migut.H00067' => 'egut', 'Migut.K00433' => 'egut', 'Migut.K00606' => 'egut', 'Migut.K01410' => 'egut', 'MSTRG.13347' => 'ama', 'MSTRG.24045' => 'ama', 'MSTRG.2428' => 'ama', 'MSTRG.26410' => 'ama', 'MSTRG.3139' => 'ama', 'MSTRG.3286' => 'ama', 'MSTRG.563' => 'ama', 'MSTRG.7941' => 'ama', 'Nitab4.5_0000028g0060' => 'nta', 'Nitab4.5_0000065g0260' => 'nta', 'Nitab4.5_0000112g0060' => 'nta', 'Nitab4.5_0000489g0120' => 'nta', 'Nitab4.5_0001776g0050' => 'nta', 'Nitab4.5_0001854g0010' => 'nta', 'Nitab4.5_0001860g0020' => 'nta', 'Nitab4.5_0004352g0010' => 'nta', 'Nitab4.5_0008716g0020' => 'nta', 'Nitab4.5_0008922g0010' => 'nta', 'Nn3g16693' => 'nnu', 'Nn4g22596' => 'nnu', 'Nn7g37639' => 'nnu', 'Oeu001701.1' => 'oeu', 'Oeu018149.1' => 'oeu', 'Oeu026220.1' => 'oeu', 'Oeu038635.1' => 'oeu', 'Oeu049176.1' => 'oeu', 'Oeu056706.1' => 'oeu', 'Oeu056937.1' => 'oeu', 'Oeu057540.1' => 'oeu', 'Os02g0594900' => 'osa', 'Os02g0595100' => 'osa', 'Os04g0477500' => 'osa', 'Os12g0611900' => 'osa', 'Peaxi162Scf00076g00020' => 'pax', 'Peaxi162Scf00128g00217' => 'pax', 'Peaxi162Scf00129g01640' => 'pax', 'Peaxi162Scf00669g00007' => 'pax', 'Peaxi162Scf00700g00421' => 'pax', 'Peaxi162Scf00801g00038' => 'pax', 'Peaxi162Scf00891g00025' => 'pax', 'PGR083G0909' => 'pgr', 'PGR119G1005' => 'pgr', 'PGR142G2236' => 'pgr', 'PGR142G3388' => 'pgr', 'PGSC0003DMG400004514' => 'stu', 'PGSC0003DMG400012635' => 'stu', 'PGSC0003DMG400015730' => 'stu', 'PGSC0003DMG400018611' => 'stu', 'PGSC0003DMG400030897' => 'stu', 'Phvul.001G254800' => 'pvu', 'Phvul.002G260100' => 'pvu', 'Phvul.003G167600' => 'pvu', 'Phvul.004G005100' => 'pvu', 'Potri.001G343600' => 'ptr', 'Potri.006G066700' => 'ptr', 'Potri.008G186000' => 'ptr', 'Potri.010G046900' => 'ptr', 'Potri.018G127900' => 'ptr', 'Pp3c20_17750' => 'ppa', 'Pp3c24_4380' => 'ppa', 'Prupe.1G245800' => 'ppe', 'Prupe.3G293400' => 'ppe', 'Prupe.7G247400' => 'ppe', 'Psat0s145g0120' => 'psa', 'Psat0s595g0040' => 'psa', 'Psat0s595g0120' => 'psa', 'Psat3g175040' => 'psa', 'Psat7g058120' => 'psa', 'PSO017G0428' => 'pso', 'PSO063G7510' => 'pso', 'PSO067G0046' => 'pso', 'PSO478G1073' => 'pso', 'PSO675G3677' => 'pso', 'PSO675G6558' => 'pso', 'PSO675G7520' => 'pso', 'PSO675G8959' => 'pso', 'QL02p074089' => 'qlo', 'QL02p089614' => 'qlo', 'QL03p057736' => 'qlo', 'RcHm_v2.0_Chr1g0364131' => 'rch', 'RcHm_v2.0_Chr2g0087801' => 'rch', 'RcHm_v2.0_Chr2g0087821' => 'rch', 'RcHm_v2.0_Chr2g0173231' => 'rch', 'RcHm_v2.0_Chr4g0433111' => 'rch', 'Rhsim03G0250300' => 'rsi', 'Rhsim08G0048400' => 'rsi', 'Rhsim10G0014800' => 'rsi', 'Rhsim12G0040100' => 'rsi', 'Rhsim12G0109700' => 'rsi', 'Sabra06G0049600' => 'sbr', 'Sabra08G0141000' => 'sbr', 'Sabra10G0021400' => 'sbr', 'Sabra16G0222900' => 'sbr', 'Sabra18G0108600' => 'sbr', 'SalBow1G0433' => 'sbo', 'SalBow1G2038' => 'sbo', 'SalBow1G5003' => 'sbo', 'SalBow7G1197' => 'sbo', 'SalBow8G3506' => 'sbo', 'Sc03g0007300' => 'sci', 'Sc11g0000950' => 'sci', 'Sc14g0008750' => 'sci', 'Sc18g0000420' => 'sci', 'Sed0006754' => 'sed', 'Sed0008741' => 'sed', 'Sed0017172' => 'sed', 'Sed0018925' => 'sed', 'Sed0023326' => 'sed', 'Sed0025909' => 'sed', 'SEGI_05333' => 'sgi', 'SEGI_10362' => 'sgi', 'SEGI_13380' => 'sgi', 'SEGI_24306' => 'sgi', 'SEGI_29077' => 'sgi', 'SEGI_29095' => 'sgi', 'SEGI_36534' => 'sgi', 'SEGI_37506' => 'sgi', 'SEGI_38321' => 'sgi', 'SGA_v2.0_scaffold307G48031' => 'sas', 'SGA_v2.0_scaffold47G17507' => 'sas', 'SGA_v2.0_scaffold63G21736' => 'sas', 'SGA_v2.0_scaffold87G27070' => 'sas', 'SHI17794' => 'shi', 'SHI28851' => 'shi', 'SMO165G0155' => 'smo', 'SMO340G0217' => 'smo', 'SMO367G1210' => 'smo', 'Solyc02g093430.3' => 'sly', 'Solyc05g013580.4' => 'sly', 'Solyc07g008030.3' => 'sly', 'Solyc12g035470.2' => 'sly', 'Sopen02g038020' => 'spe', 'Sopen05g008490' => 'spe', 'Sopen07g003910' => 'spe', 'Sopen12g015240' => 'spe', 'Sp1g11550' => 'spa', 'Sp2g16710' => 'spa', 'Sp3g00430' => 'spa', 'Sp3g26780' => 'spa', 'Sp5g22900' => 'spa', 'Sp6g29530' => 'spa', 'TAR371G0794' => 'tar', 'TAR374G0164' => 'tar', 'TAR622G0165' => 'tar', 'TAR626G0929' => 'tar', 'TAR629G2155' => 'tar', 'THA.LOC104805282' => 'tha', 'THA.LOC104805363' => 'tha', 'THA.LOC104808968' => 'tha', 'THA.LOC104821093' => 'tha', 'THA.LOC104823953' => 'tha', 'THA.LOC104825562' => 'tha', 'THA.LOC104825665' => 'tha', 'Thecc.02G261400' => 'tca', 'Thecc.04G019200' => 'tca', 'Thecc.09G130400' => 'tca', 'Thhalv10004374m.g' => 'esa', 'Thhalv10007850m.g' => 'esa', 'Thhalv10013782m.g' => 'esa', 'Thhalv10018686m.g' => 'esa', 'Thhalv10020899m.g' => 'esa', 'Thhalv10022755m.g' => 'esa', 'TPR.G23851' => 'tpr', 'TPR.G26500' => 'tpr', 'TPR.G27267' => 'tpr', 'TPR.G32001' => 'tpr', 'TPR.G6251' => 'tpr', 'TPR.G8167' => 'tpr', 'TWI12G1330' => 'twi', 'TWI18G1239' => 'twi', 'TWI34G0979' => 'twi', 'TWI36G0670' => 'twi', 'TWI36G0707' => 'twi', 'TWI56G0233' => 'twi', 'TWI75G1809' => 'twi', 'unitig_21.g20874' => 'ugi', 'unitig_26.g10343' => 'ugi', 'unitig_46.g18392' => 'ugi', 'unitig_52.g17178' => 'ugi', 'unitig_8.g2934' => 'ugi', 'vmacro01122' => 'vma', 'vmacro05875' => 'vma', 'vmacro06147' => 'vma', 'vmacro16191' => 'vma', 'vmacro18293' => 'vma', 'VMungo0251G3707' => 'vmu', 'VMungo0464G1521' => 'vmu', 'VMungo1215G0205' => 'vmu', 'VMungo1383G2484' => 'vmu', 'Zm00001eb079610' => 'zma', 'Zm00001eb135990' => 'zma', 'Zm00001eb183710' => 'zma', 'Zm00001eb246020' => 'zma' ) $gf_id = 'HOM05D001124' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001124' ) $data_identifier = 'HOM05D001124' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 6, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 7, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 21, 'bol' => (int) 10, 'bra' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 6, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 9, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 21, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 8, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 10, 'lsa' => (int) 8, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 8, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 9, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb246020' $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' => 'HOM05D001124', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '548', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02520' => 'bna', 'A03p06630' => 'bna', 'A05p44460' => 'bna', 'A06p08710' => 'bna', 'A06p41090' => 'bna', 'A07p32320' => 'bna', 'A08p32520' => 'bna', 'A09p10360' => 'bna', 'A10p24080' => 'bna', 'Aa31LG11G15250' => 'aar', 'Aa31LG1G1800' => 'aar', 'Aa31LG2G5120' => 'aar', 'Aa31LG2G6070' => 'aar', 'Aa31LG5G10770' => 'aar', 'Aa31sc61G90' => 'aar', 'Actinidia01352' => 'ach', 'Actinidia05983' => 'ach', 'Actinidia08133' => 'ach', 'Actinidia15101' => 'ach', 'Actinidia26379' => 'ach', 'Actinidia35778' => 'ach', 'Actinidia36123' => 'ach', 'Actinidia37436' => 'ach', 'Actinidia38730' => 'ach', 'Ah.02g128210' => 'amhyb', 'Ah.03g132990' => 'amhyb', 'Ah.14g079410' => 'amhyb', 'AL1G24640' => 'aly', 'AL2G26680' => 'aly', 'AL3G10530' => 'aly', 'AL3G45230' => 'aly', 'AL5G15230' => 'aly', 'AL5G16960' => 'aly', 'AL6G25210' => 'aly', 'Aqoxy2G00441' => 'aox', 'Aqoxy3G01236' => 'aox', 'Aqoxy5G03746' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3RQ047' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C7GMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9C8JER' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MBL6KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YXCZ83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZANX40' => 'arhy', 'AT1G12990' => 'ath', 'AT1G67880' => 'ath', 'AT2G13290' => 'ath', 'AT3G01620' => 'ath', 'AT3G26445' => 'ath', 'AT3G27540' => 'ath', 'AT5G14480' => 'ath', 'ATR0824G026' => 'atr', 'ATR1098G019' => 'atr', 'Atru.chr11.2145' => 'acertr', 'Atru.chr2.3636' => 'acertr', 'Atru.chr2.3644' => 'acertr', 'Atru.chr6.2422' => 'acertr', 'Atru.chr7.1112' => 'acertr', 'AUR62005469' => 'cqu', 'AUR62011166' => 'cqu', 'AUR62013319' => 'cqu', 'AUR62024273' => 'cqu', 'AUR62028420' => 'cqu', 'AUR62041942' => 'cqu', 'BcaB01g04969' => 'bca', 'BcaB01g06371' => 'bca', 'BcaB02g11494' => 'bca', 'BcaB03g15382' => 'bca', 'BcaB08g36994' => 'bca', 'BcaC03g13477' => 'bca', 'BcaC03g13478' => 'bca', 'BcaC03g13480' => 'bca', 'BcaC03g13481' => 'bca', 'BcaC03g13486' => 'bca', 'BcaC04g19031' => 'bca', 'BcaC04g23085' => 'bca', 'BcaC05g25094' => 'bca', 'BcaC05g25096' => 'bca', 'BcaC05g25138' => 'bca', 'BcaC05g30416' => 'bca', 'BcaC05g30455' => 'bca', 'BcaC06g30979' => 'bca', 'BcaC06g33805' => 'bca', 'BcaC08g46021' => 'bca', 'BcaNung03154' => 'bca', 'BolC2t06623H' => 'bol', 'BolC2t06632H' => 'bol', 'BolC2t06635H' => 'bol', 'BolC2t06638H' => 'bol', 'BolC3t13266H' => 'bol', 'BolC5t29776H' => 'bol', 'BolC6t38912H' => 'bol', 'BolC7t44183H' => 'bol', 'BolC9t54123H' => 'bol', 'BolC9t59107H' => 'bol', 'BraA02t05221Z' => 'bra', 'BraA03t09996Z' => 'bra', 'BraA05t23210Z' => 'bra', 'BraA06t24068Z' => 'bra', 'BraA06t27032Z' => 'bra', 'BraA08t35176Z' => 'bra', 'BraA09t36680Z' => 'bra', 'BraA10t44471Z' => 'bra', 'C02p06760' => 'bna', 'C02p06890' => 'bna', 'C02p07010' => 'bna', 'C03p07660' => 'bna', 'C05p10300' => 'bna', 'C06p38150' => 'bna', 'C07p36650' => 'bna', 'C08p15770' => 'bna', 'C09p12300' => 'bna', 'C09p62700' => 'bna', 'C09p75040' => 'bna', 'CAN.G13.1' => 'can', 'CAN.G138.4' => 'can', 'CAN.G44.6' => 'can', 'CAN.G473.19' => 'can', 'CANSAT01G0835' => 'cansat', 'CANSAT11G0246' => 'cansat', 'CANSAT11G1766' => 'cansat', 'CANSAT64G1954' => 'cansat', 'CARHR013330' => 'chi', 'CARHR060530' => 'chi', 'CARHR075300' => 'chi', 'CARHR105120' => 'chi', 'CARHR148910' => 'chi', 'CARHR198830' => 'chi', 'Carub.0001s1275' => 'cru', 'Carub.0002s1437' => 'cru', 'Carub.0003s0044' => 'cru', 'Carub.0003s2787' => 'cru', 'Carub.0005s0597' => 'cru', 'Carub.0006s1266' => 'cru', 'Ca_06935_v3' => 'car', 'Ca_13559_v3' => 'car', 'Ca_16941_v3' => 'car', 'Ca_16960_v3' => 'car', 'Ca_17775_v3' => 'car', 'Ca_30464_v3' => 'car', 'Cc06_g08160' => 'ccan', 'Cc07_g01520' => 'ccan', 'Cc11_g15810' => 'ccan', 'CDE02G2840' => 'cde', 'CDE03G0093' => 'cde', 'CDE04G2127' => 'cde', 'CDE07G1857' => 'cde', 'CDE09G1246' => 'cde', 'Cfa003412' => 'cfa', 'Cfa007341' => 'cfa', 'Cfa009220' => 'cfa', 'Ciclev10008737m.g' => 'ccl', 'Ciclev10015565m.g' => 'ccl', 'Ciclev10031761m.g' => 'ccl', 'CiPaw.03G045300' => 'cil', 'CiPaw.03G247200' => 'cil', 'CiPaw.04G029500' => 'cil', 'CiPaw.04G174000' => 'cil', 'CiPaw.05G181200' => 'cil', 'CiPaw.06G067100' => 'cil', 'ClCG05G025800' => 'cla', 'ClCG06G011400' => 'cla', 'ClCG09G019360' => 'cla', 'COL.COLO4_04827' => 'col', 'COL.COLO4_29170' => 'col', 'COL.COLO4_35131' => 'col', 'COL.COLO4_35132' => 'col', 'Cpa.g.sc33.32' => 'cpa', 'Cpa.g.sc46.29' => 'cpa', 'Cpa.g.sc796.1' => 'cpa', 'CsaV3_1G030420' => 'csa', 'CsaV3_5G027050' => 'csa', 'CsaV3_5G031040' => 'csa', 'CsaV3_UNG023130' => 'csa', 'CSS0007726' => 'camsi', 'CSS0016433' => 'camsi', 'CSS0017656' => 'camsi', 'CSS0025364' => 'camsi', 'CSS0027582' => 'camsi', 'CSS0047288' => 'camsi', 'CSS0049950' => 'camsi', 'DCAR_003843' => 'dca', 'DCAR_007052' => 'dca', 'DCAR_020884' => 'dca', 'DCAR_021730' => 'dca', 'DCAR_024423' => 'dca', 'DCAR_026509' => 'dca', 'DCAR_031158' => 'dca', 'Dinv14728' => 'din', 'Dinv15219' => 'din', 'Dinv25728' => 'din', 'Dinv33428' => 'din', 'Dinv36489' => 'din', 'Dinv41486' => 'din', 'Duzib147G0469' => 'dzi', 'Duzib168G0060' => 'dzi', 'Duzib187G1215' => 'dzi', 'Duzib248G0692' => 'dzi', 'Duzib251G0767' => 'dzi', 'Duzib264G0446' => 'dzi', 'Duzib268G0691' => 'dzi', 'ECA232G4767' => 'eca', 'ECA233G2838' => 'eca', 'ECA234G0391' => 'eca', 'ECA234G0857' => 'eca', 'ECA236G1593' => 'eca', 'ECA238G0565' => 'eca', 'ECA246G1027' => 'eca', 'ECA246G3223' => 'eca', 'ECA246G3470' => 'eca', 'EL10Ac6g13829' => 'bvu', 'EL10Ac6g14093' => 'bvu', 'EL10Ac8g18707' => 'bvu', 'Eucgr.C01369' => 'egr', 'Eucgr.H02492' => 'egr', 'Eucgr.I01733' => 'egr', 'Eucgr.J02255' => 'egr', 'Eucgr.J02257' => 'egr', 'Eucgr.J02258' => 'egr', 'FAN02G1601' => 'fan', 'FAN03G1586' => 'fan', 'FAN03G2986' => 'fan', 'FAN05G4837' => 'fan', 'FAN06G0146' => 'fan', 'FAN07G0858' => 'fan', 'FAN09G3179' => 'fan', 'FAN10G0669' => 'fan', 'FAN12G2358' => 'fan', 'FAN14G4198' => 'fan', 'FAN14G5112' => 'fan', 'FAN17G0342' => 'fan', 'FAN19G0342' => 'fan', 'FAN19G0962' => 'fan', 'FAN19G1101' => 'fan', 'FAN19G1872' => 'fan', 'FAN22G0356' => 'fan', 'FAN23G0744' => 'fan', 'FAN23G1914' => 'fan', 'FAN26G0032' => 'fan', 'FAN28G0625' => 'fan', 'FvH4_1g02710' => 'fve', 'FvH4_1g02720' => 'fve', 'FvH4_4g25670' => 'fve', 'FvH4_6g51700' => 'fve', 'FvH4_7g20170' => 'fve', 'Glyma.05G175000' => 'gma', 'Glyma.08G132300' => 'gma', 'Glyma.11G243000' => 'gma', 'Glyma.13G158900' => 'gma', 'Glyma.17G112400' => 'gma', 'Glyma.18G014100' => 'gma', 'Glyma.19G003100' => 'gma', 'Glyma.19G056500' => 'gma', 'Gohir.A01G158900' => 'ghi', 'Gohir.A05G312600' => 'ghi', 'Gohir.A05G354900' => 'ghi', 'Gohir.A07G037200' => 'ghi', 'Gohir.A09G030000' => 'ghi', 'Gohir.A12G145200' => 'ghi', 'Gohir.D01G151500' => 'ghi', 'Gohir.D04G058300' => 'ghi', 'Gohir.D05G314100' => 'ghi', 'Gohir.D07G041400' => 'ghi', 'Gohir.D09G029700' => 'ghi', 'Gohir.D12G149700' => 'ghi', 'Gorai.001G043800' => 'gra', 'Gorai.002G187800' => 'gra', 'Gorai.006G034700' => 'gra', 'Gorai.008G161200' => 'gra', 'Gorai.009G335700' => 'gra', 'Gorai.012G065000' => 'gra', 'GSVIVG01000535001' => 'vvi', 'GSVIVG01015572001' => 'vvi', 'GSVIVG01032386001' => 'vvi', 'HanXRQChr05g0138531' => 'han', 'HanXRQChr06g0174391' => 'han', 'HanXRQChr07g0199021' => 'han', 'HanXRQChr08g0208211' => 'han', 'HanXRQChr09g0255471' => 'han', 'HanXRQChr10g0315791' => 'han', 'HanXRQChr12g0371991' => 'han', 'HanXRQChr15g0475251' => 'han', 'HanXRQChr17g0540001' => 'han', 'HanXRQChr17g0548631' => 'han', 'HanXRQChr17g0569561' => 'han', 'Haze_12256' => 'cav', 'Haze_14756' => 'cav', 'Haze_25528' => 'cav', 'Hma1.2p1_0079F.1_g041020' => 'hma', 'Hma1.2p1_0818F.1_g223260' => 'hma', 'Hma1.2p1_1747F.1_g300530' => 'hma', 'HPP92_004607' => 'vpl', 'HPP92_004608' => 'vpl', 'HPP92_006181' => 'vpl', 'HPP92_012192' => 'vpl', 'HPP92_015680' => 'vpl', 'HPP92_020249' => 'vpl', 'HPP92_021376' => 'vpl', 'HPP92_024275' => 'vpl', 'Hund06031' => 'sun', 'Hund25391' => 'sun', 'Lalb_Chr07g0185371' => 'lal', 'Lalb_Chr07g0185381' => 'lal', 'Lalb_Chr12g0204011' => 'lal', 'Lalb_Chr13g0301671' => 'lal', 'Lalb_Chr14g0362851' => 'lal', 'Lalb_Chr24g0403581' => 'lal', 'Lj1g0000233' => 'lja', 'Lj2g0018120' => 'lja', 'Lj3C621T0' => 'lonja', 'Lj3P1059T14' => 'lonja', 'Lj3P611T9' => 'lonja', 'Lj3P614T13' => 'lonja', 'Lj3P615T5' => 'lonja', 'Lj4g0012315' => 'lja', 'Lj4g0026182' => 'lja', 'Lj6P813T16' => 'lonja', 'Lj7C427T7' => 'lonja', 'Lj7C427T8' => 'lonja', 'Lj7P600T41' => 'lonja', 'Lju41C42G17' => 'lonja', 'Lsat_1_v5_gn_0_47300' => 'lsa', 'Lsat_1_v5_gn_2_91280' => 'lsa', 'Lsat_1_v5_gn_3_30561' => 'lsa', 'Lsat_1_v5_gn_4_184321' => 'lsa', 'Lsat_1_v5_gn_4_4041' => 'lsa', 'Lsat_1_v5_gn_5_92000' => 'lsa', 'Lsat_1_v5_gn_8_152940' => 'lsa', 'Lsat_1_v5_gn_8_62401' => 'lsa', 'Manes.06G055900' => 'mes', 'Manes.12G022200' => 'mes', 'Manes.13G023300' => 'mes', 'Manes.14G115000' => 'mes', 'Manes.15G151700' => 'mes', 'Manes.17G111300' => 'mes', 'Mapoly0226s0009' => 'mpo', 'MBI02_g25363_MAGBIO' => 'mbi', 'MBI06_g00027_MAGBIO' => 'mbi', 'MBI10_g13034_MAGBIO' => 'mbi', 'MD09G1023400' => 'mdo', 'MD13G1100100' => 'mdo', 'MD15G1169200' => 'mdo', 'MD16G1101100' => 'mdo', 'MD17G1022900' => 'mdo', 'Medtr3g096150' => 'mtr', 'Medtr4g115070' => 'mtr', 'Medtr7g033325' => 'mtr', 'Medtr8g089840' => 'mtr', 'MELO3C010319.2' => 'cme', 'MELO3C011944.2' => 'cme', 'MELO3C021589.2' => 'cme', 'Migut.E00207' => 'egut', 'Migut.H00067' => 'egut', 'Migut.K00433' => 'egut', 'Migut.K00606' => 'egut', 'Migut.K01410' => 'egut', 'MSTRG.13347' => 'ama', 'MSTRG.24045' => 'ama', 'MSTRG.2428' => 'ama', 'MSTRG.26410' => 'ama', 'MSTRG.3139' => 'ama', 'MSTRG.3286' => 'ama', 'MSTRG.563' => 'ama', 'MSTRG.7941' => 'ama', 'Nitab4.5_0000028g0060' => 'nta', 'Nitab4.5_0000065g0260' => 'nta', 'Nitab4.5_0000112g0060' => 'nta', 'Nitab4.5_0000489g0120' => 'nta', 'Nitab4.5_0001776g0050' => 'nta', 'Nitab4.5_0001854g0010' => 'nta', 'Nitab4.5_0001860g0020' => 'nta', 'Nitab4.5_0004352g0010' => 'nta', 'Nitab4.5_0008716g0020' => 'nta', 'Nitab4.5_0008922g0010' => 'nta', 'Nn3g16693' => 'nnu', 'Nn4g22596' => 'nnu', 'Nn7g37639' => 'nnu', 'Oeu001701.1' => 'oeu', 'Oeu018149.1' => 'oeu', 'Oeu026220.1' => 'oeu', 'Oeu038635.1' => 'oeu', 'Oeu049176.1' => 'oeu', 'Oeu056706.1' => 'oeu', 'Oeu056937.1' => 'oeu', 'Oeu057540.1' => 'oeu', 'Os02g0594900' => 'osa', 'Os02g0595100' => 'osa', 'Os04g0477500' => 'osa', 'Os12g0611900' => 'osa', 'Peaxi162Scf00076g00020' => 'pax', 'Peaxi162Scf00128g00217' => 'pax', 'Peaxi162Scf00129g01640' => 'pax', 'Peaxi162Scf00669g00007' => 'pax', 'Peaxi162Scf00700g00421' => 'pax', 'Peaxi162Scf00801g00038' => 'pax', 'Peaxi162Scf00891g00025' => 'pax', 'PGR083G0909' => 'pgr', 'PGR119G1005' => 'pgr', 'PGR142G2236' => 'pgr', 'PGR142G3388' => 'pgr', 'PGSC0003DMG400004514' => 'stu', 'PGSC0003DMG400012635' => 'stu', 'PGSC0003DMG400015730' => 'stu', 'PGSC0003DMG400018611' => 'stu', 'PGSC0003DMG400030897' => 'stu', 'Phvul.001G254800' => 'pvu', 'Phvul.002G260100' => 'pvu', 'Phvul.003G167600' => 'pvu', 'Phvul.004G005100' => 'pvu', 'Potri.001G343600' => 'ptr', 'Potri.006G066700' => 'ptr', 'Potri.008G186000' => 'ptr', 'Potri.010G046900' => 'ptr', 'Potri.018G127900' => 'ptr', 'Pp3c20_17750' => 'ppa', 'Pp3c24_4380' => 'ppa', 'Prupe.1G245800' => 'ppe', 'Prupe.3G293400' => 'ppe', 'Prupe.7G247400' => 'ppe', 'Psat0s145g0120' => 'psa', 'Psat0s595g0040' => 'psa', 'Psat0s595g0120' => 'psa', 'Psat3g175040' => 'psa', 'Psat7g058120' => 'psa', 'PSO017G0428' => 'pso', 'PSO063G7510' => 'pso', 'PSO067G0046' => 'pso', 'PSO478G1073' => 'pso', 'PSO675G3677' => 'pso', 'PSO675G6558' => 'pso', 'PSO675G7520' => 'pso', 'PSO675G8959' => 'pso', 'QL02p074089' => 'qlo', 'QL02p089614' => 'qlo', 'QL03p057736' => 'qlo', 'RcHm_v2.0_Chr1g0364131' => 'rch', 'RcHm_v2.0_Chr2g0087801' => 'rch', 'RcHm_v2.0_Chr2g0087821' => 'rch', 'RcHm_v2.0_Chr2g0173231' => 'rch', 'RcHm_v2.0_Chr4g0433111' => 'rch', 'Rhsim03G0250300' => 'rsi', 'Rhsim08G0048400' => 'rsi', 'Rhsim10G0014800' => 'rsi', 'Rhsim12G0040100' => 'rsi', 'Rhsim12G0109700' => 'rsi', 'Sabra06G0049600' => 'sbr', 'Sabra08G0141000' => 'sbr', 'Sabra10G0021400' => 'sbr', 'Sabra16G0222900' => 'sbr', 'Sabra18G0108600' => 'sbr', 'SalBow1G0433' => 'sbo', 'SalBow1G2038' => 'sbo', 'SalBow1G5003' => 'sbo', 'SalBow7G1197' => 'sbo', 'SalBow8G3506' => 'sbo', 'Sc03g0007300' => 'sci', 'Sc11g0000950' => 'sci', 'Sc14g0008750' => 'sci', 'Sc18g0000420' => 'sci', 'Sed0006754' => 'sed', 'Sed0008741' => 'sed', 'Sed0017172' => 'sed', 'Sed0018925' => 'sed', 'Sed0023326' => 'sed', 'Sed0025909' => 'sed', 'SEGI_05333' => 'sgi', 'SEGI_10362' => 'sgi', 'SEGI_13380' => 'sgi', 'SEGI_24306' => 'sgi', 'SEGI_29077' => 'sgi', 'SEGI_29095' => 'sgi', 'SEGI_36534' => 'sgi', 'SEGI_37506' => 'sgi', 'SEGI_38321' => 'sgi', 'SGA_v2.0_scaffold307G48031' => 'sas', 'SGA_v2.0_scaffold47G17507' => 'sas', 'SGA_v2.0_scaffold63G21736' => 'sas', 'SGA_v2.0_scaffold87G27070' => 'sas', 'SHI17794' => 'shi', 'SHI28851' => 'shi', 'SMO165G0155' => 'smo', 'SMO340G0217' => 'smo', 'SMO367G1210' => 'smo', 'Solyc02g093430.3' => 'sly', 'Solyc05g013580.4' => 'sly', 'Solyc07g008030.3' => 'sly', 'Solyc12g035470.2' => 'sly', 'Sopen02g038020' => 'spe', 'Sopen05g008490' => 'spe', 'Sopen07g003910' => 'spe', 'Sopen12g015240' => 'spe', 'Sp1g11550' => 'spa', 'Sp2g16710' => 'spa', 'Sp3g00430' => 'spa', 'Sp3g26780' => 'spa', 'Sp5g22900' => 'spa', 'Sp6g29530' => 'spa', 'TAR371G0794' => 'tar', 'TAR374G0164' => 'tar', 'TAR622G0165' => 'tar', 'TAR626G0929' => 'tar', 'TAR629G2155' => 'tar', 'THA.LOC104805282' => 'tha', 'THA.LOC104805363' => 'tha', 'THA.LOC104808968' => 'tha', 'THA.LOC104821093' => 'tha', 'THA.LOC104823953' => 'tha', 'THA.LOC104825562' => 'tha', 'THA.LOC104825665' => 'tha', 'Thecc.02G261400' => 'tca', 'Thecc.04G019200' => 'tca', 'Thecc.09G130400' => 'tca', 'Thhalv10004374m.g' => 'esa', 'Thhalv10007850m.g' => 'esa', 'Thhalv10013782m.g' => 'esa', 'Thhalv10018686m.g' => 'esa', 'Thhalv10020899m.g' => 'esa', 'Thhalv10022755m.g' => 'esa', 'TPR.G23851' => 'tpr', 'TPR.G26500' => 'tpr', 'TPR.G27267' => 'tpr', 'TPR.G32001' => 'tpr', 'TPR.G6251' => 'tpr', 'TPR.G8167' => 'tpr', 'TWI12G1330' => 'twi', 'TWI18G1239' => 'twi', 'TWI34G0979' => 'twi', 'TWI36G0670' => 'twi', 'TWI36G0707' => 'twi', 'TWI56G0233' => 'twi', 'TWI75G1809' => 'twi', 'unitig_21.g20874' => 'ugi', 'unitig_26.g10343' => 'ugi', 'unitig_46.g18392' => 'ugi', 'unitig_52.g17178' => 'ugi', 'unitig_8.g2934' => 'ugi', 'vmacro01122' => 'vma', 'vmacro05875' => 'vma', 'vmacro06147' => 'vma', 'vmacro16191' => 'vma', 'vmacro18293' => 'vma', 'VMungo0251G3707' => 'vmu', 'VMungo0464G1521' => 'vmu', 'VMungo1215G0205' => 'vmu', 'VMungo1383G2484' => 'vmu', 'Zm00001eb079610' => 'zma', 'Zm00001eb135990' => 'zma', 'Zm00001eb183710' => 'zma', 'Zm00001eb246020' => 'zma' ), 'gf_id' => 'HOM05D001124', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001124' ), 'data_identifier' => 'HOM05D001124', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001124', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '548', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02520' => 'bna', 'A03p06630' => 'bna', 'A05p44460' => 'bna', 'A06p08710' => 'bna', 'A06p41090' => 'bna', 'A07p32320' => 'bna', 'A08p32520' => 'bna', 'A09p10360' => 'bna', 'A10p24080' => 'bna', 'Aa31LG11G15250' => 'aar', 'Aa31LG1G1800' => 'aar', 'Aa31LG2G5120' => 'aar', 'Aa31LG2G6070' => 'aar', 'Aa31LG5G10770' => 'aar', 'Aa31sc61G90' => 'aar', 'Actinidia01352' => 'ach', 'Actinidia05983' => 'ach', 'Actinidia08133' => 'ach', 'Actinidia15101' => 'ach', 'Actinidia26379' => 'ach', 'Actinidia35778' => 'ach', 'Actinidia36123' => 'ach', 'Actinidia37436' => 'ach', 'Actinidia38730' => 'ach', 'Ah.02g128210' => 'amhyb', 'Ah.03g132990' => 'amhyb', 'Ah.14g079410' => 'amhyb', 'AL1G24640' => 'aly', 'AL2G26680' => 'aly', 'AL3G10530' => 'aly', 'AL3G45230' => 'aly', 'AL5G15230' => 'aly', 'AL5G16960' => 'aly', 'AL6G25210' => 'aly', 'Aqoxy2G00441' => 'aox', 'Aqoxy3G01236' => 'aox', 'Aqoxy5G03746' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3RQ047' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C7GMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9C8JER' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MBL6KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YXCZ83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZANX40' => 'arhy', 'AT1G12990' => 'ath', 'AT1G67880' => 'ath', 'AT2G13290' => 'ath', 'AT3G01620' => 'ath', 'AT3G26445' => 'ath', 'AT3G27540' => 'ath', 'AT5G14480' => 'ath', 'ATR0824G026' => 'atr', 'ATR1098G019' => 'atr', 'Atru.chr11.2145' => 'acertr', 'Atru.chr2.3636' => 'acertr', 'Atru.chr2.3644' => 'acertr', 'Atru.chr6.2422' => 'acertr', 'Atru.chr7.1112' => 'acertr', 'AUR62005469' => 'cqu', 'AUR62011166' => 'cqu', 'AUR62013319' => 'cqu', 'AUR62024273' => 'cqu', 'AUR62028420' => 'cqu', 'AUR62041942' => 'cqu', 'BcaB01g04969' => 'bca', 'BcaB01g06371' => 'bca', 'BcaB02g11494' => 'bca', 'BcaB03g15382' => 'bca', 'BcaB08g36994' => 'bca', 'BcaC03g13477' => 'bca', 'BcaC03g13478' => 'bca', 'BcaC03g13480' => 'bca', 'BcaC03g13481' => 'bca', 'BcaC03g13486' => 'bca', 'BcaC04g19031' => 'bca', 'BcaC04g23085' => 'bca', 'BcaC05g25094' => 'bca', 'BcaC05g25096' => 'bca', 'BcaC05g25138' => 'bca', 'BcaC05g30416' => 'bca', 'BcaC05g30455' => 'bca', 'BcaC06g30979' => 'bca', 'BcaC06g33805' => 'bca', 'BcaC08g46021' => 'bca', 'BcaNung03154' => 'bca', 'BolC2t06623H' => 'bol', 'BolC2t06632H' => 'bol', 'BolC2t06635H' => 'bol', 'BolC2t06638H' => 'bol', 'BolC3t13266H' => 'bol', 'BolC5t29776H' => 'bol', 'BolC6t38912H' => 'bol', 'BolC7t44183H' => 'bol', 'BolC9t54123H' => 'bol', 'BolC9t59107H' => 'bol', 'BraA02t05221Z' => 'bra', 'BraA03t09996Z' => 'bra', 'BraA05t23210Z' => 'bra', 'BraA06t24068Z' => 'bra', 'BraA06t27032Z' => 'bra', 'BraA08t35176Z' => 'bra', 'BraA09t36680Z' => 'bra', 'BraA10t44471Z' => 'bra', 'C02p06760' => 'bna', 'C02p06890' => 'bna', 'C02p07010' => 'bna', 'C03p07660' => 'bna', 'C05p10300' => 'bna', 'C06p38150' => 'bna', 'C07p36650' => 'bna', 'C08p15770' => 'bna', 'C09p12300' => 'bna', 'C09p62700' => 'bna', 'C09p75040' => 'bna', 'CAN.G13.1' => 'can', 'CAN.G138.4' => 'can', 'CAN.G44.6' => 'can', 'CAN.G473.19' => 'can', 'CANSAT01G0835' => 'cansat', 'CANSAT11G0246' => 'cansat', 'CANSAT11G1766' => 'cansat', 'CANSAT64G1954' => 'cansat', 'CARHR013330' => 'chi', 'CARHR060530' => 'chi', 'CARHR075300' => 'chi', 'CARHR105120' => 'chi', 'CARHR148910' => 'chi', 'CARHR198830' => 'chi', 'Carub.0001s1275' => 'cru', 'Carub.0002s1437' => 'cru', 'Carub.0003s0044' => 'cru', 'Carub.0003s2787' => 'cru', 'Carub.0005s0597' => 'cru', 'Carub.0006s1266' => 'cru', 'Ca_06935_v3' => 'car', 'Ca_13559_v3' => 'car', 'Ca_16941_v3' => 'car', 'Ca_16960_v3' => 'car', 'Ca_17775_v3' => 'car', 'Ca_30464_v3' => 'car', 'Cc06_g08160' => 'ccan', 'Cc07_g01520' => 'ccan', 'Cc11_g15810' => 'ccan', 'CDE02G2840' => 'cde', 'CDE03G0093' => 'cde', 'CDE04G2127' => 'cde', 'CDE07G1857' => 'cde', 'CDE09G1246' => 'cde', 'Cfa003412' => 'cfa', 'Cfa007341' => 'cfa', 'Cfa009220' => 'cfa', 'Ciclev10008737m.g' => 'ccl', 'Ciclev10015565m.g' => 'ccl', 'Ciclev10031761m.g' => 'ccl', 'CiPaw.03G045300' => 'cil', 'CiPaw.03G247200' => 'cil', 'CiPaw.04G029500' => 'cil', 'CiPaw.04G174000' => 'cil', 'CiPaw.05G181200' => 'cil', 'CiPaw.06G067100' => 'cil', 'ClCG05G025800' => 'cla', 'ClCG06G011400' => 'cla', 'ClCG09G019360' => 'cla', 'COL.COLO4_04827' => 'col', 'COL.COLO4_29170' => 'col', 'COL.COLO4_35131' => 'col', 'COL.COLO4_35132' => 'col', 'Cpa.g.sc33.32' => 'cpa', 'Cpa.g.sc46.29' => 'cpa', 'Cpa.g.sc796.1' => 'cpa', 'CsaV3_1G030420' => 'csa', 'CsaV3_5G027050' => 'csa', 'CsaV3_5G031040' => 'csa', 'CsaV3_UNG023130' => 'csa', 'CSS0007726' => 'camsi', 'CSS0016433' => 'camsi', 'CSS0017656' => 'camsi', 'CSS0025364' => 'camsi', 'CSS0027582' => 'camsi', 'CSS0047288' => 'camsi', 'CSS0049950' => 'camsi', 'DCAR_003843' => 'dca', 'DCAR_007052' => 'dca', 'DCAR_020884' => 'dca', 'DCAR_021730' => 'dca', 'DCAR_024423' => 'dca', 'DCAR_026509' => 'dca', 'DCAR_031158' => 'dca', 'Dinv14728' => 'din', 'Dinv15219' => 'din', 'Dinv25728' => 'din', 'Dinv33428' => 'din', 'Dinv36489' => 'din', 'Dinv41486' => 'din', 'Duzib147G0469' => 'dzi', 'Duzib168G0060' => 'dzi', 'Duzib187G1215' => 'dzi', 'Duzib248G0692' => 'dzi', 'Duzib251G0767' => 'dzi', 'Duzib264G0446' => 'dzi', 'Duzib268G0691' => 'dzi', 'ECA232G4767' => 'eca', 'ECA233G2838' => 'eca', 'ECA234G0391' => 'eca', 'ECA234G0857' => 'eca', 'ECA236G1593' => 'eca', 'ECA238G0565' => 'eca', 'ECA246G1027' => 'eca', 'ECA246G3223' => 'eca', 'ECA246G3470' => 'eca', 'EL10Ac6g13829' => 'bvu', 'EL10Ac6g14093' => 'bvu', 'EL10Ac8g18707' => 'bvu', 'Eucgr.C01369' => 'egr', 'Eucgr.H02492' => 'egr', 'Eucgr.I01733' => 'egr', 'Eucgr.J02255' => 'egr', 'Eucgr.J02257' => 'egr', 'Eucgr.J02258' => 'egr', 'FAN02G1601' => 'fan', 'FAN03G1586' => 'fan', 'FAN03G2986' => 'fan', 'FAN05G4837' => 'fan', 'FAN06G0146' => 'fan', 'FAN07G0858' => 'fan', 'FAN09G3179' => 'fan', 'FAN10G0669' => 'fan', 'FAN12G2358' => 'fan', 'FAN14G4198' => 'fan', 'FAN14G5112' => 'fan', 'FAN17G0342' => 'fan', 'FAN19G0342' => 'fan', 'FAN19G0962' => 'fan', 'FAN19G1101' => 'fan', 'FAN19G1872' => 'fan', 'FAN22G0356' => 'fan', 'FAN23G0744' => 'fan', 'FAN23G1914' => 'fan', 'FAN26G0032' => 'fan', 'FAN28G0625' => 'fan', 'FvH4_1g02710' => 'fve', 'FvH4_1g02720' => 'fve', 'FvH4_4g25670' => 'fve', 'FvH4_6g51700' => 'fve', 'FvH4_7g20170' => 'fve', 'Glyma.05G175000' => 'gma', 'Glyma.08G132300' => 'gma', 'Glyma.11G243000' => 'gma', 'Glyma.13G158900' => 'gma', 'Glyma.17G112400' => 'gma', 'Glyma.18G014100' => 'gma', 'Glyma.19G003100' => 'gma', 'Glyma.19G056500' => 'gma', 'Gohir.A01G158900' => 'ghi', 'Gohir.A05G312600' => 'ghi', 'Gohir.A05G354900' => 'ghi', 'Gohir.A07G037200' => 'ghi', 'Gohir.A09G030000' => 'ghi', 'Gohir.A12G145200' => 'ghi', 'Gohir.D01G151500' => 'ghi', 'Gohir.D04G058300' => 'ghi', 'Gohir.D05G314100' => 'ghi', 'Gohir.D07G041400' => 'ghi', 'Gohir.D09G029700' => 'ghi', 'Gohir.D12G149700' => 'ghi', 'Gorai.001G043800' => 'gra', 'Gorai.002G187800' => 'gra', 'Gorai.006G034700' => 'gra', 'Gorai.008G161200' => 'gra', 'Gorai.009G335700' => 'gra', 'Gorai.012G065000' => 'gra', 'GSVIVG01000535001' => 'vvi', 'GSVIVG01015572001' => 'vvi', 'GSVIVG01032386001' => 'vvi', 'HanXRQChr05g0138531' => 'han', 'HanXRQChr06g0174391' => 'han', 'HanXRQChr07g0199021' => 'han', 'HanXRQChr08g0208211' => 'han', 'HanXRQChr09g0255471' => 'han', 'HanXRQChr10g0315791' => 'han', 'HanXRQChr12g0371991' => 'han', 'HanXRQChr15g0475251' => 'han', 'HanXRQChr17g0540001' => 'han', 'HanXRQChr17g0548631' => 'han', 'HanXRQChr17g0569561' => 'han', 'Haze_12256' => 'cav', 'Haze_14756' => 'cav', 'Haze_25528' => 'cav', 'Hma1.2p1_0079F.1_g041020' => 'hma', 'Hma1.2p1_0818F.1_g223260' => 'hma', 'Hma1.2p1_1747F.1_g300530' => 'hma', 'HPP92_004607' => 'vpl', 'HPP92_004608' => 'vpl', 'HPP92_006181' => 'vpl', 'HPP92_012192' => 'vpl', 'HPP92_015680' => 'vpl', 'HPP92_020249' => 'vpl', 'HPP92_021376' => 'vpl', 'HPP92_024275' => 'vpl', 'Hund06031' => 'sun', 'Hund25391' => 'sun', 'Lalb_Chr07g0185371' => 'lal', 'Lalb_Chr07g0185381' => 'lal', 'Lalb_Chr12g0204011' => 'lal', 'Lalb_Chr13g0301671' => 'lal', 'Lalb_Chr14g0362851' => 'lal', 'Lalb_Chr24g0403581' => 'lal', 'Lj1g0000233' => 'lja', 'Lj2g0018120' => 'lja', 'Lj3C621T0' => 'lonja', 'Lj3P1059T14' => 'lonja', 'Lj3P611T9' => 'lonja', 'Lj3P614T13' => 'lonja', 'Lj3P615T5' => 'lonja', 'Lj4g0012315' => 'lja', 'Lj4g0026182' => 'lja', 'Lj6P813T16' => 'lonja', 'Lj7C427T7' => 'lonja', 'Lj7C427T8' => 'lonja', 'Lj7P600T41' => 'lonja', 'Lju41C42G17' => 'lonja', 'Lsat_1_v5_gn_0_47300' => 'lsa', 'Lsat_1_v5_gn_2_91280' => 'lsa', 'Lsat_1_v5_gn_3_30561' => 'lsa', 'Lsat_1_v5_gn_4_184321' => 'lsa', 'Lsat_1_v5_gn_4_4041' => 'lsa', 'Lsat_1_v5_gn_5_92000' => 'lsa', 'Lsat_1_v5_gn_8_152940' => 'lsa', 'Lsat_1_v5_gn_8_62401' => 'lsa', 'Manes.06G055900' => 'mes', 'Manes.12G022200' => 'mes', 'Manes.13G023300' => 'mes', 'Manes.14G115000' => 'mes', 'Manes.15G151700' => 'mes', 'Manes.17G111300' => 'mes', 'Mapoly0226s0009' => 'mpo', 'MBI02_g25363_MAGBIO' => 'mbi', 'MBI06_g00027_MAGBIO' => 'mbi', 'MBI10_g13034_MAGBIO' => 'mbi', 'MD09G1023400' => 'mdo', 'MD13G1100100' => 'mdo', 'MD15G1169200' => 'mdo', 'MD16G1101100' => 'mdo', 'MD17G1022900' => 'mdo', 'Medtr3g096150' => 'mtr', 'Medtr4g115070' => 'mtr', 'Medtr7g033325' => 'mtr', 'Medtr8g089840' => 'mtr', 'MELO3C010319.2' => 'cme', 'MELO3C011944.2' => 'cme', 'MELO3C021589.2' => 'cme', 'Migut.E00207' => 'egut', 'Migut.H00067' => 'egut', 'Migut.K00433' => 'egut', 'Migut.K00606' => 'egut', 'Migut.K01410' => 'egut', 'MSTRG.13347' => 'ama', 'MSTRG.24045' => 'ama', 'MSTRG.2428' => 'ama', 'MSTRG.26410' => 'ama', 'MSTRG.3139' => 'ama', 'MSTRG.3286' => 'ama', 'MSTRG.563' => 'ama', 'MSTRG.7941' => 'ama', 'Nitab4.5_0000028g0060' => 'nta', 'Nitab4.5_0000065g0260' => 'nta', 'Nitab4.5_0000112g0060' => 'nta', 'Nitab4.5_0000489g0120' => 'nta', 'Nitab4.5_0001776g0050' => 'nta', 'Nitab4.5_0001854g0010' => 'nta', 'Nitab4.5_0001860g0020' => 'nta', 'Nitab4.5_0004352g0010' => 'nta', 'Nitab4.5_0008716g0020' => 'nta', 'Nitab4.5_0008922g0010' => 'nta', 'Nn3g16693' => 'nnu', 'Nn4g22596' => 'nnu', 'Nn7g37639' => 'nnu', 'Oeu001701.1' => 'oeu', 'Oeu018149.1' => 'oeu', 'Oeu026220.1' => 'oeu', 'Oeu038635.1' => 'oeu', 'Oeu049176.1' => 'oeu', 'Oeu056706.1' => 'oeu', 'Oeu056937.1' => 'oeu', 'Oeu057540.1' => 'oeu', 'Os02g0594900' => 'osa', 'Os02g0595100' => 'osa', 'Os04g0477500' => 'osa', 'Os12g0611900' => 'osa', 'Peaxi162Scf00076g00020' => 'pax', 'Peaxi162Scf00128g00217' => 'pax', 'Peaxi162Scf00129g01640' => 'pax', 'Peaxi162Scf00669g00007' => 'pax', 'Peaxi162Scf00700g00421' => 'pax', 'Peaxi162Scf00801g00038' => 'pax', 'Peaxi162Scf00891g00025' => 'pax', 'PGR083G0909' => 'pgr', 'PGR119G1005' => 'pgr', 'PGR142G2236' => 'pgr', 'PGR142G3388' => 'pgr', 'PGSC0003DMG400004514' => 'stu', 'PGSC0003DMG400012635' => 'stu', 'PGSC0003DMG400015730' => 'stu', 'PGSC0003DMG400018611' => 'stu', 'PGSC0003DMG400030897' => 'stu', 'Phvul.001G254800' => 'pvu', 'Phvul.002G260100' => 'pvu', 'Phvul.003G167600' => 'pvu', 'Phvul.004G005100' => 'pvu', 'Potri.001G343600' => 'ptr', 'Potri.006G066700' => 'ptr', 'Potri.008G186000' => 'ptr', 'Potri.010G046900' => 'ptr', 'Potri.018G127900' => 'ptr', 'Pp3c20_17750' => 'ppa', 'Pp3c24_4380' => 'ppa', 'Prupe.1G245800' => 'ppe', 'Prupe.3G293400' => 'ppe', 'Prupe.7G247400' => 'ppe', 'Psat0s145g0120' => 'psa', 'Psat0s595g0040' => 'psa', 'Psat0s595g0120' => 'psa', 'Psat3g175040' => 'psa', 'Psat7g058120' => 'psa', 'PSO017G0428' => 'pso', 'PSO063G7510' => 'pso', 'PSO067G0046' => 'pso', 'PSO478G1073' => 'pso', 'PSO675G3677' => 'pso', 'PSO675G6558' => 'pso', 'PSO675G7520' => 'pso', 'PSO675G8959' => 'pso', 'QL02p074089' => 'qlo', 'QL02p089614' => 'qlo', 'QL03p057736' => 'qlo', 'RcHm_v2.0_Chr1g0364131' => 'rch', 'RcHm_v2.0_Chr2g0087801' => 'rch', 'RcHm_v2.0_Chr2g0087821' => 'rch', 'RcHm_v2.0_Chr2g0173231' => 'rch', 'RcHm_v2.0_Chr4g0433111' => 'rch', 'Rhsim03G0250300' => 'rsi', 'Rhsim08G0048400' => 'rsi', 'Rhsim10G0014800' => 'rsi', 'Rhsim12G0040100' => 'rsi', 'Rhsim12G0109700' => 'rsi', 'Sabra06G0049600' => 'sbr', 'Sabra08G0141000' => 'sbr', 'Sabra10G0021400' => 'sbr', 'Sabra16G0222900' => 'sbr', 'Sabra18G0108600' => 'sbr', 'SalBow1G0433' => 'sbo', 'SalBow1G2038' => 'sbo', 'SalBow1G5003' => 'sbo', 'SalBow7G1197' => 'sbo', 'SalBow8G3506' => 'sbo', 'Sc03g0007300' => 'sci', 'Sc11g0000950' => 'sci', 'Sc14g0008750' => 'sci', 'Sc18g0000420' => 'sci', 'Sed0006754' => 'sed', 'Sed0008741' => 'sed', 'Sed0017172' => 'sed', 'Sed0018925' => 'sed', 'Sed0023326' => 'sed', 'Sed0025909' => 'sed', 'SEGI_05333' => 'sgi', 'SEGI_10362' => 'sgi', 'SEGI_13380' => 'sgi', 'SEGI_24306' => 'sgi', 'SEGI_29077' => 'sgi', 'SEGI_29095' => 'sgi', 'SEGI_36534' => 'sgi', 'SEGI_37506' => 'sgi', 'SEGI_38321' => 'sgi', 'SGA_v2.0_scaffold307G48031' => 'sas', 'SGA_v2.0_scaffold47G17507' => 'sas', 'SGA_v2.0_scaffold63G21736' => 'sas', 'SGA_v2.0_scaffold87G27070' => 'sas', 'SHI17794' => 'shi', 'SHI28851' => 'shi', 'SMO165G0155' => 'smo', 'SMO340G0217' => 'smo', 'SMO367G1210' => 'smo', 'Solyc02g093430.3' => 'sly', 'Solyc05g013580.4' => 'sly', 'Solyc07g008030.3' => 'sly', 'Solyc12g035470.2' => 'sly', 'Sopen02g038020' => 'spe', 'Sopen05g008490' => 'spe', 'Sopen07g003910' => 'spe', 'Sopen12g015240' => 'spe', 'Sp1g11550' => 'spa', 'Sp2g16710' => 'spa', 'Sp3g00430' => 'spa', 'Sp3g26780' => 'spa', 'Sp5g22900' => 'spa', 'Sp6g29530' => 'spa', 'TAR371G0794' => 'tar', 'TAR374G0164' => 'tar', 'TAR622G0165' => 'tar', 'TAR626G0929' => 'tar', 'TAR629G2155' => 'tar', 'THA.LOC104805282' => 'tha', 'THA.LOC104805363' => 'tha', 'THA.LOC104808968' => 'tha', 'THA.LOC104821093' => 'tha', 'THA.LOC104823953' => 'tha', 'THA.LOC104825562' => 'tha', 'THA.LOC104825665' => 'tha', 'Thecc.02G261400' => 'tca', 'Thecc.04G019200' => 'tca', 'Thecc.09G130400' => 'tca', 'Thhalv10004374m.g' => 'esa', 'Thhalv10007850m.g' => 'esa', 'Thhalv10013782m.g' => 'esa', 'Thhalv10018686m.g' => 'esa', 'Thhalv10020899m.g' => 'esa', 'Thhalv10022755m.g' => 'esa', 'TPR.G23851' => 'tpr', 'TPR.G26500' => 'tpr', 'TPR.G27267' => 'tpr', 'TPR.G32001' => 'tpr', 'TPR.G6251' => 'tpr', 'TPR.G8167' => 'tpr', 'TWI12G1330' => 'twi', 'TWI18G1239' => 'twi', 'TWI34G0979' => 'twi', 'TWI36G0670' => 'twi', 'TWI36G0707' => 'twi', 'TWI56G0233' => 'twi', 'TWI75G1809' => 'twi', 'unitig_21.g20874' => 'ugi', 'unitig_26.g10343' => 'ugi', 'unitig_46.g18392' => 'ugi', 'unitig_52.g17178' => 'ugi', 'unitig_8.g2934' => 'ugi', 'vmacro01122' => 'vma', 'vmacro05875' => 'vma', 'vmacro06147' => 'vma', 'vmacro16191' => 'vma', 'vmacro18293' => 'vma', 'VMungo0251G3707' => 'vmu', 'VMungo0464G1521' => 'vmu', 'VMungo1215G0205' => 'vmu', 'VMungo1383G2484' => 'vmu', 'Zm00001eb079610' => 'zma', 'Zm00001eb135990' => 'zma', 'Zm00001eb183710' => 'zma', 'Zm00001eb246020' => 'zma' ) $gf_id = 'HOM05D001124' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001124' ) $data_identifier = 'HOM05D001124' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 6, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 7, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 21, 'bol' => (int) 10, 'bra' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 6, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 9, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 21, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 8, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 10, 'lsa' => (int) 8, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 8, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 9, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb246020' $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' => 'HOM05D001124', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '548', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02520' => 'bna', 'A03p06630' => 'bna', 'A05p44460' => 'bna', 'A06p08710' => 'bna', 'A06p41090' => 'bna', 'A07p32320' => 'bna', 'A08p32520' => 'bna', 'A09p10360' => 'bna', 'A10p24080' => 'bna', 'Aa31LG11G15250' => 'aar', 'Aa31LG1G1800' => 'aar', 'Aa31LG2G5120' => 'aar', 'Aa31LG2G6070' => 'aar', 'Aa31LG5G10770' => 'aar', 'Aa31sc61G90' => 'aar', 'Actinidia01352' => 'ach', 'Actinidia05983' => 'ach', 'Actinidia08133' => 'ach', 'Actinidia15101' => 'ach', 'Actinidia26379' => 'ach', 'Actinidia35778' => 'ach', 'Actinidia36123' => 'ach', 'Actinidia37436' => 'ach', 'Actinidia38730' => 'ach', 'Ah.02g128210' => 'amhyb', 'Ah.03g132990' => 'amhyb', 'Ah.14g079410' => 'amhyb', 'AL1G24640' => 'aly', 'AL2G26680' => 'aly', 'AL3G10530' => 'aly', 'AL3G45230' => 'aly', 'AL5G15230' => 'aly', 'AL5G16960' => 'aly', 'AL6G25210' => 'aly', 'Aqoxy2G00441' => 'aox', 'Aqoxy3G01236' => 'aox', 'Aqoxy5G03746' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3RQ047' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C7GMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9C8JER' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MBL6KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YXCZ83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZANX40' => 'arhy', 'AT1G12990' => 'ath', 'AT1G67880' => 'ath', 'AT2G13290' => 'ath', 'AT3G01620' => 'ath', 'AT3G26445' => 'ath', 'AT3G27540' => 'ath', 'AT5G14480' => 'ath', 'ATR0824G026' => 'atr', 'ATR1098G019' => 'atr', 'Atru.chr11.2145' => 'acertr', 'Atru.chr2.3636' => 'acertr', 'Atru.chr2.3644' => 'acertr', 'Atru.chr6.2422' => 'acertr', 'Atru.chr7.1112' => 'acertr', 'AUR62005469' => 'cqu', 'AUR62011166' => 'cqu', 'AUR62013319' => 'cqu', 'AUR62024273' => 'cqu', 'AUR62028420' => 'cqu', 'AUR62041942' => 'cqu', 'BcaB01g04969' => 'bca', 'BcaB01g06371' => 'bca', 'BcaB02g11494' => 'bca', 'BcaB03g15382' => 'bca', 'BcaB08g36994' => 'bca', 'BcaC03g13477' => 'bca', 'BcaC03g13478' => 'bca', 'BcaC03g13480' => 'bca', 'BcaC03g13481' => 'bca', 'BcaC03g13486' => 'bca', 'BcaC04g19031' => 'bca', 'BcaC04g23085' => 'bca', 'BcaC05g25094' => 'bca', 'BcaC05g25096' => 'bca', 'BcaC05g25138' => 'bca', 'BcaC05g30416' => 'bca', 'BcaC05g30455' => 'bca', 'BcaC06g30979' => 'bca', 'BcaC06g33805' => 'bca', 'BcaC08g46021' => 'bca', 'BcaNung03154' => 'bca', 'BolC2t06623H' => 'bol', 'BolC2t06632H' => 'bol', 'BolC2t06635H' => 'bol', 'BolC2t06638H' => 'bol', 'BolC3t13266H' => 'bol', 'BolC5t29776H' => 'bol', 'BolC6t38912H' => 'bol', 'BolC7t44183H' => 'bol', 'BolC9t54123H' => 'bol', 'BolC9t59107H' => 'bol', 'BraA02t05221Z' => 'bra', 'BraA03t09996Z' => 'bra', 'BraA05t23210Z' => 'bra', 'BraA06t24068Z' => 'bra', 'BraA06t27032Z' => 'bra', 'BraA08t35176Z' => 'bra', 'BraA09t36680Z' => 'bra', 'BraA10t44471Z' => 'bra', 'C02p06760' => 'bna', 'C02p06890' => 'bna', 'C02p07010' => 'bna', 'C03p07660' => 'bna', 'C05p10300' => 'bna', 'C06p38150' => 'bna', 'C07p36650' => 'bna', 'C08p15770' => 'bna', 'C09p12300' => 'bna', 'C09p62700' => 'bna', 'C09p75040' => 'bna', 'CAN.G13.1' => 'can', 'CAN.G138.4' => 'can', 'CAN.G44.6' => 'can', 'CAN.G473.19' => 'can', 'CANSAT01G0835' => 'cansat', 'CANSAT11G0246' => 'cansat', 'CANSAT11G1766' => 'cansat', 'CANSAT64G1954' => 'cansat', 'CARHR013330' => 'chi', 'CARHR060530' => 'chi', 'CARHR075300' => 'chi', 'CARHR105120' => 'chi', 'CARHR148910' => 'chi', 'CARHR198830' => 'chi', 'Carub.0001s1275' => 'cru', 'Carub.0002s1437' => 'cru', 'Carub.0003s0044' => 'cru', 'Carub.0003s2787' => 'cru', 'Carub.0005s0597' => 'cru', 'Carub.0006s1266' => 'cru', 'Ca_06935_v3' => 'car', 'Ca_13559_v3' => 'car', 'Ca_16941_v3' => 'car', 'Ca_16960_v3' => 'car', 'Ca_17775_v3' => 'car', 'Ca_30464_v3' => 'car', 'Cc06_g08160' => 'ccan', 'Cc07_g01520' => 'ccan', 'Cc11_g15810' => 'ccan', 'CDE02G2840' => 'cde', 'CDE03G0093' => 'cde', 'CDE04G2127' => 'cde', 'CDE07G1857' => 'cde', 'CDE09G1246' => 'cde', 'Cfa003412' => 'cfa', 'Cfa007341' => 'cfa', 'Cfa009220' => 'cfa', 'Ciclev10008737m.g' => 'ccl', 'Ciclev10015565m.g' => 'ccl', 'Ciclev10031761m.g' => 'ccl', 'CiPaw.03G045300' => 'cil', 'CiPaw.03G247200' => 'cil', 'CiPaw.04G029500' => 'cil', 'CiPaw.04G174000' => 'cil', 'CiPaw.05G181200' => 'cil', 'CiPaw.06G067100' => 'cil', 'ClCG05G025800' => 'cla', 'ClCG06G011400' => 'cla', 'ClCG09G019360' => 'cla', 'COL.COLO4_04827' => 'col', 'COL.COLO4_29170' => 'col', 'COL.COLO4_35131' => 'col', 'COL.COLO4_35132' => 'col', 'Cpa.g.sc33.32' => 'cpa', 'Cpa.g.sc46.29' => 'cpa', 'Cpa.g.sc796.1' => 'cpa', 'CsaV3_1G030420' => 'csa', 'CsaV3_5G027050' => 'csa', 'CsaV3_5G031040' => 'csa', 'CsaV3_UNG023130' => 'csa', 'CSS0007726' => 'camsi', 'CSS0016433' => 'camsi', 'CSS0017656' => 'camsi', 'CSS0025364' => 'camsi', 'CSS0027582' => 'camsi', 'CSS0047288' => 'camsi', 'CSS0049950' => 'camsi', 'DCAR_003843' => 'dca', 'DCAR_007052' => 'dca', 'DCAR_020884' => 'dca', 'DCAR_021730' => 'dca', 'DCAR_024423' => 'dca', 'DCAR_026509' => 'dca', 'DCAR_031158' => 'dca', 'Dinv14728' => 'din', 'Dinv15219' => 'din', 'Dinv25728' => 'din', 'Dinv33428' => 'din', 'Dinv36489' => 'din', 'Dinv41486' => 'din', 'Duzib147G0469' => 'dzi', 'Duzib168G0060' => 'dzi', 'Duzib187G1215' => 'dzi', 'Duzib248G0692' => 'dzi', 'Duzib251G0767' => 'dzi', 'Duzib264G0446' => 'dzi', 'Duzib268G0691' => 'dzi', 'ECA232G4767' => 'eca', 'ECA233G2838' => 'eca', 'ECA234G0391' => 'eca', 'ECA234G0857' => 'eca', 'ECA236G1593' => 'eca', 'ECA238G0565' => 'eca', 'ECA246G1027' => 'eca', 'ECA246G3223' => 'eca', 'ECA246G3470' => 'eca', 'EL10Ac6g13829' => 'bvu', 'EL10Ac6g14093' => 'bvu', 'EL10Ac8g18707' => 'bvu', 'Eucgr.C01369' => 'egr', 'Eucgr.H02492' => 'egr', 'Eucgr.I01733' => 'egr', 'Eucgr.J02255' => 'egr', 'Eucgr.J02257' => 'egr', 'Eucgr.J02258' => 'egr', 'FAN02G1601' => 'fan', 'FAN03G1586' => 'fan', 'FAN03G2986' => 'fan', 'FAN05G4837' => 'fan', 'FAN06G0146' => 'fan', 'FAN07G0858' => 'fan', 'FAN09G3179' => 'fan', 'FAN10G0669' => 'fan', 'FAN12G2358' => 'fan', 'FAN14G4198' => 'fan', 'FAN14G5112' => 'fan', 'FAN17G0342' => 'fan', 'FAN19G0342' => 'fan', 'FAN19G0962' => 'fan', 'FAN19G1101' => 'fan', 'FAN19G1872' => 'fan', 'FAN22G0356' => 'fan', 'FAN23G0744' => 'fan', 'FAN23G1914' => 'fan', 'FAN26G0032' => 'fan', 'FAN28G0625' => 'fan', 'FvH4_1g02710' => 'fve', 'FvH4_1g02720' => 'fve', 'FvH4_4g25670' => 'fve', 'FvH4_6g51700' => 'fve', 'FvH4_7g20170' => 'fve', 'Glyma.05G175000' => 'gma', 'Glyma.08G132300' => 'gma', 'Glyma.11G243000' => 'gma', 'Glyma.13G158900' => 'gma', 'Glyma.17G112400' => 'gma', 'Glyma.18G014100' => 'gma', 'Glyma.19G003100' => 'gma', 'Glyma.19G056500' => 'gma', 'Gohir.A01G158900' => 'ghi', 'Gohir.A05G312600' => 'ghi', 'Gohir.A05G354900' => 'ghi', 'Gohir.A07G037200' => 'ghi', 'Gohir.A09G030000' => 'ghi', 'Gohir.A12G145200' => 'ghi', 'Gohir.D01G151500' => 'ghi', 'Gohir.D04G058300' => 'ghi', 'Gohir.D05G314100' => 'ghi', 'Gohir.D07G041400' => 'ghi', 'Gohir.D09G029700' => 'ghi', 'Gohir.D12G149700' => 'ghi', 'Gorai.001G043800' => 'gra', 'Gorai.002G187800' => 'gra', 'Gorai.006G034700' => 'gra', 'Gorai.008G161200' => 'gra', 'Gorai.009G335700' => 'gra', 'Gorai.012G065000' => 'gra', 'GSVIVG01000535001' => 'vvi', 'GSVIVG01015572001' => 'vvi', 'GSVIVG01032386001' => 'vvi', 'HanXRQChr05g0138531' => 'han', 'HanXRQChr06g0174391' => 'han', 'HanXRQChr07g0199021' => 'han', 'HanXRQChr08g0208211' => 'han', 'HanXRQChr09g0255471' => 'han', 'HanXRQChr10g0315791' => 'han', 'HanXRQChr12g0371991' => 'han', 'HanXRQChr15g0475251' => 'han', 'HanXRQChr17g0540001' => 'han', 'HanXRQChr17g0548631' => 'han', 'HanXRQChr17g0569561' => 'han', 'Haze_12256' => 'cav', 'Haze_14756' => 'cav', 'Haze_25528' => 'cav', 'Hma1.2p1_0079F.1_g041020' => 'hma', 'Hma1.2p1_0818F.1_g223260' => 'hma', 'Hma1.2p1_1747F.1_g300530' => 'hma', 'HPP92_004607' => 'vpl', 'HPP92_004608' => 'vpl', 'HPP92_006181' => 'vpl', 'HPP92_012192' => 'vpl', 'HPP92_015680' => 'vpl', 'HPP92_020249' => 'vpl', 'HPP92_021376' => 'vpl', 'HPP92_024275' => 'vpl', 'Hund06031' => 'sun', 'Hund25391' => 'sun', 'Lalb_Chr07g0185371' => 'lal', 'Lalb_Chr07g0185381' => 'lal', 'Lalb_Chr12g0204011' => 'lal', 'Lalb_Chr13g0301671' => 'lal', 'Lalb_Chr14g0362851' => 'lal', 'Lalb_Chr24g0403581' => 'lal', 'Lj1g0000233' => 'lja', 'Lj2g0018120' => 'lja', 'Lj3C621T0' => 'lonja', 'Lj3P1059T14' => 'lonja', 'Lj3P611T9' => 'lonja', 'Lj3P614T13' => 'lonja', 'Lj3P615T5' => 'lonja', 'Lj4g0012315' => 'lja', 'Lj4g0026182' => 'lja', 'Lj6P813T16' => 'lonja', 'Lj7C427T7' => 'lonja', 'Lj7C427T8' => 'lonja', 'Lj7P600T41' => 'lonja', 'Lju41C42G17' => 'lonja', 'Lsat_1_v5_gn_0_47300' => 'lsa', 'Lsat_1_v5_gn_2_91280' => 'lsa', 'Lsat_1_v5_gn_3_30561' => 'lsa', 'Lsat_1_v5_gn_4_184321' => 'lsa', 'Lsat_1_v5_gn_4_4041' => 'lsa', 'Lsat_1_v5_gn_5_92000' => 'lsa', 'Lsat_1_v5_gn_8_152940' => 'lsa', 'Lsat_1_v5_gn_8_62401' => 'lsa', 'Manes.06G055900' => 'mes', 'Manes.12G022200' => 'mes', 'Manes.13G023300' => 'mes', 'Manes.14G115000' => 'mes', 'Manes.15G151700' => 'mes', 'Manes.17G111300' => 'mes', 'Mapoly0226s0009' => 'mpo', 'MBI02_g25363_MAGBIO' => 'mbi', 'MBI06_g00027_MAGBIO' => 'mbi', 'MBI10_g13034_MAGBIO' => 'mbi', 'MD09G1023400' => 'mdo', 'MD13G1100100' => 'mdo', 'MD15G1169200' => 'mdo', 'MD16G1101100' => 'mdo', 'MD17G1022900' => 'mdo', 'Medtr3g096150' => 'mtr', 'Medtr4g115070' => 'mtr', 'Medtr7g033325' => 'mtr', 'Medtr8g089840' => 'mtr', 'MELO3C010319.2' => 'cme', 'MELO3C011944.2' => 'cme', 'MELO3C021589.2' => 'cme', 'Migut.E00207' => 'egut', 'Migut.H00067' => 'egut', 'Migut.K00433' => 'egut', 'Migut.K00606' => 'egut', 'Migut.K01410' => 'egut', 'MSTRG.13347' => 'ama', 'MSTRG.24045' => 'ama', 'MSTRG.2428' => 'ama', 'MSTRG.26410' => 'ama', 'MSTRG.3139' => 'ama', 'MSTRG.3286' => 'ama', 'MSTRG.563' => 'ama', 'MSTRG.7941' => 'ama', 'Nitab4.5_0000028g0060' => 'nta', 'Nitab4.5_0000065g0260' => 'nta', 'Nitab4.5_0000112g0060' => 'nta', 'Nitab4.5_0000489g0120' => 'nta', 'Nitab4.5_0001776g0050' => 'nta', 'Nitab4.5_0001854g0010' => 'nta', 'Nitab4.5_0001860g0020' => 'nta', 'Nitab4.5_0004352g0010' => 'nta', 'Nitab4.5_0008716g0020' => 'nta', 'Nitab4.5_0008922g0010' => 'nta', 'Nn3g16693' => 'nnu', 'Nn4g22596' => 'nnu', 'Nn7g37639' => 'nnu', 'Oeu001701.1' => 'oeu', 'Oeu018149.1' => 'oeu', 'Oeu026220.1' => 'oeu', 'Oeu038635.1' => 'oeu', 'Oeu049176.1' => 'oeu', 'Oeu056706.1' => 'oeu', 'Oeu056937.1' => 'oeu', 'Oeu057540.1' => 'oeu', 'Os02g0594900' => 'osa', 'Os02g0595100' => 'osa', 'Os04g0477500' => 'osa', 'Os12g0611900' => 'osa', 'Peaxi162Scf00076g00020' => 'pax', 'Peaxi162Scf00128g00217' => 'pax', 'Peaxi162Scf00129g01640' => 'pax', 'Peaxi162Scf00669g00007' => 'pax', 'Peaxi162Scf00700g00421' => 'pax', 'Peaxi162Scf00801g00038' => 'pax', 'Peaxi162Scf00891g00025' => 'pax', 'PGR083G0909' => 'pgr', 'PGR119G1005' => 'pgr', 'PGR142G2236' => 'pgr', 'PGR142G3388' => 'pgr', 'PGSC0003DMG400004514' => 'stu', 'PGSC0003DMG400012635' => 'stu', 'PGSC0003DMG400015730' => 'stu', 'PGSC0003DMG400018611' => 'stu', 'PGSC0003DMG400030897' => 'stu', 'Phvul.001G254800' => 'pvu', 'Phvul.002G260100' => 'pvu', 'Phvul.003G167600' => 'pvu', 'Phvul.004G005100' => 'pvu', 'Potri.001G343600' => 'ptr', 'Potri.006G066700' => 'ptr', 'Potri.008G186000' => 'ptr', 'Potri.010G046900' => 'ptr', 'Potri.018G127900' => 'ptr', 'Pp3c20_17750' => 'ppa', 'Pp3c24_4380' => 'ppa', 'Prupe.1G245800' => 'ppe', 'Prupe.3G293400' => 'ppe', 'Prupe.7G247400' => 'ppe', 'Psat0s145g0120' => 'psa', 'Psat0s595g0040' => 'psa', 'Psat0s595g0120' => 'psa', 'Psat3g175040' => 'psa', 'Psat7g058120' => 'psa', 'PSO017G0428' => 'pso', 'PSO063G7510' => 'pso', 'PSO067G0046' => 'pso', 'PSO478G1073' => 'pso', 'PSO675G3677' => 'pso', 'PSO675G6558' => 'pso', 'PSO675G7520' => 'pso', 'PSO675G8959' => 'pso', 'QL02p074089' => 'qlo', 'QL02p089614' => 'qlo', 'QL03p057736' => 'qlo', 'RcHm_v2.0_Chr1g0364131' => 'rch', 'RcHm_v2.0_Chr2g0087801' => 'rch', 'RcHm_v2.0_Chr2g0087821' => 'rch', 'RcHm_v2.0_Chr2g0173231' => 'rch', 'RcHm_v2.0_Chr4g0433111' => 'rch', 'Rhsim03G0250300' => 'rsi', 'Rhsim08G0048400' => 'rsi', 'Rhsim10G0014800' => 'rsi', 'Rhsim12G0040100' => 'rsi', 'Rhsim12G0109700' => 'rsi', 'Sabra06G0049600' => 'sbr', 'Sabra08G0141000' => 'sbr', 'Sabra10G0021400' => 'sbr', 'Sabra16G0222900' => 'sbr', 'Sabra18G0108600' => 'sbr', 'SalBow1G0433' => 'sbo', 'SalBow1G2038' => 'sbo', 'SalBow1G5003' => 'sbo', 'SalBow7G1197' => 'sbo', 'SalBow8G3506' => 'sbo', 'Sc03g0007300' => 'sci', 'Sc11g0000950' => 'sci', 'Sc14g0008750' => 'sci', 'Sc18g0000420' => 'sci', 'Sed0006754' => 'sed', 'Sed0008741' => 'sed', 'Sed0017172' => 'sed', 'Sed0018925' => 'sed', 'Sed0023326' => 'sed', 'Sed0025909' => 'sed', 'SEGI_05333' => 'sgi', 'SEGI_10362' => 'sgi', 'SEGI_13380' => 'sgi', 'SEGI_24306' => 'sgi', 'SEGI_29077' => 'sgi', 'SEGI_29095' => 'sgi', 'SEGI_36534' => 'sgi', 'SEGI_37506' => 'sgi', 'SEGI_38321' => 'sgi', 'SGA_v2.0_scaffold307G48031' => 'sas', 'SGA_v2.0_scaffold47G17507' => 'sas', 'SGA_v2.0_scaffold63G21736' => 'sas', 'SGA_v2.0_scaffold87G27070' => 'sas', 'SHI17794' => 'shi', 'SHI28851' => 'shi', 'SMO165G0155' => 'smo', 'SMO340G0217' => 'smo', 'SMO367G1210' => 'smo', 'Solyc02g093430.3' => 'sly', 'Solyc05g013580.4' => 'sly', 'Solyc07g008030.3' => 'sly', 'Solyc12g035470.2' => 'sly', 'Sopen02g038020' => 'spe', 'Sopen05g008490' => 'spe', 'Sopen07g003910' => 'spe', 'Sopen12g015240' => 'spe', 'Sp1g11550' => 'spa', 'Sp2g16710' => 'spa', 'Sp3g00430' => 'spa', 'Sp3g26780' => 'spa', 'Sp5g22900' => 'spa', 'Sp6g29530' => 'spa', 'TAR371G0794' => 'tar', 'TAR374G0164' => 'tar', 'TAR622G0165' => 'tar', 'TAR626G0929' => 'tar', 'TAR629G2155' => 'tar', 'THA.LOC104805282' => 'tha', 'THA.LOC104805363' => 'tha', 'THA.LOC104808968' => 'tha', 'THA.LOC104821093' => 'tha', 'THA.LOC104823953' => 'tha', 'THA.LOC104825562' => 'tha', 'THA.LOC104825665' => 'tha', 'Thecc.02G261400' => 'tca', 'Thecc.04G019200' => 'tca', 'Thecc.09G130400' => 'tca', 'Thhalv10004374m.g' => 'esa', 'Thhalv10007850m.g' => 'esa', 'Thhalv10013782m.g' => 'esa', 'Thhalv10018686m.g' => 'esa', 'Thhalv10020899m.g' => 'esa', 'Thhalv10022755m.g' => 'esa', 'TPR.G23851' => 'tpr', 'TPR.G26500' => 'tpr', 'TPR.G27267' => 'tpr', 'TPR.G32001' => 'tpr', 'TPR.G6251' => 'tpr', 'TPR.G8167' => 'tpr', 'TWI12G1330' => 'twi', 'TWI18G1239' => 'twi', 'TWI34G0979' => 'twi', 'TWI36G0670' => 'twi', 'TWI36G0707' => 'twi', 'TWI56G0233' => 'twi', 'TWI75G1809' => 'twi', 'unitig_21.g20874' => 'ugi', 'unitig_26.g10343' => 'ugi', 'unitig_46.g18392' => 'ugi', 'unitig_52.g17178' => 'ugi', 'unitig_8.g2934' => 'ugi', 'vmacro01122' => 'vma', 'vmacro05875' => 'vma', 'vmacro06147' => 'vma', 'vmacro16191' => 'vma', 'vmacro18293' => 'vma', 'VMungo0251G3707' => 'vmu', 'VMungo0464G1521' => 'vmu', 'VMungo1215G0205' => 'vmu', 'VMungo1383G2484' => 'vmu', 'Zm00001eb079610' => 'zma', 'Zm00001eb135990' => 'zma', 'Zm00001eb183710' => 'zma', 'Zm00001eb246020' => 'zma' ), 'gf_id' => 'HOM05D001124', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001124' ), 'data_identifier' => 'HOM05D001124', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001124', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '548', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02520' => 'bna', 'A03p06630' => 'bna', 'A05p44460' => 'bna', 'A06p08710' => 'bna', 'A06p41090' => 'bna', 'A07p32320' => 'bna', 'A08p32520' => 'bna', 'A09p10360' => 'bna', 'A10p24080' => 'bna', 'Aa31LG11G15250' => 'aar', 'Aa31LG1G1800' => 'aar', 'Aa31LG2G5120' => 'aar', 'Aa31LG2G6070' => 'aar', 'Aa31LG5G10770' => 'aar', 'Aa31sc61G90' => 'aar', 'Actinidia01352' => 'ach', 'Actinidia05983' => 'ach', 'Actinidia08133' => 'ach', 'Actinidia15101' => 'ach', 'Actinidia26379' => 'ach', 'Actinidia35778' => 'ach', 'Actinidia36123' => 'ach', 'Actinidia37436' => 'ach', 'Actinidia38730' => 'ach', 'Ah.02g128210' => 'amhyb', 'Ah.03g132990' => 'amhyb', 'Ah.14g079410' => 'amhyb', 'AL1G24640' => 'aly', 'AL2G26680' => 'aly', 'AL3G10530' => 'aly', 'AL3G45230' => 'aly', 'AL5G15230' => 'aly', 'AL5G16960' => 'aly', 'AL6G25210' => 'aly', 'Aqoxy2G00441' => 'aox', 'Aqoxy3G01236' => 'aox', 'Aqoxy5G03746' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3RQ047' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C7GMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9C8JER' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MBL6KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YXCZ83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZANX40' => 'arhy', 'AT1G12990' => 'ath', 'AT1G67880' => 'ath', 'AT2G13290' => 'ath', 'AT3G01620' => 'ath', 'AT3G26445' => 'ath', 'AT3G27540' => 'ath', 'AT5G14480' => 'ath', 'ATR0824G026' => 'atr', 'ATR1098G019' => 'atr', 'Atru.chr11.2145' => 'acertr', 'Atru.chr2.3636' => 'acertr', 'Atru.chr2.3644' => 'acertr', 'Atru.chr6.2422' => 'acertr', 'Atru.chr7.1112' => 'acertr', 'AUR62005469' => 'cqu', 'AUR62011166' => 'cqu', 'AUR62013319' => 'cqu', 'AUR62024273' => 'cqu', 'AUR62028420' => 'cqu', 'AUR62041942' => 'cqu', 'BcaB01g04969' => 'bca', 'BcaB01g06371' => 'bca', 'BcaB02g11494' => 'bca', 'BcaB03g15382' => 'bca', 'BcaB08g36994' => 'bca', 'BcaC03g13477' => 'bca', 'BcaC03g13478' => 'bca', 'BcaC03g13480' => 'bca', 'BcaC03g13481' => 'bca', 'BcaC03g13486' => 'bca', 'BcaC04g19031' => 'bca', 'BcaC04g23085' => 'bca', 'BcaC05g25094' => 'bca', 'BcaC05g25096' => 'bca', 'BcaC05g25138' => 'bca', 'BcaC05g30416' => 'bca', 'BcaC05g30455' => 'bca', 'BcaC06g30979' => 'bca', 'BcaC06g33805' => 'bca', 'BcaC08g46021' => 'bca', 'BcaNung03154' => 'bca', 'BolC2t06623H' => 'bol', 'BolC2t06632H' => 'bol', 'BolC2t06635H' => 'bol', 'BolC2t06638H' => 'bol', 'BolC3t13266H' => 'bol', 'BolC5t29776H' => 'bol', 'BolC6t38912H' => 'bol', 'BolC7t44183H' => 'bol', 'BolC9t54123H' => 'bol', 'BolC9t59107H' => 'bol', 'BraA02t05221Z' => 'bra', 'BraA03t09996Z' => 'bra', 'BraA05t23210Z' => 'bra', 'BraA06t24068Z' => 'bra', 'BraA06t27032Z' => 'bra', 'BraA08t35176Z' => 'bra', 'BraA09t36680Z' => 'bra', 'BraA10t44471Z' => 'bra', 'C02p06760' => 'bna', 'C02p06890' => 'bna', 'C02p07010' => 'bna', 'C03p07660' => 'bna', 'C05p10300' => 'bna', 'C06p38150' => 'bna', 'C07p36650' => 'bna', 'C08p15770' => 'bna', 'C09p12300' => 'bna', 'C09p62700' => 'bna', 'C09p75040' => 'bna', 'CAN.G13.1' => 'can', 'CAN.G138.4' => 'can', 'CAN.G44.6' => 'can', 'CAN.G473.19' => 'can', 'CANSAT01G0835' => 'cansat', 'CANSAT11G0246' => 'cansat', 'CANSAT11G1766' => 'cansat', 'CANSAT64G1954' => 'cansat', 'CARHR013330' => 'chi', 'CARHR060530' => 'chi', 'CARHR075300' => 'chi', 'CARHR105120' => 'chi', 'CARHR148910' => 'chi', 'CARHR198830' => 'chi', 'Carub.0001s1275' => 'cru', 'Carub.0002s1437' => 'cru', 'Carub.0003s0044' => 'cru', 'Carub.0003s2787' => 'cru', 'Carub.0005s0597' => 'cru', 'Carub.0006s1266' => 'cru', 'Ca_06935_v3' => 'car', 'Ca_13559_v3' => 'car', 'Ca_16941_v3' => 'car', 'Ca_16960_v3' => 'car', 'Ca_17775_v3' => 'car', 'Ca_30464_v3' => 'car', 'Cc06_g08160' => 'ccan', 'Cc07_g01520' => 'ccan', 'Cc11_g15810' => 'ccan', 'CDE02G2840' => 'cde', 'CDE03G0093' => 'cde', 'CDE04G2127' => 'cde', 'CDE07G1857' => 'cde', 'CDE09G1246' => 'cde', 'Cfa003412' => 'cfa', 'Cfa007341' => 'cfa', 'Cfa009220' => 'cfa', 'Ciclev10008737m.g' => 'ccl', 'Ciclev10015565m.g' => 'ccl', 'Ciclev10031761m.g' => 'ccl', 'CiPaw.03G045300' => 'cil', 'CiPaw.03G247200' => 'cil', 'CiPaw.04G029500' => 'cil', 'CiPaw.04G174000' => 'cil', 'CiPaw.05G181200' => 'cil', 'CiPaw.06G067100' => 'cil', 'ClCG05G025800' => 'cla', 'ClCG06G011400' => 'cla', 'ClCG09G019360' => 'cla', 'COL.COLO4_04827' => 'col', 'COL.COLO4_29170' => 'col', 'COL.COLO4_35131' => 'col', 'COL.COLO4_35132' => 'col', 'Cpa.g.sc33.32' => 'cpa', 'Cpa.g.sc46.29' => 'cpa', 'Cpa.g.sc796.1' => 'cpa', 'CsaV3_1G030420' => 'csa', 'CsaV3_5G027050' => 'csa', 'CsaV3_5G031040' => 'csa', 'CsaV3_UNG023130' => 'csa', 'CSS0007726' => 'camsi', 'CSS0016433' => 'camsi', 'CSS0017656' => 'camsi', 'CSS0025364' => 'camsi', 'CSS0027582' => 'camsi', 'CSS0047288' => 'camsi', 'CSS0049950' => 'camsi', 'DCAR_003843' => 'dca', 'DCAR_007052' => 'dca', 'DCAR_020884' => 'dca', 'DCAR_021730' => 'dca', 'DCAR_024423' => 'dca', 'DCAR_026509' => 'dca', 'DCAR_031158' => 'dca', 'Dinv14728' => 'din', 'Dinv15219' => 'din', 'Dinv25728' => 'din', 'Dinv33428' => 'din', 'Dinv36489' => 'din', 'Dinv41486' => 'din', 'Duzib147G0469' => 'dzi', 'Duzib168G0060' => 'dzi', 'Duzib187G1215' => 'dzi', 'Duzib248G0692' => 'dzi', 'Duzib251G0767' => 'dzi', 'Duzib264G0446' => 'dzi', 'Duzib268G0691' => 'dzi', 'ECA232G4767' => 'eca', 'ECA233G2838' => 'eca', 'ECA234G0391' => 'eca', 'ECA234G0857' => 'eca', 'ECA236G1593' => 'eca', 'ECA238G0565' => 'eca', 'ECA246G1027' => 'eca', 'ECA246G3223' => 'eca', 'ECA246G3470' => 'eca', 'EL10Ac6g13829' => 'bvu', 'EL10Ac6g14093' => 'bvu', 'EL10Ac8g18707' => 'bvu', 'Eucgr.C01369' => 'egr', 'Eucgr.H02492' => 'egr', 'Eucgr.I01733' => 'egr', 'Eucgr.J02255' => 'egr', 'Eucgr.J02257' => 'egr', 'Eucgr.J02258' => 'egr', 'FAN02G1601' => 'fan', 'FAN03G1586' => 'fan', 'FAN03G2986' => 'fan', 'FAN05G4837' => 'fan', 'FAN06G0146' => 'fan', 'FAN07G0858' => 'fan', 'FAN09G3179' => 'fan', 'FAN10G0669' => 'fan', 'FAN12G2358' => 'fan', 'FAN14G4198' => 'fan', 'FAN14G5112' => 'fan', 'FAN17G0342' => 'fan', 'FAN19G0342' => 'fan', 'FAN19G0962' => 'fan', 'FAN19G1101' => 'fan', 'FAN19G1872' => 'fan', 'FAN22G0356' => 'fan', 'FAN23G0744' => 'fan', 'FAN23G1914' => 'fan', 'FAN26G0032' => 'fan', 'FAN28G0625' => 'fan', 'FvH4_1g02710' => 'fve', 'FvH4_1g02720' => 'fve', 'FvH4_4g25670' => 'fve', 'FvH4_6g51700' => 'fve', 'FvH4_7g20170' => 'fve', 'Glyma.05G175000' => 'gma', 'Glyma.08G132300' => 'gma', 'Glyma.11G243000' => 'gma', 'Glyma.13G158900' => 'gma', 'Glyma.17G112400' => 'gma', 'Glyma.18G014100' => 'gma', 'Glyma.19G003100' => 'gma', 'Glyma.19G056500' => 'gma', 'Gohir.A01G158900' => 'ghi', 'Gohir.A05G312600' => 'ghi', 'Gohir.A05G354900' => 'ghi', 'Gohir.A07G037200' => 'ghi', 'Gohir.A09G030000' => 'ghi', 'Gohir.A12G145200' => 'ghi', 'Gohir.D01G151500' => 'ghi', 'Gohir.D04G058300' => 'ghi', 'Gohir.D05G314100' => 'ghi', 'Gohir.D07G041400' => 'ghi', 'Gohir.D09G029700' => 'ghi', 'Gohir.D12G149700' => 'ghi', 'Gorai.001G043800' => 'gra', 'Gorai.002G187800' => 'gra', 'Gorai.006G034700' => 'gra', 'Gorai.008G161200' => 'gra', 'Gorai.009G335700' => 'gra', 'Gorai.012G065000' => 'gra', 'GSVIVG01000535001' => 'vvi', 'GSVIVG01015572001' => 'vvi', 'GSVIVG01032386001' => 'vvi', 'HanXRQChr05g0138531' => 'han', 'HanXRQChr06g0174391' => 'han', 'HanXRQChr07g0199021' => 'han', 'HanXRQChr08g0208211' => 'han', 'HanXRQChr09g0255471' => 'han', 'HanXRQChr10g0315791' => 'han', 'HanXRQChr12g0371991' => 'han', 'HanXRQChr15g0475251' => 'han', 'HanXRQChr17g0540001' => 'han', 'HanXRQChr17g0548631' => 'han', 'HanXRQChr17g0569561' => 'han', 'Haze_12256' => 'cav', 'Haze_14756' => 'cav', 'Haze_25528' => 'cav', 'Hma1.2p1_0079F.1_g041020' => 'hma', 'Hma1.2p1_0818F.1_g223260' => 'hma', 'Hma1.2p1_1747F.1_g300530' => 'hma', 'HPP92_004607' => 'vpl', 'HPP92_004608' => 'vpl', 'HPP92_006181' => 'vpl', 'HPP92_012192' => 'vpl', 'HPP92_015680' => 'vpl', 'HPP92_020249' => 'vpl', 'HPP92_021376' => 'vpl', 'HPP92_024275' => 'vpl', 'Hund06031' => 'sun', 'Hund25391' => 'sun', 'Lalb_Chr07g0185371' => 'lal', 'Lalb_Chr07g0185381' => 'lal', 'Lalb_Chr12g0204011' => 'lal', 'Lalb_Chr13g0301671' => 'lal', 'Lalb_Chr14g0362851' => 'lal', 'Lalb_Chr24g0403581' => 'lal', 'Lj1g0000233' => 'lja', 'Lj2g0018120' => 'lja', 'Lj3C621T0' => 'lonja', 'Lj3P1059T14' => 'lonja', 'Lj3P611T9' => 'lonja', 'Lj3P614T13' => 'lonja', 'Lj3P615T5' => 'lonja', 'Lj4g0012315' => 'lja', 'Lj4g0026182' => 'lja', 'Lj6P813T16' => 'lonja', 'Lj7C427T7' => 'lonja', 'Lj7C427T8' => 'lonja', 'Lj7P600T41' => 'lonja', 'Lju41C42G17' => 'lonja', 'Lsat_1_v5_gn_0_47300' => 'lsa', 'Lsat_1_v5_gn_2_91280' => 'lsa', 'Lsat_1_v5_gn_3_30561' => 'lsa', 'Lsat_1_v5_gn_4_184321' => 'lsa', 'Lsat_1_v5_gn_4_4041' => 'lsa', 'Lsat_1_v5_gn_5_92000' => 'lsa', 'Lsat_1_v5_gn_8_152940' => 'lsa', 'Lsat_1_v5_gn_8_62401' => 'lsa', 'Manes.06G055900' => 'mes', 'Manes.12G022200' => 'mes', 'Manes.13G023300' => 'mes', 'Manes.14G115000' => 'mes', 'Manes.15G151700' => 'mes', 'Manes.17G111300' => 'mes', 'Mapoly0226s0009' => 'mpo', 'MBI02_g25363_MAGBIO' => 'mbi', 'MBI06_g00027_MAGBIO' => 'mbi', 'MBI10_g13034_MAGBIO' => 'mbi', 'MD09G1023400' => 'mdo', 'MD13G1100100' => 'mdo', 'MD15G1169200' => 'mdo', 'MD16G1101100' => 'mdo', 'MD17G1022900' => 'mdo', 'Medtr3g096150' => 'mtr', 'Medtr4g115070' => 'mtr', 'Medtr7g033325' => 'mtr', 'Medtr8g089840' => 'mtr', 'MELO3C010319.2' => 'cme', 'MELO3C011944.2' => 'cme', 'MELO3C021589.2' => 'cme', 'Migut.E00207' => 'egut', 'Migut.H00067' => 'egut', 'Migut.K00433' => 'egut', 'Migut.K00606' => 'egut', 'Migut.K01410' => 'egut', 'MSTRG.13347' => 'ama', 'MSTRG.24045' => 'ama', 'MSTRG.2428' => 'ama', 'MSTRG.26410' => 'ama', 'MSTRG.3139' => 'ama', 'MSTRG.3286' => 'ama', 'MSTRG.563' => 'ama', 'MSTRG.7941' => 'ama', 'Nitab4.5_0000028g0060' => 'nta', 'Nitab4.5_0000065g0260' => 'nta', 'Nitab4.5_0000112g0060' => 'nta', 'Nitab4.5_0000489g0120' => 'nta', 'Nitab4.5_0001776g0050' => 'nta', 'Nitab4.5_0001854g0010' => 'nta', 'Nitab4.5_0001860g0020' => 'nta', 'Nitab4.5_0004352g0010' => 'nta', 'Nitab4.5_0008716g0020' => 'nta', 'Nitab4.5_0008922g0010' => 'nta', 'Nn3g16693' => 'nnu', 'Nn4g22596' => 'nnu', 'Nn7g37639' => 'nnu', 'Oeu001701.1' => 'oeu', 'Oeu018149.1' => 'oeu', 'Oeu026220.1' => 'oeu', 'Oeu038635.1' => 'oeu', 'Oeu049176.1' => 'oeu', 'Oeu056706.1' => 'oeu', 'Oeu056937.1' => 'oeu', 'Oeu057540.1' => 'oeu', 'Os02g0594900' => 'osa', 'Os02g0595100' => 'osa', 'Os04g0477500' => 'osa', 'Os12g0611900' => 'osa', 'Peaxi162Scf00076g00020' => 'pax', 'Peaxi162Scf00128g00217' => 'pax', 'Peaxi162Scf00129g01640' => 'pax', 'Peaxi162Scf00669g00007' => 'pax', 'Peaxi162Scf00700g00421' => 'pax', 'Peaxi162Scf00801g00038' => 'pax', 'Peaxi162Scf00891g00025' => 'pax', 'PGR083G0909' => 'pgr', 'PGR119G1005' => 'pgr', 'PGR142G2236' => 'pgr', 'PGR142G3388' => 'pgr', 'PGSC0003DMG400004514' => 'stu', 'PGSC0003DMG400012635' => 'stu', 'PGSC0003DMG400015730' => 'stu', 'PGSC0003DMG400018611' => 'stu', 'PGSC0003DMG400030897' => 'stu', 'Phvul.001G254800' => 'pvu', 'Phvul.002G260100' => 'pvu', 'Phvul.003G167600' => 'pvu', 'Phvul.004G005100' => 'pvu', 'Potri.001G343600' => 'ptr', 'Potri.006G066700' => 'ptr', 'Potri.008G186000' => 'ptr', 'Potri.010G046900' => 'ptr', 'Potri.018G127900' => 'ptr', 'Pp3c20_17750' => 'ppa', 'Pp3c24_4380' => 'ppa', 'Prupe.1G245800' => 'ppe', 'Prupe.3G293400' => 'ppe', 'Prupe.7G247400' => 'ppe', 'Psat0s145g0120' => 'psa', 'Psat0s595g0040' => 'psa', 'Psat0s595g0120' => 'psa', 'Psat3g175040' => 'psa', 'Psat7g058120' => 'psa', 'PSO017G0428' => 'pso', 'PSO063G7510' => 'pso', 'PSO067G0046' => 'pso', 'PSO478G1073' => 'pso', 'PSO675G3677' => 'pso', 'PSO675G6558' => 'pso', 'PSO675G7520' => 'pso', 'PSO675G8959' => 'pso', 'QL02p074089' => 'qlo', 'QL02p089614' => 'qlo', 'QL03p057736' => 'qlo', 'RcHm_v2.0_Chr1g0364131' => 'rch', 'RcHm_v2.0_Chr2g0087801' => 'rch', 'RcHm_v2.0_Chr2g0087821' => 'rch', 'RcHm_v2.0_Chr2g0173231' => 'rch', 'RcHm_v2.0_Chr4g0433111' => 'rch', 'Rhsim03G0250300' => 'rsi', 'Rhsim08G0048400' => 'rsi', 'Rhsim10G0014800' => 'rsi', 'Rhsim12G0040100' => 'rsi', 'Rhsim12G0109700' => 'rsi', 'Sabra06G0049600' => 'sbr', 'Sabra08G0141000' => 'sbr', 'Sabra10G0021400' => 'sbr', 'Sabra16G0222900' => 'sbr', 'Sabra18G0108600' => 'sbr', 'SalBow1G0433' => 'sbo', 'SalBow1G2038' => 'sbo', 'SalBow1G5003' => 'sbo', 'SalBow7G1197' => 'sbo', 'SalBow8G3506' => 'sbo', 'Sc03g0007300' => 'sci', 'Sc11g0000950' => 'sci', 'Sc14g0008750' => 'sci', 'Sc18g0000420' => 'sci', 'Sed0006754' => 'sed', 'Sed0008741' => 'sed', 'Sed0017172' => 'sed', 'Sed0018925' => 'sed', 'Sed0023326' => 'sed', 'Sed0025909' => 'sed', 'SEGI_05333' => 'sgi', 'SEGI_10362' => 'sgi', 'SEGI_13380' => 'sgi', 'SEGI_24306' => 'sgi', 'SEGI_29077' => 'sgi', 'SEGI_29095' => 'sgi', 'SEGI_36534' => 'sgi', 'SEGI_37506' => 'sgi', 'SEGI_38321' => 'sgi', 'SGA_v2.0_scaffold307G48031' => 'sas', 'SGA_v2.0_scaffold47G17507' => 'sas', 'SGA_v2.0_scaffold63G21736' => 'sas', 'SGA_v2.0_scaffold87G27070' => 'sas', 'SHI17794' => 'shi', 'SHI28851' => 'shi', 'SMO165G0155' => 'smo', 'SMO340G0217' => 'smo', 'SMO367G1210' => 'smo', 'Solyc02g093430.3' => 'sly', 'Solyc05g013580.4' => 'sly', 'Solyc07g008030.3' => 'sly', 'Solyc12g035470.2' => 'sly', 'Sopen02g038020' => 'spe', 'Sopen05g008490' => 'spe', 'Sopen07g003910' => 'spe', 'Sopen12g015240' => 'spe', 'Sp1g11550' => 'spa', 'Sp2g16710' => 'spa', 'Sp3g00430' => 'spa', 'Sp3g26780' => 'spa', 'Sp5g22900' => 'spa', 'Sp6g29530' => 'spa', 'TAR371G0794' => 'tar', 'TAR374G0164' => 'tar', 'TAR622G0165' => 'tar', 'TAR626G0929' => 'tar', 'TAR629G2155' => 'tar', 'THA.LOC104805282' => 'tha', 'THA.LOC104805363' => 'tha', 'THA.LOC104808968' => 'tha', 'THA.LOC104821093' => 'tha', 'THA.LOC104823953' => 'tha', 'THA.LOC104825562' => 'tha', 'THA.LOC104825665' => 'tha', 'Thecc.02G261400' => 'tca', 'Thecc.04G019200' => 'tca', 'Thecc.09G130400' => 'tca', 'Thhalv10004374m.g' => 'esa', 'Thhalv10007850m.g' => 'esa', 'Thhalv10013782m.g' => 'esa', 'Thhalv10018686m.g' => 'esa', 'Thhalv10020899m.g' => 'esa', 'Thhalv10022755m.g' => 'esa', 'TPR.G23851' => 'tpr', 'TPR.G26500' => 'tpr', 'TPR.G27267' => 'tpr', 'TPR.G32001' => 'tpr', 'TPR.G6251' => 'tpr', 'TPR.G8167' => 'tpr', 'TWI12G1330' => 'twi', 'TWI18G1239' => 'twi', 'TWI34G0979' => 'twi', 'TWI36G0670' => 'twi', 'TWI36G0707' => 'twi', 'TWI56G0233' => 'twi', 'TWI75G1809' => 'twi', 'unitig_21.g20874' => 'ugi', 'unitig_26.g10343' => 'ugi', 'unitig_46.g18392' => 'ugi', 'unitig_52.g17178' => 'ugi', 'unitig_8.g2934' => 'ugi', 'vmacro01122' => 'vma', 'vmacro05875' => 'vma', 'vmacro06147' => 'vma', 'vmacro16191' => 'vma', 'vmacro18293' => 'vma', 'VMungo0251G3707' => 'vmu', 'VMungo0464G1521' => 'vmu', 'VMungo1215G0205' => 'vmu', 'VMungo1383G2484' => 'vmu', 'Zm00001eb079610' => 'zma', 'Zm00001eb135990' => 'zma', 'Zm00001eb183710' => 'zma', 'Zm00001eb246020' => 'zma' ) $gf_id = 'HOM05D001124' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001124' ) $data_identifier = 'HOM05D001124' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 6, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 7, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 21, 'bol' => (int) 10, 'bra' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 6, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 9, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 21, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 8, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 10, 'lsa' => (int) 8, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 8, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 9, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb246020' $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' => 'HOM05D001124', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '548', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02520' => 'bna', 'A03p06630' => 'bna', 'A05p44460' => 'bna', 'A06p08710' => 'bna', 'A06p41090' => 'bna', 'A07p32320' => 'bna', 'A08p32520' => 'bna', 'A09p10360' => 'bna', 'A10p24080' => 'bna', 'Aa31LG11G15250' => 'aar', 'Aa31LG1G1800' => 'aar', 'Aa31LG2G5120' => 'aar', 'Aa31LG2G6070' => 'aar', 'Aa31LG5G10770' => 'aar', 'Aa31sc61G90' => 'aar', 'Actinidia01352' => 'ach', 'Actinidia05983' => 'ach', 'Actinidia08133' => 'ach', 'Actinidia15101' => 'ach', 'Actinidia26379' => 'ach', 'Actinidia35778' => 'ach', 'Actinidia36123' => 'ach', 'Actinidia37436' => 'ach', 'Actinidia38730' => 'ach', 'Ah.02g128210' => 'amhyb', 'Ah.03g132990' => 'amhyb', 'Ah.14g079410' => 'amhyb', 'AL1G24640' => 'aly', 'AL2G26680' => 'aly', 'AL3G10530' => 'aly', 'AL3G45230' => 'aly', 'AL5G15230' => 'aly', 'AL5G16960' => 'aly', 'AL6G25210' => 'aly', 'Aqoxy2G00441' => 'aox', 'Aqoxy3G01236' => 'aox', 'Aqoxy5G03746' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3RQ047' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C7GMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9C8JER' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MBL6KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YXCZ83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZANX40' => 'arhy', 'AT1G12990' => 'ath', 'AT1G67880' => 'ath', 'AT2G13290' => 'ath', 'AT3G01620' => 'ath', 'AT3G26445' => 'ath', 'AT3G27540' => 'ath', 'AT5G14480' => 'ath', 'ATR0824G026' => 'atr', 'ATR1098G019' => 'atr', 'Atru.chr11.2145' => 'acertr', 'Atru.chr2.3636' => 'acertr', 'Atru.chr2.3644' => 'acertr', 'Atru.chr6.2422' => 'acertr', 'Atru.chr7.1112' => 'acertr', 'AUR62005469' => 'cqu', 'AUR62011166' => 'cqu', 'AUR62013319' => 'cqu', 'AUR62024273' => 'cqu', 'AUR62028420' => 'cqu', 'AUR62041942' => 'cqu', 'BcaB01g04969' => 'bca', 'BcaB01g06371' => 'bca', 'BcaB02g11494' => 'bca', 'BcaB03g15382' => 'bca', 'BcaB08g36994' => 'bca', 'BcaC03g13477' => 'bca', 'BcaC03g13478' => 'bca', 'BcaC03g13480' => 'bca', 'BcaC03g13481' => 'bca', 'BcaC03g13486' => 'bca', 'BcaC04g19031' => 'bca', 'BcaC04g23085' => 'bca', 'BcaC05g25094' => 'bca', 'BcaC05g25096' => 'bca', 'BcaC05g25138' => 'bca', 'BcaC05g30416' => 'bca', 'BcaC05g30455' => 'bca', 'BcaC06g30979' => 'bca', 'BcaC06g33805' => 'bca', 'BcaC08g46021' => 'bca', 'BcaNung03154' => 'bca', 'BolC2t06623H' => 'bol', 'BolC2t06632H' => 'bol', 'BolC2t06635H' => 'bol', 'BolC2t06638H' => 'bol', 'BolC3t13266H' => 'bol', 'BolC5t29776H' => 'bol', 'BolC6t38912H' => 'bol', 'BolC7t44183H' => 'bol', 'BolC9t54123H' => 'bol', 'BolC9t59107H' => 'bol', 'BraA02t05221Z' => 'bra', 'BraA03t09996Z' => 'bra', 'BraA05t23210Z' => 'bra', 'BraA06t24068Z' => 'bra', 'BraA06t27032Z' => 'bra', 'BraA08t35176Z' => 'bra', 'BraA09t36680Z' => 'bra', 'BraA10t44471Z' => 'bra', 'C02p06760' => 'bna', 'C02p06890' => 'bna', 'C02p07010' => 'bna', 'C03p07660' => 'bna', 'C05p10300' => 'bna', 'C06p38150' => 'bna', 'C07p36650' => 'bna', 'C08p15770' => 'bna', 'C09p12300' => 'bna', 'C09p62700' => 'bna', 'C09p75040' => 'bna', 'CAN.G13.1' => 'can', 'CAN.G138.4' => 'can', 'CAN.G44.6' => 'can', 'CAN.G473.19' => 'can', 'CANSAT01G0835' => 'cansat', 'CANSAT11G0246' => 'cansat', 'CANSAT11G1766' => 'cansat', 'CANSAT64G1954' => 'cansat', 'CARHR013330' => 'chi', 'CARHR060530' => 'chi', 'CARHR075300' => 'chi', 'CARHR105120' => 'chi', 'CARHR148910' => 'chi', 'CARHR198830' => 'chi', 'Carub.0001s1275' => 'cru', 'Carub.0002s1437' => 'cru', 'Carub.0003s0044' => 'cru', 'Carub.0003s2787' => 'cru', 'Carub.0005s0597' => 'cru', 'Carub.0006s1266' => 'cru', 'Ca_06935_v3' => 'car', 'Ca_13559_v3' => 'car', 'Ca_16941_v3' => 'car', 'Ca_16960_v3' => 'car', 'Ca_17775_v3' => 'car', 'Ca_30464_v3' => 'car', 'Cc06_g08160' => 'ccan', 'Cc07_g01520' => 'ccan', 'Cc11_g15810' => 'ccan', 'CDE02G2840' => 'cde', 'CDE03G0093' => 'cde', 'CDE04G2127' => 'cde', 'CDE07G1857' => 'cde', 'CDE09G1246' => 'cde', 'Cfa003412' => 'cfa', 'Cfa007341' => 'cfa', 'Cfa009220' => 'cfa', 'Ciclev10008737m.g' => 'ccl', 'Ciclev10015565m.g' => 'ccl', 'Ciclev10031761m.g' => 'ccl', 'CiPaw.03G045300' => 'cil', 'CiPaw.03G247200' => 'cil', 'CiPaw.04G029500' => 'cil', 'CiPaw.04G174000' => 'cil', 'CiPaw.05G181200' => 'cil', 'CiPaw.06G067100' => 'cil', 'ClCG05G025800' => 'cla', 'ClCG06G011400' => 'cla', 'ClCG09G019360' => 'cla', 'COL.COLO4_04827' => 'col', 'COL.COLO4_29170' => 'col', 'COL.COLO4_35131' => 'col', 'COL.COLO4_35132' => 'col', 'Cpa.g.sc33.32' => 'cpa', 'Cpa.g.sc46.29' => 'cpa', 'Cpa.g.sc796.1' => 'cpa', 'CsaV3_1G030420' => 'csa', 'CsaV3_5G027050' => 'csa', 'CsaV3_5G031040' => 'csa', 'CsaV3_UNG023130' => 'csa', 'CSS0007726' => 'camsi', 'CSS0016433' => 'camsi', 'CSS0017656' => 'camsi', 'CSS0025364' => 'camsi', 'CSS0027582' => 'camsi', 'CSS0047288' => 'camsi', 'CSS0049950' => 'camsi', 'DCAR_003843' => 'dca', 'DCAR_007052' => 'dca', 'DCAR_020884' => 'dca', 'DCAR_021730' => 'dca', 'DCAR_024423' => 'dca', 'DCAR_026509' => 'dca', 'DCAR_031158' => 'dca', 'Dinv14728' => 'din', 'Dinv15219' => 'din', 'Dinv25728' => 'din', 'Dinv33428' => 'din', 'Dinv36489' => 'din', 'Dinv41486' => 'din', 'Duzib147G0469' => 'dzi', 'Duzib168G0060' => 'dzi', 'Duzib187G1215' => 'dzi', 'Duzib248G0692' => 'dzi', 'Duzib251G0767' => 'dzi', 'Duzib264G0446' => 'dzi', 'Duzib268G0691' => 'dzi', 'ECA232G4767' => 'eca', 'ECA233G2838' => 'eca', 'ECA234G0391' => 'eca', 'ECA234G0857' => 'eca', 'ECA236G1593' => 'eca', 'ECA238G0565' => 'eca', 'ECA246G1027' => 'eca', 'ECA246G3223' => 'eca', 'ECA246G3470' => 'eca', 'EL10Ac6g13829' => 'bvu', 'EL10Ac6g14093' => 'bvu', 'EL10Ac8g18707' => 'bvu', 'Eucgr.C01369' => 'egr', 'Eucgr.H02492' => 'egr', 'Eucgr.I01733' => 'egr', 'Eucgr.J02255' => 'egr', 'Eucgr.J02257' => 'egr', 'Eucgr.J02258' => 'egr', 'FAN02G1601' => 'fan', 'FAN03G1586' => 'fan', 'FAN03G2986' => 'fan', 'FAN05G4837' => 'fan', 'FAN06G0146' => 'fan', 'FAN07G0858' => 'fan', 'FAN09G3179' => 'fan', 'FAN10G0669' => 'fan', 'FAN12G2358' => 'fan', 'FAN14G4198' => 'fan', 'FAN14G5112' => 'fan', 'FAN17G0342' => 'fan', 'FAN19G0342' => 'fan', 'FAN19G0962' => 'fan', 'FAN19G1101' => 'fan', 'FAN19G1872' => 'fan', 'FAN22G0356' => 'fan', 'FAN23G0744' => 'fan', 'FAN23G1914' => 'fan', 'FAN26G0032' => 'fan', 'FAN28G0625' => 'fan', 'FvH4_1g02710' => 'fve', 'FvH4_1g02720' => 'fve', 'FvH4_4g25670' => 'fve', 'FvH4_6g51700' => 'fve', 'FvH4_7g20170' => 'fve', 'Glyma.05G175000' => 'gma', 'Glyma.08G132300' => 'gma', 'Glyma.11G243000' => 'gma', 'Glyma.13G158900' => 'gma', 'Glyma.17G112400' => 'gma', 'Glyma.18G014100' => 'gma', 'Glyma.19G003100' => 'gma', 'Glyma.19G056500' => 'gma', 'Gohir.A01G158900' => 'ghi', 'Gohir.A05G312600' => 'ghi', 'Gohir.A05G354900' => 'ghi', 'Gohir.A07G037200' => 'ghi', 'Gohir.A09G030000' => 'ghi', 'Gohir.A12G145200' => 'ghi', 'Gohir.D01G151500' => 'ghi', 'Gohir.D04G058300' => 'ghi', 'Gohir.D05G314100' => 'ghi', 'Gohir.D07G041400' => 'ghi', 'Gohir.D09G029700' => 'ghi', 'Gohir.D12G149700' => 'ghi', 'Gorai.001G043800' => 'gra', 'Gorai.002G187800' => 'gra', 'Gorai.006G034700' => 'gra', 'Gorai.008G161200' => 'gra', 'Gorai.009G335700' => 'gra', 'Gorai.012G065000' => 'gra', 'GSVIVG01000535001' => 'vvi', 'GSVIVG01015572001' => 'vvi', 'GSVIVG01032386001' => 'vvi', 'HanXRQChr05g0138531' => 'han', 'HanXRQChr06g0174391' => 'han', 'HanXRQChr07g0199021' => 'han', 'HanXRQChr08g0208211' => 'han', 'HanXRQChr09g0255471' => 'han', 'HanXRQChr10g0315791' => 'han', 'HanXRQChr12g0371991' => 'han', 'HanXRQChr15g0475251' => 'han', 'HanXRQChr17g0540001' => 'han', 'HanXRQChr17g0548631' => 'han', 'HanXRQChr17g0569561' => 'han', 'Haze_12256' => 'cav', 'Haze_14756' => 'cav', 'Haze_25528' => 'cav', 'Hma1.2p1_0079F.1_g041020' => 'hma', 'Hma1.2p1_0818F.1_g223260' => 'hma', 'Hma1.2p1_1747F.1_g300530' => 'hma', 'HPP92_004607' => 'vpl', 'HPP92_004608' => 'vpl', 'HPP92_006181' => 'vpl', 'HPP92_012192' => 'vpl', 'HPP92_015680' => 'vpl', 'HPP92_020249' => 'vpl', 'HPP92_021376' => 'vpl', 'HPP92_024275' => 'vpl', 'Hund06031' => 'sun', 'Hund25391' => 'sun', 'Lalb_Chr07g0185371' => 'lal', 'Lalb_Chr07g0185381' => 'lal', 'Lalb_Chr12g0204011' => 'lal', 'Lalb_Chr13g0301671' => 'lal', 'Lalb_Chr14g0362851' => 'lal', 'Lalb_Chr24g0403581' => 'lal', 'Lj1g0000233' => 'lja', 'Lj2g0018120' => 'lja', 'Lj3C621T0' => 'lonja', 'Lj3P1059T14' => 'lonja', 'Lj3P611T9' => 'lonja', 'Lj3P614T13' => 'lonja', 'Lj3P615T5' => 'lonja', 'Lj4g0012315' => 'lja', 'Lj4g0026182' => 'lja', 'Lj6P813T16' => 'lonja', 'Lj7C427T7' => 'lonja', 'Lj7C427T8' => 'lonja', 'Lj7P600T41' => 'lonja', 'Lju41C42G17' => 'lonja', 'Lsat_1_v5_gn_0_47300' => 'lsa', 'Lsat_1_v5_gn_2_91280' => 'lsa', 'Lsat_1_v5_gn_3_30561' => 'lsa', 'Lsat_1_v5_gn_4_184321' => 'lsa', 'Lsat_1_v5_gn_4_4041' => 'lsa', 'Lsat_1_v5_gn_5_92000' => 'lsa', 'Lsat_1_v5_gn_8_152940' => 'lsa', 'Lsat_1_v5_gn_8_62401' => 'lsa', 'Manes.06G055900' => 'mes', 'Manes.12G022200' => 'mes', 'Manes.13G023300' => 'mes', 'Manes.14G115000' => 'mes', 'Manes.15G151700' => 'mes', 'Manes.17G111300' => 'mes', 'Mapoly0226s0009' => 'mpo', 'MBI02_g25363_MAGBIO' => 'mbi', 'MBI06_g00027_MAGBIO' => 'mbi', 'MBI10_g13034_MAGBIO' => 'mbi', 'MD09G1023400' => 'mdo', 'MD13G1100100' => 'mdo', 'MD15G1169200' => 'mdo', 'MD16G1101100' => 'mdo', 'MD17G1022900' => 'mdo', 'Medtr3g096150' => 'mtr', 'Medtr4g115070' => 'mtr', 'Medtr7g033325' => 'mtr', 'Medtr8g089840' => 'mtr', 'MELO3C010319.2' => 'cme', 'MELO3C011944.2' => 'cme', 'MELO3C021589.2' => 'cme', 'Migut.E00207' => 'egut', 'Migut.H00067' => 'egut', 'Migut.K00433' => 'egut', 'Migut.K00606' => 'egut', 'Migut.K01410' => 'egut', 'MSTRG.13347' => 'ama', 'MSTRG.24045' => 'ama', 'MSTRG.2428' => 'ama', 'MSTRG.26410' => 'ama', 'MSTRG.3139' => 'ama', 'MSTRG.3286' => 'ama', 'MSTRG.563' => 'ama', 'MSTRG.7941' => 'ama', 'Nitab4.5_0000028g0060' => 'nta', 'Nitab4.5_0000065g0260' => 'nta', 'Nitab4.5_0000112g0060' => 'nta', 'Nitab4.5_0000489g0120' => 'nta', 'Nitab4.5_0001776g0050' => 'nta', 'Nitab4.5_0001854g0010' => 'nta', 'Nitab4.5_0001860g0020' => 'nta', 'Nitab4.5_0004352g0010' => 'nta', 'Nitab4.5_0008716g0020' => 'nta', 'Nitab4.5_0008922g0010' => 'nta', 'Nn3g16693' => 'nnu', 'Nn4g22596' => 'nnu', 'Nn7g37639' => 'nnu', 'Oeu001701.1' => 'oeu', 'Oeu018149.1' => 'oeu', 'Oeu026220.1' => 'oeu', 'Oeu038635.1' => 'oeu', 'Oeu049176.1' => 'oeu', 'Oeu056706.1' => 'oeu', 'Oeu056937.1' => 'oeu', 'Oeu057540.1' => 'oeu', 'Os02g0594900' => 'osa', 'Os02g0595100' => 'osa', 'Os04g0477500' => 'osa', 'Os12g0611900' => 'osa', 'Peaxi162Scf00076g00020' => 'pax', 'Peaxi162Scf00128g00217' => 'pax', 'Peaxi162Scf00129g01640' => 'pax', 'Peaxi162Scf00669g00007' => 'pax', 'Peaxi162Scf00700g00421' => 'pax', 'Peaxi162Scf00801g00038' => 'pax', 'Peaxi162Scf00891g00025' => 'pax', 'PGR083G0909' => 'pgr', 'PGR119G1005' => 'pgr', 'PGR142G2236' => 'pgr', 'PGR142G3388' => 'pgr', 'PGSC0003DMG400004514' => 'stu', 'PGSC0003DMG400012635' => 'stu', 'PGSC0003DMG400015730' => 'stu', 'PGSC0003DMG400018611' => 'stu', 'PGSC0003DMG400030897' => 'stu', 'Phvul.001G254800' => 'pvu', 'Phvul.002G260100' => 'pvu', 'Phvul.003G167600' => 'pvu', 'Phvul.004G005100' => 'pvu', 'Potri.001G343600' => 'ptr', 'Potri.006G066700' => 'ptr', 'Potri.008G186000' => 'ptr', 'Potri.010G046900' => 'ptr', 'Potri.018G127900' => 'ptr', 'Pp3c20_17750' => 'ppa', 'Pp3c24_4380' => 'ppa', 'Prupe.1G245800' => 'ppe', 'Prupe.3G293400' => 'ppe', 'Prupe.7G247400' => 'ppe', 'Psat0s145g0120' => 'psa', 'Psat0s595g0040' => 'psa', 'Psat0s595g0120' => 'psa', 'Psat3g175040' => 'psa', 'Psat7g058120' => 'psa', 'PSO017G0428' => 'pso', 'PSO063G7510' => 'pso', 'PSO067G0046' => 'pso', 'PSO478G1073' => 'pso', 'PSO675G3677' => 'pso', 'PSO675G6558' => 'pso', 'PSO675G7520' => 'pso', 'PSO675G8959' => 'pso', 'QL02p074089' => 'qlo', 'QL02p089614' => 'qlo', 'QL03p057736' => 'qlo', 'RcHm_v2.0_Chr1g0364131' => 'rch', 'RcHm_v2.0_Chr2g0087801' => 'rch', 'RcHm_v2.0_Chr2g0087821' => 'rch', 'RcHm_v2.0_Chr2g0173231' => 'rch', 'RcHm_v2.0_Chr4g0433111' => 'rch', 'Rhsim03G0250300' => 'rsi', 'Rhsim08G0048400' => 'rsi', 'Rhsim10G0014800' => 'rsi', 'Rhsim12G0040100' => 'rsi', 'Rhsim12G0109700' => 'rsi', 'Sabra06G0049600' => 'sbr', 'Sabra08G0141000' => 'sbr', 'Sabra10G0021400' => 'sbr', 'Sabra16G0222900' => 'sbr', 'Sabra18G0108600' => 'sbr', 'SalBow1G0433' => 'sbo', 'SalBow1G2038' => 'sbo', 'SalBow1G5003' => 'sbo', 'SalBow7G1197' => 'sbo', 'SalBow8G3506' => 'sbo', 'Sc03g0007300' => 'sci', 'Sc11g0000950' => 'sci', 'Sc14g0008750' => 'sci', 'Sc18g0000420' => 'sci', 'Sed0006754' => 'sed', 'Sed0008741' => 'sed', 'Sed0017172' => 'sed', 'Sed0018925' => 'sed', 'Sed0023326' => 'sed', 'Sed0025909' => 'sed', 'SEGI_05333' => 'sgi', 'SEGI_10362' => 'sgi', 'SEGI_13380' => 'sgi', 'SEGI_24306' => 'sgi', 'SEGI_29077' => 'sgi', 'SEGI_29095' => 'sgi', 'SEGI_36534' => 'sgi', 'SEGI_37506' => 'sgi', 'SEGI_38321' => 'sgi', 'SGA_v2.0_scaffold307G48031' => 'sas', 'SGA_v2.0_scaffold47G17507' => 'sas', 'SGA_v2.0_scaffold63G21736' => 'sas', 'SGA_v2.0_scaffold87G27070' => 'sas', 'SHI17794' => 'shi', 'SHI28851' => 'shi', 'SMO165G0155' => 'smo', 'SMO340G0217' => 'smo', 'SMO367G1210' => 'smo', 'Solyc02g093430.3' => 'sly', 'Solyc05g013580.4' => 'sly', 'Solyc07g008030.3' => 'sly', 'Solyc12g035470.2' => 'sly', 'Sopen02g038020' => 'spe', 'Sopen05g008490' => 'spe', 'Sopen07g003910' => 'spe', 'Sopen12g015240' => 'spe', 'Sp1g11550' => 'spa', 'Sp2g16710' => 'spa', 'Sp3g00430' => 'spa', 'Sp3g26780' => 'spa', 'Sp5g22900' => 'spa', 'Sp6g29530' => 'spa', 'TAR371G0794' => 'tar', 'TAR374G0164' => 'tar', 'TAR622G0165' => 'tar', 'TAR626G0929' => 'tar', 'TAR629G2155' => 'tar', 'THA.LOC104805282' => 'tha', 'THA.LOC104805363' => 'tha', 'THA.LOC104808968' => 'tha', 'THA.LOC104821093' => 'tha', 'THA.LOC104823953' => 'tha', 'THA.LOC104825562' => 'tha', 'THA.LOC104825665' => 'tha', 'Thecc.02G261400' => 'tca', 'Thecc.04G019200' => 'tca', 'Thecc.09G130400' => 'tca', 'Thhalv10004374m.g' => 'esa', 'Thhalv10007850m.g' => 'esa', 'Thhalv10013782m.g' => 'esa', 'Thhalv10018686m.g' => 'esa', 'Thhalv10020899m.g' => 'esa', 'Thhalv10022755m.g' => 'esa', 'TPR.G23851' => 'tpr', 'TPR.G26500' => 'tpr', 'TPR.G27267' => 'tpr', 'TPR.G32001' => 'tpr', 'TPR.G6251' => 'tpr', 'TPR.G8167' => 'tpr', 'TWI12G1330' => 'twi', 'TWI18G1239' => 'twi', 'TWI34G0979' => 'twi', 'TWI36G0670' => 'twi', 'TWI36G0707' => 'twi', 'TWI56G0233' => 'twi', 'TWI75G1809' => 'twi', 'unitig_21.g20874' => 'ugi', 'unitig_26.g10343' => 'ugi', 'unitig_46.g18392' => 'ugi', 'unitig_52.g17178' => 'ugi', 'unitig_8.g2934' => 'ugi', 'vmacro01122' => 'vma', 'vmacro05875' => 'vma', 'vmacro06147' => 'vma', 'vmacro16191' => 'vma', 'vmacro18293' => 'vma', 'VMungo0251G3707' => 'vmu', 'VMungo0464G1521' => 'vmu', 'VMungo1215G0205' => 'vmu', 'VMungo1383G2484' => 'vmu', 'Zm00001eb079610' => 'zma', 'Zm00001eb135990' => 'zma', 'Zm00001eb183710' => 'zma', 'Zm00001eb246020' => 'zma' ), 'gf_id' => 'HOM05D001124', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001124' ), 'data_identifier' => 'HOM05D001124', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001124', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '548', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02520' => 'bna', 'A03p06630' => 'bna', 'A05p44460' => 'bna', 'A06p08710' => 'bna', 'A06p41090' => 'bna', 'A07p32320' => 'bna', 'A08p32520' => 'bna', 'A09p10360' => 'bna', 'A10p24080' => 'bna', 'Aa31LG11G15250' => 'aar', 'Aa31LG1G1800' => 'aar', 'Aa31LG2G5120' => 'aar', 'Aa31LG2G6070' => 'aar', 'Aa31LG5G10770' => 'aar', 'Aa31sc61G90' => 'aar', 'Actinidia01352' => 'ach', 'Actinidia05983' => 'ach', 'Actinidia08133' => 'ach', 'Actinidia15101' => 'ach', 'Actinidia26379' => 'ach', 'Actinidia35778' => 'ach', 'Actinidia36123' => 'ach', 'Actinidia37436' => 'ach', 'Actinidia38730' => 'ach', 'Ah.02g128210' => 'amhyb', 'Ah.03g132990' => 'amhyb', 'Ah.14g079410' => 'amhyb', 'AL1G24640' => 'aly', 'AL2G26680' => 'aly', 'AL3G10530' => 'aly', 'AL3G45230' => 'aly', 'AL5G15230' => 'aly', 'AL5G16960' => 'aly', 'AL6G25210' => 'aly', 'Aqoxy2G00441' => 'aox', 'Aqoxy3G01236' => 'aox', 'Aqoxy5G03746' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3RQ047' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C7GMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9C8JER' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MBL6KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YXCZ83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZANX40' => 'arhy', 'AT1G12990' => 'ath', 'AT1G67880' => 'ath', 'AT2G13290' => 'ath', 'AT3G01620' => 'ath', 'AT3G26445' => 'ath', 'AT3G27540' => 'ath', 'AT5G14480' => 'ath', 'ATR0824G026' => 'atr', 'ATR1098G019' => 'atr', 'Atru.chr11.2145' => 'acertr', 'Atru.chr2.3636' => 'acertr', 'Atru.chr2.3644' => 'acertr', 'Atru.chr6.2422' => 'acertr', 'Atru.chr7.1112' => 'acertr', 'AUR62005469' => 'cqu', 'AUR62011166' => 'cqu', 'AUR62013319' => 'cqu', 'AUR62024273' => 'cqu', 'AUR62028420' => 'cqu', 'AUR62041942' => 'cqu', 'BcaB01g04969' => 'bca', 'BcaB01g06371' => 'bca', 'BcaB02g11494' => 'bca', 'BcaB03g15382' => 'bca', 'BcaB08g36994' => 'bca', 'BcaC03g13477' => 'bca', 'BcaC03g13478' => 'bca', 'BcaC03g13480' => 'bca', 'BcaC03g13481' => 'bca', 'BcaC03g13486' => 'bca', 'BcaC04g19031' => 'bca', 'BcaC04g23085' => 'bca', 'BcaC05g25094' => 'bca', 'BcaC05g25096' => 'bca', 'BcaC05g25138' => 'bca', 'BcaC05g30416' => 'bca', 'BcaC05g30455' => 'bca', 'BcaC06g30979' => 'bca', 'BcaC06g33805' => 'bca', 'BcaC08g46021' => 'bca', 'BcaNung03154' => 'bca', 'BolC2t06623H' => 'bol', 'BolC2t06632H' => 'bol', 'BolC2t06635H' => 'bol', 'BolC2t06638H' => 'bol', 'BolC3t13266H' => 'bol', 'BolC5t29776H' => 'bol', 'BolC6t38912H' => 'bol', 'BolC7t44183H' => 'bol', 'BolC9t54123H' => 'bol', 'BolC9t59107H' => 'bol', 'BraA02t05221Z' => 'bra', 'BraA03t09996Z' => 'bra', 'BraA05t23210Z' => 'bra', 'BraA06t24068Z' => 'bra', 'BraA06t27032Z' => 'bra', 'BraA08t35176Z' => 'bra', 'BraA09t36680Z' => 'bra', 'BraA10t44471Z' => 'bra', 'C02p06760' => 'bna', 'C02p06890' => 'bna', 'C02p07010' => 'bna', 'C03p07660' => 'bna', 'C05p10300' => 'bna', 'C06p38150' => 'bna', 'C07p36650' => 'bna', 'C08p15770' => 'bna', 'C09p12300' => 'bna', 'C09p62700' => 'bna', 'C09p75040' => 'bna', 'CAN.G13.1' => 'can', 'CAN.G138.4' => 'can', 'CAN.G44.6' => 'can', 'CAN.G473.19' => 'can', 'CANSAT01G0835' => 'cansat', 'CANSAT11G0246' => 'cansat', 'CANSAT11G1766' => 'cansat', 'CANSAT64G1954' => 'cansat', 'CARHR013330' => 'chi', 'CARHR060530' => 'chi', 'CARHR075300' => 'chi', 'CARHR105120' => 'chi', 'CARHR148910' => 'chi', 'CARHR198830' => 'chi', 'Carub.0001s1275' => 'cru', 'Carub.0002s1437' => 'cru', 'Carub.0003s0044' => 'cru', 'Carub.0003s2787' => 'cru', 'Carub.0005s0597' => 'cru', 'Carub.0006s1266' => 'cru', 'Ca_06935_v3' => 'car', 'Ca_13559_v3' => 'car', 'Ca_16941_v3' => 'car', 'Ca_16960_v3' => 'car', 'Ca_17775_v3' => 'car', 'Ca_30464_v3' => 'car', 'Cc06_g08160' => 'ccan', 'Cc07_g01520' => 'ccan', 'Cc11_g15810' => 'ccan', 'CDE02G2840' => 'cde', 'CDE03G0093' => 'cde', 'CDE04G2127' => 'cde', 'CDE07G1857' => 'cde', 'CDE09G1246' => 'cde', 'Cfa003412' => 'cfa', 'Cfa007341' => 'cfa', 'Cfa009220' => 'cfa', 'Ciclev10008737m.g' => 'ccl', 'Ciclev10015565m.g' => 'ccl', 'Ciclev10031761m.g' => 'ccl', 'CiPaw.03G045300' => 'cil', 'CiPaw.03G247200' => 'cil', 'CiPaw.04G029500' => 'cil', 'CiPaw.04G174000' => 'cil', 'CiPaw.05G181200' => 'cil', 'CiPaw.06G067100' => 'cil', 'ClCG05G025800' => 'cla', 'ClCG06G011400' => 'cla', 'ClCG09G019360' => 'cla', 'COL.COLO4_04827' => 'col', 'COL.COLO4_29170' => 'col', 'COL.COLO4_35131' => 'col', 'COL.COLO4_35132' => 'col', 'Cpa.g.sc33.32' => 'cpa', 'Cpa.g.sc46.29' => 'cpa', 'Cpa.g.sc796.1' => 'cpa', 'CsaV3_1G030420' => 'csa', 'CsaV3_5G027050' => 'csa', 'CsaV3_5G031040' => 'csa', 'CsaV3_UNG023130' => 'csa', 'CSS0007726' => 'camsi', 'CSS0016433' => 'camsi', 'CSS0017656' => 'camsi', 'CSS0025364' => 'camsi', 'CSS0027582' => 'camsi', 'CSS0047288' => 'camsi', 'CSS0049950' => 'camsi', 'DCAR_003843' => 'dca', 'DCAR_007052' => 'dca', 'DCAR_020884' => 'dca', 'DCAR_021730' => 'dca', 'DCAR_024423' => 'dca', 'DCAR_026509' => 'dca', 'DCAR_031158' => 'dca', 'Dinv14728' => 'din', 'Dinv15219' => 'din', 'Dinv25728' => 'din', 'Dinv33428' => 'din', 'Dinv36489' => 'din', 'Dinv41486' => 'din', 'Duzib147G0469' => 'dzi', 'Duzib168G0060' => 'dzi', 'Duzib187G1215' => 'dzi', 'Duzib248G0692' => 'dzi', 'Duzib251G0767' => 'dzi', 'Duzib264G0446' => 'dzi', 'Duzib268G0691' => 'dzi', 'ECA232G4767' => 'eca', 'ECA233G2838' => 'eca', 'ECA234G0391' => 'eca', 'ECA234G0857' => 'eca', 'ECA236G1593' => 'eca', 'ECA238G0565' => 'eca', 'ECA246G1027' => 'eca', 'ECA246G3223' => 'eca', 'ECA246G3470' => 'eca', 'EL10Ac6g13829' => 'bvu', 'EL10Ac6g14093' => 'bvu', 'EL10Ac8g18707' => 'bvu', 'Eucgr.C01369' => 'egr', 'Eucgr.H02492' => 'egr', 'Eucgr.I01733' => 'egr', 'Eucgr.J02255' => 'egr', 'Eucgr.J02257' => 'egr', 'Eucgr.J02258' => 'egr', 'FAN02G1601' => 'fan', 'FAN03G1586' => 'fan', 'FAN03G2986' => 'fan', 'FAN05G4837' => 'fan', 'FAN06G0146' => 'fan', 'FAN07G0858' => 'fan', 'FAN09G3179' => 'fan', 'FAN10G0669' => 'fan', 'FAN12G2358' => 'fan', 'FAN14G4198' => 'fan', 'FAN14G5112' => 'fan', 'FAN17G0342' => 'fan', 'FAN19G0342' => 'fan', 'FAN19G0962' => 'fan', 'FAN19G1101' => 'fan', 'FAN19G1872' => 'fan', 'FAN22G0356' => 'fan', 'FAN23G0744' => 'fan', 'FAN23G1914' => 'fan', 'FAN26G0032' => 'fan', 'FAN28G0625' => 'fan', 'FvH4_1g02710' => 'fve', 'FvH4_1g02720' => 'fve', 'FvH4_4g25670' => 'fve', 'FvH4_6g51700' => 'fve', 'FvH4_7g20170' => 'fve', 'Glyma.05G175000' => 'gma', 'Glyma.08G132300' => 'gma', 'Glyma.11G243000' => 'gma', 'Glyma.13G158900' => 'gma', 'Glyma.17G112400' => 'gma', 'Glyma.18G014100' => 'gma', 'Glyma.19G003100' => 'gma', 'Glyma.19G056500' => 'gma', 'Gohir.A01G158900' => 'ghi', 'Gohir.A05G312600' => 'ghi', 'Gohir.A05G354900' => 'ghi', 'Gohir.A07G037200' => 'ghi', 'Gohir.A09G030000' => 'ghi', 'Gohir.A12G145200' => 'ghi', 'Gohir.D01G151500' => 'ghi', 'Gohir.D04G058300' => 'ghi', 'Gohir.D05G314100' => 'ghi', 'Gohir.D07G041400' => 'ghi', 'Gohir.D09G029700' => 'ghi', 'Gohir.D12G149700' => 'ghi', 'Gorai.001G043800' => 'gra', 'Gorai.002G187800' => 'gra', 'Gorai.006G034700' => 'gra', 'Gorai.008G161200' => 'gra', 'Gorai.009G335700' => 'gra', 'Gorai.012G065000' => 'gra', 'GSVIVG01000535001' => 'vvi', 'GSVIVG01015572001' => 'vvi', 'GSVIVG01032386001' => 'vvi', 'HanXRQChr05g0138531' => 'han', 'HanXRQChr06g0174391' => 'han', 'HanXRQChr07g0199021' => 'han', 'HanXRQChr08g0208211' => 'han', 'HanXRQChr09g0255471' => 'han', 'HanXRQChr10g0315791' => 'han', 'HanXRQChr12g0371991' => 'han', 'HanXRQChr15g0475251' => 'han', 'HanXRQChr17g0540001' => 'han', 'HanXRQChr17g0548631' => 'han', 'HanXRQChr17g0569561' => 'han', 'Haze_12256' => 'cav', 'Haze_14756' => 'cav', 'Haze_25528' => 'cav', 'Hma1.2p1_0079F.1_g041020' => 'hma', 'Hma1.2p1_0818F.1_g223260' => 'hma', 'Hma1.2p1_1747F.1_g300530' => 'hma', 'HPP92_004607' => 'vpl', 'HPP92_004608' => 'vpl', 'HPP92_006181' => 'vpl', 'HPP92_012192' => 'vpl', 'HPP92_015680' => 'vpl', 'HPP92_020249' => 'vpl', 'HPP92_021376' => 'vpl', 'HPP92_024275' => 'vpl', 'Hund06031' => 'sun', 'Hund25391' => 'sun', 'Lalb_Chr07g0185371' => 'lal', 'Lalb_Chr07g0185381' => 'lal', 'Lalb_Chr12g0204011' => 'lal', 'Lalb_Chr13g0301671' => 'lal', 'Lalb_Chr14g0362851' => 'lal', 'Lalb_Chr24g0403581' => 'lal', 'Lj1g0000233' => 'lja', 'Lj2g0018120' => 'lja', 'Lj3C621T0' => 'lonja', 'Lj3P1059T14' => 'lonja', 'Lj3P611T9' => 'lonja', 'Lj3P614T13' => 'lonja', 'Lj3P615T5' => 'lonja', 'Lj4g0012315' => 'lja', 'Lj4g0026182' => 'lja', 'Lj6P813T16' => 'lonja', 'Lj7C427T7' => 'lonja', 'Lj7C427T8' => 'lonja', 'Lj7P600T41' => 'lonja', 'Lju41C42G17' => 'lonja', 'Lsat_1_v5_gn_0_47300' => 'lsa', 'Lsat_1_v5_gn_2_91280' => 'lsa', 'Lsat_1_v5_gn_3_30561' => 'lsa', 'Lsat_1_v5_gn_4_184321' => 'lsa', 'Lsat_1_v5_gn_4_4041' => 'lsa', 'Lsat_1_v5_gn_5_92000' => 'lsa', 'Lsat_1_v5_gn_8_152940' => 'lsa', 'Lsat_1_v5_gn_8_62401' => 'lsa', 'Manes.06G055900' => 'mes', 'Manes.12G022200' => 'mes', 'Manes.13G023300' => 'mes', 'Manes.14G115000' => 'mes', 'Manes.15G151700' => 'mes', 'Manes.17G111300' => 'mes', 'Mapoly0226s0009' => 'mpo', 'MBI02_g25363_MAGBIO' => 'mbi', 'MBI06_g00027_MAGBIO' => 'mbi', 'MBI10_g13034_MAGBIO' => 'mbi', 'MD09G1023400' => 'mdo', 'MD13G1100100' => 'mdo', 'MD15G1169200' => 'mdo', 'MD16G1101100' => 'mdo', 'MD17G1022900' => 'mdo', 'Medtr3g096150' => 'mtr', 'Medtr4g115070' => 'mtr', 'Medtr7g033325' => 'mtr', 'Medtr8g089840' => 'mtr', 'MELO3C010319.2' => 'cme', 'MELO3C011944.2' => 'cme', 'MELO3C021589.2' => 'cme', 'Migut.E00207' => 'egut', 'Migut.H00067' => 'egut', 'Migut.K00433' => 'egut', 'Migut.K00606' => 'egut', 'Migut.K01410' => 'egut', 'MSTRG.13347' => 'ama', 'MSTRG.24045' => 'ama', 'MSTRG.2428' => 'ama', 'MSTRG.26410' => 'ama', 'MSTRG.3139' => 'ama', 'MSTRG.3286' => 'ama', 'MSTRG.563' => 'ama', 'MSTRG.7941' => 'ama', 'Nitab4.5_0000028g0060' => 'nta', 'Nitab4.5_0000065g0260' => 'nta', 'Nitab4.5_0000112g0060' => 'nta', 'Nitab4.5_0000489g0120' => 'nta', 'Nitab4.5_0001776g0050' => 'nta', 'Nitab4.5_0001854g0010' => 'nta', 'Nitab4.5_0001860g0020' => 'nta', 'Nitab4.5_0004352g0010' => 'nta', 'Nitab4.5_0008716g0020' => 'nta', 'Nitab4.5_0008922g0010' => 'nta', 'Nn3g16693' => 'nnu', 'Nn4g22596' => 'nnu', 'Nn7g37639' => 'nnu', 'Oeu001701.1' => 'oeu', 'Oeu018149.1' => 'oeu', 'Oeu026220.1' => 'oeu', 'Oeu038635.1' => 'oeu', 'Oeu049176.1' => 'oeu', 'Oeu056706.1' => 'oeu', 'Oeu056937.1' => 'oeu', 'Oeu057540.1' => 'oeu', 'Os02g0594900' => 'osa', 'Os02g0595100' => 'osa', 'Os04g0477500' => 'osa', 'Os12g0611900' => 'osa', 'Peaxi162Scf00076g00020' => 'pax', 'Peaxi162Scf00128g00217' => 'pax', 'Peaxi162Scf00129g01640' => 'pax', 'Peaxi162Scf00669g00007' => 'pax', 'Peaxi162Scf00700g00421' => 'pax', 'Peaxi162Scf00801g00038' => 'pax', 'Peaxi162Scf00891g00025' => 'pax', 'PGR083G0909' => 'pgr', 'PGR119G1005' => 'pgr', 'PGR142G2236' => 'pgr', 'PGR142G3388' => 'pgr', 'PGSC0003DMG400004514' => 'stu', 'PGSC0003DMG400012635' => 'stu', 'PGSC0003DMG400015730' => 'stu', 'PGSC0003DMG400018611' => 'stu', 'PGSC0003DMG400030897' => 'stu', 'Phvul.001G254800' => 'pvu', 'Phvul.002G260100' => 'pvu', 'Phvul.003G167600' => 'pvu', 'Phvul.004G005100' => 'pvu', 'Potri.001G343600' => 'ptr', 'Potri.006G066700' => 'ptr', 'Potri.008G186000' => 'ptr', 'Potri.010G046900' => 'ptr', 'Potri.018G127900' => 'ptr', 'Pp3c20_17750' => 'ppa', 'Pp3c24_4380' => 'ppa', 'Prupe.1G245800' => 'ppe', 'Prupe.3G293400' => 'ppe', 'Prupe.7G247400' => 'ppe', 'Psat0s145g0120' => 'psa', 'Psat0s595g0040' => 'psa', 'Psat0s595g0120' => 'psa', 'Psat3g175040' => 'psa', 'Psat7g058120' => 'psa', 'PSO017G0428' => 'pso', 'PSO063G7510' => 'pso', 'PSO067G0046' => 'pso', 'PSO478G1073' => 'pso', 'PSO675G3677' => 'pso', 'PSO675G6558' => 'pso', 'PSO675G7520' => 'pso', 'PSO675G8959' => 'pso', 'QL02p074089' => 'qlo', 'QL02p089614' => 'qlo', 'QL03p057736' => 'qlo', 'RcHm_v2.0_Chr1g0364131' => 'rch', 'RcHm_v2.0_Chr2g0087801' => 'rch', 'RcHm_v2.0_Chr2g0087821' => 'rch', 'RcHm_v2.0_Chr2g0173231' => 'rch', 'RcHm_v2.0_Chr4g0433111' => 'rch', 'Rhsim03G0250300' => 'rsi', 'Rhsim08G0048400' => 'rsi', 'Rhsim10G0014800' => 'rsi', 'Rhsim12G0040100' => 'rsi', 'Rhsim12G0109700' => 'rsi', 'Sabra06G0049600' => 'sbr', 'Sabra08G0141000' => 'sbr', 'Sabra10G0021400' => 'sbr', 'Sabra16G0222900' => 'sbr', 'Sabra18G0108600' => 'sbr', 'SalBow1G0433' => 'sbo', 'SalBow1G2038' => 'sbo', 'SalBow1G5003' => 'sbo', 'SalBow7G1197' => 'sbo', 'SalBow8G3506' => 'sbo', 'Sc03g0007300' => 'sci', 'Sc11g0000950' => 'sci', 'Sc14g0008750' => 'sci', 'Sc18g0000420' => 'sci', 'Sed0006754' => 'sed', 'Sed0008741' => 'sed', 'Sed0017172' => 'sed', 'Sed0018925' => 'sed', 'Sed0023326' => 'sed', 'Sed0025909' => 'sed', 'SEGI_05333' => 'sgi', 'SEGI_10362' => 'sgi', 'SEGI_13380' => 'sgi', 'SEGI_24306' => 'sgi', 'SEGI_29077' => 'sgi', 'SEGI_29095' => 'sgi', 'SEGI_36534' => 'sgi', 'SEGI_37506' => 'sgi', 'SEGI_38321' => 'sgi', 'SGA_v2.0_scaffold307G48031' => 'sas', 'SGA_v2.0_scaffold47G17507' => 'sas', 'SGA_v2.0_scaffold63G21736' => 'sas', 'SGA_v2.0_scaffold87G27070' => 'sas', 'SHI17794' => 'shi', 'SHI28851' => 'shi', 'SMO165G0155' => 'smo', 'SMO340G0217' => 'smo', 'SMO367G1210' => 'smo', 'Solyc02g093430.3' => 'sly', 'Solyc05g013580.4' => 'sly', 'Solyc07g008030.3' => 'sly', 'Solyc12g035470.2' => 'sly', 'Sopen02g038020' => 'spe', 'Sopen05g008490' => 'spe', 'Sopen07g003910' => 'spe', 'Sopen12g015240' => 'spe', 'Sp1g11550' => 'spa', 'Sp2g16710' => 'spa', 'Sp3g00430' => 'spa', 'Sp3g26780' => 'spa', 'Sp5g22900' => 'spa', 'Sp6g29530' => 'spa', 'TAR371G0794' => 'tar', 'TAR374G0164' => 'tar', 'TAR622G0165' => 'tar', 'TAR626G0929' => 'tar', 'TAR629G2155' => 'tar', 'THA.LOC104805282' => 'tha', 'THA.LOC104805363' => 'tha', 'THA.LOC104808968' => 'tha', 'THA.LOC104821093' => 'tha', 'THA.LOC104823953' => 'tha', 'THA.LOC104825562' => 'tha', 'THA.LOC104825665' => 'tha', 'Thecc.02G261400' => 'tca', 'Thecc.04G019200' => 'tca', 'Thecc.09G130400' => 'tca', 'Thhalv10004374m.g' => 'esa', 'Thhalv10007850m.g' => 'esa', 'Thhalv10013782m.g' => 'esa', 'Thhalv10018686m.g' => 'esa', 'Thhalv10020899m.g' => 'esa', 'Thhalv10022755m.g' => 'esa', 'TPR.G23851' => 'tpr', 'TPR.G26500' => 'tpr', 'TPR.G27267' => 'tpr', 'TPR.G32001' => 'tpr', 'TPR.G6251' => 'tpr', 'TPR.G8167' => 'tpr', 'TWI12G1330' => 'twi', 'TWI18G1239' => 'twi', 'TWI34G0979' => 'twi', 'TWI36G0670' => 'twi', 'TWI36G0707' => 'twi', 'TWI56G0233' => 'twi', 'TWI75G1809' => 'twi', 'unitig_21.g20874' => 'ugi', 'unitig_26.g10343' => 'ugi', 'unitig_46.g18392' => 'ugi', 'unitig_52.g17178' => 'ugi', 'unitig_8.g2934' => 'ugi', 'vmacro01122' => 'vma', 'vmacro05875' => 'vma', 'vmacro06147' => 'vma', 'vmacro16191' => 'vma', 'vmacro18293' => 'vma', 'VMungo0251G3707' => 'vmu', 'VMungo0464G1521' => 'vmu', 'VMungo1215G0205' => 'vmu', 'VMungo1383G2484' => 'vmu', 'Zm00001eb079610' => 'zma', 'Zm00001eb135990' => 'zma', 'Zm00001eb183710' => 'zma', 'Zm00001eb246020' => 'zma' ) $gf_id = 'HOM05D001124' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001124' ) $data_identifier = 'HOM05D001124' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 6, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 7, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 21, 'bol' => (int) 10, 'bra' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 6, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 9, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 21, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 8, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 10, 'lsa' => (int) 8, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 8, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 9, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb246020' $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' => 'HOM05D001124', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '548', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02520' => 'bna', 'A03p06630' => 'bna', 'A05p44460' => 'bna', 'A06p08710' => 'bna', 'A06p41090' => 'bna', 'A07p32320' => 'bna', 'A08p32520' => 'bna', 'A09p10360' => 'bna', 'A10p24080' => 'bna', 'Aa31LG11G15250' => 'aar', 'Aa31LG1G1800' => 'aar', 'Aa31LG2G5120' => 'aar', 'Aa31LG2G6070' => 'aar', 'Aa31LG5G10770' => 'aar', 'Aa31sc61G90' => 'aar', 'Actinidia01352' => 'ach', 'Actinidia05983' => 'ach', 'Actinidia08133' => 'ach', 'Actinidia15101' => 'ach', 'Actinidia26379' => 'ach', 'Actinidia35778' => 'ach', 'Actinidia36123' => 'ach', 'Actinidia37436' => 'ach', 'Actinidia38730' => 'ach', 'Ah.02g128210' => 'amhyb', 'Ah.03g132990' => 'amhyb', 'Ah.14g079410' => 'amhyb', 'AL1G24640' => 'aly', 'AL2G26680' => 'aly', 'AL3G10530' => 'aly', 'AL3G45230' => 'aly', 'AL5G15230' => 'aly', 'AL5G16960' => 'aly', 'AL6G25210' => 'aly', 'Aqoxy2G00441' => 'aox', 'Aqoxy3G01236' => 'aox', 'Aqoxy5G03746' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3RQ047' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C7GMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9C8JER' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MBL6KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YXCZ83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZANX40' => 'arhy', 'AT1G12990' => 'ath', 'AT1G67880' => 'ath', 'AT2G13290' => 'ath', 'AT3G01620' => 'ath', 'AT3G26445' => 'ath', 'AT3G27540' => 'ath', 'AT5G14480' => 'ath', 'ATR0824G026' => 'atr', 'ATR1098G019' => 'atr', 'Atru.chr11.2145' => 'acertr', 'Atru.chr2.3636' => 'acertr', 'Atru.chr2.3644' => 'acertr', 'Atru.chr6.2422' => 'acertr', 'Atru.chr7.1112' => 'acertr', 'AUR62005469' => 'cqu', 'AUR62011166' => 'cqu', 'AUR62013319' => 'cqu', 'AUR62024273' => 'cqu', 'AUR62028420' => 'cqu', 'AUR62041942' => 'cqu', 'BcaB01g04969' => 'bca', 'BcaB01g06371' => 'bca', 'BcaB02g11494' => 'bca', 'BcaB03g15382' => 'bca', 'BcaB08g36994' => 'bca', 'BcaC03g13477' => 'bca', 'BcaC03g13478' => 'bca', 'BcaC03g13480' => 'bca', 'BcaC03g13481' => 'bca', 'BcaC03g13486' => 'bca', 'BcaC04g19031' => 'bca', 'BcaC04g23085' => 'bca', 'BcaC05g25094' => 'bca', 'BcaC05g25096' => 'bca', 'BcaC05g25138' => 'bca', 'BcaC05g30416' => 'bca', 'BcaC05g30455' => 'bca', 'BcaC06g30979' => 'bca', 'BcaC06g33805' => 'bca', 'BcaC08g46021' => 'bca', 'BcaNung03154' => 'bca', 'BolC2t06623H' => 'bol', 'BolC2t06632H' => 'bol', 'BolC2t06635H' => 'bol', 'BolC2t06638H' => 'bol', 'BolC3t13266H' => 'bol', 'BolC5t29776H' => 'bol', 'BolC6t38912H' => 'bol', 'BolC7t44183H' => 'bol', 'BolC9t54123H' => 'bol', 'BolC9t59107H' => 'bol', 'BraA02t05221Z' => 'bra', 'BraA03t09996Z' => 'bra', 'BraA05t23210Z' => 'bra', 'BraA06t24068Z' => 'bra', 'BraA06t27032Z' => 'bra', 'BraA08t35176Z' => 'bra', 'BraA09t36680Z' => 'bra', 'BraA10t44471Z' => 'bra', 'C02p06760' => 'bna', 'C02p06890' => 'bna', 'C02p07010' => 'bna', 'C03p07660' => 'bna', 'C05p10300' => 'bna', 'C06p38150' => 'bna', 'C07p36650' => 'bna', 'C08p15770' => 'bna', 'C09p12300' => 'bna', 'C09p62700' => 'bna', 'C09p75040' => 'bna', 'CAN.G13.1' => 'can', 'CAN.G138.4' => 'can', 'CAN.G44.6' => 'can', 'CAN.G473.19' => 'can', 'CANSAT01G0835' => 'cansat', 'CANSAT11G0246' => 'cansat', 'CANSAT11G1766' => 'cansat', 'CANSAT64G1954' => 'cansat', 'CARHR013330' => 'chi', 'CARHR060530' => 'chi', 'CARHR075300' => 'chi', 'CARHR105120' => 'chi', 'CARHR148910' => 'chi', 'CARHR198830' => 'chi', 'Carub.0001s1275' => 'cru', 'Carub.0002s1437' => 'cru', 'Carub.0003s0044' => 'cru', 'Carub.0003s2787' => 'cru', 'Carub.0005s0597' => 'cru', 'Carub.0006s1266' => 'cru', 'Ca_06935_v3' => 'car', 'Ca_13559_v3' => 'car', 'Ca_16941_v3' => 'car', 'Ca_16960_v3' => 'car', 'Ca_17775_v3' => 'car', 'Ca_30464_v3' => 'car', 'Cc06_g08160' => 'ccan', 'Cc07_g01520' => 'ccan', 'Cc11_g15810' => 'ccan', 'CDE02G2840' => 'cde', 'CDE03G0093' => 'cde', 'CDE04G2127' => 'cde', 'CDE07G1857' => 'cde', 'CDE09G1246' => 'cde', 'Cfa003412' => 'cfa', 'Cfa007341' => 'cfa', 'Cfa009220' => 'cfa', 'Ciclev10008737m.g' => 'ccl', 'Ciclev10015565m.g' => 'ccl', 'Ciclev10031761m.g' => 'ccl', 'CiPaw.03G045300' => 'cil', 'CiPaw.03G247200' => 'cil', 'CiPaw.04G029500' => 'cil', 'CiPaw.04G174000' => 'cil', 'CiPaw.05G181200' => 'cil', 'CiPaw.06G067100' => 'cil', 'ClCG05G025800' => 'cla', 'ClCG06G011400' => 'cla', 'ClCG09G019360' => 'cla', 'COL.COLO4_04827' => 'col', 'COL.COLO4_29170' => 'col', 'COL.COLO4_35131' => 'col', 'COL.COLO4_35132' => 'col', 'Cpa.g.sc33.32' => 'cpa', 'Cpa.g.sc46.29' => 'cpa', 'Cpa.g.sc796.1' => 'cpa', 'CsaV3_1G030420' => 'csa', 'CsaV3_5G027050' => 'csa', 'CsaV3_5G031040' => 'csa', 'CsaV3_UNG023130' => 'csa', 'CSS0007726' => 'camsi', 'CSS0016433' => 'camsi', 'CSS0017656' => 'camsi', 'CSS0025364' => 'camsi', 'CSS0027582' => 'camsi', 'CSS0047288' => 'camsi', 'CSS0049950' => 'camsi', 'DCAR_003843' => 'dca', 'DCAR_007052' => 'dca', 'DCAR_020884' => 'dca', 'DCAR_021730' => 'dca', 'DCAR_024423' => 'dca', 'DCAR_026509' => 'dca', 'DCAR_031158' => 'dca', 'Dinv14728' => 'din', 'Dinv15219' => 'din', 'Dinv25728' => 'din', 'Dinv33428' => 'din', 'Dinv36489' => 'din', 'Dinv41486' => 'din', 'Duzib147G0469' => 'dzi', 'Duzib168G0060' => 'dzi', 'Duzib187G1215' => 'dzi', 'Duzib248G0692' => 'dzi', 'Duzib251G0767' => 'dzi', 'Duzib264G0446' => 'dzi', 'Duzib268G0691' => 'dzi', 'ECA232G4767' => 'eca', 'ECA233G2838' => 'eca', 'ECA234G0391' => 'eca', 'ECA234G0857' => 'eca', 'ECA236G1593' => 'eca', 'ECA238G0565' => 'eca', 'ECA246G1027' => 'eca', 'ECA246G3223' => 'eca', 'ECA246G3470' => 'eca', 'EL10Ac6g13829' => 'bvu', 'EL10Ac6g14093' => 'bvu', 'EL10Ac8g18707' => 'bvu', 'Eucgr.C01369' => 'egr', 'Eucgr.H02492' => 'egr', 'Eucgr.I01733' => 'egr', 'Eucgr.J02255' => 'egr', 'Eucgr.J02257' => 'egr', 'Eucgr.J02258' => 'egr', 'FAN02G1601' => 'fan', 'FAN03G1586' => 'fan', 'FAN03G2986' => 'fan', 'FAN05G4837' => 'fan', 'FAN06G0146' => 'fan', 'FAN07G0858' => 'fan', 'FAN09G3179' => 'fan', 'FAN10G0669' => 'fan', 'FAN12G2358' => 'fan', 'FAN14G4198' => 'fan', 'FAN14G5112' => 'fan', 'FAN17G0342' => 'fan', 'FAN19G0342' => 'fan', 'FAN19G0962' => 'fan', 'FAN19G1101' => 'fan', 'FAN19G1872' => 'fan', 'FAN22G0356' => 'fan', 'FAN23G0744' => 'fan', 'FAN23G1914' => 'fan', 'FAN26G0032' => 'fan', 'FAN28G0625' => 'fan', 'FvH4_1g02710' => 'fve', 'FvH4_1g02720' => 'fve', 'FvH4_4g25670' => 'fve', 'FvH4_6g51700' => 'fve', 'FvH4_7g20170' => 'fve', 'Glyma.05G175000' => 'gma', 'Glyma.08G132300' => 'gma', 'Glyma.11G243000' => 'gma', 'Glyma.13G158900' => 'gma', 'Glyma.17G112400' => 'gma', 'Glyma.18G014100' => 'gma', 'Glyma.19G003100' => 'gma', 'Glyma.19G056500' => 'gma', 'Gohir.A01G158900' => 'ghi', 'Gohir.A05G312600' => 'ghi', 'Gohir.A05G354900' => 'ghi', 'Gohir.A07G037200' => 'ghi', 'Gohir.A09G030000' => 'ghi', 'Gohir.A12G145200' => 'ghi', 'Gohir.D01G151500' => 'ghi', 'Gohir.D04G058300' => 'ghi', 'Gohir.D05G314100' => 'ghi', 'Gohir.D07G041400' => 'ghi', 'Gohir.D09G029700' => 'ghi', 'Gohir.D12G149700' => 'ghi', 'Gorai.001G043800' => 'gra', 'Gorai.002G187800' => 'gra', 'Gorai.006G034700' => 'gra', 'Gorai.008G161200' => 'gra', 'Gorai.009G335700' => 'gra', 'Gorai.012G065000' => 'gra', 'GSVIVG01000535001' => 'vvi', 'GSVIVG01015572001' => 'vvi', 'GSVIVG01032386001' => 'vvi', 'HanXRQChr05g0138531' => 'han', 'HanXRQChr06g0174391' => 'han', 'HanXRQChr07g0199021' => 'han', 'HanXRQChr08g0208211' => 'han', 'HanXRQChr09g0255471' => 'han', 'HanXRQChr10g0315791' => 'han', 'HanXRQChr12g0371991' => 'han', 'HanXRQChr15g0475251' => 'han', 'HanXRQChr17g0540001' => 'han', 'HanXRQChr17g0548631' => 'han', 'HanXRQChr17g0569561' => 'han', 'Haze_12256' => 'cav', 'Haze_14756' => 'cav', 'Haze_25528' => 'cav', 'Hma1.2p1_0079F.1_g041020' => 'hma', 'Hma1.2p1_0818F.1_g223260' => 'hma', 'Hma1.2p1_1747F.1_g300530' => 'hma', 'HPP92_004607' => 'vpl', 'HPP92_004608' => 'vpl', 'HPP92_006181' => 'vpl', 'HPP92_012192' => 'vpl', 'HPP92_015680' => 'vpl', 'HPP92_020249' => 'vpl', 'HPP92_021376' => 'vpl', 'HPP92_024275' => 'vpl', 'Hund06031' => 'sun', 'Hund25391' => 'sun', 'Lalb_Chr07g0185371' => 'lal', 'Lalb_Chr07g0185381' => 'lal', 'Lalb_Chr12g0204011' => 'lal', 'Lalb_Chr13g0301671' => 'lal', 'Lalb_Chr14g0362851' => 'lal', 'Lalb_Chr24g0403581' => 'lal', 'Lj1g0000233' => 'lja', 'Lj2g0018120' => 'lja', 'Lj3C621T0' => 'lonja', 'Lj3P1059T14' => 'lonja', 'Lj3P611T9' => 'lonja', 'Lj3P614T13' => 'lonja', 'Lj3P615T5' => 'lonja', 'Lj4g0012315' => 'lja', 'Lj4g0026182' => 'lja', 'Lj6P813T16' => 'lonja', 'Lj7C427T7' => 'lonja', 'Lj7C427T8' => 'lonja', 'Lj7P600T41' => 'lonja', 'Lju41C42G17' => 'lonja', 'Lsat_1_v5_gn_0_47300' => 'lsa', 'Lsat_1_v5_gn_2_91280' => 'lsa', 'Lsat_1_v5_gn_3_30561' => 'lsa', 'Lsat_1_v5_gn_4_184321' => 'lsa', 'Lsat_1_v5_gn_4_4041' => 'lsa', 'Lsat_1_v5_gn_5_92000' => 'lsa', 'Lsat_1_v5_gn_8_152940' => 'lsa', 'Lsat_1_v5_gn_8_62401' => 'lsa', 'Manes.06G055900' => 'mes', 'Manes.12G022200' => 'mes', 'Manes.13G023300' => 'mes', 'Manes.14G115000' => 'mes', 'Manes.15G151700' => 'mes', 'Manes.17G111300' => 'mes', 'Mapoly0226s0009' => 'mpo', 'MBI02_g25363_MAGBIO' => 'mbi', 'MBI06_g00027_MAGBIO' => 'mbi', 'MBI10_g13034_MAGBIO' => 'mbi', 'MD09G1023400' => 'mdo', 'MD13G1100100' => 'mdo', 'MD15G1169200' => 'mdo', 'MD16G1101100' => 'mdo', 'MD17G1022900' => 'mdo', 'Medtr3g096150' => 'mtr', 'Medtr4g115070' => 'mtr', 'Medtr7g033325' => 'mtr', 'Medtr8g089840' => 'mtr', 'MELO3C010319.2' => 'cme', 'MELO3C011944.2' => 'cme', 'MELO3C021589.2' => 'cme', 'Migut.E00207' => 'egut', 'Migut.H00067' => 'egut', 'Migut.K00433' => 'egut', 'Migut.K00606' => 'egut', 'Migut.K01410' => 'egut', 'MSTRG.13347' => 'ama', 'MSTRG.24045' => 'ama', 'MSTRG.2428' => 'ama', 'MSTRG.26410' => 'ama', 'MSTRG.3139' => 'ama', 'MSTRG.3286' => 'ama', 'MSTRG.563' => 'ama', 'MSTRG.7941' => 'ama', 'Nitab4.5_0000028g0060' => 'nta', 'Nitab4.5_0000065g0260' => 'nta', 'Nitab4.5_0000112g0060' => 'nta', 'Nitab4.5_0000489g0120' => 'nta', 'Nitab4.5_0001776g0050' => 'nta', 'Nitab4.5_0001854g0010' => 'nta', 'Nitab4.5_0001860g0020' => 'nta', 'Nitab4.5_0004352g0010' => 'nta', 'Nitab4.5_0008716g0020' => 'nta', 'Nitab4.5_0008922g0010' => 'nta', 'Nn3g16693' => 'nnu', 'Nn4g22596' => 'nnu', 'Nn7g37639' => 'nnu', 'Oeu001701.1' => 'oeu', 'Oeu018149.1' => 'oeu', 'Oeu026220.1' => 'oeu', 'Oeu038635.1' => 'oeu', 'Oeu049176.1' => 'oeu', 'Oeu056706.1' => 'oeu', 'Oeu056937.1' => 'oeu', 'Oeu057540.1' => 'oeu', 'Os02g0594900' => 'osa', 'Os02g0595100' => 'osa', 'Os04g0477500' => 'osa', 'Os12g0611900' => 'osa', 'Peaxi162Scf00076g00020' => 'pax', 'Peaxi162Scf00128g00217' => 'pax', 'Peaxi162Scf00129g01640' => 'pax', 'Peaxi162Scf00669g00007' => 'pax', 'Peaxi162Scf00700g00421' => 'pax', 'Peaxi162Scf00801g00038' => 'pax', 'Peaxi162Scf00891g00025' => 'pax', 'PGR083G0909' => 'pgr', 'PGR119G1005' => 'pgr', 'PGR142G2236' => 'pgr', 'PGR142G3388' => 'pgr', 'PGSC0003DMG400004514' => 'stu', 'PGSC0003DMG400012635' => 'stu', 'PGSC0003DMG400015730' => 'stu', 'PGSC0003DMG400018611' => 'stu', 'PGSC0003DMG400030897' => 'stu', 'Phvul.001G254800' => 'pvu', 'Phvul.002G260100' => 'pvu', 'Phvul.003G167600' => 'pvu', 'Phvul.004G005100' => 'pvu', 'Potri.001G343600' => 'ptr', 'Potri.006G066700' => 'ptr', 'Potri.008G186000' => 'ptr', 'Potri.010G046900' => 'ptr', 'Potri.018G127900' => 'ptr', 'Pp3c20_17750' => 'ppa', 'Pp3c24_4380' => 'ppa', 'Prupe.1G245800' => 'ppe', 'Prupe.3G293400' => 'ppe', 'Prupe.7G247400' => 'ppe', 'Psat0s145g0120' => 'psa', 'Psat0s595g0040' => 'psa', 'Psat0s595g0120' => 'psa', 'Psat3g175040' => 'psa', 'Psat7g058120' => 'psa', 'PSO017G0428' => 'pso', 'PSO063G7510' => 'pso', 'PSO067G0046' => 'pso', 'PSO478G1073' => 'pso', 'PSO675G3677' => 'pso', 'PSO675G6558' => 'pso', 'PSO675G7520' => 'pso', 'PSO675G8959' => 'pso', 'QL02p074089' => 'qlo', 'QL02p089614' => 'qlo', 'QL03p057736' => 'qlo', 'RcHm_v2.0_Chr1g0364131' => 'rch', 'RcHm_v2.0_Chr2g0087801' => 'rch', 'RcHm_v2.0_Chr2g0087821' => 'rch', 'RcHm_v2.0_Chr2g0173231' => 'rch', 'RcHm_v2.0_Chr4g0433111' => 'rch', 'Rhsim03G0250300' => 'rsi', 'Rhsim08G0048400' => 'rsi', 'Rhsim10G0014800' => 'rsi', 'Rhsim12G0040100' => 'rsi', 'Rhsim12G0109700' => 'rsi', 'Sabra06G0049600' => 'sbr', 'Sabra08G0141000' => 'sbr', 'Sabra10G0021400' => 'sbr', 'Sabra16G0222900' => 'sbr', 'Sabra18G0108600' => 'sbr', 'SalBow1G0433' => 'sbo', 'SalBow1G2038' => 'sbo', 'SalBow1G5003' => 'sbo', 'SalBow7G1197' => 'sbo', 'SalBow8G3506' => 'sbo', 'Sc03g0007300' => 'sci', 'Sc11g0000950' => 'sci', 'Sc14g0008750' => 'sci', 'Sc18g0000420' => 'sci', 'Sed0006754' => 'sed', 'Sed0008741' => 'sed', 'Sed0017172' => 'sed', 'Sed0018925' => 'sed', 'Sed0023326' => 'sed', 'Sed0025909' => 'sed', 'SEGI_05333' => 'sgi', 'SEGI_10362' => 'sgi', 'SEGI_13380' => 'sgi', 'SEGI_24306' => 'sgi', 'SEGI_29077' => 'sgi', 'SEGI_29095' => 'sgi', 'SEGI_36534' => 'sgi', 'SEGI_37506' => 'sgi', 'SEGI_38321' => 'sgi', 'SGA_v2.0_scaffold307G48031' => 'sas', 'SGA_v2.0_scaffold47G17507' => 'sas', 'SGA_v2.0_scaffold63G21736' => 'sas', 'SGA_v2.0_scaffold87G27070' => 'sas', 'SHI17794' => 'shi', 'SHI28851' => 'shi', 'SMO165G0155' => 'smo', 'SMO340G0217' => 'smo', 'SMO367G1210' => 'smo', 'Solyc02g093430.3' => 'sly', 'Solyc05g013580.4' => 'sly', 'Solyc07g008030.3' => 'sly', 'Solyc12g035470.2' => 'sly', 'Sopen02g038020' => 'spe', 'Sopen05g008490' => 'spe', 'Sopen07g003910' => 'spe', 'Sopen12g015240' => 'spe', 'Sp1g11550' => 'spa', 'Sp2g16710' => 'spa', 'Sp3g00430' => 'spa', 'Sp3g26780' => 'spa', 'Sp5g22900' => 'spa', 'Sp6g29530' => 'spa', 'TAR371G0794' => 'tar', 'TAR374G0164' => 'tar', 'TAR622G0165' => 'tar', 'TAR626G0929' => 'tar', 'TAR629G2155' => 'tar', 'THA.LOC104805282' => 'tha', 'THA.LOC104805363' => 'tha', 'THA.LOC104808968' => 'tha', 'THA.LOC104821093' => 'tha', 'THA.LOC104823953' => 'tha', 'THA.LOC104825562' => 'tha', 'THA.LOC104825665' => 'tha', 'Thecc.02G261400' => 'tca', 'Thecc.04G019200' => 'tca', 'Thecc.09G130400' => 'tca', 'Thhalv10004374m.g' => 'esa', 'Thhalv10007850m.g' => 'esa', 'Thhalv10013782m.g' => 'esa', 'Thhalv10018686m.g' => 'esa', 'Thhalv10020899m.g' => 'esa', 'Thhalv10022755m.g' => 'esa', 'TPR.G23851' => 'tpr', 'TPR.G26500' => 'tpr', 'TPR.G27267' => 'tpr', 'TPR.G32001' => 'tpr', 'TPR.G6251' => 'tpr', 'TPR.G8167' => 'tpr', 'TWI12G1330' => 'twi', 'TWI18G1239' => 'twi', 'TWI34G0979' => 'twi', 'TWI36G0670' => 'twi', 'TWI36G0707' => 'twi', 'TWI56G0233' => 'twi', 'TWI75G1809' => 'twi', 'unitig_21.g20874' => 'ugi', 'unitig_26.g10343' => 'ugi', 'unitig_46.g18392' => 'ugi', 'unitig_52.g17178' => 'ugi', 'unitig_8.g2934' => 'ugi', 'vmacro01122' => 'vma', 'vmacro05875' => 'vma', 'vmacro06147' => 'vma', 'vmacro16191' => 'vma', 'vmacro18293' => 'vma', 'VMungo0251G3707' => 'vmu', 'VMungo0464G1521' => 'vmu', 'VMungo1215G0205' => 'vmu', 'VMungo1383G2484' => 'vmu', 'Zm00001eb079610' => 'zma', 'Zm00001eb135990' => 'zma', 'Zm00001eb183710' => 'zma', 'Zm00001eb246020' => 'zma' ), 'gf_id' => 'HOM05D001124', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001124' ), 'data_identifier' => 'HOM05D001124', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001124', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '548', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02520' => 'bna', 'A03p06630' => 'bna', 'A05p44460' => 'bna', 'A06p08710' => 'bna', 'A06p41090' => 'bna', 'A07p32320' => 'bna', 'A08p32520' => 'bna', 'A09p10360' => 'bna', 'A10p24080' => 'bna', 'Aa31LG11G15250' => 'aar', 'Aa31LG1G1800' => 'aar', 'Aa31LG2G5120' => 'aar', 'Aa31LG2G6070' => 'aar', 'Aa31LG5G10770' => 'aar', 'Aa31sc61G90' => 'aar', 'Actinidia01352' => 'ach', 'Actinidia05983' => 'ach', 'Actinidia08133' => 'ach', 'Actinidia15101' => 'ach', 'Actinidia26379' => 'ach', 'Actinidia35778' => 'ach', 'Actinidia36123' => 'ach', 'Actinidia37436' => 'ach', 'Actinidia38730' => 'ach', 'Ah.02g128210' => 'amhyb', 'Ah.03g132990' => 'amhyb', 'Ah.14g079410' => 'amhyb', 'AL1G24640' => 'aly', 'AL2G26680' => 'aly', 'AL3G10530' => 'aly', 'AL3G45230' => 'aly', 'AL5G15230' => 'aly', 'AL5G16960' => 'aly', 'AL6G25210' => 'aly', 'Aqoxy2G00441' => 'aox', 'Aqoxy3G01236' => 'aox', 'Aqoxy5G03746' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3RQ047' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C7GMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9C8JER' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MBL6KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YXCZ83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZANX40' => 'arhy', 'AT1G12990' => 'ath', 'AT1G67880' => 'ath', 'AT2G13290' => 'ath', 'AT3G01620' => 'ath', 'AT3G26445' => 'ath', 'AT3G27540' => 'ath', 'AT5G14480' => 'ath', 'ATR0824G026' => 'atr', 'ATR1098G019' => 'atr', 'Atru.chr11.2145' => 'acertr', 'Atru.chr2.3636' => 'acertr', 'Atru.chr2.3644' => 'acertr', 'Atru.chr6.2422' => 'acertr', 'Atru.chr7.1112' => 'acertr', 'AUR62005469' => 'cqu', 'AUR62011166' => 'cqu', 'AUR62013319' => 'cqu', 'AUR62024273' => 'cqu', 'AUR62028420' => 'cqu', 'AUR62041942' => 'cqu', 'BcaB01g04969' => 'bca', 'BcaB01g06371' => 'bca', 'BcaB02g11494' => 'bca', 'BcaB03g15382' => 'bca', 'BcaB08g36994' => 'bca', 'BcaC03g13477' => 'bca', 'BcaC03g13478' => 'bca', 'BcaC03g13480' => 'bca', 'BcaC03g13481' => 'bca', 'BcaC03g13486' => 'bca', 'BcaC04g19031' => 'bca', 'BcaC04g23085' => 'bca', 'BcaC05g25094' => 'bca', 'BcaC05g25096' => 'bca', 'BcaC05g25138' => 'bca', 'BcaC05g30416' => 'bca', 'BcaC05g30455' => 'bca', 'BcaC06g30979' => 'bca', 'BcaC06g33805' => 'bca', 'BcaC08g46021' => 'bca', 'BcaNung03154' => 'bca', 'BolC2t06623H' => 'bol', 'BolC2t06632H' => 'bol', 'BolC2t06635H' => 'bol', 'BolC2t06638H' => 'bol', 'BolC3t13266H' => 'bol', 'BolC5t29776H' => 'bol', 'BolC6t38912H' => 'bol', 'BolC7t44183H' => 'bol', 'BolC9t54123H' => 'bol', 'BolC9t59107H' => 'bol', 'BraA02t05221Z' => 'bra', 'BraA03t09996Z' => 'bra', 'BraA05t23210Z' => 'bra', 'BraA06t24068Z' => 'bra', 'BraA06t27032Z' => 'bra', 'BraA08t35176Z' => 'bra', 'BraA09t36680Z' => 'bra', 'BraA10t44471Z' => 'bra', 'C02p06760' => 'bna', 'C02p06890' => 'bna', 'C02p07010' => 'bna', 'C03p07660' => 'bna', 'C05p10300' => 'bna', 'C06p38150' => 'bna', 'C07p36650' => 'bna', 'C08p15770' => 'bna', 'C09p12300' => 'bna', 'C09p62700' => 'bna', 'C09p75040' => 'bna', 'CAN.G13.1' => 'can', 'CAN.G138.4' => 'can', 'CAN.G44.6' => 'can', 'CAN.G473.19' => 'can', 'CANSAT01G0835' => 'cansat', 'CANSAT11G0246' => 'cansat', 'CANSAT11G1766' => 'cansat', 'CANSAT64G1954' => 'cansat', 'CARHR013330' => 'chi', 'CARHR060530' => 'chi', 'CARHR075300' => 'chi', 'CARHR105120' => 'chi', 'CARHR148910' => 'chi', 'CARHR198830' => 'chi', 'Carub.0001s1275' => 'cru', 'Carub.0002s1437' => 'cru', 'Carub.0003s0044' => 'cru', 'Carub.0003s2787' => 'cru', 'Carub.0005s0597' => 'cru', 'Carub.0006s1266' => 'cru', 'Ca_06935_v3' => 'car', 'Ca_13559_v3' => 'car', 'Ca_16941_v3' => 'car', 'Ca_16960_v3' => 'car', 'Ca_17775_v3' => 'car', 'Ca_30464_v3' => 'car', 'Cc06_g08160' => 'ccan', 'Cc07_g01520' => 'ccan', 'Cc11_g15810' => 'ccan', 'CDE02G2840' => 'cde', 'CDE03G0093' => 'cde', 'CDE04G2127' => 'cde', 'CDE07G1857' => 'cde', 'CDE09G1246' => 'cde', 'Cfa003412' => 'cfa', 'Cfa007341' => 'cfa', 'Cfa009220' => 'cfa', 'Ciclev10008737m.g' => 'ccl', 'Ciclev10015565m.g' => 'ccl', 'Ciclev10031761m.g' => 'ccl', 'CiPaw.03G045300' => 'cil', 'CiPaw.03G247200' => 'cil', 'CiPaw.04G029500' => 'cil', 'CiPaw.04G174000' => 'cil', 'CiPaw.05G181200' => 'cil', 'CiPaw.06G067100' => 'cil', 'ClCG05G025800' => 'cla', 'ClCG06G011400' => 'cla', 'ClCG09G019360' => 'cla', 'COL.COLO4_04827' => 'col', 'COL.COLO4_29170' => 'col', 'COL.COLO4_35131' => 'col', 'COL.COLO4_35132' => 'col', 'Cpa.g.sc33.32' => 'cpa', 'Cpa.g.sc46.29' => 'cpa', 'Cpa.g.sc796.1' => 'cpa', 'CsaV3_1G030420' => 'csa', 'CsaV3_5G027050' => 'csa', 'CsaV3_5G031040' => 'csa', 'CsaV3_UNG023130' => 'csa', 'CSS0007726' => 'camsi', 'CSS0016433' => 'camsi', 'CSS0017656' => 'camsi', 'CSS0025364' => 'camsi', 'CSS0027582' => 'camsi', 'CSS0047288' => 'camsi', 'CSS0049950' => 'camsi', 'DCAR_003843' => 'dca', 'DCAR_007052' => 'dca', 'DCAR_020884' => 'dca', 'DCAR_021730' => 'dca', 'DCAR_024423' => 'dca', 'DCAR_026509' => 'dca', 'DCAR_031158' => 'dca', 'Dinv14728' => 'din', 'Dinv15219' => 'din', 'Dinv25728' => 'din', 'Dinv33428' => 'din', 'Dinv36489' => 'din', 'Dinv41486' => 'din', 'Duzib147G0469' => 'dzi', 'Duzib168G0060' => 'dzi', 'Duzib187G1215' => 'dzi', 'Duzib248G0692' => 'dzi', 'Duzib251G0767' => 'dzi', 'Duzib264G0446' => 'dzi', 'Duzib268G0691' => 'dzi', 'ECA232G4767' => 'eca', 'ECA233G2838' => 'eca', 'ECA234G0391' => 'eca', 'ECA234G0857' => 'eca', 'ECA236G1593' => 'eca', 'ECA238G0565' => 'eca', 'ECA246G1027' => 'eca', 'ECA246G3223' => 'eca', 'ECA246G3470' => 'eca', 'EL10Ac6g13829' => 'bvu', 'EL10Ac6g14093' => 'bvu', 'EL10Ac8g18707' => 'bvu', 'Eucgr.C01369' => 'egr', 'Eucgr.H02492' => 'egr', 'Eucgr.I01733' => 'egr', 'Eucgr.J02255' => 'egr', 'Eucgr.J02257' => 'egr', 'Eucgr.J02258' => 'egr', 'FAN02G1601' => 'fan', 'FAN03G1586' => 'fan', 'FAN03G2986' => 'fan', 'FAN05G4837' => 'fan', 'FAN06G0146' => 'fan', 'FAN07G0858' => 'fan', 'FAN09G3179' => 'fan', 'FAN10G0669' => 'fan', 'FAN12G2358' => 'fan', 'FAN14G4198' => 'fan', 'FAN14G5112' => 'fan', 'FAN17G0342' => 'fan', 'FAN19G0342' => 'fan', 'FAN19G0962' => 'fan', 'FAN19G1101' => 'fan', 'FAN19G1872' => 'fan', 'FAN22G0356' => 'fan', 'FAN23G0744' => 'fan', 'FAN23G1914' => 'fan', 'FAN26G0032' => 'fan', 'FAN28G0625' => 'fan', 'FvH4_1g02710' => 'fve', 'FvH4_1g02720' => 'fve', 'FvH4_4g25670' => 'fve', 'FvH4_6g51700' => 'fve', 'FvH4_7g20170' => 'fve', 'Glyma.05G175000' => 'gma', 'Glyma.08G132300' => 'gma', 'Glyma.11G243000' => 'gma', 'Glyma.13G158900' => 'gma', 'Glyma.17G112400' => 'gma', 'Glyma.18G014100' => 'gma', 'Glyma.19G003100' => 'gma', 'Glyma.19G056500' => 'gma', 'Gohir.A01G158900' => 'ghi', 'Gohir.A05G312600' => 'ghi', 'Gohir.A05G354900' => 'ghi', 'Gohir.A07G037200' => 'ghi', 'Gohir.A09G030000' => 'ghi', 'Gohir.A12G145200' => 'ghi', 'Gohir.D01G151500' => 'ghi', 'Gohir.D04G058300' => 'ghi', 'Gohir.D05G314100' => 'ghi', 'Gohir.D07G041400' => 'ghi', 'Gohir.D09G029700' => 'ghi', 'Gohir.D12G149700' => 'ghi', 'Gorai.001G043800' => 'gra', 'Gorai.002G187800' => 'gra', 'Gorai.006G034700' => 'gra', 'Gorai.008G161200' => 'gra', 'Gorai.009G335700' => 'gra', 'Gorai.012G065000' => 'gra', 'GSVIVG01000535001' => 'vvi', 'GSVIVG01015572001' => 'vvi', 'GSVIVG01032386001' => 'vvi', 'HanXRQChr05g0138531' => 'han', 'HanXRQChr06g0174391' => 'han', 'HanXRQChr07g0199021' => 'han', 'HanXRQChr08g0208211' => 'han', 'HanXRQChr09g0255471' => 'han', 'HanXRQChr10g0315791' => 'han', 'HanXRQChr12g0371991' => 'han', 'HanXRQChr15g0475251' => 'han', 'HanXRQChr17g0540001' => 'han', 'HanXRQChr17g0548631' => 'han', 'HanXRQChr17g0569561' => 'han', 'Haze_12256' => 'cav', 'Haze_14756' => 'cav', 'Haze_25528' => 'cav', 'Hma1.2p1_0079F.1_g041020' => 'hma', 'Hma1.2p1_0818F.1_g223260' => 'hma', 'Hma1.2p1_1747F.1_g300530' => 'hma', 'HPP92_004607' => 'vpl', 'HPP92_004608' => 'vpl', 'HPP92_006181' => 'vpl', 'HPP92_012192' => 'vpl', 'HPP92_015680' => 'vpl', 'HPP92_020249' => 'vpl', 'HPP92_021376' => 'vpl', 'HPP92_024275' => 'vpl', 'Hund06031' => 'sun', 'Hund25391' => 'sun', 'Lalb_Chr07g0185371' => 'lal', 'Lalb_Chr07g0185381' => 'lal', 'Lalb_Chr12g0204011' => 'lal', 'Lalb_Chr13g0301671' => 'lal', 'Lalb_Chr14g0362851' => 'lal', 'Lalb_Chr24g0403581' => 'lal', 'Lj1g0000233' => 'lja', 'Lj2g0018120' => 'lja', 'Lj3C621T0' => 'lonja', 'Lj3P1059T14' => 'lonja', 'Lj3P611T9' => 'lonja', 'Lj3P614T13' => 'lonja', 'Lj3P615T5' => 'lonja', 'Lj4g0012315' => 'lja', 'Lj4g0026182' => 'lja', 'Lj6P813T16' => 'lonja', 'Lj7C427T7' => 'lonja', 'Lj7C427T8' => 'lonja', 'Lj7P600T41' => 'lonja', 'Lju41C42G17' => 'lonja', 'Lsat_1_v5_gn_0_47300' => 'lsa', 'Lsat_1_v5_gn_2_91280' => 'lsa', 'Lsat_1_v5_gn_3_30561' => 'lsa', 'Lsat_1_v5_gn_4_184321' => 'lsa', 'Lsat_1_v5_gn_4_4041' => 'lsa', 'Lsat_1_v5_gn_5_92000' => 'lsa', 'Lsat_1_v5_gn_8_152940' => 'lsa', 'Lsat_1_v5_gn_8_62401' => 'lsa', 'Manes.06G055900' => 'mes', 'Manes.12G022200' => 'mes', 'Manes.13G023300' => 'mes', 'Manes.14G115000' => 'mes', 'Manes.15G151700' => 'mes', 'Manes.17G111300' => 'mes', 'Mapoly0226s0009' => 'mpo', 'MBI02_g25363_MAGBIO' => 'mbi', 'MBI06_g00027_MAGBIO' => 'mbi', 'MBI10_g13034_MAGBIO' => 'mbi', 'MD09G1023400' => 'mdo', 'MD13G1100100' => 'mdo', 'MD15G1169200' => 'mdo', 'MD16G1101100' => 'mdo', 'MD17G1022900' => 'mdo', 'Medtr3g096150' => 'mtr', 'Medtr4g115070' => 'mtr', 'Medtr7g033325' => 'mtr', 'Medtr8g089840' => 'mtr', 'MELO3C010319.2' => 'cme', 'MELO3C011944.2' => 'cme', 'MELO3C021589.2' => 'cme', 'Migut.E00207' => 'egut', 'Migut.H00067' => 'egut', 'Migut.K00433' => 'egut', 'Migut.K00606' => 'egut', 'Migut.K01410' => 'egut', 'MSTRG.13347' => 'ama', 'MSTRG.24045' => 'ama', 'MSTRG.2428' => 'ama', 'MSTRG.26410' => 'ama', 'MSTRG.3139' => 'ama', 'MSTRG.3286' => 'ama', 'MSTRG.563' => 'ama', 'MSTRG.7941' => 'ama', 'Nitab4.5_0000028g0060' => 'nta', 'Nitab4.5_0000065g0260' => 'nta', 'Nitab4.5_0000112g0060' => 'nta', 'Nitab4.5_0000489g0120' => 'nta', 'Nitab4.5_0001776g0050' => 'nta', 'Nitab4.5_0001854g0010' => 'nta', 'Nitab4.5_0001860g0020' => 'nta', 'Nitab4.5_0004352g0010' => 'nta', 'Nitab4.5_0008716g0020' => 'nta', 'Nitab4.5_0008922g0010' => 'nta', 'Nn3g16693' => 'nnu', 'Nn4g22596' => 'nnu', 'Nn7g37639' => 'nnu', 'Oeu001701.1' => 'oeu', 'Oeu018149.1' => 'oeu', 'Oeu026220.1' => 'oeu', 'Oeu038635.1' => 'oeu', 'Oeu049176.1' => 'oeu', 'Oeu056706.1' => 'oeu', 'Oeu056937.1' => 'oeu', 'Oeu057540.1' => 'oeu', 'Os02g0594900' => 'osa', 'Os02g0595100' => 'osa', 'Os04g0477500' => 'osa', 'Os12g0611900' => 'osa', 'Peaxi162Scf00076g00020' => 'pax', 'Peaxi162Scf00128g00217' => 'pax', 'Peaxi162Scf00129g01640' => 'pax', 'Peaxi162Scf00669g00007' => 'pax', 'Peaxi162Scf00700g00421' => 'pax', 'Peaxi162Scf00801g00038' => 'pax', 'Peaxi162Scf00891g00025' => 'pax', 'PGR083G0909' => 'pgr', 'PGR119G1005' => 'pgr', 'PGR142G2236' => 'pgr', 'PGR142G3388' => 'pgr', 'PGSC0003DMG400004514' => 'stu', 'PGSC0003DMG400012635' => 'stu', 'PGSC0003DMG400015730' => 'stu', 'PGSC0003DMG400018611' => 'stu', 'PGSC0003DMG400030897' => 'stu', 'Phvul.001G254800' => 'pvu', 'Phvul.002G260100' => 'pvu', 'Phvul.003G167600' => 'pvu', 'Phvul.004G005100' => 'pvu', 'Potri.001G343600' => 'ptr', 'Potri.006G066700' => 'ptr', 'Potri.008G186000' => 'ptr', 'Potri.010G046900' => 'ptr', 'Potri.018G127900' => 'ptr', 'Pp3c20_17750' => 'ppa', 'Pp3c24_4380' => 'ppa', 'Prupe.1G245800' => 'ppe', 'Prupe.3G293400' => 'ppe', 'Prupe.7G247400' => 'ppe', 'Psat0s145g0120' => 'psa', 'Psat0s595g0040' => 'psa', 'Psat0s595g0120' => 'psa', 'Psat3g175040' => 'psa', 'Psat7g058120' => 'psa', 'PSO017G0428' => 'pso', 'PSO063G7510' => 'pso', 'PSO067G0046' => 'pso', 'PSO478G1073' => 'pso', 'PSO675G3677' => 'pso', 'PSO675G6558' => 'pso', 'PSO675G7520' => 'pso', 'PSO675G8959' => 'pso', 'QL02p074089' => 'qlo', 'QL02p089614' => 'qlo', 'QL03p057736' => 'qlo', 'RcHm_v2.0_Chr1g0364131' => 'rch', 'RcHm_v2.0_Chr2g0087801' => 'rch', 'RcHm_v2.0_Chr2g0087821' => 'rch', 'RcHm_v2.0_Chr2g0173231' => 'rch', 'RcHm_v2.0_Chr4g0433111' => 'rch', 'Rhsim03G0250300' => 'rsi', 'Rhsim08G0048400' => 'rsi', 'Rhsim10G0014800' => 'rsi', 'Rhsim12G0040100' => 'rsi', 'Rhsim12G0109700' => 'rsi', 'Sabra06G0049600' => 'sbr', 'Sabra08G0141000' => 'sbr', 'Sabra10G0021400' => 'sbr', 'Sabra16G0222900' => 'sbr', 'Sabra18G0108600' => 'sbr', 'SalBow1G0433' => 'sbo', 'SalBow1G2038' => 'sbo', 'SalBow1G5003' => 'sbo', 'SalBow7G1197' => 'sbo', 'SalBow8G3506' => 'sbo', 'Sc03g0007300' => 'sci', 'Sc11g0000950' => 'sci', 'Sc14g0008750' => 'sci', 'Sc18g0000420' => 'sci', 'Sed0006754' => 'sed', 'Sed0008741' => 'sed', 'Sed0017172' => 'sed', 'Sed0018925' => 'sed', 'Sed0023326' => 'sed', 'Sed0025909' => 'sed', 'SEGI_05333' => 'sgi', 'SEGI_10362' => 'sgi', 'SEGI_13380' => 'sgi', 'SEGI_24306' => 'sgi', 'SEGI_29077' => 'sgi', 'SEGI_29095' => 'sgi', 'SEGI_36534' => 'sgi', 'SEGI_37506' => 'sgi', 'SEGI_38321' => 'sgi', 'SGA_v2.0_scaffold307G48031' => 'sas', 'SGA_v2.0_scaffold47G17507' => 'sas', 'SGA_v2.0_scaffold63G21736' => 'sas', 'SGA_v2.0_scaffold87G27070' => 'sas', 'SHI17794' => 'shi', 'SHI28851' => 'shi', 'SMO165G0155' => 'smo', 'SMO340G0217' => 'smo', 'SMO367G1210' => 'smo', 'Solyc02g093430.3' => 'sly', 'Solyc05g013580.4' => 'sly', 'Solyc07g008030.3' => 'sly', 'Solyc12g035470.2' => 'sly', 'Sopen02g038020' => 'spe', 'Sopen05g008490' => 'spe', 'Sopen07g003910' => 'spe', 'Sopen12g015240' => 'spe', 'Sp1g11550' => 'spa', 'Sp2g16710' => 'spa', 'Sp3g00430' => 'spa', 'Sp3g26780' => 'spa', 'Sp5g22900' => 'spa', 'Sp6g29530' => 'spa', 'TAR371G0794' => 'tar', 'TAR374G0164' => 'tar', 'TAR622G0165' => 'tar', 'TAR626G0929' => 'tar', 'TAR629G2155' => 'tar', 'THA.LOC104805282' => 'tha', 'THA.LOC104805363' => 'tha', 'THA.LOC104808968' => 'tha', 'THA.LOC104821093' => 'tha', 'THA.LOC104823953' => 'tha', 'THA.LOC104825562' => 'tha', 'THA.LOC104825665' => 'tha', 'Thecc.02G261400' => 'tca', 'Thecc.04G019200' => 'tca', 'Thecc.09G130400' => 'tca', 'Thhalv10004374m.g' => 'esa', 'Thhalv10007850m.g' => 'esa', 'Thhalv10013782m.g' => 'esa', 'Thhalv10018686m.g' => 'esa', 'Thhalv10020899m.g' => 'esa', 'Thhalv10022755m.g' => 'esa', 'TPR.G23851' => 'tpr', 'TPR.G26500' => 'tpr', 'TPR.G27267' => 'tpr', 'TPR.G32001' => 'tpr', 'TPR.G6251' => 'tpr', 'TPR.G8167' => 'tpr', 'TWI12G1330' => 'twi', 'TWI18G1239' => 'twi', 'TWI34G0979' => 'twi', 'TWI36G0670' => 'twi', 'TWI36G0707' => 'twi', 'TWI56G0233' => 'twi', 'TWI75G1809' => 'twi', 'unitig_21.g20874' => 'ugi', 'unitig_26.g10343' => 'ugi', 'unitig_46.g18392' => 'ugi', 'unitig_52.g17178' => 'ugi', 'unitig_8.g2934' => 'ugi', 'vmacro01122' => 'vma', 'vmacro05875' => 'vma', 'vmacro06147' => 'vma', 'vmacro16191' => 'vma', 'vmacro18293' => 'vma', 'VMungo0251G3707' => 'vmu', 'VMungo0464G1521' => 'vmu', 'VMungo1215G0205' => 'vmu', 'VMungo1383G2484' => 'vmu', 'Zm00001eb079610' => 'zma', 'Zm00001eb135990' => 'zma', 'Zm00001eb183710' => 'zma', 'Zm00001eb246020' => 'zma' ) $gf_id = 'HOM05D001124' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001124' ) $data_identifier = 'HOM05D001124' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 6, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 7, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 21, 'bol' => (int) 10, 'bra' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 6, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 9, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 21, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 8, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 10, 'lsa' => (int) 8, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 8, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 9, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb246020' $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' => 'HOM05D001124', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '548', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02520' => 'bna', 'A03p06630' => 'bna', 'A05p44460' => 'bna', 'A06p08710' => 'bna', 'A06p41090' => 'bna', 'A07p32320' => 'bna', 'A08p32520' => 'bna', 'A09p10360' => 'bna', 'A10p24080' => 'bna', 'Aa31LG11G15250' => 'aar', 'Aa31LG1G1800' => 'aar', 'Aa31LG2G5120' => 'aar', 'Aa31LG2G6070' => 'aar', 'Aa31LG5G10770' => 'aar', 'Aa31sc61G90' => 'aar', 'Actinidia01352' => 'ach', 'Actinidia05983' => 'ach', 'Actinidia08133' => 'ach', 'Actinidia15101' => 'ach', 'Actinidia26379' => 'ach', 'Actinidia35778' => 'ach', 'Actinidia36123' => 'ach', 'Actinidia37436' => 'ach', 'Actinidia38730' => 'ach', 'Ah.02g128210' => 'amhyb', 'Ah.03g132990' => 'amhyb', 'Ah.14g079410' => 'amhyb', 'AL1G24640' => 'aly', 'AL2G26680' => 'aly', 'AL3G10530' => 'aly', 'AL3G45230' => 'aly', 'AL5G15230' => 'aly', 'AL5G16960' => 'aly', 'AL6G25210' => 'aly', 'Aqoxy2G00441' => 'aox', 'Aqoxy3G01236' => 'aox', 'Aqoxy5G03746' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3RQ047' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C7GMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9C8JER' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MBL6KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YXCZ83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZANX40' => 'arhy', 'AT1G12990' => 'ath', 'AT1G67880' => 'ath', 'AT2G13290' => 'ath', 'AT3G01620' => 'ath', 'AT3G26445' => 'ath', 'AT3G27540' => 'ath', 'AT5G14480' => 'ath', 'ATR0824G026' => 'atr', 'ATR1098G019' => 'atr', 'Atru.chr11.2145' => 'acertr', 'Atru.chr2.3636' => 'acertr', 'Atru.chr2.3644' => 'acertr', 'Atru.chr6.2422' => 'acertr', 'Atru.chr7.1112' => 'acertr', 'AUR62005469' => 'cqu', 'AUR62011166' => 'cqu', 'AUR62013319' => 'cqu', 'AUR62024273' => 'cqu', 'AUR62028420' => 'cqu', 'AUR62041942' => 'cqu', 'BcaB01g04969' => 'bca', 'BcaB01g06371' => 'bca', 'BcaB02g11494' => 'bca', 'BcaB03g15382' => 'bca', 'BcaB08g36994' => 'bca', 'BcaC03g13477' => 'bca', 'BcaC03g13478' => 'bca', 'BcaC03g13480' => 'bca', 'BcaC03g13481' => 'bca', 'BcaC03g13486' => 'bca', 'BcaC04g19031' => 'bca', 'BcaC04g23085' => 'bca', 'BcaC05g25094' => 'bca', 'BcaC05g25096' => 'bca', 'BcaC05g25138' => 'bca', 'BcaC05g30416' => 'bca', 'BcaC05g30455' => 'bca', 'BcaC06g30979' => 'bca', 'BcaC06g33805' => 'bca', 'BcaC08g46021' => 'bca', 'BcaNung03154' => 'bca', 'BolC2t06623H' => 'bol', 'BolC2t06632H' => 'bol', 'BolC2t06635H' => 'bol', 'BolC2t06638H' => 'bol', 'BolC3t13266H' => 'bol', 'BolC5t29776H' => 'bol', 'BolC6t38912H' => 'bol', 'BolC7t44183H' => 'bol', 'BolC9t54123H' => 'bol', 'BolC9t59107H' => 'bol', 'BraA02t05221Z' => 'bra', 'BraA03t09996Z' => 'bra', 'BraA05t23210Z' => 'bra', 'BraA06t24068Z' => 'bra', 'BraA06t27032Z' => 'bra', 'BraA08t35176Z' => 'bra', 'BraA09t36680Z' => 'bra', 'BraA10t44471Z' => 'bra', 'C02p06760' => 'bna', 'C02p06890' => 'bna', 'C02p07010' => 'bna', 'C03p07660' => 'bna', 'C05p10300' => 'bna', 'C06p38150' => 'bna', 'C07p36650' => 'bna', 'C08p15770' => 'bna', 'C09p12300' => 'bna', 'C09p62700' => 'bna', 'C09p75040' => 'bna', 'CAN.G13.1' => 'can', 'CAN.G138.4' => 'can', 'CAN.G44.6' => 'can', 'CAN.G473.19' => 'can', 'CANSAT01G0835' => 'cansat', 'CANSAT11G0246' => 'cansat', 'CANSAT11G1766' => 'cansat', 'CANSAT64G1954' => 'cansat', 'CARHR013330' => 'chi', 'CARHR060530' => 'chi', 'CARHR075300' => 'chi', 'CARHR105120' => 'chi', 'CARHR148910' => 'chi', 'CARHR198830' => 'chi', 'Carub.0001s1275' => 'cru', 'Carub.0002s1437' => 'cru', 'Carub.0003s0044' => 'cru', 'Carub.0003s2787' => 'cru', 'Carub.0005s0597' => 'cru', 'Carub.0006s1266' => 'cru', 'Ca_06935_v3' => 'car', 'Ca_13559_v3' => 'car', 'Ca_16941_v3' => 'car', 'Ca_16960_v3' => 'car', 'Ca_17775_v3' => 'car', 'Ca_30464_v3' => 'car', 'Cc06_g08160' => 'ccan', 'Cc07_g01520' => 'ccan', 'Cc11_g15810' => 'ccan', 'CDE02G2840' => 'cde', 'CDE03G0093' => 'cde', 'CDE04G2127' => 'cde', 'CDE07G1857' => 'cde', 'CDE09G1246' => 'cde', 'Cfa003412' => 'cfa', 'Cfa007341' => 'cfa', 'Cfa009220' => 'cfa', 'Ciclev10008737m.g' => 'ccl', 'Ciclev10015565m.g' => 'ccl', 'Ciclev10031761m.g' => 'ccl', 'CiPaw.03G045300' => 'cil', 'CiPaw.03G247200' => 'cil', 'CiPaw.04G029500' => 'cil', 'CiPaw.04G174000' => 'cil', 'CiPaw.05G181200' => 'cil', 'CiPaw.06G067100' => 'cil', 'ClCG05G025800' => 'cla', 'ClCG06G011400' => 'cla', 'ClCG09G019360' => 'cla', 'COL.COLO4_04827' => 'col', 'COL.COLO4_29170' => 'col', 'COL.COLO4_35131' => 'col', 'COL.COLO4_35132' => 'col', 'Cpa.g.sc33.32' => 'cpa', 'Cpa.g.sc46.29' => 'cpa', 'Cpa.g.sc796.1' => 'cpa', 'CsaV3_1G030420' => 'csa', 'CsaV3_5G027050' => 'csa', 'CsaV3_5G031040' => 'csa', 'CsaV3_UNG023130' => 'csa', 'CSS0007726' => 'camsi', 'CSS0016433' => 'camsi', 'CSS0017656' => 'camsi', 'CSS0025364' => 'camsi', 'CSS0027582' => 'camsi', 'CSS0047288' => 'camsi', 'CSS0049950' => 'camsi', 'DCAR_003843' => 'dca', 'DCAR_007052' => 'dca', 'DCAR_020884' => 'dca', 'DCAR_021730' => 'dca', 'DCAR_024423' => 'dca', 'DCAR_026509' => 'dca', 'DCAR_031158' => 'dca', 'Dinv14728' => 'din', 'Dinv15219' => 'din', 'Dinv25728' => 'din', 'Dinv33428' => 'din', 'Dinv36489' => 'din', 'Dinv41486' => 'din', 'Duzib147G0469' => 'dzi', 'Duzib168G0060' => 'dzi', 'Duzib187G1215' => 'dzi', 'Duzib248G0692' => 'dzi', 'Duzib251G0767' => 'dzi', 'Duzib264G0446' => 'dzi', 'Duzib268G0691' => 'dzi', 'ECA232G4767' => 'eca', 'ECA233G2838' => 'eca', 'ECA234G0391' => 'eca', 'ECA234G0857' => 'eca', 'ECA236G1593' => 'eca', 'ECA238G0565' => 'eca', 'ECA246G1027' => 'eca', 'ECA246G3223' => 'eca', 'ECA246G3470' => 'eca', 'EL10Ac6g13829' => 'bvu', 'EL10Ac6g14093' => 'bvu', 'EL10Ac8g18707' => 'bvu', 'Eucgr.C01369' => 'egr', 'Eucgr.H02492' => 'egr', 'Eucgr.I01733' => 'egr', 'Eucgr.J02255' => 'egr', 'Eucgr.J02257' => 'egr', 'Eucgr.J02258' => 'egr', 'FAN02G1601' => 'fan', 'FAN03G1586' => 'fan', 'FAN03G2986' => 'fan', 'FAN05G4837' => 'fan', 'FAN06G0146' => 'fan', 'FAN07G0858' => 'fan', 'FAN09G3179' => 'fan', 'FAN10G0669' => 'fan', 'FAN12G2358' => 'fan', 'FAN14G4198' => 'fan', 'FAN14G5112' => 'fan', 'FAN17G0342' => 'fan', 'FAN19G0342' => 'fan', 'FAN19G0962' => 'fan', 'FAN19G1101' => 'fan', 'FAN19G1872' => 'fan', 'FAN22G0356' => 'fan', 'FAN23G0744' => 'fan', 'FAN23G1914' => 'fan', 'FAN26G0032' => 'fan', 'FAN28G0625' => 'fan', 'FvH4_1g02710' => 'fve', 'FvH4_1g02720' => 'fve', 'FvH4_4g25670' => 'fve', 'FvH4_6g51700' => 'fve', 'FvH4_7g20170' => 'fve', 'Glyma.05G175000' => 'gma', 'Glyma.08G132300' => 'gma', 'Glyma.11G243000' => 'gma', 'Glyma.13G158900' => 'gma', 'Glyma.17G112400' => 'gma', 'Glyma.18G014100' => 'gma', 'Glyma.19G003100' => 'gma', 'Glyma.19G056500' => 'gma', 'Gohir.A01G158900' => 'ghi', 'Gohir.A05G312600' => 'ghi', 'Gohir.A05G354900' => 'ghi', 'Gohir.A07G037200' => 'ghi', 'Gohir.A09G030000' => 'ghi', 'Gohir.A12G145200' => 'ghi', 'Gohir.D01G151500' => 'ghi', 'Gohir.D04G058300' => 'ghi', 'Gohir.D05G314100' => 'ghi', 'Gohir.D07G041400' => 'ghi', 'Gohir.D09G029700' => 'ghi', 'Gohir.D12G149700' => 'ghi', 'Gorai.001G043800' => 'gra', 'Gorai.002G187800' => 'gra', 'Gorai.006G034700' => 'gra', 'Gorai.008G161200' => 'gra', 'Gorai.009G335700' => 'gra', 'Gorai.012G065000' => 'gra', 'GSVIVG01000535001' => 'vvi', 'GSVIVG01015572001' => 'vvi', 'GSVIVG01032386001' => 'vvi', 'HanXRQChr05g0138531' => 'han', 'HanXRQChr06g0174391' => 'han', 'HanXRQChr07g0199021' => 'han', 'HanXRQChr08g0208211' => 'han', 'HanXRQChr09g0255471' => 'han', 'HanXRQChr10g0315791' => 'han', 'HanXRQChr12g0371991' => 'han', 'HanXRQChr15g0475251' => 'han', 'HanXRQChr17g0540001' => 'han', 'HanXRQChr17g0548631' => 'han', 'HanXRQChr17g0569561' => 'han', 'Haze_12256' => 'cav', 'Haze_14756' => 'cav', 'Haze_25528' => 'cav', 'Hma1.2p1_0079F.1_g041020' => 'hma', 'Hma1.2p1_0818F.1_g223260' => 'hma', 'Hma1.2p1_1747F.1_g300530' => 'hma', 'HPP92_004607' => 'vpl', 'HPP92_004608' => 'vpl', 'HPP92_006181' => 'vpl', 'HPP92_012192' => 'vpl', 'HPP92_015680' => 'vpl', 'HPP92_020249' => 'vpl', 'HPP92_021376' => 'vpl', 'HPP92_024275' => 'vpl', 'Hund06031' => 'sun', 'Hund25391' => 'sun', 'Lalb_Chr07g0185371' => 'lal', 'Lalb_Chr07g0185381' => 'lal', 'Lalb_Chr12g0204011' => 'lal', 'Lalb_Chr13g0301671' => 'lal', 'Lalb_Chr14g0362851' => 'lal', 'Lalb_Chr24g0403581' => 'lal', 'Lj1g0000233' => 'lja', 'Lj2g0018120' => 'lja', 'Lj3C621T0' => 'lonja', 'Lj3P1059T14' => 'lonja', 'Lj3P611T9' => 'lonja', 'Lj3P614T13' => 'lonja', 'Lj3P615T5' => 'lonja', 'Lj4g0012315' => 'lja', 'Lj4g0026182' => 'lja', 'Lj6P813T16' => 'lonja', 'Lj7C427T7' => 'lonja', 'Lj7C427T8' => 'lonja', 'Lj7P600T41' => 'lonja', 'Lju41C42G17' => 'lonja', 'Lsat_1_v5_gn_0_47300' => 'lsa', 'Lsat_1_v5_gn_2_91280' => 'lsa', 'Lsat_1_v5_gn_3_30561' => 'lsa', 'Lsat_1_v5_gn_4_184321' => 'lsa', 'Lsat_1_v5_gn_4_4041' => 'lsa', 'Lsat_1_v5_gn_5_92000' => 'lsa', 'Lsat_1_v5_gn_8_152940' => 'lsa', 'Lsat_1_v5_gn_8_62401' => 'lsa', 'Manes.06G055900' => 'mes', 'Manes.12G022200' => 'mes', 'Manes.13G023300' => 'mes', 'Manes.14G115000' => 'mes', 'Manes.15G151700' => 'mes', 'Manes.17G111300' => 'mes', 'Mapoly0226s0009' => 'mpo', 'MBI02_g25363_MAGBIO' => 'mbi', 'MBI06_g00027_MAGBIO' => 'mbi', 'MBI10_g13034_MAGBIO' => 'mbi', 'MD09G1023400' => 'mdo', 'MD13G1100100' => 'mdo', 'MD15G1169200' => 'mdo', 'MD16G1101100' => 'mdo', 'MD17G1022900' => 'mdo', 'Medtr3g096150' => 'mtr', 'Medtr4g115070' => 'mtr', 'Medtr7g033325' => 'mtr', 'Medtr8g089840' => 'mtr', 'MELO3C010319.2' => 'cme', 'MELO3C011944.2' => 'cme', 'MELO3C021589.2' => 'cme', 'Migut.E00207' => 'egut', 'Migut.H00067' => 'egut', 'Migut.K00433' => 'egut', 'Migut.K00606' => 'egut', 'Migut.K01410' => 'egut', 'MSTRG.13347' => 'ama', 'MSTRG.24045' => 'ama', 'MSTRG.2428' => 'ama', 'MSTRG.26410' => 'ama', 'MSTRG.3139' => 'ama', 'MSTRG.3286' => 'ama', 'MSTRG.563' => 'ama', 'MSTRG.7941' => 'ama', 'Nitab4.5_0000028g0060' => 'nta', 'Nitab4.5_0000065g0260' => 'nta', 'Nitab4.5_0000112g0060' => 'nta', 'Nitab4.5_0000489g0120' => 'nta', 'Nitab4.5_0001776g0050' => 'nta', 'Nitab4.5_0001854g0010' => 'nta', 'Nitab4.5_0001860g0020' => 'nta', 'Nitab4.5_0004352g0010' => 'nta', 'Nitab4.5_0008716g0020' => 'nta', 'Nitab4.5_0008922g0010' => 'nta', 'Nn3g16693' => 'nnu', 'Nn4g22596' => 'nnu', 'Nn7g37639' => 'nnu', 'Oeu001701.1' => 'oeu', 'Oeu018149.1' => 'oeu', 'Oeu026220.1' => 'oeu', 'Oeu038635.1' => 'oeu', 'Oeu049176.1' => 'oeu', 'Oeu056706.1' => 'oeu', 'Oeu056937.1' => 'oeu', 'Oeu057540.1' => 'oeu', 'Os02g0594900' => 'osa', 'Os02g0595100' => 'osa', 'Os04g0477500' => 'osa', 'Os12g0611900' => 'osa', 'Peaxi162Scf00076g00020' => 'pax', 'Peaxi162Scf00128g00217' => 'pax', 'Peaxi162Scf00129g01640' => 'pax', 'Peaxi162Scf00669g00007' => 'pax', 'Peaxi162Scf00700g00421' => 'pax', 'Peaxi162Scf00801g00038' => 'pax', 'Peaxi162Scf00891g00025' => 'pax', 'PGR083G0909' => 'pgr', 'PGR119G1005' => 'pgr', 'PGR142G2236' => 'pgr', 'PGR142G3388' => 'pgr', 'PGSC0003DMG400004514' => 'stu', 'PGSC0003DMG400012635' => 'stu', 'PGSC0003DMG400015730' => 'stu', 'PGSC0003DMG400018611' => 'stu', 'PGSC0003DMG400030897' => 'stu', 'Phvul.001G254800' => 'pvu', 'Phvul.002G260100' => 'pvu', 'Phvul.003G167600' => 'pvu', 'Phvul.004G005100' => 'pvu', 'Potri.001G343600' => 'ptr', 'Potri.006G066700' => 'ptr', 'Potri.008G186000' => 'ptr', 'Potri.010G046900' => 'ptr', 'Potri.018G127900' => 'ptr', 'Pp3c20_17750' => 'ppa', 'Pp3c24_4380' => 'ppa', 'Prupe.1G245800' => 'ppe', 'Prupe.3G293400' => 'ppe', 'Prupe.7G247400' => 'ppe', 'Psat0s145g0120' => 'psa', 'Psat0s595g0040' => 'psa', 'Psat0s595g0120' => 'psa', 'Psat3g175040' => 'psa', 'Psat7g058120' => 'psa', 'PSO017G0428' => 'pso', 'PSO063G7510' => 'pso', 'PSO067G0046' => 'pso', 'PSO478G1073' => 'pso', 'PSO675G3677' => 'pso', 'PSO675G6558' => 'pso', 'PSO675G7520' => 'pso', 'PSO675G8959' => 'pso', 'QL02p074089' => 'qlo', 'QL02p089614' => 'qlo', 'QL03p057736' => 'qlo', 'RcHm_v2.0_Chr1g0364131' => 'rch', 'RcHm_v2.0_Chr2g0087801' => 'rch', 'RcHm_v2.0_Chr2g0087821' => 'rch', 'RcHm_v2.0_Chr2g0173231' => 'rch', 'RcHm_v2.0_Chr4g0433111' => 'rch', 'Rhsim03G0250300' => 'rsi', 'Rhsim08G0048400' => 'rsi', 'Rhsim10G0014800' => 'rsi', 'Rhsim12G0040100' => 'rsi', 'Rhsim12G0109700' => 'rsi', 'Sabra06G0049600' => 'sbr', 'Sabra08G0141000' => 'sbr', 'Sabra10G0021400' => 'sbr', 'Sabra16G0222900' => 'sbr', 'Sabra18G0108600' => 'sbr', 'SalBow1G0433' => 'sbo', 'SalBow1G2038' => 'sbo', 'SalBow1G5003' => 'sbo', 'SalBow7G1197' => 'sbo', 'SalBow8G3506' => 'sbo', 'Sc03g0007300' => 'sci', 'Sc11g0000950' => 'sci', 'Sc14g0008750' => 'sci', 'Sc18g0000420' => 'sci', 'Sed0006754' => 'sed', 'Sed0008741' => 'sed', 'Sed0017172' => 'sed', 'Sed0018925' => 'sed', 'Sed0023326' => 'sed', 'Sed0025909' => 'sed', 'SEGI_05333' => 'sgi', 'SEGI_10362' => 'sgi', 'SEGI_13380' => 'sgi', 'SEGI_24306' => 'sgi', 'SEGI_29077' => 'sgi', 'SEGI_29095' => 'sgi', 'SEGI_36534' => 'sgi', 'SEGI_37506' => 'sgi', 'SEGI_38321' => 'sgi', 'SGA_v2.0_scaffold307G48031' => 'sas', 'SGA_v2.0_scaffold47G17507' => 'sas', 'SGA_v2.0_scaffold63G21736' => 'sas', 'SGA_v2.0_scaffold87G27070' => 'sas', 'SHI17794' => 'shi', 'SHI28851' => 'shi', 'SMO165G0155' => 'smo', 'SMO340G0217' => 'smo', 'SMO367G1210' => 'smo', 'Solyc02g093430.3' => 'sly', 'Solyc05g013580.4' => 'sly', 'Solyc07g008030.3' => 'sly', 'Solyc12g035470.2' => 'sly', 'Sopen02g038020' => 'spe', 'Sopen05g008490' => 'spe', 'Sopen07g003910' => 'spe', 'Sopen12g015240' => 'spe', 'Sp1g11550' => 'spa', 'Sp2g16710' => 'spa', 'Sp3g00430' => 'spa', 'Sp3g26780' => 'spa', 'Sp5g22900' => 'spa', 'Sp6g29530' => 'spa', 'TAR371G0794' => 'tar', 'TAR374G0164' => 'tar', 'TAR622G0165' => 'tar', 'TAR626G0929' => 'tar', 'TAR629G2155' => 'tar', 'THA.LOC104805282' => 'tha', 'THA.LOC104805363' => 'tha', 'THA.LOC104808968' => 'tha', 'THA.LOC104821093' => 'tha', 'THA.LOC104823953' => 'tha', 'THA.LOC104825562' => 'tha', 'THA.LOC104825665' => 'tha', 'Thecc.02G261400' => 'tca', 'Thecc.04G019200' => 'tca', 'Thecc.09G130400' => 'tca', 'Thhalv10004374m.g' => 'esa', 'Thhalv10007850m.g' => 'esa', 'Thhalv10013782m.g' => 'esa', 'Thhalv10018686m.g' => 'esa', 'Thhalv10020899m.g' => 'esa', 'Thhalv10022755m.g' => 'esa', 'TPR.G23851' => 'tpr', 'TPR.G26500' => 'tpr', 'TPR.G27267' => 'tpr', 'TPR.G32001' => 'tpr', 'TPR.G6251' => 'tpr', 'TPR.G8167' => 'tpr', 'TWI12G1330' => 'twi', 'TWI18G1239' => 'twi', 'TWI34G0979' => 'twi', 'TWI36G0670' => 'twi', 'TWI36G0707' => 'twi', 'TWI56G0233' => 'twi', 'TWI75G1809' => 'twi', 'unitig_21.g20874' => 'ugi', 'unitig_26.g10343' => 'ugi', 'unitig_46.g18392' => 'ugi', 'unitig_52.g17178' => 'ugi', 'unitig_8.g2934' => 'ugi', 'vmacro01122' => 'vma', 'vmacro05875' => 'vma', 'vmacro06147' => 'vma', 'vmacro16191' => 'vma', 'vmacro18293' => 'vma', 'VMungo0251G3707' => 'vmu', 'VMungo0464G1521' => 'vmu', 'VMungo1215G0205' => 'vmu', 'VMungo1383G2484' => 'vmu', 'Zm00001eb079610' => 'zma', 'Zm00001eb135990' => 'zma', 'Zm00001eb183710' => 'zma', 'Zm00001eb246020' => 'zma' ), 'gf_id' => 'HOM05D001124', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001124' ), 'data_identifier' => 'HOM05D001124', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001124', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '548', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02520' => 'bna', 'A03p06630' => 'bna', 'A05p44460' => 'bna', 'A06p08710' => 'bna', 'A06p41090' => 'bna', 'A07p32320' => 'bna', 'A08p32520' => 'bna', 'A09p10360' => 'bna', 'A10p24080' => 'bna', 'Aa31LG11G15250' => 'aar', 'Aa31LG1G1800' => 'aar', 'Aa31LG2G5120' => 'aar', 'Aa31LG2G6070' => 'aar', 'Aa31LG5G10770' => 'aar', 'Aa31sc61G90' => 'aar', 'Actinidia01352' => 'ach', 'Actinidia05983' => 'ach', 'Actinidia08133' => 'ach', 'Actinidia15101' => 'ach', 'Actinidia26379' => 'ach', 'Actinidia35778' => 'ach', 'Actinidia36123' => 'ach', 'Actinidia37436' => 'ach', 'Actinidia38730' => 'ach', 'Ah.02g128210' => 'amhyb', 'Ah.03g132990' => 'amhyb', 'Ah.14g079410' => 'amhyb', 'AL1G24640' => 'aly', 'AL2G26680' => 'aly', 'AL3G10530' => 'aly', 'AL3G45230' => 'aly', 'AL5G15230' => 'aly', 'AL5G16960' => 'aly', 'AL6G25210' => 'aly', 'Aqoxy2G00441' => 'aox', 'Aqoxy3G01236' => 'aox', 'Aqoxy5G03746' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3RQ047' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C7GMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9C8JER' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MBL6KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YXCZ83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZANX40' => 'arhy', 'AT1G12990' => 'ath', 'AT1G67880' => 'ath', 'AT2G13290' => 'ath', 'AT3G01620' => 'ath', 'AT3G26445' => 'ath', 'AT3G27540' => 'ath', 'AT5G14480' => 'ath', 'ATR0824G026' => 'atr', 'ATR1098G019' => 'atr', 'Atru.chr11.2145' => 'acertr', 'Atru.chr2.3636' => 'acertr', 'Atru.chr2.3644' => 'acertr', 'Atru.chr6.2422' => 'acertr', 'Atru.chr7.1112' => 'acertr', 'AUR62005469' => 'cqu', 'AUR62011166' => 'cqu', 'AUR62013319' => 'cqu', 'AUR62024273' => 'cqu', 'AUR62028420' => 'cqu', 'AUR62041942' => 'cqu', 'BcaB01g04969' => 'bca', 'BcaB01g06371' => 'bca', 'BcaB02g11494' => 'bca', 'BcaB03g15382' => 'bca', 'BcaB08g36994' => 'bca', 'BcaC03g13477' => 'bca', 'BcaC03g13478' => 'bca', 'BcaC03g13480' => 'bca', 'BcaC03g13481' => 'bca', 'BcaC03g13486' => 'bca', 'BcaC04g19031' => 'bca', 'BcaC04g23085' => 'bca', 'BcaC05g25094' => 'bca', 'BcaC05g25096' => 'bca', 'BcaC05g25138' => 'bca', 'BcaC05g30416' => 'bca', 'BcaC05g30455' => 'bca', 'BcaC06g30979' => 'bca', 'BcaC06g33805' => 'bca', 'BcaC08g46021' => 'bca', 'BcaNung03154' => 'bca', 'BolC2t06623H' => 'bol', 'BolC2t06632H' => 'bol', 'BolC2t06635H' => 'bol', 'BolC2t06638H' => 'bol', 'BolC3t13266H' => 'bol', 'BolC5t29776H' => 'bol', 'BolC6t38912H' => 'bol', 'BolC7t44183H' => 'bol', 'BolC9t54123H' => 'bol', 'BolC9t59107H' => 'bol', 'BraA02t05221Z' => 'bra', 'BraA03t09996Z' => 'bra', 'BraA05t23210Z' => 'bra', 'BraA06t24068Z' => 'bra', 'BraA06t27032Z' => 'bra', 'BraA08t35176Z' => 'bra', 'BraA09t36680Z' => 'bra', 'BraA10t44471Z' => 'bra', 'C02p06760' => 'bna', 'C02p06890' => 'bna', 'C02p07010' => 'bna', 'C03p07660' => 'bna', 'C05p10300' => 'bna', 'C06p38150' => 'bna', 'C07p36650' => 'bna', 'C08p15770' => 'bna', 'C09p12300' => 'bna', 'C09p62700' => 'bna', 'C09p75040' => 'bna', 'CAN.G13.1' => 'can', 'CAN.G138.4' => 'can', 'CAN.G44.6' => 'can', 'CAN.G473.19' => 'can', 'CANSAT01G0835' => 'cansat', 'CANSAT11G0246' => 'cansat', 'CANSAT11G1766' => 'cansat', 'CANSAT64G1954' => 'cansat', 'CARHR013330' => 'chi', 'CARHR060530' => 'chi', 'CARHR075300' => 'chi', 'CARHR105120' => 'chi', 'CARHR148910' => 'chi', 'CARHR198830' => 'chi', 'Carub.0001s1275' => 'cru', 'Carub.0002s1437' => 'cru', 'Carub.0003s0044' => 'cru', 'Carub.0003s2787' => 'cru', 'Carub.0005s0597' => 'cru', 'Carub.0006s1266' => 'cru', 'Ca_06935_v3' => 'car', 'Ca_13559_v3' => 'car', 'Ca_16941_v3' => 'car', 'Ca_16960_v3' => 'car', 'Ca_17775_v3' => 'car', 'Ca_30464_v3' => 'car', 'Cc06_g08160' => 'ccan', 'Cc07_g01520' => 'ccan', 'Cc11_g15810' => 'ccan', 'CDE02G2840' => 'cde', 'CDE03G0093' => 'cde', 'CDE04G2127' => 'cde', 'CDE07G1857' => 'cde', 'CDE09G1246' => 'cde', 'Cfa003412' => 'cfa', 'Cfa007341' => 'cfa', 'Cfa009220' => 'cfa', 'Ciclev10008737m.g' => 'ccl', 'Ciclev10015565m.g' => 'ccl', 'Ciclev10031761m.g' => 'ccl', 'CiPaw.03G045300' => 'cil', 'CiPaw.03G247200' => 'cil', 'CiPaw.04G029500' => 'cil', 'CiPaw.04G174000' => 'cil', 'CiPaw.05G181200' => 'cil', 'CiPaw.06G067100' => 'cil', 'ClCG05G025800' => 'cla', 'ClCG06G011400' => 'cla', 'ClCG09G019360' => 'cla', 'COL.COLO4_04827' => 'col', 'COL.COLO4_29170' => 'col', 'COL.COLO4_35131' => 'col', 'COL.COLO4_35132' => 'col', 'Cpa.g.sc33.32' => 'cpa', 'Cpa.g.sc46.29' => 'cpa', 'Cpa.g.sc796.1' => 'cpa', 'CsaV3_1G030420' => 'csa', 'CsaV3_5G027050' => 'csa', 'CsaV3_5G031040' => 'csa', 'CsaV3_UNG023130' => 'csa', 'CSS0007726' => 'camsi', 'CSS0016433' => 'camsi', 'CSS0017656' => 'camsi', 'CSS0025364' => 'camsi', 'CSS0027582' => 'camsi', 'CSS0047288' => 'camsi', 'CSS0049950' => 'camsi', 'DCAR_003843' => 'dca', 'DCAR_007052' => 'dca', 'DCAR_020884' => 'dca', 'DCAR_021730' => 'dca', 'DCAR_024423' => 'dca', 'DCAR_026509' => 'dca', 'DCAR_031158' => 'dca', 'Dinv14728' => 'din', 'Dinv15219' => 'din', 'Dinv25728' => 'din', 'Dinv33428' => 'din', 'Dinv36489' => 'din', 'Dinv41486' => 'din', 'Duzib147G0469' => 'dzi', 'Duzib168G0060' => 'dzi', 'Duzib187G1215' => 'dzi', 'Duzib248G0692' => 'dzi', 'Duzib251G0767' => 'dzi', 'Duzib264G0446' => 'dzi', 'Duzib268G0691' => 'dzi', 'ECA232G4767' => 'eca', 'ECA233G2838' => 'eca', 'ECA234G0391' => 'eca', 'ECA234G0857' => 'eca', 'ECA236G1593' => 'eca', 'ECA238G0565' => 'eca', 'ECA246G1027' => 'eca', 'ECA246G3223' => 'eca', 'ECA246G3470' => 'eca', 'EL10Ac6g13829' => 'bvu', 'EL10Ac6g14093' => 'bvu', 'EL10Ac8g18707' => 'bvu', 'Eucgr.C01369' => 'egr', 'Eucgr.H02492' => 'egr', 'Eucgr.I01733' => 'egr', 'Eucgr.J02255' => 'egr', 'Eucgr.J02257' => 'egr', 'Eucgr.J02258' => 'egr', 'FAN02G1601' => 'fan', 'FAN03G1586' => 'fan', 'FAN03G2986' => 'fan', 'FAN05G4837' => 'fan', 'FAN06G0146' => 'fan', 'FAN07G0858' => 'fan', 'FAN09G3179' => 'fan', 'FAN10G0669' => 'fan', 'FAN12G2358' => 'fan', 'FAN14G4198' => 'fan', 'FAN14G5112' => 'fan', 'FAN17G0342' => 'fan', 'FAN19G0342' => 'fan', 'FAN19G0962' => 'fan', 'FAN19G1101' => 'fan', 'FAN19G1872' => 'fan', 'FAN22G0356' => 'fan', 'FAN23G0744' => 'fan', 'FAN23G1914' => 'fan', 'FAN26G0032' => 'fan', 'FAN28G0625' => 'fan', 'FvH4_1g02710' => 'fve', 'FvH4_1g02720' => 'fve', 'FvH4_4g25670' => 'fve', 'FvH4_6g51700' => 'fve', 'FvH4_7g20170' => 'fve', 'Glyma.05G175000' => 'gma', 'Glyma.08G132300' => 'gma', 'Glyma.11G243000' => 'gma', 'Glyma.13G158900' => 'gma', 'Glyma.17G112400' => 'gma', 'Glyma.18G014100' => 'gma', 'Glyma.19G003100' => 'gma', 'Glyma.19G056500' => 'gma', 'Gohir.A01G158900' => 'ghi', 'Gohir.A05G312600' => 'ghi', 'Gohir.A05G354900' => 'ghi', 'Gohir.A07G037200' => 'ghi', 'Gohir.A09G030000' => 'ghi', 'Gohir.A12G145200' => 'ghi', 'Gohir.D01G151500' => 'ghi', 'Gohir.D04G058300' => 'ghi', 'Gohir.D05G314100' => 'ghi', 'Gohir.D07G041400' => 'ghi', 'Gohir.D09G029700' => 'ghi', 'Gohir.D12G149700' => 'ghi', 'Gorai.001G043800' => 'gra', 'Gorai.002G187800' => 'gra', 'Gorai.006G034700' => 'gra', 'Gorai.008G161200' => 'gra', 'Gorai.009G335700' => 'gra', 'Gorai.012G065000' => 'gra', 'GSVIVG01000535001' => 'vvi', 'GSVIVG01015572001' => 'vvi', 'GSVIVG01032386001' => 'vvi', 'HanXRQChr05g0138531' => 'han', 'HanXRQChr06g0174391' => 'han', 'HanXRQChr07g0199021' => 'han', 'HanXRQChr08g0208211' => 'han', 'HanXRQChr09g0255471' => 'han', 'HanXRQChr10g0315791' => 'han', 'HanXRQChr12g0371991' => 'han', 'HanXRQChr15g0475251' => 'han', 'HanXRQChr17g0540001' => 'han', 'HanXRQChr17g0548631' => 'han', 'HanXRQChr17g0569561' => 'han', 'Haze_12256' => 'cav', 'Haze_14756' => 'cav', 'Haze_25528' => 'cav', 'Hma1.2p1_0079F.1_g041020' => 'hma', 'Hma1.2p1_0818F.1_g223260' => 'hma', 'Hma1.2p1_1747F.1_g300530' => 'hma', 'HPP92_004607' => 'vpl', 'HPP92_004608' => 'vpl', 'HPP92_006181' => 'vpl', 'HPP92_012192' => 'vpl', 'HPP92_015680' => 'vpl', 'HPP92_020249' => 'vpl', 'HPP92_021376' => 'vpl', 'HPP92_024275' => 'vpl', 'Hund06031' => 'sun', 'Hund25391' => 'sun', 'Lalb_Chr07g0185371' => 'lal', 'Lalb_Chr07g0185381' => 'lal', 'Lalb_Chr12g0204011' => 'lal', 'Lalb_Chr13g0301671' => 'lal', 'Lalb_Chr14g0362851' => 'lal', 'Lalb_Chr24g0403581' => 'lal', 'Lj1g0000233' => 'lja', 'Lj2g0018120' => 'lja', 'Lj3C621T0' => 'lonja', 'Lj3P1059T14' => 'lonja', 'Lj3P611T9' => 'lonja', 'Lj3P614T13' => 'lonja', 'Lj3P615T5' => 'lonja', 'Lj4g0012315' => 'lja', 'Lj4g0026182' => 'lja', 'Lj6P813T16' => 'lonja', 'Lj7C427T7' => 'lonja', 'Lj7C427T8' => 'lonja', 'Lj7P600T41' => 'lonja', 'Lju41C42G17' => 'lonja', 'Lsat_1_v5_gn_0_47300' => 'lsa', 'Lsat_1_v5_gn_2_91280' => 'lsa', 'Lsat_1_v5_gn_3_30561' => 'lsa', 'Lsat_1_v5_gn_4_184321' => 'lsa', 'Lsat_1_v5_gn_4_4041' => 'lsa', 'Lsat_1_v5_gn_5_92000' => 'lsa', 'Lsat_1_v5_gn_8_152940' => 'lsa', 'Lsat_1_v5_gn_8_62401' => 'lsa', 'Manes.06G055900' => 'mes', 'Manes.12G022200' => 'mes', 'Manes.13G023300' => 'mes', 'Manes.14G115000' => 'mes', 'Manes.15G151700' => 'mes', 'Manes.17G111300' => 'mes', 'Mapoly0226s0009' => 'mpo', 'MBI02_g25363_MAGBIO' => 'mbi', 'MBI06_g00027_MAGBIO' => 'mbi', 'MBI10_g13034_MAGBIO' => 'mbi', 'MD09G1023400' => 'mdo', 'MD13G1100100' => 'mdo', 'MD15G1169200' => 'mdo', 'MD16G1101100' => 'mdo', 'MD17G1022900' => 'mdo', 'Medtr3g096150' => 'mtr', 'Medtr4g115070' => 'mtr', 'Medtr7g033325' => 'mtr', 'Medtr8g089840' => 'mtr', 'MELO3C010319.2' => 'cme', 'MELO3C011944.2' => 'cme', 'MELO3C021589.2' => 'cme', 'Migut.E00207' => 'egut', 'Migut.H00067' => 'egut', 'Migut.K00433' => 'egut', 'Migut.K00606' => 'egut', 'Migut.K01410' => 'egut', 'MSTRG.13347' => 'ama', 'MSTRG.24045' => 'ama', 'MSTRG.2428' => 'ama', 'MSTRG.26410' => 'ama', 'MSTRG.3139' => 'ama', 'MSTRG.3286' => 'ama', 'MSTRG.563' => 'ama', 'MSTRG.7941' => 'ama', 'Nitab4.5_0000028g0060' => 'nta', 'Nitab4.5_0000065g0260' => 'nta', 'Nitab4.5_0000112g0060' => 'nta', 'Nitab4.5_0000489g0120' => 'nta', 'Nitab4.5_0001776g0050' => 'nta', 'Nitab4.5_0001854g0010' => 'nta', 'Nitab4.5_0001860g0020' => 'nta', 'Nitab4.5_0004352g0010' => 'nta', 'Nitab4.5_0008716g0020' => 'nta', 'Nitab4.5_0008922g0010' => 'nta', 'Nn3g16693' => 'nnu', 'Nn4g22596' => 'nnu', 'Nn7g37639' => 'nnu', 'Oeu001701.1' => 'oeu', 'Oeu018149.1' => 'oeu', 'Oeu026220.1' => 'oeu', 'Oeu038635.1' => 'oeu', 'Oeu049176.1' => 'oeu', 'Oeu056706.1' => 'oeu', 'Oeu056937.1' => 'oeu', 'Oeu057540.1' => 'oeu', 'Os02g0594900' => 'osa', 'Os02g0595100' => 'osa', 'Os04g0477500' => 'osa', 'Os12g0611900' => 'osa', 'Peaxi162Scf00076g00020' => 'pax', 'Peaxi162Scf00128g00217' => 'pax', 'Peaxi162Scf00129g01640' => 'pax', 'Peaxi162Scf00669g00007' => 'pax', 'Peaxi162Scf00700g00421' => 'pax', 'Peaxi162Scf00801g00038' => 'pax', 'Peaxi162Scf00891g00025' => 'pax', 'PGR083G0909' => 'pgr', 'PGR119G1005' => 'pgr', 'PGR142G2236' => 'pgr', 'PGR142G3388' => 'pgr', 'PGSC0003DMG400004514' => 'stu', 'PGSC0003DMG400012635' => 'stu', 'PGSC0003DMG400015730' => 'stu', 'PGSC0003DMG400018611' => 'stu', 'PGSC0003DMG400030897' => 'stu', 'Phvul.001G254800' => 'pvu', 'Phvul.002G260100' => 'pvu', 'Phvul.003G167600' => 'pvu', 'Phvul.004G005100' => 'pvu', 'Potri.001G343600' => 'ptr', 'Potri.006G066700' => 'ptr', 'Potri.008G186000' => 'ptr', 'Potri.010G046900' => 'ptr', 'Potri.018G127900' => 'ptr', 'Pp3c20_17750' => 'ppa', 'Pp3c24_4380' => 'ppa', 'Prupe.1G245800' => 'ppe', 'Prupe.3G293400' => 'ppe', 'Prupe.7G247400' => 'ppe', 'Psat0s145g0120' => 'psa', 'Psat0s595g0040' => 'psa', 'Psat0s595g0120' => 'psa', 'Psat3g175040' => 'psa', 'Psat7g058120' => 'psa', 'PSO017G0428' => 'pso', 'PSO063G7510' => 'pso', 'PSO067G0046' => 'pso', 'PSO478G1073' => 'pso', 'PSO675G3677' => 'pso', 'PSO675G6558' => 'pso', 'PSO675G7520' => 'pso', 'PSO675G8959' => 'pso', 'QL02p074089' => 'qlo', 'QL02p089614' => 'qlo', 'QL03p057736' => 'qlo', 'RcHm_v2.0_Chr1g0364131' => 'rch', 'RcHm_v2.0_Chr2g0087801' => 'rch', 'RcHm_v2.0_Chr2g0087821' => 'rch', 'RcHm_v2.0_Chr2g0173231' => 'rch', 'RcHm_v2.0_Chr4g0433111' => 'rch', 'Rhsim03G0250300' => 'rsi', 'Rhsim08G0048400' => 'rsi', 'Rhsim10G0014800' => 'rsi', 'Rhsim12G0040100' => 'rsi', 'Rhsim12G0109700' => 'rsi', 'Sabra06G0049600' => 'sbr', 'Sabra08G0141000' => 'sbr', 'Sabra10G0021400' => 'sbr', 'Sabra16G0222900' => 'sbr', 'Sabra18G0108600' => 'sbr', 'SalBow1G0433' => 'sbo', 'SalBow1G2038' => 'sbo', 'SalBow1G5003' => 'sbo', 'SalBow7G1197' => 'sbo', 'SalBow8G3506' => 'sbo', 'Sc03g0007300' => 'sci', 'Sc11g0000950' => 'sci', 'Sc14g0008750' => 'sci', 'Sc18g0000420' => 'sci', 'Sed0006754' => 'sed', 'Sed0008741' => 'sed', 'Sed0017172' => 'sed', 'Sed0018925' => 'sed', 'Sed0023326' => 'sed', 'Sed0025909' => 'sed', 'SEGI_05333' => 'sgi', 'SEGI_10362' => 'sgi', 'SEGI_13380' => 'sgi', 'SEGI_24306' => 'sgi', 'SEGI_29077' => 'sgi', 'SEGI_29095' => 'sgi', 'SEGI_36534' => 'sgi', 'SEGI_37506' => 'sgi', 'SEGI_38321' => 'sgi', 'SGA_v2.0_scaffold307G48031' => 'sas', 'SGA_v2.0_scaffold47G17507' => 'sas', 'SGA_v2.0_scaffold63G21736' => 'sas', 'SGA_v2.0_scaffold87G27070' => 'sas', 'SHI17794' => 'shi', 'SHI28851' => 'shi', 'SMO165G0155' => 'smo', 'SMO340G0217' => 'smo', 'SMO367G1210' => 'smo', 'Solyc02g093430.3' => 'sly', 'Solyc05g013580.4' => 'sly', 'Solyc07g008030.3' => 'sly', 'Solyc12g035470.2' => 'sly', 'Sopen02g038020' => 'spe', 'Sopen05g008490' => 'spe', 'Sopen07g003910' => 'spe', 'Sopen12g015240' => 'spe', 'Sp1g11550' => 'spa', 'Sp2g16710' => 'spa', 'Sp3g00430' => 'spa', 'Sp3g26780' => 'spa', 'Sp5g22900' => 'spa', 'Sp6g29530' => 'spa', 'TAR371G0794' => 'tar', 'TAR374G0164' => 'tar', 'TAR622G0165' => 'tar', 'TAR626G0929' => 'tar', 'TAR629G2155' => 'tar', 'THA.LOC104805282' => 'tha', 'THA.LOC104805363' => 'tha', 'THA.LOC104808968' => 'tha', 'THA.LOC104821093' => 'tha', 'THA.LOC104823953' => 'tha', 'THA.LOC104825562' => 'tha', 'THA.LOC104825665' => 'tha', 'Thecc.02G261400' => 'tca', 'Thecc.04G019200' => 'tca', 'Thecc.09G130400' => 'tca', 'Thhalv10004374m.g' => 'esa', 'Thhalv10007850m.g' => 'esa', 'Thhalv10013782m.g' => 'esa', 'Thhalv10018686m.g' => 'esa', 'Thhalv10020899m.g' => 'esa', 'Thhalv10022755m.g' => 'esa', 'TPR.G23851' => 'tpr', 'TPR.G26500' => 'tpr', 'TPR.G27267' => 'tpr', 'TPR.G32001' => 'tpr', 'TPR.G6251' => 'tpr', 'TPR.G8167' => 'tpr', 'TWI12G1330' => 'twi', 'TWI18G1239' => 'twi', 'TWI34G0979' => 'twi', 'TWI36G0670' => 'twi', 'TWI36G0707' => 'twi', 'TWI56G0233' => 'twi', 'TWI75G1809' => 'twi', 'unitig_21.g20874' => 'ugi', 'unitig_26.g10343' => 'ugi', 'unitig_46.g18392' => 'ugi', 'unitig_52.g17178' => 'ugi', 'unitig_8.g2934' => 'ugi', 'vmacro01122' => 'vma', 'vmacro05875' => 'vma', 'vmacro06147' => 'vma', 'vmacro16191' => 'vma', 'vmacro18293' => 'vma', 'VMungo0251G3707' => 'vmu', 'VMungo0464G1521' => 'vmu', 'VMungo1215G0205' => 'vmu', 'VMungo1383G2484' => 'vmu', 'Zm00001eb079610' => 'zma', 'Zm00001eb135990' => 'zma', 'Zm00001eb183710' => 'zma', 'Zm00001eb246020' => 'zma' ) $gf_id = 'HOM05D001124' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001124' ) $data_identifier = 'HOM05D001124' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 6, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 7, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 21, 'bol' => (int) 10, 'bra' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 6, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 9, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 21, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 8, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 10, 'lsa' => (int) 8, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 8, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 9, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb246020' $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' => 'HOM05D001124', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '548', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02520' => 'bna', 'A03p06630' => 'bna', 'A05p44460' => 'bna', 'A06p08710' => 'bna', 'A06p41090' => 'bna', 'A07p32320' => 'bna', 'A08p32520' => 'bna', 'A09p10360' => 'bna', 'A10p24080' => 'bna', 'Aa31LG11G15250' => 'aar', 'Aa31LG1G1800' => 'aar', 'Aa31LG2G5120' => 'aar', 'Aa31LG2G6070' => 'aar', 'Aa31LG5G10770' => 'aar', 'Aa31sc61G90' => 'aar', 'Actinidia01352' => 'ach', 'Actinidia05983' => 'ach', 'Actinidia08133' => 'ach', 'Actinidia15101' => 'ach', 'Actinidia26379' => 'ach', 'Actinidia35778' => 'ach', 'Actinidia36123' => 'ach', 'Actinidia37436' => 'ach', 'Actinidia38730' => 'ach', 'Ah.02g128210' => 'amhyb', 'Ah.03g132990' => 'amhyb', 'Ah.14g079410' => 'amhyb', 'AL1G24640' => 'aly', 'AL2G26680' => 'aly', 'AL3G10530' => 'aly', 'AL3G45230' => 'aly', 'AL5G15230' => 'aly', 'AL5G16960' => 'aly', 'AL6G25210' => 'aly', 'Aqoxy2G00441' => 'aox', 'Aqoxy3G01236' => 'aox', 'Aqoxy5G03746' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3RQ047' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C7GMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9C8JER' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MBL6KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YXCZ83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZANX40' => 'arhy', 'AT1G12990' => 'ath', 'AT1G67880' => 'ath', 'AT2G13290' => 'ath', 'AT3G01620' => 'ath', 'AT3G26445' => 'ath', 'AT3G27540' => 'ath', 'AT5G14480' => 'ath', 'ATR0824G026' => 'atr', 'ATR1098G019' => 'atr', 'Atru.chr11.2145' => 'acertr', 'Atru.chr2.3636' => 'acertr', 'Atru.chr2.3644' => 'acertr', 'Atru.chr6.2422' => 'acertr', 'Atru.chr7.1112' => 'acertr', 'AUR62005469' => 'cqu', 'AUR62011166' => 'cqu', 'AUR62013319' => 'cqu', 'AUR62024273' => 'cqu', 'AUR62028420' => 'cqu', 'AUR62041942' => 'cqu', 'BcaB01g04969' => 'bca', 'BcaB01g06371' => 'bca', 'BcaB02g11494' => 'bca', 'BcaB03g15382' => 'bca', 'BcaB08g36994' => 'bca', 'BcaC03g13477' => 'bca', 'BcaC03g13478' => 'bca', 'BcaC03g13480' => 'bca', 'BcaC03g13481' => 'bca', 'BcaC03g13486' => 'bca', 'BcaC04g19031' => 'bca', 'BcaC04g23085' => 'bca', 'BcaC05g25094' => 'bca', 'BcaC05g25096' => 'bca', 'BcaC05g25138' => 'bca', 'BcaC05g30416' => 'bca', 'BcaC05g30455' => 'bca', 'BcaC06g30979' => 'bca', 'BcaC06g33805' => 'bca', 'BcaC08g46021' => 'bca', 'BcaNung03154' => 'bca', 'BolC2t06623H' => 'bol', 'BolC2t06632H' => 'bol', 'BolC2t06635H' => 'bol', 'BolC2t06638H' => 'bol', 'BolC3t13266H' => 'bol', 'BolC5t29776H' => 'bol', 'BolC6t38912H' => 'bol', 'BolC7t44183H' => 'bol', 'BolC9t54123H' => 'bol', 'BolC9t59107H' => 'bol', 'BraA02t05221Z' => 'bra', 'BraA03t09996Z' => 'bra', 'BraA05t23210Z' => 'bra', 'BraA06t24068Z' => 'bra', 'BraA06t27032Z' => 'bra', 'BraA08t35176Z' => 'bra', 'BraA09t36680Z' => 'bra', 'BraA10t44471Z' => 'bra', 'C02p06760' => 'bna', 'C02p06890' => 'bna', 'C02p07010' => 'bna', 'C03p07660' => 'bna', 'C05p10300' => 'bna', 'C06p38150' => 'bna', 'C07p36650' => 'bna', 'C08p15770' => 'bna', 'C09p12300' => 'bna', 'C09p62700' => 'bna', 'C09p75040' => 'bna', 'CAN.G13.1' => 'can', 'CAN.G138.4' => 'can', 'CAN.G44.6' => 'can', 'CAN.G473.19' => 'can', 'CANSAT01G0835' => 'cansat', 'CANSAT11G0246' => 'cansat', 'CANSAT11G1766' => 'cansat', 'CANSAT64G1954' => 'cansat', 'CARHR013330' => 'chi', 'CARHR060530' => 'chi', 'CARHR075300' => 'chi', 'CARHR105120' => 'chi', 'CARHR148910' => 'chi', 'CARHR198830' => 'chi', 'Carub.0001s1275' => 'cru', 'Carub.0002s1437' => 'cru', 'Carub.0003s0044' => 'cru', 'Carub.0003s2787' => 'cru', 'Carub.0005s0597' => 'cru', 'Carub.0006s1266' => 'cru', 'Ca_06935_v3' => 'car', 'Ca_13559_v3' => 'car', 'Ca_16941_v3' => 'car', 'Ca_16960_v3' => 'car', 'Ca_17775_v3' => 'car', 'Ca_30464_v3' => 'car', 'Cc06_g08160' => 'ccan', 'Cc07_g01520' => 'ccan', 'Cc11_g15810' => 'ccan', 'CDE02G2840' => 'cde', 'CDE03G0093' => 'cde', 'CDE04G2127' => 'cde', 'CDE07G1857' => 'cde', 'CDE09G1246' => 'cde', 'Cfa003412' => 'cfa', 'Cfa007341' => 'cfa', 'Cfa009220' => 'cfa', 'Ciclev10008737m.g' => 'ccl', 'Ciclev10015565m.g' => 'ccl', 'Ciclev10031761m.g' => 'ccl', 'CiPaw.03G045300' => 'cil', 'CiPaw.03G247200' => 'cil', 'CiPaw.04G029500' => 'cil', 'CiPaw.04G174000' => 'cil', 'CiPaw.05G181200' => 'cil', 'CiPaw.06G067100' => 'cil', 'ClCG05G025800' => 'cla', 'ClCG06G011400' => 'cla', 'ClCG09G019360' => 'cla', 'COL.COLO4_04827' => 'col', 'COL.COLO4_29170' => 'col', 'COL.COLO4_35131' => 'col', 'COL.COLO4_35132' => 'col', 'Cpa.g.sc33.32' => 'cpa', 'Cpa.g.sc46.29' => 'cpa', 'Cpa.g.sc796.1' => 'cpa', 'CsaV3_1G030420' => 'csa', 'CsaV3_5G027050' => 'csa', 'CsaV3_5G031040' => 'csa', 'CsaV3_UNG023130' => 'csa', 'CSS0007726' => 'camsi', 'CSS0016433' => 'camsi', 'CSS0017656' => 'camsi', 'CSS0025364' => 'camsi', 'CSS0027582' => 'camsi', 'CSS0047288' => 'camsi', 'CSS0049950' => 'camsi', 'DCAR_003843' => 'dca', 'DCAR_007052' => 'dca', 'DCAR_020884' => 'dca', 'DCAR_021730' => 'dca', 'DCAR_024423' => 'dca', 'DCAR_026509' => 'dca', 'DCAR_031158' => 'dca', 'Dinv14728' => 'din', 'Dinv15219' => 'din', 'Dinv25728' => 'din', 'Dinv33428' => 'din', 'Dinv36489' => 'din', 'Dinv41486' => 'din', 'Duzib147G0469' => 'dzi', 'Duzib168G0060' => 'dzi', 'Duzib187G1215' => 'dzi', 'Duzib248G0692' => 'dzi', 'Duzib251G0767' => 'dzi', 'Duzib264G0446' => 'dzi', 'Duzib268G0691' => 'dzi', 'ECA232G4767' => 'eca', 'ECA233G2838' => 'eca', 'ECA234G0391' => 'eca', 'ECA234G0857' => 'eca', 'ECA236G1593' => 'eca', 'ECA238G0565' => 'eca', 'ECA246G1027' => 'eca', 'ECA246G3223' => 'eca', 'ECA246G3470' => 'eca', 'EL10Ac6g13829' => 'bvu', 'EL10Ac6g14093' => 'bvu', 'EL10Ac8g18707' => 'bvu', 'Eucgr.C01369' => 'egr', 'Eucgr.H02492' => 'egr', 'Eucgr.I01733' => 'egr', 'Eucgr.J02255' => 'egr', 'Eucgr.J02257' => 'egr', 'Eucgr.J02258' => 'egr', 'FAN02G1601' => 'fan', 'FAN03G1586' => 'fan', 'FAN03G2986' => 'fan', 'FAN05G4837' => 'fan', 'FAN06G0146' => 'fan', 'FAN07G0858' => 'fan', 'FAN09G3179' => 'fan', 'FAN10G0669' => 'fan', 'FAN12G2358' => 'fan', 'FAN14G4198' => 'fan', 'FAN14G5112' => 'fan', 'FAN17G0342' => 'fan', 'FAN19G0342' => 'fan', 'FAN19G0962' => 'fan', 'FAN19G1101' => 'fan', 'FAN19G1872' => 'fan', 'FAN22G0356' => 'fan', 'FAN23G0744' => 'fan', 'FAN23G1914' => 'fan', 'FAN26G0032' => 'fan', 'FAN28G0625' => 'fan', 'FvH4_1g02710' => 'fve', 'FvH4_1g02720' => 'fve', 'FvH4_4g25670' => 'fve', 'FvH4_6g51700' => 'fve', 'FvH4_7g20170' => 'fve', 'Glyma.05G175000' => 'gma', 'Glyma.08G132300' => 'gma', 'Glyma.11G243000' => 'gma', 'Glyma.13G158900' => 'gma', 'Glyma.17G112400' => 'gma', 'Glyma.18G014100' => 'gma', 'Glyma.19G003100' => 'gma', 'Glyma.19G056500' => 'gma', 'Gohir.A01G158900' => 'ghi', 'Gohir.A05G312600' => 'ghi', 'Gohir.A05G354900' => 'ghi', 'Gohir.A07G037200' => 'ghi', 'Gohir.A09G030000' => 'ghi', 'Gohir.A12G145200' => 'ghi', 'Gohir.D01G151500' => 'ghi', 'Gohir.D04G058300' => 'ghi', 'Gohir.D05G314100' => 'ghi', 'Gohir.D07G041400' => 'ghi', 'Gohir.D09G029700' => 'ghi', 'Gohir.D12G149700' => 'ghi', 'Gorai.001G043800' => 'gra', 'Gorai.002G187800' => 'gra', 'Gorai.006G034700' => 'gra', 'Gorai.008G161200' => 'gra', 'Gorai.009G335700' => 'gra', 'Gorai.012G065000' => 'gra', 'GSVIVG01000535001' => 'vvi', 'GSVIVG01015572001' => 'vvi', 'GSVIVG01032386001' => 'vvi', 'HanXRQChr05g0138531' => 'han', 'HanXRQChr06g0174391' => 'han', 'HanXRQChr07g0199021' => 'han', 'HanXRQChr08g0208211' => 'han', 'HanXRQChr09g0255471' => 'han', 'HanXRQChr10g0315791' => 'han', 'HanXRQChr12g0371991' => 'han', 'HanXRQChr15g0475251' => 'han', 'HanXRQChr17g0540001' => 'han', 'HanXRQChr17g0548631' => 'han', 'HanXRQChr17g0569561' => 'han', 'Haze_12256' => 'cav', 'Haze_14756' => 'cav', 'Haze_25528' => 'cav', 'Hma1.2p1_0079F.1_g041020' => 'hma', 'Hma1.2p1_0818F.1_g223260' => 'hma', 'Hma1.2p1_1747F.1_g300530' => 'hma', 'HPP92_004607' => 'vpl', 'HPP92_004608' => 'vpl', 'HPP92_006181' => 'vpl', 'HPP92_012192' => 'vpl', 'HPP92_015680' => 'vpl', 'HPP92_020249' => 'vpl', 'HPP92_021376' => 'vpl', 'HPP92_024275' => 'vpl', 'Hund06031' => 'sun', 'Hund25391' => 'sun', 'Lalb_Chr07g0185371' => 'lal', 'Lalb_Chr07g0185381' => 'lal', 'Lalb_Chr12g0204011' => 'lal', 'Lalb_Chr13g0301671' => 'lal', 'Lalb_Chr14g0362851' => 'lal', 'Lalb_Chr24g0403581' => 'lal', 'Lj1g0000233' => 'lja', 'Lj2g0018120' => 'lja', 'Lj3C621T0' => 'lonja', 'Lj3P1059T14' => 'lonja', 'Lj3P611T9' => 'lonja', 'Lj3P614T13' => 'lonja', 'Lj3P615T5' => 'lonja', 'Lj4g0012315' => 'lja', 'Lj4g0026182' => 'lja', 'Lj6P813T16' => 'lonja', 'Lj7C427T7' => 'lonja', 'Lj7C427T8' => 'lonja', 'Lj7P600T41' => 'lonja', 'Lju41C42G17' => 'lonja', 'Lsat_1_v5_gn_0_47300' => 'lsa', 'Lsat_1_v5_gn_2_91280' => 'lsa', 'Lsat_1_v5_gn_3_30561' => 'lsa', 'Lsat_1_v5_gn_4_184321' => 'lsa', 'Lsat_1_v5_gn_4_4041' => 'lsa', 'Lsat_1_v5_gn_5_92000' => 'lsa', 'Lsat_1_v5_gn_8_152940' => 'lsa', 'Lsat_1_v5_gn_8_62401' => 'lsa', 'Manes.06G055900' => 'mes', 'Manes.12G022200' => 'mes', 'Manes.13G023300' => 'mes', 'Manes.14G115000' => 'mes', 'Manes.15G151700' => 'mes', 'Manes.17G111300' => 'mes', 'Mapoly0226s0009' => 'mpo', 'MBI02_g25363_MAGBIO' => 'mbi', 'MBI06_g00027_MAGBIO' => 'mbi', 'MBI10_g13034_MAGBIO' => 'mbi', 'MD09G1023400' => 'mdo', 'MD13G1100100' => 'mdo', 'MD15G1169200' => 'mdo', 'MD16G1101100' => 'mdo', 'MD17G1022900' => 'mdo', 'Medtr3g096150' => 'mtr', 'Medtr4g115070' => 'mtr', 'Medtr7g033325' => 'mtr', 'Medtr8g089840' => 'mtr', 'MELO3C010319.2' => 'cme', 'MELO3C011944.2' => 'cme', 'MELO3C021589.2' => 'cme', 'Migut.E00207' => 'egut', 'Migut.H00067' => 'egut', 'Migut.K00433' => 'egut', 'Migut.K00606' => 'egut', 'Migut.K01410' => 'egut', 'MSTRG.13347' => 'ama', 'MSTRG.24045' => 'ama', 'MSTRG.2428' => 'ama', 'MSTRG.26410' => 'ama', 'MSTRG.3139' => 'ama', 'MSTRG.3286' => 'ama', 'MSTRG.563' => 'ama', 'MSTRG.7941' => 'ama', 'Nitab4.5_0000028g0060' => 'nta', 'Nitab4.5_0000065g0260' => 'nta', 'Nitab4.5_0000112g0060' => 'nta', 'Nitab4.5_0000489g0120' => 'nta', 'Nitab4.5_0001776g0050' => 'nta', 'Nitab4.5_0001854g0010' => 'nta', 'Nitab4.5_0001860g0020' => 'nta', 'Nitab4.5_0004352g0010' => 'nta', 'Nitab4.5_0008716g0020' => 'nta', 'Nitab4.5_0008922g0010' => 'nta', 'Nn3g16693' => 'nnu', 'Nn4g22596' => 'nnu', 'Nn7g37639' => 'nnu', 'Oeu001701.1' => 'oeu', 'Oeu018149.1' => 'oeu', 'Oeu026220.1' => 'oeu', 'Oeu038635.1' => 'oeu', 'Oeu049176.1' => 'oeu', 'Oeu056706.1' => 'oeu', 'Oeu056937.1' => 'oeu', 'Oeu057540.1' => 'oeu', 'Os02g0594900' => 'osa', 'Os02g0595100' => 'osa', 'Os04g0477500' => 'osa', 'Os12g0611900' => 'osa', 'Peaxi162Scf00076g00020' => 'pax', 'Peaxi162Scf00128g00217' => 'pax', 'Peaxi162Scf00129g01640' => 'pax', 'Peaxi162Scf00669g00007' => 'pax', 'Peaxi162Scf00700g00421' => 'pax', 'Peaxi162Scf00801g00038' => 'pax', 'Peaxi162Scf00891g00025' => 'pax', 'PGR083G0909' => 'pgr', 'PGR119G1005' => 'pgr', 'PGR142G2236' => 'pgr', 'PGR142G3388' => 'pgr', 'PGSC0003DMG400004514' => 'stu', 'PGSC0003DMG400012635' => 'stu', 'PGSC0003DMG400015730' => 'stu', 'PGSC0003DMG400018611' => 'stu', 'PGSC0003DMG400030897' => 'stu', 'Phvul.001G254800' => 'pvu', 'Phvul.002G260100' => 'pvu', 'Phvul.003G167600' => 'pvu', 'Phvul.004G005100' => 'pvu', 'Potri.001G343600' => 'ptr', 'Potri.006G066700' => 'ptr', 'Potri.008G186000' => 'ptr', 'Potri.010G046900' => 'ptr', 'Potri.018G127900' => 'ptr', 'Pp3c20_17750' => 'ppa', 'Pp3c24_4380' => 'ppa', 'Prupe.1G245800' => 'ppe', 'Prupe.3G293400' => 'ppe', 'Prupe.7G247400' => 'ppe', 'Psat0s145g0120' => 'psa', 'Psat0s595g0040' => 'psa', 'Psat0s595g0120' => 'psa', 'Psat3g175040' => 'psa', 'Psat7g058120' => 'psa', 'PSO017G0428' => 'pso', 'PSO063G7510' => 'pso', 'PSO067G0046' => 'pso', 'PSO478G1073' => 'pso', 'PSO675G3677' => 'pso', 'PSO675G6558' => 'pso', 'PSO675G7520' => 'pso', 'PSO675G8959' => 'pso', 'QL02p074089' => 'qlo', 'QL02p089614' => 'qlo', 'QL03p057736' => 'qlo', 'RcHm_v2.0_Chr1g0364131' => 'rch', 'RcHm_v2.0_Chr2g0087801' => 'rch', 'RcHm_v2.0_Chr2g0087821' => 'rch', 'RcHm_v2.0_Chr2g0173231' => 'rch', 'RcHm_v2.0_Chr4g0433111' => 'rch', 'Rhsim03G0250300' => 'rsi', 'Rhsim08G0048400' => 'rsi', 'Rhsim10G0014800' => 'rsi', 'Rhsim12G0040100' => 'rsi', 'Rhsim12G0109700' => 'rsi', 'Sabra06G0049600' => 'sbr', 'Sabra08G0141000' => 'sbr', 'Sabra10G0021400' => 'sbr', 'Sabra16G0222900' => 'sbr', 'Sabra18G0108600' => 'sbr', 'SalBow1G0433' => 'sbo', 'SalBow1G2038' => 'sbo', 'SalBow1G5003' => 'sbo', 'SalBow7G1197' => 'sbo', 'SalBow8G3506' => 'sbo', 'Sc03g0007300' => 'sci', 'Sc11g0000950' => 'sci', 'Sc14g0008750' => 'sci', 'Sc18g0000420' => 'sci', 'Sed0006754' => 'sed', 'Sed0008741' => 'sed', 'Sed0017172' => 'sed', 'Sed0018925' => 'sed', 'Sed0023326' => 'sed', 'Sed0025909' => 'sed', 'SEGI_05333' => 'sgi', 'SEGI_10362' => 'sgi', 'SEGI_13380' => 'sgi', 'SEGI_24306' => 'sgi', 'SEGI_29077' => 'sgi', 'SEGI_29095' => 'sgi', 'SEGI_36534' => 'sgi', 'SEGI_37506' => 'sgi', 'SEGI_38321' => 'sgi', 'SGA_v2.0_scaffold307G48031' => 'sas', 'SGA_v2.0_scaffold47G17507' => 'sas', 'SGA_v2.0_scaffold63G21736' => 'sas', 'SGA_v2.0_scaffold87G27070' => 'sas', 'SHI17794' => 'shi', 'SHI28851' => 'shi', 'SMO165G0155' => 'smo', 'SMO340G0217' => 'smo', 'SMO367G1210' => 'smo', 'Solyc02g093430.3' => 'sly', 'Solyc05g013580.4' => 'sly', 'Solyc07g008030.3' => 'sly', 'Solyc12g035470.2' => 'sly', 'Sopen02g038020' => 'spe', 'Sopen05g008490' => 'spe', 'Sopen07g003910' => 'spe', 'Sopen12g015240' => 'spe', 'Sp1g11550' => 'spa', 'Sp2g16710' => 'spa', 'Sp3g00430' => 'spa', 'Sp3g26780' => 'spa', 'Sp5g22900' => 'spa', 'Sp6g29530' => 'spa', 'TAR371G0794' => 'tar', 'TAR374G0164' => 'tar', 'TAR622G0165' => 'tar', 'TAR626G0929' => 'tar', 'TAR629G2155' => 'tar', 'THA.LOC104805282' => 'tha', 'THA.LOC104805363' => 'tha', 'THA.LOC104808968' => 'tha', 'THA.LOC104821093' => 'tha', 'THA.LOC104823953' => 'tha', 'THA.LOC104825562' => 'tha', 'THA.LOC104825665' => 'tha', 'Thecc.02G261400' => 'tca', 'Thecc.04G019200' => 'tca', 'Thecc.09G130400' => 'tca', 'Thhalv10004374m.g' => 'esa', 'Thhalv10007850m.g' => 'esa', 'Thhalv10013782m.g' => 'esa', 'Thhalv10018686m.g' => 'esa', 'Thhalv10020899m.g' => 'esa', 'Thhalv10022755m.g' => 'esa', 'TPR.G23851' => 'tpr', 'TPR.G26500' => 'tpr', 'TPR.G27267' => 'tpr', 'TPR.G32001' => 'tpr', 'TPR.G6251' => 'tpr', 'TPR.G8167' => 'tpr', 'TWI12G1330' => 'twi', 'TWI18G1239' => 'twi', 'TWI34G0979' => 'twi', 'TWI36G0670' => 'twi', 'TWI36G0707' => 'twi', 'TWI56G0233' => 'twi', 'TWI75G1809' => 'twi', 'unitig_21.g20874' => 'ugi', 'unitig_26.g10343' => 'ugi', 'unitig_46.g18392' => 'ugi', 'unitig_52.g17178' => 'ugi', 'unitig_8.g2934' => 'ugi', 'vmacro01122' => 'vma', 'vmacro05875' => 'vma', 'vmacro06147' => 'vma', 'vmacro16191' => 'vma', 'vmacro18293' => 'vma', 'VMungo0251G3707' => 'vmu', 'VMungo0464G1521' => 'vmu', 'VMungo1215G0205' => 'vmu', 'VMungo1383G2484' => 'vmu', 'Zm00001eb079610' => 'zma', 'Zm00001eb135990' => 'zma', 'Zm00001eb183710' => 'zma', 'Zm00001eb246020' => 'zma' ), 'gf_id' => 'HOM05D001124', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001124' ), 'data_identifier' => 'HOM05D001124', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001124', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '548', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02520' => 'bna', 'A03p06630' => 'bna', 'A05p44460' => 'bna', 'A06p08710' => 'bna', 'A06p41090' => 'bna', 'A07p32320' => 'bna', 'A08p32520' => 'bna', 'A09p10360' => 'bna', 'A10p24080' => 'bna', 'Aa31LG11G15250' => 'aar', 'Aa31LG1G1800' => 'aar', 'Aa31LG2G5120' => 'aar', 'Aa31LG2G6070' => 'aar', 'Aa31LG5G10770' => 'aar', 'Aa31sc61G90' => 'aar', 'Actinidia01352' => 'ach', 'Actinidia05983' => 'ach', 'Actinidia08133' => 'ach', 'Actinidia15101' => 'ach', 'Actinidia26379' => 'ach', 'Actinidia35778' => 'ach', 'Actinidia36123' => 'ach', 'Actinidia37436' => 'ach', 'Actinidia38730' => 'ach', 'Ah.02g128210' => 'amhyb', 'Ah.03g132990' => 'amhyb', 'Ah.14g079410' => 'amhyb', 'AL1G24640' => 'aly', 'AL2G26680' => 'aly', 'AL3G10530' => 'aly', 'AL3G45230' => 'aly', 'AL5G15230' => 'aly', 'AL5G16960' => 'aly', 'AL6G25210' => 'aly', 'Aqoxy2G00441' => 'aox', 'Aqoxy3G01236' => 'aox', 'Aqoxy5G03746' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3RQ047' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C7GMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9C8JER' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MBL6KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YXCZ83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZANX40' => 'arhy', 'AT1G12990' => 'ath', 'AT1G67880' => 'ath', 'AT2G13290' => 'ath', 'AT3G01620' => 'ath', 'AT3G26445' => 'ath', 'AT3G27540' => 'ath', 'AT5G14480' => 'ath', 'ATR0824G026' => 'atr', 'ATR1098G019' => 'atr', 'Atru.chr11.2145' => 'acertr', 'Atru.chr2.3636' => 'acertr', 'Atru.chr2.3644' => 'acertr', 'Atru.chr6.2422' => 'acertr', 'Atru.chr7.1112' => 'acertr', 'AUR62005469' => 'cqu', 'AUR62011166' => 'cqu', 'AUR62013319' => 'cqu', 'AUR62024273' => 'cqu', 'AUR62028420' => 'cqu', 'AUR62041942' => 'cqu', 'BcaB01g04969' => 'bca', 'BcaB01g06371' => 'bca', 'BcaB02g11494' => 'bca', 'BcaB03g15382' => 'bca', 'BcaB08g36994' => 'bca', 'BcaC03g13477' => 'bca', 'BcaC03g13478' => 'bca', 'BcaC03g13480' => 'bca', 'BcaC03g13481' => 'bca', 'BcaC03g13486' => 'bca', 'BcaC04g19031' => 'bca', 'BcaC04g23085' => 'bca', 'BcaC05g25094' => 'bca', 'BcaC05g25096' => 'bca', 'BcaC05g25138' => 'bca', 'BcaC05g30416' => 'bca', 'BcaC05g30455' => 'bca', 'BcaC06g30979' => 'bca', 'BcaC06g33805' => 'bca', 'BcaC08g46021' => 'bca', 'BcaNung03154' => 'bca', 'BolC2t06623H' => 'bol', 'BolC2t06632H' => 'bol', 'BolC2t06635H' => 'bol', 'BolC2t06638H' => 'bol', 'BolC3t13266H' => 'bol', 'BolC5t29776H' => 'bol', 'BolC6t38912H' => 'bol', 'BolC7t44183H' => 'bol', 'BolC9t54123H' => 'bol', 'BolC9t59107H' => 'bol', 'BraA02t05221Z' => 'bra', 'BraA03t09996Z' => 'bra', 'BraA05t23210Z' => 'bra', 'BraA06t24068Z' => 'bra', 'BraA06t27032Z' => 'bra', 'BraA08t35176Z' => 'bra', 'BraA09t36680Z' => 'bra', 'BraA10t44471Z' => 'bra', 'C02p06760' => 'bna', 'C02p06890' => 'bna', 'C02p07010' => 'bna', 'C03p07660' => 'bna', 'C05p10300' => 'bna', 'C06p38150' => 'bna', 'C07p36650' => 'bna', 'C08p15770' => 'bna', 'C09p12300' => 'bna', 'C09p62700' => 'bna', 'C09p75040' => 'bna', 'CAN.G13.1' => 'can', 'CAN.G138.4' => 'can', 'CAN.G44.6' => 'can', 'CAN.G473.19' => 'can', 'CANSAT01G0835' => 'cansat', 'CANSAT11G0246' => 'cansat', 'CANSAT11G1766' => 'cansat', 'CANSAT64G1954' => 'cansat', 'CARHR013330' => 'chi', 'CARHR060530' => 'chi', 'CARHR075300' => 'chi', 'CARHR105120' => 'chi', 'CARHR148910' => 'chi', 'CARHR198830' => 'chi', 'Carub.0001s1275' => 'cru', 'Carub.0002s1437' => 'cru', 'Carub.0003s0044' => 'cru', 'Carub.0003s2787' => 'cru', 'Carub.0005s0597' => 'cru', 'Carub.0006s1266' => 'cru', 'Ca_06935_v3' => 'car', 'Ca_13559_v3' => 'car', 'Ca_16941_v3' => 'car', 'Ca_16960_v3' => 'car', 'Ca_17775_v3' => 'car', 'Ca_30464_v3' => 'car', 'Cc06_g08160' => 'ccan', 'Cc07_g01520' => 'ccan', 'Cc11_g15810' => 'ccan', 'CDE02G2840' => 'cde', 'CDE03G0093' => 'cde', 'CDE04G2127' => 'cde', 'CDE07G1857' => 'cde', 'CDE09G1246' => 'cde', 'Cfa003412' => 'cfa', 'Cfa007341' => 'cfa', 'Cfa009220' => 'cfa', 'Ciclev10008737m.g' => 'ccl', 'Ciclev10015565m.g' => 'ccl', 'Ciclev10031761m.g' => 'ccl', 'CiPaw.03G045300' => 'cil', 'CiPaw.03G247200' => 'cil', 'CiPaw.04G029500' => 'cil', 'CiPaw.04G174000' => 'cil', 'CiPaw.05G181200' => 'cil', 'CiPaw.06G067100' => 'cil', 'ClCG05G025800' => 'cla', 'ClCG06G011400' => 'cla', 'ClCG09G019360' => 'cla', 'COL.COLO4_04827' => 'col', 'COL.COLO4_29170' => 'col', 'COL.COLO4_35131' => 'col', 'COL.COLO4_35132' => 'col', 'Cpa.g.sc33.32' => 'cpa', 'Cpa.g.sc46.29' => 'cpa', 'Cpa.g.sc796.1' => 'cpa', 'CsaV3_1G030420' => 'csa', 'CsaV3_5G027050' => 'csa', 'CsaV3_5G031040' => 'csa', 'CsaV3_UNG023130' => 'csa', 'CSS0007726' => 'camsi', 'CSS0016433' => 'camsi', 'CSS0017656' => 'camsi', 'CSS0025364' => 'camsi', 'CSS0027582' => 'camsi', 'CSS0047288' => 'camsi', 'CSS0049950' => 'camsi', 'DCAR_003843' => 'dca', 'DCAR_007052' => 'dca', 'DCAR_020884' => 'dca', 'DCAR_021730' => 'dca', 'DCAR_024423' => 'dca', 'DCAR_026509' => 'dca', 'DCAR_031158' => 'dca', 'Dinv14728' => 'din', 'Dinv15219' => 'din', 'Dinv25728' => 'din', 'Dinv33428' => 'din', 'Dinv36489' => 'din', 'Dinv41486' => 'din', 'Duzib147G0469' => 'dzi', 'Duzib168G0060' => 'dzi', 'Duzib187G1215' => 'dzi', 'Duzib248G0692' => 'dzi', 'Duzib251G0767' => 'dzi', 'Duzib264G0446' => 'dzi', 'Duzib268G0691' => 'dzi', 'ECA232G4767' => 'eca', 'ECA233G2838' => 'eca', 'ECA234G0391' => 'eca', 'ECA234G0857' => 'eca', 'ECA236G1593' => 'eca', 'ECA238G0565' => 'eca', 'ECA246G1027' => 'eca', 'ECA246G3223' => 'eca', 'ECA246G3470' => 'eca', 'EL10Ac6g13829' => 'bvu', 'EL10Ac6g14093' => 'bvu', 'EL10Ac8g18707' => 'bvu', 'Eucgr.C01369' => 'egr', 'Eucgr.H02492' => 'egr', 'Eucgr.I01733' => 'egr', 'Eucgr.J02255' => 'egr', 'Eucgr.J02257' => 'egr', 'Eucgr.J02258' => 'egr', 'FAN02G1601' => 'fan', 'FAN03G1586' => 'fan', 'FAN03G2986' => 'fan', 'FAN05G4837' => 'fan', 'FAN06G0146' => 'fan', 'FAN07G0858' => 'fan', 'FAN09G3179' => 'fan', 'FAN10G0669' => 'fan', 'FAN12G2358' => 'fan', 'FAN14G4198' => 'fan', 'FAN14G5112' => 'fan', 'FAN17G0342' => 'fan', 'FAN19G0342' => 'fan', 'FAN19G0962' => 'fan', 'FAN19G1101' => 'fan', 'FAN19G1872' => 'fan', 'FAN22G0356' => 'fan', 'FAN23G0744' => 'fan', 'FAN23G1914' => 'fan', 'FAN26G0032' => 'fan', 'FAN28G0625' => 'fan', 'FvH4_1g02710' => 'fve', 'FvH4_1g02720' => 'fve', 'FvH4_4g25670' => 'fve', 'FvH4_6g51700' => 'fve', 'FvH4_7g20170' => 'fve', 'Glyma.05G175000' => 'gma', 'Glyma.08G132300' => 'gma', 'Glyma.11G243000' => 'gma', 'Glyma.13G158900' => 'gma', 'Glyma.17G112400' => 'gma', 'Glyma.18G014100' => 'gma', 'Glyma.19G003100' => 'gma', 'Glyma.19G056500' => 'gma', 'Gohir.A01G158900' => 'ghi', 'Gohir.A05G312600' => 'ghi', 'Gohir.A05G354900' => 'ghi', 'Gohir.A07G037200' => 'ghi', 'Gohir.A09G030000' => 'ghi', 'Gohir.A12G145200' => 'ghi', 'Gohir.D01G151500' => 'ghi', 'Gohir.D04G058300' => 'ghi', 'Gohir.D05G314100' => 'ghi', 'Gohir.D07G041400' => 'ghi', 'Gohir.D09G029700' => 'ghi', 'Gohir.D12G149700' => 'ghi', 'Gorai.001G043800' => 'gra', 'Gorai.002G187800' => 'gra', 'Gorai.006G034700' => 'gra', 'Gorai.008G161200' => 'gra', 'Gorai.009G335700' => 'gra', 'Gorai.012G065000' => 'gra', 'GSVIVG01000535001' => 'vvi', 'GSVIVG01015572001' => 'vvi', 'GSVIVG01032386001' => 'vvi', 'HanXRQChr05g0138531' => 'han', 'HanXRQChr06g0174391' => 'han', 'HanXRQChr07g0199021' => 'han', 'HanXRQChr08g0208211' => 'han', 'HanXRQChr09g0255471' => 'han', 'HanXRQChr10g0315791' => 'han', 'HanXRQChr12g0371991' => 'han', 'HanXRQChr15g0475251' => 'han', 'HanXRQChr17g0540001' => 'han', 'HanXRQChr17g0548631' => 'han', 'HanXRQChr17g0569561' => 'han', 'Haze_12256' => 'cav', 'Haze_14756' => 'cav', 'Haze_25528' => 'cav', 'Hma1.2p1_0079F.1_g041020' => 'hma', 'Hma1.2p1_0818F.1_g223260' => 'hma', 'Hma1.2p1_1747F.1_g300530' => 'hma', 'HPP92_004607' => 'vpl', 'HPP92_004608' => 'vpl', 'HPP92_006181' => 'vpl', 'HPP92_012192' => 'vpl', 'HPP92_015680' => 'vpl', 'HPP92_020249' => 'vpl', 'HPP92_021376' => 'vpl', 'HPP92_024275' => 'vpl', 'Hund06031' => 'sun', 'Hund25391' => 'sun', 'Lalb_Chr07g0185371' => 'lal', 'Lalb_Chr07g0185381' => 'lal', 'Lalb_Chr12g0204011' => 'lal', 'Lalb_Chr13g0301671' => 'lal', 'Lalb_Chr14g0362851' => 'lal', 'Lalb_Chr24g0403581' => 'lal', 'Lj1g0000233' => 'lja', 'Lj2g0018120' => 'lja', 'Lj3C621T0' => 'lonja', 'Lj3P1059T14' => 'lonja', 'Lj3P611T9' => 'lonja', 'Lj3P614T13' => 'lonja', 'Lj3P615T5' => 'lonja', 'Lj4g0012315' => 'lja', 'Lj4g0026182' => 'lja', 'Lj6P813T16' => 'lonja', 'Lj7C427T7' => 'lonja', 'Lj7C427T8' => 'lonja', 'Lj7P600T41' => 'lonja', 'Lju41C42G17' => 'lonja', 'Lsat_1_v5_gn_0_47300' => 'lsa', 'Lsat_1_v5_gn_2_91280' => 'lsa', 'Lsat_1_v5_gn_3_30561' => 'lsa', 'Lsat_1_v5_gn_4_184321' => 'lsa', 'Lsat_1_v5_gn_4_4041' => 'lsa', 'Lsat_1_v5_gn_5_92000' => 'lsa', 'Lsat_1_v5_gn_8_152940' => 'lsa', 'Lsat_1_v5_gn_8_62401' => 'lsa', 'Manes.06G055900' => 'mes', 'Manes.12G022200' => 'mes', 'Manes.13G023300' => 'mes', 'Manes.14G115000' => 'mes', 'Manes.15G151700' => 'mes', 'Manes.17G111300' => 'mes', 'Mapoly0226s0009' => 'mpo', 'MBI02_g25363_MAGBIO' => 'mbi', 'MBI06_g00027_MAGBIO' => 'mbi', 'MBI10_g13034_MAGBIO' => 'mbi', 'MD09G1023400' => 'mdo', 'MD13G1100100' => 'mdo', 'MD15G1169200' => 'mdo', 'MD16G1101100' => 'mdo', 'MD17G1022900' => 'mdo', 'Medtr3g096150' => 'mtr', 'Medtr4g115070' => 'mtr', 'Medtr7g033325' => 'mtr', 'Medtr8g089840' => 'mtr', 'MELO3C010319.2' => 'cme', 'MELO3C011944.2' => 'cme', 'MELO3C021589.2' => 'cme', 'Migut.E00207' => 'egut', 'Migut.H00067' => 'egut', 'Migut.K00433' => 'egut', 'Migut.K00606' => 'egut', 'Migut.K01410' => 'egut', 'MSTRG.13347' => 'ama', 'MSTRG.24045' => 'ama', 'MSTRG.2428' => 'ama', 'MSTRG.26410' => 'ama', 'MSTRG.3139' => 'ama', 'MSTRG.3286' => 'ama', 'MSTRG.563' => 'ama', 'MSTRG.7941' => 'ama', 'Nitab4.5_0000028g0060' => 'nta', 'Nitab4.5_0000065g0260' => 'nta', 'Nitab4.5_0000112g0060' => 'nta', 'Nitab4.5_0000489g0120' => 'nta', 'Nitab4.5_0001776g0050' => 'nta', 'Nitab4.5_0001854g0010' => 'nta', 'Nitab4.5_0001860g0020' => 'nta', 'Nitab4.5_0004352g0010' => 'nta', 'Nitab4.5_0008716g0020' => 'nta', 'Nitab4.5_0008922g0010' => 'nta', 'Nn3g16693' => 'nnu', 'Nn4g22596' => 'nnu', 'Nn7g37639' => 'nnu', 'Oeu001701.1' => 'oeu', 'Oeu018149.1' => 'oeu', 'Oeu026220.1' => 'oeu', 'Oeu038635.1' => 'oeu', 'Oeu049176.1' => 'oeu', 'Oeu056706.1' => 'oeu', 'Oeu056937.1' => 'oeu', 'Oeu057540.1' => 'oeu', 'Os02g0594900' => 'osa', 'Os02g0595100' => 'osa', 'Os04g0477500' => 'osa', 'Os12g0611900' => 'osa', 'Peaxi162Scf00076g00020' => 'pax', 'Peaxi162Scf00128g00217' => 'pax', 'Peaxi162Scf00129g01640' => 'pax', 'Peaxi162Scf00669g00007' => 'pax', 'Peaxi162Scf00700g00421' => 'pax', 'Peaxi162Scf00801g00038' => 'pax', 'Peaxi162Scf00891g00025' => 'pax', 'PGR083G0909' => 'pgr', 'PGR119G1005' => 'pgr', 'PGR142G2236' => 'pgr', 'PGR142G3388' => 'pgr', 'PGSC0003DMG400004514' => 'stu', 'PGSC0003DMG400012635' => 'stu', 'PGSC0003DMG400015730' => 'stu', 'PGSC0003DMG400018611' => 'stu', 'PGSC0003DMG400030897' => 'stu', 'Phvul.001G254800' => 'pvu', 'Phvul.002G260100' => 'pvu', 'Phvul.003G167600' => 'pvu', 'Phvul.004G005100' => 'pvu', 'Potri.001G343600' => 'ptr', 'Potri.006G066700' => 'ptr', 'Potri.008G186000' => 'ptr', 'Potri.010G046900' => 'ptr', 'Potri.018G127900' => 'ptr', 'Pp3c20_17750' => 'ppa', 'Pp3c24_4380' => 'ppa', 'Prupe.1G245800' => 'ppe', 'Prupe.3G293400' => 'ppe', 'Prupe.7G247400' => 'ppe', 'Psat0s145g0120' => 'psa', 'Psat0s595g0040' => 'psa', 'Psat0s595g0120' => 'psa', 'Psat3g175040' => 'psa', 'Psat7g058120' => 'psa', 'PSO017G0428' => 'pso', 'PSO063G7510' => 'pso', 'PSO067G0046' => 'pso', 'PSO478G1073' => 'pso', 'PSO675G3677' => 'pso', 'PSO675G6558' => 'pso', 'PSO675G7520' => 'pso', 'PSO675G8959' => 'pso', 'QL02p074089' => 'qlo', 'QL02p089614' => 'qlo', 'QL03p057736' => 'qlo', 'RcHm_v2.0_Chr1g0364131' => 'rch', 'RcHm_v2.0_Chr2g0087801' => 'rch', 'RcHm_v2.0_Chr2g0087821' => 'rch', 'RcHm_v2.0_Chr2g0173231' => 'rch', 'RcHm_v2.0_Chr4g0433111' => 'rch', 'Rhsim03G0250300' => 'rsi', 'Rhsim08G0048400' => 'rsi', 'Rhsim10G0014800' => 'rsi', 'Rhsim12G0040100' => 'rsi', 'Rhsim12G0109700' => 'rsi', 'Sabra06G0049600' => 'sbr', 'Sabra08G0141000' => 'sbr', 'Sabra10G0021400' => 'sbr', 'Sabra16G0222900' => 'sbr', 'Sabra18G0108600' => 'sbr', 'SalBow1G0433' => 'sbo', 'SalBow1G2038' => 'sbo', 'SalBow1G5003' => 'sbo', 'SalBow7G1197' => 'sbo', 'SalBow8G3506' => 'sbo', 'Sc03g0007300' => 'sci', 'Sc11g0000950' => 'sci', 'Sc14g0008750' => 'sci', 'Sc18g0000420' => 'sci', 'Sed0006754' => 'sed', 'Sed0008741' => 'sed', 'Sed0017172' => 'sed', 'Sed0018925' => 'sed', 'Sed0023326' => 'sed', 'Sed0025909' => 'sed', 'SEGI_05333' => 'sgi', 'SEGI_10362' => 'sgi', 'SEGI_13380' => 'sgi', 'SEGI_24306' => 'sgi', 'SEGI_29077' => 'sgi', 'SEGI_29095' => 'sgi', 'SEGI_36534' => 'sgi', 'SEGI_37506' => 'sgi', 'SEGI_38321' => 'sgi', 'SGA_v2.0_scaffold307G48031' => 'sas', 'SGA_v2.0_scaffold47G17507' => 'sas', 'SGA_v2.0_scaffold63G21736' => 'sas', 'SGA_v2.0_scaffold87G27070' => 'sas', 'SHI17794' => 'shi', 'SHI28851' => 'shi', 'SMO165G0155' => 'smo', 'SMO340G0217' => 'smo', 'SMO367G1210' => 'smo', 'Solyc02g093430.3' => 'sly', 'Solyc05g013580.4' => 'sly', 'Solyc07g008030.3' => 'sly', 'Solyc12g035470.2' => 'sly', 'Sopen02g038020' => 'spe', 'Sopen05g008490' => 'spe', 'Sopen07g003910' => 'spe', 'Sopen12g015240' => 'spe', 'Sp1g11550' => 'spa', 'Sp2g16710' => 'spa', 'Sp3g00430' => 'spa', 'Sp3g26780' => 'spa', 'Sp5g22900' => 'spa', 'Sp6g29530' => 'spa', 'TAR371G0794' => 'tar', 'TAR374G0164' => 'tar', 'TAR622G0165' => 'tar', 'TAR626G0929' => 'tar', 'TAR629G2155' => 'tar', 'THA.LOC104805282' => 'tha', 'THA.LOC104805363' => 'tha', 'THA.LOC104808968' => 'tha', 'THA.LOC104821093' => 'tha', 'THA.LOC104823953' => 'tha', 'THA.LOC104825562' => 'tha', 'THA.LOC104825665' => 'tha', 'Thecc.02G261400' => 'tca', 'Thecc.04G019200' => 'tca', 'Thecc.09G130400' => 'tca', 'Thhalv10004374m.g' => 'esa', 'Thhalv10007850m.g' => 'esa', 'Thhalv10013782m.g' => 'esa', 'Thhalv10018686m.g' => 'esa', 'Thhalv10020899m.g' => 'esa', 'Thhalv10022755m.g' => 'esa', 'TPR.G23851' => 'tpr', 'TPR.G26500' => 'tpr', 'TPR.G27267' => 'tpr', 'TPR.G32001' => 'tpr', 'TPR.G6251' => 'tpr', 'TPR.G8167' => 'tpr', 'TWI12G1330' => 'twi', 'TWI18G1239' => 'twi', 'TWI34G0979' => 'twi', 'TWI36G0670' => 'twi', 'TWI36G0707' => 'twi', 'TWI56G0233' => 'twi', 'TWI75G1809' => 'twi', 'unitig_21.g20874' => 'ugi', 'unitig_26.g10343' => 'ugi', 'unitig_46.g18392' => 'ugi', 'unitig_52.g17178' => 'ugi', 'unitig_8.g2934' => 'ugi', 'vmacro01122' => 'vma', 'vmacro05875' => 'vma', 'vmacro06147' => 'vma', 'vmacro16191' => 'vma', 'vmacro18293' => 'vma', 'VMungo0251G3707' => 'vmu', 'VMungo0464G1521' => 'vmu', 'VMungo1215G0205' => 'vmu', 'VMungo1383G2484' => 'vmu', 'Zm00001eb079610' => 'zma', 'Zm00001eb135990' => 'zma', 'Zm00001eb183710' => 'zma', 'Zm00001eb246020' => 'zma' ) $gf_id = 'HOM05D001124' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001124' ) $data_identifier = 'HOM05D001124' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 6, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 7, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 21, 'bol' => (int) 10, 'bra' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 6, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 9, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 21, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 8, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 10, 'lsa' => (int) 8, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 8, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 9, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb246020' $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' => 'HOM05D001124', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '548', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02520' => 'bna', 'A03p06630' => 'bna', 'A05p44460' => 'bna', 'A06p08710' => 'bna', 'A06p41090' => 'bna', 'A07p32320' => 'bna', 'A08p32520' => 'bna', 'A09p10360' => 'bna', 'A10p24080' => 'bna', 'Aa31LG11G15250' => 'aar', 'Aa31LG1G1800' => 'aar', 'Aa31LG2G5120' => 'aar', 'Aa31LG2G6070' => 'aar', 'Aa31LG5G10770' => 'aar', 'Aa31sc61G90' => 'aar', 'Actinidia01352' => 'ach', 'Actinidia05983' => 'ach', 'Actinidia08133' => 'ach', 'Actinidia15101' => 'ach', 'Actinidia26379' => 'ach', 'Actinidia35778' => 'ach', 'Actinidia36123' => 'ach', 'Actinidia37436' => 'ach', 'Actinidia38730' => 'ach', 'Ah.02g128210' => 'amhyb', 'Ah.03g132990' => 'amhyb', 'Ah.14g079410' => 'amhyb', 'AL1G24640' => 'aly', 'AL2G26680' => 'aly', 'AL3G10530' => 'aly', 'AL3G45230' => 'aly', 'AL5G15230' => 'aly', 'AL5G16960' => 'aly', 'AL6G25210' => 'aly', 'Aqoxy2G00441' => 'aox', 'Aqoxy3G01236' => 'aox', 'Aqoxy5G03746' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3RQ047' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C7GMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9C8JER' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MBL6KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YXCZ83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZANX40' => 'arhy', 'AT1G12990' => 'ath', 'AT1G67880' => 'ath', 'AT2G13290' => 'ath', 'AT3G01620' => 'ath', 'AT3G26445' => 'ath', 'AT3G27540' => 'ath', 'AT5G14480' => 'ath', 'ATR0824G026' => 'atr', 'ATR1098G019' => 'atr', 'Atru.chr11.2145' => 'acertr', 'Atru.chr2.3636' => 'acertr', 'Atru.chr2.3644' => 'acertr', 'Atru.chr6.2422' => 'acertr', 'Atru.chr7.1112' => 'acertr', 'AUR62005469' => 'cqu', 'AUR62011166' => 'cqu', 'AUR62013319' => 'cqu', 'AUR62024273' => 'cqu', 'AUR62028420' => 'cqu', 'AUR62041942' => 'cqu', 'BcaB01g04969' => 'bca', 'BcaB01g06371' => 'bca', 'BcaB02g11494' => 'bca', 'BcaB03g15382' => 'bca', 'BcaB08g36994' => 'bca', 'BcaC03g13477' => 'bca', 'BcaC03g13478' => 'bca', 'BcaC03g13480' => 'bca', 'BcaC03g13481' => 'bca', 'BcaC03g13486' => 'bca', 'BcaC04g19031' => 'bca', 'BcaC04g23085' => 'bca', 'BcaC05g25094' => 'bca', 'BcaC05g25096' => 'bca', 'BcaC05g25138' => 'bca', 'BcaC05g30416' => 'bca', 'BcaC05g30455' => 'bca', 'BcaC06g30979' => 'bca', 'BcaC06g33805' => 'bca', 'BcaC08g46021' => 'bca', 'BcaNung03154' => 'bca', 'BolC2t06623H' => 'bol', 'BolC2t06632H' => 'bol', 'BolC2t06635H' => 'bol', 'BolC2t06638H' => 'bol', 'BolC3t13266H' => 'bol', 'BolC5t29776H' => 'bol', 'BolC6t38912H' => 'bol', 'BolC7t44183H' => 'bol', 'BolC9t54123H' => 'bol', 'BolC9t59107H' => 'bol', 'BraA02t05221Z' => 'bra', 'BraA03t09996Z' => 'bra', 'BraA05t23210Z' => 'bra', 'BraA06t24068Z' => 'bra', 'BraA06t27032Z' => 'bra', 'BraA08t35176Z' => 'bra', 'BraA09t36680Z' => 'bra', 'BraA10t44471Z' => 'bra', 'C02p06760' => 'bna', 'C02p06890' => 'bna', 'C02p07010' => 'bna', 'C03p07660' => 'bna', 'C05p10300' => 'bna', 'C06p38150' => 'bna', 'C07p36650' => 'bna', 'C08p15770' => 'bna', 'C09p12300' => 'bna', 'C09p62700' => 'bna', 'C09p75040' => 'bna', 'CAN.G13.1' => 'can', 'CAN.G138.4' => 'can', 'CAN.G44.6' => 'can', 'CAN.G473.19' => 'can', 'CANSAT01G0835' => 'cansat', 'CANSAT11G0246' => 'cansat', 'CANSAT11G1766' => 'cansat', 'CANSAT64G1954' => 'cansat', 'CARHR013330' => 'chi', 'CARHR060530' => 'chi', 'CARHR075300' => 'chi', 'CARHR105120' => 'chi', 'CARHR148910' => 'chi', 'CARHR198830' => 'chi', 'Carub.0001s1275' => 'cru', 'Carub.0002s1437' => 'cru', 'Carub.0003s0044' => 'cru', 'Carub.0003s2787' => 'cru', 'Carub.0005s0597' => 'cru', 'Carub.0006s1266' => 'cru', 'Ca_06935_v3' => 'car', 'Ca_13559_v3' => 'car', 'Ca_16941_v3' => 'car', 'Ca_16960_v3' => 'car', 'Ca_17775_v3' => 'car', 'Ca_30464_v3' => 'car', 'Cc06_g08160' => 'ccan', 'Cc07_g01520' => 'ccan', 'Cc11_g15810' => 'ccan', 'CDE02G2840' => 'cde', 'CDE03G0093' => 'cde', 'CDE04G2127' => 'cde', 'CDE07G1857' => 'cde', 'CDE09G1246' => 'cde', 'Cfa003412' => 'cfa', 'Cfa007341' => 'cfa', 'Cfa009220' => 'cfa', 'Ciclev10008737m.g' => 'ccl', 'Ciclev10015565m.g' => 'ccl', 'Ciclev10031761m.g' => 'ccl', 'CiPaw.03G045300' => 'cil', 'CiPaw.03G247200' => 'cil', 'CiPaw.04G029500' => 'cil', 'CiPaw.04G174000' => 'cil', 'CiPaw.05G181200' => 'cil', 'CiPaw.06G067100' => 'cil', 'ClCG05G025800' => 'cla', 'ClCG06G011400' => 'cla', 'ClCG09G019360' => 'cla', 'COL.COLO4_04827' => 'col', 'COL.COLO4_29170' => 'col', 'COL.COLO4_35131' => 'col', 'COL.COLO4_35132' => 'col', 'Cpa.g.sc33.32' => 'cpa', 'Cpa.g.sc46.29' => 'cpa', 'Cpa.g.sc796.1' => 'cpa', 'CsaV3_1G030420' => 'csa', 'CsaV3_5G027050' => 'csa', 'CsaV3_5G031040' => 'csa', 'CsaV3_UNG023130' => 'csa', 'CSS0007726' => 'camsi', 'CSS0016433' => 'camsi', 'CSS0017656' => 'camsi', 'CSS0025364' => 'camsi', 'CSS0027582' => 'camsi', 'CSS0047288' => 'camsi', 'CSS0049950' => 'camsi', 'DCAR_003843' => 'dca', 'DCAR_007052' => 'dca', 'DCAR_020884' => 'dca', 'DCAR_021730' => 'dca', 'DCAR_024423' => 'dca', 'DCAR_026509' => 'dca', 'DCAR_031158' => 'dca', 'Dinv14728' => 'din', 'Dinv15219' => 'din', 'Dinv25728' => 'din', 'Dinv33428' => 'din', 'Dinv36489' => 'din', 'Dinv41486' => 'din', 'Duzib147G0469' => 'dzi', 'Duzib168G0060' => 'dzi', 'Duzib187G1215' => 'dzi', 'Duzib248G0692' => 'dzi', 'Duzib251G0767' => 'dzi', 'Duzib264G0446' => 'dzi', 'Duzib268G0691' => 'dzi', 'ECA232G4767' => 'eca', 'ECA233G2838' => 'eca', 'ECA234G0391' => 'eca', 'ECA234G0857' => 'eca', 'ECA236G1593' => 'eca', 'ECA238G0565' => 'eca', 'ECA246G1027' => 'eca', 'ECA246G3223' => 'eca', 'ECA246G3470' => 'eca', 'EL10Ac6g13829' => 'bvu', 'EL10Ac6g14093' => 'bvu', 'EL10Ac8g18707' => 'bvu', 'Eucgr.C01369' => 'egr', 'Eucgr.H02492' => 'egr', 'Eucgr.I01733' => 'egr', 'Eucgr.J02255' => 'egr', 'Eucgr.J02257' => 'egr', 'Eucgr.J02258' => 'egr', 'FAN02G1601' => 'fan', 'FAN03G1586' => 'fan', 'FAN03G2986' => 'fan', 'FAN05G4837' => 'fan', 'FAN06G0146' => 'fan', 'FAN07G0858' => 'fan', 'FAN09G3179' => 'fan', 'FAN10G0669' => 'fan', 'FAN12G2358' => 'fan', 'FAN14G4198' => 'fan', 'FAN14G5112' => 'fan', 'FAN17G0342' => 'fan', 'FAN19G0342' => 'fan', 'FAN19G0962' => 'fan', 'FAN19G1101' => 'fan', 'FAN19G1872' => 'fan', 'FAN22G0356' => 'fan', 'FAN23G0744' => 'fan', 'FAN23G1914' => 'fan', 'FAN26G0032' => 'fan', 'FAN28G0625' => 'fan', 'FvH4_1g02710' => 'fve', 'FvH4_1g02720' => 'fve', 'FvH4_4g25670' => 'fve', 'FvH4_6g51700' => 'fve', 'FvH4_7g20170' => 'fve', 'Glyma.05G175000' => 'gma', 'Glyma.08G132300' => 'gma', 'Glyma.11G243000' => 'gma', 'Glyma.13G158900' => 'gma', 'Glyma.17G112400' => 'gma', 'Glyma.18G014100' => 'gma', 'Glyma.19G003100' => 'gma', 'Glyma.19G056500' => 'gma', 'Gohir.A01G158900' => 'ghi', 'Gohir.A05G312600' => 'ghi', 'Gohir.A05G354900' => 'ghi', 'Gohir.A07G037200' => 'ghi', 'Gohir.A09G030000' => 'ghi', 'Gohir.A12G145200' => 'ghi', 'Gohir.D01G151500' => 'ghi', 'Gohir.D04G058300' => 'ghi', 'Gohir.D05G314100' => 'ghi', 'Gohir.D07G041400' => 'ghi', 'Gohir.D09G029700' => 'ghi', 'Gohir.D12G149700' => 'ghi', 'Gorai.001G043800' => 'gra', 'Gorai.002G187800' => 'gra', 'Gorai.006G034700' => 'gra', 'Gorai.008G161200' => 'gra', 'Gorai.009G335700' => 'gra', 'Gorai.012G065000' => 'gra', 'GSVIVG01000535001' => 'vvi', 'GSVIVG01015572001' => 'vvi', 'GSVIVG01032386001' => 'vvi', 'HanXRQChr05g0138531' => 'han', 'HanXRQChr06g0174391' => 'han', 'HanXRQChr07g0199021' => 'han', 'HanXRQChr08g0208211' => 'han', 'HanXRQChr09g0255471' => 'han', 'HanXRQChr10g0315791' => 'han', 'HanXRQChr12g0371991' => 'han', 'HanXRQChr15g0475251' => 'han', 'HanXRQChr17g0540001' => 'han', 'HanXRQChr17g0548631' => 'han', 'HanXRQChr17g0569561' => 'han', 'Haze_12256' => 'cav', 'Haze_14756' => 'cav', 'Haze_25528' => 'cav', 'Hma1.2p1_0079F.1_g041020' => 'hma', 'Hma1.2p1_0818F.1_g223260' => 'hma', 'Hma1.2p1_1747F.1_g300530' => 'hma', 'HPP92_004607' => 'vpl', 'HPP92_004608' => 'vpl', 'HPP92_006181' => 'vpl', 'HPP92_012192' => 'vpl', 'HPP92_015680' => 'vpl', 'HPP92_020249' => 'vpl', 'HPP92_021376' => 'vpl', 'HPP92_024275' => 'vpl', 'Hund06031' => 'sun', 'Hund25391' => 'sun', 'Lalb_Chr07g0185371' => 'lal', 'Lalb_Chr07g0185381' => 'lal', 'Lalb_Chr12g0204011' => 'lal', 'Lalb_Chr13g0301671' => 'lal', 'Lalb_Chr14g0362851' => 'lal', 'Lalb_Chr24g0403581' => 'lal', 'Lj1g0000233' => 'lja', 'Lj2g0018120' => 'lja', 'Lj3C621T0' => 'lonja', 'Lj3P1059T14' => 'lonja', 'Lj3P611T9' => 'lonja', 'Lj3P614T13' => 'lonja', 'Lj3P615T5' => 'lonja', 'Lj4g0012315' => 'lja', 'Lj4g0026182' => 'lja', 'Lj6P813T16' => 'lonja', 'Lj7C427T7' => 'lonja', 'Lj7C427T8' => 'lonja', 'Lj7P600T41' => 'lonja', 'Lju41C42G17' => 'lonja', 'Lsat_1_v5_gn_0_47300' => 'lsa', 'Lsat_1_v5_gn_2_91280' => 'lsa', 'Lsat_1_v5_gn_3_30561' => 'lsa', 'Lsat_1_v5_gn_4_184321' => 'lsa', 'Lsat_1_v5_gn_4_4041' => 'lsa', 'Lsat_1_v5_gn_5_92000' => 'lsa', 'Lsat_1_v5_gn_8_152940' => 'lsa', 'Lsat_1_v5_gn_8_62401' => 'lsa', 'Manes.06G055900' => 'mes', 'Manes.12G022200' => 'mes', 'Manes.13G023300' => 'mes', 'Manes.14G115000' => 'mes', 'Manes.15G151700' => 'mes', 'Manes.17G111300' => 'mes', 'Mapoly0226s0009' => 'mpo', 'MBI02_g25363_MAGBIO' => 'mbi', 'MBI06_g00027_MAGBIO' => 'mbi', 'MBI10_g13034_MAGBIO' => 'mbi', 'MD09G1023400' => 'mdo', 'MD13G1100100' => 'mdo', 'MD15G1169200' => 'mdo', 'MD16G1101100' => 'mdo', 'MD17G1022900' => 'mdo', 'Medtr3g096150' => 'mtr', 'Medtr4g115070' => 'mtr', 'Medtr7g033325' => 'mtr', 'Medtr8g089840' => 'mtr', 'MELO3C010319.2' => 'cme', 'MELO3C011944.2' => 'cme', 'MELO3C021589.2' => 'cme', 'Migut.E00207' => 'egut', 'Migut.H00067' => 'egut', 'Migut.K00433' => 'egut', 'Migut.K00606' => 'egut', 'Migut.K01410' => 'egut', 'MSTRG.13347' => 'ama', 'MSTRG.24045' => 'ama', 'MSTRG.2428' => 'ama', 'MSTRG.26410' => 'ama', 'MSTRG.3139' => 'ama', 'MSTRG.3286' => 'ama', 'MSTRG.563' => 'ama', 'MSTRG.7941' => 'ama', 'Nitab4.5_0000028g0060' => 'nta', 'Nitab4.5_0000065g0260' => 'nta', 'Nitab4.5_0000112g0060' => 'nta', 'Nitab4.5_0000489g0120' => 'nta', 'Nitab4.5_0001776g0050' => 'nta', 'Nitab4.5_0001854g0010' => 'nta', 'Nitab4.5_0001860g0020' => 'nta', 'Nitab4.5_0004352g0010' => 'nta', 'Nitab4.5_0008716g0020' => 'nta', 'Nitab4.5_0008922g0010' => 'nta', 'Nn3g16693' => 'nnu', 'Nn4g22596' => 'nnu', 'Nn7g37639' => 'nnu', 'Oeu001701.1' => 'oeu', 'Oeu018149.1' => 'oeu', 'Oeu026220.1' => 'oeu', 'Oeu038635.1' => 'oeu', 'Oeu049176.1' => 'oeu', 'Oeu056706.1' => 'oeu', 'Oeu056937.1' => 'oeu', 'Oeu057540.1' => 'oeu', 'Os02g0594900' => 'osa', 'Os02g0595100' => 'osa', 'Os04g0477500' => 'osa', 'Os12g0611900' => 'osa', 'Peaxi162Scf00076g00020' => 'pax', 'Peaxi162Scf00128g00217' => 'pax', 'Peaxi162Scf00129g01640' => 'pax', 'Peaxi162Scf00669g00007' => 'pax', 'Peaxi162Scf00700g00421' => 'pax', 'Peaxi162Scf00801g00038' => 'pax', 'Peaxi162Scf00891g00025' => 'pax', 'PGR083G0909' => 'pgr', 'PGR119G1005' => 'pgr', 'PGR142G2236' => 'pgr', 'PGR142G3388' => 'pgr', 'PGSC0003DMG400004514' => 'stu', 'PGSC0003DMG400012635' => 'stu', 'PGSC0003DMG400015730' => 'stu', 'PGSC0003DMG400018611' => 'stu', 'PGSC0003DMG400030897' => 'stu', 'Phvul.001G254800' => 'pvu', 'Phvul.002G260100' => 'pvu', 'Phvul.003G167600' => 'pvu', 'Phvul.004G005100' => 'pvu', 'Potri.001G343600' => 'ptr', 'Potri.006G066700' => 'ptr', 'Potri.008G186000' => 'ptr', 'Potri.010G046900' => 'ptr', 'Potri.018G127900' => 'ptr', 'Pp3c20_17750' => 'ppa', 'Pp3c24_4380' => 'ppa', 'Prupe.1G245800' => 'ppe', 'Prupe.3G293400' => 'ppe', 'Prupe.7G247400' => 'ppe', 'Psat0s145g0120' => 'psa', 'Psat0s595g0040' => 'psa', 'Psat0s595g0120' => 'psa', 'Psat3g175040' => 'psa', 'Psat7g058120' => 'psa', 'PSO017G0428' => 'pso', 'PSO063G7510' => 'pso', 'PSO067G0046' => 'pso', 'PSO478G1073' => 'pso', 'PSO675G3677' => 'pso', 'PSO675G6558' => 'pso', 'PSO675G7520' => 'pso', 'PSO675G8959' => 'pso', 'QL02p074089' => 'qlo', 'QL02p089614' => 'qlo', 'QL03p057736' => 'qlo', 'RcHm_v2.0_Chr1g0364131' => 'rch', 'RcHm_v2.0_Chr2g0087801' => 'rch', 'RcHm_v2.0_Chr2g0087821' => 'rch', 'RcHm_v2.0_Chr2g0173231' => 'rch', 'RcHm_v2.0_Chr4g0433111' => 'rch', 'Rhsim03G0250300' => 'rsi', 'Rhsim08G0048400' => 'rsi', 'Rhsim10G0014800' => 'rsi', 'Rhsim12G0040100' => 'rsi', 'Rhsim12G0109700' => 'rsi', 'Sabra06G0049600' => 'sbr', 'Sabra08G0141000' => 'sbr', 'Sabra10G0021400' => 'sbr', 'Sabra16G0222900' => 'sbr', 'Sabra18G0108600' => 'sbr', 'SalBow1G0433' => 'sbo', 'SalBow1G2038' => 'sbo', 'SalBow1G5003' => 'sbo', 'SalBow7G1197' => 'sbo', 'SalBow8G3506' => 'sbo', 'Sc03g0007300' => 'sci', 'Sc11g0000950' => 'sci', 'Sc14g0008750' => 'sci', 'Sc18g0000420' => 'sci', 'Sed0006754' => 'sed', 'Sed0008741' => 'sed', 'Sed0017172' => 'sed', 'Sed0018925' => 'sed', 'Sed0023326' => 'sed', 'Sed0025909' => 'sed', 'SEGI_05333' => 'sgi', 'SEGI_10362' => 'sgi', 'SEGI_13380' => 'sgi', 'SEGI_24306' => 'sgi', 'SEGI_29077' => 'sgi', 'SEGI_29095' => 'sgi', 'SEGI_36534' => 'sgi', 'SEGI_37506' => 'sgi', 'SEGI_38321' => 'sgi', 'SGA_v2.0_scaffold307G48031' => 'sas', 'SGA_v2.0_scaffold47G17507' => 'sas', 'SGA_v2.0_scaffold63G21736' => 'sas', 'SGA_v2.0_scaffold87G27070' => 'sas', 'SHI17794' => 'shi', 'SHI28851' => 'shi', 'SMO165G0155' => 'smo', 'SMO340G0217' => 'smo', 'SMO367G1210' => 'smo', 'Solyc02g093430.3' => 'sly', 'Solyc05g013580.4' => 'sly', 'Solyc07g008030.3' => 'sly', 'Solyc12g035470.2' => 'sly', 'Sopen02g038020' => 'spe', 'Sopen05g008490' => 'spe', 'Sopen07g003910' => 'spe', 'Sopen12g015240' => 'spe', 'Sp1g11550' => 'spa', 'Sp2g16710' => 'spa', 'Sp3g00430' => 'spa', 'Sp3g26780' => 'spa', 'Sp5g22900' => 'spa', 'Sp6g29530' => 'spa', 'TAR371G0794' => 'tar', 'TAR374G0164' => 'tar', 'TAR622G0165' => 'tar', 'TAR626G0929' => 'tar', 'TAR629G2155' => 'tar', 'THA.LOC104805282' => 'tha', 'THA.LOC104805363' => 'tha', 'THA.LOC104808968' => 'tha', 'THA.LOC104821093' => 'tha', 'THA.LOC104823953' => 'tha', 'THA.LOC104825562' => 'tha', 'THA.LOC104825665' => 'tha', 'Thecc.02G261400' => 'tca', 'Thecc.04G019200' => 'tca', 'Thecc.09G130400' => 'tca', 'Thhalv10004374m.g' => 'esa', 'Thhalv10007850m.g' => 'esa', 'Thhalv10013782m.g' => 'esa', 'Thhalv10018686m.g' => 'esa', 'Thhalv10020899m.g' => 'esa', 'Thhalv10022755m.g' => 'esa', 'TPR.G23851' => 'tpr', 'TPR.G26500' => 'tpr', 'TPR.G27267' => 'tpr', 'TPR.G32001' => 'tpr', 'TPR.G6251' => 'tpr', 'TPR.G8167' => 'tpr', 'TWI12G1330' => 'twi', 'TWI18G1239' => 'twi', 'TWI34G0979' => 'twi', 'TWI36G0670' => 'twi', 'TWI36G0707' => 'twi', 'TWI56G0233' => 'twi', 'TWI75G1809' => 'twi', 'unitig_21.g20874' => 'ugi', 'unitig_26.g10343' => 'ugi', 'unitig_46.g18392' => 'ugi', 'unitig_52.g17178' => 'ugi', 'unitig_8.g2934' => 'ugi', 'vmacro01122' => 'vma', 'vmacro05875' => 'vma', 'vmacro06147' => 'vma', 'vmacro16191' => 'vma', 'vmacro18293' => 'vma', 'VMungo0251G3707' => 'vmu', 'VMungo0464G1521' => 'vmu', 'VMungo1215G0205' => 'vmu', 'VMungo1383G2484' => 'vmu', 'Zm00001eb079610' => 'zma', 'Zm00001eb135990' => 'zma', 'Zm00001eb183710' => 'zma', 'Zm00001eb246020' => 'zma' ), 'gf_id' => 'HOM05D001124', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001124' ), 'data_identifier' => 'HOM05D001124', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001124', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '548', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02520' => 'bna', 'A03p06630' => 'bna', 'A05p44460' => 'bna', 'A06p08710' => 'bna', 'A06p41090' => 'bna', 'A07p32320' => 'bna', 'A08p32520' => 'bna', 'A09p10360' => 'bna', 'A10p24080' => 'bna', 'Aa31LG11G15250' => 'aar', 'Aa31LG1G1800' => 'aar', 'Aa31LG2G5120' => 'aar', 'Aa31LG2G6070' => 'aar', 'Aa31LG5G10770' => 'aar', 'Aa31sc61G90' => 'aar', 'Actinidia01352' => 'ach', 'Actinidia05983' => 'ach', 'Actinidia08133' => 'ach', 'Actinidia15101' => 'ach', 'Actinidia26379' => 'ach', 'Actinidia35778' => 'ach', 'Actinidia36123' => 'ach', 'Actinidia37436' => 'ach', 'Actinidia38730' => 'ach', 'Ah.02g128210' => 'amhyb', 'Ah.03g132990' => 'amhyb', 'Ah.14g079410' => 'amhyb', 'AL1G24640' => 'aly', 'AL2G26680' => 'aly', 'AL3G10530' => 'aly', 'AL3G45230' => 'aly', 'AL5G15230' => 'aly', 'AL5G16960' => 'aly', 'AL6G25210' => 'aly', 'Aqoxy2G00441' => 'aox', 'Aqoxy3G01236' => 'aox', 'Aqoxy5G03746' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3RQ047' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C7GMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9C8JER' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MBL6KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YXCZ83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZANX40' => 'arhy', 'AT1G12990' => 'ath', 'AT1G67880' => 'ath', 'AT2G13290' => 'ath', 'AT3G01620' => 'ath', 'AT3G26445' => 'ath', 'AT3G27540' => 'ath', 'AT5G14480' => 'ath', 'ATR0824G026' => 'atr', 'ATR1098G019' => 'atr', 'Atru.chr11.2145' => 'acertr', 'Atru.chr2.3636' => 'acertr', 'Atru.chr2.3644' => 'acertr', 'Atru.chr6.2422' => 'acertr', 'Atru.chr7.1112' => 'acertr', 'AUR62005469' => 'cqu', 'AUR62011166' => 'cqu', 'AUR62013319' => 'cqu', 'AUR62024273' => 'cqu', 'AUR62028420' => 'cqu', 'AUR62041942' => 'cqu', 'BcaB01g04969' => 'bca', 'BcaB01g06371' => 'bca', 'BcaB02g11494' => 'bca', 'BcaB03g15382' => 'bca', 'BcaB08g36994' => 'bca', 'BcaC03g13477' => 'bca', 'BcaC03g13478' => 'bca', 'BcaC03g13480' => 'bca', 'BcaC03g13481' => 'bca', 'BcaC03g13486' => 'bca', 'BcaC04g19031' => 'bca', 'BcaC04g23085' => 'bca', 'BcaC05g25094' => 'bca', 'BcaC05g25096' => 'bca', 'BcaC05g25138' => 'bca', 'BcaC05g30416' => 'bca', 'BcaC05g30455' => 'bca', 'BcaC06g30979' => 'bca', 'BcaC06g33805' => 'bca', 'BcaC08g46021' => 'bca', 'BcaNung03154' => 'bca', 'BolC2t06623H' => 'bol', 'BolC2t06632H' => 'bol', 'BolC2t06635H' => 'bol', 'BolC2t06638H' => 'bol', 'BolC3t13266H' => 'bol', 'BolC5t29776H' => 'bol', 'BolC6t38912H' => 'bol', 'BolC7t44183H' => 'bol', 'BolC9t54123H' => 'bol', 'BolC9t59107H' => 'bol', 'BraA02t05221Z' => 'bra', 'BraA03t09996Z' => 'bra', 'BraA05t23210Z' => 'bra', 'BraA06t24068Z' => 'bra', 'BraA06t27032Z' => 'bra', 'BraA08t35176Z' => 'bra', 'BraA09t36680Z' => 'bra', 'BraA10t44471Z' => 'bra', 'C02p06760' => 'bna', 'C02p06890' => 'bna', 'C02p07010' => 'bna', 'C03p07660' => 'bna', 'C05p10300' => 'bna', 'C06p38150' => 'bna', 'C07p36650' => 'bna', 'C08p15770' => 'bna', 'C09p12300' => 'bna', 'C09p62700' => 'bna', 'C09p75040' => 'bna', 'CAN.G13.1' => 'can', 'CAN.G138.4' => 'can', 'CAN.G44.6' => 'can', 'CAN.G473.19' => 'can', 'CANSAT01G0835' => 'cansat', 'CANSAT11G0246' => 'cansat', 'CANSAT11G1766' => 'cansat', 'CANSAT64G1954' => 'cansat', 'CARHR013330' => 'chi', 'CARHR060530' => 'chi', 'CARHR075300' => 'chi', 'CARHR105120' => 'chi', 'CARHR148910' => 'chi', 'CARHR198830' => 'chi', 'Carub.0001s1275' => 'cru', 'Carub.0002s1437' => 'cru', 'Carub.0003s0044' => 'cru', 'Carub.0003s2787' => 'cru', 'Carub.0005s0597' => 'cru', 'Carub.0006s1266' => 'cru', 'Ca_06935_v3' => 'car', 'Ca_13559_v3' => 'car', 'Ca_16941_v3' => 'car', 'Ca_16960_v3' => 'car', 'Ca_17775_v3' => 'car', 'Ca_30464_v3' => 'car', 'Cc06_g08160' => 'ccan', 'Cc07_g01520' => 'ccan', 'Cc11_g15810' => 'ccan', 'CDE02G2840' => 'cde', 'CDE03G0093' => 'cde', 'CDE04G2127' => 'cde', 'CDE07G1857' => 'cde', 'CDE09G1246' => 'cde', 'Cfa003412' => 'cfa', 'Cfa007341' => 'cfa', 'Cfa009220' => 'cfa', 'Ciclev10008737m.g' => 'ccl', 'Ciclev10015565m.g' => 'ccl', 'Ciclev10031761m.g' => 'ccl', 'CiPaw.03G045300' => 'cil', 'CiPaw.03G247200' => 'cil', 'CiPaw.04G029500' => 'cil', 'CiPaw.04G174000' => 'cil', 'CiPaw.05G181200' => 'cil', 'CiPaw.06G067100' => 'cil', 'ClCG05G025800' => 'cla', 'ClCG06G011400' => 'cla', 'ClCG09G019360' => 'cla', 'COL.COLO4_04827' => 'col', 'COL.COLO4_29170' => 'col', 'COL.COLO4_35131' => 'col', 'COL.COLO4_35132' => 'col', 'Cpa.g.sc33.32' => 'cpa', 'Cpa.g.sc46.29' => 'cpa', 'Cpa.g.sc796.1' => 'cpa', 'CsaV3_1G030420' => 'csa', 'CsaV3_5G027050' => 'csa', 'CsaV3_5G031040' => 'csa', 'CsaV3_UNG023130' => 'csa', 'CSS0007726' => 'camsi', 'CSS0016433' => 'camsi', 'CSS0017656' => 'camsi', 'CSS0025364' => 'camsi', 'CSS0027582' => 'camsi', 'CSS0047288' => 'camsi', 'CSS0049950' => 'camsi', 'DCAR_003843' => 'dca', 'DCAR_007052' => 'dca', 'DCAR_020884' => 'dca', 'DCAR_021730' => 'dca', 'DCAR_024423' => 'dca', 'DCAR_026509' => 'dca', 'DCAR_031158' => 'dca', 'Dinv14728' => 'din', 'Dinv15219' => 'din', 'Dinv25728' => 'din', 'Dinv33428' => 'din', 'Dinv36489' => 'din', 'Dinv41486' => 'din', 'Duzib147G0469' => 'dzi', 'Duzib168G0060' => 'dzi', 'Duzib187G1215' => 'dzi', 'Duzib248G0692' => 'dzi', 'Duzib251G0767' => 'dzi', 'Duzib264G0446' => 'dzi', 'Duzib268G0691' => 'dzi', 'ECA232G4767' => 'eca', 'ECA233G2838' => 'eca', 'ECA234G0391' => 'eca', 'ECA234G0857' => 'eca', 'ECA236G1593' => 'eca', 'ECA238G0565' => 'eca', 'ECA246G1027' => 'eca', 'ECA246G3223' => 'eca', 'ECA246G3470' => 'eca', 'EL10Ac6g13829' => 'bvu', 'EL10Ac6g14093' => 'bvu', 'EL10Ac8g18707' => 'bvu', 'Eucgr.C01369' => 'egr', 'Eucgr.H02492' => 'egr', 'Eucgr.I01733' => 'egr', 'Eucgr.J02255' => 'egr', 'Eucgr.J02257' => 'egr', 'Eucgr.J02258' => 'egr', 'FAN02G1601' => 'fan', 'FAN03G1586' => 'fan', 'FAN03G2986' => 'fan', 'FAN05G4837' => 'fan', 'FAN06G0146' => 'fan', 'FAN07G0858' => 'fan', 'FAN09G3179' => 'fan', 'FAN10G0669' => 'fan', 'FAN12G2358' => 'fan', 'FAN14G4198' => 'fan', 'FAN14G5112' => 'fan', 'FAN17G0342' => 'fan', 'FAN19G0342' => 'fan', 'FAN19G0962' => 'fan', 'FAN19G1101' => 'fan', 'FAN19G1872' => 'fan', 'FAN22G0356' => 'fan', 'FAN23G0744' => 'fan', 'FAN23G1914' => 'fan', 'FAN26G0032' => 'fan', 'FAN28G0625' => 'fan', 'FvH4_1g02710' => 'fve', 'FvH4_1g02720' => 'fve', 'FvH4_4g25670' => 'fve', 'FvH4_6g51700' => 'fve', 'FvH4_7g20170' => 'fve', 'Glyma.05G175000' => 'gma', 'Glyma.08G132300' => 'gma', 'Glyma.11G243000' => 'gma', 'Glyma.13G158900' => 'gma', 'Glyma.17G112400' => 'gma', 'Glyma.18G014100' => 'gma', 'Glyma.19G003100' => 'gma', 'Glyma.19G056500' => 'gma', 'Gohir.A01G158900' => 'ghi', 'Gohir.A05G312600' => 'ghi', 'Gohir.A05G354900' => 'ghi', 'Gohir.A07G037200' => 'ghi', 'Gohir.A09G030000' => 'ghi', 'Gohir.A12G145200' => 'ghi', 'Gohir.D01G151500' => 'ghi', 'Gohir.D04G058300' => 'ghi', 'Gohir.D05G314100' => 'ghi', 'Gohir.D07G041400' => 'ghi', 'Gohir.D09G029700' => 'ghi', 'Gohir.D12G149700' => 'ghi', 'Gorai.001G043800' => 'gra', 'Gorai.002G187800' => 'gra', 'Gorai.006G034700' => 'gra', 'Gorai.008G161200' => 'gra', 'Gorai.009G335700' => 'gra', 'Gorai.012G065000' => 'gra', 'GSVIVG01000535001' => 'vvi', 'GSVIVG01015572001' => 'vvi', 'GSVIVG01032386001' => 'vvi', 'HanXRQChr05g0138531' => 'han', 'HanXRQChr06g0174391' => 'han', 'HanXRQChr07g0199021' => 'han', 'HanXRQChr08g0208211' => 'han', 'HanXRQChr09g0255471' => 'han', 'HanXRQChr10g0315791' => 'han', 'HanXRQChr12g0371991' => 'han', 'HanXRQChr15g0475251' => 'han', 'HanXRQChr17g0540001' => 'han', 'HanXRQChr17g0548631' => 'han', 'HanXRQChr17g0569561' => 'han', 'Haze_12256' => 'cav', 'Haze_14756' => 'cav', 'Haze_25528' => 'cav', 'Hma1.2p1_0079F.1_g041020' => 'hma', 'Hma1.2p1_0818F.1_g223260' => 'hma', 'Hma1.2p1_1747F.1_g300530' => 'hma', 'HPP92_004607' => 'vpl', 'HPP92_004608' => 'vpl', 'HPP92_006181' => 'vpl', 'HPP92_012192' => 'vpl', 'HPP92_015680' => 'vpl', 'HPP92_020249' => 'vpl', 'HPP92_021376' => 'vpl', 'HPP92_024275' => 'vpl', 'Hund06031' => 'sun', 'Hund25391' => 'sun', 'Lalb_Chr07g0185371' => 'lal', 'Lalb_Chr07g0185381' => 'lal', 'Lalb_Chr12g0204011' => 'lal', 'Lalb_Chr13g0301671' => 'lal', 'Lalb_Chr14g0362851' => 'lal', 'Lalb_Chr24g0403581' => 'lal', 'Lj1g0000233' => 'lja', 'Lj2g0018120' => 'lja', 'Lj3C621T0' => 'lonja', 'Lj3P1059T14' => 'lonja', 'Lj3P611T9' => 'lonja', 'Lj3P614T13' => 'lonja', 'Lj3P615T5' => 'lonja', 'Lj4g0012315' => 'lja', 'Lj4g0026182' => 'lja', 'Lj6P813T16' => 'lonja', 'Lj7C427T7' => 'lonja', 'Lj7C427T8' => 'lonja', 'Lj7P600T41' => 'lonja', 'Lju41C42G17' => 'lonja', 'Lsat_1_v5_gn_0_47300' => 'lsa', 'Lsat_1_v5_gn_2_91280' => 'lsa', 'Lsat_1_v5_gn_3_30561' => 'lsa', 'Lsat_1_v5_gn_4_184321' => 'lsa', 'Lsat_1_v5_gn_4_4041' => 'lsa', 'Lsat_1_v5_gn_5_92000' => 'lsa', 'Lsat_1_v5_gn_8_152940' => 'lsa', 'Lsat_1_v5_gn_8_62401' => 'lsa', 'Manes.06G055900' => 'mes', 'Manes.12G022200' => 'mes', 'Manes.13G023300' => 'mes', 'Manes.14G115000' => 'mes', 'Manes.15G151700' => 'mes', 'Manes.17G111300' => 'mes', 'Mapoly0226s0009' => 'mpo', 'MBI02_g25363_MAGBIO' => 'mbi', 'MBI06_g00027_MAGBIO' => 'mbi', 'MBI10_g13034_MAGBIO' => 'mbi', 'MD09G1023400' => 'mdo', 'MD13G1100100' => 'mdo', 'MD15G1169200' => 'mdo', 'MD16G1101100' => 'mdo', 'MD17G1022900' => 'mdo', 'Medtr3g096150' => 'mtr', 'Medtr4g115070' => 'mtr', 'Medtr7g033325' => 'mtr', 'Medtr8g089840' => 'mtr', 'MELO3C010319.2' => 'cme', 'MELO3C011944.2' => 'cme', 'MELO3C021589.2' => 'cme', 'Migut.E00207' => 'egut', 'Migut.H00067' => 'egut', 'Migut.K00433' => 'egut', 'Migut.K00606' => 'egut', 'Migut.K01410' => 'egut', 'MSTRG.13347' => 'ama', 'MSTRG.24045' => 'ama', 'MSTRG.2428' => 'ama', 'MSTRG.26410' => 'ama', 'MSTRG.3139' => 'ama', 'MSTRG.3286' => 'ama', 'MSTRG.563' => 'ama', 'MSTRG.7941' => 'ama', 'Nitab4.5_0000028g0060' => 'nta', 'Nitab4.5_0000065g0260' => 'nta', 'Nitab4.5_0000112g0060' => 'nta', 'Nitab4.5_0000489g0120' => 'nta', 'Nitab4.5_0001776g0050' => 'nta', 'Nitab4.5_0001854g0010' => 'nta', 'Nitab4.5_0001860g0020' => 'nta', 'Nitab4.5_0004352g0010' => 'nta', 'Nitab4.5_0008716g0020' => 'nta', 'Nitab4.5_0008922g0010' => 'nta', 'Nn3g16693' => 'nnu', 'Nn4g22596' => 'nnu', 'Nn7g37639' => 'nnu', 'Oeu001701.1' => 'oeu', 'Oeu018149.1' => 'oeu', 'Oeu026220.1' => 'oeu', 'Oeu038635.1' => 'oeu', 'Oeu049176.1' => 'oeu', 'Oeu056706.1' => 'oeu', 'Oeu056937.1' => 'oeu', 'Oeu057540.1' => 'oeu', 'Os02g0594900' => 'osa', 'Os02g0595100' => 'osa', 'Os04g0477500' => 'osa', 'Os12g0611900' => 'osa', 'Peaxi162Scf00076g00020' => 'pax', 'Peaxi162Scf00128g00217' => 'pax', 'Peaxi162Scf00129g01640' => 'pax', 'Peaxi162Scf00669g00007' => 'pax', 'Peaxi162Scf00700g00421' => 'pax', 'Peaxi162Scf00801g00038' => 'pax', 'Peaxi162Scf00891g00025' => 'pax', 'PGR083G0909' => 'pgr', 'PGR119G1005' => 'pgr', 'PGR142G2236' => 'pgr', 'PGR142G3388' => 'pgr', 'PGSC0003DMG400004514' => 'stu', 'PGSC0003DMG400012635' => 'stu', 'PGSC0003DMG400015730' => 'stu', 'PGSC0003DMG400018611' => 'stu', 'PGSC0003DMG400030897' => 'stu', 'Phvul.001G254800' => 'pvu', 'Phvul.002G260100' => 'pvu', 'Phvul.003G167600' => 'pvu', 'Phvul.004G005100' => 'pvu', 'Potri.001G343600' => 'ptr', 'Potri.006G066700' => 'ptr', 'Potri.008G186000' => 'ptr', 'Potri.010G046900' => 'ptr', 'Potri.018G127900' => 'ptr', 'Pp3c20_17750' => 'ppa', 'Pp3c24_4380' => 'ppa', 'Prupe.1G245800' => 'ppe', 'Prupe.3G293400' => 'ppe', 'Prupe.7G247400' => 'ppe', 'Psat0s145g0120' => 'psa', 'Psat0s595g0040' => 'psa', 'Psat0s595g0120' => 'psa', 'Psat3g175040' => 'psa', 'Psat7g058120' => 'psa', 'PSO017G0428' => 'pso', 'PSO063G7510' => 'pso', 'PSO067G0046' => 'pso', 'PSO478G1073' => 'pso', 'PSO675G3677' => 'pso', 'PSO675G6558' => 'pso', 'PSO675G7520' => 'pso', 'PSO675G8959' => 'pso', 'QL02p074089' => 'qlo', 'QL02p089614' => 'qlo', 'QL03p057736' => 'qlo', 'RcHm_v2.0_Chr1g0364131' => 'rch', 'RcHm_v2.0_Chr2g0087801' => 'rch', 'RcHm_v2.0_Chr2g0087821' => 'rch', 'RcHm_v2.0_Chr2g0173231' => 'rch', 'RcHm_v2.0_Chr4g0433111' => 'rch', 'Rhsim03G0250300' => 'rsi', 'Rhsim08G0048400' => 'rsi', 'Rhsim10G0014800' => 'rsi', 'Rhsim12G0040100' => 'rsi', 'Rhsim12G0109700' => 'rsi', 'Sabra06G0049600' => 'sbr', 'Sabra08G0141000' => 'sbr', 'Sabra10G0021400' => 'sbr', 'Sabra16G0222900' => 'sbr', 'Sabra18G0108600' => 'sbr', 'SalBow1G0433' => 'sbo', 'SalBow1G2038' => 'sbo', 'SalBow1G5003' => 'sbo', 'SalBow7G1197' => 'sbo', 'SalBow8G3506' => 'sbo', 'Sc03g0007300' => 'sci', 'Sc11g0000950' => 'sci', 'Sc14g0008750' => 'sci', 'Sc18g0000420' => 'sci', 'Sed0006754' => 'sed', 'Sed0008741' => 'sed', 'Sed0017172' => 'sed', 'Sed0018925' => 'sed', 'Sed0023326' => 'sed', 'Sed0025909' => 'sed', 'SEGI_05333' => 'sgi', 'SEGI_10362' => 'sgi', 'SEGI_13380' => 'sgi', 'SEGI_24306' => 'sgi', 'SEGI_29077' => 'sgi', 'SEGI_29095' => 'sgi', 'SEGI_36534' => 'sgi', 'SEGI_37506' => 'sgi', 'SEGI_38321' => 'sgi', 'SGA_v2.0_scaffold307G48031' => 'sas', 'SGA_v2.0_scaffold47G17507' => 'sas', 'SGA_v2.0_scaffold63G21736' => 'sas', 'SGA_v2.0_scaffold87G27070' => 'sas', 'SHI17794' => 'shi', 'SHI28851' => 'shi', 'SMO165G0155' => 'smo', 'SMO340G0217' => 'smo', 'SMO367G1210' => 'smo', 'Solyc02g093430.3' => 'sly', 'Solyc05g013580.4' => 'sly', 'Solyc07g008030.3' => 'sly', 'Solyc12g035470.2' => 'sly', 'Sopen02g038020' => 'spe', 'Sopen05g008490' => 'spe', 'Sopen07g003910' => 'spe', 'Sopen12g015240' => 'spe', 'Sp1g11550' => 'spa', 'Sp2g16710' => 'spa', 'Sp3g00430' => 'spa', 'Sp3g26780' => 'spa', 'Sp5g22900' => 'spa', 'Sp6g29530' => 'spa', 'TAR371G0794' => 'tar', 'TAR374G0164' => 'tar', 'TAR622G0165' => 'tar', 'TAR626G0929' => 'tar', 'TAR629G2155' => 'tar', 'THA.LOC104805282' => 'tha', 'THA.LOC104805363' => 'tha', 'THA.LOC104808968' => 'tha', 'THA.LOC104821093' => 'tha', 'THA.LOC104823953' => 'tha', 'THA.LOC104825562' => 'tha', 'THA.LOC104825665' => 'tha', 'Thecc.02G261400' => 'tca', 'Thecc.04G019200' => 'tca', 'Thecc.09G130400' => 'tca', 'Thhalv10004374m.g' => 'esa', 'Thhalv10007850m.g' => 'esa', 'Thhalv10013782m.g' => 'esa', 'Thhalv10018686m.g' => 'esa', 'Thhalv10020899m.g' => 'esa', 'Thhalv10022755m.g' => 'esa', 'TPR.G23851' => 'tpr', 'TPR.G26500' => 'tpr', 'TPR.G27267' => 'tpr', 'TPR.G32001' => 'tpr', 'TPR.G6251' => 'tpr', 'TPR.G8167' => 'tpr', 'TWI12G1330' => 'twi', 'TWI18G1239' => 'twi', 'TWI34G0979' => 'twi', 'TWI36G0670' => 'twi', 'TWI36G0707' => 'twi', 'TWI56G0233' => 'twi', 'TWI75G1809' => 'twi', 'unitig_21.g20874' => 'ugi', 'unitig_26.g10343' => 'ugi', 'unitig_46.g18392' => 'ugi', 'unitig_52.g17178' => 'ugi', 'unitig_8.g2934' => 'ugi', 'vmacro01122' => 'vma', 'vmacro05875' => 'vma', 'vmacro06147' => 'vma', 'vmacro16191' => 'vma', 'vmacro18293' => 'vma', 'VMungo0251G3707' => 'vmu', 'VMungo0464G1521' => 'vmu', 'VMungo1215G0205' => 'vmu', 'VMungo1383G2484' => 'vmu', 'Zm00001eb079610' => 'zma', 'Zm00001eb135990' => 'zma', 'Zm00001eb183710' => 'zma', 'Zm00001eb246020' => 'zma' ) $gf_id = 'HOM05D001124' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001124' ) $data_identifier = 'HOM05D001124' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 6, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 7, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 21, 'bol' => (int) 10, 'bra' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 6, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 9, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 21, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 8, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 10, 'lsa' => (int) 8, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 8, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 9, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb246020' $species_info = array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ) $local_species = 'ppa' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001124', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '548', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02520' => 'bna', 'A03p06630' => 'bna', 'A05p44460' => 'bna', 'A06p08710' => 'bna', 'A06p41090' => 'bna', 'A07p32320' => 'bna', 'A08p32520' => 'bna', 'A09p10360' => 'bna', 'A10p24080' => 'bna', 'Aa31LG11G15250' => 'aar', 'Aa31LG1G1800' => 'aar', 'Aa31LG2G5120' => 'aar', 'Aa31LG2G6070' => 'aar', 'Aa31LG5G10770' => 'aar', 'Aa31sc61G90' => 'aar', 'Actinidia01352' => 'ach', 'Actinidia05983' => 'ach', 'Actinidia08133' => 'ach', 'Actinidia15101' => 'ach', 'Actinidia26379' => 'ach', 'Actinidia35778' => 'ach', 'Actinidia36123' => 'ach', 'Actinidia37436' => 'ach', 'Actinidia38730' => 'ach', 'Ah.02g128210' => 'amhyb', 'Ah.03g132990' => 'amhyb', 'Ah.14g079410' => 'amhyb', 'AL1G24640' => 'aly', 'AL2G26680' => 'aly', 'AL3G10530' => 'aly', 'AL3G45230' => 'aly', 'AL5G15230' => 'aly', 'AL5G16960' => 'aly', 'AL6G25210' => 'aly', 'Aqoxy2G00441' => 'aox', 'Aqoxy3G01236' => 'aox', 'Aqoxy5G03746' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3RQ047' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C7GMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9C8JER' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MBL6KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YXCZ83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZANX40' => 'arhy', 'AT1G12990' => 'ath', 'AT1G67880' => 'ath', 'AT2G13290' => 'ath', 'AT3G01620' => 'ath', 'AT3G26445' => 'ath', 'AT3G27540' => 'ath', 'AT5G14480' => 'ath', 'ATR0824G026' => 'atr', 'ATR1098G019' => 'atr', 'Atru.chr11.2145' => 'acertr', 'Atru.chr2.3636' => 'acertr', 'Atru.chr2.3644' => 'acertr', 'Atru.chr6.2422' => 'acertr', 'Atru.chr7.1112' => 'acertr', 'AUR62005469' => 'cqu', 'AUR62011166' => 'cqu', 'AUR62013319' => 'cqu', 'AUR62024273' => 'cqu', 'AUR62028420' => 'cqu', 'AUR62041942' => 'cqu', 'BcaB01g04969' => 'bca', 'BcaB01g06371' => 'bca', 'BcaB02g11494' => 'bca', 'BcaB03g15382' => 'bca', 'BcaB08g36994' => 'bca', 'BcaC03g13477' => 'bca', 'BcaC03g13478' => 'bca', 'BcaC03g13480' => 'bca', 'BcaC03g13481' => 'bca', 'BcaC03g13486' => 'bca', 'BcaC04g19031' => 'bca', 'BcaC04g23085' => 'bca', 'BcaC05g25094' => 'bca', 'BcaC05g25096' => 'bca', 'BcaC05g25138' => 'bca', 'BcaC05g30416' => 'bca', 'BcaC05g30455' => 'bca', 'BcaC06g30979' => 'bca', 'BcaC06g33805' => 'bca', 'BcaC08g46021' => 'bca', 'BcaNung03154' => 'bca', 'BolC2t06623H' => 'bol', 'BolC2t06632H' => 'bol', 'BolC2t06635H' => 'bol', 'BolC2t06638H' => 'bol', 'BolC3t13266H' => 'bol', 'BolC5t29776H' => 'bol', 'BolC6t38912H' => 'bol', 'BolC7t44183H' => 'bol', 'BolC9t54123H' => 'bol', 'BolC9t59107H' => 'bol', 'BraA02t05221Z' => 'bra', 'BraA03t09996Z' => 'bra', 'BraA05t23210Z' => 'bra', 'BraA06t24068Z' => 'bra', 'BraA06t27032Z' => 'bra', 'BraA08t35176Z' => 'bra', 'BraA09t36680Z' => 'bra', 'BraA10t44471Z' => 'bra', 'C02p06760' => 'bna', 'C02p06890' => 'bna', 'C02p07010' => 'bna', 'C03p07660' => 'bna', 'C05p10300' => 'bna', 'C06p38150' => 'bna', 'C07p36650' => 'bna', 'C08p15770' => 'bna', 'C09p12300' => 'bna', 'C09p62700' => 'bna', 'C09p75040' => 'bna', 'CAN.G13.1' => 'can', 'CAN.G138.4' => 'can', 'CAN.G44.6' => 'can', 'CAN.G473.19' => 'can', 'CANSAT01G0835' => 'cansat', 'CANSAT11G0246' => 'cansat', 'CANSAT11G1766' => 'cansat', 'CANSAT64G1954' => 'cansat', 'CARHR013330' => 'chi', 'CARHR060530' => 'chi', 'CARHR075300' => 'chi', 'CARHR105120' => 'chi', 'CARHR148910' => 'chi', 'CARHR198830' => 'chi', 'Carub.0001s1275' => 'cru', 'Carub.0002s1437' => 'cru', 'Carub.0003s0044' => 'cru', 'Carub.0003s2787' => 'cru', 'Carub.0005s0597' => 'cru', 'Carub.0006s1266' => 'cru', 'Ca_06935_v3' => 'car', 'Ca_13559_v3' => 'car', 'Ca_16941_v3' => 'car', 'Ca_16960_v3' => 'car', 'Ca_17775_v3' => 'car', 'Ca_30464_v3' => 'car', 'Cc06_g08160' => 'ccan', 'Cc07_g01520' => 'ccan', 'Cc11_g15810' => 'ccan', 'CDE02G2840' => 'cde', 'CDE03G0093' => 'cde', 'CDE04G2127' => 'cde', 'CDE07G1857' => 'cde', 'CDE09G1246' => 'cde', 'Cfa003412' => 'cfa', 'Cfa007341' => 'cfa', 'Cfa009220' => 'cfa', 'Ciclev10008737m.g' => 'ccl', 'Ciclev10015565m.g' => 'ccl', 'Ciclev10031761m.g' => 'ccl', 'CiPaw.03G045300' => 'cil', 'CiPaw.03G247200' => 'cil', 'CiPaw.04G029500' => 'cil', 'CiPaw.04G174000' => 'cil', 'CiPaw.05G181200' => 'cil', 'CiPaw.06G067100' => 'cil', 'ClCG05G025800' => 'cla', 'ClCG06G011400' => 'cla', 'ClCG09G019360' => 'cla', 'COL.COLO4_04827' => 'col', 'COL.COLO4_29170' => 'col', 'COL.COLO4_35131' => 'col', 'COL.COLO4_35132' => 'col', 'Cpa.g.sc33.32' => 'cpa', 'Cpa.g.sc46.29' => 'cpa', 'Cpa.g.sc796.1' => 'cpa', 'CsaV3_1G030420' => 'csa', 'CsaV3_5G027050' => 'csa', 'CsaV3_5G031040' => 'csa', 'CsaV3_UNG023130' => 'csa', 'CSS0007726' => 'camsi', 'CSS0016433' => 'camsi', 'CSS0017656' => 'camsi', 'CSS0025364' => 'camsi', 'CSS0027582' => 'camsi', 'CSS0047288' => 'camsi', 'CSS0049950' => 'camsi', 'DCAR_003843' => 'dca', 'DCAR_007052' => 'dca', 'DCAR_020884' => 'dca', 'DCAR_021730' => 'dca', 'DCAR_024423' => 'dca', 'DCAR_026509' => 'dca', 'DCAR_031158' => 'dca', 'Dinv14728' => 'din', 'Dinv15219' => 'din', 'Dinv25728' => 'din', 'Dinv33428' => 'din', 'Dinv36489' => 'din', 'Dinv41486' => 'din', 'Duzib147G0469' => 'dzi', 'Duzib168G0060' => 'dzi', 'Duzib187G1215' => 'dzi', 'Duzib248G0692' => 'dzi', 'Duzib251G0767' => 'dzi', 'Duzib264G0446' => 'dzi', 'Duzib268G0691' => 'dzi', 'ECA232G4767' => 'eca', 'ECA233G2838' => 'eca', 'ECA234G0391' => 'eca', 'ECA234G0857' => 'eca', 'ECA236G1593' => 'eca', 'ECA238G0565' => 'eca', 'ECA246G1027' => 'eca', 'ECA246G3223' => 'eca', 'ECA246G3470' => 'eca', 'EL10Ac6g13829' => 'bvu', 'EL10Ac6g14093' => 'bvu', 'EL10Ac8g18707' => 'bvu', 'Eucgr.C01369' => 'egr', 'Eucgr.H02492' => 'egr', 'Eucgr.I01733' => 'egr', 'Eucgr.J02255' => 'egr', 'Eucgr.J02257' => 'egr', 'Eucgr.J02258' => 'egr', 'FAN02G1601' => 'fan', 'FAN03G1586' => 'fan', 'FAN03G2986' => 'fan', 'FAN05G4837' => 'fan', 'FAN06G0146' => 'fan', 'FAN07G0858' => 'fan', 'FAN09G3179' => 'fan', 'FAN10G0669' => 'fan', 'FAN12G2358' => 'fan', 'FAN14G4198' => 'fan', 'FAN14G5112' => 'fan', 'FAN17G0342' => 'fan', 'FAN19G0342' => 'fan', 'FAN19G0962' => 'fan', 'FAN19G1101' => 'fan', 'FAN19G1872' => 'fan', 'FAN22G0356' => 'fan', 'FAN23G0744' => 'fan', 'FAN23G1914' => 'fan', 'FAN26G0032' => 'fan', 'FAN28G0625' => 'fan', 'FvH4_1g02710' => 'fve', 'FvH4_1g02720' => 'fve', 'FvH4_4g25670' => 'fve', 'FvH4_6g51700' => 'fve', 'FvH4_7g20170' => 'fve', 'Glyma.05G175000' => 'gma', 'Glyma.08G132300' => 'gma', 'Glyma.11G243000' => 'gma', 'Glyma.13G158900' => 'gma', 'Glyma.17G112400' => 'gma', 'Glyma.18G014100' => 'gma', 'Glyma.19G003100' => 'gma', 'Glyma.19G056500' => 'gma', 'Gohir.A01G158900' => 'ghi', 'Gohir.A05G312600' => 'ghi', 'Gohir.A05G354900' => 'ghi', 'Gohir.A07G037200' => 'ghi', 'Gohir.A09G030000' => 'ghi', 'Gohir.A12G145200' => 'ghi', 'Gohir.D01G151500' => 'ghi', 'Gohir.D04G058300' => 'ghi', 'Gohir.D05G314100' => 'ghi', 'Gohir.D07G041400' => 'ghi', 'Gohir.D09G029700' => 'ghi', 'Gohir.D12G149700' => 'ghi', 'Gorai.001G043800' => 'gra', 'Gorai.002G187800' => 'gra', 'Gorai.006G034700' => 'gra', 'Gorai.008G161200' => 'gra', 'Gorai.009G335700' => 'gra', 'Gorai.012G065000' => 'gra', 'GSVIVG01000535001' => 'vvi', 'GSVIVG01015572001' => 'vvi', 'GSVIVG01032386001' => 'vvi', 'HanXRQChr05g0138531' => 'han', 'HanXRQChr06g0174391' => 'han', 'HanXRQChr07g0199021' => 'han', 'HanXRQChr08g0208211' => 'han', 'HanXRQChr09g0255471' => 'han', 'HanXRQChr10g0315791' => 'han', 'HanXRQChr12g0371991' => 'han', 'HanXRQChr15g0475251' => 'han', 'HanXRQChr17g0540001' => 'han', 'HanXRQChr17g0548631' => 'han', 'HanXRQChr17g0569561' => 'han', 'Haze_12256' => 'cav', 'Haze_14756' => 'cav', 'Haze_25528' => 'cav', 'Hma1.2p1_0079F.1_g041020' => 'hma', 'Hma1.2p1_0818F.1_g223260' => 'hma', 'Hma1.2p1_1747F.1_g300530' => 'hma', 'HPP92_004607' => 'vpl', 'HPP92_004608' => 'vpl', 'HPP92_006181' => 'vpl', 'HPP92_012192' => 'vpl', 'HPP92_015680' => 'vpl', 'HPP92_020249' => 'vpl', 'HPP92_021376' => 'vpl', 'HPP92_024275' => 'vpl', 'Hund06031' => 'sun', 'Hund25391' => 'sun', 'Lalb_Chr07g0185371' => 'lal', 'Lalb_Chr07g0185381' => 'lal', 'Lalb_Chr12g0204011' => 'lal', 'Lalb_Chr13g0301671' => 'lal', 'Lalb_Chr14g0362851' => 'lal', 'Lalb_Chr24g0403581' => 'lal', 'Lj1g0000233' => 'lja', 'Lj2g0018120' => 'lja', 'Lj3C621T0' => 'lonja', 'Lj3P1059T14' => 'lonja', 'Lj3P611T9' => 'lonja', 'Lj3P614T13' => 'lonja', 'Lj3P615T5' => 'lonja', 'Lj4g0012315' => 'lja', 'Lj4g0026182' => 'lja', 'Lj6P813T16' => 'lonja', 'Lj7C427T7' => 'lonja', 'Lj7C427T8' => 'lonja', 'Lj7P600T41' => 'lonja', 'Lju41C42G17' => 'lonja', 'Lsat_1_v5_gn_0_47300' => 'lsa', 'Lsat_1_v5_gn_2_91280' => 'lsa', 'Lsat_1_v5_gn_3_30561' => 'lsa', 'Lsat_1_v5_gn_4_184321' => 'lsa', 'Lsat_1_v5_gn_4_4041' => 'lsa', 'Lsat_1_v5_gn_5_92000' => 'lsa', 'Lsat_1_v5_gn_8_152940' => 'lsa', 'Lsat_1_v5_gn_8_62401' => 'lsa', 'Manes.06G055900' => 'mes', 'Manes.12G022200' => 'mes', 'Manes.13G023300' => 'mes', 'Manes.14G115000' => 'mes', 'Manes.15G151700' => 'mes', 'Manes.17G111300' => 'mes', 'Mapoly0226s0009' => 'mpo', 'MBI02_g25363_MAGBIO' => 'mbi', 'MBI06_g00027_MAGBIO' => 'mbi', 'MBI10_g13034_MAGBIO' => 'mbi', 'MD09G1023400' => 'mdo', 'MD13G1100100' => 'mdo', 'MD15G1169200' => 'mdo', 'MD16G1101100' => 'mdo', 'MD17G1022900' => 'mdo', 'Medtr3g096150' => 'mtr', 'Medtr4g115070' => 'mtr', 'Medtr7g033325' => 'mtr', 'Medtr8g089840' => 'mtr', 'MELO3C010319.2' => 'cme', 'MELO3C011944.2' => 'cme', 'MELO3C021589.2' => 'cme', 'Migut.E00207' => 'egut', 'Migut.H00067' => 'egut', 'Migut.K00433' => 'egut', 'Migut.K00606' => 'egut', 'Migut.K01410' => 'egut', 'MSTRG.13347' => 'ama', 'MSTRG.24045' => 'ama', 'MSTRG.2428' => 'ama', 'MSTRG.26410' => 'ama', 'MSTRG.3139' => 'ama', 'MSTRG.3286' => 'ama', 'MSTRG.563' => 'ama', 'MSTRG.7941' => 'ama', 'Nitab4.5_0000028g0060' => 'nta', 'Nitab4.5_0000065g0260' => 'nta', 'Nitab4.5_0000112g0060' => 'nta', 'Nitab4.5_0000489g0120' => 'nta', 'Nitab4.5_0001776g0050' => 'nta', 'Nitab4.5_0001854g0010' => 'nta', 'Nitab4.5_0001860g0020' => 'nta', 'Nitab4.5_0004352g0010' => 'nta', 'Nitab4.5_0008716g0020' => 'nta', 'Nitab4.5_0008922g0010' => 'nta', 'Nn3g16693' => 'nnu', 'Nn4g22596' => 'nnu', 'Nn7g37639' => 'nnu', 'Oeu001701.1' => 'oeu', 'Oeu018149.1' => 'oeu', 'Oeu026220.1' => 'oeu', 'Oeu038635.1' => 'oeu', 'Oeu049176.1' => 'oeu', 'Oeu056706.1' => 'oeu', 'Oeu056937.1' => 'oeu', 'Oeu057540.1' => 'oeu', 'Os02g0594900' => 'osa', 'Os02g0595100' => 'osa', 'Os04g0477500' => 'osa', 'Os12g0611900' => 'osa', 'Peaxi162Scf00076g00020' => 'pax', 'Peaxi162Scf00128g00217' => 'pax', 'Peaxi162Scf00129g01640' => 'pax', 'Peaxi162Scf00669g00007' => 'pax', 'Peaxi162Scf00700g00421' => 'pax', 'Peaxi162Scf00801g00038' => 'pax', 'Peaxi162Scf00891g00025' => 'pax', 'PGR083G0909' => 'pgr', 'PGR119G1005' => 'pgr', 'PGR142G2236' => 'pgr', 'PGR142G3388' => 'pgr', 'PGSC0003DMG400004514' => 'stu', 'PGSC0003DMG400012635' => 'stu', 'PGSC0003DMG400015730' => 'stu', 'PGSC0003DMG400018611' => 'stu', 'PGSC0003DMG400030897' => 'stu', 'Phvul.001G254800' => 'pvu', 'Phvul.002G260100' => 'pvu', 'Phvul.003G167600' => 'pvu', 'Phvul.004G005100' => 'pvu', 'Potri.001G343600' => 'ptr', 'Potri.006G066700' => 'ptr', 'Potri.008G186000' => 'ptr', 'Potri.010G046900' => 'ptr', 'Potri.018G127900' => 'ptr', 'Pp3c20_17750' => 'ppa', 'Pp3c24_4380' => 'ppa', 'Prupe.1G245800' => 'ppe', 'Prupe.3G293400' => 'ppe', 'Prupe.7G247400' => 'ppe', 'Psat0s145g0120' => 'psa', 'Psat0s595g0040' => 'psa', 'Psat0s595g0120' => 'psa', 'Psat3g175040' => 'psa', 'Psat7g058120' => 'psa', 'PSO017G0428' => 'pso', 'PSO063G7510' => 'pso', 'PSO067G0046' => 'pso', 'PSO478G1073' => 'pso', 'PSO675G3677' => 'pso', 'PSO675G6558' => 'pso', 'PSO675G7520' => 'pso', 'PSO675G8959' => 'pso', 'QL02p074089' => 'qlo', 'QL02p089614' => 'qlo', 'QL03p057736' => 'qlo', 'RcHm_v2.0_Chr1g0364131' => 'rch', 'RcHm_v2.0_Chr2g0087801' => 'rch', 'RcHm_v2.0_Chr2g0087821' => 'rch', 'RcHm_v2.0_Chr2g0173231' => 'rch', 'RcHm_v2.0_Chr4g0433111' => 'rch', 'Rhsim03G0250300' => 'rsi', 'Rhsim08G0048400' => 'rsi', 'Rhsim10G0014800' => 'rsi', 'Rhsim12G0040100' => 'rsi', 'Rhsim12G0109700' => 'rsi', 'Sabra06G0049600' => 'sbr', 'Sabra08G0141000' => 'sbr', 'Sabra10G0021400' => 'sbr', 'Sabra16G0222900' => 'sbr', 'Sabra18G0108600' => 'sbr', 'SalBow1G0433' => 'sbo', 'SalBow1G2038' => 'sbo', 'SalBow1G5003' => 'sbo', 'SalBow7G1197' => 'sbo', 'SalBow8G3506' => 'sbo', 'Sc03g0007300' => 'sci', 'Sc11g0000950' => 'sci', 'Sc14g0008750' => 'sci', 'Sc18g0000420' => 'sci', 'Sed0006754' => 'sed', 'Sed0008741' => 'sed', 'Sed0017172' => 'sed', 'Sed0018925' => 'sed', 'Sed0023326' => 'sed', 'Sed0025909' => 'sed', 'SEGI_05333' => 'sgi', 'SEGI_10362' => 'sgi', 'SEGI_13380' => 'sgi', 'SEGI_24306' => 'sgi', 'SEGI_29077' => 'sgi', 'SEGI_29095' => 'sgi', 'SEGI_36534' => 'sgi', 'SEGI_37506' => 'sgi', 'SEGI_38321' => 'sgi', 'SGA_v2.0_scaffold307G48031' => 'sas', 'SGA_v2.0_scaffold47G17507' => 'sas', 'SGA_v2.0_scaffold63G21736' => 'sas', 'SGA_v2.0_scaffold87G27070' => 'sas', 'SHI17794' => 'shi', 'SHI28851' => 'shi', 'SMO165G0155' => 'smo', 'SMO340G0217' => 'smo', 'SMO367G1210' => 'smo', 'Solyc02g093430.3' => 'sly', 'Solyc05g013580.4' => 'sly', 'Solyc07g008030.3' => 'sly', 'Solyc12g035470.2' => 'sly', 'Sopen02g038020' => 'spe', 'Sopen05g008490' => 'spe', 'Sopen07g003910' => 'spe', 'Sopen12g015240' => 'spe', 'Sp1g11550' => 'spa', 'Sp2g16710' => 'spa', 'Sp3g00430' => 'spa', 'Sp3g26780' => 'spa', 'Sp5g22900' => 'spa', 'Sp6g29530' => 'spa', 'TAR371G0794' => 'tar', 'TAR374G0164' => 'tar', 'TAR622G0165' => 'tar', 'TAR626G0929' => 'tar', 'TAR629G2155' => 'tar', 'THA.LOC104805282' => 'tha', 'THA.LOC104805363' => 'tha', 'THA.LOC104808968' => 'tha', 'THA.LOC104821093' => 'tha', 'THA.LOC104823953' => 'tha', 'THA.LOC104825562' => 'tha', 'THA.LOC104825665' => 'tha', 'Thecc.02G261400' => 'tca', 'Thecc.04G019200' => 'tca', 'Thecc.09G130400' => 'tca', 'Thhalv10004374m.g' => 'esa', 'Thhalv10007850m.g' => 'esa', 'Thhalv10013782m.g' => 'esa', 'Thhalv10018686m.g' => 'esa', 'Thhalv10020899m.g' => 'esa', 'Thhalv10022755m.g' => 'esa', 'TPR.G23851' => 'tpr', 'TPR.G26500' => 'tpr', 'TPR.G27267' => 'tpr', 'TPR.G32001' => 'tpr', 'TPR.G6251' => 'tpr', 'TPR.G8167' => 'tpr', 'TWI12G1330' => 'twi', 'TWI18G1239' => 'twi', 'TWI34G0979' => 'twi', 'TWI36G0670' => 'twi', 'TWI36G0707' => 'twi', 'TWI56G0233' => 'twi', 'TWI75G1809' => 'twi', 'unitig_21.g20874' => 'ugi', 'unitig_26.g10343' => 'ugi', 'unitig_46.g18392' => 'ugi', 'unitig_52.g17178' => 'ugi', 'unitig_8.g2934' => 'ugi', 'vmacro01122' => 'vma', 'vmacro05875' => 'vma', 'vmacro06147' => 'vma', 'vmacro16191' => 'vma', 'vmacro18293' => 'vma', 'VMungo0251G3707' => 'vmu', 'VMungo0464G1521' => 'vmu', 'VMungo1215G0205' => 'vmu', 'VMungo1383G2484' => 'vmu', 'Zm00001eb079610' => 'zma', 'Zm00001eb135990' => 'zma', 'Zm00001eb183710' => 'zma', 'Zm00001eb246020' => 'zma' ), 'gf_id' => 'HOM05D001124', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001124' ), 'data_identifier' => 'HOM05D001124', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001124', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '548', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02520' => 'bna', 'A03p06630' => 'bna', 'A05p44460' => 'bna', 'A06p08710' => 'bna', 'A06p41090' => 'bna', 'A07p32320' => 'bna', 'A08p32520' => 'bna', 'A09p10360' => 'bna', 'A10p24080' => 'bna', 'Aa31LG11G15250' => 'aar', 'Aa31LG1G1800' => 'aar', 'Aa31LG2G5120' => 'aar', 'Aa31LG2G6070' => 'aar', 'Aa31LG5G10770' => 'aar', 'Aa31sc61G90' => 'aar', 'Actinidia01352' => 'ach', 'Actinidia05983' => 'ach', 'Actinidia08133' => 'ach', 'Actinidia15101' => 'ach', 'Actinidia26379' => 'ach', 'Actinidia35778' => 'ach', 'Actinidia36123' => 'ach', 'Actinidia37436' => 'ach', 'Actinidia38730' => 'ach', 'Ah.02g128210' => 'amhyb', 'Ah.03g132990' => 'amhyb', 'Ah.14g079410' => 'amhyb', 'AL1G24640' => 'aly', 'AL2G26680' => 'aly', 'AL3G10530' => 'aly', 'AL3G45230' => 'aly', 'AL5G15230' => 'aly', 'AL5G16960' => 'aly', 'AL6G25210' => 'aly', 'Aqoxy2G00441' => 'aox', 'Aqoxy3G01236' => 'aox', 'Aqoxy5G03746' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3RQ047' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C7GMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9C8JER' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MBL6KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YXCZ83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZANX40' => 'arhy', 'AT1G12990' => 'ath', 'AT1G67880' => 'ath', 'AT2G13290' => 'ath', 'AT3G01620' => 'ath', 'AT3G26445' => 'ath', 'AT3G27540' => 'ath', 'AT5G14480' => 'ath', 'ATR0824G026' => 'atr', 'ATR1098G019' => 'atr', 'Atru.chr11.2145' => 'acertr', 'Atru.chr2.3636' => 'acertr', 'Atru.chr2.3644' => 'acertr', 'Atru.chr6.2422' => 'acertr', 'Atru.chr7.1112' => 'acertr', 'AUR62005469' => 'cqu', 'AUR62011166' => 'cqu', 'AUR62013319' => 'cqu', 'AUR62024273' => 'cqu', 'AUR62028420' => 'cqu', 'AUR62041942' => 'cqu', 'BcaB01g04969' => 'bca', 'BcaB01g06371' => 'bca', 'BcaB02g11494' => 'bca', 'BcaB03g15382' => 'bca', 'BcaB08g36994' => 'bca', 'BcaC03g13477' => 'bca', 'BcaC03g13478' => 'bca', 'BcaC03g13480' => 'bca', 'BcaC03g13481' => 'bca', 'BcaC03g13486' => 'bca', 'BcaC04g19031' => 'bca', 'BcaC04g23085' => 'bca', 'BcaC05g25094' => 'bca', 'BcaC05g25096' => 'bca', 'BcaC05g25138' => 'bca', 'BcaC05g30416' => 'bca', 'BcaC05g30455' => 'bca', 'BcaC06g30979' => 'bca', 'BcaC06g33805' => 'bca', 'BcaC08g46021' => 'bca', 'BcaNung03154' => 'bca', 'BolC2t06623H' => 'bol', 'BolC2t06632H' => 'bol', 'BolC2t06635H' => 'bol', 'BolC2t06638H' => 'bol', 'BolC3t13266H' => 'bol', 'BolC5t29776H' => 'bol', 'BolC6t38912H' => 'bol', 'BolC7t44183H' => 'bol', 'BolC9t54123H' => 'bol', 'BolC9t59107H' => 'bol', 'BraA02t05221Z' => 'bra', 'BraA03t09996Z' => 'bra', 'BraA05t23210Z' => 'bra', 'BraA06t24068Z' => 'bra', 'BraA06t27032Z' => 'bra', 'BraA08t35176Z' => 'bra', 'BraA09t36680Z' => 'bra', 'BraA10t44471Z' => 'bra', 'C02p06760' => 'bna', 'C02p06890' => 'bna', 'C02p07010' => 'bna', 'C03p07660' => 'bna', 'C05p10300' => 'bna', 'C06p38150' => 'bna', 'C07p36650' => 'bna', 'C08p15770' => 'bna', 'C09p12300' => 'bna', 'C09p62700' => 'bna', 'C09p75040' => 'bna', 'CAN.G13.1' => 'can', 'CAN.G138.4' => 'can', 'CAN.G44.6' => 'can', 'CAN.G473.19' => 'can', 'CANSAT01G0835' => 'cansat', 'CANSAT11G0246' => 'cansat', 'CANSAT11G1766' => 'cansat', 'CANSAT64G1954' => 'cansat', 'CARHR013330' => 'chi', 'CARHR060530' => 'chi', 'CARHR075300' => 'chi', 'CARHR105120' => 'chi', 'CARHR148910' => 'chi', 'CARHR198830' => 'chi', 'Carub.0001s1275' => 'cru', 'Carub.0002s1437' => 'cru', 'Carub.0003s0044' => 'cru', 'Carub.0003s2787' => 'cru', 'Carub.0005s0597' => 'cru', 'Carub.0006s1266' => 'cru', 'Ca_06935_v3' => 'car', 'Ca_13559_v3' => 'car', 'Ca_16941_v3' => 'car', 'Ca_16960_v3' => 'car', 'Ca_17775_v3' => 'car', 'Ca_30464_v3' => 'car', 'Cc06_g08160' => 'ccan', 'Cc07_g01520' => 'ccan', 'Cc11_g15810' => 'ccan', 'CDE02G2840' => 'cde', 'CDE03G0093' => 'cde', 'CDE04G2127' => 'cde', 'CDE07G1857' => 'cde', 'CDE09G1246' => 'cde', 'Cfa003412' => 'cfa', 'Cfa007341' => 'cfa', 'Cfa009220' => 'cfa', 'Ciclev10008737m.g' => 'ccl', 'Ciclev10015565m.g' => 'ccl', 'Ciclev10031761m.g' => 'ccl', 'CiPaw.03G045300' => 'cil', 'CiPaw.03G247200' => 'cil', 'CiPaw.04G029500' => 'cil', 'CiPaw.04G174000' => 'cil', 'CiPaw.05G181200' => 'cil', 'CiPaw.06G067100' => 'cil', 'ClCG05G025800' => 'cla', 'ClCG06G011400' => 'cla', 'ClCG09G019360' => 'cla', 'COL.COLO4_04827' => 'col', 'COL.COLO4_29170' => 'col', 'COL.COLO4_35131' => 'col', 'COL.COLO4_35132' => 'col', 'Cpa.g.sc33.32' => 'cpa', 'Cpa.g.sc46.29' => 'cpa', 'Cpa.g.sc796.1' => 'cpa', 'CsaV3_1G030420' => 'csa', 'CsaV3_5G027050' => 'csa', 'CsaV3_5G031040' => 'csa', 'CsaV3_UNG023130' => 'csa', 'CSS0007726' => 'camsi', 'CSS0016433' => 'camsi', 'CSS0017656' => 'camsi', 'CSS0025364' => 'camsi', 'CSS0027582' => 'camsi', 'CSS0047288' => 'camsi', 'CSS0049950' => 'camsi', 'DCAR_003843' => 'dca', 'DCAR_007052' => 'dca', 'DCAR_020884' => 'dca', 'DCAR_021730' => 'dca', 'DCAR_024423' => 'dca', 'DCAR_026509' => 'dca', 'DCAR_031158' => 'dca', 'Dinv14728' => 'din', 'Dinv15219' => 'din', 'Dinv25728' => 'din', 'Dinv33428' => 'din', 'Dinv36489' => 'din', 'Dinv41486' => 'din', 'Duzib147G0469' => 'dzi', 'Duzib168G0060' => 'dzi', 'Duzib187G1215' => 'dzi', 'Duzib248G0692' => 'dzi', 'Duzib251G0767' => 'dzi', 'Duzib264G0446' => 'dzi', 'Duzib268G0691' => 'dzi', 'ECA232G4767' => 'eca', 'ECA233G2838' => 'eca', 'ECA234G0391' => 'eca', 'ECA234G0857' => 'eca', 'ECA236G1593' => 'eca', 'ECA238G0565' => 'eca', 'ECA246G1027' => 'eca', 'ECA246G3223' => 'eca', 'ECA246G3470' => 'eca', 'EL10Ac6g13829' => 'bvu', 'EL10Ac6g14093' => 'bvu', 'EL10Ac8g18707' => 'bvu', 'Eucgr.C01369' => 'egr', 'Eucgr.H02492' => 'egr', 'Eucgr.I01733' => 'egr', 'Eucgr.J02255' => 'egr', 'Eucgr.J02257' => 'egr', 'Eucgr.J02258' => 'egr', 'FAN02G1601' => 'fan', 'FAN03G1586' => 'fan', 'FAN03G2986' => 'fan', 'FAN05G4837' => 'fan', 'FAN06G0146' => 'fan', 'FAN07G0858' => 'fan', 'FAN09G3179' => 'fan', 'FAN10G0669' => 'fan', 'FAN12G2358' => 'fan', 'FAN14G4198' => 'fan', 'FAN14G5112' => 'fan', 'FAN17G0342' => 'fan', 'FAN19G0342' => 'fan', 'FAN19G0962' => 'fan', 'FAN19G1101' => 'fan', 'FAN19G1872' => 'fan', 'FAN22G0356' => 'fan', 'FAN23G0744' => 'fan', 'FAN23G1914' => 'fan', 'FAN26G0032' => 'fan', 'FAN28G0625' => 'fan', 'FvH4_1g02710' => 'fve', 'FvH4_1g02720' => 'fve', 'FvH4_4g25670' => 'fve', 'FvH4_6g51700' => 'fve', 'FvH4_7g20170' => 'fve', 'Glyma.05G175000' => 'gma', 'Glyma.08G132300' => 'gma', 'Glyma.11G243000' => 'gma', 'Glyma.13G158900' => 'gma', 'Glyma.17G112400' => 'gma', 'Glyma.18G014100' => 'gma', 'Glyma.19G003100' => 'gma', 'Glyma.19G056500' => 'gma', 'Gohir.A01G158900' => 'ghi', 'Gohir.A05G312600' => 'ghi', 'Gohir.A05G354900' => 'ghi', 'Gohir.A07G037200' => 'ghi', 'Gohir.A09G030000' => 'ghi', 'Gohir.A12G145200' => 'ghi', 'Gohir.D01G151500' => 'ghi', 'Gohir.D04G058300' => 'ghi', 'Gohir.D05G314100' => 'ghi', 'Gohir.D07G041400' => 'ghi', 'Gohir.D09G029700' => 'ghi', 'Gohir.D12G149700' => 'ghi', 'Gorai.001G043800' => 'gra', 'Gorai.002G187800' => 'gra', 'Gorai.006G034700' => 'gra', 'Gorai.008G161200' => 'gra', 'Gorai.009G335700' => 'gra', 'Gorai.012G065000' => 'gra', 'GSVIVG01000535001' => 'vvi', 'GSVIVG01015572001' => 'vvi', 'GSVIVG01032386001' => 'vvi', 'HanXRQChr05g0138531' => 'han', 'HanXRQChr06g0174391' => 'han', 'HanXRQChr07g0199021' => 'han', 'HanXRQChr08g0208211' => 'han', 'HanXRQChr09g0255471' => 'han', 'HanXRQChr10g0315791' => 'han', 'HanXRQChr12g0371991' => 'han', 'HanXRQChr15g0475251' => 'han', 'HanXRQChr17g0540001' => 'han', 'HanXRQChr17g0548631' => 'han', 'HanXRQChr17g0569561' => 'han', 'Haze_12256' => 'cav', 'Haze_14756' => 'cav', 'Haze_25528' => 'cav', 'Hma1.2p1_0079F.1_g041020' => 'hma', 'Hma1.2p1_0818F.1_g223260' => 'hma', 'Hma1.2p1_1747F.1_g300530' => 'hma', 'HPP92_004607' => 'vpl', 'HPP92_004608' => 'vpl', 'HPP92_006181' => 'vpl', 'HPP92_012192' => 'vpl', 'HPP92_015680' => 'vpl', 'HPP92_020249' => 'vpl', 'HPP92_021376' => 'vpl', 'HPP92_024275' => 'vpl', 'Hund06031' => 'sun', 'Hund25391' => 'sun', 'Lalb_Chr07g0185371' => 'lal', 'Lalb_Chr07g0185381' => 'lal', 'Lalb_Chr12g0204011' => 'lal', 'Lalb_Chr13g0301671' => 'lal', 'Lalb_Chr14g0362851' => 'lal', 'Lalb_Chr24g0403581' => 'lal', 'Lj1g0000233' => 'lja', 'Lj2g0018120' => 'lja', 'Lj3C621T0' => 'lonja', 'Lj3P1059T14' => 'lonja', 'Lj3P611T9' => 'lonja', 'Lj3P614T13' => 'lonja', 'Lj3P615T5' => 'lonja', 'Lj4g0012315' => 'lja', 'Lj4g0026182' => 'lja', 'Lj6P813T16' => 'lonja', 'Lj7C427T7' => 'lonja', 'Lj7C427T8' => 'lonja', 'Lj7P600T41' => 'lonja', 'Lju41C42G17' => 'lonja', 'Lsat_1_v5_gn_0_47300' => 'lsa', 'Lsat_1_v5_gn_2_91280' => 'lsa', 'Lsat_1_v5_gn_3_30561' => 'lsa', 'Lsat_1_v5_gn_4_184321' => 'lsa', 'Lsat_1_v5_gn_4_4041' => 'lsa', 'Lsat_1_v5_gn_5_92000' => 'lsa', 'Lsat_1_v5_gn_8_152940' => 'lsa', 'Lsat_1_v5_gn_8_62401' => 'lsa', 'Manes.06G055900' => 'mes', 'Manes.12G022200' => 'mes', 'Manes.13G023300' => 'mes', 'Manes.14G115000' => 'mes', 'Manes.15G151700' => 'mes', 'Manes.17G111300' => 'mes', 'Mapoly0226s0009' => 'mpo', 'MBI02_g25363_MAGBIO' => 'mbi', 'MBI06_g00027_MAGBIO' => 'mbi', 'MBI10_g13034_MAGBIO' => 'mbi', 'MD09G1023400' => 'mdo', 'MD13G1100100' => 'mdo', 'MD15G1169200' => 'mdo', 'MD16G1101100' => 'mdo', 'MD17G1022900' => 'mdo', 'Medtr3g096150' => 'mtr', 'Medtr4g115070' => 'mtr', 'Medtr7g033325' => 'mtr', 'Medtr8g089840' => 'mtr', 'MELO3C010319.2' => 'cme', 'MELO3C011944.2' => 'cme', 'MELO3C021589.2' => 'cme', 'Migut.E00207' => 'egut', 'Migut.H00067' => 'egut', 'Migut.K00433' => 'egut', 'Migut.K00606' => 'egut', 'Migut.K01410' => 'egut', 'MSTRG.13347' => 'ama', 'MSTRG.24045' => 'ama', 'MSTRG.2428' => 'ama', 'MSTRG.26410' => 'ama', 'MSTRG.3139' => 'ama', 'MSTRG.3286' => 'ama', 'MSTRG.563' => 'ama', 'MSTRG.7941' => 'ama', 'Nitab4.5_0000028g0060' => 'nta', 'Nitab4.5_0000065g0260' => 'nta', 'Nitab4.5_0000112g0060' => 'nta', 'Nitab4.5_0000489g0120' => 'nta', 'Nitab4.5_0001776g0050' => 'nta', 'Nitab4.5_0001854g0010' => 'nta', 'Nitab4.5_0001860g0020' => 'nta', 'Nitab4.5_0004352g0010' => 'nta', 'Nitab4.5_0008716g0020' => 'nta', 'Nitab4.5_0008922g0010' => 'nta', 'Nn3g16693' => 'nnu', 'Nn4g22596' => 'nnu', 'Nn7g37639' => 'nnu', 'Oeu001701.1' => 'oeu', 'Oeu018149.1' => 'oeu', 'Oeu026220.1' => 'oeu', 'Oeu038635.1' => 'oeu', 'Oeu049176.1' => 'oeu', 'Oeu056706.1' => 'oeu', 'Oeu056937.1' => 'oeu', 'Oeu057540.1' => 'oeu', 'Os02g0594900' => 'osa', 'Os02g0595100' => 'osa', 'Os04g0477500' => 'osa', 'Os12g0611900' => 'osa', 'Peaxi162Scf00076g00020' => 'pax', 'Peaxi162Scf00128g00217' => 'pax', 'Peaxi162Scf00129g01640' => 'pax', 'Peaxi162Scf00669g00007' => 'pax', 'Peaxi162Scf00700g00421' => 'pax', 'Peaxi162Scf00801g00038' => 'pax', 'Peaxi162Scf00891g00025' => 'pax', 'PGR083G0909' => 'pgr', 'PGR119G1005' => 'pgr', 'PGR142G2236' => 'pgr', 'PGR142G3388' => 'pgr', 'PGSC0003DMG400004514' => 'stu', 'PGSC0003DMG400012635' => 'stu', 'PGSC0003DMG400015730' => 'stu', 'PGSC0003DMG400018611' => 'stu', 'PGSC0003DMG400030897' => 'stu', 'Phvul.001G254800' => 'pvu', 'Phvul.002G260100' => 'pvu', 'Phvul.003G167600' => 'pvu', 'Phvul.004G005100' => 'pvu', 'Potri.001G343600' => 'ptr', 'Potri.006G066700' => 'ptr', 'Potri.008G186000' => 'ptr', 'Potri.010G046900' => 'ptr', 'Potri.018G127900' => 'ptr', 'Pp3c20_17750' => 'ppa', 'Pp3c24_4380' => 'ppa', 'Prupe.1G245800' => 'ppe', 'Prupe.3G293400' => 'ppe', 'Prupe.7G247400' => 'ppe', 'Psat0s145g0120' => 'psa', 'Psat0s595g0040' => 'psa', 'Psat0s595g0120' => 'psa', 'Psat3g175040' => 'psa', 'Psat7g058120' => 'psa', 'PSO017G0428' => 'pso', 'PSO063G7510' => 'pso', 'PSO067G0046' => 'pso', 'PSO478G1073' => 'pso', 'PSO675G3677' => 'pso', 'PSO675G6558' => 'pso', 'PSO675G7520' => 'pso', 'PSO675G8959' => 'pso', 'QL02p074089' => 'qlo', 'QL02p089614' => 'qlo', 'QL03p057736' => 'qlo', 'RcHm_v2.0_Chr1g0364131' => 'rch', 'RcHm_v2.0_Chr2g0087801' => 'rch', 'RcHm_v2.0_Chr2g0087821' => 'rch', 'RcHm_v2.0_Chr2g0173231' => 'rch', 'RcHm_v2.0_Chr4g0433111' => 'rch', 'Rhsim03G0250300' => 'rsi', 'Rhsim08G0048400' => 'rsi', 'Rhsim10G0014800' => 'rsi', 'Rhsim12G0040100' => 'rsi', 'Rhsim12G0109700' => 'rsi', 'Sabra06G0049600' => 'sbr', 'Sabra08G0141000' => 'sbr', 'Sabra10G0021400' => 'sbr', 'Sabra16G0222900' => 'sbr', 'Sabra18G0108600' => 'sbr', 'SalBow1G0433' => 'sbo', 'SalBow1G2038' => 'sbo', 'SalBow1G5003' => 'sbo', 'SalBow7G1197' => 'sbo', 'SalBow8G3506' => 'sbo', 'Sc03g0007300' => 'sci', 'Sc11g0000950' => 'sci', 'Sc14g0008750' => 'sci', 'Sc18g0000420' => 'sci', 'Sed0006754' => 'sed', 'Sed0008741' => 'sed', 'Sed0017172' => 'sed', 'Sed0018925' => 'sed', 'Sed0023326' => 'sed', 'Sed0025909' => 'sed', 'SEGI_05333' => 'sgi', 'SEGI_10362' => 'sgi', 'SEGI_13380' => 'sgi', 'SEGI_24306' => 'sgi', 'SEGI_29077' => 'sgi', 'SEGI_29095' => 'sgi', 'SEGI_36534' => 'sgi', 'SEGI_37506' => 'sgi', 'SEGI_38321' => 'sgi', 'SGA_v2.0_scaffold307G48031' => 'sas', 'SGA_v2.0_scaffold47G17507' => 'sas', 'SGA_v2.0_scaffold63G21736' => 'sas', 'SGA_v2.0_scaffold87G27070' => 'sas', 'SHI17794' => 'shi', 'SHI28851' => 'shi', 'SMO165G0155' => 'smo', 'SMO340G0217' => 'smo', 'SMO367G1210' => 'smo', 'Solyc02g093430.3' => 'sly', 'Solyc05g013580.4' => 'sly', 'Solyc07g008030.3' => 'sly', 'Solyc12g035470.2' => 'sly', 'Sopen02g038020' => 'spe', 'Sopen05g008490' => 'spe', 'Sopen07g003910' => 'spe', 'Sopen12g015240' => 'spe', 'Sp1g11550' => 'spa', 'Sp2g16710' => 'spa', 'Sp3g00430' => 'spa', 'Sp3g26780' => 'spa', 'Sp5g22900' => 'spa', 'Sp6g29530' => 'spa', 'TAR371G0794' => 'tar', 'TAR374G0164' => 'tar', 'TAR622G0165' => 'tar', 'TAR626G0929' => 'tar', 'TAR629G2155' => 'tar', 'THA.LOC104805282' => 'tha', 'THA.LOC104805363' => 'tha', 'THA.LOC104808968' => 'tha', 'THA.LOC104821093' => 'tha', 'THA.LOC104823953' => 'tha', 'THA.LOC104825562' => 'tha', 'THA.LOC104825665' => 'tha', 'Thecc.02G261400' => 'tca', 'Thecc.04G019200' => 'tca', 'Thecc.09G130400' => 'tca', 'Thhalv10004374m.g' => 'esa', 'Thhalv10007850m.g' => 'esa', 'Thhalv10013782m.g' => 'esa', 'Thhalv10018686m.g' => 'esa', 'Thhalv10020899m.g' => 'esa', 'Thhalv10022755m.g' => 'esa', 'TPR.G23851' => 'tpr', 'TPR.G26500' => 'tpr', 'TPR.G27267' => 'tpr', 'TPR.G32001' => 'tpr', 'TPR.G6251' => 'tpr', 'TPR.G8167' => 'tpr', 'TWI12G1330' => 'twi', 'TWI18G1239' => 'twi', 'TWI34G0979' => 'twi', 'TWI36G0670' => 'twi', 'TWI36G0707' => 'twi', 'TWI56G0233' => 'twi', 'TWI75G1809' => 'twi', 'unitig_21.g20874' => 'ugi', 'unitig_26.g10343' => 'ugi', 'unitig_46.g18392' => 'ugi', 'unitig_52.g17178' => 'ugi', 'unitig_8.g2934' => 'ugi', 'vmacro01122' => 'vma', 'vmacro05875' => 'vma', 'vmacro06147' => 'vma', 'vmacro16191' => 'vma', 'vmacro18293' => 'vma', 'VMungo0251G3707' => 'vmu', 'VMungo0464G1521' => 'vmu', 'VMungo1215G0205' => 'vmu', 'VMungo1383G2484' => 'vmu', 'Zm00001eb079610' => 'zma', 'Zm00001eb135990' => 'zma', 'Zm00001eb183710' => 'zma', 'Zm00001eb246020' => 'zma' ) $gf_id = 'HOM05D001124' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001124' ) $data_identifier = 'HOM05D001124' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 6, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 7, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 21, 'bol' => (int) 10, 'bra' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 6, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 9, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 21, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 8, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 10, 'lsa' => (int) 8, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 8, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 9, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb246020' $species_info = array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ) $local_species = 'ppa' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001124', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '548', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02520' => 'bna', 'A03p06630' => 'bna', 'A05p44460' => 'bna', 'A06p08710' => 'bna', 'A06p41090' => 'bna', 'A07p32320' => 'bna', 'A08p32520' => 'bna', 'A09p10360' => 'bna', 'A10p24080' => 'bna', 'Aa31LG11G15250' => 'aar', 'Aa31LG1G1800' => 'aar', 'Aa31LG2G5120' => 'aar', 'Aa31LG2G6070' => 'aar', 'Aa31LG5G10770' => 'aar', 'Aa31sc61G90' => 'aar', 'Actinidia01352' => 'ach', 'Actinidia05983' => 'ach', 'Actinidia08133' => 'ach', 'Actinidia15101' => 'ach', 'Actinidia26379' => 'ach', 'Actinidia35778' => 'ach', 'Actinidia36123' => 'ach', 'Actinidia37436' => 'ach', 'Actinidia38730' => 'ach', 'Ah.02g128210' => 'amhyb', 'Ah.03g132990' => 'amhyb', 'Ah.14g079410' => 'amhyb', 'AL1G24640' => 'aly', 'AL2G26680' => 'aly', 'AL3G10530' => 'aly', 'AL3G45230' => 'aly', 'AL5G15230' => 'aly', 'AL5G16960' => 'aly', 'AL6G25210' => 'aly', 'Aqoxy2G00441' => 'aox', 'Aqoxy3G01236' => 'aox', 'Aqoxy5G03746' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3RQ047' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C7GMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9C8JER' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MBL6KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YXCZ83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZANX40' => 'arhy', 'AT1G12990' => 'ath', 'AT1G67880' => 'ath', 'AT2G13290' => 'ath', 'AT3G01620' => 'ath', 'AT3G26445' => 'ath', 'AT3G27540' => 'ath', 'AT5G14480' => 'ath', 'ATR0824G026' => 'atr', 'ATR1098G019' => 'atr', 'Atru.chr11.2145' => 'acertr', 'Atru.chr2.3636' => 'acertr', 'Atru.chr2.3644' => 'acertr', 'Atru.chr6.2422' => 'acertr', 'Atru.chr7.1112' => 'acertr', 'AUR62005469' => 'cqu', 'AUR62011166' => 'cqu', 'AUR62013319' => 'cqu', 'AUR62024273' => 'cqu', 'AUR62028420' => 'cqu', 'AUR62041942' => 'cqu', 'BcaB01g04969' => 'bca', 'BcaB01g06371' => 'bca', 'BcaB02g11494' => 'bca', 'BcaB03g15382' => 'bca', 'BcaB08g36994' => 'bca', 'BcaC03g13477' => 'bca', 'BcaC03g13478' => 'bca', 'BcaC03g13480' => 'bca', 'BcaC03g13481' => 'bca', 'BcaC03g13486' => 'bca', 'BcaC04g19031' => 'bca', 'BcaC04g23085' => 'bca', 'BcaC05g25094' => 'bca', 'BcaC05g25096' => 'bca', 'BcaC05g25138' => 'bca', 'BcaC05g30416' => 'bca', 'BcaC05g30455' => 'bca', 'BcaC06g30979' => 'bca', 'BcaC06g33805' => 'bca', 'BcaC08g46021' => 'bca', 'BcaNung03154' => 'bca', 'BolC2t06623H' => 'bol', 'BolC2t06632H' => 'bol', 'BolC2t06635H' => 'bol', 'BolC2t06638H' => 'bol', 'BolC3t13266H' => 'bol', 'BolC5t29776H' => 'bol', 'BolC6t38912H' => 'bol', 'BolC7t44183H' => 'bol', 'BolC9t54123H' => 'bol', 'BolC9t59107H' => 'bol', 'BraA02t05221Z' => 'bra', 'BraA03t09996Z' => 'bra', 'BraA05t23210Z' => 'bra', 'BraA06t24068Z' => 'bra', 'BraA06t27032Z' => 'bra', 'BraA08t35176Z' => 'bra', 'BraA09t36680Z' => 'bra', 'BraA10t44471Z' => 'bra', 'C02p06760' => 'bna', 'C02p06890' => 'bna', 'C02p07010' => 'bna', 'C03p07660' => 'bna', 'C05p10300' => 'bna', 'C06p38150' => 'bna', 'C07p36650' => 'bna', 'C08p15770' => 'bna', 'C09p12300' => 'bna', 'C09p62700' => 'bna', 'C09p75040' => 'bna', 'CAN.G13.1' => 'can', 'CAN.G138.4' => 'can', 'CAN.G44.6' => 'can', 'CAN.G473.19' => 'can', 'CANSAT01G0835' => 'cansat', 'CANSAT11G0246' => 'cansat', 'CANSAT11G1766' => 'cansat', 'CANSAT64G1954' => 'cansat', 'CARHR013330' => 'chi', 'CARHR060530' => 'chi', 'CARHR075300' => 'chi', 'CARHR105120' => 'chi', 'CARHR148910' => 'chi', 'CARHR198830' => 'chi', 'Carub.0001s1275' => 'cru', 'Carub.0002s1437' => 'cru', 'Carub.0003s0044' => 'cru', 'Carub.0003s2787' => 'cru', 'Carub.0005s0597' => 'cru', 'Carub.0006s1266' => 'cru', 'Ca_06935_v3' => 'car', 'Ca_13559_v3' => 'car', 'Ca_16941_v3' => 'car', 'Ca_16960_v3' => 'car', 'Ca_17775_v3' => 'car', 'Ca_30464_v3' => 'car', 'Cc06_g08160' => 'ccan', 'Cc07_g01520' => 'ccan', 'Cc11_g15810' => 'ccan', 'CDE02G2840' => 'cde', 'CDE03G0093' => 'cde', 'CDE04G2127' => 'cde', 'CDE07G1857' => 'cde', 'CDE09G1246' => 'cde', 'Cfa003412' => 'cfa', 'Cfa007341' => 'cfa', 'Cfa009220' => 'cfa', 'Ciclev10008737m.g' => 'ccl', 'Ciclev10015565m.g' => 'ccl', 'Ciclev10031761m.g' => 'ccl', 'CiPaw.03G045300' => 'cil', 'CiPaw.03G247200' => 'cil', 'CiPaw.04G029500' => 'cil', 'CiPaw.04G174000' => 'cil', 'CiPaw.05G181200' => 'cil', 'CiPaw.06G067100' => 'cil', 'ClCG05G025800' => 'cla', 'ClCG06G011400' => 'cla', 'ClCG09G019360' => 'cla', 'COL.COLO4_04827' => 'col', 'COL.COLO4_29170' => 'col', 'COL.COLO4_35131' => 'col', 'COL.COLO4_35132' => 'col', 'Cpa.g.sc33.32' => 'cpa', 'Cpa.g.sc46.29' => 'cpa', 'Cpa.g.sc796.1' => 'cpa', 'CsaV3_1G030420' => 'csa', 'CsaV3_5G027050' => 'csa', 'CsaV3_5G031040' => 'csa', 'CsaV3_UNG023130' => 'csa', 'CSS0007726' => 'camsi', 'CSS0016433' => 'camsi', 'CSS0017656' => 'camsi', 'CSS0025364' => 'camsi', 'CSS0027582' => 'camsi', 'CSS0047288' => 'camsi', 'CSS0049950' => 'camsi', 'DCAR_003843' => 'dca', 'DCAR_007052' => 'dca', 'DCAR_020884' => 'dca', 'DCAR_021730' => 'dca', 'DCAR_024423' => 'dca', 'DCAR_026509' => 'dca', 'DCAR_031158' => 'dca', 'Dinv14728' => 'din', 'Dinv15219' => 'din', 'Dinv25728' => 'din', 'Dinv33428' => 'din', 'Dinv36489' => 'din', 'Dinv41486' => 'din', 'Duzib147G0469' => 'dzi', 'Duzib168G0060' => 'dzi', 'Duzib187G1215' => 'dzi', 'Duzib248G0692' => 'dzi', 'Duzib251G0767' => 'dzi', 'Duzib264G0446' => 'dzi', 'Duzib268G0691' => 'dzi', 'ECA232G4767' => 'eca', 'ECA233G2838' => 'eca', 'ECA234G0391' => 'eca', 'ECA234G0857' => 'eca', 'ECA236G1593' => 'eca', 'ECA238G0565' => 'eca', 'ECA246G1027' => 'eca', 'ECA246G3223' => 'eca', 'ECA246G3470' => 'eca', 'EL10Ac6g13829' => 'bvu', 'EL10Ac6g14093' => 'bvu', 'EL10Ac8g18707' => 'bvu', 'Eucgr.C01369' => 'egr', 'Eucgr.H02492' => 'egr', 'Eucgr.I01733' => 'egr', 'Eucgr.J02255' => 'egr', 'Eucgr.J02257' => 'egr', 'Eucgr.J02258' => 'egr', 'FAN02G1601' => 'fan', 'FAN03G1586' => 'fan', 'FAN03G2986' => 'fan', 'FAN05G4837' => 'fan', 'FAN06G0146' => 'fan', 'FAN07G0858' => 'fan', 'FAN09G3179' => 'fan', 'FAN10G0669' => 'fan', 'FAN12G2358' => 'fan', 'FAN14G4198' => 'fan', 'FAN14G5112' => 'fan', 'FAN17G0342' => 'fan', 'FAN19G0342' => 'fan', 'FAN19G0962' => 'fan', 'FAN19G1101' => 'fan', 'FAN19G1872' => 'fan', 'FAN22G0356' => 'fan', 'FAN23G0744' => 'fan', 'FAN23G1914' => 'fan', 'FAN26G0032' => 'fan', 'FAN28G0625' => 'fan', 'FvH4_1g02710' => 'fve', 'FvH4_1g02720' => 'fve', 'FvH4_4g25670' => 'fve', 'FvH4_6g51700' => 'fve', 'FvH4_7g20170' => 'fve', 'Glyma.05G175000' => 'gma', 'Glyma.08G132300' => 'gma', 'Glyma.11G243000' => 'gma', 'Glyma.13G158900' => 'gma', 'Glyma.17G112400' => 'gma', 'Glyma.18G014100' => 'gma', 'Glyma.19G003100' => 'gma', 'Glyma.19G056500' => 'gma', 'Gohir.A01G158900' => 'ghi', 'Gohir.A05G312600' => 'ghi', 'Gohir.A05G354900' => 'ghi', 'Gohir.A07G037200' => 'ghi', 'Gohir.A09G030000' => 'ghi', 'Gohir.A12G145200' => 'ghi', 'Gohir.D01G151500' => 'ghi', 'Gohir.D04G058300' => 'ghi', 'Gohir.D05G314100' => 'ghi', 'Gohir.D07G041400' => 'ghi', 'Gohir.D09G029700' => 'ghi', 'Gohir.D12G149700' => 'ghi', 'Gorai.001G043800' => 'gra', 'Gorai.002G187800' => 'gra', 'Gorai.006G034700' => 'gra', 'Gorai.008G161200' => 'gra', 'Gorai.009G335700' => 'gra', 'Gorai.012G065000' => 'gra', 'GSVIVG01000535001' => 'vvi', 'GSVIVG01015572001' => 'vvi', 'GSVIVG01032386001' => 'vvi', 'HanXRQChr05g0138531' => 'han', 'HanXRQChr06g0174391' => 'han', 'HanXRQChr07g0199021' => 'han', 'HanXRQChr08g0208211' => 'han', 'HanXRQChr09g0255471' => 'han', 'HanXRQChr10g0315791' => 'han', 'HanXRQChr12g0371991' => 'han', 'HanXRQChr15g0475251' => 'han', 'HanXRQChr17g0540001' => 'han', 'HanXRQChr17g0548631' => 'han', 'HanXRQChr17g0569561' => 'han', 'Haze_12256' => 'cav', 'Haze_14756' => 'cav', 'Haze_25528' => 'cav', 'Hma1.2p1_0079F.1_g041020' => 'hma', 'Hma1.2p1_0818F.1_g223260' => 'hma', 'Hma1.2p1_1747F.1_g300530' => 'hma', 'HPP92_004607' => 'vpl', 'HPP92_004608' => 'vpl', 'HPP92_006181' => 'vpl', 'HPP92_012192' => 'vpl', 'HPP92_015680' => 'vpl', 'HPP92_020249' => 'vpl', 'HPP92_021376' => 'vpl', 'HPP92_024275' => 'vpl', 'Hund06031' => 'sun', 'Hund25391' => 'sun', 'Lalb_Chr07g0185371' => 'lal', 'Lalb_Chr07g0185381' => 'lal', 'Lalb_Chr12g0204011' => 'lal', 'Lalb_Chr13g0301671' => 'lal', 'Lalb_Chr14g0362851' => 'lal', 'Lalb_Chr24g0403581' => 'lal', 'Lj1g0000233' => 'lja', 'Lj2g0018120' => 'lja', 'Lj3C621T0' => 'lonja', 'Lj3P1059T14' => 'lonja', 'Lj3P611T9' => 'lonja', 'Lj3P614T13' => 'lonja', 'Lj3P615T5' => 'lonja', 'Lj4g0012315' => 'lja', 'Lj4g0026182' => 'lja', 'Lj6P813T16' => 'lonja', 'Lj7C427T7' => 'lonja', 'Lj7C427T8' => 'lonja', 'Lj7P600T41' => 'lonja', 'Lju41C42G17' => 'lonja', 'Lsat_1_v5_gn_0_47300' => 'lsa', 'Lsat_1_v5_gn_2_91280' => 'lsa', 'Lsat_1_v5_gn_3_30561' => 'lsa', 'Lsat_1_v5_gn_4_184321' => 'lsa', 'Lsat_1_v5_gn_4_4041' => 'lsa', 'Lsat_1_v5_gn_5_92000' => 'lsa', 'Lsat_1_v5_gn_8_152940' => 'lsa', 'Lsat_1_v5_gn_8_62401' => 'lsa', 'Manes.06G055900' => 'mes', 'Manes.12G022200' => 'mes', 'Manes.13G023300' => 'mes', 'Manes.14G115000' => 'mes', 'Manes.15G151700' => 'mes', 'Manes.17G111300' => 'mes', 'Mapoly0226s0009' => 'mpo', 'MBI02_g25363_MAGBIO' => 'mbi', 'MBI06_g00027_MAGBIO' => 'mbi', 'MBI10_g13034_MAGBIO' => 'mbi', 'MD09G1023400' => 'mdo', 'MD13G1100100' => 'mdo', 'MD15G1169200' => 'mdo', 'MD16G1101100' => 'mdo', 'MD17G1022900' => 'mdo', 'Medtr3g096150' => 'mtr', 'Medtr4g115070' => 'mtr', 'Medtr7g033325' => 'mtr', 'Medtr8g089840' => 'mtr', 'MELO3C010319.2' => 'cme', 'MELO3C011944.2' => 'cme', 'MELO3C021589.2' => 'cme', 'Migut.E00207' => 'egut', 'Migut.H00067' => 'egut', 'Migut.K00433' => 'egut', 'Migut.K00606' => 'egut', 'Migut.K01410' => 'egut', 'MSTRG.13347' => 'ama', 'MSTRG.24045' => 'ama', 'MSTRG.2428' => 'ama', 'MSTRG.26410' => 'ama', 'MSTRG.3139' => 'ama', 'MSTRG.3286' => 'ama', 'MSTRG.563' => 'ama', 'MSTRG.7941' => 'ama', 'Nitab4.5_0000028g0060' => 'nta', 'Nitab4.5_0000065g0260' => 'nta', 'Nitab4.5_0000112g0060' => 'nta', 'Nitab4.5_0000489g0120' => 'nta', 'Nitab4.5_0001776g0050' => 'nta', 'Nitab4.5_0001854g0010' => 'nta', 'Nitab4.5_0001860g0020' => 'nta', 'Nitab4.5_0004352g0010' => 'nta', 'Nitab4.5_0008716g0020' => 'nta', 'Nitab4.5_0008922g0010' => 'nta', 'Nn3g16693' => 'nnu', 'Nn4g22596' => 'nnu', 'Nn7g37639' => 'nnu', 'Oeu001701.1' => 'oeu', 'Oeu018149.1' => 'oeu', 'Oeu026220.1' => 'oeu', 'Oeu038635.1' => 'oeu', 'Oeu049176.1' => 'oeu', 'Oeu056706.1' => 'oeu', 'Oeu056937.1' => 'oeu', 'Oeu057540.1' => 'oeu', 'Os02g0594900' => 'osa', 'Os02g0595100' => 'osa', 'Os04g0477500' => 'osa', 'Os12g0611900' => 'osa', 'Peaxi162Scf00076g00020' => 'pax', 'Peaxi162Scf00128g00217' => 'pax', 'Peaxi162Scf00129g01640' => 'pax', 'Peaxi162Scf00669g00007' => 'pax', 'Peaxi162Scf00700g00421' => 'pax', 'Peaxi162Scf00801g00038' => 'pax', 'Peaxi162Scf00891g00025' => 'pax', 'PGR083G0909' => 'pgr', 'PGR119G1005' => 'pgr', 'PGR142G2236' => 'pgr', 'PGR142G3388' => 'pgr', 'PGSC0003DMG400004514' => 'stu', 'PGSC0003DMG400012635' => 'stu', 'PGSC0003DMG400015730' => 'stu', 'PGSC0003DMG400018611' => 'stu', 'PGSC0003DMG400030897' => 'stu', 'Phvul.001G254800' => 'pvu', 'Phvul.002G260100' => 'pvu', 'Phvul.003G167600' => 'pvu', 'Phvul.004G005100' => 'pvu', 'Potri.001G343600' => 'ptr', 'Potri.006G066700' => 'ptr', 'Potri.008G186000' => 'ptr', 'Potri.010G046900' => 'ptr', 'Potri.018G127900' => 'ptr', 'Pp3c20_17750' => 'ppa', 'Pp3c24_4380' => 'ppa', 'Prupe.1G245800' => 'ppe', 'Prupe.3G293400' => 'ppe', 'Prupe.7G247400' => 'ppe', 'Psat0s145g0120' => 'psa', 'Psat0s595g0040' => 'psa', 'Psat0s595g0120' => 'psa', 'Psat3g175040' => 'psa', 'Psat7g058120' => 'psa', 'PSO017G0428' => 'pso', 'PSO063G7510' => 'pso', 'PSO067G0046' => 'pso', 'PSO478G1073' => 'pso', 'PSO675G3677' => 'pso', 'PSO675G6558' => 'pso', 'PSO675G7520' => 'pso', 'PSO675G8959' => 'pso', 'QL02p074089' => 'qlo', 'QL02p089614' => 'qlo', 'QL03p057736' => 'qlo', 'RcHm_v2.0_Chr1g0364131' => 'rch', 'RcHm_v2.0_Chr2g0087801' => 'rch', 'RcHm_v2.0_Chr2g0087821' => 'rch', 'RcHm_v2.0_Chr2g0173231' => 'rch', 'RcHm_v2.0_Chr4g0433111' => 'rch', 'Rhsim03G0250300' => 'rsi', 'Rhsim08G0048400' => 'rsi', 'Rhsim10G0014800' => 'rsi', 'Rhsim12G0040100' => 'rsi', 'Rhsim12G0109700' => 'rsi', 'Sabra06G0049600' => 'sbr', 'Sabra08G0141000' => 'sbr', 'Sabra10G0021400' => 'sbr', 'Sabra16G0222900' => 'sbr', 'Sabra18G0108600' => 'sbr', 'SalBow1G0433' => 'sbo', 'SalBow1G2038' => 'sbo', 'SalBow1G5003' => 'sbo', 'SalBow7G1197' => 'sbo', 'SalBow8G3506' => 'sbo', 'Sc03g0007300' => 'sci', 'Sc11g0000950' => 'sci', 'Sc14g0008750' => 'sci', 'Sc18g0000420' => 'sci', 'Sed0006754' => 'sed', 'Sed0008741' => 'sed', 'Sed0017172' => 'sed', 'Sed0018925' => 'sed', 'Sed0023326' => 'sed', 'Sed0025909' => 'sed', 'SEGI_05333' => 'sgi', 'SEGI_10362' => 'sgi', 'SEGI_13380' => 'sgi', 'SEGI_24306' => 'sgi', 'SEGI_29077' => 'sgi', 'SEGI_29095' => 'sgi', 'SEGI_36534' => 'sgi', 'SEGI_37506' => 'sgi', 'SEGI_38321' => 'sgi', 'SGA_v2.0_scaffold307G48031' => 'sas', 'SGA_v2.0_scaffold47G17507' => 'sas', 'SGA_v2.0_scaffold63G21736' => 'sas', 'SGA_v2.0_scaffold87G27070' => 'sas', 'SHI17794' => 'shi', 'SHI28851' => 'shi', 'SMO165G0155' => 'smo', 'SMO340G0217' => 'smo', 'SMO367G1210' => 'smo', 'Solyc02g093430.3' => 'sly', 'Solyc05g013580.4' => 'sly', 'Solyc07g008030.3' => 'sly', 'Solyc12g035470.2' => 'sly', 'Sopen02g038020' => 'spe', 'Sopen05g008490' => 'spe', 'Sopen07g003910' => 'spe', 'Sopen12g015240' => 'spe', 'Sp1g11550' => 'spa', 'Sp2g16710' => 'spa', 'Sp3g00430' => 'spa', 'Sp3g26780' => 'spa', 'Sp5g22900' => 'spa', 'Sp6g29530' => 'spa', 'TAR371G0794' => 'tar', 'TAR374G0164' => 'tar', 'TAR622G0165' => 'tar', 'TAR626G0929' => 'tar', 'TAR629G2155' => 'tar', 'THA.LOC104805282' => 'tha', 'THA.LOC104805363' => 'tha', 'THA.LOC104808968' => 'tha', 'THA.LOC104821093' => 'tha', 'THA.LOC104823953' => 'tha', 'THA.LOC104825562' => 'tha', 'THA.LOC104825665' => 'tha', 'Thecc.02G261400' => 'tca', 'Thecc.04G019200' => 'tca', 'Thecc.09G130400' => 'tca', 'Thhalv10004374m.g' => 'esa', 'Thhalv10007850m.g' => 'esa', 'Thhalv10013782m.g' => 'esa', 'Thhalv10018686m.g' => 'esa', 'Thhalv10020899m.g' => 'esa', 'Thhalv10022755m.g' => 'esa', 'TPR.G23851' => 'tpr', 'TPR.G26500' => 'tpr', 'TPR.G27267' => 'tpr', 'TPR.G32001' => 'tpr', 'TPR.G6251' => 'tpr', 'TPR.G8167' => 'tpr', 'TWI12G1330' => 'twi', 'TWI18G1239' => 'twi', 'TWI34G0979' => 'twi', 'TWI36G0670' => 'twi', 'TWI36G0707' => 'twi', 'TWI56G0233' => 'twi', 'TWI75G1809' => 'twi', 'unitig_21.g20874' => 'ugi', 'unitig_26.g10343' => 'ugi', 'unitig_46.g18392' => 'ugi', 'unitig_52.g17178' => 'ugi', 'unitig_8.g2934' => 'ugi', 'vmacro01122' => 'vma', 'vmacro05875' => 'vma', 'vmacro06147' => 'vma', 'vmacro16191' => 'vma', 'vmacro18293' => 'vma', 'VMungo0251G3707' => 'vmu', 'VMungo0464G1521' => 'vmu', 'VMungo1215G0205' => 'vmu', 'VMungo1383G2484' => 'vmu', 'Zm00001eb079610' => 'zma', 'Zm00001eb135990' => 'zma', 'Zm00001eb183710' => 'zma', 'Zm00001eb246020' => 'zma' ), 'gf_id' => 'HOM05D001124', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001124' ), 'data_identifier' => 'HOM05D001124', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001124', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '548', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02520' => 'bna', 'A03p06630' => 'bna', 'A05p44460' => 'bna', 'A06p08710' => 'bna', 'A06p41090' => 'bna', 'A07p32320' => 'bna', 'A08p32520' => 'bna', 'A09p10360' => 'bna', 'A10p24080' => 'bna', 'Aa31LG11G15250' => 'aar', 'Aa31LG1G1800' => 'aar', 'Aa31LG2G5120' => 'aar', 'Aa31LG2G6070' => 'aar', 'Aa31LG5G10770' => 'aar', 'Aa31sc61G90' => 'aar', 'Actinidia01352' => 'ach', 'Actinidia05983' => 'ach', 'Actinidia08133' => 'ach', 'Actinidia15101' => 'ach', 'Actinidia26379' => 'ach', 'Actinidia35778' => 'ach', 'Actinidia36123' => 'ach', 'Actinidia37436' => 'ach', 'Actinidia38730' => 'ach', 'Ah.02g128210' => 'amhyb', 'Ah.03g132990' => 'amhyb', 'Ah.14g079410' => 'amhyb', 'AL1G24640' => 'aly', 'AL2G26680' => 'aly', 'AL3G10530' => 'aly', 'AL3G45230' => 'aly', 'AL5G15230' => 'aly', 'AL5G16960' => 'aly', 'AL6G25210' => 'aly', 'Aqoxy2G00441' => 'aox', 'Aqoxy3G01236' => 'aox', 'Aqoxy5G03746' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3RQ047' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C7GMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9C8JER' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MBL6KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YXCZ83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZANX40' => 'arhy', 'AT1G12990' => 'ath', 'AT1G67880' => 'ath', 'AT2G13290' => 'ath', 'AT3G01620' => 'ath', 'AT3G26445' => 'ath', 'AT3G27540' => 'ath', 'AT5G14480' => 'ath', 'ATR0824G026' => 'atr', 'ATR1098G019' => 'atr', 'Atru.chr11.2145' => 'acertr', 'Atru.chr2.3636' => 'acertr', 'Atru.chr2.3644' => 'acertr', 'Atru.chr6.2422' => 'acertr', 'Atru.chr7.1112' => 'acertr', 'AUR62005469' => 'cqu', 'AUR62011166' => 'cqu', 'AUR62013319' => 'cqu', 'AUR62024273' => 'cqu', 'AUR62028420' => 'cqu', 'AUR62041942' => 'cqu', 'BcaB01g04969' => 'bca', 'BcaB01g06371' => 'bca', 'BcaB02g11494' => 'bca', 'BcaB03g15382' => 'bca', 'BcaB08g36994' => 'bca', 'BcaC03g13477' => 'bca', 'BcaC03g13478' => 'bca', 'BcaC03g13480' => 'bca', 'BcaC03g13481' => 'bca', 'BcaC03g13486' => 'bca', 'BcaC04g19031' => 'bca', 'BcaC04g23085' => 'bca', 'BcaC05g25094' => 'bca', 'BcaC05g25096' => 'bca', 'BcaC05g25138' => 'bca', 'BcaC05g30416' => 'bca', 'BcaC05g30455' => 'bca', 'BcaC06g30979' => 'bca', 'BcaC06g33805' => 'bca', 'BcaC08g46021' => 'bca', 'BcaNung03154' => 'bca', 'BolC2t06623H' => 'bol', 'BolC2t06632H' => 'bol', 'BolC2t06635H' => 'bol', 'BolC2t06638H' => 'bol', 'BolC3t13266H' => 'bol', 'BolC5t29776H' => 'bol', 'BolC6t38912H' => 'bol', 'BolC7t44183H' => 'bol', 'BolC9t54123H' => 'bol', 'BolC9t59107H' => 'bol', 'BraA02t05221Z' => 'bra', 'BraA03t09996Z' => 'bra', 'BraA05t23210Z' => 'bra', 'BraA06t24068Z' => 'bra', 'BraA06t27032Z' => 'bra', 'BraA08t35176Z' => 'bra', 'BraA09t36680Z' => 'bra', 'BraA10t44471Z' => 'bra', 'C02p06760' => 'bna', 'C02p06890' => 'bna', 'C02p07010' => 'bna', 'C03p07660' => 'bna', 'C05p10300' => 'bna', 'C06p38150' => 'bna', 'C07p36650' => 'bna', 'C08p15770' => 'bna', 'C09p12300' => 'bna', 'C09p62700' => 'bna', 'C09p75040' => 'bna', 'CAN.G13.1' => 'can', 'CAN.G138.4' => 'can', 'CAN.G44.6' => 'can', 'CAN.G473.19' => 'can', 'CANSAT01G0835' => 'cansat', 'CANSAT11G0246' => 'cansat', 'CANSAT11G1766' => 'cansat', 'CANSAT64G1954' => 'cansat', 'CARHR013330' => 'chi', 'CARHR060530' => 'chi', 'CARHR075300' => 'chi', 'CARHR105120' => 'chi', 'CARHR148910' => 'chi', 'CARHR198830' => 'chi', 'Carub.0001s1275' => 'cru', 'Carub.0002s1437' => 'cru', 'Carub.0003s0044' => 'cru', 'Carub.0003s2787' => 'cru', 'Carub.0005s0597' => 'cru', 'Carub.0006s1266' => 'cru', 'Ca_06935_v3' => 'car', 'Ca_13559_v3' => 'car', 'Ca_16941_v3' => 'car', 'Ca_16960_v3' => 'car', 'Ca_17775_v3' => 'car', 'Ca_30464_v3' => 'car', 'Cc06_g08160' => 'ccan', 'Cc07_g01520' => 'ccan', 'Cc11_g15810' => 'ccan', 'CDE02G2840' => 'cde', 'CDE03G0093' => 'cde', 'CDE04G2127' => 'cde', 'CDE07G1857' => 'cde', 'CDE09G1246' => 'cde', 'Cfa003412' => 'cfa', 'Cfa007341' => 'cfa', 'Cfa009220' => 'cfa', 'Ciclev10008737m.g' => 'ccl', 'Ciclev10015565m.g' => 'ccl', 'Ciclev10031761m.g' => 'ccl', 'CiPaw.03G045300' => 'cil', 'CiPaw.03G247200' => 'cil', 'CiPaw.04G029500' => 'cil', 'CiPaw.04G174000' => 'cil', 'CiPaw.05G181200' => 'cil', 'CiPaw.06G067100' => 'cil', 'ClCG05G025800' => 'cla', 'ClCG06G011400' => 'cla', 'ClCG09G019360' => 'cla', 'COL.COLO4_04827' => 'col', 'COL.COLO4_29170' => 'col', 'COL.COLO4_35131' => 'col', 'COL.COLO4_35132' => 'col', 'Cpa.g.sc33.32' => 'cpa', 'Cpa.g.sc46.29' => 'cpa', 'Cpa.g.sc796.1' => 'cpa', 'CsaV3_1G030420' => 'csa', 'CsaV3_5G027050' => 'csa', 'CsaV3_5G031040' => 'csa', 'CsaV3_UNG023130' => 'csa', 'CSS0007726' => 'camsi', 'CSS0016433' => 'camsi', 'CSS0017656' => 'camsi', 'CSS0025364' => 'camsi', 'CSS0027582' => 'camsi', 'CSS0047288' => 'camsi', 'CSS0049950' => 'camsi', 'DCAR_003843' => 'dca', 'DCAR_007052' => 'dca', 'DCAR_020884' => 'dca', 'DCAR_021730' => 'dca', 'DCAR_024423' => 'dca', 'DCAR_026509' => 'dca', 'DCAR_031158' => 'dca', 'Dinv14728' => 'din', 'Dinv15219' => 'din', 'Dinv25728' => 'din', 'Dinv33428' => 'din', 'Dinv36489' => 'din', 'Dinv41486' => 'din', 'Duzib147G0469' => 'dzi', 'Duzib168G0060' => 'dzi', 'Duzib187G1215' => 'dzi', 'Duzib248G0692' => 'dzi', 'Duzib251G0767' => 'dzi', 'Duzib264G0446' => 'dzi', 'Duzib268G0691' => 'dzi', 'ECA232G4767' => 'eca', 'ECA233G2838' => 'eca', 'ECA234G0391' => 'eca', 'ECA234G0857' => 'eca', 'ECA236G1593' => 'eca', 'ECA238G0565' => 'eca', 'ECA246G1027' => 'eca', 'ECA246G3223' => 'eca', 'ECA246G3470' => 'eca', 'EL10Ac6g13829' => 'bvu', 'EL10Ac6g14093' => 'bvu', 'EL10Ac8g18707' => 'bvu', 'Eucgr.C01369' => 'egr', 'Eucgr.H02492' => 'egr', 'Eucgr.I01733' => 'egr', 'Eucgr.J02255' => 'egr', 'Eucgr.J02257' => 'egr', 'Eucgr.J02258' => 'egr', 'FAN02G1601' => 'fan', 'FAN03G1586' => 'fan', 'FAN03G2986' => 'fan', 'FAN05G4837' => 'fan', 'FAN06G0146' => 'fan', 'FAN07G0858' => 'fan', 'FAN09G3179' => 'fan', 'FAN10G0669' => 'fan', 'FAN12G2358' => 'fan', 'FAN14G4198' => 'fan', 'FAN14G5112' => 'fan', 'FAN17G0342' => 'fan', 'FAN19G0342' => 'fan', 'FAN19G0962' => 'fan', 'FAN19G1101' => 'fan', 'FAN19G1872' => 'fan', 'FAN22G0356' => 'fan', 'FAN23G0744' => 'fan', 'FAN23G1914' => 'fan', 'FAN26G0032' => 'fan', 'FAN28G0625' => 'fan', 'FvH4_1g02710' => 'fve', 'FvH4_1g02720' => 'fve', 'FvH4_4g25670' => 'fve', 'FvH4_6g51700' => 'fve', 'FvH4_7g20170' => 'fve', 'Glyma.05G175000' => 'gma', 'Glyma.08G132300' => 'gma', 'Glyma.11G243000' => 'gma', 'Glyma.13G158900' => 'gma', 'Glyma.17G112400' => 'gma', 'Glyma.18G014100' => 'gma', 'Glyma.19G003100' => 'gma', 'Glyma.19G056500' => 'gma', 'Gohir.A01G158900' => 'ghi', 'Gohir.A05G312600' => 'ghi', 'Gohir.A05G354900' => 'ghi', 'Gohir.A07G037200' => 'ghi', 'Gohir.A09G030000' => 'ghi', 'Gohir.A12G145200' => 'ghi', 'Gohir.D01G151500' => 'ghi', 'Gohir.D04G058300' => 'ghi', 'Gohir.D05G314100' => 'ghi', 'Gohir.D07G041400' => 'ghi', 'Gohir.D09G029700' => 'ghi', 'Gohir.D12G149700' => 'ghi', 'Gorai.001G043800' => 'gra', 'Gorai.002G187800' => 'gra', 'Gorai.006G034700' => 'gra', 'Gorai.008G161200' => 'gra', 'Gorai.009G335700' => 'gra', 'Gorai.012G065000' => 'gra', 'GSVIVG01000535001' => 'vvi', 'GSVIVG01015572001' => 'vvi', 'GSVIVG01032386001' => 'vvi', 'HanXRQChr05g0138531' => 'han', 'HanXRQChr06g0174391' => 'han', 'HanXRQChr07g0199021' => 'han', 'HanXRQChr08g0208211' => 'han', 'HanXRQChr09g0255471' => 'han', 'HanXRQChr10g0315791' => 'han', 'HanXRQChr12g0371991' => 'han', 'HanXRQChr15g0475251' => 'han', 'HanXRQChr17g0540001' => 'han', 'HanXRQChr17g0548631' => 'han', 'HanXRQChr17g0569561' => 'han', 'Haze_12256' => 'cav', 'Haze_14756' => 'cav', 'Haze_25528' => 'cav', 'Hma1.2p1_0079F.1_g041020' => 'hma', 'Hma1.2p1_0818F.1_g223260' => 'hma', 'Hma1.2p1_1747F.1_g300530' => 'hma', 'HPP92_004607' => 'vpl', 'HPP92_004608' => 'vpl', 'HPP92_006181' => 'vpl', 'HPP92_012192' => 'vpl', 'HPP92_015680' => 'vpl', 'HPP92_020249' => 'vpl', 'HPP92_021376' => 'vpl', 'HPP92_024275' => 'vpl', 'Hund06031' => 'sun', 'Hund25391' => 'sun', 'Lalb_Chr07g0185371' => 'lal', 'Lalb_Chr07g0185381' => 'lal', 'Lalb_Chr12g0204011' => 'lal', 'Lalb_Chr13g0301671' => 'lal', 'Lalb_Chr14g0362851' => 'lal', 'Lalb_Chr24g0403581' => 'lal', 'Lj1g0000233' => 'lja', 'Lj2g0018120' => 'lja', 'Lj3C621T0' => 'lonja', 'Lj3P1059T14' => 'lonja', 'Lj3P611T9' => 'lonja', 'Lj3P614T13' => 'lonja', 'Lj3P615T5' => 'lonja', 'Lj4g0012315' => 'lja', 'Lj4g0026182' => 'lja', 'Lj6P813T16' => 'lonja', 'Lj7C427T7' => 'lonja', 'Lj7C427T8' => 'lonja', 'Lj7P600T41' => 'lonja', 'Lju41C42G17' => 'lonja', 'Lsat_1_v5_gn_0_47300' => 'lsa', 'Lsat_1_v5_gn_2_91280' => 'lsa', 'Lsat_1_v5_gn_3_30561' => 'lsa', 'Lsat_1_v5_gn_4_184321' => 'lsa', 'Lsat_1_v5_gn_4_4041' => 'lsa', 'Lsat_1_v5_gn_5_92000' => 'lsa', 'Lsat_1_v5_gn_8_152940' => 'lsa', 'Lsat_1_v5_gn_8_62401' => 'lsa', 'Manes.06G055900' => 'mes', 'Manes.12G022200' => 'mes', 'Manes.13G023300' => 'mes', 'Manes.14G115000' => 'mes', 'Manes.15G151700' => 'mes', 'Manes.17G111300' => 'mes', 'Mapoly0226s0009' => 'mpo', 'MBI02_g25363_MAGBIO' => 'mbi', 'MBI06_g00027_MAGBIO' => 'mbi', 'MBI10_g13034_MAGBIO' => 'mbi', 'MD09G1023400' => 'mdo', 'MD13G1100100' => 'mdo', 'MD15G1169200' => 'mdo', 'MD16G1101100' => 'mdo', 'MD17G1022900' => 'mdo', 'Medtr3g096150' => 'mtr', 'Medtr4g115070' => 'mtr', 'Medtr7g033325' => 'mtr', 'Medtr8g089840' => 'mtr', 'MELO3C010319.2' => 'cme', 'MELO3C011944.2' => 'cme', 'MELO3C021589.2' => 'cme', 'Migut.E00207' => 'egut', 'Migut.H00067' => 'egut', 'Migut.K00433' => 'egut', 'Migut.K00606' => 'egut', 'Migut.K01410' => 'egut', 'MSTRG.13347' => 'ama', 'MSTRG.24045' => 'ama', 'MSTRG.2428' => 'ama', 'MSTRG.26410' => 'ama', 'MSTRG.3139' => 'ama', 'MSTRG.3286' => 'ama', 'MSTRG.563' => 'ama', 'MSTRG.7941' => 'ama', 'Nitab4.5_0000028g0060' => 'nta', 'Nitab4.5_0000065g0260' => 'nta', 'Nitab4.5_0000112g0060' => 'nta', 'Nitab4.5_0000489g0120' => 'nta', 'Nitab4.5_0001776g0050' => 'nta', 'Nitab4.5_0001854g0010' => 'nta', 'Nitab4.5_0001860g0020' => 'nta', 'Nitab4.5_0004352g0010' => 'nta', 'Nitab4.5_0008716g0020' => 'nta', 'Nitab4.5_0008922g0010' => 'nta', 'Nn3g16693' => 'nnu', 'Nn4g22596' => 'nnu', 'Nn7g37639' => 'nnu', 'Oeu001701.1' => 'oeu', 'Oeu018149.1' => 'oeu', 'Oeu026220.1' => 'oeu', 'Oeu038635.1' => 'oeu', 'Oeu049176.1' => 'oeu', 'Oeu056706.1' => 'oeu', 'Oeu056937.1' => 'oeu', 'Oeu057540.1' => 'oeu', 'Os02g0594900' => 'osa', 'Os02g0595100' => 'osa', 'Os04g0477500' => 'osa', 'Os12g0611900' => 'osa', 'Peaxi162Scf00076g00020' => 'pax', 'Peaxi162Scf00128g00217' => 'pax', 'Peaxi162Scf00129g01640' => 'pax', 'Peaxi162Scf00669g00007' => 'pax', 'Peaxi162Scf00700g00421' => 'pax', 'Peaxi162Scf00801g00038' => 'pax', 'Peaxi162Scf00891g00025' => 'pax', 'PGR083G0909' => 'pgr', 'PGR119G1005' => 'pgr', 'PGR142G2236' => 'pgr', 'PGR142G3388' => 'pgr', 'PGSC0003DMG400004514' => 'stu', 'PGSC0003DMG400012635' => 'stu', 'PGSC0003DMG400015730' => 'stu', 'PGSC0003DMG400018611' => 'stu', 'PGSC0003DMG400030897' => 'stu', 'Phvul.001G254800' => 'pvu', 'Phvul.002G260100' => 'pvu', 'Phvul.003G167600' => 'pvu', 'Phvul.004G005100' => 'pvu', 'Potri.001G343600' => 'ptr', 'Potri.006G066700' => 'ptr', 'Potri.008G186000' => 'ptr', 'Potri.010G046900' => 'ptr', 'Potri.018G127900' => 'ptr', 'Pp3c20_17750' => 'ppa', 'Pp3c24_4380' => 'ppa', 'Prupe.1G245800' => 'ppe', 'Prupe.3G293400' => 'ppe', 'Prupe.7G247400' => 'ppe', 'Psat0s145g0120' => 'psa', 'Psat0s595g0040' => 'psa', 'Psat0s595g0120' => 'psa', 'Psat3g175040' => 'psa', 'Psat7g058120' => 'psa', 'PSO017G0428' => 'pso', 'PSO063G7510' => 'pso', 'PSO067G0046' => 'pso', 'PSO478G1073' => 'pso', 'PSO675G3677' => 'pso', 'PSO675G6558' => 'pso', 'PSO675G7520' => 'pso', 'PSO675G8959' => 'pso', 'QL02p074089' => 'qlo', 'QL02p089614' => 'qlo', 'QL03p057736' => 'qlo', 'RcHm_v2.0_Chr1g0364131' => 'rch', 'RcHm_v2.0_Chr2g0087801' => 'rch', 'RcHm_v2.0_Chr2g0087821' => 'rch', 'RcHm_v2.0_Chr2g0173231' => 'rch', 'RcHm_v2.0_Chr4g0433111' => 'rch', 'Rhsim03G0250300' => 'rsi', 'Rhsim08G0048400' => 'rsi', 'Rhsim10G0014800' => 'rsi', 'Rhsim12G0040100' => 'rsi', 'Rhsim12G0109700' => 'rsi', 'Sabra06G0049600' => 'sbr', 'Sabra08G0141000' => 'sbr', 'Sabra10G0021400' => 'sbr', 'Sabra16G0222900' => 'sbr', 'Sabra18G0108600' => 'sbr', 'SalBow1G0433' => 'sbo', 'SalBow1G2038' => 'sbo', 'SalBow1G5003' => 'sbo', 'SalBow7G1197' => 'sbo', 'SalBow8G3506' => 'sbo', 'Sc03g0007300' => 'sci', 'Sc11g0000950' => 'sci', 'Sc14g0008750' => 'sci', 'Sc18g0000420' => 'sci', 'Sed0006754' => 'sed', 'Sed0008741' => 'sed', 'Sed0017172' => 'sed', 'Sed0018925' => 'sed', 'Sed0023326' => 'sed', 'Sed0025909' => 'sed', 'SEGI_05333' => 'sgi', 'SEGI_10362' => 'sgi', 'SEGI_13380' => 'sgi', 'SEGI_24306' => 'sgi', 'SEGI_29077' => 'sgi', 'SEGI_29095' => 'sgi', 'SEGI_36534' => 'sgi', 'SEGI_37506' => 'sgi', 'SEGI_38321' => 'sgi', 'SGA_v2.0_scaffold307G48031' => 'sas', 'SGA_v2.0_scaffold47G17507' => 'sas', 'SGA_v2.0_scaffold63G21736' => 'sas', 'SGA_v2.0_scaffold87G27070' => 'sas', 'SHI17794' => 'shi', 'SHI28851' => 'shi', 'SMO165G0155' => 'smo', 'SMO340G0217' => 'smo', 'SMO367G1210' => 'smo', 'Solyc02g093430.3' => 'sly', 'Solyc05g013580.4' => 'sly', 'Solyc07g008030.3' => 'sly', 'Solyc12g035470.2' => 'sly', 'Sopen02g038020' => 'spe', 'Sopen05g008490' => 'spe', 'Sopen07g003910' => 'spe', 'Sopen12g015240' => 'spe', 'Sp1g11550' => 'spa', 'Sp2g16710' => 'spa', 'Sp3g00430' => 'spa', 'Sp3g26780' => 'spa', 'Sp5g22900' => 'spa', 'Sp6g29530' => 'spa', 'TAR371G0794' => 'tar', 'TAR374G0164' => 'tar', 'TAR622G0165' => 'tar', 'TAR626G0929' => 'tar', 'TAR629G2155' => 'tar', 'THA.LOC104805282' => 'tha', 'THA.LOC104805363' => 'tha', 'THA.LOC104808968' => 'tha', 'THA.LOC104821093' => 'tha', 'THA.LOC104823953' => 'tha', 'THA.LOC104825562' => 'tha', 'THA.LOC104825665' => 'tha', 'Thecc.02G261400' => 'tca', 'Thecc.04G019200' => 'tca', 'Thecc.09G130400' => 'tca', 'Thhalv10004374m.g' => 'esa', 'Thhalv10007850m.g' => 'esa', 'Thhalv10013782m.g' => 'esa', 'Thhalv10018686m.g' => 'esa', 'Thhalv10020899m.g' => 'esa', 'Thhalv10022755m.g' => 'esa', 'TPR.G23851' => 'tpr', 'TPR.G26500' => 'tpr', 'TPR.G27267' => 'tpr', 'TPR.G32001' => 'tpr', 'TPR.G6251' => 'tpr', 'TPR.G8167' => 'tpr', 'TWI12G1330' => 'twi', 'TWI18G1239' => 'twi', 'TWI34G0979' => 'twi', 'TWI36G0670' => 'twi', 'TWI36G0707' => 'twi', 'TWI56G0233' => 'twi', 'TWI75G1809' => 'twi', 'unitig_21.g20874' => 'ugi', 'unitig_26.g10343' => 'ugi', 'unitig_46.g18392' => 'ugi', 'unitig_52.g17178' => 'ugi', 'unitig_8.g2934' => 'ugi', 'vmacro01122' => 'vma', 'vmacro05875' => 'vma', 'vmacro06147' => 'vma', 'vmacro16191' => 'vma', 'vmacro18293' => 'vma', 'VMungo0251G3707' => 'vmu', 'VMungo0464G1521' => 'vmu', 'VMungo1215G0205' => 'vmu', 'VMungo1383G2484' => 'vmu', 'Zm00001eb079610' => 'zma', 'Zm00001eb135990' => 'zma', 'Zm00001eb183710' => 'zma', 'Zm00001eb246020' => 'zma' ) $gf_id = 'HOM05D001124' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001124' ) $data_identifier = 'HOM05D001124' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 6, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 7, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 21, 'bol' => (int) 10, 'bra' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 6, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 9, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 21, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 8, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 10, 'lsa' => (int) 8, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 8, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 9, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb246020' $species_info = array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ) $local_species = 'psa' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001124', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '548', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02520' => 'bna', 'A03p06630' => 'bna', 'A05p44460' => 'bna', 'A06p08710' => 'bna', 'A06p41090' => 'bna', 'A07p32320' => 'bna', 'A08p32520' => 'bna', 'A09p10360' => 'bna', 'A10p24080' => 'bna', 'Aa31LG11G15250' => 'aar', 'Aa31LG1G1800' => 'aar', 'Aa31LG2G5120' => 'aar', 'Aa31LG2G6070' => 'aar', 'Aa31LG5G10770' => 'aar', 'Aa31sc61G90' => 'aar', 'Actinidia01352' => 'ach', 'Actinidia05983' => 'ach', 'Actinidia08133' => 'ach', 'Actinidia15101' => 'ach', 'Actinidia26379' => 'ach', 'Actinidia35778' => 'ach', 'Actinidia36123' => 'ach', 'Actinidia37436' => 'ach', 'Actinidia38730' => 'ach', 'Ah.02g128210' => 'amhyb', 'Ah.03g132990' => 'amhyb', 'Ah.14g079410' => 'amhyb', 'AL1G24640' => 'aly', 'AL2G26680' => 'aly', 'AL3G10530' => 'aly', 'AL3G45230' => 'aly', 'AL5G15230' => 'aly', 'AL5G16960' => 'aly', 'AL6G25210' => 'aly', 'Aqoxy2G00441' => 'aox', 'Aqoxy3G01236' => 'aox', 'Aqoxy5G03746' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3RQ047' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C7GMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9C8JER' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MBL6KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YXCZ83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZANX40' => 'arhy', 'AT1G12990' => 'ath', 'AT1G67880' => 'ath', 'AT2G13290' => 'ath', 'AT3G01620' => 'ath', 'AT3G26445' => 'ath', 'AT3G27540' => 'ath', 'AT5G14480' => 'ath', 'ATR0824G026' => 'atr', 'ATR1098G019' => 'atr', 'Atru.chr11.2145' => 'acertr', 'Atru.chr2.3636' => 'acertr', 'Atru.chr2.3644' => 'acertr', 'Atru.chr6.2422' => 'acertr', 'Atru.chr7.1112' => 'acertr', 'AUR62005469' => 'cqu', 'AUR62011166' => 'cqu', 'AUR62013319' => 'cqu', 'AUR62024273' => 'cqu', 'AUR62028420' => 'cqu', 'AUR62041942' => 'cqu', 'BcaB01g04969' => 'bca', 'BcaB01g06371' => 'bca', 'BcaB02g11494' => 'bca', 'BcaB03g15382' => 'bca', 'BcaB08g36994' => 'bca', 'BcaC03g13477' => 'bca', 'BcaC03g13478' => 'bca', 'BcaC03g13480' => 'bca', 'BcaC03g13481' => 'bca', 'BcaC03g13486' => 'bca', 'BcaC04g19031' => 'bca', 'BcaC04g23085' => 'bca', 'BcaC05g25094' => 'bca', 'BcaC05g25096' => 'bca', 'BcaC05g25138' => 'bca', 'BcaC05g30416' => 'bca', 'BcaC05g30455' => 'bca', 'BcaC06g30979' => 'bca', 'BcaC06g33805' => 'bca', 'BcaC08g46021' => 'bca', 'BcaNung03154' => 'bca', 'BolC2t06623H' => 'bol', 'BolC2t06632H' => 'bol', 'BolC2t06635H' => 'bol', 'BolC2t06638H' => 'bol', 'BolC3t13266H' => 'bol', 'BolC5t29776H' => 'bol', 'BolC6t38912H' => 'bol', 'BolC7t44183H' => 'bol', 'BolC9t54123H' => 'bol', 'BolC9t59107H' => 'bol', 'BraA02t05221Z' => 'bra', 'BraA03t09996Z' => 'bra', 'BraA05t23210Z' => 'bra', 'BraA06t24068Z' => 'bra', 'BraA06t27032Z' => 'bra', 'BraA08t35176Z' => 'bra', 'BraA09t36680Z' => 'bra', 'BraA10t44471Z' => 'bra', 'C02p06760' => 'bna', 'C02p06890' => 'bna', 'C02p07010' => 'bna', 'C03p07660' => 'bna', 'C05p10300' => 'bna', 'C06p38150' => 'bna', 'C07p36650' => 'bna', 'C08p15770' => 'bna', 'C09p12300' => 'bna', 'C09p62700' => 'bna', 'C09p75040' => 'bna', 'CAN.G13.1' => 'can', 'CAN.G138.4' => 'can', 'CAN.G44.6' => 'can', 'CAN.G473.19' => 'can', 'CANSAT01G0835' => 'cansat', 'CANSAT11G0246' => 'cansat', 'CANSAT11G1766' => 'cansat', 'CANSAT64G1954' => 'cansat', 'CARHR013330' => 'chi', 'CARHR060530' => 'chi', 'CARHR075300' => 'chi', 'CARHR105120' => 'chi', 'CARHR148910' => 'chi', 'CARHR198830' => 'chi', 'Carub.0001s1275' => 'cru', 'Carub.0002s1437' => 'cru', 'Carub.0003s0044' => 'cru', 'Carub.0003s2787' => 'cru', 'Carub.0005s0597' => 'cru', 'Carub.0006s1266' => 'cru', 'Ca_06935_v3' => 'car', 'Ca_13559_v3' => 'car', 'Ca_16941_v3' => 'car', 'Ca_16960_v3' => 'car', 'Ca_17775_v3' => 'car', 'Ca_30464_v3' => 'car', 'Cc06_g08160' => 'ccan', 'Cc07_g01520' => 'ccan', 'Cc11_g15810' => 'ccan', 'CDE02G2840' => 'cde', 'CDE03G0093' => 'cde', 'CDE04G2127' => 'cde', 'CDE07G1857' => 'cde', 'CDE09G1246' => 'cde', 'Cfa003412' => 'cfa', 'Cfa007341' => 'cfa', 'Cfa009220' => 'cfa', 'Ciclev10008737m.g' => 'ccl', 'Ciclev10015565m.g' => 'ccl', 'Ciclev10031761m.g' => 'ccl', 'CiPaw.03G045300' => 'cil', 'CiPaw.03G247200' => 'cil', 'CiPaw.04G029500' => 'cil', 'CiPaw.04G174000' => 'cil', 'CiPaw.05G181200' => 'cil', 'CiPaw.06G067100' => 'cil', 'ClCG05G025800' => 'cla', 'ClCG06G011400' => 'cla', 'ClCG09G019360' => 'cla', 'COL.COLO4_04827' => 'col', 'COL.COLO4_29170' => 'col', 'COL.COLO4_35131' => 'col', 'COL.COLO4_35132' => 'col', 'Cpa.g.sc33.32' => 'cpa', 'Cpa.g.sc46.29' => 'cpa', 'Cpa.g.sc796.1' => 'cpa', 'CsaV3_1G030420' => 'csa', 'CsaV3_5G027050' => 'csa', 'CsaV3_5G031040' => 'csa', 'CsaV3_UNG023130' => 'csa', 'CSS0007726' => 'camsi', 'CSS0016433' => 'camsi', 'CSS0017656' => 'camsi', 'CSS0025364' => 'camsi', 'CSS0027582' => 'camsi', 'CSS0047288' => 'camsi', 'CSS0049950' => 'camsi', 'DCAR_003843' => 'dca', 'DCAR_007052' => 'dca', 'DCAR_020884' => 'dca', 'DCAR_021730' => 'dca', 'DCAR_024423' => 'dca', 'DCAR_026509' => 'dca', 'DCAR_031158' => 'dca', 'Dinv14728' => 'din', 'Dinv15219' => 'din', 'Dinv25728' => 'din', 'Dinv33428' => 'din', 'Dinv36489' => 'din', 'Dinv41486' => 'din', 'Duzib147G0469' => 'dzi', 'Duzib168G0060' => 'dzi', 'Duzib187G1215' => 'dzi', 'Duzib248G0692' => 'dzi', 'Duzib251G0767' => 'dzi', 'Duzib264G0446' => 'dzi', 'Duzib268G0691' => 'dzi', 'ECA232G4767' => 'eca', 'ECA233G2838' => 'eca', 'ECA234G0391' => 'eca', 'ECA234G0857' => 'eca', 'ECA236G1593' => 'eca', 'ECA238G0565' => 'eca', 'ECA246G1027' => 'eca', 'ECA246G3223' => 'eca', 'ECA246G3470' => 'eca', 'EL10Ac6g13829' => 'bvu', 'EL10Ac6g14093' => 'bvu', 'EL10Ac8g18707' => 'bvu', 'Eucgr.C01369' => 'egr', 'Eucgr.H02492' => 'egr', 'Eucgr.I01733' => 'egr', 'Eucgr.J02255' => 'egr', 'Eucgr.J02257' => 'egr', 'Eucgr.J02258' => 'egr', 'FAN02G1601' => 'fan', 'FAN03G1586' => 'fan', 'FAN03G2986' => 'fan', 'FAN05G4837' => 'fan', 'FAN06G0146' => 'fan', 'FAN07G0858' => 'fan', 'FAN09G3179' => 'fan', 'FAN10G0669' => 'fan', 'FAN12G2358' => 'fan', 'FAN14G4198' => 'fan', 'FAN14G5112' => 'fan', 'FAN17G0342' => 'fan', 'FAN19G0342' => 'fan', 'FAN19G0962' => 'fan', 'FAN19G1101' => 'fan', 'FAN19G1872' => 'fan', 'FAN22G0356' => 'fan', 'FAN23G0744' => 'fan', 'FAN23G1914' => 'fan', 'FAN26G0032' => 'fan', 'FAN28G0625' => 'fan', 'FvH4_1g02710' => 'fve', 'FvH4_1g02720' => 'fve', 'FvH4_4g25670' => 'fve', 'FvH4_6g51700' => 'fve', 'FvH4_7g20170' => 'fve', 'Glyma.05G175000' => 'gma', 'Glyma.08G132300' => 'gma', 'Glyma.11G243000' => 'gma', 'Glyma.13G158900' => 'gma', 'Glyma.17G112400' => 'gma', 'Glyma.18G014100' => 'gma', 'Glyma.19G003100' => 'gma', 'Glyma.19G056500' => 'gma', 'Gohir.A01G158900' => 'ghi', 'Gohir.A05G312600' => 'ghi', 'Gohir.A05G354900' => 'ghi', 'Gohir.A07G037200' => 'ghi', 'Gohir.A09G030000' => 'ghi', 'Gohir.A12G145200' => 'ghi', 'Gohir.D01G151500' => 'ghi', 'Gohir.D04G058300' => 'ghi', 'Gohir.D05G314100' => 'ghi', 'Gohir.D07G041400' => 'ghi', 'Gohir.D09G029700' => 'ghi', 'Gohir.D12G149700' => 'ghi', 'Gorai.001G043800' => 'gra', 'Gorai.002G187800' => 'gra', 'Gorai.006G034700' => 'gra', 'Gorai.008G161200' => 'gra', 'Gorai.009G335700' => 'gra', 'Gorai.012G065000' => 'gra', 'GSVIVG01000535001' => 'vvi', 'GSVIVG01015572001' => 'vvi', 'GSVIVG01032386001' => 'vvi', 'HanXRQChr05g0138531' => 'han', 'HanXRQChr06g0174391' => 'han', 'HanXRQChr07g0199021' => 'han', 'HanXRQChr08g0208211' => 'han', 'HanXRQChr09g0255471' => 'han', 'HanXRQChr10g0315791' => 'han', 'HanXRQChr12g0371991' => 'han', 'HanXRQChr15g0475251' => 'han', 'HanXRQChr17g0540001' => 'han', 'HanXRQChr17g0548631' => 'han', 'HanXRQChr17g0569561' => 'han', 'Haze_12256' => 'cav', 'Haze_14756' => 'cav', 'Haze_25528' => 'cav', 'Hma1.2p1_0079F.1_g041020' => 'hma', 'Hma1.2p1_0818F.1_g223260' => 'hma', 'Hma1.2p1_1747F.1_g300530' => 'hma', 'HPP92_004607' => 'vpl', 'HPP92_004608' => 'vpl', 'HPP92_006181' => 'vpl', 'HPP92_012192' => 'vpl', 'HPP92_015680' => 'vpl', 'HPP92_020249' => 'vpl', 'HPP92_021376' => 'vpl', 'HPP92_024275' => 'vpl', 'Hund06031' => 'sun', 'Hund25391' => 'sun', 'Lalb_Chr07g0185371' => 'lal', 'Lalb_Chr07g0185381' => 'lal', 'Lalb_Chr12g0204011' => 'lal', 'Lalb_Chr13g0301671' => 'lal', 'Lalb_Chr14g0362851' => 'lal', 'Lalb_Chr24g0403581' => 'lal', 'Lj1g0000233' => 'lja', 'Lj2g0018120' => 'lja', 'Lj3C621T0' => 'lonja', 'Lj3P1059T14' => 'lonja', 'Lj3P611T9' => 'lonja', 'Lj3P614T13' => 'lonja', 'Lj3P615T5' => 'lonja', 'Lj4g0012315' => 'lja', 'Lj4g0026182' => 'lja', 'Lj6P813T16' => 'lonja', 'Lj7C427T7' => 'lonja', 'Lj7C427T8' => 'lonja', 'Lj7P600T41' => 'lonja', 'Lju41C42G17' => 'lonja', 'Lsat_1_v5_gn_0_47300' => 'lsa', 'Lsat_1_v5_gn_2_91280' => 'lsa', 'Lsat_1_v5_gn_3_30561' => 'lsa', 'Lsat_1_v5_gn_4_184321' => 'lsa', 'Lsat_1_v5_gn_4_4041' => 'lsa', 'Lsat_1_v5_gn_5_92000' => 'lsa', 'Lsat_1_v5_gn_8_152940' => 'lsa', 'Lsat_1_v5_gn_8_62401' => 'lsa', 'Manes.06G055900' => 'mes', 'Manes.12G022200' => 'mes', 'Manes.13G023300' => 'mes', 'Manes.14G115000' => 'mes', 'Manes.15G151700' => 'mes', 'Manes.17G111300' => 'mes', 'Mapoly0226s0009' => 'mpo', 'MBI02_g25363_MAGBIO' => 'mbi', 'MBI06_g00027_MAGBIO' => 'mbi', 'MBI10_g13034_MAGBIO' => 'mbi', 'MD09G1023400' => 'mdo', 'MD13G1100100' => 'mdo', 'MD15G1169200' => 'mdo', 'MD16G1101100' => 'mdo', 'MD17G1022900' => 'mdo', 'Medtr3g096150' => 'mtr', 'Medtr4g115070' => 'mtr', 'Medtr7g033325' => 'mtr', 'Medtr8g089840' => 'mtr', 'MELO3C010319.2' => 'cme', 'MELO3C011944.2' => 'cme', 'MELO3C021589.2' => 'cme', 'Migut.E00207' => 'egut', 'Migut.H00067' => 'egut', 'Migut.K00433' => 'egut', 'Migut.K00606' => 'egut', 'Migut.K01410' => 'egut', 'MSTRG.13347' => 'ama', 'MSTRG.24045' => 'ama', 'MSTRG.2428' => 'ama', 'MSTRG.26410' => 'ama', 'MSTRG.3139' => 'ama', 'MSTRG.3286' => 'ama', 'MSTRG.563' => 'ama', 'MSTRG.7941' => 'ama', 'Nitab4.5_0000028g0060' => 'nta', 'Nitab4.5_0000065g0260' => 'nta', 'Nitab4.5_0000112g0060' => 'nta', 'Nitab4.5_0000489g0120' => 'nta', 'Nitab4.5_0001776g0050' => 'nta', 'Nitab4.5_0001854g0010' => 'nta', 'Nitab4.5_0001860g0020' => 'nta', 'Nitab4.5_0004352g0010' => 'nta', 'Nitab4.5_0008716g0020' => 'nta', 'Nitab4.5_0008922g0010' => 'nta', 'Nn3g16693' => 'nnu', 'Nn4g22596' => 'nnu', 'Nn7g37639' => 'nnu', 'Oeu001701.1' => 'oeu', 'Oeu018149.1' => 'oeu', 'Oeu026220.1' => 'oeu', 'Oeu038635.1' => 'oeu', 'Oeu049176.1' => 'oeu', 'Oeu056706.1' => 'oeu', 'Oeu056937.1' => 'oeu', 'Oeu057540.1' => 'oeu', 'Os02g0594900' => 'osa', 'Os02g0595100' => 'osa', 'Os04g0477500' => 'osa', 'Os12g0611900' => 'osa', 'Peaxi162Scf00076g00020' => 'pax', 'Peaxi162Scf00128g00217' => 'pax', 'Peaxi162Scf00129g01640' => 'pax', 'Peaxi162Scf00669g00007' => 'pax', 'Peaxi162Scf00700g00421' => 'pax', 'Peaxi162Scf00801g00038' => 'pax', 'Peaxi162Scf00891g00025' => 'pax', 'PGR083G0909' => 'pgr', 'PGR119G1005' => 'pgr', 'PGR142G2236' => 'pgr', 'PGR142G3388' => 'pgr', 'PGSC0003DMG400004514' => 'stu', 'PGSC0003DMG400012635' => 'stu', 'PGSC0003DMG400015730' => 'stu', 'PGSC0003DMG400018611' => 'stu', 'PGSC0003DMG400030897' => 'stu', 'Phvul.001G254800' => 'pvu', 'Phvul.002G260100' => 'pvu', 'Phvul.003G167600' => 'pvu', 'Phvul.004G005100' => 'pvu', 'Potri.001G343600' => 'ptr', 'Potri.006G066700' => 'ptr', 'Potri.008G186000' => 'ptr', 'Potri.010G046900' => 'ptr', 'Potri.018G127900' => 'ptr', 'Pp3c20_17750' => 'ppa', 'Pp3c24_4380' => 'ppa', 'Prupe.1G245800' => 'ppe', 'Prupe.3G293400' => 'ppe', 'Prupe.7G247400' => 'ppe', 'Psat0s145g0120' => 'psa', 'Psat0s595g0040' => 'psa', 'Psat0s595g0120' => 'psa', 'Psat3g175040' => 'psa', 'Psat7g058120' => 'psa', 'PSO017G0428' => 'pso', 'PSO063G7510' => 'pso', 'PSO067G0046' => 'pso', 'PSO478G1073' => 'pso', 'PSO675G3677' => 'pso', 'PSO675G6558' => 'pso', 'PSO675G7520' => 'pso', 'PSO675G8959' => 'pso', 'QL02p074089' => 'qlo', 'QL02p089614' => 'qlo', 'QL03p057736' => 'qlo', 'RcHm_v2.0_Chr1g0364131' => 'rch', 'RcHm_v2.0_Chr2g0087801' => 'rch', 'RcHm_v2.0_Chr2g0087821' => 'rch', 'RcHm_v2.0_Chr2g0173231' => 'rch', 'RcHm_v2.0_Chr4g0433111' => 'rch', 'Rhsim03G0250300' => 'rsi', 'Rhsim08G0048400' => 'rsi', 'Rhsim10G0014800' => 'rsi', 'Rhsim12G0040100' => 'rsi', 'Rhsim12G0109700' => 'rsi', 'Sabra06G0049600' => 'sbr', 'Sabra08G0141000' => 'sbr', 'Sabra10G0021400' => 'sbr', 'Sabra16G0222900' => 'sbr', 'Sabra18G0108600' => 'sbr', 'SalBow1G0433' => 'sbo', 'SalBow1G2038' => 'sbo', 'SalBow1G5003' => 'sbo', 'SalBow7G1197' => 'sbo', 'SalBow8G3506' => 'sbo', 'Sc03g0007300' => 'sci', 'Sc11g0000950' => 'sci', 'Sc14g0008750' => 'sci', 'Sc18g0000420' => 'sci', 'Sed0006754' => 'sed', 'Sed0008741' => 'sed', 'Sed0017172' => 'sed', 'Sed0018925' => 'sed', 'Sed0023326' => 'sed', 'Sed0025909' => 'sed', 'SEGI_05333' => 'sgi', 'SEGI_10362' => 'sgi', 'SEGI_13380' => 'sgi', 'SEGI_24306' => 'sgi', 'SEGI_29077' => 'sgi', 'SEGI_29095' => 'sgi', 'SEGI_36534' => 'sgi', 'SEGI_37506' => 'sgi', 'SEGI_38321' => 'sgi', 'SGA_v2.0_scaffold307G48031' => 'sas', 'SGA_v2.0_scaffold47G17507' => 'sas', 'SGA_v2.0_scaffold63G21736' => 'sas', 'SGA_v2.0_scaffold87G27070' => 'sas', 'SHI17794' => 'shi', 'SHI28851' => 'shi', 'SMO165G0155' => 'smo', 'SMO340G0217' => 'smo', 'SMO367G1210' => 'smo', 'Solyc02g093430.3' => 'sly', 'Solyc05g013580.4' => 'sly', 'Solyc07g008030.3' => 'sly', 'Solyc12g035470.2' => 'sly', 'Sopen02g038020' => 'spe', 'Sopen05g008490' => 'spe', 'Sopen07g003910' => 'spe', 'Sopen12g015240' => 'spe', 'Sp1g11550' => 'spa', 'Sp2g16710' => 'spa', 'Sp3g00430' => 'spa', 'Sp3g26780' => 'spa', 'Sp5g22900' => 'spa', 'Sp6g29530' => 'spa', 'TAR371G0794' => 'tar', 'TAR374G0164' => 'tar', 'TAR622G0165' => 'tar', 'TAR626G0929' => 'tar', 'TAR629G2155' => 'tar', 'THA.LOC104805282' => 'tha', 'THA.LOC104805363' => 'tha', 'THA.LOC104808968' => 'tha', 'THA.LOC104821093' => 'tha', 'THA.LOC104823953' => 'tha', 'THA.LOC104825562' => 'tha', 'THA.LOC104825665' => 'tha', 'Thecc.02G261400' => 'tca', 'Thecc.04G019200' => 'tca', 'Thecc.09G130400' => 'tca', 'Thhalv10004374m.g' => 'esa', 'Thhalv10007850m.g' => 'esa', 'Thhalv10013782m.g' => 'esa', 'Thhalv10018686m.g' => 'esa', 'Thhalv10020899m.g' => 'esa', 'Thhalv10022755m.g' => 'esa', 'TPR.G23851' => 'tpr', 'TPR.G26500' => 'tpr', 'TPR.G27267' => 'tpr', 'TPR.G32001' => 'tpr', 'TPR.G6251' => 'tpr', 'TPR.G8167' => 'tpr', 'TWI12G1330' => 'twi', 'TWI18G1239' => 'twi', 'TWI34G0979' => 'twi', 'TWI36G0670' => 'twi', 'TWI36G0707' => 'twi', 'TWI56G0233' => 'twi', 'TWI75G1809' => 'twi', 'unitig_21.g20874' => 'ugi', 'unitig_26.g10343' => 'ugi', 'unitig_46.g18392' => 'ugi', 'unitig_52.g17178' => 'ugi', 'unitig_8.g2934' => 'ugi', 'vmacro01122' => 'vma', 'vmacro05875' => 'vma', 'vmacro06147' => 'vma', 'vmacro16191' => 'vma', 'vmacro18293' => 'vma', 'VMungo0251G3707' => 'vmu', 'VMungo0464G1521' => 'vmu', 'VMungo1215G0205' => 'vmu', 'VMungo1383G2484' => 'vmu', 'Zm00001eb079610' => 'zma', 'Zm00001eb135990' => 'zma', 'Zm00001eb183710' => 'zma', 'Zm00001eb246020' => 'zma' ), 'gf_id' => 'HOM05D001124', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001124' ), 'data_identifier' => 'HOM05D001124', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001124', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '548', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02520' => 'bna', 'A03p06630' => 'bna', 'A05p44460' => 'bna', 'A06p08710' => 'bna', 'A06p41090' => 'bna', 'A07p32320' => 'bna', 'A08p32520' => 'bna', 'A09p10360' => 'bna', 'A10p24080' => 'bna', 'Aa31LG11G15250' => 'aar', 'Aa31LG1G1800' => 'aar', 'Aa31LG2G5120' => 'aar', 'Aa31LG2G6070' => 'aar', 'Aa31LG5G10770' => 'aar', 'Aa31sc61G90' => 'aar', 'Actinidia01352' => 'ach', 'Actinidia05983' => 'ach', 'Actinidia08133' => 'ach', 'Actinidia15101' => 'ach', 'Actinidia26379' => 'ach', 'Actinidia35778' => 'ach', 'Actinidia36123' => 'ach', 'Actinidia37436' => 'ach', 'Actinidia38730' => 'ach', 'Ah.02g128210' => 'amhyb', 'Ah.03g132990' => 'amhyb', 'Ah.14g079410' => 'amhyb', 'AL1G24640' => 'aly', 'AL2G26680' => 'aly', 'AL3G10530' => 'aly', 'AL3G45230' => 'aly', 'AL5G15230' => 'aly', 'AL5G16960' => 'aly', 'AL6G25210' => 'aly', 'Aqoxy2G00441' => 'aox', 'Aqoxy3G01236' => 'aox', 'Aqoxy5G03746' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3RQ047' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C7GMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9C8JER' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MBL6KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YXCZ83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZANX40' => 'arhy', 'AT1G12990' => 'ath', 'AT1G67880' => 'ath', 'AT2G13290' => 'ath', 'AT3G01620' => 'ath', 'AT3G26445' => 'ath', 'AT3G27540' => 'ath', 'AT5G14480' => 'ath', 'ATR0824G026' => 'atr', 'ATR1098G019' => 'atr', 'Atru.chr11.2145' => 'acertr', 'Atru.chr2.3636' => 'acertr', 'Atru.chr2.3644' => 'acertr', 'Atru.chr6.2422' => 'acertr', 'Atru.chr7.1112' => 'acertr', 'AUR62005469' => 'cqu', 'AUR62011166' => 'cqu', 'AUR62013319' => 'cqu', 'AUR62024273' => 'cqu', 'AUR62028420' => 'cqu', 'AUR62041942' => 'cqu', 'BcaB01g04969' => 'bca', 'BcaB01g06371' => 'bca', 'BcaB02g11494' => 'bca', 'BcaB03g15382' => 'bca', 'BcaB08g36994' => 'bca', 'BcaC03g13477' => 'bca', 'BcaC03g13478' => 'bca', 'BcaC03g13480' => 'bca', 'BcaC03g13481' => 'bca', 'BcaC03g13486' => 'bca', 'BcaC04g19031' => 'bca', 'BcaC04g23085' => 'bca', 'BcaC05g25094' => 'bca', 'BcaC05g25096' => 'bca', 'BcaC05g25138' => 'bca', 'BcaC05g30416' => 'bca', 'BcaC05g30455' => 'bca', 'BcaC06g30979' => 'bca', 'BcaC06g33805' => 'bca', 'BcaC08g46021' => 'bca', 'BcaNung03154' => 'bca', 'BolC2t06623H' => 'bol', 'BolC2t06632H' => 'bol', 'BolC2t06635H' => 'bol', 'BolC2t06638H' => 'bol', 'BolC3t13266H' => 'bol', 'BolC5t29776H' => 'bol', 'BolC6t38912H' => 'bol', 'BolC7t44183H' => 'bol', 'BolC9t54123H' => 'bol', 'BolC9t59107H' => 'bol', 'BraA02t05221Z' => 'bra', 'BraA03t09996Z' => 'bra', 'BraA05t23210Z' => 'bra', 'BraA06t24068Z' => 'bra', 'BraA06t27032Z' => 'bra', 'BraA08t35176Z' => 'bra', 'BraA09t36680Z' => 'bra', 'BraA10t44471Z' => 'bra', 'C02p06760' => 'bna', 'C02p06890' => 'bna', 'C02p07010' => 'bna', 'C03p07660' => 'bna', 'C05p10300' => 'bna', 'C06p38150' => 'bna', 'C07p36650' => 'bna', 'C08p15770' => 'bna', 'C09p12300' => 'bna', 'C09p62700' => 'bna', 'C09p75040' => 'bna', 'CAN.G13.1' => 'can', 'CAN.G138.4' => 'can', 'CAN.G44.6' => 'can', 'CAN.G473.19' => 'can', 'CANSAT01G0835' => 'cansat', 'CANSAT11G0246' => 'cansat', 'CANSAT11G1766' => 'cansat', 'CANSAT64G1954' => 'cansat', 'CARHR013330' => 'chi', 'CARHR060530' => 'chi', 'CARHR075300' => 'chi', 'CARHR105120' => 'chi', 'CARHR148910' => 'chi', 'CARHR198830' => 'chi', 'Carub.0001s1275' => 'cru', 'Carub.0002s1437' => 'cru', 'Carub.0003s0044' => 'cru', 'Carub.0003s2787' => 'cru', 'Carub.0005s0597' => 'cru', 'Carub.0006s1266' => 'cru', 'Ca_06935_v3' => 'car', 'Ca_13559_v3' => 'car', 'Ca_16941_v3' => 'car', 'Ca_16960_v3' => 'car', 'Ca_17775_v3' => 'car', 'Ca_30464_v3' => 'car', 'Cc06_g08160' => 'ccan', 'Cc07_g01520' => 'ccan', 'Cc11_g15810' => 'ccan', 'CDE02G2840' => 'cde', 'CDE03G0093' => 'cde', 'CDE04G2127' => 'cde', 'CDE07G1857' => 'cde', 'CDE09G1246' => 'cde', 'Cfa003412' => 'cfa', 'Cfa007341' => 'cfa', 'Cfa009220' => 'cfa', 'Ciclev10008737m.g' => 'ccl', 'Ciclev10015565m.g' => 'ccl', 'Ciclev10031761m.g' => 'ccl', 'CiPaw.03G045300' => 'cil', 'CiPaw.03G247200' => 'cil', 'CiPaw.04G029500' => 'cil', 'CiPaw.04G174000' => 'cil', 'CiPaw.05G181200' => 'cil', 'CiPaw.06G067100' => 'cil', 'ClCG05G025800' => 'cla', 'ClCG06G011400' => 'cla', 'ClCG09G019360' => 'cla', 'COL.COLO4_04827' => 'col', 'COL.COLO4_29170' => 'col', 'COL.COLO4_35131' => 'col', 'COL.COLO4_35132' => 'col', 'Cpa.g.sc33.32' => 'cpa', 'Cpa.g.sc46.29' => 'cpa', 'Cpa.g.sc796.1' => 'cpa', 'CsaV3_1G030420' => 'csa', 'CsaV3_5G027050' => 'csa', 'CsaV3_5G031040' => 'csa', 'CsaV3_UNG023130' => 'csa', 'CSS0007726' => 'camsi', 'CSS0016433' => 'camsi', 'CSS0017656' => 'camsi', 'CSS0025364' => 'camsi', 'CSS0027582' => 'camsi', 'CSS0047288' => 'camsi', 'CSS0049950' => 'camsi', 'DCAR_003843' => 'dca', 'DCAR_007052' => 'dca', 'DCAR_020884' => 'dca', 'DCAR_021730' => 'dca', 'DCAR_024423' => 'dca', 'DCAR_026509' => 'dca', 'DCAR_031158' => 'dca', 'Dinv14728' => 'din', 'Dinv15219' => 'din', 'Dinv25728' => 'din', 'Dinv33428' => 'din', 'Dinv36489' => 'din', 'Dinv41486' => 'din', 'Duzib147G0469' => 'dzi', 'Duzib168G0060' => 'dzi', 'Duzib187G1215' => 'dzi', 'Duzib248G0692' => 'dzi', 'Duzib251G0767' => 'dzi', 'Duzib264G0446' => 'dzi', 'Duzib268G0691' => 'dzi', 'ECA232G4767' => 'eca', 'ECA233G2838' => 'eca', 'ECA234G0391' => 'eca', 'ECA234G0857' => 'eca', 'ECA236G1593' => 'eca', 'ECA238G0565' => 'eca', 'ECA246G1027' => 'eca', 'ECA246G3223' => 'eca', 'ECA246G3470' => 'eca', 'EL10Ac6g13829' => 'bvu', 'EL10Ac6g14093' => 'bvu', 'EL10Ac8g18707' => 'bvu', 'Eucgr.C01369' => 'egr', 'Eucgr.H02492' => 'egr', 'Eucgr.I01733' => 'egr', 'Eucgr.J02255' => 'egr', 'Eucgr.J02257' => 'egr', 'Eucgr.J02258' => 'egr', 'FAN02G1601' => 'fan', 'FAN03G1586' => 'fan', 'FAN03G2986' => 'fan', 'FAN05G4837' => 'fan', 'FAN06G0146' => 'fan', 'FAN07G0858' => 'fan', 'FAN09G3179' => 'fan', 'FAN10G0669' => 'fan', 'FAN12G2358' => 'fan', 'FAN14G4198' => 'fan', 'FAN14G5112' => 'fan', 'FAN17G0342' => 'fan', 'FAN19G0342' => 'fan', 'FAN19G0962' => 'fan', 'FAN19G1101' => 'fan', 'FAN19G1872' => 'fan', 'FAN22G0356' => 'fan', 'FAN23G0744' => 'fan', 'FAN23G1914' => 'fan', 'FAN26G0032' => 'fan', 'FAN28G0625' => 'fan', 'FvH4_1g02710' => 'fve', 'FvH4_1g02720' => 'fve', 'FvH4_4g25670' => 'fve', 'FvH4_6g51700' => 'fve', 'FvH4_7g20170' => 'fve', 'Glyma.05G175000' => 'gma', 'Glyma.08G132300' => 'gma', 'Glyma.11G243000' => 'gma', 'Glyma.13G158900' => 'gma', 'Glyma.17G112400' => 'gma', 'Glyma.18G014100' => 'gma', 'Glyma.19G003100' => 'gma', 'Glyma.19G056500' => 'gma', 'Gohir.A01G158900' => 'ghi', 'Gohir.A05G312600' => 'ghi', 'Gohir.A05G354900' => 'ghi', 'Gohir.A07G037200' => 'ghi', 'Gohir.A09G030000' => 'ghi', 'Gohir.A12G145200' => 'ghi', 'Gohir.D01G151500' => 'ghi', 'Gohir.D04G058300' => 'ghi', 'Gohir.D05G314100' => 'ghi', 'Gohir.D07G041400' => 'ghi', 'Gohir.D09G029700' => 'ghi', 'Gohir.D12G149700' => 'ghi', 'Gorai.001G043800' => 'gra', 'Gorai.002G187800' => 'gra', 'Gorai.006G034700' => 'gra', 'Gorai.008G161200' => 'gra', 'Gorai.009G335700' => 'gra', 'Gorai.012G065000' => 'gra', 'GSVIVG01000535001' => 'vvi', 'GSVIVG01015572001' => 'vvi', 'GSVIVG01032386001' => 'vvi', 'HanXRQChr05g0138531' => 'han', 'HanXRQChr06g0174391' => 'han', 'HanXRQChr07g0199021' => 'han', 'HanXRQChr08g0208211' => 'han', 'HanXRQChr09g0255471' => 'han', 'HanXRQChr10g0315791' => 'han', 'HanXRQChr12g0371991' => 'han', 'HanXRQChr15g0475251' => 'han', 'HanXRQChr17g0540001' => 'han', 'HanXRQChr17g0548631' => 'han', 'HanXRQChr17g0569561' => 'han', 'Haze_12256' => 'cav', 'Haze_14756' => 'cav', 'Haze_25528' => 'cav', 'Hma1.2p1_0079F.1_g041020' => 'hma', 'Hma1.2p1_0818F.1_g223260' => 'hma', 'Hma1.2p1_1747F.1_g300530' => 'hma', 'HPP92_004607' => 'vpl', 'HPP92_004608' => 'vpl', 'HPP92_006181' => 'vpl', 'HPP92_012192' => 'vpl', 'HPP92_015680' => 'vpl', 'HPP92_020249' => 'vpl', 'HPP92_021376' => 'vpl', 'HPP92_024275' => 'vpl', 'Hund06031' => 'sun', 'Hund25391' => 'sun', 'Lalb_Chr07g0185371' => 'lal', 'Lalb_Chr07g0185381' => 'lal', 'Lalb_Chr12g0204011' => 'lal', 'Lalb_Chr13g0301671' => 'lal', 'Lalb_Chr14g0362851' => 'lal', 'Lalb_Chr24g0403581' => 'lal', 'Lj1g0000233' => 'lja', 'Lj2g0018120' => 'lja', 'Lj3C621T0' => 'lonja', 'Lj3P1059T14' => 'lonja', 'Lj3P611T9' => 'lonja', 'Lj3P614T13' => 'lonja', 'Lj3P615T5' => 'lonja', 'Lj4g0012315' => 'lja', 'Lj4g0026182' => 'lja', 'Lj6P813T16' => 'lonja', 'Lj7C427T7' => 'lonja', 'Lj7C427T8' => 'lonja', 'Lj7P600T41' => 'lonja', 'Lju41C42G17' => 'lonja', 'Lsat_1_v5_gn_0_47300' => 'lsa', 'Lsat_1_v5_gn_2_91280' => 'lsa', 'Lsat_1_v5_gn_3_30561' => 'lsa', 'Lsat_1_v5_gn_4_184321' => 'lsa', 'Lsat_1_v5_gn_4_4041' => 'lsa', 'Lsat_1_v5_gn_5_92000' => 'lsa', 'Lsat_1_v5_gn_8_152940' => 'lsa', 'Lsat_1_v5_gn_8_62401' => 'lsa', 'Manes.06G055900' => 'mes', 'Manes.12G022200' => 'mes', 'Manes.13G023300' => 'mes', 'Manes.14G115000' => 'mes', 'Manes.15G151700' => 'mes', 'Manes.17G111300' => 'mes', 'Mapoly0226s0009' => 'mpo', 'MBI02_g25363_MAGBIO' => 'mbi', 'MBI06_g00027_MAGBIO' => 'mbi', 'MBI10_g13034_MAGBIO' => 'mbi', 'MD09G1023400' => 'mdo', 'MD13G1100100' => 'mdo', 'MD15G1169200' => 'mdo', 'MD16G1101100' => 'mdo', 'MD17G1022900' => 'mdo', 'Medtr3g096150' => 'mtr', 'Medtr4g115070' => 'mtr', 'Medtr7g033325' => 'mtr', 'Medtr8g089840' => 'mtr', 'MELO3C010319.2' => 'cme', 'MELO3C011944.2' => 'cme', 'MELO3C021589.2' => 'cme', 'Migut.E00207' => 'egut', 'Migut.H00067' => 'egut', 'Migut.K00433' => 'egut', 'Migut.K00606' => 'egut', 'Migut.K01410' => 'egut', 'MSTRG.13347' => 'ama', 'MSTRG.24045' => 'ama', 'MSTRG.2428' => 'ama', 'MSTRG.26410' => 'ama', 'MSTRG.3139' => 'ama', 'MSTRG.3286' => 'ama', 'MSTRG.563' => 'ama', 'MSTRG.7941' => 'ama', 'Nitab4.5_0000028g0060' => 'nta', 'Nitab4.5_0000065g0260' => 'nta', 'Nitab4.5_0000112g0060' => 'nta', 'Nitab4.5_0000489g0120' => 'nta', 'Nitab4.5_0001776g0050' => 'nta', 'Nitab4.5_0001854g0010' => 'nta', 'Nitab4.5_0001860g0020' => 'nta', 'Nitab4.5_0004352g0010' => 'nta', 'Nitab4.5_0008716g0020' => 'nta', 'Nitab4.5_0008922g0010' => 'nta', 'Nn3g16693' => 'nnu', 'Nn4g22596' => 'nnu', 'Nn7g37639' => 'nnu', 'Oeu001701.1' => 'oeu', 'Oeu018149.1' => 'oeu', 'Oeu026220.1' => 'oeu', 'Oeu038635.1' => 'oeu', 'Oeu049176.1' => 'oeu', 'Oeu056706.1' => 'oeu', 'Oeu056937.1' => 'oeu', 'Oeu057540.1' => 'oeu', 'Os02g0594900' => 'osa', 'Os02g0595100' => 'osa', 'Os04g0477500' => 'osa', 'Os12g0611900' => 'osa', 'Peaxi162Scf00076g00020' => 'pax', 'Peaxi162Scf00128g00217' => 'pax', 'Peaxi162Scf00129g01640' => 'pax', 'Peaxi162Scf00669g00007' => 'pax', 'Peaxi162Scf00700g00421' => 'pax', 'Peaxi162Scf00801g00038' => 'pax', 'Peaxi162Scf00891g00025' => 'pax', 'PGR083G0909' => 'pgr', 'PGR119G1005' => 'pgr', 'PGR142G2236' => 'pgr', 'PGR142G3388' => 'pgr', 'PGSC0003DMG400004514' => 'stu', 'PGSC0003DMG400012635' => 'stu', 'PGSC0003DMG400015730' => 'stu', 'PGSC0003DMG400018611' => 'stu', 'PGSC0003DMG400030897' => 'stu', 'Phvul.001G254800' => 'pvu', 'Phvul.002G260100' => 'pvu', 'Phvul.003G167600' => 'pvu', 'Phvul.004G005100' => 'pvu', 'Potri.001G343600' => 'ptr', 'Potri.006G066700' => 'ptr', 'Potri.008G186000' => 'ptr', 'Potri.010G046900' => 'ptr', 'Potri.018G127900' => 'ptr', 'Pp3c20_17750' => 'ppa', 'Pp3c24_4380' => 'ppa', 'Prupe.1G245800' => 'ppe', 'Prupe.3G293400' => 'ppe', 'Prupe.7G247400' => 'ppe', 'Psat0s145g0120' => 'psa', 'Psat0s595g0040' => 'psa', 'Psat0s595g0120' => 'psa', 'Psat3g175040' => 'psa', 'Psat7g058120' => 'psa', 'PSO017G0428' => 'pso', 'PSO063G7510' => 'pso', 'PSO067G0046' => 'pso', 'PSO478G1073' => 'pso', 'PSO675G3677' => 'pso', 'PSO675G6558' => 'pso', 'PSO675G7520' => 'pso', 'PSO675G8959' => 'pso', 'QL02p074089' => 'qlo', 'QL02p089614' => 'qlo', 'QL03p057736' => 'qlo', 'RcHm_v2.0_Chr1g0364131' => 'rch', 'RcHm_v2.0_Chr2g0087801' => 'rch', 'RcHm_v2.0_Chr2g0087821' => 'rch', 'RcHm_v2.0_Chr2g0173231' => 'rch', 'RcHm_v2.0_Chr4g0433111' => 'rch', 'Rhsim03G0250300' => 'rsi', 'Rhsim08G0048400' => 'rsi', 'Rhsim10G0014800' => 'rsi', 'Rhsim12G0040100' => 'rsi', 'Rhsim12G0109700' => 'rsi', 'Sabra06G0049600' => 'sbr', 'Sabra08G0141000' => 'sbr', 'Sabra10G0021400' => 'sbr', 'Sabra16G0222900' => 'sbr', 'Sabra18G0108600' => 'sbr', 'SalBow1G0433' => 'sbo', 'SalBow1G2038' => 'sbo', 'SalBow1G5003' => 'sbo', 'SalBow7G1197' => 'sbo', 'SalBow8G3506' => 'sbo', 'Sc03g0007300' => 'sci', 'Sc11g0000950' => 'sci', 'Sc14g0008750' => 'sci', 'Sc18g0000420' => 'sci', 'Sed0006754' => 'sed', 'Sed0008741' => 'sed', 'Sed0017172' => 'sed', 'Sed0018925' => 'sed', 'Sed0023326' => 'sed', 'Sed0025909' => 'sed', 'SEGI_05333' => 'sgi', 'SEGI_10362' => 'sgi', 'SEGI_13380' => 'sgi', 'SEGI_24306' => 'sgi', 'SEGI_29077' => 'sgi', 'SEGI_29095' => 'sgi', 'SEGI_36534' => 'sgi', 'SEGI_37506' => 'sgi', 'SEGI_38321' => 'sgi', 'SGA_v2.0_scaffold307G48031' => 'sas', 'SGA_v2.0_scaffold47G17507' => 'sas', 'SGA_v2.0_scaffold63G21736' => 'sas', 'SGA_v2.0_scaffold87G27070' => 'sas', 'SHI17794' => 'shi', 'SHI28851' => 'shi', 'SMO165G0155' => 'smo', 'SMO340G0217' => 'smo', 'SMO367G1210' => 'smo', 'Solyc02g093430.3' => 'sly', 'Solyc05g013580.4' => 'sly', 'Solyc07g008030.3' => 'sly', 'Solyc12g035470.2' => 'sly', 'Sopen02g038020' => 'spe', 'Sopen05g008490' => 'spe', 'Sopen07g003910' => 'spe', 'Sopen12g015240' => 'spe', 'Sp1g11550' => 'spa', 'Sp2g16710' => 'spa', 'Sp3g00430' => 'spa', 'Sp3g26780' => 'spa', 'Sp5g22900' => 'spa', 'Sp6g29530' => 'spa', 'TAR371G0794' => 'tar', 'TAR374G0164' => 'tar', 'TAR622G0165' => 'tar', 'TAR626G0929' => 'tar', 'TAR629G2155' => 'tar', 'THA.LOC104805282' => 'tha', 'THA.LOC104805363' => 'tha', 'THA.LOC104808968' => 'tha', 'THA.LOC104821093' => 'tha', 'THA.LOC104823953' => 'tha', 'THA.LOC104825562' => 'tha', 'THA.LOC104825665' => 'tha', 'Thecc.02G261400' => 'tca', 'Thecc.04G019200' => 'tca', 'Thecc.09G130400' => 'tca', 'Thhalv10004374m.g' => 'esa', 'Thhalv10007850m.g' => 'esa', 'Thhalv10013782m.g' => 'esa', 'Thhalv10018686m.g' => 'esa', 'Thhalv10020899m.g' => 'esa', 'Thhalv10022755m.g' => 'esa', 'TPR.G23851' => 'tpr', 'TPR.G26500' => 'tpr', 'TPR.G27267' => 'tpr', 'TPR.G32001' => 'tpr', 'TPR.G6251' => 'tpr', 'TPR.G8167' => 'tpr', 'TWI12G1330' => 'twi', 'TWI18G1239' => 'twi', 'TWI34G0979' => 'twi', 'TWI36G0670' => 'twi', 'TWI36G0707' => 'twi', 'TWI56G0233' => 'twi', 'TWI75G1809' => 'twi', 'unitig_21.g20874' => 'ugi', 'unitig_26.g10343' => 'ugi', 'unitig_46.g18392' => 'ugi', 'unitig_52.g17178' => 'ugi', 'unitig_8.g2934' => 'ugi', 'vmacro01122' => 'vma', 'vmacro05875' => 'vma', 'vmacro06147' => 'vma', 'vmacro16191' => 'vma', 'vmacro18293' => 'vma', 'VMungo0251G3707' => 'vmu', 'VMungo0464G1521' => 'vmu', 'VMungo1215G0205' => 'vmu', 'VMungo1383G2484' => 'vmu', 'Zm00001eb079610' => 'zma', 'Zm00001eb135990' => 'zma', 'Zm00001eb183710' => 'zma', 'Zm00001eb246020' => 'zma' ) $gf_id = 'HOM05D001124' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001124' ) $data_identifier = 'HOM05D001124' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 6, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 7, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 21, 'bol' => (int) 10, 'bra' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 6, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 9, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 21, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 8, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 10, 'lsa' => (int) 8, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 8, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 9, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb246020' $species_info = array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ) $local_species = 'psa' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001124', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '548', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02520' => 'bna', 'A03p06630' => 'bna', 'A05p44460' => 'bna', 'A06p08710' => 'bna', 'A06p41090' => 'bna', 'A07p32320' => 'bna', 'A08p32520' => 'bna', 'A09p10360' => 'bna', 'A10p24080' => 'bna', 'Aa31LG11G15250' => 'aar', 'Aa31LG1G1800' => 'aar', 'Aa31LG2G5120' => 'aar', 'Aa31LG2G6070' => 'aar', 'Aa31LG5G10770' => 'aar', 'Aa31sc61G90' => 'aar', 'Actinidia01352' => 'ach', 'Actinidia05983' => 'ach', 'Actinidia08133' => 'ach', 'Actinidia15101' => 'ach', 'Actinidia26379' => 'ach', 'Actinidia35778' => 'ach', 'Actinidia36123' => 'ach', 'Actinidia37436' => 'ach', 'Actinidia38730' => 'ach', 'Ah.02g128210' => 'amhyb', 'Ah.03g132990' => 'amhyb', 'Ah.14g079410' => 'amhyb', 'AL1G24640' => 'aly', 'AL2G26680' => 'aly', 'AL3G10530' => 'aly', 'AL3G45230' => 'aly', 'AL5G15230' => 'aly', 'AL5G16960' => 'aly', 'AL6G25210' => 'aly', 'Aqoxy2G00441' => 'aox', 'Aqoxy3G01236' => 'aox', 'Aqoxy5G03746' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3RQ047' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C7GMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9C8JER' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MBL6KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YXCZ83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZANX40' => 'arhy', 'AT1G12990' => 'ath', 'AT1G67880' => 'ath', 'AT2G13290' => 'ath', 'AT3G01620' => 'ath', 'AT3G26445' => 'ath', 'AT3G27540' => 'ath', 'AT5G14480' => 'ath', 'ATR0824G026' => 'atr', 'ATR1098G019' => 'atr', 'Atru.chr11.2145' => 'acertr', 'Atru.chr2.3636' => 'acertr', 'Atru.chr2.3644' => 'acertr', 'Atru.chr6.2422' => 'acertr', 'Atru.chr7.1112' => 'acertr', 'AUR62005469' => 'cqu', 'AUR62011166' => 'cqu', 'AUR62013319' => 'cqu', 'AUR62024273' => 'cqu', 'AUR62028420' => 'cqu', 'AUR62041942' => 'cqu', 'BcaB01g04969' => 'bca', 'BcaB01g06371' => 'bca', 'BcaB02g11494' => 'bca', 'BcaB03g15382' => 'bca', 'BcaB08g36994' => 'bca', 'BcaC03g13477' => 'bca', 'BcaC03g13478' => 'bca', 'BcaC03g13480' => 'bca', 'BcaC03g13481' => 'bca', 'BcaC03g13486' => 'bca', 'BcaC04g19031' => 'bca', 'BcaC04g23085' => 'bca', 'BcaC05g25094' => 'bca', 'BcaC05g25096' => 'bca', 'BcaC05g25138' => 'bca', 'BcaC05g30416' => 'bca', 'BcaC05g30455' => 'bca', 'BcaC06g30979' => 'bca', 'BcaC06g33805' => 'bca', 'BcaC08g46021' => 'bca', 'BcaNung03154' => 'bca', 'BolC2t06623H' => 'bol', 'BolC2t06632H' => 'bol', 'BolC2t06635H' => 'bol', 'BolC2t06638H' => 'bol', 'BolC3t13266H' => 'bol', 'BolC5t29776H' => 'bol', 'BolC6t38912H' => 'bol', 'BolC7t44183H' => 'bol', 'BolC9t54123H' => 'bol', 'BolC9t59107H' => 'bol', 'BraA02t05221Z' => 'bra', 'BraA03t09996Z' => 'bra', 'BraA05t23210Z' => 'bra', 'BraA06t24068Z' => 'bra', 'BraA06t27032Z' => 'bra', 'BraA08t35176Z' => 'bra', 'BraA09t36680Z' => 'bra', 'BraA10t44471Z' => 'bra', 'C02p06760' => 'bna', 'C02p06890' => 'bna', 'C02p07010' => 'bna', 'C03p07660' => 'bna', 'C05p10300' => 'bna', 'C06p38150' => 'bna', 'C07p36650' => 'bna', 'C08p15770' => 'bna', 'C09p12300' => 'bna', 'C09p62700' => 'bna', 'C09p75040' => 'bna', 'CAN.G13.1' => 'can', 'CAN.G138.4' => 'can', 'CAN.G44.6' => 'can', 'CAN.G473.19' => 'can', 'CANSAT01G0835' => 'cansat', 'CANSAT11G0246' => 'cansat', 'CANSAT11G1766' => 'cansat', 'CANSAT64G1954' => 'cansat', 'CARHR013330' => 'chi', 'CARHR060530' => 'chi', 'CARHR075300' => 'chi', 'CARHR105120' => 'chi', 'CARHR148910' => 'chi', 'CARHR198830' => 'chi', 'Carub.0001s1275' => 'cru', 'Carub.0002s1437' => 'cru', 'Carub.0003s0044' => 'cru', 'Carub.0003s2787' => 'cru', 'Carub.0005s0597' => 'cru', 'Carub.0006s1266' => 'cru', 'Ca_06935_v3' => 'car', 'Ca_13559_v3' => 'car', 'Ca_16941_v3' => 'car', 'Ca_16960_v3' => 'car', 'Ca_17775_v3' => 'car', 'Ca_30464_v3' => 'car', 'Cc06_g08160' => 'ccan', 'Cc07_g01520' => 'ccan', 'Cc11_g15810' => 'ccan', 'CDE02G2840' => 'cde', 'CDE03G0093' => 'cde', 'CDE04G2127' => 'cde', 'CDE07G1857' => 'cde', 'CDE09G1246' => 'cde', 'Cfa003412' => 'cfa', 'Cfa007341' => 'cfa', 'Cfa009220' => 'cfa', 'Ciclev10008737m.g' => 'ccl', 'Ciclev10015565m.g' => 'ccl', 'Ciclev10031761m.g' => 'ccl', 'CiPaw.03G045300' => 'cil', 'CiPaw.03G247200' => 'cil', 'CiPaw.04G029500' => 'cil', 'CiPaw.04G174000' => 'cil', 'CiPaw.05G181200' => 'cil', 'CiPaw.06G067100' => 'cil', 'ClCG05G025800' => 'cla', 'ClCG06G011400' => 'cla', 'ClCG09G019360' => 'cla', 'COL.COLO4_04827' => 'col', 'COL.COLO4_29170' => 'col', 'COL.COLO4_35131' => 'col', 'COL.COLO4_35132' => 'col', 'Cpa.g.sc33.32' => 'cpa', 'Cpa.g.sc46.29' => 'cpa', 'Cpa.g.sc796.1' => 'cpa', 'CsaV3_1G030420' => 'csa', 'CsaV3_5G027050' => 'csa', 'CsaV3_5G031040' => 'csa', 'CsaV3_UNG023130' => 'csa', 'CSS0007726' => 'camsi', 'CSS0016433' => 'camsi', 'CSS0017656' => 'camsi', 'CSS0025364' => 'camsi', 'CSS0027582' => 'camsi', 'CSS0047288' => 'camsi', 'CSS0049950' => 'camsi', 'DCAR_003843' => 'dca', 'DCAR_007052' => 'dca', 'DCAR_020884' => 'dca', 'DCAR_021730' => 'dca', 'DCAR_024423' => 'dca', 'DCAR_026509' => 'dca', 'DCAR_031158' => 'dca', 'Dinv14728' => 'din', 'Dinv15219' => 'din', 'Dinv25728' => 'din', 'Dinv33428' => 'din', 'Dinv36489' => 'din', 'Dinv41486' => 'din', 'Duzib147G0469' => 'dzi', 'Duzib168G0060' => 'dzi', 'Duzib187G1215' => 'dzi', 'Duzib248G0692' => 'dzi', 'Duzib251G0767' => 'dzi', 'Duzib264G0446' => 'dzi', 'Duzib268G0691' => 'dzi', 'ECA232G4767' => 'eca', 'ECA233G2838' => 'eca', 'ECA234G0391' => 'eca', 'ECA234G0857' => 'eca', 'ECA236G1593' => 'eca', 'ECA238G0565' => 'eca', 'ECA246G1027' => 'eca', 'ECA246G3223' => 'eca', 'ECA246G3470' => 'eca', 'EL10Ac6g13829' => 'bvu', 'EL10Ac6g14093' => 'bvu', 'EL10Ac8g18707' => 'bvu', 'Eucgr.C01369' => 'egr', 'Eucgr.H02492' => 'egr', 'Eucgr.I01733' => 'egr', 'Eucgr.J02255' => 'egr', 'Eucgr.J02257' => 'egr', 'Eucgr.J02258' => 'egr', 'FAN02G1601' => 'fan', 'FAN03G1586' => 'fan', 'FAN03G2986' => 'fan', 'FAN05G4837' => 'fan', 'FAN06G0146' => 'fan', 'FAN07G0858' => 'fan', 'FAN09G3179' => 'fan', 'FAN10G0669' => 'fan', 'FAN12G2358' => 'fan', 'FAN14G4198' => 'fan', 'FAN14G5112' => 'fan', 'FAN17G0342' => 'fan', 'FAN19G0342' => 'fan', 'FAN19G0962' => 'fan', 'FAN19G1101' => 'fan', 'FAN19G1872' => 'fan', 'FAN22G0356' => 'fan', 'FAN23G0744' => 'fan', 'FAN23G1914' => 'fan', 'FAN26G0032' => 'fan', 'FAN28G0625' => 'fan', 'FvH4_1g02710' => 'fve', 'FvH4_1g02720' => 'fve', 'FvH4_4g25670' => 'fve', 'FvH4_6g51700' => 'fve', 'FvH4_7g20170' => 'fve', 'Glyma.05G175000' => 'gma', 'Glyma.08G132300' => 'gma', 'Glyma.11G243000' => 'gma', 'Glyma.13G158900' => 'gma', 'Glyma.17G112400' => 'gma', 'Glyma.18G014100' => 'gma', 'Glyma.19G003100' => 'gma', 'Glyma.19G056500' => 'gma', 'Gohir.A01G158900' => 'ghi', 'Gohir.A05G312600' => 'ghi', 'Gohir.A05G354900' => 'ghi', 'Gohir.A07G037200' => 'ghi', 'Gohir.A09G030000' => 'ghi', 'Gohir.A12G145200' => 'ghi', 'Gohir.D01G151500' => 'ghi', 'Gohir.D04G058300' => 'ghi', 'Gohir.D05G314100' => 'ghi', 'Gohir.D07G041400' => 'ghi', 'Gohir.D09G029700' => 'ghi', 'Gohir.D12G149700' => 'ghi', 'Gorai.001G043800' => 'gra', 'Gorai.002G187800' => 'gra', 'Gorai.006G034700' => 'gra', 'Gorai.008G161200' => 'gra', 'Gorai.009G335700' => 'gra', 'Gorai.012G065000' => 'gra', 'GSVIVG01000535001' => 'vvi', 'GSVIVG01015572001' => 'vvi', 'GSVIVG01032386001' => 'vvi', 'HanXRQChr05g0138531' => 'han', 'HanXRQChr06g0174391' => 'han', 'HanXRQChr07g0199021' => 'han', 'HanXRQChr08g0208211' => 'han', 'HanXRQChr09g0255471' => 'han', 'HanXRQChr10g0315791' => 'han', 'HanXRQChr12g0371991' => 'han', 'HanXRQChr15g0475251' => 'han', 'HanXRQChr17g0540001' => 'han', 'HanXRQChr17g0548631' => 'han', 'HanXRQChr17g0569561' => 'han', 'Haze_12256' => 'cav', 'Haze_14756' => 'cav', 'Haze_25528' => 'cav', 'Hma1.2p1_0079F.1_g041020' => 'hma', 'Hma1.2p1_0818F.1_g223260' => 'hma', 'Hma1.2p1_1747F.1_g300530' => 'hma', 'HPP92_004607' => 'vpl', 'HPP92_004608' => 'vpl', 'HPP92_006181' => 'vpl', 'HPP92_012192' => 'vpl', 'HPP92_015680' => 'vpl', 'HPP92_020249' => 'vpl', 'HPP92_021376' => 'vpl', 'HPP92_024275' => 'vpl', 'Hund06031' => 'sun', 'Hund25391' => 'sun', 'Lalb_Chr07g0185371' => 'lal', 'Lalb_Chr07g0185381' => 'lal', 'Lalb_Chr12g0204011' => 'lal', 'Lalb_Chr13g0301671' => 'lal', 'Lalb_Chr14g0362851' => 'lal', 'Lalb_Chr24g0403581' => 'lal', 'Lj1g0000233' => 'lja', 'Lj2g0018120' => 'lja', 'Lj3C621T0' => 'lonja', 'Lj3P1059T14' => 'lonja', 'Lj3P611T9' => 'lonja', 'Lj3P614T13' => 'lonja', 'Lj3P615T5' => 'lonja', 'Lj4g0012315' => 'lja', 'Lj4g0026182' => 'lja', 'Lj6P813T16' => 'lonja', 'Lj7C427T7' => 'lonja', 'Lj7C427T8' => 'lonja', 'Lj7P600T41' => 'lonja', 'Lju41C42G17' => 'lonja', 'Lsat_1_v5_gn_0_47300' => 'lsa', 'Lsat_1_v5_gn_2_91280' => 'lsa', 'Lsat_1_v5_gn_3_30561' => 'lsa', 'Lsat_1_v5_gn_4_184321' => 'lsa', 'Lsat_1_v5_gn_4_4041' => 'lsa', 'Lsat_1_v5_gn_5_92000' => 'lsa', 'Lsat_1_v5_gn_8_152940' => 'lsa', 'Lsat_1_v5_gn_8_62401' => 'lsa', 'Manes.06G055900' => 'mes', 'Manes.12G022200' => 'mes', 'Manes.13G023300' => 'mes', 'Manes.14G115000' => 'mes', 'Manes.15G151700' => 'mes', 'Manes.17G111300' => 'mes', 'Mapoly0226s0009' => 'mpo', 'MBI02_g25363_MAGBIO' => 'mbi', 'MBI06_g00027_MAGBIO' => 'mbi', 'MBI10_g13034_MAGBIO' => 'mbi', 'MD09G1023400' => 'mdo', 'MD13G1100100' => 'mdo', 'MD15G1169200' => 'mdo', 'MD16G1101100' => 'mdo', 'MD17G1022900' => 'mdo', 'Medtr3g096150' => 'mtr', 'Medtr4g115070' => 'mtr', 'Medtr7g033325' => 'mtr', 'Medtr8g089840' => 'mtr', 'MELO3C010319.2' => 'cme', 'MELO3C011944.2' => 'cme', 'MELO3C021589.2' => 'cme', 'Migut.E00207' => 'egut', 'Migut.H00067' => 'egut', 'Migut.K00433' => 'egut', 'Migut.K00606' => 'egut', 'Migut.K01410' => 'egut', 'MSTRG.13347' => 'ama', 'MSTRG.24045' => 'ama', 'MSTRG.2428' => 'ama', 'MSTRG.26410' => 'ama', 'MSTRG.3139' => 'ama', 'MSTRG.3286' => 'ama', 'MSTRG.563' => 'ama', 'MSTRG.7941' => 'ama', 'Nitab4.5_0000028g0060' => 'nta', 'Nitab4.5_0000065g0260' => 'nta', 'Nitab4.5_0000112g0060' => 'nta', 'Nitab4.5_0000489g0120' => 'nta', 'Nitab4.5_0001776g0050' => 'nta', 'Nitab4.5_0001854g0010' => 'nta', 'Nitab4.5_0001860g0020' => 'nta', 'Nitab4.5_0004352g0010' => 'nta', 'Nitab4.5_0008716g0020' => 'nta', 'Nitab4.5_0008922g0010' => 'nta', 'Nn3g16693' => 'nnu', 'Nn4g22596' => 'nnu', 'Nn7g37639' => 'nnu', 'Oeu001701.1' => 'oeu', 'Oeu018149.1' => 'oeu', 'Oeu026220.1' => 'oeu', 'Oeu038635.1' => 'oeu', 'Oeu049176.1' => 'oeu', 'Oeu056706.1' => 'oeu', 'Oeu056937.1' => 'oeu', 'Oeu057540.1' => 'oeu', 'Os02g0594900' => 'osa', 'Os02g0595100' => 'osa', 'Os04g0477500' => 'osa', 'Os12g0611900' => 'osa', 'Peaxi162Scf00076g00020' => 'pax', 'Peaxi162Scf00128g00217' => 'pax', 'Peaxi162Scf00129g01640' => 'pax', 'Peaxi162Scf00669g00007' => 'pax', 'Peaxi162Scf00700g00421' => 'pax', 'Peaxi162Scf00801g00038' => 'pax', 'Peaxi162Scf00891g00025' => 'pax', 'PGR083G0909' => 'pgr', 'PGR119G1005' => 'pgr', 'PGR142G2236' => 'pgr', 'PGR142G3388' => 'pgr', 'PGSC0003DMG400004514' => 'stu', 'PGSC0003DMG400012635' => 'stu', 'PGSC0003DMG400015730' => 'stu', 'PGSC0003DMG400018611' => 'stu', 'PGSC0003DMG400030897' => 'stu', 'Phvul.001G254800' => 'pvu', 'Phvul.002G260100' => 'pvu', 'Phvul.003G167600' => 'pvu', 'Phvul.004G005100' => 'pvu', 'Potri.001G343600' => 'ptr', 'Potri.006G066700' => 'ptr', 'Potri.008G186000' => 'ptr', 'Potri.010G046900' => 'ptr', 'Potri.018G127900' => 'ptr', 'Pp3c20_17750' => 'ppa', 'Pp3c24_4380' => 'ppa', 'Prupe.1G245800' => 'ppe', 'Prupe.3G293400' => 'ppe', 'Prupe.7G247400' => 'ppe', 'Psat0s145g0120' => 'psa', 'Psat0s595g0040' => 'psa', 'Psat0s595g0120' => 'psa', 'Psat3g175040' => 'psa', 'Psat7g058120' => 'psa', 'PSO017G0428' => 'pso', 'PSO063G7510' => 'pso', 'PSO067G0046' => 'pso', 'PSO478G1073' => 'pso', 'PSO675G3677' => 'pso', 'PSO675G6558' => 'pso', 'PSO675G7520' => 'pso', 'PSO675G8959' => 'pso', 'QL02p074089' => 'qlo', 'QL02p089614' => 'qlo', 'QL03p057736' => 'qlo', 'RcHm_v2.0_Chr1g0364131' => 'rch', 'RcHm_v2.0_Chr2g0087801' => 'rch', 'RcHm_v2.0_Chr2g0087821' => 'rch', 'RcHm_v2.0_Chr2g0173231' => 'rch', 'RcHm_v2.0_Chr4g0433111' => 'rch', 'Rhsim03G0250300' => 'rsi', 'Rhsim08G0048400' => 'rsi', 'Rhsim10G0014800' => 'rsi', 'Rhsim12G0040100' => 'rsi', 'Rhsim12G0109700' => 'rsi', 'Sabra06G0049600' => 'sbr', 'Sabra08G0141000' => 'sbr', 'Sabra10G0021400' => 'sbr', 'Sabra16G0222900' => 'sbr', 'Sabra18G0108600' => 'sbr', 'SalBow1G0433' => 'sbo', 'SalBow1G2038' => 'sbo', 'SalBow1G5003' => 'sbo', 'SalBow7G1197' => 'sbo', 'SalBow8G3506' => 'sbo', 'Sc03g0007300' => 'sci', 'Sc11g0000950' => 'sci', 'Sc14g0008750' => 'sci', 'Sc18g0000420' => 'sci', 'Sed0006754' => 'sed', 'Sed0008741' => 'sed', 'Sed0017172' => 'sed', 'Sed0018925' => 'sed', 'Sed0023326' => 'sed', 'Sed0025909' => 'sed', 'SEGI_05333' => 'sgi', 'SEGI_10362' => 'sgi', 'SEGI_13380' => 'sgi', 'SEGI_24306' => 'sgi', 'SEGI_29077' => 'sgi', 'SEGI_29095' => 'sgi', 'SEGI_36534' => 'sgi', 'SEGI_37506' => 'sgi', 'SEGI_38321' => 'sgi', 'SGA_v2.0_scaffold307G48031' => 'sas', 'SGA_v2.0_scaffold47G17507' => 'sas', 'SGA_v2.0_scaffold63G21736' => 'sas', 'SGA_v2.0_scaffold87G27070' => 'sas', 'SHI17794' => 'shi', 'SHI28851' => 'shi', 'SMO165G0155' => 'smo', 'SMO340G0217' => 'smo', 'SMO367G1210' => 'smo', 'Solyc02g093430.3' => 'sly', 'Solyc05g013580.4' => 'sly', 'Solyc07g008030.3' => 'sly', 'Solyc12g035470.2' => 'sly', 'Sopen02g038020' => 'spe', 'Sopen05g008490' => 'spe', 'Sopen07g003910' => 'spe', 'Sopen12g015240' => 'spe', 'Sp1g11550' => 'spa', 'Sp2g16710' => 'spa', 'Sp3g00430' => 'spa', 'Sp3g26780' => 'spa', 'Sp5g22900' => 'spa', 'Sp6g29530' => 'spa', 'TAR371G0794' => 'tar', 'TAR374G0164' => 'tar', 'TAR622G0165' => 'tar', 'TAR626G0929' => 'tar', 'TAR629G2155' => 'tar', 'THA.LOC104805282' => 'tha', 'THA.LOC104805363' => 'tha', 'THA.LOC104808968' => 'tha', 'THA.LOC104821093' => 'tha', 'THA.LOC104823953' => 'tha', 'THA.LOC104825562' => 'tha', 'THA.LOC104825665' => 'tha', 'Thecc.02G261400' => 'tca', 'Thecc.04G019200' => 'tca', 'Thecc.09G130400' => 'tca', 'Thhalv10004374m.g' => 'esa', 'Thhalv10007850m.g' => 'esa', 'Thhalv10013782m.g' => 'esa', 'Thhalv10018686m.g' => 'esa', 'Thhalv10020899m.g' => 'esa', 'Thhalv10022755m.g' => 'esa', 'TPR.G23851' => 'tpr', 'TPR.G26500' => 'tpr', 'TPR.G27267' => 'tpr', 'TPR.G32001' => 'tpr', 'TPR.G6251' => 'tpr', 'TPR.G8167' => 'tpr', 'TWI12G1330' => 'twi', 'TWI18G1239' => 'twi', 'TWI34G0979' => 'twi', 'TWI36G0670' => 'twi', 'TWI36G0707' => 'twi', 'TWI56G0233' => 'twi', 'TWI75G1809' => 'twi', 'unitig_21.g20874' => 'ugi', 'unitig_26.g10343' => 'ugi', 'unitig_46.g18392' => 'ugi', 'unitig_52.g17178' => 'ugi', 'unitig_8.g2934' => 'ugi', 'vmacro01122' => 'vma', 'vmacro05875' => 'vma', 'vmacro06147' => 'vma', 'vmacro16191' => 'vma', 'vmacro18293' => 'vma', 'VMungo0251G3707' => 'vmu', 'VMungo0464G1521' => 'vmu', 'VMungo1215G0205' => 'vmu', 'VMungo1383G2484' => 'vmu', 'Zm00001eb079610' => 'zma', 'Zm00001eb135990' => 'zma', 'Zm00001eb183710' => 'zma', 'Zm00001eb246020' => 'zma' ), 'gf_id' => 'HOM05D001124', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001124' ), 'data_identifier' => 'HOM05D001124', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001124', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '548', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02520' => 'bna', 'A03p06630' => 'bna', 'A05p44460' => 'bna', 'A06p08710' => 'bna', 'A06p41090' => 'bna', 'A07p32320' => 'bna', 'A08p32520' => 'bna', 'A09p10360' => 'bna', 'A10p24080' => 'bna', 'Aa31LG11G15250' => 'aar', 'Aa31LG1G1800' => 'aar', 'Aa31LG2G5120' => 'aar', 'Aa31LG2G6070' => 'aar', 'Aa31LG5G10770' => 'aar', 'Aa31sc61G90' => 'aar', 'Actinidia01352' => 'ach', 'Actinidia05983' => 'ach', 'Actinidia08133' => 'ach', 'Actinidia15101' => 'ach', 'Actinidia26379' => 'ach', 'Actinidia35778' => 'ach', 'Actinidia36123' => 'ach', 'Actinidia37436' => 'ach', 'Actinidia38730' => 'ach', 'Ah.02g128210' => 'amhyb', 'Ah.03g132990' => 'amhyb', 'Ah.14g079410' => 'amhyb', 'AL1G24640' => 'aly', 'AL2G26680' => 'aly', 'AL3G10530' => 'aly', 'AL3G45230' => 'aly', 'AL5G15230' => 'aly', 'AL5G16960' => 'aly', 'AL6G25210' => 'aly', 'Aqoxy2G00441' => 'aox', 'Aqoxy3G01236' => 'aox', 'Aqoxy5G03746' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3RQ047' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C7GMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9C8JER' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MBL6KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YXCZ83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZANX40' => 'arhy', 'AT1G12990' => 'ath', 'AT1G67880' => 'ath', 'AT2G13290' => 'ath', 'AT3G01620' => 'ath', 'AT3G26445' => 'ath', 'AT3G27540' => 'ath', 'AT5G14480' => 'ath', 'ATR0824G026' => 'atr', 'ATR1098G019' => 'atr', 'Atru.chr11.2145' => 'acertr', 'Atru.chr2.3636' => 'acertr', 'Atru.chr2.3644' => 'acertr', 'Atru.chr6.2422' => 'acertr', 'Atru.chr7.1112' => 'acertr', 'AUR62005469' => 'cqu', 'AUR62011166' => 'cqu', 'AUR62013319' => 'cqu', 'AUR62024273' => 'cqu', 'AUR62028420' => 'cqu', 'AUR62041942' => 'cqu', 'BcaB01g04969' => 'bca', 'BcaB01g06371' => 'bca', 'BcaB02g11494' => 'bca', 'BcaB03g15382' => 'bca', 'BcaB08g36994' => 'bca', 'BcaC03g13477' => 'bca', 'BcaC03g13478' => 'bca', 'BcaC03g13480' => 'bca', 'BcaC03g13481' => 'bca', 'BcaC03g13486' => 'bca', 'BcaC04g19031' => 'bca', 'BcaC04g23085' => 'bca', 'BcaC05g25094' => 'bca', 'BcaC05g25096' => 'bca', 'BcaC05g25138' => 'bca', 'BcaC05g30416' => 'bca', 'BcaC05g30455' => 'bca', 'BcaC06g30979' => 'bca', 'BcaC06g33805' => 'bca', 'BcaC08g46021' => 'bca', 'BcaNung03154' => 'bca', 'BolC2t06623H' => 'bol', 'BolC2t06632H' => 'bol', 'BolC2t06635H' => 'bol', 'BolC2t06638H' => 'bol', 'BolC3t13266H' => 'bol', 'BolC5t29776H' => 'bol', 'BolC6t38912H' => 'bol', 'BolC7t44183H' => 'bol', 'BolC9t54123H' => 'bol', 'BolC9t59107H' => 'bol', 'BraA02t05221Z' => 'bra', 'BraA03t09996Z' => 'bra', 'BraA05t23210Z' => 'bra', 'BraA06t24068Z' => 'bra', 'BraA06t27032Z' => 'bra', 'BraA08t35176Z' => 'bra', 'BraA09t36680Z' => 'bra', 'BraA10t44471Z' => 'bra', 'C02p06760' => 'bna', 'C02p06890' => 'bna', 'C02p07010' => 'bna', 'C03p07660' => 'bna', 'C05p10300' => 'bna', 'C06p38150' => 'bna', 'C07p36650' => 'bna', 'C08p15770' => 'bna', 'C09p12300' => 'bna', 'C09p62700' => 'bna', 'C09p75040' => 'bna', 'CAN.G13.1' => 'can', 'CAN.G138.4' => 'can', 'CAN.G44.6' => 'can', 'CAN.G473.19' => 'can', 'CANSAT01G0835' => 'cansat', 'CANSAT11G0246' => 'cansat', 'CANSAT11G1766' => 'cansat', 'CANSAT64G1954' => 'cansat', 'CARHR013330' => 'chi', 'CARHR060530' => 'chi', 'CARHR075300' => 'chi', 'CARHR105120' => 'chi', 'CARHR148910' => 'chi', 'CARHR198830' => 'chi', 'Carub.0001s1275' => 'cru', 'Carub.0002s1437' => 'cru', 'Carub.0003s0044' => 'cru', 'Carub.0003s2787' => 'cru', 'Carub.0005s0597' => 'cru', 'Carub.0006s1266' => 'cru', 'Ca_06935_v3' => 'car', 'Ca_13559_v3' => 'car', 'Ca_16941_v3' => 'car', 'Ca_16960_v3' => 'car', 'Ca_17775_v3' => 'car', 'Ca_30464_v3' => 'car', 'Cc06_g08160' => 'ccan', 'Cc07_g01520' => 'ccan', 'Cc11_g15810' => 'ccan', 'CDE02G2840' => 'cde', 'CDE03G0093' => 'cde', 'CDE04G2127' => 'cde', 'CDE07G1857' => 'cde', 'CDE09G1246' => 'cde', 'Cfa003412' => 'cfa', 'Cfa007341' => 'cfa', 'Cfa009220' => 'cfa', 'Ciclev10008737m.g' => 'ccl', 'Ciclev10015565m.g' => 'ccl', 'Ciclev10031761m.g' => 'ccl', 'CiPaw.03G045300' => 'cil', 'CiPaw.03G247200' => 'cil', 'CiPaw.04G029500' => 'cil', 'CiPaw.04G174000' => 'cil', 'CiPaw.05G181200' => 'cil', 'CiPaw.06G067100' => 'cil', 'ClCG05G025800' => 'cla', 'ClCG06G011400' => 'cla', 'ClCG09G019360' => 'cla', 'COL.COLO4_04827' => 'col', 'COL.COLO4_29170' => 'col', 'COL.COLO4_35131' => 'col', 'COL.COLO4_35132' => 'col', 'Cpa.g.sc33.32' => 'cpa', 'Cpa.g.sc46.29' => 'cpa', 'Cpa.g.sc796.1' => 'cpa', 'CsaV3_1G030420' => 'csa', 'CsaV3_5G027050' => 'csa', 'CsaV3_5G031040' => 'csa', 'CsaV3_UNG023130' => 'csa', 'CSS0007726' => 'camsi', 'CSS0016433' => 'camsi', 'CSS0017656' => 'camsi', 'CSS0025364' => 'camsi', 'CSS0027582' => 'camsi', 'CSS0047288' => 'camsi', 'CSS0049950' => 'camsi', 'DCAR_003843' => 'dca', 'DCAR_007052' => 'dca', 'DCAR_020884' => 'dca', 'DCAR_021730' => 'dca', 'DCAR_024423' => 'dca', 'DCAR_026509' => 'dca', 'DCAR_031158' => 'dca', 'Dinv14728' => 'din', 'Dinv15219' => 'din', 'Dinv25728' => 'din', 'Dinv33428' => 'din', 'Dinv36489' => 'din', 'Dinv41486' => 'din', 'Duzib147G0469' => 'dzi', 'Duzib168G0060' => 'dzi', 'Duzib187G1215' => 'dzi', 'Duzib248G0692' => 'dzi', 'Duzib251G0767' => 'dzi', 'Duzib264G0446' => 'dzi', 'Duzib268G0691' => 'dzi', 'ECA232G4767' => 'eca', 'ECA233G2838' => 'eca', 'ECA234G0391' => 'eca', 'ECA234G0857' => 'eca', 'ECA236G1593' => 'eca', 'ECA238G0565' => 'eca', 'ECA246G1027' => 'eca', 'ECA246G3223' => 'eca', 'ECA246G3470' => 'eca', 'EL10Ac6g13829' => 'bvu', 'EL10Ac6g14093' => 'bvu', 'EL10Ac8g18707' => 'bvu', 'Eucgr.C01369' => 'egr', 'Eucgr.H02492' => 'egr', 'Eucgr.I01733' => 'egr', 'Eucgr.J02255' => 'egr', 'Eucgr.J02257' => 'egr', 'Eucgr.J02258' => 'egr', 'FAN02G1601' => 'fan', 'FAN03G1586' => 'fan', 'FAN03G2986' => 'fan', 'FAN05G4837' => 'fan', 'FAN06G0146' => 'fan', 'FAN07G0858' => 'fan', 'FAN09G3179' => 'fan', 'FAN10G0669' => 'fan', 'FAN12G2358' => 'fan', 'FAN14G4198' => 'fan', 'FAN14G5112' => 'fan', 'FAN17G0342' => 'fan', 'FAN19G0342' => 'fan', 'FAN19G0962' => 'fan', 'FAN19G1101' => 'fan', 'FAN19G1872' => 'fan', 'FAN22G0356' => 'fan', 'FAN23G0744' => 'fan', 'FAN23G1914' => 'fan', 'FAN26G0032' => 'fan', 'FAN28G0625' => 'fan', 'FvH4_1g02710' => 'fve', 'FvH4_1g02720' => 'fve', 'FvH4_4g25670' => 'fve', 'FvH4_6g51700' => 'fve', 'FvH4_7g20170' => 'fve', 'Glyma.05G175000' => 'gma', 'Glyma.08G132300' => 'gma', 'Glyma.11G243000' => 'gma', 'Glyma.13G158900' => 'gma', 'Glyma.17G112400' => 'gma', 'Glyma.18G014100' => 'gma', 'Glyma.19G003100' => 'gma', 'Glyma.19G056500' => 'gma', 'Gohir.A01G158900' => 'ghi', 'Gohir.A05G312600' => 'ghi', 'Gohir.A05G354900' => 'ghi', 'Gohir.A07G037200' => 'ghi', 'Gohir.A09G030000' => 'ghi', 'Gohir.A12G145200' => 'ghi', 'Gohir.D01G151500' => 'ghi', 'Gohir.D04G058300' => 'ghi', 'Gohir.D05G314100' => 'ghi', 'Gohir.D07G041400' => 'ghi', 'Gohir.D09G029700' => 'ghi', 'Gohir.D12G149700' => 'ghi', 'Gorai.001G043800' => 'gra', 'Gorai.002G187800' => 'gra', 'Gorai.006G034700' => 'gra', 'Gorai.008G161200' => 'gra', 'Gorai.009G335700' => 'gra', 'Gorai.012G065000' => 'gra', 'GSVIVG01000535001' => 'vvi', 'GSVIVG01015572001' => 'vvi', 'GSVIVG01032386001' => 'vvi', 'HanXRQChr05g0138531' => 'han', 'HanXRQChr06g0174391' => 'han', 'HanXRQChr07g0199021' => 'han', 'HanXRQChr08g0208211' => 'han', 'HanXRQChr09g0255471' => 'han', 'HanXRQChr10g0315791' => 'han', 'HanXRQChr12g0371991' => 'han', 'HanXRQChr15g0475251' => 'han', 'HanXRQChr17g0540001' => 'han', 'HanXRQChr17g0548631' => 'han', 'HanXRQChr17g0569561' => 'han', 'Haze_12256' => 'cav', 'Haze_14756' => 'cav', 'Haze_25528' => 'cav', 'Hma1.2p1_0079F.1_g041020' => 'hma', 'Hma1.2p1_0818F.1_g223260' => 'hma', 'Hma1.2p1_1747F.1_g300530' => 'hma', 'HPP92_004607' => 'vpl', 'HPP92_004608' => 'vpl', 'HPP92_006181' => 'vpl', 'HPP92_012192' => 'vpl', 'HPP92_015680' => 'vpl', 'HPP92_020249' => 'vpl', 'HPP92_021376' => 'vpl', 'HPP92_024275' => 'vpl', 'Hund06031' => 'sun', 'Hund25391' => 'sun', 'Lalb_Chr07g0185371' => 'lal', 'Lalb_Chr07g0185381' => 'lal', 'Lalb_Chr12g0204011' => 'lal', 'Lalb_Chr13g0301671' => 'lal', 'Lalb_Chr14g0362851' => 'lal', 'Lalb_Chr24g0403581' => 'lal', 'Lj1g0000233' => 'lja', 'Lj2g0018120' => 'lja', 'Lj3C621T0' => 'lonja', 'Lj3P1059T14' => 'lonja', 'Lj3P611T9' => 'lonja', 'Lj3P614T13' => 'lonja', 'Lj3P615T5' => 'lonja', 'Lj4g0012315' => 'lja', 'Lj4g0026182' => 'lja', 'Lj6P813T16' => 'lonja', 'Lj7C427T7' => 'lonja', 'Lj7C427T8' => 'lonja', 'Lj7P600T41' => 'lonja', 'Lju41C42G17' => 'lonja', 'Lsat_1_v5_gn_0_47300' => 'lsa', 'Lsat_1_v5_gn_2_91280' => 'lsa', 'Lsat_1_v5_gn_3_30561' => 'lsa', 'Lsat_1_v5_gn_4_184321' => 'lsa', 'Lsat_1_v5_gn_4_4041' => 'lsa', 'Lsat_1_v5_gn_5_92000' => 'lsa', 'Lsat_1_v5_gn_8_152940' => 'lsa', 'Lsat_1_v5_gn_8_62401' => 'lsa', 'Manes.06G055900' => 'mes', 'Manes.12G022200' => 'mes', 'Manes.13G023300' => 'mes', 'Manes.14G115000' => 'mes', 'Manes.15G151700' => 'mes', 'Manes.17G111300' => 'mes', 'Mapoly0226s0009' => 'mpo', 'MBI02_g25363_MAGBIO' => 'mbi', 'MBI06_g00027_MAGBIO' => 'mbi', 'MBI10_g13034_MAGBIO' => 'mbi', 'MD09G1023400' => 'mdo', 'MD13G1100100' => 'mdo', 'MD15G1169200' => 'mdo', 'MD16G1101100' => 'mdo', 'MD17G1022900' => 'mdo', 'Medtr3g096150' => 'mtr', 'Medtr4g115070' => 'mtr', 'Medtr7g033325' => 'mtr', 'Medtr8g089840' => 'mtr', 'MELO3C010319.2' => 'cme', 'MELO3C011944.2' => 'cme', 'MELO3C021589.2' => 'cme', 'Migut.E00207' => 'egut', 'Migut.H00067' => 'egut', 'Migut.K00433' => 'egut', 'Migut.K00606' => 'egut', 'Migut.K01410' => 'egut', 'MSTRG.13347' => 'ama', 'MSTRG.24045' => 'ama', 'MSTRG.2428' => 'ama', 'MSTRG.26410' => 'ama', 'MSTRG.3139' => 'ama', 'MSTRG.3286' => 'ama', 'MSTRG.563' => 'ama', 'MSTRG.7941' => 'ama', 'Nitab4.5_0000028g0060' => 'nta', 'Nitab4.5_0000065g0260' => 'nta', 'Nitab4.5_0000112g0060' => 'nta', 'Nitab4.5_0000489g0120' => 'nta', 'Nitab4.5_0001776g0050' => 'nta', 'Nitab4.5_0001854g0010' => 'nta', 'Nitab4.5_0001860g0020' => 'nta', 'Nitab4.5_0004352g0010' => 'nta', 'Nitab4.5_0008716g0020' => 'nta', 'Nitab4.5_0008922g0010' => 'nta', 'Nn3g16693' => 'nnu', 'Nn4g22596' => 'nnu', 'Nn7g37639' => 'nnu', 'Oeu001701.1' => 'oeu', 'Oeu018149.1' => 'oeu', 'Oeu026220.1' => 'oeu', 'Oeu038635.1' => 'oeu', 'Oeu049176.1' => 'oeu', 'Oeu056706.1' => 'oeu', 'Oeu056937.1' => 'oeu', 'Oeu057540.1' => 'oeu', 'Os02g0594900' => 'osa', 'Os02g0595100' => 'osa', 'Os04g0477500' => 'osa', 'Os12g0611900' => 'osa', 'Peaxi162Scf00076g00020' => 'pax', 'Peaxi162Scf00128g00217' => 'pax', 'Peaxi162Scf00129g01640' => 'pax', 'Peaxi162Scf00669g00007' => 'pax', 'Peaxi162Scf00700g00421' => 'pax', 'Peaxi162Scf00801g00038' => 'pax', 'Peaxi162Scf00891g00025' => 'pax', 'PGR083G0909' => 'pgr', 'PGR119G1005' => 'pgr', 'PGR142G2236' => 'pgr', 'PGR142G3388' => 'pgr', 'PGSC0003DMG400004514' => 'stu', 'PGSC0003DMG400012635' => 'stu', 'PGSC0003DMG400015730' => 'stu', 'PGSC0003DMG400018611' => 'stu', 'PGSC0003DMG400030897' => 'stu', 'Phvul.001G254800' => 'pvu', 'Phvul.002G260100' => 'pvu', 'Phvul.003G167600' => 'pvu', 'Phvul.004G005100' => 'pvu', 'Potri.001G343600' => 'ptr', 'Potri.006G066700' => 'ptr', 'Potri.008G186000' => 'ptr', 'Potri.010G046900' => 'ptr', 'Potri.018G127900' => 'ptr', 'Pp3c20_17750' => 'ppa', 'Pp3c24_4380' => 'ppa', 'Prupe.1G245800' => 'ppe', 'Prupe.3G293400' => 'ppe', 'Prupe.7G247400' => 'ppe', 'Psat0s145g0120' => 'psa', 'Psat0s595g0040' => 'psa', 'Psat0s595g0120' => 'psa', 'Psat3g175040' => 'psa', 'Psat7g058120' => 'psa', 'PSO017G0428' => 'pso', 'PSO063G7510' => 'pso', 'PSO067G0046' => 'pso', 'PSO478G1073' => 'pso', 'PSO675G3677' => 'pso', 'PSO675G6558' => 'pso', 'PSO675G7520' => 'pso', 'PSO675G8959' => 'pso', 'QL02p074089' => 'qlo', 'QL02p089614' => 'qlo', 'QL03p057736' => 'qlo', 'RcHm_v2.0_Chr1g0364131' => 'rch', 'RcHm_v2.0_Chr2g0087801' => 'rch', 'RcHm_v2.0_Chr2g0087821' => 'rch', 'RcHm_v2.0_Chr2g0173231' => 'rch', 'RcHm_v2.0_Chr4g0433111' => 'rch', 'Rhsim03G0250300' => 'rsi', 'Rhsim08G0048400' => 'rsi', 'Rhsim10G0014800' => 'rsi', 'Rhsim12G0040100' => 'rsi', 'Rhsim12G0109700' => 'rsi', 'Sabra06G0049600' => 'sbr', 'Sabra08G0141000' => 'sbr', 'Sabra10G0021400' => 'sbr', 'Sabra16G0222900' => 'sbr', 'Sabra18G0108600' => 'sbr', 'SalBow1G0433' => 'sbo', 'SalBow1G2038' => 'sbo', 'SalBow1G5003' => 'sbo', 'SalBow7G1197' => 'sbo', 'SalBow8G3506' => 'sbo', 'Sc03g0007300' => 'sci', 'Sc11g0000950' => 'sci', 'Sc14g0008750' => 'sci', 'Sc18g0000420' => 'sci', 'Sed0006754' => 'sed', 'Sed0008741' => 'sed', 'Sed0017172' => 'sed', 'Sed0018925' => 'sed', 'Sed0023326' => 'sed', 'Sed0025909' => 'sed', 'SEGI_05333' => 'sgi', 'SEGI_10362' => 'sgi', 'SEGI_13380' => 'sgi', 'SEGI_24306' => 'sgi', 'SEGI_29077' => 'sgi', 'SEGI_29095' => 'sgi', 'SEGI_36534' => 'sgi', 'SEGI_37506' => 'sgi', 'SEGI_38321' => 'sgi', 'SGA_v2.0_scaffold307G48031' => 'sas', 'SGA_v2.0_scaffold47G17507' => 'sas', 'SGA_v2.0_scaffold63G21736' => 'sas', 'SGA_v2.0_scaffold87G27070' => 'sas', 'SHI17794' => 'shi', 'SHI28851' => 'shi', 'SMO165G0155' => 'smo', 'SMO340G0217' => 'smo', 'SMO367G1210' => 'smo', 'Solyc02g093430.3' => 'sly', 'Solyc05g013580.4' => 'sly', 'Solyc07g008030.3' => 'sly', 'Solyc12g035470.2' => 'sly', 'Sopen02g038020' => 'spe', 'Sopen05g008490' => 'spe', 'Sopen07g003910' => 'spe', 'Sopen12g015240' => 'spe', 'Sp1g11550' => 'spa', 'Sp2g16710' => 'spa', 'Sp3g00430' => 'spa', 'Sp3g26780' => 'spa', 'Sp5g22900' => 'spa', 'Sp6g29530' => 'spa', 'TAR371G0794' => 'tar', 'TAR374G0164' => 'tar', 'TAR622G0165' => 'tar', 'TAR626G0929' => 'tar', 'TAR629G2155' => 'tar', 'THA.LOC104805282' => 'tha', 'THA.LOC104805363' => 'tha', 'THA.LOC104808968' => 'tha', 'THA.LOC104821093' => 'tha', 'THA.LOC104823953' => 'tha', 'THA.LOC104825562' => 'tha', 'THA.LOC104825665' => 'tha', 'Thecc.02G261400' => 'tca', 'Thecc.04G019200' => 'tca', 'Thecc.09G130400' => 'tca', 'Thhalv10004374m.g' => 'esa', 'Thhalv10007850m.g' => 'esa', 'Thhalv10013782m.g' => 'esa', 'Thhalv10018686m.g' => 'esa', 'Thhalv10020899m.g' => 'esa', 'Thhalv10022755m.g' => 'esa', 'TPR.G23851' => 'tpr', 'TPR.G26500' => 'tpr', 'TPR.G27267' => 'tpr', 'TPR.G32001' => 'tpr', 'TPR.G6251' => 'tpr', 'TPR.G8167' => 'tpr', 'TWI12G1330' => 'twi', 'TWI18G1239' => 'twi', 'TWI34G0979' => 'twi', 'TWI36G0670' => 'twi', 'TWI36G0707' => 'twi', 'TWI56G0233' => 'twi', 'TWI75G1809' => 'twi', 'unitig_21.g20874' => 'ugi', 'unitig_26.g10343' => 'ugi', 'unitig_46.g18392' => 'ugi', 'unitig_52.g17178' => 'ugi', 'unitig_8.g2934' => 'ugi', 'vmacro01122' => 'vma', 'vmacro05875' => 'vma', 'vmacro06147' => 'vma', 'vmacro16191' => 'vma', 'vmacro18293' => 'vma', 'VMungo0251G3707' => 'vmu', 'VMungo0464G1521' => 'vmu', 'VMungo1215G0205' => 'vmu', 'VMungo1383G2484' => 'vmu', 'Zm00001eb079610' => 'zma', 'Zm00001eb135990' => 'zma', 'Zm00001eb183710' => 'zma', 'Zm00001eb246020' => 'zma' ) $gf_id = 'HOM05D001124' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001124' ) $data_identifier = 'HOM05D001124' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 6, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 7, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 21, 'bol' => (int) 10, 'bra' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 6, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 9, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 21, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 8, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 10, 'lsa' => (int) 8, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 8, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 9, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb246020' $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' => 'HOM05D001124', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '548', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02520' => 'bna', 'A03p06630' => 'bna', 'A05p44460' => 'bna', 'A06p08710' => 'bna', 'A06p41090' => 'bna', 'A07p32320' => 'bna', 'A08p32520' => 'bna', 'A09p10360' => 'bna', 'A10p24080' => 'bna', 'Aa31LG11G15250' => 'aar', 'Aa31LG1G1800' => 'aar', 'Aa31LG2G5120' => 'aar', 'Aa31LG2G6070' => 'aar', 'Aa31LG5G10770' => 'aar', 'Aa31sc61G90' => 'aar', 'Actinidia01352' => 'ach', 'Actinidia05983' => 'ach', 'Actinidia08133' => 'ach', 'Actinidia15101' => 'ach', 'Actinidia26379' => 'ach', 'Actinidia35778' => 'ach', 'Actinidia36123' => 'ach', 'Actinidia37436' => 'ach', 'Actinidia38730' => 'ach', 'Ah.02g128210' => 'amhyb', 'Ah.03g132990' => 'amhyb', 'Ah.14g079410' => 'amhyb', 'AL1G24640' => 'aly', 'AL2G26680' => 'aly', 'AL3G10530' => 'aly', 'AL3G45230' => 'aly', 'AL5G15230' => 'aly', 'AL5G16960' => 'aly', 'AL6G25210' => 'aly', 'Aqoxy2G00441' => 'aox', 'Aqoxy3G01236' => 'aox', 'Aqoxy5G03746' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3RQ047' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C7GMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9C8JER' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MBL6KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YXCZ83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZANX40' => 'arhy', 'AT1G12990' => 'ath', 'AT1G67880' => 'ath', 'AT2G13290' => 'ath', 'AT3G01620' => 'ath', 'AT3G26445' => 'ath', 'AT3G27540' => 'ath', 'AT5G14480' => 'ath', 'ATR0824G026' => 'atr', 'ATR1098G019' => 'atr', 'Atru.chr11.2145' => 'acertr', 'Atru.chr2.3636' => 'acertr', 'Atru.chr2.3644' => 'acertr', 'Atru.chr6.2422' => 'acertr', 'Atru.chr7.1112' => 'acertr', 'AUR62005469' => 'cqu', 'AUR62011166' => 'cqu', 'AUR62013319' => 'cqu', 'AUR62024273' => 'cqu', 'AUR62028420' => 'cqu', 'AUR62041942' => 'cqu', 'BcaB01g04969' => 'bca', 'BcaB01g06371' => 'bca', 'BcaB02g11494' => 'bca', 'BcaB03g15382' => 'bca', 'BcaB08g36994' => 'bca', 'BcaC03g13477' => 'bca', 'BcaC03g13478' => 'bca', 'BcaC03g13480' => 'bca', 'BcaC03g13481' => 'bca', 'BcaC03g13486' => 'bca', 'BcaC04g19031' => 'bca', 'BcaC04g23085' => 'bca', 'BcaC05g25094' => 'bca', 'BcaC05g25096' => 'bca', 'BcaC05g25138' => 'bca', 'BcaC05g30416' => 'bca', 'BcaC05g30455' => 'bca', 'BcaC06g30979' => 'bca', 'BcaC06g33805' => 'bca', 'BcaC08g46021' => 'bca', 'BcaNung03154' => 'bca', 'BolC2t06623H' => 'bol', 'BolC2t06632H' => 'bol', 'BolC2t06635H' => 'bol', 'BolC2t06638H' => 'bol', 'BolC3t13266H' => 'bol', 'BolC5t29776H' => 'bol', 'BolC6t38912H' => 'bol', 'BolC7t44183H' => 'bol', 'BolC9t54123H' => 'bol', 'BolC9t59107H' => 'bol', 'BraA02t05221Z' => 'bra', 'BraA03t09996Z' => 'bra', 'BraA05t23210Z' => 'bra', 'BraA06t24068Z' => 'bra', 'BraA06t27032Z' => 'bra', 'BraA08t35176Z' => 'bra', 'BraA09t36680Z' => 'bra', 'BraA10t44471Z' => 'bra', 'C02p06760' => 'bna', 'C02p06890' => 'bna', 'C02p07010' => 'bna', 'C03p07660' => 'bna', 'C05p10300' => 'bna', 'C06p38150' => 'bna', 'C07p36650' => 'bna', 'C08p15770' => 'bna', 'C09p12300' => 'bna', 'C09p62700' => 'bna', 'C09p75040' => 'bna', 'CAN.G13.1' => 'can', 'CAN.G138.4' => 'can', 'CAN.G44.6' => 'can', 'CAN.G473.19' => 'can', 'CANSAT01G0835' => 'cansat', 'CANSAT11G0246' => 'cansat', 'CANSAT11G1766' => 'cansat', 'CANSAT64G1954' => 'cansat', 'CARHR013330' => 'chi', 'CARHR060530' => 'chi', 'CARHR075300' => 'chi', 'CARHR105120' => 'chi', 'CARHR148910' => 'chi', 'CARHR198830' => 'chi', 'Carub.0001s1275' => 'cru', 'Carub.0002s1437' => 'cru', 'Carub.0003s0044' => 'cru', 'Carub.0003s2787' => 'cru', 'Carub.0005s0597' => 'cru', 'Carub.0006s1266' => 'cru', 'Ca_06935_v3' => 'car', 'Ca_13559_v3' => 'car', 'Ca_16941_v3' => 'car', 'Ca_16960_v3' => 'car', 'Ca_17775_v3' => 'car', 'Ca_30464_v3' => 'car', 'Cc06_g08160' => 'ccan', 'Cc07_g01520' => 'ccan', 'Cc11_g15810' => 'ccan', 'CDE02G2840' => 'cde', 'CDE03G0093' => 'cde', 'CDE04G2127' => 'cde', 'CDE07G1857' => 'cde', 'CDE09G1246' => 'cde', 'Cfa003412' => 'cfa', 'Cfa007341' => 'cfa', 'Cfa009220' => 'cfa', 'Ciclev10008737m.g' => 'ccl', 'Ciclev10015565m.g' => 'ccl', 'Ciclev10031761m.g' => 'ccl', 'CiPaw.03G045300' => 'cil', 'CiPaw.03G247200' => 'cil', 'CiPaw.04G029500' => 'cil', 'CiPaw.04G174000' => 'cil', 'CiPaw.05G181200' => 'cil', 'CiPaw.06G067100' => 'cil', 'ClCG05G025800' => 'cla', 'ClCG06G011400' => 'cla', 'ClCG09G019360' => 'cla', 'COL.COLO4_04827' => 'col', 'COL.COLO4_29170' => 'col', 'COL.COLO4_35131' => 'col', 'COL.COLO4_35132' => 'col', 'Cpa.g.sc33.32' => 'cpa', 'Cpa.g.sc46.29' => 'cpa', 'Cpa.g.sc796.1' => 'cpa', 'CsaV3_1G030420' => 'csa', 'CsaV3_5G027050' => 'csa', 'CsaV3_5G031040' => 'csa', 'CsaV3_UNG023130' => 'csa', 'CSS0007726' => 'camsi', 'CSS0016433' => 'camsi', 'CSS0017656' => 'camsi', 'CSS0025364' => 'camsi', 'CSS0027582' => 'camsi', 'CSS0047288' => 'camsi', 'CSS0049950' => 'camsi', 'DCAR_003843' => 'dca', 'DCAR_007052' => 'dca', 'DCAR_020884' => 'dca', 'DCAR_021730' => 'dca', 'DCAR_024423' => 'dca', 'DCAR_026509' => 'dca', 'DCAR_031158' => 'dca', 'Dinv14728' => 'din', 'Dinv15219' => 'din', 'Dinv25728' => 'din', 'Dinv33428' => 'din', 'Dinv36489' => 'din', 'Dinv41486' => 'din', 'Duzib147G0469' => 'dzi', 'Duzib168G0060' => 'dzi', 'Duzib187G1215' => 'dzi', 'Duzib248G0692' => 'dzi', 'Duzib251G0767' => 'dzi', 'Duzib264G0446' => 'dzi', 'Duzib268G0691' => 'dzi', 'ECA232G4767' => 'eca', 'ECA233G2838' => 'eca', 'ECA234G0391' => 'eca', 'ECA234G0857' => 'eca', 'ECA236G1593' => 'eca', 'ECA238G0565' => 'eca', 'ECA246G1027' => 'eca', 'ECA246G3223' => 'eca', 'ECA246G3470' => 'eca', 'EL10Ac6g13829' => 'bvu', 'EL10Ac6g14093' => 'bvu', 'EL10Ac8g18707' => 'bvu', 'Eucgr.C01369' => 'egr', 'Eucgr.H02492' => 'egr', 'Eucgr.I01733' => 'egr', 'Eucgr.J02255' => 'egr', 'Eucgr.J02257' => 'egr', 'Eucgr.J02258' => 'egr', 'FAN02G1601' => 'fan', 'FAN03G1586' => 'fan', 'FAN03G2986' => 'fan', 'FAN05G4837' => 'fan', 'FAN06G0146' => 'fan', 'FAN07G0858' => 'fan', 'FAN09G3179' => 'fan', 'FAN10G0669' => 'fan', 'FAN12G2358' => 'fan', 'FAN14G4198' => 'fan', 'FAN14G5112' => 'fan', 'FAN17G0342' => 'fan', 'FAN19G0342' => 'fan', 'FAN19G0962' => 'fan', 'FAN19G1101' => 'fan', 'FAN19G1872' => 'fan', 'FAN22G0356' => 'fan', 'FAN23G0744' => 'fan', 'FAN23G1914' => 'fan', 'FAN26G0032' => 'fan', 'FAN28G0625' => 'fan', 'FvH4_1g02710' => 'fve', 'FvH4_1g02720' => 'fve', 'FvH4_4g25670' => 'fve', 'FvH4_6g51700' => 'fve', 'FvH4_7g20170' => 'fve', 'Glyma.05G175000' => 'gma', 'Glyma.08G132300' => 'gma', 'Glyma.11G243000' => 'gma', 'Glyma.13G158900' => 'gma', 'Glyma.17G112400' => 'gma', 'Glyma.18G014100' => 'gma', 'Glyma.19G003100' => 'gma', 'Glyma.19G056500' => 'gma', 'Gohir.A01G158900' => 'ghi', 'Gohir.A05G312600' => 'ghi', 'Gohir.A05G354900' => 'ghi', 'Gohir.A07G037200' => 'ghi', 'Gohir.A09G030000' => 'ghi', 'Gohir.A12G145200' => 'ghi', 'Gohir.D01G151500' => 'ghi', 'Gohir.D04G058300' => 'ghi', 'Gohir.D05G314100' => 'ghi', 'Gohir.D07G041400' => 'ghi', 'Gohir.D09G029700' => 'ghi', 'Gohir.D12G149700' => 'ghi', 'Gorai.001G043800' => 'gra', 'Gorai.002G187800' => 'gra', 'Gorai.006G034700' => 'gra', 'Gorai.008G161200' => 'gra', 'Gorai.009G335700' => 'gra', 'Gorai.012G065000' => 'gra', 'GSVIVG01000535001' => 'vvi', 'GSVIVG01015572001' => 'vvi', 'GSVIVG01032386001' => 'vvi', 'HanXRQChr05g0138531' => 'han', 'HanXRQChr06g0174391' => 'han', 'HanXRQChr07g0199021' => 'han', 'HanXRQChr08g0208211' => 'han', 'HanXRQChr09g0255471' => 'han', 'HanXRQChr10g0315791' => 'han', 'HanXRQChr12g0371991' => 'han', 'HanXRQChr15g0475251' => 'han', 'HanXRQChr17g0540001' => 'han', 'HanXRQChr17g0548631' => 'han', 'HanXRQChr17g0569561' => 'han', 'Haze_12256' => 'cav', 'Haze_14756' => 'cav', 'Haze_25528' => 'cav', 'Hma1.2p1_0079F.1_g041020' => 'hma', 'Hma1.2p1_0818F.1_g223260' => 'hma', 'Hma1.2p1_1747F.1_g300530' => 'hma', 'HPP92_004607' => 'vpl', 'HPP92_004608' => 'vpl', 'HPP92_006181' => 'vpl', 'HPP92_012192' => 'vpl', 'HPP92_015680' => 'vpl', 'HPP92_020249' => 'vpl', 'HPP92_021376' => 'vpl', 'HPP92_024275' => 'vpl', 'Hund06031' => 'sun', 'Hund25391' => 'sun', 'Lalb_Chr07g0185371' => 'lal', 'Lalb_Chr07g0185381' => 'lal', 'Lalb_Chr12g0204011' => 'lal', 'Lalb_Chr13g0301671' => 'lal', 'Lalb_Chr14g0362851' => 'lal', 'Lalb_Chr24g0403581' => 'lal', 'Lj1g0000233' => 'lja', 'Lj2g0018120' => 'lja', 'Lj3C621T0' => 'lonja', 'Lj3P1059T14' => 'lonja', 'Lj3P611T9' => 'lonja', 'Lj3P614T13' => 'lonja', 'Lj3P615T5' => 'lonja', 'Lj4g0012315' => 'lja', 'Lj4g0026182' => 'lja', 'Lj6P813T16' => 'lonja', 'Lj7C427T7' => 'lonja', 'Lj7C427T8' => 'lonja', 'Lj7P600T41' => 'lonja', 'Lju41C42G17' => 'lonja', 'Lsat_1_v5_gn_0_47300' => 'lsa', 'Lsat_1_v5_gn_2_91280' => 'lsa', 'Lsat_1_v5_gn_3_30561' => 'lsa', 'Lsat_1_v5_gn_4_184321' => 'lsa', 'Lsat_1_v5_gn_4_4041' => 'lsa', 'Lsat_1_v5_gn_5_92000' => 'lsa', 'Lsat_1_v5_gn_8_152940' => 'lsa', 'Lsat_1_v5_gn_8_62401' => 'lsa', 'Manes.06G055900' => 'mes', 'Manes.12G022200' => 'mes', 'Manes.13G023300' => 'mes', 'Manes.14G115000' => 'mes', 'Manes.15G151700' => 'mes', 'Manes.17G111300' => 'mes', 'Mapoly0226s0009' => 'mpo', 'MBI02_g25363_MAGBIO' => 'mbi', 'MBI06_g00027_MAGBIO' => 'mbi', 'MBI10_g13034_MAGBIO' => 'mbi', 'MD09G1023400' => 'mdo', 'MD13G1100100' => 'mdo', 'MD15G1169200' => 'mdo', 'MD16G1101100' => 'mdo', 'MD17G1022900' => 'mdo', 'Medtr3g096150' => 'mtr', 'Medtr4g115070' => 'mtr', 'Medtr7g033325' => 'mtr', 'Medtr8g089840' => 'mtr', 'MELO3C010319.2' => 'cme', 'MELO3C011944.2' => 'cme', 'MELO3C021589.2' => 'cme', 'Migut.E00207' => 'egut', 'Migut.H00067' => 'egut', 'Migut.K00433' => 'egut', 'Migut.K00606' => 'egut', 'Migut.K01410' => 'egut', 'MSTRG.13347' => 'ama', 'MSTRG.24045' => 'ama', 'MSTRG.2428' => 'ama', 'MSTRG.26410' => 'ama', 'MSTRG.3139' => 'ama', 'MSTRG.3286' => 'ama', 'MSTRG.563' => 'ama', 'MSTRG.7941' => 'ama', 'Nitab4.5_0000028g0060' => 'nta', 'Nitab4.5_0000065g0260' => 'nta', 'Nitab4.5_0000112g0060' => 'nta', 'Nitab4.5_0000489g0120' => 'nta', 'Nitab4.5_0001776g0050' => 'nta', 'Nitab4.5_0001854g0010' => 'nta', 'Nitab4.5_0001860g0020' => 'nta', 'Nitab4.5_0004352g0010' => 'nta', 'Nitab4.5_0008716g0020' => 'nta', 'Nitab4.5_0008922g0010' => 'nta', 'Nn3g16693' => 'nnu', 'Nn4g22596' => 'nnu', 'Nn7g37639' => 'nnu', 'Oeu001701.1' => 'oeu', 'Oeu018149.1' => 'oeu', 'Oeu026220.1' => 'oeu', 'Oeu038635.1' => 'oeu', 'Oeu049176.1' => 'oeu', 'Oeu056706.1' => 'oeu', 'Oeu056937.1' => 'oeu', 'Oeu057540.1' => 'oeu', 'Os02g0594900' => 'osa', 'Os02g0595100' => 'osa', 'Os04g0477500' => 'osa', 'Os12g0611900' => 'osa', 'Peaxi162Scf00076g00020' => 'pax', 'Peaxi162Scf00128g00217' => 'pax', 'Peaxi162Scf00129g01640' => 'pax', 'Peaxi162Scf00669g00007' => 'pax', 'Peaxi162Scf00700g00421' => 'pax', 'Peaxi162Scf00801g00038' => 'pax', 'Peaxi162Scf00891g00025' => 'pax', 'PGR083G0909' => 'pgr', 'PGR119G1005' => 'pgr', 'PGR142G2236' => 'pgr', 'PGR142G3388' => 'pgr', 'PGSC0003DMG400004514' => 'stu', 'PGSC0003DMG400012635' => 'stu', 'PGSC0003DMG400015730' => 'stu', 'PGSC0003DMG400018611' => 'stu', 'PGSC0003DMG400030897' => 'stu', 'Phvul.001G254800' => 'pvu', 'Phvul.002G260100' => 'pvu', 'Phvul.003G167600' => 'pvu', 'Phvul.004G005100' => 'pvu', 'Potri.001G343600' => 'ptr', 'Potri.006G066700' => 'ptr', 'Potri.008G186000' => 'ptr', 'Potri.010G046900' => 'ptr', 'Potri.018G127900' => 'ptr', 'Pp3c20_17750' => 'ppa', 'Pp3c24_4380' => 'ppa', 'Prupe.1G245800' => 'ppe', 'Prupe.3G293400' => 'ppe', 'Prupe.7G247400' => 'ppe', 'Psat0s145g0120' => 'psa', 'Psat0s595g0040' => 'psa', 'Psat0s595g0120' => 'psa', 'Psat3g175040' => 'psa', 'Psat7g058120' => 'psa', 'PSO017G0428' => 'pso', 'PSO063G7510' => 'pso', 'PSO067G0046' => 'pso', 'PSO478G1073' => 'pso', 'PSO675G3677' => 'pso', 'PSO675G6558' => 'pso', 'PSO675G7520' => 'pso', 'PSO675G8959' => 'pso', 'QL02p074089' => 'qlo', 'QL02p089614' => 'qlo', 'QL03p057736' => 'qlo', 'RcHm_v2.0_Chr1g0364131' => 'rch', 'RcHm_v2.0_Chr2g0087801' => 'rch', 'RcHm_v2.0_Chr2g0087821' => 'rch', 'RcHm_v2.0_Chr2g0173231' => 'rch', 'RcHm_v2.0_Chr4g0433111' => 'rch', 'Rhsim03G0250300' => 'rsi', 'Rhsim08G0048400' => 'rsi', 'Rhsim10G0014800' => 'rsi', 'Rhsim12G0040100' => 'rsi', 'Rhsim12G0109700' => 'rsi', 'Sabra06G0049600' => 'sbr', 'Sabra08G0141000' => 'sbr', 'Sabra10G0021400' => 'sbr', 'Sabra16G0222900' => 'sbr', 'Sabra18G0108600' => 'sbr', 'SalBow1G0433' => 'sbo', 'SalBow1G2038' => 'sbo', 'SalBow1G5003' => 'sbo', 'SalBow7G1197' => 'sbo', 'SalBow8G3506' => 'sbo', 'Sc03g0007300' => 'sci', 'Sc11g0000950' => 'sci', 'Sc14g0008750' => 'sci', 'Sc18g0000420' => 'sci', 'Sed0006754' => 'sed', 'Sed0008741' => 'sed', 'Sed0017172' => 'sed', 'Sed0018925' => 'sed', 'Sed0023326' => 'sed', 'Sed0025909' => 'sed', 'SEGI_05333' => 'sgi', 'SEGI_10362' => 'sgi', 'SEGI_13380' => 'sgi', 'SEGI_24306' => 'sgi', 'SEGI_29077' => 'sgi', 'SEGI_29095' => 'sgi', 'SEGI_36534' => 'sgi', 'SEGI_37506' => 'sgi', 'SEGI_38321' => 'sgi', 'SGA_v2.0_scaffold307G48031' => 'sas', 'SGA_v2.0_scaffold47G17507' => 'sas', 'SGA_v2.0_scaffold63G21736' => 'sas', 'SGA_v2.0_scaffold87G27070' => 'sas', 'SHI17794' => 'shi', 'SHI28851' => 'shi', 'SMO165G0155' => 'smo', 'SMO340G0217' => 'smo', 'SMO367G1210' => 'smo', 'Solyc02g093430.3' => 'sly', 'Solyc05g013580.4' => 'sly', 'Solyc07g008030.3' => 'sly', 'Solyc12g035470.2' => 'sly', 'Sopen02g038020' => 'spe', 'Sopen05g008490' => 'spe', 'Sopen07g003910' => 'spe', 'Sopen12g015240' => 'spe', 'Sp1g11550' => 'spa', 'Sp2g16710' => 'spa', 'Sp3g00430' => 'spa', 'Sp3g26780' => 'spa', 'Sp5g22900' => 'spa', 'Sp6g29530' => 'spa', 'TAR371G0794' => 'tar', 'TAR374G0164' => 'tar', 'TAR622G0165' => 'tar', 'TAR626G0929' => 'tar', 'TAR629G2155' => 'tar', 'THA.LOC104805282' => 'tha', 'THA.LOC104805363' => 'tha', 'THA.LOC104808968' => 'tha', 'THA.LOC104821093' => 'tha', 'THA.LOC104823953' => 'tha', 'THA.LOC104825562' => 'tha', 'THA.LOC104825665' => 'tha', 'Thecc.02G261400' => 'tca', 'Thecc.04G019200' => 'tca', 'Thecc.09G130400' => 'tca', 'Thhalv10004374m.g' => 'esa', 'Thhalv10007850m.g' => 'esa', 'Thhalv10013782m.g' => 'esa', 'Thhalv10018686m.g' => 'esa', 'Thhalv10020899m.g' => 'esa', 'Thhalv10022755m.g' => 'esa', 'TPR.G23851' => 'tpr', 'TPR.G26500' => 'tpr', 'TPR.G27267' => 'tpr', 'TPR.G32001' => 'tpr', 'TPR.G6251' => 'tpr', 'TPR.G8167' => 'tpr', 'TWI12G1330' => 'twi', 'TWI18G1239' => 'twi', 'TWI34G0979' => 'twi', 'TWI36G0670' => 'twi', 'TWI36G0707' => 'twi', 'TWI56G0233' => 'twi', 'TWI75G1809' => 'twi', 'unitig_21.g20874' => 'ugi', 'unitig_26.g10343' => 'ugi', 'unitig_46.g18392' => 'ugi', 'unitig_52.g17178' => 'ugi', 'unitig_8.g2934' => 'ugi', 'vmacro01122' => 'vma', 'vmacro05875' => 'vma', 'vmacro06147' => 'vma', 'vmacro16191' => 'vma', 'vmacro18293' => 'vma', 'VMungo0251G3707' => 'vmu', 'VMungo0464G1521' => 'vmu', 'VMungo1215G0205' => 'vmu', 'VMungo1383G2484' => 'vmu', 'Zm00001eb079610' => 'zma', 'Zm00001eb135990' => 'zma', 'Zm00001eb183710' => 'zma', 'Zm00001eb246020' => 'zma' ), 'gf_id' => 'HOM05D001124', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001124' ), 'data_identifier' => 'HOM05D001124', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001124', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '548', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02520' => 'bna', 'A03p06630' => 'bna', 'A05p44460' => 'bna', 'A06p08710' => 'bna', 'A06p41090' => 'bna', 'A07p32320' => 'bna', 'A08p32520' => 'bna', 'A09p10360' => 'bna', 'A10p24080' => 'bna', 'Aa31LG11G15250' => 'aar', 'Aa31LG1G1800' => 'aar', 'Aa31LG2G5120' => 'aar', 'Aa31LG2G6070' => 'aar', 'Aa31LG5G10770' => 'aar', 'Aa31sc61G90' => 'aar', 'Actinidia01352' => 'ach', 'Actinidia05983' => 'ach', 'Actinidia08133' => 'ach', 'Actinidia15101' => 'ach', 'Actinidia26379' => 'ach', 'Actinidia35778' => 'ach', 'Actinidia36123' => 'ach', 'Actinidia37436' => 'ach', 'Actinidia38730' => 'ach', 'Ah.02g128210' => 'amhyb', 'Ah.03g132990' => 'amhyb', 'Ah.14g079410' => 'amhyb', 'AL1G24640' => 'aly', 'AL2G26680' => 'aly', 'AL3G10530' => 'aly', 'AL3G45230' => 'aly', 'AL5G15230' => 'aly', 'AL5G16960' => 'aly', 'AL6G25210' => 'aly', 'Aqoxy2G00441' => 'aox', 'Aqoxy3G01236' => 'aox', 'Aqoxy5G03746' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3RQ047' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C7GMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9C8JER' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MBL6KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YXCZ83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZANX40' => 'arhy', 'AT1G12990' => 'ath', 'AT1G67880' => 'ath', 'AT2G13290' => 'ath', 'AT3G01620' => 'ath', 'AT3G26445' => 'ath', 'AT3G27540' => 'ath', 'AT5G14480' => 'ath', 'ATR0824G026' => 'atr', 'ATR1098G019' => 'atr', 'Atru.chr11.2145' => 'acertr', 'Atru.chr2.3636' => 'acertr', 'Atru.chr2.3644' => 'acertr', 'Atru.chr6.2422' => 'acertr', 'Atru.chr7.1112' => 'acertr', 'AUR62005469' => 'cqu', 'AUR62011166' => 'cqu', 'AUR62013319' => 'cqu', 'AUR62024273' => 'cqu', 'AUR62028420' => 'cqu', 'AUR62041942' => 'cqu', 'BcaB01g04969' => 'bca', 'BcaB01g06371' => 'bca', 'BcaB02g11494' => 'bca', 'BcaB03g15382' => 'bca', 'BcaB08g36994' => 'bca', 'BcaC03g13477' => 'bca', 'BcaC03g13478' => 'bca', 'BcaC03g13480' => 'bca', 'BcaC03g13481' => 'bca', 'BcaC03g13486' => 'bca', 'BcaC04g19031' => 'bca', 'BcaC04g23085' => 'bca', 'BcaC05g25094' => 'bca', 'BcaC05g25096' => 'bca', 'BcaC05g25138' => 'bca', 'BcaC05g30416' => 'bca', 'BcaC05g30455' => 'bca', 'BcaC06g30979' => 'bca', 'BcaC06g33805' => 'bca', 'BcaC08g46021' => 'bca', 'BcaNung03154' => 'bca', 'BolC2t06623H' => 'bol', 'BolC2t06632H' => 'bol', 'BolC2t06635H' => 'bol', 'BolC2t06638H' => 'bol', 'BolC3t13266H' => 'bol', 'BolC5t29776H' => 'bol', 'BolC6t38912H' => 'bol', 'BolC7t44183H' => 'bol', 'BolC9t54123H' => 'bol', 'BolC9t59107H' => 'bol', 'BraA02t05221Z' => 'bra', 'BraA03t09996Z' => 'bra', 'BraA05t23210Z' => 'bra', 'BraA06t24068Z' => 'bra', 'BraA06t27032Z' => 'bra', 'BraA08t35176Z' => 'bra', 'BraA09t36680Z' => 'bra', 'BraA10t44471Z' => 'bra', 'C02p06760' => 'bna', 'C02p06890' => 'bna', 'C02p07010' => 'bna', 'C03p07660' => 'bna', 'C05p10300' => 'bna', 'C06p38150' => 'bna', 'C07p36650' => 'bna', 'C08p15770' => 'bna', 'C09p12300' => 'bna', 'C09p62700' => 'bna', 'C09p75040' => 'bna', 'CAN.G13.1' => 'can', 'CAN.G138.4' => 'can', 'CAN.G44.6' => 'can', 'CAN.G473.19' => 'can', 'CANSAT01G0835' => 'cansat', 'CANSAT11G0246' => 'cansat', 'CANSAT11G1766' => 'cansat', 'CANSAT64G1954' => 'cansat', 'CARHR013330' => 'chi', 'CARHR060530' => 'chi', 'CARHR075300' => 'chi', 'CARHR105120' => 'chi', 'CARHR148910' => 'chi', 'CARHR198830' => 'chi', 'Carub.0001s1275' => 'cru', 'Carub.0002s1437' => 'cru', 'Carub.0003s0044' => 'cru', 'Carub.0003s2787' => 'cru', 'Carub.0005s0597' => 'cru', 'Carub.0006s1266' => 'cru', 'Ca_06935_v3' => 'car', 'Ca_13559_v3' => 'car', 'Ca_16941_v3' => 'car', 'Ca_16960_v3' => 'car', 'Ca_17775_v3' => 'car', 'Ca_30464_v3' => 'car', 'Cc06_g08160' => 'ccan', 'Cc07_g01520' => 'ccan', 'Cc11_g15810' => 'ccan', 'CDE02G2840' => 'cde', 'CDE03G0093' => 'cde', 'CDE04G2127' => 'cde', 'CDE07G1857' => 'cde', 'CDE09G1246' => 'cde', 'Cfa003412' => 'cfa', 'Cfa007341' => 'cfa', 'Cfa009220' => 'cfa', 'Ciclev10008737m.g' => 'ccl', 'Ciclev10015565m.g' => 'ccl', 'Ciclev10031761m.g' => 'ccl', 'CiPaw.03G045300' => 'cil', 'CiPaw.03G247200' => 'cil', 'CiPaw.04G029500' => 'cil', 'CiPaw.04G174000' => 'cil', 'CiPaw.05G181200' => 'cil', 'CiPaw.06G067100' => 'cil', 'ClCG05G025800' => 'cla', 'ClCG06G011400' => 'cla', 'ClCG09G019360' => 'cla', 'COL.COLO4_04827' => 'col', 'COL.COLO4_29170' => 'col', 'COL.COLO4_35131' => 'col', 'COL.COLO4_35132' => 'col', 'Cpa.g.sc33.32' => 'cpa', 'Cpa.g.sc46.29' => 'cpa', 'Cpa.g.sc796.1' => 'cpa', 'CsaV3_1G030420' => 'csa', 'CsaV3_5G027050' => 'csa', 'CsaV3_5G031040' => 'csa', 'CsaV3_UNG023130' => 'csa', 'CSS0007726' => 'camsi', 'CSS0016433' => 'camsi', 'CSS0017656' => 'camsi', 'CSS0025364' => 'camsi', 'CSS0027582' => 'camsi', 'CSS0047288' => 'camsi', 'CSS0049950' => 'camsi', 'DCAR_003843' => 'dca', 'DCAR_007052' => 'dca', 'DCAR_020884' => 'dca', 'DCAR_021730' => 'dca', 'DCAR_024423' => 'dca', 'DCAR_026509' => 'dca', 'DCAR_031158' => 'dca', 'Dinv14728' => 'din', 'Dinv15219' => 'din', 'Dinv25728' => 'din', 'Dinv33428' => 'din', 'Dinv36489' => 'din', 'Dinv41486' => 'din', 'Duzib147G0469' => 'dzi', 'Duzib168G0060' => 'dzi', 'Duzib187G1215' => 'dzi', 'Duzib248G0692' => 'dzi', 'Duzib251G0767' => 'dzi', 'Duzib264G0446' => 'dzi', 'Duzib268G0691' => 'dzi', 'ECA232G4767' => 'eca', 'ECA233G2838' => 'eca', 'ECA234G0391' => 'eca', 'ECA234G0857' => 'eca', 'ECA236G1593' => 'eca', 'ECA238G0565' => 'eca', 'ECA246G1027' => 'eca', 'ECA246G3223' => 'eca', 'ECA246G3470' => 'eca', 'EL10Ac6g13829' => 'bvu', 'EL10Ac6g14093' => 'bvu', 'EL10Ac8g18707' => 'bvu', 'Eucgr.C01369' => 'egr', 'Eucgr.H02492' => 'egr', 'Eucgr.I01733' => 'egr', 'Eucgr.J02255' => 'egr', 'Eucgr.J02257' => 'egr', 'Eucgr.J02258' => 'egr', 'FAN02G1601' => 'fan', 'FAN03G1586' => 'fan', 'FAN03G2986' => 'fan', 'FAN05G4837' => 'fan', 'FAN06G0146' => 'fan', 'FAN07G0858' => 'fan', 'FAN09G3179' => 'fan', 'FAN10G0669' => 'fan', 'FAN12G2358' => 'fan', 'FAN14G4198' => 'fan', 'FAN14G5112' => 'fan', 'FAN17G0342' => 'fan', 'FAN19G0342' => 'fan', 'FAN19G0962' => 'fan', 'FAN19G1101' => 'fan', 'FAN19G1872' => 'fan', 'FAN22G0356' => 'fan', 'FAN23G0744' => 'fan', 'FAN23G1914' => 'fan', 'FAN26G0032' => 'fan', 'FAN28G0625' => 'fan', 'FvH4_1g02710' => 'fve', 'FvH4_1g02720' => 'fve', 'FvH4_4g25670' => 'fve', 'FvH4_6g51700' => 'fve', 'FvH4_7g20170' => 'fve', 'Glyma.05G175000' => 'gma', 'Glyma.08G132300' => 'gma', 'Glyma.11G243000' => 'gma', 'Glyma.13G158900' => 'gma', 'Glyma.17G112400' => 'gma', 'Glyma.18G014100' => 'gma', 'Glyma.19G003100' => 'gma', 'Glyma.19G056500' => 'gma', 'Gohir.A01G158900' => 'ghi', 'Gohir.A05G312600' => 'ghi', 'Gohir.A05G354900' => 'ghi', 'Gohir.A07G037200' => 'ghi', 'Gohir.A09G030000' => 'ghi', 'Gohir.A12G145200' => 'ghi', 'Gohir.D01G151500' => 'ghi', 'Gohir.D04G058300' => 'ghi', 'Gohir.D05G314100' => 'ghi', 'Gohir.D07G041400' => 'ghi', 'Gohir.D09G029700' => 'ghi', 'Gohir.D12G149700' => 'ghi', 'Gorai.001G043800' => 'gra', 'Gorai.002G187800' => 'gra', 'Gorai.006G034700' => 'gra', 'Gorai.008G161200' => 'gra', 'Gorai.009G335700' => 'gra', 'Gorai.012G065000' => 'gra', 'GSVIVG01000535001' => 'vvi', 'GSVIVG01015572001' => 'vvi', 'GSVIVG01032386001' => 'vvi', 'HanXRQChr05g0138531' => 'han', 'HanXRQChr06g0174391' => 'han', 'HanXRQChr07g0199021' => 'han', 'HanXRQChr08g0208211' => 'han', 'HanXRQChr09g0255471' => 'han', 'HanXRQChr10g0315791' => 'han', 'HanXRQChr12g0371991' => 'han', 'HanXRQChr15g0475251' => 'han', 'HanXRQChr17g0540001' => 'han', 'HanXRQChr17g0548631' => 'han', 'HanXRQChr17g0569561' => 'han', 'Haze_12256' => 'cav', 'Haze_14756' => 'cav', 'Haze_25528' => 'cav', 'Hma1.2p1_0079F.1_g041020' => 'hma', 'Hma1.2p1_0818F.1_g223260' => 'hma', 'Hma1.2p1_1747F.1_g300530' => 'hma', 'HPP92_004607' => 'vpl', 'HPP92_004608' => 'vpl', 'HPP92_006181' => 'vpl', 'HPP92_012192' => 'vpl', 'HPP92_015680' => 'vpl', 'HPP92_020249' => 'vpl', 'HPP92_021376' => 'vpl', 'HPP92_024275' => 'vpl', 'Hund06031' => 'sun', 'Hund25391' => 'sun', 'Lalb_Chr07g0185371' => 'lal', 'Lalb_Chr07g0185381' => 'lal', 'Lalb_Chr12g0204011' => 'lal', 'Lalb_Chr13g0301671' => 'lal', 'Lalb_Chr14g0362851' => 'lal', 'Lalb_Chr24g0403581' => 'lal', 'Lj1g0000233' => 'lja', 'Lj2g0018120' => 'lja', 'Lj3C621T0' => 'lonja', 'Lj3P1059T14' => 'lonja', 'Lj3P611T9' => 'lonja', 'Lj3P614T13' => 'lonja', 'Lj3P615T5' => 'lonja', 'Lj4g0012315' => 'lja', 'Lj4g0026182' => 'lja', 'Lj6P813T16' => 'lonja', 'Lj7C427T7' => 'lonja', 'Lj7C427T8' => 'lonja', 'Lj7P600T41' => 'lonja', 'Lju41C42G17' => 'lonja', 'Lsat_1_v5_gn_0_47300' => 'lsa', 'Lsat_1_v5_gn_2_91280' => 'lsa', 'Lsat_1_v5_gn_3_30561' => 'lsa', 'Lsat_1_v5_gn_4_184321' => 'lsa', 'Lsat_1_v5_gn_4_4041' => 'lsa', 'Lsat_1_v5_gn_5_92000' => 'lsa', 'Lsat_1_v5_gn_8_152940' => 'lsa', 'Lsat_1_v5_gn_8_62401' => 'lsa', 'Manes.06G055900' => 'mes', 'Manes.12G022200' => 'mes', 'Manes.13G023300' => 'mes', 'Manes.14G115000' => 'mes', 'Manes.15G151700' => 'mes', 'Manes.17G111300' => 'mes', 'Mapoly0226s0009' => 'mpo', 'MBI02_g25363_MAGBIO' => 'mbi', 'MBI06_g00027_MAGBIO' => 'mbi', 'MBI10_g13034_MAGBIO' => 'mbi', 'MD09G1023400' => 'mdo', 'MD13G1100100' => 'mdo', 'MD15G1169200' => 'mdo', 'MD16G1101100' => 'mdo', 'MD17G1022900' => 'mdo', 'Medtr3g096150' => 'mtr', 'Medtr4g115070' => 'mtr', 'Medtr7g033325' => 'mtr', 'Medtr8g089840' => 'mtr', 'MELO3C010319.2' => 'cme', 'MELO3C011944.2' => 'cme', 'MELO3C021589.2' => 'cme', 'Migut.E00207' => 'egut', 'Migut.H00067' => 'egut', 'Migut.K00433' => 'egut', 'Migut.K00606' => 'egut', 'Migut.K01410' => 'egut', 'MSTRG.13347' => 'ama', 'MSTRG.24045' => 'ama', 'MSTRG.2428' => 'ama', 'MSTRG.26410' => 'ama', 'MSTRG.3139' => 'ama', 'MSTRG.3286' => 'ama', 'MSTRG.563' => 'ama', 'MSTRG.7941' => 'ama', 'Nitab4.5_0000028g0060' => 'nta', 'Nitab4.5_0000065g0260' => 'nta', 'Nitab4.5_0000112g0060' => 'nta', 'Nitab4.5_0000489g0120' => 'nta', 'Nitab4.5_0001776g0050' => 'nta', 'Nitab4.5_0001854g0010' => 'nta', 'Nitab4.5_0001860g0020' => 'nta', 'Nitab4.5_0004352g0010' => 'nta', 'Nitab4.5_0008716g0020' => 'nta', 'Nitab4.5_0008922g0010' => 'nta', 'Nn3g16693' => 'nnu', 'Nn4g22596' => 'nnu', 'Nn7g37639' => 'nnu', 'Oeu001701.1' => 'oeu', 'Oeu018149.1' => 'oeu', 'Oeu026220.1' => 'oeu', 'Oeu038635.1' => 'oeu', 'Oeu049176.1' => 'oeu', 'Oeu056706.1' => 'oeu', 'Oeu056937.1' => 'oeu', 'Oeu057540.1' => 'oeu', 'Os02g0594900' => 'osa', 'Os02g0595100' => 'osa', 'Os04g0477500' => 'osa', 'Os12g0611900' => 'osa', 'Peaxi162Scf00076g00020' => 'pax', 'Peaxi162Scf00128g00217' => 'pax', 'Peaxi162Scf00129g01640' => 'pax', 'Peaxi162Scf00669g00007' => 'pax', 'Peaxi162Scf00700g00421' => 'pax', 'Peaxi162Scf00801g00038' => 'pax', 'Peaxi162Scf00891g00025' => 'pax', 'PGR083G0909' => 'pgr', 'PGR119G1005' => 'pgr', 'PGR142G2236' => 'pgr', 'PGR142G3388' => 'pgr', 'PGSC0003DMG400004514' => 'stu', 'PGSC0003DMG400012635' => 'stu', 'PGSC0003DMG400015730' => 'stu', 'PGSC0003DMG400018611' => 'stu', 'PGSC0003DMG400030897' => 'stu', 'Phvul.001G254800' => 'pvu', 'Phvul.002G260100' => 'pvu', 'Phvul.003G167600' => 'pvu', 'Phvul.004G005100' => 'pvu', 'Potri.001G343600' => 'ptr', 'Potri.006G066700' => 'ptr', 'Potri.008G186000' => 'ptr', 'Potri.010G046900' => 'ptr', 'Potri.018G127900' => 'ptr', 'Pp3c20_17750' => 'ppa', 'Pp3c24_4380' => 'ppa', 'Prupe.1G245800' => 'ppe', 'Prupe.3G293400' => 'ppe', 'Prupe.7G247400' => 'ppe', 'Psat0s145g0120' => 'psa', 'Psat0s595g0040' => 'psa', 'Psat0s595g0120' => 'psa', 'Psat3g175040' => 'psa', 'Psat7g058120' => 'psa', 'PSO017G0428' => 'pso', 'PSO063G7510' => 'pso', 'PSO067G0046' => 'pso', 'PSO478G1073' => 'pso', 'PSO675G3677' => 'pso', 'PSO675G6558' => 'pso', 'PSO675G7520' => 'pso', 'PSO675G8959' => 'pso', 'QL02p074089' => 'qlo', 'QL02p089614' => 'qlo', 'QL03p057736' => 'qlo', 'RcHm_v2.0_Chr1g0364131' => 'rch', 'RcHm_v2.0_Chr2g0087801' => 'rch', 'RcHm_v2.0_Chr2g0087821' => 'rch', 'RcHm_v2.0_Chr2g0173231' => 'rch', 'RcHm_v2.0_Chr4g0433111' => 'rch', 'Rhsim03G0250300' => 'rsi', 'Rhsim08G0048400' => 'rsi', 'Rhsim10G0014800' => 'rsi', 'Rhsim12G0040100' => 'rsi', 'Rhsim12G0109700' => 'rsi', 'Sabra06G0049600' => 'sbr', 'Sabra08G0141000' => 'sbr', 'Sabra10G0021400' => 'sbr', 'Sabra16G0222900' => 'sbr', 'Sabra18G0108600' => 'sbr', 'SalBow1G0433' => 'sbo', 'SalBow1G2038' => 'sbo', 'SalBow1G5003' => 'sbo', 'SalBow7G1197' => 'sbo', 'SalBow8G3506' => 'sbo', 'Sc03g0007300' => 'sci', 'Sc11g0000950' => 'sci', 'Sc14g0008750' => 'sci', 'Sc18g0000420' => 'sci', 'Sed0006754' => 'sed', 'Sed0008741' => 'sed', 'Sed0017172' => 'sed', 'Sed0018925' => 'sed', 'Sed0023326' => 'sed', 'Sed0025909' => 'sed', 'SEGI_05333' => 'sgi', 'SEGI_10362' => 'sgi', 'SEGI_13380' => 'sgi', 'SEGI_24306' => 'sgi', 'SEGI_29077' => 'sgi', 'SEGI_29095' => 'sgi', 'SEGI_36534' => 'sgi', 'SEGI_37506' => 'sgi', 'SEGI_38321' => 'sgi', 'SGA_v2.0_scaffold307G48031' => 'sas', 'SGA_v2.0_scaffold47G17507' => 'sas', 'SGA_v2.0_scaffold63G21736' => 'sas', 'SGA_v2.0_scaffold87G27070' => 'sas', 'SHI17794' => 'shi', 'SHI28851' => 'shi', 'SMO165G0155' => 'smo', 'SMO340G0217' => 'smo', 'SMO367G1210' => 'smo', 'Solyc02g093430.3' => 'sly', 'Solyc05g013580.4' => 'sly', 'Solyc07g008030.3' => 'sly', 'Solyc12g035470.2' => 'sly', 'Sopen02g038020' => 'spe', 'Sopen05g008490' => 'spe', 'Sopen07g003910' => 'spe', 'Sopen12g015240' => 'spe', 'Sp1g11550' => 'spa', 'Sp2g16710' => 'spa', 'Sp3g00430' => 'spa', 'Sp3g26780' => 'spa', 'Sp5g22900' => 'spa', 'Sp6g29530' => 'spa', 'TAR371G0794' => 'tar', 'TAR374G0164' => 'tar', 'TAR622G0165' => 'tar', 'TAR626G0929' => 'tar', 'TAR629G2155' => 'tar', 'THA.LOC104805282' => 'tha', 'THA.LOC104805363' => 'tha', 'THA.LOC104808968' => 'tha', 'THA.LOC104821093' => 'tha', 'THA.LOC104823953' => 'tha', 'THA.LOC104825562' => 'tha', 'THA.LOC104825665' => 'tha', 'Thecc.02G261400' => 'tca', 'Thecc.04G019200' => 'tca', 'Thecc.09G130400' => 'tca', 'Thhalv10004374m.g' => 'esa', 'Thhalv10007850m.g' => 'esa', 'Thhalv10013782m.g' => 'esa', 'Thhalv10018686m.g' => 'esa', 'Thhalv10020899m.g' => 'esa', 'Thhalv10022755m.g' => 'esa', 'TPR.G23851' => 'tpr', 'TPR.G26500' => 'tpr', 'TPR.G27267' => 'tpr', 'TPR.G32001' => 'tpr', 'TPR.G6251' => 'tpr', 'TPR.G8167' => 'tpr', 'TWI12G1330' => 'twi', 'TWI18G1239' => 'twi', 'TWI34G0979' => 'twi', 'TWI36G0670' => 'twi', 'TWI36G0707' => 'twi', 'TWI56G0233' => 'twi', 'TWI75G1809' => 'twi', 'unitig_21.g20874' => 'ugi', 'unitig_26.g10343' => 'ugi', 'unitig_46.g18392' => 'ugi', 'unitig_52.g17178' => 'ugi', 'unitig_8.g2934' => 'ugi', 'vmacro01122' => 'vma', 'vmacro05875' => 'vma', 'vmacro06147' => 'vma', 'vmacro16191' => 'vma', 'vmacro18293' => 'vma', 'VMungo0251G3707' => 'vmu', 'VMungo0464G1521' => 'vmu', 'VMungo1215G0205' => 'vmu', 'VMungo1383G2484' => 'vmu', 'Zm00001eb079610' => 'zma', 'Zm00001eb135990' => 'zma', 'Zm00001eb183710' => 'zma', 'Zm00001eb246020' => 'zma' ) $gf_id = 'HOM05D001124' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001124' ) $data_identifier = 'HOM05D001124' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 6, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 7, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 21, 'bol' => (int) 10, 'bra' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 6, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 9, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 21, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 8, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 10, 'lsa' => (int) 8, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 8, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 9, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb246020' $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' => 'HOM05D001124', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '548', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02520' => 'bna', 'A03p06630' => 'bna', 'A05p44460' => 'bna', 'A06p08710' => 'bna', 'A06p41090' => 'bna', 'A07p32320' => 'bna', 'A08p32520' => 'bna', 'A09p10360' => 'bna', 'A10p24080' => 'bna', 'Aa31LG11G15250' => 'aar', 'Aa31LG1G1800' => 'aar', 'Aa31LG2G5120' => 'aar', 'Aa31LG2G6070' => 'aar', 'Aa31LG5G10770' => 'aar', 'Aa31sc61G90' => 'aar', 'Actinidia01352' => 'ach', 'Actinidia05983' => 'ach', 'Actinidia08133' => 'ach', 'Actinidia15101' => 'ach', 'Actinidia26379' => 'ach', 'Actinidia35778' => 'ach', 'Actinidia36123' => 'ach', 'Actinidia37436' => 'ach', 'Actinidia38730' => 'ach', 'Ah.02g128210' => 'amhyb', 'Ah.03g132990' => 'amhyb', 'Ah.14g079410' => 'amhyb', 'AL1G24640' => 'aly', 'AL2G26680' => 'aly', 'AL3G10530' => 'aly', 'AL3G45230' => 'aly', 'AL5G15230' => 'aly', 'AL5G16960' => 'aly', 'AL6G25210' => 'aly', 'Aqoxy2G00441' => 'aox', 'Aqoxy3G01236' => 'aox', 'Aqoxy5G03746' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3RQ047' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C7GMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9C8JER' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MBL6KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YXCZ83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZANX40' => 'arhy', 'AT1G12990' => 'ath', 'AT1G67880' => 'ath', 'AT2G13290' => 'ath', 'AT3G01620' => 'ath', 'AT3G26445' => 'ath', 'AT3G27540' => 'ath', 'AT5G14480' => 'ath', 'ATR0824G026' => 'atr', 'ATR1098G019' => 'atr', 'Atru.chr11.2145' => 'acertr', 'Atru.chr2.3636' => 'acertr', 'Atru.chr2.3644' => 'acertr', 'Atru.chr6.2422' => 'acertr', 'Atru.chr7.1112' => 'acertr', 'AUR62005469' => 'cqu', 'AUR62011166' => 'cqu', 'AUR62013319' => 'cqu', 'AUR62024273' => 'cqu', 'AUR62028420' => 'cqu', 'AUR62041942' => 'cqu', 'BcaB01g04969' => 'bca', 'BcaB01g06371' => 'bca', 'BcaB02g11494' => 'bca', 'BcaB03g15382' => 'bca', 'BcaB08g36994' => 'bca', 'BcaC03g13477' => 'bca', 'BcaC03g13478' => 'bca', 'BcaC03g13480' => 'bca', 'BcaC03g13481' => 'bca', 'BcaC03g13486' => 'bca', 'BcaC04g19031' => 'bca', 'BcaC04g23085' => 'bca', 'BcaC05g25094' => 'bca', 'BcaC05g25096' => 'bca', 'BcaC05g25138' => 'bca', 'BcaC05g30416' => 'bca', 'BcaC05g30455' => 'bca', 'BcaC06g30979' => 'bca', 'BcaC06g33805' => 'bca', 'BcaC08g46021' => 'bca', 'BcaNung03154' => 'bca', 'BolC2t06623H' => 'bol', 'BolC2t06632H' => 'bol', 'BolC2t06635H' => 'bol', 'BolC2t06638H' => 'bol', 'BolC3t13266H' => 'bol', 'BolC5t29776H' => 'bol', 'BolC6t38912H' => 'bol', 'BolC7t44183H' => 'bol', 'BolC9t54123H' => 'bol', 'BolC9t59107H' => 'bol', 'BraA02t05221Z' => 'bra', 'BraA03t09996Z' => 'bra', 'BraA05t23210Z' => 'bra', 'BraA06t24068Z' => 'bra', 'BraA06t27032Z' => 'bra', 'BraA08t35176Z' => 'bra', 'BraA09t36680Z' => 'bra', 'BraA10t44471Z' => 'bra', 'C02p06760' => 'bna', 'C02p06890' => 'bna', 'C02p07010' => 'bna', 'C03p07660' => 'bna', 'C05p10300' => 'bna', 'C06p38150' => 'bna', 'C07p36650' => 'bna', 'C08p15770' => 'bna', 'C09p12300' => 'bna', 'C09p62700' => 'bna', 'C09p75040' => 'bna', 'CAN.G13.1' => 'can', 'CAN.G138.4' => 'can', 'CAN.G44.6' => 'can', 'CAN.G473.19' => 'can', 'CANSAT01G0835' => 'cansat', 'CANSAT11G0246' => 'cansat', 'CANSAT11G1766' => 'cansat', 'CANSAT64G1954' => 'cansat', 'CARHR013330' => 'chi', 'CARHR060530' => 'chi', 'CARHR075300' => 'chi', 'CARHR105120' => 'chi', 'CARHR148910' => 'chi', 'CARHR198830' => 'chi', 'Carub.0001s1275' => 'cru', 'Carub.0002s1437' => 'cru', 'Carub.0003s0044' => 'cru', 'Carub.0003s2787' => 'cru', 'Carub.0005s0597' => 'cru', 'Carub.0006s1266' => 'cru', 'Ca_06935_v3' => 'car', 'Ca_13559_v3' => 'car', 'Ca_16941_v3' => 'car', 'Ca_16960_v3' => 'car', 'Ca_17775_v3' => 'car', 'Ca_30464_v3' => 'car', 'Cc06_g08160' => 'ccan', 'Cc07_g01520' => 'ccan', 'Cc11_g15810' => 'ccan', 'CDE02G2840' => 'cde', 'CDE03G0093' => 'cde', 'CDE04G2127' => 'cde', 'CDE07G1857' => 'cde', 'CDE09G1246' => 'cde', 'Cfa003412' => 'cfa', 'Cfa007341' => 'cfa', 'Cfa009220' => 'cfa', 'Ciclev10008737m.g' => 'ccl', 'Ciclev10015565m.g' => 'ccl', 'Ciclev10031761m.g' => 'ccl', 'CiPaw.03G045300' => 'cil', 'CiPaw.03G247200' => 'cil', 'CiPaw.04G029500' => 'cil', 'CiPaw.04G174000' => 'cil', 'CiPaw.05G181200' => 'cil', 'CiPaw.06G067100' => 'cil', 'ClCG05G025800' => 'cla', 'ClCG06G011400' => 'cla', 'ClCG09G019360' => 'cla', 'COL.COLO4_04827' => 'col', 'COL.COLO4_29170' => 'col', 'COL.COLO4_35131' => 'col', 'COL.COLO4_35132' => 'col', 'Cpa.g.sc33.32' => 'cpa', 'Cpa.g.sc46.29' => 'cpa', 'Cpa.g.sc796.1' => 'cpa', 'CsaV3_1G030420' => 'csa', 'CsaV3_5G027050' => 'csa', 'CsaV3_5G031040' => 'csa', 'CsaV3_UNG023130' => 'csa', 'CSS0007726' => 'camsi', 'CSS0016433' => 'camsi', 'CSS0017656' => 'camsi', 'CSS0025364' => 'camsi', 'CSS0027582' => 'camsi', 'CSS0047288' => 'camsi', 'CSS0049950' => 'camsi', 'DCAR_003843' => 'dca', 'DCAR_007052' => 'dca', 'DCAR_020884' => 'dca', 'DCAR_021730' => 'dca', 'DCAR_024423' => 'dca', 'DCAR_026509' => 'dca', 'DCAR_031158' => 'dca', 'Dinv14728' => 'din', 'Dinv15219' => 'din', 'Dinv25728' => 'din', 'Dinv33428' => 'din', 'Dinv36489' => 'din', 'Dinv41486' => 'din', 'Duzib147G0469' => 'dzi', 'Duzib168G0060' => 'dzi', 'Duzib187G1215' => 'dzi', 'Duzib248G0692' => 'dzi', 'Duzib251G0767' => 'dzi', 'Duzib264G0446' => 'dzi', 'Duzib268G0691' => 'dzi', 'ECA232G4767' => 'eca', 'ECA233G2838' => 'eca', 'ECA234G0391' => 'eca', 'ECA234G0857' => 'eca', 'ECA236G1593' => 'eca', 'ECA238G0565' => 'eca', 'ECA246G1027' => 'eca', 'ECA246G3223' => 'eca', 'ECA246G3470' => 'eca', 'EL10Ac6g13829' => 'bvu', 'EL10Ac6g14093' => 'bvu', 'EL10Ac8g18707' => 'bvu', 'Eucgr.C01369' => 'egr', 'Eucgr.H02492' => 'egr', 'Eucgr.I01733' => 'egr', 'Eucgr.J02255' => 'egr', 'Eucgr.J02257' => 'egr', 'Eucgr.J02258' => 'egr', 'FAN02G1601' => 'fan', 'FAN03G1586' => 'fan', 'FAN03G2986' => 'fan', 'FAN05G4837' => 'fan', 'FAN06G0146' => 'fan', 'FAN07G0858' => 'fan', 'FAN09G3179' => 'fan', 'FAN10G0669' => 'fan', 'FAN12G2358' => 'fan', 'FAN14G4198' => 'fan', 'FAN14G5112' => 'fan', 'FAN17G0342' => 'fan', 'FAN19G0342' => 'fan', 'FAN19G0962' => 'fan', 'FAN19G1101' => 'fan', 'FAN19G1872' => 'fan', 'FAN22G0356' => 'fan', 'FAN23G0744' => 'fan', 'FAN23G1914' => 'fan', 'FAN26G0032' => 'fan', 'FAN28G0625' => 'fan', 'FvH4_1g02710' => 'fve', 'FvH4_1g02720' => 'fve', 'FvH4_4g25670' => 'fve', 'FvH4_6g51700' => 'fve', 'FvH4_7g20170' => 'fve', 'Glyma.05G175000' => 'gma', 'Glyma.08G132300' => 'gma', 'Glyma.11G243000' => 'gma', 'Glyma.13G158900' => 'gma', 'Glyma.17G112400' => 'gma', 'Glyma.18G014100' => 'gma', 'Glyma.19G003100' => 'gma', 'Glyma.19G056500' => 'gma', 'Gohir.A01G158900' => 'ghi', 'Gohir.A05G312600' => 'ghi', 'Gohir.A05G354900' => 'ghi', 'Gohir.A07G037200' => 'ghi', 'Gohir.A09G030000' => 'ghi', 'Gohir.A12G145200' => 'ghi', 'Gohir.D01G151500' => 'ghi', 'Gohir.D04G058300' => 'ghi', 'Gohir.D05G314100' => 'ghi', 'Gohir.D07G041400' => 'ghi', 'Gohir.D09G029700' => 'ghi', 'Gohir.D12G149700' => 'ghi', 'Gorai.001G043800' => 'gra', 'Gorai.002G187800' => 'gra', 'Gorai.006G034700' => 'gra', 'Gorai.008G161200' => 'gra', 'Gorai.009G335700' => 'gra', 'Gorai.012G065000' => 'gra', 'GSVIVG01000535001' => 'vvi', 'GSVIVG01015572001' => 'vvi', 'GSVIVG01032386001' => 'vvi', 'HanXRQChr05g0138531' => 'han', 'HanXRQChr06g0174391' => 'han', 'HanXRQChr07g0199021' => 'han', 'HanXRQChr08g0208211' => 'han', 'HanXRQChr09g0255471' => 'han', 'HanXRQChr10g0315791' => 'han', 'HanXRQChr12g0371991' => 'han', 'HanXRQChr15g0475251' => 'han', 'HanXRQChr17g0540001' => 'han', 'HanXRQChr17g0548631' => 'han', 'HanXRQChr17g0569561' => 'han', 'Haze_12256' => 'cav', 'Haze_14756' => 'cav', 'Haze_25528' => 'cav', 'Hma1.2p1_0079F.1_g041020' => 'hma', 'Hma1.2p1_0818F.1_g223260' => 'hma', 'Hma1.2p1_1747F.1_g300530' => 'hma', 'HPP92_004607' => 'vpl', 'HPP92_004608' => 'vpl', 'HPP92_006181' => 'vpl', 'HPP92_012192' => 'vpl', 'HPP92_015680' => 'vpl', 'HPP92_020249' => 'vpl', 'HPP92_021376' => 'vpl', 'HPP92_024275' => 'vpl', 'Hund06031' => 'sun', 'Hund25391' => 'sun', 'Lalb_Chr07g0185371' => 'lal', 'Lalb_Chr07g0185381' => 'lal', 'Lalb_Chr12g0204011' => 'lal', 'Lalb_Chr13g0301671' => 'lal', 'Lalb_Chr14g0362851' => 'lal', 'Lalb_Chr24g0403581' => 'lal', 'Lj1g0000233' => 'lja', 'Lj2g0018120' => 'lja', 'Lj3C621T0' => 'lonja', 'Lj3P1059T14' => 'lonja', 'Lj3P611T9' => 'lonja', 'Lj3P614T13' => 'lonja', 'Lj3P615T5' => 'lonja', 'Lj4g0012315' => 'lja', 'Lj4g0026182' => 'lja', 'Lj6P813T16' => 'lonja', 'Lj7C427T7' => 'lonja', 'Lj7C427T8' => 'lonja', 'Lj7P600T41' => 'lonja', 'Lju41C42G17' => 'lonja', 'Lsat_1_v5_gn_0_47300' => 'lsa', 'Lsat_1_v5_gn_2_91280' => 'lsa', 'Lsat_1_v5_gn_3_30561' => 'lsa', 'Lsat_1_v5_gn_4_184321' => 'lsa', 'Lsat_1_v5_gn_4_4041' => 'lsa', 'Lsat_1_v5_gn_5_92000' => 'lsa', 'Lsat_1_v5_gn_8_152940' => 'lsa', 'Lsat_1_v5_gn_8_62401' => 'lsa', 'Manes.06G055900' => 'mes', 'Manes.12G022200' => 'mes', 'Manes.13G023300' => 'mes', 'Manes.14G115000' => 'mes', 'Manes.15G151700' => 'mes', 'Manes.17G111300' => 'mes', 'Mapoly0226s0009' => 'mpo', 'MBI02_g25363_MAGBIO' => 'mbi', 'MBI06_g00027_MAGBIO' => 'mbi', 'MBI10_g13034_MAGBIO' => 'mbi', 'MD09G1023400' => 'mdo', 'MD13G1100100' => 'mdo', 'MD15G1169200' => 'mdo', 'MD16G1101100' => 'mdo', 'MD17G1022900' => 'mdo', 'Medtr3g096150' => 'mtr', 'Medtr4g115070' => 'mtr', 'Medtr7g033325' => 'mtr', 'Medtr8g089840' => 'mtr', 'MELO3C010319.2' => 'cme', 'MELO3C011944.2' => 'cme', 'MELO3C021589.2' => 'cme', 'Migut.E00207' => 'egut', 'Migut.H00067' => 'egut', 'Migut.K00433' => 'egut', 'Migut.K00606' => 'egut', 'Migut.K01410' => 'egut', 'MSTRG.13347' => 'ama', 'MSTRG.24045' => 'ama', 'MSTRG.2428' => 'ama', 'MSTRG.26410' => 'ama', 'MSTRG.3139' => 'ama', 'MSTRG.3286' => 'ama', 'MSTRG.563' => 'ama', 'MSTRG.7941' => 'ama', 'Nitab4.5_0000028g0060' => 'nta', 'Nitab4.5_0000065g0260' => 'nta', 'Nitab4.5_0000112g0060' => 'nta', 'Nitab4.5_0000489g0120' => 'nta', 'Nitab4.5_0001776g0050' => 'nta', 'Nitab4.5_0001854g0010' => 'nta', 'Nitab4.5_0001860g0020' => 'nta', 'Nitab4.5_0004352g0010' => 'nta', 'Nitab4.5_0008716g0020' => 'nta', 'Nitab4.5_0008922g0010' => 'nta', 'Nn3g16693' => 'nnu', 'Nn4g22596' => 'nnu', 'Nn7g37639' => 'nnu', 'Oeu001701.1' => 'oeu', 'Oeu018149.1' => 'oeu', 'Oeu026220.1' => 'oeu', 'Oeu038635.1' => 'oeu', 'Oeu049176.1' => 'oeu', 'Oeu056706.1' => 'oeu', 'Oeu056937.1' => 'oeu', 'Oeu057540.1' => 'oeu', 'Os02g0594900' => 'osa', 'Os02g0595100' => 'osa', 'Os04g0477500' => 'osa', 'Os12g0611900' => 'osa', 'Peaxi162Scf00076g00020' => 'pax', 'Peaxi162Scf00128g00217' => 'pax', 'Peaxi162Scf00129g01640' => 'pax', 'Peaxi162Scf00669g00007' => 'pax', 'Peaxi162Scf00700g00421' => 'pax', 'Peaxi162Scf00801g00038' => 'pax', 'Peaxi162Scf00891g00025' => 'pax', 'PGR083G0909' => 'pgr', 'PGR119G1005' => 'pgr', 'PGR142G2236' => 'pgr', 'PGR142G3388' => 'pgr', 'PGSC0003DMG400004514' => 'stu', 'PGSC0003DMG400012635' => 'stu', 'PGSC0003DMG400015730' => 'stu', 'PGSC0003DMG400018611' => 'stu', 'PGSC0003DMG400030897' => 'stu', 'Phvul.001G254800' => 'pvu', 'Phvul.002G260100' => 'pvu', 'Phvul.003G167600' => 'pvu', 'Phvul.004G005100' => 'pvu', 'Potri.001G343600' => 'ptr', 'Potri.006G066700' => 'ptr', 'Potri.008G186000' => 'ptr', 'Potri.010G046900' => 'ptr', 'Potri.018G127900' => 'ptr', 'Pp3c20_17750' => 'ppa', 'Pp3c24_4380' => 'ppa', 'Prupe.1G245800' => 'ppe', 'Prupe.3G293400' => 'ppe', 'Prupe.7G247400' => 'ppe', 'Psat0s145g0120' => 'psa', 'Psat0s595g0040' => 'psa', 'Psat0s595g0120' => 'psa', 'Psat3g175040' => 'psa', 'Psat7g058120' => 'psa', 'PSO017G0428' => 'pso', 'PSO063G7510' => 'pso', 'PSO067G0046' => 'pso', 'PSO478G1073' => 'pso', 'PSO675G3677' => 'pso', 'PSO675G6558' => 'pso', 'PSO675G7520' => 'pso', 'PSO675G8959' => 'pso', 'QL02p074089' => 'qlo', 'QL02p089614' => 'qlo', 'QL03p057736' => 'qlo', 'RcHm_v2.0_Chr1g0364131' => 'rch', 'RcHm_v2.0_Chr2g0087801' => 'rch', 'RcHm_v2.0_Chr2g0087821' => 'rch', 'RcHm_v2.0_Chr2g0173231' => 'rch', 'RcHm_v2.0_Chr4g0433111' => 'rch', 'Rhsim03G0250300' => 'rsi', 'Rhsim08G0048400' => 'rsi', 'Rhsim10G0014800' => 'rsi', 'Rhsim12G0040100' => 'rsi', 'Rhsim12G0109700' => 'rsi', 'Sabra06G0049600' => 'sbr', 'Sabra08G0141000' => 'sbr', 'Sabra10G0021400' => 'sbr', 'Sabra16G0222900' => 'sbr', 'Sabra18G0108600' => 'sbr', 'SalBow1G0433' => 'sbo', 'SalBow1G2038' => 'sbo', 'SalBow1G5003' => 'sbo', 'SalBow7G1197' => 'sbo', 'SalBow8G3506' => 'sbo', 'Sc03g0007300' => 'sci', 'Sc11g0000950' => 'sci', 'Sc14g0008750' => 'sci', 'Sc18g0000420' => 'sci', 'Sed0006754' => 'sed', 'Sed0008741' => 'sed', 'Sed0017172' => 'sed', 'Sed0018925' => 'sed', 'Sed0023326' => 'sed', 'Sed0025909' => 'sed', 'SEGI_05333' => 'sgi', 'SEGI_10362' => 'sgi', 'SEGI_13380' => 'sgi', 'SEGI_24306' => 'sgi', 'SEGI_29077' => 'sgi', 'SEGI_29095' => 'sgi', 'SEGI_36534' => 'sgi', 'SEGI_37506' => 'sgi', 'SEGI_38321' => 'sgi', 'SGA_v2.0_scaffold307G48031' => 'sas', 'SGA_v2.0_scaffold47G17507' => 'sas', 'SGA_v2.0_scaffold63G21736' => 'sas', 'SGA_v2.0_scaffold87G27070' => 'sas', 'SHI17794' => 'shi', 'SHI28851' => 'shi', 'SMO165G0155' => 'smo', 'SMO340G0217' => 'smo', 'SMO367G1210' => 'smo', 'Solyc02g093430.3' => 'sly', 'Solyc05g013580.4' => 'sly', 'Solyc07g008030.3' => 'sly', 'Solyc12g035470.2' => 'sly', 'Sopen02g038020' => 'spe', 'Sopen05g008490' => 'spe', 'Sopen07g003910' => 'spe', 'Sopen12g015240' => 'spe', 'Sp1g11550' => 'spa', 'Sp2g16710' => 'spa', 'Sp3g00430' => 'spa', 'Sp3g26780' => 'spa', 'Sp5g22900' => 'spa', 'Sp6g29530' => 'spa', 'TAR371G0794' => 'tar', 'TAR374G0164' => 'tar', 'TAR622G0165' => 'tar', 'TAR626G0929' => 'tar', 'TAR629G2155' => 'tar', 'THA.LOC104805282' => 'tha', 'THA.LOC104805363' => 'tha', 'THA.LOC104808968' => 'tha', 'THA.LOC104821093' => 'tha', 'THA.LOC104823953' => 'tha', 'THA.LOC104825562' => 'tha', 'THA.LOC104825665' => 'tha', 'Thecc.02G261400' => 'tca', 'Thecc.04G019200' => 'tca', 'Thecc.09G130400' => 'tca', 'Thhalv10004374m.g' => 'esa', 'Thhalv10007850m.g' => 'esa', 'Thhalv10013782m.g' => 'esa', 'Thhalv10018686m.g' => 'esa', 'Thhalv10020899m.g' => 'esa', 'Thhalv10022755m.g' => 'esa', 'TPR.G23851' => 'tpr', 'TPR.G26500' => 'tpr', 'TPR.G27267' => 'tpr', 'TPR.G32001' => 'tpr', 'TPR.G6251' => 'tpr', 'TPR.G8167' => 'tpr', 'TWI12G1330' => 'twi', 'TWI18G1239' => 'twi', 'TWI34G0979' => 'twi', 'TWI36G0670' => 'twi', 'TWI36G0707' => 'twi', 'TWI56G0233' => 'twi', 'TWI75G1809' => 'twi', 'unitig_21.g20874' => 'ugi', 'unitig_26.g10343' => 'ugi', 'unitig_46.g18392' => 'ugi', 'unitig_52.g17178' => 'ugi', 'unitig_8.g2934' => 'ugi', 'vmacro01122' => 'vma', 'vmacro05875' => 'vma', 'vmacro06147' => 'vma', 'vmacro16191' => 'vma', 'vmacro18293' => 'vma', 'VMungo0251G3707' => 'vmu', 'VMungo0464G1521' => 'vmu', 'VMungo1215G0205' => 'vmu', 'VMungo1383G2484' => 'vmu', 'Zm00001eb079610' => 'zma', 'Zm00001eb135990' => 'zma', 'Zm00001eb183710' => 'zma', 'Zm00001eb246020' => 'zma' ), 'gf_id' => 'HOM05D001124', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001124' ), 'data_identifier' => 'HOM05D001124', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001124', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '548', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02520' => 'bna', 'A03p06630' => 'bna', 'A05p44460' => 'bna', 'A06p08710' => 'bna', 'A06p41090' => 'bna', 'A07p32320' => 'bna', 'A08p32520' => 'bna', 'A09p10360' => 'bna', 'A10p24080' => 'bna', 'Aa31LG11G15250' => 'aar', 'Aa31LG1G1800' => 'aar', 'Aa31LG2G5120' => 'aar', 'Aa31LG2G6070' => 'aar', 'Aa31LG5G10770' => 'aar', 'Aa31sc61G90' => 'aar', 'Actinidia01352' => 'ach', 'Actinidia05983' => 'ach', 'Actinidia08133' => 'ach', 'Actinidia15101' => 'ach', 'Actinidia26379' => 'ach', 'Actinidia35778' => 'ach', 'Actinidia36123' => 'ach', 'Actinidia37436' => 'ach', 'Actinidia38730' => 'ach', 'Ah.02g128210' => 'amhyb', 'Ah.03g132990' => 'amhyb', 'Ah.14g079410' => 'amhyb', 'AL1G24640' => 'aly', 'AL2G26680' => 'aly', 'AL3G10530' => 'aly', 'AL3G45230' => 'aly', 'AL5G15230' => 'aly', 'AL5G16960' => 'aly', 'AL6G25210' => 'aly', 'Aqoxy2G00441' => 'aox', 'Aqoxy3G01236' => 'aox', 'Aqoxy5G03746' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3RQ047' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C7GMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9C8JER' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MBL6KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YXCZ83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZANX40' => 'arhy', 'AT1G12990' => 'ath', 'AT1G67880' => 'ath', 'AT2G13290' => 'ath', 'AT3G01620' => 'ath', 'AT3G26445' => 'ath', 'AT3G27540' => 'ath', 'AT5G14480' => 'ath', 'ATR0824G026' => 'atr', 'ATR1098G019' => 'atr', 'Atru.chr11.2145' => 'acertr', 'Atru.chr2.3636' => 'acertr', 'Atru.chr2.3644' => 'acertr', 'Atru.chr6.2422' => 'acertr', 'Atru.chr7.1112' => 'acertr', 'AUR62005469' => 'cqu', 'AUR62011166' => 'cqu', 'AUR62013319' => 'cqu', 'AUR62024273' => 'cqu', 'AUR62028420' => 'cqu', 'AUR62041942' => 'cqu', 'BcaB01g04969' => 'bca', 'BcaB01g06371' => 'bca', 'BcaB02g11494' => 'bca', 'BcaB03g15382' => 'bca', 'BcaB08g36994' => 'bca', 'BcaC03g13477' => 'bca', 'BcaC03g13478' => 'bca', 'BcaC03g13480' => 'bca', 'BcaC03g13481' => 'bca', 'BcaC03g13486' => 'bca', 'BcaC04g19031' => 'bca', 'BcaC04g23085' => 'bca', 'BcaC05g25094' => 'bca', 'BcaC05g25096' => 'bca', 'BcaC05g25138' => 'bca', 'BcaC05g30416' => 'bca', 'BcaC05g30455' => 'bca', 'BcaC06g30979' => 'bca', 'BcaC06g33805' => 'bca', 'BcaC08g46021' => 'bca', 'BcaNung03154' => 'bca', 'BolC2t06623H' => 'bol', 'BolC2t06632H' => 'bol', 'BolC2t06635H' => 'bol', 'BolC2t06638H' => 'bol', 'BolC3t13266H' => 'bol', 'BolC5t29776H' => 'bol', 'BolC6t38912H' => 'bol', 'BolC7t44183H' => 'bol', 'BolC9t54123H' => 'bol', 'BolC9t59107H' => 'bol', 'BraA02t05221Z' => 'bra', 'BraA03t09996Z' => 'bra', 'BraA05t23210Z' => 'bra', 'BraA06t24068Z' => 'bra', 'BraA06t27032Z' => 'bra', 'BraA08t35176Z' => 'bra', 'BraA09t36680Z' => 'bra', 'BraA10t44471Z' => 'bra', 'C02p06760' => 'bna', 'C02p06890' => 'bna', 'C02p07010' => 'bna', 'C03p07660' => 'bna', 'C05p10300' => 'bna', 'C06p38150' => 'bna', 'C07p36650' => 'bna', 'C08p15770' => 'bna', 'C09p12300' => 'bna', 'C09p62700' => 'bna', 'C09p75040' => 'bna', 'CAN.G13.1' => 'can', 'CAN.G138.4' => 'can', 'CAN.G44.6' => 'can', 'CAN.G473.19' => 'can', 'CANSAT01G0835' => 'cansat', 'CANSAT11G0246' => 'cansat', 'CANSAT11G1766' => 'cansat', 'CANSAT64G1954' => 'cansat', 'CARHR013330' => 'chi', 'CARHR060530' => 'chi', 'CARHR075300' => 'chi', 'CARHR105120' => 'chi', 'CARHR148910' => 'chi', 'CARHR198830' => 'chi', 'Carub.0001s1275' => 'cru', 'Carub.0002s1437' => 'cru', 'Carub.0003s0044' => 'cru', 'Carub.0003s2787' => 'cru', 'Carub.0005s0597' => 'cru', 'Carub.0006s1266' => 'cru', 'Ca_06935_v3' => 'car', 'Ca_13559_v3' => 'car', 'Ca_16941_v3' => 'car', 'Ca_16960_v3' => 'car', 'Ca_17775_v3' => 'car', 'Ca_30464_v3' => 'car', 'Cc06_g08160' => 'ccan', 'Cc07_g01520' => 'ccan', 'Cc11_g15810' => 'ccan', 'CDE02G2840' => 'cde', 'CDE03G0093' => 'cde', 'CDE04G2127' => 'cde', 'CDE07G1857' => 'cde', 'CDE09G1246' => 'cde', 'Cfa003412' => 'cfa', 'Cfa007341' => 'cfa', 'Cfa009220' => 'cfa', 'Ciclev10008737m.g' => 'ccl', 'Ciclev10015565m.g' => 'ccl', 'Ciclev10031761m.g' => 'ccl', 'CiPaw.03G045300' => 'cil', 'CiPaw.03G247200' => 'cil', 'CiPaw.04G029500' => 'cil', 'CiPaw.04G174000' => 'cil', 'CiPaw.05G181200' => 'cil', 'CiPaw.06G067100' => 'cil', 'ClCG05G025800' => 'cla', 'ClCG06G011400' => 'cla', 'ClCG09G019360' => 'cla', 'COL.COLO4_04827' => 'col', 'COL.COLO4_29170' => 'col', 'COL.COLO4_35131' => 'col', 'COL.COLO4_35132' => 'col', 'Cpa.g.sc33.32' => 'cpa', 'Cpa.g.sc46.29' => 'cpa', 'Cpa.g.sc796.1' => 'cpa', 'CsaV3_1G030420' => 'csa', 'CsaV3_5G027050' => 'csa', 'CsaV3_5G031040' => 'csa', 'CsaV3_UNG023130' => 'csa', 'CSS0007726' => 'camsi', 'CSS0016433' => 'camsi', 'CSS0017656' => 'camsi', 'CSS0025364' => 'camsi', 'CSS0027582' => 'camsi', 'CSS0047288' => 'camsi', 'CSS0049950' => 'camsi', 'DCAR_003843' => 'dca', 'DCAR_007052' => 'dca', 'DCAR_020884' => 'dca', 'DCAR_021730' => 'dca', 'DCAR_024423' => 'dca', 'DCAR_026509' => 'dca', 'DCAR_031158' => 'dca', 'Dinv14728' => 'din', 'Dinv15219' => 'din', 'Dinv25728' => 'din', 'Dinv33428' => 'din', 'Dinv36489' => 'din', 'Dinv41486' => 'din', 'Duzib147G0469' => 'dzi', 'Duzib168G0060' => 'dzi', 'Duzib187G1215' => 'dzi', 'Duzib248G0692' => 'dzi', 'Duzib251G0767' => 'dzi', 'Duzib264G0446' => 'dzi', 'Duzib268G0691' => 'dzi', 'ECA232G4767' => 'eca', 'ECA233G2838' => 'eca', 'ECA234G0391' => 'eca', 'ECA234G0857' => 'eca', 'ECA236G1593' => 'eca', 'ECA238G0565' => 'eca', 'ECA246G1027' => 'eca', 'ECA246G3223' => 'eca', 'ECA246G3470' => 'eca', 'EL10Ac6g13829' => 'bvu', 'EL10Ac6g14093' => 'bvu', 'EL10Ac8g18707' => 'bvu', 'Eucgr.C01369' => 'egr', 'Eucgr.H02492' => 'egr', 'Eucgr.I01733' => 'egr', 'Eucgr.J02255' => 'egr', 'Eucgr.J02257' => 'egr', 'Eucgr.J02258' => 'egr', 'FAN02G1601' => 'fan', 'FAN03G1586' => 'fan', 'FAN03G2986' => 'fan', 'FAN05G4837' => 'fan', 'FAN06G0146' => 'fan', 'FAN07G0858' => 'fan', 'FAN09G3179' => 'fan', 'FAN10G0669' => 'fan', 'FAN12G2358' => 'fan', 'FAN14G4198' => 'fan', 'FAN14G5112' => 'fan', 'FAN17G0342' => 'fan', 'FAN19G0342' => 'fan', 'FAN19G0962' => 'fan', 'FAN19G1101' => 'fan', 'FAN19G1872' => 'fan', 'FAN22G0356' => 'fan', 'FAN23G0744' => 'fan', 'FAN23G1914' => 'fan', 'FAN26G0032' => 'fan', 'FAN28G0625' => 'fan', 'FvH4_1g02710' => 'fve', 'FvH4_1g02720' => 'fve', 'FvH4_4g25670' => 'fve', 'FvH4_6g51700' => 'fve', 'FvH4_7g20170' => 'fve', 'Glyma.05G175000' => 'gma', 'Glyma.08G132300' => 'gma', 'Glyma.11G243000' => 'gma', 'Glyma.13G158900' => 'gma', 'Glyma.17G112400' => 'gma', 'Glyma.18G014100' => 'gma', 'Glyma.19G003100' => 'gma', 'Glyma.19G056500' => 'gma', 'Gohir.A01G158900' => 'ghi', 'Gohir.A05G312600' => 'ghi', 'Gohir.A05G354900' => 'ghi', 'Gohir.A07G037200' => 'ghi', 'Gohir.A09G030000' => 'ghi', 'Gohir.A12G145200' => 'ghi', 'Gohir.D01G151500' => 'ghi', 'Gohir.D04G058300' => 'ghi', 'Gohir.D05G314100' => 'ghi', 'Gohir.D07G041400' => 'ghi', 'Gohir.D09G029700' => 'ghi', 'Gohir.D12G149700' => 'ghi', 'Gorai.001G043800' => 'gra', 'Gorai.002G187800' => 'gra', 'Gorai.006G034700' => 'gra', 'Gorai.008G161200' => 'gra', 'Gorai.009G335700' => 'gra', 'Gorai.012G065000' => 'gra', 'GSVIVG01000535001' => 'vvi', 'GSVIVG01015572001' => 'vvi', 'GSVIVG01032386001' => 'vvi', 'HanXRQChr05g0138531' => 'han', 'HanXRQChr06g0174391' => 'han', 'HanXRQChr07g0199021' => 'han', 'HanXRQChr08g0208211' => 'han', 'HanXRQChr09g0255471' => 'han', 'HanXRQChr10g0315791' => 'han', 'HanXRQChr12g0371991' => 'han', 'HanXRQChr15g0475251' => 'han', 'HanXRQChr17g0540001' => 'han', 'HanXRQChr17g0548631' => 'han', 'HanXRQChr17g0569561' => 'han', 'Haze_12256' => 'cav', 'Haze_14756' => 'cav', 'Haze_25528' => 'cav', 'Hma1.2p1_0079F.1_g041020' => 'hma', 'Hma1.2p1_0818F.1_g223260' => 'hma', 'Hma1.2p1_1747F.1_g300530' => 'hma', 'HPP92_004607' => 'vpl', 'HPP92_004608' => 'vpl', 'HPP92_006181' => 'vpl', 'HPP92_012192' => 'vpl', 'HPP92_015680' => 'vpl', 'HPP92_020249' => 'vpl', 'HPP92_021376' => 'vpl', 'HPP92_024275' => 'vpl', 'Hund06031' => 'sun', 'Hund25391' => 'sun', 'Lalb_Chr07g0185371' => 'lal', 'Lalb_Chr07g0185381' => 'lal', 'Lalb_Chr12g0204011' => 'lal', 'Lalb_Chr13g0301671' => 'lal', 'Lalb_Chr14g0362851' => 'lal', 'Lalb_Chr24g0403581' => 'lal', 'Lj1g0000233' => 'lja', 'Lj2g0018120' => 'lja', 'Lj3C621T0' => 'lonja', 'Lj3P1059T14' => 'lonja', 'Lj3P611T9' => 'lonja', 'Lj3P614T13' => 'lonja', 'Lj3P615T5' => 'lonja', 'Lj4g0012315' => 'lja', 'Lj4g0026182' => 'lja', 'Lj6P813T16' => 'lonja', 'Lj7C427T7' => 'lonja', 'Lj7C427T8' => 'lonja', 'Lj7P600T41' => 'lonja', 'Lju41C42G17' => 'lonja', 'Lsat_1_v5_gn_0_47300' => 'lsa', 'Lsat_1_v5_gn_2_91280' => 'lsa', 'Lsat_1_v5_gn_3_30561' => 'lsa', 'Lsat_1_v5_gn_4_184321' => 'lsa', 'Lsat_1_v5_gn_4_4041' => 'lsa', 'Lsat_1_v5_gn_5_92000' => 'lsa', 'Lsat_1_v5_gn_8_152940' => 'lsa', 'Lsat_1_v5_gn_8_62401' => 'lsa', 'Manes.06G055900' => 'mes', 'Manes.12G022200' => 'mes', 'Manes.13G023300' => 'mes', 'Manes.14G115000' => 'mes', 'Manes.15G151700' => 'mes', 'Manes.17G111300' => 'mes', 'Mapoly0226s0009' => 'mpo', 'MBI02_g25363_MAGBIO' => 'mbi', 'MBI06_g00027_MAGBIO' => 'mbi', 'MBI10_g13034_MAGBIO' => 'mbi', 'MD09G1023400' => 'mdo', 'MD13G1100100' => 'mdo', 'MD15G1169200' => 'mdo', 'MD16G1101100' => 'mdo', 'MD17G1022900' => 'mdo', 'Medtr3g096150' => 'mtr', 'Medtr4g115070' => 'mtr', 'Medtr7g033325' => 'mtr', 'Medtr8g089840' => 'mtr', 'MELO3C010319.2' => 'cme', 'MELO3C011944.2' => 'cme', 'MELO3C021589.2' => 'cme', 'Migut.E00207' => 'egut', 'Migut.H00067' => 'egut', 'Migut.K00433' => 'egut', 'Migut.K00606' => 'egut', 'Migut.K01410' => 'egut', 'MSTRG.13347' => 'ama', 'MSTRG.24045' => 'ama', 'MSTRG.2428' => 'ama', 'MSTRG.26410' => 'ama', 'MSTRG.3139' => 'ama', 'MSTRG.3286' => 'ama', 'MSTRG.563' => 'ama', 'MSTRG.7941' => 'ama', 'Nitab4.5_0000028g0060' => 'nta', 'Nitab4.5_0000065g0260' => 'nta', 'Nitab4.5_0000112g0060' => 'nta', 'Nitab4.5_0000489g0120' => 'nta', 'Nitab4.5_0001776g0050' => 'nta', 'Nitab4.5_0001854g0010' => 'nta', 'Nitab4.5_0001860g0020' => 'nta', 'Nitab4.5_0004352g0010' => 'nta', 'Nitab4.5_0008716g0020' => 'nta', 'Nitab4.5_0008922g0010' => 'nta', 'Nn3g16693' => 'nnu', 'Nn4g22596' => 'nnu', 'Nn7g37639' => 'nnu', 'Oeu001701.1' => 'oeu', 'Oeu018149.1' => 'oeu', 'Oeu026220.1' => 'oeu', 'Oeu038635.1' => 'oeu', 'Oeu049176.1' => 'oeu', 'Oeu056706.1' => 'oeu', 'Oeu056937.1' => 'oeu', 'Oeu057540.1' => 'oeu', 'Os02g0594900' => 'osa', 'Os02g0595100' => 'osa', 'Os04g0477500' => 'osa', 'Os12g0611900' => 'osa', 'Peaxi162Scf00076g00020' => 'pax', 'Peaxi162Scf00128g00217' => 'pax', 'Peaxi162Scf00129g01640' => 'pax', 'Peaxi162Scf00669g00007' => 'pax', 'Peaxi162Scf00700g00421' => 'pax', 'Peaxi162Scf00801g00038' => 'pax', 'Peaxi162Scf00891g00025' => 'pax', 'PGR083G0909' => 'pgr', 'PGR119G1005' => 'pgr', 'PGR142G2236' => 'pgr', 'PGR142G3388' => 'pgr', 'PGSC0003DMG400004514' => 'stu', 'PGSC0003DMG400012635' => 'stu', 'PGSC0003DMG400015730' => 'stu', 'PGSC0003DMG400018611' => 'stu', 'PGSC0003DMG400030897' => 'stu', 'Phvul.001G254800' => 'pvu', 'Phvul.002G260100' => 'pvu', 'Phvul.003G167600' => 'pvu', 'Phvul.004G005100' => 'pvu', 'Potri.001G343600' => 'ptr', 'Potri.006G066700' => 'ptr', 'Potri.008G186000' => 'ptr', 'Potri.010G046900' => 'ptr', 'Potri.018G127900' => 'ptr', 'Pp3c20_17750' => 'ppa', 'Pp3c24_4380' => 'ppa', 'Prupe.1G245800' => 'ppe', 'Prupe.3G293400' => 'ppe', 'Prupe.7G247400' => 'ppe', 'Psat0s145g0120' => 'psa', 'Psat0s595g0040' => 'psa', 'Psat0s595g0120' => 'psa', 'Psat3g175040' => 'psa', 'Psat7g058120' => 'psa', 'PSO017G0428' => 'pso', 'PSO063G7510' => 'pso', 'PSO067G0046' => 'pso', 'PSO478G1073' => 'pso', 'PSO675G3677' => 'pso', 'PSO675G6558' => 'pso', 'PSO675G7520' => 'pso', 'PSO675G8959' => 'pso', 'QL02p074089' => 'qlo', 'QL02p089614' => 'qlo', 'QL03p057736' => 'qlo', 'RcHm_v2.0_Chr1g0364131' => 'rch', 'RcHm_v2.0_Chr2g0087801' => 'rch', 'RcHm_v2.0_Chr2g0087821' => 'rch', 'RcHm_v2.0_Chr2g0173231' => 'rch', 'RcHm_v2.0_Chr4g0433111' => 'rch', 'Rhsim03G0250300' => 'rsi', 'Rhsim08G0048400' => 'rsi', 'Rhsim10G0014800' => 'rsi', 'Rhsim12G0040100' => 'rsi', 'Rhsim12G0109700' => 'rsi', 'Sabra06G0049600' => 'sbr', 'Sabra08G0141000' => 'sbr', 'Sabra10G0021400' => 'sbr', 'Sabra16G0222900' => 'sbr', 'Sabra18G0108600' => 'sbr', 'SalBow1G0433' => 'sbo', 'SalBow1G2038' => 'sbo', 'SalBow1G5003' => 'sbo', 'SalBow7G1197' => 'sbo', 'SalBow8G3506' => 'sbo', 'Sc03g0007300' => 'sci', 'Sc11g0000950' => 'sci', 'Sc14g0008750' => 'sci', 'Sc18g0000420' => 'sci', 'Sed0006754' => 'sed', 'Sed0008741' => 'sed', 'Sed0017172' => 'sed', 'Sed0018925' => 'sed', 'Sed0023326' => 'sed', 'Sed0025909' => 'sed', 'SEGI_05333' => 'sgi', 'SEGI_10362' => 'sgi', 'SEGI_13380' => 'sgi', 'SEGI_24306' => 'sgi', 'SEGI_29077' => 'sgi', 'SEGI_29095' => 'sgi', 'SEGI_36534' => 'sgi', 'SEGI_37506' => 'sgi', 'SEGI_38321' => 'sgi', 'SGA_v2.0_scaffold307G48031' => 'sas', 'SGA_v2.0_scaffold47G17507' => 'sas', 'SGA_v2.0_scaffold63G21736' => 'sas', 'SGA_v2.0_scaffold87G27070' => 'sas', 'SHI17794' => 'shi', 'SHI28851' => 'shi', 'SMO165G0155' => 'smo', 'SMO340G0217' => 'smo', 'SMO367G1210' => 'smo', 'Solyc02g093430.3' => 'sly', 'Solyc05g013580.4' => 'sly', 'Solyc07g008030.3' => 'sly', 'Solyc12g035470.2' => 'sly', 'Sopen02g038020' => 'spe', 'Sopen05g008490' => 'spe', 'Sopen07g003910' => 'spe', 'Sopen12g015240' => 'spe', 'Sp1g11550' => 'spa', 'Sp2g16710' => 'spa', 'Sp3g00430' => 'spa', 'Sp3g26780' => 'spa', 'Sp5g22900' => 'spa', 'Sp6g29530' => 'spa', 'TAR371G0794' => 'tar', 'TAR374G0164' => 'tar', 'TAR622G0165' => 'tar', 'TAR626G0929' => 'tar', 'TAR629G2155' => 'tar', 'THA.LOC104805282' => 'tha', 'THA.LOC104805363' => 'tha', 'THA.LOC104808968' => 'tha', 'THA.LOC104821093' => 'tha', 'THA.LOC104823953' => 'tha', 'THA.LOC104825562' => 'tha', 'THA.LOC104825665' => 'tha', 'Thecc.02G261400' => 'tca', 'Thecc.04G019200' => 'tca', 'Thecc.09G130400' => 'tca', 'Thhalv10004374m.g' => 'esa', 'Thhalv10007850m.g' => 'esa', 'Thhalv10013782m.g' => 'esa', 'Thhalv10018686m.g' => 'esa', 'Thhalv10020899m.g' => 'esa', 'Thhalv10022755m.g' => 'esa', 'TPR.G23851' => 'tpr', 'TPR.G26500' => 'tpr', 'TPR.G27267' => 'tpr', 'TPR.G32001' => 'tpr', 'TPR.G6251' => 'tpr', 'TPR.G8167' => 'tpr', 'TWI12G1330' => 'twi', 'TWI18G1239' => 'twi', 'TWI34G0979' => 'twi', 'TWI36G0670' => 'twi', 'TWI36G0707' => 'twi', 'TWI56G0233' => 'twi', 'TWI75G1809' => 'twi', 'unitig_21.g20874' => 'ugi', 'unitig_26.g10343' => 'ugi', 'unitig_46.g18392' => 'ugi', 'unitig_52.g17178' => 'ugi', 'unitig_8.g2934' => 'ugi', 'vmacro01122' => 'vma', 'vmacro05875' => 'vma', 'vmacro06147' => 'vma', 'vmacro16191' => 'vma', 'vmacro18293' => 'vma', 'VMungo0251G3707' => 'vmu', 'VMungo0464G1521' => 'vmu', 'VMungo1215G0205' => 'vmu', 'VMungo1383G2484' => 'vmu', 'Zm00001eb079610' => 'zma', 'Zm00001eb135990' => 'zma', 'Zm00001eb183710' => 'zma', 'Zm00001eb246020' => 'zma' ) $gf_id = 'HOM05D001124' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001124' ) $data_identifier = 'HOM05D001124' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 6, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 7, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 21, 'bol' => (int) 10, 'bra' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 6, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 9, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 21, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 8, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 10, 'lsa' => (int) 8, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 8, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 9, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb246020' $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' => 'HOM05D001124', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '548', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02520' => 'bna', 'A03p06630' => 'bna', 'A05p44460' => 'bna', 'A06p08710' => 'bna', 'A06p41090' => 'bna', 'A07p32320' => 'bna', 'A08p32520' => 'bna', 'A09p10360' => 'bna', 'A10p24080' => 'bna', 'Aa31LG11G15250' => 'aar', 'Aa31LG1G1800' => 'aar', 'Aa31LG2G5120' => 'aar', 'Aa31LG2G6070' => 'aar', 'Aa31LG5G10770' => 'aar', 'Aa31sc61G90' => 'aar', 'Actinidia01352' => 'ach', 'Actinidia05983' => 'ach', 'Actinidia08133' => 'ach', 'Actinidia15101' => 'ach', 'Actinidia26379' => 'ach', 'Actinidia35778' => 'ach', 'Actinidia36123' => 'ach', 'Actinidia37436' => 'ach', 'Actinidia38730' => 'ach', 'Ah.02g128210' => 'amhyb', 'Ah.03g132990' => 'amhyb', 'Ah.14g079410' => 'amhyb', 'AL1G24640' => 'aly', 'AL2G26680' => 'aly', 'AL3G10530' => 'aly', 'AL3G45230' => 'aly', 'AL5G15230' => 'aly', 'AL5G16960' => 'aly', 'AL6G25210' => 'aly', 'Aqoxy2G00441' => 'aox', 'Aqoxy3G01236' => 'aox', 'Aqoxy5G03746' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3RQ047' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C7GMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9C8JER' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MBL6KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YXCZ83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZANX40' => 'arhy', 'AT1G12990' => 'ath', 'AT1G67880' => 'ath', 'AT2G13290' => 'ath', 'AT3G01620' => 'ath', 'AT3G26445' => 'ath', 'AT3G27540' => 'ath', 'AT5G14480' => 'ath', 'ATR0824G026' => 'atr', 'ATR1098G019' => 'atr', 'Atru.chr11.2145' => 'acertr', 'Atru.chr2.3636' => 'acertr', 'Atru.chr2.3644' => 'acertr', 'Atru.chr6.2422' => 'acertr', 'Atru.chr7.1112' => 'acertr', 'AUR62005469' => 'cqu', 'AUR62011166' => 'cqu', 'AUR62013319' => 'cqu', 'AUR62024273' => 'cqu', 'AUR62028420' => 'cqu', 'AUR62041942' => 'cqu', 'BcaB01g04969' => 'bca', 'BcaB01g06371' => 'bca', 'BcaB02g11494' => 'bca', 'BcaB03g15382' => 'bca', 'BcaB08g36994' => 'bca', 'BcaC03g13477' => 'bca', 'BcaC03g13478' => 'bca', 'BcaC03g13480' => 'bca', 'BcaC03g13481' => 'bca', 'BcaC03g13486' => 'bca', 'BcaC04g19031' => 'bca', 'BcaC04g23085' => 'bca', 'BcaC05g25094' => 'bca', 'BcaC05g25096' => 'bca', 'BcaC05g25138' => 'bca', 'BcaC05g30416' => 'bca', 'BcaC05g30455' => 'bca', 'BcaC06g30979' => 'bca', 'BcaC06g33805' => 'bca', 'BcaC08g46021' => 'bca', 'BcaNung03154' => 'bca', 'BolC2t06623H' => 'bol', 'BolC2t06632H' => 'bol', 'BolC2t06635H' => 'bol', 'BolC2t06638H' => 'bol', 'BolC3t13266H' => 'bol', 'BolC5t29776H' => 'bol', 'BolC6t38912H' => 'bol', 'BolC7t44183H' => 'bol', 'BolC9t54123H' => 'bol', 'BolC9t59107H' => 'bol', 'BraA02t05221Z' => 'bra', 'BraA03t09996Z' => 'bra', 'BraA05t23210Z' => 'bra', 'BraA06t24068Z' => 'bra', 'BraA06t27032Z' => 'bra', 'BraA08t35176Z' => 'bra', 'BraA09t36680Z' => 'bra', 'BraA10t44471Z' => 'bra', 'C02p06760' => 'bna', 'C02p06890' => 'bna', 'C02p07010' => 'bna', 'C03p07660' => 'bna', 'C05p10300' => 'bna', 'C06p38150' => 'bna', 'C07p36650' => 'bna', 'C08p15770' => 'bna', 'C09p12300' => 'bna', 'C09p62700' => 'bna', 'C09p75040' => 'bna', 'CAN.G13.1' => 'can', 'CAN.G138.4' => 'can', 'CAN.G44.6' => 'can', 'CAN.G473.19' => 'can', 'CANSAT01G0835' => 'cansat', 'CANSAT11G0246' => 'cansat', 'CANSAT11G1766' => 'cansat', 'CANSAT64G1954' => 'cansat', 'CARHR013330' => 'chi', 'CARHR060530' => 'chi', 'CARHR075300' => 'chi', 'CARHR105120' => 'chi', 'CARHR148910' => 'chi', 'CARHR198830' => 'chi', 'Carub.0001s1275' => 'cru', 'Carub.0002s1437' => 'cru', 'Carub.0003s0044' => 'cru', 'Carub.0003s2787' => 'cru', 'Carub.0005s0597' => 'cru', 'Carub.0006s1266' => 'cru', 'Ca_06935_v3' => 'car', 'Ca_13559_v3' => 'car', 'Ca_16941_v3' => 'car', 'Ca_16960_v3' => 'car', 'Ca_17775_v3' => 'car', 'Ca_30464_v3' => 'car', 'Cc06_g08160' => 'ccan', 'Cc07_g01520' => 'ccan', 'Cc11_g15810' => 'ccan', 'CDE02G2840' => 'cde', 'CDE03G0093' => 'cde', 'CDE04G2127' => 'cde', 'CDE07G1857' => 'cde', 'CDE09G1246' => 'cde', 'Cfa003412' => 'cfa', 'Cfa007341' => 'cfa', 'Cfa009220' => 'cfa', 'Ciclev10008737m.g' => 'ccl', 'Ciclev10015565m.g' => 'ccl', 'Ciclev10031761m.g' => 'ccl', 'CiPaw.03G045300' => 'cil', 'CiPaw.03G247200' => 'cil', 'CiPaw.04G029500' => 'cil', 'CiPaw.04G174000' => 'cil', 'CiPaw.05G181200' => 'cil', 'CiPaw.06G067100' => 'cil', 'ClCG05G025800' => 'cla', 'ClCG06G011400' => 'cla', 'ClCG09G019360' => 'cla', 'COL.COLO4_04827' => 'col', 'COL.COLO4_29170' => 'col', 'COL.COLO4_35131' => 'col', 'COL.COLO4_35132' => 'col', 'Cpa.g.sc33.32' => 'cpa', 'Cpa.g.sc46.29' => 'cpa', 'Cpa.g.sc796.1' => 'cpa', 'CsaV3_1G030420' => 'csa', 'CsaV3_5G027050' => 'csa', 'CsaV3_5G031040' => 'csa', 'CsaV3_UNG023130' => 'csa', 'CSS0007726' => 'camsi', 'CSS0016433' => 'camsi', 'CSS0017656' => 'camsi', 'CSS0025364' => 'camsi', 'CSS0027582' => 'camsi', 'CSS0047288' => 'camsi', 'CSS0049950' => 'camsi', 'DCAR_003843' => 'dca', 'DCAR_007052' => 'dca', 'DCAR_020884' => 'dca', 'DCAR_021730' => 'dca', 'DCAR_024423' => 'dca', 'DCAR_026509' => 'dca', 'DCAR_031158' => 'dca', 'Dinv14728' => 'din', 'Dinv15219' => 'din', 'Dinv25728' => 'din', 'Dinv33428' => 'din', 'Dinv36489' => 'din', 'Dinv41486' => 'din', 'Duzib147G0469' => 'dzi', 'Duzib168G0060' => 'dzi', 'Duzib187G1215' => 'dzi', 'Duzib248G0692' => 'dzi', 'Duzib251G0767' => 'dzi', 'Duzib264G0446' => 'dzi', 'Duzib268G0691' => 'dzi', 'ECA232G4767' => 'eca', 'ECA233G2838' => 'eca', 'ECA234G0391' => 'eca', 'ECA234G0857' => 'eca', 'ECA236G1593' => 'eca', 'ECA238G0565' => 'eca', 'ECA246G1027' => 'eca', 'ECA246G3223' => 'eca', 'ECA246G3470' => 'eca', 'EL10Ac6g13829' => 'bvu', 'EL10Ac6g14093' => 'bvu', 'EL10Ac8g18707' => 'bvu', 'Eucgr.C01369' => 'egr', 'Eucgr.H02492' => 'egr', 'Eucgr.I01733' => 'egr', 'Eucgr.J02255' => 'egr', 'Eucgr.J02257' => 'egr', 'Eucgr.J02258' => 'egr', 'FAN02G1601' => 'fan', 'FAN03G1586' => 'fan', 'FAN03G2986' => 'fan', 'FAN05G4837' => 'fan', 'FAN06G0146' => 'fan', 'FAN07G0858' => 'fan', 'FAN09G3179' => 'fan', 'FAN10G0669' => 'fan', 'FAN12G2358' => 'fan', 'FAN14G4198' => 'fan', 'FAN14G5112' => 'fan', 'FAN17G0342' => 'fan', 'FAN19G0342' => 'fan', 'FAN19G0962' => 'fan', 'FAN19G1101' => 'fan', 'FAN19G1872' => 'fan', 'FAN22G0356' => 'fan', 'FAN23G0744' => 'fan', 'FAN23G1914' => 'fan', 'FAN26G0032' => 'fan', 'FAN28G0625' => 'fan', 'FvH4_1g02710' => 'fve', 'FvH4_1g02720' => 'fve', 'FvH4_4g25670' => 'fve', 'FvH4_6g51700' => 'fve', 'FvH4_7g20170' => 'fve', 'Glyma.05G175000' => 'gma', 'Glyma.08G132300' => 'gma', 'Glyma.11G243000' => 'gma', 'Glyma.13G158900' => 'gma', 'Glyma.17G112400' => 'gma', 'Glyma.18G014100' => 'gma', 'Glyma.19G003100' => 'gma', 'Glyma.19G056500' => 'gma', 'Gohir.A01G158900' => 'ghi', 'Gohir.A05G312600' => 'ghi', 'Gohir.A05G354900' => 'ghi', 'Gohir.A07G037200' => 'ghi', 'Gohir.A09G030000' => 'ghi', 'Gohir.A12G145200' => 'ghi', 'Gohir.D01G151500' => 'ghi', 'Gohir.D04G058300' => 'ghi', 'Gohir.D05G314100' => 'ghi', 'Gohir.D07G041400' => 'ghi', 'Gohir.D09G029700' => 'ghi', 'Gohir.D12G149700' => 'ghi', 'Gorai.001G043800' => 'gra', 'Gorai.002G187800' => 'gra', 'Gorai.006G034700' => 'gra', 'Gorai.008G161200' => 'gra', 'Gorai.009G335700' => 'gra', 'Gorai.012G065000' => 'gra', 'GSVIVG01000535001' => 'vvi', 'GSVIVG01015572001' => 'vvi', 'GSVIVG01032386001' => 'vvi', 'HanXRQChr05g0138531' => 'han', 'HanXRQChr06g0174391' => 'han', 'HanXRQChr07g0199021' => 'han', 'HanXRQChr08g0208211' => 'han', 'HanXRQChr09g0255471' => 'han', 'HanXRQChr10g0315791' => 'han', 'HanXRQChr12g0371991' => 'han', 'HanXRQChr15g0475251' => 'han', 'HanXRQChr17g0540001' => 'han', 'HanXRQChr17g0548631' => 'han', 'HanXRQChr17g0569561' => 'han', 'Haze_12256' => 'cav', 'Haze_14756' => 'cav', 'Haze_25528' => 'cav', 'Hma1.2p1_0079F.1_g041020' => 'hma', 'Hma1.2p1_0818F.1_g223260' => 'hma', 'Hma1.2p1_1747F.1_g300530' => 'hma', 'HPP92_004607' => 'vpl', 'HPP92_004608' => 'vpl', 'HPP92_006181' => 'vpl', 'HPP92_012192' => 'vpl', 'HPP92_015680' => 'vpl', 'HPP92_020249' => 'vpl', 'HPP92_021376' => 'vpl', 'HPP92_024275' => 'vpl', 'Hund06031' => 'sun', 'Hund25391' => 'sun', 'Lalb_Chr07g0185371' => 'lal', 'Lalb_Chr07g0185381' => 'lal', 'Lalb_Chr12g0204011' => 'lal', 'Lalb_Chr13g0301671' => 'lal', 'Lalb_Chr14g0362851' => 'lal', 'Lalb_Chr24g0403581' => 'lal', 'Lj1g0000233' => 'lja', 'Lj2g0018120' => 'lja', 'Lj3C621T0' => 'lonja', 'Lj3P1059T14' => 'lonja', 'Lj3P611T9' => 'lonja', 'Lj3P614T13' => 'lonja', 'Lj3P615T5' => 'lonja', 'Lj4g0012315' => 'lja', 'Lj4g0026182' => 'lja', 'Lj6P813T16' => 'lonja', 'Lj7C427T7' => 'lonja', 'Lj7C427T8' => 'lonja', 'Lj7P600T41' => 'lonja', 'Lju41C42G17' => 'lonja', 'Lsat_1_v5_gn_0_47300' => 'lsa', 'Lsat_1_v5_gn_2_91280' => 'lsa', 'Lsat_1_v5_gn_3_30561' => 'lsa', 'Lsat_1_v5_gn_4_184321' => 'lsa', 'Lsat_1_v5_gn_4_4041' => 'lsa', 'Lsat_1_v5_gn_5_92000' => 'lsa', 'Lsat_1_v5_gn_8_152940' => 'lsa', 'Lsat_1_v5_gn_8_62401' => 'lsa', 'Manes.06G055900' => 'mes', 'Manes.12G022200' => 'mes', 'Manes.13G023300' => 'mes', 'Manes.14G115000' => 'mes', 'Manes.15G151700' => 'mes', 'Manes.17G111300' => 'mes', 'Mapoly0226s0009' => 'mpo', 'MBI02_g25363_MAGBIO' => 'mbi', 'MBI06_g00027_MAGBIO' => 'mbi', 'MBI10_g13034_MAGBIO' => 'mbi', 'MD09G1023400' => 'mdo', 'MD13G1100100' => 'mdo', 'MD15G1169200' => 'mdo', 'MD16G1101100' => 'mdo', 'MD17G1022900' => 'mdo', 'Medtr3g096150' => 'mtr', 'Medtr4g115070' => 'mtr', 'Medtr7g033325' => 'mtr', 'Medtr8g089840' => 'mtr', 'MELO3C010319.2' => 'cme', 'MELO3C011944.2' => 'cme', 'MELO3C021589.2' => 'cme', 'Migut.E00207' => 'egut', 'Migut.H00067' => 'egut', 'Migut.K00433' => 'egut', 'Migut.K00606' => 'egut', 'Migut.K01410' => 'egut', 'MSTRG.13347' => 'ama', 'MSTRG.24045' => 'ama', 'MSTRG.2428' => 'ama', 'MSTRG.26410' => 'ama', 'MSTRG.3139' => 'ama', 'MSTRG.3286' => 'ama', 'MSTRG.563' => 'ama', 'MSTRG.7941' => 'ama', 'Nitab4.5_0000028g0060' => 'nta', 'Nitab4.5_0000065g0260' => 'nta', 'Nitab4.5_0000112g0060' => 'nta', 'Nitab4.5_0000489g0120' => 'nta', 'Nitab4.5_0001776g0050' => 'nta', 'Nitab4.5_0001854g0010' => 'nta', 'Nitab4.5_0001860g0020' => 'nta', 'Nitab4.5_0004352g0010' => 'nta', 'Nitab4.5_0008716g0020' => 'nta', 'Nitab4.5_0008922g0010' => 'nta', 'Nn3g16693' => 'nnu', 'Nn4g22596' => 'nnu', 'Nn7g37639' => 'nnu', 'Oeu001701.1' => 'oeu', 'Oeu018149.1' => 'oeu', 'Oeu026220.1' => 'oeu', 'Oeu038635.1' => 'oeu', 'Oeu049176.1' => 'oeu', 'Oeu056706.1' => 'oeu', 'Oeu056937.1' => 'oeu', 'Oeu057540.1' => 'oeu', 'Os02g0594900' => 'osa', 'Os02g0595100' => 'osa', 'Os04g0477500' => 'osa', 'Os12g0611900' => 'osa', 'Peaxi162Scf00076g00020' => 'pax', 'Peaxi162Scf00128g00217' => 'pax', 'Peaxi162Scf00129g01640' => 'pax', 'Peaxi162Scf00669g00007' => 'pax', 'Peaxi162Scf00700g00421' => 'pax', 'Peaxi162Scf00801g00038' => 'pax', 'Peaxi162Scf00891g00025' => 'pax', 'PGR083G0909' => 'pgr', 'PGR119G1005' => 'pgr', 'PGR142G2236' => 'pgr', 'PGR142G3388' => 'pgr', 'PGSC0003DMG400004514' => 'stu', 'PGSC0003DMG400012635' => 'stu', 'PGSC0003DMG400015730' => 'stu', 'PGSC0003DMG400018611' => 'stu', 'PGSC0003DMG400030897' => 'stu', 'Phvul.001G254800' => 'pvu', 'Phvul.002G260100' => 'pvu', 'Phvul.003G167600' => 'pvu', 'Phvul.004G005100' => 'pvu', 'Potri.001G343600' => 'ptr', 'Potri.006G066700' => 'ptr', 'Potri.008G186000' => 'ptr', 'Potri.010G046900' => 'ptr', 'Potri.018G127900' => 'ptr', 'Pp3c20_17750' => 'ppa', 'Pp3c24_4380' => 'ppa', 'Prupe.1G245800' => 'ppe', 'Prupe.3G293400' => 'ppe', 'Prupe.7G247400' => 'ppe', 'Psat0s145g0120' => 'psa', 'Psat0s595g0040' => 'psa', 'Psat0s595g0120' => 'psa', 'Psat3g175040' => 'psa', 'Psat7g058120' => 'psa', 'PSO017G0428' => 'pso', 'PSO063G7510' => 'pso', 'PSO067G0046' => 'pso', 'PSO478G1073' => 'pso', 'PSO675G3677' => 'pso', 'PSO675G6558' => 'pso', 'PSO675G7520' => 'pso', 'PSO675G8959' => 'pso', 'QL02p074089' => 'qlo', 'QL02p089614' => 'qlo', 'QL03p057736' => 'qlo', 'RcHm_v2.0_Chr1g0364131' => 'rch', 'RcHm_v2.0_Chr2g0087801' => 'rch', 'RcHm_v2.0_Chr2g0087821' => 'rch', 'RcHm_v2.0_Chr2g0173231' => 'rch', 'RcHm_v2.0_Chr4g0433111' => 'rch', 'Rhsim03G0250300' => 'rsi', 'Rhsim08G0048400' => 'rsi', 'Rhsim10G0014800' => 'rsi', 'Rhsim12G0040100' => 'rsi', 'Rhsim12G0109700' => 'rsi', 'Sabra06G0049600' => 'sbr', 'Sabra08G0141000' => 'sbr', 'Sabra10G0021400' => 'sbr', 'Sabra16G0222900' => 'sbr', 'Sabra18G0108600' => 'sbr', 'SalBow1G0433' => 'sbo', 'SalBow1G2038' => 'sbo', 'SalBow1G5003' => 'sbo', 'SalBow7G1197' => 'sbo', 'SalBow8G3506' => 'sbo', 'Sc03g0007300' => 'sci', 'Sc11g0000950' => 'sci', 'Sc14g0008750' => 'sci', 'Sc18g0000420' => 'sci', 'Sed0006754' => 'sed', 'Sed0008741' => 'sed', 'Sed0017172' => 'sed', 'Sed0018925' => 'sed', 'Sed0023326' => 'sed', 'Sed0025909' => 'sed', 'SEGI_05333' => 'sgi', 'SEGI_10362' => 'sgi', 'SEGI_13380' => 'sgi', 'SEGI_24306' => 'sgi', 'SEGI_29077' => 'sgi', 'SEGI_29095' => 'sgi', 'SEGI_36534' => 'sgi', 'SEGI_37506' => 'sgi', 'SEGI_38321' => 'sgi', 'SGA_v2.0_scaffold307G48031' => 'sas', 'SGA_v2.0_scaffold47G17507' => 'sas', 'SGA_v2.0_scaffold63G21736' => 'sas', 'SGA_v2.0_scaffold87G27070' => 'sas', 'SHI17794' => 'shi', 'SHI28851' => 'shi', 'SMO165G0155' => 'smo', 'SMO340G0217' => 'smo', 'SMO367G1210' => 'smo', 'Solyc02g093430.3' => 'sly', 'Solyc05g013580.4' => 'sly', 'Solyc07g008030.3' => 'sly', 'Solyc12g035470.2' => 'sly', 'Sopen02g038020' => 'spe', 'Sopen05g008490' => 'spe', 'Sopen07g003910' => 'spe', 'Sopen12g015240' => 'spe', 'Sp1g11550' => 'spa', 'Sp2g16710' => 'spa', 'Sp3g00430' => 'spa', 'Sp3g26780' => 'spa', 'Sp5g22900' => 'spa', 'Sp6g29530' => 'spa', 'TAR371G0794' => 'tar', 'TAR374G0164' => 'tar', 'TAR622G0165' => 'tar', 'TAR626G0929' => 'tar', 'TAR629G2155' => 'tar', 'THA.LOC104805282' => 'tha', 'THA.LOC104805363' => 'tha', 'THA.LOC104808968' => 'tha', 'THA.LOC104821093' => 'tha', 'THA.LOC104823953' => 'tha', 'THA.LOC104825562' => 'tha', 'THA.LOC104825665' => 'tha', 'Thecc.02G261400' => 'tca', 'Thecc.04G019200' => 'tca', 'Thecc.09G130400' => 'tca', 'Thhalv10004374m.g' => 'esa', 'Thhalv10007850m.g' => 'esa', 'Thhalv10013782m.g' => 'esa', 'Thhalv10018686m.g' => 'esa', 'Thhalv10020899m.g' => 'esa', 'Thhalv10022755m.g' => 'esa', 'TPR.G23851' => 'tpr', 'TPR.G26500' => 'tpr', 'TPR.G27267' => 'tpr', 'TPR.G32001' => 'tpr', 'TPR.G6251' => 'tpr', 'TPR.G8167' => 'tpr', 'TWI12G1330' => 'twi', 'TWI18G1239' => 'twi', 'TWI34G0979' => 'twi', 'TWI36G0670' => 'twi', 'TWI36G0707' => 'twi', 'TWI56G0233' => 'twi', 'TWI75G1809' => 'twi', 'unitig_21.g20874' => 'ugi', 'unitig_26.g10343' => 'ugi', 'unitig_46.g18392' => 'ugi', 'unitig_52.g17178' => 'ugi', 'unitig_8.g2934' => 'ugi', 'vmacro01122' => 'vma', 'vmacro05875' => 'vma', 'vmacro06147' => 'vma', 'vmacro16191' => 'vma', 'vmacro18293' => 'vma', 'VMungo0251G3707' => 'vmu', 'VMungo0464G1521' => 'vmu', 'VMungo1215G0205' => 'vmu', 'VMungo1383G2484' => 'vmu', 'Zm00001eb079610' => 'zma', 'Zm00001eb135990' => 'zma', 'Zm00001eb183710' => 'zma', 'Zm00001eb246020' => 'zma' ), 'gf_id' => 'HOM05D001124', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001124' ), 'data_identifier' => 'HOM05D001124', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001124', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '548', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02520' => 'bna', 'A03p06630' => 'bna', 'A05p44460' => 'bna', 'A06p08710' => 'bna', 'A06p41090' => 'bna', 'A07p32320' => 'bna', 'A08p32520' => 'bna', 'A09p10360' => 'bna', 'A10p24080' => 'bna', 'Aa31LG11G15250' => 'aar', 'Aa31LG1G1800' => 'aar', 'Aa31LG2G5120' => 'aar', 'Aa31LG2G6070' => 'aar', 'Aa31LG5G10770' => 'aar', 'Aa31sc61G90' => 'aar', 'Actinidia01352' => 'ach', 'Actinidia05983' => 'ach', 'Actinidia08133' => 'ach', 'Actinidia15101' => 'ach', 'Actinidia26379' => 'ach', 'Actinidia35778' => 'ach', 'Actinidia36123' => 'ach', 'Actinidia37436' => 'ach', 'Actinidia38730' => 'ach', 'Ah.02g128210' => 'amhyb', 'Ah.03g132990' => 'amhyb', 'Ah.14g079410' => 'amhyb', 'AL1G24640' => 'aly', 'AL2G26680' => 'aly', 'AL3G10530' => 'aly', 'AL3G45230' => 'aly', 'AL5G15230' => 'aly', 'AL5G16960' => 'aly', 'AL6G25210' => 'aly', 'Aqoxy2G00441' => 'aox', 'Aqoxy3G01236' => 'aox', 'Aqoxy5G03746' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3RQ047' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C7GMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9C8JER' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MBL6KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YXCZ83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZANX40' => 'arhy', 'AT1G12990' => 'ath', 'AT1G67880' => 'ath', 'AT2G13290' => 'ath', 'AT3G01620' => 'ath', 'AT3G26445' => 'ath', 'AT3G27540' => 'ath', 'AT5G14480' => 'ath', 'ATR0824G026' => 'atr', 'ATR1098G019' => 'atr', 'Atru.chr11.2145' => 'acertr', 'Atru.chr2.3636' => 'acertr', 'Atru.chr2.3644' => 'acertr', 'Atru.chr6.2422' => 'acertr', 'Atru.chr7.1112' => 'acertr', 'AUR62005469' => 'cqu', 'AUR62011166' => 'cqu', 'AUR62013319' => 'cqu', 'AUR62024273' => 'cqu', 'AUR62028420' => 'cqu', 'AUR62041942' => 'cqu', 'BcaB01g04969' => 'bca', 'BcaB01g06371' => 'bca', 'BcaB02g11494' => 'bca', 'BcaB03g15382' => 'bca', 'BcaB08g36994' => 'bca', 'BcaC03g13477' => 'bca', 'BcaC03g13478' => 'bca', 'BcaC03g13480' => 'bca', 'BcaC03g13481' => 'bca', 'BcaC03g13486' => 'bca', 'BcaC04g19031' => 'bca', 'BcaC04g23085' => 'bca', 'BcaC05g25094' => 'bca', 'BcaC05g25096' => 'bca', 'BcaC05g25138' => 'bca', 'BcaC05g30416' => 'bca', 'BcaC05g30455' => 'bca', 'BcaC06g30979' => 'bca', 'BcaC06g33805' => 'bca', 'BcaC08g46021' => 'bca', 'BcaNung03154' => 'bca', 'BolC2t06623H' => 'bol', 'BolC2t06632H' => 'bol', 'BolC2t06635H' => 'bol', 'BolC2t06638H' => 'bol', 'BolC3t13266H' => 'bol', 'BolC5t29776H' => 'bol', 'BolC6t38912H' => 'bol', 'BolC7t44183H' => 'bol', 'BolC9t54123H' => 'bol', 'BolC9t59107H' => 'bol', 'BraA02t05221Z' => 'bra', 'BraA03t09996Z' => 'bra', 'BraA05t23210Z' => 'bra', 'BraA06t24068Z' => 'bra', 'BraA06t27032Z' => 'bra', 'BraA08t35176Z' => 'bra', 'BraA09t36680Z' => 'bra', 'BraA10t44471Z' => 'bra', 'C02p06760' => 'bna', 'C02p06890' => 'bna', 'C02p07010' => 'bna', 'C03p07660' => 'bna', 'C05p10300' => 'bna', 'C06p38150' => 'bna', 'C07p36650' => 'bna', 'C08p15770' => 'bna', 'C09p12300' => 'bna', 'C09p62700' => 'bna', 'C09p75040' => 'bna', 'CAN.G13.1' => 'can', 'CAN.G138.4' => 'can', 'CAN.G44.6' => 'can', 'CAN.G473.19' => 'can', 'CANSAT01G0835' => 'cansat', 'CANSAT11G0246' => 'cansat', 'CANSAT11G1766' => 'cansat', 'CANSAT64G1954' => 'cansat', 'CARHR013330' => 'chi', 'CARHR060530' => 'chi', 'CARHR075300' => 'chi', 'CARHR105120' => 'chi', 'CARHR148910' => 'chi', 'CARHR198830' => 'chi', 'Carub.0001s1275' => 'cru', 'Carub.0002s1437' => 'cru', 'Carub.0003s0044' => 'cru', 'Carub.0003s2787' => 'cru', 'Carub.0005s0597' => 'cru', 'Carub.0006s1266' => 'cru', 'Ca_06935_v3' => 'car', 'Ca_13559_v3' => 'car', 'Ca_16941_v3' => 'car', 'Ca_16960_v3' => 'car', 'Ca_17775_v3' => 'car', 'Ca_30464_v3' => 'car', 'Cc06_g08160' => 'ccan', 'Cc07_g01520' => 'ccan', 'Cc11_g15810' => 'ccan', 'CDE02G2840' => 'cde', 'CDE03G0093' => 'cde', 'CDE04G2127' => 'cde', 'CDE07G1857' => 'cde', 'CDE09G1246' => 'cde', 'Cfa003412' => 'cfa', 'Cfa007341' => 'cfa', 'Cfa009220' => 'cfa', 'Ciclev10008737m.g' => 'ccl', 'Ciclev10015565m.g' => 'ccl', 'Ciclev10031761m.g' => 'ccl', 'CiPaw.03G045300' => 'cil', 'CiPaw.03G247200' => 'cil', 'CiPaw.04G029500' => 'cil', 'CiPaw.04G174000' => 'cil', 'CiPaw.05G181200' => 'cil', 'CiPaw.06G067100' => 'cil', 'ClCG05G025800' => 'cla', 'ClCG06G011400' => 'cla', 'ClCG09G019360' => 'cla', 'COL.COLO4_04827' => 'col', 'COL.COLO4_29170' => 'col', 'COL.COLO4_35131' => 'col', 'COL.COLO4_35132' => 'col', 'Cpa.g.sc33.32' => 'cpa', 'Cpa.g.sc46.29' => 'cpa', 'Cpa.g.sc796.1' => 'cpa', 'CsaV3_1G030420' => 'csa', 'CsaV3_5G027050' => 'csa', 'CsaV3_5G031040' => 'csa', 'CsaV3_UNG023130' => 'csa', 'CSS0007726' => 'camsi', 'CSS0016433' => 'camsi', 'CSS0017656' => 'camsi', 'CSS0025364' => 'camsi', 'CSS0027582' => 'camsi', 'CSS0047288' => 'camsi', 'CSS0049950' => 'camsi', 'DCAR_003843' => 'dca', 'DCAR_007052' => 'dca', 'DCAR_020884' => 'dca', 'DCAR_021730' => 'dca', 'DCAR_024423' => 'dca', 'DCAR_026509' => 'dca', 'DCAR_031158' => 'dca', 'Dinv14728' => 'din', 'Dinv15219' => 'din', 'Dinv25728' => 'din', 'Dinv33428' => 'din', 'Dinv36489' => 'din', 'Dinv41486' => 'din', 'Duzib147G0469' => 'dzi', 'Duzib168G0060' => 'dzi', 'Duzib187G1215' => 'dzi', 'Duzib248G0692' => 'dzi', 'Duzib251G0767' => 'dzi', 'Duzib264G0446' => 'dzi', 'Duzib268G0691' => 'dzi', 'ECA232G4767' => 'eca', 'ECA233G2838' => 'eca', 'ECA234G0391' => 'eca', 'ECA234G0857' => 'eca', 'ECA236G1593' => 'eca', 'ECA238G0565' => 'eca', 'ECA246G1027' => 'eca', 'ECA246G3223' => 'eca', 'ECA246G3470' => 'eca', 'EL10Ac6g13829' => 'bvu', 'EL10Ac6g14093' => 'bvu', 'EL10Ac8g18707' => 'bvu', 'Eucgr.C01369' => 'egr', 'Eucgr.H02492' => 'egr', 'Eucgr.I01733' => 'egr', 'Eucgr.J02255' => 'egr', 'Eucgr.J02257' => 'egr', 'Eucgr.J02258' => 'egr', 'FAN02G1601' => 'fan', 'FAN03G1586' => 'fan', 'FAN03G2986' => 'fan', 'FAN05G4837' => 'fan', 'FAN06G0146' => 'fan', 'FAN07G0858' => 'fan', 'FAN09G3179' => 'fan', 'FAN10G0669' => 'fan', 'FAN12G2358' => 'fan', 'FAN14G4198' => 'fan', 'FAN14G5112' => 'fan', 'FAN17G0342' => 'fan', 'FAN19G0342' => 'fan', 'FAN19G0962' => 'fan', 'FAN19G1101' => 'fan', 'FAN19G1872' => 'fan', 'FAN22G0356' => 'fan', 'FAN23G0744' => 'fan', 'FAN23G1914' => 'fan', 'FAN26G0032' => 'fan', 'FAN28G0625' => 'fan', 'FvH4_1g02710' => 'fve', 'FvH4_1g02720' => 'fve', 'FvH4_4g25670' => 'fve', 'FvH4_6g51700' => 'fve', 'FvH4_7g20170' => 'fve', 'Glyma.05G175000' => 'gma', 'Glyma.08G132300' => 'gma', 'Glyma.11G243000' => 'gma', 'Glyma.13G158900' => 'gma', 'Glyma.17G112400' => 'gma', 'Glyma.18G014100' => 'gma', 'Glyma.19G003100' => 'gma', 'Glyma.19G056500' => 'gma', 'Gohir.A01G158900' => 'ghi', 'Gohir.A05G312600' => 'ghi', 'Gohir.A05G354900' => 'ghi', 'Gohir.A07G037200' => 'ghi', 'Gohir.A09G030000' => 'ghi', 'Gohir.A12G145200' => 'ghi', 'Gohir.D01G151500' => 'ghi', 'Gohir.D04G058300' => 'ghi', 'Gohir.D05G314100' => 'ghi', 'Gohir.D07G041400' => 'ghi', 'Gohir.D09G029700' => 'ghi', 'Gohir.D12G149700' => 'ghi', 'Gorai.001G043800' => 'gra', 'Gorai.002G187800' => 'gra', 'Gorai.006G034700' => 'gra', 'Gorai.008G161200' => 'gra', 'Gorai.009G335700' => 'gra', 'Gorai.012G065000' => 'gra', 'GSVIVG01000535001' => 'vvi', 'GSVIVG01015572001' => 'vvi', 'GSVIVG01032386001' => 'vvi', 'HanXRQChr05g0138531' => 'han', 'HanXRQChr06g0174391' => 'han', 'HanXRQChr07g0199021' => 'han', 'HanXRQChr08g0208211' => 'han', 'HanXRQChr09g0255471' => 'han', 'HanXRQChr10g0315791' => 'han', 'HanXRQChr12g0371991' => 'han', 'HanXRQChr15g0475251' => 'han', 'HanXRQChr17g0540001' => 'han', 'HanXRQChr17g0548631' => 'han', 'HanXRQChr17g0569561' => 'han', 'Haze_12256' => 'cav', 'Haze_14756' => 'cav', 'Haze_25528' => 'cav', 'Hma1.2p1_0079F.1_g041020' => 'hma', 'Hma1.2p1_0818F.1_g223260' => 'hma', 'Hma1.2p1_1747F.1_g300530' => 'hma', 'HPP92_004607' => 'vpl', 'HPP92_004608' => 'vpl', 'HPP92_006181' => 'vpl', 'HPP92_012192' => 'vpl', 'HPP92_015680' => 'vpl', 'HPP92_020249' => 'vpl', 'HPP92_021376' => 'vpl', 'HPP92_024275' => 'vpl', 'Hund06031' => 'sun', 'Hund25391' => 'sun', 'Lalb_Chr07g0185371' => 'lal', 'Lalb_Chr07g0185381' => 'lal', 'Lalb_Chr12g0204011' => 'lal', 'Lalb_Chr13g0301671' => 'lal', 'Lalb_Chr14g0362851' => 'lal', 'Lalb_Chr24g0403581' => 'lal', 'Lj1g0000233' => 'lja', 'Lj2g0018120' => 'lja', 'Lj3C621T0' => 'lonja', 'Lj3P1059T14' => 'lonja', 'Lj3P611T9' => 'lonja', 'Lj3P614T13' => 'lonja', 'Lj3P615T5' => 'lonja', 'Lj4g0012315' => 'lja', 'Lj4g0026182' => 'lja', 'Lj6P813T16' => 'lonja', 'Lj7C427T7' => 'lonja', 'Lj7C427T8' => 'lonja', 'Lj7P600T41' => 'lonja', 'Lju41C42G17' => 'lonja', 'Lsat_1_v5_gn_0_47300' => 'lsa', 'Lsat_1_v5_gn_2_91280' => 'lsa', 'Lsat_1_v5_gn_3_30561' => 'lsa', 'Lsat_1_v5_gn_4_184321' => 'lsa', 'Lsat_1_v5_gn_4_4041' => 'lsa', 'Lsat_1_v5_gn_5_92000' => 'lsa', 'Lsat_1_v5_gn_8_152940' => 'lsa', 'Lsat_1_v5_gn_8_62401' => 'lsa', 'Manes.06G055900' => 'mes', 'Manes.12G022200' => 'mes', 'Manes.13G023300' => 'mes', 'Manes.14G115000' => 'mes', 'Manes.15G151700' => 'mes', 'Manes.17G111300' => 'mes', 'Mapoly0226s0009' => 'mpo', 'MBI02_g25363_MAGBIO' => 'mbi', 'MBI06_g00027_MAGBIO' => 'mbi', 'MBI10_g13034_MAGBIO' => 'mbi', 'MD09G1023400' => 'mdo', 'MD13G1100100' => 'mdo', 'MD15G1169200' => 'mdo', 'MD16G1101100' => 'mdo', 'MD17G1022900' => 'mdo', 'Medtr3g096150' => 'mtr', 'Medtr4g115070' => 'mtr', 'Medtr7g033325' => 'mtr', 'Medtr8g089840' => 'mtr', 'MELO3C010319.2' => 'cme', 'MELO3C011944.2' => 'cme', 'MELO3C021589.2' => 'cme', 'Migut.E00207' => 'egut', 'Migut.H00067' => 'egut', 'Migut.K00433' => 'egut', 'Migut.K00606' => 'egut', 'Migut.K01410' => 'egut', 'MSTRG.13347' => 'ama', 'MSTRG.24045' => 'ama', 'MSTRG.2428' => 'ama', 'MSTRG.26410' => 'ama', 'MSTRG.3139' => 'ama', 'MSTRG.3286' => 'ama', 'MSTRG.563' => 'ama', 'MSTRG.7941' => 'ama', 'Nitab4.5_0000028g0060' => 'nta', 'Nitab4.5_0000065g0260' => 'nta', 'Nitab4.5_0000112g0060' => 'nta', 'Nitab4.5_0000489g0120' => 'nta', 'Nitab4.5_0001776g0050' => 'nta', 'Nitab4.5_0001854g0010' => 'nta', 'Nitab4.5_0001860g0020' => 'nta', 'Nitab4.5_0004352g0010' => 'nta', 'Nitab4.5_0008716g0020' => 'nta', 'Nitab4.5_0008922g0010' => 'nta', 'Nn3g16693' => 'nnu', 'Nn4g22596' => 'nnu', 'Nn7g37639' => 'nnu', 'Oeu001701.1' => 'oeu', 'Oeu018149.1' => 'oeu', 'Oeu026220.1' => 'oeu', 'Oeu038635.1' => 'oeu', 'Oeu049176.1' => 'oeu', 'Oeu056706.1' => 'oeu', 'Oeu056937.1' => 'oeu', 'Oeu057540.1' => 'oeu', 'Os02g0594900' => 'osa', 'Os02g0595100' => 'osa', 'Os04g0477500' => 'osa', 'Os12g0611900' => 'osa', 'Peaxi162Scf00076g00020' => 'pax', 'Peaxi162Scf00128g00217' => 'pax', 'Peaxi162Scf00129g01640' => 'pax', 'Peaxi162Scf00669g00007' => 'pax', 'Peaxi162Scf00700g00421' => 'pax', 'Peaxi162Scf00801g00038' => 'pax', 'Peaxi162Scf00891g00025' => 'pax', 'PGR083G0909' => 'pgr', 'PGR119G1005' => 'pgr', 'PGR142G2236' => 'pgr', 'PGR142G3388' => 'pgr', 'PGSC0003DMG400004514' => 'stu', 'PGSC0003DMG400012635' => 'stu', 'PGSC0003DMG400015730' => 'stu', 'PGSC0003DMG400018611' => 'stu', 'PGSC0003DMG400030897' => 'stu', 'Phvul.001G254800' => 'pvu', 'Phvul.002G260100' => 'pvu', 'Phvul.003G167600' => 'pvu', 'Phvul.004G005100' => 'pvu', 'Potri.001G343600' => 'ptr', 'Potri.006G066700' => 'ptr', 'Potri.008G186000' => 'ptr', 'Potri.010G046900' => 'ptr', 'Potri.018G127900' => 'ptr', 'Pp3c20_17750' => 'ppa', 'Pp3c24_4380' => 'ppa', 'Prupe.1G245800' => 'ppe', 'Prupe.3G293400' => 'ppe', 'Prupe.7G247400' => 'ppe', 'Psat0s145g0120' => 'psa', 'Psat0s595g0040' => 'psa', 'Psat0s595g0120' => 'psa', 'Psat3g175040' => 'psa', 'Psat7g058120' => 'psa', 'PSO017G0428' => 'pso', 'PSO063G7510' => 'pso', 'PSO067G0046' => 'pso', 'PSO478G1073' => 'pso', 'PSO675G3677' => 'pso', 'PSO675G6558' => 'pso', 'PSO675G7520' => 'pso', 'PSO675G8959' => 'pso', 'QL02p074089' => 'qlo', 'QL02p089614' => 'qlo', 'QL03p057736' => 'qlo', 'RcHm_v2.0_Chr1g0364131' => 'rch', 'RcHm_v2.0_Chr2g0087801' => 'rch', 'RcHm_v2.0_Chr2g0087821' => 'rch', 'RcHm_v2.0_Chr2g0173231' => 'rch', 'RcHm_v2.0_Chr4g0433111' => 'rch', 'Rhsim03G0250300' => 'rsi', 'Rhsim08G0048400' => 'rsi', 'Rhsim10G0014800' => 'rsi', 'Rhsim12G0040100' => 'rsi', 'Rhsim12G0109700' => 'rsi', 'Sabra06G0049600' => 'sbr', 'Sabra08G0141000' => 'sbr', 'Sabra10G0021400' => 'sbr', 'Sabra16G0222900' => 'sbr', 'Sabra18G0108600' => 'sbr', 'SalBow1G0433' => 'sbo', 'SalBow1G2038' => 'sbo', 'SalBow1G5003' => 'sbo', 'SalBow7G1197' => 'sbo', 'SalBow8G3506' => 'sbo', 'Sc03g0007300' => 'sci', 'Sc11g0000950' => 'sci', 'Sc14g0008750' => 'sci', 'Sc18g0000420' => 'sci', 'Sed0006754' => 'sed', 'Sed0008741' => 'sed', 'Sed0017172' => 'sed', 'Sed0018925' => 'sed', 'Sed0023326' => 'sed', 'Sed0025909' => 'sed', 'SEGI_05333' => 'sgi', 'SEGI_10362' => 'sgi', 'SEGI_13380' => 'sgi', 'SEGI_24306' => 'sgi', 'SEGI_29077' => 'sgi', 'SEGI_29095' => 'sgi', 'SEGI_36534' => 'sgi', 'SEGI_37506' => 'sgi', 'SEGI_38321' => 'sgi', 'SGA_v2.0_scaffold307G48031' => 'sas', 'SGA_v2.0_scaffold47G17507' => 'sas', 'SGA_v2.0_scaffold63G21736' => 'sas', 'SGA_v2.0_scaffold87G27070' => 'sas', 'SHI17794' => 'shi', 'SHI28851' => 'shi', 'SMO165G0155' => 'smo', 'SMO340G0217' => 'smo', 'SMO367G1210' => 'smo', 'Solyc02g093430.3' => 'sly', 'Solyc05g013580.4' => 'sly', 'Solyc07g008030.3' => 'sly', 'Solyc12g035470.2' => 'sly', 'Sopen02g038020' => 'spe', 'Sopen05g008490' => 'spe', 'Sopen07g003910' => 'spe', 'Sopen12g015240' => 'spe', 'Sp1g11550' => 'spa', 'Sp2g16710' => 'spa', 'Sp3g00430' => 'spa', 'Sp3g26780' => 'spa', 'Sp5g22900' => 'spa', 'Sp6g29530' => 'spa', 'TAR371G0794' => 'tar', 'TAR374G0164' => 'tar', 'TAR622G0165' => 'tar', 'TAR626G0929' => 'tar', 'TAR629G2155' => 'tar', 'THA.LOC104805282' => 'tha', 'THA.LOC104805363' => 'tha', 'THA.LOC104808968' => 'tha', 'THA.LOC104821093' => 'tha', 'THA.LOC104823953' => 'tha', 'THA.LOC104825562' => 'tha', 'THA.LOC104825665' => 'tha', 'Thecc.02G261400' => 'tca', 'Thecc.04G019200' => 'tca', 'Thecc.09G130400' => 'tca', 'Thhalv10004374m.g' => 'esa', 'Thhalv10007850m.g' => 'esa', 'Thhalv10013782m.g' => 'esa', 'Thhalv10018686m.g' => 'esa', 'Thhalv10020899m.g' => 'esa', 'Thhalv10022755m.g' => 'esa', 'TPR.G23851' => 'tpr', 'TPR.G26500' => 'tpr', 'TPR.G27267' => 'tpr', 'TPR.G32001' => 'tpr', 'TPR.G6251' => 'tpr', 'TPR.G8167' => 'tpr', 'TWI12G1330' => 'twi', 'TWI18G1239' => 'twi', 'TWI34G0979' => 'twi', 'TWI36G0670' => 'twi', 'TWI36G0707' => 'twi', 'TWI56G0233' => 'twi', 'TWI75G1809' => 'twi', 'unitig_21.g20874' => 'ugi', 'unitig_26.g10343' => 'ugi', 'unitig_46.g18392' => 'ugi', 'unitig_52.g17178' => 'ugi', 'unitig_8.g2934' => 'ugi', 'vmacro01122' => 'vma', 'vmacro05875' => 'vma', 'vmacro06147' => 'vma', 'vmacro16191' => 'vma', 'vmacro18293' => 'vma', 'VMungo0251G3707' => 'vmu', 'VMungo0464G1521' => 'vmu', 'VMungo1215G0205' => 'vmu', 'VMungo1383G2484' => 'vmu', 'Zm00001eb079610' => 'zma', 'Zm00001eb135990' => 'zma', 'Zm00001eb183710' => 'zma', 'Zm00001eb246020' => 'zma' ) $gf_id = 'HOM05D001124' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001124' ) $data_identifier = 'HOM05D001124' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 6, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 7, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 21, 'bol' => (int) 10, 'bra' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 6, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 9, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 21, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 8, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 10, 'lsa' => (int) 8, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 8, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 9, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb246020' $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' => 'HOM05D001124', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '548', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02520' => 'bna', 'A03p06630' => 'bna', 'A05p44460' => 'bna', 'A06p08710' => 'bna', 'A06p41090' => 'bna', 'A07p32320' => 'bna', 'A08p32520' => 'bna', 'A09p10360' => 'bna', 'A10p24080' => 'bna', 'Aa31LG11G15250' => 'aar', 'Aa31LG1G1800' => 'aar', 'Aa31LG2G5120' => 'aar', 'Aa31LG2G6070' => 'aar', 'Aa31LG5G10770' => 'aar', 'Aa31sc61G90' => 'aar', 'Actinidia01352' => 'ach', 'Actinidia05983' => 'ach', 'Actinidia08133' => 'ach', 'Actinidia15101' => 'ach', 'Actinidia26379' => 'ach', 'Actinidia35778' => 'ach', 'Actinidia36123' => 'ach', 'Actinidia37436' => 'ach', 'Actinidia38730' => 'ach', 'Ah.02g128210' => 'amhyb', 'Ah.03g132990' => 'amhyb', 'Ah.14g079410' => 'amhyb', 'AL1G24640' => 'aly', 'AL2G26680' => 'aly', 'AL3G10530' => 'aly', 'AL3G45230' => 'aly', 'AL5G15230' => 'aly', 'AL5G16960' => 'aly', 'AL6G25210' => 'aly', 'Aqoxy2G00441' => 'aox', 'Aqoxy3G01236' => 'aox', 'Aqoxy5G03746' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3RQ047' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C7GMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9C8JER' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MBL6KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YXCZ83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZANX40' => 'arhy', 'AT1G12990' => 'ath', 'AT1G67880' => 'ath', 'AT2G13290' => 'ath', 'AT3G01620' => 'ath', 'AT3G26445' => 'ath', 'AT3G27540' => 'ath', 'AT5G14480' => 'ath', 'ATR0824G026' => 'atr', 'ATR1098G019' => 'atr', 'Atru.chr11.2145' => 'acertr', 'Atru.chr2.3636' => 'acertr', 'Atru.chr2.3644' => 'acertr', 'Atru.chr6.2422' => 'acertr', 'Atru.chr7.1112' => 'acertr', 'AUR62005469' => 'cqu', 'AUR62011166' => 'cqu', 'AUR62013319' => 'cqu', 'AUR62024273' => 'cqu', 'AUR62028420' => 'cqu', 'AUR62041942' => 'cqu', 'BcaB01g04969' => 'bca', 'BcaB01g06371' => 'bca', 'BcaB02g11494' => 'bca', 'BcaB03g15382' => 'bca', 'BcaB08g36994' => 'bca', 'BcaC03g13477' => 'bca', 'BcaC03g13478' => 'bca', 'BcaC03g13480' => 'bca', 'BcaC03g13481' => 'bca', 'BcaC03g13486' => 'bca', 'BcaC04g19031' => 'bca', 'BcaC04g23085' => 'bca', 'BcaC05g25094' => 'bca', 'BcaC05g25096' => 'bca', 'BcaC05g25138' => 'bca', 'BcaC05g30416' => 'bca', 'BcaC05g30455' => 'bca', 'BcaC06g30979' => 'bca', 'BcaC06g33805' => 'bca', 'BcaC08g46021' => 'bca', 'BcaNung03154' => 'bca', 'BolC2t06623H' => 'bol', 'BolC2t06632H' => 'bol', 'BolC2t06635H' => 'bol', 'BolC2t06638H' => 'bol', 'BolC3t13266H' => 'bol', 'BolC5t29776H' => 'bol', 'BolC6t38912H' => 'bol', 'BolC7t44183H' => 'bol', 'BolC9t54123H' => 'bol', 'BolC9t59107H' => 'bol', 'BraA02t05221Z' => 'bra', 'BraA03t09996Z' => 'bra', 'BraA05t23210Z' => 'bra', 'BraA06t24068Z' => 'bra', 'BraA06t27032Z' => 'bra', 'BraA08t35176Z' => 'bra', 'BraA09t36680Z' => 'bra', 'BraA10t44471Z' => 'bra', 'C02p06760' => 'bna', 'C02p06890' => 'bna', 'C02p07010' => 'bna', 'C03p07660' => 'bna', 'C05p10300' => 'bna', 'C06p38150' => 'bna', 'C07p36650' => 'bna', 'C08p15770' => 'bna', 'C09p12300' => 'bna', 'C09p62700' => 'bna', 'C09p75040' => 'bna', 'CAN.G13.1' => 'can', 'CAN.G138.4' => 'can', 'CAN.G44.6' => 'can', 'CAN.G473.19' => 'can', 'CANSAT01G0835' => 'cansat', 'CANSAT11G0246' => 'cansat', 'CANSAT11G1766' => 'cansat', 'CANSAT64G1954' => 'cansat', 'CARHR013330' => 'chi', 'CARHR060530' => 'chi', 'CARHR075300' => 'chi', 'CARHR105120' => 'chi', 'CARHR148910' => 'chi', 'CARHR198830' => 'chi', 'Carub.0001s1275' => 'cru', 'Carub.0002s1437' => 'cru', 'Carub.0003s0044' => 'cru', 'Carub.0003s2787' => 'cru', 'Carub.0005s0597' => 'cru', 'Carub.0006s1266' => 'cru', 'Ca_06935_v3' => 'car', 'Ca_13559_v3' => 'car', 'Ca_16941_v3' => 'car', 'Ca_16960_v3' => 'car', 'Ca_17775_v3' => 'car', 'Ca_30464_v3' => 'car', 'Cc06_g08160' => 'ccan', 'Cc07_g01520' => 'ccan', 'Cc11_g15810' => 'ccan', 'CDE02G2840' => 'cde', 'CDE03G0093' => 'cde', 'CDE04G2127' => 'cde', 'CDE07G1857' => 'cde', 'CDE09G1246' => 'cde', 'Cfa003412' => 'cfa', 'Cfa007341' => 'cfa', 'Cfa009220' => 'cfa', 'Ciclev10008737m.g' => 'ccl', 'Ciclev10015565m.g' => 'ccl', 'Ciclev10031761m.g' => 'ccl', 'CiPaw.03G045300' => 'cil', 'CiPaw.03G247200' => 'cil', 'CiPaw.04G029500' => 'cil', 'CiPaw.04G174000' => 'cil', 'CiPaw.05G181200' => 'cil', 'CiPaw.06G067100' => 'cil', 'ClCG05G025800' => 'cla', 'ClCG06G011400' => 'cla', 'ClCG09G019360' => 'cla', 'COL.COLO4_04827' => 'col', 'COL.COLO4_29170' => 'col', 'COL.COLO4_35131' => 'col', 'COL.COLO4_35132' => 'col', 'Cpa.g.sc33.32' => 'cpa', 'Cpa.g.sc46.29' => 'cpa', 'Cpa.g.sc796.1' => 'cpa', 'CsaV3_1G030420' => 'csa', 'CsaV3_5G027050' => 'csa', 'CsaV3_5G031040' => 'csa', 'CsaV3_UNG023130' => 'csa', 'CSS0007726' => 'camsi', 'CSS0016433' => 'camsi', 'CSS0017656' => 'camsi', 'CSS0025364' => 'camsi', 'CSS0027582' => 'camsi', 'CSS0047288' => 'camsi', 'CSS0049950' => 'camsi', 'DCAR_003843' => 'dca', 'DCAR_007052' => 'dca', 'DCAR_020884' => 'dca', 'DCAR_021730' => 'dca', 'DCAR_024423' => 'dca', 'DCAR_026509' => 'dca', 'DCAR_031158' => 'dca', 'Dinv14728' => 'din', 'Dinv15219' => 'din', 'Dinv25728' => 'din', 'Dinv33428' => 'din', 'Dinv36489' => 'din', 'Dinv41486' => 'din', 'Duzib147G0469' => 'dzi', 'Duzib168G0060' => 'dzi', 'Duzib187G1215' => 'dzi', 'Duzib248G0692' => 'dzi', 'Duzib251G0767' => 'dzi', 'Duzib264G0446' => 'dzi', 'Duzib268G0691' => 'dzi', 'ECA232G4767' => 'eca', 'ECA233G2838' => 'eca', 'ECA234G0391' => 'eca', 'ECA234G0857' => 'eca', 'ECA236G1593' => 'eca', 'ECA238G0565' => 'eca', 'ECA246G1027' => 'eca', 'ECA246G3223' => 'eca', 'ECA246G3470' => 'eca', 'EL10Ac6g13829' => 'bvu', 'EL10Ac6g14093' => 'bvu', 'EL10Ac8g18707' => 'bvu', 'Eucgr.C01369' => 'egr', 'Eucgr.H02492' => 'egr', 'Eucgr.I01733' => 'egr', 'Eucgr.J02255' => 'egr', 'Eucgr.J02257' => 'egr', 'Eucgr.J02258' => 'egr', 'FAN02G1601' => 'fan', 'FAN03G1586' => 'fan', 'FAN03G2986' => 'fan', 'FAN05G4837' => 'fan', 'FAN06G0146' => 'fan', 'FAN07G0858' => 'fan', 'FAN09G3179' => 'fan', 'FAN10G0669' => 'fan', 'FAN12G2358' => 'fan', 'FAN14G4198' => 'fan', 'FAN14G5112' => 'fan', 'FAN17G0342' => 'fan', 'FAN19G0342' => 'fan', 'FAN19G0962' => 'fan', 'FAN19G1101' => 'fan', 'FAN19G1872' => 'fan', 'FAN22G0356' => 'fan', 'FAN23G0744' => 'fan', 'FAN23G1914' => 'fan', 'FAN26G0032' => 'fan', 'FAN28G0625' => 'fan', 'FvH4_1g02710' => 'fve', 'FvH4_1g02720' => 'fve', 'FvH4_4g25670' => 'fve', 'FvH4_6g51700' => 'fve', 'FvH4_7g20170' => 'fve', 'Glyma.05G175000' => 'gma', 'Glyma.08G132300' => 'gma', 'Glyma.11G243000' => 'gma', 'Glyma.13G158900' => 'gma', 'Glyma.17G112400' => 'gma', 'Glyma.18G014100' => 'gma', 'Glyma.19G003100' => 'gma', 'Glyma.19G056500' => 'gma', 'Gohir.A01G158900' => 'ghi', 'Gohir.A05G312600' => 'ghi', 'Gohir.A05G354900' => 'ghi', 'Gohir.A07G037200' => 'ghi', 'Gohir.A09G030000' => 'ghi', 'Gohir.A12G145200' => 'ghi', 'Gohir.D01G151500' => 'ghi', 'Gohir.D04G058300' => 'ghi', 'Gohir.D05G314100' => 'ghi', 'Gohir.D07G041400' => 'ghi', 'Gohir.D09G029700' => 'ghi', 'Gohir.D12G149700' => 'ghi', 'Gorai.001G043800' => 'gra', 'Gorai.002G187800' => 'gra', 'Gorai.006G034700' => 'gra', 'Gorai.008G161200' => 'gra', 'Gorai.009G335700' => 'gra', 'Gorai.012G065000' => 'gra', 'GSVIVG01000535001' => 'vvi', 'GSVIVG01015572001' => 'vvi', 'GSVIVG01032386001' => 'vvi', 'HanXRQChr05g0138531' => 'han', 'HanXRQChr06g0174391' => 'han', 'HanXRQChr07g0199021' => 'han', 'HanXRQChr08g0208211' => 'han', 'HanXRQChr09g0255471' => 'han', 'HanXRQChr10g0315791' => 'han', 'HanXRQChr12g0371991' => 'han', 'HanXRQChr15g0475251' => 'han', 'HanXRQChr17g0540001' => 'han', 'HanXRQChr17g0548631' => 'han', 'HanXRQChr17g0569561' => 'han', 'Haze_12256' => 'cav', 'Haze_14756' => 'cav', 'Haze_25528' => 'cav', 'Hma1.2p1_0079F.1_g041020' => 'hma', 'Hma1.2p1_0818F.1_g223260' => 'hma', 'Hma1.2p1_1747F.1_g300530' => 'hma', 'HPP92_004607' => 'vpl', 'HPP92_004608' => 'vpl', 'HPP92_006181' => 'vpl', 'HPP92_012192' => 'vpl', 'HPP92_015680' => 'vpl', 'HPP92_020249' => 'vpl', 'HPP92_021376' => 'vpl', 'HPP92_024275' => 'vpl', 'Hund06031' => 'sun', 'Hund25391' => 'sun', 'Lalb_Chr07g0185371' => 'lal', 'Lalb_Chr07g0185381' => 'lal', 'Lalb_Chr12g0204011' => 'lal', 'Lalb_Chr13g0301671' => 'lal', 'Lalb_Chr14g0362851' => 'lal', 'Lalb_Chr24g0403581' => 'lal', 'Lj1g0000233' => 'lja', 'Lj2g0018120' => 'lja', 'Lj3C621T0' => 'lonja', 'Lj3P1059T14' => 'lonja', 'Lj3P611T9' => 'lonja', 'Lj3P614T13' => 'lonja', 'Lj3P615T5' => 'lonja', 'Lj4g0012315' => 'lja', 'Lj4g0026182' => 'lja', 'Lj6P813T16' => 'lonja', 'Lj7C427T7' => 'lonja', 'Lj7C427T8' => 'lonja', 'Lj7P600T41' => 'lonja', 'Lju41C42G17' => 'lonja', 'Lsat_1_v5_gn_0_47300' => 'lsa', 'Lsat_1_v5_gn_2_91280' => 'lsa', 'Lsat_1_v5_gn_3_30561' => 'lsa', 'Lsat_1_v5_gn_4_184321' => 'lsa', 'Lsat_1_v5_gn_4_4041' => 'lsa', 'Lsat_1_v5_gn_5_92000' => 'lsa', 'Lsat_1_v5_gn_8_152940' => 'lsa', 'Lsat_1_v5_gn_8_62401' => 'lsa', 'Manes.06G055900' => 'mes', 'Manes.12G022200' => 'mes', 'Manes.13G023300' => 'mes', 'Manes.14G115000' => 'mes', 'Manes.15G151700' => 'mes', 'Manes.17G111300' => 'mes', 'Mapoly0226s0009' => 'mpo', 'MBI02_g25363_MAGBIO' => 'mbi', 'MBI06_g00027_MAGBIO' => 'mbi', 'MBI10_g13034_MAGBIO' => 'mbi', 'MD09G1023400' => 'mdo', 'MD13G1100100' => 'mdo', 'MD15G1169200' => 'mdo', 'MD16G1101100' => 'mdo', 'MD17G1022900' => 'mdo', 'Medtr3g096150' => 'mtr', 'Medtr4g115070' => 'mtr', 'Medtr7g033325' => 'mtr', 'Medtr8g089840' => 'mtr', 'MELO3C010319.2' => 'cme', 'MELO3C011944.2' => 'cme', 'MELO3C021589.2' => 'cme', 'Migut.E00207' => 'egut', 'Migut.H00067' => 'egut', 'Migut.K00433' => 'egut', 'Migut.K00606' => 'egut', 'Migut.K01410' => 'egut', 'MSTRG.13347' => 'ama', 'MSTRG.24045' => 'ama', 'MSTRG.2428' => 'ama', 'MSTRG.26410' => 'ama', 'MSTRG.3139' => 'ama', 'MSTRG.3286' => 'ama', 'MSTRG.563' => 'ama', 'MSTRG.7941' => 'ama', 'Nitab4.5_0000028g0060' => 'nta', 'Nitab4.5_0000065g0260' => 'nta', 'Nitab4.5_0000112g0060' => 'nta', 'Nitab4.5_0000489g0120' => 'nta', 'Nitab4.5_0001776g0050' => 'nta', 'Nitab4.5_0001854g0010' => 'nta', 'Nitab4.5_0001860g0020' => 'nta', 'Nitab4.5_0004352g0010' => 'nta', 'Nitab4.5_0008716g0020' => 'nta', 'Nitab4.5_0008922g0010' => 'nta', 'Nn3g16693' => 'nnu', 'Nn4g22596' => 'nnu', 'Nn7g37639' => 'nnu', 'Oeu001701.1' => 'oeu', 'Oeu018149.1' => 'oeu', 'Oeu026220.1' => 'oeu', 'Oeu038635.1' => 'oeu', 'Oeu049176.1' => 'oeu', 'Oeu056706.1' => 'oeu', 'Oeu056937.1' => 'oeu', 'Oeu057540.1' => 'oeu', 'Os02g0594900' => 'osa', 'Os02g0595100' => 'osa', 'Os04g0477500' => 'osa', 'Os12g0611900' => 'osa', 'Peaxi162Scf00076g00020' => 'pax', 'Peaxi162Scf00128g00217' => 'pax', 'Peaxi162Scf00129g01640' => 'pax', 'Peaxi162Scf00669g00007' => 'pax', 'Peaxi162Scf00700g00421' => 'pax', 'Peaxi162Scf00801g00038' => 'pax', 'Peaxi162Scf00891g00025' => 'pax', 'PGR083G0909' => 'pgr', 'PGR119G1005' => 'pgr', 'PGR142G2236' => 'pgr', 'PGR142G3388' => 'pgr', 'PGSC0003DMG400004514' => 'stu', 'PGSC0003DMG400012635' => 'stu', 'PGSC0003DMG400015730' => 'stu', 'PGSC0003DMG400018611' => 'stu', 'PGSC0003DMG400030897' => 'stu', 'Phvul.001G254800' => 'pvu', 'Phvul.002G260100' => 'pvu', 'Phvul.003G167600' => 'pvu', 'Phvul.004G005100' => 'pvu', 'Potri.001G343600' => 'ptr', 'Potri.006G066700' => 'ptr', 'Potri.008G186000' => 'ptr', 'Potri.010G046900' => 'ptr', 'Potri.018G127900' => 'ptr', 'Pp3c20_17750' => 'ppa', 'Pp3c24_4380' => 'ppa', 'Prupe.1G245800' => 'ppe', 'Prupe.3G293400' => 'ppe', 'Prupe.7G247400' => 'ppe', 'Psat0s145g0120' => 'psa', 'Psat0s595g0040' => 'psa', 'Psat0s595g0120' => 'psa', 'Psat3g175040' => 'psa', 'Psat7g058120' => 'psa', 'PSO017G0428' => 'pso', 'PSO063G7510' => 'pso', 'PSO067G0046' => 'pso', 'PSO478G1073' => 'pso', 'PSO675G3677' => 'pso', 'PSO675G6558' => 'pso', 'PSO675G7520' => 'pso', 'PSO675G8959' => 'pso', 'QL02p074089' => 'qlo', 'QL02p089614' => 'qlo', 'QL03p057736' => 'qlo', 'RcHm_v2.0_Chr1g0364131' => 'rch', 'RcHm_v2.0_Chr2g0087801' => 'rch', 'RcHm_v2.0_Chr2g0087821' => 'rch', 'RcHm_v2.0_Chr2g0173231' => 'rch', 'RcHm_v2.0_Chr4g0433111' => 'rch', 'Rhsim03G0250300' => 'rsi', 'Rhsim08G0048400' => 'rsi', 'Rhsim10G0014800' => 'rsi', 'Rhsim12G0040100' => 'rsi', 'Rhsim12G0109700' => 'rsi', 'Sabra06G0049600' => 'sbr', 'Sabra08G0141000' => 'sbr', 'Sabra10G0021400' => 'sbr', 'Sabra16G0222900' => 'sbr', 'Sabra18G0108600' => 'sbr', 'SalBow1G0433' => 'sbo', 'SalBow1G2038' => 'sbo', 'SalBow1G5003' => 'sbo', 'SalBow7G1197' => 'sbo', 'SalBow8G3506' => 'sbo', 'Sc03g0007300' => 'sci', 'Sc11g0000950' => 'sci', 'Sc14g0008750' => 'sci', 'Sc18g0000420' => 'sci', 'Sed0006754' => 'sed', 'Sed0008741' => 'sed', 'Sed0017172' => 'sed', 'Sed0018925' => 'sed', 'Sed0023326' => 'sed', 'Sed0025909' => 'sed', 'SEGI_05333' => 'sgi', 'SEGI_10362' => 'sgi', 'SEGI_13380' => 'sgi', 'SEGI_24306' => 'sgi', 'SEGI_29077' => 'sgi', 'SEGI_29095' => 'sgi', 'SEGI_36534' => 'sgi', 'SEGI_37506' => 'sgi', 'SEGI_38321' => 'sgi', 'SGA_v2.0_scaffold307G48031' => 'sas', 'SGA_v2.0_scaffold47G17507' => 'sas', 'SGA_v2.0_scaffold63G21736' => 'sas', 'SGA_v2.0_scaffold87G27070' => 'sas', 'SHI17794' => 'shi', 'SHI28851' => 'shi', 'SMO165G0155' => 'smo', 'SMO340G0217' => 'smo', 'SMO367G1210' => 'smo', 'Solyc02g093430.3' => 'sly', 'Solyc05g013580.4' => 'sly', 'Solyc07g008030.3' => 'sly', 'Solyc12g035470.2' => 'sly', 'Sopen02g038020' => 'spe', 'Sopen05g008490' => 'spe', 'Sopen07g003910' => 'spe', 'Sopen12g015240' => 'spe', 'Sp1g11550' => 'spa', 'Sp2g16710' => 'spa', 'Sp3g00430' => 'spa', 'Sp3g26780' => 'spa', 'Sp5g22900' => 'spa', 'Sp6g29530' => 'spa', 'TAR371G0794' => 'tar', 'TAR374G0164' => 'tar', 'TAR622G0165' => 'tar', 'TAR626G0929' => 'tar', 'TAR629G2155' => 'tar', 'THA.LOC104805282' => 'tha', 'THA.LOC104805363' => 'tha', 'THA.LOC104808968' => 'tha', 'THA.LOC104821093' => 'tha', 'THA.LOC104823953' => 'tha', 'THA.LOC104825562' => 'tha', 'THA.LOC104825665' => 'tha', 'Thecc.02G261400' => 'tca', 'Thecc.04G019200' => 'tca', 'Thecc.09G130400' => 'tca', 'Thhalv10004374m.g' => 'esa', 'Thhalv10007850m.g' => 'esa', 'Thhalv10013782m.g' => 'esa', 'Thhalv10018686m.g' => 'esa', 'Thhalv10020899m.g' => 'esa', 'Thhalv10022755m.g' => 'esa', 'TPR.G23851' => 'tpr', 'TPR.G26500' => 'tpr', 'TPR.G27267' => 'tpr', 'TPR.G32001' => 'tpr', 'TPR.G6251' => 'tpr', 'TPR.G8167' => 'tpr', 'TWI12G1330' => 'twi', 'TWI18G1239' => 'twi', 'TWI34G0979' => 'twi', 'TWI36G0670' => 'twi', 'TWI36G0707' => 'twi', 'TWI56G0233' => 'twi', 'TWI75G1809' => 'twi', 'unitig_21.g20874' => 'ugi', 'unitig_26.g10343' => 'ugi', 'unitig_46.g18392' => 'ugi', 'unitig_52.g17178' => 'ugi', 'unitig_8.g2934' => 'ugi', 'vmacro01122' => 'vma', 'vmacro05875' => 'vma', 'vmacro06147' => 'vma', 'vmacro16191' => 'vma', 'vmacro18293' => 'vma', 'VMungo0251G3707' => 'vmu', 'VMungo0464G1521' => 'vmu', 'VMungo1215G0205' => 'vmu', 'VMungo1383G2484' => 'vmu', 'Zm00001eb079610' => 'zma', 'Zm00001eb135990' => 'zma', 'Zm00001eb183710' => 'zma', 'Zm00001eb246020' => 'zma' ), 'gf_id' => 'HOM05D001124', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001124' ), 'data_identifier' => 'HOM05D001124', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001124', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '548', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02520' => 'bna', 'A03p06630' => 'bna', 'A05p44460' => 'bna', 'A06p08710' => 'bna', 'A06p41090' => 'bna', 'A07p32320' => 'bna', 'A08p32520' => 'bna', 'A09p10360' => 'bna', 'A10p24080' => 'bna', 'Aa31LG11G15250' => 'aar', 'Aa31LG1G1800' => 'aar', 'Aa31LG2G5120' => 'aar', 'Aa31LG2G6070' => 'aar', 'Aa31LG5G10770' => 'aar', 'Aa31sc61G90' => 'aar', 'Actinidia01352' => 'ach', 'Actinidia05983' => 'ach', 'Actinidia08133' => 'ach', 'Actinidia15101' => 'ach', 'Actinidia26379' => 'ach', 'Actinidia35778' => 'ach', 'Actinidia36123' => 'ach', 'Actinidia37436' => 'ach', 'Actinidia38730' => 'ach', 'Ah.02g128210' => 'amhyb', 'Ah.03g132990' => 'amhyb', 'Ah.14g079410' => 'amhyb', 'AL1G24640' => 'aly', 'AL2G26680' => 'aly', 'AL3G10530' => 'aly', 'AL3G45230' => 'aly', 'AL5G15230' => 'aly', 'AL5G16960' => 'aly', 'AL6G25210' => 'aly', 'Aqoxy2G00441' => 'aox', 'Aqoxy3G01236' => 'aox', 'Aqoxy5G03746' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3RQ047' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C7GMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9C8JER' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MBL6KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YXCZ83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZANX40' => 'arhy', 'AT1G12990' => 'ath', 'AT1G67880' => 'ath', 'AT2G13290' => 'ath', 'AT3G01620' => 'ath', 'AT3G26445' => 'ath', 'AT3G27540' => 'ath', 'AT5G14480' => 'ath', 'ATR0824G026' => 'atr', 'ATR1098G019' => 'atr', 'Atru.chr11.2145' => 'acertr', 'Atru.chr2.3636' => 'acertr', 'Atru.chr2.3644' => 'acertr', 'Atru.chr6.2422' => 'acertr', 'Atru.chr7.1112' => 'acertr', 'AUR62005469' => 'cqu', 'AUR62011166' => 'cqu', 'AUR62013319' => 'cqu', 'AUR62024273' => 'cqu', 'AUR62028420' => 'cqu', 'AUR62041942' => 'cqu', 'BcaB01g04969' => 'bca', 'BcaB01g06371' => 'bca', 'BcaB02g11494' => 'bca', 'BcaB03g15382' => 'bca', 'BcaB08g36994' => 'bca', 'BcaC03g13477' => 'bca', 'BcaC03g13478' => 'bca', 'BcaC03g13480' => 'bca', 'BcaC03g13481' => 'bca', 'BcaC03g13486' => 'bca', 'BcaC04g19031' => 'bca', 'BcaC04g23085' => 'bca', 'BcaC05g25094' => 'bca', 'BcaC05g25096' => 'bca', 'BcaC05g25138' => 'bca', 'BcaC05g30416' => 'bca', 'BcaC05g30455' => 'bca', 'BcaC06g30979' => 'bca', 'BcaC06g33805' => 'bca', 'BcaC08g46021' => 'bca', 'BcaNung03154' => 'bca', 'BolC2t06623H' => 'bol', 'BolC2t06632H' => 'bol', 'BolC2t06635H' => 'bol', 'BolC2t06638H' => 'bol', 'BolC3t13266H' => 'bol', 'BolC5t29776H' => 'bol', 'BolC6t38912H' => 'bol', 'BolC7t44183H' => 'bol', 'BolC9t54123H' => 'bol', 'BolC9t59107H' => 'bol', 'BraA02t05221Z' => 'bra', 'BraA03t09996Z' => 'bra', 'BraA05t23210Z' => 'bra', 'BraA06t24068Z' => 'bra', 'BraA06t27032Z' => 'bra', 'BraA08t35176Z' => 'bra', 'BraA09t36680Z' => 'bra', 'BraA10t44471Z' => 'bra', 'C02p06760' => 'bna', 'C02p06890' => 'bna', 'C02p07010' => 'bna', 'C03p07660' => 'bna', 'C05p10300' => 'bna', 'C06p38150' => 'bna', 'C07p36650' => 'bna', 'C08p15770' => 'bna', 'C09p12300' => 'bna', 'C09p62700' => 'bna', 'C09p75040' => 'bna', 'CAN.G13.1' => 'can', 'CAN.G138.4' => 'can', 'CAN.G44.6' => 'can', 'CAN.G473.19' => 'can', 'CANSAT01G0835' => 'cansat', 'CANSAT11G0246' => 'cansat', 'CANSAT11G1766' => 'cansat', 'CANSAT64G1954' => 'cansat', 'CARHR013330' => 'chi', 'CARHR060530' => 'chi', 'CARHR075300' => 'chi', 'CARHR105120' => 'chi', 'CARHR148910' => 'chi', 'CARHR198830' => 'chi', 'Carub.0001s1275' => 'cru', 'Carub.0002s1437' => 'cru', 'Carub.0003s0044' => 'cru', 'Carub.0003s2787' => 'cru', 'Carub.0005s0597' => 'cru', 'Carub.0006s1266' => 'cru', 'Ca_06935_v3' => 'car', 'Ca_13559_v3' => 'car', 'Ca_16941_v3' => 'car', 'Ca_16960_v3' => 'car', 'Ca_17775_v3' => 'car', 'Ca_30464_v3' => 'car', 'Cc06_g08160' => 'ccan', 'Cc07_g01520' => 'ccan', 'Cc11_g15810' => 'ccan', 'CDE02G2840' => 'cde', 'CDE03G0093' => 'cde', 'CDE04G2127' => 'cde', 'CDE07G1857' => 'cde', 'CDE09G1246' => 'cde', 'Cfa003412' => 'cfa', 'Cfa007341' => 'cfa', 'Cfa009220' => 'cfa', 'Ciclev10008737m.g' => 'ccl', 'Ciclev10015565m.g' => 'ccl', 'Ciclev10031761m.g' => 'ccl', 'CiPaw.03G045300' => 'cil', 'CiPaw.03G247200' => 'cil', 'CiPaw.04G029500' => 'cil', 'CiPaw.04G174000' => 'cil', 'CiPaw.05G181200' => 'cil', 'CiPaw.06G067100' => 'cil', 'ClCG05G025800' => 'cla', 'ClCG06G011400' => 'cla', 'ClCG09G019360' => 'cla', 'COL.COLO4_04827' => 'col', 'COL.COLO4_29170' => 'col', 'COL.COLO4_35131' => 'col', 'COL.COLO4_35132' => 'col', 'Cpa.g.sc33.32' => 'cpa', 'Cpa.g.sc46.29' => 'cpa', 'Cpa.g.sc796.1' => 'cpa', 'CsaV3_1G030420' => 'csa', 'CsaV3_5G027050' => 'csa', 'CsaV3_5G031040' => 'csa', 'CsaV3_UNG023130' => 'csa', 'CSS0007726' => 'camsi', 'CSS0016433' => 'camsi', 'CSS0017656' => 'camsi', 'CSS0025364' => 'camsi', 'CSS0027582' => 'camsi', 'CSS0047288' => 'camsi', 'CSS0049950' => 'camsi', 'DCAR_003843' => 'dca', 'DCAR_007052' => 'dca', 'DCAR_020884' => 'dca', 'DCAR_021730' => 'dca', 'DCAR_024423' => 'dca', 'DCAR_026509' => 'dca', 'DCAR_031158' => 'dca', 'Dinv14728' => 'din', 'Dinv15219' => 'din', 'Dinv25728' => 'din', 'Dinv33428' => 'din', 'Dinv36489' => 'din', 'Dinv41486' => 'din', 'Duzib147G0469' => 'dzi', 'Duzib168G0060' => 'dzi', 'Duzib187G1215' => 'dzi', 'Duzib248G0692' => 'dzi', 'Duzib251G0767' => 'dzi', 'Duzib264G0446' => 'dzi', 'Duzib268G0691' => 'dzi', 'ECA232G4767' => 'eca', 'ECA233G2838' => 'eca', 'ECA234G0391' => 'eca', 'ECA234G0857' => 'eca', 'ECA236G1593' => 'eca', 'ECA238G0565' => 'eca', 'ECA246G1027' => 'eca', 'ECA246G3223' => 'eca', 'ECA246G3470' => 'eca', 'EL10Ac6g13829' => 'bvu', 'EL10Ac6g14093' => 'bvu', 'EL10Ac8g18707' => 'bvu', 'Eucgr.C01369' => 'egr', 'Eucgr.H02492' => 'egr', 'Eucgr.I01733' => 'egr', 'Eucgr.J02255' => 'egr', 'Eucgr.J02257' => 'egr', 'Eucgr.J02258' => 'egr', 'FAN02G1601' => 'fan', 'FAN03G1586' => 'fan', 'FAN03G2986' => 'fan', 'FAN05G4837' => 'fan', 'FAN06G0146' => 'fan', 'FAN07G0858' => 'fan', 'FAN09G3179' => 'fan', 'FAN10G0669' => 'fan', 'FAN12G2358' => 'fan', 'FAN14G4198' => 'fan', 'FAN14G5112' => 'fan', 'FAN17G0342' => 'fan', 'FAN19G0342' => 'fan', 'FAN19G0962' => 'fan', 'FAN19G1101' => 'fan', 'FAN19G1872' => 'fan', 'FAN22G0356' => 'fan', 'FAN23G0744' => 'fan', 'FAN23G1914' => 'fan', 'FAN26G0032' => 'fan', 'FAN28G0625' => 'fan', 'FvH4_1g02710' => 'fve', 'FvH4_1g02720' => 'fve', 'FvH4_4g25670' => 'fve', 'FvH4_6g51700' => 'fve', 'FvH4_7g20170' => 'fve', 'Glyma.05G175000' => 'gma', 'Glyma.08G132300' => 'gma', 'Glyma.11G243000' => 'gma', 'Glyma.13G158900' => 'gma', 'Glyma.17G112400' => 'gma', 'Glyma.18G014100' => 'gma', 'Glyma.19G003100' => 'gma', 'Glyma.19G056500' => 'gma', 'Gohir.A01G158900' => 'ghi', 'Gohir.A05G312600' => 'ghi', 'Gohir.A05G354900' => 'ghi', 'Gohir.A07G037200' => 'ghi', 'Gohir.A09G030000' => 'ghi', 'Gohir.A12G145200' => 'ghi', 'Gohir.D01G151500' => 'ghi', 'Gohir.D04G058300' => 'ghi', 'Gohir.D05G314100' => 'ghi', 'Gohir.D07G041400' => 'ghi', 'Gohir.D09G029700' => 'ghi', 'Gohir.D12G149700' => 'ghi', 'Gorai.001G043800' => 'gra', 'Gorai.002G187800' => 'gra', 'Gorai.006G034700' => 'gra', 'Gorai.008G161200' => 'gra', 'Gorai.009G335700' => 'gra', 'Gorai.012G065000' => 'gra', 'GSVIVG01000535001' => 'vvi', 'GSVIVG01015572001' => 'vvi', 'GSVIVG01032386001' => 'vvi', 'HanXRQChr05g0138531' => 'han', 'HanXRQChr06g0174391' => 'han', 'HanXRQChr07g0199021' => 'han', 'HanXRQChr08g0208211' => 'han', 'HanXRQChr09g0255471' => 'han', 'HanXRQChr10g0315791' => 'han', 'HanXRQChr12g0371991' => 'han', 'HanXRQChr15g0475251' => 'han', 'HanXRQChr17g0540001' => 'han', 'HanXRQChr17g0548631' => 'han', 'HanXRQChr17g0569561' => 'han', 'Haze_12256' => 'cav', 'Haze_14756' => 'cav', 'Haze_25528' => 'cav', 'Hma1.2p1_0079F.1_g041020' => 'hma', 'Hma1.2p1_0818F.1_g223260' => 'hma', 'Hma1.2p1_1747F.1_g300530' => 'hma', 'HPP92_004607' => 'vpl', 'HPP92_004608' => 'vpl', 'HPP92_006181' => 'vpl', 'HPP92_012192' => 'vpl', 'HPP92_015680' => 'vpl', 'HPP92_020249' => 'vpl', 'HPP92_021376' => 'vpl', 'HPP92_024275' => 'vpl', 'Hund06031' => 'sun', 'Hund25391' => 'sun', 'Lalb_Chr07g0185371' => 'lal', 'Lalb_Chr07g0185381' => 'lal', 'Lalb_Chr12g0204011' => 'lal', 'Lalb_Chr13g0301671' => 'lal', 'Lalb_Chr14g0362851' => 'lal', 'Lalb_Chr24g0403581' => 'lal', 'Lj1g0000233' => 'lja', 'Lj2g0018120' => 'lja', 'Lj3C621T0' => 'lonja', 'Lj3P1059T14' => 'lonja', 'Lj3P611T9' => 'lonja', 'Lj3P614T13' => 'lonja', 'Lj3P615T5' => 'lonja', 'Lj4g0012315' => 'lja', 'Lj4g0026182' => 'lja', 'Lj6P813T16' => 'lonja', 'Lj7C427T7' => 'lonja', 'Lj7C427T8' => 'lonja', 'Lj7P600T41' => 'lonja', 'Lju41C42G17' => 'lonja', 'Lsat_1_v5_gn_0_47300' => 'lsa', 'Lsat_1_v5_gn_2_91280' => 'lsa', 'Lsat_1_v5_gn_3_30561' => 'lsa', 'Lsat_1_v5_gn_4_184321' => 'lsa', 'Lsat_1_v5_gn_4_4041' => 'lsa', 'Lsat_1_v5_gn_5_92000' => 'lsa', 'Lsat_1_v5_gn_8_152940' => 'lsa', 'Lsat_1_v5_gn_8_62401' => 'lsa', 'Manes.06G055900' => 'mes', 'Manes.12G022200' => 'mes', 'Manes.13G023300' => 'mes', 'Manes.14G115000' => 'mes', 'Manes.15G151700' => 'mes', 'Manes.17G111300' => 'mes', 'Mapoly0226s0009' => 'mpo', 'MBI02_g25363_MAGBIO' => 'mbi', 'MBI06_g00027_MAGBIO' => 'mbi', 'MBI10_g13034_MAGBIO' => 'mbi', 'MD09G1023400' => 'mdo', 'MD13G1100100' => 'mdo', 'MD15G1169200' => 'mdo', 'MD16G1101100' => 'mdo', 'MD17G1022900' => 'mdo', 'Medtr3g096150' => 'mtr', 'Medtr4g115070' => 'mtr', 'Medtr7g033325' => 'mtr', 'Medtr8g089840' => 'mtr', 'MELO3C010319.2' => 'cme', 'MELO3C011944.2' => 'cme', 'MELO3C021589.2' => 'cme', 'Migut.E00207' => 'egut', 'Migut.H00067' => 'egut', 'Migut.K00433' => 'egut', 'Migut.K00606' => 'egut', 'Migut.K01410' => 'egut', 'MSTRG.13347' => 'ama', 'MSTRG.24045' => 'ama', 'MSTRG.2428' => 'ama', 'MSTRG.26410' => 'ama', 'MSTRG.3139' => 'ama', 'MSTRG.3286' => 'ama', 'MSTRG.563' => 'ama', 'MSTRG.7941' => 'ama', 'Nitab4.5_0000028g0060' => 'nta', 'Nitab4.5_0000065g0260' => 'nta', 'Nitab4.5_0000112g0060' => 'nta', 'Nitab4.5_0000489g0120' => 'nta', 'Nitab4.5_0001776g0050' => 'nta', 'Nitab4.5_0001854g0010' => 'nta', 'Nitab4.5_0001860g0020' => 'nta', 'Nitab4.5_0004352g0010' => 'nta', 'Nitab4.5_0008716g0020' => 'nta', 'Nitab4.5_0008922g0010' => 'nta', 'Nn3g16693' => 'nnu', 'Nn4g22596' => 'nnu', 'Nn7g37639' => 'nnu', 'Oeu001701.1' => 'oeu', 'Oeu018149.1' => 'oeu', 'Oeu026220.1' => 'oeu', 'Oeu038635.1' => 'oeu', 'Oeu049176.1' => 'oeu', 'Oeu056706.1' => 'oeu', 'Oeu056937.1' => 'oeu', 'Oeu057540.1' => 'oeu', 'Os02g0594900' => 'osa', 'Os02g0595100' => 'osa', 'Os04g0477500' => 'osa', 'Os12g0611900' => 'osa', 'Peaxi162Scf00076g00020' => 'pax', 'Peaxi162Scf00128g00217' => 'pax', 'Peaxi162Scf00129g01640' => 'pax', 'Peaxi162Scf00669g00007' => 'pax', 'Peaxi162Scf00700g00421' => 'pax', 'Peaxi162Scf00801g00038' => 'pax', 'Peaxi162Scf00891g00025' => 'pax', 'PGR083G0909' => 'pgr', 'PGR119G1005' => 'pgr', 'PGR142G2236' => 'pgr', 'PGR142G3388' => 'pgr', 'PGSC0003DMG400004514' => 'stu', 'PGSC0003DMG400012635' => 'stu', 'PGSC0003DMG400015730' => 'stu', 'PGSC0003DMG400018611' => 'stu', 'PGSC0003DMG400030897' => 'stu', 'Phvul.001G254800' => 'pvu', 'Phvul.002G260100' => 'pvu', 'Phvul.003G167600' => 'pvu', 'Phvul.004G005100' => 'pvu', 'Potri.001G343600' => 'ptr', 'Potri.006G066700' => 'ptr', 'Potri.008G186000' => 'ptr', 'Potri.010G046900' => 'ptr', 'Potri.018G127900' => 'ptr', 'Pp3c20_17750' => 'ppa', 'Pp3c24_4380' => 'ppa', 'Prupe.1G245800' => 'ppe', 'Prupe.3G293400' => 'ppe', 'Prupe.7G247400' => 'ppe', 'Psat0s145g0120' => 'psa', 'Psat0s595g0040' => 'psa', 'Psat0s595g0120' => 'psa', 'Psat3g175040' => 'psa', 'Psat7g058120' => 'psa', 'PSO017G0428' => 'pso', 'PSO063G7510' => 'pso', 'PSO067G0046' => 'pso', 'PSO478G1073' => 'pso', 'PSO675G3677' => 'pso', 'PSO675G6558' => 'pso', 'PSO675G7520' => 'pso', 'PSO675G8959' => 'pso', 'QL02p074089' => 'qlo', 'QL02p089614' => 'qlo', 'QL03p057736' => 'qlo', 'RcHm_v2.0_Chr1g0364131' => 'rch', 'RcHm_v2.0_Chr2g0087801' => 'rch', 'RcHm_v2.0_Chr2g0087821' => 'rch', 'RcHm_v2.0_Chr2g0173231' => 'rch', 'RcHm_v2.0_Chr4g0433111' => 'rch', 'Rhsim03G0250300' => 'rsi', 'Rhsim08G0048400' => 'rsi', 'Rhsim10G0014800' => 'rsi', 'Rhsim12G0040100' => 'rsi', 'Rhsim12G0109700' => 'rsi', 'Sabra06G0049600' => 'sbr', 'Sabra08G0141000' => 'sbr', 'Sabra10G0021400' => 'sbr', 'Sabra16G0222900' => 'sbr', 'Sabra18G0108600' => 'sbr', 'SalBow1G0433' => 'sbo', 'SalBow1G2038' => 'sbo', 'SalBow1G5003' => 'sbo', 'SalBow7G1197' => 'sbo', 'SalBow8G3506' => 'sbo', 'Sc03g0007300' => 'sci', 'Sc11g0000950' => 'sci', 'Sc14g0008750' => 'sci', 'Sc18g0000420' => 'sci', 'Sed0006754' => 'sed', 'Sed0008741' => 'sed', 'Sed0017172' => 'sed', 'Sed0018925' => 'sed', 'Sed0023326' => 'sed', 'Sed0025909' => 'sed', 'SEGI_05333' => 'sgi', 'SEGI_10362' => 'sgi', 'SEGI_13380' => 'sgi', 'SEGI_24306' => 'sgi', 'SEGI_29077' => 'sgi', 'SEGI_29095' => 'sgi', 'SEGI_36534' => 'sgi', 'SEGI_37506' => 'sgi', 'SEGI_38321' => 'sgi', 'SGA_v2.0_scaffold307G48031' => 'sas', 'SGA_v2.0_scaffold47G17507' => 'sas', 'SGA_v2.0_scaffold63G21736' => 'sas', 'SGA_v2.0_scaffold87G27070' => 'sas', 'SHI17794' => 'shi', 'SHI28851' => 'shi', 'SMO165G0155' => 'smo', 'SMO340G0217' => 'smo', 'SMO367G1210' => 'smo', 'Solyc02g093430.3' => 'sly', 'Solyc05g013580.4' => 'sly', 'Solyc07g008030.3' => 'sly', 'Solyc12g035470.2' => 'sly', 'Sopen02g038020' => 'spe', 'Sopen05g008490' => 'spe', 'Sopen07g003910' => 'spe', 'Sopen12g015240' => 'spe', 'Sp1g11550' => 'spa', 'Sp2g16710' => 'spa', 'Sp3g00430' => 'spa', 'Sp3g26780' => 'spa', 'Sp5g22900' => 'spa', 'Sp6g29530' => 'spa', 'TAR371G0794' => 'tar', 'TAR374G0164' => 'tar', 'TAR622G0165' => 'tar', 'TAR626G0929' => 'tar', 'TAR629G2155' => 'tar', 'THA.LOC104805282' => 'tha', 'THA.LOC104805363' => 'tha', 'THA.LOC104808968' => 'tha', 'THA.LOC104821093' => 'tha', 'THA.LOC104823953' => 'tha', 'THA.LOC104825562' => 'tha', 'THA.LOC104825665' => 'tha', 'Thecc.02G261400' => 'tca', 'Thecc.04G019200' => 'tca', 'Thecc.09G130400' => 'tca', 'Thhalv10004374m.g' => 'esa', 'Thhalv10007850m.g' => 'esa', 'Thhalv10013782m.g' => 'esa', 'Thhalv10018686m.g' => 'esa', 'Thhalv10020899m.g' => 'esa', 'Thhalv10022755m.g' => 'esa', 'TPR.G23851' => 'tpr', 'TPR.G26500' => 'tpr', 'TPR.G27267' => 'tpr', 'TPR.G32001' => 'tpr', 'TPR.G6251' => 'tpr', 'TPR.G8167' => 'tpr', 'TWI12G1330' => 'twi', 'TWI18G1239' => 'twi', 'TWI34G0979' => 'twi', 'TWI36G0670' => 'twi', 'TWI36G0707' => 'twi', 'TWI56G0233' => 'twi', 'TWI75G1809' => 'twi', 'unitig_21.g20874' => 'ugi', 'unitig_26.g10343' => 'ugi', 'unitig_46.g18392' => 'ugi', 'unitig_52.g17178' => 'ugi', 'unitig_8.g2934' => 'ugi', 'vmacro01122' => 'vma', 'vmacro05875' => 'vma', 'vmacro06147' => 'vma', 'vmacro16191' => 'vma', 'vmacro18293' => 'vma', 'VMungo0251G3707' => 'vmu', 'VMungo0464G1521' => 'vmu', 'VMungo1215G0205' => 'vmu', 'VMungo1383G2484' => 'vmu', 'Zm00001eb079610' => 'zma', 'Zm00001eb135990' => 'zma', 'Zm00001eb183710' => 'zma', 'Zm00001eb246020' => 'zma' ) $gf_id = 'HOM05D001124' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001124' ) $data_identifier = 'HOM05D001124' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 6, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 7, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 21, 'bol' => (int) 10, 'bra' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 6, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 9, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 21, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 8, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 10, 'lsa' => (int) 8, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 8, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 9, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb246020' $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' => 'HOM05D001124', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '548', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02520' => 'bna', 'A03p06630' => 'bna', 'A05p44460' => 'bna', 'A06p08710' => 'bna', 'A06p41090' => 'bna', 'A07p32320' => 'bna', 'A08p32520' => 'bna', 'A09p10360' => 'bna', 'A10p24080' => 'bna', 'Aa31LG11G15250' => 'aar', 'Aa31LG1G1800' => 'aar', 'Aa31LG2G5120' => 'aar', 'Aa31LG2G6070' => 'aar', 'Aa31LG5G10770' => 'aar', 'Aa31sc61G90' => 'aar', 'Actinidia01352' => 'ach', 'Actinidia05983' => 'ach', 'Actinidia08133' => 'ach', 'Actinidia15101' => 'ach', 'Actinidia26379' => 'ach', 'Actinidia35778' => 'ach', 'Actinidia36123' => 'ach', 'Actinidia37436' => 'ach', 'Actinidia38730' => 'ach', 'Ah.02g128210' => 'amhyb', 'Ah.03g132990' => 'amhyb', 'Ah.14g079410' => 'amhyb', 'AL1G24640' => 'aly', 'AL2G26680' => 'aly', 'AL3G10530' => 'aly', 'AL3G45230' => 'aly', 'AL5G15230' => 'aly', 'AL5G16960' => 'aly', 'AL6G25210' => 'aly', 'Aqoxy2G00441' => 'aox', 'Aqoxy3G01236' => 'aox', 'Aqoxy5G03746' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3RQ047' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C7GMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9C8JER' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MBL6KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YXCZ83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZANX40' => 'arhy', 'AT1G12990' => 'ath', 'AT1G67880' => 'ath', 'AT2G13290' => 'ath', 'AT3G01620' => 'ath', 'AT3G26445' => 'ath', 'AT3G27540' => 'ath', 'AT5G14480' => 'ath', 'ATR0824G026' => 'atr', 'ATR1098G019' => 'atr', 'Atru.chr11.2145' => 'acertr', 'Atru.chr2.3636' => 'acertr', 'Atru.chr2.3644' => 'acertr', 'Atru.chr6.2422' => 'acertr', 'Atru.chr7.1112' => 'acertr', 'AUR62005469' => 'cqu', 'AUR62011166' => 'cqu', 'AUR62013319' => 'cqu', 'AUR62024273' => 'cqu', 'AUR62028420' => 'cqu', 'AUR62041942' => 'cqu', 'BcaB01g04969' => 'bca', 'BcaB01g06371' => 'bca', 'BcaB02g11494' => 'bca', 'BcaB03g15382' => 'bca', 'BcaB08g36994' => 'bca', 'BcaC03g13477' => 'bca', 'BcaC03g13478' => 'bca', 'BcaC03g13480' => 'bca', 'BcaC03g13481' => 'bca', 'BcaC03g13486' => 'bca', 'BcaC04g19031' => 'bca', 'BcaC04g23085' => 'bca', 'BcaC05g25094' => 'bca', 'BcaC05g25096' => 'bca', 'BcaC05g25138' => 'bca', 'BcaC05g30416' => 'bca', 'BcaC05g30455' => 'bca', 'BcaC06g30979' => 'bca', 'BcaC06g33805' => 'bca', 'BcaC08g46021' => 'bca', 'BcaNung03154' => 'bca', 'BolC2t06623H' => 'bol', 'BolC2t06632H' => 'bol', 'BolC2t06635H' => 'bol', 'BolC2t06638H' => 'bol', 'BolC3t13266H' => 'bol', 'BolC5t29776H' => 'bol', 'BolC6t38912H' => 'bol', 'BolC7t44183H' => 'bol', 'BolC9t54123H' => 'bol', 'BolC9t59107H' => 'bol', 'BraA02t05221Z' => 'bra', 'BraA03t09996Z' => 'bra', 'BraA05t23210Z' => 'bra', 'BraA06t24068Z' => 'bra', 'BraA06t27032Z' => 'bra', 'BraA08t35176Z' => 'bra', 'BraA09t36680Z' => 'bra', 'BraA10t44471Z' => 'bra', 'C02p06760' => 'bna', 'C02p06890' => 'bna', 'C02p07010' => 'bna', 'C03p07660' => 'bna', 'C05p10300' => 'bna', 'C06p38150' => 'bna', 'C07p36650' => 'bna', 'C08p15770' => 'bna', 'C09p12300' => 'bna', 'C09p62700' => 'bna', 'C09p75040' => 'bna', 'CAN.G13.1' => 'can', 'CAN.G138.4' => 'can', 'CAN.G44.6' => 'can', 'CAN.G473.19' => 'can', 'CANSAT01G0835' => 'cansat', 'CANSAT11G0246' => 'cansat', 'CANSAT11G1766' => 'cansat', 'CANSAT64G1954' => 'cansat', 'CARHR013330' => 'chi', 'CARHR060530' => 'chi', 'CARHR075300' => 'chi', 'CARHR105120' => 'chi', 'CARHR148910' => 'chi', 'CARHR198830' => 'chi', 'Carub.0001s1275' => 'cru', 'Carub.0002s1437' => 'cru', 'Carub.0003s0044' => 'cru', 'Carub.0003s2787' => 'cru', 'Carub.0005s0597' => 'cru', 'Carub.0006s1266' => 'cru', 'Ca_06935_v3' => 'car', 'Ca_13559_v3' => 'car', 'Ca_16941_v3' => 'car', 'Ca_16960_v3' => 'car', 'Ca_17775_v3' => 'car', 'Ca_30464_v3' => 'car', 'Cc06_g08160' => 'ccan', 'Cc07_g01520' => 'ccan', 'Cc11_g15810' => 'ccan', 'CDE02G2840' => 'cde', 'CDE03G0093' => 'cde', 'CDE04G2127' => 'cde', 'CDE07G1857' => 'cde', 'CDE09G1246' => 'cde', 'Cfa003412' => 'cfa', 'Cfa007341' => 'cfa', 'Cfa009220' => 'cfa', 'Ciclev10008737m.g' => 'ccl', 'Ciclev10015565m.g' => 'ccl', 'Ciclev10031761m.g' => 'ccl', 'CiPaw.03G045300' => 'cil', 'CiPaw.03G247200' => 'cil', 'CiPaw.04G029500' => 'cil', 'CiPaw.04G174000' => 'cil', 'CiPaw.05G181200' => 'cil', 'CiPaw.06G067100' => 'cil', 'ClCG05G025800' => 'cla', 'ClCG06G011400' => 'cla', 'ClCG09G019360' => 'cla', 'COL.COLO4_04827' => 'col', 'COL.COLO4_29170' => 'col', 'COL.COLO4_35131' => 'col', 'COL.COLO4_35132' => 'col', 'Cpa.g.sc33.32' => 'cpa', 'Cpa.g.sc46.29' => 'cpa', 'Cpa.g.sc796.1' => 'cpa', 'CsaV3_1G030420' => 'csa', 'CsaV3_5G027050' => 'csa', 'CsaV3_5G031040' => 'csa', 'CsaV3_UNG023130' => 'csa', 'CSS0007726' => 'camsi', 'CSS0016433' => 'camsi', 'CSS0017656' => 'camsi', 'CSS0025364' => 'camsi', 'CSS0027582' => 'camsi', 'CSS0047288' => 'camsi', 'CSS0049950' => 'camsi', 'DCAR_003843' => 'dca', 'DCAR_007052' => 'dca', 'DCAR_020884' => 'dca', 'DCAR_021730' => 'dca', 'DCAR_024423' => 'dca', 'DCAR_026509' => 'dca', 'DCAR_031158' => 'dca', 'Dinv14728' => 'din', 'Dinv15219' => 'din', 'Dinv25728' => 'din', 'Dinv33428' => 'din', 'Dinv36489' => 'din', 'Dinv41486' => 'din', 'Duzib147G0469' => 'dzi', 'Duzib168G0060' => 'dzi', 'Duzib187G1215' => 'dzi', 'Duzib248G0692' => 'dzi', 'Duzib251G0767' => 'dzi', 'Duzib264G0446' => 'dzi', 'Duzib268G0691' => 'dzi', 'ECA232G4767' => 'eca', 'ECA233G2838' => 'eca', 'ECA234G0391' => 'eca', 'ECA234G0857' => 'eca', 'ECA236G1593' => 'eca', 'ECA238G0565' => 'eca', 'ECA246G1027' => 'eca', 'ECA246G3223' => 'eca', 'ECA246G3470' => 'eca', 'EL10Ac6g13829' => 'bvu', 'EL10Ac6g14093' => 'bvu', 'EL10Ac8g18707' => 'bvu', 'Eucgr.C01369' => 'egr', 'Eucgr.H02492' => 'egr', 'Eucgr.I01733' => 'egr', 'Eucgr.J02255' => 'egr', 'Eucgr.J02257' => 'egr', 'Eucgr.J02258' => 'egr', 'FAN02G1601' => 'fan', 'FAN03G1586' => 'fan', 'FAN03G2986' => 'fan', 'FAN05G4837' => 'fan', 'FAN06G0146' => 'fan', 'FAN07G0858' => 'fan', 'FAN09G3179' => 'fan', 'FAN10G0669' => 'fan', 'FAN12G2358' => 'fan', 'FAN14G4198' => 'fan', 'FAN14G5112' => 'fan', 'FAN17G0342' => 'fan', 'FAN19G0342' => 'fan', 'FAN19G0962' => 'fan', 'FAN19G1101' => 'fan', 'FAN19G1872' => 'fan', 'FAN22G0356' => 'fan', 'FAN23G0744' => 'fan', 'FAN23G1914' => 'fan', 'FAN26G0032' => 'fan', 'FAN28G0625' => 'fan', 'FvH4_1g02710' => 'fve', 'FvH4_1g02720' => 'fve', 'FvH4_4g25670' => 'fve', 'FvH4_6g51700' => 'fve', 'FvH4_7g20170' => 'fve', 'Glyma.05G175000' => 'gma', 'Glyma.08G132300' => 'gma', 'Glyma.11G243000' => 'gma', 'Glyma.13G158900' => 'gma', 'Glyma.17G112400' => 'gma', 'Glyma.18G014100' => 'gma', 'Glyma.19G003100' => 'gma', 'Glyma.19G056500' => 'gma', 'Gohir.A01G158900' => 'ghi', 'Gohir.A05G312600' => 'ghi', 'Gohir.A05G354900' => 'ghi', 'Gohir.A07G037200' => 'ghi', 'Gohir.A09G030000' => 'ghi', 'Gohir.A12G145200' => 'ghi', 'Gohir.D01G151500' => 'ghi', 'Gohir.D04G058300' => 'ghi', 'Gohir.D05G314100' => 'ghi', 'Gohir.D07G041400' => 'ghi', 'Gohir.D09G029700' => 'ghi', 'Gohir.D12G149700' => 'ghi', 'Gorai.001G043800' => 'gra', 'Gorai.002G187800' => 'gra', 'Gorai.006G034700' => 'gra', 'Gorai.008G161200' => 'gra', 'Gorai.009G335700' => 'gra', 'Gorai.012G065000' => 'gra', 'GSVIVG01000535001' => 'vvi', 'GSVIVG01015572001' => 'vvi', 'GSVIVG01032386001' => 'vvi', 'HanXRQChr05g0138531' => 'han', 'HanXRQChr06g0174391' => 'han', 'HanXRQChr07g0199021' => 'han', 'HanXRQChr08g0208211' => 'han', 'HanXRQChr09g0255471' => 'han', 'HanXRQChr10g0315791' => 'han', 'HanXRQChr12g0371991' => 'han', 'HanXRQChr15g0475251' => 'han', 'HanXRQChr17g0540001' => 'han', 'HanXRQChr17g0548631' => 'han', 'HanXRQChr17g0569561' => 'han', 'Haze_12256' => 'cav', 'Haze_14756' => 'cav', 'Haze_25528' => 'cav', 'Hma1.2p1_0079F.1_g041020' => 'hma', 'Hma1.2p1_0818F.1_g223260' => 'hma', 'Hma1.2p1_1747F.1_g300530' => 'hma', 'HPP92_004607' => 'vpl', 'HPP92_004608' => 'vpl', 'HPP92_006181' => 'vpl', 'HPP92_012192' => 'vpl', 'HPP92_015680' => 'vpl', 'HPP92_020249' => 'vpl', 'HPP92_021376' => 'vpl', 'HPP92_024275' => 'vpl', 'Hund06031' => 'sun', 'Hund25391' => 'sun', 'Lalb_Chr07g0185371' => 'lal', 'Lalb_Chr07g0185381' => 'lal', 'Lalb_Chr12g0204011' => 'lal', 'Lalb_Chr13g0301671' => 'lal', 'Lalb_Chr14g0362851' => 'lal', 'Lalb_Chr24g0403581' => 'lal', 'Lj1g0000233' => 'lja', 'Lj2g0018120' => 'lja', 'Lj3C621T0' => 'lonja', 'Lj3P1059T14' => 'lonja', 'Lj3P611T9' => 'lonja', 'Lj3P614T13' => 'lonja', 'Lj3P615T5' => 'lonja', 'Lj4g0012315' => 'lja', 'Lj4g0026182' => 'lja', 'Lj6P813T16' => 'lonja', 'Lj7C427T7' => 'lonja', 'Lj7C427T8' => 'lonja', 'Lj7P600T41' => 'lonja', 'Lju41C42G17' => 'lonja', 'Lsat_1_v5_gn_0_47300' => 'lsa', 'Lsat_1_v5_gn_2_91280' => 'lsa', 'Lsat_1_v5_gn_3_30561' => 'lsa', 'Lsat_1_v5_gn_4_184321' => 'lsa', 'Lsat_1_v5_gn_4_4041' => 'lsa', 'Lsat_1_v5_gn_5_92000' => 'lsa', 'Lsat_1_v5_gn_8_152940' => 'lsa', 'Lsat_1_v5_gn_8_62401' => 'lsa', 'Manes.06G055900' => 'mes', 'Manes.12G022200' => 'mes', 'Manes.13G023300' => 'mes', 'Manes.14G115000' => 'mes', 'Manes.15G151700' => 'mes', 'Manes.17G111300' => 'mes', 'Mapoly0226s0009' => 'mpo', 'MBI02_g25363_MAGBIO' => 'mbi', 'MBI06_g00027_MAGBIO' => 'mbi', 'MBI10_g13034_MAGBIO' => 'mbi', 'MD09G1023400' => 'mdo', 'MD13G1100100' => 'mdo', 'MD15G1169200' => 'mdo', 'MD16G1101100' => 'mdo', 'MD17G1022900' => 'mdo', 'Medtr3g096150' => 'mtr', 'Medtr4g115070' => 'mtr', 'Medtr7g033325' => 'mtr', 'Medtr8g089840' => 'mtr', 'MELO3C010319.2' => 'cme', 'MELO3C011944.2' => 'cme', 'MELO3C021589.2' => 'cme', 'Migut.E00207' => 'egut', 'Migut.H00067' => 'egut', 'Migut.K00433' => 'egut', 'Migut.K00606' => 'egut', 'Migut.K01410' => 'egut', 'MSTRG.13347' => 'ama', 'MSTRG.24045' => 'ama', 'MSTRG.2428' => 'ama', 'MSTRG.26410' => 'ama', 'MSTRG.3139' => 'ama', 'MSTRG.3286' => 'ama', 'MSTRG.563' => 'ama', 'MSTRG.7941' => 'ama', 'Nitab4.5_0000028g0060' => 'nta', 'Nitab4.5_0000065g0260' => 'nta', 'Nitab4.5_0000112g0060' => 'nta', 'Nitab4.5_0000489g0120' => 'nta', 'Nitab4.5_0001776g0050' => 'nta', 'Nitab4.5_0001854g0010' => 'nta', 'Nitab4.5_0001860g0020' => 'nta', 'Nitab4.5_0004352g0010' => 'nta', 'Nitab4.5_0008716g0020' => 'nta', 'Nitab4.5_0008922g0010' => 'nta', 'Nn3g16693' => 'nnu', 'Nn4g22596' => 'nnu', 'Nn7g37639' => 'nnu', 'Oeu001701.1' => 'oeu', 'Oeu018149.1' => 'oeu', 'Oeu026220.1' => 'oeu', 'Oeu038635.1' => 'oeu', 'Oeu049176.1' => 'oeu', 'Oeu056706.1' => 'oeu', 'Oeu056937.1' => 'oeu', 'Oeu057540.1' => 'oeu', 'Os02g0594900' => 'osa', 'Os02g0595100' => 'osa', 'Os04g0477500' => 'osa', 'Os12g0611900' => 'osa', 'Peaxi162Scf00076g00020' => 'pax', 'Peaxi162Scf00128g00217' => 'pax', 'Peaxi162Scf00129g01640' => 'pax', 'Peaxi162Scf00669g00007' => 'pax', 'Peaxi162Scf00700g00421' => 'pax', 'Peaxi162Scf00801g00038' => 'pax', 'Peaxi162Scf00891g00025' => 'pax', 'PGR083G0909' => 'pgr', 'PGR119G1005' => 'pgr', 'PGR142G2236' => 'pgr', 'PGR142G3388' => 'pgr', 'PGSC0003DMG400004514' => 'stu', 'PGSC0003DMG400012635' => 'stu', 'PGSC0003DMG400015730' => 'stu', 'PGSC0003DMG400018611' => 'stu', 'PGSC0003DMG400030897' => 'stu', 'Phvul.001G254800' => 'pvu', 'Phvul.002G260100' => 'pvu', 'Phvul.003G167600' => 'pvu', 'Phvul.004G005100' => 'pvu', 'Potri.001G343600' => 'ptr', 'Potri.006G066700' => 'ptr', 'Potri.008G186000' => 'ptr', 'Potri.010G046900' => 'ptr', 'Potri.018G127900' => 'ptr', 'Pp3c20_17750' => 'ppa', 'Pp3c24_4380' => 'ppa', 'Prupe.1G245800' => 'ppe', 'Prupe.3G293400' => 'ppe', 'Prupe.7G247400' => 'ppe', 'Psat0s145g0120' => 'psa', 'Psat0s595g0040' => 'psa', 'Psat0s595g0120' => 'psa', 'Psat3g175040' => 'psa', 'Psat7g058120' => 'psa', 'PSO017G0428' => 'pso', 'PSO063G7510' => 'pso', 'PSO067G0046' => 'pso', 'PSO478G1073' => 'pso', 'PSO675G3677' => 'pso', 'PSO675G6558' => 'pso', 'PSO675G7520' => 'pso', 'PSO675G8959' => 'pso', 'QL02p074089' => 'qlo', 'QL02p089614' => 'qlo', 'QL03p057736' => 'qlo', 'RcHm_v2.0_Chr1g0364131' => 'rch', 'RcHm_v2.0_Chr2g0087801' => 'rch', 'RcHm_v2.0_Chr2g0087821' => 'rch', 'RcHm_v2.0_Chr2g0173231' => 'rch', 'RcHm_v2.0_Chr4g0433111' => 'rch', 'Rhsim03G0250300' => 'rsi', 'Rhsim08G0048400' => 'rsi', 'Rhsim10G0014800' => 'rsi', 'Rhsim12G0040100' => 'rsi', 'Rhsim12G0109700' => 'rsi', 'Sabra06G0049600' => 'sbr', 'Sabra08G0141000' => 'sbr', 'Sabra10G0021400' => 'sbr', 'Sabra16G0222900' => 'sbr', 'Sabra18G0108600' => 'sbr', 'SalBow1G0433' => 'sbo', 'SalBow1G2038' => 'sbo', 'SalBow1G5003' => 'sbo', 'SalBow7G1197' => 'sbo', 'SalBow8G3506' => 'sbo', 'Sc03g0007300' => 'sci', 'Sc11g0000950' => 'sci', 'Sc14g0008750' => 'sci', 'Sc18g0000420' => 'sci', 'Sed0006754' => 'sed', 'Sed0008741' => 'sed', 'Sed0017172' => 'sed', 'Sed0018925' => 'sed', 'Sed0023326' => 'sed', 'Sed0025909' => 'sed', 'SEGI_05333' => 'sgi', 'SEGI_10362' => 'sgi', 'SEGI_13380' => 'sgi', 'SEGI_24306' => 'sgi', 'SEGI_29077' => 'sgi', 'SEGI_29095' => 'sgi', 'SEGI_36534' => 'sgi', 'SEGI_37506' => 'sgi', 'SEGI_38321' => 'sgi', 'SGA_v2.0_scaffold307G48031' => 'sas', 'SGA_v2.0_scaffold47G17507' => 'sas', 'SGA_v2.0_scaffold63G21736' => 'sas', 'SGA_v2.0_scaffold87G27070' => 'sas', 'SHI17794' => 'shi', 'SHI28851' => 'shi', 'SMO165G0155' => 'smo', 'SMO340G0217' => 'smo', 'SMO367G1210' => 'smo', 'Solyc02g093430.3' => 'sly', 'Solyc05g013580.4' => 'sly', 'Solyc07g008030.3' => 'sly', 'Solyc12g035470.2' => 'sly', 'Sopen02g038020' => 'spe', 'Sopen05g008490' => 'spe', 'Sopen07g003910' => 'spe', 'Sopen12g015240' => 'spe', 'Sp1g11550' => 'spa', 'Sp2g16710' => 'spa', 'Sp3g00430' => 'spa', 'Sp3g26780' => 'spa', 'Sp5g22900' => 'spa', 'Sp6g29530' => 'spa', 'TAR371G0794' => 'tar', 'TAR374G0164' => 'tar', 'TAR622G0165' => 'tar', 'TAR626G0929' => 'tar', 'TAR629G2155' => 'tar', 'THA.LOC104805282' => 'tha', 'THA.LOC104805363' => 'tha', 'THA.LOC104808968' => 'tha', 'THA.LOC104821093' => 'tha', 'THA.LOC104823953' => 'tha', 'THA.LOC104825562' => 'tha', 'THA.LOC104825665' => 'tha', 'Thecc.02G261400' => 'tca', 'Thecc.04G019200' => 'tca', 'Thecc.09G130400' => 'tca', 'Thhalv10004374m.g' => 'esa', 'Thhalv10007850m.g' => 'esa', 'Thhalv10013782m.g' => 'esa', 'Thhalv10018686m.g' => 'esa', 'Thhalv10020899m.g' => 'esa', 'Thhalv10022755m.g' => 'esa', 'TPR.G23851' => 'tpr', 'TPR.G26500' => 'tpr', 'TPR.G27267' => 'tpr', 'TPR.G32001' => 'tpr', 'TPR.G6251' => 'tpr', 'TPR.G8167' => 'tpr', 'TWI12G1330' => 'twi', 'TWI18G1239' => 'twi', 'TWI34G0979' => 'twi', 'TWI36G0670' => 'twi', 'TWI36G0707' => 'twi', 'TWI56G0233' => 'twi', 'TWI75G1809' => 'twi', 'unitig_21.g20874' => 'ugi', 'unitig_26.g10343' => 'ugi', 'unitig_46.g18392' => 'ugi', 'unitig_52.g17178' => 'ugi', 'unitig_8.g2934' => 'ugi', 'vmacro01122' => 'vma', 'vmacro05875' => 'vma', 'vmacro06147' => 'vma', 'vmacro16191' => 'vma', 'vmacro18293' => 'vma', 'VMungo0251G3707' => 'vmu', 'VMungo0464G1521' => 'vmu', 'VMungo1215G0205' => 'vmu', 'VMungo1383G2484' => 'vmu', 'Zm00001eb079610' => 'zma', 'Zm00001eb135990' => 'zma', 'Zm00001eb183710' => 'zma', 'Zm00001eb246020' => 'zma' ), 'gf_id' => 'HOM05D001124', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001124' ), 'data_identifier' => 'HOM05D001124', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001124', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '548', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02520' => 'bna', 'A03p06630' => 'bna', 'A05p44460' => 'bna', 'A06p08710' => 'bna', 'A06p41090' => 'bna', 'A07p32320' => 'bna', 'A08p32520' => 'bna', 'A09p10360' => 'bna', 'A10p24080' => 'bna', 'Aa31LG11G15250' => 'aar', 'Aa31LG1G1800' => 'aar', 'Aa31LG2G5120' => 'aar', 'Aa31LG2G6070' => 'aar', 'Aa31LG5G10770' => 'aar', 'Aa31sc61G90' => 'aar', 'Actinidia01352' => 'ach', 'Actinidia05983' => 'ach', 'Actinidia08133' => 'ach', 'Actinidia15101' => 'ach', 'Actinidia26379' => 'ach', 'Actinidia35778' => 'ach', 'Actinidia36123' => 'ach', 'Actinidia37436' => 'ach', 'Actinidia38730' => 'ach', 'Ah.02g128210' => 'amhyb', 'Ah.03g132990' => 'amhyb', 'Ah.14g079410' => 'amhyb', 'AL1G24640' => 'aly', 'AL2G26680' => 'aly', 'AL3G10530' => 'aly', 'AL3G45230' => 'aly', 'AL5G15230' => 'aly', 'AL5G16960' => 'aly', 'AL6G25210' => 'aly', 'Aqoxy2G00441' => 'aox', 'Aqoxy3G01236' => 'aox', 'Aqoxy5G03746' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3RQ047' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C7GMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9C8JER' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MBL6KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YXCZ83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZANX40' => 'arhy', 'AT1G12990' => 'ath', 'AT1G67880' => 'ath', 'AT2G13290' => 'ath', 'AT3G01620' => 'ath', 'AT3G26445' => 'ath', 'AT3G27540' => 'ath', 'AT5G14480' => 'ath', 'ATR0824G026' => 'atr', 'ATR1098G019' => 'atr', 'Atru.chr11.2145' => 'acertr', 'Atru.chr2.3636' => 'acertr', 'Atru.chr2.3644' => 'acertr', 'Atru.chr6.2422' => 'acertr', 'Atru.chr7.1112' => 'acertr', 'AUR62005469' => 'cqu', 'AUR62011166' => 'cqu', 'AUR62013319' => 'cqu', 'AUR62024273' => 'cqu', 'AUR62028420' => 'cqu', 'AUR62041942' => 'cqu', 'BcaB01g04969' => 'bca', 'BcaB01g06371' => 'bca', 'BcaB02g11494' => 'bca', 'BcaB03g15382' => 'bca', 'BcaB08g36994' => 'bca', 'BcaC03g13477' => 'bca', 'BcaC03g13478' => 'bca', 'BcaC03g13480' => 'bca', 'BcaC03g13481' => 'bca', 'BcaC03g13486' => 'bca', 'BcaC04g19031' => 'bca', 'BcaC04g23085' => 'bca', 'BcaC05g25094' => 'bca', 'BcaC05g25096' => 'bca', 'BcaC05g25138' => 'bca', 'BcaC05g30416' => 'bca', 'BcaC05g30455' => 'bca', 'BcaC06g30979' => 'bca', 'BcaC06g33805' => 'bca', 'BcaC08g46021' => 'bca', 'BcaNung03154' => 'bca', 'BolC2t06623H' => 'bol', 'BolC2t06632H' => 'bol', 'BolC2t06635H' => 'bol', 'BolC2t06638H' => 'bol', 'BolC3t13266H' => 'bol', 'BolC5t29776H' => 'bol', 'BolC6t38912H' => 'bol', 'BolC7t44183H' => 'bol', 'BolC9t54123H' => 'bol', 'BolC9t59107H' => 'bol', 'BraA02t05221Z' => 'bra', 'BraA03t09996Z' => 'bra', 'BraA05t23210Z' => 'bra', 'BraA06t24068Z' => 'bra', 'BraA06t27032Z' => 'bra', 'BraA08t35176Z' => 'bra', 'BraA09t36680Z' => 'bra', 'BraA10t44471Z' => 'bra', 'C02p06760' => 'bna', 'C02p06890' => 'bna', 'C02p07010' => 'bna', 'C03p07660' => 'bna', 'C05p10300' => 'bna', 'C06p38150' => 'bna', 'C07p36650' => 'bna', 'C08p15770' => 'bna', 'C09p12300' => 'bna', 'C09p62700' => 'bna', 'C09p75040' => 'bna', 'CAN.G13.1' => 'can', 'CAN.G138.4' => 'can', 'CAN.G44.6' => 'can', 'CAN.G473.19' => 'can', 'CANSAT01G0835' => 'cansat', 'CANSAT11G0246' => 'cansat', 'CANSAT11G1766' => 'cansat', 'CANSAT64G1954' => 'cansat', 'CARHR013330' => 'chi', 'CARHR060530' => 'chi', 'CARHR075300' => 'chi', 'CARHR105120' => 'chi', 'CARHR148910' => 'chi', 'CARHR198830' => 'chi', 'Carub.0001s1275' => 'cru', 'Carub.0002s1437' => 'cru', 'Carub.0003s0044' => 'cru', 'Carub.0003s2787' => 'cru', 'Carub.0005s0597' => 'cru', 'Carub.0006s1266' => 'cru', 'Ca_06935_v3' => 'car', 'Ca_13559_v3' => 'car', 'Ca_16941_v3' => 'car', 'Ca_16960_v3' => 'car', 'Ca_17775_v3' => 'car', 'Ca_30464_v3' => 'car', 'Cc06_g08160' => 'ccan', 'Cc07_g01520' => 'ccan', 'Cc11_g15810' => 'ccan', 'CDE02G2840' => 'cde', 'CDE03G0093' => 'cde', 'CDE04G2127' => 'cde', 'CDE07G1857' => 'cde', 'CDE09G1246' => 'cde', 'Cfa003412' => 'cfa', 'Cfa007341' => 'cfa', 'Cfa009220' => 'cfa', 'Ciclev10008737m.g' => 'ccl', 'Ciclev10015565m.g' => 'ccl', 'Ciclev10031761m.g' => 'ccl', 'CiPaw.03G045300' => 'cil', 'CiPaw.03G247200' => 'cil', 'CiPaw.04G029500' => 'cil', 'CiPaw.04G174000' => 'cil', 'CiPaw.05G181200' => 'cil', 'CiPaw.06G067100' => 'cil', 'ClCG05G025800' => 'cla', 'ClCG06G011400' => 'cla', 'ClCG09G019360' => 'cla', 'COL.COLO4_04827' => 'col', 'COL.COLO4_29170' => 'col', 'COL.COLO4_35131' => 'col', 'COL.COLO4_35132' => 'col', 'Cpa.g.sc33.32' => 'cpa', 'Cpa.g.sc46.29' => 'cpa', 'Cpa.g.sc796.1' => 'cpa', 'CsaV3_1G030420' => 'csa', 'CsaV3_5G027050' => 'csa', 'CsaV3_5G031040' => 'csa', 'CsaV3_UNG023130' => 'csa', 'CSS0007726' => 'camsi', 'CSS0016433' => 'camsi', 'CSS0017656' => 'camsi', 'CSS0025364' => 'camsi', 'CSS0027582' => 'camsi', 'CSS0047288' => 'camsi', 'CSS0049950' => 'camsi', 'DCAR_003843' => 'dca', 'DCAR_007052' => 'dca', 'DCAR_020884' => 'dca', 'DCAR_021730' => 'dca', 'DCAR_024423' => 'dca', 'DCAR_026509' => 'dca', 'DCAR_031158' => 'dca', 'Dinv14728' => 'din', 'Dinv15219' => 'din', 'Dinv25728' => 'din', 'Dinv33428' => 'din', 'Dinv36489' => 'din', 'Dinv41486' => 'din', 'Duzib147G0469' => 'dzi', 'Duzib168G0060' => 'dzi', 'Duzib187G1215' => 'dzi', 'Duzib248G0692' => 'dzi', 'Duzib251G0767' => 'dzi', 'Duzib264G0446' => 'dzi', 'Duzib268G0691' => 'dzi', 'ECA232G4767' => 'eca', 'ECA233G2838' => 'eca', 'ECA234G0391' => 'eca', 'ECA234G0857' => 'eca', 'ECA236G1593' => 'eca', 'ECA238G0565' => 'eca', 'ECA246G1027' => 'eca', 'ECA246G3223' => 'eca', 'ECA246G3470' => 'eca', 'EL10Ac6g13829' => 'bvu', 'EL10Ac6g14093' => 'bvu', 'EL10Ac8g18707' => 'bvu', 'Eucgr.C01369' => 'egr', 'Eucgr.H02492' => 'egr', 'Eucgr.I01733' => 'egr', 'Eucgr.J02255' => 'egr', 'Eucgr.J02257' => 'egr', 'Eucgr.J02258' => 'egr', 'FAN02G1601' => 'fan', 'FAN03G1586' => 'fan', 'FAN03G2986' => 'fan', 'FAN05G4837' => 'fan', 'FAN06G0146' => 'fan', 'FAN07G0858' => 'fan', 'FAN09G3179' => 'fan', 'FAN10G0669' => 'fan', 'FAN12G2358' => 'fan', 'FAN14G4198' => 'fan', 'FAN14G5112' => 'fan', 'FAN17G0342' => 'fan', 'FAN19G0342' => 'fan', 'FAN19G0962' => 'fan', 'FAN19G1101' => 'fan', 'FAN19G1872' => 'fan', 'FAN22G0356' => 'fan', 'FAN23G0744' => 'fan', 'FAN23G1914' => 'fan', 'FAN26G0032' => 'fan', 'FAN28G0625' => 'fan', 'FvH4_1g02710' => 'fve', 'FvH4_1g02720' => 'fve', 'FvH4_4g25670' => 'fve', 'FvH4_6g51700' => 'fve', 'FvH4_7g20170' => 'fve', 'Glyma.05G175000' => 'gma', 'Glyma.08G132300' => 'gma', 'Glyma.11G243000' => 'gma', 'Glyma.13G158900' => 'gma', 'Glyma.17G112400' => 'gma', 'Glyma.18G014100' => 'gma', 'Glyma.19G003100' => 'gma', 'Glyma.19G056500' => 'gma', 'Gohir.A01G158900' => 'ghi', 'Gohir.A05G312600' => 'ghi', 'Gohir.A05G354900' => 'ghi', 'Gohir.A07G037200' => 'ghi', 'Gohir.A09G030000' => 'ghi', 'Gohir.A12G145200' => 'ghi', 'Gohir.D01G151500' => 'ghi', 'Gohir.D04G058300' => 'ghi', 'Gohir.D05G314100' => 'ghi', 'Gohir.D07G041400' => 'ghi', 'Gohir.D09G029700' => 'ghi', 'Gohir.D12G149700' => 'ghi', 'Gorai.001G043800' => 'gra', 'Gorai.002G187800' => 'gra', 'Gorai.006G034700' => 'gra', 'Gorai.008G161200' => 'gra', 'Gorai.009G335700' => 'gra', 'Gorai.012G065000' => 'gra', 'GSVIVG01000535001' => 'vvi', 'GSVIVG01015572001' => 'vvi', 'GSVIVG01032386001' => 'vvi', 'HanXRQChr05g0138531' => 'han', 'HanXRQChr06g0174391' => 'han', 'HanXRQChr07g0199021' => 'han', 'HanXRQChr08g0208211' => 'han', 'HanXRQChr09g0255471' => 'han', 'HanXRQChr10g0315791' => 'han', 'HanXRQChr12g0371991' => 'han', 'HanXRQChr15g0475251' => 'han', 'HanXRQChr17g0540001' => 'han', 'HanXRQChr17g0548631' => 'han', 'HanXRQChr17g0569561' => 'han', 'Haze_12256' => 'cav', 'Haze_14756' => 'cav', 'Haze_25528' => 'cav', 'Hma1.2p1_0079F.1_g041020' => 'hma', 'Hma1.2p1_0818F.1_g223260' => 'hma', 'Hma1.2p1_1747F.1_g300530' => 'hma', 'HPP92_004607' => 'vpl', 'HPP92_004608' => 'vpl', 'HPP92_006181' => 'vpl', 'HPP92_012192' => 'vpl', 'HPP92_015680' => 'vpl', 'HPP92_020249' => 'vpl', 'HPP92_021376' => 'vpl', 'HPP92_024275' => 'vpl', 'Hund06031' => 'sun', 'Hund25391' => 'sun', 'Lalb_Chr07g0185371' => 'lal', 'Lalb_Chr07g0185381' => 'lal', 'Lalb_Chr12g0204011' => 'lal', 'Lalb_Chr13g0301671' => 'lal', 'Lalb_Chr14g0362851' => 'lal', 'Lalb_Chr24g0403581' => 'lal', 'Lj1g0000233' => 'lja', 'Lj2g0018120' => 'lja', 'Lj3C621T0' => 'lonja', 'Lj3P1059T14' => 'lonja', 'Lj3P611T9' => 'lonja', 'Lj3P614T13' => 'lonja', 'Lj3P615T5' => 'lonja', 'Lj4g0012315' => 'lja', 'Lj4g0026182' => 'lja', 'Lj6P813T16' => 'lonja', 'Lj7C427T7' => 'lonja', 'Lj7C427T8' => 'lonja', 'Lj7P600T41' => 'lonja', 'Lju41C42G17' => 'lonja', 'Lsat_1_v5_gn_0_47300' => 'lsa', 'Lsat_1_v5_gn_2_91280' => 'lsa', 'Lsat_1_v5_gn_3_30561' => 'lsa', 'Lsat_1_v5_gn_4_184321' => 'lsa', 'Lsat_1_v5_gn_4_4041' => 'lsa', 'Lsat_1_v5_gn_5_92000' => 'lsa', 'Lsat_1_v5_gn_8_152940' => 'lsa', 'Lsat_1_v5_gn_8_62401' => 'lsa', 'Manes.06G055900' => 'mes', 'Manes.12G022200' => 'mes', 'Manes.13G023300' => 'mes', 'Manes.14G115000' => 'mes', 'Manes.15G151700' => 'mes', 'Manes.17G111300' => 'mes', 'Mapoly0226s0009' => 'mpo', 'MBI02_g25363_MAGBIO' => 'mbi', 'MBI06_g00027_MAGBIO' => 'mbi', 'MBI10_g13034_MAGBIO' => 'mbi', 'MD09G1023400' => 'mdo', 'MD13G1100100' => 'mdo', 'MD15G1169200' => 'mdo', 'MD16G1101100' => 'mdo', 'MD17G1022900' => 'mdo', 'Medtr3g096150' => 'mtr', 'Medtr4g115070' => 'mtr', 'Medtr7g033325' => 'mtr', 'Medtr8g089840' => 'mtr', 'MELO3C010319.2' => 'cme', 'MELO3C011944.2' => 'cme', 'MELO3C021589.2' => 'cme', 'Migut.E00207' => 'egut', 'Migut.H00067' => 'egut', 'Migut.K00433' => 'egut', 'Migut.K00606' => 'egut', 'Migut.K01410' => 'egut', 'MSTRG.13347' => 'ama', 'MSTRG.24045' => 'ama', 'MSTRG.2428' => 'ama', 'MSTRG.26410' => 'ama', 'MSTRG.3139' => 'ama', 'MSTRG.3286' => 'ama', 'MSTRG.563' => 'ama', 'MSTRG.7941' => 'ama', 'Nitab4.5_0000028g0060' => 'nta', 'Nitab4.5_0000065g0260' => 'nta', 'Nitab4.5_0000112g0060' => 'nta', 'Nitab4.5_0000489g0120' => 'nta', 'Nitab4.5_0001776g0050' => 'nta', 'Nitab4.5_0001854g0010' => 'nta', 'Nitab4.5_0001860g0020' => 'nta', 'Nitab4.5_0004352g0010' => 'nta', 'Nitab4.5_0008716g0020' => 'nta', 'Nitab4.5_0008922g0010' => 'nta', 'Nn3g16693' => 'nnu', 'Nn4g22596' => 'nnu', 'Nn7g37639' => 'nnu', 'Oeu001701.1' => 'oeu', 'Oeu018149.1' => 'oeu', 'Oeu026220.1' => 'oeu', 'Oeu038635.1' => 'oeu', 'Oeu049176.1' => 'oeu', 'Oeu056706.1' => 'oeu', 'Oeu056937.1' => 'oeu', 'Oeu057540.1' => 'oeu', 'Os02g0594900' => 'osa', 'Os02g0595100' => 'osa', 'Os04g0477500' => 'osa', 'Os12g0611900' => 'osa', 'Peaxi162Scf00076g00020' => 'pax', 'Peaxi162Scf00128g00217' => 'pax', 'Peaxi162Scf00129g01640' => 'pax', 'Peaxi162Scf00669g00007' => 'pax', 'Peaxi162Scf00700g00421' => 'pax', 'Peaxi162Scf00801g00038' => 'pax', 'Peaxi162Scf00891g00025' => 'pax', 'PGR083G0909' => 'pgr', 'PGR119G1005' => 'pgr', 'PGR142G2236' => 'pgr', 'PGR142G3388' => 'pgr', 'PGSC0003DMG400004514' => 'stu', 'PGSC0003DMG400012635' => 'stu', 'PGSC0003DMG400015730' => 'stu', 'PGSC0003DMG400018611' => 'stu', 'PGSC0003DMG400030897' => 'stu', 'Phvul.001G254800' => 'pvu', 'Phvul.002G260100' => 'pvu', 'Phvul.003G167600' => 'pvu', 'Phvul.004G005100' => 'pvu', 'Potri.001G343600' => 'ptr', 'Potri.006G066700' => 'ptr', 'Potri.008G186000' => 'ptr', 'Potri.010G046900' => 'ptr', 'Potri.018G127900' => 'ptr', 'Pp3c20_17750' => 'ppa', 'Pp3c24_4380' => 'ppa', 'Prupe.1G245800' => 'ppe', 'Prupe.3G293400' => 'ppe', 'Prupe.7G247400' => 'ppe', 'Psat0s145g0120' => 'psa', 'Psat0s595g0040' => 'psa', 'Psat0s595g0120' => 'psa', 'Psat3g175040' => 'psa', 'Psat7g058120' => 'psa', 'PSO017G0428' => 'pso', 'PSO063G7510' => 'pso', 'PSO067G0046' => 'pso', 'PSO478G1073' => 'pso', 'PSO675G3677' => 'pso', 'PSO675G6558' => 'pso', 'PSO675G7520' => 'pso', 'PSO675G8959' => 'pso', 'QL02p074089' => 'qlo', 'QL02p089614' => 'qlo', 'QL03p057736' => 'qlo', 'RcHm_v2.0_Chr1g0364131' => 'rch', 'RcHm_v2.0_Chr2g0087801' => 'rch', 'RcHm_v2.0_Chr2g0087821' => 'rch', 'RcHm_v2.0_Chr2g0173231' => 'rch', 'RcHm_v2.0_Chr4g0433111' => 'rch', 'Rhsim03G0250300' => 'rsi', 'Rhsim08G0048400' => 'rsi', 'Rhsim10G0014800' => 'rsi', 'Rhsim12G0040100' => 'rsi', 'Rhsim12G0109700' => 'rsi', 'Sabra06G0049600' => 'sbr', 'Sabra08G0141000' => 'sbr', 'Sabra10G0021400' => 'sbr', 'Sabra16G0222900' => 'sbr', 'Sabra18G0108600' => 'sbr', 'SalBow1G0433' => 'sbo', 'SalBow1G2038' => 'sbo', 'SalBow1G5003' => 'sbo', 'SalBow7G1197' => 'sbo', 'SalBow8G3506' => 'sbo', 'Sc03g0007300' => 'sci', 'Sc11g0000950' => 'sci', 'Sc14g0008750' => 'sci', 'Sc18g0000420' => 'sci', 'Sed0006754' => 'sed', 'Sed0008741' => 'sed', 'Sed0017172' => 'sed', 'Sed0018925' => 'sed', 'Sed0023326' => 'sed', 'Sed0025909' => 'sed', 'SEGI_05333' => 'sgi', 'SEGI_10362' => 'sgi', 'SEGI_13380' => 'sgi', 'SEGI_24306' => 'sgi', 'SEGI_29077' => 'sgi', 'SEGI_29095' => 'sgi', 'SEGI_36534' => 'sgi', 'SEGI_37506' => 'sgi', 'SEGI_38321' => 'sgi', 'SGA_v2.0_scaffold307G48031' => 'sas', 'SGA_v2.0_scaffold47G17507' => 'sas', 'SGA_v2.0_scaffold63G21736' => 'sas', 'SGA_v2.0_scaffold87G27070' => 'sas', 'SHI17794' => 'shi', 'SHI28851' => 'shi', 'SMO165G0155' => 'smo', 'SMO340G0217' => 'smo', 'SMO367G1210' => 'smo', 'Solyc02g093430.3' => 'sly', 'Solyc05g013580.4' => 'sly', 'Solyc07g008030.3' => 'sly', 'Solyc12g035470.2' => 'sly', 'Sopen02g038020' => 'spe', 'Sopen05g008490' => 'spe', 'Sopen07g003910' => 'spe', 'Sopen12g015240' => 'spe', 'Sp1g11550' => 'spa', 'Sp2g16710' => 'spa', 'Sp3g00430' => 'spa', 'Sp3g26780' => 'spa', 'Sp5g22900' => 'spa', 'Sp6g29530' => 'spa', 'TAR371G0794' => 'tar', 'TAR374G0164' => 'tar', 'TAR622G0165' => 'tar', 'TAR626G0929' => 'tar', 'TAR629G2155' => 'tar', 'THA.LOC104805282' => 'tha', 'THA.LOC104805363' => 'tha', 'THA.LOC104808968' => 'tha', 'THA.LOC104821093' => 'tha', 'THA.LOC104823953' => 'tha', 'THA.LOC104825562' => 'tha', 'THA.LOC104825665' => 'tha', 'Thecc.02G261400' => 'tca', 'Thecc.04G019200' => 'tca', 'Thecc.09G130400' => 'tca', 'Thhalv10004374m.g' => 'esa', 'Thhalv10007850m.g' => 'esa', 'Thhalv10013782m.g' => 'esa', 'Thhalv10018686m.g' => 'esa', 'Thhalv10020899m.g' => 'esa', 'Thhalv10022755m.g' => 'esa', 'TPR.G23851' => 'tpr', 'TPR.G26500' => 'tpr', 'TPR.G27267' => 'tpr', 'TPR.G32001' => 'tpr', 'TPR.G6251' => 'tpr', 'TPR.G8167' => 'tpr', 'TWI12G1330' => 'twi', 'TWI18G1239' => 'twi', 'TWI34G0979' => 'twi', 'TWI36G0670' => 'twi', 'TWI36G0707' => 'twi', 'TWI56G0233' => 'twi', 'TWI75G1809' => 'twi', 'unitig_21.g20874' => 'ugi', 'unitig_26.g10343' => 'ugi', 'unitig_46.g18392' => 'ugi', 'unitig_52.g17178' => 'ugi', 'unitig_8.g2934' => 'ugi', 'vmacro01122' => 'vma', 'vmacro05875' => 'vma', 'vmacro06147' => 'vma', 'vmacro16191' => 'vma', 'vmacro18293' => 'vma', 'VMungo0251G3707' => 'vmu', 'VMungo0464G1521' => 'vmu', 'VMungo1215G0205' => 'vmu', 'VMungo1383G2484' => 'vmu', 'Zm00001eb079610' => 'zma', 'Zm00001eb135990' => 'zma', 'Zm00001eb183710' => 'zma', 'Zm00001eb246020' => 'zma' ) $gf_id = 'HOM05D001124' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001124' ) $data_identifier = 'HOM05D001124' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 6, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 7, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 21, 'bol' => (int) 10, 'bra' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 6, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 9, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 21, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 8, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 10, 'lsa' => (int) 8, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 8, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 9, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb246020' $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' => 'HOM05D001124', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '548', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02520' => 'bna', 'A03p06630' => 'bna', 'A05p44460' => 'bna', 'A06p08710' => 'bna', 'A06p41090' => 'bna', 'A07p32320' => 'bna', 'A08p32520' => 'bna', 'A09p10360' => 'bna', 'A10p24080' => 'bna', 'Aa31LG11G15250' => 'aar', 'Aa31LG1G1800' => 'aar', 'Aa31LG2G5120' => 'aar', 'Aa31LG2G6070' => 'aar', 'Aa31LG5G10770' => 'aar', 'Aa31sc61G90' => 'aar', 'Actinidia01352' => 'ach', 'Actinidia05983' => 'ach', 'Actinidia08133' => 'ach', 'Actinidia15101' => 'ach', 'Actinidia26379' => 'ach', 'Actinidia35778' => 'ach', 'Actinidia36123' => 'ach', 'Actinidia37436' => 'ach', 'Actinidia38730' => 'ach', 'Ah.02g128210' => 'amhyb', 'Ah.03g132990' => 'amhyb', 'Ah.14g079410' => 'amhyb', 'AL1G24640' => 'aly', 'AL2G26680' => 'aly', 'AL3G10530' => 'aly', 'AL3G45230' => 'aly', 'AL5G15230' => 'aly', 'AL5G16960' => 'aly', 'AL6G25210' => 'aly', 'Aqoxy2G00441' => 'aox', 'Aqoxy3G01236' => 'aox', 'Aqoxy5G03746' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3RQ047' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C7GMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9C8JER' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MBL6KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YXCZ83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZANX40' => 'arhy', 'AT1G12990' => 'ath', 'AT1G67880' => 'ath', 'AT2G13290' => 'ath', 'AT3G01620' => 'ath', 'AT3G26445' => 'ath', 'AT3G27540' => 'ath', 'AT5G14480' => 'ath', 'ATR0824G026' => 'atr', 'ATR1098G019' => 'atr', 'Atru.chr11.2145' => 'acertr', 'Atru.chr2.3636' => 'acertr', 'Atru.chr2.3644' => 'acertr', 'Atru.chr6.2422' => 'acertr', 'Atru.chr7.1112' => 'acertr', 'AUR62005469' => 'cqu', 'AUR62011166' => 'cqu', 'AUR62013319' => 'cqu', 'AUR62024273' => 'cqu', 'AUR62028420' => 'cqu', 'AUR62041942' => 'cqu', 'BcaB01g04969' => 'bca', 'BcaB01g06371' => 'bca', 'BcaB02g11494' => 'bca', 'BcaB03g15382' => 'bca', 'BcaB08g36994' => 'bca', 'BcaC03g13477' => 'bca', 'BcaC03g13478' => 'bca', 'BcaC03g13480' => 'bca', 'BcaC03g13481' => 'bca', 'BcaC03g13486' => 'bca', 'BcaC04g19031' => 'bca', 'BcaC04g23085' => 'bca', 'BcaC05g25094' => 'bca', 'BcaC05g25096' => 'bca', 'BcaC05g25138' => 'bca', 'BcaC05g30416' => 'bca', 'BcaC05g30455' => 'bca', 'BcaC06g30979' => 'bca', 'BcaC06g33805' => 'bca', 'BcaC08g46021' => 'bca', 'BcaNung03154' => 'bca', 'BolC2t06623H' => 'bol', 'BolC2t06632H' => 'bol', 'BolC2t06635H' => 'bol', 'BolC2t06638H' => 'bol', 'BolC3t13266H' => 'bol', 'BolC5t29776H' => 'bol', 'BolC6t38912H' => 'bol', 'BolC7t44183H' => 'bol', 'BolC9t54123H' => 'bol', 'BolC9t59107H' => 'bol', 'BraA02t05221Z' => 'bra', 'BraA03t09996Z' => 'bra', 'BraA05t23210Z' => 'bra', 'BraA06t24068Z' => 'bra', 'BraA06t27032Z' => 'bra', 'BraA08t35176Z' => 'bra', 'BraA09t36680Z' => 'bra', 'BraA10t44471Z' => 'bra', 'C02p06760' => 'bna', 'C02p06890' => 'bna', 'C02p07010' => 'bna', 'C03p07660' => 'bna', 'C05p10300' => 'bna', 'C06p38150' => 'bna', 'C07p36650' => 'bna', 'C08p15770' => 'bna', 'C09p12300' => 'bna', 'C09p62700' => 'bna', 'C09p75040' => 'bna', 'CAN.G13.1' => 'can', 'CAN.G138.4' => 'can', 'CAN.G44.6' => 'can', 'CAN.G473.19' => 'can', 'CANSAT01G0835' => 'cansat', 'CANSAT11G0246' => 'cansat', 'CANSAT11G1766' => 'cansat', 'CANSAT64G1954' => 'cansat', 'CARHR013330' => 'chi', 'CARHR060530' => 'chi', 'CARHR075300' => 'chi', 'CARHR105120' => 'chi', 'CARHR148910' => 'chi', 'CARHR198830' => 'chi', 'Carub.0001s1275' => 'cru', 'Carub.0002s1437' => 'cru', 'Carub.0003s0044' => 'cru', 'Carub.0003s2787' => 'cru', 'Carub.0005s0597' => 'cru', 'Carub.0006s1266' => 'cru', 'Ca_06935_v3' => 'car', 'Ca_13559_v3' => 'car', 'Ca_16941_v3' => 'car', 'Ca_16960_v3' => 'car', 'Ca_17775_v3' => 'car', 'Ca_30464_v3' => 'car', 'Cc06_g08160' => 'ccan', 'Cc07_g01520' => 'ccan', 'Cc11_g15810' => 'ccan', 'CDE02G2840' => 'cde', 'CDE03G0093' => 'cde', 'CDE04G2127' => 'cde', 'CDE07G1857' => 'cde', 'CDE09G1246' => 'cde', 'Cfa003412' => 'cfa', 'Cfa007341' => 'cfa', 'Cfa009220' => 'cfa', 'Ciclev10008737m.g' => 'ccl', 'Ciclev10015565m.g' => 'ccl', 'Ciclev10031761m.g' => 'ccl', 'CiPaw.03G045300' => 'cil', 'CiPaw.03G247200' => 'cil', 'CiPaw.04G029500' => 'cil', 'CiPaw.04G174000' => 'cil', 'CiPaw.05G181200' => 'cil', 'CiPaw.06G067100' => 'cil', 'ClCG05G025800' => 'cla', 'ClCG06G011400' => 'cla', 'ClCG09G019360' => 'cla', 'COL.COLO4_04827' => 'col', 'COL.COLO4_29170' => 'col', 'COL.COLO4_35131' => 'col', 'COL.COLO4_35132' => 'col', 'Cpa.g.sc33.32' => 'cpa', 'Cpa.g.sc46.29' => 'cpa', 'Cpa.g.sc796.1' => 'cpa', 'CsaV3_1G030420' => 'csa', 'CsaV3_5G027050' => 'csa', 'CsaV3_5G031040' => 'csa', 'CsaV3_UNG023130' => 'csa', 'CSS0007726' => 'camsi', 'CSS0016433' => 'camsi', 'CSS0017656' => 'camsi', 'CSS0025364' => 'camsi', 'CSS0027582' => 'camsi', 'CSS0047288' => 'camsi', 'CSS0049950' => 'camsi', 'DCAR_003843' => 'dca', 'DCAR_007052' => 'dca', 'DCAR_020884' => 'dca', 'DCAR_021730' => 'dca', 'DCAR_024423' => 'dca', 'DCAR_026509' => 'dca', 'DCAR_031158' => 'dca', 'Dinv14728' => 'din', 'Dinv15219' => 'din', 'Dinv25728' => 'din', 'Dinv33428' => 'din', 'Dinv36489' => 'din', 'Dinv41486' => 'din', 'Duzib147G0469' => 'dzi', 'Duzib168G0060' => 'dzi', 'Duzib187G1215' => 'dzi', 'Duzib248G0692' => 'dzi', 'Duzib251G0767' => 'dzi', 'Duzib264G0446' => 'dzi', 'Duzib268G0691' => 'dzi', 'ECA232G4767' => 'eca', 'ECA233G2838' => 'eca', 'ECA234G0391' => 'eca', 'ECA234G0857' => 'eca', 'ECA236G1593' => 'eca', 'ECA238G0565' => 'eca', 'ECA246G1027' => 'eca', 'ECA246G3223' => 'eca', 'ECA246G3470' => 'eca', 'EL10Ac6g13829' => 'bvu', 'EL10Ac6g14093' => 'bvu', 'EL10Ac8g18707' => 'bvu', 'Eucgr.C01369' => 'egr', 'Eucgr.H02492' => 'egr', 'Eucgr.I01733' => 'egr', 'Eucgr.J02255' => 'egr', 'Eucgr.J02257' => 'egr', 'Eucgr.J02258' => 'egr', 'FAN02G1601' => 'fan', 'FAN03G1586' => 'fan', 'FAN03G2986' => 'fan', 'FAN05G4837' => 'fan', 'FAN06G0146' => 'fan', 'FAN07G0858' => 'fan', 'FAN09G3179' => 'fan', 'FAN10G0669' => 'fan', 'FAN12G2358' => 'fan', 'FAN14G4198' => 'fan', 'FAN14G5112' => 'fan', 'FAN17G0342' => 'fan', 'FAN19G0342' => 'fan', 'FAN19G0962' => 'fan', 'FAN19G1101' => 'fan', 'FAN19G1872' => 'fan', 'FAN22G0356' => 'fan', 'FAN23G0744' => 'fan', 'FAN23G1914' => 'fan', 'FAN26G0032' => 'fan', 'FAN28G0625' => 'fan', 'FvH4_1g02710' => 'fve', 'FvH4_1g02720' => 'fve', 'FvH4_4g25670' => 'fve', 'FvH4_6g51700' => 'fve', 'FvH4_7g20170' => 'fve', 'Glyma.05G175000' => 'gma', 'Glyma.08G132300' => 'gma', 'Glyma.11G243000' => 'gma', 'Glyma.13G158900' => 'gma', 'Glyma.17G112400' => 'gma', 'Glyma.18G014100' => 'gma', 'Glyma.19G003100' => 'gma', 'Glyma.19G056500' => 'gma', 'Gohir.A01G158900' => 'ghi', 'Gohir.A05G312600' => 'ghi', 'Gohir.A05G354900' => 'ghi', 'Gohir.A07G037200' => 'ghi', 'Gohir.A09G030000' => 'ghi', 'Gohir.A12G145200' => 'ghi', 'Gohir.D01G151500' => 'ghi', 'Gohir.D04G058300' => 'ghi', 'Gohir.D05G314100' => 'ghi', 'Gohir.D07G041400' => 'ghi', 'Gohir.D09G029700' => 'ghi', 'Gohir.D12G149700' => 'ghi', 'Gorai.001G043800' => 'gra', 'Gorai.002G187800' => 'gra', 'Gorai.006G034700' => 'gra', 'Gorai.008G161200' => 'gra', 'Gorai.009G335700' => 'gra', 'Gorai.012G065000' => 'gra', 'GSVIVG01000535001' => 'vvi', 'GSVIVG01015572001' => 'vvi', 'GSVIVG01032386001' => 'vvi', 'HanXRQChr05g0138531' => 'han', 'HanXRQChr06g0174391' => 'han', 'HanXRQChr07g0199021' => 'han', 'HanXRQChr08g0208211' => 'han', 'HanXRQChr09g0255471' => 'han', 'HanXRQChr10g0315791' => 'han', 'HanXRQChr12g0371991' => 'han', 'HanXRQChr15g0475251' => 'han', 'HanXRQChr17g0540001' => 'han', 'HanXRQChr17g0548631' => 'han', 'HanXRQChr17g0569561' => 'han', 'Haze_12256' => 'cav', 'Haze_14756' => 'cav', 'Haze_25528' => 'cav', 'Hma1.2p1_0079F.1_g041020' => 'hma', 'Hma1.2p1_0818F.1_g223260' => 'hma', 'Hma1.2p1_1747F.1_g300530' => 'hma', 'HPP92_004607' => 'vpl', 'HPP92_004608' => 'vpl', 'HPP92_006181' => 'vpl', 'HPP92_012192' => 'vpl', 'HPP92_015680' => 'vpl', 'HPP92_020249' => 'vpl', 'HPP92_021376' => 'vpl', 'HPP92_024275' => 'vpl', 'Hund06031' => 'sun', 'Hund25391' => 'sun', 'Lalb_Chr07g0185371' => 'lal', 'Lalb_Chr07g0185381' => 'lal', 'Lalb_Chr12g0204011' => 'lal', 'Lalb_Chr13g0301671' => 'lal', 'Lalb_Chr14g0362851' => 'lal', 'Lalb_Chr24g0403581' => 'lal', 'Lj1g0000233' => 'lja', 'Lj2g0018120' => 'lja', 'Lj3C621T0' => 'lonja', 'Lj3P1059T14' => 'lonja', 'Lj3P611T9' => 'lonja', 'Lj3P614T13' => 'lonja', 'Lj3P615T5' => 'lonja', 'Lj4g0012315' => 'lja', 'Lj4g0026182' => 'lja', 'Lj6P813T16' => 'lonja', 'Lj7C427T7' => 'lonja', 'Lj7C427T8' => 'lonja', 'Lj7P600T41' => 'lonja', 'Lju41C42G17' => 'lonja', 'Lsat_1_v5_gn_0_47300' => 'lsa', 'Lsat_1_v5_gn_2_91280' => 'lsa', 'Lsat_1_v5_gn_3_30561' => 'lsa', 'Lsat_1_v5_gn_4_184321' => 'lsa', 'Lsat_1_v5_gn_4_4041' => 'lsa', 'Lsat_1_v5_gn_5_92000' => 'lsa', 'Lsat_1_v5_gn_8_152940' => 'lsa', 'Lsat_1_v5_gn_8_62401' => 'lsa', 'Manes.06G055900' => 'mes', 'Manes.12G022200' => 'mes', 'Manes.13G023300' => 'mes', 'Manes.14G115000' => 'mes', 'Manes.15G151700' => 'mes', 'Manes.17G111300' => 'mes', 'Mapoly0226s0009' => 'mpo', 'MBI02_g25363_MAGBIO' => 'mbi', 'MBI06_g00027_MAGBIO' => 'mbi', 'MBI10_g13034_MAGBIO' => 'mbi', 'MD09G1023400' => 'mdo', 'MD13G1100100' => 'mdo', 'MD15G1169200' => 'mdo', 'MD16G1101100' => 'mdo', 'MD17G1022900' => 'mdo', 'Medtr3g096150' => 'mtr', 'Medtr4g115070' => 'mtr', 'Medtr7g033325' => 'mtr', 'Medtr8g089840' => 'mtr', 'MELO3C010319.2' => 'cme', 'MELO3C011944.2' => 'cme', 'MELO3C021589.2' => 'cme', 'Migut.E00207' => 'egut', 'Migut.H00067' => 'egut', 'Migut.K00433' => 'egut', 'Migut.K00606' => 'egut', 'Migut.K01410' => 'egut', 'MSTRG.13347' => 'ama', 'MSTRG.24045' => 'ama', 'MSTRG.2428' => 'ama', 'MSTRG.26410' => 'ama', 'MSTRG.3139' => 'ama', 'MSTRG.3286' => 'ama', 'MSTRG.563' => 'ama', 'MSTRG.7941' => 'ama', 'Nitab4.5_0000028g0060' => 'nta', 'Nitab4.5_0000065g0260' => 'nta', 'Nitab4.5_0000112g0060' => 'nta', 'Nitab4.5_0000489g0120' => 'nta', 'Nitab4.5_0001776g0050' => 'nta', 'Nitab4.5_0001854g0010' => 'nta', 'Nitab4.5_0001860g0020' => 'nta', 'Nitab4.5_0004352g0010' => 'nta', 'Nitab4.5_0008716g0020' => 'nta', 'Nitab4.5_0008922g0010' => 'nta', 'Nn3g16693' => 'nnu', 'Nn4g22596' => 'nnu', 'Nn7g37639' => 'nnu', 'Oeu001701.1' => 'oeu', 'Oeu018149.1' => 'oeu', 'Oeu026220.1' => 'oeu', 'Oeu038635.1' => 'oeu', 'Oeu049176.1' => 'oeu', 'Oeu056706.1' => 'oeu', 'Oeu056937.1' => 'oeu', 'Oeu057540.1' => 'oeu', 'Os02g0594900' => 'osa', 'Os02g0595100' => 'osa', 'Os04g0477500' => 'osa', 'Os12g0611900' => 'osa', 'Peaxi162Scf00076g00020' => 'pax', 'Peaxi162Scf00128g00217' => 'pax', 'Peaxi162Scf00129g01640' => 'pax', 'Peaxi162Scf00669g00007' => 'pax', 'Peaxi162Scf00700g00421' => 'pax', 'Peaxi162Scf00801g00038' => 'pax', 'Peaxi162Scf00891g00025' => 'pax', 'PGR083G0909' => 'pgr', 'PGR119G1005' => 'pgr', 'PGR142G2236' => 'pgr', 'PGR142G3388' => 'pgr', 'PGSC0003DMG400004514' => 'stu', 'PGSC0003DMG400012635' => 'stu', 'PGSC0003DMG400015730' => 'stu', 'PGSC0003DMG400018611' => 'stu', 'PGSC0003DMG400030897' => 'stu', 'Phvul.001G254800' => 'pvu', 'Phvul.002G260100' => 'pvu', 'Phvul.003G167600' => 'pvu', 'Phvul.004G005100' => 'pvu', 'Potri.001G343600' => 'ptr', 'Potri.006G066700' => 'ptr', 'Potri.008G186000' => 'ptr', 'Potri.010G046900' => 'ptr', 'Potri.018G127900' => 'ptr', 'Pp3c20_17750' => 'ppa', 'Pp3c24_4380' => 'ppa', 'Prupe.1G245800' => 'ppe', 'Prupe.3G293400' => 'ppe', 'Prupe.7G247400' => 'ppe', 'Psat0s145g0120' => 'psa', 'Psat0s595g0040' => 'psa', 'Psat0s595g0120' => 'psa', 'Psat3g175040' => 'psa', 'Psat7g058120' => 'psa', 'PSO017G0428' => 'pso', 'PSO063G7510' => 'pso', 'PSO067G0046' => 'pso', 'PSO478G1073' => 'pso', 'PSO675G3677' => 'pso', 'PSO675G6558' => 'pso', 'PSO675G7520' => 'pso', 'PSO675G8959' => 'pso', 'QL02p074089' => 'qlo', 'QL02p089614' => 'qlo', 'QL03p057736' => 'qlo', 'RcHm_v2.0_Chr1g0364131' => 'rch', 'RcHm_v2.0_Chr2g0087801' => 'rch', 'RcHm_v2.0_Chr2g0087821' => 'rch', 'RcHm_v2.0_Chr2g0173231' => 'rch', 'RcHm_v2.0_Chr4g0433111' => 'rch', 'Rhsim03G0250300' => 'rsi', 'Rhsim08G0048400' => 'rsi', 'Rhsim10G0014800' => 'rsi', 'Rhsim12G0040100' => 'rsi', 'Rhsim12G0109700' => 'rsi', 'Sabra06G0049600' => 'sbr', 'Sabra08G0141000' => 'sbr', 'Sabra10G0021400' => 'sbr', 'Sabra16G0222900' => 'sbr', 'Sabra18G0108600' => 'sbr', 'SalBow1G0433' => 'sbo', 'SalBow1G2038' => 'sbo', 'SalBow1G5003' => 'sbo', 'SalBow7G1197' => 'sbo', 'SalBow8G3506' => 'sbo', 'Sc03g0007300' => 'sci', 'Sc11g0000950' => 'sci', 'Sc14g0008750' => 'sci', 'Sc18g0000420' => 'sci', 'Sed0006754' => 'sed', 'Sed0008741' => 'sed', 'Sed0017172' => 'sed', 'Sed0018925' => 'sed', 'Sed0023326' => 'sed', 'Sed0025909' => 'sed', 'SEGI_05333' => 'sgi', 'SEGI_10362' => 'sgi', 'SEGI_13380' => 'sgi', 'SEGI_24306' => 'sgi', 'SEGI_29077' => 'sgi', 'SEGI_29095' => 'sgi', 'SEGI_36534' => 'sgi', 'SEGI_37506' => 'sgi', 'SEGI_38321' => 'sgi', 'SGA_v2.0_scaffold307G48031' => 'sas', 'SGA_v2.0_scaffold47G17507' => 'sas', 'SGA_v2.0_scaffold63G21736' => 'sas', 'SGA_v2.0_scaffold87G27070' => 'sas', 'SHI17794' => 'shi', 'SHI28851' => 'shi', 'SMO165G0155' => 'smo', 'SMO340G0217' => 'smo', 'SMO367G1210' => 'smo', 'Solyc02g093430.3' => 'sly', 'Solyc05g013580.4' => 'sly', 'Solyc07g008030.3' => 'sly', 'Solyc12g035470.2' => 'sly', 'Sopen02g038020' => 'spe', 'Sopen05g008490' => 'spe', 'Sopen07g003910' => 'spe', 'Sopen12g015240' => 'spe', 'Sp1g11550' => 'spa', 'Sp2g16710' => 'spa', 'Sp3g00430' => 'spa', 'Sp3g26780' => 'spa', 'Sp5g22900' => 'spa', 'Sp6g29530' => 'spa', 'TAR371G0794' => 'tar', 'TAR374G0164' => 'tar', 'TAR622G0165' => 'tar', 'TAR626G0929' => 'tar', 'TAR629G2155' => 'tar', 'THA.LOC104805282' => 'tha', 'THA.LOC104805363' => 'tha', 'THA.LOC104808968' => 'tha', 'THA.LOC104821093' => 'tha', 'THA.LOC104823953' => 'tha', 'THA.LOC104825562' => 'tha', 'THA.LOC104825665' => 'tha', 'Thecc.02G261400' => 'tca', 'Thecc.04G019200' => 'tca', 'Thecc.09G130400' => 'tca', 'Thhalv10004374m.g' => 'esa', 'Thhalv10007850m.g' => 'esa', 'Thhalv10013782m.g' => 'esa', 'Thhalv10018686m.g' => 'esa', 'Thhalv10020899m.g' => 'esa', 'Thhalv10022755m.g' => 'esa', 'TPR.G23851' => 'tpr', 'TPR.G26500' => 'tpr', 'TPR.G27267' => 'tpr', 'TPR.G32001' => 'tpr', 'TPR.G6251' => 'tpr', 'TPR.G8167' => 'tpr', 'TWI12G1330' => 'twi', 'TWI18G1239' => 'twi', 'TWI34G0979' => 'twi', 'TWI36G0670' => 'twi', 'TWI36G0707' => 'twi', 'TWI56G0233' => 'twi', 'TWI75G1809' => 'twi', 'unitig_21.g20874' => 'ugi', 'unitig_26.g10343' => 'ugi', 'unitig_46.g18392' => 'ugi', 'unitig_52.g17178' => 'ugi', 'unitig_8.g2934' => 'ugi', 'vmacro01122' => 'vma', 'vmacro05875' => 'vma', 'vmacro06147' => 'vma', 'vmacro16191' => 'vma', 'vmacro18293' => 'vma', 'VMungo0251G3707' => 'vmu', 'VMungo0464G1521' => 'vmu', 'VMungo1215G0205' => 'vmu', 'VMungo1383G2484' => 'vmu', 'Zm00001eb079610' => 'zma', 'Zm00001eb135990' => 'zma', 'Zm00001eb183710' => 'zma', 'Zm00001eb246020' => 'zma' ), 'gf_id' => 'HOM05D001124', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001124' ), 'data_identifier' => 'HOM05D001124', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001124', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '548', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02520' => 'bna', 'A03p06630' => 'bna', 'A05p44460' => 'bna', 'A06p08710' => 'bna', 'A06p41090' => 'bna', 'A07p32320' => 'bna', 'A08p32520' => 'bna', 'A09p10360' => 'bna', 'A10p24080' => 'bna', 'Aa31LG11G15250' => 'aar', 'Aa31LG1G1800' => 'aar', 'Aa31LG2G5120' => 'aar', 'Aa31LG2G6070' => 'aar', 'Aa31LG5G10770' => 'aar', 'Aa31sc61G90' => 'aar', 'Actinidia01352' => 'ach', 'Actinidia05983' => 'ach', 'Actinidia08133' => 'ach', 'Actinidia15101' => 'ach', 'Actinidia26379' => 'ach', 'Actinidia35778' => 'ach', 'Actinidia36123' => 'ach', 'Actinidia37436' => 'ach', 'Actinidia38730' => 'ach', 'Ah.02g128210' => 'amhyb', 'Ah.03g132990' => 'amhyb', 'Ah.14g079410' => 'amhyb', 'AL1G24640' => 'aly', 'AL2G26680' => 'aly', 'AL3G10530' => 'aly', 'AL3G45230' => 'aly', 'AL5G15230' => 'aly', 'AL5G16960' => 'aly', 'AL6G25210' => 'aly', 'Aqoxy2G00441' => 'aox', 'Aqoxy3G01236' => 'aox', 'Aqoxy5G03746' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3RQ047' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C7GMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9C8JER' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MBL6KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YXCZ83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZANX40' => 'arhy', 'AT1G12990' => 'ath', 'AT1G67880' => 'ath', 'AT2G13290' => 'ath', 'AT3G01620' => 'ath', 'AT3G26445' => 'ath', 'AT3G27540' => 'ath', 'AT5G14480' => 'ath', 'ATR0824G026' => 'atr', 'ATR1098G019' => 'atr', 'Atru.chr11.2145' => 'acertr', 'Atru.chr2.3636' => 'acertr', 'Atru.chr2.3644' => 'acertr', 'Atru.chr6.2422' => 'acertr', 'Atru.chr7.1112' => 'acertr', 'AUR62005469' => 'cqu', 'AUR62011166' => 'cqu', 'AUR62013319' => 'cqu', 'AUR62024273' => 'cqu', 'AUR62028420' => 'cqu', 'AUR62041942' => 'cqu', 'BcaB01g04969' => 'bca', 'BcaB01g06371' => 'bca', 'BcaB02g11494' => 'bca', 'BcaB03g15382' => 'bca', 'BcaB08g36994' => 'bca', 'BcaC03g13477' => 'bca', 'BcaC03g13478' => 'bca', 'BcaC03g13480' => 'bca', 'BcaC03g13481' => 'bca', 'BcaC03g13486' => 'bca', 'BcaC04g19031' => 'bca', 'BcaC04g23085' => 'bca', 'BcaC05g25094' => 'bca', 'BcaC05g25096' => 'bca', 'BcaC05g25138' => 'bca', 'BcaC05g30416' => 'bca', 'BcaC05g30455' => 'bca', 'BcaC06g30979' => 'bca', 'BcaC06g33805' => 'bca', 'BcaC08g46021' => 'bca', 'BcaNung03154' => 'bca', 'BolC2t06623H' => 'bol', 'BolC2t06632H' => 'bol', 'BolC2t06635H' => 'bol', 'BolC2t06638H' => 'bol', 'BolC3t13266H' => 'bol', 'BolC5t29776H' => 'bol', 'BolC6t38912H' => 'bol', 'BolC7t44183H' => 'bol', 'BolC9t54123H' => 'bol', 'BolC9t59107H' => 'bol', 'BraA02t05221Z' => 'bra', 'BraA03t09996Z' => 'bra', 'BraA05t23210Z' => 'bra', 'BraA06t24068Z' => 'bra', 'BraA06t27032Z' => 'bra', 'BraA08t35176Z' => 'bra', 'BraA09t36680Z' => 'bra', 'BraA10t44471Z' => 'bra', 'C02p06760' => 'bna', 'C02p06890' => 'bna', 'C02p07010' => 'bna', 'C03p07660' => 'bna', 'C05p10300' => 'bna', 'C06p38150' => 'bna', 'C07p36650' => 'bna', 'C08p15770' => 'bna', 'C09p12300' => 'bna', 'C09p62700' => 'bna', 'C09p75040' => 'bna', 'CAN.G13.1' => 'can', 'CAN.G138.4' => 'can', 'CAN.G44.6' => 'can', 'CAN.G473.19' => 'can', 'CANSAT01G0835' => 'cansat', 'CANSAT11G0246' => 'cansat', 'CANSAT11G1766' => 'cansat', 'CANSAT64G1954' => 'cansat', 'CARHR013330' => 'chi', 'CARHR060530' => 'chi', 'CARHR075300' => 'chi', 'CARHR105120' => 'chi', 'CARHR148910' => 'chi', 'CARHR198830' => 'chi', 'Carub.0001s1275' => 'cru', 'Carub.0002s1437' => 'cru', 'Carub.0003s0044' => 'cru', 'Carub.0003s2787' => 'cru', 'Carub.0005s0597' => 'cru', 'Carub.0006s1266' => 'cru', 'Ca_06935_v3' => 'car', 'Ca_13559_v3' => 'car', 'Ca_16941_v3' => 'car', 'Ca_16960_v3' => 'car', 'Ca_17775_v3' => 'car', 'Ca_30464_v3' => 'car', 'Cc06_g08160' => 'ccan', 'Cc07_g01520' => 'ccan', 'Cc11_g15810' => 'ccan', 'CDE02G2840' => 'cde', 'CDE03G0093' => 'cde', 'CDE04G2127' => 'cde', 'CDE07G1857' => 'cde', 'CDE09G1246' => 'cde', 'Cfa003412' => 'cfa', 'Cfa007341' => 'cfa', 'Cfa009220' => 'cfa', 'Ciclev10008737m.g' => 'ccl', 'Ciclev10015565m.g' => 'ccl', 'Ciclev10031761m.g' => 'ccl', 'CiPaw.03G045300' => 'cil', 'CiPaw.03G247200' => 'cil', 'CiPaw.04G029500' => 'cil', 'CiPaw.04G174000' => 'cil', 'CiPaw.05G181200' => 'cil', 'CiPaw.06G067100' => 'cil', 'ClCG05G025800' => 'cla', 'ClCG06G011400' => 'cla', 'ClCG09G019360' => 'cla', 'COL.COLO4_04827' => 'col', 'COL.COLO4_29170' => 'col', 'COL.COLO4_35131' => 'col', 'COL.COLO4_35132' => 'col', 'Cpa.g.sc33.32' => 'cpa', 'Cpa.g.sc46.29' => 'cpa', 'Cpa.g.sc796.1' => 'cpa', 'CsaV3_1G030420' => 'csa', 'CsaV3_5G027050' => 'csa', 'CsaV3_5G031040' => 'csa', 'CsaV3_UNG023130' => 'csa', 'CSS0007726' => 'camsi', 'CSS0016433' => 'camsi', 'CSS0017656' => 'camsi', 'CSS0025364' => 'camsi', 'CSS0027582' => 'camsi', 'CSS0047288' => 'camsi', 'CSS0049950' => 'camsi', 'DCAR_003843' => 'dca', 'DCAR_007052' => 'dca', 'DCAR_020884' => 'dca', 'DCAR_021730' => 'dca', 'DCAR_024423' => 'dca', 'DCAR_026509' => 'dca', 'DCAR_031158' => 'dca', 'Dinv14728' => 'din', 'Dinv15219' => 'din', 'Dinv25728' => 'din', 'Dinv33428' => 'din', 'Dinv36489' => 'din', 'Dinv41486' => 'din', 'Duzib147G0469' => 'dzi', 'Duzib168G0060' => 'dzi', 'Duzib187G1215' => 'dzi', 'Duzib248G0692' => 'dzi', 'Duzib251G0767' => 'dzi', 'Duzib264G0446' => 'dzi', 'Duzib268G0691' => 'dzi', 'ECA232G4767' => 'eca', 'ECA233G2838' => 'eca', 'ECA234G0391' => 'eca', 'ECA234G0857' => 'eca', 'ECA236G1593' => 'eca', 'ECA238G0565' => 'eca', 'ECA246G1027' => 'eca', 'ECA246G3223' => 'eca', 'ECA246G3470' => 'eca', 'EL10Ac6g13829' => 'bvu', 'EL10Ac6g14093' => 'bvu', 'EL10Ac8g18707' => 'bvu', 'Eucgr.C01369' => 'egr', 'Eucgr.H02492' => 'egr', 'Eucgr.I01733' => 'egr', 'Eucgr.J02255' => 'egr', 'Eucgr.J02257' => 'egr', 'Eucgr.J02258' => 'egr', 'FAN02G1601' => 'fan', 'FAN03G1586' => 'fan', 'FAN03G2986' => 'fan', 'FAN05G4837' => 'fan', 'FAN06G0146' => 'fan', 'FAN07G0858' => 'fan', 'FAN09G3179' => 'fan', 'FAN10G0669' => 'fan', 'FAN12G2358' => 'fan', 'FAN14G4198' => 'fan', 'FAN14G5112' => 'fan', 'FAN17G0342' => 'fan', 'FAN19G0342' => 'fan', 'FAN19G0962' => 'fan', 'FAN19G1101' => 'fan', 'FAN19G1872' => 'fan', 'FAN22G0356' => 'fan', 'FAN23G0744' => 'fan', 'FAN23G1914' => 'fan', 'FAN26G0032' => 'fan', 'FAN28G0625' => 'fan', 'FvH4_1g02710' => 'fve', 'FvH4_1g02720' => 'fve', 'FvH4_4g25670' => 'fve', 'FvH4_6g51700' => 'fve', 'FvH4_7g20170' => 'fve', 'Glyma.05G175000' => 'gma', 'Glyma.08G132300' => 'gma', 'Glyma.11G243000' => 'gma', 'Glyma.13G158900' => 'gma', 'Glyma.17G112400' => 'gma', 'Glyma.18G014100' => 'gma', 'Glyma.19G003100' => 'gma', 'Glyma.19G056500' => 'gma', 'Gohir.A01G158900' => 'ghi', 'Gohir.A05G312600' => 'ghi', 'Gohir.A05G354900' => 'ghi', 'Gohir.A07G037200' => 'ghi', 'Gohir.A09G030000' => 'ghi', 'Gohir.A12G145200' => 'ghi', 'Gohir.D01G151500' => 'ghi', 'Gohir.D04G058300' => 'ghi', 'Gohir.D05G314100' => 'ghi', 'Gohir.D07G041400' => 'ghi', 'Gohir.D09G029700' => 'ghi', 'Gohir.D12G149700' => 'ghi', 'Gorai.001G043800' => 'gra', 'Gorai.002G187800' => 'gra', 'Gorai.006G034700' => 'gra', 'Gorai.008G161200' => 'gra', 'Gorai.009G335700' => 'gra', 'Gorai.012G065000' => 'gra', 'GSVIVG01000535001' => 'vvi', 'GSVIVG01015572001' => 'vvi', 'GSVIVG01032386001' => 'vvi', 'HanXRQChr05g0138531' => 'han', 'HanXRQChr06g0174391' => 'han', 'HanXRQChr07g0199021' => 'han', 'HanXRQChr08g0208211' => 'han', 'HanXRQChr09g0255471' => 'han', 'HanXRQChr10g0315791' => 'han', 'HanXRQChr12g0371991' => 'han', 'HanXRQChr15g0475251' => 'han', 'HanXRQChr17g0540001' => 'han', 'HanXRQChr17g0548631' => 'han', 'HanXRQChr17g0569561' => 'han', 'Haze_12256' => 'cav', 'Haze_14756' => 'cav', 'Haze_25528' => 'cav', 'Hma1.2p1_0079F.1_g041020' => 'hma', 'Hma1.2p1_0818F.1_g223260' => 'hma', 'Hma1.2p1_1747F.1_g300530' => 'hma', 'HPP92_004607' => 'vpl', 'HPP92_004608' => 'vpl', 'HPP92_006181' => 'vpl', 'HPP92_012192' => 'vpl', 'HPP92_015680' => 'vpl', 'HPP92_020249' => 'vpl', 'HPP92_021376' => 'vpl', 'HPP92_024275' => 'vpl', 'Hund06031' => 'sun', 'Hund25391' => 'sun', 'Lalb_Chr07g0185371' => 'lal', 'Lalb_Chr07g0185381' => 'lal', 'Lalb_Chr12g0204011' => 'lal', 'Lalb_Chr13g0301671' => 'lal', 'Lalb_Chr14g0362851' => 'lal', 'Lalb_Chr24g0403581' => 'lal', 'Lj1g0000233' => 'lja', 'Lj2g0018120' => 'lja', 'Lj3C621T0' => 'lonja', 'Lj3P1059T14' => 'lonja', 'Lj3P611T9' => 'lonja', 'Lj3P614T13' => 'lonja', 'Lj3P615T5' => 'lonja', 'Lj4g0012315' => 'lja', 'Lj4g0026182' => 'lja', 'Lj6P813T16' => 'lonja', 'Lj7C427T7' => 'lonja', 'Lj7C427T8' => 'lonja', 'Lj7P600T41' => 'lonja', 'Lju41C42G17' => 'lonja', 'Lsat_1_v5_gn_0_47300' => 'lsa', 'Lsat_1_v5_gn_2_91280' => 'lsa', 'Lsat_1_v5_gn_3_30561' => 'lsa', 'Lsat_1_v5_gn_4_184321' => 'lsa', 'Lsat_1_v5_gn_4_4041' => 'lsa', 'Lsat_1_v5_gn_5_92000' => 'lsa', 'Lsat_1_v5_gn_8_152940' => 'lsa', 'Lsat_1_v5_gn_8_62401' => 'lsa', 'Manes.06G055900' => 'mes', 'Manes.12G022200' => 'mes', 'Manes.13G023300' => 'mes', 'Manes.14G115000' => 'mes', 'Manes.15G151700' => 'mes', 'Manes.17G111300' => 'mes', 'Mapoly0226s0009' => 'mpo', 'MBI02_g25363_MAGBIO' => 'mbi', 'MBI06_g00027_MAGBIO' => 'mbi', 'MBI10_g13034_MAGBIO' => 'mbi', 'MD09G1023400' => 'mdo', 'MD13G1100100' => 'mdo', 'MD15G1169200' => 'mdo', 'MD16G1101100' => 'mdo', 'MD17G1022900' => 'mdo', 'Medtr3g096150' => 'mtr', 'Medtr4g115070' => 'mtr', 'Medtr7g033325' => 'mtr', 'Medtr8g089840' => 'mtr', 'MELO3C010319.2' => 'cme', 'MELO3C011944.2' => 'cme', 'MELO3C021589.2' => 'cme', 'Migut.E00207' => 'egut', 'Migut.H00067' => 'egut', 'Migut.K00433' => 'egut', 'Migut.K00606' => 'egut', 'Migut.K01410' => 'egut', 'MSTRG.13347' => 'ama', 'MSTRG.24045' => 'ama', 'MSTRG.2428' => 'ama', 'MSTRG.26410' => 'ama', 'MSTRG.3139' => 'ama', 'MSTRG.3286' => 'ama', 'MSTRG.563' => 'ama', 'MSTRG.7941' => 'ama', 'Nitab4.5_0000028g0060' => 'nta', 'Nitab4.5_0000065g0260' => 'nta', 'Nitab4.5_0000112g0060' => 'nta', 'Nitab4.5_0000489g0120' => 'nta', 'Nitab4.5_0001776g0050' => 'nta', 'Nitab4.5_0001854g0010' => 'nta', 'Nitab4.5_0001860g0020' => 'nta', 'Nitab4.5_0004352g0010' => 'nta', 'Nitab4.5_0008716g0020' => 'nta', 'Nitab4.5_0008922g0010' => 'nta', 'Nn3g16693' => 'nnu', 'Nn4g22596' => 'nnu', 'Nn7g37639' => 'nnu', 'Oeu001701.1' => 'oeu', 'Oeu018149.1' => 'oeu', 'Oeu026220.1' => 'oeu', 'Oeu038635.1' => 'oeu', 'Oeu049176.1' => 'oeu', 'Oeu056706.1' => 'oeu', 'Oeu056937.1' => 'oeu', 'Oeu057540.1' => 'oeu', 'Os02g0594900' => 'osa', 'Os02g0595100' => 'osa', 'Os04g0477500' => 'osa', 'Os12g0611900' => 'osa', 'Peaxi162Scf00076g00020' => 'pax', 'Peaxi162Scf00128g00217' => 'pax', 'Peaxi162Scf00129g01640' => 'pax', 'Peaxi162Scf00669g00007' => 'pax', 'Peaxi162Scf00700g00421' => 'pax', 'Peaxi162Scf00801g00038' => 'pax', 'Peaxi162Scf00891g00025' => 'pax', 'PGR083G0909' => 'pgr', 'PGR119G1005' => 'pgr', 'PGR142G2236' => 'pgr', 'PGR142G3388' => 'pgr', 'PGSC0003DMG400004514' => 'stu', 'PGSC0003DMG400012635' => 'stu', 'PGSC0003DMG400015730' => 'stu', 'PGSC0003DMG400018611' => 'stu', 'PGSC0003DMG400030897' => 'stu', 'Phvul.001G254800' => 'pvu', 'Phvul.002G260100' => 'pvu', 'Phvul.003G167600' => 'pvu', 'Phvul.004G005100' => 'pvu', 'Potri.001G343600' => 'ptr', 'Potri.006G066700' => 'ptr', 'Potri.008G186000' => 'ptr', 'Potri.010G046900' => 'ptr', 'Potri.018G127900' => 'ptr', 'Pp3c20_17750' => 'ppa', 'Pp3c24_4380' => 'ppa', 'Prupe.1G245800' => 'ppe', 'Prupe.3G293400' => 'ppe', 'Prupe.7G247400' => 'ppe', 'Psat0s145g0120' => 'psa', 'Psat0s595g0040' => 'psa', 'Psat0s595g0120' => 'psa', 'Psat3g175040' => 'psa', 'Psat7g058120' => 'psa', 'PSO017G0428' => 'pso', 'PSO063G7510' => 'pso', 'PSO067G0046' => 'pso', 'PSO478G1073' => 'pso', 'PSO675G3677' => 'pso', 'PSO675G6558' => 'pso', 'PSO675G7520' => 'pso', 'PSO675G8959' => 'pso', 'QL02p074089' => 'qlo', 'QL02p089614' => 'qlo', 'QL03p057736' => 'qlo', 'RcHm_v2.0_Chr1g0364131' => 'rch', 'RcHm_v2.0_Chr2g0087801' => 'rch', 'RcHm_v2.0_Chr2g0087821' => 'rch', 'RcHm_v2.0_Chr2g0173231' => 'rch', 'RcHm_v2.0_Chr4g0433111' => 'rch', 'Rhsim03G0250300' => 'rsi', 'Rhsim08G0048400' => 'rsi', 'Rhsim10G0014800' => 'rsi', 'Rhsim12G0040100' => 'rsi', 'Rhsim12G0109700' => 'rsi', 'Sabra06G0049600' => 'sbr', 'Sabra08G0141000' => 'sbr', 'Sabra10G0021400' => 'sbr', 'Sabra16G0222900' => 'sbr', 'Sabra18G0108600' => 'sbr', 'SalBow1G0433' => 'sbo', 'SalBow1G2038' => 'sbo', 'SalBow1G5003' => 'sbo', 'SalBow7G1197' => 'sbo', 'SalBow8G3506' => 'sbo', 'Sc03g0007300' => 'sci', 'Sc11g0000950' => 'sci', 'Sc14g0008750' => 'sci', 'Sc18g0000420' => 'sci', 'Sed0006754' => 'sed', 'Sed0008741' => 'sed', 'Sed0017172' => 'sed', 'Sed0018925' => 'sed', 'Sed0023326' => 'sed', 'Sed0025909' => 'sed', 'SEGI_05333' => 'sgi', 'SEGI_10362' => 'sgi', 'SEGI_13380' => 'sgi', 'SEGI_24306' => 'sgi', 'SEGI_29077' => 'sgi', 'SEGI_29095' => 'sgi', 'SEGI_36534' => 'sgi', 'SEGI_37506' => 'sgi', 'SEGI_38321' => 'sgi', 'SGA_v2.0_scaffold307G48031' => 'sas', 'SGA_v2.0_scaffold47G17507' => 'sas', 'SGA_v2.0_scaffold63G21736' => 'sas', 'SGA_v2.0_scaffold87G27070' => 'sas', 'SHI17794' => 'shi', 'SHI28851' => 'shi', 'SMO165G0155' => 'smo', 'SMO340G0217' => 'smo', 'SMO367G1210' => 'smo', 'Solyc02g093430.3' => 'sly', 'Solyc05g013580.4' => 'sly', 'Solyc07g008030.3' => 'sly', 'Solyc12g035470.2' => 'sly', 'Sopen02g038020' => 'spe', 'Sopen05g008490' => 'spe', 'Sopen07g003910' => 'spe', 'Sopen12g015240' => 'spe', 'Sp1g11550' => 'spa', 'Sp2g16710' => 'spa', 'Sp3g00430' => 'spa', 'Sp3g26780' => 'spa', 'Sp5g22900' => 'spa', 'Sp6g29530' => 'spa', 'TAR371G0794' => 'tar', 'TAR374G0164' => 'tar', 'TAR622G0165' => 'tar', 'TAR626G0929' => 'tar', 'TAR629G2155' => 'tar', 'THA.LOC104805282' => 'tha', 'THA.LOC104805363' => 'tha', 'THA.LOC104808968' => 'tha', 'THA.LOC104821093' => 'tha', 'THA.LOC104823953' => 'tha', 'THA.LOC104825562' => 'tha', 'THA.LOC104825665' => 'tha', 'Thecc.02G261400' => 'tca', 'Thecc.04G019200' => 'tca', 'Thecc.09G130400' => 'tca', 'Thhalv10004374m.g' => 'esa', 'Thhalv10007850m.g' => 'esa', 'Thhalv10013782m.g' => 'esa', 'Thhalv10018686m.g' => 'esa', 'Thhalv10020899m.g' => 'esa', 'Thhalv10022755m.g' => 'esa', 'TPR.G23851' => 'tpr', 'TPR.G26500' => 'tpr', 'TPR.G27267' => 'tpr', 'TPR.G32001' => 'tpr', 'TPR.G6251' => 'tpr', 'TPR.G8167' => 'tpr', 'TWI12G1330' => 'twi', 'TWI18G1239' => 'twi', 'TWI34G0979' => 'twi', 'TWI36G0670' => 'twi', 'TWI36G0707' => 'twi', 'TWI56G0233' => 'twi', 'TWI75G1809' => 'twi', 'unitig_21.g20874' => 'ugi', 'unitig_26.g10343' => 'ugi', 'unitig_46.g18392' => 'ugi', 'unitig_52.g17178' => 'ugi', 'unitig_8.g2934' => 'ugi', 'vmacro01122' => 'vma', 'vmacro05875' => 'vma', 'vmacro06147' => 'vma', 'vmacro16191' => 'vma', 'vmacro18293' => 'vma', 'VMungo0251G3707' => 'vmu', 'VMungo0464G1521' => 'vmu', 'VMungo1215G0205' => 'vmu', 'VMungo1383G2484' => 'vmu', 'Zm00001eb079610' => 'zma', 'Zm00001eb135990' => 'zma', 'Zm00001eb183710' => 'zma', 'Zm00001eb246020' => 'zma' ) $gf_id = 'HOM05D001124' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001124' ) $data_identifier = 'HOM05D001124' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 6, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 7, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 21, 'bol' => (int) 10, 'bra' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 6, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 9, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 21, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 8, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 10, 'lsa' => (int) 8, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 8, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 9, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb246020' $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' => 'HOM05D001124', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '548', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02520' => 'bna', 'A03p06630' => 'bna', 'A05p44460' => 'bna', 'A06p08710' => 'bna', 'A06p41090' => 'bna', 'A07p32320' => 'bna', 'A08p32520' => 'bna', 'A09p10360' => 'bna', 'A10p24080' => 'bna', 'Aa31LG11G15250' => 'aar', 'Aa31LG1G1800' => 'aar', 'Aa31LG2G5120' => 'aar', 'Aa31LG2G6070' => 'aar', 'Aa31LG5G10770' => 'aar', 'Aa31sc61G90' => 'aar', 'Actinidia01352' => 'ach', 'Actinidia05983' => 'ach', 'Actinidia08133' => 'ach', 'Actinidia15101' => 'ach', 'Actinidia26379' => 'ach', 'Actinidia35778' => 'ach', 'Actinidia36123' => 'ach', 'Actinidia37436' => 'ach', 'Actinidia38730' => 'ach', 'Ah.02g128210' => 'amhyb', 'Ah.03g132990' => 'amhyb', 'Ah.14g079410' => 'amhyb', 'AL1G24640' => 'aly', 'AL2G26680' => 'aly', 'AL3G10530' => 'aly', 'AL3G45230' => 'aly', 'AL5G15230' => 'aly', 'AL5G16960' => 'aly', 'AL6G25210' => 'aly', 'Aqoxy2G00441' => 'aox', 'Aqoxy3G01236' => 'aox', 'Aqoxy5G03746' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3RQ047' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C7GMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9C8JER' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MBL6KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YXCZ83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZANX40' => 'arhy', 'AT1G12990' => 'ath', 'AT1G67880' => 'ath', 'AT2G13290' => 'ath', 'AT3G01620' => 'ath', 'AT3G26445' => 'ath', 'AT3G27540' => 'ath', 'AT5G14480' => 'ath', 'ATR0824G026' => 'atr', 'ATR1098G019' => 'atr', 'Atru.chr11.2145' => 'acertr', 'Atru.chr2.3636' => 'acertr', 'Atru.chr2.3644' => 'acertr', 'Atru.chr6.2422' => 'acertr', 'Atru.chr7.1112' => 'acertr', 'AUR62005469' => 'cqu', 'AUR62011166' => 'cqu', 'AUR62013319' => 'cqu', 'AUR62024273' => 'cqu', 'AUR62028420' => 'cqu', 'AUR62041942' => 'cqu', 'BcaB01g04969' => 'bca', 'BcaB01g06371' => 'bca', 'BcaB02g11494' => 'bca', 'BcaB03g15382' => 'bca', 'BcaB08g36994' => 'bca', 'BcaC03g13477' => 'bca', 'BcaC03g13478' => 'bca', 'BcaC03g13480' => 'bca', 'BcaC03g13481' => 'bca', 'BcaC03g13486' => 'bca', 'BcaC04g19031' => 'bca', 'BcaC04g23085' => 'bca', 'BcaC05g25094' => 'bca', 'BcaC05g25096' => 'bca', 'BcaC05g25138' => 'bca', 'BcaC05g30416' => 'bca', 'BcaC05g30455' => 'bca', 'BcaC06g30979' => 'bca', 'BcaC06g33805' => 'bca', 'BcaC08g46021' => 'bca', 'BcaNung03154' => 'bca', 'BolC2t06623H' => 'bol', 'BolC2t06632H' => 'bol', 'BolC2t06635H' => 'bol', 'BolC2t06638H' => 'bol', 'BolC3t13266H' => 'bol', 'BolC5t29776H' => 'bol', 'BolC6t38912H' => 'bol', 'BolC7t44183H' => 'bol', 'BolC9t54123H' => 'bol', 'BolC9t59107H' => 'bol', 'BraA02t05221Z' => 'bra', 'BraA03t09996Z' => 'bra', 'BraA05t23210Z' => 'bra', 'BraA06t24068Z' => 'bra', 'BraA06t27032Z' => 'bra', 'BraA08t35176Z' => 'bra', 'BraA09t36680Z' => 'bra', 'BraA10t44471Z' => 'bra', 'C02p06760' => 'bna', 'C02p06890' => 'bna', 'C02p07010' => 'bna', 'C03p07660' => 'bna', 'C05p10300' => 'bna', 'C06p38150' => 'bna', 'C07p36650' => 'bna', 'C08p15770' => 'bna', 'C09p12300' => 'bna', 'C09p62700' => 'bna', 'C09p75040' => 'bna', 'CAN.G13.1' => 'can', 'CAN.G138.4' => 'can', 'CAN.G44.6' => 'can', 'CAN.G473.19' => 'can', 'CANSAT01G0835' => 'cansat', 'CANSAT11G0246' => 'cansat', 'CANSAT11G1766' => 'cansat', 'CANSAT64G1954' => 'cansat', 'CARHR013330' => 'chi', 'CARHR060530' => 'chi', 'CARHR075300' => 'chi', 'CARHR105120' => 'chi', 'CARHR148910' => 'chi', 'CARHR198830' => 'chi', 'Carub.0001s1275' => 'cru', 'Carub.0002s1437' => 'cru', 'Carub.0003s0044' => 'cru', 'Carub.0003s2787' => 'cru', 'Carub.0005s0597' => 'cru', 'Carub.0006s1266' => 'cru', 'Ca_06935_v3' => 'car', 'Ca_13559_v3' => 'car', 'Ca_16941_v3' => 'car', 'Ca_16960_v3' => 'car', 'Ca_17775_v3' => 'car', 'Ca_30464_v3' => 'car', 'Cc06_g08160' => 'ccan', 'Cc07_g01520' => 'ccan', 'Cc11_g15810' => 'ccan', 'CDE02G2840' => 'cde', 'CDE03G0093' => 'cde', 'CDE04G2127' => 'cde', 'CDE07G1857' => 'cde', 'CDE09G1246' => 'cde', 'Cfa003412' => 'cfa', 'Cfa007341' => 'cfa', 'Cfa009220' => 'cfa', 'Ciclev10008737m.g' => 'ccl', 'Ciclev10015565m.g' => 'ccl', 'Ciclev10031761m.g' => 'ccl', 'CiPaw.03G045300' => 'cil', 'CiPaw.03G247200' => 'cil', 'CiPaw.04G029500' => 'cil', 'CiPaw.04G174000' => 'cil', 'CiPaw.05G181200' => 'cil', 'CiPaw.06G067100' => 'cil', 'ClCG05G025800' => 'cla', 'ClCG06G011400' => 'cla', 'ClCG09G019360' => 'cla', 'COL.COLO4_04827' => 'col', 'COL.COLO4_29170' => 'col', 'COL.COLO4_35131' => 'col', 'COL.COLO4_35132' => 'col', 'Cpa.g.sc33.32' => 'cpa', 'Cpa.g.sc46.29' => 'cpa', 'Cpa.g.sc796.1' => 'cpa', 'CsaV3_1G030420' => 'csa', 'CsaV3_5G027050' => 'csa', 'CsaV3_5G031040' => 'csa', 'CsaV3_UNG023130' => 'csa', 'CSS0007726' => 'camsi', 'CSS0016433' => 'camsi', 'CSS0017656' => 'camsi', 'CSS0025364' => 'camsi', 'CSS0027582' => 'camsi', 'CSS0047288' => 'camsi', 'CSS0049950' => 'camsi', 'DCAR_003843' => 'dca', 'DCAR_007052' => 'dca', 'DCAR_020884' => 'dca', 'DCAR_021730' => 'dca', 'DCAR_024423' => 'dca', 'DCAR_026509' => 'dca', 'DCAR_031158' => 'dca', 'Dinv14728' => 'din', 'Dinv15219' => 'din', 'Dinv25728' => 'din', 'Dinv33428' => 'din', 'Dinv36489' => 'din', 'Dinv41486' => 'din', 'Duzib147G0469' => 'dzi', 'Duzib168G0060' => 'dzi', 'Duzib187G1215' => 'dzi', 'Duzib248G0692' => 'dzi', 'Duzib251G0767' => 'dzi', 'Duzib264G0446' => 'dzi', 'Duzib268G0691' => 'dzi', 'ECA232G4767' => 'eca', 'ECA233G2838' => 'eca', 'ECA234G0391' => 'eca', 'ECA234G0857' => 'eca', 'ECA236G1593' => 'eca', 'ECA238G0565' => 'eca', 'ECA246G1027' => 'eca', 'ECA246G3223' => 'eca', 'ECA246G3470' => 'eca', 'EL10Ac6g13829' => 'bvu', 'EL10Ac6g14093' => 'bvu', 'EL10Ac8g18707' => 'bvu', 'Eucgr.C01369' => 'egr', 'Eucgr.H02492' => 'egr', 'Eucgr.I01733' => 'egr', 'Eucgr.J02255' => 'egr', 'Eucgr.J02257' => 'egr', 'Eucgr.J02258' => 'egr', 'FAN02G1601' => 'fan', 'FAN03G1586' => 'fan', 'FAN03G2986' => 'fan', 'FAN05G4837' => 'fan', 'FAN06G0146' => 'fan', 'FAN07G0858' => 'fan', 'FAN09G3179' => 'fan', 'FAN10G0669' => 'fan', 'FAN12G2358' => 'fan', 'FAN14G4198' => 'fan', 'FAN14G5112' => 'fan', 'FAN17G0342' => 'fan', 'FAN19G0342' => 'fan', 'FAN19G0962' => 'fan', 'FAN19G1101' => 'fan', 'FAN19G1872' => 'fan', 'FAN22G0356' => 'fan', 'FAN23G0744' => 'fan', 'FAN23G1914' => 'fan', 'FAN26G0032' => 'fan', 'FAN28G0625' => 'fan', 'FvH4_1g02710' => 'fve', 'FvH4_1g02720' => 'fve', 'FvH4_4g25670' => 'fve', 'FvH4_6g51700' => 'fve', 'FvH4_7g20170' => 'fve', 'Glyma.05G175000' => 'gma', 'Glyma.08G132300' => 'gma', 'Glyma.11G243000' => 'gma', 'Glyma.13G158900' => 'gma', 'Glyma.17G112400' => 'gma', 'Glyma.18G014100' => 'gma', 'Glyma.19G003100' => 'gma', 'Glyma.19G056500' => 'gma', 'Gohir.A01G158900' => 'ghi', 'Gohir.A05G312600' => 'ghi', 'Gohir.A05G354900' => 'ghi', 'Gohir.A07G037200' => 'ghi', 'Gohir.A09G030000' => 'ghi', 'Gohir.A12G145200' => 'ghi', 'Gohir.D01G151500' => 'ghi', 'Gohir.D04G058300' => 'ghi', 'Gohir.D05G314100' => 'ghi', 'Gohir.D07G041400' => 'ghi', 'Gohir.D09G029700' => 'ghi', 'Gohir.D12G149700' => 'ghi', 'Gorai.001G043800' => 'gra', 'Gorai.002G187800' => 'gra', 'Gorai.006G034700' => 'gra', 'Gorai.008G161200' => 'gra', 'Gorai.009G335700' => 'gra', 'Gorai.012G065000' => 'gra', 'GSVIVG01000535001' => 'vvi', 'GSVIVG01015572001' => 'vvi', 'GSVIVG01032386001' => 'vvi', 'HanXRQChr05g0138531' => 'han', 'HanXRQChr06g0174391' => 'han', 'HanXRQChr07g0199021' => 'han', 'HanXRQChr08g0208211' => 'han', 'HanXRQChr09g0255471' => 'han', 'HanXRQChr10g0315791' => 'han', 'HanXRQChr12g0371991' => 'han', 'HanXRQChr15g0475251' => 'han', 'HanXRQChr17g0540001' => 'han', 'HanXRQChr17g0548631' => 'han', 'HanXRQChr17g0569561' => 'han', 'Haze_12256' => 'cav', 'Haze_14756' => 'cav', 'Haze_25528' => 'cav', 'Hma1.2p1_0079F.1_g041020' => 'hma', 'Hma1.2p1_0818F.1_g223260' => 'hma', 'Hma1.2p1_1747F.1_g300530' => 'hma', 'HPP92_004607' => 'vpl', 'HPP92_004608' => 'vpl', 'HPP92_006181' => 'vpl', 'HPP92_012192' => 'vpl', 'HPP92_015680' => 'vpl', 'HPP92_020249' => 'vpl', 'HPP92_021376' => 'vpl', 'HPP92_024275' => 'vpl', 'Hund06031' => 'sun', 'Hund25391' => 'sun', 'Lalb_Chr07g0185371' => 'lal', 'Lalb_Chr07g0185381' => 'lal', 'Lalb_Chr12g0204011' => 'lal', 'Lalb_Chr13g0301671' => 'lal', 'Lalb_Chr14g0362851' => 'lal', 'Lalb_Chr24g0403581' => 'lal', 'Lj1g0000233' => 'lja', 'Lj2g0018120' => 'lja', 'Lj3C621T0' => 'lonja', 'Lj3P1059T14' => 'lonja', 'Lj3P611T9' => 'lonja', 'Lj3P614T13' => 'lonja', 'Lj3P615T5' => 'lonja', 'Lj4g0012315' => 'lja', 'Lj4g0026182' => 'lja', 'Lj6P813T16' => 'lonja', 'Lj7C427T7' => 'lonja', 'Lj7C427T8' => 'lonja', 'Lj7P600T41' => 'lonja', 'Lju41C42G17' => 'lonja', 'Lsat_1_v5_gn_0_47300' => 'lsa', 'Lsat_1_v5_gn_2_91280' => 'lsa', 'Lsat_1_v5_gn_3_30561' => 'lsa', 'Lsat_1_v5_gn_4_184321' => 'lsa', 'Lsat_1_v5_gn_4_4041' => 'lsa', 'Lsat_1_v5_gn_5_92000' => 'lsa', 'Lsat_1_v5_gn_8_152940' => 'lsa', 'Lsat_1_v5_gn_8_62401' => 'lsa', 'Manes.06G055900' => 'mes', 'Manes.12G022200' => 'mes', 'Manes.13G023300' => 'mes', 'Manes.14G115000' => 'mes', 'Manes.15G151700' => 'mes', 'Manes.17G111300' => 'mes', 'Mapoly0226s0009' => 'mpo', 'MBI02_g25363_MAGBIO' => 'mbi', 'MBI06_g00027_MAGBIO' => 'mbi', 'MBI10_g13034_MAGBIO' => 'mbi', 'MD09G1023400' => 'mdo', 'MD13G1100100' => 'mdo', 'MD15G1169200' => 'mdo', 'MD16G1101100' => 'mdo', 'MD17G1022900' => 'mdo', 'Medtr3g096150' => 'mtr', 'Medtr4g115070' => 'mtr', 'Medtr7g033325' => 'mtr', 'Medtr8g089840' => 'mtr', 'MELO3C010319.2' => 'cme', 'MELO3C011944.2' => 'cme', 'MELO3C021589.2' => 'cme', 'Migut.E00207' => 'egut', 'Migut.H00067' => 'egut', 'Migut.K00433' => 'egut', 'Migut.K00606' => 'egut', 'Migut.K01410' => 'egut', 'MSTRG.13347' => 'ama', 'MSTRG.24045' => 'ama', 'MSTRG.2428' => 'ama', 'MSTRG.26410' => 'ama', 'MSTRG.3139' => 'ama', 'MSTRG.3286' => 'ama', 'MSTRG.563' => 'ama', 'MSTRG.7941' => 'ama', 'Nitab4.5_0000028g0060' => 'nta', 'Nitab4.5_0000065g0260' => 'nta', 'Nitab4.5_0000112g0060' => 'nta', 'Nitab4.5_0000489g0120' => 'nta', 'Nitab4.5_0001776g0050' => 'nta', 'Nitab4.5_0001854g0010' => 'nta', 'Nitab4.5_0001860g0020' => 'nta', 'Nitab4.5_0004352g0010' => 'nta', 'Nitab4.5_0008716g0020' => 'nta', 'Nitab4.5_0008922g0010' => 'nta', 'Nn3g16693' => 'nnu', 'Nn4g22596' => 'nnu', 'Nn7g37639' => 'nnu', 'Oeu001701.1' => 'oeu', 'Oeu018149.1' => 'oeu', 'Oeu026220.1' => 'oeu', 'Oeu038635.1' => 'oeu', 'Oeu049176.1' => 'oeu', 'Oeu056706.1' => 'oeu', 'Oeu056937.1' => 'oeu', 'Oeu057540.1' => 'oeu', 'Os02g0594900' => 'osa', 'Os02g0595100' => 'osa', 'Os04g0477500' => 'osa', 'Os12g0611900' => 'osa', 'Peaxi162Scf00076g00020' => 'pax', 'Peaxi162Scf00128g00217' => 'pax', 'Peaxi162Scf00129g01640' => 'pax', 'Peaxi162Scf00669g00007' => 'pax', 'Peaxi162Scf00700g00421' => 'pax', 'Peaxi162Scf00801g00038' => 'pax', 'Peaxi162Scf00891g00025' => 'pax', 'PGR083G0909' => 'pgr', 'PGR119G1005' => 'pgr', 'PGR142G2236' => 'pgr', 'PGR142G3388' => 'pgr', 'PGSC0003DMG400004514' => 'stu', 'PGSC0003DMG400012635' => 'stu', 'PGSC0003DMG400015730' => 'stu', 'PGSC0003DMG400018611' => 'stu', 'PGSC0003DMG400030897' => 'stu', 'Phvul.001G254800' => 'pvu', 'Phvul.002G260100' => 'pvu', 'Phvul.003G167600' => 'pvu', 'Phvul.004G005100' => 'pvu', 'Potri.001G343600' => 'ptr', 'Potri.006G066700' => 'ptr', 'Potri.008G186000' => 'ptr', 'Potri.010G046900' => 'ptr', 'Potri.018G127900' => 'ptr', 'Pp3c20_17750' => 'ppa', 'Pp3c24_4380' => 'ppa', 'Prupe.1G245800' => 'ppe', 'Prupe.3G293400' => 'ppe', 'Prupe.7G247400' => 'ppe', 'Psat0s145g0120' => 'psa', 'Psat0s595g0040' => 'psa', 'Psat0s595g0120' => 'psa', 'Psat3g175040' => 'psa', 'Psat7g058120' => 'psa', 'PSO017G0428' => 'pso', 'PSO063G7510' => 'pso', 'PSO067G0046' => 'pso', 'PSO478G1073' => 'pso', 'PSO675G3677' => 'pso', 'PSO675G6558' => 'pso', 'PSO675G7520' => 'pso', 'PSO675G8959' => 'pso', 'QL02p074089' => 'qlo', 'QL02p089614' => 'qlo', 'QL03p057736' => 'qlo', 'RcHm_v2.0_Chr1g0364131' => 'rch', 'RcHm_v2.0_Chr2g0087801' => 'rch', 'RcHm_v2.0_Chr2g0087821' => 'rch', 'RcHm_v2.0_Chr2g0173231' => 'rch', 'RcHm_v2.0_Chr4g0433111' => 'rch', 'Rhsim03G0250300' => 'rsi', 'Rhsim08G0048400' => 'rsi', 'Rhsim10G0014800' => 'rsi', 'Rhsim12G0040100' => 'rsi', 'Rhsim12G0109700' => 'rsi', 'Sabra06G0049600' => 'sbr', 'Sabra08G0141000' => 'sbr', 'Sabra10G0021400' => 'sbr', 'Sabra16G0222900' => 'sbr', 'Sabra18G0108600' => 'sbr', 'SalBow1G0433' => 'sbo', 'SalBow1G2038' => 'sbo', 'SalBow1G5003' => 'sbo', 'SalBow7G1197' => 'sbo', 'SalBow8G3506' => 'sbo', 'Sc03g0007300' => 'sci', 'Sc11g0000950' => 'sci', 'Sc14g0008750' => 'sci', 'Sc18g0000420' => 'sci', 'Sed0006754' => 'sed', 'Sed0008741' => 'sed', 'Sed0017172' => 'sed', 'Sed0018925' => 'sed', 'Sed0023326' => 'sed', 'Sed0025909' => 'sed', 'SEGI_05333' => 'sgi', 'SEGI_10362' => 'sgi', 'SEGI_13380' => 'sgi', 'SEGI_24306' => 'sgi', 'SEGI_29077' => 'sgi', 'SEGI_29095' => 'sgi', 'SEGI_36534' => 'sgi', 'SEGI_37506' => 'sgi', 'SEGI_38321' => 'sgi', 'SGA_v2.0_scaffold307G48031' => 'sas', 'SGA_v2.0_scaffold47G17507' => 'sas', 'SGA_v2.0_scaffold63G21736' => 'sas', 'SGA_v2.0_scaffold87G27070' => 'sas', 'SHI17794' => 'shi', 'SHI28851' => 'shi', 'SMO165G0155' => 'smo', 'SMO340G0217' => 'smo', 'SMO367G1210' => 'smo', 'Solyc02g093430.3' => 'sly', 'Solyc05g013580.4' => 'sly', 'Solyc07g008030.3' => 'sly', 'Solyc12g035470.2' => 'sly', 'Sopen02g038020' => 'spe', 'Sopen05g008490' => 'spe', 'Sopen07g003910' => 'spe', 'Sopen12g015240' => 'spe', 'Sp1g11550' => 'spa', 'Sp2g16710' => 'spa', 'Sp3g00430' => 'spa', 'Sp3g26780' => 'spa', 'Sp5g22900' => 'spa', 'Sp6g29530' => 'spa', 'TAR371G0794' => 'tar', 'TAR374G0164' => 'tar', 'TAR622G0165' => 'tar', 'TAR626G0929' => 'tar', 'TAR629G2155' => 'tar', 'THA.LOC104805282' => 'tha', 'THA.LOC104805363' => 'tha', 'THA.LOC104808968' => 'tha', 'THA.LOC104821093' => 'tha', 'THA.LOC104823953' => 'tha', 'THA.LOC104825562' => 'tha', 'THA.LOC104825665' => 'tha', 'Thecc.02G261400' => 'tca', 'Thecc.04G019200' => 'tca', 'Thecc.09G130400' => 'tca', 'Thhalv10004374m.g' => 'esa', 'Thhalv10007850m.g' => 'esa', 'Thhalv10013782m.g' => 'esa', 'Thhalv10018686m.g' => 'esa', 'Thhalv10020899m.g' => 'esa', 'Thhalv10022755m.g' => 'esa', 'TPR.G23851' => 'tpr', 'TPR.G26500' => 'tpr', 'TPR.G27267' => 'tpr', 'TPR.G32001' => 'tpr', 'TPR.G6251' => 'tpr', 'TPR.G8167' => 'tpr', 'TWI12G1330' => 'twi', 'TWI18G1239' => 'twi', 'TWI34G0979' => 'twi', 'TWI36G0670' => 'twi', 'TWI36G0707' => 'twi', 'TWI56G0233' => 'twi', 'TWI75G1809' => 'twi', 'unitig_21.g20874' => 'ugi', 'unitig_26.g10343' => 'ugi', 'unitig_46.g18392' => 'ugi', 'unitig_52.g17178' => 'ugi', 'unitig_8.g2934' => 'ugi', 'vmacro01122' => 'vma', 'vmacro05875' => 'vma', 'vmacro06147' => 'vma', 'vmacro16191' => 'vma', 'vmacro18293' => 'vma', 'VMungo0251G3707' => 'vmu', 'VMungo0464G1521' => 'vmu', 'VMungo1215G0205' => 'vmu', 'VMungo1383G2484' => 'vmu', 'Zm00001eb079610' => 'zma', 'Zm00001eb135990' => 'zma', 'Zm00001eb183710' => 'zma', 'Zm00001eb246020' => 'zma' ), 'gf_id' => 'HOM05D001124', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001124' ), 'data_identifier' => 'HOM05D001124', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001124', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '548', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02520' => 'bna', 'A03p06630' => 'bna', 'A05p44460' => 'bna', 'A06p08710' => 'bna', 'A06p41090' => 'bna', 'A07p32320' => 'bna', 'A08p32520' => 'bna', 'A09p10360' => 'bna', 'A10p24080' => 'bna', 'Aa31LG11G15250' => 'aar', 'Aa31LG1G1800' => 'aar', 'Aa31LG2G5120' => 'aar', 'Aa31LG2G6070' => 'aar', 'Aa31LG5G10770' => 'aar', 'Aa31sc61G90' => 'aar', 'Actinidia01352' => 'ach', 'Actinidia05983' => 'ach', 'Actinidia08133' => 'ach', 'Actinidia15101' => 'ach', 'Actinidia26379' => 'ach', 'Actinidia35778' => 'ach', 'Actinidia36123' => 'ach', 'Actinidia37436' => 'ach', 'Actinidia38730' => 'ach', 'Ah.02g128210' => 'amhyb', 'Ah.03g132990' => 'amhyb', 'Ah.14g079410' => 'amhyb', 'AL1G24640' => 'aly', 'AL2G26680' => 'aly', 'AL3G10530' => 'aly', 'AL3G45230' => 'aly', 'AL5G15230' => 'aly', 'AL5G16960' => 'aly', 'AL6G25210' => 'aly', 'Aqoxy2G00441' => 'aox', 'Aqoxy3G01236' => 'aox', 'Aqoxy5G03746' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3RQ047' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C7GMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9C8JER' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MBL6KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YXCZ83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZANX40' => 'arhy', 'AT1G12990' => 'ath', 'AT1G67880' => 'ath', 'AT2G13290' => 'ath', 'AT3G01620' => 'ath', 'AT3G26445' => 'ath', 'AT3G27540' => 'ath', 'AT5G14480' => 'ath', 'ATR0824G026' => 'atr', 'ATR1098G019' => 'atr', 'Atru.chr11.2145' => 'acertr', 'Atru.chr2.3636' => 'acertr', 'Atru.chr2.3644' => 'acertr', 'Atru.chr6.2422' => 'acertr', 'Atru.chr7.1112' => 'acertr', 'AUR62005469' => 'cqu', 'AUR62011166' => 'cqu', 'AUR62013319' => 'cqu', 'AUR62024273' => 'cqu', 'AUR62028420' => 'cqu', 'AUR62041942' => 'cqu', 'BcaB01g04969' => 'bca', 'BcaB01g06371' => 'bca', 'BcaB02g11494' => 'bca', 'BcaB03g15382' => 'bca', 'BcaB08g36994' => 'bca', 'BcaC03g13477' => 'bca', 'BcaC03g13478' => 'bca', 'BcaC03g13480' => 'bca', 'BcaC03g13481' => 'bca', 'BcaC03g13486' => 'bca', 'BcaC04g19031' => 'bca', 'BcaC04g23085' => 'bca', 'BcaC05g25094' => 'bca', 'BcaC05g25096' => 'bca', 'BcaC05g25138' => 'bca', 'BcaC05g30416' => 'bca', 'BcaC05g30455' => 'bca', 'BcaC06g30979' => 'bca', 'BcaC06g33805' => 'bca', 'BcaC08g46021' => 'bca', 'BcaNung03154' => 'bca', 'BolC2t06623H' => 'bol', 'BolC2t06632H' => 'bol', 'BolC2t06635H' => 'bol', 'BolC2t06638H' => 'bol', 'BolC3t13266H' => 'bol', 'BolC5t29776H' => 'bol', 'BolC6t38912H' => 'bol', 'BolC7t44183H' => 'bol', 'BolC9t54123H' => 'bol', 'BolC9t59107H' => 'bol', 'BraA02t05221Z' => 'bra', 'BraA03t09996Z' => 'bra', 'BraA05t23210Z' => 'bra', 'BraA06t24068Z' => 'bra', 'BraA06t27032Z' => 'bra', 'BraA08t35176Z' => 'bra', 'BraA09t36680Z' => 'bra', 'BraA10t44471Z' => 'bra', 'C02p06760' => 'bna', 'C02p06890' => 'bna', 'C02p07010' => 'bna', 'C03p07660' => 'bna', 'C05p10300' => 'bna', 'C06p38150' => 'bna', 'C07p36650' => 'bna', 'C08p15770' => 'bna', 'C09p12300' => 'bna', 'C09p62700' => 'bna', 'C09p75040' => 'bna', 'CAN.G13.1' => 'can', 'CAN.G138.4' => 'can', 'CAN.G44.6' => 'can', 'CAN.G473.19' => 'can', 'CANSAT01G0835' => 'cansat', 'CANSAT11G0246' => 'cansat', 'CANSAT11G1766' => 'cansat', 'CANSAT64G1954' => 'cansat', 'CARHR013330' => 'chi', 'CARHR060530' => 'chi', 'CARHR075300' => 'chi', 'CARHR105120' => 'chi', 'CARHR148910' => 'chi', 'CARHR198830' => 'chi', 'Carub.0001s1275' => 'cru', 'Carub.0002s1437' => 'cru', 'Carub.0003s0044' => 'cru', 'Carub.0003s2787' => 'cru', 'Carub.0005s0597' => 'cru', 'Carub.0006s1266' => 'cru', 'Ca_06935_v3' => 'car', 'Ca_13559_v3' => 'car', 'Ca_16941_v3' => 'car', 'Ca_16960_v3' => 'car', 'Ca_17775_v3' => 'car', 'Ca_30464_v3' => 'car', 'Cc06_g08160' => 'ccan', 'Cc07_g01520' => 'ccan', 'Cc11_g15810' => 'ccan', 'CDE02G2840' => 'cde', 'CDE03G0093' => 'cde', 'CDE04G2127' => 'cde', 'CDE07G1857' => 'cde', 'CDE09G1246' => 'cde', 'Cfa003412' => 'cfa', 'Cfa007341' => 'cfa', 'Cfa009220' => 'cfa', 'Ciclev10008737m.g' => 'ccl', 'Ciclev10015565m.g' => 'ccl', 'Ciclev10031761m.g' => 'ccl', 'CiPaw.03G045300' => 'cil', 'CiPaw.03G247200' => 'cil', 'CiPaw.04G029500' => 'cil', 'CiPaw.04G174000' => 'cil', 'CiPaw.05G181200' => 'cil', 'CiPaw.06G067100' => 'cil', 'ClCG05G025800' => 'cla', 'ClCG06G011400' => 'cla', 'ClCG09G019360' => 'cla', 'COL.COLO4_04827' => 'col', 'COL.COLO4_29170' => 'col', 'COL.COLO4_35131' => 'col', 'COL.COLO4_35132' => 'col', 'Cpa.g.sc33.32' => 'cpa', 'Cpa.g.sc46.29' => 'cpa', 'Cpa.g.sc796.1' => 'cpa', 'CsaV3_1G030420' => 'csa', 'CsaV3_5G027050' => 'csa', 'CsaV3_5G031040' => 'csa', 'CsaV3_UNG023130' => 'csa', 'CSS0007726' => 'camsi', 'CSS0016433' => 'camsi', 'CSS0017656' => 'camsi', 'CSS0025364' => 'camsi', 'CSS0027582' => 'camsi', 'CSS0047288' => 'camsi', 'CSS0049950' => 'camsi', 'DCAR_003843' => 'dca', 'DCAR_007052' => 'dca', 'DCAR_020884' => 'dca', 'DCAR_021730' => 'dca', 'DCAR_024423' => 'dca', 'DCAR_026509' => 'dca', 'DCAR_031158' => 'dca', 'Dinv14728' => 'din', 'Dinv15219' => 'din', 'Dinv25728' => 'din', 'Dinv33428' => 'din', 'Dinv36489' => 'din', 'Dinv41486' => 'din', 'Duzib147G0469' => 'dzi', 'Duzib168G0060' => 'dzi', 'Duzib187G1215' => 'dzi', 'Duzib248G0692' => 'dzi', 'Duzib251G0767' => 'dzi', 'Duzib264G0446' => 'dzi', 'Duzib268G0691' => 'dzi', 'ECA232G4767' => 'eca', 'ECA233G2838' => 'eca', 'ECA234G0391' => 'eca', 'ECA234G0857' => 'eca', 'ECA236G1593' => 'eca', 'ECA238G0565' => 'eca', 'ECA246G1027' => 'eca', 'ECA246G3223' => 'eca', 'ECA246G3470' => 'eca', 'EL10Ac6g13829' => 'bvu', 'EL10Ac6g14093' => 'bvu', 'EL10Ac8g18707' => 'bvu', 'Eucgr.C01369' => 'egr', 'Eucgr.H02492' => 'egr', 'Eucgr.I01733' => 'egr', 'Eucgr.J02255' => 'egr', 'Eucgr.J02257' => 'egr', 'Eucgr.J02258' => 'egr', 'FAN02G1601' => 'fan', 'FAN03G1586' => 'fan', 'FAN03G2986' => 'fan', 'FAN05G4837' => 'fan', 'FAN06G0146' => 'fan', 'FAN07G0858' => 'fan', 'FAN09G3179' => 'fan', 'FAN10G0669' => 'fan', 'FAN12G2358' => 'fan', 'FAN14G4198' => 'fan', 'FAN14G5112' => 'fan', 'FAN17G0342' => 'fan', 'FAN19G0342' => 'fan', 'FAN19G0962' => 'fan', 'FAN19G1101' => 'fan', 'FAN19G1872' => 'fan', 'FAN22G0356' => 'fan', 'FAN23G0744' => 'fan', 'FAN23G1914' => 'fan', 'FAN26G0032' => 'fan', 'FAN28G0625' => 'fan', 'FvH4_1g02710' => 'fve', 'FvH4_1g02720' => 'fve', 'FvH4_4g25670' => 'fve', 'FvH4_6g51700' => 'fve', 'FvH4_7g20170' => 'fve', 'Glyma.05G175000' => 'gma', 'Glyma.08G132300' => 'gma', 'Glyma.11G243000' => 'gma', 'Glyma.13G158900' => 'gma', 'Glyma.17G112400' => 'gma', 'Glyma.18G014100' => 'gma', 'Glyma.19G003100' => 'gma', 'Glyma.19G056500' => 'gma', 'Gohir.A01G158900' => 'ghi', 'Gohir.A05G312600' => 'ghi', 'Gohir.A05G354900' => 'ghi', 'Gohir.A07G037200' => 'ghi', 'Gohir.A09G030000' => 'ghi', 'Gohir.A12G145200' => 'ghi', 'Gohir.D01G151500' => 'ghi', 'Gohir.D04G058300' => 'ghi', 'Gohir.D05G314100' => 'ghi', 'Gohir.D07G041400' => 'ghi', 'Gohir.D09G029700' => 'ghi', 'Gohir.D12G149700' => 'ghi', 'Gorai.001G043800' => 'gra', 'Gorai.002G187800' => 'gra', 'Gorai.006G034700' => 'gra', 'Gorai.008G161200' => 'gra', 'Gorai.009G335700' => 'gra', 'Gorai.012G065000' => 'gra', 'GSVIVG01000535001' => 'vvi', 'GSVIVG01015572001' => 'vvi', 'GSVIVG01032386001' => 'vvi', 'HanXRQChr05g0138531' => 'han', 'HanXRQChr06g0174391' => 'han', 'HanXRQChr07g0199021' => 'han', 'HanXRQChr08g0208211' => 'han', 'HanXRQChr09g0255471' => 'han', 'HanXRQChr10g0315791' => 'han', 'HanXRQChr12g0371991' => 'han', 'HanXRQChr15g0475251' => 'han', 'HanXRQChr17g0540001' => 'han', 'HanXRQChr17g0548631' => 'han', 'HanXRQChr17g0569561' => 'han', 'Haze_12256' => 'cav', 'Haze_14756' => 'cav', 'Haze_25528' => 'cav', 'Hma1.2p1_0079F.1_g041020' => 'hma', 'Hma1.2p1_0818F.1_g223260' => 'hma', 'Hma1.2p1_1747F.1_g300530' => 'hma', 'HPP92_004607' => 'vpl', 'HPP92_004608' => 'vpl', 'HPP92_006181' => 'vpl', 'HPP92_012192' => 'vpl', 'HPP92_015680' => 'vpl', 'HPP92_020249' => 'vpl', 'HPP92_021376' => 'vpl', 'HPP92_024275' => 'vpl', 'Hund06031' => 'sun', 'Hund25391' => 'sun', 'Lalb_Chr07g0185371' => 'lal', 'Lalb_Chr07g0185381' => 'lal', 'Lalb_Chr12g0204011' => 'lal', 'Lalb_Chr13g0301671' => 'lal', 'Lalb_Chr14g0362851' => 'lal', 'Lalb_Chr24g0403581' => 'lal', 'Lj1g0000233' => 'lja', 'Lj2g0018120' => 'lja', 'Lj3C621T0' => 'lonja', 'Lj3P1059T14' => 'lonja', 'Lj3P611T9' => 'lonja', 'Lj3P614T13' => 'lonja', 'Lj3P615T5' => 'lonja', 'Lj4g0012315' => 'lja', 'Lj4g0026182' => 'lja', 'Lj6P813T16' => 'lonja', 'Lj7C427T7' => 'lonja', 'Lj7C427T8' => 'lonja', 'Lj7P600T41' => 'lonja', 'Lju41C42G17' => 'lonja', 'Lsat_1_v5_gn_0_47300' => 'lsa', 'Lsat_1_v5_gn_2_91280' => 'lsa', 'Lsat_1_v5_gn_3_30561' => 'lsa', 'Lsat_1_v5_gn_4_184321' => 'lsa', 'Lsat_1_v5_gn_4_4041' => 'lsa', 'Lsat_1_v5_gn_5_92000' => 'lsa', 'Lsat_1_v5_gn_8_152940' => 'lsa', 'Lsat_1_v5_gn_8_62401' => 'lsa', 'Manes.06G055900' => 'mes', 'Manes.12G022200' => 'mes', 'Manes.13G023300' => 'mes', 'Manes.14G115000' => 'mes', 'Manes.15G151700' => 'mes', 'Manes.17G111300' => 'mes', 'Mapoly0226s0009' => 'mpo', 'MBI02_g25363_MAGBIO' => 'mbi', 'MBI06_g00027_MAGBIO' => 'mbi', 'MBI10_g13034_MAGBIO' => 'mbi', 'MD09G1023400' => 'mdo', 'MD13G1100100' => 'mdo', 'MD15G1169200' => 'mdo', 'MD16G1101100' => 'mdo', 'MD17G1022900' => 'mdo', 'Medtr3g096150' => 'mtr', 'Medtr4g115070' => 'mtr', 'Medtr7g033325' => 'mtr', 'Medtr8g089840' => 'mtr', 'MELO3C010319.2' => 'cme', 'MELO3C011944.2' => 'cme', 'MELO3C021589.2' => 'cme', 'Migut.E00207' => 'egut', 'Migut.H00067' => 'egut', 'Migut.K00433' => 'egut', 'Migut.K00606' => 'egut', 'Migut.K01410' => 'egut', 'MSTRG.13347' => 'ama', 'MSTRG.24045' => 'ama', 'MSTRG.2428' => 'ama', 'MSTRG.26410' => 'ama', 'MSTRG.3139' => 'ama', 'MSTRG.3286' => 'ama', 'MSTRG.563' => 'ama', 'MSTRG.7941' => 'ama', 'Nitab4.5_0000028g0060' => 'nta', 'Nitab4.5_0000065g0260' => 'nta', 'Nitab4.5_0000112g0060' => 'nta', 'Nitab4.5_0000489g0120' => 'nta', 'Nitab4.5_0001776g0050' => 'nta', 'Nitab4.5_0001854g0010' => 'nta', 'Nitab4.5_0001860g0020' => 'nta', 'Nitab4.5_0004352g0010' => 'nta', 'Nitab4.5_0008716g0020' => 'nta', 'Nitab4.5_0008922g0010' => 'nta', 'Nn3g16693' => 'nnu', 'Nn4g22596' => 'nnu', 'Nn7g37639' => 'nnu', 'Oeu001701.1' => 'oeu', 'Oeu018149.1' => 'oeu', 'Oeu026220.1' => 'oeu', 'Oeu038635.1' => 'oeu', 'Oeu049176.1' => 'oeu', 'Oeu056706.1' => 'oeu', 'Oeu056937.1' => 'oeu', 'Oeu057540.1' => 'oeu', 'Os02g0594900' => 'osa', 'Os02g0595100' => 'osa', 'Os04g0477500' => 'osa', 'Os12g0611900' => 'osa', 'Peaxi162Scf00076g00020' => 'pax', 'Peaxi162Scf00128g00217' => 'pax', 'Peaxi162Scf00129g01640' => 'pax', 'Peaxi162Scf00669g00007' => 'pax', 'Peaxi162Scf00700g00421' => 'pax', 'Peaxi162Scf00801g00038' => 'pax', 'Peaxi162Scf00891g00025' => 'pax', 'PGR083G0909' => 'pgr', 'PGR119G1005' => 'pgr', 'PGR142G2236' => 'pgr', 'PGR142G3388' => 'pgr', 'PGSC0003DMG400004514' => 'stu', 'PGSC0003DMG400012635' => 'stu', 'PGSC0003DMG400015730' => 'stu', 'PGSC0003DMG400018611' => 'stu', 'PGSC0003DMG400030897' => 'stu', 'Phvul.001G254800' => 'pvu', 'Phvul.002G260100' => 'pvu', 'Phvul.003G167600' => 'pvu', 'Phvul.004G005100' => 'pvu', 'Potri.001G343600' => 'ptr', 'Potri.006G066700' => 'ptr', 'Potri.008G186000' => 'ptr', 'Potri.010G046900' => 'ptr', 'Potri.018G127900' => 'ptr', 'Pp3c20_17750' => 'ppa', 'Pp3c24_4380' => 'ppa', 'Prupe.1G245800' => 'ppe', 'Prupe.3G293400' => 'ppe', 'Prupe.7G247400' => 'ppe', 'Psat0s145g0120' => 'psa', 'Psat0s595g0040' => 'psa', 'Psat0s595g0120' => 'psa', 'Psat3g175040' => 'psa', 'Psat7g058120' => 'psa', 'PSO017G0428' => 'pso', 'PSO063G7510' => 'pso', 'PSO067G0046' => 'pso', 'PSO478G1073' => 'pso', 'PSO675G3677' => 'pso', 'PSO675G6558' => 'pso', 'PSO675G7520' => 'pso', 'PSO675G8959' => 'pso', 'QL02p074089' => 'qlo', 'QL02p089614' => 'qlo', 'QL03p057736' => 'qlo', 'RcHm_v2.0_Chr1g0364131' => 'rch', 'RcHm_v2.0_Chr2g0087801' => 'rch', 'RcHm_v2.0_Chr2g0087821' => 'rch', 'RcHm_v2.0_Chr2g0173231' => 'rch', 'RcHm_v2.0_Chr4g0433111' => 'rch', 'Rhsim03G0250300' => 'rsi', 'Rhsim08G0048400' => 'rsi', 'Rhsim10G0014800' => 'rsi', 'Rhsim12G0040100' => 'rsi', 'Rhsim12G0109700' => 'rsi', 'Sabra06G0049600' => 'sbr', 'Sabra08G0141000' => 'sbr', 'Sabra10G0021400' => 'sbr', 'Sabra16G0222900' => 'sbr', 'Sabra18G0108600' => 'sbr', 'SalBow1G0433' => 'sbo', 'SalBow1G2038' => 'sbo', 'SalBow1G5003' => 'sbo', 'SalBow7G1197' => 'sbo', 'SalBow8G3506' => 'sbo', 'Sc03g0007300' => 'sci', 'Sc11g0000950' => 'sci', 'Sc14g0008750' => 'sci', 'Sc18g0000420' => 'sci', 'Sed0006754' => 'sed', 'Sed0008741' => 'sed', 'Sed0017172' => 'sed', 'Sed0018925' => 'sed', 'Sed0023326' => 'sed', 'Sed0025909' => 'sed', 'SEGI_05333' => 'sgi', 'SEGI_10362' => 'sgi', 'SEGI_13380' => 'sgi', 'SEGI_24306' => 'sgi', 'SEGI_29077' => 'sgi', 'SEGI_29095' => 'sgi', 'SEGI_36534' => 'sgi', 'SEGI_37506' => 'sgi', 'SEGI_38321' => 'sgi', 'SGA_v2.0_scaffold307G48031' => 'sas', 'SGA_v2.0_scaffold47G17507' => 'sas', 'SGA_v2.0_scaffold63G21736' => 'sas', 'SGA_v2.0_scaffold87G27070' => 'sas', 'SHI17794' => 'shi', 'SHI28851' => 'shi', 'SMO165G0155' => 'smo', 'SMO340G0217' => 'smo', 'SMO367G1210' => 'smo', 'Solyc02g093430.3' => 'sly', 'Solyc05g013580.4' => 'sly', 'Solyc07g008030.3' => 'sly', 'Solyc12g035470.2' => 'sly', 'Sopen02g038020' => 'spe', 'Sopen05g008490' => 'spe', 'Sopen07g003910' => 'spe', 'Sopen12g015240' => 'spe', 'Sp1g11550' => 'spa', 'Sp2g16710' => 'spa', 'Sp3g00430' => 'spa', 'Sp3g26780' => 'spa', 'Sp5g22900' => 'spa', 'Sp6g29530' => 'spa', 'TAR371G0794' => 'tar', 'TAR374G0164' => 'tar', 'TAR622G0165' => 'tar', 'TAR626G0929' => 'tar', 'TAR629G2155' => 'tar', 'THA.LOC104805282' => 'tha', 'THA.LOC104805363' => 'tha', 'THA.LOC104808968' => 'tha', 'THA.LOC104821093' => 'tha', 'THA.LOC104823953' => 'tha', 'THA.LOC104825562' => 'tha', 'THA.LOC104825665' => 'tha', 'Thecc.02G261400' => 'tca', 'Thecc.04G019200' => 'tca', 'Thecc.09G130400' => 'tca', 'Thhalv10004374m.g' => 'esa', 'Thhalv10007850m.g' => 'esa', 'Thhalv10013782m.g' => 'esa', 'Thhalv10018686m.g' => 'esa', 'Thhalv10020899m.g' => 'esa', 'Thhalv10022755m.g' => 'esa', 'TPR.G23851' => 'tpr', 'TPR.G26500' => 'tpr', 'TPR.G27267' => 'tpr', 'TPR.G32001' => 'tpr', 'TPR.G6251' => 'tpr', 'TPR.G8167' => 'tpr', 'TWI12G1330' => 'twi', 'TWI18G1239' => 'twi', 'TWI34G0979' => 'twi', 'TWI36G0670' => 'twi', 'TWI36G0707' => 'twi', 'TWI56G0233' => 'twi', 'TWI75G1809' => 'twi', 'unitig_21.g20874' => 'ugi', 'unitig_26.g10343' => 'ugi', 'unitig_46.g18392' => 'ugi', 'unitig_52.g17178' => 'ugi', 'unitig_8.g2934' => 'ugi', 'vmacro01122' => 'vma', 'vmacro05875' => 'vma', 'vmacro06147' => 'vma', 'vmacro16191' => 'vma', 'vmacro18293' => 'vma', 'VMungo0251G3707' => 'vmu', 'VMungo0464G1521' => 'vmu', 'VMungo1215G0205' => 'vmu', 'VMungo1383G2484' => 'vmu', 'Zm00001eb079610' => 'zma', 'Zm00001eb135990' => 'zma', 'Zm00001eb183710' => 'zma', 'Zm00001eb246020' => 'zma' ) $gf_id = 'HOM05D001124' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001124' ) $data_identifier = 'HOM05D001124' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 6, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 7, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 21, 'bol' => (int) 10, 'bra' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 6, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 9, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 21, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 8, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 10, 'lsa' => (int) 8, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 8, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 9, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb246020' $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' => 'HOM05D001124', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '548', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02520' => 'bna', 'A03p06630' => 'bna', 'A05p44460' => 'bna', 'A06p08710' => 'bna', 'A06p41090' => 'bna', 'A07p32320' => 'bna', 'A08p32520' => 'bna', 'A09p10360' => 'bna', 'A10p24080' => 'bna', 'Aa31LG11G15250' => 'aar', 'Aa31LG1G1800' => 'aar', 'Aa31LG2G5120' => 'aar', 'Aa31LG2G6070' => 'aar', 'Aa31LG5G10770' => 'aar', 'Aa31sc61G90' => 'aar', 'Actinidia01352' => 'ach', 'Actinidia05983' => 'ach', 'Actinidia08133' => 'ach', 'Actinidia15101' => 'ach', 'Actinidia26379' => 'ach', 'Actinidia35778' => 'ach', 'Actinidia36123' => 'ach', 'Actinidia37436' => 'ach', 'Actinidia38730' => 'ach', 'Ah.02g128210' => 'amhyb', 'Ah.03g132990' => 'amhyb', 'Ah.14g079410' => 'amhyb', 'AL1G24640' => 'aly', 'AL2G26680' => 'aly', 'AL3G10530' => 'aly', 'AL3G45230' => 'aly', 'AL5G15230' => 'aly', 'AL5G16960' => 'aly', 'AL6G25210' => 'aly', 'Aqoxy2G00441' => 'aox', 'Aqoxy3G01236' => 'aox', 'Aqoxy5G03746' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3RQ047' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C7GMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9C8JER' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MBL6KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YXCZ83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZANX40' => 'arhy', 'AT1G12990' => 'ath', 'AT1G67880' => 'ath', 'AT2G13290' => 'ath', 'AT3G01620' => 'ath', 'AT3G26445' => 'ath', 'AT3G27540' => 'ath', 'AT5G14480' => 'ath', 'ATR0824G026' => 'atr', 'ATR1098G019' => 'atr', 'Atru.chr11.2145' => 'acertr', 'Atru.chr2.3636' => 'acertr', 'Atru.chr2.3644' => 'acertr', 'Atru.chr6.2422' => 'acertr', 'Atru.chr7.1112' => 'acertr', 'AUR62005469' => 'cqu', 'AUR62011166' => 'cqu', 'AUR62013319' => 'cqu', 'AUR62024273' => 'cqu', 'AUR62028420' => 'cqu', 'AUR62041942' => 'cqu', 'BcaB01g04969' => 'bca', 'BcaB01g06371' => 'bca', 'BcaB02g11494' => 'bca', 'BcaB03g15382' => 'bca', 'BcaB08g36994' => 'bca', 'BcaC03g13477' => 'bca', 'BcaC03g13478' => 'bca', 'BcaC03g13480' => 'bca', 'BcaC03g13481' => 'bca', 'BcaC03g13486' => 'bca', 'BcaC04g19031' => 'bca', 'BcaC04g23085' => 'bca', 'BcaC05g25094' => 'bca', 'BcaC05g25096' => 'bca', 'BcaC05g25138' => 'bca', 'BcaC05g30416' => 'bca', 'BcaC05g30455' => 'bca', 'BcaC06g30979' => 'bca', 'BcaC06g33805' => 'bca', 'BcaC08g46021' => 'bca', 'BcaNung03154' => 'bca', 'BolC2t06623H' => 'bol', 'BolC2t06632H' => 'bol', 'BolC2t06635H' => 'bol', 'BolC2t06638H' => 'bol', 'BolC3t13266H' => 'bol', 'BolC5t29776H' => 'bol', 'BolC6t38912H' => 'bol', 'BolC7t44183H' => 'bol', 'BolC9t54123H' => 'bol', 'BolC9t59107H' => 'bol', 'BraA02t05221Z' => 'bra', 'BraA03t09996Z' => 'bra', 'BraA05t23210Z' => 'bra', 'BraA06t24068Z' => 'bra', 'BraA06t27032Z' => 'bra', 'BraA08t35176Z' => 'bra', 'BraA09t36680Z' => 'bra', 'BraA10t44471Z' => 'bra', 'C02p06760' => 'bna', 'C02p06890' => 'bna', 'C02p07010' => 'bna', 'C03p07660' => 'bna', 'C05p10300' => 'bna', 'C06p38150' => 'bna', 'C07p36650' => 'bna', 'C08p15770' => 'bna', 'C09p12300' => 'bna', 'C09p62700' => 'bna', 'C09p75040' => 'bna', 'CAN.G13.1' => 'can', 'CAN.G138.4' => 'can', 'CAN.G44.6' => 'can', 'CAN.G473.19' => 'can', 'CANSAT01G0835' => 'cansat', 'CANSAT11G0246' => 'cansat', 'CANSAT11G1766' => 'cansat', 'CANSAT64G1954' => 'cansat', 'CARHR013330' => 'chi', 'CARHR060530' => 'chi', 'CARHR075300' => 'chi', 'CARHR105120' => 'chi', 'CARHR148910' => 'chi', 'CARHR198830' => 'chi', 'Carub.0001s1275' => 'cru', 'Carub.0002s1437' => 'cru', 'Carub.0003s0044' => 'cru', 'Carub.0003s2787' => 'cru', 'Carub.0005s0597' => 'cru', 'Carub.0006s1266' => 'cru', 'Ca_06935_v3' => 'car', 'Ca_13559_v3' => 'car', 'Ca_16941_v3' => 'car', 'Ca_16960_v3' => 'car', 'Ca_17775_v3' => 'car', 'Ca_30464_v3' => 'car', 'Cc06_g08160' => 'ccan', 'Cc07_g01520' => 'ccan', 'Cc11_g15810' => 'ccan', 'CDE02G2840' => 'cde', 'CDE03G0093' => 'cde', 'CDE04G2127' => 'cde', 'CDE07G1857' => 'cde', 'CDE09G1246' => 'cde', 'Cfa003412' => 'cfa', 'Cfa007341' => 'cfa', 'Cfa009220' => 'cfa', 'Ciclev10008737m.g' => 'ccl', 'Ciclev10015565m.g' => 'ccl', 'Ciclev10031761m.g' => 'ccl', 'CiPaw.03G045300' => 'cil', 'CiPaw.03G247200' => 'cil', 'CiPaw.04G029500' => 'cil', 'CiPaw.04G174000' => 'cil', 'CiPaw.05G181200' => 'cil', 'CiPaw.06G067100' => 'cil', 'ClCG05G025800' => 'cla', 'ClCG06G011400' => 'cla', 'ClCG09G019360' => 'cla', 'COL.COLO4_04827' => 'col', 'COL.COLO4_29170' => 'col', 'COL.COLO4_35131' => 'col', 'COL.COLO4_35132' => 'col', 'Cpa.g.sc33.32' => 'cpa', 'Cpa.g.sc46.29' => 'cpa', 'Cpa.g.sc796.1' => 'cpa', 'CsaV3_1G030420' => 'csa', 'CsaV3_5G027050' => 'csa', 'CsaV3_5G031040' => 'csa', 'CsaV3_UNG023130' => 'csa', 'CSS0007726' => 'camsi', 'CSS0016433' => 'camsi', 'CSS0017656' => 'camsi', 'CSS0025364' => 'camsi', 'CSS0027582' => 'camsi', 'CSS0047288' => 'camsi', 'CSS0049950' => 'camsi', 'DCAR_003843' => 'dca', 'DCAR_007052' => 'dca', 'DCAR_020884' => 'dca', 'DCAR_021730' => 'dca', 'DCAR_024423' => 'dca', 'DCAR_026509' => 'dca', 'DCAR_031158' => 'dca', 'Dinv14728' => 'din', 'Dinv15219' => 'din', 'Dinv25728' => 'din', 'Dinv33428' => 'din', 'Dinv36489' => 'din', 'Dinv41486' => 'din', 'Duzib147G0469' => 'dzi', 'Duzib168G0060' => 'dzi', 'Duzib187G1215' => 'dzi', 'Duzib248G0692' => 'dzi', 'Duzib251G0767' => 'dzi', 'Duzib264G0446' => 'dzi', 'Duzib268G0691' => 'dzi', 'ECA232G4767' => 'eca', 'ECA233G2838' => 'eca', 'ECA234G0391' => 'eca', 'ECA234G0857' => 'eca', 'ECA236G1593' => 'eca', 'ECA238G0565' => 'eca', 'ECA246G1027' => 'eca', 'ECA246G3223' => 'eca', 'ECA246G3470' => 'eca', 'EL10Ac6g13829' => 'bvu', 'EL10Ac6g14093' => 'bvu', 'EL10Ac8g18707' => 'bvu', 'Eucgr.C01369' => 'egr', 'Eucgr.H02492' => 'egr', 'Eucgr.I01733' => 'egr', 'Eucgr.J02255' => 'egr', 'Eucgr.J02257' => 'egr', 'Eucgr.J02258' => 'egr', 'FAN02G1601' => 'fan', 'FAN03G1586' => 'fan', 'FAN03G2986' => 'fan', 'FAN05G4837' => 'fan', 'FAN06G0146' => 'fan', 'FAN07G0858' => 'fan', 'FAN09G3179' => 'fan', 'FAN10G0669' => 'fan', 'FAN12G2358' => 'fan', 'FAN14G4198' => 'fan', 'FAN14G5112' => 'fan', 'FAN17G0342' => 'fan', 'FAN19G0342' => 'fan', 'FAN19G0962' => 'fan', 'FAN19G1101' => 'fan', 'FAN19G1872' => 'fan', 'FAN22G0356' => 'fan', 'FAN23G0744' => 'fan', 'FAN23G1914' => 'fan', 'FAN26G0032' => 'fan', 'FAN28G0625' => 'fan', 'FvH4_1g02710' => 'fve', 'FvH4_1g02720' => 'fve', 'FvH4_4g25670' => 'fve', 'FvH4_6g51700' => 'fve', 'FvH4_7g20170' => 'fve', 'Glyma.05G175000' => 'gma', 'Glyma.08G132300' => 'gma', 'Glyma.11G243000' => 'gma', 'Glyma.13G158900' => 'gma', 'Glyma.17G112400' => 'gma', 'Glyma.18G014100' => 'gma', 'Glyma.19G003100' => 'gma', 'Glyma.19G056500' => 'gma', 'Gohir.A01G158900' => 'ghi', 'Gohir.A05G312600' => 'ghi', 'Gohir.A05G354900' => 'ghi', 'Gohir.A07G037200' => 'ghi', 'Gohir.A09G030000' => 'ghi', 'Gohir.A12G145200' => 'ghi', 'Gohir.D01G151500' => 'ghi', 'Gohir.D04G058300' => 'ghi', 'Gohir.D05G314100' => 'ghi', 'Gohir.D07G041400' => 'ghi', 'Gohir.D09G029700' => 'ghi', 'Gohir.D12G149700' => 'ghi', 'Gorai.001G043800' => 'gra', 'Gorai.002G187800' => 'gra', 'Gorai.006G034700' => 'gra', 'Gorai.008G161200' => 'gra', 'Gorai.009G335700' => 'gra', 'Gorai.012G065000' => 'gra', 'GSVIVG01000535001' => 'vvi', 'GSVIVG01015572001' => 'vvi', 'GSVIVG01032386001' => 'vvi', 'HanXRQChr05g0138531' => 'han', 'HanXRQChr06g0174391' => 'han', 'HanXRQChr07g0199021' => 'han', 'HanXRQChr08g0208211' => 'han', 'HanXRQChr09g0255471' => 'han', 'HanXRQChr10g0315791' => 'han', 'HanXRQChr12g0371991' => 'han', 'HanXRQChr15g0475251' => 'han', 'HanXRQChr17g0540001' => 'han', 'HanXRQChr17g0548631' => 'han', 'HanXRQChr17g0569561' => 'han', 'Haze_12256' => 'cav', 'Haze_14756' => 'cav', 'Haze_25528' => 'cav', 'Hma1.2p1_0079F.1_g041020' => 'hma', 'Hma1.2p1_0818F.1_g223260' => 'hma', 'Hma1.2p1_1747F.1_g300530' => 'hma', 'HPP92_004607' => 'vpl', 'HPP92_004608' => 'vpl', 'HPP92_006181' => 'vpl', 'HPP92_012192' => 'vpl', 'HPP92_015680' => 'vpl', 'HPP92_020249' => 'vpl', 'HPP92_021376' => 'vpl', 'HPP92_024275' => 'vpl', 'Hund06031' => 'sun', 'Hund25391' => 'sun', 'Lalb_Chr07g0185371' => 'lal', 'Lalb_Chr07g0185381' => 'lal', 'Lalb_Chr12g0204011' => 'lal', 'Lalb_Chr13g0301671' => 'lal', 'Lalb_Chr14g0362851' => 'lal', 'Lalb_Chr24g0403581' => 'lal', 'Lj1g0000233' => 'lja', 'Lj2g0018120' => 'lja', 'Lj3C621T0' => 'lonja', 'Lj3P1059T14' => 'lonja', 'Lj3P611T9' => 'lonja', 'Lj3P614T13' => 'lonja', 'Lj3P615T5' => 'lonja', 'Lj4g0012315' => 'lja', 'Lj4g0026182' => 'lja', 'Lj6P813T16' => 'lonja', 'Lj7C427T7' => 'lonja', 'Lj7C427T8' => 'lonja', 'Lj7P600T41' => 'lonja', 'Lju41C42G17' => 'lonja', 'Lsat_1_v5_gn_0_47300' => 'lsa', 'Lsat_1_v5_gn_2_91280' => 'lsa', 'Lsat_1_v5_gn_3_30561' => 'lsa', 'Lsat_1_v5_gn_4_184321' => 'lsa', 'Lsat_1_v5_gn_4_4041' => 'lsa', 'Lsat_1_v5_gn_5_92000' => 'lsa', 'Lsat_1_v5_gn_8_152940' => 'lsa', 'Lsat_1_v5_gn_8_62401' => 'lsa', 'Manes.06G055900' => 'mes', 'Manes.12G022200' => 'mes', 'Manes.13G023300' => 'mes', 'Manes.14G115000' => 'mes', 'Manes.15G151700' => 'mes', 'Manes.17G111300' => 'mes', 'Mapoly0226s0009' => 'mpo', 'MBI02_g25363_MAGBIO' => 'mbi', 'MBI06_g00027_MAGBIO' => 'mbi', 'MBI10_g13034_MAGBIO' => 'mbi', 'MD09G1023400' => 'mdo', 'MD13G1100100' => 'mdo', 'MD15G1169200' => 'mdo', 'MD16G1101100' => 'mdo', 'MD17G1022900' => 'mdo', 'Medtr3g096150' => 'mtr', 'Medtr4g115070' => 'mtr', 'Medtr7g033325' => 'mtr', 'Medtr8g089840' => 'mtr', 'MELO3C010319.2' => 'cme', 'MELO3C011944.2' => 'cme', 'MELO3C021589.2' => 'cme', 'Migut.E00207' => 'egut', 'Migut.H00067' => 'egut', 'Migut.K00433' => 'egut', 'Migut.K00606' => 'egut', 'Migut.K01410' => 'egut', 'MSTRG.13347' => 'ama', 'MSTRG.24045' => 'ama', 'MSTRG.2428' => 'ama', 'MSTRG.26410' => 'ama', 'MSTRG.3139' => 'ama', 'MSTRG.3286' => 'ama', 'MSTRG.563' => 'ama', 'MSTRG.7941' => 'ama', 'Nitab4.5_0000028g0060' => 'nta', 'Nitab4.5_0000065g0260' => 'nta', 'Nitab4.5_0000112g0060' => 'nta', 'Nitab4.5_0000489g0120' => 'nta', 'Nitab4.5_0001776g0050' => 'nta', 'Nitab4.5_0001854g0010' => 'nta', 'Nitab4.5_0001860g0020' => 'nta', 'Nitab4.5_0004352g0010' => 'nta', 'Nitab4.5_0008716g0020' => 'nta', 'Nitab4.5_0008922g0010' => 'nta', 'Nn3g16693' => 'nnu', 'Nn4g22596' => 'nnu', 'Nn7g37639' => 'nnu', 'Oeu001701.1' => 'oeu', 'Oeu018149.1' => 'oeu', 'Oeu026220.1' => 'oeu', 'Oeu038635.1' => 'oeu', 'Oeu049176.1' => 'oeu', 'Oeu056706.1' => 'oeu', 'Oeu056937.1' => 'oeu', 'Oeu057540.1' => 'oeu', 'Os02g0594900' => 'osa', 'Os02g0595100' => 'osa', 'Os04g0477500' => 'osa', 'Os12g0611900' => 'osa', 'Peaxi162Scf00076g00020' => 'pax', 'Peaxi162Scf00128g00217' => 'pax', 'Peaxi162Scf00129g01640' => 'pax', 'Peaxi162Scf00669g00007' => 'pax', 'Peaxi162Scf00700g00421' => 'pax', 'Peaxi162Scf00801g00038' => 'pax', 'Peaxi162Scf00891g00025' => 'pax', 'PGR083G0909' => 'pgr', 'PGR119G1005' => 'pgr', 'PGR142G2236' => 'pgr', 'PGR142G3388' => 'pgr', 'PGSC0003DMG400004514' => 'stu', 'PGSC0003DMG400012635' => 'stu', 'PGSC0003DMG400015730' => 'stu', 'PGSC0003DMG400018611' => 'stu', 'PGSC0003DMG400030897' => 'stu', 'Phvul.001G254800' => 'pvu', 'Phvul.002G260100' => 'pvu', 'Phvul.003G167600' => 'pvu', 'Phvul.004G005100' => 'pvu', 'Potri.001G343600' => 'ptr', 'Potri.006G066700' => 'ptr', 'Potri.008G186000' => 'ptr', 'Potri.010G046900' => 'ptr', 'Potri.018G127900' => 'ptr', 'Pp3c20_17750' => 'ppa', 'Pp3c24_4380' => 'ppa', 'Prupe.1G245800' => 'ppe', 'Prupe.3G293400' => 'ppe', 'Prupe.7G247400' => 'ppe', 'Psat0s145g0120' => 'psa', 'Psat0s595g0040' => 'psa', 'Psat0s595g0120' => 'psa', 'Psat3g175040' => 'psa', 'Psat7g058120' => 'psa', 'PSO017G0428' => 'pso', 'PSO063G7510' => 'pso', 'PSO067G0046' => 'pso', 'PSO478G1073' => 'pso', 'PSO675G3677' => 'pso', 'PSO675G6558' => 'pso', 'PSO675G7520' => 'pso', 'PSO675G8959' => 'pso', 'QL02p074089' => 'qlo', 'QL02p089614' => 'qlo', 'QL03p057736' => 'qlo', 'RcHm_v2.0_Chr1g0364131' => 'rch', 'RcHm_v2.0_Chr2g0087801' => 'rch', 'RcHm_v2.0_Chr2g0087821' => 'rch', 'RcHm_v2.0_Chr2g0173231' => 'rch', 'RcHm_v2.0_Chr4g0433111' => 'rch', 'Rhsim03G0250300' => 'rsi', 'Rhsim08G0048400' => 'rsi', 'Rhsim10G0014800' => 'rsi', 'Rhsim12G0040100' => 'rsi', 'Rhsim12G0109700' => 'rsi', 'Sabra06G0049600' => 'sbr', 'Sabra08G0141000' => 'sbr', 'Sabra10G0021400' => 'sbr', 'Sabra16G0222900' => 'sbr', 'Sabra18G0108600' => 'sbr', 'SalBow1G0433' => 'sbo', 'SalBow1G2038' => 'sbo', 'SalBow1G5003' => 'sbo', 'SalBow7G1197' => 'sbo', 'SalBow8G3506' => 'sbo', 'Sc03g0007300' => 'sci', 'Sc11g0000950' => 'sci', 'Sc14g0008750' => 'sci', 'Sc18g0000420' => 'sci', 'Sed0006754' => 'sed', 'Sed0008741' => 'sed', 'Sed0017172' => 'sed', 'Sed0018925' => 'sed', 'Sed0023326' => 'sed', 'Sed0025909' => 'sed', 'SEGI_05333' => 'sgi', 'SEGI_10362' => 'sgi', 'SEGI_13380' => 'sgi', 'SEGI_24306' => 'sgi', 'SEGI_29077' => 'sgi', 'SEGI_29095' => 'sgi', 'SEGI_36534' => 'sgi', 'SEGI_37506' => 'sgi', 'SEGI_38321' => 'sgi', 'SGA_v2.0_scaffold307G48031' => 'sas', 'SGA_v2.0_scaffold47G17507' => 'sas', 'SGA_v2.0_scaffold63G21736' => 'sas', 'SGA_v2.0_scaffold87G27070' => 'sas', 'SHI17794' => 'shi', 'SHI28851' => 'shi', 'SMO165G0155' => 'smo', 'SMO340G0217' => 'smo', 'SMO367G1210' => 'smo', 'Solyc02g093430.3' => 'sly', 'Solyc05g013580.4' => 'sly', 'Solyc07g008030.3' => 'sly', 'Solyc12g035470.2' => 'sly', 'Sopen02g038020' => 'spe', 'Sopen05g008490' => 'spe', 'Sopen07g003910' => 'spe', 'Sopen12g015240' => 'spe', 'Sp1g11550' => 'spa', 'Sp2g16710' => 'spa', 'Sp3g00430' => 'spa', 'Sp3g26780' => 'spa', 'Sp5g22900' => 'spa', 'Sp6g29530' => 'spa', 'TAR371G0794' => 'tar', 'TAR374G0164' => 'tar', 'TAR622G0165' => 'tar', 'TAR626G0929' => 'tar', 'TAR629G2155' => 'tar', 'THA.LOC104805282' => 'tha', 'THA.LOC104805363' => 'tha', 'THA.LOC104808968' => 'tha', 'THA.LOC104821093' => 'tha', 'THA.LOC104823953' => 'tha', 'THA.LOC104825562' => 'tha', 'THA.LOC104825665' => 'tha', 'Thecc.02G261400' => 'tca', 'Thecc.04G019200' => 'tca', 'Thecc.09G130400' => 'tca', 'Thhalv10004374m.g' => 'esa', 'Thhalv10007850m.g' => 'esa', 'Thhalv10013782m.g' => 'esa', 'Thhalv10018686m.g' => 'esa', 'Thhalv10020899m.g' => 'esa', 'Thhalv10022755m.g' => 'esa', 'TPR.G23851' => 'tpr', 'TPR.G26500' => 'tpr', 'TPR.G27267' => 'tpr', 'TPR.G32001' => 'tpr', 'TPR.G6251' => 'tpr', 'TPR.G8167' => 'tpr', 'TWI12G1330' => 'twi', 'TWI18G1239' => 'twi', 'TWI34G0979' => 'twi', 'TWI36G0670' => 'twi', 'TWI36G0707' => 'twi', 'TWI56G0233' => 'twi', 'TWI75G1809' => 'twi', 'unitig_21.g20874' => 'ugi', 'unitig_26.g10343' => 'ugi', 'unitig_46.g18392' => 'ugi', 'unitig_52.g17178' => 'ugi', 'unitig_8.g2934' => 'ugi', 'vmacro01122' => 'vma', 'vmacro05875' => 'vma', 'vmacro06147' => 'vma', 'vmacro16191' => 'vma', 'vmacro18293' => 'vma', 'VMungo0251G3707' => 'vmu', 'VMungo0464G1521' => 'vmu', 'VMungo1215G0205' => 'vmu', 'VMungo1383G2484' => 'vmu', 'Zm00001eb079610' => 'zma', 'Zm00001eb135990' => 'zma', 'Zm00001eb183710' => 'zma', 'Zm00001eb246020' => 'zma' ), 'gf_id' => 'HOM05D001124', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001124' ), 'data_identifier' => 'HOM05D001124', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001124', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '548', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02520' => 'bna', 'A03p06630' => 'bna', 'A05p44460' => 'bna', 'A06p08710' => 'bna', 'A06p41090' => 'bna', 'A07p32320' => 'bna', 'A08p32520' => 'bna', 'A09p10360' => 'bna', 'A10p24080' => 'bna', 'Aa31LG11G15250' => 'aar', 'Aa31LG1G1800' => 'aar', 'Aa31LG2G5120' => 'aar', 'Aa31LG2G6070' => 'aar', 'Aa31LG5G10770' => 'aar', 'Aa31sc61G90' => 'aar', 'Actinidia01352' => 'ach', 'Actinidia05983' => 'ach', 'Actinidia08133' => 'ach', 'Actinidia15101' => 'ach', 'Actinidia26379' => 'ach', 'Actinidia35778' => 'ach', 'Actinidia36123' => 'ach', 'Actinidia37436' => 'ach', 'Actinidia38730' => 'ach', 'Ah.02g128210' => 'amhyb', 'Ah.03g132990' => 'amhyb', 'Ah.14g079410' => 'amhyb', 'AL1G24640' => 'aly', 'AL2G26680' => 'aly', 'AL3G10530' => 'aly', 'AL3G45230' => 'aly', 'AL5G15230' => 'aly', 'AL5G16960' => 'aly', 'AL6G25210' => 'aly', 'Aqoxy2G00441' => 'aox', 'Aqoxy3G01236' => 'aox', 'Aqoxy5G03746' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3RQ047' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C7GMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9C8JER' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MBL6KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YXCZ83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZANX40' => 'arhy', 'AT1G12990' => 'ath', 'AT1G67880' => 'ath', 'AT2G13290' => 'ath', 'AT3G01620' => 'ath', 'AT3G26445' => 'ath', 'AT3G27540' => 'ath', 'AT5G14480' => 'ath', 'ATR0824G026' => 'atr', 'ATR1098G019' => 'atr', 'Atru.chr11.2145' => 'acertr', 'Atru.chr2.3636' => 'acertr', 'Atru.chr2.3644' => 'acertr', 'Atru.chr6.2422' => 'acertr', 'Atru.chr7.1112' => 'acertr', 'AUR62005469' => 'cqu', 'AUR62011166' => 'cqu', 'AUR62013319' => 'cqu', 'AUR62024273' => 'cqu', 'AUR62028420' => 'cqu', 'AUR62041942' => 'cqu', 'BcaB01g04969' => 'bca', 'BcaB01g06371' => 'bca', 'BcaB02g11494' => 'bca', 'BcaB03g15382' => 'bca', 'BcaB08g36994' => 'bca', 'BcaC03g13477' => 'bca', 'BcaC03g13478' => 'bca', 'BcaC03g13480' => 'bca', 'BcaC03g13481' => 'bca', 'BcaC03g13486' => 'bca', 'BcaC04g19031' => 'bca', 'BcaC04g23085' => 'bca', 'BcaC05g25094' => 'bca', 'BcaC05g25096' => 'bca', 'BcaC05g25138' => 'bca', 'BcaC05g30416' => 'bca', 'BcaC05g30455' => 'bca', 'BcaC06g30979' => 'bca', 'BcaC06g33805' => 'bca', 'BcaC08g46021' => 'bca', 'BcaNung03154' => 'bca', 'BolC2t06623H' => 'bol', 'BolC2t06632H' => 'bol', 'BolC2t06635H' => 'bol', 'BolC2t06638H' => 'bol', 'BolC3t13266H' => 'bol', 'BolC5t29776H' => 'bol', 'BolC6t38912H' => 'bol', 'BolC7t44183H' => 'bol', 'BolC9t54123H' => 'bol', 'BolC9t59107H' => 'bol', 'BraA02t05221Z' => 'bra', 'BraA03t09996Z' => 'bra', 'BraA05t23210Z' => 'bra', 'BraA06t24068Z' => 'bra', 'BraA06t27032Z' => 'bra', 'BraA08t35176Z' => 'bra', 'BraA09t36680Z' => 'bra', 'BraA10t44471Z' => 'bra', 'C02p06760' => 'bna', 'C02p06890' => 'bna', 'C02p07010' => 'bna', 'C03p07660' => 'bna', 'C05p10300' => 'bna', 'C06p38150' => 'bna', 'C07p36650' => 'bna', 'C08p15770' => 'bna', 'C09p12300' => 'bna', 'C09p62700' => 'bna', 'C09p75040' => 'bna', 'CAN.G13.1' => 'can', 'CAN.G138.4' => 'can', 'CAN.G44.6' => 'can', 'CAN.G473.19' => 'can', 'CANSAT01G0835' => 'cansat', 'CANSAT11G0246' => 'cansat', 'CANSAT11G1766' => 'cansat', 'CANSAT64G1954' => 'cansat', 'CARHR013330' => 'chi', 'CARHR060530' => 'chi', 'CARHR075300' => 'chi', 'CARHR105120' => 'chi', 'CARHR148910' => 'chi', 'CARHR198830' => 'chi', 'Carub.0001s1275' => 'cru', 'Carub.0002s1437' => 'cru', 'Carub.0003s0044' => 'cru', 'Carub.0003s2787' => 'cru', 'Carub.0005s0597' => 'cru', 'Carub.0006s1266' => 'cru', 'Ca_06935_v3' => 'car', 'Ca_13559_v3' => 'car', 'Ca_16941_v3' => 'car', 'Ca_16960_v3' => 'car', 'Ca_17775_v3' => 'car', 'Ca_30464_v3' => 'car', 'Cc06_g08160' => 'ccan', 'Cc07_g01520' => 'ccan', 'Cc11_g15810' => 'ccan', 'CDE02G2840' => 'cde', 'CDE03G0093' => 'cde', 'CDE04G2127' => 'cde', 'CDE07G1857' => 'cde', 'CDE09G1246' => 'cde', 'Cfa003412' => 'cfa', 'Cfa007341' => 'cfa', 'Cfa009220' => 'cfa', 'Ciclev10008737m.g' => 'ccl', 'Ciclev10015565m.g' => 'ccl', 'Ciclev10031761m.g' => 'ccl', 'CiPaw.03G045300' => 'cil', 'CiPaw.03G247200' => 'cil', 'CiPaw.04G029500' => 'cil', 'CiPaw.04G174000' => 'cil', 'CiPaw.05G181200' => 'cil', 'CiPaw.06G067100' => 'cil', 'ClCG05G025800' => 'cla', 'ClCG06G011400' => 'cla', 'ClCG09G019360' => 'cla', 'COL.COLO4_04827' => 'col', 'COL.COLO4_29170' => 'col', 'COL.COLO4_35131' => 'col', 'COL.COLO4_35132' => 'col', 'Cpa.g.sc33.32' => 'cpa', 'Cpa.g.sc46.29' => 'cpa', 'Cpa.g.sc796.1' => 'cpa', 'CsaV3_1G030420' => 'csa', 'CsaV3_5G027050' => 'csa', 'CsaV3_5G031040' => 'csa', 'CsaV3_UNG023130' => 'csa', 'CSS0007726' => 'camsi', 'CSS0016433' => 'camsi', 'CSS0017656' => 'camsi', 'CSS0025364' => 'camsi', 'CSS0027582' => 'camsi', 'CSS0047288' => 'camsi', 'CSS0049950' => 'camsi', 'DCAR_003843' => 'dca', 'DCAR_007052' => 'dca', 'DCAR_020884' => 'dca', 'DCAR_021730' => 'dca', 'DCAR_024423' => 'dca', 'DCAR_026509' => 'dca', 'DCAR_031158' => 'dca', 'Dinv14728' => 'din', 'Dinv15219' => 'din', 'Dinv25728' => 'din', 'Dinv33428' => 'din', 'Dinv36489' => 'din', 'Dinv41486' => 'din', 'Duzib147G0469' => 'dzi', 'Duzib168G0060' => 'dzi', 'Duzib187G1215' => 'dzi', 'Duzib248G0692' => 'dzi', 'Duzib251G0767' => 'dzi', 'Duzib264G0446' => 'dzi', 'Duzib268G0691' => 'dzi', 'ECA232G4767' => 'eca', 'ECA233G2838' => 'eca', 'ECA234G0391' => 'eca', 'ECA234G0857' => 'eca', 'ECA236G1593' => 'eca', 'ECA238G0565' => 'eca', 'ECA246G1027' => 'eca', 'ECA246G3223' => 'eca', 'ECA246G3470' => 'eca', 'EL10Ac6g13829' => 'bvu', 'EL10Ac6g14093' => 'bvu', 'EL10Ac8g18707' => 'bvu', 'Eucgr.C01369' => 'egr', 'Eucgr.H02492' => 'egr', 'Eucgr.I01733' => 'egr', 'Eucgr.J02255' => 'egr', 'Eucgr.J02257' => 'egr', 'Eucgr.J02258' => 'egr', 'FAN02G1601' => 'fan', 'FAN03G1586' => 'fan', 'FAN03G2986' => 'fan', 'FAN05G4837' => 'fan', 'FAN06G0146' => 'fan', 'FAN07G0858' => 'fan', 'FAN09G3179' => 'fan', 'FAN10G0669' => 'fan', 'FAN12G2358' => 'fan', 'FAN14G4198' => 'fan', 'FAN14G5112' => 'fan', 'FAN17G0342' => 'fan', 'FAN19G0342' => 'fan', 'FAN19G0962' => 'fan', 'FAN19G1101' => 'fan', 'FAN19G1872' => 'fan', 'FAN22G0356' => 'fan', 'FAN23G0744' => 'fan', 'FAN23G1914' => 'fan', 'FAN26G0032' => 'fan', 'FAN28G0625' => 'fan', 'FvH4_1g02710' => 'fve', 'FvH4_1g02720' => 'fve', 'FvH4_4g25670' => 'fve', 'FvH4_6g51700' => 'fve', 'FvH4_7g20170' => 'fve', 'Glyma.05G175000' => 'gma', 'Glyma.08G132300' => 'gma', 'Glyma.11G243000' => 'gma', 'Glyma.13G158900' => 'gma', 'Glyma.17G112400' => 'gma', 'Glyma.18G014100' => 'gma', 'Glyma.19G003100' => 'gma', 'Glyma.19G056500' => 'gma', 'Gohir.A01G158900' => 'ghi', 'Gohir.A05G312600' => 'ghi', 'Gohir.A05G354900' => 'ghi', 'Gohir.A07G037200' => 'ghi', 'Gohir.A09G030000' => 'ghi', 'Gohir.A12G145200' => 'ghi', 'Gohir.D01G151500' => 'ghi', 'Gohir.D04G058300' => 'ghi', 'Gohir.D05G314100' => 'ghi', 'Gohir.D07G041400' => 'ghi', 'Gohir.D09G029700' => 'ghi', 'Gohir.D12G149700' => 'ghi', 'Gorai.001G043800' => 'gra', 'Gorai.002G187800' => 'gra', 'Gorai.006G034700' => 'gra', 'Gorai.008G161200' => 'gra', 'Gorai.009G335700' => 'gra', 'Gorai.012G065000' => 'gra', 'GSVIVG01000535001' => 'vvi', 'GSVIVG01015572001' => 'vvi', 'GSVIVG01032386001' => 'vvi', 'HanXRQChr05g0138531' => 'han', 'HanXRQChr06g0174391' => 'han', 'HanXRQChr07g0199021' => 'han', 'HanXRQChr08g0208211' => 'han', 'HanXRQChr09g0255471' => 'han', 'HanXRQChr10g0315791' => 'han', 'HanXRQChr12g0371991' => 'han', 'HanXRQChr15g0475251' => 'han', 'HanXRQChr17g0540001' => 'han', 'HanXRQChr17g0548631' => 'han', 'HanXRQChr17g0569561' => 'han', 'Haze_12256' => 'cav', 'Haze_14756' => 'cav', 'Haze_25528' => 'cav', 'Hma1.2p1_0079F.1_g041020' => 'hma', 'Hma1.2p1_0818F.1_g223260' => 'hma', 'Hma1.2p1_1747F.1_g300530' => 'hma', 'HPP92_004607' => 'vpl', 'HPP92_004608' => 'vpl', 'HPP92_006181' => 'vpl', 'HPP92_012192' => 'vpl', 'HPP92_015680' => 'vpl', 'HPP92_020249' => 'vpl', 'HPP92_021376' => 'vpl', 'HPP92_024275' => 'vpl', 'Hund06031' => 'sun', 'Hund25391' => 'sun', 'Lalb_Chr07g0185371' => 'lal', 'Lalb_Chr07g0185381' => 'lal', 'Lalb_Chr12g0204011' => 'lal', 'Lalb_Chr13g0301671' => 'lal', 'Lalb_Chr14g0362851' => 'lal', 'Lalb_Chr24g0403581' => 'lal', 'Lj1g0000233' => 'lja', 'Lj2g0018120' => 'lja', 'Lj3C621T0' => 'lonja', 'Lj3P1059T14' => 'lonja', 'Lj3P611T9' => 'lonja', 'Lj3P614T13' => 'lonja', 'Lj3P615T5' => 'lonja', 'Lj4g0012315' => 'lja', 'Lj4g0026182' => 'lja', 'Lj6P813T16' => 'lonja', 'Lj7C427T7' => 'lonja', 'Lj7C427T8' => 'lonja', 'Lj7P600T41' => 'lonja', 'Lju41C42G17' => 'lonja', 'Lsat_1_v5_gn_0_47300' => 'lsa', 'Lsat_1_v5_gn_2_91280' => 'lsa', 'Lsat_1_v5_gn_3_30561' => 'lsa', 'Lsat_1_v5_gn_4_184321' => 'lsa', 'Lsat_1_v5_gn_4_4041' => 'lsa', 'Lsat_1_v5_gn_5_92000' => 'lsa', 'Lsat_1_v5_gn_8_152940' => 'lsa', 'Lsat_1_v5_gn_8_62401' => 'lsa', 'Manes.06G055900' => 'mes', 'Manes.12G022200' => 'mes', 'Manes.13G023300' => 'mes', 'Manes.14G115000' => 'mes', 'Manes.15G151700' => 'mes', 'Manes.17G111300' => 'mes', 'Mapoly0226s0009' => 'mpo', 'MBI02_g25363_MAGBIO' => 'mbi', 'MBI06_g00027_MAGBIO' => 'mbi', 'MBI10_g13034_MAGBIO' => 'mbi', 'MD09G1023400' => 'mdo', 'MD13G1100100' => 'mdo', 'MD15G1169200' => 'mdo', 'MD16G1101100' => 'mdo', 'MD17G1022900' => 'mdo', 'Medtr3g096150' => 'mtr', 'Medtr4g115070' => 'mtr', 'Medtr7g033325' => 'mtr', 'Medtr8g089840' => 'mtr', 'MELO3C010319.2' => 'cme', 'MELO3C011944.2' => 'cme', 'MELO3C021589.2' => 'cme', 'Migut.E00207' => 'egut', 'Migut.H00067' => 'egut', 'Migut.K00433' => 'egut', 'Migut.K00606' => 'egut', 'Migut.K01410' => 'egut', 'MSTRG.13347' => 'ama', 'MSTRG.24045' => 'ama', 'MSTRG.2428' => 'ama', 'MSTRG.26410' => 'ama', 'MSTRG.3139' => 'ama', 'MSTRG.3286' => 'ama', 'MSTRG.563' => 'ama', 'MSTRG.7941' => 'ama', 'Nitab4.5_0000028g0060' => 'nta', 'Nitab4.5_0000065g0260' => 'nta', 'Nitab4.5_0000112g0060' => 'nta', 'Nitab4.5_0000489g0120' => 'nta', 'Nitab4.5_0001776g0050' => 'nta', 'Nitab4.5_0001854g0010' => 'nta', 'Nitab4.5_0001860g0020' => 'nta', 'Nitab4.5_0004352g0010' => 'nta', 'Nitab4.5_0008716g0020' => 'nta', 'Nitab4.5_0008922g0010' => 'nta', 'Nn3g16693' => 'nnu', 'Nn4g22596' => 'nnu', 'Nn7g37639' => 'nnu', 'Oeu001701.1' => 'oeu', 'Oeu018149.1' => 'oeu', 'Oeu026220.1' => 'oeu', 'Oeu038635.1' => 'oeu', 'Oeu049176.1' => 'oeu', 'Oeu056706.1' => 'oeu', 'Oeu056937.1' => 'oeu', 'Oeu057540.1' => 'oeu', 'Os02g0594900' => 'osa', 'Os02g0595100' => 'osa', 'Os04g0477500' => 'osa', 'Os12g0611900' => 'osa', 'Peaxi162Scf00076g00020' => 'pax', 'Peaxi162Scf00128g00217' => 'pax', 'Peaxi162Scf00129g01640' => 'pax', 'Peaxi162Scf00669g00007' => 'pax', 'Peaxi162Scf00700g00421' => 'pax', 'Peaxi162Scf00801g00038' => 'pax', 'Peaxi162Scf00891g00025' => 'pax', 'PGR083G0909' => 'pgr', 'PGR119G1005' => 'pgr', 'PGR142G2236' => 'pgr', 'PGR142G3388' => 'pgr', 'PGSC0003DMG400004514' => 'stu', 'PGSC0003DMG400012635' => 'stu', 'PGSC0003DMG400015730' => 'stu', 'PGSC0003DMG400018611' => 'stu', 'PGSC0003DMG400030897' => 'stu', 'Phvul.001G254800' => 'pvu', 'Phvul.002G260100' => 'pvu', 'Phvul.003G167600' => 'pvu', 'Phvul.004G005100' => 'pvu', 'Potri.001G343600' => 'ptr', 'Potri.006G066700' => 'ptr', 'Potri.008G186000' => 'ptr', 'Potri.010G046900' => 'ptr', 'Potri.018G127900' => 'ptr', 'Pp3c20_17750' => 'ppa', 'Pp3c24_4380' => 'ppa', 'Prupe.1G245800' => 'ppe', 'Prupe.3G293400' => 'ppe', 'Prupe.7G247400' => 'ppe', 'Psat0s145g0120' => 'psa', 'Psat0s595g0040' => 'psa', 'Psat0s595g0120' => 'psa', 'Psat3g175040' => 'psa', 'Psat7g058120' => 'psa', 'PSO017G0428' => 'pso', 'PSO063G7510' => 'pso', 'PSO067G0046' => 'pso', 'PSO478G1073' => 'pso', 'PSO675G3677' => 'pso', 'PSO675G6558' => 'pso', 'PSO675G7520' => 'pso', 'PSO675G8959' => 'pso', 'QL02p074089' => 'qlo', 'QL02p089614' => 'qlo', 'QL03p057736' => 'qlo', 'RcHm_v2.0_Chr1g0364131' => 'rch', 'RcHm_v2.0_Chr2g0087801' => 'rch', 'RcHm_v2.0_Chr2g0087821' => 'rch', 'RcHm_v2.0_Chr2g0173231' => 'rch', 'RcHm_v2.0_Chr4g0433111' => 'rch', 'Rhsim03G0250300' => 'rsi', 'Rhsim08G0048400' => 'rsi', 'Rhsim10G0014800' => 'rsi', 'Rhsim12G0040100' => 'rsi', 'Rhsim12G0109700' => 'rsi', 'Sabra06G0049600' => 'sbr', 'Sabra08G0141000' => 'sbr', 'Sabra10G0021400' => 'sbr', 'Sabra16G0222900' => 'sbr', 'Sabra18G0108600' => 'sbr', 'SalBow1G0433' => 'sbo', 'SalBow1G2038' => 'sbo', 'SalBow1G5003' => 'sbo', 'SalBow7G1197' => 'sbo', 'SalBow8G3506' => 'sbo', 'Sc03g0007300' => 'sci', 'Sc11g0000950' => 'sci', 'Sc14g0008750' => 'sci', 'Sc18g0000420' => 'sci', 'Sed0006754' => 'sed', 'Sed0008741' => 'sed', 'Sed0017172' => 'sed', 'Sed0018925' => 'sed', 'Sed0023326' => 'sed', 'Sed0025909' => 'sed', 'SEGI_05333' => 'sgi', 'SEGI_10362' => 'sgi', 'SEGI_13380' => 'sgi', 'SEGI_24306' => 'sgi', 'SEGI_29077' => 'sgi', 'SEGI_29095' => 'sgi', 'SEGI_36534' => 'sgi', 'SEGI_37506' => 'sgi', 'SEGI_38321' => 'sgi', 'SGA_v2.0_scaffold307G48031' => 'sas', 'SGA_v2.0_scaffold47G17507' => 'sas', 'SGA_v2.0_scaffold63G21736' => 'sas', 'SGA_v2.0_scaffold87G27070' => 'sas', 'SHI17794' => 'shi', 'SHI28851' => 'shi', 'SMO165G0155' => 'smo', 'SMO340G0217' => 'smo', 'SMO367G1210' => 'smo', 'Solyc02g093430.3' => 'sly', 'Solyc05g013580.4' => 'sly', 'Solyc07g008030.3' => 'sly', 'Solyc12g035470.2' => 'sly', 'Sopen02g038020' => 'spe', 'Sopen05g008490' => 'spe', 'Sopen07g003910' => 'spe', 'Sopen12g015240' => 'spe', 'Sp1g11550' => 'spa', 'Sp2g16710' => 'spa', 'Sp3g00430' => 'spa', 'Sp3g26780' => 'spa', 'Sp5g22900' => 'spa', 'Sp6g29530' => 'spa', 'TAR371G0794' => 'tar', 'TAR374G0164' => 'tar', 'TAR622G0165' => 'tar', 'TAR626G0929' => 'tar', 'TAR629G2155' => 'tar', 'THA.LOC104805282' => 'tha', 'THA.LOC104805363' => 'tha', 'THA.LOC104808968' => 'tha', 'THA.LOC104821093' => 'tha', 'THA.LOC104823953' => 'tha', 'THA.LOC104825562' => 'tha', 'THA.LOC104825665' => 'tha', 'Thecc.02G261400' => 'tca', 'Thecc.04G019200' => 'tca', 'Thecc.09G130400' => 'tca', 'Thhalv10004374m.g' => 'esa', 'Thhalv10007850m.g' => 'esa', 'Thhalv10013782m.g' => 'esa', 'Thhalv10018686m.g' => 'esa', 'Thhalv10020899m.g' => 'esa', 'Thhalv10022755m.g' => 'esa', 'TPR.G23851' => 'tpr', 'TPR.G26500' => 'tpr', 'TPR.G27267' => 'tpr', 'TPR.G32001' => 'tpr', 'TPR.G6251' => 'tpr', 'TPR.G8167' => 'tpr', 'TWI12G1330' => 'twi', 'TWI18G1239' => 'twi', 'TWI34G0979' => 'twi', 'TWI36G0670' => 'twi', 'TWI36G0707' => 'twi', 'TWI56G0233' => 'twi', 'TWI75G1809' => 'twi', 'unitig_21.g20874' => 'ugi', 'unitig_26.g10343' => 'ugi', 'unitig_46.g18392' => 'ugi', 'unitig_52.g17178' => 'ugi', 'unitig_8.g2934' => 'ugi', 'vmacro01122' => 'vma', 'vmacro05875' => 'vma', 'vmacro06147' => 'vma', 'vmacro16191' => 'vma', 'vmacro18293' => 'vma', 'VMungo0251G3707' => 'vmu', 'VMungo0464G1521' => 'vmu', 'VMungo1215G0205' => 'vmu', 'VMungo1383G2484' => 'vmu', 'Zm00001eb079610' => 'zma', 'Zm00001eb135990' => 'zma', 'Zm00001eb183710' => 'zma', 'Zm00001eb246020' => 'zma' ) $gf_id = 'HOM05D001124' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001124' ) $data_identifier = 'HOM05D001124' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 6, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 7, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 21, 'bol' => (int) 10, 'bra' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 6, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 9, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 21, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 8, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 10, 'lsa' => (int) 8, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 8, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 9, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb246020' $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' => 'HOM05D001124', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '548', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02520' => 'bna', 'A03p06630' => 'bna', 'A05p44460' => 'bna', 'A06p08710' => 'bna', 'A06p41090' => 'bna', 'A07p32320' => 'bna', 'A08p32520' => 'bna', 'A09p10360' => 'bna', 'A10p24080' => 'bna', 'Aa31LG11G15250' => 'aar', 'Aa31LG1G1800' => 'aar', 'Aa31LG2G5120' => 'aar', 'Aa31LG2G6070' => 'aar', 'Aa31LG5G10770' => 'aar', 'Aa31sc61G90' => 'aar', 'Actinidia01352' => 'ach', 'Actinidia05983' => 'ach', 'Actinidia08133' => 'ach', 'Actinidia15101' => 'ach', 'Actinidia26379' => 'ach', 'Actinidia35778' => 'ach', 'Actinidia36123' => 'ach', 'Actinidia37436' => 'ach', 'Actinidia38730' => 'ach', 'Ah.02g128210' => 'amhyb', 'Ah.03g132990' => 'amhyb', 'Ah.14g079410' => 'amhyb', 'AL1G24640' => 'aly', 'AL2G26680' => 'aly', 'AL3G10530' => 'aly', 'AL3G45230' => 'aly', 'AL5G15230' => 'aly', 'AL5G16960' => 'aly', 'AL6G25210' => 'aly', 'Aqoxy2G00441' => 'aox', 'Aqoxy3G01236' => 'aox', 'Aqoxy5G03746' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3RQ047' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C7GMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9C8JER' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MBL6KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YXCZ83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZANX40' => 'arhy', 'AT1G12990' => 'ath', 'AT1G67880' => 'ath', 'AT2G13290' => 'ath', 'AT3G01620' => 'ath', 'AT3G26445' => 'ath', 'AT3G27540' => 'ath', 'AT5G14480' => 'ath', 'ATR0824G026' => 'atr', 'ATR1098G019' => 'atr', 'Atru.chr11.2145' => 'acertr', 'Atru.chr2.3636' => 'acertr', 'Atru.chr2.3644' => 'acertr', 'Atru.chr6.2422' => 'acertr', 'Atru.chr7.1112' => 'acertr', 'AUR62005469' => 'cqu', 'AUR62011166' => 'cqu', 'AUR62013319' => 'cqu', 'AUR62024273' => 'cqu', 'AUR62028420' => 'cqu', 'AUR62041942' => 'cqu', 'BcaB01g04969' => 'bca', 'BcaB01g06371' => 'bca', 'BcaB02g11494' => 'bca', 'BcaB03g15382' => 'bca', 'BcaB08g36994' => 'bca', 'BcaC03g13477' => 'bca', 'BcaC03g13478' => 'bca', 'BcaC03g13480' => 'bca', 'BcaC03g13481' => 'bca', 'BcaC03g13486' => 'bca', 'BcaC04g19031' => 'bca', 'BcaC04g23085' => 'bca', 'BcaC05g25094' => 'bca', 'BcaC05g25096' => 'bca', 'BcaC05g25138' => 'bca', 'BcaC05g30416' => 'bca', 'BcaC05g30455' => 'bca', 'BcaC06g30979' => 'bca', 'BcaC06g33805' => 'bca', 'BcaC08g46021' => 'bca', 'BcaNung03154' => 'bca', 'BolC2t06623H' => 'bol', 'BolC2t06632H' => 'bol', 'BolC2t06635H' => 'bol', 'BolC2t06638H' => 'bol', 'BolC3t13266H' => 'bol', 'BolC5t29776H' => 'bol', 'BolC6t38912H' => 'bol', 'BolC7t44183H' => 'bol', 'BolC9t54123H' => 'bol', 'BolC9t59107H' => 'bol', 'BraA02t05221Z' => 'bra', 'BraA03t09996Z' => 'bra', 'BraA05t23210Z' => 'bra', 'BraA06t24068Z' => 'bra', 'BraA06t27032Z' => 'bra', 'BraA08t35176Z' => 'bra', 'BraA09t36680Z' => 'bra', 'BraA10t44471Z' => 'bra', 'C02p06760' => 'bna', 'C02p06890' => 'bna', 'C02p07010' => 'bna', 'C03p07660' => 'bna', 'C05p10300' => 'bna', 'C06p38150' => 'bna', 'C07p36650' => 'bna', 'C08p15770' => 'bna', 'C09p12300' => 'bna', 'C09p62700' => 'bna', 'C09p75040' => 'bna', 'CAN.G13.1' => 'can', 'CAN.G138.4' => 'can', 'CAN.G44.6' => 'can', 'CAN.G473.19' => 'can', 'CANSAT01G0835' => 'cansat', 'CANSAT11G0246' => 'cansat', 'CANSAT11G1766' => 'cansat', 'CANSAT64G1954' => 'cansat', 'CARHR013330' => 'chi', 'CARHR060530' => 'chi', 'CARHR075300' => 'chi', 'CARHR105120' => 'chi', 'CARHR148910' => 'chi', 'CARHR198830' => 'chi', 'Carub.0001s1275' => 'cru', 'Carub.0002s1437' => 'cru', 'Carub.0003s0044' => 'cru', 'Carub.0003s2787' => 'cru', 'Carub.0005s0597' => 'cru', 'Carub.0006s1266' => 'cru', 'Ca_06935_v3' => 'car', 'Ca_13559_v3' => 'car', 'Ca_16941_v3' => 'car', 'Ca_16960_v3' => 'car', 'Ca_17775_v3' => 'car', 'Ca_30464_v3' => 'car', 'Cc06_g08160' => 'ccan', 'Cc07_g01520' => 'ccan', 'Cc11_g15810' => 'ccan', 'CDE02G2840' => 'cde', 'CDE03G0093' => 'cde', 'CDE04G2127' => 'cde', 'CDE07G1857' => 'cde', 'CDE09G1246' => 'cde', 'Cfa003412' => 'cfa', 'Cfa007341' => 'cfa', 'Cfa009220' => 'cfa', 'Ciclev10008737m.g' => 'ccl', 'Ciclev10015565m.g' => 'ccl', 'Ciclev10031761m.g' => 'ccl', 'CiPaw.03G045300' => 'cil', 'CiPaw.03G247200' => 'cil', 'CiPaw.04G029500' => 'cil', 'CiPaw.04G174000' => 'cil', 'CiPaw.05G181200' => 'cil', 'CiPaw.06G067100' => 'cil', 'ClCG05G025800' => 'cla', 'ClCG06G011400' => 'cla', 'ClCG09G019360' => 'cla', 'COL.COLO4_04827' => 'col', 'COL.COLO4_29170' => 'col', 'COL.COLO4_35131' => 'col', 'COL.COLO4_35132' => 'col', 'Cpa.g.sc33.32' => 'cpa', 'Cpa.g.sc46.29' => 'cpa', 'Cpa.g.sc796.1' => 'cpa', 'CsaV3_1G030420' => 'csa', 'CsaV3_5G027050' => 'csa', 'CsaV3_5G031040' => 'csa', 'CsaV3_UNG023130' => 'csa', 'CSS0007726' => 'camsi', 'CSS0016433' => 'camsi', 'CSS0017656' => 'camsi', 'CSS0025364' => 'camsi', 'CSS0027582' => 'camsi', 'CSS0047288' => 'camsi', 'CSS0049950' => 'camsi', 'DCAR_003843' => 'dca', 'DCAR_007052' => 'dca', 'DCAR_020884' => 'dca', 'DCAR_021730' => 'dca', 'DCAR_024423' => 'dca', 'DCAR_026509' => 'dca', 'DCAR_031158' => 'dca', 'Dinv14728' => 'din', 'Dinv15219' => 'din', 'Dinv25728' => 'din', 'Dinv33428' => 'din', 'Dinv36489' => 'din', 'Dinv41486' => 'din', 'Duzib147G0469' => 'dzi', 'Duzib168G0060' => 'dzi', 'Duzib187G1215' => 'dzi', 'Duzib248G0692' => 'dzi', 'Duzib251G0767' => 'dzi', 'Duzib264G0446' => 'dzi', 'Duzib268G0691' => 'dzi', 'ECA232G4767' => 'eca', 'ECA233G2838' => 'eca', 'ECA234G0391' => 'eca', 'ECA234G0857' => 'eca', 'ECA236G1593' => 'eca', 'ECA238G0565' => 'eca', 'ECA246G1027' => 'eca', 'ECA246G3223' => 'eca', 'ECA246G3470' => 'eca', 'EL10Ac6g13829' => 'bvu', 'EL10Ac6g14093' => 'bvu', 'EL10Ac8g18707' => 'bvu', 'Eucgr.C01369' => 'egr', 'Eucgr.H02492' => 'egr', 'Eucgr.I01733' => 'egr', 'Eucgr.J02255' => 'egr', 'Eucgr.J02257' => 'egr', 'Eucgr.J02258' => 'egr', 'FAN02G1601' => 'fan', 'FAN03G1586' => 'fan', 'FAN03G2986' => 'fan', 'FAN05G4837' => 'fan', 'FAN06G0146' => 'fan', 'FAN07G0858' => 'fan', 'FAN09G3179' => 'fan', 'FAN10G0669' => 'fan', 'FAN12G2358' => 'fan', 'FAN14G4198' => 'fan', 'FAN14G5112' => 'fan', 'FAN17G0342' => 'fan', 'FAN19G0342' => 'fan', 'FAN19G0962' => 'fan', 'FAN19G1101' => 'fan', 'FAN19G1872' => 'fan', 'FAN22G0356' => 'fan', 'FAN23G0744' => 'fan', 'FAN23G1914' => 'fan', 'FAN26G0032' => 'fan', 'FAN28G0625' => 'fan', 'FvH4_1g02710' => 'fve', 'FvH4_1g02720' => 'fve', 'FvH4_4g25670' => 'fve', 'FvH4_6g51700' => 'fve', 'FvH4_7g20170' => 'fve', 'Glyma.05G175000' => 'gma', 'Glyma.08G132300' => 'gma', 'Glyma.11G243000' => 'gma', 'Glyma.13G158900' => 'gma', 'Glyma.17G112400' => 'gma', 'Glyma.18G014100' => 'gma', 'Glyma.19G003100' => 'gma', 'Glyma.19G056500' => 'gma', 'Gohir.A01G158900' => 'ghi', 'Gohir.A05G312600' => 'ghi', 'Gohir.A05G354900' => 'ghi', 'Gohir.A07G037200' => 'ghi', 'Gohir.A09G030000' => 'ghi', 'Gohir.A12G145200' => 'ghi', 'Gohir.D01G151500' => 'ghi', 'Gohir.D04G058300' => 'ghi', 'Gohir.D05G314100' => 'ghi', 'Gohir.D07G041400' => 'ghi', 'Gohir.D09G029700' => 'ghi', 'Gohir.D12G149700' => 'ghi', 'Gorai.001G043800' => 'gra', 'Gorai.002G187800' => 'gra', 'Gorai.006G034700' => 'gra', 'Gorai.008G161200' => 'gra', 'Gorai.009G335700' => 'gra', 'Gorai.012G065000' => 'gra', 'GSVIVG01000535001' => 'vvi', 'GSVIVG01015572001' => 'vvi', 'GSVIVG01032386001' => 'vvi', 'HanXRQChr05g0138531' => 'han', 'HanXRQChr06g0174391' => 'han', 'HanXRQChr07g0199021' => 'han', 'HanXRQChr08g0208211' => 'han', 'HanXRQChr09g0255471' => 'han', 'HanXRQChr10g0315791' => 'han', 'HanXRQChr12g0371991' => 'han', 'HanXRQChr15g0475251' => 'han', 'HanXRQChr17g0540001' => 'han', 'HanXRQChr17g0548631' => 'han', 'HanXRQChr17g0569561' => 'han', 'Haze_12256' => 'cav', 'Haze_14756' => 'cav', 'Haze_25528' => 'cav', 'Hma1.2p1_0079F.1_g041020' => 'hma', 'Hma1.2p1_0818F.1_g223260' => 'hma', 'Hma1.2p1_1747F.1_g300530' => 'hma', 'HPP92_004607' => 'vpl', 'HPP92_004608' => 'vpl', 'HPP92_006181' => 'vpl', 'HPP92_012192' => 'vpl', 'HPP92_015680' => 'vpl', 'HPP92_020249' => 'vpl', 'HPP92_021376' => 'vpl', 'HPP92_024275' => 'vpl', 'Hund06031' => 'sun', 'Hund25391' => 'sun', 'Lalb_Chr07g0185371' => 'lal', 'Lalb_Chr07g0185381' => 'lal', 'Lalb_Chr12g0204011' => 'lal', 'Lalb_Chr13g0301671' => 'lal', 'Lalb_Chr14g0362851' => 'lal', 'Lalb_Chr24g0403581' => 'lal', 'Lj1g0000233' => 'lja', 'Lj2g0018120' => 'lja', 'Lj3C621T0' => 'lonja', 'Lj3P1059T14' => 'lonja', 'Lj3P611T9' => 'lonja', 'Lj3P614T13' => 'lonja', 'Lj3P615T5' => 'lonja', 'Lj4g0012315' => 'lja', 'Lj4g0026182' => 'lja', 'Lj6P813T16' => 'lonja', 'Lj7C427T7' => 'lonja', 'Lj7C427T8' => 'lonja', 'Lj7P600T41' => 'lonja', 'Lju41C42G17' => 'lonja', 'Lsat_1_v5_gn_0_47300' => 'lsa', 'Lsat_1_v5_gn_2_91280' => 'lsa', 'Lsat_1_v5_gn_3_30561' => 'lsa', 'Lsat_1_v5_gn_4_184321' => 'lsa', 'Lsat_1_v5_gn_4_4041' => 'lsa', 'Lsat_1_v5_gn_5_92000' => 'lsa', 'Lsat_1_v5_gn_8_152940' => 'lsa', 'Lsat_1_v5_gn_8_62401' => 'lsa', 'Manes.06G055900' => 'mes', 'Manes.12G022200' => 'mes', 'Manes.13G023300' => 'mes', 'Manes.14G115000' => 'mes', 'Manes.15G151700' => 'mes', 'Manes.17G111300' => 'mes', 'Mapoly0226s0009' => 'mpo', 'MBI02_g25363_MAGBIO' => 'mbi', 'MBI06_g00027_MAGBIO' => 'mbi', 'MBI10_g13034_MAGBIO' => 'mbi', 'MD09G1023400' => 'mdo', 'MD13G1100100' => 'mdo', 'MD15G1169200' => 'mdo', 'MD16G1101100' => 'mdo', 'MD17G1022900' => 'mdo', 'Medtr3g096150' => 'mtr', 'Medtr4g115070' => 'mtr', 'Medtr7g033325' => 'mtr', 'Medtr8g089840' => 'mtr', 'MELO3C010319.2' => 'cme', 'MELO3C011944.2' => 'cme', 'MELO3C021589.2' => 'cme', 'Migut.E00207' => 'egut', 'Migut.H00067' => 'egut', 'Migut.K00433' => 'egut', 'Migut.K00606' => 'egut', 'Migut.K01410' => 'egut', 'MSTRG.13347' => 'ama', 'MSTRG.24045' => 'ama', 'MSTRG.2428' => 'ama', 'MSTRG.26410' => 'ama', 'MSTRG.3139' => 'ama', 'MSTRG.3286' => 'ama', 'MSTRG.563' => 'ama', 'MSTRG.7941' => 'ama', 'Nitab4.5_0000028g0060' => 'nta', 'Nitab4.5_0000065g0260' => 'nta', 'Nitab4.5_0000112g0060' => 'nta', 'Nitab4.5_0000489g0120' => 'nta', 'Nitab4.5_0001776g0050' => 'nta', 'Nitab4.5_0001854g0010' => 'nta', 'Nitab4.5_0001860g0020' => 'nta', 'Nitab4.5_0004352g0010' => 'nta', 'Nitab4.5_0008716g0020' => 'nta', 'Nitab4.5_0008922g0010' => 'nta', 'Nn3g16693' => 'nnu', 'Nn4g22596' => 'nnu', 'Nn7g37639' => 'nnu', 'Oeu001701.1' => 'oeu', 'Oeu018149.1' => 'oeu', 'Oeu026220.1' => 'oeu', 'Oeu038635.1' => 'oeu', 'Oeu049176.1' => 'oeu', 'Oeu056706.1' => 'oeu', 'Oeu056937.1' => 'oeu', 'Oeu057540.1' => 'oeu', 'Os02g0594900' => 'osa', 'Os02g0595100' => 'osa', 'Os04g0477500' => 'osa', 'Os12g0611900' => 'osa', 'Peaxi162Scf00076g00020' => 'pax', 'Peaxi162Scf00128g00217' => 'pax', 'Peaxi162Scf00129g01640' => 'pax', 'Peaxi162Scf00669g00007' => 'pax', 'Peaxi162Scf00700g00421' => 'pax', 'Peaxi162Scf00801g00038' => 'pax', 'Peaxi162Scf00891g00025' => 'pax', 'PGR083G0909' => 'pgr', 'PGR119G1005' => 'pgr', 'PGR142G2236' => 'pgr', 'PGR142G3388' => 'pgr', 'PGSC0003DMG400004514' => 'stu', 'PGSC0003DMG400012635' => 'stu', 'PGSC0003DMG400015730' => 'stu', 'PGSC0003DMG400018611' => 'stu', 'PGSC0003DMG400030897' => 'stu', 'Phvul.001G254800' => 'pvu', 'Phvul.002G260100' => 'pvu', 'Phvul.003G167600' => 'pvu', 'Phvul.004G005100' => 'pvu', 'Potri.001G343600' => 'ptr', 'Potri.006G066700' => 'ptr', 'Potri.008G186000' => 'ptr', 'Potri.010G046900' => 'ptr', 'Potri.018G127900' => 'ptr', 'Pp3c20_17750' => 'ppa', 'Pp3c24_4380' => 'ppa', 'Prupe.1G245800' => 'ppe', 'Prupe.3G293400' => 'ppe', 'Prupe.7G247400' => 'ppe', 'Psat0s145g0120' => 'psa', 'Psat0s595g0040' => 'psa', 'Psat0s595g0120' => 'psa', 'Psat3g175040' => 'psa', 'Psat7g058120' => 'psa', 'PSO017G0428' => 'pso', 'PSO063G7510' => 'pso', 'PSO067G0046' => 'pso', 'PSO478G1073' => 'pso', 'PSO675G3677' => 'pso', 'PSO675G6558' => 'pso', 'PSO675G7520' => 'pso', 'PSO675G8959' => 'pso', 'QL02p074089' => 'qlo', 'QL02p089614' => 'qlo', 'QL03p057736' => 'qlo', 'RcHm_v2.0_Chr1g0364131' => 'rch', 'RcHm_v2.0_Chr2g0087801' => 'rch', 'RcHm_v2.0_Chr2g0087821' => 'rch', 'RcHm_v2.0_Chr2g0173231' => 'rch', 'RcHm_v2.0_Chr4g0433111' => 'rch', 'Rhsim03G0250300' => 'rsi', 'Rhsim08G0048400' => 'rsi', 'Rhsim10G0014800' => 'rsi', 'Rhsim12G0040100' => 'rsi', 'Rhsim12G0109700' => 'rsi', 'Sabra06G0049600' => 'sbr', 'Sabra08G0141000' => 'sbr', 'Sabra10G0021400' => 'sbr', 'Sabra16G0222900' => 'sbr', 'Sabra18G0108600' => 'sbr', 'SalBow1G0433' => 'sbo', 'SalBow1G2038' => 'sbo', 'SalBow1G5003' => 'sbo', 'SalBow7G1197' => 'sbo', 'SalBow8G3506' => 'sbo', 'Sc03g0007300' => 'sci', 'Sc11g0000950' => 'sci', 'Sc14g0008750' => 'sci', 'Sc18g0000420' => 'sci', 'Sed0006754' => 'sed', 'Sed0008741' => 'sed', 'Sed0017172' => 'sed', 'Sed0018925' => 'sed', 'Sed0023326' => 'sed', 'Sed0025909' => 'sed', 'SEGI_05333' => 'sgi', 'SEGI_10362' => 'sgi', 'SEGI_13380' => 'sgi', 'SEGI_24306' => 'sgi', 'SEGI_29077' => 'sgi', 'SEGI_29095' => 'sgi', 'SEGI_36534' => 'sgi', 'SEGI_37506' => 'sgi', 'SEGI_38321' => 'sgi', 'SGA_v2.0_scaffold307G48031' => 'sas', 'SGA_v2.0_scaffold47G17507' => 'sas', 'SGA_v2.0_scaffold63G21736' => 'sas', 'SGA_v2.0_scaffold87G27070' => 'sas', 'SHI17794' => 'shi', 'SHI28851' => 'shi', 'SMO165G0155' => 'smo', 'SMO340G0217' => 'smo', 'SMO367G1210' => 'smo', 'Solyc02g093430.3' => 'sly', 'Solyc05g013580.4' => 'sly', 'Solyc07g008030.3' => 'sly', 'Solyc12g035470.2' => 'sly', 'Sopen02g038020' => 'spe', 'Sopen05g008490' => 'spe', 'Sopen07g003910' => 'spe', 'Sopen12g015240' => 'spe', 'Sp1g11550' => 'spa', 'Sp2g16710' => 'spa', 'Sp3g00430' => 'spa', 'Sp3g26780' => 'spa', 'Sp5g22900' => 'spa', 'Sp6g29530' => 'spa', 'TAR371G0794' => 'tar', 'TAR374G0164' => 'tar', 'TAR622G0165' => 'tar', 'TAR626G0929' => 'tar', 'TAR629G2155' => 'tar', 'THA.LOC104805282' => 'tha', 'THA.LOC104805363' => 'tha', 'THA.LOC104808968' => 'tha', 'THA.LOC104821093' => 'tha', 'THA.LOC104823953' => 'tha', 'THA.LOC104825562' => 'tha', 'THA.LOC104825665' => 'tha', 'Thecc.02G261400' => 'tca', 'Thecc.04G019200' => 'tca', 'Thecc.09G130400' => 'tca', 'Thhalv10004374m.g' => 'esa', 'Thhalv10007850m.g' => 'esa', 'Thhalv10013782m.g' => 'esa', 'Thhalv10018686m.g' => 'esa', 'Thhalv10020899m.g' => 'esa', 'Thhalv10022755m.g' => 'esa', 'TPR.G23851' => 'tpr', 'TPR.G26500' => 'tpr', 'TPR.G27267' => 'tpr', 'TPR.G32001' => 'tpr', 'TPR.G6251' => 'tpr', 'TPR.G8167' => 'tpr', 'TWI12G1330' => 'twi', 'TWI18G1239' => 'twi', 'TWI34G0979' => 'twi', 'TWI36G0670' => 'twi', 'TWI36G0707' => 'twi', 'TWI56G0233' => 'twi', 'TWI75G1809' => 'twi', 'unitig_21.g20874' => 'ugi', 'unitig_26.g10343' => 'ugi', 'unitig_46.g18392' => 'ugi', 'unitig_52.g17178' => 'ugi', 'unitig_8.g2934' => 'ugi', 'vmacro01122' => 'vma', 'vmacro05875' => 'vma', 'vmacro06147' => 'vma', 'vmacro16191' => 'vma', 'vmacro18293' => 'vma', 'VMungo0251G3707' => 'vmu', 'VMungo0464G1521' => 'vmu', 'VMungo1215G0205' => 'vmu', 'VMungo1383G2484' => 'vmu', 'Zm00001eb079610' => 'zma', 'Zm00001eb135990' => 'zma', 'Zm00001eb183710' => 'zma', 'Zm00001eb246020' => 'zma' ), 'gf_id' => 'HOM05D001124', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001124' ), 'data_identifier' => 'HOM05D001124', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001124', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '548', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02520' => 'bna', 'A03p06630' => 'bna', 'A05p44460' => 'bna', 'A06p08710' => 'bna', 'A06p41090' => 'bna', 'A07p32320' => 'bna', 'A08p32520' => 'bna', 'A09p10360' => 'bna', 'A10p24080' => 'bna', 'Aa31LG11G15250' => 'aar', 'Aa31LG1G1800' => 'aar', 'Aa31LG2G5120' => 'aar', 'Aa31LG2G6070' => 'aar', 'Aa31LG5G10770' => 'aar', 'Aa31sc61G90' => 'aar', 'Actinidia01352' => 'ach', 'Actinidia05983' => 'ach', 'Actinidia08133' => 'ach', 'Actinidia15101' => 'ach', 'Actinidia26379' => 'ach', 'Actinidia35778' => 'ach', 'Actinidia36123' => 'ach', 'Actinidia37436' => 'ach', 'Actinidia38730' => 'ach', 'Ah.02g128210' => 'amhyb', 'Ah.03g132990' => 'amhyb', 'Ah.14g079410' => 'amhyb', 'AL1G24640' => 'aly', 'AL2G26680' => 'aly', 'AL3G10530' => 'aly', 'AL3G45230' => 'aly', 'AL5G15230' => 'aly', 'AL5G16960' => 'aly', 'AL6G25210' => 'aly', 'Aqoxy2G00441' => 'aox', 'Aqoxy3G01236' => 'aox', 'Aqoxy5G03746' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3RQ047' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C7GMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9C8JER' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MBL6KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YXCZ83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZANX40' => 'arhy', 'AT1G12990' => 'ath', 'AT1G67880' => 'ath', 'AT2G13290' => 'ath', 'AT3G01620' => 'ath', 'AT3G26445' => 'ath', 'AT3G27540' => 'ath', 'AT5G14480' => 'ath', 'ATR0824G026' => 'atr', 'ATR1098G019' => 'atr', 'Atru.chr11.2145' => 'acertr', 'Atru.chr2.3636' => 'acertr', 'Atru.chr2.3644' => 'acertr', 'Atru.chr6.2422' => 'acertr', 'Atru.chr7.1112' => 'acertr', 'AUR62005469' => 'cqu', 'AUR62011166' => 'cqu', 'AUR62013319' => 'cqu', 'AUR62024273' => 'cqu', 'AUR62028420' => 'cqu', 'AUR62041942' => 'cqu', 'BcaB01g04969' => 'bca', 'BcaB01g06371' => 'bca', 'BcaB02g11494' => 'bca', 'BcaB03g15382' => 'bca', 'BcaB08g36994' => 'bca', 'BcaC03g13477' => 'bca', 'BcaC03g13478' => 'bca', 'BcaC03g13480' => 'bca', 'BcaC03g13481' => 'bca', 'BcaC03g13486' => 'bca', 'BcaC04g19031' => 'bca', 'BcaC04g23085' => 'bca', 'BcaC05g25094' => 'bca', 'BcaC05g25096' => 'bca', 'BcaC05g25138' => 'bca', 'BcaC05g30416' => 'bca', 'BcaC05g30455' => 'bca', 'BcaC06g30979' => 'bca', 'BcaC06g33805' => 'bca', 'BcaC08g46021' => 'bca', 'BcaNung03154' => 'bca', 'BolC2t06623H' => 'bol', 'BolC2t06632H' => 'bol', 'BolC2t06635H' => 'bol', 'BolC2t06638H' => 'bol', 'BolC3t13266H' => 'bol', 'BolC5t29776H' => 'bol', 'BolC6t38912H' => 'bol', 'BolC7t44183H' => 'bol', 'BolC9t54123H' => 'bol', 'BolC9t59107H' => 'bol', 'BraA02t05221Z' => 'bra', 'BraA03t09996Z' => 'bra', 'BraA05t23210Z' => 'bra', 'BraA06t24068Z' => 'bra', 'BraA06t27032Z' => 'bra', 'BraA08t35176Z' => 'bra', 'BraA09t36680Z' => 'bra', 'BraA10t44471Z' => 'bra', 'C02p06760' => 'bna', 'C02p06890' => 'bna', 'C02p07010' => 'bna', 'C03p07660' => 'bna', 'C05p10300' => 'bna', 'C06p38150' => 'bna', 'C07p36650' => 'bna', 'C08p15770' => 'bna', 'C09p12300' => 'bna', 'C09p62700' => 'bna', 'C09p75040' => 'bna', 'CAN.G13.1' => 'can', 'CAN.G138.4' => 'can', 'CAN.G44.6' => 'can', 'CAN.G473.19' => 'can', 'CANSAT01G0835' => 'cansat', 'CANSAT11G0246' => 'cansat', 'CANSAT11G1766' => 'cansat', 'CANSAT64G1954' => 'cansat', 'CARHR013330' => 'chi', 'CARHR060530' => 'chi', 'CARHR075300' => 'chi', 'CARHR105120' => 'chi', 'CARHR148910' => 'chi', 'CARHR198830' => 'chi', 'Carub.0001s1275' => 'cru', 'Carub.0002s1437' => 'cru', 'Carub.0003s0044' => 'cru', 'Carub.0003s2787' => 'cru', 'Carub.0005s0597' => 'cru', 'Carub.0006s1266' => 'cru', 'Ca_06935_v3' => 'car', 'Ca_13559_v3' => 'car', 'Ca_16941_v3' => 'car', 'Ca_16960_v3' => 'car', 'Ca_17775_v3' => 'car', 'Ca_30464_v3' => 'car', 'Cc06_g08160' => 'ccan', 'Cc07_g01520' => 'ccan', 'Cc11_g15810' => 'ccan', 'CDE02G2840' => 'cde', 'CDE03G0093' => 'cde', 'CDE04G2127' => 'cde', 'CDE07G1857' => 'cde', 'CDE09G1246' => 'cde', 'Cfa003412' => 'cfa', 'Cfa007341' => 'cfa', 'Cfa009220' => 'cfa', 'Ciclev10008737m.g' => 'ccl', 'Ciclev10015565m.g' => 'ccl', 'Ciclev10031761m.g' => 'ccl', 'CiPaw.03G045300' => 'cil', 'CiPaw.03G247200' => 'cil', 'CiPaw.04G029500' => 'cil', 'CiPaw.04G174000' => 'cil', 'CiPaw.05G181200' => 'cil', 'CiPaw.06G067100' => 'cil', 'ClCG05G025800' => 'cla', 'ClCG06G011400' => 'cla', 'ClCG09G019360' => 'cla', 'COL.COLO4_04827' => 'col', 'COL.COLO4_29170' => 'col', 'COL.COLO4_35131' => 'col', 'COL.COLO4_35132' => 'col', 'Cpa.g.sc33.32' => 'cpa', 'Cpa.g.sc46.29' => 'cpa', 'Cpa.g.sc796.1' => 'cpa', 'CsaV3_1G030420' => 'csa', 'CsaV3_5G027050' => 'csa', 'CsaV3_5G031040' => 'csa', 'CsaV3_UNG023130' => 'csa', 'CSS0007726' => 'camsi', 'CSS0016433' => 'camsi', 'CSS0017656' => 'camsi', 'CSS0025364' => 'camsi', 'CSS0027582' => 'camsi', 'CSS0047288' => 'camsi', 'CSS0049950' => 'camsi', 'DCAR_003843' => 'dca', 'DCAR_007052' => 'dca', 'DCAR_020884' => 'dca', 'DCAR_021730' => 'dca', 'DCAR_024423' => 'dca', 'DCAR_026509' => 'dca', 'DCAR_031158' => 'dca', 'Dinv14728' => 'din', 'Dinv15219' => 'din', 'Dinv25728' => 'din', 'Dinv33428' => 'din', 'Dinv36489' => 'din', 'Dinv41486' => 'din', 'Duzib147G0469' => 'dzi', 'Duzib168G0060' => 'dzi', 'Duzib187G1215' => 'dzi', 'Duzib248G0692' => 'dzi', 'Duzib251G0767' => 'dzi', 'Duzib264G0446' => 'dzi', 'Duzib268G0691' => 'dzi', 'ECA232G4767' => 'eca', 'ECA233G2838' => 'eca', 'ECA234G0391' => 'eca', 'ECA234G0857' => 'eca', 'ECA236G1593' => 'eca', 'ECA238G0565' => 'eca', 'ECA246G1027' => 'eca', 'ECA246G3223' => 'eca', 'ECA246G3470' => 'eca', 'EL10Ac6g13829' => 'bvu', 'EL10Ac6g14093' => 'bvu', 'EL10Ac8g18707' => 'bvu', 'Eucgr.C01369' => 'egr', 'Eucgr.H02492' => 'egr', 'Eucgr.I01733' => 'egr', 'Eucgr.J02255' => 'egr', 'Eucgr.J02257' => 'egr', 'Eucgr.J02258' => 'egr', 'FAN02G1601' => 'fan', 'FAN03G1586' => 'fan', 'FAN03G2986' => 'fan', 'FAN05G4837' => 'fan', 'FAN06G0146' => 'fan', 'FAN07G0858' => 'fan', 'FAN09G3179' => 'fan', 'FAN10G0669' => 'fan', 'FAN12G2358' => 'fan', 'FAN14G4198' => 'fan', 'FAN14G5112' => 'fan', 'FAN17G0342' => 'fan', 'FAN19G0342' => 'fan', 'FAN19G0962' => 'fan', 'FAN19G1101' => 'fan', 'FAN19G1872' => 'fan', 'FAN22G0356' => 'fan', 'FAN23G0744' => 'fan', 'FAN23G1914' => 'fan', 'FAN26G0032' => 'fan', 'FAN28G0625' => 'fan', 'FvH4_1g02710' => 'fve', 'FvH4_1g02720' => 'fve', 'FvH4_4g25670' => 'fve', 'FvH4_6g51700' => 'fve', 'FvH4_7g20170' => 'fve', 'Glyma.05G175000' => 'gma', 'Glyma.08G132300' => 'gma', 'Glyma.11G243000' => 'gma', 'Glyma.13G158900' => 'gma', 'Glyma.17G112400' => 'gma', 'Glyma.18G014100' => 'gma', 'Glyma.19G003100' => 'gma', 'Glyma.19G056500' => 'gma', 'Gohir.A01G158900' => 'ghi', 'Gohir.A05G312600' => 'ghi', 'Gohir.A05G354900' => 'ghi', 'Gohir.A07G037200' => 'ghi', 'Gohir.A09G030000' => 'ghi', 'Gohir.A12G145200' => 'ghi', 'Gohir.D01G151500' => 'ghi', 'Gohir.D04G058300' => 'ghi', 'Gohir.D05G314100' => 'ghi', 'Gohir.D07G041400' => 'ghi', 'Gohir.D09G029700' => 'ghi', 'Gohir.D12G149700' => 'ghi', 'Gorai.001G043800' => 'gra', 'Gorai.002G187800' => 'gra', 'Gorai.006G034700' => 'gra', 'Gorai.008G161200' => 'gra', 'Gorai.009G335700' => 'gra', 'Gorai.012G065000' => 'gra', 'GSVIVG01000535001' => 'vvi', 'GSVIVG01015572001' => 'vvi', 'GSVIVG01032386001' => 'vvi', 'HanXRQChr05g0138531' => 'han', 'HanXRQChr06g0174391' => 'han', 'HanXRQChr07g0199021' => 'han', 'HanXRQChr08g0208211' => 'han', 'HanXRQChr09g0255471' => 'han', 'HanXRQChr10g0315791' => 'han', 'HanXRQChr12g0371991' => 'han', 'HanXRQChr15g0475251' => 'han', 'HanXRQChr17g0540001' => 'han', 'HanXRQChr17g0548631' => 'han', 'HanXRQChr17g0569561' => 'han', 'Haze_12256' => 'cav', 'Haze_14756' => 'cav', 'Haze_25528' => 'cav', 'Hma1.2p1_0079F.1_g041020' => 'hma', 'Hma1.2p1_0818F.1_g223260' => 'hma', 'Hma1.2p1_1747F.1_g300530' => 'hma', 'HPP92_004607' => 'vpl', 'HPP92_004608' => 'vpl', 'HPP92_006181' => 'vpl', 'HPP92_012192' => 'vpl', 'HPP92_015680' => 'vpl', 'HPP92_020249' => 'vpl', 'HPP92_021376' => 'vpl', 'HPP92_024275' => 'vpl', 'Hund06031' => 'sun', 'Hund25391' => 'sun', 'Lalb_Chr07g0185371' => 'lal', 'Lalb_Chr07g0185381' => 'lal', 'Lalb_Chr12g0204011' => 'lal', 'Lalb_Chr13g0301671' => 'lal', 'Lalb_Chr14g0362851' => 'lal', 'Lalb_Chr24g0403581' => 'lal', 'Lj1g0000233' => 'lja', 'Lj2g0018120' => 'lja', 'Lj3C621T0' => 'lonja', 'Lj3P1059T14' => 'lonja', 'Lj3P611T9' => 'lonja', 'Lj3P614T13' => 'lonja', 'Lj3P615T5' => 'lonja', 'Lj4g0012315' => 'lja', 'Lj4g0026182' => 'lja', 'Lj6P813T16' => 'lonja', 'Lj7C427T7' => 'lonja', 'Lj7C427T8' => 'lonja', 'Lj7P600T41' => 'lonja', 'Lju41C42G17' => 'lonja', 'Lsat_1_v5_gn_0_47300' => 'lsa', 'Lsat_1_v5_gn_2_91280' => 'lsa', 'Lsat_1_v5_gn_3_30561' => 'lsa', 'Lsat_1_v5_gn_4_184321' => 'lsa', 'Lsat_1_v5_gn_4_4041' => 'lsa', 'Lsat_1_v5_gn_5_92000' => 'lsa', 'Lsat_1_v5_gn_8_152940' => 'lsa', 'Lsat_1_v5_gn_8_62401' => 'lsa', 'Manes.06G055900' => 'mes', 'Manes.12G022200' => 'mes', 'Manes.13G023300' => 'mes', 'Manes.14G115000' => 'mes', 'Manes.15G151700' => 'mes', 'Manes.17G111300' => 'mes', 'Mapoly0226s0009' => 'mpo', 'MBI02_g25363_MAGBIO' => 'mbi', 'MBI06_g00027_MAGBIO' => 'mbi', 'MBI10_g13034_MAGBIO' => 'mbi', 'MD09G1023400' => 'mdo', 'MD13G1100100' => 'mdo', 'MD15G1169200' => 'mdo', 'MD16G1101100' => 'mdo', 'MD17G1022900' => 'mdo', 'Medtr3g096150' => 'mtr', 'Medtr4g115070' => 'mtr', 'Medtr7g033325' => 'mtr', 'Medtr8g089840' => 'mtr', 'MELO3C010319.2' => 'cme', 'MELO3C011944.2' => 'cme', 'MELO3C021589.2' => 'cme', 'Migut.E00207' => 'egut', 'Migut.H00067' => 'egut', 'Migut.K00433' => 'egut', 'Migut.K00606' => 'egut', 'Migut.K01410' => 'egut', 'MSTRG.13347' => 'ama', 'MSTRG.24045' => 'ama', 'MSTRG.2428' => 'ama', 'MSTRG.26410' => 'ama', 'MSTRG.3139' => 'ama', 'MSTRG.3286' => 'ama', 'MSTRG.563' => 'ama', 'MSTRG.7941' => 'ama', 'Nitab4.5_0000028g0060' => 'nta', 'Nitab4.5_0000065g0260' => 'nta', 'Nitab4.5_0000112g0060' => 'nta', 'Nitab4.5_0000489g0120' => 'nta', 'Nitab4.5_0001776g0050' => 'nta', 'Nitab4.5_0001854g0010' => 'nta', 'Nitab4.5_0001860g0020' => 'nta', 'Nitab4.5_0004352g0010' => 'nta', 'Nitab4.5_0008716g0020' => 'nta', 'Nitab4.5_0008922g0010' => 'nta', 'Nn3g16693' => 'nnu', 'Nn4g22596' => 'nnu', 'Nn7g37639' => 'nnu', 'Oeu001701.1' => 'oeu', 'Oeu018149.1' => 'oeu', 'Oeu026220.1' => 'oeu', 'Oeu038635.1' => 'oeu', 'Oeu049176.1' => 'oeu', 'Oeu056706.1' => 'oeu', 'Oeu056937.1' => 'oeu', 'Oeu057540.1' => 'oeu', 'Os02g0594900' => 'osa', 'Os02g0595100' => 'osa', 'Os04g0477500' => 'osa', 'Os12g0611900' => 'osa', 'Peaxi162Scf00076g00020' => 'pax', 'Peaxi162Scf00128g00217' => 'pax', 'Peaxi162Scf00129g01640' => 'pax', 'Peaxi162Scf00669g00007' => 'pax', 'Peaxi162Scf00700g00421' => 'pax', 'Peaxi162Scf00801g00038' => 'pax', 'Peaxi162Scf00891g00025' => 'pax', 'PGR083G0909' => 'pgr', 'PGR119G1005' => 'pgr', 'PGR142G2236' => 'pgr', 'PGR142G3388' => 'pgr', 'PGSC0003DMG400004514' => 'stu', 'PGSC0003DMG400012635' => 'stu', 'PGSC0003DMG400015730' => 'stu', 'PGSC0003DMG400018611' => 'stu', 'PGSC0003DMG400030897' => 'stu', 'Phvul.001G254800' => 'pvu', 'Phvul.002G260100' => 'pvu', 'Phvul.003G167600' => 'pvu', 'Phvul.004G005100' => 'pvu', 'Potri.001G343600' => 'ptr', 'Potri.006G066700' => 'ptr', 'Potri.008G186000' => 'ptr', 'Potri.010G046900' => 'ptr', 'Potri.018G127900' => 'ptr', 'Pp3c20_17750' => 'ppa', 'Pp3c24_4380' => 'ppa', 'Prupe.1G245800' => 'ppe', 'Prupe.3G293400' => 'ppe', 'Prupe.7G247400' => 'ppe', 'Psat0s145g0120' => 'psa', 'Psat0s595g0040' => 'psa', 'Psat0s595g0120' => 'psa', 'Psat3g175040' => 'psa', 'Psat7g058120' => 'psa', 'PSO017G0428' => 'pso', 'PSO063G7510' => 'pso', 'PSO067G0046' => 'pso', 'PSO478G1073' => 'pso', 'PSO675G3677' => 'pso', 'PSO675G6558' => 'pso', 'PSO675G7520' => 'pso', 'PSO675G8959' => 'pso', 'QL02p074089' => 'qlo', 'QL02p089614' => 'qlo', 'QL03p057736' => 'qlo', 'RcHm_v2.0_Chr1g0364131' => 'rch', 'RcHm_v2.0_Chr2g0087801' => 'rch', 'RcHm_v2.0_Chr2g0087821' => 'rch', 'RcHm_v2.0_Chr2g0173231' => 'rch', 'RcHm_v2.0_Chr4g0433111' => 'rch', 'Rhsim03G0250300' => 'rsi', 'Rhsim08G0048400' => 'rsi', 'Rhsim10G0014800' => 'rsi', 'Rhsim12G0040100' => 'rsi', 'Rhsim12G0109700' => 'rsi', 'Sabra06G0049600' => 'sbr', 'Sabra08G0141000' => 'sbr', 'Sabra10G0021400' => 'sbr', 'Sabra16G0222900' => 'sbr', 'Sabra18G0108600' => 'sbr', 'SalBow1G0433' => 'sbo', 'SalBow1G2038' => 'sbo', 'SalBow1G5003' => 'sbo', 'SalBow7G1197' => 'sbo', 'SalBow8G3506' => 'sbo', 'Sc03g0007300' => 'sci', 'Sc11g0000950' => 'sci', 'Sc14g0008750' => 'sci', 'Sc18g0000420' => 'sci', 'Sed0006754' => 'sed', 'Sed0008741' => 'sed', 'Sed0017172' => 'sed', 'Sed0018925' => 'sed', 'Sed0023326' => 'sed', 'Sed0025909' => 'sed', 'SEGI_05333' => 'sgi', 'SEGI_10362' => 'sgi', 'SEGI_13380' => 'sgi', 'SEGI_24306' => 'sgi', 'SEGI_29077' => 'sgi', 'SEGI_29095' => 'sgi', 'SEGI_36534' => 'sgi', 'SEGI_37506' => 'sgi', 'SEGI_38321' => 'sgi', 'SGA_v2.0_scaffold307G48031' => 'sas', 'SGA_v2.0_scaffold47G17507' => 'sas', 'SGA_v2.0_scaffold63G21736' => 'sas', 'SGA_v2.0_scaffold87G27070' => 'sas', 'SHI17794' => 'shi', 'SHI28851' => 'shi', 'SMO165G0155' => 'smo', 'SMO340G0217' => 'smo', 'SMO367G1210' => 'smo', 'Solyc02g093430.3' => 'sly', 'Solyc05g013580.4' => 'sly', 'Solyc07g008030.3' => 'sly', 'Solyc12g035470.2' => 'sly', 'Sopen02g038020' => 'spe', 'Sopen05g008490' => 'spe', 'Sopen07g003910' => 'spe', 'Sopen12g015240' => 'spe', 'Sp1g11550' => 'spa', 'Sp2g16710' => 'spa', 'Sp3g00430' => 'spa', 'Sp3g26780' => 'spa', 'Sp5g22900' => 'spa', 'Sp6g29530' => 'spa', 'TAR371G0794' => 'tar', 'TAR374G0164' => 'tar', 'TAR622G0165' => 'tar', 'TAR626G0929' => 'tar', 'TAR629G2155' => 'tar', 'THA.LOC104805282' => 'tha', 'THA.LOC104805363' => 'tha', 'THA.LOC104808968' => 'tha', 'THA.LOC104821093' => 'tha', 'THA.LOC104823953' => 'tha', 'THA.LOC104825562' => 'tha', 'THA.LOC104825665' => 'tha', 'Thecc.02G261400' => 'tca', 'Thecc.04G019200' => 'tca', 'Thecc.09G130400' => 'tca', 'Thhalv10004374m.g' => 'esa', 'Thhalv10007850m.g' => 'esa', 'Thhalv10013782m.g' => 'esa', 'Thhalv10018686m.g' => 'esa', 'Thhalv10020899m.g' => 'esa', 'Thhalv10022755m.g' => 'esa', 'TPR.G23851' => 'tpr', 'TPR.G26500' => 'tpr', 'TPR.G27267' => 'tpr', 'TPR.G32001' => 'tpr', 'TPR.G6251' => 'tpr', 'TPR.G8167' => 'tpr', 'TWI12G1330' => 'twi', 'TWI18G1239' => 'twi', 'TWI34G0979' => 'twi', 'TWI36G0670' => 'twi', 'TWI36G0707' => 'twi', 'TWI56G0233' => 'twi', 'TWI75G1809' => 'twi', 'unitig_21.g20874' => 'ugi', 'unitig_26.g10343' => 'ugi', 'unitig_46.g18392' => 'ugi', 'unitig_52.g17178' => 'ugi', 'unitig_8.g2934' => 'ugi', 'vmacro01122' => 'vma', 'vmacro05875' => 'vma', 'vmacro06147' => 'vma', 'vmacro16191' => 'vma', 'vmacro18293' => 'vma', 'VMungo0251G3707' => 'vmu', 'VMungo0464G1521' => 'vmu', 'VMungo1215G0205' => 'vmu', 'VMungo1383G2484' => 'vmu', 'Zm00001eb079610' => 'zma', 'Zm00001eb135990' => 'zma', 'Zm00001eb183710' => 'zma', 'Zm00001eb246020' => 'zma' ) $gf_id = 'HOM05D001124' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001124' ) $data_identifier = 'HOM05D001124' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 6, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 7, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 21, 'bol' => (int) 10, 'bra' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 6, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 9, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 21, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 8, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 10, 'lsa' => (int) 8, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 8, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 9, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb246020' $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' => 'HOM05D001124', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '548', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02520' => 'bna', 'A03p06630' => 'bna', 'A05p44460' => 'bna', 'A06p08710' => 'bna', 'A06p41090' => 'bna', 'A07p32320' => 'bna', 'A08p32520' => 'bna', 'A09p10360' => 'bna', 'A10p24080' => 'bna', 'Aa31LG11G15250' => 'aar', 'Aa31LG1G1800' => 'aar', 'Aa31LG2G5120' => 'aar', 'Aa31LG2G6070' => 'aar', 'Aa31LG5G10770' => 'aar', 'Aa31sc61G90' => 'aar', 'Actinidia01352' => 'ach', 'Actinidia05983' => 'ach', 'Actinidia08133' => 'ach', 'Actinidia15101' => 'ach', 'Actinidia26379' => 'ach', 'Actinidia35778' => 'ach', 'Actinidia36123' => 'ach', 'Actinidia37436' => 'ach', 'Actinidia38730' => 'ach', 'Ah.02g128210' => 'amhyb', 'Ah.03g132990' => 'amhyb', 'Ah.14g079410' => 'amhyb', 'AL1G24640' => 'aly', 'AL2G26680' => 'aly', 'AL3G10530' => 'aly', 'AL3G45230' => 'aly', 'AL5G15230' => 'aly', 'AL5G16960' => 'aly', 'AL6G25210' => 'aly', 'Aqoxy2G00441' => 'aox', 'Aqoxy3G01236' => 'aox', 'Aqoxy5G03746' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3RQ047' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C7GMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9C8JER' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MBL6KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YXCZ83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZANX40' => 'arhy', 'AT1G12990' => 'ath', 'AT1G67880' => 'ath', 'AT2G13290' => 'ath', 'AT3G01620' => 'ath', 'AT3G26445' => 'ath', 'AT3G27540' => 'ath', 'AT5G14480' => 'ath', 'ATR0824G026' => 'atr', 'ATR1098G019' => 'atr', 'Atru.chr11.2145' => 'acertr', 'Atru.chr2.3636' => 'acertr', 'Atru.chr2.3644' => 'acertr', 'Atru.chr6.2422' => 'acertr', 'Atru.chr7.1112' => 'acertr', 'AUR62005469' => 'cqu', 'AUR62011166' => 'cqu', 'AUR62013319' => 'cqu', 'AUR62024273' => 'cqu', 'AUR62028420' => 'cqu', 'AUR62041942' => 'cqu', 'BcaB01g04969' => 'bca', 'BcaB01g06371' => 'bca', 'BcaB02g11494' => 'bca', 'BcaB03g15382' => 'bca', 'BcaB08g36994' => 'bca', 'BcaC03g13477' => 'bca', 'BcaC03g13478' => 'bca', 'BcaC03g13480' => 'bca', 'BcaC03g13481' => 'bca', 'BcaC03g13486' => 'bca', 'BcaC04g19031' => 'bca', 'BcaC04g23085' => 'bca', 'BcaC05g25094' => 'bca', 'BcaC05g25096' => 'bca', 'BcaC05g25138' => 'bca', 'BcaC05g30416' => 'bca', 'BcaC05g30455' => 'bca', 'BcaC06g30979' => 'bca', 'BcaC06g33805' => 'bca', 'BcaC08g46021' => 'bca', 'BcaNung03154' => 'bca', 'BolC2t06623H' => 'bol', 'BolC2t06632H' => 'bol', 'BolC2t06635H' => 'bol', 'BolC2t06638H' => 'bol', 'BolC3t13266H' => 'bol', 'BolC5t29776H' => 'bol', 'BolC6t38912H' => 'bol', 'BolC7t44183H' => 'bol', 'BolC9t54123H' => 'bol', 'BolC9t59107H' => 'bol', 'BraA02t05221Z' => 'bra', 'BraA03t09996Z' => 'bra', 'BraA05t23210Z' => 'bra', 'BraA06t24068Z' => 'bra', 'BraA06t27032Z' => 'bra', 'BraA08t35176Z' => 'bra', 'BraA09t36680Z' => 'bra', 'BraA10t44471Z' => 'bra', 'C02p06760' => 'bna', 'C02p06890' => 'bna', 'C02p07010' => 'bna', 'C03p07660' => 'bna', 'C05p10300' => 'bna', 'C06p38150' => 'bna', 'C07p36650' => 'bna', 'C08p15770' => 'bna', 'C09p12300' => 'bna', 'C09p62700' => 'bna', 'C09p75040' => 'bna', 'CAN.G13.1' => 'can', 'CAN.G138.4' => 'can', 'CAN.G44.6' => 'can', 'CAN.G473.19' => 'can', 'CANSAT01G0835' => 'cansat', 'CANSAT11G0246' => 'cansat', 'CANSAT11G1766' => 'cansat', 'CANSAT64G1954' => 'cansat', 'CARHR013330' => 'chi', 'CARHR060530' => 'chi', 'CARHR075300' => 'chi', 'CARHR105120' => 'chi', 'CARHR148910' => 'chi', 'CARHR198830' => 'chi', 'Carub.0001s1275' => 'cru', 'Carub.0002s1437' => 'cru', 'Carub.0003s0044' => 'cru', 'Carub.0003s2787' => 'cru', 'Carub.0005s0597' => 'cru', 'Carub.0006s1266' => 'cru', 'Ca_06935_v3' => 'car', 'Ca_13559_v3' => 'car', 'Ca_16941_v3' => 'car', 'Ca_16960_v3' => 'car', 'Ca_17775_v3' => 'car', 'Ca_30464_v3' => 'car', 'Cc06_g08160' => 'ccan', 'Cc07_g01520' => 'ccan', 'Cc11_g15810' => 'ccan', 'CDE02G2840' => 'cde', 'CDE03G0093' => 'cde', 'CDE04G2127' => 'cde', 'CDE07G1857' => 'cde', 'CDE09G1246' => 'cde', 'Cfa003412' => 'cfa', 'Cfa007341' => 'cfa', 'Cfa009220' => 'cfa', 'Ciclev10008737m.g' => 'ccl', 'Ciclev10015565m.g' => 'ccl', 'Ciclev10031761m.g' => 'ccl', 'CiPaw.03G045300' => 'cil', 'CiPaw.03G247200' => 'cil', 'CiPaw.04G029500' => 'cil', 'CiPaw.04G174000' => 'cil', 'CiPaw.05G181200' => 'cil', 'CiPaw.06G067100' => 'cil', 'ClCG05G025800' => 'cla', 'ClCG06G011400' => 'cla', 'ClCG09G019360' => 'cla', 'COL.COLO4_04827' => 'col', 'COL.COLO4_29170' => 'col', 'COL.COLO4_35131' => 'col', 'COL.COLO4_35132' => 'col', 'Cpa.g.sc33.32' => 'cpa', 'Cpa.g.sc46.29' => 'cpa', 'Cpa.g.sc796.1' => 'cpa', 'CsaV3_1G030420' => 'csa', 'CsaV3_5G027050' => 'csa', 'CsaV3_5G031040' => 'csa', 'CsaV3_UNG023130' => 'csa', 'CSS0007726' => 'camsi', 'CSS0016433' => 'camsi', 'CSS0017656' => 'camsi', 'CSS0025364' => 'camsi', 'CSS0027582' => 'camsi', 'CSS0047288' => 'camsi', 'CSS0049950' => 'camsi', 'DCAR_003843' => 'dca', 'DCAR_007052' => 'dca', 'DCAR_020884' => 'dca', 'DCAR_021730' => 'dca', 'DCAR_024423' => 'dca', 'DCAR_026509' => 'dca', 'DCAR_031158' => 'dca', 'Dinv14728' => 'din', 'Dinv15219' => 'din', 'Dinv25728' => 'din', 'Dinv33428' => 'din', 'Dinv36489' => 'din', 'Dinv41486' => 'din', 'Duzib147G0469' => 'dzi', 'Duzib168G0060' => 'dzi', 'Duzib187G1215' => 'dzi', 'Duzib248G0692' => 'dzi', 'Duzib251G0767' => 'dzi', 'Duzib264G0446' => 'dzi', 'Duzib268G0691' => 'dzi', 'ECA232G4767' => 'eca', 'ECA233G2838' => 'eca', 'ECA234G0391' => 'eca', 'ECA234G0857' => 'eca', 'ECA236G1593' => 'eca', 'ECA238G0565' => 'eca', 'ECA246G1027' => 'eca', 'ECA246G3223' => 'eca', 'ECA246G3470' => 'eca', 'EL10Ac6g13829' => 'bvu', 'EL10Ac6g14093' => 'bvu', 'EL10Ac8g18707' => 'bvu', 'Eucgr.C01369' => 'egr', 'Eucgr.H02492' => 'egr', 'Eucgr.I01733' => 'egr', 'Eucgr.J02255' => 'egr', 'Eucgr.J02257' => 'egr', 'Eucgr.J02258' => 'egr', 'FAN02G1601' => 'fan', 'FAN03G1586' => 'fan', 'FAN03G2986' => 'fan', 'FAN05G4837' => 'fan', 'FAN06G0146' => 'fan', 'FAN07G0858' => 'fan', 'FAN09G3179' => 'fan', 'FAN10G0669' => 'fan', 'FAN12G2358' => 'fan', 'FAN14G4198' => 'fan', 'FAN14G5112' => 'fan', 'FAN17G0342' => 'fan', 'FAN19G0342' => 'fan', 'FAN19G0962' => 'fan', 'FAN19G1101' => 'fan', 'FAN19G1872' => 'fan', 'FAN22G0356' => 'fan', 'FAN23G0744' => 'fan', 'FAN23G1914' => 'fan', 'FAN26G0032' => 'fan', 'FAN28G0625' => 'fan', 'FvH4_1g02710' => 'fve', 'FvH4_1g02720' => 'fve', 'FvH4_4g25670' => 'fve', 'FvH4_6g51700' => 'fve', 'FvH4_7g20170' => 'fve', 'Glyma.05G175000' => 'gma', 'Glyma.08G132300' => 'gma', 'Glyma.11G243000' => 'gma', 'Glyma.13G158900' => 'gma', 'Glyma.17G112400' => 'gma', 'Glyma.18G014100' => 'gma', 'Glyma.19G003100' => 'gma', 'Glyma.19G056500' => 'gma', 'Gohir.A01G158900' => 'ghi', 'Gohir.A05G312600' => 'ghi', 'Gohir.A05G354900' => 'ghi', 'Gohir.A07G037200' => 'ghi', 'Gohir.A09G030000' => 'ghi', 'Gohir.A12G145200' => 'ghi', 'Gohir.D01G151500' => 'ghi', 'Gohir.D04G058300' => 'ghi', 'Gohir.D05G314100' => 'ghi', 'Gohir.D07G041400' => 'ghi', 'Gohir.D09G029700' => 'ghi', 'Gohir.D12G149700' => 'ghi', 'Gorai.001G043800' => 'gra', 'Gorai.002G187800' => 'gra', 'Gorai.006G034700' => 'gra', 'Gorai.008G161200' => 'gra', 'Gorai.009G335700' => 'gra', 'Gorai.012G065000' => 'gra', 'GSVIVG01000535001' => 'vvi', 'GSVIVG01015572001' => 'vvi', 'GSVIVG01032386001' => 'vvi', 'HanXRQChr05g0138531' => 'han', 'HanXRQChr06g0174391' => 'han', 'HanXRQChr07g0199021' => 'han', 'HanXRQChr08g0208211' => 'han', 'HanXRQChr09g0255471' => 'han', 'HanXRQChr10g0315791' => 'han', 'HanXRQChr12g0371991' => 'han', 'HanXRQChr15g0475251' => 'han', 'HanXRQChr17g0540001' => 'han', 'HanXRQChr17g0548631' => 'han', 'HanXRQChr17g0569561' => 'han', 'Haze_12256' => 'cav', 'Haze_14756' => 'cav', 'Haze_25528' => 'cav', 'Hma1.2p1_0079F.1_g041020' => 'hma', 'Hma1.2p1_0818F.1_g223260' => 'hma', 'Hma1.2p1_1747F.1_g300530' => 'hma', 'HPP92_004607' => 'vpl', 'HPP92_004608' => 'vpl', 'HPP92_006181' => 'vpl', 'HPP92_012192' => 'vpl', 'HPP92_015680' => 'vpl', 'HPP92_020249' => 'vpl', 'HPP92_021376' => 'vpl', 'HPP92_024275' => 'vpl', 'Hund06031' => 'sun', 'Hund25391' => 'sun', 'Lalb_Chr07g0185371' => 'lal', 'Lalb_Chr07g0185381' => 'lal', 'Lalb_Chr12g0204011' => 'lal', 'Lalb_Chr13g0301671' => 'lal', 'Lalb_Chr14g0362851' => 'lal', 'Lalb_Chr24g0403581' => 'lal', 'Lj1g0000233' => 'lja', 'Lj2g0018120' => 'lja', 'Lj3C621T0' => 'lonja', 'Lj3P1059T14' => 'lonja', 'Lj3P611T9' => 'lonja', 'Lj3P614T13' => 'lonja', 'Lj3P615T5' => 'lonja', 'Lj4g0012315' => 'lja', 'Lj4g0026182' => 'lja', 'Lj6P813T16' => 'lonja', 'Lj7C427T7' => 'lonja', 'Lj7C427T8' => 'lonja', 'Lj7P600T41' => 'lonja', 'Lju41C42G17' => 'lonja', 'Lsat_1_v5_gn_0_47300' => 'lsa', 'Lsat_1_v5_gn_2_91280' => 'lsa', 'Lsat_1_v5_gn_3_30561' => 'lsa', 'Lsat_1_v5_gn_4_184321' => 'lsa', 'Lsat_1_v5_gn_4_4041' => 'lsa', 'Lsat_1_v5_gn_5_92000' => 'lsa', 'Lsat_1_v5_gn_8_152940' => 'lsa', 'Lsat_1_v5_gn_8_62401' => 'lsa', 'Manes.06G055900' => 'mes', 'Manes.12G022200' => 'mes', 'Manes.13G023300' => 'mes', 'Manes.14G115000' => 'mes', 'Manes.15G151700' => 'mes', 'Manes.17G111300' => 'mes', 'Mapoly0226s0009' => 'mpo', 'MBI02_g25363_MAGBIO' => 'mbi', 'MBI06_g00027_MAGBIO' => 'mbi', 'MBI10_g13034_MAGBIO' => 'mbi', 'MD09G1023400' => 'mdo', 'MD13G1100100' => 'mdo', 'MD15G1169200' => 'mdo', 'MD16G1101100' => 'mdo', 'MD17G1022900' => 'mdo', 'Medtr3g096150' => 'mtr', 'Medtr4g115070' => 'mtr', 'Medtr7g033325' => 'mtr', 'Medtr8g089840' => 'mtr', 'MELO3C010319.2' => 'cme', 'MELO3C011944.2' => 'cme', 'MELO3C021589.2' => 'cme', 'Migut.E00207' => 'egut', 'Migut.H00067' => 'egut', 'Migut.K00433' => 'egut', 'Migut.K00606' => 'egut', 'Migut.K01410' => 'egut', 'MSTRG.13347' => 'ama', 'MSTRG.24045' => 'ama', 'MSTRG.2428' => 'ama', 'MSTRG.26410' => 'ama', 'MSTRG.3139' => 'ama', 'MSTRG.3286' => 'ama', 'MSTRG.563' => 'ama', 'MSTRG.7941' => 'ama', 'Nitab4.5_0000028g0060' => 'nta', 'Nitab4.5_0000065g0260' => 'nta', 'Nitab4.5_0000112g0060' => 'nta', 'Nitab4.5_0000489g0120' => 'nta', 'Nitab4.5_0001776g0050' => 'nta', 'Nitab4.5_0001854g0010' => 'nta', 'Nitab4.5_0001860g0020' => 'nta', 'Nitab4.5_0004352g0010' => 'nta', 'Nitab4.5_0008716g0020' => 'nta', 'Nitab4.5_0008922g0010' => 'nta', 'Nn3g16693' => 'nnu', 'Nn4g22596' => 'nnu', 'Nn7g37639' => 'nnu', 'Oeu001701.1' => 'oeu', 'Oeu018149.1' => 'oeu', 'Oeu026220.1' => 'oeu', 'Oeu038635.1' => 'oeu', 'Oeu049176.1' => 'oeu', 'Oeu056706.1' => 'oeu', 'Oeu056937.1' => 'oeu', 'Oeu057540.1' => 'oeu', 'Os02g0594900' => 'osa', 'Os02g0595100' => 'osa', 'Os04g0477500' => 'osa', 'Os12g0611900' => 'osa', 'Peaxi162Scf00076g00020' => 'pax', 'Peaxi162Scf00128g00217' => 'pax', 'Peaxi162Scf00129g01640' => 'pax', 'Peaxi162Scf00669g00007' => 'pax', 'Peaxi162Scf00700g00421' => 'pax', 'Peaxi162Scf00801g00038' => 'pax', 'Peaxi162Scf00891g00025' => 'pax', 'PGR083G0909' => 'pgr', 'PGR119G1005' => 'pgr', 'PGR142G2236' => 'pgr', 'PGR142G3388' => 'pgr', 'PGSC0003DMG400004514' => 'stu', 'PGSC0003DMG400012635' => 'stu', 'PGSC0003DMG400015730' => 'stu', 'PGSC0003DMG400018611' => 'stu', 'PGSC0003DMG400030897' => 'stu', 'Phvul.001G254800' => 'pvu', 'Phvul.002G260100' => 'pvu', 'Phvul.003G167600' => 'pvu', 'Phvul.004G005100' => 'pvu', 'Potri.001G343600' => 'ptr', 'Potri.006G066700' => 'ptr', 'Potri.008G186000' => 'ptr', 'Potri.010G046900' => 'ptr', 'Potri.018G127900' => 'ptr', 'Pp3c20_17750' => 'ppa', 'Pp3c24_4380' => 'ppa', 'Prupe.1G245800' => 'ppe', 'Prupe.3G293400' => 'ppe', 'Prupe.7G247400' => 'ppe', 'Psat0s145g0120' => 'psa', 'Psat0s595g0040' => 'psa', 'Psat0s595g0120' => 'psa', 'Psat3g175040' => 'psa', 'Psat7g058120' => 'psa', 'PSO017G0428' => 'pso', 'PSO063G7510' => 'pso', 'PSO067G0046' => 'pso', 'PSO478G1073' => 'pso', 'PSO675G3677' => 'pso', 'PSO675G6558' => 'pso', 'PSO675G7520' => 'pso', 'PSO675G8959' => 'pso', 'QL02p074089' => 'qlo', 'QL02p089614' => 'qlo', 'QL03p057736' => 'qlo', 'RcHm_v2.0_Chr1g0364131' => 'rch', 'RcHm_v2.0_Chr2g0087801' => 'rch', 'RcHm_v2.0_Chr2g0087821' => 'rch', 'RcHm_v2.0_Chr2g0173231' => 'rch', 'RcHm_v2.0_Chr4g0433111' => 'rch', 'Rhsim03G0250300' => 'rsi', 'Rhsim08G0048400' => 'rsi', 'Rhsim10G0014800' => 'rsi', 'Rhsim12G0040100' => 'rsi', 'Rhsim12G0109700' => 'rsi', 'Sabra06G0049600' => 'sbr', 'Sabra08G0141000' => 'sbr', 'Sabra10G0021400' => 'sbr', 'Sabra16G0222900' => 'sbr', 'Sabra18G0108600' => 'sbr', 'SalBow1G0433' => 'sbo', 'SalBow1G2038' => 'sbo', 'SalBow1G5003' => 'sbo', 'SalBow7G1197' => 'sbo', 'SalBow8G3506' => 'sbo', 'Sc03g0007300' => 'sci', 'Sc11g0000950' => 'sci', 'Sc14g0008750' => 'sci', 'Sc18g0000420' => 'sci', 'Sed0006754' => 'sed', 'Sed0008741' => 'sed', 'Sed0017172' => 'sed', 'Sed0018925' => 'sed', 'Sed0023326' => 'sed', 'Sed0025909' => 'sed', 'SEGI_05333' => 'sgi', 'SEGI_10362' => 'sgi', 'SEGI_13380' => 'sgi', 'SEGI_24306' => 'sgi', 'SEGI_29077' => 'sgi', 'SEGI_29095' => 'sgi', 'SEGI_36534' => 'sgi', 'SEGI_37506' => 'sgi', 'SEGI_38321' => 'sgi', 'SGA_v2.0_scaffold307G48031' => 'sas', 'SGA_v2.0_scaffold47G17507' => 'sas', 'SGA_v2.0_scaffold63G21736' => 'sas', 'SGA_v2.0_scaffold87G27070' => 'sas', 'SHI17794' => 'shi', 'SHI28851' => 'shi', 'SMO165G0155' => 'smo', 'SMO340G0217' => 'smo', 'SMO367G1210' => 'smo', 'Solyc02g093430.3' => 'sly', 'Solyc05g013580.4' => 'sly', 'Solyc07g008030.3' => 'sly', 'Solyc12g035470.2' => 'sly', 'Sopen02g038020' => 'spe', 'Sopen05g008490' => 'spe', 'Sopen07g003910' => 'spe', 'Sopen12g015240' => 'spe', 'Sp1g11550' => 'spa', 'Sp2g16710' => 'spa', 'Sp3g00430' => 'spa', 'Sp3g26780' => 'spa', 'Sp5g22900' => 'spa', 'Sp6g29530' => 'spa', 'TAR371G0794' => 'tar', 'TAR374G0164' => 'tar', 'TAR622G0165' => 'tar', 'TAR626G0929' => 'tar', 'TAR629G2155' => 'tar', 'THA.LOC104805282' => 'tha', 'THA.LOC104805363' => 'tha', 'THA.LOC104808968' => 'tha', 'THA.LOC104821093' => 'tha', 'THA.LOC104823953' => 'tha', 'THA.LOC104825562' => 'tha', 'THA.LOC104825665' => 'tha', 'Thecc.02G261400' => 'tca', 'Thecc.04G019200' => 'tca', 'Thecc.09G130400' => 'tca', 'Thhalv10004374m.g' => 'esa', 'Thhalv10007850m.g' => 'esa', 'Thhalv10013782m.g' => 'esa', 'Thhalv10018686m.g' => 'esa', 'Thhalv10020899m.g' => 'esa', 'Thhalv10022755m.g' => 'esa', 'TPR.G23851' => 'tpr', 'TPR.G26500' => 'tpr', 'TPR.G27267' => 'tpr', 'TPR.G32001' => 'tpr', 'TPR.G6251' => 'tpr', 'TPR.G8167' => 'tpr', 'TWI12G1330' => 'twi', 'TWI18G1239' => 'twi', 'TWI34G0979' => 'twi', 'TWI36G0670' => 'twi', 'TWI36G0707' => 'twi', 'TWI56G0233' => 'twi', 'TWI75G1809' => 'twi', 'unitig_21.g20874' => 'ugi', 'unitig_26.g10343' => 'ugi', 'unitig_46.g18392' => 'ugi', 'unitig_52.g17178' => 'ugi', 'unitig_8.g2934' => 'ugi', 'vmacro01122' => 'vma', 'vmacro05875' => 'vma', 'vmacro06147' => 'vma', 'vmacro16191' => 'vma', 'vmacro18293' => 'vma', 'VMungo0251G3707' => 'vmu', 'VMungo0464G1521' => 'vmu', 'VMungo1215G0205' => 'vmu', 'VMungo1383G2484' => 'vmu', 'Zm00001eb079610' => 'zma', 'Zm00001eb135990' => 'zma', 'Zm00001eb183710' => 'zma', 'Zm00001eb246020' => 'zma' ), 'gf_id' => 'HOM05D001124', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001124' ), 'data_identifier' => 'HOM05D001124', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001124', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '548', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02520' => 'bna', 'A03p06630' => 'bna', 'A05p44460' => 'bna', 'A06p08710' => 'bna', 'A06p41090' => 'bna', 'A07p32320' => 'bna', 'A08p32520' => 'bna', 'A09p10360' => 'bna', 'A10p24080' => 'bna', 'Aa31LG11G15250' => 'aar', 'Aa31LG1G1800' => 'aar', 'Aa31LG2G5120' => 'aar', 'Aa31LG2G6070' => 'aar', 'Aa31LG5G10770' => 'aar', 'Aa31sc61G90' => 'aar', 'Actinidia01352' => 'ach', 'Actinidia05983' => 'ach', 'Actinidia08133' => 'ach', 'Actinidia15101' => 'ach', 'Actinidia26379' => 'ach', 'Actinidia35778' => 'ach', 'Actinidia36123' => 'ach', 'Actinidia37436' => 'ach', 'Actinidia38730' => 'ach', 'Ah.02g128210' => 'amhyb', 'Ah.03g132990' => 'amhyb', 'Ah.14g079410' => 'amhyb', 'AL1G24640' => 'aly', 'AL2G26680' => 'aly', 'AL3G10530' => 'aly', 'AL3G45230' => 'aly', 'AL5G15230' => 'aly', 'AL5G16960' => 'aly', 'AL6G25210' => 'aly', 'Aqoxy2G00441' => 'aox', 'Aqoxy3G01236' => 'aox', 'Aqoxy5G03746' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3RQ047' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C7GMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9C8JER' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MBL6KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YXCZ83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZANX40' => 'arhy', 'AT1G12990' => 'ath', 'AT1G67880' => 'ath', 'AT2G13290' => 'ath', 'AT3G01620' => 'ath', 'AT3G26445' => 'ath', 'AT3G27540' => 'ath', 'AT5G14480' => 'ath', 'ATR0824G026' => 'atr', 'ATR1098G019' => 'atr', 'Atru.chr11.2145' => 'acertr', 'Atru.chr2.3636' => 'acertr', 'Atru.chr2.3644' => 'acertr', 'Atru.chr6.2422' => 'acertr', 'Atru.chr7.1112' => 'acertr', 'AUR62005469' => 'cqu', 'AUR62011166' => 'cqu', 'AUR62013319' => 'cqu', 'AUR62024273' => 'cqu', 'AUR62028420' => 'cqu', 'AUR62041942' => 'cqu', 'BcaB01g04969' => 'bca', 'BcaB01g06371' => 'bca', 'BcaB02g11494' => 'bca', 'BcaB03g15382' => 'bca', 'BcaB08g36994' => 'bca', 'BcaC03g13477' => 'bca', 'BcaC03g13478' => 'bca', 'BcaC03g13480' => 'bca', 'BcaC03g13481' => 'bca', 'BcaC03g13486' => 'bca', 'BcaC04g19031' => 'bca', 'BcaC04g23085' => 'bca', 'BcaC05g25094' => 'bca', 'BcaC05g25096' => 'bca', 'BcaC05g25138' => 'bca', 'BcaC05g30416' => 'bca', 'BcaC05g30455' => 'bca', 'BcaC06g30979' => 'bca', 'BcaC06g33805' => 'bca', 'BcaC08g46021' => 'bca', 'BcaNung03154' => 'bca', 'BolC2t06623H' => 'bol', 'BolC2t06632H' => 'bol', 'BolC2t06635H' => 'bol', 'BolC2t06638H' => 'bol', 'BolC3t13266H' => 'bol', 'BolC5t29776H' => 'bol', 'BolC6t38912H' => 'bol', 'BolC7t44183H' => 'bol', 'BolC9t54123H' => 'bol', 'BolC9t59107H' => 'bol', 'BraA02t05221Z' => 'bra', 'BraA03t09996Z' => 'bra', 'BraA05t23210Z' => 'bra', 'BraA06t24068Z' => 'bra', 'BraA06t27032Z' => 'bra', 'BraA08t35176Z' => 'bra', 'BraA09t36680Z' => 'bra', 'BraA10t44471Z' => 'bra', 'C02p06760' => 'bna', 'C02p06890' => 'bna', 'C02p07010' => 'bna', 'C03p07660' => 'bna', 'C05p10300' => 'bna', 'C06p38150' => 'bna', 'C07p36650' => 'bna', 'C08p15770' => 'bna', 'C09p12300' => 'bna', 'C09p62700' => 'bna', 'C09p75040' => 'bna', 'CAN.G13.1' => 'can', 'CAN.G138.4' => 'can', 'CAN.G44.6' => 'can', 'CAN.G473.19' => 'can', 'CANSAT01G0835' => 'cansat', 'CANSAT11G0246' => 'cansat', 'CANSAT11G1766' => 'cansat', 'CANSAT64G1954' => 'cansat', 'CARHR013330' => 'chi', 'CARHR060530' => 'chi', 'CARHR075300' => 'chi', 'CARHR105120' => 'chi', 'CARHR148910' => 'chi', 'CARHR198830' => 'chi', 'Carub.0001s1275' => 'cru', 'Carub.0002s1437' => 'cru', 'Carub.0003s0044' => 'cru', 'Carub.0003s2787' => 'cru', 'Carub.0005s0597' => 'cru', 'Carub.0006s1266' => 'cru', 'Ca_06935_v3' => 'car', 'Ca_13559_v3' => 'car', 'Ca_16941_v3' => 'car', 'Ca_16960_v3' => 'car', 'Ca_17775_v3' => 'car', 'Ca_30464_v3' => 'car', 'Cc06_g08160' => 'ccan', 'Cc07_g01520' => 'ccan', 'Cc11_g15810' => 'ccan', 'CDE02G2840' => 'cde', 'CDE03G0093' => 'cde', 'CDE04G2127' => 'cde', 'CDE07G1857' => 'cde', 'CDE09G1246' => 'cde', 'Cfa003412' => 'cfa', 'Cfa007341' => 'cfa', 'Cfa009220' => 'cfa', 'Ciclev10008737m.g' => 'ccl', 'Ciclev10015565m.g' => 'ccl', 'Ciclev10031761m.g' => 'ccl', 'CiPaw.03G045300' => 'cil', 'CiPaw.03G247200' => 'cil', 'CiPaw.04G029500' => 'cil', 'CiPaw.04G174000' => 'cil', 'CiPaw.05G181200' => 'cil', 'CiPaw.06G067100' => 'cil', 'ClCG05G025800' => 'cla', 'ClCG06G011400' => 'cla', 'ClCG09G019360' => 'cla', 'COL.COLO4_04827' => 'col', 'COL.COLO4_29170' => 'col', 'COL.COLO4_35131' => 'col', 'COL.COLO4_35132' => 'col', 'Cpa.g.sc33.32' => 'cpa', 'Cpa.g.sc46.29' => 'cpa', 'Cpa.g.sc796.1' => 'cpa', 'CsaV3_1G030420' => 'csa', 'CsaV3_5G027050' => 'csa', 'CsaV3_5G031040' => 'csa', 'CsaV3_UNG023130' => 'csa', 'CSS0007726' => 'camsi', 'CSS0016433' => 'camsi', 'CSS0017656' => 'camsi', 'CSS0025364' => 'camsi', 'CSS0027582' => 'camsi', 'CSS0047288' => 'camsi', 'CSS0049950' => 'camsi', 'DCAR_003843' => 'dca', 'DCAR_007052' => 'dca', 'DCAR_020884' => 'dca', 'DCAR_021730' => 'dca', 'DCAR_024423' => 'dca', 'DCAR_026509' => 'dca', 'DCAR_031158' => 'dca', 'Dinv14728' => 'din', 'Dinv15219' => 'din', 'Dinv25728' => 'din', 'Dinv33428' => 'din', 'Dinv36489' => 'din', 'Dinv41486' => 'din', 'Duzib147G0469' => 'dzi', 'Duzib168G0060' => 'dzi', 'Duzib187G1215' => 'dzi', 'Duzib248G0692' => 'dzi', 'Duzib251G0767' => 'dzi', 'Duzib264G0446' => 'dzi', 'Duzib268G0691' => 'dzi', 'ECA232G4767' => 'eca', 'ECA233G2838' => 'eca', 'ECA234G0391' => 'eca', 'ECA234G0857' => 'eca', 'ECA236G1593' => 'eca', 'ECA238G0565' => 'eca', 'ECA246G1027' => 'eca', 'ECA246G3223' => 'eca', 'ECA246G3470' => 'eca', 'EL10Ac6g13829' => 'bvu', 'EL10Ac6g14093' => 'bvu', 'EL10Ac8g18707' => 'bvu', 'Eucgr.C01369' => 'egr', 'Eucgr.H02492' => 'egr', 'Eucgr.I01733' => 'egr', 'Eucgr.J02255' => 'egr', 'Eucgr.J02257' => 'egr', 'Eucgr.J02258' => 'egr', 'FAN02G1601' => 'fan', 'FAN03G1586' => 'fan', 'FAN03G2986' => 'fan', 'FAN05G4837' => 'fan', 'FAN06G0146' => 'fan', 'FAN07G0858' => 'fan', 'FAN09G3179' => 'fan', 'FAN10G0669' => 'fan', 'FAN12G2358' => 'fan', 'FAN14G4198' => 'fan', 'FAN14G5112' => 'fan', 'FAN17G0342' => 'fan', 'FAN19G0342' => 'fan', 'FAN19G0962' => 'fan', 'FAN19G1101' => 'fan', 'FAN19G1872' => 'fan', 'FAN22G0356' => 'fan', 'FAN23G0744' => 'fan', 'FAN23G1914' => 'fan', 'FAN26G0032' => 'fan', 'FAN28G0625' => 'fan', 'FvH4_1g02710' => 'fve', 'FvH4_1g02720' => 'fve', 'FvH4_4g25670' => 'fve', 'FvH4_6g51700' => 'fve', 'FvH4_7g20170' => 'fve', 'Glyma.05G175000' => 'gma', 'Glyma.08G132300' => 'gma', 'Glyma.11G243000' => 'gma', 'Glyma.13G158900' => 'gma', 'Glyma.17G112400' => 'gma', 'Glyma.18G014100' => 'gma', 'Glyma.19G003100' => 'gma', 'Glyma.19G056500' => 'gma', 'Gohir.A01G158900' => 'ghi', 'Gohir.A05G312600' => 'ghi', 'Gohir.A05G354900' => 'ghi', 'Gohir.A07G037200' => 'ghi', 'Gohir.A09G030000' => 'ghi', 'Gohir.A12G145200' => 'ghi', 'Gohir.D01G151500' => 'ghi', 'Gohir.D04G058300' => 'ghi', 'Gohir.D05G314100' => 'ghi', 'Gohir.D07G041400' => 'ghi', 'Gohir.D09G029700' => 'ghi', 'Gohir.D12G149700' => 'ghi', 'Gorai.001G043800' => 'gra', 'Gorai.002G187800' => 'gra', 'Gorai.006G034700' => 'gra', 'Gorai.008G161200' => 'gra', 'Gorai.009G335700' => 'gra', 'Gorai.012G065000' => 'gra', 'GSVIVG01000535001' => 'vvi', 'GSVIVG01015572001' => 'vvi', 'GSVIVG01032386001' => 'vvi', 'HanXRQChr05g0138531' => 'han', 'HanXRQChr06g0174391' => 'han', 'HanXRQChr07g0199021' => 'han', 'HanXRQChr08g0208211' => 'han', 'HanXRQChr09g0255471' => 'han', 'HanXRQChr10g0315791' => 'han', 'HanXRQChr12g0371991' => 'han', 'HanXRQChr15g0475251' => 'han', 'HanXRQChr17g0540001' => 'han', 'HanXRQChr17g0548631' => 'han', 'HanXRQChr17g0569561' => 'han', 'Haze_12256' => 'cav', 'Haze_14756' => 'cav', 'Haze_25528' => 'cav', 'Hma1.2p1_0079F.1_g041020' => 'hma', 'Hma1.2p1_0818F.1_g223260' => 'hma', 'Hma1.2p1_1747F.1_g300530' => 'hma', 'HPP92_004607' => 'vpl', 'HPP92_004608' => 'vpl', 'HPP92_006181' => 'vpl', 'HPP92_012192' => 'vpl', 'HPP92_015680' => 'vpl', 'HPP92_020249' => 'vpl', 'HPP92_021376' => 'vpl', 'HPP92_024275' => 'vpl', 'Hund06031' => 'sun', 'Hund25391' => 'sun', 'Lalb_Chr07g0185371' => 'lal', 'Lalb_Chr07g0185381' => 'lal', 'Lalb_Chr12g0204011' => 'lal', 'Lalb_Chr13g0301671' => 'lal', 'Lalb_Chr14g0362851' => 'lal', 'Lalb_Chr24g0403581' => 'lal', 'Lj1g0000233' => 'lja', 'Lj2g0018120' => 'lja', 'Lj3C621T0' => 'lonja', 'Lj3P1059T14' => 'lonja', 'Lj3P611T9' => 'lonja', 'Lj3P614T13' => 'lonja', 'Lj3P615T5' => 'lonja', 'Lj4g0012315' => 'lja', 'Lj4g0026182' => 'lja', 'Lj6P813T16' => 'lonja', 'Lj7C427T7' => 'lonja', 'Lj7C427T8' => 'lonja', 'Lj7P600T41' => 'lonja', 'Lju41C42G17' => 'lonja', 'Lsat_1_v5_gn_0_47300' => 'lsa', 'Lsat_1_v5_gn_2_91280' => 'lsa', 'Lsat_1_v5_gn_3_30561' => 'lsa', 'Lsat_1_v5_gn_4_184321' => 'lsa', 'Lsat_1_v5_gn_4_4041' => 'lsa', 'Lsat_1_v5_gn_5_92000' => 'lsa', 'Lsat_1_v5_gn_8_152940' => 'lsa', 'Lsat_1_v5_gn_8_62401' => 'lsa', 'Manes.06G055900' => 'mes', 'Manes.12G022200' => 'mes', 'Manes.13G023300' => 'mes', 'Manes.14G115000' => 'mes', 'Manes.15G151700' => 'mes', 'Manes.17G111300' => 'mes', 'Mapoly0226s0009' => 'mpo', 'MBI02_g25363_MAGBIO' => 'mbi', 'MBI06_g00027_MAGBIO' => 'mbi', 'MBI10_g13034_MAGBIO' => 'mbi', 'MD09G1023400' => 'mdo', 'MD13G1100100' => 'mdo', 'MD15G1169200' => 'mdo', 'MD16G1101100' => 'mdo', 'MD17G1022900' => 'mdo', 'Medtr3g096150' => 'mtr', 'Medtr4g115070' => 'mtr', 'Medtr7g033325' => 'mtr', 'Medtr8g089840' => 'mtr', 'MELO3C010319.2' => 'cme', 'MELO3C011944.2' => 'cme', 'MELO3C021589.2' => 'cme', 'Migut.E00207' => 'egut', 'Migut.H00067' => 'egut', 'Migut.K00433' => 'egut', 'Migut.K00606' => 'egut', 'Migut.K01410' => 'egut', 'MSTRG.13347' => 'ama', 'MSTRG.24045' => 'ama', 'MSTRG.2428' => 'ama', 'MSTRG.26410' => 'ama', 'MSTRG.3139' => 'ama', 'MSTRG.3286' => 'ama', 'MSTRG.563' => 'ama', 'MSTRG.7941' => 'ama', 'Nitab4.5_0000028g0060' => 'nta', 'Nitab4.5_0000065g0260' => 'nta', 'Nitab4.5_0000112g0060' => 'nta', 'Nitab4.5_0000489g0120' => 'nta', 'Nitab4.5_0001776g0050' => 'nta', 'Nitab4.5_0001854g0010' => 'nta', 'Nitab4.5_0001860g0020' => 'nta', 'Nitab4.5_0004352g0010' => 'nta', 'Nitab4.5_0008716g0020' => 'nta', 'Nitab4.5_0008922g0010' => 'nta', 'Nn3g16693' => 'nnu', 'Nn4g22596' => 'nnu', 'Nn7g37639' => 'nnu', 'Oeu001701.1' => 'oeu', 'Oeu018149.1' => 'oeu', 'Oeu026220.1' => 'oeu', 'Oeu038635.1' => 'oeu', 'Oeu049176.1' => 'oeu', 'Oeu056706.1' => 'oeu', 'Oeu056937.1' => 'oeu', 'Oeu057540.1' => 'oeu', 'Os02g0594900' => 'osa', 'Os02g0595100' => 'osa', 'Os04g0477500' => 'osa', 'Os12g0611900' => 'osa', 'Peaxi162Scf00076g00020' => 'pax', 'Peaxi162Scf00128g00217' => 'pax', 'Peaxi162Scf00129g01640' => 'pax', 'Peaxi162Scf00669g00007' => 'pax', 'Peaxi162Scf00700g00421' => 'pax', 'Peaxi162Scf00801g00038' => 'pax', 'Peaxi162Scf00891g00025' => 'pax', 'PGR083G0909' => 'pgr', 'PGR119G1005' => 'pgr', 'PGR142G2236' => 'pgr', 'PGR142G3388' => 'pgr', 'PGSC0003DMG400004514' => 'stu', 'PGSC0003DMG400012635' => 'stu', 'PGSC0003DMG400015730' => 'stu', 'PGSC0003DMG400018611' => 'stu', 'PGSC0003DMG400030897' => 'stu', 'Phvul.001G254800' => 'pvu', 'Phvul.002G260100' => 'pvu', 'Phvul.003G167600' => 'pvu', 'Phvul.004G005100' => 'pvu', 'Potri.001G343600' => 'ptr', 'Potri.006G066700' => 'ptr', 'Potri.008G186000' => 'ptr', 'Potri.010G046900' => 'ptr', 'Potri.018G127900' => 'ptr', 'Pp3c20_17750' => 'ppa', 'Pp3c24_4380' => 'ppa', 'Prupe.1G245800' => 'ppe', 'Prupe.3G293400' => 'ppe', 'Prupe.7G247400' => 'ppe', 'Psat0s145g0120' => 'psa', 'Psat0s595g0040' => 'psa', 'Psat0s595g0120' => 'psa', 'Psat3g175040' => 'psa', 'Psat7g058120' => 'psa', 'PSO017G0428' => 'pso', 'PSO063G7510' => 'pso', 'PSO067G0046' => 'pso', 'PSO478G1073' => 'pso', 'PSO675G3677' => 'pso', 'PSO675G6558' => 'pso', 'PSO675G7520' => 'pso', 'PSO675G8959' => 'pso', 'QL02p074089' => 'qlo', 'QL02p089614' => 'qlo', 'QL03p057736' => 'qlo', 'RcHm_v2.0_Chr1g0364131' => 'rch', 'RcHm_v2.0_Chr2g0087801' => 'rch', 'RcHm_v2.0_Chr2g0087821' => 'rch', 'RcHm_v2.0_Chr2g0173231' => 'rch', 'RcHm_v2.0_Chr4g0433111' => 'rch', 'Rhsim03G0250300' => 'rsi', 'Rhsim08G0048400' => 'rsi', 'Rhsim10G0014800' => 'rsi', 'Rhsim12G0040100' => 'rsi', 'Rhsim12G0109700' => 'rsi', 'Sabra06G0049600' => 'sbr', 'Sabra08G0141000' => 'sbr', 'Sabra10G0021400' => 'sbr', 'Sabra16G0222900' => 'sbr', 'Sabra18G0108600' => 'sbr', 'SalBow1G0433' => 'sbo', 'SalBow1G2038' => 'sbo', 'SalBow1G5003' => 'sbo', 'SalBow7G1197' => 'sbo', 'SalBow8G3506' => 'sbo', 'Sc03g0007300' => 'sci', 'Sc11g0000950' => 'sci', 'Sc14g0008750' => 'sci', 'Sc18g0000420' => 'sci', 'Sed0006754' => 'sed', 'Sed0008741' => 'sed', 'Sed0017172' => 'sed', 'Sed0018925' => 'sed', 'Sed0023326' => 'sed', 'Sed0025909' => 'sed', 'SEGI_05333' => 'sgi', 'SEGI_10362' => 'sgi', 'SEGI_13380' => 'sgi', 'SEGI_24306' => 'sgi', 'SEGI_29077' => 'sgi', 'SEGI_29095' => 'sgi', 'SEGI_36534' => 'sgi', 'SEGI_37506' => 'sgi', 'SEGI_38321' => 'sgi', 'SGA_v2.0_scaffold307G48031' => 'sas', 'SGA_v2.0_scaffold47G17507' => 'sas', 'SGA_v2.0_scaffold63G21736' => 'sas', 'SGA_v2.0_scaffold87G27070' => 'sas', 'SHI17794' => 'shi', 'SHI28851' => 'shi', 'SMO165G0155' => 'smo', 'SMO340G0217' => 'smo', 'SMO367G1210' => 'smo', 'Solyc02g093430.3' => 'sly', 'Solyc05g013580.4' => 'sly', 'Solyc07g008030.3' => 'sly', 'Solyc12g035470.2' => 'sly', 'Sopen02g038020' => 'spe', 'Sopen05g008490' => 'spe', 'Sopen07g003910' => 'spe', 'Sopen12g015240' => 'spe', 'Sp1g11550' => 'spa', 'Sp2g16710' => 'spa', 'Sp3g00430' => 'spa', 'Sp3g26780' => 'spa', 'Sp5g22900' => 'spa', 'Sp6g29530' => 'spa', 'TAR371G0794' => 'tar', 'TAR374G0164' => 'tar', 'TAR622G0165' => 'tar', 'TAR626G0929' => 'tar', 'TAR629G2155' => 'tar', 'THA.LOC104805282' => 'tha', 'THA.LOC104805363' => 'tha', 'THA.LOC104808968' => 'tha', 'THA.LOC104821093' => 'tha', 'THA.LOC104823953' => 'tha', 'THA.LOC104825562' => 'tha', 'THA.LOC104825665' => 'tha', 'Thecc.02G261400' => 'tca', 'Thecc.04G019200' => 'tca', 'Thecc.09G130400' => 'tca', 'Thhalv10004374m.g' => 'esa', 'Thhalv10007850m.g' => 'esa', 'Thhalv10013782m.g' => 'esa', 'Thhalv10018686m.g' => 'esa', 'Thhalv10020899m.g' => 'esa', 'Thhalv10022755m.g' => 'esa', 'TPR.G23851' => 'tpr', 'TPR.G26500' => 'tpr', 'TPR.G27267' => 'tpr', 'TPR.G32001' => 'tpr', 'TPR.G6251' => 'tpr', 'TPR.G8167' => 'tpr', 'TWI12G1330' => 'twi', 'TWI18G1239' => 'twi', 'TWI34G0979' => 'twi', 'TWI36G0670' => 'twi', 'TWI36G0707' => 'twi', 'TWI56G0233' => 'twi', 'TWI75G1809' => 'twi', 'unitig_21.g20874' => 'ugi', 'unitig_26.g10343' => 'ugi', 'unitig_46.g18392' => 'ugi', 'unitig_52.g17178' => 'ugi', 'unitig_8.g2934' => 'ugi', 'vmacro01122' => 'vma', 'vmacro05875' => 'vma', 'vmacro06147' => 'vma', 'vmacro16191' => 'vma', 'vmacro18293' => 'vma', 'VMungo0251G3707' => 'vmu', 'VMungo0464G1521' => 'vmu', 'VMungo1215G0205' => 'vmu', 'VMungo1383G2484' => 'vmu', 'Zm00001eb079610' => 'zma', 'Zm00001eb135990' => 'zma', 'Zm00001eb183710' => 'zma', 'Zm00001eb246020' => 'zma' ) $gf_id = 'HOM05D001124' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001124' ) $data_identifier = 'HOM05D001124' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 6, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 7, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 21, 'bol' => (int) 10, 'bra' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 6, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 9, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 21, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 8, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 10, 'lsa' => (int) 8, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 8, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 9, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb246020' $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' => 'HOM05D001124', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '548', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02520' => 'bna', 'A03p06630' => 'bna', 'A05p44460' => 'bna', 'A06p08710' => 'bna', 'A06p41090' => 'bna', 'A07p32320' => 'bna', 'A08p32520' => 'bna', 'A09p10360' => 'bna', 'A10p24080' => 'bna', 'Aa31LG11G15250' => 'aar', 'Aa31LG1G1800' => 'aar', 'Aa31LG2G5120' => 'aar', 'Aa31LG2G6070' => 'aar', 'Aa31LG5G10770' => 'aar', 'Aa31sc61G90' => 'aar', 'Actinidia01352' => 'ach', 'Actinidia05983' => 'ach', 'Actinidia08133' => 'ach', 'Actinidia15101' => 'ach', 'Actinidia26379' => 'ach', 'Actinidia35778' => 'ach', 'Actinidia36123' => 'ach', 'Actinidia37436' => 'ach', 'Actinidia38730' => 'ach', 'Ah.02g128210' => 'amhyb', 'Ah.03g132990' => 'amhyb', 'Ah.14g079410' => 'amhyb', 'AL1G24640' => 'aly', 'AL2G26680' => 'aly', 'AL3G10530' => 'aly', 'AL3G45230' => 'aly', 'AL5G15230' => 'aly', 'AL5G16960' => 'aly', 'AL6G25210' => 'aly', 'Aqoxy2G00441' => 'aox', 'Aqoxy3G01236' => 'aox', 'Aqoxy5G03746' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3RQ047' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C7GMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9C8JER' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MBL6KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YXCZ83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZANX40' => 'arhy', 'AT1G12990' => 'ath', 'AT1G67880' => 'ath', 'AT2G13290' => 'ath', 'AT3G01620' => 'ath', 'AT3G26445' => 'ath', 'AT3G27540' => 'ath', 'AT5G14480' => 'ath', 'ATR0824G026' => 'atr', 'ATR1098G019' => 'atr', 'Atru.chr11.2145' => 'acertr', 'Atru.chr2.3636' => 'acertr', 'Atru.chr2.3644' => 'acertr', 'Atru.chr6.2422' => 'acertr', 'Atru.chr7.1112' => 'acertr', 'AUR62005469' => 'cqu', 'AUR62011166' => 'cqu', 'AUR62013319' => 'cqu', 'AUR62024273' => 'cqu', 'AUR62028420' => 'cqu', 'AUR62041942' => 'cqu', 'BcaB01g04969' => 'bca', 'BcaB01g06371' => 'bca', 'BcaB02g11494' => 'bca', 'BcaB03g15382' => 'bca', 'BcaB08g36994' => 'bca', 'BcaC03g13477' => 'bca', 'BcaC03g13478' => 'bca', 'BcaC03g13480' => 'bca', 'BcaC03g13481' => 'bca', 'BcaC03g13486' => 'bca', 'BcaC04g19031' => 'bca', 'BcaC04g23085' => 'bca', 'BcaC05g25094' => 'bca', 'BcaC05g25096' => 'bca', 'BcaC05g25138' => 'bca', 'BcaC05g30416' => 'bca', 'BcaC05g30455' => 'bca', 'BcaC06g30979' => 'bca', 'BcaC06g33805' => 'bca', 'BcaC08g46021' => 'bca', 'BcaNung03154' => 'bca', 'BolC2t06623H' => 'bol', 'BolC2t06632H' => 'bol', 'BolC2t06635H' => 'bol', 'BolC2t06638H' => 'bol', 'BolC3t13266H' => 'bol', 'BolC5t29776H' => 'bol', 'BolC6t38912H' => 'bol', 'BolC7t44183H' => 'bol', 'BolC9t54123H' => 'bol', 'BolC9t59107H' => 'bol', 'BraA02t05221Z' => 'bra', 'BraA03t09996Z' => 'bra', 'BraA05t23210Z' => 'bra', 'BraA06t24068Z' => 'bra', 'BraA06t27032Z' => 'bra', 'BraA08t35176Z' => 'bra', 'BraA09t36680Z' => 'bra', 'BraA10t44471Z' => 'bra', 'C02p06760' => 'bna', 'C02p06890' => 'bna', 'C02p07010' => 'bna', 'C03p07660' => 'bna', 'C05p10300' => 'bna', 'C06p38150' => 'bna', 'C07p36650' => 'bna', 'C08p15770' => 'bna', 'C09p12300' => 'bna', 'C09p62700' => 'bna', 'C09p75040' => 'bna', 'CAN.G13.1' => 'can', 'CAN.G138.4' => 'can', 'CAN.G44.6' => 'can', 'CAN.G473.19' => 'can', 'CANSAT01G0835' => 'cansat', 'CANSAT11G0246' => 'cansat', 'CANSAT11G1766' => 'cansat', 'CANSAT64G1954' => 'cansat', 'CARHR013330' => 'chi', 'CARHR060530' => 'chi', 'CARHR075300' => 'chi', 'CARHR105120' => 'chi', 'CARHR148910' => 'chi', 'CARHR198830' => 'chi', 'Carub.0001s1275' => 'cru', 'Carub.0002s1437' => 'cru', 'Carub.0003s0044' => 'cru', 'Carub.0003s2787' => 'cru', 'Carub.0005s0597' => 'cru', 'Carub.0006s1266' => 'cru', 'Ca_06935_v3' => 'car', 'Ca_13559_v3' => 'car', 'Ca_16941_v3' => 'car', 'Ca_16960_v3' => 'car', 'Ca_17775_v3' => 'car', 'Ca_30464_v3' => 'car', 'Cc06_g08160' => 'ccan', 'Cc07_g01520' => 'ccan', 'Cc11_g15810' => 'ccan', 'CDE02G2840' => 'cde', 'CDE03G0093' => 'cde', 'CDE04G2127' => 'cde', 'CDE07G1857' => 'cde', 'CDE09G1246' => 'cde', 'Cfa003412' => 'cfa', 'Cfa007341' => 'cfa', 'Cfa009220' => 'cfa', 'Ciclev10008737m.g' => 'ccl', 'Ciclev10015565m.g' => 'ccl', 'Ciclev10031761m.g' => 'ccl', 'CiPaw.03G045300' => 'cil', 'CiPaw.03G247200' => 'cil', 'CiPaw.04G029500' => 'cil', 'CiPaw.04G174000' => 'cil', 'CiPaw.05G181200' => 'cil', 'CiPaw.06G067100' => 'cil', 'ClCG05G025800' => 'cla', 'ClCG06G011400' => 'cla', 'ClCG09G019360' => 'cla', 'COL.COLO4_04827' => 'col', 'COL.COLO4_29170' => 'col', 'COL.COLO4_35131' => 'col', 'COL.COLO4_35132' => 'col', 'Cpa.g.sc33.32' => 'cpa', 'Cpa.g.sc46.29' => 'cpa', 'Cpa.g.sc796.1' => 'cpa', 'CsaV3_1G030420' => 'csa', 'CsaV3_5G027050' => 'csa', 'CsaV3_5G031040' => 'csa', 'CsaV3_UNG023130' => 'csa', 'CSS0007726' => 'camsi', 'CSS0016433' => 'camsi', 'CSS0017656' => 'camsi', 'CSS0025364' => 'camsi', 'CSS0027582' => 'camsi', 'CSS0047288' => 'camsi', 'CSS0049950' => 'camsi', 'DCAR_003843' => 'dca', 'DCAR_007052' => 'dca', 'DCAR_020884' => 'dca', 'DCAR_021730' => 'dca', 'DCAR_024423' => 'dca', 'DCAR_026509' => 'dca', 'DCAR_031158' => 'dca', 'Dinv14728' => 'din', 'Dinv15219' => 'din', 'Dinv25728' => 'din', 'Dinv33428' => 'din', 'Dinv36489' => 'din', 'Dinv41486' => 'din', 'Duzib147G0469' => 'dzi', 'Duzib168G0060' => 'dzi', 'Duzib187G1215' => 'dzi', 'Duzib248G0692' => 'dzi', 'Duzib251G0767' => 'dzi', 'Duzib264G0446' => 'dzi', 'Duzib268G0691' => 'dzi', 'ECA232G4767' => 'eca', 'ECA233G2838' => 'eca', 'ECA234G0391' => 'eca', 'ECA234G0857' => 'eca', 'ECA236G1593' => 'eca', 'ECA238G0565' => 'eca', 'ECA246G1027' => 'eca', 'ECA246G3223' => 'eca', 'ECA246G3470' => 'eca', 'EL10Ac6g13829' => 'bvu', 'EL10Ac6g14093' => 'bvu', 'EL10Ac8g18707' => 'bvu', 'Eucgr.C01369' => 'egr', 'Eucgr.H02492' => 'egr', 'Eucgr.I01733' => 'egr', 'Eucgr.J02255' => 'egr', 'Eucgr.J02257' => 'egr', 'Eucgr.J02258' => 'egr', 'FAN02G1601' => 'fan', 'FAN03G1586' => 'fan', 'FAN03G2986' => 'fan', 'FAN05G4837' => 'fan', 'FAN06G0146' => 'fan', 'FAN07G0858' => 'fan', 'FAN09G3179' => 'fan', 'FAN10G0669' => 'fan', 'FAN12G2358' => 'fan', 'FAN14G4198' => 'fan', 'FAN14G5112' => 'fan', 'FAN17G0342' => 'fan', 'FAN19G0342' => 'fan', 'FAN19G0962' => 'fan', 'FAN19G1101' => 'fan', 'FAN19G1872' => 'fan', 'FAN22G0356' => 'fan', 'FAN23G0744' => 'fan', 'FAN23G1914' => 'fan', 'FAN26G0032' => 'fan', 'FAN28G0625' => 'fan', 'FvH4_1g02710' => 'fve', 'FvH4_1g02720' => 'fve', 'FvH4_4g25670' => 'fve', 'FvH4_6g51700' => 'fve', 'FvH4_7g20170' => 'fve', 'Glyma.05G175000' => 'gma', 'Glyma.08G132300' => 'gma', 'Glyma.11G243000' => 'gma', 'Glyma.13G158900' => 'gma', 'Glyma.17G112400' => 'gma', 'Glyma.18G014100' => 'gma', 'Glyma.19G003100' => 'gma', 'Glyma.19G056500' => 'gma', 'Gohir.A01G158900' => 'ghi', 'Gohir.A05G312600' => 'ghi', 'Gohir.A05G354900' => 'ghi', 'Gohir.A07G037200' => 'ghi', 'Gohir.A09G030000' => 'ghi', 'Gohir.A12G145200' => 'ghi', 'Gohir.D01G151500' => 'ghi', 'Gohir.D04G058300' => 'ghi', 'Gohir.D05G314100' => 'ghi', 'Gohir.D07G041400' => 'ghi', 'Gohir.D09G029700' => 'ghi', 'Gohir.D12G149700' => 'ghi', 'Gorai.001G043800' => 'gra', 'Gorai.002G187800' => 'gra', 'Gorai.006G034700' => 'gra', 'Gorai.008G161200' => 'gra', 'Gorai.009G335700' => 'gra', 'Gorai.012G065000' => 'gra', 'GSVIVG01000535001' => 'vvi', 'GSVIVG01015572001' => 'vvi', 'GSVIVG01032386001' => 'vvi', 'HanXRQChr05g0138531' => 'han', 'HanXRQChr06g0174391' => 'han', 'HanXRQChr07g0199021' => 'han', 'HanXRQChr08g0208211' => 'han', 'HanXRQChr09g0255471' => 'han', 'HanXRQChr10g0315791' => 'han', 'HanXRQChr12g0371991' => 'han', 'HanXRQChr15g0475251' => 'han', 'HanXRQChr17g0540001' => 'han', 'HanXRQChr17g0548631' => 'han', 'HanXRQChr17g0569561' => 'han', 'Haze_12256' => 'cav', 'Haze_14756' => 'cav', 'Haze_25528' => 'cav', 'Hma1.2p1_0079F.1_g041020' => 'hma', 'Hma1.2p1_0818F.1_g223260' => 'hma', 'Hma1.2p1_1747F.1_g300530' => 'hma', 'HPP92_004607' => 'vpl', 'HPP92_004608' => 'vpl', 'HPP92_006181' => 'vpl', 'HPP92_012192' => 'vpl', 'HPP92_015680' => 'vpl', 'HPP92_020249' => 'vpl', 'HPP92_021376' => 'vpl', 'HPP92_024275' => 'vpl', 'Hund06031' => 'sun', 'Hund25391' => 'sun', 'Lalb_Chr07g0185371' => 'lal', 'Lalb_Chr07g0185381' => 'lal', 'Lalb_Chr12g0204011' => 'lal', 'Lalb_Chr13g0301671' => 'lal', 'Lalb_Chr14g0362851' => 'lal', 'Lalb_Chr24g0403581' => 'lal', 'Lj1g0000233' => 'lja', 'Lj2g0018120' => 'lja', 'Lj3C621T0' => 'lonja', 'Lj3P1059T14' => 'lonja', 'Lj3P611T9' => 'lonja', 'Lj3P614T13' => 'lonja', 'Lj3P615T5' => 'lonja', 'Lj4g0012315' => 'lja', 'Lj4g0026182' => 'lja', 'Lj6P813T16' => 'lonja', 'Lj7C427T7' => 'lonja', 'Lj7C427T8' => 'lonja', 'Lj7P600T41' => 'lonja', 'Lju41C42G17' => 'lonja', 'Lsat_1_v5_gn_0_47300' => 'lsa', 'Lsat_1_v5_gn_2_91280' => 'lsa', 'Lsat_1_v5_gn_3_30561' => 'lsa', 'Lsat_1_v5_gn_4_184321' => 'lsa', 'Lsat_1_v5_gn_4_4041' => 'lsa', 'Lsat_1_v5_gn_5_92000' => 'lsa', 'Lsat_1_v5_gn_8_152940' => 'lsa', 'Lsat_1_v5_gn_8_62401' => 'lsa', 'Manes.06G055900' => 'mes', 'Manes.12G022200' => 'mes', 'Manes.13G023300' => 'mes', 'Manes.14G115000' => 'mes', 'Manes.15G151700' => 'mes', 'Manes.17G111300' => 'mes', 'Mapoly0226s0009' => 'mpo', 'MBI02_g25363_MAGBIO' => 'mbi', 'MBI06_g00027_MAGBIO' => 'mbi', 'MBI10_g13034_MAGBIO' => 'mbi', 'MD09G1023400' => 'mdo', 'MD13G1100100' => 'mdo', 'MD15G1169200' => 'mdo', 'MD16G1101100' => 'mdo', 'MD17G1022900' => 'mdo', 'Medtr3g096150' => 'mtr', 'Medtr4g115070' => 'mtr', 'Medtr7g033325' => 'mtr', 'Medtr8g089840' => 'mtr', 'MELO3C010319.2' => 'cme', 'MELO3C011944.2' => 'cme', 'MELO3C021589.2' => 'cme', 'Migut.E00207' => 'egut', 'Migut.H00067' => 'egut', 'Migut.K00433' => 'egut', 'Migut.K00606' => 'egut', 'Migut.K01410' => 'egut', 'MSTRG.13347' => 'ama', 'MSTRG.24045' => 'ama', 'MSTRG.2428' => 'ama', 'MSTRG.26410' => 'ama', 'MSTRG.3139' => 'ama', 'MSTRG.3286' => 'ama', 'MSTRG.563' => 'ama', 'MSTRG.7941' => 'ama', 'Nitab4.5_0000028g0060' => 'nta', 'Nitab4.5_0000065g0260' => 'nta', 'Nitab4.5_0000112g0060' => 'nta', 'Nitab4.5_0000489g0120' => 'nta', 'Nitab4.5_0001776g0050' => 'nta', 'Nitab4.5_0001854g0010' => 'nta', 'Nitab4.5_0001860g0020' => 'nta', 'Nitab4.5_0004352g0010' => 'nta', 'Nitab4.5_0008716g0020' => 'nta', 'Nitab4.5_0008922g0010' => 'nta', 'Nn3g16693' => 'nnu', 'Nn4g22596' => 'nnu', 'Nn7g37639' => 'nnu', 'Oeu001701.1' => 'oeu', 'Oeu018149.1' => 'oeu', 'Oeu026220.1' => 'oeu', 'Oeu038635.1' => 'oeu', 'Oeu049176.1' => 'oeu', 'Oeu056706.1' => 'oeu', 'Oeu056937.1' => 'oeu', 'Oeu057540.1' => 'oeu', 'Os02g0594900' => 'osa', 'Os02g0595100' => 'osa', 'Os04g0477500' => 'osa', 'Os12g0611900' => 'osa', 'Peaxi162Scf00076g00020' => 'pax', 'Peaxi162Scf00128g00217' => 'pax', 'Peaxi162Scf00129g01640' => 'pax', 'Peaxi162Scf00669g00007' => 'pax', 'Peaxi162Scf00700g00421' => 'pax', 'Peaxi162Scf00801g00038' => 'pax', 'Peaxi162Scf00891g00025' => 'pax', 'PGR083G0909' => 'pgr', 'PGR119G1005' => 'pgr', 'PGR142G2236' => 'pgr', 'PGR142G3388' => 'pgr', 'PGSC0003DMG400004514' => 'stu', 'PGSC0003DMG400012635' => 'stu', 'PGSC0003DMG400015730' => 'stu', 'PGSC0003DMG400018611' => 'stu', 'PGSC0003DMG400030897' => 'stu', 'Phvul.001G254800' => 'pvu', 'Phvul.002G260100' => 'pvu', 'Phvul.003G167600' => 'pvu', 'Phvul.004G005100' => 'pvu', 'Potri.001G343600' => 'ptr', 'Potri.006G066700' => 'ptr', 'Potri.008G186000' => 'ptr', 'Potri.010G046900' => 'ptr', 'Potri.018G127900' => 'ptr', 'Pp3c20_17750' => 'ppa', 'Pp3c24_4380' => 'ppa', 'Prupe.1G245800' => 'ppe', 'Prupe.3G293400' => 'ppe', 'Prupe.7G247400' => 'ppe', 'Psat0s145g0120' => 'psa', 'Psat0s595g0040' => 'psa', 'Psat0s595g0120' => 'psa', 'Psat3g175040' => 'psa', 'Psat7g058120' => 'psa', 'PSO017G0428' => 'pso', 'PSO063G7510' => 'pso', 'PSO067G0046' => 'pso', 'PSO478G1073' => 'pso', 'PSO675G3677' => 'pso', 'PSO675G6558' => 'pso', 'PSO675G7520' => 'pso', 'PSO675G8959' => 'pso', 'QL02p074089' => 'qlo', 'QL02p089614' => 'qlo', 'QL03p057736' => 'qlo', 'RcHm_v2.0_Chr1g0364131' => 'rch', 'RcHm_v2.0_Chr2g0087801' => 'rch', 'RcHm_v2.0_Chr2g0087821' => 'rch', 'RcHm_v2.0_Chr2g0173231' => 'rch', 'RcHm_v2.0_Chr4g0433111' => 'rch', 'Rhsim03G0250300' => 'rsi', 'Rhsim08G0048400' => 'rsi', 'Rhsim10G0014800' => 'rsi', 'Rhsim12G0040100' => 'rsi', 'Rhsim12G0109700' => 'rsi', 'Sabra06G0049600' => 'sbr', 'Sabra08G0141000' => 'sbr', 'Sabra10G0021400' => 'sbr', 'Sabra16G0222900' => 'sbr', 'Sabra18G0108600' => 'sbr', 'SalBow1G0433' => 'sbo', 'SalBow1G2038' => 'sbo', 'SalBow1G5003' => 'sbo', 'SalBow7G1197' => 'sbo', 'SalBow8G3506' => 'sbo', 'Sc03g0007300' => 'sci', 'Sc11g0000950' => 'sci', 'Sc14g0008750' => 'sci', 'Sc18g0000420' => 'sci', 'Sed0006754' => 'sed', 'Sed0008741' => 'sed', 'Sed0017172' => 'sed', 'Sed0018925' => 'sed', 'Sed0023326' => 'sed', 'Sed0025909' => 'sed', 'SEGI_05333' => 'sgi', 'SEGI_10362' => 'sgi', 'SEGI_13380' => 'sgi', 'SEGI_24306' => 'sgi', 'SEGI_29077' => 'sgi', 'SEGI_29095' => 'sgi', 'SEGI_36534' => 'sgi', 'SEGI_37506' => 'sgi', 'SEGI_38321' => 'sgi', 'SGA_v2.0_scaffold307G48031' => 'sas', 'SGA_v2.0_scaffold47G17507' => 'sas', 'SGA_v2.0_scaffold63G21736' => 'sas', 'SGA_v2.0_scaffold87G27070' => 'sas', 'SHI17794' => 'shi', 'SHI28851' => 'shi', 'SMO165G0155' => 'smo', 'SMO340G0217' => 'smo', 'SMO367G1210' => 'smo', 'Solyc02g093430.3' => 'sly', 'Solyc05g013580.4' => 'sly', 'Solyc07g008030.3' => 'sly', 'Solyc12g035470.2' => 'sly', 'Sopen02g038020' => 'spe', 'Sopen05g008490' => 'spe', 'Sopen07g003910' => 'spe', 'Sopen12g015240' => 'spe', 'Sp1g11550' => 'spa', 'Sp2g16710' => 'spa', 'Sp3g00430' => 'spa', 'Sp3g26780' => 'spa', 'Sp5g22900' => 'spa', 'Sp6g29530' => 'spa', 'TAR371G0794' => 'tar', 'TAR374G0164' => 'tar', 'TAR622G0165' => 'tar', 'TAR626G0929' => 'tar', 'TAR629G2155' => 'tar', 'THA.LOC104805282' => 'tha', 'THA.LOC104805363' => 'tha', 'THA.LOC104808968' => 'tha', 'THA.LOC104821093' => 'tha', 'THA.LOC104823953' => 'tha', 'THA.LOC104825562' => 'tha', 'THA.LOC104825665' => 'tha', 'Thecc.02G261400' => 'tca', 'Thecc.04G019200' => 'tca', 'Thecc.09G130400' => 'tca', 'Thhalv10004374m.g' => 'esa', 'Thhalv10007850m.g' => 'esa', 'Thhalv10013782m.g' => 'esa', 'Thhalv10018686m.g' => 'esa', 'Thhalv10020899m.g' => 'esa', 'Thhalv10022755m.g' => 'esa', 'TPR.G23851' => 'tpr', 'TPR.G26500' => 'tpr', 'TPR.G27267' => 'tpr', 'TPR.G32001' => 'tpr', 'TPR.G6251' => 'tpr', 'TPR.G8167' => 'tpr', 'TWI12G1330' => 'twi', 'TWI18G1239' => 'twi', 'TWI34G0979' => 'twi', 'TWI36G0670' => 'twi', 'TWI36G0707' => 'twi', 'TWI56G0233' => 'twi', 'TWI75G1809' => 'twi', 'unitig_21.g20874' => 'ugi', 'unitig_26.g10343' => 'ugi', 'unitig_46.g18392' => 'ugi', 'unitig_52.g17178' => 'ugi', 'unitig_8.g2934' => 'ugi', 'vmacro01122' => 'vma', 'vmacro05875' => 'vma', 'vmacro06147' => 'vma', 'vmacro16191' => 'vma', 'vmacro18293' => 'vma', 'VMungo0251G3707' => 'vmu', 'VMungo0464G1521' => 'vmu', 'VMungo1215G0205' => 'vmu', 'VMungo1383G2484' => 'vmu', 'Zm00001eb079610' => 'zma', 'Zm00001eb135990' => 'zma', 'Zm00001eb183710' => 'zma', 'Zm00001eb246020' => 'zma' ), 'gf_id' => 'HOM05D001124', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001124' ), 'data_identifier' => 'HOM05D001124', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001124', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '548', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02520' => 'bna', 'A03p06630' => 'bna', 'A05p44460' => 'bna', 'A06p08710' => 'bna', 'A06p41090' => 'bna', 'A07p32320' => 'bna', 'A08p32520' => 'bna', 'A09p10360' => 'bna', 'A10p24080' => 'bna', 'Aa31LG11G15250' => 'aar', 'Aa31LG1G1800' => 'aar', 'Aa31LG2G5120' => 'aar', 'Aa31LG2G6070' => 'aar', 'Aa31LG5G10770' => 'aar', 'Aa31sc61G90' => 'aar', 'Actinidia01352' => 'ach', 'Actinidia05983' => 'ach', 'Actinidia08133' => 'ach', 'Actinidia15101' => 'ach', 'Actinidia26379' => 'ach', 'Actinidia35778' => 'ach', 'Actinidia36123' => 'ach', 'Actinidia37436' => 'ach', 'Actinidia38730' => 'ach', 'Ah.02g128210' => 'amhyb', 'Ah.03g132990' => 'amhyb', 'Ah.14g079410' => 'amhyb', 'AL1G24640' => 'aly', 'AL2G26680' => 'aly', 'AL3G10530' => 'aly', 'AL3G45230' => 'aly', 'AL5G15230' => 'aly', 'AL5G16960' => 'aly', 'AL6G25210' => 'aly', 'Aqoxy2G00441' => 'aox', 'Aqoxy3G01236' => 'aox', 'Aqoxy5G03746' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3RQ047' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C7GMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9C8JER' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MBL6KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YXCZ83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZANX40' => 'arhy', 'AT1G12990' => 'ath', 'AT1G67880' => 'ath', 'AT2G13290' => 'ath', 'AT3G01620' => 'ath', 'AT3G26445' => 'ath', 'AT3G27540' => 'ath', 'AT5G14480' => 'ath', 'ATR0824G026' => 'atr', 'ATR1098G019' => 'atr', 'Atru.chr11.2145' => 'acertr', 'Atru.chr2.3636' => 'acertr', 'Atru.chr2.3644' => 'acertr', 'Atru.chr6.2422' => 'acertr', 'Atru.chr7.1112' => 'acertr', 'AUR62005469' => 'cqu', 'AUR62011166' => 'cqu', 'AUR62013319' => 'cqu', 'AUR62024273' => 'cqu', 'AUR62028420' => 'cqu', 'AUR62041942' => 'cqu', 'BcaB01g04969' => 'bca', 'BcaB01g06371' => 'bca', 'BcaB02g11494' => 'bca', 'BcaB03g15382' => 'bca', 'BcaB08g36994' => 'bca', 'BcaC03g13477' => 'bca', 'BcaC03g13478' => 'bca', 'BcaC03g13480' => 'bca', 'BcaC03g13481' => 'bca', 'BcaC03g13486' => 'bca', 'BcaC04g19031' => 'bca', 'BcaC04g23085' => 'bca', 'BcaC05g25094' => 'bca', 'BcaC05g25096' => 'bca', 'BcaC05g25138' => 'bca', 'BcaC05g30416' => 'bca', 'BcaC05g30455' => 'bca', 'BcaC06g30979' => 'bca', 'BcaC06g33805' => 'bca', 'BcaC08g46021' => 'bca', 'BcaNung03154' => 'bca', 'BolC2t06623H' => 'bol', 'BolC2t06632H' => 'bol', 'BolC2t06635H' => 'bol', 'BolC2t06638H' => 'bol', 'BolC3t13266H' => 'bol', 'BolC5t29776H' => 'bol', 'BolC6t38912H' => 'bol', 'BolC7t44183H' => 'bol', 'BolC9t54123H' => 'bol', 'BolC9t59107H' => 'bol', 'BraA02t05221Z' => 'bra', 'BraA03t09996Z' => 'bra', 'BraA05t23210Z' => 'bra', 'BraA06t24068Z' => 'bra', 'BraA06t27032Z' => 'bra', 'BraA08t35176Z' => 'bra', 'BraA09t36680Z' => 'bra', 'BraA10t44471Z' => 'bra', 'C02p06760' => 'bna', 'C02p06890' => 'bna', 'C02p07010' => 'bna', 'C03p07660' => 'bna', 'C05p10300' => 'bna', 'C06p38150' => 'bna', 'C07p36650' => 'bna', 'C08p15770' => 'bna', 'C09p12300' => 'bna', 'C09p62700' => 'bna', 'C09p75040' => 'bna', 'CAN.G13.1' => 'can', 'CAN.G138.4' => 'can', 'CAN.G44.6' => 'can', 'CAN.G473.19' => 'can', 'CANSAT01G0835' => 'cansat', 'CANSAT11G0246' => 'cansat', 'CANSAT11G1766' => 'cansat', 'CANSAT64G1954' => 'cansat', 'CARHR013330' => 'chi', 'CARHR060530' => 'chi', 'CARHR075300' => 'chi', 'CARHR105120' => 'chi', 'CARHR148910' => 'chi', 'CARHR198830' => 'chi', 'Carub.0001s1275' => 'cru', 'Carub.0002s1437' => 'cru', 'Carub.0003s0044' => 'cru', 'Carub.0003s2787' => 'cru', 'Carub.0005s0597' => 'cru', 'Carub.0006s1266' => 'cru', 'Ca_06935_v3' => 'car', 'Ca_13559_v3' => 'car', 'Ca_16941_v3' => 'car', 'Ca_16960_v3' => 'car', 'Ca_17775_v3' => 'car', 'Ca_30464_v3' => 'car', 'Cc06_g08160' => 'ccan', 'Cc07_g01520' => 'ccan', 'Cc11_g15810' => 'ccan', 'CDE02G2840' => 'cde', 'CDE03G0093' => 'cde', 'CDE04G2127' => 'cde', 'CDE07G1857' => 'cde', 'CDE09G1246' => 'cde', 'Cfa003412' => 'cfa', 'Cfa007341' => 'cfa', 'Cfa009220' => 'cfa', 'Ciclev10008737m.g' => 'ccl', 'Ciclev10015565m.g' => 'ccl', 'Ciclev10031761m.g' => 'ccl', 'CiPaw.03G045300' => 'cil', 'CiPaw.03G247200' => 'cil', 'CiPaw.04G029500' => 'cil', 'CiPaw.04G174000' => 'cil', 'CiPaw.05G181200' => 'cil', 'CiPaw.06G067100' => 'cil', 'ClCG05G025800' => 'cla', 'ClCG06G011400' => 'cla', 'ClCG09G019360' => 'cla', 'COL.COLO4_04827' => 'col', 'COL.COLO4_29170' => 'col', 'COL.COLO4_35131' => 'col', 'COL.COLO4_35132' => 'col', 'Cpa.g.sc33.32' => 'cpa', 'Cpa.g.sc46.29' => 'cpa', 'Cpa.g.sc796.1' => 'cpa', 'CsaV3_1G030420' => 'csa', 'CsaV3_5G027050' => 'csa', 'CsaV3_5G031040' => 'csa', 'CsaV3_UNG023130' => 'csa', 'CSS0007726' => 'camsi', 'CSS0016433' => 'camsi', 'CSS0017656' => 'camsi', 'CSS0025364' => 'camsi', 'CSS0027582' => 'camsi', 'CSS0047288' => 'camsi', 'CSS0049950' => 'camsi', 'DCAR_003843' => 'dca', 'DCAR_007052' => 'dca', 'DCAR_020884' => 'dca', 'DCAR_021730' => 'dca', 'DCAR_024423' => 'dca', 'DCAR_026509' => 'dca', 'DCAR_031158' => 'dca', 'Dinv14728' => 'din', 'Dinv15219' => 'din', 'Dinv25728' => 'din', 'Dinv33428' => 'din', 'Dinv36489' => 'din', 'Dinv41486' => 'din', 'Duzib147G0469' => 'dzi', 'Duzib168G0060' => 'dzi', 'Duzib187G1215' => 'dzi', 'Duzib248G0692' => 'dzi', 'Duzib251G0767' => 'dzi', 'Duzib264G0446' => 'dzi', 'Duzib268G0691' => 'dzi', 'ECA232G4767' => 'eca', 'ECA233G2838' => 'eca', 'ECA234G0391' => 'eca', 'ECA234G0857' => 'eca', 'ECA236G1593' => 'eca', 'ECA238G0565' => 'eca', 'ECA246G1027' => 'eca', 'ECA246G3223' => 'eca', 'ECA246G3470' => 'eca', 'EL10Ac6g13829' => 'bvu', 'EL10Ac6g14093' => 'bvu', 'EL10Ac8g18707' => 'bvu', 'Eucgr.C01369' => 'egr', 'Eucgr.H02492' => 'egr', 'Eucgr.I01733' => 'egr', 'Eucgr.J02255' => 'egr', 'Eucgr.J02257' => 'egr', 'Eucgr.J02258' => 'egr', 'FAN02G1601' => 'fan', 'FAN03G1586' => 'fan', 'FAN03G2986' => 'fan', 'FAN05G4837' => 'fan', 'FAN06G0146' => 'fan', 'FAN07G0858' => 'fan', 'FAN09G3179' => 'fan', 'FAN10G0669' => 'fan', 'FAN12G2358' => 'fan', 'FAN14G4198' => 'fan', 'FAN14G5112' => 'fan', 'FAN17G0342' => 'fan', 'FAN19G0342' => 'fan', 'FAN19G0962' => 'fan', 'FAN19G1101' => 'fan', 'FAN19G1872' => 'fan', 'FAN22G0356' => 'fan', 'FAN23G0744' => 'fan', 'FAN23G1914' => 'fan', 'FAN26G0032' => 'fan', 'FAN28G0625' => 'fan', 'FvH4_1g02710' => 'fve', 'FvH4_1g02720' => 'fve', 'FvH4_4g25670' => 'fve', 'FvH4_6g51700' => 'fve', 'FvH4_7g20170' => 'fve', 'Glyma.05G175000' => 'gma', 'Glyma.08G132300' => 'gma', 'Glyma.11G243000' => 'gma', 'Glyma.13G158900' => 'gma', 'Glyma.17G112400' => 'gma', 'Glyma.18G014100' => 'gma', 'Glyma.19G003100' => 'gma', 'Glyma.19G056500' => 'gma', 'Gohir.A01G158900' => 'ghi', 'Gohir.A05G312600' => 'ghi', 'Gohir.A05G354900' => 'ghi', 'Gohir.A07G037200' => 'ghi', 'Gohir.A09G030000' => 'ghi', 'Gohir.A12G145200' => 'ghi', 'Gohir.D01G151500' => 'ghi', 'Gohir.D04G058300' => 'ghi', 'Gohir.D05G314100' => 'ghi', 'Gohir.D07G041400' => 'ghi', 'Gohir.D09G029700' => 'ghi', 'Gohir.D12G149700' => 'ghi', 'Gorai.001G043800' => 'gra', 'Gorai.002G187800' => 'gra', 'Gorai.006G034700' => 'gra', 'Gorai.008G161200' => 'gra', 'Gorai.009G335700' => 'gra', 'Gorai.012G065000' => 'gra', 'GSVIVG01000535001' => 'vvi', 'GSVIVG01015572001' => 'vvi', 'GSVIVG01032386001' => 'vvi', 'HanXRQChr05g0138531' => 'han', 'HanXRQChr06g0174391' => 'han', 'HanXRQChr07g0199021' => 'han', 'HanXRQChr08g0208211' => 'han', 'HanXRQChr09g0255471' => 'han', 'HanXRQChr10g0315791' => 'han', 'HanXRQChr12g0371991' => 'han', 'HanXRQChr15g0475251' => 'han', 'HanXRQChr17g0540001' => 'han', 'HanXRQChr17g0548631' => 'han', 'HanXRQChr17g0569561' => 'han', 'Haze_12256' => 'cav', 'Haze_14756' => 'cav', 'Haze_25528' => 'cav', 'Hma1.2p1_0079F.1_g041020' => 'hma', 'Hma1.2p1_0818F.1_g223260' => 'hma', 'Hma1.2p1_1747F.1_g300530' => 'hma', 'HPP92_004607' => 'vpl', 'HPP92_004608' => 'vpl', 'HPP92_006181' => 'vpl', 'HPP92_012192' => 'vpl', 'HPP92_015680' => 'vpl', 'HPP92_020249' => 'vpl', 'HPP92_021376' => 'vpl', 'HPP92_024275' => 'vpl', 'Hund06031' => 'sun', 'Hund25391' => 'sun', 'Lalb_Chr07g0185371' => 'lal', 'Lalb_Chr07g0185381' => 'lal', 'Lalb_Chr12g0204011' => 'lal', 'Lalb_Chr13g0301671' => 'lal', 'Lalb_Chr14g0362851' => 'lal', 'Lalb_Chr24g0403581' => 'lal', 'Lj1g0000233' => 'lja', 'Lj2g0018120' => 'lja', 'Lj3C621T0' => 'lonja', 'Lj3P1059T14' => 'lonja', 'Lj3P611T9' => 'lonja', 'Lj3P614T13' => 'lonja', 'Lj3P615T5' => 'lonja', 'Lj4g0012315' => 'lja', 'Lj4g0026182' => 'lja', 'Lj6P813T16' => 'lonja', 'Lj7C427T7' => 'lonja', 'Lj7C427T8' => 'lonja', 'Lj7P600T41' => 'lonja', 'Lju41C42G17' => 'lonja', 'Lsat_1_v5_gn_0_47300' => 'lsa', 'Lsat_1_v5_gn_2_91280' => 'lsa', 'Lsat_1_v5_gn_3_30561' => 'lsa', 'Lsat_1_v5_gn_4_184321' => 'lsa', 'Lsat_1_v5_gn_4_4041' => 'lsa', 'Lsat_1_v5_gn_5_92000' => 'lsa', 'Lsat_1_v5_gn_8_152940' => 'lsa', 'Lsat_1_v5_gn_8_62401' => 'lsa', 'Manes.06G055900' => 'mes', 'Manes.12G022200' => 'mes', 'Manes.13G023300' => 'mes', 'Manes.14G115000' => 'mes', 'Manes.15G151700' => 'mes', 'Manes.17G111300' => 'mes', 'Mapoly0226s0009' => 'mpo', 'MBI02_g25363_MAGBIO' => 'mbi', 'MBI06_g00027_MAGBIO' => 'mbi', 'MBI10_g13034_MAGBIO' => 'mbi', 'MD09G1023400' => 'mdo', 'MD13G1100100' => 'mdo', 'MD15G1169200' => 'mdo', 'MD16G1101100' => 'mdo', 'MD17G1022900' => 'mdo', 'Medtr3g096150' => 'mtr', 'Medtr4g115070' => 'mtr', 'Medtr7g033325' => 'mtr', 'Medtr8g089840' => 'mtr', 'MELO3C010319.2' => 'cme', 'MELO3C011944.2' => 'cme', 'MELO3C021589.2' => 'cme', 'Migut.E00207' => 'egut', 'Migut.H00067' => 'egut', 'Migut.K00433' => 'egut', 'Migut.K00606' => 'egut', 'Migut.K01410' => 'egut', 'MSTRG.13347' => 'ama', 'MSTRG.24045' => 'ama', 'MSTRG.2428' => 'ama', 'MSTRG.26410' => 'ama', 'MSTRG.3139' => 'ama', 'MSTRG.3286' => 'ama', 'MSTRG.563' => 'ama', 'MSTRG.7941' => 'ama', 'Nitab4.5_0000028g0060' => 'nta', 'Nitab4.5_0000065g0260' => 'nta', 'Nitab4.5_0000112g0060' => 'nta', 'Nitab4.5_0000489g0120' => 'nta', 'Nitab4.5_0001776g0050' => 'nta', 'Nitab4.5_0001854g0010' => 'nta', 'Nitab4.5_0001860g0020' => 'nta', 'Nitab4.5_0004352g0010' => 'nta', 'Nitab4.5_0008716g0020' => 'nta', 'Nitab4.5_0008922g0010' => 'nta', 'Nn3g16693' => 'nnu', 'Nn4g22596' => 'nnu', 'Nn7g37639' => 'nnu', 'Oeu001701.1' => 'oeu', 'Oeu018149.1' => 'oeu', 'Oeu026220.1' => 'oeu', 'Oeu038635.1' => 'oeu', 'Oeu049176.1' => 'oeu', 'Oeu056706.1' => 'oeu', 'Oeu056937.1' => 'oeu', 'Oeu057540.1' => 'oeu', 'Os02g0594900' => 'osa', 'Os02g0595100' => 'osa', 'Os04g0477500' => 'osa', 'Os12g0611900' => 'osa', 'Peaxi162Scf00076g00020' => 'pax', 'Peaxi162Scf00128g00217' => 'pax', 'Peaxi162Scf00129g01640' => 'pax', 'Peaxi162Scf00669g00007' => 'pax', 'Peaxi162Scf00700g00421' => 'pax', 'Peaxi162Scf00801g00038' => 'pax', 'Peaxi162Scf00891g00025' => 'pax', 'PGR083G0909' => 'pgr', 'PGR119G1005' => 'pgr', 'PGR142G2236' => 'pgr', 'PGR142G3388' => 'pgr', 'PGSC0003DMG400004514' => 'stu', 'PGSC0003DMG400012635' => 'stu', 'PGSC0003DMG400015730' => 'stu', 'PGSC0003DMG400018611' => 'stu', 'PGSC0003DMG400030897' => 'stu', 'Phvul.001G254800' => 'pvu', 'Phvul.002G260100' => 'pvu', 'Phvul.003G167600' => 'pvu', 'Phvul.004G005100' => 'pvu', 'Potri.001G343600' => 'ptr', 'Potri.006G066700' => 'ptr', 'Potri.008G186000' => 'ptr', 'Potri.010G046900' => 'ptr', 'Potri.018G127900' => 'ptr', 'Pp3c20_17750' => 'ppa', 'Pp3c24_4380' => 'ppa', 'Prupe.1G245800' => 'ppe', 'Prupe.3G293400' => 'ppe', 'Prupe.7G247400' => 'ppe', 'Psat0s145g0120' => 'psa', 'Psat0s595g0040' => 'psa', 'Psat0s595g0120' => 'psa', 'Psat3g175040' => 'psa', 'Psat7g058120' => 'psa', 'PSO017G0428' => 'pso', 'PSO063G7510' => 'pso', 'PSO067G0046' => 'pso', 'PSO478G1073' => 'pso', 'PSO675G3677' => 'pso', 'PSO675G6558' => 'pso', 'PSO675G7520' => 'pso', 'PSO675G8959' => 'pso', 'QL02p074089' => 'qlo', 'QL02p089614' => 'qlo', 'QL03p057736' => 'qlo', 'RcHm_v2.0_Chr1g0364131' => 'rch', 'RcHm_v2.0_Chr2g0087801' => 'rch', 'RcHm_v2.0_Chr2g0087821' => 'rch', 'RcHm_v2.0_Chr2g0173231' => 'rch', 'RcHm_v2.0_Chr4g0433111' => 'rch', 'Rhsim03G0250300' => 'rsi', 'Rhsim08G0048400' => 'rsi', 'Rhsim10G0014800' => 'rsi', 'Rhsim12G0040100' => 'rsi', 'Rhsim12G0109700' => 'rsi', 'Sabra06G0049600' => 'sbr', 'Sabra08G0141000' => 'sbr', 'Sabra10G0021400' => 'sbr', 'Sabra16G0222900' => 'sbr', 'Sabra18G0108600' => 'sbr', 'SalBow1G0433' => 'sbo', 'SalBow1G2038' => 'sbo', 'SalBow1G5003' => 'sbo', 'SalBow7G1197' => 'sbo', 'SalBow8G3506' => 'sbo', 'Sc03g0007300' => 'sci', 'Sc11g0000950' => 'sci', 'Sc14g0008750' => 'sci', 'Sc18g0000420' => 'sci', 'Sed0006754' => 'sed', 'Sed0008741' => 'sed', 'Sed0017172' => 'sed', 'Sed0018925' => 'sed', 'Sed0023326' => 'sed', 'Sed0025909' => 'sed', 'SEGI_05333' => 'sgi', 'SEGI_10362' => 'sgi', 'SEGI_13380' => 'sgi', 'SEGI_24306' => 'sgi', 'SEGI_29077' => 'sgi', 'SEGI_29095' => 'sgi', 'SEGI_36534' => 'sgi', 'SEGI_37506' => 'sgi', 'SEGI_38321' => 'sgi', 'SGA_v2.0_scaffold307G48031' => 'sas', 'SGA_v2.0_scaffold47G17507' => 'sas', 'SGA_v2.0_scaffold63G21736' => 'sas', 'SGA_v2.0_scaffold87G27070' => 'sas', 'SHI17794' => 'shi', 'SHI28851' => 'shi', 'SMO165G0155' => 'smo', 'SMO340G0217' => 'smo', 'SMO367G1210' => 'smo', 'Solyc02g093430.3' => 'sly', 'Solyc05g013580.4' => 'sly', 'Solyc07g008030.3' => 'sly', 'Solyc12g035470.2' => 'sly', 'Sopen02g038020' => 'spe', 'Sopen05g008490' => 'spe', 'Sopen07g003910' => 'spe', 'Sopen12g015240' => 'spe', 'Sp1g11550' => 'spa', 'Sp2g16710' => 'spa', 'Sp3g00430' => 'spa', 'Sp3g26780' => 'spa', 'Sp5g22900' => 'spa', 'Sp6g29530' => 'spa', 'TAR371G0794' => 'tar', 'TAR374G0164' => 'tar', 'TAR622G0165' => 'tar', 'TAR626G0929' => 'tar', 'TAR629G2155' => 'tar', 'THA.LOC104805282' => 'tha', 'THA.LOC104805363' => 'tha', 'THA.LOC104808968' => 'tha', 'THA.LOC104821093' => 'tha', 'THA.LOC104823953' => 'tha', 'THA.LOC104825562' => 'tha', 'THA.LOC104825665' => 'tha', 'Thecc.02G261400' => 'tca', 'Thecc.04G019200' => 'tca', 'Thecc.09G130400' => 'tca', 'Thhalv10004374m.g' => 'esa', 'Thhalv10007850m.g' => 'esa', 'Thhalv10013782m.g' => 'esa', 'Thhalv10018686m.g' => 'esa', 'Thhalv10020899m.g' => 'esa', 'Thhalv10022755m.g' => 'esa', 'TPR.G23851' => 'tpr', 'TPR.G26500' => 'tpr', 'TPR.G27267' => 'tpr', 'TPR.G32001' => 'tpr', 'TPR.G6251' => 'tpr', 'TPR.G8167' => 'tpr', 'TWI12G1330' => 'twi', 'TWI18G1239' => 'twi', 'TWI34G0979' => 'twi', 'TWI36G0670' => 'twi', 'TWI36G0707' => 'twi', 'TWI56G0233' => 'twi', 'TWI75G1809' => 'twi', 'unitig_21.g20874' => 'ugi', 'unitig_26.g10343' => 'ugi', 'unitig_46.g18392' => 'ugi', 'unitig_52.g17178' => 'ugi', 'unitig_8.g2934' => 'ugi', 'vmacro01122' => 'vma', 'vmacro05875' => 'vma', 'vmacro06147' => 'vma', 'vmacro16191' => 'vma', 'vmacro18293' => 'vma', 'VMungo0251G3707' => 'vmu', 'VMungo0464G1521' => 'vmu', 'VMungo1215G0205' => 'vmu', 'VMungo1383G2484' => 'vmu', 'Zm00001eb079610' => 'zma', 'Zm00001eb135990' => 'zma', 'Zm00001eb183710' => 'zma', 'Zm00001eb246020' => 'zma' ) $gf_id = 'HOM05D001124' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001124' ) $data_identifier = 'HOM05D001124' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 6, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 7, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 21, 'bol' => (int) 10, 'bra' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 6, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 9, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 21, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 8, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 10, 'lsa' => (int) 8, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 8, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 9, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb246020' $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' => 'HOM05D001124', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '548', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02520' => 'bna', 'A03p06630' => 'bna', 'A05p44460' => 'bna', 'A06p08710' => 'bna', 'A06p41090' => 'bna', 'A07p32320' => 'bna', 'A08p32520' => 'bna', 'A09p10360' => 'bna', 'A10p24080' => 'bna', 'Aa31LG11G15250' => 'aar', 'Aa31LG1G1800' => 'aar', 'Aa31LG2G5120' => 'aar', 'Aa31LG2G6070' => 'aar', 'Aa31LG5G10770' => 'aar', 'Aa31sc61G90' => 'aar', 'Actinidia01352' => 'ach', 'Actinidia05983' => 'ach', 'Actinidia08133' => 'ach', 'Actinidia15101' => 'ach', 'Actinidia26379' => 'ach', 'Actinidia35778' => 'ach', 'Actinidia36123' => 'ach', 'Actinidia37436' => 'ach', 'Actinidia38730' => 'ach', 'Ah.02g128210' => 'amhyb', 'Ah.03g132990' => 'amhyb', 'Ah.14g079410' => 'amhyb', 'AL1G24640' => 'aly', 'AL2G26680' => 'aly', 'AL3G10530' => 'aly', 'AL3G45230' => 'aly', 'AL5G15230' => 'aly', 'AL5G16960' => 'aly', 'AL6G25210' => 'aly', 'Aqoxy2G00441' => 'aox', 'Aqoxy3G01236' => 'aox', 'Aqoxy5G03746' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3RQ047' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C7GMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9C8JER' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MBL6KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YXCZ83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZANX40' => 'arhy', 'AT1G12990' => 'ath', 'AT1G67880' => 'ath', 'AT2G13290' => 'ath', 'AT3G01620' => 'ath', 'AT3G26445' => 'ath', 'AT3G27540' => 'ath', 'AT5G14480' => 'ath', 'ATR0824G026' => 'atr', 'ATR1098G019' => 'atr', 'Atru.chr11.2145' => 'acertr', 'Atru.chr2.3636' => 'acertr', 'Atru.chr2.3644' => 'acertr', 'Atru.chr6.2422' => 'acertr', 'Atru.chr7.1112' => 'acertr', 'AUR62005469' => 'cqu', 'AUR62011166' => 'cqu', 'AUR62013319' => 'cqu', 'AUR62024273' => 'cqu', 'AUR62028420' => 'cqu', 'AUR62041942' => 'cqu', 'BcaB01g04969' => 'bca', 'BcaB01g06371' => 'bca', 'BcaB02g11494' => 'bca', 'BcaB03g15382' => 'bca', 'BcaB08g36994' => 'bca', 'BcaC03g13477' => 'bca', 'BcaC03g13478' => 'bca', 'BcaC03g13480' => 'bca', 'BcaC03g13481' => 'bca', 'BcaC03g13486' => 'bca', 'BcaC04g19031' => 'bca', 'BcaC04g23085' => 'bca', 'BcaC05g25094' => 'bca', 'BcaC05g25096' => 'bca', 'BcaC05g25138' => 'bca', 'BcaC05g30416' => 'bca', 'BcaC05g30455' => 'bca', 'BcaC06g30979' => 'bca', 'BcaC06g33805' => 'bca', 'BcaC08g46021' => 'bca', 'BcaNung03154' => 'bca', 'BolC2t06623H' => 'bol', 'BolC2t06632H' => 'bol', 'BolC2t06635H' => 'bol', 'BolC2t06638H' => 'bol', 'BolC3t13266H' => 'bol', 'BolC5t29776H' => 'bol', 'BolC6t38912H' => 'bol', 'BolC7t44183H' => 'bol', 'BolC9t54123H' => 'bol', 'BolC9t59107H' => 'bol', 'BraA02t05221Z' => 'bra', 'BraA03t09996Z' => 'bra', 'BraA05t23210Z' => 'bra', 'BraA06t24068Z' => 'bra', 'BraA06t27032Z' => 'bra', 'BraA08t35176Z' => 'bra', 'BraA09t36680Z' => 'bra', 'BraA10t44471Z' => 'bra', 'C02p06760' => 'bna', 'C02p06890' => 'bna', 'C02p07010' => 'bna', 'C03p07660' => 'bna', 'C05p10300' => 'bna', 'C06p38150' => 'bna', 'C07p36650' => 'bna', 'C08p15770' => 'bna', 'C09p12300' => 'bna', 'C09p62700' => 'bna', 'C09p75040' => 'bna', 'CAN.G13.1' => 'can', 'CAN.G138.4' => 'can', 'CAN.G44.6' => 'can', 'CAN.G473.19' => 'can', 'CANSAT01G0835' => 'cansat', 'CANSAT11G0246' => 'cansat', 'CANSAT11G1766' => 'cansat', 'CANSAT64G1954' => 'cansat', 'CARHR013330' => 'chi', 'CARHR060530' => 'chi', 'CARHR075300' => 'chi', 'CARHR105120' => 'chi', 'CARHR148910' => 'chi', 'CARHR198830' => 'chi', 'Carub.0001s1275' => 'cru', 'Carub.0002s1437' => 'cru', 'Carub.0003s0044' => 'cru', 'Carub.0003s2787' => 'cru', 'Carub.0005s0597' => 'cru', 'Carub.0006s1266' => 'cru', 'Ca_06935_v3' => 'car', 'Ca_13559_v3' => 'car', 'Ca_16941_v3' => 'car', 'Ca_16960_v3' => 'car', 'Ca_17775_v3' => 'car', 'Ca_30464_v3' => 'car', 'Cc06_g08160' => 'ccan', 'Cc07_g01520' => 'ccan', 'Cc11_g15810' => 'ccan', 'CDE02G2840' => 'cde', 'CDE03G0093' => 'cde', 'CDE04G2127' => 'cde', 'CDE07G1857' => 'cde', 'CDE09G1246' => 'cde', 'Cfa003412' => 'cfa', 'Cfa007341' => 'cfa', 'Cfa009220' => 'cfa', 'Ciclev10008737m.g' => 'ccl', 'Ciclev10015565m.g' => 'ccl', 'Ciclev10031761m.g' => 'ccl', 'CiPaw.03G045300' => 'cil', 'CiPaw.03G247200' => 'cil', 'CiPaw.04G029500' => 'cil', 'CiPaw.04G174000' => 'cil', 'CiPaw.05G181200' => 'cil', 'CiPaw.06G067100' => 'cil', 'ClCG05G025800' => 'cla', 'ClCG06G011400' => 'cla', 'ClCG09G019360' => 'cla', 'COL.COLO4_04827' => 'col', 'COL.COLO4_29170' => 'col', 'COL.COLO4_35131' => 'col', 'COL.COLO4_35132' => 'col', 'Cpa.g.sc33.32' => 'cpa', 'Cpa.g.sc46.29' => 'cpa', 'Cpa.g.sc796.1' => 'cpa', 'CsaV3_1G030420' => 'csa', 'CsaV3_5G027050' => 'csa', 'CsaV3_5G031040' => 'csa', 'CsaV3_UNG023130' => 'csa', 'CSS0007726' => 'camsi', 'CSS0016433' => 'camsi', 'CSS0017656' => 'camsi', 'CSS0025364' => 'camsi', 'CSS0027582' => 'camsi', 'CSS0047288' => 'camsi', 'CSS0049950' => 'camsi', 'DCAR_003843' => 'dca', 'DCAR_007052' => 'dca', 'DCAR_020884' => 'dca', 'DCAR_021730' => 'dca', 'DCAR_024423' => 'dca', 'DCAR_026509' => 'dca', 'DCAR_031158' => 'dca', 'Dinv14728' => 'din', 'Dinv15219' => 'din', 'Dinv25728' => 'din', 'Dinv33428' => 'din', 'Dinv36489' => 'din', 'Dinv41486' => 'din', 'Duzib147G0469' => 'dzi', 'Duzib168G0060' => 'dzi', 'Duzib187G1215' => 'dzi', 'Duzib248G0692' => 'dzi', 'Duzib251G0767' => 'dzi', 'Duzib264G0446' => 'dzi', 'Duzib268G0691' => 'dzi', 'ECA232G4767' => 'eca', 'ECA233G2838' => 'eca', 'ECA234G0391' => 'eca', 'ECA234G0857' => 'eca', 'ECA236G1593' => 'eca', 'ECA238G0565' => 'eca', 'ECA246G1027' => 'eca', 'ECA246G3223' => 'eca', 'ECA246G3470' => 'eca', 'EL10Ac6g13829' => 'bvu', 'EL10Ac6g14093' => 'bvu', 'EL10Ac8g18707' => 'bvu', 'Eucgr.C01369' => 'egr', 'Eucgr.H02492' => 'egr', 'Eucgr.I01733' => 'egr', 'Eucgr.J02255' => 'egr', 'Eucgr.J02257' => 'egr', 'Eucgr.J02258' => 'egr', 'FAN02G1601' => 'fan', 'FAN03G1586' => 'fan', 'FAN03G2986' => 'fan', 'FAN05G4837' => 'fan', 'FAN06G0146' => 'fan', 'FAN07G0858' => 'fan', 'FAN09G3179' => 'fan', 'FAN10G0669' => 'fan', 'FAN12G2358' => 'fan', 'FAN14G4198' => 'fan', 'FAN14G5112' => 'fan', 'FAN17G0342' => 'fan', 'FAN19G0342' => 'fan', 'FAN19G0962' => 'fan', 'FAN19G1101' => 'fan', 'FAN19G1872' => 'fan', 'FAN22G0356' => 'fan', 'FAN23G0744' => 'fan', 'FAN23G1914' => 'fan', 'FAN26G0032' => 'fan', 'FAN28G0625' => 'fan', 'FvH4_1g02710' => 'fve', 'FvH4_1g02720' => 'fve', 'FvH4_4g25670' => 'fve', 'FvH4_6g51700' => 'fve', 'FvH4_7g20170' => 'fve', 'Glyma.05G175000' => 'gma', 'Glyma.08G132300' => 'gma', 'Glyma.11G243000' => 'gma', 'Glyma.13G158900' => 'gma', 'Glyma.17G112400' => 'gma', 'Glyma.18G014100' => 'gma', 'Glyma.19G003100' => 'gma', 'Glyma.19G056500' => 'gma', 'Gohir.A01G158900' => 'ghi', 'Gohir.A05G312600' => 'ghi', 'Gohir.A05G354900' => 'ghi', 'Gohir.A07G037200' => 'ghi', 'Gohir.A09G030000' => 'ghi', 'Gohir.A12G145200' => 'ghi', 'Gohir.D01G151500' => 'ghi', 'Gohir.D04G058300' => 'ghi', 'Gohir.D05G314100' => 'ghi', 'Gohir.D07G041400' => 'ghi', 'Gohir.D09G029700' => 'ghi', 'Gohir.D12G149700' => 'ghi', 'Gorai.001G043800' => 'gra', 'Gorai.002G187800' => 'gra', 'Gorai.006G034700' => 'gra', 'Gorai.008G161200' => 'gra', 'Gorai.009G335700' => 'gra', 'Gorai.012G065000' => 'gra', 'GSVIVG01000535001' => 'vvi', 'GSVIVG01015572001' => 'vvi', 'GSVIVG01032386001' => 'vvi', 'HanXRQChr05g0138531' => 'han', 'HanXRQChr06g0174391' => 'han', 'HanXRQChr07g0199021' => 'han', 'HanXRQChr08g0208211' => 'han', 'HanXRQChr09g0255471' => 'han', 'HanXRQChr10g0315791' => 'han', 'HanXRQChr12g0371991' => 'han', 'HanXRQChr15g0475251' => 'han', 'HanXRQChr17g0540001' => 'han', 'HanXRQChr17g0548631' => 'han', 'HanXRQChr17g0569561' => 'han', 'Haze_12256' => 'cav', 'Haze_14756' => 'cav', 'Haze_25528' => 'cav', 'Hma1.2p1_0079F.1_g041020' => 'hma', 'Hma1.2p1_0818F.1_g223260' => 'hma', 'Hma1.2p1_1747F.1_g300530' => 'hma', 'HPP92_004607' => 'vpl', 'HPP92_004608' => 'vpl', 'HPP92_006181' => 'vpl', 'HPP92_012192' => 'vpl', 'HPP92_015680' => 'vpl', 'HPP92_020249' => 'vpl', 'HPP92_021376' => 'vpl', 'HPP92_024275' => 'vpl', 'Hund06031' => 'sun', 'Hund25391' => 'sun', 'Lalb_Chr07g0185371' => 'lal', 'Lalb_Chr07g0185381' => 'lal', 'Lalb_Chr12g0204011' => 'lal', 'Lalb_Chr13g0301671' => 'lal', 'Lalb_Chr14g0362851' => 'lal', 'Lalb_Chr24g0403581' => 'lal', 'Lj1g0000233' => 'lja', 'Lj2g0018120' => 'lja', 'Lj3C621T0' => 'lonja', 'Lj3P1059T14' => 'lonja', 'Lj3P611T9' => 'lonja', 'Lj3P614T13' => 'lonja', 'Lj3P615T5' => 'lonja', 'Lj4g0012315' => 'lja', 'Lj4g0026182' => 'lja', 'Lj6P813T16' => 'lonja', 'Lj7C427T7' => 'lonja', 'Lj7C427T8' => 'lonja', 'Lj7P600T41' => 'lonja', 'Lju41C42G17' => 'lonja', 'Lsat_1_v5_gn_0_47300' => 'lsa', 'Lsat_1_v5_gn_2_91280' => 'lsa', 'Lsat_1_v5_gn_3_30561' => 'lsa', 'Lsat_1_v5_gn_4_184321' => 'lsa', 'Lsat_1_v5_gn_4_4041' => 'lsa', 'Lsat_1_v5_gn_5_92000' => 'lsa', 'Lsat_1_v5_gn_8_152940' => 'lsa', 'Lsat_1_v5_gn_8_62401' => 'lsa', 'Manes.06G055900' => 'mes', 'Manes.12G022200' => 'mes', 'Manes.13G023300' => 'mes', 'Manes.14G115000' => 'mes', 'Manes.15G151700' => 'mes', 'Manes.17G111300' => 'mes', 'Mapoly0226s0009' => 'mpo', 'MBI02_g25363_MAGBIO' => 'mbi', 'MBI06_g00027_MAGBIO' => 'mbi', 'MBI10_g13034_MAGBIO' => 'mbi', 'MD09G1023400' => 'mdo', 'MD13G1100100' => 'mdo', 'MD15G1169200' => 'mdo', 'MD16G1101100' => 'mdo', 'MD17G1022900' => 'mdo', 'Medtr3g096150' => 'mtr', 'Medtr4g115070' => 'mtr', 'Medtr7g033325' => 'mtr', 'Medtr8g089840' => 'mtr', 'MELO3C010319.2' => 'cme', 'MELO3C011944.2' => 'cme', 'MELO3C021589.2' => 'cme', 'Migut.E00207' => 'egut', 'Migut.H00067' => 'egut', 'Migut.K00433' => 'egut', 'Migut.K00606' => 'egut', 'Migut.K01410' => 'egut', 'MSTRG.13347' => 'ama', 'MSTRG.24045' => 'ama', 'MSTRG.2428' => 'ama', 'MSTRG.26410' => 'ama', 'MSTRG.3139' => 'ama', 'MSTRG.3286' => 'ama', 'MSTRG.563' => 'ama', 'MSTRG.7941' => 'ama', 'Nitab4.5_0000028g0060' => 'nta', 'Nitab4.5_0000065g0260' => 'nta', 'Nitab4.5_0000112g0060' => 'nta', 'Nitab4.5_0000489g0120' => 'nta', 'Nitab4.5_0001776g0050' => 'nta', 'Nitab4.5_0001854g0010' => 'nta', 'Nitab4.5_0001860g0020' => 'nta', 'Nitab4.5_0004352g0010' => 'nta', 'Nitab4.5_0008716g0020' => 'nta', 'Nitab4.5_0008922g0010' => 'nta', 'Nn3g16693' => 'nnu', 'Nn4g22596' => 'nnu', 'Nn7g37639' => 'nnu', 'Oeu001701.1' => 'oeu', 'Oeu018149.1' => 'oeu', 'Oeu026220.1' => 'oeu', 'Oeu038635.1' => 'oeu', 'Oeu049176.1' => 'oeu', 'Oeu056706.1' => 'oeu', 'Oeu056937.1' => 'oeu', 'Oeu057540.1' => 'oeu', 'Os02g0594900' => 'osa', 'Os02g0595100' => 'osa', 'Os04g0477500' => 'osa', 'Os12g0611900' => 'osa', 'Peaxi162Scf00076g00020' => 'pax', 'Peaxi162Scf00128g00217' => 'pax', 'Peaxi162Scf00129g01640' => 'pax', 'Peaxi162Scf00669g00007' => 'pax', 'Peaxi162Scf00700g00421' => 'pax', 'Peaxi162Scf00801g00038' => 'pax', 'Peaxi162Scf00891g00025' => 'pax', 'PGR083G0909' => 'pgr', 'PGR119G1005' => 'pgr', 'PGR142G2236' => 'pgr', 'PGR142G3388' => 'pgr', 'PGSC0003DMG400004514' => 'stu', 'PGSC0003DMG400012635' => 'stu', 'PGSC0003DMG400015730' => 'stu', 'PGSC0003DMG400018611' => 'stu', 'PGSC0003DMG400030897' => 'stu', 'Phvul.001G254800' => 'pvu', 'Phvul.002G260100' => 'pvu', 'Phvul.003G167600' => 'pvu', 'Phvul.004G005100' => 'pvu', 'Potri.001G343600' => 'ptr', 'Potri.006G066700' => 'ptr', 'Potri.008G186000' => 'ptr', 'Potri.010G046900' => 'ptr', 'Potri.018G127900' => 'ptr', 'Pp3c20_17750' => 'ppa', 'Pp3c24_4380' => 'ppa', 'Prupe.1G245800' => 'ppe', 'Prupe.3G293400' => 'ppe', 'Prupe.7G247400' => 'ppe', 'Psat0s145g0120' => 'psa', 'Psat0s595g0040' => 'psa', 'Psat0s595g0120' => 'psa', 'Psat3g175040' => 'psa', 'Psat7g058120' => 'psa', 'PSO017G0428' => 'pso', 'PSO063G7510' => 'pso', 'PSO067G0046' => 'pso', 'PSO478G1073' => 'pso', 'PSO675G3677' => 'pso', 'PSO675G6558' => 'pso', 'PSO675G7520' => 'pso', 'PSO675G8959' => 'pso', 'QL02p074089' => 'qlo', 'QL02p089614' => 'qlo', 'QL03p057736' => 'qlo', 'RcHm_v2.0_Chr1g0364131' => 'rch', 'RcHm_v2.0_Chr2g0087801' => 'rch', 'RcHm_v2.0_Chr2g0087821' => 'rch', 'RcHm_v2.0_Chr2g0173231' => 'rch', 'RcHm_v2.0_Chr4g0433111' => 'rch', 'Rhsim03G0250300' => 'rsi', 'Rhsim08G0048400' => 'rsi', 'Rhsim10G0014800' => 'rsi', 'Rhsim12G0040100' => 'rsi', 'Rhsim12G0109700' => 'rsi', 'Sabra06G0049600' => 'sbr', 'Sabra08G0141000' => 'sbr', 'Sabra10G0021400' => 'sbr', 'Sabra16G0222900' => 'sbr', 'Sabra18G0108600' => 'sbr', 'SalBow1G0433' => 'sbo', 'SalBow1G2038' => 'sbo', 'SalBow1G5003' => 'sbo', 'SalBow7G1197' => 'sbo', 'SalBow8G3506' => 'sbo', 'Sc03g0007300' => 'sci', 'Sc11g0000950' => 'sci', 'Sc14g0008750' => 'sci', 'Sc18g0000420' => 'sci', 'Sed0006754' => 'sed', 'Sed0008741' => 'sed', 'Sed0017172' => 'sed', 'Sed0018925' => 'sed', 'Sed0023326' => 'sed', 'Sed0025909' => 'sed', 'SEGI_05333' => 'sgi', 'SEGI_10362' => 'sgi', 'SEGI_13380' => 'sgi', 'SEGI_24306' => 'sgi', 'SEGI_29077' => 'sgi', 'SEGI_29095' => 'sgi', 'SEGI_36534' => 'sgi', 'SEGI_37506' => 'sgi', 'SEGI_38321' => 'sgi', 'SGA_v2.0_scaffold307G48031' => 'sas', 'SGA_v2.0_scaffold47G17507' => 'sas', 'SGA_v2.0_scaffold63G21736' => 'sas', 'SGA_v2.0_scaffold87G27070' => 'sas', 'SHI17794' => 'shi', 'SHI28851' => 'shi', 'SMO165G0155' => 'smo', 'SMO340G0217' => 'smo', 'SMO367G1210' => 'smo', 'Solyc02g093430.3' => 'sly', 'Solyc05g013580.4' => 'sly', 'Solyc07g008030.3' => 'sly', 'Solyc12g035470.2' => 'sly', 'Sopen02g038020' => 'spe', 'Sopen05g008490' => 'spe', 'Sopen07g003910' => 'spe', 'Sopen12g015240' => 'spe', 'Sp1g11550' => 'spa', 'Sp2g16710' => 'spa', 'Sp3g00430' => 'spa', 'Sp3g26780' => 'spa', 'Sp5g22900' => 'spa', 'Sp6g29530' => 'spa', 'TAR371G0794' => 'tar', 'TAR374G0164' => 'tar', 'TAR622G0165' => 'tar', 'TAR626G0929' => 'tar', 'TAR629G2155' => 'tar', 'THA.LOC104805282' => 'tha', 'THA.LOC104805363' => 'tha', 'THA.LOC104808968' => 'tha', 'THA.LOC104821093' => 'tha', 'THA.LOC104823953' => 'tha', 'THA.LOC104825562' => 'tha', 'THA.LOC104825665' => 'tha', 'Thecc.02G261400' => 'tca', 'Thecc.04G019200' => 'tca', 'Thecc.09G130400' => 'tca', 'Thhalv10004374m.g' => 'esa', 'Thhalv10007850m.g' => 'esa', 'Thhalv10013782m.g' => 'esa', 'Thhalv10018686m.g' => 'esa', 'Thhalv10020899m.g' => 'esa', 'Thhalv10022755m.g' => 'esa', 'TPR.G23851' => 'tpr', 'TPR.G26500' => 'tpr', 'TPR.G27267' => 'tpr', 'TPR.G32001' => 'tpr', 'TPR.G6251' => 'tpr', 'TPR.G8167' => 'tpr', 'TWI12G1330' => 'twi', 'TWI18G1239' => 'twi', 'TWI34G0979' => 'twi', 'TWI36G0670' => 'twi', 'TWI36G0707' => 'twi', 'TWI56G0233' => 'twi', 'TWI75G1809' => 'twi', 'unitig_21.g20874' => 'ugi', 'unitig_26.g10343' => 'ugi', 'unitig_46.g18392' => 'ugi', 'unitig_52.g17178' => 'ugi', 'unitig_8.g2934' => 'ugi', 'vmacro01122' => 'vma', 'vmacro05875' => 'vma', 'vmacro06147' => 'vma', 'vmacro16191' => 'vma', 'vmacro18293' => 'vma', 'VMungo0251G3707' => 'vmu', 'VMungo0464G1521' => 'vmu', 'VMungo1215G0205' => 'vmu', 'VMungo1383G2484' => 'vmu', 'Zm00001eb079610' => 'zma', 'Zm00001eb135990' => 'zma', 'Zm00001eb183710' => 'zma', 'Zm00001eb246020' => 'zma' ), 'gf_id' => 'HOM05D001124', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001124' ), 'data_identifier' => 'HOM05D001124', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001124', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '548', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02520' => 'bna', 'A03p06630' => 'bna', 'A05p44460' => 'bna', 'A06p08710' => 'bna', 'A06p41090' => 'bna', 'A07p32320' => 'bna', 'A08p32520' => 'bna', 'A09p10360' => 'bna', 'A10p24080' => 'bna', 'Aa31LG11G15250' => 'aar', 'Aa31LG1G1800' => 'aar', 'Aa31LG2G5120' => 'aar', 'Aa31LG2G6070' => 'aar', 'Aa31LG5G10770' => 'aar', 'Aa31sc61G90' => 'aar', 'Actinidia01352' => 'ach', 'Actinidia05983' => 'ach', 'Actinidia08133' => 'ach', 'Actinidia15101' => 'ach', 'Actinidia26379' => 'ach', 'Actinidia35778' => 'ach', 'Actinidia36123' => 'ach', 'Actinidia37436' => 'ach', 'Actinidia38730' => 'ach', 'Ah.02g128210' => 'amhyb', 'Ah.03g132990' => 'amhyb', 'Ah.14g079410' => 'amhyb', 'AL1G24640' => 'aly', 'AL2G26680' => 'aly', 'AL3G10530' => 'aly', 'AL3G45230' => 'aly', 'AL5G15230' => 'aly', 'AL5G16960' => 'aly', 'AL6G25210' => 'aly', 'Aqoxy2G00441' => 'aox', 'Aqoxy3G01236' => 'aox', 'Aqoxy5G03746' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3RQ047' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C7GMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9C8JER' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MBL6KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YXCZ83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZANX40' => 'arhy', 'AT1G12990' => 'ath', 'AT1G67880' => 'ath', 'AT2G13290' => 'ath', 'AT3G01620' => 'ath', 'AT3G26445' => 'ath', 'AT3G27540' => 'ath', 'AT5G14480' => 'ath', 'ATR0824G026' => 'atr', 'ATR1098G019' => 'atr', 'Atru.chr11.2145' => 'acertr', 'Atru.chr2.3636' => 'acertr', 'Atru.chr2.3644' => 'acertr', 'Atru.chr6.2422' => 'acertr', 'Atru.chr7.1112' => 'acertr', 'AUR62005469' => 'cqu', 'AUR62011166' => 'cqu', 'AUR62013319' => 'cqu', 'AUR62024273' => 'cqu', 'AUR62028420' => 'cqu', 'AUR62041942' => 'cqu', 'BcaB01g04969' => 'bca', 'BcaB01g06371' => 'bca', 'BcaB02g11494' => 'bca', 'BcaB03g15382' => 'bca', 'BcaB08g36994' => 'bca', 'BcaC03g13477' => 'bca', 'BcaC03g13478' => 'bca', 'BcaC03g13480' => 'bca', 'BcaC03g13481' => 'bca', 'BcaC03g13486' => 'bca', 'BcaC04g19031' => 'bca', 'BcaC04g23085' => 'bca', 'BcaC05g25094' => 'bca', 'BcaC05g25096' => 'bca', 'BcaC05g25138' => 'bca', 'BcaC05g30416' => 'bca', 'BcaC05g30455' => 'bca', 'BcaC06g30979' => 'bca', 'BcaC06g33805' => 'bca', 'BcaC08g46021' => 'bca', 'BcaNung03154' => 'bca', 'BolC2t06623H' => 'bol', 'BolC2t06632H' => 'bol', 'BolC2t06635H' => 'bol', 'BolC2t06638H' => 'bol', 'BolC3t13266H' => 'bol', 'BolC5t29776H' => 'bol', 'BolC6t38912H' => 'bol', 'BolC7t44183H' => 'bol', 'BolC9t54123H' => 'bol', 'BolC9t59107H' => 'bol', 'BraA02t05221Z' => 'bra', 'BraA03t09996Z' => 'bra', 'BraA05t23210Z' => 'bra', 'BraA06t24068Z' => 'bra', 'BraA06t27032Z' => 'bra', 'BraA08t35176Z' => 'bra', 'BraA09t36680Z' => 'bra', 'BraA10t44471Z' => 'bra', 'C02p06760' => 'bna', 'C02p06890' => 'bna', 'C02p07010' => 'bna', 'C03p07660' => 'bna', 'C05p10300' => 'bna', 'C06p38150' => 'bna', 'C07p36650' => 'bna', 'C08p15770' => 'bna', 'C09p12300' => 'bna', 'C09p62700' => 'bna', 'C09p75040' => 'bna', 'CAN.G13.1' => 'can', 'CAN.G138.4' => 'can', 'CAN.G44.6' => 'can', 'CAN.G473.19' => 'can', 'CANSAT01G0835' => 'cansat', 'CANSAT11G0246' => 'cansat', 'CANSAT11G1766' => 'cansat', 'CANSAT64G1954' => 'cansat', 'CARHR013330' => 'chi', 'CARHR060530' => 'chi', 'CARHR075300' => 'chi', 'CARHR105120' => 'chi', 'CARHR148910' => 'chi', 'CARHR198830' => 'chi', 'Carub.0001s1275' => 'cru', 'Carub.0002s1437' => 'cru', 'Carub.0003s0044' => 'cru', 'Carub.0003s2787' => 'cru', 'Carub.0005s0597' => 'cru', 'Carub.0006s1266' => 'cru', 'Ca_06935_v3' => 'car', 'Ca_13559_v3' => 'car', 'Ca_16941_v3' => 'car', 'Ca_16960_v3' => 'car', 'Ca_17775_v3' => 'car', 'Ca_30464_v3' => 'car', 'Cc06_g08160' => 'ccan', 'Cc07_g01520' => 'ccan', 'Cc11_g15810' => 'ccan', 'CDE02G2840' => 'cde', 'CDE03G0093' => 'cde', 'CDE04G2127' => 'cde', 'CDE07G1857' => 'cde', 'CDE09G1246' => 'cde', 'Cfa003412' => 'cfa', 'Cfa007341' => 'cfa', 'Cfa009220' => 'cfa', 'Ciclev10008737m.g' => 'ccl', 'Ciclev10015565m.g' => 'ccl', 'Ciclev10031761m.g' => 'ccl', 'CiPaw.03G045300' => 'cil', 'CiPaw.03G247200' => 'cil', 'CiPaw.04G029500' => 'cil', 'CiPaw.04G174000' => 'cil', 'CiPaw.05G181200' => 'cil', 'CiPaw.06G067100' => 'cil', 'ClCG05G025800' => 'cla', 'ClCG06G011400' => 'cla', 'ClCG09G019360' => 'cla', 'COL.COLO4_04827' => 'col', 'COL.COLO4_29170' => 'col', 'COL.COLO4_35131' => 'col', 'COL.COLO4_35132' => 'col', 'Cpa.g.sc33.32' => 'cpa', 'Cpa.g.sc46.29' => 'cpa', 'Cpa.g.sc796.1' => 'cpa', 'CsaV3_1G030420' => 'csa', 'CsaV3_5G027050' => 'csa', 'CsaV3_5G031040' => 'csa', 'CsaV3_UNG023130' => 'csa', 'CSS0007726' => 'camsi', 'CSS0016433' => 'camsi', 'CSS0017656' => 'camsi', 'CSS0025364' => 'camsi', 'CSS0027582' => 'camsi', 'CSS0047288' => 'camsi', 'CSS0049950' => 'camsi', 'DCAR_003843' => 'dca', 'DCAR_007052' => 'dca', 'DCAR_020884' => 'dca', 'DCAR_021730' => 'dca', 'DCAR_024423' => 'dca', 'DCAR_026509' => 'dca', 'DCAR_031158' => 'dca', 'Dinv14728' => 'din', 'Dinv15219' => 'din', 'Dinv25728' => 'din', 'Dinv33428' => 'din', 'Dinv36489' => 'din', 'Dinv41486' => 'din', 'Duzib147G0469' => 'dzi', 'Duzib168G0060' => 'dzi', 'Duzib187G1215' => 'dzi', 'Duzib248G0692' => 'dzi', 'Duzib251G0767' => 'dzi', 'Duzib264G0446' => 'dzi', 'Duzib268G0691' => 'dzi', 'ECA232G4767' => 'eca', 'ECA233G2838' => 'eca', 'ECA234G0391' => 'eca', 'ECA234G0857' => 'eca', 'ECA236G1593' => 'eca', 'ECA238G0565' => 'eca', 'ECA246G1027' => 'eca', 'ECA246G3223' => 'eca', 'ECA246G3470' => 'eca', 'EL10Ac6g13829' => 'bvu', 'EL10Ac6g14093' => 'bvu', 'EL10Ac8g18707' => 'bvu', 'Eucgr.C01369' => 'egr', 'Eucgr.H02492' => 'egr', 'Eucgr.I01733' => 'egr', 'Eucgr.J02255' => 'egr', 'Eucgr.J02257' => 'egr', 'Eucgr.J02258' => 'egr', 'FAN02G1601' => 'fan', 'FAN03G1586' => 'fan', 'FAN03G2986' => 'fan', 'FAN05G4837' => 'fan', 'FAN06G0146' => 'fan', 'FAN07G0858' => 'fan', 'FAN09G3179' => 'fan', 'FAN10G0669' => 'fan', 'FAN12G2358' => 'fan', 'FAN14G4198' => 'fan', 'FAN14G5112' => 'fan', 'FAN17G0342' => 'fan', 'FAN19G0342' => 'fan', 'FAN19G0962' => 'fan', 'FAN19G1101' => 'fan', 'FAN19G1872' => 'fan', 'FAN22G0356' => 'fan', 'FAN23G0744' => 'fan', 'FAN23G1914' => 'fan', 'FAN26G0032' => 'fan', 'FAN28G0625' => 'fan', 'FvH4_1g02710' => 'fve', 'FvH4_1g02720' => 'fve', 'FvH4_4g25670' => 'fve', 'FvH4_6g51700' => 'fve', 'FvH4_7g20170' => 'fve', 'Glyma.05G175000' => 'gma', 'Glyma.08G132300' => 'gma', 'Glyma.11G243000' => 'gma', 'Glyma.13G158900' => 'gma', 'Glyma.17G112400' => 'gma', 'Glyma.18G014100' => 'gma', 'Glyma.19G003100' => 'gma', 'Glyma.19G056500' => 'gma', 'Gohir.A01G158900' => 'ghi', 'Gohir.A05G312600' => 'ghi', 'Gohir.A05G354900' => 'ghi', 'Gohir.A07G037200' => 'ghi', 'Gohir.A09G030000' => 'ghi', 'Gohir.A12G145200' => 'ghi', 'Gohir.D01G151500' => 'ghi', 'Gohir.D04G058300' => 'ghi', 'Gohir.D05G314100' => 'ghi', 'Gohir.D07G041400' => 'ghi', 'Gohir.D09G029700' => 'ghi', 'Gohir.D12G149700' => 'ghi', 'Gorai.001G043800' => 'gra', 'Gorai.002G187800' => 'gra', 'Gorai.006G034700' => 'gra', 'Gorai.008G161200' => 'gra', 'Gorai.009G335700' => 'gra', 'Gorai.012G065000' => 'gra', 'GSVIVG01000535001' => 'vvi', 'GSVIVG01015572001' => 'vvi', 'GSVIVG01032386001' => 'vvi', 'HanXRQChr05g0138531' => 'han', 'HanXRQChr06g0174391' => 'han', 'HanXRQChr07g0199021' => 'han', 'HanXRQChr08g0208211' => 'han', 'HanXRQChr09g0255471' => 'han', 'HanXRQChr10g0315791' => 'han', 'HanXRQChr12g0371991' => 'han', 'HanXRQChr15g0475251' => 'han', 'HanXRQChr17g0540001' => 'han', 'HanXRQChr17g0548631' => 'han', 'HanXRQChr17g0569561' => 'han', 'Haze_12256' => 'cav', 'Haze_14756' => 'cav', 'Haze_25528' => 'cav', 'Hma1.2p1_0079F.1_g041020' => 'hma', 'Hma1.2p1_0818F.1_g223260' => 'hma', 'Hma1.2p1_1747F.1_g300530' => 'hma', 'HPP92_004607' => 'vpl', 'HPP92_004608' => 'vpl', 'HPP92_006181' => 'vpl', 'HPP92_012192' => 'vpl', 'HPP92_015680' => 'vpl', 'HPP92_020249' => 'vpl', 'HPP92_021376' => 'vpl', 'HPP92_024275' => 'vpl', 'Hund06031' => 'sun', 'Hund25391' => 'sun', 'Lalb_Chr07g0185371' => 'lal', 'Lalb_Chr07g0185381' => 'lal', 'Lalb_Chr12g0204011' => 'lal', 'Lalb_Chr13g0301671' => 'lal', 'Lalb_Chr14g0362851' => 'lal', 'Lalb_Chr24g0403581' => 'lal', 'Lj1g0000233' => 'lja', 'Lj2g0018120' => 'lja', 'Lj3C621T0' => 'lonja', 'Lj3P1059T14' => 'lonja', 'Lj3P611T9' => 'lonja', 'Lj3P614T13' => 'lonja', 'Lj3P615T5' => 'lonja', 'Lj4g0012315' => 'lja', 'Lj4g0026182' => 'lja', 'Lj6P813T16' => 'lonja', 'Lj7C427T7' => 'lonja', 'Lj7C427T8' => 'lonja', 'Lj7P600T41' => 'lonja', 'Lju41C42G17' => 'lonja', 'Lsat_1_v5_gn_0_47300' => 'lsa', 'Lsat_1_v5_gn_2_91280' => 'lsa', 'Lsat_1_v5_gn_3_30561' => 'lsa', 'Lsat_1_v5_gn_4_184321' => 'lsa', 'Lsat_1_v5_gn_4_4041' => 'lsa', 'Lsat_1_v5_gn_5_92000' => 'lsa', 'Lsat_1_v5_gn_8_152940' => 'lsa', 'Lsat_1_v5_gn_8_62401' => 'lsa', 'Manes.06G055900' => 'mes', 'Manes.12G022200' => 'mes', 'Manes.13G023300' => 'mes', 'Manes.14G115000' => 'mes', 'Manes.15G151700' => 'mes', 'Manes.17G111300' => 'mes', 'Mapoly0226s0009' => 'mpo', 'MBI02_g25363_MAGBIO' => 'mbi', 'MBI06_g00027_MAGBIO' => 'mbi', 'MBI10_g13034_MAGBIO' => 'mbi', 'MD09G1023400' => 'mdo', 'MD13G1100100' => 'mdo', 'MD15G1169200' => 'mdo', 'MD16G1101100' => 'mdo', 'MD17G1022900' => 'mdo', 'Medtr3g096150' => 'mtr', 'Medtr4g115070' => 'mtr', 'Medtr7g033325' => 'mtr', 'Medtr8g089840' => 'mtr', 'MELO3C010319.2' => 'cme', 'MELO3C011944.2' => 'cme', 'MELO3C021589.2' => 'cme', 'Migut.E00207' => 'egut', 'Migut.H00067' => 'egut', 'Migut.K00433' => 'egut', 'Migut.K00606' => 'egut', 'Migut.K01410' => 'egut', 'MSTRG.13347' => 'ama', 'MSTRG.24045' => 'ama', 'MSTRG.2428' => 'ama', 'MSTRG.26410' => 'ama', 'MSTRG.3139' => 'ama', 'MSTRG.3286' => 'ama', 'MSTRG.563' => 'ama', 'MSTRG.7941' => 'ama', 'Nitab4.5_0000028g0060' => 'nta', 'Nitab4.5_0000065g0260' => 'nta', 'Nitab4.5_0000112g0060' => 'nta', 'Nitab4.5_0000489g0120' => 'nta', 'Nitab4.5_0001776g0050' => 'nta', 'Nitab4.5_0001854g0010' => 'nta', 'Nitab4.5_0001860g0020' => 'nta', 'Nitab4.5_0004352g0010' => 'nta', 'Nitab4.5_0008716g0020' => 'nta', 'Nitab4.5_0008922g0010' => 'nta', 'Nn3g16693' => 'nnu', 'Nn4g22596' => 'nnu', 'Nn7g37639' => 'nnu', 'Oeu001701.1' => 'oeu', 'Oeu018149.1' => 'oeu', 'Oeu026220.1' => 'oeu', 'Oeu038635.1' => 'oeu', 'Oeu049176.1' => 'oeu', 'Oeu056706.1' => 'oeu', 'Oeu056937.1' => 'oeu', 'Oeu057540.1' => 'oeu', 'Os02g0594900' => 'osa', 'Os02g0595100' => 'osa', 'Os04g0477500' => 'osa', 'Os12g0611900' => 'osa', 'Peaxi162Scf00076g00020' => 'pax', 'Peaxi162Scf00128g00217' => 'pax', 'Peaxi162Scf00129g01640' => 'pax', 'Peaxi162Scf00669g00007' => 'pax', 'Peaxi162Scf00700g00421' => 'pax', 'Peaxi162Scf00801g00038' => 'pax', 'Peaxi162Scf00891g00025' => 'pax', 'PGR083G0909' => 'pgr', 'PGR119G1005' => 'pgr', 'PGR142G2236' => 'pgr', 'PGR142G3388' => 'pgr', 'PGSC0003DMG400004514' => 'stu', 'PGSC0003DMG400012635' => 'stu', 'PGSC0003DMG400015730' => 'stu', 'PGSC0003DMG400018611' => 'stu', 'PGSC0003DMG400030897' => 'stu', 'Phvul.001G254800' => 'pvu', 'Phvul.002G260100' => 'pvu', 'Phvul.003G167600' => 'pvu', 'Phvul.004G005100' => 'pvu', 'Potri.001G343600' => 'ptr', 'Potri.006G066700' => 'ptr', 'Potri.008G186000' => 'ptr', 'Potri.010G046900' => 'ptr', 'Potri.018G127900' => 'ptr', 'Pp3c20_17750' => 'ppa', 'Pp3c24_4380' => 'ppa', 'Prupe.1G245800' => 'ppe', 'Prupe.3G293400' => 'ppe', 'Prupe.7G247400' => 'ppe', 'Psat0s145g0120' => 'psa', 'Psat0s595g0040' => 'psa', 'Psat0s595g0120' => 'psa', 'Psat3g175040' => 'psa', 'Psat7g058120' => 'psa', 'PSO017G0428' => 'pso', 'PSO063G7510' => 'pso', 'PSO067G0046' => 'pso', 'PSO478G1073' => 'pso', 'PSO675G3677' => 'pso', 'PSO675G6558' => 'pso', 'PSO675G7520' => 'pso', 'PSO675G8959' => 'pso', 'QL02p074089' => 'qlo', 'QL02p089614' => 'qlo', 'QL03p057736' => 'qlo', 'RcHm_v2.0_Chr1g0364131' => 'rch', 'RcHm_v2.0_Chr2g0087801' => 'rch', 'RcHm_v2.0_Chr2g0087821' => 'rch', 'RcHm_v2.0_Chr2g0173231' => 'rch', 'RcHm_v2.0_Chr4g0433111' => 'rch', 'Rhsim03G0250300' => 'rsi', 'Rhsim08G0048400' => 'rsi', 'Rhsim10G0014800' => 'rsi', 'Rhsim12G0040100' => 'rsi', 'Rhsim12G0109700' => 'rsi', 'Sabra06G0049600' => 'sbr', 'Sabra08G0141000' => 'sbr', 'Sabra10G0021400' => 'sbr', 'Sabra16G0222900' => 'sbr', 'Sabra18G0108600' => 'sbr', 'SalBow1G0433' => 'sbo', 'SalBow1G2038' => 'sbo', 'SalBow1G5003' => 'sbo', 'SalBow7G1197' => 'sbo', 'SalBow8G3506' => 'sbo', 'Sc03g0007300' => 'sci', 'Sc11g0000950' => 'sci', 'Sc14g0008750' => 'sci', 'Sc18g0000420' => 'sci', 'Sed0006754' => 'sed', 'Sed0008741' => 'sed', 'Sed0017172' => 'sed', 'Sed0018925' => 'sed', 'Sed0023326' => 'sed', 'Sed0025909' => 'sed', 'SEGI_05333' => 'sgi', 'SEGI_10362' => 'sgi', 'SEGI_13380' => 'sgi', 'SEGI_24306' => 'sgi', 'SEGI_29077' => 'sgi', 'SEGI_29095' => 'sgi', 'SEGI_36534' => 'sgi', 'SEGI_37506' => 'sgi', 'SEGI_38321' => 'sgi', 'SGA_v2.0_scaffold307G48031' => 'sas', 'SGA_v2.0_scaffold47G17507' => 'sas', 'SGA_v2.0_scaffold63G21736' => 'sas', 'SGA_v2.0_scaffold87G27070' => 'sas', 'SHI17794' => 'shi', 'SHI28851' => 'shi', 'SMO165G0155' => 'smo', 'SMO340G0217' => 'smo', 'SMO367G1210' => 'smo', 'Solyc02g093430.3' => 'sly', 'Solyc05g013580.4' => 'sly', 'Solyc07g008030.3' => 'sly', 'Solyc12g035470.2' => 'sly', 'Sopen02g038020' => 'spe', 'Sopen05g008490' => 'spe', 'Sopen07g003910' => 'spe', 'Sopen12g015240' => 'spe', 'Sp1g11550' => 'spa', 'Sp2g16710' => 'spa', 'Sp3g00430' => 'spa', 'Sp3g26780' => 'spa', 'Sp5g22900' => 'spa', 'Sp6g29530' => 'spa', 'TAR371G0794' => 'tar', 'TAR374G0164' => 'tar', 'TAR622G0165' => 'tar', 'TAR626G0929' => 'tar', 'TAR629G2155' => 'tar', 'THA.LOC104805282' => 'tha', 'THA.LOC104805363' => 'tha', 'THA.LOC104808968' => 'tha', 'THA.LOC104821093' => 'tha', 'THA.LOC104823953' => 'tha', 'THA.LOC104825562' => 'tha', 'THA.LOC104825665' => 'tha', 'Thecc.02G261400' => 'tca', 'Thecc.04G019200' => 'tca', 'Thecc.09G130400' => 'tca', 'Thhalv10004374m.g' => 'esa', 'Thhalv10007850m.g' => 'esa', 'Thhalv10013782m.g' => 'esa', 'Thhalv10018686m.g' => 'esa', 'Thhalv10020899m.g' => 'esa', 'Thhalv10022755m.g' => 'esa', 'TPR.G23851' => 'tpr', 'TPR.G26500' => 'tpr', 'TPR.G27267' => 'tpr', 'TPR.G32001' => 'tpr', 'TPR.G6251' => 'tpr', 'TPR.G8167' => 'tpr', 'TWI12G1330' => 'twi', 'TWI18G1239' => 'twi', 'TWI34G0979' => 'twi', 'TWI36G0670' => 'twi', 'TWI36G0707' => 'twi', 'TWI56G0233' => 'twi', 'TWI75G1809' => 'twi', 'unitig_21.g20874' => 'ugi', 'unitig_26.g10343' => 'ugi', 'unitig_46.g18392' => 'ugi', 'unitig_52.g17178' => 'ugi', 'unitig_8.g2934' => 'ugi', 'vmacro01122' => 'vma', 'vmacro05875' => 'vma', 'vmacro06147' => 'vma', 'vmacro16191' => 'vma', 'vmacro18293' => 'vma', 'VMungo0251G3707' => 'vmu', 'VMungo0464G1521' => 'vmu', 'VMungo1215G0205' => 'vmu', 'VMungo1383G2484' => 'vmu', 'Zm00001eb079610' => 'zma', 'Zm00001eb135990' => 'zma', 'Zm00001eb183710' => 'zma', 'Zm00001eb246020' => 'zma' ) $gf_id = 'HOM05D001124' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001124' ) $data_identifier = 'HOM05D001124' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 6, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 7, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 21, 'bol' => (int) 10, 'bra' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 6, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 9, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 21, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 8, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 10, 'lsa' => (int) 8, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 8, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 9, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb246020' $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' => 'HOM05D001124', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '548', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02520' => 'bna', 'A03p06630' => 'bna', 'A05p44460' => 'bna', 'A06p08710' => 'bna', 'A06p41090' => 'bna', 'A07p32320' => 'bna', 'A08p32520' => 'bna', 'A09p10360' => 'bna', 'A10p24080' => 'bna', 'Aa31LG11G15250' => 'aar', 'Aa31LG1G1800' => 'aar', 'Aa31LG2G5120' => 'aar', 'Aa31LG2G6070' => 'aar', 'Aa31LG5G10770' => 'aar', 'Aa31sc61G90' => 'aar', 'Actinidia01352' => 'ach', 'Actinidia05983' => 'ach', 'Actinidia08133' => 'ach', 'Actinidia15101' => 'ach', 'Actinidia26379' => 'ach', 'Actinidia35778' => 'ach', 'Actinidia36123' => 'ach', 'Actinidia37436' => 'ach', 'Actinidia38730' => 'ach', 'Ah.02g128210' => 'amhyb', 'Ah.03g132990' => 'amhyb', 'Ah.14g079410' => 'amhyb', 'AL1G24640' => 'aly', 'AL2G26680' => 'aly', 'AL3G10530' => 'aly', 'AL3G45230' => 'aly', 'AL5G15230' => 'aly', 'AL5G16960' => 'aly', 'AL6G25210' => 'aly', 'Aqoxy2G00441' => 'aox', 'Aqoxy3G01236' => 'aox', 'Aqoxy5G03746' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3RQ047' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C7GMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9C8JER' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MBL6KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YXCZ83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZANX40' => 'arhy', 'AT1G12990' => 'ath', 'AT1G67880' => 'ath', 'AT2G13290' => 'ath', 'AT3G01620' => 'ath', 'AT3G26445' => 'ath', 'AT3G27540' => 'ath', 'AT5G14480' => 'ath', 'ATR0824G026' => 'atr', 'ATR1098G019' => 'atr', 'Atru.chr11.2145' => 'acertr', 'Atru.chr2.3636' => 'acertr', 'Atru.chr2.3644' => 'acertr', 'Atru.chr6.2422' => 'acertr', 'Atru.chr7.1112' => 'acertr', 'AUR62005469' => 'cqu', 'AUR62011166' => 'cqu', 'AUR62013319' => 'cqu', 'AUR62024273' => 'cqu', 'AUR62028420' => 'cqu', 'AUR62041942' => 'cqu', 'BcaB01g04969' => 'bca', 'BcaB01g06371' => 'bca', 'BcaB02g11494' => 'bca', 'BcaB03g15382' => 'bca', 'BcaB08g36994' => 'bca', 'BcaC03g13477' => 'bca', 'BcaC03g13478' => 'bca', 'BcaC03g13480' => 'bca', 'BcaC03g13481' => 'bca', 'BcaC03g13486' => 'bca', 'BcaC04g19031' => 'bca', 'BcaC04g23085' => 'bca', 'BcaC05g25094' => 'bca', 'BcaC05g25096' => 'bca', 'BcaC05g25138' => 'bca', 'BcaC05g30416' => 'bca', 'BcaC05g30455' => 'bca', 'BcaC06g30979' => 'bca', 'BcaC06g33805' => 'bca', 'BcaC08g46021' => 'bca', 'BcaNung03154' => 'bca', 'BolC2t06623H' => 'bol', 'BolC2t06632H' => 'bol', 'BolC2t06635H' => 'bol', 'BolC2t06638H' => 'bol', 'BolC3t13266H' => 'bol', 'BolC5t29776H' => 'bol', 'BolC6t38912H' => 'bol', 'BolC7t44183H' => 'bol', 'BolC9t54123H' => 'bol', 'BolC9t59107H' => 'bol', 'BraA02t05221Z' => 'bra', 'BraA03t09996Z' => 'bra', 'BraA05t23210Z' => 'bra', 'BraA06t24068Z' => 'bra', 'BraA06t27032Z' => 'bra', 'BraA08t35176Z' => 'bra', 'BraA09t36680Z' => 'bra', 'BraA10t44471Z' => 'bra', 'C02p06760' => 'bna', 'C02p06890' => 'bna', 'C02p07010' => 'bna', 'C03p07660' => 'bna', 'C05p10300' => 'bna', 'C06p38150' => 'bna', 'C07p36650' => 'bna', 'C08p15770' => 'bna', 'C09p12300' => 'bna', 'C09p62700' => 'bna', 'C09p75040' => 'bna', 'CAN.G13.1' => 'can', 'CAN.G138.4' => 'can', 'CAN.G44.6' => 'can', 'CAN.G473.19' => 'can', 'CANSAT01G0835' => 'cansat', 'CANSAT11G0246' => 'cansat', 'CANSAT11G1766' => 'cansat', 'CANSAT64G1954' => 'cansat', 'CARHR013330' => 'chi', 'CARHR060530' => 'chi', 'CARHR075300' => 'chi', 'CARHR105120' => 'chi', 'CARHR148910' => 'chi', 'CARHR198830' => 'chi', 'Carub.0001s1275' => 'cru', 'Carub.0002s1437' => 'cru', 'Carub.0003s0044' => 'cru', 'Carub.0003s2787' => 'cru', 'Carub.0005s0597' => 'cru', 'Carub.0006s1266' => 'cru', 'Ca_06935_v3' => 'car', 'Ca_13559_v3' => 'car', 'Ca_16941_v3' => 'car', 'Ca_16960_v3' => 'car', 'Ca_17775_v3' => 'car', 'Ca_30464_v3' => 'car', 'Cc06_g08160' => 'ccan', 'Cc07_g01520' => 'ccan', 'Cc11_g15810' => 'ccan', 'CDE02G2840' => 'cde', 'CDE03G0093' => 'cde', 'CDE04G2127' => 'cde', 'CDE07G1857' => 'cde', 'CDE09G1246' => 'cde', 'Cfa003412' => 'cfa', 'Cfa007341' => 'cfa', 'Cfa009220' => 'cfa', 'Ciclev10008737m.g' => 'ccl', 'Ciclev10015565m.g' => 'ccl', 'Ciclev10031761m.g' => 'ccl', 'CiPaw.03G045300' => 'cil', 'CiPaw.03G247200' => 'cil', 'CiPaw.04G029500' => 'cil', 'CiPaw.04G174000' => 'cil', 'CiPaw.05G181200' => 'cil', 'CiPaw.06G067100' => 'cil', 'ClCG05G025800' => 'cla', 'ClCG06G011400' => 'cla', 'ClCG09G019360' => 'cla', 'COL.COLO4_04827' => 'col', 'COL.COLO4_29170' => 'col', 'COL.COLO4_35131' => 'col', 'COL.COLO4_35132' => 'col', 'Cpa.g.sc33.32' => 'cpa', 'Cpa.g.sc46.29' => 'cpa', 'Cpa.g.sc796.1' => 'cpa', 'CsaV3_1G030420' => 'csa', 'CsaV3_5G027050' => 'csa', 'CsaV3_5G031040' => 'csa', 'CsaV3_UNG023130' => 'csa', 'CSS0007726' => 'camsi', 'CSS0016433' => 'camsi', 'CSS0017656' => 'camsi', 'CSS0025364' => 'camsi', 'CSS0027582' => 'camsi', 'CSS0047288' => 'camsi', 'CSS0049950' => 'camsi', 'DCAR_003843' => 'dca', 'DCAR_007052' => 'dca', 'DCAR_020884' => 'dca', 'DCAR_021730' => 'dca', 'DCAR_024423' => 'dca', 'DCAR_026509' => 'dca', 'DCAR_031158' => 'dca', 'Dinv14728' => 'din', 'Dinv15219' => 'din', 'Dinv25728' => 'din', 'Dinv33428' => 'din', 'Dinv36489' => 'din', 'Dinv41486' => 'din', 'Duzib147G0469' => 'dzi', 'Duzib168G0060' => 'dzi', 'Duzib187G1215' => 'dzi', 'Duzib248G0692' => 'dzi', 'Duzib251G0767' => 'dzi', 'Duzib264G0446' => 'dzi', 'Duzib268G0691' => 'dzi', 'ECA232G4767' => 'eca', 'ECA233G2838' => 'eca', 'ECA234G0391' => 'eca', 'ECA234G0857' => 'eca', 'ECA236G1593' => 'eca', 'ECA238G0565' => 'eca', 'ECA246G1027' => 'eca', 'ECA246G3223' => 'eca', 'ECA246G3470' => 'eca', 'EL10Ac6g13829' => 'bvu', 'EL10Ac6g14093' => 'bvu', 'EL10Ac8g18707' => 'bvu', 'Eucgr.C01369' => 'egr', 'Eucgr.H02492' => 'egr', 'Eucgr.I01733' => 'egr', 'Eucgr.J02255' => 'egr', 'Eucgr.J02257' => 'egr', 'Eucgr.J02258' => 'egr', 'FAN02G1601' => 'fan', 'FAN03G1586' => 'fan', 'FAN03G2986' => 'fan', 'FAN05G4837' => 'fan', 'FAN06G0146' => 'fan', 'FAN07G0858' => 'fan', 'FAN09G3179' => 'fan', 'FAN10G0669' => 'fan', 'FAN12G2358' => 'fan', 'FAN14G4198' => 'fan', 'FAN14G5112' => 'fan', 'FAN17G0342' => 'fan', 'FAN19G0342' => 'fan', 'FAN19G0962' => 'fan', 'FAN19G1101' => 'fan', 'FAN19G1872' => 'fan', 'FAN22G0356' => 'fan', 'FAN23G0744' => 'fan', 'FAN23G1914' => 'fan', 'FAN26G0032' => 'fan', 'FAN28G0625' => 'fan', 'FvH4_1g02710' => 'fve', 'FvH4_1g02720' => 'fve', 'FvH4_4g25670' => 'fve', 'FvH4_6g51700' => 'fve', 'FvH4_7g20170' => 'fve', 'Glyma.05G175000' => 'gma', 'Glyma.08G132300' => 'gma', 'Glyma.11G243000' => 'gma', 'Glyma.13G158900' => 'gma', 'Glyma.17G112400' => 'gma', 'Glyma.18G014100' => 'gma', 'Glyma.19G003100' => 'gma', 'Glyma.19G056500' => 'gma', 'Gohir.A01G158900' => 'ghi', 'Gohir.A05G312600' => 'ghi', 'Gohir.A05G354900' => 'ghi', 'Gohir.A07G037200' => 'ghi', 'Gohir.A09G030000' => 'ghi', 'Gohir.A12G145200' => 'ghi', 'Gohir.D01G151500' => 'ghi', 'Gohir.D04G058300' => 'ghi', 'Gohir.D05G314100' => 'ghi', 'Gohir.D07G041400' => 'ghi', 'Gohir.D09G029700' => 'ghi', 'Gohir.D12G149700' => 'ghi', 'Gorai.001G043800' => 'gra', 'Gorai.002G187800' => 'gra', 'Gorai.006G034700' => 'gra', 'Gorai.008G161200' => 'gra', 'Gorai.009G335700' => 'gra', 'Gorai.012G065000' => 'gra', 'GSVIVG01000535001' => 'vvi', 'GSVIVG01015572001' => 'vvi', 'GSVIVG01032386001' => 'vvi', 'HanXRQChr05g0138531' => 'han', 'HanXRQChr06g0174391' => 'han', 'HanXRQChr07g0199021' => 'han', 'HanXRQChr08g0208211' => 'han', 'HanXRQChr09g0255471' => 'han', 'HanXRQChr10g0315791' => 'han', 'HanXRQChr12g0371991' => 'han', 'HanXRQChr15g0475251' => 'han', 'HanXRQChr17g0540001' => 'han', 'HanXRQChr17g0548631' => 'han', 'HanXRQChr17g0569561' => 'han', 'Haze_12256' => 'cav', 'Haze_14756' => 'cav', 'Haze_25528' => 'cav', 'Hma1.2p1_0079F.1_g041020' => 'hma', 'Hma1.2p1_0818F.1_g223260' => 'hma', 'Hma1.2p1_1747F.1_g300530' => 'hma', 'HPP92_004607' => 'vpl', 'HPP92_004608' => 'vpl', 'HPP92_006181' => 'vpl', 'HPP92_012192' => 'vpl', 'HPP92_015680' => 'vpl', 'HPP92_020249' => 'vpl', 'HPP92_021376' => 'vpl', 'HPP92_024275' => 'vpl', 'Hund06031' => 'sun', 'Hund25391' => 'sun', 'Lalb_Chr07g0185371' => 'lal', 'Lalb_Chr07g0185381' => 'lal', 'Lalb_Chr12g0204011' => 'lal', 'Lalb_Chr13g0301671' => 'lal', 'Lalb_Chr14g0362851' => 'lal', 'Lalb_Chr24g0403581' => 'lal', 'Lj1g0000233' => 'lja', 'Lj2g0018120' => 'lja', 'Lj3C621T0' => 'lonja', 'Lj3P1059T14' => 'lonja', 'Lj3P611T9' => 'lonja', 'Lj3P614T13' => 'lonja', 'Lj3P615T5' => 'lonja', 'Lj4g0012315' => 'lja', 'Lj4g0026182' => 'lja', 'Lj6P813T16' => 'lonja', 'Lj7C427T7' => 'lonja', 'Lj7C427T8' => 'lonja', 'Lj7P600T41' => 'lonja', 'Lju41C42G17' => 'lonja', 'Lsat_1_v5_gn_0_47300' => 'lsa', 'Lsat_1_v5_gn_2_91280' => 'lsa', 'Lsat_1_v5_gn_3_30561' => 'lsa', 'Lsat_1_v5_gn_4_184321' => 'lsa', 'Lsat_1_v5_gn_4_4041' => 'lsa', 'Lsat_1_v5_gn_5_92000' => 'lsa', 'Lsat_1_v5_gn_8_152940' => 'lsa', 'Lsat_1_v5_gn_8_62401' => 'lsa', 'Manes.06G055900' => 'mes', 'Manes.12G022200' => 'mes', 'Manes.13G023300' => 'mes', 'Manes.14G115000' => 'mes', 'Manes.15G151700' => 'mes', 'Manes.17G111300' => 'mes', 'Mapoly0226s0009' => 'mpo', 'MBI02_g25363_MAGBIO' => 'mbi', 'MBI06_g00027_MAGBIO' => 'mbi', 'MBI10_g13034_MAGBIO' => 'mbi', 'MD09G1023400' => 'mdo', 'MD13G1100100' => 'mdo', 'MD15G1169200' => 'mdo', 'MD16G1101100' => 'mdo', 'MD17G1022900' => 'mdo', 'Medtr3g096150' => 'mtr', 'Medtr4g115070' => 'mtr', 'Medtr7g033325' => 'mtr', 'Medtr8g089840' => 'mtr', 'MELO3C010319.2' => 'cme', 'MELO3C011944.2' => 'cme', 'MELO3C021589.2' => 'cme', 'Migut.E00207' => 'egut', 'Migut.H00067' => 'egut', 'Migut.K00433' => 'egut', 'Migut.K00606' => 'egut', 'Migut.K01410' => 'egut', 'MSTRG.13347' => 'ama', 'MSTRG.24045' => 'ama', 'MSTRG.2428' => 'ama', 'MSTRG.26410' => 'ama', 'MSTRG.3139' => 'ama', 'MSTRG.3286' => 'ama', 'MSTRG.563' => 'ama', 'MSTRG.7941' => 'ama', 'Nitab4.5_0000028g0060' => 'nta', 'Nitab4.5_0000065g0260' => 'nta', 'Nitab4.5_0000112g0060' => 'nta', 'Nitab4.5_0000489g0120' => 'nta', 'Nitab4.5_0001776g0050' => 'nta', 'Nitab4.5_0001854g0010' => 'nta', 'Nitab4.5_0001860g0020' => 'nta', 'Nitab4.5_0004352g0010' => 'nta', 'Nitab4.5_0008716g0020' => 'nta', 'Nitab4.5_0008922g0010' => 'nta', 'Nn3g16693' => 'nnu', 'Nn4g22596' => 'nnu', 'Nn7g37639' => 'nnu', 'Oeu001701.1' => 'oeu', 'Oeu018149.1' => 'oeu', 'Oeu026220.1' => 'oeu', 'Oeu038635.1' => 'oeu', 'Oeu049176.1' => 'oeu', 'Oeu056706.1' => 'oeu', 'Oeu056937.1' => 'oeu', 'Oeu057540.1' => 'oeu', 'Os02g0594900' => 'osa', 'Os02g0595100' => 'osa', 'Os04g0477500' => 'osa', 'Os12g0611900' => 'osa', 'Peaxi162Scf00076g00020' => 'pax', 'Peaxi162Scf00128g00217' => 'pax', 'Peaxi162Scf00129g01640' => 'pax', 'Peaxi162Scf00669g00007' => 'pax', 'Peaxi162Scf00700g00421' => 'pax', 'Peaxi162Scf00801g00038' => 'pax', 'Peaxi162Scf00891g00025' => 'pax', 'PGR083G0909' => 'pgr', 'PGR119G1005' => 'pgr', 'PGR142G2236' => 'pgr', 'PGR142G3388' => 'pgr', 'PGSC0003DMG400004514' => 'stu', 'PGSC0003DMG400012635' => 'stu', 'PGSC0003DMG400015730' => 'stu', 'PGSC0003DMG400018611' => 'stu', 'PGSC0003DMG400030897' => 'stu', 'Phvul.001G254800' => 'pvu', 'Phvul.002G260100' => 'pvu', 'Phvul.003G167600' => 'pvu', 'Phvul.004G005100' => 'pvu', 'Potri.001G343600' => 'ptr', 'Potri.006G066700' => 'ptr', 'Potri.008G186000' => 'ptr', 'Potri.010G046900' => 'ptr', 'Potri.018G127900' => 'ptr', 'Pp3c20_17750' => 'ppa', 'Pp3c24_4380' => 'ppa', 'Prupe.1G245800' => 'ppe', 'Prupe.3G293400' => 'ppe', 'Prupe.7G247400' => 'ppe', 'Psat0s145g0120' => 'psa', 'Psat0s595g0040' => 'psa', 'Psat0s595g0120' => 'psa', 'Psat3g175040' => 'psa', 'Psat7g058120' => 'psa', 'PSO017G0428' => 'pso', 'PSO063G7510' => 'pso', 'PSO067G0046' => 'pso', 'PSO478G1073' => 'pso', 'PSO675G3677' => 'pso', 'PSO675G6558' => 'pso', 'PSO675G7520' => 'pso', 'PSO675G8959' => 'pso', 'QL02p074089' => 'qlo', 'QL02p089614' => 'qlo', 'QL03p057736' => 'qlo', 'RcHm_v2.0_Chr1g0364131' => 'rch', 'RcHm_v2.0_Chr2g0087801' => 'rch', 'RcHm_v2.0_Chr2g0087821' => 'rch', 'RcHm_v2.0_Chr2g0173231' => 'rch', 'RcHm_v2.0_Chr4g0433111' => 'rch', 'Rhsim03G0250300' => 'rsi', 'Rhsim08G0048400' => 'rsi', 'Rhsim10G0014800' => 'rsi', 'Rhsim12G0040100' => 'rsi', 'Rhsim12G0109700' => 'rsi', 'Sabra06G0049600' => 'sbr', 'Sabra08G0141000' => 'sbr', 'Sabra10G0021400' => 'sbr', 'Sabra16G0222900' => 'sbr', 'Sabra18G0108600' => 'sbr', 'SalBow1G0433' => 'sbo', 'SalBow1G2038' => 'sbo', 'SalBow1G5003' => 'sbo', 'SalBow7G1197' => 'sbo', 'SalBow8G3506' => 'sbo', 'Sc03g0007300' => 'sci', 'Sc11g0000950' => 'sci', 'Sc14g0008750' => 'sci', 'Sc18g0000420' => 'sci', 'Sed0006754' => 'sed', 'Sed0008741' => 'sed', 'Sed0017172' => 'sed', 'Sed0018925' => 'sed', 'Sed0023326' => 'sed', 'Sed0025909' => 'sed', 'SEGI_05333' => 'sgi', 'SEGI_10362' => 'sgi', 'SEGI_13380' => 'sgi', 'SEGI_24306' => 'sgi', 'SEGI_29077' => 'sgi', 'SEGI_29095' => 'sgi', 'SEGI_36534' => 'sgi', 'SEGI_37506' => 'sgi', 'SEGI_38321' => 'sgi', 'SGA_v2.0_scaffold307G48031' => 'sas', 'SGA_v2.0_scaffold47G17507' => 'sas', 'SGA_v2.0_scaffold63G21736' => 'sas', 'SGA_v2.0_scaffold87G27070' => 'sas', 'SHI17794' => 'shi', 'SHI28851' => 'shi', 'SMO165G0155' => 'smo', 'SMO340G0217' => 'smo', 'SMO367G1210' => 'smo', 'Solyc02g093430.3' => 'sly', 'Solyc05g013580.4' => 'sly', 'Solyc07g008030.3' => 'sly', 'Solyc12g035470.2' => 'sly', 'Sopen02g038020' => 'spe', 'Sopen05g008490' => 'spe', 'Sopen07g003910' => 'spe', 'Sopen12g015240' => 'spe', 'Sp1g11550' => 'spa', 'Sp2g16710' => 'spa', 'Sp3g00430' => 'spa', 'Sp3g26780' => 'spa', 'Sp5g22900' => 'spa', 'Sp6g29530' => 'spa', 'TAR371G0794' => 'tar', 'TAR374G0164' => 'tar', 'TAR622G0165' => 'tar', 'TAR626G0929' => 'tar', 'TAR629G2155' => 'tar', 'THA.LOC104805282' => 'tha', 'THA.LOC104805363' => 'tha', 'THA.LOC104808968' => 'tha', 'THA.LOC104821093' => 'tha', 'THA.LOC104823953' => 'tha', 'THA.LOC104825562' => 'tha', 'THA.LOC104825665' => 'tha', 'Thecc.02G261400' => 'tca', 'Thecc.04G019200' => 'tca', 'Thecc.09G130400' => 'tca', 'Thhalv10004374m.g' => 'esa', 'Thhalv10007850m.g' => 'esa', 'Thhalv10013782m.g' => 'esa', 'Thhalv10018686m.g' => 'esa', 'Thhalv10020899m.g' => 'esa', 'Thhalv10022755m.g' => 'esa', 'TPR.G23851' => 'tpr', 'TPR.G26500' => 'tpr', 'TPR.G27267' => 'tpr', 'TPR.G32001' => 'tpr', 'TPR.G6251' => 'tpr', 'TPR.G8167' => 'tpr', 'TWI12G1330' => 'twi', 'TWI18G1239' => 'twi', 'TWI34G0979' => 'twi', 'TWI36G0670' => 'twi', 'TWI36G0707' => 'twi', 'TWI56G0233' => 'twi', 'TWI75G1809' => 'twi', 'unitig_21.g20874' => 'ugi', 'unitig_26.g10343' => 'ugi', 'unitig_46.g18392' => 'ugi', 'unitig_52.g17178' => 'ugi', 'unitig_8.g2934' => 'ugi', 'vmacro01122' => 'vma', 'vmacro05875' => 'vma', 'vmacro06147' => 'vma', 'vmacro16191' => 'vma', 'vmacro18293' => 'vma', 'VMungo0251G3707' => 'vmu', 'VMungo0464G1521' => 'vmu', 'VMungo1215G0205' => 'vmu', 'VMungo1383G2484' => 'vmu', 'Zm00001eb079610' => 'zma', 'Zm00001eb135990' => 'zma', 'Zm00001eb183710' => 'zma', 'Zm00001eb246020' => 'zma' ), 'gf_id' => 'HOM05D001124', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001124' ), 'data_identifier' => 'HOM05D001124', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001124', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '548', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02520' => 'bna', 'A03p06630' => 'bna', 'A05p44460' => 'bna', 'A06p08710' => 'bna', 'A06p41090' => 'bna', 'A07p32320' => 'bna', 'A08p32520' => 'bna', 'A09p10360' => 'bna', 'A10p24080' => 'bna', 'Aa31LG11G15250' => 'aar', 'Aa31LG1G1800' => 'aar', 'Aa31LG2G5120' => 'aar', 'Aa31LG2G6070' => 'aar', 'Aa31LG5G10770' => 'aar', 'Aa31sc61G90' => 'aar', 'Actinidia01352' => 'ach', 'Actinidia05983' => 'ach', 'Actinidia08133' => 'ach', 'Actinidia15101' => 'ach', 'Actinidia26379' => 'ach', 'Actinidia35778' => 'ach', 'Actinidia36123' => 'ach', 'Actinidia37436' => 'ach', 'Actinidia38730' => 'ach', 'Ah.02g128210' => 'amhyb', 'Ah.03g132990' => 'amhyb', 'Ah.14g079410' => 'amhyb', 'AL1G24640' => 'aly', 'AL2G26680' => 'aly', 'AL3G10530' => 'aly', 'AL3G45230' => 'aly', 'AL5G15230' => 'aly', 'AL5G16960' => 'aly', 'AL6G25210' => 'aly', 'Aqoxy2G00441' => 'aox', 'Aqoxy3G01236' => 'aox', 'Aqoxy5G03746' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3RQ047' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C7GMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9C8JER' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MBL6KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YXCZ83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZANX40' => 'arhy', 'AT1G12990' => 'ath', 'AT1G67880' => 'ath', 'AT2G13290' => 'ath', 'AT3G01620' => 'ath', 'AT3G26445' => 'ath', 'AT3G27540' => 'ath', 'AT5G14480' => 'ath', 'ATR0824G026' => 'atr', 'ATR1098G019' => 'atr', 'Atru.chr11.2145' => 'acertr', 'Atru.chr2.3636' => 'acertr', 'Atru.chr2.3644' => 'acertr', 'Atru.chr6.2422' => 'acertr', 'Atru.chr7.1112' => 'acertr', 'AUR62005469' => 'cqu', 'AUR62011166' => 'cqu', 'AUR62013319' => 'cqu', 'AUR62024273' => 'cqu', 'AUR62028420' => 'cqu', 'AUR62041942' => 'cqu', 'BcaB01g04969' => 'bca', 'BcaB01g06371' => 'bca', 'BcaB02g11494' => 'bca', 'BcaB03g15382' => 'bca', 'BcaB08g36994' => 'bca', 'BcaC03g13477' => 'bca', 'BcaC03g13478' => 'bca', 'BcaC03g13480' => 'bca', 'BcaC03g13481' => 'bca', 'BcaC03g13486' => 'bca', 'BcaC04g19031' => 'bca', 'BcaC04g23085' => 'bca', 'BcaC05g25094' => 'bca', 'BcaC05g25096' => 'bca', 'BcaC05g25138' => 'bca', 'BcaC05g30416' => 'bca', 'BcaC05g30455' => 'bca', 'BcaC06g30979' => 'bca', 'BcaC06g33805' => 'bca', 'BcaC08g46021' => 'bca', 'BcaNung03154' => 'bca', 'BolC2t06623H' => 'bol', 'BolC2t06632H' => 'bol', 'BolC2t06635H' => 'bol', 'BolC2t06638H' => 'bol', 'BolC3t13266H' => 'bol', 'BolC5t29776H' => 'bol', 'BolC6t38912H' => 'bol', 'BolC7t44183H' => 'bol', 'BolC9t54123H' => 'bol', 'BolC9t59107H' => 'bol', 'BraA02t05221Z' => 'bra', 'BraA03t09996Z' => 'bra', 'BraA05t23210Z' => 'bra', 'BraA06t24068Z' => 'bra', 'BraA06t27032Z' => 'bra', 'BraA08t35176Z' => 'bra', 'BraA09t36680Z' => 'bra', 'BraA10t44471Z' => 'bra', 'C02p06760' => 'bna', 'C02p06890' => 'bna', 'C02p07010' => 'bna', 'C03p07660' => 'bna', 'C05p10300' => 'bna', 'C06p38150' => 'bna', 'C07p36650' => 'bna', 'C08p15770' => 'bna', 'C09p12300' => 'bna', 'C09p62700' => 'bna', 'C09p75040' => 'bna', 'CAN.G13.1' => 'can', 'CAN.G138.4' => 'can', 'CAN.G44.6' => 'can', 'CAN.G473.19' => 'can', 'CANSAT01G0835' => 'cansat', 'CANSAT11G0246' => 'cansat', 'CANSAT11G1766' => 'cansat', 'CANSAT64G1954' => 'cansat', 'CARHR013330' => 'chi', 'CARHR060530' => 'chi', 'CARHR075300' => 'chi', 'CARHR105120' => 'chi', 'CARHR148910' => 'chi', 'CARHR198830' => 'chi', 'Carub.0001s1275' => 'cru', 'Carub.0002s1437' => 'cru', 'Carub.0003s0044' => 'cru', 'Carub.0003s2787' => 'cru', 'Carub.0005s0597' => 'cru', 'Carub.0006s1266' => 'cru', 'Ca_06935_v3' => 'car', 'Ca_13559_v3' => 'car', 'Ca_16941_v3' => 'car', 'Ca_16960_v3' => 'car', 'Ca_17775_v3' => 'car', 'Ca_30464_v3' => 'car', 'Cc06_g08160' => 'ccan', 'Cc07_g01520' => 'ccan', 'Cc11_g15810' => 'ccan', 'CDE02G2840' => 'cde', 'CDE03G0093' => 'cde', 'CDE04G2127' => 'cde', 'CDE07G1857' => 'cde', 'CDE09G1246' => 'cde', 'Cfa003412' => 'cfa', 'Cfa007341' => 'cfa', 'Cfa009220' => 'cfa', 'Ciclev10008737m.g' => 'ccl', 'Ciclev10015565m.g' => 'ccl', 'Ciclev10031761m.g' => 'ccl', 'CiPaw.03G045300' => 'cil', 'CiPaw.03G247200' => 'cil', 'CiPaw.04G029500' => 'cil', 'CiPaw.04G174000' => 'cil', 'CiPaw.05G181200' => 'cil', 'CiPaw.06G067100' => 'cil', 'ClCG05G025800' => 'cla', 'ClCG06G011400' => 'cla', 'ClCG09G019360' => 'cla', 'COL.COLO4_04827' => 'col', 'COL.COLO4_29170' => 'col', 'COL.COLO4_35131' => 'col', 'COL.COLO4_35132' => 'col', 'Cpa.g.sc33.32' => 'cpa', 'Cpa.g.sc46.29' => 'cpa', 'Cpa.g.sc796.1' => 'cpa', 'CsaV3_1G030420' => 'csa', 'CsaV3_5G027050' => 'csa', 'CsaV3_5G031040' => 'csa', 'CsaV3_UNG023130' => 'csa', 'CSS0007726' => 'camsi', 'CSS0016433' => 'camsi', 'CSS0017656' => 'camsi', 'CSS0025364' => 'camsi', 'CSS0027582' => 'camsi', 'CSS0047288' => 'camsi', 'CSS0049950' => 'camsi', 'DCAR_003843' => 'dca', 'DCAR_007052' => 'dca', 'DCAR_020884' => 'dca', 'DCAR_021730' => 'dca', 'DCAR_024423' => 'dca', 'DCAR_026509' => 'dca', 'DCAR_031158' => 'dca', 'Dinv14728' => 'din', 'Dinv15219' => 'din', 'Dinv25728' => 'din', 'Dinv33428' => 'din', 'Dinv36489' => 'din', 'Dinv41486' => 'din', 'Duzib147G0469' => 'dzi', 'Duzib168G0060' => 'dzi', 'Duzib187G1215' => 'dzi', 'Duzib248G0692' => 'dzi', 'Duzib251G0767' => 'dzi', 'Duzib264G0446' => 'dzi', 'Duzib268G0691' => 'dzi', 'ECA232G4767' => 'eca', 'ECA233G2838' => 'eca', 'ECA234G0391' => 'eca', 'ECA234G0857' => 'eca', 'ECA236G1593' => 'eca', 'ECA238G0565' => 'eca', 'ECA246G1027' => 'eca', 'ECA246G3223' => 'eca', 'ECA246G3470' => 'eca', 'EL10Ac6g13829' => 'bvu', 'EL10Ac6g14093' => 'bvu', 'EL10Ac8g18707' => 'bvu', 'Eucgr.C01369' => 'egr', 'Eucgr.H02492' => 'egr', 'Eucgr.I01733' => 'egr', 'Eucgr.J02255' => 'egr', 'Eucgr.J02257' => 'egr', 'Eucgr.J02258' => 'egr', 'FAN02G1601' => 'fan', 'FAN03G1586' => 'fan', 'FAN03G2986' => 'fan', 'FAN05G4837' => 'fan', 'FAN06G0146' => 'fan', 'FAN07G0858' => 'fan', 'FAN09G3179' => 'fan', 'FAN10G0669' => 'fan', 'FAN12G2358' => 'fan', 'FAN14G4198' => 'fan', 'FAN14G5112' => 'fan', 'FAN17G0342' => 'fan', 'FAN19G0342' => 'fan', 'FAN19G0962' => 'fan', 'FAN19G1101' => 'fan', 'FAN19G1872' => 'fan', 'FAN22G0356' => 'fan', 'FAN23G0744' => 'fan', 'FAN23G1914' => 'fan', 'FAN26G0032' => 'fan', 'FAN28G0625' => 'fan', 'FvH4_1g02710' => 'fve', 'FvH4_1g02720' => 'fve', 'FvH4_4g25670' => 'fve', 'FvH4_6g51700' => 'fve', 'FvH4_7g20170' => 'fve', 'Glyma.05G175000' => 'gma', 'Glyma.08G132300' => 'gma', 'Glyma.11G243000' => 'gma', 'Glyma.13G158900' => 'gma', 'Glyma.17G112400' => 'gma', 'Glyma.18G014100' => 'gma', 'Glyma.19G003100' => 'gma', 'Glyma.19G056500' => 'gma', 'Gohir.A01G158900' => 'ghi', 'Gohir.A05G312600' => 'ghi', 'Gohir.A05G354900' => 'ghi', 'Gohir.A07G037200' => 'ghi', 'Gohir.A09G030000' => 'ghi', 'Gohir.A12G145200' => 'ghi', 'Gohir.D01G151500' => 'ghi', 'Gohir.D04G058300' => 'ghi', 'Gohir.D05G314100' => 'ghi', 'Gohir.D07G041400' => 'ghi', 'Gohir.D09G029700' => 'ghi', 'Gohir.D12G149700' => 'ghi', 'Gorai.001G043800' => 'gra', 'Gorai.002G187800' => 'gra', 'Gorai.006G034700' => 'gra', 'Gorai.008G161200' => 'gra', 'Gorai.009G335700' => 'gra', 'Gorai.012G065000' => 'gra', 'GSVIVG01000535001' => 'vvi', 'GSVIVG01015572001' => 'vvi', 'GSVIVG01032386001' => 'vvi', 'HanXRQChr05g0138531' => 'han', 'HanXRQChr06g0174391' => 'han', 'HanXRQChr07g0199021' => 'han', 'HanXRQChr08g0208211' => 'han', 'HanXRQChr09g0255471' => 'han', 'HanXRQChr10g0315791' => 'han', 'HanXRQChr12g0371991' => 'han', 'HanXRQChr15g0475251' => 'han', 'HanXRQChr17g0540001' => 'han', 'HanXRQChr17g0548631' => 'han', 'HanXRQChr17g0569561' => 'han', 'Haze_12256' => 'cav', 'Haze_14756' => 'cav', 'Haze_25528' => 'cav', 'Hma1.2p1_0079F.1_g041020' => 'hma', 'Hma1.2p1_0818F.1_g223260' => 'hma', 'Hma1.2p1_1747F.1_g300530' => 'hma', 'HPP92_004607' => 'vpl', 'HPP92_004608' => 'vpl', 'HPP92_006181' => 'vpl', 'HPP92_012192' => 'vpl', 'HPP92_015680' => 'vpl', 'HPP92_020249' => 'vpl', 'HPP92_021376' => 'vpl', 'HPP92_024275' => 'vpl', 'Hund06031' => 'sun', 'Hund25391' => 'sun', 'Lalb_Chr07g0185371' => 'lal', 'Lalb_Chr07g0185381' => 'lal', 'Lalb_Chr12g0204011' => 'lal', 'Lalb_Chr13g0301671' => 'lal', 'Lalb_Chr14g0362851' => 'lal', 'Lalb_Chr24g0403581' => 'lal', 'Lj1g0000233' => 'lja', 'Lj2g0018120' => 'lja', 'Lj3C621T0' => 'lonja', 'Lj3P1059T14' => 'lonja', 'Lj3P611T9' => 'lonja', 'Lj3P614T13' => 'lonja', 'Lj3P615T5' => 'lonja', 'Lj4g0012315' => 'lja', 'Lj4g0026182' => 'lja', 'Lj6P813T16' => 'lonja', 'Lj7C427T7' => 'lonja', 'Lj7C427T8' => 'lonja', 'Lj7P600T41' => 'lonja', 'Lju41C42G17' => 'lonja', 'Lsat_1_v5_gn_0_47300' => 'lsa', 'Lsat_1_v5_gn_2_91280' => 'lsa', 'Lsat_1_v5_gn_3_30561' => 'lsa', 'Lsat_1_v5_gn_4_184321' => 'lsa', 'Lsat_1_v5_gn_4_4041' => 'lsa', 'Lsat_1_v5_gn_5_92000' => 'lsa', 'Lsat_1_v5_gn_8_152940' => 'lsa', 'Lsat_1_v5_gn_8_62401' => 'lsa', 'Manes.06G055900' => 'mes', 'Manes.12G022200' => 'mes', 'Manes.13G023300' => 'mes', 'Manes.14G115000' => 'mes', 'Manes.15G151700' => 'mes', 'Manes.17G111300' => 'mes', 'Mapoly0226s0009' => 'mpo', 'MBI02_g25363_MAGBIO' => 'mbi', 'MBI06_g00027_MAGBIO' => 'mbi', 'MBI10_g13034_MAGBIO' => 'mbi', 'MD09G1023400' => 'mdo', 'MD13G1100100' => 'mdo', 'MD15G1169200' => 'mdo', 'MD16G1101100' => 'mdo', 'MD17G1022900' => 'mdo', 'Medtr3g096150' => 'mtr', 'Medtr4g115070' => 'mtr', 'Medtr7g033325' => 'mtr', 'Medtr8g089840' => 'mtr', 'MELO3C010319.2' => 'cme', 'MELO3C011944.2' => 'cme', 'MELO3C021589.2' => 'cme', 'Migut.E00207' => 'egut', 'Migut.H00067' => 'egut', 'Migut.K00433' => 'egut', 'Migut.K00606' => 'egut', 'Migut.K01410' => 'egut', 'MSTRG.13347' => 'ama', 'MSTRG.24045' => 'ama', 'MSTRG.2428' => 'ama', 'MSTRG.26410' => 'ama', 'MSTRG.3139' => 'ama', 'MSTRG.3286' => 'ama', 'MSTRG.563' => 'ama', 'MSTRG.7941' => 'ama', 'Nitab4.5_0000028g0060' => 'nta', 'Nitab4.5_0000065g0260' => 'nta', 'Nitab4.5_0000112g0060' => 'nta', 'Nitab4.5_0000489g0120' => 'nta', 'Nitab4.5_0001776g0050' => 'nta', 'Nitab4.5_0001854g0010' => 'nta', 'Nitab4.5_0001860g0020' => 'nta', 'Nitab4.5_0004352g0010' => 'nta', 'Nitab4.5_0008716g0020' => 'nta', 'Nitab4.5_0008922g0010' => 'nta', 'Nn3g16693' => 'nnu', 'Nn4g22596' => 'nnu', 'Nn7g37639' => 'nnu', 'Oeu001701.1' => 'oeu', 'Oeu018149.1' => 'oeu', 'Oeu026220.1' => 'oeu', 'Oeu038635.1' => 'oeu', 'Oeu049176.1' => 'oeu', 'Oeu056706.1' => 'oeu', 'Oeu056937.1' => 'oeu', 'Oeu057540.1' => 'oeu', 'Os02g0594900' => 'osa', 'Os02g0595100' => 'osa', 'Os04g0477500' => 'osa', 'Os12g0611900' => 'osa', 'Peaxi162Scf00076g00020' => 'pax', 'Peaxi162Scf00128g00217' => 'pax', 'Peaxi162Scf00129g01640' => 'pax', 'Peaxi162Scf00669g00007' => 'pax', 'Peaxi162Scf00700g00421' => 'pax', 'Peaxi162Scf00801g00038' => 'pax', 'Peaxi162Scf00891g00025' => 'pax', 'PGR083G0909' => 'pgr', 'PGR119G1005' => 'pgr', 'PGR142G2236' => 'pgr', 'PGR142G3388' => 'pgr', 'PGSC0003DMG400004514' => 'stu', 'PGSC0003DMG400012635' => 'stu', 'PGSC0003DMG400015730' => 'stu', 'PGSC0003DMG400018611' => 'stu', 'PGSC0003DMG400030897' => 'stu', 'Phvul.001G254800' => 'pvu', 'Phvul.002G260100' => 'pvu', 'Phvul.003G167600' => 'pvu', 'Phvul.004G005100' => 'pvu', 'Potri.001G343600' => 'ptr', 'Potri.006G066700' => 'ptr', 'Potri.008G186000' => 'ptr', 'Potri.010G046900' => 'ptr', 'Potri.018G127900' => 'ptr', 'Pp3c20_17750' => 'ppa', 'Pp3c24_4380' => 'ppa', 'Prupe.1G245800' => 'ppe', 'Prupe.3G293400' => 'ppe', 'Prupe.7G247400' => 'ppe', 'Psat0s145g0120' => 'psa', 'Psat0s595g0040' => 'psa', 'Psat0s595g0120' => 'psa', 'Psat3g175040' => 'psa', 'Psat7g058120' => 'psa', 'PSO017G0428' => 'pso', 'PSO063G7510' => 'pso', 'PSO067G0046' => 'pso', 'PSO478G1073' => 'pso', 'PSO675G3677' => 'pso', 'PSO675G6558' => 'pso', 'PSO675G7520' => 'pso', 'PSO675G8959' => 'pso', 'QL02p074089' => 'qlo', 'QL02p089614' => 'qlo', 'QL03p057736' => 'qlo', 'RcHm_v2.0_Chr1g0364131' => 'rch', 'RcHm_v2.0_Chr2g0087801' => 'rch', 'RcHm_v2.0_Chr2g0087821' => 'rch', 'RcHm_v2.0_Chr2g0173231' => 'rch', 'RcHm_v2.0_Chr4g0433111' => 'rch', 'Rhsim03G0250300' => 'rsi', 'Rhsim08G0048400' => 'rsi', 'Rhsim10G0014800' => 'rsi', 'Rhsim12G0040100' => 'rsi', 'Rhsim12G0109700' => 'rsi', 'Sabra06G0049600' => 'sbr', 'Sabra08G0141000' => 'sbr', 'Sabra10G0021400' => 'sbr', 'Sabra16G0222900' => 'sbr', 'Sabra18G0108600' => 'sbr', 'SalBow1G0433' => 'sbo', 'SalBow1G2038' => 'sbo', 'SalBow1G5003' => 'sbo', 'SalBow7G1197' => 'sbo', 'SalBow8G3506' => 'sbo', 'Sc03g0007300' => 'sci', 'Sc11g0000950' => 'sci', 'Sc14g0008750' => 'sci', 'Sc18g0000420' => 'sci', 'Sed0006754' => 'sed', 'Sed0008741' => 'sed', 'Sed0017172' => 'sed', 'Sed0018925' => 'sed', 'Sed0023326' => 'sed', 'Sed0025909' => 'sed', 'SEGI_05333' => 'sgi', 'SEGI_10362' => 'sgi', 'SEGI_13380' => 'sgi', 'SEGI_24306' => 'sgi', 'SEGI_29077' => 'sgi', 'SEGI_29095' => 'sgi', 'SEGI_36534' => 'sgi', 'SEGI_37506' => 'sgi', 'SEGI_38321' => 'sgi', 'SGA_v2.0_scaffold307G48031' => 'sas', 'SGA_v2.0_scaffold47G17507' => 'sas', 'SGA_v2.0_scaffold63G21736' => 'sas', 'SGA_v2.0_scaffold87G27070' => 'sas', 'SHI17794' => 'shi', 'SHI28851' => 'shi', 'SMO165G0155' => 'smo', 'SMO340G0217' => 'smo', 'SMO367G1210' => 'smo', 'Solyc02g093430.3' => 'sly', 'Solyc05g013580.4' => 'sly', 'Solyc07g008030.3' => 'sly', 'Solyc12g035470.2' => 'sly', 'Sopen02g038020' => 'spe', 'Sopen05g008490' => 'spe', 'Sopen07g003910' => 'spe', 'Sopen12g015240' => 'spe', 'Sp1g11550' => 'spa', 'Sp2g16710' => 'spa', 'Sp3g00430' => 'spa', 'Sp3g26780' => 'spa', 'Sp5g22900' => 'spa', 'Sp6g29530' => 'spa', 'TAR371G0794' => 'tar', 'TAR374G0164' => 'tar', 'TAR622G0165' => 'tar', 'TAR626G0929' => 'tar', 'TAR629G2155' => 'tar', 'THA.LOC104805282' => 'tha', 'THA.LOC104805363' => 'tha', 'THA.LOC104808968' => 'tha', 'THA.LOC104821093' => 'tha', 'THA.LOC104823953' => 'tha', 'THA.LOC104825562' => 'tha', 'THA.LOC104825665' => 'tha', 'Thecc.02G261400' => 'tca', 'Thecc.04G019200' => 'tca', 'Thecc.09G130400' => 'tca', 'Thhalv10004374m.g' => 'esa', 'Thhalv10007850m.g' => 'esa', 'Thhalv10013782m.g' => 'esa', 'Thhalv10018686m.g' => 'esa', 'Thhalv10020899m.g' => 'esa', 'Thhalv10022755m.g' => 'esa', 'TPR.G23851' => 'tpr', 'TPR.G26500' => 'tpr', 'TPR.G27267' => 'tpr', 'TPR.G32001' => 'tpr', 'TPR.G6251' => 'tpr', 'TPR.G8167' => 'tpr', 'TWI12G1330' => 'twi', 'TWI18G1239' => 'twi', 'TWI34G0979' => 'twi', 'TWI36G0670' => 'twi', 'TWI36G0707' => 'twi', 'TWI56G0233' => 'twi', 'TWI75G1809' => 'twi', 'unitig_21.g20874' => 'ugi', 'unitig_26.g10343' => 'ugi', 'unitig_46.g18392' => 'ugi', 'unitig_52.g17178' => 'ugi', 'unitig_8.g2934' => 'ugi', 'vmacro01122' => 'vma', 'vmacro05875' => 'vma', 'vmacro06147' => 'vma', 'vmacro16191' => 'vma', 'vmacro18293' => 'vma', 'VMungo0251G3707' => 'vmu', 'VMungo0464G1521' => 'vmu', 'VMungo1215G0205' => 'vmu', 'VMungo1383G2484' => 'vmu', 'Zm00001eb079610' => 'zma', 'Zm00001eb135990' => 'zma', 'Zm00001eb183710' => 'zma', 'Zm00001eb246020' => 'zma' ) $gf_id = 'HOM05D001124' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001124' ) $data_identifier = 'HOM05D001124' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 6, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 7, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 21, 'bol' => (int) 10, 'bra' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 6, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 9, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 21, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 8, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 10, 'lsa' => (int) 8, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 8, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 9, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb246020' $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' => 'HOM05D001124', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '548', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02520' => 'bna', 'A03p06630' => 'bna', 'A05p44460' => 'bna', 'A06p08710' => 'bna', 'A06p41090' => 'bna', 'A07p32320' => 'bna', 'A08p32520' => 'bna', 'A09p10360' => 'bna', 'A10p24080' => 'bna', 'Aa31LG11G15250' => 'aar', 'Aa31LG1G1800' => 'aar', 'Aa31LG2G5120' => 'aar', 'Aa31LG2G6070' => 'aar', 'Aa31LG5G10770' => 'aar', 'Aa31sc61G90' => 'aar', 'Actinidia01352' => 'ach', 'Actinidia05983' => 'ach', 'Actinidia08133' => 'ach', 'Actinidia15101' => 'ach', 'Actinidia26379' => 'ach', 'Actinidia35778' => 'ach', 'Actinidia36123' => 'ach', 'Actinidia37436' => 'ach', 'Actinidia38730' => 'ach', 'Ah.02g128210' => 'amhyb', 'Ah.03g132990' => 'amhyb', 'Ah.14g079410' => 'amhyb', 'AL1G24640' => 'aly', 'AL2G26680' => 'aly', 'AL3G10530' => 'aly', 'AL3G45230' => 'aly', 'AL5G15230' => 'aly', 'AL5G16960' => 'aly', 'AL6G25210' => 'aly', 'Aqoxy2G00441' => 'aox', 'Aqoxy3G01236' => 'aox', 'Aqoxy5G03746' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3RQ047' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C7GMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9C8JER' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MBL6KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YXCZ83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZANX40' => 'arhy', 'AT1G12990' => 'ath', 'AT1G67880' => 'ath', 'AT2G13290' => 'ath', 'AT3G01620' => 'ath', 'AT3G26445' => 'ath', 'AT3G27540' => 'ath', 'AT5G14480' => 'ath', 'ATR0824G026' => 'atr', 'ATR1098G019' => 'atr', 'Atru.chr11.2145' => 'acertr', 'Atru.chr2.3636' => 'acertr', 'Atru.chr2.3644' => 'acertr', 'Atru.chr6.2422' => 'acertr', 'Atru.chr7.1112' => 'acertr', 'AUR62005469' => 'cqu', 'AUR62011166' => 'cqu', 'AUR62013319' => 'cqu', 'AUR62024273' => 'cqu', 'AUR62028420' => 'cqu', 'AUR62041942' => 'cqu', 'BcaB01g04969' => 'bca', 'BcaB01g06371' => 'bca', 'BcaB02g11494' => 'bca', 'BcaB03g15382' => 'bca', 'BcaB08g36994' => 'bca', 'BcaC03g13477' => 'bca', 'BcaC03g13478' => 'bca', 'BcaC03g13480' => 'bca', 'BcaC03g13481' => 'bca', 'BcaC03g13486' => 'bca', 'BcaC04g19031' => 'bca', 'BcaC04g23085' => 'bca', 'BcaC05g25094' => 'bca', 'BcaC05g25096' => 'bca', 'BcaC05g25138' => 'bca', 'BcaC05g30416' => 'bca', 'BcaC05g30455' => 'bca', 'BcaC06g30979' => 'bca', 'BcaC06g33805' => 'bca', 'BcaC08g46021' => 'bca', 'BcaNung03154' => 'bca', 'BolC2t06623H' => 'bol', 'BolC2t06632H' => 'bol', 'BolC2t06635H' => 'bol', 'BolC2t06638H' => 'bol', 'BolC3t13266H' => 'bol', 'BolC5t29776H' => 'bol', 'BolC6t38912H' => 'bol', 'BolC7t44183H' => 'bol', 'BolC9t54123H' => 'bol', 'BolC9t59107H' => 'bol', 'BraA02t05221Z' => 'bra', 'BraA03t09996Z' => 'bra', 'BraA05t23210Z' => 'bra', 'BraA06t24068Z' => 'bra', 'BraA06t27032Z' => 'bra', 'BraA08t35176Z' => 'bra', 'BraA09t36680Z' => 'bra', 'BraA10t44471Z' => 'bra', 'C02p06760' => 'bna', 'C02p06890' => 'bna', 'C02p07010' => 'bna', 'C03p07660' => 'bna', 'C05p10300' => 'bna', 'C06p38150' => 'bna', 'C07p36650' => 'bna', 'C08p15770' => 'bna', 'C09p12300' => 'bna', 'C09p62700' => 'bna', 'C09p75040' => 'bna', 'CAN.G13.1' => 'can', 'CAN.G138.4' => 'can', 'CAN.G44.6' => 'can', 'CAN.G473.19' => 'can', 'CANSAT01G0835' => 'cansat', 'CANSAT11G0246' => 'cansat', 'CANSAT11G1766' => 'cansat', 'CANSAT64G1954' => 'cansat', 'CARHR013330' => 'chi', 'CARHR060530' => 'chi', 'CARHR075300' => 'chi', 'CARHR105120' => 'chi', 'CARHR148910' => 'chi', 'CARHR198830' => 'chi', 'Carub.0001s1275' => 'cru', 'Carub.0002s1437' => 'cru', 'Carub.0003s0044' => 'cru', 'Carub.0003s2787' => 'cru', 'Carub.0005s0597' => 'cru', 'Carub.0006s1266' => 'cru', 'Ca_06935_v3' => 'car', 'Ca_13559_v3' => 'car', 'Ca_16941_v3' => 'car', 'Ca_16960_v3' => 'car', 'Ca_17775_v3' => 'car', 'Ca_30464_v3' => 'car', 'Cc06_g08160' => 'ccan', 'Cc07_g01520' => 'ccan', 'Cc11_g15810' => 'ccan', 'CDE02G2840' => 'cde', 'CDE03G0093' => 'cde', 'CDE04G2127' => 'cde', 'CDE07G1857' => 'cde', 'CDE09G1246' => 'cde', 'Cfa003412' => 'cfa', 'Cfa007341' => 'cfa', 'Cfa009220' => 'cfa', 'Ciclev10008737m.g' => 'ccl', 'Ciclev10015565m.g' => 'ccl', 'Ciclev10031761m.g' => 'ccl', 'CiPaw.03G045300' => 'cil', 'CiPaw.03G247200' => 'cil', 'CiPaw.04G029500' => 'cil', 'CiPaw.04G174000' => 'cil', 'CiPaw.05G181200' => 'cil', 'CiPaw.06G067100' => 'cil', 'ClCG05G025800' => 'cla', 'ClCG06G011400' => 'cla', 'ClCG09G019360' => 'cla', 'COL.COLO4_04827' => 'col', 'COL.COLO4_29170' => 'col', 'COL.COLO4_35131' => 'col', 'COL.COLO4_35132' => 'col', 'Cpa.g.sc33.32' => 'cpa', 'Cpa.g.sc46.29' => 'cpa', 'Cpa.g.sc796.1' => 'cpa', 'CsaV3_1G030420' => 'csa', 'CsaV3_5G027050' => 'csa', 'CsaV3_5G031040' => 'csa', 'CsaV3_UNG023130' => 'csa', 'CSS0007726' => 'camsi', 'CSS0016433' => 'camsi', 'CSS0017656' => 'camsi', 'CSS0025364' => 'camsi', 'CSS0027582' => 'camsi', 'CSS0047288' => 'camsi', 'CSS0049950' => 'camsi', 'DCAR_003843' => 'dca', 'DCAR_007052' => 'dca', 'DCAR_020884' => 'dca', 'DCAR_021730' => 'dca', 'DCAR_024423' => 'dca', 'DCAR_026509' => 'dca', 'DCAR_031158' => 'dca', 'Dinv14728' => 'din', 'Dinv15219' => 'din', 'Dinv25728' => 'din', 'Dinv33428' => 'din', 'Dinv36489' => 'din', 'Dinv41486' => 'din', 'Duzib147G0469' => 'dzi', 'Duzib168G0060' => 'dzi', 'Duzib187G1215' => 'dzi', 'Duzib248G0692' => 'dzi', 'Duzib251G0767' => 'dzi', 'Duzib264G0446' => 'dzi', 'Duzib268G0691' => 'dzi', 'ECA232G4767' => 'eca', 'ECA233G2838' => 'eca', 'ECA234G0391' => 'eca', 'ECA234G0857' => 'eca', 'ECA236G1593' => 'eca', 'ECA238G0565' => 'eca', 'ECA246G1027' => 'eca', 'ECA246G3223' => 'eca', 'ECA246G3470' => 'eca', 'EL10Ac6g13829' => 'bvu', 'EL10Ac6g14093' => 'bvu', 'EL10Ac8g18707' => 'bvu', 'Eucgr.C01369' => 'egr', 'Eucgr.H02492' => 'egr', 'Eucgr.I01733' => 'egr', 'Eucgr.J02255' => 'egr', 'Eucgr.J02257' => 'egr', 'Eucgr.J02258' => 'egr', 'FAN02G1601' => 'fan', 'FAN03G1586' => 'fan', 'FAN03G2986' => 'fan', 'FAN05G4837' => 'fan', 'FAN06G0146' => 'fan', 'FAN07G0858' => 'fan', 'FAN09G3179' => 'fan', 'FAN10G0669' => 'fan', 'FAN12G2358' => 'fan', 'FAN14G4198' => 'fan', 'FAN14G5112' => 'fan', 'FAN17G0342' => 'fan', 'FAN19G0342' => 'fan', 'FAN19G0962' => 'fan', 'FAN19G1101' => 'fan', 'FAN19G1872' => 'fan', 'FAN22G0356' => 'fan', 'FAN23G0744' => 'fan', 'FAN23G1914' => 'fan', 'FAN26G0032' => 'fan', 'FAN28G0625' => 'fan', 'FvH4_1g02710' => 'fve', 'FvH4_1g02720' => 'fve', 'FvH4_4g25670' => 'fve', 'FvH4_6g51700' => 'fve', 'FvH4_7g20170' => 'fve', 'Glyma.05G175000' => 'gma', 'Glyma.08G132300' => 'gma', 'Glyma.11G243000' => 'gma', 'Glyma.13G158900' => 'gma', 'Glyma.17G112400' => 'gma', 'Glyma.18G014100' => 'gma', 'Glyma.19G003100' => 'gma', 'Glyma.19G056500' => 'gma', 'Gohir.A01G158900' => 'ghi', 'Gohir.A05G312600' => 'ghi', 'Gohir.A05G354900' => 'ghi', 'Gohir.A07G037200' => 'ghi', 'Gohir.A09G030000' => 'ghi', 'Gohir.A12G145200' => 'ghi', 'Gohir.D01G151500' => 'ghi', 'Gohir.D04G058300' => 'ghi', 'Gohir.D05G314100' => 'ghi', 'Gohir.D07G041400' => 'ghi', 'Gohir.D09G029700' => 'ghi', 'Gohir.D12G149700' => 'ghi', 'Gorai.001G043800' => 'gra', 'Gorai.002G187800' => 'gra', 'Gorai.006G034700' => 'gra', 'Gorai.008G161200' => 'gra', 'Gorai.009G335700' => 'gra', 'Gorai.012G065000' => 'gra', 'GSVIVG01000535001' => 'vvi', 'GSVIVG01015572001' => 'vvi', 'GSVIVG01032386001' => 'vvi', 'HanXRQChr05g0138531' => 'han', 'HanXRQChr06g0174391' => 'han', 'HanXRQChr07g0199021' => 'han', 'HanXRQChr08g0208211' => 'han', 'HanXRQChr09g0255471' => 'han', 'HanXRQChr10g0315791' => 'han', 'HanXRQChr12g0371991' => 'han', 'HanXRQChr15g0475251' => 'han', 'HanXRQChr17g0540001' => 'han', 'HanXRQChr17g0548631' => 'han', 'HanXRQChr17g0569561' => 'han', 'Haze_12256' => 'cav', 'Haze_14756' => 'cav', 'Haze_25528' => 'cav', 'Hma1.2p1_0079F.1_g041020' => 'hma', 'Hma1.2p1_0818F.1_g223260' => 'hma', 'Hma1.2p1_1747F.1_g300530' => 'hma', 'HPP92_004607' => 'vpl', 'HPP92_004608' => 'vpl', 'HPP92_006181' => 'vpl', 'HPP92_012192' => 'vpl', 'HPP92_015680' => 'vpl', 'HPP92_020249' => 'vpl', 'HPP92_021376' => 'vpl', 'HPP92_024275' => 'vpl', 'Hund06031' => 'sun', 'Hund25391' => 'sun', 'Lalb_Chr07g0185371' => 'lal', 'Lalb_Chr07g0185381' => 'lal', 'Lalb_Chr12g0204011' => 'lal', 'Lalb_Chr13g0301671' => 'lal', 'Lalb_Chr14g0362851' => 'lal', 'Lalb_Chr24g0403581' => 'lal', 'Lj1g0000233' => 'lja', 'Lj2g0018120' => 'lja', 'Lj3C621T0' => 'lonja', 'Lj3P1059T14' => 'lonja', 'Lj3P611T9' => 'lonja', 'Lj3P614T13' => 'lonja', 'Lj3P615T5' => 'lonja', 'Lj4g0012315' => 'lja', 'Lj4g0026182' => 'lja', 'Lj6P813T16' => 'lonja', 'Lj7C427T7' => 'lonja', 'Lj7C427T8' => 'lonja', 'Lj7P600T41' => 'lonja', 'Lju41C42G17' => 'lonja', 'Lsat_1_v5_gn_0_47300' => 'lsa', 'Lsat_1_v5_gn_2_91280' => 'lsa', 'Lsat_1_v5_gn_3_30561' => 'lsa', 'Lsat_1_v5_gn_4_184321' => 'lsa', 'Lsat_1_v5_gn_4_4041' => 'lsa', 'Lsat_1_v5_gn_5_92000' => 'lsa', 'Lsat_1_v5_gn_8_152940' => 'lsa', 'Lsat_1_v5_gn_8_62401' => 'lsa', 'Manes.06G055900' => 'mes', 'Manes.12G022200' => 'mes', 'Manes.13G023300' => 'mes', 'Manes.14G115000' => 'mes', 'Manes.15G151700' => 'mes', 'Manes.17G111300' => 'mes', 'Mapoly0226s0009' => 'mpo', 'MBI02_g25363_MAGBIO' => 'mbi', 'MBI06_g00027_MAGBIO' => 'mbi', 'MBI10_g13034_MAGBIO' => 'mbi', 'MD09G1023400' => 'mdo', 'MD13G1100100' => 'mdo', 'MD15G1169200' => 'mdo', 'MD16G1101100' => 'mdo', 'MD17G1022900' => 'mdo', 'Medtr3g096150' => 'mtr', 'Medtr4g115070' => 'mtr', 'Medtr7g033325' => 'mtr', 'Medtr8g089840' => 'mtr', 'MELO3C010319.2' => 'cme', 'MELO3C011944.2' => 'cme', 'MELO3C021589.2' => 'cme', 'Migut.E00207' => 'egut', 'Migut.H00067' => 'egut', 'Migut.K00433' => 'egut', 'Migut.K00606' => 'egut', 'Migut.K01410' => 'egut', 'MSTRG.13347' => 'ama', 'MSTRG.24045' => 'ama', 'MSTRG.2428' => 'ama', 'MSTRG.26410' => 'ama', 'MSTRG.3139' => 'ama', 'MSTRG.3286' => 'ama', 'MSTRG.563' => 'ama', 'MSTRG.7941' => 'ama', 'Nitab4.5_0000028g0060' => 'nta', 'Nitab4.5_0000065g0260' => 'nta', 'Nitab4.5_0000112g0060' => 'nta', 'Nitab4.5_0000489g0120' => 'nta', 'Nitab4.5_0001776g0050' => 'nta', 'Nitab4.5_0001854g0010' => 'nta', 'Nitab4.5_0001860g0020' => 'nta', 'Nitab4.5_0004352g0010' => 'nta', 'Nitab4.5_0008716g0020' => 'nta', 'Nitab4.5_0008922g0010' => 'nta', 'Nn3g16693' => 'nnu', 'Nn4g22596' => 'nnu', 'Nn7g37639' => 'nnu', 'Oeu001701.1' => 'oeu', 'Oeu018149.1' => 'oeu', 'Oeu026220.1' => 'oeu', 'Oeu038635.1' => 'oeu', 'Oeu049176.1' => 'oeu', 'Oeu056706.1' => 'oeu', 'Oeu056937.1' => 'oeu', 'Oeu057540.1' => 'oeu', 'Os02g0594900' => 'osa', 'Os02g0595100' => 'osa', 'Os04g0477500' => 'osa', 'Os12g0611900' => 'osa', 'Peaxi162Scf00076g00020' => 'pax', 'Peaxi162Scf00128g00217' => 'pax', 'Peaxi162Scf00129g01640' => 'pax', 'Peaxi162Scf00669g00007' => 'pax', 'Peaxi162Scf00700g00421' => 'pax', 'Peaxi162Scf00801g00038' => 'pax', 'Peaxi162Scf00891g00025' => 'pax', 'PGR083G0909' => 'pgr', 'PGR119G1005' => 'pgr', 'PGR142G2236' => 'pgr', 'PGR142G3388' => 'pgr', 'PGSC0003DMG400004514' => 'stu', 'PGSC0003DMG400012635' => 'stu', 'PGSC0003DMG400015730' => 'stu', 'PGSC0003DMG400018611' => 'stu', 'PGSC0003DMG400030897' => 'stu', 'Phvul.001G254800' => 'pvu', 'Phvul.002G260100' => 'pvu', 'Phvul.003G167600' => 'pvu', 'Phvul.004G005100' => 'pvu', 'Potri.001G343600' => 'ptr', 'Potri.006G066700' => 'ptr', 'Potri.008G186000' => 'ptr', 'Potri.010G046900' => 'ptr', 'Potri.018G127900' => 'ptr', 'Pp3c20_17750' => 'ppa', 'Pp3c24_4380' => 'ppa', 'Prupe.1G245800' => 'ppe', 'Prupe.3G293400' => 'ppe', 'Prupe.7G247400' => 'ppe', 'Psat0s145g0120' => 'psa', 'Psat0s595g0040' => 'psa', 'Psat0s595g0120' => 'psa', 'Psat3g175040' => 'psa', 'Psat7g058120' => 'psa', 'PSO017G0428' => 'pso', 'PSO063G7510' => 'pso', 'PSO067G0046' => 'pso', 'PSO478G1073' => 'pso', 'PSO675G3677' => 'pso', 'PSO675G6558' => 'pso', 'PSO675G7520' => 'pso', 'PSO675G8959' => 'pso', 'QL02p074089' => 'qlo', 'QL02p089614' => 'qlo', 'QL03p057736' => 'qlo', 'RcHm_v2.0_Chr1g0364131' => 'rch', 'RcHm_v2.0_Chr2g0087801' => 'rch', 'RcHm_v2.0_Chr2g0087821' => 'rch', 'RcHm_v2.0_Chr2g0173231' => 'rch', 'RcHm_v2.0_Chr4g0433111' => 'rch', 'Rhsim03G0250300' => 'rsi', 'Rhsim08G0048400' => 'rsi', 'Rhsim10G0014800' => 'rsi', 'Rhsim12G0040100' => 'rsi', 'Rhsim12G0109700' => 'rsi', 'Sabra06G0049600' => 'sbr', 'Sabra08G0141000' => 'sbr', 'Sabra10G0021400' => 'sbr', 'Sabra16G0222900' => 'sbr', 'Sabra18G0108600' => 'sbr', 'SalBow1G0433' => 'sbo', 'SalBow1G2038' => 'sbo', 'SalBow1G5003' => 'sbo', 'SalBow7G1197' => 'sbo', 'SalBow8G3506' => 'sbo', 'Sc03g0007300' => 'sci', 'Sc11g0000950' => 'sci', 'Sc14g0008750' => 'sci', 'Sc18g0000420' => 'sci', 'Sed0006754' => 'sed', 'Sed0008741' => 'sed', 'Sed0017172' => 'sed', 'Sed0018925' => 'sed', 'Sed0023326' => 'sed', 'Sed0025909' => 'sed', 'SEGI_05333' => 'sgi', 'SEGI_10362' => 'sgi', 'SEGI_13380' => 'sgi', 'SEGI_24306' => 'sgi', 'SEGI_29077' => 'sgi', 'SEGI_29095' => 'sgi', 'SEGI_36534' => 'sgi', 'SEGI_37506' => 'sgi', 'SEGI_38321' => 'sgi', 'SGA_v2.0_scaffold307G48031' => 'sas', 'SGA_v2.0_scaffold47G17507' => 'sas', 'SGA_v2.0_scaffold63G21736' => 'sas', 'SGA_v2.0_scaffold87G27070' => 'sas', 'SHI17794' => 'shi', 'SHI28851' => 'shi', 'SMO165G0155' => 'smo', 'SMO340G0217' => 'smo', 'SMO367G1210' => 'smo', 'Solyc02g093430.3' => 'sly', 'Solyc05g013580.4' => 'sly', 'Solyc07g008030.3' => 'sly', 'Solyc12g035470.2' => 'sly', 'Sopen02g038020' => 'spe', 'Sopen05g008490' => 'spe', 'Sopen07g003910' => 'spe', 'Sopen12g015240' => 'spe', 'Sp1g11550' => 'spa', 'Sp2g16710' => 'spa', 'Sp3g00430' => 'spa', 'Sp3g26780' => 'spa', 'Sp5g22900' => 'spa', 'Sp6g29530' => 'spa', 'TAR371G0794' => 'tar', 'TAR374G0164' => 'tar', 'TAR622G0165' => 'tar', 'TAR626G0929' => 'tar', 'TAR629G2155' => 'tar', 'THA.LOC104805282' => 'tha', 'THA.LOC104805363' => 'tha', 'THA.LOC104808968' => 'tha', 'THA.LOC104821093' => 'tha', 'THA.LOC104823953' => 'tha', 'THA.LOC104825562' => 'tha', 'THA.LOC104825665' => 'tha', 'Thecc.02G261400' => 'tca', 'Thecc.04G019200' => 'tca', 'Thecc.09G130400' => 'tca', 'Thhalv10004374m.g' => 'esa', 'Thhalv10007850m.g' => 'esa', 'Thhalv10013782m.g' => 'esa', 'Thhalv10018686m.g' => 'esa', 'Thhalv10020899m.g' => 'esa', 'Thhalv10022755m.g' => 'esa', 'TPR.G23851' => 'tpr', 'TPR.G26500' => 'tpr', 'TPR.G27267' => 'tpr', 'TPR.G32001' => 'tpr', 'TPR.G6251' => 'tpr', 'TPR.G8167' => 'tpr', 'TWI12G1330' => 'twi', 'TWI18G1239' => 'twi', 'TWI34G0979' => 'twi', 'TWI36G0670' => 'twi', 'TWI36G0707' => 'twi', 'TWI56G0233' => 'twi', 'TWI75G1809' => 'twi', 'unitig_21.g20874' => 'ugi', 'unitig_26.g10343' => 'ugi', 'unitig_46.g18392' => 'ugi', 'unitig_52.g17178' => 'ugi', 'unitig_8.g2934' => 'ugi', 'vmacro01122' => 'vma', 'vmacro05875' => 'vma', 'vmacro06147' => 'vma', 'vmacro16191' => 'vma', 'vmacro18293' => 'vma', 'VMungo0251G3707' => 'vmu', 'VMungo0464G1521' => 'vmu', 'VMungo1215G0205' => 'vmu', 'VMungo1383G2484' => 'vmu', 'Zm00001eb079610' => 'zma', 'Zm00001eb135990' => 'zma', 'Zm00001eb183710' => 'zma', 'Zm00001eb246020' => 'zma' ), 'gf_id' => 'HOM05D001124', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001124' ), 'data_identifier' => 'HOM05D001124', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001124', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '548', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02520' => 'bna', 'A03p06630' => 'bna', 'A05p44460' => 'bna', 'A06p08710' => 'bna', 'A06p41090' => 'bna', 'A07p32320' => 'bna', 'A08p32520' => 'bna', 'A09p10360' => 'bna', 'A10p24080' => 'bna', 'Aa31LG11G15250' => 'aar', 'Aa31LG1G1800' => 'aar', 'Aa31LG2G5120' => 'aar', 'Aa31LG2G6070' => 'aar', 'Aa31LG5G10770' => 'aar', 'Aa31sc61G90' => 'aar', 'Actinidia01352' => 'ach', 'Actinidia05983' => 'ach', 'Actinidia08133' => 'ach', 'Actinidia15101' => 'ach', 'Actinidia26379' => 'ach', 'Actinidia35778' => 'ach', 'Actinidia36123' => 'ach', 'Actinidia37436' => 'ach', 'Actinidia38730' => 'ach', 'Ah.02g128210' => 'amhyb', 'Ah.03g132990' => 'amhyb', 'Ah.14g079410' => 'amhyb', 'AL1G24640' => 'aly', 'AL2G26680' => 'aly', 'AL3G10530' => 'aly', 'AL3G45230' => 'aly', 'AL5G15230' => 'aly', 'AL5G16960' => 'aly', 'AL6G25210' => 'aly', 'Aqoxy2G00441' => 'aox', 'Aqoxy3G01236' => 'aox', 'Aqoxy5G03746' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3RQ047' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C7GMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9C8JER' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MBL6KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YXCZ83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZANX40' => 'arhy', 'AT1G12990' => 'ath', 'AT1G67880' => 'ath', 'AT2G13290' => 'ath', 'AT3G01620' => 'ath', 'AT3G26445' => 'ath', 'AT3G27540' => 'ath', 'AT5G14480' => 'ath', 'ATR0824G026' => 'atr', 'ATR1098G019' => 'atr', 'Atru.chr11.2145' => 'acertr', 'Atru.chr2.3636' => 'acertr', 'Atru.chr2.3644' => 'acertr', 'Atru.chr6.2422' => 'acertr', 'Atru.chr7.1112' => 'acertr', 'AUR62005469' => 'cqu', 'AUR62011166' => 'cqu', 'AUR62013319' => 'cqu', 'AUR62024273' => 'cqu', 'AUR62028420' => 'cqu', 'AUR62041942' => 'cqu', 'BcaB01g04969' => 'bca', 'BcaB01g06371' => 'bca', 'BcaB02g11494' => 'bca', 'BcaB03g15382' => 'bca', 'BcaB08g36994' => 'bca', 'BcaC03g13477' => 'bca', 'BcaC03g13478' => 'bca', 'BcaC03g13480' => 'bca', 'BcaC03g13481' => 'bca', 'BcaC03g13486' => 'bca', 'BcaC04g19031' => 'bca', 'BcaC04g23085' => 'bca', 'BcaC05g25094' => 'bca', 'BcaC05g25096' => 'bca', 'BcaC05g25138' => 'bca', 'BcaC05g30416' => 'bca', 'BcaC05g30455' => 'bca', 'BcaC06g30979' => 'bca', 'BcaC06g33805' => 'bca', 'BcaC08g46021' => 'bca', 'BcaNung03154' => 'bca', 'BolC2t06623H' => 'bol', 'BolC2t06632H' => 'bol', 'BolC2t06635H' => 'bol', 'BolC2t06638H' => 'bol', 'BolC3t13266H' => 'bol', 'BolC5t29776H' => 'bol', 'BolC6t38912H' => 'bol', 'BolC7t44183H' => 'bol', 'BolC9t54123H' => 'bol', 'BolC9t59107H' => 'bol', 'BraA02t05221Z' => 'bra', 'BraA03t09996Z' => 'bra', 'BraA05t23210Z' => 'bra', 'BraA06t24068Z' => 'bra', 'BraA06t27032Z' => 'bra', 'BraA08t35176Z' => 'bra', 'BraA09t36680Z' => 'bra', 'BraA10t44471Z' => 'bra', 'C02p06760' => 'bna', 'C02p06890' => 'bna', 'C02p07010' => 'bna', 'C03p07660' => 'bna', 'C05p10300' => 'bna', 'C06p38150' => 'bna', 'C07p36650' => 'bna', 'C08p15770' => 'bna', 'C09p12300' => 'bna', 'C09p62700' => 'bna', 'C09p75040' => 'bna', 'CAN.G13.1' => 'can', 'CAN.G138.4' => 'can', 'CAN.G44.6' => 'can', 'CAN.G473.19' => 'can', 'CANSAT01G0835' => 'cansat', 'CANSAT11G0246' => 'cansat', 'CANSAT11G1766' => 'cansat', 'CANSAT64G1954' => 'cansat', 'CARHR013330' => 'chi', 'CARHR060530' => 'chi', 'CARHR075300' => 'chi', 'CARHR105120' => 'chi', 'CARHR148910' => 'chi', 'CARHR198830' => 'chi', 'Carub.0001s1275' => 'cru', 'Carub.0002s1437' => 'cru', 'Carub.0003s0044' => 'cru', 'Carub.0003s2787' => 'cru', 'Carub.0005s0597' => 'cru', 'Carub.0006s1266' => 'cru', 'Ca_06935_v3' => 'car', 'Ca_13559_v3' => 'car', 'Ca_16941_v3' => 'car', 'Ca_16960_v3' => 'car', 'Ca_17775_v3' => 'car', 'Ca_30464_v3' => 'car', 'Cc06_g08160' => 'ccan', 'Cc07_g01520' => 'ccan', 'Cc11_g15810' => 'ccan', 'CDE02G2840' => 'cde', 'CDE03G0093' => 'cde', 'CDE04G2127' => 'cde', 'CDE07G1857' => 'cde', 'CDE09G1246' => 'cde', 'Cfa003412' => 'cfa', 'Cfa007341' => 'cfa', 'Cfa009220' => 'cfa', 'Ciclev10008737m.g' => 'ccl', 'Ciclev10015565m.g' => 'ccl', 'Ciclev10031761m.g' => 'ccl', 'CiPaw.03G045300' => 'cil', 'CiPaw.03G247200' => 'cil', 'CiPaw.04G029500' => 'cil', 'CiPaw.04G174000' => 'cil', 'CiPaw.05G181200' => 'cil', 'CiPaw.06G067100' => 'cil', 'ClCG05G025800' => 'cla', 'ClCG06G011400' => 'cla', 'ClCG09G019360' => 'cla', 'COL.COLO4_04827' => 'col', 'COL.COLO4_29170' => 'col', 'COL.COLO4_35131' => 'col', 'COL.COLO4_35132' => 'col', 'Cpa.g.sc33.32' => 'cpa', 'Cpa.g.sc46.29' => 'cpa', 'Cpa.g.sc796.1' => 'cpa', 'CsaV3_1G030420' => 'csa', 'CsaV3_5G027050' => 'csa', 'CsaV3_5G031040' => 'csa', 'CsaV3_UNG023130' => 'csa', 'CSS0007726' => 'camsi', 'CSS0016433' => 'camsi', 'CSS0017656' => 'camsi', 'CSS0025364' => 'camsi', 'CSS0027582' => 'camsi', 'CSS0047288' => 'camsi', 'CSS0049950' => 'camsi', 'DCAR_003843' => 'dca', 'DCAR_007052' => 'dca', 'DCAR_020884' => 'dca', 'DCAR_021730' => 'dca', 'DCAR_024423' => 'dca', 'DCAR_026509' => 'dca', 'DCAR_031158' => 'dca', 'Dinv14728' => 'din', 'Dinv15219' => 'din', 'Dinv25728' => 'din', 'Dinv33428' => 'din', 'Dinv36489' => 'din', 'Dinv41486' => 'din', 'Duzib147G0469' => 'dzi', 'Duzib168G0060' => 'dzi', 'Duzib187G1215' => 'dzi', 'Duzib248G0692' => 'dzi', 'Duzib251G0767' => 'dzi', 'Duzib264G0446' => 'dzi', 'Duzib268G0691' => 'dzi', 'ECA232G4767' => 'eca', 'ECA233G2838' => 'eca', 'ECA234G0391' => 'eca', 'ECA234G0857' => 'eca', 'ECA236G1593' => 'eca', 'ECA238G0565' => 'eca', 'ECA246G1027' => 'eca', 'ECA246G3223' => 'eca', 'ECA246G3470' => 'eca', 'EL10Ac6g13829' => 'bvu', 'EL10Ac6g14093' => 'bvu', 'EL10Ac8g18707' => 'bvu', 'Eucgr.C01369' => 'egr', 'Eucgr.H02492' => 'egr', 'Eucgr.I01733' => 'egr', 'Eucgr.J02255' => 'egr', 'Eucgr.J02257' => 'egr', 'Eucgr.J02258' => 'egr', 'FAN02G1601' => 'fan', 'FAN03G1586' => 'fan', 'FAN03G2986' => 'fan', 'FAN05G4837' => 'fan', 'FAN06G0146' => 'fan', 'FAN07G0858' => 'fan', 'FAN09G3179' => 'fan', 'FAN10G0669' => 'fan', 'FAN12G2358' => 'fan', 'FAN14G4198' => 'fan', 'FAN14G5112' => 'fan', 'FAN17G0342' => 'fan', 'FAN19G0342' => 'fan', 'FAN19G0962' => 'fan', 'FAN19G1101' => 'fan', 'FAN19G1872' => 'fan', 'FAN22G0356' => 'fan', 'FAN23G0744' => 'fan', 'FAN23G1914' => 'fan', 'FAN26G0032' => 'fan', 'FAN28G0625' => 'fan', 'FvH4_1g02710' => 'fve', 'FvH4_1g02720' => 'fve', 'FvH4_4g25670' => 'fve', 'FvH4_6g51700' => 'fve', 'FvH4_7g20170' => 'fve', 'Glyma.05G175000' => 'gma', 'Glyma.08G132300' => 'gma', 'Glyma.11G243000' => 'gma', 'Glyma.13G158900' => 'gma', 'Glyma.17G112400' => 'gma', 'Glyma.18G014100' => 'gma', 'Glyma.19G003100' => 'gma', 'Glyma.19G056500' => 'gma', 'Gohir.A01G158900' => 'ghi', 'Gohir.A05G312600' => 'ghi', 'Gohir.A05G354900' => 'ghi', 'Gohir.A07G037200' => 'ghi', 'Gohir.A09G030000' => 'ghi', 'Gohir.A12G145200' => 'ghi', 'Gohir.D01G151500' => 'ghi', 'Gohir.D04G058300' => 'ghi', 'Gohir.D05G314100' => 'ghi', 'Gohir.D07G041400' => 'ghi', 'Gohir.D09G029700' => 'ghi', 'Gohir.D12G149700' => 'ghi', 'Gorai.001G043800' => 'gra', 'Gorai.002G187800' => 'gra', 'Gorai.006G034700' => 'gra', 'Gorai.008G161200' => 'gra', 'Gorai.009G335700' => 'gra', 'Gorai.012G065000' => 'gra', 'GSVIVG01000535001' => 'vvi', 'GSVIVG01015572001' => 'vvi', 'GSVIVG01032386001' => 'vvi', 'HanXRQChr05g0138531' => 'han', 'HanXRQChr06g0174391' => 'han', 'HanXRQChr07g0199021' => 'han', 'HanXRQChr08g0208211' => 'han', 'HanXRQChr09g0255471' => 'han', 'HanXRQChr10g0315791' => 'han', 'HanXRQChr12g0371991' => 'han', 'HanXRQChr15g0475251' => 'han', 'HanXRQChr17g0540001' => 'han', 'HanXRQChr17g0548631' => 'han', 'HanXRQChr17g0569561' => 'han', 'Haze_12256' => 'cav', 'Haze_14756' => 'cav', 'Haze_25528' => 'cav', 'Hma1.2p1_0079F.1_g041020' => 'hma', 'Hma1.2p1_0818F.1_g223260' => 'hma', 'Hma1.2p1_1747F.1_g300530' => 'hma', 'HPP92_004607' => 'vpl', 'HPP92_004608' => 'vpl', 'HPP92_006181' => 'vpl', 'HPP92_012192' => 'vpl', 'HPP92_015680' => 'vpl', 'HPP92_020249' => 'vpl', 'HPP92_021376' => 'vpl', 'HPP92_024275' => 'vpl', 'Hund06031' => 'sun', 'Hund25391' => 'sun', 'Lalb_Chr07g0185371' => 'lal', 'Lalb_Chr07g0185381' => 'lal', 'Lalb_Chr12g0204011' => 'lal', 'Lalb_Chr13g0301671' => 'lal', 'Lalb_Chr14g0362851' => 'lal', 'Lalb_Chr24g0403581' => 'lal', 'Lj1g0000233' => 'lja', 'Lj2g0018120' => 'lja', 'Lj3C621T0' => 'lonja', 'Lj3P1059T14' => 'lonja', 'Lj3P611T9' => 'lonja', 'Lj3P614T13' => 'lonja', 'Lj3P615T5' => 'lonja', 'Lj4g0012315' => 'lja', 'Lj4g0026182' => 'lja', 'Lj6P813T16' => 'lonja', 'Lj7C427T7' => 'lonja', 'Lj7C427T8' => 'lonja', 'Lj7P600T41' => 'lonja', 'Lju41C42G17' => 'lonja', 'Lsat_1_v5_gn_0_47300' => 'lsa', 'Lsat_1_v5_gn_2_91280' => 'lsa', 'Lsat_1_v5_gn_3_30561' => 'lsa', 'Lsat_1_v5_gn_4_184321' => 'lsa', 'Lsat_1_v5_gn_4_4041' => 'lsa', 'Lsat_1_v5_gn_5_92000' => 'lsa', 'Lsat_1_v5_gn_8_152940' => 'lsa', 'Lsat_1_v5_gn_8_62401' => 'lsa', 'Manes.06G055900' => 'mes', 'Manes.12G022200' => 'mes', 'Manes.13G023300' => 'mes', 'Manes.14G115000' => 'mes', 'Manes.15G151700' => 'mes', 'Manes.17G111300' => 'mes', 'Mapoly0226s0009' => 'mpo', 'MBI02_g25363_MAGBIO' => 'mbi', 'MBI06_g00027_MAGBIO' => 'mbi', 'MBI10_g13034_MAGBIO' => 'mbi', 'MD09G1023400' => 'mdo', 'MD13G1100100' => 'mdo', 'MD15G1169200' => 'mdo', 'MD16G1101100' => 'mdo', 'MD17G1022900' => 'mdo', 'Medtr3g096150' => 'mtr', 'Medtr4g115070' => 'mtr', 'Medtr7g033325' => 'mtr', 'Medtr8g089840' => 'mtr', 'MELO3C010319.2' => 'cme', 'MELO3C011944.2' => 'cme', 'MELO3C021589.2' => 'cme', 'Migut.E00207' => 'egut', 'Migut.H00067' => 'egut', 'Migut.K00433' => 'egut', 'Migut.K00606' => 'egut', 'Migut.K01410' => 'egut', 'MSTRG.13347' => 'ama', 'MSTRG.24045' => 'ama', 'MSTRG.2428' => 'ama', 'MSTRG.26410' => 'ama', 'MSTRG.3139' => 'ama', 'MSTRG.3286' => 'ama', 'MSTRG.563' => 'ama', 'MSTRG.7941' => 'ama', 'Nitab4.5_0000028g0060' => 'nta', 'Nitab4.5_0000065g0260' => 'nta', 'Nitab4.5_0000112g0060' => 'nta', 'Nitab4.5_0000489g0120' => 'nta', 'Nitab4.5_0001776g0050' => 'nta', 'Nitab4.5_0001854g0010' => 'nta', 'Nitab4.5_0001860g0020' => 'nta', 'Nitab4.5_0004352g0010' => 'nta', 'Nitab4.5_0008716g0020' => 'nta', 'Nitab4.5_0008922g0010' => 'nta', 'Nn3g16693' => 'nnu', 'Nn4g22596' => 'nnu', 'Nn7g37639' => 'nnu', 'Oeu001701.1' => 'oeu', 'Oeu018149.1' => 'oeu', 'Oeu026220.1' => 'oeu', 'Oeu038635.1' => 'oeu', 'Oeu049176.1' => 'oeu', 'Oeu056706.1' => 'oeu', 'Oeu056937.1' => 'oeu', 'Oeu057540.1' => 'oeu', 'Os02g0594900' => 'osa', 'Os02g0595100' => 'osa', 'Os04g0477500' => 'osa', 'Os12g0611900' => 'osa', 'Peaxi162Scf00076g00020' => 'pax', 'Peaxi162Scf00128g00217' => 'pax', 'Peaxi162Scf00129g01640' => 'pax', 'Peaxi162Scf00669g00007' => 'pax', 'Peaxi162Scf00700g00421' => 'pax', 'Peaxi162Scf00801g00038' => 'pax', 'Peaxi162Scf00891g00025' => 'pax', 'PGR083G0909' => 'pgr', 'PGR119G1005' => 'pgr', 'PGR142G2236' => 'pgr', 'PGR142G3388' => 'pgr', 'PGSC0003DMG400004514' => 'stu', 'PGSC0003DMG400012635' => 'stu', 'PGSC0003DMG400015730' => 'stu', 'PGSC0003DMG400018611' => 'stu', 'PGSC0003DMG400030897' => 'stu', 'Phvul.001G254800' => 'pvu', 'Phvul.002G260100' => 'pvu', 'Phvul.003G167600' => 'pvu', 'Phvul.004G005100' => 'pvu', 'Potri.001G343600' => 'ptr', 'Potri.006G066700' => 'ptr', 'Potri.008G186000' => 'ptr', 'Potri.010G046900' => 'ptr', 'Potri.018G127900' => 'ptr', 'Pp3c20_17750' => 'ppa', 'Pp3c24_4380' => 'ppa', 'Prupe.1G245800' => 'ppe', 'Prupe.3G293400' => 'ppe', 'Prupe.7G247400' => 'ppe', 'Psat0s145g0120' => 'psa', 'Psat0s595g0040' => 'psa', 'Psat0s595g0120' => 'psa', 'Psat3g175040' => 'psa', 'Psat7g058120' => 'psa', 'PSO017G0428' => 'pso', 'PSO063G7510' => 'pso', 'PSO067G0046' => 'pso', 'PSO478G1073' => 'pso', 'PSO675G3677' => 'pso', 'PSO675G6558' => 'pso', 'PSO675G7520' => 'pso', 'PSO675G8959' => 'pso', 'QL02p074089' => 'qlo', 'QL02p089614' => 'qlo', 'QL03p057736' => 'qlo', 'RcHm_v2.0_Chr1g0364131' => 'rch', 'RcHm_v2.0_Chr2g0087801' => 'rch', 'RcHm_v2.0_Chr2g0087821' => 'rch', 'RcHm_v2.0_Chr2g0173231' => 'rch', 'RcHm_v2.0_Chr4g0433111' => 'rch', 'Rhsim03G0250300' => 'rsi', 'Rhsim08G0048400' => 'rsi', 'Rhsim10G0014800' => 'rsi', 'Rhsim12G0040100' => 'rsi', 'Rhsim12G0109700' => 'rsi', 'Sabra06G0049600' => 'sbr', 'Sabra08G0141000' => 'sbr', 'Sabra10G0021400' => 'sbr', 'Sabra16G0222900' => 'sbr', 'Sabra18G0108600' => 'sbr', 'SalBow1G0433' => 'sbo', 'SalBow1G2038' => 'sbo', 'SalBow1G5003' => 'sbo', 'SalBow7G1197' => 'sbo', 'SalBow8G3506' => 'sbo', 'Sc03g0007300' => 'sci', 'Sc11g0000950' => 'sci', 'Sc14g0008750' => 'sci', 'Sc18g0000420' => 'sci', 'Sed0006754' => 'sed', 'Sed0008741' => 'sed', 'Sed0017172' => 'sed', 'Sed0018925' => 'sed', 'Sed0023326' => 'sed', 'Sed0025909' => 'sed', 'SEGI_05333' => 'sgi', 'SEGI_10362' => 'sgi', 'SEGI_13380' => 'sgi', 'SEGI_24306' => 'sgi', 'SEGI_29077' => 'sgi', 'SEGI_29095' => 'sgi', 'SEGI_36534' => 'sgi', 'SEGI_37506' => 'sgi', 'SEGI_38321' => 'sgi', 'SGA_v2.0_scaffold307G48031' => 'sas', 'SGA_v2.0_scaffold47G17507' => 'sas', 'SGA_v2.0_scaffold63G21736' => 'sas', 'SGA_v2.0_scaffold87G27070' => 'sas', 'SHI17794' => 'shi', 'SHI28851' => 'shi', 'SMO165G0155' => 'smo', 'SMO340G0217' => 'smo', 'SMO367G1210' => 'smo', 'Solyc02g093430.3' => 'sly', 'Solyc05g013580.4' => 'sly', 'Solyc07g008030.3' => 'sly', 'Solyc12g035470.2' => 'sly', 'Sopen02g038020' => 'spe', 'Sopen05g008490' => 'spe', 'Sopen07g003910' => 'spe', 'Sopen12g015240' => 'spe', 'Sp1g11550' => 'spa', 'Sp2g16710' => 'spa', 'Sp3g00430' => 'spa', 'Sp3g26780' => 'spa', 'Sp5g22900' => 'spa', 'Sp6g29530' => 'spa', 'TAR371G0794' => 'tar', 'TAR374G0164' => 'tar', 'TAR622G0165' => 'tar', 'TAR626G0929' => 'tar', 'TAR629G2155' => 'tar', 'THA.LOC104805282' => 'tha', 'THA.LOC104805363' => 'tha', 'THA.LOC104808968' => 'tha', 'THA.LOC104821093' => 'tha', 'THA.LOC104823953' => 'tha', 'THA.LOC104825562' => 'tha', 'THA.LOC104825665' => 'tha', 'Thecc.02G261400' => 'tca', 'Thecc.04G019200' => 'tca', 'Thecc.09G130400' => 'tca', 'Thhalv10004374m.g' => 'esa', 'Thhalv10007850m.g' => 'esa', 'Thhalv10013782m.g' => 'esa', 'Thhalv10018686m.g' => 'esa', 'Thhalv10020899m.g' => 'esa', 'Thhalv10022755m.g' => 'esa', 'TPR.G23851' => 'tpr', 'TPR.G26500' => 'tpr', 'TPR.G27267' => 'tpr', 'TPR.G32001' => 'tpr', 'TPR.G6251' => 'tpr', 'TPR.G8167' => 'tpr', 'TWI12G1330' => 'twi', 'TWI18G1239' => 'twi', 'TWI34G0979' => 'twi', 'TWI36G0670' => 'twi', 'TWI36G0707' => 'twi', 'TWI56G0233' => 'twi', 'TWI75G1809' => 'twi', 'unitig_21.g20874' => 'ugi', 'unitig_26.g10343' => 'ugi', 'unitig_46.g18392' => 'ugi', 'unitig_52.g17178' => 'ugi', 'unitig_8.g2934' => 'ugi', 'vmacro01122' => 'vma', 'vmacro05875' => 'vma', 'vmacro06147' => 'vma', 'vmacro16191' => 'vma', 'vmacro18293' => 'vma', 'VMungo0251G3707' => 'vmu', 'VMungo0464G1521' => 'vmu', 'VMungo1215G0205' => 'vmu', 'VMungo1383G2484' => 'vmu', 'Zm00001eb079610' => 'zma', 'Zm00001eb135990' => 'zma', 'Zm00001eb183710' => 'zma', 'Zm00001eb246020' => 'zma' ) $gf_id = 'HOM05D001124' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001124' ) $data_identifier = 'HOM05D001124' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 6, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 7, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 21, 'bol' => (int) 10, 'bra' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 6, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 9, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 21, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 8, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 10, 'lsa' => (int) 8, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 8, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 9, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb246020' $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' => 'HOM05D001124', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '548', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02520' => 'bna', 'A03p06630' => 'bna', 'A05p44460' => 'bna', 'A06p08710' => 'bna', 'A06p41090' => 'bna', 'A07p32320' => 'bna', 'A08p32520' => 'bna', 'A09p10360' => 'bna', 'A10p24080' => 'bna', 'Aa31LG11G15250' => 'aar', 'Aa31LG1G1800' => 'aar', 'Aa31LG2G5120' => 'aar', 'Aa31LG2G6070' => 'aar', 'Aa31LG5G10770' => 'aar', 'Aa31sc61G90' => 'aar', 'Actinidia01352' => 'ach', 'Actinidia05983' => 'ach', 'Actinidia08133' => 'ach', 'Actinidia15101' => 'ach', 'Actinidia26379' => 'ach', 'Actinidia35778' => 'ach', 'Actinidia36123' => 'ach', 'Actinidia37436' => 'ach', 'Actinidia38730' => 'ach', 'Ah.02g128210' => 'amhyb', 'Ah.03g132990' => 'amhyb', 'Ah.14g079410' => 'amhyb', 'AL1G24640' => 'aly', 'AL2G26680' => 'aly', 'AL3G10530' => 'aly', 'AL3G45230' => 'aly', 'AL5G15230' => 'aly', 'AL5G16960' => 'aly', 'AL6G25210' => 'aly', 'Aqoxy2G00441' => 'aox', 'Aqoxy3G01236' => 'aox', 'Aqoxy5G03746' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3RQ047' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C7GMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9C8JER' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MBL6KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YXCZ83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZANX40' => 'arhy', 'AT1G12990' => 'ath', 'AT1G67880' => 'ath', 'AT2G13290' => 'ath', 'AT3G01620' => 'ath', 'AT3G26445' => 'ath', 'AT3G27540' => 'ath', 'AT5G14480' => 'ath', 'ATR0824G026' => 'atr', 'ATR1098G019' => 'atr', 'Atru.chr11.2145' => 'acertr', 'Atru.chr2.3636' => 'acertr', 'Atru.chr2.3644' => 'acertr', 'Atru.chr6.2422' => 'acertr', 'Atru.chr7.1112' => 'acertr', 'AUR62005469' => 'cqu', 'AUR62011166' => 'cqu', 'AUR62013319' => 'cqu', 'AUR62024273' => 'cqu', 'AUR62028420' => 'cqu', 'AUR62041942' => 'cqu', 'BcaB01g04969' => 'bca', 'BcaB01g06371' => 'bca', 'BcaB02g11494' => 'bca', 'BcaB03g15382' => 'bca', 'BcaB08g36994' => 'bca', 'BcaC03g13477' => 'bca', 'BcaC03g13478' => 'bca', 'BcaC03g13480' => 'bca', 'BcaC03g13481' => 'bca', 'BcaC03g13486' => 'bca', 'BcaC04g19031' => 'bca', 'BcaC04g23085' => 'bca', 'BcaC05g25094' => 'bca', 'BcaC05g25096' => 'bca', 'BcaC05g25138' => 'bca', 'BcaC05g30416' => 'bca', 'BcaC05g30455' => 'bca', 'BcaC06g30979' => 'bca', 'BcaC06g33805' => 'bca', 'BcaC08g46021' => 'bca', 'BcaNung03154' => 'bca', 'BolC2t06623H' => 'bol', 'BolC2t06632H' => 'bol', 'BolC2t06635H' => 'bol', 'BolC2t06638H' => 'bol', 'BolC3t13266H' => 'bol', 'BolC5t29776H' => 'bol', 'BolC6t38912H' => 'bol', 'BolC7t44183H' => 'bol', 'BolC9t54123H' => 'bol', 'BolC9t59107H' => 'bol', 'BraA02t05221Z' => 'bra', 'BraA03t09996Z' => 'bra', 'BraA05t23210Z' => 'bra', 'BraA06t24068Z' => 'bra', 'BraA06t27032Z' => 'bra', 'BraA08t35176Z' => 'bra', 'BraA09t36680Z' => 'bra', 'BraA10t44471Z' => 'bra', 'C02p06760' => 'bna', 'C02p06890' => 'bna', 'C02p07010' => 'bna', 'C03p07660' => 'bna', 'C05p10300' => 'bna', 'C06p38150' => 'bna', 'C07p36650' => 'bna', 'C08p15770' => 'bna', 'C09p12300' => 'bna', 'C09p62700' => 'bna', 'C09p75040' => 'bna', 'CAN.G13.1' => 'can', 'CAN.G138.4' => 'can', 'CAN.G44.6' => 'can', 'CAN.G473.19' => 'can', 'CANSAT01G0835' => 'cansat', 'CANSAT11G0246' => 'cansat', 'CANSAT11G1766' => 'cansat', 'CANSAT64G1954' => 'cansat', 'CARHR013330' => 'chi', 'CARHR060530' => 'chi', 'CARHR075300' => 'chi', 'CARHR105120' => 'chi', 'CARHR148910' => 'chi', 'CARHR198830' => 'chi', 'Carub.0001s1275' => 'cru', 'Carub.0002s1437' => 'cru', 'Carub.0003s0044' => 'cru', 'Carub.0003s2787' => 'cru', 'Carub.0005s0597' => 'cru', 'Carub.0006s1266' => 'cru', 'Ca_06935_v3' => 'car', 'Ca_13559_v3' => 'car', 'Ca_16941_v3' => 'car', 'Ca_16960_v3' => 'car', 'Ca_17775_v3' => 'car', 'Ca_30464_v3' => 'car', 'Cc06_g08160' => 'ccan', 'Cc07_g01520' => 'ccan', 'Cc11_g15810' => 'ccan', 'CDE02G2840' => 'cde', 'CDE03G0093' => 'cde', 'CDE04G2127' => 'cde', 'CDE07G1857' => 'cde', 'CDE09G1246' => 'cde', 'Cfa003412' => 'cfa', 'Cfa007341' => 'cfa', 'Cfa009220' => 'cfa', 'Ciclev10008737m.g' => 'ccl', 'Ciclev10015565m.g' => 'ccl', 'Ciclev10031761m.g' => 'ccl', 'CiPaw.03G045300' => 'cil', 'CiPaw.03G247200' => 'cil', 'CiPaw.04G029500' => 'cil', 'CiPaw.04G174000' => 'cil', 'CiPaw.05G181200' => 'cil', 'CiPaw.06G067100' => 'cil', 'ClCG05G025800' => 'cla', 'ClCG06G011400' => 'cla', 'ClCG09G019360' => 'cla', 'COL.COLO4_04827' => 'col', 'COL.COLO4_29170' => 'col', 'COL.COLO4_35131' => 'col', 'COL.COLO4_35132' => 'col', 'Cpa.g.sc33.32' => 'cpa', 'Cpa.g.sc46.29' => 'cpa', 'Cpa.g.sc796.1' => 'cpa', 'CsaV3_1G030420' => 'csa', 'CsaV3_5G027050' => 'csa', 'CsaV3_5G031040' => 'csa', 'CsaV3_UNG023130' => 'csa', 'CSS0007726' => 'camsi', 'CSS0016433' => 'camsi', 'CSS0017656' => 'camsi', 'CSS0025364' => 'camsi', 'CSS0027582' => 'camsi', 'CSS0047288' => 'camsi', 'CSS0049950' => 'camsi', 'DCAR_003843' => 'dca', 'DCAR_007052' => 'dca', 'DCAR_020884' => 'dca', 'DCAR_021730' => 'dca', 'DCAR_024423' => 'dca', 'DCAR_026509' => 'dca', 'DCAR_031158' => 'dca', 'Dinv14728' => 'din', 'Dinv15219' => 'din', 'Dinv25728' => 'din', 'Dinv33428' => 'din', 'Dinv36489' => 'din', 'Dinv41486' => 'din', 'Duzib147G0469' => 'dzi', 'Duzib168G0060' => 'dzi', 'Duzib187G1215' => 'dzi', 'Duzib248G0692' => 'dzi', 'Duzib251G0767' => 'dzi', 'Duzib264G0446' => 'dzi', 'Duzib268G0691' => 'dzi', 'ECA232G4767' => 'eca', 'ECA233G2838' => 'eca', 'ECA234G0391' => 'eca', 'ECA234G0857' => 'eca', 'ECA236G1593' => 'eca', 'ECA238G0565' => 'eca', 'ECA246G1027' => 'eca', 'ECA246G3223' => 'eca', 'ECA246G3470' => 'eca', 'EL10Ac6g13829' => 'bvu', 'EL10Ac6g14093' => 'bvu', 'EL10Ac8g18707' => 'bvu', 'Eucgr.C01369' => 'egr', 'Eucgr.H02492' => 'egr', 'Eucgr.I01733' => 'egr', 'Eucgr.J02255' => 'egr', 'Eucgr.J02257' => 'egr', 'Eucgr.J02258' => 'egr', 'FAN02G1601' => 'fan', 'FAN03G1586' => 'fan', 'FAN03G2986' => 'fan', 'FAN05G4837' => 'fan', 'FAN06G0146' => 'fan', 'FAN07G0858' => 'fan', 'FAN09G3179' => 'fan', 'FAN10G0669' => 'fan', 'FAN12G2358' => 'fan', 'FAN14G4198' => 'fan', 'FAN14G5112' => 'fan', 'FAN17G0342' => 'fan', 'FAN19G0342' => 'fan', 'FAN19G0962' => 'fan', 'FAN19G1101' => 'fan', 'FAN19G1872' => 'fan', 'FAN22G0356' => 'fan', 'FAN23G0744' => 'fan', 'FAN23G1914' => 'fan', 'FAN26G0032' => 'fan', 'FAN28G0625' => 'fan', 'FvH4_1g02710' => 'fve', 'FvH4_1g02720' => 'fve', 'FvH4_4g25670' => 'fve', 'FvH4_6g51700' => 'fve', 'FvH4_7g20170' => 'fve', 'Glyma.05G175000' => 'gma', 'Glyma.08G132300' => 'gma', 'Glyma.11G243000' => 'gma', 'Glyma.13G158900' => 'gma', 'Glyma.17G112400' => 'gma', 'Glyma.18G014100' => 'gma', 'Glyma.19G003100' => 'gma', 'Glyma.19G056500' => 'gma', 'Gohir.A01G158900' => 'ghi', 'Gohir.A05G312600' => 'ghi', 'Gohir.A05G354900' => 'ghi', 'Gohir.A07G037200' => 'ghi', 'Gohir.A09G030000' => 'ghi', 'Gohir.A12G145200' => 'ghi', 'Gohir.D01G151500' => 'ghi', 'Gohir.D04G058300' => 'ghi', 'Gohir.D05G314100' => 'ghi', 'Gohir.D07G041400' => 'ghi', 'Gohir.D09G029700' => 'ghi', 'Gohir.D12G149700' => 'ghi', 'Gorai.001G043800' => 'gra', 'Gorai.002G187800' => 'gra', 'Gorai.006G034700' => 'gra', 'Gorai.008G161200' => 'gra', 'Gorai.009G335700' => 'gra', 'Gorai.012G065000' => 'gra', 'GSVIVG01000535001' => 'vvi', 'GSVIVG01015572001' => 'vvi', 'GSVIVG01032386001' => 'vvi', 'HanXRQChr05g0138531' => 'han', 'HanXRQChr06g0174391' => 'han', 'HanXRQChr07g0199021' => 'han', 'HanXRQChr08g0208211' => 'han', 'HanXRQChr09g0255471' => 'han', 'HanXRQChr10g0315791' => 'han', 'HanXRQChr12g0371991' => 'han', 'HanXRQChr15g0475251' => 'han', 'HanXRQChr17g0540001' => 'han', 'HanXRQChr17g0548631' => 'han', 'HanXRQChr17g0569561' => 'han', 'Haze_12256' => 'cav', 'Haze_14756' => 'cav', 'Haze_25528' => 'cav', 'Hma1.2p1_0079F.1_g041020' => 'hma', 'Hma1.2p1_0818F.1_g223260' => 'hma', 'Hma1.2p1_1747F.1_g300530' => 'hma', 'HPP92_004607' => 'vpl', 'HPP92_004608' => 'vpl', 'HPP92_006181' => 'vpl', 'HPP92_012192' => 'vpl', 'HPP92_015680' => 'vpl', 'HPP92_020249' => 'vpl', 'HPP92_021376' => 'vpl', 'HPP92_024275' => 'vpl', 'Hund06031' => 'sun', 'Hund25391' => 'sun', 'Lalb_Chr07g0185371' => 'lal', 'Lalb_Chr07g0185381' => 'lal', 'Lalb_Chr12g0204011' => 'lal', 'Lalb_Chr13g0301671' => 'lal', 'Lalb_Chr14g0362851' => 'lal', 'Lalb_Chr24g0403581' => 'lal', 'Lj1g0000233' => 'lja', 'Lj2g0018120' => 'lja', 'Lj3C621T0' => 'lonja', 'Lj3P1059T14' => 'lonja', 'Lj3P611T9' => 'lonja', 'Lj3P614T13' => 'lonja', 'Lj3P615T5' => 'lonja', 'Lj4g0012315' => 'lja', 'Lj4g0026182' => 'lja', 'Lj6P813T16' => 'lonja', 'Lj7C427T7' => 'lonja', 'Lj7C427T8' => 'lonja', 'Lj7P600T41' => 'lonja', 'Lju41C42G17' => 'lonja', 'Lsat_1_v5_gn_0_47300' => 'lsa', 'Lsat_1_v5_gn_2_91280' => 'lsa', 'Lsat_1_v5_gn_3_30561' => 'lsa', 'Lsat_1_v5_gn_4_184321' => 'lsa', 'Lsat_1_v5_gn_4_4041' => 'lsa', 'Lsat_1_v5_gn_5_92000' => 'lsa', 'Lsat_1_v5_gn_8_152940' => 'lsa', 'Lsat_1_v5_gn_8_62401' => 'lsa', 'Manes.06G055900' => 'mes', 'Manes.12G022200' => 'mes', 'Manes.13G023300' => 'mes', 'Manes.14G115000' => 'mes', 'Manes.15G151700' => 'mes', 'Manes.17G111300' => 'mes', 'Mapoly0226s0009' => 'mpo', 'MBI02_g25363_MAGBIO' => 'mbi', 'MBI06_g00027_MAGBIO' => 'mbi', 'MBI10_g13034_MAGBIO' => 'mbi', 'MD09G1023400' => 'mdo', 'MD13G1100100' => 'mdo', 'MD15G1169200' => 'mdo', 'MD16G1101100' => 'mdo', 'MD17G1022900' => 'mdo', 'Medtr3g096150' => 'mtr', 'Medtr4g115070' => 'mtr', 'Medtr7g033325' => 'mtr', 'Medtr8g089840' => 'mtr', 'MELO3C010319.2' => 'cme', 'MELO3C011944.2' => 'cme', 'MELO3C021589.2' => 'cme', 'Migut.E00207' => 'egut', 'Migut.H00067' => 'egut', 'Migut.K00433' => 'egut', 'Migut.K00606' => 'egut', 'Migut.K01410' => 'egut', 'MSTRG.13347' => 'ama', 'MSTRG.24045' => 'ama', 'MSTRG.2428' => 'ama', 'MSTRG.26410' => 'ama', 'MSTRG.3139' => 'ama', 'MSTRG.3286' => 'ama', 'MSTRG.563' => 'ama', 'MSTRG.7941' => 'ama', 'Nitab4.5_0000028g0060' => 'nta', 'Nitab4.5_0000065g0260' => 'nta', 'Nitab4.5_0000112g0060' => 'nta', 'Nitab4.5_0000489g0120' => 'nta', 'Nitab4.5_0001776g0050' => 'nta', 'Nitab4.5_0001854g0010' => 'nta', 'Nitab4.5_0001860g0020' => 'nta', 'Nitab4.5_0004352g0010' => 'nta', 'Nitab4.5_0008716g0020' => 'nta', 'Nitab4.5_0008922g0010' => 'nta', 'Nn3g16693' => 'nnu', 'Nn4g22596' => 'nnu', 'Nn7g37639' => 'nnu', 'Oeu001701.1' => 'oeu', 'Oeu018149.1' => 'oeu', 'Oeu026220.1' => 'oeu', 'Oeu038635.1' => 'oeu', 'Oeu049176.1' => 'oeu', 'Oeu056706.1' => 'oeu', 'Oeu056937.1' => 'oeu', 'Oeu057540.1' => 'oeu', 'Os02g0594900' => 'osa', 'Os02g0595100' => 'osa', 'Os04g0477500' => 'osa', 'Os12g0611900' => 'osa', 'Peaxi162Scf00076g00020' => 'pax', 'Peaxi162Scf00128g00217' => 'pax', 'Peaxi162Scf00129g01640' => 'pax', 'Peaxi162Scf00669g00007' => 'pax', 'Peaxi162Scf00700g00421' => 'pax', 'Peaxi162Scf00801g00038' => 'pax', 'Peaxi162Scf00891g00025' => 'pax', 'PGR083G0909' => 'pgr', 'PGR119G1005' => 'pgr', 'PGR142G2236' => 'pgr', 'PGR142G3388' => 'pgr', 'PGSC0003DMG400004514' => 'stu', 'PGSC0003DMG400012635' => 'stu', 'PGSC0003DMG400015730' => 'stu', 'PGSC0003DMG400018611' => 'stu', 'PGSC0003DMG400030897' => 'stu', 'Phvul.001G254800' => 'pvu', 'Phvul.002G260100' => 'pvu', 'Phvul.003G167600' => 'pvu', 'Phvul.004G005100' => 'pvu', 'Potri.001G343600' => 'ptr', 'Potri.006G066700' => 'ptr', 'Potri.008G186000' => 'ptr', 'Potri.010G046900' => 'ptr', 'Potri.018G127900' => 'ptr', 'Pp3c20_17750' => 'ppa', 'Pp3c24_4380' => 'ppa', 'Prupe.1G245800' => 'ppe', 'Prupe.3G293400' => 'ppe', 'Prupe.7G247400' => 'ppe', 'Psat0s145g0120' => 'psa', 'Psat0s595g0040' => 'psa', 'Psat0s595g0120' => 'psa', 'Psat3g175040' => 'psa', 'Psat7g058120' => 'psa', 'PSO017G0428' => 'pso', 'PSO063G7510' => 'pso', 'PSO067G0046' => 'pso', 'PSO478G1073' => 'pso', 'PSO675G3677' => 'pso', 'PSO675G6558' => 'pso', 'PSO675G7520' => 'pso', 'PSO675G8959' => 'pso', 'QL02p074089' => 'qlo', 'QL02p089614' => 'qlo', 'QL03p057736' => 'qlo', 'RcHm_v2.0_Chr1g0364131' => 'rch', 'RcHm_v2.0_Chr2g0087801' => 'rch', 'RcHm_v2.0_Chr2g0087821' => 'rch', 'RcHm_v2.0_Chr2g0173231' => 'rch', 'RcHm_v2.0_Chr4g0433111' => 'rch', 'Rhsim03G0250300' => 'rsi', 'Rhsim08G0048400' => 'rsi', 'Rhsim10G0014800' => 'rsi', 'Rhsim12G0040100' => 'rsi', 'Rhsim12G0109700' => 'rsi', 'Sabra06G0049600' => 'sbr', 'Sabra08G0141000' => 'sbr', 'Sabra10G0021400' => 'sbr', 'Sabra16G0222900' => 'sbr', 'Sabra18G0108600' => 'sbr', 'SalBow1G0433' => 'sbo', 'SalBow1G2038' => 'sbo', 'SalBow1G5003' => 'sbo', 'SalBow7G1197' => 'sbo', 'SalBow8G3506' => 'sbo', 'Sc03g0007300' => 'sci', 'Sc11g0000950' => 'sci', 'Sc14g0008750' => 'sci', 'Sc18g0000420' => 'sci', 'Sed0006754' => 'sed', 'Sed0008741' => 'sed', 'Sed0017172' => 'sed', 'Sed0018925' => 'sed', 'Sed0023326' => 'sed', 'Sed0025909' => 'sed', 'SEGI_05333' => 'sgi', 'SEGI_10362' => 'sgi', 'SEGI_13380' => 'sgi', 'SEGI_24306' => 'sgi', 'SEGI_29077' => 'sgi', 'SEGI_29095' => 'sgi', 'SEGI_36534' => 'sgi', 'SEGI_37506' => 'sgi', 'SEGI_38321' => 'sgi', 'SGA_v2.0_scaffold307G48031' => 'sas', 'SGA_v2.0_scaffold47G17507' => 'sas', 'SGA_v2.0_scaffold63G21736' => 'sas', 'SGA_v2.0_scaffold87G27070' => 'sas', 'SHI17794' => 'shi', 'SHI28851' => 'shi', 'SMO165G0155' => 'smo', 'SMO340G0217' => 'smo', 'SMO367G1210' => 'smo', 'Solyc02g093430.3' => 'sly', 'Solyc05g013580.4' => 'sly', 'Solyc07g008030.3' => 'sly', 'Solyc12g035470.2' => 'sly', 'Sopen02g038020' => 'spe', 'Sopen05g008490' => 'spe', 'Sopen07g003910' => 'spe', 'Sopen12g015240' => 'spe', 'Sp1g11550' => 'spa', 'Sp2g16710' => 'spa', 'Sp3g00430' => 'spa', 'Sp3g26780' => 'spa', 'Sp5g22900' => 'spa', 'Sp6g29530' => 'spa', 'TAR371G0794' => 'tar', 'TAR374G0164' => 'tar', 'TAR622G0165' => 'tar', 'TAR626G0929' => 'tar', 'TAR629G2155' => 'tar', 'THA.LOC104805282' => 'tha', 'THA.LOC104805363' => 'tha', 'THA.LOC104808968' => 'tha', 'THA.LOC104821093' => 'tha', 'THA.LOC104823953' => 'tha', 'THA.LOC104825562' => 'tha', 'THA.LOC104825665' => 'tha', 'Thecc.02G261400' => 'tca', 'Thecc.04G019200' => 'tca', 'Thecc.09G130400' => 'tca', 'Thhalv10004374m.g' => 'esa', 'Thhalv10007850m.g' => 'esa', 'Thhalv10013782m.g' => 'esa', 'Thhalv10018686m.g' => 'esa', 'Thhalv10020899m.g' => 'esa', 'Thhalv10022755m.g' => 'esa', 'TPR.G23851' => 'tpr', 'TPR.G26500' => 'tpr', 'TPR.G27267' => 'tpr', 'TPR.G32001' => 'tpr', 'TPR.G6251' => 'tpr', 'TPR.G8167' => 'tpr', 'TWI12G1330' => 'twi', 'TWI18G1239' => 'twi', 'TWI34G0979' => 'twi', 'TWI36G0670' => 'twi', 'TWI36G0707' => 'twi', 'TWI56G0233' => 'twi', 'TWI75G1809' => 'twi', 'unitig_21.g20874' => 'ugi', 'unitig_26.g10343' => 'ugi', 'unitig_46.g18392' => 'ugi', 'unitig_52.g17178' => 'ugi', 'unitig_8.g2934' => 'ugi', 'vmacro01122' => 'vma', 'vmacro05875' => 'vma', 'vmacro06147' => 'vma', 'vmacro16191' => 'vma', 'vmacro18293' => 'vma', 'VMungo0251G3707' => 'vmu', 'VMungo0464G1521' => 'vmu', 'VMungo1215G0205' => 'vmu', 'VMungo1383G2484' => 'vmu', 'Zm00001eb079610' => 'zma', 'Zm00001eb135990' => 'zma', 'Zm00001eb183710' => 'zma', 'Zm00001eb246020' => 'zma' ), 'gf_id' => 'HOM05D001124', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001124' ), 'data_identifier' => 'HOM05D001124', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001124', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '548', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02520' => 'bna', 'A03p06630' => 'bna', 'A05p44460' => 'bna', 'A06p08710' => 'bna', 'A06p41090' => 'bna', 'A07p32320' => 'bna', 'A08p32520' => 'bna', 'A09p10360' => 'bna', 'A10p24080' => 'bna', 'Aa31LG11G15250' => 'aar', 'Aa31LG1G1800' => 'aar', 'Aa31LG2G5120' => 'aar', 'Aa31LG2G6070' => 'aar', 'Aa31LG5G10770' => 'aar', 'Aa31sc61G90' => 'aar', 'Actinidia01352' => 'ach', 'Actinidia05983' => 'ach', 'Actinidia08133' => 'ach', 'Actinidia15101' => 'ach', 'Actinidia26379' => 'ach', 'Actinidia35778' => 'ach', 'Actinidia36123' => 'ach', 'Actinidia37436' => 'ach', 'Actinidia38730' => 'ach', 'Ah.02g128210' => 'amhyb', 'Ah.03g132990' => 'amhyb', 'Ah.14g079410' => 'amhyb', 'AL1G24640' => 'aly', 'AL2G26680' => 'aly', 'AL3G10530' => 'aly', 'AL3G45230' => 'aly', 'AL5G15230' => 'aly', 'AL5G16960' => 'aly', 'AL6G25210' => 'aly', 'Aqoxy2G00441' => 'aox', 'Aqoxy3G01236' => 'aox', 'Aqoxy5G03746' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3RQ047' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C7GMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9C8JER' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MBL6KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YXCZ83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZANX40' => 'arhy', 'AT1G12990' => 'ath', 'AT1G67880' => 'ath', 'AT2G13290' => 'ath', 'AT3G01620' => 'ath', 'AT3G26445' => 'ath', 'AT3G27540' => 'ath', 'AT5G14480' => 'ath', 'ATR0824G026' => 'atr', 'ATR1098G019' => 'atr', 'Atru.chr11.2145' => 'acertr', 'Atru.chr2.3636' => 'acertr', 'Atru.chr2.3644' => 'acertr', 'Atru.chr6.2422' => 'acertr', 'Atru.chr7.1112' => 'acertr', 'AUR62005469' => 'cqu', 'AUR62011166' => 'cqu', 'AUR62013319' => 'cqu', 'AUR62024273' => 'cqu', 'AUR62028420' => 'cqu', 'AUR62041942' => 'cqu', 'BcaB01g04969' => 'bca', 'BcaB01g06371' => 'bca', 'BcaB02g11494' => 'bca', 'BcaB03g15382' => 'bca', 'BcaB08g36994' => 'bca', 'BcaC03g13477' => 'bca', 'BcaC03g13478' => 'bca', 'BcaC03g13480' => 'bca', 'BcaC03g13481' => 'bca', 'BcaC03g13486' => 'bca', 'BcaC04g19031' => 'bca', 'BcaC04g23085' => 'bca', 'BcaC05g25094' => 'bca', 'BcaC05g25096' => 'bca', 'BcaC05g25138' => 'bca', 'BcaC05g30416' => 'bca', 'BcaC05g30455' => 'bca', 'BcaC06g30979' => 'bca', 'BcaC06g33805' => 'bca', 'BcaC08g46021' => 'bca', 'BcaNung03154' => 'bca', 'BolC2t06623H' => 'bol', 'BolC2t06632H' => 'bol', 'BolC2t06635H' => 'bol', 'BolC2t06638H' => 'bol', 'BolC3t13266H' => 'bol', 'BolC5t29776H' => 'bol', 'BolC6t38912H' => 'bol', 'BolC7t44183H' => 'bol', 'BolC9t54123H' => 'bol', 'BolC9t59107H' => 'bol', 'BraA02t05221Z' => 'bra', 'BraA03t09996Z' => 'bra', 'BraA05t23210Z' => 'bra', 'BraA06t24068Z' => 'bra', 'BraA06t27032Z' => 'bra', 'BraA08t35176Z' => 'bra', 'BraA09t36680Z' => 'bra', 'BraA10t44471Z' => 'bra', 'C02p06760' => 'bna', 'C02p06890' => 'bna', 'C02p07010' => 'bna', 'C03p07660' => 'bna', 'C05p10300' => 'bna', 'C06p38150' => 'bna', 'C07p36650' => 'bna', 'C08p15770' => 'bna', 'C09p12300' => 'bna', 'C09p62700' => 'bna', 'C09p75040' => 'bna', 'CAN.G13.1' => 'can', 'CAN.G138.4' => 'can', 'CAN.G44.6' => 'can', 'CAN.G473.19' => 'can', 'CANSAT01G0835' => 'cansat', 'CANSAT11G0246' => 'cansat', 'CANSAT11G1766' => 'cansat', 'CANSAT64G1954' => 'cansat', 'CARHR013330' => 'chi', 'CARHR060530' => 'chi', 'CARHR075300' => 'chi', 'CARHR105120' => 'chi', 'CARHR148910' => 'chi', 'CARHR198830' => 'chi', 'Carub.0001s1275' => 'cru', 'Carub.0002s1437' => 'cru', 'Carub.0003s0044' => 'cru', 'Carub.0003s2787' => 'cru', 'Carub.0005s0597' => 'cru', 'Carub.0006s1266' => 'cru', 'Ca_06935_v3' => 'car', 'Ca_13559_v3' => 'car', 'Ca_16941_v3' => 'car', 'Ca_16960_v3' => 'car', 'Ca_17775_v3' => 'car', 'Ca_30464_v3' => 'car', 'Cc06_g08160' => 'ccan', 'Cc07_g01520' => 'ccan', 'Cc11_g15810' => 'ccan', 'CDE02G2840' => 'cde', 'CDE03G0093' => 'cde', 'CDE04G2127' => 'cde', 'CDE07G1857' => 'cde', 'CDE09G1246' => 'cde', 'Cfa003412' => 'cfa', 'Cfa007341' => 'cfa', 'Cfa009220' => 'cfa', 'Ciclev10008737m.g' => 'ccl', 'Ciclev10015565m.g' => 'ccl', 'Ciclev10031761m.g' => 'ccl', 'CiPaw.03G045300' => 'cil', 'CiPaw.03G247200' => 'cil', 'CiPaw.04G029500' => 'cil', 'CiPaw.04G174000' => 'cil', 'CiPaw.05G181200' => 'cil', 'CiPaw.06G067100' => 'cil', 'ClCG05G025800' => 'cla', 'ClCG06G011400' => 'cla', 'ClCG09G019360' => 'cla', 'COL.COLO4_04827' => 'col', 'COL.COLO4_29170' => 'col', 'COL.COLO4_35131' => 'col', 'COL.COLO4_35132' => 'col', 'Cpa.g.sc33.32' => 'cpa', 'Cpa.g.sc46.29' => 'cpa', 'Cpa.g.sc796.1' => 'cpa', 'CsaV3_1G030420' => 'csa', 'CsaV3_5G027050' => 'csa', 'CsaV3_5G031040' => 'csa', 'CsaV3_UNG023130' => 'csa', 'CSS0007726' => 'camsi', 'CSS0016433' => 'camsi', 'CSS0017656' => 'camsi', 'CSS0025364' => 'camsi', 'CSS0027582' => 'camsi', 'CSS0047288' => 'camsi', 'CSS0049950' => 'camsi', 'DCAR_003843' => 'dca', 'DCAR_007052' => 'dca', 'DCAR_020884' => 'dca', 'DCAR_021730' => 'dca', 'DCAR_024423' => 'dca', 'DCAR_026509' => 'dca', 'DCAR_031158' => 'dca', 'Dinv14728' => 'din', 'Dinv15219' => 'din', 'Dinv25728' => 'din', 'Dinv33428' => 'din', 'Dinv36489' => 'din', 'Dinv41486' => 'din', 'Duzib147G0469' => 'dzi', 'Duzib168G0060' => 'dzi', 'Duzib187G1215' => 'dzi', 'Duzib248G0692' => 'dzi', 'Duzib251G0767' => 'dzi', 'Duzib264G0446' => 'dzi', 'Duzib268G0691' => 'dzi', 'ECA232G4767' => 'eca', 'ECA233G2838' => 'eca', 'ECA234G0391' => 'eca', 'ECA234G0857' => 'eca', 'ECA236G1593' => 'eca', 'ECA238G0565' => 'eca', 'ECA246G1027' => 'eca', 'ECA246G3223' => 'eca', 'ECA246G3470' => 'eca', 'EL10Ac6g13829' => 'bvu', 'EL10Ac6g14093' => 'bvu', 'EL10Ac8g18707' => 'bvu', 'Eucgr.C01369' => 'egr', 'Eucgr.H02492' => 'egr', 'Eucgr.I01733' => 'egr', 'Eucgr.J02255' => 'egr', 'Eucgr.J02257' => 'egr', 'Eucgr.J02258' => 'egr', 'FAN02G1601' => 'fan', 'FAN03G1586' => 'fan', 'FAN03G2986' => 'fan', 'FAN05G4837' => 'fan', 'FAN06G0146' => 'fan', 'FAN07G0858' => 'fan', 'FAN09G3179' => 'fan', 'FAN10G0669' => 'fan', 'FAN12G2358' => 'fan', 'FAN14G4198' => 'fan', 'FAN14G5112' => 'fan', 'FAN17G0342' => 'fan', 'FAN19G0342' => 'fan', 'FAN19G0962' => 'fan', 'FAN19G1101' => 'fan', 'FAN19G1872' => 'fan', 'FAN22G0356' => 'fan', 'FAN23G0744' => 'fan', 'FAN23G1914' => 'fan', 'FAN26G0032' => 'fan', 'FAN28G0625' => 'fan', 'FvH4_1g02710' => 'fve', 'FvH4_1g02720' => 'fve', 'FvH4_4g25670' => 'fve', 'FvH4_6g51700' => 'fve', 'FvH4_7g20170' => 'fve', 'Glyma.05G175000' => 'gma', 'Glyma.08G132300' => 'gma', 'Glyma.11G243000' => 'gma', 'Glyma.13G158900' => 'gma', 'Glyma.17G112400' => 'gma', 'Glyma.18G014100' => 'gma', 'Glyma.19G003100' => 'gma', 'Glyma.19G056500' => 'gma', 'Gohir.A01G158900' => 'ghi', 'Gohir.A05G312600' => 'ghi', 'Gohir.A05G354900' => 'ghi', 'Gohir.A07G037200' => 'ghi', 'Gohir.A09G030000' => 'ghi', 'Gohir.A12G145200' => 'ghi', 'Gohir.D01G151500' => 'ghi', 'Gohir.D04G058300' => 'ghi', 'Gohir.D05G314100' => 'ghi', 'Gohir.D07G041400' => 'ghi', 'Gohir.D09G029700' => 'ghi', 'Gohir.D12G149700' => 'ghi', 'Gorai.001G043800' => 'gra', 'Gorai.002G187800' => 'gra', 'Gorai.006G034700' => 'gra', 'Gorai.008G161200' => 'gra', 'Gorai.009G335700' => 'gra', 'Gorai.012G065000' => 'gra', 'GSVIVG01000535001' => 'vvi', 'GSVIVG01015572001' => 'vvi', 'GSVIVG01032386001' => 'vvi', 'HanXRQChr05g0138531' => 'han', 'HanXRQChr06g0174391' => 'han', 'HanXRQChr07g0199021' => 'han', 'HanXRQChr08g0208211' => 'han', 'HanXRQChr09g0255471' => 'han', 'HanXRQChr10g0315791' => 'han', 'HanXRQChr12g0371991' => 'han', 'HanXRQChr15g0475251' => 'han', 'HanXRQChr17g0540001' => 'han', 'HanXRQChr17g0548631' => 'han', 'HanXRQChr17g0569561' => 'han', 'Haze_12256' => 'cav', 'Haze_14756' => 'cav', 'Haze_25528' => 'cav', 'Hma1.2p1_0079F.1_g041020' => 'hma', 'Hma1.2p1_0818F.1_g223260' => 'hma', 'Hma1.2p1_1747F.1_g300530' => 'hma', 'HPP92_004607' => 'vpl', 'HPP92_004608' => 'vpl', 'HPP92_006181' => 'vpl', 'HPP92_012192' => 'vpl', 'HPP92_015680' => 'vpl', 'HPP92_020249' => 'vpl', 'HPP92_021376' => 'vpl', 'HPP92_024275' => 'vpl', 'Hund06031' => 'sun', 'Hund25391' => 'sun', 'Lalb_Chr07g0185371' => 'lal', 'Lalb_Chr07g0185381' => 'lal', 'Lalb_Chr12g0204011' => 'lal', 'Lalb_Chr13g0301671' => 'lal', 'Lalb_Chr14g0362851' => 'lal', 'Lalb_Chr24g0403581' => 'lal', 'Lj1g0000233' => 'lja', 'Lj2g0018120' => 'lja', 'Lj3C621T0' => 'lonja', 'Lj3P1059T14' => 'lonja', 'Lj3P611T9' => 'lonja', 'Lj3P614T13' => 'lonja', 'Lj3P615T5' => 'lonja', 'Lj4g0012315' => 'lja', 'Lj4g0026182' => 'lja', 'Lj6P813T16' => 'lonja', 'Lj7C427T7' => 'lonja', 'Lj7C427T8' => 'lonja', 'Lj7P600T41' => 'lonja', 'Lju41C42G17' => 'lonja', 'Lsat_1_v5_gn_0_47300' => 'lsa', 'Lsat_1_v5_gn_2_91280' => 'lsa', 'Lsat_1_v5_gn_3_30561' => 'lsa', 'Lsat_1_v5_gn_4_184321' => 'lsa', 'Lsat_1_v5_gn_4_4041' => 'lsa', 'Lsat_1_v5_gn_5_92000' => 'lsa', 'Lsat_1_v5_gn_8_152940' => 'lsa', 'Lsat_1_v5_gn_8_62401' => 'lsa', 'Manes.06G055900' => 'mes', 'Manes.12G022200' => 'mes', 'Manes.13G023300' => 'mes', 'Manes.14G115000' => 'mes', 'Manes.15G151700' => 'mes', 'Manes.17G111300' => 'mes', 'Mapoly0226s0009' => 'mpo', 'MBI02_g25363_MAGBIO' => 'mbi', 'MBI06_g00027_MAGBIO' => 'mbi', 'MBI10_g13034_MAGBIO' => 'mbi', 'MD09G1023400' => 'mdo', 'MD13G1100100' => 'mdo', 'MD15G1169200' => 'mdo', 'MD16G1101100' => 'mdo', 'MD17G1022900' => 'mdo', 'Medtr3g096150' => 'mtr', 'Medtr4g115070' => 'mtr', 'Medtr7g033325' => 'mtr', 'Medtr8g089840' => 'mtr', 'MELO3C010319.2' => 'cme', 'MELO3C011944.2' => 'cme', 'MELO3C021589.2' => 'cme', 'Migut.E00207' => 'egut', 'Migut.H00067' => 'egut', 'Migut.K00433' => 'egut', 'Migut.K00606' => 'egut', 'Migut.K01410' => 'egut', 'MSTRG.13347' => 'ama', 'MSTRG.24045' => 'ama', 'MSTRG.2428' => 'ama', 'MSTRG.26410' => 'ama', 'MSTRG.3139' => 'ama', 'MSTRG.3286' => 'ama', 'MSTRG.563' => 'ama', 'MSTRG.7941' => 'ama', 'Nitab4.5_0000028g0060' => 'nta', 'Nitab4.5_0000065g0260' => 'nta', 'Nitab4.5_0000112g0060' => 'nta', 'Nitab4.5_0000489g0120' => 'nta', 'Nitab4.5_0001776g0050' => 'nta', 'Nitab4.5_0001854g0010' => 'nta', 'Nitab4.5_0001860g0020' => 'nta', 'Nitab4.5_0004352g0010' => 'nta', 'Nitab4.5_0008716g0020' => 'nta', 'Nitab4.5_0008922g0010' => 'nta', 'Nn3g16693' => 'nnu', 'Nn4g22596' => 'nnu', 'Nn7g37639' => 'nnu', 'Oeu001701.1' => 'oeu', 'Oeu018149.1' => 'oeu', 'Oeu026220.1' => 'oeu', 'Oeu038635.1' => 'oeu', 'Oeu049176.1' => 'oeu', 'Oeu056706.1' => 'oeu', 'Oeu056937.1' => 'oeu', 'Oeu057540.1' => 'oeu', 'Os02g0594900' => 'osa', 'Os02g0595100' => 'osa', 'Os04g0477500' => 'osa', 'Os12g0611900' => 'osa', 'Peaxi162Scf00076g00020' => 'pax', 'Peaxi162Scf00128g00217' => 'pax', 'Peaxi162Scf00129g01640' => 'pax', 'Peaxi162Scf00669g00007' => 'pax', 'Peaxi162Scf00700g00421' => 'pax', 'Peaxi162Scf00801g00038' => 'pax', 'Peaxi162Scf00891g00025' => 'pax', 'PGR083G0909' => 'pgr', 'PGR119G1005' => 'pgr', 'PGR142G2236' => 'pgr', 'PGR142G3388' => 'pgr', 'PGSC0003DMG400004514' => 'stu', 'PGSC0003DMG400012635' => 'stu', 'PGSC0003DMG400015730' => 'stu', 'PGSC0003DMG400018611' => 'stu', 'PGSC0003DMG400030897' => 'stu', 'Phvul.001G254800' => 'pvu', 'Phvul.002G260100' => 'pvu', 'Phvul.003G167600' => 'pvu', 'Phvul.004G005100' => 'pvu', 'Potri.001G343600' => 'ptr', 'Potri.006G066700' => 'ptr', 'Potri.008G186000' => 'ptr', 'Potri.010G046900' => 'ptr', 'Potri.018G127900' => 'ptr', 'Pp3c20_17750' => 'ppa', 'Pp3c24_4380' => 'ppa', 'Prupe.1G245800' => 'ppe', 'Prupe.3G293400' => 'ppe', 'Prupe.7G247400' => 'ppe', 'Psat0s145g0120' => 'psa', 'Psat0s595g0040' => 'psa', 'Psat0s595g0120' => 'psa', 'Psat3g175040' => 'psa', 'Psat7g058120' => 'psa', 'PSO017G0428' => 'pso', 'PSO063G7510' => 'pso', 'PSO067G0046' => 'pso', 'PSO478G1073' => 'pso', 'PSO675G3677' => 'pso', 'PSO675G6558' => 'pso', 'PSO675G7520' => 'pso', 'PSO675G8959' => 'pso', 'QL02p074089' => 'qlo', 'QL02p089614' => 'qlo', 'QL03p057736' => 'qlo', 'RcHm_v2.0_Chr1g0364131' => 'rch', 'RcHm_v2.0_Chr2g0087801' => 'rch', 'RcHm_v2.0_Chr2g0087821' => 'rch', 'RcHm_v2.0_Chr2g0173231' => 'rch', 'RcHm_v2.0_Chr4g0433111' => 'rch', 'Rhsim03G0250300' => 'rsi', 'Rhsim08G0048400' => 'rsi', 'Rhsim10G0014800' => 'rsi', 'Rhsim12G0040100' => 'rsi', 'Rhsim12G0109700' => 'rsi', 'Sabra06G0049600' => 'sbr', 'Sabra08G0141000' => 'sbr', 'Sabra10G0021400' => 'sbr', 'Sabra16G0222900' => 'sbr', 'Sabra18G0108600' => 'sbr', 'SalBow1G0433' => 'sbo', 'SalBow1G2038' => 'sbo', 'SalBow1G5003' => 'sbo', 'SalBow7G1197' => 'sbo', 'SalBow8G3506' => 'sbo', 'Sc03g0007300' => 'sci', 'Sc11g0000950' => 'sci', 'Sc14g0008750' => 'sci', 'Sc18g0000420' => 'sci', 'Sed0006754' => 'sed', 'Sed0008741' => 'sed', 'Sed0017172' => 'sed', 'Sed0018925' => 'sed', 'Sed0023326' => 'sed', 'Sed0025909' => 'sed', 'SEGI_05333' => 'sgi', 'SEGI_10362' => 'sgi', 'SEGI_13380' => 'sgi', 'SEGI_24306' => 'sgi', 'SEGI_29077' => 'sgi', 'SEGI_29095' => 'sgi', 'SEGI_36534' => 'sgi', 'SEGI_37506' => 'sgi', 'SEGI_38321' => 'sgi', 'SGA_v2.0_scaffold307G48031' => 'sas', 'SGA_v2.0_scaffold47G17507' => 'sas', 'SGA_v2.0_scaffold63G21736' => 'sas', 'SGA_v2.0_scaffold87G27070' => 'sas', 'SHI17794' => 'shi', 'SHI28851' => 'shi', 'SMO165G0155' => 'smo', 'SMO340G0217' => 'smo', 'SMO367G1210' => 'smo', 'Solyc02g093430.3' => 'sly', 'Solyc05g013580.4' => 'sly', 'Solyc07g008030.3' => 'sly', 'Solyc12g035470.2' => 'sly', 'Sopen02g038020' => 'spe', 'Sopen05g008490' => 'spe', 'Sopen07g003910' => 'spe', 'Sopen12g015240' => 'spe', 'Sp1g11550' => 'spa', 'Sp2g16710' => 'spa', 'Sp3g00430' => 'spa', 'Sp3g26780' => 'spa', 'Sp5g22900' => 'spa', 'Sp6g29530' => 'spa', 'TAR371G0794' => 'tar', 'TAR374G0164' => 'tar', 'TAR622G0165' => 'tar', 'TAR626G0929' => 'tar', 'TAR629G2155' => 'tar', 'THA.LOC104805282' => 'tha', 'THA.LOC104805363' => 'tha', 'THA.LOC104808968' => 'tha', 'THA.LOC104821093' => 'tha', 'THA.LOC104823953' => 'tha', 'THA.LOC104825562' => 'tha', 'THA.LOC104825665' => 'tha', 'Thecc.02G261400' => 'tca', 'Thecc.04G019200' => 'tca', 'Thecc.09G130400' => 'tca', 'Thhalv10004374m.g' => 'esa', 'Thhalv10007850m.g' => 'esa', 'Thhalv10013782m.g' => 'esa', 'Thhalv10018686m.g' => 'esa', 'Thhalv10020899m.g' => 'esa', 'Thhalv10022755m.g' => 'esa', 'TPR.G23851' => 'tpr', 'TPR.G26500' => 'tpr', 'TPR.G27267' => 'tpr', 'TPR.G32001' => 'tpr', 'TPR.G6251' => 'tpr', 'TPR.G8167' => 'tpr', 'TWI12G1330' => 'twi', 'TWI18G1239' => 'twi', 'TWI34G0979' => 'twi', 'TWI36G0670' => 'twi', 'TWI36G0707' => 'twi', 'TWI56G0233' => 'twi', 'TWI75G1809' => 'twi', 'unitig_21.g20874' => 'ugi', 'unitig_26.g10343' => 'ugi', 'unitig_46.g18392' => 'ugi', 'unitig_52.g17178' => 'ugi', 'unitig_8.g2934' => 'ugi', 'vmacro01122' => 'vma', 'vmacro05875' => 'vma', 'vmacro06147' => 'vma', 'vmacro16191' => 'vma', 'vmacro18293' => 'vma', 'VMungo0251G3707' => 'vmu', 'VMungo0464G1521' => 'vmu', 'VMungo1215G0205' => 'vmu', 'VMungo1383G2484' => 'vmu', 'Zm00001eb079610' => 'zma', 'Zm00001eb135990' => 'zma', 'Zm00001eb183710' => 'zma', 'Zm00001eb246020' => 'zma' ) $gf_id = 'HOM05D001124' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001124' ) $data_identifier = 'HOM05D001124' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 6, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 7, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 21, 'bol' => (int) 10, 'bra' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 6, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 9, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 21, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 8, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 10, 'lsa' => (int) 8, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 8, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 9, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb246020' $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' => 'HOM05D001124', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '548', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02520' => 'bna', 'A03p06630' => 'bna', 'A05p44460' => 'bna', 'A06p08710' => 'bna', 'A06p41090' => 'bna', 'A07p32320' => 'bna', 'A08p32520' => 'bna', 'A09p10360' => 'bna', 'A10p24080' => 'bna', 'Aa31LG11G15250' => 'aar', 'Aa31LG1G1800' => 'aar', 'Aa31LG2G5120' => 'aar', 'Aa31LG2G6070' => 'aar', 'Aa31LG5G10770' => 'aar', 'Aa31sc61G90' => 'aar', 'Actinidia01352' => 'ach', 'Actinidia05983' => 'ach', 'Actinidia08133' => 'ach', 'Actinidia15101' => 'ach', 'Actinidia26379' => 'ach', 'Actinidia35778' => 'ach', 'Actinidia36123' => 'ach', 'Actinidia37436' => 'ach', 'Actinidia38730' => 'ach', 'Ah.02g128210' => 'amhyb', 'Ah.03g132990' => 'amhyb', 'Ah.14g079410' => 'amhyb', 'AL1G24640' => 'aly', 'AL2G26680' => 'aly', 'AL3G10530' => 'aly', 'AL3G45230' => 'aly', 'AL5G15230' => 'aly', 'AL5G16960' => 'aly', 'AL6G25210' => 'aly', 'Aqoxy2G00441' => 'aox', 'Aqoxy3G01236' => 'aox', 'Aqoxy5G03746' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3RQ047' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C7GMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9C8JER' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MBL6KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YXCZ83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZANX40' => 'arhy', 'AT1G12990' => 'ath', 'AT1G67880' => 'ath', 'AT2G13290' => 'ath', 'AT3G01620' => 'ath', 'AT3G26445' => 'ath', 'AT3G27540' => 'ath', 'AT5G14480' => 'ath', 'ATR0824G026' => 'atr', 'ATR1098G019' => 'atr', 'Atru.chr11.2145' => 'acertr', 'Atru.chr2.3636' => 'acertr', 'Atru.chr2.3644' => 'acertr', 'Atru.chr6.2422' => 'acertr', 'Atru.chr7.1112' => 'acertr', 'AUR62005469' => 'cqu', 'AUR62011166' => 'cqu', 'AUR62013319' => 'cqu', 'AUR62024273' => 'cqu', 'AUR62028420' => 'cqu', 'AUR62041942' => 'cqu', 'BcaB01g04969' => 'bca', 'BcaB01g06371' => 'bca', 'BcaB02g11494' => 'bca', 'BcaB03g15382' => 'bca', 'BcaB08g36994' => 'bca', 'BcaC03g13477' => 'bca', 'BcaC03g13478' => 'bca', 'BcaC03g13480' => 'bca', 'BcaC03g13481' => 'bca', 'BcaC03g13486' => 'bca', 'BcaC04g19031' => 'bca', 'BcaC04g23085' => 'bca', 'BcaC05g25094' => 'bca', 'BcaC05g25096' => 'bca', 'BcaC05g25138' => 'bca', 'BcaC05g30416' => 'bca', 'BcaC05g30455' => 'bca', 'BcaC06g30979' => 'bca', 'BcaC06g33805' => 'bca', 'BcaC08g46021' => 'bca', 'BcaNung03154' => 'bca', 'BolC2t06623H' => 'bol', 'BolC2t06632H' => 'bol', 'BolC2t06635H' => 'bol', 'BolC2t06638H' => 'bol', 'BolC3t13266H' => 'bol', 'BolC5t29776H' => 'bol', 'BolC6t38912H' => 'bol', 'BolC7t44183H' => 'bol', 'BolC9t54123H' => 'bol', 'BolC9t59107H' => 'bol', 'BraA02t05221Z' => 'bra', 'BraA03t09996Z' => 'bra', 'BraA05t23210Z' => 'bra', 'BraA06t24068Z' => 'bra', 'BraA06t27032Z' => 'bra', 'BraA08t35176Z' => 'bra', 'BraA09t36680Z' => 'bra', 'BraA10t44471Z' => 'bra', 'C02p06760' => 'bna', 'C02p06890' => 'bna', 'C02p07010' => 'bna', 'C03p07660' => 'bna', 'C05p10300' => 'bna', 'C06p38150' => 'bna', 'C07p36650' => 'bna', 'C08p15770' => 'bna', 'C09p12300' => 'bna', 'C09p62700' => 'bna', 'C09p75040' => 'bna', 'CAN.G13.1' => 'can', 'CAN.G138.4' => 'can', 'CAN.G44.6' => 'can', 'CAN.G473.19' => 'can', 'CANSAT01G0835' => 'cansat', 'CANSAT11G0246' => 'cansat', 'CANSAT11G1766' => 'cansat', 'CANSAT64G1954' => 'cansat', 'CARHR013330' => 'chi', 'CARHR060530' => 'chi', 'CARHR075300' => 'chi', 'CARHR105120' => 'chi', 'CARHR148910' => 'chi', 'CARHR198830' => 'chi', 'Carub.0001s1275' => 'cru', 'Carub.0002s1437' => 'cru', 'Carub.0003s0044' => 'cru', 'Carub.0003s2787' => 'cru', 'Carub.0005s0597' => 'cru', 'Carub.0006s1266' => 'cru', 'Ca_06935_v3' => 'car', 'Ca_13559_v3' => 'car', 'Ca_16941_v3' => 'car', 'Ca_16960_v3' => 'car', 'Ca_17775_v3' => 'car', 'Ca_30464_v3' => 'car', 'Cc06_g08160' => 'ccan', 'Cc07_g01520' => 'ccan', 'Cc11_g15810' => 'ccan', 'CDE02G2840' => 'cde', 'CDE03G0093' => 'cde', 'CDE04G2127' => 'cde', 'CDE07G1857' => 'cde', 'CDE09G1246' => 'cde', 'Cfa003412' => 'cfa', 'Cfa007341' => 'cfa', 'Cfa009220' => 'cfa', 'Ciclev10008737m.g' => 'ccl', 'Ciclev10015565m.g' => 'ccl', 'Ciclev10031761m.g' => 'ccl', 'CiPaw.03G045300' => 'cil', 'CiPaw.03G247200' => 'cil', 'CiPaw.04G029500' => 'cil', 'CiPaw.04G174000' => 'cil', 'CiPaw.05G181200' => 'cil', 'CiPaw.06G067100' => 'cil', 'ClCG05G025800' => 'cla', 'ClCG06G011400' => 'cla', 'ClCG09G019360' => 'cla', 'COL.COLO4_04827' => 'col', 'COL.COLO4_29170' => 'col', 'COL.COLO4_35131' => 'col', 'COL.COLO4_35132' => 'col', 'Cpa.g.sc33.32' => 'cpa', 'Cpa.g.sc46.29' => 'cpa', 'Cpa.g.sc796.1' => 'cpa', 'CsaV3_1G030420' => 'csa', 'CsaV3_5G027050' => 'csa', 'CsaV3_5G031040' => 'csa', 'CsaV3_UNG023130' => 'csa', 'CSS0007726' => 'camsi', 'CSS0016433' => 'camsi', 'CSS0017656' => 'camsi', 'CSS0025364' => 'camsi', 'CSS0027582' => 'camsi', 'CSS0047288' => 'camsi', 'CSS0049950' => 'camsi', 'DCAR_003843' => 'dca', 'DCAR_007052' => 'dca', 'DCAR_020884' => 'dca', 'DCAR_021730' => 'dca', 'DCAR_024423' => 'dca', 'DCAR_026509' => 'dca', 'DCAR_031158' => 'dca', 'Dinv14728' => 'din', 'Dinv15219' => 'din', 'Dinv25728' => 'din', 'Dinv33428' => 'din', 'Dinv36489' => 'din', 'Dinv41486' => 'din', 'Duzib147G0469' => 'dzi', 'Duzib168G0060' => 'dzi', 'Duzib187G1215' => 'dzi', 'Duzib248G0692' => 'dzi', 'Duzib251G0767' => 'dzi', 'Duzib264G0446' => 'dzi', 'Duzib268G0691' => 'dzi', 'ECA232G4767' => 'eca', 'ECA233G2838' => 'eca', 'ECA234G0391' => 'eca', 'ECA234G0857' => 'eca', 'ECA236G1593' => 'eca', 'ECA238G0565' => 'eca', 'ECA246G1027' => 'eca', 'ECA246G3223' => 'eca', 'ECA246G3470' => 'eca', 'EL10Ac6g13829' => 'bvu', 'EL10Ac6g14093' => 'bvu', 'EL10Ac8g18707' => 'bvu', 'Eucgr.C01369' => 'egr', 'Eucgr.H02492' => 'egr', 'Eucgr.I01733' => 'egr', 'Eucgr.J02255' => 'egr', 'Eucgr.J02257' => 'egr', 'Eucgr.J02258' => 'egr', 'FAN02G1601' => 'fan', 'FAN03G1586' => 'fan', 'FAN03G2986' => 'fan', 'FAN05G4837' => 'fan', 'FAN06G0146' => 'fan', 'FAN07G0858' => 'fan', 'FAN09G3179' => 'fan', 'FAN10G0669' => 'fan', 'FAN12G2358' => 'fan', 'FAN14G4198' => 'fan', 'FAN14G5112' => 'fan', 'FAN17G0342' => 'fan', 'FAN19G0342' => 'fan', 'FAN19G0962' => 'fan', 'FAN19G1101' => 'fan', 'FAN19G1872' => 'fan', 'FAN22G0356' => 'fan', 'FAN23G0744' => 'fan', 'FAN23G1914' => 'fan', 'FAN26G0032' => 'fan', 'FAN28G0625' => 'fan', 'FvH4_1g02710' => 'fve', 'FvH4_1g02720' => 'fve', 'FvH4_4g25670' => 'fve', 'FvH4_6g51700' => 'fve', 'FvH4_7g20170' => 'fve', 'Glyma.05G175000' => 'gma', 'Glyma.08G132300' => 'gma', 'Glyma.11G243000' => 'gma', 'Glyma.13G158900' => 'gma', 'Glyma.17G112400' => 'gma', 'Glyma.18G014100' => 'gma', 'Glyma.19G003100' => 'gma', 'Glyma.19G056500' => 'gma', 'Gohir.A01G158900' => 'ghi', 'Gohir.A05G312600' => 'ghi', 'Gohir.A05G354900' => 'ghi', 'Gohir.A07G037200' => 'ghi', 'Gohir.A09G030000' => 'ghi', 'Gohir.A12G145200' => 'ghi', 'Gohir.D01G151500' => 'ghi', 'Gohir.D04G058300' => 'ghi', 'Gohir.D05G314100' => 'ghi', 'Gohir.D07G041400' => 'ghi', 'Gohir.D09G029700' => 'ghi', 'Gohir.D12G149700' => 'ghi', 'Gorai.001G043800' => 'gra', 'Gorai.002G187800' => 'gra', 'Gorai.006G034700' => 'gra', 'Gorai.008G161200' => 'gra', 'Gorai.009G335700' => 'gra', 'Gorai.012G065000' => 'gra', 'GSVIVG01000535001' => 'vvi', 'GSVIVG01015572001' => 'vvi', 'GSVIVG01032386001' => 'vvi', 'HanXRQChr05g0138531' => 'han', 'HanXRQChr06g0174391' => 'han', 'HanXRQChr07g0199021' => 'han', 'HanXRQChr08g0208211' => 'han', 'HanXRQChr09g0255471' => 'han', 'HanXRQChr10g0315791' => 'han', 'HanXRQChr12g0371991' => 'han', 'HanXRQChr15g0475251' => 'han', 'HanXRQChr17g0540001' => 'han', 'HanXRQChr17g0548631' => 'han', 'HanXRQChr17g0569561' => 'han', 'Haze_12256' => 'cav', 'Haze_14756' => 'cav', 'Haze_25528' => 'cav', 'Hma1.2p1_0079F.1_g041020' => 'hma', 'Hma1.2p1_0818F.1_g223260' => 'hma', 'Hma1.2p1_1747F.1_g300530' => 'hma', 'HPP92_004607' => 'vpl', 'HPP92_004608' => 'vpl', 'HPP92_006181' => 'vpl', 'HPP92_012192' => 'vpl', 'HPP92_015680' => 'vpl', 'HPP92_020249' => 'vpl', 'HPP92_021376' => 'vpl', 'HPP92_024275' => 'vpl', 'Hund06031' => 'sun', 'Hund25391' => 'sun', 'Lalb_Chr07g0185371' => 'lal', 'Lalb_Chr07g0185381' => 'lal', 'Lalb_Chr12g0204011' => 'lal', 'Lalb_Chr13g0301671' => 'lal', 'Lalb_Chr14g0362851' => 'lal', 'Lalb_Chr24g0403581' => 'lal', 'Lj1g0000233' => 'lja', 'Lj2g0018120' => 'lja', 'Lj3C621T0' => 'lonja', 'Lj3P1059T14' => 'lonja', 'Lj3P611T9' => 'lonja', 'Lj3P614T13' => 'lonja', 'Lj3P615T5' => 'lonja', 'Lj4g0012315' => 'lja', 'Lj4g0026182' => 'lja', 'Lj6P813T16' => 'lonja', 'Lj7C427T7' => 'lonja', 'Lj7C427T8' => 'lonja', 'Lj7P600T41' => 'lonja', 'Lju41C42G17' => 'lonja', 'Lsat_1_v5_gn_0_47300' => 'lsa', 'Lsat_1_v5_gn_2_91280' => 'lsa', 'Lsat_1_v5_gn_3_30561' => 'lsa', 'Lsat_1_v5_gn_4_184321' => 'lsa', 'Lsat_1_v5_gn_4_4041' => 'lsa', 'Lsat_1_v5_gn_5_92000' => 'lsa', 'Lsat_1_v5_gn_8_152940' => 'lsa', 'Lsat_1_v5_gn_8_62401' => 'lsa', 'Manes.06G055900' => 'mes', 'Manes.12G022200' => 'mes', 'Manes.13G023300' => 'mes', 'Manes.14G115000' => 'mes', 'Manes.15G151700' => 'mes', 'Manes.17G111300' => 'mes', 'Mapoly0226s0009' => 'mpo', 'MBI02_g25363_MAGBIO' => 'mbi', 'MBI06_g00027_MAGBIO' => 'mbi', 'MBI10_g13034_MAGBIO' => 'mbi', 'MD09G1023400' => 'mdo', 'MD13G1100100' => 'mdo', 'MD15G1169200' => 'mdo', 'MD16G1101100' => 'mdo', 'MD17G1022900' => 'mdo', 'Medtr3g096150' => 'mtr', 'Medtr4g115070' => 'mtr', 'Medtr7g033325' => 'mtr', 'Medtr8g089840' => 'mtr', 'MELO3C010319.2' => 'cme', 'MELO3C011944.2' => 'cme', 'MELO3C021589.2' => 'cme', 'Migut.E00207' => 'egut', 'Migut.H00067' => 'egut', 'Migut.K00433' => 'egut', 'Migut.K00606' => 'egut', 'Migut.K01410' => 'egut', 'MSTRG.13347' => 'ama', 'MSTRG.24045' => 'ama', 'MSTRG.2428' => 'ama', 'MSTRG.26410' => 'ama', 'MSTRG.3139' => 'ama', 'MSTRG.3286' => 'ama', 'MSTRG.563' => 'ama', 'MSTRG.7941' => 'ama', 'Nitab4.5_0000028g0060' => 'nta', 'Nitab4.5_0000065g0260' => 'nta', 'Nitab4.5_0000112g0060' => 'nta', 'Nitab4.5_0000489g0120' => 'nta', 'Nitab4.5_0001776g0050' => 'nta', 'Nitab4.5_0001854g0010' => 'nta', 'Nitab4.5_0001860g0020' => 'nta', 'Nitab4.5_0004352g0010' => 'nta', 'Nitab4.5_0008716g0020' => 'nta', 'Nitab4.5_0008922g0010' => 'nta', 'Nn3g16693' => 'nnu', 'Nn4g22596' => 'nnu', 'Nn7g37639' => 'nnu', 'Oeu001701.1' => 'oeu', 'Oeu018149.1' => 'oeu', 'Oeu026220.1' => 'oeu', 'Oeu038635.1' => 'oeu', 'Oeu049176.1' => 'oeu', 'Oeu056706.1' => 'oeu', 'Oeu056937.1' => 'oeu', 'Oeu057540.1' => 'oeu', 'Os02g0594900' => 'osa', 'Os02g0595100' => 'osa', 'Os04g0477500' => 'osa', 'Os12g0611900' => 'osa', 'Peaxi162Scf00076g00020' => 'pax', 'Peaxi162Scf00128g00217' => 'pax', 'Peaxi162Scf00129g01640' => 'pax', 'Peaxi162Scf00669g00007' => 'pax', 'Peaxi162Scf00700g00421' => 'pax', 'Peaxi162Scf00801g00038' => 'pax', 'Peaxi162Scf00891g00025' => 'pax', 'PGR083G0909' => 'pgr', 'PGR119G1005' => 'pgr', 'PGR142G2236' => 'pgr', 'PGR142G3388' => 'pgr', 'PGSC0003DMG400004514' => 'stu', 'PGSC0003DMG400012635' => 'stu', 'PGSC0003DMG400015730' => 'stu', 'PGSC0003DMG400018611' => 'stu', 'PGSC0003DMG400030897' => 'stu', 'Phvul.001G254800' => 'pvu', 'Phvul.002G260100' => 'pvu', 'Phvul.003G167600' => 'pvu', 'Phvul.004G005100' => 'pvu', 'Potri.001G343600' => 'ptr', 'Potri.006G066700' => 'ptr', 'Potri.008G186000' => 'ptr', 'Potri.010G046900' => 'ptr', 'Potri.018G127900' => 'ptr', 'Pp3c20_17750' => 'ppa', 'Pp3c24_4380' => 'ppa', 'Prupe.1G245800' => 'ppe', 'Prupe.3G293400' => 'ppe', 'Prupe.7G247400' => 'ppe', 'Psat0s145g0120' => 'psa', 'Psat0s595g0040' => 'psa', 'Psat0s595g0120' => 'psa', 'Psat3g175040' => 'psa', 'Psat7g058120' => 'psa', 'PSO017G0428' => 'pso', 'PSO063G7510' => 'pso', 'PSO067G0046' => 'pso', 'PSO478G1073' => 'pso', 'PSO675G3677' => 'pso', 'PSO675G6558' => 'pso', 'PSO675G7520' => 'pso', 'PSO675G8959' => 'pso', 'QL02p074089' => 'qlo', 'QL02p089614' => 'qlo', 'QL03p057736' => 'qlo', 'RcHm_v2.0_Chr1g0364131' => 'rch', 'RcHm_v2.0_Chr2g0087801' => 'rch', 'RcHm_v2.0_Chr2g0087821' => 'rch', 'RcHm_v2.0_Chr2g0173231' => 'rch', 'RcHm_v2.0_Chr4g0433111' => 'rch', 'Rhsim03G0250300' => 'rsi', 'Rhsim08G0048400' => 'rsi', 'Rhsim10G0014800' => 'rsi', 'Rhsim12G0040100' => 'rsi', 'Rhsim12G0109700' => 'rsi', 'Sabra06G0049600' => 'sbr', 'Sabra08G0141000' => 'sbr', 'Sabra10G0021400' => 'sbr', 'Sabra16G0222900' => 'sbr', 'Sabra18G0108600' => 'sbr', 'SalBow1G0433' => 'sbo', 'SalBow1G2038' => 'sbo', 'SalBow1G5003' => 'sbo', 'SalBow7G1197' => 'sbo', 'SalBow8G3506' => 'sbo', 'Sc03g0007300' => 'sci', 'Sc11g0000950' => 'sci', 'Sc14g0008750' => 'sci', 'Sc18g0000420' => 'sci', 'Sed0006754' => 'sed', 'Sed0008741' => 'sed', 'Sed0017172' => 'sed', 'Sed0018925' => 'sed', 'Sed0023326' => 'sed', 'Sed0025909' => 'sed', 'SEGI_05333' => 'sgi', 'SEGI_10362' => 'sgi', 'SEGI_13380' => 'sgi', 'SEGI_24306' => 'sgi', 'SEGI_29077' => 'sgi', 'SEGI_29095' => 'sgi', 'SEGI_36534' => 'sgi', 'SEGI_37506' => 'sgi', 'SEGI_38321' => 'sgi', 'SGA_v2.0_scaffold307G48031' => 'sas', 'SGA_v2.0_scaffold47G17507' => 'sas', 'SGA_v2.0_scaffold63G21736' => 'sas', 'SGA_v2.0_scaffold87G27070' => 'sas', 'SHI17794' => 'shi', 'SHI28851' => 'shi', 'SMO165G0155' => 'smo', 'SMO340G0217' => 'smo', 'SMO367G1210' => 'smo', 'Solyc02g093430.3' => 'sly', 'Solyc05g013580.4' => 'sly', 'Solyc07g008030.3' => 'sly', 'Solyc12g035470.2' => 'sly', 'Sopen02g038020' => 'spe', 'Sopen05g008490' => 'spe', 'Sopen07g003910' => 'spe', 'Sopen12g015240' => 'spe', 'Sp1g11550' => 'spa', 'Sp2g16710' => 'spa', 'Sp3g00430' => 'spa', 'Sp3g26780' => 'spa', 'Sp5g22900' => 'spa', 'Sp6g29530' => 'spa', 'TAR371G0794' => 'tar', 'TAR374G0164' => 'tar', 'TAR622G0165' => 'tar', 'TAR626G0929' => 'tar', 'TAR629G2155' => 'tar', 'THA.LOC104805282' => 'tha', 'THA.LOC104805363' => 'tha', 'THA.LOC104808968' => 'tha', 'THA.LOC104821093' => 'tha', 'THA.LOC104823953' => 'tha', 'THA.LOC104825562' => 'tha', 'THA.LOC104825665' => 'tha', 'Thecc.02G261400' => 'tca', 'Thecc.04G019200' => 'tca', 'Thecc.09G130400' => 'tca', 'Thhalv10004374m.g' => 'esa', 'Thhalv10007850m.g' => 'esa', 'Thhalv10013782m.g' => 'esa', 'Thhalv10018686m.g' => 'esa', 'Thhalv10020899m.g' => 'esa', 'Thhalv10022755m.g' => 'esa', 'TPR.G23851' => 'tpr', 'TPR.G26500' => 'tpr', 'TPR.G27267' => 'tpr', 'TPR.G32001' => 'tpr', 'TPR.G6251' => 'tpr', 'TPR.G8167' => 'tpr', 'TWI12G1330' => 'twi', 'TWI18G1239' => 'twi', 'TWI34G0979' => 'twi', 'TWI36G0670' => 'twi', 'TWI36G0707' => 'twi', 'TWI56G0233' => 'twi', 'TWI75G1809' => 'twi', 'unitig_21.g20874' => 'ugi', 'unitig_26.g10343' => 'ugi', 'unitig_46.g18392' => 'ugi', 'unitig_52.g17178' => 'ugi', 'unitig_8.g2934' => 'ugi', 'vmacro01122' => 'vma', 'vmacro05875' => 'vma', 'vmacro06147' => 'vma', 'vmacro16191' => 'vma', 'vmacro18293' => 'vma', 'VMungo0251G3707' => 'vmu', 'VMungo0464G1521' => 'vmu', 'VMungo1215G0205' => 'vmu', 'VMungo1383G2484' => 'vmu', 'Zm00001eb079610' => 'zma', 'Zm00001eb135990' => 'zma', 'Zm00001eb183710' => 'zma', 'Zm00001eb246020' => 'zma' ), 'gf_id' => 'HOM05D001124', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001124' ), 'data_identifier' => 'HOM05D001124', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001124', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '548', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02520' => 'bna', 'A03p06630' => 'bna', 'A05p44460' => 'bna', 'A06p08710' => 'bna', 'A06p41090' => 'bna', 'A07p32320' => 'bna', 'A08p32520' => 'bna', 'A09p10360' => 'bna', 'A10p24080' => 'bna', 'Aa31LG11G15250' => 'aar', 'Aa31LG1G1800' => 'aar', 'Aa31LG2G5120' => 'aar', 'Aa31LG2G6070' => 'aar', 'Aa31LG5G10770' => 'aar', 'Aa31sc61G90' => 'aar', 'Actinidia01352' => 'ach', 'Actinidia05983' => 'ach', 'Actinidia08133' => 'ach', 'Actinidia15101' => 'ach', 'Actinidia26379' => 'ach', 'Actinidia35778' => 'ach', 'Actinidia36123' => 'ach', 'Actinidia37436' => 'ach', 'Actinidia38730' => 'ach', 'Ah.02g128210' => 'amhyb', 'Ah.03g132990' => 'amhyb', 'Ah.14g079410' => 'amhyb', 'AL1G24640' => 'aly', 'AL2G26680' => 'aly', 'AL3G10530' => 'aly', 'AL3G45230' => 'aly', 'AL5G15230' => 'aly', 'AL5G16960' => 'aly', 'AL6G25210' => 'aly', 'Aqoxy2G00441' => 'aox', 'Aqoxy3G01236' => 'aox', 'Aqoxy5G03746' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3RQ047' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C7GMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9C8JER' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MBL6KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YXCZ83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZANX40' => 'arhy', 'AT1G12990' => 'ath', 'AT1G67880' => 'ath', 'AT2G13290' => 'ath', 'AT3G01620' => 'ath', 'AT3G26445' => 'ath', 'AT3G27540' => 'ath', 'AT5G14480' => 'ath', 'ATR0824G026' => 'atr', 'ATR1098G019' => 'atr', 'Atru.chr11.2145' => 'acertr', 'Atru.chr2.3636' => 'acertr', 'Atru.chr2.3644' => 'acertr', 'Atru.chr6.2422' => 'acertr', 'Atru.chr7.1112' => 'acertr', 'AUR62005469' => 'cqu', 'AUR62011166' => 'cqu', 'AUR62013319' => 'cqu', 'AUR62024273' => 'cqu', 'AUR62028420' => 'cqu', 'AUR62041942' => 'cqu', 'BcaB01g04969' => 'bca', 'BcaB01g06371' => 'bca', 'BcaB02g11494' => 'bca', 'BcaB03g15382' => 'bca', 'BcaB08g36994' => 'bca', 'BcaC03g13477' => 'bca', 'BcaC03g13478' => 'bca', 'BcaC03g13480' => 'bca', 'BcaC03g13481' => 'bca', 'BcaC03g13486' => 'bca', 'BcaC04g19031' => 'bca', 'BcaC04g23085' => 'bca', 'BcaC05g25094' => 'bca', 'BcaC05g25096' => 'bca', 'BcaC05g25138' => 'bca', 'BcaC05g30416' => 'bca', 'BcaC05g30455' => 'bca', 'BcaC06g30979' => 'bca', 'BcaC06g33805' => 'bca', 'BcaC08g46021' => 'bca', 'BcaNung03154' => 'bca', 'BolC2t06623H' => 'bol', 'BolC2t06632H' => 'bol', 'BolC2t06635H' => 'bol', 'BolC2t06638H' => 'bol', 'BolC3t13266H' => 'bol', 'BolC5t29776H' => 'bol', 'BolC6t38912H' => 'bol', 'BolC7t44183H' => 'bol', 'BolC9t54123H' => 'bol', 'BolC9t59107H' => 'bol', 'BraA02t05221Z' => 'bra', 'BraA03t09996Z' => 'bra', 'BraA05t23210Z' => 'bra', 'BraA06t24068Z' => 'bra', 'BraA06t27032Z' => 'bra', 'BraA08t35176Z' => 'bra', 'BraA09t36680Z' => 'bra', 'BraA10t44471Z' => 'bra', 'C02p06760' => 'bna', 'C02p06890' => 'bna', 'C02p07010' => 'bna', 'C03p07660' => 'bna', 'C05p10300' => 'bna', 'C06p38150' => 'bna', 'C07p36650' => 'bna', 'C08p15770' => 'bna', 'C09p12300' => 'bna', 'C09p62700' => 'bna', 'C09p75040' => 'bna', 'CAN.G13.1' => 'can', 'CAN.G138.4' => 'can', 'CAN.G44.6' => 'can', 'CAN.G473.19' => 'can', 'CANSAT01G0835' => 'cansat', 'CANSAT11G0246' => 'cansat', 'CANSAT11G1766' => 'cansat', 'CANSAT64G1954' => 'cansat', 'CARHR013330' => 'chi', 'CARHR060530' => 'chi', 'CARHR075300' => 'chi', 'CARHR105120' => 'chi', 'CARHR148910' => 'chi', 'CARHR198830' => 'chi', 'Carub.0001s1275' => 'cru', 'Carub.0002s1437' => 'cru', 'Carub.0003s0044' => 'cru', 'Carub.0003s2787' => 'cru', 'Carub.0005s0597' => 'cru', 'Carub.0006s1266' => 'cru', 'Ca_06935_v3' => 'car', 'Ca_13559_v3' => 'car', 'Ca_16941_v3' => 'car', 'Ca_16960_v3' => 'car', 'Ca_17775_v3' => 'car', 'Ca_30464_v3' => 'car', 'Cc06_g08160' => 'ccan', 'Cc07_g01520' => 'ccan', 'Cc11_g15810' => 'ccan', 'CDE02G2840' => 'cde', 'CDE03G0093' => 'cde', 'CDE04G2127' => 'cde', 'CDE07G1857' => 'cde', 'CDE09G1246' => 'cde', 'Cfa003412' => 'cfa', 'Cfa007341' => 'cfa', 'Cfa009220' => 'cfa', 'Ciclev10008737m.g' => 'ccl', 'Ciclev10015565m.g' => 'ccl', 'Ciclev10031761m.g' => 'ccl', 'CiPaw.03G045300' => 'cil', 'CiPaw.03G247200' => 'cil', 'CiPaw.04G029500' => 'cil', 'CiPaw.04G174000' => 'cil', 'CiPaw.05G181200' => 'cil', 'CiPaw.06G067100' => 'cil', 'ClCG05G025800' => 'cla', 'ClCG06G011400' => 'cla', 'ClCG09G019360' => 'cla', 'COL.COLO4_04827' => 'col', 'COL.COLO4_29170' => 'col', 'COL.COLO4_35131' => 'col', 'COL.COLO4_35132' => 'col', 'Cpa.g.sc33.32' => 'cpa', 'Cpa.g.sc46.29' => 'cpa', 'Cpa.g.sc796.1' => 'cpa', 'CsaV3_1G030420' => 'csa', 'CsaV3_5G027050' => 'csa', 'CsaV3_5G031040' => 'csa', 'CsaV3_UNG023130' => 'csa', 'CSS0007726' => 'camsi', 'CSS0016433' => 'camsi', 'CSS0017656' => 'camsi', 'CSS0025364' => 'camsi', 'CSS0027582' => 'camsi', 'CSS0047288' => 'camsi', 'CSS0049950' => 'camsi', 'DCAR_003843' => 'dca', 'DCAR_007052' => 'dca', 'DCAR_020884' => 'dca', 'DCAR_021730' => 'dca', 'DCAR_024423' => 'dca', 'DCAR_026509' => 'dca', 'DCAR_031158' => 'dca', 'Dinv14728' => 'din', 'Dinv15219' => 'din', 'Dinv25728' => 'din', 'Dinv33428' => 'din', 'Dinv36489' => 'din', 'Dinv41486' => 'din', 'Duzib147G0469' => 'dzi', 'Duzib168G0060' => 'dzi', 'Duzib187G1215' => 'dzi', 'Duzib248G0692' => 'dzi', 'Duzib251G0767' => 'dzi', 'Duzib264G0446' => 'dzi', 'Duzib268G0691' => 'dzi', 'ECA232G4767' => 'eca', 'ECA233G2838' => 'eca', 'ECA234G0391' => 'eca', 'ECA234G0857' => 'eca', 'ECA236G1593' => 'eca', 'ECA238G0565' => 'eca', 'ECA246G1027' => 'eca', 'ECA246G3223' => 'eca', 'ECA246G3470' => 'eca', 'EL10Ac6g13829' => 'bvu', 'EL10Ac6g14093' => 'bvu', 'EL10Ac8g18707' => 'bvu', 'Eucgr.C01369' => 'egr', 'Eucgr.H02492' => 'egr', 'Eucgr.I01733' => 'egr', 'Eucgr.J02255' => 'egr', 'Eucgr.J02257' => 'egr', 'Eucgr.J02258' => 'egr', 'FAN02G1601' => 'fan', 'FAN03G1586' => 'fan', 'FAN03G2986' => 'fan', 'FAN05G4837' => 'fan', 'FAN06G0146' => 'fan', 'FAN07G0858' => 'fan', 'FAN09G3179' => 'fan', 'FAN10G0669' => 'fan', 'FAN12G2358' => 'fan', 'FAN14G4198' => 'fan', 'FAN14G5112' => 'fan', 'FAN17G0342' => 'fan', 'FAN19G0342' => 'fan', 'FAN19G0962' => 'fan', 'FAN19G1101' => 'fan', 'FAN19G1872' => 'fan', 'FAN22G0356' => 'fan', 'FAN23G0744' => 'fan', 'FAN23G1914' => 'fan', 'FAN26G0032' => 'fan', 'FAN28G0625' => 'fan', 'FvH4_1g02710' => 'fve', 'FvH4_1g02720' => 'fve', 'FvH4_4g25670' => 'fve', 'FvH4_6g51700' => 'fve', 'FvH4_7g20170' => 'fve', 'Glyma.05G175000' => 'gma', 'Glyma.08G132300' => 'gma', 'Glyma.11G243000' => 'gma', 'Glyma.13G158900' => 'gma', 'Glyma.17G112400' => 'gma', 'Glyma.18G014100' => 'gma', 'Glyma.19G003100' => 'gma', 'Glyma.19G056500' => 'gma', 'Gohir.A01G158900' => 'ghi', 'Gohir.A05G312600' => 'ghi', 'Gohir.A05G354900' => 'ghi', 'Gohir.A07G037200' => 'ghi', 'Gohir.A09G030000' => 'ghi', 'Gohir.A12G145200' => 'ghi', 'Gohir.D01G151500' => 'ghi', 'Gohir.D04G058300' => 'ghi', 'Gohir.D05G314100' => 'ghi', 'Gohir.D07G041400' => 'ghi', 'Gohir.D09G029700' => 'ghi', 'Gohir.D12G149700' => 'ghi', 'Gorai.001G043800' => 'gra', 'Gorai.002G187800' => 'gra', 'Gorai.006G034700' => 'gra', 'Gorai.008G161200' => 'gra', 'Gorai.009G335700' => 'gra', 'Gorai.012G065000' => 'gra', 'GSVIVG01000535001' => 'vvi', 'GSVIVG01015572001' => 'vvi', 'GSVIVG01032386001' => 'vvi', 'HanXRQChr05g0138531' => 'han', 'HanXRQChr06g0174391' => 'han', 'HanXRQChr07g0199021' => 'han', 'HanXRQChr08g0208211' => 'han', 'HanXRQChr09g0255471' => 'han', 'HanXRQChr10g0315791' => 'han', 'HanXRQChr12g0371991' => 'han', 'HanXRQChr15g0475251' => 'han', 'HanXRQChr17g0540001' => 'han', 'HanXRQChr17g0548631' => 'han', 'HanXRQChr17g0569561' => 'han', 'Haze_12256' => 'cav', 'Haze_14756' => 'cav', 'Haze_25528' => 'cav', 'Hma1.2p1_0079F.1_g041020' => 'hma', 'Hma1.2p1_0818F.1_g223260' => 'hma', 'Hma1.2p1_1747F.1_g300530' => 'hma', 'HPP92_004607' => 'vpl', 'HPP92_004608' => 'vpl', 'HPP92_006181' => 'vpl', 'HPP92_012192' => 'vpl', 'HPP92_015680' => 'vpl', 'HPP92_020249' => 'vpl', 'HPP92_021376' => 'vpl', 'HPP92_024275' => 'vpl', 'Hund06031' => 'sun', 'Hund25391' => 'sun', 'Lalb_Chr07g0185371' => 'lal', 'Lalb_Chr07g0185381' => 'lal', 'Lalb_Chr12g0204011' => 'lal', 'Lalb_Chr13g0301671' => 'lal', 'Lalb_Chr14g0362851' => 'lal', 'Lalb_Chr24g0403581' => 'lal', 'Lj1g0000233' => 'lja', 'Lj2g0018120' => 'lja', 'Lj3C621T0' => 'lonja', 'Lj3P1059T14' => 'lonja', 'Lj3P611T9' => 'lonja', 'Lj3P614T13' => 'lonja', 'Lj3P615T5' => 'lonja', 'Lj4g0012315' => 'lja', 'Lj4g0026182' => 'lja', 'Lj6P813T16' => 'lonja', 'Lj7C427T7' => 'lonja', 'Lj7C427T8' => 'lonja', 'Lj7P600T41' => 'lonja', 'Lju41C42G17' => 'lonja', 'Lsat_1_v5_gn_0_47300' => 'lsa', 'Lsat_1_v5_gn_2_91280' => 'lsa', 'Lsat_1_v5_gn_3_30561' => 'lsa', 'Lsat_1_v5_gn_4_184321' => 'lsa', 'Lsat_1_v5_gn_4_4041' => 'lsa', 'Lsat_1_v5_gn_5_92000' => 'lsa', 'Lsat_1_v5_gn_8_152940' => 'lsa', 'Lsat_1_v5_gn_8_62401' => 'lsa', 'Manes.06G055900' => 'mes', 'Manes.12G022200' => 'mes', 'Manes.13G023300' => 'mes', 'Manes.14G115000' => 'mes', 'Manes.15G151700' => 'mes', 'Manes.17G111300' => 'mes', 'Mapoly0226s0009' => 'mpo', 'MBI02_g25363_MAGBIO' => 'mbi', 'MBI06_g00027_MAGBIO' => 'mbi', 'MBI10_g13034_MAGBIO' => 'mbi', 'MD09G1023400' => 'mdo', 'MD13G1100100' => 'mdo', 'MD15G1169200' => 'mdo', 'MD16G1101100' => 'mdo', 'MD17G1022900' => 'mdo', 'Medtr3g096150' => 'mtr', 'Medtr4g115070' => 'mtr', 'Medtr7g033325' => 'mtr', 'Medtr8g089840' => 'mtr', 'MELO3C010319.2' => 'cme', 'MELO3C011944.2' => 'cme', 'MELO3C021589.2' => 'cme', 'Migut.E00207' => 'egut', 'Migut.H00067' => 'egut', 'Migut.K00433' => 'egut', 'Migut.K00606' => 'egut', 'Migut.K01410' => 'egut', 'MSTRG.13347' => 'ama', 'MSTRG.24045' => 'ama', 'MSTRG.2428' => 'ama', 'MSTRG.26410' => 'ama', 'MSTRG.3139' => 'ama', 'MSTRG.3286' => 'ama', 'MSTRG.563' => 'ama', 'MSTRG.7941' => 'ama', 'Nitab4.5_0000028g0060' => 'nta', 'Nitab4.5_0000065g0260' => 'nta', 'Nitab4.5_0000112g0060' => 'nta', 'Nitab4.5_0000489g0120' => 'nta', 'Nitab4.5_0001776g0050' => 'nta', 'Nitab4.5_0001854g0010' => 'nta', 'Nitab4.5_0001860g0020' => 'nta', 'Nitab4.5_0004352g0010' => 'nta', 'Nitab4.5_0008716g0020' => 'nta', 'Nitab4.5_0008922g0010' => 'nta', 'Nn3g16693' => 'nnu', 'Nn4g22596' => 'nnu', 'Nn7g37639' => 'nnu', 'Oeu001701.1' => 'oeu', 'Oeu018149.1' => 'oeu', 'Oeu026220.1' => 'oeu', 'Oeu038635.1' => 'oeu', 'Oeu049176.1' => 'oeu', 'Oeu056706.1' => 'oeu', 'Oeu056937.1' => 'oeu', 'Oeu057540.1' => 'oeu', 'Os02g0594900' => 'osa', 'Os02g0595100' => 'osa', 'Os04g0477500' => 'osa', 'Os12g0611900' => 'osa', 'Peaxi162Scf00076g00020' => 'pax', 'Peaxi162Scf00128g00217' => 'pax', 'Peaxi162Scf00129g01640' => 'pax', 'Peaxi162Scf00669g00007' => 'pax', 'Peaxi162Scf00700g00421' => 'pax', 'Peaxi162Scf00801g00038' => 'pax', 'Peaxi162Scf00891g00025' => 'pax', 'PGR083G0909' => 'pgr', 'PGR119G1005' => 'pgr', 'PGR142G2236' => 'pgr', 'PGR142G3388' => 'pgr', 'PGSC0003DMG400004514' => 'stu', 'PGSC0003DMG400012635' => 'stu', 'PGSC0003DMG400015730' => 'stu', 'PGSC0003DMG400018611' => 'stu', 'PGSC0003DMG400030897' => 'stu', 'Phvul.001G254800' => 'pvu', 'Phvul.002G260100' => 'pvu', 'Phvul.003G167600' => 'pvu', 'Phvul.004G005100' => 'pvu', 'Potri.001G343600' => 'ptr', 'Potri.006G066700' => 'ptr', 'Potri.008G186000' => 'ptr', 'Potri.010G046900' => 'ptr', 'Potri.018G127900' => 'ptr', 'Pp3c20_17750' => 'ppa', 'Pp3c24_4380' => 'ppa', 'Prupe.1G245800' => 'ppe', 'Prupe.3G293400' => 'ppe', 'Prupe.7G247400' => 'ppe', 'Psat0s145g0120' => 'psa', 'Psat0s595g0040' => 'psa', 'Psat0s595g0120' => 'psa', 'Psat3g175040' => 'psa', 'Psat7g058120' => 'psa', 'PSO017G0428' => 'pso', 'PSO063G7510' => 'pso', 'PSO067G0046' => 'pso', 'PSO478G1073' => 'pso', 'PSO675G3677' => 'pso', 'PSO675G6558' => 'pso', 'PSO675G7520' => 'pso', 'PSO675G8959' => 'pso', 'QL02p074089' => 'qlo', 'QL02p089614' => 'qlo', 'QL03p057736' => 'qlo', 'RcHm_v2.0_Chr1g0364131' => 'rch', 'RcHm_v2.0_Chr2g0087801' => 'rch', 'RcHm_v2.0_Chr2g0087821' => 'rch', 'RcHm_v2.0_Chr2g0173231' => 'rch', 'RcHm_v2.0_Chr4g0433111' => 'rch', 'Rhsim03G0250300' => 'rsi', 'Rhsim08G0048400' => 'rsi', 'Rhsim10G0014800' => 'rsi', 'Rhsim12G0040100' => 'rsi', 'Rhsim12G0109700' => 'rsi', 'Sabra06G0049600' => 'sbr', 'Sabra08G0141000' => 'sbr', 'Sabra10G0021400' => 'sbr', 'Sabra16G0222900' => 'sbr', 'Sabra18G0108600' => 'sbr', 'SalBow1G0433' => 'sbo', 'SalBow1G2038' => 'sbo', 'SalBow1G5003' => 'sbo', 'SalBow7G1197' => 'sbo', 'SalBow8G3506' => 'sbo', 'Sc03g0007300' => 'sci', 'Sc11g0000950' => 'sci', 'Sc14g0008750' => 'sci', 'Sc18g0000420' => 'sci', 'Sed0006754' => 'sed', 'Sed0008741' => 'sed', 'Sed0017172' => 'sed', 'Sed0018925' => 'sed', 'Sed0023326' => 'sed', 'Sed0025909' => 'sed', 'SEGI_05333' => 'sgi', 'SEGI_10362' => 'sgi', 'SEGI_13380' => 'sgi', 'SEGI_24306' => 'sgi', 'SEGI_29077' => 'sgi', 'SEGI_29095' => 'sgi', 'SEGI_36534' => 'sgi', 'SEGI_37506' => 'sgi', 'SEGI_38321' => 'sgi', 'SGA_v2.0_scaffold307G48031' => 'sas', 'SGA_v2.0_scaffold47G17507' => 'sas', 'SGA_v2.0_scaffold63G21736' => 'sas', 'SGA_v2.0_scaffold87G27070' => 'sas', 'SHI17794' => 'shi', 'SHI28851' => 'shi', 'SMO165G0155' => 'smo', 'SMO340G0217' => 'smo', 'SMO367G1210' => 'smo', 'Solyc02g093430.3' => 'sly', 'Solyc05g013580.4' => 'sly', 'Solyc07g008030.3' => 'sly', 'Solyc12g035470.2' => 'sly', 'Sopen02g038020' => 'spe', 'Sopen05g008490' => 'spe', 'Sopen07g003910' => 'spe', 'Sopen12g015240' => 'spe', 'Sp1g11550' => 'spa', 'Sp2g16710' => 'spa', 'Sp3g00430' => 'spa', 'Sp3g26780' => 'spa', 'Sp5g22900' => 'spa', 'Sp6g29530' => 'spa', 'TAR371G0794' => 'tar', 'TAR374G0164' => 'tar', 'TAR622G0165' => 'tar', 'TAR626G0929' => 'tar', 'TAR629G2155' => 'tar', 'THA.LOC104805282' => 'tha', 'THA.LOC104805363' => 'tha', 'THA.LOC104808968' => 'tha', 'THA.LOC104821093' => 'tha', 'THA.LOC104823953' => 'tha', 'THA.LOC104825562' => 'tha', 'THA.LOC104825665' => 'tha', 'Thecc.02G261400' => 'tca', 'Thecc.04G019200' => 'tca', 'Thecc.09G130400' => 'tca', 'Thhalv10004374m.g' => 'esa', 'Thhalv10007850m.g' => 'esa', 'Thhalv10013782m.g' => 'esa', 'Thhalv10018686m.g' => 'esa', 'Thhalv10020899m.g' => 'esa', 'Thhalv10022755m.g' => 'esa', 'TPR.G23851' => 'tpr', 'TPR.G26500' => 'tpr', 'TPR.G27267' => 'tpr', 'TPR.G32001' => 'tpr', 'TPR.G6251' => 'tpr', 'TPR.G8167' => 'tpr', 'TWI12G1330' => 'twi', 'TWI18G1239' => 'twi', 'TWI34G0979' => 'twi', 'TWI36G0670' => 'twi', 'TWI36G0707' => 'twi', 'TWI56G0233' => 'twi', 'TWI75G1809' => 'twi', 'unitig_21.g20874' => 'ugi', 'unitig_26.g10343' => 'ugi', 'unitig_46.g18392' => 'ugi', 'unitig_52.g17178' => 'ugi', 'unitig_8.g2934' => 'ugi', 'vmacro01122' => 'vma', 'vmacro05875' => 'vma', 'vmacro06147' => 'vma', 'vmacro16191' => 'vma', 'vmacro18293' => 'vma', 'VMungo0251G3707' => 'vmu', 'VMungo0464G1521' => 'vmu', 'VMungo1215G0205' => 'vmu', 'VMungo1383G2484' => 'vmu', 'Zm00001eb079610' => 'zma', 'Zm00001eb135990' => 'zma', 'Zm00001eb183710' => 'zma', 'Zm00001eb246020' => 'zma' ) $gf_id = 'HOM05D001124' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001124' ) $data_identifier = 'HOM05D001124' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 6, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 7, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 21, 'bol' => (int) 10, 'bra' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 6, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 9, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 21, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 8, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 10, 'lsa' => (int) 8, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 8, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 9, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb246020' $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' => 'HOM05D001124', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '548', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02520' => 'bna', 'A03p06630' => 'bna', 'A05p44460' => 'bna', 'A06p08710' => 'bna', 'A06p41090' => 'bna', 'A07p32320' => 'bna', 'A08p32520' => 'bna', 'A09p10360' => 'bna', 'A10p24080' => 'bna', 'Aa31LG11G15250' => 'aar', 'Aa31LG1G1800' => 'aar', 'Aa31LG2G5120' => 'aar', 'Aa31LG2G6070' => 'aar', 'Aa31LG5G10770' => 'aar', 'Aa31sc61G90' => 'aar', 'Actinidia01352' => 'ach', 'Actinidia05983' => 'ach', 'Actinidia08133' => 'ach', 'Actinidia15101' => 'ach', 'Actinidia26379' => 'ach', 'Actinidia35778' => 'ach', 'Actinidia36123' => 'ach', 'Actinidia37436' => 'ach', 'Actinidia38730' => 'ach', 'Ah.02g128210' => 'amhyb', 'Ah.03g132990' => 'amhyb', 'Ah.14g079410' => 'amhyb', 'AL1G24640' => 'aly', 'AL2G26680' => 'aly', 'AL3G10530' => 'aly', 'AL3G45230' => 'aly', 'AL5G15230' => 'aly', 'AL5G16960' => 'aly', 'AL6G25210' => 'aly', 'Aqoxy2G00441' => 'aox', 'Aqoxy3G01236' => 'aox', 'Aqoxy5G03746' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3RQ047' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C7GMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9C8JER' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MBL6KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YXCZ83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZANX40' => 'arhy', 'AT1G12990' => 'ath', 'AT1G67880' => 'ath', 'AT2G13290' => 'ath', 'AT3G01620' => 'ath', 'AT3G26445' => 'ath', 'AT3G27540' => 'ath', 'AT5G14480' => 'ath', 'ATR0824G026' => 'atr', 'ATR1098G019' => 'atr', 'Atru.chr11.2145' => 'acertr', 'Atru.chr2.3636' => 'acertr', 'Atru.chr2.3644' => 'acertr', 'Atru.chr6.2422' => 'acertr', 'Atru.chr7.1112' => 'acertr', 'AUR62005469' => 'cqu', 'AUR62011166' => 'cqu', 'AUR62013319' => 'cqu', 'AUR62024273' => 'cqu', 'AUR62028420' => 'cqu', 'AUR62041942' => 'cqu', 'BcaB01g04969' => 'bca', 'BcaB01g06371' => 'bca', 'BcaB02g11494' => 'bca', 'BcaB03g15382' => 'bca', 'BcaB08g36994' => 'bca', 'BcaC03g13477' => 'bca', 'BcaC03g13478' => 'bca', 'BcaC03g13480' => 'bca', 'BcaC03g13481' => 'bca', 'BcaC03g13486' => 'bca', 'BcaC04g19031' => 'bca', 'BcaC04g23085' => 'bca', 'BcaC05g25094' => 'bca', 'BcaC05g25096' => 'bca', 'BcaC05g25138' => 'bca', 'BcaC05g30416' => 'bca', 'BcaC05g30455' => 'bca', 'BcaC06g30979' => 'bca', 'BcaC06g33805' => 'bca', 'BcaC08g46021' => 'bca', 'BcaNung03154' => 'bca', 'BolC2t06623H' => 'bol', 'BolC2t06632H' => 'bol', 'BolC2t06635H' => 'bol', 'BolC2t06638H' => 'bol', 'BolC3t13266H' => 'bol', 'BolC5t29776H' => 'bol', 'BolC6t38912H' => 'bol', 'BolC7t44183H' => 'bol', 'BolC9t54123H' => 'bol', 'BolC9t59107H' => 'bol', 'BraA02t05221Z' => 'bra', 'BraA03t09996Z' => 'bra', 'BraA05t23210Z' => 'bra', 'BraA06t24068Z' => 'bra', 'BraA06t27032Z' => 'bra', 'BraA08t35176Z' => 'bra', 'BraA09t36680Z' => 'bra', 'BraA10t44471Z' => 'bra', 'C02p06760' => 'bna', 'C02p06890' => 'bna', 'C02p07010' => 'bna', 'C03p07660' => 'bna', 'C05p10300' => 'bna', 'C06p38150' => 'bna', 'C07p36650' => 'bna', 'C08p15770' => 'bna', 'C09p12300' => 'bna', 'C09p62700' => 'bna', 'C09p75040' => 'bna', 'CAN.G13.1' => 'can', 'CAN.G138.4' => 'can', 'CAN.G44.6' => 'can', 'CAN.G473.19' => 'can', 'CANSAT01G0835' => 'cansat', 'CANSAT11G0246' => 'cansat', 'CANSAT11G1766' => 'cansat', 'CANSAT64G1954' => 'cansat', 'CARHR013330' => 'chi', 'CARHR060530' => 'chi', 'CARHR075300' => 'chi', 'CARHR105120' => 'chi', 'CARHR148910' => 'chi', 'CARHR198830' => 'chi', 'Carub.0001s1275' => 'cru', 'Carub.0002s1437' => 'cru', 'Carub.0003s0044' => 'cru', 'Carub.0003s2787' => 'cru', 'Carub.0005s0597' => 'cru', 'Carub.0006s1266' => 'cru', 'Ca_06935_v3' => 'car', 'Ca_13559_v3' => 'car', 'Ca_16941_v3' => 'car', 'Ca_16960_v3' => 'car', 'Ca_17775_v3' => 'car', 'Ca_30464_v3' => 'car', 'Cc06_g08160' => 'ccan', 'Cc07_g01520' => 'ccan', 'Cc11_g15810' => 'ccan', 'CDE02G2840' => 'cde', 'CDE03G0093' => 'cde', 'CDE04G2127' => 'cde', 'CDE07G1857' => 'cde', 'CDE09G1246' => 'cde', 'Cfa003412' => 'cfa', 'Cfa007341' => 'cfa', 'Cfa009220' => 'cfa', 'Ciclev10008737m.g' => 'ccl', 'Ciclev10015565m.g' => 'ccl', 'Ciclev10031761m.g' => 'ccl', 'CiPaw.03G045300' => 'cil', 'CiPaw.03G247200' => 'cil', 'CiPaw.04G029500' => 'cil', 'CiPaw.04G174000' => 'cil', 'CiPaw.05G181200' => 'cil', 'CiPaw.06G067100' => 'cil', 'ClCG05G025800' => 'cla', 'ClCG06G011400' => 'cla', 'ClCG09G019360' => 'cla', 'COL.COLO4_04827' => 'col', 'COL.COLO4_29170' => 'col', 'COL.COLO4_35131' => 'col', 'COL.COLO4_35132' => 'col', 'Cpa.g.sc33.32' => 'cpa', 'Cpa.g.sc46.29' => 'cpa', 'Cpa.g.sc796.1' => 'cpa', 'CsaV3_1G030420' => 'csa', 'CsaV3_5G027050' => 'csa', 'CsaV3_5G031040' => 'csa', 'CsaV3_UNG023130' => 'csa', 'CSS0007726' => 'camsi', 'CSS0016433' => 'camsi', 'CSS0017656' => 'camsi', 'CSS0025364' => 'camsi', 'CSS0027582' => 'camsi', 'CSS0047288' => 'camsi', 'CSS0049950' => 'camsi', 'DCAR_003843' => 'dca', 'DCAR_007052' => 'dca', 'DCAR_020884' => 'dca', 'DCAR_021730' => 'dca', 'DCAR_024423' => 'dca', 'DCAR_026509' => 'dca', 'DCAR_031158' => 'dca', 'Dinv14728' => 'din', 'Dinv15219' => 'din', 'Dinv25728' => 'din', 'Dinv33428' => 'din', 'Dinv36489' => 'din', 'Dinv41486' => 'din', 'Duzib147G0469' => 'dzi', 'Duzib168G0060' => 'dzi', 'Duzib187G1215' => 'dzi', 'Duzib248G0692' => 'dzi', 'Duzib251G0767' => 'dzi', 'Duzib264G0446' => 'dzi', 'Duzib268G0691' => 'dzi', 'ECA232G4767' => 'eca', 'ECA233G2838' => 'eca', 'ECA234G0391' => 'eca', 'ECA234G0857' => 'eca', 'ECA236G1593' => 'eca', 'ECA238G0565' => 'eca', 'ECA246G1027' => 'eca', 'ECA246G3223' => 'eca', 'ECA246G3470' => 'eca', 'EL10Ac6g13829' => 'bvu', 'EL10Ac6g14093' => 'bvu', 'EL10Ac8g18707' => 'bvu', 'Eucgr.C01369' => 'egr', 'Eucgr.H02492' => 'egr', 'Eucgr.I01733' => 'egr', 'Eucgr.J02255' => 'egr', 'Eucgr.J02257' => 'egr', 'Eucgr.J02258' => 'egr', 'FAN02G1601' => 'fan', 'FAN03G1586' => 'fan', 'FAN03G2986' => 'fan', 'FAN05G4837' => 'fan', 'FAN06G0146' => 'fan', 'FAN07G0858' => 'fan', 'FAN09G3179' => 'fan', 'FAN10G0669' => 'fan', 'FAN12G2358' => 'fan', 'FAN14G4198' => 'fan', 'FAN14G5112' => 'fan', 'FAN17G0342' => 'fan', 'FAN19G0342' => 'fan', 'FAN19G0962' => 'fan', 'FAN19G1101' => 'fan', 'FAN19G1872' => 'fan', 'FAN22G0356' => 'fan', 'FAN23G0744' => 'fan', 'FAN23G1914' => 'fan', 'FAN26G0032' => 'fan', 'FAN28G0625' => 'fan', 'FvH4_1g02710' => 'fve', 'FvH4_1g02720' => 'fve', 'FvH4_4g25670' => 'fve', 'FvH4_6g51700' => 'fve', 'FvH4_7g20170' => 'fve', 'Glyma.05G175000' => 'gma', 'Glyma.08G132300' => 'gma', 'Glyma.11G243000' => 'gma', 'Glyma.13G158900' => 'gma', 'Glyma.17G112400' => 'gma', 'Glyma.18G014100' => 'gma', 'Glyma.19G003100' => 'gma', 'Glyma.19G056500' => 'gma', 'Gohir.A01G158900' => 'ghi', 'Gohir.A05G312600' => 'ghi', 'Gohir.A05G354900' => 'ghi', 'Gohir.A07G037200' => 'ghi', 'Gohir.A09G030000' => 'ghi', 'Gohir.A12G145200' => 'ghi', 'Gohir.D01G151500' => 'ghi', 'Gohir.D04G058300' => 'ghi', 'Gohir.D05G314100' => 'ghi', 'Gohir.D07G041400' => 'ghi', 'Gohir.D09G029700' => 'ghi', 'Gohir.D12G149700' => 'ghi', 'Gorai.001G043800' => 'gra', 'Gorai.002G187800' => 'gra', 'Gorai.006G034700' => 'gra', 'Gorai.008G161200' => 'gra', 'Gorai.009G335700' => 'gra', 'Gorai.012G065000' => 'gra', 'GSVIVG01000535001' => 'vvi', 'GSVIVG01015572001' => 'vvi', 'GSVIVG01032386001' => 'vvi', 'HanXRQChr05g0138531' => 'han', 'HanXRQChr06g0174391' => 'han', 'HanXRQChr07g0199021' => 'han', 'HanXRQChr08g0208211' => 'han', 'HanXRQChr09g0255471' => 'han', 'HanXRQChr10g0315791' => 'han', 'HanXRQChr12g0371991' => 'han', 'HanXRQChr15g0475251' => 'han', 'HanXRQChr17g0540001' => 'han', 'HanXRQChr17g0548631' => 'han', 'HanXRQChr17g0569561' => 'han', 'Haze_12256' => 'cav', 'Haze_14756' => 'cav', 'Haze_25528' => 'cav', 'Hma1.2p1_0079F.1_g041020' => 'hma', 'Hma1.2p1_0818F.1_g223260' => 'hma', 'Hma1.2p1_1747F.1_g300530' => 'hma', 'HPP92_004607' => 'vpl', 'HPP92_004608' => 'vpl', 'HPP92_006181' => 'vpl', 'HPP92_012192' => 'vpl', 'HPP92_015680' => 'vpl', 'HPP92_020249' => 'vpl', 'HPP92_021376' => 'vpl', 'HPP92_024275' => 'vpl', 'Hund06031' => 'sun', 'Hund25391' => 'sun', 'Lalb_Chr07g0185371' => 'lal', 'Lalb_Chr07g0185381' => 'lal', 'Lalb_Chr12g0204011' => 'lal', 'Lalb_Chr13g0301671' => 'lal', 'Lalb_Chr14g0362851' => 'lal', 'Lalb_Chr24g0403581' => 'lal', 'Lj1g0000233' => 'lja', 'Lj2g0018120' => 'lja', 'Lj3C621T0' => 'lonja', 'Lj3P1059T14' => 'lonja', 'Lj3P611T9' => 'lonja', 'Lj3P614T13' => 'lonja', 'Lj3P615T5' => 'lonja', 'Lj4g0012315' => 'lja', 'Lj4g0026182' => 'lja', 'Lj6P813T16' => 'lonja', 'Lj7C427T7' => 'lonja', 'Lj7C427T8' => 'lonja', 'Lj7P600T41' => 'lonja', 'Lju41C42G17' => 'lonja', 'Lsat_1_v5_gn_0_47300' => 'lsa', 'Lsat_1_v5_gn_2_91280' => 'lsa', 'Lsat_1_v5_gn_3_30561' => 'lsa', 'Lsat_1_v5_gn_4_184321' => 'lsa', 'Lsat_1_v5_gn_4_4041' => 'lsa', 'Lsat_1_v5_gn_5_92000' => 'lsa', 'Lsat_1_v5_gn_8_152940' => 'lsa', 'Lsat_1_v5_gn_8_62401' => 'lsa', 'Manes.06G055900' => 'mes', 'Manes.12G022200' => 'mes', 'Manes.13G023300' => 'mes', 'Manes.14G115000' => 'mes', 'Manes.15G151700' => 'mes', 'Manes.17G111300' => 'mes', 'Mapoly0226s0009' => 'mpo', 'MBI02_g25363_MAGBIO' => 'mbi', 'MBI06_g00027_MAGBIO' => 'mbi', 'MBI10_g13034_MAGBIO' => 'mbi', 'MD09G1023400' => 'mdo', 'MD13G1100100' => 'mdo', 'MD15G1169200' => 'mdo', 'MD16G1101100' => 'mdo', 'MD17G1022900' => 'mdo', 'Medtr3g096150' => 'mtr', 'Medtr4g115070' => 'mtr', 'Medtr7g033325' => 'mtr', 'Medtr8g089840' => 'mtr', 'MELO3C010319.2' => 'cme', 'MELO3C011944.2' => 'cme', 'MELO3C021589.2' => 'cme', 'Migut.E00207' => 'egut', 'Migut.H00067' => 'egut', 'Migut.K00433' => 'egut', 'Migut.K00606' => 'egut', 'Migut.K01410' => 'egut', 'MSTRG.13347' => 'ama', 'MSTRG.24045' => 'ama', 'MSTRG.2428' => 'ama', 'MSTRG.26410' => 'ama', 'MSTRG.3139' => 'ama', 'MSTRG.3286' => 'ama', 'MSTRG.563' => 'ama', 'MSTRG.7941' => 'ama', 'Nitab4.5_0000028g0060' => 'nta', 'Nitab4.5_0000065g0260' => 'nta', 'Nitab4.5_0000112g0060' => 'nta', 'Nitab4.5_0000489g0120' => 'nta', 'Nitab4.5_0001776g0050' => 'nta', 'Nitab4.5_0001854g0010' => 'nta', 'Nitab4.5_0001860g0020' => 'nta', 'Nitab4.5_0004352g0010' => 'nta', 'Nitab4.5_0008716g0020' => 'nta', 'Nitab4.5_0008922g0010' => 'nta', 'Nn3g16693' => 'nnu', 'Nn4g22596' => 'nnu', 'Nn7g37639' => 'nnu', 'Oeu001701.1' => 'oeu', 'Oeu018149.1' => 'oeu', 'Oeu026220.1' => 'oeu', 'Oeu038635.1' => 'oeu', 'Oeu049176.1' => 'oeu', 'Oeu056706.1' => 'oeu', 'Oeu056937.1' => 'oeu', 'Oeu057540.1' => 'oeu', 'Os02g0594900' => 'osa', 'Os02g0595100' => 'osa', 'Os04g0477500' => 'osa', 'Os12g0611900' => 'osa', 'Peaxi162Scf00076g00020' => 'pax', 'Peaxi162Scf00128g00217' => 'pax', 'Peaxi162Scf00129g01640' => 'pax', 'Peaxi162Scf00669g00007' => 'pax', 'Peaxi162Scf00700g00421' => 'pax', 'Peaxi162Scf00801g00038' => 'pax', 'Peaxi162Scf00891g00025' => 'pax', 'PGR083G0909' => 'pgr', 'PGR119G1005' => 'pgr', 'PGR142G2236' => 'pgr', 'PGR142G3388' => 'pgr', 'PGSC0003DMG400004514' => 'stu', 'PGSC0003DMG400012635' => 'stu', 'PGSC0003DMG400015730' => 'stu', 'PGSC0003DMG400018611' => 'stu', 'PGSC0003DMG400030897' => 'stu', 'Phvul.001G254800' => 'pvu', 'Phvul.002G260100' => 'pvu', 'Phvul.003G167600' => 'pvu', 'Phvul.004G005100' => 'pvu', 'Potri.001G343600' => 'ptr', 'Potri.006G066700' => 'ptr', 'Potri.008G186000' => 'ptr', 'Potri.010G046900' => 'ptr', 'Potri.018G127900' => 'ptr', 'Pp3c20_17750' => 'ppa', 'Pp3c24_4380' => 'ppa', 'Prupe.1G245800' => 'ppe', 'Prupe.3G293400' => 'ppe', 'Prupe.7G247400' => 'ppe', 'Psat0s145g0120' => 'psa', 'Psat0s595g0040' => 'psa', 'Psat0s595g0120' => 'psa', 'Psat3g175040' => 'psa', 'Psat7g058120' => 'psa', 'PSO017G0428' => 'pso', 'PSO063G7510' => 'pso', 'PSO067G0046' => 'pso', 'PSO478G1073' => 'pso', 'PSO675G3677' => 'pso', 'PSO675G6558' => 'pso', 'PSO675G7520' => 'pso', 'PSO675G8959' => 'pso', 'QL02p074089' => 'qlo', 'QL02p089614' => 'qlo', 'QL03p057736' => 'qlo', 'RcHm_v2.0_Chr1g0364131' => 'rch', 'RcHm_v2.0_Chr2g0087801' => 'rch', 'RcHm_v2.0_Chr2g0087821' => 'rch', 'RcHm_v2.0_Chr2g0173231' => 'rch', 'RcHm_v2.0_Chr4g0433111' => 'rch', 'Rhsim03G0250300' => 'rsi', 'Rhsim08G0048400' => 'rsi', 'Rhsim10G0014800' => 'rsi', 'Rhsim12G0040100' => 'rsi', 'Rhsim12G0109700' => 'rsi', 'Sabra06G0049600' => 'sbr', 'Sabra08G0141000' => 'sbr', 'Sabra10G0021400' => 'sbr', 'Sabra16G0222900' => 'sbr', 'Sabra18G0108600' => 'sbr', 'SalBow1G0433' => 'sbo', 'SalBow1G2038' => 'sbo', 'SalBow1G5003' => 'sbo', 'SalBow7G1197' => 'sbo', 'SalBow8G3506' => 'sbo', 'Sc03g0007300' => 'sci', 'Sc11g0000950' => 'sci', 'Sc14g0008750' => 'sci', 'Sc18g0000420' => 'sci', 'Sed0006754' => 'sed', 'Sed0008741' => 'sed', 'Sed0017172' => 'sed', 'Sed0018925' => 'sed', 'Sed0023326' => 'sed', 'Sed0025909' => 'sed', 'SEGI_05333' => 'sgi', 'SEGI_10362' => 'sgi', 'SEGI_13380' => 'sgi', 'SEGI_24306' => 'sgi', 'SEGI_29077' => 'sgi', 'SEGI_29095' => 'sgi', 'SEGI_36534' => 'sgi', 'SEGI_37506' => 'sgi', 'SEGI_38321' => 'sgi', 'SGA_v2.0_scaffold307G48031' => 'sas', 'SGA_v2.0_scaffold47G17507' => 'sas', 'SGA_v2.0_scaffold63G21736' => 'sas', 'SGA_v2.0_scaffold87G27070' => 'sas', 'SHI17794' => 'shi', 'SHI28851' => 'shi', 'SMO165G0155' => 'smo', 'SMO340G0217' => 'smo', 'SMO367G1210' => 'smo', 'Solyc02g093430.3' => 'sly', 'Solyc05g013580.4' => 'sly', 'Solyc07g008030.3' => 'sly', 'Solyc12g035470.2' => 'sly', 'Sopen02g038020' => 'spe', 'Sopen05g008490' => 'spe', 'Sopen07g003910' => 'spe', 'Sopen12g015240' => 'spe', 'Sp1g11550' => 'spa', 'Sp2g16710' => 'spa', 'Sp3g00430' => 'spa', 'Sp3g26780' => 'spa', 'Sp5g22900' => 'spa', 'Sp6g29530' => 'spa', 'TAR371G0794' => 'tar', 'TAR374G0164' => 'tar', 'TAR622G0165' => 'tar', 'TAR626G0929' => 'tar', 'TAR629G2155' => 'tar', 'THA.LOC104805282' => 'tha', 'THA.LOC104805363' => 'tha', 'THA.LOC104808968' => 'tha', 'THA.LOC104821093' => 'tha', 'THA.LOC104823953' => 'tha', 'THA.LOC104825562' => 'tha', 'THA.LOC104825665' => 'tha', 'Thecc.02G261400' => 'tca', 'Thecc.04G019200' => 'tca', 'Thecc.09G130400' => 'tca', 'Thhalv10004374m.g' => 'esa', 'Thhalv10007850m.g' => 'esa', 'Thhalv10013782m.g' => 'esa', 'Thhalv10018686m.g' => 'esa', 'Thhalv10020899m.g' => 'esa', 'Thhalv10022755m.g' => 'esa', 'TPR.G23851' => 'tpr', 'TPR.G26500' => 'tpr', 'TPR.G27267' => 'tpr', 'TPR.G32001' => 'tpr', 'TPR.G6251' => 'tpr', 'TPR.G8167' => 'tpr', 'TWI12G1330' => 'twi', 'TWI18G1239' => 'twi', 'TWI34G0979' => 'twi', 'TWI36G0670' => 'twi', 'TWI36G0707' => 'twi', 'TWI56G0233' => 'twi', 'TWI75G1809' => 'twi', 'unitig_21.g20874' => 'ugi', 'unitig_26.g10343' => 'ugi', 'unitig_46.g18392' => 'ugi', 'unitig_52.g17178' => 'ugi', 'unitig_8.g2934' => 'ugi', 'vmacro01122' => 'vma', 'vmacro05875' => 'vma', 'vmacro06147' => 'vma', 'vmacro16191' => 'vma', 'vmacro18293' => 'vma', 'VMungo0251G3707' => 'vmu', 'VMungo0464G1521' => 'vmu', 'VMungo1215G0205' => 'vmu', 'VMungo1383G2484' => 'vmu', 'Zm00001eb079610' => 'zma', 'Zm00001eb135990' => 'zma', 'Zm00001eb183710' => 'zma', 'Zm00001eb246020' => 'zma' ), 'gf_id' => 'HOM05D001124', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001124' ), 'data_identifier' => 'HOM05D001124', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001124', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '548', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02520' => 'bna', 'A03p06630' => 'bna', 'A05p44460' => 'bna', 'A06p08710' => 'bna', 'A06p41090' => 'bna', 'A07p32320' => 'bna', 'A08p32520' => 'bna', 'A09p10360' => 'bna', 'A10p24080' => 'bna', 'Aa31LG11G15250' => 'aar', 'Aa31LG1G1800' => 'aar', 'Aa31LG2G5120' => 'aar', 'Aa31LG2G6070' => 'aar', 'Aa31LG5G10770' => 'aar', 'Aa31sc61G90' => 'aar', 'Actinidia01352' => 'ach', 'Actinidia05983' => 'ach', 'Actinidia08133' => 'ach', 'Actinidia15101' => 'ach', 'Actinidia26379' => 'ach', 'Actinidia35778' => 'ach', 'Actinidia36123' => 'ach', 'Actinidia37436' => 'ach', 'Actinidia38730' => 'ach', 'Ah.02g128210' => 'amhyb', 'Ah.03g132990' => 'amhyb', 'Ah.14g079410' => 'amhyb', 'AL1G24640' => 'aly', 'AL2G26680' => 'aly', 'AL3G10530' => 'aly', 'AL3G45230' => 'aly', 'AL5G15230' => 'aly', 'AL5G16960' => 'aly', 'AL6G25210' => 'aly', 'Aqoxy2G00441' => 'aox', 'Aqoxy3G01236' => 'aox', 'Aqoxy5G03746' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3RQ047' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C7GMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9C8JER' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MBL6KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YXCZ83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZANX40' => 'arhy', 'AT1G12990' => 'ath', 'AT1G67880' => 'ath', 'AT2G13290' => 'ath', 'AT3G01620' => 'ath', 'AT3G26445' => 'ath', 'AT3G27540' => 'ath', 'AT5G14480' => 'ath', 'ATR0824G026' => 'atr', 'ATR1098G019' => 'atr', 'Atru.chr11.2145' => 'acertr', 'Atru.chr2.3636' => 'acertr', 'Atru.chr2.3644' => 'acertr', 'Atru.chr6.2422' => 'acertr', 'Atru.chr7.1112' => 'acertr', 'AUR62005469' => 'cqu', 'AUR62011166' => 'cqu', 'AUR62013319' => 'cqu', 'AUR62024273' => 'cqu', 'AUR62028420' => 'cqu', 'AUR62041942' => 'cqu', 'BcaB01g04969' => 'bca', 'BcaB01g06371' => 'bca', 'BcaB02g11494' => 'bca', 'BcaB03g15382' => 'bca', 'BcaB08g36994' => 'bca', 'BcaC03g13477' => 'bca', 'BcaC03g13478' => 'bca', 'BcaC03g13480' => 'bca', 'BcaC03g13481' => 'bca', 'BcaC03g13486' => 'bca', 'BcaC04g19031' => 'bca', 'BcaC04g23085' => 'bca', 'BcaC05g25094' => 'bca', 'BcaC05g25096' => 'bca', 'BcaC05g25138' => 'bca', 'BcaC05g30416' => 'bca', 'BcaC05g30455' => 'bca', 'BcaC06g30979' => 'bca', 'BcaC06g33805' => 'bca', 'BcaC08g46021' => 'bca', 'BcaNung03154' => 'bca', 'BolC2t06623H' => 'bol', 'BolC2t06632H' => 'bol', 'BolC2t06635H' => 'bol', 'BolC2t06638H' => 'bol', 'BolC3t13266H' => 'bol', 'BolC5t29776H' => 'bol', 'BolC6t38912H' => 'bol', 'BolC7t44183H' => 'bol', 'BolC9t54123H' => 'bol', 'BolC9t59107H' => 'bol', 'BraA02t05221Z' => 'bra', 'BraA03t09996Z' => 'bra', 'BraA05t23210Z' => 'bra', 'BraA06t24068Z' => 'bra', 'BraA06t27032Z' => 'bra', 'BraA08t35176Z' => 'bra', 'BraA09t36680Z' => 'bra', 'BraA10t44471Z' => 'bra', 'C02p06760' => 'bna', 'C02p06890' => 'bna', 'C02p07010' => 'bna', 'C03p07660' => 'bna', 'C05p10300' => 'bna', 'C06p38150' => 'bna', 'C07p36650' => 'bna', 'C08p15770' => 'bna', 'C09p12300' => 'bna', 'C09p62700' => 'bna', 'C09p75040' => 'bna', 'CAN.G13.1' => 'can', 'CAN.G138.4' => 'can', 'CAN.G44.6' => 'can', 'CAN.G473.19' => 'can', 'CANSAT01G0835' => 'cansat', 'CANSAT11G0246' => 'cansat', 'CANSAT11G1766' => 'cansat', 'CANSAT64G1954' => 'cansat', 'CARHR013330' => 'chi', 'CARHR060530' => 'chi', 'CARHR075300' => 'chi', 'CARHR105120' => 'chi', 'CARHR148910' => 'chi', 'CARHR198830' => 'chi', 'Carub.0001s1275' => 'cru', 'Carub.0002s1437' => 'cru', 'Carub.0003s0044' => 'cru', 'Carub.0003s2787' => 'cru', 'Carub.0005s0597' => 'cru', 'Carub.0006s1266' => 'cru', 'Ca_06935_v3' => 'car', 'Ca_13559_v3' => 'car', 'Ca_16941_v3' => 'car', 'Ca_16960_v3' => 'car', 'Ca_17775_v3' => 'car', 'Ca_30464_v3' => 'car', 'Cc06_g08160' => 'ccan', 'Cc07_g01520' => 'ccan', 'Cc11_g15810' => 'ccan', 'CDE02G2840' => 'cde', 'CDE03G0093' => 'cde', 'CDE04G2127' => 'cde', 'CDE07G1857' => 'cde', 'CDE09G1246' => 'cde', 'Cfa003412' => 'cfa', 'Cfa007341' => 'cfa', 'Cfa009220' => 'cfa', 'Ciclev10008737m.g' => 'ccl', 'Ciclev10015565m.g' => 'ccl', 'Ciclev10031761m.g' => 'ccl', 'CiPaw.03G045300' => 'cil', 'CiPaw.03G247200' => 'cil', 'CiPaw.04G029500' => 'cil', 'CiPaw.04G174000' => 'cil', 'CiPaw.05G181200' => 'cil', 'CiPaw.06G067100' => 'cil', 'ClCG05G025800' => 'cla', 'ClCG06G011400' => 'cla', 'ClCG09G019360' => 'cla', 'COL.COLO4_04827' => 'col', 'COL.COLO4_29170' => 'col', 'COL.COLO4_35131' => 'col', 'COL.COLO4_35132' => 'col', 'Cpa.g.sc33.32' => 'cpa', 'Cpa.g.sc46.29' => 'cpa', 'Cpa.g.sc796.1' => 'cpa', 'CsaV3_1G030420' => 'csa', 'CsaV3_5G027050' => 'csa', 'CsaV3_5G031040' => 'csa', 'CsaV3_UNG023130' => 'csa', 'CSS0007726' => 'camsi', 'CSS0016433' => 'camsi', 'CSS0017656' => 'camsi', 'CSS0025364' => 'camsi', 'CSS0027582' => 'camsi', 'CSS0047288' => 'camsi', 'CSS0049950' => 'camsi', 'DCAR_003843' => 'dca', 'DCAR_007052' => 'dca', 'DCAR_020884' => 'dca', 'DCAR_021730' => 'dca', 'DCAR_024423' => 'dca', 'DCAR_026509' => 'dca', 'DCAR_031158' => 'dca', 'Dinv14728' => 'din', 'Dinv15219' => 'din', 'Dinv25728' => 'din', 'Dinv33428' => 'din', 'Dinv36489' => 'din', 'Dinv41486' => 'din', 'Duzib147G0469' => 'dzi', 'Duzib168G0060' => 'dzi', 'Duzib187G1215' => 'dzi', 'Duzib248G0692' => 'dzi', 'Duzib251G0767' => 'dzi', 'Duzib264G0446' => 'dzi', 'Duzib268G0691' => 'dzi', 'ECA232G4767' => 'eca', 'ECA233G2838' => 'eca', 'ECA234G0391' => 'eca', 'ECA234G0857' => 'eca', 'ECA236G1593' => 'eca', 'ECA238G0565' => 'eca', 'ECA246G1027' => 'eca', 'ECA246G3223' => 'eca', 'ECA246G3470' => 'eca', 'EL10Ac6g13829' => 'bvu', 'EL10Ac6g14093' => 'bvu', 'EL10Ac8g18707' => 'bvu', 'Eucgr.C01369' => 'egr', 'Eucgr.H02492' => 'egr', 'Eucgr.I01733' => 'egr', 'Eucgr.J02255' => 'egr', 'Eucgr.J02257' => 'egr', 'Eucgr.J02258' => 'egr', 'FAN02G1601' => 'fan', 'FAN03G1586' => 'fan', 'FAN03G2986' => 'fan', 'FAN05G4837' => 'fan', 'FAN06G0146' => 'fan', 'FAN07G0858' => 'fan', 'FAN09G3179' => 'fan', 'FAN10G0669' => 'fan', 'FAN12G2358' => 'fan', 'FAN14G4198' => 'fan', 'FAN14G5112' => 'fan', 'FAN17G0342' => 'fan', 'FAN19G0342' => 'fan', 'FAN19G0962' => 'fan', 'FAN19G1101' => 'fan', 'FAN19G1872' => 'fan', 'FAN22G0356' => 'fan', 'FAN23G0744' => 'fan', 'FAN23G1914' => 'fan', 'FAN26G0032' => 'fan', 'FAN28G0625' => 'fan', 'FvH4_1g02710' => 'fve', 'FvH4_1g02720' => 'fve', 'FvH4_4g25670' => 'fve', 'FvH4_6g51700' => 'fve', 'FvH4_7g20170' => 'fve', 'Glyma.05G175000' => 'gma', 'Glyma.08G132300' => 'gma', 'Glyma.11G243000' => 'gma', 'Glyma.13G158900' => 'gma', 'Glyma.17G112400' => 'gma', 'Glyma.18G014100' => 'gma', 'Glyma.19G003100' => 'gma', 'Glyma.19G056500' => 'gma', 'Gohir.A01G158900' => 'ghi', 'Gohir.A05G312600' => 'ghi', 'Gohir.A05G354900' => 'ghi', 'Gohir.A07G037200' => 'ghi', 'Gohir.A09G030000' => 'ghi', 'Gohir.A12G145200' => 'ghi', 'Gohir.D01G151500' => 'ghi', 'Gohir.D04G058300' => 'ghi', 'Gohir.D05G314100' => 'ghi', 'Gohir.D07G041400' => 'ghi', 'Gohir.D09G029700' => 'ghi', 'Gohir.D12G149700' => 'ghi', 'Gorai.001G043800' => 'gra', 'Gorai.002G187800' => 'gra', 'Gorai.006G034700' => 'gra', 'Gorai.008G161200' => 'gra', 'Gorai.009G335700' => 'gra', 'Gorai.012G065000' => 'gra', 'GSVIVG01000535001' => 'vvi', 'GSVIVG01015572001' => 'vvi', 'GSVIVG01032386001' => 'vvi', 'HanXRQChr05g0138531' => 'han', 'HanXRQChr06g0174391' => 'han', 'HanXRQChr07g0199021' => 'han', 'HanXRQChr08g0208211' => 'han', 'HanXRQChr09g0255471' => 'han', 'HanXRQChr10g0315791' => 'han', 'HanXRQChr12g0371991' => 'han', 'HanXRQChr15g0475251' => 'han', 'HanXRQChr17g0540001' => 'han', 'HanXRQChr17g0548631' => 'han', 'HanXRQChr17g0569561' => 'han', 'Haze_12256' => 'cav', 'Haze_14756' => 'cav', 'Haze_25528' => 'cav', 'Hma1.2p1_0079F.1_g041020' => 'hma', 'Hma1.2p1_0818F.1_g223260' => 'hma', 'Hma1.2p1_1747F.1_g300530' => 'hma', 'HPP92_004607' => 'vpl', 'HPP92_004608' => 'vpl', 'HPP92_006181' => 'vpl', 'HPP92_012192' => 'vpl', 'HPP92_015680' => 'vpl', 'HPP92_020249' => 'vpl', 'HPP92_021376' => 'vpl', 'HPP92_024275' => 'vpl', 'Hund06031' => 'sun', 'Hund25391' => 'sun', 'Lalb_Chr07g0185371' => 'lal', 'Lalb_Chr07g0185381' => 'lal', 'Lalb_Chr12g0204011' => 'lal', 'Lalb_Chr13g0301671' => 'lal', 'Lalb_Chr14g0362851' => 'lal', 'Lalb_Chr24g0403581' => 'lal', 'Lj1g0000233' => 'lja', 'Lj2g0018120' => 'lja', 'Lj3C621T0' => 'lonja', 'Lj3P1059T14' => 'lonja', 'Lj3P611T9' => 'lonja', 'Lj3P614T13' => 'lonja', 'Lj3P615T5' => 'lonja', 'Lj4g0012315' => 'lja', 'Lj4g0026182' => 'lja', 'Lj6P813T16' => 'lonja', 'Lj7C427T7' => 'lonja', 'Lj7C427T8' => 'lonja', 'Lj7P600T41' => 'lonja', 'Lju41C42G17' => 'lonja', 'Lsat_1_v5_gn_0_47300' => 'lsa', 'Lsat_1_v5_gn_2_91280' => 'lsa', 'Lsat_1_v5_gn_3_30561' => 'lsa', 'Lsat_1_v5_gn_4_184321' => 'lsa', 'Lsat_1_v5_gn_4_4041' => 'lsa', 'Lsat_1_v5_gn_5_92000' => 'lsa', 'Lsat_1_v5_gn_8_152940' => 'lsa', 'Lsat_1_v5_gn_8_62401' => 'lsa', 'Manes.06G055900' => 'mes', 'Manes.12G022200' => 'mes', 'Manes.13G023300' => 'mes', 'Manes.14G115000' => 'mes', 'Manes.15G151700' => 'mes', 'Manes.17G111300' => 'mes', 'Mapoly0226s0009' => 'mpo', 'MBI02_g25363_MAGBIO' => 'mbi', 'MBI06_g00027_MAGBIO' => 'mbi', 'MBI10_g13034_MAGBIO' => 'mbi', 'MD09G1023400' => 'mdo', 'MD13G1100100' => 'mdo', 'MD15G1169200' => 'mdo', 'MD16G1101100' => 'mdo', 'MD17G1022900' => 'mdo', 'Medtr3g096150' => 'mtr', 'Medtr4g115070' => 'mtr', 'Medtr7g033325' => 'mtr', 'Medtr8g089840' => 'mtr', 'MELO3C010319.2' => 'cme', 'MELO3C011944.2' => 'cme', 'MELO3C021589.2' => 'cme', 'Migut.E00207' => 'egut', 'Migut.H00067' => 'egut', 'Migut.K00433' => 'egut', 'Migut.K00606' => 'egut', 'Migut.K01410' => 'egut', 'MSTRG.13347' => 'ama', 'MSTRG.24045' => 'ama', 'MSTRG.2428' => 'ama', 'MSTRG.26410' => 'ama', 'MSTRG.3139' => 'ama', 'MSTRG.3286' => 'ama', 'MSTRG.563' => 'ama', 'MSTRG.7941' => 'ama', 'Nitab4.5_0000028g0060' => 'nta', 'Nitab4.5_0000065g0260' => 'nta', 'Nitab4.5_0000112g0060' => 'nta', 'Nitab4.5_0000489g0120' => 'nta', 'Nitab4.5_0001776g0050' => 'nta', 'Nitab4.5_0001854g0010' => 'nta', 'Nitab4.5_0001860g0020' => 'nta', 'Nitab4.5_0004352g0010' => 'nta', 'Nitab4.5_0008716g0020' => 'nta', 'Nitab4.5_0008922g0010' => 'nta', 'Nn3g16693' => 'nnu', 'Nn4g22596' => 'nnu', 'Nn7g37639' => 'nnu', 'Oeu001701.1' => 'oeu', 'Oeu018149.1' => 'oeu', 'Oeu026220.1' => 'oeu', 'Oeu038635.1' => 'oeu', 'Oeu049176.1' => 'oeu', 'Oeu056706.1' => 'oeu', 'Oeu056937.1' => 'oeu', 'Oeu057540.1' => 'oeu', 'Os02g0594900' => 'osa', 'Os02g0595100' => 'osa', 'Os04g0477500' => 'osa', 'Os12g0611900' => 'osa', 'Peaxi162Scf00076g00020' => 'pax', 'Peaxi162Scf00128g00217' => 'pax', 'Peaxi162Scf00129g01640' => 'pax', 'Peaxi162Scf00669g00007' => 'pax', 'Peaxi162Scf00700g00421' => 'pax', 'Peaxi162Scf00801g00038' => 'pax', 'Peaxi162Scf00891g00025' => 'pax', 'PGR083G0909' => 'pgr', 'PGR119G1005' => 'pgr', 'PGR142G2236' => 'pgr', 'PGR142G3388' => 'pgr', 'PGSC0003DMG400004514' => 'stu', 'PGSC0003DMG400012635' => 'stu', 'PGSC0003DMG400015730' => 'stu', 'PGSC0003DMG400018611' => 'stu', 'PGSC0003DMG400030897' => 'stu', 'Phvul.001G254800' => 'pvu', 'Phvul.002G260100' => 'pvu', 'Phvul.003G167600' => 'pvu', 'Phvul.004G005100' => 'pvu', 'Potri.001G343600' => 'ptr', 'Potri.006G066700' => 'ptr', 'Potri.008G186000' => 'ptr', 'Potri.010G046900' => 'ptr', 'Potri.018G127900' => 'ptr', 'Pp3c20_17750' => 'ppa', 'Pp3c24_4380' => 'ppa', 'Prupe.1G245800' => 'ppe', 'Prupe.3G293400' => 'ppe', 'Prupe.7G247400' => 'ppe', 'Psat0s145g0120' => 'psa', 'Psat0s595g0040' => 'psa', 'Psat0s595g0120' => 'psa', 'Psat3g175040' => 'psa', 'Psat7g058120' => 'psa', 'PSO017G0428' => 'pso', 'PSO063G7510' => 'pso', 'PSO067G0046' => 'pso', 'PSO478G1073' => 'pso', 'PSO675G3677' => 'pso', 'PSO675G6558' => 'pso', 'PSO675G7520' => 'pso', 'PSO675G8959' => 'pso', 'QL02p074089' => 'qlo', 'QL02p089614' => 'qlo', 'QL03p057736' => 'qlo', 'RcHm_v2.0_Chr1g0364131' => 'rch', 'RcHm_v2.0_Chr2g0087801' => 'rch', 'RcHm_v2.0_Chr2g0087821' => 'rch', 'RcHm_v2.0_Chr2g0173231' => 'rch', 'RcHm_v2.0_Chr4g0433111' => 'rch', 'Rhsim03G0250300' => 'rsi', 'Rhsim08G0048400' => 'rsi', 'Rhsim10G0014800' => 'rsi', 'Rhsim12G0040100' => 'rsi', 'Rhsim12G0109700' => 'rsi', 'Sabra06G0049600' => 'sbr', 'Sabra08G0141000' => 'sbr', 'Sabra10G0021400' => 'sbr', 'Sabra16G0222900' => 'sbr', 'Sabra18G0108600' => 'sbr', 'SalBow1G0433' => 'sbo', 'SalBow1G2038' => 'sbo', 'SalBow1G5003' => 'sbo', 'SalBow7G1197' => 'sbo', 'SalBow8G3506' => 'sbo', 'Sc03g0007300' => 'sci', 'Sc11g0000950' => 'sci', 'Sc14g0008750' => 'sci', 'Sc18g0000420' => 'sci', 'Sed0006754' => 'sed', 'Sed0008741' => 'sed', 'Sed0017172' => 'sed', 'Sed0018925' => 'sed', 'Sed0023326' => 'sed', 'Sed0025909' => 'sed', 'SEGI_05333' => 'sgi', 'SEGI_10362' => 'sgi', 'SEGI_13380' => 'sgi', 'SEGI_24306' => 'sgi', 'SEGI_29077' => 'sgi', 'SEGI_29095' => 'sgi', 'SEGI_36534' => 'sgi', 'SEGI_37506' => 'sgi', 'SEGI_38321' => 'sgi', 'SGA_v2.0_scaffold307G48031' => 'sas', 'SGA_v2.0_scaffold47G17507' => 'sas', 'SGA_v2.0_scaffold63G21736' => 'sas', 'SGA_v2.0_scaffold87G27070' => 'sas', 'SHI17794' => 'shi', 'SHI28851' => 'shi', 'SMO165G0155' => 'smo', 'SMO340G0217' => 'smo', 'SMO367G1210' => 'smo', 'Solyc02g093430.3' => 'sly', 'Solyc05g013580.4' => 'sly', 'Solyc07g008030.3' => 'sly', 'Solyc12g035470.2' => 'sly', 'Sopen02g038020' => 'spe', 'Sopen05g008490' => 'spe', 'Sopen07g003910' => 'spe', 'Sopen12g015240' => 'spe', 'Sp1g11550' => 'spa', 'Sp2g16710' => 'spa', 'Sp3g00430' => 'spa', 'Sp3g26780' => 'spa', 'Sp5g22900' => 'spa', 'Sp6g29530' => 'spa', 'TAR371G0794' => 'tar', 'TAR374G0164' => 'tar', 'TAR622G0165' => 'tar', 'TAR626G0929' => 'tar', 'TAR629G2155' => 'tar', 'THA.LOC104805282' => 'tha', 'THA.LOC104805363' => 'tha', 'THA.LOC104808968' => 'tha', 'THA.LOC104821093' => 'tha', 'THA.LOC104823953' => 'tha', 'THA.LOC104825562' => 'tha', 'THA.LOC104825665' => 'tha', 'Thecc.02G261400' => 'tca', 'Thecc.04G019200' => 'tca', 'Thecc.09G130400' => 'tca', 'Thhalv10004374m.g' => 'esa', 'Thhalv10007850m.g' => 'esa', 'Thhalv10013782m.g' => 'esa', 'Thhalv10018686m.g' => 'esa', 'Thhalv10020899m.g' => 'esa', 'Thhalv10022755m.g' => 'esa', 'TPR.G23851' => 'tpr', 'TPR.G26500' => 'tpr', 'TPR.G27267' => 'tpr', 'TPR.G32001' => 'tpr', 'TPR.G6251' => 'tpr', 'TPR.G8167' => 'tpr', 'TWI12G1330' => 'twi', 'TWI18G1239' => 'twi', 'TWI34G0979' => 'twi', 'TWI36G0670' => 'twi', 'TWI36G0707' => 'twi', 'TWI56G0233' => 'twi', 'TWI75G1809' => 'twi', 'unitig_21.g20874' => 'ugi', 'unitig_26.g10343' => 'ugi', 'unitig_46.g18392' => 'ugi', 'unitig_52.g17178' => 'ugi', 'unitig_8.g2934' => 'ugi', 'vmacro01122' => 'vma', 'vmacro05875' => 'vma', 'vmacro06147' => 'vma', 'vmacro16191' => 'vma', 'vmacro18293' => 'vma', 'VMungo0251G3707' => 'vmu', 'VMungo0464G1521' => 'vmu', 'VMungo1215G0205' => 'vmu', 'VMungo1383G2484' => 'vmu', 'Zm00001eb079610' => 'zma', 'Zm00001eb135990' => 'zma', 'Zm00001eb183710' => 'zma', 'Zm00001eb246020' => 'zma' ) $gf_id = 'HOM05D001124' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001124' ) $data_identifier = 'HOM05D001124' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 6, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 7, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 21, 'bol' => (int) 10, 'bra' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 6, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 9, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 21, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 8, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 10, 'lsa' => (int) 8, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 8, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 9, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb246020' $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' => 'HOM05D001124', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '548', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02520' => 'bna', 'A03p06630' => 'bna', 'A05p44460' => 'bna', 'A06p08710' => 'bna', 'A06p41090' => 'bna', 'A07p32320' => 'bna', 'A08p32520' => 'bna', 'A09p10360' => 'bna', 'A10p24080' => 'bna', 'Aa31LG11G15250' => 'aar', 'Aa31LG1G1800' => 'aar', 'Aa31LG2G5120' => 'aar', 'Aa31LG2G6070' => 'aar', 'Aa31LG5G10770' => 'aar', 'Aa31sc61G90' => 'aar', 'Actinidia01352' => 'ach', 'Actinidia05983' => 'ach', 'Actinidia08133' => 'ach', 'Actinidia15101' => 'ach', 'Actinidia26379' => 'ach', 'Actinidia35778' => 'ach', 'Actinidia36123' => 'ach', 'Actinidia37436' => 'ach', 'Actinidia38730' => 'ach', 'Ah.02g128210' => 'amhyb', 'Ah.03g132990' => 'amhyb', 'Ah.14g079410' => 'amhyb', 'AL1G24640' => 'aly', 'AL2G26680' => 'aly', 'AL3G10530' => 'aly', 'AL3G45230' => 'aly', 'AL5G15230' => 'aly', 'AL5G16960' => 'aly', 'AL6G25210' => 'aly', 'Aqoxy2G00441' => 'aox', 'Aqoxy3G01236' => 'aox', 'Aqoxy5G03746' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3RQ047' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C7GMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9C8JER' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MBL6KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YXCZ83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZANX40' => 'arhy', 'AT1G12990' => 'ath', 'AT1G67880' => 'ath', 'AT2G13290' => 'ath', 'AT3G01620' => 'ath', 'AT3G26445' => 'ath', 'AT3G27540' => 'ath', 'AT5G14480' => 'ath', 'ATR0824G026' => 'atr', 'ATR1098G019' => 'atr', 'Atru.chr11.2145' => 'acertr', 'Atru.chr2.3636' => 'acertr', 'Atru.chr2.3644' => 'acertr', 'Atru.chr6.2422' => 'acertr', 'Atru.chr7.1112' => 'acertr', 'AUR62005469' => 'cqu', 'AUR62011166' => 'cqu', 'AUR62013319' => 'cqu', 'AUR62024273' => 'cqu', 'AUR62028420' => 'cqu', 'AUR62041942' => 'cqu', 'BcaB01g04969' => 'bca', 'BcaB01g06371' => 'bca', 'BcaB02g11494' => 'bca', 'BcaB03g15382' => 'bca', 'BcaB08g36994' => 'bca', 'BcaC03g13477' => 'bca', 'BcaC03g13478' => 'bca', 'BcaC03g13480' => 'bca', 'BcaC03g13481' => 'bca', 'BcaC03g13486' => 'bca', 'BcaC04g19031' => 'bca', 'BcaC04g23085' => 'bca', 'BcaC05g25094' => 'bca', 'BcaC05g25096' => 'bca', 'BcaC05g25138' => 'bca', 'BcaC05g30416' => 'bca', 'BcaC05g30455' => 'bca', 'BcaC06g30979' => 'bca', 'BcaC06g33805' => 'bca', 'BcaC08g46021' => 'bca', 'BcaNung03154' => 'bca', 'BolC2t06623H' => 'bol', 'BolC2t06632H' => 'bol', 'BolC2t06635H' => 'bol', 'BolC2t06638H' => 'bol', 'BolC3t13266H' => 'bol', 'BolC5t29776H' => 'bol', 'BolC6t38912H' => 'bol', 'BolC7t44183H' => 'bol', 'BolC9t54123H' => 'bol', 'BolC9t59107H' => 'bol', 'BraA02t05221Z' => 'bra', 'BraA03t09996Z' => 'bra', 'BraA05t23210Z' => 'bra', 'BraA06t24068Z' => 'bra', 'BraA06t27032Z' => 'bra', 'BraA08t35176Z' => 'bra', 'BraA09t36680Z' => 'bra', 'BraA10t44471Z' => 'bra', 'C02p06760' => 'bna', 'C02p06890' => 'bna', 'C02p07010' => 'bna', 'C03p07660' => 'bna', 'C05p10300' => 'bna', 'C06p38150' => 'bna', 'C07p36650' => 'bna', 'C08p15770' => 'bna', 'C09p12300' => 'bna', 'C09p62700' => 'bna', 'C09p75040' => 'bna', 'CAN.G13.1' => 'can', 'CAN.G138.4' => 'can', 'CAN.G44.6' => 'can', 'CAN.G473.19' => 'can', 'CANSAT01G0835' => 'cansat', 'CANSAT11G0246' => 'cansat', 'CANSAT11G1766' => 'cansat', 'CANSAT64G1954' => 'cansat', 'CARHR013330' => 'chi', 'CARHR060530' => 'chi', 'CARHR075300' => 'chi', 'CARHR105120' => 'chi', 'CARHR148910' => 'chi', 'CARHR198830' => 'chi', 'Carub.0001s1275' => 'cru', 'Carub.0002s1437' => 'cru', 'Carub.0003s0044' => 'cru', 'Carub.0003s2787' => 'cru', 'Carub.0005s0597' => 'cru', 'Carub.0006s1266' => 'cru', 'Ca_06935_v3' => 'car', 'Ca_13559_v3' => 'car', 'Ca_16941_v3' => 'car', 'Ca_16960_v3' => 'car', 'Ca_17775_v3' => 'car', 'Ca_30464_v3' => 'car', 'Cc06_g08160' => 'ccan', 'Cc07_g01520' => 'ccan', 'Cc11_g15810' => 'ccan', 'CDE02G2840' => 'cde', 'CDE03G0093' => 'cde', 'CDE04G2127' => 'cde', 'CDE07G1857' => 'cde', 'CDE09G1246' => 'cde', 'Cfa003412' => 'cfa', 'Cfa007341' => 'cfa', 'Cfa009220' => 'cfa', 'Ciclev10008737m.g' => 'ccl', 'Ciclev10015565m.g' => 'ccl', 'Ciclev10031761m.g' => 'ccl', 'CiPaw.03G045300' => 'cil', 'CiPaw.03G247200' => 'cil', 'CiPaw.04G029500' => 'cil', 'CiPaw.04G174000' => 'cil', 'CiPaw.05G181200' => 'cil', 'CiPaw.06G067100' => 'cil', 'ClCG05G025800' => 'cla', 'ClCG06G011400' => 'cla', 'ClCG09G019360' => 'cla', 'COL.COLO4_04827' => 'col', 'COL.COLO4_29170' => 'col', 'COL.COLO4_35131' => 'col', 'COL.COLO4_35132' => 'col', 'Cpa.g.sc33.32' => 'cpa', 'Cpa.g.sc46.29' => 'cpa', 'Cpa.g.sc796.1' => 'cpa', 'CsaV3_1G030420' => 'csa', 'CsaV3_5G027050' => 'csa', 'CsaV3_5G031040' => 'csa', 'CsaV3_UNG023130' => 'csa', 'CSS0007726' => 'camsi', 'CSS0016433' => 'camsi', 'CSS0017656' => 'camsi', 'CSS0025364' => 'camsi', 'CSS0027582' => 'camsi', 'CSS0047288' => 'camsi', 'CSS0049950' => 'camsi', 'DCAR_003843' => 'dca', 'DCAR_007052' => 'dca', 'DCAR_020884' => 'dca', 'DCAR_021730' => 'dca', 'DCAR_024423' => 'dca', 'DCAR_026509' => 'dca', 'DCAR_031158' => 'dca', 'Dinv14728' => 'din', 'Dinv15219' => 'din', 'Dinv25728' => 'din', 'Dinv33428' => 'din', 'Dinv36489' => 'din', 'Dinv41486' => 'din', 'Duzib147G0469' => 'dzi', 'Duzib168G0060' => 'dzi', 'Duzib187G1215' => 'dzi', 'Duzib248G0692' => 'dzi', 'Duzib251G0767' => 'dzi', 'Duzib264G0446' => 'dzi', 'Duzib268G0691' => 'dzi', 'ECA232G4767' => 'eca', 'ECA233G2838' => 'eca', 'ECA234G0391' => 'eca', 'ECA234G0857' => 'eca', 'ECA236G1593' => 'eca', 'ECA238G0565' => 'eca', 'ECA246G1027' => 'eca', 'ECA246G3223' => 'eca', 'ECA246G3470' => 'eca', 'EL10Ac6g13829' => 'bvu', 'EL10Ac6g14093' => 'bvu', 'EL10Ac8g18707' => 'bvu', 'Eucgr.C01369' => 'egr', 'Eucgr.H02492' => 'egr', 'Eucgr.I01733' => 'egr', 'Eucgr.J02255' => 'egr', 'Eucgr.J02257' => 'egr', 'Eucgr.J02258' => 'egr', 'FAN02G1601' => 'fan', 'FAN03G1586' => 'fan', 'FAN03G2986' => 'fan', 'FAN05G4837' => 'fan', 'FAN06G0146' => 'fan', 'FAN07G0858' => 'fan', 'FAN09G3179' => 'fan', 'FAN10G0669' => 'fan', 'FAN12G2358' => 'fan', 'FAN14G4198' => 'fan', 'FAN14G5112' => 'fan', 'FAN17G0342' => 'fan', 'FAN19G0342' => 'fan', 'FAN19G0962' => 'fan', 'FAN19G1101' => 'fan', 'FAN19G1872' => 'fan', 'FAN22G0356' => 'fan', 'FAN23G0744' => 'fan', 'FAN23G1914' => 'fan', 'FAN26G0032' => 'fan', 'FAN28G0625' => 'fan', 'FvH4_1g02710' => 'fve', 'FvH4_1g02720' => 'fve', 'FvH4_4g25670' => 'fve', 'FvH4_6g51700' => 'fve', 'FvH4_7g20170' => 'fve', 'Glyma.05G175000' => 'gma', 'Glyma.08G132300' => 'gma', 'Glyma.11G243000' => 'gma', 'Glyma.13G158900' => 'gma', 'Glyma.17G112400' => 'gma', 'Glyma.18G014100' => 'gma', 'Glyma.19G003100' => 'gma', 'Glyma.19G056500' => 'gma', 'Gohir.A01G158900' => 'ghi', 'Gohir.A05G312600' => 'ghi', 'Gohir.A05G354900' => 'ghi', 'Gohir.A07G037200' => 'ghi', 'Gohir.A09G030000' => 'ghi', 'Gohir.A12G145200' => 'ghi', 'Gohir.D01G151500' => 'ghi', 'Gohir.D04G058300' => 'ghi', 'Gohir.D05G314100' => 'ghi', 'Gohir.D07G041400' => 'ghi', 'Gohir.D09G029700' => 'ghi', 'Gohir.D12G149700' => 'ghi', 'Gorai.001G043800' => 'gra', 'Gorai.002G187800' => 'gra', 'Gorai.006G034700' => 'gra', 'Gorai.008G161200' => 'gra', 'Gorai.009G335700' => 'gra', 'Gorai.012G065000' => 'gra', 'GSVIVG01000535001' => 'vvi', 'GSVIVG01015572001' => 'vvi', 'GSVIVG01032386001' => 'vvi', 'HanXRQChr05g0138531' => 'han', 'HanXRQChr06g0174391' => 'han', 'HanXRQChr07g0199021' => 'han', 'HanXRQChr08g0208211' => 'han', 'HanXRQChr09g0255471' => 'han', 'HanXRQChr10g0315791' => 'han', 'HanXRQChr12g0371991' => 'han', 'HanXRQChr15g0475251' => 'han', 'HanXRQChr17g0540001' => 'han', 'HanXRQChr17g0548631' => 'han', 'HanXRQChr17g0569561' => 'han', 'Haze_12256' => 'cav', 'Haze_14756' => 'cav', 'Haze_25528' => 'cav', 'Hma1.2p1_0079F.1_g041020' => 'hma', 'Hma1.2p1_0818F.1_g223260' => 'hma', 'Hma1.2p1_1747F.1_g300530' => 'hma', 'HPP92_004607' => 'vpl', 'HPP92_004608' => 'vpl', 'HPP92_006181' => 'vpl', 'HPP92_012192' => 'vpl', 'HPP92_015680' => 'vpl', 'HPP92_020249' => 'vpl', 'HPP92_021376' => 'vpl', 'HPP92_024275' => 'vpl', 'Hund06031' => 'sun', 'Hund25391' => 'sun', 'Lalb_Chr07g0185371' => 'lal', 'Lalb_Chr07g0185381' => 'lal', 'Lalb_Chr12g0204011' => 'lal', 'Lalb_Chr13g0301671' => 'lal', 'Lalb_Chr14g0362851' => 'lal', 'Lalb_Chr24g0403581' => 'lal', 'Lj1g0000233' => 'lja', 'Lj2g0018120' => 'lja', 'Lj3C621T0' => 'lonja', 'Lj3P1059T14' => 'lonja', 'Lj3P611T9' => 'lonja', 'Lj3P614T13' => 'lonja', 'Lj3P615T5' => 'lonja', 'Lj4g0012315' => 'lja', 'Lj4g0026182' => 'lja', 'Lj6P813T16' => 'lonja', 'Lj7C427T7' => 'lonja', 'Lj7C427T8' => 'lonja', 'Lj7P600T41' => 'lonja', 'Lju41C42G17' => 'lonja', 'Lsat_1_v5_gn_0_47300' => 'lsa', 'Lsat_1_v5_gn_2_91280' => 'lsa', 'Lsat_1_v5_gn_3_30561' => 'lsa', 'Lsat_1_v5_gn_4_184321' => 'lsa', 'Lsat_1_v5_gn_4_4041' => 'lsa', 'Lsat_1_v5_gn_5_92000' => 'lsa', 'Lsat_1_v5_gn_8_152940' => 'lsa', 'Lsat_1_v5_gn_8_62401' => 'lsa', 'Manes.06G055900' => 'mes', 'Manes.12G022200' => 'mes', 'Manes.13G023300' => 'mes', 'Manes.14G115000' => 'mes', 'Manes.15G151700' => 'mes', 'Manes.17G111300' => 'mes', 'Mapoly0226s0009' => 'mpo', 'MBI02_g25363_MAGBIO' => 'mbi', 'MBI06_g00027_MAGBIO' => 'mbi', 'MBI10_g13034_MAGBIO' => 'mbi', 'MD09G1023400' => 'mdo', 'MD13G1100100' => 'mdo', 'MD15G1169200' => 'mdo', 'MD16G1101100' => 'mdo', 'MD17G1022900' => 'mdo', 'Medtr3g096150' => 'mtr', 'Medtr4g115070' => 'mtr', 'Medtr7g033325' => 'mtr', 'Medtr8g089840' => 'mtr', 'MELO3C010319.2' => 'cme', 'MELO3C011944.2' => 'cme', 'MELO3C021589.2' => 'cme', 'Migut.E00207' => 'egut', 'Migut.H00067' => 'egut', 'Migut.K00433' => 'egut', 'Migut.K00606' => 'egut', 'Migut.K01410' => 'egut', 'MSTRG.13347' => 'ama', 'MSTRG.24045' => 'ama', 'MSTRG.2428' => 'ama', 'MSTRG.26410' => 'ama', 'MSTRG.3139' => 'ama', 'MSTRG.3286' => 'ama', 'MSTRG.563' => 'ama', 'MSTRG.7941' => 'ama', 'Nitab4.5_0000028g0060' => 'nta', 'Nitab4.5_0000065g0260' => 'nta', 'Nitab4.5_0000112g0060' => 'nta', 'Nitab4.5_0000489g0120' => 'nta', 'Nitab4.5_0001776g0050' => 'nta', 'Nitab4.5_0001854g0010' => 'nta', 'Nitab4.5_0001860g0020' => 'nta', 'Nitab4.5_0004352g0010' => 'nta', 'Nitab4.5_0008716g0020' => 'nta', 'Nitab4.5_0008922g0010' => 'nta', 'Nn3g16693' => 'nnu', 'Nn4g22596' => 'nnu', 'Nn7g37639' => 'nnu', 'Oeu001701.1' => 'oeu', 'Oeu018149.1' => 'oeu', 'Oeu026220.1' => 'oeu', 'Oeu038635.1' => 'oeu', 'Oeu049176.1' => 'oeu', 'Oeu056706.1' => 'oeu', 'Oeu056937.1' => 'oeu', 'Oeu057540.1' => 'oeu', 'Os02g0594900' => 'osa', 'Os02g0595100' => 'osa', 'Os04g0477500' => 'osa', 'Os12g0611900' => 'osa', 'Peaxi162Scf00076g00020' => 'pax', 'Peaxi162Scf00128g00217' => 'pax', 'Peaxi162Scf00129g01640' => 'pax', 'Peaxi162Scf00669g00007' => 'pax', 'Peaxi162Scf00700g00421' => 'pax', 'Peaxi162Scf00801g00038' => 'pax', 'Peaxi162Scf00891g00025' => 'pax', 'PGR083G0909' => 'pgr', 'PGR119G1005' => 'pgr', 'PGR142G2236' => 'pgr', 'PGR142G3388' => 'pgr', 'PGSC0003DMG400004514' => 'stu', 'PGSC0003DMG400012635' => 'stu', 'PGSC0003DMG400015730' => 'stu', 'PGSC0003DMG400018611' => 'stu', 'PGSC0003DMG400030897' => 'stu', 'Phvul.001G254800' => 'pvu', 'Phvul.002G260100' => 'pvu', 'Phvul.003G167600' => 'pvu', 'Phvul.004G005100' => 'pvu', 'Potri.001G343600' => 'ptr', 'Potri.006G066700' => 'ptr', 'Potri.008G186000' => 'ptr', 'Potri.010G046900' => 'ptr', 'Potri.018G127900' => 'ptr', 'Pp3c20_17750' => 'ppa', 'Pp3c24_4380' => 'ppa', 'Prupe.1G245800' => 'ppe', 'Prupe.3G293400' => 'ppe', 'Prupe.7G247400' => 'ppe', 'Psat0s145g0120' => 'psa', 'Psat0s595g0040' => 'psa', 'Psat0s595g0120' => 'psa', 'Psat3g175040' => 'psa', 'Psat7g058120' => 'psa', 'PSO017G0428' => 'pso', 'PSO063G7510' => 'pso', 'PSO067G0046' => 'pso', 'PSO478G1073' => 'pso', 'PSO675G3677' => 'pso', 'PSO675G6558' => 'pso', 'PSO675G7520' => 'pso', 'PSO675G8959' => 'pso', 'QL02p074089' => 'qlo', 'QL02p089614' => 'qlo', 'QL03p057736' => 'qlo', 'RcHm_v2.0_Chr1g0364131' => 'rch', 'RcHm_v2.0_Chr2g0087801' => 'rch', 'RcHm_v2.0_Chr2g0087821' => 'rch', 'RcHm_v2.0_Chr2g0173231' => 'rch', 'RcHm_v2.0_Chr4g0433111' => 'rch', 'Rhsim03G0250300' => 'rsi', 'Rhsim08G0048400' => 'rsi', 'Rhsim10G0014800' => 'rsi', 'Rhsim12G0040100' => 'rsi', 'Rhsim12G0109700' => 'rsi', 'Sabra06G0049600' => 'sbr', 'Sabra08G0141000' => 'sbr', 'Sabra10G0021400' => 'sbr', 'Sabra16G0222900' => 'sbr', 'Sabra18G0108600' => 'sbr', 'SalBow1G0433' => 'sbo', 'SalBow1G2038' => 'sbo', 'SalBow1G5003' => 'sbo', 'SalBow7G1197' => 'sbo', 'SalBow8G3506' => 'sbo', 'Sc03g0007300' => 'sci', 'Sc11g0000950' => 'sci', 'Sc14g0008750' => 'sci', 'Sc18g0000420' => 'sci', 'Sed0006754' => 'sed', 'Sed0008741' => 'sed', 'Sed0017172' => 'sed', 'Sed0018925' => 'sed', 'Sed0023326' => 'sed', 'Sed0025909' => 'sed', 'SEGI_05333' => 'sgi', 'SEGI_10362' => 'sgi', 'SEGI_13380' => 'sgi', 'SEGI_24306' => 'sgi', 'SEGI_29077' => 'sgi', 'SEGI_29095' => 'sgi', 'SEGI_36534' => 'sgi', 'SEGI_37506' => 'sgi', 'SEGI_38321' => 'sgi', 'SGA_v2.0_scaffold307G48031' => 'sas', 'SGA_v2.0_scaffold47G17507' => 'sas', 'SGA_v2.0_scaffold63G21736' => 'sas', 'SGA_v2.0_scaffold87G27070' => 'sas', 'SHI17794' => 'shi', 'SHI28851' => 'shi', 'SMO165G0155' => 'smo', 'SMO340G0217' => 'smo', 'SMO367G1210' => 'smo', 'Solyc02g093430.3' => 'sly', 'Solyc05g013580.4' => 'sly', 'Solyc07g008030.3' => 'sly', 'Solyc12g035470.2' => 'sly', 'Sopen02g038020' => 'spe', 'Sopen05g008490' => 'spe', 'Sopen07g003910' => 'spe', 'Sopen12g015240' => 'spe', 'Sp1g11550' => 'spa', 'Sp2g16710' => 'spa', 'Sp3g00430' => 'spa', 'Sp3g26780' => 'spa', 'Sp5g22900' => 'spa', 'Sp6g29530' => 'spa', 'TAR371G0794' => 'tar', 'TAR374G0164' => 'tar', 'TAR622G0165' => 'tar', 'TAR626G0929' => 'tar', 'TAR629G2155' => 'tar', 'THA.LOC104805282' => 'tha', 'THA.LOC104805363' => 'tha', 'THA.LOC104808968' => 'tha', 'THA.LOC104821093' => 'tha', 'THA.LOC104823953' => 'tha', 'THA.LOC104825562' => 'tha', 'THA.LOC104825665' => 'tha', 'Thecc.02G261400' => 'tca', 'Thecc.04G019200' => 'tca', 'Thecc.09G130400' => 'tca', 'Thhalv10004374m.g' => 'esa', 'Thhalv10007850m.g' => 'esa', 'Thhalv10013782m.g' => 'esa', 'Thhalv10018686m.g' => 'esa', 'Thhalv10020899m.g' => 'esa', 'Thhalv10022755m.g' => 'esa', 'TPR.G23851' => 'tpr', 'TPR.G26500' => 'tpr', 'TPR.G27267' => 'tpr', 'TPR.G32001' => 'tpr', 'TPR.G6251' => 'tpr', 'TPR.G8167' => 'tpr', 'TWI12G1330' => 'twi', 'TWI18G1239' => 'twi', 'TWI34G0979' => 'twi', 'TWI36G0670' => 'twi', 'TWI36G0707' => 'twi', 'TWI56G0233' => 'twi', 'TWI75G1809' => 'twi', 'unitig_21.g20874' => 'ugi', 'unitig_26.g10343' => 'ugi', 'unitig_46.g18392' => 'ugi', 'unitig_52.g17178' => 'ugi', 'unitig_8.g2934' => 'ugi', 'vmacro01122' => 'vma', 'vmacro05875' => 'vma', 'vmacro06147' => 'vma', 'vmacro16191' => 'vma', 'vmacro18293' => 'vma', 'VMungo0251G3707' => 'vmu', 'VMungo0464G1521' => 'vmu', 'VMungo1215G0205' => 'vmu', 'VMungo1383G2484' => 'vmu', 'Zm00001eb079610' => 'zma', 'Zm00001eb135990' => 'zma', 'Zm00001eb183710' => 'zma', 'Zm00001eb246020' => 'zma' ), 'gf_id' => 'HOM05D001124', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001124' ), 'data_identifier' => 'HOM05D001124', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001124', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '548', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02520' => 'bna', 'A03p06630' => 'bna', 'A05p44460' => 'bna', 'A06p08710' => 'bna', 'A06p41090' => 'bna', 'A07p32320' => 'bna', 'A08p32520' => 'bna', 'A09p10360' => 'bna', 'A10p24080' => 'bna', 'Aa31LG11G15250' => 'aar', 'Aa31LG1G1800' => 'aar', 'Aa31LG2G5120' => 'aar', 'Aa31LG2G6070' => 'aar', 'Aa31LG5G10770' => 'aar', 'Aa31sc61G90' => 'aar', 'Actinidia01352' => 'ach', 'Actinidia05983' => 'ach', 'Actinidia08133' => 'ach', 'Actinidia15101' => 'ach', 'Actinidia26379' => 'ach', 'Actinidia35778' => 'ach', 'Actinidia36123' => 'ach', 'Actinidia37436' => 'ach', 'Actinidia38730' => 'ach', 'Ah.02g128210' => 'amhyb', 'Ah.03g132990' => 'amhyb', 'Ah.14g079410' => 'amhyb', 'AL1G24640' => 'aly', 'AL2G26680' => 'aly', 'AL3G10530' => 'aly', 'AL3G45230' => 'aly', 'AL5G15230' => 'aly', 'AL5G16960' => 'aly', 'AL6G25210' => 'aly', 'Aqoxy2G00441' => 'aox', 'Aqoxy3G01236' => 'aox', 'Aqoxy5G03746' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3RQ047' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C7GMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9C8JER' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MBL6KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YXCZ83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZANX40' => 'arhy', 'AT1G12990' => 'ath', 'AT1G67880' => 'ath', 'AT2G13290' => 'ath', 'AT3G01620' => 'ath', 'AT3G26445' => 'ath', 'AT3G27540' => 'ath', 'AT5G14480' => 'ath', 'ATR0824G026' => 'atr', 'ATR1098G019' => 'atr', 'Atru.chr11.2145' => 'acertr', 'Atru.chr2.3636' => 'acertr', 'Atru.chr2.3644' => 'acertr', 'Atru.chr6.2422' => 'acertr', 'Atru.chr7.1112' => 'acertr', 'AUR62005469' => 'cqu', 'AUR62011166' => 'cqu', 'AUR62013319' => 'cqu', 'AUR62024273' => 'cqu', 'AUR62028420' => 'cqu', 'AUR62041942' => 'cqu', 'BcaB01g04969' => 'bca', 'BcaB01g06371' => 'bca', 'BcaB02g11494' => 'bca', 'BcaB03g15382' => 'bca', 'BcaB08g36994' => 'bca', 'BcaC03g13477' => 'bca', 'BcaC03g13478' => 'bca', 'BcaC03g13480' => 'bca', 'BcaC03g13481' => 'bca', 'BcaC03g13486' => 'bca', 'BcaC04g19031' => 'bca', 'BcaC04g23085' => 'bca', 'BcaC05g25094' => 'bca', 'BcaC05g25096' => 'bca', 'BcaC05g25138' => 'bca', 'BcaC05g30416' => 'bca', 'BcaC05g30455' => 'bca', 'BcaC06g30979' => 'bca', 'BcaC06g33805' => 'bca', 'BcaC08g46021' => 'bca', 'BcaNung03154' => 'bca', 'BolC2t06623H' => 'bol', 'BolC2t06632H' => 'bol', 'BolC2t06635H' => 'bol', 'BolC2t06638H' => 'bol', 'BolC3t13266H' => 'bol', 'BolC5t29776H' => 'bol', 'BolC6t38912H' => 'bol', 'BolC7t44183H' => 'bol', 'BolC9t54123H' => 'bol', 'BolC9t59107H' => 'bol', 'BraA02t05221Z' => 'bra', 'BraA03t09996Z' => 'bra', 'BraA05t23210Z' => 'bra', 'BraA06t24068Z' => 'bra', 'BraA06t27032Z' => 'bra', 'BraA08t35176Z' => 'bra', 'BraA09t36680Z' => 'bra', 'BraA10t44471Z' => 'bra', 'C02p06760' => 'bna', 'C02p06890' => 'bna', 'C02p07010' => 'bna', 'C03p07660' => 'bna', 'C05p10300' => 'bna', 'C06p38150' => 'bna', 'C07p36650' => 'bna', 'C08p15770' => 'bna', 'C09p12300' => 'bna', 'C09p62700' => 'bna', 'C09p75040' => 'bna', 'CAN.G13.1' => 'can', 'CAN.G138.4' => 'can', 'CAN.G44.6' => 'can', 'CAN.G473.19' => 'can', 'CANSAT01G0835' => 'cansat', 'CANSAT11G0246' => 'cansat', 'CANSAT11G1766' => 'cansat', 'CANSAT64G1954' => 'cansat', 'CARHR013330' => 'chi', 'CARHR060530' => 'chi', 'CARHR075300' => 'chi', 'CARHR105120' => 'chi', 'CARHR148910' => 'chi', 'CARHR198830' => 'chi', 'Carub.0001s1275' => 'cru', 'Carub.0002s1437' => 'cru', 'Carub.0003s0044' => 'cru', 'Carub.0003s2787' => 'cru', 'Carub.0005s0597' => 'cru', 'Carub.0006s1266' => 'cru', 'Ca_06935_v3' => 'car', 'Ca_13559_v3' => 'car', 'Ca_16941_v3' => 'car', 'Ca_16960_v3' => 'car', 'Ca_17775_v3' => 'car', 'Ca_30464_v3' => 'car', 'Cc06_g08160' => 'ccan', 'Cc07_g01520' => 'ccan', 'Cc11_g15810' => 'ccan', 'CDE02G2840' => 'cde', 'CDE03G0093' => 'cde', 'CDE04G2127' => 'cde', 'CDE07G1857' => 'cde', 'CDE09G1246' => 'cde', 'Cfa003412' => 'cfa', 'Cfa007341' => 'cfa', 'Cfa009220' => 'cfa', 'Ciclev10008737m.g' => 'ccl', 'Ciclev10015565m.g' => 'ccl', 'Ciclev10031761m.g' => 'ccl', 'CiPaw.03G045300' => 'cil', 'CiPaw.03G247200' => 'cil', 'CiPaw.04G029500' => 'cil', 'CiPaw.04G174000' => 'cil', 'CiPaw.05G181200' => 'cil', 'CiPaw.06G067100' => 'cil', 'ClCG05G025800' => 'cla', 'ClCG06G011400' => 'cla', 'ClCG09G019360' => 'cla', 'COL.COLO4_04827' => 'col', 'COL.COLO4_29170' => 'col', 'COL.COLO4_35131' => 'col', 'COL.COLO4_35132' => 'col', 'Cpa.g.sc33.32' => 'cpa', 'Cpa.g.sc46.29' => 'cpa', 'Cpa.g.sc796.1' => 'cpa', 'CsaV3_1G030420' => 'csa', 'CsaV3_5G027050' => 'csa', 'CsaV3_5G031040' => 'csa', 'CsaV3_UNG023130' => 'csa', 'CSS0007726' => 'camsi', 'CSS0016433' => 'camsi', 'CSS0017656' => 'camsi', 'CSS0025364' => 'camsi', 'CSS0027582' => 'camsi', 'CSS0047288' => 'camsi', 'CSS0049950' => 'camsi', 'DCAR_003843' => 'dca', 'DCAR_007052' => 'dca', 'DCAR_020884' => 'dca', 'DCAR_021730' => 'dca', 'DCAR_024423' => 'dca', 'DCAR_026509' => 'dca', 'DCAR_031158' => 'dca', 'Dinv14728' => 'din', 'Dinv15219' => 'din', 'Dinv25728' => 'din', 'Dinv33428' => 'din', 'Dinv36489' => 'din', 'Dinv41486' => 'din', 'Duzib147G0469' => 'dzi', 'Duzib168G0060' => 'dzi', 'Duzib187G1215' => 'dzi', 'Duzib248G0692' => 'dzi', 'Duzib251G0767' => 'dzi', 'Duzib264G0446' => 'dzi', 'Duzib268G0691' => 'dzi', 'ECA232G4767' => 'eca', 'ECA233G2838' => 'eca', 'ECA234G0391' => 'eca', 'ECA234G0857' => 'eca', 'ECA236G1593' => 'eca', 'ECA238G0565' => 'eca', 'ECA246G1027' => 'eca', 'ECA246G3223' => 'eca', 'ECA246G3470' => 'eca', 'EL10Ac6g13829' => 'bvu', 'EL10Ac6g14093' => 'bvu', 'EL10Ac8g18707' => 'bvu', 'Eucgr.C01369' => 'egr', 'Eucgr.H02492' => 'egr', 'Eucgr.I01733' => 'egr', 'Eucgr.J02255' => 'egr', 'Eucgr.J02257' => 'egr', 'Eucgr.J02258' => 'egr', 'FAN02G1601' => 'fan', 'FAN03G1586' => 'fan', 'FAN03G2986' => 'fan', 'FAN05G4837' => 'fan', 'FAN06G0146' => 'fan', 'FAN07G0858' => 'fan', 'FAN09G3179' => 'fan', 'FAN10G0669' => 'fan', 'FAN12G2358' => 'fan', 'FAN14G4198' => 'fan', 'FAN14G5112' => 'fan', 'FAN17G0342' => 'fan', 'FAN19G0342' => 'fan', 'FAN19G0962' => 'fan', 'FAN19G1101' => 'fan', 'FAN19G1872' => 'fan', 'FAN22G0356' => 'fan', 'FAN23G0744' => 'fan', 'FAN23G1914' => 'fan', 'FAN26G0032' => 'fan', 'FAN28G0625' => 'fan', 'FvH4_1g02710' => 'fve', 'FvH4_1g02720' => 'fve', 'FvH4_4g25670' => 'fve', 'FvH4_6g51700' => 'fve', 'FvH4_7g20170' => 'fve', 'Glyma.05G175000' => 'gma', 'Glyma.08G132300' => 'gma', 'Glyma.11G243000' => 'gma', 'Glyma.13G158900' => 'gma', 'Glyma.17G112400' => 'gma', 'Glyma.18G014100' => 'gma', 'Glyma.19G003100' => 'gma', 'Glyma.19G056500' => 'gma', 'Gohir.A01G158900' => 'ghi', 'Gohir.A05G312600' => 'ghi', 'Gohir.A05G354900' => 'ghi', 'Gohir.A07G037200' => 'ghi', 'Gohir.A09G030000' => 'ghi', 'Gohir.A12G145200' => 'ghi', 'Gohir.D01G151500' => 'ghi', 'Gohir.D04G058300' => 'ghi', 'Gohir.D05G314100' => 'ghi', 'Gohir.D07G041400' => 'ghi', 'Gohir.D09G029700' => 'ghi', 'Gohir.D12G149700' => 'ghi', 'Gorai.001G043800' => 'gra', 'Gorai.002G187800' => 'gra', 'Gorai.006G034700' => 'gra', 'Gorai.008G161200' => 'gra', 'Gorai.009G335700' => 'gra', 'Gorai.012G065000' => 'gra', 'GSVIVG01000535001' => 'vvi', 'GSVIVG01015572001' => 'vvi', 'GSVIVG01032386001' => 'vvi', 'HanXRQChr05g0138531' => 'han', 'HanXRQChr06g0174391' => 'han', 'HanXRQChr07g0199021' => 'han', 'HanXRQChr08g0208211' => 'han', 'HanXRQChr09g0255471' => 'han', 'HanXRQChr10g0315791' => 'han', 'HanXRQChr12g0371991' => 'han', 'HanXRQChr15g0475251' => 'han', 'HanXRQChr17g0540001' => 'han', 'HanXRQChr17g0548631' => 'han', 'HanXRQChr17g0569561' => 'han', 'Haze_12256' => 'cav', 'Haze_14756' => 'cav', 'Haze_25528' => 'cav', 'Hma1.2p1_0079F.1_g041020' => 'hma', 'Hma1.2p1_0818F.1_g223260' => 'hma', 'Hma1.2p1_1747F.1_g300530' => 'hma', 'HPP92_004607' => 'vpl', 'HPP92_004608' => 'vpl', 'HPP92_006181' => 'vpl', 'HPP92_012192' => 'vpl', 'HPP92_015680' => 'vpl', 'HPP92_020249' => 'vpl', 'HPP92_021376' => 'vpl', 'HPP92_024275' => 'vpl', 'Hund06031' => 'sun', 'Hund25391' => 'sun', 'Lalb_Chr07g0185371' => 'lal', 'Lalb_Chr07g0185381' => 'lal', 'Lalb_Chr12g0204011' => 'lal', 'Lalb_Chr13g0301671' => 'lal', 'Lalb_Chr14g0362851' => 'lal', 'Lalb_Chr24g0403581' => 'lal', 'Lj1g0000233' => 'lja', 'Lj2g0018120' => 'lja', 'Lj3C621T0' => 'lonja', 'Lj3P1059T14' => 'lonja', 'Lj3P611T9' => 'lonja', 'Lj3P614T13' => 'lonja', 'Lj3P615T5' => 'lonja', 'Lj4g0012315' => 'lja', 'Lj4g0026182' => 'lja', 'Lj6P813T16' => 'lonja', 'Lj7C427T7' => 'lonja', 'Lj7C427T8' => 'lonja', 'Lj7P600T41' => 'lonja', 'Lju41C42G17' => 'lonja', 'Lsat_1_v5_gn_0_47300' => 'lsa', 'Lsat_1_v5_gn_2_91280' => 'lsa', 'Lsat_1_v5_gn_3_30561' => 'lsa', 'Lsat_1_v5_gn_4_184321' => 'lsa', 'Lsat_1_v5_gn_4_4041' => 'lsa', 'Lsat_1_v5_gn_5_92000' => 'lsa', 'Lsat_1_v5_gn_8_152940' => 'lsa', 'Lsat_1_v5_gn_8_62401' => 'lsa', 'Manes.06G055900' => 'mes', 'Manes.12G022200' => 'mes', 'Manes.13G023300' => 'mes', 'Manes.14G115000' => 'mes', 'Manes.15G151700' => 'mes', 'Manes.17G111300' => 'mes', 'Mapoly0226s0009' => 'mpo', 'MBI02_g25363_MAGBIO' => 'mbi', 'MBI06_g00027_MAGBIO' => 'mbi', 'MBI10_g13034_MAGBIO' => 'mbi', 'MD09G1023400' => 'mdo', 'MD13G1100100' => 'mdo', 'MD15G1169200' => 'mdo', 'MD16G1101100' => 'mdo', 'MD17G1022900' => 'mdo', 'Medtr3g096150' => 'mtr', 'Medtr4g115070' => 'mtr', 'Medtr7g033325' => 'mtr', 'Medtr8g089840' => 'mtr', 'MELO3C010319.2' => 'cme', 'MELO3C011944.2' => 'cme', 'MELO3C021589.2' => 'cme', 'Migut.E00207' => 'egut', 'Migut.H00067' => 'egut', 'Migut.K00433' => 'egut', 'Migut.K00606' => 'egut', 'Migut.K01410' => 'egut', 'MSTRG.13347' => 'ama', 'MSTRG.24045' => 'ama', 'MSTRG.2428' => 'ama', 'MSTRG.26410' => 'ama', 'MSTRG.3139' => 'ama', 'MSTRG.3286' => 'ama', 'MSTRG.563' => 'ama', 'MSTRG.7941' => 'ama', 'Nitab4.5_0000028g0060' => 'nta', 'Nitab4.5_0000065g0260' => 'nta', 'Nitab4.5_0000112g0060' => 'nta', 'Nitab4.5_0000489g0120' => 'nta', 'Nitab4.5_0001776g0050' => 'nta', 'Nitab4.5_0001854g0010' => 'nta', 'Nitab4.5_0001860g0020' => 'nta', 'Nitab4.5_0004352g0010' => 'nta', 'Nitab4.5_0008716g0020' => 'nta', 'Nitab4.5_0008922g0010' => 'nta', 'Nn3g16693' => 'nnu', 'Nn4g22596' => 'nnu', 'Nn7g37639' => 'nnu', 'Oeu001701.1' => 'oeu', 'Oeu018149.1' => 'oeu', 'Oeu026220.1' => 'oeu', 'Oeu038635.1' => 'oeu', 'Oeu049176.1' => 'oeu', 'Oeu056706.1' => 'oeu', 'Oeu056937.1' => 'oeu', 'Oeu057540.1' => 'oeu', 'Os02g0594900' => 'osa', 'Os02g0595100' => 'osa', 'Os04g0477500' => 'osa', 'Os12g0611900' => 'osa', 'Peaxi162Scf00076g00020' => 'pax', 'Peaxi162Scf00128g00217' => 'pax', 'Peaxi162Scf00129g01640' => 'pax', 'Peaxi162Scf00669g00007' => 'pax', 'Peaxi162Scf00700g00421' => 'pax', 'Peaxi162Scf00801g00038' => 'pax', 'Peaxi162Scf00891g00025' => 'pax', 'PGR083G0909' => 'pgr', 'PGR119G1005' => 'pgr', 'PGR142G2236' => 'pgr', 'PGR142G3388' => 'pgr', 'PGSC0003DMG400004514' => 'stu', 'PGSC0003DMG400012635' => 'stu', 'PGSC0003DMG400015730' => 'stu', 'PGSC0003DMG400018611' => 'stu', 'PGSC0003DMG400030897' => 'stu', 'Phvul.001G254800' => 'pvu', 'Phvul.002G260100' => 'pvu', 'Phvul.003G167600' => 'pvu', 'Phvul.004G005100' => 'pvu', 'Potri.001G343600' => 'ptr', 'Potri.006G066700' => 'ptr', 'Potri.008G186000' => 'ptr', 'Potri.010G046900' => 'ptr', 'Potri.018G127900' => 'ptr', 'Pp3c20_17750' => 'ppa', 'Pp3c24_4380' => 'ppa', 'Prupe.1G245800' => 'ppe', 'Prupe.3G293400' => 'ppe', 'Prupe.7G247400' => 'ppe', 'Psat0s145g0120' => 'psa', 'Psat0s595g0040' => 'psa', 'Psat0s595g0120' => 'psa', 'Psat3g175040' => 'psa', 'Psat7g058120' => 'psa', 'PSO017G0428' => 'pso', 'PSO063G7510' => 'pso', 'PSO067G0046' => 'pso', 'PSO478G1073' => 'pso', 'PSO675G3677' => 'pso', 'PSO675G6558' => 'pso', 'PSO675G7520' => 'pso', 'PSO675G8959' => 'pso', 'QL02p074089' => 'qlo', 'QL02p089614' => 'qlo', 'QL03p057736' => 'qlo', 'RcHm_v2.0_Chr1g0364131' => 'rch', 'RcHm_v2.0_Chr2g0087801' => 'rch', 'RcHm_v2.0_Chr2g0087821' => 'rch', 'RcHm_v2.0_Chr2g0173231' => 'rch', 'RcHm_v2.0_Chr4g0433111' => 'rch', 'Rhsim03G0250300' => 'rsi', 'Rhsim08G0048400' => 'rsi', 'Rhsim10G0014800' => 'rsi', 'Rhsim12G0040100' => 'rsi', 'Rhsim12G0109700' => 'rsi', 'Sabra06G0049600' => 'sbr', 'Sabra08G0141000' => 'sbr', 'Sabra10G0021400' => 'sbr', 'Sabra16G0222900' => 'sbr', 'Sabra18G0108600' => 'sbr', 'SalBow1G0433' => 'sbo', 'SalBow1G2038' => 'sbo', 'SalBow1G5003' => 'sbo', 'SalBow7G1197' => 'sbo', 'SalBow8G3506' => 'sbo', 'Sc03g0007300' => 'sci', 'Sc11g0000950' => 'sci', 'Sc14g0008750' => 'sci', 'Sc18g0000420' => 'sci', 'Sed0006754' => 'sed', 'Sed0008741' => 'sed', 'Sed0017172' => 'sed', 'Sed0018925' => 'sed', 'Sed0023326' => 'sed', 'Sed0025909' => 'sed', 'SEGI_05333' => 'sgi', 'SEGI_10362' => 'sgi', 'SEGI_13380' => 'sgi', 'SEGI_24306' => 'sgi', 'SEGI_29077' => 'sgi', 'SEGI_29095' => 'sgi', 'SEGI_36534' => 'sgi', 'SEGI_37506' => 'sgi', 'SEGI_38321' => 'sgi', 'SGA_v2.0_scaffold307G48031' => 'sas', 'SGA_v2.0_scaffold47G17507' => 'sas', 'SGA_v2.0_scaffold63G21736' => 'sas', 'SGA_v2.0_scaffold87G27070' => 'sas', 'SHI17794' => 'shi', 'SHI28851' => 'shi', 'SMO165G0155' => 'smo', 'SMO340G0217' => 'smo', 'SMO367G1210' => 'smo', 'Solyc02g093430.3' => 'sly', 'Solyc05g013580.4' => 'sly', 'Solyc07g008030.3' => 'sly', 'Solyc12g035470.2' => 'sly', 'Sopen02g038020' => 'spe', 'Sopen05g008490' => 'spe', 'Sopen07g003910' => 'spe', 'Sopen12g015240' => 'spe', 'Sp1g11550' => 'spa', 'Sp2g16710' => 'spa', 'Sp3g00430' => 'spa', 'Sp3g26780' => 'spa', 'Sp5g22900' => 'spa', 'Sp6g29530' => 'spa', 'TAR371G0794' => 'tar', 'TAR374G0164' => 'tar', 'TAR622G0165' => 'tar', 'TAR626G0929' => 'tar', 'TAR629G2155' => 'tar', 'THA.LOC104805282' => 'tha', 'THA.LOC104805363' => 'tha', 'THA.LOC104808968' => 'tha', 'THA.LOC104821093' => 'tha', 'THA.LOC104823953' => 'tha', 'THA.LOC104825562' => 'tha', 'THA.LOC104825665' => 'tha', 'Thecc.02G261400' => 'tca', 'Thecc.04G019200' => 'tca', 'Thecc.09G130400' => 'tca', 'Thhalv10004374m.g' => 'esa', 'Thhalv10007850m.g' => 'esa', 'Thhalv10013782m.g' => 'esa', 'Thhalv10018686m.g' => 'esa', 'Thhalv10020899m.g' => 'esa', 'Thhalv10022755m.g' => 'esa', 'TPR.G23851' => 'tpr', 'TPR.G26500' => 'tpr', 'TPR.G27267' => 'tpr', 'TPR.G32001' => 'tpr', 'TPR.G6251' => 'tpr', 'TPR.G8167' => 'tpr', 'TWI12G1330' => 'twi', 'TWI18G1239' => 'twi', 'TWI34G0979' => 'twi', 'TWI36G0670' => 'twi', 'TWI36G0707' => 'twi', 'TWI56G0233' => 'twi', 'TWI75G1809' => 'twi', 'unitig_21.g20874' => 'ugi', 'unitig_26.g10343' => 'ugi', 'unitig_46.g18392' => 'ugi', 'unitig_52.g17178' => 'ugi', 'unitig_8.g2934' => 'ugi', 'vmacro01122' => 'vma', 'vmacro05875' => 'vma', 'vmacro06147' => 'vma', 'vmacro16191' => 'vma', 'vmacro18293' => 'vma', 'VMungo0251G3707' => 'vmu', 'VMungo0464G1521' => 'vmu', 'VMungo1215G0205' => 'vmu', 'VMungo1383G2484' => 'vmu', 'Zm00001eb079610' => 'zma', 'Zm00001eb135990' => 'zma', 'Zm00001eb183710' => 'zma', 'Zm00001eb246020' => 'zma' ) $gf_id = 'HOM05D001124' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001124' ) $data_identifier = 'HOM05D001124' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 6, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 7, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 21, 'bol' => (int) 10, 'bra' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 6, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 9, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 21, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 8, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 10, 'lsa' => (int) 8, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 8, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 9, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb246020' $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' => 'HOM05D001124', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '548', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02520' => 'bna', 'A03p06630' => 'bna', 'A05p44460' => 'bna', 'A06p08710' => 'bna', 'A06p41090' => 'bna', 'A07p32320' => 'bna', 'A08p32520' => 'bna', 'A09p10360' => 'bna', 'A10p24080' => 'bna', 'Aa31LG11G15250' => 'aar', 'Aa31LG1G1800' => 'aar', 'Aa31LG2G5120' => 'aar', 'Aa31LG2G6070' => 'aar', 'Aa31LG5G10770' => 'aar', 'Aa31sc61G90' => 'aar', 'Actinidia01352' => 'ach', 'Actinidia05983' => 'ach', 'Actinidia08133' => 'ach', 'Actinidia15101' => 'ach', 'Actinidia26379' => 'ach', 'Actinidia35778' => 'ach', 'Actinidia36123' => 'ach', 'Actinidia37436' => 'ach', 'Actinidia38730' => 'ach', 'Ah.02g128210' => 'amhyb', 'Ah.03g132990' => 'amhyb', 'Ah.14g079410' => 'amhyb', 'AL1G24640' => 'aly', 'AL2G26680' => 'aly', 'AL3G10530' => 'aly', 'AL3G45230' => 'aly', 'AL5G15230' => 'aly', 'AL5G16960' => 'aly', 'AL6G25210' => 'aly', 'Aqoxy2G00441' => 'aox', 'Aqoxy3G01236' => 'aox', 'Aqoxy5G03746' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3RQ047' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C7GMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9C8JER' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MBL6KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YXCZ83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZANX40' => 'arhy', 'AT1G12990' => 'ath', 'AT1G67880' => 'ath', 'AT2G13290' => 'ath', 'AT3G01620' => 'ath', 'AT3G26445' => 'ath', 'AT3G27540' => 'ath', 'AT5G14480' => 'ath', 'ATR0824G026' => 'atr', 'ATR1098G019' => 'atr', 'Atru.chr11.2145' => 'acertr', 'Atru.chr2.3636' => 'acertr', 'Atru.chr2.3644' => 'acertr', 'Atru.chr6.2422' => 'acertr', 'Atru.chr7.1112' => 'acertr', 'AUR62005469' => 'cqu', 'AUR62011166' => 'cqu', 'AUR62013319' => 'cqu', 'AUR62024273' => 'cqu', 'AUR62028420' => 'cqu', 'AUR62041942' => 'cqu', 'BcaB01g04969' => 'bca', 'BcaB01g06371' => 'bca', 'BcaB02g11494' => 'bca', 'BcaB03g15382' => 'bca', 'BcaB08g36994' => 'bca', 'BcaC03g13477' => 'bca', 'BcaC03g13478' => 'bca', 'BcaC03g13480' => 'bca', 'BcaC03g13481' => 'bca', 'BcaC03g13486' => 'bca', 'BcaC04g19031' => 'bca', 'BcaC04g23085' => 'bca', 'BcaC05g25094' => 'bca', 'BcaC05g25096' => 'bca', 'BcaC05g25138' => 'bca', 'BcaC05g30416' => 'bca', 'BcaC05g30455' => 'bca', 'BcaC06g30979' => 'bca', 'BcaC06g33805' => 'bca', 'BcaC08g46021' => 'bca', 'BcaNung03154' => 'bca', 'BolC2t06623H' => 'bol', 'BolC2t06632H' => 'bol', 'BolC2t06635H' => 'bol', 'BolC2t06638H' => 'bol', 'BolC3t13266H' => 'bol', 'BolC5t29776H' => 'bol', 'BolC6t38912H' => 'bol', 'BolC7t44183H' => 'bol', 'BolC9t54123H' => 'bol', 'BolC9t59107H' => 'bol', 'BraA02t05221Z' => 'bra', 'BraA03t09996Z' => 'bra', 'BraA05t23210Z' => 'bra', 'BraA06t24068Z' => 'bra', 'BraA06t27032Z' => 'bra', 'BraA08t35176Z' => 'bra', 'BraA09t36680Z' => 'bra', 'BraA10t44471Z' => 'bra', 'C02p06760' => 'bna', 'C02p06890' => 'bna', 'C02p07010' => 'bna', 'C03p07660' => 'bna', 'C05p10300' => 'bna', 'C06p38150' => 'bna', 'C07p36650' => 'bna', 'C08p15770' => 'bna', 'C09p12300' => 'bna', 'C09p62700' => 'bna', 'C09p75040' => 'bna', 'CAN.G13.1' => 'can', 'CAN.G138.4' => 'can', 'CAN.G44.6' => 'can', 'CAN.G473.19' => 'can', 'CANSAT01G0835' => 'cansat', 'CANSAT11G0246' => 'cansat', 'CANSAT11G1766' => 'cansat', 'CANSAT64G1954' => 'cansat', 'CARHR013330' => 'chi', 'CARHR060530' => 'chi', 'CARHR075300' => 'chi', 'CARHR105120' => 'chi', 'CARHR148910' => 'chi', 'CARHR198830' => 'chi', 'Carub.0001s1275' => 'cru', 'Carub.0002s1437' => 'cru', 'Carub.0003s0044' => 'cru', 'Carub.0003s2787' => 'cru', 'Carub.0005s0597' => 'cru', 'Carub.0006s1266' => 'cru', 'Ca_06935_v3' => 'car', 'Ca_13559_v3' => 'car', 'Ca_16941_v3' => 'car', 'Ca_16960_v3' => 'car', 'Ca_17775_v3' => 'car', 'Ca_30464_v3' => 'car', 'Cc06_g08160' => 'ccan', 'Cc07_g01520' => 'ccan', 'Cc11_g15810' => 'ccan', 'CDE02G2840' => 'cde', 'CDE03G0093' => 'cde', 'CDE04G2127' => 'cde', 'CDE07G1857' => 'cde', 'CDE09G1246' => 'cde', 'Cfa003412' => 'cfa', 'Cfa007341' => 'cfa', 'Cfa009220' => 'cfa', 'Ciclev10008737m.g' => 'ccl', 'Ciclev10015565m.g' => 'ccl', 'Ciclev10031761m.g' => 'ccl', 'CiPaw.03G045300' => 'cil', 'CiPaw.03G247200' => 'cil', 'CiPaw.04G029500' => 'cil', 'CiPaw.04G174000' => 'cil', 'CiPaw.05G181200' => 'cil', 'CiPaw.06G067100' => 'cil', 'ClCG05G025800' => 'cla', 'ClCG06G011400' => 'cla', 'ClCG09G019360' => 'cla', 'COL.COLO4_04827' => 'col', 'COL.COLO4_29170' => 'col', 'COL.COLO4_35131' => 'col', 'COL.COLO4_35132' => 'col', 'Cpa.g.sc33.32' => 'cpa', 'Cpa.g.sc46.29' => 'cpa', 'Cpa.g.sc796.1' => 'cpa', 'CsaV3_1G030420' => 'csa', 'CsaV3_5G027050' => 'csa', 'CsaV3_5G031040' => 'csa', 'CsaV3_UNG023130' => 'csa', 'CSS0007726' => 'camsi', 'CSS0016433' => 'camsi', 'CSS0017656' => 'camsi', 'CSS0025364' => 'camsi', 'CSS0027582' => 'camsi', 'CSS0047288' => 'camsi', 'CSS0049950' => 'camsi', 'DCAR_003843' => 'dca', 'DCAR_007052' => 'dca', 'DCAR_020884' => 'dca', 'DCAR_021730' => 'dca', 'DCAR_024423' => 'dca', 'DCAR_026509' => 'dca', 'DCAR_031158' => 'dca', 'Dinv14728' => 'din', 'Dinv15219' => 'din', 'Dinv25728' => 'din', 'Dinv33428' => 'din', 'Dinv36489' => 'din', 'Dinv41486' => 'din', 'Duzib147G0469' => 'dzi', 'Duzib168G0060' => 'dzi', 'Duzib187G1215' => 'dzi', 'Duzib248G0692' => 'dzi', 'Duzib251G0767' => 'dzi', 'Duzib264G0446' => 'dzi', 'Duzib268G0691' => 'dzi', 'ECA232G4767' => 'eca', 'ECA233G2838' => 'eca', 'ECA234G0391' => 'eca', 'ECA234G0857' => 'eca', 'ECA236G1593' => 'eca', 'ECA238G0565' => 'eca', 'ECA246G1027' => 'eca', 'ECA246G3223' => 'eca', 'ECA246G3470' => 'eca', 'EL10Ac6g13829' => 'bvu', 'EL10Ac6g14093' => 'bvu', 'EL10Ac8g18707' => 'bvu', 'Eucgr.C01369' => 'egr', 'Eucgr.H02492' => 'egr', 'Eucgr.I01733' => 'egr', 'Eucgr.J02255' => 'egr', 'Eucgr.J02257' => 'egr', 'Eucgr.J02258' => 'egr', 'FAN02G1601' => 'fan', 'FAN03G1586' => 'fan', 'FAN03G2986' => 'fan', 'FAN05G4837' => 'fan', 'FAN06G0146' => 'fan', 'FAN07G0858' => 'fan', 'FAN09G3179' => 'fan', 'FAN10G0669' => 'fan', 'FAN12G2358' => 'fan', 'FAN14G4198' => 'fan', 'FAN14G5112' => 'fan', 'FAN17G0342' => 'fan', 'FAN19G0342' => 'fan', 'FAN19G0962' => 'fan', 'FAN19G1101' => 'fan', 'FAN19G1872' => 'fan', 'FAN22G0356' => 'fan', 'FAN23G0744' => 'fan', 'FAN23G1914' => 'fan', 'FAN26G0032' => 'fan', 'FAN28G0625' => 'fan', 'FvH4_1g02710' => 'fve', 'FvH4_1g02720' => 'fve', 'FvH4_4g25670' => 'fve', 'FvH4_6g51700' => 'fve', 'FvH4_7g20170' => 'fve', 'Glyma.05G175000' => 'gma', 'Glyma.08G132300' => 'gma', 'Glyma.11G243000' => 'gma', 'Glyma.13G158900' => 'gma', 'Glyma.17G112400' => 'gma', 'Glyma.18G014100' => 'gma', 'Glyma.19G003100' => 'gma', 'Glyma.19G056500' => 'gma', 'Gohir.A01G158900' => 'ghi', 'Gohir.A05G312600' => 'ghi', 'Gohir.A05G354900' => 'ghi', 'Gohir.A07G037200' => 'ghi', 'Gohir.A09G030000' => 'ghi', 'Gohir.A12G145200' => 'ghi', 'Gohir.D01G151500' => 'ghi', 'Gohir.D04G058300' => 'ghi', 'Gohir.D05G314100' => 'ghi', 'Gohir.D07G041400' => 'ghi', 'Gohir.D09G029700' => 'ghi', 'Gohir.D12G149700' => 'ghi', 'Gorai.001G043800' => 'gra', 'Gorai.002G187800' => 'gra', 'Gorai.006G034700' => 'gra', 'Gorai.008G161200' => 'gra', 'Gorai.009G335700' => 'gra', 'Gorai.012G065000' => 'gra', 'GSVIVG01000535001' => 'vvi', 'GSVIVG01015572001' => 'vvi', 'GSVIVG01032386001' => 'vvi', 'HanXRQChr05g0138531' => 'han', 'HanXRQChr06g0174391' => 'han', 'HanXRQChr07g0199021' => 'han', 'HanXRQChr08g0208211' => 'han', 'HanXRQChr09g0255471' => 'han', 'HanXRQChr10g0315791' => 'han', 'HanXRQChr12g0371991' => 'han', 'HanXRQChr15g0475251' => 'han', 'HanXRQChr17g0540001' => 'han', 'HanXRQChr17g0548631' => 'han', 'HanXRQChr17g0569561' => 'han', 'Haze_12256' => 'cav', 'Haze_14756' => 'cav', 'Haze_25528' => 'cav', 'Hma1.2p1_0079F.1_g041020' => 'hma', 'Hma1.2p1_0818F.1_g223260' => 'hma', 'Hma1.2p1_1747F.1_g300530' => 'hma', 'HPP92_004607' => 'vpl', 'HPP92_004608' => 'vpl', 'HPP92_006181' => 'vpl', 'HPP92_012192' => 'vpl', 'HPP92_015680' => 'vpl', 'HPP92_020249' => 'vpl', 'HPP92_021376' => 'vpl', 'HPP92_024275' => 'vpl', 'Hund06031' => 'sun', 'Hund25391' => 'sun', 'Lalb_Chr07g0185371' => 'lal', 'Lalb_Chr07g0185381' => 'lal', 'Lalb_Chr12g0204011' => 'lal', 'Lalb_Chr13g0301671' => 'lal', 'Lalb_Chr14g0362851' => 'lal', 'Lalb_Chr24g0403581' => 'lal', 'Lj1g0000233' => 'lja', 'Lj2g0018120' => 'lja', 'Lj3C621T0' => 'lonja', 'Lj3P1059T14' => 'lonja', 'Lj3P611T9' => 'lonja', 'Lj3P614T13' => 'lonja', 'Lj3P615T5' => 'lonja', 'Lj4g0012315' => 'lja', 'Lj4g0026182' => 'lja', 'Lj6P813T16' => 'lonja', 'Lj7C427T7' => 'lonja', 'Lj7C427T8' => 'lonja', 'Lj7P600T41' => 'lonja', 'Lju41C42G17' => 'lonja', 'Lsat_1_v5_gn_0_47300' => 'lsa', 'Lsat_1_v5_gn_2_91280' => 'lsa', 'Lsat_1_v5_gn_3_30561' => 'lsa', 'Lsat_1_v5_gn_4_184321' => 'lsa', 'Lsat_1_v5_gn_4_4041' => 'lsa', 'Lsat_1_v5_gn_5_92000' => 'lsa', 'Lsat_1_v5_gn_8_152940' => 'lsa', 'Lsat_1_v5_gn_8_62401' => 'lsa', 'Manes.06G055900' => 'mes', 'Manes.12G022200' => 'mes', 'Manes.13G023300' => 'mes', 'Manes.14G115000' => 'mes', 'Manes.15G151700' => 'mes', 'Manes.17G111300' => 'mes', 'Mapoly0226s0009' => 'mpo', 'MBI02_g25363_MAGBIO' => 'mbi', 'MBI06_g00027_MAGBIO' => 'mbi', 'MBI10_g13034_MAGBIO' => 'mbi', 'MD09G1023400' => 'mdo', 'MD13G1100100' => 'mdo', 'MD15G1169200' => 'mdo', 'MD16G1101100' => 'mdo', 'MD17G1022900' => 'mdo', 'Medtr3g096150' => 'mtr', 'Medtr4g115070' => 'mtr', 'Medtr7g033325' => 'mtr', 'Medtr8g089840' => 'mtr', 'MELO3C010319.2' => 'cme', 'MELO3C011944.2' => 'cme', 'MELO3C021589.2' => 'cme', 'Migut.E00207' => 'egut', 'Migut.H00067' => 'egut', 'Migut.K00433' => 'egut', 'Migut.K00606' => 'egut', 'Migut.K01410' => 'egut', 'MSTRG.13347' => 'ama', 'MSTRG.24045' => 'ama', 'MSTRG.2428' => 'ama', 'MSTRG.26410' => 'ama', 'MSTRG.3139' => 'ama', 'MSTRG.3286' => 'ama', 'MSTRG.563' => 'ama', 'MSTRG.7941' => 'ama', 'Nitab4.5_0000028g0060' => 'nta', 'Nitab4.5_0000065g0260' => 'nta', 'Nitab4.5_0000112g0060' => 'nta', 'Nitab4.5_0000489g0120' => 'nta', 'Nitab4.5_0001776g0050' => 'nta', 'Nitab4.5_0001854g0010' => 'nta', 'Nitab4.5_0001860g0020' => 'nta', 'Nitab4.5_0004352g0010' => 'nta', 'Nitab4.5_0008716g0020' => 'nta', 'Nitab4.5_0008922g0010' => 'nta', 'Nn3g16693' => 'nnu', 'Nn4g22596' => 'nnu', 'Nn7g37639' => 'nnu', 'Oeu001701.1' => 'oeu', 'Oeu018149.1' => 'oeu', 'Oeu026220.1' => 'oeu', 'Oeu038635.1' => 'oeu', 'Oeu049176.1' => 'oeu', 'Oeu056706.1' => 'oeu', 'Oeu056937.1' => 'oeu', 'Oeu057540.1' => 'oeu', 'Os02g0594900' => 'osa', 'Os02g0595100' => 'osa', 'Os04g0477500' => 'osa', 'Os12g0611900' => 'osa', 'Peaxi162Scf00076g00020' => 'pax', 'Peaxi162Scf00128g00217' => 'pax', 'Peaxi162Scf00129g01640' => 'pax', 'Peaxi162Scf00669g00007' => 'pax', 'Peaxi162Scf00700g00421' => 'pax', 'Peaxi162Scf00801g00038' => 'pax', 'Peaxi162Scf00891g00025' => 'pax', 'PGR083G0909' => 'pgr', 'PGR119G1005' => 'pgr', 'PGR142G2236' => 'pgr', 'PGR142G3388' => 'pgr', 'PGSC0003DMG400004514' => 'stu', 'PGSC0003DMG400012635' => 'stu', 'PGSC0003DMG400015730' => 'stu', 'PGSC0003DMG400018611' => 'stu', 'PGSC0003DMG400030897' => 'stu', 'Phvul.001G254800' => 'pvu', 'Phvul.002G260100' => 'pvu', 'Phvul.003G167600' => 'pvu', 'Phvul.004G005100' => 'pvu', 'Potri.001G343600' => 'ptr', 'Potri.006G066700' => 'ptr', 'Potri.008G186000' => 'ptr', 'Potri.010G046900' => 'ptr', 'Potri.018G127900' => 'ptr', 'Pp3c20_17750' => 'ppa', 'Pp3c24_4380' => 'ppa', 'Prupe.1G245800' => 'ppe', 'Prupe.3G293400' => 'ppe', 'Prupe.7G247400' => 'ppe', 'Psat0s145g0120' => 'psa', 'Psat0s595g0040' => 'psa', 'Psat0s595g0120' => 'psa', 'Psat3g175040' => 'psa', 'Psat7g058120' => 'psa', 'PSO017G0428' => 'pso', 'PSO063G7510' => 'pso', 'PSO067G0046' => 'pso', 'PSO478G1073' => 'pso', 'PSO675G3677' => 'pso', 'PSO675G6558' => 'pso', 'PSO675G7520' => 'pso', 'PSO675G8959' => 'pso', 'QL02p074089' => 'qlo', 'QL02p089614' => 'qlo', 'QL03p057736' => 'qlo', 'RcHm_v2.0_Chr1g0364131' => 'rch', 'RcHm_v2.0_Chr2g0087801' => 'rch', 'RcHm_v2.0_Chr2g0087821' => 'rch', 'RcHm_v2.0_Chr2g0173231' => 'rch', 'RcHm_v2.0_Chr4g0433111' => 'rch', 'Rhsim03G0250300' => 'rsi', 'Rhsim08G0048400' => 'rsi', 'Rhsim10G0014800' => 'rsi', 'Rhsim12G0040100' => 'rsi', 'Rhsim12G0109700' => 'rsi', 'Sabra06G0049600' => 'sbr', 'Sabra08G0141000' => 'sbr', 'Sabra10G0021400' => 'sbr', 'Sabra16G0222900' => 'sbr', 'Sabra18G0108600' => 'sbr', 'SalBow1G0433' => 'sbo', 'SalBow1G2038' => 'sbo', 'SalBow1G5003' => 'sbo', 'SalBow7G1197' => 'sbo', 'SalBow8G3506' => 'sbo', 'Sc03g0007300' => 'sci', 'Sc11g0000950' => 'sci', 'Sc14g0008750' => 'sci', 'Sc18g0000420' => 'sci', 'Sed0006754' => 'sed', 'Sed0008741' => 'sed', 'Sed0017172' => 'sed', 'Sed0018925' => 'sed', 'Sed0023326' => 'sed', 'Sed0025909' => 'sed', 'SEGI_05333' => 'sgi', 'SEGI_10362' => 'sgi', 'SEGI_13380' => 'sgi', 'SEGI_24306' => 'sgi', 'SEGI_29077' => 'sgi', 'SEGI_29095' => 'sgi', 'SEGI_36534' => 'sgi', 'SEGI_37506' => 'sgi', 'SEGI_38321' => 'sgi', 'SGA_v2.0_scaffold307G48031' => 'sas', 'SGA_v2.0_scaffold47G17507' => 'sas', 'SGA_v2.0_scaffold63G21736' => 'sas', 'SGA_v2.0_scaffold87G27070' => 'sas', 'SHI17794' => 'shi', 'SHI28851' => 'shi', 'SMO165G0155' => 'smo', 'SMO340G0217' => 'smo', 'SMO367G1210' => 'smo', 'Solyc02g093430.3' => 'sly', 'Solyc05g013580.4' => 'sly', 'Solyc07g008030.3' => 'sly', 'Solyc12g035470.2' => 'sly', 'Sopen02g038020' => 'spe', 'Sopen05g008490' => 'spe', 'Sopen07g003910' => 'spe', 'Sopen12g015240' => 'spe', 'Sp1g11550' => 'spa', 'Sp2g16710' => 'spa', 'Sp3g00430' => 'spa', 'Sp3g26780' => 'spa', 'Sp5g22900' => 'spa', 'Sp6g29530' => 'spa', 'TAR371G0794' => 'tar', 'TAR374G0164' => 'tar', 'TAR622G0165' => 'tar', 'TAR626G0929' => 'tar', 'TAR629G2155' => 'tar', 'THA.LOC104805282' => 'tha', 'THA.LOC104805363' => 'tha', 'THA.LOC104808968' => 'tha', 'THA.LOC104821093' => 'tha', 'THA.LOC104823953' => 'tha', 'THA.LOC104825562' => 'tha', 'THA.LOC104825665' => 'tha', 'Thecc.02G261400' => 'tca', 'Thecc.04G019200' => 'tca', 'Thecc.09G130400' => 'tca', 'Thhalv10004374m.g' => 'esa', 'Thhalv10007850m.g' => 'esa', 'Thhalv10013782m.g' => 'esa', 'Thhalv10018686m.g' => 'esa', 'Thhalv10020899m.g' => 'esa', 'Thhalv10022755m.g' => 'esa', 'TPR.G23851' => 'tpr', 'TPR.G26500' => 'tpr', 'TPR.G27267' => 'tpr', 'TPR.G32001' => 'tpr', 'TPR.G6251' => 'tpr', 'TPR.G8167' => 'tpr', 'TWI12G1330' => 'twi', 'TWI18G1239' => 'twi', 'TWI34G0979' => 'twi', 'TWI36G0670' => 'twi', 'TWI36G0707' => 'twi', 'TWI56G0233' => 'twi', 'TWI75G1809' => 'twi', 'unitig_21.g20874' => 'ugi', 'unitig_26.g10343' => 'ugi', 'unitig_46.g18392' => 'ugi', 'unitig_52.g17178' => 'ugi', 'unitig_8.g2934' => 'ugi', 'vmacro01122' => 'vma', 'vmacro05875' => 'vma', 'vmacro06147' => 'vma', 'vmacro16191' => 'vma', 'vmacro18293' => 'vma', 'VMungo0251G3707' => 'vmu', 'VMungo0464G1521' => 'vmu', 'VMungo1215G0205' => 'vmu', 'VMungo1383G2484' => 'vmu', 'Zm00001eb079610' => 'zma', 'Zm00001eb135990' => 'zma', 'Zm00001eb183710' => 'zma', 'Zm00001eb246020' => 'zma' ), 'gf_id' => 'HOM05D001124', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001124' ), 'data_identifier' => 'HOM05D001124', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001124', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '548', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02520' => 'bna', 'A03p06630' => 'bna', 'A05p44460' => 'bna', 'A06p08710' => 'bna', 'A06p41090' => 'bna', 'A07p32320' => 'bna', 'A08p32520' => 'bna', 'A09p10360' => 'bna', 'A10p24080' => 'bna', 'Aa31LG11G15250' => 'aar', 'Aa31LG1G1800' => 'aar', 'Aa31LG2G5120' => 'aar', 'Aa31LG2G6070' => 'aar', 'Aa31LG5G10770' => 'aar', 'Aa31sc61G90' => 'aar', 'Actinidia01352' => 'ach', 'Actinidia05983' => 'ach', 'Actinidia08133' => 'ach', 'Actinidia15101' => 'ach', 'Actinidia26379' => 'ach', 'Actinidia35778' => 'ach', 'Actinidia36123' => 'ach', 'Actinidia37436' => 'ach', 'Actinidia38730' => 'ach', 'Ah.02g128210' => 'amhyb', 'Ah.03g132990' => 'amhyb', 'Ah.14g079410' => 'amhyb', 'AL1G24640' => 'aly', 'AL2G26680' => 'aly', 'AL3G10530' => 'aly', 'AL3G45230' => 'aly', 'AL5G15230' => 'aly', 'AL5G16960' => 'aly', 'AL6G25210' => 'aly', 'Aqoxy2G00441' => 'aox', 'Aqoxy3G01236' => 'aox', 'Aqoxy5G03746' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3RQ047' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C7GMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9C8JER' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MBL6KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YXCZ83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZANX40' => 'arhy', 'AT1G12990' => 'ath', 'AT1G67880' => 'ath', 'AT2G13290' => 'ath', 'AT3G01620' => 'ath', 'AT3G26445' => 'ath', 'AT3G27540' => 'ath', 'AT5G14480' => 'ath', 'ATR0824G026' => 'atr', 'ATR1098G019' => 'atr', 'Atru.chr11.2145' => 'acertr', 'Atru.chr2.3636' => 'acertr', 'Atru.chr2.3644' => 'acertr', 'Atru.chr6.2422' => 'acertr', 'Atru.chr7.1112' => 'acertr', 'AUR62005469' => 'cqu', 'AUR62011166' => 'cqu', 'AUR62013319' => 'cqu', 'AUR62024273' => 'cqu', 'AUR62028420' => 'cqu', 'AUR62041942' => 'cqu', 'BcaB01g04969' => 'bca', 'BcaB01g06371' => 'bca', 'BcaB02g11494' => 'bca', 'BcaB03g15382' => 'bca', 'BcaB08g36994' => 'bca', 'BcaC03g13477' => 'bca', 'BcaC03g13478' => 'bca', 'BcaC03g13480' => 'bca', 'BcaC03g13481' => 'bca', 'BcaC03g13486' => 'bca', 'BcaC04g19031' => 'bca', 'BcaC04g23085' => 'bca', 'BcaC05g25094' => 'bca', 'BcaC05g25096' => 'bca', 'BcaC05g25138' => 'bca', 'BcaC05g30416' => 'bca', 'BcaC05g30455' => 'bca', 'BcaC06g30979' => 'bca', 'BcaC06g33805' => 'bca', 'BcaC08g46021' => 'bca', 'BcaNung03154' => 'bca', 'BolC2t06623H' => 'bol', 'BolC2t06632H' => 'bol', 'BolC2t06635H' => 'bol', 'BolC2t06638H' => 'bol', 'BolC3t13266H' => 'bol', 'BolC5t29776H' => 'bol', 'BolC6t38912H' => 'bol', 'BolC7t44183H' => 'bol', 'BolC9t54123H' => 'bol', 'BolC9t59107H' => 'bol', 'BraA02t05221Z' => 'bra', 'BraA03t09996Z' => 'bra', 'BraA05t23210Z' => 'bra', 'BraA06t24068Z' => 'bra', 'BraA06t27032Z' => 'bra', 'BraA08t35176Z' => 'bra', 'BraA09t36680Z' => 'bra', 'BraA10t44471Z' => 'bra', 'C02p06760' => 'bna', 'C02p06890' => 'bna', 'C02p07010' => 'bna', 'C03p07660' => 'bna', 'C05p10300' => 'bna', 'C06p38150' => 'bna', 'C07p36650' => 'bna', 'C08p15770' => 'bna', 'C09p12300' => 'bna', 'C09p62700' => 'bna', 'C09p75040' => 'bna', 'CAN.G13.1' => 'can', 'CAN.G138.4' => 'can', 'CAN.G44.6' => 'can', 'CAN.G473.19' => 'can', 'CANSAT01G0835' => 'cansat', 'CANSAT11G0246' => 'cansat', 'CANSAT11G1766' => 'cansat', 'CANSAT64G1954' => 'cansat', 'CARHR013330' => 'chi', 'CARHR060530' => 'chi', 'CARHR075300' => 'chi', 'CARHR105120' => 'chi', 'CARHR148910' => 'chi', 'CARHR198830' => 'chi', 'Carub.0001s1275' => 'cru', 'Carub.0002s1437' => 'cru', 'Carub.0003s0044' => 'cru', 'Carub.0003s2787' => 'cru', 'Carub.0005s0597' => 'cru', 'Carub.0006s1266' => 'cru', 'Ca_06935_v3' => 'car', 'Ca_13559_v3' => 'car', 'Ca_16941_v3' => 'car', 'Ca_16960_v3' => 'car', 'Ca_17775_v3' => 'car', 'Ca_30464_v3' => 'car', 'Cc06_g08160' => 'ccan', 'Cc07_g01520' => 'ccan', 'Cc11_g15810' => 'ccan', 'CDE02G2840' => 'cde', 'CDE03G0093' => 'cde', 'CDE04G2127' => 'cde', 'CDE07G1857' => 'cde', 'CDE09G1246' => 'cde', 'Cfa003412' => 'cfa', 'Cfa007341' => 'cfa', 'Cfa009220' => 'cfa', 'Ciclev10008737m.g' => 'ccl', 'Ciclev10015565m.g' => 'ccl', 'Ciclev10031761m.g' => 'ccl', 'CiPaw.03G045300' => 'cil', 'CiPaw.03G247200' => 'cil', 'CiPaw.04G029500' => 'cil', 'CiPaw.04G174000' => 'cil', 'CiPaw.05G181200' => 'cil', 'CiPaw.06G067100' => 'cil', 'ClCG05G025800' => 'cla', 'ClCG06G011400' => 'cla', 'ClCG09G019360' => 'cla', 'COL.COLO4_04827' => 'col', 'COL.COLO4_29170' => 'col', 'COL.COLO4_35131' => 'col', 'COL.COLO4_35132' => 'col', 'Cpa.g.sc33.32' => 'cpa', 'Cpa.g.sc46.29' => 'cpa', 'Cpa.g.sc796.1' => 'cpa', 'CsaV3_1G030420' => 'csa', 'CsaV3_5G027050' => 'csa', 'CsaV3_5G031040' => 'csa', 'CsaV3_UNG023130' => 'csa', 'CSS0007726' => 'camsi', 'CSS0016433' => 'camsi', 'CSS0017656' => 'camsi', 'CSS0025364' => 'camsi', 'CSS0027582' => 'camsi', 'CSS0047288' => 'camsi', 'CSS0049950' => 'camsi', 'DCAR_003843' => 'dca', 'DCAR_007052' => 'dca', 'DCAR_020884' => 'dca', 'DCAR_021730' => 'dca', 'DCAR_024423' => 'dca', 'DCAR_026509' => 'dca', 'DCAR_031158' => 'dca', 'Dinv14728' => 'din', 'Dinv15219' => 'din', 'Dinv25728' => 'din', 'Dinv33428' => 'din', 'Dinv36489' => 'din', 'Dinv41486' => 'din', 'Duzib147G0469' => 'dzi', 'Duzib168G0060' => 'dzi', 'Duzib187G1215' => 'dzi', 'Duzib248G0692' => 'dzi', 'Duzib251G0767' => 'dzi', 'Duzib264G0446' => 'dzi', 'Duzib268G0691' => 'dzi', 'ECA232G4767' => 'eca', 'ECA233G2838' => 'eca', 'ECA234G0391' => 'eca', 'ECA234G0857' => 'eca', 'ECA236G1593' => 'eca', 'ECA238G0565' => 'eca', 'ECA246G1027' => 'eca', 'ECA246G3223' => 'eca', 'ECA246G3470' => 'eca', 'EL10Ac6g13829' => 'bvu', 'EL10Ac6g14093' => 'bvu', 'EL10Ac8g18707' => 'bvu', 'Eucgr.C01369' => 'egr', 'Eucgr.H02492' => 'egr', 'Eucgr.I01733' => 'egr', 'Eucgr.J02255' => 'egr', 'Eucgr.J02257' => 'egr', 'Eucgr.J02258' => 'egr', 'FAN02G1601' => 'fan', 'FAN03G1586' => 'fan', 'FAN03G2986' => 'fan', 'FAN05G4837' => 'fan', 'FAN06G0146' => 'fan', 'FAN07G0858' => 'fan', 'FAN09G3179' => 'fan', 'FAN10G0669' => 'fan', 'FAN12G2358' => 'fan', 'FAN14G4198' => 'fan', 'FAN14G5112' => 'fan', 'FAN17G0342' => 'fan', 'FAN19G0342' => 'fan', 'FAN19G0962' => 'fan', 'FAN19G1101' => 'fan', 'FAN19G1872' => 'fan', 'FAN22G0356' => 'fan', 'FAN23G0744' => 'fan', 'FAN23G1914' => 'fan', 'FAN26G0032' => 'fan', 'FAN28G0625' => 'fan', 'FvH4_1g02710' => 'fve', 'FvH4_1g02720' => 'fve', 'FvH4_4g25670' => 'fve', 'FvH4_6g51700' => 'fve', 'FvH4_7g20170' => 'fve', 'Glyma.05G175000' => 'gma', 'Glyma.08G132300' => 'gma', 'Glyma.11G243000' => 'gma', 'Glyma.13G158900' => 'gma', 'Glyma.17G112400' => 'gma', 'Glyma.18G014100' => 'gma', 'Glyma.19G003100' => 'gma', 'Glyma.19G056500' => 'gma', 'Gohir.A01G158900' => 'ghi', 'Gohir.A05G312600' => 'ghi', 'Gohir.A05G354900' => 'ghi', 'Gohir.A07G037200' => 'ghi', 'Gohir.A09G030000' => 'ghi', 'Gohir.A12G145200' => 'ghi', 'Gohir.D01G151500' => 'ghi', 'Gohir.D04G058300' => 'ghi', 'Gohir.D05G314100' => 'ghi', 'Gohir.D07G041400' => 'ghi', 'Gohir.D09G029700' => 'ghi', 'Gohir.D12G149700' => 'ghi', 'Gorai.001G043800' => 'gra', 'Gorai.002G187800' => 'gra', 'Gorai.006G034700' => 'gra', 'Gorai.008G161200' => 'gra', 'Gorai.009G335700' => 'gra', 'Gorai.012G065000' => 'gra', 'GSVIVG01000535001' => 'vvi', 'GSVIVG01015572001' => 'vvi', 'GSVIVG01032386001' => 'vvi', 'HanXRQChr05g0138531' => 'han', 'HanXRQChr06g0174391' => 'han', 'HanXRQChr07g0199021' => 'han', 'HanXRQChr08g0208211' => 'han', 'HanXRQChr09g0255471' => 'han', 'HanXRQChr10g0315791' => 'han', 'HanXRQChr12g0371991' => 'han', 'HanXRQChr15g0475251' => 'han', 'HanXRQChr17g0540001' => 'han', 'HanXRQChr17g0548631' => 'han', 'HanXRQChr17g0569561' => 'han', 'Haze_12256' => 'cav', 'Haze_14756' => 'cav', 'Haze_25528' => 'cav', 'Hma1.2p1_0079F.1_g041020' => 'hma', 'Hma1.2p1_0818F.1_g223260' => 'hma', 'Hma1.2p1_1747F.1_g300530' => 'hma', 'HPP92_004607' => 'vpl', 'HPP92_004608' => 'vpl', 'HPP92_006181' => 'vpl', 'HPP92_012192' => 'vpl', 'HPP92_015680' => 'vpl', 'HPP92_020249' => 'vpl', 'HPP92_021376' => 'vpl', 'HPP92_024275' => 'vpl', 'Hund06031' => 'sun', 'Hund25391' => 'sun', 'Lalb_Chr07g0185371' => 'lal', 'Lalb_Chr07g0185381' => 'lal', 'Lalb_Chr12g0204011' => 'lal', 'Lalb_Chr13g0301671' => 'lal', 'Lalb_Chr14g0362851' => 'lal', 'Lalb_Chr24g0403581' => 'lal', 'Lj1g0000233' => 'lja', 'Lj2g0018120' => 'lja', 'Lj3C621T0' => 'lonja', 'Lj3P1059T14' => 'lonja', 'Lj3P611T9' => 'lonja', 'Lj3P614T13' => 'lonja', 'Lj3P615T5' => 'lonja', 'Lj4g0012315' => 'lja', 'Lj4g0026182' => 'lja', 'Lj6P813T16' => 'lonja', 'Lj7C427T7' => 'lonja', 'Lj7C427T8' => 'lonja', 'Lj7P600T41' => 'lonja', 'Lju41C42G17' => 'lonja', 'Lsat_1_v5_gn_0_47300' => 'lsa', 'Lsat_1_v5_gn_2_91280' => 'lsa', 'Lsat_1_v5_gn_3_30561' => 'lsa', 'Lsat_1_v5_gn_4_184321' => 'lsa', 'Lsat_1_v5_gn_4_4041' => 'lsa', 'Lsat_1_v5_gn_5_92000' => 'lsa', 'Lsat_1_v5_gn_8_152940' => 'lsa', 'Lsat_1_v5_gn_8_62401' => 'lsa', 'Manes.06G055900' => 'mes', 'Manes.12G022200' => 'mes', 'Manes.13G023300' => 'mes', 'Manes.14G115000' => 'mes', 'Manes.15G151700' => 'mes', 'Manes.17G111300' => 'mes', 'Mapoly0226s0009' => 'mpo', 'MBI02_g25363_MAGBIO' => 'mbi', 'MBI06_g00027_MAGBIO' => 'mbi', 'MBI10_g13034_MAGBIO' => 'mbi', 'MD09G1023400' => 'mdo', 'MD13G1100100' => 'mdo', 'MD15G1169200' => 'mdo', 'MD16G1101100' => 'mdo', 'MD17G1022900' => 'mdo', 'Medtr3g096150' => 'mtr', 'Medtr4g115070' => 'mtr', 'Medtr7g033325' => 'mtr', 'Medtr8g089840' => 'mtr', 'MELO3C010319.2' => 'cme', 'MELO3C011944.2' => 'cme', 'MELO3C021589.2' => 'cme', 'Migut.E00207' => 'egut', 'Migut.H00067' => 'egut', 'Migut.K00433' => 'egut', 'Migut.K00606' => 'egut', 'Migut.K01410' => 'egut', 'MSTRG.13347' => 'ama', 'MSTRG.24045' => 'ama', 'MSTRG.2428' => 'ama', 'MSTRG.26410' => 'ama', 'MSTRG.3139' => 'ama', 'MSTRG.3286' => 'ama', 'MSTRG.563' => 'ama', 'MSTRG.7941' => 'ama', 'Nitab4.5_0000028g0060' => 'nta', 'Nitab4.5_0000065g0260' => 'nta', 'Nitab4.5_0000112g0060' => 'nta', 'Nitab4.5_0000489g0120' => 'nta', 'Nitab4.5_0001776g0050' => 'nta', 'Nitab4.5_0001854g0010' => 'nta', 'Nitab4.5_0001860g0020' => 'nta', 'Nitab4.5_0004352g0010' => 'nta', 'Nitab4.5_0008716g0020' => 'nta', 'Nitab4.5_0008922g0010' => 'nta', 'Nn3g16693' => 'nnu', 'Nn4g22596' => 'nnu', 'Nn7g37639' => 'nnu', 'Oeu001701.1' => 'oeu', 'Oeu018149.1' => 'oeu', 'Oeu026220.1' => 'oeu', 'Oeu038635.1' => 'oeu', 'Oeu049176.1' => 'oeu', 'Oeu056706.1' => 'oeu', 'Oeu056937.1' => 'oeu', 'Oeu057540.1' => 'oeu', 'Os02g0594900' => 'osa', 'Os02g0595100' => 'osa', 'Os04g0477500' => 'osa', 'Os12g0611900' => 'osa', 'Peaxi162Scf00076g00020' => 'pax', 'Peaxi162Scf00128g00217' => 'pax', 'Peaxi162Scf00129g01640' => 'pax', 'Peaxi162Scf00669g00007' => 'pax', 'Peaxi162Scf00700g00421' => 'pax', 'Peaxi162Scf00801g00038' => 'pax', 'Peaxi162Scf00891g00025' => 'pax', 'PGR083G0909' => 'pgr', 'PGR119G1005' => 'pgr', 'PGR142G2236' => 'pgr', 'PGR142G3388' => 'pgr', 'PGSC0003DMG400004514' => 'stu', 'PGSC0003DMG400012635' => 'stu', 'PGSC0003DMG400015730' => 'stu', 'PGSC0003DMG400018611' => 'stu', 'PGSC0003DMG400030897' => 'stu', 'Phvul.001G254800' => 'pvu', 'Phvul.002G260100' => 'pvu', 'Phvul.003G167600' => 'pvu', 'Phvul.004G005100' => 'pvu', 'Potri.001G343600' => 'ptr', 'Potri.006G066700' => 'ptr', 'Potri.008G186000' => 'ptr', 'Potri.010G046900' => 'ptr', 'Potri.018G127900' => 'ptr', 'Pp3c20_17750' => 'ppa', 'Pp3c24_4380' => 'ppa', 'Prupe.1G245800' => 'ppe', 'Prupe.3G293400' => 'ppe', 'Prupe.7G247400' => 'ppe', 'Psat0s145g0120' => 'psa', 'Psat0s595g0040' => 'psa', 'Psat0s595g0120' => 'psa', 'Psat3g175040' => 'psa', 'Psat7g058120' => 'psa', 'PSO017G0428' => 'pso', 'PSO063G7510' => 'pso', 'PSO067G0046' => 'pso', 'PSO478G1073' => 'pso', 'PSO675G3677' => 'pso', 'PSO675G6558' => 'pso', 'PSO675G7520' => 'pso', 'PSO675G8959' => 'pso', 'QL02p074089' => 'qlo', 'QL02p089614' => 'qlo', 'QL03p057736' => 'qlo', 'RcHm_v2.0_Chr1g0364131' => 'rch', 'RcHm_v2.0_Chr2g0087801' => 'rch', 'RcHm_v2.0_Chr2g0087821' => 'rch', 'RcHm_v2.0_Chr2g0173231' => 'rch', 'RcHm_v2.0_Chr4g0433111' => 'rch', 'Rhsim03G0250300' => 'rsi', 'Rhsim08G0048400' => 'rsi', 'Rhsim10G0014800' => 'rsi', 'Rhsim12G0040100' => 'rsi', 'Rhsim12G0109700' => 'rsi', 'Sabra06G0049600' => 'sbr', 'Sabra08G0141000' => 'sbr', 'Sabra10G0021400' => 'sbr', 'Sabra16G0222900' => 'sbr', 'Sabra18G0108600' => 'sbr', 'SalBow1G0433' => 'sbo', 'SalBow1G2038' => 'sbo', 'SalBow1G5003' => 'sbo', 'SalBow7G1197' => 'sbo', 'SalBow8G3506' => 'sbo', 'Sc03g0007300' => 'sci', 'Sc11g0000950' => 'sci', 'Sc14g0008750' => 'sci', 'Sc18g0000420' => 'sci', 'Sed0006754' => 'sed', 'Sed0008741' => 'sed', 'Sed0017172' => 'sed', 'Sed0018925' => 'sed', 'Sed0023326' => 'sed', 'Sed0025909' => 'sed', 'SEGI_05333' => 'sgi', 'SEGI_10362' => 'sgi', 'SEGI_13380' => 'sgi', 'SEGI_24306' => 'sgi', 'SEGI_29077' => 'sgi', 'SEGI_29095' => 'sgi', 'SEGI_36534' => 'sgi', 'SEGI_37506' => 'sgi', 'SEGI_38321' => 'sgi', 'SGA_v2.0_scaffold307G48031' => 'sas', 'SGA_v2.0_scaffold47G17507' => 'sas', 'SGA_v2.0_scaffold63G21736' => 'sas', 'SGA_v2.0_scaffold87G27070' => 'sas', 'SHI17794' => 'shi', 'SHI28851' => 'shi', 'SMO165G0155' => 'smo', 'SMO340G0217' => 'smo', 'SMO367G1210' => 'smo', 'Solyc02g093430.3' => 'sly', 'Solyc05g013580.4' => 'sly', 'Solyc07g008030.3' => 'sly', 'Solyc12g035470.2' => 'sly', 'Sopen02g038020' => 'spe', 'Sopen05g008490' => 'spe', 'Sopen07g003910' => 'spe', 'Sopen12g015240' => 'spe', 'Sp1g11550' => 'spa', 'Sp2g16710' => 'spa', 'Sp3g00430' => 'spa', 'Sp3g26780' => 'spa', 'Sp5g22900' => 'spa', 'Sp6g29530' => 'spa', 'TAR371G0794' => 'tar', 'TAR374G0164' => 'tar', 'TAR622G0165' => 'tar', 'TAR626G0929' => 'tar', 'TAR629G2155' => 'tar', 'THA.LOC104805282' => 'tha', 'THA.LOC104805363' => 'tha', 'THA.LOC104808968' => 'tha', 'THA.LOC104821093' => 'tha', 'THA.LOC104823953' => 'tha', 'THA.LOC104825562' => 'tha', 'THA.LOC104825665' => 'tha', 'Thecc.02G261400' => 'tca', 'Thecc.04G019200' => 'tca', 'Thecc.09G130400' => 'tca', 'Thhalv10004374m.g' => 'esa', 'Thhalv10007850m.g' => 'esa', 'Thhalv10013782m.g' => 'esa', 'Thhalv10018686m.g' => 'esa', 'Thhalv10020899m.g' => 'esa', 'Thhalv10022755m.g' => 'esa', 'TPR.G23851' => 'tpr', 'TPR.G26500' => 'tpr', 'TPR.G27267' => 'tpr', 'TPR.G32001' => 'tpr', 'TPR.G6251' => 'tpr', 'TPR.G8167' => 'tpr', 'TWI12G1330' => 'twi', 'TWI18G1239' => 'twi', 'TWI34G0979' => 'twi', 'TWI36G0670' => 'twi', 'TWI36G0707' => 'twi', 'TWI56G0233' => 'twi', 'TWI75G1809' => 'twi', 'unitig_21.g20874' => 'ugi', 'unitig_26.g10343' => 'ugi', 'unitig_46.g18392' => 'ugi', 'unitig_52.g17178' => 'ugi', 'unitig_8.g2934' => 'ugi', 'vmacro01122' => 'vma', 'vmacro05875' => 'vma', 'vmacro06147' => 'vma', 'vmacro16191' => 'vma', 'vmacro18293' => 'vma', 'VMungo0251G3707' => 'vmu', 'VMungo0464G1521' => 'vmu', 'VMungo1215G0205' => 'vmu', 'VMungo1383G2484' => 'vmu', 'Zm00001eb079610' => 'zma', 'Zm00001eb135990' => 'zma', 'Zm00001eb183710' => 'zma', 'Zm00001eb246020' => 'zma' ) $gf_id = 'HOM05D001124' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001124' ) $data_identifier = 'HOM05D001124' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 6, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 7, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 21, 'bol' => (int) 10, 'bra' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 6, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 9, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 21, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 8, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 10, 'lsa' => (int) 8, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 8, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 9, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb246020' $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' => 'HOM05D001124', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '548', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02520' => 'bna', 'A03p06630' => 'bna', 'A05p44460' => 'bna', 'A06p08710' => 'bna', 'A06p41090' => 'bna', 'A07p32320' => 'bna', 'A08p32520' => 'bna', 'A09p10360' => 'bna', 'A10p24080' => 'bna', 'Aa31LG11G15250' => 'aar', 'Aa31LG1G1800' => 'aar', 'Aa31LG2G5120' => 'aar', 'Aa31LG2G6070' => 'aar', 'Aa31LG5G10770' => 'aar', 'Aa31sc61G90' => 'aar', 'Actinidia01352' => 'ach', 'Actinidia05983' => 'ach', 'Actinidia08133' => 'ach', 'Actinidia15101' => 'ach', 'Actinidia26379' => 'ach', 'Actinidia35778' => 'ach', 'Actinidia36123' => 'ach', 'Actinidia37436' => 'ach', 'Actinidia38730' => 'ach', 'Ah.02g128210' => 'amhyb', 'Ah.03g132990' => 'amhyb', 'Ah.14g079410' => 'amhyb', 'AL1G24640' => 'aly', 'AL2G26680' => 'aly', 'AL3G10530' => 'aly', 'AL3G45230' => 'aly', 'AL5G15230' => 'aly', 'AL5G16960' => 'aly', 'AL6G25210' => 'aly', 'Aqoxy2G00441' => 'aox', 'Aqoxy3G01236' => 'aox', 'Aqoxy5G03746' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3RQ047' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C7GMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9C8JER' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MBL6KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YXCZ83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZANX40' => 'arhy', 'AT1G12990' => 'ath', 'AT1G67880' => 'ath', 'AT2G13290' => 'ath', 'AT3G01620' => 'ath', 'AT3G26445' => 'ath', 'AT3G27540' => 'ath', 'AT5G14480' => 'ath', 'ATR0824G026' => 'atr', 'ATR1098G019' => 'atr', 'Atru.chr11.2145' => 'acertr', 'Atru.chr2.3636' => 'acertr', 'Atru.chr2.3644' => 'acertr', 'Atru.chr6.2422' => 'acertr', 'Atru.chr7.1112' => 'acertr', 'AUR62005469' => 'cqu', 'AUR62011166' => 'cqu', 'AUR62013319' => 'cqu', 'AUR62024273' => 'cqu', 'AUR62028420' => 'cqu', 'AUR62041942' => 'cqu', 'BcaB01g04969' => 'bca', 'BcaB01g06371' => 'bca', 'BcaB02g11494' => 'bca', 'BcaB03g15382' => 'bca', 'BcaB08g36994' => 'bca', 'BcaC03g13477' => 'bca', 'BcaC03g13478' => 'bca', 'BcaC03g13480' => 'bca', 'BcaC03g13481' => 'bca', 'BcaC03g13486' => 'bca', 'BcaC04g19031' => 'bca', 'BcaC04g23085' => 'bca', 'BcaC05g25094' => 'bca', 'BcaC05g25096' => 'bca', 'BcaC05g25138' => 'bca', 'BcaC05g30416' => 'bca', 'BcaC05g30455' => 'bca', 'BcaC06g30979' => 'bca', 'BcaC06g33805' => 'bca', 'BcaC08g46021' => 'bca', 'BcaNung03154' => 'bca', 'BolC2t06623H' => 'bol', 'BolC2t06632H' => 'bol', 'BolC2t06635H' => 'bol', 'BolC2t06638H' => 'bol', 'BolC3t13266H' => 'bol', 'BolC5t29776H' => 'bol', 'BolC6t38912H' => 'bol', 'BolC7t44183H' => 'bol', 'BolC9t54123H' => 'bol', 'BolC9t59107H' => 'bol', 'BraA02t05221Z' => 'bra', 'BraA03t09996Z' => 'bra', 'BraA05t23210Z' => 'bra', 'BraA06t24068Z' => 'bra', 'BraA06t27032Z' => 'bra', 'BraA08t35176Z' => 'bra', 'BraA09t36680Z' => 'bra', 'BraA10t44471Z' => 'bra', 'C02p06760' => 'bna', 'C02p06890' => 'bna', 'C02p07010' => 'bna', 'C03p07660' => 'bna', 'C05p10300' => 'bna', 'C06p38150' => 'bna', 'C07p36650' => 'bna', 'C08p15770' => 'bna', 'C09p12300' => 'bna', 'C09p62700' => 'bna', 'C09p75040' => 'bna', 'CAN.G13.1' => 'can', 'CAN.G138.4' => 'can', 'CAN.G44.6' => 'can', 'CAN.G473.19' => 'can', 'CANSAT01G0835' => 'cansat', 'CANSAT11G0246' => 'cansat', 'CANSAT11G1766' => 'cansat', 'CANSAT64G1954' => 'cansat', 'CARHR013330' => 'chi', 'CARHR060530' => 'chi', 'CARHR075300' => 'chi', 'CARHR105120' => 'chi', 'CARHR148910' => 'chi', 'CARHR198830' => 'chi', 'Carub.0001s1275' => 'cru', 'Carub.0002s1437' => 'cru', 'Carub.0003s0044' => 'cru', 'Carub.0003s2787' => 'cru', 'Carub.0005s0597' => 'cru', 'Carub.0006s1266' => 'cru', 'Ca_06935_v3' => 'car', 'Ca_13559_v3' => 'car', 'Ca_16941_v3' => 'car', 'Ca_16960_v3' => 'car', 'Ca_17775_v3' => 'car', 'Ca_30464_v3' => 'car', 'Cc06_g08160' => 'ccan', 'Cc07_g01520' => 'ccan', 'Cc11_g15810' => 'ccan', 'CDE02G2840' => 'cde', 'CDE03G0093' => 'cde', 'CDE04G2127' => 'cde', 'CDE07G1857' => 'cde', 'CDE09G1246' => 'cde', 'Cfa003412' => 'cfa', 'Cfa007341' => 'cfa', 'Cfa009220' => 'cfa', 'Ciclev10008737m.g' => 'ccl', 'Ciclev10015565m.g' => 'ccl', 'Ciclev10031761m.g' => 'ccl', 'CiPaw.03G045300' => 'cil', 'CiPaw.03G247200' => 'cil', 'CiPaw.04G029500' => 'cil', 'CiPaw.04G174000' => 'cil', 'CiPaw.05G181200' => 'cil', 'CiPaw.06G067100' => 'cil', 'ClCG05G025800' => 'cla', 'ClCG06G011400' => 'cla', 'ClCG09G019360' => 'cla', 'COL.COLO4_04827' => 'col', 'COL.COLO4_29170' => 'col', 'COL.COLO4_35131' => 'col', 'COL.COLO4_35132' => 'col', 'Cpa.g.sc33.32' => 'cpa', 'Cpa.g.sc46.29' => 'cpa', 'Cpa.g.sc796.1' => 'cpa', 'CsaV3_1G030420' => 'csa', 'CsaV3_5G027050' => 'csa', 'CsaV3_5G031040' => 'csa', 'CsaV3_UNG023130' => 'csa', 'CSS0007726' => 'camsi', 'CSS0016433' => 'camsi', 'CSS0017656' => 'camsi', 'CSS0025364' => 'camsi', 'CSS0027582' => 'camsi', 'CSS0047288' => 'camsi', 'CSS0049950' => 'camsi', 'DCAR_003843' => 'dca', 'DCAR_007052' => 'dca', 'DCAR_020884' => 'dca', 'DCAR_021730' => 'dca', 'DCAR_024423' => 'dca', 'DCAR_026509' => 'dca', 'DCAR_031158' => 'dca', 'Dinv14728' => 'din', 'Dinv15219' => 'din', 'Dinv25728' => 'din', 'Dinv33428' => 'din', 'Dinv36489' => 'din', 'Dinv41486' => 'din', 'Duzib147G0469' => 'dzi', 'Duzib168G0060' => 'dzi', 'Duzib187G1215' => 'dzi', 'Duzib248G0692' => 'dzi', 'Duzib251G0767' => 'dzi', 'Duzib264G0446' => 'dzi', 'Duzib268G0691' => 'dzi', 'ECA232G4767' => 'eca', 'ECA233G2838' => 'eca', 'ECA234G0391' => 'eca', 'ECA234G0857' => 'eca', 'ECA236G1593' => 'eca', 'ECA238G0565' => 'eca', 'ECA246G1027' => 'eca', 'ECA246G3223' => 'eca', 'ECA246G3470' => 'eca', 'EL10Ac6g13829' => 'bvu', 'EL10Ac6g14093' => 'bvu', 'EL10Ac8g18707' => 'bvu', 'Eucgr.C01369' => 'egr', 'Eucgr.H02492' => 'egr', 'Eucgr.I01733' => 'egr', 'Eucgr.J02255' => 'egr', 'Eucgr.J02257' => 'egr', 'Eucgr.J02258' => 'egr', 'FAN02G1601' => 'fan', 'FAN03G1586' => 'fan', 'FAN03G2986' => 'fan', 'FAN05G4837' => 'fan', 'FAN06G0146' => 'fan', 'FAN07G0858' => 'fan', 'FAN09G3179' => 'fan', 'FAN10G0669' => 'fan', 'FAN12G2358' => 'fan', 'FAN14G4198' => 'fan', 'FAN14G5112' => 'fan', 'FAN17G0342' => 'fan', 'FAN19G0342' => 'fan', 'FAN19G0962' => 'fan', 'FAN19G1101' => 'fan', 'FAN19G1872' => 'fan', 'FAN22G0356' => 'fan', 'FAN23G0744' => 'fan', 'FAN23G1914' => 'fan', 'FAN26G0032' => 'fan', 'FAN28G0625' => 'fan', 'FvH4_1g02710' => 'fve', 'FvH4_1g02720' => 'fve', 'FvH4_4g25670' => 'fve', 'FvH4_6g51700' => 'fve', 'FvH4_7g20170' => 'fve', 'Glyma.05G175000' => 'gma', 'Glyma.08G132300' => 'gma', 'Glyma.11G243000' => 'gma', 'Glyma.13G158900' => 'gma', 'Glyma.17G112400' => 'gma', 'Glyma.18G014100' => 'gma', 'Glyma.19G003100' => 'gma', 'Glyma.19G056500' => 'gma', 'Gohir.A01G158900' => 'ghi', 'Gohir.A05G312600' => 'ghi', 'Gohir.A05G354900' => 'ghi', 'Gohir.A07G037200' => 'ghi', 'Gohir.A09G030000' => 'ghi', 'Gohir.A12G145200' => 'ghi', 'Gohir.D01G151500' => 'ghi', 'Gohir.D04G058300' => 'ghi', 'Gohir.D05G314100' => 'ghi', 'Gohir.D07G041400' => 'ghi', 'Gohir.D09G029700' => 'ghi', 'Gohir.D12G149700' => 'ghi', 'Gorai.001G043800' => 'gra', 'Gorai.002G187800' => 'gra', 'Gorai.006G034700' => 'gra', 'Gorai.008G161200' => 'gra', 'Gorai.009G335700' => 'gra', 'Gorai.012G065000' => 'gra', 'GSVIVG01000535001' => 'vvi', 'GSVIVG01015572001' => 'vvi', 'GSVIVG01032386001' => 'vvi', 'HanXRQChr05g0138531' => 'han', 'HanXRQChr06g0174391' => 'han', 'HanXRQChr07g0199021' => 'han', 'HanXRQChr08g0208211' => 'han', 'HanXRQChr09g0255471' => 'han', 'HanXRQChr10g0315791' => 'han', 'HanXRQChr12g0371991' => 'han', 'HanXRQChr15g0475251' => 'han', 'HanXRQChr17g0540001' => 'han', 'HanXRQChr17g0548631' => 'han', 'HanXRQChr17g0569561' => 'han', 'Haze_12256' => 'cav', 'Haze_14756' => 'cav', 'Haze_25528' => 'cav', 'Hma1.2p1_0079F.1_g041020' => 'hma', 'Hma1.2p1_0818F.1_g223260' => 'hma', 'Hma1.2p1_1747F.1_g300530' => 'hma', 'HPP92_004607' => 'vpl', 'HPP92_004608' => 'vpl', 'HPP92_006181' => 'vpl', 'HPP92_012192' => 'vpl', 'HPP92_015680' => 'vpl', 'HPP92_020249' => 'vpl', 'HPP92_021376' => 'vpl', 'HPP92_024275' => 'vpl', 'Hund06031' => 'sun', 'Hund25391' => 'sun', 'Lalb_Chr07g0185371' => 'lal', 'Lalb_Chr07g0185381' => 'lal', 'Lalb_Chr12g0204011' => 'lal', 'Lalb_Chr13g0301671' => 'lal', 'Lalb_Chr14g0362851' => 'lal', 'Lalb_Chr24g0403581' => 'lal', 'Lj1g0000233' => 'lja', 'Lj2g0018120' => 'lja', 'Lj3C621T0' => 'lonja', 'Lj3P1059T14' => 'lonja', 'Lj3P611T9' => 'lonja', 'Lj3P614T13' => 'lonja', 'Lj3P615T5' => 'lonja', 'Lj4g0012315' => 'lja', 'Lj4g0026182' => 'lja', 'Lj6P813T16' => 'lonja', 'Lj7C427T7' => 'lonja', 'Lj7C427T8' => 'lonja', 'Lj7P600T41' => 'lonja', 'Lju41C42G17' => 'lonja', 'Lsat_1_v5_gn_0_47300' => 'lsa', 'Lsat_1_v5_gn_2_91280' => 'lsa', 'Lsat_1_v5_gn_3_30561' => 'lsa', 'Lsat_1_v5_gn_4_184321' => 'lsa', 'Lsat_1_v5_gn_4_4041' => 'lsa', 'Lsat_1_v5_gn_5_92000' => 'lsa', 'Lsat_1_v5_gn_8_152940' => 'lsa', 'Lsat_1_v5_gn_8_62401' => 'lsa', 'Manes.06G055900' => 'mes', 'Manes.12G022200' => 'mes', 'Manes.13G023300' => 'mes', 'Manes.14G115000' => 'mes', 'Manes.15G151700' => 'mes', 'Manes.17G111300' => 'mes', 'Mapoly0226s0009' => 'mpo', 'MBI02_g25363_MAGBIO' => 'mbi', 'MBI06_g00027_MAGBIO' => 'mbi', 'MBI10_g13034_MAGBIO' => 'mbi', 'MD09G1023400' => 'mdo', 'MD13G1100100' => 'mdo', 'MD15G1169200' => 'mdo', 'MD16G1101100' => 'mdo', 'MD17G1022900' => 'mdo', 'Medtr3g096150' => 'mtr', 'Medtr4g115070' => 'mtr', 'Medtr7g033325' => 'mtr', 'Medtr8g089840' => 'mtr', 'MELO3C010319.2' => 'cme', 'MELO3C011944.2' => 'cme', 'MELO3C021589.2' => 'cme', 'Migut.E00207' => 'egut', 'Migut.H00067' => 'egut', 'Migut.K00433' => 'egut', 'Migut.K00606' => 'egut', 'Migut.K01410' => 'egut', 'MSTRG.13347' => 'ama', 'MSTRG.24045' => 'ama', 'MSTRG.2428' => 'ama', 'MSTRG.26410' => 'ama', 'MSTRG.3139' => 'ama', 'MSTRG.3286' => 'ama', 'MSTRG.563' => 'ama', 'MSTRG.7941' => 'ama', 'Nitab4.5_0000028g0060' => 'nta', 'Nitab4.5_0000065g0260' => 'nta', 'Nitab4.5_0000112g0060' => 'nta', 'Nitab4.5_0000489g0120' => 'nta', 'Nitab4.5_0001776g0050' => 'nta', 'Nitab4.5_0001854g0010' => 'nta', 'Nitab4.5_0001860g0020' => 'nta', 'Nitab4.5_0004352g0010' => 'nta', 'Nitab4.5_0008716g0020' => 'nta', 'Nitab4.5_0008922g0010' => 'nta', 'Nn3g16693' => 'nnu', 'Nn4g22596' => 'nnu', 'Nn7g37639' => 'nnu', 'Oeu001701.1' => 'oeu', 'Oeu018149.1' => 'oeu', 'Oeu026220.1' => 'oeu', 'Oeu038635.1' => 'oeu', 'Oeu049176.1' => 'oeu', 'Oeu056706.1' => 'oeu', 'Oeu056937.1' => 'oeu', 'Oeu057540.1' => 'oeu', 'Os02g0594900' => 'osa', 'Os02g0595100' => 'osa', 'Os04g0477500' => 'osa', 'Os12g0611900' => 'osa', 'Peaxi162Scf00076g00020' => 'pax', 'Peaxi162Scf00128g00217' => 'pax', 'Peaxi162Scf00129g01640' => 'pax', 'Peaxi162Scf00669g00007' => 'pax', 'Peaxi162Scf00700g00421' => 'pax', 'Peaxi162Scf00801g00038' => 'pax', 'Peaxi162Scf00891g00025' => 'pax', 'PGR083G0909' => 'pgr', 'PGR119G1005' => 'pgr', 'PGR142G2236' => 'pgr', 'PGR142G3388' => 'pgr', 'PGSC0003DMG400004514' => 'stu', 'PGSC0003DMG400012635' => 'stu', 'PGSC0003DMG400015730' => 'stu', 'PGSC0003DMG400018611' => 'stu', 'PGSC0003DMG400030897' => 'stu', 'Phvul.001G254800' => 'pvu', 'Phvul.002G260100' => 'pvu', 'Phvul.003G167600' => 'pvu', 'Phvul.004G005100' => 'pvu', 'Potri.001G343600' => 'ptr', 'Potri.006G066700' => 'ptr', 'Potri.008G186000' => 'ptr', 'Potri.010G046900' => 'ptr', 'Potri.018G127900' => 'ptr', 'Pp3c20_17750' => 'ppa', 'Pp3c24_4380' => 'ppa', 'Prupe.1G245800' => 'ppe', 'Prupe.3G293400' => 'ppe', 'Prupe.7G247400' => 'ppe', 'Psat0s145g0120' => 'psa', 'Psat0s595g0040' => 'psa', 'Psat0s595g0120' => 'psa', 'Psat3g175040' => 'psa', 'Psat7g058120' => 'psa', 'PSO017G0428' => 'pso', 'PSO063G7510' => 'pso', 'PSO067G0046' => 'pso', 'PSO478G1073' => 'pso', 'PSO675G3677' => 'pso', 'PSO675G6558' => 'pso', 'PSO675G7520' => 'pso', 'PSO675G8959' => 'pso', 'QL02p074089' => 'qlo', 'QL02p089614' => 'qlo', 'QL03p057736' => 'qlo', 'RcHm_v2.0_Chr1g0364131' => 'rch', 'RcHm_v2.0_Chr2g0087801' => 'rch', 'RcHm_v2.0_Chr2g0087821' => 'rch', 'RcHm_v2.0_Chr2g0173231' => 'rch', 'RcHm_v2.0_Chr4g0433111' => 'rch', 'Rhsim03G0250300' => 'rsi', 'Rhsim08G0048400' => 'rsi', 'Rhsim10G0014800' => 'rsi', 'Rhsim12G0040100' => 'rsi', 'Rhsim12G0109700' => 'rsi', 'Sabra06G0049600' => 'sbr', 'Sabra08G0141000' => 'sbr', 'Sabra10G0021400' => 'sbr', 'Sabra16G0222900' => 'sbr', 'Sabra18G0108600' => 'sbr', 'SalBow1G0433' => 'sbo', 'SalBow1G2038' => 'sbo', 'SalBow1G5003' => 'sbo', 'SalBow7G1197' => 'sbo', 'SalBow8G3506' => 'sbo', 'Sc03g0007300' => 'sci', 'Sc11g0000950' => 'sci', 'Sc14g0008750' => 'sci', 'Sc18g0000420' => 'sci', 'Sed0006754' => 'sed', 'Sed0008741' => 'sed', 'Sed0017172' => 'sed', 'Sed0018925' => 'sed', 'Sed0023326' => 'sed', 'Sed0025909' => 'sed', 'SEGI_05333' => 'sgi', 'SEGI_10362' => 'sgi', 'SEGI_13380' => 'sgi', 'SEGI_24306' => 'sgi', 'SEGI_29077' => 'sgi', 'SEGI_29095' => 'sgi', 'SEGI_36534' => 'sgi', 'SEGI_37506' => 'sgi', 'SEGI_38321' => 'sgi', 'SGA_v2.0_scaffold307G48031' => 'sas', 'SGA_v2.0_scaffold47G17507' => 'sas', 'SGA_v2.0_scaffold63G21736' => 'sas', 'SGA_v2.0_scaffold87G27070' => 'sas', 'SHI17794' => 'shi', 'SHI28851' => 'shi', 'SMO165G0155' => 'smo', 'SMO340G0217' => 'smo', 'SMO367G1210' => 'smo', 'Solyc02g093430.3' => 'sly', 'Solyc05g013580.4' => 'sly', 'Solyc07g008030.3' => 'sly', 'Solyc12g035470.2' => 'sly', 'Sopen02g038020' => 'spe', 'Sopen05g008490' => 'spe', 'Sopen07g003910' => 'spe', 'Sopen12g015240' => 'spe', 'Sp1g11550' => 'spa', 'Sp2g16710' => 'spa', 'Sp3g00430' => 'spa', 'Sp3g26780' => 'spa', 'Sp5g22900' => 'spa', 'Sp6g29530' => 'spa', 'TAR371G0794' => 'tar', 'TAR374G0164' => 'tar', 'TAR622G0165' => 'tar', 'TAR626G0929' => 'tar', 'TAR629G2155' => 'tar', 'THA.LOC104805282' => 'tha', 'THA.LOC104805363' => 'tha', 'THA.LOC104808968' => 'tha', 'THA.LOC104821093' => 'tha', 'THA.LOC104823953' => 'tha', 'THA.LOC104825562' => 'tha', 'THA.LOC104825665' => 'tha', 'Thecc.02G261400' => 'tca', 'Thecc.04G019200' => 'tca', 'Thecc.09G130400' => 'tca', 'Thhalv10004374m.g' => 'esa', 'Thhalv10007850m.g' => 'esa', 'Thhalv10013782m.g' => 'esa', 'Thhalv10018686m.g' => 'esa', 'Thhalv10020899m.g' => 'esa', 'Thhalv10022755m.g' => 'esa', 'TPR.G23851' => 'tpr', 'TPR.G26500' => 'tpr', 'TPR.G27267' => 'tpr', 'TPR.G32001' => 'tpr', 'TPR.G6251' => 'tpr', 'TPR.G8167' => 'tpr', 'TWI12G1330' => 'twi', 'TWI18G1239' => 'twi', 'TWI34G0979' => 'twi', 'TWI36G0670' => 'twi', 'TWI36G0707' => 'twi', 'TWI56G0233' => 'twi', 'TWI75G1809' => 'twi', 'unitig_21.g20874' => 'ugi', 'unitig_26.g10343' => 'ugi', 'unitig_46.g18392' => 'ugi', 'unitig_52.g17178' => 'ugi', 'unitig_8.g2934' => 'ugi', 'vmacro01122' => 'vma', 'vmacro05875' => 'vma', 'vmacro06147' => 'vma', 'vmacro16191' => 'vma', 'vmacro18293' => 'vma', 'VMungo0251G3707' => 'vmu', 'VMungo0464G1521' => 'vmu', 'VMungo1215G0205' => 'vmu', 'VMungo1383G2484' => 'vmu', 'Zm00001eb079610' => 'zma', 'Zm00001eb135990' => 'zma', 'Zm00001eb183710' => 'zma', 'Zm00001eb246020' => 'zma' ), 'gf_id' => 'HOM05D001124', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001124' ), 'data_identifier' => 'HOM05D001124', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001124', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '548', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02520' => 'bna', 'A03p06630' => 'bna', 'A05p44460' => 'bna', 'A06p08710' => 'bna', 'A06p41090' => 'bna', 'A07p32320' => 'bna', 'A08p32520' => 'bna', 'A09p10360' => 'bna', 'A10p24080' => 'bna', 'Aa31LG11G15250' => 'aar', 'Aa31LG1G1800' => 'aar', 'Aa31LG2G5120' => 'aar', 'Aa31LG2G6070' => 'aar', 'Aa31LG5G10770' => 'aar', 'Aa31sc61G90' => 'aar', 'Actinidia01352' => 'ach', 'Actinidia05983' => 'ach', 'Actinidia08133' => 'ach', 'Actinidia15101' => 'ach', 'Actinidia26379' => 'ach', 'Actinidia35778' => 'ach', 'Actinidia36123' => 'ach', 'Actinidia37436' => 'ach', 'Actinidia38730' => 'ach', 'Ah.02g128210' => 'amhyb', 'Ah.03g132990' => 'amhyb', 'Ah.14g079410' => 'amhyb', 'AL1G24640' => 'aly', 'AL2G26680' => 'aly', 'AL3G10530' => 'aly', 'AL3G45230' => 'aly', 'AL5G15230' => 'aly', 'AL5G16960' => 'aly', 'AL6G25210' => 'aly', 'Aqoxy2G00441' => 'aox', 'Aqoxy3G01236' => 'aox', 'Aqoxy5G03746' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3RQ047' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C7GMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9C8JER' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MBL6KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YXCZ83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZANX40' => 'arhy', 'AT1G12990' => 'ath', 'AT1G67880' => 'ath', 'AT2G13290' => 'ath', 'AT3G01620' => 'ath', 'AT3G26445' => 'ath', 'AT3G27540' => 'ath', 'AT5G14480' => 'ath', 'ATR0824G026' => 'atr', 'ATR1098G019' => 'atr', 'Atru.chr11.2145' => 'acertr', 'Atru.chr2.3636' => 'acertr', 'Atru.chr2.3644' => 'acertr', 'Atru.chr6.2422' => 'acertr', 'Atru.chr7.1112' => 'acertr', 'AUR62005469' => 'cqu', 'AUR62011166' => 'cqu', 'AUR62013319' => 'cqu', 'AUR62024273' => 'cqu', 'AUR62028420' => 'cqu', 'AUR62041942' => 'cqu', 'BcaB01g04969' => 'bca', 'BcaB01g06371' => 'bca', 'BcaB02g11494' => 'bca', 'BcaB03g15382' => 'bca', 'BcaB08g36994' => 'bca', 'BcaC03g13477' => 'bca', 'BcaC03g13478' => 'bca', 'BcaC03g13480' => 'bca', 'BcaC03g13481' => 'bca', 'BcaC03g13486' => 'bca', 'BcaC04g19031' => 'bca', 'BcaC04g23085' => 'bca', 'BcaC05g25094' => 'bca', 'BcaC05g25096' => 'bca', 'BcaC05g25138' => 'bca', 'BcaC05g30416' => 'bca', 'BcaC05g30455' => 'bca', 'BcaC06g30979' => 'bca', 'BcaC06g33805' => 'bca', 'BcaC08g46021' => 'bca', 'BcaNung03154' => 'bca', 'BolC2t06623H' => 'bol', 'BolC2t06632H' => 'bol', 'BolC2t06635H' => 'bol', 'BolC2t06638H' => 'bol', 'BolC3t13266H' => 'bol', 'BolC5t29776H' => 'bol', 'BolC6t38912H' => 'bol', 'BolC7t44183H' => 'bol', 'BolC9t54123H' => 'bol', 'BolC9t59107H' => 'bol', 'BraA02t05221Z' => 'bra', 'BraA03t09996Z' => 'bra', 'BraA05t23210Z' => 'bra', 'BraA06t24068Z' => 'bra', 'BraA06t27032Z' => 'bra', 'BraA08t35176Z' => 'bra', 'BraA09t36680Z' => 'bra', 'BraA10t44471Z' => 'bra', 'C02p06760' => 'bna', 'C02p06890' => 'bna', 'C02p07010' => 'bna', 'C03p07660' => 'bna', 'C05p10300' => 'bna', 'C06p38150' => 'bna', 'C07p36650' => 'bna', 'C08p15770' => 'bna', 'C09p12300' => 'bna', 'C09p62700' => 'bna', 'C09p75040' => 'bna', 'CAN.G13.1' => 'can', 'CAN.G138.4' => 'can', 'CAN.G44.6' => 'can', 'CAN.G473.19' => 'can', 'CANSAT01G0835' => 'cansat', 'CANSAT11G0246' => 'cansat', 'CANSAT11G1766' => 'cansat', 'CANSAT64G1954' => 'cansat', 'CARHR013330' => 'chi', 'CARHR060530' => 'chi', 'CARHR075300' => 'chi', 'CARHR105120' => 'chi', 'CARHR148910' => 'chi', 'CARHR198830' => 'chi', 'Carub.0001s1275' => 'cru', 'Carub.0002s1437' => 'cru', 'Carub.0003s0044' => 'cru', 'Carub.0003s2787' => 'cru', 'Carub.0005s0597' => 'cru', 'Carub.0006s1266' => 'cru', 'Ca_06935_v3' => 'car', 'Ca_13559_v3' => 'car', 'Ca_16941_v3' => 'car', 'Ca_16960_v3' => 'car', 'Ca_17775_v3' => 'car', 'Ca_30464_v3' => 'car', 'Cc06_g08160' => 'ccan', 'Cc07_g01520' => 'ccan', 'Cc11_g15810' => 'ccan', 'CDE02G2840' => 'cde', 'CDE03G0093' => 'cde', 'CDE04G2127' => 'cde', 'CDE07G1857' => 'cde', 'CDE09G1246' => 'cde', 'Cfa003412' => 'cfa', 'Cfa007341' => 'cfa', 'Cfa009220' => 'cfa', 'Ciclev10008737m.g' => 'ccl', 'Ciclev10015565m.g' => 'ccl', 'Ciclev10031761m.g' => 'ccl', 'CiPaw.03G045300' => 'cil', 'CiPaw.03G247200' => 'cil', 'CiPaw.04G029500' => 'cil', 'CiPaw.04G174000' => 'cil', 'CiPaw.05G181200' => 'cil', 'CiPaw.06G067100' => 'cil', 'ClCG05G025800' => 'cla', 'ClCG06G011400' => 'cla', 'ClCG09G019360' => 'cla', 'COL.COLO4_04827' => 'col', 'COL.COLO4_29170' => 'col', 'COL.COLO4_35131' => 'col', 'COL.COLO4_35132' => 'col', 'Cpa.g.sc33.32' => 'cpa', 'Cpa.g.sc46.29' => 'cpa', 'Cpa.g.sc796.1' => 'cpa', 'CsaV3_1G030420' => 'csa', 'CsaV3_5G027050' => 'csa', 'CsaV3_5G031040' => 'csa', 'CsaV3_UNG023130' => 'csa', 'CSS0007726' => 'camsi', 'CSS0016433' => 'camsi', 'CSS0017656' => 'camsi', 'CSS0025364' => 'camsi', 'CSS0027582' => 'camsi', 'CSS0047288' => 'camsi', 'CSS0049950' => 'camsi', 'DCAR_003843' => 'dca', 'DCAR_007052' => 'dca', 'DCAR_020884' => 'dca', 'DCAR_021730' => 'dca', 'DCAR_024423' => 'dca', 'DCAR_026509' => 'dca', 'DCAR_031158' => 'dca', 'Dinv14728' => 'din', 'Dinv15219' => 'din', 'Dinv25728' => 'din', 'Dinv33428' => 'din', 'Dinv36489' => 'din', 'Dinv41486' => 'din', 'Duzib147G0469' => 'dzi', 'Duzib168G0060' => 'dzi', 'Duzib187G1215' => 'dzi', 'Duzib248G0692' => 'dzi', 'Duzib251G0767' => 'dzi', 'Duzib264G0446' => 'dzi', 'Duzib268G0691' => 'dzi', 'ECA232G4767' => 'eca', 'ECA233G2838' => 'eca', 'ECA234G0391' => 'eca', 'ECA234G0857' => 'eca', 'ECA236G1593' => 'eca', 'ECA238G0565' => 'eca', 'ECA246G1027' => 'eca', 'ECA246G3223' => 'eca', 'ECA246G3470' => 'eca', 'EL10Ac6g13829' => 'bvu', 'EL10Ac6g14093' => 'bvu', 'EL10Ac8g18707' => 'bvu', 'Eucgr.C01369' => 'egr', 'Eucgr.H02492' => 'egr', 'Eucgr.I01733' => 'egr', 'Eucgr.J02255' => 'egr', 'Eucgr.J02257' => 'egr', 'Eucgr.J02258' => 'egr', 'FAN02G1601' => 'fan', 'FAN03G1586' => 'fan', 'FAN03G2986' => 'fan', 'FAN05G4837' => 'fan', 'FAN06G0146' => 'fan', 'FAN07G0858' => 'fan', 'FAN09G3179' => 'fan', 'FAN10G0669' => 'fan', 'FAN12G2358' => 'fan', 'FAN14G4198' => 'fan', 'FAN14G5112' => 'fan', 'FAN17G0342' => 'fan', 'FAN19G0342' => 'fan', 'FAN19G0962' => 'fan', 'FAN19G1101' => 'fan', 'FAN19G1872' => 'fan', 'FAN22G0356' => 'fan', 'FAN23G0744' => 'fan', 'FAN23G1914' => 'fan', 'FAN26G0032' => 'fan', 'FAN28G0625' => 'fan', 'FvH4_1g02710' => 'fve', 'FvH4_1g02720' => 'fve', 'FvH4_4g25670' => 'fve', 'FvH4_6g51700' => 'fve', 'FvH4_7g20170' => 'fve', 'Glyma.05G175000' => 'gma', 'Glyma.08G132300' => 'gma', 'Glyma.11G243000' => 'gma', 'Glyma.13G158900' => 'gma', 'Glyma.17G112400' => 'gma', 'Glyma.18G014100' => 'gma', 'Glyma.19G003100' => 'gma', 'Glyma.19G056500' => 'gma', 'Gohir.A01G158900' => 'ghi', 'Gohir.A05G312600' => 'ghi', 'Gohir.A05G354900' => 'ghi', 'Gohir.A07G037200' => 'ghi', 'Gohir.A09G030000' => 'ghi', 'Gohir.A12G145200' => 'ghi', 'Gohir.D01G151500' => 'ghi', 'Gohir.D04G058300' => 'ghi', 'Gohir.D05G314100' => 'ghi', 'Gohir.D07G041400' => 'ghi', 'Gohir.D09G029700' => 'ghi', 'Gohir.D12G149700' => 'ghi', 'Gorai.001G043800' => 'gra', 'Gorai.002G187800' => 'gra', 'Gorai.006G034700' => 'gra', 'Gorai.008G161200' => 'gra', 'Gorai.009G335700' => 'gra', 'Gorai.012G065000' => 'gra', 'GSVIVG01000535001' => 'vvi', 'GSVIVG01015572001' => 'vvi', 'GSVIVG01032386001' => 'vvi', 'HanXRQChr05g0138531' => 'han', 'HanXRQChr06g0174391' => 'han', 'HanXRQChr07g0199021' => 'han', 'HanXRQChr08g0208211' => 'han', 'HanXRQChr09g0255471' => 'han', 'HanXRQChr10g0315791' => 'han', 'HanXRQChr12g0371991' => 'han', 'HanXRQChr15g0475251' => 'han', 'HanXRQChr17g0540001' => 'han', 'HanXRQChr17g0548631' => 'han', 'HanXRQChr17g0569561' => 'han', 'Haze_12256' => 'cav', 'Haze_14756' => 'cav', 'Haze_25528' => 'cav', 'Hma1.2p1_0079F.1_g041020' => 'hma', 'Hma1.2p1_0818F.1_g223260' => 'hma', 'Hma1.2p1_1747F.1_g300530' => 'hma', 'HPP92_004607' => 'vpl', 'HPP92_004608' => 'vpl', 'HPP92_006181' => 'vpl', 'HPP92_012192' => 'vpl', 'HPP92_015680' => 'vpl', 'HPP92_020249' => 'vpl', 'HPP92_021376' => 'vpl', 'HPP92_024275' => 'vpl', 'Hund06031' => 'sun', 'Hund25391' => 'sun', 'Lalb_Chr07g0185371' => 'lal', 'Lalb_Chr07g0185381' => 'lal', 'Lalb_Chr12g0204011' => 'lal', 'Lalb_Chr13g0301671' => 'lal', 'Lalb_Chr14g0362851' => 'lal', 'Lalb_Chr24g0403581' => 'lal', 'Lj1g0000233' => 'lja', 'Lj2g0018120' => 'lja', 'Lj3C621T0' => 'lonja', 'Lj3P1059T14' => 'lonja', 'Lj3P611T9' => 'lonja', 'Lj3P614T13' => 'lonja', 'Lj3P615T5' => 'lonja', 'Lj4g0012315' => 'lja', 'Lj4g0026182' => 'lja', 'Lj6P813T16' => 'lonja', 'Lj7C427T7' => 'lonja', 'Lj7C427T8' => 'lonja', 'Lj7P600T41' => 'lonja', 'Lju41C42G17' => 'lonja', 'Lsat_1_v5_gn_0_47300' => 'lsa', 'Lsat_1_v5_gn_2_91280' => 'lsa', 'Lsat_1_v5_gn_3_30561' => 'lsa', 'Lsat_1_v5_gn_4_184321' => 'lsa', 'Lsat_1_v5_gn_4_4041' => 'lsa', 'Lsat_1_v5_gn_5_92000' => 'lsa', 'Lsat_1_v5_gn_8_152940' => 'lsa', 'Lsat_1_v5_gn_8_62401' => 'lsa', 'Manes.06G055900' => 'mes', 'Manes.12G022200' => 'mes', 'Manes.13G023300' => 'mes', 'Manes.14G115000' => 'mes', 'Manes.15G151700' => 'mes', 'Manes.17G111300' => 'mes', 'Mapoly0226s0009' => 'mpo', 'MBI02_g25363_MAGBIO' => 'mbi', 'MBI06_g00027_MAGBIO' => 'mbi', 'MBI10_g13034_MAGBIO' => 'mbi', 'MD09G1023400' => 'mdo', 'MD13G1100100' => 'mdo', 'MD15G1169200' => 'mdo', 'MD16G1101100' => 'mdo', 'MD17G1022900' => 'mdo', 'Medtr3g096150' => 'mtr', 'Medtr4g115070' => 'mtr', 'Medtr7g033325' => 'mtr', 'Medtr8g089840' => 'mtr', 'MELO3C010319.2' => 'cme', 'MELO3C011944.2' => 'cme', 'MELO3C021589.2' => 'cme', 'Migut.E00207' => 'egut', 'Migut.H00067' => 'egut', 'Migut.K00433' => 'egut', 'Migut.K00606' => 'egut', 'Migut.K01410' => 'egut', 'MSTRG.13347' => 'ama', 'MSTRG.24045' => 'ama', 'MSTRG.2428' => 'ama', 'MSTRG.26410' => 'ama', 'MSTRG.3139' => 'ama', 'MSTRG.3286' => 'ama', 'MSTRG.563' => 'ama', 'MSTRG.7941' => 'ama', 'Nitab4.5_0000028g0060' => 'nta', 'Nitab4.5_0000065g0260' => 'nta', 'Nitab4.5_0000112g0060' => 'nta', 'Nitab4.5_0000489g0120' => 'nta', 'Nitab4.5_0001776g0050' => 'nta', 'Nitab4.5_0001854g0010' => 'nta', 'Nitab4.5_0001860g0020' => 'nta', 'Nitab4.5_0004352g0010' => 'nta', 'Nitab4.5_0008716g0020' => 'nta', 'Nitab4.5_0008922g0010' => 'nta', 'Nn3g16693' => 'nnu', 'Nn4g22596' => 'nnu', 'Nn7g37639' => 'nnu', 'Oeu001701.1' => 'oeu', 'Oeu018149.1' => 'oeu', 'Oeu026220.1' => 'oeu', 'Oeu038635.1' => 'oeu', 'Oeu049176.1' => 'oeu', 'Oeu056706.1' => 'oeu', 'Oeu056937.1' => 'oeu', 'Oeu057540.1' => 'oeu', 'Os02g0594900' => 'osa', 'Os02g0595100' => 'osa', 'Os04g0477500' => 'osa', 'Os12g0611900' => 'osa', 'Peaxi162Scf00076g00020' => 'pax', 'Peaxi162Scf00128g00217' => 'pax', 'Peaxi162Scf00129g01640' => 'pax', 'Peaxi162Scf00669g00007' => 'pax', 'Peaxi162Scf00700g00421' => 'pax', 'Peaxi162Scf00801g00038' => 'pax', 'Peaxi162Scf00891g00025' => 'pax', 'PGR083G0909' => 'pgr', 'PGR119G1005' => 'pgr', 'PGR142G2236' => 'pgr', 'PGR142G3388' => 'pgr', 'PGSC0003DMG400004514' => 'stu', 'PGSC0003DMG400012635' => 'stu', 'PGSC0003DMG400015730' => 'stu', 'PGSC0003DMG400018611' => 'stu', 'PGSC0003DMG400030897' => 'stu', 'Phvul.001G254800' => 'pvu', 'Phvul.002G260100' => 'pvu', 'Phvul.003G167600' => 'pvu', 'Phvul.004G005100' => 'pvu', 'Potri.001G343600' => 'ptr', 'Potri.006G066700' => 'ptr', 'Potri.008G186000' => 'ptr', 'Potri.010G046900' => 'ptr', 'Potri.018G127900' => 'ptr', 'Pp3c20_17750' => 'ppa', 'Pp3c24_4380' => 'ppa', 'Prupe.1G245800' => 'ppe', 'Prupe.3G293400' => 'ppe', 'Prupe.7G247400' => 'ppe', 'Psat0s145g0120' => 'psa', 'Psat0s595g0040' => 'psa', 'Psat0s595g0120' => 'psa', 'Psat3g175040' => 'psa', 'Psat7g058120' => 'psa', 'PSO017G0428' => 'pso', 'PSO063G7510' => 'pso', 'PSO067G0046' => 'pso', 'PSO478G1073' => 'pso', 'PSO675G3677' => 'pso', 'PSO675G6558' => 'pso', 'PSO675G7520' => 'pso', 'PSO675G8959' => 'pso', 'QL02p074089' => 'qlo', 'QL02p089614' => 'qlo', 'QL03p057736' => 'qlo', 'RcHm_v2.0_Chr1g0364131' => 'rch', 'RcHm_v2.0_Chr2g0087801' => 'rch', 'RcHm_v2.0_Chr2g0087821' => 'rch', 'RcHm_v2.0_Chr2g0173231' => 'rch', 'RcHm_v2.0_Chr4g0433111' => 'rch', 'Rhsim03G0250300' => 'rsi', 'Rhsim08G0048400' => 'rsi', 'Rhsim10G0014800' => 'rsi', 'Rhsim12G0040100' => 'rsi', 'Rhsim12G0109700' => 'rsi', 'Sabra06G0049600' => 'sbr', 'Sabra08G0141000' => 'sbr', 'Sabra10G0021400' => 'sbr', 'Sabra16G0222900' => 'sbr', 'Sabra18G0108600' => 'sbr', 'SalBow1G0433' => 'sbo', 'SalBow1G2038' => 'sbo', 'SalBow1G5003' => 'sbo', 'SalBow7G1197' => 'sbo', 'SalBow8G3506' => 'sbo', 'Sc03g0007300' => 'sci', 'Sc11g0000950' => 'sci', 'Sc14g0008750' => 'sci', 'Sc18g0000420' => 'sci', 'Sed0006754' => 'sed', 'Sed0008741' => 'sed', 'Sed0017172' => 'sed', 'Sed0018925' => 'sed', 'Sed0023326' => 'sed', 'Sed0025909' => 'sed', 'SEGI_05333' => 'sgi', 'SEGI_10362' => 'sgi', 'SEGI_13380' => 'sgi', 'SEGI_24306' => 'sgi', 'SEGI_29077' => 'sgi', 'SEGI_29095' => 'sgi', 'SEGI_36534' => 'sgi', 'SEGI_37506' => 'sgi', 'SEGI_38321' => 'sgi', 'SGA_v2.0_scaffold307G48031' => 'sas', 'SGA_v2.0_scaffold47G17507' => 'sas', 'SGA_v2.0_scaffold63G21736' => 'sas', 'SGA_v2.0_scaffold87G27070' => 'sas', 'SHI17794' => 'shi', 'SHI28851' => 'shi', 'SMO165G0155' => 'smo', 'SMO340G0217' => 'smo', 'SMO367G1210' => 'smo', 'Solyc02g093430.3' => 'sly', 'Solyc05g013580.4' => 'sly', 'Solyc07g008030.3' => 'sly', 'Solyc12g035470.2' => 'sly', 'Sopen02g038020' => 'spe', 'Sopen05g008490' => 'spe', 'Sopen07g003910' => 'spe', 'Sopen12g015240' => 'spe', 'Sp1g11550' => 'spa', 'Sp2g16710' => 'spa', 'Sp3g00430' => 'spa', 'Sp3g26780' => 'spa', 'Sp5g22900' => 'spa', 'Sp6g29530' => 'spa', 'TAR371G0794' => 'tar', 'TAR374G0164' => 'tar', 'TAR622G0165' => 'tar', 'TAR626G0929' => 'tar', 'TAR629G2155' => 'tar', 'THA.LOC104805282' => 'tha', 'THA.LOC104805363' => 'tha', 'THA.LOC104808968' => 'tha', 'THA.LOC104821093' => 'tha', 'THA.LOC104823953' => 'tha', 'THA.LOC104825562' => 'tha', 'THA.LOC104825665' => 'tha', 'Thecc.02G261400' => 'tca', 'Thecc.04G019200' => 'tca', 'Thecc.09G130400' => 'tca', 'Thhalv10004374m.g' => 'esa', 'Thhalv10007850m.g' => 'esa', 'Thhalv10013782m.g' => 'esa', 'Thhalv10018686m.g' => 'esa', 'Thhalv10020899m.g' => 'esa', 'Thhalv10022755m.g' => 'esa', 'TPR.G23851' => 'tpr', 'TPR.G26500' => 'tpr', 'TPR.G27267' => 'tpr', 'TPR.G32001' => 'tpr', 'TPR.G6251' => 'tpr', 'TPR.G8167' => 'tpr', 'TWI12G1330' => 'twi', 'TWI18G1239' => 'twi', 'TWI34G0979' => 'twi', 'TWI36G0670' => 'twi', 'TWI36G0707' => 'twi', 'TWI56G0233' => 'twi', 'TWI75G1809' => 'twi', 'unitig_21.g20874' => 'ugi', 'unitig_26.g10343' => 'ugi', 'unitig_46.g18392' => 'ugi', 'unitig_52.g17178' => 'ugi', 'unitig_8.g2934' => 'ugi', 'vmacro01122' => 'vma', 'vmacro05875' => 'vma', 'vmacro06147' => 'vma', 'vmacro16191' => 'vma', 'vmacro18293' => 'vma', 'VMungo0251G3707' => 'vmu', 'VMungo0464G1521' => 'vmu', 'VMungo1215G0205' => 'vmu', 'VMungo1383G2484' => 'vmu', 'Zm00001eb079610' => 'zma', 'Zm00001eb135990' => 'zma', 'Zm00001eb183710' => 'zma', 'Zm00001eb246020' => 'zma' ) $gf_id = 'HOM05D001124' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001124' ) $data_identifier = 'HOM05D001124' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 6, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 7, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 21, 'bol' => (int) 10, 'bra' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 6, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 9, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 21, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 8, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 10, 'lsa' => (int) 8, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 8, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 9, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb246020' $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' => 'HOM05D001124', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '548', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02520' => 'bna', 'A03p06630' => 'bna', 'A05p44460' => 'bna', 'A06p08710' => 'bna', 'A06p41090' => 'bna', 'A07p32320' => 'bna', 'A08p32520' => 'bna', 'A09p10360' => 'bna', 'A10p24080' => 'bna', 'Aa31LG11G15250' => 'aar', 'Aa31LG1G1800' => 'aar', 'Aa31LG2G5120' => 'aar', 'Aa31LG2G6070' => 'aar', 'Aa31LG5G10770' => 'aar', 'Aa31sc61G90' => 'aar', 'Actinidia01352' => 'ach', 'Actinidia05983' => 'ach', 'Actinidia08133' => 'ach', 'Actinidia15101' => 'ach', 'Actinidia26379' => 'ach', 'Actinidia35778' => 'ach', 'Actinidia36123' => 'ach', 'Actinidia37436' => 'ach', 'Actinidia38730' => 'ach', 'Ah.02g128210' => 'amhyb', 'Ah.03g132990' => 'amhyb', 'Ah.14g079410' => 'amhyb', 'AL1G24640' => 'aly', 'AL2G26680' => 'aly', 'AL3G10530' => 'aly', 'AL3G45230' => 'aly', 'AL5G15230' => 'aly', 'AL5G16960' => 'aly', 'AL6G25210' => 'aly', 'Aqoxy2G00441' => 'aox', 'Aqoxy3G01236' => 'aox', 'Aqoxy5G03746' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3RQ047' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C7GMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9C8JER' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MBL6KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YXCZ83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZANX40' => 'arhy', 'AT1G12990' => 'ath', 'AT1G67880' => 'ath', 'AT2G13290' => 'ath', 'AT3G01620' => 'ath', 'AT3G26445' => 'ath', 'AT3G27540' => 'ath', 'AT5G14480' => 'ath', 'ATR0824G026' => 'atr', 'ATR1098G019' => 'atr', 'Atru.chr11.2145' => 'acertr', 'Atru.chr2.3636' => 'acertr', 'Atru.chr2.3644' => 'acertr', 'Atru.chr6.2422' => 'acertr', 'Atru.chr7.1112' => 'acertr', 'AUR62005469' => 'cqu', 'AUR62011166' => 'cqu', 'AUR62013319' => 'cqu', 'AUR62024273' => 'cqu', 'AUR62028420' => 'cqu', 'AUR62041942' => 'cqu', 'BcaB01g04969' => 'bca', 'BcaB01g06371' => 'bca', 'BcaB02g11494' => 'bca', 'BcaB03g15382' => 'bca', 'BcaB08g36994' => 'bca', 'BcaC03g13477' => 'bca', 'BcaC03g13478' => 'bca', 'BcaC03g13480' => 'bca', 'BcaC03g13481' => 'bca', 'BcaC03g13486' => 'bca', 'BcaC04g19031' => 'bca', 'BcaC04g23085' => 'bca', 'BcaC05g25094' => 'bca', 'BcaC05g25096' => 'bca', 'BcaC05g25138' => 'bca', 'BcaC05g30416' => 'bca', 'BcaC05g30455' => 'bca', 'BcaC06g30979' => 'bca', 'BcaC06g33805' => 'bca', 'BcaC08g46021' => 'bca', 'BcaNung03154' => 'bca', 'BolC2t06623H' => 'bol', 'BolC2t06632H' => 'bol', 'BolC2t06635H' => 'bol', 'BolC2t06638H' => 'bol', 'BolC3t13266H' => 'bol', 'BolC5t29776H' => 'bol', 'BolC6t38912H' => 'bol', 'BolC7t44183H' => 'bol', 'BolC9t54123H' => 'bol', 'BolC9t59107H' => 'bol', 'BraA02t05221Z' => 'bra', 'BraA03t09996Z' => 'bra', 'BraA05t23210Z' => 'bra', 'BraA06t24068Z' => 'bra', 'BraA06t27032Z' => 'bra', 'BraA08t35176Z' => 'bra', 'BraA09t36680Z' => 'bra', 'BraA10t44471Z' => 'bra', 'C02p06760' => 'bna', 'C02p06890' => 'bna', 'C02p07010' => 'bna', 'C03p07660' => 'bna', 'C05p10300' => 'bna', 'C06p38150' => 'bna', 'C07p36650' => 'bna', 'C08p15770' => 'bna', 'C09p12300' => 'bna', 'C09p62700' => 'bna', 'C09p75040' => 'bna', 'CAN.G13.1' => 'can', 'CAN.G138.4' => 'can', 'CAN.G44.6' => 'can', 'CAN.G473.19' => 'can', 'CANSAT01G0835' => 'cansat', 'CANSAT11G0246' => 'cansat', 'CANSAT11G1766' => 'cansat', 'CANSAT64G1954' => 'cansat', 'CARHR013330' => 'chi', 'CARHR060530' => 'chi', 'CARHR075300' => 'chi', 'CARHR105120' => 'chi', 'CARHR148910' => 'chi', 'CARHR198830' => 'chi', 'Carub.0001s1275' => 'cru', 'Carub.0002s1437' => 'cru', 'Carub.0003s0044' => 'cru', 'Carub.0003s2787' => 'cru', 'Carub.0005s0597' => 'cru', 'Carub.0006s1266' => 'cru', 'Ca_06935_v3' => 'car', 'Ca_13559_v3' => 'car', 'Ca_16941_v3' => 'car', 'Ca_16960_v3' => 'car', 'Ca_17775_v3' => 'car', 'Ca_30464_v3' => 'car', 'Cc06_g08160' => 'ccan', 'Cc07_g01520' => 'ccan', 'Cc11_g15810' => 'ccan', 'CDE02G2840' => 'cde', 'CDE03G0093' => 'cde', 'CDE04G2127' => 'cde', 'CDE07G1857' => 'cde', 'CDE09G1246' => 'cde', 'Cfa003412' => 'cfa', 'Cfa007341' => 'cfa', 'Cfa009220' => 'cfa', 'Ciclev10008737m.g' => 'ccl', 'Ciclev10015565m.g' => 'ccl', 'Ciclev10031761m.g' => 'ccl', 'CiPaw.03G045300' => 'cil', 'CiPaw.03G247200' => 'cil', 'CiPaw.04G029500' => 'cil', 'CiPaw.04G174000' => 'cil', 'CiPaw.05G181200' => 'cil', 'CiPaw.06G067100' => 'cil', 'ClCG05G025800' => 'cla', 'ClCG06G011400' => 'cla', 'ClCG09G019360' => 'cla', 'COL.COLO4_04827' => 'col', 'COL.COLO4_29170' => 'col', 'COL.COLO4_35131' => 'col', 'COL.COLO4_35132' => 'col', 'Cpa.g.sc33.32' => 'cpa', 'Cpa.g.sc46.29' => 'cpa', 'Cpa.g.sc796.1' => 'cpa', 'CsaV3_1G030420' => 'csa', 'CsaV3_5G027050' => 'csa', 'CsaV3_5G031040' => 'csa', 'CsaV3_UNG023130' => 'csa', 'CSS0007726' => 'camsi', 'CSS0016433' => 'camsi', 'CSS0017656' => 'camsi', 'CSS0025364' => 'camsi', 'CSS0027582' => 'camsi', 'CSS0047288' => 'camsi', 'CSS0049950' => 'camsi', 'DCAR_003843' => 'dca', 'DCAR_007052' => 'dca', 'DCAR_020884' => 'dca', 'DCAR_021730' => 'dca', 'DCAR_024423' => 'dca', 'DCAR_026509' => 'dca', 'DCAR_031158' => 'dca', 'Dinv14728' => 'din', 'Dinv15219' => 'din', 'Dinv25728' => 'din', 'Dinv33428' => 'din', 'Dinv36489' => 'din', 'Dinv41486' => 'din', 'Duzib147G0469' => 'dzi', 'Duzib168G0060' => 'dzi', 'Duzib187G1215' => 'dzi', 'Duzib248G0692' => 'dzi', 'Duzib251G0767' => 'dzi', 'Duzib264G0446' => 'dzi', 'Duzib268G0691' => 'dzi', 'ECA232G4767' => 'eca', 'ECA233G2838' => 'eca', 'ECA234G0391' => 'eca', 'ECA234G0857' => 'eca', 'ECA236G1593' => 'eca', 'ECA238G0565' => 'eca', 'ECA246G1027' => 'eca', 'ECA246G3223' => 'eca', 'ECA246G3470' => 'eca', 'EL10Ac6g13829' => 'bvu', 'EL10Ac6g14093' => 'bvu', 'EL10Ac8g18707' => 'bvu', 'Eucgr.C01369' => 'egr', 'Eucgr.H02492' => 'egr', 'Eucgr.I01733' => 'egr', 'Eucgr.J02255' => 'egr', 'Eucgr.J02257' => 'egr', 'Eucgr.J02258' => 'egr', 'FAN02G1601' => 'fan', 'FAN03G1586' => 'fan', 'FAN03G2986' => 'fan', 'FAN05G4837' => 'fan', 'FAN06G0146' => 'fan', 'FAN07G0858' => 'fan', 'FAN09G3179' => 'fan', 'FAN10G0669' => 'fan', 'FAN12G2358' => 'fan', 'FAN14G4198' => 'fan', 'FAN14G5112' => 'fan', 'FAN17G0342' => 'fan', 'FAN19G0342' => 'fan', 'FAN19G0962' => 'fan', 'FAN19G1101' => 'fan', 'FAN19G1872' => 'fan', 'FAN22G0356' => 'fan', 'FAN23G0744' => 'fan', 'FAN23G1914' => 'fan', 'FAN26G0032' => 'fan', 'FAN28G0625' => 'fan', 'FvH4_1g02710' => 'fve', 'FvH4_1g02720' => 'fve', 'FvH4_4g25670' => 'fve', 'FvH4_6g51700' => 'fve', 'FvH4_7g20170' => 'fve', 'Glyma.05G175000' => 'gma', 'Glyma.08G132300' => 'gma', 'Glyma.11G243000' => 'gma', 'Glyma.13G158900' => 'gma', 'Glyma.17G112400' => 'gma', 'Glyma.18G014100' => 'gma', 'Glyma.19G003100' => 'gma', 'Glyma.19G056500' => 'gma', 'Gohir.A01G158900' => 'ghi', 'Gohir.A05G312600' => 'ghi', 'Gohir.A05G354900' => 'ghi', 'Gohir.A07G037200' => 'ghi', 'Gohir.A09G030000' => 'ghi', 'Gohir.A12G145200' => 'ghi', 'Gohir.D01G151500' => 'ghi', 'Gohir.D04G058300' => 'ghi', 'Gohir.D05G314100' => 'ghi', 'Gohir.D07G041400' => 'ghi', 'Gohir.D09G029700' => 'ghi', 'Gohir.D12G149700' => 'ghi', 'Gorai.001G043800' => 'gra', 'Gorai.002G187800' => 'gra', 'Gorai.006G034700' => 'gra', 'Gorai.008G161200' => 'gra', 'Gorai.009G335700' => 'gra', 'Gorai.012G065000' => 'gra', 'GSVIVG01000535001' => 'vvi', 'GSVIVG01015572001' => 'vvi', 'GSVIVG01032386001' => 'vvi', 'HanXRQChr05g0138531' => 'han', 'HanXRQChr06g0174391' => 'han', 'HanXRQChr07g0199021' => 'han', 'HanXRQChr08g0208211' => 'han', 'HanXRQChr09g0255471' => 'han', 'HanXRQChr10g0315791' => 'han', 'HanXRQChr12g0371991' => 'han', 'HanXRQChr15g0475251' => 'han', 'HanXRQChr17g0540001' => 'han', 'HanXRQChr17g0548631' => 'han', 'HanXRQChr17g0569561' => 'han', 'Haze_12256' => 'cav', 'Haze_14756' => 'cav', 'Haze_25528' => 'cav', 'Hma1.2p1_0079F.1_g041020' => 'hma', 'Hma1.2p1_0818F.1_g223260' => 'hma', 'Hma1.2p1_1747F.1_g300530' => 'hma', 'HPP92_004607' => 'vpl', 'HPP92_004608' => 'vpl', 'HPP92_006181' => 'vpl', 'HPP92_012192' => 'vpl', 'HPP92_015680' => 'vpl', 'HPP92_020249' => 'vpl', 'HPP92_021376' => 'vpl', 'HPP92_024275' => 'vpl', 'Hund06031' => 'sun', 'Hund25391' => 'sun', 'Lalb_Chr07g0185371' => 'lal', 'Lalb_Chr07g0185381' => 'lal', 'Lalb_Chr12g0204011' => 'lal', 'Lalb_Chr13g0301671' => 'lal', 'Lalb_Chr14g0362851' => 'lal', 'Lalb_Chr24g0403581' => 'lal', 'Lj1g0000233' => 'lja', 'Lj2g0018120' => 'lja', 'Lj3C621T0' => 'lonja', 'Lj3P1059T14' => 'lonja', 'Lj3P611T9' => 'lonja', 'Lj3P614T13' => 'lonja', 'Lj3P615T5' => 'lonja', 'Lj4g0012315' => 'lja', 'Lj4g0026182' => 'lja', 'Lj6P813T16' => 'lonja', 'Lj7C427T7' => 'lonja', 'Lj7C427T8' => 'lonja', 'Lj7P600T41' => 'lonja', 'Lju41C42G17' => 'lonja', 'Lsat_1_v5_gn_0_47300' => 'lsa', 'Lsat_1_v5_gn_2_91280' => 'lsa', 'Lsat_1_v5_gn_3_30561' => 'lsa', 'Lsat_1_v5_gn_4_184321' => 'lsa', 'Lsat_1_v5_gn_4_4041' => 'lsa', 'Lsat_1_v5_gn_5_92000' => 'lsa', 'Lsat_1_v5_gn_8_152940' => 'lsa', 'Lsat_1_v5_gn_8_62401' => 'lsa', 'Manes.06G055900' => 'mes', 'Manes.12G022200' => 'mes', 'Manes.13G023300' => 'mes', 'Manes.14G115000' => 'mes', 'Manes.15G151700' => 'mes', 'Manes.17G111300' => 'mes', 'Mapoly0226s0009' => 'mpo', 'MBI02_g25363_MAGBIO' => 'mbi', 'MBI06_g00027_MAGBIO' => 'mbi', 'MBI10_g13034_MAGBIO' => 'mbi', 'MD09G1023400' => 'mdo', 'MD13G1100100' => 'mdo', 'MD15G1169200' => 'mdo', 'MD16G1101100' => 'mdo', 'MD17G1022900' => 'mdo', 'Medtr3g096150' => 'mtr', 'Medtr4g115070' => 'mtr', 'Medtr7g033325' => 'mtr', 'Medtr8g089840' => 'mtr', 'MELO3C010319.2' => 'cme', 'MELO3C011944.2' => 'cme', 'MELO3C021589.2' => 'cme', 'Migut.E00207' => 'egut', 'Migut.H00067' => 'egut', 'Migut.K00433' => 'egut', 'Migut.K00606' => 'egut', 'Migut.K01410' => 'egut', 'MSTRG.13347' => 'ama', 'MSTRG.24045' => 'ama', 'MSTRG.2428' => 'ama', 'MSTRG.26410' => 'ama', 'MSTRG.3139' => 'ama', 'MSTRG.3286' => 'ama', 'MSTRG.563' => 'ama', 'MSTRG.7941' => 'ama', 'Nitab4.5_0000028g0060' => 'nta', 'Nitab4.5_0000065g0260' => 'nta', 'Nitab4.5_0000112g0060' => 'nta', 'Nitab4.5_0000489g0120' => 'nta', 'Nitab4.5_0001776g0050' => 'nta', 'Nitab4.5_0001854g0010' => 'nta', 'Nitab4.5_0001860g0020' => 'nta', 'Nitab4.5_0004352g0010' => 'nta', 'Nitab4.5_0008716g0020' => 'nta', 'Nitab4.5_0008922g0010' => 'nta', 'Nn3g16693' => 'nnu', 'Nn4g22596' => 'nnu', 'Nn7g37639' => 'nnu', 'Oeu001701.1' => 'oeu', 'Oeu018149.1' => 'oeu', 'Oeu026220.1' => 'oeu', 'Oeu038635.1' => 'oeu', 'Oeu049176.1' => 'oeu', 'Oeu056706.1' => 'oeu', 'Oeu056937.1' => 'oeu', 'Oeu057540.1' => 'oeu', 'Os02g0594900' => 'osa', 'Os02g0595100' => 'osa', 'Os04g0477500' => 'osa', 'Os12g0611900' => 'osa', 'Peaxi162Scf00076g00020' => 'pax', 'Peaxi162Scf00128g00217' => 'pax', 'Peaxi162Scf00129g01640' => 'pax', 'Peaxi162Scf00669g00007' => 'pax', 'Peaxi162Scf00700g00421' => 'pax', 'Peaxi162Scf00801g00038' => 'pax', 'Peaxi162Scf00891g00025' => 'pax', 'PGR083G0909' => 'pgr', 'PGR119G1005' => 'pgr', 'PGR142G2236' => 'pgr', 'PGR142G3388' => 'pgr', 'PGSC0003DMG400004514' => 'stu', 'PGSC0003DMG400012635' => 'stu', 'PGSC0003DMG400015730' => 'stu', 'PGSC0003DMG400018611' => 'stu', 'PGSC0003DMG400030897' => 'stu', 'Phvul.001G254800' => 'pvu', 'Phvul.002G260100' => 'pvu', 'Phvul.003G167600' => 'pvu', 'Phvul.004G005100' => 'pvu', 'Potri.001G343600' => 'ptr', 'Potri.006G066700' => 'ptr', 'Potri.008G186000' => 'ptr', 'Potri.010G046900' => 'ptr', 'Potri.018G127900' => 'ptr', 'Pp3c20_17750' => 'ppa', 'Pp3c24_4380' => 'ppa', 'Prupe.1G245800' => 'ppe', 'Prupe.3G293400' => 'ppe', 'Prupe.7G247400' => 'ppe', 'Psat0s145g0120' => 'psa', 'Psat0s595g0040' => 'psa', 'Psat0s595g0120' => 'psa', 'Psat3g175040' => 'psa', 'Psat7g058120' => 'psa', 'PSO017G0428' => 'pso', 'PSO063G7510' => 'pso', 'PSO067G0046' => 'pso', 'PSO478G1073' => 'pso', 'PSO675G3677' => 'pso', 'PSO675G6558' => 'pso', 'PSO675G7520' => 'pso', 'PSO675G8959' => 'pso', 'QL02p074089' => 'qlo', 'QL02p089614' => 'qlo', 'QL03p057736' => 'qlo', 'RcHm_v2.0_Chr1g0364131' => 'rch', 'RcHm_v2.0_Chr2g0087801' => 'rch', 'RcHm_v2.0_Chr2g0087821' => 'rch', 'RcHm_v2.0_Chr2g0173231' => 'rch', 'RcHm_v2.0_Chr4g0433111' => 'rch', 'Rhsim03G0250300' => 'rsi', 'Rhsim08G0048400' => 'rsi', 'Rhsim10G0014800' => 'rsi', 'Rhsim12G0040100' => 'rsi', 'Rhsim12G0109700' => 'rsi', 'Sabra06G0049600' => 'sbr', 'Sabra08G0141000' => 'sbr', 'Sabra10G0021400' => 'sbr', 'Sabra16G0222900' => 'sbr', 'Sabra18G0108600' => 'sbr', 'SalBow1G0433' => 'sbo', 'SalBow1G2038' => 'sbo', 'SalBow1G5003' => 'sbo', 'SalBow7G1197' => 'sbo', 'SalBow8G3506' => 'sbo', 'Sc03g0007300' => 'sci', 'Sc11g0000950' => 'sci', 'Sc14g0008750' => 'sci', 'Sc18g0000420' => 'sci', 'Sed0006754' => 'sed', 'Sed0008741' => 'sed', 'Sed0017172' => 'sed', 'Sed0018925' => 'sed', 'Sed0023326' => 'sed', 'Sed0025909' => 'sed', 'SEGI_05333' => 'sgi', 'SEGI_10362' => 'sgi', 'SEGI_13380' => 'sgi', 'SEGI_24306' => 'sgi', 'SEGI_29077' => 'sgi', 'SEGI_29095' => 'sgi', 'SEGI_36534' => 'sgi', 'SEGI_37506' => 'sgi', 'SEGI_38321' => 'sgi', 'SGA_v2.0_scaffold307G48031' => 'sas', 'SGA_v2.0_scaffold47G17507' => 'sas', 'SGA_v2.0_scaffold63G21736' => 'sas', 'SGA_v2.0_scaffold87G27070' => 'sas', 'SHI17794' => 'shi', 'SHI28851' => 'shi', 'SMO165G0155' => 'smo', 'SMO340G0217' => 'smo', 'SMO367G1210' => 'smo', 'Solyc02g093430.3' => 'sly', 'Solyc05g013580.4' => 'sly', 'Solyc07g008030.3' => 'sly', 'Solyc12g035470.2' => 'sly', 'Sopen02g038020' => 'spe', 'Sopen05g008490' => 'spe', 'Sopen07g003910' => 'spe', 'Sopen12g015240' => 'spe', 'Sp1g11550' => 'spa', 'Sp2g16710' => 'spa', 'Sp3g00430' => 'spa', 'Sp3g26780' => 'spa', 'Sp5g22900' => 'spa', 'Sp6g29530' => 'spa', 'TAR371G0794' => 'tar', 'TAR374G0164' => 'tar', 'TAR622G0165' => 'tar', 'TAR626G0929' => 'tar', 'TAR629G2155' => 'tar', 'THA.LOC104805282' => 'tha', 'THA.LOC104805363' => 'tha', 'THA.LOC104808968' => 'tha', 'THA.LOC104821093' => 'tha', 'THA.LOC104823953' => 'tha', 'THA.LOC104825562' => 'tha', 'THA.LOC104825665' => 'tha', 'Thecc.02G261400' => 'tca', 'Thecc.04G019200' => 'tca', 'Thecc.09G130400' => 'tca', 'Thhalv10004374m.g' => 'esa', 'Thhalv10007850m.g' => 'esa', 'Thhalv10013782m.g' => 'esa', 'Thhalv10018686m.g' => 'esa', 'Thhalv10020899m.g' => 'esa', 'Thhalv10022755m.g' => 'esa', 'TPR.G23851' => 'tpr', 'TPR.G26500' => 'tpr', 'TPR.G27267' => 'tpr', 'TPR.G32001' => 'tpr', 'TPR.G6251' => 'tpr', 'TPR.G8167' => 'tpr', 'TWI12G1330' => 'twi', 'TWI18G1239' => 'twi', 'TWI34G0979' => 'twi', 'TWI36G0670' => 'twi', 'TWI36G0707' => 'twi', 'TWI56G0233' => 'twi', 'TWI75G1809' => 'twi', 'unitig_21.g20874' => 'ugi', 'unitig_26.g10343' => 'ugi', 'unitig_46.g18392' => 'ugi', 'unitig_52.g17178' => 'ugi', 'unitig_8.g2934' => 'ugi', 'vmacro01122' => 'vma', 'vmacro05875' => 'vma', 'vmacro06147' => 'vma', 'vmacro16191' => 'vma', 'vmacro18293' => 'vma', 'VMungo0251G3707' => 'vmu', 'VMungo0464G1521' => 'vmu', 'VMungo1215G0205' => 'vmu', 'VMungo1383G2484' => 'vmu', 'Zm00001eb079610' => 'zma', 'Zm00001eb135990' => 'zma', 'Zm00001eb183710' => 'zma', 'Zm00001eb246020' => 'zma' ), 'gf_id' => 'HOM05D001124', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001124' ), 'data_identifier' => 'HOM05D001124', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001124', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '548', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02520' => 'bna', 'A03p06630' => 'bna', 'A05p44460' => 'bna', 'A06p08710' => 'bna', 'A06p41090' => 'bna', 'A07p32320' => 'bna', 'A08p32520' => 'bna', 'A09p10360' => 'bna', 'A10p24080' => 'bna', 'Aa31LG11G15250' => 'aar', 'Aa31LG1G1800' => 'aar', 'Aa31LG2G5120' => 'aar', 'Aa31LG2G6070' => 'aar', 'Aa31LG5G10770' => 'aar', 'Aa31sc61G90' => 'aar', 'Actinidia01352' => 'ach', 'Actinidia05983' => 'ach', 'Actinidia08133' => 'ach', 'Actinidia15101' => 'ach', 'Actinidia26379' => 'ach', 'Actinidia35778' => 'ach', 'Actinidia36123' => 'ach', 'Actinidia37436' => 'ach', 'Actinidia38730' => 'ach', 'Ah.02g128210' => 'amhyb', 'Ah.03g132990' => 'amhyb', 'Ah.14g079410' => 'amhyb', 'AL1G24640' => 'aly', 'AL2G26680' => 'aly', 'AL3G10530' => 'aly', 'AL3G45230' => 'aly', 'AL5G15230' => 'aly', 'AL5G16960' => 'aly', 'AL6G25210' => 'aly', 'Aqoxy2G00441' => 'aox', 'Aqoxy3G01236' => 'aox', 'Aqoxy5G03746' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3RQ047' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C7GMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9C8JER' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MBL6KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YXCZ83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZANX40' => 'arhy', 'AT1G12990' => 'ath', 'AT1G67880' => 'ath', 'AT2G13290' => 'ath', 'AT3G01620' => 'ath', 'AT3G26445' => 'ath', 'AT3G27540' => 'ath', 'AT5G14480' => 'ath', 'ATR0824G026' => 'atr', 'ATR1098G019' => 'atr', 'Atru.chr11.2145' => 'acertr', 'Atru.chr2.3636' => 'acertr', 'Atru.chr2.3644' => 'acertr', 'Atru.chr6.2422' => 'acertr', 'Atru.chr7.1112' => 'acertr', 'AUR62005469' => 'cqu', 'AUR62011166' => 'cqu', 'AUR62013319' => 'cqu', 'AUR62024273' => 'cqu', 'AUR62028420' => 'cqu', 'AUR62041942' => 'cqu', 'BcaB01g04969' => 'bca', 'BcaB01g06371' => 'bca', 'BcaB02g11494' => 'bca', 'BcaB03g15382' => 'bca', 'BcaB08g36994' => 'bca', 'BcaC03g13477' => 'bca', 'BcaC03g13478' => 'bca', 'BcaC03g13480' => 'bca', 'BcaC03g13481' => 'bca', 'BcaC03g13486' => 'bca', 'BcaC04g19031' => 'bca', 'BcaC04g23085' => 'bca', 'BcaC05g25094' => 'bca', 'BcaC05g25096' => 'bca', 'BcaC05g25138' => 'bca', 'BcaC05g30416' => 'bca', 'BcaC05g30455' => 'bca', 'BcaC06g30979' => 'bca', 'BcaC06g33805' => 'bca', 'BcaC08g46021' => 'bca', 'BcaNung03154' => 'bca', 'BolC2t06623H' => 'bol', 'BolC2t06632H' => 'bol', 'BolC2t06635H' => 'bol', 'BolC2t06638H' => 'bol', 'BolC3t13266H' => 'bol', 'BolC5t29776H' => 'bol', 'BolC6t38912H' => 'bol', 'BolC7t44183H' => 'bol', 'BolC9t54123H' => 'bol', 'BolC9t59107H' => 'bol', 'BraA02t05221Z' => 'bra', 'BraA03t09996Z' => 'bra', 'BraA05t23210Z' => 'bra', 'BraA06t24068Z' => 'bra', 'BraA06t27032Z' => 'bra', 'BraA08t35176Z' => 'bra', 'BraA09t36680Z' => 'bra', 'BraA10t44471Z' => 'bra', 'C02p06760' => 'bna', 'C02p06890' => 'bna', 'C02p07010' => 'bna', 'C03p07660' => 'bna', 'C05p10300' => 'bna', 'C06p38150' => 'bna', 'C07p36650' => 'bna', 'C08p15770' => 'bna', 'C09p12300' => 'bna', 'C09p62700' => 'bna', 'C09p75040' => 'bna', 'CAN.G13.1' => 'can', 'CAN.G138.4' => 'can', 'CAN.G44.6' => 'can', 'CAN.G473.19' => 'can', 'CANSAT01G0835' => 'cansat', 'CANSAT11G0246' => 'cansat', 'CANSAT11G1766' => 'cansat', 'CANSAT64G1954' => 'cansat', 'CARHR013330' => 'chi', 'CARHR060530' => 'chi', 'CARHR075300' => 'chi', 'CARHR105120' => 'chi', 'CARHR148910' => 'chi', 'CARHR198830' => 'chi', 'Carub.0001s1275' => 'cru', 'Carub.0002s1437' => 'cru', 'Carub.0003s0044' => 'cru', 'Carub.0003s2787' => 'cru', 'Carub.0005s0597' => 'cru', 'Carub.0006s1266' => 'cru', 'Ca_06935_v3' => 'car', 'Ca_13559_v3' => 'car', 'Ca_16941_v3' => 'car', 'Ca_16960_v3' => 'car', 'Ca_17775_v3' => 'car', 'Ca_30464_v3' => 'car', 'Cc06_g08160' => 'ccan', 'Cc07_g01520' => 'ccan', 'Cc11_g15810' => 'ccan', 'CDE02G2840' => 'cde', 'CDE03G0093' => 'cde', 'CDE04G2127' => 'cde', 'CDE07G1857' => 'cde', 'CDE09G1246' => 'cde', 'Cfa003412' => 'cfa', 'Cfa007341' => 'cfa', 'Cfa009220' => 'cfa', 'Ciclev10008737m.g' => 'ccl', 'Ciclev10015565m.g' => 'ccl', 'Ciclev10031761m.g' => 'ccl', 'CiPaw.03G045300' => 'cil', 'CiPaw.03G247200' => 'cil', 'CiPaw.04G029500' => 'cil', 'CiPaw.04G174000' => 'cil', 'CiPaw.05G181200' => 'cil', 'CiPaw.06G067100' => 'cil', 'ClCG05G025800' => 'cla', 'ClCG06G011400' => 'cla', 'ClCG09G019360' => 'cla', 'COL.COLO4_04827' => 'col', 'COL.COLO4_29170' => 'col', 'COL.COLO4_35131' => 'col', 'COL.COLO4_35132' => 'col', 'Cpa.g.sc33.32' => 'cpa', 'Cpa.g.sc46.29' => 'cpa', 'Cpa.g.sc796.1' => 'cpa', 'CsaV3_1G030420' => 'csa', 'CsaV3_5G027050' => 'csa', 'CsaV3_5G031040' => 'csa', 'CsaV3_UNG023130' => 'csa', 'CSS0007726' => 'camsi', 'CSS0016433' => 'camsi', 'CSS0017656' => 'camsi', 'CSS0025364' => 'camsi', 'CSS0027582' => 'camsi', 'CSS0047288' => 'camsi', 'CSS0049950' => 'camsi', 'DCAR_003843' => 'dca', 'DCAR_007052' => 'dca', 'DCAR_020884' => 'dca', 'DCAR_021730' => 'dca', 'DCAR_024423' => 'dca', 'DCAR_026509' => 'dca', 'DCAR_031158' => 'dca', 'Dinv14728' => 'din', 'Dinv15219' => 'din', 'Dinv25728' => 'din', 'Dinv33428' => 'din', 'Dinv36489' => 'din', 'Dinv41486' => 'din', 'Duzib147G0469' => 'dzi', 'Duzib168G0060' => 'dzi', 'Duzib187G1215' => 'dzi', 'Duzib248G0692' => 'dzi', 'Duzib251G0767' => 'dzi', 'Duzib264G0446' => 'dzi', 'Duzib268G0691' => 'dzi', 'ECA232G4767' => 'eca', 'ECA233G2838' => 'eca', 'ECA234G0391' => 'eca', 'ECA234G0857' => 'eca', 'ECA236G1593' => 'eca', 'ECA238G0565' => 'eca', 'ECA246G1027' => 'eca', 'ECA246G3223' => 'eca', 'ECA246G3470' => 'eca', 'EL10Ac6g13829' => 'bvu', 'EL10Ac6g14093' => 'bvu', 'EL10Ac8g18707' => 'bvu', 'Eucgr.C01369' => 'egr', 'Eucgr.H02492' => 'egr', 'Eucgr.I01733' => 'egr', 'Eucgr.J02255' => 'egr', 'Eucgr.J02257' => 'egr', 'Eucgr.J02258' => 'egr', 'FAN02G1601' => 'fan', 'FAN03G1586' => 'fan', 'FAN03G2986' => 'fan', 'FAN05G4837' => 'fan', 'FAN06G0146' => 'fan', 'FAN07G0858' => 'fan', 'FAN09G3179' => 'fan', 'FAN10G0669' => 'fan', 'FAN12G2358' => 'fan', 'FAN14G4198' => 'fan', 'FAN14G5112' => 'fan', 'FAN17G0342' => 'fan', 'FAN19G0342' => 'fan', 'FAN19G0962' => 'fan', 'FAN19G1101' => 'fan', 'FAN19G1872' => 'fan', 'FAN22G0356' => 'fan', 'FAN23G0744' => 'fan', 'FAN23G1914' => 'fan', 'FAN26G0032' => 'fan', 'FAN28G0625' => 'fan', 'FvH4_1g02710' => 'fve', 'FvH4_1g02720' => 'fve', 'FvH4_4g25670' => 'fve', 'FvH4_6g51700' => 'fve', 'FvH4_7g20170' => 'fve', 'Glyma.05G175000' => 'gma', 'Glyma.08G132300' => 'gma', 'Glyma.11G243000' => 'gma', 'Glyma.13G158900' => 'gma', 'Glyma.17G112400' => 'gma', 'Glyma.18G014100' => 'gma', 'Glyma.19G003100' => 'gma', 'Glyma.19G056500' => 'gma', 'Gohir.A01G158900' => 'ghi', 'Gohir.A05G312600' => 'ghi', 'Gohir.A05G354900' => 'ghi', 'Gohir.A07G037200' => 'ghi', 'Gohir.A09G030000' => 'ghi', 'Gohir.A12G145200' => 'ghi', 'Gohir.D01G151500' => 'ghi', 'Gohir.D04G058300' => 'ghi', 'Gohir.D05G314100' => 'ghi', 'Gohir.D07G041400' => 'ghi', 'Gohir.D09G029700' => 'ghi', 'Gohir.D12G149700' => 'ghi', 'Gorai.001G043800' => 'gra', 'Gorai.002G187800' => 'gra', 'Gorai.006G034700' => 'gra', 'Gorai.008G161200' => 'gra', 'Gorai.009G335700' => 'gra', 'Gorai.012G065000' => 'gra', 'GSVIVG01000535001' => 'vvi', 'GSVIVG01015572001' => 'vvi', 'GSVIVG01032386001' => 'vvi', 'HanXRQChr05g0138531' => 'han', 'HanXRQChr06g0174391' => 'han', 'HanXRQChr07g0199021' => 'han', 'HanXRQChr08g0208211' => 'han', 'HanXRQChr09g0255471' => 'han', 'HanXRQChr10g0315791' => 'han', 'HanXRQChr12g0371991' => 'han', 'HanXRQChr15g0475251' => 'han', 'HanXRQChr17g0540001' => 'han', 'HanXRQChr17g0548631' => 'han', 'HanXRQChr17g0569561' => 'han', 'Haze_12256' => 'cav', 'Haze_14756' => 'cav', 'Haze_25528' => 'cav', 'Hma1.2p1_0079F.1_g041020' => 'hma', 'Hma1.2p1_0818F.1_g223260' => 'hma', 'Hma1.2p1_1747F.1_g300530' => 'hma', 'HPP92_004607' => 'vpl', 'HPP92_004608' => 'vpl', 'HPP92_006181' => 'vpl', 'HPP92_012192' => 'vpl', 'HPP92_015680' => 'vpl', 'HPP92_020249' => 'vpl', 'HPP92_021376' => 'vpl', 'HPP92_024275' => 'vpl', 'Hund06031' => 'sun', 'Hund25391' => 'sun', 'Lalb_Chr07g0185371' => 'lal', 'Lalb_Chr07g0185381' => 'lal', 'Lalb_Chr12g0204011' => 'lal', 'Lalb_Chr13g0301671' => 'lal', 'Lalb_Chr14g0362851' => 'lal', 'Lalb_Chr24g0403581' => 'lal', 'Lj1g0000233' => 'lja', 'Lj2g0018120' => 'lja', 'Lj3C621T0' => 'lonja', 'Lj3P1059T14' => 'lonja', 'Lj3P611T9' => 'lonja', 'Lj3P614T13' => 'lonja', 'Lj3P615T5' => 'lonja', 'Lj4g0012315' => 'lja', 'Lj4g0026182' => 'lja', 'Lj6P813T16' => 'lonja', 'Lj7C427T7' => 'lonja', 'Lj7C427T8' => 'lonja', 'Lj7P600T41' => 'lonja', 'Lju41C42G17' => 'lonja', 'Lsat_1_v5_gn_0_47300' => 'lsa', 'Lsat_1_v5_gn_2_91280' => 'lsa', 'Lsat_1_v5_gn_3_30561' => 'lsa', 'Lsat_1_v5_gn_4_184321' => 'lsa', 'Lsat_1_v5_gn_4_4041' => 'lsa', 'Lsat_1_v5_gn_5_92000' => 'lsa', 'Lsat_1_v5_gn_8_152940' => 'lsa', 'Lsat_1_v5_gn_8_62401' => 'lsa', 'Manes.06G055900' => 'mes', 'Manes.12G022200' => 'mes', 'Manes.13G023300' => 'mes', 'Manes.14G115000' => 'mes', 'Manes.15G151700' => 'mes', 'Manes.17G111300' => 'mes', 'Mapoly0226s0009' => 'mpo', 'MBI02_g25363_MAGBIO' => 'mbi', 'MBI06_g00027_MAGBIO' => 'mbi', 'MBI10_g13034_MAGBIO' => 'mbi', 'MD09G1023400' => 'mdo', 'MD13G1100100' => 'mdo', 'MD15G1169200' => 'mdo', 'MD16G1101100' => 'mdo', 'MD17G1022900' => 'mdo', 'Medtr3g096150' => 'mtr', 'Medtr4g115070' => 'mtr', 'Medtr7g033325' => 'mtr', 'Medtr8g089840' => 'mtr', 'MELO3C010319.2' => 'cme', 'MELO3C011944.2' => 'cme', 'MELO3C021589.2' => 'cme', 'Migut.E00207' => 'egut', 'Migut.H00067' => 'egut', 'Migut.K00433' => 'egut', 'Migut.K00606' => 'egut', 'Migut.K01410' => 'egut', 'MSTRG.13347' => 'ama', 'MSTRG.24045' => 'ama', 'MSTRG.2428' => 'ama', 'MSTRG.26410' => 'ama', 'MSTRG.3139' => 'ama', 'MSTRG.3286' => 'ama', 'MSTRG.563' => 'ama', 'MSTRG.7941' => 'ama', 'Nitab4.5_0000028g0060' => 'nta', 'Nitab4.5_0000065g0260' => 'nta', 'Nitab4.5_0000112g0060' => 'nta', 'Nitab4.5_0000489g0120' => 'nta', 'Nitab4.5_0001776g0050' => 'nta', 'Nitab4.5_0001854g0010' => 'nta', 'Nitab4.5_0001860g0020' => 'nta', 'Nitab4.5_0004352g0010' => 'nta', 'Nitab4.5_0008716g0020' => 'nta', 'Nitab4.5_0008922g0010' => 'nta', 'Nn3g16693' => 'nnu', 'Nn4g22596' => 'nnu', 'Nn7g37639' => 'nnu', 'Oeu001701.1' => 'oeu', 'Oeu018149.1' => 'oeu', 'Oeu026220.1' => 'oeu', 'Oeu038635.1' => 'oeu', 'Oeu049176.1' => 'oeu', 'Oeu056706.1' => 'oeu', 'Oeu056937.1' => 'oeu', 'Oeu057540.1' => 'oeu', 'Os02g0594900' => 'osa', 'Os02g0595100' => 'osa', 'Os04g0477500' => 'osa', 'Os12g0611900' => 'osa', 'Peaxi162Scf00076g00020' => 'pax', 'Peaxi162Scf00128g00217' => 'pax', 'Peaxi162Scf00129g01640' => 'pax', 'Peaxi162Scf00669g00007' => 'pax', 'Peaxi162Scf00700g00421' => 'pax', 'Peaxi162Scf00801g00038' => 'pax', 'Peaxi162Scf00891g00025' => 'pax', 'PGR083G0909' => 'pgr', 'PGR119G1005' => 'pgr', 'PGR142G2236' => 'pgr', 'PGR142G3388' => 'pgr', 'PGSC0003DMG400004514' => 'stu', 'PGSC0003DMG400012635' => 'stu', 'PGSC0003DMG400015730' => 'stu', 'PGSC0003DMG400018611' => 'stu', 'PGSC0003DMG400030897' => 'stu', 'Phvul.001G254800' => 'pvu', 'Phvul.002G260100' => 'pvu', 'Phvul.003G167600' => 'pvu', 'Phvul.004G005100' => 'pvu', 'Potri.001G343600' => 'ptr', 'Potri.006G066700' => 'ptr', 'Potri.008G186000' => 'ptr', 'Potri.010G046900' => 'ptr', 'Potri.018G127900' => 'ptr', 'Pp3c20_17750' => 'ppa', 'Pp3c24_4380' => 'ppa', 'Prupe.1G245800' => 'ppe', 'Prupe.3G293400' => 'ppe', 'Prupe.7G247400' => 'ppe', 'Psat0s145g0120' => 'psa', 'Psat0s595g0040' => 'psa', 'Psat0s595g0120' => 'psa', 'Psat3g175040' => 'psa', 'Psat7g058120' => 'psa', 'PSO017G0428' => 'pso', 'PSO063G7510' => 'pso', 'PSO067G0046' => 'pso', 'PSO478G1073' => 'pso', 'PSO675G3677' => 'pso', 'PSO675G6558' => 'pso', 'PSO675G7520' => 'pso', 'PSO675G8959' => 'pso', 'QL02p074089' => 'qlo', 'QL02p089614' => 'qlo', 'QL03p057736' => 'qlo', 'RcHm_v2.0_Chr1g0364131' => 'rch', 'RcHm_v2.0_Chr2g0087801' => 'rch', 'RcHm_v2.0_Chr2g0087821' => 'rch', 'RcHm_v2.0_Chr2g0173231' => 'rch', 'RcHm_v2.0_Chr4g0433111' => 'rch', 'Rhsim03G0250300' => 'rsi', 'Rhsim08G0048400' => 'rsi', 'Rhsim10G0014800' => 'rsi', 'Rhsim12G0040100' => 'rsi', 'Rhsim12G0109700' => 'rsi', 'Sabra06G0049600' => 'sbr', 'Sabra08G0141000' => 'sbr', 'Sabra10G0021400' => 'sbr', 'Sabra16G0222900' => 'sbr', 'Sabra18G0108600' => 'sbr', 'SalBow1G0433' => 'sbo', 'SalBow1G2038' => 'sbo', 'SalBow1G5003' => 'sbo', 'SalBow7G1197' => 'sbo', 'SalBow8G3506' => 'sbo', 'Sc03g0007300' => 'sci', 'Sc11g0000950' => 'sci', 'Sc14g0008750' => 'sci', 'Sc18g0000420' => 'sci', 'Sed0006754' => 'sed', 'Sed0008741' => 'sed', 'Sed0017172' => 'sed', 'Sed0018925' => 'sed', 'Sed0023326' => 'sed', 'Sed0025909' => 'sed', 'SEGI_05333' => 'sgi', 'SEGI_10362' => 'sgi', 'SEGI_13380' => 'sgi', 'SEGI_24306' => 'sgi', 'SEGI_29077' => 'sgi', 'SEGI_29095' => 'sgi', 'SEGI_36534' => 'sgi', 'SEGI_37506' => 'sgi', 'SEGI_38321' => 'sgi', 'SGA_v2.0_scaffold307G48031' => 'sas', 'SGA_v2.0_scaffold47G17507' => 'sas', 'SGA_v2.0_scaffold63G21736' => 'sas', 'SGA_v2.0_scaffold87G27070' => 'sas', 'SHI17794' => 'shi', 'SHI28851' => 'shi', 'SMO165G0155' => 'smo', 'SMO340G0217' => 'smo', 'SMO367G1210' => 'smo', 'Solyc02g093430.3' => 'sly', 'Solyc05g013580.4' => 'sly', 'Solyc07g008030.3' => 'sly', 'Solyc12g035470.2' => 'sly', 'Sopen02g038020' => 'spe', 'Sopen05g008490' => 'spe', 'Sopen07g003910' => 'spe', 'Sopen12g015240' => 'spe', 'Sp1g11550' => 'spa', 'Sp2g16710' => 'spa', 'Sp3g00430' => 'spa', 'Sp3g26780' => 'spa', 'Sp5g22900' => 'spa', 'Sp6g29530' => 'spa', 'TAR371G0794' => 'tar', 'TAR374G0164' => 'tar', 'TAR622G0165' => 'tar', 'TAR626G0929' => 'tar', 'TAR629G2155' => 'tar', 'THA.LOC104805282' => 'tha', 'THA.LOC104805363' => 'tha', 'THA.LOC104808968' => 'tha', 'THA.LOC104821093' => 'tha', 'THA.LOC104823953' => 'tha', 'THA.LOC104825562' => 'tha', 'THA.LOC104825665' => 'tha', 'Thecc.02G261400' => 'tca', 'Thecc.04G019200' => 'tca', 'Thecc.09G130400' => 'tca', 'Thhalv10004374m.g' => 'esa', 'Thhalv10007850m.g' => 'esa', 'Thhalv10013782m.g' => 'esa', 'Thhalv10018686m.g' => 'esa', 'Thhalv10020899m.g' => 'esa', 'Thhalv10022755m.g' => 'esa', 'TPR.G23851' => 'tpr', 'TPR.G26500' => 'tpr', 'TPR.G27267' => 'tpr', 'TPR.G32001' => 'tpr', 'TPR.G6251' => 'tpr', 'TPR.G8167' => 'tpr', 'TWI12G1330' => 'twi', 'TWI18G1239' => 'twi', 'TWI34G0979' => 'twi', 'TWI36G0670' => 'twi', 'TWI36G0707' => 'twi', 'TWI56G0233' => 'twi', 'TWI75G1809' => 'twi', 'unitig_21.g20874' => 'ugi', 'unitig_26.g10343' => 'ugi', 'unitig_46.g18392' => 'ugi', 'unitig_52.g17178' => 'ugi', 'unitig_8.g2934' => 'ugi', 'vmacro01122' => 'vma', 'vmacro05875' => 'vma', 'vmacro06147' => 'vma', 'vmacro16191' => 'vma', 'vmacro18293' => 'vma', 'VMungo0251G3707' => 'vmu', 'VMungo0464G1521' => 'vmu', 'VMungo1215G0205' => 'vmu', 'VMungo1383G2484' => 'vmu', 'Zm00001eb079610' => 'zma', 'Zm00001eb135990' => 'zma', 'Zm00001eb183710' => 'zma', 'Zm00001eb246020' => 'zma' ) $gf_id = 'HOM05D001124' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001124' ) $data_identifier = 'HOM05D001124' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 6, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 7, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 21, 'bol' => (int) 10, 'bra' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 6, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 9, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 21, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 8, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 10, 'lsa' => (int) 8, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 8, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 9, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb246020' $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' => 'HOM05D001124', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '548', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02520' => 'bna', 'A03p06630' => 'bna', 'A05p44460' => 'bna', 'A06p08710' => 'bna', 'A06p41090' => 'bna', 'A07p32320' => 'bna', 'A08p32520' => 'bna', 'A09p10360' => 'bna', 'A10p24080' => 'bna', 'Aa31LG11G15250' => 'aar', 'Aa31LG1G1800' => 'aar', 'Aa31LG2G5120' => 'aar', 'Aa31LG2G6070' => 'aar', 'Aa31LG5G10770' => 'aar', 'Aa31sc61G90' => 'aar', 'Actinidia01352' => 'ach', 'Actinidia05983' => 'ach', 'Actinidia08133' => 'ach', 'Actinidia15101' => 'ach', 'Actinidia26379' => 'ach', 'Actinidia35778' => 'ach', 'Actinidia36123' => 'ach', 'Actinidia37436' => 'ach', 'Actinidia38730' => 'ach', 'Ah.02g128210' => 'amhyb', 'Ah.03g132990' => 'amhyb', 'Ah.14g079410' => 'amhyb', 'AL1G24640' => 'aly', 'AL2G26680' => 'aly', 'AL3G10530' => 'aly', 'AL3G45230' => 'aly', 'AL5G15230' => 'aly', 'AL5G16960' => 'aly', 'AL6G25210' => 'aly', 'Aqoxy2G00441' => 'aox', 'Aqoxy3G01236' => 'aox', 'Aqoxy5G03746' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3RQ047' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C7GMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9C8JER' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MBL6KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YXCZ83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZANX40' => 'arhy', 'AT1G12990' => 'ath', 'AT1G67880' => 'ath', 'AT2G13290' => 'ath', 'AT3G01620' => 'ath', 'AT3G26445' => 'ath', 'AT3G27540' => 'ath', 'AT5G14480' => 'ath', 'ATR0824G026' => 'atr', 'ATR1098G019' => 'atr', 'Atru.chr11.2145' => 'acertr', 'Atru.chr2.3636' => 'acertr', 'Atru.chr2.3644' => 'acertr', 'Atru.chr6.2422' => 'acertr', 'Atru.chr7.1112' => 'acertr', 'AUR62005469' => 'cqu', 'AUR62011166' => 'cqu', 'AUR62013319' => 'cqu', 'AUR62024273' => 'cqu', 'AUR62028420' => 'cqu', 'AUR62041942' => 'cqu', 'BcaB01g04969' => 'bca', 'BcaB01g06371' => 'bca', 'BcaB02g11494' => 'bca', 'BcaB03g15382' => 'bca', 'BcaB08g36994' => 'bca', 'BcaC03g13477' => 'bca', 'BcaC03g13478' => 'bca', 'BcaC03g13480' => 'bca', 'BcaC03g13481' => 'bca', 'BcaC03g13486' => 'bca', 'BcaC04g19031' => 'bca', 'BcaC04g23085' => 'bca', 'BcaC05g25094' => 'bca', 'BcaC05g25096' => 'bca', 'BcaC05g25138' => 'bca', 'BcaC05g30416' => 'bca', 'BcaC05g30455' => 'bca', 'BcaC06g30979' => 'bca', 'BcaC06g33805' => 'bca', 'BcaC08g46021' => 'bca', 'BcaNung03154' => 'bca', 'BolC2t06623H' => 'bol', 'BolC2t06632H' => 'bol', 'BolC2t06635H' => 'bol', 'BolC2t06638H' => 'bol', 'BolC3t13266H' => 'bol', 'BolC5t29776H' => 'bol', 'BolC6t38912H' => 'bol', 'BolC7t44183H' => 'bol', 'BolC9t54123H' => 'bol', 'BolC9t59107H' => 'bol', 'BraA02t05221Z' => 'bra', 'BraA03t09996Z' => 'bra', 'BraA05t23210Z' => 'bra', 'BraA06t24068Z' => 'bra', 'BraA06t27032Z' => 'bra', 'BraA08t35176Z' => 'bra', 'BraA09t36680Z' => 'bra', 'BraA10t44471Z' => 'bra', 'C02p06760' => 'bna', 'C02p06890' => 'bna', 'C02p07010' => 'bna', 'C03p07660' => 'bna', 'C05p10300' => 'bna', 'C06p38150' => 'bna', 'C07p36650' => 'bna', 'C08p15770' => 'bna', 'C09p12300' => 'bna', 'C09p62700' => 'bna', 'C09p75040' => 'bna', 'CAN.G13.1' => 'can', 'CAN.G138.4' => 'can', 'CAN.G44.6' => 'can', 'CAN.G473.19' => 'can', 'CANSAT01G0835' => 'cansat', 'CANSAT11G0246' => 'cansat', 'CANSAT11G1766' => 'cansat', 'CANSAT64G1954' => 'cansat', 'CARHR013330' => 'chi', 'CARHR060530' => 'chi', 'CARHR075300' => 'chi', 'CARHR105120' => 'chi', 'CARHR148910' => 'chi', 'CARHR198830' => 'chi', 'Carub.0001s1275' => 'cru', 'Carub.0002s1437' => 'cru', 'Carub.0003s0044' => 'cru', 'Carub.0003s2787' => 'cru', 'Carub.0005s0597' => 'cru', 'Carub.0006s1266' => 'cru', 'Ca_06935_v3' => 'car', 'Ca_13559_v3' => 'car', 'Ca_16941_v3' => 'car', 'Ca_16960_v3' => 'car', 'Ca_17775_v3' => 'car', 'Ca_30464_v3' => 'car', 'Cc06_g08160' => 'ccan', 'Cc07_g01520' => 'ccan', 'Cc11_g15810' => 'ccan', 'CDE02G2840' => 'cde', 'CDE03G0093' => 'cde', 'CDE04G2127' => 'cde', 'CDE07G1857' => 'cde', 'CDE09G1246' => 'cde', 'Cfa003412' => 'cfa', 'Cfa007341' => 'cfa', 'Cfa009220' => 'cfa', 'Ciclev10008737m.g' => 'ccl', 'Ciclev10015565m.g' => 'ccl', 'Ciclev10031761m.g' => 'ccl', 'CiPaw.03G045300' => 'cil', 'CiPaw.03G247200' => 'cil', 'CiPaw.04G029500' => 'cil', 'CiPaw.04G174000' => 'cil', 'CiPaw.05G181200' => 'cil', 'CiPaw.06G067100' => 'cil', 'ClCG05G025800' => 'cla', 'ClCG06G011400' => 'cla', 'ClCG09G019360' => 'cla', 'COL.COLO4_04827' => 'col', 'COL.COLO4_29170' => 'col', 'COL.COLO4_35131' => 'col', 'COL.COLO4_35132' => 'col', 'Cpa.g.sc33.32' => 'cpa', 'Cpa.g.sc46.29' => 'cpa', 'Cpa.g.sc796.1' => 'cpa', 'CsaV3_1G030420' => 'csa', 'CsaV3_5G027050' => 'csa', 'CsaV3_5G031040' => 'csa', 'CsaV3_UNG023130' => 'csa', 'CSS0007726' => 'camsi', 'CSS0016433' => 'camsi', 'CSS0017656' => 'camsi', 'CSS0025364' => 'camsi', 'CSS0027582' => 'camsi', 'CSS0047288' => 'camsi', 'CSS0049950' => 'camsi', 'DCAR_003843' => 'dca', 'DCAR_007052' => 'dca', 'DCAR_020884' => 'dca', 'DCAR_021730' => 'dca', 'DCAR_024423' => 'dca', 'DCAR_026509' => 'dca', 'DCAR_031158' => 'dca', 'Dinv14728' => 'din', 'Dinv15219' => 'din', 'Dinv25728' => 'din', 'Dinv33428' => 'din', 'Dinv36489' => 'din', 'Dinv41486' => 'din', 'Duzib147G0469' => 'dzi', 'Duzib168G0060' => 'dzi', 'Duzib187G1215' => 'dzi', 'Duzib248G0692' => 'dzi', 'Duzib251G0767' => 'dzi', 'Duzib264G0446' => 'dzi', 'Duzib268G0691' => 'dzi', 'ECA232G4767' => 'eca', 'ECA233G2838' => 'eca', 'ECA234G0391' => 'eca', 'ECA234G0857' => 'eca', 'ECA236G1593' => 'eca', 'ECA238G0565' => 'eca', 'ECA246G1027' => 'eca', 'ECA246G3223' => 'eca', 'ECA246G3470' => 'eca', 'EL10Ac6g13829' => 'bvu', 'EL10Ac6g14093' => 'bvu', 'EL10Ac8g18707' => 'bvu', 'Eucgr.C01369' => 'egr', 'Eucgr.H02492' => 'egr', 'Eucgr.I01733' => 'egr', 'Eucgr.J02255' => 'egr', 'Eucgr.J02257' => 'egr', 'Eucgr.J02258' => 'egr', 'FAN02G1601' => 'fan', 'FAN03G1586' => 'fan', 'FAN03G2986' => 'fan', 'FAN05G4837' => 'fan', 'FAN06G0146' => 'fan', 'FAN07G0858' => 'fan', 'FAN09G3179' => 'fan', 'FAN10G0669' => 'fan', 'FAN12G2358' => 'fan', 'FAN14G4198' => 'fan', 'FAN14G5112' => 'fan', 'FAN17G0342' => 'fan', 'FAN19G0342' => 'fan', 'FAN19G0962' => 'fan', 'FAN19G1101' => 'fan', 'FAN19G1872' => 'fan', 'FAN22G0356' => 'fan', 'FAN23G0744' => 'fan', 'FAN23G1914' => 'fan', 'FAN26G0032' => 'fan', 'FAN28G0625' => 'fan', 'FvH4_1g02710' => 'fve', 'FvH4_1g02720' => 'fve', 'FvH4_4g25670' => 'fve', 'FvH4_6g51700' => 'fve', 'FvH4_7g20170' => 'fve', 'Glyma.05G175000' => 'gma', 'Glyma.08G132300' => 'gma', 'Glyma.11G243000' => 'gma', 'Glyma.13G158900' => 'gma', 'Glyma.17G112400' => 'gma', 'Glyma.18G014100' => 'gma', 'Glyma.19G003100' => 'gma', 'Glyma.19G056500' => 'gma', 'Gohir.A01G158900' => 'ghi', 'Gohir.A05G312600' => 'ghi', 'Gohir.A05G354900' => 'ghi', 'Gohir.A07G037200' => 'ghi', 'Gohir.A09G030000' => 'ghi', 'Gohir.A12G145200' => 'ghi', 'Gohir.D01G151500' => 'ghi', 'Gohir.D04G058300' => 'ghi', 'Gohir.D05G314100' => 'ghi', 'Gohir.D07G041400' => 'ghi', 'Gohir.D09G029700' => 'ghi', 'Gohir.D12G149700' => 'ghi', 'Gorai.001G043800' => 'gra', 'Gorai.002G187800' => 'gra', 'Gorai.006G034700' => 'gra', 'Gorai.008G161200' => 'gra', 'Gorai.009G335700' => 'gra', 'Gorai.012G065000' => 'gra', 'GSVIVG01000535001' => 'vvi', 'GSVIVG01015572001' => 'vvi', 'GSVIVG01032386001' => 'vvi', 'HanXRQChr05g0138531' => 'han', 'HanXRQChr06g0174391' => 'han', 'HanXRQChr07g0199021' => 'han', 'HanXRQChr08g0208211' => 'han', 'HanXRQChr09g0255471' => 'han', 'HanXRQChr10g0315791' => 'han', 'HanXRQChr12g0371991' => 'han', 'HanXRQChr15g0475251' => 'han', 'HanXRQChr17g0540001' => 'han', 'HanXRQChr17g0548631' => 'han', 'HanXRQChr17g0569561' => 'han', 'Haze_12256' => 'cav', 'Haze_14756' => 'cav', 'Haze_25528' => 'cav', 'Hma1.2p1_0079F.1_g041020' => 'hma', 'Hma1.2p1_0818F.1_g223260' => 'hma', 'Hma1.2p1_1747F.1_g300530' => 'hma', 'HPP92_004607' => 'vpl', 'HPP92_004608' => 'vpl', 'HPP92_006181' => 'vpl', 'HPP92_012192' => 'vpl', 'HPP92_015680' => 'vpl', 'HPP92_020249' => 'vpl', 'HPP92_021376' => 'vpl', 'HPP92_024275' => 'vpl', 'Hund06031' => 'sun', 'Hund25391' => 'sun', 'Lalb_Chr07g0185371' => 'lal', 'Lalb_Chr07g0185381' => 'lal', 'Lalb_Chr12g0204011' => 'lal', 'Lalb_Chr13g0301671' => 'lal', 'Lalb_Chr14g0362851' => 'lal', 'Lalb_Chr24g0403581' => 'lal', 'Lj1g0000233' => 'lja', 'Lj2g0018120' => 'lja', 'Lj3C621T0' => 'lonja', 'Lj3P1059T14' => 'lonja', 'Lj3P611T9' => 'lonja', 'Lj3P614T13' => 'lonja', 'Lj3P615T5' => 'lonja', 'Lj4g0012315' => 'lja', 'Lj4g0026182' => 'lja', 'Lj6P813T16' => 'lonja', 'Lj7C427T7' => 'lonja', 'Lj7C427T8' => 'lonja', 'Lj7P600T41' => 'lonja', 'Lju41C42G17' => 'lonja', 'Lsat_1_v5_gn_0_47300' => 'lsa', 'Lsat_1_v5_gn_2_91280' => 'lsa', 'Lsat_1_v5_gn_3_30561' => 'lsa', 'Lsat_1_v5_gn_4_184321' => 'lsa', 'Lsat_1_v5_gn_4_4041' => 'lsa', 'Lsat_1_v5_gn_5_92000' => 'lsa', 'Lsat_1_v5_gn_8_152940' => 'lsa', 'Lsat_1_v5_gn_8_62401' => 'lsa', 'Manes.06G055900' => 'mes', 'Manes.12G022200' => 'mes', 'Manes.13G023300' => 'mes', 'Manes.14G115000' => 'mes', 'Manes.15G151700' => 'mes', 'Manes.17G111300' => 'mes', 'Mapoly0226s0009' => 'mpo', 'MBI02_g25363_MAGBIO' => 'mbi', 'MBI06_g00027_MAGBIO' => 'mbi', 'MBI10_g13034_MAGBIO' => 'mbi', 'MD09G1023400' => 'mdo', 'MD13G1100100' => 'mdo', 'MD15G1169200' => 'mdo', 'MD16G1101100' => 'mdo', 'MD17G1022900' => 'mdo', 'Medtr3g096150' => 'mtr', 'Medtr4g115070' => 'mtr', 'Medtr7g033325' => 'mtr', 'Medtr8g089840' => 'mtr', 'MELO3C010319.2' => 'cme', 'MELO3C011944.2' => 'cme', 'MELO3C021589.2' => 'cme', 'Migut.E00207' => 'egut', 'Migut.H00067' => 'egut', 'Migut.K00433' => 'egut', 'Migut.K00606' => 'egut', 'Migut.K01410' => 'egut', 'MSTRG.13347' => 'ama', 'MSTRG.24045' => 'ama', 'MSTRG.2428' => 'ama', 'MSTRG.26410' => 'ama', 'MSTRG.3139' => 'ama', 'MSTRG.3286' => 'ama', 'MSTRG.563' => 'ama', 'MSTRG.7941' => 'ama', 'Nitab4.5_0000028g0060' => 'nta', 'Nitab4.5_0000065g0260' => 'nta', 'Nitab4.5_0000112g0060' => 'nta', 'Nitab4.5_0000489g0120' => 'nta', 'Nitab4.5_0001776g0050' => 'nta', 'Nitab4.5_0001854g0010' => 'nta', 'Nitab4.5_0001860g0020' => 'nta', 'Nitab4.5_0004352g0010' => 'nta', 'Nitab4.5_0008716g0020' => 'nta', 'Nitab4.5_0008922g0010' => 'nta', 'Nn3g16693' => 'nnu', 'Nn4g22596' => 'nnu', 'Nn7g37639' => 'nnu', 'Oeu001701.1' => 'oeu', 'Oeu018149.1' => 'oeu', 'Oeu026220.1' => 'oeu', 'Oeu038635.1' => 'oeu', 'Oeu049176.1' => 'oeu', 'Oeu056706.1' => 'oeu', 'Oeu056937.1' => 'oeu', 'Oeu057540.1' => 'oeu', 'Os02g0594900' => 'osa', 'Os02g0595100' => 'osa', 'Os04g0477500' => 'osa', 'Os12g0611900' => 'osa', 'Peaxi162Scf00076g00020' => 'pax', 'Peaxi162Scf00128g00217' => 'pax', 'Peaxi162Scf00129g01640' => 'pax', 'Peaxi162Scf00669g00007' => 'pax', 'Peaxi162Scf00700g00421' => 'pax', 'Peaxi162Scf00801g00038' => 'pax', 'Peaxi162Scf00891g00025' => 'pax', 'PGR083G0909' => 'pgr', 'PGR119G1005' => 'pgr', 'PGR142G2236' => 'pgr', 'PGR142G3388' => 'pgr', 'PGSC0003DMG400004514' => 'stu', 'PGSC0003DMG400012635' => 'stu', 'PGSC0003DMG400015730' => 'stu', 'PGSC0003DMG400018611' => 'stu', 'PGSC0003DMG400030897' => 'stu', 'Phvul.001G254800' => 'pvu', 'Phvul.002G260100' => 'pvu', 'Phvul.003G167600' => 'pvu', 'Phvul.004G005100' => 'pvu', 'Potri.001G343600' => 'ptr', 'Potri.006G066700' => 'ptr', 'Potri.008G186000' => 'ptr', 'Potri.010G046900' => 'ptr', 'Potri.018G127900' => 'ptr', 'Pp3c20_17750' => 'ppa', 'Pp3c24_4380' => 'ppa', 'Prupe.1G245800' => 'ppe', 'Prupe.3G293400' => 'ppe', 'Prupe.7G247400' => 'ppe', 'Psat0s145g0120' => 'psa', 'Psat0s595g0040' => 'psa', 'Psat0s595g0120' => 'psa', 'Psat3g175040' => 'psa', 'Psat7g058120' => 'psa', 'PSO017G0428' => 'pso', 'PSO063G7510' => 'pso', 'PSO067G0046' => 'pso', 'PSO478G1073' => 'pso', 'PSO675G3677' => 'pso', 'PSO675G6558' => 'pso', 'PSO675G7520' => 'pso', 'PSO675G8959' => 'pso', 'QL02p074089' => 'qlo', 'QL02p089614' => 'qlo', 'QL03p057736' => 'qlo', 'RcHm_v2.0_Chr1g0364131' => 'rch', 'RcHm_v2.0_Chr2g0087801' => 'rch', 'RcHm_v2.0_Chr2g0087821' => 'rch', 'RcHm_v2.0_Chr2g0173231' => 'rch', 'RcHm_v2.0_Chr4g0433111' => 'rch', 'Rhsim03G0250300' => 'rsi', 'Rhsim08G0048400' => 'rsi', 'Rhsim10G0014800' => 'rsi', 'Rhsim12G0040100' => 'rsi', 'Rhsim12G0109700' => 'rsi', 'Sabra06G0049600' => 'sbr', 'Sabra08G0141000' => 'sbr', 'Sabra10G0021400' => 'sbr', 'Sabra16G0222900' => 'sbr', 'Sabra18G0108600' => 'sbr', 'SalBow1G0433' => 'sbo', 'SalBow1G2038' => 'sbo', 'SalBow1G5003' => 'sbo', 'SalBow7G1197' => 'sbo', 'SalBow8G3506' => 'sbo', 'Sc03g0007300' => 'sci', 'Sc11g0000950' => 'sci', 'Sc14g0008750' => 'sci', 'Sc18g0000420' => 'sci', 'Sed0006754' => 'sed', 'Sed0008741' => 'sed', 'Sed0017172' => 'sed', 'Sed0018925' => 'sed', 'Sed0023326' => 'sed', 'Sed0025909' => 'sed', 'SEGI_05333' => 'sgi', 'SEGI_10362' => 'sgi', 'SEGI_13380' => 'sgi', 'SEGI_24306' => 'sgi', 'SEGI_29077' => 'sgi', 'SEGI_29095' => 'sgi', 'SEGI_36534' => 'sgi', 'SEGI_37506' => 'sgi', 'SEGI_38321' => 'sgi', 'SGA_v2.0_scaffold307G48031' => 'sas', 'SGA_v2.0_scaffold47G17507' => 'sas', 'SGA_v2.0_scaffold63G21736' => 'sas', 'SGA_v2.0_scaffold87G27070' => 'sas', 'SHI17794' => 'shi', 'SHI28851' => 'shi', 'SMO165G0155' => 'smo', 'SMO340G0217' => 'smo', 'SMO367G1210' => 'smo', 'Solyc02g093430.3' => 'sly', 'Solyc05g013580.4' => 'sly', 'Solyc07g008030.3' => 'sly', 'Solyc12g035470.2' => 'sly', 'Sopen02g038020' => 'spe', 'Sopen05g008490' => 'spe', 'Sopen07g003910' => 'spe', 'Sopen12g015240' => 'spe', 'Sp1g11550' => 'spa', 'Sp2g16710' => 'spa', 'Sp3g00430' => 'spa', 'Sp3g26780' => 'spa', 'Sp5g22900' => 'spa', 'Sp6g29530' => 'spa', 'TAR371G0794' => 'tar', 'TAR374G0164' => 'tar', 'TAR622G0165' => 'tar', 'TAR626G0929' => 'tar', 'TAR629G2155' => 'tar', 'THA.LOC104805282' => 'tha', 'THA.LOC104805363' => 'tha', 'THA.LOC104808968' => 'tha', 'THA.LOC104821093' => 'tha', 'THA.LOC104823953' => 'tha', 'THA.LOC104825562' => 'tha', 'THA.LOC104825665' => 'tha', 'Thecc.02G261400' => 'tca', 'Thecc.04G019200' => 'tca', 'Thecc.09G130400' => 'tca', 'Thhalv10004374m.g' => 'esa', 'Thhalv10007850m.g' => 'esa', 'Thhalv10013782m.g' => 'esa', 'Thhalv10018686m.g' => 'esa', 'Thhalv10020899m.g' => 'esa', 'Thhalv10022755m.g' => 'esa', 'TPR.G23851' => 'tpr', 'TPR.G26500' => 'tpr', 'TPR.G27267' => 'tpr', 'TPR.G32001' => 'tpr', 'TPR.G6251' => 'tpr', 'TPR.G8167' => 'tpr', 'TWI12G1330' => 'twi', 'TWI18G1239' => 'twi', 'TWI34G0979' => 'twi', 'TWI36G0670' => 'twi', 'TWI36G0707' => 'twi', 'TWI56G0233' => 'twi', 'TWI75G1809' => 'twi', 'unitig_21.g20874' => 'ugi', 'unitig_26.g10343' => 'ugi', 'unitig_46.g18392' => 'ugi', 'unitig_52.g17178' => 'ugi', 'unitig_8.g2934' => 'ugi', 'vmacro01122' => 'vma', 'vmacro05875' => 'vma', 'vmacro06147' => 'vma', 'vmacro16191' => 'vma', 'vmacro18293' => 'vma', 'VMungo0251G3707' => 'vmu', 'VMungo0464G1521' => 'vmu', 'VMungo1215G0205' => 'vmu', 'VMungo1383G2484' => 'vmu', 'Zm00001eb079610' => 'zma', 'Zm00001eb135990' => 'zma', 'Zm00001eb183710' => 'zma', 'Zm00001eb246020' => 'zma' ), 'gf_id' => 'HOM05D001124', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001124' ), 'data_identifier' => 'HOM05D001124', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001124', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '548', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02520' => 'bna', 'A03p06630' => 'bna', 'A05p44460' => 'bna', 'A06p08710' => 'bna', 'A06p41090' => 'bna', 'A07p32320' => 'bna', 'A08p32520' => 'bna', 'A09p10360' => 'bna', 'A10p24080' => 'bna', 'Aa31LG11G15250' => 'aar', 'Aa31LG1G1800' => 'aar', 'Aa31LG2G5120' => 'aar', 'Aa31LG2G6070' => 'aar', 'Aa31LG5G10770' => 'aar', 'Aa31sc61G90' => 'aar', 'Actinidia01352' => 'ach', 'Actinidia05983' => 'ach', 'Actinidia08133' => 'ach', 'Actinidia15101' => 'ach', 'Actinidia26379' => 'ach', 'Actinidia35778' => 'ach', 'Actinidia36123' => 'ach', 'Actinidia37436' => 'ach', 'Actinidia38730' => 'ach', 'Ah.02g128210' => 'amhyb', 'Ah.03g132990' => 'amhyb', 'Ah.14g079410' => 'amhyb', 'AL1G24640' => 'aly', 'AL2G26680' => 'aly', 'AL3G10530' => 'aly', 'AL3G45230' => 'aly', 'AL5G15230' => 'aly', 'AL5G16960' => 'aly', 'AL6G25210' => 'aly', 'Aqoxy2G00441' => 'aox', 'Aqoxy3G01236' => 'aox', 'Aqoxy5G03746' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3RQ047' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C7GMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9C8JER' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MBL6KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YXCZ83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZANX40' => 'arhy', 'AT1G12990' => 'ath', 'AT1G67880' => 'ath', 'AT2G13290' => 'ath', 'AT3G01620' => 'ath', 'AT3G26445' => 'ath', 'AT3G27540' => 'ath', 'AT5G14480' => 'ath', 'ATR0824G026' => 'atr', 'ATR1098G019' => 'atr', 'Atru.chr11.2145' => 'acertr', 'Atru.chr2.3636' => 'acertr', 'Atru.chr2.3644' => 'acertr', 'Atru.chr6.2422' => 'acertr', 'Atru.chr7.1112' => 'acertr', 'AUR62005469' => 'cqu', 'AUR62011166' => 'cqu', 'AUR62013319' => 'cqu', 'AUR62024273' => 'cqu', 'AUR62028420' => 'cqu', 'AUR62041942' => 'cqu', 'BcaB01g04969' => 'bca', 'BcaB01g06371' => 'bca', 'BcaB02g11494' => 'bca', 'BcaB03g15382' => 'bca', 'BcaB08g36994' => 'bca', 'BcaC03g13477' => 'bca', 'BcaC03g13478' => 'bca', 'BcaC03g13480' => 'bca', 'BcaC03g13481' => 'bca', 'BcaC03g13486' => 'bca', 'BcaC04g19031' => 'bca', 'BcaC04g23085' => 'bca', 'BcaC05g25094' => 'bca', 'BcaC05g25096' => 'bca', 'BcaC05g25138' => 'bca', 'BcaC05g30416' => 'bca', 'BcaC05g30455' => 'bca', 'BcaC06g30979' => 'bca', 'BcaC06g33805' => 'bca', 'BcaC08g46021' => 'bca', 'BcaNung03154' => 'bca', 'BolC2t06623H' => 'bol', 'BolC2t06632H' => 'bol', 'BolC2t06635H' => 'bol', 'BolC2t06638H' => 'bol', 'BolC3t13266H' => 'bol', 'BolC5t29776H' => 'bol', 'BolC6t38912H' => 'bol', 'BolC7t44183H' => 'bol', 'BolC9t54123H' => 'bol', 'BolC9t59107H' => 'bol', 'BraA02t05221Z' => 'bra', 'BraA03t09996Z' => 'bra', 'BraA05t23210Z' => 'bra', 'BraA06t24068Z' => 'bra', 'BraA06t27032Z' => 'bra', 'BraA08t35176Z' => 'bra', 'BraA09t36680Z' => 'bra', 'BraA10t44471Z' => 'bra', 'C02p06760' => 'bna', 'C02p06890' => 'bna', 'C02p07010' => 'bna', 'C03p07660' => 'bna', 'C05p10300' => 'bna', 'C06p38150' => 'bna', 'C07p36650' => 'bna', 'C08p15770' => 'bna', 'C09p12300' => 'bna', 'C09p62700' => 'bna', 'C09p75040' => 'bna', 'CAN.G13.1' => 'can', 'CAN.G138.4' => 'can', 'CAN.G44.6' => 'can', 'CAN.G473.19' => 'can', 'CANSAT01G0835' => 'cansat', 'CANSAT11G0246' => 'cansat', 'CANSAT11G1766' => 'cansat', 'CANSAT64G1954' => 'cansat', 'CARHR013330' => 'chi', 'CARHR060530' => 'chi', 'CARHR075300' => 'chi', 'CARHR105120' => 'chi', 'CARHR148910' => 'chi', 'CARHR198830' => 'chi', 'Carub.0001s1275' => 'cru', 'Carub.0002s1437' => 'cru', 'Carub.0003s0044' => 'cru', 'Carub.0003s2787' => 'cru', 'Carub.0005s0597' => 'cru', 'Carub.0006s1266' => 'cru', 'Ca_06935_v3' => 'car', 'Ca_13559_v3' => 'car', 'Ca_16941_v3' => 'car', 'Ca_16960_v3' => 'car', 'Ca_17775_v3' => 'car', 'Ca_30464_v3' => 'car', 'Cc06_g08160' => 'ccan', 'Cc07_g01520' => 'ccan', 'Cc11_g15810' => 'ccan', 'CDE02G2840' => 'cde', 'CDE03G0093' => 'cde', 'CDE04G2127' => 'cde', 'CDE07G1857' => 'cde', 'CDE09G1246' => 'cde', 'Cfa003412' => 'cfa', 'Cfa007341' => 'cfa', 'Cfa009220' => 'cfa', 'Ciclev10008737m.g' => 'ccl', 'Ciclev10015565m.g' => 'ccl', 'Ciclev10031761m.g' => 'ccl', 'CiPaw.03G045300' => 'cil', 'CiPaw.03G247200' => 'cil', 'CiPaw.04G029500' => 'cil', 'CiPaw.04G174000' => 'cil', 'CiPaw.05G181200' => 'cil', 'CiPaw.06G067100' => 'cil', 'ClCG05G025800' => 'cla', 'ClCG06G011400' => 'cla', 'ClCG09G019360' => 'cla', 'COL.COLO4_04827' => 'col', 'COL.COLO4_29170' => 'col', 'COL.COLO4_35131' => 'col', 'COL.COLO4_35132' => 'col', 'Cpa.g.sc33.32' => 'cpa', 'Cpa.g.sc46.29' => 'cpa', 'Cpa.g.sc796.1' => 'cpa', 'CsaV3_1G030420' => 'csa', 'CsaV3_5G027050' => 'csa', 'CsaV3_5G031040' => 'csa', 'CsaV3_UNG023130' => 'csa', 'CSS0007726' => 'camsi', 'CSS0016433' => 'camsi', 'CSS0017656' => 'camsi', 'CSS0025364' => 'camsi', 'CSS0027582' => 'camsi', 'CSS0047288' => 'camsi', 'CSS0049950' => 'camsi', 'DCAR_003843' => 'dca', 'DCAR_007052' => 'dca', 'DCAR_020884' => 'dca', 'DCAR_021730' => 'dca', 'DCAR_024423' => 'dca', 'DCAR_026509' => 'dca', 'DCAR_031158' => 'dca', 'Dinv14728' => 'din', 'Dinv15219' => 'din', 'Dinv25728' => 'din', 'Dinv33428' => 'din', 'Dinv36489' => 'din', 'Dinv41486' => 'din', 'Duzib147G0469' => 'dzi', 'Duzib168G0060' => 'dzi', 'Duzib187G1215' => 'dzi', 'Duzib248G0692' => 'dzi', 'Duzib251G0767' => 'dzi', 'Duzib264G0446' => 'dzi', 'Duzib268G0691' => 'dzi', 'ECA232G4767' => 'eca', 'ECA233G2838' => 'eca', 'ECA234G0391' => 'eca', 'ECA234G0857' => 'eca', 'ECA236G1593' => 'eca', 'ECA238G0565' => 'eca', 'ECA246G1027' => 'eca', 'ECA246G3223' => 'eca', 'ECA246G3470' => 'eca', 'EL10Ac6g13829' => 'bvu', 'EL10Ac6g14093' => 'bvu', 'EL10Ac8g18707' => 'bvu', 'Eucgr.C01369' => 'egr', 'Eucgr.H02492' => 'egr', 'Eucgr.I01733' => 'egr', 'Eucgr.J02255' => 'egr', 'Eucgr.J02257' => 'egr', 'Eucgr.J02258' => 'egr', 'FAN02G1601' => 'fan', 'FAN03G1586' => 'fan', 'FAN03G2986' => 'fan', 'FAN05G4837' => 'fan', 'FAN06G0146' => 'fan', 'FAN07G0858' => 'fan', 'FAN09G3179' => 'fan', 'FAN10G0669' => 'fan', 'FAN12G2358' => 'fan', 'FAN14G4198' => 'fan', 'FAN14G5112' => 'fan', 'FAN17G0342' => 'fan', 'FAN19G0342' => 'fan', 'FAN19G0962' => 'fan', 'FAN19G1101' => 'fan', 'FAN19G1872' => 'fan', 'FAN22G0356' => 'fan', 'FAN23G0744' => 'fan', 'FAN23G1914' => 'fan', 'FAN26G0032' => 'fan', 'FAN28G0625' => 'fan', 'FvH4_1g02710' => 'fve', 'FvH4_1g02720' => 'fve', 'FvH4_4g25670' => 'fve', 'FvH4_6g51700' => 'fve', 'FvH4_7g20170' => 'fve', 'Glyma.05G175000' => 'gma', 'Glyma.08G132300' => 'gma', 'Glyma.11G243000' => 'gma', 'Glyma.13G158900' => 'gma', 'Glyma.17G112400' => 'gma', 'Glyma.18G014100' => 'gma', 'Glyma.19G003100' => 'gma', 'Glyma.19G056500' => 'gma', 'Gohir.A01G158900' => 'ghi', 'Gohir.A05G312600' => 'ghi', 'Gohir.A05G354900' => 'ghi', 'Gohir.A07G037200' => 'ghi', 'Gohir.A09G030000' => 'ghi', 'Gohir.A12G145200' => 'ghi', 'Gohir.D01G151500' => 'ghi', 'Gohir.D04G058300' => 'ghi', 'Gohir.D05G314100' => 'ghi', 'Gohir.D07G041400' => 'ghi', 'Gohir.D09G029700' => 'ghi', 'Gohir.D12G149700' => 'ghi', 'Gorai.001G043800' => 'gra', 'Gorai.002G187800' => 'gra', 'Gorai.006G034700' => 'gra', 'Gorai.008G161200' => 'gra', 'Gorai.009G335700' => 'gra', 'Gorai.012G065000' => 'gra', 'GSVIVG01000535001' => 'vvi', 'GSVIVG01015572001' => 'vvi', 'GSVIVG01032386001' => 'vvi', 'HanXRQChr05g0138531' => 'han', 'HanXRQChr06g0174391' => 'han', 'HanXRQChr07g0199021' => 'han', 'HanXRQChr08g0208211' => 'han', 'HanXRQChr09g0255471' => 'han', 'HanXRQChr10g0315791' => 'han', 'HanXRQChr12g0371991' => 'han', 'HanXRQChr15g0475251' => 'han', 'HanXRQChr17g0540001' => 'han', 'HanXRQChr17g0548631' => 'han', 'HanXRQChr17g0569561' => 'han', 'Haze_12256' => 'cav', 'Haze_14756' => 'cav', 'Haze_25528' => 'cav', 'Hma1.2p1_0079F.1_g041020' => 'hma', 'Hma1.2p1_0818F.1_g223260' => 'hma', 'Hma1.2p1_1747F.1_g300530' => 'hma', 'HPP92_004607' => 'vpl', 'HPP92_004608' => 'vpl', 'HPP92_006181' => 'vpl', 'HPP92_012192' => 'vpl', 'HPP92_015680' => 'vpl', 'HPP92_020249' => 'vpl', 'HPP92_021376' => 'vpl', 'HPP92_024275' => 'vpl', 'Hund06031' => 'sun', 'Hund25391' => 'sun', 'Lalb_Chr07g0185371' => 'lal', 'Lalb_Chr07g0185381' => 'lal', 'Lalb_Chr12g0204011' => 'lal', 'Lalb_Chr13g0301671' => 'lal', 'Lalb_Chr14g0362851' => 'lal', 'Lalb_Chr24g0403581' => 'lal', 'Lj1g0000233' => 'lja', 'Lj2g0018120' => 'lja', 'Lj3C621T0' => 'lonja', 'Lj3P1059T14' => 'lonja', 'Lj3P611T9' => 'lonja', 'Lj3P614T13' => 'lonja', 'Lj3P615T5' => 'lonja', 'Lj4g0012315' => 'lja', 'Lj4g0026182' => 'lja', 'Lj6P813T16' => 'lonja', 'Lj7C427T7' => 'lonja', 'Lj7C427T8' => 'lonja', 'Lj7P600T41' => 'lonja', 'Lju41C42G17' => 'lonja', 'Lsat_1_v5_gn_0_47300' => 'lsa', 'Lsat_1_v5_gn_2_91280' => 'lsa', 'Lsat_1_v5_gn_3_30561' => 'lsa', 'Lsat_1_v5_gn_4_184321' => 'lsa', 'Lsat_1_v5_gn_4_4041' => 'lsa', 'Lsat_1_v5_gn_5_92000' => 'lsa', 'Lsat_1_v5_gn_8_152940' => 'lsa', 'Lsat_1_v5_gn_8_62401' => 'lsa', 'Manes.06G055900' => 'mes', 'Manes.12G022200' => 'mes', 'Manes.13G023300' => 'mes', 'Manes.14G115000' => 'mes', 'Manes.15G151700' => 'mes', 'Manes.17G111300' => 'mes', 'Mapoly0226s0009' => 'mpo', 'MBI02_g25363_MAGBIO' => 'mbi', 'MBI06_g00027_MAGBIO' => 'mbi', 'MBI10_g13034_MAGBIO' => 'mbi', 'MD09G1023400' => 'mdo', 'MD13G1100100' => 'mdo', 'MD15G1169200' => 'mdo', 'MD16G1101100' => 'mdo', 'MD17G1022900' => 'mdo', 'Medtr3g096150' => 'mtr', 'Medtr4g115070' => 'mtr', 'Medtr7g033325' => 'mtr', 'Medtr8g089840' => 'mtr', 'MELO3C010319.2' => 'cme', 'MELO3C011944.2' => 'cme', 'MELO3C021589.2' => 'cme', 'Migut.E00207' => 'egut', 'Migut.H00067' => 'egut', 'Migut.K00433' => 'egut', 'Migut.K00606' => 'egut', 'Migut.K01410' => 'egut', 'MSTRG.13347' => 'ama', 'MSTRG.24045' => 'ama', 'MSTRG.2428' => 'ama', 'MSTRG.26410' => 'ama', 'MSTRG.3139' => 'ama', 'MSTRG.3286' => 'ama', 'MSTRG.563' => 'ama', 'MSTRG.7941' => 'ama', 'Nitab4.5_0000028g0060' => 'nta', 'Nitab4.5_0000065g0260' => 'nta', 'Nitab4.5_0000112g0060' => 'nta', 'Nitab4.5_0000489g0120' => 'nta', 'Nitab4.5_0001776g0050' => 'nta', 'Nitab4.5_0001854g0010' => 'nta', 'Nitab4.5_0001860g0020' => 'nta', 'Nitab4.5_0004352g0010' => 'nta', 'Nitab4.5_0008716g0020' => 'nta', 'Nitab4.5_0008922g0010' => 'nta', 'Nn3g16693' => 'nnu', 'Nn4g22596' => 'nnu', 'Nn7g37639' => 'nnu', 'Oeu001701.1' => 'oeu', 'Oeu018149.1' => 'oeu', 'Oeu026220.1' => 'oeu', 'Oeu038635.1' => 'oeu', 'Oeu049176.1' => 'oeu', 'Oeu056706.1' => 'oeu', 'Oeu056937.1' => 'oeu', 'Oeu057540.1' => 'oeu', 'Os02g0594900' => 'osa', 'Os02g0595100' => 'osa', 'Os04g0477500' => 'osa', 'Os12g0611900' => 'osa', 'Peaxi162Scf00076g00020' => 'pax', 'Peaxi162Scf00128g00217' => 'pax', 'Peaxi162Scf00129g01640' => 'pax', 'Peaxi162Scf00669g00007' => 'pax', 'Peaxi162Scf00700g00421' => 'pax', 'Peaxi162Scf00801g00038' => 'pax', 'Peaxi162Scf00891g00025' => 'pax', 'PGR083G0909' => 'pgr', 'PGR119G1005' => 'pgr', 'PGR142G2236' => 'pgr', 'PGR142G3388' => 'pgr', 'PGSC0003DMG400004514' => 'stu', 'PGSC0003DMG400012635' => 'stu', 'PGSC0003DMG400015730' => 'stu', 'PGSC0003DMG400018611' => 'stu', 'PGSC0003DMG400030897' => 'stu', 'Phvul.001G254800' => 'pvu', 'Phvul.002G260100' => 'pvu', 'Phvul.003G167600' => 'pvu', 'Phvul.004G005100' => 'pvu', 'Potri.001G343600' => 'ptr', 'Potri.006G066700' => 'ptr', 'Potri.008G186000' => 'ptr', 'Potri.010G046900' => 'ptr', 'Potri.018G127900' => 'ptr', 'Pp3c20_17750' => 'ppa', 'Pp3c24_4380' => 'ppa', 'Prupe.1G245800' => 'ppe', 'Prupe.3G293400' => 'ppe', 'Prupe.7G247400' => 'ppe', 'Psat0s145g0120' => 'psa', 'Psat0s595g0040' => 'psa', 'Psat0s595g0120' => 'psa', 'Psat3g175040' => 'psa', 'Psat7g058120' => 'psa', 'PSO017G0428' => 'pso', 'PSO063G7510' => 'pso', 'PSO067G0046' => 'pso', 'PSO478G1073' => 'pso', 'PSO675G3677' => 'pso', 'PSO675G6558' => 'pso', 'PSO675G7520' => 'pso', 'PSO675G8959' => 'pso', 'QL02p074089' => 'qlo', 'QL02p089614' => 'qlo', 'QL03p057736' => 'qlo', 'RcHm_v2.0_Chr1g0364131' => 'rch', 'RcHm_v2.0_Chr2g0087801' => 'rch', 'RcHm_v2.0_Chr2g0087821' => 'rch', 'RcHm_v2.0_Chr2g0173231' => 'rch', 'RcHm_v2.0_Chr4g0433111' => 'rch', 'Rhsim03G0250300' => 'rsi', 'Rhsim08G0048400' => 'rsi', 'Rhsim10G0014800' => 'rsi', 'Rhsim12G0040100' => 'rsi', 'Rhsim12G0109700' => 'rsi', 'Sabra06G0049600' => 'sbr', 'Sabra08G0141000' => 'sbr', 'Sabra10G0021400' => 'sbr', 'Sabra16G0222900' => 'sbr', 'Sabra18G0108600' => 'sbr', 'SalBow1G0433' => 'sbo', 'SalBow1G2038' => 'sbo', 'SalBow1G5003' => 'sbo', 'SalBow7G1197' => 'sbo', 'SalBow8G3506' => 'sbo', 'Sc03g0007300' => 'sci', 'Sc11g0000950' => 'sci', 'Sc14g0008750' => 'sci', 'Sc18g0000420' => 'sci', 'Sed0006754' => 'sed', 'Sed0008741' => 'sed', 'Sed0017172' => 'sed', 'Sed0018925' => 'sed', 'Sed0023326' => 'sed', 'Sed0025909' => 'sed', 'SEGI_05333' => 'sgi', 'SEGI_10362' => 'sgi', 'SEGI_13380' => 'sgi', 'SEGI_24306' => 'sgi', 'SEGI_29077' => 'sgi', 'SEGI_29095' => 'sgi', 'SEGI_36534' => 'sgi', 'SEGI_37506' => 'sgi', 'SEGI_38321' => 'sgi', 'SGA_v2.0_scaffold307G48031' => 'sas', 'SGA_v2.0_scaffold47G17507' => 'sas', 'SGA_v2.0_scaffold63G21736' => 'sas', 'SGA_v2.0_scaffold87G27070' => 'sas', 'SHI17794' => 'shi', 'SHI28851' => 'shi', 'SMO165G0155' => 'smo', 'SMO340G0217' => 'smo', 'SMO367G1210' => 'smo', 'Solyc02g093430.3' => 'sly', 'Solyc05g013580.4' => 'sly', 'Solyc07g008030.3' => 'sly', 'Solyc12g035470.2' => 'sly', 'Sopen02g038020' => 'spe', 'Sopen05g008490' => 'spe', 'Sopen07g003910' => 'spe', 'Sopen12g015240' => 'spe', 'Sp1g11550' => 'spa', 'Sp2g16710' => 'spa', 'Sp3g00430' => 'spa', 'Sp3g26780' => 'spa', 'Sp5g22900' => 'spa', 'Sp6g29530' => 'spa', 'TAR371G0794' => 'tar', 'TAR374G0164' => 'tar', 'TAR622G0165' => 'tar', 'TAR626G0929' => 'tar', 'TAR629G2155' => 'tar', 'THA.LOC104805282' => 'tha', 'THA.LOC104805363' => 'tha', 'THA.LOC104808968' => 'tha', 'THA.LOC104821093' => 'tha', 'THA.LOC104823953' => 'tha', 'THA.LOC104825562' => 'tha', 'THA.LOC104825665' => 'tha', 'Thecc.02G261400' => 'tca', 'Thecc.04G019200' => 'tca', 'Thecc.09G130400' => 'tca', 'Thhalv10004374m.g' => 'esa', 'Thhalv10007850m.g' => 'esa', 'Thhalv10013782m.g' => 'esa', 'Thhalv10018686m.g' => 'esa', 'Thhalv10020899m.g' => 'esa', 'Thhalv10022755m.g' => 'esa', 'TPR.G23851' => 'tpr', 'TPR.G26500' => 'tpr', 'TPR.G27267' => 'tpr', 'TPR.G32001' => 'tpr', 'TPR.G6251' => 'tpr', 'TPR.G8167' => 'tpr', 'TWI12G1330' => 'twi', 'TWI18G1239' => 'twi', 'TWI34G0979' => 'twi', 'TWI36G0670' => 'twi', 'TWI36G0707' => 'twi', 'TWI56G0233' => 'twi', 'TWI75G1809' => 'twi', 'unitig_21.g20874' => 'ugi', 'unitig_26.g10343' => 'ugi', 'unitig_46.g18392' => 'ugi', 'unitig_52.g17178' => 'ugi', 'unitig_8.g2934' => 'ugi', 'vmacro01122' => 'vma', 'vmacro05875' => 'vma', 'vmacro06147' => 'vma', 'vmacro16191' => 'vma', 'vmacro18293' => 'vma', 'VMungo0251G3707' => 'vmu', 'VMungo0464G1521' => 'vmu', 'VMungo1215G0205' => 'vmu', 'VMungo1383G2484' => 'vmu', 'Zm00001eb079610' => 'zma', 'Zm00001eb135990' => 'zma', 'Zm00001eb183710' => 'zma', 'Zm00001eb246020' => 'zma' ) $gf_id = 'HOM05D001124' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001124' ) $data_identifier = 'HOM05D001124' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 6, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 7, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 21, 'bol' => (int) 10, 'bra' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 6, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 9, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 21, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 8, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 10, 'lsa' => (int) 8, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 8, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 9, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb246020' $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' => 'HOM05D001124', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '548', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02520' => 'bna', 'A03p06630' => 'bna', 'A05p44460' => 'bna', 'A06p08710' => 'bna', 'A06p41090' => 'bna', 'A07p32320' => 'bna', 'A08p32520' => 'bna', 'A09p10360' => 'bna', 'A10p24080' => 'bna', 'Aa31LG11G15250' => 'aar', 'Aa31LG1G1800' => 'aar', 'Aa31LG2G5120' => 'aar', 'Aa31LG2G6070' => 'aar', 'Aa31LG5G10770' => 'aar', 'Aa31sc61G90' => 'aar', 'Actinidia01352' => 'ach', 'Actinidia05983' => 'ach', 'Actinidia08133' => 'ach', 'Actinidia15101' => 'ach', 'Actinidia26379' => 'ach', 'Actinidia35778' => 'ach', 'Actinidia36123' => 'ach', 'Actinidia37436' => 'ach', 'Actinidia38730' => 'ach', 'Ah.02g128210' => 'amhyb', 'Ah.03g132990' => 'amhyb', 'Ah.14g079410' => 'amhyb', 'AL1G24640' => 'aly', 'AL2G26680' => 'aly', 'AL3G10530' => 'aly', 'AL3G45230' => 'aly', 'AL5G15230' => 'aly', 'AL5G16960' => 'aly', 'AL6G25210' => 'aly', 'Aqoxy2G00441' => 'aox', 'Aqoxy3G01236' => 'aox', 'Aqoxy5G03746' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3RQ047' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C7GMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9C8JER' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MBL6KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YXCZ83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZANX40' => 'arhy', 'AT1G12990' => 'ath', 'AT1G67880' => 'ath', 'AT2G13290' => 'ath', 'AT3G01620' => 'ath', 'AT3G26445' => 'ath', 'AT3G27540' => 'ath', 'AT5G14480' => 'ath', 'ATR0824G026' => 'atr', 'ATR1098G019' => 'atr', 'Atru.chr11.2145' => 'acertr', 'Atru.chr2.3636' => 'acertr', 'Atru.chr2.3644' => 'acertr', 'Atru.chr6.2422' => 'acertr', 'Atru.chr7.1112' => 'acertr', 'AUR62005469' => 'cqu', 'AUR62011166' => 'cqu', 'AUR62013319' => 'cqu', 'AUR62024273' => 'cqu', 'AUR62028420' => 'cqu', 'AUR62041942' => 'cqu', 'BcaB01g04969' => 'bca', 'BcaB01g06371' => 'bca', 'BcaB02g11494' => 'bca', 'BcaB03g15382' => 'bca', 'BcaB08g36994' => 'bca', 'BcaC03g13477' => 'bca', 'BcaC03g13478' => 'bca', 'BcaC03g13480' => 'bca', 'BcaC03g13481' => 'bca', 'BcaC03g13486' => 'bca', 'BcaC04g19031' => 'bca', 'BcaC04g23085' => 'bca', 'BcaC05g25094' => 'bca', 'BcaC05g25096' => 'bca', 'BcaC05g25138' => 'bca', 'BcaC05g30416' => 'bca', 'BcaC05g30455' => 'bca', 'BcaC06g30979' => 'bca', 'BcaC06g33805' => 'bca', 'BcaC08g46021' => 'bca', 'BcaNung03154' => 'bca', 'BolC2t06623H' => 'bol', 'BolC2t06632H' => 'bol', 'BolC2t06635H' => 'bol', 'BolC2t06638H' => 'bol', 'BolC3t13266H' => 'bol', 'BolC5t29776H' => 'bol', 'BolC6t38912H' => 'bol', 'BolC7t44183H' => 'bol', 'BolC9t54123H' => 'bol', 'BolC9t59107H' => 'bol', 'BraA02t05221Z' => 'bra', 'BraA03t09996Z' => 'bra', 'BraA05t23210Z' => 'bra', 'BraA06t24068Z' => 'bra', 'BraA06t27032Z' => 'bra', 'BraA08t35176Z' => 'bra', 'BraA09t36680Z' => 'bra', 'BraA10t44471Z' => 'bra', 'C02p06760' => 'bna', 'C02p06890' => 'bna', 'C02p07010' => 'bna', 'C03p07660' => 'bna', 'C05p10300' => 'bna', 'C06p38150' => 'bna', 'C07p36650' => 'bna', 'C08p15770' => 'bna', 'C09p12300' => 'bna', 'C09p62700' => 'bna', 'C09p75040' => 'bna', 'CAN.G13.1' => 'can', 'CAN.G138.4' => 'can', 'CAN.G44.6' => 'can', 'CAN.G473.19' => 'can', 'CANSAT01G0835' => 'cansat', 'CANSAT11G0246' => 'cansat', 'CANSAT11G1766' => 'cansat', 'CANSAT64G1954' => 'cansat', 'CARHR013330' => 'chi', 'CARHR060530' => 'chi', 'CARHR075300' => 'chi', 'CARHR105120' => 'chi', 'CARHR148910' => 'chi', 'CARHR198830' => 'chi', 'Carub.0001s1275' => 'cru', 'Carub.0002s1437' => 'cru', 'Carub.0003s0044' => 'cru', 'Carub.0003s2787' => 'cru', 'Carub.0005s0597' => 'cru', 'Carub.0006s1266' => 'cru', 'Ca_06935_v3' => 'car', 'Ca_13559_v3' => 'car', 'Ca_16941_v3' => 'car', 'Ca_16960_v3' => 'car', 'Ca_17775_v3' => 'car', 'Ca_30464_v3' => 'car', 'Cc06_g08160' => 'ccan', 'Cc07_g01520' => 'ccan', 'Cc11_g15810' => 'ccan', 'CDE02G2840' => 'cde', 'CDE03G0093' => 'cde', 'CDE04G2127' => 'cde', 'CDE07G1857' => 'cde', 'CDE09G1246' => 'cde', 'Cfa003412' => 'cfa', 'Cfa007341' => 'cfa', 'Cfa009220' => 'cfa', 'Ciclev10008737m.g' => 'ccl', 'Ciclev10015565m.g' => 'ccl', 'Ciclev10031761m.g' => 'ccl', 'CiPaw.03G045300' => 'cil', 'CiPaw.03G247200' => 'cil', 'CiPaw.04G029500' => 'cil', 'CiPaw.04G174000' => 'cil', 'CiPaw.05G181200' => 'cil', 'CiPaw.06G067100' => 'cil', 'ClCG05G025800' => 'cla', 'ClCG06G011400' => 'cla', 'ClCG09G019360' => 'cla', 'COL.COLO4_04827' => 'col', 'COL.COLO4_29170' => 'col', 'COL.COLO4_35131' => 'col', 'COL.COLO4_35132' => 'col', 'Cpa.g.sc33.32' => 'cpa', 'Cpa.g.sc46.29' => 'cpa', 'Cpa.g.sc796.1' => 'cpa', 'CsaV3_1G030420' => 'csa', 'CsaV3_5G027050' => 'csa', 'CsaV3_5G031040' => 'csa', 'CsaV3_UNG023130' => 'csa', 'CSS0007726' => 'camsi', 'CSS0016433' => 'camsi', 'CSS0017656' => 'camsi', 'CSS0025364' => 'camsi', 'CSS0027582' => 'camsi', 'CSS0047288' => 'camsi', 'CSS0049950' => 'camsi', 'DCAR_003843' => 'dca', 'DCAR_007052' => 'dca', 'DCAR_020884' => 'dca', 'DCAR_021730' => 'dca', 'DCAR_024423' => 'dca', 'DCAR_026509' => 'dca', 'DCAR_031158' => 'dca', 'Dinv14728' => 'din', 'Dinv15219' => 'din', 'Dinv25728' => 'din', 'Dinv33428' => 'din', 'Dinv36489' => 'din', 'Dinv41486' => 'din', 'Duzib147G0469' => 'dzi', 'Duzib168G0060' => 'dzi', 'Duzib187G1215' => 'dzi', 'Duzib248G0692' => 'dzi', 'Duzib251G0767' => 'dzi', 'Duzib264G0446' => 'dzi', 'Duzib268G0691' => 'dzi', 'ECA232G4767' => 'eca', 'ECA233G2838' => 'eca', 'ECA234G0391' => 'eca', 'ECA234G0857' => 'eca', 'ECA236G1593' => 'eca', 'ECA238G0565' => 'eca', 'ECA246G1027' => 'eca', 'ECA246G3223' => 'eca', 'ECA246G3470' => 'eca', 'EL10Ac6g13829' => 'bvu', 'EL10Ac6g14093' => 'bvu', 'EL10Ac8g18707' => 'bvu', 'Eucgr.C01369' => 'egr', 'Eucgr.H02492' => 'egr', 'Eucgr.I01733' => 'egr', 'Eucgr.J02255' => 'egr', 'Eucgr.J02257' => 'egr', 'Eucgr.J02258' => 'egr', 'FAN02G1601' => 'fan', 'FAN03G1586' => 'fan', 'FAN03G2986' => 'fan', 'FAN05G4837' => 'fan', 'FAN06G0146' => 'fan', 'FAN07G0858' => 'fan', 'FAN09G3179' => 'fan', 'FAN10G0669' => 'fan', 'FAN12G2358' => 'fan', 'FAN14G4198' => 'fan', 'FAN14G5112' => 'fan', 'FAN17G0342' => 'fan', 'FAN19G0342' => 'fan', 'FAN19G0962' => 'fan', 'FAN19G1101' => 'fan', 'FAN19G1872' => 'fan', 'FAN22G0356' => 'fan', 'FAN23G0744' => 'fan', 'FAN23G1914' => 'fan', 'FAN26G0032' => 'fan', 'FAN28G0625' => 'fan', 'FvH4_1g02710' => 'fve', 'FvH4_1g02720' => 'fve', 'FvH4_4g25670' => 'fve', 'FvH4_6g51700' => 'fve', 'FvH4_7g20170' => 'fve', 'Glyma.05G175000' => 'gma', 'Glyma.08G132300' => 'gma', 'Glyma.11G243000' => 'gma', 'Glyma.13G158900' => 'gma', 'Glyma.17G112400' => 'gma', 'Glyma.18G014100' => 'gma', 'Glyma.19G003100' => 'gma', 'Glyma.19G056500' => 'gma', 'Gohir.A01G158900' => 'ghi', 'Gohir.A05G312600' => 'ghi', 'Gohir.A05G354900' => 'ghi', 'Gohir.A07G037200' => 'ghi', 'Gohir.A09G030000' => 'ghi', 'Gohir.A12G145200' => 'ghi', 'Gohir.D01G151500' => 'ghi', 'Gohir.D04G058300' => 'ghi', 'Gohir.D05G314100' => 'ghi', 'Gohir.D07G041400' => 'ghi', 'Gohir.D09G029700' => 'ghi', 'Gohir.D12G149700' => 'ghi', 'Gorai.001G043800' => 'gra', 'Gorai.002G187800' => 'gra', 'Gorai.006G034700' => 'gra', 'Gorai.008G161200' => 'gra', 'Gorai.009G335700' => 'gra', 'Gorai.012G065000' => 'gra', 'GSVIVG01000535001' => 'vvi', 'GSVIVG01015572001' => 'vvi', 'GSVIVG01032386001' => 'vvi', 'HanXRQChr05g0138531' => 'han', 'HanXRQChr06g0174391' => 'han', 'HanXRQChr07g0199021' => 'han', 'HanXRQChr08g0208211' => 'han', 'HanXRQChr09g0255471' => 'han', 'HanXRQChr10g0315791' => 'han', 'HanXRQChr12g0371991' => 'han', 'HanXRQChr15g0475251' => 'han', 'HanXRQChr17g0540001' => 'han', 'HanXRQChr17g0548631' => 'han', 'HanXRQChr17g0569561' => 'han', 'Haze_12256' => 'cav', 'Haze_14756' => 'cav', 'Haze_25528' => 'cav', 'Hma1.2p1_0079F.1_g041020' => 'hma', 'Hma1.2p1_0818F.1_g223260' => 'hma', 'Hma1.2p1_1747F.1_g300530' => 'hma', 'HPP92_004607' => 'vpl', 'HPP92_004608' => 'vpl', 'HPP92_006181' => 'vpl', 'HPP92_012192' => 'vpl', 'HPP92_015680' => 'vpl', 'HPP92_020249' => 'vpl', 'HPP92_021376' => 'vpl', 'HPP92_024275' => 'vpl', 'Hund06031' => 'sun', 'Hund25391' => 'sun', 'Lalb_Chr07g0185371' => 'lal', 'Lalb_Chr07g0185381' => 'lal', 'Lalb_Chr12g0204011' => 'lal', 'Lalb_Chr13g0301671' => 'lal', 'Lalb_Chr14g0362851' => 'lal', 'Lalb_Chr24g0403581' => 'lal', 'Lj1g0000233' => 'lja', 'Lj2g0018120' => 'lja', 'Lj3C621T0' => 'lonja', 'Lj3P1059T14' => 'lonja', 'Lj3P611T9' => 'lonja', 'Lj3P614T13' => 'lonja', 'Lj3P615T5' => 'lonja', 'Lj4g0012315' => 'lja', 'Lj4g0026182' => 'lja', 'Lj6P813T16' => 'lonja', 'Lj7C427T7' => 'lonja', 'Lj7C427T8' => 'lonja', 'Lj7P600T41' => 'lonja', 'Lju41C42G17' => 'lonja', 'Lsat_1_v5_gn_0_47300' => 'lsa', 'Lsat_1_v5_gn_2_91280' => 'lsa', 'Lsat_1_v5_gn_3_30561' => 'lsa', 'Lsat_1_v5_gn_4_184321' => 'lsa', 'Lsat_1_v5_gn_4_4041' => 'lsa', 'Lsat_1_v5_gn_5_92000' => 'lsa', 'Lsat_1_v5_gn_8_152940' => 'lsa', 'Lsat_1_v5_gn_8_62401' => 'lsa', 'Manes.06G055900' => 'mes', 'Manes.12G022200' => 'mes', 'Manes.13G023300' => 'mes', 'Manes.14G115000' => 'mes', 'Manes.15G151700' => 'mes', 'Manes.17G111300' => 'mes', 'Mapoly0226s0009' => 'mpo', 'MBI02_g25363_MAGBIO' => 'mbi', 'MBI06_g00027_MAGBIO' => 'mbi', 'MBI10_g13034_MAGBIO' => 'mbi', 'MD09G1023400' => 'mdo', 'MD13G1100100' => 'mdo', 'MD15G1169200' => 'mdo', 'MD16G1101100' => 'mdo', 'MD17G1022900' => 'mdo', 'Medtr3g096150' => 'mtr', 'Medtr4g115070' => 'mtr', 'Medtr7g033325' => 'mtr', 'Medtr8g089840' => 'mtr', 'MELO3C010319.2' => 'cme', 'MELO3C011944.2' => 'cme', 'MELO3C021589.2' => 'cme', 'Migut.E00207' => 'egut', 'Migut.H00067' => 'egut', 'Migut.K00433' => 'egut', 'Migut.K00606' => 'egut', 'Migut.K01410' => 'egut', 'MSTRG.13347' => 'ama', 'MSTRG.24045' => 'ama', 'MSTRG.2428' => 'ama', 'MSTRG.26410' => 'ama', 'MSTRG.3139' => 'ama', 'MSTRG.3286' => 'ama', 'MSTRG.563' => 'ama', 'MSTRG.7941' => 'ama', 'Nitab4.5_0000028g0060' => 'nta', 'Nitab4.5_0000065g0260' => 'nta', 'Nitab4.5_0000112g0060' => 'nta', 'Nitab4.5_0000489g0120' => 'nta', 'Nitab4.5_0001776g0050' => 'nta', 'Nitab4.5_0001854g0010' => 'nta', 'Nitab4.5_0001860g0020' => 'nta', 'Nitab4.5_0004352g0010' => 'nta', 'Nitab4.5_0008716g0020' => 'nta', 'Nitab4.5_0008922g0010' => 'nta', 'Nn3g16693' => 'nnu', 'Nn4g22596' => 'nnu', 'Nn7g37639' => 'nnu', 'Oeu001701.1' => 'oeu', 'Oeu018149.1' => 'oeu', 'Oeu026220.1' => 'oeu', 'Oeu038635.1' => 'oeu', 'Oeu049176.1' => 'oeu', 'Oeu056706.1' => 'oeu', 'Oeu056937.1' => 'oeu', 'Oeu057540.1' => 'oeu', 'Os02g0594900' => 'osa', 'Os02g0595100' => 'osa', 'Os04g0477500' => 'osa', 'Os12g0611900' => 'osa', 'Peaxi162Scf00076g00020' => 'pax', 'Peaxi162Scf00128g00217' => 'pax', 'Peaxi162Scf00129g01640' => 'pax', 'Peaxi162Scf00669g00007' => 'pax', 'Peaxi162Scf00700g00421' => 'pax', 'Peaxi162Scf00801g00038' => 'pax', 'Peaxi162Scf00891g00025' => 'pax', 'PGR083G0909' => 'pgr', 'PGR119G1005' => 'pgr', 'PGR142G2236' => 'pgr', 'PGR142G3388' => 'pgr', 'PGSC0003DMG400004514' => 'stu', 'PGSC0003DMG400012635' => 'stu', 'PGSC0003DMG400015730' => 'stu', 'PGSC0003DMG400018611' => 'stu', 'PGSC0003DMG400030897' => 'stu', 'Phvul.001G254800' => 'pvu', 'Phvul.002G260100' => 'pvu', 'Phvul.003G167600' => 'pvu', 'Phvul.004G005100' => 'pvu', 'Potri.001G343600' => 'ptr', 'Potri.006G066700' => 'ptr', 'Potri.008G186000' => 'ptr', 'Potri.010G046900' => 'ptr', 'Potri.018G127900' => 'ptr', 'Pp3c20_17750' => 'ppa', 'Pp3c24_4380' => 'ppa', 'Prupe.1G245800' => 'ppe', 'Prupe.3G293400' => 'ppe', 'Prupe.7G247400' => 'ppe', 'Psat0s145g0120' => 'psa', 'Psat0s595g0040' => 'psa', 'Psat0s595g0120' => 'psa', 'Psat3g175040' => 'psa', 'Psat7g058120' => 'psa', 'PSO017G0428' => 'pso', 'PSO063G7510' => 'pso', 'PSO067G0046' => 'pso', 'PSO478G1073' => 'pso', 'PSO675G3677' => 'pso', 'PSO675G6558' => 'pso', 'PSO675G7520' => 'pso', 'PSO675G8959' => 'pso', 'QL02p074089' => 'qlo', 'QL02p089614' => 'qlo', 'QL03p057736' => 'qlo', 'RcHm_v2.0_Chr1g0364131' => 'rch', 'RcHm_v2.0_Chr2g0087801' => 'rch', 'RcHm_v2.0_Chr2g0087821' => 'rch', 'RcHm_v2.0_Chr2g0173231' => 'rch', 'RcHm_v2.0_Chr4g0433111' => 'rch', 'Rhsim03G0250300' => 'rsi', 'Rhsim08G0048400' => 'rsi', 'Rhsim10G0014800' => 'rsi', 'Rhsim12G0040100' => 'rsi', 'Rhsim12G0109700' => 'rsi', 'Sabra06G0049600' => 'sbr', 'Sabra08G0141000' => 'sbr', 'Sabra10G0021400' => 'sbr', 'Sabra16G0222900' => 'sbr', 'Sabra18G0108600' => 'sbr', 'SalBow1G0433' => 'sbo', 'SalBow1G2038' => 'sbo', 'SalBow1G5003' => 'sbo', 'SalBow7G1197' => 'sbo', 'SalBow8G3506' => 'sbo', 'Sc03g0007300' => 'sci', 'Sc11g0000950' => 'sci', 'Sc14g0008750' => 'sci', 'Sc18g0000420' => 'sci', 'Sed0006754' => 'sed', 'Sed0008741' => 'sed', 'Sed0017172' => 'sed', 'Sed0018925' => 'sed', 'Sed0023326' => 'sed', 'Sed0025909' => 'sed', 'SEGI_05333' => 'sgi', 'SEGI_10362' => 'sgi', 'SEGI_13380' => 'sgi', 'SEGI_24306' => 'sgi', 'SEGI_29077' => 'sgi', 'SEGI_29095' => 'sgi', 'SEGI_36534' => 'sgi', 'SEGI_37506' => 'sgi', 'SEGI_38321' => 'sgi', 'SGA_v2.0_scaffold307G48031' => 'sas', 'SGA_v2.0_scaffold47G17507' => 'sas', 'SGA_v2.0_scaffold63G21736' => 'sas', 'SGA_v2.0_scaffold87G27070' => 'sas', 'SHI17794' => 'shi', 'SHI28851' => 'shi', 'SMO165G0155' => 'smo', 'SMO340G0217' => 'smo', 'SMO367G1210' => 'smo', 'Solyc02g093430.3' => 'sly', 'Solyc05g013580.4' => 'sly', 'Solyc07g008030.3' => 'sly', 'Solyc12g035470.2' => 'sly', 'Sopen02g038020' => 'spe', 'Sopen05g008490' => 'spe', 'Sopen07g003910' => 'spe', 'Sopen12g015240' => 'spe', 'Sp1g11550' => 'spa', 'Sp2g16710' => 'spa', 'Sp3g00430' => 'spa', 'Sp3g26780' => 'spa', 'Sp5g22900' => 'spa', 'Sp6g29530' => 'spa', 'TAR371G0794' => 'tar', 'TAR374G0164' => 'tar', 'TAR622G0165' => 'tar', 'TAR626G0929' => 'tar', 'TAR629G2155' => 'tar', 'THA.LOC104805282' => 'tha', 'THA.LOC104805363' => 'tha', 'THA.LOC104808968' => 'tha', 'THA.LOC104821093' => 'tha', 'THA.LOC104823953' => 'tha', 'THA.LOC104825562' => 'tha', 'THA.LOC104825665' => 'tha', 'Thecc.02G261400' => 'tca', 'Thecc.04G019200' => 'tca', 'Thecc.09G130400' => 'tca', 'Thhalv10004374m.g' => 'esa', 'Thhalv10007850m.g' => 'esa', 'Thhalv10013782m.g' => 'esa', 'Thhalv10018686m.g' => 'esa', 'Thhalv10020899m.g' => 'esa', 'Thhalv10022755m.g' => 'esa', 'TPR.G23851' => 'tpr', 'TPR.G26500' => 'tpr', 'TPR.G27267' => 'tpr', 'TPR.G32001' => 'tpr', 'TPR.G6251' => 'tpr', 'TPR.G8167' => 'tpr', 'TWI12G1330' => 'twi', 'TWI18G1239' => 'twi', 'TWI34G0979' => 'twi', 'TWI36G0670' => 'twi', 'TWI36G0707' => 'twi', 'TWI56G0233' => 'twi', 'TWI75G1809' => 'twi', 'unitig_21.g20874' => 'ugi', 'unitig_26.g10343' => 'ugi', 'unitig_46.g18392' => 'ugi', 'unitig_52.g17178' => 'ugi', 'unitig_8.g2934' => 'ugi', 'vmacro01122' => 'vma', 'vmacro05875' => 'vma', 'vmacro06147' => 'vma', 'vmacro16191' => 'vma', 'vmacro18293' => 'vma', 'VMungo0251G3707' => 'vmu', 'VMungo0464G1521' => 'vmu', 'VMungo1215G0205' => 'vmu', 'VMungo1383G2484' => 'vmu', 'Zm00001eb079610' => 'zma', 'Zm00001eb135990' => 'zma', 'Zm00001eb183710' => 'zma', 'Zm00001eb246020' => 'zma' ), 'gf_id' => 'HOM05D001124', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001124' ), 'data_identifier' => 'HOM05D001124', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001124', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '548', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02520' => 'bna', 'A03p06630' => 'bna', 'A05p44460' => 'bna', 'A06p08710' => 'bna', 'A06p41090' => 'bna', 'A07p32320' => 'bna', 'A08p32520' => 'bna', 'A09p10360' => 'bna', 'A10p24080' => 'bna', 'Aa31LG11G15250' => 'aar', 'Aa31LG1G1800' => 'aar', 'Aa31LG2G5120' => 'aar', 'Aa31LG2G6070' => 'aar', 'Aa31LG5G10770' => 'aar', 'Aa31sc61G90' => 'aar', 'Actinidia01352' => 'ach', 'Actinidia05983' => 'ach', 'Actinidia08133' => 'ach', 'Actinidia15101' => 'ach', 'Actinidia26379' => 'ach', 'Actinidia35778' => 'ach', 'Actinidia36123' => 'ach', 'Actinidia37436' => 'ach', 'Actinidia38730' => 'ach', 'Ah.02g128210' => 'amhyb', 'Ah.03g132990' => 'amhyb', 'Ah.14g079410' => 'amhyb', 'AL1G24640' => 'aly', 'AL2G26680' => 'aly', 'AL3G10530' => 'aly', 'AL3G45230' => 'aly', 'AL5G15230' => 'aly', 'AL5G16960' => 'aly', 'AL6G25210' => 'aly', 'Aqoxy2G00441' => 'aox', 'Aqoxy3G01236' => 'aox', 'Aqoxy5G03746' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3RQ047' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C7GMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9C8JER' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MBL6KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YXCZ83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZANX40' => 'arhy', 'AT1G12990' => 'ath', 'AT1G67880' => 'ath', 'AT2G13290' => 'ath', 'AT3G01620' => 'ath', 'AT3G26445' => 'ath', 'AT3G27540' => 'ath', 'AT5G14480' => 'ath', 'ATR0824G026' => 'atr', 'ATR1098G019' => 'atr', 'Atru.chr11.2145' => 'acertr', 'Atru.chr2.3636' => 'acertr', 'Atru.chr2.3644' => 'acertr', 'Atru.chr6.2422' => 'acertr', 'Atru.chr7.1112' => 'acertr', 'AUR62005469' => 'cqu', 'AUR62011166' => 'cqu', 'AUR62013319' => 'cqu', 'AUR62024273' => 'cqu', 'AUR62028420' => 'cqu', 'AUR62041942' => 'cqu', 'BcaB01g04969' => 'bca', 'BcaB01g06371' => 'bca', 'BcaB02g11494' => 'bca', 'BcaB03g15382' => 'bca', 'BcaB08g36994' => 'bca', 'BcaC03g13477' => 'bca', 'BcaC03g13478' => 'bca', 'BcaC03g13480' => 'bca', 'BcaC03g13481' => 'bca', 'BcaC03g13486' => 'bca', 'BcaC04g19031' => 'bca', 'BcaC04g23085' => 'bca', 'BcaC05g25094' => 'bca', 'BcaC05g25096' => 'bca', 'BcaC05g25138' => 'bca', 'BcaC05g30416' => 'bca', 'BcaC05g30455' => 'bca', 'BcaC06g30979' => 'bca', 'BcaC06g33805' => 'bca', 'BcaC08g46021' => 'bca', 'BcaNung03154' => 'bca', 'BolC2t06623H' => 'bol', 'BolC2t06632H' => 'bol', 'BolC2t06635H' => 'bol', 'BolC2t06638H' => 'bol', 'BolC3t13266H' => 'bol', 'BolC5t29776H' => 'bol', 'BolC6t38912H' => 'bol', 'BolC7t44183H' => 'bol', 'BolC9t54123H' => 'bol', 'BolC9t59107H' => 'bol', 'BraA02t05221Z' => 'bra', 'BraA03t09996Z' => 'bra', 'BraA05t23210Z' => 'bra', 'BraA06t24068Z' => 'bra', 'BraA06t27032Z' => 'bra', 'BraA08t35176Z' => 'bra', 'BraA09t36680Z' => 'bra', 'BraA10t44471Z' => 'bra', 'C02p06760' => 'bna', 'C02p06890' => 'bna', 'C02p07010' => 'bna', 'C03p07660' => 'bna', 'C05p10300' => 'bna', 'C06p38150' => 'bna', 'C07p36650' => 'bna', 'C08p15770' => 'bna', 'C09p12300' => 'bna', 'C09p62700' => 'bna', 'C09p75040' => 'bna', 'CAN.G13.1' => 'can', 'CAN.G138.4' => 'can', 'CAN.G44.6' => 'can', 'CAN.G473.19' => 'can', 'CANSAT01G0835' => 'cansat', 'CANSAT11G0246' => 'cansat', 'CANSAT11G1766' => 'cansat', 'CANSAT64G1954' => 'cansat', 'CARHR013330' => 'chi', 'CARHR060530' => 'chi', 'CARHR075300' => 'chi', 'CARHR105120' => 'chi', 'CARHR148910' => 'chi', 'CARHR198830' => 'chi', 'Carub.0001s1275' => 'cru', 'Carub.0002s1437' => 'cru', 'Carub.0003s0044' => 'cru', 'Carub.0003s2787' => 'cru', 'Carub.0005s0597' => 'cru', 'Carub.0006s1266' => 'cru', 'Ca_06935_v3' => 'car', 'Ca_13559_v3' => 'car', 'Ca_16941_v3' => 'car', 'Ca_16960_v3' => 'car', 'Ca_17775_v3' => 'car', 'Ca_30464_v3' => 'car', 'Cc06_g08160' => 'ccan', 'Cc07_g01520' => 'ccan', 'Cc11_g15810' => 'ccan', 'CDE02G2840' => 'cde', 'CDE03G0093' => 'cde', 'CDE04G2127' => 'cde', 'CDE07G1857' => 'cde', 'CDE09G1246' => 'cde', 'Cfa003412' => 'cfa', 'Cfa007341' => 'cfa', 'Cfa009220' => 'cfa', 'Ciclev10008737m.g' => 'ccl', 'Ciclev10015565m.g' => 'ccl', 'Ciclev10031761m.g' => 'ccl', 'CiPaw.03G045300' => 'cil', 'CiPaw.03G247200' => 'cil', 'CiPaw.04G029500' => 'cil', 'CiPaw.04G174000' => 'cil', 'CiPaw.05G181200' => 'cil', 'CiPaw.06G067100' => 'cil', 'ClCG05G025800' => 'cla', 'ClCG06G011400' => 'cla', 'ClCG09G019360' => 'cla', 'COL.COLO4_04827' => 'col', 'COL.COLO4_29170' => 'col', 'COL.COLO4_35131' => 'col', 'COL.COLO4_35132' => 'col', 'Cpa.g.sc33.32' => 'cpa', 'Cpa.g.sc46.29' => 'cpa', 'Cpa.g.sc796.1' => 'cpa', 'CsaV3_1G030420' => 'csa', 'CsaV3_5G027050' => 'csa', 'CsaV3_5G031040' => 'csa', 'CsaV3_UNG023130' => 'csa', 'CSS0007726' => 'camsi', 'CSS0016433' => 'camsi', 'CSS0017656' => 'camsi', 'CSS0025364' => 'camsi', 'CSS0027582' => 'camsi', 'CSS0047288' => 'camsi', 'CSS0049950' => 'camsi', 'DCAR_003843' => 'dca', 'DCAR_007052' => 'dca', 'DCAR_020884' => 'dca', 'DCAR_021730' => 'dca', 'DCAR_024423' => 'dca', 'DCAR_026509' => 'dca', 'DCAR_031158' => 'dca', 'Dinv14728' => 'din', 'Dinv15219' => 'din', 'Dinv25728' => 'din', 'Dinv33428' => 'din', 'Dinv36489' => 'din', 'Dinv41486' => 'din', 'Duzib147G0469' => 'dzi', 'Duzib168G0060' => 'dzi', 'Duzib187G1215' => 'dzi', 'Duzib248G0692' => 'dzi', 'Duzib251G0767' => 'dzi', 'Duzib264G0446' => 'dzi', 'Duzib268G0691' => 'dzi', 'ECA232G4767' => 'eca', 'ECA233G2838' => 'eca', 'ECA234G0391' => 'eca', 'ECA234G0857' => 'eca', 'ECA236G1593' => 'eca', 'ECA238G0565' => 'eca', 'ECA246G1027' => 'eca', 'ECA246G3223' => 'eca', 'ECA246G3470' => 'eca', 'EL10Ac6g13829' => 'bvu', 'EL10Ac6g14093' => 'bvu', 'EL10Ac8g18707' => 'bvu', 'Eucgr.C01369' => 'egr', 'Eucgr.H02492' => 'egr', 'Eucgr.I01733' => 'egr', 'Eucgr.J02255' => 'egr', 'Eucgr.J02257' => 'egr', 'Eucgr.J02258' => 'egr', 'FAN02G1601' => 'fan', 'FAN03G1586' => 'fan', 'FAN03G2986' => 'fan', 'FAN05G4837' => 'fan', 'FAN06G0146' => 'fan', 'FAN07G0858' => 'fan', 'FAN09G3179' => 'fan', 'FAN10G0669' => 'fan', 'FAN12G2358' => 'fan', 'FAN14G4198' => 'fan', 'FAN14G5112' => 'fan', 'FAN17G0342' => 'fan', 'FAN19G0342' => 'fan', 'FAN19G0962' => 'fan', 'FAN19G1101' => 'fan', 'FAN19G1872' => 'fan', 'FAN22G0356' => 'fan', 'FAN23G0744' => 'fan', 'FAN23G1914' => 'fan', 'FAN26G0032' => 'fan', 'FAN28G0625' => 'fan', 'FvH4_1g02710' => 'fve', 'FvH4_1g02720' => 'fve', 'FvH4_4g25670' => 'fve', 'FvH4_6g51700' => 'fve', 'FvH4_7g20170' => 'fve', 'Glyma.05G175000' => 'gma', 'Glyma.08G132300' => 'gma', 'Glyma.11G243000' => 'gma', 'Glyma.13G158900' => 'gma', 'Glyma.17G112400' => 'gma', 'Glyma.18G014100' => 'gma', 'Glyma.19G003100' => 'gma', 'Glyma.19G056500' => 'gma', 'Gohir.A01G158900' => 'ghi', 'Gohir.A05G312600' => 'ghi', 'Gohir.A05G354900' => 'ghi', 'Gohir.A07G037200' => 'ghi', 'Gohir.A09G030000' => 'ghi', 'Gohir.A12G145200' => 'ghi', 'Gohir.D01G151500' => 'ghi', 'Gohir.D04G058300' => 'ghi', 'Gohir.D05G314100' => 'ghi', 'Gohir.D07G041400' => 'ghi', 'Gohir.D09G029700' => 'ghi', 'Gohir.D12G149700' => 'ghi', 'Gorai.001G043800' => 'gra', 'Gorai.002G187800' => 'gra', 'Gorai.006G034700' => 'gra', 'Gorai.008G161200' => 'gra', 'Gorai.009G335700' => 'gra', 'Gorai.012G065000' => 'gra', 'GSVIVG01000535001' => 'vvi', 'GSVIVG01015572001' => 'vvi', 'GSVIVG01032386001' => 'vvi', 'HanXRQChr05g0138531' => 'han', 'HanXRQChr06g0174391' => 'han', 'HanXRQChr07g0199021' => 'han', 'HanXRQChr08g0208211' => 'han', 'HanXRQChr09g0255471' => 'han', 'HanXRQChr10g0315791' => 'han', 'HanXRQChr12g0371991' => 'han', 'HanXRQChr15g0475251' => 'han', 'HanXRQChr17g0540001' => 'han', 'HanXRQChr17g0548631' => 'han', 'HanXRQChr17g0569561' => 'han', 'Haze_12256' => 'cav', 'Haze_14756' => 'cav', 'Haze_25528' => 'cav', 'Hma1.2p1_0079F.1_g041020' => 'hma', 'Hma1.2p1_0818F.1_g223260' => 'hma', 'Hma1.2p1_1747F.1_g300530' => 'hma', 'HPP92_004607' => 'vpl', 'HPP92_004608' => 'vpl', 'HPP92_006181' => 'vpl', 'HPP92_012192' => 'vpl', 'HPP92_015680' => 'vpl', 'HPP92_020249' => 'vpl', 'HPP92_021376' => 'vpl', 'HPP92_024275' => 'vpl', 'Hund06031' => 'sun', 'Hund25391' => 'sun', 'Lalb_Chr07g0185371' => 'lal', 'Lalb_Chr07g0185381' => 'lal', 'Lalb_Chr12g0204011' => 'lal', 'Lalb_Chr13g0301671' => 'lal', 'Lalb_Chr14g0362851' => 'lal', 'Lalb_Chr24g0403581' => 'lal', 'Lj1g0000233' => 'lja', 'Lj2g0018120' => 'lja', 'Lj3C621T0' => 'lonja', 'Lj3P1059T14' => 'lonja', 'Lj3P611T9' => 'lonja', 'Lj3P614T13' => 'lonja', 'Lj3P615T5' => 'lonja', 'Lj4g0012315' => 'lja', 'Lj4g0026182' => 'lja', 'Lj6P813T16' => 'lonja', 'Lj7C427T7' => 'lonja', 'Lj7C427T8' => 'lonja', 'Lj7P600T41' => 'lonja', 'Lju41C42G17' => 'lonja', 'Lsat_1_v5_gn_0_47300' => 'lsa', 'Lsat_1_v5_gn_2_91280' => 'lsa', 'Lsat_1_v5_gn_3_30561' => 'lsa', 'Lsat_1_v5_gn_4_184321' => 'lsa', 'Lsat_1_v5_gn_4_4041' => 'lsa', 'Lsat_1_v5_gn_5_92000' => 'lsa', 'Lsat_1_v5_gn_8_152940' => 'lsa', 'Lsat_1_v5_gn_8_62401' => 'lsa', 'Manes.06G055900' => 'mes', 'Manes.12G022200' => 'mes', 'Manes.13G023300' => 'mes', 'Manes.14G115000' => 'mes', 'Manes.15G151700' => 'mes', 'Manes.17G111300' => 'mes', 'Mapoly0226s0009' => 'mpo', 'MBI02_g25363_MAGBIO' => 'mbi', 'MBI06_g00027_MAGBIO' => 'mbi', 'MBI10_g13034_MAGBIO' => 'mbi', 'MD09G1023400' => 'mdo', 'MD13G1100100' => 'mdo', 'MD15G1169200' => 'mdo', 'MD16G1101100' => 'mdo', 'MD17G1022900' => 'mdo', 'Medtr3g096150' => 'mtr', 'Medtr4g115070' => 'mtr', 'Medtr7g033325' => 'mtr', 'Medtr8g089840' => 'mtr', 'MELO3C010319.2' => 'cme', 'MELO3C011944.2' => 'cme', 'MELO3C021589.2' => 'cme', 'Migut.E00207' => 'egut', 'Migut.H00067' => 'egut', 'Migut.K00433' => 'egut', 'Migut.K00606' => 'egut', 'Migut.K01410' => 'egut', 'MSTRG.13347' => 'ama', 'MSTRG.24045' => 'ama', 'MSTRG.2428' => 'ama', 'MSTRG.26410' => 'ama', 'MSTRG.3139' => 'ama', 'MSTRG.3286' => 'ama', 'MSTRG.563' => 'ama', 'MSTRG.7941' => 'ama', 'Nitab4.5_0000028g0060' => 'nta', 'Nitab4.5_0000065g0260' => 'nta', 'Nitab4.5_0000112g0060' => 'nta', 'Nitab4.5_0000489g0120' => 'nta', 'Nitab4.5_0001776g0050' => 'nta', 'Nitab4.5_0001854g0010' => 'nta', 'Nitab4.5_0001860g0020' => 'nta', 'Nitab4.5_0004352g0010' => 'nta', 'Nitab4.5_0008716g0020' => 'nta', 'Nitab4.5_0008922g0010' => 'nta', 'Nn3g16693' => 'nnu', 'Nn4g22596' => 'nnu', 'Nn7g37639' => 'nnu', 'Oeu001701.1' => 'oeu', 'Oeu018149.1' => 'oeu', 'Oeu026220.1' => 'oeu', 'Oeu038635.1' => 'oeu', 'Oeu049176.1' => 'oeu', 'Oeu056706.1' => 'oeu', 'Oeu056937.1' => 'oeu', 'Oeu057540.1' => 'oeu', 'Os02g0594900' => 'osa', 'Os02g0595100' => 'osa', 'Os04g0477500' => 'osa', 'Os12g0611900' => 'osa', 'Peaxi162Scf00076g00020' => 'pax', 'Peaxi162Scf00128g00217' => 'pax', 'Peaxi162Scf00129g01640' => 'pax', 'Peaxi162Scf00669g00007' => 'pax', 'Peaxi162Scf00700g00421' => 'pax', 'Peaxi162Scf00801g00038' => 'pax', 'Peaxi162Scf00891g00025' => 'pax', 'PGR083G0909' => 'pgr', 'PGR119G1005' => 'pgr', 'PGR142G2236' => 'pgr', 'PGR142G3388' => 'pgr', 'PGSC0003DMG400004514' => 'stu', 'PGSC0003DMG400012635' => 'stu', 'PGSC0003DMG400015730' => 'stu', 'PGSC0003DMG400018611' => 'stu', 'PGSC0003DMG400030897' => 'stu', 'Phvul.001G254800' => 'pvu', 'Phvul.002G260100' => 'pvu', 'Phvul.003G167600' => 'pvu', 'Phvul.004G005100' => 'pvu', 'Potri.001G343600' => 'ptr', 'Potri.006G066700' => 'ptr', 'Potri.008G186000' => 'ptr', 'Potri.010G046900' => 'ptr', 'Potri.018G127900' => 'ptr', 'Pp3c20_17750' => 'ppa', 'Pp3c24_4380' => 'ppa', 'Prupe.1G245800' => 'ppe', 'Prupe.3G293400' => 'ppe', 'Prupe.7G247400' => 'ppe', 'Psat0s145g0120' => 'psa', 'Psat0s595g0040' => 'psa', 'Psat0s595g0120' => 'psa', 'Psat3g175040' => 'psa', 'Psat7g058120' => 'psa', 'PSO017G0428' => 'pso', 'PSO063G7510' => 'pso', 'PSO067G0046' => 'pso', 'PSO478G1073' => 'pso', 'PSO675G3677' => 'pso', 'PSO675G6558' => 'pso', 'PSO675G7520' => 'pso', 'PSO675G8959' => 'pso', 'QL02p074089' => 'qlo', 'QL02p089614' => 'qlo', 'QL03p057736' => 'qlo', 'RcHm_v2.0_Chr1g0364131' => 'rch', 'RcHm_v2.0_Chr2g0087801' => 'rch', 'RcHm_v2.0_Chr2g0087821' => 'rch', 'RcHm_v2.0_Chr2g0173231' => 'rch', 'RcHm_v2.0_Chr4g0433111' => 'rch', 'Rhsim03G0250300' => 'rsi', 'Rhsim08G0048400' => 'rsi', 'Rhsim10G0014800' => 'rsi', 'Rhsim12G0040100' => 'rsi', 'Rhsim12G0109700' => 'rsi', 'Sabra06G0049600' => 'sbr', 'Sabra08G0141000' => 'sbr', 'Sabra10G0021400' => 'sbr', 'Sabra16G0222900' => 'sbr', 'Sabra18G0108600' => 'sbr', 'SalBow1G0433' => 'sbo', 'SalBow1G2038' => 'sbo', 'SalBow1G5003' => 'sbo', 'SalBow7G1197' => 'sbo', 'SalBow8G3506' => 'sbo', 'Sc03g0007300' => 'sci', 'Sc11g0000950' => 'sci', 'Sc14g0008750' => 'sci', 'Sc18g0000420' => 'sci', 'Sed0006754' => 'sed', 'Sed0008741' => 'sed', 'Sed0017172' => 'sed', 'Sed0018925' => 'sed', 'Sed0023326' => 'sed', 'Sed0025909' => 'sed', 'SEGI_05333' => 'sgi', 'SEGI_10362' => 'sgi', 'SEGI_13380' => 'sgi', 'SEGI_24306' => 'sgi', 'SEGI_29077' => 'sgi', 'SEGI_29095' => 'sgi', 'SEGI_36534' => 'sgi', 'SEGI_37506' => 'sgi', 'SEGI_38321' => 'sgi', 'SGA_v2.0_scaffold307G48031' => 'sas', 'SGA_v2.0_scaffold47G17507' => 'sas', 'SGA_v2.0_scaffold63G21736' => 'sas', 'SGA_v2.0_scaffold87G27070' => 'sas', 'SHI17794' => 'shi', 'SHI28851' => 'shi', 'SMO165G0155' => 'smo', 'SMO340G0217' => 'smo', 'SMO367G1210' => 'smo', 'Solyc02g093430.3' => 'sly', 'Solyc05g013580.4' => 'sly', 'Solyc07g008030.3' => 'sly', 'Solyc12g035470.2' => 'sly', 'Sopen02g038020' => 'spe', 'Sopen05g008490' => 'spe', 'Sopen07g003910' => 'spe', 'Sopen12g015240' => 'spe', 'Sp1g11550' => 'spa', 'Sp2g16710' => 'spa', 'Sp3g00430' => 'spa', 'Sp3g26780' => 'spa', 'Sp5g22900' => 'spa', 'Sp6g29530' => 'spa', 'TAR371G0794' => 'tar', 'TAR374G0164' => 'tar', 'TAR622G0165' => 'tar', 'TAR626G0929' => 'tar', 'TAR629G2155' => 'tar', 'THA.LOC104805282' => 'tha', 'THA.LOC104805363' => 'tha', 'THA.LOC104808968' => 'tha', 'THA.LOC104821093' => 'tha', 'THA.LOC104823953' => 'tha', 'THA.LOC104825562' => 'tha', 'THA.LOC104825665' => 'tha', 'Thecc.02G261400' => 'tca', 'Thecc.04G019200' => 'tca', 'Thecc.09G130400' => 'tca', 'Thhalv10004374m.g' => 'esa', 'Thhalv10007850m.g' => 'esa', 'Thhalv10013782m.g' => 'esa', 'Thhalv10018686m.g' => 'esa', 'Thhalv10020899m.g' => 'esa', 'Thhalv10022755m.g' => 'esa', 'TPR.G23851' => 'tpr', 'TPR.G26500' => 'tpr', 'TPR.G27267' => 'tpr', 'TPR.G32001' => 'tpr', 'TPR.G6251' => 'tpr', 'TPR.G8167' => 'tpr', 'TWI12G1330' => 'twi', 'TWI18G1239' => 'twi', 'TWI34G0979' => 'twi', 'TWI36G0670' => 'twi', 'TWI36G0707' => 'twi', 'TWI56G0233' => 'twi', 'TWI75G1809' => 'twi', 'unitig_21.g20874' => 'ugi', 'unitig_26.g10343' => 'ugi', 'unitig_46.g18392' => 'ugi', 'unitig_52.g17178' => 'ugi', 'unitig_8.g2934' => 'ugi', 'vmacro01122' => 'vma', 'vmacro05875' => 'vma', 'vmacro06147' => 'vma', 'vmacro16191' => 'vma', 'vmacro18293' => 'vma', 'VMungo0251G3707' => 'vmu', 'VMungo0464G1521' => 'vmu', 'VMungo1215G0205' => 'vmu', 'VMungo1383G2484' => 'vmu', 'Zm00001eb079610' => 'zma', 'Zm00001eb135990' => 'zma', 'Zm00001eb183710' => 'zma', 'Zm00001eb246020' => 'zma' ) $gf_id = 'HOM05D001124' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001124' ) $data_identifier = 'HOM05D001124' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 6, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 7, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 21, 'bol' => (int) 10, 'bra' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 6, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 9, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 21, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 8, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 10, 'lsa' => (int) 8, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 8, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 9, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb246020' $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' => 'HOM05D001124', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '548', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02520' => 'bna', 'A03p06630' => 'bna', 'A05p44460' => 'bna', 'A06p08710' => 'bna', 'A06p41090' => 'bna', 'A07p32320' => 'bna', 'A08p32520' => 'bna', 'A09p10360' => 'bna', 'A10p24080' => 'bna', 'Aa31LG11G15250' => 'aar', 'Aa31LG1G1800' => 'aar', 'Aa31LG2G5120' => 'aar', 'Aa31LG2G6070' => 'aar', 'Aa31LG5G10770' => 'aar', 'Aa31sc61G90' => 'aar', 'Actinidia01352' => 'ach', 'Actinidia05983' => 'ach', 'Actinidia08133' => 'ach', 'Actinidia15101' => 'ach', 'Actinidia26379' => 'ach', 'Actinidia35778' => 'ach', 'Actinidia36123' => 'ach', 'Actinidia37436' => 'ach', 'Actinidia38730' => 'ach', 'Ah.02g128210' => 'amhyb', 'Ah.03g132990' => 'amhyb', 'Ah.14g079410' => 'amhyb', 'AL1G24640' => 'aly', 'AL2G26680' => 'aly', 'AL3G10530' => 'aly', 'AL3G45230' => 'aly', 'AL5G15230' => 'aly', 'AL5G16960' => 'aly', 'AL6G25210' => 'aly', 'Aqoxy2G00441' => 'aox', 'Aqoxy3G01236' => 'aox', 'Aqoxy5G03746' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3RQ047' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C7GMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9C8JER' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MBL6KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YXCZ83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZANX40' => 'arhy', 'AT1G12990' => 'ath', 'AT1G67880' => 'ath', 'AT2G13290' => 'ath', 'AT3G01620' => 'ath', 'AT3G26445' => 'ath', 'AT3G27540' => 'ath', 'AT5G14480' => 'ath', 'ATR0824G026' => 'atr', 'ATR1098G019' => 'atr', 'Atru.chr11.2145' => 'acertr', 'Atru.chr2.3636' => 'acertr', 'Atru.chr2.3644' => 'acertr', 'Atru.chr6.2422' => 'acertr', 'Atru.chr7.1112' => 'acertr', 'AUR62005469' => 'cqu', 'AUR62011166' => 'cqu', 'AUR62013319' => 'cqu', 'AUR62024273' => 'cqu', 'AUR62028420' => 'cqu', 'AUR62041942' => 'cqu', 'BcaB01g04969' => 'bca', 'BcaB01g06371' => 'bca', 'BcaB02g11494' => 'bca', 'BcaB03g15382' => 'bca', 'BcaB08g36994' => 'bca', 'BcaC03g13477' => 'bca', 'BcaC03g13478' => 'bca', 'BcaC03g13480' => 'bca', 'BcaC03g13481' => 'bca', 'BcaC03g13486' => 'bca', 'BcaC04g19031' => 'bca', 'BcaC04g23085' => 'bca', 'BcaC05g25094' => 'bca', 'BcaC05g25096' => 'bca', 'BcaC05g25138' => 'bca', 'BcaC05g30416' => 'bca', 'BcaC05g30455' => 'bca', 'BcaC06g30979' => 'bca', 'BcaC06g33805' => 'bca', 'BcaC08g46021' => 'bca', 'BcaNung03154' => 'bca', 'BolC2t06623H' => 'bol', 'BolC2t06632H' => 'bol', 'BolC2t06635H' => 'bol', 'BolC2t06638H' => 'bol', 'BolC3t13266H' => 'bol', 'BolC5t29776H' => 'bol', 'BolC6t38912H' => 'bol', 'BolC7t44183H' => 'bol', 'BolC9t54123H' => 'bol', 'BolC9t59107H' => 'bol', 'BraA02t05221Z' => 'bra', 'BraA03t09996Z' => 'bra', 'BraA05t23210Z' => 'bra', 'BraA06t24068Z' => 'bra', 'BraA06t27032Z' => 'bra', 'BraA08t35176Z' => 'bra', 'BraA09t36680Z' => 'bra', 'BraA10t44471Z' => 'bra', 'C02p06760' => 'bna', 'C02p06890' => 'bna', 'C02p07010' => 'bna', 'C03p07660' => 'bna', 'C05p10300' => 'bna', 'C06p38150' => 'bna', 'C07p36650' => 'bna', 'C08p15770' => 'bna', 'C09p12300' => 'bna', 'C09p62700' => 'bna', 'C09p75040' => 'bna', 'CAN.G13.1' => 'can', 'CAN.G138.4' => 'can', 'CAN.G44.6' => 'can', 'CAN.G473.19' => 'can', 'CANSAT01G0835' => 'cansat', 'CANSAT11G0246' => 'cansat', 'CANSAT11G1766' => 'cansat', 'CANSAT64G1954' => 'cansat', 'CARHR013330' => 'chi', 'CARHR060530' => 'chi', 'CARHR075300' => 'chi', 'CARHR105120' => 'chi', 'CARHR148910' => 'chi', 'CARHR198830' => 'chi', 'Carub.0001s1275' => 'cru', 'Carub.0002s1437' => 'cru', 'Carub.0003s0044' => 'cru', 'Carub.0003s2787' => 'cru', 'Carub.0005s0597' => 'cru', 'Carub.0006s1266' => 'cru', 'Ca_06935_v3' => 'car', 'Ca_13559_v3' => 'car', 'Ca_16941_v3' => 'car', 'Ca_16960_v3' => 'car', 'Ca_17775_v3' => 'car', 'Ca_30464_v3' => 'car', 'Cc06_g08160' => 'ccan', 'Cc07_g01520' => 'ccan', 'Cc11_g15810' => 'ccan', 'CDE02G2840' => 'cde', 'CDE03G0093' => 'cde', 'CDE04G2127' => 'cde', 'CDE07G1857' => 'cde', 'CDE09G1246' => 'cde', 'Cfa003412' => 'cfa', 'Cfa007341' => 'cfa', 'Cfa009220' => 'cfa', 'Ciclev10008737m.g' => 'ccl', 'Ciclev10015565m.g' => 'ccl', 'Ciclev10031761m.g' => 'ccl', 'CiPaw.03G045300' => 'cil', 'CiPaw.03G247200' => 'cil', 'CiPaw.04G029500' => 'cil', 'CiPaw.04G174000' => 'cil', 'CiPaw.05G181200' => 'cil', 'CiPaw.06G067100' => 'cil', 'ClCG05G025800' => 'cla', 'ClCG06G011400' => 'cla', 'ClCG09G019360' => 'cla', 'COL.COLO4_04827' => 'col', 'COL.COLO4_29170' => 'col', 'COL.COLO4_35131' => 'col', 'COL.COLO4_35132' => 'col', 'Cpa.g.sc33.32' => 'cpa', 'Cpa.g.sc46.29' => 'cpa', 'Cpa.g.sc796.1' => 'cpa', 'CsaV3_1G030420' => 'csa', 'CsaV3_5G027050' => 'csa', 'CsaV3_5G031040' => 'csa', 'CsaV3_UNG023130' => 'csa', 'CSS0007726' => 'camsi', 'CSS0016433' => 'camsi', 'CSS0017656' => 'camsi', 'CSS0025364' => 'camsi', 'CSS0027582' => 'camsi', 'CSS0047288' => 'camsi', 'CSS0049950' => 'camsi', 'DCAR_003843' => 'dca', 'DCAR_007052' => 'dca', 'DCAR_020884' => 'dca', 'DCAR_021730' => 'dca', 'DCAR_024423' => 'dca', 'DCAR_026509' => 'dca', 'DCAR_031158' => 'dca', 'Dinv14728' => 'din', 'Dinv15219' => 'din', 'Dinv25728' => 'din', 'Dinv33428' => 'din', 'Dinv36489' => 'din', 'Dinv41486' => 'din', 'Duzib147G0469' => 'dzi', 'Duzib168G0060' => 'dzi', 'Duzib187G1215' => 'dzi', 'Duzib248G0692' => 'dzi', 'Duzib251G0767' => 'dzi', 'Duzib264G0446' => 'dzi', 'Duzib268G0691' => 'dzi', 'ECA232G4767' => 'eca', 'ECA233G2838' => 'eca', 'ECA234G0391' => 'eca', 'ECA234G0857' => 'eca', 'ECA236G1593' => 'eca', 'ECA238G0565' => 'eca', 'ECA246G1027' => 'eca', 'ECA246G3223' => 'eca', 'ECA246G3470' => 'eca', 'EL10Ac6g13829' => 'bvu', 'EL10Ac6g14093' => 'bvu', 'EL10Ac8g18707' => 'bvu', 'Eucgr.C01369' => 'egr', 'Eucgr.H02492' => 'egr', 'Eucgr.I01733' => 'egr', 'Eucgr.J02255' => 'egr', 'Eucgr.J02257' => 'egr', 'Eucgr.J02258' => 'egr', 'FAN02G1601' => 'fan', 'FAN03G1586' => 'fan', 'FAN03G2986' => 'fan', 'FAN05G4837' => 'fan', 'FAN06G0146' => 'fan', 'FAN07G0858' => 'fan', 'FAN09G3179' => 'fan', 'FAN10G0669' => 'fan', 'FAN12G2358' => 'fan', 'FAN14G4198' => 'fan', 'FAN14G5112' => 'fan', 'FAN17G0342' => 'fan', 'FAN19G0342' => 'fan', 'FAN19G0962' => 'fan', 'FAN19G1101' => 'fan', 'FAN19G1872' => 'fan', 'FAN22G0356' => 'fan', 'FAN23G0744' => 'fan', 'FAN23G1914' => 'fan', 'FAN26G0032' => 'fan', 'FAN28G0625' => 'fan', 'FvH4_1g02710' => 'fve', 'FvH4_1g02720' => 'fve', 'FvH4_4g25670' => 'fve', 'FvH4_6g51700' => 'fve', 'FvH4_7g20170' => 'fve', 'Glyma.05G175000' => 'gma', 'Glyma.08G132300' => 'gma', 'Glyma.11G243000' => 'gma', 'Glyma.13G158900' => 'gma', 'Glyma.17G112400' => 'gma', 'Glyma.18G014100' => 'gma', 'Glyma.19G003100' => 'gma', 'Glyma.19G056500' => 'gma', 'Gohir.A01G158900' => 'ghi', 'Gohir.A05G312600' => 'ghi', 'Gohir.A05G354900' => 'ghi', 'Gohir.A07G037200' => 'ghi', 'Gohir.A09G030000' => 'ghi', 'Gohir.A12G145200' => 'ghi', 'Gohir.D01G151500' => 'ghi', 'Gohir.D04G058300' => 'ghi', 'Gohir.D05G314100' => 'ghi', 'Gohir.D07G041400' => 'ghi', 'Gohir.D09G029700' => 'ghi', 'Gohir.D12G149700' => 'ghi', 'Gorai.001G043800' => 'gra', 'Gorai.002G187800' => 'gra', 'Gorai.006G034700' => 'gra', 'Gorai.008G161200' => 'gra', 'Gorai.009G335700' => 'gra', 'Gorai.012G065000' => 'gra', 'GSVIVG01000535001' => 'vvi', 'GSVIVG01015572001' => 'vvi', 'GSVIVG01032386001' => 'vvi', 'HanXRQChr05g0138531' => 'han', 'HanXRQChr06g0174391' => 'han', 'HanXRQChr07g0199021' => 'han', 'HanXRQChr08g0208211' => 'han', 'HanXRQChr09g0255471' => 'han', 'HanXRQChr10g0315791' => 'han', 'HanXRQChr12g0371991' => 'han', 'HanXRQChr15g0475251' => 'han', 'HanXRQChr17g0540001' => 'han', 'HanXRQChr17g0548631' => 'han', 'HanXRQChr17g0569561' => 'han', 'Haze_12256' => 'cav', 'Haze_14756' => 'cav', 'Haze_25528' => 'cav', 'Hma1.2p1_0079F.1_g041020' => 'hma', 'Hma1.2p1_0818F.1_g223260' => 'hma', 'Hma1.2p1_1747F.1_g300530' => 'hma', 'HPP92_004607' => 'vpl', 'HPP92_004608' => 'vpl', 'HPP92_006181' => 'vpl', 'HPP92_012192' => 'vpl', 'HPP92_015680' => 'vpl', 'HPP92_020249' => 'vpl', 'HPP92_021376' => 'vpl', 'HPP92_024275' => 'vpl', 'Hund06031' => 'sun', 'Hund25391' => 'sun', 'Lalb_Chr07g0185371' => 'lal', 'Lalb_Chr07g0185381' => 'lal', 'Lalb_Chr12g0204011' => 'lal', 'Lalb_Chr13g0301671' => 'lal', 'Lalb_Chr14g0362851' => 'lal', 'Lalb_Chr24g0403581' => 'lal', 'Lj1g0000233' => 'lja', 'Lj2g0018120' => 'lja', 'Lj3C621T0' => 'lonja', 'Lj3P1059T14' => 'lonja', 'Lj3P611T9' => 'lonja', 'Lj3P614T13' => 'lonja', 'Lj3P615T5' => 'lonja', 'Lj4g0012315' => 'lja', 'Lj4g0026182' => 'lja', 'Lj6P813T16' => 'lonja', 'Lj7C427T7' => 'lonja', 'Lj7C427T8' => 'lonja', 'Lj7P600T41' => 'lonja', 'Lju41C42G17' => 'lonja', 'Lsat_1_v5_gn_0_47300' => 'lsa', 'Lsat_1_v5_gn_2_91280' => 'lsa', 'Lsat_1_v5_gn_3_30561' => 'lsa', 'Lsat_1_v5_gn_4_184321' => 'lsa', 'Lsat_1_v5_gn_4_4041' => 'lsa', 'Lsat_1_v5_gn_5_92000' => 'lsa', 'Lsat_1_v5_gn_8_152940' => 'lsa', 'Lsat_1_v5_gn_8_62401' => 'lsa', 'Manes.06G055900' => 'mes', 'Manes.12G022200' => 'mes', 'Manes.13G023300' => 'mes', 'Manes.14G115000' => 'mes', 'Manes.15G151700' => 'mes', 'Manes.17G111300' => 'mes', 'Mapoly0226s0009' => 'mpo', 'MBI02_g25363_MAGBIO' => 'mbi', 'MBI06_g00027_MAGBIO' => 'mbi', 'MBI10_g13034_MAGBIO' => 'mbi', 'MD09G1023400' => 'mdo', 'MD13G1100100' => 'mdo', 'MD15G1169200' => 'mdo', 'MD16G1101100' => 'mdo', 'MD17G1022900' => 'mdo', 'Medtr3g096150' => 'mtr', 'Medtr4g115070' => 'mtr', 'Medtr7g033325' => 'mtr', 'Medtr8g089840' => 'mtr', 'MELO3C010319.2' => 'cme', 'MELO3C011944.2' => 'cme', 'MELO3C021589.2' => 'cme', 'Migut.E00207' => 'egut', 'Migut.H00067' => 'egut', 'Migut.K00433' => 'egut', 'Migut.K00606' => 'egut', 'Migut.K01410' => 'egut', 'MSTRG.13347' => 'ama', 'MSTRG.24045' => 'ama', 'MSTRG.2428' => 'ama', 'MSTRG.26410' => 'ama', 'MSTRG.3139' => 'ama', 'MSTRG.3286' => 'ama', 'MSTRG.563' => 'ama', 'MSTRG.7941' => 'ama', 'Nitab4.5_0000028g0060' => 'nta', 'Nitab4.5_0000065g0260' => 'nta', 'Nitab4.5_0000112g0060' => 'nta', 'Nitab4.5_0000489g0120' => 'nta', 'Nitab4.5_0001776g0050' => 'nta', 'Nitab4.5_0001854g0010' => 'nta', 'Nitab4.5_0001860g0020' => 'nta', 'Nitab4.5_0004352g0010' => 'nta', 'Nitab4.5_0008716g0020' => 'nta', 'Nitab4.5_0008922g0010' => 'nta', 'Nn3g16693' => 'nnu', 'Nn4g22596' => 'nnu', 'Nn7g37639' => 'nnu', 'Oeu001701.1' => 'oeu', 'Oeu018149.1' => 'oeu', 'Oeu026220.1' => 'oeu', 'Oeu038635.1' => 'oeu', 'Oeu049176.1' => 'oeu', 'Oeu056706.1' => 'oeu', 'Oeu056937.1' => 'oeu', 'Oeu057540.1' => 'oeu', 'Os02g0594900' => 'osa', 'Os02g0595100' => 'osa', 'Os04g0477500' => 'osa', 'Os12g0611900' => 'osa', 'Peaxi162Scf00076g00020' => 'pax', 'Peaxi162Scf00128g00217' => 'pax', 'Peaxi162Scf00129g01640' => 'pax', 'Peaxi162Scf00669g00007' => 'pax', 'Peaxi162Scf00700g00421' => 'pax', 'Peaxi162Scf00801g00038' => 'pax', 'Peaxi162Scf00891g00025' => 'pax', 'PGR083G0909' => 'pgr', 'PGR119G1005' => 'pgr', 'PGR142G2236' => 'pgr', 'PGR142G3388' => 'pgr', 'PGSC0003DMG400004514' => 'stu', 'PGSC0003DMG400012635' => 'stu', 'PGSC0003DMG400015730' => 'stu', 'PGSC0003DMG400018611' => 'stu', 'PGSC0003DMG400030897' => 'stu', 'Phvul.001G254800' => 'pvu', 'Phvul.002G260100' => 'pvu', 'Phvul.003G167600' => 'pvu', 'Phvul.004G005100' => 'pvu', 'Potri.001G343600' => 'ptr', 'Potri.006G066700' => 'ptr', 'Potri.008G186000' => 'ptr', 'Potri.010G046900' => 'ptr', 'Potri.018G127900' => 'ptr', 'Pp3c20_17750' => 'ppa', 'Pp3c24_4380' => 'ppa', 'Prupe.1G245800' => 'ppe', 'Prupe.3G293400' => 'ppe', 'Prupe.7G247400' => 'ppe', 'Psat0s145g0120' => 'psa', 'Psat0s595g0040' => 'psa', 'Psat0s595g0120' => 'psa', 'Psat3g175040' => 'psa', 'Psat7g058120' => 'psa', 'PSO017G0428' => 'pso', 'PSO063G7510' => 'pso', 'PSO067G0046' => 'pso', 'PSO478G1073' => 'pso', 'PSO675G3677' => 'pso', 'PSO675G6558' => 'pso', 'PSO675G7520' => 'pso', 'PSO675G8959' => 'pso', 'QL02p074089' => 'qlo', 'QL02p089614' => 'qlo', 'QL03p057736' => 'qlo', 'RcHm_v2.0_Chr1g0364131' => 'rch', 'RcHm_v2.0_Chr2g0087801' => 'rch', 'RcHm_v2.0_Chr2g0087821' => 'rch', 'RcHm_v2.0_Chr2g0173231' => 'rch', 'RcHm_v2.0_Chr4g0433111' => 'rch', 'Rhsim03G0250300' => 'rsi', 'Rhsim08G0048400' => 'rsi', 'Rhsim10G0014800' => 'rsi', 'Rhsim12G0040100' => 'rsi', 'Rhsim12G0109700' => 'rsi', 'Sabra06G0049600' => 'sbr', 'Sabra08G0141000' => 'sbr', 'Sabra10G0021400' => 'sbr', 'Sabra16G0222900' => 'sbr', 'Sabra18G0108600' => 'sbr', 'SalBow1G0433' => 'sbo', 'SalBow1G2038' => 'sbo', 'SalBow1G5003' => 'sbo', 'SalBow7G1197' => 'sbo', 'SalBow8G3506' => 'sbo', 'Sc03g0007300' => 'sci', 'Sc11g0000950' => 'sci', 'Sc14g0008750' => 'sci', 'Sc18g0000420' => 'sci', 'Sed0006754' => 'sed', 'Sed0008741' => 'sed', 'Sed0017172' => 'sed', 'Sed0018925' => 'sed', 'Sed0023326' => 'sed', 'Sed0025909' => 'sed', 'SEGI_05333' => 'sgi', 'SEGI_10362' => 'sgi', 'SEGI_13380' => 'sgi', 'SEGI_24306' => 'sgi', 'SEGI_29077' => 'sgi', 'SEGI_29095' => 'sgi', 'SEGI_36534' => 'sgi', 'SEGI_37506' => 'sgi', 'SEGI_38321' => 'sgi', 'SGA_v2.0_scaffold307G48031' => 'sas', 'SGA_v2.0_scaffold47G17507' => 'sas', 'SGA_v2.0_scaffold63G21736' => 'sas', 'SGA_v2.0_scaffold87G27070' => 'sas', 'SHI17794' => 'shi', 'SHI28851' => 'shi', 'SMO165G0155' => 'smo', 'SMO340G0217' => 'smo', 'SMO367G1210' => 'smo', 'Solyc02g093430.3' => 'sly', 'Solyc05g013580.4' => 'sly', 'Solyc07g008030.3' => 'sly', 'Solyc12g035470.2' => 'sly', 'Sopen02g038020' => 'spe', 'Sopen05g008490' => 'spe', 'Sopen07g003910' => 'spe', 'Sopen12g015240' => 'spe', 'Sp1g11550' => 'spa', 'Sp2g16710' => 'spa', 'Sp3g00430' => 'spa', 'Sp3g26780' => 'spa', 'Sp5g22900' => 'spa', 'Sp6g29530' => 'spa', 'TAR371G0794' => 'tar', 'TAR374G0164' => 'tar', 'TAR622G0165' => 'tar', 'TAR626G0929' => 'tar', 'TAR629G2155' => 'tar', 'THA.LOC104805282' => 'tha', 'THA.LOC104805363' => 'tha', 'THA.LOC104808968' => 'tha', 'THA.LOC104821093' => 'tha', 'THA.LOC104823953' => 'tha', 'THA.LOC104825562' => 'tha', 'THA.LOC104825665' => 'tha', 'Thecc.02G261400' => 'tca', 'Thecc.04G019200' => 'tca', 'Thecc.09G130400' => 'tca', 'Thhalv10004374m.g' => 'esa', 'Thhalv10007850m.g' => 'esa', 'Thhalv10013782m.g' => 'esa', 'Thhalv10018686m.g' => 'esa', 'Thhalv10020899m.g' => 'esa', 'Thhalv10022755m.g' => 'esa', 'TPR.G23851' => 'tpr', 'TPR.G26500' => 'tpr', 'TPR.G27267' => 'tpr', 'TPR.G32001' => 'tpr', 'TPR.G6251' => 'tpr', 'TPR.G8167' => 'tpr', 'TWI12G1330' => 'twi', 'TWI18G1239' => 'twi', 'TWI34G0979' => 'twi', 'TWI36G0670' => 'twi', 'TWI36G0707' => 'twi', 'TWI56G0233' => 'twi', 'TWI75G1809' => 'twi', 'unitig_21.g20874' => 'ugi', 'unitig_26.g10343' => 'ugi', 'unitig_46.g18392' => 'ugi', 'unitig_52.g17178' => 'ugi', 'unitig_8.g2934' => 'ugi', 'vmacro01122' => 'vma', 'vmacro05875' => 'vma', 'vmacro06147' => 'vma', 'vmacro16191' => 'vma', 'vmacro18293' => 'vma', 'VMungo0251G3707' => 'vmu', 'VMungo0464G1521' => 'vmu', 'VMungo1215G0205' => 'vmu', 'VMungo1383G2484' => 'vmu', 'Zm00001eb079610' => 'zma', 'Zm00001eb135990' => 'zma', 'Zm00001eb183710' => 'zma', 'Zm00001eb246020' => 'zma' ), 'gf_id' => 'HOM05D001124', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001124' ), 'data_identifier' => 'HOM05D001124', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001124', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '548', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02520' => 'bna', 'A03p06630' => 'bna', 'A05p44460' => 'bna', 'A06p08710' => 'bna', 'A06p41090' => 'bna', 'A07p32320' => 'bna', 'A08p32520' => 'bna', 'A09p10360' => 'bna', 'A10p24080' => 'bna', 'Aa31LG11G15250' => 'aar', 'Aa31LG1G1800' => 'aar', 'Aa31LG2G5120' => 'aar', 'Aa31LG2G6070' => 'aar', 'Aa31LG5G10770' => 'aar', 'Aa31sc61G90' => 'aar', 'Actinidia01352' => 'ach', 'Actinidia05983' => 'ach', 'Actinidia08133' => 'ach', 'Actinidia15101' => 'ach', 'Actinidia26379' => 'ach', 'Actinidia35778' => 'ach', 'Actinidia36123' => 'ach', 'Actinidia37436' => 'ach', 'Actinidia38730' => 'ach', 'Ah.02g128210' => 'amhyb', 'Ah.03g132990' => 'amhyb', 'Ah.14g079410' => 'amhyb', 'AL1G24640' => 'aly', 'AL2G26680' => 'aly', 'AL3G10530' => 'aly', 'AL3G45230' => 'aly', 'AL5G15230' => 'aly', 'AL5G16960' => 'aly', 'AL6G25210' => 'aly', 'Aqoxy2G00441' => 'aox', 'Aqoxy3G01236' => 'aox', 'Aqoxy5G03746' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3RQ047' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C7GMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9C8JER' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MBL6KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YXCZ83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZANX40' => 'arhy', 'AT1G12990' => 'ath', 'AT1G67880' => 'ath', 'AT2G13290' => 'ath', 'AT3G01620' => 'ath', 'AT3G26445' => 'ath', 'AT3G27540' => 'ath', 'AT5G14480' => 'ath', 'ATR0824G026' => 'atr', 'ATR1098G019' => 'atr', 'Atru.chr11.2145' => 'acertr', 'Atru.chr2.3636' => 'acertr', 'Atru.chr2.3644' => 'acertr', 'Atru.chr6.2422' => 'acertr', 'Atru.chr7.1112' => 'acertr', 'AUR62005469' => 'cqu', 'AUR62011166' => 'cqu', 'AUR62013319' => 'cqu', 'AUR62024273' => 'cqu', 'AUR62028420' => 'cqu', 'AUR62041942' => 'cqu', 'BcaB01g04969' => 'bca', 'BcaB01g06371' => 'bca', 'BcaB02g11494' => 'bca', 'BcaB03g15382' => 'bca', 'BcaB08g36994' => 'bca', 'BcaC03g13477' => 'bca', 'BcaC03g13478' => 'bca', 'BcaC03g13480' => 'bca', 'BcaC03g13481' => 'bca', 'BcaC03g13486' => 'bca', 'BcaC04g19031' => 'bca', 'BcaC04g23085' => 'bca', 'BcaC05g25094' => 'bca', 'BcaC05g25096' => 'bca', 'BcaC05g25138' => 'bca', 'BcaC05g30416' => 'bca', 'BcaC05g30455' => 'bca', 'BcaC06g30979' => 'bca', 'BcaC06g33805' => 'bca', 'BcaC08g46021' => 'bca', 'BcaNung03154' => 'bca', 'BolC2t06623H' => 'bol', 'BolC2t06632H' => 'bol', 'BolC2t06635H' => 'bol', 'BolC2t06638H' => 'bol', 'BolC3t13266H' => 'bol', 'BolC5t29776H' => 'bol', 'BolC6t38912H' => 'bol', 'BolC7t44183H' => 'bol', 'BolC9t54123H' => 'bol', 'BolC9t59107H' => 'bol', 'BraA02t05221Z' => 'bra', 'BraA03t09996Z' => 'bra', 'BraA05t23210Z' => 'bra', 'BraA06t24068Z' => 'bra', 'BraA06t27032Z' => 'bra', 'BraA08t35176Z' => 'bra', 'BraA09t36680Z' => 'bra', 'BraA10t44471Z' => 'bra', 'C02p06760' => 'bna', 'C02p06890' => 'bna', 'C02p07010' => 'bna', 'C03p07660' => 'bna', 'C05p10300' => 'bna', 'C06p38150' => 'bna', 'C07p36650' => 'bna', 'C08p15770' => 'bna', 'C09p12300' => 'bna', 'C09p62700' => 'bna', 'C09p75040' => 'bna', 'CAN.G13.1' => 'can', 'CAN.G138.4' => 'can', 'CAN.G44.6' => 'can', 'CAN.G473.19' => 'can', 'CANSAT01G0835' => 'cansat', 'CANSAT11G0246' => 'cansat', 'CANSAT11G1766' => 'cansat', 'CANSAT64G1954' => 'cansat', 'CARHR013330' => 'chi', 'CARHR060530' => 'chi', 'CARHR075300' => 'chi', 'CARHR105120' => 'chi', 'CARHR148910' => 'chi', 'CARHR198830' => 'chi', 'Carub.0001s1275' => 'cru', 'Carub.0002s1437' => 'cru', 'Carub.0003s0044' => 'cru', 'Carub.0003s2787' => 'cru', 'Carub.0005s0597' => 'cru', 'Carub.0006s1266' => 'cru', 'Ca_06935_v3' => 'car', 'Ca_13559_v3' => 'car', 'Ca_16941_v3' => 'car', 'Ca_16960_v3' => 'car', 'Ca_17775_v3' => 'car', 'Ca_30464_v3' => 'car', 'Cc06_g08160' => 'ccan', 'Cc07_g01520' => 'ccan', 'Cc11_g15810' => 'ccan', 'CDE02G2840' => 'cde', 'CDE03G0093' => 'cde', 'CDE04G2127' => 'cde', 'CDE07G1857' => 'cde', 'CDE09G1246' => 'cde', 'Cfa003412' => 'cfa', 'Cfa007341' => 'cfa', 'Cfa009220' => 'cfa', 'Ciclev10008737m.g' => 'ccl', 'Ciclev10015565m.g' => 'ccl', 'Ciclev10031761m.g' => 'ccl', 'CiPaw.03G045300' => 'cil', 'CiPaw.03G247200' => 'cil', 'CiPaw.04G029500' => 'cil', 'CiPaw.04G174000' => 'cil', 'CiPaw.05G181200' => 'cil', 'CiPaw.06G067100' => 'cil', 'ClCG05G025800' => 'cla', 'ClCG06G011400' => 'cla', 'ClCG09G019360' => 'cla', 'COL.COLO4_04827' => 'col', 'COL.COLO4_29170' => 'col', 'COL.COLO4_35131' => 'col', 'COL.COLO4_35132' => 'col', 'Cpa.g.sc33.32' => 'cpa', 'Cpa.g.sc46.29' => 'cpa', 'Cpa.g.sc796.1' => 'cpa', 'CsaV3_1G030420' => 'csa', 'CsaV3_5G027050' => 'csa', 'CsaV3_5G031040' => 'csa', 'CsaV3_UNG023130' => 'csa', 'CSS0007726' => 'camsi', 'CSS0016433' => 'camsi', 'CSS0017656' => 'camsi', 'CSS0025364' => 'camsi', 'CSS0027582' => 'camsi', 'CSS0047288' => 'camsi', 'CSS0049950' => 'camsi', 'DCAR_003843' => 'dca', 'DCAR_007052' => 'dca', 'DCAR_020884' => 'dca', 'DCAR_021730' => 'dca', 'DCAR_024423' => 'dca', 'DCAR_026509' => 'dca', 'DCAR_031158' => 'dca', 'Dinv14728' => 'din', 'Dinv15219' => 'din', 'Dinv25728' => 'din', 'Dinv33428' => 'din', 'Dinv36489' => 'din', 'Dinv41486' => 'din', 'Duzib147G0469' => 'dzi', 'Duzib168G0060' => 'dzi', 'Duzib187G1215' => 'dzi', 'Duzib248G0692' => 'dzi', 'Duzib251G0767' => 'dzi', 'Duzib264G0446' => 'dzi', 'Duzib268G0691' => 'dzi', 'ECA232G4767' => 'eca', 'ECA233G2838' => 'eca', 'ECA234G0391' => 'eca', 'ECA234G0857' => 'eca', 'ECA236G1593' => 'eca', 'ECA238G0565' => 'eca', 'ECA246G1027' => 'eca', 'ECA246G3223' => 'eca', 'ECA246G3470' => 'eca', 'EL10Ac6g13829' => 'bvu', 'EL10Ac6g14093' => 'bvu', 'EL10Ac8g18707' => 'bvu', 'Eucgr.C01369' => 'egr', 'Eucgr.H02492' => 'egr', 'Eucgr.I01733' => 'egr', 'Eucgr.J02255' => 'egr', 'Eucgr.J02257' => 'egr', 'Eucgr.J02258' => 'egr', 'FAN02G1601' => 'fan', 'FAN03G1586' => 'fan', 'FAN03G2986' => 'fan', 'FAN05G4837' => 'fan', 'FAN06G0146' => 'fan', 'FAN07G0858' => 'fan', 'FAN09G3179' => 'fan', 'FAN10G0669' => 'fan', 'FAN12G2358' => 'fan', 'FAN14G4198' => 'fan', 'FAN14G5112' => 'fan', 'FAN17G0342' => 'fan', 'FAN19G0342' => 'fan', 'FAN19G0962' => 'fan', 'FAN19G1101' => 'fan', 'FAN19G1872' => 'fan', 'FAN22G0356' => 'fan', 'FAN23G0744' => 'fan', 'FAN23G1914' => 'fan', 'FAN26G0032' => 'fan', 'FAN28G0625' => 'fan', 'FvH4_1g02710' => 'fve', 'FvH4_1g02720' => 'fve', 'FvH4_4g25670' => 'fve', 'FvH4_6g51700' => 'fve', 'FvH4_7g20170' => 'fve', 'Glyma.05G175000' => 'gma', 'Glyma.08G132300' => 'gma', 'Glyma.11G243000' => 'gma', 'Glyma.13G158900' => 'gma', 'Glyma.17G112400' => 'gma', 'Glyma.18G014100' => 'gma', 'Glyma.19G003100' => 'gma', 'Glyma.19G056500' => 'gma', 'Gohir.A01G158900' => 'ghi', 'Gohir.A05G312600' => 'ghi', 'Gohir.A05G354900' => 'ghi', 'Gohir.A07G037200' => 'ghi', 'Gohir.A09G030000' => 'ghi', 'Gohir.A12G145200' => 'ghi', 'Gohir.D01G151500' => 'ghi', 'Gohir.D04G058300' => 'ghi', 'Gohir.D05G314100' => 'ghi', 'Gohir.D07G041400' => 'ghi', 'Gohir.D09G029700' => 'ghi', 'Gohir.D12G149700' => 'ghi', 'Gorai.001G043800' => 'gra', 'Gorai.002G187800' => 'gra', 'Gorai.006G034700' => 'gra', 'Gorai.008G161200' => 'gra', 'Gorai.009G335700' => 'gra', 'Gorai.012G065000' => 'gra', 'GSVIVG01000535001' => 'vvi', 'GSVIVG01015572001' => 'vvi', 'GSVIVG01032386001' => 'vvi', 'HanXRQChr05g0138531' => 'han', 'HanXRQChr06g0174391' => 'han', 'HanXRQChr07g0199021' => 'han', 'HanXRQChr08g0208211' => 'han', 'HanXRQChr09g0255471' => 'han', 'HanXRQChr10g0315791' => 'han', 'HanXRQChr12g0371991' => 'han', 'HanXRQChr15g0475251' => 'han', 'HanXRQChr17g0540001' => 'han', 'HanXRQChr17g0548631' => 'han', 'HanXRQChr17g0569561' => 'han', 'Haze_12256' => 'cav', 'Haze_14756' => 'cav', 'Haze_25528' => 'cav', 'Hma1.2p1_0079F.1_g041020' => 'hma', 'Hma1.2p1_0818F.1_g223260' => 'hma', 'Hma1.2p1_1747F.1_g300530' => 'hma', 'HPP92_004607' => 'vpl', 'HPP92_004608' => 'vpl', 'HPP92_006181' => 'vpl', 'HPP92_012192' => 'vpl', 'HPP92_015680' => 'vpl', 'HPP92_020249' => 'vpl', 'HPP92_021376' => 'vpl', 'HPP92_024275' => 'vpl', 'Hund06031' => 'sun', 'Hund25391' => 'sun', 'Lalb_Chr07g0185371' => 'lal', 'Lalb_Chr07g0185381' => 'lal', 'Lalb_Chr12g0204011' => 'lal', 'Lalb_Chr13g0301671' => 'lal', 'Lalb_Chr14g0362851' => 'lal', 'Lalb_Chr24g0403581' => 'lal', 'Lj1g0000233' => 'lja', 'Lj2g0018120' => 'lja', 'Lj3C621T0' => 'lonja', 'Lj3P1059T14' => 'lonja', 'Lj3P611T9' => 'lonja', 'Lj3P614T13' => 'lonja', 'Lj3P615T5' => 'lonja', 'Lj4g0012315' => 'lja', 'Lj4g0026182' => 'lja', 'Lj6P813T16' => 'lonja', 'Lj7C427T7' => 'lonja', 'Lj7C427T8' => 'lonja', 'Lj7P600T41' => 'lonja', 'Lju41C42G17' => 'lonja', 'Lsat_1_v5_gn_0_47300' => 'lsa', 'Lsat_1_v5_gn_2_91280' => 'lsa', 'Lsat_1_v5_gn_3_30561' => 'lsa', 'Lsat_1_v5_gn_4_184321' => 'lsa', 'Lsat_1_v5_gn_4_4041' => 'lsa', 'Lsat_1_v5_gn_5_92000' => 'lsa', 'Lsat_1_v5_gn_8_152940' => 'lsa', 'Lsat_1_v5_gn_8_62401' => 'lsa', 'Manes.06G055900' => 'mes', 'Manes.12G022200' => 'mes', 'Manes.13G023300' => 'mes', 'Manes.14G115000' => 'mes', 'Manes.15G151700' => 'mes', 'Manes.17G111300' => 'mes', 'Mapoly0226s0009' => 'mpo', 'MBI02_g25363_MAGBIO' => 'mbi', 'MBI06_g00027_MAGBIO' => 'mbi', 'MBI10_g13034_MAGBIO' => 'mbi', 'MD09G1023400' => 'mdo', 'MD13G1100100' => 'mdo', 'MD15G1169200' => 'mdo', 'MD16G1101100' => 'mdo', 'MD17G1022900' => 'mdo', 'Medtr3g096150' => 'mtr', 'Medtr4g115070' => 'mtr', 'Medtr7g033325' => 'mtr', 'Medtr8g089840' => 'mtr', 'MELO3C010319.2' => 'cme', 'MELO3C011944.2' => 'cme', 'MELO3C021589.2' => 'cme', 'Migut.E00207' => 'egut', 'Migut.H00067' => 'egut', 'Migut.K00433' => 'egut', 'Migut.K00606' => 'egut', 'Migut.K01410' => 'egut', 'MSTRG.13347' => 'ama', 'MSTRG.24045' => 'ama', 'MSTRG.2428' => 'ama', 'MSTRG.26410' => 'ama', 'MSTRG.3139' => 'ama', 'MSTRG.3286' => 'ama', 'MSTRG.563' => 'ama', 'MSTRG.7941' => 'ama', 'Nitab4.5_0000028g0060' => 'nta', 'Nitab4.5_0000065g0260' => 'nta', 'Nitab4.5_0000112g0060' => 'nta', 'Nitab4.5_0000489g0120' => 'nta', 'Nitab4.5_0001776g0050' => 'nta', 'Nitab4.5_0001854g0010' => 'nta', 'Nitab4.5_0001860g0020' => 'nta', 'Nitab4.5_0004352g0010' => 'nta', 'Nitab4.5_0008716g0020' => 'nta', 'Nitab4.5_0008922g0010' => 'nta', 'Nn3g16693' => 'nnu', 'Nn4g22596' => 'nnu', 'Nn7g37639' => 'nnu', 'Oeu001701.1' => 'oeu', 'Oeu018149.1' => 'oeu', 'Oeu026220.1' => 'oeu', 'Oeu038635.1' => 'oeu', 'Oeu049176.1' => 'oeu', 'Oeu056706.1' => 'oeu', 'Oeu056937.1' => 'oeu', 'Oeu057540.1' => 'oeu', 'Os02g0594900' => 'osa', 'Os02g0595100' => 'osa', 'Os04g0477500' => 'osa', 'Os12g0611900' => 'osa', 'Peaxi162Scf00076g00020' => 'pax', 'Peaxi162Scf00128g00217' => 'pax', 'Peaxi162Scf00129g01640' => 'pax', 'Peaxi162Scf00669g00007' => 'pax', 'Peaxi162Scf00700g00421' => 'pax', 'Peaxi162Scf00801g00038' => 'pax', 'Peaxi162Scf00891g00025' => 'pax', 'PGR083G0909' => 'pgr', 'PGR119G1005' => 'pgr', 'PGR142G2236' => 'pgr', 'PGR142G3388' => 'pgr', 'PGSC0003DMG400004514' => 'stu', 'PGSC0003DMG400012635' => 'stu', 'PGSC0003DMG400015730' => 'stu', 'PGSC0003DMG400018611' => 'stu', 'PGSC0003DMG400030897' => 'stu', 'Phvul.001G254800' => 'pvu', 'Phvul.002G260100' => 'pvu', 'Phvul.003G167600' => 'pvu', 'Phvul.004G005100' => 'pvu', 'Potri.001G343600' => 'ptr', 'Potri.006G066700' => 'ptr', 'Potri.008G186000' => 'ptr', 'Potri.010G046900' => 'ptr', 'Potri.018G127900' => 'ptr', 'Pp3c20_17750' => 'ppa', 'Pp3c24_4380' => 'ppa', 'Prupe.1G245800' => 'ppe', 'Prupe.3G293400' => 'ppe', 'Prupe.7G247400' => 'ppe', 'Psat0s145g0120' => 'psa', 'Psat0s595g0040' => 'psa', 'Psat0s595g0120' => 'psa', 'Psat3g175040' => 'psa', 'Psat7g058120' => 'psa', 'PSO017G0428' => 'pso', 'PSO063G7510' => 'pso', 'PSO067G0046' => 'pso', 'PSO478G1073' => 'pso', 'PSO675G3677' => 'pso', 'PSO675G6558' => 'pso', 'PSO675G7520' => 'pso', 'PSO675G8959' => 'pso', 'QL02p074089' => 'qlo', 'QL02p089614' => 'qlo', 'QL03p057736' => 'qlo', 'RcHm_v2.0_Chr1g0364131' => 'rch', 'RcHm_v2.0_Chr2g0087801' => 'rch', 'RcHm_v2.0_Chr2g0087821' => 'rch', 'RcHm_v2.0_Chr2g0173231' => 'rch', 'RcHm_v2.0_Chr4g0433111' => 'rch', 'Rhsim03G0250300' => 'rsi', 'Rhsim08G0048400' => 'rsi', 'Rhsim10G0014800' => 'rsi', 'Rhsim12G0040100' => 'rsi', 'Rhsim12G0109700' => 'rsi', 'Sabra06G0049600' => 'sbr', 'Sabra08G0141000' => 'sbr', 'Sabra10G0021400' => 'sbr', 'Sabra16G0222900' => 'sbr', 'Sabra18G0108600' => 'sbr', 'SalBow1G0433' => 'sbo', 'SalBow1G2038' => 'sbo', 'SalBow1G5003' => 'sbo', 'SalBow7G1197' => 'sbo', 'SalBow8G3506' => 'sbo', 'Sc03g0007300' => 'sci', 'Sc11g0000950' => 'sci', 'Sc14g0008750' => 'sci', 'Sc18g0000420' => 'sci', 'Sed0006754' => 'sed', 'Sed0008741' => 'sed', 'Sed0017172' => 'sed', 'Sed0018925' => 'sed', 'Sed0023326' => 'sed', 'Sed0025909' => 'sed', 'SEGI_05333' => 'sgi', 'SEGI_10362' => 'sgi', 'SEGI_13380' => 'sgi', 'SEGI_24306' => 'sgi', 'SEGI_29077' => 'sgi', 'SEGI_29095' => 'sgi', 'SEGI_36534' => 'sgi', 'SEGI_37506' => 'sgi', 'SEGI_38321' => 'sgi', 'SGA_v2.0_scaffold307G48031' => 'sas', 'SGA_v2.0_scaffold47G17507' => 'sas', 'SGA_v2.0_scaffold63G21736' => 'sas', 'SGA_v2.0_scaffold87G27070' => 'sas', 'SHI17794' => 'shi', 'SHI28851' => 'shi', 'SMO165G0155' => 'smo', 'SMO340G0217' => 'smo', 'SMO367G1210' => 'smo', 'Solyc02g093430.3' => 'sly', 'Solyc05g013580.4' => 'sly', 'Solyc07g008030.3' => 'sly', 'Solyc12g035470.2' => 'sly', 'Sopen02g038020' => 'spe', 'Sopen05g008490' => 'spe', 'Sopen07g003910' => 'spe', 'Sopen12g015240' => 'spe', 'Sp1g11550' => 'spa', 'Sp2g16710' => 'spa', 'Sp3g00430' => 'spa', 'Sp3g26780' => 'spa', 'Sp5g22900' => 'spa', 'Sp6g29530' => 'spa', 'TAR371G0794' => 'tar', 'TAR374G0164' => 'tar', 'TAR622G0165' => 'tar', 'TAR626G0929' => 'tar', 'TAR629G2155' => 'tar', 'THA.LOC104805282' => 'tha', 'THA.LOC104805363' => 'tha', 'THA.LOC104808968' => 'tha', 'THA.LOC104821093' => 'tha', 'THA.LOC104823953' => 'tha', 'THA.LOC104825562' => 'tha', 'THA.LOC104825665' => 'tha', 'Thecc.02G261400' => 'tca', 'Thecc.04G019200' => 'tca', 'Thecc.09G130400' => 'tca', 'Thhalv10004374m.g' => 'esa', 'Thhalv10007850m.g' => 'esa', 'Thhalv10013782m.g' => 'esa', 'Thhalv10018686m.g' => 'esa', 'Thhalv10020899m.g' => 'esa', 'Thhalv10022755m.g' => 'esa', 'TPR.G23851' => 'tpr', 'TPR.G26500' => 'tpr', 'TPR.G27267' => 'tpr', 'TPR.G32001' => 'tpr', 'TPR.G6251' => 'tpr', 'TPR.G8167' => 'tpr', 'TWI12G1330' => 'twi', 'TWI18G1239' => 'twi', 'TWI34G0979' => 'twi', 'TWI36G0670' => 'twi', 'TWI36G0707' => 'twi', 'TWI56G0233' => 'twi', 'TWI75G1809' => 'twi', 'unitig_21.g20874' => 'ugi', 'unitig_26.g10343' => 'ugi', 'unitig_46.g18392' => 'ugi', 'unitig_52.g17178' => 'ugi', 'unitig_8.g2934' => 'ugi', 'vmacro01122' => 'vma', 'vmacro05875' => 'vma', 'vmacro06147' => 'vma', 'vmacro16191' => 'vma', 'vmacro18293' => 'vma', 'VMungo0251G3707' => 'vmu', 'VMungo0464G1521' => 'vmu', 'VMungo1215G0205' => 'vmu', 'VMungo1383G2484' => 'vmu', 'Zm00001eb079610' => 'zma', 'Zm00001eb135990' => 'zma', 'Zm00001eb183710' => 'zma', 'Zm00001eb246020' => 'zma' ) $gf_id = 'HOM05D001124' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001124' ) $data_identifier = 'HOM05D001124' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 6, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 7, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 21, 'bol' => (int) 10, 'bra' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 6, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 9, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 21, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 8, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 10, 'lsa' => (int) 8, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 8, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 9, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb246020' $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' => 'HOM05D001124', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '548', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02520' => 'bna', 'A03p06630' => 'bna', 'A05p44460' => 'bna', 'A06p08710' => 'bna', 'A06p41090' => 'bna', 'A07p32320' => 'bna', 'A08p32520' => 'bna', 'A09p10360' => 'bna', 'A10p24080' => 'bna', 'Aa31LG11G15250' => 'aar', 'Aa31LG1G1800' => 'aar', 'Aa31LG2G5120' => 'aar', 'Aa31LG2G6070' => 'aar', 'Aa31LG5G10770' => 'aar', 'Aa31sc61G90' => 'aar', 'Actinidia01352' => 'ach', 'Actinidia05983' => 'ach', 'Actinidia08133' => 'ach', 'Actinidia15101' => 'ach', 'Actinidia26379' => 'ach', 'Actinidia35778' => 'ach', 'Actinidia36123' => 'ach', 'Actinidia37436' => 'ach', 'Actinidia38730' => 'ach', 'Ah.02g128210' => 'amhyb', 'Ah.03g132990' => 'amhyb', 'Ah.14g079410' => 'amhyb', 'AL1G24640' => 'aly', 'AL2G26680' => 'aly', 'AL3G10530' => 'aly', 'AL3G45230' => 'aly', 'AL5G15230' => 'aly', 'AL5G16960' => 'aly', 'AL6G25210' => 'aly', 'Aqoxy2G00441' => 'aox', 'Aqoxy3G01236' => 'aox', 'Aqoxy5G03746' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3RQ047' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C7GMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9C8JER' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MBL6KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YXCZ83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZANX40' => 'arhy', 'AT1G12990' => 'ath', 'AT1G67880' => 'ath', 'AT2G13290' => 'ath', 'AT3G01620' => 'ath', 'AT3G26445' => 'ath', 'AT3G27540' => 'ath', 'AT5G14480' => 'ath', 'ATR0824G026' => 'atr', 'ATR1098G019' => 'atr', 'Atru.chr11.2145' => 'acertr', 'Atru.chr2.3636' => 'acertr', 'Atru.chr2.3644' => 'acertr', 'Atru.chr6.2422' => 'acertr', 'Atru.chr7.1112' => 'acertr', 'AUR62005469' => 'cqu', 'AUR62011166' => 'cqu', 'AUR62013319' => 'cqu', 'AUR62024273' => 'cqu', 'AUR62028420' => 'cqu', 'AUR62041942' => 'cqu', 'BcaB01g04969' => 'bca', 'BcaB01g06371' => 'bca', 'BcaB02g11494' => 'bca', 'BcaB03g15382' => 'bca', 'BcaB08g36994' => 'bca', 'BcaC03g13477' => 'bca', 'BcaC03g13478' => 'bca', 'BcaC03g13480' => 'bca', 'BcaC03g13481' => 'bca', 'BcaC03g13486' => 'bca', 'BcaC04g19031' => 'bca', 'BcaC04g23085' => 'bca', 'BcaC05g25094' => 'bca', 'BcaC05g25096' => 'bca', 'BcaC05g25138' => 'bca', 'BcaC05g30416' => 'bca', 'BcaC05g30455' => 'bca', 'BcaC06g30979' => 'bca', 'BcaC06g33805' => 'bca', 'BcaC08g46021' => 'bca', 'BcaNung03154' => 'bca', 'BolC2t06623H' => 'bol', 'BolC2t06632H' => 'bol', 'BolC2t06635H' => 'bol', 'BolC2t06638H' => 'bol', 'BolC3t13266H' => 'bol', 'BolC5t29776H' => 'bol', 'BolC6t38912H' => 'bol', 'BolC7t44183H' => 'bol', 'BolC9t54123H' => 'bol', 'BolC9t59107H' => 'bol', 'BraA02t05221Z' => 'bra', 'BraA03t09996Z' => 'bra', 'BraA05t23210Z' => 'bra', 'BraA06t24068Z' => 'bra', 'BraA06t27032Z' => 'bra', 'BraA08t35176Z' => 'bra', 'BraA09t36680Z' => 'bra', 'BraA10t44471Z' => 'bra', 'C02p06760' => 'bna', 'C02p06890' => 'bna', 'C02p07010' => 'bna', 'C03p07660' => 'bna', 'C05p10300' => 'bna', 'C06p38150' => 'bna', 'C07p36650' => 'bna', 'C08p15770' => 'bna', 'C09p12300' => 'bna', 'C09p62700' => 'bna', 'C09p75040' => 'bna', 'CAN.G13.1' => 'can', 'CAN.G138.4' => 'can', 'CAN.G44.6' => 'can', 'CAN.G473.19' => 'can', 'CANSAT01G0835' => 'cansat', 'CANSAT11G0246' => 'cansat', 'CANSAT11G1766' => 'cansat', 'CANSAT64G1954' => 'cansat', 'CARHR013330' => 'chi', 'CARHR060530' => 'chi', 'CARHR075300' => 'chi', 'CARHR105120' => 'chi', 'CARHR148910' => 'chi', 'CARHR198830' => 'chi', 'Carub.0001s1275' => 'cru', 'Carub.0002s1437' => 'cru', 'Carub.0003s0044' => 'cru', 'Carub.0003s2787' => 'cru', 'Carub.0005s0597' => 'cru', 'Carub.0006s1266' => 'cru', 'Ca_06935_v3' => 'car', 'Ca_13559_v3' => 'car', 'Ca_16941_v3' => 'car', 'Ca_16960_v3' => 'car', 'Ca_17775_v3' => 'car', 'Ca_30464_v3' => 'car', 'Cc06_g08160' => 'ccan', 'Cc07_g01520' => 'ccan', 'Cc11_g15810' => 'ccan', 'CDE02G2840' => 'cde', 'CDE03G0093' => 'cde', 'CDE04G2127' => 'cde', 'CDE07G1857' => 'cde', 'CDE09G1246' => 'cde', 'Cfa003412' => 'cfa', 'Cfa007341' => 'cfa', 'Cfa009220' => 'cfa', 'Ciclev10008737m.g' => 'ccl', 'Ciclev10015565m.g' => 'ccl', 'Ciclev10031761m.g' => 'ccl', 'CiPaw.03G045300' => 'cil', 'CiPaw.03G247200' => 'cil', 'CiPaw.04G029500' => 'cil', 'CiPaw.04G174000' => 'cil', 'CiPaw.05G181200' => 'cil', 'CiPaw.06G067100' => 'cil', 'ClCG05G025800' => 'cla', 'ClCG06G011400' => 'cla', 'ClCG09G019360' => 'cla', 'COL.COLO4_04827' => 'col', 'COL.COLO4_29170' => 'col', 'COL.COLO4_35131' => 'col', 'COL.COLO4_35132' => 'col', 'Cpa.g.sc33.32' => 'cpa', 'Cpa.g.sc46.29' => 'cpa', 'Cpa.g.sc796.1' => 'cpa', 'CsaV3_1G030420' => 'csa', 'CsaV3_5G027050' => 'csa', 'CsaV3_5G031040' => 'csa', 'CsaV3_UNG023130' => 'csa', 'CSS0007726' => 'camsi', 'CSS0016433' => 'camsi', 'CSS0017656' => 'camsi', 'CSS0025364' => 'camsi', 'CSS0027582' => 'camsi', 'CSS0047288' => 'camsi', 'CSS0049950' => 'camsi', 'DCAR_003843' => 'dca', 'DCAR_007052' => 'dca', 'DCAR_020884' => 'dca', 'DCAR_021730' => 'dca', 'DCAR_024423' => 'dca', 'DCAR_026509' => 'dca', 'DCAR_031158' => 'dca', 'Dinv14728' => 'din', 'Dinv15219' => 'din', 'Dinv25728' => 'din', 'Dinv33428' => 'din', 'Dinv36489' => 'din', 'Dinv41486' => 'din', 'Duzib147G0469' => 'dzi', 'Duzib168G0060' => 'dzi', 'Duzib187G1215' => 'dzi', 'Duzib248G0692' => 'dzi', 'Duzib251G0767' => 'dzi', 'Duzib264G0446' => 'dzi', 'Duzib268G0691' => 'dzi', 'ECA232G4767' => 'eca', 'ECA233G2838' => 'eca', 'ECA234G0391' => 'eca', 'ECA234G0857' => 'eca', 'ECA236G1593' => 'eca', 'ECA238G0565' => 'eca', 'ECA246G1027' => 'eca', 'ECA246G3223' => 'eca', 'ECA246G3470' => 'eca', 'EL10Ac6g13829' => 'bvu', 'EL10Ac6g14093' => 'bvu', 'EL10Ac8g18707' => 'bvu', 'Eucgr.C01369' => 'egr', 'Eucgr.H02492' => 'egr', 'Eucgr.I01733' => 'egr', 'Eucgr.J02255' => 'egr', 'Eucgr.J02257' => 'egr', 'Eucgr.J02258' => 'egr', 'FAN02G1601' => 'fan', 'FAN03G1586' => 'fan', 'FAN03G2986' => 'fan', 'FAN05G4837' => 'fan', 'FAN06G0146' => 'fan', 'FAN07G0858' => 'fan', 'FAN09G3179' => 'fan', 'FAN10G0669' => 'fan', 'FAN12G2358' => 'fan', 'FAN14G4198' => 'fan', 'FAN14G5112' => 'fan', 'FAN17G0342' => 'fan', 'FAN19G0342' => 'fan', 'FAN19G0962' => 'fan', 'FAN19G1101' => 'fan', 'FAN19G1872' => 'fan', 'FAN22G0356' => 'fan', 'FAN23G0744' => 'fan', 'FAN23G1914' => 'fan', 'FAN26G0032' => 'fan', 'FAN28G0625' => 'fan', 'FvH4_1g02710' => 'fve', 'FvH4_1g02720' => 'fve', 'FvH4_4g25670' => 'fve', 'FvH4_6g51700' => 'fve', 'FvH4_7g20170' => 'fve', 'Glyma.05G175000' => 'gma', 'Glyma.08G132300' => 'gma', 'Glyma.11G243000' => 'gma', 'Glyma.13G158900' => 'gma', 'Glyma.17G112400' => 'gma', 'Glyma.18G014100' => 'gma', 'Glyma.19G003100' => 'gma', 'Glyma.19G056500' => 'gma', 'Gohir.A01G158900' => 'ghi', 'Gohir.A05G312600' => 'ghi', 'Gohir.A05G354900' => 'ghi', 'Gohir.A07G037200' => 'ghi', 'Gohir.A09G030000' => 'ghi', 'Gohir.A12G145200' => 'ghi', 'Gohir.D01G151500' => 'ghi', 'Gohir.D04G058300' => 'ghi', 'Gohir.D05G314100' => 'ghi', 'Gohir.D07G041400' => 'ghi', 'Gohir.D09G029700' => 'ghi', 'Gohir.D12G149700' => 'ghi', 'Gorai.001G043800' => 'gra', 'Gorai.002G187800' => 'gra', 'Gorai.006G034700' => 'gra', 'Gorai.008G161200' => 'gra', 'Gorai.009G335700' => 'gra', 'Gorai.012G065000' => 'gra', 'GSVIVG01000535001' => 'vvi', 'GSVIVG01015572001' => 'vvi', 'GSVIVG01032386001' => 'vvi', 'HanXRQChr05g0138531' => 'han', 'HanXRQChr06g0174391' => 'han', 'HanXRQChr07g0199021' => 'han', 'HanXRQChr08g0208211' => 'han', 'HanXRQChr09g0255471' => 'han', 'HanXRQChr10g0315791' => 'han', 'HanXRQChr12g0371991' => 'han', 'HanXRQChr15g0475251' => 'han', 'HanXRQChr17g0540001' => 'han', 'HanXRQChr17g0548631' => 'han', 'HanXRQChr17g0569561' => 'han', 'Haze_12256' => 'cav', 'Haze_14756' => 'cav', 'Haze_25528' => 'cav', 'Hma1.2p1_0079F.1_g041020' => 'hma', 'Hma1.2p1_0818F.1_g223260' => 'hma', 'Hma1.2p1_1747F.1_g300530' => 'hma', 'HPP92_004607' => 'vpl', 'HPP92_004608' => 'vpl', 'HPP92_006181' => 'vpl', 'HPP92_012192' => 'vpl', 'HPP92_015680' => 'vpl', 'HPP92_020249' => 'vpl', 'HPP92_021376' => 'vpl', 'HPP92_024275' => 'vpl', 'Hund06031' => 'sun', 'Hund25391' => 'sun', 'Lalb_Chr07g0185371' => 'lal', 'Lalb_Chr07g0185381' => 'lal', 'Lalb_Chr12g0204011' => 'lal', 'Lalb_Chr13g0301671' => 'lal', 'Lalb_Chr14g0362851' => 'lal', 'Lalb_Chr24g0403581' => 'lal', 'Lj1g0000233' => 'lja', 'Lj2g0018120' => 'lja', 'Lj3C621T0' => 'lonja', 'Lj3P1059T14' => 'lonja', 'Lj3P611T9' => 'lonja', 'Lj3P614T13' => 'lonja', 'Lj3P615T5' => 'lonja', 'Lj4g0012315' => 'lja', 'Lj4g0026182' => 'lja', 'Lj6P813T16' => 'lonja', 'Lj7C427T7' => 'lonja', 'Lj7C427T8' => 'lonja', 'Lj7P600T41' => 'lonja', 'Lju41C42G17' => 'lonja', 'Lsat_1_v5_gn_0_47300' => 'lsa', 'Lsat_1_v5_gn_2_91280' => 'lsa', 'Lsat_1_v5_gn_3_30561' => 'lsa', 'Lsat_1_v5_gn_4_184321' => 'lsa', 'Lsat_1_v5_gn_4_4041' => 'lsa', 'Lsat_1_v5_gn_5_92000' => 'lsa', 'Lsat_1_v5_gn_8_152940' => 'lsa', 'Lsat_1_v5_gn_8_62401' => 'lsa', 'Manes.06G055900' => 'mes', 'Manes.12G022200' => 'mes', 'Manes.13G023300' => 'mes', 'Manes.14G115000' => 'mes', 'Manes.15G151700' => 'mes', 'Manes.17G111300' => 'mes', 'Mapoly0226s0009' => 'mpo', 'MBI02_g25363_MAGBIO' => 'mbi', 'MBI06_g00027_MAGBIO' => 'mbi', 'MBI10_g13034_MAGBIO' => 'mbi', 'MD09G1023400' => 'mdo', 'MD13G1100100' => 'mdo', 'MD15G1169200' => 'mdo', 'MD16G1101100' => 'mdo', 'MD17G1022900' => 'mdo', 'Medtr3g096150' => 'mtr', 'Medtr4g115070' => 'mtr', 'Medtr7g033325' => 'mtr', 'Medtr8g089840' => 'mtr', 'MELO3C010319.2' => 'cme', 'MELO3C011944.2' => 'cme', 'MELO3C021589.2' => 'cme', 'Migut.E00207' => 'egut', 'Migut.H00067' => 'egut', 'Migut.K00433' => 'egut', 'Migut.K00606' => 'egut', 'Migut.K01410' => 'egut', 'MSTRG.13347' => 'ama', 'MSTRG.24045' => 'ama', 'MSTRG.2428' => 'ama', 'MSTRG.26410' => 'ama', 'MSTRG.3139' => 'ama', 'MSTRG.3286' => 'ama', 'MSTRG.563' => 'ama', 'MSTRG.7941' => 'ama', 'Nitab4.5_0000028g0060' => 'nta', 'Nitab4.5_0000065g0260' => 'nta', 'Nitab4.5_0000112g0060' => 'nta', 'Nitab4.5_0000489g0120' => 'nta', 'Nitab4.5_0001776g0050' => 'nta', 'Nitab4.5_0001854g0010' => 'nta', 'Nitab4.5_0001860g0020' => 'nta', 'Nitab4.5_0004352g0010' => 'nta', 'Nitab4.5_0008716g0020' => 'nta', 'Nitab4.5_0008922g0010' => 'nta', 'Nn3g16693' => 'nnu', 'Nn4g22596' => 'nnu', 'Nn7g37639' => 'nnu', 'Oeu001701.1' => 'oeu', 'Oeu018149.1' => 'oeu', 'Oeu026220.1' => 'oeu', 'Oeu038635.1' => 'oeu', 'Oeu049176.1' => 'oeu', 'Oeu056706.1' => 'oeu', 'Oeu056937.1' => 'oeu', 'Oeu057540.1' => 'oeu', 'Os02g0594900' => 'osa', 'Os02g0595100' => 'osa', 'Os04g0477500' => 'osa', 'Os12g0611900' => 'osa', 'Peaxi162Scf00076g00020' => 'pax', 'Peaxi162Scf00128g00217' => 'pax', 'Peaxi162Scf00129g01640' => 'pax', 'Peaxi162Scf00669g00007' => 'pax', 'Peaxi162Scf00700g00421' => 'pax', 'Peaxi162Scf00801g00038' => 'pax', 'Peaxi162Scf00891g00025' => 'pax', 'PGR083G0909' => 'pgr', 'PGR119G1005' => 'pgr', 'PGR142G2236' => 'pgr', 'PGR142G3388' => 'pgr', 'PGSC0003DMG400004514' => 'stu', 'PGSC0003DMG400012635' => 'stu', 'PGSC0003DMG400015730' => 'stu', 'PGSC0003DMG400018611' => 'stu', 'PGSC0003DMG400030897' => 'stu', 'Phvul.001G254800' => 'pvu', 'Phvul.002G260100' => 'pvu', 'Phvul.003G167600' => 'pvu', 'Phvul.004G005100' => 'pvu', 'Potri.001G343600' => 'ptr', 'Potri.006G066700' => 'ptr', 'Potri.008G186000' => 'ptr', 'Potri.010G046900' => 'ptr', 'Potri.018G127900' => 'ptr', 'Pp3c20_17750' => 'ppa', 'Pp3c24_4380' => 'ppa', 'Prupe.1G245800' => 'ppe', 'Prupe.3G293400' => 'ppe', 'Prupe.7G247400' => 'ppe', 'Psat0s145g0120' => 'psa', 'Psat0s595g0040' => 'psa', 'Psat0s595g0120' => 'psa', 'Psat3g175040' => 'psa', 'Psat7g058120' => 'psa', 'PSO017G0428' => 'pso', 'PSO063G7510' => 'pso', 'PSO067G0046' => 'pso', 'PSO478G1073' => 'pso', 'PSO675G3677' => 'pso', 'PSO675G6558' => 'pso', 'PSO675G7520' => 'pso', 'PSO675G8959' => 'pso', 'QL02p074089' => 'qlo', 'QL02p089614' => 'qlo', 'QL03p057736' => 'qlo', 'RcHm_v2.0_Chr1g0364131' => 'rch', 'RcHm_v2.0_Chr2g0087801' => 'rch', 'RcHm_v2.0_Chr2g0087821' => 'rch', 'RcHm_v2.0_Chr2g0173231' => 'rch', 'RcHm_v2.0_Chr4g0433111' => 'rch', 'Rhsim03G0250300' => 'rsi', 'Rhsim08G0048400' => 'rsi', 'Rhsim10G0014800' => 'rsi', 'Rhsim12G0040100' => 'rsi', 'Rhsim12G0109700' => 'rsi', 'Sabra06G0049600' => 'sbr', 'Sabra08G0141000' => 'sbr', 'Sabra10G0021400' => 'sbr', 'Sabra16G0222900' => 'sbr', 'Sabra18G0108600' => 'sbr', 'SalBow1G0433' => 'sbo', 'SalBow1G2038' => 'sbo', 'SalBow1G5003' => 'sbo', 'SalBow7G1197' => 'sbo', 'SalBow8G3506' => 'sbo', 'Sc03g0007300' => 'sci', 'Sc11g0000950' => 'sci', 'Sc14g0008750' => 'sci', 'Sc18g0000420' => 'sci', 'Sed0006754' => 'sed', 'Sed0008741' => 'sed', 'Sed0017172' => 'sed', 'Sed0018925' => 'sed', 'Sed0023326' => 'sed', 'Sed0025909' => 'sed', 'SEGI_05333' => 'sgi', 'SEGI_10362' => 'sgi', 'SEGI_13380' => 'sgi', 'SEGI_24306' => 'sgi', 'SEGI_29077' => 'sgi', 'SEGI_29095' => 'sgi', 'SEGI_36534' => 'sgi', 'SEGI_37506' => 'sgi', 'SEGI_38321' => 'sgi', 'SGA_v2.0_scaffold307G48031' => 'sas', 'SGA_v2.0_scaffold47G17507' => 'sas', 'SGA_v2.0_scaffold63G21736' => 'sas', 'SGA_v2.0_scaffold87G27070' => 'sas', 'SHI17794' => 'shi', 'SHI28851' => 'shi', 'SMO165G0155' => 'smo', 'SMO340G0217' => 'smo', 'SMO367G1210' => 'smo', 'Solyc02g093430.3' => 'sly', 'Solyc05g013580.4' => 'sly', 'Solyc07g008030.3' => 'sly', 'Solyc12g035470.2' => 'sly', 'Sopen02g038020' => 'spe', 'Sopen05g008490' => 'spe', 'Sopen07g003910' => 'spe', 'Sopen12g015240' => 'spe', 'Sp1g11550' => 'spa', 'Sp2g16710' => 'spa', 'Sp3g00430' => 'spa', 'Sp3g26780' => 'spa', 'Sp5g22900' => 'spa', 'Sp6g29530' => 'spa', 'TAR371G0794' => 'tar', 'TAR374G0164' => 'tar', 'TAR622G0165' => 'tar', 'TAR626G0929' => 'tar', 'TAR629G2155' => 'tar', 'THA.LOC104805282' => 'tha', 'THA.LOC104805363' => 'tha', 'THA.LOC104808968' => 'tha', 'THA.LOC104821093' => 'tha', 'THA.LOC104823953' => 'tha', 'THA.LOC104825562' => 'tha', 'THA.LOC104825665' => 'tha', 'Thecc.02G261400' => 'tca', 'Thecc.04G019200' => 'tca', 'Thecc.09G130400' => 'tca', 'Thhalv10004374m.g' => 'esa', 'Thhalv10007850m.g' => 'esa', 'Thhalv10013782m.g' => 'esa', 'Thhalv10018686m.g' => 'esa', 'Thhalv10020899m.g' => 'esa', 'Thhalv10022755m.g' => 'esa', 'TPR.G23851' => 'tpr', 'TPR.G26500' => 'tpr', 'TPR.G27267' => 'tpr', 'TPR.G32001' => 'tpr', 'TPR.G6251' => 'tpr', 'TPR.G8167' => 'tpr', 'TWI12G1330' => 'twi', 'TWI18G1239' => 'twi', 'TWI34G0979' => 'twi', 'TWI36G0670' => 'twi', 'TWI36G0707' => 'twi', 'TWI56G0233' => 'twi', 'TWI75G1809' => 'twi', 'unitig_21.g20874' => 'ugi', 'unitig_26.g10343' => 'ugi', 'unitig_46.g18392' => 'ugi', 'unitig_52.g17178' => 'ugi', 'unitig_8.g2934' => 'ugi', 'vmacro01122' => 'vma', 'vmacro05875' => 'vma', 'vmacro06147' => 'vma', 'vmacro16191' => 'vma', 'vmacro18293' => 'vma', 'VMungo0251G3707' => 'vmu', 'VMungo0464G1521' => 'vmu', 'VMungo1215G0205' => 'vmu', 'VMungo1383G2484' => 'vmu', 'Zm00001eb079610' => 'zma', 'Zm00001eb135990' => 'zma', 'Zm00001eb183710' => 'zma', 'Zm00001eb246020' => 'zma' ), 'gf_id' => 'HOM05D001124', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001124' ), 'data_identifier' => 'HOM05D001124', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001124', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '548', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02520' => 'bna', 'A03p06630' => 'bna', 'A05p44460' => 'bna', 'A06p08710' => 'bna', 'A06p41090' => 'bna', 'A07p32320' => 'bna', 'A08p32520' => 'bna', 'A09p10360' => 'bna', 'A10p24080' => 'bna', 'Aa31LG11G15250' => 'aar', 'Aa31LG1G1800' => 'aar', 'Aa31LG2G5120' => 'aar', 'Aa31LG2G6070' => 'aar', 'Aa31LG5G10770' => 'aar', 'Aa31sc61G90' => 'aar', 'Actinidia01352' => 'ach', 'Actinidia05983' => 'ach', 'Actinidia08133' => 'ach', 'Actinidia15101' => 'ach', 'Actinidia26379' => 'ach', 'Actinidia35778' => 'ach', 'Actinidia36123' => 'ach', 'Actinidia37436' => 'ach', 'Actinidia38730' => 'ach', 'Ah.02g128210' => 'amhyb', 'Ah.03g132990' => 'amhyb', 'Ah.14g079410' => 'amhyb', 'AL1G24640' => 'aly', 'AL2G26680' => 'aly', 'AL3G10530' => 'aly', 'AL3G45230' => 'aly', 'AL5G15230' => 'aly', 'AL5G16960' => 'aly', 'AL6G25210' => 'aly', 'Aqoxy2G00441' => 'aox', 'Aqoxy3G01236' => 'aox', 'Aqoxy5G03746' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3RQ047' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C7GMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9C8JER' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MBL6KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YXCZ83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZANX40' => 'arhy', 'AT1G12990' => 'ath', 'AT1G67880' => 'ath', 'AT2G13290' => 'ath', 'AT3G01620' => 'ath', 'AT3G26445' => 'ath', 'AT3G27540' => 'ath', 'AT5G14480' => 'ath', 'ATR0824G026' => 'atr', 'ATR1098G019' => 'atr', 'Atru.chr11.2145' => 'acertr', 'Atru.chr2.3636' => 'acertr', 'Atru.chr2.3644' => 'acertr', 'Atru.chr6.2422' => 'acertr', 'Atru.chr7.1112' => 'acertr', 'AUR62005469' => 'cqu', 'AUR62011166' => 'cqu', 'AUR62013319' => 'cqu', 'AUR62024273' => 'cqu', 'AUR62028420' => 'cqu', 'AUR62041942' => 'cqu', 'BcaB01g04969' => 'bca', 'BcaB01g06371' => 'bca', 'BcaB02g11494' => 'bca', 'BcaB03g15382' => 'bca', 'BcaB08g36994' => 'bca', 'BcaC03g13477' => 'bca', 'BcaC03g13478' => 'bca', 'BcaC03g13480' => 'bca', 'BcaC03g13481' => 'bca', 'BcaC03g13486' => 'bca', 'BcaC04g19031' => 'bca', 'BcaC04g23085' => 'bca', 'BcaC05g25094' => 'bca', 'BcaC05g25096' => 'bca', 'BcaC05g25138' => 'bca', 'BcaC05g30416' => 'bca', 'BcaC05g30455' => 'bca', 'BcaC06g30979' => 'bca', 'BcaC06g33805' => 'bca', 'BcaC08g46021' => 'bca', 'BcaNung03154' => 'bca', 'BolC2t06623H' => 'bol', 'BolC2t06632H' => 'bol', 'BolC2t06635H' => 'bol', 'BolC2t06638H' => 'bol', 'BolC3t13266H' => 'bol', 'BolC5t29776H' => 'bol', 'BolC6t38912H' => 'bol', 'BolC7t44183H' => 'bol', 'BolC9t54123H' => 'bol', 'BolC9t59107H' => 'bol', 'BraA02t05221Z' => 'bra', 'BraA03t09996Z' => 'bra', 'BraA05t23210Z' => 'bra', 'BraA06t24068Z' => 'bra', 'BraA06t27032Z' => 'bra', 'BraA08t35176Z' => 'bra', 'BraA09t36680Z' => 'bra', 'BraA10t44471Z' => 'bra', 'C02p06760' => 'bna', 'C02p06890' => 'bna', 'C02p07010' => 'bna', 'C03p07660' => 'bna', 'C05p10300' => 'bna', 'C06p38150' => 'bna', 'C07p36650' => 'bna', 'C08p15770' => 'bna', 'C09p12300' => 'bna', 'C09p62700' => 'bna', 'C09p75040' => 'bna', 'CAN.G13.1' => 'can', 'CAN.G138.4' => 'can', 'CAN.G44.6' => 'can', 'CAN.G473.19' => 'can', 'CANSAT01G0835' => 'cansat', 'CANSAT11G0246' => 'cansat', 'CANSAT11G1766' => 'cansat', 'CANSAT64G1954' => 'cansat', 'CARHR013330' => 'chi', 'CARHR060530' => 'chi', 'CARHR075300' => 'chi', 'CARHR105120' => 'chi', 'CARHR148910' => 'chi', 'CARHR198830' => 'chi', 'Carub.0001s1275' => 'cru', 'Carub.0002s1437' => 'cru', 'Carub.0003s0044' => 'cru', 'Carub.0003s2787' => 'cru', 'Carub.0005s0597' => 'cru', 'Carub.0006s1266' => 'cru', 'Ca_06935_v3' => 'car', 'Ca_13559_v3' => 'car', 'Ca_16941_v3' => 'car', 'Ca_16960_v3' => 'car', 'Ca_17775_v3' => 'car', 'Ca_30464_v3' => 'car', 'Cc06_g08160' => 'ccan', 'Cc07_g01520' => 'ccan', 'Cc11_g15810' => 'ccan', 'CDE02G2840' => 'cde', 'CDE03G0093' => 'cde', 'CDE04G2127' => 'cde', 'CDE07G1857' => 'cde', 'CDE09G1246' => 'cde', 'Cfa003412' => 'cfa', 'Cfa007341' => 'cfa', 'Cfa009220' => 'cfa', 'Ciclev10008737m.g' => 'ccl', 'Ciclev10015565m.g' => 'ccl', 'Ciclev10031761m.g' => 'ccl', 'CiPaw.03G045300' => 'cil', 'CiPaw.03G247200' => 'cil', 'CiPaw.04G029500' => 'cil', 'CiPaw.04G174000' => 'cil', 'CiPaw.05G181200' => 'cil', 'CiPaw.06G067100' => 'cil', 'ClCG05G025800' => 'cla', 'ClCG06G011400' => 'cla', 'ClCG09G019360' => 'cla', 'COL.COLO4_04827' => 'col', 'COL.COLO4_29170' => 'col', 'COL.COLO4_35131' => 'col', 'COL.COLO4_35132' => 'col', 'Cpa.g.sc33.32' => 'cpa', 'Cpa.g.sc46.29' => 'cpa', 'Cpa.g.sc796.1' => 'cpa', 'CsaV3_1G030420' => 'csa', 'CsaV3_5G027050' => 'csa', 'CsaV3_5G031040' => 'csa', 'CsaV3_UNG023130' => 'csa', 'CSS0007726' => 'camsi', 'CSS0016433' => 'camsi', 'CSS0017656' => 'camsi', 'CSS0025364' => 'camsi', 'CSS0027582' => 'camsi', 'CSS0047288' => 'camsi', 'CSS0049950' => 'camsi', 'DCAR_003843' => 'dca', 'DCAR_007052' => 'dca', 'DCAR_020884' => 'dca', 'DCAR_021730' => 'dca', 'DCAR_024423' => 'dca', 'DCAR_026509' => 'dca', 'DCAR_031158' => 'dca', 'Dinv14728' => 'din', 'Dinv15219' => 'din', 'Dinv25728' => 'din', 'Dinv33428' => 'din', 'Dinv36489' => 'din', 'Dinv41486' => 'din', 'Duzib147G0469' => 'dzi', 'Duzib168G0060' => 'dzi', 'Duzib187G1215' => 'dzi', 'Duzib248G0692' => 'dzi', 'Duzib251G0767' => 'dzi', 'Duzib264G0446' => 'dzi', 'Duzib268G0691' => 'dzi', 'ECA232G4767' => 'eca', 'ECA233G2838' => 'eca', 'ECA234G0391' => 'eca', 'ECA234G0857' => 'eca', 'ECA236G1593' => 'eca', 'ECA238G0565' => 'eca', 'ECA246G1027' => 'eca', 'ECA246G3223' => 'eca', 'ECA246G3470' => 'eca', 'EL10Ac6g13829' => 'bvu', 'EL10Ac6g14093' => 'bvu', 'EL10Ac8g18707' => 'bvu', 'Eucgr.C01369' => 'egr', 'Eucgr.H02492' => 'egr', 'Eucgr.I01733' => 'egr', 'Eucgr.J02255' => 'egr', 'Eucgr.J02257' => 'egr', 'Eucgr.J02258' => 'egr', 'FAN02G1601' => 'fan', 'FAN03G1586' => 'fan', 'FAN03G2986' => 'fan', 'FAN05G4837' => 'fan', 'FAN06G0146' => 'fan', 'FAN07G0858' => 'fan', 'FAN09G3179' => 'fan', 'FAN10G0669' => 'fan', 'FAN12G2358' => 'fan', 'FAN14G4198' => 'fan', 'FAN14G5112' => 'fan', 'FAN17G0342' => 'fan', 'FAN19G0342' => 'fan', 'FAN19G0962' => 'fan', 'FAN19G1101' => 'fan', 'FAN19G1872' => 'fan', 'FAN22G0356' => 'fan', 'FAN23G0744' => 'fan', 'FAN23G1914' => 'fan', 'FAN26G0032' => 'fan', 'FAN28G0625' => 'fan', 'FvH4_1g02710' => 'fve', 'FvH4_1g02720' => 'fve', 'FvH4_4g25670' => 'fve', 'FvH4_6g51700' => 'fve', 'FvH4_7g20170' => 'fve', 'Glyma.05G175000' => 'gma', 'Glyma.08G132300' => 'gma', 'Glyma.11G243000' => 'gma', 'Glyma.13G158900' => 'gma', 'Glyma.17G112400' => 'gma', 'Glyma.18G014100' => 'gma', 'Glyma.19G003100' => 'gma', 'Glyma.19G056500' => 'gma', 'Gohir.A01G158900' => 'ghi', 'Gohir.A05G312600' => 'ghi', 'Gohir.A05G354900' => 'ghi', 'Gohir.A07G037200' => 'ghi', 'Gohir.A09G030000' => 'ghi', 'Gohir.A12G145200' => 'ghi', 'Gohir.D01G151500' => 'ghi', 'Gohir.D04G058300' => 'ghi', 'Gohir.D05G314100' => 'ghi', 'Gohir.D07G041400' => 'ghi', 'Gohir.D09G029700' => 'ghi', 'Gohir.D12G149700' => 'ghi', 'Gorai.001G043800' => 'gra', 'Gorai.002G187800' => 'gra', 'Gorai.006G034700' => 'gra', 'Gorai.008G161200' => 'gra', 'Gorai.009G335700' => 'gra', 'Gorai.012G065000' => 'gra', 'GSVIVG01000535001' => 'vvi', 'GSVIVG01015572001' => 'vvi', 'GSVIVG01032386001' => 'vvi', 'HanXRQChr05g0138531' => 'han', 'HanXRQChr06g0174391' => 'han', 'HanXRQChr07g0199021' => 'han', 'HanXRQChr08g0208211' => 'han', 'HanXRQChr09g0255471' => 'han', 'HanXRQChr10g0315791' => 'han', 'HanXRQChr12g0371991' => 'han', 'HanXRQChr15g0475251' => 'han', 'HanXRQChr17g0540001' => 'han', 'HanXRQChr17g0548631' => 'han', 'HanXRQChr17g0569561' => 'han', 'Haze_12256' => 'cav', 'Haze_14756' => 'cav', 'Haze_25528' => 'cav', 'Hma1.2p1_0079F.1_g041020' => 'hma', 'Hma1.2p1_0818F.1_g223260' => 'hma', 'Hma1.2p1_1747F.1_g300530' => 'hma', 'HPP92_004607' => 'vpl', 'HPP92_004608' => 'vpl', 'HPP92_006181' => 'vpl', 'HPP92_012192' => 'vpl', 'HPP92_015680' => 'vpl', 'HPP92_020249' => 'vpl', 'HPP92_021376' => 'vpl', 'HPP92_024275' => 'vpl', 'Hund06031' => 'sun', 'Hund25391' => 'sun', 'Lalb_Chr07g0185371' => 'lal', 'Lalb_Chr07g0185381' => 'lal', 'Lalb_Chr12g0204011' => 'lal', 'Lalb_Chr13g0301671' => 'lal', 'Lalb_Chr14g0362851' => 'lal', 'Lalb_Chr24g0403581' => 'lal', 'Lj1g0000233' => 'lja', 'Lj2g0018120' => 'lja', 'Lj3C621T0' => 'lonja', 'Lj3P1059T14' => 'lonja', 'Lj3P611T9' => 'lonja', 'Lj3P614T13' => 'lonja', 'Lj3P615T5' => 'lonja', 'Lj4g0012315' => 'lja', 'Lj4g0026182' => 'lja', 'Lj6P813T16' => 'lonja', 'Lj7C427T7' => 'lonja', 'Lj7C427T8' => 'lonja', 'Lj7P600T41' => 'lonja', 'Lju41C42G17' => 'lonja', 'Lsat_1_v5_gn_0_47300' => 'lsa', 'Lsat_1_v5_gn_2_91280' => 'lsa', 'Lsat_1_v5_gn_3_30561' => 'lsa', 'Lsat_1_v5_gn_4_184321' => 'lsa', 'Lsat_1_v5_gn_4_4041' => 'lsa', 'Lsat_1_v5_gn_5_92000' => 'lsa', 'Lsat_1_v5_gn_8_152940' => 'lsa', 'Lsat_1_v5_gn_8_62401' => 'lsa', 'Manes.06G055900' => 'mes', 'Manes.12G022200' => 'mes', 'Manes.13G023300' => 'mes', 'Manes.14G115000' => 'mes', 'Manes.15G151700' => 'mes', 'Manes.17G111300' => 'mes', 'Mapoly0226s0009' => 'mpo', 'MBI02_g25363_MAGBIO' => 'mbi', 'MBI06_g00027_MAGBIO' => 'mbi', 'MBI10_g13034_MAGBIO' => 'mbi', 'MD09G1023400' => 'mdo', 'MD13G1100100' => 'mdo', 'MD15G1169200' => 'mdo', 'MD16G1101100' => 'mdo', 'MD17G1022900' => 'mdo', 'Medtr3g096150' => 'mtr', 'Medtr4g115070' => 'mtr', 'Medtr7g033325' => 'mtr', 'Medtr8g089840' => 'mtr', 'MELO3C010319.2' => 'cme', 'MELO3C011944.2' => 'cme', 'MELO3C021589.2' => 'cme', 'Migut.E00207' => 'egut', 'Migut.H00067' => 'egut', 'Migut.K00433' => 'egut', 'Migut.K00606' => 'egut', 'Migut.K01410' => 'egut', 'MSTRG.13347' => 'ama', 'MSTRG.24045' => 'ama', 'MSTRG.2428' => 'ama', 'MSTRG.26410' => 'ama', 'MSTRG.3139' => 'ama', 'MSTRG.3286' => 'ama', 'MSTRG.563' => 'ama', 'MSTRG.7941' => 'ama', 'Nitab4.5_0000028g0060' => 'nta', 'Nitab4.5_0000065g0260' => 'nta', 'Nitab4.5_0000112g0060' => 'nta', 'Nitab4.5_0000489g0120' => 'nta', 'Nitab4.5_0001776g0050' => 'nta', 'Nitab4.5_0001854g0010' => 'nta', 'Nitab4.5_0001860g0020' => 'nta', 'Nitab4.5_0004352g0010' => 'nta', 'Nitab4.5_0008716g0020' => 'nta', 'Nitab4.5_0008922g0010' => 'nta', 'Nn3g16693' => 'nnu', 'Nn4g22596' => 'nnu', 'Nn7g37639' => 'nnu', 'Oeu001701.1' => 'oeu', 'Oeu018149.1' => 'oeu', 'Oeu026220.1' => 'oeu', 'Oeu038635.1' => 'oeu', 'Oeu049176.1' => 'oeu', 'Oeu056706.1' => 'oeu', 'Oeu056937.1' => 'oeu', 'Oeu057540.1' => 'oeu', 'Os02g0594900' => 'osa', 'Os02g0595100' => 'osa', 'Os04g0477500' => 'osa', 'Os12g0611900' => 'osa', 'Peaxi162Scf00076g00020' => 'pax', 'Peaxi162Scf00128g00217' => 'pax', 'Peaxi162Scf00129g01640' => 'pax', 'Peaxi162Scf00669g00007' => 'pax', 'Peaxi162Scf00700g00421' => 'pax', 'Peaxi162Scf00801g00038' => 'pax', 'Peaxi162Scf00891g00025' => 'pax', 'PGR083G0909' => 'pgr', 'PGR119G1005' => 'pgr', 'PGR142G2236' => 'pgr', 'PGR142G3388' => 'pgr', 'PGSC0003DMG400004514' => 'stu', 'PGSC0003DMG400012635' => 'stu', 'PGSC0003DMG400015730' => 'stu', 'PGSC0003DMG400018611' => 'stu', 'PGSC0003DMG400030897' => 'stu', 'Phvul.001G254800' => 'pvu', 'Phvul.002G260100' => 'pvu', 'Phvul.003G167600' => 'pvu', 'Phvul.004G005100' => 'pvu', 'Potri.001G343600' => 'ptr', 'Potri.006G066700' => 'ptr', 'Potri.008G186000' => 'ptr', 'Potri.010G046900' => 'ptr', 'Potri.018G127900' => 'ptr', 'Pp3c20_17750' => 'ppa', 'Pp3c24_4380' => 'ppa', 'Prupe.1G245800' => 'ppe', 'Prupe.3G293400' => 'ppe', 'Prupe.7G247400' => 'ppe', 'Psat0s145g0120' => 'psa', 'Psat0s595g0040' => 'psa', 'Psat0s595g0120' => 'psa', 'Psat3g175040' => 'psa', 'Psat7g058120' => 'psa', 'PSO017G0428' => 'pso', 'PSO063G7510' => 'pso', 'PSO067G0046' => 'pso', 'PSO478G1073' => 'pso', 'PSO675G3677' => 'pso', 'PSO675G6558' => 'pso', 'PSO675G7520' => 'pso', 'PSO675G8959' => 'pso', 'QL02p074089' => 'qlo', 'QL02p089614' => 'qlo', 'QL03p057736' => 'qlo', 'RcHm_v2.0_Chr1g0364131' => 'rch', 'RcHm_v2.0_Chr2g0087801' => 'rch', 'RcHm_v2.0_Chr2g0087821' => 'rch', 'RcHm_v2.0_Chr2g0173231' => 'rch', 'RcHm_v2.0_Chr4g0433111' => 'rch', 'Rhsim03G0250300' => 'rsi', 'Rhsim08G0048400' => 'rsi', 'Rhsim10G0014800' => 'rsi', 'Rhsim12G0040100' => 'rsi', 'Rhsim12G0109700' => 'rsi', 'Sabra06G0049600' => 'sbr', 'Sabra08G0141000' => 'sbr', 'Sabra10G0021400' => 'sbr', 'Sabra16G0222900' => 'sbr', 'Sabra18G0108600' => 'sbr', 'SalBow1G0433' => 'sbo', 'SalBow1G2038' => 'sbo', 'SalBow1G5003' => 'sbo', 'SalBow7G1197' => 'sbo', 'SalBow8G3506' => 'sbo', 'Sc03g0007300' => 'sci', 'Sc11g0000950' => 'sci', 'Sc14g0008750' => 'sci', 'Sc18g0000420' => 'sci', 'Sed0006754' => 'sed', 'Sed0008741' => 'sed', 'Sed0017172' => 'sed', 'Sed0018925' => 'sed', 'Sed0023326' => 'sed', 'Sed0025909' => 'sed', 'SEGI_05333' => 'sgi', 'SEGI_10362' => 'sgi', 'SEGI_13380' => 'sgi', 'SEGI_24306' => 'sgi', 'SEGI_29077' => 'sgi', 'SEGI_29095' => 'sgi', 'SEGI_36534' => 'sgi', 'SEGI_37506' => 'sgi', 'SEGI_38321' => 'sgi', 'SGA_v2.0_scaffold307G48031' => 'sas', 'SGA_v2.0_scaffold47G17507' => 'sas', 'SGA_v2.0_scaffold63G21736' => 'sas', 'SGA_v2.0_scaffold87G27070' => 'sas', 'SHI17794' => 'shi', 'SHI28851' => 'shi', 'SMO165G0155' => 'smo', 'SMO340G0217' => 'smo', 'SMO367G1210' => 'smo', 'Solyc02g093430.3' => 'sly', 'Solyc05g013580.4' => 'sly', 'Solyc07g008030.3' => 'sly', 'Solyc12g035470.2' => 'sly', 'Sopen02g038020' => 'spe', 'Sopen05g008490' => 'spe', 'Sopen07g003910' => 'spe', 'Sopen12g015240' => 'spe', 'Sp1g11550' => 'spa', 'Sp2g16710' => 'spa', 'Sp3g00430' => 'spa', 'Sp3g26780' => 'spa', 'Sp5g22900' => 'spa', 'Sp6g29530' => 'spa', 'TAR371G0794' => 'tar', 'TAR374G0164' => 'tar', 'TAR622G0165' => 'tar', 'TAR626G0929' => 'tar', 'TAR629G2155' => 'tar', 'THA.LOC104805282' => 'tha', 'THA.LOC104805363' => 'tha', 'THA.LOC104808968' => 'tha', 'THA.LOC104821093' => 'tha', 'THA.LOC104823953' => 'tha', 'THA.LOC104825562' => 'tha', 'THA.LOC104825665' => 'tha', 'Thecc.02G261400' => 'tca', 'Thecc.04G019200' => 'tca', 'Thecc.09G130400' => 'tca', 'Thhalv10004374m.g' => 'esa', 'Thhalv10007850m.g' => 'esa', 'Thhalv10013782m.g' => 'esa', 'Thhalv10018686m.g' => 'esa', 'Thhalv10020899m.g' => 'esa', 'Thhalv10022755m.g' => 'esa', 'TPR.G23851' => 'tpr', 'TPR.G26500' => 'tpr', 'TPR.G27267' => 'tpr', 'TPR.G32001' => 'tpr', 'TPR.G6251' => 'tpr', 'TPR.G8167' => 'tpr', 'TWI12G1330' => 'twi', 'TWI18G1239' => 'twi', 'TWI34G0979' => 'twi', 'TWI36G0670' => 'twi', 'TWI36G0707' => 'twi', 'TWI56G0233' => 'twi', 'TWI75G1809' => 'twi', 'unitig_21.g20874' => 'ugi', 'unitig_26.g10343' => 'ugi', 'unitig_46.g18392' => 'ugi', 'unitig_52.g17178' => 'ugi', 'unitig_8.g2934' => 'ugi', 'vmacro01122' => 'vma', 'vmacro05875' => 'vma', 'vmacro06147' => 'vma', 'vmacro16191' => 'vma', 'vmacro18293' => 'vma', 'VMungo0251G3707' => 'vmu', 'VMungo0464G1521' => 'vmu', 'VMungo1215G0205' => 'vmu', 'VMungo1383G2484' => 'vmu', 'Zm00001eb079610' => 'zma', 'Zm00001eb135990' => 'zma', 'Zm00001eb183710' => 'zma', 'Zm00001eb246020' => 'zma' ) $gf_id = 'HOM05D001124' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001124' ) $data_identifier = 'HOM05D001124' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 6, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 7, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 21, 'bol' => (int) 10, 'bra' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 6, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 9, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 21, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 8, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 10, 'lsa' => (int) 8, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 8, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 9, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb246020' $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' => 'HOM05D001124', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '548', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02520' => 'bna', 'A03p06630' => 'bna', 'A05p44460' => 'bna', 'A06p08710' => 'bna', 'A06p41090' => 'bna', 'A07p32320' => 'bna', 'A08p32520' => 'bna', 'A09p10360' => 'bna', 'A10p24080' => 'bna', 'Aa31LG11G15250' => 'aar', 'Aa31LG1G1800' => 'aar', 'Aa31LG2G5120' => 'aar', 'Aa31LG2G6070' => 'aar', 'Aa31LG5G10770' => 'aar', 'Aa31sc61G90' => 'aar', 'Actinidia01352' => 'ach', 'Actinidia05983' => 'ach', 'Actinidia08133' => 'ach', 'Actinidia15101' => 'ach', 'Actinidia26379' => 'ach', 'Actinidia35778' => 'ach', 'Actinidia36123' => 'ach', 'Actinidia37436' => 'ach', 'Actinidia38730' => 'ach', 'Ah.02g128210' => 'amhyb', 'Ah.03g132990' => 'amhyb', 'Ah.14g079410' => 'amhyb', 'AL1G24640' => 'aly', 'AL2G26680' => 'aly', 'AL3G10530' => 'aly', 'AL3G45230' => 'aly', 'AL5G15230' => 'aly', 'AL5G16960' => 'aly', 'AL6G25210' => 'aly', 'Aqoxy2G00441' => 'aox', 'Aqoxy3G01236' => 'aox', 'Aqoxy5G03746' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3RQ047' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C7GMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9C8JER' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MBL6KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YXCZ83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZANX40' => 'arhy', 'AT1G12990' => 'ath', 'AT1G67880' => 'ath', 'AT2G13290' => 'ath', 'AT3G01620' => 'ath', 'AT3G26445' => 'ath', 'AT3G27540' => 'ath', 'AT5G14480' => 'ath', 'ATR0824G026' => 'atr', 'ATR1098G019' => 'atr', 'Atru.chr11.2145' => 'acertr', 'Atru.chr2.3636' => 'acertr', 'Atru.chr2.3644' => 'acertr', 'Atru.chr6.2422' => 'acertr', 'Atru.chr7.1112' => 'acertr', 'AUR62005469' => 'cqu', 'AUR62011166' => 'cqu', 'AUR62013319' => 'cqu', 'AUR62024273' => 'cqu', 'AUR62028420' => 'cqu', 'AUR62041942' => 'cqu', 'BcaB01g04969' => 'bca', 'BcaB01g06371' => 'bca', 'BcaB02g11494' => 'bca', 'BcaB03g15382' => 'bca', 'BcaB08g36994' => 'bca', 'BcaC03g13477' => 'bca', 'BcaC03g13478' => 'bca', 'BcaC03g13480' => 'bca', 'BcaC03g13481' => 'bca', 'BcaC03g13486' => 'bca', 'BcaC04g19031' => 'bca', 'BcaC04g23085' => 'bca', 'BcaC05g25094' => 'bca', 'BcaC05g25096' => 'bca', 'BcaC05g25138' => 'bca', 'BcaC05g30416' => 'bca', 'BcaC05g30455' => 'bca', 'BcaC06g30979' => 'bca', 'BcaC06g33805' => 'bca', 'BcaC08g46021' => 'bca', 'BcaNung03154' => 'bca', 'BolC2t06623H' => 'bol', 'BolC2t06632H' => 'bol', 'BolC2t06635H' => 'bol', 'BolC2t06638H' => 'bol', 'BolC3t13266H' => 'bol', 'BolC5t29776H' => 'bol', 'BolC6t38912H' => 'bol', 'BolC7t44183H' => 'bol', 'BolC9t54123H' => 'bol', 'BolC9t59107H' => 'bol', 'BraA02t05221Z' => 'bra', 'BraA03t09996Z' => 'bra', 'BraA05t23210Z' => 'bra', 'BraA06t24068Z' => 'bra', 'BraA06t27032Z' => 'bra', 'BraA08t35176Z' => 'bra', 'BraA09t36680Z' => 'bra', 'BraA10t44471Z' => 'bra', 'C02p06760' => 'bna', 'C02p06890' => 'bna', 'C02p07010' => 'bna', 'C03p07660' => 'bna', 'C05p10300' => 'bna', 'C06p38150' => 'bna', 'C07p36650' => 'bna', 'C08p15770' => 'bna', 'C09p12300' => 'bna', 'C09p62700' => 'bna', 'C09p75040' => 'bna', 'CAN.G13.1' => 'can', 'CAN.G138.4' => 'can', 'CAN.G44.6' => 'can', 'CAN.G473.19' => 'can', 'CANSAT01G0835' => 'cansat', 'CANSAT11G0246' => 'cansat', 'CANSAT11G1766' => 'cansat', 'CANSAT64G1954' => 'cansat', 'CARHR013330' => 'chi', 'CARHR060530' => 'chi', 'CARHR075300' => 'chi', 'CARHR105120' => 'chi', 'CARHR148910' => 'chi', 'CARHR198830' => 'chi', 'Carub.0001s1275' => 'cru', 'Carub.0002s1437' => 'cru', 'Carub.0003s0044' => 'cru', 'Carub.0003s2787' => 'cru', 'Carub.0005s0597' => 'cru', 'Carub.0006s1266' => 'cru', 'Ca_06935_v3' => 'car', 'Ca_13559_v3' => 'car', 'Ca_16941_v3' => 'car', 'Ca_16960_v3' => 'car', 'Ca_17775_v3' => 'car', 'Ca_30464_v3' => 'car', 'Cc06_g08160' => 'ccan', 'Cc07_g01520' => 'ccan', 'Cc11_g15810' => 'ccan', 'CDE02G2840' => 'cde', 'CDE03G0093' => 'cde', 'CDE04G2127' => 'cde', 'CDE07G1857' => 'cde', 'CDE09G1246' => 'cde', 'Cfa003412' => 'cfa', 'Cfa007341' => 'cfa', 'Cfa009220' => 'cfa', 'Ciclev10008737m.g' => 'ccl', 'Ciclev10015565m.g' => 'ccl', 'Ciclev10031761m.g' => 'ccl', 'CiPaw.03G045300' => 'cil', 'CiPaw.03G247200' => 'cil', 'CiPaw.04G029500' => 'cil', 'CiPaw.04G174000' => 'cil', 'CiPaw.05G181200' => 'cil', 'CiPaw.06G067100' => 'cil', 'ClCG05G025800' => 'cla', 'ClCG06G011400' => 'cla', 'ClCG09G019360' => 'cla', 'COL.COLO4_04827' => 'col', 'COL.COLO4_29170' => 'col', 'COL.COLO4_35131' => 'col', 'COL.COLO4_35132' => 'col', 'Cpa.g.sc33.32' => 'cpa', 'Cpa.g.sc46.29' => 'cpa', 'Cpa.g.sc796.1' => 'cpa', 'CsaV3_1G030420' => 'csa', 'CsaV3_5G027050' => 'csa', 'CsaV3_5G031040' => 'csa', 'CsaV3_UNG023130' => 'csa', 'CSS0007726' => 'camsi', 'CSS0016433' => 'camsi', 'CSS0017656' => 'camsi', 'CSS0025364' => 'camsi', 'CSS0027582' => 'camsi', 'CSS0047288' => 'camsi', 'CSS0049950' => 'camsi', 'DCAR_003843' => 'dca', 'DCAR_007052' => 'dca', 'DCAR_020884' => 'dca', 'DCAR_021730' => 'dca', 'DCAR_024423' => 'dca', 'DCAR_026509' => 'dca', 'DCAR_031158' => 'dca', 'Dinv14728' => 'din', 'Dinv15219' => 'din', 'Dinv25728' => 'din', 'Dinv33428' => 'din', 'Dinv36489' => 'din', 'Dinv41486' => 'din', 'Duzib147G0469' => 'dzi', 'Duzib168G0060' => 'dzi', 'Duzib187G1215' => 'dzi', 'Duzib248G0692' => 'dzi', 'Duzib251G0767' => 'dzi', 'Duzib264G0446' => 'dzi', 'Duzib268G0691' => 'dzi', 'ECA232G4767' => 'eca', 'ECA233G2838' => 'eca', 'ECA234G0391' => 'eca', 'ECA234G0857' => 'eca', 'ECA236G1593' => 'eca', 'ECA238G0565' => 'eca', 'ECA246G1027' => 'eca', 'ECA246G3223' => 'eca', 'ECA246G3470' => 'eca', 'EL10Ac6g13829' => 'bvu', 'EL10Ac6g14093' => 'bvu', 'EL10Ac8g18707' => 'bvu', 'Eucgr.C01369' => 'egr', 'Eucgr.H02492' => 'egr', 'Eucgr.I01733' => 'egr', 'Eucgr.J02255' => 'egr', 'Eucgr.J02257' => 'egr', 'Eucgr.J02258' => 'egr', 'FAN02G1601' => 'fan', 'FAN03G1586' => 'fan', 'FAN03G2986' => 'fan', 'FAN05G4837' => 'fan', 'FAN06G0146' => 'fan', 'FAN07G0858' => 'fan', 'FAN09G3179' => 'fan', 'FAN10G0669' => 'fan', 'FAN12G2358' => 'fan', 'FAN14G4198' => 'fan', 'FAN14G5112' => 'fan', 'FAN17G0342' => 'fan', 'FAN19G0342' => 'fan', 'FAN19G0962' => 'fan', 'FAN19G1101' => 'fan', 'FAN19G1872' => 'fan', 'FAN22G0356' => 'fan', 'FAN23G0744' => 'fan', 'FAN23G1914' => 'fan', 'FAN26G0032' => 'fan', 'FAN28G0625' => 'fan', 'FvH4_1g02710' => 'fve', 'FvH4_1g02720' => 'fve', 'FvH4_4g25670' => 'fve', 'FvH4_6g51700' => 'fve', 'FvH4_7g20170' => 'fve', 'Glyma.05G175000' => 'gma', 'Glyma.08G132300' => 'gma', 'Glyma.11G243000' => 'gma', 'Glyma.13G158900' => 'gma', 'Glyma.17G112400' => 'gma', 'Glyma.18G014100' => 'gma', 'Glyma.19G003100' => 'gma', 'Glyma.19G056500' => 'gma', 'Gohir.A01G158900' => 'ghi', 'Gohir.A05G312600' => 'ghi', 'Gohir.A05G354900' => 'ghi', 'Gohir.A07G037200' => 'ghi', 'Gohir.A09G030000' => 'ghi', 'Gohir.A12G145200' => 'ghi', 'Gohir.D01G151500' => 'ghi', 'Gohir.D04G058300' => 'ghi', 'Gohir.D05G314100' => 'ghi', 'Gohir.D07G041400' => 'ghi', 'Gohir.D09G029700' => 'ghi', 'Gohir.D12G149700' => 'ghi', 'Gorai.001G043800' => 'gra', 'Gorai.002G187800' => 'gra', 'Gorai.006G034700' => 'gra', 'Gorai.008G161200' => 'gra', 'Gorai.009G335700' => 'gra', 'Gorai.012G065000' => 'gra', 'GSVIVG01000535001' => 'vvi', 'GSVIVG01015572001' => 'vvi', 'GSVIVG01032386001' => 'vvi', 'HanXRQChr05g0138531' => 'han', 'HanXRQChr06g0174391' => 'han', 'HanXRQChr07g0199021' => 'han', 'HanXRQChr08g0208211' => 'han', 'HanXRQChr09g0255471' => 'han', 'HanXRQChr10g0315791' => 'han', 'HanXRQChr12g0371991' => 'han', 'HanXRQChr15g0475251' => 'han', 'HanXRQChr17g0540001' => 'han', 'HanXRQChr17g0548631' => 'han', 'HanXRQChr17g0569561' => 'han', 'Haze_12256' => 'cav', 'Haze_14756' => 'cav', 'Haze_25528' => 'cav', 'Hma1.2p1_0079F.1_g041020' => 'hma', 'Hma1.2p1_0818F.1_g223260' => 'hma', 'Hma1.2p1_1747F.1_g300530' => 'hma', 'HPP92_004607' => 'vpl', 'HPP92_004608' => 'vpl', 'HPP92_006181' => 'vpl', 'HPP92_012192' => 'vpl', 'HPP92_015680' => 'vpl', 'HPP92_020249' => 'vpl', 'HPP92_021376' => 'vpl', 'HPP92_024275' => 'vpl', 'Hund06031' => 'sun', 'Hund25391' => 'sun', 'Lalb_Chr07g0185371' => 'lal', 'Lalb_Chr07g0185381' => 'lal', 'Lalb_Chr12g0204011' => 'lal', 'Lalb_Chr13g0301671' => 'lal', 'Lalb_Chr14g0362851' => 'lal', 'Lalb_Chr24g0403581' => 'lal', 'Lj1g0000233' => 'lja', 'Lj2g0018120' => 'lja', 'Lj3C621T0' => 'lonja', 'Lj3P1059T14' => 'lonja', 'Lj3P611T9' => 'lonja', 'Lj3P614T13' => 'lonja', 'Lj3P615T5' => 'lonja', 'Lj4g0012315' => 'lja', 'Lj4g0026182' => 'lja', 'Lj6P813T16' => 'lonja', 'Lj7C427T7' => 'lonja', 'Lj7C427T8' => 'lonja', 'Lj7P600T41' => 'lonja', 'Lju41C42G17' => 'lonja', 'Lsat_1_v5_gn_0_47300' => 'lsa', 'Lsat_1_v5_gn_2_91280' => 'lsa', 'Lsat_1_v5_gn_3_30561' => 'lsa', 'Lsat_1_v5_gn_4_184321' => 'lsa', 'Lsat_1_v5_gn_4_4041' => 'lsa', 'Lsat_1_v5_gn_5_92000' => 'lsa', 'Lsat_1_v5_gn_8_152940' => 'lsa', 'Lsat_1_v5_gn_8_62401' => 'lsa', 'Manes.06G055900' => 'mes', 'Manes.12G022200' => 'mes', 'Manes.13G023300' => 'mes', 'Manes.14G115000' => 'mes', 'Manes.15G151700' => 'mes', 'Manes.17G111300' => 'mes', 'Mapoly0226s0009' => 'mpo', 'MBI02_g25363_MAGBIO' => 'mbi', 'MBI06_g00027_MAGBIO' => 'mbi', 'MBI10_g13034_MAGBIO' => 'mbi', 'MD09G1023400' => 'mdo', 'MD13G1100100' => 'mdo', 'MD15G1169200' => 'mdo', 'MD16G1101100' => 'mdo', 'MD17G1022900' => 'mdo', 'Medtr3g096150' => 'mtr', 'Medtr4g115070' => 'mtr', 'Medtr7g033325' => 'mtr', 'Medtr8g089840' => 'mtr', 'MELO3C010319.2' => 'cme', 'MELO3C011944.2' => 'cme', 'MELO3C021589.2' => 'cme', 'Migut.E00207' => 'egut', 'Migut.H00067' => 'egut', 'Migut.K00433' => 'egut', 'Migut.K00606' => 'egut', 'Migut.K01410' => 'egut', 'MSTRG.13347' => 'ama', 'MSTRG.24045' => 'ama', 'MSTRG.2428' => 'ama', 'MSTRG.26410' => 'ama', 'MSTRG.3139' => 'ama', 'MSTRG.3286' => 'ama', 'MSTRG.563' => 'ama', 'MSTRG.7941' => 'ama', 'Nitab4.5_0000028g0060' => 'nta', 'Nitab4.5_0000065g0260' => 'nta', 'Nitab4.5_0000112g0060' => 'nta', 'Nitab4.5_0000489g0120' => 'nta', 'Nitab4.5_0001776g0050' => 'nta', 'Nitab4.5_0001854g0010' => 'nta', 'Nitab4.5_0001860g0020' => 'nta', 'Nitab4.5_0004352g0010' => 'nta', 'Nitab4.5_0008716g0020' => 'nta', 'Nitab4.5_0008922g0010' => 'nta', 'Nn3g16693' => 'nnu', 'Nn4g22596' => 'nnu', 'Nn7g37639' => 'nnu', 'Oeu001701.1' => 'oeu', 'Oeu018149.1' => 'oeu', 'Oeu026220.1' => 'oeu', 'Oeu038635.1' => 'oeu', 'Oeu049176.1' => 'oeu', 'Oeu056706.1' => 'oeu', 'Oeu056937.1' => 'oeu', 'Oeu057540.1' => 'oeu', 'Os02g0594900' => 'osa', 'Os02g0595100' => 'osa', 'Os04g0477500' => 'osa', 'Os12g0611900' => 'osa', 'Peaxi162Scf00076g00020' => 'pax', 'Peaxi162Scf00128g00217' => 'pax', 'Peaxi162Scf00129g01640' => 'pax', 'Peaxi162Scf00669g00007' => 'pax', 'Peaxi162Scf00700g00421' => 'pax', 'Peaxi162Scf00801g00038' => 'pax', 'Peaxi162Scf00891g00025' => 'pax', 'PGR083G0909' => 'pgr', 'PGR119G1005' => 'pgr', 'PGR142G2236' => 'pgr', 'PGR142G3388' => 'pgr', 'PGSC0003DMG400004514' => 'stu', 'PGSC0003DMG400012635' => 'stu', 'PGSC0003DMG400015730' => 'stu', 'PGSC0003DMG400018611' => 'stu', 'PGSC0003DMG400030897' => 'stu', 'Phvul.001G254800' => 'pvu', 'Phvul.002G260100' => 'pvu', 'Phvul.003G167600' => 'pvu', 'Phvul.004G005100' => 'pvu', 'Potri.001G343600' => 'ptr', 'Potri.006G066700' => 'ptr', 'Potri.008G186000' => 'ptr', 'Potri.010G046900' => 'ptr', 'Potri.018G127900' => 'ptr', 'Pp3c20_17750' => 'ppa', 'Pp3c24_4380' => 'ppa', 'Prupe.1G245800' => 'ppe', 'Prupe.3G293400' => 'ppe', 'Prupe.7G247400' => 'ppe', 'Psat0s145g0120' => 'psa', 'Psat0s595g0040' => 'psa', 'Psat0s595g0120' => 'psa', 'Psat3g175040' => 'psa', 'Psat7g058120' => 'psa', 'PSO017G0428' => 'pso', 'PSO063G7510' => 'pso', 'PSO067G0046' => 'pso', 'PSO478G1073' => 'pso', 'PSO675G3677' => 'pso', 'PSO675G6558' => 'pso', 'PSO675G7520' => 'pso', 'PSO675G8959' => 'pso', 'QL02p074089' => 'qlo', 'QL02p089614' => 'qlo', 'QL03p057736' => 'qlo', 'RcHm_v2.0_Chr1g0364131' => 'rch', 'RcHm_v2.0_Chr2g0087801' => 'rch', 'RcHm_v2.0_Chr2g0087821' => 'rch', 'RcHm_v2.0_Chr2g0173231' => 'rch', 'RcHm_v2.0_Chr4g0433111' => 'rch', 'Rhsim03G0250300' => 'rsi', 'Rhsim08G0048400' => 'rsi', 'Rhsim10G0014800' => 'rsi', 'Rhsim12G0040100' => 'rsi', 'Rhsim12G0109700' => 'rsi', 'Sabra06G0049600' => 'sbr', 'Sabra08G0141000' => 'sbr', 'Sabra10G0021400' => 'sbr', 'Sabra16G0222900' => 'sbr', 'Sabra18G0108600' => 'sbr', 'SalBow1G0433' => 'sbo', 'SalBow1G2038' => 'sbo', 'SalBow1G5003' => 'sbo', 'SalBow7G1197' => 'sbo', 'SalBow8G3506' => 'sbo', 'Sc03g0007300' => 'sci', 'Sc11g0000950' => 'sci', 'Sc14g0008750' => 'sci', 'Sc18g0000420' => 'sci', 'Sed0006754' => 'sed', 'Sed0008741' => 'sed', 'Sed0017172' => 'sed', 'Sed0018925' => 'sed', 'Sed0023326' => 'sed', 'Sed0025909' => 'sed', 'SEGI_05333' => 'sgi', 'SEGI_10362' => 'sgi', 'SEGI_13380' => 'sgi', 'SEGI_24306' => 'sgi', 'SEGI_29077' => 'sgi', 'SEGI_29095' => 'sgi', 'SEGI_36534' => 'sgi', 'SEGI_37506' => 'sgi', 'SEGI_38321' => 'sgi', 'SGA_v2.0_scaffold307G48031' => 'sas', 'SGA_v2.0_scaffold47G17507' => 'sas', 'SGA_v2.0_scaffold63G21736' => 'sas', 'SGA_v2.0_scaffold87G27070' => 'sas', 'SHI17794' => 'shi', 'SHI28851' => 'shi', 'SMO165G0155' => 'smo', 'SMO340G0217' => 'smo', 'SMO367G1210' => 'smo', 'Solyc02g093430.3' => 'sly', 'Solyc05g013580.4' => 'sly', 'Solyc07g008030.3' => 'sly', 'Solyc12g035470.2' => 'sly', 'Sopen02g038020' => 'spe', 'Sopen05g008490' => 'spe', 'Sopen07g003910' => 'spe', 'Sopen12g015240' => 'spe', 'Sp1g11550' => 'spa', 'Sp2g16710' => 'spa', 'Sp3g00430' => 'spa', 'Sp3g26780' => 'spa', 'Sp5g22900' => 'spa', 'Sp6g29530' => 'spa', 'TAR371G0794' => 'tar', 'TAR374G0164' => 'tar', 'TAR622G0165' => 'tar', 'TAR626G0929' => 'tar', 'TAR629G2155' => 'tar', 'THA.LOC104805282' => 'tha', 'THA.LOC104805363' => 'tha', 'THA.LOC104808968' => 'tha', 'THA.LOC104821093' => 'tha', 'THA.LOC104823953' => 'tha', 'THA.LOC104825562' => 'tha', 'THA.LOC104825665' => 'tha', 'Thecc.02G261400' => 'tca', 'Thecc.04G019200' => 'tca', 'Thecc.09G130400' => 'tca', 'Thhalv10004374m.g' => 'esa', 'Thhalv10007850m.g' => 'esa', 'Thhalv10013782m.g' => 'esa', 'Thhalv10018686m.g' => 'esa', 'Thhalv10020899m.g' => 'esa', 'Thhalv10022755m.g' => 'esa', 'TPR.G23851' => 'tpr', 'TPR.G26500' => 'tpr', 'TPR.G27267' => 'tpr', 'TPR.G32001' => 'tpr', 'TPR.G6251' => 'tpr', 'TPR.G8167' => 'tpr', 'TWI12G1330' => 'twi', 'TWI18G1239' => 'twi', 'TWI34G0979' => 'twi', 'TWI36G0670' => 'twi', 'TWI36G0707' => 'twi', 'TWI56G0233' => 'twi', 'TWI75G1809' => 'twi', 'unitig_21.g20874' => 'ugi', 'unitig_26.g10343' => 'ugi', 'unitig_46.g18392' => 'ugi', 'unitig_52.g17178' => 'ugi', 'unitig_8.g2934' => 'ugi', 'vmacro01122' => 'vma', 'vmacro05875' => 'vma', 'vmacro06147' => 'vma', 'vmacro16191' => 'vma', 'vmacro18293' => 'vma', 'VMungo0251G3707' => 'vmu', 'VMungo0464G1521' => 'vmu', 'VMungo1215G0205' => 'vmu', 'VMungo1383G2484' => 'vmu', 'Zm00001eb079610' => 'zma', 'Zm00001eb135990' => 'zma', 'Zm00001eb183710' => 'zma', 'Zm00001eb246020' => 'zma' ), 'gf_id' => 'HOM05D001124', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001124' ), 'data_identifier' => 'HOM05D001124', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001124', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '548', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02520' => 'bna', 'A03p06630' => 'bna', 'A05p44460' => 'bna', 'A06p08710' => 'bna', 'A06p41090' => 'bna', 'A07p32320' => 'bna', 'A08p32520' => 'bna', 'A09p10360' => 'bna', 'A10p24080' => 'bna', 'Aa31LG11G15250' => 'aar', 'Aa31LG1G1800' => 'aar', 'Aa31LG2G5120' => 'aar', 'Aa31LG2G6070' => 'aar', 'Aa31LG5G10770' => 'aar', 'Aa31sc61G90' => 'aar', 'Actinidia01352' => 'ach', 'Actinidia05983' => 'ach', 'Actinidia08133' => 'ach', 'Actinidia15101' => 'ach', 'Actinidia26379' => 'ach', 'Actinidia35778' => 'ach', 'Actinidia36123' => 'ach', 'Actinidia37436' => 'ach', 'Actinidia38730' => 'ach', 'Ah.02g128210' => 'amhyb', 'Ah.03g132990' => 'amhyb', 'Ah.14g079410' => 'amhyb', 'AL1G24640' => 'aly', 'AL2G26680' => 'aly', 'AL3G10530' => 'aly', 'AL3G45230' => 'aly', 'AL5G15230' => 'aly', 'AL5G16960' => 'aly', 'AL6G25210' => 'aly', 'Aqoxy2G00441' => 'aox', 'Aqoxy3G01236' => 'aox', 'Aqoxy5G03746' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3RQ047' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C7GMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9C8JER' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MBL6KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YXCZ83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZANX40' => 'arhy', 'AT1G12990' => 'ath', 'AT1G67880' => 'ath', 'AT2G13290' => 'ath', 'AT3G01620' => 'ath', 'AT3G26445' => 'ath', 'AT3G27540' => 'ath', 'AT5G14480' => 'ath', 'ATR0824G026' => 'atr', 'ATR1098G019' => 'atr', 'Atru.chr11.2145' => 'acertr', 'Atru.chr2.3636' => 'acertr', 'Atru.chr2.3644' => 'acertr', 'Atru.chr6.2422' => 'acertr', 'Atru.chr7.1112' => 'acertr', 'AUR62005469' => 'cqu', 'AUR62011166' => 'cqu', 'AUR62013319' => 'cqu', 'AUR62024273' => 'cqu', 'AUR62028420' => 'cqu', 'AUR62041942' => 'cqu', 'BcaB01g04969' => 'bca', 'BcaB01g06371' => 'bca', 'BcaB02g11494' => 'bca', 'BcaB03g15382' => 'bca', 'BcaB08g36994' => 'bca', 'BcaC03g13477' => 'bca', 'BcaC03g13478' => 'bca', 'BcaC03g13480' => 'bca', 'BcaC03g13481' => 'bca', 'BcaC03g13486' => 'bca', 'BcaC04g19031' => 'bca', 'BcaC04g23085' => 'bca', 'BcaC05g25094' => 'bca', 'BcaC05g25096' => 'bca', 'BcaC05g25138' => 'bca', 'BcaC05g30416' => 'bca', 'BcaC05g30455' => 'bca', 'BcaC06g30979' => 'bca', 'BcaC06g33805' => 'bca', 'BcaC08g46021' => 'bca', 'BcaNung03154' => 'bca', 'BolC2t06623H' => 'bol', 'BolC2t06632H' => 'bol', 'BolC2t06635H' => 'bol', 'BolC2t06638H' => 'bol', 'BolC3t13266H' => 'bol', 'BolC5t29776H' => 'bol', 'BolC6t38912H' => 'bol', 'BolC7t44183H' => 'bol', 'BolC9t54123H' => 'bol', 'BolC9t59107H' => 'bol', 'BraA02t05221Z' => 'bra', 'BraA03t09996Z' => 'bra', 'BraA05t23210Z' => 'bra', 'BraA06t24068Z' => 'bra', 'BraA06t27032Z' => 'bra', 'BraA08t35176Z' => 'bra', 'BraA09t36680Z' => 'bra', 'BraA10t44471Z' => 'bra', 'C02p06760' => 'bna', 'C02p06890' => 'bna', 'C02p07010' => 'bna', 'C03p07660' => 'bna', 'C05p10300' => 'bna', 'C06p38150' => 'bna', 'C07p36650' => 'bna', 'C08p15770' => 'bna', 'C09p12300' => 'bna', 'C09p62700' => 'bna', 'C09p75040' => 'bna', 'CAN.G13.1' => 'can', 'CAN.G138.4' => 'can', 'CAN.G44.6' => 'can', 'CAN.G473.19' => 'can', 'CANSAT01G0835' => 'cansat', 'CANSAT11G0246' => 'cansat', 'CANSAT11G1766' => 'cansat', 'CANSAT64G1954' => 'cansat', 'CARHR013330' => 'chi', 'CARHR060530' => 'chi', 'CARHR075300' => 'chi', 'CARHR105120' => 'chi', 'CARHR148910' => 'chi', 'CARHR198830' => 'chi', 'Carub.0001s1275' => 'cru', 'Carub.0002s1437' => 'cru', 'Carub.0003s0044' => 'cru', 'Carub.0003s2787' => 'cru', 'Carub.0005s0597' => 'cru', 'Carub.0006s1266' => 'cru', 'Ca_06935_v3' => 'car', 'Ca_13559_v3' => 'car', 'Ca_16941_v3' => 'car', 'Ca_16960_v3' => 'car', 'Ca_17775_v3' => 'car', 'Ca_30464_v3' => 'car', 'Cc06_g08160' => 'ccan', 'Cc07_g01520' => 'ccan', 'Cc11_g15810' => 'ccan', 'CDE02G2840' => 'cde', 'CDE03G0093' => 'cde', 'CDE04G2127' => 'cde', 'CDE07G1857' => 'cde', 'CDE09G1246' => 'cde', 'Cfa003412' => 'cfa', 'Cfa007341' => 'cfa', 'Cfa009220' => 'cfa', 'Ciclev10008737m.g' => 'ccl', 'Ciclev10015565m.g' => 'ccl', 'Ciclev10031761m.g' => 'ccl', 'CiPaw.03G045300' => 'cil', 'CiPaw.03G247200' => 'cil', 'CiPaw.04G029500' => 'cil', 'CiPaw.04G174000' => 'cil', 'CiPaw.05G181200' => 'cil', 'CiPaw.06G067100' => 'cil', 'ClCG05G025800' => 'cla', 'ClCG06G011400' => 'cla', 'ClCG09G019360' => 'cla', 'COL.COLO4_04827' => 'col', 'COL.COLO4_29170' => 'col', 'COL.COLO4_35131' => 'col', 'COL.COLO4_35132' => 'col', 'Cpa.g.sc33.32' => 'cpa', 'Cpa.g.sc46.29' => 'cpa', 'Cpa.g.sc796.1' => 'cpa', 'CsaV3_1G030420' => 'csa', 'CsaV3_5G027050' => 'csa', 'CsaV3_5G031040' => 'csa', 'CsaV3_UNG023130' => 'csa', 'CSS0007726' => 'camsi', 'CSS0016433' => 'camsi', 'CSS0017656' => 'camsi', 'CSS0025364' => 'camsi', 'CSS0027582' => 'camsi', 'CSS0047288' => 'camsi', 'CSS0049950' => 'camsi', 'DCAR_003843' => 'dca', 'DCAR_007052' => 'dca', 'DCAR_020884' => 'dca', 'DCAR_021730' => 'dca', 'DCAR_024423' => 'dca', 'DCAR_026509' => 'dca', 'DCAR_031158' => 'dca', 'Dinv14728' => 'din', 'Dinv15219' => 'din', 'Dinv25728' => 'din', 'Dinv33428' => 'din', 'Dinv36489' => 'din', 'Dinv41486' => 'din', 'Duzib147G0469' => 'dzi', 'Duzib168G0060' => 'dzi', 'Duzib187G1215' => 'dzi', 'Duzib248G0692' => 'dzi', 'Duzib251G0767' => 'dzi', 'Duzib264G0446' => 'dzi', 'Duzib268G0691' => 'dzi', 'ECA232G4767' => 'eca', 'ECA233G2838' => 'eca', 'ECA234G0391' => 'eca', 'ECA234G0857' => 'eca', 'ECA236G1593' => 'eca', 'ECA238G0565' => 'eca', 'ECA246G1027' => 'eca', 'ECA246G3223' => 'eca', 'ECA246G3470' => 'eca', 'EL10Ac6g13829' => 'bvu', 'EL10Ac6g14093' => 'bvu', 'EL10Ac8g18707' => 'bvu', 'Eucgr.C01369' => 'egr', 'Eucgr.H02492' => 'egr', 'Eucgr.I01733' => 'egr', 'Eucgr.J02255' => 'egr', 'Eucgr.J02257' => 'egr', 'Eucgr.J02258' => 'egr', 'FAN02G1601' => 'fan', 'FAN03G1586' => 'fan', 'FAN03G2986' => 'fan', 'FAN05G4837' => 'fan', 'FAN06G0146' => 'fan', 'FAN07G0858' => 'fan', 'FAN09G3179' => 'fan', 'FAN10G0669' => 'fan', 'FAN12G2358' => 'fan', 'FAN14G4198' => 'fan', 'FAN14G5112' => 'fan', 'FAN17G0342' => 'fan', 'FAN19G0342' => 'fan', 'FAN19G0962' => 'fan', 'FAN19G1101' => 'fan', 'FAN19G1872' => 'fan', 'FAN22G0356' => 'fan', 'FAN23G0744' => 'fan', 'FAN23G1914' => 'fan', 'FAN26G0032' => 'fan', 'FAN28G0625' => 'fan', 'FvH4_1g02710' => 'fve', 'FvH4_1g02720' => 'fve', 'FvH4_4g25670' => 'fve', 'FvH4_6g51700' => 'fve', 'FvH4_7g20170' => 'fve', 'Glyma.05G175000' => 'gma', 'Glyma.08G132300' => 'gma', 'Glyma.11G243000' => 'gma', 'Glyma.13G158900' => 'gma', 'Glyma.17G112400' => 'gma', 'Glyma.18G014100' => 'gma', 'Glyma.19G003100' => 'gma', 'Glyma.19G056500' => 'gma', 'Gohir.A01G158900' => 'ghi', 'Gohir.A05G312600' => 'ghi', 'Gohir.A05G354900' => 'ghi', 'Gohir.A07G037200' => 'ghi', 'Gohir.A09G030000' => 'ghi', 'Gohir.A12G145200' => 'ghi', 'Gohir.D01G151500' => 'ghi', 'Gohir.D04G058300' => 'ghi', 'Gohir.D05G314100' => 'ghi', 'Gohir.D07G041400' => 'ghi', 'Gohir.D09G029700' => 'ghi', 'Gohir.D12G149700' => 'ghi', 'Gorai.001G043800' => 'gra', 'Gorai.002G187800' => 'gra', 'Gorai.006G034700' => 'gra', 'Gorai.008G161200' => 'gra', 'Gorai.009G335700' => 'gra', 'Gorai.012G065000' => 'gra', 'GSVIVG01000535001' => 'vvi', 'GSVIVG01015572001' => 'vvi', 'GSVIVG01032386001' => 'vvi', 'HanXRQChr05g0138531' => 'han', 'HanXRQChr06g0174391' => 'han', 'HanXRQChr07g0199021' => 'han', 'HanXRQChr08g0208211' => 'han', 'HanXRQChr09g0255471' => 'han', 'HanXRQChr10g0315791' => 'han', 'HanXRQChr12g0371991' => 'han', 'HanXRQChr15g0475251' => 'han', 'HanXRQChr17g0540001' => 'han', 'HanXRQChr17g0548631' => 'han', 'HanXRQChr17g0569561' => 'han', 'Haze_12256' => 'cav', 'Haze_14756' => 'cav', 'Haze_25528' => 'cav', 'Hma1.2p1_0079F.1_g041020' => 'hma', 'Hma1.2p1_0818F.1_g223260' => 'hma', 'Hma1.2p1_1747F.1_g300530' => 'hma', 'HPP92_004607' => 'vpl', 'HPP92_004608' => 'vpl', 'HPP92_006181' => 'vpl', 'HPP92_012192' => 'vpl', 'HPP92_015680' => 'vpl', 'HPP92_020249' => 'vpl', 'HPP92_021376' => 'vpl', 'HPP92_024275' => 'vpl', 'Hund06031' => 'sun', 'Hund25391' => 'sun', 'Lalb_Chr07g0185371' => 'lal', 'Lalb_Chr07g0185381' => 'lal', 'Lalb_Chr12g0204011' => 'lal', 'Lalb_Chr13g0301671' => 'lal', 'Lalb_Chr14g0362851' => 'lal', 'Lalb_Chr24g0403581' => 'lal', 'Lj1g0000233' => 'lja', 'Lj2g0018120' => 'lja', 'Lj3C621T0' => 'lonja', 'Lj3P1059T14' => 'lonja', 'Lj3P611T9' => 'lonja', 'Lj3P614T13' => 'lonja', 'Lj3P615T5' => 'lonja', 'Lj4g0012315' => 'lja', 'Lj4g0026182' => 'lja', 'Lj6P813T16' => 'lonja', 'Lj7C427T7' => 'lonja', 'Lj7C427T8' => 'lonja', 'Lj7P600T41' => 'lonja', 'Lju41C42G17' => 'lonja', 'Lsat_1_v5_gn_0_47300' => 'lsa', 'Lsat_1_v5_gn_2_91280' => 'lsa', 'Lsat_1_v5_gn_3_30561' => 'lsa', 'Lsat_1_v5_gn_4_184321' => 'lsa', 'Lsat_1_v5_gn_4_4041' => 'lsa', 'Lsat_1_v5_gn_5_92000' => 'lsa', 'Lsat_1_v5_gn_8_152940' => 'lsa', 'Lsat_1_v5_gn_8_62401' => 'lsa', 'Manes.06G055900' => 'mes', 'Manes.12G022200' => 'mes', 'Manes.13G023300' => 'mes', 'Manes.14G115000' => 'mes', 'Manes.15G151700' => 'mes', 'Manes.17G111300' => 'mes', 'Mapoly0226s0009' => 'mpo', 'MBI02_g25363_MAGBIO' => 'mbi', 'MBI06_g00027_MAGBIO' => 'mbi', 'MBI10_g13034_MAGBIO' => 'mbi', 'MD09G1023400' => 'mdo', 'MD13G1100100' => 'mdo', 'MD15G1169200' => 'mdo', 'MD16G1101100' => 'mdo', 'MD17G1022900' => 'mdo', 'Medtr3g096150' => 'mtr', 'Medtr4g115070' => 'mtr', 'Medtr7g033325' => 'mtr', 'Medtr8g089840' => 'mtr', 'MELO3C010319.2' => 'cme', 'MELO3C011944.2' => 'cme', 'MELO3C021589.2' => 'cme', 'Migut.E00207' => 'egut', 'Migut.H00067' => 'egut', 'Migut.K00433' => 'egut', 'Migut.K00606' => 'egut', 'Migut.K01410' => 'egut', 'MSTRG.13347' => 'ama', 'MSTRG.24045' => 'ama', 'MSTRG.2428' => 'ama', 'MSTRG.26410' => 'ama', 'MSTRG.3139' => 'ama', 'MSTRG.3286' => 'ama', 'MSTRG.563' => 'ama', 'MSTRG.7941' => 'ama', 'Nitab4.5_0000028g0060' => 'nta', 'Nitab4.5_0000065g0260' => 'nta', 'Nitab4.5_0000112g0060' => 'nta', 'Nitab4.5_0000489g0120' => 'nta', 'Nitab4.5_0001776g0050' => 'nta', 'Nitab4.5_0001854g0010' => 'nta', 'Nitab4.5_0001860g0020' => 'nta', 'Nitab4.5_0004352g0010' => 'nta', 'Nitab4.5_0008716g0020' => 'nta', 'Nitab4.5_0008922g0010' => 'nta', 'Nn3g16693' => 'nnu', 'Nn4g22596' => 'nnu', 'Nn7g37639' => 'nnu', 'Oeu001701.1' => 'oeu', 'Oeu018149.1' => 'oeu', 'Oeu026220.1' => 'oeu', 'Oeu038635.1' => 'oeu', 'Oeu049176.1' => 'oeu', 'Oeu056706.1' => 'oeu', 'Oeu056937.1' => 'oeu', 'Oeu057540.1' => 'oeu', 'Os02g0594900' => 'osa', 'Os02g0595100' => 'osa', 'Os04g0477500' => 'osa', 'Os12g0611900' => 'osa', 'Peaxi162Scf00076g00020' => 'pax', 'Peaxi162Scf00128g00217' => 'pax', 'Peaxi162Scf00129g01640' => 'pax', 'Peaxi162Scf00669g00007' => 'pax', 'Peaxi162Scf00700g00421' => 'pax', 'Peaxi162Scf00801g00038' => 'pax', 'Peaxi162Scf00891g00025' => 'pax', 'PGR083G0909' => 'pgr', 'PGR119G1005' => 'pgr', 'PGR142G2236' => 'pgr', 'PGR142G3388' => 'pgr', 'PGSC0003DMG400004514' => 'stu', 'PGSC0003DMG400012635' => 'stu', 'PGSC0003DMG400015730' => 'stu', 'PGSC0003DMG400018611' => 'stu', 'PGSC0003DMG400030897' => 'stu', 'Phvul.001G254800' => 'pvu', 'Phvul.002G260100' => 'pvu', 'Phvul.003G167600' => 'pvu', 'Phvul.004G005100' => 'pvu', 'Potri.001G343600' => 'ptr', 'Potri.006G066700' => 'ptr', 'Potri.008G186000' => 'ptr', 'Potri.010G046900' => 'ptr', 'Potri.018G127900' => 'ptr', 'Pp3c20_17750' => 'ppa', 'Pp3c24_4380' => 'ppa', 'Prupe.1G245800' => 'ppe', 'Prupe.3G293400' => 'ppe', 'Prupe.7G247400' => 'ppe', 'Psat0s145g0120' => 'psa', 'Psat0s595g0040' => 'psa', 'Psat0s595g0120' => 'psa', 'Psat3g175040' => 'psa', 'Psat7g058120' => 'psa', 'PSO017G0428' => 'pso', 'PSO063G7510' => 'pso', 'PSO067G0046' => 'pso', 'PSO478G1073' => 'pso', 'PSO675G3677' => 'pso', 'PSO675G6558' => 'pso', 'PSO675G7520' => 'pso', 'PSO675G8959' => 'pso', 'QL02p074089' => 'qlo', 'QL02p089614' => 'qlo', 'QL03p057736' => 'qlo', 'RcHm_v2.0_Chr1g0364131' => 'rch', 'RcHm_v2.0_Chr2g0087801' => 'rch', 'RcHm_v2.0_Chr2g0087821' => 'rch', 'RcHm_v2.0_Chr2g0173231' => 'rch', 'RcHm_v2.0_Chr4g0433111' => 'rch', 'Rhsim03G0250300' => 'rsi', 'Rhsim08G0048400' => 'rsi', 'Rhsim10G0014800' => 'rsi', 'Rhsim12G0040100' => 'rsi', 'Rhsim12G0109700' => 'rsi', 'Sabra06G0049600' => 'sbr', 'Sabra08G0141000' => 'sbr', 'Sabra10G0021400' => 'sbr', 'Sabra16G0222900' => 'sbr', 'Sabra18G0108600' => 'sbr', 'SalBow1G0433' => 'sbo', 'SalBow1G2038' => 'sbo', 'SalBow1G5003' => 'sbo', 'SalBow7G1197' => 'sbo', 'SalBow8G3506' => 'sbo', 'Sc03g0007300' => 'sci', 'Sc11g0000950' => 'sci', 'Sc14g0008750' => 'sci', 'Sc18g0000420' => 'sci', 'Sed0006754' => 'sed', 'Sed0008741' => 'sed', 'Sed0017172' => 'sed', 'Sed0018925' => 'sed', 'Sed0023326' => 'sed', 'Sed0025909' => 'sed', 'SEGI_05333' => 'sgi', 'SEGI_10362' => 'sgi', 'SEGI_13380' => 'sgi', 'SEGI_24306' => 'sgi', 'SEGI_29077' => 'sgi', 'SEGI_29095' => 'sgi', 'SEGI_36534' => 'sgi', 'SEGI_37506' => 'sgi', 'SEGI_38321' => 'sgi', 'SGA_v2.0_scaffold307G48031' => 'sas', 'SGA_v2.0_scaffold47G17507' => 'sas', 'SGA_v2.0_scaffold63G21736' => 'sas', 'SGA_v2.0_scaffold87G27070' => 'sas', 'SHI17794' => 'shi', 'SHI28851' => 'shi', 'SMO165G0155' => 'smo', 'SMO340G0217' => 'smo', 'SMO367G1210' => 'smo', 'Solyc02g093430.3' => 'sly', 'Solyc05g013580.4' => 'sly', 'Solyc07g008030.3' => 'sly', 'Solyc12g035470.2' => 'sly', 'Sopen02g038020' => 'spe', 'Sopen05g008490' => 'spe', 'Sopen07g003910' => 'spe', 'Sopen12g015240' => 'spe', 'Sp1g11550' => 'spa', 'Sp2g16710' => 'spa', 'Sp3g00430' => 'spa', 'Sp3g26780' => 'spa', 'Sp5g22900' => 'spa', 'Sp6g29530' => 'spa', 'TAR371G0794' => 'tar', 'TAR374G0164' => 'tar', 'TAR622G0165' => 'tar', 'TAR626G0929' => 'tar', 'TAR629G2155' => 'tar', 'THA.LOC104805282' => 'tha', 'THA.LOC104805363' => 'tha', 'THA.LOC104808968' => 'tha', 'THA.LOC104821093' => 'tha', 'THA.LOC104823953' => 'tha', 'THA.LOC104825562' => 'tha', 'THA.LOC104825665' => 'tha', 'Thecc.02G261400' => 'tca', 'Thecc.04G019200' => 'tca', 'Thecc.09G130400' => 'tca', 'Thhalv10004374m.g' => 'esa', 'Thhalv10007850m.g' => 'esa', 'Thhalv10013782m.g' => 'esa', 'Thhalv10018686m.g' => 'esa', 'Thhalv10020899m.g' => 'esa', 'Thhalv10022755m.g' => 'esa', 'TPR.G23851' => 'tpr', 'TPR.G26500' => 'tpr', 'TPR.G27267' => 'tpr', 'TPR.G32001' => 'tpr', 'TPR.G6251' => 'tpr', 'TPR.G8167' => 'tpr', 'TWI12G1330' => 'twi', 'TWI18G1239' => 'twi', 'TWI34G0979' => 'twi', 'TWI36G0670' => 'twi', 'TWI36G0707' => 'twi', 'TWI56G0233' => 'twi', 'TWI75G1809' => 'twi', 'unitig_21.g20874' => 'ugi', 'unitig_26.g10343' => 'ugi', 'unitig_46.g18392' => 'ugi', 'unitig_52.g17178' => 'ugi', 'unitig_8.g2934' => 'ugi', 'vmacro01122' => 'vma', 'vmacro05875' => 'vma', 'vmacro06147' => 'vma', 'vmacro16191' => 'vma', 'vmacro18293' => 'vma', 'VMungo0251G3707' => 'vmu', 'VMungo0464G1521' => 'vmu', 'VMungo1215G0205' => 'vmu', 'VMungo1383G2484' => 'vmu', 'Zm00001eb079610' => 'zma', 'Zm00001eb135990' => 'zma', 'Zm00001eb183710' => 'zma', 'Zm00001eb246020' => 'zma' ) $gf_id = 'HOM05D001124' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001124' ) $data_identifier = 'HOM05D001124' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 6, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 7, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 21, 'bol' => (int) 10, 'bra' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 6, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 9, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 21, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 8, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 10, 'lsa' => (int) 8, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 8, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 9, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb246020' $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' => 'HOM05D001124', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '548', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02520' => 'bna', 'A03p06630' => 'bna', 'A05p44460' => 'bna', 'A06p08710' => 'bna', 'A06p41090' => 'bna', 'A07p32320' => 'bna', 'A08p32520' => 'bna', 'A09p10360' => 'bna', 'A10p24080' => 'bna', 'Aa31LG11G15250' => 'aar', 'Aa31LG1G1800' => 'aar', 'Aa31LG2G5120' => 'aar', 'Aa31LG2G6070' => 'aar', 'Aa31LG5G10770' => 'aar', 'Aa31sc61G90' => 'aar', 'Actinidia01352' => 'ach', 'Actinidia05983' => 'ach', 'Actinidia08133' => 'ach', 'Actinidia15101' => 'ach', 'Actinidia26379' => 'ach', 'Actinidia35778' => 'ach', 'Actinidia36123' => 'ach', 'Actinidia37436' => 'ach', 'Actinidia38730' => 'ach', 'Ah.02g128210' => 'amhyb', 'Ah.03g132990' => 'amhyb', 'Ah.14g079410' => 'amhyb', 'AL1G24640' => 'aly', 'AL2G26680' => 'aly', 'AL3G10530' => 'aly', 'AL3G45230' => 'aly', 'AL5G15230' => 'aly', 'AL5G16960' => 'aly', 'AL6G25210' => 'aly', 'Aqoxy2G00441' => 'aox', 'Aqoxy3G01236' => 'aox', 'Aqoxy5G03746' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3RQ047' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C7GMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9C8JER' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MBL6KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YXCZ83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZANX40' => 'arhy', 'AT1G12990' => 'ath', 'AT1G67880' => 'ath', 'AT2G13290' => 'ath', 'AT3G01620' => 'ath', 'AT3G26445' => 'ath', 'AT3G27540' => 'ath', 'AT5G14480' => 'ath', 'ATR0824G026' => 'atr', 'ATR1098G019' => 'atr', 'Atru.chr11.2145' => 'acertr', 'Atru.chr2.3636' => 'acertr', 'Atru.chr2.3644' => 'acertr', 'Atru.chr6.2422' => 'acertr', 'Atru.chr7.1112' => 'acertr', 'AUR62005469' => 'cqu', 'AUR62011166' => 'cqu', 'AUR62013319' => 'cqu', 'AUR62024273' => 'cqu', 'AUR62028420' => 'cqu', 'AUR62041942' => 'cqu', 'BcaB01g04969' => 'bca', 'BcaB01g06371' => 'bca', 'BcaB02g11494' => 'bca', 'BcaB03g15382' => 'bca', 'BcaB08g36994' => 'bca', 'BcaC03g13477' => 'bca', 'BcaC03g13478' => 'bca', 'BcaC03g13480' => 'bca', 'BcaC03g13481' => 'bca', 'BcaC03g13486' => 'bca', 'BcaC04g19031' => 'bca', 'BcaC04g23085' => 'bca', 'BcaC05g25094' => 'bca', 'BcaC05g25096' => 'bca', 'BcaC05g25138' => 'bca', 'BcaC05g30416' => 'bca', 'BcaC05g30455' => 'bca', 'BcaC06g30979' => 'bca', 'BcaC06g33805' => 'bca', 'BcaC08g46021' => 'bca', 'BcaNung03154' => 'bca', 'BolC2t06623H' => 'bol', 'BolC2t06632H' => 'bol', 'BolC2t06635H' => 'bol', 'BolC2t06638H' => 'bol', 'BolC3t13266H' => 'bol', 'BolC5t29776H' => 'bol', 'BolC6t38912H' => 'bol', 'BolC7t44183H' => 'bol', 'BolC9t54123H' => 'bol', 'BolC9t59107H' => 'bol', 'BraA02t05221Z' => 'bra', 'BraA03t09996Z' => 'bra', 'BraA05t23210Z' => 'bra', 'BraA06t24068Z' => 'bra', 'BraA06t27032Z' => 'bra', 'BraA08t35176Z' => 'bra', 'BraA09t36680Z' => 'bra', 'BraA10t44471Z' => 'bra', 'C02p06760' => 'bna', 'C02p06890' => 'bna', 'C02p07010' => 'bna', 'C03p07660' => 'bna', 'C05p10300' => 'bna', 'C06p38150' => 'bna', 'C07p36650' => 'bna', 'C08p15770' => 'bna', 'C09p12300' => 'bna', 'C09p62700' => 'bna', 'C09p75040' => 'bna', 'CAN.G13.1' => 'can', 'CAN.G138.4' => 'can', 'CAN.G44.6' => 'can', 'CAN.G473.19' => 'can', 'CANSAT01G0835' => 'cansat', 'CANSAT11G0246' => 'cansat', 'CANSAT11G1766' => 'cansat', 'CANSAT64G1954' => 'cansat', 'CARHR013330' => 'chi', 'CARHR060530' => 'chi', 'CARHR075300' => 'chi', 'CARHR105120' => 'chi', 'CARHR148910' => 'chi', 'CARHR198830' => 'chi', 'Carub.0001s1275' => 'cru', 'Carub.0002s1437' => 'cru', 'Carub.0003s0044' => 'cru', 'Carub.0003s2787' => 'cru', 'Carub.0005s0597' => 'cru', 'Carub.0006s1266' => 'cru', 'Ca_06935_v3' => 'car', 'Ca_13559_v3' => 'car', 'Ca_16941_v3' => 'car', 'Ca_16960_v3' => 'car', 'Ca_17775_v3' => 'car', 'Ca_30464_v3' => 'car', 'Cc06_g08160' => 'ccan', 'Cc07_g01520' => 'ccan', 'Cc11_g15810' => 'ccan', 'CDE02G2840' => 'cde', 'CDE03G0093' => 'cde', 'CDE04G2127' => 'cde', 'CDE07G1857' => 'cde', 'CDE09G1246' => 'cde', 'Cfa003412' => 'cfa', 'Cfa007341' => 'cfa', 'Cfa009220' => 'cfa', 'Ciclev10008737m.g' => 'ccl', 'Ciclev10015565m.g' => 'ccl', 'Ciclev10031761m.g' => 'ccl', 'CiPaw.03G045300' => 'cil', 'CiPaw.03G247200' => 'cil', 'CiPaw.04G029500' => 'cil', 'CiPaw.04G174000' => 'cil', 'CiPaw.05G181200' => 'cil', 'CiPaw.06G067100' => 'cil', 'ClCG05G025800' => 'cla', 'ClCG06G011400' => 'cla', 'ClCG09G019360' => 'cla', 'COL.COLO4_04827' => 'col', 'COL.COLO4_29170' => 'col', 'COL.COLO4_35131' => 'col', 'COL.COLO4_35132' => 'col', 'Cpa.g.sc33.32' => 'cpa', 'Cpa.g.sc46.29' => 'cpa', 'Cpa.g.sc796.1' => 'cpa', 'CsaV3_1G030420' => 'csa', 'CsaV3_5G027050' => 'csa', 'CsaV3_5G031040' => 'csa', 'CsaV3_UNG023130' => 'csa', 'CSS0007726' => 'camsi', 'CSS0016433' => 'camsi', 'CSS0017656' => 'camsi', 'CSS0025364' => 'camsi', 'CSS0027582' => 'camsi', 'CSS0047288' => 'camsi', 'CSS0049950' => 'camsi', 'DCAR_003843' => 'dca', 'DCAR_007052' => 'dca', 'DCAR_020884' => 'dca', 'DCAR_021730' => 'dca', 'DCAR_024423' => 'dca', 'DCAR_026509' => 'dca', 'DCAR_031158' => 'dca', 'Dinv14728' => 'din', 'Dinv15219' => 'din', 'Dinv25728' => 'din', 'Dinv33428' => 'din', 'Dinv36489' => 'din', 'Dinv41486' => 'din', 'Duzib147G0469' => 'dzi', 'Duzib168G0060' => 'dzi', 'Duzib187G1215' => 'dzi', 'Duzib248G0692' => 'dzi', 'Duzib251G0767' => 'dzi', 'Duzib264G0446' => 'dzi', 'Duzib268G0691' => 'dzi', 'ECA232G4767' => 'eca', 'ECA233G2838' => 'eca', 'ECA234G0391' => 'eca', 'ECA234G0857' => 'eca', 'ECA236G1593' => 'eca', 'ECA238G0565' => 'eca', 'ECA246G1027' => 'eca', 'ECA246G3223' => 'eca', 'ECA246G3470' => 'eca', 'EL10Ac6g13829' => 'bvu', 'EL10Ac6g14093' => 'bvu', 'EL10Ac8g18707' => 'bvu', 'Eucgr.C01369' => 'egr', 'Eucgr.H02492' => 'egr', 'Eucgr.I01733' => 'egr', 'Eucgr.J02255' => 'egr', 'Eucgr.J02257' => 'egr', 'Eucgr.J02258' => 'egr', 'FAN02G1601' => 'fan', 'FAN03G1586' => 'fan', 'FAN03G2986' => 'fan', 'FAN05G4837' => 'fan', 'FAN06G0146' => 'fan', 'FAN07G0858' => 'fan', 'FAN09G3179' => 'fan', 'FAN10G0669' => 'fan', 'FAN12G2358' => 'fan', 'FAN14G4198' => 'fan', 'FAN14G5112' => 'fan', 'FAN17G0342' => 'fan', 'FAN19G0342' => 'fan', 'FAN19G0962' => 'fan', 'FAN19G1101' => 'fan', 'FAN19G1872' => 'fan', 'FAN22G0356' => 'fan', 'FAN23G0744' => 'fan', 'FAN23G1914' => 'fan', 'FAN26G0032' => 'fan', 'FAN28G0625' => 'fan', 'FvH4_1g02710' => 'fve', 'FvH4_1g02720' => 'fve', 'FvH4_4g25670' => 'fve', 'FvH4_6g51700' => 'fve', 'FvH4_7g20170' => 'fve', 'Glyma.05G175000' => 'gma', 'Glyma.08G132300' => 'gma', 'Glyma.11G243000' => 'gma', 'Glyma.13G158900' => 'gma', 'Glyma.17G112400' => 'gma', 'Glyma.18G014100' => 'gma', 'Glyma.19G003100' => 'gma', 'Glyma.19G056500' => 'gma', 'Gohir.A01G158900' => 'ghi', 'Gohir.A05G312600' => 'ghi', 'Gohir.A05G354900' => 'ghi', 'Gohir.A07G037200' => 'ghi', 'Gohir.A09G030000' => 'ghi', 'Gohir.A12G145200' => 'ghi', 'Gohir.D01G151500' => 'ghi', 'Gohir.D04G058300' => 'ghi', 'Gohir.D05G314100' => 'ghi', 'Gohir.D07G041400' => 'ghi', 'Gohir.D09G029700' => 'ghi', 'Gohir.D12G149700' => 'ghi', 'Gorai.001G043800' => 'gra', 'Gorai.002G187800' => 'gra', 'Gorai.006G034700' => 'gra', 'Gorai.008G161200' => 'gra', 'Gorai.009G335700' => 'gra', 'Gorai.012G065000' => 'gra', 'GSVIVG01000535001' => 'vvi', 'GSVIVG01015572001' => 'vvi', 'GSVIVG01032386001' => 'vvi', 'HanXRQChr05g0138531' => 'han', 'HanXRQChr06g0174391' => 'han', 'HanXRQChr07g0199021' => 'han', 'HanXRQChr08g0208211' => 'han', 'HanXRQChr09g0255471' => 'han', 'HanXRQChr10g0315791' => 'han', 'HanXRQChr12g0371991' => 'han', 'HanXRQChr15g0475251' => 'han', 'HanXRQChr17g0540001' => 'han', 'HanXRQChr17g0548631' => 'han', 'HanXRQChr17g0569561' => 'han', 'Haze_12256' => 'cav', 'Haze_14756' => 'cav', 'Haze_25528' => 'cav', 'Hma1.2p1_0079F.1_g041020' => 'hma', 'Hma1.2p1_0818F.1_g223260' => 'hma', 'Hma1.2p1_1747F.1_g300530' => 'hma', 'HPP92_004607' => 'vpl', 'HPP92_004608' => 'vpl', 'HPP92_006181' => 'vpl', 'HPP92_012192' => 'vpl', 'HPP92_015680' => 'vpl', 'HPP92_020249' => 'vpl', 'HPP92_021376' => 'vpl', 'HPP92_024275' => 'vpl', 'Hund06031' => 'sun', 'Hund25391' => 'sun', 'Lalb_Chr07g0185371' => 'lal', 'Lalb_Chr07g0185381' => 'lal', 'Lalb_Chr12g0204011' => 'lal', 'Lalb_Chr13g0301671' => 'lal', 'Lalb_Chr14g0362851' => 'lal', 'Lalb_Chr24g0403581' => 'lal', 'Lj1g0000233' => 'lja', 'Lj2g0018120' => 'lja', 'Lj3C621T0' => 'lonja', 'Lj3P1059T14' => 'lonja', 'Lj3P611T9' => 'lonja', 'Lj3P614T13' => 'lonja', 'Lj3P615T5' => 'lonja', 'Lj4g0012315' => 'lja', 'Lj4g0026182' => 'lja', 'Lj6P813T16' => 'lonja', 'Lj7C427T7' => 'lonja', 'Lj7C427T8' => 'lonja', 'Lj7P600T41' => 'lonja', 'Lju41C42G17' => 'lonja', 'Lsat_1_v5_gn_0_47300' => 'lsa', 'Lsat_1_v5_gn_2_91280' => 'lsa', 'Lsat_1_v5_gn_3_30561' => 'lsa', 'Lsat_1_v5_gn_4_184321' => 'lsa', 'Lsat_1_v5_gn_4_4041' => 'lsa', 'Lsat_1_v5_gn_5_92000' => 'lsa', 'Lsat_1_v5_gn_8_152940' => 'lsa', 'Lsat_1_v5_gn_8_62401' => 'lsa', 'Manes.06G055900' => 'mes', 'Manes.12G022200' => 'mes', 'Manes.13G023300' => 'mes', 'Manes.14G115000' => 'mes', 'Manes.15G151700' => 'mes', 'Manes.17G111300' => 'mes', 'Mapoly0226s0009' => 'mpo', 'MBI02_g25363_MAGBIO' => 'mbi', 'MBI06_g00027_MAGBIO' => 'mbi', 'MBI10_g13034_MAGBIO' => 'mbi', 'MD09G1023400' => 'mdo', 'MD13G1100100' => 'mdo', 'MD15G1169200' => 'mdo', 'MD16G1101100' => 'mdo', 'MD17G1022900' => 'mdo', 'Medtr3g096150' => 'mtr', 'Medtr4g115070' => 'mtr', 'Medtr7g033325' => 'mtr', 'Medtr8g089840' => 'mtr', 'MELO3C010319.2' => 'cme', 'MELO3C011944.2' => 'cme', 'MELO3C021589.2' => 'cme', 'Migut.E00207' => 'egut', 'Migut.H00067' => 'egut', 'Migut.K00433' => 'egut', 'Migut.K00606' => 'egut', 'Migut.K01410' => 'egut', 'MSTRG.13347' => 'ama', 'MSTRG.24045' => 'ama', 'MSTRG.2428' => 'ama', 'MSTRG.26410' => 'ama', 'MSTRG.3139' => 'ama', 'MSTRG.3286' => 'ama', 'MSTRG.563' => 'ama', 'MSTRG.7941' => 'ama', 'Nitab4.5_0000028g0060' => 'nta', 'Nitab4.5_0000065g0260' => 'nta', 'Nitab4.5_0000112g0060' => 'nta', 'Nitab4.5_0000489g0120' => 'nta', 'Nitab4.5_0001776g0050' => 'nta', 'Nitab4.5_0001854g0010' => 'nta', 'Nitab4.5_0001860g0020' => 'nta', 'Nitab4.5_0004352g0010' => 'nta', 'Nitab4.5_0008716g0020' => 'nta', 'Nitab4.5_0008922g0010' => 'nta', 'Nn3g16693' => 'nnu', 'Nn4g22596' => 'nnu', 'Nn7g37639' => 'nnu', 'Oeu001701.1' => 'oeu', 'Oeu018149.1' => 'oeu', 'Oeu026220.1' => 'oeu', 'Oeu038635.1' => 'oeu', 'Oeu049176.1' => 'oeu', 'Oeu056706.1' => 'oeu', 'Oeu056937.1' => 'oeu', 'Oeu057540.1' => 'oeu', 'Os02g0594900' => 'osa', 'Os02g0595100' => 'osa', 'Os04g0477500' => 'osa', 'Os12g0611900' => 'osa', 'Peaxi162Scf00076g00020' => 'pax', 'Peaxi162Scf00128g00217' => 'pax', 'Peaxi162Scf00129g01640' => 'pax', 'Peaxi162Scf00669g00007' => 'pax', 'Peaxi162Scf00700g00421' => 'pax', 'Peaxi162Scf00801g00038' => 'pax', 'Peaxi162Scf00891g00025' => 'pax', 'PGR083G0909' => 'pgr', 'PGR119G1005' => 'pgr', 'PGR142G2236' => 'pgr', 'PGR142G3388' => 'pgr', 'PGSC0003DMG400004514' => 'stu', 'PGSC0003DMG400012635' => 'stu', 'PGSC0003DMG400015730' => 'stu', 'PGSC0003DMG400018611' => 'stu', 'PGSC0003DMG400030897' => 'stu', 'Phvul.001G254800' => 'pvu', 'Phvul.002G260100' => 'pvu', 'Phvul.003G167600' => 'pvu', 'Phvul.004G005100' => 'pvu', 'Potri.001G343600' => 'ptr', 'Potri.006G066700' => 'ptr', 'Potri.008G186000' => 'ptr', 'Potri.010G046900' => 'ptr', 'Potri.018G127900' => 'ptr', 'Pp3c20_17750' => 'ppa', 'Pp3c24_4380' => 'ppa', 'Prupe.1G245800' => 'ppe', 'Prupe.3G293400' => 'ppe', 'Prupe.7G247400' => 'ppe', 'Psat0s145g0120' => 'psa', 'Psat0s595g0040' => 'psa', 'Psat0s595g0120' => 'psa', 'Psat3g175040' => 'psa', 'Psat7g058120' => 'psa', 'PSO017G0428' => 'pso', 'PSO063G7510' => 'pso', 'PSO067G0046' => 'pso', 'PSO478G1073' => 'pso', 'PSO675G3677' => 'pso', 'PSO675G6558' => 'pso', 'PSO675G7520' => 'pso', 'PSO675G8959' => 'pso', 'QL02p074089' => 'qlo', 'QL02p089614' => 'qlo', 'QL03p057736' => 'qlo', 'RcHm_v2.0_Chr1g0364131' => 'rch', 'RcHm_v2.0_Chr2g0087801' => 'rch', 'RcHm_v2.0_Chr2g0087821' => 'rch', 'RcHm_v2.0_Chr2g0173231' => 'rch', 'RcHm_v2.0_Chr4g0433111' => 'rch', 'Rhsim03G0250300' => 'rsi', 'Rhsim08G0048400' => 'rsi', 'Rhsim10G0014800' => 'rsi', 'Rhsim12G0040100' => 'rsi', 'Rhsim12G0109700' => 'rsi', 'Sabra06G0049600' => 'sbr', 'Sabra08G0141000' => 'sbr', 'Sabra10G0021400' => 'sbr', 'Sabra16G0222900' => 'sbr', 'Sabra18G0108600' => 'sbr', 'SalBow1G0433' => 'sbo', 'SalBow1G2038' => 'sbo', 'SalBow1G5003' => 'sbo', 'SalBow7G1197' => 'sbo', 'SalBow8G3506' => 'sbo', 'Sc03g0007300' => 'sci', 'Sc11g0000950' => 'sci', 'Sc14g0008750' => 'sci', 'Sc18g0000420' => 'sci', 'Sed0006754' => 'sed', 'Sed0008741' => 'sed', 'Sed0017172' => 'sed', 'Sed0018925' => 'sed', 'Sed0023326' => 'sed', 'Sed0025909' => 'sed', 'SEGI_05333' => 'sgi', 'SEGI_10362' => 'sgi', 'SEGI_13380' => 'sgi', 'SEGI_24306' => 'sgi', 'SEGI_29077' => 'sgi', 'SEGI_29095' => 'sgi', 'SEGI_36534' => 'sgi', 'SEGI_37506' => 'sgi', 'SEGI_38321' => 'sgi', 'SGA_v2.0_scaffold307G48031' => 'sas', 'SGA_v2.0_scaffold47G17507' => 'sas', 'SGA_v2.0_scaffold63G21736' => 'sas', 'SGA_v2.0_scaffold87G27070' => 'sas', 'SHI17794' => 'shi', 'SHI28851' => 'shi', 'SMO165G0155' => 'smo', 'SMO340G0217' => 'smo', 'SMO367G1210' => 'smo', 'Solyc02g093430.3' => 'sly', 'Solyc05g013580.4' => 'sly', 'Solyc07g008030.3' => 'sly', 'Solyc12g035470.2' => 'sly', 'Sopen02g038020' => 'spe', 'Sopen05g008490' => 'spe', 'Sopen07g003910' => 'spe', 'Sopen12g015240' => 'spe', 'Sp1g11550' => 'spa', 'Sp2g16710' => 'spa', 'Sp3g00430' => 'spa', 'Sp3g26780' => 'spa', 'Sp5g22900' => 'spa', 'Sp6g29530' => 'spa', 'TAR371G0794' => 'tar', 'TAR374G0164' => 'tar', 'TAR622G0165' => 'tar', 'TAR626G0929' => 'tar', 'TAR629G2155' => 'tar', 'THA.LOC104805282' => 'tha', 'THA.LOC104805363' => 'tha', 'THA.LOC104808968' => 'tha', 'THA.LOC104821093' => 'tha', 'THA.LOC104823953' => 'tha', 'THA.LOC104825562' => 'tha', 'THA.LOC104825665' => 'tha', 'Thecc.02G261400' => 'tca', 'Thecc.04G019200' => 'tca', 'Thecc.09G130400' => 'tca', 'Thhalv10004374m.g' => 'esa', 'Thhalv10007850m.g' => 'esa', 'Thhalv10013782m.g' => 'esa', 'Thhalv10018686m.g' => 'esa', 'Thhalv10020899m.g' => 'esa', 'Thhalv10022755m.g' => 'esa', 'TPR.G23851' => 'tpr', 'TPR.G26500' => 'tpr', 'TPR.G27267' => 'tpr', 'TPR.G32001' => 'tpr', 'TPR.G6251' => 'tpr', 'TPR.G8167' => 'tpr', 'TWI12G1330' => 'twi', 'TWI18G1239' => 'twi', 'TWI34G0979' => 'twi', 'TWI36G0670' => 'twi', 'TWI36G0707' => 'twi', 'TWI56G0233' => 'twi', 'TWI75G1809' => 'twi', 'unitig_21.g20874' => 'ugi', 'unitig_26.g10343' => 'ugi', 'unitig_46.g18392' => 'ugi', 'unitig_52.g17178' => 'ugi', 'unitig_8.g2934' => 'ugi', 'vmacro01122' => 'vma', 'vmacro05875' => 'vma', 'vmacro06147' => 'vma', 'vmacro16191' => 'vma', 'vmacro18293' => 'vma', 'VMungo0251G3707' => 'vmu', 'VMungo0464G1521' => 'vmu', 'VMungo1215G0205' => 'vmu', 'VMungo1383G2484' => 'vmu', 'Zm00001eb079610' => 'zma', 'Zm00001eb135990' => 'zma', 'Zm00001eb183710' => 'zma', 'Zm00001eb246020' => 'zma' ), 'gf_id' => 'HOM05D001124', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001124' ), 'data_identifier' => 'HOM05D001124', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001124', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '548', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02520' => 'bna', 'A03p06630' => 'bna', 'A05p44460' => 'bna', 'A06p08710' => 'bna', 'A06p41090' => 'bna', 'A07p32320' => 'bna', 'A08p32520' => 'bna', 'A09p10360' => 'bna', 'A10p24080' => 'bna', 'Aa31LG11G15250' => 'aar', 'Aa31LG1G1800' => 'aar', 'Aa31LG2G5120' => 'aar', 'Aa31LG2G6070' => 'aar', 'Aa31LG5G10770' => 'aar', 'Aa31sc61G90' => 'aar', 'Actinidia01352' => 'ach', 'Actinidia05983' => 'ach', 'Actinidia08133' => 'ach', 'Actinidia15101' => 'ach', 'Actinidia26379' => 'ach', 'Actinidia35778' => 'ach', 'Actinidia36123' => 'ach', 'Actinidia37436' => 'ach', 'Actinidia38730' => 'ach', 'Ah.02g128210' => 'amhyb', 'Ah.03g132990' => 'amhyb', 'Ah.14g079410' => 'amhyb', 'AL1G24640' => 'aly', 'AL2G26680' => 'aly', 'AL3G10530' => 'aly', 'AL3G45230' => 'aly', 'AL5G15230' => 'aly', 'AL5G16960' => 'aly', 'AL6G25210' => 'aly', 'Aqoxy2G00441' => 'aox', 'Aqoxy3G01236' => 'aox', 'Aqoxy5G03746' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3RQ047' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C7GMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9C8JER' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MBL6KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YXCZ83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZANX40' => 'arhy', 'AT1G12990' => 'ath', 'AT1G67880' => 'ath', 'AT2G13290' => 'ath', 'AT3G01620' => 'ath', 'AT3G26445' => 'ath', 'AT3G27540' => 'ath', 'AT5G14480' => 'ath', 'ATR0824G026' => 'atr', 'ATR1098G019' => 'atr', 'Atru.chr11.2145' => 'acertr', 'Atru.chr2.3636' => 'acertr', 'Atru.chr2.3644' => 'acertr', 'Atru.chr6.2422' => 'acertr', 'Atru.chr7.1112' => 'acertr', 'AUR62005469' => 'cqu', 'AUR62011166' => 'cqu', 'AUR62013319' => 'cqu', 'AUR62024273' => 'cqu', 'AUR62028420' => 'cqu', 'AUR62041942' => 'cqu', 'BcaB01g04969' => 'bca', 'BcaB01g06371' => 'bca', 'BcaB02g11494' => 'bca', 'BcaB03g15382' => 'bca', 'BcaB08g36994' => 'bca', 'BcaC03g13477' => 'bca', 'BcaC03g13478' => 'bca', 'BcaC03g13480' => 'bca', 'BcaC03g13481' => 'bca', 'BcaC03g13486' => 'bca', 'BcaC04g19031' => 'bca', 'BcaC04g23085' => 'bca', 'BcaC05g25094' => 'bca', 'BcaC05g25096' => 'bca', 'BcaC05g25138' => 'bca', 'BcaC05g30416' => 'bca', 'BcaC05g30455' => 'bca', 'BcaC06g30979' => 'bca', 'BcaC06g33805' => 'bca', 'BcaC08g46021' => 'bca', 'BcaNung03154' => 'bca', 'BolC2t06623H' => 'bol', 'BolC2t06632H' => 'bol', 'BolC2t06635H' => 'bol', 'BolC2t06638H' => 'bol', 'BolC3t13266H' => 'bol', 'BolC5t29776H' => 'bol', 'BolC6t38912H' => 'bol', 'BolC7t44183H' => 'bol', 'BolC9t54123H' => 'bol', 'BolC9t59107H' => 'bol', 'BraA02t05221Z' => 'bra', 'BraA03t09996Z' => 'bra', 'BraA05t23210Z' => 'bra', 'BraA06t24068Z' => 'bra', 'BraA06t27032Z' => 'bra', 'BraA08t35176Z' => 'bra', 'BraA09t36680Z' => 'bra', 'BraA10t44471Z' => 'bra', 'C02p06760' => 'bna', 'C02p06890' => 'bna', 'C02p07010' => 'bna', 'C03p07660' => 'bna', 'C05p10300' => 'bna', 'C06p38150' => 'bna', 'C07p36650' => 'bna', 'C08p15770' => 'bna', 'C09p12300' => 'bna', 'C09p62700' => 'bna', 'C09p75040' => 'bna', 'CAN.G13.1' => 'can', 'CAN.G138.4' => 'can', 'CAN.G44.6' => 'can', 'CAN.G473.19' => 'can', 'CANSAT01G0835' => 'cansat', 'CANSAT11G0246' => 'cansat', 'CANSAT11G1766' => 'cansat', 'CANSAT64G1954' => 'cansat', 'CARHR013330' => 'chi', 'CARHR060530' => 'chi', 'CARHR075300' => 'chi', 'CARHR105120' => 'chi', 'CARHR148910' => 'chi', 'CARHR198830' => 'chi', 'Carub.0001s1275' => 'cru', 'Carub.0002s1437' => 'cru', 'Carub.0003s0044' => 'cru', 'Carub.0003s2787' => 'cru', 'Carub.0005s0597' => 'cru', 'Carub.0006s1266' => 'cru', 'Ca_06935_v3' => 'car', 'Ca_13559_v3' => 'car', 'Ca_16941_v3' => 'car', 'Ca_16960_v3' => 'car', 'Ca_17775_v3' => 'car', 'Ca_30464_v3' => 'car', 'Cc06_g08160' => 'ccan', 'Cc07_g01520' => 'ccan', 'Cc11_g15810' => 'ccan', 'CDE02G2840' => 'cde', 'CDE03G0093' => 'cde', 'CDE04G2127' => 'cde', 'CDE07G1857' => 'cde', 'CDE09G1246' => 'cde', 'Cfa003412' => 'cfa', 'Cfa007341' => 'cfa', 'Cfa009220' => 'cfa', 'Ciclev10008737m.g' => 'ccl', 'Ciclev10015565m.g' => 'ccl', 'Ciclev10031761m.g' => 'ccl', 'CiPaw.03G045300' => 'cil', 'CiPaw.03G247200' => 'cil', 'CiPaw.04G029500' => 'cil', 'CiPaw.04G174000' => 'cil', 'CiPaw.05G181200' => 'cil', 'CiPaw.06G067100' => 'cil', 'ClCG05G025800' => 'cla', 'ClCG06G011400' => 'cla', 'ClCG09G019360' => 'cla', 'COL.COLO4_04827' => 'col', 'COL.COLO4_29170' => 'col', 'COL.COLO4_35131' => 'col', 'COL.COLO4_35132' => 'col', 'Cpa.g.sc33.32' => 'cpa', 'Cpa.g.sc46.29' => 'cpa', 'Cpa.g.sc796.1' => 'cpa', 'CsaV3_1G030420' => 'csa', 'CsaV3_5G027050' => 'csa', 'CsaV3_5G031040' => 'csa', 'CsaV3_UNG023130' => 'csa', 'CSS0007726' => 'camsi', 'CSS0016433' => 'camsi', 'CSS0017656' => 'camsi', 'CSS0025364' => 'camsi', 'CSS0027582' => 'camsi', 'CSS0047288' => 'camsi', 'CSS0049950' => 'camsi', 'DCAR_003843' => 'dca', 'DCAR_007052' => 'dca', 'DCAR_020884' => 'dca', 'DCAR_021730' => 'dca', 'DCAR_024423' => 'dca', 'DCAR_026509' => 'dca', 'DCAR_031158' => 'dca', 'Dinv14728' => 'din', 'Dinv15219' => 'din', 'Dinv25728' => 'din', 'Dinv33428' => 'din', 'Dinv36489' => 'din', 'Dinv41486' => 'din', 'Duzib147G0469' => 'dzi', 'Duzib168G0060' => 'dzi', 'Duzib187G1215' => 'dzi', 'Duzib248G0692' => 'dzi', 'Duzib251G0767' => 'dzi', 'Duzib264G0446' => 'dzi', 'Duzib268G0691' => 'dzi', 'ECA232G4767' => 'eca', 'ECA233G2838' => 'eca', 'ECA234G0391' => 'eca', 'ECA234G0857' => 'eca', 'ECA236G1593' => 'eca', 'ECA238G0565' => 'eca', 'ECA246G1027' => 'eca', 'ECA246G3223' => 'eca', 'ECA246G3470' => 'eca', 'EL10Ac6g13829' => 'bvu', 'EL10Ac6g14093' => 'bvu', 'EL10Ac8g18707' => 'bvu', 'Eucgr.C01369' => 'egr', 'Eucgr.H02492' => 'egr', 'Eucgr.I01733' => 'egr', 'Eucgr.J02255' => 'egr', 'Eucgr.J02257' => 'egr', 'Eucgr.J02258' => 'egr', 'FAN02G1601' => 'fan', 'FAN03G1586' => 'fan', 'FAN03G2986' => 'fan', 'FAN05G4837' => 'fan', 'FAN06G0146' => 'fan', 'FAN07G0858' => 'fan', 'FAN09G3179' => 'fan', 'FAN10G0669' => 'fan', 'FAN12G2358' => 'fan', 'FAN14G4198' => 'fan', 'FAN14G5112' => 'fan', 'FAN17G0342' => 'fan', 'FAN19G0342' => 'fan', 'FAN19G0962' => 'fan', 'FAN19G1101' => 'fan', 'FAN19G1872' => 'fan', 'FAN22G0356' => 'fan', 'FAN23G0744' => 'fan', 'FAN23G1914' => 'fan', 'FAN26G0032' => 'fan', 'FAN28G0625' => 'fan', 'FvH4_1g02710' => 'fve', 'FvH4_1g02720' => 'fve', 'FvH4_4g25670' => 'fve', 'FvH4_6g51700' => 'fve', 'FvH4_7g20170' => 'fve', 'Glyma.05G175000' => 'gma', 'Glyma.08G132300' => 'gma', 'Glyma.11G243000' => 'gma', 'Glyma.13G158900' => 'gma', 'Glyma.17G112400' => 'gma', 'Glyma.18G014100' => 'gma', 'Glyma.19G003100' => 'gma', 'Glyma.19G056500' => 'gma', 'Gohir.A01G158900' => 'ghi', 'Gohir.A05G312600' => 'ghi', 'Gohir.A05G354900' => 'ghi', 'Gohir.A07G037200' => 'ghi', 'Gohir.A09G030000' => 'ghi', 'Gohir.A12G145200' => 'ghi', 'Gohir.D01G151500' => 'ghi', 'Gohir.D04G058300' => 'ghi', 'Gohir.D05G314100' => 'ghi', 'Gohir.D07G041400' => 'ghi', 'Gohir.D09G029700' => 'ghi', 'Gohir.D12G149700' => 'ghi', 'Gorai.001G043800' => 'gra', 'Gorai.002G187800' => 'gra', 'Gorai.006G034700' => 'gra', 'Gorai.008G161200' => 'gra', 'Gorai.009G335700' => 'gra', 'Gorai.012G065000' => 'gra', 'GSVIVG01000535001' => 'vvi', 'GSVIVG01015572001' => 'vvi', 'GSVIVG01032386001' => 'vvi', 'HanXRQChr05g0138531' => 'han', 'HanXRQChr06g0174391' => 'han', 'HanXRQChr07g0199021' => 'han', 'HanXRQChr08g0208211' => 'han', 'HanXRQChr09g0255471' => 'han', 'HanXRQChr10g0315791' => 'han', 'HanXRQChr12g0371991' => 'han', 'HanXRQChr15g0475251' => 'han', 'HanXRQChr17g0540001' => 'han', 'HanXRQChr17g0548631' => 'han', 'HanXRQChr17g0569561' => 'han', 'Haze_12256' => 'cav', 'Haze_14756' => 'cav', 'Haze_25528' => 'cav', 'Hma1.2p1_0079F.1_g041020' => 'hma', 'Hma1.2p1_0818F.1_g223260' => 'hma', 'Hma1.2p1_1747F.1_g300530' => 'hma', 'HPP92_004607' => 'vpl', 'HPP92_004608' => 'vpl', 'HPP92_006181' => 'vpl', 'HPP92_012192' => 'vpl', 'HPP92_015680' => 'vpl', 'HPP92_020249' => 'vpl', 'HPP92_021376' => 'vpl', 'HPP92_024275' => 'vpl', 'Hund06031' => 'sun', 'Hund25391' => 'sun', 'Lalb_Chr07g0185371' => 'lal', 'Lalb_Chr07g0185381' => 'lal', 'Lalb_Chr12g0204011' => 'lal', 'Lalb_Chr13g0301671' => 'lal', 'Lalb_Chr14g0362851' => 'lal', 'Lalb_Chr24g0403581' => 'lal', 'Lj1g0000233' => 'lja', 'Lj2g0018120' => 'lja', 'Lj3C621T0' => 'lonja', 'Lj3P1059T14' => 'lonja', 'Lj3P611T9' => 'lonja', 'Lj3P614T13' => 'lonja', 'Lj3P615T5' => 'lonja', 'Lj4g0012315' => 'lja', 'Lj4g0026182' => 'lja', 'Lj6P813T16' => 'lonja', 'Lj7C427T7' => 'lonja', 'Lj7C427T8' => 'lonja', 'Lj7P600T41' => 'lonja', 'Lju41C42G17' => 'lonja', 'Lsat_1_v5_gn_0_47300' => 'lsa', 'Lsat_1_v5_gn_2_91280' => 'lsa', 'Lsat_1_v5_gn_3_30561' => 'lsa', 'Lsat_1_v5_gn_4_184321' => 'lsa', 'Lsat_1_v5_gn_4_4041' => 'lsa', 'Lsat_1_v5_gn_5_92000' => 'lsa', 'Lsat_1_v5_gn_8_152940' => 'lsa', 'Lsat_1_v5_gn_8_62401' => 'lsa', 'Manes.06G055900' => 'mes', 'Manes.12G022200' => 'mes', 'Manes.13G023300' => 'mes', 'Manes.14G115000' => 'mes', 'Manes.15G151700' => 'mes', 'Manes.17G111300' => 'mes', 'Mapoly0226s0009' => 'mpo', 'MBI02_g25363_MAGBIO' => 'mbi', 'MBI06_g00027_MAGBIO' => 'mbi', 'MBI10_g13034_MAGBIO' => 'mbi', 'MD09G1023400' => 'mdo', 'MD13G1100100' => 'mdo', 'MD15G1169200' => 'mdo', 'MD16G1101100' => 'mdo', 'MD17G1022900' => 'mdo', 'Medtr3g096150' => 'mtr', 'Medtr4g115070' => 'mtr', 'Medtr7g033325' => 'mtr', 'Medtr8g089840' => 'mtr', 'MELO3C010319.2' => 'cme', 'MELO3C011944.2' => 'cme', 'MELO3C021589.2' => 'cme', 'Migut.E00207' => 'egut', 'Migut.H00067' => 'egut', 'Migut.K00433' => 'egut', 'Migut.K00606' => 'egut', 'Migut.K01410' => 'egut', 'MSTRG.13347' => 'ama', 'MSTRG.24045' => 'ama', 'MSTRG.2428' => 'ama', 'MSTRG.26410' => 'ama', 'MSTRG.3139' => 'ama', 'MSTRG.3286' => 'ama', 'MSTRG.563' => 'ama', 'MSTRG.7941' => 'ama', 'Nitab4.5_0000028g0060' => 'nta', 'Nitab4.5_0000065g0260' => 'nta', 'Nitab4.5_0000112g0060' => 'nta', 'Nitab4.5_0000489g0120' => 'nta', 'Nitab4.5_0001776g0050' => 'nta', 'Nitab4.5_0001854g0010' => 'nta', 'Nitab4.5_0001860g0020' => 'nta', 'Nitab4.5_0004352g0010' => 'nta', 'Nitab4.5_0008716g0020' => 'nta', 'Nitab4.5_0008922g0010' => 'nta', 'Nn3g16693' => 'nnu', 'Nn4g22596' => 'nnu', 'Nn7g37639' => 'nnu', 'Oeu001701.1' => 'oeu', 'Oeu018149.1' => 'oeu', 'Oeu026220.1' => 'oeu', 'Oeu038635.1' => 'oeu', 'Oeu049176.1' => 'oeu', 'Oeu056706.1' => 'oeu', 'Oeu056937.1' => 'oeu', 'Oeu057540.1' => 'oeu', 'Os02g0594900' => 'osa', 'Os02g0595100' => 'osa', 'Os04g0477500' => 'osa', 'Os12g0611900' => 'osa', 'Peaxi162Scf00076g00020' => 'pax', 'Peaxi162Scf00128g00217' => 'pax', 'Peaxi162Scf00129g01640' => 'pax', 'Peaxi162Scf00669g00007' => 'pax', 'Peaxi162Scf00700g00421' => 'pax', 'Peaxi162Scf00801g00038' => 'pax', 'Peaxi162Scf00891g00025' => 'pax', 'PGR083G0909' => 'pgr', 'PGR119G1005' => 'pgr', 'PGR142G2236' => 'pgr', 'PGR142G3388' => 'pgr', 'PGSC0003DMG400004514' => 'stu', 'PGSC0003DMG400012635' => 'stu', 'PGSC0003DMG400015730' => 'stu', 'PGSC0003DMG400018611' => 'stu', 'PGSC0003DMG400030897' => 'stu', 'Phvul.001G254800' => 'pvu', 'Phvul.002G260100' => 'pvu', 'Phvul.003G167600' => 'pvu', 'Phvul.004G005100' => 'pvu', 'Potri.001G343600' => 'ptr', 'Potri.006G066700' => 'ptr', 'Potri.008G186000' => 'ptr', 'Potri.010G046900' => 'ptr', 'Potri.018G127900' => 'ptr', 'Pp3c20_17750' => 'ppa', 'Pp3c24_4380' => 'ppa', 'Prupe.1G245800' => 'ppe', 'Prupe.3G293400' => 'ppe', 'Prupe.7G247400' => 'ppe', 'Psat0s145g0120' => 'psa', 'Psat0s595g0040' => 'psa', 'Psat0s595g0120' => 'psa', 'Psat3g175040' => 'psa', 'Psat7g058120' => 'psa', 'PSO017G0428' => 'pso', 'PSO063G7510' => 'pso', 'PSO067G0046' => 'pso', 'PSO478G1073' => 'pso', 'PSO675G3677' => 'pso', 'PSO675G6558' => 'pso', 'PSO675G7520' => 'pso', 'PSO675G8959' => 'pso', 'QL02p074089' => 'qlo', 'QL02p089614' => 'qlo', 'QL03p057736' => 'qlo', 'RcHm_v2.0_Chr1g0364131' => 'rch', 'RcHm_v2.0_Chr2g0087801' => 'rch', 'RcHm_v2.0_Chr2g0087821' => 'rch', 'RcHm_v2.0_Chr2g0173231' => 'rch', 'RcHm_v2.0_Chr4g0433111' => 'rch', 'Rhsim03G0250300' => 'rsi', 'Rhsim08G0048400' => 'rsi', 'Rhsim10G0014800' => 'rsi', 'Rhsim12G0040100' => 'rsi', 'Rhsim12G0109700' => 'rsi', 'Sabra06G0049600' => 'sbr', 'Sabra08G0141000' => 'sbr', 'Sabra10G0021400' => 'sbr', 'Sabra16G0222900' => 'sbr', 'Sabra18G0108600' => 'sbr', 'SalBow1G0433' => 'sbo', 'SalBow1G2038' => 'sbo', 'SalBow1G5003' => 'sbo', 'SalBow7G1197' => 'sbo', 'SalBow8G3506' => 'sbo', 'Sc03g0007300' => 'sci', 'Sc11g0000950' => 'sci', 'Sc14g0008750' => 'sci', 'Sc18g0000420' => 'sci', 'Sed0006754' => 'sed', 'Sed0008741' => 'sed', 'Sed0017172' => 'sed', 'Sed0018925' => 'sed', 'Sed0023326' => 'sed', 'Sed0025909' => 'sed', 'SEGI_05333' => 'sgi', 'SEGI_10362' => 'sgi', 'SEGI_13380' => 'sgi', 'SEGI_24306' => 'sgi', 'SEGI_29077' => 'sgi', 'SEGI_29095' => 'sgi', 'SEGI_36534' => 'sgi', 'SEGI_37506' => 'sgi', 'SEGI_38321' => 'sgi', 'SGA_v2.0_scaffold307G48031' => 'sas', 'SGA_v2.0_scaffold47G17507' => 'sas', 'SGA_v2.0_scaffold63G21736' => 'sas', 'SGA_v2.0_scaffold87G27070' => 'sas', 'SHI17794' => 'shi', 'SHI28851' => 'shi', 'SMO165G0155' => 'smo', 'SMO340G0217' => 'smo', 'SMO367G1210' => 'smo', 'Solyc02g093430.3' => 'sly', 'Solyc05g013580.4' => 'sly', 'Solyc07g008030.3' => 'sly', 'Solyc12g035470.2' => 'sly', 'Sopen02g038020' => 'spe', 'Sopen05g008490' => 'spe', 'Sopen07g003910' => 'spe', 'Sopen12g015240' => 'spe', 'Sp1g11550' => 'spa', 'Sp2g16710' => 'spa', 'Sp3g00430' => 'spa', 'Sp3g26780' => 'spa', 'Sp5g22900' => 'spa', 'Sp6g29530' => 'spa', 'TAR371G0794' => 'tar', 'TAR374G0164' => 'tar', 'TAR622G0165' => 'tar', 'TAR626G0929' => 'tar', 'TAR629G2155' => 'tar', 'THA.LOC104805282' => 'tha', 'THA.LOC104805363' => 'tha', 'THA.LOC104808968' => 'tha', 'THA.LOC104821093' => 'tha', 'THA.LOC104823953' => 'tha', 'THA.LOC104825562' => 'tha', 'THA.LOC104825665' => 'tha', 'Thecc.02G261400' => 'tca', 'Thecc.04G019200' => 'tca', 'Thecc.09G130400' => 'tca', 'Thhalv10004374m.g' => 'esa', 'Thhalv10007850m.g' => 'esa', 'Thhalv10013782m.g' => 'esa', 'Thhalv10018686m.g' => 'esa', 'Thhalv10020899m.g' => 'esa', 'Thhalv10022755m.g' => 'esa', 'TPR.G23851' => 'tpr', 'TPR.G26500' => 'tpr', 'TPR.G27267' => 'tpr', 'TPR.G32001' => 'tpr', 'TPR.G6251' => 'tpr', 'TPR.G8167' => 'tpr', 'TWI12G1330' => 'twi', 'TWI18G1239' => 'twi', 'TWI34G0979' => 'twi', 'TWI36G0670' => 'twi', 'TWI36G0707' => 'twi', 'TWI56G0233' => 'twi', 'TWI75G1809' => 'twi', 'unitig_21.g20874' => 'ugi', 'unitig_26.g10343' => 'ugi', 'unitig_46.g18392' => 'ugi', 'unitig_52.g17178' => 'ugi', 'unitig_8.g2934' => 'ugi', 'vmacro01122' => 'vma', 'vmacro05875' => 'vma', 'vmacro06147' => 'vma', 'vmacro16191' => 'vma', 'vmacro18293' => 'vma', 'VMungo0251G3707' => 'vmu', 'VMungo0464G1521' => 'vmu', 'VMungo1215G0205' => 'vmu', 'VMungo1383G2484' => 'vmu', 'Zm00001eb079610' => 'zma', 'Zm00001eb135990' => 'zma', 'Zm00001eb183710' => 'zma', 'Zm00001eb246020' => 'zma' ) $gf_id = 'HOM05D001124' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001124' ) $data_identifier = 'HOM05D001124' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 6, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 7, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 21, 'bol' => (int) 10, 'bra' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 6, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 9, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 21, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 8, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 10, 'lsa' => (int) 8, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 8, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 9, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb246020' $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' => 'HOM05D001124', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '548', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02520' => 'bna', 'A03p06630' => 'bna', 'A05p44460' => 'bna', 'A06p08710' => 'bna', 'A06p41090' => 'bna', 'A07p32320' => 'bna', 'A08p32520' => 'bna', 'A09p10360' => 'bna', 'A10p24080' => 'bna', 'Aa31LG11G15250' => 'aar', 'Aa31LG1G1800' => 'aar', 'Aa31LG2G5120' => 'aar', 'Aa31LG2G6070' => 'aar', 'Aa31LG5G10770' => 'aar', 'Aa31sc61G90' => 'aar', 'Actinidia01352' => 'ach', 'Actinidia05983' => 'ach', 'Actinidia08133' => 'ach', 'Actinidia15101' => 'ach', 'Actinidia26379' => 'ach', 'Actinidia35778' => 'ach', 'Actinidia36123' => 'ach', 'Actinidia37436' => 'ach', 'Actinidia38730' => 'ach', 'Ah.02g128210' => 'amhyb', 'Ah.03g132990' => 'amhyb', 'Ah.14g079410' => 'amhyb', 'AL1G24640' => 'aly', 'AL2G26680' => 'aly', 'AL3G10530' => 'aly', 'AL3G45230' => 'aly', 'AL5G15230' => 'aly', 'AL5G16960' => 'aly', 'AL6G25210' => 'aly', 'Aqoxy2G00441' => 'aox', 'Aqoxy3G01236' => 'aox', 'Aqoxy5G03746' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3RQ047' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C7GMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9C8JER' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MBL6KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YXCZ83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZANX40' => 'arhy', 'AT1G12990' => 'ath', 'AT1G67880' => 'ath', 'AT2G13290' => 'ath', 'AT3G01620' => 'ath', 'AT3G26445' => 'ath', 'AT3G27540' => 'ath', 'AT5G14480' => 'ath', 'ATR0824G026' => 'atr', 'ATR1098G019' => 'atr', 'Atru.chr11.2145' => 'acertr', 'Atru.chr2.3636' => 'acertr', 'Atru.chr2.3644' => 'acertr', 'Atru.chr6.2422' => 'acertr', 'Atru.chr7.1112' => 'acertr', 'AUR62005469' => 'cqu', 'AUR62011166' => 'cqu', 'AUR62013319' => 'cqu', 'AUR62024273' => 'cqu', 'AUR62028420' => 'cqu', 'AUR62041942' => 'cqu', 'BcaB01g04969' => 'bca', 'BcaB01g06371' => 'bca', 'BcaB02g11494' => 'bca', 'BcaB03g15382' => 'bca', 'BcaB08g36994' => 'bca', 'BcaC03g13477' => 'bca', 'BcaC03g13478' => 'bca', 'BcaC03g13480' => 'bca', 'BcaC03g13481' => 'bca', 'BcaC03g13486' => 'bca', 'BcaC04g19031' => 'bca', 'BcaC04g23085' => 'bca', 'BcaC05g25094' => 'bca', 'BcaC05g25096' => 'bca', 'BcaC05g25138' => 'bca', 'BcaC05g30416' => 'bca', 'BcaC05g30455' => 'bca', 'BcaC06g30979' => 'bca', 'BcaC06g33805' => 'bca', 'BcaC08g46021' => 'bca', 'BcaNung03154' => 'bca', 'BolC2t06623H' => 'bol', 'BolC2t06632H' => 'bol', 'BolC2t06635H' => 'bol', 'BolC2t06638H' => 'bol', 'BolC3t13266H' => 'bol', 'BolC5t29776H' => 'bol', 'BolC6t38912H' => 'bol', 'BolC7t44183H' => 'bol', 'BolC9t54123H' => 'bol', 'BolC9t59107H' => 'bol', 'BraA02t05221Z' => 'bra', 'BraA03t09996Z' => 'bra', 'BraA05t23210Z' => 'bra', 'BraA06t24068Z' => 'bra', 'BraA06t27032Z' => 'bra', 'BraA08t35176Z' => 'bra', 'BraA09t36680Z' => 'bra', 'BraA10t44471Z' => 'bra', 'C02p06760' => 'bna', 'C02p06890' => 'bna', 'C02p07010' => 'bna', 'C03p07660' => 'bna', 'C05p10300' => 'bna', 'C06p38150' => 'bna', 'C07p36650' => 'bna', 'C08p15770' => 'bna', 'C09p12300' => 'bna', 'C09p62700' => 'bna', 'C09p75040' => 'bna', 'CAN.G13.1' => 'can', 'CAN.G138.4' => 'can', 'CAN.G44.6' => 'can', 'CAN.G473.19' => 'can', 'CANSAT01G0835' => 'cansat', 'CANSAT11G0246' => 'cansat', 'CANSAT11G1766' => 'cansat', 'CANSAT64G1954' => 'cansat', 'CARHR013330' => 'chi', 'CARHR060530' => 'chi', 'CARHR075300' => 'chi', 'CARHR105120' => 'chi', 'CARHR148910' => 'chi', 'CARHR198830' => 'chi', 'Carub.0001s1275' => 'cru', 'Carub.0002s1437' => 'cru', 'Carub.0003s0044' => 'cru', 'Carub.0003s2787' => 'cru', 'Carub.0005s0597' => 'cru', 'Carub.0006s1266' => 'cru', 'Ca_06935_v3' => 'car', 'Ca_13559_v3' => 'car', 'Ca_16941_v3' => 'car', 'Ca_16960_v3' => 'car', 'Ca_17775_v3' => 'car', 'Ca_30464_v3' => 'car', 'Cc06_g08160' => 'ccan', 'Cc07_g01520' => 'ccan', 'Cc11_g15810' => 'ccan', 'CDE02G2840' => 'cde', 'CDE03G0093' => 'cde', 'CDE04G2127' => 'cde', 'CDE07G1857' => 'cde', 'CDE09G1246' => 'cde', 'Cfa003412' => 'cfa', 'Cfa007341' => 'cfa', 'Cfa009220' => 'cfa', 'Ciclev10008737m.g' => 'ccl', 'Ciclev10015565m.g' => 'ccl', 'Ciclev10031761m.g' => 'ccl', 'CiPaw.03G045300' => 'cil', 'CiPaw.03G247200' => 'cil', 'CiPaw.04G029500' => 'cil', 'CiPaw.04G174000' => 'cil', 'CiPaw.05G181200' => 'cil', 'CiPaw.06G067100' => 'cil', 'ClCG05G025800' => 'cla', 'ClCG06G011400' => 'cla', 'ClCG09G019360' => 'cla', 'COL.COLO4_04827' => 'col', 'COL.COLO4_29170' => 'col', 'COL.COLO4_35131' => 'col', 'COL.COLO4_35132' => 'col', 'Cpa.g.sc33.32' => 'cpa', 'Cpa.g.sc46.29' => 'cpa', 'Cpa.g.sc796.1' => 'cpa', 'CsaV3_1G030420' => 'csa', 'CsaV3_5G027050' => 'csa', 'CsaV3_5G031040' => 'csa', 'CsaV3_UNG023130' => 'csa', 'CSS0007726' => 'camsi', 'CSS0016433' => 'camsi', 'CSS0017656' => 'camsi', 'CSS0025364' => 'camsi', 'CSS0027582' => 'camsi', 'CSS0047288' => 'camsi', 'CSS0049950' => 'camsi', 'DCAR_003843' => 'dca', 'DCAR_007052' => 'dca', 'DCAR_020884' => 'dca', 'DCAR_021730' => 'dca', 'DCAR_024423' => 'dca', 'DCAR_026509' => 'dca', 'DCAR_031158' => 'dca', 'Dinv14728' => 'din', 'Dinv15219' => 'din', 'Dinv25728' => 'din', 'Dinv33428' => 'din', 'Dinv36489' => 'din', 'Dinv41486' => 'din', 'Duzib147G0469' => 'dzi', 'Duzib168G0060' => 'dzi', 'Duzib187G1215' => 'dzi', 'Duzib248G0692' => 'dzi', 'Duzib251G0767' => 'dzi', 'Duzib264G0446' => 'dzi', 'Duzib268G0691' => 'dzi', 'ECA232G4767' => 'eca', 'ECA233G2838' => 'eca', 'ECA234G0391' => 'eca', 'ECA234G0857' => 'eca', 'ECA236G1593' => 'eca', 'ECA238G0565' => 'eca', 'ECA246G1027' => 'eca', 'ECA246G3223' => 'eca', 'ECA246G3470' => 'eca', 'EL10Ac6g13829' => 'bvu', 'EL10Ac6g14093' => 'bvu', 'EL10Ac8g18707' => 'bvu', 'Eucgr.C01369' => 'egr', 'Eucgr.H02492' => 'egr', 'Eucgr.I01733' => 'egr', 'Eucgr.J02255' => 'egr', 'Eucgr.J02257' => 'egr', 'Eucgr.J02258' => 'egr', 'FAN02G1601' => 'fan', 'FAN03G1586' => 'fan', 'FAN03G2986' => 'fan', 'FAN05G4837' => 'fan', 'FAN06G0146' => 'fan', 'FAN07G0858' => 'fan', 'FAN09G3179' => 'fan', 'FAN10G0669' => 'fan', 'FAN12G2358' => 'fan', 'FAN14G4198' => 'fan', 'FAN14G5112' => 'fan', 'FAN17G0342' => 'fan', 'FAN19G0342' => 'fan', 'FAN19G0962' => 'fan', 'FAN19G1101' => 'fan', 'FAN19G1872' => 'fan', 'FAN22G0356' => 'fan', 'FAN23G0744' => 'fan', 'FAN23G1914' => 'fan', 'FAN26G0032' => 'fan', 'FAN28G0625' => 'fan', 'FvH4_1g02710' => 'fve', 'FvH4_1g02720' => 'fve', 'FvH4_4g25670' => 'fve', 'FvH4_6g51700' => 'fve', 'FvH4_7g20170' => 'fve', 'Glyma.05G175000' => 'gma', 'Glyma.08G132300' => 'gma', 'Glyma.11G243000' => 'gma', 'Glyma.13G158900' => 'gma', 'Glyma.17G112400' => 'gma', 'Glyma.18G014100' => 'gma', 'Glyma.19G003100' => 'gma', 'Glyma.19G056500' => 'gma', 'Gohir.A01G158900' => 'ghi', 'Gohir.A05G312600' => 'ghi', 'Gohir.A05G354900' => 'ghi', 'Gohir.A07G037200' => 'ghi', 'Gohir.A09G030000' => 'ghi', 'Gohir.A12G145200' => 'ghi', 'Gohir.D01G151500' => 'ghi', 'Gohir.D04G058300' => 'ghi', 'Gohir.D05G314100' => 'ghi', 'Gohir.D07G041400' => 'ghi', 'Gohir.D09G029700' => 'ghi', 'Gohir.D12G149700' => 'ghi', 'Gorai.001G043800' => 'gra', 'Gorai.002G187800' => 'gra', 'Gorai.006G034700' => 'gra', 'Gorai.008G161200' => 'gra', 'Gorai.009G335700' => 'gra', 'Gorai.012G065000' => 'gra', 'GSVIVG01000535001' => 'vvi', 'GSVIVG01015572001' => 'vvi', 'GSVIVG01032386001' => 'vvi', 'HanXRQChr05g0138531' => 'han', 'HanXRQChr06g0174391' => 'han', 'HanXRQChr07g0199021' => 'han', 'HanXRQChr08g0208211' => 'han', 'HanXRQChr09g0255471' => 'han', 'HanXRQChr10g0315791' => 'han', 'HanXRQChr12g0371991' => 'han', 'HanXRQChr15g0475251' => 'han', 'HanXRQChr17g0540001' => 'han', 'HanXRQChr17g0548631' => 'han', 'HanXRQChr17g0569561' => 'han', 'Haze_12256' => 'cav', 'Haze_14756' => 'cav', 'Haze_25528' => 'cav', 'Hma1.2p1_0079F.1_g041020' => 'hma', 'Hma1.2p1_0818F.1_g223260' => 'hma', 'Hma1.2p1_1747F.1_g300530' => 'hma', 'HPP92_004607' => 'vpl', 'HPP92_004608' => 'vpl', 'HPP92_006181' => 'vpl', 'HPP92_012192' => 'vpl', 'HPP92_015680' => 'vpl', 'HPP92_020249' => 'vpl', 'HPP92_021376' => 'vpl', 'HPP92_024275' => 'vpl', 'Hund06031' => 'sun', 'Hund25391' => 'sun', 'Lalb_Chr07g0185371' => 'lal', 'Lalb_Chr07g0185381' => 'lal', 'Lalb_Chr12g0204011' => 'lal', 'Lalb_Chr13g0301671' => 'lal', 'Lalb_Chr14g0362851' => 'lal', 'Lalb_Chr24g0403581' => 'lal', 'Lj1g0000233' => 'lja', 'Lj2g0018120' => 'lja', 'Lj3C621T0' => 'lonja', 'Lj3P1059T14' => 'lonja', 'Lj3P611T9' => 'lonja', 'Lj3P614T13' => 'lonja', 'Lj3P615T5' => 'lonja', 'Lj4g0012315' => 'lja', 'Lj4g0026182' => 'lja', 'Lj6P813T16' => 'lonja', 'Lj7C427T7' => 'lonja', 'Lj7C427T8' => 'lonja', 'Lj7P600T41' => 'lonja', 'Lju41C42G17' => 'lonja', 'Lsat_1_v5_gn_0_47300' => 'lsa', 'Lsat_1_v5_gn_2_91280' => 'lsa', 'Lsat_1_v5_gn_3_30561' => 'lsa', 'Lsat_1_v5_gn_4_184321' => 'lsa', 'Lsat_1_v5_gn_4_4041' => 'lsa', 'Lsat_1_v5_gn_5_92000' => 'lsa', 'Lsat_1_v5_gn_8_152940' => 'lsa', 'Lsat_1_v5_gn_8_62401' => 'lsa', 'Manes.06G055900' => 'mes', 'Manes.12G022200' => 'mes', 'Manes.13G023300' => 'mes', 'Manes.14G115000' => 'mes', 'Manes.15G151700' => 'mes', 'Manes.17G111300' => 'mes', 'Mapoly0226s0009' => 'mpo', 'MBI02_g25363_MAGBIO' => 'mbi', 'MBI06_g00027_MAGBIO' => 'mbi', 'MBI10_g13034_MAGBIO' => 'mbi', 'MD09G1023400' => 'mdo', 'MD13G1100100' => 'mdo', 'MD15G1169200' => 'mdo', 'MD16G1101100' => 'mdo', 'MD17G1022900' => 'mdo', 'Medtr3g096150' => 'mtr', 'Medtr4g115070' => 'mtr', 'Medtr7g033325' => 'mtr', 'Medtr8g089840' => 'mtr', 'MELO3C010319.2' => 'cme', 'MELO3C011944.2' => 'cme', 'MELO3C021589.2' => 'cme', 'Migut.E00207' => 'egut', 'Migut.H00067' => 'egut', 'Migut.K00433' => 'egut', 'Migut.K00606' => 'egut', 'Migut.K01410' => 'egut', 'MSTRG.13347' => 'ama', 'MSTRG.24045' => 'ama', 'MSTRG.2428' => 'ama', 'MSTRG.26410' => 'ama', 'MSTRG.3139' => 'ama', 'MSTRG.3286' => 'ama', 'MSTRG.563' => 'ama', 'MSTRG.7941' => 'ama', 'Nitab4.5_0000028g0060' => 'nta', 'Nitab4.5_0000065g0260' => 'nta', 'Nitab4.5_0000112g0060' => 'nta', 'Nitab4.5_0000489g0120' => 'nta', 'Nitab4.5_0001776g0050' => 'nta', 'Nitab4.5_0001854g0010' => 'nta', 'Nitab4.5_0001860g0020' => 'nta', 'Nitab4.5_0004352g0010' => 'nta', 'Nitab4.5_0008716g0020' => 'nta', 'Nitab4.5_0008922g0010' => 'nta', 'Nn3g16693' => 'nnu', 'Nn4g22596' => 'nnu', 'Nn7g37639' => 'nnu', 'Oeu001701.1' => 'oeu', 'Oeu018149.1' => 'oeu', 'Oeu026220.1' => 'oeu', 'Oeu038635.1' => 'oeu', 'Oeu049176.1' => 'oeu', 'Oeu056706.1' => 'oeu', 'Oeu056937.1' => 'oeu', 'Oeu057540.1' => 'oeu', 'Os02g0594900' => 'osa', 'Os02g0595100' => 'osa', 'Os04g0477500' => 'osa', 'Os12g0611900' => 'osa', 'Peaxi162Scf00076g00020' => 'pax', 'Peaxi162Scf00128g00217' => 'pax', 'Peaxi162Scf00129g01640' => 'pax', 'Peaxi162Scf00669g00007' => 'pax', 'Peaxi162Scf00700g00421' => 'pax', 'Peaxi162Scf00801g00038' => 'pax', 'Peaxi162Scf00891g00025' => 'pax', 'PGR083G0909' => 'pgr', 'PGR119G1005' => 'pgr', 'PGR142G2236' => 'pgr', 'PGR142G3388' => 'pgr', 'PGSC0003DMG400004514' => 'stu', 'PGSC0003DMG400012635' => 'stu', 'PGSC0003DMG400015730' => 'stu', 'PGSC0003DMG400018611' => 'stu', 'PGSC0003DMG400030897' => 'stu', 'Phvul.001G254800' => 'pvu', 'Phvul.002G260100' => 'pvu', 'Phvul.003G167600' => 'pvu', 'Phvul.004G005100' => 'pvu', 'Potri.001G343600' => 'ptr', 'Potri.006G066700' => 'ptr', 'Potri.008G186000' => 'ptr', 'Potri.010G046900' => 'ptr', 'Potri.018G127900' => 'ptr', 'Pp3c20_17750' => 'ppa', 'Pp3c24_4380' => 'ppa', 'Prupe.1G245800' => 'ppe', 'Prupe.3G293400' => 'ppe', 'Prupe.7G247400' => 'ppe', 'Psat0s145g0120' => 'psa', 'Psat0s595g0040' => 'psa', 'Psat0s595g0120' => 'psa', 'Psat3g175040' => 'psa', 'Psat7g058120' => 'psa', 'PSO017G0428' => 'pso', 'PSO063G7510' => 'pso', 'PSO067G0046' => 'pso', 'PSO478G1073' => 'pso', 'PSO675G3677' => 'pso', 'PSO675G6558' => 'pso', 'PSO675G7520' => 'pso', 'PSO675G8959' => 'pso', 'QL02p074089' => 'qlo', 'QL02p089614' => 'qlo', 'QL03p057736' => 'qlo', 'RcHm_v2.0_Chr1g0364131' => 'rch', 'RcHm_v2.0_Chr2g0087801' => 'rch', 'RcHm_v2.0_Chr2g0087821' => 'rch', 'RcHm_v2.0_Chr2g0173231' => 'rch', 'RcHm_v2.0_Chr4g0433111' => 'rch', 'Rhsim03G0250300' => 'rsi', 'Rhsim08G0048400' => 'rsi', 'Rhsim10G0014800' => 'rsi', 'Rhsim12G0040100' => 'rsi', 'Rhsim12G0109700' => 'rsi', 'Sabra06G0049600' => 'sbr', 'Sabra08G0141000' => 'sbr', 'Sabra10G0021400' => 'sbr', 'Sabra16G0222900' => 'sbr', 'Sabra18G0108600' => 'sbr', 'SalBow1G0433' => 'sbo', 'SalBow1G2038' => 'sbo', 'SalBow1G5003' => 'sbo', 'SalBow7G1197' => 'sbo', 'SalBow8G3506' => 'sbo', 'Sc03g0007300' => 'sci', 'Sc11g0000950' => 'sci', 'Sc14g0008750' => 'sci', 'Sc18g0000420' => 'sci', 'Sed0006754' => 'sed', 'Sed0008741' => 'sed', 'Sed0017172' => 'sed', 'Sed0018925' => 'sed', 'Sed0023326' => 'sed', 'Sed0025909' => 'sed', 'SEGI_05333' => 'sgi', 'SEGI_10362' => 'sgi', 'SEGI_13380' => 'sgi', 'SEGI_24306' => 'sgi', 'SEGI_29077' => 'sgi', 'SEGI_29095' => 'sgi', 'SEGI_36534' => 'sgi', 'SEGI_37506' => 'sgi', 'SEGI_38321' => 'sgi', 'SGA_v2.0_scaffold307G48031' => 'sas', 'SGA_v2.0_scaffold47G17507' => 'sas', 'SGA_v2.0_scaffold63G21736' => 'sas', 'SGA_v2.0_scaffold87G27070' => 'sas', 'SHI17794' => 'shi', 'SHI28851' => 'shi', 'SMO165G0155' => 'smo', 'SMO340G0217' => 'smo', 'SMO367G1210' => 'smo', 'Solyc02g093430.3' => 'sly', 'Solyc05g013580.4' => 'sly', 'Solyc07g008030.3' => 'sly', 'Solyc12g035470.2' => 'sly', 'Sopen02g038020' => 'spe', 'Sopen05g008490' => 'spe', 'Sopen07g003910' => 'spe', 'Sopen12g015240' => 'spe', 'Sp1g11550' => 'spa', 'Sp2g16710' => 'spa', 'Sp3g00430' => 'spa', 'Sp3g26780' => 'spa', 'Sp5g22900' => 'spa', 'Sp6g29530' => 'spa', 'TAR371G0794' => 'tar', 'TAR374G0164' => 'tar', 'TAR622G0165' => 'tar', 'TAR626G0929' => 'tar', 'TAR629G2155' => 'tar', 'THA.LOC104805282' => 'tha', 'THA.LOC104805363' => 'tha', 'THA.LOC104808968' => 'tha', 'THA.LOC104821093' => 'tha', 'THA.LOC104823953' => 'tha', 'THA.LOC104825562' => 'tha', 'THA.LOC104825665' => 'tha', 'Thecc.02G261400' => 'tca', 'Thecc.04G019200' => 'tca', 'Thecc.09G130400' => 'tca', 'Thhalv10004374m.g' => 'esa', 'Thhalv10007850m.g' => 'esa', 'Thhalv10013782m.g' => 'esa', 'Thhalv10018686m.g' => 'esa', 'Thhalv10020899m.g' => 'esa', 'Thhalv10022755m.g' => 'esa', 'TPR.G23851' => 'tpr', 'TPR.G26500' => 'tpr', 'TPR.G27267' => 'tpr', 'TPR.G32001' => 'tpr', 'TPR.G6251' => 'tpr', 'TPR.G8167' => 'tpr', 'TWI12G1330' => 'twi', 'TWI18G1239' => 'twi', 'TWI34G0979' => 'twi', 'TWI36G0670' => 'twi', 'TWI36G0707' => 'twi', 'TWI56G0233' => 'twi', 'TWI75G1809' => 'twi', 'unitig_21.g20874' => 'ugi', 'unitig_26.g10343' => 'ugi', 'unitig_46.g18392' => 'ugi', 'unitig_52.g17178' => 'ugi', 'unitig_8.g2934' => 'ugi', 'vmacro01122' => 'vma', 'vmacro05875' => 'vma', 'vmacro06147' => 'vma', 'vmacro16191' => 'vma', 'vmacro18293' => 'vma', 'VMungo0251G3707' => 'vmu', 'VMungo0464G1521' => 'vmu', 'VMungo1215G0205' => 'vmu', 'VMungo1383G2484' => 'vmu', 'Zm00001eb079610' => 'zma', 'Zm00001eb135990' => 'zma', 'Zm00001eb183710' => 'zma', 'Zm00001eb246020' => 'zma' ), 'gf_id' => 'HOM05D001124', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001124' ), 'data_identifier' => 'HOM05D001124', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001124', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '548', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02520' => 'bna', 'A03p06630' => 'bna', 'A05p44460' => 'bna', 'A06p08710' => 'bna', 'A06p41090' => 'bna', 'A07p32320' => 'bna', 'A08p32520' => 'bna', 'A09p10360' => 'bna', 'A10p24080' => 'bna', 'Aa31LG11G15250' => 'aar', 'Aa31LG1G1800' => 'aar', 'Aa31LG2G5120' => 'aar', 'Aa31LG2G6070' => 'aar', 'Aa31LG5G10770' => 'aar', 'Aa31sc61G90' => 'aar', 'Actinidia01352' => 'ach', 'Actinidia05983' => 'ach', 'Actinidia08133' => 'ach', 'Actinidia15101' => 'ach', 'Actinidia26379' => 'ach', 'Actinidia35778' => 'ach', 'Actinidia36123' => 'ach', 'Actinidia37436' => 'ach', 'Actinidia38730' => 'ach', 'Ah.02g128210' => 'amhyb', 'Ah.03g132990' => 'amhyb', 'Ah.14g079410' => 'amhyb', 'AL1G24640' => 'aly', 'AL2G26680' => 'aly', 'AL3G10530' => 'aly', 'AL3G45230' => 'aly', 'AL5G15230' => 'aly', 'AL5G16960' => 'aly', 'AL6G25210' => 'aly', 'Aqoxy2G00441' => 'aox', 'Aqoxy3G01236' => 'aox', 'Aqoxy5G03746' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3RQ047' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C7GMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9C8JER' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MBL6KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YXCZ83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZANX40' => 'arhy', 'AT1G12990' => 'ath', 'AT1G67880' => 'ath', 'AT2G13290' => 'ath', 'AT3G01620' => 'ath', 'AT3G26445' => 'ath', 'AT3G27540' => 'ath', 'AT5G14480' => 'ath', 'ATR0824G026' => 'atr', 'ATR1098G019' => 'atr', 'Atru.chr11.2145' => 'acertr', 'Atru.chr2.3636' => 'acertr', 'Atru.chr2.3644' => 'acertr', 'Atru.chr6.2422' => 'acertr', 'Atru.chr7.1112' => 'acertr', 'AUR62005469' => 'cqu', 'AUR62011166' => 'cqu', 'AUR62013319' => 'cqu', 'AUR62024273' => 'cqu', 'AUR62028420' => 'cqu', 'AUR62041942' => 'cqu', 'BcaB01g04969' => 'bca', 'BcaB01g06371' => 'bca', 'BcaB02g11494' => 'bca', 'BcaB03g15382' => 'bca', 'BcaB08g36994' => 'bca', 'BcaC03g13477' => 'bca', 'BcaC03g13478' => 'bca', 'BcaC03g13480' => 'bca', 'BcaC03g13481' => 'bca', 'BcaC03g13486' => 'bca', 'BcaC04g19031' => 'bca', 'BcaC04g23085' => 'bca', 'BcaC05g25094' => 'bca', 'BcaC05g25096' => 'bca', 'BcaC05g25138' => 'bca', 'BcaC05g30416' => 'bca', 'BcaC05g30455' => 'bca', 'BcaC06g30979' => 'bca', 'BcaC06g33805' => 'bca', 'BcaC08g46021' => 'bca', 'BcaNung03154' => 'bca', 'BolC2t06623H' => 'bol', 'BolC2t06632H' => 'bol', 'BolC2t06635H' => 'bol', 'BolC2t06638H' => 'bol', 'BolC3t13266H' => 'bol', 'BolC5t29776H' => 'bol', 'BolC6t38912H' => 'bol', 'BolC7t44183H' => 'bol', 'BolC9t54123H' => 'bol', 'BolC9t59107H' => 'bol', 'BraA02t05221Z' => 'bra', 'BraA03t09996Z' => 'bra', 'BraA05t23210Z' => 'bra', 'BraA06t24068Z' => 'bra', 'BraA06t27032Z' => 'bra', 'BraA08t35176Z' => 'bra', 'BraA09t36680Z' => 'bra', 'BraA10t44471Z' => 'bra', 'C02p06760' => 'bna', 'C02p06890' => 'bna', 'C02p07010' => 'bna', 'C03p07660' => 'bna', 'C05p10300' => 'bna', 'C06p38150' => 'bna', 'C07p36650' => 'bna', 'C08p15770' => 'bna', 'C09p12300' => 'bna', 'C09p62700' => 'bna', 'C09p75040' => 'bna', 'CAN.G13.1' => 'can', 'CAN.G138.4' => 'can', 'CAN.G44.6' => 'can', 'CAN.G473.19' => 'can', 'CANSAT01G0835' => 'cansat', 'CANSAT11G0246' => 'cansat', 'CANSAT11G1766' => 'cansat', 'CANSAT64G1954' => 'cansat', 'CARHR013330' => 'chi', 'CARHR060530' => 'chi', 'CARHR075300' => 'chi', 'CARHR105120' => 'chi', 'CARHR148910' => 'chi', 'CARHR198830' => 'chi', 'Carub.0001s1275' => 'cru', 'Carub.0002s1437' => 'cru', 'Carub.0003s0044' => 'cru', 'Carub.0003s2787' => 'cru', 'Carub.0005s0597' => 'cru', 'Carub.0006s1266' => 'cru', 'Ca_06935_v3' => 'car', 'Ca_13559_v3' => 'car', 'Ca_16941_v3' => 'car', 'Ca_16960_v3' => 'car', 'Ca_17775_v3' => 'car', 'Ca_30464_v3' => 'car', 'Cc06_g08160' => 'ccan', 'Cc07_g01520' => 'ccan', 'Cc11_g15810' => 'ccan', 'CDE02G2840' => 'cde', 'CDE03G0093' => 'cde', 'CDE04G2127' => 'cde', 'CDE07G1857' => 'cde', 'CDE09G1246' => 'cde', 'Cfa003412' => 'cfa', 'Cfa007341' => 'cfa', 'Cfa009220' => 'cfa', 'Ciclev10008737m.g' => 'ccl', 'Ciclev10015565m.g' => 'ccl', 'Ciclev10031761m.g' => 'ccl', 'CiPaw.03G045300' => 'cil', 'CiPaw.03G247200' => 'cil', 'CiPaw.04G029500' => 'cil', 'CiPaw.04G174000' => 'cil', 'CiPaw.05G181200' => 'cil', 'CiPaw.06G067100' => 'cil', 'ClCG05G025800' => 'cla', 'ClCG06G011400' => 'cla', 'ClCG09G019360' => 'cla', 'COL.COLO4_04827' => 'col', 'COL.COLO4_29170' => 'col', 'COL.COLO4_35131' => 'col', 'COL.COLO4_35132' => 'col', 'Cpa.g.sc33.32' => 'cpa', 'Cpa.g.sc46.29' => 'cpa', 'Cpa.g.sc796.1' => 'cpa', 'CsaV3_1G030420' => 'csa', 'CsaV3_5G027050' => 'csa', 'CsaV3_5G031040' => 'csa', 'CsaV3_UNG023130' => 'csa', 'CSS0007726' => 'camsi', 'CSS0016433' => 'camsi', 'CSS0017656' => 'camsi', 'CSS0025364' => 'camsi', 'CSS0027582' => 'camsi', 'CSS0047288' => 'camsi', 'CSS0049950' => 'camsi', 'DCAR_003843' => 'dca', 'DCAR_007052' => 'dca', 'DCAR_020884' => 'dca', 'DCAR_021730' => 'dca', 'DCAR_024423' => 'dca', 'DCAR_026509' => 'dca', 'DCAR_031158' => 'dca', 'Dinv14728' => 'din', 'Dinv15219' => 'din', 'Dinv25728' => 'din', 'Dinv33428' => 'din', 'Dinv36489' => 'din', 'Dinv41486' => 'din', 'Duzib147G0469' => 'dzi', 'Duzib168G0060' => 'dzi', 'Duzib187G1215' => 'dzi', 'Duzib248G0692' => 'dzi', 'Duzib251G0767' => 'dzi', 'Duzib264G0446' => 'dzi', 'Duzib268G0691' => 'dzi', 'ECA232G4767' => 'eca', 'ECA233G2838' => 'eca', 'ECA234G0391' => 'eca', 'ECA234G0857' => 'eca', 'ECA236G1593' => 'eca', 'ECA238G0565' => 'eca', 'ECA246G1027' => 'eca', 'ECA246G3223' => 'eca', 'ECA246G3470' => 'eca', 'EL10Ac6g13829' => 'bvu', 'EL10Ac6g14093' => 'bvu', 'EL10Ac8g18707' => 'bvu', 'Eucgr.C01369' => 'egr', 'Eucgr.H02492' => 'egr', 'Eucgr.I01733' => 'egr', 'Eucgr.J02255' => 'egr', 'Eucgr.J02257' => 'egr', 'Eucgr.J02258' => 'egr', 'FAN02G1601' => 'fan', 'FAN03G1586' => 'fan', 'FAN03G2986' => 'fan', 'FAN05G4837' => 'fan', 'FAN06G0146' => 'fan', 'FAN07G0858' => 'fan', 'FAN09G3179' => 'fan', 'FAN10G0669' => 'fan', 'FAN12G2358' => 'fan', 'FAN14G4198' => 'fan', 'FAN14G5112' => 'fan', 'FAN17G0342' => 'fan', 'FAN19G0342' => 'fan', 'FAN19G0962' => 'fan', 'FAN19G1101' => 'fan', 'FAN19G1872' => 'fan', 'FAN22G0356' => 'fan', 'FAN23G0744' => 'fan', 'FAN23G1914' => 'fan', 'FAN26G0032' => 'fan', 'FAN28G0625' => 'fan', 'FvH4_1g02710' => 'fve', 'FvH4_1g02720' => 'fve', 'FvH4_4g25670' => 'fve', 'FvH4_6g51700' => 'fve', 'FvH4_7g20170' => 'fve', 'Glyma.05G175000' => 'gma', 'Glyma.08G132300' => 'gma', 'Glyma.11G243000' => 'gma', 'Glyma.13G158900' => 'gma', 'Glyma.17G112400' => 'gma', 'Glyma.18G014100' => 'gma', 'Glyma.19G003100' => 'gma', 'Glyma.19G056500' => 'gma', 'Gohir.A01G158900' => 'ghi', 'Gohir.A05G312600' => 'ghi', 'Gohir.A05G354900' => 'ghi', 'Gohir.A07G037200' => 'ghi', 'Gohir.A09G030000' => 'ghi', 'Gohir.A12G145200' => 'ghi', 'Gohir.D01G151500' => 'ghi', 'Gohir.D04G058300' => 'ghi', 'Gohir.D05G314100' => 'ghi', 'Gohir.D07G041400' => 'ghi', 'Gohir.D09G029700' => 'ghi', 'Gohir.D12G149700' => 'ghi', 'Gorai.001G043800' => 'gra', 'Gorai.002G187800' => 'gra', 'Gorai.006G034700' => 'gra', 'Gorai.008G161200' => 'gra', 'Gorai.009G335700' => 'gra', 'Gorai.012G065000' => 'gra', 'GSVIVG01000535001' => 'vvi', 'GSVIVG01015572001' => 'vvi', 'GSVIVG01032386001' => 'vvi', 'HanXRQChr05g0138531' => 'han', 'HanXRQChr06g0174391' => 'han', 'HanXRQChr07g0199021' => 'han', 'HanXRQChr08g0208211' => 'han', 'HanXRQChr09g0255471' => 'han', 'HanXRQChr10g0315791' => 'han', 'HanXRQChr12g0371991' => 'han', 'HanXRQChr15g0475251' => 'han', 'HanXRQChr17g0540001' => 'han', 'HanXRQChr17g0548631' => 'han', 'HanXRQChr17g0569561' => 'han', 'Haze_12256' => 'cav', 'Haze_14756' => 'cav', 'Haze_25528' => 'cav', 'Hma1.2p1_0079F.1_g041020' => 'hma', 'Hma1.2p1_0818F.1_g223260' => 'hma', 'Hma1.2p1_1747F.1_g300530' => 'hma', 'HPP92_004607' => 'vpl', 'HPP92_004608' => 'vpl', 'HPP92_006181' => 'vpl', 'HPP92_012192' => 'vpl', 'HPP92_015680' => 'vpl', 'HPP92_020249' => 'vpl', 'HPP92_021376' => 'vpl', 'HPP92_024275' => 'vpl', 'Hund06031' => 'sun', 'Hund25391' => 'sun', 'Lalb_Chr07g0185371' => 'lal', 'Lalb_Chr07g0185381' => 'lal', 'Lalb_Chr12g0204011' => 'lal', 'Lalb_Chr13g0301671' => 'lal', 'Lalb_Chr14g0362851' => 'lal', 'Lalb_Chr24g0403581' => 'lal', 'Lj1g0000233' => 'lja', 'Lj2g0018120' => 'lja', 'Lj3C621T0' => 'lonja', 'Lj3P1059T14' => 'lonja', 'Lj3P611T9' => 'lonja', 'Lj3P614T13' => 'lonja', 'Lj3P615T5' => 'lonja', 'Lj4g0012315' => 'lja', 'Lj4g0026182' => 'lja', 'Lj6P813T16' => 'lonja', 'Lj7C427T7' => 'lonja', 'Lj7C427T8' => 'lonja', 'Lj7P600T41' => 'lonja', 'Lju41C42G17' => 'lonja', 'Lsat_1_v5_gn_0_47300' => 'lsa', 'Lsat_1_v5_gn_2_91280' => 'lsa', 'Lsat_1_v5_gn_3_30561' => 'lsa', 'Lsat_1_v5_gn_4_184321' => 'lsa', 'Lsat_1_v5_gn_4_4041' => 'lsa', 'Lsat_1_v5_gn_5_92000' => 'lsa', 'Lsat_1_v5_gn_8_152940' => 'lsa', 'Lsat_1_v5_gn_8_62401' => 'lsa', 'Manes.06G055900' => 'mes', 'Manes.12G022200' => 'mes', 'Manes.13G023300' => 'mes', 'Manes.14G115000' => 'mes', 'Manes.15G151700' => 'mes', 'Manes.17G111300' => 'mes', 'Mapoly0226s0009' => 'mpo', 'MBI02_g25363_MAGBIO' => 'mbi', 'MBI06_g00027_MAGBIO' => 'mbi', 'MBI10_g13034_MAGBIO' => 'mbi', 'MD09G1023400' => 'mdo', 'MD13G1100100' => 'mdo', 'MD15G1169200' => 'mdo', 'MD16G1101100' => 'mdo', 'MD17G1022900' => 'mdo', 'Medtr3g096150' => 'mtr', 'Medtr4g115070' => 'mtr', 'Medtr7g033325' => 'mtr', 'Medtr8g089840' => 'mtr', 'MELO3C010319.2' => 'cme', 'MELO3C011944.2' => 'cme', 'MELO3C021589.2' => 'cme', 'Migut.E00207' => 'egut', 'Migut.H00067' => 'egut', 'Migut.K00433' => 'egut', 'Migut.K00606' => 'egut', 'Migut.K01410' => 'egut', 'MSTRG.13347' => 'ama', 'MSTRG.24045' => 'ama', 'MSTRG.2428' => 'ama', 'MSTRG.26410' => 'ama', 'MSTRG.3139' => 'ama', 'MSTRG.3286' => 'ama', 'MSTRG.563' => 'ama', 'MSTRG.7941' => 'ama', 'Nitab4.5_0000028g0060' => 'nta', 'Nitab4.5_0000065g0260' => 'nta', 'Nitab4.5_0000112g0060' => 'nta', 'Nitab4.5_0000489g0120' => 'nta', 'Nitab4.5_0001776g0050' => 'nta', 'Nitab4.5_0001854g0010' => 'nta', 'Nitab4.5_0001860g0020' => 'nta', 'Nitab4.5_0004352g0010' => 'nta', 'Nitab4.5_0008716g0020' => 'nta', 'Nitab4.5_0008922g0010' => 'nta', 'Nn3g16693' => 'nnu', 'Nn4g22596' => 'nnu', 'Nn7g37639' => 'nnu', 'Oeu001701.1' => 'oeu', 'Oeu018149.1' => 'oeu', 'Oeu026220.1' => 'oeu', 'Oeu038635.1' => 'oeu', 'Oeu049176.1' => 'oeu', 'Oeu056706.1' => 'oeu', 'Oeu056937.1' => 'oeu', 'Oeu057540.1' => 'oeu', 'Os02g0594900' => 'osa', 'Os02g0595100' => 'osa', 'Os04g0477500' => 'osa', 'Os12g0611900' => 'osa', 'Peaxi162Scf00076g00020' => 'pax', 'Peaxi162Scf00128g00217' => 'pax', 'Peaxi162Scf00129g01640' => 'pax', 'Peaxi162Scf00669g00007' => 'pax', 'Peaxi162Scf00700g00421' => 'pax', 'Peaxi162Scf00801g00038' => 'pax', 'Peaxi162Scf00891g00025' => 'pax', 'PGR083G0909' => 'pgr', 'PGR119G1005' => 'pgr', 'PGR142G2236' => 'pgr', 'PGR142G3388' => 'pgr', 'PGSC0003DMG400004514' => 'stu', 'PGSC0003DMG400012635' => 'stu', 'PGSC0003DMG400015730' => 'stu', 'PGSC0003DMG400018611' => 'stu', 'PGSC0003DMG400030897' => 'stu', 'Phvul.001G254800' => 'pvu', 'Phvul.002G260100' => 'pvu', 'Phvul.003G167600' => 'pvu', 'Phvul.004G005100' => 'pvu', 'Potri.001G343600' => 'ptr', 'Potri.006G066700' => 'ptr', 'Potri.008G186000' => 'ptr', 'Potri.010G046900' => 'ptr', 'Potri.018G127900' => 'ptr', 'Pp3c20_17750' => 'ppa', 'Pp3c24_4380' => 'ppa', 'Prupe.1G245800' => 'ppe', 'Prupe.3G293400' => 'ppe', 'Prupe.7G247400' => 'ppe', 'Psat0s145g0120' => 'psa', 'Psat0s595g0040' => 'psa', 'Psat0s595g0120' => 'psa', 'Psat3g175040' => 'psa', 'Psat7g058120' => 'psa', 'PSO017G0428' => 'pso', 'PSO063G7510' => 'pso', 'PSO067G0046' => 'pso', 'PSO478G1073' => 'pso', 'PSO675G3677' => 'pso', 'PSO675G6558' => 'pso', 'PSO675G7520' => 'pso', 'PSO675G8959' => 'pso', 'QL02p074089' => 'qlo', 'QL02p089614' => 'qlo', 'QL03p057736' => 'qlo', 'RcHm_v2.0_Chr1g0364131' => 'rch', 'RcHm_v2.0_Chr2g0087801' => 'rch', 'RcHm_v2.0_Chr2g0087821' => 'rch', 'RcHm_v2.0_Chr2g0173231' => 'rch', 'RcHm_v2.0_Chr4g0433111' => 'rch', 'Rhsim03G0250300' => 'rsi', 'Rhsim08G0048400' => 'rsi', 'Rhsim10G0014800' => 'rsi', 'Rhsim12G0040100' => 'rsi', 'Rhsim12G0109700' => 'rsi', 'Sabra06G0049600' => 'sbr', 'Sabra08G0141000' => 'sbr', 'Sabra10G0021400' => 'sbr', 'Sabra16G0222900' => 'sbr', 'Sabra18G0108600' => 'sbr', 'SalBow1G0433' => 'sbo', 'SalBow1G2038' => 'sbo', 'SalBow1G5003' => 'sbo', 'SalBow7G1197' => 'sbo', 'SalBow8G3506' => 'sbo', 'Sc03g0007300' => 'sci', 'Sc11g0000950' => 'sci', 'Sc14g0008750' => 'sci', 'Sc18g0000420' => 'sci', 'Sed0006754' => 'sed', 'Sed0008741' => 'sed', 'Sed0017172' => 'sed', 'Sed0018925' => 'sed', 'Sed0023326' => 'sed', 'Sed0025909' => 'sed', 'SEGI_05333' => 'sgi', 'SEGI_10362' => 'sgi', 'SEGI_13380' => 'sgi', 'SEGI_24306' => 'sgi', 'SEGI_29077' => 'sgi', 'SEGI_29095' => 'sgi', 'SEGI_36534' => 'sgi', 'SEGI_37506' => 'sgi', 'SEGI_38321' => 'sgi', 'SGA_v2.0_scaffold307G48031' => 'sas', 'SGA_v2.0_scaffold47G17507' => 'sas', 'SGA_v2.0_scaffold63G21736' => 'sas', 'SGA_v2.0_scaffold87G27070' => 'sas', 'SHI17794' => 'shi', 'SHI28851' => 'shi', 'SMO165G0155' => 'smo', 'SMO340G0217' => 'smo', 'SMO367G1210' => 'smo', 'Solyc02g093430.3' => 'sly', 'Solyc05g013580.4' => 'sly', 'Solyc07g008030.3' => 'sly', 'Solyc12g035470.2' => 'sly', 'Sopen02g038020' => 'spe', 'Sopen05g008490' => 'spe', 'Sopen07g003910' => 'spe', 'Sopen12g015240' => 'spe', 'Sp1g11550' => 'spa', 'Sp2g16710' => 'spa', 'Sp3g00430' => 'spa', 'Sp3g26780' => 'spa', 'Sp5g22900' => 'spa', 'Sp6g29530' => 'spa', 'TAR371G0794' => 'tar', 'TAR374G0164' => 'tar', 'TAR622G0165' => 'tar', 'TAR626G0929' => 'tar', 'TAR629G2155' => 'tar', 'THA.LOC104805282' => 'tha', 'THA.LOC104805363' => 'tha', 'THA.LOC104808968' => 'tha', 'THA.LOC104821093' => 'tha', 'THA.LOC104823953' => 'tha', 'THA.LOC104825562' => 'tha', 'THA.LOC104825665' => 'tha', 'Thecc.02G261400' => 'tca', 'Thecc.04G019200' => 'tca', 'Thecc.09G130400' => 'tca', 'Thhalv10004374m.g' => 'esa', 'Thhalv10007850m.g' => 'esa', 'Thhalv10013782m.g' => 'esa', 'Thhalv10018686m.g' => 'esa', 'Thhalv10020899m.g' => 'esa', 'Thhalv10022755m.g' => 'esa', 'TPR.G23851' => 'tpr', 'TPR.G26500' => 'tpr', 'TPR.G27267' => 'tpr', 'TPR.G32001' => 'tpr', 'TPR.G6251' => 'tpr', 'TPR.G8167' => 'tpr', 'TWI12G1330' => 'twi', 'TWI18G1239' => 'twi', 'TWI34G0979' => 'twi', 'TWI36G0670' => 'twi', 'TWI36G0707' => 'twi', 'TWI56G0233' => 'twi', 'TWI75G1809' => 'twi', 'unitig_21.g20874' => 'ugi', 'unitig_26.g10343' => 'ugi', 'unitig_46.g18392' => 'ugi', 'unitig_52.g17178' => 'ugi', 'unitig_8.g2934' => 'ugi', 'vmacro01122' => 'vma', 'vmacro05875' => 'vma', 'vmacro06147' => 'vma', 'vmacro16191' => 'vma', 'vmacro18293' => 'vma', 'VMungo0251G3707' => 'vmu', 'VMungo0464G1521' => 'vmu', 'VMungo1215G0205' => 'vmu', 'VMungo1383G2484' => 'vmu', 'Zm00001eb079610' => 'zma', 'Zm00001eb135990' => 'zma', 'Zm00001eb183710' => 'zma', 'Zm00001eb246020' => 'zma' ) $gf_id = 'HOM05D001124' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001124' ) $data_identifier = 'HOM05D001124' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 6, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 7, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 21, 'bol' => (int) 10, 'bra' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 6, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 9, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 21, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 8, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 10, 'lsa' => (int) 8, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 8, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 9, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb246020' $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' => 'HOM05D001124', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '548', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02520' => 'bna', 'A03p06630' => 'bna', 'A05p44460' => 'bna', 'A06p08710' => 'bna', 'A06p41090' => 'bna', 'A07p32320' => 'bna', 'A08p32520' => 'bna', 'A09p10360' => 'bna', 'A10p24080' => 'bna', 'Aa31LG11G15250' => 'aar', 'Aa31LG1G1800' => 'aar', 'Aa31LG2G5120' => 'aar', 'Aa31LG2G6070' => 'aar', 'Aa31LG5G10770' => 'aar', 'Aa31sc61G90' => 'aar', 'Actinidia01352' => 'ach', 'Actinidia05983' => 'ach', 'Actinidia08133' => 'ach', 'Actinidia15101' => 'ach', 'Actinidia26379' => 'ach', 'Actinidia35778' => 'ach', 'Actinidia36123' => 'ach', 'Actinidia37436' => 'ach', 'Actinidia38730' => 'ach', 'Ah.02g128210' => 'amhyb', 'Ah.03g132990' => 'amhyb', 'Ah.14g079410' => 'amhyb', 'AL1G24640' => 'aly', 'AL2G26680' => 'aly', 'AL3G10530' => 'aly', 'AL3G45230' => 'aly', 'AL5G15230' => 'aly', 'AL5G16960' => 'aly', 'AL6G25210' => 'aly', 'Aqoxy2G00441' => 'aox', 'Aqoxy3G01236' => 'aox', 'Aqoxy5G03746' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3RQ047' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C7GMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9C8JER' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MBL6KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YXCZ83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZANX40' => 'arhy', 'AT1G12990' => 'ath', 'AT1G67880' => 'ath', 'AT2G13290' => 'ath', 'AT3G01620' => 'ath', 'AT3G26445' => 'ath', 'AT3G27540' => 'ath', 'AT5G14480' => 'ath', 'ATR0824G026' => 'atr', 'ATR1098G019' => 'atr', 'Atru.chr11.2145' => 'acertr', 'Atru.chr2.3636' => 'acertr', 'Atru.chr2.3644' => 'acertr', 'Atru.chr6.2422' => 'acertr', 'Atru.chr7.1112' => 'acertr', 'AUR62005469' => 'cqu', 'AUR62011166' => 'cqu', 'AUR62013319' => 'cqu', 'AUR62024273' => 'cqu', 'AUR62028420' => 'cqu', 'AUR62041942' => 'cqu', 'BcaB01g04969' => 'bca', 'BcaB01g06371' => 'bca', 'BcaB02g11494' => 'bca', 'BcaB03g15382' => 'bca', 'BcaB08g36994' => 'bca', 'BcaC03g13477' => 'bca', 'BcaC03g13478' => 'bca', 'BcaC03g13480' => 'bca', 'BcaC03g13481' => 'bca', 'BcaC03g13486' => 'bca', 'BcaC04g19031' => 'bca', 'BcaC04g23085' => 'bca', 'BcaC05g25094' => 'bca', 'BcaC05g25096' => 'bca', 'BcaC05g25138' => 'bca', 'BcaC05g30416' => 'bca', 'BcaC05g30455' => 'bca', 'BcaC06g30979' => 'bca', 'BcaC06g33805' => 'bca', 'BcaC08g46021' => 'bca', 'BcaNung03154' => 'bca', 'BolC2t06623H' => 'bol', 'BolC2t06632H' => 'bol', 'BolC2t06635H' => 'bol', 'BolC2t06638H' => 'bol', 'BolC3t13266H' => 'bol', 'BolC5t29776H' => 'bol', 'BolC6t38912H' => 'bol', 'BolC7t44183H' => 'bol', 'BolC9t54123H' => 'bol', 'BolC9t59107H' => 'bol', 'BraA02t05221Z' => 'bra', 'BraA03t09996Z' => 'bra', 'BraA05t23210Z' => 'bra', 'BraA06t24068Z' => 'bra', 'BraA06t27032Z' => 'bra', 'BraA08t35176Z' => 'bra', 'BraA09t36680Z' => 'bra', 'BraA10t44471Z' => 'bra', 'C02p06760' => 'bna', 'C02p06890' => 'bna', 'C02p07010' => 'bna', 'C03p07660' => 'bna', 'C05p10300' => 'bna', 'C06p38150' => 'bna', 'C07p36650' => 'bna', 'C08p15770' => 'bna', 'C09p12300' => 'bna', 'C09p62700' => 'bna', 'C09p75040' => 'bna', 'CAN.G13.1' => 'can', 'CAN.G138.4' => 'can', 'CAN.G44.6' => 'can', 'CAN.G473.19' => 'can', 'CANSAT01G0835' => 'cansat', 'CANSAT11G0246' => 'cansat', 'CANSAT11G1766' => 'cansat', 'CANSAT64G1954' => 'cansat', 'CARHR013330' => 'chi', 'CARHR060530' => 'chi', 'CARHR075300' => 'chi', 'CARHR105120' => 'chi', 'CARHR148910' => 'chi', 'CARHR198830' => 'chi', 'Carub.0001s1275' => 'cru', 'Carub.0002s1437' => 'cru', 'Carub.0003s0044' => 'cru', 'Carub.0003s2787' => 'cru', 'Carub.0005s0597' => 'cru', 'Carub.0006s1266' => 'cru', 'Ca_06935_v3' => 'car', 'Ca_13559_v3' => 'car', 'Ca_16941_v3' => 'car', 'Ca_16960_v3' => 'car', 'Ca_17775_v3' => 'car', 'Ca_30464_v3' => 'car', 'Cc06_g08160' => 'ccan', 'Cc07_g01520' => 'ccan', 'Cc11_g15810' => 'ccan', 'CDE02G2840' => 'cde', 'CDE03G0093' => 'cde', 'CDE04G2127' => 'cde', 'CDE07G1857' => 'cde', 'CDE09G1246' => 'cde', 'Cfa003412' => 'cfa', 'Cfa007341' => 'cfa', 'Cfa009220' => 'cfa', 'Ciclev10008737m.g' => 'ccl', 'Ciclev10015565m.g' => 'ccl', 'Ciclev10031761m.g' => 'ccl', 'CiPaw.03G045300' => 'cil', 'CiPaw.03G247200' => 'cil', 'CiPaw.04G029500' => 'cil', 'CiPaw.04G174000' => 'cil', 'CiPaw.05G181200' => 'cil', 'CiPaw.06G067100' => 'cil', 'ClCG05G025800' => 'cla', 'ClCG06G011400' => 'cla', 'ClCG09G019360' => 'cla', 'COL.COLO4_04827' => 'col', 'COL.COLO4_29170' => 'col', 'COL.COLO4_35131' => 'col', 'COL.COLO4_35132' => 'col', 'Cpa.g.sc33.32' => 'cpa', 'Cpa.g.sc46.29' => 'cpa', 'Cpa.g.sc796.1' => 'cpa', 'CsaV3_1G030420' => 'csa', 'CsaV3_5G027050' => 'csa', 'CsaV3_5G031040' => 'csa', 'CsaV3_UNG023130' => 'csa', 'CSS0007726' => 'camsi', 'CSS0016433' => 'camsi', 'CSS0017656' => 'camsi', 'CSS0025364' => 'camsi', 'CSS0027582' => 'camsi', 'CSS0047288' => 'camsi', 'CSS0049950' => 'camsi', 'DCAR_003843' => 'dca', 'DCAR_007052' => 'dca', 'DCAR_020884' => 'dca', 'DCAR_021730' => 'dca', 'DCAR_024423' => 'dca', 'DCAR_026509' => 'dca', 'DCAR_031158' => 'dca', 'Dinv14728' => 'din', 'Dinv15219' => 'din', 'Dinv25728' => 'din', 'Dinv33428' => 'din', 'Dinv36489' => 'din', 'Dinv41486' => 'din', 'Duzib147G0469' => 'dzi', 'Duzib168G0060' => 'dzi', 'Duzib187G1215' => 'dzi', 'Duzib248G0692' => 'dzi', 'Duzib251G0767' => 'dzi', 'Duzib264G0446' => 'dzi', 'Duzib268G0691' => 'dzi', 'ECA232G4767' => 'eca', 'ECA233G2838' => 'eca', 'ECA234G0391' => 'eca', 'ECA234G0857' => 'eca', 'ECA236G1593' => 'eca', 'ECA238G0565' => 'eca', 'ECA246G1027' => 'eca', 'ECA246G3223' => 'eca', 'ECA246G3470' => 'eca', 'EL10Ac6g13829' => 'bvu', 'EL10Ac6g14093' => 'bvu', 'EL10Ac8g18707' => 'bvu', 'Eucgr.C01369' => 'egr', 'Eucgr.H02492' => 'egr', 'Eucgr.I01733' => 'egr', 'Eucgr.J02255' => 'egr', 'Eucgr.J02257' => 'egr', 'Eucgr.J02258' => 'egr', 'FAN02G1601' => 'fan', 'FAN03G1586' => 'fan', 'FAN03G2986' => 'fan', 'FAN05G4837' => 'fan', 'FAN06G0146' => 'fan', 'FAN07G0858' => 'fan', 'FAN09G3179' => 'fan', 'FAN10G0669' => 'fan', 'FAN12G2358' => 'fan', 'FAN14G4198' => 'fan', 'FAN14G5112' => 'fan', 'FAN17G0342' => 'fan', 'FAN19G0342' => 'fan', 'FAN19G0962' => 'fan', 'FAN19G1101' => 'fan', 'FAN19G1872' => 'fan', 'FAN22G0356' => 'fan', 'FAN23G0744' => 'fan', 'FAN23G1914' => 'fan', 'FAN26G0032' => 'fan', 'FAN28G0625' => 'fan', 'FvH4_1g02710' => 'fve', 'FvH4_1g02720' => 'fve', 'FvH4_4g25670' => 'fve', 'FvH4_6g51700' => 'fve', 'FvH4_7g20170' => 'fve', 'Glyma.05G175000' => 'gma', 'Glyma.08G132300' => 'gma', 'Glyma.11G243000' => 'gma', 'Glyma.13G158900' => 'gma', 'Glyma.17G112400' => 'gma', 'Glyma.18G014100' => 'gma', 'Glyma.19G003100' => 'gma', 'Glyma.19G056500' => 'gma', 'Gohir.A01G158900' => 'ghi', 'Gohir.A05G312600' => 'ghi', 'Gohir.A05G354900' => 'ghi', 'Gohir.A07G037200' => 'ghi', 'Gohir.A09G030000' => 'ghi', 'Gohir.A12G145200' => 'ghi', 'Gohir.D01G151500' => 'ghi', 'Gohir.D04G058300' => 'ghi', 'Gohir.D05G314100' => 'ghi', 'Gohir.D07G041400' => 'ghi', 'Gohir.D09G029700' => 'ghi', 'Gohir.D12G149700' => 'ghi', 'Gorai.001G043800' => 'gra', 'Gorai.002G187800' => 'gra', 'Gorai.006G034700' => 'gra', 'Gorai.008G161200' => 'gra', 'Gorai.009G335700' => 'gra', 'Gorai.012G065000' => 'gra', 'GSVIVG01000535001' => 'vvi', 'GSVIVG01015572001' => 'vvi', 'GSVIVG01032386001' => 'vvi', 'HanXRQChr05g0138531' => 'han', 'HanXRQChr06g0174391' => 'han', 'HanXRQChr07g0199021' => 'han', 'HanXRQChr08g0208211' => 'han', 'HanXRQChr09g0255471' => 'han', 'HanXRQChr10g0315791' => 'han', 'HanXRQChr12g0371991' => 'han', 'HanXRQChr15g0475251' => 'han', 'HanXRQChr17g0540001' => 'han', 'HanXRQChr17g0548631' => 'han', 'HanXRQChr17g0569561' => 'han', 'Haze_12256' => 'cav', 'Haze_14756' => 'cav', 'Haze_25528' => 'cav', 'Hma1.2p1_0079F.1_g041020' => 'hma', 'Hma1.2p1_0818F.1_g223260' => 'hma', 'Hma1.2p1_1747F.1_g300530' => 'hma', 'HPP92_004607' => 'vpl', 'HPP92_004608' => 'vpl', 'HPP92_006181' => 'vpl', 'HPP92_012192' => 'vpl', 'HPP92_015680' => 'vpl', 'HPP92_020249' => 'vpl', 'HPP92_021376' => 'vpl', 'HPP92_024275' => 'vpl', 'Hund06031' => 'sun', 'Hund25391' => 'sun', 'Lalb_Chr07g0185371' => 'lal', 'Lalb_Chr07g0185381' => 'lal', 'Lalb_Chr12g0204011' => 'lal', 'Lalb_Chr13g0301671' => 'lal', 'Lalb_Chr14g0362851' => 'lal', 'Lalb_Chr24g0403581' => 'lal', 'Lj1g0000233' => 'lja', 'Lj2g0018120' => 'lja', 'Lj3C621T0' => 'lonja', 'Lj3P1059T14' => 'lonja', 'Lj3P611T9' => 'lonja', 'Lj3P614T13' => 'lonja', 'Lj3P615T5' => 'lonja', 'Lj4g0012315' => 'lja', 'Lj4g0026182' => 'lja', 'Lj6P813T16' => 'lonja', 'Lj7C427T7' => 'lonja', 'Lj7C427T8' => 'lonja', 'Lj7P600T41' => 'lonja', 'Lju41C42G17' => 'lonja', 'Lsat_1_v5_gn_0_47300' => 'lsa', 'Lsat_1_v5_gn_2_91280' => 'lsa', 'Lsat_1_v5_gn_3_30561' => 'lsa', 'Lsat_1_v5_gn_4_184321' => 'lsa', 'Lsat_1_v5_gn_4_4041' => 'lsa', 'Lsat_1_v5_gn_5_92000' => 'lsa', 'Lsat_1_v5_gn_8_152940' => 'lsa', 'Lsat_1_v5_gn_8_62401' => 'lsa', 'Manes.06G055900' => 'mes', 'Manes.12G022200' => 'mes', 'Manes.13G023300' => 'mes', 'Manes.14G115000' => 'mes', 'Manes.15G151700' => 'mes', 'Manes.17G111300' => 'mes', 'Mapoly0226s0009' => 'mpo', 'MBI02_g25363_MAGBIO' => 'mbi', 'MBI06_g00027_MAGBIO' => 'mbi', 'MBI10_g13034_MAGBIO' => 'mbi', 'MD09G1023400' => 'mdo', 'MD13G1100100' => 'mdo', 'MD15G1169200' => 'mdo', 'MD16G1101100' => 'mdo', 'MD17G1022900' => 'mdo', 'Medtr3g096150' => 'mtr', 'Medtr4g115070' => 'mtr', 'Medtr7g033325' => 'mtr', 'Medtr8g089840' => 'mtr', 'MELO3C010319.2' => 'cme', 'MELO3C011944.2' => 'cme', 'MELO3C021589.2' => 'cme', 'Migut.E00207' => 'egut', 'Migut.H00067' => 'egut', 'Migut.K00433' => 'egut', 'Migut.K00606' => 'egut', 'Migut.K01410' => 'egut', 'MSTRG.13347' => 'ama', 'MSTRG.24045' => 'ama', 'MSTRG.2428' => 'ama', 'MSTRG.26410' => 'ama', 'MSTRG.3139' => 'ama', 'MSTRG.3286' => 'ama', 'MSTRG.563' => 'ama', 'MSTRG.7941' => 'ama', 'Nitab4.5_0000028g0060' => 'nta', 'Nitab4.5_0000065g0260' => 'nta', 'Nitab4.5_0000112g0060' => 'nta', 'Nitab4.5_0000489g0120' => 'nta', 'Nitab4.5_0001776g0050' => 'nta', 'Nitab4.5_0001854g0010' => 'nta', 'Nitab4.5_0001860g0020' => 'nta', 'Nitab4.5_0004352g0010' => 'nta', 'Nitab4.5_0008716g0020' => 'nta', 'Nitab4.5_0008922g0010' => 'nta', 'Nn3g16693' => 'nnu', 'Nn4g22596' => 'nnu', 'Nn7g37639' => 'nnu', 'Oeu001701.1' => 'oeu', 'Oeu018149.1' => 'oeu', 'Oeu026220.1' => 'oeu', 'Oeu038635.1' => 'oeu', 'Oeu049176.1' => 'oeu', 'Oeu056706.1' => 'oeu', 'Oeu056937.1' => 'oeu', 'Oeu057540.1' => 'oeu', 'Os02g0594900' => 'osa', 'Os02g0595100' => 'osa', 'Os04g0477500' => 'osa', 'Os12g0611900' => 'osa', 'Peaxi162Scf00076g00020' => 'pax', 'Peaxi162Scf00128g00217' => 'pax', 'Peaxi162Scf00129g01640' => 'pax', 'Peaxi162Scf00669g00007' => 'pax', 'Peaxi162Scf00700g00421' => 'pax', 'Peaxi162Scf00801g00038' => 'pax', 'Peaxi162Scf00891g00025' => 'pax', 'PGR083G0909' => 'pgr', 'PGR119G1005' => 'pgr', 'PGR142G2236' => 'pgr', 'PGR142G3388' => 'pgr', 'PGSC0003DMG400004514' => 'stu', 'PGSC0003DMG400012635' => 'stu', 'PGSC0003DMG400015730' => 'stu', 'PGSC0003DMG400018611' => 'stu', 'PGSC0003DMG400030897' => 'stu', 'Phvul.001G254800' => 'pvu', 'Phvul.002G260100' => 'pvu', 'Phvul.003G167600' => 'pvu', 'Phvul.004G005100' => 'pvu', 'Potri.001G343600' => 'ptr', 'Potri.006G066700' => 'ptr', 'Potri.008G186000' => 'ptr', 'Potri.010G046900' => 'ptr', 'Potri.018G127900' => 'ptr', 'Pp3c20_17750' => 'ppa', 'Pp3c24_4380' => 'ppa', 'Prupe.1G245800' => 'ppe', 'Prupe.3G293400' => 'ppe', 'Prupe.7G247400' => 'ppe', 'Psat0s145g0120' => 'psa', 'Psat0s595g0040' => 'psa', 'Psat0s595g0120' => 'psa', 'Psat3g175040' => 'psa', 'Psat7g058120' => 'psa', 'PSO017G0428' => 'pso', 'PSO063G7510' => 'pso', 'PSO067G0046' => 'pso', 'PSO478G1073' => 'pso', 'PSO675G3677' => 'pso', 'PSO675G6558' => 'pso', 'PSO675G7520' => 'pso', 'PSO675G8959' => 'pso', 'QL02p074089' => 'qlo', 'QL02p089614' => 'qlo', 'QL03p057736' => 'qlo', 'RcHm_v2.0_Chr1g0364131' => 'rch', 'RcHm_v2.0_Chr2g0087801' => 'rch', 'RcHm_v2.0_Chr2g0087821' => 'rch', 'RcHm_v2.0_Chr2g0173231' => 'rch', 'RcHm_v2.0_Chr4g0433111' => 'rch', 'Rhsim03G0250300' => 'rsi', 'Rhsim08G0048400' => 'rsi', 'Rhsim10G0014800' => 'rsi', 'Rhsim12G0040100' => 'rsi', 'Rhsim12G0109700' => 'rsi', 'Sabra06G0049600' => 'sbr', 'Sabra08G0141000' => 'sbr', 'Sabra10G0021400' => 'sbr', 'Sabra16G0222900' => 'sbr', 'Sabra18G0108600' => 'sbr', 'SalBow1G0433' => 'sbo', 'SalBow1G2038' => 'sbo', 'SalBow1G5003' => 'sbo', 'SalBow7G1197' => 'sbo', 'SalBow8G3506' => 'sbo', 'Sc03g0007300' => 'sci', 'Sc11g0000950' => 'sci', 'Sc14g0008750' => 'sci', 'Sc18g0000420' => 'sci', 'Sed0006754' => 'sed', 'Sed0008741' => 'sed', 'Sed0017172' => 'sed', 'Sed0018925' => 'sed', 'Sed0023326' => 'sed', 'Sed0025909' => 'sed', 'SEGI_05333' => 'sgi', 'SEGI_10362' => 'sgi', 'SEGI_13380' => 'sgi', 'SEGI_24306' => 'sgi', 'SEGI_29077' => 'sgi', 'SEGI_29095' => 'sgi', 'SEGI_36534' => 'sgi', 'SEGI_37506' => 'sgi', 'SEGI_38321' => 'sgi', 'SGA_v2.0_scaffold307G48031' => 'sas', 'SGA_v2.0_scaffold47G17507' => 'sas', 'SGA_v2.0_scaffold63G21736' => 'sas', 'SGA_v2.0_scaffold87G27070' => 'sas', 'SHI17794' => 'shi', 'SHI28851' => 'shi', 'SMO165G0155' => 'smo', 'SMO340G0217' => 'smo', 'SMO367G1210' => 'smo', 'Solyc02g093430.3' => 'sly', 'Solyc05g013580.4' => 'sly', 'Solyc07g008030.3' => 'sly', 'Solyc12g035470.2' => 'sly', 'Sopen02g038020' => 'spe', 'Sopen05g008490' => 'spe', 'Sopen07g003910' => 'spe', 'Sopen12g015240' => 'spe', 'Sp1g11550' => 'spa', 'Sp2g16710' => 'spa', 'Sp3g00430' => 'spa', 'Sp3g26780' => 'spa', 'Sp5g22900' => 'spa', 'Sp6g29530' => 'spa', 'TAR371G0794' => 'tar', 'TAR374G0164' => 'tar', 'TAR622G0165' => 'tar', 'TAR626G0929' => 'tar', 'TAR629G2155' => 'tar', 'THA.LOC104805282' => 'tha', 'THA.LOC104805363' => 'tha', 'THA.LOC104808968' => 'tha', 'THA.LOC104821093' => 'tha', 'THA.LOC104823953' => 'tha', 'THA.LOC104825562' => 'tha', 'THA.LOC104825665' => 'tha', 'Thecc.02G261400' => 'tca', 'Thecc.04G019200' => 'tca', 'Thecc.09G130400' => 'tca', 'Thhalv10004374m.g' => 'esa', 'Thhalv10007850m.g' => 'esa', 'Thhalv10013782m.g' => 'esa', 'Thhalv10018686m.g' => 'esa', 'Thhalv10020899m.g' => 'esa', 'Thhalv10022755m.g' => 'esa', 'TPR.G23851' => 'tpr', 'TPR.G26500' => 'tpr', 'TPR.G27267' => 'tpr', 'TPR.G32001' => 'tpr', 'TPR.G6251' => 'tpr', 'TPR.G8167' => 'tpr', 'TWI12G1330' => 'twi', 'TWI18G1239' => 'twi', 'TWI34G0979' => 'twi', 'TWI36G0670' => 'twi', 'TWI36G0707' => 'twi', 'TWI56G0233' => 'twi', 'TWI75G1809' => 'twi', 'unitig_21.g20874' => 'ugi', 'unitig_26.g10343' => 'ugi', 'unitig_46.g18392' => 'ugi', 'unitig_52.g17178' => 'ugi', 'unitig_8.g2934' => 'ugi', 'vmacro01122' => 'vma', 'vmacro05875' => 'vma', 'vmacro06147' => 'vma', 'vmacro16191' => 'vma', 'vmacro18293' => 'vma', 'VMungo0251G3707' => 'vmu', 'VMungo0464G1521' => 'vmu', 'VMungo1215G0205' => 'vmu', 'VMungo1383G2484' => 'vmu', 'Zm00001eb079610' => 'zma', 'Zm00001eb135990' => 'zma', 'Zm00001eb183710' => 'zma', 'Zm00001eb246020' => 'zma' ), 'gf_id' => 'HOM05D001124', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001124' ), 'data_identifier' => 'HOM05D001124', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001124', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '548', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02520' => 'bna', 'A03p06630' => 'bna', 'A05p44460' => 'bna', 'A06p08710' => 'bna', 'A06p41090' => 'bna', 'A07p32320' => 'bna', 'A08p32520' => 'bna', 'A09p10360' => 'bna', 'A10p24080' => 'bna', 'Aa31LG11G15250' => 'aar', 'Aa31LG1G1800' => 'aar', 'Aa31LG2G5120' => 'aar', 'Aa31LG2G6070' => 'aar', 'Aa31LG5G10770' => 'aar', 'Aa31sc61G90' => 'aar', 'Actinidia01352' => 'ach', 'Actinidia05983' => 'ach', 'Actinidia08133' => 'ach', 'Actinidia15101' => 'ach', 'Actinidia26379' => 'ach', 'Actinidia35778' => 'ach', 'Actinidia36123' => 'ach', 'Actinidia37436' => 'ach', 'Actinidia38730' => 'ach', 'Ah.02g128210' => 'amhyb', 'Ah.03g132990' => 'amhyb', 'Ah.14g079410' => 'amhyb', 'AL1G24640' => 'aly', 'AL2G26680' => 'aly', 'AL3G10530' => 'aly', 'AL3G45230' => 'aly', 'AL5G15230' => 'aly', 'AL5G16960' => 'aly', 'AL6G25210' => 'aly', 'Aqoxy2G00441' => 'aox', 'Aqoxy3G01236' => 'aox', 'Aqoxy5G03746' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3RQ047' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C7GMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9C8JER' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MBL6KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YXCZ83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZANX40' => 'arhy', 'AT1G12990' => 'ath', 'AT1G67880' => 'ath', 'AT2G13290' => 'ath', 'AT3G01620' => 'ath', 'AT3G26445' => 'ath', 'AT3G27540' => 'ath', 'AT5G14480' => 'ath', 'ATR0824G026' => 'atr', 'ATR1098G019' => 'atr', 'Atru.chr11.2145' => 'acertr', 'Atru.chr2.3636' => 'acertr', 'Atru.chr2.3644' => 'acertr', 'Atru.chr6.2422' => 'acertr', 'Atru.chr7.1112' => 'acertr', 'AUR62005469' => 'cqu', 'AUR62011166' => 'cqu', 'AUR62013319' => 'cqu', 'AUR62024273' => 'cqu', 'AUR62028420' => 'cqu', 'AUR62041942' => 'cqu', 'BcaB01g04969' => 'bca', 'BcaB01g06371' => 'bca', 'BcaB02g11494' => 'bca', 'BcaB03g15382' => 'bca', 'BcaB08g36994' => 'bca', 'BcaC03g13477' => 'bca', 'BcaC03g13478' => 'bca', 'BcaC03g13480' => 'bca', 'BcaC03g13481' => 'bca', 'BcaC03g13486' => 'bca', 'BcaC04g19031' => 'bca', 'BcaC04g23085' => 'bca', 'BcaC05g25094' => 'bca', 'BcaC05g25096' => 'bca', 'BcaC05g25138' => 'bca', 'BcaC05g30416' => 'bca', 'BcaC05g30455' => 'bca', 'BcaC06g30979' => 'bca', 'BcaC06g33805' => 'bca', 'BcaC08g46021' => 'bca', 'BcaNung03154' => 'bca', 'BolC2t06623H' => 'bol', 'BolC2t06632H' => 'bol', 'BolC2t06635H' => 'bol', 'BolC2t06638H' => 'bol', 'BolC3t13266H' => 'bol', 'BolC5t29776H' => 'bol', 'BolC6t38912H' => 'bol', 'BolC7t44183H' => 'bol', 'BolC9t54123H' => 'bol', 'BolC9t59107H' => 'bol', 'BraA02t05221Z' => 'bra', 'BraA03t09996Z' => 'bra', 'BraA05t23210Z' => 'bra', 'BraA06t24068Z' => 'bra', 'BraA06t27032Z' => 'bra', 'BraA08t35176Z' => 'bra', 'BraA09t36680Z' => 'bra', 'BraA10t44471Z' => 'bra', 'C02p06760' => 'bna', 'C02p06890' => 'bna', 'C02p07010' => 'bna', 'C03p07660' => 'bna', 'C05p10300' => 'bna', 'C06p38150' => 'bna', 'C07p36650' => 'bna', 'C08p15770' => 'bna', 'C09p12300' => 'bna', 'C09p62700' => 'bna', 'C09p75040' => 'bna', 'CAN.G13.1' => 'can', 'CAN.G138.4' => 'can', 'CAN.G44.6' => 'can', 'CAN.G473.19' => 'can', 'CANSAT01G0835' => 'cansat', 'CANSAT11G0246' => 'cansat', 'CANSAT11G1766' => 'cansat', 'CANSAT64G1954' => 'cansat', 'CARHR013330' => 'chi', 'CARHR060530' => 'chi', 'CARHR075300' => 'chi', 'CARHR105120' => 'chi', 'CARHR148910' => 'chi', 'CARHR198830' => 'chi', 'Carub.0001s1275' => 'cru', 'Carub.0002s1437' => 'cru', 'Carub.0003s0044' => 'cru', 'Carub.0003s2787' => 'cru', 'Carub.0005s0597' => 'cru', 'Carub.0006s1266' => 'cru', 'Ca_06935_v3' => 'car', 'Ca_13559_v3' => 'car', 'Ca_16941_v3' => 'car', 'Ca_16960_v3' => 'car', 'Ca_17775_v3' => 'car', 'Ca_30464_v3' => 'car', 'Cc06_g08160' => 'ccan', 'Cc07_g01520' => 'ccan', 'Cc11_g15810' => 'ccan', 'CDE02G2840' => 'cde', 'CDE03G0093' => 'cde', 'CDE04G2127' => 'cde', 'CDE07G1857' => 'cde', 'CDE09G1246' => 'cde', 'Cfa003412' => 'cfa', 'Cfa007341' => 'cfa', 'Cfa009220' => 'cfa', 'Ciclev10008737m.g' => 'ccl', 'Ciclev10015565m.g' => 'ccl', 'Ciclev10031761m.g' => 'ccl', 'CiPaw.03G045300' => 'cil', 'CiPaw.03G247200' => 'cil', 'CiPaw.04G029500' => 'cil', 'CiPaw.04G174000' => 'cil', 'CiPaw.05G181200' => 'cil', 'CiPaw.06G067100' => 'cil', 'ClCG05G025800' => 'cla', 'ClCG06G011400' => 'cla', 'ClCG09G019360' => 'cla', 'COL.COLO4_04827' => 'col', 'COL.COLO4_29170' => 'col', 'COL.COLO4_35131' => 'col', 'COL.COLO4_35132' => 'col', 'Cpa.g.sc33.32' => 'cpa', 'Cpa.g.sc46.29' => 'cpa', 'Cpa.g.sc796.1' => 'cpa', 'CsaV3_1G030420' => 'csa', 'CsaV3_5G027050' => 'csa', 'CsaV3_5G031040' => 'csa', 'CsaV3_UNG023130' => 'csa', 'CSS0007726' => 'camsi', 'CSS0016433' => 'camsi', 'CSS0017656' => 'camsi', 'CSS0025364' => 'camsi', 'CSS0027582' => 'camsi', 'CSS0047288' => 'camsi', 'CSS0049950' => 'camsi', 'DCAR_003843' => 'dca', 'DCAR_007052' => 'dca', 'DCAR_020884' => 'dca', 'DCAR_021730' => 'dca', 'DCAR_024423' => 'dca', 'DCAR_026509' => 'dca', 'DCAR_031158' => 'dca', 'Dinv14728' => 'din', 'Dinv15219' => 'din', 'Dinv25728' => 'din', 'Dinv33428' => 'din', 'Dinv36489' => 'din', 'Dinv41486' => 'din', 'Duzib147G0469' => 'dzi', 'Duzib168G0060' => 'dzi', 'Duzib187G1215' => 'dzi', 'Duzib248G0692' => 'dzi', 'Duzib251G0767' => 'dzi', 'Duzib264G0446' => 'dzi', 'Duzib268G0691' => 'dzi', 'ECA232G4767' => 'eca', 'ECA233G2838' => 'eca', 'ECA234G0391' => 'eca', 'ECA234G0857' => 'eca', 'ECA236G1593' => 'eca', 'ECA238G0565' => 'eca', 'ECA246G1027' => 'eca', 'ECA246G3223' => 'eca', 'ECA246G3470' => 'eca', 'EL10Ac6g13829' => 'bvu', 'EL10Ac6g14093' => 'bvu', 'EL10Ac8g18707' => 'bvu', 'Eucgr.C01369' => 'egr', 'Eucgr.H02492' => 'egr', 'Eucgr.I01733' => 'egr', 'Eucgr.J02255' => 'egr', 'Eucgr.J02257' => 'egr', 'Eucgr.J02258' => 'egr', 'FAN02G1601' => 'fan', 'FAN03G1586' => 'fan', 'FAN03G2986' => 'fan', 'FAN05G4837' => 'fan', 'FAN06G0146' => 'fan', 'FAN07G0858' => 'fan', 'FAN09G3179' => 'fan', 'FAN10G0669' => 'fan', 'FAN12G2358' => 'fan', 'FAN14G4198' => 'fan', 'FAN14G5112' => 'fan', 'FAN17G0342' => 'fan', 'FAN19G0342' => 'fan', 'FAN19G0962' => 'fan', 'FAN19G1101' => 'fan', 'FAN19G1872' => 'fan', 'FAN22G0356' => 'fan', 'FAN23G0744' => 'fan', 'FAN23G1914' => 'fan', 'FAN26G0032' => 'fan', 'FAN28G0625' => 'fan', 'FvH4_1g02710' => 'fve', 'FvH4_1g02720' => 'fve', 'FvH4_4g25670' => 'fve', 'FvH4_6g51700' => 'fve', 'FvH4_7g20170' => 'fve', 'Glyma.05G175000' => 'gma', 'Glyma.08G132300' => 'gma', 'Glyma.11G243000' => 'gma', 'Glyma.13G158900' => 'gma', 'Glyma.17G112400' => 'gma', 'Glyma.18G014100' => 'gma', 'Glyma.19G003100' => 'gma', 'Glyma.19G056500' => 'gma', 'Gohir.A01G158900' => 'ghi', 'Gohir.A05G312600' => 'ghi', 'Gohir.A05G354900' => 'ghi', 'Gohir.A07G037200' => 'ghi', 'Gohir.A09G030000' => 'ghi', 'Gohir.A12G145200' => 'ghi', 'Gohir.D01G151500' => 'ghi', 'Gohir.D04G058300' => 'ghi', 'Gohir.D05G314100' => 'ghi', 'Gohir.D07G041400' => 'ghi', 'Gohir.D09G029700' => 'ghi', 'Gohir.D12G149700' => 'ghi', 'Gorai.001G043800' => 'gra', 'Gorai.002G187800' => 'gra', 'Gorai.006G034700' => 'gra', 'Gorai.008G161200' => 'gra', 'Gorai.009G335700' => 'gra', 'Gorai.012G065000' => 'gra', 'GSVIVG01000535001' => 'vvi', 'GSVIVG01015572001' => 'vvi', 'GSVIVG01032386001' => 'vvi', 'HanXRQChr05g0138531' => 'han', 'HanXRQChr06g0174391' => 'han', 'HanXRQChr07g0199021' => 'han', 'HanXRQChr08g0208211' => 'han', 'HanXRQChr09g0255471' => 'han', 'HanXRQChr10g0315791' => 'han', 'HanXRQChr12g0371991' => 'han', 'HanXRQChr15g0475251' => 'han', 'HanXRQChr17g0540001' => 'han', 'HanXRQChr17g0548631' => 'han', 'HanXRQChr17g0569561' => 'han', 'Haze_12256' => 'cav', 'Haze_14756' => 'cav', 'Haze_25528' => 'cav', 'Hma1.2p1_0079F.1_g041020' => 'hma', 'Hma1.2p1_0818F.1_g223260' => 'hma', 'Hma1.2p1_1747F.1_g300530' => 'hma', 'HPP92_004607' => 'vpl', 'HPP92_004608' => 'vpl', 'HPP92_006181' => 'vpl', 'HPP92_012192' => 'vpl', 'HPP92_015680' => 'vpl', 'HPP92_020249' => 'vpl', 'HPP92_021376' => 'vpl', 'HPP92_024275' => 'vpl', 'Hund06031' => 'sun', 'Hund25391' => 'sun', 'Lalb_Chr07g0185371' => 'lal', 'Lalb_Chr07g0185381' => 'lal', 'Lalb_Chr12g0204011' => 'lal', 'Lalb_Chr13g0301671' => 'lal', 'Lalb_Chr14g0362851' => 'lal', 'Lalb_Chr24g0403581' => 'lal', 'Lj1g0000233' => 'lja', 'Lj2g0018120' => 'lja', 'Lj3C621T0' => 'lonja', 'Lj3P1059T14' => 'lonja', 'Lj3P611T9' => 'lonja', 'Lj3P614T13' => 'lonja', 'Lj3P615T5' => 'lonja', 'Lj4g0012315' => 'lja', 'Lj4g0026182' => 'lja', 'Lj6P813T16' => 'lonja', 'Lj7C427T7' => 'lonja', 'Lj7C427T8' => 'lonja', 'Lj7P600T41' => 'lonja', 'Lju41C42G17' => 'lonja', 'Lsat_1_v5_gn_0_47300' => 'lsa', 'Lsat_1_v5_gn_2_91280' => 'lsa', 'Lsat_1_v5_gn_3_30561' => 'lsa', 'Lsat_1_v5_gn_4_184321' => 'lsa', 'Lsat_1_v5_gn_4_4041' => 'lsa', 'Lsat_1_v5_gn_5_92000' => 'lsa', 'Lsat_1_v5_gn_8_152940' => 'lsa', 'Lsat_1_v5_gn_8_62401' => 'lsa', 'Manes.06G055900' => 'mes', 'Manes.12G022200' => 'mes', 'Manes.13G023300' => 'mes', 'Manes.14G115000' => 'mes', 'Manes.15G151700' => 'mes', 'Manes.17G111300' => 'mes', 'Mapoly0226s0009' => 'mpo', 'MBI02_g25363_MAGBIO' => 'mbi', 'MBI06_g00027_MAGBIO' => 'mbi', 'MBI10_g13034_MAGBIO' => 'mbi', 'MD09G1023400' => 'mdo', 'MD13G1100100' => 'mdo', 'MD15G1169200' => 'mdo', 'MD16G1101100' => 'mdo', 'MD17G1022900' => 'mdo', 'Medtr3g096150' => 'mtr', 'Medtr4g115070' => 'mtr', 'Medtr7g033325' => 'mtr', 'Medtr8g089840' => 'mtr', 'MELO3C010319.2' => 'cme', 'MELO3C011944.2' => 'cme', 'MELO3C021589.2' => 'cme', 'Migut.E00207' => 'egut', 'Migut.H00067' => 'egut', 'Migut.K00433' => 'egut', 'Migut.K00606' => 'egut', 'Migut.K01410' => 'egut', 'MSTRG.13347' => 'ama', 'MSTRG.24045' => 'ama', 'MSTRG.2428' => 'ama', 'MSTRG.26410' => 'ama', 'MSTRG.3139' => 'ama', 'MSTRG.3286' => 'ama', 'MSTRG.563' => 'ama', 'MSTRG.7941' => 'ama', 'Nitab4.5_0000028g0060' => 'nta', 'Nitab4.5_0000065g0260' => 'nta', 'Nitab4.5_0000112g0060' => 'nta', 'Nitab4.5_0000489g0120' => 'nta', 'Nitab4.5_0001776g0050' => 'nta', 'Nitab4.5_0001854g0010' => 'nta', 'Nitab4.5_0001860g0020' => 'nta', 'Nitab4.5_0004352g0010' => 'nta', 'Nitab4.5_0008716g0020' => 'nta', 'Nitab4.5_0008922g0010' => 'nta', 'Nn3g16693' => 'nnu', 'Nn4g22596' => 'nnu', 'Nn7g37639' => 'nnu', 'Oeu001701.1' => 'oeu', 'Oeu018149.1' => 'oeu', 'Oeu026220.1' => 'oeu', 'Oeu038635.1' => 'oeu', 'Oeu049176.1' => 'oeu', 'Oeu056706.1' => 'oeu', 'Oeu056937.1' => 'oeu', 'Oeu057540.1' => 'oeu', 'Os02g0594900' => 'osa', 'Os02g0595100' => 'osa', 'Os04g0477500' => 'osa', 'Os12g0611900' => 'osa', 'Peaxi162Scf00076g00020' => 'pax', 'Peaxi162Scf00128g00217' => 'pax', 'Peaxi162Scf00129g01640' => 'pax', 'Peaxi162Scf00669g00007' => 'pax', 'Peaxi162Scf00700g00421' => 'pax', 'Peaxi162Scf00801g00038' => 'pax', 'Peaxi162Scf00891g00025' => 'pax', 'PGR083G0909' => 'pgr', 'PGR119G1005' => 'pgr', 'PGR142G2236' => 'pgr', 'PGR142G3388' => 'pgr', 'PGSC0003DMG400004514' => 'stu', 'PGSC0003DMG400012635' => 'stu', 'PGSC0003DMG400015730' => 'stu', 'PGSC0003DMG400018611' => 'stu', 'PGSC0003DMG400030897' => 'stu', 'Phvul.001G254800' => 'pvu', 'Phvul.002G260100' => 'pvu', 'Phvul.003G167600' => 'pvu', 'Phvul.004G005100' => 'pvu', 'Potri.001G343600' => 'ptr', 'Potri.006G066700' => 'ptr', 'Potri.008G186000' => 'ptr', 'Potri.010G046900' => 'ptr', 'Potri.018G127900' => 'ptr', 'Pp3c20_17750' => 'ppa', 'Pp3c24_4380' => 'ppa', 'Prupe.1G245800' => 'ppe', 'Prupe.3G293400' => 'ppe', 'Prupe.7G247400' => 'ppe', 'Psat0s145g0120' => 'psa', 'Psat0s595g0040' => 'psa', 'Psat0s595g0120' => 'psa', 'Psat3g175040' => 'psa', 'Psat7g058120' => 'psa', 'PSO017G0428' => 'pso', 'PSO063G7510' => 'pso', 'PSO067G0046' => 'pso', 'PSO478G1073' => 'pso', 'PSO675G3677' => 'pso', 'PSO675G6558' => 'pso', 'PSO675G7520' => 'pso', 'PSO675G8959' => 'pso', 'QL02p074089' => 'qlo', 'QL02p089614' => 'qlo', 'QL03p057736' => 'qlo', 'RcHm_v2.0_Chr1g0364131' => 'rch', 'RcHm_v2.0_Chr2g0087801' => 'rch', 'RcHm_v2.0_Chr2g0087821' => 'rch', 'RcHm_v2.0_Chr2g0173231' => 'rch', 'RcHm_v2.0_Chr4g0433111' => 'rch', 'Rhsim03G0250300' => 'rsi', 'Rhsim08G0048400' => 'rsi', 'Rhsim10G0014800' => 'rsi', 'Rhsim12G0040100' => 'rsi', 'Rhsim12G0109700' => 'rsi', 'Sabra06G0049600' => 'sbr', 'Sabra08G0141000' => 'sbr', 'Sabra10G0021400' => 'sbr', 'Sabra16G0222900' => 'sbr', 'Sabra18G0108600' => 'sbr', 'SalBow1G0433' => 'sbo', 'SalBow1G2038' => 'sbo', 'SalBow1G5003' => 'sbo', 'SalBow7G1197' => 'sbo', 'SalBow8G3506' => 'sbo', 'Sc03g0007300' => 'sci', 'Sc11g0000950' => 'sci', 'Sc14g0008750' => 'sci', 'Sc18g0000420' => 'sci', 'Sed0006754' => 'sed', 'Sed0008741' => 'sed', 'Sed0017172' => 'sed', 'Sed0018925' => 'sed', 'Sed0023326' => 'sed', 'Sed0025909' => 'sed', 'SEGI_05333' => 'sgi', 'SEGI_10362' => 'sgi', 'SEGI_13380' => 'sgi', 'SEGI_24306' => 'sgi', 'SEGI_29077' => 'sgi', 'SEGI_29095' => 'sgi', 'SEGI_36534' => 'sgi', 'SEGI_37506' => 'sgi', 'SEGI_38321' => 'sgi', 'SGA_v2.0_scaffold307G48031' => 'sas', 'SGA_v2.0_scaffold47G17507' => 'sas', 'SGA_v2.0_scaffold63G21736' => 'sas', 'SGA_v2.0_scaffold87G27070' => 'sas', 'SHI17794' => 'shi', 'SHI28851' => 'shi', 'SMO165G0155' => 'smo', 'SMO340G0217' => 'smo', 'SMO367G1210' => 'smo', 'Solyc02g093430.3' => 'sly', 'Solyc05g013580.4' => 'sly', 'Solyc07g008030.3' => 'sly', 'Solyc12g035470.2' => 'sly', 'Sopen02g038020' => 'spe', 'Sopen05g008490' => 'spe', 'Sopen07g003910' => 'spe', 'Sopen12g015240' => 'spe', 'Sp1g11550' => 'spa', 'Sp2g16710' => 'spa', 'Sp3g00430' => 'spa', 'Sp3g26780' => 'spa', 'Sp5g22900' => 'spa', 'Sp6g29530' => 'spa', 'TAR371G0794' => 'tar', 'TAR374G0164' => 'tar', 'TAR622G0165' => 'tar', 'TAR626G0929' => 'tar', 'TAR629G2155' => 'tar', 'THA.LOC104805282' => 'tha', 'THA.LOC104805363' => 'tha', 'THA.LOC104808968' => 'tha', 'THA.LOC104821093' => 'tha', 'THA.LOC104823953' => 'tha', 'THA.LOC104825562' => 'tha', 'THA.LOC104825665' => 'tha', 'Thecc.02G261400' => 'tca', 'Thecc.04G019200' => 'tca', 'Thecc.09G130400' => 'tca', 'Thhalv10004374m.g' => 'esa', 'Thhalv10007850m.g' => 'esa', 'Thhalv10013782m.g' => 'esa', 'Thhalv10018686m.g' => 'esa', 'Thhalv10020899m.g' => 'esa', 'Thhalv10022755m.g' => 'esa', 'TPR.G23851' => 'tpr', 'TPR.G26500' => 'tpr', 'TPR.G27267' => 'tpr', 'TPR.G32001' => 'tpr', 'TPR.G6251' => 'tpr', 'TPR.G8167' => 'tpr', 'TWI12G1330' => 'twi', 'TWI18G1239' => 'twi', 'TWI34G0979' => 'twi', 'TWI36G0670' => 'twi', 'TWI36G0707' => 'twi', 'TWI56G0233' => 'twi', 'TWI75G1809' => 'twi', 'unitig_21.g20874' => 'ugi', 'unitig_26.g10343' => 'ugi', 'unitig_46.g18392' => 'ugi', 'unitig_52.g17178' => 'ugi', 'unitig_8.g2934' => 'ugi', 'vmacro01122' => 'vma', 'vmacro05875' => 'vma', 'vmacro06147' => 'vma', 'vmacro16191' => 'vma', 'vmacro18293' => 'vma', 'VMungo0251G3707' => 'vmu', 'VMungo0464G1521' => 'vmu', 'VMungo1215G0205' => 'vmu', 'VMungo1383G2484' => 'vmu', 'Zm00001eb079610' => 'zma', 'Zm00001eb135990' => 'zma', 'Zm00001eb183710' => 'zma', 'Zm00001eb246020' => 'zma' ) $gf_id = 'HOM05D001124' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001124' ) $data_identifier = 'HOM05D001124' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 6, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 7, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 21, 'bol' => (int) 10, 'bra' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 6, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 9, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 21, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 8, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 10, 'lsa' => (int) 8, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 8, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 9, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb246020' $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' => 'HOM05D001124', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '548', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02520' => 'bna', 'A03p06630' => 'bna', 'A05p44460' => 'bna', 'A06p08710' => 'bna', 'A06p41090' => 'bna', 'A07p32320' => 'bna', 'A08p32520' => 'bna', 'A09p10360' => 'bna', 'A10p24080' => 'bna', 'Aa31LG11G15250' => 'aar', 'Aa31LG1G1800' => 'aar', 'Aa31LG2G5120' => 'aar', 'Aa31LG2G6070' => 'aar', 'Aa31LG5G10770' => 'aar', 'Aa31sc61G90' => 'aar', 'Actinidia01352' => 'ach', 'Actinidia05983' => 'ach', 'Actinidia08133' => 'ach', 'Actinidia15101' => 'ach', 'Actinidia26379' => 'ach', 'Actinidia35778' => 'ach', 'Actinidia36123' => 'ach', 'Actinidia37436' => 'ach', 'Actinidia38730' => 'ach', 'Ah.02g128210' => 'amhyb', 'Ah.03g132990' => 'amhyb', 'Ah.14g079410' => 'amhyb', 'AL1G24640' => 'aly', 'AL2G26680' => 'aly', 'AL3G10530' => 'aly', 'AL3G45230' => 'aly', 'AL5G15230' => 'aly', 'AL5G16960' => 'aly', 'AL6G25210' => 'aly', 'Aqoxy2G00441' => 'aox', 'Aqoxy3G01236' => 'aox', 'Aqoxy5G03746' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3RQ047' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C7GMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9C8JER' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MBL6KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YXCZ83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZANX40' => 'arhy', 'AT1G12990' => 'ath', 'AT1G67880' => 'ath', 'AT2G13290' => 'ath', 'AT3G01620' => 'ath', 'AT3G26445' => 'ath', 'AT3G27540' => 'ath', 'AT5G14480' => 'ath', 'ATR0824G026' => 'atr', 'ATR1098G019' => 'atr', 'Atru.chr11.2145' => 'acertr', 'Atru.chr2.3636' => 'acertr', 'Atru.chr2.3644' => 'acertr', 'Atru.chr6.2422' => 'acertr', 'Atru.chr7.1112' => 'acertr', 'AUR62005469' => 'cqu', 'AUR62011166' => 'cqu', 'AUR62013319' => 'cqu', 'AUR62024273' => 'cqu', 'AUR62028420' => 'cqu', 'AUR62041942' => 'cqu', 'BcaB01g04969' => 'bca', 'BcaB01g06371' => 'bca', 'BcaB02g11494' => 'bca', 'BcaB03g15382' => 'bca', 'BcaB08g36994' => 'bca', 'BcaC03g13477' => 'bca', 'BcaC03g13478' => 'bca', 'BcaC03g13480' => 'bca', 'BcaC03g13481' => 'bca', 'BcaC03g13486' => 'bca', 'BcaC04g19031' => 'bca', 'BcaC04g23085' => 'bca', 'BcaC05g25094' => 'bca', 'BcaC05g25096' => 'bca', 'BcaC05g25138' => 'bca', 'BcaC05g30416' => 'bca', 'BcaC05g30455' => 'bca', 'BcaC06g30979' => 'bca', 'BcaC06g33805' => 'bca', 'BcaC08g46021' => 'bca', 'BcaNung03154' => 'bca', 'BolC2t06623H' => 'bol', 'BolC2t06632H' => 'bol', 'BolC2t06635H' => 'bol', 'BolC2t06638H' => 'bol', 'BolC3t13266H' => 'bol', 'BolC5t29776H' => 'bol', 'BolC6t38912H' => 'bol', 'BolC7t44183H' => 'bol', 'BolC9t54123H' => 'bol', 'BolC9t59107H' => 'bol', 'BraA02t05221Z' => 'bra', 'BraA03t09996Z' => 'bra', 'BraA05t23210Z' => 'bra', 'BraA06t24068Z' => 'bra', 'BraA06t27032Z' => 'bra', 'BraA08t35176Z' => 'bra', 'BraA09t36680Z' => 'bra', 'BraA10t44471Z' => 'bra', 'C02p06760' => 'bna', 'C02p06890' => 'bna', 'C02p07010' => 'bna', 'C03p07660' => 'bna', 'C05p10300' => 'bna', 'C06p38150' => 'bna', 'C07p36650' => 'bna', 'C08p15770' => 'bna', 'C09p12300' => 'bna', 'C09p62700' => 'bna', 'C09p75040' => 'bna', 'CAN.G13.1' => 'can', 'CAN.G138.4' => 'can', 'CAN.G44.6' => 'can', 'CAN.G473.19' => 'can', 'CANSAT01G0835' => 'cansat', 'CANSAT11G0246' => 'cansat', 'CANSAT11G1766' => 'cansat', 'CANSAT64G1954' => 'cansat', 'CARHR013330' => 'chi', 'CARHR060530' => 'chi', 'CARHR075300' => 'chi', 'CARHR105120' => 'chi', 'CARHR148910' => 'chi', 'CARHR198830' => 'chi', 'Carub.0001s1275' => 'cru', 'Carub.0002s1437' => 'cru', 'Carub.0003s0044' => 'cru', 'Carub.0003s2787' => 'cru', 'Carub.0005s0597' => 'cru', 'Carub.0006s1266' => 'cru', 'Ca_06935_v3' => 'car', 'Ca_13559_v3' => 'car', 'Ca_16941_v3' => 'car', 'Ca_16960_v3' => 'car', 'Ca_17775_v3' => 'car', 'Ca_30464_v3' => 'car', 'Cc06_g08160' => 'ccan', 'Cc07_g01520' => 'ccan', 'Cc11_g15810' => 'ccan', 'CDE02G2840' => 'cde', 'CDE03G0093' => 'cde', 'CDE04G2127' => 'cde', 'CDE07G1857' => 'cde', 'CDE09G1246' => 'cde', 'Cfa003412' => 'cfa', 'Cfa007341' => 'cfa', 'Cfa009220' => 'cfa', 'Ciclev10008737m.g' => 'ccl', 'Ciclev10015565m.g' => 'ccl', 'Ciclev10031761m.g' => 'ccl', 'CiPaw.03G045300' => 'cil', 'CiPaw.03G247200' => 'cil', 'CiPaw.04G029500' => 'cil', 'CiPaw.04G174000' => 'cil', 'CiPaw.05G181200' => 'cil', 'CiPaw.06G067100' => 'cil', 'ClCG05G025800' => 'cla', 'ClCG06G011400' => 'cla', 'ClCG09G019360' => 'cla', 'COL.COLO4_04827' => 'col', 'COL.COLO4_29170' => 'col', 'COL.COLO4_35131' => 'col', 'COL.COLO4_35132' => 'col', 'Cpa.g.sc33.32' => 'cpa', 'Cpa.g.sc46.29' => 'cpa', 'Cpa.g.sc796.1' => 'cpa', 'CsaV3_1G030420' => 'csa', 'CsaV3_5G027050' => 'csa', 'CsaV3_5G031040' => 'csa', 'CsaV3_UNG023130' => 'csa', 'CSS0007726' => 'camsi', 'CSS0016433' => 'camsi', 'CSS0017656' => 'camsi', 'CSS0025364' => 'camsi', 'CSS0027582' => 'camsi', 'CSS0047288' => 'camsi', 'CSS0049950' => 'camsi', 'DCAR_003843' => 'dca', 'DCAR_007052' => 'dca', 'DCAR_020884' => 'dca', 'DCAR_021730' => 'dca', 'DCAR_024423' => 'dca', 'DCAR_026509' => 'dca', 'DCAR_031158' => 'dca', 'Dinv14728' => 'din', 'Dinv15219' => 'din', 'Dinv25728' => 'din', 'Dinv33428' => 'din', 'Dinv36489' => 'din', 'Dinv41486' => 'din', 'Duzib147G0469' => 'dzi', 'Duzib168G0060' => 'dzi', 'Duzib187G1215' => 'dzi', 'Duzib248G0692' => 'dzi', 'Duzib251G0767' => 'dzi', 'Duzib264G0446' => 'dzi', 'Duzib268G0691' => 'dzi', 'ECA232G4767' => 'eca', 'ECA233G2838' => 'eca', 'ECA234G0391' => 'eca', 'ECA234G0857' => 'eca', 'ECA236G1593' => 'eca', 'ECA238G0565' => 'eca', 'ECA246G1027' => 'eca', 'ECA246G3223' => 'eca', 'ECA246G3470' => 'eca', 'EL10Ac6g13829' => 'bvu', 'EL10Ac6g14093' => 'bvu', 'EL10Ac8g18707' => 'bvu', 'Eucgr.C01369' => 'egr', 'Eucgr.H02492' => 'egr', 'Eucgr.I01733' => 'egr', 'Eucgr.J02255' => 'egr', 'Eucgr.J02257' => 'egr', 'Eucgr.J02258' => 'egr', 'FAN02G1601' => 'fan', 'FAN03G1586' => 'fan', 'FAN03G2986' => 'fan', 'FAN05G4837' => 'fan', 'FAN06G0146' => 'fan', 'FAN07G0858' => 'fan', 'FAN09G3179' => 'fan', 'FAN10G0669' => 'fan', 'FAN12G2358' => 'fan', 'FAN14G4198' => 'fan', 'FAN14G5112' => 'fan', 'FAN17G0342' => 'fan', 'FAN19G0342' => 'fan', 'FAN19G0962' => 'fan', 'FAN19G1101' => 'fan', 'FAN19G1872' => 'fan', 'FAN22G0356' => 'fan', 'FAN23G0744' => 'fan', 'FAN23G1914' => 'fan', 'FAN26G0032' => 'fan', 'FAN28G0625' => 'fan', 'FvH4_1g02710' => 'fve', 'FvH4_1g02720' => 'fve', 'FvH4_4g25670' => 'fve', 'FvH4_6g51700' => 'fve', 'FvH4_7g20170' => 'fve', 'Glyma.05G175000' => 'gma', 'Glyma.08G132300' => 'gma', 'Glyma.11G243000' => 'gma', 'Glyma.13G158900' => 'gma', 'Glyma.17G112400' => 'gma', 'Glyma.18G014100' => 'gma', 'Glyma.19G003100' => 'gma', 'Glyma.19G056500' => 'gma', 'Gohir.A01G158900' => 'ghi', 'Gohir.A05G312600' => 'ghi', 'Gohir.A05G354900' => 'ghi', 'Gohir.A07G037200' => 'ghi', 'Gohir.A09G030000' => 'ghi', 'Gohir.A12G145200' => 'ghi', 'Gohir.D01G151500' => 'ghi', 'Gohir.D04G058300' => 'ghi', 'Gohir.D05G314100' => 'ghi', 'Gohir.D07G041400' => 'ghi', 'Gohir.D09G029700' => 'ghi', 'Gohir.D12G149700' => 'ghi', 'Gorai.001G043800' => 'gra', 'Gorai.002G187800' => 'gra', 'Gorai.006G034700' => 'gra', 'Gorai.008G161200' => 'gra', 'Gorai.009G335700' => 'gra', 'Gorai.012G065000' => 'gra', 'GSVIVG01000535001' => 'vvi', 'GSVIVG01015572001' => 'vvi', 'GSVIVG01032386001' => 'vvi', 'HanXRQChr05g0138531' => 'han', 'HanXRQChr06g0174391' => 'han', 'HanXRQChr07g0199021' => 'han', 'HanXRQChr08g0208211' => 'han', 'HanXRQChr09g0255471' => 'han', 'HanXRQChr10g0315791' => 'han', 'HanXRQChr12g0371991' => 'han', 'HanXRQChr15g0475251' => 'han', 'HanXRQChr17g0540001' => 'han', 'HanXRQChr17g0548631' => 'han', 'HanXRQChr17g0569561' => 'han', 'Haze_12256' => 'cav', 'Haze_14756' => 'cav', 'Haze_25528' => 'cav', 'Hma1.2p1_0079F.1_g041020' => 'hma', 'Hma1.2p1_0818F.1_g223260' => 'hma', 'Hma1.2p1_1747F.1_g300530' => 'hma', 'HPP92_004607' => 'vpl', 'HPP92_004608' => 'vpl', 'HPP92_006181' => 'vpl', 'HPP92_012192' => 'vpl', 'HPP92_015680' => 'vpl', 'HPP92_020249' => 'vpl', 'HPP92_021376' => 'vpl', 'HPP92_024275' => 'vpl', 'Hund06031' => 'sun', 'Hund25391' => 'sun', 'Lalb_Chr07g0185371' => 'lal', 'Lalb_Chr07g0185381' => 'lal', 'Lalb_Chr12g0204011' => 'lal', 'Lalb_Chr13g0301671' => 'lal', 'Lalb_Chr14g0362851' => 'lal', 'Lalb_Chr24g0403581' => 'lal', 'Lj1g0000233' => 'lja', 'Lj2g0018120' => 'lja', 'Lj3C621T0' => 'lonja', 'Lj3P1059T14' => 'lonja', 'Lj3P611T9' => 'lonja', 'Lj3P614T13' => 'lonja', 'Lj3P615T5' => 'lonja', 'Lj4g0012315' => 'lja', 'Lj4g0026182' => 'lja', 'Lj6P813T16' => 'lonja', 'Lj7C427T7' => 'lonja', 'Lj7C427T8' => 'lonja', 'Lj7P600T41' => 'lonja', 'Lju41C42G17' => 'lonja', 'Lsat_1_v5_gn_0_47300' => 'lsa', 'Lsat_1_v5_gn_2_91280' => 'lsa', 'Lsat_1_v5_gn_3_30561' => 'lsa', 'Lsat_1_v5_gn_4_184321' => 'lsa', 'Lsat_1_v5_gn_4_4041' => 'lsa', 'Lsat_1_v5_gn_5_92000' => 'lsa', 'Lsat_1_v5_gn_8_152940' => 'lsa', 'Lsat_1_v5_gn_8_62401' => 'lsa', 'Manes.06G055900' => 'mes', 'Manes.12G022200' => 'mes', 'Manes.13G023300' => 'mes', 'Manes.14G115000' => 'mes', 'Manes.15G151700' => 'mes', 'Manes.17G111300' => 'mes', 'Mapoly0226s0009' => 'mpo', 'MBI02_g25363_MAGBIO' => 'mbi', 'MBI06_g00027_MAGBIO' => 'mbi', 'MBI10_g13034_MAGBIO' => 'mbi', 'MD09G1023400' => 'mdo', 'MD13G1100100' => 'mdo', 'MD15G1169200' => 'mdo', 'MD16G1101100' => 'mdo', 'MD17G1022900' => 'mdo', 'Medtr3g096150' => 'mtr', 'Medtr4g115070' => 'mtr', 'Medtr7g033325' => 'mtr', 'Medtr8g089840' => 'mtr', 'MELO3C010319.2' => 'cme', 'MELO3C011944.2' => 'cme', 'MELO3C021589.2' => 'cme', 'Migut.E00207' => 'egut', 'Migut.H00067' => 'egut', 'Migut.K00433' => 'egut', 'Migut.K00606' => 'egut', 'Migut.K01410' => 'egut', 'MSTRG.13347' => 'ama', 'MSTRG.24045' => 'ama', 'MSTRG.2428' => 'ama', 'MSTRG.26410' => 'ama', 'MSTRG.3139' => 'ama', 'MSTRG.3286' => 'ama', 'MSTRG.563' => 'ama', 'MSTRG.7941' => 'ama', 'Nitab4.5_0000028g0060' => 'nta', 'Nitab4.5_0000065g0260' => 'nta', 'Nitab4.5_0000112g0060' => 'nta', 'Nitab4.5_0000489g0120' => 'nta', 'Nitab4.5_0001776g0050' => 'nta', 'Nitab4.5_0001854g0010' => 'nta', 'Nitab4.5_0001860g0020' => 'nta', 'Nitab4.5_0004352g0010' => 'nta', 'Nitab4.5_0008716g0020' => 'nta', 'Nitab4.5_0008922g0010' => 'nta', 'Nn3g16693' => 'nnu', 'Nn4g22596' => 'nnu', 'Nn7g37639' => 'nnu', 'Oeu001701.1' => 'oeu', 'Oeu018149.1' => 'oeu', 'Oeu026220.1' => 'oeu', 'Oeu038635.1' => 'oeu', 'Oeu049176.1' => 'oeu', 'Oeu056706.1' => 'oeu', 'Oeu056937.1' => 'oeu', 'Oeu057540.1' => 'oeu', 'Os02g0594900' => 'osa', 'Os02g0595100' => 'osa', 'Os04g0477500' => 'osa', 'Os12g0611900' => 'osa', 'Peaxi162Scf00076g00020' => 'pax', 'Peaxi162Scf00128g00217' => 'pax', 'Peaxi162Scf00129g01640' => 'pax', 'Peaxi162Scf00669g00007' => 'pax', 'Peaxi162Scf00700g00421' => 'pax', 'Peaxi162Scf00801g00038' => 'pax', 'Peaxi162Scf00891g00025' => 'pax', 'PGR083G0909' => 'pgr', 'PGR119G1005' => 'pgr', 'PGR142G2236' => 'pgr', 'PGR142G3388' => 'pgr', 'PGSC0003DMG400004514' => 'stu', 'PGSC0003DMG400012635' => 'stu', 'PGSC0003DMG400015730' => 'stu', 'PGSC0003DMG400018611' => 'stu', 'PGSC0003DMG400030897' => 'stu', 'Phvul.001G254800' => 'pvu', 'Phvul.002G260100' => 'pvu', 'Phvul.003G167600' => 'pvu', 'Phvul.004G005100' => 'pvu', 'Potri.001G343600' => 'ptr', 'Potri.006G066700' => 'ptr', 'Potri.008G186000' => 'ptr', 'Potri.010G046900' => 'ptr', 'Potri.018G127900' => 'ptr', 'Pp3c20_17750' => 'ppa', 'Pp3c24_4380' => 'ppa', 'Prupe.1G245800' => 'ppe', 'Prupe.3G293400' => 'ppe', 'Prupe.7G247400' => 'ppe', 'Psat0s145g0120' => 'psa', 'Psat0s595g0040' => 'psa', 'Psat0s595g0120' => 'psa', 'Psat3g175040' => 'psa', 'Psat7g058120' => 'psa', 'PSO017G0428' => 'pso', 'PSO063G7510' => 'pso', 'PSO067G0046' => 'pso', 'PSO478G1073' => 'pso', 'PSO675G3677' => 'pso', 'PSO675G6558' => 'pso', 'PSO675G7520' => 'pso', 'PSO675G8959' => 'pso', 'QL02p074089' => 'qlo', 'QL02p089614' => 'qlo', 'QL03p057736' => 'qlo', 'RcHm_v2.0_Chr1g0364131' => 'rch', 'RcHm_v2.0_Chr2g0087801' => 'rch', 'RcHm_v2.0_Chr2g0087821' => 'rch', 'RcHm_v2.0_Chr2g0173231' => 'rch', 'RcHm_v2.0_Chr4g0433111' => 'rch', 'Rhsim03G0250300' => 'rsi', 'Rhsim08G0048400' => 'rsi', 'Rhsim10G0014800' => 'rsi', 'Rhsim12G0040100' => 'rsi', 'Rhsim12G0109700' => 'rsi', 'Sabra06G0049600' => 'sbr', 'Sabra08G0141000' => 'sbr', 'Sabra10G0021400' => 'sbr', 'Sabra16G0222900' => 'sbr', 'Sabra18G0108600' => 'sbr', 'SalBow1G0433' => 'sbo', 'SalBow1G2038' => 'sbo', 'SalBow1G5003' => 'sbo', 'SalBow7G1197' => 'sbo', 'SalBow8G3506' => 'sbo', 'Sc03g0007300' => 'sci', 'Sc11g0000950' => 'sci', 'Sc14g0008750' => 'sci', 'Sc18g0000420' => 'sci', 'Sed0006754' => 'sed', 'Sed0008741' => 'sed', 'Sed0017172' => 'sed', 'Sed0018925' => 'sed', 'Sed0023326' => 'sed', 'Sed0025909' => 'sed', 'SEGI_05333' => 'sgi', 'SEGI_10362' => 'sgi', 'SEGI_13380' => 'sgi', 'SEGI_24306' => 'sgi', 'SEGI_29077' => 'sgi', 'SEGI_29095' => 'sgi', 'SEGI_36534' => 'sgi', 'SEGI_37506' => 'sgi', 'SEGI_38321' => 'sgi', 'SGA_v2.0_scaffold307G48031' => 'sas', 'SGA_v2.0_scaffold47G17507' => 'sas', 'SGA_v2.0_scaffold63G21736' => 'sas', 'SGA_v2.0_scaffold87G27070' => 'sas', 'SHI17794' => 'shi', 'SHI28851' => 'shi', 'SMO165G0155' => 'smo', 'SMO340G0217' => 'smo', 'SMO367G1210' => 'smo', 'Solyc02g093430.3' => 'sly', 'Solyc05g013580.4' => 'sly', 'Solyc07g008030.3' => 'sly', 'Solyc12g035470.2' => 'sly', 'Sopen02g038020' => 'spe', 'Sopen05g008490' => 'spe', 'Sopen07g003910' => 'spe', 'Sopen12g015240' => 'spe', 'Sp1g11550' => 'spa', 'Sp2g16710' => 'spa', 'Sp3g00430' => 'spa', 'Sp3g26780' => 'spa', 'Sp5g22900' => 'spa', 'Sp6g29530' => 'spa', 'TAR371G0794' => 'tar', 'TAR374G0164' => 'tar', 'TAR622G0165' => 'tar', 'TAR626G0929' => 'tar', 'TAR629G2155' => 'tar', 'THA.LOC104805282' => 'tha', 'THA.LOC104805363' => 'tha', 'THA.LOC104808968' => 'tha', 'THA.LOC104821093' => 'tha', 'THA.LOC104823953' => 'tha', 'THA.LOC104825562' => 'tha', 'THA.LOC104825665' => 'tha', 'Thecc.02G261400' => 'tca', 'Thecc.04G019200' => 'tca', 'Thecc.09G130400' => 'tca', 'Thhalv10004374m.g' => 'esa', 'Thhalv10007850m.g' => 'esa', 'Thhalv10013782m.g' => 'esa', 'Thhalv10018686m.g' => 'esa', 'Thhalv10020899m.g' => 'esa', 'Thhalv10022755m.g' => 'esa', 'TPR.G23851' => 'tpr', 'TPR.G26500' => 'tpr', 'TPR.G27267' => 'tpr', 'TPR.G32001' => 'tpr', 'TPR.G6251' => 'tpr', 'TPR.G8167' => 'tpr', 'TWI12G1330' => 'twi', 'TWI18G1239' => 'twi', 'TWI34G0979' => 'twi', 'TWI36G0670' => 'twi', 'TWI36G0707' => 'twi', 'TWI56G0233' => 'twi', 'TWI75G1809' => 'twi', 'unitig_21.g20874' => 'ugi', 'unitig_26.g10343' => 'ugi', 'unitig_46.g18392' => 'ugi', 'unitig_52.g17178' => 'ugi', 'unitig_8.g2934' => 'ugi', 'vmacro01122' => 'vma', 'vmacro05875' => 'vma', 'vmacro06147' => 'vma', 'vmacro16191' => 'vma', 'vmacro18293' => 'vma', 'VMungo0251G3707' => 'vmu', 'VMungo0464G1521' => 'vmu', 'VMungo1215G0205' => 'vmu', 'VMungo1383G2484' => 'vmu', 'Zm00001eb079610' => 'zma', 'Zm00001eb135990' => 'zma', 'Zm00001eb183710' => 'zma', 'Zm00001eb246020' => 'zma' ), 'gf_id' => 'HOM05D001124', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001124' ), 'data_identifier' => 'HOM05D001124', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001124', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '548', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02520' => 'bna', 'A03p06630' => 'bna', 'A05p44460' => 'bna', 'A06p08710' => 'bna', 'A06p41090' => 'bna', 'A07p32320' => 'bna', 'A08p32520' => 'bna', 'A09p10360' => 'bna', 'A10p24080' => 'bna', 'Aa31LG11G15250' => 'aar', 'Aa31LG1G1800' => 'aar', 'Aa31LG2G5120' => 'aar', 'Aa31LG2G6070' => 'aar', 'Aa31LG5G10770' => 'aar', 'Aa31sc61G90' => 'aar', 'Actinidia01352' => 'ach', 'Actinidia05983' => 'ach', 'Actinidia08133' => 'ach', 'Actinidia15101' => 'ach', 'Actinidia26379' => 'ach', 'Actinidia35778' => 'ach', 'Actinidia36123' => 'ach', 'Actinidia37436' => 'ach', 'Actinidia38730' => 'ach', 'Ah.02g128210' => 'amhyb', 'Ah.03g132990' => 'amhyb', 'Ah.14g079410' => 'amhyb', 'AL1G24640' => 'aly', 'AL2G26680' => 'aly', 'AL3G10530' => 'aly', 'AL3G45230' => 'aly', 'AL5G15230' => 'aly', 'AL5G16960' => 'aly', 'AL6G25210' => 'aly', 'Aqoxy2G00441' => 'aox', 'Aqoxy3G01236' => 'aox', 'Aqoxy5G03746' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3RQ047' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C7GMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9C8JER' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MBL6KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YXCZ83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZANX40' => 'arhy', 'AT1G12990' => 'ath', 'AT1G67880' => 'ath', 'AT2G13290' => 'ath', 'AT3G01620' => 'ath', 'AT3G26445' => 'ath', 'AT3G27540' => 'ath', 'AT5G14480' => 'ath', 'ATR0824G026' => 'atr', 'ATR1098G019' => 'atr', 'Atru.chr11.2145' => 'acertr', 'Atru.chr2.3636' => 'acertr', 'Atru.chr2.3644' => 'acertr', 'Atru.chr6.2422' => 'acertr', 'Atru.chr7.1112' => 'acertr', 'AUR62005469' => 'cqu', 'AUR62011166' => 'cqu', 'AUR62013319' => 'cqu', 'AUR62024273' => 'cqu', 'AUR62028420' => 'cqu', 'AUR62041942' => 'cqu', 'BcaB01g04969' => 'bca', 'BcaB01g06371' => 'bca', 'BcaB02g11494' => 'bca', 'BcaB03g15382' => 'bca', 'BcaB08g36994' => 'bca', 'BcaC03g13477' => 'bca', 'BcaC03g13478' => 'bca', 'BcaC03g13480' => 'bca', 'BcaC03g13481' => 'bca', 'BcaC03g13486' => 'bca', 'BcaC04g19031' => 'bca', 'BcaC04g23085' => 'bca', 'BcaC05g25094' => 'bca', 'BcaC05g25096' => 'bca', 'BcaC05g25138' => 'bca', 'BcaC05g30416' => 'bca', 'BcaC05g30455' => 'bca', 'BcaC06g30979' => 'bca', 'BcaC06g33805' => 'bca', 'BcaC08g46021' => 'bca', 'BcaNung03154' => 'bca', 'BolC2t06623H' => 'bol', 'BolC2t06632H' => 'bol', 'BolC2t06635H' => 'bol', 'BolC2t06638H' => 'bol', 'BolC3t13266H' => 'bol', 'BolC5t29776H' => 'bol', 'BolC6t38912H' => 'bol', 'BolC7t44183H' => 'bol', 'BolC9t54123H' => 'bol', 'BolC9t59107H' => 'bol', 'BraA02t05221Z' => 'bra', 'BraA03t09996Z' => 'bra', 'BraA05t23210Z' => 'bra', 'BraA06t24068Z' => 'bra', 'BraA06t27032Z' => 'bra', 'BraA08t35176Z' => 'bra', 'BraA09t36680Z' => 'bra', 'BraA10t44471Z' => 'bra', 'C02p06760' => 'bna', 'C02p06890' => 'bna', 'C02p07010' => 'bna', 'C03p07660' => 'bna', 'C05p10300' => 'bna', 'C06p38150' => 'bna', 'C07p36650' => 'bna', 'C08p15770' => 'bna', 'C09p12300' => 'bna', 'C09p62700' => 'bna', 'C09p75040' => 'bna', 'CAN.G13.1' => 'can', 'CAN.G138.4' => 'can', 'CAN.G44.6' => 'can', 'CAN.G473.19' => 'can', 'CANSAT01G0835' => 'cansat', 'CANSAT11G0246' => 'cansat', 'CANSAT11G1766' => 'cansat', 'CANSAT64G1954' => 'cansat', 'CARHR013330' => 'chi', 'CARHR060530' => 'chi', 'CARHR075300' => 'chi', 'CARHR105120' => 'chi', 'CARHR148910' => 'chi', 'CARHR198830' => 'chi', 'Carub.0001s1275' => 'cru', 'Carub.0002s1437' => 'cru', 'Carub.0003s0044' => 'cru', 'Carub.0003s2787' => 'cru', 'Carub.0005s0597' => 'cru', 'Carub.0006s1266' => 'cru', 'Ca_06935_v3' => 'car', 'Ca_13559_v3' => 'car', 'Ca_16941_v3' => 'car', 'Ca_16960_v3' => 'car', 'Ca_17775_v3' => 'car', 'Ca_30464_v3' => 'car', 'Cc06_g08160' => 'ccan', 'Cc07_g01520' => 'ccan', 'Cc11_g15810' => 'ccan', 'CDE02G2840' => 'cde', 'CDE03G0093' => 'cde', 'CDE04G2127' => 'cde', 'CDE07G1857' => 'cde', 'CDE09G1246' => 'cde', 'Cfa003412' => 'cfa', 'Cfa007341' => 'cfa', 'Cfa009220' => 'cfa', 'Ciclev10008737m.g' => 'ccl', 'Ciclev10015565m.g' => 'ccl', 'Ciclev10031761m.g' => 'ccl', 'CiPaw.03G045300' => 'cil', 'CiPaw.03G247200' => 'cil', 'CiPaw.04G029500' => 'cil', 'CiPaw.04G174000' => 'cil', 'CiPaw.05G181200' => 'cil', 'CiPaw.06G067100' => 'cil', 'ClCG05G025800' => 'cla', 'ClCG06G011400' => 'cla', 'ClCG09G019360' => 'cla', 'COL.COLO4_04827' => 'col', 'COL.COLO4_29170' => 'col', 'COL.COLO4_35131' => 'col', 'COL.COLO4_35132' => 'col', 'Cpa.g.sc33.32' => 'cpa', 'Cpa.g.sc46.29' => 'cpa', 'Cpa.g.sc796.1' => 'cpa', 'CsaV3_1G030420' => 'csa', 'CsaV3_5G027050' => 'csa', 'CsaV3_5G031040' => 'csa', 'CsaV3_UNG023130' => 'csa', 'CSS0007726' => 'camsi', 'CSS0016433' => 'camsi', 'CSS0017656' => 'camsi', 'CSS0025364' => 'camsi', 'CSS0027582' => 'camsi', 'CSS0047288' => 'camsi', 'CSS0049950' => 'camsi', 'DCAR_003843' => 'dca', 'DCAR_007052' => 'dca', 'DCAR_020884' => 'dca', 'DCAR_021730' => 'dca', 'DCAR_024423' => 'dca', 'DCAR_026509' => 'dca', 'DCAR_031158' => 'dca', 'Dinv14728' => 'din', 'Dinv15219' => 'din', 'Dinv25728' => 'din', 'Dinv33428' => 'din', 'Dinv36489' => 'din', 'Dinv41486' => 'din', 'Duzib147G0469' => 'dzi', 'Duzib168G0060' => 'dzi', 'Duzib187G1215' => 'dzi', 'Duzib248G0692' => 'dzi', 'Duzib251G0767' => 'dzi', 'Duzib264G0446' => 'dzi', 'Duzib268G0691' => 'dzi', 'ECA232G4767' => 'eca', 'ECA233G2838' => 'eca', 'ECA234G0391' => 'eca', 'ECA234G0857' => 'eca', 'ECA236G1593' => 'eca', 'ECA238G0565' => 'eca', 'ECA246G1027' => 'eca', 'ECA246G3223' => 'eca', 'ECA246G3470' => 'eca', 'EL10Ac6g13829' => 'bvu', 'EL10Ac6g14093' => 'bvu', 'EL10Ac8g18707' => 'bvu', 'Eucgr.C01369' => 'egr', 'Eucgr.H02492' => 'egr', 'Eucgr.I01733' => 'egr', 'Eucgr.J02255' => 'egr', 'Eucgr.J02257' => 'egr', 'Eucgr.J02258' => 'egr', 'FAN02G1601' => 'fan', 'FAN03G1586' => 'fan', 'FAN03G2986' => 'fan', 'FAN05G4837' => 'fan', 'FAN06G0146' => 'fan', 'FAN07G0858' => 'fan', 'FAN09G3179' => 'fan', 'FAN10G0669' => 'fan', 'FAN12G2358' => 'fan', 'FAN14G4198' => 'fan', 'FAN14G5112' => 'fan', 'FAN17G0342' => 'fan', 'FAN19G0342' => 'fan', 'FAN19G0962' => 'fan', 'FAN19G1101' => 'fan', 'FAN19G1872' => 'fan', 'FAN22G0356' => 'fan', 'FAN23G0744' => 'fan', 'FAN23G1914' => 'fan', 'FAN26G0032' => 'fan', 'FAN28G0625' => 'fan', 'FvH4_1g02710' => 'fve', 'FvH4_1g02720' => 'fve', 'FvH4_4g25670' => 'fve', 'FvH4_6g51700' => 'fve', 'FvH4_7g20170' => 'fve', 'Glyma.05G175000' => 'gma', 'Glyma.08G132300' => 'gma', 'Glyma.11G243000' => 'gma', 'Glyma.13G158900' => 'gma', 'Glyma.17G112400' => 'gma', 'Glyma.18G014100' => 'gma', 'Glyma.19G003100' => 'gma', 'Glyma.19G056500' => 'gma', 'Gohir.A01G158900' => 'ghi', 'Gohir.A05G312600' => 'ghi', 'Gohir.A05G354900' => 'ghi', 'Gohir.A07G037200' => 'ghi', 'Gohir.A09G030000' => 'ghi', 'Gohir.A12G145200' => 'ghi', 'Gohir.D01G151500' => 'ghi', 'Gohir.D04G058300' => 'ghi', 'Gohir.D05G314100' => 'ghi', 'Gohir.D07G041400' => 'ghi', 'Gohir.D09G029700' => 'ghi', 'Gohir.D12G149700' => 'ghi', 'Gorai.001G043800' => 'gra', 'Gorai.002G187800' => 'gra', 'Gorai.006G034700' => 'gra', 'Gorai.008G161200' => 'gra', 'Gorai.009G335700' => 'gra', 'Gorai.012G065000' => 'gra', 'GSVIVG01000535001' => 'vvi', 'GSVIVG01015572001' => 'vvi', 'GSVIVG01032386001' => 'vvi', 'HanXRQChr05g0138531' => 'han', 'HanXRQChr06g0174391' => 'han', 'HanXRQChr07g0199021' => 'han', 'HanXRQChr08g0208211' => 'han', 'HanXRQChr09g0255471' => 'han', 'HanXRQChr10g0315791' => 'han', 'HanXRQChr12g0371991' => 'han', 'HanXRQChr15g0475251' => 'han', 'HanXRQChr17g0540001' => 'han', 'HanXRQChr17g0548631' => 'han', 'HanXRQChr17g0569561' => 'han', 'Haze_12256' => 'cav', 'Haze_14756' => 'cav', 'Haze_25528' => 'cav', 'Hma1.2p1_0079F.1_g041020' => 'hma', 'Hma1.2p1_0818F.1_g223260' => 'hma', 'Hma1.2p1_1747F.1_g300530' => 'hma', 'HPP92_004607' => 'vpl', 'HPP92_004608' => 'vpl', 'HPP92_006181' => 'vpl', 'HPP92_012192' => 'vpl', 'HPP92_015680' => 'vpl', 'HPP92_020249' => 'vpl', 'HPP92_021376' => 'vpl', 'HPP92_024275' => 'vpl', 'Hund06031' => 'sun', 'Hund25391' => 'sun', 'Lalb_Chr07g0185371' => 'lal', 'Lalb_Chr07g0185381' => 'lal', 'Lalb_Chr12g0204011' => 'lal', 'Lalb_Chr13g0301671' => 'lal', 'Lalb_Chr14g0362851' => 'lal', 'Lalb_Chr24g0403581' => 'lal', 'Lj1g0000233' => 'lja', 'Lj2g0018120' => 'lja', 'Lj3C621T0' => 'lonja', 'Lj3P1059T14' => 'lonja', 'Lj3P611T9' => 'lonja', 'Lj3P614T13' => 'lonja', 'Lj3P615T5' => 'lonja', 'Lj4g0012315' => 'lja', 'Lj4g0026182' => 'lja', 'Lj6P813T16' => 'lonja', 'Lj7C427T7' => 'lonja', 'Lj7C427T8' => 'lonja', 'Lj7P600T41' => 'lonja', 'Lju41C42G17' => 'lonja', 'Lsat_1_v5_gn_0_47300' => 'lsa', 'Lsat_1_v5_gn_2_91280' => 'lsa', 'Lsat_1_v5_gn_3_30561' => 'lsa', 'Lsat_1_v5_gn_4_184321' => 'lsa', 'Lsat_1_v5_gn_4_4041' => 'lsa', 'Lsat_1_v5_gn_5_92000' => 'lsa', 'Lsat_1_v5_gn_8_152940' => 'lsa', 'Lsat_1_v5_gn_8_62401' => 'lsa', 'Manes.06G055900' => 'mes', 'Manes.12G022200' => 'mes', 'Manes.13G023300' => 'mes', 'Manes.14G115000' => 'mes', 'Manes.15G151700' => 'mes', 'Manes.17G111300' => 'mes', 'Mapoly0226s0009' => 'mpo', 'MBI02_g25363_MAGBIO' => 'mbi', 'MBI06_g00027_MAGBIO' => 'mbi', 'MBI10_g13034_MAGBIO' => 'mbi', 'MD09G1023400' => 'mdo', 'MD13G1100100' => 'mdo', 'MD15G1169200' => 'mdo', 'MD16G1101100' => 'mdo', 'MD17G1022900' => 'mdo', 'Medtr3g096150' => 'mtr', 'Medtr4g115070' => 'mtr', 'Medtr7g033325' => 'mtr', 'Medtr8g089840' => 'mtr', 'MELO3C010319.2' => 'cme', 'MELO3C011944.2' => 'cme', 'MELO3C021589.2' => 'cme', 'Migut.E00207' => 'egut', 'Migut.H00067' => 'egut', 'Migut.K00433' => 'egut', 'Migut.K00606' => 'egut', 'Migut.K01410' => 'egut', 'MSTRG.13347' => 'ama', 'MSTRG.24045' => 'ama', 'MSTRG.2428' => 'ama', 'MSTRG.26410' => 'ama', 'MSTRG.3139' => 'ama', 'MSTRG.3286' => 'ama', 'MSTRG.563' => 'ama', 'MSTRG.7941' => 'ama', 'Nitab4.5_0000028g0060' => 'nta', 'Nitab4.5_0000065g0260' => 'nta', 'Nitab4.5_0000112g0060' => 'nta', 'Nitab4.5_0000489g0120' => 'nta', 'Nitab4.5_0001776g0050' => 'nta', 'Nitab4.5_0001854g0010' => 'nta', 'Nitab4.5_0001860g0020' => 'nta', 'Nitab4.5_0004352g0010' => 'nta', 'Nitab4.5_0008716g0020' => 'nta', 'Nitab4.5_0008922g0010' => 'nta', 'Nn3g16693' => 'nnu', 'Nn4g22596' => 'nnu', 'Nn7g37639' => 'nnu', 'Oeu001701.1' => 'oeu', 'Oeu018149.1' => 'oeu', 'Oeu026220.1' => 'oeu', 'Oeu038635.1' => 'oeu', 'Oeu049176.1' => 'oeu', 'Oeu056706.1' => 'oeu', 'Oeu056937.1' => 'oeu', 'Oeu057540.1' => 'oeu', 'Os02g0594900' => 'osa', 'Os02g0595100' => 'osa', 'Os04g0477500' => 'osa', 'Os12g0611900' => 'osa', 'Peaxi162Scf00076g00020' => 'pax', 'Peaxi162Scf00128g00217' => 'pax', 'Peaxi162Scf00129g01640' => 'pax', 'Peaxi162Scf00669g00007' => 'pax', 'Peaxi162Scf00700g00421' => 'pax', 'Peaxi162Scf00801g00038' => 'pax', 'Peaxi162Scf00891g00025' => 'pax', 'PGR083G0909' => 'pgr', 'PGR119G1005' => 'pgr', 'PGR142G2236' => 'pgr', 'PGR142G3388' => 'pgr', 'PGSC0003DMG400004514' => 'stu', 'PGSC0003DMG400012635' => 'stu', 'PGSC0003DMG400015730' => 'stu', 'PGSC0003DMG400018611' => 'stu', 'PGSC0003DMG400030897' => 'stu', 'Phvul.001G254800' => 'pvu', 'Phvul.002G260100' => 'pvu', 'Phvul.003G167600' => 'pvu', 'Phvul.004G005100' => 'pvu', 'Potri.001G343600' => 'ptr', 'Potri.006G066700' => 'ptr', 'Potri.008G186000' => 'ptr', 'Potri.010G046900' => 'ptr', 'Potri.018G127900' => 'ptr', 'Pp3c20_17750' => 'ppa', 'Pp3c24_4380' => 'ppa', 'Prupe.1G245800' => 'ppe', 'Prupe.3G293400' => 'ppe', 'Prupe.7G247400' => 'ppe', 'Psat0s145g0120' => 'psa', 'Psat0s595g0040' => 'psa', 'Psat0s595g0120' => 'psa', 'Psat3g175040' => 'psa', 'Psat7g058120' => 'psa', 'PSO017G0428' => 'pso', 'PSO063G7510' => 'pso', 'PSO067G0046' => 'pso', 'PSO478G1073' => 'pso', 'PSO675G3677' => 'pso', 'PSO675G6558' => 'pso', 'PSO675G7520' => 'pso', 'PSO675G8959' => 'pso', 'QL02p074089' => 'qlo', 'QL02p089614' => 'qlo', 'QL03p057736' => 'qlo', 'RcHm_v2.0_Chr1g0364131' => 'rch', 'RcHm_v2.0_Chr2g0087801' => 'rch', 'RcHm_v2.0_Chr2g0087821' => 'rch', 'RcHm_v2.0_Chr2g0173231' => 'rch', 'RcHm_v2.0_Chr4g0433111' => 'rch', 'Rhsim03G0250300' => 'rsi', 'Rhsim08G0048400' => 'rsi', 'Rhsim10G0014800' => 'rsi', 'Rhsim12G0040100' => 'rsi', 'Rhsim12G0109700' => 'rsi', 'Sabra06G0049600' => 'sbr', 'Sabra08G0141000' => 'sbr', 'Sabra10G0021400' => 'sbr', 'Sabra16G0222900' => 'sbr', 'Sabra18G0108600' => 'sbr', 'SalBow1G0433' => 'sbo', 'SalBow1G2038' => 'sbo', 'SalBow1G5003' => 'sbo', 'SalBow7G1197' => 'sbo', 'SalBow8G3506' => 'sbo', 'Sc03g0007300' => 'sci', 'Sc11g0000950' => 'sci', 'Sc14g0008750' => 'sci', 'Sc18g0000420' => 'sci', 'Sed0006754' => 'sed', 'Sed0008741' => 'sed', 'Sed0017172' => 'sed', 'Sed0018925' => 'sed', 'Sed0023326' => 'sed', 'Sed0025909' => 'sed', 'SEGI_05333' => 'sgi', 'SEGI_10362' => 'sgi', 'SEGI_13380' => 'sgi', 'SEGI_24306' => 'sgi', 'SEGI_29077' => 'sgi', 'SEGI_29095' => 'sgi', 'SEGI_36534' => 'sgi', 'SEGI_37506' => 'sgi', 'SEGI_38321' => 'sgi', 'SGA_v2.0_scaffold307G48031' => 'sas', 'SGA_v2.0_scaffold47G17507' => 'sas', 'SGA_v2.0_scaffold63G21736' => 'sas', 'SGA_v2.0_scaffold87G27070' => 'sas', 'SHI17794' => 'shi', 'SHI28851' => 'shi', 'SMO165G0155' => 'smo', 'SMO340G0217' => 'smo', 'SMO367G1210' => 'smo', 'Solyc02g093430.3' => 'sly', 'Solyc05g013580.4' => 'sly', 'Solyc07g008030.3' => 'sly', 'Solyc12g035470.2' => 'sly', 'Sopen02g038020' => 'spe', 'Sopen05g008490' => 'spe', 'Sopen07g003910' => 'spe', 'Sopen12g015240' => 'spe', 'Sp1g11550' => 'spa', 'Sp2g16710' => 'spa', 'Sp3g00430' => 'spa', 'Sp3g26780' => 'spa', 'Sp5g22900' => 'spa', 'Sp6g29530' => 'spa', 'TAR371G0794' => 'tar', 'TAR374G0164' => 'tar', 'TAR622G0165' => 'tar', 'TAR626G0929' => 'tar', 'TAR629G2155' => 'tar', 'THA.LOC104805282' => 'tha', 'THA.LOC104805363' => 'tha', 'THA.LOC104808968' => 'tha', 'THA.LOC104821093' => 'tha', 'THA.LOC104823953' => 'tha', 'THA.LOC104825562' => 'tha', 'THA.LOC104825665' => 'tha', 'Thecc.02G261400' => 'tca', 'Thecc.04G019200' => 'tca', 'Thecc.09G130400' => 'tca', 'Thhalv10004374m.g' => 'esa', 'Thhalv10007850m.g' => 'esa', 'Thhalv10013782m.g' => 'esa', 'Thhalv10018686m.g' => 'esa', 'Thhalv10020899m.g' => 'esa', 'Thhalv10022755m.g' => 'esa', 'TPR.G23851' => 'tpr', 'TPR.G26500' => 'tpr', 'TPR.G27267' => 'tpr', 'TPR.G32001' => 'tpr', 'TPR.G6251' => 'tpr', 'TPR.G8167' => 'tpr', 'TWI12G1330' => 'twi', 'TWI18G1239' => 'twi', 'TWI34G0979' => 'twi', 'TWI36G0670' => 'twi', 'TWI36G0707' => 'twi', 'TWI56G0233' => 'twi', 'TWI75G1809' => 'twi', 'unitig_21.g20874' => 'ugi', 'unitig_26.g10343' => 'ugi', 'unitig_46.g18392' => 'ugi', 'unitig_52.g17178' => 'ugi', 'unitig_8.g2934' => 'ugi', 'vmacro01122' => 'vma', 'vmacro05875' => 'vma', 'vmacro06147' => 'vma', 'vmacro16191' => 'vma', 'vmacro18293' => 'vma', 'VMungo0251G3707' => 'vmu', 'VMungo0464G1521' => 'vmu', 'VMungo1215G0205' => 'vmu', 'VMungo1383G2484' => 'vmu', 'Zm00001eb079610' => 'zma', 'Zm00001eb135990' => 'zma', 'Zm00001eb183710' => 'zma', 'Zm00001eb246020' => 'zma' ) $gf_id = 'HOM05D001124' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001124' ) $data_identifier = 'HOM05D001124' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 6, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 7, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 21, 'bol' => (int) 10, 'bra' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 6, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 9, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 21, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 8, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 10, 'lsa' => (int) 8, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 8, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 9, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb246020' $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' => 'HOM05D001124', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '548', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02520' => 'bna', 'A03p06630' => 'bna', 'A05p44460' => 'bna', 'A06p08710' => 'bna', 'A06p41090' => 'bna', 'A07p32320' => 'bna', 'A08p32520' => 'bna', 'A09p10360' => 'bna', 'A10p24080' => 'bna', 'Aa31LG11G15250' => 'aar', 'Aa31LG1G1800' => 'aar', 'Aa31LG2G5120' => 'aar', 'Aa31LG2G6070' => 'aar', 'Aa31LG5G10770' => 'aar', 'Aa31sc61G90' => 'aar', 'Actinidia01352' => 'ach', 'Actinidia05983' => 'ach', 'Actinidia08133' => 'ach', 'Actinidia15101' => 'ach', 'Actinidia26379' => 'ach', 'Actinidia35778' => 'ach', 'Actinidia36123' => 'ach', 'Actinidia37436' => 'ach', 'Actinidia38730' => 'ach', 'Ah.02g128210' => 'amhyb', 'Ah.03g132990' => 'amhyb', 'Ah.14g079410' => 'amhyb', 'AL1G24640' => 'aly', 'AL2G26680' => 'aly', 'AL3G10530' => 'aly', 'AL3G45230' => 'aly', 'AL5G15230' => 'aly', 'AL5G16960' => 'aly', 'AL6G25210' => 'aly', 'Aqoxy2G00441' => 'aox', 'Aqoxy3G01236' => 'aox', 'Aqoxy5G03746' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3RQ047' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C7GMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9C8JER' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MBL6KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YXCZ83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZANX40' => 'arhy', 'AT1G12990' => 'ath', 'AT1G67880' => 'ath', 'AT2G13290' => 'ath', 'AT3G01620' => 'ath', 'AT3G26445' => 'ath', 'AT3G27540' => 'ath', 'AT5G14480' => 'ath', 'ATR0824G026' => 'atr', 'ATR1098G019' => 'atr', 'Atru.chr11.2145' => 'acertr', 'Atru.chr2.3636' => 'acertr', 'Atru.chr2.3644' => 'acertr', 'Atru.chr6.2422' => 'acertr', 'Atru.chr7.1112' => 'acertr', 'AUR62005469' => 'cqu', 'AUR62011166' => 'cqu', 'AUR62013319' => 'cqu', 'AUR62024273' => 'cqu', 'AUR62028420' => 'cqu', 'AUR62041942' => 'cqu', 'BcaB01g04969' => 'bca', 'BcaB01g06371' => 'bca', 'BcaB02g11494' => 'bca', 'BcaB03g15382' => 'bca', 'BcaB08g36994' => 'bca', 'BcaC03g13477' => 'bca', 'BcaC03g13478' => 'bca', 'BcaC03g13480' => 'bca', 'BcaC03g13481' => 'bca', 'BcaC03g13486' => 'bca', 'BcaC04g19031' => 'bca', 'BcaC04g23085' => 'bca', 'BcaC05g25094' => 'bca', 'BcaC05g25096' => 'bca', 'BcaC05g25138' => 'bca', 'BcaC05g30416' => 'bca', 'BcaC05g30455' => 'bca', 'BcaC06g30979' => 'bca', 'BcaC06g33805' => 'bca', 'BcaC08g46021' => 'bca', 'BcaNung03154' => 'bca', 'BolC2t06623H' => 'bol', 'BolC2t06632H' => 'bol', 'BolC2t06635H' => 'bol', 'BolC2t06638H' => 'bol', 'BolC3t13266H' => 'bol', 'BolC5t29776H' => 'bol', 'BolC6t38912H' => 'bol', 'BolC7t44183H' => 'bol', 'BolC9t54123H' => 'bol', 'BolC9t59107H' => 'bol', 'BraA02t05221Z' => 'bra', 'BraA03t09996Z' => 'bra', 'BraA05t23210Z' => 'bra', 'BraA06t24068Z' => 'bra', 'BraA06t27032Z' => 'bra', 'BraA08t35176Z' => 'bra', 'BraA09t36680Z' => 'bra', 'BraA10t44471Z' => 'bra', 'C02p06760' => 'bna', 'C02p06890' => 'bna', 'C02p07010' => 'bna', 'C03p07660' => 'bna', 'C05p10300' => 'bna', 'C06p38150' => 'bna', 'C07p36650' => 'bna', 'C08p15770' => 'bna', 'C09p12300' => 'bna', 'C09p62700' => 'bna', 'C09p75040' => 'bna', 'CAN.G13.1' => 'can', 'CAN.G138.4' => 'can', 'CAN.G44.6' => 'can', 'CAN.G473.19' => 'can', 'CANSAT01G0835' => 'cansat', 'CANSAT11G0246' => 'cansat', 'CANSAT11G1766' => 'cansat', 'CANSAT64G1954' => 'cansat', 'CARHR013330' => 'chi', 'CARHR060530' => 'chi', 'CARHR075300' => 'chi', 'CARHR105120' => 'chi', 'CARHR148910' => 'chi', 'CARHR198830' => 'chi', 'Carub.0001s1275' => 'cru', 'Carub.0002s1437' => 'cru', 'Carub.0003s0044' => 'cru', 'Carub.0003s2787' => 'cru', 'Carub.0005s0597' => 'cru', 'Carub.0006s1266' => 'cru', 'Ca_06935_v3' => 'car', 'Ca_13559_v3' => 'car', 'Ca_16941_v3' => 'car', 'Ca_16960_v3' => 'car', 'Ca_17775_v3' => 'car', 'Ca_30464_v3' => 'car', 'Cc06_g08160' => 'ccan', 'Cc07_g01520' => 'ccan', 'Cc11_g15810' => 'ccan', 'CDE02G2840' => 'cde', 'CDE03G0093' => 'cde', 'CDE04G2127' => 'cde', 'CDE07G1857' => 'cde', 'CDE09G1246' => 'cde', 'Cfa003412' => 'cfa', 'Cfa007341' => 'cfa', 'Cfa009220' => 'cfa', 'Ciclev10008737m.g' => 'ccl', 'Ciclev10015565m.g' => 'ccl', 'Ciclev10031761m.g' => 'ccl', 'CiPaw.03G045300' => 'cil', 'CiPaw.03G247200' => 'cil', 'CiPaw.04G029500' => 'cil', 'CiPaw.04G174000' => 'cil', 'CiPaw.05G181200' => 'cil', 'CiPaw.06G067100' => 'cil', 'ClCG05G025800' => 'cla', 'ClCG06G011400' => 'cla', 'ClCG09G019360' => 'cla', 'COL.COLO4_04827' => 'col', 'COL.COLO4_29170' => 'col', 'COL.COLO4_35131' => 'col', 'COL.COLO4_35132' => 'col', 'Cpa.g.sc33.32' => 'cpa', 'Cpa.g.sc46.29' => 'cpa', 'Cpa.g.sc796.1' => 'cpa', 'CsaV3_1G030420' => 'csa', 'CsaV3_5G027050' => 'csa', 'CsaV3_5G031040' => 'csa', 'CsaV3_UNG023130' => 'csa', 'CSS0007726' => 'camsi', 'CSS0016433' => 'camsi', 'CSS0017656' => 'camsi', 'CSS0025364' => 'camsi', 'CSS0027582' => 'camsi', 'CSS0047288' => 'camsi', 'CSS0049950' => 'camsi', 'DCAR_003843' => 'dca', 'DCAR_007052' => 'dca', 'DCAR_020884' => 'dca', 'DCAR_021730' => 'dca', 'DCAR_024423' => 'dca', 'DCAR_026509' => 'dca', 'DCAR_031158' => 'dca', 'Dinv14728' => 'din', 'Dinv15219' => 'din', 'Dinv25728' => 'din', 'Dinv33428' => 'din', 'Dinv36489' => 'din', 'Dinv41486' => 'din', 'Duzib147G0469' => 'dzi', 'Duzib168G0060' => 'dzi', 'Duzib187G1215' => 'dzi', 'Duzib248G0692' => 'dzi', 'Duzib251G0767' => 'dzi', 'Duzib264G0446' => 'dzi', 'Duzib268G0691' => 'dzi', 'ECA232G4767' => 'eca', 'ECA233G2838' => 'eca', 'ECA234G0391' => 'eca', 'ECA234G0857' => 'eca', 'ECA236G1593' => 'eca', 'ECA238G0565' => 'eca', 'ECA246G1027' => 'eca', 'ECA246G3223' => 'eca', 'ECA246G3470' => 'eca', 'EL10Ac6g13829' => 'bvu', 'EL10Ac6g14093' => 'bvu', 'EL10Ac8g18707' => 'bvu', 'Eucgr.C01369' => 'egr', 'Eucgr.H02492' => 'egr', 'Eucgr.I01733' => 'egr', 'Eucgr.J02255' => 'egr', 'Eucgr.J02257' => 'egr', 'Eucgr.J02258' => 'egr', 'FAN02G1601' => 'fan', 'FAN03G1586' => 'fan', 'FAN03G2986' => 'fan', 'FAN05G4837' => 'fan', 'FAN06G0146' => 'fan', 'FAN07G0858' => 'fan', 'FAN09G3179' => 'fan', 'FAN10G0669' => 'fan', 'FAN12G2358' => 'fan', 'FAN14G4198' => 'fan', 'FAN14G5112' => 'fan', 'FAN17G0342' => 'fan', 'FAN19G0342' => 'fan', 'FAN19G0962' => 'fan', 'FAN19G1101' => 'fan', 'FAN19G1872' => 'fan', 'FAN22G0356' => 'fan', 'FAN23G0744' => 'fan', 'FAN23G1914' => 'fan', 'FAN26G0032' => 'fan', 'FAN28G0625' => 'fan', 'FvH4_1g02710' => 'fve', 'FvH4_1g02720' => 'fve', 'FvH4_4g25670' => 'fve', 'FvH4_6g51700' => 'fve', 'FvH4_7g20170' => 'fve', 'Glyma.05G175000' => 'gma', 'Glyma.08G132300' => 'gma', 'Glyma.11G243000' => 'gma', 'Glyma.13G158900' => 'gma', 'Glyma.17G112400' => 'gma', 'Glyma.18G014100' => 'gma', 'Glyma.19G003100' => 'gma', 'Glyma.19G056500' => 'gma', 'Gohir.A01G158900' => 'ghi', 'Gohir.A05G312600' => 'ghi', 'Gohir.A05G354900' => 'ghi', 'Gohir.A07G037200' => 'ghi', 'Gohir.A09G030000' => 'ghi', 'Gohir.A12G145200' => 'ghi', 'Gohir.D01G151500' => 'ghi', 'Gohir.D04G058300' => 'ghi', 'Gohir.D05G314100' => 'ghi', 'Gohir.D07G041400' => 'ghi', 'Gohir.D09G029700' => 'ghi', 'Gohir.D12G149700' => 'ghi', 'Gorai.001G043800' => 'gra', 'Gorai.002G187800' => 'gra', 'Gorai.006G034700' => 'gra', 'Gorai.008G161200' => 'gra', 'Gorai.009G335700' => 'gra', 'Gorai.012G065000' => 'gra', 'GSVIVG01000535001' => 'vvi', 'GSVIVG01015572001' => 'vvi', 'GSVIVG01032386001' => 'vvi', 'HanXRQChr05g0138531' => 'han', 'HanXRQChr06g0174391' => 'han', 'HanXRQChr07g0199021' => 'han', 'HanXRQChr08g0208211' => 'han', 'HanXRQChr09g0255471' => 'han', 'HanXRQChr10g0315791' => 'han', 'HanXRQChr12g0371991' => 'han', 'HanXRQChr15g0475251' => 'han', 'HanXRQChr17g0540001' => 'han', 'HanXRQChr17g0548631' => 'han', 'HanXRQChr17g0569561' => 'han', 'Haze_12256' => 'cav', 'Haze_14756' => 'cav', 'Haze_25528' => 'cav', 'Hma1.2p1_0079F.1_g041020' => 'hma', 'Hma1.2p1_0818F.1_g223260' => 'hma', 'Hma1.2p1_1747F.1_g300530' => 'hma', 'HPP92_004607' => 'vpl', 'HPP92_004608' => 'vpl', 'HPP92_006181' => 'vpl', 'HPP92_012192' => 'vpl', 'HPP92_015680' => 'vpl', 'HPP92_020249' => 'vpl', 'HPP92_021376' => 'vpl', 'HPP92_024275' => 'vpl', 'Hund06031' => 'sun', 'Hund25391' => 'sun', 'Lalb_Chr07g0185371' => 'lal', 'Lalb_Chr07g0185381' => 'lal', 'Lalb_Chr12g0204011' => 'lal', 'Lalb_Chr13g0301671' => 'lal', 'Lalb_Chr14g0362851' => 'lal', 'Lalb_Chr24g0403581' => 'lal', 'Lj1g0000233' => 'lja', 'Lj2g0018120' => 'lja', 'Lj3C621T0' => 'lonja', 'Lj3P1059T14' => 'lonja', 'Lj3P611T9' => 'lonja', 'Lj3P614T13' => 'lonja', 'Lj3P615T5' => 'lonja', 'Lj4g0012315' => 'lja', 'Lj4g0026182' => 'lja', 'Lj6P813T16' => 'lonja', 'Lj7C427T7' => 'lonja', 'Lj7C427T8' => 'lonja', 'Lj7P600T41' => 'lonja', 'Lju41C42G17' => 'lonja', 'Lsat_1_v5_gn_0_47300' => 'lsa', 'Lsat_1_v5_gn_2_91280' => 'lsa', 'Lsat_1_v5_gn_3_30561' => 'lsa', 'Lsat_1_v5_gn_4_184321' => 'lsa', 'Lsat_1_v5_gn_4_4041' => 'lsa', 'Lsat_1_v5_gn_5_92000' => 'lsa', 'Lsat_1_v5_gn_8_152940' => 'lsa', 'Lsat_1_v5_gn_8_62401' => 'lsa', 'Manes.06G055900' => 'mes', 'Manes.12G022200' => 'mes', 'Manes.13G023300' => 'mes', 'Manes.14G115000' => 'mes', 'Manes.15G151700' => 'mes', 'Manes.17G111300' => 'mes', 'Mapoly0226s0009' => 'mpo', 'MBI02_g25363_MAGBIO' => 'mbi', 'MBI06_g00027_MAGBIO' => 'mbi', 'MBI10_g13034_MAGBIO' => 'mbi', 'MD09G1023400' => 'mdo', 'MD13G1100100' => 'mdo', 'MD15G1169200' => 'mdo', 'MD16G1101100' => 'mdo', 'MD17G1022900' => 'mdo', 'Medtr3g096150' => 'mtr', 'Medtr4g115070' => 'mtr', 'Medtr7g033325' => 'mtr', 'Medtr8g089840' => 'mtr', 'MELO3C010319.2' => 'cme', 'MELO3C011944.2' => 'cme', 'MELO3C021589.2' => 'cme', 'Migut.E00207' => 'egut', 'Migut.H00067' => 'egut', 'Migut.K00433' => 'egut', 'Migut.K00606' => 'egut', 'Migut.K01410' => 'egut', 'MSTRG.13347' => 'ama', 'MSTRG.24045' => 'ama', 'MSTRG.2428' => 'ama', 'MSTRG.26410' => 'ama', 'MSTRG.3139' => 'ama', 'MSTRG.3286' => 'ama', 'MSTRG.563' => 'ama', 'MSTRG.7941' => 'ama', 'Nitab4.5_0000028g0060' => 'nta', 'Nitab4.5_0000065g0260' => 'nta', 'Nitab4.5_0000112g0060' => 'nta', 'Nitab4.5_0000489g0120' => 'nta', 'Nitab4.5_0001776g0050' => 'nta', 'Nitab4.5_0001854g0010' => 'nta', 'Nitab4.5_0001860g0020' => 'nta', 'Nitab4.5_0004352g0010' => 'nta', 'Nitab4.5_0008716g0020' => 'nta', 'Nitab4.5_0008922g0010' => 'nta', 'Nn3g16693' => 'nnu', 'Nn4g22596' => 'nnu', 'Nn7g37639' => 'nnu', 'Oeu001701.1' => 'oeu', 'Oeu018149.1' => 'oeu', 'Oeu026220.1' => 'oeu', 'Oeu038635.1' => 'oeu', 'Oeu049176.1' => 'oeu', 'Oeu056706.1' => 'oeu', 'Oeu056937.1' => 'oeu', 'Oeu057540.1' => 'oeu', 'Os02g0594900' => 'osa', 'Os02g0595100' => 'osa', 'Os04g0477500' => 'osa', 'Os12g0611900' => 'osa', 'Peaxi162Scf00076g00020' => 'pax', 'Peaxi162Scf00128g00217' => 'pax', 'Peaxi162Scf00129g01640' => 'pax', 'Peaxi162Scf00669g00007' => 'pax', 'Peaxi162Scf00700g00421' => 'pax', 'Peaxi162Scf00801g00038' => 'pax', 'Peaxi162Scf00891g00025' => 'pax', 'PGR083G0909' => 'pgr', 'PGR119G1005' => 'pgr', 'PGR142G2236' => 'pgr', 'PGR142G3388' => 'pgr', 'PGSC0003DMG400004514' => 'stu', 'PGSC0003DMG400012635' => 'stu', 'PGSC0003DMG400015730' => 'stu', 'PGSC0003DMG400018611' => 'stu', 'PGSC0003DMG400030897' => 'stu', 'Phvul.001G254800' => 'pvu', 'Phvul.002G260100' => 'pvu', 'Phvul.003G167600' => 'pvu', 'Phvul.004G005100' => 'pvu', 'Potri.001G343600' => 'ptr', 'Potri.006G066700' => 'ptr', 'Potri.008G186000' => 'ptr', 'Potri.010G046900' => 'ptr', 'Potri.018G127900' => 'ptr', 'Pp3c20_17750' => 'ppa', 'Pp3c24_4380' => 'ppa', 'Prupe.1G245800' => 'ppe', 'Prupe.3G293400' => 'ppe', 'Prupe.7G247400' => 'ppe', 'Psat0s145g0120' => 'psa', 'Psat0s595g0040' => 'psa', 'Psat0s595g0120' => 'psa', 'Psat3g175040' => 'psa', 'Psat7g058120' => 'psa', 'PSO017G0428' => 'pso', 'PSO063G7510' => 'pso', 'PSO067G0046' => 'pso', 'PSO478G1073' => 'pso', 'PSO675G3677' => 'pso', 'PSO675G6558' => 'pso', 'PSO675G7520' => 'pso', 'PSO675G8959' => 'pso', 'QL02p074089' => 'qlo', 'QL02p089614' => 'qlo', 'QL03p057736' => 'qlo', 'RcHm_v2.0_Chr1g0364131' => 'rch', 'RcHm_v2.0_Chr2g0087801' => 'rch', 'RcHm_v2.0_Chr2g0087821' => 'rch', 'RcHm_v2.0_Chr2g0173231' => 'rch', 'RcHm_v2.0_Chr4g0433111' => 'rch', 'Rhsim03G0250300' => 'rsi', 'Rhsim08G0048400' => 'rsi', 'Rhsim10G0014800' => 'rsi', 'Rhsim12G0040100' => 'rsi', 'Rhsim12G0109700' => 'rsi', 'Sabra06G0049600' => 'sbr', 'Sabra08G0141000' => 'sbr', 'Sabra10G0021400' => 'sbr', 'Sabra16G0222900' => 'sbr', 'Sabra18G0108600' => 'sbr', 'SalBow1G0433' => 'sbo', 'SalBow1G2038' => 'sbo', 'SalBow1G5003' => 'sbo', 'SalBow7G1197' => 'sbo', 'SalBow8G3506' => 'sbo', 'Sc03g0007300' => 'sci', 'Sc11g0000950' => 'sci', 'Sc14g0008750' => 'sci', 'Sc18g0000420' => 'sci', 'Sed0006754' => 'sed', 'Sed0008741' => 'sed', 'Sed0017172' => 'sed', 'Sed0018925' => 'sed', 'Sed0023326' => 'sed', 'Sed0025909' => 'sed', 'SEGI_05333' => 'sgi', 'SEGI_10362' => 'sgi', 'SEGI_13380' => 'sgi', 'SEGI_24306' => 'sgi', 'SEGI_29077' => 'sgi', 'SEGI_29095' => 'sgi', 'SEGI_36534' => 'sgi', 'SEGI_37506' => 'sgi', 'SEGI_38321' => 'sgi', 'SGA_v2.0_scaffold307G48031' => 'sas', 'SGA_v2.0_scaffold47G17507' => 'sas', 'SGA_v2.0_scaffold63G21736' => 'sas', 'SGA_v2.0_scaffold87G27070' => 'sas', 'SHI17794' => 'shi', 'SHI28851' => 'shi', 'SMO165G0155' => 'smo', 'SMO340G0217' => 'smo', 'SMO367G1210' => 'smo', 'Solyc02g093430.3' => 'sly', 'Solyc05g013580.4' => 'sly', 'Solyc07g008030.3' => 'sly', 'Solyc12g035470.2' => 'sly', 'Sopen02g038020' => 'spe', 'Sopen05g008490' => 'spe', 'Sopen07g003910' => 'spe', 'Sopen12g015240' => 'spe', 'Sp1g11550' => 'spa', 'Sp2g16710' => 'spa', 'Sp3g00430' => 'spa', 'Sp3g26780' => 'spa', 'Sp5g22900' => 'spa', 'Sp6g29530' => 'spa', 'TAR371G0794' => 'tar', 'TAR374G0164' => 'tar', 'TAR622G0165' => 'tar', 'TAR626G0929' => 'tar', 'TAR629G2155' => 'tar', 'THA.LOC104805282' => 'tha', 'THA.LOC104805363' => 'tha', 'THA.LOC104808968' => 'tha', 'THA.LOC104821093' => 'tha', 'THA.LOC104823953' => 'tha', 'THA.LOC104825562' => 'tha', 'THA.LOC104825665' => 'tha', 'Thecc.02G261400' => 'tca', 'Thecc.04G019200' => 'tca', 'Thecc.09G130400' => 'tca', 'Thhalv10004374m.g' => 'esa', 'Thhalv10007850m.g' => 'esa', 'Thhalv10013782m.g' => 'esa', 'Thhalv10018686m.g' => 'esa', 'Thhalv10020899m.g' => 'esa', 'Thhalv10022755m.g' => 'esa', 'TPR.G23851' => 'tpr', 'TPR.G26500' => 'tpr', 'TPR.G27267' => 'tpr', 'TPR.G32001' => 'tpr', 'TPR.G6251' => 'tpr', 'TPR.G8167' => 'tpr', 'TWI12G1330' => 'twi', 'TWI18G1239' => 'twi', 'TWI34G0979' => 'twi', 'TWI36G0670' => 'twi', 'TWI36G0707' => 'twi', 'TWI56G0233' => 'twi', 'TWI75G1809' => 'twi', 'unitig_21.g20874' => 'ugi', 'unitig_26.g10343' => 'ugi', 'unitig_46.g18392' => 'ugi', 'unitig_52.g17178' => 'ugi', 'unitig_8.g2934' => 'ugi', 'vmacro01122' => 'vma', 'vmacro05875' => 'vma', 'vmacro06147' => 'vma', 'vmacro16191' => 'vma', 'vmacro18293' => 'vma', 'VMungo0251G3707' => 'vmu', 'VMungo0464G1521' => 'vmu', 'VMungo1215G0205' => 'vmu', 'VMungo1383G2484' => 'vmu', 'Zm00001eb079610' => 'zma', 'Zm00001eb135990' => 'zma', 'Zm00001eb183710' => 'zma', 'Zm00001eb246020' => 'zma' ), 'gf_id' => 'HOM05D001124', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001124' ), 'data_identifier' => 'HOM05D001124', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001124', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '548', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02520' => 'bna', 'A03p06630' => 'bna', 'A05p44460' => 'bna', 'A06p08710' => 'bna', 'A06p41090' => 'bna', 'A07p32320' => 'bna', 'A08p32520' => 'bna', 'A09p10360' => 'bna', 'A10p24080' => 'bna', 'Aa31LG11G15250' => 'aar', 'Aa31LG1G1800' => 'aar', 'Aa31LG2G5120' => 'aar', 'Aa31LG2G6070' => 'aar', 'Aa31LG5G10770' => 'aar', 'Aa31sc61G90' => 'aar', 'Actinidia01352' => 'ach', 'Actinidia05983' => 'ach', 'Actinidia08133' => 'ach', 'Actinidia15101' => 'ach', 'Actinidia26379' => 'ach', 'Actinidia35778' => 'ach', 'Actinidia36123' => 'ach', 'Actinidia37436' => 'ach', 'Actinidia38730' => 'ach', 'Ah.02g128210' => 'amhyb', 'Ah.03g132990' => 'amhyb', 'Ah.14g079410' => 'amhyb', 'AL1G24640' => 'aly', 'AL2G26680' => 'aly', 'AL3G10530' => 'aly', 'AL3G45230' => 'aly', 'AL5G15230' => 'aly', 'AL5G16960' => 'aly', 'AL6G25210' => 'aly', 'Aqoxy2G00441' => 'aox', 'Aqoxy3G01236' => 'aox', 'Aqoxy5G03746' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3RQ047' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C7GMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9C8JER' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MBL6KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YXCZ83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZANX40' => 'arhy', 'AT1G12990' => 'ath', 'AT1G67880' => 'ath', 'AT2G13290' => 'ath', 'AT3G01620' => 'ath', 'AT3G26445' => 'ath', 'AT3G27540' => 'ath', 'AT5G14480' => 'ath', 'ATR0824G026' => 'atr', 'ATR1098G019' => 'atr', 'Atru.chr11.2145' => 'acertr', 'Atru.chr2.3636' => 'acertr', 'Atru.chr2.3644' => 'acertr', 'Atru.chr6.2422' => 'acertr', 'Atru.chr7.1112' => 'acertr', 'AUR62005469' => 'cqu', 'AUR62011166' => 'cqu', 'AUR62013319' => 'cqu', 'AUR62024273' => 'cqu', 'AUR62028420' => 'cqu', 'AUR62041942' => 'cqu', 'BcaB01g04969' => 'bca', 'BcaB01g06371' => 'bca', 'BcaB02g11494' => 'bca', 'BcaB03g15382' => 'bca', 'BcaB08g36994' => 'bca', 'BcaC03g13477' => 'bca', 'BcaC03g13478' => 'bca', 'BcaC03g13480' => 'bca', 'BcaC03g13481' => 'bca', 'BcaC03g13486' => 'bca', 'BcaC04g19031' => 'bca', 'BcaC04g23085' => 'bca', 'BcaC05g25094' => 'bca', 'BcaC05g25096' => 'bca', 'BcaC05g25138' => 'bca', 'BcaC05g30416' => 'bca', 'BcaC05g30455' => 'bca', 'BcaC06g30979' => 'bca', 'BcaC06g33805' => 'bca', 'BcaC08g46021' => 'bca', 'BcaNung03154' => 'bca', 'BolC2t06623H' => 'bol', 'BolC2t06632H' => 'bol', 'BolC2t06635H' => 'bol', 'BolC2t06638H' => 'bol', 'BolC3t13266H' => 'bol', 'BolC5t29776H' => 'bol', 'BolC6t38912H' => 'bol', 'BolC7t44183H' => 'bol', 'BolC9t54123H' => 'bol', 'BolC9t59107H' => 'bol', 'BraA02t05221Z' => 'bra', 'BraA03t09996Z' => 'bra', 'BraA05t23210Z' => 'bra', 'BraA06t24068Z' => 'bra', 'BraA06t27032Z' => 'bra', 'BraA08t35176Z' => 'bra', 'BraA09t36680Z' => 'bra', 'BraA10t44471Z' => 'bra', 'C02p06760' => 'bna', 'C02p06890' => 'bna', 'C02p07010' => 'bna', 'C03p07660' => 'bna', 'C05p10300' => 'bna', 'C06p38150' => 'bna', 'C07p36650' => 'bna', 'C08p15770' => 'bna', 'C09p12300' => 'bna', 'C09p62700' => 'bna', 'C09p75040' => 'bna', 'CAN.G13.1' => 'can', 'CAN.G138.4' => 'can', 'CAN.G44.6' => 'can', 'CAN.G473.19' => 'can', 'CANSAT01G0835' => 'cansat', 'CANSAT11G0246' => 'cansat', 'CANSAT11G1766' => 'cansat', 'CANSAT64G1954' => 'cansat', 'CARHR013330' => 'chi', 'CARHR060530' => 'chi', 'CARHR075300' => 'chi', 'CARHR105120' => 'chi', 'CARHR148910' => 'chi', 'CARHR198830' => 'chi', 'Carub.0001s1275' => 'cru', 'Carub.0002s1437' => 'cru', 'Carub.0003s0044' => 'cru', 'Carub.0003s2787' => 'cru', 'Carub.0005s0597' => 'cru', 'Carub.0006s1266' => 'cru', 'Ca_06935_v3' => 'car', 'Ca_13559_v3' => 'car', 'Ca_16941_v3' => 'car', 'Ca_16960_v3' => 'car', 'Ca_17775_v3' => 'car', 'Ca_30464_v3' => 'car', 'Cc06_g08160' => 'ccan', 'Cc07_g01520' => 'ccan', 'Cc11_g15810' => 'ccan', 'CDE02G2840' => 'cde', 'CDE03G0093' => 'cde', 'CDE04G2127' => 'cde', 'CDE07G1857' => 'cde', 'CDE09G1246' => 'cde', 'Cfa003412' => 'cfa', 'Cfa007341' => 'cfa', 'Cfa009220' => 'cfa', 'Ciclev10008737m.g' => 'ccl', 'Ciclev10015565m.g' => 'ccl', 'Ciclev10031761m.g' => 'ccl', 'CiPaw.03G045300' => 'cil', 'CiPaw.03G247200' => 'cil', 'CiPaw.04G029500' => 'cil', 'CiPaw.04G174000' => 'cil', 'CiPaw.05G181200' => 'cil', 'CiPaw.06G067100' => 'cil', 'ClCG05G025800' => 'cla', 'ClCG06G011400' => 'cla', 'ClCG09G019360' => 'cla', 'COL.COLO4_04827' => 'col', 'COL.COLO4_29170' => 'col', 'COL.COLO4_35131' => 'col', 'COL.COLO4_35132' => 'col', 'Cpa.g.sc33.32' => 'cpa', 'Cpa.g.sc46.29' => 'cpa', 'Cpa.g.sc796.1' => 'cpa', 'CsaV3_1G030420' => 'csa', 'CsaV3_5G027050' => 'csa', 'CsaV3_5G031040' => 'csa', 'CsaV3_UNG023130' => 'csa', 'CSS0007726' => 'camsi', 'CSS0016433' => 'camsi', 'CSS0017656' => 'camsi', 'CSS0025364' => 'camsi', 'CSS0027582' => 'camsi', 'CSS0047288' => 'camsi', 'CSS0049950' => 'camsi', 'DCAR_003843' => 'dca', 'DCAR_007052' => 'dca', 'DCAR_020884' => 'dca', 'DCAR_021730' => 'dca', 'DCAR_024423' => 'dca', 'DCAR_026509' => 'dca', 'DCAR_031158' => 'dca', 'Dinv14728' => 'din', 'Dinv15219' => 'din', 'Dinv25728' => 'din', 'Dinv33428' => 'din', 'Dinv36489' => 'din', 'Dinv41486' => 'din', 'Duzib147G0469' => 'dzi', 'Duzib168G0060' => 'dzi', 'Duzib187G1215' => 'dzi', 'Duzib248G0692' => 'dzi', 'Duzib251G0767' => 'dzi', 'Duzib264G0446' => 'dzi', 'Duzib268G0691' => 'dzi', 'ECA232G4767' => 'eca', 'ECA233G2838' => 'eca', 'ECA234G0391' => 'eca', 'ECA234G0857' => 'eca', 'ECA236G1593' => 'eca', 'ECA238G0565' => 'eca', 'ECA246G1027' => 'eca', 'ECA246G3223' => 'eca', 'ECA246G3470' => 'eca', 'EL10Ac6g13829' => 'bvu', 'EL10Ac6g14093' => 'bvu', 'EL10Ac8g18707' => 'bvu', 'Eucgr.C01369' => 'egr', 'Eucgr.H02492' => 'egr', 'Eucgr.I01733' => 'egr', 'Eucgr.J02255' => 'egr', 'Eucgr.J02257' => 'egr', 'Eucgr.J02258' => 'egr', 'FAN02G1601' => 'fan', 'FAN03G1586' => 'fan', 'FAN03G2986' => 'fan', 'FAN05G4837' => 'fan', 'FAN06G0146' => 'fan', 'FAN07G0858' => 'fan', 'FAN09G3179' => 'fan', 'FAN10G0669' => 'fan', 'FAN12G2358' => 'fan', 'FAN14G4198' => 'fan', 'FAN14G5112' => 'fan', 'FAN17G0342' => 'fan', 'FAN19G0342' => 'fan', 'FAN19G0962' => 'fan', 'FAN19G1101' => 'fan', 'FAN19G1872' => 'fan', 'FAN22G0356' => 'fan', 'FAN23G0744' => 'fan', 'FAN23G1914' => 'fan', 'FAN26G0032' => 'fan', 'FAN28G0625' => 'fan', 'FvH4_1g02710' => 'fve', 'FvH4_1g02720' => 'fve', 'FvH4_4g25670' => 'fve', 'FvH4_6g51700' => 'fve', 'FvH4_7g20170' => 'fve', 'Glyma.05G175000' => 'gma', 'Glyma.08G132300' => 'gma', 'Glyma.11G243000' => 'gma', 'Glyma.13G158900' => 'gma', 'Glyma.17G112400' => 'gma', 'Glyma.18G014100' => 'gma', 'Glyma.19G003100' => 'gma', 'Glyma.19G056500' => 'gma', 'Gohir.A01G158900' => 'ghi', 'Gohir.A05G312600' => 'ghi', 'Gohir.A05G354900' => 'ghi', 'Gohir.A07G037200' => 'ghi', 'Gohir.A09G030000' => 'ghi', 'Gohir.A12G145200' => 'ghi', 'Gohir.D01G151500' => 'ghi', 'Gohir.D04G058300' => 'ghi', 'Gohir.D05G314100' => 'ghi', 'Gohir.D07G041400' => 'ghi', 'Gohir.D09G029700' => 'ghi', 'Gohir.D12G149700' => 'ghi', 'Gorai.001G043800' => 'gra', 'Gorai.002G187800' => 'gra', 'Gorai.006G034700' => 'gra', 'Gorai.008G161200' => 'gra', 'Gorai.009G335700' => 'gra', 'Gorai.012G065000' => 'gra', 'GSVIVG01000535001' => 'vvi', 'GSVIVG01015572001' => 'vvi', 'GSVIVG01032386001' => 'vvi', 'HanXRQChr05g0138531' => 'han', 'HanXRQChr06g0174391' => 'han', 'HanXRQChr07g0199021' => 'han', 'HanXRQChr08g0208211' => 'han', 'HanXRQChr09g0255471' => 'han', 'HanXRQChr10g0315791' => 'han', 'HanXRQChr12g0371991' => 'han', 'HanXRQChr15g0475251' => 'han', 'HanXRQChr17g0540001' => 'han', 'HanXRQChr17g0548631' => 'han', 'HanXRQChr17g0569561' => 'han', 'Haze_12256' => 'cav', 'Haze_14756' => 'cav', 'Haze_25528' => 'cav', 'Hma1.2p1_0079F.1_g041020' => 'hma', 'Hma1.2p1_0818F.1_g223260' => 'hma', 'Hma1.2p1_1747F.1_g300530' => 'hma', 'HPP92_004607' => 'vpl', 'HPP92_004608' => 'vpl', 'HPP92_006181' => 'vpl', 'HPP92_012192' => 'vpl', 'HPP92_015680' => 'vpl', 'HPP92_020249' => 'vpl', 'HPP92_021376' => 'vpl', 'HPP92_024275' => 'vpl', 'Hund06031' => 'sun', 'Hund25391' => 'sun', 'Lalb_Chr07g0185371' => 'lal', 'Lalb_Chr07g0185381' => 'lal', 'Lalb_Chr12g0204011' => 'lal', 'Lalb_Chr13g0301671' => 'lal', 'Lalb_Chr14g0362851' => 'lal', 'Lalb_Chr24g0403581' => 'lal', 'Lj1g0000233' => 'lja', 'Lj2g0018120' => 'lja', 'Lj3C621T0' => 'lonja', 'Lj3P1059T14' => 'lonja', 'Lj3P611T9' => 'lonja', 'Lj3P614T13' => 'lonja', 'Lj3P615T5' => 'lonja', 'Lj4g0012315' => 'lja', 'Lj4g0026182' => 'lja', 'Lj6P813T16' => 'lonja', 'Lj7C427T7' => 'lonja', 'Lj7C427T8' => 'lonja', 'Lj7P600T41' => 'lonja', 'Lju41C42G17' => 'lonja', 'Lsat_1_v5_gn_0_47300' => 'lsa', 'Lsat_1_v5_gn_2_91280' => 'lsa', 'Lsat_1_v5_gn_3_30561' => 'lsa', 'Lsat_1_v5_gn_4_184321' => 'lsa', 'Lsat_1_v5_gn_4_4041' => 'lsa', 'Lsat_1_v5_gn_5_92000' => 'lsa', 'Lsat_1_v5_gn_8_152940' => 'lsa', 'Lsat_1_v5_gn_8_62401' => 'lsa', 'Manes.06G055900' => 'mes', 'Manes.12G022200' => 'mes', 'Manes.13G023300' => 'mes', 'Manes.14G115000' => 'mes', 'Manes.15G151700' => 'mes', 'Manes.17G111300' => 'mes', 'Mapoly0226s0009' => 'mpo', 'MBI02_g25363_MAGBIO' => 'mbi', 'MBI06_g00027_MAGBIO' => 'mbi', 'MBI10_g13034_MAGBIO' => 'mbi', 'MD09G1023400' => 'mdo', 'MD13G1100100' => 'mdo', 'MD15G1169200' => 'mdo', 'MD16G1101100' => 'mdo', 'MD17G1022900' => 'mdo', 'Medtr3g096150' => 'mtr', 'Medtr4g115070' => 'mtr', 'Medtr7g033325' => 'mtr', 'Medtr8g089840' => 'mtr', 'MELO3C010319.2' => 'cme', 'MELO3C011944.2' => 'cme', 'MELO3C021589.2' => 'cme', 'Migut.E00207' => 'egut', 'Migut.H00067' => 'egut', 'Migut.K00433' => 'egut', 'Migut.K00606' => 'egut', 'Migut.K01410' => 'egut', 'MSTRG.13347' => 'ama', 'MSTRG.24045' => 'ama', 'MSTRG.2428' => 'ama', 'MSTRG.26410' => 'ama', 'MSTRG.3139' => 'ama', 'MSTRG.3286' => 'ama', 'MSTRG.563' => 'ama', 'MSTRG.7941' => 'ama', 'Nitab4.5_0000028g0060' => 'nta', 'Nitab4.5_0000065g0260' => 'nta', 'Nitab4.5_0000112g0060' => 'nta', 'Nitab4.5_0000489g0120' => 'nta', 'Nitab4.5_0001776g0050' => 'nta', 'Nitab4.5_0001854g0010' => 'nta', 'Nitab4.5_0001860g0020' => 'nta', 'Nitab4.5_0004352g0010' => 'nta', 'Nitab4.5_0008716g0020' => 'nta', 'Nitab4.5_0008922g0010' => 'nta', 'Nn3g16693' => 'nnu', 'Nn4g22596' => 'nnu', 'Nn7g37639' => 'nnu', 'Oeu001701.1' => 'oeu', 'Oeu018149.1' => 'oeu', 'Oeu026220.1' => 'oeu', 'Oeu038635.1' => 'oeu', 'Oeu049176.1' => 'oeu', 'Oeu056706.1' => 'oeu', 'Oeu056937.1' => 'oeu', 'Oeu057540.1' => 'oeu', 'Os02g0594900' => 'osa', 'Os02g0595100' => 'osa', 'Os04g0477500' => 'osa', 'Os12g0611900' => 'osa', 'Peaxi162Scf00076g00020' => 'pax', 'Peaxi162Scf00128g00217' => 'pax', 'Peaxi162Scf00129g01640' => 'pax', 'Peaxi162Scf00669g00007' => 'pax', 'Peaxi162Scf00700g00421' => 'pax', 'Peaxi162Scf00801g00038' => 'pax', 'Peaxi162Scf00891g00025' => 'pax', 'PGR083G0909' => 'pgr', 'PGR119G1005' => 'pgr', 'PGR142G2236' => 'pgr', 'PGR142G3388' => 'pgr', 'PGSC0003DMG400004514' => 'stu', 'PGSC0003DMG400012635' => 'stu', 'PGSC0003DMG400015730' => 'stu', 'PGSC0003DMG400018611' => 'stu', 'PGSC0003DMG400030897' => 'stu', 'Phvul.001G254800' => 'pvu', 'Phvul.002G260100' => 'pvu', 'Phvul.003G167600' => 'pvu', 'Phvul.004G005100' => 'pvu', 'Potri.001G343600' => 'ptr', 'Potri.006G066700' => 'ptr', 'Potri.008G186000' => 'ptr', 'Potri.010G046900' => 'ptr', 'Potri.018G127900' => 'ptr', 'Pp3c20_17750' => 'ppa', 'Pp3c24_4380' => 'ppa', 'Prupe.1G245800' => 'ppe', 'Prupe.3G293400' => 'ppe', 'Prupe.7G247400' => 'ppe', 'Psat0s145g0120' => 'psa', 'Psat0s595g0040' => 'psa', 'Psat0s595g0120' => 'psa', 'Psat3g175040' => 'psa', 'Psat7g058120' => 'psa', 'PSO017G0428' => 'pso', 'PSO063G7510' => 'pso', 'PSO067G0046' => 'pso', 'PSO478G1073' => 'pso', 'PSO675G3677' => 'pso', 'PSO675G6558' => 'pso', 'PSO675G7520' => 'pso', 'PSO675G8959' => 'pso', 'QL02p074089' => 'qlo', 'QL02p089614' => 'qlo', 'QL03p057736' => 'qlo', 'RcHm_v2.0_Chr1g0364131' => 'rch', 'RcHm_v2.0_Chr2g0087801' => 'rch', 'RcHm_v2.0_Chr2g0087821' => 'rch', 'RcHm_v2.0_Chr2g0173231' => 'rch', 'RcHm_v2.0_Chr4g0433111' => 'rch', 'Rhsim03G0250300' => 'rsi', 'Rhsim08G0048400' => 'rsi', 'Rhsim10G0014800' => 'rsi', 'Rhsim12G0040100' => 'rsi', 'Rhsim12G0109700' => 'rsi', 'Sabra06G0049600' => 'sbr', 'Sabra08G0141000' => 'sbr', 'Sabra10G0021400' => 'sbr', 'Sabra16G0222900' => 'sbr', 'Sabra18G0108600' => 'sbr', 'SalBow1G0433' => 'sbo', 'SalBow1G2038' => 'sbo', 'SalBow1G5003' => 'sbo', 'SalBow7G1197' => 'sbo', 'SalBow8G3506' => 'sbo', 'Sc03g0007300' => 'sci', 'Sc11g0000950' => 'sci', 'Sc14g0008750' => 'sci', 'Sc18g0000420' => 'sci', 'Sed0006754' => 'sed', 'Sed0008741' => 'sed', 'Sed0017172' => 'sed', 'Sed0018925' => 'sed', 'Sed0023326' => 'sed', 'Sed0025909' => 'sed', 'SEGI_05333' => 'sgi', 'SEGI_10362' => 'sgi', 'SEGI_13380' => 'sgi', 'SEGI_24306' => 'sgi', 'SEGI_29077' => 'sgi', 'SEGI_29095' => 'sgi', 'SEGI_36534' => 'sgi', 'SEGI_37506' => 'sgi', 'SEGI_38321' => 'sgi', 'SGA_v2.0_scaffold307G48031' => 'sas', 'SGA_v2.0_scaffold47G17507' => 'sas', 'SGA_v2.0_scaffold63G21736' => 'sas', 'SGA_v2.0_scaffold87G27070' => 'sas', 'SHI17794' => 'shi', 'SHI28851' => 'shi', 'SMO165G0155' => 'smo', 'SMO340G0217' => 'smo', 'SMO367G1210' => 'smo', 'Solyc02g093430.3' => 'sly', 'Solyc05g013580.4' => 'sly', 'Solyc07g008030.3' => 'sly', 'Solyc12g035470.2' => 'sly', 'Sopen02g038020' => 'spe', 'Sopen05g008490' => 'spe', 'Sopen07g003910' => 'spe', 'Sopen12g015240' => 'spe', 'Sp1g11550' => 'spa', 'Sp2g16710' => 'spa', 'Sp3g00430' => 'spa', 'Sp3g26780' => 'spa', 'Sp5g22900' => 'spa', 'Sp6g29530' => 'spa', 'TAR371G0794' => 'tar', 'TAR374G0164' => 'tar', 'TAR622G0165' => 'tar', 'TAR626G0929' => 'tar', 'TAR629G2155' => 'tar', 'THA.LOC104805282' => 'tha', 'THA.LOC104805363' => 'tha', 'THA.LOC104808968' => 'tha', 'THA.LOC104821093' => 'tha', 'THA.LOC104823953' => 'tha', 'THA.LOC104825562' => 'tha', 'THA.LOC104825665' => 'tha', 'Thecc.02G261400' => 'tca', 'Thecc.04G019200' => 'tca', 'Thecc.09G130400' => 'tca', 'Thhalv10004374m.g' => 'esa', 'Thhalv10007850m.g' => 'esa', 'Thhalv10013782m.g' => 'esa', 'Thhalv10018686m.g' => 'esa', 'Thhalv10020899m.g' => 'esa', 'Thhalv10022755m.g' => 'esa', 'TPR.G23851' => 'tpr', 'TPR.G26500' => 'tpr', 'TPR.G27267' => 'tpr', 'TPR.G32001' => 'tpr', 'TPR.G6251' => 'tpr', 'TPR.G8167' => 'tpr', 'TWI12G1330' => 'twi', 'TWI18G1239' => 'twi', 'TWI34G0979' => 'twi', 'TWI36G0670' => 'twi', 'TWI36G0707' => 'twi', 'TWI56G0233' => 'twi', 'TWI75G1809' => 'twi', 'unitig_21.g20874' => 'ugi', 'unitig_26.g10343' => 'ugi', 'unitig_46.g18392' => 'ugi', 'unitig_52.g17178' => 'ugi', 'unitig_8.g2934' => 'ugi', 'vmacro01122' => 'vma', 'vmacro05875' => 'vma', 'vmacro06147' => 'vma', 'vmacro16191' => 'vma', 'vmacro18293' => 'vma', 'VMungo0251G3707' => 'vmu', 'VMungo0464G1521' => 'vmu', 'VMungo1215G0205' => 'vmu', 'VMungo1383G2484' => 'vmu', 'Zm00001eb079610' => 'zma', 'Zm00001eb135990' => 'zma', 'Zm00001eb183710' => 'zma', 'Zm00001eb246020' => 'zma' ) $gf_id = 'HOM05D001124' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001124' ) $data_identifier = 'HOM05D001124' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 6, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 7, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 21, 'bol' => (int) 10, 'bra' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 6, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 9, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 21, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 8, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 10, 'lsa' => (int) 8, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 8, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 9, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb246020' $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' => 'HOM05D001124', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '548', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02520' => 'bna', 'A03p06630' => 'bna', 'A05p44460' => 'bna', 'A06p08710' => 'bna', 'A06p41090' => 'bna', 'A07p32320' => 'bna', 'A08p32520' => 'bna', 'A09p10360' => 'bna', 'A10p24080' => 'bna', 'Aa31LG11G15250' => 'aar', 'Aa31LG1G1800' => 'aar', 'Aa31LG2G5120' => 'aar', 'Aa31LG2G6070' => 'aar', 'Aa31LG5G10770' => 'aar', 'Aa31sc61G90' => 'aar', 'Actinidia01352' => 'ach', 'Actinidia05983' => 'ach', 'Actinidia08133' => 'ach', 'Actinidia15101' => 'ach', 'Actinidia26379' => 'ach', 'Actinidia35778' => 'ach', 'Actinidia36123' => 'ach', 'Actinidia37436' => 'ach', 'Actinidia38730' => 'ach', 'Ah.02g128210' => 'amhyb', 'Ah.03g132990' => 'amhyb', 'Ah.14g079410' => 'amhyb', 'AL1G24640' => 'aly', 'AL2G26680' => 'aly', 'AL3G10530' => 'aly', 'AL3G45230' => 'aly', 'AL5G15230' => 'aly', 'AL5G16960' => 'aly', 'AL6G25210' => 'aly', 'Aqoxy2G00441' => 'aox', 'Aqoxy3G01236' => 'aox', 'Aqoxy5G03746' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3RQ047' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C7GMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9C8JER' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MBL6KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YXCZ83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZANX40' => 'arhy', 'AT1G12990' => 'ath', 'AT1G67880' => 'ath', 'AT2G13290' => 'ath', 'AT3G01620' => 'ath', 'AT3G26445' => 'ath', 'AT3G27540' => 'ath', 'AT5G14480' => 'ath', 'ATR0824G026' => 'atr', 'ATR1098G019' => 'atr', 'Atru.chr11.2145' => 'acertr', 'Atru.chr2.3636' => 'acertr', 'Atru.chr2.3644' => 'acertr', 'Atru.chr6.2422' => 'acertr', 'Atru.chr7.1112' => 'acertr', 'AUR62005469' => 'cqu', 'AUR62011166' => 'cqu', 'AUR62013319' => 'cqu', 'AUR62024273' => 'cqu', 'AUR62028420' => 'cqu', 'AUR62041942' => 'cqu', 'BcaB01g04969' => 'bca', 'BcaB01g06371' => 'bca', 'BcaB02g11494' => 'bca', 'BcaB03g15382' => 'bca', 'BcaB08g36994' => 'bca', 'BcaC03g13477' => 'bca', 'BcaC03g13478' => 'bca', 'BcaC03g13480' => 'bca', 'BcaC03g13481' => 'bca', 'BcaC03g13486' => 'bca', 'BcaC04g19031' => 'bca', 'BcaC04g23085' => 'bca', 'BcaC05g25094' => 'bca', 'BcaC05g25096' => 'bca', 'BcaC05g25138' => 'bca', 'BcaC05g30416' => 'bca', 'BcaC05g30455' => 'bca', 'BcaC06g30979' => 'bca', 'BcaC06g33805' => 'bca', 'BcaC08g46021' => 'bca', 'BcaNung03154' => 'bca', 'BolC2t06623H' => 'bol', 'BolC2t06632H' => 'bol', 'BolC2t06635H' => 'bol', 'BolC2t06638H' => 'bol', 'BolC3t13266H' => 'bol', 'BolC5t29776H' => 'bol', 'BolC6t38912H' => 'bol', 'BolC7t44183H' => 'bol', 'BolC9t54123H' => 'bol', 'BolC9t59107H' => 'bol', 'BraA02t05221Z' => 'bra', 'BraA03t09996Z' => 'bra', 'BraA05t23210Z' => 'bra', 'BraA06t24068Z' => 'bra', 'BraA06t27032Z' => 'bra', 'BraA08t35176Z' => 'bra', 'BraA09t36680Z' => 'bra', 'BraA10t44471Z' => 'bra', 'C02p06760' => 'bna', 'C02p06890' => 'bna', 'C02p07010' => 'bna', 'C03p07660' => 'bna', 'C05p10300' => 'bna', 'C06p38150' => 'bna', 'C07p36650' => 'bna', 'C08p15770' => 'bna', 'C09p12300' => 'bna', 'C09p62700' => 'bna', 'C09p75040' => 'bna', 'CAN.G13.1' => 'can', 'CAN.G138.4' => 'can', 'CAN.G44.6' => 'can', 'CAN.G473.19' => 'can', 'CANSAT01G0835' => 'cansat', 'CANSAT11G0246' => 'cansat', 'CANSAT11G1766' => 'cansat', 'CANSAT64G1954' => 'cansat', 'CARHR013330' => 'chi', 'CARHR060530' => 'chi', 'CARHR075300' => 'chi', 'CARHR105120' => 'chi', 'CARHR148910' => 'chi', 'CARHR198830' => 'chi', 'Carub.0001s1275' => 'cru', 'Carub.0002s1437' => 'cru', 'Carub.0003s0044' => 'cru', 'Carub.0003s2787' => 'cru', 'Carub.0005s0597' => 'cru', 'Carub.0006s1266' => 'cru', 'Ca_06935_v3' => 'car', 'Ca_13559_v3' => 'car', 'Ca_16941_v3' => 'car', 'Ca_16960_v3' => 'car', 'Ca_17775_v3' => 'car', 'Ca_30464_v3' => 'car', 'Cc06_g08160' => 'ccan', 'Cc07_g01520' => 'ccan', 'Cc11_g15810' => 'ccan', 'CDE02G2840' => 'cde', 'CDE03G0093' => 'cde', 'CDE04G2127' => 'cde', 'CDE07G1857' => 'cde', 'CDE09G1246' => 'cde', 'Cfa003412' => 'cfa', 'Cfa007341' => 'cfa', 'Cfa009220' => 'cfa', 'Ciclev10008737m.g' => 'ccl', 'Ciclev10015565m.g' => 'ccl', 'Ciclev10031761m.g' => 'ccl', 'CiPaw.03G045300' => 'cil', 'CiPaw.03G247200' => 'cil', 'CiPaw.04G029500' => 'cil', 'CiPaw.04G174000' => 'cil', 'CiPaw.05G181200' => 'cil', 'CiPaw.06G067100' => 'cil', 'ClCG05G025800' => 'cla', 'ClCG06G011400' => 'cla', 'ClCG09G019360' => 'cla', 'COL.COLO4_04827' => 'col', 'COL.COLO4_29170' => 'col', 'COL.COLO4_35131' => 'col', 'COL.COLO4_35132' => 'col', 'Cpa.g.sc33.32' => 'cpa', 'Cpa.g.sc46.29' => 'cpa', 'Cpa.g.sc796.1' => 'cpa', 'CsaV3_1G030420' => 'csa', 'CsaV3_5G027050' => 'csa', 'CsaV3_5G031040' => 'csa', 'CsaV3_UNG023130' => 'csa', 'CSS0007726' => 'camsi', 'CSS0016433' => 'camsi', 'CSS0017656' => 'camsi', 'CSS0025364' => 'camsi', 'CSS0027582' => 'camsi', 'CSS0047288' => 'camsi', 'CSS0049950' => 'camsi', 'DCAR_003843' => 'dca', 'DCAR_007052' => 'dca', 'DCAR_020884' => 'dca', 'DCAR_021730' => 'dca', 'DCAR_024423' => 'dca', 'DCAR_026509' => 'dca', 'DCAR_031158' => 'dca', 'Dinv14728' => 'din', 'Dinv15219' => 'din', 'Dinv25728' => 'din', 'Dinv33428' => 'din', 'Dinv36489' => 'din', 'Dinv41486' => 'din', 'Duzib147G0469' => 'dzi', 'Duzib168G0060' => 'dzi', 'Duzib187G1215' => 'dzi', 'Duzib248G0692' => 'dzi', 'Duzib251G0767' => 'dzi', 'Duzib264G0446' => 'dzi', 'Duzib268G0691' => 'dzi', 'ECA232G4767' => 'eca', 'ECA233G2838' => 'eca', 'ECA234G0391' => 'eca', 'ECA234G0857' => 'eca', 'ECA236G1593' => 'eca', 'ECA238G0565' => 'eca', 'ECA246G1027' => 'eca', 'ECA246G3223' => 'eca', 'ECA246G3470' => 'eca', 'EL10Ac6g13829' => 'bvu', 'EL10Ac6g14093' => 'bvu', 'EL10Ac8g18707' => 'bvu', 'Eucgr.C01369' => 'egr', 'Eucgr.H02492' => 'egr', 'Eucgr.I01733' => 'egr', 'Eucgr.J02255' => 'egr', 'Eucgr.J02257' => 'egr', 'Eucgr.J02258' => 'egr', 'FAN02G1601' => 'fan', 'FAN03G1586' => 'fan', 'FAN03G2986' => 'fan', 'FAN05G4837' => 'fan', 'FAN06G0146' => 'fan', 'FAN07G0858' => 'fan', 'FAN09G3179' => 'fan', 'FAN10G0669' => 'fan', 'FAN12G2358' => 'fan', 'FAN14G4198' => 'fan', 'FAN14G5112' => 'fan', 'FAN17G0342' => 'fan', 'FAN19G0342' => 'fan', 'FAN19G0962' => 'fan', 'FAN19G1101' => 'fan', 'FAN19G1872' => 'fan', 'FAN22G0356' => 'fan', 'FAN23G0744' => 'fan', 'FAN23G1914' => 'fan', 'FAN26G0032' => 'fan', 'FAN28G0625' => 'fan', 'FvH4_1g02710' => 'fve', 'FvH4_1g02720' => 'fve', 'FvH4_4g25670' => 'fve', 'FvH4_6g51700' => 'fve', 'FvH4_7g20170' => 'fve', 'Glyma.05G175000' => 'gma', 'Glyma.08G132300' => 'gma', 'Glyma.11G243000' => 'gma', 'Glyma.13G158900' => 'gma', 'Glyma.17G112400' => 'gma', 'Glyma.18G014100' => 'gma', 'Glyma.19G003100' => 'gma', 'Glyma.19G056500' => 'gma', 'Gohir.A01G158900' => 'ghi', 'Gohir.A05G312600' => 'ghi', 'Gohir.A05G354900' => 'ghi', 'Gohir.A07G037200' => 'ghi', 'Gohir.A09G030000' => 'ghi', 'Gohir.A12G145200' => 'ghi', 'Gohir.D01G151500' => 'ghi', 'Gohir.D04G058300' => 'ghi', 'Gohir.D05G314100' => 'ghi', 'Gohir.D07G041400' => 'ghi', 'Gohir.D09G029700' => 'ghi', 'Gohir.D12G149700' => 'ghi', 'Gorai.001G043800' => 'gra', 'Gorai.002G187800' => 'gra', 'Gorai.006G034700' => 'gra', 'Gorai.008G161200' => 'gra', 'Gorai.009G335700' => 'gra', 'Gorai.012G065000' => 'gra', 'GSVIVG01000535001' => 'vvi', 'GSVIVG01015572001' => 'vvi', 'GSVIVG01032386001' => 'vvi', 'HanXRQChr05g0138531' => 'han', 'HanXRQChr06g0174391' => 'han', 'HanXRQChr07g0199021' => 'han', 'HanXRQChr08g0208211' => 'han', 'HanXRQChr09g0255471' => 'han', 'HanXRQChr10g0315791' => 'han', 'HanXRQChr12g0371991' => 'han', 'HanXRQChr15g0475251' => 'han', 'HanXRQChr17g0540001' => 'han', 'HanXRQChr17g0548631' => 'han', 'HanXRQChr17g0569561' => 'han', 'Haze_12256' => 'cav', 'Haze_14756' => 'cav', 'Haze_25528' => 'cav', 'Hma1.2p1_0079F.1_g041020' => 'hma', 'Hma1.2p1_0818F.1_g223260' => 'hma', 'Hma1.2p1_1747F.1_g300530' => 'hma', 'HPP92_004607' => 'vpl', 'HPP92_004608' => 'vpl', 'HPP92_006181' => 'vpl', 'HPP92_012192' => 'vpl', 'HPP92_015680' => 'vpl', 'HPP92_020249' => 'vpl', 'HPP92_021376' => 'vpl', 'HPP92_024275' => 'vpl', 'Hund06031' => 'sun', 'Hund25391' => 'sun', 'Lalb_Chr07g0185371' => 'lal', 'Lalb_Chr07g0185381' => 'lal', 'Lalb_Chr12g0204011' => 'lal', 'Lalb_Chr13g0301671' => 'lal', 'Lalb_Chr14g0362851' => 'lal', 'Lalb_Chr24g0403581' => 'lal', 'Lj1g0000233' => 'lja', 'Lj2g0018120' => 'lja', 'Lj3C621T0' => 'lonja', 'Lj3P1059T14' => 'lonja', 'Lj3P611T9' => 'lonja', 'Lj3P614T13' => 'lonja', 'Lj3P615T5' => 'lonja', 'Lj4g0012315' => 'lja', 'Lj4g0026182' => 'lja', 'Lj6P813T16' => 'lonja', 'Lj7C427T7' => 'lonja', 'Lj7C427T8' => 'lonja', 'Lj7P600T41' => 'lonja', 'Lju41C42G17' => 'lonja', 'Lsat_1_v5_gn_0_47300' => 'lsa', 'Lsat_1_v5_gn_2_91280' => 'lsa', 'Lsat_1_v5_gn_3_30561' => 'lsa', 'Lsat_1_v5_gn_4_184321' => 'lsa', 'Lsat_1_v5_gn_4_4041' => 'lsa', 'Lsat_1_v5_gn_5_92000' => 'lsa', 'Lsat_1_v5_gn_8_152940' => 'lsa', 'Lsat_1_v5_gn_8_62401' => 'lsa', 'Manes.06G055900' => 'mes', 'Manes.12G022200' => 'mes', 'Manes.13G023300' => 'mes', 'Manes.14G115000' => 'mes', 'Manes.15G151700' => 'mes', 'Manes.17G111300' => 'mes', 'Mapoly0226s0009' => 'mpo', 'MBI02_g25363_MAGBIO' => 'mbi', 'MBI06_g00027_MAGBIO' => 'mbi', 'MBI10_g13034_MAGBIO' => 'mbi', 'MD09G1023400' => 'mdo', 'MD13G1100100' => 'mdo', 'MD15G1169200' => 'mdo', 'MD16G1101100' => 'mdo', 'MD17G1022900' => 'mdo', 'Medtr3g096150' => 'mtr', 'Medtr4g115070' => 'mtr', 'Medtr7g033325' => 'mtr', 'Medtr8g089840' => 'mtr', 'MELO3C010319.2' => 'cme', 'MELO3C011944.2' => 'cme', 'MELO3C021589.2' => 'cme', 'Migut.E00207' => 'egut', 'Migut.H00067' => 'egut', 'Migut.K00433' => 'egut', 'Migut.K00606' => 'egut', 'Migut.K01410' => 'egut', 'MSTRG.13347' => 'ama', 'MSTRG.24045' => 'ama', 'MSTRG.2428' => 'ama', 'MSTRG.26410' => 'ama', 'MSTRG.3139' => 'ama', 'MSTRG.3286' => 'ama', 'MSTRG.563' => 'ama', 'MSTRG.7941' => 'ama', 'Nitab4.5_0000028g0060' => 'nta', 'Nitab4.5_0000065g0260' => 'nta', 'Nitab4.5_0000112g0060' => 'nta', 'Nitab4.5_0000489g0120' => 'nta', 'Nitab4.5_0001776g0050' => 'nta', 'Nitab4.5_0001854g0010' => 'nta', 'Nitab4.5_0001860g0020' => 'nta', 'Nitab4.5_0004352g0010' => 'nta', 'Nitab4.5_0008716g0020' => 'nta', 'Nitab4.5_0008922g0010' => 'nta', 'Nn3g16693' => 'nnu', 'Nn4g22596' => 'nnu', 'Nn7g37639' => 'nnu', 'Oeu001701.1' => 'oeu', 'Oeu018149.1' => 'oeu', 'Oeu026220.1' => 'oeu', 'Oeu038635.1' => 'oeu', 'Oeu049176.1' => 'oeu', 'Oeu056706.1' => 'oeu', 'Oeu056937.1' => 'oeu', 'Oeu057540.1' => 'oeu', 'Os02g0594900' => 'osa', 'Os02g0595100' => 'osa', 'Os04g0477500' => 'osa', 'Os12g0611900' => 'osa', 'Peaxi162Scf00076g00020' => 'pax', 'Peaxi162Scf00128g00217' => 'pax', 'Peaxi162Scf00129g01640' => 'pax', 'Peaxi162Scf00669g00007' => 'pax', 'Peaxi162Scf00700g00421' => 'pax', 'Peaxi162Scf00801g00038' => 'pax', 'Peaxi162Scf00891g00025' => 'pax', 'PGR083G0909' => 'pgr', 'PGR119G1005' => 'pgr', 'PGR142G2236' => 'pgr', 'PGR142G3388' => 'pgr', 'PGSC0003DMG400004514' => 'stu', 'PGSC0003DMG400012635' => 'stu', 'PGSC0003DMG400015730' => 'stu', 'PGSC0003DMG400018611' => 'stu', 'PGSC0003DMG400030897' => 'stu', 'Phvul.001G254800' => 'pvu', 'Phvul.002G260100' => 'pvu', 'Phvul.003G167600' => 'pvu', 'Phvul.004G005100' => 'pvu', 'Potri.001G343600' => 'ptr', 'Potri.006G066700' => 'ptr', 'Potri.008G186000' => 'ptr', 'Potri.010G046900' => 'ptr', 'Potri.018G127900' => 'ptr', 'Pp3c20_17750' => 'ppa', 'Pp3c24_4380' => 'ppa', 'Prupe.1G245800' => 'ppe', 'Prupe.3G293400' => 'ppe', 'Prupe.7G247400' => 'ppe', 'Psat0s145g0120' => 'psa', 'Psat0s595g0040' => 'psa', 'Psat0s595g0120' => 'psa', 'Psat3g175040' => 'psa', 'Psat7g058120' => 'psa', 'PSO017G0428' => 'pso', 'PSO063G7510' => 'pso', 'PSO067G0046' => 'pso', 'PSO478G1073' => 'pso', 'PSO675G3677' => 'pso', 'PSO675G6558' => 'pso', 'PSO675G7520' => 'pso', 'PSO675G8959' => 'pso', 'QL02p074089' => 'qlo', 'QL02p089614' => 'qlo', 'QL03p057736' => 'qlo', 'RcHm_v2.0_Chr1g0364131' => 'rch', 'RcHm_v2.0_Chr2g0087801' => 'rch', 'RcHm_v2.0_Chr2g0087821' => 'rch', 'RcHm_v2.0_Chr2g0173231' => 'rch', 'RcHm_v2.0_Chr4g0433111' => 'rch', 'Rhsim03G0250300' => 'rsi', 'Rhsim08G0048400' => 'rsi', 'Rhsim10G0014800' => 'rsi', 'Rhsim12G0040100' => 'rsi', 'Rhsim12G0109700' => 'rsi', 'Sabra06G0049600' => 'sbr', 'Sabra08G0141000' => 'sbr', 'Sabra10G0021400' => 'sbr', 'Sabra16G0222900' => 'sbr', 'Sabra18G0108600' => 'sbr', 'SalBow1G0433' => 'sbo', 'SalBow1G2038' => 'sbo', 'SalBow1G5003' => 'sbo', 'SalBow7G1197' => 'sbo', 'SalBow8G3506' => 'sbo', 'Sc03g0007300' => 'sci', 'Sc11g0000950' => 'sci', 'Sc14g0008750' => 'sci', 'Sc18g0000420' => 'sci', 'Sed0006754' => 'sed', 'Sed0008741' => 'sed', 'Sed0017172' => 'sed', 'Sed0018925' => 'sed', 'Sed0023326' => 'sed', 'Sed0025909' => 'sed', 'SEGI_05333' => 'sgi', 'SEGI_10362' => 'sgi', 'SEGI_13380' => 'sgi', 'SEGI_24306' => 'sgi', 'SEGI_29077' => 'sgi', 'SEGI_29095' => 'sgi', 'SEGI_36534' => 'sgi', 'SEGI_37506' => 'sgi', 'SEGI_38321' => 'sgi', 'SGA_v2.0_scaffold307G48031' => 'sas', 'SGA_v2.0_scaffold47G17507' => 'sas', 'SGA_v2.0_scaffold63G21736' => 'sas', 'SGA_v2.0_scaffold87G27070' => 'sas', 'SHI17794' => 'shi', 'SHI28851' => 'shi', 'SMO165G0155' => 'smo', 'SMO340G0217' => 'smo', 'SMO367G1210' => 'smo', 'Solyc02g093430.3' => 'sly', 'Solyc05g013580.4' => 'sly', 'Solyc07g008030.3' => 'sly', 'Solyc12g035470.2' => 'sly', 'Sopen02g038020' => 'spe', 'Sopen05g008490' => 'spe', 'Sopen07g003910' => 'spe', 'Sopen12g015240' => 'spe', 'Sp1g11550' => 'spa', 'Sp2g16710' => 'spa', 'Sp3g00430' => 'spa', 'Sp3g26780' => 'spa', 'Sp5g22900' => 'spa', 'Sp6g29530' => 'spa', 'TAR371G0794' => 'tar', 'TAR374G0164' => 'tar', 'TAR622G0165' => 'tar', 'TAR626G0929' => 'tar', 'TAR629G2155' => 'tar', 'THA.LOC104805282' => 'tha', 'THA.LOC104805363' => 'tha', 'THA.LOC104808968' => 'tha', 'THA.LOC104821093' => 'tha', 'THA.LOC104823953' => 'tha', 'THA.LOC104825562' => 'tha', 'THA.LOC104825665' => 'tha', 'Thecc.02G261400' => 'tca', 'Thecc.04G019200' => 'tca', 'Thecc.09G130400' => 'tca', 'Thhalv10004374m.g' => 'esa', 'Thhalv10007850m.g' => 'esa', 'Thhalv10013782m.g' => 'esa', 'Thhalv10018686m.g' => 'esa', 'Thhalv10020899m.g' => 'esa', 'Thhalv10022755m.g' => 'esa', 'TPR.G23851' => 'tpr', 'TPR.G26500' => 'tpr', 'TPR.G27267' => 'tpr', 'TPR.G32001' => 'tpr', 'TPR.G6251' => 'tpr', 'TPR.G8167' => 'tpr', 'TWI12G1330' => 'twi', 'TWI18G1239' => 'twi', 'TWI34G0979' => 'twi', 'TWI36G0670' => 'twi', 'TWI36G0707' => 'twi', 'TWI56G0233' => 'twi', 'TWI75G1809' => 'twi', 'unitig_21.g20874' => 'ugi', 'unitig_26.g10343' => 'ugi', 'unitig_46.g18392' => 'ugi', 'unitig_52.g17178' => 'ugi', 'unitig_8.g2934' => 'ugi', 'vmacro01122' => 'vma', 'vmacro05875' => 'vma', 'vmacro06147' => 'vma', 'vmacro16191' => 'vma', 'vmacro18293' => 'vma', 'VMungo0251G3707' => 'vmu', 'VMungo0464G1521' => 'vmu', 'VMungo1215G0205' => 'vmu', 'VMungo1383G2484' => 'vmu', 'Zm00001eb079610' => 'zma', 'Zm00001eb135990' => 'zma', 'Zm00001eb183710' => 'zma', 'Zm00001eb246020' => 'zma' ), 'gf_id' => 'HOM05D001124', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001124' ), 'data_identifier' => 'HOM05D001124', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001124', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '548', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02520' => 'bna', 'A03p06630' => 'bna', 'A05p44460' => 'bna', 'A06p08710' => 'bna', 'A06p41090' => 'bna', 'A07p32320' => 'bna', 'A08p32520' => 'bna', 'A09p10360' => 'bna', 'A10p24080' => 'bna', 'Aa31LG11G15250' => 'aar', 'Aa31LG1G1800' => 'aar', 'Aa31LG2G5120' => 'aar', 'Aa31LG2G6070' => 'aar', 'Aa31LG5G10770' => 'aar', 'Aa31sc61G90' => 'aar', 'Actinidia01352' => 'ach', 'Actinidia05983' => 'ach', 'Actinidia08133' => 'ach', 'Actinidia15101' => 'ach', 'Actinidia26379' => 'ach', 'Actinidia35778' => 'ach', 'Actinidia36123' => 'ach', 'Actinidia37436' => 'ach', 'Actinidia38730' => 'ach', 'Ah.02g128210' => 'amhyb', 'Ah.03g132990' => 'amhyb', 'Ah.14g079410' => 'amhyb', 'AL1G24640' => 'aly', 'AL2G26680' => 'aly', 'AL3G10530' => 'aly', 'AL3G45230' => 'aly', 'AL5G15230' => 'aly', 'AL5G16960' => 'aly', 'AL6G25210' => 'aly', 'Aqoxy2G00441' => 'aox', 'Aqoxy3G01236' => 'aox', 'Aqoxy5G03746' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3RQ047' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C7GMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9C8JER' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MBL6KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YXCZ83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZANX40' => 'arhy', 'AT1G12990' => 'ath', 'AT1G67880' => 'ath', 'AT2G13290' => 'ath', 'AT3G01620' => 'ath', 'AT3G26445' => 'ath', 'AT3G27540' => 'ath', 'AT5G14480' => 'ath', 'ATR0824G026' => 'atr', 'ATR1098G019' => 'atr', 'Atru.chr11.2145' => 'acertr', 'Atru.chr2.3636' => 'acertr', 'Atru.chr2.3644' => 'acertr', 'Atru.chr6.2422' => 'acertr', 'Atru.chr7.1112' => 'acertr', 'AUR62005469' => 'cqu', 'AUR62011166' => 'cqu', 'AUR62013319' => 'cqu', 'AUR62024273' => 'cqu', 'AUR62028420' => 'cqu', 'AUR62041942' => 'cqu', 'BcaB01g04969' => 'bca', 'BcaB01g06371' => 'bca', 'BcaB02g11494' => 'bca', 'BcaB03g15382' => 'bca', 'BcaB08g36994' => 'bca', 'BcaC03g13477' => 'bca', 'BcaC03g13478' => 'bca', 'BcaC03g13480' => 'bca', 'BcaC03g13481' => 'bca', 'BcaC03g13486' => 'bca', 'BcaC04g19031' => 'bca', 'BcaC04g23085' => 'bca', 'BcaC05g25094' => 'bca', 'BcaC05g25096' => 'bca', 'BcaC05g25138' => 'bca', 'BcaC05g30416' => 'bca', 'BcaC05g30455' => 'bca', 'BcaC06g30979' => 'bca', 'BcaC06g33805' => 'bca', 'BcaC08g46021' => 'bca', 'BcaNung03154' => 'bca', 'BolC2t06623H' => 'bol', 'BolC2t06632H' => 'bol', 'BolC2t06635H' => 'bol', 'BolC2t06638H' => 'bol', 'BolC3t13266H' => 'bol', 'BolC5t29776H' => 'bol', 'BolC6t38912H' => 'bol', 'BolC7t44183H' => 'bol', 'BolC9t54123H' => 'bol', 'BolC9t59107H' => 'bol', 'BraA02t05221Z' => 'bra', 'BraA03t09996Z' => 'bra', 'BraA05t23210Z' => 'bra', 'BraA06t24068Z' => 'bra', 'BraA06t27032Z' => 'bra', 'BraA08t35176Z' => 'bra', 'BraA09t36680Z' => 'bra', 'BraA10t44471Z' => 'bra', 'C02p06760' => 'bna', 'C02p06890' => 'bna', 'C02p07010' => 'bna', 'C03p07660' => 'bna', 'C05p10300' => 'bna', 'C06p38150' => 'bna', 'C07p36650' => 'bna', 'C08p15770' => 'bna', 'C09p12300' => 'bna', 'C09p62700' => 'bna', 'C09p75040' => 'bna', 'CAN.G13.1' => 'can', 'CAN.G138.4' => 'can', 'CAN.G44.6' => 'can', 'CAN.G473.19' => 'can', 'CANSAT01G0835' => 'cansat', 'CANSAT11G0246' => 'cansat', 'CANSAT11G1766' => 'cansat', 'CANSAT64G1954' => 'cansat', 'CARHR013330' => 'chi', 'CARHR060530' => 'chi', 'CARHR075300' => 'chi', 'CARHR105120' => 'chi', 'CARHR148910' => 'chi', 'CARHR198830' => 'chi', 'Carub.0001s1275' => 'cru', 'Carub.0002s1437' => 'cru', 'Carub.0003s0044' => 'cru', 'Carub.0003s2787' => 'cru', 'Carub.0005s0597' => 'cru', 'Carub.0006s1266' => 'cru', 'Ca_06935_v3' => 'car', 'Ca_13559_v3' => 'car', 'Ca_16941_v3' => 'car', 'Ca_16960_v3' => 'car', 'Ca_17775_v3' => 'car', 'Ca_30464_v3' => 'car', 'Cc06_g08160' => 'ccan', 'Cc07_g01520' => 'ccan', 'Cc11_g15810' => 'ccan', 'CDE02G2840' => 'cde', 'CDE03G0093' => 'cde', 'CDE04G2127' => 'cde', 'CDE07G1857' => 'cde', 'CDE09G1246' => 'cde', 'Cfa003412' => 'cfa', 'Cfa007341' => 'cfa', 'Cfa009220' => 'cfa', 'Ciclev10008737m.g' => 'ccl', 'Ciclev10015565m.g' => 'ccl', 'Ciclev10031761m.g' => 'ccl', 'CiPaw.03G045300' => 'cil', 'CiPaw.03G247200' => 'cil', 'CiPaw.04G029500' => 'cil', 'CiPaw.04G174000' => 'cil', 'CiPaw.05G181200' => 'cil', 'CiPaw.06G067100' => 'cil', 'ClCG05G025800' => 'cla', 'ClCG06G011400' => 'cla', 'ClCG09G019360' => 'cla', 'COL.COLO4_04827' => 'col', 'COL.COLO4_29170' => 'col', 'COL.COLO4_35131' => 'col', 'COL.COLO4_35132' => 'col', 'Cpa.g.sc33.32' => 'cpa', 'Cpa.g.sc46.29' => 'cpa', 'Cpa.g.sc796.1' => 'cpa', 'CsaV3_1G030420' => 'csa', 'CsaV3_5G027050' => 'csa', 'CsaV3_5G031040' => 'csa', 'CsaV3_UNG023130' => 'csa', 'CSS0007726' => 'camsi', 'CSS0016433' => 'camsi', 'CSS0017656' => 'camsi', 'CSS0025364' => 'camsi', 'CSS0027582' => 'camsi', 'CSS0047288' => 'camsi', 'CSS0049950' => 'camsi', 'DCAR_003843' => 'dca', 'DCAR_007052' => 'dca', 'DCAR_020884' => 'dca', 'DCAR_021730' => 'dca', 'DCAR_024423' => 'dca', 'DCAR_026509' => 'dca', 'DCAR_031158' => 'dca', 'Dinv14728' => 'din', 'Dinv15219' => 'din', 'Dinv25728' => 'din', 'Dinv33428' => 'din', 'Dinv36489' => 'din', 'Dinv41486' => 'din', 'Duzib147G0469' => 'dzi', 'Duzib168G0060' => 'dzi', 'Duzib187G1215' => 'dzi', 'Duzib248G0692' => 'dzi', 'Duzib251G0767' => 'dzi', 'Duzib264G0446' => 'dzi', 'Duzib268G0691' => 'dzi', 'ECA232G4767' => 'eca', 'ECA233G2838' => 'eca', 'ECA234G0391' => 'eca', 'ECA234G0857' => 'eca', 'ECA236G1593' => 'eca', 'ECA238G0565' => 'eca', 'ECA246G1027' => 'eca', 'ECA246G3223' => 'eca', 'ECA246G3470' => 'eca', 'EL10Ac6g13829' => 'bvu', 'EL10Ac6g14093' => 'bvu', 'EL10Ac8g18707' => 'bvu', 'Eucgr.C01369' => 'egr', 'Eucgr.H02492' => 'egr', 'Eucgr.I01733' => 'egr', 'Eucgr.J02255' => 'egr', 'Eucgr.J02257' => 'egr', 'Eucgr.J02258' => 'egr', 'FAN02G1601' => 'fan', 'FAN03G1586' => 'fan', 'FAN03G2986' => 'fan', 'FAN05G4837' => 'fan', 'FAN06G0146' => 'fan', 'FAN07G0858' => 'fan', 'FAN09G3179' => 'fan', 'FAN10G0669' => 'fan', 'FAN12G2358' => 'fan', 'FAN14G4198' => 'fan', 'FAN14G5112' => 'fan', 'FAN17G0342' => 'fan', 'FAN19G0342' => 'fan', 'FAN19G0962' => 'fan', 'FAN19G1101' => 'fan', 'FAN19G1872' => 'fan', 'FAN22G0356' => 'fan', 'FAN23G0744' => 'fan', 'FAN23G1914' => 'fan', 'FAN26G0032' => 'fan', 'FAN28G0625' => 'fan', 'FvH4_1g02710' => 'fve', 'FvH4_1g02720' => 'fve', 'FvH4_4g25670' => 'fve', 'FvH4_6g51700' => 'fve', 'FvH4_7g20170' => 'fve', 'Glyma.05G175000' => 'gma', 'Glyma.08G132300' => 'gma', 'Glyma.11G243000' => 'gma', 'Glyma.13G158900' => 'gma', 'Glyma.17G112400' => 'gma', 'Glyma.18G014100' => 'gma', 'Glyma.19G003100' => 'gma', 'Glyma.19G056500' => 'gma', 'Gohir.A01G158900' => 'ghi', 'Gohir.A05G312600' => 'ghi', 'Gohir.A05G354900' => 'ghi', 'Gohir.A07G037200' => 'ghi', 'Gohir.A09G030000' => 'ghi', 'Gohir.A12G145200' => 'ghi', 'Gohir.D01G151500' => 'ghi', 'Gohir.D04G058300' => 'ghi', 'Gohir.D05G314100' => 'ghi', 'Gohir.D07G041400' => 'ghi', 'Gohir.D09G029700' => 'ghi', 'Gohir.D12G149700' => 'ghi', 'Gorai.001G043800' => 'gra', 'Gorai.002G187800' => 'gra', 'Gorai.006G034700' => 'gra', 'Gorai.008G161200' => 'gra', 'Gorai.009G335700' => 'gra', 'Gorai.012G065000' => 'gra', 'GSVIVG01000535001' => 'vvi', 'GSVIVG01015572001' => 'vvi', 'GSVIVG01032386001' => 'vvi', 'HanXRQChr05g0138531' => 'han', 'HanXRQChr06g0174391' => 'han', 'HanXRQChr07g0199021' => 'han', 'HanXRQChr08g0208211' => 'han', 'HanXRQChr09g0255471' => 'han', 'HanXRQChr10g0315791' => 'han', 'HanXRQChr12g0371991' => 'han', 'HanXRQChr15g0475251' => 'han', 'HanXRQChr17g0540001' => 'han', 'HanXRQChr17g0548631' => 'han', 'HanXRQChr17g0569561' => 'han', 'Haze_12256' => 'cav', 'Haze_14756' => 'cav', 'Haze_25528' => 'cav', 'Hma1.2p1_0079F.1_g041020' => 'hma', 'Hma1.2p1_0818F.1_g223260' => 'hma', 'Hma1.2p1_1747F.1_g300530' => 'hma', 'HPP92_004607' => 'vpl', 'HPP92_004608' => 'vpl', 'HPP92_006181' => 'vpl', 'HPP92_012192' => 'vpl', 'HPP92_015680' => 'vpl', 'HPP92_020249' => 'vpl', 'HPP92_021376' => 'vpl', 'HPP92_024275' => 'vpl', 'Hund06031' => 'sun', 'Hund25391' => 'sun', 'Lalb_Chr07g0185371' => 'lal', 'Lalb_Chr07g0185381' => 'lal', 'Lalb_Chr12g0204011' => 'lal', 'Lalb_Chr13g0301671' => 'lal', 'Lalb_Chr14g0362851' => 'lal', 'Lalb_Chr24g0403581' => 'lal', 'Lj1g0000233' => 'lja', 'Lj2g0018120' => 'lja', 'Lj3C621T0' => 'lonja', 'Lj3P1059T14' => 'lonja', 'Lj3P611T9' => 'lonja', 'Lj3P614T13' => 'lonja', 'Lj3P615T5' => 'lonja', 'Lj4g0012315' => 'lja', 'Lj4g0026182' => 'lja', 'Lj6P813T16' => 'lonja', 'Lj7C427T7' => 'lonja', 'Lj7C427T8' => 'lonja', 'Lj7P600T41' => 'lonja', 'Lju41C42G17' => 'lonja', 'Lsat_1_v5_gn_0_47300' => 'lsa', 'Lsat_1_v5_gn_2_91280' => 'lsa', 'Lsat_1_v5_gn_3_30561' => 'lsa', 'Lsat_1_v5_gn_4_184321' => 'lsa', 'Lsat_1_v5_gn_4_4041' => 'lsa', 'Lsat_1_v5_gn_5_92000' => 'lsa', 'Lsat_1_v5_gn_8_152940' => 'lsa', 'Lsat_1_v5_gn_8_62401' => 'lsa', 'Manes.06G055900' => 'mes', 'Manes.12G022200' => 'mes', 'Manes.13G023300' => 'mes', 'Manes.14G115000' => 'mes', 'Manes.15G151700' => 'mes', 'Manes.17G111300' => 'mes', 'Mapoly0226s0009' => 'mpo', 'MBI02_g25363_MAGBIO' => 'mbi', 'MBI06_g00027_MAGBIO' => 'mbi', 'MBI10_g13034_MAGBIO' => 'mbi', 'MD09G1023400' => 'mdo', 'MD13G1100100' => 'mdo', 'MD15G1169200' => 'mdo', 'MD16G1101100' => 'mdo', 'MD17G1022900' => 'mdo', 'Medtr3g096150' => 'mtr', 'Medtr4g115070' => 'mtr', 'Medtr7g033325' => 'mtr', 'Medtr8g089840' => 'mtr', 'MELO3C010319.2' => 'cme', 'MELO3C011944.2' => 'cme', 'MELO3C021589.2' => 'cme', 'Migut.E00207' => 'egut', 'Migut.H00067' => 'egut', 'Migut.K00433' => 'egut', 'Migut.K00606' => 'egut', 'Migut.K01410' => 'egut', 'MSTRG.13347' => 'ama', 'MSTRG.24045' => 'ama', 'MSTRG.2428' => 'ama', 'MSTRG.26410' => 'ama', 'MSTRG.3139' => 'ama', 'MSTRG.3286' => 'ama', 'MSTRG.563' => 'ama', 'MSTRG.7941' => 'ama', 'Nitab4.5_0000028g0060' => 'nta', 'Nitab4.5_0000065g0260' => 'nta', 'Nitab4.5_0000112g0060' => 'nta', 'Nitab4.5_0000489g0120' => 'nta', 'Nitab4.5_0001776g0050' => 'nta', 'Nitab4.5_0001854g0010' => 'nta', 'Nitab4.5_0001860g0020' => 'nta', 'Nitab4.5_0004352g0010' => 'nta', 'Nitab4.5_0008716g0020' => 'nta', 'Nitab4.5_0008922g0010' => 'nta', 'Nn3g16693' => 'nnu', 'Nn4g22596' => 'nnu', 'Nn7g37639' => 'nnu', 'Oeu001701.1' => 'oeu', 'Oeu018149.1' => 'oeu', 'Oeu026220.1' => 'oeu', 'Oeu038635.1' => 'oeu', 'Oeu049176.1' => 'oeu', 'Oeu056706.1' => 'oeu', 'Oeu056937.1' => 'oeu', 'Oeu057540.1' => 'oeu', 'Os02g0594900' => 'osa', 'Os02g0595100' => 'osa', 'Os04g0477500' => 'osa', 'Os12g0611900' => 'osa', 'Peaxi162Scf00076g00020' => 'pax', 'Peaxi162Scf00128g00217' => 'pax', 'Peaxi162Scf00129g01640' => 'pax', 'Peaxi162Scf00669g00007' => 'pax', 'Peaxi162Scf00700g00421' => 'pax', 'Peaxi162Scf00801g00038' => 'pax', 'Peaxi162Scf00891g00025' => 'pax', 'PGR083G0909' => 'pgr', 'PGR119G1005' => 'pgr', 'PGR142G2236' => 'pgr', 'PGR142G3388' => 'pgr', 'PGSC0003DMG400004514' => 'stu', 'PGSC0003DMG400012635' => 'stu', 'PGSC0003DMG400015730' => 'stu', 'PGSC0003DMG400018611' => 'stu', 'PGSC0003DMG400030897' => 'stu', 'Phvul.001G254800' => 'pvu', 'Phvul.002G260100' => 'pvu', 'Phvul.003G167600' => 'pvu', 'Phvul.004G005100' => 'pvu', 'Potri.001G343600' => 'ptr', 'Potri.006G066700' => 'ptr', 'Potri.008G186000' => 'ptr', 'Potri.010G046900' => 'ptr', 'Potri.018G127900' => 'ptr', 'Pp3c20_17750' => 'ppa', 'Pp3c24_4380' => 'ppa', 'Prupe.1G245800' => 'ppe', 'Prupe.3G293400' => 'ppe', 'Prupe.7G247400' => 'ppe', 'Psat0s145g0120' => 'psa', 'Psat0s595g0040' => 'psa', 'Psat0s595g0120' => 'psa', 'Psat3g175040' => 'psa', 'Psat7g058120' => 'psa', 'PSO017G0428' => 'pso', 'PSO063G7510' => 'pso', 'PSO067G0046' => 'pso', 'PSO478G1073' => 'pso', 'PSO675G3677' => 'pso', 'PSO675G6558' => 'pso', 'PSO675G7520' => 'pso', 'PSO675G8959' => 'pso', 'QL02p074089' => 'qlo', 'QL02p089614' => 'qlo', 'QL03p057736' => 'qlo', 'RcHm_v2.0_Chr1g0364131' => 'rch', 'RcHm_v2.0_Chr2g0087801' => 'rch', 'RcHm_v2.0_Chr2g0087821' => 'rch', 'RcHm_v2.0_Chr2g0173231' => 'rch', 'RcHm_v2.0_Chr4g0433111' => 'rch', 'Rhsim03G0250300' => 'rsi', 'Rhsim08G0048400' => 'rsi', 'Rhsim10G0014800' => 'rsi', 'Rhsim12G0040100' => 'rsi', 'Rhsim12G0109700' => 'rsi', 'Sabra06G0049600' => 'sbr', 'Sabra08G0141000' => 'sbr', 'Sabra10G0021400' => 'sbr', 'Sabra16G0222900' => 'sbr', 'Sabra18G0108600' => 'sbr', 'SalBow1G0433' => 'sbo', 'SalBow1G2038' => 'sbo', 'SalBow1G5003' => 'sbo', 'SalBow7G1197' => 'sbo', 'SalBow8G3506' => 'sbo', 'Sc03g0007300' => 'sci', 'Sc11g0000950' => 'sci', 'Sc14g0008750' => 'sci', 'Sc18g0000420' => 'sci', 'Sed0006754' => 'sed', 'Sed0008741' => 'sed', 'Sed0017172' => 'sed', 'Sed0018925' => 'sed', 'Sed0023326' => 'sed', 'Sed0025909' => 'sed', 'SEGI_05333' => 'sgi', 'SEGI_10362' => 'sgi', 'SEGI_13380' => 'sgi', 'SEGI_24306' => 'sgi', 'SEGI_29077' => 'sgi', 'SEGI_29095' => 'sgi', 'SEGI_36534' => 'sgi', 'SEGI_37506' => 'sgi', 'SEGI_38321' => 'sgi', 'SGA_v2.0_scaffold307G48031' => 'sas', 'SGA_v2.0_scaffold47G17507' => 'sas', 'SGA_v2.0_scaffold63G21736' => 'sas', 'SGA_v2.0_scaffold87G27070' => 'sas', 'SHI17794' => 'shi', 'SHI28851' => 'shi', 'SMO165G0155' => 'smo', 'SMO340G0217' => 'smo', 'SMO367G1210' => 'smo', 'Solyc02g093430.3' => 'sly', 'Solyc05g013580.4' => 'sly', 'Solyc07g008030.3' => 'sly', 'Solyc12g035470.2' => 'sly', 'Sopen02g038020' => 'spe', 'Sopen05g008490' => 'spe', 'Sopen07g003910' => 'spe', 'Sopen12g015240' => 'spe', 'Sp1g11550' => 'spa', 'Sp2g16710' => 'spa', 'Sp3g00430' => 'spa', 'Sp3g26780' => 'spa', 'Sp5g22900' => 'spa', 'Sp6g29530' => 'spa', 'TAR371G0794' => 'tar', 'TAR374G0164' => 'tar', 'TAR622G0165' => 'tar', 'TAR626G0929' => 'tar', 'TAR629G2155' => 'tar', 'THA.LOC104805282' => 'tha', 'THA.LOC104805363' => 'tha', 'THA.LOC104808968' => 'tha', 'THA.LOC104821093' => 'tha', 'THA.LOC104823953' => 'tha', 'THA.LOC104825562' => 'tha', 'THA.LOC104825665' => 'tha', 'Thecc.02G261400' => 'tca', 'Thecc.04G019200' => 'tca', 'Thecc.09G130400' => 'tca', 'Thhalv10004374m.g' => 'esa', 'Thhalv10007850m.g' => 'esa', 'Thhalv10013782m.g' => 'esa', 'Thhalv10018686m.g' => 'esa', 'Thhalv10020899m.g' => 'esa', 'Thhalv10022755m.g' => 'esa', 'TPR.G23851' => 'tpr', 'TPR.G26500' => 'tpr', 'TPR.G27267' => 'tpr', 'TPR.G32001' => 'tpr', 'TPR.G6251' => 'tpr', 'TPR.G8167' => 'tpr', 'TWI12G1330' => 'twi', 'TWI18G1239' => 'twi', 'TWI34G0979' => 'twi', 'TWI36G0670' => 'twi', 'TWI36G0707' => 'twi', 'TWI56G0233' => 'twi', 'TWI75G1809' => 'twi', 'unitig_21.g20874' => 'ugi', 'unitig_26.g10343' => 'ugi', 'unitig_46.g18392' => 'ugi', 'unitig_52.g17178' => 'ugi', 'unitig_8.g2934' => 'ugi', 'vmacro01122' => 'vma', 'vmacro05875' => 'vma', 'vmacro06147' => 'vma', 'vmacro16191' => 'vma', 'vmacro18293' => 'vma', 'VMungo0251G3707' => 'vmu', 'VMungo0464G1521' => 'vmu', 'VMungo1215G0205' => 'vmu', 'VMungo1383G2484' => 'vmu', 'Zm00001eb079610' => 'zma', 'Zm00001eb135990' => 'zma', 'Zm00001eb183710' => 'zma', 'Zm00001eb246020' => 'zma' ) $gf_id = 'HOM05D001124' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001124' ) $data_identifier = 'HOM05D001124' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 6, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 7, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 21, 'bol' => (int) 10, 'bra' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 6, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 9, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 21, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 8, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 10, 'lsa' => (int) 8, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 8, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 9, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb246020' $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' => 'HOM05D001124', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '548', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02520' => 'bna', 'A03p06630' => 'bna', 'A05p44460' => 'bna', 'A06p08710' => 'bna', 'A06p41090' => 'bna', 'A07p32320' => 'bna', 'A08p32520' => 'bna', 'A09p10360' => 'bna', 'A10p24080' => 'bna', 'Aa31LG11G15250' => 'aar', 'Aa31LG1G1800' => 'aar', 'Aa31LG2G5120' => 'aar', 'Aa31LG2G6070' => 'aar', 'Aa31LG5G10770' => 'aar', 'Aa31sc61G90' => 'aar', 'Actinidia01352' => 'ach', 'Actinidia05983' => 'ach', 'Actinidia08133' => 'ach', 'Actinidia15101' => 'ach', 'Actinidia26379' => 'ach', 'Actinidia35778' => 'ach', 'Actinidia36123' => 'ach', 'Actinidia37436' => 'ach', 'Actinidia38730' => 'ach', 'Ah.02g128210' => 'amhyb', 'Ah.03g132990' => 'amhyb', 'Ah.14g079410' => 'amhyb', 'AL1G24640' => 'aly', 'AL2G26680' => 'aly', 'AL3G10530' => 'aly', 'AL3G45230' => 'aly', 'AL5G15230' => 'aly', 'AL5G16960' => 'aly', 'AL6G25210' => 'aly', 'Aqoxy2G00441' => 'aox', 'Aqoxy3G01236' => 'aox', 'Aqoxy5G03746' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3RQ047' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C7GMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9C8JER' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MBL6KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YXCZ83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZANX40' => 'arhy', 'AT1G12990' => 'ath', 'AT1G67880' => 'ath', 'AT2G13290' => 'ath', 'AT3G01620' => 'ath', 'AT3G26445' => 'ath', 'AT3G27540' => 'ath', 'AT5G14480' => 'ath', 'ATR0824G026' => 'atr', 'ATR1098G019' => 'atr', 'Atru.chr11.2145' => 'acertr', 'Atru.chr2.3636' => 'acertr', 'Atru.chr2.3644' => 'acertr', 'Atru.chr6.2422' => 'acertr', 'Atru.chr7.1112' => 'acertr', 'AUR62005469' => 'cqu', 'AUR62011166' => 'cqu', 'AUR62013319' => 'cqu', 'AUR62024273' => 'cqu', 'AUR62028420' => 'cqu', 'AUR62041942' => 'cqu', 'BcaB01g04969' => 'bca', 'BcaB01g06371' => 'bca', 'BcaB02g11494' => 'bca', 'BcaB03g15382' => 'bca', 'BcaB08g36994' => 'bca', 'BcaC03g13477' => 'bca', 'BcaC03g13478' => 'bca', 'BcaC03g13480' => 'bca', 'BcaC03g13481' => 'bca', 'BcaC03g13486' => 'bca', 'BcaC04g19031' => 'bca', 'BcaC04g23085' => 'bca', 'BcaC05g25094' => 'bca', 'BcaC05g25096' => 'bca', 'BcaC05g25138' => 'bca', 'BcaC05g30416' => 'bca', 'BcaC05g30455' => 'bca', 'BcaC06g30979' => 'bca', 'BcaC06g33805' => 'bca', 'BcaC08g46021' => 'bca', 'BcaNung03154' => 'bca', 'BolC2t06623H' => 'bol', 'BolC2t06632H' => 'bol', 'BolC2t06635H' => 'bol', 'BolC2t06638H' => 'bol', 'BolC3t13266H' => 'bol', 'BolC5t29776H' => 'bol', 'BolC6t38912H' => 'bol', 'BolC7t44183H' => 'bol', 'BolC9t54123H' => 'bol', 'BolC9t59107H' => 'bol', 'BraA02t05221Z' => 'bra', 'BraA03t09996Z' => 'bra', 'BraA05t23210Z' => 'bra', 'BraA06t24068Z' => 'bra', 'BraA06t27032Z' => 'bra', 'BraA08t35176Z' => 'bra', 'BraA09t36680Z' => 'bra', 'BraA10t44471Z' => 'bra', 'C02p06760' => 'bna', 'C02p06890' => 'bna', 'C02p07010' => 'bna', 'C03p07660' => 'bna', 'C05p10300' => 'bna', 'C06p38150' => 'bna', 'C07p36650' => 'bna', 'C08p15770' => 'bna', 'C09p12300' => 'bna', 'C09p62700' => 'bna', 'C09p75040' => 'bna', 'CAN.G13.1' => 'can', 'CAN.G138.4' => 'can', 'CAN.G44.6' => 'can', 'CAN.G473.19' => 'can', 'CANSAT01G0835' => 'cansat', 'CANSAT11G0246' => 'cansat', 'CANSAT11G1766' => 'cansat', 'CANSAT64G1954' => 'cansat', 'CARHR013330' => 'chi', 'CARHR060530' => 'chi', 'CARHR075300' => 'chi', 'CARHR105120' => 'chi', 'CARHR148910' => 'chi', 'CARHR198830' => 'chi', 'Carub.0001s1275' => 'cru', 'Carub.0002s1437' => 'cru', 'Carub.0003s0044' => 'cru', 'Carub.0003s2787' => 'cru', 'Carub.0005s0597' => 'cru', 'Carub.0006s1266' => 'cru', 'Ca_06935_v3' => 'car', 'Ca_13559_v3' => 'car', 'Ca_16941_v3' => 'car', 'Ca_16960_v3' => 'car', 'Ca_17775_v3' => 'car', 'Ca_30464_v3' => 'car', 'Cc06_g08160' => 'ccan', 'Cc07_g01520' => 'ccan', 'Cc11_g15810' => 'ccan', 'CDE02G2840' => 'cde', 'CDE03G0093' => 'cde', 'CDE04G2127' => 'cde', 'CDE07G1857' => 'cde', 'CDE09G1246' => 'cde', 'Cfa003412' => 'cfa', 'Cfa007341' => 'cfa', 'Cfa009220' => 'cfa', 'Ciclev10008737m.g' => 'ccl', 'Ciclev10015565m.g' => 'ccl', 'Ciclev10031761m.g' => 'ccl', 'CiPaw.03G045300' => 'cil', 'CiPaw.03G247200' => 'cil', 'CiPaw.04G029500' => 'cil', 'CiPaw.04G174000' => 'cil', 'CiPaw.05G181200' => 'cil', 'CiPaw.06G067100' => 'cil', 'ClCG05G025800' => 'cla', 'ClCG06G011400' => 'cla', 'ClCG09G019360' => 'cla', 'COL.COLO4_04827' => 'col', 'COL.COLO4_29170' => 'col', 'COL.COLO4_35131' => 'col', 'COL.COLO4_35132' => 'col', 'Cpa.g.sc33.32' => 'cpa', 'Cpa.g.sc46.29' => 'cpa', 'Cpa.g.sc796.1' => 'cpa', 'CsaV3_1G030420' => 'csa', 'CsaV3_5G027050' => 'csa', 'CsaV3_5G031040' => 'csa', 'CsaV3_UNG023130' => 'csa', 'CSS0007726' => 'camsi', 'CSS0016433' => 'camsi', 'CSS0017656' => 'camsi', 'CSS0025364' => 'camsi', 'CSS0027582' => 'camsi', 'CSS0047288' => 'camsi', 'CSS0049950' => 'camsi', 'DCAR_003843' => 'dca', 'DCAR_007052' => 'dca', 'DCAR_020884' => 'dca', 'DCAR_021730' => 'dca', 'DCAR_024423' => 'dca', 'DCAR_026509' => 'dca', 'DCAR_031158' => 'dca', 'Dinv14728' => 'din', 'Dinv15219' => 'din', 'Dinv25728' => 'din', 'Dinv33428' => 'din', 'Dinv36489' => 'din', 'Dinv41486' => 'din', 'Duzib147G0469' => 'dzi', 'Duzib168G0060' => 'dzi', 'Duzib187G1215' => 'dzi', 'Duzib248G0692' => 'dzi', 'Duzib251G0767' => 'dzi', 'Duzib264G0446' => 'dzi', 'Duzib268G0691' => 'dzi', 'ECA232G4767' => 'eca', 'ECA233G2838' => 'eca', 'ECA234G0391' => 'eca', 'ECA234G0857' => 'eca', 'ECA236G1593' => 'eca', 'ECA238G0565' => 'eca', 'ECA246G1027' => 'eca', 'ECA246G3223' => 'eca', 'ECA246G3470' => 'eca', 'EL10Ac6g13829' => 'bvu', 'EL10Ac6g14093' => 'bvu', 'EL10Ac8g18707' => 'bvu', 'Eucgr.C01369' => 'egr', 'Eucgr.H02492' => 'egr', 'Eucgr.I01733' => 'egr', 'Eucgr.J02255' => 'egr', 'Eucgr.J02257' => 'egr', 'Eucgr.J02258' => 'egr', 'FAN02G1601' => 'fan', 'FAN03G1586' => 'fan', 'FAN03G2986' => 'fan', 'FAN05G4837' => 'fan', 'FAN06G0146' => 'fan', 'FAN07G0858' => 'fan', 'FAN09G3179' => 'fan', 'FAN10G0669' => 'fan', 'FAN12G2358' => 'fan', 'FAN14G4198' => 'fan', 'FAN14G5112' => 'fan', 'FAN17G0342' => 'fan', 'FAN19G0342' => 'fan', 'FAN19G0962' => 'fan', 'FAN19G1101' => 'fan', 'FAN19G1872' => 'fan', 'FAN22G0356' => 'fan', 'FAN23G0744' => 'fan', 'FAN23G1914' => 'fan', 'FAN26G0032' => 'fan', 'FAN28G0625' => 'fan', 'FvH4_1g02710' => 'fve', 'FvH4_1g02720' => 'fve', 'FvH4_4g25670' => 'fve', 'FvH4_6g51700' => 'fve', 'FvH4_7g20170' => 'fve', 'Glyma.05G175000' => 'gma', 'Glyma.08G132300' => 'gma', 'Glyma.11G243000' => 'gma', 'Glyma.13G158900' => 'gma', 'Glyma.17G112400' => 'gma', 'Glyma.18G014100' => 'gma', 'Glyma.19G003100' => 'gma', 'Glyma.19G056500' => 'gma', 'Gohir.A01G158900' => 'ghi', 'Gohir.A05G312600' => 'ghi', 'Gohir.A05G354900' => 'ghi', 'Gohir.A07G037200' => 'ghi', 'Gohir.A09G030000' => 'ghi', 'Gohir.A12G145200' => 'ghi', 'Gohir.D01G151500' => 'ghi', 'Gohir.D04G058300' => 'ghi', 'Gohir.D05G314100' => 'ghi', 'Gohir.D07G041400' => 'ghi', 'Gohir.D09G029700' => 'ghi', 'Gohir.D12G149700' => 'ghi', 'Gorai.001G043800' => 'gra', 'Gorai.002G187800' => 'gra', 'Gorai.006G034700' => 'gra', 'Gorai.008G161200' => 'gra', 'Gorai.009G335700' => 'gra', 'Gorai.012G065000' => 'gra', 'GSVIVG01000535001' => 'vvi', 'GSVIVG01015572001' => 'vvi', 'GSVIVG01032386001' => 'vvi', 'HanXRQChr05g0138531' => 'han', 'HanXRQChr06g0174391' => 'han', 'HanXRQChr07g0199021' => 'han', 'HanXRQChr08g0208211' => 'han', 'HanXRQChr09g0255471' => 'han', 'HanXRQChr10g0315791' => 'han', 'HanXRQChr12g0371991' => 'han', 'HanXRQChr15g0475251' => 'han', 'HanXRQChr17g0540001' => 'han', 'HanXRQChr17g0548631' => 'han', 'HanXRQChr17g0569561' => 'han', 'Haze_12256' => 'cav', 'Haze_14756' => 'cav', 'Haze_25528' => 'cav', 'Hma1.2p1_0079F.1_g041020' => 'hma', 'Hma1.2p1_0818F.1_g223260' => 'hma', 'Hma1.2p1_1747F.1_g300530' => 'hma', 'HPP92_004607' => 'vpl', 'HPP92_004608' => 'vpl', 'HPP92_006181' => 'vpl', 'HPP92_012192' => 'vpl', 'HPP92_015680' => 'vpl', 'HPP92_020249' => 'vpl', 'HPP92_021376' => 'vpl', 'HPP92_024275' => 'vpl', 'Hund06031' => 'sun', 'Hund25391' => 'sun', 'Lalb_Chr07g0185371' => 'lal', 'Lalb_Chr07g0185381' => 'lal', 'Lalb_Chr12g0204011' => 'lal', 'Lalb_Chr13g0301671' => 'lal', 'Lalb_Chr14g0362851' => 'lal', 'Lalb_Chr24g0403581' => 'lal', 'Lj1g0000233' => 'lja', 'Lj2g0018120' => 'lja', 'Lj3C621T0' => 'lonja', 'Lj3P1059T14' => 'lonja', 'Lj3P611T9' => 'lonja', 'Lj3P614T13' => 'lonja', 'Lj3P615T5' => 'lonja', 'Lj4g0012315' => 'lja', 'Lj4g0026182' => 'lja', 'Lj6P813T16' => 'lonja', 'Lj7C427T7' => 'lonja', 'Lj7C427T8' => 'lonja', 'Lj7P600T41' => 'lonja', 'Lju41C42G17' => 'lonja', 'Lsat_1_v5_gn_0_47300' => 'lsa', 'Lsat_1_v5_gn_2_91280' => 'lsa', 'Lsat_1_v5_gn_3_30561' => 'lsa', 'Lsat_1_v5_gn_4_184321' => 'lsa', 'Lsat_1_v5_gn_4_4041' => 'lsa', 'Lsat_1_v5_gn_5_92000' => 'lsa', 'Lsat_1_v5_gn_8_152940' => 'lsa', 'Lsat_1_v5_gn_8_62401' => 'lsa', 'Manes.06G055900' => 'mes', 'Manes.12G022200' => 'mes', 'Manes.13G023300' => 'mes', 'Manes.14G115000' => 'mes', 'Manes.15G151700' => 'mes', 'Manes.17G111300' => 'mes', 'Mapoly0226s0009' => 'mpo', 'MBI02_g25363_MAGBIO' => 'mbi', 'MBI06_g00027_MAGBIO' => 'mbi', 'MBI10_g13034_MAGBIO' => 'mbi', 'MD09G1023400' => 'mdo', 'MD13G1100100' => 'mdo', 'MD15G1169200' => 'mdo', 'MD16G1101100' => 'mdo', 'MD17G1022900' => 'mdo', 'Medtr3g096150' => 'mtr', 'Medtr4g115070' => 'mtr', 'Medtr7g033325' => 'mtr', 'Medtr8g089840' => 'mtr', 'MELO3C010319.2' => 'cme', 'MELO3C011944.2' => 'cme', 'MELO3C021589.2' => 'cme', 'Migut.E00207' => 'egut', 'Migut.H00067' => 'egut', 'Migut.K00433' => 'egut', 'Migut.K00606' => 'egut', 'Migut.K01410' => 'egut', 'MSTRG.13347' => 'ama', 'MSTRG.24045' => 'ama', 'MSTRG.2428' => 'ama', 'MSTRG.26410' => 'ama', 'MSTRG.3139' => 'ama', 'MSTRG.3286' => 'ama', 'MSTRG.563' => 'ama', 'MSTRG.7941' => 'ama', 'Nitab4.5_0000028g0060' => 'nta', 'Nitab4.5_0000065g0260' => 'nta', 'Nitab4.5_0000112g0060' => 'nta', 'Nitab4.5_0000489g0120' => 'nta', 'Nitab4.5_0001776g0050' => 'nta', 'Nitab4.5_0001854g0010' => 'nta', 'Nitab4.5_0001860g0020' => 'nta', 'Nitab4.5_0004352g0010' => 'nta', 'Nitab4.5_0008716g0020' => 'nta', 'Nitab4.5_0008922g0010' => 'nta', 'Nn3g16693' => 'nnu', 'Nn4g22596' => 'nnu', 'Nn7g37639' => 'nnu', 'Oeu001701.1' => 'oeu', 'Oeu018149.1' => 'oeu', 'Oeu026220.1' => 'oeu', 'Oeu038635.1' => 'oeu', 'Oeu049176.1' => 'oeu', 'Oeu056706.1' => 'oeu', 'Oeu056937.1' => 'oeu', 'Oeu057540.1' => 'oeu', 'Os02g0594900' => 'osa', 'Os02g0595100' => 'osa', 'Os04g0477500' => 'osa', 'Os12g0611900' => 'osa', 'Peaxi162Scf00076g00020' => 'pax', 'Peaxi162Scf00128g00217' => 'pax', 'Peaxi162Scf00129g01640' => 'pax', 'Peaxi162Scf00669g00007' => 'pax', 'Peaxi162Scf00700g00421' => 'pax', 'Peaxi162Scf00801g00038' => 'pax', 'Peaxi162Scf00891g00025' => 'pax', 'PGR083G0909' => 'pgr', 'PGR119G1005' => 'pgr', 'PGR142G2236' => 'pgr', 'PGR142G3388' => 'pgr', 'PGSC0003DMG400004514' => 'stu', 'PGSC0003DMG400012635' => 'stu', 'PGSC0003DMG400015730' => 'stu', 'PGSC0003DMG400018611' => 'stu', 'PGSC0003DMG400030897' => 'stu', 'Phvul.001G254800' => 'pvu', 'Phvul.002G260100' => 'pvu', 'Phvul.003G167600' => 'pvu', 'Phvul.004G005100' => 'pvu', 'Potri.001G343600' => 'ptr', 'Potri.006G066700' => 'ptr', 'Potri.008G186000' => 'ptr', 'Potri.010G046900' => 'ptr', 'Potri.018G127900' => 'ptr', 'Pp3c20_17750' => 'ppa', 'Pp3c24_4380' => 'ppa', 'Prupe.1G245800' => 'ppe', 'Prupe.3G293400' => 'ppe', 'Prupe.7G247400' => 'ppe', 'Psat0s145g0120' => 'psa', 'Psat0s595g0040' => 'psa', 'Psat0s595g0120' => 'psa', 'Psat3g175040' => 'psa', 'Psat7g058120' => 'psa', 'PSO017G0428' => 'pso', 'PSO063G7510' => 'pso', 'PSO067G0046' => 'pso', 'PSO478G1073' => 'pso', 'PSO675G3677' => 'pso', 'PSO675G6558' => 'pso', 'PSO675G7520' => 'pso', 'PSO675G8959' => 'pso', 'QL02p074089' => 'qlo', 'QL02p089614' => 'qlo', 'QL03p057736' => 'qlo', 'RcHm_v2.0_Chr1g0364131' => 'rch', 'RcHm_v2.0_Chr2g0087801' => 'rch', 'RcHm_v2.0_Chr2g0087821' => 'rch', 'RcHm_v2.0_Chr2g0173231' => 'rch', 'RcHm_v2.0_Chr4g0433111' => 'rch', 'Rhsim03G0250300' => 'rsi', 'Rhsim08G0048400' => 'rsi', 'Rhsim10G0014800' => 'rsi', 'Rhsim12G0040100' => 'rsi', 'Rhsim12G0109700' => 'rsi', 'Sabra06G0049600' => 'sbr', 'Sabra08G0141000' => 'sbr', 'Sabra10G0021400' => 'sbr', 'Sabra16G0222900' => 'sbr', 'Sabra18G0108600' => 'sbr', 'SalBow1G0433' => 'sbo', 'SalBow1G2038' => 'sbo', 'SalBow1G5003' => 'sbo', 'SalBow7G1197' => 'sbo', 'SalBow8G3506' => 'sbo', 'Sc03g0007300' => 'sci', 'Sc11g0000950' => 'sci', 'Sc14g0008750' => 'sci', 'Sc18g0000420' => 'sci', 'Sed0006754' => 'sed', 'Sed0008741' => 'sed', 'Sed0017172' => 'sed', 'Sed0018925' => 'sed', 'Sed0023326' => 'sed', 'Sed0025909' => 'sed', 'SEGI_05333' => 'sgi', 'SEGI_10362' => 'sgi', 'SEGI_13380' => 'sgi', 'SEGI_24306' => 'sgi', 'SEGI_29077' => 'sgi', 'SEGI_29095' => 'sgi', 'SEGI_36534' => 'sgi', 'SEGI_37506' => 'sgi', 'SEGI_38321' => 'sgi', 'SGA_v2.0_scaffold307G48031' => 'sas', 'SGA_v2.0_scaffold47G17507' => 'sas', 'SGA_v2.0_scaffold63G21736' => 'sas', 'SGA_v2.0_scaffold87G27070' => 'sas', 'SHI17794' => 'shi', 'SHI28851' => 'shi', 'SMO165G0155' => 'smo', 'SMO340G0217' => 'smo', 'SMO367G1210' => 'smo', 'Solyc02g093430.3' => 'sly', 'Solyc05g013580.4' => 'sly', 'Solyc07g008030.3' => 'sly', 'Solyc12g035470.2' => 'sly', 'Sopen02g038020' => 'spe', 'Sopen05g008490' => 'spe', 'Sopen07g003910' => 'spe', 'Sopen12g015240' => 'spe', 'Sp1g11550' => 'spa', 'Sp2g16710' => 'spa', 'Sp3g00430' => 'spa', 'Sp3g26780' => 'spa', 'Sp5g22900' => 'spa', 'Sp6g29530' => 'spa', 'TAR371G0794' => 'tar', 'TAR374G0164' => 'tar', 'TAR622G0165' => 'tar', 'TAR626G0929' => 'tar', 'TAR629G2155' => 'tar', 'THA.LOC104805282' => 'tha', 'THA.LOC104805363' => 'tha', 'THA.LOC104808968' => 'tha', 'THA.LOC104821093' => 'tha', 'THA.LOC104823953' => 'tha', 'THA.LOC104825562' => 'tha', 'THA.LOC104825665' => 'tha', 'Thecc.02G261400' => 'tca', 'Thecc.04G019200' => 'tca', 'Thecc.09G130400' => 'tca', 'Thhalv10004374m.g' => 'esa', 'Thhalv10007850m.g' => 'esa', 'Thhalv10013782m.g' => 'esa', 'Thhalv10018686m.g' => 'esa', 'Thhalv10020899m.g' => 'esa', 'Thhalv10022755m.g' => 'esa', 'TPR.G23851' => 'tpr', 'TPR.G26500' => 'tpr', 'TPR.G27267' => 'tpr', 'TPR.G32001' => 'tpr', 'TPR.G6251' => 'tpr', 'TPR.G8167' => 'tpr', 'TWI12G1330' => 'twi', 'TWI18G1239' => 'twi', 'TWI34G0979' => 'twi', 'TWI36G0670' => 'twi', 'TWI36G0707' => 'twi', 'TWI56G0233' => 'twi', 'TWI75G1809' => 'twi', 'unitig_21.g20874' => 'ugi', 'unitig_26.g10343' => 'ugi', 'unitig_46.g18392' => 'ugi', 'unitig_52.g17178' => 'ugi', 'unitig_8.g2934' => 'ugi', 'vmacro01122' => 'vma', 'vmacro05875' => 'vma', 'vmacro06147' => 'vma', 'vmacro16191' => 'vma', 'vmacro18293' => 'vma', 'VMungo0251G3707' => 'vmu', 'VMungo0464G1521' => 'vmu', 'VMungo1215G0205' => 'vmu', 'VMungo1383G2484' => 'vmu', 'Zm00001eb079610' => 'zma', 'Zm00001eb135990' => 'zma', 'Zm00001eb183710' => 'zma', 'Zm00001eb246020' => 'zma' ), 'gf_id' => 'HOM05D001124', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001124' ), 'data_identifier' => 'HOM05D001124', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001124', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '548', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02520' => 'bna', 'A03p06630' => 'bna', 'A05p44460' => 'bna', 'A06p08710' => 'bna', 'A06p41090' => 'bna', 'A07p32320' => 'bna', 'A08p32520' => 'bna', 'A09p10360' => 'bna', 'A10p24080' => 'bna', 'Aa31LG11G15250' => 'aar', 'Aa31LG1G1800' => 'aar', 'Aa31LG2G5120' => 'aar', 'Aa31LG2G6070' => 'aar', 'Aa31LG5G10770' => 'aar', 'Aa31sc61G90' => 'aar', 'Actinidia01352' => 'ach', 'Actinidia05983' => 'ach', 'Actinidia08133' => 'ach', 'Actinidia15101' => 'ach', 'Actinidia26379' => 'ach', 'Actinidia35778' => 'ach', 'Actinidia36123' => 'ach', 'Actinidia37436' => 'ach', 'Actinidia38730' => 'ach', 'Ah.02g128210' => 'amhyb', 'Ah.03g132990' => 'amhyb', 'Ah.14g079410' => 'amhyb', 'AL1G24640' => 'aly', 'AL2G26680' => 'aly', 'AL3G10530' => 'aly', 'AL3G45230' => 'aly', 'AL5G15230' => 'aly', 'AL5G16960' => 'aly', 'AL6G25210' => 'aly', 'Aqoxy2G00441' => 'aox', 'Aqoxy3G01236' => 'aox', 'Aqoxy5G03746' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3RQ047' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C7GMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9C8JER' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MBL6KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YXCZ83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZANX40' => 'arhy', 'AT1G12990' => 'ath', 'AT1G67880' => 'ath', 'AT2G13290' => 'ath', 'AT3G01620' => 'ath', 'AT3G26445' => 'ath', 'AT3G27540' => 'ath', 'AT5G14480' => 'ath', 'ATR0824G026' => 'atr', 'ATR1098G019' => 'atr', 'Atru.chr11.2145' => 'acertr', 'Atru.chr2.3636' => 'acertr', 'Atru.chr2.3644' => 'acertr', 'Atru.chr6.2422' => 'acertr', 'Atru.chr7.1112' => 'acertr', 'AUR62005469' => 'cqu', 'AUR62011166' => 'cqu', 'AUR62013319' => 'cqu', 'AUR62024273' => 'cqu', 'AUR62028420' => 'cqu', 'AUR62041942' => 'cqu', 'BcaB01g04969' => 'bca', 'BcaB01g06371' => 'bca', 'BcaB02g11494' => 'bca', 'BcaB03g15382' => 'bca', 'BcaB08g36994' => 'bca', 'BcaC03g13477' => 'bca', 'BcaC03g13478' => 'bca', 'BcaC03g13480' => 'bca', 'BcaC03g13481' => 'bca', 'BcaC03g13486' => 'bca', 'BcaC04g19031' => 'bca', 'BcaC04g23085' => 'bca', 'BcaC05g25094' => 'bca', 'BcaC05g25096' => 'bca', 'BcaC05g25138' => 'bca', 'BcaC05g30416' => 'bca', 'BcaC05g30455' => 'bca', 'BcaC06g30979' => 'bca', 'BcaC06g33805' => 'bca', 'BcaC08g46021' => 'bca', 'BcaNung03154' => 'bca', 'BolC2t06623H' => 'bol', 'BolC2t06632H' => 'bol', 'BolC2t06635H' => 'bol', 'BolC2t06638H' => 'bol', 'BolC3t13266H' => 'bol', 'BolC5t29776H' => 'bol', 'BolC6t38912H' => 'bol', 'BolC7t44183H' => 'bol', 'BolC9t54123H' => 'bol', 'BolC9t59107H' => 'bol', 'BraA02t05221Z' => 'bra', 'BraA03t09996Z' => 'bra', 'BraA05t23210Z' => 'bra', 'BraA06t24068Z' => 'bra', 'BraA06t27032Z' => 'bra', 'BraA08t35176Z' => 'bra', 'BraA09t36680Z' => 'bra', 'BraA10t44471Z' => 'bra', 'C02p06760' => 'bna', 'C02p06890' => 'bna', 'C02p07010' => 'bna', 'C03p07660' => 'bna', 'C05p10300' => 'bna', 'C06p38150' => 'bna', 'C07p36650' => 'bna', 'C08p15770' => 'bna', 'C09p12300' => 'bna', 'C09p62700' => 'bna', 'C09p75040' => 'bna', 'CAN.G13.1' => 'can', 'CAN.G138.4' => 'can', 'CAN.G44.6' => 'can', 'CAN.G473.19' => 'can', 'CANSAT01G0835' => 'cansat', 'CANSAT11G0246' => 'cansat', 'CANSAT11G1766' => 'cansat', 'CANSAT64G1954' => 'cansat', 'CARHR013330' => 'chi', 'CARHR060530' => 'chi', 'CARHR075300' => 'chi', 'CARHR105120' => 'chi', 'CARHR148910' => 'chi', 'CARHR198830' => 'chi', 'Carub.0001s1275' => 'cru', 'Carub.0002s1437' => 'cru', 'Carub.0003s0044' => 'cru', 'Carub.0003s2787' => 'cru', 'Carub.0005s0597' => 'cru', 'Carub.0006s1266' => 'cru', 'Ca_06935_v3' => 'car', 'Ca_13559_v3' => 'car', 'Ca_16941_v3' => 'car', 'Ca_16960_v3' => 'car', 'Ca_17775_v3' => 'car', 'Ca_30464_v3' => 'car', 'Cc06_g08160' => 'ccan', 'Cc07_g01520' => 'ccan', 'Cc11_g15810' => 'ccan', 'CDE02G2840' => 'cde', 'CDE03G0093' => 'cde', 'CDE04G2127' => 'cde', 'CDE07G1857' => 'cde', 'CDE09G1246' => 'cde', 'Cfa003412' => 'cfa', 'Cfa007341' => 'cfa', 'Cfa009220' => 'cfa', 'Ciclev10008737m.g' => 'ccl', 'Ciclev10015565m.g' => 'ccl', 'Ciclev10031761m.g' => 'ccl', 'CiPaw.03G045300' => 'cil', 'CiPaw.03G247200' => 'cil', 'CiPaw.04G029500' => 'cil', 'CiPaw.04G174000' => 'cil', 'CiPaw.05G181200' => 'cil', 'CiPaw.06G067100' => 'cil', 'ClCG05G025800' => 'cla', 'ClCG06G011400' => 'cla', 'ClCG09G019360' => 'cla', 'COL.COLO4_04827' => 'col', 'COL.COLO4_29170' => 'col', 'COL.COLO4_35131' => 'col', 'COL.COLO4_35132' => 'col', 'Cpa.g.sc33.32' => 'cpa', 'Cpa.g.sc46.29' => 'cpa', 'Cpa.g.sc796.1' => 'cpa', 'CsaV3_1G030420' => 'csa', 'CsaV3_5G027050' => 'csa', 'CsaV3_5G031040' => 'csa', 'CsaV3_UNG023130' => 'csa', 'CSS0007726' => 'camsi', 'CSS0016433' => 'camsi', 'CSS0017656' => 'camsi', 'CSS0025364' => 'camsi', 'CSS0027582' => 'camsi', 'CSS0047288' => 'camsi', 'CSS0049950' => 'camsi', 'DCAR_003843' => 'dca', 'DCAR_007052' => 'dca', 'DCAR_020884' => 'dca', 'DCAR_021730' => 'dca', 'DCAR_024423' => 'dca', 'DCAR_026509' => 'dca', 'DCAR_031158' => 'dca', 'Dinv14728' => 'din', 'Dinv15219' => 'din', 'Dinv25728' => 'din', 'Dinv33428' => 'din', 'Dinv36489' => 'din', 'Dinv41486' => 'din', 'Duzib147G0469' => 'dzi', 'Duzib168G0060' => 'dzi', 'Duzib187G1215' => 'dzi', 'Duzib248G0692' => 'dzi', 'Duzib251G0767' => 'dzi', 'Duzib264G0446' => 'dzi', 'Duzib268G0691' => 'dzi', 'ECA232G4767' => 'eca', 'ECA233G2838' => 'eca', 'ECA234G0391' => 'eca', 'ECA234G0857' => 'eca', 'ECA236G1593' => 'eca', 'ECA238G0565' => 'eca', 'ECA246G1027' => 'eca', 'ECA246G3223' => 'eca', 'ECA246G3470' => 'eca', 'EL10Ac6g13829' => 'bvu', 'EL10Ac6g14093' => 'bvu', 'EL10Ac8g18707' => 'bvu', 'Eucgr.C01369' => 'egr', 'Eucgr.H02492' => 'egr', 'Eucgr.I01733' => 'egr', 'Eucgr.J02255' => 'egr', 'Eucgr.J02257' => 'egr', 'Eucgr.J02258' => 'egr', 'FAN02G1601' => 'fan', 'FAN03G1586' => 'fan', 'FAN03G2986' => 'fan', 'FAN05G4837' => 'fan', 'FAN06G0146' => 'fan', 'FAN07G0858' => 'fan', 'FAN09G3179' => 'fan', 'FAN10G0669' => 'fan', 'FAN12G2358' => 'fan', 'FAN14G4198' => 'fan', 'FAN14G5112' => 'fan', 'FAN17G0342' => 'fan', 'FAN19G0342' => 'fan', 'FAN19G0962' => 'fan', 'FAN19G1101' => 'fan', 'FAN19G1872' => 'fan', 'FAN22G0356' => 'fan', 'FAN23G0744' => 'fan', 'FAN23G1914' => 'fan', 'FAN26G0032' => 'fan', 'FAN28G0625' => 'fan', 'FvH4_1g02710' => 'fve', 'FvH4_1g02720' => 'fve', 'FvH4_4g25670' => 'fve', 'FvH4_6g51700' => 'fve', 'FvH4_7g20170' => 'fve', 'Glyma.05G175000' => 'gma', 'Glyma.08G132300' => 'gma', 'Glyma.11G243000' => 'gma', 'Glyma.13G158900' => 'gma', 'Glyma.17G112400' => 'gma', 'Glyma.18G014100' => 'gma', 'Glyma.19G003100' => 'gma', 'Glyma.19G056500' => 'gma', 'Gohir.A01G158900' => 'ghi', 'Gohir.A05G312600' => 'ghi', 'Gohir.A05G354900' => 'ghi', 'Gohir.A07G037200' => 'ghi', 'Gohir.A09G030000' => 'ghi', 'Gohir.A12G145200' => 'ghi', 'Gohir.D01G151500' => 'ghi', 'Gohir.D04G058300' => 'ghi', 'Gohir.D05G314100' => 'ghi', 'Gohir.D07G041400' => 'ghi', 'Gohir.D09G029700' => 'ghi', 'Gohir.D12G149700' => 'ghi', 'Gorai.001G043800' => 'gra', 'Gorai.002G187800' => 'gra', 'Gorai.006G034700' => 'gra', 'Gorai.008G161200' => 'gra', 'Gorai.009G335700' => 'gra', 'Gorai.012G065000' => 'gra', 'GSVIVG01000535001' => 'vvi', 'GSVIVG01015572001' => 'vvi', 'GSVIVG01032386001' => 'vvi', 'HanXRQChr05g0138531' => 'han', 'HanXRQChr06g0174391' => 'han', 'HanXRQChr07g0199021' => 'han', 'HanXRQChr08g0208211' => 'han', 'HanXRQChr09g0255471' => 'han', 'HanXRQChr10g0315791' => 'han', 'HanXRQChr12g0371991' => 'han', 'HanXRQChr15g0475251' => 'han', 'HanXRQChr17g0540001' => 'han', 'HanXRQChr17g0548631' => 'han', 'HanXRQChr17g0569561' => 'han', 'Haze_12256' => 'cav', 'Haze_14756' => 'cav', 'Haze_25528' => 'cav', 'Hma1.2p1_0079F.1_g041020' => 'hma', 'Hma1.2p1_0818F.1_g223260' => 'hma', 'Hma1.2p1_1747F.1_g300530' => 'hma', 'HPP92_004607' => 'vpl', 'HPP92_004608' => 'vpl', 'HPP92_006181' => 'vpl', 'HPP92_012192' => 'vpl', 'HPP92_015680' => 'vpl', 'HPP92_020249' => 'vpl', 'HPP92_021376' => 'vpl', 'HPP92_024275' => 'vpl', 'Hund06031' => 'sun', 'Hund25391' => 'sun', 'Lalb_Chr07g0185371' => 'lal', 'Lalb_Chr07g0185381' => 'lal', 'Lalb_Chr12g0204011' => 'lal', 'Lalb_Chr13g0301671' => 'lal', 'Lalb_Chr14g0362851' => 'lal', 'Lalb_Chr24g0403581' => 'lal', 'Lj1g0000233' => 'lja', 'Lj2g0018120' => 'lja', 'Lj3C621T0' => 'lonja', 'Lj3P1059T14' => 'lonja', 'Lj3P611T9' => 'lonja', 'Lj3P614T13' => 'lonja', 'Lj3P615T5' => 'lonja', 'Lj4g0012315' => 'lja', 'Lj4g0026182' => 'lja', 'Lj6P813T16' => 'lonja', 'Lj7C427T7' => 'lonja', 'Lj7C427T8' => 'lonja', 'Lj7P600T41' => 'lonja', 'Lju41C42G17' => 'lonja', 'Lsat_1_v5_gn_0_47300' => 'lsa', 'Lsat_1_v5_gn_2_91280' => 'lsa', 'Lsat_1_v5_gn_3_30561' => 'lsa', 'Lsat_1_v5_gn_4_184321' => 'lsa', 'Lsat_1_v5_gn_4_4041' => 'lsa', 'Lsat_1_v5_gn_5_92000' => 'lsa', 'Lsat_1_v5_gn_8_152940' => 'lsa', 'Lsat_1_v5_gn_8_62401' => 'lsa', 'Manes.06G055900' => 'mes', 'Manes.12G022200' => 'mes', 'Manes.13G023300' => 'mes', 'Manes.14G115000' => 'mes', 'Manes.15G151700' => 'mes', 'Manes.17G111300' => 'mes', 'Mapoly0226s0009' => 'mpo', 'MBI02_g25363_MAGBIO' => 'mbi', 'MBI06_g00027_MAGBIO' => 'mbi', 'MBI10_g13034_MAGBIO' => 'mbi', 'MD09G1023400' => 'mdo', 'MD13G1100100' => 'mdo', 'MD15G1169200' => 'mdo', 'MD16G1101100' => 'mdo', 'MD17G1022900' => 'mdo', 'Medtr3g096150' => 'mtr', 'Medtr4g115070' => 'mtr', 'Medtr7g033325' => 'mtr', 'Medtr8g089840' => 'mtr', 'MELO3C010319.2' => 'cme', 'MELO3C011944.2' => 'cme', 'MELO3C021589.2' => 'cme', 'Migut.E00207' => 'egut', 'Migut.H00067' => 'egut', 'Migut.K00433' => 'egut', 'Migut.K00606' => 'egut', 'Migut.K01410' => 'egut', 'MSTRG.13347' => 'ama', 'MSTRG.24045' => 'ama', 'MSTRG.2428' => 'ama', 'MSTRG.26410' => 'ama', 'MSTRG.3139' => 'ama', 'MSTRG.3286' => 'ama', 'MSTRG.563' => 'ama', 'MSTRG.7941' => 'ama', 'Nitab4.5_0000028g0060' => 'nta', 'Nitab4.5_0000065g0260' => 'nta', 'Nitab4.5_0000112g0060' => 'nta', 'Nitab4.5_0000489g0120' => 'nta', 'Nitab4.5_0001776g0050' => 'nta', 'Nitab4.5_0001854g0010' => 'nta', 'Nitab4.5_0001860g0020' => 'nta', 'Nitab4.5_0004352g0010' => 'nta', 'Nitab4.5_0008716g0020' => 'nta', 'Nitab4.5_0008922g0010' => 'nta', 'Nn3g16693' => 'nnu', 'Nn4g22596' => 'nnu', 'Nn7g37639' => 'nnu', 'Oeu001701.1' => 'oeu', 'Oeu018149.1' => 'oeu', 'Oeu026220.1' => 'oeu', 'Oeu038635.1' => 'oeu', 'Oeu049176.1' => 'oeu', 'Oeu056706.1' => 'oeu', 'Oeu056937.1' => 'oeu', 'Oeu057540.1' => 'oeu', 'Os02g0594900' => 'osa', 'Os02g0595100' => 'osa', 'Os04g0477500' => 'osa', 'Os12g0611900' => 'osa', 'Peaxi162Scf00076g00020' => 'pax', 'Peaxi162Scf00128g00217' => 'pax', 'Peaxi162Scf00129g01640' => 'pax', 'Peaxi162Scf00669g00007' => 'pax', 'Peaxi162Scf00700g00421' => 'pax', 'Peaxi162Scf00801g00038' => 'pax', 'Peaxi162Scf00891g00025' => 'pax', 'PGR083G0909' => 'pgr', 'PGR119G1005' => 'pgr', 'PGR142G2236' => 'pgr', 'PGR142G3388' => 'pgr', 'PGSC0003DMG400004514' => 'stu', 'PGSC0003DMG400012635' => 'stu', 'PGSC0003DMG400015730' => 'stu', 'PGSC0003DMG400018611' => 'stu', 'PGSC0003DMG400030897' => 'stu', 'Phvul.001G254800' => 'pvu', 'Phvul.002G260100' => 'pvu', 'Phvul.003G167600' => 'pvu', 'Phvul.004G005100' => 'pvu', 'Potri.001G343600' => 'ptr', 'Potri.006G066700' => 'ptr', 'Potri.008G186000' => 'ptr', 'Potri.010G046900' => 'ptr', 'Potri.018G127900' => 'ptr', 'Pp3c20_17750' => 'ppa', 'Pp3c24_4380' => 'ppa', 'Prupe.1G245800' => 'ppe', 'Prupe.3G293400' => 'ppe', 'Prupe.7G247400' => 'ppe', 'Psat0s145g0120' => 'psa', 'Psat0s595g0040' => 'psa', 'Psat0s595g0120' => 'psa', 'Psat3g175040' => 'psa', 'Psat7g058120' => 'psa', 'PSO017G0428' => 'pso', 'PSO063G7510' => 'pso', 'PSO067G0046' => 'pso', 'PSO478G1073' => 'pso', 'PSO675G3677' => 'pso', 'PSO675G6558' => 'pso', 'PSO675G7520' => 'pso', 'PSO675G8959' => 'pso', 'QL02p074089' => 'qlo', 'QL02p089614' => 'qlo', 'QL03p057736' => 'qlo', 'RcHm_v2.0_Chr1g0364131' => 'rch', 'RcHm_v2.0_Chr2g0087801' => 'rch', 'RcHm_v2.0_Chr2g0087821' => 'rch', 'RcHm_v2.0_Chr2g0173231' => 'rch', 'RcHm_v2.0_Chr4g0433111' => 'rch', 'Rhsim03G0250300' => 'rsi', 'Rhsim08G0048400' => 'rsi', 'Rhsim10G0014800' => 'rsi', 'Rhsim12G0040100' => 'rsi', 'Rhsim12G0109700' => 'rsi', 'Sabra06G0049600' => 'sbr', 'Sabra08G0141000' => 'sbr', 'Sabra10G0021400' => 'sbr', 'Sabra16G0222900' => 'sbr', 'Sabra18G0108600' => 'sbr', 'SalBow1G0433' => 'sbo', 'SalBow1G2038' => 'sbo', 'SalBow1G5003' => 'sbo', 'SalBow7G1197' => 'sbo', 'SalBow8G3506' => 'sbo', 'Sc03g0007300' => 'sci', 'Sc11g0000950' => 'sci', 'Sc14g0008750' => 'sci', 'Sc18g0000420' => 'sci', 'Sed0006754' => 'sed', 'Sed0008741' => 'sed', 'Sed0017172' => 'sed', 'Sed0018925' => 'sed', 'Sed0023326' => 'sed', 'Sed0025909' => 'sed', 'SEGI_05333' => 'sgi', 'SEGI_10362' => 'sgi', 'SEGI_13380' => 'sgi', 'SEGI_24306' => 'sgi', 'SEGI_29077' => 'sgi', 'SEGI_29095' => 'sgi', 'SEGI_36534' => 'sgi', 'SEGI_37506' => 'sgi', 'SEGI_38321' => 'sgi', 'SGA_v2.0_scaffold307G48031' => 'sas', 'SGA_v2.0_scaffold47G17507' => 'sas', 'SGA_v2.0_scaffold63G21736' => 'sas', 'SGA_v2.0_scaffold87G27070' => 'sas', 'SHI17794' => 'shi', 'SHI28851' => 'shi', 'SMO165G0155' => 'smo', 'SMO340G0217' => 'smo', 'SMO367G1210' => 'smo', 'Solyc02g093430.3' => 'sly', 'Solyc05g013580.4' => 'sly', 'Solyc07g008030.3' => 'sly', 'Solyc12g035470.2' => 'sly', 'Sopen02g038020' => 'spe', 'Sopen05g008490' => 'spe', 'Sopen07g003910' => 'spe', 'Sopen12g015240' => 'spe', 'Sp1g11550' => 'spa', 'Sp2g16710' => 'spa', 'Sp3g00430' => 'spa', 'Sp3g26780' => 'spa', 'Sp5g22900' => 'spa', 'Sp6g29530' => 'spa', 'TAR371G0794' => 'tar', 'TAR374G0164' => 'tar', 'TAR622G0165' => 'tar', 'TAR626G0929' => 'tar', 'TAR629G2155' => 'tar', 'THA.LOC104805282' => 'tha', 'THA.LOC104805363' => 'tha', 'THA.LOC104808968' => 'tha', 'THA.LOC104821093' => 'tha', 'THA.LOC104823953' => 'tha', 'THA.LOC104825562' => 'tha', 'THA.LOC104825665' => 'tha', 'Thecc.02G261400' => 'tca', 'Thecc.04G019200' => 'tca', 'Thecc.09G130400' => 'tca', 'Thhalv10004374m.g' => 'esa', 'Thhalv10007850m.g' => 'esa', 'Thhalv10013782m.g' => 'esa', 'Thhalv10018686m.g' => 'esa', 'Thhalv10020899m.g' => 'esa', 'Thhalv10022755m.g' => 'esa', 'TPR.G23851' => 'tpr', 'TPR.G26500' => 'tpr', 'TPR.G27267' => 'tpr', 'TPR.G32001' => 'tpr', 'TPR.G6251' => 'tpr', 'TPR.G8167' => 'tpr', 'TWI12G1330' => 'twi', 'TWI18G1239' => 'twi', 'TWI34G0979' => 'twi', 'TWI36G0670' => 'twi', 'TWI36G0707' => 'twi', 'TWI56G0233' => 'twi', 'TWI75G1809' => 'twi', 'unitig_21.g20874' => 'ugi', 'unitig_26.g10343' => 'ugi', 'unitig_46.g18392' => 'ugi', 'unitig_52.g17178' => 'ugi', 'unitig_8.g2934' => 'ugi', 'vmacro01122' => 'vma', 'vmacro05875' => 'vma', 'vmacro06147' => 'vma', 'vmacro16191' => 'vma', 'vmacro18293' => 'vma', 'VMungo0251G3707' => 'vmu', 'VMungo0464G1521' => 'vmu', 'VMungo1215G0205' => 'vmu', 'VMungo1383G2484' => 'vmu', 'Zm00001eb079610' => 'zma', 'Zm00001eb135990' => 'zma', 'Zm00001eb183710' => 'zma', 'Zm00001eb246020' => 'zma' ) $gf_id = 'HOM05D001124' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001124' ) $data_identifier = 'HOM05D001124' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 6, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 7, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 21, 'bol' => (int) 10, 'bra' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 6, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 9, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 21, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 8, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 10, 'lsa' => (int) 8, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 8, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 9, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb246020' $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' => 'HOM05D001124', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '548', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02520' => 'bna', 'A03p06630' => 'bna', 'A05p44460' => 'bna', 'A06p08710' => 'bna', 'A06p41090' => 'bna', 'A07p32320' => 'bna', 'A08p32520' => 'bna', 'A09p10360' => 'bna', 'A10p24080' => 'bna', 'Aa31LG11G15250' => 'aar', 'Aa31LG1G1800' => 'aar', 'Aa31LG2G5120' => 'aar', 'Aa31LG2G6070' => 'aar', 'Aa31LG5G10770' => 'aar', 'Aa31sc61G90' => 'aar', 'Actinidia01352' => 'ach', 'Actinidia05983' => 'ach', 'Actinidia08133' => 'ach', 'Actinidia15101' => 'ach', 'Actinidia26379' => 'ach', 'Actinidia35778' => 'ach', 'Actinidia36123' => 'ach', 'Actinidia37436' => 'ach', 'Actinidia38730' => 'ach', 'Ah.02g128210' => 'amhyb', 'Ah.03g132990' => 'amhyb', 'Ah.14g079410' => 'amhyb', 'AL1G24640' => 'aly', 'AL2G26680' => 'aly', 'AL3G10530' => 'aly', 'AL3G45230' => 'aly', 'AL5G15230' => 'aly', 'AL5G16960' => 'aly', 'AL6G25210' => 'aly', 'Aqoxy2G00441' => 'aox', 'Aqoxy3G01236' => 'aox', 'Aqoxy5G03746' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3RQ047' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C7GMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9C8JER' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MBL6KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YXCZ83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZANX40' => 'arhy', 'AT1G12990' => 'ath', 'AT1G67880' => 'ath', 'AT2G13290' => 'ath', 'AT3G01620' => 'ath', 'AT3G26445' => 'ath', 'AT3G27540' => 'ath', 'AT5G14480' => 'ath', 'ATR0824G026' => 'atr', 'ATR1098G019' => 'atr', 'Atru.chr11.2145' => 'acertr', 'Atru.chr2.3636' => 'acertr', 'Atru.chr2.3644' => 'acertr', 'Atru.chr6.2422' => 'acertr', 'Atru.chr7.1112' => 'acertr', 'AUR62005469' => 'cqu', 'AUR62011166' => 'cqu', 'AUR62013319' => 'cqu', 'AUR62024273' => 'cqu', 'AUR62028420' => 'cqu', 'AUR62041942' => 'cqu', 'BcaB01g04969' => 'bca', 'BcaB01g06371' => 'bca', 'BcaB02g11494' => 'bca', 'BcaB03g15382' => 'bca', 'BcaB08g36994' => 'bca', 'BcaC03g13477' => 'bca', 'BcaC03g13478' => 'bca', 'BcaC03g13480' => 'bca', 'BcaC03g13481' => 'bca', 'BcaC03g13486' => 'bca', 'BcaC04g19031' => 'bca', 'BcaC04g23085' => 'bca', 'BcaC05g25094' => 'bca', 'BcaC05g25096' => 'bca', 'BcaC05g25138' => 'bca', 'BcaC05g30416' => 'bca', 'BcaC05g30455' => 'bca', 'BcaC06g30979' => 'bca', 'BcaC06g33805' => 'bca', 'BcaC08g46021' => 'bca', 'BcaNung03154' => 'bca', 'BolC2t06623H' => 'bol', 'BolC2t06632H' => 'bol', 'BolC2t06635H' => 'bol', 'BolC2t06638H' => 'bol', 'BolC3t13266H' => 'bol', 'BolC5t29776H' => 'bol', 'BolC6t38912H' => 'bol', 'BolC7t44183H' => 'bol', 'BolC9t54123H' => 'bol', 'BolC9t59107H' => 'bol', 'BraA02t05221Z' => 'bra', 'BraA03t09996Z' => 'bra', 'BraA05t23210Z' => 'bra', 'BraA06t24068Z' => 'bra', 'BraA06t27032Z' => 'bra', 'BraA08t35176Z' => 'bra', 'BraA09t36680Z' => 'bra', 'BraA10t44471Z' => 'bra', 'C02p06760' => 'bna', 'C02p06890' => 'bna', 'C02p07010' => 'bna', 'C03p07660' => 'bna', 'C05p10300' => 'bna', 'C06p38150' => 'bna', 'C07p36650' => 'bna', 'C08p15770' => 'bna', 'C09p12300' => 'bna', 'C09p62700' => 'bna', 'C09p75040' => 'bna', 'CAN.G13.1' => 'can', 'CAN.G138.4' => 'can', 'CAN.G44.6' => 'can', 'CAN.G473.19' => 'can', 'CANSAT01G0835' => 'cansat', 'CANSAT11G0246' => 'cansat', 'CANSAT11G1766' => 'cansat', 'CANSAT64G1954' => 'cansat', 'CARHR013330' => 'chi', 'CARHR060530' => 'chi', 'CARHR075300' => 'chi', 'CARHR105120' => 'chi', 'CARHR148910' => 'chi', 'CARHR198830' => 'chi', 'Carub.0001s1275' => 'cru', 'Carub.0002s1437' => 'cru', 'Carub.0003s0044' => 'cru', 'Carub.0003s2787' => 'cru', 'Carub.0005s0597' => 'cru', 'Carub.0006s1266' => 'cru', 'Ca_06935_v3' => 'car', 'Ca_13559_v3' => 'car', 'Ca_16941_v3' => 'car', 'Ca_16960_v3' => 'car', 'Ca_17775_v3' => 'car', 'Ca_30464_v3' => 'car', 'Cc06_g08160' => 'ccan', 'Cc07_g01520' => 'ccan', 'Cc11_g15810' => 'ccan', 'CDE02G2840' => 'cde', 'CDE03G0093' => 'cde', 'CDE04G2127' => 'cde', 'CDE07G1857' => 'cde', 'CDE09G1246' => 'cde', 'Cfa003412' => 'cfa', 'Cfa007341' => 'cfa', 'Cfa009220' => 'cfa', 'Ciclev10008737m.g' => 'ccl', 'Ciclev10015565m.g' => 'ccl', 'Ciclev10031761m.g' => 'ccl', 'CiPaw.03G045300' => 'cil', 'CiPaw.03G247200' => 'cil', 'CiPaw.04G029500' => 'cil', 'CiPaw.04G174000' => 'cil', 'CiPaw.05G181200' => 'cil', 'CiPaw.06G067100' => 'cil', 'ClCG05G025800' => 'cla', 'ClCG06G011400' => 'cla', 'ClCG09G019360' => 'cla', 'COL.COLO4_04827' => 'col', 'COL.COLO4_29170' => 'col', 'COL.COLO4_35131' => 'col', 'COL.COLO4_35132' => 'col', 'Cpa.g.sc33.32' => 'cpa', 'Cpa.g.sc46.29' => 'cpa', 'Cpa.g.sc796.1' => 'cpa', 'CsaV3_1G030420' => 'csa', 'CsaV3_5G027050' => 'csa', 'CsaV3_5G031040' => 'csa', 'CsaV3_UNG023130' => 'csa', 'CSS0007726' => 'camsi', 'CSS0016433' => 'camsi', 'CSS0017656' => 'camsi', 'CSS0025364' => 'camsi', 'CSS0027582' => 'camsi', 'CSS0047288' => 'camsi', 'CSS0049950' => 'camsi', 'DCAR_003843' => 'dca', 'DCAR_007052' => 'dca', 'DCAR_020884' => 'dca', 'DCAR_021730' => 'dca', 'DCAR_024423' => 'dca', 'DCAR_026509' => 'dca', 'DCAR_031158' => 'dca', 'Dinv14728' => 'din', 'Dinv15219' => 'din', 'Dinv25728' => 'din', 'Dinv33428' => 'din', 'Dinv36489' => 'din', 'Dinv41486' => 'din', 'Duzib147G0469' => 'dzi', 'Duzib168G0060' => 'dzi', 'Duzib187G1215' => 'dzi', 'Duzib248G0692' => 'dzi', 'Duzib251G0767' => 'dzi', 'Duzib264G0446' => 'dzi', 'Duzib268G0691' => 'dzi', 'ECA232G4767' => 'eca', 'ECA233G2838' => 'eca', 'ECA234G0391' => 'eca', 'ECA234G0857' => 'eca', 'ECA236G1593' => 'eca', 'ECA238G0565' => 'eca', 'ECA246G1027' => 'eca', 'ECA246G3223' => 'eca', 'ECA246G3470' => 'eca', 'EL10Ac6g13829' => 'bvu', 'EL10Ac6g14093' => 'bvu', 'EL10Ac8g18707' => 'bvu', 'Eucgr.C01369' => 'egr', 'Eucgr.H02492' => 'egr', 'Eucgr.I01733' => 'egr', 'Eucgr.J02255' => 'egr', 'Eucgr.J02257' => 'egr', 'Eucgr.J02258' => 'egr', 'FAN02G1601' => 'fan', 'FAN03G1586' => 'fan', 'FAN03G2986' => 'fan', 'FAN05G4837' => 'fan', 'FAN06G0146' => 'fan', 'FAN07G0858' => 'fan', 'FAN09G3179' => 'fan', 'FAN10G0669' => 'fan', 'FAN12G2358' => 'fan', 'FAN14G4198' => 'fan', 'FAN14G5112' => 'fan', 'FAN17G0342' => 'fan', 'FAN19G0342' => 'fan', 'FAN19G0962' => 'fan', 'FAN19G1101' => 'fan', 'FAN19G1872' => 'fan', 'FAN22G0356' => 'fan', 'FAN23G0744' => 'fan', 'FAN23G1914' => 'fan', 'FAN26G0032' => 'fan', 'FAN28G0625' => 'fan', 'FvH4_1g02710' => 'fve', 'FvH4_1g02720' => 'fve', 'FvH4_4g25670' => 'fve', 'FvH4_6g51700' => 'fve', 'FvH4_7g20170' => 'fve', 'Glyma.05G175000' => 'gma', 'Glyma.08G132300' => 'gma', 'Glyma.11G243000' => 'gma', 'Glyma.13G158900' => 'gma', 'Glyma.17G112400' => 'gma', 'Glyma.18G014100' => 'gma', 'Glyma.19G003100' => 'gma', 'Glyma.19G056500' => 'gma', 'Gohir.A01G158900' => 'ghi', 'Gohir.A05G312600' => 'ghi', 'Gohir.A05G354900' => 'ghi', 'Gohir.A07G037200' => 'ghi', 'Gohir.A09G030000' => 'ghi', 'Gohir.A12G145200' => 'ghi', 'Gohir.D01G151500' => 'ghi', 'Gohir.D04G058300' => 'ghi', 'Gohir.D05G314100' => 'ghi', 'Gohir.D07G041400' => 'ghi', 'Gohir.D09G029700' => 'ghi', 'Gohir.D12G149700' => 'ghi', 'Gorai.001G043800' => 'gra', 'Gorai.002G187800' => 'gra', 'Gorai.006G034700' => 'gra', 'Gorai.008G161200' => 'gra', 'Gorai.009G335700' => 'gra', 'Gorai.012G065000' => 'gra', 'GSVIVG01000535001' => 'vvi', 'GSVIVG01015572001' => 'vvi', 'GSVIVG01032386001' => 'vvi', 'HanXRQChr05g0138531' => 'han', 'HanXRQChr06g0174391' => 'han', 'HanXRQChr07g0199021' => 'han', 'HanXRQChr08g0208211' => 'han', 'HanXRQChr09g0255471' => 'han', 'HanXRQChr10g0315791' => 'han', 'HanXRQChr12g0371991' => 'han', 'HanXRQChr15g0475251' => 'han', 'HanXRQChr17g0540001' => 'han', 'HanXRQChr17g0548631' => 'han', 'HanXRQChr17g0569561' => 'han', 'Haze_12256' => 'cav', 'Haze_14756' => 'cav', 'Haze_25528' => 'cav', 'Hma1.2p1_0079F.1_g041020' => 'hma', 'Hma1.2p1_0818F.1_g223260' => 'hma', 'Hma1.2p1_1747F.1_g300530' => 'hma', 'HPP92_004607' => 'vpl', 'HPP92_004608' => 'vpl', 'HPP92_006181' => 'vpl', 'HPP92_012192' => 'vpl', 'HPP92_015680' => 'vpl', 'HPP92_020249' => 'vpl', 'HPP92_021376' => 'vpl', 'HPP92_024275' => 'vpl', 'Hund06031' => 'sun', 'Hund25391' => 'sun', 'Lalb_Chr07g0185371' => 'lal', 'Lalb_Chr07g0185381' => 'lal', 'Lalb_Chr12g0204011' => 'lal', 'Lalb_Chr13g0301671' => 'lal', 'Lalb_Chr14g0362851' => 'lal', 'Lalb_Chr24g0403581' => 'lal', 'Lj1g0000233' => 'lja', 'Lj2g0018120' => 'lja', 'Lj3C621T0' => 'lonja', 'Lj3P1059T14' => 'lonja', 'Lj3P611T9' => 'lonja', 'Lj3P614T13' => 'lonja', 'Lj3P615T5' => 'lonja', 'Lj4g0012315' => 'lja', 'Lj4g0026182' => 'lja', 'Lj6P813T16' => 'lonja', 'Lj7C427T7' => 'lonja', 'Lj7C427T8' => 'lonja', 'Lj7P600T41' => 'lonja', 'Lju41C42G17' => 'lonja', 'Lsat_1_v5_gn_0_47300' => 'lsa', 'Lsat_1_v5_gn_2_91280' => 'lsa', 'Lsat_1_v5_gn_3_30561' => 'lsa', 'Lsat_1_v5_gn_4_184321' => 'lsa', 'Lsat_1_v5_gn_4_4041' => 'lsa', 'Lsat_1_v5_gn_5_92000' => 'lsa', 'Lsat_1_v5_gn_8_152940' => 'lsa', 'Lsat_1_v5_gn_8_62401' => 'lsa', 'Manes.06G055900' => 'mes', 'Manes.12G022200' => 'mes', 'Manes.13G023300' => 'mes', 'Manes.14G115000' => 'mes', 'Manes.15G151700' => 'mes', 'Manes.17G111300' => 'mes', 'Mapoly0226s0009' => 'mpo', 'MBI02_g25363_MAGBIO' => 'mbi', 'MBI06_g00027_MAGBIO' => 'mbi', 'MBI10_g13034_MAGBIO' => 'mbi', 'MD09G1023400' => 'mdo', 'MD13G1100100' => 'mdo', 'MD15G1169200' => 'mdo', 'MD16G1101100' => 'mdo', 'MD17G1022900' => 'mdo', 'Medtr3g096150' => 'mtr', 'Medtr4g115070' => 'mtr', 'Medtr7g033325' => 'mtr', 'Medtr8g089840' => 'mtr', 'MELO3C010319.2' => 'cme', 'MELO3C011944.2' => 'cme', 'MELO3C021589.2' => 'cme', 'Migut.E00207' => 'egut', 'Migut.H00067' => 'egut', 'Migut.K00433' => 'egut', 'Migut.K00606' => 'egut', 'Migut.K01410' => 'egut', 'MSTRG.13347' => 'ama', 'MSTRG.24045' => 'ama', 'MSTRG.2428' => 'ama', 'MSTRG.26410' => 'ama', 'MSTRG.3139' => 'ama', 'MSTRG.3286' => 'ama', 'MSTRG.563' => 'ama', 'MSTRG.7941' => 'ama', 'Nitab4.5_0000028g0060' => 'nta', 'Nitab4.5_0000065g0260' => 'nta', 'Nitab4.5_0000112g0060' => 'nta', 'Nitab4.5_0000489g0120' => 'nta', 'Nitab4.5_0001776g0050' => 'nta', 'Nitab4.5_0001854g0010' => 'nta', 'Nitab4.5_0001860g0020' => 'nta', 'Nitab4.5_0004352g0010' => 'nta', 'Nitab4.5_0008716g0020' => 'nta', 'Nitab4.5_0008922g0010' => 'nta', 'Nn3g16693' => 'nnu', 'Nn4g22596' => 'nnu', 'Nn7g37639' => 'nnu', 'Oeu001701.1' => 'oeu', 'Oeu018149.1' => 'oeu', 'Oeu026220.1' => 'oeu', 'Oeu038635.1' => 'oeu', 'Oeu049176.1' => 'oeu', 'Oeu056706.1' => 'oeu', 'Oeu056937.1' => 'oeu', 'Oeu057540.1' => 'oeu', 'Os02g0594900' => 'osa', 'Os02g0595100' => 'osa', 'Os04g0477500' => 'osa', 'Os12g0611900' => 'osa', 'Peaxi162Scf00076g00020' => 'pax', 'Peaxi162Scf00128g00217' => 'pax', 'Peaxi162Scf00129g01640' => 'pax', 'Peaxi162Scf00669g00007' => 'pax', 'Peaxi162Scf00700g00421' => 'pax', 'Peaxi162Scf00801g00038' => 'pax', 'Peaxi162Scf00891g00025' => 'pax', 'PGR083G0909' => 'pgr', 'PGR119G1005' => 'pgr', 'PGR142G2236' => 'pgr', 'PGR142G3388' => 'pgr', 'PGSC0003DMG400004514' => 'stu', 'PGSC0003DMG400012635' => 'stu', 'PGSC0003DMG400015730' => 'stu', 'PGSC0003DMG400018611' => 'stu', 'PGSC0003DMG400030897' => 'stu', 'Phvul.001G254800' => 'pvu', 'Phvul.002G260100' => 'pvu', 'Phvul.003G167600' => 'pvu', 'Phvul.004G005100' => 'pvu', 'Potri.001G343600' => 'ptr', 'Potri.006G066700' => 'ptr', 'Potri.008G186000' => 'ptr', 'Potri.010G046900' => 'ptr', 'Potri.018G127900' => 'ptr', 'Pp3c20_17750' => 'ppa', 'Pp3c24_4380' => 'ppa', 'Prupe.1G245800' => 'ppe', 'Prupe.3G293400' => 'ppe', 'Prupe.7G247400' => 'ppe', 'Psat0s145g0120' => 'psa', 'Psat0s595g0040' => 'psa', 'Psat0s595g0120' => 'psa', 'Psat3g175040' => 'psa', 'Psat7g058120' => 'psa', 'PSO017G0428' => 'pso', 'PSO063G7510' => 'pso', 'PSO067G0046' => 'pso', 'PSO478G1073' => 'pso', 'PSO675G3677' => 'pso', 'PSO675G6558' => 'pso', 'PSO675G7520' => 'pso', 'PSO675G8959' => 'pso', 'QL02p074089' => 'qlo', 'QL02p089614' => 'qlo', 'QL03p057736' => 'qlo', 'RcHm_v2.0_Chr1g0364131' => 'rch', 'RcHm_v2.0_Chr2g0087801' => 'rch', 'RcHm_v2.0_Chr2g0087821' => 'rch', 'RcHm_v2.0_Chr2g0173231' => 'rch', 'RcHm_v2.0_Chr4g0433111' => 'rch', 'Rhsim03G0250300' => 'rsi', 'Rhsim08G0048400' => 'rsi', 'Rhsim10G0014800' => 'rsi', 'Rhsim12G0040100' => 'rsi', 'Rhsim12G0109700' => 'rsi', 'Sabra06G0049600' => 'sbr', 'Sabra08G0141000' => 'sbr', 'Sabra10G0021400' => 'sbr', 'Sabra16G0222900' => 'sbr', 'Sabra18G0108600' => 'sbr', 'SalBow1G0433' => 'sbo', 'SalBow1G2038' => 'sbo', 'SalBow1G5003' => 'sbo', 'SalBow7G1197' => 'sbo', 'SalBow8G3506' => 'sbo', 'Sc03g0007300' => 'sci', 'Sc11g0000950' => 'sci', 'Sc14g0008750' => 'sci', 'Sc18g0000420' => 'sci', 'Sed0006754' => 'sed', 'Sed0008741' => 'sed', 'Sed0017172' => 'sed', 'Sed0018925' => 'sed', 'Sed0023326' => 'sed', 'Sed0025909' => 'sed', 'SEGI_05333' => 'sgi', 'SEGI_10362' => 'sgi', 'SEGI_13380' => 'sgi', 'SEGI_24306' => 'sgi', 'SEGI_29077' => 'sgi', 'SEGI_29095' => 'sgi', 'SEGI_36534' => 'sgi', 'SEGI_37506' => 'sgi', 'SEGI_38321' => 'sgi', 'SGA_v2.0_scaffold307G48031' => 'sas', 'SGA_v2.0_scaffold47G17507' => 'sas', 'SGA_v2.0_scaffold63G21736' => 'sas', 'SGA_v2.0_scaffold87G27070' => 'sas', 'SHI17794' => 'shi', 'SHI28851' => 'shi', 'SMO165G0155' => 'smo', 'SMO340G0217' => 'smo', 'SMO367G1210' => 'smo', 'Solyc02g093430.3' => 'sly', 'Solyc05g013580.4' => 'sly', 'Solyc07g008030.3' => 'sly', 'Solyc12g035470.2' => 'sly', 'Sopen02g038020' => 'spe', 'Sopen05g008490' => 'spe', 'Sopen07g003910' => 'spe', 'Sopen12g015240' => 'spe', 'Sp1g11550' => 'spa', 'Sp2g16710' => 'spa', 'Sp3g00430' => 'spa', 'Sp3g26780' => 'spa', 'Sp5g22900' => 'spa', 'Sp6g29530' => 'spa', 'TAR371G0794' => 'tar', 'TAR374G0164' => 'tar', 'TAR622G0165' => 'tar', 'TAR626G0929' => 'tar', 'TAR629G2155' => 'tar', 'THA.LOC104805282' => 'tha', 'THA.LOC104805363' => 'tha', 'THA.LOC104808968' => 'tha', 'THA.LOC104821093' => 'tha', 'THA.LOC104823953' => 'tha', 'THA.LOC104825562' => 'tha', 'THA.LOC104825665' => 'tha', 'Thecc.02G261400' => 'tca', 'Thecc.04G019200' => 'tca', 'Thecc.09G130400' => 'tca', 'Thhalv10004374m.g' => 'esa', 'Thhalv10007850m.g' => 'esa', 'Thhalv10013782m.g' => 'esa', 'Thhalv10018686m.g' => 'esa', 'Thhalv10020899m.g' => 'esa', 'Thhalv10022755m.g' => 'esa', 'TPR.G23851' => 'tpr', 'TPR.G26500' => 'tpr', 'TPR.G27267' => 'tpr', 'TPR.G32001' => 'tpr', 'TPR.G6251' => 'tpr', 'TPR.G8167' => 'tpr', 'TWI12G1330' => 'twi', 'TWI18G1239' => 'twi', 'TWI34G0979' => 'twi', 'TWI36G0670' => 'twi', 'TWI36G0707' => 'twi', 'TWI56G0233' => 'twi', 'TWI75G1809' => 'twi', 'unitig_21.g20874' => 'ugi', 'unitig_26.g10343' => 'ugi', 'unitig_46.g18392' => 'ugi', 'unitig_52.g17178' => 'ugi', 'unitig_8.g2934' => 'ugi', 'vmacro01122' => 'vma', 'vmacro05875' => 'vma', 'vmacro06147' => 'vma', 'vmacro16191' => 'vma', 'vmacro18293' => 'vma', 'VMungo0251G3707' => 'vmu', 'VMungo0464G1521' => 'vmu', 'VMungo1215G0205' => 'vmu', 'VMungo1383G2484' => 'vmu', 'Zm00001eb079610' => 'zma', 'Zm00001eb135990' => 'zma', 'Zm00001eb183710' => 'zma', 'Zm00001eb246020' => 'zma' ), 'gf_id' => 'HOM05D001124', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001124' ), 'data_identifier' => 'HOM05D001124', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001124', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '548', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02520' => 'bna', 'A03p06630' => 'bna', 'A05p44460' => 'bna', 'A06p08710' => 'bna', 'A06p41090' => 'bna', 'A07p32320' => 'bna', 'A08p32520' => 'bna', 'A09p10360' => 'bna', 'A10p24080' => 'bna', 'Aa31LG11G15250' => 'aar', 'Aa31LG1G1800' => 'aar', 'Aa31LG2G5120' => 'aar', 'Aa31LG2G6070' => 'aar', 'Aa31LG5G10770' => 'aar', 'Aa31sc61G90' => 'aar', 'Actinidia01352' => 'ach', 'Actinidia05983' => 'ach', 'Actinidia08133' => 'ach', 'Actinidia15101' => 'ach', 'Actinidia26379' => 'ach', 'Actinidia35778' => 'ach', 'Actinidia36123' => 'ach', 'Actinidia37436' => 'ach', 'Actinidia38730' => 'ach', 'Ah.02g128210' => 'amhyb', 'Ah.03g132990' => 'amhyb', 'Ah.14g079410' => 'amhyb', 'AL1G24640' => 'aly', 'AL2G26680' => 'aly', 'AL3G10530' => 'aly', 'AL3G45230' => 'aly', 'AL5G15230' => 'aly', 'AL5G16960' => 'aly', 'AL6G25210' => 'aly', 'Aqoxy2G00441' => 'aox', 'Aqoxy3G01236' => 'aox', 'Aqoxy5G03746' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3RQ047' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C7GMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9C8JER' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MBL6KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YXCZ83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZANX40' => 'arhy', 'AT1G12990' => 'ath', 'AT1G67880' => 'ath', 'AT2G13290' => 'ath', 'AT3G01620' => 'ath', 'AT3G26445' => 'ath', 'AT3G27540' => 'ath', 'AT5G14480' => 'ath', 'ATR0824G026' => 'atr', 'ATR1098G019' => 'atr', 'Atru.chr11.2145' => 'acertr', 'Atru.chr2.3636' => 'acertr', 'Atru.chr2.3644' => 'acertr', 'Atru.chr6.2422' => 'acertr', 'Atru.chr7.1112' => 'acertr', 'AUR62005469' => 'cqu', 'AUR62011166' => 'cqu', 'AUR62013319' => 'cqu', 'AUR62024273' => 'cqu', 'AUR62028420' => 'cqu', 'AUR62041942' => 'cqu', 'BcaB01g04969' => 'bca', 'BcaB01g06371' => 'bca', 'BcaB02g11494' => 'bca', 'BcaB03g15382' => 'bca', 'BcaB08g36994' => 'bca', 'BcaC03g13477' => 'bca', 'BcaC03g13478' => 'bca', 'BcaC03g13480' => 'bca', 'BcaC03g13481' => 'bca', 'BcaC03g13486' => 'bca', 'BcaC04g19031' => 'bca', 'BcaC04g23085' => 'bca', 'BcaC05g25094' => 'bca', 'BcaC05g25096' => 'bca', 'BcaC05g25138' => 'bca', 'BcaC05g30416' => 'bca', 'BcaC05g30455' => 'bca', 'BcaC06g30979' => 'bca', 'BcaC06g33805' => 'bca', 'BcaC08g46021' => 'bca', 'BcaNung03154' => 'bca', 'BolC2t06623H' => 'bol', 'BolC2t06632H' => 'bol', 'BolC2t06635H' => 'bol', 'BolC2t06638H' => 'bol', 'BolC3t13266H' => 'bol', 'BolC5t29776H' => 'bol', 'BolC6t38912H' => 'bol', 'BolC7t44183H' => 'bol', 'BolC9t54123H' => 'bol', 'BolC9t59107H' => 'bol', 'BraA02t05221Z' => 'bra', 'BraA03t09996Z' => 'bra', 'BraA05t23210Z' => 'bra', 'BraA06t24068Z' => 'bra', 'BraA06t27032Z' => 'bra', 'BraA08t35176Z' => 'bra', 'BraA09t36680Z' => 'bra', 'BraA10t44471Z' => 'bra', 'C02p06760' => 'bna', 'C02p06890' => 'bna', 'C02p07010' => 'bna', 'C03p07660' => 'bna', 'C05p10300' => 'bna', 'C06p38150' => 'bna', 'C07p36650' => 'bna', 'C08p15770' => 'bna', 'C09p12300' => 'bna', 'C09p62700' => 'bna', 'C09p75040' => 'bna', 'CAN.G13.1' => 'can', 'CAN.G138.4' => 'can', 'CAN.G44.6' => 'can', 'CAN.G473.19' => 'can', 'CANSAT01G0835' => 'cansat', 'CANSAT11G0246' => 'cansat', 'CANSAT11G1766' => 'cansat', 'CANSAT64G1954' => 'cansat', 'CARHR013330' => 'chi', 'CARHR060530' => 'chi', 'CARHR075300' => 'chi', 'CARHR105120' => 'chi', 'CARHR148910' => 'chi', 'CARHR198830' => 'chi', 'Carub.0001s1275' => 'cru', 'Carub.0002s1437' => 'cru', 'Carub.0003s0044' => 'cru', 'Carub.0003s2787' => 'cru', 'Carub.0005s0597' => 'cru', 'Carub.0006s1266' => 'cru', 'Ca_06935_v3' => 'car', 'Ca_13559_v3' => 'car', 'Ca_16941_v3' => 'car', 'Ca_16960_v3' => 'car', 'Ca_17775_v3' => 'car', 'Ca_30464_v3' => 'car', 'Cc06_g08160' => 'ccan', 'Cc07_g01520' => 'ccan', 'Cc11_g15810' => 'ccan', 'CDE02G2840' => 'cde', 'CDE03G0093' => 'cde', 'CDE04G2127' => 'cde', 'CDE07G1857' => 'cde', 'CDE09G1246' => 'cde', 'Cfa003412' => 'cfa', 'Cfa007341' => 'cfa', 'Cfa009220' => 'cfa', 'Ciclev10008737m.g' => 'ccl', 'Ciclev10015565m.g' => 'ccl', 'Ciclev10031761m.g' => 'ccl', 'CiPaw.03G045300' => 'cil', 'CiPaw.03G247200' => 'cil', 'CiPaw.04G029500' => 'cil', 'CiPaw.04G174000' => 'cil', 'CiPaw.05G181200' => 'cil', 'CiPaw.06G067100' => 'cil', 'ClCG05G025800' => 'cla', 'ClCG06G011400' => 'cla', 'ClCG09G019360' => 'cla', 'COL.COLO4_04827' => 'col', 'COL.COLO4_29170' => 'col', 'COL.COLO4_35131' => 'col', 'COL.COLO4_35132' => 'col', 'Cpa.g.sc33.32' => 'cpa', 'Cpa.g.sc46.29' => 'cpa', 'Cpa.g.sc796.1' => 'cpa', 'CsaV3_1G030420' => 'csa', 'CsaV3_5G027050' => 'csa', 'CsaV3_5G031040' => 'csa', 'CsaV3_UNG023130' => 'csa', 'CSS0007726' => 'camsi', 'CSS0016433' => 'camsi', 'CSS0017656' => 'camsi', 'CSS0025364' => 'camsi', 'CSS0027582' => 'camsi', 'CSS0047288' => 'camsi', 'CSS0049950' => 'camsi', 'DCAR_003843' => 'dca', 'DCAR_007052' => 'dca', 'DCAR_020884' => 'dca', 'DCAR_021730' => 'dca', 'DCAR_024423' => 'dca', 'DCAR_026509' => 'dca', 'DCAR_031158' => 'dca', 'Dinv14728' => 'din', 'Dinv15219' => 'din', 'Dinv25728' => 'din', 'Dinv33428' => 'din', 'Dinv36489' => 'din', 'Dinv41486' => 'din', 'Duzib147G0469' => 'dzi', 'Duzib168G0060' => 'dzi', 'Duzib187G1215' => 'dzi', 'Duzib248G0692' => 'dzi', 'Duzib251G0767' => 'dzi', 'Duzib264G0446' => 'dzi', 'Duzib268G0691' => 'dzi', 'ECA232G4767' => 'eca', 'ECA233G2838' => 'eca', 'ECA234G0391' => 'eca', 'ECA234G0857' => 'eca', 'ECA236G1593' => 'eca', 'ECA238G0565' => 'eca', 'ECA246G1027' => 'eca', 'ECA246G3223' => 'eca', 'ECA246G3470' => 'eca', 'EL10Ac6g13829' => 'bvu', 'EL10Ac6g14093' => 'bvu', 'EL10Ac8g18707' => 'bvu', 'Eucgr.C01369' => 'egr', 'Eucgr.H02492' => 'egr', 'Eucgr.I01733' => 'egr', 'Eucgr.J02255' => 'egr', 'Eucgr.J02257' => 'egr', 'Eucgr.J02258' => 'egr', 'FAN02G1601' => 'fan', 'FAN03G1586' => 'fan', 'FAN03G2986' => 'fan', 'FAN05G4837' => 'fan', 'FAN06G0146' => 'fan', 'FAN07G0858' => 'fan', 'FAN09G3179' => 'fan', 'FAN10G0669' => 'fan', 'FAN12G2358' => 'fan', 'FAN14G4198' => 'fan', 'FAN14G5112' => 'fan', 'FAN17G0342' => 'fan', 'FAN19G0342' => 'fan', 'FAN19G0962' => 'fan', 'FAN19G1101' => 'fan', 'FAN19G1872' => 'fan', 'FAN22G0356' => 'fan', 'FAN23G0744' => 'fan', 'FAN23G1914' => 'fan', 'FAN26G0032' => 'fan', 'FAN28G0625' => 'fan', 'FvH4_1g02710' => 'fve', 'FvH4_1g02720' => 'fve', 'FvH4_4g25670' => 'fve', 'FvH4_6g51700' => 'fve', 'FvH4_7g20170' => 'fve', 'Glyma.05G175000' => 'gma', 'Glyma.08G132300' => 'gma', 'Glyma.11G243000' => 'gma', 'Glyma.13G158900' => 'gma', 'Glyma.17G112400' => 'gma', 'Glyma.18G014100' => 'gma', 'Glyma.19G003100' => 'gma', 'Glyma.19G056500' => 'gma', 'Gohir.A01G158900' => 'ghi', 'Gohir.A05G312600' => 'ghi', 'Gohir.A05G354900' => 'ghi', 'Gohir.A07G037200' => 'ghi', 'Gohir.A09G030000' => 'ghi', 'Gohir.A12G145200' => 'ghi', 'Gohir.D01G151500' => 'ghi', 'Gohir.D04G058300' => 'ghi', 'Gohir.D05G314100' => 'ghi', 'Gohir.D07G041400' => 'ghi', 'Gohir.D09G029700' => 'ghi', 'Gohir.D12G149700' => 'ghi', 'Gorai.001G043800' => 'gra', 'Gorai.002G187800' => 'gra', 'Gorai.006G034700' => 'gra', 'Gorai.008G161200' => 'gra', 'Gorai.009G335700' => 'gra', 'Gorai.012G065000' => 'gra', 'GSVIVG01000535001' => 'vvi', 'GSVIVG01015572001' => 'vvi', 'GSVIVG01032386001' => 'vvi', 'HanXRQChr05g0138531' => 'han', 'HanXRQChr06g0174391' => 'han', 'HanXRQChr07g0199021' => 'han', 'HanXRQChr08g0208211' => 'han', 'HanXRQChr09g0255471' => 'han', 'HanXRQChr10g0315791' => 'han', 'HanXRQChr12g0371991' => 'han', 'HanXRQChr15g0475251' => 'han', 'HanXRQChr17g0540001' => 'han', 'HanXRQChr17g0548631' => 'han', 'HanXRQChr17g0569561' => 'han', 'Haze_12256' => 'cav', 'Haze_14756' => 'cav', 'Haze_25528' => 'cav', 'Hma1.2p1_0079F.1_g041020' => 'hma', 'Hma1.2p1_0818F.1_g223260' => 'hma', 'Hma1.2p1_1747F.1_g300530' => 'hma', 'HPP92_004607' => 'vpl', 'HPP92_004608' => 'vpl', 'HPP92_006181' => 'vpl', 'HPP92_012192' => 'vpl', 'HPP92_015680' => 'vpl', 'HPP92_020249' => 'vpl', 'HPP92_021376' => 'vpl', 'HPP92_024275' => 'vpl', 'Hund06031' => 'sun', 'Hund25391' => 'sun', 'Lalb_Chr07g0185371' => 'lal', 'Lalb_Chr07g0185381' => 'lal', 'Lalb_Chr12g0204011' => 'lal', 'Lalb_Chr13g0301671' => 'lal', 'Lalb_Chr14g0362851' => 'lal', 'Lalb_Chr24g0403581' => 'lal', 'Lj1g0000233' => 'lja', 'Lj2g0018120' => 'lja', 'Lj3C621T0' => 'lonja', 'Lj3P1059T14' => 'lonja', 'Lj3P611T9' => 'lonja', 'Lj3P614T13' => 'lonja', 'Lj3P615T5' => 'lonja', 'Lj4g0012315' => 'lja', 'Lj4g0026182' => 'lja', 'Lj6P813T16' => 'lonja', 'Lj7C427T7' => 'lonja', 'Lj7C427T8' => 'lonja', 'Lj7P600T41' => 'lonja', 'Lju41C42G17' => 'lonja', 'Lsat_1_v5_gn_0_47300' => 'lsa', 'Lsat_1_v5_gn_2_91280' => 'lsa', 'Lsat_1_v5_gn_3_30561' => 'lsa', 'Lsat_1_v5_gn_4_184321' => 'lsa', 'Lsat_1_v5_gn_4_4041' => 'lsa', 'Lsat_1_v5_gn_5_92000' => 'lsa', 'Lsat_1_v5_gn_8_152940' => 'lsa', 'Lsat_1_v5_gn_8_62401' => 'lsa', 'Manes.06G055900' => 'mes', 'Manes.12G022200' => 'mes', 'Manes.13G023300' => 'mes', 'Manes.14G115000' => 'mes', 'Manes.15G151700' => 'mes', 'Manes.17G111300' => 'mes', 'Mapoly0226s0009' => 'mpo', 'MBI02_g25363_MAGBIO' => 'mbi', 'MBI06_g00027_MAGBIO' => 'mbi', 'MBI10_g13034_MAGBIO' => 'mbi', 'MD09G1023400' => 'mdo', 'MD13G1100100' => 'mdo', 'MD15G1169200' => 'mdo', 'MD16G1101100' => 'mdo', 'MD17G1022900' => 'mdo', 'Medtr3g096150' => 'mtr', 'Medtr4g115070' => 'mtr', 'Medtr7g033325' => 'mtr', 'Medtr8g089840' => 'mtr', 'MELO3C010319.2' => 'cme', 'MELO3C011944.2' => 'cme', 'MELO3C021589.2' => 'cme', 'Migut.E00207' => 'egut', 'Migut.H00067' => 'egut', 'Migut.K00433' => 'egut', 'Migut.K00606' => 'egut', 'Migut.K01410' => 'egut', 'MSTRG.13347' => 'ama', 'MSTRG.24045' => 'ama', 'MSTRG.2428' => 'ama', 'MSTRG.26410' => 'ama', 'MSTRG.3139' => 'ama', 'MSTRG.3286' => 'ama', 'MSTRG.563' => 'ama', 'MSTRG.7941' => 'ama', 'Nitab4.5_0000028g0060' => 'nta', 'Nitab4.5_0000065g0260' => 'nta', 'Nitab4.5_0000112g0060' => 'nta', 'Nitab4.5_0000489g0120' => 'nta', 'Nitab4.5_0001776g0050' => 'nta', 'Nitab4.5_0001854g0010' => 'nta', 'Nitab4.5_0001860g0020' => 'nta', 'Nitab4.5_0004352g0010' => 'nta', 'Nitab4.5_0008716g0020' => 'nta', 'Nitab4.5_0008922g0010' => 'nta', 'Nn3g16693' => 'nnu', 'Nn4g22596' => 'nnu', 'Nn7g37639' => 'nnu', 'Oeu001701.1' => 'oeu', 'Oeu018149.1' => 'oeu', 'Oeu026220.1' => 'oeu', 'Oeu038635.1' => 'oeu', 'Oeu049176.1' => 'oeu', 'Oeu056706.1' => 'oeu', 'Oeu056937.1' => 'oeu', 'Oeu057540.1' => 'oeu', 'Os02g0594900' => 'osa', 'Os02g0595100' => 'osa', 'Os04g0477500' => 'osa', 'Os12g0611900' => 'osa', 'Peaxi162Scf00076g00020' => 'pax', 'Peaxi162Scf00128g00217' => 'pax', 'Peaxi162Scf00129g01640' => 'pax', 'Peaxi162Scf00669g00007' => 'pax', 'Peaxi162Scf00700g00421' => 'pax', 'Peaxi162Scf00801g00038' => 'pax', 'Peaxi162Scf00891g00025' => 'pax', 'PGR083G0909' => 'pgr', 'PGR119G1005' => 'pgr', 'PGR142G2236' => 'pgr', 'PGR142G3388' => 'pgr', 'PGSC0003DMG400004514' => 'stu', 'PGSC0003DMG400012635' => 'stu', 'PGSC0003DMG400015730' => 'stu', 'PGSC0003DMG400018611' => 'stu', 'PGSC0003DMG400030897' => 'stu', 'Phvul.001G254800' => 'pvu', 'Phvul.002G260100' => 'pvu', 'Phvul.003G167600' => 'pvu', 'Phvul.004G005100' => 'pvu', 'Potri.001G343600' => 'ptr', 'Potri.006G066700' => 'ptr', 'Potri.008G186000' => 'ptr', 'Potri.010G046900' => 'ptr', 'Potri.018G127900' => 'ptr', 'Pp3c20_17750' => 'ppa', 'Pp3c24_4380' => 'ppa', 'Prupe.1G245800' => 'ppe', 'Prupe.3G293400' => 'ppe', 'Prupe.7G247400' => 'ppe', 'Psat0s145g0120' => 'psa', 'Psat0s595g0040' => 'psa', 'Psat0s595g0120' => 'psa', 'Psat3g175040' => 'psa', 'Psat7g058120' => 'psa', 'PSO017G0428' => 'pso', 'PSO063G7510' => 'pso', 'PSO067G0046' => 'pso', 'PSO478G1073' => 'pso', 'PSO675G3677' => 'pso', 'PSO675G6558' => 'pso', 'PSO675G7520' => 'pso', 'PSO675G8959' => 'pso', 'QL02p074089' => 'qlo', 'QL02p089614' => 'qlo', 'QL03p057736' => 'qlo', 'RcHm_v2.0_Chr1g0364131' => 'rch', 'RcHm_v2.0_Chr2g0087801' => 'rch', 'RcHm_v2.0_Chr2g0087821' => 'rch', 'RcHm_v2.0_Chr2g0173231' => 'rch', 'RcHm_v2.0_Chr4g0433111' => 'rch', 'Rhsim03G0250300' => 'rsi', 'Rhsim08G0048400' => 'rsi', 'Rhsim10G0014800' => 'rsi', 'Rhsim12G0040100' => 'rsi', 'Rhsim12G0109700' => 'rsi', 'Sabra06G0049600' => 'sbr', 'Sabra08G0141000' => 'sbr', 'Sabra10G0021400' => 'sbr', 'Sabra16G0222900' => 'sbr', 'Sabra18G0108600' => 'sbr', 'SalBow1G0433' => 'sbo', 'SalBow1G2038' => 'sbo', 'SalBow1G5003' => 'sbo', 'SalBow7G1197' => 'sbo', 'SalBow8G3506' => 'sbo', 'Sc03g0007300' => 'sci', 'Sc11g0000950' => 'sci', 'Sc14g0008750' => 'sci', 'Sc18g0000420' => 'sci', 'Sed0006754' => 'sed', 'Sed0008741' => 'sed', 'Sed0017172' => 'sed', 'Sed0018925' => 'sed', 'Sed0023326' => 'sed', 'Sed0025909' => 'sed', 'SEGI_05333' => 'sgi', 'SEGI_10362' => 'sgi', 'SEGI_13380' => 'sgi', 'SEGI_24306' => 'sgi', 'SEGI_29077' => 'sgi', 'SEGI_29095' => 'sgi', 'SEGI_36534' => 'sgi', 'SEGI_37506' => 'sgi', 'SEGI_38321' => 'sgi', 'SGA_v2.0_scaffold307G48031' => 'sas', 'SGA_v2.0_scaffold47G17507' => 'sas', 'SGA_v2.0_scaffold63G21736' => 'sas', 'SGA_v2.0_scaffold87G27070' => 'sas', 'SHI17794' => 'shi', 'SHI28851' => 'shi', 'SMO165G0155' => 'smo', 'SMO340G0217' => 'smo', 'SMO367G1210' => 'smo', 'Solyc02g093430.3' => 'sly', 'Solyc05g013580.4' => 'sly', 'Solyc07g008030.3' => 'sly', 'Solyc12g035470.2' => 'sly', 'Sopen02g038020' => 'spe', 'Sopen05g008490' => 'spe', 'Sopen07g003910' => 'spe', 'Sopen12g015240' => 'spe', 'Sp1g11550' => 'spa', 'Sp2g16710' => 'spa', 'Sp3g00430' => 'spa', 'Sp3g26780' => 'spa', 'Sp5g22900' => 'spa', 'Sp6g29530' => 'spa', 'TAR371G0794' => 'tar', 'TAR374G0164' => 'tar', 'TAR622G0165' => 'tar', 'TAR626G0929' => 'tar', 'TAR629G2155' => 'tar', 'THA.LOC104805282' => 'tha', 'THA.LOC104805363' => 'tha', 'THA.LOC104808968' => 'tha', 'THA.LOC104821093' => 'tha', 'THA.LOC104823953' => 'tha', 'THA.LOC104825562' => 'tha', 'THA.LOC104825665' => 'tha', 'Thecc.02G261400' => 'tca', 'Thecc.04G019200' => 'tca', 'Thecc.09G130400' => 'tca', 'Thhalv10004374m.g' => 'esa', 'Thhalv10007850m.g' => 'esa', 'Thhalv10013782m.g' => 'esa', 'Thhalv10018686m.g' => 'esa', 'Thhalv10020899m.g' => 'esa', 'Thhalv10022755m.g' => 'esa', 'TPR.G23851' => 'tpr', 'TPR.G26500' => 'tpr', 'TPR.G27267' => 'tpr', 'TPR.G32001' => 'tpr', 'TPR.G6251' => 'tpr', 'TPR.G8167' => 'tpr', 'TWI12G1330' => 'twi', 'TWI18G1239' => 'twi', 'TWI34G0979' => 'twi', 'TWI36G0670' => 'twi', 'TWI36G0707' => 'twi', 'TWI56G0233' => 'twi', 'TWI75G1809' => 'twi', 'unitig_21.g20874' => 'ugi', 'unitig_26.g10343' => 'ugi', 'unitig_46.g18392' => 'ugi', 'unitig_52.g17178' => 'ugi', 'unitig_8.g2934' => 'ugi', 'vmacro01122' => 'vma', 'vmacro05875' => 'vma', 'vmacro06147' => 'vma', 'vmacro16191' => 'vma', 'vmacro18293' => 'vma', 'VMungo0251G3707' => 'vmu', 'VMungo0464G1521' => 'vmu', 'VMungo1215G0205' => 'vmu', 'VMungo1383G2484' => 'vmu', 'Zm00001eb079610' => 'zma', 'Zm00001eb135990' => 'zma', 'Zm00001eb183710' => 'zma', 'Zm00001eb246020' => 'zma' ) $gf_id = 'HOM05D001124' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001124' ) $data_identifier = 'HOM05D001124' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 6, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 7, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 21, 'bol' => (int) 10, 'bra' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 6, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 9, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 21, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 8, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 10, 'lsa' => (int) 8, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 8, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 9, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb246020' $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' => 'HOM05D001124', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '548', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02520' => 'bna', 'A03p06630' => 'bna', 'A05p44460' => 'bna', 'A06p08710' => 'bna', 'A06p41090' => 'bna', 'A07p32320' => 'bna', 'A08p32520' => 'bna', 'A09p10360' => 'bna', 'A10p24080' => 'bna', 'Aa31LG11G15250' => 'aar', 'Aa31LG1G1800' => 'aar', 'Aa31LG2G5120' => 'aar', 'Aa31LG2G6070' => 'aar', 'Aa31LG5G10770' => 'aar', 'Aa31sc61G90' => 'aar', 'Actinidia01352' => 'ach', 'Actinidia05983' => 'ach', 'Actinidia08133' => 'ach', 'Actinidia15101' => 'ach', 'Actinidia26379' => 'ach', 'Actinidia35778' => 'ach', 'Actinidia36123' => 'ach', 'Actinidia37436' => 'ach', 'Actinidia38730' => 'ach', 'Ah.02g128210' => 'amhyb', 'Ah.03g132990' => 'amhyb', 'Ah.14g079410' => 'amhyb', 'AL1G24640' => 'aly', 'AL2G26680' => 'aly', 'AL3G10530' => 'aly', 'AL3G45230' => 'aly', 'AL5G15230' => 'aly', 'AL5G16960' => 'aly', 'AL6G25210' => 'aly', 'Aqoxy2G00441' => 'aox', 'Aqoxy3G01236' => 'aox', 'Aqoxy5G03746' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3RQ047' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C7GMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9C8JER' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MBL6KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YXCZ83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZANX40' => 'arhy', 'AT1G12990' => 'ath', 'AT1G67880' => 'ath', 'AT2G13290' => 'ath', 'AT3G01620' => 'ath', 'AT3G26445' => 'ath', 'AT3G27540' => 'ath', 'AT5G14480' => 'ath', 'ATR0824G026' => 'atr', 'ATR1098G019' => 'atr', 'Atru.chr11.2145' => 'acertr', 'Atru.chr2.3636' => 'acertr', 'Atru.chr2.3644' => 'acertr', 'Atru.chr6.2422' => 'acertr', 'Atru.chr7.1112' => 'acertr', 'AUR62005469' => 'cqu', 'AUR62011166' => 'cqu', 'AUR62013319' => 'cqu', 'AUR62024273' => 'cqu', 'AUR62028420' => 'cqu', 'AUR62041942' => 'cqu', 'BcaB01g04969' => 'bca', 'BcaB01g06371' => 'bca', 'BcaB02g11494' => 'bca', 'BcaB03g15382' => 'bca', 'BcaB08g36994' => 'bca', 'BcaC03g13477' => 'bca', 'BcaC03g13478' => 'bca', 'BcaC03g13480' => 'bca', 'BcaC03g13481' => 'bca', 'BcaC03g13486' => 'bca', 'BcaC04g19031' => 'bca', 'BcaC04g23085' => 'bca', 'BcaC05g25094' => 'bca', 'BcaC05g25096' => 'bca', 'BcaC05g25138' => 'bca', 'BcaC05g30416' => 'bca', 'BcaC05g30455' => 'bca', 'BcaC06g30979' => 'bca', 'BcaC06g33805' => 'bca', 'BcaC08g46021' => 'bca', 'BcaNung03154' => 'bca', 'BolC2t06623H' => 'bol', 'BolC2t06632H' => 'bol', 'BolC2t06635H' => 'bol', 'BolC2t06638H' => 'bol', 'BolC3t13266H' => 'bol', 'BolC5t29776H' => 'bol', 'BolC6t38912H' => 'bol', 'BolC7t44183H' => 'bol', 'BolC9t54123H' => 'bol', 'BolC9t59107H' => 'bol', 'BraA02t05221Z' => 'bra', 'BraA03t09996Z' => 'bra', 'BraA05t23210Z' => 'bra', 'BraA06t24068Z' => 'bra', 'BraA06t27032Z' => 'bra', 'BraA08t35176Z' => 'bra', 'BraA09t36680Z' => 'bra', 'BraA10t44471Z' => 'bra', 'C02p06760' => 'bna', 'C02p06890' => 'bna', 'C02p07010' => 'bna', 'C03p07660' => 'bna', 'C05p10300' => 'bna', 'C06p38150' => 'bna', 'C07p36650' => 'bna', 'C08p15770' => 'bna', 'C09p12300' => 'bna', 'C09p62700' => 'bna', 'C09p75040' => 'bna', 'CAN.G13.1' => 'can', 'CAN.G138.4' => 'can', 'CAN.G44.6' => 'can', 'CAN.G473.19' => 'can', 'CANSAT01G0835' => 'cansat', 'CANSAT11G0246' => 'cansat', 'CANSAT11G1766' => 'cansat', 'CANSAT64G1954' => 'cansat', 'CARHR013330' => 'chi', 'CARHR060530' => 'chi', 'CARHR075300' => 'chi', 'CARHR105120' => 'chi', 'CARHR148910' => 'chi', 'CARHR198830' => 'chi', 'Carub.0001s1275' => 'cru', 'Carub.0002s1437' => 'cru', 'Carub.0003s0044' => 'cru', 'Carub.0003s2787' => 'cru', 'Carub.0005s0597' => 'cru', 'Carub.0006s1266' => 'cru', 'Ca_06935_v3' => 'car', 'Ca_13559_v3' => 'car', 'Ca_16941_v3' => 'car', 'Ca_16960_v3' => 'car', 'Ca_17775_v3' => 'car', 'Ca_30464_v3' => 'car', 'Cc06_g08160' => 'ccan', 'Cc07_g01520' => 'ccan', 'Cc11_g15810' => 'ccan', 'CDE02G2840' => 'cde', 'CDE03G0093' => 'cde', 'CDE04G2127' => 'cde', 'CDE07G1857' => 'cde', 'CDE09G1246' => 'cde', 'Cfa003412' => 'cfa', 'Cfa007341' => 'cfa', 'Cfa009220' => 'cfa', 'Ciclev10008737m.g' => 'ccl', 'Ciclev10015565m.g' => 'ccl', 'Ciclev10031761m.g' => 'ccl', 'CiPaw.03G045300' => 'cil', 'CiPaw.03G247200' => 'cil', 'CiPaw.04G029500' => 'cil', 'CiPaw.04G174000' => 'cil', 'CiPaw.05G181200' => 'cil', 'CiPaw.06G067100' => 'cil', 'ClCG05G025800' => 'cla', 'ClCG06G011400' => 'cla', 'ClCG09G019360' => 'cla', 'COL.COLO4_04827' => 'col', 'COL.COLO4_29170' => 'col', 'COL.COLO4_35131' => 'col', 'COL.COLO4_35132' => 'col', 'Cpa.g.sc33.32' => 'cpa', 'Cpa.g.sc46.29' => 'cpa', 'Cpa.g.sc796.1' => 'cpa', 'CsaV3_1G030420' => 'csa', 'CsaV3_5G027050' => 'csa', 'CsaV3_5G031040' => 'csa', 'CsaV3_UNG023130' => 'csa', 'CSS0007726' => 'camsi', 'CSS0016433' => 'camsi', 'CSS0017656' => 'camsi', 'CSS0025364' => 'camsi', 'CSS0027582' => 'camsi', 'CSS0047288' => 'camsi', 'CSS0049950' => 'camsi', 'DCAR_003843' => 'dca', 'DCAR_007052' => 'dca', 'DCAR_020884' => 'dca', 'DCAR_021730' => 'dca', 'DCAR_024423' => 'dca', 'DCAR_026509' => 'dca', 'DCAR_031158' => 'dca', 'Dinv14728' => 'din', 'Dinv15219' => 'din', 'Dinv25728' => 'din', 'Dinv33428' => 'din', 'Dinv36489' => 'din', 'Dinv41486' => 'din', 'Duzib147G0469' => 'dzi', 'Duzib168G0060' => 'dzi', 'Duzib187G1215' => 'dzi', 'Duzib248G0692' => 'dzi', 'Duzib251G0767' => 'dzi', 'Duzib264G0446' => 'dzi', 'Duzib268G0691' => 'dzi', 'ECA232G4767' => 'eca', 'ECA233G2838' => 'eca', 'ECA234G0391' => 'eca', 'ECA234G0857' => 'eca', 'ECA236G1593' => 'eca', 'ECA238G0565' => 'eca', 'ECA246G1027' => 'eca', 'ECA246G3223' => 'eca', 'ECA246G3470' => 'eca', 'EL10Ac6g13829' => 'bvu', 'EL10Ac6g14093' => 'bvu', 'EL10Ac8g18707' => 'bvu', 'Eucgr.C01369' => 'egr', 'Eucgr.H02492' => 'egr', 'Eucgr.I01733' => 'egr', 'Eucgr.J02255' => 'egr', 'Eucgr.J02257' => 'egr', 'Eucgr.J02258' => 'egr', 'FAN02G1601' => 'fan', 'FAN03G1586' => 'fan', 'FAN03G2986' => 'fan', 'FAN05G4837' => 'fan', 'FAN06G0146' => 'fan', 'FAN07G0858' => 'fan', 'FAN09G3179' => 'fan', 'FAN10G0669' => 'fan', 'FAN12G2358' => 'fan', 'FAN14G4198' => 'fan', 'FAN14G5112' => 'fan', 'FAN17G0342' => 'fan', 'FAN19G0342' => 'fan', 'FAN19G0962' => 'fan', 'FAN19G1101' => 'fan', 'FAN19G1872' => 'fan', 'FAN22G0356' => 'fan', 'FAN23G0744' => 'fan', 'FAN23G1914' => 'fan', 'FAN26G0032' => 'fan', 'FAN28G0625' => 'fan', 'FvH4_1g02710' => 'fve', 'FvH4_1g02720' => 'fve', 'FvH4_4g25670' => 'fve', 'FvH4_6g51700' => 'fve', 'FvH4_7g20170' => 'fve', 'Glyma.05G175000' => 'gma', 'Glyma.08G132300' => 'gma', 'Glyma.11G243000' => 'gma', 'Glyma.13G158900' => 'gma', 'Glyma.17G112400' => 'gma', 'Glyma.18G014100' => 'gma', 'Glyma.19G003100' => 'gma', 'Glyma.19G056500' => 'gma', 'Gohir.A01G158900' => 'ghi', 'Gohir.A05G312600' => 'ghi', 'Gohir.A05G354900' => 'ghi', 'Gohir.A07G037200' => 'ghi', 'Gohir.A09G030000' => 'ghi', 'Gohir.A12G145200' => 'ghi', 'Gohir.D01G151500' => 'ghi', 'Gohir.D04G058300' => 'ghi', 'Gohir.D05G314100' => 'ghi', 'Gohir.D07G041400' => 'ghi', 'Gohir.D09G029700' => 'ghi', 'Gohir.D12G149700' => 'ghi', 'Gorai.001G043800' => 'gra', 'Gorai.002G187800' => 'gra', 'Gorai.006G034700' => 'gra', 'Gorai.008G161200' => 'gra', 'Gorai.009G335700' => 'gra', 'Gorai.012G065000' => 'gra', 'GSVIVG01000535001' => 'vvi', 'GSVIVG01015572001' => 'vvi', 'GSVIVG01032386001' => 'vvi', 'HanXRQChr05g0138531' => 'han', 'HanXRQChr06g0174391' => 'han', 'HanXRQChr07g0199021' => 'han', 'HanXRQChr08g0208211' => 'han', 'HanXRQChr09g0255471' => 'han', 'HanXRQChr10g0315791' => 'han', 'HanXRQChr12g0371991' => 'han', 'HanXRQChr15g0475251' => 'han', 'HanXRQChr17g0540001' => 'han', 'HanXRQChr17g0548631' => 'han', 'HanXRQChr17g0569561' => 'han', 'Haze_12256' => 'cav', 'Haze_14756' => 'cav', 'Haze_25528' => 'cav', 'Hma1.2p1_0079F.1_g041020' => 'hma', 'Hma1.2p1_0818F.1_g223260' => 'hma', 'Hma1.2p1_1747F.1_g300530' => 'hma', 'HPP92_004607' => 'vpl', 'HPP92_004608' => 'vpl', 'HPP92_006181' => 'vpl', 'HPP92_012192' => 'vpl', 'HPP92_015680' => 'vpl', 'HPP92_020249' => 'vpl', 'HPP92_021376' => 'vpl', 'HPP92_024275' => 'vpl', 'Hund06031' => 'sun', 'Hund25391' => 'sun', 'Lalb_Chr07g0185371' => 'lal', 'Lalb_Chr07g0185381' => 'lal', 'Lalb_Chr12g0204011' => 'lal', 'Lalb_Chr13g0301671' => 'lal', 'Lalb_Chr14g0362851' => 'lal', 'Lalb_Chr24g0403581' => 'lal', 'Lj1g0000233' => 'lja', 'Lj2g0018120' => 'lja', 'Lj3C621T0' => 'lonja', 'Lj3P1059T14' => 'lonja', 'Lj3P611T9' => 'lonja', 'Lj3P614T13' => 'lonja', 'Lj3P615T5' => 'lonja', 'Lj4g0012315' => 'lja', 'Lj4g0026182' => 'lja', 'Lj6P813T16' => 'lonja', 'Lj7C427T7' => 'lonja', 'Lj7C427T8' => 'lonja', 'Lj7P600T41' => 'lonja', 'Lju41C42G17' => 'lonja', 'Lsat_1_v5_gn_0_47300' => 'lsa', 'Lsat_1_v5_gn_2_91280' => 'lsa', 'Lsat_1_v5_gn_3_30561' => 'lsa', 'Lsat_1_v5_gn_4_184321' => 'lsa', 'Lsat_1_v5_gn_4_4041' => 'lsa', 'Lsat_1_v5_gn_5_92000' => 'lsa', 'Lsat_1_v5_gn_8_152940' => 'lsa', 'Lsat_1_v5_gn_8_62401' => 'lsa', 'Manes.06G055900' => 'mes', 'Manes.12G022200' => 'mes', 'Manes.13G023300' => 'mes', 'Manes.14G115000' => 'mes', 'Manes.15G151700' => 'mes', 'Manes.17G111300' => 'mes', 'Mapoly0226s0009' => 'mpo', 'MBI02_g25363_MAGBIO' => 'mbi', 'MBI06_g00027_MAGBIO' => 'mbi', 'MBI10_g13034_MAGBIO' => 'mbi', 'MD09G1023400' => 'mdo', 'MD13G1100100' => 'mdo', 'MD15G1169200' => 'mdo', 'MD16G1101100' => 'mdo', 'MD17G1022900' => 'mdo', 'Medtr3g096150' => 'mtr', 'Medtr4g115070' => 'mtr', 'Medtr7g033325' => 'mtr', 'Medtr8g089840' => 'mtr', 'MELO3C010319.2' => 'cme', 'MELO3C011944.2' => 'cme', 'MELO3C021589.2' => 'cme', 'Migut.E00207' => 'egut', 'Migut.H00067' => 'egut', 'Migut.K00433' => 'egut', 'Migut.K00606' => 'egut', 'Migut.K01410' => 'egut', 'MSTRG.13347' => 'ama', 'MSTRG.24045' => 'ama', 'MSTRG.2428' => 'ama', 'MSTRG.26410' => 'ama', 'MSTRG.3139' => 'ama', 'MSTRG.3286' => 'ama', 'MSTRG.563' => 'ama', 'MSTRG.7941' => 'ama', 'Nitab4.5_0000028g0060' => 'nta', 'Nitab4.5_0000065g0260' => 'nta', 'Nitab4.5_0000112g0060' => 'nta', 'Nitab4.5_0000489g0120' => 'nta', 'Nitab4.5_0001776g0050' => 'nta', 'Nitab4.5_0001854g0010' => 'nta', 'Nitab4.5_0001860g0020' => 'nta', 'Nitab4.5_0004352g0010' => 'nta', 'Nitab4.5_0008716g0020' => 'nta', 'Nitab4.5_0008922g0010' => 'nta', 'Nn3g16693' => 'nnu', 'Nn4g22596' => 'nnu', 'Nn7g37639' => 'nnu', 'Oeu001701.1' => 'oeu', 'Oeu018149.1' => 'oeu', 'Oeu026220.1' => 'oeu', 'Oeu038635.1' => 'oeu', 'Oeu049176.1' => 'oeu', 'Oeu056706.1' => 'oeu', 'Oeu056937.1' => 'oeu', 'Oeu057540.1' => 'oeu', 'Os02g0594900' => 'osa', 'Os02g0595100' => 'osa', 'Os04g0477500' => 'osa', 'Os12g0611900' => 'osa', 'Peaxi162Scf00076g00020' => 'pax', 'Peaxi162Scf00128g00217' => 'pax', 'Peaxi162Scf00129g01640' => 'pax', 'Peaxi162Scf00669g00007' => 'pax', 'Peaxi162Scf00700g00421' => 'pax', 'Peaxi162Scf00801g00038' => 'pax', 'Peaxi162Scf00891g00025' => 'pax', 'PGR083G0909' => 'pgr', 'PGR119G1005' => 'pgr', 'PGR142G2236' => 'pgr', 'PGR142G3388' => 'pgr', 'PGSC0003DMG400004514' => 'stu', 'PGSC0003DMG400012635' => 'stu', 'PGSC0003DMG400015730' => 'stu', 'PGSC0003DMG400018611' => 'stu', 'PGSC0003DMG400030897' => 'stu', 'Phvul.001G254800' => 'pvu', 'Phvul.002G260100' => 'pvu', 'Phvul.003G167600' => 'pvu', 'Phvul.004G005100' => 'pvu', 'Potri.001G343600' => 'ptr', 'Potri.006G066700' => 'ptr', 'Potri.008G186000' => 'ptr', 'Potri.010G046900' => 'ptr', 'Potri.018G127900' => 'ptr', 'Pp3c20_17750' => 'ppa', 'Pp3c24_4380' => 'ppa', 'Prupe.1G245800' => 'ppe', 'Prupe.3G293400' => 'ppe', 'Prupe.7G247400' => 'ppe', 'Psat0s145g0120' => 'psa', 'Psat0s595g0040' => 'psa', 'Psat0s595g0120' => 'psa', 'Psat3g175040' => 'psa', 'Psat7g058120' => 'psa', 'PSO017G0428' => 'pso', 'PSO063G7510' => 'pso', 'PSO067G0046' => 'pso', 'PSO478G1073' => 'pso', 'PSO675G3677' => 'pso', 'PSO675G6558' => 'pso', 'PSO675G7520' => 'pso', 'PSO675G8959' => 'pso', 'QL02p074089' => 'qlo', 'QL02p089614' => 'qlo', 'QL03p057736' => 'qlo', 'RcHm_v2.0_Chr1g0364131' => 'rch', 'RcHm_v2.0_Chr2g0087801' => 'rch', 'RcHm_v2.0_Chr2g0087821' => 'rch', 'RcHm_v2.0_Chr2g0173231' => 'rch', 'RcHm_v2.0_Chr4g0433111' => 'rch', 'Rhsim03G0250300' => 'rsi', 'Rhsim08G0048400' => 'rsi', 'Rhsim10G0014800' => 'rsi', 'Rhsim12G0040100' => 'rsi', 'Rhsim12G0109700' => 'rsi', 'Sabra06G0049600' => 'sbr', 'Sabra08G0141000' => 'sbr', 'Sabra10G0021400' => 'sbr', 'Sabra16G0222900' => 'sbr', 'Sabra18G0108600' => 'sbr', 'SalBow1G0433' => 'sbo', 'SalBow1G2038' => 'sbo', 'SalBow1G5003' => 'sbo', 'SalBow7G1197' => 'sbo', 'SalBow8G3506' => 'sbo', 'Sc03g0007300' => 'sci', 'Sc11g0000950' => 'sci', 'Sc14g0008750' => 'sci', 'Sc18g0000420' => 'sci', 'Sed0006754' => 'sed', 'Sed0008741' => 'sed', 'Sed0017172' => 'sed', 'Sed0018925' => 'sed', 'Sed0023326' => 'sed', 'Sed0025909' => 'sed', 'SEGI_05333' => 'sgi', 'SEGI_10362' => 'sgi', 'SEGI_13380' => 'sgi', 'SEGI_24306' => 'sgi', 'SEGI_29077' => 'sgi', 'SEGI_29095' => 'sgi', 'SEGI_36534' => 'sgi', 'SEGI_37506' => 'sgi', 'SEGI_38321' => 'sgi', 'SGA_v2.0_scaffold307G48031' => 'sas', 'SGA_v2.0_scaffold47G17507' => 'sas', 'SGA_v2.0_scaffold63G21736' => 'sas', 'SGA_v2.0_scaffold87G27070' => 'sas', 'SHI17794' => 'shi', 'SHI28851' => 'shi', 'SMO165G0155' => 'smo', 'SMO340G0217' => 'smo', 'SMO367G1210' => 'smo', 'Solyc02g093430.3' => 'sly', 'Solyc05g013580.4' => 'sly', 'Solyc07g008030.3' => 'sly', 'Solyc12g035470.2' => 'sly', 'Sopen02g038020' => 'spe', 'Sopen05g008490' => 'spe', 'Sopen07g003910' => 'spe', 'Sopen12g015240' => 'spe', 'Sp1g11550' => 'spa', 'Sp2g16710' => 'spa', 'Sp3g00430' => 'spa', 'Sp3g26780' => 'spa', 'Sp5g22900' => 'spa', 'Sp6g29530' => 'spa', 'TAR371G0794' => 'tar', 'TAR374G0164' => 'tar', 'TAR622G0165' => 'tar', 'TAR626G0929' => 'tar', 'TAR629G2155' => 'tar', 'THA.LOC104805282' => 'tha', 'THA.LOC104805363' => 'tha', 'THA.LOC104808968' => 'tha', 'THA.LOC104821093' => 'tha', 'THA.LOC104823953' => 'tha', 'THA.LOC104825562' => 'tha', 'THA.LOC104825665' => 'tha', 'Thecc.02G261400' => 'tca', 'Thecc.04G019200' => 'tca', 'Thecc.09G130400' => 'tca', 'Thhalv10004374m.g' => 'esa', 'Thhalv10007850m.g' => 'esa', 'Thhalv10013782m.g' => 'esa', 'Thhalv10018686m.g' => 'esa', 'Thhalv10020899m.g' => 'esa', 'Thhalv10022755m.g' => 'esa', 'TPR.G23851' => 'tpr', 'TPR.G26500' => 'tpr', 'TPR.G27267' => 'tpr', 'TPR.G32001' => 'tpr', 'TPR.G6251' => 'tpr', 'TPR.G8167' => 'tpr', 'TWI12G1330' => 'twi', 'TWI18G1239' => 'twi', 'TWI34G0979' => 'twi', 'TWI36G0670' => 'twi', 'TWI36G0707' => 'twi', 'TWI56G0233' => 'twi', 'TWI75G1809' => 'twi', 'unitig_21.g20874' => 'ugi', 'unitig_26.g10343' => 'ugi', 'unitig_46.g18392' => 'ugi', 'unitig_52.g17178' => 'ugi', 'unitig_8.g2934' => 'ugi', 'vmacro01122' => 'vma', 'vmacro05875' => 'vma', 'vmacro06147' => 'vma', 'vmacro16191' => 'vma', 'vmacro18293' => 'vma', 'VMungo0251G3707' => 'vmu', 'VMungo0464G1521' => 'vmu', 'VMungo1215G0205' => 'vmu', 'VMungo1383G2484' => 'vmu', 'Zm00001eb079610' => 'zma', 'Zm00001eb135990' => 'zma', 'Zm00001eb183710' => 'zma', 'Zm00001eb246020' => 'zma' ), 'gf_id' => 'HOM05D001124', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001124' ), 'data_identifier' => 'HOM05D001124', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001124', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '548', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02520' => 'bna', 'A03p06630' => 'bna', 'A05p44460' => 'bna', 'A06p08710' => 'bna', 'A06p41090' => 'bna', 'A07p32320' => 'bna', 'A08p32520' => 'bna', 'A09p10360' => 'bna', 'A10p24080' => 'bna', 'Aa31LG11G15250' => 'aar', 'Aa31LG1G1800' => 'aar', 'Aa31LG2G5120' => 'aar', 'Aa31LG2G6070' => 'aar', 'Aa31LG5G10770' => 'aar', 'Aa31sc61G90' => 'aar', 'Actinidia01352' => 'ach', 'Actinidia05983' => 'ach', 'Actinidia08133' => 'ach', 'Actinidia15101' => 'ach', 'Actinidia26379' => 'ach', 'Actinidia35778' => 'ach', 'Actinidia36123' => 'ach', 'Actinidia37436' => 'ach', 'Actinidia38730' => 'ach', 'Ah.02g128210' => 'amhyb', 'Ah.03g132990' => 'amhyb', 'Ah.14g079410' => 'amhyb', 'AL1G24640' => 'aly', 'AL2G26680' => 'aly', 'AL3G10530' => 'aly', 'AL3G45230' => 'aly', 'AL5G15230' => 'aly', 'AL5G16960' => 'aly', 'AL6G25210' => 'aly', 'Aqoxy2G00441' => 'aox', 'Aqoxy3G01236' => 'aox', 'Aqoxy5G03746' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3RQ047' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C7GMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9C8JER' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MBL6KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YXCZ83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZANX40' => 'arhy', 'AT1G12990' => 'ath', 'AT1G67880' => 'ath', 'AT2G13290' => 'ath', 'AT3G01620' => 'ath', 'AT3G26445' => 'ath', 'AT3G27540' => 'ath', 'AT5G14480' => 'ath', 'ATR0824G026' => 'atr', 'ATR1098G019' => 'atr', 'Atru.chr11.2145' => 'acertr', 'Atru.chr2.3636' => 'acertr', 'Atru.chr2.3644' => 'acertr', 'Atru.chr6.2422' => 'acertr', 'Atru.chr7.1112' => 'acertr', 'AUR62005469' => 'cqu', 'AUR62011166' => 'cqu', 'AUR62013319' => 'cqu', 'AUR62024273' => 'cqu', 'AUR62028420' => 'cqu', 'AUR62041942' => 'cqu', 'BcaB01g04969' => 'bca', 'BcaB01g06371' => 'bca', 'BcaB02g11494' => 'bca', 'BcaB03g15382' => 'bca', 'BcaB08g36994' => 'bca', 'BcaC03g13477' => 'bca', 'BcaC03g13478' => 'bca', 'BcaC03g13480' => 'bca', 'BcaC03g13481' => 'bca', 'BcaC03g13486' => 'bca', 'BcaC04g19031' => 'bca', 'BcaC04g23085' => 'bca', 'BcaC05g25094' => 'bca', 'BcaC05g25096' => 'bca', 'BcaC05g25138' => 'bca', 'BcaC05g30416' => 'bca', 'BcaC05g30455' => 'bca', 'BcaC06g30979' => 'bca', 'BcaC06g33805' => 'bca', 'BcaC08g46021' => 'bca', 'BcaNung03154' => 'bca', 'BolC2t06623H' => 'bol', 'BolC2t06632H' => 'bol', 'BolC2t06635H' => 'bol', 'BolC2t06638H' => 'bol', 'BolC3t13266H' => 'bol', 'BolC5t29776H' => 'bol', 'BolC6t38912H' => 'bol', 'BolC7t44183H' => 'bol', 'BolC9t54123H' => 'bol', 'BolC9t59107H' => 'bol', 'BraA02t05221Z' => 'bra', 'BraA03t09996Z' => 'bra', 'BraA05t23210Z' => 'bra', 'BraA06t24068Z' => 'bra', 'BraA06t27032Z' => 'bra', 'BraA08t35176Z' => 'bra', 'BraA09t36680Z' => 'bra', 'BraA10t44471Z' => 'bra', 'C02p06760' => 'bna', 'C02p06890' => 'bna', 'C02p07010' => 'bna', 'C03p07660' => 'bna', 'C05p10300' => 'bna', 'C06p38150' => 'bna', 'C07p36650' => 'bna', 'C08p15770' => 'bna', 'C09p12300' => 'bna', 'C09p62700' => 'bna', 'C09p75040' => 'bna', 'CAN.G13.1' => 'can', 'CAN.G138.4' => 'can', 'CAN.G44.6' => 'can', 'CAN.G473.19' => 'can', 'CANSAT01G0835' => 'cansat', 'CANSAT11G0246' => 'cansat', 'CANSAT11G1766' => 'cansat', 'CANSAT64G1954' => 'cansat', 'CARHR013330' => 'chi', 'CARHR060530' => 'chi', 'CARHR075300' => 'chi', 'CARHR105120' => 'chi', 'CARHR148910' => 'chi', 'CARHR198830' => 'chi', 'Carub.0001s1275' => 'cru', 'Carub.0002s1437' => 'cru', 'Carub.0003s0044' => 'cru', 'Carub.0003s2787' => 'cru', 'Carub.0005s0597' => 'cru', 'Carub.0006s1266' => 'cru', 'Ca_06935_v3' => 'car', 'Ca_13559_v3' => 'car', 'Ca_16941_v3' => 'car', 'Ca_16960_v3' => 'car', 'Ca_17775_v3' => 'car', 'Ca_30464_v3' => 'car', 'Cc06_g08160' => 'ccan', 'Cc07_g01520' => 'ccan', 'Cc11_g15810' => 'ccan', 'CDE02G2840' => 'cde', 'CDE03G0093' => 'cde', 'CDE04G2127' => 'cde', 'CDE07G1857' => 'cde', 'CDE09G1246' => 'cde', 'Cfa003412' => 'cfa', 'Cfa007341' => 'cfa', 'Cfa009220' => 'cfa', 'Ciclev10008737m.g' => 'ccl', 'Ciclev10015565m.g' => 'ccl', 'Ciclev10031761m.g' => 'ccl', 'CiPaw.03G045300' => 'cil', 'CiPaw.03G247200' => 'cil', 'CiPaw.04G029500' => 'cil', 'CiPaw.04G174000' => 'cil', 'CiPaw.05G181200' => 'cil', 'CiPaw.06G067100' => 'cil', 'ClCG05G025800' => 'cla', 'ClCG06G011400' => 'cla', 'ClCG09G019360' => 'cla', 'COL.COLO4_04827' => 'col', 'COL.COLO4_29170' => 'col', 'COL.COLO4_35131' => 'col', 'COL.COLO4_35132' => 'col', 'Cpa.g.sc33.32' => 'cpa', 'Cpa.g.sc46.29' => 'cpa', 'Cpa.g.sc796.1' => 'cpa', 'CsaV3_1G030420' => 'csa', 'CsaV3_5G027050' => 'csa', 'CsaV3_5G031040' => 'csa', 'CsaV3_UNG023130' => 'csa', 'CSS0007726' => 'camsi', 'CSS0016433' => 'camsi', 'CSS0017656' => 'camsi', 'CSS0025364' => 'camsi', 'CSS0027582' => 'camsi', 'CSS0047288' => 'camsi', 'CSS0049950' => 'camsi', 'DCAR_003843' => 'dca', 'DCAR_007052' => 'dca', 'DCAR_020884' => 'dca', 'DCAR_021730' => 'dca', 'DCAR_024423' => 'dca', 'DCAR_026509' => 'dca', 'DCAR_031158' => 'dca', 'Dinv14728' => 'din', 'Dinv15219' => 'din', 'Dinv25728' => 'din', 'Dinv33428' => 'din', 'Dinv36489' => 'din', 'Dinv41486' => 'din', 'Duzib147G0469' => 'dzi', 'Duzib168G0060' => 'dzi', 'Duzib187G1215' => 'dzi', 'Duzib248G0692' => 'dzi', 'Duzib251G0767' => 'dzi', 'Duzib264G0446' => 'dzi', 'Duzib268G0691' => 'dzi', 'ECA232G4767' => 'eca', 'ECA233G2838' => 'eca', 'ECA234G0391' => 'eca', 'ECA234G0857' => 'eca', 'ECA236G1593' => 'eca', 'ECA238G0565' => 'eca', 'ECA246G1027' => 'eca', 'ECA246G3223' => 'eca', 'ECA246G3470' => 'eca', 'EL10Ac6g13829' => 'bvu', 'EL10Ac6g14093' => 'bvu', 'EL10Ac8g18707' => 'bvu', 'Eucgr.C01369' => 'egr', 'Eucgr.H02492' => 'egr', 'Eucgr.I01733' => 'egr', 'Eucgr.J02255' => 'egr', 'Eucgr.J02257' => 'egr', 'Eucgr.J02258' => 'egr', 'FAN02G1601' => 'fan', 'FAN03G1586' => 'fan', 'FAN03G2986' => 'fan', 'FAN05G4837' => 'fan', 'FAN06G0146' => 'fan', 'FAN07G0858' => 'fan', 'FAN09G3179' => 'fan', 'FAN10G0669' => 'fan', 'FAN12G2358' => 'fan', 'FAN14G4198' => 'fan', 'FAN14G5112' => 'fan', 'FAN17G0342' => 'fan', 'FAN19G0342' => 'fan', 'FAN19G0962' => 'fan', 'FAN19G1101' => 'fan', 'FAN19G1872' => 'fan', 'FAN22G0356' => 'fan', 'FAN23G0744' => 'fan', 'FAN23G1914' => 'fan', 'FAN26G0032' => 'fan', 'FAN28G0625' => 'fan', 'FvH4_1g02710' => 'fve', 'FvH4_1g02720' => 'fve', 'FvH4_4g25670' => 'fve', 'FvH4_6g51700' => 'fve', 'FvH4_7g20170' => 'fve', 'Glyma.05G175000' => 'gma', 'Glyma.08G132300' => 'gma', 'Glyma.11G243000' => 'gma', 'Glyma.13G158900' => 'gma', 'Glyma.17G112400' => 'gma', 'Glyma.18G014100' => 'gma', 'Glyma.19G003100' => 'gma', 'Glyma.19G056500' => 'gma', 'Gohir.A01G158900' => 'ghi', 'Gohir.A05G312600' => 'ghi', 'Gohir.A05G354900' => 'ghi', 'Gohir.A07G037200' => 'ghi', 'Gohir.A09G030000' => 'ghi', 'Gohir.A12G145200' => 'ghi', 'Gohir.D01G151500' => 'ghi', 'Gohir.D04G058300' => 'ghi', 'Gohir.D05G314100' => 'ghi', 'Gohir.D07G041400' => 'ghi', 'Gohir.D09G029700' => 'ghi', 'Gohir.D12G149700' => 'ghi', 'Gorai.001G043800' => 'gra', 'Gorai.002G187800' => 'gra', 'Gorai.006G034700' => 'gra', 'Gorai.008G161200' => 'gra', 'Gorai.009G335700' => 'gra', 'Gorai.012G065000' => 'gra', 'GSVIVG01000535001' => 'vvi', 'GSVIVG01015572001' => 'vvi', 'GSVIVG01032386001' => 'vvi', 'HanXRQChr05g0138531' => 'han', 'HanXRQChr06g0174391' => 'han', 'HanXRQChr07g0199021' => 'han', 'HanXRQChr08g0208211' => 'han', 'HanXRQChr09g0255471' => 'han', 'HanXRQChr10g0315791' => 'han', 'HanXRQChr12g0371991' => 'han', 'HanXRQChr15g0475251' => 'han', 'HanXRQChr17g0540001' => 'han', 'HanXRQChr17g0548631' => 'han', 'HanXRQChr17g0569561' => 'han', 'Haze_12256' => 'cav', 'Haze_14756' => 'cav', 'Haze_25528' => 'cav', 'Hma1.2p1_0079F.1_g041020' => 'hma', 'Hma1.2p1_0818F.1_g223260' => 'hma', 'Hma1.2p1_1747F.1_g300530' => 'hma', 'HPP92_004607' => 'vpl', 'HPP92_004608' => 'vpl', 'HPP92_006181' => 'vpl', 'HPP92_012192' => 'vpl', 'HPP92_015680' => 'vpl', 'HPP92_020249' => 'vpl', 'HPP92_021376' => 'vpl', 'HPP92_024275' => 'vpl', 'Hund06031' => 'sun', 'Hund25391' => 'sun', 'Lalb_Chr07g0185371' => 'lal', 'Lalb_Chr07g0185381' => 'lal', 'Lalb_Chr12g0204011' => 'lal', 'Lalb_Chr13g0301671' => 'lal', 'Lalb_Chr14g0362851' => 'lal', 'Lalb_Chr24g0403581' => 'lal', 'Lj1g0000233' => 'lja', 'Lj2g0018120' => 'lja', 'Lj3C621T0' => 'lonja', 'Lj3P1059T14' => 'lonja', 'Lj3P611T9' => 'lonja', 'Lj3P614T13' => 'lonja', 'Lj3P615T5' => 'lonja', 'Lj4g0012315' => 'lja', 'Lj4g0026182' => 'lja', 'Lj6P813T16' => 'lonja', 'Lj7C427T7' => 'lonja', 'Lj7C427T8' => 'lonja', 'Lj7P600T41' => 'lonja', 'Lju41C42G17' => 'lonja', 'Lsat_1_v5_gn_0_47300' => 'lsa', 'Lsat_1_v5_gn_2_91280' => 'lsa', 'Lsat_1_v5_gn_3_30561' => 'lsa', 'Lsat_1_v5_gn_4_184321' => 'lsa', 'Lsat_1_v5_gn_4_4041' => 'lsa', 'Lsat_1_v5_gn_5_92000' => 'lsa', 'Lsat_1_v5_gn_8_152940' => 'lsa', 'Lsat_1_v5_gn_8_62401' => 'lsa', 'Manes.06G055900' => 'mes', 'Manes.12G022200' => 'mes', 'Manes.13G023300' => 'mes', 'Manes.14G115000' => 'mes', 'Manes.15G151700' => 'mes', 'Manes.17G111300' => 'mes', 'Mapoly0226s0009' => 'mpo', 'MBI02_g25363_MAGBIO' => 'mbi', 'MBI06_g00027_MAGBIO' => 'mbi', 'MBI10_g13034_MAGBIO' => 'mbi', 'MD09G1023400' => 'mdo', 'MD13G1100100' => 'mdo', 'MD15G1169200' => 'mdo', 'MD16G1101100' => 'mdo', 'MD17G1022900' => 'mdo', 'Medtr3g096150' => 'mtr', 'Medtr4g115070' => 'mtr', 'Medtr7g033325' => 'mtr', 'Medtr8g089840' => 'mtr', 'MELO3C010319.2' => 'cme', 'MELO3C011944.2' => 'cme', 'MELO3C021589.2' => 'cme', 'Migut.E00207' => 'egut', 'Migut.H00067' => 'egut', 'Migut.K00433' => 'egut', 'Migut.K00606' => 'egut', 'Migut.K01410' => 'egut', 'MSTRG.13347' => 'ama', 'MSTRG.24045' => 'ama', 'MSTRG.2428' => 'ama', 'MSTRG.26410' => 'ama', 'MSTRG.3139' => 'ama', 'MSTRG.3286' => 'ama', 'MSTRG.563' => 'ama', 'MSTRG.7941' => 'ama', 'Nitab4.5_0000028g0060' => 'nta', 'Nitab4.5_0000065g0260' => 'nta', 'Nitab4.5_0000112g0060' => 'nta', 'Nitab4.5_0000489g0120' => 'nta', 'Nitab4.5_0001776g0050' => 'nta', 'Nitab4.5_0001854g0010' => 'nta', 'Nitab4.5_0001860g0020' => 'nta', 'Nitab4.5_0004352g0010' => 'nta', 'Nitab4.5_0008716g0020' => 'nta', 'Nitab4.5_0008922g0010' => 'nta', 'Nn3g16693' => 'nnu', 'Nn4g22596' => 'nnu', 'Nn7g37639' => 'nnu', 'Oeu001701.1' => 'oeu', 'Oeu018149.1' => 'oeu', 'Oeu026220.1' => 'oeu', 'Oeu038635.1' => 'oeu', 'Oeu049176.1' => 'oeu', 'Oeu056706.1' => 'oeu', 'Oeu056937.1' => 'oeu', 'Oeu057540.1' => 'oeu', 'Os02g0594900' => 'osa', 'Os02g0595100' => 'osa', 'Os04g0477500' => 'osa', 'Os12g0611900' => 'osa', 'Peaxi162Scf00076g00020' => 'pax', 'Peaxi162Scf00128g00217' => 'pax', 'Peaxi162Scf00129g01640' => 'pax', 'Peaxi162Scf00669g00007' => 'pax', 'Peaxi162Scf00700g00421' => 'pax', 'Peaxi162Scf00801g00038' => 'pax', 'Peaxi162Scf00891g00025' => 'pax', 'PGR083G0909' => 'pgr', 'PGR119G1005' => 'pgr', 'PGR142G2236' => 'pgr', 'PGR142G3388' => 'pgr', 'PGSC0003DMG400004514' => 'stu', 'PGSC0003DMG400012635' => 'stu', 'PGSC0003DMG400015730' => 'stu', 'PGSC0003DMG400018611' => 'stu', 'PGSC0003DMG400030897' => 'stu', 'Phvul.001G254800' => 'pvu', 'Phvul.002G260100' => 'pvu', 'Phvul.003G167600' => 'pvu', 'Phvul.004G005100' => 'pvu', 'Potri.001G343600' => 'ptr', 'Potri.006G066700' => 'ptr', 'Potri.008G186000' => 'ptr', 'Potri.010G046900' => 'ptr', 'Potri.018G127900' => 'ptr', 'Pp3c20_17750' => 'ppa', 'Pp3c24_4380' => 'ppa', 'Prupe.1G245800' => 'ppe', 'Prupe.3G293400' => 'ppe', 'Prupe.7G247400' => 'ppe', 'Psat0s145g0120' => 'psa', 'Psat0s595g0040' => 'psa', 'Psat0s595g0120' => 'psa', 'Psat3g175040' => 'psa', 'Psat7g058120' => 'psa', 'PSO017G0428' => 'pso', 'PSO063G7510' => 'pso', 'PSO067G0046' => 'pso', 'PSO478G1073' => 'pso', 'PSO675G3677' => 'pso', 'PSO675G6558' => 'pso', 'PSO675G7520' => 'pso', 'PSO675G8959' => 'pso', 'QL02p074089' => 'qlo', 'QL02p089614' => 'qlo', 'QL03p057736' => 'qlo', 'RcHm_v2.0_Chr1g0364131' => 'rch', 'RcHm_v2.0_Chr2g0087801' => 'rch', 'RcHm_v2.0_Chr2g0087821' => 'rch', 'RcHm_v2.0_Chr2g0173231' => 'rch', 'RcHm_v2.0_Chr4g0433111' => 'rch', 'Rhsim03G0250300' => 'rsi', 'Rhsim08G0048400' => 'rsi', 'Rhsim10G0014800' => 'rsi', 'Rhsim12G0040100' => 'rsi', 'Rhsim12G0109700' => 'rsi', 'Sabra06G0049600' => 'sbr', 'Sabra08G0141000' => 'sbr', 'Sabra10G0021400' => 'sbr', 'Sabra16G0222900' => 'sbr', 'Sabra18G0108600' => 'sbr', 'SalBow1G0433' => 'sbo', 'SalBow1G2038' => 'sbo', 'SalBow1G5003' => 'sbo', 'SalBow7G1197' => 'sbo', 'SalBow8G3506' => 'sbo', 'Sc03g0007300' => 'sci', 'Sc11g0000950' => 'sci', 'Sc14g0008750' => 'sci', 'Sc18g0000420' => 'sci', 'Sed0006754' => 'sed', 'Sed0008741' => 'sed', 'Sed0017172' => 'sed', 'Sed0018925' => 'sed', 'Sed0023326' => 'sed', 'Sed0025909' => 'sed', 'SEGI_05333' => 'sgi', 'SEGI_10362' => 'sgi', 'SEGI_13380' => 'sgi', 'SEGI_24306' => 'sgi', 'SEGI_29077' => 'sgi', 'SEGI_29095' => 'sgi', 'SEGI_36534' => 'sgi', 'SEGI_37506' => 'sgi', 'SEGI_38321' => 'sgi', 'SGA_v2.0_scaffold307G48031' => 'sas', 'SGA_v2.0_scaffold47G17507' => 'sas', 'SGA_v2.0_scaffold63G21736' => 'sas', 'SGA_v2.0_scaffold87G27070' => 'sas', 'SHI17794' => 'shi', 'SHI28851' => 'shi', 'SMO165G0155' => 'smo', 'SMO340G0217' => 'smo', 'SMO367G1210' => 'smo', 'Solyc02g093430.3' => 'sly', 'Solyc05g013580.4' => 'sly', 'Solyc07g008030.3' => 'sly', 'Solyc12g035470.2' => 'sly', 'Sopen02g038020' => 'spe', 'Sopen05g008490' => 'spe', 'Sopen07g003910' => 'spe', 'Sopen12g015240' => 'spe', 'Sp1g11550' => 'spa', 'Sp2g16710' => 'spa', 'Sp3g00430' => 'spa', 'Sp3g26780' => 'spa', 'Sp5g22900' => 'spa', 'Sp6g29530' => 'spa', 'TAR371G0794' => 'tar', 'TAR374G0164' => 'tar', 'TAR622G0165' => 'tar', 'TAR626G0929' => 'tar', 'TAR629G2155' => 'tar', 'THA.LOC104805282' => 'tha', 'THA.LOC104805363' => 'tha', 'THA.LOC104808968' => 'tha', 'THA.LOC104821093' => 'tha', 'THA.LOC104823953' => 'tha', 'THA.LOC104825562' => 'tha', 'THA.LOC104825665' => 'tha', 'Thecc.02G261400' => 'tca', 'Thecc.04G019200' => 'tca', 'Thecc.09G130400' => 'tca', 'Thhalv10004374m.g' => 'esa', 'Thhalv10007850m.g' => 'esa', 'Thhalv10013782m.g' => 'esa', 'Thhalv10018686m.g' => 'esa', 'Thhalv10020899m.g' => 'esa', 'Thhalv10022755m.g' => 'esa', 'TPR.G23851' => 'tpr', 'TPR.G26500' => 'tpr', 'TPR.G27267' => 'tpr', 'TPR.G32001' => 'tpr', 'TPR.G6251' => 'tpr', 'TPR.G8167' => 'tpr', 'TWI12G1330' => 'twi', 'TWI18G1239' => 'twi', 'TWI34G0979' => 'twi', 'TWI36G0670' => 'twi', 'TWI36G0707' => 'twi', 'TWI56G0233' => 'twi', 'TWI75G1809' => 'twi', 'unitig_21.g20874' => 'ugi', 'unitig_26.g10343' => 'ugi', 'unitig_46.g18392' => 'ugi', 'unitig_52.g17178' => 'ugi', 'unitig_8.g2934' => 'ugi', 'vmacro01122' => 'vma', 'vmacro05875' => 'vma', 'vmacro06147' => 'vma', 'vmacro16191' => 'vma', 'vmacro18293' => 'vma', 'VMungo0251G3707' => 'vmu', 'VMungo0464G1521' => 'vmu', 'VMungo1215G0205' => 'vmu', 'VMungo1383G2484' => 'vmu', 'Zm00001eb079610' => 'zma', 'Zm00001eb135990' => 'zma', 'Zm00001eb183710' => 'zma', 'Zm00001eb246020' => 'zma' ) $gf_id = 'HOM05D001124' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001124' ) $data_identifier = 'HOM05D001124' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 6, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 7, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 21, 'bol' => (int) 10, 'bra' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 6, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 9, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 21, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 8, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 10, 'lsa' => (int) 8, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 8, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 9, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb246020' $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' => 'HOM05D001124', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '548', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02520' => 'bna', 'A03p06630' => 'bna', 'A05p44460' => 'bna', 'A06p08710' => 'bna', 'A06p41090' => 'bna', 'A07p32320' => 'bna', 'A08p32520' => 'bna', 'A09p10360' => 'bna', 'A10p24080' => 'bna', 'Aa31LG11G15250' => 'aar', 'Aa31LG1G1800' => 'aar', 'Aa31LG2G5120' => 'aar', 'Aa31LG2G6070' => 'aar', 'Aa31LG5G10770' => 'aar', 'Aa31sc61G90' => 'aar', 'Actinidia01352' => 'ach', 'Actinidia05983' => 'ach', 'Actinidia08133' => 'ach', 'Actinidia15101' => 'ach', 'Actinidia26379' => 'ach', 'Actinidia35778' => 'ach', 'Actinidia36123' => 'ach', 'Actinidia37436' => 'ach', 'Actinidia38730' => 'ach', 'Ah.02g128210' => 'amhyb', 'Ah.03g132990' => 'amhyb', 'Ah.14g079410' => 'amhyb', 'AL1G24640' => 'aly', 'AL2G26680' => 'aly', 'AL3G10530' => 'aly', 'AL3G45230' => 'aly', 'AL5G15230' => 'aly', 'AL5G16960' => 'aly', 'AL6G25210' => 'aly', 'Aqoxy2G00441' => 'aox', 'Aqoxy3G01236' => 'aox', 'Aqoxy5G03746' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3RQ047' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C7GMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9C8JER' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MBL6KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YXCZ83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZANX40' => 'arhy', 'AT1G12990' => 'ath', 'AT1G67880' => 'ath', 'AT2G13290' => 'ath', 'AT3G01620' => 'ath', 'AT3G26445' => 'ath', 'AT3G27540' => 'ath', 'AT5G14480' => 'ath', 'ATR0824G026' => 'atr', 'ATR1098G019' => 'atr', 'Atru.chr11.2145' => 'acertr', 'Atru.chr2.3636' => 'acertr', 'Atru.chr2.3644' => 'acertr', 'Atru.chr6.2422' => 'acertr', 'Atru.chr7.1112' => 'acertr', 'AUR62005469' => 'cqu', 'AUR62011166' => 'cqu', 'AUR62013319' => 'cqu', 'AUR62024273' => 'cqu', 'AUR62028420' => 'cqu', 'AUR62041942' => 'cqu', 'BcaB01g04969' => 'bca', 'BcaB01g06371' => 'bca', 'BcaB02g11494' => 'bca', 'BcaB03g15382' => 'bca', 'BcaB08g36994' => 'bca', 'BcaC03g13477' => 'bca', 'BcaC03g13478' => 'bca', 'BcaC03g13480' => 'bca', 'BcaC03g13481' => 'bca', 'BcaC03g13486' => 'bca', 'BcaC04g19031' => 'bca', 'BcaC04g23085' => 'bca', 'BcaC05g25094' => 'bca', 'BcaC05g25096' => 'bca', 'BcaC05g25138' => 'bca', 'BcaC05g30416' => 'bca', 'BcaC05g30455' => 'bca', 'BcaC06g30979' => 'bca', 'BcaC06g33805' => 'bca', 'BcaC08g46021' => 'bca', 'BcaNung03154' => 'bca', 'BolC2t06623H' => 'bol', 'BolC2t06632H' => 'bol', 'BolC2t06635H' => 'bol', 'BolC2t06638H' => 'bol', 'BolC3t13266H' => 'bol', 'BolC5t29776H' => 'bol', 'BolC6t38912H' => 'bol', 'BolC7t44183H' => 'bol', 'BolC9t54123H' => 'bol', 'BolC9t59107H' => 'bol', 'BraA02t05221Z' => 'bra', 'BraA03t09996Z' => 'bra', 'BraA05t23210Z' => 'bra', 'BraA06t24068Z' => 'bra', 'BraA06t27032Z' => 'bra', 'BraA08t35176Z' => 'bra', 'BraA09t36680Z' => 'bra', 'BraA10t44471Z' => 'bra', 'C02p06760' => 'bna', 'C02p06890' => 'bna', 'C02p07010' => 'bna', 'C03p07660' => 'bna', 'C05p10300' => 'bna', 'C06p38150' => 'bna', 'C07p36650' => 'bna', 'C08p15770' => 'bna', 'C09p12300' => 'bna', 'C09p62700' => 'bna', 'C09p75040' => 'bna', 'CAN.G13.1' => 'can', 'CAN.G138.4' => 'can', 'CAN.G44.6' => 'can', 'CAN.G473.19' => 'can', 'CANSAT01G0835' => 'cansat', 'CANSAT11G0246' => 'cansat', 'CANSAT11G1766' => 'cansat', 'CANSAT64G1954' => 'cansat', 'CARHR013330' => 'chi', 'CARHR060530' => 'chi', 'CARHR075300' => 'chi', 'CARHR105120' => 'chi', 'CARHR148910' => 'chi', 'CARHR198830' => 'chi', 'Carub.0001s1275' => 'cru', 'Carub.0002s1437' => 'cru', 'Carub.0003s0044' => 'cru', 'Carub.0003s2787' => 'cru', 'Carub.0005s0597' => 'cru', 'Carub.0006s1266' => 'cru', 'Ca_06935_v3' => 'car', 'Ca_13559_v3' => 'car', 'Ca_16941_v3' => 'car', 'Ca_16960_v3' => 'car', 'Ca_17775_v3' => 'car', 'Ca_30464_v3' => 'car', 'Cc06_g08160' => 'ccan', 'Cc07_g01520' => 'ccan', 'Cc11_g15810' => 'ccan', 'CDE02G2840' => 'cde', 'CDE03G0093' => 'cde', 'CDE04G2127' => 'cde', 'CDE07G1857' => 'cde', 'CDE09G1246' => 'cde', 'Cfa003412' => 'cfa', 'Cfa007341' => 'cfa', 'Cfa009220' => 'cfa', 'Ciclev10008737m.g' => 'ccl', 'Ciclev10015565m.g' => 'ccl', 'Ciclev10031761m.g' => 'ccl', 'CiPaw.03G045300' => 'cil', 'CiPaw.03G247200' => 'cil', 'CiPaw.04G029500' => 'cil', 'CiPaw.04G174000' => 'cil', 'CiPaw.05G181200' => 'cil', 'CiPaw.06G067100' => 'cil', 'ClCG05G025800' => 'cla', 'ClCG06G011400' => 'cla', 'ClCG09G019360' => 'cla', 'COL.COLO4_04827' => 'col', 'COL.COLO4_29170' => 'col', 'COL.COLO4_35131' => 'col', 'COL.COLO4_35132' => 'col', 'Cpa.g.sc33.32' => 'cpa', 'Cpa.g.sc46.29' => 'cpa', 'Cpa.g.sc796.1' => 'cpa', 'CsaV3_1G030420' => 'csa', 'CsaV3_5G027050' => 'csa', 'CsaV3_5G031040' => 'csa', 'CsaV3_UNG023130' => 'csa', 'CSS0007726' => 'camsi', 'CSS0016433' => 'camsi', 'CSS0017656' => 'camsi', 'CSS0025364' => 'camsi', 'CSS0027582' => 'camsi', 'CSS0047288' => 'camsi', 'CSS0049950' => 'camsi', 'DCAR_003843' => 'dca', 'DCAR_007052' => 'dca', 'DCAR_020884' => 'dca', 'DCAR_021730' => 'dca', 'DCAR_024423' => 'dca', 'DCAR_026509' => 'dca', 'DCAR_031158' => 'dca', 'Dinv14728' => 'din', 'Dinv15219' => 'din', 'Dinv25728' => 'din', 'Dinv33428' => 'din', 'Dinv36489' => 'din', 'Dinv41486' => 'din', 'Duzib147G0469' => 'dzi', 'Duzib168G0060' => 'dzi', 'Duzib187G1215' => 'dzi', 'Duzib248G0692' => 'dzi', 'Duzib251G0767' => 'dzi', 'Duzib264G0446' => 'dzi', 'Duzib268G0691' => 'dzi', 'ECA232G4767' => 'eca', 'ECA233G2838' => 'eca', 'ECA234G0391' => 'eca', 'ECA234G0857' => 'eca', 'ECA236G1593' => 'eca', 'ECA238G0565' => 'eca', 'ECA246G1027' => 'eca', 'ECA246G3223' => 'eca', 'ECA246G3470' => 'eca', 'EL10Ac6g13829' => 'bvu', 'EL10Ac6g14093' => 'bvu', 'EL10Ac8g18707' => 'bvu', 'Eucgr.C01369' => 'egr', 'Eucgr.H02492' => 'egr', 'Eucgr.I01733' => 'egr', 'Eucgr.J02255' => 'egr', 'Eucgr.J02257' => 'egr', 'Eucgr.J02258' => 'egr', 'FAN02G1601' => 'fan', 'FAN03G1586' => 'fan', 'FAN03G2986' => 'fan', 'FAN05G4837' => 'fan', 'FAN06G0146' => 'fan', 'FAN07G0858' => 'fan', 'FAN09G3179' => 'fan', 'FAN10G0669' => 'fan', 'FAN12G2358' => 'fan', 'FAN14G4198' => 'fan', 'FAN14G5112' => 'fan', 'FAN17G0342' => 'fan', 'FAN19G0342' => 'fan', 'FAN19G0962' => 'fan', 'FAN19G1101' => 'fan', 'FAN19G1872' => 'fan', 'FAN22G0356' => 'fan', 'FAN23G0744' => 'fan', 'FAN23G1914' => 'fan', 'FAN26G0032' => 'fan', 'FAN28G0625' => 'fan', 'FvH4_1g02710' => 'fve', 'FvH4_1g02720' => 'fve', 'FvH4_4g25670' => 'fve', 'FvH4_6g51700' => 'fve', 'FvH4_7g20170' => 'fve', 'Glyma.05G175000' => 'gma', 'Glyma.08G132300' => 'gma', 'Glyma.11G243000' => 'gma', 'Glyma.13G158900' => 'gma', 'Glyma.17G112400' => 'gma', 'Glyma.18G014100' => 'gma', 'Glyma.19G003100' => 'gma', 'Glyma.19G056500' => 'gma', 'Gohir.A01G158900' => 'ghi', 'Gohir.A05G312600' => 'ghi', 'Gohir.A05G354900' => 'ghi', 'Gohir.A07G037200' => 'ghi', 'Gohir.A09G030000' => 'ghi', 'Gohir.A12G145200' => 'ghi', 'Gohir.D01G151500' => 'ghi', 'Gohir.D04G058300' => 'ghi', 'Gohir.D05G314100' => 'ghi', 'Gohir.D07G041400' => 'ghi', 'Gohir.D09G029700' => 'ghi', 'Gohir.D12G149700' => 'ghi', 'Gorai.001G043800' => 'gra', 'Gorai.002G187800' => 'gra', 'Gorai.006G034700' => 'gra', 'Gorai.008G161200' => 'gra', 'Gorai.009G335700' => 'gra', 'Gorai.012G065000' => 'gra', 'GSVIVG01000535001' => 'vvi', 'GSVIVG01015572001' => 'vvi', 'GSVIVG01032386001' => 'vvi', 'HanXRQChr05g0138531' => 'han', 'HanXRQChr06g0174391' => 'han', 'HanXRQChr07g0199021' => 'han', 'HanXRQChr08g0208211' => 'han', 'HanXRQChr09g0255471' => 'han', 'HanXRQChr10g0315791' => 'han', 'HanXRQChr12g0371991' => 'han', 'HanXRQChr15g0475251' => 'han', 'HanXRQChr17g0540001' => 'han', 'HanXRQChr17g0548631' => 'han', 'HanXRQChr17g0569561' => 'han', 'Haze_12256' => 'cav', 'Haze_14756' => 'cav', 'Haze_25528' => 'cav', 'Hma1.2p1_0079F.1_g041020' => 'hma', 'Hma1.2p1_0818F.1_g223260' => 'hma', 'Hma1.2p1_1747F.1_g300530' => 'hma', 'HPP92_004607' => 'vpl', 'HPP92_004608' => 'vpl', 'HPP92_006181' => 'vpl', 'HPP92_012192' => 'vpl', 'HPP92_015680' => 'vpl', 'HPP92_020249' => 'vpl', 'HPP92_021376' => 'vpl', 'HPP92_024275' => 'vpl', 'Hund06031' => 'sun', 'Hund25391' => 'sun', 'Lalb_Chr07g0185371' => 'lal', 'Lalb_Chr07g0185381' => 'lal', 'Lalb_Chr12g0204011' => 'lal', 'Lalb_Chr13g0301671' => 'lal', 'Lalb_Chr14g0362851' => 'lal', 'Lalb_Chr24g0403581' => 'lal', 'Lj1g0000233' => 'lja', 'Lj2g0018120' => 'lja', 'Lj3C621T0' => 'lonja', 'Lj3P1059T14' => 'lonja', 'Lj3P611T9' => 'lonja', 'Lj3P614T13' => 'lonja', 'Lj3P615T5' => 'lonja', 'Lj4g0012315' => 'lja', 'Lj4g0026182' => 'lja', 'Lj6P813T16' => 'lonja', 'Lj7C427T7' => 'lonja', 'Lj7C427T8' => 'lonja', 'Lj7P600T41' => 'lonja', 'Lju41C42G17' => 'lonja', 'Lsat_1_v5_gn_0_47300' => 'lsa', 'Lsat_1_v5_gn_2_91280' => 'lsa', 'Lsat_1_v5_gn_3_30561' => 'lsa', 'Lsat_1_v5_gn_4_184321' => 'lsa', 'Lsat_1_v5_gn_4_4041' => 'lsa', 'Lsat_1_v5_gn_5_92000' => 'lsa', 'Lsat_1_v5_gn_8_152940' => 'lsa', 'Lsat_1_v5_gn_8_62401' => 'lsa', 'Manes.06G055900' => 'mes', 'Manes.12G022200' => 'mes', 'Manes.13G023300' => 'mes', 'Manes.14G115000' => 'mes', 'Manes.15G151700' => 'mes', 'Manes.17G111300' => 'mes', 'Mapoly0226s0009' => 'mpo', 'MBI02_g25363_MAGBIO' => 'mbi', 'MBI06_g00027_MAGBIO' => 'mbi', 'MBI10_g13034_MAGBIO' => 'mbi', 'MD09G1023400' => 'mdo', 'MD13G1100100' => 'mdo', 'MD15G1169200' => 'mdo', 'MD16G1101100' => 'mdo', 'MD17G1022900' => 'mdo', 'Medtr3g096150' => 'mtr', 'Medtr4g115070' => 'mtr', 'Medtr7g033325' => 'mtr', 'Medtr8g089840' => 'mtr', 'MELO3C010319.2' => 'cme', 'MELO3C011944.2' => 'cme', 'MELO3C021589.2' => 'cme', 'Migut.E00207' => 'egut', 'Migut.H00067' => 'egut', 'Migut.K00433' => 'egut', 'Migut.K00606' => 'egut', 'Migut.K01410' => 'egut', 'MSTRG.13347' => 'ama', 'MSTRG.24045' => 'ama', 'MSTRG.2428' => 'ama', 'MSTRG.26410' => 'ama', 'MSTRG.3139' => 'ama', 'MSTRG.3286' => 'ama', 'MSTRG.563' => 'ama', 'MSTRG.7941' => 'ama', 'Nitab4.5_0000028g0060' => 'nta', 'Nitab4.5_0000065g0260' => 'nta', 'Nitab4.5_0000112g0060' => 'nta', 'Nitab4.5_0000489g0120' => 'nta', 'Nitab4.5_0001776g0050' => 'nta', 'Nitab4.5_0001854g0010' => 'nta', 'Nitab4.5_0001860g0020' => 'nta', 'Nitab4.5_0004352g0010' => 'nta', 'Nitab4.5_0008716g0020' => 'nta', 'Nitab4.5_0008922g0010' => 'nta', 'Nn3g16693' => 'nnu', 'Nn4g22596' => 'nnu', 'Nn7g37639' => 'nnu', 'Oeu001701.1' => 'oeu', 'Oeu018149.1' => 'oeu', 'Oeu026220.1' => 'oeu', 'Oeu038635.1' => 'oeu', 'Oeu049176.1' => 'oeu', 'Oeu056706.1' => 'oeu', 'Oeu056937.1' => 'oeu', 'Oeu057540.1' => 'oeu', 'Os02g0594900' => 'osa', 'Os02g0595100' => 'osa', 'Os04g0477500' => 'osa', 'Os12g0611900' => 'osa', 'Peaxi162Scf00076g00020' => 'pax', 'Peaxi162Scf00128g00217' => 'pax', 'Peaxi162Scf00129g01640' => 'pax', 'Peaxi162Scf00669g00007' => 'pax', 'Peaxi162Scf00700g00421' => 'pax', 'Peaxi162Scf00801g00038' => 'pax', 'Peaxi162Scf00891g00025' => 'pax', 'PGR083G0909' => 'pgr', 'PGR119G1005' => 'pgr', 'PGR142G2236' => 'pgr', 'PGR142G3388' => 'pgr', 'PGSC0003DMG400004514' => 'stu', 'PGSC0003DMG400012635' => 'stu', 'PGSC0003DMG400015730' => 'stu', 'PGSC0003DMG400018611' => 'stu', 'PGSC0003DMG400030897' => 'stu', 'Phvul.001G254800' => 'pvu', 'Phvul.002G260100' => 'pvu', 'Phvul.003G167600' => 'pvu', 'Phvul.004G005100' => 'pvu', 'Potri.001G343600' => 'ptr', 'Potri.006G066700' => 'ptr', 'Potri.008G186000' => 'ptr', 'Potri.010G046900' => 'ptr', 'Potri.018G127900' => 'ptr', 'Pp3c20_17750' => 'ppa', 'Pp3c24_4380' => 'ppa', 'Prupe.1G245800' => 'ppe', 'Prupe.3G293400' => 'ppe', 'Prupe.7G247400' => 'ppe', 'Psat0s145g0120' => 'psa', 'Psat0s595g0040' => 'psa', 'Psat0s595g0120' => 'psa', 'Psat3g175040' => 'psa', 'Psat7g058120' => 'psa', 'PSO017G0428' => 'pso', 'PSO063G7510' => 'pso', 'PSO067G0046' => 'pso', 'PSO478G1073' => 'pso', 'PSO675G3677' => 'pso', 'PSO675G6558' => 'pso', 'PSO675G7520' => 'pso', 'PSO675G8959' => 'pso', 'QL02p074089' => 'qlo', 'QL02p089614' => 'qlo', 'QL03p057736' => 'qlo', 'RcHm_v2.0_Chr1g0364131' => 'rch', 'RcHm_v2.0_Chr2g0087801' => 'rch', 'RcHm_v2.0_Chr2g0087821' => 'rch', 'RcHm_v2.0_Chr2g0173231' => 'rch', 'RcHm_v2.0_Chr4g0433111' => 'rch', 'Rhsim03G0250300' => 'rsi', 'Rhsim08G0048400' => 'rsi', 'Rhsim10G0014800' => 'rsi', 'Rhsim12G0040100' => 'rsi', 'Rhsim12G0109700' => 'rsi', 'Sabra06G0049600' => 'sbr', 'Sabra08G0141000' => 'sbr', 'Sabra10G0021400' => 'sbr', 'Sabra16G0222900' => 'sbr', 'Sabra18G0108600' => 'sbr', 'SalBow1G0433' => 'sbo', 'SalBow1G2038' => 'sbo', 'SalBow1G5003' => 'sbo', 'SalBow7G1197' => 'sbo', 'SalBow8G3506' => 'sbo', 'Sc03g0007300' => 'sci', 'Sc11g0000950' => 'sci', 'Sc14g0008750' => 'sci', 'Sc18g0000420' => 'sci', 'Sed0006754' => 'sed', 'Sed0008741' => 'sed', 'Sed0017172' => 'sed', 'Sed0018925' => 'sed', 'Sed0023326' => 'sed', 'Sed0025909' => 'sed', 'SEGI_05333' => 'sgi', 'SEGI_10362' => 'sgi', 'SEGI_13380' => 'sgi', 'SEGI_24306' => 'sgi', 'SEGI_29077' => 'sgi', 'SEGI_29095' => 'sgi', 'SEGI_36534' => 'sgi', 'SEGI_37506' => 'sgi', 'SEGI_38321' => 'sgi', 'SGA_v2.0_scaffold307G48031' => 'sas', 'SGA_v2.0_scaffold47G17507' => 'sas', 'SGA_v2.0_scaffold63G21736' => 'sas', 'SGA_v2.0_scaffold87G27070' => 'sas', 'SHI17794' => 'shi', 'SHI28851' => 'shi', 'SMO165G0155' => 'smo', 'SMO340G0217' => 'smo', 'SMO367G1210' => 'smo', 'Solyc02g093430.3' => 'sly', 'Solyc05g013580.4' => 'sly', 'Solyc07g008030.3' => 'sly', 'Solyc12g035470.2' => 'sly', 'Sopen02g038020' => 'spe', 'Sopen05g008490' => 'spe', 'Sopen07g003910' => 'spe', 'Sopen12g015240' => 'spe', 'Sp1g11550' => 'spa', 'Sp2g16710' => 'spa', 'Sp3g00430' => 'spa', 'Sp3g26780' => 'spa', 'Sp5g22900' => 'spa', 'Sp6g29530' => 'spa', 'TAR371G0794' => 'tar', 'TAR374G0164' => 'tar', 'TAR622G0165' => 'tar', 'TAR626G0929' => 'tar', 'TAR629G2155' => 'tar', 'THA.LOC104805282' => 'tha', 'THA.LOC104805363' => 'tha', 'THA.LOC104808968' => 'tha', 'THA.LOC104821093' => 'tha', 'THA.LOC104823953' => 'tha', 'THA.LOC104825562' => 'tha', 'THA.LOC104825665' => 'tha', 'Thecc.02G261400' => 'tca', 'Thecc.04G019200' => 'tca', 'Thecc.09G130400' => 'tca', 'Thhalv10004374m.g' => 'esa', 'Thhalv10007850m.g' => 'esa', 'Thhalv10013782m.g' => 'esa', 'Thhalv10018686m.g' => 'esa', 'Thhalv10020899m.g' => 'esa', 'Thhalv10022755m.g' => 'esa', 'TPR.G23851' => 'tpr', 'TPR.G26500' => 'tpr', 'TPR.G27267' => 'tpr', 'TPR.G32001' => 'tpr', 'TPR.G6251' => 'tpr', 'TPR.G8167' => 'tpr', 'TWI12G1330' => 'twi', 'TWI18G1239' => 'twi', 'TWI34G0979' => 'twi', 'TWI36G0670' => 'twi', 'TWI36G0707' => 'twi', 'TWI56G0233' => 'twi', 'TWI75G1809' => 'twi', 'unitig_21.g20874' => 'ugi', 'unitig_26.g10343' => 'ugi', 'unitig_46.g18392' => 'ugi', 'unitig_52.g17178' => 'ugi', 'unitig_8.g2934' => 'ugi', 'vmacro01122' => 'vma', 'vmacro05875' => 'vma', 'vmacro06147' => 'vma', 'vmacro16191' => 'vma', 'vmacro18293' => 'vma', 'VMungo0251G3707' => 'vmu', 'VMungo0464G1521' => 'vmu', 'VMungo1215G0205' => 'vmu', 'VMungo1383G2484' => 'vmu', 'Zm00001eb079610' => 'zma', 'Zm00001eb135990' => 'zma', 'Zm00001eb183710' => 'zma', 'Zm00001eb246020' => 'zma' ), 'gf_id' => 'HOM05D001124', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001124' ), 'data_identifier' => 'HOM05D001124', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001124', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '548', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02520' => 'bna', 'A03p06630' => 'bna', 'A05p44460' => 'bna', 'A06p08710' => 'bna', 'A06p41090' => 'bna', 'A07p32320' => 'bna', 'A08p32520' => 'bna', 'A09p10360' => 'bna', 'A10p24080' => 'bna', 'Aa31LG11G15250' => 'aar', 'Aa31LG1G1800' => 'aar', 'Aa31LG2G5120' => 'aar', 'Aa31LG2G6070' => 'aar', 'Aa31LG5G10770' => 'aar', 'Aa31sc61G90' => 'aar', 'Actinidia01352' => 'ach', 'Actinidia05983' => 'ach', 'Actinidia08133' => 'ach', 'Actinidia15101' => 'ach', 'Actinidia26379' => 'ach', 'Actinidia35778' => 'ach', 'Actinidia36123' => 'ach', 'Actinidia37436' => 'ach', 'Actinidia38730' => 'ach', 'Ah.02g128210' => 'amhyb', 'Ah.03g132990' => 'amhyb', 'Ah.14g079410' => 'amhyb', 'AL1G24640' => 'aly', 'AL2G26680' => 'aly', 'AL3G10530' => 'aly', 'AL3G45230' => 'aly', 'AL5G15230' => 'aly', 'AL5G16960' => 'aly', 'AL6G25210' => 'aly', 'Aqoxy2G00441' => 'aox', 'Aqoxy3G01236' => 'aox', 'Aqoxy5G03746' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3RQ047' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C7GMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9C8JER' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MBL6KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YXCZ83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZANX40' => 'arhy', 'AT1G12990' => 'ath', 'AT1G67880' => 'ath', 'AT2G13290' => 'ath', 'AT3G01620' => 'ath', 'AT3G26445' => 'ath', 'AT3G27540' => 'ath', 'AT5G14480' => 'ath', 'ATR0824G026' => 'atr', 'ATR1098G019' => 'atr', 'Atru.chr11.2145' => 'acertr', 'Atru.chr2.3636' => 'acertr', 'Atru.chr2.3644' => 'acertr', 'Atru.chr6.2422' => 'acertr', 'Atru.chr7.1112' => 'acertr', 'AUR62005469' => 'cqu', 'AUR62011166' => 'cqu', 'AUR62013319' => 'cqu', 'AUR62024273' => 'cqu', 'AUR62028420' => 'cqu', 'AUR62041942' => 'cqu', 'BcaB01g04969' => 'bca', 'BcaB01g06371' => 'bca', 'BcaB02g11494' => 'bca', 'BcaB03g15382' => 'bca', 'BcaB08g36994' => 'bca', 'BcaC03g13477' => 'bca', 'BcaC03g13478' => 'bca', 'BcaC03g13480' => 'bca', 'BcaC03g13481' => 'bca', 'BcaC03g13486' => 'bca', 'BcaC04g19031' => 'bca', 'BcaC04g23085' => 'bca', 'BcaC05g25094' => 'bca', 'BcaC05g25096' => 'bca', 'BcaC05g25138' => 'bca', 'BcaC05g30416' => 'bca', 'BcaC05g30455' => 'bca', 'BcaC06g30979' => 'bca', 'BcaC06g33805' => 'bca', 'BcaC08g46021' => 'bca', 'BcaNung03154' => 'bca', 'BolC2t06623H' => 'bol', 'BolC2t06632H' => 'bol', 'BolC2t06635H' => 'bol', 'BolC2t06638H' => 'bol', 'BolC3t13266H' => 'bol', 'BolC5t29776H' => 'bol', 'BolC6t38912H' => 'bol', 'BolC7t44183H' => 'bol', 'BolC9t54123H' => 'bol', 'BolC9t59107H' => 'bol', 'BraA02t05221Z' => 'bra', 'BraA03t09996Z' => 'bra', 'BraA05t23210Z' => 'bra', 'BraA06t24068Z' => 'bra', 'BraA06t27032Z' => 'bra', 'BraA08t35176Z' => 'bra', 'BraA09t36680Z' => 'bra', 'BraA10t44471Z' => 'bra', 'C02p06760' => 'bna', 'C02p06890' => 'bna', 'C02p07010' => 'bna', 'C03p07660' => 'bna', 'C05p10300' => 'bna', 'C06p38150' => 'bna', 'C07p36650' => 'bna', 'C08p15770' => 'bna', 'C09p12300' => 'bna', 'C09p62700' => 'bna', 'C09p75040' => 'bna', 'CAN.G13.1' => 'can', 'CAN.G138.4' => 'can', 'CAN.G44.6' => 'can', 'CAN.G473.19' => 'can', 'CANSAT01G0835' => 'cansat', 'CANSAT11G0246' => 'cansat', 'CANSAT11G1766' => 'cansat', 'CANSAT64G1954' => 'cansat', 'CARHR013330' => 'chi', 'CARHR060530' => 'chi', 'CARHR075300' => 'chi', 'CARHR105120' => 'chi', 'CARHR148910' => 'chi', 'CARHR198830' => 'chi', 'Carub.0001s1275' => 'cru', 'Carub.0002s1437' => 'cru', 'Carub.0003s0044' => 'cru', 'Carub.0003s2787' => 'cru', 'Carub.0005s0597' => 'cru', 'Carub.0006s1266' => 'cru', 'Ca_06935_v3' => 'car', 'Ca_13559_v3' => 'car', 'Ca_16941_v3' => 'car', 'Ca_16960_v3' => 'car', 'Ca_17775_v3' => 'car', 'Ca_30464_v3' => 'car', 'Cc06_g08160' => 'ccan', 'Cc07_g01520' => 'ccan', 'Cc11_g15810' => 'ccan', 'CDE02G2840' => 'cde', 'CDE03G0093' => 'cde', 'CDE04G2127' => 'cde', 'CDE07G1857' => 'cde', 'CDE09G1246' => 'cde', 'Cfa003412' => 'cfa', 'Cfa007341' => 'cfa', 'Cfa009220' => 'cfa', 'Ciclev10008737m.g' => 'ccl', 'Ciclev10015565m.g' => 'ccl', 'Ciclev10031761m.g' => 'ccl', 'CiPaw.03G045300' => 'cil', 'CiPaw.03G247200' => 'cil', 'CiPaw.04G029500' => 'cil', 'CiPaw.04G174000' => 'cil', 'CiPaw.05G181200' => 'cil', 'CiPaw.06G067100' => 'cil', 'ClCG05G025800' => 'cla', 'ClCG06G011400' => 'cla', 'ClCG09G019360' => 'cla', 'COL.COLO4_04827' => 'col', 'COL.COLO4_29170' => 'col', 'COL.COLO4_35131' => 'col', 'COL.COLO4_35132' => 'col', 'Cpa.g.sc33.32' => 'cpa', 'Cpa.g.sc46.29' => 'cpa', 'Cpa.g.sc796.1' => 'cpa', 'CsaV3_1G030420' => 'csa', 'CsaV3_5G027050' => 'csa', 'CsaV3_5G031040' => 'csa', 'CsaV3_UNG023130' => 'csa', 'CSS0007726' => 'camsi', 'CSS0016433' => 'camsi', 'CSS0017656' => 'camsi', 'CSS0025364' => 'camsi', 'CSS0027582' => 'camsi', 'CSS0047288' => 'camsi', 'CSS0049950' => 'camsi', 'DCAR_003843' => 'dca', 'DCAR_007052' => 'dca', 'DCAR_020884' => 'dca', 'DCAR_021730' => 'dca', 'DCAR_024423' => 'dca', 'DCAR_026509' => 'dca', 'DCAR_031158' => 'dca', 'Dinv14728' => 'din', 'Dinv15219' => 'din', 'Dinv25728' => 'din', 'Dinv33428' => 'din', 'Dinv36489' => 'din', 'Dinv41486' => 'din', 'Duzib147G0469' => 'dzi', 'Duzib168G0060' => 'dzi', 'Duzib187G1215' => 'dzi', 'Duzib248G0692' => 'dzi', 'Duzib251G0767' => 'dzi', 'Duzib264G0446' => 'dzi', 'Duzib268G0691' => 'dzi', 'ECA232G4767' => 'eca', 'ECA233G2838' => 'eca', 'ECA234G0391' => 'eca', 'ECA234G0857' => 'eca', 'ECA236G1593' => 'eca', 'ECA238G0565' => 'eca', 'ECA246G1027' => 'eca', 'ECA246G3223' => 'eca', 'ECA246G3470' => 'eca', 'EL10Ac6g13829' => 'bvu', 'EL10Ac6g14093' => 'bvu', 'EL10Ac8g18707' => 'bvu', 'Eucgr.C01369' => 'egr', 'Eucgr.H02492' => 'egr', 'Eucgr.I01733' => 'egr', 'Eucgr.J02255' => 'egr', 'Eucgr.J02257' => 'egr', 'Eucgr.J02258' => 'egr', 'FAN02G1601' => 'fan', 'FAN03G1586' => 'fan', 'FAN03G2986' => 'fan', 'FAN05G4837' => 'fan', 'FAN06G0146' => 'fan', 'FAN07G0858' => 'fan', 'FAN09G3179' => 'fan', 'FAN10G0669' => 'fan', 'FAN12G2358' => 'fan', 'FAN14G4198' => 'fan', 'FAN14G5112' => 'fan', 'FAN17G0342' => 'fan', 'FAN19G0342' => 'fan', 'FAN19G0962' => 'fan', 'FAN19G1101' => 'fan', 'FAN19G1872' => 'fan', 'FAN22G0356' => 'fan', 'FAN23G0744' => 'fan', 'FAN23G1914' => 'fan', 'FAN26G0032' => 'fan', 'FAN28G0625' => 'fan', 'FvH4_1g02710' => 'fve', 'FvH4_1g02720' => 'fve', 'FvH4_4g25670' => 'fve', 'FvH4_6g51700' => 'fve', 'FvH4_7g20170' => 'fve', 'Glyma.05G175000' => 'gma', 'Glyma.08G132300' => 'gma', 'Glyma.11G243000' => 'gma', 'Glyma.13G158900' => 'gma', 'Glyma.17G112400' => 'gma', 'Glyma.18G014100' => 'gma', 'Glyma.19G003100' => 'gma', 'Glyma.19G056500' => 'gma', 'Gohir.A01G158900' => 'ghi', 'Gohir.A05G312600' => 'ghi', 'Gohir.A05G354900' => 'ghi', 'Gohir.A07G037200' => 'ghi', 'Gohir.A09G030000' => 'ghi', 'Gohir.A12G145200' => 'ghi', 'Gohir.D01G151500' => 'ghi', 'Gohir.D04G058300' => 'ghi', 'Gohir.D05G314100' => 'ghi', 'Gohir.D07G041400' => 'ghi', 'Gohir.D09G029700' => 'ghi', 'Gohir.D12G149700' => 'ghi', 'Gorai.001G043800' => 'gra', 'Gorai.002G187800' => 'gra', 'Gorai.006G034700' => 'gra', 'Gorai.008G161200' => 'gra', 'Gorai.009G335700' => 'gra', 'Gorai.012G065000' => 'gra', 'GSVIVG01000535001' => 'vvi', 'GSVIVG01015572001' => 'vvi', 'GSVIVG01032386001' => 'vvi', 'HanXRQChr05g0138531' => 'han', 'HanXRQChr06g0174391' => 'han', 'HanXRQChr07g0199021' => 'han', 'HanXRQChr08g0208211' => 'han', 'HanXRQChr09g0255471' => 'han', 'HanXRQChr10g0315791' => 'han', 'HanXRQChr12g0371991' => 'han', 'HanXRQChr15g0475251' => 'han', 'HanXRQChr17g0540001' => 'han', 'HanXRQChr17g0548631' => 'han', 'HanXRQChr17g0569561' => 'han', 'Haze_12256' => 'cav', 'Haze_14756' => 'cav', 'Haze_25528' => 'cav', 'Hma1.2p1_0079F.1_g041020' => 'hma', 'Hma1.2p1_0818F.1_g223260' => 'hma', 'Hma1.2p1_1747F.1_g300530' => 'hma', 'HPP92_004607' => 'vpl', 'HPP92_004608' => 'vpl', 'HPP92_006181' => 'vpl', 'HPP92_012192' => 'vpl', 'HPP92_015680' => 'vpl', 'HPP92_020249' => 'vpl', 'HPP92_021376' => 'vpl', 'HPP92_024275' => 'vpl', 'Hund06031' => 'sun', 'Hund25391' => 'sun', 'Lalb_Chr07g0185371' => 'lal', 'Lalb_Chr07g0185381' => 'lal', 'Lalb_Chr12g0204011' => 'lal', 'Lalb_Chr13g0301671' => 'lal', 'Lalb_Chr14g0362851' => 'lal', 'Lalb_Chr24g0403581' => 'lal', 'Lj1g0000233' => 'lja', 'Lj2g0018120' => 'lja', 'Lj3C621T0' => 'lonja', 'Lj3P1059T14' => 'lonja', 'Lj3P611T9' => 'lonja', 'Lj3P614T13' => 'lonja', 'Lj3P615T5' => 'lonja', 'Lj4g0012315' => 'lja', 'Lj4g0026182' => 'lja', 'Lj6P813T16' => 'lonja', 'Lj7C427T7' => 'lonja', 'Lj7C427T8' => 'lonja', 'Lj7P600T41' => 'lonja', 'Lju41C42G17' => 'lonja', 'Lsat_1_v5_gn_0_47300' => 'lsa', 'Lsat_1_v5_gn_2_91280' => 'lsa', 'Lsat_1_v5_gn_3_30561' => 'lsa', 'Lsat_1_v5_gn_4_184321' => 'lsa', 'Lsat_1_v5_gn_4_4041' => 'lsa', 'Lsat_1_v5_gn_5_92000' => 'lsa', 'Lsat_1_v5_gn_8_152940' => 'lsa', 'Lsat_1_v5_gn_8_62401' => 'lsa', 'Manes.06G055900' => 'mes', 'Manes.12G022200' => 'mes', 'Manes.13G023300' => 'mes', 'Manes.14G115000' => 'mes', 'Manes.15G151700' => 'mes', 'Manes.17G111300' => 'mes', 'Mapoly0226s0009' => 'mpo', 'MBI02_g25363_MAGBIO' => 'mbi', 'MBI06_g00027_MAGBIO' => 'mbi', 'MBI10_g13034_MAGBIO' => 'mbi', 'MD09G1023400' => 'mdo', 'MD13G1100100' => 'mdo', 'MD15G1169200' => 'mdo', 'MD16G1101100' => 'mdo', 'MD17G1022900' => 'mdo', 'Medtr3g096150' => 'mtr', 'Medtr4g115070' => 'mtr', 'Medtr7g033325' => 'mtr', 'Medtr8g089840' => 'mtr', 'MELO3C010319.2' => 'cme', 'MELO3C011944.2' => 'cme', 'MELO3C021589.2' => 'cme', 'Migut.E00207' => 'egut', 'Migut.H00067' => 'egut', 'Migut.K00433' => 'egut', 'Migut.K00606' => 'egut', 'Migut.K01410' => 'egut', 'MSTRG.13347' => 'ama', 'MSTRG.24045' => 'ama', 'MSTRG.2428' => 'ama', 'MSTRG.26410' => 'ama', 'MSTRG.3139' => 'ama', 'MSTRG.3286' => 'ama', 'MSTRG.563' => 'ama', 'MSTRG.7941' => 'ama', 'Nitab4.5_0000028g0060' => 'nta', 'Nitab4.5_0000065g0260' => 'nta', 'Nitab4.5_0000112g0060' => 'nta', 'Nitab4.5_0000489g0120' => 'nta', 'Nitab4.5_0001776g0050' => 'nta', 'Nitab4.5_0001854g0010' => 'nta', 'Nitab4.5_0001860g0020' => 'nta', 'Nitab4.5_0004352g0010' => 'nta', 'Nitab4.5_0008716g0020' => 'nta', 'Nitab4.5_0008922g0010' => 'nta', 'Nn3g16693' => 'nnu', 'Nn4g22596' => 'nnu', 'Nn7g37639' => 'nnu', 'Oeu001701.1' => 'oeu', 'Oeu018149.1' => 'oeu', 'Oeu026220.1' => 'oeu', 'Oeu038635.1' => 'oeu', 'Oeu049176.1' => 'oeu', 'Oeu056706.1' => 'oeu', 'Oeu056937.1' => 'oeu', 'Oeu057540.1' => 'oeu', 'Os02g0594900' => 'osa', 'Os02g0595100' => 'osa', 'Os04g0477500' => 'osa', 'Os12g0611900' => 'osa', 'Peaxi162Scf00076g00020' => 'pax', 'Peaxi162Scf00128g00217' => 'pax', 'Peaxi162Scf00129g01640' => 'pax', 'Peaxi162Scf00669g00007' => 'pax', 'Peaxi162Scf00700g00421' => 'pax', 'Peaxi162Scf00801g00038' => 'pax', 'Peaxi162Scf00891g00025' => 'pax', 'PGR083G0909' => 'pgr', 'PGR119G1005' => 'pgr', 'PGR142G2236' => 'pgr', 'PGR142G3388' => 'pgr', 'PGSC0003DMG400004514' => 'stu', 'PGSC0003DMG400012635' => 'stu', 'PGSC0003DMG400015730' => 'stu', 'PGSC0003DMG400018611' => 'stu', 'PGSC0003DMG400030897' => 'stu', 'Phvul.001G254800' => 'pvu', 'Phvul.002G260100' => 'pvu', 'Phvul.003G167600' => 'pvu', 'Phvul.004G005100' => 'pvu', 'Potri.001G343600' => 'ptr', 'Potri.006G066700' => 'ptr', 'Potri.008G186000' => 'ptr', 'Potri.010G046900' => 'ptr', 'Potri.018G127900' => 'ptr', 'Pp3c20_17750' => 'ppa', 'Pp3c24_4380' => 'ppa', 'Prupe.1G245800' => 'ppe', 'Prupe.3G293400' => 'ppe', 'Prupe.7G247400' => 'ppe', 'Psat0s145g0120' => 'psa', 'Psat0s595g0040' => 'psa', 'Psat0s595g0120' => 'psa', 'Psat3g175040' => 'psa', 'Psat7g058120' => 'psa', 'PSO017G0428' => 'pso', 'PSO063G7510' => 'pso', 'PSO067G0046' => 'pso', 'PSO478G1073' => 'pso', 'PSO675G3677' => 'pso', 'PSO675G6558' => 'pso', 'PSO675G7520' => 'pso', 'PSO675G8959' => 'pso', 'QL02p074089' => 'qlo', 'QL02p089614' => 'qlo', 'QL03p057736' => 'qlo', 'RcHm_v2.0_Chr1g0364131' => 'rch', 'RcHm_v2.0_Chr2g0087801' => 'rch', 'RcHm_v2.0_Chr2g0087821' => 'rch', 'RcHm_v2.0_Chr2g0173231' => 'rch', 'RcHm_v2.0_Chr4g0433111' => 'rch', 'Rhsim03G0250300' => 'rsi', 'Rhsim08G0048400' => 'rsi', 'Rhsim10G0014800' => 'rsi', 'Rhsim12G0040100' => 'rsi', 'Rhsim12G0109700' => 'rsi', 'Sabra06G0049600' => 'sbr', 'Sabra08G0141000' => 'sbr', 'Sabra10G0021400' => 'sbr', 'Sabra16G0222900' => 'sbr', 'Sabra18G0108600' => 'sbr', 'SalBow1G0433' => 'sbo', 'SalBow1G2038' => 'sbo', 'SalBow1G5003' => 'sbo', 'SalBow7G1197' => 'sbo', 'SalBow8G3506' => 'sbo', 'Sc03g0007300' => 'sci', 'Sc11g0000950' => 'sci', 'Sc14g0008750' => 'sci', 'Sc18g0000420' => 'sci', 'Sed0006754' => 'sed', 'Sed0008741' => 'sed', 'Sed0017172' => 'sed', 'Sed0018925' => 'sed', 'Sed0023326' => 'sed', 'Sed0025909' => 'sed', 'SEGI_05333' => 'sgi', 'SEGI_10362' => 'sgi', 'SEGI_13380' => 'sgi', 'SEGI_24306' => 'sgi', 'SEGI_29077' => 'sgi', 'SEGI_29095' => 'sgi', 'SEGI_36534' => 'sgi', 'SEGI_37506' => 'sgi', 'SEGI_38321' => 'sgi', 'SGA_v2.0_scaffold307G48031' => 'sas', 'SGA_v2.0_scaffold47G17507' => 'sas', 'SGA_v2.0_scaffold63G21736' => 'sas', 'SGA_v2.0_scaffold87G27070' => 'sas', 'SHI17794' => 'shi', 'SHI28851' => 'shi', 'SMO165G0155' => 'smo', 'SMO340G0217' => 'smo', 'SMO367G1210' => 'smo', 'Solyc02g093430.3' => 'sly', 'Solyc05g013580.4' => 'sly', 'Solyc07g008030.3' => 'sly', 'Solyc12g035470.2' => 'sly', 'Sopen02g038020' => 'spe', 'Sopen05g008490' => 'spe', 'Sopen07g003910' => 'spe', 'Sopen12g015240' => 'spe', 'Sp1g11550' => 'spa', 'Sp2g16710' => 'spa', 'Sp3g00430' => 'spa', 'Sp3g26780' => 'spa', 'Sp5g22900' => 'spa', 'Sp6g29530' => 'spa', 'TAR371G0794' => 'tar', 'TAR374G0164' => 'tar', 'TAR622G0165' => 'tar', 'TAR626G0929' => 'tar', 'TAR629G2155' => 'tar', 'THA.LOC104805282' => 'tha', 'THA.LOC104805363' => 'tha', 'THA.LOC104808968' => 'tha', 'THA.LOC104821093' => 'tha', 'THA.LOC104823953' => 'tha', 'THA.LOC104825562' => 'tha', 'THA.LOC104825665' => 'tha', 'Thecc.02G261400' => 'tca', 'Thecc.04G019200' => 'tca', 'Thecc.09G130400' => 'tca', 'Thhalv10004374m.g' => 'esa', 'Thhalv10007850m.g' => 'esa', 'Thhalv10013782m.g' => 'esa', 'Thhalv10018686m.g' => 'esa', 'Thhalv10020899m.g' => 'esa', 'Thhalv10022755m.g' => 'esa', 'TPR.G23851' => 'tpr', 'TPR.G26500' => 'tpr', 'TPR.G27267' => 'tpr', 'TPR.G32001' => 'tpr', 'TPR.G6251' => 'tpr', 'TPR.G8167' => 'tpr', 'TWI12G1330' => 'twi', 'TWI18G1239' => 'twi', 'TWI34G0979' => 'twi', 'TWI36G0670' => 'twi', 'TWI36G0707' => 'twi', 'TWI56G0233' => 'twi', 'TWI75G1809' => 'twi', 'unitig_21.g20874' => 'ugi', 'unitig_26.g10343' => 'ugi', 'unitig_46.g18392' => 'ugi', 'unitig_52.g17178' => 'ugi', 'unitig_8.g2934' => 'ugi', 'vmacro01122' => 'vma', 'vmacro05875' => 'vma', 'vmacro06147' => 'vma', 'vmacro16191' => 'vma', 'vmacro18293' => 'vma', 'VMungo0251G3707' => 'vmu', 'VMungo0464G1521' => 'vmu', 'VMungo1215G0205' => 'vmu', 'VMungo1383G2484' => 'vmu', 'Zm00001eb079610' => 'zma', 'Zm00001eb135990' => 'zma', 'Zm00001eb183710' => 'zma', 'Zm00001eb246020' => 'zma' ) $gf_id = 'HOM05D001124' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001124' ) $data_identifier = 'HOM05D001124' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 6, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 7, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 21, 'bol' => (int) 10, 'bra' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 6, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 9, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 21, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 8, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 10, 'lsa' => (int) 8, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 8, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 9, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb246020' $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' => 'HOM05D001124', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '548', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02520' => 'bna', 'A03p06630' => 'bna', 'A05p44460' => 'bna', 'A06p08710' => 'bna', 'A06p41090' => 'bna', 'A07p32320' => 'bna', 'A08p32520' => 'bna', 'A09p10360' => 'bna', 'A10p24080' => 'bna', 'Aa31LG11G15250' => 'aar', 'Aa31LG1G1800' => 'aar', 'Aa31LG2G5120' => 'aar', 'Aa31LG2G6070' => 'aar', 'Aa31LG5G10770' => 'aar', 'Aa31sc61G90' => 'aar', 'Actinidia01352' => 'ach', 'Actinidia05983' => 'ach', 'Actinidia08133' => 'ach', 'Actinidia15101' => 'ach', 'Actinidia26379' => 'ach', 'Actinidia35778' => 'ach', 'Actinidia36123' => 'ach', 'Actinidia37436' => 'ach', 'Actinidia38730' => 'ach', 'Ah.02g128210' => 'amhyb', 'Ah.03g132990' => 'amhyb', 'Ah.14g079410' => 'amhyb', 'AL1G24640' => 'aly', 'AL2G26680' => 'aly', 'AL3G10530' => 'aly', 'AL3G45230' => 'aly', 'AL5G15230' => 'aly', 'AL5G16960' => 'aly', 'AL6G25210' => 'aly', 'Aqoxy2G00441' => 'aox', 'Aqoxy3G01236' => 'aox', 'Aqoxy5G03746' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3RQ047' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C7GMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9C8JER' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MBL6KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YXCZ83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZANX40' => 'arhy', 'AT1G12990' => 'ath', 'AT1G67880' => 'ath', 'AT2G13290' => 'ath', 'AT3G01620' => 'ath', 'AT3G26445' => 'ath', 'AT3G27540' => 'ath', 'AT5G14480' => 'ath', 'ATR0824G026' => 'atr', 'ATR1098G019' => 'atr', 'Atru.chr11.2145' => 'acertr', 'Atru.chr2.3636' => 'acertr', 'Atru.chr2.3644' => 'acertr', 'Atru.chr6.2422' => 'acertr', 'Atru.chr7.1112' => 'acertr', 'AUR62005469' => 'cqu', 'AUR62011166' => 'cqu', 'AUR62013319' => 'cqu', 'AUR62024273' => 'cqu', 'AUR62028420' => 'cqu', 'AUR62041942' => 'cqu', 'BcaB01g04969' => 'bca', 'BcaB01g06371' => 'bca', 'BcaB02g11494' => 'bca', 'BcaB03g15382' => 'bca', 'BcaB08g36994' => 'bca', 'BcaC03g13477' => 'bca', 'BcaC03g13478' => 'bca', 'BcaC03g13480' => 'bca', 'BcaC03g13481' => 'bca', 'BcaC03g13486' => 'bca', 'BcaC04g19031' => 'bca', 'BcaC04g23085' => 'bca', 'BcaC05g25094' => 'bca', 'BcaC05g25096' => 'bca', 'BcaC05g25138' => 'bca', 'BcaC05g30416' => 'bca', 'BcaC05g30455' => 'bca', 'BcaC06g30979' => 'bca', 'BcaC06g33805' => 'bca', 'BcaC08g46021' => 'bca', 'BcaNung03154' => 'bca', 'BolC2t06623H' => 'bol', 'BolC2t06632H' => 'bol', 'BolC2t06635H' => 'bol', 'BolC2t06638H' => 'bol', 'BolC3t13266H' => 'bol', 'BolC5t29776H' => 'bol', 'BolC6t38912H' => 'bol', 'BolC7t44183H' => 'bol', 'BolC9t54123H' => 'bol', 'BolC9t59107H' => 'bol', 'BraA02t05221Z' => 'bra', 'BraA03t09996Z' => 'bra', 'BraA05t23210Z' => 'bra', 'BraA06t24068Z' => 'bra', 'BraA06t27032Z' => 'bra', 'BraA08t35176Z' => 'bra', 'BraA09t36680Z' => 'bra', 'BraA10t44471Z' => 'bra', 'C02p06760' => 'bna', 'C02p06890' => 'bna', 'C02p07010' => 'bna', 'C03p07660' => 'bna', 'C05p10300' => 'bna', 'C06p38150' => 'bna', 'C07p36650' => 'bna', 'C08p15770' => 'bna', 'C09p12300' => 'bna', 'C09p62700' => 'bna', 'C09p75040' => 'bna', 'CAN.G13.1' => 'can', 'CAN.G138.4' => 'can', 'CAN.G44.6' => 'can', 'CAN.G473.19' => 'can', 'CANSAT01G0835' => 'cansat', 'CANSAT11G0246' => 'cansat', 'CANSAT11G1766' => 'cansat', 'CANSAT64G1954' => 'cansat', 'CARHR013330' => 'chi', 'CARHR060530' => 'chi', 'CARHR075300' => 'chi', 'CARHR105120' => 'chi', 'CARHR148910' => 'chi', 'CARHR198830' => 'chi', 'Carub.0001s1275' => 'cru', 'Carub.0002s1437' => 'cru', 'Carub.0003s0044' => 'cru', 'Carub.0003s2787' => 'cru', 'Carub.0005s0597' => 'cru', 'Carub.0006s1266' => 'cru', 'Ca_06935_v3' => 'car', 'Ca_13559_v3' => 'car', 'Ca_16941_v3' => 'car', 'Ca_16960_v3' => 'car', 'Ca_17775_v3' => 'car', 'Ca_30464_v3' => 'car', 'Cc06_g08160' => 'ccan', 'Cc07_g01520' => 'ccan', 'Cc11_g15810' => 'ccan', 'CDE02G2840' => 'cde', 'CDE03G0093' => 'cde', 'CDE04G2127' => 'cde', 'CDE07G1857' => 'cde', 'CDE09G1246' => 'cde', 'Cfa003412' => 'cfa', 'Cfa007341' => 'cfa', 'Cfa009220' => 'cfa', 'Ciclev10008737m.g' => 'ccl', 'Ciclev10015565m.g' => 'ccl', 'Ciclev10031761m.g' => 'ccl', 'CiPaw.03G045300' => 'cil', 'CiPaw.03G247200' => 'cil', 'CiPaw.04G029500' => 'cil', 'CiPaw.04G174000' => 'cil', 'CiPaw.05G181200' => 'cil', 'CiPaw.06G067100' => 'cil', 'ClCG05G025800' => 'cla', 'ClCG06G011400' => 'cla', 'ClCG09G019360' => 'cla', 'COL.COLO4_04827' => 'col', 'COL.COLO4_29170' => 'col', 'COL.COLO4_35131' => 'col', 'COL.COLO4_35132' => 'col', 'Cpa.g.sc33.32' => 'cpa', 'Cpa.g.sc46.29' => 'cpa', 'Cpa.g.sc796.1' => 'cpa', 'CsaV3_1G030420' => 'csa', 'CsaV3_5G027050' => 'csa', 'CsaV3_5G031040' => 'csa', 'CsaV3_UNG023130' => 'csa', 'CSS0007726' => 'camsi', 'CSS0016433' => 'camsi', 'CSS0017656' => 'camsi', 'CSS0025364' => 'camsi', 'CSS0027582' => 'camsi', 'CSS0047288' => 'camsi', 'CSS0049950' => 'camsi', 'DCAR_003843' => 'dca', 'DCAR_007052' => 'dca', 'DCAR_020884' => 'dca', 'DCAR_021730' => 'dca', 'DCAR_024423' => 'dca', 'DCAR_026509' => 'dca', 'DCAR_031158' => 'dca', 'Dinv14728' => 'din', 'Dinv15219' => 'din', 'Dinv25728' => 'din', 'Dinv33428' => 'din', 'Dinv36489' => 'din', 'Dinv41486' => 'din', 'Duzib147G0469' => 'dzi', 'Duzib168G0060' => 'dzi', 'Duzib187G1215' => 'dzi', 'Duzib248G0692' => 'dzi', 'Duzib251G0767' => 'dzi', 'Duzib264G0446' => 'dzi', 'Duzib268G0691' => 'dzi', 'ECA232G4767' => 'eca', 'ECA233G2838' => 'eca', 'ECA234G0391' => 'eca', 'ECA234G0857' => 'eca', 'ECA236G1593' => 'eca', 'ECA238G0565' => 'eca', 'ECA246G1027' => 'eca', 'ECA246G3223' => 'eca', 'ECA246G3470' => 'eca', 'EL10Ac6g13829' => 'bvu', 'EL10Ac6g14093' => 'bvu', 'EL10Ac8g18707' => 'bvu', 'Eucgr.C01369' => 'egr', 'Eucgr.H02492' => 'egr', 'Eucgr.I01733' => 'egr', 'Eucgr.J02255' => 'egr', 'Eucgr.J02257' => 'egr', 'Eucgr.J02258' => 'egr', 'FAN02G1601' => 'fan', 'FAN03G1586' => 'fan', 'FAN03G2986' => 'fan', 'FAN05G4837' => 'fan', 'FAN06G0146' => 'fan', 'FAN07G0858' => 'fan', 'FAN09G3179' => 'fan', 'FAN10G0669' => 'fan', 'FAN12G2358' => 'fan', 'FAN14G4198' => 'fan', 'FAN14G5112' => 'fan', 'FAN17G0342' => 'fan', 'FAN19G0342' => 'fan', 'FAN19G0962' => 'fan', 'FAN19G1101' => 'fan', 'FAN19G1872' => 'fan', 'FAN22G0356' => 'fan', 'FAN23G0744' => 'fan', 'FAN23G1914' => 'fan', 'FAN26G0032' => 'fan', 'FAN28G0625' => 'fan', 'FvH4_1g02710' => 'fve', 'FvH4_1g02720' => 'fve', 'FvH4_4g25670' => 'fve', 'FvH4_6g51700' => 'fve', 'FvH4_7g20170' => 'fve', 'Glyma.05G175000' => 'gma', 'Glyma.08G132300' => 'gma', 'Glyma.11G243000' => 'gma', 'Glyma.13G158900' => 'gma', 'Glyma.17G112400' => 'gma', 'Glyma.18G014100' => 'gma', 'Glyma.19G003100' => 'gma', 'Glyma.19G056500' => 'gma', 'Gohir.A01G158900' => 'ghi', 'Gohir.A05G312600' => 'ghi', 'Gohir.A05G354900' => 'ghi', 'Gohir.A07G037200' => 'ghi', 'Gohir.A09G030000' => 'ghi', 'Gohir.A12G145200' => 'ghi', 'Gohir.D01G151500' => 'ghi', 'Gohir.D04G058300' => 'ghi', 'Gohir.D05G314100' => 'ghi', 'Gohir.D07G041400' => 'ghi', 'Gohir.D09G029700' => 'ghi', 'Gohir.D12G149700' => 'ghi', 'Gorai.001G043800' => 'gra', 'Gorai.002G187800' => 'gra', 'Gorai.006G034700' => 'gra', 'Gorai.008G161200' => 'gra', 'Gorai.009G335700' => 'gra', 'Gorai.012G065000' => 'gra', 'GSVIVG01000535001' => 'vvi', 'GSVIVG01015572001' => 'vvi', 'GSVIVG01032386001' => 'vvi', 'HanXRQChr05g0138531' => 'han', 'HanXRQChr06g0174391' => 'han', 'HanXRQChr07g0199021' => 'han', 'HanXRQChr08g0208211' => 'han', 'HanXRQChr09g0255471' => 'han', 'HanXRQChr10g0315791' => 'han', 'HanXRQChr12g0371991' => 'han', 'HanXRQChr15g0475251' => 'han', 'HanXRQChr17g0540001' => 'han', 'HanXRQChr17g0548631' => 'han', 'HanXRQChr17g0569561' => 'han', 'Haze_12256' => 'cav', 'Haze_14756' => 'cav', 'Haze_25528' => 'cav', 'Hma1.2p1_0079F.1_g041020' => 'hma', 'Hma1.2p1_0818F.1_g223260' => 'hma', 'Hma1.2p1_1747F.1_g300530' => 'hma', 'HPP92_004607' => 'vpl', 'HPP92_004608' => 'vpl', 'HPP92_006181' => 'vpl', 'HPP92_012192' => 'vpl', 'HPP92_015680' => 'vpl', 'HPP92_020249' => 'vpl', 'HPP92_021376' => 'vpl', 'HPP92_024275' => 'vpl', 'Hund06031' => 'sun', 'Hund25391' => 'sun', 'Lalb_Chr07g0185371' => 'lal', 'Lalb_Chr07g0185381' => 'lal', 'Lalb_Chr12g0204011' => 'lal', 'Lalb_Chr13g0301671' => 'lal', 'Lalb_Chr14g0362851' => 'lal', 'Lalb_Chr24g0403581' => 'lal', 'Lj1g0000233' => 'lja', 'Lj2g0018120' => 'lja', 'Lj3C621T0' => 'lonja', 'Lj3P1059T14' => 'lonja', 'Lj3P611T9' => 'lonja', 'Lj3P614T13' => 'lonja', 'Lj3P615T5' => 'lonja', 'Lj4g0012315' => 'lja', 'Lj4g0026182' => 'lja', 'Lj6P813T16' => 'lonja', 'Lj7C427T7' => 'lonja', 'Lj7C427T8' => 'lonja', 'Lj7P600T41' => 'lonja', 'Lju41C42G17' => 'lonja', 'Lsat_1_v5_gn_0_47300' => 'lsa', 'Lsat_1_v5_gn_2_91280' => 'lsa', 'Lsat_1_v5_gn_3_30561' => 'lsa', 'Lsat_1_v5_gn_4_184321' => 'lsa', 'Lsat_1_v5_gn_4_4041' => 'lsa', 'Lsat_1_v5_gn_5_92000' => 'lsa', 'Lsat_1_v5_gn_8_152940' => 'lsa', 'Lsat_1_v5_gn_8_62401' => 'lsa', 'Manes.06G055900' => 'mes', 'Manes.12G022200' => 'mes', 'Manes.13G023300' => 'mes', 'Manes.14G115000' => 'mes', 'Manes.15G151700' => 'mes', 'Manes.17G111300' => 'mes', 'Mapoly0226s0009' => 'mpo', 'MBI02_g25363_MAGBIO' => 'mbi', 'MBI06_g00027_MAGBIO' => 'mbi', 'MBI10_g13034_MAGBIO' => 'mbi', 'MD09G1023400' => 'mdo', 'MD13G1100100' => 'mdo', 'MD15G1169200' => 'mdo', 'MD16G1101100' => 'mdo', 'MD17G1022900' => 'mdo', 'Medtr3g096150' => 'mtr', 'Medtr4g115070' => 'mtr', 'Medtr7g033325' => 'mtr', 'Medtr8g089840' => 'mtr', 'MELO3C010319.2' => 'cme', 'MELO3C011944.2' => 'cme', 'MELO3C021589.2' => 'cme', 'Migut.E00207' => 'egut', 'Migut.H00067' => 'egut', 'Migut.K00433' => 'egut', 'Migut.K00606' => 'egut', 'Migut.K01410' => 'egut', 'MSTRG.13347' => 'ama', 'MSTRG.24045' => 'ama', 'MSTRG.2428' => 'ama', 'MSTRG.26410' => 'ama', 'MSTRG.3139' => 'ama', 'MSTRG.3286' => 'ama', 'MSTRG.563' => 'ama', 'MSTRG.7941' => 'ama', 'Nitab4.5_0000028g0060' => 'nta', 'Nitab4.5_0000065g0260' => 'nta', 'Nitab4.5_0000112g0060' => 'nta', 'Nitab4.5_0000489g0120' => 'nta', 'Nitab4.5_0001776g0050' => 'nta', 'Nitab4.5_0001854g0010' => 'nta', 'Nitab4.5_0001860g0020' => 'nta', 'Nitab4.5_0004352g0010' => 'nta', 'Nitab4.5_0008716g0020' => 'nta', 'Nitab4.5_0008922g0010' => 'nta', 'Nn3g16693' => 'nnu', 'Nn4g22596' => 'nnu', 'Nn7g37639' => 'nnu', 'Oeu001701.1' => 'oeu', 'Oeu018149.1' => 'oeu', 'Oeu026220.1' => 'oeu', 'Oeu038635.1' => 'oeu', 'Oeu049176.1' => 'oeu', 'Oeu056706.1' => 'oeu', 'Oeu056937.1' => 'oeu', 'Oeu057540.1' => 'oeu', 'Os02g0594900' => 'osa', 'Os02g0595100' => 'osa', 'Os04g0477500' => 'osa', 'Os12g0611900' => 'osa', 'Peaxi162Scf00076g00020' => 'pax', 'Peaxi162Scf00128g00217' => 'pax', 'Peaxi162Scf00129g01640' => 'pax', 'Peaxi162Scf00669g00007' => 'pax', 'Peaxi162Scf00700g00421' => 'pax', 'Peaxi162Scf00801g00038' => 'pax', 'Peaxi162Scf00891g00025' => 'pax', 'PGR083G0909' => 'pgr', 'PGR119G1005' => 'pgr', 'PGR142G2236' => 'pgr', 'PGR142G3388' => 'pgr', 'PGSC0003DMG400004514' => 'stu', 'PGSC0003DMG400012635' => 'stu', 'PGSC0003DMG400015730' => 'stu', 'PGSC0003DMG400018611' => 'stu', 'PGSC0003DMG400030897' => 'stu', 'Phvul.001G254800' => 'pvu', 'Phvul.002G260100' => 'pvu', 'Phvul.003G167600' => 'pvu', 'Phvul.004G005100' => 'pvu', 'Potri.001G343600' => 'ptr', 'Potri.006G066700' => 'ptr', 'Potri.008G186000' => 'ptr', 'Potri.010G046900' => 'ptr', 'Potri.018G127900' => 'ptr', 'Pp3c20_17750' => 'ppa', 'Pp3c24_4380' => 'ppa', 'Prupe.1G245800' => 'ppe', 'Prupe.3G293400' => 'ppe', 'Prupe.7G247400' => 'ppe', 'Psat0s145g0120' => 'psa', 'Psat0s595g0040' => 'psa', 'Psat0s595g0120' => 'psa', 'Psat3g175040' => 'psa', 'Psat7g058120' => 'psa', 'PSO017G0428' => 'pso', 'PSO063G7510' => 'pso', 'PSO067G0046' => 'pso', 'PSO478G1073' => 'pso', 'PSO675G3677' => 'pso', 'PSO675G6558' => 'pso', 'PSO675G7520' => 'pso', 'PSO675G8959' => 'pso', 'QL02p074089' => 'qlo', 'QL02p089614' => 'qlo', 'QL03p057736' => 'qlo', 'RcHm_v2.0_Chr1g0364131' => 'rch', 'RcHm_v2.0_Chr2g0087801' => 'rch', 'RcHm_v2.0_Chr2g0087821' => 'rch', 'RcHm_v2.0_Chr2g0173231' => 'rch', 'RcHm_v2.0_Chr4g0433111' => 'rch', 'Rhsim03G0250300' => 'rsi', 'Rhsim08G0048400' => 'rsi', 'Rhsim10G0014800' => 'rsi', 'Rhsim12G0040100' => 'rsi', 'Rhsim12G0109700' => 'rsi', 'Sabra06G0049600' => 'sbr', 'Sabra08G0141000' => 'sbr', 'Sabra10G0021400' => 'sbr', 'Sabra16G0222900' => 'sbr', 'Sabra18G0108600' => 'sbr', 'SalBow1G0433' => 'sbo', 'SalBow1G2038' => 'sbo', 'SalBow1G5003' => 'sbo', 'SalBow7G1197' => 'sbo', 'SalBow8G3506' => 'sbo', 'Sc03g0007300' => 'sci', 'Sc11g0000950' => 'sci', 'Sc14g0008750' => 'sci', 'Sc18g0000420' => 'sci', 'Sed0006754' => 'sed', 'Sed0008741' => 'sed', 'Sed0017172' => 'sed', 'Sed0018925' => 'sed', 'Sed0023326' => 'sed', 'Sed0025909' => 'sed', 'SEGI_05333' => 'sgi', 'SEGI_10362' => 'sgi', 'SEGI_13380' => 'sgi', 'SEGI_24306' => 'sgi', 'SEGI_29077' => 'sgi', 'SEGI_29095' => 'sgi', 'SEGI_36534' => 'sgi', 'SEGI_37506' => 'sgi', 'SEGI_38321' => 'sgi', 'SGA_v2.0_scaffold307G48031' => 'sas', 'SGA_v2.0_scaffold47G17507' => 'sas', 'SGA_v2.0_scaffold63G21736' => 'sas', 'SGA_v2.0_scaffold87G27070' => 'sas', 'SHI17794' => 'shi', 'SHI28851' => 'shi', 'SMO165G0155' => 'smo', 'SMO340G0217' => 'smo', 'SMO367G1210' => 'smo', 'Solyc02g093430.3' => 'sly', 'Solyc05g013580.4' => 'sly', 'Solyc07g008030.3' => 'sly', 'Solyc12g035470.2' => 'sly', 'Sopen02g038020' => 'spe', 'Sopen05g008490' => 'spe', 'Sopen07g003910' => 'spe', 'Sopen12g015240' => 'spe', 'Sp1g11550' => 'spa', 'Sp2g16710' => 'spa', 'Sp3g00430' => 'spa', 'Sp3g26780' => 'spa', 'Sp5g22900' => 'spa', 'Sp6g29530' => 'spa', 'TAR371G0794' => 'tar', 'TAR374G0164' => 'tar', 'TAR622G0165' => 'tar', 'TAR626G0929' => 'tar', 'TAR629G2155' => 'tar', 'THA.LOC104805282' => 'tha', 'THA.LOC104805363' => 'tha', 'THA.LOC104808968' => 'tha', 'THA.LOC104821093' => 'tha', 'THA.LOC104823953' => 'tha', 'THA.LOC104825562' => 'tha', 'THA.LOC104825665' => 'tha', 'Thecc.02G261400' => 'tca', 'Thecc.04G019200' => 'tca', 'Thecc.09G130400' => 'tca', 'Thhalv10004374m.g' => 'esa', 'Thhalv10007850m.g' => 'esa', 'Thhalv10013782m.g' => 'esa', 'Thhalv10018686m.g' => 'esa', 'Thhalv10020899m.g' => 'esa', 'Thhalv10022755m.g' => 'esa', 'TPR.G23851' => 'tpr', 'TPR.G26500' => 'tpr', 'TPR.G27267' => 'tpr', 'TPR.G32001' => 'tpr', 'TPR.G6251' => 'tpr', 'TPR.G8167' => 'tpr', 'TWI12G1330' => 'twi', 'TWI18G1239' => 'twi', 'TWI34G0979' => 'twi', 'TWI36G0670' => 'twi', 'TWI36G0707' => 'twi', 'TWI56G0233' => 'twi', 'TWI75G1809' => 'twi', 'unitig_21.g20874' => 'ugi', 'unitig_26.g10343' => 'ugi', 'unitig_46.g18392' => 'ugi', 'unitig_52.g17178' => 'ugi', 'unitig_8.g2934' => 'ugi', 'vmacro01122' => 'vma', 'vmacro05875' => 'vma', 'vmacro06147' => 'vma', 'vmacro16191' => 'vma', 'vmacro18293' => 'vma', 'VMungo0251G3707' => 'vmu', 'VMungo0464G1521' => 'vmu', 'VMungo1215G0205' => 'vmu', 'VMungo1383G2484' => 'vmu', 'Zm00001eb079610' => 'zma', 'Zm00001eb135990' => 'zma', 'Zm00001eb183710' => 'zma', 'Zm00001eb246020' => 'zma' ), 'gf_id' => 'HOM05D001124', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001124' ), 'data_identifier' => 'HOM05D001124', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001124', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '548', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02520' => 'bna', 'A03p06630' => 'bna', 'A05p44460' => 'bna', 'A06p08710' => 'bna', 'A06p41090' => 'bna', 'A07p32320' => 'bna', 'A08p32520' => 'bna', 'A09p10360' => 'bna', 'A10p24080' => 'bna', 'Aa31LG11G15250' => 'aar', 'Aa31LG1G1800' => 'aar', 'Aa31LG2G5120' => 'aar', 'Aa31LG2G6070' => 'aar', 'Aa31LG5G10770' => 'aar', 'Aa31sc61G90' => 'aar', 'Actinidia01352' => 'ach', 'Actinidia05983' => 'ach', 'Actinidia08133' => 'ach', 'Actinidia15101' => 'ach', 'Actinidia26379' => 'ach', 'Actinidia35778' => 'ach', 'Actinidia36123' => 'ach', 'Actinidia37436' => 'ach', 'Actinidia38730' => 'ach', 'Ah.02g128210' => 'amhyb', 'Ah.03g132990' => 'amhyb', 'Ah.14g079410' => 'amhyb', 'AL1G24640' => 'aly', 'AL2G26680' => 'aly', 'AL3G10530' => 'aly', 'AL3G45230' => 'aly', 'AL5G15230' => 'aly', 'AL5G16960' => 'aly', 'AL6G25210' => 'aly', 'Aqoxy2G00441' => 'aox', 'Aqoxy3G01236' => 'aox', 'Aqoxy5G03746' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3RQ047' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C7GMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9C8JER' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MBL6KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YXCZ83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZANX40' => 'arhy', 'AT1G12990' => 'ath', 'AT1G67880' => 'ath', 'AT2G13290' => 'ath', 'AT3G01620' => 'ath', 'AT3G26445' => 'ath', 'AT3G27540' => 'ath', 'AT5G14480' => 'ath', 'ATR0824G026' => 'atr', 'ATR1098G019' => 'atr', 'Atru.chr11.2145' => 'acertr', 'Atru.chr2.3636' => 'acertr', 'Atru.chr2.3644' => 'acertr', 'Atru.chr6.2422' => 'acertr', 'Atru.chr7.1112' => 'acertr', 'AUR62005469' => 'cqu', 'AUR62011166' => 'cqu', 'AUR62013319' => 'cqu', 'AUR62024273' => 'cqu', 'AUR62028420' => 'cqu', 'AUR62041942' => 'cqu', 'BcaB01g04969' => 'bca', 'BcaB01g06371' => 'bca', 'BcaB02g11494' => 'bca', 'BcaB03g15382' => 'bca', 'BcaB08g36994' => 'bca', 'BcaC03g13477' => 'bca', 'BcaC03g13478' => 'bca', 'BcaC03g13480' => 'bca', 'BcaC03g13481' => 'bca', 'BcaC03g13486' => 'bca', 'BcaC04g19031' => 'bca', 'BcaC04g23085' => 'bca', 'BcaC05g25094' => 'bca', 'BcaC05g25096' => 'bca', 'BcaC05g25138' => 'bca', 'BcaC05g30416' => 'bca', 'BcaC05g30455' => 'bca', 'BcaC06g30979' => 'bca', 'BcaC06g33805' => 'bca', 'BcaC08g46021' => 'bca', 'BcaNung03154' => 'bca', 'BolC2t06623H' => 'bol', 'BolC2t06632H' => 'bol', 'BolC2t06635H' => 'bol', 'BolC2t06638H' => 'bol', 'BolC3t13266H' => 'bol', 'BolC5t29776H' => 'bol', 'BolC6t38912H' => 'bol', 'BolC7t44183H' => 'bol', 'BolC9t54123H' => 'bol', 'BolC9t59107H' => 'bol', 'BraA02t05221Z' => 'bra', 'BraA03t09996Z' => 'bra', 'BraA05t23210Z' => 'bra', 'BraA06t24068Z' => 'bra', 'BraA06t27032Z' => 'bra', 'BraA08t35176Z' => 'bra', 'BraA09t36680Z' => 'bra', 'BraA10t44471Z' => 'bra', 'C02p06760' => 'bna', 'C02p06890' => 'bna', 'C02p07010' => 'bna', 'C03p07660' => 'bna', 'C05p10300' => 'bna', 'C06p38150' => 'bna', 'C07p36650' => 'bna', 'C08p15770' => 'bna', 'C09p12300' => 'bna', 'C09p62700' => 'bna', 'C09p75040' => 'bna', 'CAN.G13.1' => 'can', 'CAN.G138.4' => 'can', 'CAN.G44.6' => 'can', 'CAN.G473.19' => 'can', 'CANSAT01G0835' => 'cansat', 'CANSAT11G0246' => 'cansat', 'CANSAT11G1766' => 'cansat', 'CANSAT64G1954' => 'cansat', 'CARHR013330' => 'chi', 'CARHR060530' => 'chi', 'CARHR075300' => 'chi', 'CARHR105120' => 'chi', 'CARHR148910' => 'chi', 'CARHR198830' => 'chi', 'Carub.0001s1275' => 'cru', 'Carub.0002s1437' => 'cru', 'Carub.0003s0044' => 'cru', 'Carub.0003s2787' => 'cru', 'Carub.0005s0597' => 'cru', 'Carub.0006s1266' => 'cru', 'Ca_06935_v3' => 'car', 'Ca_13559_v3' => 'car', 'Ca_16941_v3' => 'car', 'Ca_16960_v3' => 'car', 'Ca_17775_v3' => 'car', 'Ca_30464_v3' => 'car', 'Cc06_g08160' => 'ccan', 'Cc07_g01520' => 'ccan', 'Cc11_g15810' => 'ccan', 'CDE02G2840' => 'cde', 'CDE03G0093' => 'cde', 'CDE04G2127' => 'cde', 'CDE07G1857' => 'cde', 'CDE09G1246' => 'cde', 'Cfa003412' => 'cfa', 'Cfa007341' => 'cfa', 'Cfa009220' => 'cfa', 'Ciclev10008737m.g' => 'ccl', 'Ciclev10015565m.g' => 'ccl', 'Ciclev10031761m.g' => 'ccl', 'CiPaw.03G045300' => 'cil', 'CiPaw.03G247200' => 'cil', 'CiPaw.04G029500' => 'cil', 'CiPaw.04G174000' => 'cil', 'CiPaw.05G181200' => 'cil', 'CiPaw.06G067100' => 'cil', 'ClCG05G025800' => 'cla', 'ClCG06G011400' => 'cla', 'ClCG09G019360' => 'cla', 'COL.COLO4_04827' => 'col', 'COL.COLO4_29170' => 'col', 'COL.COLO4_35131' => 'col', 'COL.COLO4_35132' => 'col', 'Cpa.g.sc33.32' => 'cpa', 'Cpa.g.sc46.29' => 'cpa', 'Cpa.g.sc796.1' => 'cpa', 'CsaV3_1G030420' => 'csa', 'CsaV3_5G027050' => 'csa', 'CsaV3_5G031040' => 'csa', 'CsaV3_UNG023130' => 'csa', 'CSS0007726' => 'camsi', 'CSS0016433' => 'camsi', 'CSS0017656' => 'camsi', 'CSS0025364' => 'camsi', 'CSS0027582' => 'camsi', 'CSS0047288' => 'camsi', 'CSS0049950' => 'camsi', 'DCAR_003843' => 'dca', 'DCAR_007052' => 'dca', 'DCAR_020884' => 'dca', 'DCAR_021730' => 'dca', 'DCAR_024423' => 'dca', 'DCAR_026509' => 'dca', 'DCAR_031158' => 'dca', 'Dinv14728' => 'din', 'Dinv15219' => 'din', 'Dinv25728' => 'din', 'Dinv33428' => 'din', 'Dinv36489' => 'din', 'Dinv41486' => 'din', 'Duzib147G0469' => 'dzi', 'Duzib168G0060' => 'dzi', 'Duzib187G1215' => 'dzi', 'Duzib248G0692' => 'dzi', 'Duzib251G0767' => 'dzi', 'Duzib264G0446' => 'dzi', 'Duzib268G0691' => 'dzi', 'ECA232G4767' => 'eca', 'ECA233G2838' => 'eca', 'ECA234G0391' => 'eca', 'ECA234G0857' => 'eca', 'ECA236G1593' => 'eca', 'ECA238G0565' => 'eca', 'ECA246G1027' => 'eca', 'ECA246G3223' => 'eca', 'ECA246G3470' => 'eca', 'EL10Ac6g13829' => 'bvu', 'EL10Ac6g14093' => 'bvu', 'EL10Ac8g18707' => 'bvu', 'Eucgr.C01369' => 'egr', 'Eucgr.H02492' => 'egr', 'Eucgr.I01733' => 'egr', 'Eucgr.J02255' => 'egr', 'Eucgr.J02257' => 'egr', 'Eucgr.J02258' => 'egr', 'FAN02G1601' => 'fan', 'FAN03G1586' => 'fan', 'FAN03G2986' => 'fan', 'FAN05G4837' => 'fan', 'FAN06G0146' => 'fan', 'FAN07G0858' => 'fan', 'FAN09G3179' => 'fan', 'FAN10G0669' => 'fan', 'FAN12G2358' => 'fan', 'FAN14G4198' => 'fan', 'FAN14G5112' => 'fan', 'FAN17G0342' => 'fan', 'FAN19G0342' => 'fan', 'FAN19G0962' => 'fan', 'FAN19G1101' => 'fan', 'FAN19G1872' => 'fan', 'FAN22G0356' => 'fan', 'FAN23G0744' => 'fan', 'FAN23G1914' => 'fan', 'FAN26G0032' => 'fan', 'FAN28G0625' => 'fan', 'FvH4_1g02710' => 'fve', 'FvH4_1g02720' => 'fve', 'FvH4_4g25670' => 'fve', 'FvH4_6g51700' => 'fve', 'FvH4_7g20170' => 'fve', 'Glyma.05G175000' => 'gma', 'Glyma.08G132300' => 'gma', 'Glyma.11G243000' => 'gma', 'Glyma.13G158900' => 'gma', 'Glyma.17G112400' => 'gma', 'Glyma.18G014100' => 'gma', 'Glyma.19G003100' => 'gma', 'Glyma.19G056500' => 'gma', 'Gohir.A01G158900' => 'ghi', 'Gohir.A05G312600' => 'ghi', 'Gohir.A05G354900' => 'ghi', 'Gohir.A07G037200' => 'ghi', 'Gohir.A09G030000' => 'ghi', 'Gohir.A12G145200' => 'ghi', 'Gohir.D01G151500' => 'ghi', 'Gohir.D04G058300' => 'ghi', 'Gohir.D05G314100' => 'ghi', 'Gohir.D07G041400' => 'ghi', 'Gohir.D09G029700' => 'ghi', 'Gohir.D12G149700' => 'ghi', 'Gorai.001G043800' => 'gra', 'Gorai.002G187800' => 'gra', 'Gorai.006G034700' => 'gra', 'Gorai.008G161200' => 'gra', 'Gorai.009G335700' => 'gra', 'Gorai.012G065000' => 'gra', 'GSVIVG01000535001' => 'vvi', 'GSVIVG01015572001' => 'vvi', 'GSVIVG01032386001' => 'vvi', 'HanXRQChr05g0138531' => 'han', 'HanXRQChr06g0174391' => 'han', 'HanXRQChr07g0199021' => 'han', 'HanXRQChr08g0208211' => 'han', 'HanXRQChr09g0255471' => 'han', 'HanXRQChr10g0315791' => 'han', 'HanXRQChr12g0371991' => 'han', 'HanXRQChr15g0475251' => 'han', 'HanXRQChr17g0540001' => 'han', 'HanXRQChr17g0548631' => 'han', 'HanXRQChr17g0569561' => 'han', 'Haze_12256' => 'cav', 'Haze_14756' => 'cav', 'Haze_25528' => 'cav', 'Hma1.2p1_0079F.1_g041020' => 'hma', 'Hma1.2p1_0818F.1_g223260' => 'hma', 'Hma1.2p1_1747F.1_g300530' => 'hma', 'HPP92_004607' => 'vpl', 'HPP92_004608' => 'vpl', 'HPP92_006181' => 'vpl', 'HPP92_012192' => 'vpl', 'HPP92_015680' => 'vpl', 'HPP92_020249' => 'vpl', 'HPP92_021376' => 'vpl', 'HPP92_024275' => 'vpl', 'Hund06031' => 'sun', 'Hund25391' => 'sun', 'Lalb_Chr07g0185371' => 'lal', 'Lalb_Chr07g0185381' => 'lal', 'Lalb_Chr12g0204011' => 'lal', 'Lalb_Chr13g0301671' => 'lal', 'Lalb_Chr14g0362851' => 'lal', 'Lalb_Chr24g0403581' => 'lal', 'Lj1g0000233' => 'lja', 'Lj2g0018120' => 'lja', 'Lj3C621T0' => 'lonja', 'Lj3P1059T14' => 'lonja', 'Lj3P611T9' => 'lonja', 'Lj3P614T13' => 'lonja', 'Lj3P615T5' => 'lonja', 'Lj4g0012315' => 'lja', 'Lj4g0026182' => 'lja', 'Lj6P813T16' => 'lonja', 'Lj7C427T7' => 'lonja', 'Lj7C427T8' => 'lonja', 'Lj7P600T41' => 'lonja', 'Lju41C42G17' => 'lonja', 'Lsat_1_v5_gn_0_47300' => 'lsa', 'Lsat_1_v5_gn_2_91280' => 'lsa', 'Lsat_1_v5_gn_3_30561' => 'lsa', 'Lsat_1_v5_gn_4_184321' => 'lsa', 'Lsat_1_v5_gn_4_4041' => 'lsa', 'Lsat_1_v5_gn_5_92000' => 'lsa', 'Lsat_1_v5_gn_8_152940' => 'lsa', 'Lsat_1_v5_gn_8_62401' => 'lsa', 'Manes.06G055900' => 'mes', 'Manes.12G022200' => 'mes', 'Manes.13G023300' => 'mes', 'Manes.14G115000' => 'mes', 'Manes.15G151700' => 'mes', 'Manes.17G111300' => 'mes', 'Mapoly0226s0009' => 'mpo', 'MBI02_g25363_MAGBIO' => 'mbi', 'MBI06_g00027_MAGBIO' => 'mbi', 'MBI10_g13034_MAGBIO' => 'mbi', 'MD09G1023400' => 'mdo', 'MD13G1100100' => 'mdo', 'MD15G1169200' => 'mdo', 'MD16G1101100' => 'mdo', 'MD17G1022900' => 'mdo', 'Medtr3g096150' => 'mtr', 'Medtr4g115070' => 'mtr', 'Medtr7g033325' => 'mtr', 'Medtr8g089840' => 'mtr', 'MELO3C010319.2' => 'cme', 'MELO3C011944.2' => 'cme', 'MELO3C021589.2' => 'cme', 'Migut.E00207' => 'egut', 'Migut.H00067' => 'egut', 'Migut.K00433' => 'egut', 'Migut.K00606' => 'egut', 'Migut.K01410' => 'egut', 'MSTRG.13347' => 'ama', 'MSTRG.24045' => 'ama', 'MSTRG.2428' => 'ama', 'MSTRG.26410' => 'ama', 'MSTRG.3139' => 'ama', 'MSTRG.3286' => 'ama', 'MSTRG.563' => 'ama', 'MSTRG.7941' => 'ama', 'Nitab4.5_0000028g0060' => 'nta', 'Nitab4.5_0000065g0260' => 'nta', 'Nitab4.5_0000112g0060' => 'nta', 'Nitab4.5_0000489g0120' => 'nta', 'Nitab4.5_0001776g0050' => 'nta', 'Nitab4.5_0001854g0010' => 'nta', 'Nitab4.5_0001860g0020' => 'nta', 'Nitab4.5_0004352g0010' => 'nta', 'Nitab4.5_0008716g0020' => 'nta', 'Nitab4.5_0008922g0010' => 'nta', 'Nn3g16693' => 'nnu', 'Nn4g22596' => 'nnu', 'Nn7g37639' => 'nnu', 'Oeu001701.1' => 'oeu', 'Oeu018149.1' => 'oeu', 'Oeu026220.1' => 'oeu', 'Oeu038635.1' => 'oeu', 'Oeu049176.1' => 'oeu', 'Oeu056706.1' => 'oeu', 'Oeu056937.1' => 'oeu', 'Oeu057540.1' => 'oeu', 'Os02g0594900' => 'osa', 'Os02g0595100' => 'osa', 'Os04g0477500' => 'osa', 'Os12g0611900' => 'osa', 'Peaxi162Scf00076g00020' => 'pax', 'Peaxi162Scf00128g00217' => 'pax', 'Peaxi162Scf00129g01640' => 'pax', 'Peaxi162Scf00669g00007' => 'pax', 'Peaxi162Scf00700g00421' => 'pax', 'Peaxi162Scf00801g00038' => 'pax', 'Peaxi162Scf00891g00025' => 'pax', 'PGR083G0909' => 'pgr', 'PGR119G1005' => 'pgr', 'PGR142G2236' => 'pgr', 'PGR142G3388' => 'pgr', 'PGSC0003DMG400004514' => 'stu', 'PGSC0003DMG400012635' => 'stu', 'PGSC0003DMG400015730' => 'stu', 'PGSC0003DMG400018611' => 'stu', 'PGSC0003DMG400030897' => 'stu', 'Phvul.001G254800' => 'pvu', 'Phvul.002G260100' => 'pvu', 'Phvul.003G167600' => 'pvu', 'Phvul.004G005100' => 'pvu', 'Potri.001G343600' => 'ptr', 'Potri.006G066700' => 'ptr', 'Potri.008G186000' => 'ptr', 'Potri.010G046900' => 'ptr', 'Potri.018G127900' => 'ptr', 'Pp3c20_17750' => 'ppa', 'Pp3c24_4380' => 'ppa', 'Prupe.1G245800' => 'ppe', 'Prupe.3G293400' => 'ppe', 'Prupe.7G247400' => 'ppe', 'Psat0s145g0120' => 'psa', 'Psat0s595g0040' => 'psa', 'Psat0s595g0120' => 'psa', 'Psat3g175040' => 'psa', 'Psat7g058120' => 'psa', 'PSO017G0428' => 'pso', 'PSO063G7510' => 'pso', 'PSO067G0046' => 'pso', 'PSO478G1073' => 'pso', 'PSO675G3677' => 'pso', 'PSO675G6558' => 'pso', 'PSO675G7520' => 'pso', 'PSO675G8959' => 'pso', 'QL02p074089' => 'qlo', 'QL02p089614' => 'qlo', 'QL03p057736' => 'qlo', 'RcHm_v2.0_Chr1g0364131' => 'rch', 'RcHm_v2.0_Chr2g0087801' => 'rch', 'RcHm_v2.0_Chr2g0087821' => 'rch', 'RcHm_v2.0_Chr2g0173231' => 'rch', 'RcHm_v2.0_Chr4g0433111' => 'rch', 'Rhsim03G0250300' => 'rsi', 'Rhsim08G0048400' => 'rsi', 'Rhsim10G0014800' => 'rsi', 'Rhsim12G0040100' => 'rsi', 'Rhsim12G0109700' => 'rsi', 'Sabra06G0049600' => 'sbr', 'Sabra08G0141000' => 'sbr', 'Sabra10G0021400' => 'sbr', 'Sabra16G0222900' => 'sbr', 'Sabra18G0108600' => 'sbr', 'SalBow1G0433' => 'sbo', 'SalBow1G2038' => 'sbo', 'SalBow1G5003' => 'sbo', 'SalBow7G1197' => 'sbo', 'SalBow8G3506' => 'sbo', 'Sc03g0007300' => 'sci', 'Sc11g0000950' => 'sci', 'Sc14g0008750' => 'sci', 'Sc18g0000420' => 'sci', 'Sed0006754' => 'sed', 'Sed0008741' => 'sed', 'Sed0017172' => 'sed', 'Sed0018925' => 'sed', 'Sed0023326' => 'sed', 'Sed0025909' => 'sed', 'SEGI_05333' => 'sgi', 'SEGI_10362' => 'sgi', 'SEGI_13380' => 'sgi', 'SEGI_24306' => 'sgi', 'SEGI_29077' => 'sgi', 'SEGI_29095' => 'sgi', 'SEGI_36534' => 'sgi', 'SEGI_37506' => 'sgi', 'SEGI_38321' => 'sgi', 'SGA_v2.0_scaffold307G48031' => 'sas', 'SGA_v2.0_scaffold47G17507' => 'sas', 'SGA_v2.0_scaffold63G21736' => 'sas', 'SGA_v2.0_scaffold87G27070' => 'sas', 'SHI17794' => 'shi', 'SHI28851' => 'shi', 'SMO165G0155' => 'smo', 'SMO340G0217' => 'smo', 'SMO367G1210' => 'smo', 'Solyc02g093430.3' => 'sly', 'Solyc05g013580.4' => 'sly', 'Solyc07g008030.3' => 'sly', 'Solyc12g035470.2' => 'sly', 'Sopen02g038020' => 'spe', 'Sopen05g008490' => 'spe', 'Sopen07g003910' => 'spe', 'Sopen12g015240' => 'spe', 'Sp1g11550' => 'spa', 'Sp2g16710' => 'spa', 'Sp3g00430' => 'spa', 'Sp3g26780' => 'spa', 'Sp5g22900' => 'spa', 'Sp6g29530' => 'spa', 'TAR371G0794' => 'tar', 'TAR374G0164' => 'tar', 'TAR622G0165' => 'tar', 'TAR626G0929' => 'tar', 'TAR629G2155' => 'tar', 'THA.LOC104805282' => 'tha', 'THA.LOC104805363' => 'tha', 'THA.LOC104808968' => 'tha', 'THA.LOC104821093' => 'tha', 'THA.LOC104823953' => 'tha', 'THA.LOC104825562' => 'tha', 'THA.LOC104825665' => 'tha', 'Thecc.02G261400' => 'tca', 'Thecc.04G019200' => 'tca', 'Thecc.09G130400' => 'tca', 'Thhalv10004374m.g' => 'esa', 'Thhalv10007850m.g' => 'esa', 'Thhalv10013782m.g' => 'esa', 'Thhalv10018686m.g' => 'esa', 'Thhalv10020899m.g' => 'esa', 'Thhalv10022755m.g' => 'esa', 'TPR.G23851' => 'tpr', 'TPR.G26500' => 'tpr', 'TPR.G27267' => 'tpr', 'TPR.G32001' => 'tpr', 'TPR.G6251' => 'tpr', 'TPR.G8167' => 'tpr', 'TWI12G1330' => 'twi', 'TWI18G1239' => 'twi', 'TWI34G0979' => 'twi', 'TWI36G0670' => 'twi', 'TWI36G0707' => 'twi', 'TWI56G0233' => 'twi', 'TWI75G1809' => 'twi', 'unitig_21.g20874' => 'ugi', 'unitig_26.g10343' => 'ugi', 'unitig_46.g18392' => 'ugi', 'unitig_52.g17178' => 'ugi', 'unitig_8.g2934' => 'ugi', 'vmacro01122' => 'vma', 'vmacro05875' => 'vma', 'vmacro06147' => 'vma', 'vmacro16191' => 'vma', 'vmacro18293' => 'vma', 'VMungo0251G3707' => 'vmu', 'VMungo0464G1521' => 'vmu', 'VMungo1215G0205' => 'vmu', 'VMungo1383G2484' => 'vmu', 'Zm00001eb079610' => 'zma', 'Zm00001eb135990' => 'zma', 'Zm00001eb183710' => 'zma', 'Zm00001eb246020' => 'zma' ) $gf_id = 'HOM05D001124' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001124' ) $data_identifier = 'HOM05D001124' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 6, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 7, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 21, 'bol' => (int) 10, 'bra' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 6, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 9, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 21, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 8, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 10, 'lsa' => (int) 8, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 8, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 9, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb246020' $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' => 'HOM05D001124', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '548', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02520' => 'bna', 'A03p06630' => 'bna', 'A05p44460' => 'bna', 'A06p08710' => 'bna', 'A06p41090' => 'bna', 'A07p32320' => 'bna', 'A08p32520' => 'bna', 'A09p10360' => 'bna', 'A10p24080' => 'bna', 'Aa31LG11G15250' => 'aar', 'Aa31LG1G1800' => 'aar', 'Aa31LG2G5120' => 'aar', 'Aa31LG2G6070' => 'aar', 'Aa31LG5G10770' => 'aar', 'Aa31sc61G90' => 'aar', 'Actinidia01352' => 'ach', 'Actinidia05983' => 'ach', 'Actinidia08133' => 'ach', 'Actinidia15101' => 'ach', 'Actinidia26379' => 'ach', 'Actinidia35778' => 'ach', 'Actinidia36123' => 'ach', 'Actinidia37436' => 'ach', 'Actinidia38730' => 'ach', 'Ah.02g128210' => 'amhyb', 'Ah.03g132990' => 'amhyb', 'Ah.14g079410' => 'amhyb', 'AL1G24640' => 'aly', 'AL2G26680' => 'aly', 'AL3G10530' => 'aly', 'AL3G45230' => 'aly', 'AL5G15230' => 'aly', 'AL5G16960' => 'aly', 'AL6G25210' => 'aly', 'Aqoxy2G00441' => 'aox', 'Aqoxy3G01236' => 'aox', 'Aqoxy5G03746' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3RQ047' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C7GMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9C8JER' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MBL6KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YXCZ83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZANX40' => 'arhy', 'AT1G12990' => 'ath', 'AT1G67880' => 'ath', 'AT2G13290' => 'ath', 'AT3G01620' => 'ath', 'AT3G26445' => 'ath', 'AT3G27540' => 'ath', 'AT5G14480' => 'ath', 'ATR0824G026' => 'atr', 'ATR1098G019' => 'atr', 'Atru.chr11.2145' => 'acertr', 'Atru.chr2.3636' => 'acertr', 'Atru.chr2.3644' => 'acertr', 'Atru.chr6.2422' => 'acertr', 'Atru.chr7.1112' => 'acertr', 'AUR62005469' => 'cqu', 'AUR62011166' => 'cqu', 'AUR62013319' => 'cqu', 'AUR62024273' => 'cqu', 'AUR62028420' => 'cqu', 'AUR62041942' => 'cqu', 'BcaB01g04969' => 'bca', 'BcaB01g06371' => 'bca', 'BcaB02g11494' => 'bca', 'BcaB03g15382' => 'bca', 'BcaB08g36994' => 'bca', 'BcaC03g13477' => 'bca', 'BcaC03g13478' => 'bca', 'BcaC03g13480' => 'bca', 'BcaC03g13481' => 'bca', 'BcaC03g13486' => 'bca', 'BcaC04g19031' => 'bca', 'BcaC04g23085' => 'bca', 'BcaC05g25094' => 'bca', 'BcaC05g25096' => 'bca', 'BcaC05g25138' => 'bca', 'BcaC05g30416' => 'bca', 'BcaC05g30455' => 'bca', 'BcaC06g30979' => 'bca', 'BcaC06g33805' => 'bca', 'BcaC08g46021' => 'bca', 'BcaNung03154' => 'bca', 'BolC2t06623H' => 'bol', 'BolC2t06632H' => 'bol', 'BolC2t06635H' => 'bol', 'BolC2t06638H' => 'bol', 'BolC3t13266H' => 'bol', 'BolC5t29776H' => 'bol', 'BolC6t38912H' => 'bol', 'BolC7t44183H' => 'bol', 'BolC9t54123H' => 'bol', 'BolC9t59107H' => 'bol', 'BraA02t05221Z' => 'bra', 'BraA03t09996Z' => 'bra', 'BraA05t23210Z' => 'bra', 'BraA06t24068Z' => 'bra', 'BraA06t27032Z' => 'bra', 'BraA08t35176Z' => 'bra', 'BraA09t36680Z' => 'bra', 'BraA10t44471Z' => 'bra', 'C02p06760' => 'bna', 'C02p06890' => 'bna', 'C02p07010' => 'bna', 'C03p07660' => 'bna', 'C05p10300' => 'bna', 'C06p38150' => 'bna', 'C07p36650' => 'bna', 'C08p15770' => 'bna', 'C09p12300' => 'bna', 'C09p62700' => 'bna', 'C09p75040' => 'bna', 'CAN.G13.1' => 'can', 'CAN.G138.4' => 'can', 'CAN.G44.6' => 'can', 'CAN.G473.19' => 'can', 'CANSAT01G0835' => 'cansat', 'CANSAT11G0246' => 'cansat', 'CANSAT11G1766' => 'cansat', 'CANSAT64G1954' => 'cansat', 'CARHR013330' => 'chi', 'CARHR060530' => 'chi', 'CARHR075300' => 'chi', 'CARHR105120' => 'chi', 'CARHR148910' => 'chi', 'CARHR198830' => 'chi', 'Carub.0001s1275' => 'cru', 'Carub.0002s1437' => 'cru', 'Carub.0003s0044' => 'cru', 'Carub.0003s2787' => 'cru', 'Carub.0005s0597' => 'cru', 'Carub.0006s1266' => 'cru', 'Ca_06935_v3' => 'car', 'Ca_13559_v3' => 'car', 'Ca_16941_v3' => 'car', 'Ca_16960_v3' => 'car', 'Ca_17775_v3' => 'car', 'Ca_30464_v3' => 'car', 'Cc06_g08160' => 'ccan', 'Cc07_g01520' => 'ccan', 'Cc11_g15810' => 'ccan', 'CDE02G2840' => 'cde', 'CDE03G0093' => 'cde', 'CDE04G2127' => 'cde', 'CDE07G1857' => 'cde', 'CDE09G1246' => 'cde', 'Cfa003412' => 'cfa', 'Cfa007341' => 'cfa', 'Cfa009220' => 'cfa', 'Ciclev10008737m.g' => 'ccl', 'Ciclev10015565m.g' => 'ccl', 'Ciclev10031761m.g' => 'ccl', 'CiPaw.03G045300' => 'cil', 'CiPaw.03G247200' => 'cil', 'CiPaw.04G029500' => 'cil', 'CiPaw.04G174000' => 'cil', 'CiPaw.05G181200' => 'cil', 'CiPaw.06G067100' => 'cil', 'ClCG05G025800' => 'cla', 'ClCG06G011400' => 'cla', 'ClCG09G019360' => 'cla', 'COL.COLO4_04827' => 'col', 'COL.COLO4_29170' => 'col', 'COL.COLO4_35131' => 'col', 'COL.COLO4_35132' => 'col', 'Cpa.g.sc33.32' => 'cpa', 'Cpa.g.sc46.29' => 'cpa', 'Cpa.g.sc796.1' => 'cpa', 'CsaV3_1G030420' => 'csa', 'CsaV3_5G027050' => 'csa', 'CsaV3_5G031040' => 'csa', 'CsaV3_UNG023130' => 'csa', 'CSS0007726' => 'camsi', 'CSS0016433' => 'camsi', 'CSS0017656' => 'camsi', 'CSS0025364' => 'camsi', 'CSS0027582' => 'camsi', 'CSS0047288' => 'camsi', 'CSS0049950' => 'camsi', 'DCAR_003843' => 'dca', 'DCAR_007052' => 'dca', 'DCAR_020884' => 'dca', 'DCAR_021730' => 'dca', 'DCAR_024423' => 'dca', 'DCAR_026509' => 'dca', 'DCAR_031158' => 'dca', 'Dinv14728' => 'din', 'Dinv15219' => 'din', 'Dinv25728' => 'din', 'Dinv33428' => 'din', 'Dinv36489' => 'din', 'Dinv41486' => 'din', 'Duzib147G0469' => 'dzi', 'Duzib168G0060' => 'dzi', 'Duzib187G1215' => 'dzi', 'Duzib248G0692' => 'dzi', 'Duzib251G0767' => 'dzi', 'Duzib264G0446' => 'dzi', 'Duzib268G0691' => 'dzi', 'ECA232G4767' => 'eca', 'ECA233G2838' => 'eca', 'ECA234G0391' => 'eca', 'ECA234G0857' => 'eca', 'ECA236G1593' => 'eca', 'ECA238G0565' => 'eca', 'ECA246G1027' => 'eca', 'ECA246G3223' => 'eca', 'ECA246G3470' => 'eca', 'EL10Ac6g13829' => 'bvu', 'EL10Ac6g14093' => 'bvu', 'EL10Ac8g18707' => 'bvu', 'Eucgr.C01369' => 'egr', 'Eucgr.H02492' => 'egr', 'Eucgr.I01733' => 'egr', 'Eucgr.J02255' => 'egr', 'Eucgr.J02257' => 'egr', 'Eucgr.J02258' => 'egr', 'FAN02G1601' => 'fan', 'FAN03G1586' => 'fan', 'FAN03G2986' => 'fan', 'FAN05G4837' => 'fan', 'FAN06G0146' => 'fan', 'FAN07G0858' => 'fan', 'FAN09G3179' => 'fan', 'FAN10G0669' => 'fan', 'FAN12G2358' => 'fan', 'FAN14G4198' => 'fan', 'FAN14G5112' => 'fan', 'FAN17G0342' => 'fan', 'FAN19G0342' => 'fan', 'FAN19G0962' => 'fan', 'FAN19G1101' => 'fan', 'FAN19G1872' => 'fan', 'FAN22G0356' => 'fan', 'FAN23G0744' => 'fan', 'FAN23G1914' => 'fan', 'FAN26G0032' => 'fan', 'FAN28G0625' => 'fan', 'FvH4_1g02710' => 'fve', 'FvH4_1g02720' => 'fve', 'FvH4_4g25670' => 'fve', 'FvH4_6g51700' => 'fve', 'FvH4_7g20170' => 'fve', 'Glyma.05G175000' => 'gma', 'Glyma.08G132300' => 'gma', 'Glyma.11G243000' => 'gma', 'Glyma.13G158900' => 'gma', 'Glyma.17G112400' => 'gma', 'Glyma.18G014100' => 'gma', 'Glyma.19G003100' => 'gma', 'Glyma.19G056500' => 'gma', 'Gohir.A01G158900' => 'ghi', 'Gohir.A05G312600' => 'ghi', 'Gohir.A05G354900' => 'ghi', 'Gohir.A07G037200' => 'ghi', 'Gohir.A09G030000' => 'ghi', 'Gohir.A12G145200' => 'ghi', 'Gohir.D01G151500' => 'ghi', 'Gohir.D04G058300' => 'ghi', 'Gohir.D05G314100' => 'ghi', 'Gohir.D07G041400' => 'ghi', 'Gohir.D09G029700' => 'ghi', 'Gohir.D12G149700' => 'ghi', 'Gorai.001G043800' => 'gra', 'Gorai.002G187800' => 'gra', 'Gorai.006G034700' => 'gra', 'Gorai.008G161200' => 'gra', 'Gorai.009G335700' => 'gra', 'Gorai.012G065000' => 'gra', 'GSVIVG01000535001' => 'vvi', 'GSVIVG01015572001' => 'vvi', 'GSVIVG01032386001' => 'vvi', 'HanXRQChr05g0138531' => 'han', 'HanXRQChr06g0174391' => 'han', 'HanXRQChr07g0199021' => 'han', 'HanXRQChr08g0208211' => 'han', 'HanXRQChr09g0255471' => 'han', 'HanXRQChr10g0315791' => 'han', 'HanXRQChr12g0371991' => 'han', 'HanXRQChr15g0475251' => 'han', 'HanXRQChr17g0540001' => 'han', 'HanXRQChr17g0548631' => 'han', 'HanXRQChr17g0569561' => 'han', 'Haze_12256' => 'cav', 'Haze_14756' => 'cav', 'Haze_25528' => 'cav', 'Hma1.2p1_0079F.1_g041020' => 'hma', 'Hma1.2p1_0818F.1_g223260' => 'hma', 'Hma1.2p1_1747F.1_g300530' => 'hma', 'HPP92_004607' => 'vpl', 'HPP92_004608' => 'vpl', 'HPP92_006181' => 'vpl', 'HPP92_012192' => 'vpl', 'HPP92_015680' => 'vpl', 'HPP92_020249' => 'vpl', 'HPP92_021376' => 'vpl', 'HPP92_024275' => 'vpl', 'Hund06031' => 'sun', 'Hund25391' => 'sun', 'Lalb_Chr07g0185371' => 'lal', 'Lalb_Chr07g0185381' => 'lal', 'Lalb_Chr12g0204011' => 'lal', 'Lalb_Chr13g0301671' => 'lal', 'Lalb_Chr14g0362851' => 'lal', 'Lalb_Chr24g0403581' => 'lal', 'Lj1g0000233' => 'lja', 'Lj2g0018120' => 'lja', 'Lj3C621T0' => 'lonja', 'Lj3P1059T14' => 'lonja', 'Lj3P611T9' => 'lonja', 'Lj3P614T13' => 'lonja', 'Lj3P615T5' => 'lonja', 'Lj4g0012315' => 'lja', 'Lj4g0026182' => 'lja', 'Lj6P813T16' => 'lonja', 'Lj7C427T7' => 'lonja', 'Lj7C427T8' => 'lonja', 'Lj7P600T41' => 'lonja', 'Lju41C42G17' => 'lonja', 'Lsat_1_v5_gn_0_47300' => 'lsa', 'Lsat_1_v5_gn_2_91280' => 'lsa', 'Lsat_1_v5_gn_3_30561' => 'lsa', 'Lsat_1_v5_gn_4_184321' => 'lsa', 'Lsat_1_v5_gn_4_4041' => 'lsa', 'Lsat_1_v5_gn_5_92000' => 'lsa', 'Lsat_1_v5_gn_8_152940' => 'lsa', 'Lsat_1_v5_gn_8_62401' => 'lsa', 'Manes.06G055900' => 'mes', 'Manes.12G022200' => 'mes', 'Manes.13G023300' => 'mes', 'Manes.14G115000' => 'mes', 'Manes.15G151700' => 'mes', 'Manes.17G111300' => 'mes', 'Mapoly0226s0009' => 'mpo', 'MBI02_g25363_MAGBIO' => 'mbi', 'MBI06_g00027_MAGBIO' => 'mbi', 'MBI10_g13034_MAGBIO' => 'mbi', 'MD09G1023400' => 'mdo', 'MD13G1100100' => 'mdo', 'MD15G1169200' => 'mdo', 'MD16G1101100' => 'mdo', 'MD17G1022900' => 'mdo', 'Medtr3g096150' => 'mtr', 'Medtr4g115070' => 'mtr', 'Medtr7g033325' => 'mtr', 'Medtr8g089840' => 'mtr', 'MELO3C010319.2' => 'cme', 'MELO3C011944.2' => 'cme', 'MELO3C021589.2' => 'cme', 'Migut.E00207' => 'egut', 'Migut.H00067' => 'egut', 'Migut.K00433' => 'egut', 'Migut.K00606' => 'egut', 'Migut.K01410' => 'egut', 'MSTRG.13347' => 'ama', 'MSTRG.24045' => 'ama', 'MSTRG.2428' => 'ama', 'MSTRG.26410' => 'ama', 'MSTRG.3139' => 'ama', 'MSTRG.3286' => 'ama', 'MSTRG.563' => 'ama', 'MSTRG.7941' => 'ama', 'Nitab4.5_0000028g0060' => 'nta', 'Nitab4.5_0000065g0260' => 'nta', 'Nitab4.5_0000112g0060' => 'nta', 'Nitab4.5_0000489g0120' => 'nta', 'Nitab4.5_0001776g0050' => 'nta', 'Nitab4.5_0001854g0010' => 'nta', 'Nitab4.5_0001860g0020' => 'nta', 'Nitab4.5_0004352g0010' => 'nta', 'Nitab4.5_0008716g0020' => 'nta', 'Nitab4.5_0008922g0010' => 'nta', 'Nn3g16693' => 'nnu', 'Nn4g22596' => 'nnu', 'Nn7g37639' => 'nnu', 'Oeu001701.1' => 'oeu', 'Oeu018149.1' => 'oeu', 'Oeu026220.1' => 'oeu', 'Oeu038635.1' => 'oeu', 'Oeu049176.1' => 'oeu', 'Oeu056706.1' => 'oeu', 'Oeu056937.1' => 'oeu', 'Oeu057540.1' => 'oeu', 'Os02g0594900' => 'osa', 'Os02g0595100' => 'osa', 'Os04g0477500' => 'osa', 'Os12g0611900' => 'osa', 'Peaxi162Scf00076g00020' => 'pax', 'Peaxi162Scf00128g00217' => 'pax', 'Peaxi162Scf00129g01640' => 'pax', 'Peaxi162Scf00669g00007' => 'pax', 'Peaxi162Scf00700g00421' => 'pax', 'Peaxi162Scf00801g00038' => 'pax', 'Peaxi162Scf00891g00025' => 'pax', 'PGR083G0909' => 'pgr', 'PGR119G1005' => 'pgr', 'PGR142G2236' => 'pgr', 'PGR142G3388' => 'pgr', 'PGSC0003DMG400004514' => 'stu', 'PGSC0003DMG400012635' => 'stu', 'PGSC0003DMG400015730' => 'stu', 'PGSC0003DMG400018611' => 'stu', 'PGSC0003DMG400030897' => 'stu', 'Phvul.001G254800' => 'pvu', 'Phvul.002G260100' => 'pvu', 'Phvul.003G167600' => 'pvu', 'Phvul.004G005100' => 'pvu', 'Potri.001G343600' => 'ptr', 'Potri.006G066700' => 'ptr', 'Potri.008G186000' => 'ptr', 'Potri.010G046900' => 'ptr', 'Potri.018G127900' => 'ptr', 'Pp3c20_17750' => 'ppa', 'Pp3c24_4380' => 'ppa', 'Prupe.1G245800' => 'ppe', 'Prupe.3G293400' => 'ppe', 'Prupe.7G247400' => 'ppe', 'Psat0s145g0120' => 'psa', 'Psat0s595g0040' => 'psa', 'Psat0s595g0120' => 'psa', 'Psat3g175040' => 'psa', 'Psat7g058120' => 'psa', 'PSO017G0428' => 'pso', 'PSO063G7510' => 'pso', 'PSO067G0046' => 'pso', 'PSO478G1073' => 'pso', 'PSO675G3677' => 'pso', 'PSO675G6558' => 'pso', 'PSO675G7520' => 'pso', 'PSO675G8959' => 'pso', 'QL02p074089' => 'qlo', 'QL02p089614' => 'qlo', 'QL03p057736' => 'qlo', 'RcHm_v2.0_Chr1g0364131' => 'rch', 'RcHm_v2.0_Chr2g0087801' => 'rch', 'RcHm_v2.0_Chr2g0087821' => 'rch', 'RcHm_v2.0_Chr2g0173231' => 'rch', 'RcHm_v2.0_Chr4g0433111' => 'rch', 'Rhsim03G0250300' => 'rsi', 'Rhsim08G0048400' => 'rsi', 'Rhsim10G0014800' => 'rsi', 'Rhsim12G0040100' => 'rsi', 'Rhsim12G0109700' => 'rsi', 'Sabra06G0049600' => 'sbr', 'Sabra08G0141000' => 'sbr', 'Sabra10G0021400' => 'sbr', 'Sabra16G0222900' => 'sbr', 'Sabra18G0108600' => 'sbr', 'SalBow1G0433' => 'sbo', 'SalBow1G2038' => 'sbo', 'SalBow1G5003' => 'sbo', 'SalBow7G1197' => 'sbo', 'SalBow8G3506' => 'sbo', 'Sc03g0007300' => 'sci', 'Sc11g0000950' => 'sci', 'Sc14g0008750' => 'sci', 'Sc18g0000420' => 'sci', 'Sed0006754' => 'sed', 'Sed0008741' => 'sed', 'Sed0017172' => 'sed', 'Sed0018925' => 'sed', 'Sed0023326' => 'sed', 'Sed0025909' => 'sed', 'SEGI_05333' => 'sgi', 'SEGI_10362' => 'sgi', 'SEGI_13380' => 'sgi', 'SEGI_24306' => 'sgi', 'SEGI_29077' => 'sgi', 'SEGI_29095' => 'sgi', 'SEGI_36534' => 'sgi', 'SEGI_37506' => 'sgi', 'SEGI_38321' => 'sgi', 'SGA_v2.0_scaffold307G48031' => 'sas', 'SGA_v2.0_scaffold47G17507' => 'sas', 'SGA_v2.0_scaffold63G21736' => 'sas', 'SGA_v2.0_scaffold87G27070' => 'sas', 'SHI17794' => 'shi', 'SHI28851' => 'shi', 'SMO165G0155' => 'smo', 'SMO340G0217' => 'smo', 'SMO367G1210' => 'smo', 'Solyc02g093430.3' => 'sly', 'Solyc05g013580.4' => 'sly', 'Solyc07g008030.3' => 'sly', 'Solyc12g035470.2' => 'sly', 'Sopen02g038020' => 'spe', 'Sopen05g008490' => 'spe', 'Sopen07g003910' => 'spe', 'Sopen12g015240' => 'spe', 'Sp1g11550' => 'spa', 'Sp2g16710' => 'spa', 'Sp3g00430' => 'spa', 'Sp3g26780' => 'spa', 'Sp5g22900' => 'spa', 'Sp6g29530' => 'spa', 'TAR371G0794' => 'tar', 'TAR374G0164' => 'tar', 'TAR622G0165' => 'tar', 'TAR626G0929' => 'tar', 'TAR629G2155' => 'tar', 'THA.LOC104805282' => 'tha', 'THA.LOC104805363' => 'tha', 'THA.LOC104808968' => 'tha', 'THA.LOC104821093' => 'tha', 'THA.LOC104823953' => 'tha', 'THA.LOC104825562' => 'tha', 'THA.LOC104825665' => 'tha', 'Thecc.02G261400' => 'tca', 'Thecc.04G019200' => 'tca', 'Thecc.09G130400' => 'tca', 'Thhalv10004374m.g' => 'esa', 'Thhalv10007850m.g' => 'esa', 'Thhalv10013782m.g' => 'esa', 'Thhalv10018686m.g' => 'esa', 'Thhalv10020899m.g' => 'esa', 'Thhalv10022755m.g' => 'esa', 'TPR.G23851' => 'tpr', 'TPR.G26500' => 'tpr', 'TPR.G27267' => 'tpr', 'TPR.G32001' => 'tpr', 'TPR.G6251' => 'tpr', 'TPR.G8167' => 'tpr', 'TWI12G1330' => 'twi', 'TWI18G1239' => 'twi', 'TWI34G0979' => 'twi', 'TWI36G0670' => 'twi', 'TWI36G0707' => 'twi', 'TWI56G0233' => 'twi', 'TWI75G1809' => 'twi', 'unitig_21.g20874' => 'ugi', 'unitig_26.g10343' => 'ugi', 'unitig_46.g18392' => 'ugi', 'unitig_52.g17178' => 'ugi', 'unitig_8.g2934' => 'ugi', 'vmacro01122' => 'vma', 'vmacro05875' => 'vma', 'vmacro06147' => 'vma', 'vmacro16191' => 'vma', 'vmacro18293' => 'vma', 'VMungo0251G3707' => 'vmu', 'VMungo0464G1521' => 'vmu', 'VMungo1215G0205' => 'vmu', 'VMungo1383G2484' => 'vmu', 'Zm00001eb079610' => 'zma', 'Zm00001eb135990' => 'zma', 'Zm00001eb183710' => 'zma', 'Zm00001eb246020' => 'zma' ), 'gf_id' => 'HOM05D001124', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001124' ), 'data_identifier' => 'HOM05D001124', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001124', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '548', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02520' => 'bna', 'A03p06630' => 'bna', 'A05p44460' => 'bna', 'A06p08710' => 'bna', 'A06p41090' => 'bna', 'A07p32320' => 'bna', 'A08p32520' => 'bna', 'A09p10360' => 'bna', 'A10p24080' => 'bna', 'Aa31LG11G15250' => 'aar', 'Aa31LG1G1800' => 'aar', 'Aa31LG2G5120' => 'aar', 'Aa31LG2G6070' => 'aar', 'Aa31LG5G10770' => 'aar', 'Aa31sc61G90' => 'aar', 'Actinidia01352' => 'ach', 'Actinidia05983' => 'ach', 'Actinidia08133' => 'ach', 'Actinidia15101' => 'ach', 'Actinidia26379' => 'ach', 'Actinidia35778' => 'ach', 'Actinidia36123' => 'ach', 'Actinidia37436' => 'ach', 'Actinidia38730' => 'ach', 'Ah.02g128210' => 'amhyb', 'Ah.03g132990' => 'amhyb', 'Ah.14g079410' => 'amhyb', 'AL1G24640' => 'aly', 'AL2G26680' => 'aly', 'AL3G10530' => 'aly', 'AL3G45230' => 'aly', 'AL5G15230' => 'aly', 'AL5G16960' => 'aly', 'AL6G25210' => 'aly', 'Aqoxy2G00441' => 'aox', 'Aqoxy3G01236' => 'aox', 'Aqoxy5G03746' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3RQ047' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C7GMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9C8JER' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MBL6KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YXCZ83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZANX40' => 'arhy', 'AT1G12990' => 'ath', 'AT1G67880' => 'ath', 'AT2G13290' => 'ath', 'AT3G01620' => 'ath', 'AT3G26445' => 'ath', 'AT3G27540' => 'ath', 'AT5G14480' => 'ath', 'ATR0824G026' => 'atr', 'ATR1098G019' => 'atr', 'Atru.chr11.2145' => 'acertr', 'Atru.chr2.3636' => 'acertr', 'Atru.chr2.3644' => 'acertr', 'Atru.chr6.2422' => 'acertr', 'Atru.chr7.1112' => 'acertr', 'AUR62005469' => 'cqu', 'AUR62011166' => 'cqu', 'AUR62013319' => 'cqu', 'AUR62024273' => 'cqu', 'AUR62028420' => 'cqu', 'AUR62041942' => 'cqu', 'BcaB01g04969' => 'bca', 'BcaB01g06371' => 'bca', 'BcaB02g11494' => 'bca', 'BcaB03g15382' => 'bca', 'BcaB08g36994' => 'bca', 'BcaC03g13477' => 'bca', 'BcaC03g13478' => 'bca', 'BcaC03g13480' => 'bca', 'BcaC03g13481' => 'bca', 'BcaC03g13486' => 'bca', 'BcaC04g19031' => 'bca', 'BcaC04g23085' => 'bca', 'BcaC05g25094' => 'bca', 'BcaC05g25096' => 'bca', 'BcaC05g25138' => 'bca', 'BcaC05g30416' => 'bca', 'BcaC05g30455' => 'bca', 'BcaC06g30979' => 'bca', 'BcaC06g33805' => 'bca', 'BcaC08g46021' => 'bca', 'BcaNung03154' => 'bca', 'BolC2t06623H' => 'bol', 'BolC2t06632H' => 'bol', 'BolC2t06635H' => 'bol', 'BolC2t06638H' => 'bol', 'BolC3t13266H' => 'bol', 'BolC5t29776H' => 'bol', 'BolC6t38912H' => 'bol', 'BolC7t44183H' => 'bol', 'BolC9t54123H' => 'bol', 'BolC9t59107H' => 'bol', 'BraA02t05221Z' => 'bra', 'BraA03t09996Z' => 'bra', 'BraA05t23210Z' => 'bra', 'BraA06t24068Z' => 'bra', 'BraA06t27032Z' => 'bra', 'BraA08t35176Z' => 'bra', 'BraA09t36680Z' => 'bra', 'BraA10t44471Z' => 'bra', 'C02p06760' => 'bna', 'C02p06890' => 'bna', 'C02p07010' => 'bna', 'C03p07660' => 'bna', 'C05p10300' => 'bna', 'C06p38150' => 'bna', 'C07p36650' => 'bna', 'C08p15770' => 'bna', 'C09p12300' => 'bna', 'C09p62700' => 'bna', 'C09p75040' => 'bna', 'CAN.G13.1' => 'can', 'CAN.G138.4' => 'can', 'CAN.G44.6' => 'can', 'CAN.G473.19' => 'can', 'CANSAT01G0835' => 'cansat', 'CANSAT11G0246' => 'cansat', 'CANSAT11G1766' => 'cansat', 'CANSAT64G1954' => 'cansat', 'CARHR013330' => 'chi', 'CARHR060530' => 'chi', 'CARHR075300' => 'chi', 'CARHR105120' => 'chi', 'CARHR148910' => 'chi', 'CARHR198830' => 'chi', 'Carub.0001s1275' => 'cru', 'Carub.0002s1437' => 'cru', 'Carub.0003s0044' => 'cru', 'Carub.0003s2787' => 'cru', 'Carub.0005s0597' => 'cru', 'Carub.0006s1266' => 'cru', 'Ca_06935_v3' => 'car', 'Ca_13559_v3' => 'car', 'Ca_16941_v3' => 'car', 'Ca_16960_v3' => 'car', 'Ca_17775_v3' => 'car', 'Ca_30464_v3' => 'car', 'Cc06_g08160' => 'ccan', 'Cc07_g01520' => 'ccan', 'Cc11_g15810' => 'ccan', 'CDE02G2840' => 'cde', 'CDE03G0093' => 'cde', 'CDE04G2127' => 'cde', 'CDE07G1857' => 'cde', 'CDE09G1246' => 'cde', 'Cfa003412' => 'cfa', 'Cfa007341' => 'cfa', 'Cfa009220' => 'cfa', 'Ciclev10008737m.g' => 'ccl', 'Ciclev10015565m.g' => 'ccl', 'Ciclev10031761m.g' => 'ccl', 'CiPaw.03G045300' => 'cil', 'CiPaw.03G247200' => 'cil', 'CiPaw.04G029500' => 'cil', 'CiPaw.04G174000' => 'cil', 'CiPaw.05G181200' => 'cil', 'CiPaw.06G067100' => 'cil', 'ClCG05G025800' => 'cla', 'ClCG06G011400' => 'cla', 'ClCG09G019360' => 'cla', 'COL.COLO4_04827' => 'col', 'COL.COLO4_29170' => 'col', 'COL.COLO4_35131' => 'col', 'COL.COLO4_35132' => 'col', 'Cpa.g.sc33.32' => 'cpa', 'Cpa.g.sc46.29' => 'cpa', 'Cpa.g.sc796.1' => 'cpa', 'CsaV3_1G030420' => 'csa', 'CsaV3_5G027050' => 'csa', 'CsaV3_5G031040' => 'csa', 'CsaV3_UNG023130' => 'csa', 'CSS0007726' => 'camsi', 'CSS0016433' => 'camsi', 'CSS0017656' => 'camsi', 'CSS0025364' => 'camsi', 'CSS0027582' => 'camsi', 'CSS0047288' => 'camsi', 'CSS0049950' => 'camsi', 'DCAR_003843' => 'dca', 'DCAR_007052' => 'dca', 'DCAR_020884' => 'dca', 'DCAR_021730' => 'dca', 'DCAR_024423' => 'dca', 'DCAR_026509' => 'dca', 'DCAR_031158' => 'dca', 'Dinv14728' => 'din', 'Dinv15219' => 'din', 'Dinv25728' => 'din', 'Dinv33428' => 'din', 'Dinv36489' => 'din', 'Dinv41486' => 'din', 'Duzib147G0469' => 'dzi', 'Duzib168G0060' => 'dzi', 'Duzib187G1215' => 'dzi', 'Duzib248G0692' => 'dzi', 'Duzib251G0767' => 'dzi', 'Duzib264G0446' => 'dzi', 'Duzib268G0691' => 'dzi', 'ECA232G4767' => 'eca', 'ECA233G2838' => 'eca', 'ECA234G0391' => 'eca', 'ECA234G0857' => 'eca', 'ECA236G1593' => 'eca', 'ECA238G0565' => 'eca', 'ECA246G1027' => 'eca', 'ECA246G3223' => 'eca', 'ECA246G3470' => 'eca', 'EL10Ac6g13829' => 'bvu', 'EL10Ac6g14093' => 'bvu', 'EL10Ac8g18707' => 'bvu', 'Eucgr.C01369' => 'egr', 'Eucgr.H02492' => 'egr', 'Eucgr.I01733' => 'egr', 'Eucgr.J02255' => 'egr', 'Eucgr.J02257' => 'egr', 'Eucgr.J02258' => 'egr', 'FAN02G1601' => 'fan', 'FAN03G1586' => 'fan', 'FAN03G2986' => 'fan', 'FAN05G4837' => 'fan', 'FAN06G0146' => 'fan', 'FAN07G0858' => 'fan', 'FAN09G3179' => 'fan', 'FAN10G0669' => 'fan', 'FAN12G2358' => 'fan', 'FAN14G4198' => 'fan', 'FAN14G5112' => 'fan', 'FAN17G0342' => 'fan', 'FAN19G0342' => 'fan', 'FAN19G0962' => 'fan', 'FAN19G1101' => 'fan', 'FAN19G1872' => 'fan', 'FAN22G0356' => 'fan', 'FAN23G0744' => 'fan', 'FAN23G1914' => 'fan', 'FAN26G0032' => 'fan', 'FAN28G0625' => 'fan', 'FvH4_1g02710' => 'fve', 'FvH4_1g02720' => 'fve', 'FvH4_4g25670' => 'fve', 'FvH4_6g51700' => 'fve', 'FvH4_7g20170' => 'fve', 'Glyma.05G175000' => 'gma', 'Glyma.08G132300' => 'gma', 'Glyma.11G243000' => 'gma', 'Glyma.13G158900' => 'gma', 'Glyma.17G112400' => 'gma', 'Glyma.18G014100' => 'gma', 'Glyma.19G003100' => 'gma', 'Glyma.19G056500' => 'gma', 'Gohir.A01G158900' => 'ghi', 'Gohir.A05G312600' => 'ghi', 'Gohir.A05G354900' => 'ghi', 'Gohir.A07G037200' => 'ghi', 'Gohir.A09G030000' => 'ghi', 'Gohir.A12G145200' => 'ghi', 'Gohir.D01G151500' => 'ghi', 'Gohir.D04G058300' => 'ghi', 'Gohir.D05G314100' => 'ghi', 'Gohir.D07G041400' => 'ghi', 'Gohir.D09G029700' => 'ghi', 'Gohir.D12G149700' => 'ghi', 'Gorai.001G043800' => 'gra', 'Gorai.002G187800' => 'gra', 'Gorai.006G034700' => 'gra', 'Gorai.008G161200' => 'gra', 'Gorai.009G335700' => 'gra', 'Gorai.012G065000' => 'gra', 'GSVIVG01000535001' => 'vvi', 'GSVIVG01015572001' => 'vvi', 'GSVIVG01032386001' => 'vvi', 'HanXRQChr05g0138531' => 'han', 'HanXRQChr06g0174391' => 'han', 'HanXRQChr07g0199021' => 'han', 'HanXRQChr08g0208211' => 'han', 'HanXRQChr09g0255471' => 'han', 'HanXRQChr10g0315791' => 'han', 'HanXRQChr12g0371991' => 'han', 'HanXRQChr15g0475251' => 'han', 'HanXRQChr17g0540001' => 'han', 'HanXRQChr17g0548631' => 'han', 'HanXRQChr17g0569561' => 'han', 'Haze_12256' => 'cav', 'Haze_14756' => 'cav', 'Haze_25528' => 'cav', 'Hma1.2p1_0079F.1_g041020' => 'hma', 'Hma1.2p1_0818F.1_g223260' => 'hma', 'Hma1.2p1_1747F.1_g300530' => 'hma', 'HPP92_004607' => 'vpl', 'HPP92_004608' => 'vpl', 'HPP92_006181' => 'vpl', 'HPP92_012192' => 'vpl', 'HPP92_015680' => 'vpl', 'HPP92_020249' => 'vpl', 'HPP92_021376' => 'vpl', 'HPP92_024275' => 'vpl', 'Hund06031' => 'sun', 'Hund25391' => 'sun', 'Lalb_Chr07g0185371' => 'lal', 'Lalb_Chr07g0185381' => 'lal', 'Lalb_Chr12g0204011' => 'lal', 'Lalb_Chr13g0301671' => 'lal', 'Lalb_Chr14g0362851' => 'lal', 'Lalb_Chr24g0403581' => 'lal', 'Lj1g0000233' => 'lja', 'Lj2g0018120' => 'lja', 'Lj3C621T0' => 'lonja', 'Lj3P1059T14' => 'lonja', 'Lj3P611T9' => 'lonja', 'Lj3P614T13' => 'lonja', 'Lj3P615T5' => 'lonja', 'Lj4g0012315' => 'lja', 'Lj4g0026182' => 'lja', 'Lj6P813T16' => 'lonja', 'Lj7C427T7' => 'lonja', 'Lj7C427T8' => 'lonja', 'Lj7P600T41' => 'lonja', 'Lju41C42G17' => 'lonja', 'Lsat_1_v5_gn_0_47300' => 'lsa', 'Lsat_1_v5_gn_2_91280' => 'lsa', 'Lsat_1_v5_gn_3_30561' => 'lsa', 'Lsat_1_v5_gn_4_184321' => 'lsa', 'Lsat_1_v5_gn_4_4041' => 'lsa', 'Lsat_1_v5_gn_5_92000' => 'lsa', 'Lsat_1_v5_gn_8_152940' => 'lsa', 'Lsat_1_v5_gn_8_62401' => 'lsa', 'Manes.06G055900' => 'mes', 'Manes.12G022200' => 'mes', 'Manes.13G023300' => 'mes', 'Manes.14G115000' => 'mes', 'Manes.15G151700' => 'mes', 'Manes.17G111300' => 'mes', 'Mapoly0226s0009' => 'mpo', 'MBI02_g25363_MAGBIO' => 'mbi', 'MBI06_g00027_MAGBIO' => 'mbi', 'MBI10_g13034_MAGBIO' => 'mbi', 'MD09G1023400' => 'mdo', 'MD13G1100100' => 'mdo', 'MD15G1169200' => 'mdo', 'MD16G1101100' => 'mdo', 'MD17G1022900' => 'mdo', 'Medtr3g096150' => 'mtr', 'Medtr4g115070' => 'mtr', 'Medtr7g033325' => 'mtr', 'Medtr8g089840' => 'mtr', 'MELO3C010319.2' => 'cme', 'MELO3C011944.2' => 'cme', 'MELO3C021589.2' => 'cme', 'Migut.E00207' => 'egut', 'Migut.H00067' => 'egut', 'Migut.K00433' => 'egut', 'Migut.K00606' => 'egut', 'Migut.K01410' => 'egut', 'MSTRG.13347' => 'ama', 'MSTRG.24045' => 'ama', 'MSTRG.2428' => 'ama', 'MSTRG.26410' => 'ama', 'MSTRG.3139' => 'ama', 'MSTRG.3286' => 'ama', 'MSTRG.563' => 'ama', 'MSTRG.7941' => 'ama', 'Nitab4.5_0000028g0060' => 'nta', 'Nitab4.5_0000065g0260' => 'nta', 'Nitab4.5_0000112g0060' => 'nta', 'Nitab4.5_0000489g0120' => 'nta', 'Nitab4.5_0001776g0050' => 'nta', 'Nitab4.5_0001854g0010' => 'nta', 'Nitab4.5_0001860g0020' => 'nta', 'Nitab4.5_0004352g0010' => 'nta', 'Nitab4.5_0008716g0020' => 'nta', 'Nitab4.5_0008922g0010' => 'nta', 'Nn3g16693' => 'nnu', 'Nn4g22596' => 'nnu', 'Nn7g37639' => 'nnu', 'Oeu001701.1' => 'oeu', 'Oeu018149.1' => 'oeu', 'Oeu026220.1' => 'oeu', 'Oeu038635.1' => 'oeu', 'Oeu049176.1' => 'oeu', 'Oeu056706.1' => 'oeu', 'Oeu056937.1' => 'oeu', 'Oeu057540.1' => 'oeu', 'Os02g0594900' => 'osa', 'Os02g0595100' => 'osa', 'Os04g0477500' => 'osa', 'Os12g0611900' => 'osa', 'Peaxi162Scf00076g00020' => 'pax', 'Peaxi162Scf00128g00217' => 'pax', 'Peaxi162Scf00129g01640' => 'pax', 'Peaxi162Scf00669g00007' => 'pax', 'Peaxi162Scf00700g00421' => 'pax', 'Peaxi162Scf00801g00038' => 'pax', 'Peaxi162Scf00891g00025' => 'pax', 'PGR083G0909' => 'pgr', 'PGR119G1005' => 'pgr', 'PGR142G2236' => 'pgr', 'PGR142G3388' => 'pgr', 'PGSC0003DMG400004514' => 'stu', 'PGSC0003DMG400012635' => 'stu', 'PGSC0003DMG400015730' => 'stu', 'PGSC0003DMG400018611' => 'stu', 'PGSC0003DMG400030897' => 'stu', 'Phvul.001G254800' => 'pvu', 'Phvul.002G260100' => 'pvu', 'Phvul.003G167600' => 'pvu', 'Phvul.004G005100' => 'pvu', 'Potri.001G343600' => 'ptr', 'Potri.006G066700' => 'ptr', 'Potri.008G186000' => 'ptr', 'Potri.010G046900' => 'ptr', 'Potri.018G127900' => 'ptr', 'Pp3c20_17750' => 'ppa', 'Pp3c24_4380' => 'ppa', 'Prupe.1G245800' => 'ppe', 'Prupe.3G293400' => 'ppe', 'Prupe.7G247400' => 'ppe', 'Psat0s145g0120' => 'psa', 'Psat0s595g0040' => 'psa', 'Psat0s595g0120' => 'psa', 'Psat3g175040' => 'psa', 'Psat7g058120' => 'psa', 'PSO017G0428' => 'pso', 'PSO063G7510' => 'pso', 'PSO067G0046' => 'pso', 'PSO478G1073' => 'pso', 'PSO675G3677' => 'pso', 'PSO675G6558' => 'pso', 'PSO675G7520' => 'pso', 'PSO675G8959' => 'pso', 'QL02p074089' => 'qlo', 'QL02p089614' => 'qlo', 'QL03p057736' => 'qlo', 'RcHm_v2.0_Chr1g0364131' => 'rch', 'RcHm_v2.0_Chr2g0087801' => 'rch', 'RcHm_v2.0_Chr2g0087821' => 'rch', 'RcHm_v2.0_Chr2g0173231' => 'rch', 'RcHm_v2.0_Chr4g0433111' => 'rch', 'Rhsim03G0250300' => 'rsi', 'Rhsim08G0048400' => 'rsi', 'Rhsim10G0014800' => 'rsi', 'Rhsim12G0040100' => 'rsi', 'Rhsim12G0109700' => 'rsi', 'Sabra06G0049600' => 'sbr', 'Sabra08G0141000' => 'sbr', 'Sabra10G0021400' => 'sbr', 'Sabra16G0222900' => 'sbr', 'Sabra18G0108600' => 'sbr', 'SalBow1G0433' => 'sbo', 'SalBow1G2038' => 'sbo', 'SalBow1G5003' => 'sbo', 'SalBow7G1197' => 'sbo', 'SalBow8G3506' => 'sbo', 'Sc03g0007300' => 'sci', 'Sc11g0000950' => 'sci', 'Sc14g0008750' => 'sci', 'Sc18g0000420' => 'sci', 'Sed0006754' => 'sed', 'Sed0008741' => 'sed', 'Sed0017172' => 'sed', 'Sed0018925' => 'sed', 'Sed0023326' => 'sed', 'Sed0025909' => 'sed', 'SEGI_05333' => 'sgi', 'SEGI_10362' => 'sgi', 'SEGI_13380' => 'sgi', 'SEGI_24306' => 'sgi', 'SEGI_29077' => 'sgi', 'SEGI_29095' => 'sgi', 'SEGI_36534' => 'sgi', 'SEGI_37506' => 'sgi', 'SEGI_38321' => 'sgi', 'SGA_v2.0_scaffold307G48031' => 'sas', 'SGA_v2.0_scaffold47G17507' => 'sas', 'SGA_v2.0_scaffold63G21736' => 'sas', 'SGA_v2.0_scaffold87G27070' => 'sas', 'SHI17794' => 'shi', 'SHI28851' => 'shi', 'SMO165G0155' => 'smo', 'SMO340G0217' => 'smo', 'SMO367G1210' => 'smo', 'Solyc02g093430.3' => 'sly', 'Solyc05g013580.4' => 'sly', 'Solyc07g008030.3' => 'sly', 'Solyc12g035470.2' => 'sly', 'Sopen02g038020' => 'spe', 'Sopen05g008490' => 'spe', 'Sopen07g003910' => 'spe', 'Sopen12g015240' => 'spe', 'Sp1g11550' => 'spa', 'Sp2g16710' => 'spa', 'Sp3g00430' => 'spa', 'Sp3g26780' => 'spa', 'Sp5g22900' => 'spa', 'Sp6g29530' => 'spa', 'TAR371G0794' => 'tar', 'TAR374G0164' => 'tar', 'TAR622G0165' => 'tar', 'TAR626G0929' => 'tar', 'TAR629G2155' => 'tar', 'THA.LOC104805282' => 'tha', 'THA.LOC104805363' => 'tha', 'THA.LOC104808968' => 'tha', 'THA.LOC104821093' => 'tha', 'THA.LOC104823953' => 'tha', 'THA.LOC104825562' => 'tha', 'THA.LOC104825665' => 'tha', 'Thecc.02G261400' => 'tca', 'Thecc.04G019200' => 'tca', 'Thecc.09G130400' => 'tca', 'Thhalv10004374m.g' => 'esa', 'Thhalv10007850m.g' => 'esa', 'Thhalv10013782m.g' => 'esa', 'Thhalv10018686m.g' => 'esa', 'Thhalv10020899m.g' => 'esa', 'Thhalv10022755m.g' => 'esa', 'TPR.G23851' => 'tpr', 'TPR.G26500' => 'tpr', 'TPR.G27267' => 'tpr', 'TPR.G32001' => 'tpr', 'TPR.G6251' => 'tpr', 'TPR.G8167' => 'tpr', 'TWI12G1330' => 'twi', 'TWI18G1239' => 'twi', 'TWI34G0979' => 'twi', 'TWI36G0670' => 'twi', 'TWI36G0707' => 'twi', 'TWI56G0233' => 'twi', 'TWI75G1809' => 'twi', 'unitig_21.g20874' => 'ugi', 'unitig_26.g10343' => 'ugi', 'unitig_46.g18392' => 'ugi', 'unitig_52.g17178' => 'ugi', 'unitig_8.g2934' => 'ugi', 'vmacro01122' => 'vma', 'vmacro05875' => 'vma', 'vmacro06147' => 'vma', 'vmacro16191' => 'vma', 'vmacro18293' => 'vma', 'VMungo0251G3707' => 'vmu', 'VMungo0464G1521' => 'vmu', 'VMungo1215G0205' => 'vmu', 'VMungo1383G2484' => 'vmu', 'Zm00001eb079610' => 'zma', 'Zm00001eb135990' => 'zma', 'Zm00001eb183710' => 'zma', 'Zm00001eb246020' => 'zma' ) $gf_id = 'HOM05D001124' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001124' ) $data_identifier = 'HOM05D001124' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 6, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 7, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 21, 'bol' => (int) 10, 'bra' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 6, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 9, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 21, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 8, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 10, 'lsa' => (int) 8, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 8, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 9, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb246020' $species_info = array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ) $local_species = 'tha' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001124', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '548', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02520' => 'bna', 'A03p06630' => 'bna', 'A05p44460' => 'bna', 'A06p08710' => 'bna', 'A06p41090' => 'bna', 'A07p32320' => 'bna', 'A08p32520' => 'bna', 'A09p10360' => 'bna', 'A10p24080' => 'bna', 'Aa31LG11G15250' => 'aar', 'Aa31LG1G1800' => 'aar', 'Aa31LG2G5120' => 'aar', 'Aa31LG2G6070' => 'aar', 'Aa31LG5G10770' => 'aar', 'Aa31sc61G90' => 'aar', 'Actinidia01352' => 'ach', 'Actinidia05983' => 'ach', 'Actinidia08133' => 'ach', 'Actinidia15101' => 'ach', 'Actinidia26379' => 'ach', 'Actinidia35778' => 'ach', 'Actinidia36123' => 'ach', 'Actinidia37436' => 'ach', 'Actinidia38730' => 'ach', 'Ah.02g128210' => 'amhyb', 'Ah.03g132990' => 'amhyb', 'Ah.14g079410' => 'amhyb', 'AL1G24640' => 'aly', 'AL2G26680' => 'aly', 'AL3G10530' => 'aly', 'AL3G45230' => 'aly', 'AL5G15230' => 'aly', 'AL5G16960' => 'aly', 'AL6G25210' => 'aly', 'Aqoxy2G00441' => 'aox', 'Aqoxy3G01236' => 'aox', 'Aqoxy5G03746' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3RQ047' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C7GMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9C8JER' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MBL6KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YXCZ83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZANX40' => 'arhy', 'AT1G12990' => 'ath', 'AT1G67880' => 'ath', 'AT2G13290' => 'ath', 'AT3G01620' => 'ath', 'AT3G26445' => 'ath', 'AT3G27540' => 'ath', 'AT5G14480' => 'ath', 'ATR0824G026' => 'atr', 'ATR1098G019' => 'atr', 'Atru.chr11.2145' => 'acertr', 'Atru.chr2.3636' => 'acertr', 'Atru.chr2.3644' => 'acertr', 'Atru.chr6.2422' => 'acertr', 'Atru.chr7.1112' => 'acertr', 'AUR62005469' => 'cqu', 'AUR62011166' => 'cqu', 'AUR62013319' => 'cqu', 'AUR62024273' => 'cqu', 'AUR62028420' => 'cqu', 'AUR62041942' => 'cqu', 'BcaB01g04969' => 'bca', 'BcaB01g06371' => 'bca', 'BcaB02g11494' => 'bca', 'BcaB03g15382' => 'bca', 'BcaB08g36994' => 'bca', 'BcaC03g13477' => 'bca', 'BcaC03g13478' => 'bca', 'BcaC03g13480' => 'bca', 'BcaC03g13481' => 'bca', 'BcaC03g13486' => 'bca', 'BcaC04g19031' => 'bca', 'BcaC04g23085' => 'bca', 'BcaC05g25094' => 'bca', 'BcaC05g25096' => 'bca', 'BcaC05g25138' => 'bca', 'BcaC05g30416' => 'bca', 'BcaC05g30455' => 'bca', 'BcaC06g30979' => 'bca', 'BcaC06g33805' => 'bca', 'BcaC08g46021' => 'bca', 'BcaNung03154' => 'bca', 'BolC2t06623H' => 'bol', 'BolC2t06632H' => 'bol', 'BolC2t06635H' => 'bol', 'BolC2t06638H' => 'bol', 'BolC3t13266H' => 'bol', 'BolC5t29776H' => 'bol', 'BolC6t38912H' => 'bol', 'BolC7t44183H' => 'bol', 'BolC9t54123H' => 'bol', 'BolC9t59107H' => 'bol', 'BraA02t05221Z' => 'bra', 'BraA03t09996Z' => 'bra', 'BraA05t23210Z' => 'bra', 'BraA06t24068Z' => 'bra', 'BraA06t27032Z' => 'bra', 'BraA08t35176Z' => 'bra', 'BraA09t36680Z' => 'bra', 'BraA10t44471Z' => 'bra', 'C02p06760' => 'bna', 'C02p06890' => 'bna', 'C02p07010' => 'bna', 'C03p07660' => 'bna', 'C05p10300' => 'bna', 'C06p38150' => 'bna', 'C07p36650' => 'bna', 'C08p15770' => 'bna', 'C09p12300' => 'bna', 'C09p62700' => 'bna', 'C09p75040' => 'bna', 'CAN.G13.1' => 'can', 'CAN.G138.4' => 'can', 'CAN.G44.6' => 'can', 'CAN.G473.19' => 'can', 'CANSAT01G0835' => 'cansat', 'CANSAT11G0246' => 'cansat', 'CANSAT11G1766' => 'cansat', 'CANSAT64G1954' => 'cansat', 'CARHR013330' => 'chi', 'CARHR060530' => 'chi', 'CARHR075300' => 'chi', 'CARHR105120' => 'chi', 'CARHR148910' => 'chi', 'CARHR198830' => 'chi', 'Carub.0001s1275' => 'cru', 'Carub.0002s1437' => 'cru', 'Carub.0003s0044' => 'cru', 'Carub.0003s2787' => 'cru', 'Carub.0005s0597' => 'cru', 'Carub.0006s1266' => 'cru', 'Ca_06935_v3' => 'car', 'Ca_13559_v3' => 'car', 'Ca_16941_v3' => 'car', 'Ca_16960_v3' => 'car', 'Ca_17775_v3' => 'car', 'Ca_30464_v3' => 'car', 'Cc06_g08160' => 'ccan', 'Cc07_g01520' => 'ccan', 'Cc11_g15810' => 'ccan', 'CDE02G2840' => 'cde', 'CDE03G0093' => 'cde', 'CDE04G2127' => 'cde', 'CDE07G1857' => 'cde', 'CDE09G1246' => 'cde', 'Cfa003412' => 'cfa', 'Cfa007341' => 'cfa', 'Cfa009220' => 'cfa', 'Ciclev10008737m.g' => 'ccl', 'Ciclev10015565m.g' => 'ccl', 'Ciclev10031761m.g' => 'ccl', 'CiPaw.03G045300' => 'cil', 'CiPaw.03G247200' => 'cil', 'CiPaw.04G029500' => 'cil', 'CiPaw.04G174000' => 'cil', 'CiPaw.05G181200' => 'cil', 'CiPaw.06G067100' => 'cil', 'ClCG05G025800' => 'cla', 'ClCG06G011400' => 'cla', 'ClCG09G019360' => 'cla', 'COL.COLO4_04827' => 'col', 'COL.COLO4_29170' => 'col', 'COL.COLO4_35131' => 'col', 'COL.COLO4_35132' => 'col', 'Cpa.g.sc33.32' => 'cpa', 'Cpa.g.sc46.29' => 'cpa', 'Cpa.g.sc796.1' => 'cpa', 'CsaV3_1G030420' => 'csa', 'CsaV3_5G027050' => 'csa', 'CsaV3_5G031040' => 'csa', 'CsaV3_UNG023130' => 'csa', 'CSS0007726' => 'camsi', 'CSS0016433' => 'camsi', 'CSS0017656' => 'camsi', 'CSS0025364' => 'camsi', 'CSS0027582' => 'camsi', 'CSS0047288' => 'camsi', 'CSS0049950' => 'camsi', 'DCAR_003843' => 'dca', 'DCAR_007052' => 'dca', 'DCAR_020884' => 'dca', 'DCAR_021730' => 'dca', 'DCAR_024423' => 'dca', 'DCAR_026509' => 'dca', 'DCAR_031158' => 'dca', 'Dinv14728' => 'din', 'Dinv15219' => 'din', 'Dinv25728' => 'din', 'Dinv33428' => 'din', 'Dinv36489' => 'din', 'Dinv41486' => 'din', 'Duzib147G0469' => 'dzi', 'Duzib168G0060' => 'dzi', 'Duzib187G1215' => 'dzi', 'Duzib248G0692' => 'dzi', 'Duzib251G0767' => 'dzi', 'Duzib264G0446' => 'dzi', 'Duzib268G0691' => 'dzi', 'ECA232G4767' => 'eca', 'ECA233G2838' => 'eca', 'ECA234G0391' => 'eca', 'ECA234G0857' => 'eca', 'ECA236G1593' => 'eca', 'ECA238G0565' => 'eca', 'ECA246G1027' => 'eca', 'ECA246G3223' => 'eca', 'ECA246G3470' => 'eca', 'EL10Ac6g13829' => 'bvu', 'EL10Ac6g14093' => 'bvu', 'EL10Ac8g18707' => 'bvu', 'Eucgr.C01369' => 'egr', 'Eucgr.H02492' => 'egr', 'Eucgr.I01733' => 'egr', 'Eucgr.J02255' => 'egr', 'Eucgr.J02257' => 'egr', 'Eucgr.J02258' => 'egr', 'FAN02G1601' => 'fan', 'FAN03G1586' => 'fan', 'FAN03G2986' => 'fan', 'FAN05G4837' => 'fan', 'FAN06G0146' => 'fan', 'FAN07G0858' => 'fan', 'FAN09G3179' => 'fan', 'FAN10G0669' => 'fan', 'FAN12G2358' => 'fan', 'FAN14G4198' => 'fan', 'FAN14G5112' => 'fan', 'FAN17G0342' => 'fan', 'FAN19G0342' => 'fan', 'FAN19G0962' => 'fan', 'FAN19G1101' => 'fan', 'FAN19G1872' => 'fan', 'FAN22G0356' => 'fan', 'FAN23G0744' => 'fan', 'FAN23G1914' => 'fan', 'FAN26G0032' => 'fan', 'FAN28G0625' => 'fan', 'FvH4_1g02710' => 'fve', 'FvH4_1g02720' => 'fve', 'FvH4_4g25670' => 'fve', 'FvH4_6g51700' => 'fve', 'FvH4_7g20170' => 'fve', 'Glyma.05G175000' => 'gma', 'Glyma.08G132300' => 'gma', 'Glyma.11G243000' => 'gma', 'Glyma.13G158900' => 'gma', 'Glyma.17G112400' => 'gma', 'Glyma.18G014100' => 'gma', 'Glyma.19G003100' => 'gma', 'Glyma.19G056500' => 'gma', 'Gohir.A01G158900' => 'ghi', 'Gohir.A05G312600' => 'ghi', 'Gohir.A05G354900' => 'ghi', 'Gohir.A07G037200' => 'ghi', 'Gohir.A09G030000' => 'ghi', 'Gohir.A12G145200' => 'ghi', 'Gohir.D01G151500' => 'ghi', 'Gohir.D04G058300' => 'ghi', 'Gohir.D05G314100' => 'ghi', 'Gohir.D07G041400' => 'ghi', 'Gohir.D09G029700' => 'ghi', 'Gohir.D12G149700' => 'ghi', 'Gorai.001G043800' => 'gra', 'Gorai.002G187800' => 'gra', 'Gorai.006G034700' => 'gra', 'Gorai.008G161200' => 'gra', 'Gorai.009G335700' => 'gra', 'Gorai.012G065000' => 'gra', 'GSVIVG01000535001' => 'vvi', 'GSVIVG01015572001' => 'vvi', 'GSVIVG01032386001' => 'vvi', 'HanXRQChr05g0138531' => 'han', 'HanXRQChr06g0174391' => 'han', 'HanXRQChr07g0199021' => 'han', 'HanXRQChr08g0208211' => 'han', 'HanXRQChr09g0255471' => 'han', 'HanXRQChr10g0315791' => 'han', 'HanXRQChr12g0371991' => 'han', 'HanXRQChr15g0475251' => 'han', 'HanXRQChr17g0540001' => 'han', 'HanXRQChr17g0548631' => 'han', 'HanXRQChr17g0569561' => 'han', 'Haze_12256' => 'cav', 'Haze_14756' => 'cav', 'Haze_25528' => 'cav', 'Hma1.2p1_0079F.1_g041020' => 'hma', 'Hma1.2p1_0818F.1_g223260' => 'hma', 'Hma1.2p1_1747F.1_g300530' => 'hma', 'HPP92_004607' => 'vpl', 'HPP92_004608' => 'vpl', 'HPP92_006181' => 'vpl', 'HPP92_012192' => 'vpl', 'HPP92_015680' => 'vpl', 'HPP92_020249' => 'vpl', 'HPP92_021376' => 'vpl', 'HPP92_024275' => 'vpl', 'Hund06031' => 'sun', 'Hund25391' => 'sun', 'Lalb_Chr07g0185371' => 'lal', 'Lalb_Chr07g0185381' => 'lal', 'Lalb_Chr12g0204011' => 'lal', 'Lalb_Chr13g0301671' => 'lal', 'Lalb_Chr14g0362851' => 'lal', 'Lalb_Chr24g0403581' => 'lal', 'Lj1g0000233' => 'lja', 'Lj2g0018120' => 'lja', 'Lj3C621T0' => 'lonja', 'Lj3P1059T14' => 'lonja', 'Lj3P611T9' => 'lonja', 'Lj3P614T13' => 'lonja', 'Lj3P615T5' => 'lonja', 'Lj4g0012315' => 'lja', 'Lj4g0026182' => 'lja', 'Lj6P813T16' => 'lonja', 'Lj7C427T7' => 'lonja', 'Lj7C427T8' => 'lonja', 'Lj7P600T41' => 'lonja', 'Lju41C42G17' => 'lonja', 'Lsat_1_v5_gn_0_47300' => 'lsa', 'Lsat_1_v5_gn_2_91280' => 'lsa', 'Lsat_1_v5_gn_3_30561' => 'lsa', 'Lsat_1_v5_gn_4_184321' => 'lsa', 'Lsat_1_v5_gn_4_4041' => 'lsa', 'Lsat_1_v5_gn_5_92000' => 'lsa', 'Lsat_1_v5_gn_8_152940' => 'lsa', 'Lsat_1_v5_gn_8_62401' => 'lsa', 'Manes.06G055900' => 'mes', 'Manes.12G022200' => 'mes', 'Manes.13G023300' => 'mes', 'Manes.14G115000' => 'mes', 'Manes.15G151700' => 'mes', 'Manes.17G111300' => 'mes', 'Mapoly0226s0009' => 'mpo', 'MBI02_g25363_MAGBIO' => 'mbi', 'MBI06_g00027_MAGBIO' => 'mbi', 'MBI10_g13034_MAGBIO' => 'mbi', 'MD09G1023400' => 'mdo', 'MD13G1100100' => 'mdo', 'MD15G1169200' => 'mdo', 'MD16G1101100' => 'mdo', 'MD17G1022900' => 'mdo', 'Medtr3g096150' => 'mtr', 'Medtr4g115070' => 'mtr', 'Medtr7g033325' => 'mtr', 'Medtr8g089840' => 'mtr', 'MELO3C010319.2' => 'cme', 'MELO3C011944.2' => 'cme', 'MELO3C021589.2' => 'cme', 'Migut.E00207' => 'egut', 'Migut.H00067' => 'egut', 'Migut.K00433' => 'egut', 'Migut.K00606' => 'egut', 'Migut.K01410' => 'egut', 'MSTRG.13347' => 'ama', 'MSTRG.24045' => 'ama', 'MSTRG.2428' => 'ama', 'MSTRG.26410' => 'ama', 'MSTRG.3139' => 'ama', 'MSTRG.3286' => 'ama', 'MSTRG.563' => 'ama', 'MSTRG.7941' => 'ama', 'Nitab4.5_0000028g0060' => 'nta', 'Nitab4.5_0000065g0260' => 'nta', 'Nitab4.5_0000112g0060' => 'nta', 'Nitab4.5_0000489g0120' => 'nta', 'Nitab4.5_0001776g0050' => 'nta', 'Nitab4.5_0001854g0010' => 'nta', 'Nitab4.5_0001860g0020' => 'nta', 'Nitab4.5_0004352g0010' => 'nta', 'Nitab4.5_0008716g0020' => 'nta', 'Nitab4.5_0008922g0010' => 'nta', 'Nn3g16693' => 'nnu', 'Nn4g22596' => 'nnu', 'Nn7g37639' => 'nnu', 'Oeu001701.1' => 'oeu', 'Oeu018149.1' => 'oeu', 'Oeu026220.1' => 'oeu', 'Oeu038635.1' => 'oeu', 'Oeu049176.1' => 'oeu', 'Oeu056706.1' => 'oeu', 'Oeu056937.1' => 'oeu', 'Oeu057540.1' => 'oeu', 'Os02g0594900' => 'osa', 'Os02g0595100' => 'osa', 'Os04g0477500' => 'osa', 'Os12g0611900' => 'osa', 'Peaxi162Scf00076g00020' => 'pax', 'Peaxi162Scf00128g00217' => 'pax', 'Peaxi162Scf00129g01640' => 'pax', 'Peaxi162Scf00669g00007' => 'pax', 'Peaxi162Scf00700g00421' => 'pax', 'Peaxi162Scf00801g00038' => 'pax', 'Peaxi162Scf00891g00025' => 'pax', 'PGR083G0909' => 'pgr', 'PGR119G1005' => 'pgr', 'PGR142G2236' => 'pgr', 'PGR142G3388' => 'pgr', 'PGSC0003DMG400004514' => 'stu', 'PGSC0003DMG400012635' => 'stu', 'PGSC0003DMG400015730' => 'stu', 'PGSC0003DMG400018611' => 'stu', 'PGSC0003DMG400030897' => 'stu', 'Phvul.001G254800' => 'pvu', 'Phvul.002G260100' => 'pvu', 'Phvul.003G167600' => 'pvu', 'Phvul.004G005100' => 'pvu', 'Potri.001G343600' => 'ptr', 'Potri.006G066700' => 'ptr', 'Potri.008G186000' => 'ptr', 'Potri.010G046900' => 'ptr', 'Potri.018G127900' => 'ptr', 'Pp3c20_17750' => 'ppa', 'Pp3c24_4380' => 'ppa', 'Prupe.1G245800' => 'ppe', 'Prupe.3G293400' => 'ppe', 'Prupe.7G247400' => 'ppe', 'Psat0s145g0120' => 'psa', 'Psat0s595g0040' => 'psa', 'Psat0s595g0120' => 'psa', 'Psat3g175040' => 'psa', 'Psat7g058120' => 'psa', 'PSO017G0428' => 'pso', 'PSO063G7510' => 'pso', 'PSO067G0046' => 'pso', 'PSO478G1073' => 'pso', 'PSO675G3677' => 'pso', 'PSO675G6558' => 'pso', 'PSO675G7520' => 'pso', 'PSO675G8959' => 'pso', 'QL02p074089' => 'qlo', 'QL02p089614' => 'qlo', 'QL03p057736' => 'qlo', 'RcHm_v2.0_Chr1g0364131' => 'rch', 'RcHm_v2.0_Chr2g0087801' => 'rch', 'RcHm_v2.0_Chr2g0087821' => 'rch', 'RcHm_v2.0_Chr2g0173231' => 'rch', 'RcHm_v2.0_Chr4g0433111' => 'rch', 'Rhsim03G0250300' => 'rsi', 'Rhsim08G0048400' => 'rsi', 'Rhsim10G0014800' => 'rsi', 'Rhsim12G0040100' => 'rsi', 'Rhsim12G0109700' => 'rsi', 'Sabra06G0049600' => 'sbr', 'Sabra08G0141000' => 'sbr', 'Sabra10G0021400' => 'sbr', 'Sabra16G0222900' => 'sbr', 'Sabra18G0108600' => 'sbr', 'SalBow1G0433' => 'sbo', 'SalBow1G2038' => 'sbo', 'SalBow1G5003' => 'sbo', 'SalBow7G1197' => 'sbo', 'SalBow8G3506' => 'sbo', 'Sc03g0007300' => 'sci', 'Sc11g0000950' => 'sci', 'Sc14g0008750' => 'sci', 'Sc18g0000420' => 'sci', 'Sed0006754' => 'sed', 'Sed0008741' => 'sed', 'Sed0017172' => 'sed', 'Sed0018925' => 'sed', 'Sed0023326' => 'sed', 'Sed0025909' => 'sed', 'SEGI_05333' => 'sgi', 'SEGI_10362' => 'sgi', 'SEGI_13380' => 'sgi', 'SEGI_24306' => 'sgi', 'SEGI_29077' => 'sgi', 'SEGI_29095' => 'sgi', 'SEGI_36534' => 'sgi', 'SEGI_37506' => 'sgi', 'SEGI_38321' => 'sgi', 'SGA_v2.0_scaffold307G48031' => 'sas', 'SGA_v2.0_scaffold47G17507' => 'sas', 'SGA_v2.0_scaffold63G21736' => 'sas', 'SGA_v2.0_scaffold87G27070' => 'sas', 'SHI17794' => 'shi', 'SHI28851' => 'shi', 'SMO165G0155' => 'smo', 'SMO340G0217' => 'smo', 'SMO367G1210' => 'smo', 'Solyc02g093430.3' => 'sly', 'Solyc05g013580.4' => 'sly', 'Solyc07g008030.3' => 'sly', 'Solyc12g035470.2' => 'sly', 'Sopen02g038020' => 'spe', 'Sopen05g008490' => 'spe', 'Sopen07g003910' => 'spe', 'Sopen12g015240' => 'spe', 'Sp1g11550' => 'spa', 'Sp2g16710' => 'spa', 'Sp3g00430' => 'spa', 'Sp3g26780' => 'spa', 'Sp5g22900' => 'spa', 'Sp6g29530' => 'spa', 'TAR371G0794' => 'tar', 'TAR374G0164' => 'tar', 'TAR622G0165' => 'tar', 'TAR626G0929' => 'tar', 'TAR629G2155' => 'tar', 'THA.LOC104805282' => 'tha', 'THA.LOC104805363' => 'tha', 'THA.LOC104808968' => 'tha', 'THA.LOC104821093' => 'tha', 'THA.LOC104823953' => 'tha', 'THA.LOC104825562' => 'tha', 'THA.LOC104825665' => 'tha', 'Thecc.02G261400' => 'tca', 'Thecc.04G019200' => 'tca', 'Thecc.09G130400' => 'tca', 'Thhalv10004374m.g' => 'esa', 'Thhalv10007850m.g' => 'esa', 'Thhalv10013782m.g' => 'esa', 'Thhalv10018686m.g' => 'esa', 'Thhalv10020899m.g' => 'esa', 'Thhalv10022755m.g' => 'esa', 'TPR.G23851' => 'tpr', 'TPR.G26500' => 'tpr', 'TPR.G27267' => 'tpr', 'TPR.G32001' => 'tpr', 'TPR.G6251' => 'tpr', 'TPR.G8167' => 'tpr', 'TWI12G1330' => 'twi', 'TWI18G1239' => 'twi', 'TWI34G0979' => 'twi', 'TWI36G0670' => 'twi', 'TWI36G0707' => 'twi', 'TWI56G0233' => 'twi', 'TWI75G1809' => 'twi', 'unitig_21.g20874' => 'ugi', 'unitig_26.g10343' => 'ugi', 'unitig_46.g18392' => 'ugi', 'unitig_52.g17178' => 'ugi', 'unitig_8.g2934' => 'ugi', 'vmacro01122' => 'vma', 'vmacro05875' => 'vma', 'vmacro06147' => 'vma', 'vmacro16191' => 'vma', 'vmacro18293' => 'vma', 'VMungo0251G3707' => 'vmu', 'VMungo0464G1521' => 'vmu', 'VMungo1215G0205' => 'vmu', 'VMungo1383G2484' => 'vmu', 'Zm00001eb079610' => 'zma', 'Zm00001eb135990' => 'zma', 'Zm00001eb183710' => 'zma', 'Zm00001eb246020' => 'zma' ), 'gf_id' => 'HOM05D001124', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001124' ), 'data_identifier' => 'HOM05D001124', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001124', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '548', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02520' => 'bna', 'A03p06630' => 'bna', 'A05p44460' => 'bna', 'A06p08710' => 'bna', 'A06p41090' => 'bna', 'A07p32320' => 'bna', 'A08p32520' => 'bna', 'A09p10360' => 'bna', 'A10p24080' => 'bna', 'Aa31LG11G15250' => 'aar', 'Aa31LG1G1800' => 'aar', 'Aa31LG2G5120' => 'aar', 'Aa31LG2G6070' => 'aar', 'Aa31LG5G10770' => 'aar', 'Aa31sc61G90' => 'aar', 'Actinidia01352' => 'ach', 'Actinidia05983' => 'ach', 'Actinidia08133' => 'ach', 'Actinidia15101' => 'ach', 'Actinidia26379' => 'ach', 'Actinidia35778' => 'ach', 'Actinidia36123' => 'ach', 'Actinidia37436' => 'ach', 'Actinidia38730' => 'ach', 'Ah.02g128210' => 'amhyb', 'Ah.03g132990' => 'amhyb', 'Ah.14g079410' => 'amhyb', 'AL1G24640' => 'aly', 'AL2G26680' => 'aly', 'AL3G10530' => 'aly', 'AL3G45230' => 'aly', 'AL5G15230' => 'aly', 'AL5G16960' => 'aly', 'AL6G25210' => 'aly', 'Aqoxy2G00441' => 'aox', 'Aqoxy3G01236' => 'aox', 'Aqoxy5G03746' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3RQ047' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C7GMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9C8JER' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MBL6KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YXCZ83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZANX40' => 'arhy', 'AT1G12990' => 'ath', 'AT1G67880' => 'ath', 'AT2G13290' => 'ath', 'AT3G01620' => 'ath', 'AT3G26445' => 'ath', 'AT3G27540' => 'ath', 'AT5G14480' => 'ath', 'ATR0824G026' => 'atr', 'ATR1098G019' => 'atr', 'Atru.chr11.2145' => 'acertr', 'Atru.chr2.3636' => 'acertr', 'Atru.chr2.3644' => 'acertr', 'Atru.chr6.2422' => 'acertr', 'Atru.chr7.1112' => 'acertr', 'AUR62005469' => 'cqu', 'AUR62011166' => 'cqu', 'AUR62013319' => 'cqu', 'AUR62024273' => 'cqu', 'AUR62028420' => 'cqu', 'AUR62041942' => 'cqu', 'BcaB01g04969' => 'bca', 'BcaB01g06371' => 'bca', 'BcaB02g11494' => 'bca', 'BcaB03g15382' => 'bca', 'BcaB08g36994' => 'bca', 'BcaC03g13477' => 'bca', 'BcaC03g13478' => 'bca', 'BcaC03g13480' => 'bca', 'BcaC03g13481' => 'bca', 'BcaC03g13486' => 'bca', 'BcaC04g19031' => 'bca', 'BcaC04g23085' => 'bca', 'BcaC05g25094' => 'bca', 'BcaC05g25096' => 'bca', 'BcaC05g25138' => 'bca', 'BcaC05g30416' => 'bca', 'BcaC05g30455' => 'bca', 'BcaC06g30979' => 'bca', 'BcaC06g33805' => 'bca', 'BcaC08g46021' => 'bca', 'BcaNung03154' => 'bca', 'BolC2t06623H' => 'bol', 'BolC2t06632H' => 'bol', 'BolC2t06635H' => 'bol', 'BolC2t06638H' => 'bol', 'BolC3t13266H' => 'bol', 'BolC5t29776H' => 'bol', 'BolC6t38912H' => 'bol', 'BolC7t44183H' => 'bol', 'BolC9t54123H' => 'bol', 'BolC9t59107H' => 'bol', 'BraA02t05221Z' => 'bra', 'BraA03t09996Z' => 'bra', 'BraA05t23210Z' => 'bra', 'BraA06t24068Z' => 'bra', 'BraA06t27032Z' => 'bra', 'BraA08t35176Z' => 'bra', 'BraA09t36680Z' => 'bra', 'BraA10t44471Z' => 'bra', 'C02p06760' => 'bna', 'C02p06890' => 'bna', 'C02p07010' => 'bna', 'C03p07660' => 'bna', 'C05p10300' => 'bna', 'C06p38150' => 'bna', 'C07p36650' => 'bna', 'C08p15770' => 'bna', 'C09p12300' => 'bna', 'C09p62700' => 'bna', 'C09p75040' => 'bna', 'CAN.G13.1' => 'can', 'CAN.G138.4' => 'can', 'CAN.G44.6' => 'can', 'CAN.G473.19' => 'can', 'CANSAT01G0835' => 'cansat', 'CANSAT11G0246' => 'cansat', 'CANSAT11G1766' => 'cansat', 'CANSAT64G1954' => 'cansat', 'CARHR013330' => 'chi', 'CARHR060530' => 'chi', 'CARHR075300' => 'chi', 'CARHR105120' => 'chi', 'CARHR148910' => 'chi', 'CARHR198830' => 'chi', 'Carub.0001s1275' => 'cru', 'Carub.0002s1437' => 'cru', 'Carub.0003s0044' => 'cru', 'Carub.0003s2787' => 'cru', 'Carub.0005s0597' => 'cru', 'Carub.0006s1266' => 'cru', 'Ca_06935_v3' => 'car', 'Ca_13559_v3' => 'car', 'Ca_16941_v3' => 'car', 'Ca_16960_v3' => 'car', 'Ca_17775_v3' => 'car', 'Ca_30464_v3' => 'car', 'Cc06_g08160' => 'ccan', 'Cc07_g01520' => 'ccan', 'Cc11_g15810' => 'ccan', 'CDE02G2840' => 'cde', 'CDE03G0093' => 'cde', 'CDE04G2127' => 'cde', 'CDE07G1857' => 'cde', 'CDE09G1246' => 'cde', 'Cfa003412' => 'cfa', 'Cfa007341' => 'cfa', 'Cfa009220' => 'cfa', 'Ciclev10008737m.g' => 'ccl', 'Ciclev10015565m.g' => 'ccl', 'Ciclev10031761m.g' => 'ccl', 'CiPaw.03G045300' => 'cil', 'CiPaw.03G247200' => 'cil', 'CiPaw.04G029500' => 'cil', 'CiPaw.04G174000' => 'cil', 'CiPaw.05G181200' => 'cil', 'CiPaw.06G067100' => 'cil', 'ClCG05G025800' => 'cla', 'ClCG06G011400' => 'cla', 'ClCG09G019360' => 'cla', 'COL.COLO4_04827' => 'col', 'COL.COLO4_29170' => 'col', 'COL.COLO4_35131' => 'col', 'COL.COLO4_35132' => 'col', 'Cpa.g.sc33.32' => 'cpa', 'Cpa.g.sc46.29' => 'cpa', 'Cpa.g.sc796.1' => 'cpa', 'CsaV3_1G030420' => 'csa', 'CsaV3_5G027050' => 'csa', 'CsaV3_5G031040' => 'csa', 'CsaV3_UNG023130' => 'csa', 'CSS0007726' => 'camsi', 'CSS0016433' => 'camsi', 'CSS0017656' => 'camsi', 'CSS0025364' => 'camsi', 'CSS0027582' => 'camsi', 'CSS0047288' => 'camsi', 'CSS0049950' => 'camsi', 'DCAR_003843' => 'dca', 'DCAR_007052' => 'dca', 'DCAR_020884' => 'dca', 'DCAR_021730' => 'dca', 'DCAR_024423' => 'dca', 'DCAR_026509' => 'dca', 'DCAR_031158' => 'dca', 'Dinv14728' => 'din', 'Dinv15219' => 'din', 'Dinv25728' => 'din', 'Dinv33428' => 'din', 'Dinv36489' => 'din', 'Dinv41486' => 'din', 'Duzib147G0469' => 'dzi', 'Duzib168G0060' => 'dzi', 'Duzib187G1215' => 'dzi', 'Duzib248G0692' => 'dzi', 'Duzib251G0767' => 'dzi', 'Duzib264G0446' => 'dzi', 'Duzib268G0691' => 'dzi', 'ECA232G4767' => 'eca', 'ECA233G2838' => 'eca', 'ECA234G0391' => 'eca', 'ECA234G0857' => 'eca', 'ECA236G1593' => 'eca', 'ECA238G0565' => 'eca', 'ECA246G1027' => 'eca', 'ECA246G3223' => 'eca', 'ECA246G3470' => 'eca', 'EL10Ac6g13829' => 'bvu', 'EL10Ac6g14093' => 'bvu', 'EL10Ac8g18707' => 'bvu', 'Eucgr.C01369' => 'egr', 'Eucgr.H02492' => 'egr', 'Eucgr.I01733' => 'egr', 'Eucgr.J02255' => 'egr', 'Eucgr.J02257' => 'egr', 'Eucgr.J02258' => 'egr', 'FAN02G1601' => 'fan', 'FAN03G1586' => 'fan', 'FAN03G2986' => 'fan', 'FAN05G4837' => 'fan', 'FAN06G0146' => 'fan', 'FAN07G0858' => 'fan', 'FAN09G3179' => 'fan', 'FAN10G0669' => 'fan', 'FAN12G2358' => 'fan', 'FAN14G4198' => 'fan', 'FAN14G5112' => 'fan', 'FAN17G0342' => 'fan', 'FAN19G0342' => 'fan', 'FAN19G0962' => 'fan', 'FAN19G1101' => 'fan', 'FAN19G1872' => 'fan', 'FAN22G0356' => 'fan', 'FAN23G0744' => 'fan', 'FAN23G1914' => 'fan', 'FAN26G0032' => 'fan', 'FAN28G0625' => 'fan', 'FvH4_1g02710' => 'fve', 'FvH4_1g02720' => 'fve', 'FvH4_4g25670' => 'fve', 'FvH4_6g51700' => 'fve', 'FvH4_7g20170' => 'fve', 'Glyma.05G175000' => 'gma', 'Glyma.08G132300' => 'gma', 'Glyma.11G243000' => 'gma', 'Glyma.13G158900' => 'gma', 'Glyma.17G112400' => 'gma', 'Glyma.18G014100' => 'gma', 'Glyma.19G003100' => 'gma', 'Glyma.19G056500' => 'gma', 'Gohir.A01G158900' => 'ghi', 'Gohir.A05G312600' => 'ghi', 'Gohir.A05G354900' => 'ghi', 'Gohir.A07G037200' => 'ghi', 'Gohir.A09G030000' => 'ghi', 'Gohir.A12G145200' => 'ghi', 'Gohir.D01G151500' => 'ghi', 'Gohir.D04G058300' => 'ghi', 'Gohir.D05G314100' => 'ghi', 'Gohir.D07G041400' => 'ghi', 'Gohir.D09G029700' => 'ghi', 'Gohir.D12G149700' => 'ghi', 'Gorai.001G043800' => 'gra', 'Gorai.002G187800' => 'gra', 'Gorai.006G034700' => 'gra', 'Gorai.008G161200' => 'gra', 'Gorai.009G335700' => 'gra', 'Gorai.012G065000' => 'gra', 'GSVIVG01000535001' => 'vvi', 'GSVIVG01015572001' => 'vvi', 'GSVIVG01032386001' => 'vvi', 'HanXRQChr05g0138531' => 'han', 'HanXRQChr06g0174391' => 'han', 'HanXRQChr07g0199021' => 'han', 'HanXRQChr08g0208211' => 'han', 'HanXRQChr09g0255471' => 'han', 'HanXRQChr10g0315791' => 'han', 'HanXRQChr12g0371991' => 'han', 'HanXRQChr15g0475251' => 'han', 'HanXRQChr17g0540001' => 'han', 'HanXRQChr17g0548631' => 'han', 'HanXRQChr17g0569561' => 'han', 'Haze_12256' => 'cav', 'Haze_14756' => 'cav', 'Haze_25528' => 'cav', 'Hma1.2p1_0079F.1_g041020' => 'hma', 'Hma1.2p1_0818F.1_g223260' => 'hma', 'Hma1.2p1_1747F.1_g300530' => 'hma', 'HPP92_004607' => 'vpl', 'HPP92_004608' => 'vpl', 'HPP92_006181' => 'vpl', 'HPP92_012192' => 'vpl', 'HPP92_015680' => 'vpl', 'HPP92_020249' => 'vpl', 'HPP92_021376' => 'vpl', 'HPP92_024275' => 'vpl', 'Hund06031' => 'sun', 'Hund25391' => 'sun', 'Lalb_Chr07g0185371' => 'lal', 'Lalb_Chr07g0185381' => 'lal', 'Lalb_Chr12g0204011' => 'lal', 'Lalb_Chr13g0301671' => 'lal', 'Lalb_Chr14g0362851' => 'lal', 'Lalb_Chr24g0403581' => 'lal', 'Lj1g0000233' => 'lja', 'Lj2g0018120' => 'lja', 'Lj3C621T0' => 'lonja', 'Lj3P1059T14' => 'lonja', 'Lj3P611T9' => 'lonja', 'Lj3P614T13' => 'lonja', 'Lj3P615T5' => 'lonja', 'Lj4g0012315' => 'lja', 'Lj4g0026182' => 'lja', 'Lj6P813T16' => 'lonja', 'Lj7C427T7' => 'lonja', 'Lj7C427T8' => 'lonja', 'Lj7P600T41' => 'lonja', 'Lju41C42G17' => 'lonja', 'Lsat_1_v5_gn_0_47300' => 'lsa', 'Lsat_1_v5_gn_2_91280' => 'lsa', 'Lsat_1_v5_gn_3_30561' => 'lsa', 'Lsat_1_v5_gn_4_184321' => 'lsa', 'Lsat_1_v5_gn_4_4041' => 'lsa', 'Lsat_1_v5_gn_5_92000' => 'lsa', 'Lsat_1_v5_gn_8_152940' => 'lsa', 'Lsat_1_v5_gn_8_62401' => 'lsa', 'Manes.06G055900' => 'mes', 'Manes.12G022200' => 'mes', 'Manes.13G023300' => 'mes', 'Manes.14G115000' => 'mes', 'Manes.15G151700' => 'mes', 'Manes.17G111300' => 'mes', 'Mapoly0226s0009' => 'mpo', 'MBI02_g25363_MAGBIO' => 'mbi', 'MBI06_g00027_MAGBIO' => 'mbi', 'MBI10_g13034_MAGBIO' => 'mbi', 'MD09G1023400' => 'mdo', 'MD13G1100100' => 'mdo', 'MD15G1169200' => 'mdo', 'MD16G1101100' => 'mdo', 'MD17G1022900' => 'mdo', 'Medtr3g096150' => 'mtr', 'Medtr4g115070' => 'mtr', 'Medtr7g033325' => 'mtr', 'Medtr8g089840' => 'mtr', 'MELO3C010319.2' => 'cme', 'MELO3C011944.2' => 'cme', 'MELO3C021589.2' => 'cme', 'Migut.E00207' => 'egut', 'Migut.H00067' => 'egut', 'Migut.K00433' => 'egut', 'Migut.K00606' => 'egut', 'Migut.K01410' => 'egut', 'MSTRG.13347' => 'ama', 'MSTRG.24045' => 'ama', 'MSTRG.2428' => 'ama', 'MSTRG.26410' => 'ama', 'MSTRG.3139' => 'ama', 'MSTRG.3286' => 'ama', 'MSTRG.563' => 'ama', 'MSTRG.7941' => 'ama', 'Nitab4.5_0000028g0060' => 'nta', 'Nitab4.5_0000065g0260' => 'nta', 'Nitab4.5_0000112g0060' => 'nta', 'Nitab4.5_0000489g0120' => 'nta', 'Nitab4.5_0001776g0050' => 'nta', 'Nitab4.5_0001854g0010' => 'nta', 'Nitab4.5_0001860g0020' => 'nta', 'Nitab4.5_0004352g0010' => 'nta', 'Nitab4.5_0008716g0020' => 'nta', 'Nitab4.5_0008922g0010' => 'nta', 'Nn3g16693' => 'nnu', 'Nn4g22596' => 'nnu', 'Nn7g37639' => 'nnu', 'Oeu001701.1' => 'oeu', 'Oeu018149.1' => 'oeu', 'Oeu026220.1' => 'oeu', 'Oeu038635.1' => 'oeu', 'Oeu049176.1' => 'oeu', 'Oeu056706.1' => 'oeu', 'Oeu056937.1' => 'oeu', 'Oeu057540.1' => 'oeu', 'Os02g0594900' => 'osa', 'Os02g0595100' => 'osa', 'Os04g0477500' => 'osa', 'Os12g0611900' => 'osa', 'Peaxi162Scf00076g00020' => 'pax', 'Peaxi162Scf00128g00217' => 'pax', 'Peaxi162Scf00129g01640' => 'pax', 'Peaxi162Scf00669g00007' => 'pax', 'Peaxi162Scf00700g00421' => 'pax', 'Peaxi162Scf00801g00038' => 'pax', 'Peaxi162Scf00891g00025' => 'pax', 'PGR083G0909' => 'pgr', 'PGR119G1005' => 'pgr', 'PGR142G2236' => 'pgr', 'PGR142G3388' => 'pgr', 'PGSC0003DMG400004514' => 'stu', 'PGSC0003DMG400012635' => 'stu', 'PGSC0003DMG400015730' => 'stu', 'PGSC0003DMG400018611' => 'stu', 'PGSC0003DMG400030897' => 'stu', 'Phvul.001G254800' => 'pvu', 'Phvul.002G260100' => 'pvu', 'Phvul.003G167600' => 'pvu', 'Phvul.004G005100' => 'pvu', 'Potri.001G343600' => 'ptr', 'Potri.006G066700' => 'ptr', 'Potri.008G186000' => 'ptr', 'Potri.010G046900' => 'ptr', 'Potri.018G127900' => 'ptr', 'Pp3c20_17750' => 'ppa', 'Pp3c24_4380' => 'ppa', 'Prupe.1G245800' => 'ppe', 'Prupe.3G293400' => 'ppe', 'Prupe.7G247400' => 'ppe', 'Psat0s145g0120' => 'psa', 'Psat0s595g0040' => 'psa', 'Psat0s595g0120' => 'psa', 'Psat3g175040' => 'psa', 'Psat7g058120' => 'psa', 'PSO017G0428' => 'pso', 'PSO063G7510' => 'pso', 'PSO067G0046' => 'pso', 'PSO478G1073' => 'pso', 'PSO675G3677' => 'pso', 'PSO675G6558' => 'pso', 'PSO675G7520' => 'pso', 'PSO675G8959' => 'pso', 'QL02p074089' => 'qlo', 'QL02p089614' => 'qlo', 'QL03p057736' => 'qlo', 'RcHm_v2.0_Chr1g0364131' => 'rch', 'RcHm_v2.0_Chr2g0087801' => 'rch', 'RcHm_v2.0_Chr2g0087821' => 'rch', 'RcHm_v2.0_Chr2g0173231' => 'rch', 'RcHm_v2.0_Chr4g0433111' => 'rch', 'Rhsim03G0250300' => 'rsi', 'Rhsim08G0048400' => 'rsi', 'Rhsim10G0014800' => 'rsi', 'Rhsim12G0040100' => 'rsi', 'Rhsim12G0109700' => 'rsi', 'Sabra06G0049600' => 'sbr', 'Sabra08G0141000' => 'sbr', 'Sabra10G0021400' => 'sbr', 'Sabra16G0222900' => 'sbr', 'Sabra18G0108600' => 'sbr', 'SalBow1G0433' => 'sbo', 'SalBow1G2038' => 'sbo', 'SalBow1G5003' => 'sbo', 'SalBow7G1197' => 'sbo', 'SalBow8G3506' => 'sbo', 'Sc03g0007300' => 'sci', 'Sc11g0000950' => 'sci', 'Sc14g0008750' => 'sci', 'Sc18g0000420' => 'sci', 'Sed0006754' => 'sed', 'Sed0008741' => 'sed', 'Sed0017172' => 'sed', 'Sed0018925' => 'sed', 'Sed0023326' => 'sed', 'Sed0025909' => 'sed', 'SEGI_05333' => 'sgi', 'SEGI_10362' => 'sgi', 'SEGI_13380' => 'sgi', 'SEGI_24306' => 'sgi', 'SEGI_29077' => 'sgi', 'SEGI_29095' => 'sgi', 'SEGI_36534' => 'sgi', 'SEGI_37506' => 'sgi', 'SEGI_38321' => 'sgi', 'SGA_v2.0_scaffold307G48031' => 'sas', 'SGA_v2.0_scaffold47G17507' => 'sas', 'SGA_v2.0_scaffold63G21736' => 'sas', 'SGA_v2.0_scaffold87G27070' => 'sas', 'SHI17794' => 'shi', 'SHI28851' => 'shi', 'SMO165G0155' => 'smo', 'SMO340G0217' => 'smo', 'SMO367G1210' => 'smo', 'Solyc02g093430.3' => 'sly', 'Solyc05g013580.4' => 'sly', 'Solyc07g008030.3' => 'sly', 'Solyc12g035470.2' => 'sly', 'Sopen02g038020' => 'spe', 'Sopen05g008490' => 'spe', 'Sopen07g003910' => 'spe', 'Sopen12g015240' => 'spe', 'Sp1g11550' => 'spa', 'Sp2g16710' => 'spa', 'Sp3g00430' => 'spa', 'Sp3g26780' => 'spa', 'Sp5g22900' => 'spa', 'Sp6g29530' => 'spa', 'TAR371G0794' => 'tar', 'TAR374G0164' => 'tar', 'TAR622G0165' => 'tar', 'TAR626G0929' => 'tar', 'TAR629G2155' => 'tar', 'THA.LOC104805282' => 'tha', 'THA.LOC104805363' => 'tha', 'THA.LOC104808968' => 'tha', 'THA.LOC104821093' => 'tha', 'THA.LOC104823953' => 'tha', 'THA.LOC104825562' => 'tha', 'THA.LOC104825665' => 'tha', 'Thecc.02G261400' => 'tca', 'Thecc.04G019200' => 'tca', 'Thecc.09G130400' => 'tca', 'Thhalv10004374m.g' => 'esa', 'Thhalv10007850m.g' => 'esa', 'Thhalv10013782m.g' => 'esa', 'Thhalv10018686m.g' => 'esa', 'Thhalv10020899m.g' => 'esa', 'Thhalv10022755m.g' => 'esa', 'TPR.G23851' => 'tpr', 'TPR.G26500' => 'tpr', 'TPR.G27267' => 'tpr', 'TPR.G32001' => 'tpr', 'TPR.G6251' => 'tpr', 'TPR.G8167' => 'tpr', 'TWI12G1330' => 'twi', 'TWI18G1239' => 'twi', 'TWI34G0979' => 'twi', 'TWI36G0670' => 'twi', 'TWI36G0707' => 'twi', 'TWI56G0233' => 'twi', 'TWI75G1809' => 'twi', 'unitig_21.g20874' => 'ugi', 'unitig_26.g10343' => 'ugi', 'unitig_46.g18392' => 'ugi', 'unitig_52.g17178' => 'ugi', 'unitig_8.g2934' => 'ugi', 'vmacro01122' => 'vma', 'vmacro05875' => 'vma', 'vmacro06147' => 'vma', 'vmacro16191' => 'vma', 'vmacro18293' => 'vma', 'VMungo0251G3707' => 'vmu', 'VMungo0464G1521' => 'vmu', 'VMungo1215G0205' => 'vmu', 'VMungo1383G2484' => 'vmu', 'Zm00001eb079610' => 'zma', 'Zm00001eb135990' => 'zma', 'Zm00001eb183710' => 'zma', 'Zm00001eb246020' => 'zma' ) $gf_id = 'HOM05D001124' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001124' ) $data_identifier = 'HOM05D001124' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 6, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 7, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 21, 'bol' => (int) 10, 'bra' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 6, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 9, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 21, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 8, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 10, 'lsa' => (int) 8, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 8, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 9, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb246020' $species_info = array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ) $local_species = 'tha' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001124', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '548', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02520' => 'bna', 'A03p06630' => 'bna', 'A05p44460' => 'bna', 'A06p08710' => 'bna', 'A06p41090' => 'bna', 'A07p32320' => 'bna', 'A08p32520' => 'bna', 'A09p10360' => 'bna', 'A10p24080' => 'bna', 'Aa31LG11G15250' => 'aar', 'Aa31LG1G1800' => 'aar', 'Aa31LG2G5120' => 'aar', 'Aa31LG2G6070' => 'aar', 'Aa31LG5G10770' => 'aar', 'Aa31sc61G90' => 'aar', 'Actinidia01352' => 'ach', 'Actinidia05983' => 'ach', 'Actinidia08133' => 'ach', 'Actinidia15101' => 'ach', 'Actinidia26379' => 'ach', 'Actinidia35778' => 'ach', 'Actinidia36123' => 'ach', 'Actinidia37436' => 'ach', 'Actinidia38730' => 'ach', 'Ah.02g128210' => 'amhyb', 'Ah.03g132990' => 'amhyb', 'Ah.14g079410' => 'amhyb', 'AL1G24640' => 'aly', 'AL2G26680' => 'aly', 'AL3G10530' => 'aly', 'AL3G45230' => 'aly', 'AL5G15230' => 'aly', 'AL5G16960' => 'aly', 'AL6G25210' => 'aly', 'Aqoxy2G00441' => 'aox', 'Aqoxy3G01236' => 'aox', 'Aqoxy5G03746' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3RQ047' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C7GMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9C8JER' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MBL6KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YXCZ83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZANX40' => 'arhy', 'AT1G12990' => 'ath', 'AT1G67880' => 'ath', 'AT2G13290' => 'ath', 'AT3G01620' => 'ath', 'AT3G26445' => 'ath', 'AT3G27540' => 'ath', 'AT5G14480' => 'ath', 'ATR0824G026' => 'atr', 'ATR1098G019' => 'atr', 'Atru.chr11.2145' => 'acertr', 'Atru.chr2.3636' => 'acertr', 'Atru.chr2.3644' => 'acertr', 'Atru.chr6.2422' => 'acertr', 'Atru.chr7.1112' => 'acertr', 'AUR62005469' => 'cqu', 'AUR62011166' => 'cqu', 'AUR62013319' => 'cqu', 'AUR62024273' => 'cqu', 'AUR62028420' => 'cqu', 'AUR62041942' => 'cqu', 'BcaB01g04969' => 'bca', 'BcaB01g06371' => 'bca', 'BcaB02g11494' => 'bca', 'BcaB03g15382' => 'bca', 'BcaB08g36994' => 'bca', 'BcaC03g13477' => 'bca', 'BcaC03g13478' => 'bca', 'BcaC03g13480' => 'bca', 'BcaC03g13481' => 'bca', 'BcaC03g13486' => 'bca', 'BcaC04g19031' => 'bca', 'BcaC04g23085' => 'bca', 'BcaC05g25094' => 'bca', 'BcaC05g25096' => 'bca', 'BcaC05g25138' => 'bca', 'BcaC05g30416' => 'bca', 'BcaC05g30455' => 'bca', 'BcaC06g30979' => 'bca', 'BcaC06g33805' => 'bca', 'BcaC08g46021' => 'bca', 'BcaNung03154' => 'bca', 'BolC2t06623H' => 'bol', 'BolC2t06632H' => 'bol', 'BolC2t06635H' => 'bol', 'BolC2t06638H' => 'bol', 'BolC3t13266H' => 'bol', 'BolC5t29776H' => 'bol', 'BolC6t38912H' => 'bol', 'BolC7t44183H' => 'bol', 'BolC9t54123H' => 'bol', 'BolC9t59107H' => 'bol', 'BraA02t05221Z' => 'bra', 'BraA03t09996Z' => 'bra', 'BraA05t23210Z' => 'bra', 'BraA06t24068Z' => 'bra', 'BraA06t27032Z' => 'bra', 'BraA08t35176Z' => 'bra', 'BraA09t36680Z' => 'bra', 'BraA10t44471Z' => 'bra', 'C02p06760' => 'bna', 'C02p06890' => 'bna', 'C02p07010' => 'bna', 'C03p07660' => 'bna', 'C05p10300' => 'bna', 'C06p38150' => 'bna', 'C07p36650' => 'bna', 'C08p15770' => 'bna', 'C09p12300' => 'bna', 'C09p62700' => 'bna', 'C09p75040' => 'bna', 'CAN.G13.1' => 'can', 'CAN.G138.4' => 'can', 'CAN.G44.6' => 'can', 'CAN.G473.19' => 'can', 'CANSAT01G0835' => 'cansat', 'CANSAT11G0246' => 'cansat', 'CANSAT11G1766' => 'cansat', 'CANSAT64G1954' => 'cansat', 'CARHR013330' => 'chi', 'CARHR060530' => 'chi', 'CARHR075300' => 'chi', 'CARHR105120' => 'chi', 'CARHR148910' => 'chi', 'CARHR198830' => 'chi', 'Carub.0001s1275' => 'cru', 'Carub.0002s1437' => 'cru', 'Carub.0003s0044' => 'cru', 'Carub.0003s2787' => 'cru', 'Carub.0005s0597' => 'cru', 'Carub.0006s1266' => 'cru', 'Ca_06935_v3' => 'car', 'Ca_13559_v3' => 'car', 'Ca_16941_v3' => 'car', 'Ca_16960_v3' => 'car', 'Ca_17775_v3' => 'car', 'Ca_30464_v3' => 'car', 'Cc06_g08160' => 'ccan', 'Cc07_g01520' => 'ccan', 'Cc11_g15810' => 'ccan', 'CDE02G2840' => 'cde', 'CDE03G0093' => 'cde', 'CDE04G2127' => 'cde', 'CDE07G1857' => 'cde', 'CDE09G1246' => 'cde', 'Cfa003412' => 'cfa', 'Cfa007341' => 'cfa', 'Cfa009220' => 'cfa', 'Ciclev10008737m.g' => 'ccl', 'Ciclev10015565m.g' => 'ccl', 'Ciclev10031761m.g' => 'ccl', 'CiPaw.03G045300' => 'cil', 'CiPaw.03G247200' => 'cil', 'CiPaw.04G029500' => 'cil', 'CiPaw.04G174000' => 'cil', 'CiPaw.05G181200' => 'cil', 'CiPaw.06G067100' => 'cil', 'ClCG05G025800' => 'cla', 'ClCG06G011400' => 'cla', 'ClCG09G019360' => 'cla', 'COL.COLO4_04827' => 'col', 'COL.COLO4_29170' => 'col', 'COL.COLO4_35131' => 'col', 'COL.COLO4_35132' => 'col', 'Cpa.g.sc33.32' => 'cpa', 'Cpa.g.sc46.29' => 'cpa', 'Cpa.g.sc796.1' => 'cpa', 'CsaV3_1G030420' => 'csa', 'CsaV3_5G027050' => 'csa', 'CsaV3_5G031040' => 'csa', 'CsaV3_UNG023130' => 'csa', 'CSS0007726' => 'camsi', 'CSS0016433' => 'camsi', 'CSS0017656' => 'camsi', 'CSS0025364' => 'camsi', 'CSS0027582' => 'camsi', 'CSS0047288' => 'camsi', 'CSS0049950' => 'camsi', 'DCAR_003843' => 'dca', 'DCAR_007052' => 'dca', 'DCAR_020884' => 'dca', 'DCAR_021730' => 'dca', 'DCAR_024423' => 'dca', 'DCAR_026509' => 'dca', 'DCAR_031158' => 'dca', 'Dinv14728' => 'din', 'Dinv15219' => 'din', 'Dinv25728' => 'din', 'Dinv33428' => 'din', 'Dinv36489' => 'din', 'Dinv41486' => 'din', 'Duzib147G0469' => 'dzi', 'Duzib168G0060' => 'dzi', 'Duzib187G1215' => 'dzi', 'Duzib248G0692' => 'dzi', 'Duzib251G0767' => 'dzi', 'Duzib264G0446' => 'dzi', 'Duzib268G0691' => 'dzi', 'ECA232G4767' => 'eca', 'ECA233G2838' => 'eca', 'ECA234G0391' => 'eca', 'ECA234G0857' => 'eca', 'ECA236G1593' => 'eca', 'ECA238G0565' => 'eca', 'ECA246G1027' => 'eca', 'ECA246G3223' => 'eca', 'ECA246G3470' => 'eca', 'EL10Ac6g13829' => 'bvu', 'EL10Ac6g14093' => 'bvu', 'EL10Ac8g18707' => 'bvu', 'Eucgr.C01369' => 'egr', 'Eucgr.H02492' => 'egr', 'Eucgr.I01733' => 'egr', 'Eucgr.J02255' => 'egr', 'Eucgr.J02257' => 'egr', 'Eucgr.J02258' => 'egr', 'FAN02G1601' => 'fan', 'FAN03G1586' => 'fan', 'FAN03G2986' => 'fan', 'FAN05G4837' => 'fan', 'FAN06G0146' => 'fan', 'FAN07G0858' => 'fan', 'FAN09G3179' => 'fan', 'FAN10G0669' => 'fan', 'FAN12G2358' => 'fan', 'FAN14G4198' => 'fan', 'FAN14G5112' => 'fan', 'FAN17G0342' => 'fan', 'FAN19G0342' => 'fan', 'FAN19G0962' => 'fan', 'FAN19G1101' => 'fan', 'FAN19G1872' => 'fan', 'FAN22G0356' => 'fan', 'FAN23G0744' => 'fan', 'FAN23G1914' => 'fan', 'FAN26G0032' => 'fan', 'FAN28G0625' => 'fan', 'FvH4_1g02710' => 'fve', 'FvH4_1g02720' => 'fve', 'FvH4_4g25670' => 'fve', 'FvH4_6g51700' => 'fve', 'FvH4_7g20170' => 'fve', 'Glyma.05G175000' => 'gma', 'Glyma.08G132300' => 'gma', 'Glyma.11G243000' => 'gma', 'Glyma.13G158900' => 'gma', 'Glyma.17G112400' => 'gma', 'Glyma.18G014100' => 'gma', 'Glyma.19G003100' => 'gma', 'Glyma.19G056500' => 'gma', 'Gohir.A01G158900' => 'ghi', 'Gohir.A05G312600' => 'ghi', 'Gohir.A05G354900' => 'ghi', 'Gohir.A07G037200' => 'ghi', 'Gohir.A09G030000' => 'ghi', 'Gohir.A12G145200' => 'ghi', 'Gohir.D01G151500' => 'ghi', 'Gohir.D04G058300' => 'ghi', 'Gohir.D05G314100' => 'ghi', 'Gohir.D07G041400' => 'ghi', 'Gohir.D09G029700' => 'ghi', 'Gohir.D12G149700' => 'ghi', 'Gorai.001G043800' => 'gra', 'Gorai.002G187800' => 'gra', 'Gorai.006G034700' => 'gra', 'Gorai.008G161200' => 'gra', 'Gorai.009G335700' => 'gra', 'Gorai.012G065000' => 'gra', 'GSVIVG01000535001' => 'vvi', 'GSVIVG01015572001' => 'vvi', 'GSVIVG01032386001' => 'vvi', 'HanXRQChr05g0138531' => 'han', 'HanXRQChr06g0174391' => 'han', 'HanXRQChr07g0199021' => 'han', 'HanXRQChr08g0208211' => 'han', 'HanXRQChr09g0255471' => 'han', 'HanXRQChr10g0315791' => 'han', 'HanXRQChr12g0371991' => 'han', 'HanXRQChr15g0475251' => 'han', 'HanXRQChr17g0540001' => 'han', 'HanXRQChr17g0548631' => 'han', 'HanXRQChr17g0569561' => 'han', 'Haze_12256' => 'cav', 'Haze_14756' => 'cav', 'Haze_25528' => 'cav', 'Hma1.2p1_0079F.1_g041020' => 'hma', 'Hma1.2p1_0818F.1_g223260' => 'hma', 'Hma1.2p1_1747F.1_g300530' => 'hma', 'HPP92_004607' => 'vpl', 'HPP92_004608' => 'vpl', 'HPP92_006181' => 'vpl', 'HPP92_012192' => 'vpl', 'HPP92_015680' => 'vpl', 'HPP92_020249' => 'vpl', 'HPP92_021376' => 'vpl', 'HPP92_024275' => 'vpl', 'Hund06031' => 'sun', 'Hund25391' => 'sun', 'Lalb_Chr07g0185371' => 'lal', 'Lalb_Chr07g0185381' => 'lal', 'Lalb_Chr12g0204011' => 'lal', 'Lalb_Chr13g0301671' => 'lal', 'Lalb_Chr14g0362851' => 'lal', 'Lalb_Chr24g0403581' => 'lal', 'Lj1g0000233' => 'lja', 'Lj2g0018120' => 'lja', 'Lj3C621T0' => 'lonja', 'Lj3P1059T14' => 'lonja', 'Lj3P611T9' => 'lonja', 'Lj3P614T13' => 'lonja', 'Lj3P615T5' => 'lonja', 'Lj4g0012315' => 'lja', 'Lj4g0026182' => 'lja', 'Lj6P813T16' => 'lonja', 'Lj7C427T7' => 'lonja', 'Lj7C427T8' => 'lonja', 'Lj7P600T41' => 'lonja', 'Lju41C42G17' => 'lonja', 'Lsat_1_v5_gn_0_47300' => 'lsa', 'Lsat_1_v5_gn_2_91280' => 'lsa', 'Lsat_1_v5_gn_3_30561' => 'lsa', 'Lsat_1_v5_gn_4_184321' => 'lsa', 'Lsat_1_v5_gn_4_4041' => 'lsa', 'Lsat_1_v5_gn_5_92000' => 'lsa', 'Lsat_1_v5_gn_8_152940' => 'lsa', 'Lsat_1_v5_gn_8_62401' => 'lsa', 'Manes.06G055900' => 'mes', 'Manes.12G022200' => 'mes', 'Manes.13G023300' => 'mes', 'Manes.14G115000' => 'mes', 'Manes.15G151700' => 'mes', 'Manes.17G111300' => 'mes', 'Mapoly0226s0009' => 'mpo', 'MBI02_g25363_MAGBIO' => 'mbi', 'MBI06_g00027_MAGBIO' => 'mbi', 'MBI10_g13034_MAGBIO' => 'mbi', 'MD09G1023400' => 'mdo', 'MD13G1100100' => 'mdo', 'MD15G1169200' => 'mdo', 'MD16G1101100' => 'mdo', 'MD17G1022900' => 'mdo', 'Medtr3g096150' => 'mtr', 'Medtr4g115070' => 'mtr', 'Medtr7g033325' => 'mtr', 'Medtr8g089840' => 'mtr', 'MELO3C010319.2' => 'cme', 'MELO3C011944.2' => 'cme', 'MELO3C021589.2' => 'cme', 'Migut.E00207' => 'egut', 'Migut.H00067' => 'egut', 'Migut.K00433' => 'egut', 'Migut.K00606' => 'egut', 'Migut.K01410' => 'egut', 'MSTRG.13347' => 'ama', 'MSTRG.24045' => 'ama', 'MSTRG.2428' => 'ama', 'MSTRG.26410' => 'ama', 'MSTRG.3139' => 'ama', 'MSTRG.3286' => 'ama', 'MSTRG.563' => 'ama', 'MSTRG.7941' => 'ama', 'Nitab4.5_0000028g0060' => 'nta', 'Nitab4.5_0000065g0260' => 'nta', 'Nitab4.5_0000112g0060' => 'nta', 'Nitab4.5_0000489g0120' => 'nta', 'Nitab4.5_0001776g0050' => 'nta', 'Nitab4.5_0001854g0010' => 'nta', 'Nitab4.5_0001860g0020' => 'nta', 'Nitab4.5_0004352g0010' => 'nta', 'Nitab4.5_0008716g0020' => 'nta', 'Nitab4.5_0008922g0010' => 'nta', 'Nn3g16693' => 'nnu', 'Nn4g22596' => 'nnu', 'Nn7g37639' => 'nnu', 'Oeu001701.1' => 'oeu', 'Oeu018149.1' => 'oeu', 'Oeu026220.1' => 'oeu', 'Oeu038635.1' => 'oeu', 'Oeu049176.1' => 'oeu', 'Oeu056706.1' => 'oeu', 'Oeu056937.1' => 'oeu', 'Oeu057540.1' => 'oeu', 'Os02g0594900' => 'osa', 'Os02g0595100' => 'osa', 'Os04g0477500' => 'osa', 'Os12g0611900' => 'osa', 'Peaxi162Scf00076g00020' => 'pax', 'Peaxi162Scf00128g00217' => 'pax', 'Peaxi162Scf00129g01640' => 'pax', 'Peaxi162Scf00669g00007' => 'pax', 'Peaxi162Scf00700g00421' => 'pax', 'Peaxi162Scf00801g00038' => 'pax', 'Peaxi162Scf00891g00025' => 'pax', 'PGR083G0909' => 'pgr', 'PGR119G1005' => 'pgr', 'PGR142G2236' => 'pgr', 'PGR142G3388' => 'pgr', 'PGSC0003DMG400004514' => 'stu', 'PGSC0003DMG400012635' => 'stu', 'PGSC0003DMG400015730' => 'stu', 'PGSC0003DMG400018611' => 'stu', 'PGSC0003DMG400030897' => 'stu', 'Phvul.001G254800' => 'pvu', 'Phvul.002G260100' => 'pvu', 'Phvul.003G167600' => 'pvu', 'Phvul.004G005100' => 'pvu', 'Potri.001G343600' => 'ptr', 'Potri.006G066700' => 'ptr', 'Potri.008G186000' => 'ptr', 'Potri.010G046900' => 'ptr', 'Potri.018G127900' => 'ptr', 'Pp3c20_17750' => 'ppa', 'Pp3c24_4380' => 'ppa', 'Prupe.1G245800' => 'ppe', 'Prupe.3G293400' => 'ppe', 'Prupe.7G247400' => 'ppe', 'Psat0s145g0120' => 'psa', 'Psat0s595g0040' => 'psa', 'Psat0s595g0120' => 'psa', 'Psat3g175040' => 'psa', 'Psat7g058120' => 'psa', 'PSO017G0428' => 'pso', 'PSO063G7510' => 'pso', 'PSO067G0046' => 'pso', 'PSO478G1073' => 'pso', 'PSO675G3677' => 'pso', 'PSO675G6558' => 'pso', 'PSO675G7520' => 'pso', 'PSO675G8959' => 'pso', 'QL02p074089' => 'qlo', 'QL02p089614' => 'qlo', 'QL03p057736' => 'qlo', 'RcHm_v2.0_Chr1g0364131' => 'rch', 'RcHm_v2.0_Chr2g0087801' => 'rch', 'RcHm_v2.0_Chr2g0087821' => 'rch', 'RcHm_v2.0_Chr2g0173231' => 'rch', 'RcHm_v2.0_Chr4g0433111' => 'rch', 'Rhsim03G0250300' => 'rsi', 'Rhsim08G0048400' => 'rsi', 'Rhsim10G0014800' => 'rsi', 'Rhsim12G0040100' => 'rsi', 'Rhsim12G0109700' => 'rsi', 'Sabra06G0049600' => 'sbr', 'Sabra08G0141000' => 'sbr', 'Sabra10G0021400' => 'sbr', 'Sabra16G0222900' => 'sbr', 'Sabra18G0108600' => 'sbr', 'SalBow1G0433' => 'sbo', 'SalBow1G2038' => 'sbo', 'SalBow1G5003' => 'sbo', 'SalBow7G1197' => 'sbo', 'SalBow8G3506' => 'sbo', 'Sc03g0007300' => 'sci', 'Sc11g0000950' => 'sci', 'Sc14g0008750' => 'sci', 'Sc18g0000420' => 'sci', 'Sed0006754' => 'sed', 'Sed0008741' => 'sed', 'Sed0017172' => 'sed', 'Sed0018925' => 'sed', 'Sed0023326' => 'sed', 'Sed0025909' => 'sed', 'SEGI_05333' => 'sgi', 'SEGI_10362' => 'sgi', 'SEGI_13380' => 'sgi', 'SEGI_24306' => 'sgi', 'SEGI_29077' => 'sgi', 'SEGI_29095' => 'sgi', 'SEGI_36534' => 'sgi', 'SEGI_37506' => 'sgi', 'SEGI_38321' => 'sgi', 'SGA_v2.0_scaffold307G48031' => 'sas', 'SGA_v2.0_scaffold47G17507' => 'sas', 'SGA_v2.0_scaffold63G21736' => 'sas', 'SGA_v2.0_scaffold87G27070' => 'sas', 'SHI17794' => 'shi', 'SHI28851' => 'shi', 'SMO165G0155' => 'smo', 'SMO340G0217' => 'smo', 'SMO367G1210' => 'smo', 'Solyc02g093430.3' => 'sly', 'Solyc05g013580.4' => 'sly', 'Solyc07g008030.3' => 'sly', 'Solyc12g035470.2' => 'sly', 'Sopen02g038020' => 'spe', 'Sopen05g008490' => 'spe', 'Sopen07g003910' => 'spe', 'Sopen12g015240' => 'spe', 'Sp1g11550' => 'spa', 'Sp2g16710' => 'spa', 'Sp3g00430' => 'spa', 'Sp3g26780' => 'spa', 'Sp5g22900' => 'spa', 'Sp6g29530' => 'spa', 'TAR371G0794' => 'tar', 'TAR374G0164' => 'tar', 'TAR622G0165' => 'tar', 'TAR626G0929' => 'tar', 'TAR629G2155' => 'tar', 'THA.LOC104805282' => 'tha', 'THA.LOC104805363' => 'tha', 'THA.LOC104808968' => 'tha', 'THA.LOC104821093' => 'tha', 'THA.LOC104823953' => 'tha', 'THA.LOC104825562' => 'tha', 'THA.LOC104825665' => 'tha', 'Thecc.02G261400' => 'tca', 'Thecc.04G019200' => 'tca', 'Thecc.09G130400' => 'tca', 'Thhalv10004374m.g' => 'esa', 'Thhalv10007850m.g' => 'esa', 'Thhalv10013782m.g' => 'esa', 'Thhalv10018686m.g' => 'esa', 'Thhalv10020899m.g' => 'esa', 'Thhalv10022755m.g' => 'esa', 'TPR.G23851' => 'tpr', 'TPR.G26500' => 'tpr', 'TPR.G27267' => 'tpr', 'TPR.G32001' => 'tpr', 'TPR.G6251' => 'tpr', 'TPR.G8167' => 'tpr', 'TWI12G1330' => 'twi', 'TWI18G1239' => 'twi', 'TWI34G0979' => 'twi', 'TWI36G0670' => 'twi', 'TWI36G0707' => 'twi', 'TWI56G0233' => 'twi', 'TWI75G1809' => 'twi', 'unitig_21.g20874' => 'ugi', 'unitig_26.g10343' => 'ugi', 'unitig_46.g18392' => 'ugi', 'unitig_52.g17178' => 'ugi', 'unitig_8.g2934' => 'ugi', 'vmacro01122' => 'vma', 'vmacro05875' => 'vma', 'vmacro06147' => 'vma', 'vmacro16191' => 'vma', 'vmacro18293' => 'vma', 'VMungo0251G3707' => 'vmu', 'VMungo0464G1521' => 'vmu', 'VMungo1215G0205' => 'vmu', 'VMungo1383G2484' => 'vmu', 'Zm00001eb079610' => 'zma', 'Zm00001eb135990' => 'zma', 'Zm00001eb183710' => 'zma', 'Zm00001eb246020' => 'zma' ), 'gf_id' => 'HOM05D001124', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001124' ), 'data_identifier' => 'HOM05D001124', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001124', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '548', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02520' => 'bna', 'A03p06630' => 'bna', 'A05p44460' => 'bna', 'A06p08710' => 'bna', 'A06p41090' => 'bna', 'A07p32320' => 'bna', 'A08p32520' => 'bna', 'A09p10360' => 'bna', 'A10p24080' => 'bna', 'Aa31LG11G15250' => 'aar', 'Aa31LG1G1800' => 'aar', 'Aa31LG2G5120' => 'aar', 'Aa31LG2G6070' => 'aar', 'Aa31LG5G10770' => 'aar', 'Aa31sc61G90' => 'aar', 'Actinidia01352' => 'ach', 'Actinidia05983' => 'ach', 'Actinidia08133' => 'ach', 'Actinidia15101' => 'ach', 'Actinidia26379' => 'ach', 'Actinidia35778' => 'ach', 'Actinidia36123' => 'ach', 'Actinidia37436' => 'ach', 'Actinidia38730' => 'ach', 'Ah.02g128210' => 'amhyb', 'Ah.03g132990' => 'amhyb', 'Ah.14g079410' => 'amhyb', 'AL1G24640' => 'aly', 'AL2G26680' => 'aly', 'AL3G10530' => 'aly', 'AL3G45230' => 'aly', 'AL5G15230' => 'aly', 'AL5G16960' => 'aly', 'AL6G25210' => 'aly', 'Aqoxy2G00441' => 'aox', 'Aqoxy3G01236' => 'aox', 'Aqoxy5G03746' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3RQ047' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C7GMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9C8JER' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MBL6KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YXCZ83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZANX40' => 'arhy', 'AT1G12990' => 'ath', 'AT1G67880' => 'ath', 'AT2G13290' => 'ath', 'AT3G01620' => 'ath', 'AT3G26445' => 'ath', 'AT3G27540' => 'ath', 'AT5G14480' => 'ath', 'ATR0824G026' => 'atr', 'ATR1098G019' => 'atr', 'Atru.chr11.2145' => 'acertr', 'Atru.chr2.3636' => 'acertr', 'Atru.chr2.3644' => 'acertr', 'Atru.chr6.2422' => 'acertr', 'Atru.chr7.1112' => 'acertr', 'AUR62005469' => 'cqu', 'AUR62011166' => 'cqu', 'AUR62013319' => 'cqu', 'AUR62024273' => 'cqu', 'AUR62028420' => 'cqu', 'AUR62041942' => 'cqu', 'BcaB01g04969' => 'bca', 'BcaB01g06371' => 'bca', 'BcaB02g11494' => 'bca', 'BcaB03g15382' => 'bca', 'BcaB08g36994' => 'bca', 'BcaC03g13477' => 'bca', 'BcaC03g13478' => 'bca', 'BcaC03g13480' => 'bca', 'BcaC03g13481' => 'bca', 'BcaC03g13486' => 'bca', 'BcaC04g19031' => 'bca', 'BcaC04g23085' => 'bca', 'BcaC05g25094' => 'bca', 'BcaC05g25096' => 'bca', 'BcaC05g25138' => 'bca', 'BcaC05g30416' => 'bca', 'BcaC05g30455' => 'bca', 'BcaC06g30979' => 'bca', 'BcaC06g33805' => 'bca', 'BcaC08g46021' => 'bca', 'BcaNung03154' => 'bca', 'BolC2t06623H' => 'bol', 'BolC2t06632H' => 'bol', 'BolC2t06635H' => 'bol', 'BolC2t06638H' => 'bol', 'BolC3t13266H' => 'bol', 'BolC5t29776H' => 'bol', 'BolC6t38912H' => 'bol', 'BolC7t44183H' => 'bol', 'BolC9t54123H' => 'bol', 'BolC9t59107H' => 'bol', 'BraA02t05221Z' => 'bra', 'BraA03t09996Z' => 'bra', 'BraA05t23210Z' => 'bra', 'BraA06t24068Z' => 'bra', 'BraA06t27032Z' => 'bra', 'BraA08t35176Z' => 'bra', 'BraA09t36680Z' => 'bra', 'BraA10t44471Z' => 'bra', 'C02p06760' => 'bna', 'C02p06890' => 'bna', 'C02p07010' => 'bna', 'C03p07660' => 'bna', 'C05p10300' => 'bna', 'C06p38150' => 'bna', 'C07p36650' => 'bna', 'C08p15770' => 'bna', 'C09p12300' => 'bna', 'C09p62700' => 'bna', 'C09p75040' => 'bna', 'CAN.G13.1' => 'can', 'CAN.G138.4' => 'can', 'CAN.G44.6' => 'can', 'CAN.G473.19' => 'can', 'CANSAT01G0835' => 'cansat', 'CANSAT11G0246' => 'cansat', 'CANSAT11G1766' => 'cansat', 'CANSAT64G1954' => 'cansat', 'CARHR013330' => 'chi', 'CARHR060530' => 'chi', 'CARHR075300' => 'chi', 'CARHR105120' => 'chi', 'CARHR148910' => 'chi', 'CARHR198830' => 'chi', 'Carub.0001s1275' => 'cru', 'Carub.0002s1437' => 'cru', 'Carub.0003s0044' => 'cru', 'Carub.0003s2787' => 'cru', 'Carub.0005s0597' => 'cru', 'Carub.0006s1266' => 'cru', 'Ca_06935_v3' => 'car', 'Ca_13559_v3' => 'car', 'Ca_16941_v3' => 'car', 'Ca_16960_v3' => 'car', 'Ca_17775_v3' => 'car', 'Ca_30464_v3' => 'car', 'Cc06_g08160' => 'ccan', 'Cc07_g01520' => 'ccan', 'Cc11_g15810' => 'ccan', 'CDE02G2840' => 'cde', 'CDE03G0093' => 'cde', 'CDE04G2127' => 'cde', 'CDE07G1857' => 'cde', 'CDE09G1246' => 'cde', 'Cfa003412' => 'cfa', 'Cfa007341' => 'cfa', 'Cfa009220' => 'cfa', 'Ciclev10008737m.g' => 'ccl', 'Ciclev10015565m.g' => 'ccl', 'Ciclev10031761m.g' => 'ccl', 'CiPaw.03G045300' => 'cil', 'CiPaw.03G247200' => 'cil', 'CiPaw.04G029500' => 'cil', 'CiPaw.04G174000' => 'cil', 'CiPaw.05G181200' => 'cil', 'CiPaw.06G067100' => 'cil', 'ClCG05G025800' => 'cla', 'ClCG06G011400' => 'cla', 'ClCG09G019360' => 'cla', 'COL.COLO4_04827' => 'col', 'COL.COLO4_29170' => 'col', 'COL.COLO4_35131' => 'col', 'COL.COLO4_35132' => 'col', 'Cpa.g.sc33.32' => 'cpa', 'Cpa.g.sc46.29' => 'cpa', 'Cpa.g.sc796.1' => 'cpa', 'CsaV3_1G030420' => 'csa', 'CsaV3_5G027050' => 'csa', 'CsaV3_5G031040' => 'csa', 'CsaV3_UNG023130' => 'csa', 'CSS0007726' => 'camsi', 'CSS0016433' => 'camsi', 'CSS0017656' => 'camsi', 'CSS0025364' => 'camsi', 'CSS0027582' => 'camsi', 'CSS0047288' => 'camsi', 'CSS0049950' => 'camsi', 'DCAR_003843' => 'dca', 'DCAR_007052' => 'dca', 'DCAR_020884' => 'dca', 'DCAR_021730' => 'dca', 'DCAR_024423' => 'dca', 'DCAR_026509' => 'dca', 'DCAR_031158' => 'dca', 'Dinv14728' => 'din', 'Dinv15219' => 'din', 'Dinv25728' => 'din', 'Dinv33428' => 'din', 'Dinv36489' => 'din', 'Dinv41486' => 'din', 'Duzib147G0469' => 'dzi', 'Duzib168G0060' => 'dzi', 'Duzib187G1215' => 'dzi', 'Duzib248G0692' => 'dzi', 'Duzib251G0767' => 'dzi', 'Duzib264G0446' => 'dzi', 'Duzib268G0691' => 'dzi', 'ECA232G4767' => 'eca', 'ECA233G2838' => 'eca', 'ECA234G0391' => 'eca', 'ECA234G0857' => 'eca', 'ECA236G1593' => 'eca', 'ECA238G0565' => 'eca', 'ECA246G1027' => 'eca', 'ECA246G3223' => 'eca', 'ECA246G3470' => 'eca', 'EL10Ac6g13829' => 'bvu', 'EL10Ac6g14093' => 'bvu', 'EL10Ac8g18707' => 'bvu', 'Eucgr.C01369' => 'egr', 'Eucgr.H02492' => 'egr', 'Eucgr.I01733' => 'egr', 'Eucgr.J02255' => 'egr', 'Eucgr.J02257' => 'egr', 'Eucgr.J02258' => 'egr', 'FAN02G1601' => 'fan', 'FAN03G1586' => 'fan', 'FAN03G2986' => 'fan', 'FAN05G4837' => 'fan', 'FAN06G0146' => 'fan', 'FAN07G0858' => 'fan', 'FAN09G3179' => 'fan', 'FAN10G0669' => 'fan', 'FAN12G2358' => 'fan', 'FAN14G4198' => 'fan', 'FAN14G5112' => 'fan', 'FAN17G0342' => 'fan', 'FAN19G0342' => 'fan', 'FAN19G0962' => 'fan', 'FAN19G1101' => 'fan', 'FAN19G1872' => 'fan', 'FAN22G0356' => 'fan', 'FAN23G0744' => 'fan', 'FAN23G1914' => 'fan', 'FAN26G0032' => 'fan', 'FAN28G0625' => 'fan', 'FvH4_1g02710' => 'fve', 'FvH4_1g02720' => 'fve', 'FvH4_4g25670' => 'fve', 'FvH4_6g51700' => 'fve', 'FvH4_7g20170' => 'fve', 'Glyma.05G175000' => 'gma', 'Glyma.08G132300' => 'gma', 'Glyma.11G243000' => 'gma', 'Glyma.13G158900' => 'gma', 'Glyma.17G112400' => 'gma', 'Glyma.18G014100' => 'gma', 'Glyma.19G003100' => 'gma', 'Glyma.19G056500' => 'gma', 'Gohir.A01G158900' => 'ghi', 'Gohir.A05G312600' => 'ghi', 'Gohir.A05G354900' => 'ghi', 'Gohir.A07G037200' => 'ghi', 'Gohir.A09G030000' => 'ghi', 'Gohir.A12G145200' => 'ghi', 'Gohir.D01G151500' => 'ghi', 'Gohir.D04G058300' => 'ghi', 'Gohir.D05G314100' => 'ghi', 'Gohir.D07G041400' => 'ghi', 'Gohir.D09G029700' => 'ghi', 'Gohir.D12G149700' => 'ghi', 'Gorai.001G043800' => 'gra', 'Gorai.002G187800' => 'gra', 'Gorai.006G034700' => 'gra', 'Gorai.008G161200' => 'gra', 'Gorai.009G335700' => 'gra', 'Gorai.012G065000' => 'gra', 'GSVIVG01000535001' => 'vvi', 'GSVIVG01015572001' => 'vvi', 'GSVIVG01032386001' => 'vvi', 'HanXRQChr05g0138531' => 'han', 'HanXRQChr06g0174391' => 'han', 'HanXRQChr07g0199021' => 'han', 'HanXRQChr08g0208211' => 'han', 'HanXRQChr09g0255471' => 'han', 'HanXRQChr10g0315791' => 'han', 'HanXRQChr12g0371991' => 'han', 'HanXRQChr15g0475251' => 'han', 'HanXRQChr17g0540001' => 'han', 'HanXRQChr17g0548631' => 'han', 'HanXRQChr17g0569561' => 'han', 'Haze_12256' => 'cav', 'Haze_14756' => 'cav', 'Haze_25528' => 'cav', 'Hma1.2p1_0079F.1_g041020' => 'hma', 'Hma1.2p1_0818F.1_g223260' => 'hma', 'Hma1.2p1_1747F.1_g300530' => 'hma', 'HPP92_004607' => 'vpl', 'HPP92_004608' => 'vpl', 'HPP92_006181' => 'vpl', 'HPP92_012192' => 'vpl', 'HPP92_015680' => 'vpl', 'HPP92_020249' => 'vpl', 'HPP92_021376' => 'vpl', 'HPP92_024275' => 'vpl', 'Hund06031' => 'sun', 'Hund25391' => 'sun', 'Lalb_Chr07g0185371' => 'lal', 'Lalb_Chr07g0185381' => 'lal', 'Lalb_Chr12g0204011' => 'lal', 'Lalb_Chr13g0301671' => 'lal', 'Lalb_Chr14g0362851' => 'lal', 'Lalb_Chr24g0403581' => 'lal', 'Lj1g0000233' => 'lja', 'Lj2g0018120' => 'lja', 'Lj3C621T0' => 'lonja', 'Lj3P1059T14' => 'lonja', 'Lj3P611T9' => 'lonja', 'Lj3P614T13' => 'lonja', 'Lj3P615T5' => 'lonja', 'Lj4g0012315' => 'lja', 'Lj4g0026182' => 'lja', 'Lj6P813T16' => 'lonja', 'Lj7C427T7' => 'lonja', 'Lj7C427T8' => 'lonja', 'Lj7P600T41' => 'lonja', 'Lju41C42G17' => 'lonja', 'Lsat_1_v5_gn_0_47300' => 'lsa', 'Lsat_1_v5_gn_2_91280' => 'lsa', 'Lsat_1_v5_gn_3_30561' => 'lsa', 'Lsat_1_v5_gn_4_184321' => 'lsa', 'Lsat_1_v5_gn_4_4041' => 'lsa', 'Lsat_1_v5_gn_5_92000' => 'lsa', 'Lsat_1_v5_gn_8_152940' => 'lsa', 'Lsat_1_v5_gn_8_62401' => 'lsa', 'Manes.06G055900' => 'mes', 'Manes.12G022200' => 'mes', 'Manes.13G023300' => 'mes', 'Manes.14G115000' => 'mes', 'Manes.15G151700' => 'mes', 'Manes.17G111300' => 'mes', 'Mapoly0226s0009' => 'mpo', 'MBI02_g25363_MAGBIO' => 'mbi', 'MBI06_g00027_MAGBIO' => 'mbi', 'MBI10_g13034_MAGBIO' => 'mbi', 'MD09G1023400' => 'mdo', 'MD13G1100100' => 'mdo', 'MD15G1169200' => 'mdo', 'MD16G1101100' => 'mdo', 'MD17G1022900' => 'mdo', 'Medtr3g096150' => 'mtr', 'Medtr4g115070' => 'mtr', 'Medtr7g033325' => 'mtr', 'Medtr8g089840' => 'mtr', 'MELO3C010319.2' => 'cme', 'MELO3C011944.2' => 'cme', 'MELO3C021589.2' => 'cme', 'Migut.E00207' => 'egut', 'Migut.H00067' => 'egut', 'Migut.K00433' => 'egut', 'Migut.K00606' => 'egut', 'Migut.K01410' => 'egut', 'MSTRG.13347' => 'ama', 'MSTRG.24045' => 'ama', 'MSTRG.2428' => 'ama', 'MSTRG.26410' => 'ama', 'MSTRG.3139' => 'ama', 'MSTRG.3286' => 'ama', 'MSTRG.563' => 'ama', 'MSTRG.7941' => 'ama', 'Nitab4.5_0000028g0060' => 'nta', 'Nitab4.5_0000065g0260' => 'nta', 'Nitab4.5_0000112g0060' => 'nta', 'Nitab4.5_0000489g0120' => 'nta', 'Nitab4.5_0001776g0050' => 'nta', 'Nitab4.5_0001854g0010' => 'nta', 'Nitab4.5_0001860g0020' => 'nta', 'Nitab4.5_0004352g0010' => 'nta', 'Nitab4.5_0008716g0020' => 'nta', 'Nitab4.5_0008922g0010' => 'nta', 'Nn3g16693' => 'nnu', 'Nn4g22596' => 'nnu', 'Nn7g37639' => 'nnu', 'Oeu001701.1' => 'oeu', 'Oeu018149.1' => 'oeu', 'Oeu026220.1' => 'oeu', 'Oeu038635.1' => 'oeu', 'Oeu049176.1' => 'oeu', 'Oeu056706.1' => 'oeu', 'Oeu056937.1' => 'oeu', 'Oeu057540.1' => 'oeu', 'Os02g0594900' => 'osa', 'Os02g0595100' => 'osa', 'Os04g0477500' => 'osa', 'Os12g0611900' => 'osa', 'Peaxi162Scf00076g00020' => 'pax', 'Peaxi162Scf00128g00217' => 'pax', 'Peaxi162Scf00129g01640' => 'pax', 'Peaxi162Scf00669g00007' => 'pax', 'Peaxi162Scf00700g00421' => 'pax', 'Peaxi162Scf00801g00038' => 'pax', 'Peaxi162Scf00891g00025' => 'pax', 'PGR083G0909' => 'pgr', 'PGR119G1005' => 'pgr', 'PGR142G2236' => 'pgr', 'PGR142G3388' => 'pgr', 'PGSC0003DMG400004514' => 'stu', 'PGSC0003DMG400012635' => 'stu', 'PGSC0003DMG400015730' => 'stu', 'PGSC0003DMG400018611' => 'stu', 'PGSC0003DMG400030897' => 'stu', 'Phvul.001G254800' => 'pvu', 'Phvul.002G260100' => 'pvu', 'Phvul.003G167600' => 'pvu', 'Phvul.004G005100' => 'pvu', 'Potri.001G343600' => 'ptr', 'Potri.006G066700' => 'ptr', 'Potri.008G186000' => 'ptr', 'Potri.010G046900' => 'ptr', 'Potri.018G127900' => 'ptr', 'Pp3c20_17750' => 'ppa', 'Pp3c24_4380' => 'ppa', 'Prupe.1G245800' => 'ppe', 'Prupe.3G293400' => 'ppe', 'Prupe.7G247400' => 'ppe', 'Psat0s145g0120' => 'psa', 'Psat0s595g0040' => 'psa', 'Psat0s595g0120' => 'psa', 'Psat3g175040' => 'psa', 'Psat7g058120' => 'psa', 'PSO017G0428' => 'pso', 'PSO063G7510' => 'pso', 'PSO067G0046' => 'pso', 'PSO478G1073' => 'pso', 'PSO675G3677' => 'pso', 'PSO675G6558' => 'pso', 'PSO675G7520' => 'pso', 'PSO675G8959' => 'pso', 'QL02p074089' => 'qlo', 'QL02p089614' => 'qlo', 'QL03p057736' => 'qlo', 'RcHm_v2.0_Chr1g0364131' => 'rch', 'RcHm_v2.0_Chr2g0087801' => 'rch', 'RcHm_v2.0_Chr2g0087821' => 'rch', 'RcHm_v2.0_Chr2g0173231' => 'rch', 'RcHm_v2.0_Chr4g0433111' => 'rch', 'Rhsim03G0250300' => 'rsi', 'Rhsim08G0048400' => 'rsi', 'Rhsim10G0014800' => 'rsi', 'Rhsim12G0040100' => 'rsi', 'Rhsim12G0109700' => 'rsi', 'Sabra06G0049600' => 'sbr', 'Sabra08G0141000' => 'sbr', 'Sabra10G0021400' => 'sbr', 'Sabra16G0222900' => 'sbr', 'Sabra18G0108600' => 'sbr', 'SalBow1G0433' => 'sbo', 'SalBow1G2038' => 'sbo', 'SalBow1G5003' => 'sbo', 'SalBow7G1197' => 'sbo', 'SalBow8G3506' => 'sbo', 'Sc03g0007300' => 'sci', 'Sc11g0000950' => 'sci', 'Sc14g0008750' => 'sci', 'Sc18g0000420' => 'sci', 'Sed0006754' => 'sed', 'Sed0008741' => 'sed', 'Sed0017172' => 'sed', 'Sed0018925' => 'sed', 'Sed0023326' => 'sed', 'Sed0025909' => 'sed', 'SEGI_05333' => 'sgi', 'SEGI_10362' => 'sgi', 'SEGI_13380' => 'sgi', 'SEGI_24306' => 'sgi', 'SEGI_29077' => 'sgi', 'SEGI_29095' => 'sgi', 'SEGI_36534' => 'sgi', 'SEGI_37506' => 'sgi', 'SEGI_38321' => 'sgi', 'SGA_v2.0_scaffold307G48031' => 'sas', 'SGA_v2.0_scaffold47G17507' => 'sas', 'SGA_v2.0_scaffold63G21736' => 'sas', 'SGA_v2.0_scaffold87G27070' => 'sas', 'SHI17794' => 'shi', 'SHI28851' => 'shi', 'SMO165G0155' => 'smo', 'SMO340G0217' => 'smo', 'SMO367G1210' => 'smo', 'Solyc02g093430.3' => 'sly', 'Solyc05g013580.4' => 'sly', 'Solyc07g008030.3' => 'sly', 'Solyc12g035470.2' => 'sly', 'Sopen02g038020' => 'spe', 'Sopen05g008490' => 'spe', 'Sopen07g003910' => 'spe', 'Sopen12g015240' => 'spe', 'Sp1g11550' => 'spa', 'Sp2g16710' => 'spa', 'Sp3g00430' => 'spa', 'Sp3g26780' => 'spa', 'Sp5g22900' => 'spa', 'Sp6g29530' => 'spa', 'TAR371G0794' => 'tar', 'TAR374G0164' => 'tar', 'TAR622G0165' => 'tar', 'TAR626G0929' => 'tar', 'TAR629G2155' => 'tar', 'THA.LOC104805282' => 'tha', 'THA.LOC104805363' => 'tha', 'THA.LOC104808968' => 'tha', 'THA.LOC104821093' => 'tha', 'THA.LOC104823953' => 'tha', 'THA.LOC104825562' => 'tha', 'THA.LOC104825665' => 'tha', 'Thecc.02G261400' => 'tca', 'Thecc.04G019200' => 'tca', 'Thecc.09G130400' => 'tca', 'Thhalv10004374m.g' => 'esa', 'Thhalv10007850m.g' => 'esa', 'Thhalv10013782m.g' => 'esa', 'Thhalv10018686m.g' => 'esa', 'Thhalv10020899m.g' => 'esa', 'Thhalv10022755m.g' => 'esa', 'TPR.G23851' => 'tpr', 'TPR.G26500' => 'tpr', 'TPR.G27267' => 'tpr', 'TPR.G32001' => 'tpr', 'TPR.G6251' => 'tpr', 'TPR.G8167' => 'tpr', 'TWI12G1330' => 'twi', 'TWI18G1239' => 'twi', 'TWI34G0979' => 'twi', 'TWI36G0670' => 'twi', 'TWI36G0707' => 'twi', 'TWI56G0233' => 'twi', 'TWI75G1809' => 'twi', 'unitig_21.g20874' => 'ugi', 'unitig_26.g10343' => 'ugi', 'unitig_46.g18392' => 'ugi', 'unitig_52.g17178' => 'ugi', 'unitig_8.g2934' => 'ugi', 'vmacro01122' => 'vma', 'vmacro05875' => 'vma', 'vmacro06147' => 'vma', 'vmacro16191' => 'vma', 'vmacro18293' => 'vma', 'VMungo0251G3707' => 'vmu', 'VMungo0464G1521' => 'vmu', 'VMungo1215G0205' => 'vmu', 'VMungo1383G2484' => 'vmu', 'Zm00001eb079610' => 'zma', 'Zm00001eb135990' => 'zma', 'Zm00001eb183710' => 'zma', 'Zm00001eb246020' => 'zma' ) $gf_id = 'HOM05D001124' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001124' ) $data_identifier = 'HOM05D001124' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 6, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 7, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 21, 'bol' => (int) 10, 'bra' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 6, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 9, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 21, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 8, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 10, 'lsa' => (int) 8, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 8, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 9, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb246020' $species_info = array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ) $local_species = 'tca' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001124', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '548', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02520' => 'bna', 'A03p06630' => 'bna', 'A05p44460' => 'bna', 'A06p08710' => 'bna', 'A06p41090' => 'bna', 'A07p32320' => 'bna', 'A08p32520' => 'bna', 'A09p10360' => 'bna', 'A10p24080' => 'bna', 'Aa31LG11G15250' => 'aar', 'Aa31LG1G1800' => 'aar', 'Aa31LG2G5120' => 'aar', 'Aa31LG2G6070' => 'aar', 'Aa31LG5G10770' => 'aar', 'Aa31sc61G90' => 'aar', 'Actinidia01352' => 'ach', 'Actinidia05983' => 'ach', 'Actinidia08133' => 'ach', 'Actinidia15101' => 'ach', 'Actinidia26379' => 'ach', 'Actinidia35778' => 'ach', 'Actinidia36123' => 'ach', 'Actinidia37436' => 'ach', 'Actinidia38730' => 'ach', 'Ah.02g128210' => 'amhyb', 'Ah.03g132990' => 'amhyb', 'Ah.14g079410' => 'amhyb', 'AL1G24640' => 'aly', 'AL2G26680' => 'aly', 'AL3G10530' => 'aly', 'AL3G45230' => 'aly', 'AL5G15230' => 'aly', 'AL5G16960' => 'aly', 'AL6G25210' => 'aly', 'Aqoxy2G00441' => 'aox', 'Aqoxy3G01236' => 'aox', 'Aqoxy5G03746' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3RQ047' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C7GMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9C8JER' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MBL6KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YXCZ83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZANX40' => 'arhy', 'AT1G12990' => 'ath', 'AT1G67880' => 'ath', 'AT2G13290' => 'ath', 'AT3G01620' => 'ath', 'AT3G26445' => 'ath', 'AT3G27540' => 'ath', 'AT5G14480' => 'ath', 'ATR0824G026' => 'atr', 'ATR1098G019' => 'atr', 'Atru.chr11.2145' => 'acertr', 'Atru.chr2.3636' => 'acertr', 'Atru.chr2.3644' => 'acertr', 'Atru.chr6.2422' => 'acertr', 'Atru.chr7.1112' => 'acertr', 'AUR62005469' => 'cqu', 'AUR62011166' => 'cqu', 'AUR62013319' => 'cqu', 'AUR62024273' => 'cqu', 'AUR62028420' => 'cqu', 'AUR62041942' => 'cqu', 'BcaB01g04969' => 'bca', 'BcaB01g06371' => 'bca', 'BcaB02g11494' => 'bca', 'BcaB03g15382' => 'bca', 'BcaB08g36994' => 'bca', 'BcaC03g13477' => 'bca', 'BcaC03g13478' => 'bca', 'BcaC03g13480' => 'bca', 'BcaC03g13481' => 'bca', 'BcaC03g13486' => 'bca', 'BcaC04g19031' => 'bca', 'BcaC04g23085' => 'bca', 'BcaC05g25094' => 'bca', 'BcaC05g25096' => 'bca', 'BcaC05g25138' => 'bca', 'BcaC05g30416' => 'bca', 'BcaC05g30455' => 'bca', 'BcaC06g30979' => 'bca', 'BcaC06g33805' => 'bca', 'BcaC08g46021' => 'bca', 'BcaNung03154' => 'bca', 'BolC2t06623H' => 'bol', 'BolC2t06632H' => 'bol', 'BolC2t06635H' => 'bol', 'BolC2t06638H' => 'bol', 'BolC3t13266H' => 'bol', 'BolC5t29776H' => 'bol', 'BolC6t38912H' => 'bol', 'BolC7t44183H' => 'bol', 'BolC9t54123H' => 'bol', 'BolC9t59107H' => 'bol', 'BraA02t05221Z' => 'bra', 'BraA03t09996Z' => 'bra', 'BraA05t23210Z' => 'bra', 'BraA06t24068Z' => 'bra', 'BraA06t27032Z' => 'bra', 'BraA08t35176Z' => 'bra', 'BraA09t36680Z' => 'bra', 'BraA10t44471Z' => 'bra', 'C02p06760' => 'bna', 'C02p06890' => 'bna', 'C02p07010' => 'bna', 'C03p07660' => 'bna', 'C05p10300' => 'bna', 'C06p38150' => 'bna', 'C07p36650' => 'bna', 'C08p15770' => 'bna', 'C09p12300' => 'bna', 'C09p62700' => 'bna', 'C09p75040' => 'bna', 'CAN.G13.1' => 'can', 'CAN.G138.4' => 'can', 'CAN.G44.6' => 'can', 'CAN.G473.19' => 'can', 'CANSAT01G0835' => 'cansat', 'CANSAT11G0246' => 'cansat', 'CANSAT11G1766' => 'cansat', 'CANSAT64G1954' => 'cansat', 'CARHR013330' => 'chi', 'CARHR060530' => 'chi', 'CARHR075300' => 'chi', 'CARHR105120' => 'chi', 'CARHR148910' => 'chi', 'CARHR198830' => 'chi', 'Carub.0001s1275' => 'cru', 'Carub.0002s1437' => 'cru', 'Carub.0003s0044' => 'cru', 'Carub.0003s2787' => 'cru', 'Carub.0005s0597' => 'cru', 'Carub.0006s1266' => 'cru', 'Ca_06935_v3' => 'car', 'Ca_13559_v3' => 'car', 'Ca_16941_v3' => 'car', 'Ca_16960_v3' => 'car', 'Ca_17775_v3' => 'car', 'Ca_30464_v3' => 'car', 'Cc06_g08160' => 'ccan', 'Cc07_g01520' => 'ccan', 'Cc11_g15810' => 'ccan', 'CDE02G2840' => 'cde', 'CDE03G0093' => 'cde', 'CDE04G2127' => 'cde', 'CDE07G1857' => 'cde', 'CDE09G1246' => 'cde', 'Cfa003412' => 'cfa', 'Cfa007341' => 'cfa', 'Cfa009220' => 'cfa', 'Ciclev10008737m.g' => 'ccl', 'Ciclev10015565m.g' => 'ccl', 'Ciclev10031761m.g' => 'ccl', 'CiPaw.03G045300' => 'cil', 'CiPaw.03G247200' => 'cil', 'CiPaw.04G029500' => 'cil', 'CiPaw.04G174000' => 'cil', 'CiPaw.05G181200' => 'cil', 'CiPaw.06G067100' => 'cil', 'ClCG05G025800' => 'cla', 'ClCG06G011400' => 'cla', 'ClCG09G019360' => 'cla', 'COL.COLO4_04827' => 'col', 'COL.COLO4_29170' => 'col', 'COL.COLO4_35131' => 'col', 'COL.COLO4_35132' => 'col', 'Cpa.g.sc33.32' => 'cpa', 'Cpa.g.sc46.29' => 'cpa', 'Cpa.g.sc796.1' => 'cpa', 'CsaV3_1G030420' => 'csa', 'CsaV3_5G027050' => 'csa', 'CsaV3_5G031040' => 'csa', 'CsaV3_UNG023130' => 'csa', 'CSS0007726' => 'camsi', 'CSS0016433' => 'camsi', 'CSS0017656' => 'camsi', 'CSS0025364' => 'camsi', 'CSS0027582' => 'camsi', 'CSS0047288' => 'camsi', 'CSS0049950' => 'camsi', 'DCAR_003843' => 'dca', 'DCAR_007052' => 'dca', 'DCAR_020884' => 'dca', 'DCAR_021730' => 'dca', 'DCAR_024423' => 'dca', 'DCAR_026509' => 'dca', 'DCAR_031158' => 'dca', 'Dinv14728' => 'din', 'Dinv15219' => 'din', 'Dinv25728' => 'din', 'Dinv33428' => 'din', 'Dinv36489' => 'din', 'Dinv41486' => 'din', 'Duzib147G0469' => 'dzi', 'Duzib168G0060' => 'dzi', 'Duzib187G1215' => 'dzi', 'Duzib248G0692' => 'dzi', 'Duzib251G0767' => 'dzi', 'Duzib264G0446' => 'dzi', 'Duzib268G0691' => 'dzi', 'ECA232G4767' => 'eca', 'ECA233G2838' => 'eca', 'ECA234G0391' => 'eca', 'ECA234G0857' => 'eca', 'ECA236G1593' => 'eca', 'ECA238G0565' => 'eca', 'ECA246G1027' => 'eca', 'ECA246G3223' => 'eca', 'ECA246G3470' => 'eca', 'EL10Ac6g13829' => 'bvu', 'EL10Ac6g14093' => 'bvu', 'EL10Ac8g18707' => 'bvu', 'Eucgr.C01369' => 'egr', 'Eucgr.H02492' => 'egr', 'Eucgr.I01733' => 'egr', 'Eucgr.J02255' => 'egr', 'Eucgr.J02257' => 'egr', 'Eucgr.J02258' => 'egr', 'FAN02G1601' => 'fan', 'FAN03G1586' => 'fan', 'FAN03G2986' => 'fan', 'FAN05G4837' => 'fan', 'FAN06G0146' => 'fan', 'FAN07G0858' => 'fan', 'FAN09G3179' => 'fan', 'FAN10G0669' => 'fan', 'FAN12G2358' => 'fan', 'FAN14G4198' => 'fan', 'FAN14G5112' => 'fan', 'FAN17G0342' => 'fan', 'FAN19G0342' => 'fan', 'FAN19G0962' => 'fan', 'FAN19G1101' => 'fan', 'FAN19G1872' => 'fan', 'FAN22G0356' => 'fan', 'FAN23G0744' => 'fan', 'FAN23G1914' => 'fan', 'FAN26G0032' => 'fan', 'FAN28G0625' => 'fan', 'FvH4_1g02710' => 'fve', 'FvH4_1g02720' => 'fve', 'FvH4_4g25670' => 'fve', 'FvH4_6g51700' => 'fve', 'FvH4_7g20170' => 'fve', 'Glyma.05G175000' => 'gma', 'Glyma.08G132300' => 'gma', 'Glyma.11G243000' => 'gma', 'Glyma.13G158900' => 'gma', 'Glyma.17G112400' => 'gma', 'Glyma.18G014100' => 'gma', 'Glyma.19G003100' => 'gma', 'Glyma.19G056500' => 'gma', 'Gohir.A01G158900' => 'ghi', 'Gohir.A05G312600' => 'ghi', 'Gohir.A05G354900' => 'ghi', 'Gohir.A07G037200' => 'ghi', 'Gohir.A09G030000' => 'ghi', 'Gohir.A12G145200' => 'ghi', 'Gohir.D01G151500' => 'ghi', 'Gohir.D04G058300' => 'ghi', 'Gohir.D05G314100' => 'ghi', 'Gohir.D07G041400' => 'ghi', 'Gohir.D09G029700' => 'ghi', 'Gohir.D12G149700' => 'ghi', 'Gorai.001G043800' => 'gra', 'Gorai.002G187800' => 'gra', 'Gorai.006G034700' => 'gra', 'Gorai.008G161200' => 'gra', 'Gorai.009G335700' => 'gra', 'Gorai.012G065000' => 'gra', 'GSVIVG01000535001' => 'vvi', 'GSVIVG01015572001' => 'vvi', 'GSVIVG01032386001' => 'vvi', 'HanXRQChr05g0138531' => 'han', 'HanXRQChr06g0174391' => 'han', 'HanXRQChr07g0199021' => 'han', 'HanXRQChr08g0208211' => 'han', 'HanXRQChr09g0255471' => 'han', 'HanXRQChr10g0315791' => 'han', 'HanXRQChr12g0371991' => 'han', 'HanXRQChr15g0475251' => 'han', 'HanXRQChr17g0540001' => 'han', 'HanXRQChr17g0548631' => 'han', 'HanXRQChr17g0569561' => 'han', 'Haze_12256' => 'cav', 'Haze_14756' => 'cav', 'Haze_25528' => 'cav', 'Hma1.2p1_0079F.1_g041020' => 'hma', 'Hma1.2p1_0818F.1_g223260' => 'hma', 'Hma1.2p1_1747F.1_g300530' => 'hma', 'HPP92_004607' => 'vpl', 'HPP92_004608' => 'vpl', 'HPP92_006181' => 'vpl', 'HPP92_012192' => 'vpl', 'HPP92_015680' => 'vpl', 'HPP92_020249' => 'vpl', 'HPP92_021376' => 'vpl', 'HPP92_024275' => 'vpl', 'Hund06031' => 'sun', 'Hund25391' => 'sun', 'Lalb_Chr07g0185371' => 'lal', 'Lalb_Chr07g0185381' => 'lal', 'Lalb_Chr12g0204011' => 'lal', 'Lalb_Chr13g0301671' => 'lal', 'Lalb_Chr14g0362851' => 'lal', 'Lalb_Chr24g0403581' => 'lal', 'Lj1g0000233' => 'lja', 'Lj2g0018120' => 'lja', 'Lj3C621T0' => 'lonja', 'Lj3P1059T14' => 'lonja', 'Lj3P611T9' => 'lonja', 'Lj3P614T13' => 'lonja', 'Lj3P615T5' => 'lonja', 'Lj4g0012315' => 'lja', 'Lj4g0026182' => 'lja', 'Lj6P813T16' => 'lonja', 'Lj7C427T7' => 'lonja', 'Lj7C427T8' => 'lonja', 'Lj7P600T41' => 'lonja', 'Lju41C42G17' => 'lonja', 'Lsat_1_v5_gn_0_47300' => 'lsa', 'Lsat_1_v5_gn_2_91280' => 'lsa', 'Lsat_1_v5_gn_3_30561' => 'lsa', 'Lsat_1_v5_gn_4_184321' => 'lsa', 'Lsat_1_v5_gn_4_4041' => 'lsa', 'Lsat_1_v5_gn_5_92000' => 'lsa', 'Lsat_1_v5_gn_8_152940' => 'lsa', 'Lsat_1_v5_gn_8_62401' => 'lsa', 'Manes.06G055900' => 'mes', 'Manes.12G022200' => 'mes', 'Manes.13G023300' => 'mes', 'Manes.14G115000' => 'mes', 'Manes.15G151700' => 'mes', 'Manes.17G111300' => 'mes', 'Mapoly0226s0009' => 'mpo', 'MBI02_g25363_MAGBIO' => 'mbi', 'MBI06_g00027_MAGBIO' => 'mbi', 'MBI10_g13034_MAGBIO' => 'mbi', 'MD09G1023400' => 'mdo', 'MD13G1100100' => 'mdo', 'MD15G1169200' => 'mdo', 'MD16G1101100' => 'mdo', 'MD17G1022900' => 'mdo', 'Medtr3g096150' => 'mtr', 'Medtr4g115070' => 'mtr', 'Medtr7g033325' => 'mtr', 'Medtr8g089840' => 'mtr', 'MELO3C010319.2' => 'cme', 'MELO3C011944.2' => 'cme', 'MELO3C021589.2' => 'cme', 'Migut.E00207' => 'egut', 'Migut.H00067' => 'egut', 'Migut.K00433' => 'egut', 'Migut.K00606' => 'egut', 'Migut.K01410' => 'egut', 'MSTRG.13347' => 'ama', 'MSTRG.24045' => 'ama', 'MSTRG.2428' => 'ama', 'MSTRG.26410' => 'ama', 'MSTRG.3139' => 'ama', 'MSTRG.3286' => 'ama', 'MSTRG.563' => 'ama', 'MSTRG.7941' => 'ama', 'Nitab4.5_0000028g0060' => 'nta', 'Nitab4.5_0000065g0260' => 'nta', 'Nitab4.5_0000112g0060' => 'nta', 'Nitab4.5_0000489g0120' => 'nta', 'Nitab4.5_0001776g0050' => 'nta', 'Nitab4.5_0001854g0010' => 'nta', 'Nitab4.5_0001860g0020' => 'nta', 'Nitab4.5_0004352g0010' => 'nta', 'Nitab4.5_0008716g0020' => 'nta', 'Nitab4.5_0008922g0010' => 'nta', 'Nn3g16693' => 'nnu', 'Nn4g22596' => 'nnu', 'Nn7g37639' => 'nnu', 'Oeu001701.1' => 'oeu', 'Oeu018149.1' => 'oeu', 'Oeu026220.1' => 'oeu', 'Oeu038635.1' => 'oeu', 'Oeu049176.1' => 'oeu', 'Oeu056706.1' => 'oeu', 'Oeu056937.1' => 'oeu', 'Oeu057540.1' => 'oeu', 'Os02g0594900' => 'osa', 'Os02g0595100' => 'osa', 'Os04g0477500' => 'osa', 'Os12g0611900' => 'osa', 'Peaxi162Scf00076g00020' => 'pax', 'Peaxi162Scf00128g00217' => 'pax', 'Peaxi162Scf00129g01640' => 'pax', 'Peaxi162Scf00669g00007' => 'pax', 'Peaxi162Scf00700g00421' => 'pax', 'Peaxi162Scf00801g00038' => 'pax', 'Peaxi162Scf00891g00025' => 'pax', 'PGR083G0909' => 'pgr', 'PGR119G1005' => 'pgr', 'PGR142G2236' => 'pgr', 'PGR142G3388' => 'pgr', 'PGSC0003DMG400004514' => 'stu', 'PGSC0003DMG400012635' => 'stu', 'PGSC0003DMG400015730' => 'stu', 'PGSC0003DMG400018611' => 'stu', 'PGSC0003DMG400030897' => 'stu', 'Phvul.001G254800' => 'pvu', 'Phvul.002G260100' => 'pvu', 'Phvul.003G167600' => 'pvu', 'Phvul.004G005100' => 'pvu', 'Potri.001G343600' => 'ptr', 'Potri.006G066700' => 'ptr', 'Potri.008G186000' => 'ptr', 'Potri.010G046900' => 'ptr', 'Potri.018G127900' => 'ptr', 'Pp3c20_17750' => 'ppa', 'Pp3c24_4380' => 'ppa', 'Prupe.1G245800' => 'ppe', 'Prupe.3G293400' => 'ppe', 'Prupe.7G247400' => 'ppe', 'Psat0s145g0120' => 'psa', 'Psat0s595g0040' => 'psa', 'Psat0s595g0120' => 'psa', 'Psat3g175040' => 'psa', 'Psat7g058120' => 'psa', 'PSO017G0428' => 'pso', 'PSO063G7510' => 'pso', 'PSO067G0046' => 'pso', 'PSO478G1073' => 'pso', 'PSO675G3677' => 'pso', 'PSO675G6558' => 'pso', 'PSO675G7520' => 'pso', 'PSO675G8959' => 'pso', 'QL02p074089' => 'qlo', 'QL02p089614' => 'qlo', 'QL03p057736' => 'qlo', 'RcHm_v2.0_Chr1g0364131' => 'rch', 'RcHm_v2.0_Chr2g0087801' => 'rch', 'RcHm_v2.0_Chr2g0087821' => 'rch', 'RcHm_v2.0_Chr2g0173231' => 'rch', 'RcHm_v2.0_Chr4g0433111' => 'rch', 'Rhsim03G0250300' => 'rsi', 'Rhsim08G0048400' => 'rsi', 'Rhsim10G0014800' => 'rsi', 'Rhsim12G0040100' => 'rsi', 'Rhsim12G0109700' => 'rsi', 'Sabra06G0049600' => 'sbr', 'Sabra08G0141000' => 'sbr', 'Sabra10G0021400' => 'sbr', 'Sabra16G0222900' => 'sbr', 'Sabra18G0108600' => 'sbr', 'SalBow1G0433' => 'sbo', 'SalBow1G2038' => 'sbo', 'SalBow1G5003' => 'sbo', 'SalBow7G1197' => 'sbo', 'SalBow8G3506' => 'sbo', 'Sc03g0007300' => 'sci', 'Sc11g0000950' => 'sci', 'Sc14g0008750' => 'sci', 'Sc18g0000420' => 'sci', 'Sed0006754' => 'sed', 'Sed0008741' => 'sed', 'Sed0017172' => 'sed', 'Sed0018925' => 'sed', 'Sed0023326' => 'sed', 'Sed0025909' => 'sed', 'SEGI_05333' => 'sgi', 'SEGI_10362' => 'sgi', 'SEGI_13380' => 'sgi', 'SEGI_24306' => 'sgi', 'SEGI_29077' => 'sgi', 'SEGI_29095' => 'sgi', 'SEGI_36534' => 'sgi', 'SEGI_37506' => 'sgi', 'SEGI_38321' => 'sgi', 'SGA_v2.0_scaffold307G48031' => 'sas', 'SGA_v2.0_scaffold47G17507' => 'sas', 'SGA_v2.0_scaffold63G21736' => 'sas', 'SGA_v2.0_scaffold87G27070' => 'sas', 'SHI17794' => 'shi', 'SHI28851' => 'shi', 'SMO165G0155' => 'smo', 'SMO340G0217' => 'smo', 'SMO367G1210' => 'smo', 'Solyc02g093430.3' => 'sly', 'Solyc05g013580.4' => 'sly', 'Solyc07g008030.3' => 'sly', 'Solyc12g035470.2' => 'sly', 'Sopen02g038020' => 'spe', 'Sopen05g008490' => 'spe', 'Sopen07g003910' => 'spe', 'Sopen12g015240' => 'spe', 'Sp1g11550' => 'spa', 'Sp2g16710' => 'spa', 'Sp3g00430' => 'spa', 'Sp3g26780' => 'spa', 'Sp5g22900' => 'spa', 'Sp6g29530' => 'spa', 'TAR371G0794' => 'tar', 'TAR374G0164' => 'tar', 'TAR622G0165' => 'tar', 'TAR626G0929' => 'tar', 'TAR629G2155' => 'tar', 'THA.LOC104805282' => 'tha', 'THA.LOC104805363' => 'tha', 'THA.LOC104808968' => 'tha', 'THA.LOC104821093' => 'tha', 'THA.LOC104823953' => 'tha', 'THA.LOC104825562' => 'tha', 'THA.LOC104825665' => 'tha', 'Thecc.02G261400' => 'tca', 'Thecc.04G019200' => 'tca', 'Thecc.09G130400' => 'tca', 'Thhalv10004374m.g' => 'esa', 'Thhalv10007850m.g' => 'esa', 'Thhalv10013782m.g' => 'esa', 'Thhalv10018686m.g' => 'esa', 'Thhalv10020899m.g' => 'esa', 'Thhalv10022755m.g' => 'esa', 'TPR.G23851' => 'tpr', 'TPR.G26500' => 'tpr', 'TPR.G27267' => 'tpr', 'TPR.G32001' => 'tpr', 'TPR.G6251' => 'tpr', 'TPR.G8167' => 'tpr', 'TWI12G1330' => 'twi', 'TWI18G1239' => 'twi', 'TWI34G0979' => 'twi', 'TWI36G0670' => 'twi', 'TWI36G0707' => 'twi', 'TWI56G0233' => 'twi', 'TWI75G1809' => 'twi', 'unitig_21.g20874' => 'ugi', 'unitig_26.g10343' => 'ugi', 'unitig_46.g18392' => 'ugi', 'unitig_52.g17178' => 'ugi', 'unitig_8.g2934' => 'ugi', 'vmacro01122' => 'vma', 'vmacro05875' => 'vma', 'vmacro06147' => 'vma', 'vmacro16191' => 'vma', 'vmacro18293' => 'vma', 'VMungo0251G3707' => 'vmu', 'VMungo0464G1521' => 'vmu', 'VMungo1215G0205' => 'vmu', 'VMungo1383G2484' => 'vmu', 'Zm00001eb079610' => 'zma', 'Zm00001eb135990' => 'zma', 'Zm00001eb183710' => 'zma', 'Zm00001eb246020' => 'zma' ), 'gf_id' => 'HOM05D001124', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001124' ), 'data_identifier' => 'HOM05D001124', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001124', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '548', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02520' => 'bna', 'A03p06630' => 'bna', 'A05p44460' => 'bna', 'A06p08710' => 'bna', 'A06p41090' => 'bna', 'A07p32320' => 'bna', 'A08p32520' => 'bna', 'A09p10360' => 'bna', 'A10p24080' => 'bna', 'Aa31LG11G15250' => 'aar', 'Aa31LG1G1800' => 'aar', 'Aa31LG2G5120' => 'aar', 'Aa31LG2G6070' => 'aar', 'Aa31LG5G10770' => 'aar', 'Aa31sc61G90' => 'aar', 'Actinidia01352' => 'ach', 'Actinidia05983' => 'ach', 'Actinidia08133' => 'ach', 'Actinidia15101' => 'ach', 'Actinidia26379' => 'ach', 'Actinidia35778' => 'ach', 'Actinidia36123' => 'ach', 'Actinidia37436' => 'ach', 'Actinidia38730' => 'ach', 'Ah.02g128210' => 'amhyb', 'Ah.03g132990' => 'amhyb', 'Ah.14g079410' => 'amhyb', 'AL1G24640' => 'aly', 'AL2G26680' => 'aly', 'AL3G10530' => 'aly', 'AL3G45230' => 'aly', 'AL5G15230' => 'aly', 'AL5G16960' => 'aly', 'AL6G25210' => 'aly', 'Aqoxy2G00441' => 'aox', 'Aqoxy3G01236' => 'aox', 'Aqoxy5G03746' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3RQ047' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C7GMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9C8JER' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MBL6KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YXCZ83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZANX40' => 'arhy', 'AT1G12990' => 'ath', 'AT1G67880' => 'ath', 'AT2G13290' => 'ath', 'AT3G01620' => 'ath', 'AT3G26445' => 'ath', 'AT3G27540' => 'ath', 'AT5G14480' => 'ath', 'ATR0824G026' => 'atr', 'ATR1098G019' => 'atr', 'Atru.chr11.2145' => 'acertr', 'Atru.chr2.3636' => 'acertr', 'Atru.chr2.3644' => 'acertr', 'Atru.chr6.2422' => 'acertr', 'Atru.chr7.1112' => 'acertr', 'AUR62005469' => 'cqu', 'AUR62011166' => 'cqu', 'AUR62013319' => 'cqu', 'AUR62024273' => 'cqu', 'AUR62028420' => 'cqu', 'AUR62041942' => 'cqu', 'BcaB01g04969' => 'bca', 'BcaB01g06371' => 'bca', 'BcaB02g11494' => 'bca', 'BcaB03g15382' => 'bca', 'BcaB08g36994' => 'bca', 'BcaC03g13477' => 'bca', 'BcaC03g13478' => 'bca', 'BcaC03g13480' => 'bca', 'BcaC03g13481' => 'bca', 'BcaC03g13486' => 'bca', 'BcaC04g19031' => 'bca', 'BcaC04g23085' => 'bca', 'BcaC05g25094' => 'bca', 'BcaC05g25096' => 'bca', 'BcaC05g25138' => 'bca', 'BcaC05g30416' => 'bca', 'BcaC05g30455' => 'bca', 'BcaC06g30979' => 'bca', 'BcaC06g33805' => 'bca', 'BcaC08g46021' => 'bca', 'BcaNung03154' => 'bca', 'BolC2t06623H' => 'bol', 'BolC2t06632H' => 'bol', 'BolC2t06635H' => 'bol', 'BolC2t06638H' => 'bol', 'BolC3t13266H' => 'bol', 'BolC5t29776H' => 'bol', 'BolC6t38912H' => 'bol', 'BolC7t44183H' => 'bol', 'BolC9t54123H' => 'bol', 'BolC9t59107H' => 'bol', 'BraA02t05221Z' => 'bra', 'BraA03t09996Z' => 'bra', 'BraA05t23210Z' => 'bra', 'BraA06t24068Z' => 'bra', 'BraA06t27032Z' => 'bra', 'BraA08t35176Z' => 'bra', 'BraA09t36680Z' => 'bra', 'BraA10t44471Z' => 'bra', 'C02p06760' => 'bna', 'C02p06890' => 'bna', 'C02p07010' => 'bna', 'C03p07660' => 'bna', 'C05p10300' => 'bna', 'C06p38150' => 'bna', 'C07p36650' => 'bna', 'C08p15770' => 'bna', 'C09p12300' => 'bna', 'C09p62700' => 'bna', 'C09p75040' => 'bna', 'CAN.G13.1' => 'can', 'CAN.G138.4' => 'can', 'CAN.G44.6' => 'can', 'CAN.G473.19' => 'can', 'CANSAT01G0835' => 'cansat', 'CANSAT11G0246' => 'cansat', 'CANSAT11G1766' => 'cansat', 'CANSAT64G1954' => 'cansat', 'CARHR013330' => 'chi', 'CARHR060530' => 'chi', 'CARHR075300' => 'chi', 'CARHR105120' => 'chi', 'CARHR148910' => 'chi', 'CARHR198830' => 'chi', 'Carub.0001s1275' => 'cru', 'Carub.0002s1437' => 'cru', 'Carub.0003s0044' => 'cru', 'Carub.0003s2787' => 'cru', 'Carub.0005s0597' => 'cru', 'Carub.0006s1266' => 'cru', 'Ca_06935_v3' => 'car', 'Ca_13559_v3' => 'car', 'Ca_16941_v3' => 'car', 'Ca_16960_v3' => 'car', 'Ca_17775_v3' => 'car', 'Ca_30464_v3' => 'car', 'Cc06_g08160' => 'ccan', 'Cc07_g01520' => 'ccan', 'Cc11_g15810' => 'ccan', 'CDE02G2840' => 'cde', 'CDE03G0093' => 'cde', 'CDE04G2127' => 'cde', 'CDE07G1857' => 'cde', 'CDE09G1246' => 'cde', 'Cfa003412' => 'cfa', 'Cfa007341' => 'cfa', 'Cfa009220' => 'cfa', 'Ciclev10008737m.g' => 'ccl', 'Ciclev10015565m.g' => 'ccl', 'Ciclev10031761m.g' => 'ccl', 'CiPaw.03G045300' => 'cil', 'CiPaw.03G247200' => 'cil', 'CiPaw.04G029500' => 'cil', 'CiPaw.04G174000' => 'cil', 'CiPaw.05G181200' => 'cil', 'CiPaw.06G067100' => 'cil', 'ClCG05G025800' => 'cla', 'ClCG06G011400' => 'cla', 'ClCG09G019360' => 'cla', 'COL.COLO4_04827' => 'col', 'COL.COLO4_29170' => 'col', 'COL.COLO4_35131' => 'col', 'COL.COLO4_35132' => 'col', 'Cpa.g.sc33.32' => 'cpa', 'Cpa.g.sc46.29' => 'cpa', 'Cpa.g.sc796.1' => 'cpa', 'CsaV3_1G030420' => 'csa', 'CsaV3_5G027050' => 'csa', 'CsaV3_5G031040' => 'csa', 'CsaV3_UNG023130' => 'csa', 'CSS0007726' => 'camsi', 'CSS0016433' => 'camsi', 'CSS0017656' => 'camsi', 'CSS0025364' => 'camsi', 'CSS0027582' => 'camsi', 'CSS0047288' => 'camsi', 'CSS0049950' => 'camsi', 'DCAR_003843' => 'dca', 'DCAR_007052' => 'dca', 'DCAR_020884' => 'dca', 'DCAR_021730' => 'dca', 'DCAR_024423' => 'dca', 'DCAR_026509' => 'dca', 'DCAR_031158' => 'dca', 'Dinv14728' => 'din', 'Dinv15219' => 'din', 'Dinv25728' => 'din', 'Dinv33428' => 'din', 'Dinv36489' => 'din', 'Dinv41486' => 'din', 'Duzib147G0469' => 'dzi', 'Duzib168G0060' => 'dzi', 'Duzib187G1215' => 'dzi', 'Duzib248G0692' => 'dzi', 'Duzib251G0767' => 'dzi', 'Duzib264G0446' => 'dzi', 'Duzib268G0691' => 'dzi', 'ECA232G4767' => 'eca', 'ECA233G2838' => 'eca', 'ECA234G0391' => 'eca', 'ECA234G0857' => 'eca', 'ECA236G1593' => 'eca', 'ECA238G0565' => 'eca', 'ECA246G1027' => 'eca', 'ECA246G3223' => 'eca', 'ECA246G3470' => 'eca', 'EL10Ac6g13829' => 'bvu', 'EL10Ac6g14093' => 'bvu', 'EL10Ac8g18707' => 'bvu', 'Eucgr.C01369' => 'egr', 'Eucgr.H02492' => 'egr', 'Eucgr.I01733' => 'egr', 'Eucgr.J02255' => 'egr', 'Eucgr.J02257' => 'egr', 'Eucgr.J02258' => 'egr', 'FAN02G1601' => 'fan', 'FAN03G1586' => 'fan', 'FAN03G2986' => 'fan', 'FAN05G4837' => 'fan', 'FAN06G0146' => 'fan', 'FAN07G0858' => 'fan', 'FAN09G3179' => 'fan', 'FAN10G0669' => 'fan', 'FAN12G2358' => 'fan', 'FAN14G4198' => 'fan', 'FAN14G5112' => 'fan', 'FAN17G0342' => 'fan', 'FAN19G0342' => 'fan', 'FAN19G0962' => 'fan', 'FAN19G1101' => 'fan', 'FAN19G1872' => 'fan', 'FAN22G0356' => 'fan', 'FAN23G0744' => 'fan', 'FAN23G1914' => 'fan', 'FAN26G0032' => 'fan', 'FAN28G0625' => 'fan', 'FvH4_1g02710' => 'fve', 'FvH4_1g02720' => 'fve', 'FvH4_4g25670' => 'fve', 'FvH4_6g51700' => 'fve', 'FvH4_7g20170' => 'fve', 'Glyma.05G175000' => 'gma', 'Glyma.08G132300' => 'gma', 'Glyma.11G243000' => 'gma', 'Glyma.13G158900' => 'gma', 'Glyma.17G112400' => 'gma', 'Glyma.18G014100' => 'gma', 'Glyma.19G003100' => 'gma', 'Glyma.19G056500' => 'gma', 'Gohir.A01G158900' => 'ghi', 'Gohir.A05G312600' => 'ghi', 'Gohir.A05G354900' => 'ghi', 'Gohir.A07G037200' => 'ghi', 'Gohir.A09G030000' => 'ghi', 'Gohir.A12G145200' => 'ghi', 'Gohir.D01G151500' => 'ghi', 'Gohir.D04G058300' => 'ghi', 'Gohir.D05G314100' => 'ghi', 'Gohir.D07G041400' => 'ghi', 'Gohir.D09G029700' => 'ghi', 'Gohir.D12G149700' => 'ghi', 'Gorai.001G043800' => 'gra', 'Gorai.002G187800' => 'gra', 'Gorai.006G034700' => 'gra', 'Gorai.008G161200' => 'gra', 'Gorai.009G335700' => 'gra', 'Gorai.012G065000' => 'gra', 'GSVIVG01000535001' => 'vvi', 'GSVIVG01015572001' => 'vvi', 'GSVIVG01032386001' => 'vvi', 'HanXRQChr05g0138531' => 'han', 'HanXRQChr06g0174391' => 'han', 'HanXRQChr07g0199021' => 'han', 'HanXRQChr08g0208211' => 'han', 'HanXRQChr09g0255471' => 'han', 'HanXRQChr10g0315791' => 'han', 'HanXRQChr12g0371991' => 'han', 'HanXRQChr15g0475251' => 'han', 'HanXRQChr17g0540001' => 'han', 'HanXRQChr17g0548631' => 'han', 'HanXRQChr17g0569561' => 'han', 'Haze_12256' => 'cav', 'Haze_14756' => 'cav', 'Haze_25528' => 'cav', 'Hma1.2p1_0079F.1_g041020' => 'hma', 'Hma1.2p1_0818F.1_g223260' => 'hma', 'Hma1.2p1_1747F.1_g300530' => 'hma', 'HPP92_004607' => 'vpl', 'HPP92_004608' => 'vpl', 'HPP92_006181' => 'vpl', 'HPP92_012192' => 'vpl', 'HPP92_015680' => 'vpl', 'HPP92_020249' => 'vpl', 'HPP92_021376' => 'vpl', 'HPP92_024275' => 'vpl', 'Hund06031' => 'sun', 'Hund25391' => 'sun', 'Lalb_Chr07g0185371' => 'lal', 'Lalb_Chr07g0185381' => 'lal', 'Lalb_Chr12g0204011' => 'lal', 'Lalb_Chr13g0301671' => 'lal', 'Lalb_Chr14g0362851' => 'lal', 'Lalb_Chr24g0403581' => 'lal', 'Lj1g0000233' => 'lja', 'Lj2g0018120' => 'lja', 'Lj3C621T0' => 'lonja', 'Lj3P1059T14' => 'lonja', 'Lj3P611T9' => 'lonja', 'Lj3P614T13' => 'lonja', 'Lj3P615T5' => 'lonja', 'Lj4g0012315' => 'lja', 'Lj4g0026182' => 'lja', 'Lj6P813T16' => 'lonja', 'Lj7C427T7' => 'lonja', 'Lj7C427T8' => 'lonja', 'Lj7P600T41' => 'lonja', 'Lju41C42G17' => 'lonja', 'Lsat_1_v5_gn_0_47300' => 'lsa', 'Lsat_1_v5_gn_2_91280' => 'lsa', 'Lsat_1_v5_gn_3_30561' => 'lsa', 'Lsat_1_v5_gn_4_184321' => 'lsa', 'Lsat_1_v5_gn_4_4041' => 'lsa', 'Lsat_1_v5_gn_5_92000' => 'lsa', 'Lsat_1_v5_gn_8_152940' => 'lsa', 'Lsat_1_v5_gn_8_62401' => 'lsa', 'Manes.06G055900' => 'mes', 'Manes.12G022200' => 'mes', 'Manes.13G023300' => 'mes', 'Manes.14G115000' => 'mes', 'Manes.15G151700' => 'mes', 'Manes.17G111300' => 'mes', 'Mapoly0226s0009' => 'mpo', 'MBI02_g25363_MAGBIO' => 'mbi', 'MBI06_g00027_MAGBIO' => 'mbi', 'MBI10_g13034_MAGBIO' => 'mbi', 'MD09G1023400' => 'mdo', 'MD13G1100100' => 'mdo', 'MD15G1169200' => 'mdo', 'MD16G1101100' => 'mdo', 'MD17G1022900' => 'mdo', 'Medtr3g096150' => 'mtr', 'Medtr4g115070' => 'mtr', 'Medtr7g033325' => 'mtr', 'Medtr8g089840' => 'mtr', 'MELO3C010319.2' => 'cme', 'MELO3C011944.2' => 'cme', 'MELO3C021589.2' => 'cme', 'Migut.E00207' => 'egut', 'Migut.H00067' => 'egut', 'Migut.K00433' => 'egut', 'Migut.K00606' => 'egut', 'Migut.K01410' => 'egut', 'MSTRG.13347' => 'ama', 'MSTRG.24045' => 'ama', 'MSTRG.2428' => 'ama', 'MSTRG.26410' => 'ama', 'MSTRG.3139' => 'ama', 'MSTRG.3286' => 'ama', 'MSTRG.563' => 'ama', 'MSTRG.7941' => 'ama', 'Nitab4.5_0000028g0060' => 'nta', 'Nitab4.5_0000065g0260' => 'nta', 'Nitab4.5_0000112g0060' => 'nta', 'Nitab4.5_0000489g0120' => 'nta', 'Nitab4.5_0001776g0050' => 'nta', 'Nitab4.5_0001854g0010' => 'nta', 'Nitab4.5_0001860g0020' => 'nta', 'Nitab4.5_0004352g0010' => 'nta', 'Nitab4.5_0008716g0020' => 'nta', 'Nitab4.5_0008922g0010' => 'nta', 'Nn3g16693' => 'nnu', 'Nn4g22596' => 'nnu', 'Nn7g37639' => 'nnu', 'Oeu001701.1' => 'oeu', 'Oeu018149.1' => 'oeu', 'Oeu026220.1' => 'oeu', 'Oeu038635.1' => 'oeu', 'Oeu049176.1' => 'oeu', 'Oeu056706.1' => 'oeu', 'Oeu056937.1' => 'oeu', 'Oeu057540.1' => 'oeu', 'Os02g0594900' => 'osa', 'Os02g0595100' => 'osa', 'Os04g0477500' => 'osa', 'Os12g0611900' => 'osa', 'Peaxi162Scf00076g00020' => 'pax', 'Peaxi162Scf00128g00217' => 'pax', 'Peaxi162Scf00129g01640' => 'pax', 'Peaxi162Scf00669g00007' => 'pax', 'Peaxi162Scf00700g00421' => 'pax', 'Peaxi162Scf00801g00038' => 'pax', 'Peaxi162Scf00891g00025' => 'pax', 'PGR083G0909' => 'pgr', 'PGR119G1005' => 'pgr', 'PGR142G2236' => 'pgr', 'PGR142G3388' => 'pgr', 'PGSC0003DMG400004514' => 'stu', 'PGSC0003DMG400012635' => 'stu', 'PGSC0003DMG400015730' => 'stu', 'PGSC0003DMG400018611' => 'stu', 'PGSC0003DMG400030897' => 'stu', 'Phvul.001G254800' => 'pvu', 'Phvul.002G260100' => 'pvu', 'Phvul.003G167600' => 'pvu', 'Phvul.004G005100' => 'pvu', 'Potri.001G343600' => 'ptr', 'Potri.006G066700' => 'ptr', 'Potri.008G186000' => 'ptr', 'Potri.010G046900' => 'ptr', 'Potri.018G127900' => 'ptr', 'Pp3c20_17750' => 'ppa', 'Pp3c24_4380' => 'ppa', 'Prupe.1G245800' => 'ppe', 'Prupe.3G293400' => 'ppe', 'Prupe.7G247400' => 'ppe', 'Psat0s145g0120' => 'psa', 'Psat0s595g0040' => 'psa', 'Psat0s595g0120' => 'psa', 'Psat3g175040' => 'psa', 'Psat7g058120' => 'psa', 'PSO017G0428' => 'pso', 'PSO063G7510' => 'pso', 'PSO067G0046' => 'pso', 'PSO478G1073' => 'pso', 'PSO675G3677' => 'pso', 'PSO675G6558' => 'pso', 'PSO675G7520' => 'pso', 'PSO675G8959' => 'pso', 'QL02p074089' => 'qlo', 'QL02p089614' => 'qlo', 'QL03p057736' => 'qlo', 'RcHm_v2.0_Chr1g0364131' => 'rch', 'RcHm_v2.0_Chr2g0087801' => 'rch', 'RcHm_v2.0_Chr2g0087821' => 'rch', 'RcHm_v2.0_Chr2g0173231' => 'rch', 'RcHm_v2.0_Chr4g0433111' => 'rch', 'Rhsim03G0250300' => 'rsi', 'Rhsim08G0048400' => 'rsi', 'Rhsim10G0014800' => 'rsi', 'Rhsim12G0040100' => 'rsi', 'Rhsim12G0109700' => 'rsi', 'Sabra06G0049600' => 'sbr', 'Sabra08G0141000' => 'sbr', 'Sabra10G0021400' => 'sbr', 'Sabra16G0222900' => 'sbr', 'Sabra18G0108600' => 'sbr', 'SalBow1G0433' => 'sbo', 'SalBow1G2038' => 'sbo', 'SalBow1G5003' => 'sbo', 'SalBow7G1197' => 'sbo', 'SalBow8G3506' => 'sbo', 'Sc03g0007300' => 'sci', 'Sc11g0000950' => 'sci', 'Sc14g0008750' => 'sci', 'Sc18g0000420' => 'sci', 'Sed0006754' => 'sed', 'Sed0008741' => 'sed', 'Sed0017172' => 'sed', 'Sed0018925' => 'sed', 'Sed0023326' => 'sed', 'Sed0025909' => 'sed', 'SEGI_05333' => 'sgi', 'SEGI_10362' => 'sgi', 'SEGI_13380' => 'sgi', 'SEGI_24306' => 'sgi', 'SEGI_29077' => 'sgi', 'SEGI_29095' => 'sgi', 'SEGI_36534' => 'sgi', 'SEGI_37506' => 'sgi', 'SEGI_38321' => 'sgi', 'SGA_v2.0_scaffold307G48031' => 'sas', 'SGA_v2.0_scaffold47G17507' => 'sas', 'SGA_v2.0_scaffold63G21736' => 'sas', 'SGA_v2.0_scaffold87G27070' => 'sas', 'SHI17794' => 'shi', 'SHI28851' => 'shi', 'SMO165G0155' => 'smo', 'SMO340G0217' => 'smo', 'SMO367G1210' => 'smo', 'Solyc02g093430.3' => 'sly', 'Solyc05g013580.4' => 'sly', 'Solyc07g008030.3' => 'sly', 'Solyc12g035470.2' => 'sly', 'Sopen02g038020' => 'spe', 'Sopen05g008490' => 'spe', 'Sopen07g003910' => 'spe', 'Sopen12g015240' => 'spe', 'Sp1g11550' => 'spa', 'Sp2g16710' => 'spa', 'Sp3g00430' => 'spa', 'Sp3g26780' => 'spa', 'Sp5g22900' => 'spa', 'Sp6g29530' => 'spa', 'TAR371G0794' => 'tar', 'TAR374G0164' => 'tar', 'TAR622G0165' => 'tar', 'TAR626G0929' => 'tar', 'TAR629G2155' => 'tar', 'THA.LOC104805282' => 'tha', 'THA.LOC104805363' => 'tha', 'THA.LOC104808968' => 'tha', 'THA.LOC104821093' => 'tha', 'THA.LOC104823953' => 'tha', 'THA.LOC104825562' => 'tha', 'THA.LOC104825665' => 'tha', 'Thecc.02G261400' => 'tca', 'Thecc.04G019200' => 'tca', 'Thecc.09G130400' => 'tca', 'Thhalv10004374m.g' => 'esa', 'Thhalv10007850m.g' => 'esa', 'Thhalv10013782m.g' => 'esa', 'Thhalv10018686m.g' => 'esa', 'Thhalv10020899m.g' => 'esa', 'Thhalv10022755m.g' => 'esa', 'TPR.G23851' => 'tpr', 'TPR.G26500' => 'tpr', 'TPR.G27267' => 'tpr', 'TPR.G32001' => 'tpr', 'TPR.G6251' => 'tpr', 'TPR.G8167' => 'tpr', 'TWI12G1330' => 'twi', 'TWI18G1239' => 'twi', 'TWI34G0979' => 'twi', 'TWI36G0670' => 'twi', 'TWI36G0707' => 'twi', 'TWI56G0233' => 'twi', 'TWI75G1809' => 'twi', 'unitig_21.g20874' => 'ugi', 'unitig_26.g10343' => 'ugi', 'unitig_46.g18392' => 'ugi', 'unitig_52.g17178' => 'ugi', 'unitig_8.g2934' => 'ugi', 'vmacro01122' => 'vma', 'vmacro05875' => 'vma', 'vmacro06147' => 'vma', 'vmacro16191' => 'vma', 'vmacro18293' => 'vma', 'VMungo0251G3707' => 'vmu', 'VMungo0464G1521' => 'vmu', 'VMungo1215G0205' => 'vmu', 'VMungo1383G2484' => 'vmu', 'Zm00001eb079610' => 'zma', 'Zm00001eb135990' => 'zma', 'Zm00001eb183710' => 'zma', 'Zm00001eb246020' => 'zma' ) $gf_id = 'HOM05D001124' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001124' ) $data_identifier = 'HOM05D001124' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 6, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 7, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 21, 'bol' => (int) 10, 'bra' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 6, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 9, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 21, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 8, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 10, 'lsa' => (int) 8, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 8, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 9, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb246020' $species_info = array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ) $local_species = 'tca' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001124', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '548', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02520' => 'bna', 'A03p06630' => 'bna', 'A05p44460' => 'bna', 'A06p08710' => 'bna', 'A06p41090' => 'bna', 'A07p32320' => 'bna', 'A08p32520' => 'bna', 'A09p10360' => 'bna', 'A10p24080' => 'bna', 'Aa31LG11G15250' => 'aar', 'Aa31LG1G1800' => 'aar', 'Aa31LG2G5120' => 'aar', 'Aa31LG2G6070' => 'aar', 'Aa31LG5G10770' => 'aar', 'Aa31sc61G90' => 'aar', 'Actinidia01352' => 'ach', 'Actinidia05983' => 'ach', 'Actinidia08133' => 'ach', 'Actinidia15101' => 'ach', 'Actinidia26379' => 'ach', 'Actinidia35778' => 'ach', 'Actinidia36123' => 'ach', 'Actinidia37436' => 'ach', 'Actinidia38730' => 'ach', 'Ah.02g128210' => 'amhyb', 'Ah.03g132990' => 'amhyb', 'Ah.14g079410' => 'amhyb', 'AL1G24640' => 'aly', 'AL2G26680' => 'aly', 'AL3G10530' => 'aly', 'AL3G45230' => 'aly', 'AL5G15230' => 'aly', 'AL5G16960' => 'aly', 'AL6G25210' => 'aly', 'Aqoxy2G00441' => 'aox', 'Aqoxy3G01236' => 'aox', 'Aqoxy5G03746' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3RQ047' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C7GMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9C8JER' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MBL6KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YXCZ83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZANX40' => 'arhy', 'AT1G12990' => 'ath', 'AT1G67880' => 'ath', 'AT2G13290' => 'ath', 'AT3G01620' => 'ath', 'AT3G26445' => 'ath', 'AT3G27540' => 'ath', 'AT5G14480' => 'ath', 'ATR0824G026' => 'atr', 'ATR1098G019' => 'atr', 'Atru.chr11.2145' => 'acertr', 'Atru.chr2.3636' => 'acertr', 'Atru.chr2.3644' => 'acertr', 'Atru.chr6.2422' => 'acertr', 'Atru.chr7.1112' => 'acertr', 'AUR62005469' => 'cqu', 'AUR62011166' => 'cqu', 'AUR62013319' => 'cqu', 'AUR62024273' => 'cqu', 'AUR62028420' => 'cqu', 'AUR62041942' => 'cqu', 'BcaB01g04969' => 'bca', 'BcaB01g06371' => 'bca', 'BcaB02g11494' => 'bca', 'BcaB03g15382' => 'bca', 'BcaB08g36994' => 'bca', 'BcaC03g13477' => 'bca', 'BcaC03g13478' => 'bca', 'BcaC03g13480' => 'bca', 'BcaC03g13481' => 'bca', 'BcaC03g13486' => 'bca', 'BcaC04g19031' => 'bca', 'BcaC04g23085' => 'bca', 'BcaC05g25094' => 'bca', 'BcaC05g25096' => 'bca', 'BcaC05g25138' => 'bca', 'BcaC05g30416' => 'bca', 'BcaC05g30455' => 'bca', 'BcaC06g30979' => 'bca', 'BcaC06g33805' => 'bca', 'BcaC08g46021' => 'bca', 'BcaNung03154' => 'bca', 'BolC2t06623H' => 'bol', 'BolC2t06632H' => 'bol', 'BolC2t06635H' => 'bol', 'BolC2t06638H' => 'bol', 'BolC3t13266H' => 'bol', 'BolC5t29776H' => 'bol', 'BolC6t38912H' => 'bol', 'BolC7t44183H' => 'bol', 'BolC9t54123H' => 'bol', 'BolC9t59107H' => 'bol', 'BraA02t05221Z' => 'bra', 'BraA03t09996Z' => 'bra', 'BraA05t23210Z' => 'bra', 'BraA06t24068Z' => 'bra', 'BraA06t27032Z' => 'bra', 'BraA08t35176Z' => 'bra', 'BraA09t36680Z' => 'bra', 'BraA10t44471Z' => 'bra', 'C02p06760' => 'bna', 'C02p06890' => 'bna', 'C02p07010' => 'bna', 'C03p07660' => 'bna', 'C05p10300' => 'bna', 'C06p38150' => 'bna', 'C07p36650' => 'bna', 'C08p15770' => 'bna', 'C09p12300' => 'bna', 'C09p62700' => 'bna', 'C09p75040' => 'bna', 'CAN.G13.1' => 'can', 'CAN.G138.4' => 'can', 'CAN.G44.6' => 'can', 'CAN.G473.19' => 'can', 'CANSAT01G0835' => 'cansat', 'CANSAT11G0246' => 'cansat', 'CANSAT11G1766' => 'cansat', 'CANSAT64G1954' => 'cansat', 'CARHR013330' => 'chi', 'CARHR060530' => 'chi', 'CARHR075300' => 'chi', 'CARHR105120' => 'chi', 'CARHR148910' => 'chi', 'CARHR198830' => 'chi', 'Carub.0001s1275' => 'cru', 'Carub.0002s1437' => 'cru', 'Carub.0003s0044' => 'cru', 'Carub.0003s2787' => 'cru', 'Carub.0005s0597' => 'cru', 'Carub.0006s1266' => 'cru', 'Ca_06935_v3' => 'car', 'Ca_13559_v3' => 'car', 'Ca_16941_v3' => 'car', 'Ca_16960_v3' => 'car', 'Ca_17775_v3' => 'car', 'Ca_30464_v3' => 'car', 'Cc06_g08160' => 'ccan', 'Cc07_g01520' => 'ccan', 'Cc11_g15810' => 'ccan', 'CDE02G2840' => 'cde', 'CDE03G0093' => 'cde', 'CDE04G2127' => 'cde', 'CDE07G1857' => 'cde', 'CDE09G1246' => 'cde', 'Cfa003412' => 'cfa', 'Cfa007341' => 'cfa', 'Cfa009220' => 'cfa', 'Ciclev10008737m.g' => 'ccl', 'Ciclev10015565m.g' => 'ccl', 'Ciclev10031761m.g' => 'ccl', 'CiPaw.03G045300' => 'cil', 'CiPaw.03G247200' => 'cil', 'CiPaw.04G029500' => 'cil', 'CiPaw.04G174000' => 'cil', 'CiPaw.05G181200' => 'cil', 'CiPaw.06G067100' => 'cil', 'ClCG05G025800' => 'cla', 'ClCG06G011400' => 'cla', 'ClCG09G019360' => 'cla', 'COL.COLO4_04827' => 'col', 'COL.COLO4_29170' => 'col', 'COL.COLO4_35131' => 'col', 'COL.COLO4_35132' => 'col', 'Cpa.g.sc33.32' => 'cpa', 'Cpa.g.sc46.29' => 'cpa', 'Cpa.g.sc796.1' => 'cpa', 'CsaV3_1G030420' => 'csa', 'CsaV3_5G027050' => 'csa', 'CsaV3_5G031040' => 'csa', 'CsaV3_UNG023130' => 'csa', 'CSS0007726' => 'camsi', 'CSS0016433' => 'camsi', 'CSS0017656' => 'camsi', 'CSS0025364' => 'camsi', 'CSS0027582' => 'camsi', 'CSS0047288' => 'camsi', 'CSS0049950' => 'camsi', 'DCAR_003843' => 'dca', 'DCAR_007052' => 'dca', 'DCAR_020884' => 'dca', 'DCAR_021730' => 'dca', 'DCAR_024423' => 'dca', 'DCAR_026509' => 'dca', 'DCAR_031158' => 'dca', 'Dinv14728' => 'din', 'Dinv15219' => 'din', 'Dinv25728' => 'din', 'Dinv33428' => 'din', 'Dinv36489' => 'din', 'Dinv41486' => 'din', 'Duzib147G0469' => 'dzi', 'Duzib168G0060' => 'dzi', 'Duzib187G1215' => 'dzi', 'Duzib248G0692' => 'dzi', 'Duzib251G0767' => 'dzi', 'Duzib264G0446' => 'dzi', 'Duzib268G0691' => 'dzi', 'ECA232G4767' => 'eca', 'ECA233G2838' => 'eca', 'ECA234G0391' => 'eca', 'ECA234G0857' => 'eca', 'ECA236G1593' => 'eca', 'ECA238G0565' => 'eca', 'ECA246G1027' => 'eca', 'ECA246G3223' => 'eca', 'ECA246G3470' => 'eca', 'EL10Ac6g13829' => 'bvu', 'EL10Ac6g14093' => 'bvu', 'EL10Ac8g18707' => 'bvu', 'Eucgr.C01369' => 'egr', 'Eucgr.H02492' => 'egr', 'Eucgr.I01733' => 'egr', 'Eucgr.J02255' => 'egr', 'Eucgr.J02257' => 'egr', 'Eucgr.J02258' => 'egr', 'FAN02G1601' => 'fan', 'FAN03G1586' => 'fan', 'FAN03G2986' => 'fan', 'FAN05G4837' => 'fan', 'FAN06G0146' => 'fan', 'FAN07G0858' => 'fan', 'FAN09G3179' => 'fan', 'FAN10G0669' => 'fan', 'FAN12G2358' => 'fan', 'FAN14G4198' => 'fan', 'FAN14G5112' => 'fan', 'FAN17G0342' => 'fan', 'FAN19G0342' => 'fan', 'FAN19G0962' => 'fan', 'FAN19G1101' => 'fan', 'FAN19G1872' => 'fan', 'FAN22G0356' => 'fan', 'FAN23G0744' => 'fan', 'FAN23G1914' => 'fan', 'FAN26G0032' => 'fan', 'FAN28G0625' => 'fan', 'FvH4_1g02710' => 'fve', 'FvH4_1g02720' => 'fve', 'FvH4_4g25670' => 'fve', 'FvH4_6g51700' => 'fve', 'FvH4_7g20170' => 'fve', 'Glyma.05G175000' => 'gma', 'Glyma.08G132300' => 'gma', 'Glyma.11G243000' => 'gma', 'Glyma.13G158900' => 'gma', 'Glyma.17G112400' => 'gma', 'Glyma.18G014100' => 'gma', 'Glyma.19G003100' => 'gma', 'Glyma.19G056500' => 'gma', 'Gohir.A01G158900' => 'ghi', 'Gohir.A05G312600' => 'ghi', 'Gohir.A05G354900' => 'ghi', 'Gohir.A07G037200' => 'ghi', 'Gohir.A09G030000' => 'ghi', 'Gohir.A12G145200' => 'ghi', 'Gohir.D01G151500' => 'ghi', 'Gohir.D04G058300' => 'ghi', 'Gohir.D05G314100' => 'ghi', 'Gohir.D07G041400' => 'ghi', 'Gohir.D09G029700' => 'ghi', 'Gohir.D12G149700' => 'ghi', 'Gorai.001G043800' => 'gra', 'Gorai.002G187800' => 'gra', 'Gorai.006G034700' => 'gra', 'Gorai.008G161200' => 'gra', 'Gorai.009G335700' => 'gra', 'Gorai.012G065000' => 'gra', 'GSVIVG01000535001' => 'vvi', 'GSVIVG01015572001' => 'vvi', 'GSVIVG01032386001' => 'vvi', 'HanXRQChr05g0138531' => 'han', 'HanXRQChr06g0174391' => 'han', 'HanXRQChr07g0199021' => 'han', 'HanXRQChr08g0208211' => 'han', 'HanXRQChr09g0255471' => 'han', 'HanXRQChr10g0315791' => 'han', 'HanXRQChr12g0371991' => 'han', 'HanXRQChr15g0475251' => 'han', 'HanXRQChr17g0540001' => 'han', 'HanXRQChr17g0548631' => 'han', 'HanXRQChr17g0569561' => 'han', 'Haze_12256' => 'cav', 'Haze_14756' => 'cav', 'Haze_25528' => 'cav', 'Hma1.2p1_0079F.1_g041020' => 'hma', 'Hma1.2p1_0818F.1_g223260' => 'hma', 'Hma1.2p1_1747F.1_g300530' => 'hma', 'HPP92_004607' => 'vpl', 'HPP92_004608' => 'vpl', 'HPP92_006181' => 'vpl', 'HPP92_012192' => 'vpl', 'HPP92_015680' => 'vpl', 'HPP92_020249' => 'vpl', 'HPP92_021376' => 'vpl', 'HPP92_024275' => 'vpl', 'Hund06031' => 'sun', 'Hund25391' => 'sun', 'Lalb_Chr07g0185371' => 'lal', 'Lalb_Chr07g0185381' => 'lal', 'Lalb_Chr12g0204011' => 'lal', 'Lalb_Chr13g0301671' => 'lal', 'Lalb_Chr14g0362851' => 'lal', 'Lalb_Chr24g0403581' => 'lal', 'Lj1g0000233' => 'lja', 'Lj2g0018120' => 'lja', 'Lj3C621T0' => 'lonja', 'Lj3P1059T14' => 'lonja', 'Lj3P611T9' => 'lonja', 'Lj3P614T13' => 'lonja', 'Lj3P615T5' => 'lonja', 'Lj4g0012315' => 'lja', 'Lj4g0026182' => 'lja', 'Lj6P813T16' => 'lonja', 'Lj7C427T7' => 'lonja', 'Lj7C427T8' => 'lonja', 'Lj7P600T41' => 'lonja', 'Lju41C42G17' => 'lonja', 'Lsat_1_v5_gn_0_47300' => 'lsa', 'Lsat_1_v5_gn_2_91280' => 'lsa', 'Lsat_1_v5_gn_3_30561' => 'lsa', 'Lsat_1_v5_gn_4_184321' => 'lsa', 'Lsat_1_v5_gn_4_4041' => 'lsa', 'Lsat_1_v5_gn_5_92000' => 'lsa', 'Lsat_1_v5_gn_8_152940' => 'lsa', 'Lsat_1_v5_gn_8_62401' => 'lsa', 'Manes.06G055900' => 'mes', 'Manes.12G022200' => 'mes', 'Manes.13G023300' => 'mes', 'Manes.14G115000' => 'mes', 'Manes.15G151700' => 'mes', 'Manes.17G111300' => 'mes', 'Mapoly0226s0009' => 'mpo', 'MBI02_g25363_MAGBIO' => 'mbi', 'MBI06_g00027_MAGBIO' => 'mbi', 'MBI10_g13034_MAGBIO' => 'mbi', 'MD09G1023400' => 'mdo', 'MD13G1100100' => 'mdo', 'MD15G1169200' => 'mdo', 'MD16G1101100' => 'mdo', 'MD17G1022900' => 'mdo', 'Medtr3g096150' => 'mtr', 'Medtr4g115070' => 'mtr', 'Medtr7g033325' => 'mtr', 'Medtr8g089840' => 'mtr', 'MELO3C010319.2' => 'cme', 'MELO3C011944.2' => 'cme', 'MELO3C021589.2' => 'cme', 'Migut.E00207' => 'egut', 'Migut.H00067' => 'egut', 'Migut.K00433' => 'egut', 'Migut.K00606' => 'egut', 'Migut.K01410' => 'egut', 'MSTRG.13347' => 'ama', 'MSTRG.24045' => 'ama', 'MSTRG.2428' => 'ama', 'MSTRG.26410' => 'ama', 'MSTRG.3139' => 'ama', 'MSTRG.3286' => 'ama', 'MSTRG.563' => 'ama', 'MSTRG.7941' => 'ama', 'Nitab4.5_0000028g0060' => 'nta', 'Nitab4.5_0000065g0260' => 'nta', 'Nitab4.5_0000112g0060' => 'nta', 'Nitab4.5_0000489g0120' => 'nta', 'Nitab4.5_0001776g0050' => 'nta', 'Nitab4.5_0001854g0010' => 'nta', 'Nitab4.5_0001860g0020' => 'nta', 'Nitab4.5_0004352g0010' => 'nta', 'Nitab4.5_0008716g0020' => 'nta', 'Nitab4.5_0008922g0010' => 'nta', 'Nn3g16693' => 'nnu', 'Nn4g22596' => 'nnu', 'Nn7g37639' => 'nnu', 'Oeu001701.1' => 'oeu', 'Oeu018149.1' => 'oeu', 'Oeu026220.1' => 'oeu', 'Oeu038635.1' => 'oeu', 'Oeu049176.1' => 'oeu', 'Oeu056706.1' => 'oeu', 'Oeu056937.1' => 'oeu', 'Oeu057540.1' => 'oeu', 'Os02g0594900' => 'osa', 'Os02g0595100' => 'osa', 'Os04g0477500' => 'osa', 'Os12g0611900' => 'osa', 'Peaxi162Scf00076g00020' => 'pax', 'Peaxi162Scf00128g00217' => 'pax', 'Peaxi162Scf00129g01640' => 'pax', 'Peaxi162Scf00669g00007' => 'pax', 'Peaxi162Scf00700g00421' => 'pax', 'Peaxi162Scf00801g00038' => 'pax', 'Peaxi162Scf00891g00025' => 'pax', 'PGR083G0909' => 'pgr', 'PGR119G1005' => 'pgr', 'PGR142G2236' => 'pgr', 'PGR142G3388' => 'pgr', 'PGSC0003DMG400004514' => 'stu', 'PGSC0003DMG400012635' => 'stu', 'PGSC0003DMG400015730' => 'stu', 'PGSC0003DMG400018611' => 'stu', 'PGSC0003DMG400030897' => 'stu', 'Phvul.001G254800' => 'pvu', 'Phvul.002G260100' => 'pvu', 'Phvul.003G167600' => 'pvu', 'Phvul.004G005100' => 'pvu', 'Potri.001G343600' => 'ptr', 'Potri.006G066700' => 'ptr', 'Potri.008G186000' => 'ptr', 'Potri.010G046900' => 'ptr', 'Potri.018G127900' => 'ptr', 'Pp3c20_17750' => 'ppa', 'Pp3c24_4380' => 'ppa', 'Prupe.1G245800' => 'ppe', 'Prupe.3G293400' => 'ppe', 'Prupe.7G247400' => 'ppe', 'Psat0s145g0120' => 'psa', 'Psat0s595g0040' => 'psa', 'Psat0s595g0120' => 'psa', 'Psat3g175040' => 'psa', 'Psat7g058120' => 'psa', 'PSO017G0428' => 'pso', 'PSO063G7510' => 'pso', 'PSO067G0046' => 'pso', 'PSO478G1073' => 'pso', 'PSO675G3677' => 'pso', 'PSO675G6558' => 'pso', 'PSO675G7520' => 'pso', 'PSO675G8959' => 'pso', 'QL02p074089' => 'qlo', 'QL02p089614' => 'qlo', 'QL03p057736' => 'qlo', 'RcHm_v2.0_Chr1g0364131' => 'rch', 'RcHm_v2.0_Chr2g0087801' => 'rch', 'RcHm_v2.0_Chr2g0087821' => 'rch', 'RcHm_v2.0_Chr2g0173231' => 'rch', 'RcHm_v2.0_Chr4g0433111' => 'rch', 'Rhsim03G0250300' => 'rsi', 'Rhsim08G0048400' => 'rsi', 'Rhsim10G0014800' => 'rsi', 'Rhsim12G0040100' => 'rsi', 'Rhsim12G0109700' => 'rsi', 'Sabra06G0049600' => 'sbr', 'Sabra08G0141000' => 'sbr', 'Sabra10G0021400' => 'sbr', 'Sabra16G0222900' => 'sbr', 'Sabra18G0108600' => 'sbr', 'SalBow1G0433' => 'sbo', 'SalBow1G2038' => 'sbo', 'SalBow1G5003' => 'sbo', 'SalBow7G1197' => 'sbo', 'SalBow8G3506' => 'sbo', 'Sc03g0007300' => 'sci', 'Sc11g0000950' => 'sci', 'Sc14g0008750' => 'sci', 'Sc18g0000420' => 'sci', 'Sed0006754' => 'sed', 'Sed0008741' => 'sed', 'Sed0017172' => 'sed', 'Sed0018925' => 'sed', 'Sed0023326' => 'sed', 'Sed0025909' => 'sed', 'SEGI_05333' => 'sgi', 'SEGI_10362' => 'sgi', 'SEGI_13380' => 'sgi', 'SEGI_24306' => 'sgi', 'SEGI_29077' => 'sgi', 'SEGI_29095' => 'sgi', 'SEGI_36534' => 'sgi', 'SEGI_37506' => 'sgi', 'SEGI_38321' => 'sgi', 'SGA_v2.0_scaffold307G48031' => 'sas', 'SGA_v2.0_scaffold47G17507' => 'sas', 'SGA_v2.0_scaffold63G21736' => 'sas', 'SGA_v2.0_scaffold87G27070' => 'sas', 'SHI17794' => 'shi', 'SHI28851' => 'shi', 'SMO165G0155' => 'smo', 'SMO340G0217' => 'smo', 'SMO367G1210' => 'smo', 'Solyc02g093430.3' => 'sly', 'Solyc05g013580.4' => 'sly', 'Solyc07g008030.3' => 'sly', 'Solyc12g035470.2' => 'sly', 'Sopen02g038020' => 'spe', 'Sopen05g008490' => 'spe', 'Sopen07g003910' => 'spe', 'Sopen12g015240' => 'spe', 'Sp1g11550' => 'spa', 'Sp2g16710' => 'spa', 'Sp3g00430' => 'spa', 'Sp3g26780' => 'spa', 'Sp5g22900' => 'spa', 'Sp6g29530' => 'spa', 'TAR371G0794' => 'tar', 'TAR374G0164' => 'tar', 'TAR622G0165' => 'tar', 'TAR626G0929' => 'tar', 'TAR629G2155' => 'tar', 'THA.LOC104805282' => 'tha', 'THA.LOC104805363' => 'tha', 'THA.LOC104808968' => 'tha', 'THA.LOC104821093' => 'tha', 'THA.LOC104823953' => 'tha', 'THA.LOC104825562' => 'tha', 'THA.LOC104825665' => 'tha', 'Thecc.02G261400' => 'tca', 'Thecc.04G019200' => 'tca', 'Thecc.09G130400' => 'tca', 'Thhalv10004374m.g' => 'esa', 'Thhalv10007850m.g' => 'esa', 'Thhalv10013782m.g' => 'esa', 'Thhalv10018686m.g' => 'esa', 'Thhalv10020899m.g' => 'esa', 'Thhalv10022755m.g' => 'esa', 'TPR.G23851' => 'tpr', 'TPR.G26500' => 'tpr', 'TPR.G27267' => 'tpr', 'TPR.G32001' => 'tpr', 'TPR.G6251' => 'tpr', 'TPR.G8167' => 'tpr', 'TWI12G1330' => 'twi', 'TWI18G1239' => 'twi', 'TWI34G0979' => 'twi', 'TWI36G0670' => 'twi', 'TWI36G0707' => 'twi', 'TWI56G0233' => 'twi', 'TWI75G1809' => 'twi', 'unitig_21.g20874' => 'ugi', 'unitig_26.g10343' => 'ugi', 'unitig_46.g18392' => 'ugi', 'unitig_52.g17178' => 'ugi', 'unitig_8.g2934' => 'ugi', 'vmacro01122' => 'vma', 'vmacro05875' => 'vma', 'vmacro06147' => 'vma', 'vmacro16191' => 'vma', 'vmacro18293' => 'vma', 'VMungo0251G3707' => 'vmu', 'VMungo0464G1521' => 'vmu', 'VMungo1215G0205' => 'vmu', 'VMungo1383G2484' => 'vmu', 'Zm00001eb079610' => 'zma', 'Zm00001eb135990' => 'zma', 'Zm00001eb183710' => 'zma', 'Zm00001eb246020' => 'zma' ), 'gf_id' => 'HOM05D001124', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001124' ), 'data_identifier' => 'HOM05D001124', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001124', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '548', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02520' => 'bna', 'A03p06630' => 'bna', 'A05p44460' => 'bna', 'A06p08710' => 'bna', 'A06p41090' => 'bna', 'A07p32320' => 'bna', 'A08p32520' => 'bna', 'A09p10360' => 'bna', 'A10p24080' => 'bna', 'Aa31LG11G15250' => 'aar', 'Aa31LG1G1800' => 'aar', 'Aa31LG2G5120' => 'aar', 'Aa31LG2G6070' => 'aar', 'Aa31LG5G10770' => 'aar', 'Aa31sc61G90' => 'aar', 'Actinidia01352' => 'ach', 'Actinidia05983' => 'ach', 'Actinidia08133' => 'ach', 'Actinidia15101' => 'ach', 'Actinidia26379' => 'ach', 'Actinidia35778' => 'ach', 'Actinidia36123' => 'ach', 'Actinidia37436' => 'ach', 'Actinidia38730' => 'ach', 'Ah.02g128210' => 'amhyb', 'Ah.03g132990' => 'amhyb', 'Ah.14g079410' => 'amhyb', 'AL1G24640' => 'aly', 'AL2G26680' => 'aly', 'AL3G10530' => 'aly', 'AL3G45230' => 'aly', 'AL5G15230' => 'aly', 'AL5G16960' => 'aly', 'AL6G25210' => 'aly', 'Aqoxy2G00441' => 'aox', 'Aqoxy3G01236' => 'aox', 'Aqoxy5G03746' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3RQ047' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C7GMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9C8JER' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MBL6KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YXCZ83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZANX40' => 'arhy', 'AT1G12990' => 'ath', 'AT1G67880' => 'ath', 'AT2G13290' => 'ath', 'AT3G01620' => 'ath', 'AT3G26445' => 'ath', 'AT3G27540' => 'ath', 'AT5G14480' => 'ath', 'ATR0824G026' => 'atr', 'ATR1098G019' => 'atr', 'Atru.chr11.2145' => 'acertr', 'Atru.chr2.3636' => 'acertr', 'Atru.chr2.3644' => 'acertr', 'Atru.chr6.2422' => 'acertr', 'Atru.chr7.1112' => 'acertr', 'AUR62005469' => 'cqu', 'AUR62011166' => 'cqu', 'AUR62013319' => 'cqu', 'AUR62024273' => 'cqu', 'AUR62028420' => 'cqu', 'AUR62041942' => 'cqu', 'BcaB01g04969' => 'bca', 'BcaB01g06371' => 'bca', 'BcaB02g11494' => 'bca', 'BcaB03g15382' => 'bca', 'BcaB08g36994' => 'bca', 'BcaC03g13477' => 'bca', 'BcaC03g13478' => 'bca', 'BcaC03g13480' => 'bca', 'BcaC03g13481' => 'bca', 'BcaC03g13486' => 'bca', 'BcaC04g19031' => 'bca', 'BcaC04g23085' => 'bca', 'BcaC05g25094' => 'bca', 'BcaC05g25096' => 'bca', 'BcaC05g25138' => 'bca', 'BcaC05g30416' => 'bca', 'BcaC05g30455' => 'bca', 'BcaC06g30979' => 'bca', 'BcaC06g33805' => 'bca', 'BcaC08g46021' => 'bca', 'BcaNung03154' => 'bca', 'BolC2t06623H' => 'bol', 'BolC2t06632H' => 'bol', 'BolC2t06635H' => 'bol', 'BolC2t06638H' => 'bol', 'BolC3t13266H' => 'bol', 'BolC5t29776H' => 'bol', 'BolC6t38912H' => 'bol', 'BolC7t44183H' => 'bol', 'BolC9t54123H' => 'bol', 'BolC9t59107H' => 'bol', 'BraA02t05221Z' => 'bra', 'BraA03t09996Z' => 'bra', 'BraA05t23210Z' => 'bra', 'BraA06t24068Z' => 'bra', 'BraA06t27032Z' => 'bra', 'BraA08t35176Z' => 'bra', 'BraA09t36680Z' => 'bra', 'BraA10t44471Z' => 'bra', 'C02p06760' => 'bna', 'C02p06890' => 'bna', 'C02p07010' => 'bna', 'C03p07660' => 'bna', 'C05p10300' => 'bna', 'C06p38150' => 'bna', 'C07p36650' => 'bna', 'C08p15770' => 'bna', 'C09p12300' => 'bna', 'C09p62700' => 'bna', 'C09p75040' => 'bna', 'CAN.G13.1' => 'can', 'CAN.G138.4' => 'can', 'CAN.G44.6' => 'can', 'CAN.G473.19' => 'can', 'CANSAT01G0835' => 'cansat', 'CANSAT11G0246' => 'cansat', 'CANSAT11G1766' => 'cansat', 'CANSAT64G1954' => 'cansat', 'CARHR013330' => 'chi', 'CARHR060530' => 'chi', 'CARHR075300' => 'chi', 'CARHR105120' => 'chi', 'CARHR148910' => 'chi', 'CARHR198830' => 'chi', 'Carub.0001s1275' => 'cru', 'Carub.0002s1437' => 'cru', 'Carub.0003s0044' => 'cru', 'Carub.0003s2787' => 'cru', 'Carub.0005s0597' => 'cru', 'Carub.0006s1266' => 'cru', 'Ca_06935_v3' => 'car', 'Ca_13559_v3' => 'car', 'Ca_16941_v3' => 'car', 'Ca_16960_v3' => 'car', 'Ca_17775_v3' => 'car', 'Ca_30464_v3' => 'car', 'Cc06_g08160' => 'ccan', 'Cc07_g01520' => 'ccan', 'Cc11_g15810' => 'ccan', 'CDE02G2840' => 'cde', 'CDE03G0093' => 'cde', 'CDE04G2127' => 'cde', 'CDE07G1857' => 'cde', 'CDE09G1246' => 'cde', 'Cfa003412' => 'cfa', 'Cfa007341' => 'cfa', 'Cfa009220' => 'cfa', 'Ciclev10008737m.g' => 'ccl', 'Ciclev10015565m.g' => 'ccl', 'Ciclev10031761m.g' => 'ccl', 'CiPaw.03G045300' => 'cil', 'CiPaw.03G247200' => 'cil', 'CiPaw.04G029500' => 'cil', 'CiPaw.04G174000' => 'cil', 'CiPaw.05G181200' => 'cil', 'CiPaw.06G067100' => 'cil', 'ClCG05G025800' => 'cla', 'ClCG06G011400' => 'cla', 'ClCG09G019360' => 'cla', 'COL.COLO4_04827' => 'col', 'COL.COLO4_29170' => 'col', 'COL.COLO4_35131' => 'col', 'COL.COLO4_35132' => 'col', 'Cpa.g.sc33.32' => 'cpa', 'Cpa.g.sc46.29' => 'cpa', 'Cpa.g.sc796.1' => 'cpa', 'CsaV3_1G030420' => 'csa', 'CsaV3_5G027050' => 'csa', 'CsaV3_5G031040' => 'csa', 'CsaV3_UNG023130' => 'csa', 'CSS0007726' => 'camsi', 'CSS0016433' => 'camsi', 'CSS0017656' => 'camsi', 'CSS0025364' => 'camsi', 'CSS0027582' => 'camsi', 'CSS0047288' => 'camsi', 'CSS0049950' => 'camsi', 'DCAR_003843' => 'dca', 'DCAR_007052' => 'dca', 'DCAR_020884' => 'dca', 'DCAR_021730' => 'dca', 'DCAR_024423' => 'dca', 'DCAR_026509' => 'dca', 'DCAR_031158' => 'dca', 'Dinv14728' => 'din', 'Dinv15219' => 'din', 'Dinv25728' => 'din', 'Dinv33428' => 'din', 'Dinv36489' => 'din', 'Dinv41486' => 'din', 'Duzib147G0469' => 'dzi', 'Duzib168G0060' => 'dzi', 'Duzib187G1215' => 'dzi', 'Duzib248G0692' => 'dzi', 'Duzib251G0767' => 'dzi', 'Duzib264G0446' => 'dzi', 'Duzib268G0691' => 'dzi', 'ECA232G4767' => 'eca', 'ECA233G2838' => 'eca', 'ECA234G0391' => 'eca', 'ECA234G0857' => 'eca', 'ECA236G1593' => 'eca', 'ECA238G0565' => 'eca', 'ECA246G1027' => 'eca', 'ECA246G3223' => 'eca', 'ECA246G3470' => 'eca', 'EL10Ac6g13829' => 'bvu', 'EL10Ac6g14093' => 'bvu', 'EL10Ac8g18707' => 'bvu', 'Eucgr.C01369' => 'egr', 'Eucgr.H02492' => 'egr', 'Eucgr.I01733' => 'egr', 'Eucgr.J02255' => 'egr', 'Eucgr.J02257' => 'egr', 'Eucgr.J02258' => 'egr', 'FAN02G1601' => 'fan', 'FAN03G1586' => 'fan', 'FAN03G2986' => 'fan', 'FAN05G4837' => 'fan', 'FAN06G0146' => 'fan', 'FAN07G0858' => 'fan', 'FAN09G3179' => 'fan', 'FAN10G0669' => 'fan', 'FAN12G2358' => 'fan', 'FAN14G4198' => 'fan', 'FAN14G5112' => 'fan', 'FAN17G0342' => 'fan', 'FAN19G0342' => 'fan', 'FAN19G0962' => 'fan', 'FAN19G1101' => 'fan', 'FAN19G1872' => 'fan', 'FAN22G0356' => 'fan', 'FAN23G0744' => 'fan', 'FAN23G1914' => 'fan', 'FAN26G0032' => 'fan', 'FAN28G0625' => 'fan', 'FvH4_1g02710' => 'fve', 'FvH4_1g02720' => 'fve', 'FvH4_4g25670' => 'fve', 'FvH4_6g51700' => 'fve', 'FvH4_7g20170' => 'fve', 'Glyma.05G175000' => 'gma', 'Glyma.08G132300' => 'gma', 'Glyma.11G243000' => 'gma', 'Glyma.13G158900' => 'gma', 'Glyma.17G112400' => 'gma', 'Glyma.18G014100' => 'gma', 'Glyma.19G003100' => 'gma', 'Glyma.19G056500' => 'gma', 'Gohir.A01G158900' => 'ghi', 'Gohir.A05G312600' => 'ghi', 'Gohir.A05G354900' => 'ghi', 'Gohir.A07G037200' => 'ghi', 'Gohir.A09G030000' => 'ghi', 'Gohir.A12G145200' => 'ghi', 'Gohir.D01G151500' => 'ghi', 'Gohir.D04G058300' => 'ghi', 'Gohir.D05G314100' => 'ghi', 'Gohir.D07G041400' => 'ghi', 'Gohir.D09G029700' => 'ghi', 'Gohir.D12G149700' => 'ghi', 'Gorai.001G043800' => 'gra', 'Gorai.002G187800' => 'gra', 'Gorai.006G034700' => 'gra', 'Gorai.008G161200' => 'gra', 'Gorai.009G335700' => 'gra', 'Gorai.012G065000' => 'gra', 'GSVIVG01000535001' => 'vvi', 'GSVIVG01015572001' => 'vvi', 'GSVIVG01032386001' => 'vvi', 'HanXRQChr05g0138531' => 'han', 'HanXRQChr06g0174391' => 'han', 'HanXRQChr07g0199021' => 'han', 'HanXRQChr08g0208211' => 'han', 'HanXRQChr09g0255471' => 'han', 'HanXRQChr10g0315791' => 'han', 'HanXRQChr12g0371991' => 'han', 'HanXRQChr15g0475251' => 'han', 'HanXRQChr17g0540001' => 'han', 'HanXRQChr17g0548631' => 'han', 'HanXRQChr17g0569561' => 'han', 'Haze_12256' => 'cav', 'Haze_14756' => 'cav', 'Haze_25528' => 'cav', 'Hma1.2p1_0079F.1_g041020' => 'hma', 'Hma1.2p1_0818F.1_g223260' => 'hma', 'Hma1.2p1_1747F.1_g300530' => 'hma', 'HPP92_004607' => 'vpl', 'HPP92_004608' => 'vpl', 'HPP92_006181' => 'vpl', 'HPP92_012192' => 'vpl', 'HPP92_015680' => 'vpl', 'HPP92_020249' => 'vpl', 'HPP92_021376' => 'vpl', 'HPP92_024275' => 'vpl', 'Hund06031' => 'sun', 'Hund25391' => 'sun', 'Lalb_Chr07g0185371' => 'lal', 'Lalb_Chr07g0185381' => 'lal', 'Lalb_Chr12g0204011' => 'lal', 'Lalb_Chr13g0301671' => 'lal', 'Lalb_Chr14g0362851' => 'lal', 'Lalb_Chr24g0403581' => 'lal', 'Lj1g0000233' => 'lja', 'Lj2g0018120' => 'lja', 'Lj3C621T0' => 'lonja', 'Lj3P1059T14' => 'lonja', 'Lj3P611T9' => 'lonja', 'Lj3P614T13' => 'lonja', 'Lj3P615T5' => 'lonja', 'Lj4g0012315' => 'lja', 'Lj4g0026182' => 'lja', 'Lj6P813T16' => 'lonja', 'Lj7C427T7' => 'lonja', 'Lj7C427T8' => 'lonja', 'Lj7P600T41' => 'lonja', 'Lju41C42G17' => 'lonja', 'Lsat_1_v5_gn_0_47300' => 'lsa', 'Lsat_1_v5_gn_2_91280' => 'lsa', 'Lsat_1_v5_gn_3_30561' => 'lsa', 'Lsat_1_v5_gn_4_184321' => 'lsa', 'Lsat_1_v5_gn_4_4041' => 'lsa', 'Lsat_1_v5_gn_5_92000' => 'lsa', 'Lsat_1_v5_gn_8_152940' => 'lsa', 'Lsat_1_v5_gn_8_62401' => 'lsa', 'Manes.06G055900' => 'mes', 'Manes.12G022200' => 'mes', 'Manes.13G023300' => 'mes', 'Manes.14G115000' => 'mes', 'Manes.15G151700' => 'mes', 'Manes.17G111300' => 'mes', 'Mapoly0226s0009' => 'mpo', 'MBI02_g25363_MAGBIO' => 'mbi', 'MBI06_g00027_MAGBIO' => 'mbi', 'MBI10_g13034_MAGBIO' => 'mbi', 'MD09G1023400' => 'mdo', 'MD13G1100100' => 'mdo', 'MD15G1169200' => 'mdo', 'MD16G1101100' => 'mdo', 'MD17G1022900' => 'mdo', 'Medtr3g096150' => 'mtr', 'Medtr4g115070' => 'mtr', 'Medtr7g033325' => 'mtr', 'Medtr8g089840' => 'mtr', 'MELO3C010319.2' => 'cme', 'MELO3C011944.2' => 'cme', 'MELO3C021589.2' => 'cme', 'Migut.E00207' => 'egut', 'Migut.H00067' => 'egut', 'Migut.K00433' => 'egut', 'Migut.K00606' => 'egut', 'Migut.K01410' => 'egut', 'MSTRG.13347' => 'ama', 'MSTRG.24045' => 'ama', 'MSTRG.2428' => 'ama', 'MSTRG.26410' => 'ama', 'MSTRG.3139' => 'ama', 'MSTRG.3286' => 'ama', 'MSTRG.563' => 'ama', 'MSTRG.7941' => 'ama', 'Nitab4.5_0000028g0060' => 'nta', 'Nitab4.5_0000065g0260' => 'nta', 'Nitab4.5_0000112g0060' => 'nta', 'Nitab4.5_0000489g0120' => 'nta', 'Nitab4.5_0001776g0050' => 'nta', 'Nitab4.5_0001854g0010' => 'nta', 'Nitab4.5_0001860g0020' => 'nta', 'Nitab4.5_0004352g0010' => 'nta', 'Nitab4.5_0008716g0020' => 'nta', 'Nitab4.5_0008922g0010' => 'nta', 'Nn3g16693' => 'nnu', 'Nn4g22596' => 'nnu', 'Nn7g37639' => 'nnu', 'Oeu001701.1' => 'oeu', 'Oeu018149.1' => 'oeu', 'Oeu026220.1' => 'oeu', 'Oeu038635.1' => 'oeu', 'Oeu049176.1' => 'oeu', 'Oeu056706.1' => 'oeu', 'Oeu056937.1' => 'oeu', 'Oeu057540.1' => 'oeu', 'Os02g0594900' => 'osa', 'Os02g0595100' => 'osa', 'Os04g0477500' => 'osa', 'Os12g0611900' => 'osa', 'Peaxi162Scf00076g00020' => 'pax', 'Peaxi162Scf00128g00217' => 'pax', 'Peaxi162Scf00129g01640' => 'pax', 'Peaxi162Scf00669g00007' => 'pax', 'Peaxi162Scf00700g00421' => 'pax', 'Peaxi162Scf00801g00038' => 'pax', 'Peaxi162Scf00891g00025' => 'pax', 'PGR083G0909' => 'pgr', 'PGR119G1005' => 'pgr', 'PGR142G2236' => 'pgr', 'PGR142G3388' => 'pgr', 'PGSC0003DMG400004514' => 'stu', 'PGSC0003DMG400012635' => 'stu', 'PGSC0003DMG400015730' => 'stu', 'PGSC0003DMG400018611' => 'stu', 'PGSC0003DMG400030897' => 'stu', 'Phvul.001G254800' => 'pvu', 'Phvul.002G260100' => 'pvu', 'Phvul.003G167600' => 'pvu', 'Phvul.004G005100' => 'pvu', 'Potri.001G343600' => 'ptr', 'Potri.006G066700' => 'ptr', 'Potri.008G186000' => 'ptr', 'Potri.010G046900' => 'ptr', 'Potri.018G127900' => 'ptr', 'Pp3c20_17750' => 'ppa', 'Pp3c24_4380' => 'ppa', 'Prupe.1G245800' => 'ppe', 'Prupe.3G293400' => 'ppe', 'Prupe.7G247400' => 'ppe', 'Psat0s145g0120' => 'psa', 'Psat0s595g0040' => 'psa', 'Psat0s595g0120' => 'psa', 'Psat3g175040' => 'psa', 'Psat7g058120' => 'psa', 'PSO017G0428' => 'pso', 'PSO063G7510' => 'pso', 'PSO067G0046' => 'pso', 'PSO478G1073' => 'pso', 'PSO675G3677' => 'pso', 'PSO675G6558' => 'pso', 'PSO675G7520' => 'pso', 'PSO675G8959' => 'pso', 'QL02p074089' => 'qlo', 'QL02p089614' => 'qlo', 'QL03p057736' => 'qlo', 'RcHm_v2.0_Chr1g0364131' => 'rch', 'RcHm_v2.0_Chr2g0087801' => 'rch', 'RcHm_v2.0_Chr2g0087821' => 'rch', 'RcHm_v2.0_Chr2g0173231' => 'rch', 'RcHm_v2.0_Chr4g0433111' => 'rch', 'Rhsim03G0250300' => 'rsi', 'Rhsim08G0048400' => 'rsi', 'Rhsim10G0014800' => 'rsi', 'Rhsim12G0040100' => 'rsi', 'Rhsim12G0109700' => 'rsi', 'Sabra06G0049600' => 'sbr', 'Sabra08G0141000' => 'sbr', 'Sabra10G0021400' => 'sbr', 'Sabra16G0222900' => 'sbr', 'Sabra18G0108600' => 'sbr', 'SalBow1G0433' => 'sbo', 'SalBow1G2038' => 'sbo', 'SalBow1G5003' => 'sbo', 'SalBow7G1197' => 'sbo', 'SalBow8G3506' => 'sbo', 'Sc03g0007300' => 'sci', 'Sc11g0000950' => 'sci', 'Sc14g0008750' => 'sci', 'Sc18g0000420' => 'sci', 'Sed0006754' => 'sed', 'Sed0008741' => 'sed', 'Sed0017172' => 'sed', 'Sed0018925' => 'sed', 'Sed0023326' => 'sed', 'Sed0025909' => 'sed', 'SEGI_05333' => 'sgi', 'SEGI_10362' => 'sgi', 'SEGI_13380' => 'sgi', 'SEGI_24306' => 'sgi', 'SEGI_29077' => 'sgi', 'SEGI_29095' => 'sgi', 'SEGI_36534' => 'sgi', 'SEGI_37506' => 'sgi', 'SEGI_38321' => 'sgi', 'SGA_v2.0_scaffold307G48031' => 'sas', 'SGA_v2.0_scaffold47G17507' => 'sas', 'SGA_v2.0_scaffold63G21736' => 'sas', 'SGA_v2.0_scaffold87G27070' => 'sas', 'SHI17794' => 'shi', 'SHI28851' => 'shi', 'SMO165G0155' => 'smo', 'SMO340G0217' => 'smo', 'SMO367G1210' => 'smo', 'Solyc02g093430.3' => 'sly', 'Solyc05g013580.4' => 'sly', 'Solyc07g008030.3' => 'sly', 'Solyc12g035470.2' => 'sly', 'Sopen02g038020' => 'spe', 'Sopen05g008490' => 'spe', 'Sopen07g003910' => 'spe', 'Sopen12g015240' => 'spe', 'Sp1g11550' => 'spa', 'Sp2g16710' => 'spa', 'Sp3g00430' => 'spa', 'Sp3g26780' => 'spa', 'Sp5g22900' => 'spa', 'Sp6g29530' => 'spa', 'TAR371G0794' => 'tar', 'TAR374G0164' => 'tar', 'TAR622G0165' => 'tar', 'TAR626G0929' => 'tar', 'TAR629G2155' => 'tar', 'THA.LOC104805282' => 'tha', 'THA.LOC104805363' => 'tha', 'THA.LOC104808968' => 'tha', 'THA.LOC104821093' => 'tha', 'THA.LOC104823953' => 'tha', 'THA.LOC104825562' => 'tha', 'THA.LOC104825665' => 'tha', 'Thecc.02G261400' => 'tca', 'Thecc.04G019200' => 'tca', 'Thecc.09G130400' => 'tca', 'Thhalv10004374m.g' => 'esa', 'Thhalv10007850m.g' => 'esa', 'Thhalv10013782m.g' => 'esa', 'Thhalv10018686m.g' => 'esa', 'Thhalv10020899m.g' => 'esa', 'Thhalv10022755m.g' => 'esa', 'TPR.G23851' => 'tpr', 'TPR.G26500' => 'tpr', 'TPR.G27267' => 'tpr', 'TPR.G32001' => 'tpr', 'TPR.G6251' => 'tpr', 'TPR.G8167' => 'tpr', 'TWI12G1330' => 'twi', 'TWI18G1239' => 'twi', 'TWI34G0979' => 'twi', 'TWI36G0670' => 'twi', 'TWI36G0707' => 'twi', 'TWI56G0233' => 'twi', 'TWI75G1809' => 'twi', 'unitig_21.g20874' => 'ugi', 'unitig_26.g10343' => 'ugi', 'unitig_46.g18392' => 'ugi', 'unitig_52.g17178' => 'ugi', 'unitig_8.g2934' => 'ugi', 'vmacro01122' => 'vma', 'vmacro05875' => 'vma', 'vmacro06147' => 'vma', 'vmacro16191' => 'vma', 'vmacro18293' => 'vma', 'VMungo0251G3707' => 'vmu', 'VMungo0464G1521' => 'vmu', 'VMungo1215G0205' => 'vmu', 'VMungo1383G2484' => 'vmu', 'Zm00001eb079610' => 'zma', 'Zm00001eb135990' => 'zma', 'Zm00001eb183710' => 'zma', 'Zm00001eb246020' => 'zma' ) $gf_id = 'HOM05D001124' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001124' ) $data_identifier = 'HOM05D001124' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 6, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 7, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 21, 'bol' => (int) 10, 'bra' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 6, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 9, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 21, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 8, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 10, 'lsa' => (int) 8, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 8, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 9, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb246020' $species_info = array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ) $local_species = 'tpr' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001124', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '548', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02520' => 'bna', 'A03p06630' => 'bna', 'A05p44460' => 'bna', 'A06p08710' => 'bna', 'A06p41090' => 'bna', 'A07p32320' => 'bna', 'A08p32520' => 'bna', 'A09p10360' => 'bna', 'A10p24080' => 'bna', 'Aa31LG11G15250' => 'aar', 'Aa31LG1G1800' => 'aar', 'Aa31LG2G5120' => 'aar', 'Aa31LG2G6070' => 'aar', 'Aa31LG5G10770' => 'aar', 'Aa31sc61G90' => 'aar', 'Actinidia01352' => 'ach', 'Actinidia05983' => 'ach', 'Actinidia08133' => 'ach', 'Actinidia15101' => 'ach', 'Actinidia26379' => 'ach', 'Actinidia35778' => 'ach', 'Actinidia36123' => 'ach', 'Actinidia37436' => 'ach', 'Actinidia38730' => 'ach', 'Ah.02g128210' => 'amhyb', 'Ah.03g132990' => 'amhyb', 'Ah.14g079410' => 'amhyb', 'AL1G24640' => 'aly', 'AL2G26680' => 'aly', 'AL3G10530' => 'aly', 'AL3G45230' => 'aly', 'AL5G15230' => 'aly', 'AL5G16960' => 'aly', 'AL6G25210' => 'aly', 'Aqoxy2G00441' => 'aox', 'Aqoxy3G01236' => 'aox', 'Aqoxy5G03746' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3RQ047' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C7GMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9C8JER' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MBL6KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YXCZ83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZANX40' => 'arhy', 'AT1G12990' => 'ath', 'AT1G67880' => 'ath', 'AT2G13290' => 'ath', 'AT3G01620' => 'ath', 'AT3G26445' => 'ath', 'AT3G27540' => 'ath', 'AT5G14480' => 'ath', 'ATR0824G026' => 'atr', 'ATR1098G019' => 'atr', 'Atru.chr11.2145' => 'acertr', 'Atru.chr2.3636' => 'acertr', 'Atru.chr2.3644' => 'acertr', 'Atru.chr6.2422' => 'acertr', 'Atru.chr7.1112' => 'acertr', 'AUR62005469' => 'cqu', 'AUR62011166' => 'cqu', 'AUR62013319' => 'cqu', 'AUR62024273' => 'cqu', 'AUR62028420' => 'cqu', 'AUR62041942' => 'cqu', 'BcaB01g04969' => 'bca', 'BcaB01g06371' => 'bca', 'BcaB02g11494' => 'bca', 'BcaB03g15382' => 'bca', 'BcaB08g36994' => 'bca', 'BcaC03g13477' => 'bca', 'BcaC03g13478' => 'bca', 'BcaC03g13480' => 'bca', 'BcaC03g13481' => 'bca', 'BcaC03g13486' => 'bca', 'BcaC04g19031' => 'bca', 'BcaC04g23085' => 'bca', 'BcaC05g25094' => 'bca', 'BcaC05g25096' => 'bca', 'BcaC05g25138' => 'bca', 'BcaC05g30416' => 'bca', 'BcaC05g30455' => 'bca', 'BcaC06g30979' => 'bca', 'BcaC06g33805' => 'bca', 'BcaC08g46021' => 'bca', 'BcaNung03154' => 'bca', 'BolC2t06623H' => 'bol', 'BolC2t06632H' => 'bol', 'BolC2t06635H' => 'bol', 'BolC2t06638H' => 'bol', 'BolC3t13266H' => 'bol', 'BolC5t29776H' => 'bol', 'BolC6t38912H' => 'bol', 'BolC7t44183H' => 'bol', 'BolC9t54123H' => 'bol', 'BolC9t59107H' => 'bol', 'BraA02t05221Z' => 'bra', 'BraA03t09996Z' => 'bra', 'BraA05t23210Z' => 'bra', 'BraA06t24068Z' => 'bra', 'BraA06t27032Z' => 'bra', 'BraA08t35176Z' => 'bra', 'BraA09t36680Z' => 'bra', 'BraA10t44471Z' => 'bra', 'C02p06760' => 'bna', 'C02p06890' => 'bna', 'C02p07010' => 'bna', 'C03p07660' => 'bna', 'C05p10300' => 'bna', 'C06p38150' => 'bna', 'C07p36650' => 'bna', 'C08p15770' => 'bna', 'C09p12300' => 'bna', 'C09p62700' => 'bna', 'C09p75040' => 'bna', 'CAN.G13.1' => 'can', 'CAN.G138.4' => 'can', 'CAN.G44.6' => 'can', 'CAN.G473.19' => 'can', 'CANSAT01G0835' => 'cansat', 'CANSAT11G0246' => 'cansat', 'CANSAT11G1766' => 'cansat', 'CANSAT64G1954' => 'cansat', 'CARHR013330' => 'chi', 'CARHR060530' => 'chi', 'CARHR075300' => 'chi', 'CARHR105120' => 'chi', 'CARHR148910' => 'chi', 'CARHR198830' => 'chi', 'Carub.0001s1275' => 'cru', 'Carub.0002s1437' => 'cru', 'Carub.0003s0044' => 'cru', 'Carub.0003s2787' => 'cru', 'Carub.0005s0597' => 'cru', 'Carub.0006s1266' => 'cru', 'Ca_06935_v3' => 'car', 'Ca_13559_v3' => 'car', 'Ca_16941_v3' => 'car', 'Ca_16960_v3' => 'car', 'Ca_17775_v3' => 'car', 'Ca_30464_v3' => 'car', 'Cc06_g08160' => 'ccan', 'Cc07_g01520' => 'ccan', 'Cc11_g15810' => 'ccan', 'CDE02G2840' => 'cde', 'CDE03G0093' => 'cde', 'CDE04G2127' => 'cde', 'CDE07G1857' => 'cde', 'CDE09G1246' => 'cde', 'Cfa003412' => 'cfa', 'Cfa007341' => 'cfa', 'Cfa009220' => 'cfa', 'Ciclev10008737m.g' => 'ccl', 'Ciclev10015565m.g' => 'ccl', 'Ciclev10031761m.g' => 'ccl', 'CiPaw.03G045300' => 'cil', 'CiPaw.03G247200' => 'cil', 'CiPaw.04G029500' => 'cil', 'CiPaw.04G174000' => 'cil', 'CiPaw.05G181200' => 'cil', 'CiPaw.06G067100' => 'cil', 'ClCG05G025800' => 'cla', 'ClCG06G011400' => 'cla', 'ClCG09G019360' => 'cla', 'COL.COLO4_04827' => 'col', 'COL.COLO4_29170' => 'col', 'COL.COLO4_35131' => 'col', 'COL.COLO4_35132' => 'col', 'Cpa.g.sc33.32' => 'cpa', 'Cpa.g.sc46.29' => 'cpa', 'Cpa.g.sc796.1' => 'cpa', 'CsaV3_1G030420' => 'csa', 'CsaV3_5G027050' => 'csa', 'CsaV3_5G031040' => 'csa', 'CsaV3_UNG023130' => 'csa', 'CSS0007726' => 'camsi', 'CSS0016433' => 'camsi', 'CSS0017656' => 'camsi', 'CSS0025364' => 'camsi', 'CSS0027582' => 'camsi', 'CSS0047288' => 'camsi', 'CSS0049950' => 'camsi', 'DCAR_003843' => 'dca', 'DCAR_007052' => 'dca', 'DCAR_020884' => 'dca', 'DCAR_021730' => 'dca', 'DCAR_024423' => 'dca', 'DCAR_026509' => 'dca', 'DCAR_031158' => 'dca', 'Dinv14728' => 'din', 'Dinv15219' => 'din', 'Dinv25728' => 'din', 'Dinv33428' => 'din', 'Dinv36489' => 'din', 'Dinv41486' => 'din', 'Duzib147G0469' => 'dzi', 'Duzib168G0060' => 'dzi', 'Duzib187G1215' => 'dzi', 'Duzib248G0692' => 'dzi', 'Duzib251G0767' => 'dzi', 'Duzib264G0446' => 'dzi', 'Duzib268G0691' => 'dzi', 'ECA232G4767' => 'eca', 'ECA233G2838' => 'eca', 'ECA234G0391' => 'eca', 'ECA234G0857' => 'eca', 'ECA236G1593' => 'eca', 'ECA238G0565' => 'eca', 'ECA246G1027' => 'eca', 'ECA246G3223' => 'eca', 'ECA246G3470' => 'eca', 'EL10Ac6g13829' => 'bvu', 'EL10Ac6g14093' => 'bvu', 'EL10Ac8g18707' => 'bvu', 'Eucgr.C01369' => 'egr', 'Eucgr.H02492' => 'egr', 'Eucgr.I01733' => 'egr', 'Eucgr.J02255' => 'egr', 'Eucgr.J02257' => 'egr', 'Eucgr.J02258' => 'egr', 'FAN02G1601' => 'fan', 'FAN03G1586' => 'fan', 'FAN03G2986' => 'fan', 'FAN05G4837' => 'fan', 'FAN06G0146' => 'fan', 'FAN07G0858' => 'fan', 'FAN09G3179' => 'fan', 'FAN10G0669' => 'fan', 'FAN12G2358' => 'fan', 'FAN14G4198' => 'fan', 'FAN14G5112' => 'fan', 'FAN17G0342' => 'fan', 'FAN19G0342' => 'fan', 'FAN19G0962' => 'fan', 'FAN19G1101' => 'fan', 'FAN19G1872' => 'fan', 'FAN22G0356' => 'fan', 'FAN23G0744' => 'fan', 'FAN23G1914' => 'fan', 'FAN26G0032' => 'fan', 'FAN28G0625' => 'fan', 'FvH4_1g02710' => 'fve', 'FvH4_1g02720' => 'fve', 'FvH4_4g25670' => 'fve', 'FvH4_6g51700' => 'fve', 'FvH4_7g20170' => 'fve', 'Glyma.05G175000' => 'gma', 'Glyma.08G132300' => 'gma', 'Glyma.11G243000' => 'gma', 'Glyma.13G158900' => 'gma', 'Glyma.17G112400' => 'gma', 'Glyma.18G014100' => 'gma', 'Glyma.19G003100' => 'gma', 'Glyma.19G056500' => 'gma', 'Gohir.A01G158900' => 'ghi', 'Gohir.A05G312600' => 'ghi', 'Gohir.A05G354900' => 'ghi', 'Gohir.A07G037200' => 'ghi', 'Gohir.A09G030000' => 'ghi', 'Gohir.A12G145200' => 'ghi', 'Gohir.D01G151500' => 'ghi', 'Gohir.D04G058300' => 'ghi', 'Gohir.D05G314100' => 'ghi', 'Gohir.D07G041400' => 'ghi', 'Gohir.D09G029700' => 'ghi', 'Gohir.D12G149700' => 'ghi', 'Gorai.001G043800' => 'gra', 'Gorai.002G187800' => 'gra', 'Gorai.006G034700' => 'gra', 'Gorai.008G161200' => 'gra', 'Gorai.009G335700' => 'gra', 'Gorai.012G065000' => 'gra', 'GSVIVG01000535001' => 'vvi', 'GSVIVG01015572001' => 'vvi', 'GSVIVG01032386001' => 'vvi', 'HanXRQChr05g0138531' => 'han', 'HanXRQChr06g0174391' => 'han', 'HanXRQChr07g0199021' => 'han', 'HanXRQChr08g0208211' => 'han', 'HanXRQChr09g0255471' => 'han', 'HanXRQChr10g0315791' => 'han', 'HanXRQChr12g0371991' => 'han', 'HanXRQChr15g0475251' => 'han', 'HanXRQChr17g0540001' => 'han', 'HanXRQChr17g0548631' => 'han', 'HanXRQChr17g0569561' => 'han', 'Haze_12256' => 'cav', 'Haze_14756' => 'cav', 'Haze_25528' => 'cav', 'Hma1.2p1_0079F.1_g041020' => 'hma', 'Hma1.2p1_0818F.1_g223260' => 'hma', 'Hma1.2p1_1747F.1_g300530' => 'hma', 'HPP92_004607' => 'vpl', 'HPP92_004608' => 'vpl', 'HPP92_006181' => 'vpl', 'HPP92_012192' => 'vpl', 'HPP92_015680' => 'vpl', 'HPP92_020249' => 'vpl', 'HPP92_021376' => 'vpl', 'HPP92_024275' => 'vpl', 'Hund06031' => 'sun', 'Hund25391' => 'sun', 'Lalb_Chr07g0185371' => 'lal', 'Lalb_Chr07g0185381' => 'lal', 'Lalb_Chr12g0204011' => 'lal', 'Lalb_Chr13g0301671' => 'lal', 'Lalb_Chr14g0362851' => 'lal', 'Lalb_Chr24g0403581' => 'lal', 'Lj1g0000233' => 'lja', 'Lj2g0018120' => 'lja', 'Lj3C621T0' => 'lonja', 'Lj3P1059T14' => 'lonja', 'Lj3P611T9' => 'lonja', 'Lj3P614T13' => 'lonja', 'Lj3P615T5' => 'lonja', 'Lj4g0012315' => 'lja', 'Lj4g0026182' => 'lja', 'Lj6P813T16' => 'lonja', 'Lj7C427T7' => 'lonja', 'Lj7C427T8' => 'lonja', 'Lj7P600T41' => 'lonja', 'Lju41C42G17' => 'lonja', 'Lsat_1_v5_gn_0_47300' => 'lsa', 'Lsat_1_v5_gn_2_91280' => 'lsa', 'Lsat_1_v5_gn_3_30561' => 'lsa', 'Lsat_1_v5_gn_4_184321' => 'lsa', 'Lsat_1_v5_gn_4_4041' => 'lsa', 'Lsat_1_v5_gn_5_92000' => 'lsa', 'Lsat_1_v5_gn_8_152940' => 'lsa', 'Lsat_1_v5_gn_8_62401' => 'lsa', 'Manes.06G055900' => 'mes', 'Manes.12G022200' => 'mes', 'Manes.13G023300' => 'mes', 'Manes.14G115000' => 'mes', 'Manes.15G151700' => 'mes', 'Manes.17G111300' => 'mes', 'Mapoly0226s0009' => 'mpo', 'MBI02_g25363_MAGBIO' => 'mbi', 'MBI06_g00027_MAGBIO' => 'mbi', 'MBI10_g13034_MAGBIO' => 'mbi', 'MD09G1023400' => 'mdo', 'MD13G1100100' => 'mdo', 'MD15G1169200' => 'mdo', 'MD16G1101100' => 'mdo', 'MD17G1022900' => 'mdo', 'Medtr3g096150' => 'mtr', 'Medtr4g115070' => 'mtr', 'Medtr7g033325' => 'mtr', 'Medtr8g089840' => 'mtr', 'MELO3C010319.2' => 'cme', 'MELO3C011944.2' => 'cme', 'MELO3C021589.2' => 'cme', 'Migut.E00207' => 'egut', 'Migut.H00067' => 'egut', 'Migut.K00433' => 'egut', 'Migut.K00606' => 'egut', 'Migut.K01410' => 'egut', 'MSTRG.13347' => 'ama', 'MSTRG.24045' => 'ama', 'MSTRG.2428' => 'ama', 'MSTRG.26410' => 'ama', 'MSTRG.3139' => 'ama', 'MSTRG.3286' => 'ama', 'MSTRG.563' => 'ama', 'MSTRG.7941' => 'ama', 'Nitab4.5_0000028g0060' => 'nta', 'Nitab4.5_0000065g0260' => 'nta', 'Nitab4.5_0000112g0060' => 'nta', 'Nitab4.5_0000489g0120' => 'nta', 'Nitab4.5_0001776g0050' => 'nta', 'Nitab4.5_0001854g0010' => 'nta', 'Nitab4.5_0001860g0020' => 'nta', 'Nitab4.5_0004352g0010' => 'nta', 'Nitab4.5_0008716g0020' => 'nta', 'Nitab4.5_0008922g0010' => 'nta', 'Nn3g16693' => 'nnu', 'Nn4g22596' => 'nnu', 'Nn7g37639' => 'nnu', 'Oeu001701.1' => 'oeu', 'Oeu018149.1' => 'oeu', 'Oeu026220.1' => 'oeu', 'Oeu038635.1' => 'oeu', 'Oeu049176.1' => 'oeu', 'Oeu056706.1' => 'oeu', 'Oeu056937.1' => 'oeu', 'Oeu057540.1' => 'oeu', 'Os02g0594900' => 'osa', 'Os02g0595100' => 'osa', 'Os04g0477500' => 'osa', 'Os12g0611900' => 'osa', 'Peaxi162Scf00076g00020' => 'pax', 'Peaxi162Scf00128g00217' => 'pax', 'Peaxi162Scf00129g01640' => 'pax', 'Peaxi162Scf00669g00007' => 'pax', 'Peaxi162Scf00700g00421' => 'pax', 'Peaxi162Scf00801g00038' => 'pax', 'Peaxi162Scf00891g00025' => 'pax', 'PGR083G0909' => 'pgr', 'PGR119G1005' => 'pgr', 'PGR142G2236' => 'pgr', 'PGR142G3388' => 'pgr', 'PGSC0003DMG400004514' => 'stu', 'PGSC0003DMG400012635' => 'stu', 'PGSC0003DMG400015730' => 'stu', 'PGSC0003DMG400018611' => 'stu', 'PGSC0003DMG400030897' => 'stu', 'Phvul.001G254800' => 'pvu', 'Phvul.002G260100' => 'pvu', 'Phvul.003G167600' => 'pvu', 'Phvul.004G005100' => 'pvu', 'Potri.001G343600' => 'ptr', 'Potri.006G066700' => 'ptr', 'Potri.008G186000' => 'ptr', 'Potri.010G046900' => 'ptr', 'Potri.018G127900' => 'ptr', 'Pp3c20_17750' => 'ppa', 'Pp3c24_4380' => 'ppa', 'Prupe.1G245800' => 'ppe', 'Prupe.3G293400' => 'ppe', 'Prupe.7G247400' => 'ppe', 'Psat0s145g0120' => 'psa', 'Psat0s595g0040' => 'psa', 'Psat0s595g0120' => 'psa', 'Psat3g175040' => 'psa', 'Psat7g058120' => 'psa', 'PSO017G0428' => 'pso', 'PSO063G7510' => 'pso', 'PSO067G0046' => 'pso', 'PSO478G1073' => 'pso', 'PSO675G3677' => 'pso', 'PSO675G6558' => 'pso', 'PSO675G7520' => 'pso', 'PSO675G8959' => 'pso', 'QL02p074089' => 'qlo', 'QL02p089614' => 'qlo', 'QL03p057736' => 'qlo', 'RcHm_v2.0_Chr1g0364131' => 'rch', 'RcHm_v2.0_Chr2g0087801' => 'rch', 'RcHm_v2.0_Chr2g0087821' => 'rch', 'RcHm_v2.0_Chr2g0173231' => 'rch', 'RcHm_v2.0_Chr4g0433111' => 'rch', 'Rhsim03G0250300' => 'rsi', 'Rhsim08G0048400' => 'rsi', 'Rhsim10G0014800' => 'rsi', 'Rhsim12G0040100' => 'rsi', 'Rhsim12G0109700' => 'rsi', 'Sabra06G0049600' => 'sbr', 'Sabra08G0141000' => 'sbr', 'Sabra10G0021400' => 'sbr', 'Sabra16G0222900' => 'sbr', 'Sabra18G0108600' => 'sbr', 'SalBow1G0433' => 'sbo', 'SalBow1G2038' => 'sbo', 'SalBow1G5003' => 'sbo', 'SalBow7G1197' => 'sbo', 'SalBow8G3506' => 'sbo', 'Sc03g0007300' => 'sci', 'Sc11g0000950' => 'sci', 'Sc14g0008750' => 'sci', 'Sc18g0000420' => 'sci', 'Sed0006754' => 'sed', 'Sed0008741' => 'sed', 'Sed0017172' => 'sed', 'Sed0018925' => 'sed', 'Sed0023326' => 'sed', 'Sed0025909' => 'sed', 'SEGI_05333' => 'sgi', 'SEGI_10362' => 'sgi', 'SEGI_13380' => 'sgi', 'SEGI_24306' => 'sgi', 'SEGI_29077' => 'sgi', 'SEGI_29095' => 'sgi', 'SEGI_36534' => 'sgi', 'SEGI_37506' => 'sgi', 'SEGI_38321' => 'sgi', 'SGA_v2.0_scaffold307G48031' => 'sas', 'SGA_v2.0_scaffold47G17507' => 'sas', 'SGA_v2.0_scaffold63G21736' => 'sas', 'SGA_v2.0_scaffold87G27070' => 'sas', 'SHI17794' => 'shi', 'SHI28851' => 'shi', 'SMO165G0155' => 'smo', 'SMO340G0217' => 'smo', 'SMO367G1210' => 'smo', 'Solyc02g093430.3' => 'sly', 'Solyc05g013580.4' => 'sly', 'Solyc07g008030.3' => 'sly', 'Solyc12g035470.2' => 'sly', 'Sopen02g038020' => 'spe', 'Sopen05g008490' => 'spe', 'Sopen07g003910' => 'spe', 'Sopen12g015240' => 'spe', 'Sp1g11550' => 'spa', 'Sp2g16710' => 'spa', 'Sp3g00430' => 'spa', 'Sp3g26780' => 'spa', 'Sp5g22900' => 'spa', 'Sp6g29530' => 'spa', 'TAR371G0794' => 'tar', 'TAR374G0164' => 'tar', 'TAR622G0165' => 'tar', 'TAR626G0929' => 'tar', 'TAR629G2155' => 'tar', 'THA.LOC104805282' => 'tha', 'THA.LOC104805363' => 'tha', 'THA.LOC104808968' => 'tha', 'THA.LOC104821093' => 'tha', 'THA.LOC104823953' => 'tha', 'THA.LOC104825562' => 'tha', 'THA.LOC104825665' => 'tha', 'Thecc.02G261400' => 'tca', 'Thecc.04G019200' => 'tca', 'Thecc.09G130400' => 'tca', 'Thhalv10004374m.g' => 'esa', 'Thhalv10007850m.g' => 'esa', 'Thhalv10013782m.g' => 'esa', 'Thhalv10018686m.g' => 'esa', 'Thhalv10020899m.g' => 'esa', 'Thhalv10022755m.g' => 'esa', 'TPR.G23851' => 'tpr', 'TPR.G26500' => 'tpr', 'TPR.G27267' => 'tpr', 'TPR.G32001' => 'tpr', 'TPR.G6251' => 'tpr', 'TPR.G8167' => 'tpr', 'TWI12G1330' => 'twi', 'TWI18G1239' => 'twi', 'TWI34G0979' => 'twi', 'TWI36G0670' => 'twi', 'TWI36G0707' => 'twi', 'TWI56G0233' => 'twi', 'TWI75G1809' => 'twi', 'unitig_21.g20874' => 'ugi', 'unitig_26.g10343' => 'ugi', 'unitig_46.g18392' => 'ugi', 'unitig_52.g17178' => 'ugi', 'unitig_8.g2934' => 'ugi', 'vmacro01122' => 'vma', 'vmacro05875' => 'vma', 'vmacro06147' => 'vma', 'vmacro16191' => 'vma', 'vmacro18293' => 'vma', 'VMungo0251G3707' => 'vmu', 'VMungo0464G1521' => 'vmu', 'VMungo1215G0205' => 'vmu', 'VMungo1383G2484' => 'vmu', 'Zm00001eb079610' => 'zma', 'Zm00001eb135990' => 'zma', 'Zm00001eb183710' => 'zma', 'Zm00001eb246020' => 'zma' ), 'gf_id' => 'HOM05D001124', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001124' ), 'data_identifier' => 'HOM05D001124', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001124', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '548', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02520' => 'bna', 'A03p06630' => 'bna', 'A05p44460' => 'bna', 'A06p08710' => 'bna', 'A06p41090' => 'bna', 'A07p32320' => 'bna', 'A08p32520' => 'bna', 'A09p10360' => 'bna', 'A10p24080' => 'bna', 'Aa31LG11G15250' => 'aar', 'Aa31LG1G1800' => 'aar', 'Aa31LG2G5120' => 'aar', 'Aa31LG2G6070' => 'aar', 'Aa31LG5G10770' => 'aar', 'Aa31sc61G90' => 'aar', 'Actinidia01352' => 'ach', 'Actinidia05983' => 'ach', 'Actinidia08133' => 'ach', 'Actinidia15101' => 'ach', 'Actinidia26379' => 'ach', 'Actinidia35778' => 'ach', 'Actinidia36123' => 'ach', 'Actinidia37436' => 'ach', 'Actinidia38730' => 'ach', 'Ah.02g128210' => 'amhyb', 'Ah.03g132990' => 'amhyb', 'Ah.14g079410' => 'amhyb', 'AL1G24640' => 'aly', 'AL2G26680' => 'aly', 'AL3G10530' => 'aly', 'AL3G45230' => 'aly', 'AL5G15230' => 'aly', 'AL5G16960' => 'aly', 'AL6G25210' => 'aly', 'Aqoxy2G00441' => 'aox', 'Aqoxy3G01236' => 'aox', 'Aqoxy5G03746' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3RQ047' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C7GMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9C8JER' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MBL6KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YXCZ83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZANX40' => 'arhy', 'AT1G12990' => 'ath', 'AT1G67880' => 'ath', 'AT2G13290' => 'ath', 'AT3G01620' => 'ath', 'AT3G26445' => 'ath', 'AT3G27540' => 'ath', 'AT5G14480' => 'ath', 'ATR0824G026' => 'atr', 'ATR1098G019' => 'atr', 'Atru.chr11.2145' => 'acertr', 'Atru.chr2.3636' => 'acertr', 'Atru.chr2.3644' => 'acertr', 'Atru.chr6.2422' => 'acertr', 'Atru.chr7.1112' => 'acertr', 'AUR62005469' => 'cqu', 'AUR62011166' => 'cqu', 'AUR62013319' => 'cqu', 'AUR62024273' => 'cqu', 'AUR62028420' => 'cqu', 'AUR62041942' => 'cqu', 'BcaB01g04969' => 'bca', 'BcaB01g06371' => 'bca', 'BcaB02g11494' => 'bca', 'BcaB03g15382' => 'bca', 'BcaB08g36994' => 'bca', 'BcaC03g13477' => 'bca', 'BcaC03g13478' => 'bca', 'BcaC03g13480' => 'bca', 'BcaC03g13481' => 'bca', 'BcaC03g13486' => 'bca', 'BcaC04g19031' => 'bca', 'BcaC04g23085' => 'bca', 'BcaC05g25094' => 'bca', 'BcaC05g25096' => 'bca', 'BcaC05g25138' => 'bca', 'BcaC05g30416' => 'bca', 'BcaC05g30455' => 'bca', 'BcaC06g30979' => 'bca', 'BcaC06g33805' => 'bca', 'BcaC08g46021' => 'bca', 'BcaNung03154' => 'bca', 'BolC2t06623H' => 'bol', 'BolC2t06632H' => 'bol', 'BolC2t06635H' => 'bol', 'BolC2t06638H' => 'bol', 'BolC3t13266H' => 'bol', 'BolC5t29776H' => 'bol', 'BolC6t38912H' => 'bol', 'BolC7t44183H' => 'bol', 'BolC9t54123H' => 'bol', 'BolC9t59107H' => 'bol', 'BraA02t05221Z' => 'bra', 'BraA03t09996Z' => 'bra', 'BraA05t23210Z' => 'bra', 'BraA06t24068Z' => 'bra', 'BraA06t27032Z' => 'bra', 'BraA08t35176Z' => 'bra', 'BraA09t36680Z' => 'bra', 'BraA10t44471Z' => 'bra', 'C02p06760' => 'bna', 'C02p06890' => 'bna', 'C02p07010' => 'bna', 'C03p07660' => 'bna', 'C05p10300' => 'bna', 'C06p38150' => 'bna', 'C07p36650' => 'bna', 'C08p15770' => 'bna', 'C09p12300' => 'bna', 'C09p62700' => 'bna', 'C09p75040' => 'bna', 'CAN.G13.1' => 'can', 'CAN.G138.4' => 'can', 'CAN.G44.6' => 'can', 'CAN.G473.19' => 'can', 'CANSAT01G0835' => 'cansat', 'CANSAT11G0246' => 'cansat', 'CANSAT11G1766' => 'cansat', 'CANSAT64G1954' => 'cansat', 'CARHR013330' => 'chi', 'CARHR060530' => 'chi', 'CARHR075300' => 'chi', 'CARHR105120' => 'chi', 'CARHR148910' => 'chi', 'CARHR198830' => 'chi', 'Carub.0001s1275' => 'cru', 'Carub.0002s1437' => 'cru', 'Carub.0003s0044' => 'cru', 'Carub.0003s2787' => 'cru', 'Carub.0005s0597' => 'cru', 'Carub.0006s1266' => 'cru', 'Ca_06935_v3' => 'car', 'Ca_13559_v3' => 'car', 'Ca_16941_v3' => 'car', 'Ca_16960_v3' => 'car', 'Ca_17775_v3' => 'car', 'Ca_30464_v3' => 'car', 'Cc06_g08160' => 'ccan', 'Cc07_g01520' => 'ccan', 'Cc11_g15810' => 'ccan', 'CDE02G2840' => 'cde', 'CDE03G0093' => 'cde', 'CDE04G2127' => 'cde', 'CDE07G1857' => 'cde', 'CDE09G1246' => 'cde', 'Cfa003412' => 'cfa', 'Cfa007341' => 'cfa', 'Cfa009220' => 'cfa', 'Ciclev10008737m.g' => 'ccl', 'Ciclev10015565m.g' => 'ccl', 'Ciclev10031761m.g' => 'ccl', 'CiPaw.03G045300' => 'cil', 'CiPaw.03G247200' => 'cil', 'CiPaw.04G029500' => 'cil', 'CiPaw.04G174000' => 'cil', 'CiPaw.05G181200' => 'cil', 'CiPaw.06G067100' => 'cil', 'ClCG05G025800' => 'cla', 'ClCG06G011400' => 'cla', 'ClCG09G019360' => 'cla', 'COL.COLO4_04827' => 'col', 'COL.COLO4_29170' => 'col', 'COL.COLO4_35131' => 'col', 'COL.COLO4_35132' => 'col', 'Cpa.g.sc33.32' => 'cpa', 'Cpa.g.sc46.29' => 'cpa', 'Cpa.g.sc796.1' => 'cpa', 'CsaV3_1G030420' => 'csa', 'CsaV3_5G027050' => 'csa', 'CsaV3_5G031040' => 'csa', 'CsaV3_UNG023130' => 'csa', 'CSS0007726' => 'camsi', 'CSS0016433' => 'camsi', 'CSS0017656' => 'camsi', 'CSS0025364' => 'camsi', 'CSS0027582' => 'camsi', 'CSS0047288' => 'camsi', 'CSS0049950' => 'camsi', 'DCAR_003843' => 'dca', 'DCAR_007052' => 'dca', 'DCAR_020884' => 'dca', 'DCAR_021730' => 'dca', 'DCAR_024423' => 'dca', 'DCAR_026509' => 'dca', 'DCAR_031158' => 'dca', 'Dinv14728' => 'din', 'Dinv15219' => 'din', 'Dinv25728' => 'din', 'Dinv33428' => 'din', 'Dinv36489' => 'din', 'Dinv41486' => 'din', 'Duzib147G0469' => 'dzi', 'Duzib168G0060' => 'dzi', 'Duzib187G1215' => 'dzi', 'Duzib248G0692' => 'dzi', 'Duzib251G0767' => 'dzi', 'Duzib264G0446' => 'dzi', 'Duzib268G0691' => 'dzi', 'ECA232G4767' => 'eca', 'ECA233G2838' => 'eca', 'ECA234G0391' => 'eca', 'ECA234G0857' => 'eca', 'ECA236G1593' => 'eca', 'ECA238G0565' => 'eca', 'ECA246G1027' => 'eca', 'ECA246G3223' => 'eca', 'ECA246G3470' => 'eca', 'EL10Ac6g13829' => 'bvu', 'EL10Ac6g14093' => 'bvu', 'EL10Ac8g18707' => 'bvu', 'Eucgr.C01369' => 'egr', 'Eucgr.H02492' => 'egr', 'Eucgr.I01733' => 'egr', 'Eucgr.J02255' => 'egr', 'Eucgr.J02257' => 'egr', 'Eucgr.J02258' => 'egr', 'FAN02G1601' => 'fan', 'FAN03G1586' => 'fan', 'FAN03G2986' => 'fan', 'FAN05G4837' => 'fan', 'FAN06G0146' => 'fan', 'FAN07G0858' => 'fan', 'FAN09G3179' => 'fan', 'FAN10G0669' => 'fan', 'FAN12G2358' => 'fan', 'FAN14G4198' => 'fan', 'FAN14G5112' => 'fan', 'FAN17G0342' => 'fan', 'FAN19G0342' => 'fan', 'FAN19G0962' => 'fan', 'FAN19G1101' => 'fan', 'FAN19G1872' => 'fan', 'FAN22G0356' => 'fan', 'FAN23G0744' => 'fan', 'FAN23G1914' => 'fan', 'FAN26G0032' => 'fan', 'FAN28G0625' => 'fan', 'FvH4_1g02710' => 'fve', 'FvH4_1g02720' => 'fve', 'FvH4_4g25670' => 'fve', 'FvH4_6g51700' => 'fve', 'FvH4_7g20170' => 'fve', 'Glyma.05G175000' => 'gma', 'Glyma.08G132300' => 'gma', 'Glyma.11G243000' => 'gma', 'Glyma.13G158900' => 'gma', 'Glyma.17G112400' => 'gma', 'Glyma.18G014100' => 'gma', 'Glyma.19G003100' => 'gma', 'Glyma.19G056500' => 'gma', 'Gohir.A01G158900' => 'ghi', 'Gohir.A05G312600' => 'ghi', 'Gohir.A05G354900' => 'ghi', 'Gohir.A07G037200' => 'ghi', 'Gohir.A09G030000' => 'ghi', 'Gohir.A12G145200' => 'ghi', 'Gohir.D01G151500' => 'ghi', 'Gohir.D04G058300' => 'ghi', 'Gohir.D05G314100' => 'ghi', 'Gohir.D07G041400' => 'ghi', 'Gohir.D09G029700' => 'ghi', 'Gohir.D12G149700' => 'ghi', 'Gorai.001G043800' => 'gra', 'Gorai.002G187800' => 'gra', 'Gorai.006G034700' => 'gra', 'Gorai.008G161200' => 'gra', 'Gorai.009G335700' => 'gra', 'Gorai.012G065000' => 'gra', 'GSVIVG01000535001' => 'vvi', 'GSVIVG01015572001' => 'vvi', 'GSVIVG01032386001' => 'vvi', 'HanXRQChr05g0138531' => 'han', 'HanXRQChr06g0174391' => 'han', 'HanXRQChr07g0199021' => 'han', 'HanXRQChr08g0208211' => 'han', 'HanXRQChr09g0255471' => 'han', 'HanXRQChr10g0315791' => 'han', 'HanXRQChr12g0371991' => 'han', 'HanXRQChr15g0475251' => 'han', 'HanXRQChr17g0540001' => 'han', 'HanXRQChr17g0548631' => 'han', 'HanXRQChr17g0569561' => 'han', 'Haze_12256' => 'cav', 'Haze_14756' => 'cav', 'Haze_25528' => 'cav', 'Hma1.2p1_0079F.1_g041020' => 'hma', 'Hma1.2p1_0818F.1_g223260' => 'hma', 'Hma1.2p1_1747F.1_g300530' => 'hma', 'HPP92_004607' => 'vpl', 'HPP92_004608' => 'vpl', 'HPP92_006181' => 'vpl', 'HPP92_012192' => 'vpl', 'HPP92_015680' => 'vpl', 'HPP92_020249' => 'vpl', 'HPP92_021376' => 'vpl', 'HPP92_024275' => 'vpl', 'Hund06031' => 'sun', 'Hund25391' => 'sun', 'Lalb_Chr07g0185371' => 'lal', 'Lalb_Chr07g0185381' => 'lal', 'Lalb_Chr12g0204011' => 'lal', 'Lalb_Chr13g0301671' => 'lal', 'Lalb_Chr14g0362851' => 'lal', 'Lalb_Chr24g0403581' => 'lal', 'Lj1g0000233' => 'lja', 'Lj2g0018120' => 'lja', 'Lj3C621T0' => 'lonja', 'Lj3P1059T14' => 'lonja', 'Lj3P611T9' => 'lonja', 'Lj3P614T13' => 'lonja', 'Lj3P615T5' => 'lonja', 'Lj4g0012315' => 'lja', 'Lj4g0026182' => 'lja', 'Lj6P813T16' => 'lonja', 'Lj7C427T7' => 'lonja', 'Lj7C427T8' => 'lonja', 'Lj7P600T41' => 'lonja', 'Lju41C42G17' => 'lonja', 'Lsat_1_v5_gn_0_47300' => 'lsa', 'Lsat_1_v5_gn_2_91280' => 'lsa', 'Lsat_1_v5_gn_3_30561' => 'lsa', 'Lsat_1_v5_gn_4_184321' => 'lsa', 'Lsat_1_v5_gn_4_4041' => 'lsa', 'Lsat_1_v5_gn_5_92000' => 'lsa', 'Lsat_1_v5_gn_8_152940' => 'lsa', 'Lsat_1_v5_gn_8_62401' => 'lsa', 'Manes.06G055900' => 'mes', 'Manes.12G022200' => 'mes', 'Manes.13G023300' => 'mes', 'Manes.14G115000' => 'mes', 'Manes.15G151700' => 'mes', 'Manes.17G111300' => 'mes', 'Mapoly0226s0009' => 'mpo', 'MBI02_g25363_MAGBIO' => 'mbi', 'MBI06_g00027_MAGBIO' => 'mbi', 'MBI10_g13034_MAGBIO' => 'mbi', 'MD09G1023400' => 'mdo', 'MD13G1100100' => 'mdo', 'MD15G1169200' => 'mdo', 'MD16G1101100' => 'mdo', 'MD17G1022900' => 'mdo', 'Medtr3g096150' => 'mtr', 'Medtr4g115070' => 'mtr', 'Medtr7g033325' => 'mtr', 'Medtr8g089840' => 'mtr', 'MELO3C010319.2' => 'cme', 'MELO3C011944.2' => 'cme', 'MELO3C021589.2' => 'cme', 'Migut.E00207' => 'egut', 'Migut.H00067' => 'egut', 'Migut.K00433' => 'egut', 'Migut.K00606' => 'egut', 'Migut.K01410' => 'egut', 'MSTRG.13347' => 'ama', 'MSTRG.24045' => 'ama', 'MSTRG.2428' => 'ama', 'MSTRG.26410' => 'ama', 'MSTRG.3139' => 'ama', 'MSTRG.3286' => 'ama', 'MSTRG.563' => 'ama', 'MSTRG.7941' => 'ama', 'Nitab4.5_0000028g0060' => 'nta', 'Nitab4.5_0000065g0260' => 'nta', 'Nitab4.5_0000112g0060' => 'nta', 'Nitab4.5_0000489g0120' => 'nta', 'Nitab4.5_0001776g0050' => 'nta', 'Nitab4.5_0001854g0010' => 'nta', 'Nitab4.5_0001860g0020' => 'nta', 'Nitab4.5_0004352g0010' => 'nta', 'Nitab4.5_0008716g0020' => 'nta', 'Nitab4.5_0008922g0010' => 'nta', 'Nn3g16693' => 'nnu', 'Nn4g22596' => 'nnu', 'Nn7g37639' => 'nnu', 'Oeu001701.1' => 'oeu', 'Oeu018149.1' => 'oeu', 'Oeu026220.1' => 'oeu', 'Oeu038635.1' => 'oeu', 'Oeu049176.1' => 'oeu', 'Oeu056706.1' => 'oeu', 'Oeu056937.1' => 'oeu', 'Oeu057540.1' => 'oeu', 'Os02g0594900' => 'osa', 'Os02g0595100' => 'osa', 'Os04g0477500' => 'osa', 'Os12g0611900' => 'osa', 'Peaxi162Scf00076g00020' => 'pax', 'Peaxi162Scf00128g00217' => 'pax', 'Peaxi162Scf00129g01640' => 'pax', 'Peaxi162Scf00669g00007' => 'pax', 'Peaxi162Scf00700g00421' => 'pax', 'Peaxi162Scf00801g00038' => 'pax', 'Peaxi162Scf00891g00025' => 'pax', 'PGR083G0909' => 'pgr', 'PGR119G1005' => 'pgr', 'PGR142G2236' => 'pgr', 'PGR142G3388' => 'pgr', 'PGSC0003DMG400004514' => 'stu', 'PGSC0003DMG400012635' => 'stu', 'PGSC0003DMG400015730' => 'stu', 'PGSC0003DMG400018611' => 'stu', 'PGSC0003DMG400030897' => 'stu', 'Phvul.001G254800' => 'pvu', 'Phvul.002G260100' => 'pvu', 'Phvul.003G167600' => 'pvu', 'Phvul.004G005100' => 'pvu', 'Potri.001G343600' => 'ptr', 'Potri.006G066700' => 'ptr', 'Potri.008G186000' => 'ptr', 'Potri.010G046900' => 'ptr', 'Potri.018G127900' => 'ptr', 'Pp3c20_17750' => 'ppa', 'Pp3c24_4380' => 'ppa', 'Prupe.1G245800' => 'ppe', 'Prupe.3G293400' => 'ppe', 'Prupe.7G247400' => 'ppe', 'Psat0s145g0120' => 'psa', 'Psat0s595g0040' => 'psa', 'Psat0s595g0120' => 'psa', 'Psat3g175040' => 'psa', 'Psat7g058120' => 'psa', 'PSO017G0428' => 'pso', 'PSO063G7510' => 'pso', 'PSO067G0046' => 'pso', 'PSO478G1073' => 'pso', 'PSO675G3677' => 'pso', 'PSO675G6558' => 'pso', 'PSO675G7520' => 'pso', 'PSO675G8959' => 'pso', 'QL02p074089' => 'qlo', 'QL02p089614' => 'qlo', 'QL03p057736' => 'qlo', 'RcHm_v2.0_Chr1g0364131' => 'rch', 'RcHm_v2.0_Chr2g0087801' => 'rch', 'RcHm_v2.0_Chr2g0087821' => 'rch', 'RcHm_v2.0_Chr2g0173231' => 'rch', 'RcHm_v2.0_Chr4g0433111' => 'rch', 'Rhsim03G0250300' => 'rsi', 'Rhsim08G0048400' => 'rsi', 'Rhsim10G0014800' => 'rsi', 'Rhsim12G0040100' => 'rsi', 'Rhsim12G0109700' => 'rsi', 'Sabra06G0049600' => 'sbr', 'Sabra08G0141000' => 'sbr', 'Sabra10G0021400' => 'sbr', 'Sabra16G0222900' => 'sbr', 'Sabra18G0108600' => 'sbr', 'SalBow1G0433' => 'sbo', 'SalBow1G2038' => 'sbo', 'SalBow1G5003' => 'sbo', 'SalBow7G1197' => 'sbo', 'SalBow8G3506' => 'sbo', 'Sc03g0007300' => 'sci', 'Sc11g0000950' => 'sci', 'Sc14g0008750' => 'sci', 'Sc18g0000420' => 'sci', 'Sed0006754' => 'sed', 'Sed0008741' => 'sed', 'Sed0017172' => 'sed', 'Sed0018925' => 'sed', 'Sed0023326' => 'sed', 'Sed0025909' => 'sed', 'SEGI_05333' => 'sgi', 'SEGI_10362' => 'sgi', 'SEGI_13380' => 'sgi', 'SEGI_24306' => 'sgi', 'SEGI_29077' => 'sgi', 'SEGI_29095' => 'sgi', 'SEGI_36534' => 'sgi', 'SEGI_37506' => 'sgi', 'SEGI_38321' => 'sgi', 'SGA_v2.0_scaffold307G48031' => 'sas', 'SGA_v2.0_scaffold47G17507' => 'sas', 'SGA_v2.0_scaffold63G21736' => 'sas', 'SGA_v2.0_scaffold87G27070' => 'sas', 'SHI17794' => 'shi', 'SHI28851' => 'shi', 'SMO165G0155' => 'smo', 'SMO340G0217' => 'smo', 'SMO367G1210' => 'smo', 'Solyc02g093430.3' => 'sly', 'Solyc05g013580.4' => 'sly', 'Solyc07g008030.3' => 'sly', 'Solyc12g035470.2' => 'sly', 'Sopen02g038020' => 'spe', 'Sopen05g008490' => 'spe', 'Sopen07g003910' => 'spe', 'Sopen12g015240' => 'spe', 'Sp1g11550' => 'spa', 'Sp2g16710' => 'spa', 'Sp3g00430' => 'spa', 'Sp3g26780' => 'spa', 'Sp5g22900' => 'spa', 'Sp6g29530' => 'spa', 'TAR371G0794' => 'tar', 'TAR374G0164' => 'tar', 'TAR622G0165' => 'tar', 'TAR626G0929' => 'tar', 'TAR629G2155' => 'tar', 'THA.LOC104805282' => 'tha', 'THA.LOC104805363' => 'tha', 'THA.LOC104808968' => 'tha', 'THA.LOC104821093' => 'tha', 'THA.LOC104823953' => 'tha', 'THA.LOC104825562' => 'tha', 'THA.LOC104825665' => 'tha', 'Thecc.02G261400' => 'tca', 'Thecc.04G019200' => 'tca', 'Thecc.09G130400' => 'tca', 'Thhalv10004374m.g' => 'esa', 'Thhalv10007850m.g' => 'esa', 'Thhalv10013782m.g' => 'esa', 'Thhalv10018686m.g' => 'esa', 'Thhalv10020899m.g' => 'esa', 'Thhalv10022755m.g' => 'esa', 'TPR.G23851' => 'tpr', 'TPR.G26500' => 'tpr', 'TPR.G27267' => 'tpr', 'TPR.G32001' => 'tpr', 'TPR.G6251' => 'tpr', 'TPR.G8167' => 'tpr', 'TWI12G1330' => 'twi', 'TWI18G1239' => 'twi', 'TWI34G0979' => 'twi', 'TWI36G0670' => 'twi', 'TWI36G0707' => 'twi', 'TWI56G0233' => 'twi', 'TWI75G1809' => 'twi', 'unitig_21.g20874' => 'ugi', 'unitig_26.g10343' => 'ugi', 'unitig_46.g18392' => 'ugi', 'unitig_52.g17178' => 'ugi', 'unitig_8.g2934' => 'ugi', 'vmacro01122' => 'vma', 'vmacro05875' => 'vma', 'vmacro06147' => 'vma', 'vmacro16191' => 'vma', 'vmacro18293' => 'vma', 'VMungo0251G3707' => 'vmu', 'VMungo0464G1521' => 'vmu', 'VMungo1215G0205' => 'vmu', 'VMungo1383G2484' => 'vmu', 'Zm00001eb079610' => 'zma', 'Zm00001eb135990' => 'zma', 'Zm00001eb183710' => 'zma', 'Zm00001eb246020' => 'zma' ) $gf_id = 'HOM05D001124' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001124' ) $data_identifier = 'HOM05D001124' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 6, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 7, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 21, 'bol' => (int) 10, 'bra' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 6, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 9, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 21, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 8, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 10, 'lsa' => (int) 8, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 8, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 9, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb246020' $species_info = array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ) $local_species = 'tpr' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001124', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '548', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02520' => 'bna', 'A03p06630' => 'bna', 'A05p44460' => 'bna', 'A06p08710' => 'bna', 'A06p41090' => 'bna', 'A07p32320' => 'bna', 'A08p32520' => 'bna', 'A09p10360' => 'bna', 'A10p24080' => 'bna', 'Aa31LG11G15250' => 'aar', 'Aa31LG1G1800' => 'aar', 'Aa31LG2G5120' => 'aar', 'Aa31LG2G6070' => 'aar', 'Aa31LG5G10770' => 'aar', 'Aa31sc61G90' => 'aar', 'Actinidia01352' => 'ach', 'Actinidia05983' => 'ach', 'Actinidia08133' => 'ach', 'Actinidia15101' => 'ach', 'Actinidia26379' => 'ach', 'Actinidia35778' => 'ach', 'Actinidia36123' => 'ach', 'Actinidia37436' => 'ach', 'Actinidia38730' => 'ach', 'Ah.02g128210' => 'amhyb', 'Ah.03g132990' => 'amhyb', 'Ah.14g079410' => 'amhyb', 'AL1G24640' => 'aly', 'AL2G26680' => 'aly', 'AL3G10530' => 'aly', 'AL3G45230' => 'aly', 'AL5G15230' => 'aly', 'AL5G16960' => 'aly', 'AL6G25210' => 'aly', 'Aqoxy2G00441' => 'aox', 'Aqoxy3G01236' => 'aox', 'Aqoxy5G03746' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3RQ047' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C7GMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9C8JER' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MBL6KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YXCZ83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZANX40' => 'arhy', 'AT1G12990' => 'ath', 'AT1G67880' => 'ath', 'AT2G13290' => 'ath', 'AT3G01620' => 'ath', 'AT3G26445' => 'ath', 'AT3G27540' => 'ath', 'AT5G14480' => 'ath', 'ATR0824G026' => 'atr', 'ATR1098G019' => 'atr', 'Atru.chr11.2145' => 'acertr', 'Atru.chr2.3636' => 'acertr', 'Atru.chr2.3644' => 'acertr', 'Atru.chr6.2422' => 'acertr', 'Atru.chr7.1112' => 'acertr', 'AUR62005469' => 'cqu', 'AUR62011166' => 'cqu', 'AUR62013319' => 'cqu', 'AUR62024273' => 'cqu', 'AUR62028420' => 'cqu', 'AUR62041942' => 'cqu', 'BcaB01g04969' => 'bca', 'BcaB01g06371' => 'bca', 'BcaB02g11494' => 'bca', 'BcaB03g15382' => 'bca', 'BcaB08g36994' => 'bca', 'BcaC03g13477' => 'bca', 'BcaC03g13478' => 'bca', 'BcaC03g13480' => 'bca', 'BcaC03g13481' => 'bca', 'BcaC03g13486' => 'bca', 'BcaC04g19031' => 'bca', 'BcaC04g23085' => 'bca', 'BcaC05g25094' => 'bca', 'BcaC05g25096' => 'bca', 'BcaC05g25138' => 'bca', 'BcaC05g30416' => 'bca', 'BcaC05g30455' => 'bca', 'BcaC06g30979' => 'bca', 'BcaC06g33805' => 'bca', 'BcaC08g46021' => 'bca', 'BcaNung03154' => 'bca', 'BolC2t06623H' => 'bol', 'BolC2t06632H' => 'bol', 'BolC2t06635H' => 'bol', 'BolC2t06638H' => 'bol', 'BolC3t13266H' => 'bol', 'BolC5t29776H' => 'bol', 'BolC6t38912H' => 'bol', 'BolC7t44183H' => 'bol', 'BolC9t54123H' => 'bol', 'BolC9t59107H' => 'bol', 'BraA02t05221Z' => 'bra', 'BraA03t09996Z' => 'bra', 'BraA05t23210Z' => 'bra', 'BraA06t24068Z' => 'bra', 'BraA06t27032Z' => 'bra', 'BraA08t35176Z' => 'bra', 'BraA09t36680Z' => 'bra', 'BraA10t44471Z' => 'bra', 'C02p06760' => 'bna', 'C02p06890' => 'bna', 'C02p07010' => 'bna', 'C03p07660' => 'bna', 'C05p10300' => 'bna', 'C06p38150' => 'bna', 'C07p36650' => 'bna', 'C08p15770' => 'bna', 'C09p12300' => 'bna', 'C09p62700' => 'bna', 'C09p75040' => 'bna', 'CAN.G13.1' => 'can', 'CAN.G138.4' => 'can', 'CAN.G44.6' => 'can', 'CAN.G473.19' => 'can', 'CANSAT01G0835' => 'cansat', 'CANSAT11G0246' => 'cansat', 'CANSAT11G1766' => 'cansat', 'CANSAT64G1954' => 'cansat', 'CARHR013330' => 'chi', 'CARHR060530' => 'chi', 'CARHR075300' => 'chi', 'CARHR105120' => 'chi', 'CARHR148910' => 'chi', 'CARHR198830' => 'chi', 'Carub.0001s1275' => 'cru', 'Carub.0002s1437' => 'cru', 'Carub.0003s0044' => 'cru', 'Carub.0003s2787' => 'cru', 'Carub.0005s0597' => 'cru', 'Carub.0006s1266' => 'cru', 'Ca_06935_v3' => 'car', 'Ca_13559_v3' => 'car', 'Ca_16941_v3' => 'car', 'Ca_16960_v3' => 'car', 'Ca_17775_v3' => 'car', 'Ca_30464_v3' => 'car', 'Cc06_g08160' => 'ccan', 'Cc07_g01520' => 'ccan', 'Cc11_g15810' => 'ccan', 'CDE02G2840' => 'cde', 'CDE03G0093' => 'cde', 'CDE04G2127' => 'cde', 'CDE07G1857' => 'cde', 'CDE09G1246' => 'cde', 'Cfa003412' => 'cfa', 'Cfa007341' => 'cfa', 'Cfa009220' => 'cfa', 'Ciclev10008737m.g' => 'ccl', 'Ciclev10015565m.g' => 'ccl', 'Ciclev10031761m.g' => 'ccl', 'CiPaw.03G045300' => 'cil', 'CiPaw.03G247200' => 'cil', 'CiPaw.04G029500' => 'cil', 'CiPaw.04G174000' => 'cil', 'CiPaw.05G181200' => 'cil', 'CiPaw.06G067100' => 'cil', 'ClCG05G025800' => 'cla', 'ClCG06G011400' => 'cla', 'ClCG09G019360' => 'cla', 'COL.COLO4_04827' => 'col', 'COL.COLO4_29170' => 'col', 'COL.COLO4_35131' => 'col', 'COL.COLO4_35132' => 'col', 'Cpa.g.sc33.32' => 'cpa', 'Cpa.g.sc46.29' => 'cpa', 'Cpa.g.sc796.1' => 'cpa', 'CsaV3_1G030420' => 'csa', 'CsaV3_5G027050' => 'csa', 'CsaV3_5G031040' => 'csa', 'CsaV3_UNG023130' => 'csa', 'CSS0007726' => 'camsi', 'CSS0016433' => 'camsi', 'CSS0017656' => 'camsi', 'CSS0025364' => 'camsi', 'CSS0027582' => 'camsi', 'CSS0047288' => 'camsi', 'CSS0049950' => 'camsi', 'DCAR_003843' => 'dca', 'DCAR_007052' => 'dca', 'DCAR_020884' => 'dca', 'DCAR_021730' => 'dca', 'DCAR_024423' => 'dca', 'DCAR_026509' => 'dca', 'DCAR_031158' => 'dca', 'Dinv14728' => 'din', 'Dinv15219' => 'din', 'Dinv25728' => 'din', 'Dinv33428' => 'din', 'Dinv36489' => 'din', 'Dinv41486' => 'din', 'Duzib147G0469' => 'dzi', 'Duzib168G0060' => 'dzi', 'Duzib187G1215' => 'dzi', 'Duzib248G0692' => 'dzi', 'Duzib251G0767' => 'dzi', 'Duzib264G0446' => 'dzi', 'Duzib268G0691' => 'dzi', 'ECA232G4767' => 'eca', 'ECA233G2838' => 'eca', 'ECA234G0391' => 'eca', 'ECA234G0857' => 'eca', 'ECA236G1593' => 'eca', 'ECA238G0565' => 'eca', 'ECA246G1027' => 'eca', 'ECA246G3223' => 'eca', 'ECA246G3470' => 'eca', 'EL10Ac6g13829' => 'bvu', 'EL10Ac6g14093' => 'bvu', 'EL10Ac8g18707' => 'bvu', 'Eucgr.C01369' => 'egr', 'Eucgr.H02492' => 'egr', 'Eucgr.I01733' => 'egr', 'Eucgr.J02255' => 'egr', 'Eucgr.J02257' => 'egr', 'Eucgr.J02258' => 'egr', 'FAN02G1601' => 'fan', 'FAN03G1586' => 'fan', 'FAN03G2986' => 'fan', 'FAN05G4837' => 'fan', 'FAN06G0146' => 'fan', 'FAN07G0858' => 'fan', 'FAN09G3179' => 'fan', 'FAN10G0669' => 'fan', 'FAN12G2358' => 'fan', 'FAN14G4198' => 'fan', 'FAN14G5112' => 'fan', 'FAN17G0342' => 'fan', 'FAN19G0342' => 'fan', 'FAN19G0962' => 'fan', 'FAN19G1101' => 'fan', 'FAN19G1872' => 'fan', 'FAN22G0356' => 'fan', 'FAN23G0744' => 'fan', 'FAN23G1914' => 'fan', 'FAN26G0032' => 'fan', 'FAN28G0625' => 'fan', 'FvH4_1g02710' => 'fve', 'FvH4_1g02720' => 'fve', 'FvH4_4g25670' => 'fve', 'FvH4_6g51700' => 'fve', 'FvH4_7g20170' => 'fve', 'Glyma.05G175000' => 'gma', 'Glyma.08G132300' => 'gma', 'Glyma.11G243000' => 'gma', 'Glyma.13G158900' => 'gma', 'Glyma.17G112400' => 'gma', 'Glyma.18G014100' => 'gma', 'Glyma.19G003100' => 'gma', 'Glyma.19G056500' => 'gma', 'Gohir.A01G158900' => 'ghi', 'Gohir.A05G312600' => 'ghi', 'Gohir.A05G354900' => 'ghi', 'Gohir.A07G037200' => 'ghi', 'Gohir.A09G030000' => 'ghi', 'Gohir.A12G145200' => 'ghi', 'Gohir.D01G151500' => 'ghi', 'Gohir.D04G058300' => 'ghi', 'Gohir.D05G314100' => 'ghi', 'Gohir.D07G041400' => 'ghi', 'Gohir.D09G029700' => 'ghi', 'Gohir.D12G149700' => 'ghi', 'Gorai.001G043800' => 'gra', 'Gorai.002G187800' => 'gra', 'Gorai.006G034700' => 'gra', 'Gorai.008G161200' => 'gra', 'Gorai.009G335700' => 'gra', 'Gorai.012G065000' => 'gra', 'GSVIVG01000535001' => 'vvi', 'GSVIVG01015572001' => 'vvi', 'GSVIVG01032386001' => 'vvi', 'HanXRQChr05g0138531' => 'han', 'HanXRQChr06g0174391' => 'han', 'HanXRQChr07g0199021' => 'han', 'HanXRQChr08g0208211' => 'han', 'HanXRQChr09g0255471' => 'han', 'HanXRQChr10g0315791' => 'han', 'HanXRQChr12g0371991' => 'han', 'HanXRQChr15g0475251' => 'han', 'HanXRQChr17g0540001' => 'han', 'HanXRQChr17g0548631' => 'han', 'HanXRQChr17g0569561' => 'han', 'Haze_12256' => 'cav', 'Haze_14756' => 'cav', 'Haze_25528' => 'cav', 'Hma1.2p1_0079F.1_g041020' => 'hma', 'Hma1.2p1_0818F.1_g223260' => 'hma', 'Hma1.2p1_1747F.1_g300530' => 'hma', 'HPP92_004607' => 'vpl', 'HPP92_004608' => 'vpl', 'HPP92_006181' => 'vpl', 'HPP92_012192' => 'vpl', 'HPP92_015680' => 'vpl', 'HPP92_020249' => 'vpl', 'HPP92_021376' => 'vpl', 'HPP92_024275' => 'vpl', 'Hund06031' => 'sun', 'Hund25391' => 'sun', 'Lalb_Chr07g0185371' => 'lal', 'Lalb_Chr07g0185381' => 'lal', 'Lalb_Chr12g0204011' => 'lal', 'Lalb_Chr13g0301671' => 'lal', 'Lalb_Chr14g0362851' => 'lal', 'Lalb_Chr24g0403581' => 'lal', 'Lj1g0000233' => 'lja', 'Lj2g0018120' => 'lja', 'Lj3C621T0' => 'lonja', 'Lj3P1059T14' => 'lonja', 'Lj3P611T9' => 'lonja', 'Lj3P614T13' => 'lonja', 'Lj3P615T5' => 'lonja', 'Lj4g0012315' => 'lja', 'Lj4g0026182' => 'lja', 'Lj6P813T16' => 'lonja', 'Lj7C427T7' => 'lonja', 'Lj7C427T8' => 'lonja', 'Lj7P600T41' => 'lonja', 'Lju41C42G17' => 'lonja', 'Lsat_1_v5_gn_0_47300' => 'lsa', 'Lsat_1_v5_gn_2_91280' => 'lsa', 'Lsat_1_v5_gn_3_30561' => 'lsa', 'Lsat_1_v5_gn_4_184321' => 'lsa', 'Lsat_1_v5_gn_4_4041' => 'lsa', 'Lsat_1_v5_gn_5_92000' => 'lsa', 'Lsat_1_v5_gn_8_152940' => 'lsa', 'Lsat_1_v5_gn_8_62401' => 'lsa', 'Manes.06G055900' => 'mes', 'Manes.12G022200' => 'mes', 'Manes.13G023300' => 'mes', 'Manes.14G115000' => 'mes', 'Manes.15G151700' => 'mes', 'Manes.17G111300' => 'mes', 'Mapoly0226s0009' => 'mpo', 'MBI02_g25363_MAGBIO' => 'mbi', 'MBI06_g00027_MAGBIO' => 'mbi', 'MBI10_g13034_MAGBIO' => 'mbi', 'MD09G1023400' => 'mdo', 'MD13G1100100' => 'mdo', 'MD15G1169200' => 'mdo', 'MD16G1101100' => 'mdo', 'MD17G1022900' => 'mdo', 'Medtr3g096150' => 'mtr', 'Medtr4g115070' => 'mtr', 'Medtr7g033325' => 'mtr', 'Medtr8g089840' => 'mtr', 'MELO3C010319.2' => 'cme', 'MELO3C011944.2' => 'cme', 'MELO3C021589.2' => 'cme', 'Migut.E00207' => 'egut', 'Migut.H00067' => 'egut', 'Migut.K00433' => 'egut', 'Migut.K00606' => 'egut', 'Migut.K01410' => 'egut', 'MSTRG.13347' => 'ama', 'MSTRG.24045' => 'ama', 'MSTRG.2428' => 'ama', 'MSTRG.26410' => 'ama', 'MSTRG.3139' => 'ama', 'MSTRG.3286' => 'ama', 'MSTRG.563' => 'ama', 'MSTRG.7941' => 'ama', 'Nitab4.5_0000028g0060' => 'nta', 'Nitab4.5_0000065g0260' => 'nta', 'Nitab4.5_0000112g0060' => 'nta', 'Nitab4.5_0000489g0120' => 'nta', 'Nitab4.5_0001776g0050' => 'nta', 'Nitab4.5_0001854g0010' => 'nta', 'Nitab4.5_0001860g0020' => 'nta', 'Nitab4.5_0004352g0010' => 'nta', 'Nitab4.5_0008716g0020' => 'nta', 'Nitab4.5_0008922g0010' => 'nta', 'Nn3g16693' => 'nnu', 'Nn4g22596' => 'nnu', 'Nn7g37639' => 'nnu', 'Oeu001701.1' => 'oeu', 'Oeu018149.1' => 'oeu', 'Oeu026220.1' => 'oeu', 'Oeu038635.1' => 'oeu', 'Oeu049176.1' => 'oeu', 'Oeu056706.1' => 'oeu', 'Oeu056937.1' => 'oeu', 'Oeu057540.1' => 'oeu', 'Os02g0594900' => 'osa', 'Os02g0595100' => 'osa', 'Os04g0477500' => 'osa', 'Os12g0611900' => 'osa', 'Peaxi162Scf00076g00020' => 'pax', 'Peaxi162Scf00128g00217' => 'pax', 'Peaxi162Scf00129g01640' => 'pax', 'Peaxi162Scf00669g00007' => 'pax', 'Peaxi162Scf00700g00421' => 'pax', 'Peaxi162Scf00801g00038' => 'pax', 'Peaxi162Scf00891g00025' => 'pax', 'PGR083G0909' => 'pgr', 'PGR119G1005' => 'pgr', 'PGR142G2236' => 'pgr', 'PGR142G3388' => 'pgr', 'PGSC0003DMG400004514' => 'stu', 'PGSC0003DMG400012635' => 'stu', 'PGSC0003DMG400015730' => 'stu', 'PGSC0003DMG400018611' => 'stu', 'PGSC0003DMG400030897' => 'stu', 'Phvul.001G254800' => 'pvu', 'Phvul.002G260100' => 'pvu', 'Phvul.003G167600' => 'pvu', 'Phvul.004G005100' => 'pvu', 'Potri.001G343600' => 'ptr', 'Potri.006G066700' => 'ptr', 'Potri.008G186000' => 'ptr', 'Potri.010G046900' => 'ptr', 'Potri.018G127900' => 'ptr', 'Pp3c20_17750' => 'ppa', 'Pp3c24_4380' => 'ppa', 'Prupe.1G245800' => 'ppe', 'Prupe.3G293400' => 'ppe', 'Prupe.7G247400' => 'ppe', 'Psat0s145g0120' => 'psa', 'Psat0s595g0040' => 'psa', 'Psat0s595g0120' => 'psa', 'Psat3g175040' => 'psa', 'Psat7g058120' => 'psa', 'PSO017G0428' => 'pso', 'PSO063G7510' => 'pso', 'PSO067G0046' => 'pso', 'PSO478G1073' => 'pso', 'PSO675G3677' => 'pso', 'PSO675G6558' => 'pso', 'PSO675G7520' => 'pso', 'PSO675G8959' => 'pso', 'QL02p074089' => 'qlo', 'QL02p089614' => 'qlo', 'QL03p057736' => 'qlo', 'RcHm_v2.0_Chr1g0364131' => 'rch', 'RcHm_v2.0_Chr2g0087801' => 'rch', 'RcHm_v2.0_Chr2g0087821' => 'rch', 'RcHm_v2.0_Chr2g0173231' => 'rch', 'RcHm_v2.0_Chr4g0433111' => 'rch', 'Rhsim03G0250300' => 'rsi', 'Rhsim08G0048400' => 'rsi', 'Rhsim10G0014800' => 'rsi', 'Rhsim12G0040100' => 'rsi', 'Rhsim12G0109700' => 'rsi', 'Sabra06G0049600' => 'sbr', 'Sabra08G0141000' => 'sbr', 'Sabra10G0021400' => 'sbr', 'Sabra16G0222900' => 'sbr', 'Sabra18G0108600' => 'sbr', 'SalBow1G0433' => 'sbo', 'SalBow1G2038' => 'sbo', 'SalBow1G5003' => 'sbo', 'SalBow7G1197' => 'sbo', 'SalBow8G3506' => 'sbo', 'Sc03g0007300' => 'sci', 'Sc11g0000950' => 'sci', 'Sc14g0008750' => 'sci', 'Sc18g0000420' => 'sci', 'Sed0006754' => 'sed', 'Sed0008741' => 'sed', 'Sed0017172' => 'sed', 'Sed0018925' => 'sed', 'Sed0023326' => 'sed', 'Sed0025909' => 'sed', 'SEGI_05333' => 'sgi', 'SEGI_10362' => 'sgi', 'SEGI_13380' => 'sgi', 'SEGI_24306' => 'sgi', 'SEGI_29077' => 'sgi', 'SEGI_29095' => 'sgi', 'SEGI_36534' => 'sgi', 'SEGI_37506' => 'sgi', 'SEGI_38321' => 'sgi', 'SGA_v2.0_scaffold307G48031' => 'sas', 'SGA_v2.0_scaffold47G17507' => 'sas', 'SGA_v2.0_scaffold63G21736' => 'sas', 'SGA_v2.0_scaffold87G27070' => 'sas', 'SHI17794' => 'shi', 'SHI28851' => 'shi', 'SMO165G0155' => 'smo', 'SMO340G0217' => 'smo', 'SMO367G1210' => 'smo', 'Solyc02g093430.3' => 'sly', 'Solyc05g013580.4' => 'sly', 'Solyc07g008030.3' => 'sly', 'Solyc12g035470.2' => 'sly', 'Sopen02g038020' => 'spe', 'Sopen05g008490' => 'spe', 'Sopen07g003910' => 'spe', 'Sopen12g015240' => 'spe', 'Sp1g11550' => 'spa', 'Sp2g16710' => 'spa', 'Sp3g00430' => 'spa', 'Sp3g26780' => 'spa', 'Sp5g22900' => 'spa', 'Sp6g29530' => 'spa', 'TAR371G0794' => 'tar', 'TAR374G0164' => 'tar', 'TAR622G0165' => 'tar', 'TAR626G0929' => 'tar', 'TAR629G2155' => 'tar', 'THA.LOC104805282' => 'tha', 'THA.LOC104805363' => 'tha', 'THA.LOC104808968' => 'tha', 'THA.LOC104821093' => 'tha', 'THA.LOC104823953' => 'tha', 'THA.LOC104825562' => 'tha', 'THA.LOC104825665' => 'tha', 'Thecc.02G261400' => 'tca', 'Thecc.04G019200' => 'tca', 'Thecc.09G130400' => 'tca', 'Thhalv10004374m.g' => 'esa', 'Thhalv10007850m.g' => 'esa', 'Thhalv10013782m.g' => 'esa', 'Thhalv10018686m.g' => 'esa', 'Thhalv10020899m.g' => 'esa', 'Thhalv10022755m.g' => 'esa', 'TPR.G23851' => 'tpr', 'TPR.G26500' => 'tpr', 'TPR.G27267' => 'tpr', 'TPR.G32001' => 'tpr', 'TPR.G6251' => 'tpr', 'TPR.G8167' => 'tpr', 'TWI12G1330' => 'twi', 'TWI18G1239' => 'twi', 'TWI34G0979' => 'twi', 'TWI36G0670' => 'twi', 'TWI36G0707' => 'twi', 'TWI56G0233' => 'twi', 'TWI75G1809' => 'twi', 'unitig_21.g20874' => 'ugi', 'unitig_26.g10343' => 'ugi', 'unitig_46.g18392' => 'ugi', 'unitig_52.g17178' => 'ugi', 'unitig_8.g2934' => 'ugi', 'vmacro01122' => 'vma', 'vmacro05875' => 'vma', 'vmacro06147' => 'vma', 'vmacro16191' => 'vma', 'vmacro18293' => 'vma', 'VMungo0251G3707' => 'vmu', 'VMungo0464G1521' => 'vmu', 'VMungo1215G0205' => 'vmu', 'VMungo1383G2484' => 'vmu', 'Zm00001eb079610' => 'zma', 'Zm00001eb135990' => 'zma', 'Zm00001eb183710' => 'zma', 'Zm00001eb246020' => 'zma' ), 'gf_id' => 'HOM05D001124', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001124' ), 'data_identifier' => 'HOM05D001124', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001124', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '548', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02520' => 'bna', 'A03p06630' => 'bna', 'A05p44460' => 'bna', 'A06p08710' => 'bna', 'A06p41090' => 'bna', 'A07p32320' => 'bna', 'A08p32520' => 'bna', 'A09p10360' => 'bna', 'A10p24080' => 'bna', 'Aa31LG11G15250' => 'aar', 'Aa31LG1G1800' => 'aar', 'Aa31LG2G5120' => 'aar', 'Aa31LG2G6070' => 'aar', 'Aa31LG5G10770' => 'aar', 'Aa31sc61G90' => 'aar', 'Actinidia01352' => 'ach', 'Actinidia05983' => 'ach', 'Actinidia08133' => 'ach', 'Actinidia15101' => 'ach', 'Actinidia26379' => 'ach', 'Actinidia35778' => 'ach', 'Actinidia36123' => 'ach', 'Actinidia37436' => 'ach', 'Actinidia38730' => 'ach', 'Ah.02g128210' => 'amhyb', 'Ah.03g132990' => 'amhyb', 'Ah.14g079410' => 'amhyb', 'AL1G24640' => 'aly', 'AL2G26680' => 'aly', 'AL3G10530' => 'aly', 'AL3G45230' => 'aly', 'AL5G15230' => 'aly', 'AL5G16960' => 'aly', 'AL6G25210' => 'aly', 'Aqoxy2G00441' => 'aox', 'Aqoxy3G01236' => 'aox', 'Aqoxy5G03746' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3RQ047' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C7GMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9C8JER' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MBL6KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YXCZ83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZANX40' => 'arhy', 'AT1G12990' => 'ath', 'AT1G67880' => 'ath', 'AT2G13290' => 'ath', 'AT3G01620' => 'ath', 'AT3G26445' => 'ath', 'AT3G27540' => 'ath', 'AT5G14480' => 'ath', 'ATR0824G026' => 'atr', 'ATR1098G019' => 'atr', 'Atru.chr11.2145' => 'acertr', 'Atru.chr2.3636' => 'acertr', 'Atru.chr2.3644' => 'acertr', 'Atru.chr6.2422' => 'acertr', 'Atru.chr7.1112' => 'acertr', 'AUR62005469' => 'cqu', 'AUR62011166' => 'cqu', 'AUR62013319' => 'cqu', 'AUR62024273' => 'cqu', 'AUR62028420' => 'cqu', 'AUR62041942' => 'cqu', 'BcaB01g04969' => 'bca', 'BcaB01g06371' => 'bca', 'BcaB02g11494' => 'bca', 'BcaB03g15382' => 'bca', 'BcaB08g36994' => 'bca', 'BcaC03g13477' => 'bca', 'BcaC03g13478' => 'bca', 'BcaC03g13480' => 'bca', 'BcaC03g13481' => 'bca', 'BcaC03g13486' => 'bca', 'BcaC04g19031' => 'bca', 'BcaC04g23085' => 'bca', 'BcaC05g25094' => 'bca', 'BcaC05g25096' => 'bca', 'BcaC05g25138' => 'bca', 'BcaC05g30416' => 'bca', 'BcaC05g30455' => 'bca', 'BcaC06g30979' => 'bca', 'BcaC06g33805' => 'bca', 'BcaC08g46021' => 'bca', 'BcaNung03154' => 'bca', 'BolC2t06623H' => 'bol', 'BolC2t06632H' => 'bol', 'BolC2t06635H' => 'bol', 'BolC2t06638H' => 'bol', 'BolC3t13266H' => 'bol', 'BolC5t29776H' => 'bol', 'BolC6t38912H' => 'bol', 'BolC7t44183H' => 'bol', 'BolC9t54123H' => 'bol', 'BolC9t59107H' => 'bol', 'BraA02t05221Z' => 'bra', 'BraA03t09996Z' => 'bra', 'BraA05t23210Z' => 'bra', 'BraA06t24068Z' => 'bra', 'BraA06t27032Z' => 'bra', 'BraA08t35176Z' => 'bra', 'BraA09t36680Z' => 'bra', 'BraA10t44471Z' => 'bra', 'C02p06760' => 'bna', 'C02p06890' => 'bna', 'C02p07010' => 'bna', 'C03p07660' => 'bna', 'C05p10300' => 'bna', 'C06p38150' => 'bna', 'C07p36650' => 'bna', 'C08p15770' => 'bna', 'C09p12300' => 'bna', 'C09p62700' => 'bna', 'C09p75040' => 'bna', 'CAN.G13.1' => 'can', 'CAN.G138.4' => 'can', 'CAN.G44.6' => 'can', 'CAN.G473.19' => 'can', 'CANSAT01G0835' => 'cansat', 'CANSAT11G0246' => 'cansat', 'CANSAT11G1766' => 'cansat', 'CANSAT64G1954' => 'cansat', 'CARHR013330' => 'chi', 'CARHR060530' => 'chi', 'CARHR075300' => 'chi', 'CARHR105120' => 'chi', 'CARHR148910' => 'chi', 'CARHR198830' => 'chi', 'Carub.0001s1275' => 'cru', 'Carub.0002s1437' => 'cru', 'Carub.0003s0044' => 'cru', 'Carub.0003s2787' => 'cru', 'Carub.0005s0597' => 'cru', 'Carub.0006s1266' => 'cru', 'Ca_06935_v3' => 'car', 'Ca_13559_v3' => 'car', 'Ca_16941_v3' => 'car', 'Ca_16960_v3' => 'car', 'Ca_17775_v3' => 'car', 'Ca_30464_v3' => 'car', 'Cc06_g08160' => 'ccan', 'Cc07_g01520' => 'ccan', 'Cc11_g15810' => 'ccan', 'CDE02G2840' => 'cde', 'CDE03G0093' => 'cde', 'CDE04G2127' => 'cde', 'CDE07G1857' => 'cde', 'CDE09G1246' => 'cde', 'Cfa003412' => 'cfa', 'Cfa007341' => 'cfa', 'Cfa009220' => 'cfa', 'Ciclev10008737m.g' => 'ccl', 'Ciclev10015565m.g' => 'ccl', 'Ciclev10031761m.g' => 'ccl', 'CiPaw.03G045300' => 'cil', 'CiPaw.03G247200' => 'cil', 'CiPaw.04G029500' => 'cil', 'CiPaw.04G174000' => 'cil', 'CiPaw.05G181200' => 'cil', 'CiPaw.06G067100' => 'cil', 'ClCG05G025800' => 'cla', 'ClCG06G011400' => 'cla', 'ClCG09G019360' => 'cla', 'COL.COLO4_04827' => 'col', 'COL.COLO4_29170' => 'col', 'COL.COLO4_35131' => 'col', 'COL.COLO4_35132' => 'col', 'Cpa.g.sc33.32' => 'cpa', 'Cpa.g.sc46.29' => 'cpa', 'Cpa.g.sc796.1' => 'cpa', 'CsaV3_1G030420' => 'csa', 'CsaV3_5G027050' => 'csa', 'CsaV3_5G031040' => 'csa', 'CsaV3_UNG023130' => 'csa', 'CSS0007726' => 'camsi', 'CSS0016433' => 'camsi', 'CSS0017656' => 'camsi', 'CSS0025364' => 'camsi', 'CSS0027582' => 'camsi', 'CSS0047288' => 'camsi', 'CSS0049950' => 'camsi', 'DCAR_003843' => 'dca', 'DCAR_007052' => 'dca', 'DCAR_020884' => 'dca', 'DCAR_021730' => 'dca', 'DCAR_024423' => 'dca', 'DCAR_026509' => 'dca', 'DCAR_031158' => 'dca', 'Dinv14728' => 'din', 'Dinv15219' => 'din', 'Dinv25728' => 'din', 'Dinv33428' => 'din', 'Dinv36489' => 'din', 'Dinv41486' => 'din', 'Duzib147G0469' => 'dzi', 'Duzib168G0060' => 'dzi', 'Duzib187G1215' => 'dzi', 'Duzib248G0692' => 'dzi', 'Duzib251G0767' => 'dzi', 'Duzib264G0446' => 'dzi', 'Duzib268G0691' => 'dzi', 'ECA232G4767' => 'eca', 'ECA233G2838' => 'eca', 'ECA234G0391' => 'eca', 'ECA234G0857' => 'eca', 'ECA236G1593' => 'eca', 'ECA238G0565' => 'eca', 'ECA246G1027' => 'eca', 'ECA246G3223' => 'eca', 'ECA246G3470' => 'eca', 'EL10Ac6g13829' => 'bvu', 'EL10Ac6g14093' => 'bvu', 'EL10Ac8g18707' => 'bvu', 'Eucgr.C01369' => 'egr', 'Eucgr.H02492' => 'egr', 'Eucgr.I01733' => 'egr', 'Eucgr.J02255' => 'egr', 'Eucgr.J02257' => 'egr', 'Eucgr.J02258' => 'egr', 'FAN02G1601' => 'fan', 'FAN03G1586' => 'fan', 'FAN03G2986' => 'fan', 'FAN05G4837' => 'fan', 'FAN06G0146' => 'fan', 'FAN07G0858' => 'fan', 'FAN09G3179' => 'fan', 'FAN10G0669' => 'fan', 'FAN12G2358' => 'fan', 'FAN14G4198' => 'fan', 'FAN14G5112' => 'fan', 'FAN17G0342' => 'fan', 'FAN19G0342' => 'fan', 'FAN19G0962' => 'fan', 'FAN19G1101' => 'fan', 'FAN19G1872' => 'fan', 'FAN22G0356' => 'fan', 'FAN23G0744' => 'fan', 'FAN23G1914' => 'fan', 'FAN26G0032' => 'fan', 'FAN28G0625' => 'fan', 'FvH4_1g02710' => 'fve', 'FvH4_1g02720' => 'fve', 'FvH4_4g25670' => 'fve', 'FvH4_6g51700' => 'fve', 'FvH4_7g20170' => 'fve', 'Glyma.05G175000' => 'gma', 'Glyma.08G132300' => 'gma', 'Glyma.11G243000' => 'gma', 'Glyma.13G158900' => 'gma', 'Glyma.17G112400' => 'gma', 'Glyma.18G014100' => 'gma', 'Glyma.19G003100' => 'gma', 'Glyma.19G056500' => 'gma', 'Gohir.A01G158900' => 'ghi', 'Gohir.A05G312600' => 'ghi', 'Gohir.A05G354900' => 'ghi', 'Gohir.A07G037200' => 'ghi', 'Gohir.A09G030000' => 'ghi', 'Gohir.A12G145200' => 'ghi', 'Gohir.D01G151500' => 'ghi', 'Gohir.D04G058300' => 'ghi', 'Gohir.D05G314100' => 'ghi', 'Gohir.D07G041400' => 'ghi', 'Gohir.D09G029700' => 'ghi', 'Gohir.D12G149700' => 'ghi', 'Gorai.001G043800' => 'gra', 'Gorai.002G187800' => 'gra', 'Gorai.006G034700' => 'gra', 'Gorai.008G161200' => 'gra', 'Gorai.009G335700' => 'gra', 'Gorai.012G065000' => 'gra', 'GSVIVG01000535001' => 'vvi', 'GSVIVG01015572001' => 'vvi', 'GSVIVG01032386001' => 'vvi', 'HanXRQChr05g0138531' => 'han', 'HanXRQChr06g0174391' => 'han', 'HanXRQChr07g0199021' => 'han', 'HanXRQChr08g0208211' => 'han', 'HanXRQChr09g0255471' => 'han', 'HanXRQChr10g0315791' => 'han', 'HanXRQChr12g0371991' => 'han', 'HanXRQChr15g0475251' => 'han', 'HanXRQChr17g0540001' => 'han', 'HanXRQChr17g0548631' => 'han', 'HanXRQChr17g0569561' => 'han', 'Haze_12256' => 'cav', 'Haze_14756' => 'cav', 'Haze_25528' => 'cav', 'Hma1.2p1_0079F.1_g041020' => 'hma', 'Hma1.2p1_0818F.1_g223260' => 'hma', 'Hma1.2p1_1747F.1_g300530' => 'hma', 'HPP92_004607' => 'vpl', 'HPP92_004608' => 'vpl', 'HPP92_006181' => 'vpl', 'HPP92_012192' => 'vpl', 'HPP92_015680' => 'vpl', 'HPP92_020249' => 'vpl', 'HPP92_021376' => 'vpl', 'HPP92_024275' => 'vpl', 'Hund06031' => 'sun', 'Hund25391' => 'sun', 'Lalb_Chr07g0185371' => 'lal', 'Lalb_Chr07g0185381' => 'lal', 'Lalb_Chr12g0204011' => 'lal', 'Lalb_Chr13g0301671' => 'lal', 'Lalb_Chr14g0362851' => 'lal', 'Lalb_Chr24g0403581' => 'lal', 'Lj1g0000233' => 'lja', 'Lj2g0018120' => 'lja', 'Lj3C621T0' => 'lonja', 'Lj3P1059T14' => 'lonja', 'Lj3P611T9' => 'lonja', 'Lj3P614T13' => 'lonja', 'Lj3P615T5' => 'lonja', 'Lj4g0012315' => 'lja', 'Lj4g0026182' => 'lja', 'Lj6P813T16' => 'lonja', 'Lj7C427T7' => 'lonja', 'Lj7C427T8' => 'lonja', 'Lj7P600T41' => 'lonja', 'Lju41C42G17' => 'lonja', 'Lsat_1_v5_gn_0_47300' => 'lsa', 'Lsat_1_v5_gn_2_91280' => 'lsa', 'Lsat_1_v5_gn_3_30561' => 'lsa', 'Lsat_1_v5_gn_4_184321' => 'lsa', 'Lsat_1_v5_gn_4_4041' => 'lsa', 'Lsat_1_v5_gn_5_92000' => 'lsa', 'Lsat_1_v5_gn_8_152940' => 'lsa', 'Lsat_1_v5_gn_8_62401' => 'lsa', 'Manes.06G055900' => 'mes', 'Manes.12G022200' => 'mes', 'Manes.13G023300' => 'mes', 'Manes.14G115000' => 'mes', 'Manes.15G151700' => 'mes', 'Manes.17G111300' => 'mes', 'Mapoly0226s0009' => 'mpo', 'MBI02_g25363_MAGBIO' => 'mbi', 'MBI06_g00027_MAGBIO' => 'mbi', 'MBI10_g13034_MAGBIO' => 'mbi', 'MD09G1023400' => 'mdo', 'MD13G1100100' => 'mdo', 'MD15G1169200' => 'mdo', 'MD16G1101100' => 'mdo', 'MD17G1022900' => 'mdo', 'Medtr3g096150' => 'mtr', 'Medtr4g115070' => 'mtr', 'Medtr7g033325' => 'mtr', 'Medtr8g089840' => 'mtr', 'MELO3C010319.2' => 'cme', 'MELO3C011944.2' => 'cme', 'MELO3C021589.2' => 'cme', 'Migut.E00207' => 'egut', 'Migut.H00067' => 'egut', 'Migut.K00433' => 'egut', 'Migut.K00606' => 'egut', 'Migut.K01410' => 'egut', 'MSTRG.13347' => 'ama', 'MSTRG.24045' => 'ama', 'MSTRG.2428' => 'ama', 'MSTRG.26410' => 'ama', 'MSTRG.3139' => 'ama', 'MSTRG.3286' => 'ama', 'MSTRG.563' => 'ama', 'MSTRG.7941' => 'ama', 'Nitab4.5_0000028g0060' => 'nta', 'Nitab4.5_0000065g0260' => 'nta', 'Nitab4.5_0000112g0060' => 'nta', 'Nitab4.5_0000489g0120' => 'nta', 'Nitab4.5_0001776g0050' => 'nta', 'Nitab4.5_0001854g0010' => 'nta', 'Nitab4.5_0001860g0020' => 'nta', 'Nitab4.5_0004352g0010' => 'nta', 'Nitab4.5_0008716g0020' => 'nta', 'Nitab4.5_0008922g0010' => 'nta', 'Nn3g16693' => 'nnu', 'Nn4g22596' => 'nnu', 'Nn7g37639' => 'nnu', 'Oeu001701.1' => 'oeu', 'Oeu018149.1' => 'oeu', 'Oeu026220.1' => 'oeu', 'Oeu038635.1' => 'oeu', 'Oeu049176.1' => 'oeu', 'Oeu056706.1' => 'oeu', 'Oeu056937.1' => 'oeu', 'Oeu057540.1' => 'oeu', 'Os02g0594900' => 'osa', 'Os02g0595100' => 'osa', 'Os04g0477500' => 'osa', 'Os12g0611900' => 'osa', 'Peaxi162Scf00076g00020' => 'pax', 'Peaxi162Scf00128g00217' => 'pax', 'Peaxi162Scf00129g01640' => 'pax', 'Peaxi162Scf00669g00007' => 'pax', 'Peaxi162Scf00700g00421' => 'pax', 'Peaxi162Scf00801g00038' => 'pax', 'Peaxi162Scf00891g00025' => 'pax', 'PGR083G0909' => 'pgr', 'PGR119G1005' => 'pgr', 'PGR142G2236' => 'pgr', 'PGR142G3388' => 'pgr', 'PGSC0003DMG400004514' => 'stu', 'PGSC0003DMG400012635' => 'stu', 'PGSC0003DMG400015730' => 'stu', 'PGSC0003DMG400018611' => 'stu', 'PGSC0003DMG400030897' => 'stu', 'Phvul.001G254800' => 'pvu', 'Phvul.002G260100' => 'pvu', 'Phvul.003G167600' => 'pvu', 'Phvul.004G005100' => 'pvu', 'Potri.001G343600' => 'ptr', 'Potri.006G066700' => 'ptr', 'Potri.008G186000' => 'ptr', 'Potri.010G046900' => 'ptr', 'Potri.018G127900' => 'ptr', 'Pp3c20_17750' => 'ppa', 'Pp3c24_4380' => 'ppa', 'Prupe.1G245800' => 'ppe', 'Prupe.3G293400' => 'ppe', 'Prupe.7G247400' => 'ppe', 'Psat0s145g0120' => 'psa', 'Psat0s595g0040' => 'psa', 'Psat0s595g0120' => 'psa', 'Psat3g175040' => 'psa', 'Psat7g058120' => 'psa', 'PSO017G0428' => 'pso', 'PSO063G7510' => 'pso', 'PSO067G0046' => 'pso', 'PSO478G1073' => 'pso', 'PSO675G3677' => 'pso', 'PSO675G6558' => 'pso', 'PSO675G7520' => 'pso', 'PSO675G8959' => 'pso', 'QL02p074089' => 'qlo', 'QL02p089614' => 'qlo', 'QL03p057736' => 'qlo', 'RcHm_v2.0_Chr1g0364131' => 'rch', 'RcHm_v2.0_Chr2g0087801' => 'rch', 'RcHm_v2.0_Chr2g0087821' => 'rch', 'RcHm_v2.0_Chr2g0173231' => 'rch', 'RcHm_v2.0_Chr4g0433111' => 'rch', 'Rhsim03G0250300' => 'rsi', 'Rhsim08G0048400' => 'rsi', 'Rhsim10G0014800' => 'rsi', 'Rhsim12G0040100' => 'rsi', 'Rhsim12G0109700' => 'rsi', 'Sabra06G0049600' => 'sbr', 'Sabra08G0141000' => 'sbr', 'Sabra10G0021400' => 'sbr', 'Sabra16G0222900' => 'sbr', 'Sabra18G0108600' => 'sbr', 'SalBow1G0433' => 'sbo', 'SalBow1G2038' => 'sbo', 'SalBow1G5003' => 'sbo', 'SalBow7G1197' => 'sbo', 'SalBow8G3506' => 'sbo', 'Sc03g0007300' => 'sci', 'Sc11g0000950' => 'sci', 'Sc14g0008750' => 'sci', 'Sc18g0000420' => 'sci', 'Sed0006754' => 'sed', 'Sed0008741' => 'sed', 'Sed0017172' => 'sed', 'Sed0018925' => 'sed', 'Sed0023326' => 'sed', 'Sed0025909' => 'sed', 'SEGI_05333' => 'sgi', 'SEGI_10362' => 'sgi', 'SEGI_13380' => 'sgi', 'SEGI_24306' => 'sgi', 'SEGI_29077' => 'sgi', 'SEGI_29095' => 'sgi', 'SEGI_36534' => 'sgi', 'SEGI_37506' => 'sgi', 'SEGI_38321' => 'sgi', 'SGA_v2.0_scaffold307G48031' => 'sas', 'SGA_v2.0_scaffold47G17507' => 'sas', 'SGA_v2.0_scaffold63G21736' => 'sas', 'SGA_v2.0_scaffold87G27070' => 'sas', 'SHI17794' => 'shi', 'SHI28851' => 'shi', 'SMO165G0155' => 'smo', 'SMO340G0217' => 'smo', 'SMO367G1210' => 'smo', 'Solyc02g093430.3' => 'sly', 'Solyc05g013580.4' => 'sly', 'Solyc07g008030.3' => 'sly', 'Solyc12g035470.2' => 'sly', 'Sopen02g038020' => 'spe', 'Sopen05g008490' => 'spe', 'Sopen07g003910' => 'spe', 'Sopen12g015240' => 'spe', 'Sp1g11550' => 'spa', 'Sp2g16710' => 'spa', 'Sp3g00430' => 'spa', 'Sp3g26780' => 'spa', 'Sp5g22900' => 'spa', 'Sp6g29530' => 'spa', 'TAR371G0794' => 'tar', 'TAR374G0164' => 'tar', 'TAR622G0165' => 'tar', 'TAR626G0929' => 'tar', 'TAR629G2155' => 'tar', 'THA.LOC104805282' => 'tha', 'THA.LOC104805363' => 'tha', 'THA.LOC104808968' => 'tha', 'THA.LOC104821093' => 'tha', 'THA.LOC104823953' => 'tha', 'THA.LOC104825562' => 'tha', 'THA.LOC104825665' => 'tha', 'Thecc.02G261400' => 'tca', 'Thecc.04G019200' => 'tca', 'Thecc.09G130400' => 'tca', 'Thhalv10004374m.g' => 'esa', 'Thhalv10007850m.g' => 'esa', 'Thhalv10013782m.g' => 'esa', 'Thhalv10018686m.g' => 'esa', 'Thhalv10020899m.g' => 'esa', 'Thhalv10022755m.g' => 'esa', 'TPR.G23851' => 'tpr', 'TPR.G26500' => 'tpr', 'TPR.G27267' => 'tpr', 'TPR.G32001' => 'tpr', 'TPR.G6251' => 'tpr', 'TPR.G8167' => 'tpr', 'TWI12G1330' => 'twi', 'TWI18G1239' => 'twi', 'TWI34G0979' => 'twi', 'TWI36G0670' => 'twi', 'TWI36G0707' => 'twi', 'TWI56G0233' => 'twi', 'TWI75G1809' => 'twi', 'unitig_21.g20874' => 'ugi', 'unitig_26.g10343' => 'ugi', 'unitig_46.g18392' => 'ugi', 'unitig_52.g17178' => 'ugi', 'unitig_8.g2934' => 'ugi', 'vmacro01122' => 'vma', 'vmacro05875' => 'vma', 'vmacro06147' => 'vma', 'vmacro16191' => 'vma', 'vmacro18293' => 'vma', 'VMungo0251G3707' => 'vmu', 'VMungo0464G1521' => 'vmu', 'VMungo1215G0205' => 'vmu', 'VMungo1383G2484' => 'vmu', 'Zm00001eb079610' => 'zma', 'Zm00001eb135990' => 'zma', 'Zm00001eb183710' => 'zma', 'Zm00001eb246020' => 'zma' ) $gf_id = 'HOM05D001124' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001124' ) $data_identifier = 'HOM05D001124' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 6, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 7, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 21, 'bol' => (int) 10, 'bra' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 6, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 9, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 21, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 8, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 10, 'lsa' => (int) 8, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 8, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 9, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb246020' $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' => 'HOM05D001124', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '548', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02520' => 'bna', 'A03p06630' => 'bna', 'A05p44460' => 'bna', 'A06p08710' => 'bna', 'A06p41090' => 'bna', 'A07p32320' => 'bna', 'A08p32520' => 'bna', 'A09p10360' => 'bna', 'A10p24080' => 'bna', 'Aa31LG11G15250' => 'aar', 'Aa31LG1G1800' => 'aar', 'Aa31LG2G5120' => 'aar', 'Aa31LG2G6070' => 'aar', 'Aa31LG5G10770' => 'aar', 'Aa31sc61G90' => 'aar', 'Actinidia01352' => 'ach', 'Actinidia05983' => 'ach', 'Actinidia08133' => 'ach', 'Actinidia15101' => 'ach', 'Actinidia26379' => 'ach', 'Actinidia35778' => 'ach', 'Actinidia36123' => 'ach', 'Actinidia37436' => 'ach', 'Actinidia38730' => 'ach', 'Ah.02g128210' => 'amhyb', 'Ah.03g132990' => 'amhyb', 'Ah.14g079410' => 'amhyb', 'AL1G24640' => 'aly', 'AL2G26680' => 'aly', 'AL3G10530' => 'aly', 'AL3G45230' => 'aly', 'AL5G15230' => 'aly', 'AL5G16960' => 'aly', 'AL6G25210' => 'aly', 'Aqoxy2G00441' => 'aox', 'Aqoxy3G01236' => 'aox', 'Aqoxy5G03746' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3RQ047' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C7GMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9C8JER' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MBL6KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YXCZ83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZANX40' => 'arhy', 'AT1G12990' => 'ath', 'AT1G67880' => 'ath', 'AT2G13290' => 'ath', 'AT3G01620' => 'ath', 'AT3G26445' => 'ath', 'AT3G27540' => 'ath', 'AT5G14480' => 'ath', 'ATR0824G026' => 'atr', 'ATR1098G019' => 'atr', 'Atru.chr11.2145' => 'acertr', 'Atru.chr2.3636' => 'acertr', 'Atru.chr2.3644' => 'acertr', 'Atru.chr6.2422' => 'acertr', 'Atru.chr7.1112' => 'acertr', 'AUR62005469' => 'cqu', 'AUR62011166' => 'cqu', 'AUR62013319' => 'cqu', 'AUR62024273' => 'cqu', 'AUR62028420' => 'cqu', 'AUR62041942' => 'cqu', 'BcaB01g04969' => 'bca', 'BcaB01g06371' => 'bca', 'BcaB02g11494' => 'bca', 'BcaB03g15382' => 'bca', 'BcaB08g36994' => 'bca', 'BcaC03g13477' => 'bca', 'BcaC03g13478' => 'bca', 'BcaC03g13480' => 'bca', 'BcaC03g13481' => 'bca', 'BcaC03g13486' => 'bca', 'BcaC04g19031' => 'bca', 'BcaC04g23085' => 'bca', 'BcaC05g25094' => 'bca', 'BcaC05g25096' => 'bca', 'BcaC05g25138' => 'bca', 'BcaC05g30416' => 'bca', 'BcaC05g30455' => 'bca', 'BcaC06g30979' => 'bca', 'BcaC06g33805' => 'bca', 'BcaC08g46021' => 'bca', 'BcaNung03154' => 'bca', 'BolC2t06623H' => 'bol', 'BolC2t06632H' => 'bol', 'BolC2t06635H' => 'bol', 'BolC2t06638H' => 'bol', 'BolC3t13266H' => 'bol', 'BolC5t29776H' => 'bol', 'BolC6t38912H' => 'bol', 'BolC7t44183H' => 'bol', 'BolC9t54123H' => 'bol', 'BolC9t59107H' => 'bol', 'BraA02t05221Z' => 'bra', 'BraA03t09996Z' => 'bra', 'BraA05t23210Z' => 'bra', 'BraA06t24068Z' => 'bra', 'BraA06t27032Z' => 'bra', 'BraA08t35176Z' => 'bra', 'BraA09t36680Z' => 'bra', 'BraA10t44471Z' => 'bra', 'C02p06760' => 'bna', 'C02p06890' => 'bna', 'C02p07010' => 'bna', 'C03p07660' => 'bna', 'C05p10300' => 'bna', 'C06p38150' => 'bna', 'C07p36650' => 'bna', 'C08p15770' => 'bna', 'C09p12300' => 'bna', 'C09p62700' => 'bna', 'C09p75040' => 'bna', 'CAN.G13.1' => 'can', 'CAN.G138.4' => 'can', 'CAN.G44.6' => 'can', 'CAN.G473.19' => 'can', 'CANSAT01G0835' => 'cansat', 'CANSAT11G0246' => 'cansat', 'CANSAT11G1766' => 'cansat', 'CANSAT64G1954' => 'cansat', 'CARHR013330' => 'chi', 'CARHR060530' => 'chi', 'CARHR075300' => 'chi', 'CARHR105120' => 'chi', 'CARHR148910' => 'chi', 'CARHR198830' => 'chi', 'Carub.0001s1275' => 'cru', 'Carub.0002s1437' => 'cru', 'Carub.0003s0044' => 'cru', 'Carub.0003s2787' => 'cru', 'Carub.0005s0597' => 'cru', 'Carub.0006s1266' => 'cru', 'Ca_06935_v3' => 'car', 'Ca_13559_v3' => 'car', 'Ca_16941_v3' => 'car', 'Ca_16960_v3' => 'car', 'Ca_17775_v3' => 'car', 'Ca_30464_v3' => 'car', 'Cc06_g08160' => 'ccan', 'Cc07_g01520' => 'ccan', 'Cc11_g15810' => 'ccan', 'CDE02G2840' => 'cde', 'CDE03G0093' => 'cde', 'CDE04G2127' => 'cde', 'CDE07G1857' => 'cde', 'CDE09G1246' => 'cde', 'Cfa003412' => 'cfa', 'Cfa007341' => 'cfa', 'Cfa009220' => 'cfa', 'Ciclev10008737m.g' => 'ccl', 'Ciclev10015565m.g' => 'ccl', 'Ciclev10031761m.g' => 'ccl', 'CiPaw.03G045300' => 'cil', 'CiPaw.03G247200' => 'cil', 'CiPaw.04G029500' => 'cil', 'CiPaw.04G174000' => 'cil', 'CiPaw.05G181200' => 'cil', 'CiPaw.06G067100' => 'cil', 'ClCG05G025800' => 'cla', 'ClCG06G011400' => 'cla', 'ClCG09G019360' => 'cla', 'COL.COLO4_04827' => 'col', 'COL.COLO4_29170' => 'col', 'COL.COLO4_35131' => 'col', 'COL.COLO4_35132' => 'col', 'Cpa.g.sc33.32' => 'cpa', 'Cpa.g.sc46.29' => 'cpa', 'Cpa.g.sc796.1' => 'cpa', 'CsaV3_1G030420' => 'csa', 'CsaV3_5G027050' => 'csa', 'CsaV3_5G031040' => 'csa', 'CsaV3_UNG023130' => 'csa', 'CSS0007726' => 'camsi', 'CSS0016433' => 'camsi', 'CSS0017656' => 'camsi', 'CSS0025364' => 'camsi', 'CSS0027582' => 'camsi', 'CSS0047288' => 'camsi', 'CSS0049950' => 'camsi', 'DCAR_003843' => 'dca', 'DCAR_007052' => 'dca', 'DCAR_020884' => 'dca', 'DCAR_021730' => 'dca', 'DCAR_024423' => 'dca', 'DCAR_026509' => 'dca', 'DCAR_031158' => 'dca', 'Dinv14728' => 'din', 'Dinv15219' => 'din', 'Dinv25728' => 'din', 'Dinv33428' => 'din', 'Dinv36489' => 'din', 'Dinv41486' => 'din', 'Duzib147G0469' => 'dzi', 'Duzib168G0060' => 'dzi', 'Duzib187G1215' => 'dzi', 'Duzib248G0692' => 'dzi', 'Duzib251G0767' => 'dzi', 'Duzib264G0446' => 'dzi', 'Duzib268G0691' => 'dzi', 'ECA232G4767' => 'eca', 'ECA233G2838' => 'eca', 'ECA234G0391' => 'eca', 'ECA234G0857' => 'eca', 'ECA236G1593' => 'eca', 'ECA238G0565' => 'eca', 'ECA246G1027' => 'eca', 'ECA246G3223' => 'eca', 'ECA246G3470' => 'eca', 'EL10Ac6g13829' => 'bvu', 'EL10Ac6g14093' => 'bvu', 'EL10Ac8g18707' => 'bvu', 'Eucgr.C01369' => 'egr', 'Eucgr.H02492' => 'egr', 'Eucgr.I01733' => 'egr', 'Eucgr.J02255' => 'egr', 'Eucgr.J02257' => 'egr', 'Eucgr.J02258' => 'egr', 'FAN02G1601' => 'fan', 'FAN03G1586' => 'fan', 'FAN03G2986' => 'fan', 'FAN05G4837' => 'fan', 'FAN06G0146' => 'fan', 'FAN07G0858' => 'fan', 'FAN09G3179' => 'fan', 'FAN10G0669' => 'fan', 'FAN12G2358' => 'fan', 'FAN14G4198' => 'fan', 'FAN14G5112' => 'fan', 'FAN17G0342' => 'fan', 'FAN19G0342' => 'fan', 'FAN19G0962' => 'fan', 'FAN19G1101' => 'fan', 'FAN19G1872' => 'fan', 'FAN22G0356' => 'fan', 'FAN23G0744' => 'fan', 'FAN23G1914' => 'fan', 'FAN26G0032' => 'fan', 'FAN28G0625' => 'fan', 'FvH4_1g02710' => 'fve', 'FvH4_1g02720' => 'fve', 'FvH4_4g25670' => 'fve', 'FvH4_6g51700' => 'fve', 'FvH4_7g20170' => 'fve', 'Glyma.05G175000' => 'gma', 'Glyma.08G132300' => 'gma', 'Glyma.11G243000' => 'gma', 'Glyma.13G158900' => 'gma', 'Glyma.17G112400' => 'gma', 'Glyma.18G014100' => 'gma', 'Glyma.19G003100' => 'gma', 'Glyma.19G056500' => 'gma', 'Gohir.A01G158900' => 'ghi', 'Gohir.A05G312600' => 'ghi', 'Gohir.A05G354900' => 'ghi', 'Gohir.A07G037200' => 'ghi', 'Gohir.A09G030000' => 'ghi', 'Gohir.A12G145200' => 'ghi', 'Gohir.D01G151500' => 'ghi', 'Gohir.D04G058300' => 'ghi', 'Gohir.D05G314100' => 'ghi', 'Gohir.D07G041400' => 'ghi', 'Gohir.D09G029700' => 'ghi', 'Gohir.D12G149700' => 'ghi', 'Gorai.001G043800' => 'gra', 'Gorai.002G187800' => 'gra', 'Gorai.006G034700' => 'gra', 'Gorai.008G161200' => 'gra', 'Gorai.009G335700' => 'gra', 'Gorai.012G065000' => 'gra', 'GSVIVG01000535001' => 'vvi', 'GSVIVG01015572001' => 'vvi', 'GSVIVG01032386001' => 'vvi', 'HanXRQChr05g0138531' => 'han', 'HanXRQChr06g0174391' => 'han', 'HanXRQChr07g0199021' => 'han', 'HanXRQChr08g0208211' => 'han', 'HanXRQChr09g0255471' => 'han', 'HanXRQChr10g0315791' => 'han', 'HanXRQChr12g0371991' => 'han', 'HanXRQChr15g0475251' => 'han', 'HanXRQChr17g0540001' => 'han', 'HanXRQChr17g0548631' => 'han', 'HanXRQChr17g0569561' => 'han', 'Haze_12256' => 'cav', 'Haze_14756' => 'cav', 'Haze_25528' => 'cav', 'Hma1.2p1_0079F.1_g041020' => 'hma', 'Hma1.2p1_0818F.1_g223260' => 'hma', 'Hma1.2p1_1747F.1_g300530' => 'hma', 'HPP92_004607' => 'vpl', 'HPP92_004608' => 'vpl', 'HPP92_006181' => 'vpl', 'HPP92_012192' => 'vpl', 'HPP92_015680' => 'vpl', 'HPP92_020249' => 'vpl', 'HPP92_021376' => 'vpl', 'HPP92_024275' => 'vpl', 'Hund06031' => 'sun', 'Hund25391' => 'sun', 'Lalb_Chr07g0185371' => 'lal', 'Lalb_Chr07g0185381' => 'lal', 'Lalb_Chr12g0204011' => 'lal', 'Lalb_Chr13g0301671' => 'lal', 'Lalb_Chr14g0362851' => 'lal', 'Lalb_Chr24g0403581' => 'lal', 'Lj1g0000233' => 'lja', 'Lj2g0018120' => 'lja', 'Lj3C621T0' => 'lonja', 'Lj3P1059T14' => 'lonja', 'Lj3P611T9' => 'lonja', 'Lj3P614T13' => 'lonja', 'Lj3P615T5' => 'lonja', 'Lj4g0012315' => 'lja', 'Lj4g0026182' => 'lja', 'Lj6P813T16' => 'lonja', 'Lj7C427T7' => 'lonja', 'Lj7C427T8' => 'lonja', 'Lj7P600T41' => 'lonja', 'Lju41C42G17' => 'lonja', 'Lsat_1_v5_gn_0_47300' => 'lsa', 'Lsat_1_v5_gn_2_91280' => 'lsa', 'Lsat_1_v5_gn_3_30561' => 'lsa', 'Lsat_1_v5_gn_4_184321' => 'lsa', 'Lsat_1_v5_gn_4_4041' => 'lsa', 'Lsat_1_v5_gn_5_92000' => 'lsa', 'Lsat_1_v5_gn_8_152940' => 'lsa', 'Lsat_1_v5_gn_8_62401' => 'lsa', 'Manes.06G055900' => 'mes', 'Manes.12G022200' => 'mes', 'Manes.13G023300' => 'mes', 'Manes.14G115000' => 'mes', 'Manes.15G151700' => 'mes', 'Manes.17G111300' => 'mes', 'Mapoly0226s0009' => 'mpo', 'MBI02_g25363_MAGBIO' => 'mbi', 'MBI06_g00027_MAGBIO' => 'mbi', 'MBI10_g13034_MAGBIO' => 'mbi', 'MD09G1023400' => 'mdo', 'MD13G1100100' => 'mdo', 'MD15G1169200' => 'mdo', 'MD16G1101100' => 'mdo', 'MD17G1022900' => 'mdo', 'Medtr3g096150' => 'mtr', 'Medtr4g115070' => 'mtr', 'Medtr7g033325' => 'mtr', 'Medtr8g089840' => 'mtr', 'MELO3C010319.2' => 'cme', 'MELO3C011944.2' => 'cme', 'MELO3C021589.2' => 'cme', 'Migut.E00207' => 'egut', 'Migut.H00067' => 'egut', 'Migut.K00433' => 'egut', 'Migut.K00606' => 'egut', 'Migut.K01410' => 'egut', 'MSTRG.13347' => 'ama', 'MSTRG.24045' => 'ama', 'MSTRG.2428' => 'ama', 'MSTRG.26410' => 'ama', 'MSTRG.3139' => 'ama', 'MSTRG.3286' => 'ama', 'MSTRG.563' => 'ama', 'MSTRG.7941' => 'ama', 'Nitab4.5_0000028g0060' => 'nta', 'Nitab4.5_0000065g0260' => 'nta', 'Nitab4.5_0000112g0060' => 'nta', 'Nitab4.5_0000489g0120' => 'nta', 'Nitab4.5_0001776g0050' => 'nta', 'Nitab4.5_0001854g0010' => 'nta', 'Nitab4.5_0001860g0020' => 'nta', 'Nitab4.5_0004352g0010' => 'nta', 'Nitab4.5_0008716g0020' => 'nta', 'Nitab4.5_0008922g0010' => 'nta', 'Nn3g16693' => 'nnu', 'Nn4g22596' => 'nnu', 'Nn7g37639' => 'nnu', 'Oeu001701.1' => 'oeu', 'Oeu018149.1' => 'oeu', 'Oeu026220.1' => 'oeu', 'Oeu038635.1' => 'oeu', 'Oeu049176.1' => 'oeu', 'Oeu056706.1' => 'oeu', 'Oeu056937.1' => 'oeu', 'Oeu057540.1' => 'oeu', 'Os02g0594900' => 'osa', 'Os02g0595100' => 'osa', 'Os04g0477500' => 'osa', 'Os12g0611900' => 'osa', 'Peaxi162Scf00076g00020' => 'pax', 'Peaxi162Scf00128g00217' => 'pax', 'Peaxi162Scf00129g01640' => 'pax', 'Peaxi162Scf00669g00007' => 'pax', 'Peaxi162Scf00700g00421' => 'pax', 'Peaxi162Scf00801g00038' => 'pax', 'Peaxi162Scf00891g00025' => 'pax', 'PGR083G0909' => 'pgr', 'PGR119G1005' => 'pgr', 'PGR142G2236' => 'pgr', 'PGR142G3388' => 'pgr', 'PGSC0003DMG400004514' => 'stu', 'PGSC0003DMG400012635' => 'stu', 'PGSC0003DMG400015730' => 'stu', 'PGSC0003DMG400018611' => 'stu', 'PGSC0003DMG400030897' => 'stu', 'Phvul.001G254800' => 'pvu', 'Phvul.002G260100' => 'pvu', 'Phvul.003G167600' => 'pvu', 'Phvul.004G005100' => 'pvu', 'Potri.001G343600' => 'ptr', 'Potri.006G066700' => 'ptr', 'Potri.008G186000' => 'ptr', 'Potri.010G046900' => 'ptr', 'Potri.018G127900' => 'ptr', 'Pp3c20_17750' => 'ppa', 'Pp3c24_4380' => 'ppa', 'Prupe.1G245800' => 'ppe', 'Prupe.3G293400' => 'ppe', 'Prupe.7G247400' => 'ppe', 'Psat0s145g0120' => 'psa', 'Psat0s595g0040' => 'psa', 'Psat0s595g0120' => 'psa', 'Psat3g175040' => 'psa', 'Psat7g058120' => 'psa', 'PSO017G0428' => 'pso', 'PSO063G7510' => 'pso', 'PSO067G0046' => 'pso', 'PSO478G1073' => 'pso', 'PSO675G3677' => 'pso', 'PSO675G6558' => 'pso', 'PSO675G7520' => 'pso', 'PSO675G8959' => 'pso', 'QL02p074089' => 'qlo', 'QL02p089614' => 'qlo', 'QL03p057736' => 'qlo', 'RcHm_v2.0_Chr1g0364131' => 'rch', 'RcHm_v2.0_Chr2g0087801' => 'rch', 'RcHm_v2.0_Chr2g0087821' => 'rch', 'RcHm_v2.0_Chr2g0173231' => 'rch', 'RcHm_v2.0_Chr4g0433111' => 'rch', 'Rhsim03G0250300' => 'rsi', 'Rhsim08G0048400' => 'rsi', 'Rhsim10G0014800' => 'rsi', 'Rhsim12G0040100' => 'rsi', 'Rhsim12G0109700' => 'rsi', 'Sabra06G0049600' => 'sbr', 'Sabra08G0141000' => 'sbr', 'Sabra10G0021400' => 'sbr', 'Sabra16G0222900' => 'sbr', 'Sabra18G0108600' => 'sbr', 'SalBow1G0433' => 'sbo', 'SalBow1G2038' => 'sbo', 'SalBow1G5003' => 'sbo', 'SalBow7G1197' => 'sbo', 'SalBow8G3506' => 'sbo', 'Sc03g0007300' => 'sci', 'Sc11g0000950' => 'sci', 'Sc14g0008750' => 'sci', 'Sc18g0000420' => 'sci', 'Sed0006754' => 'sed', 'Sed0008741' => 'sed', 'Sed0017172' => 'sed', 'Sed0018925' => 'sed', 'Sed0023326' => 'sed', 'Sed0025909' => 'sed', 'SEGI_05333' => 'sgi', 'SEGI_10362' => 'sgi', 'SEGI_13380' => 'sgi', 'SEGI_24306' => 'sgi', 'SEGI_29077' => 'sgi', 'SEGI_29095' => 'sgi', 'SEGI_36534' => 'sgi', 'SEGI_37506' => 'sgi', 'SEGI_38321' => 'sgi', 'SGA_v2.0_scaffold307G48031' => 'sas', 'SGA_v2.0_scaffold47G17507' => 'sas', 'SGA_v2.0_scaffold63G21736' => 'sas', 'SGA_v2.0_scaffold87G27070' => 'sas', 'SHI17794' => 'shi', 'SHI28851' => 'shi', 'SMO165G0155' => 'smo', 'SMO340G0217' => 'smo', 'SMO367G1210' => 'smo', 'Solyc02g093430.3' => 'sly', 'Solyc05g013580.4' => 'sly', 'Solyc07g008030.3' => 'sly', 'Solyc12g035470.2' => 'sly', 'Sopen02g038020' => 'spe', 'Sopen05g008490' => 'spe', 'Sopen07g003910' => 'spe', 'Sopen12g015240' => 'spe', 'Sp1g11550' => 'spa', 'Sp2g16710' => 'spa', 'Sp3g00430' => 'spa', 'Sp3g26780' => 'spa', 'Sp5g22900' => 'spa', 'Sp6g29530' => 'spa', 'TAR371G0794' => 'tar', 'TAR374G0164' => 'tar', 'TAR622G0165' => 'tar', 'TAR626G0929' => 'tar', 'TAR629G2155' => 'tar', 'THA.LOC104805282' => 'tha', 'THA.LOC104805363' => 'tha', 'THA.LOC104808968' => 'tha', 'THA.LOC104821093' => 'tha', 'THA.LOC104823953' => 'tha', 'THA.LOC104825562' => 'tha', 'THA.LOC104825665' => 'tha', 'Thecc.02G261400' => 'tca', 'Thecc.04G019200' => 'tca', 'Thecc.09G130400' => 'tca', 'Thhalv10004374m.g' => 'esa', 'Thhalv10007850m.g' => 'esa', 'Thhalv10013782m.g' => 'esa', 'Thhalv10018686m.g' => 'esa', 'Thhalv10020899m.g' => 'esa', 'Thhalv10022755m.g' => 'esa', 'TPR.G23851' => 'tpr', 'TPR.G26500' => 'tpr', 'TPR.G27267' => 'tpr', 'TPR.G32001' => 'tpr', 'TPR.G6251' => 'tpr', 'TPR.G8167' => 'tpr', 'TWI12G1330' => 'twi', 'TWI18G1239' => 'twi', 'TWI34G0979' => 'twi', 'TWI36G0670' => 'twi', 'TWI36G0707' => 'twi', 'TWI56G0233' => 'twi', 'TWI75G1809' => 'twi', 'unitig_21.g20874' => 'ugi', 'unitig_26.g10343' => 'ugi', 'unitig_46.g18392' => 'ugi', 'unitig_52.g17178' => 'ugi', 'unitig_8.g2934' => 'ugi', 'vmacro01122' => 'vma', 'vmacro05875' => 'vma', 'vmacro06147' => 'vma', 'vmacro16191' => 'vma', 'vmacro18293' => 'vma', 'VMungo0251G3707' => 'vmu', 'VMungo0464G1521' => 'vmu', 'VMungo1215G0205' => 'vmu', 'VMungo1383G2484' => 'vmu', 'Zm00001eb079610' => 'zma', 'Zm00001eb135990' => 'zma', 'Zm00001eb183710' => 'zma', 'Zm00001eb246020' => 'zma' ), 'gf_id' => 'HOM05D001124', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001124' ), 'data_identifier' => 'HOM05D001124', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001124', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '548', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02520' => 'bna', 'A03p06630' => 'bna', 'A05p44460' => 'bna', 'A06p08710' => 'bna', 'A06p41090' => 'bna', 'A07p32320' => 'bna', 'A08p32520' => 'bna', 'A09p10360' => 'bna', 'A10p24080' => 'bna', 'Aa31LG11G15250' => 'aar', 'Aa31LG1G1800' => 'aar', 'Aa31LG2G5120' => 'aar', 'Aa31LG2G6070' => 'aar', 'Aa31LG5G10770' => 'aar', 'Aa31sc61G90' => 'aar', 'Actinidia01352' => 'ach', 'Actinidia05983' => 'ach', 'Actinidia08133' => 'ach', 'Actinidia15101' => 'ach', 'Actinidia26379' => 'ach', 'Actinidia35778' => 'ach', 'Actinidia36123' => 'ach', 'Actinidia37436' => 'ach', 'Actinidia38730' => 'ach', 'Ah.02g128210' => 'amhyb', 'Ah.03g132990' => 'amhyb', 'Ah.14g079410' => 'amhyb', 'AL1G24640' => 'aly', 'AL2G26680' => 'aly', 'AL3G10530' => 'aly', 'AL3G45230' => 'aly', 'AL5G15230' => 'aly', 'AL5G16960' => 'aly', 'AL6G25210' => 'aly', 'Aqoxy2G00441' => 'aox', 'Aqoxy3G01236' => 'aox', 'Aqoxy5G03746' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3RQ047' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C7GMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9C8JER' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MBL6KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YXCZ83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZANX40' => 'arhy', 'AT1G12990' => 'ath', 'AT1G67880' => 'ath', 'AT2G13290' => 'ath', 'AT3G01620' => 'ath', 'AT3G26445' => 'ath', 'AT3G27540' => 'ath', 'AT5G14480' => 'ath', 'ATR0824G026' => 'atr', 'ATR1098G019' => 'atr', 'Atru.chr11.2145' => 'acertr', 'Atru.chr2.3636' => 'acertr', 'Atru.chr2.3644' => 'acertr', 'Atru.chr6.2422' => 'acertr', 'Atru.chr7.1112' => 'acertr', 'AUR62005469' => 'cqu', 'AUR62011166' => 'cqu', 'AUR62013319' => 'cqu', 'AUR62024273' => 'cqu', 'AUR62028420' => 'cqu', 'AUR62041942' => 'cqu', 'BcaB01g04969' => 'bca', 'BcaB01g06371' => 'bca', 'BcaB02g11494' => 'bca', 'BcaB03g15382' => 'bca', 'BcaB08g36994' => 'bca', 'BcaC03g13477' => 'bca', 'BcaC03g13478' => 'bca', 'BcaC03g13480' => 'bca', 'BcaC03g13481' => 'bca', 'BcaC03g13486' => 'bca', 'BcaC04g19031' => 'bca', 'BcaC04g23085' => 'bca', 'BcaC05g25094' => 'bca', 'BcaC05g25096' => 'bca', 'BcaC05g25138' => 'bca', 'BcaC05g30416' => 'bca', 'BcaC05g30455' => 'bca', 'BcaC06g30979' => 'bca', 'BcaC06g33805' => 'bca', 'BcaC08g46021' => 'bca', 'BcaNung03154' => 'bca', 'BolC2t06623H' => 'bol', 'BolC2t06632H' => 'bol', 'BolC2t06635H' => 'bol', 'BolC2t06638H' => 'bol', 'BolC3t13266H' => 'bol', 'BolC5t29776H' => 'bol', 'BolC6t38912H' => 'bol', 'BolC7t44183H' => 'bol', 'BolC9t54123H' => 'bol', 'BolC9t59107H' => 'bol', 'BraA02t05221Z' => 'bra', 'BraA03t09996Z' => 'bra', 'BraA05t23210Z' => 'bra', 'BraA06t24068Z' => 'bra', 'BraA06t27032Z' => 'bra', 'BraA08t35176Z' => 'bra', 'BraA09t36680Z' => 'bra', 'BraA10t44471Z' => 'bra', 'C02p06760' => 'bna', 'C02p06890' => 'bna', 'C02p07010' => 'bna', 'C03p07660' => 'bna', 'C05p10300' => 'bna', 'C06p38150' => 'bna', 'C07p36650' => 'bna', 'C08p15770' => 'bna', 'C09p12300' => 'bna', 'C09p62700' => 'bna', 'C09p75040' => 'bna', 'CAN.G13.1' => 'can', 'CAN.G138.4' => 'can', 'CAN.G44.6' => 'can', 'CAN.G473.19' => 'can', 'CANSAT01G0835' => 'cansat', 'CANSAT11G0246' => 'cansat', 'CANSAT11G1766' => 'cansat', 'CANSAT64G1954' => 'cansat', 'CARHR013330' => 'chi', 'CARHR060530' => 'chi', 'CARHR075300' => 'chi', 'CARHR105120' => 'chi', 'CARHR148910' => 'chi', 'CARHR198830' => 'chi', 'Carub.0001s1275' => 'cru', 'Carub.0002s1437' => 'cru', 'Carub.0003s0044' => 'cru', 'Carub.0003s2787' => 'cru', 'Carub.0005s0597' => 'cru', 'Carub.0006s1266' => 'cru', 'Ca_06935_v3' => 'car', 'Ca_13559_v3' => 'car', 'Ca_16941_v3' => 'car', 'Ca_16960_v3' => 'car', 'Ca_17775_v3' => 'car', 'Ca_30464_v3' => 'car', 'Cc06_g08160' => 'ccan', 'Cc07_g01520' => 'ccan', 'Cc11_g15810' => 'ccan', 'CDE02G2840' => 'cde', 'CDE03G0093' => 'cde', 'CDE04G2127' => 'cde', 'CDE07G1857' => 'cde', 'CDE09G1246' => 'cde', 'Cfa003412' => 'cfa', 'Cfa007341' => 'cfa', 'Cfa009220' => 'cfa', 'Ciclev10008737m.g' => 'ccl', 'Ciclev10015565m.g' => 'ccl', 'Ciclev10031761m.g' => 'ccl', 'CiPaw.03G045300' => 'cil', 'CiPaw.03G247200' => 'cil', 'CiPaw.04G029500' => 'cil', 'CiPaw.04G174000' => 'cil', 'CiPaw.05G181200' => 'cil', 'CiPaw.06G067100' => 'cil', 'ClCG05G025800' => 'cla', 'ClCG06G011400' => 'cla', 'ClCG09G019360' => 'cla', 'COL.COLO4_04827' => 'col', 'COL.COLO4_29170' => 'col', 'COL.COLO4_35131' => 'col', 'COL.COLO4_35132' => 'col', 'Cpa.g.sc33.32' => 'cpa', 'Cpa.g.sc46.29' => 'cpa', 'Cpa.g.sc796.1' => 'cpa', 'CsaV3_1G030420' => 'csa', 'CsaV3_5G027050' => 'csa', 'CsaV3_5G031040' => 'csa', 'CsaV3_UNG023130' => 'csa', 'CSS0007726' => 'camsi', 'CSS0016433' => 'camsi', 'CSS0017656' => 'camsi', 'CSS0025364' => 'camsi', 'CSS0027582' => 'camsi', 'CSS0047288' => 'camsi', 'CSS0049950' => 'camsi', 'DCAR_003843' => 'dca', 'DCAR_007052' => 'dca', 'DCAR_020884' => 'dca', 'DCAR_021730' => 'dca', 'DCAR_024423' => 'dca', 'DCAR_026509' => 'dca', 'DCAR_031158' => 'dca', 'Dinv14728' => 'din', 'Dinv15219' => 'din', 'Dinv25728' => 'din', 'Dinv33428' => 'din', 'Dinv36489' => 'din', 'Dinv41486' => 'din', 'Duzib147G0469' => 'dzi', 'Duzib168G0060' => 'dzi', 'Duzib187G1215' => 'dzi', 'Duzib248G0692' => 'dzi', 'Duzib251G0767' => 'dzi', 'Duzib264G0446' => 'dzi', 'Duzib268G0691' => 'dzi', 'ECA232G4767' => 'eca', 'ECA233G2838' => 'eca', 'ECA234G0391' => 'eca', 'ECA234G0857' => 'eca', 'ECA236G1593' => 'eca', 'ECA238G0565' => 'eca', 'ECA246G1027' => 'eca', 'ECA246G3223' => 'eca', 'ECA246G3470' => 'eca', 'EL10Ac6g13829' => 'bvu', 'EL10Ac6g14093' => 'bvu', 'EL10Ac8g18707' => 'bvu', 'Eucgr.C01369' => 'egr', 'Eucgr.H02492' => 'egr', 'Eucgr.I01733' => 'egr', 'Eucgr.J02255' => 'egr', 'Eucgr.J02257' => 'egr', 'Eucgr.J02258' => 'egr', 'FAN02G1601' => 'fan', 'FAN03G1586' => 'fan', 'FAN03G2986' => 'fan', 'FAN05G4837' => 'fan', 'FAN06G0146' => 'fan', 'FAN07G0858' => 'fan', 'FAN09G3179' => 'fan', 'FAN10G0669' => 'fan', 'FAN12G2358' => 'fan', 'FAN14G4198' => 'fan', 'FAN14G5112' => 'fan', 'FAN17G0342' => 'fan', 'FAN19G0342' => 'fan', 'FAN19G0962' => 'fan', 'FAN19G1101' => 'fan', 'FAN19G1872' => 'fan', 'FAN22G0356' => 'fan', 'FAN23G0744' => 'fan', 'FAN23G1914' => 'fan', 'FAN26G0032' => 'fan', 'FAN28G0625' => 'fan', 'FvH4_1g02710' => 'fve', 'FvH4_1g02720' => 'fve', 'FvH4_4g25670' => 'fve', 'FvH4_6g51700' => 'fve', 'FvH4_7g20170' => 'fve', 'Glyma.05G175000' => 'gma', 'Glyma.08G132300' => 'gma', 'Glyma.11G243000' => 'gma', 'Glyma.13G158900' => 'gma', 'Glyma.17G112400' => 'gma', 'Glyma.18G014100' => 'gma', 'Glyma.19G003100' => 'gma', 'Glyma.19G056500' => 'gma', 'Gohir.A01G158900' => 'ghi', 'Gohir.A05G312600' => 'ghi', 'Gohir.A05G354900' => 'ghi', 'Gohir.A07G037200' => 'ghi', 'Gohir.A09G030000' => 'ghi', 'Gohir.A12G145200' => 'ghi', 'Gohir.D01G151500' => 'ghi', 'Gohir.D04G058300' => 'ghi', 'Gohir.D05G314100' => 'ghi', 'Gohir.D07G041400' => 'ghi', 'Gohir.D09G029700' => 'ghi', 'Gohir.D12G149700' => 'ghi', 'Gorai.001G043800' => 'gra', 'Gorai.002G187800' => 'gra', 'Gorai.006G034700' => 'gra', 'Gorai.008G161200' => 'gra', 'Gorai.009G335700' => 'gra', 'Gorai.012G065000' => 'gra', 'GSVIVG01000535001' => 'vvi', 'GSVIVG01015572001' => 'vvi', 'GSVIVG01032386001' => 'vvi', 'HanXRQChr05g0138531' => 'han', 'HanXRQChr06g0174391' => 'han', 'HanXRQChr07g0199021' => 'han', 'HanXRQChr08g0208211' => 'han', 'HanXRQChr09g0255471' => 'han', 'HanXRQChr10g0315791' => 'han', 'HanXRQChr12g0371991' => 'han', 'HanXRQChr15g0475251' => 'han', 'HanXRQChr17g0540001' => 'han', 'HanXRQChr17g0548631' => 'han', 'HanXRQChr17g0569561' => 'han', 'Haze_12256' => 'cav', 'Haze_14756' => 'cav', 'Haze_25528' => 'cav', 'Hma1.2p1_0079F.1_g041020' => 'hma', 'Hma1.2p1_0818F.1_g223260' => 'hma', 'Hma1.2p1_1747F.1_g300530' => 'hma', 'HPP92_004607' => 'vpl', 'HPP92_004608' => 'vpl', 'HPP92_006181' => 'vpl', 'HPP92_012192' => 'vpl', 'HPP92_015680' => 'vpl', 'HPP92_020249' => 'vpl', 'HPP92_021376' => 'vpl', 'HPP92_024275' => 'vpl', 'Hund06031' => 'sun', 'Hund25391' => 'sun', 'Lalb_Chr07g0185371' => 'lal', 'Lalb_Chr07g0185381' => 'lal', 'Lalb_Chr12g0204011' => 'lal', 'Lalb_Chr13g0301671' => 'lal', 'Lalb_Chr14g0362851' => 'lal', 'Lalb_Chr24g0403581' => 'lal', 'Lj1g0000233' => 'lja', 'Lj2g0018120' => 'lja', 'Lj3C621T0' => 'lonja', 'Lj3P1059T14' => 'lonja', 'Lj3P611T9' => 'lonja', 'Lj3P614T13' => 'lonja', 'Lj3P615T5' => 'lonja', 'Lj4g0012315' => 'lja', 'Lj4g0026182' => 'lja', 'Lj6P813T16' => 'lonja', 'Lj7C427T7' => 'lonja', 'Lj7C427T8' => 'lonja', 'Lj7P600T41' => 'lonja', 'Lju41C42G17' => 'lonja', 'Lsat_1_v5_gn_0_47300' => 'lsa', 'Lsat_1_v5_gn_2_91280' => 'lsa', 'Lsat_1_v5_gn_3_30561' => 'lsa', 'Lsat_1_v5_gn_4_184321' => 'lsa', 'Lsat_1_v5_gn_4_4041' => 'lsa', 'Lsat_1_v5_gn_5_92000' => 'lsa', 'Lsat_1_v5_gn_8_152940' => 'lsa', 'Lsat_1_v5_gn_8_62401' => 'lsa', 'Manes.06G055900' => 'mes', 'Manes.12G022200' => 'mes', 'Manes.13G023300' => 'mes', 'Manes.14G115000' => 'mes', 'Manes.15G151700' => 'mes', 'Manes.17G111300' => 'mes', 'Mapoly0226s0009' => 'mpo', 'MBI02_g25363_MAGBIO' => 'mbi', 'MBI06_g00027_MAGBIO' => 'mbi', 'MBI10_g13034_MAGBIO' => 'mbi', 'MD09G1023400' => 'mdo', 'MD13G1100100' => 'mdo', 'MD15G1169200' => 'mdo', 'MD16G1101100' => 'mdo', 'MD17G1022900' => 'mdo', 'Medtr3g096150' => 'mtr', 'Medtr4g115070' => 'mtr', 'Medtr7g033325' => 'mtr', 'Medtr8g089840' => 'mtr', 'MELO3C010319.2' => 'cme', 'MELO3C011944.2' => 'cme', 'MELO3C021589.2' => 'cme', 'Migut.E00207' => 'egut', 'Migut.H00067' => 'egut', 'Migut.K00433' => 'egut', 'Migut.K00606' => 'egut', 'Migut.K01410' => 'egut', 'MSTRG.13347' => 'ama', 'MSTRG.24045' => 'ama', 'MSTRG.2428' => 'ama', 'MSTRG.26410' => 'ama', 'MSTRG.3139' => 'ama', 'MSTRG.3286' => 'ama', 'MSTRG.563' => 'ama', 'MSTRG.7941' => 'ama', 'Nitab4.5_0000028g0060' => 'nta', 'Nitab4.5_0000065g0260' => 'nta', 'Nitab4.5_0000112g0060' => 'nta', 'Nitab4.5_0000489g0120' => 'nta', 'Nitab4.5_0001776g0050' => 'nta', 'Nitab4.5_0001854g0010' => 'nta', 'Nitab4.5_0001860g0020' => 'nta', 'Nitab4.5_0004352g0010' => 'nta', 'Nitab4.5_0008716g0020' => 'nta', 'Nitab4.5_0008922g0010' => 'nta', 'Nn3g16693' => 'nnu', 'Nn4g22596' => 'nnu', 'Nn7g37639' => 'nnu', 'Oeu001701.1' => 'oeu', 'Oeu018149.1' => 'oeu', 'Oeu026220.1' => 'oeu', 'Oeu038635.1' => 'oeu', 'Oeu049176.1' => 'oeu', 'Oeu056706.1' => 'oeu', 'Oeu056937.1' => 'oeu', 'Oeu057540.1' => 'oeu', 'Os02g0594900' => 'osa', 'Os02g0595100' => 'osa', 'Os04g0477500' => 'osa', 'Os12g0611900' => 'osa', 'Peaxi162Scf00076g00020' => 'pax', 'Peaxi162Scf00128g00217' => 'pax', 'Peaxi162Scf00129g01640' => 'pax', 'Peaxi162Scf00669g00007' => 'pax', 'Peaxi162Scf00700g00421' => 'pax', 'Peaxi162Scf00801g00038' => 'pax', 'Peaxi162Scf00891g00025' => 'pax', 'PGR083G0909' => 'pgr', 'PGR119G1005' => 'pgr', 'PGR142G2236' => 'pgr', 'PGR142G3388' => 'pgr', 'PGSC0003DMG400004514' => 'stu', 'PGSC0003DMG400012635' => 'stu', 'PGSC0003DMG400015730' => 'stu', 'PGSC0003DMG400018611' => 'stu', 'PGSC0003DMG400030897' => 'stu', 'Phvul.001G254800' => 'pvu', 'Phvul.002G260100' => 'pvu', 'Phvul.003G167600' => 'pvu', 'Phvul.004G005100' => 'pvu', 'Potri.001G343600' => 'ptr', 'Potri.006G066700' => 'ptr', 'Potri.008G186000' => 'ptr', 'Potri.010G046900' => 'ptr', 'Potri.018G127900' => 'ptr', 'Pp3c20_17750' => 'ppa', 'Pp3c24_4380' => 'ppa', 'Prupe.1G245800' => 'ppe', 'Prupe.3G293400' => 'ppe', 'Prupe.7G247400' => 'ppe', 'Psat0s145g0120' => 'psa', 'Psat0s595g0040' => 'psa', 'Psat0s595g0120' => 'psa', 'Psat3g175040' => 'psa', 'Psat7g058120' => 'psa', 'PSO017G0428' => 'pso', 'PSO063G7510' => 'pso', 'PSO067G0046' => 'pso', 'PSO478G1073' => 'pso', 'PSO675G3677' => 'pso', 'PSO675G6558' => 'pso', 'PSO675G7520' => 'pso', 'PSO675G8959' => 'pso', 'QL02p074089' => 'qlo', 'QL02p089614' => 'qlo', 'QL03p057736' => 'qlo', 'RcHm_v2.0_Chr1g0364131' => 'rch', 'RcHm_v2.0_Chr2g0087801' => 'rch', 'RcHm_v2.0_Chr2g0087821' => 'rch', 'RcHm_v2.0_Chr2g0173231' => 'rch', 'RcHm_v2.0_Chr4g0433111' => 'rch', 'Rhsim03G0250300' => 'rsi', 'Rhsim08G0048400' => 'rsi', 'Rhsim10G0014800' => 'rsi', 'Rhsim12G0040100' => 'rsi', 'Rhsim12G0109700' => 'rsi', 'Sabra06G0049600' => 'sbr', 'Sabra08G0141000' => 'sbr', 'Sabra10G0021400' => 'sbr', 'Sabra16G0222900' => 'sbr', 'Sabra18G0108600' => 'sbr', 'SalBow1G0433' => 'sbo', 'SalBow1G2038' => 'sbo', 'SalBow1G5003' => 'sbo', 'SalBow7G1197' => 'sbo', 'SalBow8G3506' => 'sbo', 'Sc03g0007300' => 'sci', 'Sc11g0000950' => 'sci', 'Sc14g0008750' => 'sci', 'Sc18g0000420' => 'sci', 'Sed0006754' => 'sed', 'Sed0008741' => 'sed', 'Sed0017172' => 'sed', 'Sed0018925' => 'sed', 'Sed0023326' => 'sed', 'Sed0025909' => 'sed', 'SEGI_05333' => 'sgi', 'SEGI_10362' => 'sgi', 'SEGI_13380' => 'sgi', 'SEGI_24306' => 'sgi', 'SEGI_29077' => 'sgi', 'SEGI_29095' => 'sgi', 'SEGI_36534' => 'sgi', 'SEGI_37506' => 'sgi', 'SEGI_38321' => 'sgi', 'SGA_v2.0_scaffold307G48031' => 'sas', 'SGA_v2.0_scaffold47G17507' => 'sas', 'SGA_v2.0_scaffold63G21736' => 'sas', 'SGA_v2.0_scaffold87G27070' => 'sas', 'SHI17794' => 'shi', 'SHI28851' => 'shi', 'SMO165G0155' => 'smo', 'SMO340G0217' => 'smo', 'SMO367G1210' => 'smo', 'Solyc02g093430.3' => 'sly', 'Solyc05g013580.4' => 'sly', 'Solyc07g008030.3' => 'sly', 'Solyc12g035470.2' => 'sly', 'Sopen02g038020' => 'spe', 'Sopen05g008490' => 'spe', 'Sopen07g003910' => 'spe', 'Sopen12g015240' => 'spe', 'Sp1g11550' => 'spa', 'Sp2g16710' => 'spa', 'Sp3g00430' => 'spa', 'Sp3g26780' => 'spa', 'Sp5g22900' => 'spa', 'Sp6g29530' => 'spa', 'TAR371G0794' => 'tar', 'TAR374G0164' => 'tar', 'TAR622G0165' => 'tar', 'TAR626G0929' => 'tar', 'TAR629G2155' => 'tar', 'THA.LOC104805282' => 'tha', 'THA.LOC104805363' => 'tha', 'THA.LOC104808968' => 'tha', 'THA.LOC104821093' => 'tha', 'THA.LOC104823953' => 'tha', 'THA.LOC104825562' => 'tha', 'THA.LOC104825665' => 'tha', 'Thecc.02G261400' => 'tca', 'Thecc.04G019200' => 'tca', 'Thecc.09G130400' => 'tca', 'Thhalv10004374m.g' => 'esa', 'Thhalv10007850m.g' => 'esa', 'Thhalv10013782m.g' => 'esa', 'Thhalv10018686m.g' => 'esa', 'Thhalv10020899m.g' => 'esa', 'Thhalv10022755m.g' => 'esa', 'TPR.G23851' => 'tpr', 'TPR.G26500' => 'tpr', 'TPR.G27267' => 'tpr', 'TPR.G32001' => 'tpr', 'TPR.G6251' => 'tpr', 'TPR.G8167' => 'tpr', 'TWI12G1330' => 'twi', 'TWI18G1239' => 'twi', 'TWI34G0979' => 'twi', 'TWI36G0670' => 'twi', 'TWI36G0707' => 'twi', 'TWI56G0233' => 'twi', 'TWI75G1809' => 'twi', 'unitig_21.g20874' => 'ugi', 'unitig_26.g10343' => 'ugi', 'unitig_46.g18392' => 'ugi', 'unitig_52.g17178' => 'ugi', 'unitig_8.g2934' => 'ugi', 'vmacro01122' => 'vma', 'vmacro05875' => 'vma', 'vmacro06147' => 'vma', 'vmacro16191' => 'vma', 'vmacro18293' => 'vma', 'VMungo0251G3707' => 'vmu', 'VMungo0464G1521' => 'vmu', 'VMungo1215G0205' => 'vmu', 'VMungo1383G2484' => 'vmu', 'Zm00001eb079610' => 'zma', 'Zm00001eb135990' => 'zma', 'Zm00001eb183710' => 'zma', 'Zm00001eb246020' => 'zma' ) $gf_id = 'HOM05D001124' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001124' ) $data_identifier = 'HOM05D001124' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 6, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 7, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 21, 'bol' => (int) 10, 'bra' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 6, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 9, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 21, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 8, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 10, 'lsa' => (int) 8, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 8, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 9, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb246020' $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' => 'HOM05D001124', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '548', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02520' => 'bna', 'A03p06630' => 'bna', 'A05p44460' => 'bna', 'A06p08710' => 'bna', 'A06p41090' => 'bna', 'A07p32320' => 'bna', 'A08p32520' => 'bna', 'A09p10360' => 'bna', 'A10p24080' => 'bna', 'Aa31LG11G15250' => 'aar', 'Aa31LG1G1800' => 'aar', 'Aa31LG2G5120' => 'aar', 'Aa31LG2G6070' => 'aar', 'Aa31LG5G10770' => 'aar', 'Aa31sc61G90' => 'aar', 'Actinidia01352' => 'ach', 'Actinidia05983' => 'ach', 'Actinidia08133' => 'ach', 'Actinidia15101' => 'ach', 'Actinidia26379' => 'ach', 'Actinidia35778' => 'ach', 'Actinidia36123' => 'ach', 'Actinidia37436' => 'ach', 'Actinidia38730' => 'ach', 'Ah.02g128210' => 'amhyb', 'Ah.03g132990' => 'amhyb', 'Ah.14g079410' => 'amhyb', 'AL1G24640' => 'aly', 'AL2G26680' => 'aly', 'AL3G10530' => 'aly', 'AL3G45230' => 'aly', 'AL5G15230' => 'aly', 'AL5G16960' => 'aly', 'AL6G25210' => 'aly', 'Aqoxy2G00441' => 'aox', 'Aqoxy3G01236' => 'aox', 'Aqoxy5G03746' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3RQ047' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C7GMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9C8JER' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MBL6KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YXCZ83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZANX40' => 'arhy', 'AT1G12990' => 'ath', 'AT1G67880' => 'ath', 'AT2G13290' => 'ath', 'AT3G01620' => 'ath', 'AT3G26445' => 'ath', 'AT3G27540' => 'ath', 'AT5G14480' => 'ath', 'ATR0824G026' => 'atr', 'ATR1098G019' => 'atr', 'Atru.chr11.2145' => 'acertr', 'Atru.chr2.3636' => 'acertr', 'Atru.chr2.3644' => 'acertr', 'Atru.chr6.2422' => 'acertr', 'Atru.chr7.1112' => 'acertr', 'AUR62005469' => 'cqu', 'AUR62011166' => 'cqu', 'AUR62013319' => 'cqu', 'AUR62024273' => 'cqu', 'AUR62028420' => 'cqu', 'AUR62041942' => 'cqu', 'BcaB01g04969' => 'bca', 'BcaB01g06371' => 'bca', 'BcaB02g11494' => 'bca', 'BcaB03g15382' => 'bca', 'BcaB08g36994' => 'bca', 'BcaC03g13477' => 'bca', 'BcaC03g13478' => 'bca', 'BcaC03g13480' => 'bca', 'BcaC03g13481' => 'bca', 'BcaC03g13486' => 'bca', 'BcaC04g19031' => 'bca', 'BcaC04g23085' => 'bca', 'BcaC05g25094' => 'bca', 'BcaC05g25096' => 'bca', 'BcaC05g25138' => 'bca', 'BcaC05g30416' => 'bca', 'BcaC05g30455' => 'bca', 'BcaC06g30979' => 'bca', 'BcaC06g33805' => 'bca', 'BcaC08g46021' => 'bca', 'BcaNung03154' => 'bca', 'BolC2t06623H' => 'bol', 'BolC2t06632H' => 'bol', 'BolC2t06635H' => 'bol', 'BolC2t06638H' => 'bol', 'BolC3t13266H' => 'bol', 'BolC5t29776H' => 'bol', 'BolC6t38912H' => 'bol', 'BolC7t44183H' => 'bol', 'BolC9t54123H' => 'bol', 'BolC9t59107H' => 'bol', 'BraA02t05221Z' => 'bra', 'BraA03t09996Z' => 'bra', 'BraA05t23210Z' => 'bra', 'BraA06t24068Z' => 'bra', 'BraA06t27032Z' => 'bra', 'BraA08t35176Z' => 'bra', 'BraA09t36680Z' => 'bra', 'BraA10t44471Z' => 'bra', 'C02p06760' => 'bna', 'C02p06890' => 'bna', 'C02p07010' => 'bna', 'C03p07660' => 'bna', 'C05p10300' => 'bna', 'C06p38150' => 'bna', 'C07p36650' => 'bna', 'C08p15770' => 'bna', 'C09p12300' => 'bna', 'C09p62700' => 'bna', 'C09p75040' => 'bna', 'CAN.G13.1' => 'can', 'CAN.G138.4' => 'can', 'CAN.G44.6' => 'can', 'CAN.G473.19' => 'can', 'CANSAT01G0835' => 'cansat', 'CANSAT11G0246' => 'cansat', 'CANSAT11G1766' => 'cansat', 'CANSAT64G1954' => 'cansat', 'CARHR013330' => 'chi', 'CARHR060530' => 'chi', 'CARHR075300' => 'chi', 'CARHR105120' => 'chi', 'CARHR148910' => 'chi', 'CARHR198830' => 'chi', 'Carub.0001s1275' => 'cru', 'Carub.0002s1437' => 'cru', 'Carub.0003s0044' => 'cru', 'Carub.0003s2787' => 'cru', 'Carub.0005s0597' => 'cru', 'Carub.0006s1266' => 'cru', 'Ca_06935_v3' => 'car', 'Ca_13559_v3' => 'car', 'Ca_16941_v3' => 'car', 'Ca_16960_v3' => 'car', 'Ca_17775_v3' => 'car', 'Ca_30464_v3' => 'car', 'Cc06_g08160' => 'ccan', 'Cc07_g01520' => 'ccan', 'Cc11_g15810' => 'ccan', 'CDE02G2840' => 'cde', 'CDE03G0093' => 'cde', 'CDE04G2127' => 'cde', 'CDE07G1857' => 'cde', 'CDE09G1246' => 'cde', 'Cfa003412' => 'cfa', 'Cfa007341' => 'cfa', 'Cfa009220' => 'cfa', 'Ciclev10008737m.g' => 'ccl', 'Ciclev10015565m.g' => 'ccl', 'Ciclev10031761m.g' => 'ccl', 'CiPaw.03G045300' => 'cil', 'CiPaw.03G247200' => 'cil', 'CiPaw.04G029500' => 'cil', 'CiPaw.04G174000' => 'cil', 'CiPaw.05G181200' => 'cil', 'CiPaw.06G067100' => 'cil', 'ClCG05G025800' => 'cla', 'ClCG06G011400' => 'cla', 'ClCG09G019360' => 'cla', 'COL.COLO4_04827' => 'col', 'COL.COLO4_29170' => 'col', 'COL.COLO4_35131' => 'col', 'COL.COLO4_35132' => 'col', 'Cpa.g.sc33.32' => 'cpa', 'Cpa.g.sc46.29' => 'cpa', 'Cpa.g.sc796.1' => 'cpa', 'CsaV3_1G030420' => 'csa', 'CsaV3_5G027050' => 'csa', 'CsaV3_5G031040' => 'csa', 'CsaV3_UNG023130' => 'csa', 'CSS0007726' => 'camsi', 'CSS0016433' => 'camsi', 'CSS0017656' => 'camsi', 'CSS0025364' => 'camsi', 'CSS0027582' => 'camsi', 'CSS0047288' => 'camsi', 'CSS0049950' => 'camsi', 'DCAR_003843' => 'dca', 'DCAR_007052' => 'dca', 'DCAR_020884' => 'dca', 'DCAR_021730' => 'dca', 'DCAR_024423' => 'dca', 'DCAR_026509' => 'dca', 'DCAR_031158' => 'dca', 'Dinv14728' => 'din', 'Dinv15219' => 'din', 'Dinv25728' => 'din', 'Dinv33428' => 'din', 'Dinv36489' => 'din', 'Dinv41486' => 'din', 'Duzib147G0469' => 'dzi', 'Duzib168G0060' => 'dzi', 'Duzib187G1215' => 'dzi', 'Duzib248G0692' => 'dzi', 'Duzib251G0767' => 'dzi', 'Duzib264G0446' => 'dzi', 'Duzib268G0691' => 'dzi', 'ECA232G4767' => 'eca', 'ECA233G2838' => 'eca', 'ECA234G0391' => 'eca', 'ECA234G0857' => 'eca', 'ECA236G1593' => 'eca', 'ECA238G0565' => 'eca', 'ECA246G1027' => 'eca', 'ECA246G3223' => 'eca', 'ECA246G3470' => 'eca', 'EL10Ac6g13829' => 'bvu', 'EL10Ac6g14093' => 'bvu', 'EL10Ac8g18707' => 'bvu', 'Eucgr.C01369' => 'egr', 'Eucgr.H02492' => 'egr', 'Eucgr.I01733' => 'egr', 'Eucgr.J02255' => 'egr', 'Eucgr.J02257' => 'egr', 'Eucgr.J02258' => 'egr', 'FAN02G1601' => 'fan', 'FAN03G1586' => 'fan', 'FAN03G2986' => 'fan', 'FAN05G4837' => 'fan', 'FAN06G0146' => 'fan', 'FAN07G0858' => 'fan', 'FAN09G3179' => 'fan', 'FAN10G0669' => 'fan', 'FAN12G2358' => 'fan', 'FAN14G4198' => 'fan', 'FAN14G5112' => 'fan', 'FAN17G0342' => 'fan', 'FAN19G0342' => 'fan', 'FAN19G0962' => 'fan', 'FAN19G1101' => 'fan', 'FAN19G1872' => 'fan', 'FAN22G0356' => 'fan', 'FAN23G0744' => 'fan', 'FAN23G1914' => 'fan', 'FAN26G0032' => 'fan', 'FAN28G0625' => 'fan', 'FvH4_1g02710' => 'fve', 'FvH4_1g02720' => 'fve', 'FvH4_4g25670' => 'fve', 'FvH4_6g51700' => 'fve', 'FvH4_7g20170' => 'fve', 'Glyma.05G175000' => 'gma', 'Glyma.08G132300' => 'gma', 'Glyma.11G243000' => 'gma', 'Glyma.13G158900' => 'gma', 'Glyma.17G112400' => 'gma', 'Glyma.18G014100' => 'gma', 'Glyma.19G003100' => 'gma', 'Glyma.19G056500' => 'gma', 'Gohir.A01G158900' => 'ghi', 'Gohir.A05G312600' => 'ghi', 'Gohir.A05G354900' => 'ghi', 'Gohir.A07G037200' => 'ghi', 'Gohir.A09G030000' => 'ghi', 'Gohir.A12G145200' => 'ghi', 'Gohir.D01G151500' => 'ghi', 'Gohir.D04G058300' => 'ghi', 'Gohir.D05G314100' => 'ghi', 'Gohir.D07G041400' => 'ghi', 'Gohir.D09G029700' => 'ghi', 'Gohir.D12G149700' => 'ghi', 'Gorai.001G043800' => 'gra', 'Gorai.002G187800' => 'gra', 'Gorai.006G034700' => 'gra', 'Gorai.008G161200' => 'gra', 'Gorai.009G335700' => 'gra', 'Gorai.012G065000' => 'gra', 'GSVIVG01000535001' => 'vvi', 'GSVIVG01015572001' => 'vvi', 'GSVIVG01032386001' => 'vvi', 'HanXRQChr05g0138531' => 'han', 'HanXRQChr06g0174391' => 'han', 'HanXRQChr07g0199021' => 'han', 'HanXRQChr08g0208211' => 'han', 'HanXRQChr09g0255471' => 'han', 'HanXRQChr10g0315791' => 'han', 'HanXRQChr12g0371991' => 'han', 'HanXRQChr15g0475251' => 'han', 'HanXRQChr17g0540001' => 'han', 'HanXRQChr17g0548631' => 'han', 'HanXRQChr17g0569561' => 'han', 'Haze_12256' => 'cav', 'Haze_14756' => 'cav', 'Haze_25528' => 'cav', 'Hma1.2p1_0079F.1_g041020' => 'hma', 'Hma1.2p1_0818F.1_g223260' => 'hma', 'Hma1.2p1_1747F.1_g300530' => 'hma', 'HPP92_004607' => 'vpl', 'HPP92_004608' => 'vpl', 'HPP92_006181' => 'vpl', 'HPP92_012192' => 'vpl', 'HPP92_015680' => 'vpl', 'HPP92_020249' => 'vpl', 'HPP92_021376' => 'vpl', 'HPP92_024275' => 'vpl', 'Hund06031' => 'sun', 'Hund25391' => 'sun', 'Lalb_Chr07g0185371' => 'lal', 'Lalb_Chr07g0185381' => 'lal', 'Lalb_Chr12g0204011' => 'lal', 'Lalb_Chr13g0301671' => 'lal', 'Lalb_Chr14g0362851' => 'lal', 'Lalb_Chr24g0403581' => 'lal', 'Lj1g0000233' => 'lja', 'Lj2g0018120' => 'lja', 'Lj3C621T0' => 'lonja', 'Lj3P1059T14' => 'lonja', 'Lj3P611T9' => 'lonja', 'Lj3P614T13' => 'lonja', 'Lj3P615T5' => 'lonja', 'Lj4g0012315' => 'lja', 'Lj4g0026182' => 'lja', 'Lj6P813T16' => 'lonja', 'Lj7C427T7' => 'lonja', 'Lj7C427T8' => 'lonja', 'Lj7P600T41' => 'lonja', 'Lju41C42G17' => 'lonja', 'Lsat_1_v5_gn_0_47300' => 'lsa', 'Lsat_1_v5_gn_2_91280' => 'lsa', 'Lsat_1_v5_gn_3_30561' => 'lsa', 'Lsat_1_v5_gn_4_184321' => 'lsa', 'Lsat_1_v5_gn_4_4041' => 'lsa', 'Lsat_1_v5_gn_5_92000' => 'lsa', 'Lsat_1_v5_gn_8_152940' => 'lsa', 'Lsat_1_v5_gn_8_62401' => 'lsa', 'Manes.06G055900' => 'mes', 'Manes.12G022200' => 'mes', 'Manes.13G023300' => 'mes', 'Manes.14G115000' => 'mes', 'Manes.15G151700' => 'mes', 'Manes.17G111300' => 'mes', 'Mapoly0226s0009' => 'mpo', 'MBI02_g25363_MAGBIO' => 'mbi', 'MBI06_g00027_MAGBIO' => 'mbi', 'MBI10_g13034_MAGBIO' => 'mbi', 'MD09G1023400' => 'mdo', 'MD13G1100100' => 'mdo', 'MD15G1169200' => 'mdo', 'MD16G1101100' => 'mdo', 'MD17G1022900' => 'mdo', 'Medtr3g096150' => 'mtr', 'Medtr4g115070' => 'mtr', 'Medtr7g033325' => 'mtr', 'Medtr8g089840' => 'mtr', 'MELO3C010319.2' => 'cme', 'MELO3C011944.2' => 'cme', 'MELO3C021589.2' => 'cme', 'Migut.E00207' => 'egut', 'Migut.H00067' => 'egut', 'Migut.K00433' => 'egut', 'Migut.K00606' => 'egut', 'Migut.K01410' => 'egut', 'MSTRG.13347' => 'ama', 'MSTRG.24045' => 'ama', 'MSTRG.2428' => 'ama', 'MSTRG.26410' => 'ama', 'MSTRG.3139' => 'ama', 'MSTRG.3286' => 'ama', 'MSTRG.563' => 'ama', 'MSTRG.7941' => 'ama', 'Nitab4.5_0000028g0060' => 'nta', 'Nitab4.5_0000065g0260' => 'nta', 'Nitab4.5_0000112g0060' => 'nta', 'Nitab4.5_0000489g0120' => 'nta', 'Nitab4.5_0001776g0050' => 'nta', 'Nitab4.5_0001854g0010' => 'nta', 'Nitab4.5_0001860g0020' => 'nta', 'Nitab4.5_0004352g0010' => 'nta', 'Nitab4.5_0008716g0020' => 'nta', 'Nitab4.5_0008922g0010' => 'nta', 'Nn3g16693' => 'nnu', 'Nn4g22596' => 'nnu', 'Nn7g37639' => 'nnu', 'Oeu001701.1' => 'oeu', 'Oeu018149.1' => 'oeu', 'Oeu026220.1' => 'oeu', 'Oeu038635.1' => 'oeu', 'Oeu049176.1' => 'oeu', 'Oeu056706.1' => 'oeu', 'Oeu056937.1' => 'oeu', 'Oeu057540.1' => 'oeu', 'Os02g0594900' => 'osa', 'Os02g0595100' => 'osa', 'Os04g0477500' => 'osa', 'Os12g0611900' => 'osa', 'Peaxi162Scf00076g00020' => 'pax', 'Peaxi162Scf00128g00217' => 'pax', 'Peaxi162Scf00129g01640' => 'pax', 'Peaxi162Scf00669g00007' => 'pax', 'Peaxi162Scf00700g00421' => 'pax', 'Peaxi162Scf00801g00038' => 'pax', 'Peaxi162Scf00891g00025' => 'pax', 'PGR083G0909' => 'pgr', 'PGR119G1005' => 'pgr', 'PGR142G2236' => 'pgr', 'PGR142G3388' => 'pgr', 'PGSC0003DMG400004514' => 'stu', 'PGSC0003DMG400012635' => 'stu', 'PGSC0003DMG400015730' => 'stu', 'PGSC0003DMG400018611' => 'stu', 'PGSC0003DMG400030897' => 'stu', 'Phvul.001G254800' => 'pvu', 'Phvul.002G260100' => 'pvu', 'Phvul.003G167600' => 'pvu', 'Phvul.004G005100' => 'pvu', 'Potri.001G343600' => 'ptr', 'Potri.006G066700' => 'ptr', 'Potri.008G186000' => 'ptr', 'Potri.010G046900' => 'ptr', 'Potri.018G127900' => 'ptr', 'Pp3c20_17750' => 'ppa', 'Pp3c24_4380' => 'ppa', 'Prupe.1G245800' => 'ppe', 'Prupe.3G293400' => 'ppe', 'Prupe.7G247400' => 'ppe', 'Psat0s145g0120' => 'psa', 'Psat0s595g0040' => 'psa', 'Psat0s595g0120' => 'psa', 'Psat3g175040' => 'psa', 'Psat7g058120' => 'psa', 'PSO017G0428' => 'pso', 'PSO063G7510' => 'pso', 'PSO067G0046' => 'pso', 'PSO478G1073' => 'pso', 'PSO675G3677' => 'pso', 'PSO675G6558' => 'pso', 'PSO675G7520' => 'pso', 'PSO675G8959' => 'pso', 'QL02p074089' => 'qlo', 'QL02p089614' => 'qlo', 'QL03p057736' => 'qlo', 'RcHm_v2.0_Chr1g0364131' => 'rch', 'RcHm_v2.0_Chr2g0087801' => 'rch', 'RcHm_v2.0_Chr2g0087821' => 'rch', 'RcHm_v2.0_Chr2g0173231' => 'rch', 'RcHm_v2.0_Chr4g0433111' => 'rch', 'Rhsim03G0250300' => 'rsi', 'Rhsim08G0048400' => 'rsi', 'Rhsim10G0014800' => 'rsi', 'Rhsim12G0040100' => 'rsi', 'Rhsim12G0109700' => 'rsi', 'Sabra06G0049600' => 'sbr', 'Sabra08G0141000' => 'sbr', 'Sabra10G0021400' => 'sbr', 'Sabra16G0222900' => 'sbr', 'Sabra18G0108600' => 'sbr', 'SalBow1G0433' => 'sbo', 'SalBow1G2038' => 'sbo', 'SalBow1G5003' => 'sbo', 'SalBow7G1197' => 'sbo', 'SalBow8G3506' => 'sbo', 'Sc03g0007300' => 'sci', 'Sc11g0000950' => 'sci', 'Sc14g0008750' => 'sci', 'Sc18g0000420' => 'sci', 'Sed0006754' => 'sed', 'Sed0008741' => 'sed', 'Sed0017172' => 'sed', 'Sed0018925' => 'sed', 'Sed0023326' => 'sed', 'Sed0025909' => 'sed', 'SEGI_05333' => 'sgi', 'SEGI_10362' => 'sgi', 'SEGI_13380' => 'sgi', 'SEGI_24306' => 'sgi', 'SEGI_29077' => 'sgi', 'SEGI_29095' => 'sgi', 'SEGI_36534' => 'sgi', 'SEGI_37506' => 'sgi', 'SEGI_38321' => 'sgi', 'SGA_v2.0_scaffold307G48031' => 'sas', 'SGA_v2.0_scaffold47G17507' => 'sas', 'SGA_v2.0_scaffold63G21736' => 'sas', 'SGA_v2.0_scaffold87G27070' => 'sas', 'SHI17794' => 'shi', 'SHI28851' => 'shi', 'SMO165G0155' => 'smo', 'SMO340G0217' => 'smo', 'SMO367G1210' => 'smo', 'Solyc02g093430.3' => 'sly', 'Solyc05g013580.4' => 'sly', 'Solyc07g008030.3' => 'sly', 'Solyc12g035470.2' => 'sly', 'Sopen02g038020' => 'spe', 'Sopen05g008490' => 'spe', 'Sopen07g003910' => 'spe', 'Sopen12g015240' => 'spe', 'Sp1g11550' => 'spa', 'Sp2g16710' => 'spa', 'Sp3g00430' => 'spa', 'Sp3g26780' => 'spa', 'Sp5g22900' => 'spa', 'Sp6g29530' => 'spa', 'TAR371G0794' => 'tar', 'TAR374G0164' => 'tar', 'TAR622G0165' => 'tar', 'TAR626G0929' => 'tar', 'TAR629G2155' => 'tar', 'THA.LOC104805282' => 'tha', 'THA.LOC104805363' => 'tha', 'THA.LOC104808968' => 'tha', 'THA.LOC104821093' => 'tha', 'THA.LOC104823953' => 'tha', 'THA.LOC104825562' => 'tha', 'THA.LOC104825665' => 'tha', 'Thecc.02G261400' => 'tca', 'Thecc.04G019200' => 'tca', 'Thecc.09G130400' => 'tca', 'Thhalv10004374m.g' => 'esa', 'Thhalv10007850m.g' => 'esa', 'Thhalv10013782m.g' => 'esa', 'Thhalv10018686m.g' => 'esa', 'Thhalv10020899m.g' => 'esa', 'Thhalv10022755m.g' => 'esa', 'TPR.G23851' => 'tpr', 'TPR.G26500' => 'tpr', 'TPR.G27267' => 'tpr', 'TPR.G32001' => 'tpr', 'TPR.G6251' => 'tpr', 'TPR.G8167' => 'tpr', 'TWI12G1330' => 'twi', 'TWI18G1239' => 'twi', 'TWI34G0979' => 'twi', 'TWI36G0670' => 'twi', 'TWI36G0707' => 'twi', 'TWI56G0233' => 'twi', 'TWI75G1809' => 'twi', 'unitig_21.g20874' => 'ugi', 'unitig_26.g10343' => 'ugi', 'unitig_46.g18392' => 'ugi', 'unitig_52.g17178' => 'ugi', 'unitig_8.g2934' => 'ugi', 'vmacro01122' => 'vma', 'vmacro05875' => 'vma', 'vmacro06147' => 'vma', 'vmacro16191' => 'vma', 'vmacro18293' => 'vma', 'VMungo0251G3707' => 'vmu', 'VMungo0464G1521' => 'vmu', 'VMungo1215G0205' => 'vmu', 'VMungo1383G2484' => 'vmu', 'Zm00001eb079610' => 'zma', 'Zm00001eb135990' => 'zma', 'Zm00001eb183710' => 'zma', 'Zm00001eb246020' => 'zma' ), 'gf_id' => 'HOM05D001124', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001124' ), 'data_identifier' => 'HOM05D001124', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001124', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '548', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02520' => 'bna', 'A03p06630' => 'bna', 'A05p44460' => 'bna', 'A06p08710' => 'bna', 'A06p41090' => 'bna', 'A07p32320' => 'bna', 'A08p32520' => 'bna', 'A09p10360' => 'bna', 'A10p24080' => 'bna', 'Aa31LG11G15250' => 'aar', 'Aa31LG1G1800' => 'aar', 'Aa31LG2G5120' => 'aar', 'Aa31LG2G6070' => 'aar', 'Aa31LG5G10770' => 'aar', 'Aa31sc61G90' => 'aar', 'Actinidia01352' => 'ach', 'Actinidia05983' => 'ach', 'Actinidia08133' => 'ach', 'Actinidia15101' => 'ach', 'Actinidia26379' => 'ach', 'Actinidia35778' => 'ach', 'Actinidia36123' => 'ach', 'Actinidia37436' => 'ach', 'Actinidia38730' => 'ach', 'Ah.02g128210' => 'amhyb', 'Ah.03g132990' => 'amhyb', 'Ah.14g079410' => 'amhyb', 'AL1G24640' => 'aly', 'AL2G26680' => 'aly', 'AL3G10530' => 'aly', 'AL3G45230' => 'aly', 'AL5G15230' => 'aly', 'AL5G16960' => 'aly', 'AL6G25210' => 'aly', 'Aqoxy2G00441' => 'aox', 'Aqoxy3G01236' => 'aox', 'Aqoxy5G03746' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3RQ047' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C7GMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9C8JER' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MBL6KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YXCZ83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZANX40' => 'arhy', 'AT1G12990' => 'ath', 'AT1G67880' => 'ath', 'AT2G13290' => 'ath', 'AT3G01620' => 'ath', 'AT3G26445' => 'ath', 'AT3G27540' => 'ath', 'AT5G14480' => 'ath', 'ATR0824G026' => 'atr', 'ATR1098G019' => 'atr', 'Atru.chr11.2145' => 'acertr', 'Atru.chr2.3636' => 'acertr', 'Atru.chr2.3644' => 'acertr', 'Atru.chr6.2422' => 'acertr', 'Atru.chr7.1112' => 'acertr', 'AUR62005469' => 'cqu', 'AUR62011166' => 'cqu', 'AUR62013319' => 'cqu', 'AUR62024273' => 'cqu', 'AUR62028420' => 'cqu', 'AUR62041942' => 'cqu', 'BcaB01g04969' => 'bca', 'BcaB01g06371' => 'bca', 'BcaB02g11494' => 'bca', 'BcaB03g15382' => 'bca', 'BcaB08g36994' => 'bca', 'BcaC03g13477' => 'bca', 'BcaC03g13478' => 'bca', 'BcaC03g13480' => 'bca', 'BcaC03g13481' => 'bca', 'BcaC03g13486' => 'bca', 'BcaC04g19031' => 'bca', 'BcaC04g23085' => 'bca', 'BcaC05g25094' => 'bca', 'BcaC05g25096' => 'bca', 'BcaC05g25138' => 'bca', 'BcaC05g30416' => 'bca', 'BcaC05g30455' => 'bca', 'BcaC06g30979' => 'bca', 'BcaC06g33805' => 'bca', 'BcaC08g46021' => 'bca', 'BcaNung03154' => 'bca', 'BolC2t06623H' => 'bol', 'BolC2t06632H' => 'bol', 'BolC2t06635H' => 'bol', 'BolC2t06638H' => 'bol', 'BolC3t13266H' => 'bol', 'BolC5t29776H' => 'bol', 'BolC6t38912H' => 'bol', 'BolC7t44183H' => 'bol', 'BolC9t54123H' => 'bol', 'BolC9t59107H' => 'bol', 'BraA02t05221Z' => 'bra', 'BraA03t09996Z' => 'bra', 'BraA05t23210Z' => 'bra', 'BraA06t24068Z' => 'bra', 'BraA06t27032Z' => 'bra', 'BraA08t35176Z' => 'bra', 'BraA09t36680Z' => 'bra', 'BraA10t44471Z' => 'bra', 'C02p06760' => 'bna', 'C02p06890' => 'bna', 'C02p07010' => 'bna', 'C03p07660' => 'bna', 'C05p10300' => 'bna', 'C06p38150' => 'bna', 'C07p36650' => 'bna', 'C08p15770' => 'bna', 'C09p12300' => 'bna', 'C09p62700' => 'bna', 'C09p75040' => 'bna', 'CAN.G13.1' => 'can', 'CAN.G138.4' => 'can', 'CAN.G44.6' => 'can', 'CAN.G473.19' => 'can', 'CANSAT01G0835' => 'cansat', 'CANSAT11G0246' => 'cansat', 'CANSAT11G1766' => 'cansat', 'CANSAT64G1954' => 'cansat', 'CARHR013330' => 'chi', 'CARHR060530' => 'chi', 'CARHR075300' => 'chi', 'CARHR105120' => 'chi', 'CARHR148910' => 'chi', 'CARHR198830' => 'chi', 'Carub.0001s1275' => 'cru', 'Carub.0002s1437' => 'cru', 'Carub.0003s0044' => 'cru', 'Carub.0003s2787' => 'cru', 'Carub.0005s0597' => 'cru', 'Carub.0006s1266' => 'cru', 'Ca_06935_v3' => 'car', 'Ca_13559_v3' => 'car', 'Ca_16941_v3' => 'car', 'Ca_16960_v3' => 'car', 'Ca_17775_v3' => 'car', 'Ca_30464_v3' => 'car', 'Cc06_g08160' => 'ccan', 'Cc07_g01520' => 'ccan', 'Cc11_g15810' => 'ccan', 'CDE02G2840' => 'cde', 'CDE03G0093' => 'cde', 'CDE04G2127' => 'cde', 'CDE07G1857' => 'cde', 'CDE09G1246' => 'cde', 'Cfa003412' => 'cfa', 'Cfa007341' => 'cfa', 'Cfa009220' => 'cfa', 'Ciclev10008737m.g' => 'ccl', 'Ciclev10015565m.g' => 'ccl', 'Ciclev10031761m.g' => 'ccl', 'CiPaw.03G045300' => 'cil', 'CiPaw.03G247200' => 'cil', 'CiPaw.04G029500' => 'cil', 'CiPaw.04G174000' => 'cil', 'CiPaw.05G181200' => 'cil', 'CiPaw.06G067100' => 'cil', 'ClCG05G025800' => 'cla', 'ClCG06G011400' => 'cla', 'ClCG09G019360' => 'cla', 'COL.COLO4_04827' => 'col', 'COL.COLO4_29170' => 'col', 'COL.COLO4_35131' => 'col', 'COL.COLO4_35132' => 'col', 'Cpa.g.sc33.32' => 'cpa', 'Cpa.g.sc46.29' => 'cpa', 'Cpa.g.sc796.1' => 'cpa', 'CsaV3_1G030420' => 'csa', 'CsaV3_5G027050' => 'csa', 'CsaV3_5G031040' => 'csa', 'CsaV3_UNG023130' => 'csa', 'CSS0007726' => 'camsi', 'CSS0016433' => 'camsi', 'CSS0017656' => 'camsi', 'CSS0025364' => 'camsi', 'CSS0027582' => 'camsi', 'CSS0047288' => 'camsi', 'CSS0049950' => 'camsi', 'DCAR_003843' => 'dca', 'DCAR_007052' => 'dca', 'DCAR_020884' => 'dca', 'DCAR_021730' => 'dca', 'DCAR_024423' => 'dca', 'DCAR_026509' => 'dca', 'DCAR_031158' => 'dca', 'Dinv14728' => 'din', 'Dinv15219' => 'din', 'Dinv25728' => 'din', 'Dinv33428' => 'din', 'Dinv36489' => 'din', 'Dinv41486' => 'din', 'Duzib147G0469' => 'dzi', 'Duzib168G0060' => 'dzi', 'Duzib187G1215' => 'dzi', 'Duzib248G0692' => 'dzi', 'Duzib251G0767' => 'dzi', 'Duzib264G0446' => 'dzi', 'Duzib268G0691' => 'dzi', 'ECA232G4767' => 'eca', 'ECA233G2838' => 'eca', 'ECA234G0391' => 'eca', 'ECA234G0857' => 'eca', 'ECA236G1593' => 'eca', 'ECA238G0565' => 'eca', 'ECA246G1027' => 'eca', 'ECA246G3223' => 'eca', 'ECA246G3470' => 'eca', 'EL10Ac6g13829' => 'bvu', 'EL10Ac6g14093' => 'bvu', 'EL10Ac8g18707' => 'bvu', 'Eucgr.C01369' => 'egr', 'Eucgr.H02492' => 'egr', 'Eucgr.I01733' => 'egr', 'Eucgr.J02255' => 'egr', 'Eucgr.J02257' => 'egr', 'Eucgr.J02258' => 'egr', 'FAN02G1601' => 'fan', 'FAN03G1586' => 'fan', 'FAN03G2986' => 'fan', 'FAN05G4837' => 'fan', 'FAN06G0146' => 'fan', 'FAN07G0858' => 'fan', 'FAN09G3179' => 'fan', 'FAN10G0669' => 'fan', 'FAN12G2358' => 'fan', 'FAN14G4198' => 'fan', 'FAN14G5112' => 'fan', 'FAN17G0342' => 'fan', 'FAN19G0342' => 'fan', 'FAN19G0962' => 'fan', 'FAN19G1101' => 'fan', 'FAN19G1872' => 'fan', 'FAN22G0356' => 'fan', 'FAN23G0744' => 'fan', 'FAN23G1914' => 'fan', 'FAN26G0032' => 'fan', 'FAN28G0625' => 'fan', 'FvH4_1g02710' => 'fve', 'FvH4_1g02720' => 'fve', 'FvH4_4g25670' => 'fve', 'FvH4_6g51700' => 'fve', 'FvH4_7g20170' => 'fve', 'Glyma.05G175000' => 'gma', 'Glyma.08G132300' => 'gma', 'Glyma.11G243000' => 'gma', 'Glyma.13G158900' => 'gma', 'Glyma.17G112400' => 'gma', 'Glyma.18G014100' => 'gma', 'Glyma.19G003100' => 'gma', 'Glyma.19G056500' => 'gma', 'Gohir.A01G158900' => 'ghi', 'Gohir.A05G312600' => 'ghi', 'Gohir.A05G354900' => 'ghi', 'Gohir.A07G037200' => 'ghi', 'Gohir.A09G030000' => 'ghi', 'Gohir.A12G145200' => 'ghi', 'Gohir.D01G151500' => 'ghi', 'Gohir.D04G058300' => 'ghi', 'Gohir.D05G314100' => 'ghi', 'Gohir.D07G041400' => 'ghi', 'Gohir.D09G029700' => 'ghi', 'Gohir.D12G149700' => 'ghi', 'Gorai.001G043800' => 'gra', 'Gorai.002G187800' => 'gra', 'Gorai.006G034700' => 'gra', 'Gorai.008G161200' => 'gra', 'Gorai.009G335700' => 'gra', 'Gorai.012G065000' => 'gra', 'GSVIVG01000535001' => 'vvi', 'GSVIVG01015572001' => 'vvi', 'GSVIVG01032386001' => 'vvi', 'HanXRQChr05g0138531' => 'han', 'HanXRQChr06g0174391' => 'han', 'HanXRQChr07g0199021' => 'han', 'HanXRQChr08g0208211' => 'han', 'HanXRQChr09g0255471' => 'han', 'HanXRQChr10g0315791' => 'han', 'HanXRQChr12g0371991' => 'han', 'HanXRQChr15g0475251' => 'han', 'HanXRQChr17g0540001' => 'han', 'HanXRQChr17g0548631' => 'han', 'HanXRQChr17g0569561' => 'han', 'Haze_12256' => 'cav', 'Haze_14756' => 'cav', 'Haze_25528' => 'cav', 'Hma1.2p1_0079F.1_g041020' => 'hma', 'Hma1.2p1_0818F.1_g223260' => 'hma', 'Hma1.2p1_1747F.1_g300530' => 'hma', 'HPP92_004607' => 'vpl', 'HPP92_004608' => 'vpl', 'HPP92_006181' => 'vpl', 'HPP92_012192' => 'vpl', 'HPP92_015680' => 'vpl', 'HPP92_020249' => 'vpl', 'HPP92_021376' => 'vpl', 'HPP92_024275' => 'vpl', 'Hund06031' => 'sun', 'Hund25391' => 'sun', 'Lalb_Chr07g0185371' => 'lal', 'Lalb_Chr07g0185381' => 'lal', 'Lalb_Chr12g0204011' => 'lal', 'Lalb_Chr13g0301671' => 'lal', 'Lalb_Chr14g0362851' => 'lal', 'Lalb_Chr24g0403581' => 'lal', 'Lj1g0000233' => 'lja', 'Lj2g0018120' => 'lja', 'Lj3C621T0' => 'lonja', 'Lj3P1059T14' => 'lonja', 'Lj3P611T9' => 'lonja', 'Lj3P614T13' => 'lonja', 'Lj3P615T5' => 'lonja', 'Lj4g0012315' => 'lja', 'Lj4g0026182' => 'lja', 'Lj6P813T16' => 'lonja', 'Lj7C427T7' => 'lonja', 'Lj7C427T8' => 'lonja', 'Lj7P600T41' => 'lonja', 'Lju41C42G17' => 'lonja', 'Lsat_1_v5_gn_0_47300' => 'lsa', 'Lsat_1_v5_gn_2_91280' => 'lsa', 'Lsat_1_v5_gn_3_30561' => 'lsa', 'Lsat_1_v5_gn_4_184321' => 'lsa', 'Lsat_1_v5_gn_4_4041' => 'lsa', 'Lsat_1_v5_gn_5_92000' => 'lsa', 'Lsat_1_v5_gn_8_152940' => 'lsa', 'Lsat_1_v5_gn_8_62401' => 'lsa', 'Manes.06G055900' => 'mes', 'Manes.12G022200' => 'mes', 'Manes.13G023300' => 'mes', 'Manes.14G115000' => 'mes', 'Manes.15G151700' => 'mes', 'Manes.17G111300' => 'mes', 'Mapoly0226s0009' => 'mpo', 'MBI02_g25363_MAGBIO' => 'mbi', 'MBI06_g00027_MAGBIO' => 'mbi', 'MBI10_g13034_MAGBIO' => 'mbi', 'MD09G1023400' => 'mdo', 'MD13G1100100' => 'mdo', 'MD15G1169200' => 'mdo', 'MD16G1101100' => 'mdo', 'MD17G1022900' => 'mdo', 'Medtr3g096150' => 'mtr', 'Medtr4g115070' => 'mtr', 'Medtr7g033325' => 'mtr', 'Medtr8g089840' => 'mtr', 'MELO3C010319.2' => 'cme', 'MELO3C011944.2' => 'cme', 'MELO3C021589.2' => 'cme', 'Migut.E00207' => 'egut', 'Migut.H00067' => 'egut', 'Migut.K00433' => 'egut', 'Migut.K00606' => 'egut', 'Migut.K01410' => 'egut', 'MSTRG.13347' => 'ama', 'MSTRG.24045' => 'ama', 'MSTRG.2428' => 'ama', 'MSTRG.26410' => 'ama', 'MSTRG.3139' => 'ama', 'MSTRG.3286' => 'ama', 'MSTRG.563' => 'ama', 'MSTRG.7941' => 'ama', 'Nitab4.5_0000028g0060' => 'nta', 'Nitab4.5_0000065g0260' => 'nta', 'Nitab4.5_0000112g0060' => 'nta', 'Nitab4.5_0000489g0120' => 'nta', 'Nitab4.5_0001776g0050' => 'nta', 'Nitab4.5_0001854g0010' => 'nta', 'Nitab4.5_0001860g0020' => 'nta', 'Nitab4.5_0004352g0010' => 'nta', 'Nitab4.5_0008716g0020' => 'nta', 'Nitab4.5_0008922g0010' => 'nta', 'Nn3g16693' => 'nnu', 'Nn4g22596' => 'nnu', 'Nn7g37639' => 'nnu', 'Oeu001701.1' => 'oeu', 'Oeu018149.1' => 'oeu', 'Oeu026220.1' => 'oeu', 'Oeu038635.1' => 'oeu', 'Oeu049176.1' => 'oeu', 'Oeu056706.1' => 'oeu', 'Oeu056937.1' => 'oeu', 'Oeu057540.1' => 'oeu', 'Os02g0594900' => 'osa', 'Os02g0595100' => 'osa', 'Os04g0477500' => 'osa', 'Os12g0611900' => 'osa', 'Peaxi162Scf00076g00020' => 'pax', 'Peaxi162Scf00128g00217' => 'pax', 'Peaxi162Scf00129g01640' => 'pax', 'Peaxi162Scf00669g00007' => 'pax', 'Peaxi162Scf00700g00421' => 'pax', 'Peaxi162Scf00801g00038' => 'pax', 'Peaxi162Scf00891g00025' => 'pax', 'PGR083G0909' => 'pgr', 'PGR119G1005' => 'pgr', 'PGR142G2236' => 'pgr', 'PGR142G3388' => 'pgr', 'PGSC0003DMG400004514' => 'stu', 'PGSC0003DMG400012635' => 'stu', 'PGSC0003DMG400015730' => 'stu', 'PGSC0003DMG400018611' => 'stu', 'PGSC0003DMG400030897' => 'stu', 'Phvul.001G254800' => 'pvu', 'Phvul.002G260100' => 'pvu', 'Phvul.003G167600' => 'pvu', 'Phvul.004G005100' => 'pvu', 'Potri.001G343600' => 'ptr', 'Potri.006G066700' => 'ptr', 'Potri.008G186000' => 'ptr', 'Potri.010G046900' => 'ptr', 'Potri.018G127900' => 'ptr', 'Pp3c20_17750' => 'ppa', 'Pp3c24_4380' => 'ppa', 'Prupe.1G245800' => 'ppe', 'Prupe.3G293400' => 'ppe', 'Prupe.7G247400' => 'ppe', 'Psat0s145g0120' => 'psa', 'Psat0s595g0040' => 'psa', 'Psat0s595g0120' => 'psa', 'Psat3g175040' => 'psa', 'Psat7g058120' => 'psa', 'PSO017G0428' => 'pso', 'PSO063G7510' => 'pso', 'PSO067G0046' => 'pso', 'PSO478G1073' => 'pso', 'PSO675G3677' => 'pso', 'PSO675G6558' => 'pso', 'PSO675G7520' => 'pso', 'PSO675G8959' => 'pso', 'QL02p074089' => 'qlo', 'QL02p089614' => 'qlo', 'QL03p057736' => 'qlo', 'RcHm_v2.0_Chr1g0364131' => 'rch', 'RcHm_v2.0_Chr2g0087801' => 'rch', 'RcHm_v2.0_Chr2g0087821' => 'rch', 'RcHm_v2.0_Chr2g0173231' => 'rch', 'RcHm_v2.0_Chr4g0433111' => 'rch', 'Rhsim03G0250300' => 'rsi', 'Rhsim08G0048400' => 'rsi', 'Rhsim10G0014800' => 'rsi', 'Rhsim12G0040100' => 'rsi', 'Rhsim12G0109700' => 'rsi', 'Sabra06G0049600' => 'sbr', 'Sabra08G0141000' => 'sbr', 'Sabra10G0021400' => 'sbr', 'Sabra16G0222900' => 'sbr', 'Sabra18G0108600' => 'sbr', 'SalBow1G0433' => 'sbo', 'SalBow1G2038' => 'sbo', 'SalBow1G5003' => 'sbo', 'SalBow7G1197' => 'sbo', 'SalBow8G3506' => 'sbo', 'Sc03g0007300' => 'sci', 'Sc11g0000950' => 'sci', 'Sc14g0008750' => 'sci', 'Sc18g0000420' => 'sci', 'Sed0006754' => 'sed', 'Sed0008741' => 'sed', 'Sed0017172' => 'sed', 'Sed0018925' => 'sed', 'Sed0023326' => 'sed', 'Sed0025909' => 'sed', 'SEGI_05333' => 'sgi', 'SEGI_10362' => 'sgi', 'SEGI_13380' => 'sgi', 'SEGI_24306' => 'sgi', 'SEGI_29077' => 'sgi', 'SEGI_29095' => 'sgi', 'SEGI_36534' => 'sgi', 'SEGI_37506' => 'sgi', 'SEGI_38321' => 'sgi', 'SGA_v2.0_scaffold307G48031' => 'sas', 'SGA_v2.0_scaffold47G17507' => 'sas', 'SGA_v2.0_scaffold63G21736' => 'sas', 'SGA_v2.0_scaffold87G27070' => 'sas', 'SHI17794' => 'shi', 'SHI28851' => 'shi', 'SMO165G0155' => 'smo', 'SMO340G0217' => 'smo', 'SMO367G1210' => 'smo', 'Solyc02g093430.3' => 'sly', 'Solyc05g013580.4' => 'sly', 'Solyc07g008030.3' => 'sly', 'Solyc12g035470.2' => 'sly', 'Sopen02g038020' => 'spe', 'Sopen05g008490' => 'spe', 'Sopen07g003910' => 'spe', 'Sopen12g015240' => 'spe', 'Sp1g11550' => 'spa', 'Sp2g16710' => 'spa', 'Sp3g00430' => 'spa', 'Sp3g26780' => 'spa', 'Sp5g22900' => 'spa', 'Sp6g29530' => 'spa', 'TAR371G0794' => 'tar', 'TAR374G0164' => 'tar', 'TAR622G0165' => 'tar', 'TAR626G0929' => 'tar', 'TAR629G2155' => 'tar', 'THA.LOC104805282' => 'tha', 'THA.LOC104805363' => 'tha', 'THA.LOC104808968' => 'tha', 'THA.LOC104821093' => 'tha', 'THA.LOC104823953' => 'tha', 'THA.LOC104825562' => 'tha', 'THA.LOC104825665' => 'tha', 'Thecc.02G261400' => 'tca', 'Thecc.04G019200' => 'tca', 'Thecc.09G130400' => 'tca', 'Thhalv10004374m.g' => 'esa', 'Thhalv10007850m.g' => 'esa', 'Thhalv10013782m.g' => 'esa', 'Thhalv10018686m.g' => 'esa', 'Thhalv10020899m.g' => 'esa', 'Thhalv10022755m.g' => 'esa', 'TPR.G23851' => 'tpr', 'TPR.G26500' => 'tpr', 'TPR.G27267' => 'tpr', 'TPR.G32001' => 'tpr', 'TPR.G6251' => 'tpr', 'TPR.G8167' => 'tpr', 'TWI12G1330' => 'twi', 'TWI18G1239' => 'twi', 'TWI34G0979' => 'twi', 'TWI36G0670' => 'twi', 'TWI36G0707' => 'twi', 'TWI56G0233' => 'twi', 'TWI75G1809' => 'twi', 'unitig_21.g20874' => 'ugi', 'unitig_26.g10343' => 'ugi', 'unitig_46.g18392' => 'ugi', 'unitig_52.g17178' => 'ugi', 'unitig_8.g2934' => 'ugi', 'vmacro01122' => 'vma', 'vmacro05875' => 'vma', 'vmacro06147' => 'vma', 'vmacro16191' => 'vma', 'vmacro18293' => 'vma', 'VMungo0251G3707' => 'vmu', 'VMungo0464G1521' => 'vmu', 'VMungo1215G0205' => 'vmu', 'VMungo1383G2484' => 'vmu', 'Zm00001eb079610' => 'zma', 'Zm00001eb135990' => 'zma', 'Zm00001eb183710' => 'zma', 'Zm00001eb246020' => 'zma' ) $gf_id = 'HOM05D001124' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001124' ) $data_identifier = 'HOM05D001124' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 6, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 7, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 21, 'bol' => (int) 10, 'bra' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 6, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 9, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 21, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 8, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 10, 'lsa' => (int) 8, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 8, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 9, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb246020' $species_info = array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ) $local_species = 'tar' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001124', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '548', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02520' => 'bna', 'A03p06630' => 'bna', 'A05p44460' => 'bna', 'A06p08710' => 'bna', 'A06p41090' => 'bna', 'A07p32320' => 'bna', 'A08p32520' => 'bna', 'A09p10360' => 'bna', 'A10p24080' => 'bna', 'Aa31LG11G15250' => 'aar', 'Aa31LG1G1800' => 'aar', 'Aa31LG2G5120' => 'aar', 'Aa31LG2G6070' => 'aar', 'Aa31LG5G10770' => 'aar', 'Aa31sc61G90' => 'aar', 'Actinidia01352' => 'ach', 'Actinidia05983' => 'ach', 'Actinidia08133' => 'ach', 'Actinidia15101' => 'ach', 'Actinidia26379' => 'ach', 'Actinidia35778' => 'ach', 'Actinidia36123' => 'ach', 'Actinidia37436' => 'ach', 'Actinidia38730' => 'ach', 'Ah.02g128210' => 'amhyb', 'Ah.03g132990' => 'amhyb', 'Ah.14g079410' => 'amhyb', 'AL1G24640' => 'aly', 'AL2G26680' => 'aly', 'AL3G10530' => 'aly', 'AL3G45230' => 'aly', 'AL5G15230' => 'aly', 'AL5G16960' => 'aly', 'AL6G25210' => 'aly', 'Aqoxy2G00441' => 'aox', 'Aqoxy3G01236' => 'aox', 'Aqoxy5G03746' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3RQ047' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C7GMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9C8JER' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MBL6KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YXCZ83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZANX40' => 'arhy', 'AT1G12990' => 'ath', 'AT1G67880' => 'ath', 'AT2G13290' => 'ath', 'AT3G01620' => 'ath', 'AT3G26445' => 'ath', 'AT3G27540' => 'ath', 'AT5G14480' => 'ath', 'ATR0824G026' => 'atr', 'ATR1098G019' => 'atr', 'Atru.chr11.2145' => 'acertr', 'Atru.chr2.3636' => 'acertr', 'Atru.chr2.3644' => 'acertr', 'Atru.chr6.2422' => 'acertr', 'Atru.chr7.1112' => 'acertr', 'AUR62005469' => 'cqu', 'AUR62011166' => 'cqu', 'AUR62013319' => 'cqu', 'AUR62024273' => 'cqu', 'AUR62028420' => 'cqu', 'AUR62041942' => 'cqu', 'BcaB01g04969' => 'bca', 'BcaB01g06371' => 'bca', 'BcaB02g11494' => 'bca', 'BcaB03g15382' => 'bca', 'BcaB08g36994' => 'bca', 'BcaC03g13477' => 'bca', 'BcaC03g13478' => 'bca', 'BcaC03g13480' => 'bca', 'BcaC03g13481' => 'bca', 'BcaC03g13486' => 'bca', 'BcaC04g19031' => 'bca', 'BcaC04g23085' => 'bca', 'BcaC05g25094' => 'bca', 'BcaC05g25096' => 'bca', 'BcaC05g25138' => 'bca', 'BcaC05g30416' => 'bca', 'BcaC05g30455' => 'bca', 'BcaC06g30979' => 'bca', 'BcaC06g33805' => 'bca', 'BcaC08g46021' => 'bca', 'BcaNung03154' => 'bca', 'BolC2t06623H' => 'bol', 'BolC2t06632H' => 'bol', 'BolC2t06635H' => 'bol', 'BolC2t06638H' => 'bol', 'BolC3t13266H' => 'bol', 'BolC5t29776H' => 'bol', 'BolC6t38912H' => 'bol', 'BolC7t44183H' => 'bol', 'BolC9t54123H' => 'bol', 'BolC9t59107H' => 'bol', 'BraA02t05221Z' => 'bra', 'BraA03t09996Z' => 'bra', 'BraA05t23210Z' => 'bra', 'BraA06t24068Z' => 'bra', 'BraA06t27032Z' => 'bra', 'BraA08t35176Z' => 'bra', 'BraA09t36680Z' => 'bra', 'BraA10t44471Z' => 'bra', 'C02p06760' => 'bna', 'C02p06890' => 'bna', 'C02p07010' => 'bna', 'C03p07660' => 'bna', 'C05p10300' => 'bna', 'C06p38150' => 'bna', 'C07p36650' => 'bna', 'C08p15770' => 'bna', 'C09p12300' => 'bna', 'C09p62700' => 'bna', 'C09p75040' => 'bna', 'CAN.G13.1' => 'can', 'CAN.G138.4' => 'can', 'CAN.G44.6' => 'can', 'CAN.G473.19' => 'can', 'CANSAT01G0835' => 'cansat', 'CANSAT11G0246' => 'cansat', 'CANSAT11G1766' => 'cansat', 'CANSAT64G1954' => 'cansat', 'CARHR013330' => 'chi', 'CARHR060530' => 'chi', 'CARHR075300' => 'chi', 'CARHR105120' => 'chi', 'CARHR148910' => 'chi', 'CARHR198830' => 'chi', 'Carub.0001s1275' => 'cru', 'Carub.0002s1437' => 'cru', 'Carub.0003s0044' => 'cru', 'Carub.0003s2787' => 'cru', 'Carub.0005s0597' => 'cru', 'Carub.0006s1266' => 'cru', 'Ca_06935_v3' => 'car', 'Ca_13559_v3' => 'car', 'Ca_16941_v3' => 'car', 'Ca_16960_v3' => 'car', 'Ca_17775_v3' => 'car', 'Ca_30464_v3' => 'car', 'Cc06_g08160' => 'ccan', 'Cc07_g01520' => 'ccan', 'Cc11_g15810' => 'ccan', 'CDE02G2840' => 'cde', 'CDE03G0093' => 'cde', 'CDE04G2127' => 'cde', 'CDE07G1857' => 'cde', 'CDE09G1246' => 'cde', 'Cfa003412' => 'cfa', 'Cfa007341' => 'cfa', 'Cfa009220' => 'cfa', 'Ciclev10008737m.g' => 'ccl', 'Ciclev10015565m.g' => 'ccl', 'Ciclev10031761m.g' => 'ccl', 'CiPaw.03G045300' => 'cil', 'CiPaw.03G247200' => 'cil', 'CiPaw.04G029500' => 'cil', 'CiPaw.04G174000' => 'cil', 'CiPaw.05G181200' => 'cil', 'CiPaw.06G067100' => 'cil', 'ClCG05G025800' => 'cla', 'ClCG06G011400' => 'cla', 'ClCG09G019360' => 'cla', 'COL.COLO4_04827' => 'col', 'COL.COLO4_29170' => 'col', 'COL.COLO4_35131' => 'col', 'COL.COLO4_35132' => 'col', 'Cpa.g.sc33.32' => 'cpa', 'Cpa.g.sc46.29' => 'cpa', 'Cpa.g.sc796.1' => 'cpa', 'CsaV3_1G030420' => 'csa', 'CsaV3_5G027050' => 'csa', 'CsaV3_5G031040' => 'csa', 'CsaV3_UNG023130' => 'csa', 'CSS0007726' => 'camsi', 'CSS0016433' => 'camsi', 'CSS0017656' => 'camsi', 'CSS0025364' => 'camsi', 'CSS0027582' => 'camsi', 'CSS0047288' => 'camsi', 'CSS0049950' => 'camsi', 'DCAR_003843' => 'dca', 'DCAR_007052' => 'dca', 'DCAR_020884' => 'dca', 'DCAR_021730' => 'dca', 'DCAR_024423' => 'dca', 'DCAR_026509' => 'dca', 'DCAR_031158' => 'dca', 'Dinv14728' => 'din', 'Dinv15219' => 'din', 'Dinv25728' => 'din', 'Dinv33428' => 'din', 'Dinv36489' => 'din', 'Dinv41486' => 'din', 'Duzib147G0469' => 'dzi', 'Duzib168G0060' => 'dzi', 'Duzib187G1215' => 'dzi', 'Duzib248G0692' => 'dzi', 'Duzib251G0767' => 'dzi', 'Duzib264G0446' => 'dzi', 'Duzib268G0691' => 'dzi', 'ECA232G4767' => 'eca', 'ECA233G2838' => 'eca', 'ECA234G0391' => 'eca', 'ECA234G0857' => 'eca', 'ECA236G1593' => 'eca', 'ECA238G0565' => 'eca', 'ECA246G1027' => 'eca', 'ECA246G3223' => 'eca', 'ECA246G3470' => 'eca', 'EL10Ac6g13829' => 'bvu', 'EL10Ac6g14093' => 'bvu', 'EL10Ac8g18707' => 'bvu', 'Eucgr.C01369' => 'egr', 'Eucgr.H02492' => 'egr', 'Eucgr.I01733' => 'egr', 'Eucgr.J02255' => 'egr', 'Eucgr.J02257' => 'egr', 'Eucgr.J02258' => 'egr', 'FAN02G1601' => 'fan', 'FAN03G1586' => 'fan', 'FAN03G2986' => 'fan', 'FAN05G4837' => 'fan', 'FAN06G0146' => 'fan', 'FAN07G0858' => 'fan', 'FAN09G3179' => 'fan', 'FAN10G0669' => 'fan', 'FAN12G2358' => 'fan', 'FAN14G4198' => 'fan', 'FAN14G5112' => 'fan', 'FAN17G0342' => 'fan', 'FAN19G0342' => 'fan', 'FAN19G0962' => 'fan', 'FAN19G1101' => 'fan', 'FAN19G1872' => 'fan', 'FAN22G0356' => 'fan', 'FAN23G0744' => 'fan', 'FAN23G1914' => 'fan', 'FAN26G0032' => 'fan', 'FAN28G0625' => 'fan', 'FvH4_1g02710' => 'fve', 'FvH4_1g02720' => 'fve', 'FvH4_4g25670' => 'fve', 'FvH4_6g51700' => 'fve', 'FvH4_7g20170' => 'fve', 'Glyma.05G175000' => 'gma', 'Glyma.08G132300' => 'gma', 'Glyma.11G243000' => 'gma', 'Glyma.13G158900' => 'gma', 'Glyma.17G112400' => 'gma', 'Glyma.18G014100' => 'gma', 'Glyma.19G003100' => 'gma', 'Glyma.19G056500' => 'gma', 'Gohir.A01G158900' => 'ghi', 'Gohir.A05G312600' => 'ghi', 'Gohir.A05G354900' => 'ghi', 'Gohir.A07G037200' => 'ghi', 'Gohir.A09G030000' => 'ghi', 'Gohir.A12G145200' => 'ghi', 'Gohir.D01G151500' => 'ghi', 'Gohir.D04G058300' => 'ghi', 'Gohir.D05G314100' => 'ghi', 'Gohir.D07G041400' => 'ghi', 'Gohir.D09G029700' => 'ghi', 'Gohir.D12G149700' => 'ghi', 'Gorai.001G043800' => 'gra', 'Gorai.002G187800' => 'gra', 'Gorai.006G034700' => 'gra', 'Gorai.008G161200' => 'gra', 'Gorai.009G335700' => 'gra', 'Gorai.012G065000' => 'gra', 'GSVIVG01000535001' => 'vvi', 'GSVIVG01015572001' => 'vvi', 'GSVIVG01032386001' => 'vvi', 'HanXRQChr05g0138531' => 'han', 'HanXRQChr06g0174391' => 'han', 'HanXRQChr07g0199021' => 'han', 'HanXRQChr08g0208211' => 'han', 'HanXRQChr09g0255471' => 'han', 'HanXRQChr10g0315791' => 'han', 'HanXRQChr12g0371991' => 'han', 'HanXRQChr15g0475251' => 'han', 'HanXRQChr17g0540001' => 'han', 'HanXRQChr17g0548631' => 'han', 'HanXRQChr17g0569561' => 'han', 'Haze_12256' => 'cav', 'Haze_14756' => 'cav', 'Haze_25528' => 'cav', 'Hma1.2p1_0079F.1_g041020' => 'hma', 'Hma1.2p1_0818F.1_g223260' => 'hma', 'Hma1.2p1_1747F.1_g300530' => 'hma', 'HPP92_004607' => 'vpl', 'HPP92_004608' => 'vpl', 'HPP92_006181' => 'vpl', 'HPP92_012192' => 'vpl', 'HPP92_015680' => 'vpl', 'HPP92_020249' => 'vpl', 'HPP92_021376' => 'vpl', 'HPP92_024275' => 'vpl', 'Hund06031' => 'sun', 'Hund25391' => 'sun', 'Lalb_Chr07g0185371' => 'lal', 'Lalb_Chr07g0185381' => 'lal', 'Lalb_Chr12g0204011' => 'lal', 'Lalb_Chr13g0301671' => 'lal', 'Lalb_Chr14g0362851' => 'lal', 'Lalb_Chr24g0403581' => 'lal', 'Lj1g0000233' => 'lja', 'Lj2g0018120' => 'lja', 'Lj3C621T0' => 'lonja', 'Lj3P1059T14' => 'lonja', 'Lj3P611T9' => 'lonja', 'Lj3P614T13' => 'lonja', 'Lj3P615T5' => 'lonja', 'Lj4g0012315' => 'lja', 'Lj4g0026182' => 'lja', 'Lj6P813T16' => 'lonja', 'Lj7C427T7' => 'lonja', 'Lj7C427T8' => 'lonja', 'Lj7P600T41' => 'lonja', 'Lju41C42G17' => 'lonja', 'Lsat_1_v5_gn_0_47300' => 'lsa', 'Lsat_1_v5_gn_2_91280' => 'lsa', 'Lsat_1_v5_gn_3_30561' => 'lsa', 'Lsat_1_v5_gn_4_184321' => 'lsa', 'Lsat_1_v5_gn_4_4041' => 'lsa', 'Lsat_1_v5_gn_5_92000' => 'lsa', 'Lsat_1_v5_gn_8_152940' => 'lsa', 'Lsat_1_v5_gn_8_62401' => 'lsa', 'Manes.06G055900' => 'mes', 'Manes.12G022200' => 'mes', 'Manes.13G023300' => 'mes', 'Manes.14G115000' => 'mes', 'Manes.15G151700' => 'mes', 'Manes.17G111300' => 'mes', 'Mapoly0226s0009' => 'mpo', 'MBI02_g25363_MAGBIO' => 'mbi', 'MBI06_g00027_MAGBIO' => 'mbi', 'MBI10_g13034_MAGBIO' => 'mbi', 'MD09G1023400' => 'mdo', 'MD13G1100100' => 'mdo', 'MD15G1169200' => 'mdo', 'MD16G1101100' => 'mdo', 'MD17G1022900' => 'mdo', 'Medtr3g096150' => 'mtr', 'Medtr4g115070' => 'mtr', 'Medtr7g033325' => 'mtr', 'Medtr8g089840' => 'mtr', 'MELO3C010319.2' => 'cme', 'MELO3C011944.2' => 'cme', 'MELO3C021589.2' => 'cme', 'Migut.E00207' => 'egut', 'Migut.H00067' => 'egut', 'Migut.K00433' => 'egut', 'Migut.K00606' => 'egut', 'Migut.K01410' => 'egut', 'MSTRG.13347' => 'ama', 'MSTRG.24045' => 'ama', 'MSTRG.2428' => 'ama', 'MSTRG.26410' => 'ama', 'MSTRG.3139' => 'ama', 'MSTRG.3286' => 'ama', 'MSTRG.563' => 'ama', 'MSTRG.7941' => 'ama', 'Nitab4.5_0000028g0060' => 'nta', 'Nitab4.5_0000065g0260' => 'nta', 'Nitab4.5_0000112g0060' => 'nta', 'Nitab4.5_0000489g0120' => 'nta', 'Nitab4.5_0001776g0050' => 'nta', 'Nitab4.5_0001854g0010' => 'nta', 'Nitab4.5_0001860g0020' => 'nta', 'Nitab4.5_0004352g0010' => 'nta', 'Nitab4.5_0008716g0020' => 'nta', 'Nitab4.5_0008922g0010' => 'nta', 'Nn3g16693' => 'nnu', 'Nn4g22596' => 'nnu', 'Nn7g37639' => 'nnu', 'Oeu001701.1' => 'oeu', 'Oeu018149.1' => 'oeu', 'Oeu026220.1' => 'oeu', 'Oeu038635.1' => 'oeu', 'Oeu049176.1' => 'oeu', 'Oeu056706.1' => 'oeu', 'Oeu056937.1' => 'oeu', 'Oeu057540.1' => 'oeu', 'Os02g0594900' => 'osa', 'Os02g0595100' => 'osa', 'Os04g0477500' => 'osa', 'Os12g0611900' => 'osa', 'Peaxi162Scf00076g00020' => 'pax', 'Peaxi162Scf00128g00217' => 'pax', 'Peaxi162Scf00129g01640' => 'pax', 'Peaxi162Scf00669g00007' => 'pax', 'Peaxi162Scf00700g00421' => 'pax', 'Peaxi162Scf00801g00038' => 'pax', 'Peaxi162Scf00891g00025' => 'pax', 'PGR083G0909' => 'pgr', 'PGR119G1005' => 'pgr', 'PGR142G2236' => 'pgr', 'PGR142G3388' => 'pgr', 'PGSC0003DMG400004514' => 'stu', 'PGSC0003DMG400012635' => 'stu', 'PGSC0003DMG400015730' => 'stu', 'PGSC0003DMG400018611' => 'stu', 'PGSC0003DMG400030897' => 'stu', 'Phvul.001G254800' => 'pvu', 'Phvul.002G260100' => 'pvu', 'Phvul.003G167600' => 'pvu', 'Phvul.004G005100' => 'pvu', 'Potri.001G343600' => 'ptr', 'Potri.006G066700' => 'ptr', 'Potri.008G186000' => 'ptr', 'Potri.010G046900' => 'ptr', 'Potri.018G127900' => 'ptr', 'Pp3c20_17750' => 'ppa', 'Pp3c24_4380' => 'ppa', 'Prupe.1G245800' => 'ppe', 'Prupe.3G293400' => 'ppe', 'Prupe.7G247400' => 'ppe', 'Psat0s145g0120' => 'psa', 'Psat0s595g0040' => 'psa', 'Psat0s595g0120' => 'psa', 'Psat3g175040' => 'psa', 'Psat7g058120' => 'psa', 'PSO017G0428' => 'pso', 'PSO063G7510' => 'pso', 'PSO067G0046' => 'pso', 'PSO478G1073' => 'pso', 'PSO675G3677' => 'pso', 'PSO675G6558' => 'pso', 'PSO675G7520' => 'pso', 'PSO675G8959' => 'pso', 'QL02p074089' => 'qlo', 'QL02p089614' => 'qlo', 'QL03p057736' => 'qlo', 'RcHm_v2.0_Chr1g0364131' => 'rch', 'RcHm_v2.0_Chr2g0087801' => 'rch', 'RcHm_v2.0_Chr2g0087821' => 'rch', 'RcHm_v2.0_Chr2g0173231' => 'rch', 'RcHm_v2.0_Chr4g0433111' => 'rch', 'Rhsim03G0250300' => 'rsi', 'Rhsim08G0048400' => 'rsi', 'Rhsim10G0014800' => 'rsi', 'Rhsim12G0040100' => 'rsi', 'Rhsim12G0109700' => 'rsi', 'Sabra06G0049600' => 'sbr', 'Sabra08G0141000' => 'sbr', 'Sabra10G0021400' => 'sbr', 'Sabra16G0222900' => 'sbr', 'Sabra18G0108600' => 'sbr', 'SalBow1G0433' => 'sbo', 'SalBow1G2038' => 'sbo', 'SalBow1G5003' => 'sbo', 'SalBow7G1197' => 'sbo', 'SalBow8G3506' => 'sbo', 'Sc03g0007300' => 'sci', 'Sc11g0000950' => 'sci', 'Sc14g0008750' => 'sci', 'Sc18g0000420' => 'sci', 'Sed0006754' => 'sed', 'Sed0008741' => 'sed', 'Sed0017172' => 'sed', 'Sed0018925' => 'sed', 'Sed0023326' => 'sed', 'Sed0025909' => 'sed', 'SEGI_05333' => 'sgi', 'SEGI_10362' => 'sgi', 'SEGI_13380' => 'sgi', 'SEGI_24306' => 'sgi', 'SEGI_29077' => 'sgi', 'SEGI_29095' => 'sgi', 'SEGI_36534' => 'sgi', 'SEGI_37506' => 'sgi', 'SEGI_38321' => 'sgi', 'SGA_v2.0_scaffold307G48031' => 'sas', 'SGA_v2.0_scaffold47G17507' => 'sas', 'SGA_v2.0_scaffold63G21736' => 'sas', 'SGA_v2.0_scaffold87G27070' => 'sas', 'SHI17794' => 'shi', 'SHI28851' => 'shi', 'SMO165G0155' => 'smo', 'SMO340G0217' => 'smo', 'SMO367G1210' => 'smo', 'Solyc02g093430.3' => 'sly', 'Solyc05g013580.4' => 'sly', 'Solyc07g008030.3' => 'sly', 'Solyc12g035470.2' => 'sly', 'Sopen02g038020' => 'spe', 'Sopen05g008490' => 'spe', 'Sopen07g003910' => 'spe', 'Sopen12g015240' => 'spe', 'Sp1g11550' => 'spa', 'Sp2g16710' => 'spa', 'Sp3g00430' => 'spa', 'Sp3g26780' => 'spa', 'Sp5g22900' => 'spa', 'Sp6g29530' => 'spa', 'TAR371G0794' => 'tar', 'TAR374G0164' => 'tar', 'TAR622G0165' => 'tar', 'TAR626G0929' => 'tar', 'TAR629G2155' => 'tar', 'THA.LOC104805282' => 'tha', 'THA.LOC104805363' => 'tha', 'THA.LOC104808968' => 'tha', 'THA.LOC104821093' => 'tha', 'THA.LOC104823953' => 'tha', 'THA.LOC104825562' => 'tha', 'THA.LOC104825665' => 'tha', 'Thecc.02G261400' => 'tca', 'Thecc.04G019200' => 'tca', 'Thecc.09G130400' => 'tca', 'Thhalv10004374m.g' => 'esa', 'Thhalv10007850m.g' => 'esa', 'Thhalv10013782m.g' => 'esa', 'Thhalv10018686m.g' => 'esa', 'Thhalv10020899m.g' => 'esa', 'Thhalv10022755m.g' => 'esa', 'TPR.G23851' => 'tpr', 'TPR.G26500' => 'tpr', 'TPR.G27267' => 'tpr', 'TPR.G32001' => 'tpr', 'TPR.G6251' => 'tpr', 'TPR.G8167' => 'tpr', 'TWI12G1330' => 'twi', 'TWI18G1239' => 'twi', 'TWI34G0979' => 'twi', 'TWI36G0670' => 'twi', 'TWI36G0707' => 'twi', 'TWI56G0233' => 'twi', 'TWI75G1809' => 'twi', 'unitig_21.g20874' => 'ugi', 'unitig_26.g10343' => 'ugi', 'unitig_46.g18392' => 'ugi', 'unitig_52.g17178' => 'ugi', 'unitig_8.g2934' => 'ugi', 'vmacro01122' => 'vma', 'vmacro05875' => 'vma', 'vmacro06147' => 'vma', 'vmacro16191' => 'vma', 'vmacro18293' => 'vma', 'VMungo0251G3707' => 'vmu', 'VMungo0464G1521' => 'vmu', 'VMungo1215G0205' => 'vmu', 'VMungo1383G2484' => 'vmu', 'Zm00001eb079610' => 'zma', 'Zm00001eb135990' => 'zma', 'Zm00001eb183710' => 'zma', 'Zm00001eb246020' => 'zma' ), 'gf_id' => 'HOM05D001124', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001124' ), 'data_identifier' => 'HOM05D001124', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001124', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '548', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02520' => 'bna', 'A03p06630' => 'bna', 'A05p44460' => 'bna', 'A06p08710' => 'bna', 'A06p41090' => 'bna', 'A07p32320' => 'bna', 'A08p32520' => 'bna', 'A09p10360' => 'bna', 'A10p24080' => 'bna', 'Aa31LG11G15250' => 'aar', 'Aa31LG1G1800' => 'aar', 'Aa31LG2G5120' => 'aar', 'Aa31LG2G6070' => 'aar', 'Aa31LG5G10770' => 'aar', 'Aa31sc61G90' => 'aar', 'Actinidia01352' => 'ach', 'Actinidia05983' => 'ach', 'Actinidia08133' => 'ach', 'Actinidia15101' => 'ach', 'Actinidia26379' => 'ach', 'Actinidia35778' => 'ach', 'Actinidia36123' => 'ach', 'Actinidia37436' => 'ach', 'Actinidia38730' => 'ach', 'Ah.02g128210' => 'amhyb', 'Ah.03g132990' => 'amhyb', 'Ah.14g079410' => 'amhyb', 'AL1G24640' => 'aly', 'AL2G26680' => 'aly', 'AL3G10530' => 'aly', 'AL3G45230' => 'aly', 'AL5G15230' => 'aly', 'AL5G16960' => 'aly', 'AL6G25210' => 'aly', 'Aqoxy2G00441' => 'aox', 'Aqoxy3G01236' => 'aox', 'Aqoxy5G03746' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3RQ047' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C7GMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9C8JER' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MBL6KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YXCZ83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZANX40' => 'arhy', 'AT1G12990' => 'ath', 'AT1G67880' => 'ath', 'AT2G13290' => 'ath', 'AT3G01620' => 'ath', 'AT3G26445' => 'ath', 'AT3G27540' => 'ath', 'AT5G14480' => 'ath', 'ATR0824G026' => 'atr', 'ATR1098G019' => 'atr', 'Atru.chr11.2145' => 'acertr', 'Atru.chr2.3636' => 'acertr', 'Atru.chr2.3644' => 'acertr', 'Atru.chr6.2422' => 'acertr', 'Atru.chr7.1112' => 'acertr', 'AUR62005469' => 'cqu', 'AUR62011166' => 'cqu', 'AUR62013319' => 'cqu', 'AUR62024273' => 'cqu', 'AUR62028420' => 'cqu', 'AUR62041942' => 'cqu', 'BcaB01g04969' => 'bca', 'BcaB01g06371' => 'bca', 'BcaB02g11494' => 'bca', 'BcaB03g15382' => 'bca', 'BcaB08g36994' => 'bca', 'BcaC03g13477' => 'bca', 'BcaC03g13478' => 'bca', 'BcaC03g13480' => 'bca', 'BcaC03g13481' => 'bca', 'BcaC03g13486' => 'bca', 'BcaC04g19031' => 'bca', 'BcaC04g23085' => 'bca', 'BcaC05g25094' => 'bca', 'BcaC05g25096' => 'bca', 'BcaC05g25138' => 'bca', 'BcaC05g30416' => 'bca', 'BcaC05g30455' => 'bca', 'BcaC06g30979' => 'bca', 'BcaC06g33805' => 'bca', 'BcaC08g46021' => 'bca', 'BcaNung03154' => 'bca', 'BolC2t06623H' => 'bol', 'BolC2t06632H' => 'bol', 'BolC2t06635H' => 'bol', 'BolC2t06638H' => 'bol', 'BolC3t13266H' => 'bol', 'BolC5t29776H' => 'bol', 'BolC6t38912H' => 'bol', 'BolC7t44183H' => 'bol', 'BolC9t54123H' => 'bol', 'BolC9t59107H' => 'bol', 'BraA02t05221Z' => 'bra', 'BraA03t09996Z' => 'bra', 'BraA05t23210Z' => 'bra', 'BraA06t24068Z' => 'bra', 'BraA06t27032Z' => 'bra', 'BraA08t35176Z' => 'bra', 'BraA09t36680Z' => 'bra', 'BraA10t44471Z' => 'bra', 'C02p06760' => 'bna', 'C02p06890' => 'bna', 'C02p07010' => 'bna', 'C03p07660' => 'bna', 'C05p10300' => 'bna', 'C06p38150' => 'bna', 'C07p36650' => 'bna', 'C08p15770' => 'bna', 'C09p12300' => 'bna', 'C09p62700' => 'bna', 'C09p75040' => 'bna', 'CAN.G13.1' => 'can', 'CAN.G138.4' => 'can', 'CAN.G44.6' => 'can', 'CAN.G473.19' => 'can', 'CANSAT01G0835' => 'cansat', 'CANSAT11G0246' => 'cansat', 'CANSAT11G1766' => 'cansat', 'CANSAT64G1954' => 'cansat', 'CARHR013330' => 'chi', 'CARHR060530' => 'chi', 'CARHR075300' => 'chi', 'CARHR105120' => 'chi', 'CARHR148910' => 'chi', 'CARHR198830' => 'chi', 'Carub.0001s1275' => 'cru', 'Carub.0002s1437' => 'cru', 'Carub.0003s0044' => 'cru', 'Carub.0003s2787' => 'cru', 'Carub.0005s0597' => 'cru', 'Carub.0006s1266' => 'cru', 'Ca_06935_v3' => 'car', 'Ca_13559_v3' => 'car', 'Ca_16941_v3' => 'car', 'Ca_16960_v3' => 'car', 'Ca_17775_v3' => 'car', 'Ca_30464_v3' => 'car', 'Cc06_g08160' => 'ccan', 'Cc07_g01520' => 'ccan', 'Cc11_g15810' => 'ccan', 'CDE02G2840' => 'cde', 'CDE03G0093' => 'cde', 'CDE04G2127' => 'cde', 'CDE07G1857' => 'cde', 'CDE09G1246' => 'cde', 'Cfa003412' => 'cfa', 'Cfa007341' => 'cfa', 'Cfa009220' => 'cfa', 'Ciclev10008737m.g' => 'ccl', 'Ciclev10015565m.g' => 'ccl', 'Ciclev10031761m.g' => 'ccl', 'CiPaw.03G045300' => 'cil', 'CiPaw.03G247200' => 'cil', 'CiPaw.04G029500' => 'cil', 'CiPaw.04G174000' => 'cil', 'CiPaw.05G181200' => 'cil', 'CiPaw.06G067100' => 'cil', 'ClCG05G025800' => 'cla', 'ClCG06G011400' => 'cla', 'ClCG09G019360' => 'cla', 'COL.COLO4_04827' => 'col', 'COL.COLO4_29170' => 'col', 'COL.COLO4_35131' => 'col', 'COL.COLO4_35132' => 'col', 'Cpa.g.sc33.32' => 'cpa', 'Cpa.g.sc46.29' => 'cpa', 'Cpa.g.sc796.1' => 'cpa', 'CsaV3_1G030420' => 'csa', 'CsaV3_5G027050' => 'csa', 'CsaV3_5G031040' => 'csa', 'CsaV3_UNG023130' => 'csa', 'CSS0007726' => 'camsi', 'CSS0016433' => 'camsi', 'CSS0017656' => 'camsi', 'CSS0025364' => 'camsi', 'CSS0027582' => 'camsi', 'CSS0047288' => 'camsi', 'CSS0049950' => 'camsi', 'DCAR_003843' => 'dca', 'DCAR_007052' => 'dca', 'DCAR_020884' => 'dca', 'DCAR_021730' => 'dca', 'DCAR_024423' => 'dca', 'DCAR_026509' => 'dca', 'DCAR_031158' => 'dca', 'Dinv14728' => 'din', 'Dinv15219' => 'din', 'Dinv25728' => 'din', 'Dinv33428' => 'din', 'Dinv36489' => 'din', 'Dinv41486' => 'din', 'Duzib147G0469' => 'dzi', 'Duzib168G0060' => 'dzi', 'Duzib187G1215' => 'dzi', 'Duzib248G0692' => 'dzi', 'Duzib251G0767' => 'dzi', 'Duzib264G0446' => 'dzi', 'Duzib268G0691' => 'dzi', 'ECA232G4767' => 'eca', 'ECA233G2838' => 'eca', 'ECA234G0391' => 'eca', 'ECA234G0857' => 'eca', 'ECA236G1593' => 'eca', 'ECA238G0565' => 'eca', 'ECA246G1027' => 'eca', 'ECA246G3223' => 'eca', 'ECA246G3470' => 'eca', 'EL10Ac6g13829' => 'bvu', 'EL10Ac6g14093' => 'bvu', 'EL10Ac8g18707' => 'bvu', 'Eucgr.C01369' => 'egr', 'Eucgr.H02492' => 'egr', 'Eucgr.I01733' => 'egr', 'Eucgr.J02255' => 'egr', 'Eucgr.J02257' => 'egr', 'Eucgr.J02258' => 'egr', 'FAN02G1601' => 'fan', 'FAN03G1586' => 'fan', 'FAN03G2986' => 'fan', 'FAN05G4837' => 'fan', 'FAN06G0146' => 'fan', 'FAN07G0858' => 'fan', 'FAN09G3179' => 'fan', 'FAN10G0669' => 'fan', 'FAN12G2358' => 'fan', 'FAN14G4198' => 'fan', 'FAN14G5112' => 'fan', 'FAN17G0342' => 'fan', 'FAN19G0342' => 'fan', 'FAN19G0962' => 'fan', 'FAN19G1101' => 'fan', 'FAN19G1872' => 'fan', 'FAN22G0356' => 'fan', 'FAN23G0744' => 'fan', 'FAN23G1914' => 'fan', 'FAN26G0032' => 'fan', 'FAN28G0625' => 'fan', 'FvH4_1g02710' => 'fve', 'FvH4_1g02720' => 'fve', 'FvH4_4g25670' => 'fve', 'FvH4_6g51700' => 'fve', 'FvH4_7g20170' => 'fve', 'Glyma.05G175000' => 'gma', 'Glyma.08G132300' => 'gma', 'Glyma.11G243000' => 'gma', 'Glyma.13G158900' => 'gma', 'Glyma.17G112400' => 'gma', 'Glyma.18G014100' => 'gma', 'Glyma.19G003100' => 'gma', 'Glyma.19G056500' => 'gma', 'Gohir.A01G158900' => 'ghi', 'Gohir.A05G312600' => 'ghi', 'Gohir.A05G354900' => 'ghi', 'Gohir.A07G037200' => 'ghi', 'Gohir.A09G030000' => 'ghi', 'Gohir.A12G145200' => 'ghi', 'Gohir.D01G151500' => 'ghi', 'Gohir.D04G058300' => 'ghi', 'Gohir.D05G314100' => 'ghi', 'Gohir.D07G041400' => 'ghi', 'Gohir.D09G029700' => 'ghi', 'Gohir.D12G149700' => 'ghi', 'Gorai.001G043800' => 'gra', 'Gorai.002G187800' => 'gra', 'Gorai.006G034700' => 'gra', 'Gorai.008G161200' => 'gra', 'Gorai.009G335700' => 'gra', 'Gorai.012G065000' => 'gra', 'GSVIVG01000535001' => 'vvi', 'GSVIVG01015572001' => 'vvi', 'GSVIVG01032386001' => 'vvi', 'HanXRQChr05g0138531' => 'han', 'HanXRQChr06g0174391' => 'han', 'HanXRQChr07g0199021' => 'han', 'HanXRQChr08g0208211' => 'han', 'HanXRQChr09g0255471' => 'han', 'HanXRQChr10g0315791' => 'han', 'HanXRQChr12g0371991' => 'han', 'HanXRQChr15g0475251' => 'han', 'HanXRQChr17g0540001' => 'han', 'HanXRQChr17g0548631' => 'han', 'HanXRQChr17g0569561' => 'han', 'Haze_12256' => 'cav', 'Haze_14756' => 'cav', 'Haze_25528' => 'cav', 'Hma1.2p1_0079F.1_g041020' => 'hma', 'Hma1.2p1_0818F.1_g223260' => 'hma', 'Hma1.2p1_1747F.1_g300530' => 'hma', 'HPP92_004607' => 'vpl', 'HPP92_004608' => 'vpl', 'HPP92_006181' => 'vpl', 'HPP92_012192' => 'vpl', 'HPP92_015680' => 'vpl', 'HPP92_020249' => 'vpl', 'HPP92_021376' => 'vpl', 'HPP92_024275' => 'vpl', 'Hund06031' => 'sun', 'Hund25391' => 'sun', 'Lalb_Chr07g0185371' => 'lal', 'Lalb_Chr07g0185381' => 'lal', 'Lalb_Chr12g0204011' => 'lal', 'Lalb_Chr13g0301671' => 'lal', 'Lalb_Chr14g0362851' => 'lal', 'Lalb_Chr24g0403581' => 'lal', 'Lj1g0000233' => 'lja', 'Lj2g0018120' => 'lja', 'Lj3C621T0' => 'lonja', 'Lj3P1059T14' => 'lonja', 'Lj3P611T9' => 'lonja', 'Lj3P614T13' => 'lonja', 'Lj3P615T5' => 'lonja', 'Lj4g0012315' => 'lja', 'Lj4g0026182' => 'lja', 'Lj6P813T16' => 'lonja', 'Lj7C427T7' => 'lonja', 'Lj7C427T8' => 'lonja', 'Lj7P600T41' => 'lonja', 'Lju41C42G17' => 'lonja', 'Lsat_1_v5_gn_0_47300' => 'lsa', 'Lsat_1_v5_gn_2_91280' => 'lsa', 'Lsat_1_v5_gn_3_30561' => 'lsa', 'Lsat_1_v5_gn_4_184321' => 'lsa', 'Lsat_1_v5_gn_4_4041' => 'lsa', 'Lsat_1_v5_gn_5_92000' => 'lsa', 'Lsat_1_v5_gn_8_152940' => 'lsa', 'Lsat_1_v5_gn_8_62401' => 'lsa', 'Manes.06G055900' => 'mes', 'Manes.12G022200' => 'mes', 'Manes.13G023300' => 'mes', 'Manes.14G115000' => 'mes', 'Manes.15G151700' => 'mes', 'Manes.17G111300' => 'mes', 'Mapoly0226s0009' => 'mpo', 'MBI02_g25363_MAGBIO' => 'mbi', 'MBI06_g00027_MAGBIO' => 'mbi', 'MBI10_g13034_MAGBIO' => 'mbi', 'MD09G1023400' => 'mdo', 'MD13G1100100' => 'mdo', 'MD15G1169200' => 'mdo', 'MD16G1101100' => 'mdo', 'MD17G1022900' => 'mdo', 'Medtr3g096150' => 'mtr', 'Medtr4g115070' => 'mtr', 'Medtr7g033325' => 'mtr', 'Medtr8g089840' => 'mtr', 'MELO3C010319.2' => 'cme', 'MELO3C011944.2' => 'cme', 'MELO3C021589.2' => 'cme', 'Migut.E00207' => 'egut', 'Migut.H00067' => 'egut', 'Migut.K00433' => 'egut', 'Migut.K00606' => 'egut', 'Migut.K01410' => 'egut', 'MSTRG.13347' => 'ama', 'MSTRG.24045' => 'ama', 'MSTRG.2428' => 'ama', 'MSTRG.26410' => 'ama', 'MSTRG.3139' => 'ama', 'MSTRG.3286' => 'ama', 'MSTRG.563' => 'ama', 'MSTRG.7941' => 'ama', 'Nitab4.5_0000028g0060' => 'nta', 'Nitab4.5_0000065g0260' => 'nta', 'Nitab4.5_0000112g0060' => 'nta', 'Nitab4.5_0000489g0120' => 'nta', 'Nitab4.5_0001776g0050' => 'nta', 'Nitab4.5_0001854g0010' => 'nta', 'Nitab4.5_0001860g0020' => 'nta', 'Nitab4.5_0004352g0010' => 'nta', 'Nitab4.5_0008716g0020' => 'nta', 'Nitab4.5_0008922g0010' => 'nta', 'Nn3g16693' => 'nnu', 'Nn4g22596' => 'nnu', 'Nn7g37639' => 'nnu', 'Oeu001701.1' => 'oeu', 'Oeu018149.1' => 'oeu', 'Oeu026220.1' => 'oeu', 'Oeu038635.1' => 'oeu', 'Oeu049176.1' => 'oeu', 'Oeu056706.1' => 'oeu', 'Oeu056937.1' => 'oeu', 'Oeu057540.1' => 'oeu', 'Os02g0594900' => 'osa', 'Os02g0595100' => 'osa', 'Os04g0477500' => 'osa', 'Os12g0611900' => 'osa', 'Peaxi162Scf00076g00020' => 'pax', 'Peaxi162Scf00128g00217' => 'pax', 'Peaxi162Scf00129g01640' => 'pax', 'Peaxi162Scf00669g00007' => 'pax', 'Peaxi162Scf00700g00421' => 'pax', 'Peaxi162Scf00801g00038' => 'pax', 'Peaxi162Scf00891g00025' => 'pax', 'PGR083G0909' => 'pgr', 'PGR119G1005' => 'pgr', 'PGR142G2236' => 'pgr', 'PGR142G3388' => 'pgr', 'PGSC0003DMG400004514' => 'stu', 'PGSC0003DMG400012635' => 'stu', 'PGSC0003DMG400015730' => 'stu', 'PGSC0003DMG400018611' => 'stu', 'PGSC0003DMG400030897' => 'stu', 'Phvul.001G254800' => 'pvu', 'Phvul.002G260100' => 'pvu', 'Phvul.003G167600' => 'pvu', 'Phvul.004G005100' => 'pvu', 'Potri.001G343600' => 'ptr', 'Potri.006G066700' => 'ptr', 'Potri.008G186000' => 'ptr', 'Potri.010G046900' => 'ptr', 'Potri.018G127900' => 'ptr', 'Pp3c20_17750' => 'ppa', 'Pp3c24_4380' => 'ppa', 'Prupe.1G245800' => 'ppe', 'Prupe.3G293400' => 'ppe', 'Prupe.7G247400' => 'ppe', 'Psat0s145g0120' => 'psa', 'Psat0s595g0040' => 'psa', 'Psat0s595g0120' => 'psa', 'Psat3g175040' => 'psa', 'Psat7g058120' => 'psa', 'PSO017G0428' => 'pso', 'PSO063G7510' => 'pso', 'PSO067G0046' => 'pso', 'PSO478G1073' => 'pso', 'PSO675G3677' => 'pso', 'PSO675G6558' => 'pso', 'PSO675G7520' => 'pso', 'PSO675G8959' => 'pso', 'QL02p074089' => 'qlo', 'QL02p089614' => 'qlo', 'QL03p057736' => 'qlo', 'RcHm_v2.0_Chr1g0364131' => 'rch', 'RcHm_v2.0_Chr2g0087801' => 'rch', 'RcHm_v2.0_Chr2g0087821' => 'rch', 'RcHm_v2.0_Chr2g0173231' => 'rch', 'RcHm_v2.0_Chr4g0433111' => 'rch', 'Rhsim03G0250300' => 'rsi', 'Rhsim08G0048400' => 'rsi', 'Rhsim10G0014800' => 'rsi', 'Rhsim12G0040100' => 'rsi', 'Rhsim12G0109700' => 'rsi', 'Sabra06G0049600' => 'sbr', 'Sabra08G0141000' => 'sbr', 'Sabra10G0021400' => 'sbr', 'Sabra16G0222900' => 'sbr', 'Sabra18G0108600' => 'sbr', 'SalBow1G0433' => 'sbo', 'SalBow1G2038' => 'sbo', 'SalBow1G5003' => 'sbo', 'SalBow7G1197' => 'sbo', 'SalBow8G3506' => 'sbo', 'Sc03g0007300' => 'sci', 'Sc11g0000950' => 'sci', 'Sc14g0008750' => 'sci', 'Sc18g0000420' => 'sci', 'Sed0006754' => 'sed', 'Sed0008741' => 'sed', 'Sed0017172' => 'sed', 'Sed0018925' => 'sed', 'Sed0023326' => 'sed', 'Sed0025909' => 'sed', 'SEGI_05333' => 'sgi', 'SEGI_10362' => 'sgi', 'SEGI_13380' => 'sgi', 'SEGI_24306' => 'sgi', 'SEGI_29077' => 'sgi', 'SEGI_29095' => 'sgi', 'SEGI_36534' => 'sgi', 'SEGI_37506' => 'sgi', 'SEGI_38321' => 'sgi', 'SGA_v2.0_scaffold307G48031' => 'sas', 'SGA_v2.0_scaffold47G17507' => 'sas', 'SGA_v2.0_scaffold63G21736' => 'sas', 'SGA_v2.0_scaffold87G27070' => 'sas', 'SHI17794' => 'shi', 'SHI28851' => 'shi', 'SMO165G0155' => 'smo', 'SMO340G0217' => 'smo', 'SMO367G1210' => 'smo', 'Solyc02g093430.3' => 'sly', 'Solyc05g013580.4' => 'sly', 'Solyc07g008030.3' => 'sly', 'Solyc12g035470.2' => 'sly', 'Sopen02g038020' => 'spe', 'Sopen05g008490' => 'spe', 'Sopen07g003910' => 'spe', 'Sopen12g015240' => 'spe', 'Sp1g11550' => 'spa', 'Sp2g16710' => 'spa', 'Sp3g00430' => 'spa', 'Sp3g26780' => 'spa', 'Sp5g22900' => 'spa', 'Sp6g29530' => 'spa', 'TAR371G0794' => 'tar', 'TAR374G0164' => 'tar', 'TAR622G0165' => 'tar', 'TAR626G0929' => 'tar', 'TAR629G2155' => 'tar', 'THA.LOC104805282' => 'tha', 'THA.LOC104805363' => 'tha', 'THA.LOC104808968' => 'tha', 'THA.LOC104821093' => 'tha', 'THA.LOC104823953' => 'tha', 'THA.LOC104825562' => 'tha', 'THA.LOC104825665' => 'tha', 'Thecc.02G261400' => 'tca', 'Thecc.04G019200' => 'tca', 'Thecc.09G130400' => 'tca', 'Thhalv10004374m.g' => 'esa', 'Thhalv10007850m.g' => 'esa', 'Thhalv10013782m.g' => 'esa', 'Thhalv10018686m.g' => 'esa', 'Thhalv10020899m.g' => 'esa', 'Thhalv10022755m.g' => 'esa', 'TPR.G23851' => 'tpr', 'TPR.G26500' => 'tpr', 'TPR.G27267' => 'tpr', 'TPR.G32001' => 'tpr', 'TPR.G6251' => 'tpr', 'TPR.G8167' => 'tpr', 'TWI12G1330' => 'twi', 'TWI18G1239' => 'twi', 'TWI34G0979' => 'twi', 'TWI36G0670' => 'twi', 'TWI36G0707' => 'twi', 'TWI56G0233' => 'twi', 'TWI75G1809' => 'twi', 'unitig_21.g20874' => 'ugi', 'unitig_26.g10343' => 'ugi', 'unitig_46.g18392' => 'ugi', 'unitig_52.g17178' => 'ugi', 'unitig_8.g2934' => 'ugi', 'vmacro01122' => 'vma', 'vmacro05875' => 'vma', 'vmacro06147' => 'vma', 'vmacro16191' => 'vma', 'vmacro18293' => 'vma', 'VMungo0251G3707' => 'vmu', 'VMungo0464G1521' => 'vmu', 'VMungo1215G0205' => 'vmu', 'VMungo1383G2484' => 'vmu', 'Zm00001eb079610' => 'zma', 'Zm00001eb135990' => 'zma', 'Zm00001eb183710' => 'zma', 'Zm00001eb246020' => 'zma' ) $gf_id = 'HOM05D001124' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001124' ) $data_identifier = 'HOM05D001124' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 6, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 7, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 21, 'bol' => (int) 10, 'bra' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 6, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 9, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 21, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 8, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 10, 'lsa' => (int) 8, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 8, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 9, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb246020' $species_info = array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ) $local_species = 'tar' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001124', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '548', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02520' => 'bna', 'A03p06630' => 'bna', 'A05p44460' => 'bna', 'A06p08710' => 'bna', 'A06p41090' => 'bna', 'A07p32320' => 'bna', 'A08p32520' => 'bna', 'A09p10360' => 'bna', 'A10p24080' => 'bna', 'Aa31LG11G15250' => 'aar', 'Aa31LG1G1800' => 'aar', 'Aa31LG2G5120' => 'aar', 'Aa31LG2G6070' => 'aar', 'Aa31LG5G10770' => 'aar', 'Aa31sc61G90' => 'aar', 'Actinidia01352' => 'ach', 'Actinidia05983' => 'ach', 'Actinidia08133' => 'ach', 'Actinidia15101' => 'ach', 'Actinidia26379' => 'ach', 'Actinidia35778' => 'ach', 'Actinidia36123' => 'ach', 'Actinidia37436' => 'ach', 'Actinidia38730' => 'ach', 'Ah.02g128210' => 'amhyb', 'Ah.03g132990' => 'amhyb', 'Ah.14g079410' => 'amhyb', 'AL1G24640' => 'aly', 'AL2G26680' => 'aly', 'AL3G10530' => 'aly', 'AL3G45230' => 'aly', 'AL5G15230' => 'aly', 'AL5G16960' => 'aly', 'AL6G25210' => 'aly', 'Aqoxy2G00441' => 'aox', 'Aqoxy3G01236' => 'aox', 'Aqoxy5G03746' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3RQ047' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C7GMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9C8JER' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MBL6KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YXCZ83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZANX40' => 'arhy', 'AT1G12990' => 'ath', 'AT1G67880' => 'ath', 'AT2G13290' => 'ath', 'AT3G01620' => 'ath', 'AT3G26445' => 'ath', 'AT3G27540' => 'ath', 'AT5G14480' => 'ath', 'ATR0824G026' => 'atr', 'ATR1098G019' => 'atr', 'Atru.chr11.2145' => 'acertr', 'Atru.chr2.3636' => 'acertr', 'Atru.chr2.3644' => 'acertr', 'Atru.chr6.2422' => 'acertr', 'Atru.chr7.1112' => 'acertr', 'AUR62005469' => 'cqu', 'AUR62011166' => 'cqu', 'AUR62013319' => 'cqu', 'AUR62024273' => 'cqu', 'AUR62028420' => 'cqu', 'AUR62041942' => 'cqu', 'BcaB01g04969' => 'bca', 'BcaB01g06371' => 'bca', 'BcaB02g11494' => 'bca', 'BcaB03g15382' => 'bca', 'BcaB08g36994' => 'bca', 'BcaC03g13477' => 'bca', 'BcaC03g13478' => 'bca', 'BcaC03g13480' => 'bca', 'BcaC03g13481' => 'bca', 'BcaC03g13486' => 'bca', 'BcaC04g19031' => 'bca', 'BcaC04g23085' => 'bca', 'BcaC05g25094' => 'bca', 'BcaC05g25096' => 'bca', 'BcaC05g25138' => 'bca', 'BcaC05g30416' => 'bca', 'BcaC05g30455' => 'bca', 'BcaC06g30979' => 'bca', 'BcaC06g33805' => 'bca', 'BcaC08g46021' => 'bca', 'BcaNung03154' => 'bca', 'BolC2t06623H' => 'bol', 'BolC2t06632H' => 'bol', 'BolC2t06635H' => 'bol', 'BolC2t06638H' => 'bol', 'BolC3t13266H' => 'bol', 'BolC5t29776H' => 'bol', 'BolC6t38912H' => 'bol', 'BolC7t44183H' => 'bol', 'BolC9t54123H' => 'bol', 'BolC9t59107H' => 'bol', 'BraA02t05221Z' => 'bra', 'BraA03t09996Z' => 'bra', 'BraA05t23210Z' => 'bra', 'BraA06t24068Z' => 'bra', 'BraA06t27032Z' => 'bra', 'BraA08t35176Z' => 'bra', 'BraA09t36680Z' => 'bra', 'BraA10t44471Z' => 'bra', 'C02p06760' => 'bna', 'C02p06890' => 'bna', 'C02p07010' => 'bna', 'C03p07660' => 'bna', 'C05p10300' => 'bna', 'C06p38150' => 'bna', 'C07p36650' => 'bna', 'C08p15770' => 'bna', 'C09p12300' => 'bna', 'C09p62700' => 'bna', 'C09p75040' => 'bna', 'CAN.G13.1' => 'can', 'CAN.G138.4' => 'can', 'CAN.G44.6' => 'can', 'CAN.G473.19' => 'can', 'CANSAT01G0835' => 'cansat', 'CANSAT11G0246' => 'cansat', 'CANSAT11G1766' => 'cansat', 'CANSAT64G1954' => 'cansat', 'CARHR013330' => 'chi', 'CARHR060530' => 'chi', 'CARHR075300' => 'chi', 'CARHR105120' => 'chi', 'CARHR148910' => 'chi', 'CARHR198830' => 'chi', 'Carub.0001s1275' => 'cru', 'Carub.0002s1437' => 'cru', 'Carub.0003s0044' => 'cru', 'Carub.0003s2787' => 'cru', 'Carub.0005s0597' => 'cru', 'Carub.0006s1266' => 'cru', 'Ca_06935_v3' => 'car', 'Ca_13559_v3' => 'car', 'Ca_16941_v3' => 'car', 'Ca_16960_v3' => 'car', 'Ca_17775_v3' => 'car', 'Ca_30464_v3' => 'car', 'Cc06_g08160' => 'ccan', 'Cc07_g01520' => 'ccan', 'Cc11_g15810' => 'ccan', 'CDE02G2840' => 'cde', 'CDE03G0093' => 'cde', 'CDE04G2127' => 'cde', 'CDE07G1857' => 'cde', 'CDE09G1246' => 'cde', 'Cfa003412' => 'cfa', 'Cfa007341' => 'cfa', 'Cfa009220' => 'cfa', 'Ciclev10008737m.g' => 'ccl', 'Ciclev10015565m.g' => 'ccl', 'Ciclev10031761m.g' => 'ccl', 'CiPaw.03G045300' => 'cil', 'CiPaw.03G247200' => 'cil', 'CiPaw.04G029500' => 'cil', 'CiPaw.04G174000' => 'cil', 'CiPaw.05G181200' => 'cil', 'CiPaw.06G067100' => 'cil', 'ClCG05G025800' => 'cla', 'ClCG06G011400' => 'cla', 'ClCG09G019360' => 'cla', 'COL.COLO4_04827' => 'col', 'COL.COLO4_29170' => 'col', 'COL.COLO4_35131' => 'col', 'COL.COLO4_35132' => 'col', 'Cpa.g.sc33.32' => 'cpa', 'Cpa.g.sc46.29' => 'cpa', 'Cpa.g.sc796.1' => 'cpa', 'CsaV3_1G030420' => 'csa', 'CsaV3_5G027050' => 'csa', 'CsaV3_5G031040' => 'csa', 'CsaV3_UNG023130' => 'csa', 'CSS0007726' => 'camsi', 'CSS0016433' => 'camsi', 'CSS0017656' => 'camsi', 'CSS0025364' => 'camsi', 'CSS0027582' => 'camsi', 'CSS0047288' => 'camsi', 'CSS0049950' => 'camsi', 'DCAR_003843' => 'dca', 'DCAR_007052' => 'dca', 'DCAR_020884' => 'dca', 'DCAR_021730' => 'dca', 'DCAR_024423' => 'dca', 'DCAR_026509' => 'dca', 'DCAR_031158' => 'dca', 'Dinv14728' => 'din', 'Dinv15219' => 'din', 'Dinv25728' => 'din', 'Dinv33428' => 'din', 'Dinv36489' => 'din', 'Dinv41486' => 'din', 'Duzib147G0469' => 'dzi', 'Duzib168G0060' => 'dzi', 'Duzib187G1215' => 'dzi', 'Duzib248G0692' => 'dzi', 'Duzib251G0767' => 'dzi', 'Duzib264G0446' => 'dzi', 'Duzib268G0691' => 'dzi', 'ECA232G4767' => 'eca', 'ECA233G2838' => 'eca', 'ECA234G0391' => 'eca', 'ECA234G0857' => 'eca', 'ECA236G1593' => 'eca', 'ECA238G0565' => 'eca', 'ECA246G1027' => 'eca', 'ECA246G3223' => 'eca', 'ECA246G3470' => 'eca', 'EL10Ac6g13829' => 'bvu', 'EL10Ac6g14093' => 'bvu', 'EL10Ac8g18707' => 'bvu', 'Eucgr.C01369' => 'egr', 'Eucgr.H02492' => 'egr', 'Eucgr.I01733' => 'egr', 'Eucgr.J02255' => 'egr', 'Eucgr.J02257' => 'egr', 'Eucgr.J02258' => 'egr', 'FAN02G1601' => 'fan', 'FAN03G1586' => 'fan', 'FAN03G2986' => 'fan', 'FAN05G4837' => 'fan', 'FAN06G0146' => 'fan', 'FAN07G0858' => 'fan', 'FAN09G3179' => 'fan', 'FAN10G0669' => 'fan', 'FAN12G2358' => 'fan', 'FAN14G4198' => 'fan', 'FAN14G5112' => 'fan', 'FAN17G0342' => 'fan', 'FAN19G0342' => 'fan', 'FAN19G0962' => 'fan', 'FAN19G1101' => 'fan', 'FAN19G1872' => 'fan', 'FAN22G0356' => 'fan', 'FAN23G0744' => 'fan', 'FAN23G1914' => 'fan', 'FAN26G0032' => 'fan', 'FAN28G0625' => 'fan', 'FvH4_1g02710' => 'fve', 'FvH4_1g02720' => 'fve', 'FvH4_4g25670' => 'fve', 'FvH4_6g51700' => 'fve', 'FvH4_7g20170' => 'fve', 'Glyma.05G175000' => 'gma', 'Glyma.08G132300' => 'gma', 'Glyma.11G243000' => 'gma', 'Glyma.13G158900' => 'gma', 'Glyma.17G112400' => 'gma', 'Glyma.18G014100' => 'gma', 'Glyma.19G003100' => 'gma', 'Glyma.19G056500' => 'gma', 'Gohir.A01G158900' => 'ghi', 'Gohir.A05G312600' => 'ghi', 'Gohir.A05G354900' => 'ghi', 'Gohir.A07G037200' => 'ghi', 'Gohir.A09G030000' => 'ghi', 'Gohir.A12G145200' => 'ghi', 'Gohir.D01G151500' => 'ghi', 'Gohir.D04G058300' => 'ghi', 'Gohir.D05G314100' => 'ghi', 'Gohir.D07G041400' => 'ghi', 'Gohir.D09G029700' => 'ghi', 'Gohir.D12G149700' => 'ghi', 'Gorai.001G043800' => 'gra', 'Gorai.002G187800' => 'gra', 'Gorai.006G034700' => 'gra', 'Gorai.008G161200' => 'gra', 'Gorai.009G335700' => 'gra', 'Gorai.012G065000' => 'gra', 'GSVIVG01000535001' => 'vvi', 'GSVIVG01015572001' => 'vvi', 'GSVIVG01032386001' => 'vvi', 'HanXRQChr05g0138531' => 'han', 'HanXRQChr06g0174391' => 'han', 'HanXRQChr07g0199021' => 'han', 'HanXRQChr08g0208211' => 'han', 'HanXRQChr09g0255471' => 'han', 'HanXRQChr10g0315791' => 'han', 'HanXRQChr12g0371991' => 'han', 'HanXRQChr15g0475251' => 'han', 'HanXRQChr17g0540001' => 'han', 'HanXRQChr17g0548631' => 'han', 'HanXRQChr17g0569561' => 'han', 'Haze_12256' => 'cav', 'Haze_14756' => 'cav', 'Haze_25528' => 'cav', 'Hma1.2p1_0079F.1_g041020' => 'hma', 'Hma1.2p1_0818F.1_g223260' => 'hma', 'Hma1.2p1_1747F.1_g300530' => 'hma', 'HPP92_004607' => 'vpl', 'HPP92_004608' => 'vpl', 'HPP92_006181' => 'vpl', 'HPP92_012192' => 'vpl', 'HPP92_015680' => 'vpl', 'HPP92_020249' => 'vpl', 'HPP92_021376' => 'vpl', 'HPP92_024275' => 'vpl', 'Hund06031' => 'sun', 'Hund25391' => 'sun', 'Lalb_Chr07g0185371' => 'lal', 'Lalb_Chr07g0185381' => 'lal', 'Lalb_Chr12g0204011' => 'lal', 'Lalb_Chr13g0301671' => 'lal', 'Lalb_Chr14g0362851' => 'lal', 'Lalb_Chr24g0403581' => 'lal', 'Lj1g0000233' => 'lja', 'Lj2g0018120' => 'lja', 'Lj3C621T0' => 'lonja', 'Lj3P1059T14' => 'lonja', 'Lj3P611T9' => 'lonja', 'Lj3P614T13' => 'lonja', 'Lj3P615T5' => 'lonja', 'Lj4g0012315' => 'lja', 'Lj4g0026182' => 'lja', 'Lj6P813T16' => 'lonja', 'Lj7C427T7' => 'lonja', 'Lj7C427T8' => 'lonja', 'Lj7P600T41' => 'lonja', 'Lju41C42G17' => 'lonja', 'Lsat_1_v5_gn_0_47300' => 'lsa', 'Lsat_1_v5_gn_2_91280' => 'lsa', 'Lsat_1_v5_gn_3_30561' => 'lsa', 'Lsat_1_v5_gn_4_184321' => 'lsa', 'Lsat_1_v5_gn_4_4041' => 'lsa', 'Lsat_1_v5_gn_5_92000' => 'lsa', 'Lsat_1_v5_gn_8_152940' => 'lsa', 'Lsat_1_v5_gn_8_62401' => 'lsa', 'Manes.06G055900' => 'mes', 'Manes.12G022200' => 'mes', 'Manes.13G023300' => 'mes', 'Manes.14G115000' => 'mes', 'Manes.15G151700' => 'mes', 'Manes.17G111300' => 'mes', 'Mapoly0226s0009' => 'mpo', 'MBI02_g25363_MAGBIO' => 'mbi', 'MBI06_g00027_MAGBIO' => 'mbi', 'MBI10_g13034_MAGBIO' => 'mbi', 'MD09G1023400' => 'mdo', 'MD13G1100100' => 'mdo', 'MD15G1169200' => 'mdo', 'MD16G1101100' => 'mdo', 'MD17G1022900' => 'mdo', 'Medtr3g096150' => 'mtr', 'Medtr4g115070' => 'mtr', 'Medtr7g033325' => 'mtr', 'Medtr8g089840' => 'mtr', 'MELO3C010319.2' => 'cme', 'MELO3C011944.2' => 'cme', 'MELO3C021589.2' => 'cme', 'Migut.E00207' => 'egut', 'Migut.H00067' => 'egut', 'Migut.K00433' => 'egut', 'Migut.K00606' => 'egut', 'Migut.K01410' => 'egut', 'MSTRG.13347' => 'ama', 'MSTRG.24045' => 'ama', 'MSTRG.2428' => 'ama', 'MSTRG.26410' => 'ama', 'MSTRG.3139' => 'ama', 'MSTRG.3286' => 'ama', 'MSTRG.563' => 'ama', 'MSTRG.7941' => 'ama', 'Nitab4.5_0000028g0060' => 'nta', 'Nitab4.5_0000065g0260' => 'nta', 'Nitab4.5_0000112g0060' => 'nta', 'Nitab4.5_0000489g0120' => 'nta', 'Nitab4.5_0001776g0050' => 'nta', 'Nitab4.5_0001854g0010' => 'nta', 'Nitab4.5_0001860g0020' => 'nta', 'Nitab4.5_0004352g0010' => 'nta', 'Nitab4.5_0008716g0020' => 'nta', 'Nitab4.5_0008922g0010' => 'nta', 'Nn3g16693' => 'nnu', 'Nn4g22596' => 'nnu', 'Nn7g37639' => 'nnu', 'Oeu001701.1' => 'oeu', 'Oeu018149.1' => 'oeu', 'Oeu026220.1' => 'oeu', 'Oeu038635.1' => 'oeu', 'Oeu049176.1' => 'oeu', 'Oeu056706.1' => 'oeu', 'Oeu056937.1' => 'oeu', 'Oeu057540.1' => 'oeu', 'Os02g0594900' => 'osa', 'Os02g0595100' => 'osa', 'Os04g0477500' => 'osa', 'Os12g0611900' => 'osa', 'Peaxi162Scf00076g00020' => 'pax', 'Peaxi162Scf00128g00217' => 'pax', 'Peaxi162Scf00129g01640' => 'pax', 'Peaxi162Scf00669g00007' => 'pax', 'Peaxi162Scf00700g00421' => 'pax', 'Peaxi162Scf00801g00038' => 'pax', 'Peaxi162Scf00891g00025' => 'pax', 'PGR083G0909' => 'pgr', 'PGR119G1005' => 'pgr', 'PGR142G2236' => 'pgr', 'PGR142G3388' => 'pgr', 'PGSC0003DMG400004514' => 'stu', 'PGSC0003DMG400012635' => 'stu', 'PGSC0003DMG400015730' => 'stu', 'PGSC0003DMG400018611' => 'stu', 'PGSC0003DMG400030897' => 'stu', 'Phvul.001G254800' => 'pvu', 'Phvul.002G260100' => 'pvu', 'Phvul.003G167600' => 'pvu', 'Phvul.004G005100' => 'pvu', 'Potri.001G343600' => 'ptr', 'Potri.006G066700' => 'ptr', 'Potri.008G186000' => 'ptr', 'Potri.010G046900' => 'ptr', 'Potri.018G127900' => 'ptr', 'Pp3c20_17750' => 'ppa', 'Pp3c24_4380' => 'ppa', 'Prupe.1G245800' => 'ppe', 'Prupe.3G293400' => 'ppe', 'Prupe.7G247400' => 'ppe', 'Psat0s145g0120' => 'psa', 'Psat0s595g0040' => 'psa', 'Psat0s595g0120' => 'psa', 'Psat3g175040' => 'psa', 'Psat7g058120' => 'psa', 'PSO017G0428' => 'pso', 'PSO063G7510' => 'pso', 'PSO067G0046' => 'pso', 'PSO478G1073' => 'pso', 'PSO675G3677' => 'pso', 'PSO675G6558' => 'pso', 'PSO675G7520' => 'pso', 'PSO675G8959' => 'pso', 'QL02p074089' => 'qlo', 'QL02p089614' => 'qlo', 'QL03p057736' => 'qlo', 'RcHm_v2.0_Chr1g0364131' => 'rch', 'RcHm_v2.0_Chr2g0087801' => 'rch', 'RcHm_v2.0_Chr2g0087821' => 'rch', 'RcHm_v2.0_Chr2g0173231' => 'rch', 'RcHm_v2.0_Chr4g0433111' => 'rch', 'Rhsim03G0250300' => 'rsi', 'Rhsim08G0048400' => 'rsi', 'Rhsim10G0014800' => 'rsi', 'Rhsim12G0040100' => 'rsi', 'Rhsim12G0109700' => 'rsi', 'Sabra06G0049600' => 'sbr', 'Sabra08G0141000' => 'sbr', 'Sabra10G0021400' => 'sbr', 'Sabra16G0222900' => 'sbr', 'Sabra18G0108600' => 'sbr', 'SalBow1G0433' => 'sbo', 'SalBow1G2038' => 'sbo', 'SalBow1G5003' => 'sbo', 'SalBow7G1197' => 'sbo', 'SalBow8G3506' => 'sbo', 'Sc03g0007300' => 'sci', 'Sc11g0000950' => 'sci', 'Sc14g0008750' => 'sci', 'Sc18g0000420' => 'sci', 'Sed0006754' => 'sed', 'Sed0008741' => 'sed', 'Sed0017172' => 'sed', 'Sed0018925' => 'sed', 'Sed0023326' => 'sed', 'Sed0025909' => 'sed', 'SEGI_05333' => 'sgi', 'SEGI_10362' => 'sgi', 'SEGI_13380' => 'sgi', 'SEGI_24306' => 'sgi', 'SEGI_29077' => 'sgi', 'SEGI_29095' => 'sgi', 'SEGI_36534' => 'sgi', 'SEGI_37506' => 'sgi', 'SEGI_38321' => 'sgi', 'SGA_v2.0_scaffold307G48031' => 'sas', 'SGA_v2.0_scaffold47G17507' => 'sas', 'SGA_v2.0_scaffold63G21736' => 'sas', 'SGA_v2.0_scaffold87G27070' => 'sas', 'SHI17794' => 'shi', 'SHI28851' => 'shi', 'SMO165G0155' => 'smo', 'SMO340G0217' => 'smo', 'SMO367G1210' => 'smo', 'Solyc02g093430.3' => 'sly', 'Solyc05g013580.4' => 'sly', 'Solyc07g008030.3' => 'sly', 'Solyc12g035470.2' => 'sly', 'Sopen02g038020' => 'spe', 'Sopen05g008490' => 'spe', 'Sopen07g003910' => 'spe', 'Sopen12g015240' => 'spe', 'Sp1g11550' => 'spa', 'Sp2g16710' => 'spa', 'Sp3g00430' => 'spa', 'Sp3g26780' => 'spa', 'Sp5g22900' => 'spa', 'Sp6g29530' => 'spa', 'TAR371G0794' => 'tar', 'TAR374G0164' => 'tar', 'TAR622G0165' => 'tar', 'TAR626G0929' => 'tar', 'TAR629G2155' => 'tar', 'THA.LOC104805282' => 'tha', 'THA.LOC104805363' => 'tha', 'THA.LOC104808968' => 'tha', 'THA.LOC104821093' => 'tha', 'THA.LOC104823953' => 'tha', 'THA.LOC104825562' => 'tha', 'THA.LOC104825665' => 'tha', 'Thecc.02G261400' => 'tca', 'Thecc.04G019200' => 'tca', 'Thecc.09G130400' => 'tca', 'Thhalv10004374m.g' => 'esa', 'Thhalv10007850m.g' => 'esa', 'Thhalv10013782m.g' => 'esa', 'Thhalv10018686m.g' => 'esa', 'Thhalv10020899m.g' => 'esa', 'Thhalv10022755m.g' => 'esa', 'TPR.G23851' => 'tpr', 'TPR.G26500' => 'tpr', 'TPR.G27267' => 'tpr', 'TPR.G32001' => 'tpr', 'TPR.G6251' => 'tpr', 'TPR.G8167' => 'tpr', 'TWI12G1330' => 'twi', 'TWI18G1239' => 'twi', 'TWI34G0979' => 'twi', 'TWI36G0670' => 'twi', 'TWI36G0707' => 'twi', 'TWI56G0233' => 'twi', 'TWI75G1809' => 'twi', 'unitig_21.g20874' => 'ugi', 'unitig_26.g10343' => 'ugi', 'unitig_46.g18392' => 'ugi', 'unitig_52.g17178' => 'ugi', 'unitig_8.g2934' => 'ugi', 'vmacro01122' => 'vma', 'vmacro05875' => 'vma', 'vmacro06147' => 'vma', 'vmacro16191' => 'vma', 'vmacro18293' => 'vma', 'VMungo0251G3707' => 'vmu', 'VMungo0464G1521' => 'vmu', 'VMungo1215G0205' => 'vmu', 'VMungo1383G2484' => 'vmu', 'Zm00001eb079610' => 'zma', 'Zm00001eb135990' => 'zma', 'Zm00001eb183710' => 'zma', 'Zm00001eb246020' => 'zma' ), 'gf_id' => 'HOM05D001124', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001124' ), 'data_identifier' => 'HOM05D001124', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001124', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '548', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02520' => 'bna', 'A03p06630' => 'bna', 'A05p44460' => 'bna', 'A06p08710' => 'bna', 'A06p41090' => 'bna', 'A07p32320' => 'bna', 'A08p32520' => 'bna', 'A09p10360' => 'bna', 'A10p24080' => 'bna', 'Aa31LG11G15250' => 'aar', 'Aa31LG1G1800' => 'aar', 'Aa31LG2G5120' => 'aar', 'Aa31LG2G6070' => 'aar', 'Aa31LG5G10770' => 'aar', 'Aa31sc61G90' => 'aar', 'Actinidia01352' => 'ach', 'Actinidia05983' => 'ach', 'Actinidia08133' => 'ach', 'Actinidia15101' => 'ach', 'Actinidia26379' => 'ach', 'Actinidia35778' => 'ach', 'Actinidia36123' => 'ach', 'Actinidia37436' => 'ach', 'Actinidia38730' => 'ach', 'Ah.02g128210' => 'amhyb', 'Ah.03g132990' => 'amhyb', 'Ah.14g079410' => 'amhyb', 'AL1G24640' => 'aly', 'AL2G26680' => 'aly', 'AL3G10530' => 'aly', 'AL3G45230' => 'aly', 'AL5G15230' => 'aly', 'AL5G16960' => 'aly', 'AL6G25210' => 'aly', 'Aqoxy2G00441' => 'aox', 'Aqoxy3G01236' => 'aox', 'Aqoxy5G03746' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3RQ047' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C7GMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9C8JER' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MBL6KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YXCZ83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZANX40' => 'arhy', 'AT1G12990' => 'ath', 'AT1G67880' => 'ath', 'AT2G13290' => 'ath', 'AT3G01620' => 'ath', 'AT3G26445' => 'ath', 'AT3G27540' => 'ath', 'AT5G14480' => 'ath', 'ATR0824G026' => 'atr', 'ATR1098G019' => 'atr', 'Atru.chr11.2145' => 'acertr', 'Atru.chr2.3636' => 'acertr', 'Atru.chr2.3644' => 'acertr', 'Atru.chr6.2422' => 'acertr', 'Atru.chr7.1112' => 'acertr', 'AUR62005469' => 'cqu', 'AUR62011166' => 'cqu', 'AUR62013319' => 'cqu', 'AUR62024273' => 'cqu', 'AUR62028420' => 'cqu', 'AUR62041942' => 'cqu', 'BcaB01g04969' => 'bca', 'BcaB01g06371' => 'bca', 'BcaB02g11494' => 'bca', 'BcaB03g15382' => 'bca', 'BcaB08g36994' => 'bca', 'BcaC03g13477' => 'bca', 'BcaC03g13478' => 'bca', 'BcaC03g13480' => 'bca', 'BcaC03g13481' => 'bca', 'BcaC03g13486' => 'bca', 'BcaC04g19031' => 'bca', 'BcaC04g23085' => 'bca', 'BcaC05g25094' => 'bca', 'BcaC05g25096' => 'bca', 'BcaC05g25138' => 'bca', 'BcaC05g30416' => 'bca', 'BcaC05g30455' => 'bca', 'BcaC06g30979' => 'bca', 'BcaC06g33805' => 'bca', 'BcaC08g46021' => 'bca', 'BcaNung03154' => 'bca', 'BolC2t06623H' => 'bol', 'BolC2t06632H' => 'bol', 'BolC2t06635H' => 'bol', 'BolC2t06638H' => 'bol', 'BolC3t13266H' => 'bol', 'BolC5t29776H' => 'bol', 'BolC6t38912H' => 'bol', 'BolC7t44183H' => 'bol', 'BolC9t54123H' => 'bol', 'BolC9t59107H' => 'bol', 'BraA02t05221Z' => 'bra', 'BraA03t09996Z' => 'bra', 'BraA05t23210Z' => 'bra', 'BraA06t24068Z' => 'bra', 'BraA06t27032Z' => 'bra', 'BraA08t35176Z' => 'bra', 'BraA09t36680Z' => 'bra', 'BraA10t44471Z' => 'bra', 'C02p06760' => 'bna', 'C02p06890' => 'bna', 'C02p07010' => 'bna', 'C03p07660' => 'bna', 'C05p10300' => 'bna', 'C06p38150' => 'bna', 'C07p36650' => 'bna', 'C08p15770' => 'bna', 'C09p12300' => 'bna', 'C09p62700' => 'bna', 'C09p75040' => 'bna', 'CAN.G13.1' => 'can', 'CAN.G138.4' => 'can', 'CAN.G44.6' => 'can', 'CAN.G473.19' => 'can', 'CANSAT01G0835' => 'cansat', 'CANSAT11G0246' => 'cansat', 'CANSAT11G1766' => 'cansat', 'CANSAT64G1954' => 'cansat', 'CARHR013330' => 'chi', 'CARHR060530' => 'chi', 'CARHR075300' => 'chi', 'CARHR105120' => 'chi', 'CARHR148910' => 'chi', 'CARHR198830' => 'chi', 'Carub.0001s1275' => 'cru', 'Carub.0002s1437' => 'cru', 'Carub.0003s0044' => 'cru', 'Carub.0003s2787' => 'cru', 'Carub.0005s0597' => 'cru', 'Carub.0006s1266' => 'cru', 'Ca_06935_v3' => 'car', 'Ca_13559_v3' => 'car', 'Ca_16941_v3' => 'car', 'Ca_16960_v3' => 'car', 'Ca_17775_v3' => 'car', 'Ca_30464_v3' => 'car', 'Cc06_g08160' => 'ccan', 'Cc07_g01520' => 'ccan', 'Cc11_g15810' => 'ccan', 'CDE02G2840' => 'cde', 'CDE03G0093' => 'cde', 'CDE04G2127' => 'cde', 'CDE07G1857' => 'cde', 'CDE09G1246' => 'cde', 'Cfa003412' => 'cfa', 'Cfa007341' => 'cfa', 'Cfa009220' => 'cfa', 'Ciclev10008737m.g' => 'ccl', 'Ciclev10015565m.g' => 'ccl', 'Ciclev10031761m.g' => 'ccl', 'CiPaw.03G045300' => 'cil', 'CiPaw.03G247200' => 'cil', 'CiPaw.04G029500' => 'cil', 'CiPaw.04G174000' => 'cil', 'CiPaw.05G181200' => 'cil', 'CiPaw.06G067100' => 'cil', 'ClCG05G025800' => 'cla', 'ClCG06G011400' => 'cla', 'ClCG09G019360' => 'cla', 'COL.COLO4_04827' => 'col', 'COL.COLO4_29170' => 'col', 'COL.COLO4_35131' => 'col', 'COL.COLO4_35132' => 'col', 'Cpa.g.sc33.32' => 'cpa', 'Cpa.g.sc46.29' => 'cpa', 'Cpa.g.sc796.1' => 'cpa', 'CsaV3_1G030420' => 'csa', 'CsaV3_5G027050' => 'csa', 'CsaV3_5G031040' => 'csa', 'CsaV3_UNG023130' => 'csa', 'CSS0007726' => 'camsi', 'CSS0016433' => 'camsi', 'CSS0017656' => 'camsi', 'CSS0025364' => 'camsi', 'CSS0027582' => 'camsi', 'CSS0047288' => 'camsi', 'CSS0049950' => 'camsi', 'DCAR_003843' => 'dca', 'DCAR_007052' => 'dca', 'DCAR_020884' => 'dca', 'DCAR_021730' => 'dca', 'DCAR_024423' => 'dca', 'DCAR_026509' => 'dca', 'DCAR_031158' => 'dca', 'Dinv14728' => 'din', 'Dinv15219' => 'din', 'Dinv25728' => 'din', 'Dinv33428' => 'din', 'Dinv36489' => 'din', 'Dinv41486' => 'din', 'Duzib147G0469' => 'dzi', 'Duzib168G0060' => 'dzi', 'Duzib187G1215' => 'dzi', 'Duzib248G0692' => 'dzi', 'Duzib251G0767' => 'dzi', 'Duzib264G0446' => 'dzi', 'Duzib268G0691' => 'dzi', 'ECA232G4767' => 'eca', 'ECA233G2838' => 'eca', 'ECA234G0391' => 'eca', 'ECA234G0857' => 'eca', 'ECA236G1593' => 'eca', 'ECA238G0565' => 'eca', 'ECA246G1027' => 'eca', 'ECA246G3223' => 'eca', 'ECA246G3470' => 'eca', 'EL10Ac6g13829' => 'bvu', 'EL10Ac6g14093' => 'bvu', 'EL10Ac8g18707' => 'bvu', 'Eucgr.C01369' => 'egr', 'Eucgr.H02492' => 'egr', 'Eucgr.I01733' => 'egr', 'Eucgr.J02255' => 'egr', 'Eucgr.J02257' => 'egr', 'Eucgr.J02258' => 'egr', 'FAN02G1601' => 'fan', 'FAN03G1586' => 'fan', 'FAN03G2986' => 'fan', 'FAN05G4837' => 'fan', 'FAN06G0146' => 'fan', 'FAN07G0858' => 'fan', 'FAN09G3179' => 'fan', 'FAN10G0669' => 'fan', 'FAN12G2358' => 'fan', 'FAN14G4198' => 'fan', 'FAN14G5112' => 'fan', 'FAN17G0342' => 'fan', 'FAN19G0342' => 'fan', 'FAN19G0962' => 'fan', 'FAN19G1101' => 'fan', 'FAN19G1872' => 'fan', 'FAN22G0356' => 'fan', 'FAN23G0744' => 'fan', 'FAN23G1914' => 'fan', 'FAN26G0032' => 'fan', 'FAN28G0625' => 'fan', 'FvH4_1g02710' => 'fve', 'FvH4_1g02720' => 'fve', 'FvH4_4g25670' => 'fve', 'FvH4_6g51700' => 'fve', 'FvH4_7g20170' => 'fve', 'Glyma.05G175000' => 'gma', 'Glyma.08G132300' => 'gma', 'Glyma.11G243000' => 'gma', 'Glyma.13G158900' => 'gma', 'Glyma.17G112400' => 'gma', 'Glyma.18G014100' => 'gma', 'Glyma.19G003100' => 'gma', 'Glyma.19G056500' => 'gma', 'Gohir.A01G158900' => 'ghi', 'Gohir.A05G312600' => 'ghi', 'Gohir.A05G354900' => 'ghi', 'Gohir.A07G037200' => 'ghi', 'Gohir.A09G030000' => 'ghi', 'Gohir.A12G145200' => 'ghi', 'Gohir.D01G151500' => 'ghi', 'Gohir.D04G058300' => 'ghi', 'Gohir.D05G314100' => 'ghi', 'Gohir.D07G041400' => 'ghi', 'Gohir.D09G029700' => 'ghi', 'Gohir.D12G149700' => 'ghi', 'Gorai.001G043800' => 'gra', 'Gorai.002G187800' => 'gra', 'Gorai.006G034700' => 'gra', 'Gorai.008G161200' => 'gra', 'Gorai.009G335700' => 'gra', 'Gorai.012G065000' => 'gra', 'GSVIVG01000535001' => 'vvi', 'GSVIVG01015572001' => 'vvi', 'GSVIVG01032386001' => 'vvi', 'HanXRQChr05g0138531' => 'han', 'HanXRQChr06g0174391' => 'han', 'HanXRQChr07g0199021' => 'han', 'HanXRQChr08g0208211' => 'han', 'HanXRQChr09g0255471' => 'han', 'HanXRQChr10g0315791' => 'han', 'HanXRQChr12g0371991' => 'han', 'HanXRQChr15g0475251' => 'han', 'HanXRQChr17g0540001' => 'han', 'HanXRQChr17g0548631' => 'han', 'HanXRQChr17g0569561' => 'han', 'Haze_12256' => 'cav', 'Haze_14756' => 'cav', 'Haze_25528' => 'cav', 'Hma1.2p1_0079F.1_g041020' => 'hma', 'Hma1.2p1_0818F.1_g223260' => 'hma', 'Hma1.2p1_1747F.1_g300530' => 'hma', 'HPP92_004607' => 'vpl', 'HPP92_004608' => 'vpl', 'HPP92_006181' => 'vpl', 'HPP92_012192' => 'vpl', 'HPP92_015680' => 'vpl', 'HPP92_020249' => 'vpl', 'HPP92_021376' => 'vpl', 'HPP92_024275' => 'vpl', 'Hund06031' => 'sun', 'Hund25391' => 'sun', 'Lalb_Chr07g0185371' => 'lal', 'Lalb_Chr07g0185381' => 'lal', 'Lalb_Chr12g0204011' => 'lal', 'Lalb_Chr13g0301671' => 'lal', 'Lalb_Chr14g0362851' => 'lal', 'Lalb_Chr24g0403581' => 'lal', 'Lj1g0000233' => 'lja', 'Lj2g0018120' => 'lja', 'Lj3C621T0' => 'lonja', 'Lj3P1059T14' => 'lonja', 'Lj3P611T9' => 'lonja', 'Lj3P614T13' => 'lonja', 'Lj3P615T5' => 'lonja', 'Lj4g0012315' => 'lja', 'Lj4g0026182' => 'lja', 'Lj6P813T16' => 'lonja', 'Lj7C427T7' => 'lonja', 'Lj7C427T8' => 'lonja', 'Lj7P600T41' => 'lonja', 'Lju41C42G17' => 'lonja', 'Lsat_1_v5_gn_0_47300' => 'lsa', 'Lsat_1_v5_gn_2_91280' => 'lsa', 'Lsat_1_v5_gn_3_30561' => 'lsa', 'Lsat_1_v5_gn_4_184321' => 'lsa', 'Lsat_1_v5_gn_4_4041' => 'lsa', 'Lsat_1_v5_gn_5_92000' => 'lsa', 'Lsat_1_v5_gn_8_152940' => 'lsa', 'Lsat_1_v5_gn_8_62401' => 'lsa', 'Manes.06G055900' => 'mes', 'Manes.12G022200' => 'mes', 'Manes.13G023300' => 'mes', 'Manes.14G115000' => 'mes', 'Manes.15G151700' => 'mes', 'Manes.17G111300' => 'mes', 'Mapoly0226s0009' => 'mpo', 'MBI02_g25363_MAGBIO' => 'mbi', 'MBI06_g00027_MAGBIO' => 'mbi', 'MBI10_g13034_MAGBIO' => 'mbi', 'MD09G1023400' => 'mdo', 'MD13G1100100' => 'mdo', 'MD15G1169200' => 'mdo', 'MD16G1101100' => 'mdo', 'MD17G1022900' => 'mdo', 'Medtr3g096150' => 'mtr', 'Medtr4g115070' => 'mtr', 'Medtr7g033325' => 'mtr', 'Medtr8g089840' => 'mtr', 'MELO3C010319.2' => 'cme', 'MELO3C011944.2' => 'cme', 'MELO3C021589.2' => 'cme', 'Migut.E00207' => 'egut', 'Migut.H00067' => 'egut', 'Migut.K00433' => 'egut', 'Migut.K00606' => 'egut', 'Migut.K01410' => 'egut', 'MSTRG.13347' => 'ama', 'MSTRG.24045' => 'ama', 'MSTRG.2428' => 'ama', 'MSTRG.26410' => 'ama', 'MSTRG.3139' => 'ama', 'MSTRG.3286' => 'ama', 'MSTRG.563' => 'ama', 'MSTRG.7941' => 'ama', 'Nitab4.5_0000028g0060' => 'nta', 'Nitab4.5_0000065g0260' => 'nta', 'Nitab4.5_0000112g0060' => 'nta', 'Nitab4.5_0000489g0120' => 'nta', 'Nitab4.5_0001776g0050' => 'nta', 'Nitab4.5_0001854g0010' => 'nta', 'Nitab4.5_0001860g0020' => 'nta', 'Nitab4.5_0004352g0010' => 'nta', 'Nitab4.5_0008716g0020' => 'nta', 'Nitab4.5_0008922g0010' => 'nta', 'Nn3g16693' => 'nnu', 'Nn4g22596' => 'nnu', 'Nn7g37639' => 'nnu', 'Oeu001701.1' => 'oeu', 'Oeu018149.1' => 'oeu', 'Oeu026220.1' => 'oeu', 'Oeu038635.1' => 'oeu', 'Oeu049176.1' => 'oeu', 'Oeu056706.1' => 'oeu', 'Oeu056937.1' => 'oeu', 'Oeu057540.1' => 'oeu', 'Os02g0594900' => 'osa', 'Os02g0595100' => 'osa', 'Os04g0477500' => 'osa', 'Os12g0611900' => 'osa', 'Peaxi162Scf00076g00020' => 'pax', 'Peaxi162Scf00128g00217' => 'pax', 'Peaxi162Scf00129g01640' => 'pax', 'Peaxi162Scf00669g00007' => 'pax', 'Peaxi162Scf00700g00421' => 'pax', 'Peaxi162Scf00801g00038' => 'pax', 'Peaxi162Scf00891g00025' => 'pax', 'PGR083G0909' => 'pgr', 'PGR119G1005' => 'pgr', 'PGR142G2236' => 'pgr', 'PGR142G3388' => 'pgr', 'PGSC0003DMG400004514' => 'stu', 'PGSC0003DMG400012635' => 'stu', 'PGSC0003DMG400015730' => 'stu', 'PGSC0003DMG400018611' => 'stu', 'PGSC0003DMG400030897' => 'stu', 'Phvul.001G254800' => 'pvu', 'Phvul.002G260100' => 'pvu', 'Phvul.003G167600' => 'pvu', 'Phvul.004G005100' => 'pvu', 'Potri.001G343600' => 'ptr', 'Potri.006G066700' => 'ptr', 'Potri.008G186000' => 'ptr', 'Potri.010G046900' => 'ptr', 'Potri.018G127900' => 'ptr', 'Pp3c20_17750' => 'ppa', 'Pp3c24_4380' => 'ppa', 'Prupe.1G245800' => 'ppe', 'Prupe.3G293400' => 'ppe', 'Prupe.7G247400' => 'ppe', 'Psat0s145g0120' => 'psa', 'Psat0s595g0040' => 'psa', 'Psat0s595g0120' => 'psa', 'Psat3g175040' => 'psa', 'Psat7g058120' => 'psa', 'PSO017G0428' => 'pso', 'PSO063G7510' => 'pso', 'PSO067G0046' => 'pso', 'PSO478G1073' => 'pso', 'PSO675G3677' => 'pso', 'PSO675G6558' => 'pso', 'PSO675G7520' => 'pso', 'PSO675G8959' => 'pso', 'QL02p074089' => 'qlo', 'QL02p089614' => 'qlo', 'QL03p057736' => 'qlo', 'RcHm_v2.0_Chr1g0364131' => 'rch', 'RcHm_v2.0_Chr2g0087801' => 'rch', 'RcHm_v2.0_Chr2g0087821' => 'rch', 'RcHm_v2.0_Chr2g0173231' => 'rch', 'RcHm_v2.0_Chr4g0433111' => 'rch', 'Rhsim03G0250300' => 'rsi', 'Rhsim08G0048400' => 'rsi', 'Rhsim10G0014800' => 'rsi', 'Rhsim12G0040100' => 'rsi', 'Rhsim12G0109700' => 'rsi', 'Sabra06G0049600' => 'sbr', 'Sabra08G0141000' => 'sbr', 'Sabra10G0021400' => 'sbr', 'Sabra16G0222900' => 'sbr', 'Sabra18G0108600' => 'sbr', 'SalBow1G0433' => 'sbo', 'SalBow1G2038' => 'sbo', 'SalBow1G5003' => 'sbo', 'SalBow7G1197' => 'sbo', 'SalBow8G3506' => 'sbo', 'Sc03g0007300' => 'sci', 'Sc11g0000950' => 'sci', 'Sc14g0008750' => 'sci', 'Sc18g0000420' => 'sci', 'Sed0006754' => 'sed', 'Sed0008741' => 'sed', 'Sed0017172' => 'sed', 'Sed0018925' => 'sed', 'Sed0023326' => 'sed', 'Sed0025909' => 'sed', 'SEGI_05333' => 'sgi', 'SEGI_10362' => 'sgi', 'SEGI_13380' => 'sgi', 'SEGI_24306' => 'sgi', 'SEGI_29077' => 'sgi', 'SEGI_29095' => 'sgi', 'SEGI_36534' => 'sgi', 'SEGI_37506' => 'sgi', 'SEGI_38321' => 'sgi', 'SGA_v2.0_scaffold307G48031' => 'sas', 'SGA_v2.0_scaffold47G17507' => 'sas', 'SGA_v2.0_scaffold63G21736' => 'sas', 'SGA_v2.0_scaffold87G27070' => 'sas', 'SHI17794' => 'shi', 'SHI28851' => 'shi', 'SMO165G0155' => 'smo', 'SMO340G0217' => 'smo', 'SMO367G1210' => 'smo', 'Solyc02g093430.3' => 'sly', 'Solyc05g013580.4' => 'sly', 'Solyc07g008030.3' => 'sly', 'Solyc12g035470.2' => 'sly', 'Sopen02g038020' => 'spe', 'Sopen05g008490' => 'spe', 'Sopen07g003910' => 'spe', 'Sopen12g015240' => 'spe', 'Sp1g11550' => 'spa', 'Sp2g16710' => 'spa', 'Sp3g00430' => 'spa', 'Sp3g26780' => 'spa', 'Sp5g22900' => 'spa', 'Sp6g29530' => 'spa', 'TAR371G0794' => 'tar', 'TAR374G0164' => 'tar', 'TAR622G0165' => 'tar', 'TAR626G0929' => 'tar', 'TAR629G2155' => 'tar', 'THA.LOC104805282' => 'tha', 'THA.LOC104805363' => 'tha', 'THA.LOC104808968' => 'tha', 'THA.LOC104821093' => 'tha', 'THA.LOC104823953' => 'tha', 'THA.LOC104825562' => 'tha', 'THA.LOC104825665' => 'tha', 'Thecc.02G261400' => 'tca', 'Thecc.04G019200' => 'tca', 'Thecc.09G130400' => 'tca', 'Thhalv10004374m.g' => 'esa', 'Thhalv10007850m.g' => 'esa', 'Thhalv10013782m.g' => 'esa', 'Thhalv10018686m.g' => 'esa', 'Thhalv10020899m.g' => 'esa', 'Thhalv10022755m.g' => 'esa', 'TPR.G23851' => 'tpr', 'TPR.G26500' => 'tpr', 'TPR.G27267' => 'tpr', 'TPR.G32001' => 'tpr', 'TPR.G6251' => 'tpr', 'TPR.G8167' => 'tpr', 'TWI12G1330' => 'twi', 'TWI18G1239' => 'twi', 'TWI34G0979' => 'twi', 'TWI36G0670' => 'twi', 'TWI36G0707' => 'twi', 'TWI56G0233' => 'twi', 'TWI75G1809' => 'twi', 'unitig_21.g20874' => 'ugi', 'unitig_26.g10343' => 'ugi', 'unitig_46.g18392' => 'ugi', 'unitig_52.g17178' => 'ugi', 'unitig_8.g2934' => 'ugi', 'vmacro01122' => 'vma', 'vmacro05875' => 'vma', 'vmacro06147' => 'vma', 'vmacro16191' => 'vma', 'vmacro18293' => 'vma', 'VMungo0251G3707' => 'vmu', 'VMungo0464G1521' => 'vmu', 'VMungo1215G0205' => 'vmu', 'VMungo1383G2484' => 'vmu', 'Zm00001eb079610' => 'zma', 'Zm00001eb135990' => 'zma', 'Zm00001eb183710' => 'zma', 'Zm00001eb246020' => 'zma' ) $gf_id = 'HOM05D001124' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001124' ) $data_identifier = 'HOM05D001124' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 6, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 7, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 21, 'bol' => (int) 10, 'bra' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 6, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 9, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 21, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 8, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 10, 'lsa' => (int) 8, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 8, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 9, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb246020' $species_info = array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ) $local_species = 'ugi' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001124', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '548', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02520' => 'bna', 'A03p06630' => 'bna', 'A05p44460' => 'bna', 'A06p08710' => 'bna', 'A06p41090' => 'bna', 'A07p32320' => 'bna', 'A08p32520' => 'bna', 'A09p10360' => 'bna', 'A10p24080' => 'bna', 'Aa31LG11G15250' => 'aar', 'Aa31LG1G1800' => 'aar', 'Aa31LG2G5120' => 'aar', 'Aa31LG2G6070' => 'aar', 'Aa31LG5G10770' => 'aar', 'Aa31sc61G90' => 'aar', 'Actinidia01352' => 'ach', 'Actinidia05983' => 'ach', 'Actinidia08133' => 'ach', 'Actinidia15101' => 'ach', 'Actinidia26379' => 'ach', 'Actinidia35778' => 'ach', 'Actinidia36123' => 'ach', 'Actinidia37436' => 'ach', 'Actinidia38730' => 'ach', 'Ah.02g128210' => 'amhyb', 'Ah.03g132990' => 'amhyb', 'Ah.14g079410' => 'amhyb', 'AL1G24640' => 'aly', 'AL2G26680' => 'aly', 'AL3G10530' => 'aly', 'AL3G45230' => 'aly', 'AL5G15230' => 'aly', 'AL5G16960' => 'aly', 'AL6G25210' => 'aly', 'Aqoxy2G00441' => 'aox', 'Aqoxy3G01236' => 'aox', 'Aqoxy5G03746' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3RQ047' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C7GMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9C8JER' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MBL6KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YXCZ83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZANX40' => 'arhy', 'AT1G12990' => 'ath', 'AT1G67880' => 'ath', 'AT2G13290' => 'ath', 'AT3G01620' => 'ath', 'AT3G26445' => 'ath', 'AT3G27540' => 'ath', 'AT5G14480' => 'ath', 'ATR0824G026' => 'atr', 'ATR1098G019' => 'atr', 'Atru.chr11.2145' => 'acertr', 'Atru.chr2.3636' => 'acertr', 'Atru.chr2.3644' => 'acertr', 'Atru.chr6.2422' => 'acertr', 'Atru.chr7.1112' => 'acertr', 'AUR62005469' => 'cqu', 'AUR62011166' => 'cqu', 'AUR62013319' => 'cqu', 'AUR62024273' => 'cqu', 'AUR62028420' => 'cqu', 'AUR62041942' => 'cqu', 'BcaB01g04969' => 'bca', 'BcaB01g06371' => 'bca', 'BcaB02g11494' => 'bca', 'BcaB03g15382' => 'bca', 'BcaB08g36994' => 'bca', 'BcaC03g13477' => 'bca', 'BcaC03g13478' => 'bca', 'BcaC03g13480' => 'bca', 'BcaC03g13481' => 'bca', 'BcaC03g13486' => 'bca', 'BcaC04g19031' => 'bca', 'BcaC04g23085' => 'bca', 'BcaC05g25094' => 'bca', 'BcaC05g25096' => 'bca', 'BcaC05g25138' => 'bca', 'BcaC05g30416' => 'bca', 'BcaC05g30455' => 'bca', 'BcaC06g30979' => 'bca', 'BcaC06g33805' => 'bca', 'BcaC08g46021' => 'bca', 'BcaNung03154' => 'bca', 'BolC2t06623H' => 'bol', 'BolC2t06632H' => 'bol', 'BolC2t06635H' => 'bol', 'BolC2t06638H' => 'bol', 'BolC3t13266H' => 'bol', 'BolC5t29776H' => 'bol', 'BolC6t38912H' => 'bol', 'BolC7t44183H' => 'bol', 'BolC9t54123H' => 'bol', 'BolC9t59107H' => 'bol', 'BraA02t05221Z' => 'bra', 'BraA03t09996Z' => 'bra', 'BraA05t23210Z' => 'bra', 'BraA06t24068Z' => 'bra', 'BraA06t27032Z' => 'bra', 'BraA08t35176Z' => 'bra', 'BraA09t36680Z' => 'bra', 'BraA10t44471Z' => 'bra', 'C02p06760' => 'bna', 'C02p06890' => 'bna', 'C02p07010' => 'bna', 'C03p07660' => 'bna', 'C05p10300' => 'bna', 'C06p38150' => 'bna', 'C07p36650' => 'bna', 'C08p15770' => 'bna', 'C09p12300' => 'bna', 'C09p62700' => 'bna', 'C09p75040' => 'bna', 'CAN.G13.1' => 'can', 'CAN.G138.4' => 'can', 'CAN.G44.6' => 'can', 'CAN.G473.19' => 'can', 'CANSAT01G0835' => 'cansat', 'CANSAT11G0246' => 'cansat', 'CANSAT11G1766' => 'cansat', 'CANSAT64G1954' => 'cansat', 'CARHR013330' => 'chi', 'CARHR060530' => 'chi', 'CARHR075300' => 'chi', 'CARHR105120' => 'chi', 'CARHR148910' => 'chi', 'CARHR198830' => 'chi', 'Carub.0001s1275' => 'cru', 'Carub.0002s1437' => 'cru', 'Carub.0003s0044' => 'cru', 'Carub.0003s2787' => 'cru', 'Carub.0005s0597' => 'cru', 'Carub.0006s1266' => 'cru', 'Ca_06935_v3' => 'car', 'Ca_13559_v3' => 'car', 'Ca_16941_v3' => 'car', 'Ca_16960_v3' => 'car', 'Ca_17775_v3' => 'car', 'Ca_30464_v3' => 'car', 'Cc06_g08160' => 'ccan', 'Cc07_g01520' => 'ccan', 'Cc11_g15810' => 'ccan', 'CDE02G2840' => 'cde', 'CDE03G0093' => 'cde', 'CDE04G2127' => 'cde', 'CDE07G1857' => 'cde', 'CDE09G1246' => 'cde', 'Cfa003412' => 'cfa', 'Cfa007341' => 'cfa', 'Cfa009220' => 'cfa', 'Ciclev10008737m.g' => 'ccl', 'Ciclev10015565m.g' => 'ccl', 'Ciclev10031761m.g' => 'ccl', 'CiPaw.03G045300' => 'cil', 'CiPaw.03G247200' => 'cil', 'CiPaw.04G029500' => 'cil', 'CiPaw.04G174000' => 'cil', 'CiPaw.05G181200' => 'cil', 'CiPaw.06G067100' => 'cil', 'ClCG05G025800' => 'cla', 'ClCG06G011400' => 'cla', 'ClCG09G019360' => 'cla', 'COL.COLO4_04827' => 'col', 'COL.COLO4_29170' => 'col', 'COL.COLO4_35131' => 'col', 'COL.COLO4_35132' => 'col', 'Cpa.g.sc33.32' => 'cpa', 'Cpa.g.sc46.29' => 'cpa', 'Cpa.g.sc796.1' => 'cpa', 'CsaV3_1G030420' => 'csa', 'CsaV3_5G027050' => 'csa', 'CsaV3_5G031040' => 'csa', 'CsaV3_UNG023130' => 'csa', 'CSS0007726' => 'camsi', 'CSS0016433' => 'camsi', 'CSS0017656' => 'camsi', 'CSS0025364' => 'camsi', 'CSS0027582' => 'camsi', 'CSS0047288' => 'camsi', 'CSS0049950' => 'camsi', 'DCAR_003843' => 'dca', 'DCAR_007052' => 'dca', 'DCAR_020884' => 'dca', 'DCAR_021730' => 'dca', 'DCAR_024423' => 'dca', 'DCAR_026509' => 'dca', 'DCAR_031158' => 'dca', 'Dinv14728' => 'din', 'Dinv15219' => 'din', 'Dinv25728' => 'din', 'Dinv33428' => 'din', 'Dinv36489' => 'din', 'Dinv41486' => 'din', 'Duzib147G0469' => 'dzi', 'Duzib168G0060' => 'dzi', 'Duzib187G1215' => 'dzi', 'Duzib248G0692' => 'dzi', 'Duzib251G0767' => 'dzi', 'Duzib264G0446' => 'dzi', 'Duzib268G0691' => 'dzi', 'ECA232G4767' => 'eca', 'ECA233G2838' => 'eca', 'ECA234G0391' => 'eca', 'ECA234G0857' => 'eca', 'ECA236G1593' => 'eca', 'ECA238G0565' => 'eca', 'ECA246G1027' => 'eca', 'ECA246G3223' => 'eca', 'ECA246G3470' => 'eca', 'EL10Ac6g13829' => 'bvu', 'EL10Ac6g14093' => 'bvu', 'EL10Ac8g18707' => 'bvu', 'Eucgr.C01369' => 'egr', 'Eucgr.H02492' => 'egr', 'Eucgr.I01733' => 'egr', 'Eucgr.J02255' => 'egr', 'Eucgr.J02257' => 'egr', 'Eucgr.J02258' => 'egr', 'FAN02G1601' => 'fan', 'FAN03G1586' => 'fan', 'FAN03G2986' => 'fan', 'FAN05G4837' => 'fan', 'FAN06G0146' => 'fan', 'FAN07G0858' => 'fan', 'FAN09G3179' => 'fan', 'FAN10G0669' => 'fan', 'FAN12G2358' => 'fan', 'FAN14G4198' => 'fan', 'FAN14G5112' => 'fan', 'FAN17G0342' => 'fan', 'FAN19G0342' => 'fan', 'FAN19G0962' => 'fan', 'FAN19G1101' => 'fan', 'FAN19G1872' => 'fan', 'FAN22G0356' => 'fan', 'FAN23G0744' => 'fan', 'FAN23G1914' => 'fan', 'FAN26G0032' => 'fan', 'FAN28G0625' => 'fan', 'FvH4_1g02710' => 'fve', 'FvH4_1g02720' => 'fve', 'FvH4_4g25670' => 'fve', 'FvH4_6g51700' => 'fve', 'FvH4_7g20170' => 'fve', 'Glyma.05G175000' => 'gma', 'Glyma.08G132300' => 'gma', 'Glyma.11G243000' => 'gma', 'Glyma.13G158900' => 'gma', 'Glyma.17G112400' => 'gma', 'Glyma.18G014100' => 'gma', 'Glyma.19G003100' => 'gma', 'Glyma.19G056500' => 'gma', 'Gohir.A01G158900' => 'ghi', 'Gohir.A05G312600' => 'ghi', 'Gohir.A05G354900' => 'ghi', 'Gohir.A07G037200' => 'ghi', 'Gohir.A09G030000' => 'ghi', 'Gohir.A12G145200' => 'ghi', 'Gohir.D01G151500' => 'ghi', 'Gohir.D04G058300' => 'ghi', 'Gohir.D05G314100' => 'ghi', 'Gohir.D07G041400' => 'ghi', 'Gohir.D09G029700' => 'ghi', 'Gohir.D12G149700' => 'ghi', 'Gorai.001G043800' => 'gra', 'Gorai.002G187800' => 'gra', 'Gorai.006G034700' => 'gra', 'Gorai.008G161200' => 'gra', 'Gorai.009G335700' => 'gra', 'Gorai.012G065000' => 'gra', 'GSVIVG01000535001' => 'vvi', 'GSVIVG01015572001' => 'vvi', 'GSVIVG01032386001' => 'vvi', 'HanXRQChr05g0138531' => 'han', 'HanXRQChr06g0174391' => 'han', 'HanXRQChr07g0199021' => 'han', 'HanXRQChr08g0208211' => 'han', 'HanXRQChr09g0255471' => 'han', 'HanXRQChr10g0315791' => 'han', 'HanXRQChr12g0371991' => 'han', 'HanXRQChr15g0475251' => 'han', 'HanXRQChr17g0540001' => 'han', 'HanXRQChr17g0548631' => 'han', 'HanXRQChr17g0569561' => 'han', 'Haze_12256' => 'cav', 'Haze_14756' => 'cav', 'Haze_25528' => 'cav', 'Hma1.2p1_0079F.1_g041020' => 'hma', 'Hma1.2p1_0818F.1_g223260' => 'hma', 'Hma1.2p1_1747F.1_g300530' => 'hma', 'HPP92_004607' => 'vpl', 'HPP92_004608' => 'vpl', 'HPP92_006181' => 'vpl', 'HPP92_012192' => 'vpl', 'HPP92_015680' => 'vpl', 'HPP92_020249' => 'vpl', 'HPP92_021376' => 'vpl', 'HPP92_024275' => 'vpl', 'Hund06031' => 'sun', 'Hund25391' => 'sun', 'Lalb_Chr07g0185371' => 'lal', 'Lalb_Chr07g0185381' => 'lal', 'Lalb_Chr12g0204011' => 'lal', 'Lalb_Chr13g0301671' => 'lal', 'Lalb_Chr14g0362851' => 'lal', 'Lalb_Chr24g0403581' => 'lal', 'Lj1g0000233' => 'lja', 'Lj2g0018120' => 'lja', 'Lj3C621T0' => 'lonja', 'Lj3P1059T14' => 'lonja', 'Lj3P611T9' => 'lonja', 'Lj3P614T13' => 'lonja', 'Lj3P615T5' => 'lonja', 'Lj4g0012315' => 'lja', 'Lj4g0026182' => 'lja', 'Lj6P813T16' => 'lonja', 'Lj7C427T7' => 'lonja', 'Lj7C427T8' => 'lonja', 'Lj7P600T41' => 'lonja', 'Lju41C42G17' => 'lonja', 'Lsat_1_v5_gn_0_47300' => 'lsa', 'Lsat_1_v5_gn_2_91280' => 'lsa', 'Lsat_1_v5_gn_3_30561' => 'lsa', 'Lsat_1_v5_gn_4_184321' => 'lsa', 'Lsat_1_v5_gn_4_4041' => 'lsa', 'Lsat_1_v5_gn_5_92000' => 'lsa', 'Lsat_1_v5_gn_8_152940' => 'lsa', 'Lsat_1_v5_gn_8_62401' => 'lsa', 'Manes.06G055900' => 'mes', 'Manes.12G022200' => 'mes', 'Manes.13G023300' => 'mes', 'Manes.14G115000' => 'mes', 'Manes.15G151700' => 'mes', 'Manes.17G111300' => 'mes', 'Mapoly0226s0009' => 'mpo', 'MBI02_g25363_MAGBIO' => 'mbi', 'MBI06_g00027_MAGBIO' => 'mbi', 'MBI10_g13034_MAGBIO' => 'mbi', 'MD09G1023400' => 'mdo', 'MD13G1100100' => 'mdo', 'MD15G1169200' => 'mdo', 'MD16G1101100' => 'mdo', 'MD17G1022900' => 'mdo', 'Medtr3g096150' => 'mtr', 'Medtr4g115070' => 'mtr', 'Medtr7g033325' => 'mtr', 'Medtr8g089840' => 'mtr', 'MELO3C010319.2' => 'cme', 'MELO3C011944.2' => 'cme', 'MELO3C021589.2' => 'cme', 'Migut.E00207' => 'egut', 'Migut.H00067' => 'egut', 'Migut.K00433' => 'egut', 'Migut.K00606' => 'egut', 'Migut.K01410' => 'egut', 'MSTRG.13347' => 'ama', 'MSTRG.24045' => 'ama', 'MSTRG.2428' => 'ama', 'MSTRG.26410' => 'ama', 'MSTRG.3139' => 'ama', 'MSTRG.3286' => 'ama', 'MSTRG.563' => 'ama', 'MSTRG.7941' => 'ama', 'Nitab4.5_0000028g0060' => 'nta', 'Nitab4.5_0000065g0260' => 'nta', 'Nitab4.5_0000112g0060' => 'nta', 'Nitab4.5_0000489g0120' => 'nta', 'Nitab4.5_0001776g0050' => 'nta', 'Nitab4.5_0001854g0010' => 'nta', 'Nitab4.5_0001860g0020' => 'nta', 'Nitab4.5_0004352g0010' => 'nta', 'Nitab4.5_0008716g0020' => 'nta', 'Nitab4.5_0008922g0010' => 'nta', 'Nn3g16693' => 'nnu', 'Nn4g22596' => 'nnu', 'Nn7g37639' => 'nnu', 'Oeu001701.1' => 'oeu', 'Oeu018149.1' => 'oeu', 'Oeu026220.1' => 'oeu', 'Oeu038635.1' => 'oeu', 'Oeu049176.1' => 'oeu', 'Oeu056706.1' => 'oeu', 'Oeu056937.1' => 'oeu', 'Oeu057540.1' => 'oeu', 'Os02g0594900' => 'osa', 'Os02g0595100' => 'osa', 'Os04g0477500' => 'osa', 'Os12g0611900' => 'osa', 'Peaxi162Scf00076g00020' => 'pax', 'Peaxi162Scf00128g00217' => 'pax', 'Peaxi162Scf00129g01640' => 'pax', 'Peaxi162Scf00669g00007' => 'pax', 'Peaxi162Scf00700g00421' => 'pax', 'Peaxi162Scf00801g00038' => 'pax', 'Peaxi162Scf00891g00025' => 'pax', 'PGR083G0909' => 'pgr', 'PGR119G1005' => 'pgr', 'PGR142G2236' => 'pgr', 'PGR142G3388' => 'pgr', 'PGSC0003DMG400004514' => 'stu', 'PGSC0003DMG400012635' => 'stu', 'PGSC0003DMG400015730' => 'stu', 'PGSC0003DMG400018611' => 'stu', 'PGSC0003DMG400030897' => 'stu', 'Phvul.001G254800' => 'pvu', 'Phvul.002G260100' => 'pvu', 'Phvul.003G167600' => 'pvu', 'Phvul.004G005100' => 'pvu', 'Potri.001G343600' => 'ptr', 'Potri.006G066700' => 'ptr', 'Potri.008G186000' => 'ptr', 'Potri.010G046900' => 'ptr', 'Potri.018G127900' => 'ptr', 'Pp3c20_17750' => 'ppa', 'Pp3c24_4380' => 'ppa', 'Prupe.1G245800' => 'ppe', 'Prupe.3G293400' => 'ppe', 'Prupe.7G247400' => 'ppe', 'Psat0s145g0120' => 'psa', 'Psat0s595g0040' => 'psa', 'Psat0s595g0120' => 'psa', 'Psat3g175040' => 'psa', 'Psat7g058120' => 'psa', 'PSO017G0428' => 'pso', 'PSO063G7510' => 'pso', 'PSO067G0046' => 'pso', 'PSO478G1073' => 'pso', 'PSO675G3677' => 'pso', 'PSO675G6558' => 'pso', 'PSO675G7520' => 'pso', 'PSO675G8959' => 'pso', 'QL02p074089' => 'qlo', 'QL02p089614' => 'qlo', 'QL03p057736' => 'qlo', 'RcHm_v2.0_Chr1g0364131' => 'rch', 'RcHm_v2.0_Chr2g0087801' => 'rch', 'RcHm_v2.0_Chr2g0087821' => 'rch', 'RcHm_v2.0_Chr2g0173231' => 'rch', 'RcHm_v2.0_Chr4g0433111' => 'rch', 'Rhsim03G0250300' => 'rsi', 'Rhsim08G0048400' => 'rsi', 'Rhsim10G0014800' => 'rsi', 'Rhsim12G0040100' => 'rsi', 'Rhsim12G0109700' => 'rsi', 'Sabra06G0049600' => 'sbr', 'Sabra08G0141000' => 'sbr', 'Sabra10G0021400' => 'sbr', 'Sabra16G0222900' => 'sbr', 'Sabra18G0108600' => 'sbr', 'SalBow1G0433' => 'sbo', 'SalBow1G2038' => 'sbo', 'SalBow1G5003' => 'sbo', 'SalBow7G1197' => 'sbo', 'SalBow8G3506' => 'sbo', 'Sc03g0007300' => 'sci', 'Sc11g0000950' => 'sci', 'Sc14g0008750' => 'sci', 'Sc18g0000420' => 'sci', 'Sed0006754' => 'sed', 'Sed0008741' => 'sed', 'Sed0017172' => 'sed', 'Sed0018925' => 'sed', 'Sed0023326' => 'sed', 'Sed0025909' => 'sed', 'SEGI_05333' => 'sgi', 'SEGI_10362' => 'sgi', 'SEGI_13380' => 'sgi', 'SEGI_24306' => 'sgi', 'SEGI_29077' => 'sgi', 'SEGI_29095' => 'sgi', 'SEGI_36534' => 'sgi', 'SEGI_37506' => 'sgi', 'SEGI_38321' => 'sgi', 'SGA_v2.0_scaffold307G48031' => 'sas', 'SGA_v2.0_scaffold47G17507' => 'sas', 'SGA_v2.0_scaffold63G21736' => 'sas', 'SGA_v2.0_scaffold87G27070' => 'sas', 'SHI17794' => 'shi', 'SHI28851' => 'shi', 'SMO165G0155' => 'smo', 'SMO340G0217' => 'smo', 'SMO367G1210' => 'smo', 'Solyc02g093430.3' => 'sly', 'Solyc05g013580.4' => 'sly', 'Solyc07g008030.3' => 'sly', 'Solyc12g035470.2' => 'sly', 'Sopen02g038020' => 'spe', 'Sopen05g008490' => 'spe', 'Sopen07g003910' => 'spe', 'Sopen12g015240' => 'spe', 'Sp1g11550' => 'spa', 'Sp2g16710' => 'spa', 'Sp3g00430' => 'spa', 'Sp3g26780' => 'spa', 'Sp5g22900' => 'spa', 'Sp6g29530' => 'spa', 'TAR371G0794' => 'tar', 'TAR374G0164' => 'tar', 'TAR622G0165' => 'tar', 'TAR626G0929' => 'tar', 'TAR629G2155' => 'tar', 'THA.LOC104805282' => 'tha', 'THA.LOC104805363' => 'tha', 'THA.LOC104808968' => 'tha', 'THA.LOC104821093' => 'tha', 'THA.LOC104823953' => 'tha', 'THA.LOC104825562' => 'tha', 'THA.LOC104825665' => 'tha', 'Thecc.02G261400' => 'tca', 'Thecc.04G019200' => 'tca', 'Thecc.09G130400' => 'tca', 'Thhalv10004374m.g' => 'esa', 'Thhalv10007850m.g' => 'esa', 'Thhalv10013782m.g' => 'esa', 'Thhalv10018686m.g' => 'esa', 'Thhalv10020899m.g' => 'esa', 'Thhalv10022755m.g' => 'esa', 'TPR.G23851' => 'tpr', 'TPR.G26500' => 'tpr', 'TPR.G27267' => 'tpr', 'TPR.G32001' => 'tpr', 'TPR.G6251' => 'tpr', 'TPR.G8167' => 'tpr', 'TWI12G1330' => 'twi', 'TWI18G1239' => 'twi', 'TWI34G0979' => 'twi', 'TWI36G0670' => 'twi', 'TWI36G0707' => 'twi', 'TWI56G0233' => 'twi', 'TWI75G1809' => 'twi', 'unitig_21.g20874' => 'ugi', 'unitig_26.g10343' => 'ugi', 'unitig_46.g18392' => 'ugi', 'unitig_52.g17178' => 'ugi', 'unitig_8.g2934' => 'ugi', 'vmacro01122' => 'vma', 'vmacro05875' => 'vma', 'vmacro06147' => 'vma', 'vmacro16191' => 'vma', 'vmacro18293' => 'vma', 'VMungo0251G3707' => 'vmu', 'VMungo0464G1521' => 'vmu', 'VMungo1215G0205' => 'vmu', 'VMungo1383G2484' => 'vmu', 'Zm00001eb079610' => 'zma', 'Zm00001eb135990' => 'zma', 'Zm00001eb183710' => 'zma', 'Zm00001eb246020' => 'zma' ), 'gf_id' => 'HOM05D001124', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001124' ), 'data_identifier' => 'HOM05D001124', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001124', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '548', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02520' => 'bna', 'A03p06630' => 'bna', 'A05p44460' => 'bna', 'A06p08710' => 'bna', 'A06p41090' => 'bna', 'A07p32320' => 'bna', 'A08p32520' => 'bna', 'A09p10360' => 'bna', 'A10p24080' => 'bna', 'Aa31LG11G15250' => 'aar', 'Aa31LG1G1800' => 'aar', 'Aa31LG2G5120' => 'aar', 'Aa31LG2G6070' => 'aar', 'Aa31LG5G10770' => 'aar', 'Aa31sc61G90' => 'aar', 'Actinidia01352' => 'ach', 'Actinidia05983' => 'ach', 'Actinidia08133' => 'ach', 'Actinidia15101' => 'ach', 'Actinidia26379' => 'ach', 'Actinidia35778' => 'ach', 'Actinidia36123' => 'ach', 'Actinidia37436' => 'ach', 'Actinidia38730' => 'ach', 'Ah.02g128210' => 'amhyb', 'Ah.03g132990' => 'amhyb', 'Ah.14g079410' => 'amhyb', 'AL1G24640' => 'aly', 'AL2G26680' => 'aly', 'AL3G10530' => 'aly', 'AL3G45230' => 'aly', 'AL5G15230' => 'aly', 'AL5G16960' => 'aly', 'AL6G25210' => 'aly', 'Aqoxy2G00441' => 'aox', 'Aqoxy3G01236' => 'aox', 'Aqoxy5G03746' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3RQ047' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C7GMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9C8JER' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MBL6KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YXCZ83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZANX40' => 'arhy', 'AT1G12990' => 'ath', 'AT1G67880' => 'ath', 'AT2G13290' => 'ath', 'AT3G01620' => 'ath', 'AT3G26445' => 'ath', 'AT3G27540' => 'ath', 'AT5G14480' => 'ath', 'ATR0824G026' => 'atr', 'ATR1098G019' => 'atr', 'Atru.chr11.2145' => 'acertr', 'Atru.chr2.3636' => 'acertr', 'Atru.chr2.3644' => 'acertr', 'Atru.chr6.2422' => 'acertr', 'Atru.chr7.1112' => 'acertr', 'AUR62005469' => 'cqu', 'AUR62011166' => 'cqu', 'AUR62013319' => 'cqu', 'AUR62024273' => 'cqu', 'AUR62028420' => 'cqu', 'AUR62041942' => 'cqu', 'BcaB01g04969' => 'bca', 'BcaB01g06371' => 'bca', 'BcaB02g11494' => 'bca', 'BcaB03g15382' => 'bca', 'BcaB08g36994' => 'bca', 'BcaC03g13477' => 'bca', 'BcaC03g13478' => 'bca', 'BcaC03g13480' => 'bca', 'BcaC03g13481' => 'bca', 'BcaC03g13486' => 'bca', 'BcaC04g19031' => 'bca', 'BcaC04g23085' => 'bca', 'BcaC05g25094' => 'bca', 'BcaC05g25096' => 'bca', 'BcaC05g25138' => 'bca', 'BcaC05g30416' => 'bca', 'BcaC05g30455' => 'bca', 'BcaC06g30979' => 'bca', 'BcaC06g33805' => 'bca', 'BcaC08g46021' => 'bca', 'BcaNung03154' => 'bca', 'BolC2t06623H' => 'bol', 'BolC2t06632H' => 'bol', 'BolC2t06635H' => 'bol', 'BolC2t06638H' => 'bol', 'BolC3t13266H' => 'bol', 'BolC5t29776H' => 'bol', 'BolC6t38912H' => 'bol', 'BolC7t44183H' => 'bol', 'BolC9t54123H' => 'bol', 'BolC9t59107H' => 'bol', 'BraA02t05221Z' => 'bra', 'BraA03t09996Z' => 'bra', 'BraA05t23210Z' => 'bra', 'BraA06t24068Z' => 'bra', 'BraA06t27032Z' => 'bra', 'BraA08t35176Z' => 'bra', 'BraA09t36680Z' => 'bra', 'BraA10t44471Z' => 'bra', 'C02p06760' => 'bna', 'C02p06890' => 'bna', 'C02p07010' => 'bna', 'C03p07660' => 'bna', 'C05p10300' => 'bna', 'C06p38150' => 'bna', 'C07p36650' => 'bna', 'C08p15770' => 'bna', 'C09p12300' => 'bna', 'C09p62700' => 'bna', 'C09p75040' => 'bna', 'CAN.G13.1' => 'can', 'CAN.G138.4' => 'can', 'CAN.G44.6' => 'can', 'CAN.G473.19' => 'can', 'CANSAT01G0835' => 'cansat', 'CANSAT11G0246' => 'cansat', 'CANSAT11G1766' => 'cansat', 'CANSAT64G1954' => 'cansat', 'CARHR013330' => 'chi', 'CARHR060530' => 'chi', 'CARHR075300' => 'chi', 'CARHR105120' => 'chi', 'CARHR148910' => 'chi', 'CARHR198830' => 'chi', 'Carub.0001s1275' => 'cru', 'Carub.0002s1437' => 'cru', 'Carub.0003s0044' => 'cru', 'Carub.0003s2787' => 'cru', 'Carub.0005s0597' => 'cru', 'Carub.0006s1266' => 'cru', 'Ca_06935_v3' => 'car', 'Ca_13559_v3' => 'car', 'Ca_16941_v3' => 'car', 'Ca_16960_v3' => 'car', 'Ca_17775_v3' => 'car', 'Ca_30464_v3' => 'car', 'Cc06_g08160' => 'ccan', 'Cc07_g01520' => 'ccan', 'Cc11_g15810' => 'ccan', 'CDE02G2840' => 'cde', 'CDE03G0093' => 'cde', 'CDE04G2127' => 'cde', 'CDE07G1857' => 'cde', 'CDE09G1246' => 'cde', 'Cfa003412' => 'cfa', 'Cfa007341' => 'cfa', 'Cfa009220' => 'cfa', 'Ciclev10008737m.g' => 'ccl', 'Ciclev10015565m.g' => 'ccl', 'Ciclev10031761m.g' => 'ccl', 'CiPaw.03G045300' => 'cil', 'CiPaw.03G247200' => 'cil', 'CiPaw.04G029500' => 'cil', 'CiPaw.04G174000' => 'cil', 'CiPaw.05G181200' => 'cil', 'CiPaw.06G067100' => 'cil', 'ClCG05G025800' => 'cla', 'ClCG06G011400' => 'cla', 'ClCG09G019360' => 'cla', 'COL.COLO4_04827' => 'col', 'COL.COLO4_29170' => 'col', 'COL.COLO4_35131' => 'col', 'COL.COLO4_35132' => 'col', 'Cpa.g.sc33.32' => 'cpa', 'Cpa.g.sc46.29' => 'cpa', 'Cpa.g.sc796.1' => 'cpa', 'CsaV3_1G030420' => 'csa', 'CsaV3_5G027050' => 'csa', 'CsaV3_5G031040' => 'csa', 'CsaV3_UNG023130' => 'csa', 'CSS0007726' => 'camsi', 'CSS0016433' => 'camsi', 'CSS0017656' => 'camsi', 'CSS0025364' => 'camsi', 'CSS0027582' => 'camsi', 'CSS0047288' => 'camsi', 'CSS0049950' => 'camsi', 'DCAR_003843' => 'dca', 'DCAR_007052' => 'dca', 'DCAR_020884' => 'dca', 'DCAR_021730' => 'dca', 'DCAR_024423' => 'dca', 'DCAR_026509' => 'dca', 'DCAR_031158' => 'dca', 'Dinv14728' => 'din', 'Dinv15219' => 'din', 'Dinv25728' => 'din', 'Dinv33428' => 'din', 'Dinv36489' => 'din', 'Dinv41486' => 'din', 'Duzib147G0469' => 'dzi', 'Duzib168G0060' => 'dzi', 'Duzib187G1215' => 'dzi', 'Duzib248G0692' => 'dzi', 'Duzib251G0767' => 'dzi', 'Duzib264G0446' => 'dzi', 'Duzib268G0691' => 'dzi', 'ECA232G4767' => 'eca', 'ECA233G2838' => 'eca', 'ECA234G0391' => 'eca', 'ECA234G0857' => 'eca', 'ECA236G1593' => 'eca', 'ECA238G0565' => 'eca', 'ECA246G1027' => 'eca', 'ECA246G3223' => 'eca', 'ECA246G3470' => 'eca', 'EL10Ac6g13829' => 'bvu', 'EL10Ac6g14093' => 'bvu', 'EL10Ac8g18707' => 'bvu', 'Eucgr.C01369' => 'egr', 'Eucgr.H02492' => 'egr', 'Eucgr.I01733' => 'egr', 'Eucgr.J02255' => 'egr', 'Eucgr.J02257' => 'egr', 'Eucgr.J02258' => 'egr', 'FAN02G1601' => 'fan', 'FAN03G1586' => 'fan', 'FAN03G2986' => 'fan', 'FAN05G4837' => 'fan', 'FAN06G0146' => 'fan', 'FAN07G0858' => 'fan', 'FAN09G3179' => 'fan', 'FAN10G0669' => 'fan', 'FAN12G2358' => 'fan', 'FAN14G4198' => 'fan', 'FAN14G5112' => 'fan', 'FAN17G0342' => 'fan', 'FAN19G0342' => 'fan', 'FAN19G0962' => 'fan', 'FAN19G1101' => 'fan', 'FAN19G1872' => 'fan', 'FAN22G0356' => 'fan', 'FAN23G0744' => 'fan', 'FAN23G1914' => 'fan', 'FAN26G0032' => 'fan', 'FAN28G0625' => 'fan', 'FvH4_1g02710' => 'fve', 'FvH4_1g02720' => 'fve', 'FvH4_4g25670' => 'fve', 'FvH4_6g51700' => 'fve', 'FvH4_7g20170' => 'fve', 'Glyma.05G175000' => 'gma', 'Glyma.08G132300' => 'gma', 'Glyma.11G243000' => 'gma', 'Glyma.13G158900' => 'gma', 'Glyma.17G112400' => 'gma', 'Glyma.18G014100' => 'gma', 'Glyma.19G003100' => 'gma', 'Glyma.19G056500' => 'gma', 'Gohir.A01G158900' => 'ghi', 'Gohir.A05G312600' => 'ghi', 'Gohir.A05G354900' => 'ghi', 'Gohir.A07G037200' => 'ghi', 'Gohir.A09G030000' => 'ghi', 'Gohir.A12G145200' => 'ghi', 'Gohir.D01G151500' => 'ghi', 'Gohir.D04G058300' => 'ghi', 'Gohir.D05G314100' => 'ghi', 'Gohir.D07G041400' => 'ghi', 'Gohir.D09G029700' => 'ghi', 'Gohir.D12G149700' => 'ghi', 'Gorai.001G043800' => 'gra', 'Gorai.002G187800' => 'gra', 'Gorai.006G034700' => 'gra', 'Gorai.008G161200' => 'gra', 'Gorai.009G335700' => 'gra', 'Gorai.012G065000' => 'gra', 'GSVIVG01000535001' => 'vvi', 'GSVIVG01015572001' => 'vvi', 'GSVIVG01032386001' => 'vvi', 'HanXRQChr05g0138531' => 'han', 'HanXRQChr06g0174391' => 'han', 'HanXRQChr07g0199021' => 'han', 'HanXRQChr08g0208211' => 'han', 'HanXRQChr09g0255471' => 'han', 'HanXRQChr10g0315791' => 'han', 'HanXRQChr12g0371991' => 'han', 'HanXRQChr15g0475251' => 'han', 'HanXRQChr17g0540001' => 'han', 'HanXRQChr17g0548631' => 'han', 'HanXRQChr17g0569561' => 'han', 'Haze_12256' => 'cav', 'Haze_14756' => 'cav', 'Haze_25528' => 'cav', 'Hma1.2p1_0079F.1_g041020' => 'hma', 'Hma1.2p1_0818F.1_g223260' => 'hma', 'Hma1.2p1_1747F.1_g300530' => 'hma', 'HPP92_004607' => 'vpl', 'HPP92_004608' => 'vpl', 'HPP92_006181' => 'vpl', 'HPP92_012192' => 'vpl', 'HPP92_015680' => 'vpl', 'HPP92_020249' => 'vpl', 'HPP92_021376' => 'vpl', 'HPP92_024275' => 'vpl', 'Hund06031' => 'sun', 'Hund25391' => 'sun', 'Lalb_Chr07g0185371' => 'lal', 'Lalb_Chr07g0185381' => 'lal', 'Lalb_Chr12g0204011' => 'lal', 'Lalb_Chr13g0301671' => 'lal', 'Lalb_Chr14g0362851' => 'lal', 'Lalb_Chr24g0403581' => 'lal', 'Lj1g0000233' => 'lja', 'Lj2g0018120' => 'lja', 'Lj3C621T0' => 'lonja', 'Lj3P1059T14' => 'lonja', 'Lj3P611T9' => 'lonja', 'Lj3P614T13' => 'lonja', 'Lj3P615T5' => 'lonja', 'Lj4g0012315' => 'lja', 'Lj4g0026182' => 'lja', 'Lj6P813T16' => 'lonja', 'Lj7C427T7' => 'lonja', 'Lj7C427T8' => 'lonja', 'Lj7P600T41' => 'lonja', 'Lju41C42G17' => 'lonja', 'Lsat_1_v5_gn_0_47300' => 'lsa', 'Lsat_1_v5_gn_2_91280' => 'lsa', 'Lsat_1_v5_gn_3_30561' => 'lsa', 'Lsat_1_v5_gn_4_184321' => 'lsa', 'Lsat_1_v5_gn_4_4041' => 'lsa', 'Lsat_1_v5_gn_5_92000' => 'lsa', 'Lsat_1_v5_gn_8_152940' => 'lsa', 'Lsat_1_v5_gn_8_62401' => 'lsa', 'Manes.06G055900' => 'mes', 'Manes.12G022200' => 'mes', 'Manes.13G023300' => 'mes', 'Manes.14G115000' => 'mes', 'Manes.15G151700' => 'mes', 'Manes.17G111300' => 'mes', 'Mapoly0226s0009' => 'mpo', 'MBI02_g25363_MAGBIO' => 'mbi', 'MBI06_g00027_MAGBIO' => 'mbi', 'MBI10_g13034_MAGBIO' => 'mbi', 'MD09G1023400' => 'mdo', 'MD13G1100100' => 'mdo', 'MD15G1169200' => 'mdo', 'MD16G1101100' => 'mdo', 'MD17G1022900' => 'mdo', 'Medtr3g096150' => 'mtr', 'Medtr4g115070' => 'mtr', 'Medtr7g033325' => 'mtr', 'Medtr8g089840' => 'mtr', 'MELO3C010319.2' => 'cme', 'MELO3C011944.2' => 'cme', 'MELO3C021589.2' => 'cme', 'Migut.E00207' => 'egut', 'Migut.H00067' => 'egut', 'Migut.K00433' => 'egut', 'Migut.K00606' => 'egut', 'Migut.K01410' => 'egut', 'MSTRG.13347' => 'ama', 'MSTRG.24045' => 'ama', 'MSTRG.2428' => 'ama', 'MSTRG.26410' => 'ama', 'MSTRG.3139' => 'ama', 'MSTRG.3286' => 'ama', 'MSTRG.563' => 'ama', 'MSTRG.7941' => 'ama', 'Nitab4.5_0000028g0060' => 'nta', 'Nitab4.5_0000065g0260' => 'nta', 'Nitab4.5_0000112g0060' => 'nta', 'Nitab4.5_0000489g0120' => 'nta', 'Nitab4.5_0001776g0050' => 'nta', 'Nitab4.5_0001854g0010' => 'nta', 'Nitab4.5_0001860g0020' => 'nta', 'Nitab4.5_0004352g0010' => 'nta', 'Nitab4.5_0008716g0020' => 'nta', 'Nitab4.5_0008922g0010' => 'nta', 'Nn3g16693' => 'nnu', 'Nn4g22596' => 'nnu', 'Nn7g37639' => 'nnu', 'Oeu001701.1' => 'oeu', 'Oeu018149.1' => 'oeu', 'Oeu026220.1' => 'oeu', 'Oeu038635.1' => 'oeu', 'Oeu049176.1' => 'oeu', 'Oeu056706.1' => 'oeu', 'Oeu056937.1' => 'oeu', 'Oeu057540.1' => 'oeu', 'Os02g0594900' => 'osa', 'Os02g0595100' => 'osa', 'Os04g0477500' => 'osa', 'Os12g0611900' => 'osa', 'Peaxi162Scf00076g00020' => 'pax', 'Peaxi162Scf00128g00217' => 'pax', 'Peaxi162Scf00129g01640' => 'pax', 'Peaxi162Scf00669g00007' => 'pax', 'Peaxi162Scf00700g00421' => 'pax', 'Peaxi162Scf00801g00038' => 'pax', 'Peaxi162Scf00891g00025' => 'pax', 'PGR083G0909' => 'pgr', 'PGR119G1005' => 'pgr', 'PGR142G2236' => 'pgr', 'PGR142G3388' => 'pgr', 'PGSC0003DMG400004514' => 'stu', 'PGSC0003DMG400012635' => 'stu', 'PGSC0003DMG400015730' => 'stu', 'PGSC0003DMG400018611' => 'stu', 'PGSC0003DMG400030897' => 'stu', 'Phvul.001G254800' => 'pvu', 'Phvul.002G260100' => 'pvu', 'Phvul.003G167600' => 'pvu', 'Phvul.004G005100' => 'pvu', 'Potri.001G343600' => 'ptr', 'Potri.006G066700' => 'ptr', 'Potri.008G186000' => 'ptr', 'Potri.010G046900' => 'ptr', 'Potri.018G127900' => 'ptr', 'Pp3c20_17750' => 'ppa', 'Pp3c24_4380' => 'ppa', 'Prupe.1G245800' => 'ppe', 'Prupe.3G293400' => 'ppe', 'Prupe.7G247400' => 'ppe', 'Psat0s145g0120' => 'psa', 'Psat0s595g0040' => 'psa', 'Psat0s595g0120' => 'psa', 'Psat3g175040' => 'psa', 'Psat7g058120' => 'psa', 'PSO017G0428' => 'pso', 'PSO063G7510' => 'pso', 'PSO067G0046' => 'pso', 'PSO478G1073' => 'pso', 'PSO675G3677' => 'pso', 'PSO675G6558' => 'pso', 'PSO675G7520' => 'pso', 'PSO675G8959' => 'pso', 'QL02p074089' => 'qlo', 'QL02p089614' => 'qlo', 'QL03p057736' => 'qlo', 'RcHm_v2.0_Chr1g0364131' => 'rch', 'RcHm_v2.0_Chr2g0087801' => 'rch', 'RcHm_v2.0_Chr2g0087821' => 'rch', 'RcHm_v2.0_Chr2g0173231' => 'rch', 'RcHm_v2.0_Chr4g0433111' => 'rch', 'Rhsim03G0250300' => 'rsi', 'Rhsim08G0048400' => 'rsi', 'Rhsim10G0014800' => 'rsi', 'Rhsim12G0040100' => 'rsi', 'Rhsim12G0109700' => 'rsi', 'Sabra06G0049600' => 'sbr', 'Sabra08G0141000' => 'sbr', 'Sabra10G0021400' => 'sbr', 'Sabra16G0222900' => 'sbr', 'Sabra18G0108600' => 'sbr', 'SalBow1G0433' => 'sbo', 'SalBow1G2038' => 'sbo', 'SalBow1G5003' => 'sbo', 'SalBow7G1197' => 'sbo', 'SalBow8G3506' => 'sbo', 'Sc03g0007300' => 'sci', 'Sc11g0000950' => 'sci', 'Sc14g0008750' => 'sci', 'Sc18g0000420' => 'sci', 'Sed0006754' => 'sed', 'Sed0008741' => 'sed', 'Sed0017172' => 'sed', 'Sed0018925' => 'sed', 'Sed0023326' => 'sed', 'Sed0025909' => 'sed', 'SEGI_05333' => 'sgi', 'SEGI_10362' => 'sgi', 'SEGI_13380' => 'sgi', 'SEGI_24306' => 'sgi', 'SEGI_29077' => 'sgi', 'SEGI_29095' => 'sgi', 'SEGI_36534' => 'sgi', 'SEGI_37506' => 'sgi', 'SEGI_38321' => 'sgi', 'SGA_v2.0_scaffold307G48031' => 'sas', 'SGA_v2.0_scaffold47G17507' => 'sas', 'SGA_v2.0_scaffold63G21736' => 'sas', 'SGA_v2.0_scaffold87G27070' => 'sas', 'SHI17794' => 'shi', 'SHI28851' => 'shi', 'SMO165G0155' => 'smo', 'SMO340G0217' => 'smo', 'SMO367G1210' => 'smo', 'Solyc02g093430.3' => 'sly', 'Solyc05g013580.4' => 'sly', 'Solyc07g008030.3' => 'sly', 'Solyc12g035470.2' => 'sly', 'Sopen02g038020' => 'spe', 'Sopen05g008490' => 'spe', 'Sopen07g003910' => 'spe', 'Sopen12g015240' => 'spe', 'Sp1g11550' => 'spa', 'Sp2g16710' => 'spa', 'Sp3g00430' => 'spa', 'Sp3g26780' => 'spa', 'Sp5g22900' => 'spa', 'Sp6g29530' => 'spa', 'TAR371G0794' => 'tar', 'TAR374G0164' => 'tar', 'TAR622G0165' => 'tar', 'TAR626G0929' => 'tar', 'TAR629G2155' => 'tar', 'THA.LOC104805282' => 'tha', 'THA.LOC104805363' => 'tha', 'THA.LOC104808968' => 'tha', 'THA.LOC104821093' => 'tha', 'THA.LOC104823953' => 'tha', 'THA.LOC104825562' => 'tha', 'THA.LOC104825665' => 'tha', 'Thecc.02G261400' => 'tca', 'Thecc.04G019200' => 'tca', 'Thecc.09G130400' => 'tca', 'Thhalv10004374m.g' => 'esa', 'Thhalv10007850m.g' => 'esa', 'Thhalv10013782m.g' => 'esa', 'Thhalv10018686m.g' => 'esa', 'Thhalv10020899m.g' => 'esa', 'Thhalv10022755m.g' => 'esa', 'TPR.G23851' => 'tpr', 'TPR.G26500' => 'tpr', 'TPR.G27267' => 'tpr', 'TPR.G32001' => 'tpr', 'TPR.G6251' => 'tpr', 'TPR.G8167' => 'tpr', 'TWI12G1330' => 'twi', 'TWI18G1239' => 'twi', 'TWI34G0979' => 'twi', 'TWI36G0670' => 'twi', 'TWI36G0707' => 'twi', 'TWI56G0233' => 'twi', 'TWI75G1809' => 'twi', 'unitig_21.g20874' => 'ugi', 'unitig_26.g10343' => 'ugi', 'unitig_46.g18392' => 'ugi', 'unitig_52.g17178' => 'ugi', 'unitig_8.g2934' => 'ugi', 'vmacro01122' => 'vma', 'vmacro05875' => 'vma', 'vmacro06147' => 'vma', 'vmacro16191' => 'vma', 'vmacro18293' => 'vma', 'VMungo0251G3707' => 'vmu', 'VMungo0464G1521' => 'vmu', 'VMungo1215G0205' => 'vmu', 'VMungo1383G2484' => 'vmu', 'Zm00001eb079610' => 'zma', 'Zm00001eb135990' => 'zma', 'Zm00001eb183710' => 'zma', 'Zm00001eb246020' => 'zma' ) $gf_id = 'HOM05D001124' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001124' ) $data_identifier = 'HOM05D001124' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 6, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 7, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 21, 'bol' => (int) 10, 'bra' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 6, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 9, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 21, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 8, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 10, 'lsa' => (int) 8, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 8, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 9, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb246020' $species_info = array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ) $local_species = 'ugi' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001124', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '548', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02520' => 'bna', 'A03p06630' => 'bna', 'A05p44460' => 'bna', 'A06p08710' => 'bna', 'A06p41090' => 'bna', 'A07p32320' => 'bna', 'A08p32520' => 'bna', 'A09p10360' => 'bna', 'A10p24080' => 'bna', 'Aa31LG11G15250' => 'aar', 'Aa31LG1G1800' => 'aar', 'Aa31LG2G5120' => 'aar', 'Aa31LG2G6070' => 'aar', 'Aa31LG5G10770' => 'aar', 'Aa31sc61G90' => 'aar', 'Actinidia01352' => 'ach', 'Actinidia05983' => 'ach', 'Actinidia08133' => 'ach', 'Actinidia15101' => 'ach', 'Actinidia26379' => 'ach', 'Actinidia35778' => 'ach', 'Actinidia36123' => 'ach', 'Actinidia37436' => 'ach', 'Actinidia38730' => 'ach', 'Ah.02g128210' => 'amhyb', 'Ah.03g132990' => 'amhyb', 'Ah.14g079410' => 'amhyb', 'AL1G24640' => 'aly', 'AL2G26680' => 'aly', 'AL3G10530' => 'aly', 'AL3G45230' => 'aly', 'AL5G15230' => 'aly', 'AL5G16960' => 'aly', 'AL6G25210' => 'aly', 'Aqoxy2G00441' => 'aox', 'Aqoxy3G01236' => 'aox', 'Aqoxy5G03746' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3RQ047' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C7GMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9C8JER' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MBL6KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YXCZ83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZANX40' => 'arhy', 'AT1G12990' => 'ath', 'AT1G67880' => 'ath', 'AT2G13290' => 'ath', 'AT3G01620' => 'ath', 'AT3G26445' => 'ath', 'AT3G27540' => 'ath', 'AT5G14480' => 'ath', 'ATR0824G026' => 'atr', 'ATR1098G019' => 'atr', 'Atru.chr11.2145' => 'acertr', 'Atru.chr2.3636' => 'acertr', 'Atru.chr2.3644' => 'acertr', 'Atru.chr6.2422' => 'acertr', 'Atru.chr7.1112' => 'acertr', 'AUR62005469' => 'cqu', 'AUR62011166' => 'cqu', 'AUR62013319' => 'cqu', 'AUR62024273' => 'cqu', 'AUR62028420' => 'cqu', 'AUR62041942' => 'cqu', 'BcaB01g04969' => 'bca', 'BcaB01g06371' => 'bca', 'BcaB02g11494' => 'bca', 'BcaB03g15382' => 'bca', 'BcaB08g36994' => 'bca', 'BcaC03g13477' => 'bca', 'BcaC03g13478' => 'bca', 'BcaC03g13480' => 'bca', 'BcaC03g13481' => 'bca', 'BcaC03g13486' => 'bca', 'BcaC04g19031' => 'bca', 'BcaC04g23085' => 'bca', 'BcaC05g25094' => 'bca', 'BcaC05g25096' => 'bca', 'BcaC05g25138' => 'bca', 'BcaC05g30416' => 'bca', 'BcaC05g30455' => 'bca', 'BcaC06g30979' => 'bca', 'BcaC06g33805' => 'bca', 'BcaC08g46021' => 'bca', 'BcaNung03154' => 'bca', 'BolC2t06623H' => 'bol', 'BolC2t06632H' => 'bol', 'BolC2t06635H' => 'bol', 'BolC2t06638H' => 'bol', 'BolC3t13266H' => 'bol', 'BolC5t29776H' => 'bol', 'BolC6t38912H' => 'bol', 'BolC7t44183H' => 'bol', 'BolC9t54123H' => 'bol', 'BolC9t59107H' => 'bol', 'BraA02t05221Z' => 'bra', 'BraA03t09996Z' => 'bra', 'BraA05t23210Z' => 'bra', 'BraA06t24068Z' => 'bra', 'BraA06t27032Z' => 'bra', 'BraA08t35176Z' => 'bra', 'BraA09t36680Z' => 'bra', 'BraA10t44471Z' => 'bra', 'C02p06760' => 'bna', 'C02p06890' => 'bna', 'C02p07010' => 'bna', 'C03p07660' => 'bna', 'C05p10300' => 'bna', 'C06p38150' => 'bna', 'C07p36650' => 'bna', 'C08p15770' => 'bna', 'C09p12300' => 'bna', 'C09p62700' => 'bna', 'C09p75040' => 'bna', 'CAN.G13.1' => 'can', 'CAN.G138.4' => 'can', 'CAN.G44.6' => 'can', 'CAN.G473.19' => 'can', 'CANSAT01G0835' => 'cansat', 'CANSAT11G0246' => 'cansat', 'CANSAT11G1766' => 'cansat', 'CANSAT64G1954' => 'cansat', 'CARHR013330' => 'chi', 'CARHR060530' => 'chi', 'CARHR075300' => 'chi', 'CARHR105120' => 'chi', 'CARHR148910' => 'chi', 'CARHR198830' => 'chi', 'Carub.0001s1275' => 'cru', 'Carub.0002s1437' => 'cru', 'Carub.0003s0044' => 'cru', 'Carub.0003s2787' => 'cru', 'Carub.0005s0597' => 'cru', 'Carub.0006s1266' => 'cru', 'Ca_06935_v3' => 'car', 'Ca_13559_v3' => 'car', 'Ca_16941_v3' => 'car', 'Ca_16960_v3' => 'car', 'Ca_17775_v3' => 'car', 'Ca_30464_v3' => 'car', 'Cc06_g08160' => 'ccan', 'Cc07_g01520' => 'ccan', 'Cc11_g15810' => 'ccan', 'CDE02G2840' => 'cde', 'CDE03G0093' => 'cde', 'CDE04G2127' => 'cde', 'CDE07G1857' => 'cde', 'CDE09G1246' => 'cde', 'Cfa003412' => 'cfa', 'Cfa007341' => 'cfa', 'Cfa009220' => 'cfa', 'Ciclev10008737m.g' => 'ccl', 'Ciclev10015565m.g' => 'ccl', 'Ciclev10031761m.g' => 'ccl', 'CiPaw.03G045300' => 'cil', 'CiPaw.03G247200' => 'cil', 'CiPaw.04G029500' => 'cil', 'CiPaw.04G174000' => 'cil', 'CiPaw.05G181200' => 'cil', 'CiPaw.06G067100' => 'cil', 'ClCG05G025800' => 'cla', 'ClCG06G011400' => 'cla', 'ClCG09G019360' => 'cla', 'COL.COLO4_04827' => 'col', 'COL.COLO4_29170' => 'col', 'COL.COLO4_35131' => 'col', 'COL.COLO4_35132' => 'col', 'Cpa.g.sc33.32' => 'cpa', 'Cpa.g.sc46.29' => 'cpa', 'Cpa.g.sc796.1' => 'cpa', 'CsaV3_1G030420' => 'csa', 'CsaV3_5G027050' => 'csa', 'CsaV3_5G031040' => 'csa', 'CsaV3_UNG023130' => 'csa', 'CSS0007726' => 'camsi', 'CSS0016433' => 'camsi', 'CSS0017656' => 'camsi', 'CSS0025364' => 'camsi', 'CSS0027582' => 'camsi', 'CSS0047288' => 'camsi', 'CSS0049950' => 'camsi', 'DCAR_003843' => 'dca', 'DCAR_007052' => 'dca', 'DCAR_020884' => 'dca', 'DCAR_021730' => 'dca', 'DCAR_024423' => 'dca', 'DCAR_026509' => 'dca', 'DCAR_031158' => 'dca', 'Dinv14728' => 'din', 'Dinv15219' => 'din', 'Dinv25728' => 'din', 'Dinv33428' => 'din', 'Dinv36489' => 'din', 'Dinv41486' => 'din', 'Duzib147G0469' => 'dzi', 'Duzib168G0060' => 'dzi', 'Duzib187G1215' => 'dzi', 'Duzib248G0692' => 'dzi', 'Duzib251G0767' => 'dzi', 'Duzib264G0446' => 'dzi', 'Duzib268G0691' => 'dzi', 'ECA232G4767' => 'eca', 'ECA233G2838' => 'eca', 'ECA234G0391' => 'eca', 'ECA234G0857' => 'eca', 'ECA236G1593' => 'eca', 'ECA238G0565' => 'eca', 'ECA246G1027' => 'eca', 'ECA246G3223' => 'eca', 'ECA246G3470' => 'eca', 'EL10Ac6g13829' => 'bvu', 'EL10Ac6g14093' => 'bvu', 'EL10Ac8g18707' => 'bvu', 'Eucgr.C01369' => 'egr', 'Eucgr.H02492' => 'egr', 'Eucgr.I01733' => 'egr', 'Eucgr.J02255' => 'egr', 'Eucgr.J02257' => 'egr', 'Eucgr.J02258' => 'egr', 'FAN02G1601' => 'fan', 'FAN03G1586' => 'fan', 'FAN03G2986' => 'fan', 'FAN05G4837' => 'fan', 'FAN06G0146' => 'fan', 'FAN07G0858' => 'fan', 'FAN09G3179' => 'fan', 'FAN10G0669' => 'fan', 'FAN12G2358' => 'fan', 'FAN14G4198' => 'fan', 'FAN14G5112' => 'fan', 'FAN17G0342' => 'fan', 'FAN19G0342' => 'fan', 'FAN19G0962' => 'fan', 'FAN19G1101' => 'fan', 'FAN19G1872' => 'fan', 'FAN22G0356' => 'fan', 'FAN23G0744' => 'fan', 'FAN23G1914' => 'fan', 'FAN26G0032' => 'fan', 'FAN28G0625' => 'fan', 'FvH4_1g02710' => 'fve', 'FvH4_1g02720' => 'fve', 'FvH4_4g25670' => 'fve', 'FvH4_6g51700' => 'fve', 'FvH4_7g20170' => 'fve', 'Glyma.05G175000' => 'gma', 'Glyma.08G132300' => 'gma', 'Glyma.11G243000' => 'gma', 'Glyma.13G158900' => 'gma', 'Glyma.17G112400' => 'gma', 'Glyma.18G014100' => 'gma', 'Glyma.19G003100' => 'gma', 'Glyma.19G056500' => 'gma', 'Gohir.A01G158900' => 'ghi', 'Gohir.A05G312600' => 'ghi', 'Gohir.A05G354900' => 'ghi', 'Gohir.A07G037200' => 'ghi', 'Gohir.A09G030000' => 'ghi', 'Gohir.A12G145200' => 'ghi', 'Gohir.D01G151500' => 'ghi', 'Gohir.D04G058300' => 'ghi', 'Gohir.D05G314100' => 'ghi', 'Gohir.D07G041400' => 'ghi', 'Gohir.D09G029700' => 'ghi', 'Gohir.D12G149700' => 'ghi', 'Gorai.001G043800' => 'gra', 'Gorai.002G187800' => 'gra', 'Gorai.006G034700' => 'gra', 'Gorai.008G161200' => 'gra', 'Gorai.009G335700' => 'gra', 'Gorai.012G065000' => 'gra', 'GSVIVG01000535001' => 'vvi', 'GSVIVG01015572001' => 'vvi', 'GSVIVG01032386001' => 'vvi', 'HanXRQChr05g0138531' => 'han', 'HanXRQChr06g0174391' => 'han', 'HanXRQChr07g0199021' => 'han', 'HanXRQChr08g0208211' => 'han', 'HanXRQChr09g0255471' => 'han', 'HanXRQChr10g0315791' => 'han', 'HanXRQChr12g0371991' => 'han', 'HanXRQChr15g0475251' => 'han', 'HanXRQChr17g0540001' => 'han', 'HanXRQChr17g0548631' => 'han', 'HanXRQChr17g0569561' => 'han', 'Haze_12256' => 'cav', 'Haze_14756' => 'cav', 'Haze_25528' => 'cav', 'Hma1.2p1_0079F.1_g041020' => 'hma', 'Hma1.2p1_0818F.1_g223260' => 'hma', 'Hma1.2p1_1747F.1_g300530' => 'hma', 'HPP92_004607' => 'vpl', 'HPP92_004608' => 'vpl', 'HPP92_006181' => 'vpl', 'HPP92_012192' => 'vpl', 'HPP92_015680' => 'vpl', 'HPP92_020249' => 'vpl', 'HPP92_021376' => 'vpl', 'HPP92_024275' => 'vpl', 'Hund06031' => 'sun', 'Hund25391' => 'sun', 'Lalb_Chr07g0185371' => 'lal', 'Lalb_Chr07g0185381' => 'lal', 'Lalb_Chr12g0204011' => 'lal', 'Lalb_Chr13g0301671' => 'lal', 'Lalb_Chr14g0362851' => 'lal', 'Lalb_Chr24g0403581' => 'lal', 'Lj1g0000233' => 'lja', 'Lj2g0018120' => 'lja', 'Lj3C621T0' => 'lonja', 'Lj3P1059T14' => 'lonja', 'Lj3P611T9' => 'lonja', 'Lj3P614T13' => 'lonja', 'Lj3P615T5' => 'lonja', 'Lj4g0012315' => 'lja', 'Lj4g0026182' => 'lja', 'Lj6P813T16' => 'lonja', 'Lj7C427T7' => 'lonja', 'Lj7C427T8' => 'lonja', 'Lj7P600T41' => 'lonja', 'Lju41C42G17' => 'lonja', 'Lsat_1_v5_gn_0_47300' => 'lsa', 'Lsat_1_v5_gn_2_91280' => 'lsa', 'Lsat_1_v5_gn_3_30561' => 'lsa', 'Lsat_1_v5_gn_4_184321' => 'lsa', 'Lsat_1_v5_gn_4_4041' => 'lsa', 'Lsat_1_v5_gn_5_92000' => 'lsa', 'Lsat_1_v5_gn_8_152940' => 'lsa', 'Lsat_1_v5_gn_8_62401' => 'lsa', 'Manes.06G055900' => 'mes', 'Manes.12G022200' => 'mes', 'Manes.13G023300' => 'mes', 'Manes.14G115000' => 'mes', 'Manes.15G151700' => 'mes', 'Manes.17G111300' => 'mes', 'Mapoly0226s0009' => 'mpo', 'MBI02_g25363_MAGBIO' => 'mbi', 'MBI06_g00027_MAGBIO' => 'mbi', 'MBI10_g13034_MAGBIO' => 'mbi', 'MD09G1023400' => 'mdo', 'MD13G1100100' => 'mdo', 'MD15G1169200' => 'mdo', 'MD16G1101100' => 'mdo', 'MD17G1022900' => 'mdo', 'Medtr3g096150' => 'mtr', 'Medtr4g115070' => 'mtr', 'Medtr7g033325' => 'mtr', 'Medtr8g089840' => 'mtr', 'MELO3C010319.2' => 'cme', 'MELO3C011944.2' => 'cme', 'MELO3C021589.2' => 'cme', 'Migut.E00207' => 'egut', 'Migut.H00067' => 'egut', 'Migut.K00433' => 'egut', 'Migut.K00606' => 'egut', 'Migut.K01410' => 'egut', 'MSTRG.13347' => 'ama', 'MSTRG.24045' => 'ama', 'MSTRG.2428' => 'ama', 'MSTRG.26410' => 'ama', 'MSTRG.3139' => 'ama', 'MSTRG.3286' => 'ama', 'MSTRG.563' => 'ama', 'MSTRG.7941' => 'ama', 'Nitab4.5_0000028g0060' => 'nta', 'Nitab4.5_0000065g0260' => 'nta', 'Nitab4.5_0000112g0060' => 'nta', 'Nitab4.5_0000489g0120' => 'nta', 'Nitab4.5_0001776g0050' => 'nta', 'Nitab4.5_0001854g0010' => 'nta', 'Nitab4.5_0001860g0020' => 'nta', 'Nitab4.5_0004352g0010' => 'nta', 'Nitab4.5_0008716g0020' => 'nta', 'Nitab4.5_0008922g0010' => 'nta', 'Nn3g16693' => 'nnu', 'Nn4g22596' => 'nnu', 'Nn7g37639' => 'nnu', 'Oeu001701.1' => 'oeu', 'Oeu018149.1' => 'oeu', 'Oeu026220.1' => 'oeu', 'Oeu038635.1' => 'oeu', 'Oeu049176.1' => 'oeu', 'Oeu056706.1' => 'oeu', 'Oeu056937.1' => 'oeu', 'Oeu057540.1' => 'oeu', 'Os02g0594900' => 'osa', 'Os02g0595100' => 'osa', 'Os04g0477500' => 'osa', 'Os12g0611900' => 'osa', 'Peaxi162Scf00076g00020' => 'pax', 'Peaxi162Scf00128g00217' => 'pax', 'Peaxi162Scf00129g01640' => 'pax', 'Peaxi162Scf00669g00007' => 'pax', 'Peaxi162Scf00700g00421' => 'pax', 'Peaxi162Scf00801g00038' => 'pax', 'Peaxi162Scf00891g00025' => 'pax', 'PGR083G0909' => 'pgr', 'PGR119G1005' => 'pgr', 'PGR142G2236' => 'pgr', 'PGR142G3388' => 'pgr', 'PGSC0003DMG400004514' => 'stu', 'PGSC0003DMG400012635' => 'stu', 'PGSC0003DMG400015730' => 'stu', 'PGSC0003DMG400018611' => 'stu', 'PGSC0003DMG400030897' => 'stu', 'Phvul.001G254800' => 'pvu', 'Phvul.002G260100' => 'pvu', 'Phvul.003G167600' => 'pvu', 'Phvul.004G005100' => 'pvu', 'Potri.001G343600' => 'ptr', 'Potri.006G066700' => 'ptr', 'Potri.008G186000' => 'ptr', 'Potri.010G046900' => 'ptr', 'Potri.018G127900' => 'ptr', 'Pp3c20_17750' => 'ppa', 'Pp3c24_4380' => 'ppa', 'Prupe.1G245800' => 'ppe', 'Prupe.3G293400' => 'ppe', 'Prupe.7G247400' => 'ppe', 'Psat0s145g0120' => 'psa', 'Psat0s595g0040' => 'psa', 'Psat0s595g0120' => 'psa', 'Psat3g175040' => 'psa', 'Psat7g058120' => 'psa', 'PSO017G0428' => 'pso', 'PSO063G7510' => 'pso', 'PSO067G0046' => 'pso', 'PSO478G1073' => 'pso', 'PSO675G3677' => 'pso', 'PSO675G6558' => 'pso', 'PSO675G7520' => 'pso', 'PSO675G8959' => 'pso', 'QL02p074089' => 'qlo', 'QL02p089614' => 'qlo', 'QL03p057736' => 'qlo', 'RcHm_v2.0_Chr1g0364131' => 'rch', 'RcHm_v2.0_Chr2g0087801' => 'rch', 'RcHm_v2.0_Chr2g0087821' => 'rch', 'RcHm_v2.0_Chr2g0173231' => 'rch', 'RcHm_v2.0_Chr4g0433111' => 'rch', 'Rhsim03G0250300' => 'rsi', 'Rhsim08G0048400' => 'rsi', 'Rhsim10G0014800' => 'rsi', 'Rhsim12G0040100' => 'rsi', 'Rhsim12G0109700' => 'rsi', 'Sabra06G0049600' => 'sbr', 'Sabra08G0141000' => 'sbr', 'Sabra10G0021400' => 'sbr', 'Sabra16G0222900' => 'sbr', 'Sabra18G0108600' => 'sbr', 'SalBow1G0433' => 'sbo', 'SalBow1G2038' => 'sbo', 'SalBow1G5003' => 'sbo', 'SalBow7G1197' => 'sbo', 'SalBow8G3506' => 'sbo', 'Sc03g0007300' => 'sci', 'Sc11g0000950' => 'sci', 'Sc14g0008750' => 'sci', 'Sc18g0000420' => 'sci', 'Sed0006754' => 'sed', 'Sed0008741' => 'sed', 'Sed0017172' => 'sed', 'Sed0018925' => 'sed', 'Sed0023326' => 'sed', 'Sed0025909' => 'sed', 'SEGI_05333' => 'sgi', 'SEGI_10362' => 'sgi', 'SEGI_13380' => 'sgi', 'SEGI_24306' => 'sgi', 'SEGI_29077' => 'sgi', 'SEGI_29095' => 'sgi', 'SEGI_36534' => 'sgi', 'SEGI_37506' => 'sgi', 'SEGI_38321' => 'sgi', 'SGA_v2.0_scaffold307G48031' => 'sas', 'SGA_v2.0_scaffold47G17507' => 'sas', 'SGA_v2.0_scaffold63G21736' => 'sas', 'SGA_v2.0_scaffold87G27070' => 'sas', 'SHI17794' => 'shi', 'SHI28851' => 'shi', 'SMO165G0155' => 'smo', 'SMO340G0217' => 'smo', 'SMO367G1210' => 'smo', 'Solyc02g093430.3' => 'sly', 'Solyc05g013580.4' => 'sly', 'Solyc07g008030.3' => 'sly', 'Solyc12g035470.2' => 'sly', 'Sopen02g038020' => 'spe', 'Sopen05g008490' => 'spe', 'Sopen07g003910' => 'spe', 'Sopen12g015240' => 'spe', 'Sp1g11550' => 'spa', 'Sp2g16710' => 'spa', 'Sp3g00430' => 'spa', 'Sp3g26780' => 'spa', 'Sp5g22900' => 'spa', 'Sp6g29530' => 'spa', 'TAR371G0794' => 'tar', 'TAR374G0164' => 'tar', 'TAR622G0165' => 'tar', 'TAR626G0929' => 'tar', 'TAR629G2155' => 'tar', 'THA.LOC104805282' => 'tha', 'THA.LOC104805363' => 'tha', 'THA.LOC104808968' => 'tha', 'THA.LOC104821093' => 'tha', 'THA.LOC104823953' => 'tha', 'THA.LOC104825562' => 'tha', 'THA.LOC104825665' => 'tha', 'Thecc.02G261400' => 'tca', 'Thecc.04G019200' => 'tca', 'Thecc.09G130400' => 'tca', 'Thhalv10004374m.g' => 'esa', 'Thhalv10007850m.g' => 'esa', 'Thhalv10013782m.g' => 'esa', 'Thhalv10018686m.g' => 'esa', 'Thhalv10020899m.g' => 'esa', 'Thhalv10022755m.g' => 'esa', 'TPR.G23851' => 'tpr', 'TPR.G26500' => 'tpr', 'TPR.G27267' => 'tpr', 'TPR.G32001' => 'tpr', 'TPR.G6251' => 'tpr', 'TPR.G8167' => 'tpr', 'TWI12G1330' => 'twi', 'TWI18G1239' => 'twi', 'TWI34G0979' => 'twi', 'TWI36G0670' => 'twi', 'TWI36G0707' => 'twi', 'TWI56G0233' => 'twi', 'TWI75G1809' => 'twi', 'unitig_21.g20874' => 'ugi', 'unitig_26.g10343' => 'ugi', 'unitig_46.g18392' => 'ugi', 'unitig_52.g17178' => 'ugi', 'unitig_8.g2934' => 'ugi', 'vmacro01122' => 'vma', 'vmacro05875' => 'vma', 'vmacro06147' => 'vma', 'vmacro16191' => 'vma', 'vmacro18293' => 'vma', 'VMungo0251G3707' => 'vmu', 'VMungo0464G1521' => 'vmu', 'VMungo1215G0205' => 'vmu', 'VMungo1383G2484' => 'vmu', 'Zm00001eb079610' => 'zma', 'Zm00001eb135990' => 'zma', 'Zm00001eb183710' => 'zma', 'Zm00001eb246020' => 'zma' ), 'gf_id' => 'HOM05D001124', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001124' ), 'data_identifier' => 'HOM05D001124', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001124', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '548', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02520' => 'bna', 'A03p06630' => 'bna', 'A05p44460' => 'bna', 'A06p08710' => 'bna', 'A06p41090' => 'bna', 'A07p32320' => 'bna', 'A08p32520' => 'bna', 'A09p10360' => 'bna', 'A10p24080' => 'bna', 'Aa31LG11G15250' => 'aar', 'Aa31LG1G1800' => 'aar', 'Aa31LG2G5120' => 'aar', 'Aa31LG2G6070' => 'aar', 'Aa31LG5G10770' => 'aar', 'Aa31sc61G90' => 'aar', 'Actinidia01352' => 'ach', 'Actinidia05983' => 'ach', 'Actinidia08133' => 'ach', 'Actinidia15101' => 'ach', 'Actinidia26379' => 'ach', 'Actinidia35778' => 'ach', 'Actinidia36123' => 'ach', 'Actinidia37436' => 'ach', 'Actinidia38730' => 'ach', 'Ah.02g128210' => 'amhyb', 'Ah.03g132990' => 'amhyb', 'Ah.14g079410' => 'amhyb', 'AL1G24640' => 'aly', 'AL2G26680' => 'aly', 'AL3G10530' => 'aly', 'AL3G45230' => 'aly', 'AL5G15230' => 'aly', 'AL5G16960' => 'aly', 'AL6G25210' => 'aly', 'Aqoxy2G00441' => 'aox', 'Aqoxy3G01236' => 'aox', 'Aqoxy5G03746' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3RQ047' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C7GMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9C8JER' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MBL6KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YXCZ83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZANX40' => 'arhy', 'AT1G12990' => 'ath', 'AT1G67880' => 'ath', 'AT2G13290' => 'ath', 'AT3G01620' => 'ath', 'AT3G26445' => 'ath', 'AT3G27540' => 'ath', 'AT5G14480' => 'ath', 'ATR0824G026' => 'atr', 'ATR1098G019' => 'atr', 'Atru.chr11.2145' => 'acertr', 'Atru.chr2.3636' => 'acertr', 'Atru.chr2.3644' => 'acertr', 'Atru.chr6.2422' => 'acertr', 'Atru.chr7.1112' => 'acertr', 'AUR62005469' => 'cqu', 'AUR62011166' => 'cqu', 'AUR62013319' => 'cqu', 'AUR62024273' => 'cqu', 'AUR62028420' => 'cqu', 'AUR62041942' => 'cqu', 'BcaB01g04969' => 'bca', 'BcaB01g06371' => 'bca', 'BcaB02g11494' => 'bca', 'BcaB03g15382' => 'bca', 'BcaB08g36994' => 'bca', 'BcaC03g13477' => 'bca', 'BcaC03g13478' => 'bca', 'BcaC03g13480' => 'bca', 'BcaC03g13481' => 'bca', 'BcaC03g13486' => 'bca', 'BcaC04g19031' => 'bca', 'BcaC04g23085' => 'bca', 'BcaC05g25094' => 'bca', 'BcaC05g25096' => 'bca', 'BcaC05g25138' => 'bca', 'BcaC05g30416' => 'bca', 'BcaC05g30455' => 'bca', 'BcaC06g30979' => 'bca', 'BcaC06g33805' => 'bca', 'BcaC08g46021' => 'bca', 'BcaNung03154' => 'bca', 'BolC2t06623H' => 'bol', 'BolC2t06632H' => 'bol', 'BolC2t06635H' => 'bol', 'BolC2t06638H' => 'bol', 'BolC3t13266H' => 'bol', 'BolC5t29776H' => 'bol', 'BolC6t38912H' => 'bol', 'BolC7t44183H' => 'bol', 'BolC9t54123H' => 'bol', 'BolC9t59107H' => 'bol', 'BraA02t05221Z' => 'bra', 'BraA03t09996Z' => 'bra', 'BraA05t23210Z' => 'bra', 'BraA06t24068Z' => 'bra', 'BraA06t27032Z' => 'bra', 'BraA08t35176Z' => 'bra', 'BraA09t36680Z' => 'bra', 'BraA10t44471Z' => 'bra', 'C02p06760' => 'bna', 'C02p06890' => 'bna', 'C02p07010' => 'bna', 'C03p07660' => 'bna', 'C05p10300' => 'bna', 'C06p38150' => 'bna', 'C07p36650' => 'bna', 'C08p15770' => 'bna', 'C09p12300' => 'bna', 'C09p62700' => 'bna', 'C09p75040' => 'bna', 'CAN.G13.1' => 'can', 'CAN.G138.4' => 'can', 'CAN.G44.6' => 'can', 'CAN.G473.19' => 'can', 'CANSAT01G0835' => 'cansat', 'CANSAT11G0246' => 'cansat', 'CANSAT11G1766' => 'cansat', 'CANSAT64G1954' => 'cansat', 'CARHR013330' => 'chi', 'CARHR060530' => 'chi', 'CARHR075300' => 'chi', 'CARHR105120' => 'chi', 'CARHR148910' => 'chi', 'CARHR198830' => 'chi', 'Carub.0001s1275' => 'cru', 'Carub.0002s1437' => 'cru', 'Carub.0003s0044' => 'cru', 'Carub.0003s2787' => 'cru', 'Carub.0005s0597' => 'cru', 'Carub.0006s1266' => 'cru', 'Ca_06935_v3' => 'car', 'Ca_13559_v3' => 'car', 'Ca_16941_v3' => 'car', 'Ca_16960_v3' => 'car', 'Ca_17775_v3' => 'car', 'Ca_30464_v3' => 'car', 'Cc06_g08160' => 'ccan', 'Cc07_g01520' => 'ccan', 'Cc11_g15810' => 'ccan', 'CDE02G2840' => 'cde', 'CDE03G0093' => 'cde', 'CDE04G2127' => 'cde', 'CDE07G1857' => 'cde', 'CDE09G1246' => 'cde', 'Cfa003412' => 'cfa', 'Cfa007341' => 'cfa', 'Cfa009220' => 'cfa', 'Ciclev10008737m.g' => 'ccl', 'Ciclev10015565m.g' => 'ccl', 'Ciclev10031761m.g' => 'ccl', 'CiPaw.03G045300' => 'cil', 'CiPaw.03G247200' => 'cil', 'CiPaw.04G029500' => 'cil', 'CiPaw.04G174000' => 'cil', 'CiPaw.05G181200' => 'cil', 'CiPaw.06G067100' => 'cil', 'ClCG05G025800' => 'cla', 'ClCG06G011400' => 'cla', 'ClCG09G019360' => 'cla', 'COL.COLO4_04827' => 'col', 'COL.COLO4_29170' => 'col', 'COL.COLO4_35131' => 'col', 'COL.COLO4_35132' => 'col', 'Cpa.g.sc33.32' => 'cpa', 'Cpa.g.sc46.29' => 'cpa', 'Cpa.g.sc796.1' => 'cpa', 'CsaV3_1G030420' => 'csa', 'CsaV3_5G027050' => 'csa', 'CsaV3_5G031040' => 'csa', 'CsaV3_UNG023130' => 'csa', 'CSS0007726' => 'camsi', 'CSS0016433' => 'camsi', 'CSS0017656' => 'camsi', 'CSS0025364' => 'camsi', 'CSS0027582' => 'camsi', 'CSS0047288' => 'camsi', 'CSS0049950' => 'camsi', 'DCAR_003843' => 'dca', 'DCAR_007052' => 'dca', 'DCAR_020884' => 'dca', 'DCAR_021730' => 'dca', 'DCAR_024423' => 'dca', 'DCAR_026509' => 'dca', 'DCAR_031158' => 'dca', 'Dinv14728' => 'din', 'Dinv15219' => 'din', 'Dinv25728' => 'din', 'Dinv33428' => 'din', 'Dinv36489' => 'din', 'Dinv41486' => 'din', 'Duzib147G0469' => 'dzi', 'Duzib168G0060' => 'dzi', 'Duzib187G1215' => 'dzi', 'Duzib248G0692' => 'dzi', 'Duzib251G0767' => 'dzi', 'Duzib264G0446' => 'dzi', 'Duzib268G0691' => 'dzi', 'ECA232G4767' => 'eca', 'ECA233G2838' => 'eca', 'ECA234G0391' => 'eca', 'ECA234G0857' => 'eca', 'ECA236G1593' => 'eca', 'ECA238G0565' => 'eca', 'ECA246G1027' => 'eca', 'ECA246G3223' => 'eca', 'ECA246G3470' => 'eca', 'EL10Ac6g13829' => 'bvu', 'EL10Ac6g14093' => 'bvu', 'EL10Ac8g18707' => 'bvu', 'Eucgr.C01369' => 'egr', 'Eucgr.H02492' => 'egr', 'Eucgr.I01733' => 'egr', 'Eucgr.J02255' => 'egr', 'Eucgr.J02257' => 'egr', 'Eucgr.J02258' => 'egr', 'FAN02G1601' => 'fan', 'FAN03G1586' => 'fan', 'FAN03G2986' => 'fan', 'FAN05G4837' => 'fan', 'FAN06G0146' => 'fan', 'FAN07G0858' => 'fan', 'FAN09G3179' => 'fan', 'FAN10G0669' => 'fan', 'FAN12G2358' => 'fan', 'FAN14G4198' => 'fan', 'FAN14G5112' => 'fan', 'FAN17G0342' => 'fan', 'FAN19G0342' => 'fan', 'FAN19G0962' => 'fan', 'FAN19G1101' => 'fan', 'FAN19G1872' => 'fan', 'FAN22G0356' => 'fan', 'FAN23G0744' => 'fan', 'FAN23G1914' => 'fan', 'FAN26G0032' => 'fan', 'FAN28G0625' => 'fan', 'FvH4_1g02710' => 'fve', 'FvH4_1g02720' => 'fve', 'FvH4_4g25670' => 'fve', 'FvH4_6g51700' => 'fve', 'FvH4_7g20170' => 'fve', 'Glyma.05G175000' => 'gma', 'Glyma.08G132300' => 'gma', 'Glyma.11G243000' => 'gma', 'Glyma.13G158900' => 'gma', 'Glyma.17G112400' => 'gma', 'Glyma.18G014100' => 'gma', 'Glyma.19G003100' => 'gma', 'Glyma.19G056500' => 'gma', 'Gohir.A01G158900' => 'ghi', 'Gohir.A05G312600' => 'ghi', 'Gohir.A05G354900' => 'ghi', 'Gohir.A07G037200' => 'ghi', 'Gohir.A09G030000' => 'ghi', 'Gohir.A12G145200' => 'ghi', 'Gohir.D01G151500' => 'ghi', 'Gohir.D04G058300' => 'ghi', 'Gohir.D05G314100' => 'ghi', 'Gohir.D07G041400' => 'ghi', 'Gohir.D09G029700' => 'ghi', 'Gohir.D12G149700' => 'ghi', 'Gorai.001G043800' => 'gra', 'Gorai.002G187800' => 'gra', 'Gorai.006G034700' => 'gra', 'Gorai.008G161200' => 'gra', 'Gorai.009G335700' => 'gra', 'Gorai.012G065000' => 'gra', 'GSVIVG01000535001' => 'vvi', 'GSVIVG01015572001' => 'vvi', 'GSVIVG01032386001' => 'vvi', 'HanXRQChr05g0138531' => 'han', 'HanXRQChr06g0174391' => 'han', 'HanXRQChr07g0199021' => 'han', 'HanXRQChr08g0208211' => 'han', 'HanXRQChr09g0255471' => 'han', 'HanXRQChr10g0315791' => 'han', 'HanXRQChr12g0371991' => 'han', 'HanXRQChr15g0475251' => 'han', 'HanXRQChr17g0540001' => 'han', 'HanXRQChr17g0548631' => 'han', 'HanXRQChr17g0569561' => 'han', 'Haze_12256' => 'cav', 'Haze_14756' => 'cav', 'Haze_25528' => 'cav', 'Hma1.2p1_0079F.1_g041020' => 'hma', 'Hma1.2p1_0818F.1_g223260' => 'hma', 'Hma1.2p1_1747F.1_g300530' => 'hma', 'HPP92_004607' => 'vpl', 'HPP92_004608' => 'vpl', 'HPP92_006181' => 'vpl', 'HPP92_012192' => 'vpl', 'HPP92_015680' => 'vpl', 'HPP92_020249' => 'vpl', 'HPP92_021376' => 'vpl', 'HPP92_024275' => 'vpl', 'Hund06031' => 'sun', 'Hund25391' => 'sun', 'Lalb_Chr07g0185371' => 'lal', 'Lalb_Chr07g0185381' => 'lal', 'Lalb_Chr12g0204011' => 'lal', 'Lalb_Chr13g0301671' => 'lal', 'Lalb_Chr14g0362851' => 'lal', 'Lalb_Chr24g0403581' => 'lal', 'Lj1g0000233' => 'lja', 'Lj2g0018120' => 'lja', 'Lj3C621T0' => 'lonja', 'Lj3P1059T14' => 'lonja', 'Lj3P611T9' => 'lonja', 'Lj3P614T13' => 'lonja', 'Lj3P615T5' => 'lonja', 'Lj4g0012315' => 'lja', 'Lj4g0026182' => 'lja', 'Lj6P813T16' => 'lonja', 'Lj7C427T7' => 'lonja', 'Lj7C427T8' => 'lonja', 'Lj7P600T41' => 'lonja', 'Lju41C42G17' => 'lonja', 'Lsat_1_v5_gn_0_47300' => 'lsa', 'Lsat_1_v5_gn_2_91280' => 'lsa', 'Lsat_1_v5_gn_3_30561' => 'lsa', 'Lsat_1_v5_gn_4_184321' => 'lsa', 'Lsat_1_v5_gn_4_4041' => 'lsa', 'Lsat_1_v5_gn_5_92000' => 'lsa', 'Lsat_1_v5_gn_8_152940' => 'lsa', 'Lsat_1_v5_gn_8_62401' => 'lsa', 'Manes.06G055900' => 'mes', 'Manes.12G022200' => 'mes', 'Manes.13G023300' => 'mes', 'Manes.14G115000' => 'mes', 'Manes.15G151700' => 'mes', 'Manes.17G111300' => 'mes', 'Mapoly0226s0009' => 'mpo', 'MBI02_g25363_MAGBIO' => 'mbi', 'MBI06_g00027_MAGBIO' => 'mbi', 'MBI10_g13034_MAGBIO' => 'mbi', 'MD09G1023400' => 'mdo', 'MD13G1100100' => 'mdo', 'MD15G1169200' => 'mdo', 'MD16G1101100' => 'mdo', 'MD17G1022900' => 'mdo', 'Medtr3g096150' => 'mtr', 'Medtr4g115070' => 'mtr', 'Medtr7g033325' => 'mtr', 'Medtr8g089840' => 'mtr', 'MELO3C010319.2' => 'cme', 'MELO3C011944.2' => 'cme', 'MELO3C021589.2' => 'cme', 'Migut.E00207' => 'egut', 'Migut.H00067' => 'egut', 'Migut.K00433' => 'egut', 'Migut.K00606' => 'egut', 'Migut.K01410' => 'egut', 'MSTRG.13347' => 'ama', 'MSTRG.24045' => 'ama', 'MSTRG.2428' => 'ama', 'MSTRG.26410' => 'ama', 'MSTRG.3139' => 'ama', 'MSTRG.3286' => 'ama', 'MSTRG.563' => 'ama', 'MSTRG.7941' => 'ama', 'Nitab4.5_0000028g0060' => 'nta', 'Nitab4.5_0000065g0260' => 'nta', 'Nitab4.5_0000112g0060' => 'nta', 'Nitab4.5_0000489g0120' => 'nta', 'Nitab4.5_0001776g0050' => 'nta', 'Nitab4.5_0001854g0010' => 'nta', 'Nitab4.5_0001860g0020' => 'nta', 'Nitab4.5_0004352g0010' => 'nta', 'Nitab4.5_0008716g0020' => 'nta', 'Nitab4.5_0008922g0010' => 'nta', 'Nn3g16693' => 'nnu', 'Nn4g22596' => 'nnu', 'Nn7g37639' => 'nnu', 'Oeu001701.1' => 'oeu', 'Oeu018149.1' => 'oeu', 'Oeu026220.1' => 'oeu', 'Oeu038635.1' => 'oeu', 'Oeu049176.1' => 'oeu', 'Oeu056706.1' => 'oeu', 'Oeu056937.1' => 'oeu', 'Oeu057540.1' => 'oeu', 'Os02g0594900' => 'osa', 'Os02g0595100' => 'osa', 'Os04g0477500' => 'osa', 'Os12g0611900' => 'osa', 'Peaxi162Scf00076g00020' => 'pax', 'Peaxi162Scf00128g00217' => 'pax', 'Peaxi162Scf00129g01640' => 'pax', 'Peaxi162Scf00669g00007' => 'pax', 'Peaxi162Scf00700g00421' => 'pax', 'Peaxi162Scf00801g00038' => 'pax', 'Peaxi162Scf00891g00025' => 'pax', 'PGR083G0909' => 'pgr', 'PGR119G1005' => 'pgr', 'PGR142G2236' => 'pgr', 'PGR142G3388' => 'pgr', 'PGSC0003DMG400004514' => 'stu', 'PGSC0003DMG400012635' => 'stu', 'PGSC0003DMG400015730' => 'stu', 'PGSC0003DMG400018611' => 'stu', 'PGSC0003DMG400030897' => 'stu', 'Phvul.001G254800' => 'pvu', 'Phvul.002G260100' => 'pvu', 'Phvul.003G167600' => 'pvu', 'Phvul.004G005100' => 'pvu', 'Potri.001G343600' => 'ptr', 'Potri.006G066700' => 'ptr', 'Potri.008G186000' => 'ptr', 'Potri.010G046900' => 'ptr', 'Potri.018G127900' => 'ptr', 'Pp3c20_17750' => 'ppa', 'Pp3c24_4380' => 'ppa', 'Prupe.1G245800' => 'ppe', 'Prupe.3G293400' => 'ppe', 'Prupe.7G247400' => 'ppe', 'Psat0s145g0120' => 'psa', 'Psat0s595g0040' => 'psa', 'Psat0s595g0120' => 'psa', 'Psat3g175040' => 'psa', 'Psat7g058120' => 'psa', 'PSO017G0428' => 'pso', 'PSO063G7510' => 'pso', 'PSO067G0046' => 'pso', 'PSO478G1073' => 'pso', 'PSO675G3677' => 'pso', 'PSO675G6558' => 'pso', 'PSO675G7520' => 'pso', 'PSO675G8959' => 'pso', 'QL02p074089' => 'qlo', 'QL02p089614' => 'qlo', 'QL03p057736' => 'qlo', 'RcHm_v2.0_Chr1g0364131' => 'rch', 'RcHm_v2.0_Chr2g0087801' => 'rch', 'RcHm_v2.0_Chr2g0087821' => 'rch', 'RcHm_v2.0_Chr2g0173231' => 'rch', 'RcHm_v2.0_Chr4g0433111' => 'rch', 'Rhsim03G0250300' => 'rsi', 'Rhsim08G0048400' => 'rsi', 'Rhsim10G0014800' => 'rsi', 'Rhsim12G0040100' => 'rsi', 'Rhsim12G0109700' => 'rsi', 'Sabra06G0049600' => 'sbr', 'Sabra08G0141000' => 'sbr', 'Sabra10G0021400' => 'sbr', 'Sabra16G0222900' => 'sbr', 'Sabra18G0108600' => 'sbr', 'SalBow1G0433' => 'sbo', 'SalBow1G2038' => 'sbo', 'SalBow1G5003' => 'sbo', 'SalBow7G1197' => 'sbo', 'SalBow8G3506' => 'sbo', 'Sc03g0007300' => 'sci', 'Sc11g0000950' => 'sci', 'Sc14g0008750' => 'sci', 'Sc18g0000420' => 'sci', 'Sed0006754' => 'sed', 'Sed0008741' => 'sed', 'Sed0017172' => 'sed', 'Sed0018925' => 'sed', 'Sed0023326' => 'sed', 'Sed0025909' => 'sed', 'SEGI_05333' => 'sgi', 'SEGI_10362' => 'sgi', 'SEGI_13380' => 'sgi', 'SEGI_24306' => 'sgi', 'SEGI_29077' => 'sgi', 'SEGI_29095' => 'sgi', 'SEGI_36534' => 'sgi', 'SEGI_37506' => 'sgi', 'SEGI_38321' => 'sgi', 'SGA_v2.0_scaffold307G48031' => 'sas', 'SGA_v2.0_scaffold47G17507' => 'sas', 'SGA_v2.0_scaffold63G21736' => 'sas', 'SGA_v2.0_scaffold87G27070' => 'sas', 'SHI17794' => 'shi', 'SHI28851' => 'shi', 'SMO165G0155' => 'smo', 'SMO340G0217' => 'smo', 'SMO367G1210' => 'smo', 'Solyc02g093430.3' => 'sly', 'Solyc05g013580.4' => 'sly', 'Solyc07g008030.3' => 'sly', 'Solyc12g035470.2' => 'sly', 'Sopen02g038020' => 'spe', 'Sopen05g008490' => 'spe', 'Sopen07g003910' => 'spe', 'Sopen12g015240' => 'spe', 'Sp1g11550' => 'spa', 'Sp2g16710' => 'spa', 'Sp3g00430' => 'spa', 'Sp3g26780' => 'spa', 'Sp5g22900' => 'spa', 'Sp6g29530' => 'spa', 'TAR371G0794' => 'tar', 'TAR374G0164' => 'tar', 'TAR622G0165' => 'tar', 'TAR626G0929' => 'tar', 'TAR629G2155' => 'tar', 'THA.LOC104805282' => 'tha', 'THA.LOC104805363' => 'tha', 'THA.LOC104808968' => 'tha', 'THA.LOC104821093' => 'tha', 'THA.LOC104823953' => 'tha', 'THA.LOC104825562' => 'tha', 'THA.LOC104825665' => 'tha', 'Thecc.02G261400' => 'tca', 'Thecc.04G019200' => 'tca', 'Thecc.09G130400' => 'tca', 'Thhalv10004374m.g' => 'esa', 'Thhalv10007850m.g' => 'esa', 'Thhalv10013782m.g' => 'esa', 'Thhalv10018686m.g' => 'esa', 'Thhalv10020899m.g' => 'esa', 'Thhalv10022755m.g' => 'esa', 'TPR.G23851' => 'tpr', 'TPR.G26500' => 'tpr', 'TPR.G27267' => 'tpr', 'TPR.G32001' => 'tpr', 'TPR.G6251' => 'tpr', 'TPR.G8167' => 'tpr', 'TWI12G1330' => 'twi', 'TWI18G1239' => 'twi', 'TWI34G0979' => 'twi', 'TWI36G0670' => 'twi', 'TWI36G0707' => 'twi', 'TWI56G0233' => 'twi', 'TWI75G1809' => 'twi', 'unitig_21.g20874' => 'ugi', 'unitig_26.g10343' => 'ugi', 'unitig_46.g18392' => 'ugi', 'unitig_52.g17178' => 'ugi', 'unitig_8.g2934' => 'ugi', 'vmacro01122' => 'vma', 'vmacro05875' => 'vma', 'vmacro06147' => 'vma', 'vmacro16191' => 'vma', 'vmacro18293' => 'vma', 'VMungo0251G3707' => 'vmu', 'VMungo0464G1521' => 'vmu', 'VMungo1215G0205' => 'vmu', 'VMungo1383G2484' => 'vmu', 'Zm00001eb079610' => 'zma', 'Zm00001eb135990' => 'zma', 'Zm00001eb183710' => 'zma', 'Zm00001eb246020' => 'zma' ) $gf_id = 'HOM05D001124' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001124' ) $data_identifier = 'HOM05D001124' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 6, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 7, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 21, 'bol' => (int) 10, 'bra' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 6, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 9, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 21, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 8, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 10, 'lsa' => (int) 8, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 8, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 9, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb246020' $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' => 'HOM05D001124', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '548', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02520' => 'bna', 'A03p06630' => 'bna', 'A05p44460' => 'bna', 'A06p08710' => 'bna', 'A06p41090' => 'bna', 'A07p32320' => 'bna', 'A08p32520' => 'bna', 'A09p10360' => 'bna', 'A10p24080' => 'bna', 'Aa31LG11G15250' => 'aar', 'Aa31LG1G1800' => 'aar', 'Aa31LG2G5120' => 'aar', 'Aa31LG2G6070' => 'aar', 'Aa31LG5G10770' => 'aar', 'Aa31sc61G90' => 'aar', 'Actinidia01352' => 'ach', 'Actinidia05983' => 'ach', 'Actinidia08133' => 'ach', 'Actinidia15101' => 'ach', 'Actinidia26379' => 'ach', 'Actinidia35778' => 'ach', 'Actinidia36123' => 'ach', 'Actinidia37436' => 'ach', 'Actinidia38730' => 'ach', 'Ah.02g128210' => 'amhyb', 'Ah.03g132990' => 'amhyb', 'Ah.14g079410' => 'amhyb', 'AL1G24640' => 'aly', 'AL2G26680' => 'aly', 'AL3G10530' => 'aly', 'AL3G45230' => 'aly', 'AL5G15230' => 'aly', 'AL5G16960' => 'aly', 'AL6G25210' => 'aly', 'Aqoxy2G00441' => 'aox', 'Aqoxy3G01236' => 'aox', 'Aqoxy5G03746' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3RQ047' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C7GMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9C8JER' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MBL6KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YXCZ83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZANX40' => 'arhy', 'AT1G12990' => 'ath', 'AT1G67880' => 'ath', 'AT2G13290' => 'ath', 'AT3G01620' => 'ath', 'AT3G26445' => 'ath', 'AT3G27540' => 'ath', 'AT5G14480' => 'ath', 'ATR0824G026' => 'atr', 'ATR1098G019' => 'atr', 'Atru.chr11.2145' => 'acertr', 'Atru.chr2.3636' => 'acertr', 'Atru.chr2.3644' => 'acertr', 'Atru.chr6.2422' => 'acertr', 'Atru.chr7.1112' => 'acertr', 'AUR62005469' => 'cqu', 'AUR62011166' => 'cqu', 'AUR62013319' => 'cqu', 'AUR62024273' => 'cqu', 'AUR62028420' => 'cqu', 'AUR62041942' => 'cqu', 'BcaB01g04969' => 'bca', 'BcaB01g06371' => 'bca', 'BcaB02g11494' => 'bca', 'BcaB03g15382' => 'bca', 'BcaB08g36994' => 'bca', 'BcaC03g13477' => 'bca', 'BcaC03g13478' => 'bca', 'BcaC03g13480' => 'bca', 'BcaC03g13481' => 'bca', 'BcaC03g13486' => 'bca', 'BcaC04g19031' => 'bca', 'BcaC04g23085' => 'bca', 'BcaC05g25094' => 'bca', 'BcaC05g25096' => 'bca', 'BcaC05g25138' => 'bca', 'BcaC05g30416' => 'bca', 'BcaC05g30455' => 'bca', 'BcaC06g30979' => 'bca', 'BcaC06g33805' => 'bca', 'BcaC08g46021' => 'bca', 'BcaNung03154' => 'bca', 'BolC2t06623H' => 'bol', 'BolC2t06632H' => 'bol', 'BolC2t06635H' => 'bol', 'BolC2t06638H' => 'bol', 'BolC3t13266H' => 'bol', 'BolC5t29776H' => 'bol', 'BolC6t38912H' => 'bol', 'BolC7t44183H' => 'bol', 'BolC9t54123H' => 'bol', 'BolC9t59107H' => 'bol', 'BraA02t05221Z' => 'bra', 'BraA03t09996Z' => 'bra', 'BraA05t23210Z' => 'bra', 'BraA06t24068Z' => 'bra', 'BraA06t27032Z' => 'bra', 'BraA08t35176Z' => 'bra', 'BraA09t36680Z' => 'bra', 'BraA10t44471Z' => 'bra', 'C02p06760' => 'bna', 'C02p06890' => 'bna', 'C02p07010' => 'bna', 'C03p07660' => 'bna', 'C05p10300' => 'bna', 'C06p38150' => 'bna', 'C07p36650' => 'bna', 'C08p15770' => 'bna', 'C09p12300' => 'bna', 'C09p62700' => 'bna', 'C09p75040' => 'bna', 'CAN.G13.1' => 'can', 'CAN.G138.4' => 'can', 'CAN.G44.6' => 'can', 'CAN.G473.19' => 'can', 'CANSAT01G0835' => 'cansat', 'CANSAT11G0246' => 'cansat', 'CANSAT11G1766' => 'cansat', 'CANSAT64G1954' => 'cansat', 'CARHR013330' => 'chi', 'CARHR060530' => 'chi', 'CARHR075300' => 'chi', 'CARHR105120' => 'chi', 'CARHR148910' => 'chi', 'CARHR198830' => 'chi', 'Carub.0001s1275' => 'cru', 'Carub.0002s1437' => 'cru', 'Carub.0003s0044' => 'cru', 'Carub.0003s2787' => 'cru', 'Carub.0005s0597' => 'cru', 'Carub.0006s1266' => 'cru', 'Ca_06935_v3' => 'car', 'Ca_13559_v3' => 'car', 'Ca_16941_v3' => 'car', 'Ca_16960_v3' => 'car', 'Ca_17775_v3' => 'car', 'Ca_30464_v3' => 'car', 'Cc06_g08160' => 'ccan', 'Cc07_g01520' => 'ccan', 'Cc11_g15810' => 'ccan', 'CDE02G2840' => 'cde', 'CDE03G0093' => 'cde', 'CDE04G2127' => 'cde', 'CDE07G1857' => 'cde', 'CDE09G1246' => 'cde', 'Cfa003412' => 'cfa', 'Cfa007341' => 'cfa', 'Cfa009220' => 'cfa', 'Ciclev10008737m.g' => 'ccl', 'Ciclev10015565m.g' => 'ccl', 'Ciclev10031761m.g' => 'ccl', 'CiPaw.03G045300' => 'cil', 'CiPaw.03G247200' => 'cil', 'CiPaw.04G029500' => 'cil', 'CiPaw.04G174000' => 'cil', 'CiPaw.05G181200' => 'cil', 'CiPaw.06G067100' => 'cil', 'ClCG05G025800' => 'cla', 'ClCG06G011400' => 'cla', 'ClCG09G019360' => 'cla', 'COL.COLO4_04827' => 'col', 'COL.COLO4_29170' => 'col', 'COL.COLO4_35131' => 'col', 'COL.COLO4_35132' => 'col', 'Cpa.g.sc33.32' => 'cpa', 'Cpa.g.sc46.29' => 'cpa', 'Cpa.g.sc796.1' => 'cpa', 'CsaV3_1G030420' => 'csa', 'CsaV3_5G027050' => 'csa', 'CsaV3_5G031040' => 'csa', 'CsaV3_UNG023130' => 'csa', 'CSS0007726' => 'camsi', 'CSS0016433' => 'camsi', 'CSS0017656' => 'camsi', 'CSS0025364' => 'camsi', 'CSS0027582' => 'camsi', 'CSS0047288' => 'camsi', 'CSS0049950' => 'camsi', 'DCAR_003843' => 'dca', 'DCAR_007052' => 'dca', 'DCAR_020884' => 'dca', 'DCAR_021730' => 'dca', 'DCAR_024423' => 'dca', 'DCAR_026509' => 'dca', 'DCAR_031158' => 'dca', 'Dinv14728' => 'din', 'Dinv15219' => 'din', 'Dinv25728' => 'din', 'Dinv33428' => 'din', 'Dinv36489' => 'din', 'Dinv41486' => 'din', 'Duzib147G0469' => 'dzi', 'Duzib168G0060' => 'dzi', 'Duzib187G1215' => 'dzi', 'Duzib248G0692' => 'dzi', 'Duzib251G0767' => 'dzi', 'Duzib264G0446' => 'dzi', 'Duzib268G0691' => 'dzi', 'ECA232G4767' => 'eca', 'ECA233G2838' => 'eca', 'ECA234G0391' => 'eca', 'ECA234G0857' => 'eca', 'ECA236G1593' => 'eca', 'ECA238G0565' => 'eca', 'ECA246G1027' => 'eca', 'ECA246G3223' => 'eca', 'ECA246G3470' => 'eca', 'EL10Ac6g13829' => 'bvu', 'EL10Ac6g14093' => 'bvu', 'EL10Ac8g18707' => 'bvu', 'Eucgr.C01369' => 'egr', 'Eucgr.H02492' => 'egr', 'Eucgr.I01733' => 'egr', 'Eucgr.J02255' => 'egr', 'Eucgr.J02257' => 'egr', 'Eucgr.J02258' => 'egr', 'FAN02G1601' => 'fan', 'FAN03G1586' => 'fan', 'FAN03G2986' => 'fan', 'FAN05G4837' => 'fan', 'FAN06G0146' => 'fan', 'FAN07G0858' => 'fan', 'FAN09G3179' => 'fan', 'FAN10G0669' => 'fan', 'FAN12G2358' => 'fan', 'FAN14G4198' => 'fan', 'FAN14G5112' => 'fan', 'FAN17G0342' => 'fan', 'FAN19G0342' => 'fan', 'FAN19G0962' => 'fan', 'FAN19G1101' => 'fan', 'FAN19G1872' => 'fan', 'FAN22G0356' => 'fan', 'FAN23G0744' => 'fan', 'FAN23G1914' => 'fan', 'FAN26G0032' => 'fan', 'FAN28G0625' => 'fan', 'FvH4_1g02710' => 'fve', 'FvH4_1g02720' => 'fve', 'FvH4_4g25670' => 'fve', 'FvH4_6g51700' => 'fve', 'FvH4_7g20170' => 'fve', 'Glyma.05G175000' => 'gma', 'Glyma.08G132300' => 'gma', 'Glyma.11G243000' => 'gma', 'Glyma.13G158900' => 'gma', 'Glyma.17G112400' => 'gma', 'Glyma.18G014100' => 'gma', 'Glyma.19G003100' => 'gma', 'Glyma.19G056500' => 'gma', 'Gohir.A01G158900' => 'ghi', 'Gohir.A05G312600' => 'ghi', 'Gohir.A05G354900' => 'ghi', 'Gohir.A07G037200' => 'ghi', 'Gohir.A09G030000' => 'ghi', 'Gohir.A12G145200' => 'ghi', 'Gohir.D01G151500' => 'ghi', 'Gohir.D04G058300' => 'ghi', 'Gohir.D05G314100' => 'ghi', 'Gohir.D07G041400' => 'ghi', 'Gohir.D09G029700' => 'ghi', 'Gohir.D12G149700' => 'ghi', 'Gorai.001G043800' => 'gra', 'Gorai.002G187800' => 'gra', 'Gorai.006G034700' => 'gra', 'Gorai.008G161200' => 'gra', 'Gorai.009G335700' => 'gra', 'Gorai.012G065000' => 'gra', 'GSVIVG01000535001' => 'vvi', 'GSVIVG01015572001' => 'vvi', 'GSVIVG01032386001' => 'vvi', 'HanXRQChr05g0138531' => 'han', 'HanXRQChr06g0174391' => 'han', 'HanXRQChr07g0199021' => 'han', 'HanXRQChr08g0208211' => 'han', 'HanXRQChr09g0255471' => 'han', 'HanXRQChr10g0315791' => 'han', 'HanXRQChr12g0371991' => 'han', 'HanXRQChr15g0475251' => 'han', 'HanXRQChr17g0540001' => 'han', 'HanXRQChr17g0548631' => 'han', 'HanXRQChr17g0569561' => 'han', 'Haze_12256' => 'cav', 'Haze_14756' => 'cav', 'Haze_25528' => 'cav', 'Hma1.2p1_0079F.1_g041020' => 'hma', 'Hma1.2p1_0818F.1_g223260' => 'hma', 'Hma1.2p1_1747F.1_g300530' => 'hma', 'HPP92_004607' => 'vpl', 'HPP92_004608' => 'vpl', 'HPP92_006181' => 'vpl', 'HPP92_012192' => 'vpl', 'HPP92_015680' => 'vpl', 'HPP92_020249' => 'vpl', 'HPP92_021376' => 'vpl', 'HPP92_024275' => 'vpl', 'Hund06031' => 'sun', 'Hund25391' => 'sun', 'Lalb_Chr07g0185371' => 'lal', 'Lalb_Chr07g0185381' => 'lal', 'Lalb_Chr12g0204011' => 'lal', 'Lalb_Chr13g0301671' => 'lal', 'Lalb_Chr14g0362851' => 'lal', 'Lalb_Chr24g0403581' => 'lal', 'Lj1g0000233' => 'lja', 'Lj2g0018120' => 'lja', 'Lj3C621T0' => 'lonja', 'Lj3P1059T14' => 'lonja', 'Lj3P611T9' => 'lonja', 'Lj3P614T13' => 'lonja', 'Lj3P615T5' => 'lonja', 'Lj4g0012315' => 'lja', 'Lj4g0026182' => 'lja', 'Lj6P813T16' => 'lonja', 'Lj7C427T7' => 'lonja', 'Lj7C427T8' => 'lonja', 'Lj7P600T41' => 'lonja', 'Lju41C42G17' => 'lonja', 'Lsat_1_v5_gn_0_47300' => 'lsa', 'Lsat_1_v5_gn_2_91280' => 'lsa', 'Lsat_1_v5_gn_3_30561' => 'lsa', 'Lsat_1_v5_gn_4_184321' => 'lsa', 'Lsat_1_v5_gn_4_4041' => 'lsa', 'Lsat_1_v5_gn_5_92000' => 'lsa', 'Lsat_1_v5_gn_8_152940' => 'lsa', 'Lsat_1_v5_gn_8_62401' => 'lsa', 'Manes.06G055900' => 'mes', 'Manes.12G022200' => 'mes', 'Manes.13G023300' => 'mes', 'Manes.14G115000' => 'mes', 'Manes.15G151700' => 'mes', 'Manes.17G111300' => 'mes', 'Mapoly0226s0009' => 'mpo', 'MBI02_g25363_MAGBIO' => 'mbi', 'MBI06_g00027_MAGBIO' => 'mbi', 'MBI10_g13034_MAGBIO' => 'mbi', 'MD09G1023400' => 'mdo', 'MD13G1100100' => 'mdo', 'MD15G1169200' => 'mdo', 'MD16G1101100' => 'mdo', 'MD17G1022900' => 'mdo', 'Medtr3g096150' => 'mtr', 'Medtr4g115070' => 'mtr', 'Medtr7g033325' => 'mtr', 'Medtr8g089840' => 'mtr', 'MELO3C010319.2' => 'cme', 'MELO3C011944.2' => 'cme', 'MELO3C021589.2' => 'cme', 'Migut.E00207' => 'egut', 'Migut.H00067' => 'egut', 'Migut.K00433' => 'egut', 'Migut.K00606' => 'egut', 'Migut.K01410' => 'egut', 'MSTRG.13347' => 'ama', 'MSTRG.24045' => 'ama', 'MSTRG.2428' => 'ama', 'MSTRG.26410' => 'ama', 'MSTRG.3139' => 'ama', 'MSTRG.3286' => 'ama', 'MSTRG.563' => 'ama', 'MSTRG.7941' => 'ama', 'Nitab4.5_0000028g0060' => 'nta', 'Nitab4.5_0000065g0260' => 'nta', 'Nitab4.5_0000112g0060' => 'nta', 'Nitab4.5_0000489g0120' => 'nta', 'Nitab4.5_0001776g0050' => 'nta', 'Nitab4.5_0001854g0010' => 'nta', 'Nitab4.5_0001860g0020' => 'nta', 'Nitab4.5_0004352g0010' => 'nta', 'Nitab4.5_0008716g0020' => 'nta', 'Nitab4.5_0008922g0010' => 'nta', 'Nn3g16693' => 'nnu', 'Nn4g22596' => 'nnu', 'Nn7g37639' => 'nnu', 'Oeu001701.1' => 'oeu', 'Oeu018149.1' => 'oeu', 'Oeu026220.1' => 'oeu', 'Oeu038635.1' => 'oeu', 'Oeu049176.1' => 'oeu', 'Oeu056706.1' => 'oeu', 'Oeu056937.1' => 'oeu', 'Oeu057540.1' => 'oeu', 'Os02g0594900' => 'osa', 'Os02g0595100' => 'osa', 'Os04g0477500' => 'osa', 'Os12g0611900' => 'osa', 'Peaxi162Scf00076g00020' => 'pax', 'Peaxi162Scf00128g00217' => 'pax', 'Peaxi162Scf00129g01640' => 'pax', 'Peaxi162Scf00669g00007' => 'pax', 'Peaxi162Scf00700g00421' => 'pax', 'Peaxi162Scf00801g00038' => 'pax', 'Peaxi162Scf00891g00025' => 'pax', 'PGR083G0909' => 'pgr', 'PGR119G1005' => 'pgr', 'PGR142G2236' => 'pgr', 'PGR142G3388' => 'pgr', 'PGSC0003DMG400004514' => 'stu', 'PGSC0003DMG400012635' => 'stu', 'PGSC0003DMG400015730' => 'stu', 'PGSC0003DMG400018611' => 'stu', 'PGSC0003DMG400030897' => 'stu', 'Phvul.001G254800' => 'pvu', 'Phvul.002G260100' => 'pvu', 'Phvul.003G167600' => 'pvu', 'Phvul.004G005100' => 'pvu', 'Potri.001G343600' => 'ptr', 'Potri.006G066700' => 'ptr', 'Potri.008G186000' => 'ptr', 'Potri.010G046900' => 'ptr', 'Potri.018G127900' => 'ptr', 'Pp3c20_17750' => 'ppa', 'Pp3c24_4380' => 'ppa', 'Prupe.1G245800' => 'ppe', 'Prupe.3G293400' => 'ppe', 'Prupe.7G247400' => 'ppe', 'Psat0s145g0120' => 'psa', 'Psat0s595g0040' => 'psa', 'Psat0s595g0120' => 'psa', 'Psat3g175040' => 'psa', 'Psat7g058120' => 'psa', 'PSO017G0428' => 'pso', 'PSO063G7510' => 'pso', 'PSO067G0046' => 'pso', 'PSO478G1073' => 'pso', 'PSO675G3677' => 'pso', 'PSO675G6558' => 'pso', 'PSO675G7520' => 'pso', 'PSO675G8959' => 'pso', 'QL02p074089' => 'qlo', 'QL02p089614' => 'qlo', 'QL03p057736' => 'qlo', 'RcHm_v2.0_Chr1g0364131' => 'rch', 'RcHm_v2.0_Chr2g0087801' => 'rch', 'RcHm_v2.0_Chr2g0087821' => 'rch', 'RcHm_v2.0_Chr2g0173231' => 'rch', 'RcHm_v2.0_Chr4g0433111' => 'rch', 'Rhsim03G0250300' => 'rsi', 'Rhsim08G0048400' => 'rsi', 'Rhsim10G0014800' => 'rsi', 'Rhsim12G0040100' => 'rsi', 'Rhsim12G0109700' => 'rsi', 'Sabra06G0049600' => 'sbr', 'Sabra08G0141000' => 'sbr', 'Sabra10G0021400' => 'sbr', 'Sabra16G0222900' => 'sbr', 'Sabra18G0108600' => 'sbr', 'SalBow1G0433' => 'sbo', 'SalBow1G2038' => 'sbo', 'SalBow1G5003' => 'sbo', 'SalBow7G1197' => 'sbo', 'SalBow8G3506' => 'sbo', 'Sc03g0007300' => 'sci', 'Sc11g0000950' => 'sci', 'Sc14g0008750' => 'sci', 'Sc18g0000420' => 'sci', 'Sed0006754' => 'sed', 'Sed0008741' => 'sed', 'Sed0017172' => 'sed', 'Sed0018925' => 'sed', 'Sed0023326' => 'sed', 'Sed0025909' => 'sed', 'SEGI_05333' => 'sgi', 'SEGI_10362' => 'sgi', 'SEGI_13380' => 'sgi', 'SEGI_24306' => 'sgi', 'SEGI_29077' => 'sgi', 'SEGI_29095' => 'sgi', 'SEGI_36534' => 'sgi', 'SEGI_37506' => 'sgi', 'SEGI_38321' => 'sgi', 'SGA_v2.0_scaffold307G48031' => 'sas', 'SGA_v2.0_scaffold47G17507' => 'sas', 'SGA_v2.0_scaffold63G21736' => 'sas', 'SGA_v2.0_scaffold87G27070' => 'sas', 'SHI17794' => 'shi', 'SHI28851' => 'shi', 'SMO165G0155' => 'smo', 'SMO340G0217' => 'smo', 'SMO367G1210' => 'smo', 'Solyc02g093430.3' => 'sly', 'Solyc05g013580.4' => 'sly', 'Solyc07g008030.3' => 'sly', 'Solyc12g035470.2' => 'sly', 'Sopen02g038020' => 'spe', 'Sopen05g008490' => 'spe', 'Sopen07g003910' => 'spe', 'Sopen12g015240' => 'spe', 'Sp1g11550' => 'spa', 'Sp2g16710' => 'spa', 'Sp3g00430' => 'spa', 'Sp3g26780' => 'spa', 'Sp5g22900' => 'spa', 'Sp6g29530' => 'spa', 'TAR371G0794' => 'tar', 'TAR374G0164' => 'tar', 'TAR622G0165' => 'tar', 'TAR626G0929' => 'tar', 'TAR629G2155' => 'tar', 'THA.LOC104805282' => 'tha', 'THA.LOC104805363' => 'tha', 'THA.LOC104808968' => 'tha', 'THA.LOC104821093' => 'tha', 'THA.LOC104823953' => 'tha', 'THA.LOC104825562' => 'tha', 'THA.LOC104825665' => 'tha', 'Thecc.02G261400' => 'tca', 'Thecc.04G019200' => 'tca', 'Thecc.09G130400' => 'tca', 'Thhalv10004374m.g' => 'esa', 'Thhalv10007850m.g' => 'esa', 'Thhalv10013782m.g' => 'esa', 'Thhalv10018686m.g' => 'esa', 'Thhalv10020899m.g' => 'esa', 'Thhalv10022755m.g' => 'esa', 'TPR.G23851' => 'tpr', 'TPR.G26500' => 'tpr', 'TPR.G27267' => 'tpr', 'TPR.G32001' => 'tpr', 'TPR.G6251' => 'tpr', 'TPR.G8167' => 'tpr', 'TWI12G1330' => 'twi', 'TWI18G1239' => 'twi', 'TWI34G0979' => 'twi', 'TWI36G0670' => 'twi', 'TWI36G0707' => 'twi', 'TWI56G0233' => 'twi', 'TWI75G1809' => 'twi', 'unitig_21.g20874' => 'ugi', 'unitig_26.g10343' => 'ugi', 'unitig_46.g18392' => 'ugi', 'unitig_52.g17178' => 'ugi', 'unitig_8.g2934' => 'ugi', 'vmacro01122' => 'vma', 'vmacro05875' => 'vma', 'vmacro06147' => 'vma', 'vmacro16191' => 'vma', 'vmacro18293' => 'vma', 'VMungo0251G3707' => 'vmu', 'VMungo0464G1521' => 'vmu', 'VMungo1215G0205' => 'vmu', 'VMungo1383G2484' => 'vmu', 'Zm00001eb079610' => 'zma', 'Zm00001eb135990' => 'zma', 'Zm00001eb183710' => 'zma', 'Zm00001eb246020' => 'zma' ), 'gf_id' => 'HOM05D001124', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001124' ), 'data_identifier' => 'HOM05D001124', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001124', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '548', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02520' => 'bna', 'A03p06630' => 'bna', 'A05p44460' => 'bna', 'A06p08710' => 'bna', 'A06p41090' => 'bna', 'A07p32320' => 'bna', 'A08p32520' => 'bna', 'A09p10360' => 'bna', 'A10p24080' => 'bna', 'Aa31LG11G15250' => 'aar', 'Aa31LG1G1800' => 'aar', 'Aa31LG2G5120' => 'aar', 'Aa31LG2G6070' => 'aar', 'Aa31LG5G10770' => 'aar', 'Aa31sc61G90' => 'aar', 'Actinidia01352' => 'ach', 'Actinidia05983' => 'ach', 'Actinidia08133' => 'ach', 'Actinidia15101' => 'ach', 'Actinidia26379' => 'ach', 'Actinidia35778' => 'ach', 'Actinidia36123' => 'ach', 'Actinidia37436' => 'ach', 'Actinidia38730' => 'ach', 'Ah.02g128210' => 'amhyb', 'Ah.03g132990' => 'amhyb', 'Ah.14g079410' => 'amhyb', 'AL1G24640' => 'aly', 'AL2G26680' => 'aly', 'AL3G10530' => 'aly', 'AL3G45230' => 'aly', 'AL5G15230' => 'aly', 'AL5G16960' => 'aly', 'AL6G25210' => 'aly', 'Aqoxy2G00441' => 'aox', 'Aqoxy3G01236' => 'aox', 'Aqoxy5G03746' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3RQ047' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C7GMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9C8JER' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MBL6KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YXCZ83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZANX40' => 'arhy', 'AT1G12990' => 'ath', 'AT1G67880' => 'ath', 'AT2G13290' => 'ath', 'AT3G01620' => 'ath', 'AT3G26445' => 'ath', 'AT3G27540' => 'ath', 'AT5G14480' => 'ath', 'ATR0824G026' => 'atr', 'ATR1098G019' => 'atr', 'Atru.chr11.2145' => 'acertr', 'Atru.chr2.3636' => 'acertr', 'Atru.chr2.3644' => 'acertr', 'Atru.chr6.2422' => 'acertr', 'Atru.chr7.1112' => 'acertr', 'AUR62005469' => 'cqu', 'AUR62011166' => 'cqu', 'AUR62013319' => 'cqu', 'AUR62024273' => 'cqu', 'AUR62028420' => 'cqu', 'AUR62041942' => 'cqu', 'BcaB01g04969' => 'bca', 'BcaB01g06371' => 'bca', 'BcaB02g11494' => 'bca', 'BcaB03g15382' => 'bca', 'BcaB08g36994' => 'bca', 'BcaC03g13477' => 'bca', 'BcaC03g13478' => 'bca', 'BcaC03g13480' => 'bca', 'BcaC03g13481' => 'bca', 'BcaC03g13486' => 'bca', 'BcaC04g19031' => 'bca', 'BcaC04g23085' => 'bca', 'BcaC05g25094' => 'bca', 'BcaC05g25096' => 'bca', 'BcaC05g25138' => 'bca', 'BcaC05g30416' => 'bca', 'BcaC05g30455' => 'bca', 'BcaC06g30979' => 'bca', 'BcaC06g33805' => 'bca', 'BcaC08g46021' => 'bca', 'BcaNung03154' => 'bca', 'BolC2t06623H' => 'bol', 'BolC2t06632H' => 'bol', 'BolC2t06635H' => 'bol', 'BolC2t06638H' => 'bol', 'BolC3t13266H' => 'bol', 'BolC5t29776H' => 'bol', 'BolC6t38912H' => 'bol', 'BolC7t44183H' => 'bol', 'BolC9t54123H' => 'bol', 'BolC9t59107H' => 'bol', 'BraA02t05221Z' => 'bra', 'BraA03t09996Z' => 'bra', 'BraA05t23210Z' => 'bra', 'BraA06t24068Z' => 'bra', 'BraA06t27032Z' => 'bra', 'BraA08t35176Z' => 'bra', 'BraA09t36680Z' => 'bra', 'BraA10t44471Z' => 'bra', 'C02p06760' => 'bna', 'C02p06890' => 'bna', 'C02p07010' => 'bna', 'C03p07660' => 'bna', 'C05p10300' => 'bna', 'C06p38150' => 'bna', 'C07p36650' => 'bna', 'C08p15770' => 'bna', 'C09p12300' => 'bna', 'C09p62700' => 'bna', 'C09p75040' => 'bna', 'CAN.G13.1' => 'can', 'CAN.G138.4' => 'can', 'CAN.G44.6' => 'can', 'CAN.G473.19' => 'can', 'CANSAT01G0835' => 'cansat', 'CANSAT11G0246' => 'cansat', 'CANSAT11G1766' => 'cansat', 'CANSAT64G1954' => 'cansat', 'CARHR013330' => 'chi', 'CARHR060530' => 'chi', 'CARHR075300' => 'chi', 'CARHR105120' => 'chi', 'CARHR148910' => 'chi', 'CARHR198830' => 'chi', 'Carub.0001s1275' => 'cru', 'Carub.0002s1437' => 'cru', 'Carub.0003s0044' => 'cru', 'Carub.0003s2787' => 'cru', 'Carub.0005s0597' => 'cru', 'Carub.0006s1266' => 'cru', 'Ca_06935_v3' => 'car', 'Ca_13559_v3' => 'car', 'Ca_16941_v3' => 'car', 'Ca_16960_v3' => 'car', 'Ca_17775_v3' => 'car', 'Ca_30464_v3' => 'car', 'Cc06_g08160' => 'ccan', 'Cc07_g01520' => 'ccan', 'Cc11_g15810' => 'ccan', 'CDE02G2840' => 'cde', 'CDE03G0093' => 'cde', 'CDE04G2127' => 'cde', 'CDE07G1857' => 'cde', 'CDE09G1246' => 'cde', 'Cfa003412' => 'cfa', 'Cfa007341' => 'cfa', 'Cfa009220' => 'cfa', 'Ciclev10008737m.g' => 'ccl', 'Ciclev10015565m.g' => 'ccl', 'Ciclev10031761m.g' => 'ccl', 'CiPaw.03G045300' => 'cil', 'CiPaw.03G247200' => 'cil', 'CiPaw.04G029500' => 'cil', 'CiPaw.04G174000' => 'cil', 'CiPaw.05G181200' => 'cil', 'CiPaw.06G067100' => 'cil', 'ClCG05G025800' => 'cla', 'ClCG06G011400' => 'cla', 'ClCG09G019360' => 'cla', 'COL.COLO4_04827' => 'col', 'COL.COLO4_29170' => 'col', 'COL.COLO4_35131' => 'col', 'COL.COLO4_35132' => 'col', 'Cpa.g.sc33.32' => 'cpa', 'Cpa.g.sc46.29' => 'cpa', 'Cpa.g.sc796.1' => 'cpa', 'CsaV3_1G030420' => 'csa', 'CsaV3_5G027050' => 'csa', 'CsaV3_5G031040' => 'csa', 'CsaV3_UNG023130' => 'csa', 'CSS0007726' => 'camsi', 'CSS0016433' => 'camsi', 'CSS0017656' => 'camsi', 'CSS0025364' => 'camsi', 'CSS0027582' => 'camsi', 'CSS0047288' => 'camsi', 'CSS0049950' => 'camsi', 'DCAR_003843' => 'dca', 'DCAR_007052' => 'dca', 'DCAR_020884' => 'dca', 'DCAR_021730' => 'dca', 'DCAR_024423' => 'dca', 'DCAR_026509' => 'dca', 'DCAR_031158' => 'dca', 'Dinv14728' => 'din', 'Dinv15219' => 'din', 'Dinv25728' => 'din', 'Dinv33428' => 'din', 'Dinv36489' => 'din', 'Dinv41486' => 'din', 'Duzib147G0469' => 'dzi', 'Duzib168G0060' => 'dzi', 'Duzib187G1215' => 'dzi', 'Duzib248G0692' => 'dzi', 'Duzib251G0767' => 'dzi', 'Duzib264G0446' => 'dzi', 'Duzib268G0691' => 'dzi', 'ECA232G4767' => 'eca', 'ECA233G2838' => 'eca', 'ECA234G0391' => 'eca', 'ECA234G0857' => 'eca', 'ECA236G1593' => 'eca', 'ECA238G0565' => 'eca', 'ECA246G1027' => 'eca', 'ECA246G3223' => 'eca', 'ECA246G3470' => 'eca', 'EL10Ac6g13829' => 'bvu', 'EL10Ac6g14093' => 'bvu', 'EL10Ac8g18707' => 'bvu', 'Eucgr.C01369' => 'egr', 'Eucgr.H02492' => 'egr', 'Eucgr.I01733' => 'egr', 'Eucgr.J02255' => 'egr', 'Eucgr.J02257' => 'egr', 'Eucgr.J02258' => 'egr', 'FAN02G1601' => 'fan', 'FAN03G1586' => 'fan', 'FAN03G2986' => 'fan', 'FAN05G4837' => 'fan', 'FAN06G0146' => 'fan', 'FAN07G0858' => 'fan', 'FAN09G3179' => 'fan', 'FAN10G0669' => 'fan', 'FAN12G2358' => 'fan', 'FAN14G4198' => 'fan', 'FAN14G5112' => 'fan', 'FAN17G0342' => 'fan', 'FAN19G0342' => 'fan', 'FAN19G0962' => 'fan', 'FAN19G1101' => 'fan', 'FAN19G1872' => 'fan', 'FAN22G0356' => 'fan', 'FAN23G0744' => 'fan', 'FAN23G1914' => 'fan', 'FAN26G0032' => 'fan', 'FAN28G0625' => 'fan', 'FvH4_1g02710' => 'fve', 'FvH4_1g02720' => 'fve', 'FvH4_4g25670' => 'fve', 'FvH4_6g51700' => 'fve', 'FvH4_7g20170' => 'fve', 'Glyma.05G175000' => 'gma', 'Glyma.08G132300' => 'gma', 'Glyma.11G243000' => 'gma', 'Glyma.13G158900' => 'gma', 'Glyma.17G112400' => 'gma', 'Glyma.18G014100' => 'gma', 'Glyma.19G003100' => 'gma', 'Glyma.19G056500' => 'gma', 'Gohir.A01G158900' => 'ghi', 'Gohir.A05G312600' => 'ghi', 'Gohir.A05G354900' => 'ghi', 'Gohir.A07G037200' => 'ghi', 'Gohir.A09G030000' => 'ghi', 'Gohir.A12G145200' => 'ghi', 'Gohir.D01G151500' => 'ghi', 'Gohir.D04G058300' => 'ghi', 'Gohir.D05G314100' => 'ghi', 'Gohir.D07G041400' => 'ghi', 'Gohir.D09G029700' => 'ghi', 'Gohir.D12G149700' => 'ghi', 'Gorai.001G043800' => 'gra', 'Gorai.002G187800' => 'gra', 'Gorai.006G034700' => 'gra', 'Gorai.008G161200' => 'gra', 'Gorai.009G335700' => 'gra', 'Gorai.012G065000' => 'gra', 'GSVIVG01000535001' => 'vvi', 'GSVIVG01015572001' => 'vvi', 'GSVIVG01032386001' => 'vvi', 'HanXRQChr05g0138531' => 'han', 'HanXRQChr06g0174391' => 'han', 'HanXRQChr07g0199021' => 'han', 'HanXRQChr08g0208211' => 'han', 'HanXRQChr09g0255471' => 'han', 'HanXRQChr10g0315791' => 'han', 'HanXRQChr12g0371991' => 'han', 'HanXRQChr15g0475251' => 'han', 'HanXRQChr17g0540001' => 'han', 'HanXRQChr17g0548631' => 'han', 'HanXRQChr17g0569561' => 'han', 'Haze_12256' => 'cav', 'Haze_14756' => 'cav', 'Haze_25528' => 'cav', 'Hma1.2p1_0079F.1_g041020' => 'hma', 'Hma1.2p1_0818F.1_g223260' => 'hma', 'Hma1.2p1_1747F.1_g300530' => 'hma', 'HPP92_004607' => 'vpl', 'HPP92_004608' => 'vpl', 'HPP92_006181' => 'vpl', 'HPP92_012192' => 'vpl', 'HPP92_015680' => 'vpl', 'HPP92_020249' => 'vpl', 'HPP92_021376' => 'vpl', 'HPP92_024275' => 'vpl', 'Hund06031' => 'sun', 'Hund25391' => 'sun', 'Lalb_Chr07g0185371' => 'lal', 'Lalb_Chr07g0185381' => 'lal', 'Lalb_Chr12g0204011' => 'lal', 'Lalb_Chr13g0301671' => 'lal', 'Lalb_Chr14g0362851' => 'lal', 'Lalb_Chr24g0403581' => 'lal', 'Lj1g0000233' => 'lja', 'Lj2g0018120' => 'lja', 'Lj3C621T0' => 'lonja', 'Lj3P1059T14' => 'lonja', 'Lj3P611T9' => 'lonja', 'Lj3P614T13' => 'lonja', 'Lj3P615T5' => 'lonja', 'Lj4g0012315' => 'lja', 'Lj4g0026182' => 'lja', 'Lj6P813T16' => 'lonja', 'Lj7C427T7' => 'lonja', 'Lj7C427T8' => 'lonja', 'Lj7P600T41' => 'lonja', 'Lju41C42G17' => 'lonja', 'Lsat_1_v5_gn_0_47300' => 'lsa', 'Lsat_1_v5_gn_2_91280' => 'lsa', 'Lsat_1_v5_gn_3_30561' => 'lsa', 'Lsat_1_v5_gn_4_184321' => 'lsa', 'Lsat_1_v5_gn_4_4041' => 'lsa', 'Lsat_1_v5_gn_5_92000' => 'lsa', 'Lsat_1_v5_gn_8_152940' => 'lsa', 'Lsat_1_v5_gn_8_62401' => 'lsa', 'Manes.06G055900' => 'mes', 'Manes.12G022200' => 'mes', 'Manes.13G023300' => 'mes', 'Manes.14G115000' => 'mes', 'Manes.15G151700' => 'mes', 'Manes.17G111300' => 'mes', 'Mapoly0226s0009' => 'mpo', 'MBI02_g25363_MAGBIO' => 'mbi', 'MBI06_g00027_MAGBIO' => 'mbi', 'MBI10_g13034_MAGBIO' => 'mbi', 'MD09G1023400' => 'mdo', 'MD13G1100100' => 'mdo', 'MD15G1169200' => 'mdo', 'MD16G1101100' => 'mdo', 'MD17G1022900' => 'mdo', 'Medtr3g096150' => 'mtr', 'Medtr4g115070' => 'mtr', 'Medtr7g033325' => 'mtr', 'Medtr8g089840' => 'mtr', 'MELO3C010319.2' => 'cme', 'MELO3C011944.2' => 'cme', 'MELO3C021589.2' => 'cme', 'Migut.E00207' => 'egut', 'Migut.H00067' => 'egut', 'Migut.K00433' => 'egut', 'Migut.K00606' => 'egut', 'Migut.K01410' => 'egut', 'MSTRG.13347' => 'ama', 'MSTRG.24045' => 'ama', 'MSTRG.2428' => 'ama', 'MSTRG.26410' => 'ama', 'MSTRG.3139' => 'ama', 'MSTRG.3286' => 'ama', 'MSTRG.563' => 'ama', 'MSTRG.7941' => 'ama', 'Nitab4.5_0000028g0060' => 'nta', 'Nitab4.5_0000065g0260' => 'nta', 'Nitab4.5_0000112g0060' => 'nta', 'Nitab4.5_0000489g0120' => 'nta', 'Nitab4.5_0001776g0050' => 'nta', 'Nitab4.5_0001854g0010' => 'nta', 'Nitab4.5_0001860g0020' => 'nta', 'Nitab4.5_0004352g0010' => 'nta', 'Nitab4.5_0008716g0020' => 'nta', 'Nitab4.5_0008922g0010' => 'nta', 'Nn3g16693' => 'nnu', 'Nn4g22596' => 'nnu', 'Nn7g37639' => 'nnu', 'Oeu001701.1' => 'oeu', 'Oeu018149.1' => 'oeu', 'Oeu026220.1' => 'oeu', 'Oeu038635.1' => 'oeu', 'Oeu049176.1' => 'oeu', 'Oeu056706.1' => 'oeu', 'Oeu056937.1' => 'oeu', 'Oeu057540.1' => 'oeu', 'Os02g0594900' => 'osa', 'Os02g0595100' => 'osa', 'Os04g0477500' => 'osa', 'Os12g0611900' => 'osa', 'Peaxi162Scf00076g00020' => 'pax', 'Peaxi162Scf00128g00217' => 'pax', 'Peaxi162Scf00129g01640' => 'pax', 'Peaxi162Scf00669g00007' => 'pax', 'Peaxi162Scf00700g00421' => 'pax', 'Peaxi162Scf00801g00038' => 'pax', 'Peaxi162Scf00891g00025' => 'pax', 'PGR083G0909' => 'pgr', 'PGR119G1005' => 'pgr', 'PGR142G2236' => 'pgr', 'PGR142G3388' => 'pgr', 'PGSC0003DMG400004514' => 'stu', 'PGSC0003DMG400012635' => 'stu', 'PGSC0003DMG400015730' => 'stu', 'PGSC0003DMG400018611' => 'stu', 'PGSC0003DMG400030897' => 'stu', 'Phvul.001G254800' => 'pvu', 'Phvul.002G260100' => 'pvu', 'Phvul.003G167600' => 'pvu', 'Phvul.004G005100' => 'pvu', 'Potri.001G343600' => 'ptr', 'Potri.006G066700' => 'ptr', 'Potri.008G186000' => 'ptr', 'Potri.010G046900' => 'ptr', 'Potri.018G127900' => 'ptr', 'Pp3c20_17750' => 'ppa', 'Pp3c24_4380' => 'ppa', 'Prupe.1G245800' => 'ppe', 'Prupe.3G293400' => 'ppe', 'Prupe.7G247400' => 'ppe', 'Psat0s145g0120' => 'psa', 'Psat0s595g0040' => 'psa', 'Psat0s595g0120' => 'psa', 'Psat3g175040' => 'psa', 'Psat7g058120' => 'psa', 'PSO017G0428' => 'pso', 'PSO063G7510' => 'pso', 'PSO067G0046' => 'pso', 'PSO478G1073' => 'pso', 'PSO675G3677' => 'pso', 'PSO675G6558' => 'pso', 'PSO675G7520' => 'pso', 'PSO675G8959' => 'pso', 'QL02p074089' => 'qlo', 'QL02p089614' => 'qlo', 'QL03p057736' => 'qlo', 'RcHm_v2.0_Chr1g0364131' => 'rch', 'RcHm_v2.0_Chr2g0087801' => 'rch', 'RcHm_v2.0_Chr2g0087821' => 'rch', 'RcHm_v2.0_Chr2g0173231' => 'rch', 'RcHm_v2.0_Chr4g0433111' => 'rch', 'Rhsim03G0250300' => 'rsi', 'Rhsim08G0048400' => 'rsi', 'Rhsim10G0014800' => 'rsi', 'Rhsim12G0040100' => 'rsi', 'Rhsim12G0109700' => 'rsi', 'Sabra06G0049600' => 'sbr', 'Sabra08G0141000' => 'sbr', 'Sabra10G0021400' => 'sbr', 'Sabra16G0222900' => 'sbr', 'Sabra18G0108600' => 'sbr', 'SalBow1G0433' => 'sbo', 'SalBow1G2038' => 'sbo', 'SalBow1G5003' => 'sbo', 'SalBow7G1197' => 'sbo', 'SalBow8G3506' => 'sbo', 'Sc03g0007300' => 'sci', 'Sc11g0000950' => 'sci', 'Sc14g0008750' => 'sci', 'Sc18g0000420' => 'sci', 'Sed0006754' => 'sed', 'Sed0008741' => 'sed', 'Sed0017172' => 'sed', 'Sed0018925' => 'sed', 'Sed0023326' => 'sed', 'Sed0025909' => 'sed', 'SEGI_05333' => 'sgi', 'SEGI_10362' => 'sgi', 'SEGI_13380' => 'sgi', 'SEGI_24306' => 'sgi', 'SEGI_29077' => 'sgi', 'SEGI_29095' => 'sgi', 'SEGI_36534' => 'sgi', 'SEGI_37506' => 'sgi', 'SEGI_38321' => 'sgi', 'SGA_v2.0_scaffold307G48031' => 'sas', 'SGA_v2.0_scaffold47G17507' => 'sas', 'SGA_v2.0_scaffold63G21736' => 'sas', 'SGA_v2.0_scaffold87G27070' => 'sas', 'SHI17794' => 'shi', 'SHI28851' => 'shi', 'SMO165G0155' => 'smo', 'SMO340G0217' => 'smo', 'SMO367G1210' => 'smo', 'Solyc02g093430.3' => 'sly', 'Solyc05g013580.4' => 'sly', 'Solyc07g008030.3' => 'sly', 'Solyc12g035470.2' => 'sly', 'Sopen02g038020' => 'spe', 'Sopen05g008490' => 'spe', 'Sopen07g003910' => 'spe', 'Sopen12g015240' => 'spe', 'Sp1g11550' => 'spa', 'Sp2g16710' => 'spa', 'Sp3g00430' => 'spa', 'Sp3g26780' => 'spa', 'Sp5g22900' => 'spa', 'Sp6g29530' => 'spa', 'TAR371G0794' => 'tar', 'TAR374G0164' => 'tar', 'TAR622G0165' => 'tar', 'TAR626G0929' => 'tar', 'TAR629G2155' => 'tar', 'THA.LOC104805282' => 'tha', 'THA.LOC104805363' => 'tha', 'THA.LOC104808968' => 'tha', 'THA.LOC104821093' => 'tha', 'THA.LOC104823953' => 'tha', 'THA.LOC104825562' => 'tha', 'THA.LOC104825665' => 'tha', 'Thecc.02G261400' => 'tca', 'Thecc.04G019200' => 'tca', 'Thecc.09G130400' => 'tca', 'Thhalv10004374m.g' => 'esa', 'Thhalv10007850m.g' => 'esa', 'Thhalv10013782m.g' => 'esa', 'Thhalv10018686m.g' => 'esa', 'Thhalv10020899m.g' => 'esa', 'Thhalv10022755m.g' => 'esa', 'TPR.G23851' => 'tpr', 'TPR.G26500' => 'tpr', 'TPR.G27267' => 'tpr', 'TPR.G32001' => 'tpr', 'TPR.G6251' => 'tpr', 'TPR.G8167' => 'tpr', 'TWI12G1330' => 'twi', 'TWI18G1239' => 'twi', 'TWI34G0979' => 'twi', 'TWI36G0670' => 'twi', 'TWI36G0707' => 'twi', 'TWI56G0233' => 'twi', 'TWI75G1809' => 'twi', 'unitig_21.g20874' => 'ugi', 'unitig_26.g10343' => 'ugi', 'unitig_46.g18392' => 'ugi', 'unitig_52.g17178' => 'ugi', 'unitig_8.g2934' => 'ugi', 'vmacro01122' => 'vma', 'vmacro05875' => 'vma', 'vmacro06147' => 'vma', 'vmacro16191' => 'vma', 'vmacro18293' => 'vma', 'VMungo0251G3707' => 'vmu', 'VMungo0464G1521' => 'vmu', 'VMungo1215G0205' => 'vmu', 'VMungo1383G2484' => 'vmu', 'Zm00001eb079610' => 'zma', 'Zm00001eb135990' => 'zma', 'Zm00001eb183710' => 'zma', 'Zm00001eb246020' => 'zma' ) $gf_id = 'HOM05D001124' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001124' ) $data_identifier = 'HOM05D001124' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 6, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 7, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 21, 'bol' => (int) 10, 'bra' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 6, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 9, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 21, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 8, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 10, 'lsa' => (int) 8, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 8, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 9, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb246020' $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' => 'HOM05D001124', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '548', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02520' => 'bna', 'A03p06630' => 'bna', 'A05p44460' => 'bna', 'A06p08710' => 'bna', 'A06p41090' => 'bna', 'A07p32320' => 'bna', 'A08p32520' => 'bna', 'A09p10360' => 'bna', 'A10p24080' => 'bna', 'Aa31LG11G15250' => 'aar', 'Aa31LG1G1800' => 'aar', 'Aa31LG2G5120' => 'aar', 'Aa31LG2G6070' => 'aar', 'Aa31LG5G10770' => 'aar', 'Aa31sc61G90' => 'aar', 'Actinidia01352' => 'ach', 'Actinidia05983' => 'ach', 'Actinidia08133' => 'ach', 'Actinidia15101' => 'ach', 'Actinidia26379' => 'ach', 'Actinidia35778' => 'ach', 'Actinidia36123' => 'ach', 'Actinidia37436' => 'ach', 'Actinidia38730' => 'ach', 'Ah.02g128210' => 'amhyb', 'Ah.03g132990' => 'amhyb', 'Ah.14g079410' => 'amhyb', 'AL1G24640' => 'aly', 'AL2G26680' => 'aly', 'AL3G10530' => 'aly', 'AL3G45230' => 'aly', 'AL5G15230' => 'aly', 'AL5G16960' => 'aly', 'AL6G25210' => 'aly', 'Aqoxy2G00441' => 'aox', 'Aqoxy3G01236' => 'aox', 'Aqoxy5G03746' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3RQ047' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C7GMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9C8JER' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MBL6KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YXCZ83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZANX40' => 'arhy', 'AT1G12990' => 'ath', 'AT1G67880' => 'ath', 'AT2G13290' => 'ath', 'AT3G01620' => 'ath', 'AT3G26445' => 'ath', 'AT3G27540' => 'ath', 'AT5G14480' => 'ath', 'ATR0824G026' => 'atr', 'ATR1098G019' => 'atr', 'Atru.chr11.2145' => 'acertr', 'Atru.chr2.3636' => 'acertr', 'Atru.chr2.3644' => 'acertr', 'Atru.chr6.2422' => 'acertr', 'Atru.chr7.1112' => 'acertr', 'AUR62005469' => 'cqu', 'AUR62011166' => 'cqu', 'AUR62013319' => 'cqu', 'AUR62024273' => 'cqu', 'AUR62028420' => 'cqu', 'AUR62041942' => 'cqu', 'BcaB01g04969' => 'bca', 'BcaB01g06371' => 'bca', 'BcaB02g11494' => 'bca', 'BcaB03g15382' => 'bca', 'BcaB08g36994' => 'bca', 'BcaC03g13477' => 'bca', 'BcaC03g13478' => 'bca', 'BcaC03g13480' => 'bca', 'BcaC03g13481' => 'bca', 'BcaC03g13486' => 'bca', 'BcaC04g19031' => 'bca', 'BcaC04g23085' => 'bca', 'BcaC05g25094' => 'bca', 'BcaC05g25096' => 'bca', 'BcaC05g25138' => 'bca', 'BcaC05g30416' => 'bca', 'BcaC05g30455' => 'bca', 'BcaC06g30979' => 'bca', 'BcaC06g33805' => 'bca', 'BcaC08g46021' => 'bca', 'BcaNung03154' => 'bca', 'BolC2t06623H' => 'bol', 'BolC2t06632H' => 'bol', 'BolC2t06635H' => 'bol', 'BolC2t06638H' => 'bol', 'BolC3t13266H' => 'bol', 'BolC5t29776H' => 'bol', 'BolC6t38912H' => 'bol', 'BolC7t44183H' => 'bol', 'BolC9t54123H' => 'bol', 'BolC9t59107H' => 'bol', 'BraA02t05221Z' => 'bra', 'BraA03t09996Z' => 'bra', 'BraA05t23210Z' => 'bra', 'BraA06t24068Z' => 'bra', 'BraA06t27032Z' => 'bra', 'BraA08t35176Z' => 'bra', 'BraA09t36680Z' => 'bra', 'BraA10t44471Z' => 'bra', 'C02p06760' => 'bna', 'C02p06890' => 'bna', 'C02p07010' => 'bna', 'C03p07660' => 'bna', 'C05p10300' => 'bna', 'C06p38150' => 'bna', 'C07p36650' => 'bna', 'C08p15770' => 'bna', 'C09p12300' => 'bna', 'C09p62700' => 'bna', 'C09p75040' => 'bna', 'CAN.G13.1' => 'can', 'CAN.G138.4' => 'can', 'CAN.G44.6' => 'can', 'CAN.G473.19' => 'can', 'CANSAT01G0835' => 'cansat', 'CANSAT11G0246' => 'cansat', 'CANSAT11G1766' => 'cansat', 'CANSAT64G1954' => 'cansat', 'CARHR013330' => 'chi', 'CARHR060530' => 'chi', 'CARHR075300' => 'chi', 'CARHR105120' => 'chi', 'CARHR148910' => 'chi', 'CARHR198830' => 'chi', 'Carub.0001s1275' => 'cru', 'Carub.0002s1437' => 'cru', 'Carub.0003s0044' => 'cru', 'Carub.0003s2787' => 'cru', 'Carub.0005s0597' => 'cru', 'Carub.0006s1266' => 'cru', 'Ca_06935_v3' => 'car', 'Ca_13559_v3' => 'car', 'Ca_16941_v3' => 'car', 'Ca_16960_v3' => 'car', 'Ca_17775_v3' => 'car', 'Ca_30464_v3' => 'car', 'Cc06_g08160' => 'ccan', 'Cc07_g01520' => 'ccan', 'Cc11_g15810' => 'ccan', 'CDE02G2840' => 'cde', 'CDE03G0093' => 'cde', 'CDE04G2127' => 'cde', 'CDE07G1857' => 'cde', 'CDE09G1246' => 'cde', 'Cfa003412' => 'cfa', 'Cfa007341' => 'cfa', 'Cfa009220' => 'cfa', 'Ciclev10008737m.g' => 'ccl', 'Ciclev10015565m.g' => 'ccl', 'Ciclev10031761m.g' => 'ccl', 'CiPaw.03G045300' => 'cil', 'CiPaw.03G247200' => 'cil', 'CiPaw.04G029500' => 'cil', 'CiPaw.04G174000' => 'cil', 'CiPaw.05G181200' => 'cil', 'CiPaw.06G067100' => 'cil', 'ClCG05G025800' => 'cla', 'ClCG06G011400' => 'cla', 'ClCG09G019360' => 'cla', 'COL.COLO4_04827' => 'col', 'COL.COLO4_29170' => 'col', 'COL.COLO4_35131' => 'col', 'COL.COLO4_35132' => 'col', 'Cpa.g.sc33.32' => 'cpa', 'Cpa.g.sc46.29' => 'cpa', 'Cpa.g.sc796.1' => 'cpa', 'CsaV3_1G030420' => 'csa', 'CsaV3_5G027050' => 'csa', 'CsaV3_5G031040' => 'csa', 'CsaV3_UNG023130' => 'csa', 'CSS0007726' => 'camsi', 'CSS0016433' => 'camsi', 'CSS0017656' => 'camsi', 'CSS0025364' => 'camsi', 'CSS0027582' => 'camsi', 'CSS0047288' => 'camsi', 'CSS0049950' => 'camsi', 'DCAR_003843' => 'dca', 'DCAR_007052' => 'dca', 'DCAR_020884' => 'dca', 'DCAR_021730' => 'dca', 'DCAR_024423' => 'dca', 'DCAR_026509' => 'dca', 'DCAR_031158' => 'dca', 'Dinv14728' => 'din', 'Dinv15219' => 'din', 'Dinv25728' => 'din', 'Dinv33428' => 'din', 'Dinv36489' => 'din', 'Dinv41486' => 'din', 'Duzib147G0469' => 'dzi', 'Duzib168G0060' => 'dzi', 'Duzib187G1215' => 'dzi', 'Duzib248G0692' => 'dzi', 'Duzib251G0767' => 'dzi', 'Duzib264G0446' => 'dzi', 'Duzib268G0691' => 'dzi', 'ECA232G4767' => 'eca', 'ECA233G2838' => 'eca', 'ECA234G0391' => 'eca', 'ECA234G0857' => 'eca', 'ECA236G1593' => 'eca', 'ECA238G0565' => 'eca', 'ECA246G1027' => 'eca', 'ECA246G3223' => 'eca', 'ECA246G3470' => 'eca', 'EL10Ac6g13829' => 'bvu', 'EL10Ac6g14093' => 'bvu', 'EL10Ac8g18707' => 'bvu', 'Eucgr.C01369' => 'egr', 'Eucgr.H02492' => 'egr', 'Eucgr.I01733' => 'egr', 'Eucgr.J02255' => 'egr', 'Eucgr.J02257' => 'egr', 'Eucgr.J02258' => 'egr', 'FAN02G1601' => 'fan', 'FAN03G1586' => 'fan', 'FAN03G2986' => 'fan', 'FAN05G4837' => 'fan', 'FAN06G0146' => 'fan', 'FAN07G0858' => 'fan', 'FAN09G3179' => 'fan', 'FAN10G0669' => 'fan', 'FAN12G2358' => 'fan', 'FAN14G4198' => 'fan', 'FAN14G5112' => 'fan', 'FAN17G0342' => 'fan', 'FAN19G0342' => 'fan', 'FAN19G0962' => 'fan', 'FAN19G1101' => 'fan', 'FAN19G1872' => 'fan', 'FAN22G0356' => 'fan', 'FAN23G0744' => 'fan', 'FAN23G1914' => 'fan', 'FAN26G0032' => 'fan', 'FAN28G0625' => 'fan', 'FvH4_1g02710' => 'fve', 'FvH4_1g02720' => 'fve', 'FvH4_4g25670' => 'fve', 'FvH4_6g51700' => 'fve', 'FvH4_7g20170' => 'fve', 'Glyma.05G175000' => 'gma', 'Glyma.08G132300' => 'gma', 'Glyma.11G243000' => 'gma', 'Glyma.13G158900' => 'gma', 'Glyma.17G112400' => 'gma', 'Glyma.18G014100' => 'gma', 'Glyma.19G003100' => 'gma', 'Glyma.19G056500' => 'gma', 'Gohir.A01G158900' => 'ghi', 'Gohir.A05G312600' => 'ghi', 'Gohir.A05G354900' => 'ghi', 'Gohir.A07G037200' => 'ghi', 'Gohir.A09G030000' => 'ghi', 'Gohir.A12G145200' => 'ghi', 'Gohir.D01G151500' => 'ghi', 'Gohir.D04G058300' => 'ghi', 'Gohir.D05G314100' => 'ghi', 'Gohir.D07G041400' => 'ghi', 'Gohir.D09G029700' => 'ghi', 'Gohir.D12G149700' => 'ghi', 'Gorai.001G043800' => 'gra', 'Gorai.002G187800' => 'gra', 'Gorai.006G034700' => 'gra', 'Gorai.008G161200' => 'gra', 'Gorai.009G335700' => 'gra', 'Gorai.012G065000' => 'gra', 'GSVIVG01000535001' => 'vvi', 'GSVIVG01015572001' => 'vvi', 'GSVIVG01032386001' => 'vvi', 'HanXRQChr05g0138531' => 'han', 'HanXRQChr06g0174391' => 'han', 'HanXRQChr07g0199021' => 'han', 'HanXRQChr08g0208211' => 'han', 'HanXRQChr09g0255471' => 'han', 'HanXRQChr10g0315791' => 'han', 'HanXRQChr12g0371991' => 'han', 'HanXRQChr15g0475251' => 'han', 'HanXRQChr17g0540001' => 'han', 'HanXRQChr17g0548631' => 'han', 'HanXRQChr17g0569561' => 'han', 'Haze_12256' => 'cav', 'Haze_14756' => 'cav', 'Haze_25528' => 'cav', 'Hma1.2p1_0079F.1_g041020' => 'hma', 'Hma1.2p1_0818F.1_g223260' => 'hma', 'Hma1.2p1_1747F.1_g300530' => 'hma', 'HPP92_004607' => 'vpl', 'HPP92_004608' => 'vpl', 'HPP92_006181' => 'vpl', 'HPP92_012192' => 'vpl', 'HPP92_015680' => 'vpl', 'HPP92_020249' => 'vpl', 'HPP92_021376' => 'vpl', 'HPP92_024275' => 'vpl', 'Hund06031' => 'sun', 'Hund25391' => 'sun', 'Lalb_Chr07g0185371' => 'lal', 'Lalb_Chr07g0185381' => 'lal', 'Lalb_Chr12g0204011' => 'lal', 'Lalb_Chr13g0301671' => 'lal', 'Lalb_Chr14g0362851' => 'lal', 'Lalb_Chr24g0403581' => 'lal', 'Lj1g0000233' => 'lja', 'Lj2g0018120' => 'lja', 'Lj3C621T0' => 'lonja', 'Lj3P1059T14' => 'lonja', 'Lj3P611T9' => 'lonja', 'Lj3P614T13' => 'lonja', 'Lj3P615T5' => 'lonja', 'Lj4g0012315' => 'lja', 'Lj4g0026182' => 'lja', 'Lj6P813T16' => 'lonja', 'Lj7C427T7' => 'lonja', 'Lj7C427T8' => 'lonja', 'Lj7P600T41' => 'lonja', 'Lju41C42G17' => 'lonja', 'Lsat_1_v5_gn_0_47300' => 'lsa', 'Lsat_1_v5_gn_2_91280' => 'lsa', 'Lsat_1_v5_gn_3_30561' => 'lsa', 'Lsat_1_v5_gn_4_184321' => 'lsa', 'Lsat_1_v5_gn_4_4041' => 'lsa', 'Lsat_1_v5_gn_5_92000' => 'lsa', 'Lsat_1_v5_gn_8_152940' => 'lsa', 'Lsat_1_v5_gn_8_62401' => 'lsa', 'Manes.06G055900' => 'mes', 'Manes.12G022200' => 'mes', 'Manes.13G023300' => 'mes', 'Manes.14G115000' => 'mes', 'Manes.15G151700' => 'mes', 'Manes.17G111300' => 'mes', 'Mapoly0226s0009' => 'mpo', 'MBI02_g25363_MAGBIO' => 'mbi', 'MBI06_g00027_MAGBIO' => 'mbi', 'MBI10_g13034_MAGBIO' => 'mbi', 'MD09G1023400' => 'mdo', 'MD13G1100100' => 'mdo', 'MD15G1169200' => 'mdo', 'MD16G1101100' => 'mdo', 'MD17G1022900' => 'mdo', 'Medtr3g096150' => 'mtr', 'Medtr4g115070' => 'mtr', 'Medtr7g033325' => 'mtr', 'Medtr8g089840' => 'mtr', 'MELO3C010319.2' => 'cme', 'MELO3C011944.2' => 'cme', 'MELO3C021589.2' => 'cme', 'Migut.E00207' => 'egut', 'Migut.H00067' => 'egut', 'Migut.K00433' => 'egut', 'Migut.K00606' => 'egut', 'Migut.K01410' => 'egut', 'MSTRG.13347' => 'ama', 'MSTRG.24045' => 'ama', 'MSTRG.2428' => 'ama', 'MSTRG.26410' => 'ama', 'MSTRG.3139' => 'ama', 'MSTRG.3286' => 'ama', 'MSTRG.563' => 'ama', 'MSTRG.7941' => 'ama', 'Nitab4.5_0000028g0060' => 'nta', 'Nitab4.5_0000065g0260' => 'nta', 'Nitab4.5_0000112g0060' => 'nta', 'Nitab4.5_0000489g0120' => 'nta', 'Nitab4.5_0001776g0050' => 'nta', 'Nitab4.5_0001854g0010' => 'nta', 'Nitab4.5_0001860g0020' => 'nta', 'Nitab4.5_0004352g0010' => 'nta', 'Nitab4.5_0008716g0020' => 'nta', 'Nitab4.5_0008922g0010' => 'nta', 'Nn3g16693' => 'nnu', 'Nn4g22596' => 'nnu', 'Nn7g37639' => 'nnu', 'Oeu001701.1' => 'oeu', 'Oeu018149.1' => 'oeu', 'Oeu026220.1' => 'oeu', 'Oeu038635.1' => 'oeu', 'Oeu049176.1' => 'oeu', 'Oeu056706.1' => 'oeu', 'Oeu056937.1' => 'oeu', 'Oeu057540.1' => 'oeu', 'Os02g0594900' => 'osa', 'Os02g0595100' => 'osa', 'Os04g0477500' => 'osa', 'Os12g0611900' => 'osa', 'Peaxi162Scf00076g00020' => 'pax', 'Peaxi162Scf00128g00217' => 'pax', 'Peaxi162Scf00129g01640' => 'pax', 'Peaxi162Scf00669g00007' => 'pax', 'Peaxi162Scf00700g00421' => 'pax', 'Peaxi162Scf00801g00038' => 'pax', 'Peaxi162Scf00891g00025' => 'pax', 'PGR083G0909' => 'pgr', 'PGR119G1005' => 'pgr', 'PGR142G2236' => 'pgr', 'PGR142G3388' => 'pgr', 'PGSC0003DMG400004514' => 'stu', 'PGSC0003DMG400012635' => 'stu', 'PGSC0003DMG400015730' => 'stu', 'PGSC0003DMG400018611' => 'stu', 'PGSC0003DMG400030897' => 'stu', 'Phvul.001G254800' => 'pvu', 'Phvul.002G260100' => 'pvu', 'Phvul.003G167600' => 'pvu', 'Phvul.004G005100' => 'pvu', 'Potri.001G343600' => 'ptr', 'Potri.006G066700' => 'ptr', 'Potri.008G186000' => 'ptr', 'Potri.010G046900' => 'ptr', 'Potri.018G127900' => 'ptr', 'Pp3c20_17750' => 'ppa', 'Pp3c24_4380' => 'ppa', 'Prupe.1G245800' => 'ppe', 'Prupe.3G293400' => 'ppe', 'Prupe.7G247400' => 'ppe', 'Psat0s145g0120' => 'psa', 'Psat0s595g0040' => 'psa', 'Psat0s595g0120' => 'psa', 'Psat3g175040' => 'psa', 'Psat7g058120' => 'psa', 'PSO017G0428' => 'pso', 'PSO063G7510' => 'pso', 'PSO067G0046' => 'pso', 'PSO478G1073' => 'pso', 'PSO675G3677' => 'pso', 'PSO675G6558' => 'pso', 'PSO675G7520' => 'pso', 'PSO675G8959' => 'pso', 'QL02p074089' => 'qlo', 'QL02p089614' => 'qlo', 'QL03p057736' => 'qlo', 'RcHm_v2.0_Chr1g0364131' => 'rch', 'RcHm_v2.0_Chr2g0087801' => 'rch', 'RcHm_v2.0_Chr2g0087821' => 'rch', 'RcHm_v2.0_Chr2g0173231' => 'rch', 'RcHm_v2.0_Chr4g0433111' => 'rch', 'Rhsim03G0250300' => 'rsi', 'Rhsim08G0048400' => 'rsi', 'Rhsim10G0014800' => 'rsi', 'Rhsim12G0040100' => 'rsi', 'Rhsim12G0109700' => 'rsi', 'Sabra06G0049600' => 'sbr', 'Sabra08G0141000' => 'sbr', 'Sabra10G0021400' => 'sbr', 'Sabra16G0222900' => 'sbr', 'Sabra18G0108600' => 'sbr', 'SalBow1G0433' => 'sbo', 'SalBow1G2038' => 'sbo', 'SalBow1G5003' => 'sbo', 'SalBow7G1197' => 'sbo', 'SalBow8G3506' => 'sbo', 'Sc03g0007300' => 'sci', 'Sc11g0000950' => 'sci', 'Sc14g0008750' => 'sci', 'Sc18g0000420' => 'sci', 'Sed0006754' => 'sed', 'Sed0008741' => 'sed', 'Sed0017172' => 'sed', 'Sed0018925' => 'sed', 'Sed0023326' => 'sed', 'Sed0025909' => 'sed', 'SEGI_05333' => 'sgi', 'SEGI_10362' => 'sgi', 'SEGI_13380' => 'sgi', 'SEGI_24306' => 'sgi', 'SEGI_29077' => 'sgi', 'SEGI_29095' => 'sgi', 'SEGI_36534' => 'sgi', 'SEGI_37506' => 'sgi', 'SEGI_38321' => 'sgi', 'SGA_v2.0_scaffold307G48031' => 'sas', 'SGA_v2.0_scaffold47G17507' => 'sas', 'SGA_v2.0_scaffold63G21736' => 'sas', 'SGA_v2.0_scaffold87G27070' => 'sas', 'SHI17794' => 'shi', 'SHI28851' => 'shi', 'SMO165G0155' => 'smo', 'SMO340G0217' => 'smo', 'SMO367G1210' => 'smo', 'Solyc02g093430.3' => 'sly', 'Solyc05g013580.4' => 'sly', 'Solyc07g008030.3' => 'sly', 'Solyc12g035470.2' => 'sly', 'Sopen02g038020' => 'spe', 'Sopen05g008490' => 'spe', 'Sopen07g003910' => 'spe', 'Sopen12g015240' => 'spe', 'Sp1g11550' => 'spa', 'Sp2g16710' => 'spa', 'Sp3g00430' => 'spa', 'Sp3g26780' => 'spa', 'Sp5g22900' => 'spa', 'Sp6g29530' => 'spa', 'TAR371G0794' => 'tar', 'TAR374G0164' => 'tar', 'TAR622G0165' => 'tar', 'TAR626G0929' => 'tar', 'TAR629G2155' => 'tar', 'THA.LOC104805282' => 'tha', 'THA.LOC104805363' => 'tha', 'THA.LOC104808968' => 'tha', 'THA.LOC104821093' => 'tha', 'THA.LOC104823953' => 'tha', 'THA.LOC104825562' => 'tha', 'THA.LOC104825665' => 'tha', 'Thecc.02G261400' => 'tca', 'Thecc.04G019200' => 'tca', 'Thecc.09G130400' => 'tca', 'Thhalv10004374m.g' => 'esa', 'Thhalv10007850m.g' => 'esa', 'Thhalv10013782m.g' => 'esa', 'Thhalv10018686m.g' => 'esa', 'Thhalv10020899m.g' => 'esa', 'Thhalv10022755m.g' => 'esa', 'TPR.G23851' => 'tpr', 'TPR.G26500' => 'tpr', 'TPR.G27267' => 'tpr', 'TPR.G32001' => 'tpr', 'TPR.G6251' => 'tpr', 'TPR.G8167' => 'tpr', 'TWI12G1330' => 'twi', 'TWI18G1239' => 'twi', 'TWI34G0979' => 'twi', 'TWI36G0670' => 'twi', 'TWI36G0707' => 'twi', 'TWI56G0233' => 'twi', 'TWI75G1809' => 'twi', 'unitig_21.g20874' => 'ugi', 'unitig_26.g10343' => 'ugi', 'unitig_46.g18392' => 'ugi', 'unitig_52.g17178' => 'ugi', 'unitig_8.g2934' => 'ugi', 'vmacro01122' => 'vma', 'vmacro05875' => 'vma', 'vmacro06147' => 'vma', 'vmacro16191' => 'vma', 'vmacro18293' => 'vma', 'VMungo0251G3707' => 'vmu', 'VMungo0464G1521' => 'vmu', 'VMungo1215G0205' => 'vmu', 'VMungo1383G2484' => 'vmu', 'Zm00001eb079610' => 'zma', 'Zm00001eb135990' => 'zma', 'Zm00001eb183710' => 'zma', 'Zm00001eb246020' => 'zma' ), 'gf_id' => 'HOM05D001124', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001124' ), 'data_identifier' => 'HOM05D001124', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001124', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '548', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02520' => 'bna', 'A03p06630' => 'bna', 'A05p44460' => 'bna', 'A06p08710' => 'bna', 'A06p41090' => 'bna', 'A07p32320' => 'bna', 'A08p32520' => 'bna', 'A09p10360' => 'bna', 'A10p24080' => 'bna', 'Aa31LG11G15250' => 'aar', 'Aa31LG1G1800' => 'aar', 'Aa31LG2G5120' => 'aar', 'Aa31LG2G6070' => 'aar', 'Aa31LG5G10770' => 'aar', 'Aa31sc61G90' => 'aar', 'Actinidia01352' => 'ach', 'Actinidia05983' => 'ach', 'Actinidia08133' => 'ach', 'Actinidia15101' => 'ach', 'Actinidia26379' => 'ach', 'Actinidia35778' => 'ach', 'Actinidia36123' => 'ach', 'Actinidia37436' => 'ach', 'Actinidia38730' => 'ach', 'Ah.02g128210' => 'amhyb', 'Ah.03g132990' => 'amhyb', 'Ah.14g079410' => 'amhyb', 'AL1G24640' => 'aly', 'AL2G26680' => 'aly', 'AL3G10530' => 'aly', 'AL3G45230' => 'aly', 'AL5G15230' => 'aly', 'AL5G16960' => 'aly', 'AL6G25210' => 'aly', 'Aqoxy2G00441' => 'aox', 'Aqoxy3G01236' => 'aox', 'Aqoxy5G03746' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3RQ047' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C7GMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9C8JER' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MBL6KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YXCZ83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZANX40' => 'arhy', 'AT1G12990' => 'ath', 'AT1G67880' => 'ath', 'AT2G13290' => 'ath', 'AT3G01620' => 'ath', 'AT3G26445' => 'ath', 'AT3G27540' => 'ath', 'AT5G14480' => 'ath', 'ATR0824G026' => 'atr', 'ATR1098G019' => 'atr', 'Atru.chr11.2145' => 'acertr', 'Atru.chr2.3636' => 'acertr', 'Atru.chr2.3644' => 'acertr', 'Atru.chr6.2422' => 'acertr', 'Atru.chr7.1112' => 'acertr', 'AUR62005469' => 'cqu', 'AUR62011166' => 'cqu', 'AUR62013319' => 'cqu', 'AUR62024273' => 'cqu', 'AUR62028420' => 'cqu', 'AUR62041942' => 'cqu', 'BcaB01g04969' => 'bca', 'BcaB01g06371' => 'bca', 'BcaB02g11494' => 'bca', 'BcaB03g15382' => 'bca', 'BcaB08g36994' => 'bca', 'BcaC03g13477' => 'bca', 'BcaC03g13478' => 'bca', 'BcaC03g13480' => 'bca', 'BcaC03g13481' => 'bca', 'BcaC03g13486' => 'bca', 'BcaC04g19031' => 'bca', 'BcaC04g23085' => 'bca', 'BcaC05g25094' => 'bca', 'BcaC05g25096' => 'bca', 'BcaC05g25138' => 'bca', 'BcaC05g30416' => 'bca', 'BcaC05g30455' => 'bca', 'BcaC06g30979' => 'bca', 'BcaC06g33805' => 'bca', 'BcaC08g46021' => 'bca', 'BcaNung03154' => 'bca', 'BolC2t06623H' => 'bol', 'BolC2t06632H' => 'bol', 'BolC2t06635H' => 'bol', 'BolC2t06638H' => 'bol', 'BolC3t13266H' => 'bol', 'BolC5t29776H' => 'bol', 'BolC6t38912H' => 'bol', 'BolC7t44183H' => 'bol', 'BolC9t54123H' => 'bol', 'BolC9t59107H' => 'bol', 'BraA02t05221Z' => 'bra', 'BraA03t09996Z' => 'bra', 'BraA05t23210Z' => 'bra', 'BraA06t24068Z' => 'bra', 'BraA06t27032Z' => 'bra', 'BraA08t35176Z' => 'bra', 'BraA09t36680Z' => 'bra', 'BraA10t44471Z' => 'bra', 'C02p06760' => 'bna', 'C02p06890' => 'bna', 'C02p07010' => 'bna', 'C03p07660' => 'bna', 'C05p10300' => 'bna', 'C06p38150' => 'bna', 'C07p36650' => 'bna', 'C08p15770' => 'bna', 'C09p12300' => 'bna', 'C09p62700' => 'bna', 'C09p75040' => 'bna', 'CAN.G13.1' => 'can', 'CAN.G138.4' => 'can', 'CAN.G44.6' => 'can', 'CAN.G473.19' => 'can', 'CANSAT01G0835' => 'cansat', 'CANSAT11G0246' => 'cansat', 'CANSAT11G1766' => 'cansat', 'CANSAT64G1954' => 'cansat', 'CARHR013330' => 'chi', 'CARHR060530' => 'chi', 'CARHR075300' => 'chi', 'CARHR105120' => 'chi', 'CARHR148910' => 'chi', 'CARHR198830' => 'chi', 'Carub.0001s1275' => 'cru', 'Carub.0002s1437' => 'cru', 'Carub.0003s0044' => 'cru', 'Carub.0003s2787' => 'cru', 'Carub.0005s0597' => 'cru', 'Carub.0006s1266' => 'cru', 'Ca_06935_v3' => 'car', 'Ca_13559_v3' => 'car', 'Ca_16941_v3' => 'car', 'Ca_16960_v3' => 'car', 'Ca_17775_v3' => 'car', 'Ca_30464_v3' => 'car', 'Cc06_g08160' => 'ccan', 'Cc07_g01520' => 'ccan', 'Cc11_g15810' => 'ccan', 'CDE02G2840' => 'cde', 'CDE03G0093' => 'cde', 'CDE04G2127' => 'cde', 'CDE07G1857' => 'cde', 'CDE09G1246' => 'cde', 'Cfa003412' => 'cfa', 'Cfa007341' => 'cfa', 'Cfa009220' => 'cfa', 'Ciclev10008737m.g' => 'ccl', 'Ciclev10015565m.g' => 'ccl', 'Ciclev10031761m.g' => 'ccl', 'CiPaw.03G045300' => 'cil', 'CiPaw.03G247200' => 'cil', 'CiPaw.04G029500' => 'cil', 'CiPaw.04G174000' => 'cil', 'CiPaw.05G181200' => 'cil', 'CiPaw.06G067100' => 'cil', 'ClCG05G025800' => 'cla', 'ClCG06G011400' => 'cla', 'ClCG09G019360' => 'cla', 'COL.COLO4_04827' => 'col', 'COL.COLO4_29170' => 'col', 'COL.COLO4_35131' => 'col', 'COL.COLO4_35132' => 'col', 'Cpa.g.sc33.32' => 'cpa', 'Cpa.g.sc46.29' => 'cpa', 'Cpa.g.sc796.1' => 'cpa', 'CsaV3_1G030420' => 'csa', 'CsaV3_5G027050' => 'csa', 'CsaV3_5G031040' => 'csa', 'CsaV3_UNG023130' => 'csa', 'CSS0007726' => 'camsi', 'CSS0016433' => 'camsi', 'CSS0017656' => 'camsi', 'CSS0025364' => 'camsi', 'CSS0027582' => 'camsi', 'CSS0047288' => 'camsi', 'CSS0049950' => 'camsi', 'DCAR_003843' => 'dca', 'DCAR_007052' => 'dca', 'DCAR_020884' => 'dca', 'DCAR_021730' => 'dca', 'DCAR_024423' => 'dca', 'DCAR_026509' => 'dca', 'DCAR_031158' => 'dca', 'Dinv14728' => 'din', 'Dinv15219' => 'din', 'Dinv25728' => 'din', 'Dinv33428' => 'din', 'Dinv36489' => 'din', 'Dinv41486' => 'din', 'Duzib147G0469' => 'dzi', 'Duzib168G0060' => 'dzi', 'Duzib187G1215' => 'dzi', 'Duzib248G0692' => 'dzi', 'Duzib251G0767' => 'dzi', 'Duzib264G0446' => 'dzi', 'Duzib268G0691' => 'dzi', 'ECA232G4767' => 'eca', 'ECA233G2838' => 'eca', 'ECA234G0391' => 'eca', 'ECA234G0857' => 'eca', 'ECA236G1593' => 'eca', 'ECA238G0565' => 'eca', 'ECA246G1027' => 'eca', 'ECA246G3223' => 'eca', 'ECA246G3470' => 'eca', 'EL10Ac6g13829' => 'bvu', 'EL10Ac6g14093' => 'bvu', 'EL10Ac8g18707' => 'bvu', 'Eucgr.C01369' => 'egr', 'Eucgr.H02492' => 'egr', 'Eucgr.I01733' => 'egr', 'Eucgr.J02255' => 'egr', 'Eucgr.J02257' => 'egr', 'Eucgr.J02258' => 'egr', 'FAN02G1601' => 'fan', 'FAN03G1586' => 'fan', 'FAN03G2986' => 'fan', 'FAN05G4837' => 'fan', 'FAN06G0146' => 'fan', 'FAN07G0858' => 'fan', 'FAN09G3179' => 'fan', 'FAN10G0669' => 'fan', 'FAN12G2358' => 'fan', 'FAN14G4198' => 'fan', 'FAN14G5112' => 'fan', 'FAN17G0342' => 'fan', 'FAN19G0342' => 'fan', 'FAN19G0962' => 'fan', 'FAN19G1101' => 'fan', 'FAN19G1872' => 'fan', 'FAN22G0356' => 'fan', 'FAN23G0744' => 'fan', 'FAN23G1914' => 'fan', 'FAN26G0032' => 'fan', 'FAN28G0625' => 'fan', 'FvH4_1g02710' => 'fve', 'FvH4_1g02720' => 'fve', 'FvH4_4g25670' => 'fve', 'FvH4_6g51700' => 'fve', 'FvH4_7g20170' => 'fve', 'Glyma.05G175000' => 'gma', 'Glyma.08G132300' => 'gma', 'Glyma.11G243000' => 'gma', 'Glyma.13G158900' => 'gma', 'Glyma.17G112400' => 'gma', 'Glyma.18G014100' => 'gma', 'Glyma.19G003100' => 'gma', 'Glyma.19G056500' => 'gma', 'Gohir.A01G158900' => 'ghi', 'Gohir.A05G312600' => 'ghi', 'Gohir.A05G354900' => 'ghi', 'Gohir.A07G037200' => 'ghi', 'Gohir.A09G030000' => 'ghi', 'Gohir.A12G145200' => 'ghi', 'Gohir.D01G151500' => 'ghi', 'Gohir.D04G058300' => 'ghi', 'Gohir.D05G314100' => 'ghi', 'Gohir.D07G041400' => 'ghi', 'Gohir.D09G029700' => 'ghi', 'Gohir.D12G149700' => 'ghi', 'Gorai.001G043800' => 'gra', 'Gorai.002G187800' => 'gra', 'Gorai.006G034700' => 'gra', 'Gorai.008G161200' => 'gra', 'Gorai.009G335700' => 'gra', 'Gorai.012G065000' => 'gra', 'GSVIVG01000535001' => 'vvi', 'GSVIVG01015572001' => 'vvi', 'GSVIVG01032386001' => 'vvi', 'HanXRQChr05g0138531' => 'han', 'HanXRQChr06g0174391' => 'han', 'HanXRQChr07g0199021' => 'han', 'HanXRQChr08g0208211' => 'han', 'HanXRQChr09g0255471' => 'han', 'HanXRQChr10g0315791' => 'han', 'HanXRQChr12g0371991' => 'han', 'HanXRQChr15g0475251' => 'han', 'HanXRQChr17g0540001' => 'han', 'HanXRQChr17g0548631' => 'han', 'HanXRQChr17g0569561' => 'han', 'Haze_12256' => 'cav', 'Haze_14756' => 'cav', 'Haze_25528' => 'cav', 'Hma1.2p1_0079F.1_g041020' => 'hma', 'Hma1.2p1_0818F.1_g223260' => 'hma', 'Hma1.2p1_1747F.1_g300530' => 'hma', 'HPP92_004607' => 'vpl', 'HPP92_004608' => 'vpl', 'HPP92_006181' => 'vpl', 'HPP92_012192' => 'vpl', 'HPP92_015680' => 'vpl', 'HPP92_020249' => 'vpl', 'HPP92_021376' => 'vpl', 'HPP92_024275' => 'vpl', 'Hund06031' => 'sun', 'Hund25391' => 'sun', 'Lalb_Chr07g0185371' => 'lal', 'Lalb_Chr07g0185381' => 'lal', 'Lalb_Chr12g0204011' => 'lal', 'Lalb_Chr13g0301671' => 'lal', 'Lalb_Chr14g0362851' => 'lal', 'Lalb_Chr24g0403581' => 'lal', 'Lj1g0000233' => 'lja', 'Lj2g0018120' => 'lja', 'Lj3C621T0' => 'lonja', 'Lj3P1059T14' => 'lonja', 'Lj3P611T9' => 'lonja', 'Lj3P614T13' => 'lonja', 'Lj3P615T5' => 'lonja', 'Lj4g0012315' => 'lja', 'Lj4g0026182' => 'lja', 'Lj6P813T16' => 'lonja', 'Lj7C427T7' => 'lonja', 'Lj7C427T8' => 'lonja', 'Lj7P600T41' => 'lonja', 'Lju41C42G17' => 'lonja', 'Lsat_1_v5_gn_0_47300' => 'lsa', 'Lsat_1_v5_gn_2_91280' => 'lsa', 'Lsat_1_v5_gn_3_30561' => 'lsa', 'Lsat_1_v5_gn_4_184321' => 'lsa', 'Lsat_1_v5_gn_4_4041' => 'lsa', 'Lsat_1_v5_gn_5_92000' => 'lsa', 'Lsat_1_v5_gn_8_152940' => 'lsa', 'Lsat_1_v5_gn_8_62401' => 'lsa', 'Manes.06G055900' => 'mes', 'Manes.12G022200' => 'mes', 'Manes.13G023300' => 'mes', 'Manes.14G115000' => 'mes', 'Manes.15G151700' => 'mes', 'Manes.17G111300' => 'mes', 'Mapoly0226s0009' => 'mpo', 'MBI02_g25363_MAGBIO' => 'mbi', 'MBI06_g00027_MAGBIO' => 'mbi', 'MBI10_g13034_MAGBIO' => 'mbi', 'MD09G1023400' => 'mdo', 'MD13G1100100' => 'mdo', 'MD15G1169200' => 'mdo', 'MD16G1101100' => 'mdo', 'MD17G1022900' => 'mdo', 'Medtr3g096150' => 'mtr', 'Medtr4g115070' => 'mtr', 'Medtr7g033325' => 'mtr', 'Medtr8g089840' => 'mtr', 'MELO3C010319.2' => 'cme', 'MELO3C011944.2' => 'cme', 'MELO3C021589.2' => 'cme', 'Migut.E00207' => 'egut', 'Migut.H00067' => 'egut', 'Migut.K00433' => 'egut', 'Migut.K00606' => 'egut', 'Migut.K01410' => 'egut', 'MSTRG.13347' => 'ama', 'MSTRG.24045' => 'ama', 'MSTRG.2428' => 'ama', 'MSTRG.26410' => 'ama', 'MSTRG.3139' => 'ama', 'MSTRG.3286' => 'ama', 'MSTRG.563' => 'ama', 'MSTRG.7941' => 'ama', 'Nitab4.5_0000028g0060' => 'nta', 'Nitab4.5_0000065g0260' => 'nta', 'Nitab4.5_0000112g0060' => 'nta', 'Nitab4.5_0000489g0120' => 'nta', 'Nitab4.5_0001776g0050' => 'nta', 'Nitab4.5_0001854g0010' => 'nta', 'Nitab4.5_0001860g0020' => 'nta', 'Nitab4.5_0004352g0010' => 'nta', 'Nitab4.5_0008716g0020' => 'nta', 'Nitab4.5_0008922g0010' => 'nta', 'Nn3g16693' => 'nnu', 'Nn4g22596' => 'nnu', 'Nn7g37639' => 'nnu', 'Oeu001701.1' => 'oeu', 'Oeu018149.1' => 'oeu', 'Oeu026220.1' => 'oeu', 'Oeu038635.1' => 'oeu', 'Oeu049176.1' => 'oeu', 'Oeu056706.1' => 'oeu', 'Oeu056937.1' => 'oeu', 'Oeu057540.1' => 'oeu', 'Os02g0594900' => 'osa', 'Os02g0595100' => 'osa', 'Os04g0477500' => 'osa', 'Os12g0611900' => 'osa', 'Peaxi162Scf00076g00020' => 'pax', 'Peaxi162Scf00128g00217' => 'pax', 'Peaxi162Scf00129g01640' => 'pax', 'Peaxi162Scf00669g00007' => 'pax', 'Peaxi162Scf00700g00421' => 'pax', 'Peaxi162Scf00801g00038' => 'pax', 'Peaxi162Scf00891g00025' => 'pax', 'PGR083G0909' => 'pgr', 'PGR119G1005' => 'pgr', 'PGR142G2236' => 'pgr', 'PGR142G3388' => 'pgr', 'PGSC0003DMG400004514' => 'stu', 'PGSC0003DMG400012635' => 'stu', 'PGSC0003DMG400015730' => 'stu', 'PGSC0003DMG400018611' => 'stu', 'PGSC0003DMG400030897' => 'stu', 'Phvul.001G254800' => 'pvu', 'Phvul.002G260100' => 'pvu', 'Phvul.003G167600' => 'pvu', 'Phvul.004G005100' => 'pvu', 'Potri.001G343600' => 'ptr', 'Potri.006G066700' => 'ptr', 'Potri.008G186000' => 'ptr', 'Potri.010G046900' => 'ptr', 'Potri.018G127900' => 'ptr', 'Pp3c20_17750' => 'ppa', 'Pp3c24_4380' => 'ppa', 'Prupe.1G245800' => 'ppe', 'Prupe.3G293400' => 'ppe', 'Prupe.7G247400' => 'ppe', 'Psat0s145g0120' => 'psa', 'Psat0s595g0040' => 'psa', 'Psat0s595g0120' => 'psa', 'Psat3g175040' => 'psa', 'Psat7g058120' => 'psa', 'PSO017G0428' => 'pso', 'PSO063G7510' => 'pso', 'PSO067G0046' => 'pso', 'PSO478G1073' => 'pso', 'PSO675G3677' => 'pso', 'PSO675G6558' => 'pso', 'PSO675G7520' => 'pso', 'PSO675G8959' => 'pso', 'QL02p074089' => 'qlo', 'QL02p089614' => 'qlo', 'QL03p057736' => 'qlo', 'RcHm_v2.0_Chr1g0364131' => 'rch', 'RcHm_v2.0_Chr2g0087801' => 'rch', 'RcHm_v2.0_Chr2g0087821' => 'rch', 'RcHm_v2.0_Chr2g0173231' => 'rch', 'RcHm_v2.0_Chr4g0433111' => 'rch', 'Rhsim03G0250300' => 'rsi', 'Rhsim08G0048400' => 'rsi', 'Rhsim10G0014800' => 'rsi', 'Rhsim12G0040100' => 'rsi', 'Rhsim12G0109700' => 'rsi', 'Sabra06G0049600' => 'sbr', 'Sabra08G0141000' => 'sbr', 'Sabra10G0021400' => 'sbr', 'Sabra16G0222900' => 'sbr', 'Sabra18G0108600' => 'sbr', 'SalBow1G0433' => 'sbo', 'SalBow1G2038' => 'sbo', 'SalBow1G5003' => 'sbo', 'SalBow7G1197' => 'sbo', 'SalBow8G3506' => 'sbo', 'Sc03g0007300' => 'sci', 'Sc11g0000950' => 'sci', 'Sc14g0008750' => 'sci', 'Sc18g0000420' => 'sci', 'Sed0006754' => 'sed', 'Sed0008741' => 'sed', 'Sed0017172' => 'sed', 'Sed0018925' => 'sed', 'Sed0023326' => 'sed', 'Sed0025909' => 'sed', 'SEGI_05333' => 'sgi', 'SEGI_10362' => 'sgi', 'SEGI_13380' => 'sgi', 'SEGI_24306' => 'sgi', 'SEGI_29077' => 'sgi', 'SEGI_29095' => 'sgi', 'SEGI_36534' => 'sgi', 'SEGI_37506' => 'sgi', 'SEGI_38321' => 'sgi', 'SGA_v2.0_scaffold307G48031' => 'sas', 'SGA_v2.0_scaffold47G17507' => 'sas', 'SGA_v2.0_scaffold63G21736' => 'sas', 'SGA_v2.0_scaffold87G27070' => 'sas', 'SHI17794' => 'shi', 'SHI28851' => 'shi', 'SMO165G0155' => 'smo', 'SMO340G0217' => 'smo', 'SMO367G1210' => 'smo', 'Solyc02g093430.3' => 'sly', 'Solyc05g013580.4' => 'sly', 'Solyc07g008030.3' => 'sly', 'Solyc12g035470.2' => 'sly', 'Sopen02g038020' => 'spe', 'Sopen05g008490' => 'spe', 'Sopen07g003910' => 'spe', 'Sopen12g015240' => 'spe', 'Sp1g11550' => 'spa', 'Sp2g16710' => 'spa', 'Sp3g00430' => 'spa', 'Sp3g26780' => 'spa', 'Sp5g22900' => 'spa', 'Sp6g29530' => 'spa', 'TAR371G0794' => 'tar', 'TAR374G0164' => 'tar', 'TAR622G0165' => 'tar', 'TAR626G0929' => 'tar', 'TAR629G2155' => 'tar', 'THA.LOC104805282' => 'tha', 'THA.LOC104805363' => 'tha', 'THA.LOC104808968' => 'tha', 'THA.LOC104821093' => 'tha', 'THA.LOC104823953' => 'tha', 'THA.LOC104825562' => 'tha', 'THA.LOC104825665' => 'tha', 'Thecc.02G261400' => 'tca', 'Thecc.04G019200' => 'tca', 'Thecc.09G130400' => 'tca', 'Thhalv10004374m.g' => 'esa', 'Thhalv10007850m.g' => 'esa', 'Thhalv10013782m.g' => 'esa', 'Thhalv10018686m.g' => 'esa', 'Thhalv10020899m.g' => 'esa', 'Thhalv10022755m.g' => 'esa', 'TPR.G23851' => 'tpr', 'TPR.G26500' => 'tpr', 'TPR.G27267' => 'tpr', 'TPR.G32001' => 'tpr', 'TPR.G6251' => 'tpr', 'TPR.G8167' => 'tpr', 'TWI12G1330' => 'twi', 'TWI18G1239' => 'twi', 'TWI34G0979' => 'twi', 'TWI36G0670' => 'twi', 'TWI36G0707' => 'twi', 'TWI56G0233' => 'twi', 'TWI75G1809' => 'twi', 'unitig_21.g20874' => 'ugi', 'unitig_26.g10343' => 'ugi', 'unitig_46.g18392' => 'ugi', 'unitig_52.g17178' => 'ugi', 'unitig_8.g2934' => 'ugi', 'vmacro01122' => 'vma', 'vmacro05875' => 'vma', 'vmacro06147' => 'vma', 'vmacro16191' => 'vma', 'vmacro18293' => 'vma', 'VMungo0251G3707' => 'vmu', 'VMungo0464G1521' => 'vmu', 'VMungo1215G0205' => 'vmu', 'VMungo1383G2484' => 'vmu', 'Zm00001eb079610' => 'zma', 'Zm00001eb135990' => 'zma', 'Zm00001eb183710' => 'zma', 'Zm00001eb246020' => 'zma' ) $gf_id = 'HOM05D001124' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001124' ) $data_identifier = 'HOM05D001124' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 6, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 7, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 21, 'bol' => (int) 10, 'bra' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 6, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 9, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 21, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 8, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 10, 'lsa' => (int) 8, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 8, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 9, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb246020' $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' => 'HOM05D001124', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '548', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02520' => 'bna', 'A03p06630' => 'bna', 'A05p44460' => 'bna', 'A06p08710' => 'bna', 'A06p41090' => 'bna', 'A07p32320' => 'bna', 'A08p32520' => 'bna', 'A09p10360' => 'bna', 'A10p24080' => 'bna', 'Aa31LG11G15250' => 'aar', 'Aa31LG1G1800' => 'aar', 'Aa31LG2G5120' => 'aar', 'Aa31LG2G6070' => 'aar', 'Aa31LG5G10770' => 'aar', 'Aa31sc61G90' => 'aar', 'Actinidia01352' => 'ach', 'Actinidia05983' => 'ach', 'Actinidia08133' => 'ach', 'Actinidia15101' => 'ach', 'Actinidia26379' => 'ach', 'Actinidia35778' => 'ach', 'Actinidia36123' => 'ach', 'Actinidia37436' => 'ach', 'Actinidia38730' => 'ach', 'Ah.02g128210' => 'amhyb', 'Ah.03g132990' => 'amhyb', 'Ah.14g079410' => 'amhyb', 'AL1G24640' => 'aly', 'AL2G26680' => 'aly', 'AL3G10530' => 'aly', 'AL3G45230' => 'aly', 'AL5G15230' => 'aly', 'AL5G16960' => 'aly', 'AL6G25210' => 'aly', 'Aqoxy2G00441' => 'aox', 'Aqoxy3G01236' => 'aox', 'Aqoxy5G03746' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3RQ047' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C7GMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9C8JER' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MBL6KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YXCZ83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZANX40' => 'arhy', 'AT1G12990' => 'ath', 'AT1G67880' => 'ath', 'AT2G13290' => 'ath', 'AT3G01620' => 'ath', 'AT3G26445' => 'ath', 'AT3G27540' => 'ath', 'AT5G14480' => 'ath', 'ATR0824G026' => 'atr', 'ATR1098G019' => 'atr', 'Atru.chr11.2145' => 'acertr', 'Atru.chr2.3636' => 'acertr', 'Atru.chr2.3644' => 'acertr', 'Atru.chr6.2422' => 'acertr', 'Atru.chr7.1112' => 'acertr', 'AUR62005469' => 'cqu', 'AUR62011166' => 'cqu', 'AUR62013319' => 'cqu', 'AUR62024273' => 'cqu', 'AUR62028420' => 'cqu', 'AUR62041942' => 'cqu', 'BcaB01g04969' => 'bca', 'BcaB01g06371' => 'bca', 'BcaB02g11494' => 'bca', 'BcaB03g15382' => 'bca', 'BcaB08g36994' => 'bca', 'BcaC03g13477' => 'bca', 'BcaC03g13478' => 'bca', 'BcaC03g13480' => 'bca', 'BcaC03g13481' => 'bca', 'BcaC03g13486' => 'bca', 'BcaC04g19031' => 'bca', 'BcaC04g23085' => 'bca', 'BcaC05g25094' => 'bca', 'BcaC05g25096' => 'bca', 'BcaC05g25138' => 'bca', 'BcaC05g30416' => 'bca', 'BcaC05g30455' => 'bca', 'BcaC06g30979' => 'bca', 'BcaC06g33805' => 'bca', 'BcaC08g46021' => 'bca', 'BcaNung03154' => 'bca', 'BolC2t06623H' => 'bol', 'BolC2t06632H' => 'bol', 'BolC2t06635H' => 'bol', 'BolC2t06638H' => 'bol', 'BolC3t13266H' => 'bol', 'BolC5t29776H' => 'bol', 'BolC6t38912H' => 'bol', 'BolC7t44183H' => 'bol', 'BolC9t54123H' => 'bol', 'BolC9t59107H' => 'bol', 'BraA02t05221Z' => 'bra', 'BraA03t09996Z' => 'bra', 'BraA05t23210Z' => 'bra', 'BraA06t24068Z' => 'bra', 'BraA06t27032Z' => 'bra', 'BraA08t35176Z' => 'bra', 'BraA09t36680Z' => 'bra', 'BraA10t44471Z' => 'bra', 'C02p06760' => 'bna', 'C02p06890' => 'bna', 'C02p07010' => 'bna', 'C03p07660' => 'bna', 'C05p10300' => 'bna', 'C06p38150' => 'bna', 'C07p36650' => 'bna', 'C08p15770' => 'bna', 'C09p12300' => 'bna', 'C09p62700' => 'bna', 'C09p75040' => 'bna', 'CAN.G13.1' => 'can', 'CAN.G138.4' => 'can', 'CAN.G44.6' => 'can', 'CAN.G473.19' => 'can', 'CANSAT01G0835' => 'cansat', 'CANSAT11G0246' => 'cansat', 'CANSAT11G1766' => 'cansat', 'CANSAT64G1954' => 'cansat', 'CARHR013330' => 'chi', 'CARHR060530' => 'chi', 'CARHR075300' => 'chi', 'CARHR105120' => 'chi', 'CARHR148910' => 'chi', 'CARHR198830' => 'chi', 'Carub.0001s1275' => 'cru', 'Carub.0002s1437' => 'cru', 'Carub.0003s0044' => 'cru', 'Carub.0003s2787' => 'cru', 'Carub.0005s0597' => 'cru', 'Carub.0006s1266' => 'cru', 'Ca_06935_v3' => 'car', 'Ca_13559_v3' => 'car', 'Ca_16941_v3' => 'car', 'Ca_16960_v3' => 'car', 'Ca_17775_v3' => 'car', 'Ca_30464_v3' => 'car', 'Cc06_g08160' => 'ccan', 'Cc07_g01520' => 'ccan', 'Cc11_g15810' => 'ccan', 'CDE02G2840' => 'cde', 'CDE03G0093' => 'cde', 'CDE04G2127' => 'cde', 'CDE07G1857' => 'cde', 'CDE09G1246' => 'cde', 'Cfa003412' => 'cfa', 'Cfa007341' => 'cfa', 'Cfa009220' => 'cfa', 'Ciclev10008737m.g' => 'ccl', 'Ciclev10015565m.g' => 'ccl', 'Ciclev10031761m.g' => 'ccl', 'CiPaw.03G045300' => 'cil', 'CiPaw.03G247200' => 'cil', 'CiPaw.04G029500' => 'cil', 'CiPaw.04G174000' => 'cil', 'CiPaw.05G181200' => 'cil', 'CiPaw.06G067100' => 'cil', 'ClCG05G025800' => 'cla', 'ClCG06G011400' => 'cla', 'ClCG09G019360' => 'cla', 'COL.COLO4_04827' => 'col', 'COL.COLO4_29170' => 'col', 'COL.COLO4_35131' => 'col', 'COL.COLO4_35132' => 'col', 'Cpa.g.sc33.32' => 'cpa', 'Cpa.g.sc46.29' => 'cpa', 'Cpa.g.sc796.1' => 'cpa', 'CsaV3_1G030420' => 'csa', 'CsaV3_5G027050' => 'csa', 'CsaV3_5G031040' => 'csa', 'CsaV3_UNG023130' => 'csa', 'CSS0007726' => 'camsi', 'CSS0016433' => 'camsi', 'CSS0017656' => 'camsi', 'CSS0025364' => 'camsi', 'CSS0027582' => 'camsi', 'CSS0047288' => 'camsi', 'CSS0049950' => 'camsi', 'DCAR_003843' => 'dca', 'DCAR_007052' => 'dca', 'DCAR_020884' => 'dca', 'DCAR_021730' => 'dca', 'DCAR_024423' => 'dca', 'DCAR_026509' => 'dca', 'DCAR_031158' => 'dca', 'Dinv14728' => 'din', 'Dinv15219' => 'din', 'Dinv25728' => 'din', 'Dinv33428' => 'din', 'Dinv36489' => 'din', 'Dinv41486' => 'din', 'Duzib147G0469' => 'dzi', 'Duzib168G0060' => 'dzi', 'Duzib187G1215' => 'dzi', 'Duzib248G0692' => 'dzi', 'Duzib251G0767' => 'dzi', 'Duzib264G0446' => 'dzi', 'Duzib268G0691' => 'dzi', 'ECA232G4767' => 'eca', 'ECA233G2838' => 'eca', 'ECA234G0391' => 'eca', 'ECA234G0857' => 'eca', 'ECA236G1593' => 'eca', 'ECA238G0565' => 'eca', 'ECA246G1027' => 'eca', 'ECA246G3223' => 'eca', 'ECA246G3470' => 'eca', 'EL10Ac6g13829' => 'bvu', 'EL10Ac6g14093' => 'bvu', 'EL10Ac8g18707' => 'bvu', 'Eucgr.C01369' => 'egr', 'Eucgr.H02492' => 'egr', 'Eucgr.I01733' => 'egr', 'Eucgr.J02255' => 'egr', 'Eucgr.J02257' => 'egr', 'Eucgr.J02258' => 'egr', 'FAN02G1601' => 'fan', 'FAN03G1586' => 'fan', 'FAN03G2986' => 'fan', 'FAN05G4837' => 'fan', 'FAN06G0146' => 'fan', 'FAN07G0858' => 'fan', 'FAN09G3179' => 'fan', 'FAN10G0669' => 'fan', 'FAN12G2358' => 'fan', 'FAN14G4198' => 'fan', 'FAN14G5112' => 'fan', 'FAN17G0342' => 'fan', 'FAN19G0342' => 'fan', 'FAN19G0962' => 'fan', 'FAN19G1101' => 'fan', 'FAN19G1872' => 'fan', 'FAN22G0356' => 'fan', 'FAN23G0744' => 'fan', 'FAN23G1914' => 'fan', 'FAN26G0032' => 'fan', 'FAN28G0625' => 'fan', 'FvH4_1g02710' => 'fve', 'FvH4_1g02720' => 'fve', 'FvH4_4g25670' => 'fve', 'FvH4_6g51700' => 'fve', 'FvH4_7g20170' => 'fve', 'Glyma.05G175000' => 'gma', 'Glyma.08G132300' => 'gma', 'Glyma.11G243000' => 'gma', 'Glyma.13G158900' => 'gma', 'Glyma.17G112400' => 'gma', 'Glyma.18G014100' => 'gma', 'Glyma.19G003100' => 'gma', 'Glyma.19G056500' => 'gma', 'Gohir.A01G158900' => 'ghi', 'Gohir.A05G312600' => 'ghi', 'Gohir.A05G354900' => 'ghi', 'Gohir.A07G037200' => 'ghi', 'Gohir.A09G030000' => 'ghi', 'Gohir.A12G145200' => 'ghi', 'Gohir.D01G151500' => 'ghi', 'Gohir.D04G058300' => 'ghi', 'Gohir.D05G314100' => 'ghi', 'Gohir.D07G041400' => 'ghi', 'Gohir.D09G029700' => 'ghi', 'Gohir.D12G149700' => 'ghi', 'Gorai.001G043800' => 'gra', 'Gorai.002G187800' => 'gra', 'Gorai.006G034700' => 'gra', 'Gorai.008G161200' => 'gra', 'Gorai.009G335700' => 'gra', 'Gorai.012G065000' => 'gra', 'GSVIVG01000535001' => 'vvi', 'GSVIVG01015572001' => 'vvi', 'GSVIVG01032386001' => 'vvi', 'HanXRQChr05g0138531' => 'han', 'HanXRQChr06g0174391' => 'han', 'HanXRQChr07g0199021' => 'han', 'HanXRQChr08g0208211' => 'han', 'HanXRQChr09g0255471' => 'han', 'HanXRQChr10g0315791' => 'han', 'HanXRQChr12g0371991' => 'han', 'HanXRQChr15g0475251' => 'han', 'HanXRQChr17g0540001' => 'han', 'HanXRQChr17g0548631' => 'han', 'HanXRQChr17g0569561' => 'han', 'Haze_12256' => 'cav', 'Haze_14756' => 'cav', 'Haze_25528' => 'cav', 'Hma1.2p1_0079F.1_g041020' => 'hma', 'Hma1.2p1_0818F.1_g223260' => 'hma', 'Hma1.2p1_1747F.1_g300530' => 'hma', 'HPP92_004607' => 'vpl', 'HPP92_004608' => 'vpl', 'HPP92_006181' => 'vpl', 'HPP92_012192' => 'vpl', 'HPP92_015680' => 'vpl', 'HPP92_020249' => 'vpl', 'HPP92_021376' => 'vpl', 'HPP92_024275' => 'vpl', 'Hund06031' => 'sun', 'Hund25391' => 'sun', 'Lalb_Chr07g0185371' => 'lal', 'Lalb_Chr07g0185381' => 'lal', 'Lalb_Chr12g0204011' => 'lal', 'Lalb_Chr13g0301671' => 'lal', 'Lalb_Chr14g0362851' => 'lal', 'Lalb_Chr24g0403581' => 'lal', 'Lj1g0000233' => 'lja', 'Lj2g0018120' => 'lja', 'Lj3C621T0' => 'lonja', 'Lj3P1059T14' => 'lonja', 'Lj3P611T9' => 'lonja', 'Lj3P614T13' => 'lonja', 'Lj3P615T5' => 'lonja', 'Lj4g0012315' => 'lja', 'Lj4g0026182' => 'lja', 'Lj6P813T16' => 'lonja', 'Lj7C427T7' => 'lonja', 'Lj7C427T8' => 'lonja', 'Lj7P600T41' => 'lonja', 'Lju41C42G17' => 'lonja', 'Lsat_1_v5_gn_0_47300' => 'lsa', 'Lsat_1_v5_gn_2_91280' => 'lsa', 'Lsat_1_v5_gn_3_30561' => 'lsa', 'Lsat_1_v5_gn_4_184321' => 'lsa', 'Lsat_1_v5_gn_4_4041' => 'lsa', 'Lsat_1_v5_gn_5_92000' => 'lsa', 'Lsat_1_v5_gn_8_152940' => 'lsa', 'Lsat_1_v5_gn_8_62401' => 'lsa', 'Manes.06G055900' => 'mes', 'Manes.12G022200' => 'mes', 'Manes.13G023300' => 'mes', 'Manes.14G115000' => 'mes', 'Manes.15G151700' => 'mes', 'Manes.17G111300' => 'mes', 'Mapoly0226s0009' => 'mpo', 'MBI02_g25363_MAGBIO' => 'mbi', 'MBI06_g00027_MAGBIO' => 'mbi', 'MBI10_g13034_MAGBIO' => 'mbi', 'MD09G1023400' => 'mdo', 'MD13G1100100' => 'mdo', 'MD15G1169200' => 'mdo', 'MD16G1101100' => 'mdo', 'MD17G1022900' => 'mdo', 'Medtr3g096150' => 'mtr', 'Medtr4g115070' => 'mtr', 'Medtr7g033325' => 'mtr', 'Medtr8g089840' => 'mtr', 'MELO3C010319.2' => 'cme', 'MELO3C011944.2' => 'cme', 'MELO3C021589.2' => 'cme', 'Migut.E00207' => 'egut', 'Migut.H00067' => 'egut', 'Migut.K00433' => 'egut', 'Migut.K00606' => 'egut', 'Migut.K01410' => 'egut', 'MSTRG.13347' => 'ama', 'MSTRG.24045' => 'ama', 'MSTRG.2428' => 'ama', 'MSTRG.26410' => 'ama', 'MSTRG.3139' => 'ama', 'MSTRG.3286' => 'ama', 'MSTRG.563' => 'ama', 'MSTRG.7941' => 'ama', 'Nitab4.5_0000028g0060' => 'nta', 'Nitab4.5_0000065g0260' => 'nta', 'Nitab4.5_0000112g0060' => 'nta', 'Nitab4.5_0000489g0120' => 'nta', 'Nitab4.5_0001776g0050' => 'nta', 'Nitab4.5_0001854g0010' => 'nta', 'Nitab4.5_0001860g0020' => 'nta', 'Nitab4.5_0004352g0010' => 'nta', 'Nitab4.5_0008716g0020' => 'nta', 'Nitab4.5_0008922g0010' => 'nta', 'Nn3g16693' => 'nnu', 'Nn4g22596' => 'nnu', 'Nn7g37639' => 'nnu', 'Oeu001701.1' => 'oeu', 'Oeu018149.1' => 'oeu', 'Oeu026220.1' => 'oeu', 'Oeu038635.1' => 'oeu', 'Oeu049176.1' => 'oeu', 'Oeu056706.1' => 'oeu', 'Oeu056937.1' => 'oeu', 'Oeu057540.1' => 'oeu', 'Os02g0594900' => 'osa', 'Os02g0595100' => 'osa', 'Os04g0477500' => 'osa', 'Os12g0611900' => 'osa', 'Peaxi162Scf00076g00020' => 'pax', 'Peaxi162Scf00128g00217' => 'pax', 'Peaxi162Scf00129g01640' => 'pax', 'Peaxi162Scf00669g00007' => 'pax', 'Peaxi162Scf00700g00421' => 'pax', 'Peaxi162Scf00801g00038' => 'pax', 'Peaxi162Scf00891g00025' => 'pax', 'PGR083G0909' => 'pgr', 'PGR119G1005' => 'pgr', 'PGR142G2236' => 'pgr', 'PGR142G3388' => 'pgr', 'PGSC0003DMG400004514' => 'stu', 'PGSC0003DMG400012635' => 'stu', 'PGSC0003DMG400015730' => 'stu', 'PGSC0003DMG400018611' => 'stu', 'PGSC0003DMG400030897' => 'stu', 'Phvul.001G254800' => 'pvu', 'Phvul.002G260100' => 'pvu', 'Phvul.003G167600' => 'pvu', 'Phvul.004G005100' => 'pvu', 'Potri.001G343600' => 'ptr', 'Potri.006G066700' => 'ptr', 'Potri.008G186000' => 'ptr', 'Potri.010G046900' => 'ptr', 'Potri.018G127900' => 'ptr', 'Pp3c20_17750' => 'ppa', 'Pp3c24_4380' => 'ppa', 'Prupe.1G245800' => 'ppe', 'Prupe.3G293400' => 'ppe', 'Prupe.7G247400' => 'ppe', 'Psat0s145g0120' => 'psa', 'Psat0s595g0040' => 'psa', 'Psat0s595g0120' => 'psa', 'Psat3g175040' => 'psa', 'Psat7g058120' => 'psa', 'PSO017G0428' => 'pso', 'PSO063G7510' => 'pso', 'PSO067G0046' => 'pso', 'PSO478G1073' => 'pso', 'PSO675G3677' => 'pso', 'PSO675G6558' => 'pso', 'PSO675G7520' => 'pso', 'PSO675G8959' => 'pso', 'QL02p074089' => 'qlo', 'QL02p089614' => 'qlo', 'QL03p057736' => 'qlo', 'RcHm_v2.0_Chr1g0364131' => 'rch', 'RcHm_v2.0_Chr2g0087801' => 'rch', 'RcHm_v2.0_Chr2g0087821' => 'rch', 'RcHm_v2.0_Chr2g0173231' => 'rch', 'RcHm_v2.0_Chr4g0433111' => 'rch', 'Rhsim03G0250300' => 'rsi', 'Rhsim08G0048400' => 'rsi', 'Rhsim10G0014800' => 'rsi', 'Rhsim12G0040100' => 'rsi', 'Rhsim12G0109700' => 'rsi', 'Sabra06G0049600' => 'sbr', 'Sabra08G0141000' => 'sbr', 'Sabra10G0021400' => 'sbr', 'Sabra16G0222900' => 'sbr', 'Sabra18G0108600' => 'sbr', 'SalBow1G0433' => 'sbo', 'SalBow1G2038' => 'sbo', 'SalBow1G5003' => 'sbo', 'SalBow7G1197' => 'sbo', 'SalBow8G3506' => 'sbo', 'Sc03g0007300' => 'sci', 'Sc11g0000950' => 'sci', 'Sc14g0008750' => 'sci', 'Sc18g0000420' => 'sci', 'Sed0006754' => 'sed', 'Sed0008741' => 'sed', 'Sed0017172' => 'sed', 'Sed0018925' => 'sed', 'Sed0023326' => 'sed', 'Sed0025909' => 'sed', 'SEGI_05333' => 'sgi', 'SEGI_10362' => 'sgi', 'SEGI_13380' => 'sgi', 'SEGI_24306' => 'sgi', 'SEGI_29077' => 'sgi', 'SEGI_29095' => 'sgi', 'SEGI_36534' => 'sgi', 'SEGI_37506' => 'sgi', 'SEGI_38321' => 'sgi', 'SGA_v2.0_scaffold307G48031' => 'sas', 'SGA_v2.0_scaffold47G17507' => 'sas', 'SGA_v2.0_scaffold63G21736' => 'sas', 'SGA_v2.0_scaffold87G27070' => 'sas', 'SHI17794' => 'shi', 'SHI28851' => 'shi', 'SMO165G0155' => 'smo', 'SMO340G0217' => 'smo', 'SMO367G1210' => 'smo', 'Solyc02g093430.3' => 'sly', 'Solyc05g013580.4' => 'sly', 'Solyc07g008030.3' => 'sly', 'Solyc12g035470.2' => 'sly', 'Sopen02g038020' => 'spe', 'Sopen05g008490' => 'spe', 'Sopen07g003910' => 'spe', 'Sopen12g015240' => 'spe', 'Sp1g11550' => 'spa', 'Sp2g16710' => 'spa', 'Sp3g00430' => 'spa', 'Sp3g26780' => 'spa', 'Sp5g22900' => 'spa', 'Sp6g29530' => 'spa', 'TAR371G0794' => 'tar', 'TAR374G0164' => 'tar', 'TAR622G0165' => 'tar', 'TAR626G0929' => 'tar', 'TAR629G2155' => 'tar', 'THA.LOC104805282' => 'tha', 'THA.LOC104805363' => 'tha', 'THA.LOC104808968' => 'tha', 'THA.LOC104821093' => 'tha', 'THA.LOC104823953' => 'tha', 'THA.LOC104825562' => 'tha', 'THA.LOC104825665' => 'tha', 'Thecc.02G261400' => 'tca', 'Thecc.04G019200' => 'tca', 'Thecc.09G130400' => 'tca', 'Thhalv10004374m.g' => 'esa', 'Thhalv10007850m.g' => 'esa', 'Thhalv10013782m.g' => 'esa', 'Thhalv10018686m.g' => 'esa', 'Thhalv10020899m.g' => 'esa', 'Thhalv10022755m.g' => 'esa', 'TPR.G23851' => 'tpr', 'TPR.G26500' => 'tpr', 'TPR.G27267' => 'tpr', 'TPR.G32001' => 'tpr', 'TPR.G6251' => 'tpr', 'TPR.G8167' => 'tpr', 'TWI12G1330' => 'twi', 'TWI18G1239' => 'twi', 'TWI34G0979' => 'twi', 'TWI36G0670' => 'twi', 'TWI36G0707' => 'twi', 'TWI56G0233' => 'twi', 'TWI75G1809' => 'twi', 'unitig_21.g20874' => 'ugi', 'unitig_26.g10343' => 'ugi', 'unitig_46.g18392' => 'ugi', 'unitig_52.g17178' => 'ugi', 'unitig_8.g2934' => 'ugi', 'vmacro01122' => 'vma', 'vmacro05875' => 'vma', 'vmacro06147' => 'vma', 'vmacro16191' => 'vma', 'vmacro18293' => 'vma', 'VMungo0251G3707' => 'vmu', 'VMungo0464G1521' => 'vmu', 'VMungo1215G0205' => 'vmu', 'VMungo1383G2484' => 'vmu', 'Zm00001eb079610' => 'zma', 'Zm00001eb135990' => 'zma', 'Zm00001eb183710' => 'zma', 'Zm00001eb246020' => 'zma' ), 'gf_id' => 'HOM05D001124', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001124' ), 'data_identifier' => 'HOM05D001124', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001124', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '548', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02520' => 'bna', 'A03p06630' => 'bna', 'A05p44460' => 'bna', 'A06p08710' => 'bna', 'A06p41090' => 'bna', 'A07p32320' => 'bna', 'A08p32520' => 'bna', 'A09p10360' => 'bna', 'A10p24080' => 'bna', 'Aa31LG11G15250' => 'aar', 'Aa31LG1G1800' => 'aar', 'Aa31LG2G5120' => 'aar', 'Aa31LG2G6070' => 'aar', 'Aa31LG5G10770' => 'aar', 'Aa31sc61G90' => 'aar', 'Actinidia01352' => 'ach', 'Actinidia05983' => 'ach', 'Actinidia08133' => 'ach', 'Actinidia15101' => 'ach', 'Actinidia26379' => 'ach', 'Actinidia35778' => 'ach', 'Actinidia36123' => 'ach', 'Actinidia37436' => 'ach', 'Actinidia38730' => 'ach', 'Ah.02g128210' => 'amhyb', 'Ah.03g132990' => 'amhyb', 'Ah.14g079410' => 'amhyb', 'AL1G24640' => 'aly', 'AL2G26680' => 'aly', 'AL3G10530' => 'aly', 'AL3G45230' => 'aly', 'AL5G15230' => 'aly', 'AL5G16960' => 'aly', 'AL6G25210' => 'aly', 'Aqoxy2G00441' => 'aox', 'Aqoxy3G01236' => 'aox', 'Aqoxy5G03746' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3RQ047' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C7GMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9C8JER' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MBL6KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YXCZ83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZANX40' => 'arhy', 'AT1G12990' => 'ath', 'AT1G67880' => 'ath', 'AT2G13290' => 'ath', 'AT3G01620' => 'ath', 'AT3G26445' => 'ath', 'AT3G27540' => 'ath', 'AT5G14480' => 'ath', 'ATR0824G026' => 'atr', 'ATR1098G019' => 'atr', 'Atru.chr11.2145' => 'acertr', 'Atru.chr2.3636' => 'acertr', 'Atru.chr2.3644' => 'acertr', 'Atru.chr6.2422' => 'acertr', 'Atru.chr7.1112' => 'acertr', 'AUR62005469' => 'cqu', 'AUR62011166' => 'cqu', 'AUR62013319' => 'cqu', 'AUR62024273' => 'cqu', 'AUR62028420' => 'cqu', 'AUR62041942' => 'cqu', 'BcaB01g04969' => 'bca', 'BcaB01g06371' => 'bca', 'BcaB02g11494' => 'bca', 'BcaB03g15382' => 'bca', 'BcaB08g36994' => 'bca', 'BcaC03g13477' => 'bca', 'BcaC03g13478' => 'bca', 'BcaC03g13480' => 'bca', 'BcaC03g13481' => 'bca', 'BcaC03g13486' => 'bca', 'BcaC04g19031' => 'bca', 'BcaC04g23085' => 'bca', 'BcaC05g25094' => 'bca', 'BcaC05g25096' => 'bca', 'BcaC05g25138' => 'bca', 'BcaC05g30416' => 'bca', 'BcaC05g30455' => 'bca', 'BcaC06g30979' => 'bca', 'BcaC06g33805' => 'bca', 'BcaC08g46021' => 'bca', 'BcaNung03154' => 'bca', 'BolC2t06623H' => 'bol', 'BolC2t06632H' => 'bol', 'BolC2t06635H' => 'bol', 'BolC2t06638H' => 'bol', 'BolC3t13266H' => 'bol', 'BolC5t29776H' => 'bol', 'BolC6t38912H' => 'bol', 'BolC7t44183H' => 'bol', 'BolC9t54123H' => 'bol', 'BolC9t59107H' => 'bol', 'BraA02t05221Z' => 'bra', 'BraA03t09996Z' => 'bra', 'BraA05t23210Z' => 'bra', 'BraA06t24068Z' => 'bra', 'BraA06t27032Z' => 'bra', 'BraA08t35176Z' => 'bra', 'BraA09t36680Z' => 'bra', 'BraA10t44471Z' => 'bra', 'C02p06760' => 'bna', 'C02p06890' => 'bna', 'C02p07010' => 'bna', 'C03p07660' => 'bna', 'C05p10300' => 'bna', 'C06p38150' => 'bna', 'C07p36650' => 'bna', 'C08p15770' => 'bna', 'C09p12300' => 'bna', 'C09p62700' => 'bna', 'C09p75040' => 'bna', 'CAN.G13.1' => 'can', 'CAN.G138.4' => 'can', 'CAN.G44.6' => 'can', 'CAN.G473.19' => 'can', 'CANSAT01G0835' => 'cansat', 'CANSAT11G0246' => 'cansat', 'CANSAT11G1766' => 'cansat', 'CANSAT64G1954' => 'cansat', 'CARHR013330' => 'chi', 'CARHR060530' => 'chi', 'CARHR075300' => 'chi', 'CARHR105120' => 'chi', 'CARHR148910' => 'chi', 'CARHR198830' => 'chi', 'Carub.0001s1275' => 'cru', 'Carub.0002s1437' => 'cru', 'Carub.0003s0044' => 'cru', 'Carub.0003s2787' => 'cru', 'Carub.0005s0597' => 'cru', 'Carub.0006s1266' => 'cru', 'Ca_06935_v3' => 'car', 'Ca_13559_v3' => 'car', 'Ca_16941_v3' => 'car', 'Ca_16960_v3' => 'car', 'Ca_17775_v3' => 'car', 'Ca_30464_v3' => 'car', 'Cc06_g08160' => 'ccan', 'Cc07_g01520' => 'ccan', 'Cc11_g15810' => 'ccan', 'CDE02G2840' => 'cde', 'CDE03G0093' => 'cde', 'CDE04G2127' => 'cde', 'CDE07G1857' => 'cde', 'CDE09G1246' => 'cde', 'Cfa003412' => 'cfa', 'Cfa007341' => 'cfa', 'Cfa009220' => 'cfa', 'Ciclev10008737m.g' => 'ccl', 'Ciclev10015565m.g' => 'ccl', 'Ciclev10031761m.g' => 'ccl', 'CiPaw.03G045300' => 'cil', 'CiPaw.03G247200' => 'cil', 'CiPaw.04G029500' => 'cil', 'CiPaw.04G174000' => 'cil', 'CiPaw.05G181200' => 'cil', 'CiPaw.06G067100' => 'cil', 'ClCG05G025800' => 'cla', 'ClCG06G011400' => 'cla', 'ClCG09G019360' => 'cla', 'COL.COLO4_04827' => 'col', 'COL.COLO4_29170' => 'col', 'COL.COLO4_35131' => 'col', 'COL.COLO4_35132' => 'col', 'Cpa.g.sc33.32' => 'cpa', 'Cpa.g.sc46.29' => 'cpa', 'Cpa.g.sc796.1' => 'cpa', 'CsaV3_1G030420' => 'csa', 'CsaV3_5G027050' => 'csa', 'CsaV3_5G031040' => 'csa', 'CsaV3_UNG023130' => 'csa', 'CSS0007726' => 'camsi', 'CSS0016433' => 'camsi', 'CSS0017656' => 'camsi', 'CSS0025364' => 'camsi', 'CSS0027582' => 'camsi', 'CSS0047288' => 'camsi', 'CSS0049950' => 'camsi', 'DCAR_003843' => 'dca', 'DCAR_007052' => 'dca', 'DCAR_020884' => 'dca', 'DCAR_021730' => 'dca', 'DCAR_024423' => 'dca', 'DCAR_026509' => 'dca', 'DCAR_031158' => 'dca', 'Dinv14728' => 'din', 'Dinv15219' => 'din', 'Dinv25728' => 'din', 'Dinv33428' => 'din', 'Dinv36489' => 'din', 'Dinv41486' => 'din', 'Duzib147G0469' => 'dzi', 'Duzib168G0060' => 'dzi', 'Duzib187G1215' => 'dzi', 'Duzib248G0692' => 'dzi', 'Duzib251G0767' => 'dzi', 'Duzib264G0446' => 'dzi', 'Duzib268G0691' => 'dzi', 'ECA232G4767' => 'eca', 'ECA233G2838' => 'eca', 'ECA234G0391' => 'eca', 'ECA234G0857' => 'eca', 'ECA236G1593' => 'eca', 'ECA238G0565' => 'eca', 'ECA246G1027' => 'eca', 'ECA246G3223' => 'eca', 'ECA246G3470' => 'eca', 'EL10Ac6g13829' => 'bvu', 'EL10Ac6g14093' => 'bvu', 'EL10Ac8g18707' => 'bvu', 'Eucgr.C01369' => 'egr', 'Eucgr.H02492' => 'egr', 'Eucgr.I01733' => 'egr', 'Eucgr.J02255' => 'egr', 'Eucgr.J02257' => 'egr', 'Eucgr.J02258' => 'egr', 'FAN02G1601' => 'fan', 'FAN03G1586' => 'fan', 'FAN03G2986' => 'fan', 'FAN05G4837' => 'fan', 'FAN06G0146' => 'fan', 'FAN07G0858' => 'fan', 'FAN09G3179' => 'fan', 'FAN10G0669' => 'fan', 'FAN12G2358' => 'fan', 'FAN14G4198' => 'fan', 'FAN14G5112' => 'fan', 'FAN17G0342' => 'fan', 'FAN19G0342' => 'fan', 'FAN19G0962' => 'fan', 'FAN19G1101' => 'fan', 'FAN19G1872' => 'fan', 'FAN22G0356' => 'fan', 'FAN23G0744' => 'fan', 'FAN23G1914' => 'fan', 'FAN26G0032' => 'fan', 'FAN28G0625' => 'fan', 'FvH4_1g02710' => 'fve', 'FvH4_1g02720' => 'fve', 'FvH4_4g25670' => 'fve', 'FvH4_6g51700' => 'fve', 'FvH4_7g20170' => 'fve', 'Glyma.05G175000' => 'gma', 'Glyma.08G132300' => 'gma', 'Glyma.11G243000' => 'gma', 'Glyma.13G158900' => 'gma', 'Glyma.17G112400' => 'gma', 'Glyma.18G014100' => 'gma', 'Glyma.19G003100' => 'gma', 'Glyma.19G056500' => 'gma', 'Gohir.A01G158900' => 'ghi', 'Gohir.A05G312600' => 'ghi', 'Gohir.A05G354900' => 'ghi', 'Gohir.A07G037200' => 'ghi', 'Gohir.A09G030000' => 'ghi', 'Gohir.A12G145200' => 'ghi', 'Gohir.D01G151500' => 'ghi', 'Gohir.D04G058300' => 'ghi', 'Gohir.D05G314100' => 'ghi', 'Gohir.D07G041400' => 'ghi', 'Gohir.D09G029700' => 'ghi', 'Gohir.D12G149700' => 'ghi', 'Gorai.001G043800' => 'gra', 'Gorai.002G187800' => 'gra', 'Gorai.006G034700' => 'gra', 'Gorai.008G161200' => 'gra', 'Gorai.009G335700' => 'gra', 'Gorai.012G065000' => 'gra', 'GSVIVG01000535001' => 'vvi', 'GSVIVG01015572001' => 'vvi', 'GSVIVG01032386001' => 'vvi', 'HanXRQChr05g0138531' => 'han', 'HanXRQChr06g0174391' => 'han', 'HanXRQChr07g0199021' => 'han', 'HanXRQChr08g0208211' => 'han', 'HanXRQChr09g0255471' => 'han', 'HanXRQChr10g0315791' => 'han', 'HanXRQChr12g0371991' => 'han', 'HanXRQChr15g0475251' => 'han', 'HanXRQChr17g0540001' => 'han', 'HanXRQChr17g0548631' => 'han', 'HanXRQChr17g0569561' => 'han', 'Haze_12256' => 'cav', 'Haze_14756' => 'cav', 'Haze_25528' => 'cav', 'Hma1.2p1_0079F.1_g041020' => 'hma', 'Hma1.2p1_0818F.1_g223260' => 'hma', 'Hma1.2p1_1747F.1_g300530' => 'hma', 'HPP92_004607' => 'vpl', 'HPP92_004608' => 'vpl', 'HPP92_006181' => 'vpl', 'HPP92_012192' => 'vpl', 'HPP92_015680' => 'vpl', 'HPP92_020249' => 'vpl', 'HPP92_021376' => 'vpl', 'HPP92_024275' => 'vpl', 'Hund06031' => 'sun', 'Hund25391' => 'sun', 'Lalb_Chr07g0185371' => 'lal', 'Lalb_Chr07g0185381' => 'lal', 'Lalb_Chr12g0204011' => 'lal', 'Lalb_Chr13g0301671' => 'lal', 'Lalb_Chr14g0362851' => 'lal', 'Lalb_Chr24g0403581' => 'lal', 'Lj1g0000233' => 'lja', 'Lj2g0018120' => 'lja', 'Lj3C621T0' => 'lonja', 'Lj3P1059T14' => 'lonja', 'Lj3P611T9' => 'lonja', 'Lj3P614T13' => 'lonja', 'Lj3P615T5' => 'lonja', 'Lj4g0012315' => 'lja', 'Lj4g0026182' => 'lja', 'Lj6P813T16' => 'lonja', 'Lj7C427T7' => 'lonja', 'Lj7C427T8' => 'lonja', 'Lj7P600T41' => 'lonja', 'Lju41C42G17' => 'lonja', 'Lsat_1_v5_gn_0_47300' => 'lsa', 'Lsat_1_v5_gn_2_91280' => 'lsa', 'Lsat_1_v5_gn_3_30561' => 'lsa', 'Lsat_1_v5_gn_4_184321' => 'lsa', 'Lsat_1_v5_gn_4_4041' => 'lsa', 'Lsat_1_v5_gn_5_92000' => 'lsa', 'Lsat_1_v5_gn_8_152940' => 'lsa', 'Lsat_1_v5_gn_8_62401' => 'lsa', 'Manes.06G055900' => 'mes', 'Manes.12G022200' => 'mes', 'Manes.13G023300' => 'mes', 'Manes.14G115000' => 'mes', 'Manes.15G151700' => 'mes', 'Manes.17G111300' => 'mes', 'Mapoly0226s0009' => 'mpo', 'MBI02_g25363_MAGBIO' => 'mbi', 'MBI06_g00027_MAGBIO' => 'mbi', 'MBI10_g13034_MAGBIO' => 'mbi', 'MD09G1023400' => 'mdo', 'MD13G1100100' => 'mdo', 'MD15G1169200' => 'mdo', 'MD16G1101100' => 'mdo', 'MD17G1022900' => 'mdo', 'Medtr3g096150' => 'mtr', 'Medtr4g115070' => 'mtr', 'Medtr7g033325' => 'mtr', 'Medtr8g089840' => 'mtr', 'MELO3C010319.2' => 'cme', 'MELO3C011944.2' => 'cme', 'MELO3C021589.2' => 'cme', 'Migut.E00207' => 'egut', 'Migut.H00067' => 'egut', 'Migut.K00433' => 'egut', 'Migut.K00606' => 'egut', 'Migut.K01410' => 'egut', 'MSTRG.13347' => 'ama', 'MSTRG.24045' => 'ama', 'MSTRG.2428' => 'ama', 'MSTRG.26410' => 'ama', 'MSTRG.3139' => 'ama', 'MSTRG.3286' => 'ama', 'MSTRG.563' => 'ama', 'MSTRG.7941' => 'ama', 'Nitab4.5_0000028g0060' => 'nta', 'Nitab4.5_0000065g0260' => 'nta', 'Nitab4.5_0000112g0060' => 'nta', 'Nitab4.5_0000489g0120' => 'nta', 'Nitab4.5_0001776g0050' => 'nta', 'Nitab4.5_0001854g0010' => 'nta', 'Nitab4.5_0001860g0020' => 'nta', 'Nitab4.5_0004352g0010' => 'nta', 'Nitab4.5_0008716g0020' => 'nta', 'Nitab4.5_0008922g0010' => 'nta', 'Nn3g16693' => 'nnu', 'Nn4g22596' => 'nnu', 'Nn7g37639' => 'nnu', 'Oeu001701.1' => 'oeu', 'Oeu018149.1' => 'oeu', 'Oeu026220.1' => 'oeu', 'Oeu038635.1' => 'oeu', 'Oeu049176.1' => 'oeu', 'Oeu056706.1' => 'oeu', 'Oeu056937.1' => 'oeu', 'Oeu057540.1' => 'oeu', 'Os02g0594900' => 'osa', 'Os02g0595100' => 'osa', 'Os04g0477500' => 'osa', 'Os12g0611900' => 'osa', 'Peaxi162Scf00076g00020' => 'pax', 'Peaxi162Scf00128g00217' => 'pax', 'Peaxi162Scf00129g01640' => 'pax', 'Peaxi162Scf00669g00007' => 'pax', 'Peaxi162Scf00700g00421' => 'pax', 'Peaxi162Scf00801g00038' => 'pax', 'Peaxi162Scf00891g00025' => 'pax', 'PGR083G0909' => 'pgr', 'PGR119G1005' => 'pgr', 'PGR142G2236' => 'pgr', 'PGR142G3388' => 'pgr', 'PGSC0003DMG400004514' => 'stu', 'PGSC0003DMG400012635' => 'stu', 'PGSC0003DMG400015730' => 'stu', 'PGSC0003DMG400018611' => 'stu', 'PGSC0003DMG400030897' => 'stu', 'Phvul.001G254800' => 'pvu', 'Phvul.002G260100' => 'pvu', 'Phvul.003G167600' => 'pvu', 'Phvul.004G005100' => 'pvu', 'Potri.001G343600' => 'ptr', 'Potri.006G066700' => 'ptr', 'Potri.008G186000' => 'ptr', 'Potri.010G046900' => 'ptr', 'Potri.018G127900' => 'ptr', 'Pp3c20_17750' => 'ppa', 'Pp3c24_4380' => 'ppa', 'Prupe.1G245800' => 'ppe', 'Prupe.3G293400' => 'ppe', 'Prupe.7G247400' => 'ppe', 'Psat0s145g0120' => 'psa', 'Psat0s595g0040' => 'psa', 'Psat0s595g0120' => 'psa', 'Psat3g175040' => 'psa', 'Psat7g058120' => 'psa', 'PSO017G0428' => 'pso', 'PSO063G7510' => 'pso', 'PSO067G0046' => 'pso', 'PSO478G1073' => 'pso', 'PSO675G3677' => 'pso', 'PSO675G6558' => 'pso', 'PSO675G7520' => 'pso', 'PSO675G8959' => 'pso', 'QL02p074089' => 'qlo', 'QL02p089614' => 'qlo', 'QL03p057736' => 'qlo', 'RcHm_v2.0_Chr1g0364131' => 'rch', 'RcHm_v2.0_Chr2g0087801' => 'rch', 'RcHm_v2.0_Chr2g0087821' => 'rch', 'RcHm_v2.0_Chr2g0173231' => 'rch', 'RcHm_v2.0_Chr4g0433111' => 'rch', 'Rhsim03G0250300' => 'rsi', 'Rhsim08G0048400' => 'rsi', 'Rhsim10G0014800' => 'rsi', 'Rhsim12G0040100' => 'rsi', 'Rhsim12G0109700' => 'rsi', 'Sabra06G0049600' => 'sbr', 'Sabra08G0141000' => 'sbr', 'Sabra10G0021400' => 'sbr', 'Sabra16G0222900' => 'sbr', 'Sabra18G0108600' => 'sbr', 'SalBow1G0433' => 'sbo', 'SalBow1G2038' => 'sbo', 'SalBow1G5003' => 'sbo', 'SalBow7G1197' => 'sbo', 'SalBow8G3506' => 'sbo', 'Sc03g0007300' => 'sci', 'Sc11g0000950' => 'sci', 'Sc14g0008750' => 'sci', 'Sc18g0000420' => 'sci', 'Sed0006754' => 'sed', 'Sed0008741' => 'sed', 'Sed0017172' => 'sed', 'Sed0018925' => 'sed', 'Sed0023326' => 'sed', 'Sed0025909' => 'sed', 'SEGI_05333' => 'sgi', 'SEGI_10362' => 'sgi', 'SEGI_13380' => 'sgi', 'SEGI_24306' => 'sgi', 'SEGI_29077' => 'sgi', 'SEGI_29095' => 'sgi', 'SEGI_36534' => 'sgi', 'SEGI_37506' => 'sgi', 'SEGI_38321' => 'sgi', 'SGA_v2.0_scaffold307G48031' => 'sas', 'SGA_v2.0_scaffold47G17507' => 'sas', 'SGA_v2.0_scaffold63G21736' => 'sas', 'SGA_v2.0_scaffold87G27070' => 'sas', 'SHI17794' => 'shi', 'SHI28851' => 'shi', 'SMO165G0155' => 'smo', 'SMO340G0217' => 'smo', 'SMO367G1210' => 'smo', 'Solyc02g093430.3' => 'sly', 'Solyc05g013580.4' => 'sly', 'Solyc07g008030.3' => 'sly', 'Solyc12g035470.2' => 'sly', 'Sopen02g038020' => 'spe', 'Sopen05g008490' => 'spe', 'Sopen07g003910' => 'spe', 'Sopen12g015240' => 'spe', 'Sp1g11550' => 'spa', 'Sp2g16710' => 'spa', 'Sp3g00430' => 'spa', 'Sp3g26780' => 'spa', 'Sp5g22900' => 'spa', 'Sp6g29530' => 'spa', 'TAR371G0794' => 'tar', 'TAR374G0164' => 'tar', 'TAR622G0165' => 'tar', 'TAR626G0929' => 'tar', 'TAR629G2155' => 'tar', 'THA.LOC104805282' => 'tha', 'THA.LOC104805363' => 'tha', 'THA.LOC104808968' => 'tha', 'THA.LOC104821093' => 'tha', 'THA.LOC104823953' => 'tha', 'THA.LOC104825562' => 'tha', 'THA.LOC104825665' => 'tha', 'Thecc.02G261400' => 'tca', 'Thecc.04G019200' => 'tca', 'Thecc.09G130400' => 'tca', 'Thhalv10004374m.g' => 'esa', 'Thhalv10007850m.g' => 'esa', 'Thhalv10013782m.g' => 'esa', 'Thhalv10018686m.g' => 'esa', 'Thhalv10020899m.g' => 'esa', 'Thhalv10022755m.g' => 'esa', 'TPR.G23851' => 'tpr', 'TPR.G26500' => 'tpr', 'TPR.G27267' => 'tpr', 'TPR.G32001' => 'tpr', 'TPR.G6251' => 'tpr', 'TPR.G8167' => 'tpr', 'TWI12G1330' => 'twi', 'TWI18G1239' => 'twi', 'TWI34G0979' => 'twi', 'TWI36G0670' => 'twi', 'TWI36G0707' => 'twi', 'TWI56G0233' => 'twi', 'TWI75G1809' => 'twi', 'unitig_21.g20874' => 'ugi', 'unitig_26.g10343' => 'ugi', 'unitig_46.g18392' => 'ugi', 'unitig_52.g17178' => 'ugi', 'unitig_8.g2934' => 'ugi', 'vmacro01122' => 'vma', 'vmacro05875' => 'vma', 'vmacro06147' => 'vma', 'vmacro16191' => 'vma', 'vmacro18293' => 'vma', 'VMungo0251G3707' => 'vmu', 'VMungo0464G1521' => 'vmu', 'VMungo1215G0205' => 'vmu', 'VMungo1383G2484' => 'vmu', 'Zm00001eb079610' => 'zma', 'Zm00001eb135990' => 'zma', 'Zm00001eb183710' => 'zma', 'Zm00001eb246020' => 'zma' ) $gf_id = 'HOM05D001124' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001124' ) $data_identifier = 'HOM05D001124' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 6, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 7, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 21, 'bol' => (int) 10, 'bra' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 6, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 9, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 21, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 8, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 10, 'lsa' => (int) 8, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 8, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 9, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb246020' $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' => 'HOM05D001124', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '548', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02520' => 'bna', 'A03p06630' => 'bna', 'A05p44460' => 'bna', 'A06p08710' => 'bna', 'A06p41090' => 'bna', 'A07p32320' => 'bna', 'A08p32520' => 'bna', 'A09p10360' => 'bna', 'A10p24080' => 'bna', 'Aa31LG11G15250' => 'aar', 'Aa31LG1G1800' => 'aar', 'Aa31LG2G5120' => 'aar', 'Aa31LG2G6070' => 'aar', 'Aa31LG5G10770' => 'aar', 'Aa31sc61G90' => 'aar', 'Actinidia01352' => 'ach', 'Actinidia05983' => 'ach', 'Actinidia08133' => 'ach', 'Actinidia15101' => 'ach', 'Actinidia26379' => 'ach', 'Actinidia35778' => 'ach', 'Actinidia36123' => 'ach', 'Actinidia37436' => 'ach', 'Actinidia38730' => 'ach', 'Ah.02g128210' => 'amhyb', 'Ah.03g132990' => 'amhyb', 'Ah.14g079410' => 'amhyb', 'AL1G24640' => 'aly', 'AL2G26680' => 'aly', 'AL3G10530' => 'aly', 'AL3G45230' => 'aly', 'AL5G15230' => 'aly', 'AL5G16960' => 'aly', 'AL6G25210' => 'aly', 'Aqoxy2G00441' => 'aox', 'Aqoxy3G01236' => 'aox', 'Aqoxy5G03746' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3RQ047' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C7GMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9C8JER' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MBL6KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YXCZ83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZANX40' => 'arhy', 'AT1G12990' => 'ath', 'AT1G67880' => 'ath', 'AT2G13290' => 'ath', 'AT3G01620' => 'ath', 'AT3G26445' => 'ath', 'AT3G27540' => 'ath', 'AT5G14480' => 'ath', 'ATR0824G026' => 'atr', 'ATR1098G019' => 'atr', 'Atru.chr11.2145' => 'acertr', 'Atru.chr2.3636' => 'acertr', 'Atru.chr2.3644' => 'acertr', 'Atru.chr6.2422' => 'acertr', 'Atru.chr7.1112' => 'acertr', 'AUR62005469' => 'cqu', 'AUR62011166' => 'cqu', 'AUR62013319' => 'cqu', 'AUR62024273' => 'cqu', 'AUR62028420' => 'cqu', 'AUR62041942' => 'cqu', 'BcaB01g04969' => 'bca', 'BcaB01g06371' => 'bca', 'BcaB02g11494' => 'bca', 'BcaB03g15382' => 'bca', 'BcaB08g36994' => 'bca', 'BcaC03g13477' => 'bca', 'BcaC03g13478' => 'bca', 'BcaC03g13480' => 'bca', 'BcaC03g13481' => 'bca', 'BcaC03g13486' => 'bca', 'BcaC04g19031' => 'bca', 'BcaC04g23085' => 'bca', 'BcaC05g25094' => 'bca', 'BcaC05g25096' => 'bca', 'BcaC05g25138' => 'bca', 'BcaC05g30416' => 'bca', 'BcaC05g30455' => 'bca', 'BcaC06g30979' => 'bca', 'BcaC06g33805' => 'bca', 'BcaC08g46021' => 'bca', 'BcaNung03154' => 'bca', 'BolC2t06623H' => 'bol', 'BolC2t06632H' => 'bol', 'BolC2t06635H' => 'bol', 'BolC2t06638H' => 'bol', 'BolC3t13266H' => 'bol', 'BolC5t29776H' => 'bol', 'BolC6t38912H' => 'bol', 'BolC7t44183H' => 'bol', 'BolC9t54123H' => 'bol', 'BolC9t59107H' => 'bol', 'BraA02t05221Z' => 'bra', 'BraA03t09996Z' => 'bra', 'BraA05t23210Z' => 'bra', 'BraA06t24068Z' => 'bra', 'BraA06t27032Z' => 'bra', 'BraA08t35176Z' => 'bra', 'BraA09t36680Z' => 'bra', 'BraA10t44471Z' => 'bra', 'C02p06760' => 'bna', 'C02p06890' => 'bna', 'C02p07010' => 'bna', 'C03p07660' => 'bna', 'C05p10300' => 'bna', 'C06p38150' => 'bna', 'C07p36650' => 'bna', 'C08p15770' => 'bna', 'C09p12300' => 'bna', 'C09p62700' => 'bna', 'C09p75040' => 'bna', 'CAN.G13.1' => 'can', 'CAN.G138.4' => 'can', 'CAN.G44.6' => 'can', 'CAN.G473.19' => 'can', 'CANSAT01G0835' => 'cansat', 'CANSAT11G0246' => 'cansat', 'CANSAT11G1766' => 'cansat', 'CANSAT64G1954' => 'cansat', 'CARHR013330' => 'chi', 'CARHR060530' => 'chi', 'CARHR075300' => 'chi', 'CARHR105120' => 'chi', 'CARHR148910' => 'chi', 'CARHR198830' => 'chi', 'Carub.0001s1275' => 'cru', 'Carub.0002s1437' => 'cru', 'Carub.0003s0044' => 'cru', 'Carub.0003s2787' => 'cru', 'Carub.0005s0597' => 'cru', 'Carub.0006s1266' => 'cru', 'Ca_06935_v3' => 'car', 'Ca_13559_v3' => 'car', 'Ca_16941_v3' => 'car', 'Ca_16960_v3' => 'car', 'Ca_17775_v3' => 'car', 'Ca_30464_v3' => 'car', 'Cc06_g08160' => 'ccan', 'Cc07_g01520' => 'ccan', 'Cc11_g15810' => 'ccan', 'CDE02G2840' => 'cde', 'CDE03G0093' => 'cde', 'CDE04G2127' => 'cde', 'CDE07G1857' => 'cde', 'CDE09G1246' => 'cde', 'Cfa003412' => 'cfa', 'Cfa007341' => 'cfa', 'Cfa009220' => 'cfa', 'Ciclev10008737m.g' => 'ccl', 'Ciclev10015565m.g' => 'ccl', 'Ciclev10031761m.g' => 'ccl', 'CiPaw.03G045300' => 'cil', 'CiPaw.03G247200' => 'cil', 'CiPaw.04G029500' => 'cil', 'CiPaw.04G174000' => 'cil', 'CiPaw.05G181200' => 'cil', 'CiPaw.06G067100' => 'cil', 'ClCG05G025800' => 'cla', 'ClCG06G011400' => 'cla', 'ClCG09G019360' => 'cla', 'COL.COLO4_04827' => 'col', 'COL.COLO4_29170' => 'col', 'COL.COLO4_35131' => 'col', 'COL.COLO4_35132' => 'col', 'Cpa.g.sc33.32' => 'cpa', 'Cpa.g.sc46.29' => 'cpa', 'Cpa.g.sc796.1' => 'cpa', 'CsaV3_1G030420' => 'csa', 'CsaV3_5G027050' => 'csa', 'CsaV3_5G031040' => 'csa', 'CsaV3_UNG023130' => 'csa', 'CSS0007726' => 'camsi', 'CSS0016433' => 'camsi', 'CSS0017656' => 'camsi', 'CSS0025364' => 'camsi', 'CSS0027582' => 'camsi', 'CSS0047288' => 'camsi', 'CSS0049950' => 'camsi', 'DCAR_003843' => 'dca', 'DCAR_007052' => 'dca', 'DCAR_020884' => 'dca', 'DCAR_021730' => 'dca', 'DCAR_024423' => 'dca', 'DCAR_026509' => 'dca', 'DCAR_031158' => 'dca', 'Dinv14728' => 'din', 'Dinv15219' => 'din', 'Dinv25728' => 'din', 'Dinv33428' => 'din', 'Dinv36489' => 'din', 'Dinv41486' => 'din', 'Duzib147G0469' => 'dzi', 'Duzib168G0060' => 'dzi', 'Duzib187G1215' => 'dzi', 'Duzib248G0692' => 'dzi', 'Duzib251G0767' => 'dzi', 'Duzib264G0446' => 'dzi', 'Duzib268G0691' => 'dzi', 'ECA232G4767' => 'eca', 'ECA233G2838' => 'eca', 'ECA234G0391' => 'eca', 'ECA234G0857' => 'eca', 'ECA236G1593' => 'eca', 'ECA238G0565' => 'eca', 'ECA246G1027' => 'eca', 'ECA246G3223' => 'eca', 'ECA246G3470' => 'eca', 'EL10Ac6g13829' => 'bvu', 'EL10Ac6g14093' => 'bvu', 'EL10Ac8g18707' => 'bvu', 'Eucgr.C01369' => 'egr', 'Eucgr.H02492' => 'egr', 'Eucgr.I01733' => 'egr', 'Eucgr.J02255' => 'egr', 'Eucgr.J02257' => 'egr', 'Eucgr.J02258' => 'egr', 'FAN02G1601' => 'fan', 'FAN03G1586' => 'fan', 'FAN03G2986' => 'fan', 'FAN05G4837' => 'fan', 'FAN06G0146' => 'fan', 'FAN07G0858' => 'fan', 'FAN09G3179' => 'fan', 'FAN10G0669' => 'fan', 'FAN12G2358' => 'fan', 'FAN14G4198' => 'fan', 'FAN14G5112' => 'fan', 'FAN17G0342' => 'fan', 'FAN19G0342' => 'fan', 'FAN19G0962' => 'fan', 'FAN19G1101' => 'fan', 'FAN19G1872' => 'fan', 'FAN22G0356' => 'fan', 'FAN23G0744' => 'fan', 'FAN23G1914' => 'fan', 'FAN26G0032' => 'fan', 'FAN28G0625' => 'fan', 'FvH4_1g02710' => 'fve', 'FvH4_1g02720' => 'fve', 'FvH4_4g25670' => 'fve', 'FvH4_6g51700' => 'fve', 'FvH4_7g20170' => 'fve', 'Glyma.05G175000' => 'gma', 'Glyma.08G132300' => 'gma', 'Glyma.11G243000' => 'gma', 'Glyma.13G158900' => 'gma', 'Glyma.17G112400' => 'gma', 'Glyma.18G014100' => 'gma', 'Glyma.19G003100' => 'gma', 'Glyma.19G056500' => 'gma', 'Gohir.A01G158900' => 'ghi', 'Gohir.A05G312600' => 'ghi', 'Gohir.A05G354900' => 'ghi', 'Gohir.A07G037200' => 'ghi', 'Gohir.A09G030000' => 'ghi', 'Gohir.A12G145200' => 'ghi', 'Gohir.D01G151500' => 'ghi', 'Gohir.D04G058300' => 'ghi', 'Gohir.D05G314100' => 'ghi', 'Gohir.D07G041400' => 'ghi', 'Gohir.D09G029700' => 'ghi', 'Gohir.D12G149700' => 'ghi', 'Gorai.001G043800' => 'gra', 'Gorai.002G187800' => 'gra', 'Gorai.006G034700' => 'gra', 'Gorai.008G161200' => 'gra', 'Gorai.009G335700' => 'gra', 'Gorai.012G065000' => 'gra', 'GSVIVG01000535001' => 'vvi', 'GSVIVG01015572001' => 'vvi', 'GSVIVG01032386001' => 'vvi', 'HanXRQChr05g0138531' => 'han', 'HanXRQChr06g0174391' => 'han', 'HanXRQChr07g0199021' => 'han', 'HanXRQChr08g0208211' => 'han', 'HanXRQChr09g0255471' => 'han', 'HanXRQChr10g0315791' => 'han', 'HanXRQChr12g0371991' => 'han', 'HanXRQChr15g0475251' => 'han', 'HanXRQChr17g0540001' => 'han', 'HanXRQChr17g0548631' => 'han', 'HanXRQChr17g0569561' => 'han', 'Haze_12256' => 'cav', 'Haze_14756' => 'cav', 'Haze_25528' => 'cav', 'Hma1.2p1_0079F.1_g041020' => 'hma', 'Hma1.2p1_0818F.1_g223260' => 'hma', 'Hma1.2p1_1747F.1_g300530' => 'hma', 'HPP92_004607' => 'vpl', 'HPP92_004608' => 'vpl', 'HPP92_006181' => 'vpl', 'HPP92_012192' => 'vpl', 'HPP92_015680' => 'vpl', 'HPP92_020249' => 'vpl', 'HPP92_021376' => 'vpl', 'HPP92_024275' => 'vpl', 'Hund06031' => 'sun', 'Hund25391' => 'sun', 'Lalb_Chr07g0185371' => 'lal', 'Lalb_Chr07g0185381' => 'lal', 'Lalb_Chr12g0204011' => 'lal', 'Lalb_Chr13g0301671' => 'lal', 'Lalb_Chr14g0362851' => 'lal', 'Lalb_Chr24g0403581' => 'lal', 'Lj1g0000233' => 'lja', 'Lj2g0018120' => 'lja', 'Lj3C621T0' => 'lonja', 'Lj3P1059T14' => 'lonja', 'Lj3P611T9' => 'lonja', 'Lj3P614T13' => 'lonja', 'Lj3P615T5' => 'lonja', 'Lj4g0012315' => 'lja', 'Lj4g0026182' => 'lja', 'Lj6P813T16' => 'lonja', 'Lj7C427T7' => 'lonja', 'Lj7C427T8' => 'lonja', 'Lj7P600T41' => 'lonja', 'Lju41C42G17' => 'lonja', 'Lsat_1_v5_gn_0_47300' => 'lsa', 'Lsat_1_v5_gn_2_91280' => 'lsa', 'Lsat_1_v5_gn_3_30561' => 'lsa', 'Lsat_1_v5_gn_4_184321' => 'lsa', 'Lsat_1_v5_gn_4_4041' => 'lsa', 'Lsat_1_v5_gn_5_92000' => 'lsa', 'Lsat_1_v5_gn_8_152940' => 'lsa', 'Lsat_1_v5_gn_8_62401' => 'lsa', 'Manes.06G055900' => 'mes', 'Manes.12G022200' => 'mes', 'Manes.13G023300' => 'mes', 'Manes.14G115000' => 'mes', 'Manes.15G151700' => 'mes', 'Manes.17G111300' => 'mes', 'Mapoly0226s0009' => 'mpo', 'MBI02_g25363_MAGBIO' => 'mbi', 'MBI06_g00027_MAGBIO' => 'mbi', 'MBI10_g13034_MAGBIO' => 'mbi', 'MD09G1023400' => 'mdo', 'MD13G1100100' => 'mdo', 'MD15G1169200' => 'mdo', 'MD16G1101100' => 'mdo', 'MD17G1022900' => 'mdo', 'Medtr3g096150' => 'mtr', 'Medtr4g115070' => 'mtr', 'Medtr7g033325' => 'mtr', 'Medtr8g089840' => 'mtr', 'MELO3C010319.2' => 'cme', 'MELO3C011944.2' => 'cme', 'MELO3C021589.2' => 'cme', 'Migut.E00207' => 'egut', 'Migut.H00067' => 'egut', 'Migut.K00433' => 'egut', 'Migut.K00606' => 'egut', 'Migut.K01410' => 'egut', 'MSTRG.13347' => 'ama', 'MSTRG.24045' => 'ama', 'MSTRG.2428' => 'ama', 'MSTRG.26410' => 'ama', 'MSTRG.3139' => 'ama', 'MSTRG.3286' => 'ama', 'MSTRG.563' => 'ama', 'MSTRG.7941' => 'ama', 'Nitab4.5_0000028g0060' => 'nta', 'Nitab4.5_0000065g0260' => 'nta', 'Nitab4.5_0000112g0060' => 'nta', 'Nitab4.5_0000489g0120' => 'nta', 'Nitab4.5_0001776g0050' => 'nta', 'Nitab4.5_0001854g0010' => 'nta', 'Nitab4.5_0001860g0020' => 'nta', 'Nitab4.5_0004352g0010' => 'nta', 'Nitab4.5_0008716g0020' => 'nta', 'Nitab4.5_0008922g0010' => 'nta', 'Nn3g16693' => 'nnu', 'Nn4g22596' => 'nnu', 'Nn7g37639' => 'nnu', 'Oeu001701.1' => 'oeu', 'Oeu018149.1' => 'oeu', 'Oeu026220.1' => 'oeu', 'Oeu038635.1' => 'oeu', 'Oeu049176.1' => 'oeu', 'Oeu056706.1' => 'oeu', 'Oeu056937.1' => 'oeu', 'Oeu057540.1' => 'oeu', 'Os02g0594900' => 'osa', 'Os02g0595100' => 'osa', 'Os04g0477500' => 'osa', 'Os12g0611900' => 'osa', 'Peaxi162Scf00076g00020' => 'pax', 'Peaxi162Scf00128g00217' => 'pax', 'Peaxi162Scf00129g01640' => 'pax', 'Peaxi162Scf00669g00007' => 'pax', 'Peaxi162Scf00700g00421' => 'pax', 'Peaxi162Scf00801g00038' => 'pax', 'Peaxi162Scf00891g00025' => 'pax', 'PGR083G0909' => 'pgr', 'PGR119G1005' => 'pgr', 'PGR142G2236' => 'pgr', 'PGR142G3388' => 'pgr', 'PGSC0003DMG400004514' => 'stu', 'PGSC0003DMG400012635' => 'stu', 'PGSC0003DMG400015730' => 'stu', 'PGSC0003DMG400018611' => 'stu', 'PGSC0003DMG400030897' => 'stu', 'Phvul.001G254800' => 'pvu', 'Phvul.002G260100' => 'pvu', 'Phvul.003G167600' => 'pvu', 'Phvul.004G005100' => 'pvu', 'Potri.001G343600' => 'ptr', 'Potri.006G066700' => 'ptr', 'Potri.008G186000' => 'ptr', 'Potri.010G046900' => 'ptr', 'Potri.018G127900' => 'ptr', 'Pp3c20_17750' => 'ppa', 'Pp3c24_4380' => 'ppa', 'Prupe.1G245800' => 'ppe', 'Prupe.3G293400' => 'ppe', 'Prupe.7G247400' => 'ppe', 'Psat0s145g0120' => 'psa', 'Psat0s595g0040' => 'psa', 'Psat0s595g0120' => 'psa', 'Psat3g175040' => 'psa', 'Psat7g058120' => 'psa', 'PSO017G0428' => 'pso', 'PSO063G7510' => 'pso', 'PSO067G0046' => 'pso', 'PSO478G1073' => 'pso', 'PSO675G3677' => 'pso', 'PSO675G6558' => 'pso', 'PSO675G7520' => 'pso', 'PSO675G8959' => 'pso', 'QL02p074089' => 'qlo', 'QL02p089614' => 'qlo', 'QL03p057736' => 'qlo', 'RcHm_v2.0_Chr1g0364131' => 'rch', 'RcHm_v2.0_Chr2g0087801' => 'rch', 'RcHm_v2.0_Chr2g0087821' => 'rch', 'RcHm_v2.0_Chr2g0173231' => 'rch', 'RcHm_v2.0_Chr4g0433111' => 'rch', 'Rhsim03G0250300' => 'rsi', 'Rhsim08G0048400' => 'rsi', 'Rhsim10G0014800' => 'rsi', 'Rhsim12G0040100' => 'rsi', 'Rhsim12G0109700' => 'rsi', 'Sabra06G0049600' => 'sbr', 'Sabra08G0141000' => 'sbr', 'Sabra10G0021400' => 'sbr', 'Sabra16G0222900' => 'sbr', 'Sabra18G0108600' => 'sbr', 'SalBow1G0433' => 'sbo', 'SalBow1G2038' => 'sbo', 'SalBow1G5003' => 'sbo', 'SalBow7G1197' => 'sbo', 'SalBow8G3506' => 'sbo', 'Sc03g0007300' => 'sci', 'Sc11g0000950' => 'sci', 'Sc14g0008750' => 'sci', 'Sc18g0000420' => 'sci', 'Sed0006754' => 'sed', 'Sed0008741' => 'sed', 'Sed0017172' => 'sed', 'Sed0018925' => 'sed', 'Sed0023326' => 'sed', 'Sed0025909' => 'sed', 'SEGI_05333' => 'sgi', 'SEGI_10362' => 'sgi', 'SEGI_13380' => 'sgi', 'SEGI_24306' => 'sgi', 'SEGI_29077' => 'sgi', 'SEGI_29095' => 'sgi', 'SEGI_36534' => 'sgi', 'SEGI_37506' => 'sgi', 'SEGI_38321' => 'sgi', 'SGA_v2.0_scaffold307G48031' => 'sas', 'SGA_v2.0_scaffold47G17507' => 'sas', 'SGA_v2.0_scaffold63G21736' => 'sas', 'SGA_v2.0_scaffold87G27070' => 'sas', 'SHI17794' => 'shi', 'SHI28851' => 'shi', 'SMO165G0155' => 'smo', 'SMO340G0217' => 'smo', 'SMO367G1210' => 'smo', 'Solyc02g093430.3' => 'sly', 'Solyc05g013580.4' => 'sly', 'Solyc07g008030.3' => 'sly', 'Solyc12g035470.2' => 'sly', 'Sopen02g038020' => 'spe', 'Sopen05g008490' => 'spe', 'Sopen07g003910' => 'spe', 'Sopen12g015240' => 'spe', 'Sp1g11550' => 'spa', 'Sp2g16710' => 'spa', 'Sp3g00430' => 'spa', 'Sp3g26780' => 'spa', 'Sp5g22900' => 'spa', 'Sp6g29530' => 'spa', 'TAR371G0794' => 'tar', 'TAR374G0164' => 'tar', 'TAR622G0165' => 'tar', 'TAR626G0929' => 'tar', 'TAR629G2155' => 'tar', 'THA.LOC104805282' => 'tha', 'THA.LOC104805363' => 'tha', 'THA.LOC104808968' => 'tha', 'THA.LOC104821093' => 'tha', 'THA.LOC104823953' => 'tha', 'THA.LOC104825562' => 'tha', 'THA.LOC104825665' => 'tha', 'Thecc.02G261400' => 'tca', 'Thecc.04G019200' => 'tca', 'Thecc.09G130400' => 'tca', 'Thhalv10004374m.g' => 'esa', 'Thhalv10007850m.g' => 'esa', 'Thhalv10013782m.g' => 'esa', 'Thhalv10018686m.g' => 'esa', 'Thhalv10020899m.g' => 'esa', 'Thhalv10022755m.g' => 'esa', 'TPR.G23851' => 'tpr', 'TPR.G26500' => 'tpr', 'TPR.G27267' => 'tpr', 'TPR.G32001' => 'tpr', 'TPR.G6251' => 'tpr', 'TPR.G8167' => 'tpr', 'TWI12G1330' => 'twi', 'TWI18G1239' => 'twi', 'TWI34G0979' => 'twi', 'TWI36G0670' => 'twi', 'TWI36G0707' => 'twi', 'TWI56G0233' => 'twi', 'TWI75G1809' => 'twi', 'unitig_21.g20874' => 'ugi', 'unitig_26.g10343' => 'ugi', 'unitig_46.g18392' => 'ugi', 'unitig_52.g17178' => 'ugi', 'unitig_8.g2934' => 'ugi', 'vmacro01122' => 'vma', 'vmacro05875' => 'vma', 'vmacro06147' => 'vma', 'vmacro16191' => 'vma', 'vmacro18293' => 'vma', 'VMungo0251G3707' => 'vmu', 'VMungo0464G1521' => 'vmu', 'VMungo1215G0205' => 'vmu', 'VMungo1383G2484' => 'vmu', 'Zm00001eb079610' => 'zma', 'Zm00001eb135990' => 'zma', 'Zm00001eb183710' => 'zma', 'Zm00001eb246020' => 'zma' ), 'gf_id' => 'HOM05D001124', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001124' ), 'data_identifier' => 'HOM05D001124', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001124', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '548', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02520' => 'bna', 'A03p06630' => 'bna', 'A05p44460' => 'bna', 'A06p08710' => 'bna', 'A06p41090' => 'bna', 'A07p32320' => 'bna', 'A08p32520' => 'bna', 'A09p10360' => 'bna', 'A10p24080' => 'bna', 'Aa31LG11G15250' => 'aar', 'Aa31LG1G1800' => 'aar', 'Aa31LG2G5120' => 'aar', 'Aa31LG2G6070' => 'aar', 'Aa31LG5G10770' => 'aar', 'Aa31sc61G90' => 'aar', 'Actinidia01352' => 'ach', 'Actinidia05983' => 'ach', 'Actinidia08133' => 'ach', 'Actinidia15101' => 'ach', 'Actinidia26379' => 'ach', 'Actinidia35778' => 'ach', 'Actinidia36123' => 'ach', 'Actinidia37436' => 'ach', 'Actinidia38730' => 'ach', 'Ah.02g128210' => 'amhyb', 'Ah.03g132990' => 'amhyb', 'Ah.14g079410' => 'amhyb', 'AL1G24640' => 'aly', 'AL2G26680' => 'aly', 'AL3G10530' => 'aly', 'AL3G45230' => 'aly', 'AL5G15230' => 'aly', 'AL5G16960' => 'aly', 'AL6G25210' => 'aly', 'Aqoxy2G00441' => 'aox', 'Aqoxy3G01236' => 'aox', 'Aqoxy5G03746' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3RQ047' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C7GMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9C8JER' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MBL6KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YXCZ83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZANX40' => 'arhy', 'AT1G12990' => 'ath', 'AT1G67880' => 'ath', 'AT2G13290' => 'ath', 'AT3G01620' => 'ath', 'AT3G26445' => 'ath', 'AT3G27540' => 'ath', 'AT5G14480' => 'ath', 'ATR0824G026' => 'atr', 'ATR1098G019' => 'atr', 'Atru.chr11.2145' => 'acertr', 'Atru.chr2.3636' => 'acertr', 'Atru.chr2.3644' => 'acertr', 'Atru.chr6.2422' => 'acertr', 'Atru.chr7.1112' => 'acertr', 'AUR62005469' => 'cqu', 'AUR62011166' => 'cqu', 'AUR62013319' => 'cqu', 'AUR62024273' => 'cqu', 'AUR62028420' => 'cqu', 'AUR62041942' => 'cqu', 'BcaB01g04969' => 'bca', 'BcaB01g06371' => 'bca', 'BcaB02g11494' => 'bca', 'BcaB03g15382' => 'bca', 'BcaB08g36994' => 'bca', 'BcaC03g13477' => 'bca', 'BcaC03g13478' => 'bca', 'BcaC03g13480' => 'bca', 'BcaC03g13481' => 'bca', 'BcaC03g13486' => 'bca', 'BcaC04g19031' => 'bca', 'BcaC04g23085' => 'bca', 'BcaC05g25094' => 'bca', 'BcaC05g25096' => 'bca', 'BcaC05g25138' => 'bca', 'BcaC05g30416' => 'bca', 'BcaC05g30455' => 'bca', 'BcaC06g30979' => 'bca', 'BcaC06g33805' => 'bca', 'BcaC08g46021' => 'bca', 'BcaNung03154' => 'bca', 'BolC2t06623H' => 'bol', 'BolC2t06632H' => 'bol', 'BolC2t06635H' => 'bol', 'BolC2t06638H' => 'bol', 'BolC3t13266H' => 'bol', 'BolC5t29776H' => 'bol', 'BolC6t38912H' => 'bol', 'BolC7t44183H' => 'bol', 'BolC9t54123H' => 'bol', 'BolC9t59107H' => 'bol', 'BraA02t05221Z' => 'bra', 'BraA03t09996Z' => 'bra', 'BraA05t23210Z' => 'bra', 'BraA06t24068Z' => 'bra', 'BraA06t27032Z' => 'bra', 'BraA08t35176Z' => 'bra', 'BraA09t36680Z' => 'bra', 'BraA10t44471Z' => 'bra', 'C02p06760' => 'bna', 'C02p06890' => 'bna', 'C02p07010' => 'bna', 'C03p07660' => 'bna', 'C05p10300' => 'bna', 'C06p38150' => 'bna', 'C07p36650' => 'bna', 'C08p15770' => 'bna', 'C09p12300' => 'bna', 'C09p62700' => 'bna', 'C09p75040' => 'bna', 'CAN.G13.1' => 'can', 'CAN.G138.4' => 'can', 'CAN.G44.6' => 'can', 'CAN.G473.19' => 'can', 'CANSAT01G0835' => 'cansat', 'CANSAT11G0246' => 'cansat', 'CANSAT11G1766' => 'cansat', 'CANSAT64G1954' => 'cansat', 'CARHR013330' => 'chi', 'CARHR060530' => 'chi', 'CARHR075300' => 'chi', 'CARHR105120' => 'chi', 'CARHR148910' => 'chi', 'CARHR198830' => 'chi', 'Carub.0001s1275' => 'cru', 'Carub.0002s1437' => 'cru', 'Carub.0003s0044' => 'cru', 'Carub.0003s2787' => 'cru', 'Carub.0005s0597' => 'cru', 'Carub.0006s1266' => 'cru', 'Ca_06935_v3' => 'car', 'Ca_13559_v3' => 'car', 'Ca_16941_v3' => 'car', 'Ca_16960_v3' => 'car', 'Ca_17775_v3' => 'car', 'Ca_30464_v3' => 'car', 'Cc06_g08160' => 'ccan', 'Cc07_g01520' => 'ccan', 'Cc11_g15810' => 'ccan', 'CDE02G2840' => 'cde', 'CDE03G0093' => 'cde', 'CDE04G2127' => 'cde', 'CDE07G1857' => 'cde', 'CDE09G1246' => 'cde', 'Cfa003412' => 'cfa', 'Cfa007341' => 'cfa', 'Cfa009220' => 'cfa', 'Ciclev10008737m.g' => 'ccl', 'Ciclev10015565m.g' => 'ccl', 'Ciclev10031761m.g' => 'ccl', 'CiPaw.03G045300' => 'cil', 'CiPaw.03G247200' => 'cil', 'CiPaw.04G029500' => 'cil', 'CiPaw.04G174000' => 'cil', 'CiPaw.05G181200' => 'cil', 'CiPaw.06G067100' => 'cil', 'ClCG05G025800' => 'cla', 'ClCG06G011400' => 'cla', 'ClCG09G019360' => 'cla', 'COL.COLO4_04827' => 'col', 'COL.COLO4_29170' => 'col', 'COL.COLO4_35131' => 'col', 'COL.COLO4_35132' => 'col', 'Cpa.g.sc33.32' => 'cpa', 'Cpa.g.sc46.29' => 'cpa', 'Cpa.g.sc796.1' => 'cpa', 'CsaV3_1G030420' => 'csa', 'CsaV3_5G027050' => 'csa', 'CsaV3_5G031040' => 'csa', 'CsaV3_UNG023130' => 'csa', 'CSS0007726' => 'camsi', 'CSS0016433' => 'camsi', 'CSS0017656' => 'camsi', 'CSS0025364' => 'camsi', 'CSS0027582' => 'camsi', 'CSS0047288' => 'camsi', 'CSS0049950' => 'camsi', 'DCAR_003843' => 'dca', 'DCAR_007052' => 'dca', 'DCAR_020884' => 'dca', 'DCAR_021730' => 'dca', 'DCAR_024423' => 'dca', 'DCAR_026509' => 'dca', 'DCAR_031158' => 'dca', 'Dinv14728' => 'din', 'Dinv15219' => 'din', 'Dinv25728' => 'din', 'Dinv33428' => 'din', 'Dinv36489' => 'din', 'Dinv41486' => 'din', 'Duzib147G0469' => 'dzi', 'Duzib168G0060' => 'dzi', 'Duzib187G1215' => 'dzi', 'Duzib248G0692' => 'dzi', 'Duzib251G0767' => 'dzi', 'Duzib264G0446' => 'dzi', 'Duzib268G0691' => 'dzi', 'ECA232G4767' => 'eca', 'ECA233G2838' => 'eca', 'ECA234G0391' => 'eca', 'ECA234G0857' => 'eca', 'ECA236G1593' => 'eca', 'ECA238G0565' => 'eca', 'ECA246G1027' => 'eca', 'ECA246G3223' => 'eca', 'ECA246G3470' => 'eca', 'EL10Ac6g13829' => 'bvu', 'EL10Ac6g14093' => 'bvu', 'EL10Ac8g18707' => 'bvu', 'Eucgr.C01369' => 'egr', 'Eucgr.H02492' => 'egr', 'Eucgr.I01733' => 'egr', 'Eucgr.J02255' => 'egr', 'Eucgr.J02257' => 'egr', 'Eucgr.J02258' => 'egr', 'FAN02G1601' => 'fan', 'FAN03G1586' => 'fan', 'FAN03G2986' => 'fan', 'FAN05G4837' => 'fan', 'FAN06G0146' => 'fan', 'FAN07G0858' => 'fan', 'FAN09G3179' => 'fan', 'FAN10G0669' => 'fan', 'FAN12G2358' => 'fan', 'FAN14G4198' => 'fan', 'FAN14G5112' => 'fan', 'FAN17G0342' => 'fan', 'FAN19G0342' => 'fan', 'FAN19G0962' => 'fan', 'FAN19G1101' => 'fan', 'FAN19G1872' => 'fan', 'FAN22G0356' => 'fan', 'FAN23G0744' => 'fan', 'FAN23G1914' => 'fan', 'FAN26G0032' => 'fan', 'FAN28G0625' => 'fan', 'FvH4_1g02710' => 'fve', 'FvH4_1g02720' => 'fve', 'FvH4_4g25670' => 'fve', 'FvH4_6g51700' => 'fve', 'FvH4_7g20170' => 'fve', 'Glyma.05G175000' => 'gma', 'Glyma.08G132300' => 'gma', 'Glyma.11G243000' => 'gma', 'Glyma.13G158900' => 'gma', 'Glyma.17G112400' => 'gma', 'Glyma.18G014100' => 'gma', 'Glyma.19G003100' => 'gma', 'Glyma.19G056500' => 'gma', 'Gohir.A01G158900' => 'ghi', 'Gohir.A05G312600' => 'ghi', 'Gohir.A05G354900' => 'ghi', 'Gohir.A07G037200' => 'ghi', 'Gohir.A09G030000' => 'ghi', 'Gohir.A12G145200' => 'ghi', 'Gohir.D01G151500' => 'ghi', 'Gohir.D04G058300' => 'ghi', 'Gohir.D05G314100' => 'ghi', 'Gohir.D07G041400' => 'ghi', 'Gohir.D09G029700' => 'ghi', 'Gohir.D12G149700' => 'ghi', 'Gorai.001G043800' => 'gra', 'Gorai.002G187800' => 'gra', 'Gorai.006G034700' => 'gra', 'Gorai.008G161200' => 'gra', 'Gorai.009G335700' => 'gra', 'Gorai.012G065000' => 'gra', 'GSVIVG01000535001' => 'vvi', 'GSVIVG01015572001' => 'vvi', 'GSVIVG01032386001' => 'vvi', 'HanXRQChr05g0138531' => 'han', 'HanXRQChr06g0174391' => 'han', 'HanXRQChr07g0199021' => 'han', 'HanXRQChr08g0208211' => 'han', 'HanXRQChr09g0255471' => 'han', 'HanXRQChr10g0315791' => 'han', 'HanXRQChr12g0371991' => 'han', 'HanXRQChr15g0475251' => 'han', 'HanXRQChr17g0540001' => 'han', 'HanXRQChr17g0548631' => 'han', 'HanXRQChr17g0569561' => 'han', 'Haze_12256' => 'cav', 'Haze_14756' => 'cav', 'Haze_25528' => 'cav', 'Hma1.2p1_0079F.1_g041020' => 'hma', 'Hma1.2p1_0818F.1_g223260' => 'hma', 'Hma1.2p1_1747F.1_g300530' => 'hma', 'HPP92_004607' => 'vpl', 'HPP92_004608' => 'vpl', 'HPP92_006181' => 'vpl', 'HPP92_012192' => 'vpl', 'HPP92_015680' => 'vpl', 'HPP92_020249' => 'vpl', 'HPP92_021376' => 'vpl', 'HPP92_024275' => 'vpl', 'Hund06031' => 'sun', 'Hund25391' => 'sun', 'Lalb_Chr07g0185371' => 'lal', 'Lalb_Chr07g0185381' => 'lal', 'Lalb_Chr12g0204011' => 'lal', 'Lalb_Chr13g0301671' => 'lal', 'Lalb_Chr14g0362851' => 'lal', 'Lalb_Chr24g0403581' => 'lal', 'Lj1g0000233' => 'lja', 'Lj2g0018120' => 'lja', 'Lj3C621T0' => 'lonja', 'Lj3P1059T14' => 'lonja', 'Lj3P611T9' => 'lonja', 'Lj3P614T13' => 'lonja', 'Lj3P615T5' => 'lonja', 'Lj4g0012315' => 'lja', 'Lj4g0026182' => 'lja', 'Lj6P813T16' => 'lonja', 'Lj7C427T7' => 'lonja', 'Lj7C427T8' => 'lonja', 'Lj7P600T41' => 'lonja', 'Lju41C42G17' => 'lonja', 'Lsat_1_v5_gn_0_47300' => 'lsa', 'Lsat_1_v5_gn_2_91280' => 'lsa', 'Lsat_1_v5_gn_3_30561' => 'lsa', 'Lsat_1_v5_gn_4_184321' => 'lsa', 'Lsat_1_v5_gn_4_4041' => 'lsa', 'Lsat_1_v5_gn_5_92000' => 'lsa', 'Lsat_1_v5_gn_8_152940' => 'lsa', 'Lsat_1_v5_gn_8_62401' => 'lsa', 'Manes.06G055900' => 'mes', 'Manes.12G022200' => 'mes', 'Manes.13G023300' => 'mes', 'Manes.14G115000' => 'mes', 'Manes.15G151700' => 'mes', 'Manes.17G111300' => 'mes', 'Mapoly0226s0009' => 'mpo', 'MBI02_g25363_MAGBIO' => 'mbi', 'MBI06_g00027_MAGBIO' => 'mbi', 'MBI10_g13034_MAGBIO' => 'mbi', 'MD09G1023400' => 'mdo', 'MD13G1100100' => 'mdo', 'MD15G1169200' => 'mdo', 'MD16G1101100' => 'mdo', 'MD17G1022900' => 'mdo', 'Medtr3g096150' => 'mtr', 'Medtr4g115070' => 'mtr', 'Medtr7g033325' => 'mtr', 'Medtr8g089840' => 'mtr', 'MELO3C010319.2' => 'cme', 'MELO3C011944.2' => 'cme', 'MELO3C021589.2' => 'cme', 'Migut.E00207' => 'egut', 'Migut.H00067' => 'egut', 'Migut.K00433' => 'egut', 'Migut.K00606' => 'egut', 'Migut.K01410' => 'egut', 'MSTRG.13347' => 'ama', 'MSTRG.24045' => 'ama', 'MSTRG.2428' => 'ama', 'MSTRG.26410' => 'ama', 'MSTRG.3139' => 'ama', 'MSTRG.3286' => 'ama', 'MSTRG.563' => 'ama', 'MSTRG.7941' => 'ama', 'Nitab4.5_0000028g0060' => 'nta', 'Nitab4.5_0000065g0260' => 'nta', 'Nitab4.5_0000112g0060' => 'nta', 'Nitab4.5_0000489g0120' => 'nta', 'Nitab4.5_0001776g0050' => 'nta', 'Nitab4.5_0001854g0010' => 'nta', 'Nitab4.5_0001860g0020' => 'nta', 'Nitab4.5_0004352g0010' => 'nta', 'Nitab4.5_0008716g0020' => 'nta', 'Nitab4.5_0008922g0010' => 'nta', 'Nn3g16693' => 'nnu', 'Nn4g22596' => 'nnu', 'Nn7g37639' => 'nnu', 'Oeu001701.1' => 'oeu', 'Oeu018149.1' => 'oeu', 'Oeu026220.1' => 'oeu', 'Oeu038635.1' => 'oeu', 'Oeu049176.1' => 'oeu', 'Oeu056706.1' => 'oeu', 'Oeu056937.1' => 'oeu', 'Oeu057540.1' => 'oeu', 'Os02g0594900' => 'osa', 'Os02g0595100' => 'osa', 'Os04g0477500' => 'osa', 'Os12g0611900' => 'osa', 'Peaxi162Scf00076g00020' => 'pax', 'Peaxi162Scf00128g00217' => 'pax', 'Peaxi162Scf00129g01640' => 'pax', 'Peaxi162Scf00669g00007' => 'pax', 'Peaxi162Scf00700g00421' => 'pax', 'Peaxi162Scf00801g00038' => 'pax', 'Peaxi162Scf00891g00025' => 'pax', 'PGR083G0909' => 'pgr', 'PGR119G1005' => 'pgr', 'PGR142G2236' => 'pgr', 'PGR142G3388' => 'pgr', 'PGSC0003DMG400004514' => 'stu', 'PGSC0003DMG400012635' => 'stu', 'PGSC0003DMG400015730' => 'stu', 'PGSC0003DMG400018611' => 'stu', 'PGSC0003DMG400030897' => 'stu', 'Phvul.001G254800' => 'pvu', 'Phvul.002G260100' => 'pvu', 'Phvul.003G167600' => 'pvu', 'Phvul.004G005100' => 'pvu', 'Potri.001G343600' => 'ptr', 'Potri.006G066700' => 'ptr', 'Potri.008G186000' => 'ptr', 'Potri.010G046900' => 'ptr', 'Potri.018G127900' => 'ptr', 'Pp3c20_17750' => 'ppa', 'Pp3c24_4380' => 'ppa', 'Prupe.1G245800' => 'ppe', 'Prupe.3G293400' => 'ppe', 'Prupe.7G247400' => 'ppe', 'Psat0s145g0120' => 'psa', 'Psat0s595g0040' => 'psa', 'Psat0s595g0120' => 'psa', 'Psat3g175040' => 'psa', 'Psat7g058120' => 'psa', 'PSO017G0428' => 'pso', 'PSO063G7510' => 'pso', 'PSO067G0046' => 'pso', 'PSO478G1073' => 'pso', 'PSO675G3677' => 'pso', 'PSO675G6558' => 'pso', 'PSO675G7520' => 'pso', 'PSO675G8959' => 'pso', 'QL02p074089' => 'qlo', 'QL02p089614' => 'qlo', 'QL03p057736' => 'qlo', 'RcHm_v2.0_Chr1g0364131' => 'rch', 'RcHm_v2.0_Chr2g0087801' => 'rch', 'RcHm_v2.0_Chr2g0087821' => 'rch', 'RcHm_v2.0_Chr2g0173231' => 'rch', 'RcHm_v2.0_Chr4g0433111' => 'rch', 'Rhsim03G0250300' => 'rsi', 'Rhsim08G0048400' => 'rsi', 'Rhsim10G0014800' => 'rsi', 'Rhsim12G0040100' => 'rsi', 'Rhsim12G0109700' => 'rsi', 'Sabra06G0049600' => 'sbr', 'Sabra08G0141000' => 'sbr', 'Sabra10G0021400' => 'sbr', 'Sabra16G0222900' => 'sbr', 'Sabra18G0108600' => 'sbr', 'SalBow1G0433' => 'sbo', 'SalBow1G2038' => 'sbo', 'SalBow1G5003' => 'sbo', 'SalBow7G1197' => 'sbo', 'SalBow8G3506' => 'sbo', 'Sc03g0007300' => 'sci', 'Sc11g0000950' => 'sci', 'Sc14g0008750' => 'sci', 'Sc18g0000420' => 'sci', 'Sed0006754' => 'sed', 'Sed0008741' => 'sed', 'Sed0017172' => 'sed', 'Sed0018925' => 'sed', 'Sed0023326' => 'sed', 'Sed0025909' => 'sed', 'SEGI_05333' => 'sgi', 'SEGI_10362' => 'sgi', 'SEGI_13380' => 'sgi', 'SEGI_24306' => 'sgi', 'SEGI_29077' => 'sgi', 'SEGI_29095' => 'sgi', 'SEGI_36534' => 'sgi', 'SEGI_37506' => 'sgi', 'SEGI_38321' => 'sgi', 'SGA_v2.0_scaffold307G48031' => 'sas', 'SGA_v2.0_scaffold47G17507' => 'sas', 'SGA_v2.0_scaffold63G21736' => 'sas', 'SGA_v2.0_scaffold87G27070' => 'sas', 'SHI17794' => 'shi', 'SHI28851' => 'shi', 'SMO165G0155' => 'smo', 'SMO340G0217' => 'smo', 'SMO367G1210' => 'smo', 'Solyc02g093430.3' => 'sly', 'Solyc05g013580.4' => 'sly', 'Solyc07g008030.3' => 'sly', 'Solyc12g035470.2' => 'sly', 'Sopen02g038020' => 'spe', 'Sopen05g008490' => 'spe', 'Sopen07g003910' => 'spe', 'Sopen12g015240' => 'spe', 'Sp1g11550' => 'spa', 'Sp2g16710' => 'spa', 'Sp3g00430' => 'spa', 'Sp3g26780' => 'spa', 'Sp5g22900' => 'spa', 'Sp6g29530' => 'spa', 'TAR371G0794' => 'tar', 'TAR374G0164' => 'tar', 'TAR622G0165' => 'tar', 'TAR626G0929' => 'tar', 'TAR629G2155' => 'tar', 'THA.LOC104805282' => 'tha', 'THA.LOC104805363' => 'tha', 'THA.LOC104808968' => 'tha', 'THA.LOC104821093' => 'tha', 'THA.LOC104823953' => 'tha', 'THA.LOC104825562' => 'tha', 'THA.LOC104825665' => 'tha', 'Thecc.02G261400' => 'tca', 'Thecc.04G019200' => 'tca', 'Thecc.09G130400' => 'tca', 'Thhalv10004374m.g' => 'esa', 'Thhalv10007850m.g' => 'esa', 'Thhalv10013782m.g' => 'esa', 'Thhalv10018686m.g' => 'esa', 'Thhalv10020899m.g' => 'esa', 'Thhalv10022755m.g' => 'esa', 'TPR.G23851' => 'tpr', 'TPR.G26500' => 'tpr', 'TPR.G27267' => 'tpr', 'TPR.G32001' => 'tpr', 'TPR.G6251' => 'tpr', 'TPR.G8167' => 'tpr', 'TWI12G1330' => 'twi', 'TWI18G1239' => 'twi', 'TWI34G0979' => 'twi', 'TWI36G0670' => 'twi', 'TWI36G0707' => 'twi', 'TWI56G0233' => 'twi', 'TWI75G1809' => 'twi', 'unitig_21.g20874' => 'ugi', 'unitig_26.g10343' => 'ugi', 'unitig_46.g18392' => 'ugi', 'unitig_52.g17178' => 'ugi', 'unitig_8.g2934' => 'ugi', 'vmacro01122' => 'vma', 'vmacro05875' => 'vma', 'vmacro06147' => 'vma', 'vmacro16191' => 'vma', 'vmacro18293' => 'vma', 'VMungo0251G3707' => 'vmu', 'VMungo0464G1521' => 'vmu', 'VMungo1215G0205' => 'vmu', 'VMungo1383G2484' => 'vmu', 'Zm00001eb079610' => 'zma', 'Zm00001eb135990' => 'zma', 'Zm00001eb183710' => 'zma', 'Zm00001eb246020' => 'zma' ) $gf_id = 'HOM05D001124' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001124' ) $data_identifier = 'HOM05D001124' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 6, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 7, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 21, 'bol' => (int) 10, 'bra' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 6, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 9, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 21, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 8, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 10, 'lsa' => (int) 8, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 8, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 9, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb246020' $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' => 'HOM05D001124', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '548', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02520' => 'bna', 'A03p06630' => 'bna', 'A05p44460' => 'bna', 'A06p08710' => 'bna', 'A06p41090' => 'bna', 'A07p32320' => 'bna', 'A08p32520' => 'bna', 'A09p10360' => 'bna', 'A10p24080' => 'bna', 'Aa31LG11G15250' => 'aar', 'Aa31LG1G1800' => 'aar', 'Aa31LG2G5120' => 'aar', 'Aa31LG2G6070' => 'aar', 'Aa31LG5G10770' => 'aar', 'Aa31sc61G90' => 'aar', 'Actinidia01352' => 'ach', 'Actinidia05983' => 'ach', 'Actinidia08133' => 'ach', 'Actinidia15101' => 'ach', 'Actinidia26379' => 'ach', 'Actinidia35778' => 'ach', 'Actinidia36123' => 'ach', 'Actinidia37436' => 'ach', 'Actinidia38730' => 'ach', 'Ah.02g128210' => 'amhyb', 'Ah.03g132990' => 'amhyb', 'Ah.14g079410' => 'amhyb', 'AL1G24640' => 'aly', 'AL2G26680' => 'aly', 'AL3G10530' => 'aly', 'AL3G45230' => 'aly', 'AL5G15230' => 'aly', 'AL5G16960' => 'aly', 'AL6G25210' => 'aly', 'Aqoxy2G00441' => 'aox', 'Aqoxy3G01236' => 'aox', 'Aqoxy5G03746' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3RQ047' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C7GMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9C8JER' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MBL6KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YXCZ83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZANX40' => 'arhy', 'AT1G12990' => 'ath', 'AT1G67880' => 'ath', 'AT2G13290' => 'ath', 'AT3G01620' => 'ath', 'AT3G26445' => 'ath', 'AT3G27540' => 'ath', 'AT5G14480' => 'ath', 'ATR0824G026' => 'atr', 'ATR1098G019' => 'atr', 'Atru.chr11.2145' => 'acertr', 'Atru.chr2.3636' => 'acertr', 'Atru.chr2.3644' => 'acertr', 'Atru.chr6.2422' => 'acertr', 'Atru.chr7.1112' => 'acertr', 'AUR62005469' => 'cqu', 'AUR62011166' => 'cqu', 'AUR62013319' => 'cqu', 'AUR62024273' => 'cqu', 'AUR62028420' => 'cqu', 'AUR62041942' => 'cqu', 'BcaB01g04969' => 'bca', 'BcaB01g06371' => 'bca', 'BcaB02g11494' => 'bca', 'BcaB03g15382' => 'bca', 'BcaB08g36994' => 'bca', 'BcaC03g13477' => 'bca', 'BcaC03g13478' => 'bca', 'BcaC03g13480' => 'bca', 'BcaC03g13481' => 'bca', 'BcaC03g13486' => 'bca', 'BcaC04g19031' => 'bca', 'BcaC04g23085' => 'bca', 'BcaC05g25094' => 'bca', 'BcaC05g25096' => 'bca', 'BcaC05g25138' => 'bca', 'BcaC05g30416' => 'bca', 'BcaC05g30455' => 'bca', 'BcaC06g30979' => 'bca', 'BcaC06g33805' => 'bca', 'BcaC08g46021' => 'bca', 'BcaNung03154' => 'bca', 'BolC2t06623H' => 'bol', 'BolC2t06632H' => 'bol', 'BolC2t06635H' => 'bol', 'BolC2t06638H' => 'bol', 'BolC3t13266H' => 'bol', 'BolC5t29776H' => 'bol', 'BolC6t38912H' => 'bol', 'BolC7t44183H' => 'bol', 'BolC9t54123H' => 'bol', 'BolC9t59107H' => 'bol', 'BraA02t05221Z' => 'bra', 'BraA03t09996Z' => 'bra', 'BraA05t23210Z' => 'bra', 'BraA06t24068Z' => 'bra', 'BraA06t27032Z' => 'bra', 'BraA08t35176Z' => 'bra', 'BraA09t36680Z' => 'bra', 'BraA10t44471Z' => 'bra', 'C02p06760' => 'bna', 'C02p06890' => 'bna', 'C02p07010' => 'bna', 'C03p07660' => 'bna', 'C05p10300' => 'bna', 'C06p38150' => 'bna', 'C07p36650' => 'bna', 'C08p15770' => 'bna', 'C09p12300' => 'bna', 'C09p62700' => 'bna', 'C09p75040' => 'bna', 'CAN.G13.1' => 'can', 'CAN.G138.4' => 'can', 'CAN.G44.6' => 'can', 'CAN.G473.19' => 'can', 'CANSAT01G0835' => 'cansat', 'CANSAT11G0246' => 'cansat', 'CANSAT11G1766' => 'cansat', 'CANSAT64G1954' => 'cansat', 'CARHR013330' => 'chi', 'CARHR060530' => 'chi', 'CARHR075300' => 'chi', 'CARHR105120' => 'chi', 'CARHR148910' => 'chi', 'CARHR198830' => 'chi', 'Carub.0001s1275' => 'cru', 'Carub.0002s1437' => 'cru', 'Carub.0003s0044' => 'cru', 'Carub.0003s2787' => 'cru', 'Carub.0005s0597' => 'cru', 'Carub.0006s1266' => 'cru', 'Ca_06935_v3' => 'car', 'Ca_13559_v3' => 'car', 'Ca_16941_v3' => 'car', 'Ca_16960_v3' => 'car', 'Ca_17775_v3' => 'car', 'Ca_30464_v3' => 'car', 'Cc06_g08160' => 'ccan', 'Cc07_g01520' => 'ccan', 'Cc11_g15810' => 'ccan', 'CDE02G2840' => 'cde', 'CDE03G0093' => 'cde', 'CDE04G2127' => 'cde', 'CDE07G1857' => 'cde', 'CDE09G1246' => 'cde', 'Cfa003412' => 'cfa', 'Cfa007341' => 'cfa', 'Cfa009220' => 'cfa', 'Ciclev10008737m.g' => 'ccl', 'Ciclev10015565m.g' => 'ccl', 'Ciclev10031761m.g' => 'ccl', 'CiPaw.03G045300' => 'cil', 'CiPaw.03G247200' => 'cil', 'CiPaw.04G029500' => 'cil', 'CiPaw.04G174000' => 'cil', 'CiPaw.05G181200' => 'cil', 'CiPaw.06G067100' => 'cil', 'ClCG05G025800' => 'cla', 'ClCG06G011400' => 'cla', 'ClCG09G019360' => 'cla', 'COL.COLO4_04827' => 'col', 'COL.COLO4_29170' => 'col', 'COL.COLO4_35131' => 'col', 'COL.COLO4_35132' => 'col', 'Cpa.g.sc33.32' => 'cpa', 'Cpa.g.sc46.29' => 'cpa', 'Cpa.g.sc796.1' => 'cpa', 'CsaV3_1G030420' => 'csa', 'CsaV3_5G027050' => 'csa', 'CsaV3_5G031040' => 'csa', 'CsaV3_UNG023130' => 'csa', 'CSS0007726' => 'camsi', 'CSS0016433' => 'camsi', 'CSS0017656' => 'camsi', 'CSS0025364' => 'camsi', 'CSS0027582' => 'camsi', 'CSS0047288' => 'camsi', 'CSS0049950' => 'camsi', 'DCAR_003843' => 'dca', 'DCAR_007052' => 'dca', 'DCAR_020884' => 'dca', 'DCAR_021730' => 'dca', 'DCAR_024423' => 'dca', 'DCAR_026509' => 'dca', 'DCAR_031158' => 'dca', 'Dinv14728' => 'din', 'Dinv15219' => 'din', 'Dinv25728' => 'din', 'Dinv33428' => 'din', 'Dinv36489' => 'din', 'Dinv41486' => 'din', 'Duzib147G0469' => 'dzi', 'Duzib168G0060' => 'dzi', 'Duzib187G1215' => 'dzi', 'Duzib248G0692' => 'dzi', 'Duzib251G0767' => 'dzi', 'Duzib264G0446' => 'dzi', 'Duzib268G0691' => 'dzi', 'ECA232G4767' => 'eca', 'ECA233G2838' => 'eca', 'ECA234G0391' => 'eca', 'ECA234G0857' => 'eca', 'ECA236G1593' => 'eca', 'ECA238G0565' => 'eca', 'ECA246G1027' => 'eca', 'ECA246G3223' => 'eca', 'ECA246G3470' => 'eca', 'EL10Ac6g13829' => 'bvu', 'EL10Ac6g14093' => 'bvu', 'EL10Ac8g18707' => 'bvu', 'Eucgr.C01369' => 'egr', 'Eucgr.H02492' => 'egr', 'Eucgr.I01733' => 'egr', 'Eucgr.J02255' => 'egr', 'Eucgr.J02257' => 'egr', 'Eucgr.J02258' => 'egr', 'FAN02G1601' => 'fan', 'FAN03G1586' => 'fan', 'FAN03G2986' => 'fan', 'FAN05G4837' => 'fan', 'FAN06G0146' => 'fan', 'FAN07G0858' => 'fan', 'FAN09G3179' => 'fan', 'FAN10G0669' => 'fan', 'FAN12G2358' => 'fan', 'FAN14G4198' => 'fan', 'FAN14G5112' => 'fan', 'FAN17G0342' => 'fan', 'FAN19G0342' => 'fan', 'FAN19G0962' => 'fan', 'FAN19G1101' => 'fan', 'FAN19G1872' => 'fan', 'FAN22G0356' => 'fan', 'FAN23G0744' => 'fan', 'FAN23G1914' => 'fan', 'FAN26G0032' => 'fan', 'FAN28G0625' => 'fan', 'FvH4_1g02710' => 'fve', 'FvH4_1g02720' => 'fve', 'FvH4_4g25670' => 'fve', 'FvH4_6g51700' => 'fve', 'FvH4_7g20170' => 'fve', 'Glyma.05G175000' => 'gma', 'Glyma.08G132300' => 'gma', 'Glyma.11G243000' => 'gma', 'Glyma.13G158900' => 'gma', 'Glyma.17G112400' => 'gma', 'Glyma.18G014100' => 'gma', 'Glyma.19G003100' => 'gma', 'Glyma.19G056500' => 'gma', 'Gohir.A01G158900' => 'ghi', 'Gohir.A05G312600' => 'ghi', 'Gohir.A05G354900' => 'ghi', 'Gohir.A07G037200' => 'ghi', 'Gohir.A09G030000' => 'ghi', 'Gohir.A12G145200' => 'ghi', 'Gohir.D01G151500' => 'ghi', 'Gohir.D04G058300' => 'ghi', 'Gohir.D05G314100' => 'ghi', 'Gohir.D07G041400' => 'ghi', 'Gohir.D09G029700' => 'ghi', 'Gohir.D12G149700' => 'ghi', 'Gorai.001G043800' => 'gra', 'Gorai.002G187800' => 'gra', 'Gorai.006G034700' => 'gra', 'Gorai.008G161200' => 'gra', 'Gorai.009G335700' => 'gra', 'Gorai.012G065000' => 'gra', 'GSVIVG01000535001' => 'vvi', 'GSVIVG01015572001' => 'vvi', 'GSVIVG01032386001' => 'vvi', 'HanXRQChr05g0138531' => 'han', 'HanXRQChr06g0174391' => 'han', 'HanXRQChr07g0199021' => 'han', 'HanXRQChr08g0208211' => 'han', 'HanXRQChr09g0255471' => 'han', 'HanXRQChr10g0315791' => 'han', 'HanXRQChr12g0371991' => 'han', 'HanXRQChr15g0475251' => 'han', 'HanXRQChr17g0540001' => 'han', 'HanXRQChr17g0548631' => 'han', 'HanXRQChr17g0569561' => 'han', 'Haze_12256' => 'cav', 'Haze_14756' => 'cav', 'Haze_25528' => 'cav', 'Hma1.2p1_0079F.1_g041020' => 'hma', 'Hma1.2p1_0818F.1_g223260' => 'hma', 'Hma1.2p1_1747F.1_g300530' => 'hma', 'HPP92_004607' => 'vpl', 'HPP92_004608' => 'vpl', 'HPP92_006181' => 'vpl', 'HPP92_012192' => 'vpl', 'HPP92_015680' => 'vpl', 'HPP92_020249' => 'vpl', 'HPP92_021376' => 'vpl', 'HPP92_024275' => 'vpl', 'Hund06031' => 'sun', 'Hund25391' => 'sun', 'Lalb_Chr07g0185371' => 'lal', 'Lalb_Chr07g0185381' => 'lal', 'Lalb_Chr12g0204011' => 'lal', 'Lalb_Chr13g0301671' => 'lal', 'Lalb_Chr14g0362851' => 'lal', 'Lalb_Chr24g0403581' => 'lal', 'Lj1g0000233' => 'lja', 'Lj2g0018120' => 'lja', 'Lj3C621T0' => 'lonja', 'Lj3P1059T14' => 'lonja', 'Lj3P611T9' => 'lonja', 'Lj3P614T13' => 'lonja', 'Lj3P615T5' => 'lonja', 'Lj4g0012315' => 'lja', 'Lj4g0026182' => 'lja', 'Lj6P813T16' => 'lonja', 'Lj7C427T7' => 'lonja', 'Lj7C427T8' => 'lonja', 'Lj7P600T41' => 'lonja', 'Lju41C42G17' => 'lonja', 'Lsat_1_v5_gn_0_47300' => 'lsa', 'Lsat_1_v5_gn_2_91280' => 'lsa', 'Lsat_1_v5_gn_3_30561' => 'lsa', 'Lsat_1_v5_gn_4_184321' => 'lsa', 'Lsat_1_v5_gn_4_4041' => 'lsa', 'Lsat_1_v5_gn_5_92000' => 'lsa', 'Lsat_1_v5_gn_8_152940' => 'lsa', 'Lsat_1_v5_gn_8_62401' => 'lsa', 'Manes.06G055900' => 'mes', 'Manes.12G022200' => 'mes', 'Manes.13G023300' => 'mes', 'Manes.14G115000' => 'mes', 'Manes.15G151700' => 'mes', 'Manes.17G111300' => 'mes', 'Mapoly0226s0009' => 'mpo', 'MBI02_g25363_MAGBIO' => 'mbi', 'MBI06_g00027_MAGBIO' => 'mbi', 'MBI10_g13034_MAGBIO' => 'mbi', 'MD09G1023400' => 'mdo', 'MD13G1100100' => 'mdo', 'MD15G1169200' => 'mdo', 'MD16G1101100' => 'mdo', 'MD17G1022900' => 'mdo', 'Medtr3g096150' => 'mtr', 'Medtr4g115070' => 'mtr', 'Medtr7g033325' => 'mtr', 'Medtr8g089840' => 'mtr', 'MELO3C010319.2' => 'cme', 'MELO3C011944.2' => 'cme', 'MELO3C021589.2' => 'cme', 'Migut.E00207' => 'egut', 'Migut.H00067' => 'egut', 'Migut.K00433' => 'egut', 'Migut.K00606' => 'egut', 'Migut.K01410' => 'egut', 'MSTRG.13347' => 'ama', 'MSTRG.24045' => 'ama', 'MSTRG.2428' => 'ama', 'MSTRG.26410' => 'ama', 'MSTRG.3139' => 'ama', 'MSTRG.3286' => 'ama', 'MSTRG.563' => 'ama', 'MSTRG.7941' => 'ama', 'Nitab4.5_0000028g0060' => 'nta', 'Nitab4.5_0000065g0260' => 'nta', 'Nitab4.5_0000112g0060' => 'nta', 'Nitab4.5_0000489g0120' => 'nta', 'Nitab4.5_0001776g0050' => 'nta', 'Nitab4.5_0001854g0010' => 'nta', 'Nitab4.5_0001860g0020' => 'nta', 'Nitab4.5_0004352g0010' => 'nta', 'Nitab4.5_0008716g0020' => 'nta', 'Nitab4.5_0008922g0010' => 'nta', 'Nn3g16693' => 'nnu', 'Nn4g22596' => 'nnu', 'Nn7g37639' => 'nnu', 'Oeu001701.1' => 'oeu', 'Oeu018149.1' => 'oeu', 'Oeu026220.1' => 'oeu', 'Oeu038635.1' => 'oeu', 'Oeu049176.1' => 'oeu', 'Oeu056706.1' => 'oeu', 'Oeu056937.1' => 'oeu', 'Oeu057540.1' => 'oeu', 'Os02g0594900' => 'osa', 'Os02g0595100' => 'osa', 'Os04g0477500' => 'osa', 'Os12g0611900' => 'osa', 'Peaxi162Scf00076g00020' => 'pax', 'Peaxi162Scf00128g00217' => 'pax', 'Peaxi162Scf00129g01640' => 'pax', 'Peaxi162Scf00669g00007' => 'pax', 'Peaxi162Scf00700g00421' => 'pax', 'Peaxi162Scf00801g00038' => 'pax', 'Peaxi162Scf00891g00025' => 'pax', 'PGR083G0909' => 'pgr', 'PGR119G1005' => 'pgr', 'PGR142G2236' => 'pgr', 'PGR142G3388' => 'pgr', 'PGSC0003DMG400004514' => 'stu', 'PGSC0003DMG400012635' => 'stu', 'PGSC0003DMG400015730' => 'stu', 'PGSC0003DMG400018611' => 'stu', 'PGSC0003DMG400030897' => 'stu', 'Phvul.001G254800' => 'pvu', 'Phvul.002G260100' => 'pvu', 'Phvul.003G167600' => 'pvu', 'Phvul.004G005100' => 'pvu', 'Potri.001G343600' => 'ptr', 'Potri.006G066700' => 'ptr', 'Potri.008G186000' => 'ptr', 'Potri.010G046900' => 'ptr', 'Potri.018G127900' => 'ptr', 'Pp3c20_17750' => 'ppa', 'Pp3c24_4380' => 'ppa', 'Prupe.1G245800' => 'ppe', 'Prupe.3G293400' => 'ppe', 'Prupe.7G247400' => 'ppe', 'Psat0s145g0120' => 'psa', 'Psat0s595g0040' => 'psa', 'Psat0s595g0120' => 'psa', 'Psat3g175040' => 'psa', 'Psat7g058120' => 'psa', 'PSO017G0428' => 'pso', 'PSO063G7510' => 'pso', 'PSO067G0046' => 'pso', 'PSO478G1073' => 'pso', 'PSO675G3677' => 'pso', 'PSO675G6558' => 'pso', 'PSO675G7520' => 'pso', 'PSO675G8959' => 'pso', 'QL02p074089' => 'qlo', 'QL02p089614' => 'qlo', 'QL03p057736' => 'qlo', 'RcHm_v2.0_Chr1g0364131' => 'rch', 'RcHm_v2.0_Chr2g0087801' => 'rch', 'RcHm_v2.0_Chr2g0087821' => 'rch', 'RcHm_v2.0_Chr2g0173231' => 'rch', 'RcHm_v2.0_Chr4g0433111' => 'rch', 'Rhsim03G0250300' => 'rsi', 'Rhsim08G0048400' => 'rsi', 'Rhsim10G0014800' => 'rsi', 'Rhsim12G0040100' => 'rsi', 'Rhsim12G0109700' => 'rsi', 'Sabra06G0049600' => 'sbr', 'Sabra08G0141000' => 'sbr', 'Sabra10G0021400' => 'sbr', 'Sabra16G0222900' => 'sbr', 'Sabra18G0108600' => 'sbr', 'SalBow1G0433' => 'sbo', 'SalBow1G2038' => 'sbo', 'SalBow1G5003' => 'sbo', 'SalBow7G1197' => 'sbo', 'SalBow8G3506' => 'sbo', 'Sc03g0007300' => 'sci', 'Sc11g0000950' => 'sci', 'Sc14g0008750' => 'sci', 'Sc18g0000420' => 'sci', 'Sed0006754' => 'sed', 'Sed0008741' => 'sed', 'Sed0017172' => 'sed', 'Sed0018925' => 'sed', 'Sed0023326' => 'sed', 'Sed0025909' => 'sed', 'SEGI_05333' => 'sgi', 'SEGI_10362' => 'sgi', 'SEGI_13380' => 'sgi', 'SEGI_24306' => 'sgi', 'SEGI_29077' => 'sgi', 'SEGI_29095' => 'sgi', 'SEGI_36534' => 'sgi', 'SEGI_37506' => 'sgi', 'SEGI_38321' => 'sgi', 'SGA_v2.0_scaffold307G48031' => 'sas', 'SGA_v2.0_scaffold47G17507' => 'sas', 'SGA_v2.0_scaffold63G21736' => 'sas', 'SGA_v2.0_scaffold87G27070' => 'sas', 'SHI17794' => 'shi', 'SHI28851' => 'shi', 'SMO165G0155' => 'smo', 'SMO340G0217' => 'smo', 'SMO367G1210' => 'smo', 'Solyc02g093430.3' => 'sly', 'Solyc05g013580.4' => 'sly', 'Solyc07g008030.3' => 'sly', 'Solyc12g035470.2' => 'sly', 'Sopen02g038020' => 'spe', 'Sopen05g008490' => 'spe', 'Sopen07g003910' => 'spe', 'Sopen12g015240' => 'spe', 'Sp1g11550' => 'spa', 'Sp2g16710' => 'spa', 'Sp3g00430' => 'spa', 'Sp3g26780' => 'spa', 'Sp5g22900' => 'spa', 'Sp6g29530' => 'spa', 'TAR371G0794' => 'tar', 'TAR374G0164' => 'tar', 'TAR622G0165' => 'tar', 'TAR626G0929' => 'tar', 'TAR629G2155' => 'tar', 'THA.LOC104805282' => 'tha', 'THA.LOC104805363' => 'tha', 'THA.LOC104808968' => 'tha', 'THA.LOC104821093' => 'tha', 'THA.LOC104823953' => 'tha', 'THA.LOC104825562' => 'tha', 'THA.LOC104825665' => 'tha', 'Thecc.02G261400' => 'tca', 'Thecc.04G019200' => 'tca', 'Thecc.09G130400' => 'tca', 'Thhalv10004374m.g' => 'esa', 'Thhalv10007850m.g' => 'esa', 'Thhalv10013782m.g' => 'esa', 'Thhalv10018686m.g' => 'esa', 'Thhalv10020899m.g' => 'esa', 'Thhalv10022755m.g' => 'esa', 'TPR.G23851' => 'tpr', 'TPR.G26500' => 'tpr', 'TPR.G27267' => 'tpr', 'TPR.G32001' => 'tpr', 'TPR.G6251' => 'tpr', 'TPR.G8167' => 'tpr', 'TWI12G1330' => 'twi', 'TWI18G1239' => 'twi', 'TWI34G0979' => 'twi', 'TWI36G0670' => 'twi', 'TWI36G0707' => 'twi', 'TWI56G0233' => 'twi', 'TWI75G1809' => 'twi', 'unitig_21.g20874' => 'ugi', 'unitig_26.g10343' => 'ugi', 'unitig_46.g18392' => 'ugi', 'unitig_52.g17178' => 'ugi', 'unitig_8.g2934' => 'ugi', 'vmacro01122' => 'vma', 'vmacro05875' => 'vma', 'vmacro06147' => 'vma', 'vmacro16191' => 'vma', 'vmacro18293' => 'vma', 'VMungo0251G3707' => 'vmu', 'VMungo0464G1521' => 'vmu', 'VMungo1215G0205' => 'vmu', 'VMungo1383G2484' => 'vmu', 'Zm00001eb079610' => 'zma', 'Zm00001eb135990' => 'zma', 'Zm00001eb183710' => 'zma', 'Zm00001eb246020' => 'zma' ), 'gf_id' => 'HOM05D001124', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001124' ), 'data_identifier' => 'HOM05D001124', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001124', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '548', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02520' => 'bna', 'A03p06630' => 'bna', 'A05p44460' => 'bna', 'A06p08710' => 'bna', 'A06p41090' => 'bna', 'A07p32320' => 'bna', 'A08p32520' => 'bna', 'A09p10360' => 'bna', 'A10p24080' => 'bna', 'Aa31LG11G15250' => 'aar', 'Aa31LG1G1800' => 'aar', 'Aa31LG2G5120' => 'aar', 'Aa31LG2G6070' => 'aar', 'Aa31LG5G10770' => 'aar', 'Aa31sc61G90' => 'aar', 'Actinidia01352' => 'ach', 'Actinidia05983' => 'ach', 'Actinidia08133' => 'ach', 'Actinidia15101' => 'ach', 'Actinidia26379' => 'ach', 'Actinidia35778' => 'ach', 'Actinidia36123' => 'ach', 'Actinidia37436' => 'ach', 'Actinidia38730' => 'ach', 'Ah.02g128210' => 'amhyb', 'Ah.03g132990' => 'amhyb', 'Ah.14g079410' => 'amhyb', 'AL1G24640' => 'aly', 'AL2G26680' => 'aly', 'AL3G10530' => 'aly', 'AL3G45230' => 'aly', 'AL5G15230' => 'aly', 'AL5G16960' => 'aly', 'AL6G25210' => 'aly', 'Aqoxy2G00441' => 'aox', 'Aqoxy3G01236' => 'aox', 'Aqoxy5G03746' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3RQ047' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C7GMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9C8JER' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MBL6KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YXCZ83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZANX40' => 'arhy', 'AT1G12990' => 'ath', 'AT1G67880' => 'ath', 'AT2G13290' => 'ath', 'AT3G01620' => 'ath', 'AT3G26445' => 'ath', 'AT3G27540' => 'ath', 'AT5G14480' => 'ath', 'ATR0824G026' => 'atr', 'ATR1098G019' => 'atr', 'Atru.chr11.2145' => 'acertr', 'Atru.chr2.3636' => 'acertr', 'Atru.chr2.3644' => 'acertr', 'Atru.chr6.2422' => 'acertr', 'Atru.chr7.1112' => 'acertr', 'AUR62005469' => 'cqu', 'AUR62011166' => 'cqu', 'AUR62013319' => 'cqu', 'AUR62024273' => 'cqu', 'AUR62028420' => 'cqu', 'AUR62041942' => 'cqu', 'BcaB01g04969' => 'bca', 'BcaB01g06371' => 'bca', 'BcaB02g11494' => 'bca', 'BcaB03g15382' => 'bca', 'BcaB08g36994' => 'bca', 'BcaC03g13477' => 'bca', 'BcaC03g13478' => 'bca', 'BcaC03g13480' => 'bca', 'BcaC03g13481' => 'bca', 'BcaC03g13486' => 'bca', 'BcaC04g19031' => 'bca', 'BcaC04g23085' => 'bca', 'BcaC05g25094' => 'bca', 'BcaC05g25096' => 'bca', 'BcaC05g25138' => 'bca', 'BcaC05g30416' => 'bca', 'BcaC05g30455' => 'bca', 'BcaC06g30979' => 'bca', 'BcaC06g33805' => 'bca', 'BcaC08g46021' => 'bca', 'BcaNung03154' => 'bca', 'BolC2t06623H' => 'bol', 'BolC2t06632H' => 'bol', 'BolC2t06635H' => 'bol', 'BolC2t06638H' => 'bol', 'BolC3t13266H' => 'bol', 'BolC5t29776H' => 'bol', 'BolC6t38912H' => 'bol', 'BolC7t44183H' => 'bol', 'BolC9t54123H' => 'bol', 'BolC9t59107H' => 'bol', 'BraA02t05221Z' => 'bra', 'BraA03t09996Z' => 'bra', 'BraA05t23210Z' => 'bra', 'BraA06t24068Z' => 'bra', 'BraA06t27032Z' => 'bra', 'BraA08t35176Z' => 'bra', 'BraA09t36680Z' => 'bra', 'BraA10t44471Z' => 'bra', 'C02p06760' => 'bna', 'C02p06890' => 'bna', 'C02p07010' => 'bna', 'C03p07660' => 'bna', 'C05p10300' => 'bna', 'C06p38150' => 'bna', 'C07p36650' => 'bna', 'C08p15770' => 'bna', 'C09p12300' => 'bna', 'C09p62700' => 'bna', 'C09p75040' => 'bna', 'CAN.G13.1' => 'can', 'CAN.G138.4' => 'can', 'CAN.G44.6' => 'can', 'CAN.G473.19' => 'can', 'CANSAT01G0835' => 'cansat', 'CANSAT11G0246' => 'cansat', 'CANSAT11G1766' => 'cansat', 'CANSAT64G1954' => 'cansat', 'CARHR013330' => 'chi', 'CARHR060530' => 'chi', 'CARHR075300' => 'chi', 'CARHR105120' => 'chi', 'CARHR148910' => 'chi', 'CARHR198830' => 'chi', 'Carub.0001s1275' => 'cru', 'Carub.0002s1437' => 'cru', 'Carub.0003s0044' => 'cru', 'Carub.0003s2787' => 'cru', 'Carub.0005s0597' => 'cru', 'Carub.0006s1266' => 'cru', 'Ca_06935_v3' => 'car', 'Ca_13559_v3' => 'car', 'Ca_16941_v3' => 'car', 'Ca_16960_v3' => 'car', 'Ca_17775_v3' => 'car', 'Ca_30464_v3' => 'car', 'Cc06_g08160' => 'ccan', 'Cc07_g01520' => 'ccan', 'Cc11_g15810' => 'ccan', 'CDE02G2840' => 'cde', 'CDE03G0093' => 'cde', 'CDE04G2127' => 'cde', 'CDE07G1857' => 'cde', 'CDE09G1246' => 'cde', 'Cfa003412' => 'cfa', 'Cfa007341' => 'cfa', 'Cfa009220' => 'cfa', 'Ciclev10008737m.g' => 'ccl', 'Ciclev10015565m.g' => 'ccl', 'Ciclev10031761m.g' => 'ccl', 'CiPaw.03G045300' => 'cil', 'CiPaw.03G247200' => 'cil', 'CiPaw.04G029500' => 'cil', 'CiPaw.04G174000' => 'cil', 'CiPaw.05G181200' => 'cil', 'CiPaw.06G067100' => 'cil', 'ClCG05G025800' => 'cla', 'ClCG06G011400' => 'cla', 'ClCG09G019360' => 'cla', 'COL.COLO4_04827' => 'col', 'COL.COLO4_29170' => 'col', 'COL.COLO4_35131' => 'col', 'COL.COLO4_35132' => 'col', 'Cpa.g.sc33.32' => 'cpa', 'Cpa.g.sc46.29' => 'cpa', 'Cpa.g.sc796.1' => 'cpa', 'CsaV3_1G030420' => 'csa', 'CsaV3_5G027050' => 'csa', 'CsaV3_5G031040' => 'csa', 'CsaV3_UNG023130' => 'csa', 'CSS0007726' => 'camsi', 'CSS0016433' => 'camsi', 'CSS0017656' => 'camsi', 'CSS0025364' => 'camsi', 'CSS0027582' => 'camsi', 'CSS0047288' => 'camsi', 'CSS0049950' => 'camsi', 'DCAR_003843' => 'dca', 'DCAR_007052' => 'dca', 'DCAR_020884' => 'dca', 'DCAR_021730' => 'dca', 'DCAR_024423' => 'dca', 'DCAR_026509' => 'dca', 'DCAR_031158' => 'dca', 'Dinv14728' => 'din', 'Dinv15219' => 'din', 'Dinv25728' => 'din', 'Dinv33428' => 'din', 'Dinv36489' => 'din', 'Dinv41486' => 'din', 'Duzib147G0469' => 'dzi', 'Duzib168G0060' => 'dzi', 'Duzib187G1215' => 'dzi', 'Duzib248G0692' => 'dzi', 'Duzib251G0767' => 'dzi', 'Duzib264G0446' => 'dzi', 'Duzib268G0691' => 'dzi', 'ECA232G4767' => 'eca', 'ECA233G2838' => 'eca', 'ECA234G0391' => 'eca', 'ECA234G0857' => 'eca', 'ECA236G1593' => 'eca', 'ECA238G0565' => 'eca', 'ECA246G1027' => 'eca', 'ECA246G3223' => 'eca', 'ECA246G3470' => 'eca', 'EL10Ac6g13829' => 'bvu', 'EL10Ac6g14093' => 'bvu', 'EL10Ac8g18707' => 'bvu', 'Eucgr.C01369' => 'egr', 'Eucgr.H02492' => 'egr', 'Eucgr.I01733' => 'egr', 'Eucgr.J02255' => 'egr', 'Eucgr.J02257' => 'egr', 'Eucgr.J02258' => 'egr', 'FAN02G1601' => 'fan', 'FAN03G1586' => 'fan', 'FAN03G2986' => 'fan', 'FAN05G4837' => 'fan', 'FAN06G0146' => 'fan', 'FAN07G0858' => 'fan', 'FAN09G3179' => 'fan', 'FAN10G0669' => 'fan', 'FAN12G2358' => 'fan', 'FAN14G4198' => 'fan', 'FAN14G5112' => 'fan', 'FAN17G0342' => 'fan', 'FAN19G0342' => 'fan', 'FAN19G0962' => 'fan', 'FAN19G1101' => 'fan', 'FAN19G1872' => 'fan', 'FAN22G0356' => 'fan', 'FAN23G0744' => 'fan', 'FAN23G1914' => 'fan', 'FAN26G0032' => 'fan', 'FAN28G0625' => 'fan', 'FvH4_1g02710' => 'fve', 'FvH4_1g02720' => 'fve', 'FvH4_4g25670' => 'fve', 'FvH4_6g51700' => 'fve', 'FvH4_7g20170' => 'fve', 'Glyma.05G175000' => 'gma', 'Glyma.08G132300' => 'gma', 'Glyma.11G243000' => 'gma', 'Glyma.13G158900' => 'gma', 'Glyma.17G112400' => 'gma', 'Glyma.18G014100' => 'gma', 'Glyma.19G003100' => 'gma', 'Glyma.19G056500' => 'gma', 'Gohir.A01G158900' => 'ghi', 'Gohir.A05G312600' => 'ghi', 'Gohir.A05G354900' => 'ghi', 'Gohir.A07G037200' => 'ghi', 'Gohir.A09G030000' => 'ghi', 'Gohir.A12G145200' => 'ghi', 'Gohir.D01G151500' => 'ghi', 'Gohir.D04G058300' => 'ghi', 'Gohir.D05G314100' => 'ghi', 'Gohir.D07G041400' => 'ghi', 'Gohir.D09G029700' => 'ghi', 'Gohir.D12G149700' => 'ghi', 'Gorai.001G043800' => 'gra', 'Gorai.002G187800' => 'gra', 'Gorai.006G034700' => 'gra', 'Gorai.008G161200' => 'gra', 'Gorai.009G335700' => 'gra', 'Gorai.012G065000' => 'gra', 'GSVIVG01000535001' => 'vvi', 'GSVIVG01015572001' => 'vvi', 'GSVIVG01032386001' => 'vvi', 'HanXRQChr05g0138531' => 'han', 'HanXRQChr06g0174391' => 'han', 'HanXRQChr07g0199021' => 'han', 'HanXRQChr08g0208211' => 'han', 'HanXRQChr09g0255471' => 'han', 'HanXRQChr10g0315791' => 'han', 'HanXRQChr12g0371991' => 'han', 'HanXRQChr15g0475251' => 'han', 'HanXRQChr17g0540001' => 'han', 'HanXRQChr17g0548631' => 'han', 'HanXRQChr17g0569561' => 'han', 'Haze_12256' => 'cav', 'Haze_14756' => 'cav', 'Haze_25528' => 'cav', 'Hma1.2p1_0079F.1_g041020' => 'hma', 'Hma1.2p1_0818F.1_g223260' => 'hma', 'Hma1.2p1_1747F.1_g300530' => 'hma', 'HPP92_004607' => 'vpl', 'HPP92_004608' => 'vpl', 'HPP92_006181' => 'vpl', 'HPP92_012192' => 'vpl', 'HPP92_015680' => 'vpl', 'HPP92_020249' => 'vpl', 'HPP92_021376' => 'vpl', 'HPP92_024275' => 'vpl', 'Hund06031' => 'sun', 'Hund25391' => 'sun', 'Lalb_Chr07g0185371' => 'lal', 'Lalb_Chr07g0185381' => 'lal', 'Lalb_Chr12g0204011' => 'lal', 'Lalb_Chr13g0301671' => 'lal', 'Lalb_Chr14g0362851' => 'lal', 'Lalb_Chr24g0403581' => 'lal', 'Lj1g0000233' => 'lja', 'Lj2g0018120' => 'lja', 'Lj3C621T0' => 'lonja', 'Lj3P1059T14' => 'lonja', 'Lj3P611T9' => 'lonja', 'Lj3P614T13' => 'lonja', 'Lj3P615T5' => 'lonja', 'Lj4g0012315' => 'lja', 'Lj4g0026182' => 'lja', 'Lj6P813T16' => 'lonja', 'Lj7C427T7' => 'lonja', 'Lj7C427T8' => 'lonja', 'Lj7P600T41' => 'lonja', 'Lju41C42G17' => 'lonja', 'Lsat_1_v5_gn_0_47300' => 'lsa', 'Lsat_1_v5_gn_2_91280' => 'lsa', 'Lsat_1_v5_gn_3_30561' => 'lsa', 'Lsat_1_v5_gn_4_184321' => 'lsa', 'Lsat_1_v5_gn_4_4041' => 'lsa', 'Lsat_1_v5_gn_5_92000' => 'lsa', 'Lsat_1_v5_gn_8_152940' => 'lsa', 'Lsat_1_v5_gn_8_62401' => 'lsa', 'Manes.06G055900' => 'mes', 'Manes.12G022200' => 'mes', 'Manes.13G023300' => 'mes', 'Manes.14G115000' => 'mes', 'Manes.15G151700' => 'mes', 'Manes.17G111300' => 'mes', 'Mapoly0226s0009' => 'mpo', 'MBI02_g25363_MAGBIO' => 'mbi', 'MBI06_g00027_MAGBIO' => 'mbi', 'MBI10_g13034_MAGBIO' => 'mbi', 'MD09G1023400' => 'mdo', 'MD13G1100100' => 'mdo', 'MD15G1169200' => 'mdo', 'MD16G1101100' => 'mdo', 'MD17G1022900' => 'mdo', 'Medtr3g096150' => 'mtr', 'Medtr4g115070' => 'mtr', 'Medtr7g033325' => 'mtr', 'Medtr8g089840' => 'mtr', 'MELO3C010319.2' => 'cme', 'MELO3C011944.2' => 'cme', 'MELO3C021589.2' => 'cme', 'Migut.E00207' => 'egut', 'Migut.H00067' => 'egut', 'Migut.K00433' => 'egut', 'Migut.K00606' => 'egut', 'Migut.K01410' => 'egut', 'MSTRG.13347' => 'ama', 'MSTRG.24045' => 'ama', 'MSTRG.2428' => 'ama', 'MSTRG.26410' => 'ama', 'MSTRG.3139' => 'ama', 'MSTRG.3286' => 'ama', 'MSTRG.563' => 'ama', 'MSTRG.7941' => 'ama', 'Nitab4.5_0000028g0060' => 'nta', 'Nitab4.5_0000065g0260' => 'nta', 'Nitab4.5_0000112g0060' => 'nta', 'Nitab4.5_0000489g0120' => 'nta', 'Nitab4.5_0001776g0050' => 'nta', 'Nitab4.5_0001854g0010' => 'nta', 'Nitab4.5_0001860g0020' => 'nta', 'Nitab4.5_0004352g0010' => 'nta', 'Nitab4.5_0008716g0020' => 'nta', 'Nitab4.5_0008922g0010' => 'nta', 'Nn3g16693' => 'nnu', 'Nn4g22596' => 'nnu', 'Nn7g37639' => 'nnu', 'Oeu001701.1' => 'oeu', 'Oeu018149.1' => 'oeu', 'Oeu026220.1' => 'oeu', 'Oeu038635.1' => 'oeu', 'Oeu049176.1' => 'oeu', 'Oeu056706.1' => 'oeu', 'Oeu056937.1' => 'oeu', 'Oeu057540.1' => 'oeu', 'Os02g0594900' => 'osa', 'Os02g0595100' => 'osa', 'Os04g0477500' => 'osa', 'Os12g0611900' => 'osa', 'Peaxi162Scf00076g00020' => 'pax', 'Peaxi162Scf00128g00217' => 'pax', 'Peaxi162Scf00129g01640' => 'pax', 'Peaxi162Scf00669g00007' => 'pax', 'Peaxi162Scf00700g00421' => 'pax', 'Peaxi162Scf00801g00038' => 'pax', 'Peaxi162Scf00891g00025' => 'pax', 'PGR083G0909' => 'pgr', 'PGR119G1005' => 'pgr', 'PGR142G2236' => 'pgr', 'PGR142G3388' => 'pgr', 'PGSC0003DMG400004514' => 'stu', 'PGSC0003DMG400012635' => 'stu', 'PGSC0003DMG400015730' => 'stu', 'PGSC0003DMG400018611' => 'stu', 'PGSC0003DMG400030897' => 'stu', 'Phvul.001G254800' => 'pvu', 'Phvul.002G260100' => 'pvu', 'Phvul.003G167600' => 'pvu', 'Phvul.004G005100' => 'pvu', 'Potri.001G343600' => 'ptr', 'Potri.006G066700' => 'ptr', 'Potri.008G186000' => 'ptr', 'Potri.010G046900' => 'ptr', 'Potri.018G127900' => 'ptr', 'Pp3c20_17750' => 'ppa', 'Pp3c24_4380' => 'ppa', 'Prupe.1G245800' => 'ppe', 'Prupe.3G293400' => 'ppe', 'Prupe.7G247400' => 'ppe', 'Psat0s145g0120' => 'psa', 'Psat0s595g0040' => 'psa', 'Psat0s595g0120' => 'psa', 'Psat3g175040' => 'psa', 'Psat7g058120' => 'psa', 'PSO017G0428' => 'pso', 'PSO063G7510' => 'pso', 'PSO067G0046' => 'pso', 'PSO478G1073' => 'pso', 'PSO675G3677' => 'pso', 'PSO675G6558' => 'pso', 'PSO675G7520' => 'pso', 'PSO675G8959' => 'pso', 'QL02p074089' => 'qlo', 'QL02p089614' => 'qlo', 'QL03p057736' => 'qlo', 'RcHm_v2.0_Chr1g0364131' => 'rch', 'RcHm_v2.0_Chr2g0087801' => 'rch', 'RcHm_v2.0_Chr2g0087821' => 'rch', 'RcHm_v2.0_Chr2g0173231' => 'rch', 'RcHm_v2.0_Chr4g0433111' => 'rch', 'Rhsim03G0250300' => 'rsi', 'Rhsim08G0048400' => 'rsi', 'Rhsim10G0014800' => 'rsi', 'Rhsim12G0040100' => 'rsi', 'Rhsim12G0109700' => 'rsi', 'Sabra06G0049600' => 'sbr', 'Sabra08G0141000' => 'sbr', 'Sabra10G0021400' => 'sbr', 'Sabra16G0222900' => 'sbr', 'Sabra18G0108600' => 'sbr', 'SalBow1G0433' => 'sbo', 'SalBow1G2038' => 'sbo', 'SalBow1G5003' => 'sbo', 'SalBow7G1197' => 'sbo', 'SalBow8G3506' => 'sbo', 'Sc03g0007300' => 'sci', 'Sc11g0000950' => 'sci', 'Sc14g0008750' => 'sci', 'Sc18g0000420' => 'sci', 'Sed0006754' => 'sed', 'Sed0008741' => 'sed', 'Sed0017172' => 'sed', 'Sed0018925' => 'sed', 'Sed0023326' => 'sed', 'Sed0025909' => 'sed', 'SEGI_05333' => 'sgi', 'SEGI_10362' => 'sgi', 'SEGI_13380' => 'sgi', 'SEGI_24306' => 'sgi', 'SEGI_29077' => 'sgi', 'SEGI_29095' => 'sgi', 'SEGI_36534' => 'sgi', 'SEGI_37506' => 'sgi', 'SEGI_38321' => 'sgi', 'SGA_v2.0_scaffold307G48031' => 'sas', 'SGA_v2.0_scaffold47G17507' => 'sas', 'SGA_v2.0_scaffold63G21736' => 'sas', 'SGA_v2.0_scaffold87G27070' => 'sas', 'SHI17794' => 'shi', 'SHI28851' => 'shi', 'SMO165G0155' => 'smo', 'SMO340G0217' => 'smo', 'SMO367G1210' => 'smo', 'Solyc02g093430.3' => 'sly', 'Solyc05g013580.4' => 'sly', 'Solyc07g008030.3' => 'sly', 'Solyc12g035470.2' => 'sly', 'Sopen02g038020' => 'spe', 'Sopen05g008490' => 'spe', 'Sopen07g003910' => 'spe', 'Sopen12g015240' => 'spe', 'Sp1g11550' => 'spa', 'Sp2g16710' => 'spa', 'Sp3g00430' => 'spa', 'Sp3g26780' => 'spa', 'Sp5g22900' => 'spa', 'Sp6g29530' => 'spa', 'TAR371G0794' => 'tar', 'TAR374G0164' => 'tar', 'TAR622G0165' => 'tar', 'TAR626G0929' => 'tar', 'TAR629G2155' => 'tar', 'THA.LOC104805282' => 'tha', 'THA.LOC104805363' => 'tha', 'THA.LOC104808968' => 'tha', 'THA.LOC104821093' => 'tha', 'THA.LOC104823953' => 'tha', 'THA.LOC104825562' => 'tha', 'THA.LOC104825665' => 'tha', 'Thecc.02G261400' => 'tca', 'Thecc.04G019200' => 'tca', 'Thecc.09G130400' => 'tca', 'Thhalv10004374m.g' => 'esa', 'Thhalv10007850m.g' => 'esa', 'Thhalv10013782m.g' => 'esa', 'Thhalv10018686m.g' => 'esa', 'Thhalv10020899m.g' => 'esa', 'Thhalv10022755m.g' => 'esa', 'TPR.G23851' => 'tpr', 'TPR.G26500' => 'tpr', 'TPR.G27267' => 'tpr', 'TPR.G32001' => 'tpr', 'TPR.G6251' => 'tpr', 'TPR.G8167' => 'tpr', 'TWI12G1330' => 'twi', 'TWI18G1239' => 'twi', 'TWI34G0979' => 'twi', 'TWI36G0670' => 'twi', 'TWI36G0707' => 'twi', 'TWI56G0233' => 'twi', 'TWI75G1809' => 'twi', 'unitig_21.g20874' => 'ugi', 'unitig_26.g10343' => 'ugi', 'unitig_46.g18392' => 'ugi', 'unitig_52.g17178' => 'ugi', 'unitig_8.g2934' => 'ugi', 'vmacro01122' => 'vma', 'vmacro05875' => 'vma', 'vmacro06147' => 'vma', 'vmacro16191' => 'vma', 'vmacro18293' => 'vma', 'VMungo0251G3707' => 'vmu', 'VMungo0464G1521' => 'vmu', 'VMungo1215G0205' => 'vmu', 'VMungo1383G2484' => 'vmu', 'Zm00001eb079610' => 'zma', 'Zm00001eb135990' => 'zma', 'Zm00001eb183710' => 'zma', 'Zm00001eb246020' => 'zma' ) $gf_id = 'HOM05D001124' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001124' ) $data_identifier = 'HOM05D001124' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 6, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 7, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 21, 'bol' => (int) 10, 'bra' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 6, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 9, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 21, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 8, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 10, 'lsa' => (int) 8, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 8, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 9, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb246020' $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' => 'HOM05D001124', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '548', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02520' => 'bna', 'A03p06630' => 'bna', 'A05p44460' => 'bna', 'A06p08710' => 'bna', 'A06p41090' => 'bna', 'A07p32320' => 'bna', 'A08p32520' => 'bna', 'A09p10360' => 'bna', 'A10p24080' => 'bna', 'Aa31LG11G15250' => 'aar', 'Aa31LG1G1800' => 'aar', 'Aa31LG2G5120' => 'aar', 'Aa31LG2G6070' => 'aar', 'Aa31LG5G10770' => 'aar', 'Aa31sc61G90' => 'aar', 'Actinidia01352' => 'ach', 'Actinidia05983' => 'ach', 'Actinidia08133' => 'ach', 'Actinidia15101' => 'ach', 'Actinidia26379' => 'ach', 'Actinidia35778' => 'ach', 'Actinidia36123' => 'ach', 'Actinidia37436' => 'ach', 'Actinidia38730' => 'ach', 'Ah.02g128210' => 'amhyb', 'Ah.03g132990' => 'amhyb', 'Ah.14g079410' => 'amhyb', 'AL1G24640' => 'aly', 'AL2G26680' => 'aly', 'AL3G10530' => 'aly', 'AL3G45230' => 'aly', 'AL5G15230' => 'aly', 'AL5G16960' => 'aly', 'AL6G25210' => 'aly', 'Aqoxy2G00441' => 'aox', 'Aqoxy3G01236' => 'aox', 'Aqoxy5G03746' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3RQ047' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C7GMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9C8JER' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MBL6KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YXCZ83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZANX40' => 'arhy', 'AT1G12990' => 'ath', 'AT1G67880' => 'ath', 'AT2G13290' => 'ath', 'AT3G01620' => 'ath', 'AT3G26445' => 'ath', 'AT3G27540' => 'ath', 'AT5G14480' => 'ath', 'ATR0824G026' => 'atr', 'ATR1098G019' => 'atr', 'Atru.chr11.2145' => 'acertr', 'Atru.chr2.3636' => 'acertr', 'Atru.chr2.3644' => 'acertr', 'Atru.chr6.2422' => 'acertr', 'Atru.chr7.1112' => 'acertr', 'AUR62005469' => 'cqu', 'AUR62011166' => 'cqu', 'AUR62013319' => 'cqu', 'AUR62024273' => 'cqu', 'AUR62028420' => 'cqu', 'AUR62041942' => 'cqu', 'BcaB01g04969' => 'bca', 'BcaB01g06371' => 'bca', 'BcaB02g11494' => 'bca', 'BcaB03g15382' => 'bca', 'BcaB08g36994' => 'bca', 'BcaC03g13477' => 'bca', 'BcaC03g13478' => 'bca', 'BcaC03g13480' => 'bca', 'BcaC03g13481' => 'bca', 'BcaC03g13486' => 'bca', 'BcaC04g19031' => 'bca', 'BcaC04g23085' => 'bca', 'BcaC05g25094' => 'bca', 'BcaC05g25096' => 'bca', 'BcaC05g25138' => 'bca', 'BcaC05g30416' => 'bca', 'BcaC05g30455' => 'bca', 'BcaC06g30979' => 'bca', 'BcaC06g33805' => 'bca', 'BcaC08g46021' => 'bca', 'BcaNung03154' => 'bca', 'BolC2t06623H' => 'bol', 'BolC2t06632H' => 'bol', 'BolC2t06635H' => 'bol', 'BolC2t06638H' => 'bol', 'BolC3t13266H' => 'bol', 'BolC5t29776H' => 'bol', 'BolC6t38912H' => 'bol', 'BolC7t44183H' => 'bol', 'BolC9t54123H' => 'bol', 'BolC9t59107H' => 'bol', 'BraA02t05221Z' => 'bra', 'BraA03t09996Z' => 'bra', 'BraA05t23210Z' => 'bra', 'BraA06t24068Z' => 'bra', 'BraA06t27032Z' => 'bra', 'BraA08t35176Z' => 'bra', 'BraA09t36680Z' => 'bra', 'BraA10t44471Z' => 'bra', 'C02p06760' => 'bna', 'C02p06890' => 'bna', 'C02p07010' => 'bna', 'C03p07660' => 'bna', 'C05p10300' => 'bna', 'C06p38150' => 'bna', 'C07p36650' => 'bna', 'C08p15770' => 'bna', 'C09p12300' => 'bna', 'C09p62700' => 'bna', 'C09p75040' => 'bna', 'CAN.G13.1' => 'can', 'CAN.G138.4' => 'can', 'CAN.G44.6' => 'can', 'CAN.G473.19' => 'can', 'CANSAT01G0835' => 'cansat', 'CANSAT11G0246' => 'cansat', 'CANSAT11G1766' => 'cansat', 'CANSAT64G1954' => 'cansat', 'CARHR013330' => 'chi', 'CARHR060530' => 'chi', 'CARHR075300' => 'chi', 'CARHR105120' => 'chi', 'CARHR148910' => 'chi', 'CARHR198830' => 'chi', 'Carub.0001s1275' => 'cru', 'Carub.0002s1437' => 'cru', 'Carub.0003s0044' => 'cru', 'Carub.0003s2787' => 'cru', 'Carub.0005s0597' => 'cru', 'Carub.0006s1266' => 'cru', 'Ca_06935_v3' => 'car', 'Ca_13559_v3' => 'car', 'Ca_16941_v3' => 'car', 'Ca_16960_v3' => 'car', 'Ca_17775_v3' => 'car', 'Ca_30464_v3' => 'car', 'Cc06_g08160' => 'ccan', 'Cc07_g01520' => 'ccan', 'Cc11_g15810' => 'ccan', 'CDE02G2840' => 'cde', 'CDE03G0093' => 'cde', 'CDE04G2127' => 'cde', 'CDE07G1857' => 'cde', 'CDE09G1246' => 'cde', 'Cfa003412' => 'cfa', 'Cfa007341' => 'cfa', 'Cfa009220' => 'cfa', 'Ciclev10008737m.g' => 'ccl', 'Ciclev10015565m.g' => 'ccl', 'Ciclev10031761m.g' => 'ccl', 'CiPaw.03G045300' => 'cil', 'CiPaw.03G247200' => 'cil', 'CiPaw.04G029500' => 'cil', 'CiPaw.04G174000' => 'cil', 'CiPaw.05G181200' => 'cil', 'CiPaw.06G067100' => 'cil', 'ClCG05G025800' => 'cla', 'ClCG06G011400' => 'cla', 'ClCG09G019360' => 'cla', 'COL.COLO4_04827' => 'col', 'COL.COLO4_29170' => 'col', 'COL.COLO4_35131' => 'col', 'COL.COLO4_35132' => 'col', 'Cpa.g.sc33.32' => 'cpa', 'Cpa.g.sc46.29' => 'cpa', 'Cpa.g.sc796.1' => 'cpa', 'CsaV3_1G030420' => 'csa', 'CsaV3_5G027050' => 'csa', 'CsaV3_5G031040' => 'csa', 'CsaV3_UNG023130' => 'csa', 'CSS0007726' => 'camsi', 'CSS0016433' => 'camsi', 'CSS0017656' => 'camsi', 'CSS0025364' => 'camsi', 'CSS0027582' => 'camsi', 'CSS0047288' => 'camsi', 'CSS0049950' => 'camsi', 'DCAR_003843' => 'dca', 'DCAR_007052' => 'dca', 'DCAR_020884' => 'dca', 'DCAR_021730' => 'dca', 'DCAR_024423' => 'dca', 'DCAR_026509' => 'dca', 'DCAR_031158' => 'dca', 'Dinv14728' => 'din', 'Dinv15219' => 'din', 'Dinv25728' => 'din', 'Dinv33428' => 'din', 'Dinv36489' => 'din', 'Dinv41486' => 'din', 'Duzib147G0469' => 'dzi', 'Duzib168G0060' => 'dzi', 'Duzib187G1215' => 'dzi', 'Duzib248G0692' => 'dzi', 'Duzib251G0767' => 'dzi', 'Duzib264G0446' => 'dzi', 'Duzib268G0691' => 'dzi', 'ECA232G4767' => 'eca', 'ECA233G2838' => 'eca', 'ECA234G0391' => 'eca', 'ECA234G0857' => 'eca', 'ECA236G1593' => 'eca', 'ECA238G0565' => 'eca', 'ECA246G1027' => 'eca', 'ECA246G3223' => 'eca', 'ECA246G3470' => 'eca', 'EL10Ac6g13829' => 'bvu', 'EL10Ac6g14093' => 'bvu', 'EL10Ac8g18707' => 'bvu', 'Eucgr.C01369' => 'egr', 'Eucgr.H02492' => 'egr', 'Eucgr.I01733' => 'egr', 'Eucgr.J02255' => 'egr', 'Eucgr.J02257' => 'egr', 'Eucgr.J02258' => 'egr', 'FAN02G1601' => 'fan', 'FAN03G1586' => 'fan', 'FAN03G2986' => 'fan', 'FAN05G4837' => 'fan', 'FAN06G0146' => 'fan', 'FAN07G0858' => 'fan', 'FAN09G3179' => 'fan', 'FAN10G0669' => 'fan', 'FAN12G2358' => 'fan', 'FAN14G4198' => 'fan', 'FAN14G5112' => 'fan', 'FAN17G0342' => 'fan', 'FAN19G0342' => 'fan', 'FAN19G0962' => 'fan', 'FAN19G1101' => 'fan', 'FAN19G1872' => 'fan', 'FAN22G0356' => 'fan', 'FAN23G0744' => 'fan', 'FAN23G1914' => 'fan', 'FAN26G0032' => 'fan', 'FAN28G0625' => 'fan', 'FvH4_1g02710' => 'fve', 'FvH4_1g02720' => 'fve', 'FvH4_4g25670' => 'fve', 'FvH4_6g51700' => 'fve', 'FvH4_7g20170' => 'fve', 'Glyma.05G175000' => 'gma', 'Glyma.08G132300' => 'gma', 'Glyma.11G243000' => 'gma', 'Glyma.13G158900' => 'gma', 'Glyma.17G112400' => 'gma', 'Glyma.18G014100' => 'gma', 'Glyma.19G003100' => 'gma', 'Glyma.19G056500' => 'gma', 'Gohir.A01G158900' => 'ghi', 'Gohir.A05G312600' => 'ghi', 'Gohir.A05G354900' => 'ghi', 'Gohir.A07G037200' => 'ghi', 'Gohir.A09G030000' => 'ghi', 'Gohir.A12G145200' => 'ghi', 'Gohir.D01G151500' => 'ghi', 'Gohir.D04G058300' => 'ghi', 'Gohir.D05G314100' => 'ghi', 'Gohir.D07G041400' => 'ghi', 'Gohir.D09G029700' => 'ghi', 'Gohir.D12G149700' => 'ghi', 'Gorai.001G043800' => 'gra', 'Gorai.002G187800' => 'gra', 'Gorai.006G034700' => 'gra', 'Gorai.008G161200' => 'gra', 'Gorai.009G335700' => 'gra', 'Gorai.012G065000' => 'gra', 'GSVIVG01000535001' => 'vvi', 'GSVIVG01015572001' => 'vvi', 'GSVIVG01032386001' => 'vvi', 'HanXRQChr05g0138531' => 'han', 'HanXRQChr06g0174391' => 'han', 'HanXRQChr07g0199021' => 'han', 'HanXRQChr08g0208211' => 'han', 'HanXRQChr09g0255471' => 'han', 'HanXRQChr10g0315791' => 'han', 'HanXRQChr12g0371991' => 'han', 'HanXRQChr15g0475251' => 'han', 'HanXRQChr17g0540001' => 'han', 'HanXRQChr17g0548631' => 'han', 'HanXRQChr17g0569561' => 'han', 'Haze_12256' => 'cav', 'Haze_14756' => 'cav', 'Haze_25528' => 'cav', 'Hma1.2p1_0079F.1_g041020' => 'hma', 'Hma1.2p1_0818F.1_g223260' => 'hma', 'Hma1.2p1_1747F.1_g300530' => 'hma', 'HPP92_004607' => 'vpl', 'HPP92_004608' => 'vpl', 'HPP92_006181' => 'vpl', 'HPP92_012192' => 'vpl', 'HPP92_015680' => 'vpl', 'HPP92_020249' => 'vpl', 'HPP92_021376' => 'vpl', 'HPP92_024275' => 'vpl', 'Hund06031' => 'sun', 'Hund25391' => 'sun', 'Lalb_Chr07g0185371' => 'lal', 'Lalb_Chr07g0185381' => 'lal', 'Lalb_Chr12g0204011' => 'lal', 'Lalb_Chr13g0301671' => 'lal', 'Lalb_Chr14g0362851' => 'lal', 'Lalb_Chr24g0403581' => 'lal', 'Lj1g0000233' => 'lja', 'Lj2g0018120' => 'lja', 'Lj3C621T0' => 'lonja', 'Lj3P1059T14' => 'lonja', 'Lj3P611T9' => 'lonja', 'Lj3P614T13' => 'lonja', 'Lj3P615T5' => 'lonja', 'Lj4g0012315' => 'lja', 'Lj4g0026182' => 'lja', 'Lj6P813T16' => 'lonja', 'Lj7C427T7' => 'lonja', 'Lj7C427T8' => 'lonja', 'Lj7P600T41' => 'lonja', 'Lju41C42G17' => 'lonja', 'Lsat_1_v5_gn_0_47300' => 'lsa', 'Lsat_1_v5_gn_2_91280' => 'lsa', 'Lsat_1_v5_gn_3_30561' => 'lsa', 'Lsat_1_v5_gn_4_184321' => 'lsa', 'Lsat_1_v5_gn_4_4041' => 'lsa', 'Lsat_1_v5_gn_5_92000' => 'lsa', 'Lsat_1_v5_gn_8_152940' => 'lsa', 'Lsat_1_v5_gn_8_62401' => 'lsa', 'Manes.06G055900' => 'mes', 'Manes.12G022200' => 'mes', 'Manes.13G023300' => 'mes', 'Manes.14G115000' => 'mes', 'Manes.15G151700' => 'mes', 'Manes.17G111300' => 'mes', 'Mapoly0226s0009' => 'mpo', 'MBI02_g25363_MAGBIO' => 'mbi', 'MBI06_g00027_MAGBIO' => 'mbi', 'MBI10_g13034_MAGBIO' => 'mbi', 'MD09G1023400' => 'mdo', 'MD13G1100100' => 'mdo', 'MD15G1169200' => 'mdo', 'MD16G1101100' => 'mdo', 'MD17G1022900' => 'mdo', 'Medtr3g096150' => 'mtr', 'Medtr4g115070' => 'mtr', 'Medtr7g033325' => 'mtr', 'Medtr8g089840' => 'mtr', 'MELO3C010319.2' => 'cme', 'MELO3C011944.2' => 'cme', 'MELO3C021589.2' => 'cme', 'Migut.E00207' => 'egut', 'Migut.H00067' => 'egut', 'Migut.K00433' => 'egut', 'Migut.K00606' => 'egut', 'Migut.K01410' => 'egut', 'MSTRG.13347' => 'ama', 'MSTRG.24045' => 'ama', 'MSTRG.2428' => 'ama', 'MSTRG.26410' => 'ama', 'MSTRG.3139' => 'ama', 'MSTRG.3286' => 'ama', 'MSTRG.563' => 'ama', 'MSTRG.7941' => 'ama', 'Nitab4.5_0000028g0060' => 'nta', 'Nitab4.5_0000065g0260' => 'nta', 'Nitab4.5_0000112g0060' => 'nta', 'Nitab4.5_0000489g0120' => 'nta', 'Nitab4.5_0001776g0050' => 'nta', 'Nitab4.5_0001854g0010' => 'nta', 'Nitab4.5_0001860g0020' => 'nta', 'Nitab4.5_0004352g0010' => 'nta', 'Nitab4.5_0008716g0020' => 'nta', 'Nitab4.5_0008922g0010' => 'nta', 'Nn3g16693' => 'nnu', 'Nn4g22596' => 'nnu', 'Nn7g37639' => 'nnu', 'Oeu001701.1' => 'oeu', 'Oeu018149.1' => 'oeu', 'Oeu026220.1' => 'oeu', 'Oeu038635.1' => 'oeu', 'Oeu049176.1' => 'oeu', 'Oeu056706.1' => 'oeu', 'Oeu056937.1' => 'oeu', 'Oeu057540.1' => 'oeu', 'Os02g0594900' => 'osa', 'Os02g0595100' => 'osa', 'Os04g0477500' => 'osa', 'Os12g0611900' => 'osa', 'Peaxi162Scf00076g00020' => 'pax', 'Peaxi162Scf00128g00217' => 'pax', 'Peaxi162Scf00129g01640' => 'pax', 'Peaxi162Scf00669g00007' => 'pax', 'Peaxi162Scf00700g00421' => 'pax', 'Peaxi162Scf00801g00038' => 'pax', 'Peaxi162Scf00891g00025' => 'pax', 'PGR083G0909' => 'pgr', 'PGR119G1005' => 'pgr', 'PGR142G2236' => 'pgr', 'PGR142G3388' => 'pgr', 'PGSC0003DMG400004514' => 'stu', 'PGSC0003DMG400012635' => 'stu', 'PGSC0003DMG400015730' => 'stu', 'PGSC0003DMG400018611' => 'stu', 'PGSC0003DMG400030897' => 'stu', 'Phvul.001G254800' => 'pvu', 'Phvul.002G260100' => 'pvu', 'Phvul.003G167600' => 'pvu', 'Phvul.004G005100' => 'pvu', 'Potri.001G343600' => 'ptr', 'Potri.006G066700' => 'ptr', 'Potri.008G186000' => 'ptr', 'Potri.010G046900' => 'ptr', 'Potri.018G127900' => 'ptr', 'Pp3c20_17750' => 'ppa', 'Pp3c24_4380' => 'ppa', 'Prupe.1G245800' => 'ppe', 'Prupe.3G293400' => 'ppe', 'Prupe.7G247400' => 'ppe', 'Psat0s145g0120' => 'psa', 'Psat0s595g0040' => 'psa', 'Psat0s595g0120' => 'psa', 'Psat3g175040' => 'psa', 'Psat7g058120' => 'psa', 'PSO017G0428' => 'pso', 'PSO063G7510' => 'pso', 'PSO067G0046' => 'pso', 'PSO478G1073' => 'pso', 'PSO675G3677' => 'pso', 'PSO675G6558' => 'pso', 'PSO675G7520' => 'pso', 'PSO675G8959' => 'pso', 'QL02p074089' => 'qlo', 'QL02p089614' => 'qlo', 'QL03p057736' => 'qlo', 'RcHm_v2.0_Chr1g0364131' => 'rch', 'RcHm_v2.0_Chr2g0087801' => 'rch', 'RcHm_v2.0_Chr2g0087821' => 'rch', 'RcHm_v2.0_Chr2g0173231' => 'rch', 'RcHm_v2.0_Chr4g0433111' => 'rch', 'Rhsim03G0250300' => 'rsi', 'Rhsim08G0048400' => 'rsi', 'Rhsim10G0014800' => 'rsi', 'Rhsim12G0040100' => 'rsi', 'Rhsim12G0109700' => 'rsi', 'Sabra06G0049600' => 'sbr', 'Sabra08G0141000' => 'sbr', 'Sabra10G0021400' => 'sbr', 'Sabra16G0222900' => 'sbr', 'Sabra18G0108600' => 'sbr', 'SalBow1G0433' => 'sbo', 'SalBow1G2038' => 'sbo', 'SalBow1G5003' => 'sbo', 'SalBow7G1197' => 'sbo', 'SalBow8G3506' => 'sbo', 'Sc03g0007300' => 'sci', 'Sc11g0000950' => 'sci', 'Sc14g0008750' => 'sci', 'Sc18g0000420' => 'sci', 'Sed0006754' => 'sed', 'Sed0008741' => 'sed', 'Sed0017172' => 'sed', 'Sed0018925' => 'sed', 'Sed0023326' => 'sed', 'Sed0025909' => 'sed', 'SEGI_05333' => 'sgi', 'SEGI_10362' => 'sgi', 'SEGI_13380' => 'sgi', 'SEGI_24306' => 'sgi', 'SEGI_29077' => 'sgi', 'SEGI_29095' => 'sgi', 'SEGI_36534' => 'sgi', 'SEGI_37506' => 'sgi', 'SEGI_38321' => 'sgi', 'SGA_v2.0_scaffold307G48031' => 'sas', 'SGA_v2.0_scaffold47G17507' => 'sas', 'SGA_v2.0_scaffold63G21736' => 'sas', 'SGA_v2.0_scaffold87G27070' => 'sas', 'SHI17794' => 'shi', 'SHI28851' => 'shi', 'SMO165G0155' => 'smo', 'SMO340G0217' => 'smo', 'SMO367G1210' => 'smo', 'Solyc02g093430.3' => 'sly', 'Solyc05g013580.4' => 'sly', 'Solyc07g008030.3' => 'sly', 'Solyc12g035470.2' => 'sly', 'Sopen02g038020' => 'spe', 'Sopen05g008490' => 'spe', 'Sopen07g003910' => 'spe', 'Sopen12g015240' => 'spe', 'Sp1g11550' => 'spa', 'Sp2g16710' => 'spa', 'Sp3g00430' => 'spa', 'Sp3g26780' => 'spa', 'Sp5g22900' => 'spa', 'Sp6g29530' => 'spa', 'TAR371G0794' => 'tar', 'TAR374G0164' => 'tar', 'TAR622G0165' => 'tar', 'TAR626G0929' => 'tar', 'TAR629G2155' => 'tar', 'THA.LOC104805282' => 'tha', 'THA.LOC104805363' => 'tha', 'THA.LOC104808968' => 'tha', 'THA.LOC104821093' => 'tha', 'THA.LOC104823953' => 'tha', 'THA.LOC104825562' => 'tha', 'THA.LOC104825665' => 'tha', 'Thecc.02G261400' => 'tca', 'Thecc.04G019200' => 'tca', 'Thecc.09G130400' => 'tca', 'Thhalv10004374m.g' => 'esa', 'Thhalv10007850m.g' => 'esa', 'Thhalv10013782m.g' => 'esa', 'Thhalv10018686m.g' => 'esa', 'Thhalv10020899m.g' => 'esa', 'Thhalv10022755m.g' => 'esa', 'TPR.G23851' => 'tpr', 'TPR.G26500' => 'tpr', 'TPR.G27267' => 'tpr', 'TPR.G32001' => 'tpr', 'TPR.G6251' => 'tpr', 'TPR.G8167' => 'tpr', 'TWI12G1330' => 'twi', 'TWI18G1239' => 'twi', 'TWI34G0979' => 'twi', 'TWI36G0670' => 'twi', 'TWI36G0707' => 'twi', 'TWI56G0233' => 'twi', 'TWI75G1809' => 'twi', 'unitig_21.g20874' => 'ugi', 'unitig_26.g10343' => 'ugi', 'unitig_46.g18392' => 'ugi', 'unitig_52.g17178' => 'ugi', 'unitig_8.g2934' => 'ugi', 'vmacro01122' => 'vma', 'vmacro05875' => 'vma', 'vmacro06147' => 'vma', 'vmacro16191' => 'vma', 'vmacro18293' => 'vma', 'VMungo0251G3707' => 'vmu', 'VMungo0464G1521' => 'vmu', 'VMungo1215G0205' => 'vmu', 'VMungo1383G2484' => 'vmu', 'Zm00001eb079610' => 'zma', 'Zm00001eb135990' => 'zma', 'Zm00001eb183710' => 'zma', 'Zm00001eb246020' => 'zma' ), 'gf_id' => 'HOM05D001124', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001124' ), 'data_identifier' => 'HOM05D001124', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001124', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '548', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02520' => 'bna', 'A03p06630' => 'bna', 'A05p44460' => 'bna', 'A06p08710' => 'bna', 'A06p41090' => 'bna', 'A07p32320' => 'bna', 'A08p32520' => 'bna', 'A09p10360' => 'bna', 'A10p24080' => 'bna', 'Aa31LG11G15250' => 'aar', 'Aa31LG1G1800' => 'aar', 'Aa31LG2G5120' => 'aar', 'Aa31LG2G6070' => 'aar', 'Aa31LG5G10770' => 'aar', 'Aa31sc61G90' => 'aar', 'Actinidia01352' => 'ach', 'Actinidia05983' => 'ach', 'Actinidia08133' => 'ach', 'Actinidia15101' => 'ach', 'Actinidia26379' => 'ach', 'Actinidia35778' => 'ach', 'Actinidia36123' => 'ach', 'Actinidia37436' => 'ach', 'Actinidia38730' => 'ach', 'Ah.02g128210' => 'amhyb', 'Ah.03g132990' => 'amhyb', 'Ah.14g079410' => 'amhyb', 'AL1G24640' => 'aly', 'AL2G26680' => 'aly', 'AL3G10530' => 'aly', 'AL3G45230' => 'aly', 'AL5G15230' => 'aly', 'AL5G16960' => 'aly', 'AL6G25210' => 'aly', 'Aqoxy2G00441' => 'aox', 'Aqoxy3G01236' => 'aox', 'Aqoxy5G03746' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3RQ047' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C7GMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9C8JER' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MBL6KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YXCZ83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZANX40' => 'arhy', 'AT1G12990' => 'ath', 'AT1G67880' => 'ath', 'AT2G13290' => 'ath', 'AT3G01620' => 'ath', 'AT3G26445' => 'ath', 'AT3G27540' => 'ath', 'AT5G14480' => 'ath', 'ATR0824G026' => 'atr', 'ATR1098G019' => 'atr', 'Atru.chr11.2145' => 'acertr', 'Atru.chr2.3636' => 'acertr', 'Atru.chr2.3644' => 'acertr', 'Atru.chr6.2422' => 'acertr', 'Atru.chr7.1112' => 'acertr', 'AUR62005469' => 'cqu', 'AUR62011166' => 'cqu', 'AUR62013319' => 'cqu', 'AUR62024273' => 'cqu', 'AUR62028420' => 'cqu', 'AUR62041942' => 'cqu', 'BcaB01g04969' => 'bca', 'BcaB01g06371' => 'bca', 'BcaB02g11494' => 'bca', 'BcaB03g15382' => 'bca', 'BcaB08g36994' => 'bca', 'BcaC03g13477' => 'bca', 'BcaC03g13478' => 'bca', 'BcaC03g13480' => 'bca', 'BcaC03g13481' => 'bca', 'BcaC03g13486' => 'bca', 'BcaC04g19031' => 'bca', 'BcaC04g23085' => 'bca', 'BcaC05g25094' => 'bca', 'BcaC05g25096' => 'bca', 'BcaC05g25138' => 'bca', 'BcaC05g30416' => 'bca', 'BcaC05g30455' => 'bca', 'BcaC06g30979' => 'bca', 'BcaC06g33805' => 'bca', 'BcaC08g46021' => 'bca', 'BcaNung03154' => 'bca', 'BolC2t06623H' => 'bol', 'BolC2t06632H' => 'bol', 'BolC2t06635H' => 'bol', 'BolC2t06638H' => 'bol', 'BolC3t13266H' => 'bol', 'BolC5t29776H' => 'bol', 'BolC6t38912H' => 'bol', 'BolC7t44183H' => 'bol', 'BolC9t54123H' => 'bol', 'BolC9t59107H' => 'bol', 'BraA02t05221Z' => 'bra', 'BraA03t09996Z' => 'bra', 'BraA05t23210Z' => 'bra', 'BraA06t24068Z' => 'bra', 'BraA06t27032Z' => 'bra', 'BraA08t35176Z' => 'bra', 'BraA09t36680Z' => 'bra', 'BraA10t44471Z' => 'bra', 'C02p06760' => 'bna', 'C02p06890' => 'bna', 'C02p07010' => 'bna', 'C03p07660' => 'bna', 'C05p10300' => 'bna', 'C06p38150' => 'bna', 'C07p36650' => 'bna', 'C08p15770' => 'bna', 'C09p12300' => 'bna', 'C09p62700' => 'bna', 'C09p75040' => 'bna', 'CAN.G13.1' => 'can', 'CAN.G138.4' => 'can', 'CAN.G44.6' => 'can', 'CAN.G473.19' => 'can', 'CANSAT01G0835' => 'cansat', 'CANSAT11G0246' => 'cansat', 'CANSAT11G1766' => 'cansat', 'CANSAT64G1954' => 'cansat', 'CARHR013330' => 'chi', 'CARHR060530' => 'chi', 'CARHR075300' => 'chi', 'CARHR105120' => 'chi', 'CARHR148910' => 'chi', 'CARHR198830' => 'chi', 'Carub.0001s1275' => 'cru', 'Carub.0002s1437' => 'cru', 'Carub.0003s0044' => 'cru', 'Carub.0003s2787' => 'cru', 'Carub.0005s0597' => 'cru', 'Carub.0006s1266' => 'cru', 'Ca_06935_v3' => 'car', 'Ca_13559_v3' => 'car', 'Ca_16941_v3' => 'car', 'Ca_16960_v3' => 'car', 'Ca_17775_v3' => 'car', 'Ca_30464_v3' => 'car', 'Cc06_g08160' => 'ccan', 'Cc07_g01520' => 'ccan', 'Cc11_g15810' => 'ccan', 'CDE02G2840' => 'cde', 'CDE03G0093' => 'cde', 'CDE04G2127' => 'cde', 'CDE07G1857' => 'cde', 'CDE09G1246' => 'cde', 'Cfa003412' => 'cfa', 'Cfa007341' => 'cfa', 'Cfa009220' => 'cfa', 'Ciclev10008737m.g' => 'ccl', 'Ciclev10015565m.g' => 'ccl', 'Ciclev10031761m.g' => 'ccl', 'CiPaw.03G045300' => 'cil', 'CiPaw.03G247200' => 'cil', 'CiPaw.04G029500' => 'cil', 'CiPaw.04G174000' => 'cil', 'CiPaw.05G181200' => 'cil', 'CiPaw.06G067100' => 'cil', 'ClCG05G025800' => 'cla', 'ClCG06G011400' => 'cla', 'ClCG09G019360' => 'cla', 'COL.COLO4_04827' => 'col', 'COL.COLO4_29170' => 'col', 'COL.COLO4_35131' => 'col', 'COL.COLO4_35132' => 'col', 'Cpa.g.sc33.32' => 'cpa', 'Cpa.g.sc46.29' => 'cpa', 'Cpa.g.sc796.1' => 'cpa', 'CsaV3_1G030420' => 'csa', 'CsaV3_5G027050' => 'csa', 'CsaV3_5G031040' => 'csa', 'CsaV3_UNG023130' => 'csa', 'CSS0007726' => 'camsi', 'CSS0016433' => 'camsi', 'CSS0017656' => 'camsi', 'CSS0025364' => 'camsi', 'CSS0027582' => 'camsi', 'CSS0047288' => 'camsi', 'CSS0049950' => 'camsi', 'DCAR_003843' => 'dca', 'DCAR_007052' => 'dca', 'DCAR_020884' => 'dca', 'DCAR_021730' => 'dca', 'DCAR_024423' => 'dca', 'DCAR_026509' => 'dca', 'DCAR_031158' => 'dca', 'Dinv14728' => 'din', 'Dinv15219' => 'din', 'Dinv25728' => 'din', 'Dinv33428' => 'din', 'Dinv36489' => 'din', 'Dinv41486' => 'din', 'Duzib147G0469' => 'dzi', 'Duzib168G0060' => 'dzi', 'Duzib187G1215' => 'dzi', 'Duzib248G0692' => 'dzi', 'Duzib251G0767' => 'dzi', 'Duzib264G0446' => 'dzi', 'Duzib268G0691' => 'dzi', 'ECA232G4767' => 'eca', 'ECA233G2838' => 'eca', 'ECA234G0391' => 'eca', 'ECA234G0857' => 'eca', 'ECA236G1593' => 'eca', 'ECA238G0565' => 'eca', 'ECA246G1027' => 'eca', 'ECA246G3223' => 'eca', 'ECA246G3470' => 'eca', 'EL10Ac6g13829' => 'bvu', 'EL10Ac6g14093' => 'bvu', 'EL10Ac8g18707' => 'bvu', 'Eucgr.C01369' => 'egr', 'Eucgr.H02492' => 'egr', 'Eucgr.I01733' => 'egr', 'Eucgr.J02255' => 'egr', 'Eucgr.J02257' => 'egr', 'Eucgr.J02258' => 'egr', 'FAN02G1601' => 'fan', 'FAN03G1586' => 'fan', 'FAN03G2986' => 'fan', 'FAN05G4837' => 'fan', 'FAN06G0146' => 'fan', 'FAN07G0858' => 'fan', 'FAN09G3179' => 'fan', 'FAN10G0669' => 'fan', 'FAN12G2358' => 'fan', 'FAN14G4198' => 'fan', 'FAN14G5112' => 'fan', 'FAN17G0342' => 'fan', 'FAN19G0342' => 'fan', 'FAN19G0962' => 'fan', 'FAN19G1101' => 'fan', 'FAN19G1872' => 'fan', 'FAN22G0356' => 'fan', 'FAN23G0744' => 'fan', 'FAN23G1914' => 'fan', 'FAN26G0032' => 'fan', 'FAN28G0625' => 'fan', 'FvH4_1g02710' => 'fve', 'FvH4_1g02720' => 'fve', 'FvH4_4g25670' => 'fve', 'FvH4_6g51700' => 'fve', 'FvH4_7g20170' => 'fve', 'Glyma.05G175000' => 'gma', 'Glyma.08G132300' => 'gma', 'Glyma.11G243000' => 'gma', 'Glyma.13G158900' => 'gma', 'Glyma.17G112400' => 'gma', 'Glyma.18G014100' => 'gma', 'Glyma.19G003100' => 'gma', 'Glyma.19G056500' => 'gma', 'Gohir.A01G158900' => 'ghi', 'Gohir.A05G312600' => 'ghi', 'Gohir.A05G354900' => 'ghi', 'Gohir.A07G037200' => 'ghi', 'Gohir.A09G030000' => 'ghi', 'Gohir.A12G145200' => 'ghi', 'Gohir.D01G151500' => 'ghi', 'Gohir.D04G058300' => 'ghi', 'Gohir.D05G314100' => 'ghi', 'Gohir.D07G041400' => 'ghi', 'Gohir.D09G029700' => 'ghi', 'Gohir.D12G149700' => 'ghi', 'Gorai.001G043800' => 'gra', 'Gorai.002G187800' => 'gra', 'Gorai.006G034700' => 'gra', 'Gorai.008G161200' => 'gra', 'Gorai.009G335700' => 'gra', 'Gorai.012G065000' => 'gra', 'GSVIVG01000535001' => 'vvi', 'GSVIVG01015572001' => 'vvi', 'GSVIVG01032386001' => 'vvi', 'HanXRQChr05g0138531' => 'han', 'HanXRQChr06g0174391' => 'han', 'HanXRQChr07g0199021' => 'han', 'HanXRQChr08g0208211' => 'han', 'HanXRQChr09g0255471' => 'han', 'HanXRQChr10g0315791' => 'han', 'HanXRQChr12g0371991' => 'han', 'HanXRQChr15g0475251' => 'han', 'HanXRQChr17g0540001' => 'han', 'HanXRQChr17g0548631' => 'han', 'HanXRQChr17g0569561' => 'han', 'Haze_12256' => 'cav', 'Haze_14756' => 'cav', 'Haze_25528' => 'cav', 'Hma1.2p1_0079F.1_g041020' => 'hma', 'Hma1.2p1_0818F.1_g223260' => 'hma', 'Hma1.2p1_1747F.1_g300530' => 'hma', 'HPP92_004607' => 'vpl', 'HPP92_004608' => 'vpl', 'HPP92_006181' => 'vpl', 'HPP92_012192' => 'vpl', 'HPP92_015680' => 'vpl', 'HPP92_020249' => 'vpl', 'HPP92_021376' => 'vpl', 'HPP92_024275' => 'vpl', 'Hund06031' => 'sun', 'Hund25391' => 'sun', 'Lalb_Chr07g0185371' => 'lal', 'Lalb_Chr07g0185381' => 'lal', 'Lalb_Chr12g0204011' => 'lal', 'Lalb_Chr13g0301671' => 'lal', 'Lalb_Chr14g0362851' => 'lal', 'Lalb_Chr24g0403581' => 'lal', 'Lj1g0000233' => 'lja', 'Lj2g0018120' => 'lja', 'Lj3C621T0' => 'lonja', 'Lj3P1059T14' => 'lonja', 'Lj3P611T9' => 'lonja', 'Lj3P614T13' => 'lonja', 'Lj3P615T5' => 'lonja', 'Lj4g0012315' => 'lja', 'Lj4g0026182' => 'lja', 'Lj6P813T16' => 'lonja', 'Lj7C427T7' => 'lonja', 'Lj7C427T8' => 'lonja', 'Lj7P600T41' => 'lonja', 'Lju41C42G17' => 'lonja', 'Lsat_1_v5_gn_0_47300' => 'lsa', 'Lsat_1_v5_gn_2_91280' => 'lsa', 'Lsat_1_v5_gn_3_30561' => 'lsa', 'Lsat_1_v5_gn_4_184321' => 'lsa', 'Lsat_1_v5_gn_4_4041' => 'lsa', 'Lsat_1_v5_gn_5_92000' => 'lsa', 'Lsat_1_v5_gn_8_152940' => 'lsa', 'Lsat_1_v5_gn_8_62401' => 'lsa', 'Manes.06G055900' => 'mes', 'Manes.12G022200' => 'mes', 'Manes.13G023300' => 'mes', 'Manes.14G115000' => 'mes', 'Manes.15G151700' => 'mes', 'Manes.17G111300' => 'mes', 'Mapoly0226s0009' => 'mpo', 'MBI02_g25363_MAGBIO' => 'mbi', 'MBI06_g00027_MAGBIO' => 'mbi', 'MBI10_g13034_MAGBIO' => 'mbi', 'MD09G1023400' => 'mdo', 'MD13G1100100' => 'mdo', 'MD15G1169200' => 'mdo', 'MD16G1101100' => 'mdo', 'MD17G1022900' => 'mdo', 'Medtr3g096150' => 'mtr', 'Medtr4g115070' => 'mtr', 'Medtr7g033325' => 'mtr', 'Medtr8g089840' => 'mtr', 'MELO3C010319.2' => 'cme', 'MELO3C011944.2' => 'cme', 'MELO3C021589.2' => 'cme', 'Migut.E00207' => 'egut', 'Migut.H00067' => 'egut', 'Migut.K00433' => 'egut', 'Migut.K00606' => 'egut', 'Migut.K01410' => 'egut', 'MSTRG.13347' => 'ama', 'MSTRG.24045' => 'ama', 'MSTRG.2428' => 'ama', 'MSTRG.26410' => 'ama', 'MSTRG.3139' => 'ama', 'MSTRG.3286' => 'ama', 'MSTRG.563' => 'ama', 'MSTRG.7941' => 'ama', 'Nitab4.5_0000028g0060' => 'nta', 'Nitab4.5_0000065g0260' => 'nta', 'Nitab4.5_0000112g0060' => 'nta', 'Nitab4.5_0000489g0120' => 'nta', 'Nitab4.5_0001776g0050' => 'nta', 'Nitab4.5_0001854g0010' => 'nta', 'Nitab4.5_0001860g0020' => 'nta', 'Nitab4.5_0004352g0010' => 'nta', 'Nitab4.5_0008716g0020' => 'nta', 'Nitab4.5_0008922g0010' => 'nta', 'Nn3g16693' => 'nnu', 'Nn4g22596' => 'nnu', 'Nn7g37639' => 'nnu', 'Oeu001701.1' => 'oeu', 'Oeu018149.1' => 'oeu', 'Oeu026220.1' => 'oeu', 'Oeu038635.1' => 'oeu', 'Oeu049176.1' => 'oeu', 'Oeu056706.1' => 'oeu', 'Oeu056937.1' => 'oeu', 'Oeu057540.1' => 'oeu', 'Os02g0594900' => 'osa', 'Os02g0595100' => 'osa', 'Os04g0477500' => 'osa', 'Os12g0611900' => 'osa', 'Peaxi162Scf00076g00020' => 'pax', 'Peaxi162Scf00128g00217' => 'pax', 'Peaxi162Scf00129g01640' => 'pax', 'Peaxi162Scf00669g00007' => 'pax', 'Peaxi162Scf00700g00421' => 'pax', 'Peaxi162Scf00801g00038' => 'pax', 'Peaxi162Scf00891g00025' => 'pax', 'PGR083G0909' => 'pgr', 'PGR119G1005' => 'pgr', 'PGR142G2236' => 'pgr', 'PGR142G3388' => 'pgr', 'PGSC0003DMG400004514' => 'stu', 'PGSC0003DMG400012635' => 'stu', 'PGSC0003DMG400015730' => 'stu', 'PGSC0003DMG400018611' => 'stu', 'PGSC0003DMG400030897' => 'stu', 'Phvul.001G254800' => 'pvu', 'Phvul.002G260100' => 'pvu', 'Phvul.003G167600' => 'pvu', 'Phvul.004G005100' => 'pvu', 'Potri.001G343600' => 'ptr', 'Potri.006G066700' => 'ptr', 'Potri.008G186000' => 'ptr', 'Potri.010G046900' => 'ptr', 'Potri.018G127900' => 'ptr', 'Pp3c20_17750' => 'ppa', 'Pp3c24_4380' => 'ppa', 'Prupe.1G245800' => 'ppe', 'Prupe.3G293400' => 'ppe', 'Prupe.7G247400' => 'ppe', 'Psat0s145g0120' => 'psa', 'Psat0s595g0040' => 'psa', 'Psat0s595g0120' => 'psa', 'Psat3g175040' => 'psa', 'Psat7g058120' => 'psa', 'PSO017G0428' => 'pso', 'PSO063G7510' => 'pso', 'PSO067G0046' => 'pso', 'PSO478G1073' => 'pso', 'PSO675G3677' => 'pso', 'PSO675G6558' => 'pso', 'PSO675G7520' => 'pso', 'PSO675G8959' => 'pso', 'QL02p074089' => 'qlo', 'QL02p089614' => 'qlo', 'QL03p057736' => 'qlo', 'RcHm_v2.0_Chr1g0364131' => 'rch', 'RcHm_v2.0_Chr2g0087801' => 'rch', 'RcHm_v2.0_Chr2g0087821' => 'rch', 'RcHm_v2.0_Chr2g0173231' => 'rch', 'RcHm_v2.0_Chr4g0433111' => 'rch', 'Rhsim03G0250300' => 'rsi', 'Rhsim08G0048400' => 'rsi', 'Rhsim10G0014800' => 'rsi', 'Rhsim12G0040100' => 'rsi', 'Rhsim12G0109700' => 'rsi', 'Sabra06G0049600' => 'sbr', 'Sabra08G0141000' => 'sbr', 'Sabra10G0021400' => 'sbr', 'Sabra16G0222900' => 'sbr', 'Sabra18G0108600' => 'sbr', 'SalBow1G0433' => 'sbo', 'SalBow1G2038' => 'sbo', 'SalBow1G5003' => 'sbo', 'SalBow7G1197' => 'sbo', 'SalBow8G3506' => 'sbo', 'Sc03g0007300' => 'sci', 'Sc11g0000950' => 'sci', 'Sc14g0008750' => 'sci', 'Sc18g0000420' => 'sci', 'Sed0006754' => 'sed', 'Sed0008741' => 'sed', 'Sed0017172' => 'sed', 'Sed0018925' => 'sed', 'Sed0023326' => 'sed', 'Sed0025909' => 'sed', 'SEGI_05333' => 'sgi', 'SEGI_10362' => 'sgi', 'SEGI_13380' => 'sgi', 'SEGI_24306' => 'sgi', 'SEGI_29077' => 'sgi', 'SEGI_29095' => 'sgi', 'SEGI_36534' => 'sgi', 'SEGI_37506' => 'sgi', 'SEGI_38321' => 'sgi', 'SGA_v2.0_scaffold307G48031' => 'sas', 'SGA_v2.0_scaffold47G17507' => 'sas', 'SGA_v2.0_scaffold63G21736' => 'sas', 'SGA_v2.0_scaffold87G27070' => 'sas', 'SHI17794' => 'shi', 'SHI28851' => 'shi', 'SMO165G0155' => 'smo', 'SMO340G0217' => 'smo', 'SMO367G1210' => 'smo', 'Solyc02g093430.3' => 'sly', 'Solyc05g013580.4' => 'sly', 'Solyc07g008030.3' => 'sly', 'Solyc12g035470.2' => 'sly', 'Sopen02g038020' => 'spe', 'Sopen05g008490' => 'spe', 'Sopen07g003910' => 'spe', 'Sopen12g015240' => 'spe', 'Sp1g11550' => 'spa', 'Sp2g16710' => 'spa', 'Sp3g00430' => 'spa', 'Sp3g26780' => 'spa', 'Sp5g22900' => 'spa', 'Sp6g29530' => 'spa', 'TAR371G0794' => 'tar', 'TAR374G0164' => 'tar', 'TAR622G0165' => 'tar', 'TAR626G0929' => 'tar', 'TAR629G2155' => 'tar', 'THA.LOC104805282' => 'tha', 'THA.LOC104805363' => 'tha', 'THA.LOC104808968' => 'tha', 'THA.LOC104821093' => 'tha', 'THA.LOC104823953' => 'tha', 'THA.LOC104825562' => 'tha', 'THA.LOC104825665' => 'tha', 'Thecc.02G261400' => 'tca', 'Thecc.04G019200' => 'tca', 'Thecc.09G130400' => 'tca', 'Thhalv10004374m.g' => 'esa', 'Thhalv10007850m.g' => 'esa', 'Thhalv10013782m.g' => 'esa', 'Thhalv10018686m.g' => 'esa', 'Thhalv10020899m.g' => 'esa', 'Thhalv10022755m.g' => 'esa', 'TPR.G23851' => 'tpr', 'TPR.G26500' => 'tpr', 'TPR.G27267' => 'tpr', 'TPR.G32001' => 'tpr', 'TPR.G6251' => 'tpr', 'TPR.G8167' => 'tpr', 'TWI12G1330' => 'twi', 'TWI18G1239' => 'twi', 'TWI34G0979' => 'twi', 'TWI36G0670' => 'twi', 'TWI36G0707' => 'twi', 'TWI56G0233' => 'twi', 'TWI75G1809' => 'twi', 'unitig_21.g20874' => 'ugi', 'unitig_26.g10343' => 'ugi', 'unitig_46.g18392' => 'ugi', 'unitig_52.g17178' => 'ugi', 'unitig_8.g2934' => 'ugi', 'vmacro01122' => 'vma', 'vmacro05875' => 'vma', 'vmacro06147' => 'vma', 'vmacro16191' => 'vma', 'vmacro18293' => 'vma', 'VMungo0251G3707' => 'vmu', 'VMungo0464G1521' => 'vmu', 'VMungo1215G0205' => 'vmu', 'VMungo1383G2484' => 'vmu', 'Zm00001eb079610' => 'zma', 'Zm00001eb135990' => 'zma', 'Zm00001eb183710' => 'zma', 'Zm00001eb246020' => 'zma' ) $gf_id = 'HOM05D001124' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001124' ) $data_identifier = 'HOM05D001124' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 6, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 7, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 21, 'bol' => (int) 10, 'bra' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 6, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 9, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 21, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 8, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 10, 'lsa' => (int) 8, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 8, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 9, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb246020' $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' => 'HOM05D001124', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '548', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02520' => 'bna', 'A03p06630' => 'bna', 'A05p44460' => 'bna', 'A06p08710' => 'bna', 'A06p41090' => 'bna', 'A07p32320' => 'bna', 'A08p32520' => 'bna', 'A09p10360' => 'bna', 'A10p24080' => 'bna', 'Aa31LG11G15250' => 'aar', 'Aa31LG1G1800' => 'aar', 'Aa31LG2G5120' => 'aar', 'Aa31LG2G6070' => 'aar', 'Aa31LG5G10770' => 'aar', 'Aa31sc61G90' => 'aar', 'Actinidia01352' => 'ach', 'Actinidia05983' => 'ach', 'Actinidia08133' => 'ach', 'Actinidia15101' => 'ach', 'Actinidia26379' => 'ach', 'Actinidia35778' => 'ach', 'Actinidia36123' => 'ach', 'Actinidia37436' => 'ach', 'Actinidia38730' => 'ach', 'Ah.02g128210' => 'amhyb', 'Ah.03g132990' => 'amhyb', 'Ah.14g079410' => 'amhyb', 'AL1G24640' => 'aly', 'AL2G26680' => 'aly', 'AL3G10530' => 'aly', 'AL3G45230' => 'aly', 'AL5G15230' => 'aly', 'AL5G16960' => 'aly', 'AL6G25210' => 'aly', 'Aqoxy2G00441' => 'aox', 'Aqoxy3G01236' => 'aox', 'Aqoxy5G03746' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3RQ047' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C7GMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9C8JER' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MBL6KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YXCZ83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZANX40' => 'arhy', 'AT1G12990' => 'ath', 'AT1G67880' => 'ath', 'AT2G13290' => 'ath', 'AT3G01620' => 'ath', 'AT3G26445' => 'ath', 'AT3G27540' => 'ath', 'AT5G14480' => 'ath', 'ATR0824G026' => 'atr', 'ATR1098G019' => 'atr', 'Atru.chr11.2145' => 'acertr', 'Atru.chr2.3636' => 'acertr', 'Atru.chr2.3644' => 'acertr', 'Atru.chr6.2422' => 'acertr', 'Atru.chr7.1112' => 'acertr', 'AUR62005469' => 'cqu', 'AUR62011166' => 'cqu', 'AUR62013319' => 'cqu', 'AUR62024273' => 'cqu', 'AUR62028420' => 'cqu', 'AUR62041942' => 'cqu', 'BcaB01g04969' => 'bca', 'BcaB01g06371' => 'bca', 'BcaB02g11494' => 'bca', 'BcaB03g15382' => 'bca', 'BcaB08g36994' => 'bca', 'BcaC03g13477' => 'bca', 'BcaC03g13478' => 'bca', 'BcaC03g13480' => 'bca', 'BcaC03g13481' => 'bca', 'BcaC03g13486' => 'bca', 'BcaC04g19031' => 'bca', 'BcaC04g23085' => 'bca', 'BcaC05g25094' => 'bca', 'BcaC05g25096' => 'bca', 'BcaC05g25138' => 'bca', 'BcaC05g30416' => 'bca', 'BcaC05g30455' => 'bca', 'BcaC06g30979' => 'bca', 'BcaC06g33805' => 'bca', 'BcaC08g46021' => 'bca', 'BcaNung03154' => 'bca', 'BolC2t06623H' => 'bol', 'BolC2t06632H' => 'bol', 'BolC2t06635H' => 'bol', 'BolC2t06638H' => 'bol', 'BolC3t13266H' => 'bol', 'BolC5t29776H' => 'bol', 'BolC6t38912H' => 'bol', 'BolC7t44183H' => 'bol', 'BolC9t54123H' => 'bol', 'BolC9t59107H' => 'bol', 'BraA02t05221Z' => 'bra', 'BraA03t09996Z' => 'bra', 'BraA05t23210Z' => 'bra', 'BraA06t24068Z' => 'bra', 'BraA06t27032Z' => 'bra', 'BraA08t35176Z' => 'bra', 'BraA09t36680Z' => 'bra', 'BraA10t44471Z' => 'bra', 'C02p06760' => 'bna', 'C02p06890' => 'bna', 'C02p07010' => 'bna', 'C03p07660' => 'bna', 'C05p10300' => 'bna', 'C06p38150' => 'bna', 'C07p36650' => 'bna', 'C08p15770' => 'bna', 'C09p12300' => 'bna', 'C09p62700' => 'bna', 'C09p75040' => 'bna', 'CAN.G13.1' => 'can', 'CAN.G138.4' => 'can', 'CAN.G44.6' => 'can', 'CAN.G473.19' => 'can', 'CANSAT01G0835' => 'cansat', 'CANSAT11G0246' => 'cansat', 'CANSAT11G1766' => 'cansat', 'CANSAT64G1954' => 'cansat', 'CARHR013330' => 'chi', 'CARHR060530' => 'chi', 'CARHR075300' => 'chi', 'CARHR105120' => 'chi', 'CARHR148910' => 'chi', 'CARHR198830' => 'chi', 'Carub.0001s1275' => 'cru', 'Carub.0002s1437' => 'cru', 'Carub.0003s0044' => 'cru', 'Carub.0003s2787' => 'cru', 'Carub.0005s0597' => 'cru', 'Carub.0006s1266' => 'cru', 'Ca_06935_v3' => 'car', 'Ca_13559_v3' => 'car', 'Ca_16941_v3' => 'car', 'Ca_16960_v3' => 'car', 'Ca_17775_v3' => 'car', 'Ca_30464_v3' => 'car', 'Cc06_g08160' => 'ccan', 'Cc07_g01520' => 'ccan', 'Cc11_g15810' => 'ccan', 'CDE02G2840' => 'cde', 'CDE03G0093' => 'cde', 'CDE04G2127' => 'cde', 'CDE07G1857' => 'cde', 'CDE09G1246' => 'cde', 'Cfa003412' => 'cfa', 'Cfa007341' => 'cfa', 'Cfa009220' => 'cfa', 'Ciclev10008737m.g' => 'ccl', 'Ciclev10015565m.g' => 'ccl', 'Ciclev10031761m.g' => 'ccl', 'CiPaw.03G045300' => 'cil', 'CiPaw.03G247200' => 'cil', 'CiPaw.04G029500' => 'cil', 'CiPaw.04G174000' => 'cil', 'CiPaw.05G181200' => 'cil', 'CiPaw.06G067100' => 'cil', 'ClCG05G025800' => 'cla', 'ClCG06G011400' => 'cla', 'ClCG09G019360' => 'cla', 'COL.COLO4_04827' => 'col', 'COL.COLO4_29170' => 'col', 'COL.COLO4_35131' => 'col', 'COL.COLO4_35132' => 'col', 'Cpa.g.sc33.32' => 'cpa', 'Cpa.g.sc46.29' => 'cpa', 'Cpa.g.sc796.1' => 'cpa', 'CsaV3_1G030420' => 'csa', 'CsaV3_5G027050' => 'csa', 'CsaV3_5G031040' => 'csa', 'CsaV3_UNG023130' => 'csa', 'CSS0007726' => 'camsi', 'CSS0016433' => 'camsi', 'CSS0017656' => 'camsi', 'CSS0025364' => 'camsi', 'CSS0027582' => 'camsi', 'CSS0047288' => 'camsi', 'CSS0049950' => 'camsi', 'DCAR_003843' => 'dca', 'DCAR_007052' => 'dca', 'DCAR_020884' => 'dca', 'DCAR_021730' => 'dca', 'DCAR_024423' => 'dca', 'DCAR_026509' => 'dca', 'DCAR_031158' => 'dca', 'Dinv14728' => 'din', 'Dinv15219' => 'din', 'Dinv25728' => 'din', 'Dinv33428' => 'din', 'Dinv36489' => 'din', 'Dinv41486' => 'din', 'Duzib147G0469' => 'dzi', 'Duzib168G0060' => 'dzi', 'Duzib187G1215' => 'dzi', 'Duzib248G0692' => 'dzi', 'Duzib251G0767' => 'dzi', 'Duzib264G0446' => 'dzi', 'Duzib268G0691' => 'dzi', 'ECA232G4767' => 'eca', 'ECA233G2838' => 'eca', 'ECA234G0391' => 'eca', 'ECA234G0857' => 'eca', 'ECA236G1593' => 'eca', 'ECA238G0565' => 'eca', 'ECA246G1027' => 'eca', 'ECA246G3223' => 'eca', 'ECA246G3470' => 'eca', 'EL10Ac6g13829' => 'bvu', 'EL10Ac6g14093' => 'bvu', 'EL10Ac8g18707' => 'bvu', 'Eucgr.C01369' => 'egr', 'Eucgr.H02492' => 'egr', 'Eucgr.I01733' => 'egr', 'Eucgr.J02255' => 'egr', 'Eucgr.J02257' => 'egr', 'Eucgr.J02258' => 'egr', 'FAN02G1601' => 'fan', 'FAN03G1586' => 'fan', 'FAN03G2986' => 'fan', 'FAN05G4837' => 'fan', 'FAN06G0146' => 'fan', 'FAN07G0858' => 'fan', 'FAN09G3179' => 'fan', 'FAN10G0669' => 'fan', 'FAN12G2358' => 'fan', 'FAN14G4198' => 'fan', 'FAN14G5112' => 'fan', 'FAN17G0342' => 'fan', 'FAN19G0342' => 'fan', 'FAN19G0962' => 'fan', 'FAN19G1101' => 'fan', 'FAN19G1872' => 'fan', 'FAN22G0356' => 'fan', 'FAN23G0744' => 'fan', 'FAN23G1914' => 'fan', 'FAN26G0032' => 'fan', 'FAN28G0625' => 'fan', 'FvH4_1g02710' => 'fve', 'FvH4_1g02720' => 'fve', 'FvH4_4g25670' => 'fve', 'FvH4_6g51700' => 'fve', 'FvH4_7g20170' => 'fve', 'Glyma.05G175000' => 'gma', 'Glyma.08G132300' => 'gma', 'Glyma.11G243000' => 'gma', 'Glyma.13G158900' => 'gma', 'Glyma.17G112400' => 'gma', 'Glyma.18G014100' => 'gma', 'Glyma.19G003100' => 'gma', 'Glyma.19G056500' => 'gma', 'Gohir.A01G158900' => 'ghi', 'Gohir.A05G312600' => 'ghi', 'Gohir.A05G354900' => 'ghi', 'Gohir.A07G037200' => 'ghi', 'Gohir.A09G030000' => 'ghi', 'Gohir.A12G145200' => 'ghi', 'Gohir.D01G151500' => 'ghi', 'Gohir.D04G058300' => 'ghi', 'Gohir.D05G314100' => 'ghi', 'Gohir.D07G041400' => 'ghi', 'Gohir.D09G029700' => 'ghi', 'Gohir.D12G149700' => 'ghi', 'Gorai.001G043800' => 'gra', 'Gorai.002G187800' => 'gra', 'Gorai.006G034700' => 'gra', 'Gorai.008G161200' => 'gra', 'Gorai.009G335700' => 'gra', 'Gorai.012G065000' => 'gra', 'GSVIVG01000535001' => 'vvi', 'GSVIVG01015572001' => 'vvi', 'GSVIVG01032386001' => 'vvi', 'HanXRQChr05g0138531' => 'han', 'HanXRQChr06g0174391' => 'han', 'HanXRQChr07g0199021' => 'han', 'HanXRQChr08g0208211' => 'han', 'HanXRQChr09g0255471' => 'han', 'HanXRQChr10g0315791' => 'han', 'HanXRQChr12g0371991' => 'han', 'HanXRQChr15g0475251' => 'han', 'HanXRQChr17g0540001' => 'han', 'HanXRQChr17g0548631' => 'han', 'HanXRQChr17g0569561' => 'han', 'Haze_12256' => 'cav', 'Haze_14756' => 'cav', 'Haze_25528' => 'cav', 'Hma1.2p1_0079F.1_g041020' => 'hma', 'Hma1.2p1_0818F.1_g223260' => 'hma', 'Hma1.2p1_1747F.1_g300530' => 'hma', 'HPP92_004607' => 'vpl', 'HPP92_004608' => 'vpl', 'HPP92_006181' => 'vpl', 'HPP92_012192' => 'vpl', 'HPP92_015680' => 'vpl', 'HPP92_020249' => 'vpl', 'HPP92_021376' => 'vpl', 'HPP92_024275' => 'vpl', 'Hund06031' => 'sun', 'Hund25391' => 'sun', 'Lalb_Chr07g0185371' => 'lal', 'Lalb_Chr07g0185381' => 'lal', 'Lalb_Chr12g0204011' => 'lal', 'Lalb_Chr13g0301671' => 'lal', 'Lalb_Chr14g0362851' => 'lal', 'Lalb_Chr24g0403581' => 'lal', 'Lj1g0000233' => 'lja', 'Lj2g0018120' => 'lja', 'Lj3C621T0' => 'lonja', 'Lj3P1059T14' => 'lonja', 'Lj3P611T9' => 'lonja', 'Lj3P614T13' => 'lonja', 'Lj3P615T5' => 'lonja', 'Lj4g0012315' => 'lja', 'Lj4g0026182' => 'lja', 'Lj6P813T16' => 'lonja', 'Lj7C427T7' => 'lonja', 'Lj7C427T8' => 'lonja', 'Lj7P600T41' => 'lonja', 'Lju41C42G17' => 'lonja', 'Lsat_1_v5_gn_0_47300' => 'lsa', 'Lsat_1_v5_gn_2_91280' => 'lsa', 'Lsat_1_v5_gn_3_30561' => 'lsa', 'Lsat_1_v5_gn_4_184321' => 'lsa', 'Lsat_1_v5_gn_4_4041' => 'lsa', 'Lsat_1_v5_gn_5_92000' => 'lsa', 'Lsat_1_v5_gn_8_152940' => 'lsa', 'Lsat_1_v5_gn_8_62401' => 'lsa', 'Manes.06G055900' => 'mes', 'Manes.12G022200' => 'mes', 'Manes.13G023300' => 'mes', 'Manes.14G115000' => 'mes', 'Manes.15G151700' => 'mes', 'Manes.17G111300' => 'mes', 'Mapoly0226s0009' => 'mpo', 'MBI02_g25363_MAGBIO' => 'mbi', 'MBI06_g00027_MAGBIO' => 'mbi', 'MBI10_g13034_MAGBIO' => 'mbi', 'MD09G1023400' => 'mdo', 'MD13G1100100' => 'mdo', 'MD15G1169200' => 'mdo', 'MD16G1101100' => 'mdo', 'MD17G1022900' => 'mdo', 'Medtr3g096150' => 'mtr', 'Medtr4g115070' => 'mtr', 'Medtr7g033325' => 'mtr', 'Medtr8g089840' => 'mtr', 'MELO3C010319.2' => 'cme', 'MELO3C011944.2' => 'cme', 'MELO3C021589.2' => 'cme', 'Migut.E00207' => 'egut', 'Migut.H00067' => 'egut', 'Migut.K00433' => 'egut', 'Migut.K00606' => 'egut', 'Migut.K01410' => 'egut', 'MSTRG.13347' => 'ama', 'MSTRG.24045' => 'ama', 'MSTRG.2428' => 'ama', 'MSTRG.26410' => 'ama', 'MSTRG.3139' => 'ama', 'MSTRG.3286' => 'ama', 'MSTRG.563' => 'ama', 'MSTRG.7941' => 'ama', 'Nitab4.5_0000028g0060' => 'nta', 'Nitab4.5_0000065g0260' => 'nta', 'Nitab4.5_0000112g0060' => 'nta', 'Nitab4.5_0000489g0120' => 'nta', 'Nitab4.5_0001776g0050' => 'nta', 'Nitab4.5_0001854g0010' => 'nta', 'Nitab4.5_0001860g0020' => 'nta', 'Nitab4.5_0004352g0010' => 'nta', 'Nitab4.5_0008716g0020' => 'nta', 'Nitab4.5_0008922g0010' => 'nta', 'Nn3g16693' => 'nnu', 'Nn4g22596' => 'nnu', 'Nn7g37639' => 'nnu', 'Oeu001701.1' => 'oeu', 'Oeu018149.1' => 'oeu', 'Oeu026220.1' => 'oeu', 'Oeu038635.1' => 'oeu', 'Oeu049176.1' => 'oeu', 'Oeu056706.1' => 'oeu', 'Oeu056937.1' => 'oeu', 'Oeu057540.1' => 'oeu', 'Os02g0594900' => 'osa', 'Os02g0595100' => 'osa', 'Os04g0477500' => 'osa', 'Os12g0611900' => 'osa', 'Peaxi162Scf00076g00020' => 'pax', 'Peaxi162Scf00128g00217' => 'pax', 'Peaxi162Scf00129g01640' => 'pax', 'Peaxi162Scf00669g00007' => 'pax', 'Peaxi162Scf00700g00421' => 'pax', 'Peaxi162Scf00801g00038' => 'pax', 'Peaxi162Scf00891g00025' => 'pax', 'PGR083G0909' => 'pgr', 'PGR119G1005' => 'pgr', 'PGR142G2236' => 'pgr', 'PGR142G3388' => 'pgr', 'PGSC0003DMG400004514' => 'stu', 'PGSC0003DMG400012635' => 'stu', 'PGSC0003DMG400015730' => 'stu', 'PGSC0003DMG400018611' => 'stu', 'PGSC0003DMG400030897' => 'stu', 'Phvul.001G254800' => 'pvu', 'Phvul.002G260100' => 'pvu', 'Phvul.003G167600' => 'pvu', 'Phvul.004G005100' => 'pvu', 'Potri.001G343600' => 'ptr', 'Potri.006G066700' => 'ptr', 'Potri.008G186000' => 'ptr', 'Potri.010G046900' => 'ptr', 'Potri.018G127900' => 'ptr', 'Pp3c20_17750' => 'ppa', 'Pp3c24_4380' => 'ppa', 'Prupe.1G245800' => 'ppe', 'Prupe.3G293400' => 'ppe', 'Prupe.7G247400' => 'ppe', 'Psat0s145g0120' => 'psa', 'Psat0s595g0040' => 'psa', 'Psat0s595g0120' => 'psa', 'Psat3g175040' => 'psa', 'Psat7g058120' => 'psa', 'PSO017G0428' => 'pso', 'PSO063G7510' => 'pso', 'PSO067G0046' => 'pso', 'PSO478G1073' => 'pso', 'PSO675G3677' => 'pso', 'PSO675G6558' => 'pso', 'PSO675G7520' => 'pso', 'PSO675G8959' => 'pso', 'QL02p074089' => 'qlo', 'QL02p089614' => 'qlo', 'QL03p057736' => 'qlo', 'RcHm_v2.0_Chr1g0364131' => 'rch', 'RcHm_v2.0_Chr2g0087801' => 'rch', 'RcHm_v2.0_Chr2g0087821' => 'rch', 'RcHm_v2.0_Chr2g0173231' => 'rch', 'RcHm_v2.0_Chr4g0433111' => 'rch', 'Rhsim03G0250300' => 'rsi', 'Rhsim08G0048400' => 'rsi', 'Rhsim10G0014800' => 'rsi', 'Rhsim12G0040100' => 'rsi', 'Rhsim12G0109700' => 'rsi', 'Sabra06G0049600' => 'sbr', 'Sabra08G0141000' => 'sbr', 'Sabra10G0021400' => 'sbr', 'Sabra16G0222900' => 'sbr', 'Sabra18G0108600' => 'sbr', 'SalBow1G0433' => 'sbo', 'SalBow1G2038' => 'sbo', 'SalBow1G5003' => 'sbo', 'SalBow7G1197' => 'sbo', 'SalBow8G3506' => 'sbo', 'Sc03g0007300' => 'sci', 'Sc11g0000950' => 'sci', 'Sc14g0008750' => 'sci', 'Sc18g0000420' => 'sci', 'Sed0006754' => 'sed', 'Sed0008741' => 'sed', 'Sed0017172' => 'sed', 'Sed0018925' => 'sed', 'Sed0023326' => 'sed', 'Sed0025909' => 'sed', 'SEGI_05333' => 'sgi', 'SEGI_10362' => 'sgi', 'SEGI_13380' => 'sgi', 'SEGI_24306' => 'sgi', 'SEGI_29077' => 'sgi', 'SEGI_29095' => 'sgi', 'SEGI_36534' => 'sgi', 'SEGI_37506' => 'sgi', 'SEGI_38321' => 'sgi', 'SGA_v2.0_scaffold307G48031' => 'sas', 'SGA_v2.0_scaffold47G17507' => 'sas', 'SGA_v2.0_scaffold63G21736' => 'sas', 'SGA_v2.0_scaffold87G27070' => 'sas', 'SHI17794' => 'shi', 'SHI28851' => 'shi', 'SMO165G0155' => 'smo', 'SMO340G0217' => 'smo', 'SMO367G1210' => 'smo', 'Solyc02g093430.3' => 'sly', 'Solyc05g013580.4' => 'sly', 'Solyc07g008030.3' => 'sly', 'Solyc12g035470.2' => 'sly', 'Sopen02g038020' => 'spe', 'Sopen05g008490' => 'spe', 'Sopen07g003910' => 'spe', 'Sopen12g015240' => 'spe', 'Sp1g11550' => 'spa', 'Sp2g16710' => 'spa', 'Sp3g00430' => 'spa', 'Sp3g26780' => 'spa', 'Sp5g22900' => 'spa', 'Sp6g29530' => 'spa', 'TAR371G0794' => 'tar', 'TAR374G0164' => 'tar', 'TAR622G0165' => 'tar', 'TAR626G0929' => 'tar', 'TAR629G2155' => 'tar', 'THA.LOC104805282' => 'tha', 'THA.LOC104805363' => 'tha', 'THA.LOC104808968' => 'tha', 'THA.LOC104821093' => 'tha', 'THA.LOC104823953' => 'tha', 'THA.LOC104825562' => 'tha', 'THA.LOC104825665' => 'tha', 'Thecc.02G261400' => 'tca', 'Thecc.04G019200' => 'tca', 'Thecc.09G130400' => 'tca', 'Thhalv10004374m.g' => 'esa', 'Thhalv10007850m.g' => 'esa', 'Thhalv10013782m.g' => 'esa', 'Thhalv10018686m.g' => 'esa', 'Thhalv10020899m.g' => 'esa', 'Thhalv10022755m.g' => 'esa', 'TPR.G23851' => 'tpr', 'TPR.G26500' => 'tpr', 'TPR.G27267' => 'tpr', 'TPR.G32001' => 'tpr', 'TPR.G6251' => 'tpr', 'TPR.G8167' => 'tpr', 'TWI12G1330' => 'twi', 'TWI18G1239' => 'twi', 'TWI34G0979' => 'twi', 'TWI36G0670' => 'twi', 'TWI36G0707' => 'twi', 'TWI56G0233' => 'twi', 'TWI75G1809' => 'twi', 'unitig_21.g20874' => 'ugi', 'unitig_26.g10343' => 'ugi', 'unitig_46.g18392' => 'ugi', 'unitig_52.g17178' => 'ugi', 'unitig_8.g2934' => 'ugi', 'vmacro01122' => 'vma', 'vmacro05875' => 'vma', 'vmacro06147' => 'vma', 'vmacro16191' => 'vma', 'vmacro18293' => 'vma', 'VMungo0251G3707' => 'vmu', 'VMungo0464G1521' => 'vmu', 'VMungo1215G0205' => 'vmu', 'VMungo1383G2484' => 'vmu', 'Zm00001eb079610' => 'zma', 'Zm00001eb135990' => 'zma', 'Zm00001eb183710' => 'zma', 'Zm00001eb246020' => 'zma' ), 'gf_id' => 'HOM05D001124', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001124' ), 'data_identifier' => 'HOM05D001124', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001124', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '548', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02520' => 'bna', 'A03p06630' => 'bna', 'A05p44460' => 'bna', 'A06p08710' => 'bna', 'A06p41090' => 'bna', 'A07p32320' => 'bna', 'A08p32520' => 'bna', 'A09p10360' => 'bna', 'A10p24080' => 'bna', 'Aa31LG11G15250' => 'aar', 'Aa31LG1G1800' => 'aar', 'Aa31LG2G5120' => 'aar', 'Aa31LG2G6070' => 'aar', 'Aa31LG5G10770' => 'aar', 'Aa31sc61G90' => 'aar', 'Actinidia01352' => 'ach', 'Actinidia05983' => 'ach', 'Actinidia08133' => 'ach', 'Actinidia15101' => 'ach', 'Actinidia26379' => 'ach', 'Actinidia35778' => 'ach', 'Actinidia36123' => 'ach', 'Actinidia37436' => 'ach', 'Actinidia38730' => 'ach', 'Ah.02g128210' => 'amhyb', 'Ah.03g132990' => 'amhyb', 'Ah.14g079410' => 'amhyb', 'AL1G24640' => 'aly', 'AL2G26680' => 'aly', 'AL3G10530' => 'aly', 'AL3G45230' => 'aly', 'AL5G15230' => 'aly', 'AL5G16960' => 'aly', 'AL6G25210' => 'aly', 'Aqoxy2G00441' => 'aox', 'Aqoxy3G01236' => 'aox', 'Aqoxy5G03746' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3RQ047' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C7GMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9C8JER' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MBL6KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YXCZ83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZANX40' => 'arhy', 'AT1G12990' => 'ath', 'AT1G67880' => 'ath', 'AT2G13290' => 'ath', 'AT3G01620' => 'ath', 'AT3G26445' => 'ath', 'AT3G27540' => 'ath', 'AT5G14480' => 'ath', 'ATR0824G026' => 'atr', 'ATR1098G019' => 'atr', 'Atru.chr11.2145' => 'acertr', 'Atru.chr2.3636' => 'acertr', 'Atru.chr2.3644' => 'acertr', 'Atru.chr6.2422' => 'acertr', 'Atru.chr7.1112' => 'acertr', 'AUR62005469' => 'cqu', 'AUR62011166' => 'cqu', 'AUR62013319' => 'cqu', 'AUR62024273' => 'cqu', 'AUR62028420' => 'cqu', 'AUR62041942' => 'cqu', 'BcaB01g04969' => 'bca', 'BcaB01g06371' => 'bca', 'BcaB02g11494' => 'bca', 'BcaB03g15382' => 'bca', 'BcaB08g36994' => 'bca', 'BcaC03g13477' => 'bca', 'BcaC03g13478' => 'bca', 'BcaC03g13480' => 'bca', 'BcaC03g13481' => 'bca', 'BcaC03g13486' => 'bca', 'BcaC04g19031' => 'bca', 'BcaC04g23085' => 'bca', 'BcaC05g25094' => 'bca', 'BcaC05g25096' => 'bca', 'BcaC05g25138' => 'bca', 'BcaC05g30416' => 'bca', 'BcaC05g30455' => 'bca', 'BcaC06g30979' => 'bca', 'BcaC06g33805' => 'bca', 'BcaC08g46021' => 'bca', 'BcaNung03154' => 'bca', 'BolC2t06623H' => 'bol', 'BolC2t06632H' => 'bol', 'BolC2t06635H' => 'bol', 'BolC2t06638H' => 'bol', 'BolC3t13266H' => 'bol', 'BolC5t29776H' => 'bol', 'BolC6t38912H' => 'bol', 'BolC7t44183H' => 'bol', 'BolC9t54123H' => 'bol', 'BolC9t59107H' => 'bol', 'BraA02t05221Z' => 'bra', 'BraA03t09996Z' => 'bra', 'BraA05t23210Z' => 'bra', 'BraA06t24068Z' => 'bra', 'BraA06t27032Z' => 'bra', 'BraA08t35176Z' => 'bra', 'BraA09t36680Z' => 'bra', 'BraA10t44471Z' => 'bra', 'C02p06760' => 'bna', 'C02p06890' => 'bna', 'C02p07010' => 'bna', 'C03p07660' => 'bna', 'C05p10300' => 'bna', 'C06p38150' => 'bna', 'C07p36650' => 'bna', 'C08p15770' => 'bna', 'C09p12300' => 'bna', 'C09p62700' => 'bna', 'C09p75040' => 'bna', 'CAN.G13.1' => 'can', 'CAN.G138.4' => 'can', 'CAN.G44.6' => 'can', 'CAN.G473.19' => 'can', 'CANSAT01G0835' => 'cansat', 'CANSAT11G0246' => 'cansat', 'CANSAT11G1766' => 'cansat', 'CANSAT64G1954' => 'cansat', 'CARHR013330' => 'chi', 'CARHR060530' => 'chi', 'CARHR075300' => 'chi', 'CARHR105120' => 'chi', 'CARHR148910' => 'chi', 'CARHR198830' => 'chi', 'Carub.0001s1275' => 'cru', 'Carub.0002s1437' => 'cru', 'Carub.0003s0044' => 'cru', 'Carub.0003s2787' => 'cru', 'Carub.0005s0597' => 'cru', 'Carub.0006s1266' => 'cru', 'Ca_06935_v3' => 'car', 'Ca_13559_v3' => 'car', 'Ca_16941_v3' => 'car', 'Ca_16960_v3' => 'car', 'Ca_17775_v3' => 'car', 'Ca_30464_v3' => 'car', 'Cc06_g08160' => 'ccan', 'Cc07_g01520' => 'ccan', 'Cc11_g15810' => 'ccan', 'CDE02G2840' => 'cde', 'CDE03G0093' => 'cde', 'CDE04G2127' => 'cde', 'CDE07G1857' => 'cde', 'CDE09G1246' => 'cde', 'Cfa003412' => 'cfa', 'Cfa007341' => 'cfa', 'Cfa009220' => 'cfa', 'Ciclev10008737m.g' => 'ccl', 'Ciclev10015565m.g' => 'ccl', 'Ciclev10031761m.g' => 'ccl', 'CiPaw.03G045300' => 'cil', 'CiPaw.03G247200' => 'cil', 'CiPaw.04G029500' => 'cil', 'CiPaw.04G174000' => 'cil', 'CiPaw.05G181200' => 'cil', 'CiPaw.06G067100' => 'cil', 'ClCG05G025800' => 'cla', 'ClCG06G011400' => 'cla', 'ClCG09G019360' => 'cla', 'COL.COLO4_04827' => 'col', 'COL.COLO4_29170' => 'col', 'COL.COLO4_35131' => 'col', 'COL.COLO4_35132' => 'col', 'Cpa.g.sc33.32' => 'cpa', 'Cpa.g.sc46.29' => 'cpa', 'Cpa.g.sc796.1' => 'cpa', 'CsaV3_1G030420' => 'csa', 'CsaV3_5G027050' => 'csa', 'CsaV3_5G031040' => 'csa', 'CsaV3_UNG023130' => 'csa', 'CSS0007726' => 'camsi', 'CSS0016433' => 'camsi', 'CSS0017656' => 'camsi', 'CSS0025364' => 'camsi', 'CSS0027582' => 'camsi', 'CSS0047288' => 'camsi', 'CSS0049950' => 'camsi', 'DCAR_003843' => 'dca', 'DCAR_007052' => 'dca', 'DCAR_020884' => 'dca', 'DCAR_021730' => 'dca', 'DCAR_024423' => 'dca', 'DCAR_026509' => 'dca', 'DCAR_031158' => 'dca', 'Dinv14728' => 'din', 'Dinv15219' => 'din', 'Dinv25728' => 'din', 'Dinv33428' => 'din', 'Dinv36489' => 'din', 'Dinv41486' => 'din', 'Duzib147G0469' => 'dzi', 'Duzib168G0060' => 'dzi', 'Duzib187G1215' => 'dzi', 'Duzib248G0692' => 'dzi', 'Duzib251G0767' => 'dzi', 'Duzib264G0446' => 'dzi', 'Duzib268G0691' => 'dzi', 'ECA232G4767' => 'eca', 'ECA233G2838' => 'eca', 'ECA234G0391' => 'eca', 'ECA234G0857' => 'eca', 'ECA236G1593' => 'eca', 'ECA238G0565' => 'eca', 'ECA246G1027' => 'eca', 'ECA246G3223' => 'eca', 'ECA246G3470' => 'eca', 'EL10Ac6g13829' => 'bvu', 'EL10Ac6g14093' => 'bvu', 'EL10Ac8g18707' => 'bvu', 'Eucgr.C01369' => 'egr', 'Eucgr.H02492' => 'egr', 'Eucgr.I01733' => 'egr', 'Eucgr.J02255' => 'egr', 'Eucgr.J02257' => 'egr', 'Eucgr.J02258' => 'egr', 'FAN02G1601' => 'fan', 'FAN03G1586' => 'fan', 'FAN03G2986' => 'fan', 'FAN05G4837' => 'fan', 'FAN06G0146' => 'fan', 'FAN07G0858' => 'fan', 'FAN09G3179' => 'fan', 'FAN10G0669' => 'fan', 'FAN12G2358' => 'fan', 'FAN14G4198' => 'fan', 'FAN14G5112' => 'fan', 'FAN17G0342' => 'fan', 'FAN19G0342' => 'fan', 'FAN19G0962' => 'fan', 'FAN19G1101' => 'fan', 'FAN19G1872' => 'fan', 'FAN22G0356' => 'fan', 'FAN23G0744' => 'fan', 'FAN23G1914' => 'fan', 'FAN26G0032' => 'fan', 'FAN28G0625' => 'fan', 'FvH4_1g02710' => 'fve', 'FvH4_1g02720' => 'fve', 'FvH4_4g25670' => 'fve', 'FvH4_6g51700' => 'fve', 'FvH4_7g20170' => 'fve', 'Glyma.05G175000' => 'gma', 'Glyma.08G132300' => 'gma', 'Glyma.11G243000' => 'gma', 'Glyma.13G158900' => 'gma', 'Glyma.17G112400' => 'gma', 'Glyma.18G014100' => 'gma', 'Glyma.19G003100' => 'gma', 'Glyma.19G056500' => 'gma', 'Gohir.A01G158900' => 'ghi', 'Gohir.A05G312600' => 'ghi', 'Gohir.A05G354900' => 'ghi', 'Gohir.A07G037200' => 'ghi', 'Gohir.A09G030000' => 'ghi', 'Gohir.A12G145200' => 'ghi', 'Gohir.D01G151500' => 'ghi', 'Gohir.D04G058300' => 'ghi', 'Gohir.D05G314100' => 'ghi', 'Gohir.D07G041400' => 'ghi', 'Gohir.D09G029700' => 'ghi', 'Gohir.D12G149700' => 'ghi', 'Gorai.001G043800' => 'gra', 'Gorai.002G187800' => 'gra', 'Gorai.006G034700' => 'gra', 'Gorai.008G161200' => 'gra', 'Gorai.009G335700' => 'gra', 'Gorai.012G065000' => 'gra', 'GSVIVG01000535001' => 'vvi', 'GSVIVG01015572001' => 'vvi', 'GSVIVG01032386001' => 'vvi', 'HanXRQChr05g0138531' => 'han', 'HanXRQChr06g0174391' => 'han', 'HanXRQChr07g0199021' => 'han', 'HanXRQChr08g0208211' => 'han', 'HanXRQChr09g0255471' => 'han', 'HanXRQChr10g0315791' => 'han', 'HanXRQChr12g0371991' => 'han', 'HanXRQChr15g0475251' => 'han', 'HanXRQChr17g0540001' => 'han', 'HanXRQChr17g0548631' => 'han', 'HanXRQChr17g0569561' => 'han', 'Haze_12256' => 'cav', 'Haze_14756' => 'cav', 'Haze_25528' => 'cav', 'Hma1.2p1_0079F.1_g041020' => 'hma', 'Hma1.2p1_0818F.1_g223260' => 'hma', 'Hma1.2p1_1747F.1_g300530' => 'hma', 'HPP92_004607' => 'vpl', 'HPP92_004608' => 'vpl', 'HPP92_006181' => 'vpl', 'HPP92_012192' => 'vpl', 'HPP92_015680' => 'vpl', 'HPP92_020249' => 'vpl', 'HPP92_021376' => 'vpl', 'HPP92_024275' => 'vpl', 'Hund06031' => 'sun', 'Hund25391' => 'sun', 'Lalb_Chr07g0185371' => 'lal', 'Lalb_Chr07g0185381' => 'lal', 'Lalb_Chr12g0204011' => 'lal', 'Lalb_Chr13g0301671' => 'lal', 'Lalb_Chr14g0362851' => 'lal', 'Lalb_Chr24g0403581' => 'lal', 'Lj1g0000233' => 'lja', 'Lj2g0018120' => 'lja', 'Lj3C621T0' => 'lonja', 'Lj3P1059T14' => 'lonja', 'Lj3P611T9' => 'lonja', 'Lj3P614T13' => 'lonja', 'Lj3P615T5' => 'lonja', 'Lj4g0012315' => 'lja', 'Lj4g0026182' => 'lja', 'Lj6P813T16' => 'lonja', 'Lj7C427T7' => 'lonja', 'Lj7C427T8' => 'lonja', 'Lj7P600T41' => 'lonja', 'Lju41C42G17' => 'lonja', 'Lsat_1_v5_gn_0_47300' => 'lsa', 'Lsat_1_v5_gn_2_91280' => 'lsa', 'Lsat_1_v5_gn_3_30561' => 'lsa', 'Lsat_1_v5_gn_4_184321' => 'lsa', 'Lsat_1_v5_gn_4_4041' => 'lsa', 'Lsat_1_v5_gn_5_92000' => 'lsa', 'Lsat_1_v5_gn_8_152940' => 'lsa', 'Lsat_1_v5_gn_8_62401' => 'lsa', 'Manes.06G055900' => 'mes', 'Manes.12G022200' => 'mes', 'Manes.13G023300' => 'mes', 'Manes.14G115000' => 'mes', 'Manes.15G151700' => 'mes', 'Manes.17G111300' => 'mes', 'Mapoly0226s0009' => 'mpo', 'MBI02_g25363_MAGBIO' => 'mbi', 'MBI06_g00027_MAGBIO' => 'mbi', 'MBI10_g13034_MAGBIO' => 'mbi', 'MD09G1023400' => 'mdo', 'MD13G1100100' => 'mdo', 'MD15G1169200' => 'mdo', 'MD16G1101100' => 'mdo', 'MD17G1022900' => 'mdo', 'Medtr3g096150' => 'mtr', 'Medtr4g115070' => 'mtr', 'Medtr7g033325' => 'mtr', 'Medtr8g089840' => 'mtr', 'MELO3C010319.2' => 'cme', 'MELO3C011944.2' => 'cme', 'MELO3C021589.2' => 'cme', 'Migut.E00207' => 'egut', 'Migut.H00067' => 'egut', 'Migut.K00433' => 'egut', 'Migut.K00606' => 'egut', 'Migut.K01410' => 'egut', 'MSTRG.13347' => 'ama', 'MSTRG.24045' => 'ama', 'MSTRG.2428' => 'ama', 'MSTRG.26410' => 'ama', 'MSTRG.3139' => 'ama', 'MSTRG.3286' => 'ama', 'MSTRG.563' => 'ama', 'MSTRG.7941' => 'ama', 'Nitab4.5_0000028g0060' => 'nta', 'Nitab4.5_0000065g0260' => 'nta', 'Nitab4.5_0000112g0060' => 'nta', 'Nitab4.5_0000489g0120' => 'nta', 'Nitab4.5_0001776g0050' => 'nta', 'Nitab4.5_0001854g0010' => 'nta', 'Nitab4.5_0001860g0020' => 'nta', 'Nitab4.5_0004352g0010' => 'nta', 'Nitab4.5_0008716g0020' => 'nta', 'Nitab4.5_0008922g0010' => 'nta', 'Nn3g16693' => 'nnu', 'Nn4g22596' => 'nnu', 'Nn7g37639' => 'nnu', 'Oeu001701.1' => 'oeu', 'Oeu018149.1' => 'oeu', 'Oeu026220.1' => 'oeu', 'Oeu038635.1' => 'oeu', 'Oeu049176.1' => 'oeu', 'Oeu056706.1' => 'oeu', 'Oeu056937.1' => 'oeu', 'Oeu057540.1' => 'oeu', 'Os02g0594900' => 'osa', 'Os02g0595100' => 'osa', 'Os04g0477500' => 'osa', 'Os12g0611900' => 'osa', 'Peaxi162Scf00076g00020' => 'pax', 'Peaxi162Scf00128g00217' => 'pax', 'Peaxi162Scf00129g01640' => 'pax', 'Peaxi162Scf00669g00007' => 'pax', 'Peaxi162Scf00700g00421' => 'pax', 'Peaxi162Scf00801g00038' => 'pax', 'Peaxi162Scf00891g00025' => 'pax', 'PGR083G0909' => 'pgr', 'PGR119G1005' => 'pgr', 'PGR142G2236' => 'pgr', 'PGR142G3388' => 'pgr', 'PGSC0003DMG400004514' => 'stu', 'PGSC0003DMG400012635' => 'stu', 'PGSC0003DMG400015730' => 'stu', 'PGSC0003DMG400018611' => 'stu', 'PGSC0003DMG400030897' => 'stu', 'Phvul.001G254800' => 'pvu', 'Phvul.002G260100' => 'pvu', 'Phvul.003G167600' => 'pvu', 'Phvul.004G005100' => 'pvu', 'Potri.001G343600' => 'ptr', 'Potri.006G066700' => 'ptr', 'Potri.008G186000' => 'ptr', 'Potri.010G046900' => 'ptr', 'Potri.018G127900' => 'ptr', 'Pp3c20_17750' => 'ppa', 'Pp3c24_4380' => 'ppa', 'Prupe.1G245800' => 'ppe', 'Prupe.3G293400' => 'ppe', 'Prupe.7G247400' => 'ppe', 'Psat0s145g0120' => 'psa', 'Psat0s595g0040' => 'psa', 'Psat0s595g0120' => 'psa', 'Psat3g175040' => 'psa', 'Psat7g058120' => 'psa', 'PSO017G0428' => 'pso', 'PSO063G7510' => 'pso', 'PSO067G0046' => 'pso', 'PSO478G1073' => 'pso', 'PSO675G3677' => 'pso', 'PSO675G6558' => 'pso', 'PSO675G7520' => 'pso', 'PSO675G8959' => 'pso', 'QL02p074089' => 'qlo', 'QL02p089614' => 'qlo', 'QL03p057736' => 'qlo', 'RcHm_v2.0_Chr1g0364131' => 'rch', 'RcHm_v2.0_Chr2g0087801' => 'rch', 'RcHm_v2.0_Chr2g0087821' => 'rch', 'RcHm_v2.0_Chr2g0173231' => 'rch', 'RcHm_v2.0_Chr4g0433111' => 'rch', 'Rhsim03G0250300' => 'rsi', 'Rhsim08G0048400' => 'rsi', 'Rhsim10G0014800' => 'rsi', 'Rhsim12G0040100' => 'rsi', 'Rhsim12G0109700' => 'rsi', 'Sabra06G0049600' => 'sbr', 'Sabra08G0141000' => 'sbr', 'Sabra10G0021400' => 'sbr', 'Sabra16G0222900' => 'sbr', 'Sabra18G0108600' => 'sbr', 'SalBow1G0433' => 'sbo', 'SalBow1G2038' => 'sbo', 'SalBow1G5003' => 'sbo', 'SalBow7G1197' => 'sbo', 'SalBow8G3506' => 'sbo', 'Sc03g0007300' => 'sci', 'Sc11g0000950' => 'sci', 'Sc14g0008750' => 'sci', 'Sc18g0000420' => 'sci', 'Sed0006754' => 'sed', 'Sed0008741' => 'sed', 'Sed0017172' => 'sed', 'Sed0018925' => 'sed', 'Sed0023326' => 'sed', 'Sed0025909' => 'sed', 'SEGI_05333' => 'sgi', 'SEGI_10362' => 'sgi', 'SEGI_13380' => 'sgi', 'SEGI_24306' => 'sgi', 'SEGI_29077' => 'sgi', 'SEGI_29095' => 'sgi', 'SEGI_36534' => 'sgi', 'SEGI_37506' => 'sgi', 'SEGI_38321' => 'sgi', 'SGA_v2.0_scaffold307G48031' => 'sas', 'SGA_v2.0_scaffold47G17507' => 'sas', 'SGA_v2.0_scaffold63G21736' => 'sas', 'SGA_v2.0_scaffold87G27070' => 'sas', 'SHI17794' => 'shi', 'SHI28851' => 'shi', 'SMO165G0155' => 'smo', 'SMO340G0217' => 'smo', 'SMO367G1210' => 'smo', 'Solyc02g093430.3' => 'sly', 'Solyc05g013580.4' => 'sly', 'Solyc07g008030.3' => 'sly', 'Solyc12g035470.2' => 'sly', 'Sopen02g038020' => 'spe', 'Sopen05g008490' => 'spe', 'Sopen07g003910' => 'spe', 'Sopen12g015240' => 'spe', 'Sp1g11550' => 'spa', 'Sp2g16710' => 'spa', 'Sp3g00430' => 'spa', 'Sp3g26780' => 'spa', 'Sp5g22900' => 'spa', 'Sp6g29530' => 'spa', 'TAR371G0794' => 'tar', 'TAR374G0164' => 'tar', 'TAR622G0165' => 'tar', 'TAR626G0929' => 'tar', 'TAR629G2155' => 'tar', 'THA.LOC104805282' => 'tha', 'THA.LOC104805363' => 'tha', 'THA.LOC104808968' => 'tha', 'THA.LOC104821093' => 'tha', 'THA.LOC104823953' => 'tha', 'THA.LOC104825562' => 'tha', 'THA.LOC104825665' => 'tha', 'Thecc.02G261400' => 'tca', 'Thecc.04G019200' => 'tca', 'Thecc.09G130400' => 'tca', 'Thhalv10004374m.g' => 'esa', 'Thhalv10007850m.g' => 'esa', 'Thhalv10013782m.g' => 'esa', 'Thhalv10018686m.g' => 'esa', 'Thhalv10020899m.g' => 'esa', 'Thhalv10022755m.g' => 'esa', 'TPR.G23851' => 'tpr', 'TPR.G26500' => 'tpr', 'TPR.G27267' => 'tpr', 'TPR.G32001' => 'tpr', 'TPR.G6251' => 'tpr', 'TPR.G8167' => 'tpr', 'TWI12G1330' => 'twi', 'TWI18G1239' => 'twi', 'TWI34G0979' => 'twi', 'TWI36G0670' => 'twi', 'TWI36G0707' => 'twi', 'TWI56G0233' => 'twi', 'TWI75G1809' => 'twi', 'unitig_21.g20874' => 'ugi', 'unitig_26.g10343' => 'ugi', 'unitig_46.g18392' => 'ugi', 'unitig_52.g17178' => 'ugi', 'unitig_8.g2934' => 'ugi', 'vmacro01122' => 'vma', 'vmacro05875' => 'vma', 'vmacro06147' => 'vma', 'vmacro16191' => 'vma', 'vmacro18293' => 'vma', 'VMungo0251G3707' => 'vmu', 'VMungo0464G1521' => 'vmu', 'VMungo1215G0205' => 'vmu', 'VMungo1383G2484' => 'vmu', 'Zm00001eb079610' => 'zma', 'Zm00001eb135990' => 'zma', 'Zm00001eb183710' => 'zma', 'Zm00001eb246020' => 'zma' ) $gf_id = 'HOM05D001124' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001124' ) $data_identifier = 'HOM05D001124' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 6, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 7, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 21, 'bol' => (int) 10, 'bra' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 6, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 9, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 21, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 8, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 10, 'lsa' => (int) 8, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 8, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 9, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb246020' $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' => 'HOM05D001124', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '548', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02520' => 'bna', 'A03p06630' => 'bna', 'A05p44460' => 'bna', 'A06p08710' => 'bna', 'A06p41090' => 'bna', 'A07p32320' => 'bna', 'A08p32520' => 'bna', 'A09p10360' => 'bna', 'A10p24080' => 'bna', 'Aa31LG11G15250' => 'aar', 'Aa31LG1G1800' => 'aar', 'Aa31LG2G5120' => 'aar', 'Aa31LG2G6070' => 'aar', 'Aa31LG5G10770' => 'aar', 'Aa31sc61G90' => 'aar', 'Actinidia01352' => 'ach', 'Actinidia05983' => 'ach', 'Actinidia08133' => 'ach', 'Actinidia15101' => 'ach', 'Actinidia26379' => 'ach', 'Actinidia35778' => 'ach', 'Actinidia36123' => 'ach', 'Actinidia37436' => 'ach', 'Actinidia38730' => 'ach', 'Ah.02g128210' => 'amhyb', 'Ah.03g132990' => 'amhyb', 'Ah.14g079410' => 'amhyb', 'AL1G24640' => 'aly', 'AL2G26680' => 'aly', 'AL3G10530' => 'aly', 'AL3G45230' => 'aly', 'AL5G15230' => 'aly', 'AL5G16960' => 'aly', 'AL6G25210' => 'aly', 'Aqoxy2G00441' => 'aox', 'Aqoxy3G01236' => 'aox', 'Aqoxy5G03746' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3RQ047' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C7GMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9C8JER' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MBL6KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YXCZ83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZANX40' => 'arhy', 'AT1G12990' => 'ath', 'AT1G67880' => 'ath', 'AT2G13290' => 'ath', 'AT3G01620' => 'ath', 'AT3G26445' => 'ath', 'AT3G27540' => 'ath', 'AT5G14480' => 'ath', 'ATR0824G026' => 'atr', 'ATR1098G019' => 'atr', 'Atru.chr11.2145' => 'acertr', 'Atru.chr2.3636' => 'acertr', 'Atru.chr2.3644' => 'acertr', 'Atru.chr6.2422' => 'acertr', 'Atru.chr7.1112' => 'acertr', 'AUR62005469' => 'cqu', 'AUR62011166' => 'cqu', 'AUR62013319' => 'cqu', 'AUR62024273' => 'cqu', 'AUR62028420' => 'cqu', 'AUR62041942' => 'cqu', 'BcaB01g04969' => 'bca', 'BcaB01g06371' => 'bca', 'BcaB02g11494' => 'bca', 'BcaB03g15382' => 'bca', 'BcaB08g36994' => 'bca', 'BcaC03g13477' => 'bca', 'BcaC03g13478' => 'bca', 'BcaC03g13480' => 'bca', 'BcaC03g13481' => 'bca', 'BcaC03g13486' => 'bca', 'BcaC04g19031' => 'bca', 'BcaC04g23085' => 'bca', 'BcaC05g25094' => 'bca', 'BcaC05g25096' => 'bca', 'BcaC05g25138' => 'bca', 'BcaC05g30416' => 'bca', 'BcaC05g30455' => 'bca', 'BcaC06g30979' => 'bca', 'BcaC06g33805' => 'bca', 'BcaC08g46021' => 'bca', 'BcaNung03154' => 'bca', 'BolC2t06623H' => 'bol', 'BolC2t06632H' => 'bol', 'BolC2t06635H' => 'bol', 'BolC2t06638H' => 'bol', 'BolC3t13266H' => 'bol', 'BolC5t29776H' => 'bol', 'BolC6t38912H' => 'bol', 'BolC7t44183H' => 'bol', 'BolC9t54123H' => 'bol', 'BolC9t59107H' => 'bol', 'BraA02t05221Z' => 'bra', 'BraA03t09996Z' => 'bra', 'BraA05t23210Z' => 'bra', 'BraA06t24068Z' => 'bra', 'BraA06t27032Z' => 'bra', 'BraA08t35176Z' => 'bra', 'BraA09t36680Z' => 'bra', 'BraA10t44471Z' => 'bra', 'C02p06760' => 'bna', 'C02p06890' => 'bna', 'C02p07010' => 'bna', 'C03p07660' => 'bna', 'C05p10300' => 'bna', 'C06p38150' => 'bna', 'C07p36650' => 'bna', 'C08p15770' => 'bna', 'C09p12300' => 'bna', 'C09p62700' => 'bna', 'C09p75040' => 'bna', 'CAN.G13.1' => 'can', 'CAN.G138.4' => 'can', 'CAN.G44.6' => 'can', 'CAN.G473.19' => 'can', 'CANSAT01G0835' => 'cansat', 'CANSAT11G0246' => 'cansat', 'CANSAT11G1766' => 'cansat', 'CANSAT64G1954' => 'cansat', 'CARHR013330' => 'chi', 'CARHR060530' => 'chi', 'CARHR075300' => 'chi', 'CARHR105120' => 'chi', 'CARHR148910' => 'chi', 'CARHR198830' => 'chi', 'Carub.0001s1275' => 'cru', 'Carub.0002s1437' => 'cru', 'Carub.0003s0044' => 'cru', 'Carub.0003s2787' => 'cru', 'Carub.0005s0597' => 'cru', 'Carub.0006s1266' => 'cru', 'Ca_06935_v3' => 'car', 'Ca_13559_v3' => 'car', 'Ca_16941_v3' => 'car', 'Ca_16960_v3' => 'car', 'Ca_17775_v3' => 'car', 'Ca_30464_v3' => 'car', 'Cc06_g08160' => 'ccan', 'Cc07_g01520' => 'ccan', 'Cc11_g15810' => 'ccan', 'CDE02G2840' => 'cde', 'CDE03G0093' => 'cde', 'CDE04G2127' => 'cde', 'CDE07G1857' => 'cde', 'CDE09G1246' => 'cde', 'Cfa003412' => 'cfa', 'Cfa007341' => 'cfa', 'Cfa009220' => 'cfa', 'Ciclev10008737m.g' => 'ccl', 'Ciclev10015565m.g' => 'ccl', 'Ciclev10031761m.g' => 'ccl', 'CiPaw.03G045300' => 'cil', 'CiPaw.03G247200' => 'cil', 'CiPaw.04G029500' => 'cil', 'CiPaw.04G174000' => 'cil', 'CiPaw.05G181200' => 'cil', 'CiPaw.06G067100' => 'cil', 'ClCG05G025800' => 'cla', 'ClCG06G011400' => 'cla', 'ClCG09G019360' => 'cla', 'COL.COLO4_04827' => 'col', 'COL.COLO4_29170' => 'col', 'COL.COLO4_35131' => 'col', 'COL.COLO4_35132' => 'col', 'Cpa.g.sc33.32' => 'cpa', 'Cpa.g.sc46.29' => 'cpa', 'Cpa.g.sc796.1' => 'cpa', 'CsaV3_1G030420' => 'csa', 'CsaV3_5G027050' => 'csa', 'CsaV3_5G031040' => 'csa', 'CsaV3_UNG023130' => 'csa', 'CSS0007726' => 'camsi', 'CSS0016433' => 'camsi', 'CSS0017656' => 'camsi', 'CSS0025364' => 'camsi', 'CSS0027582' => 'camsi', 'CSS0047288' => 'camsi', 'CSS0049950' => 'camsi', 'DCAR_003843' => 'dca', 'DCAR_007052' => 'dca', 'DCAR_020884' => 'dca', 'DCAR_021730' => 'dca', 'DCAR_024423' => 'dca', 'DCAR_026509' => 'dca', 'DCAR_031158' => 'dca', 'Dinv14728' => 'din', 'Dinv15219' => 'din', 'Dinv25728' => 'din', 'Dinv33428' => 'din', 'Dinv36489' => 'din', 'Dinv41486' => 'din', 'Duzib147G0469' => 'dzi', 'Duzib168G0060' => 'dzi', 'Duzib187G1215' => 'dzi', 'Duzib248G0692' => 'dzi', 'Duzib251G0767' => 'dzi', 'Duzib264G0446' => 'dzi', 'Duzib268G0691' => 'dzi', 'ECA232G4767' => 'eca', 'ECA233G2838' => 'eca', 'ECA234G0391' => 'eca', 'ECA234G0857' => 'eca', 'ECA236G1593' => 'eca', 'ECA238G0565' => 'eca', 'ECA246G1027' => 'eca', 'ECA246G3223' => 'eca', 'ECA246G3470' => 'eca', 'EL10Ac6g13829' => 'bvu', 'EL10Ac6g14093' => 'bvu', 'EL10Ac8g18707' => 'bvu', 'Eucgr.C01369' => 'egr', 'Eucgr.H02492' => 'egr', 'Eucgr.I01733' => 'egr', 'Eucgr.J02255' => 'egr', 'Eucgr.J02257' => 'egr', 'Eucgr.J02258' => 'egr', 'FAN02G1601' => 'fan', 'FAN03G1586' => 'fan', 'FAN03G2986' => 'fan', 'FAN05G4837' => 'fan', 'FAN06G0146' => 'fan', 'FAN07G0858' => 'fan', 'FAN09G3179' => 'fan', 'FAN10G0669' => 'fan', 'FAN12G2358' => 'fan', 'FAN14G4198' => 'fan', 'FAN14G5112' => 'fan', 'FAN17G0342' => 'fan', 'FAN19G0342' => 'fan', 'FAN19G0962' => 'fan', 'FAN19G1101' => 'fan', 'FAN19G1872' => 'fan', 'FAN22G0356' => 'fan', 'FAN23G0744' => 'fan', 'FAN23G1914' => 'fan', 'FAN26G0032' => 'fan', 'FAN28G0625' => 'fan', 'FvH4_1g02710' => 'fve', 'FvH4_1g02720' => 'fve', 'FvH4_4g25670' => 'fve', 'FvH4_6g51700' => 'fve', 'FvH4_7g20170' => 'fve', 'Glyma.05G175000' => 'gma', 'Glyma.08G132300' => 'gma', 'Glyma.11G243000' => 'gma', 'Glyma.13G158900' => 'gma', 'Glyma.17G112400' => 'gma', 'Glyma.18G014100' => 'gma', 'Glyma.19G003100' => 'gma', 'Glyma.19G056500' => 'gma', 'Gohir.A01G158900' => 'ghi', 'Gohir.A05G312600' => 'ghi', 'Gohir.A05G354900' => 'ghi', 'Gohir.A07G037200' => 'ghi', 'Gohir.A09G030000' => 'ghi', 'Gohir.A12G145200' => 'ghi', 'Gohir.D01G151500' => 'ghi', 'Gohir.D04G058300' => 'ghi', 'Gohir.D05G314100' => 'ghi', 'Gohir.D07G041400' => 'ghi', 'Gohir.D09G029700' => 'ghi', 'Gohir.D12G149700' => 'ghi', 'Gorai.001G043800' => 'gra', 'Gorai.002G187800' => 'gra', 'Gorai.006G034700' => 'gra', 'Gorai.008G161200' => 'gra', 'Gorai.009G335700' => 'gra', 'Gorai.012G065000' => 'gra', 'GSVIVG01000535001' => 'vvi', 'GSVIVG01015572001' => 'vvi', 'GSVIVG01032386001' => 'vvi', 'HanXRQChr05g0138531' => 'han', 'HanXRQChr06g0174391' => 'han', 'HanXRQChr07g0199021' => 'han', 'HanXRQChr08g0208211' => 'han', 'HanXRQChr09g0255471' => 'han', 'HanXRQChr10g0315791' => 'han', 'HanXRQChr12g0371991' => 'han', 'HanXRQChr15g0475251' => 'han', 'HanXRQChr17g0540001' => 'han', 'HanXRQChr17g0548631' => 'han', 'HanXRQChr17g0569561' => 'han', 'Haze_12256' => 'cav', 'Haze_14756' => 'cav', 'Haze_25528' => 'cav', 'Hma1.2p1_0079F.1_g041020' => 'hma', 'Hma1.2p1_0818F.1_g223260' => 'hma', 'Hma1.2p1_1747F.1_g300530' => 'hma', 'HPP92_004607' => 'vpl', 'HPP92_004608' => 'vpl', 'HPP92_006181' => 'vpl', 'HPP92_012192' => 'vpl', 'HPP92_015680' => 'vpl', 'HPP92_020249' => 'vpl', 'HPP92_021376' => 'vpl', 'HPP92_024275' => 'vpl', 'Hund06031' => 'sun', 'Hund25391' => 'sun', 'Lalb_Chr07g0185371' => 'lal', 'Lalb_Chr07g0185381' => 'lal', 'Lalb_Chr12g0204011' => 'lal', 'Lalb_Chr13g0301671' => 'lal', 'Lalb_Chr14g0362851' => 'lal', 'Lalb_Chr24g0403581' => 'lal', 'Lj1g0000233' => 'lja', 'Lj2g0018120' => 'lja', 'Lj3C621T0' => 'lonja', 'Lj3P1059T14' => 'lonja', 'Lj3P611T9' => 'lonja', 'Lj3P614T13' => 'lonja', 'Lj3P615T5' => 'lonja', 'Lj4g0012315' => 'lja', 'Lj4g0026182' => 'lja', 'Lj6P813T16' => 'lonja', 'Lj7C427T7' => 'lonja', 'Lj7C427T8' => 'lonja', 'Lj7P600T41' => 'lonja', 'Lju41C42G17' => 'lonja', 'Lsat_1_v5_gn_0_47300' => 'lsa', 'Lsat_1_v5_gn_2_91280' => 'lsa', 'Lsat_1_v5_gn_3_30561' => 'lsa', 'Lsat_1_v5_gn_4_184321' => 'lsa', 'Lsat_1_v5_gn_4_4041' => 'lsa', 'Lsat_1_v5_gn_5_92000' => 'lsa', 'Lsat_1_v5_gn_8_152940' => 'lsa', 'Lsat_1_v5_gn_8_62401' => 'lsa', 'Manes.06G055900' => 'mes', 'Manes.12G022200' => 'mes', 'Manes.13G023300' => 'mes', 'Manes.14G115000' => 'mes', 'Manes.15G151700' => 'mes', 'Manes.17G111300' => 'mes', 'Mapoly0226s0009' => 'mpo', 'MBI02_g25363_MAGBIO' => 'mbi', 'MBI06_g00027_MAGBIO' => 'mbi', 'MBI10_g13034_MAGBIO' => 'mbi', 'MD09G1023400' => 'mdo', 'MD13G1100100' => 'mdo', 'MD15G1169200' => 'mdo', 'MD16G1101100' => 'mdo', 'MD17G1022900' => 'mdo', 'Medtr3g096150' => 'mtr', 'Medtr4g115070' => 'mtr', 'Medtr7g033325' => 'mtr', 'Medtr8g089840' => 'mtr', 'MELO3C010319.2' => 'cme', 'MELO3C011944.2' => 'cme', 'MELO3C021589.2' => 'cme', 'Migut.E00207' => 'egut', 'Migut.H00067' => 'egut', 'Migut.K00433' => 'egut', 'Migut.K00606' => 'egut', 'Migut.K01410' => 'egut', 'MSTRG.13347' => 'ama', 'MSTRG.24045' => 'ama', 'MSTRG.2428' => 'ama', 'MSTRG.26410' => 'ama', 'MSTRG.3139' => 'ama', 'MSTRG.3286' => 'ama', 'MSTRG.563' => 'ama', 'MSTRG.7941' => 'ama', 'Nitab4.5_0000028g0060' => 'nta', 'Nitab4.5_0000065g0260' => 'nta', 'Nitab4.5_0000112g0060' => 'nta', 'Nitab4.5_0000489g0120' => 'nta', 'Nitab4.5_0001776g0050' => 'nta', 'Nitab4.5_0001854g0010' => 'nta', 'Nitab4.5_0001860g0020' => 'nta', 'Nitab4.5_0004352g0010' => 'nta', 'Nitab4.5_0008716g0020' => 'nta', 'Nitab4.5_0008922g0010' => 'nta', 'Nn3g16693' => 'nnu', 'Nn4g22596' => 'nnu', 'Nn7g37639' => 'nnu', 'Oeu001701.1' => 'oeu', 'Oeu018149.1' => 'oeu', 'Oeu026220.1' => 'oeu', 'Oeu038635.1' => 'oeu', 'Oeu049176.1' => 'oeu', 'Oeu056706.1' => 'oeu', 'Oeu056937.1' => 'oeu', 'Oeu057540.1' => 'oeu', 'Os02g0594900' => 'osa', 'Os02g0595100' => 'osa', 'Os04g0477500' => 'osa', 'Os12g0611900' => 'osa', 'Peaxi162Scf00076g00020' => 'pax', 'Peaxi162Scf00128g00217' => 'pax', 'Peaxi162Scf00129g01640' => 'pax', 'Peaxi162Scf00669g00007' => 'pax', 'Peaxi162Scf00700g00421' => 'pax', 'Peaxi162Scf00801g00038' => 'pax', 'Peaxi162Scf00891g00025' => 'pax', 'PGR083G0909' => 'pgr', 'PGR119G1005' => 'pgr', 'PGR142G2236' => 'pgr', 'PGR142G3388' => 'pgr', 'PGSC0003DMG400004514' => 'stu', 'PGSC0003DMG400012635' => 'stu', 'PGSC0003DMG400015730' => 'stu', 'PGSC0003DMG400018611' => 'stu', 'PGSC0003DMG400030897' => 'stu', 'Phvul.001G254800' => 'pvu', 'Phvul.002G260100' => 'pvu', 'Phvul.003G167600' => 'pvu', 'Phvul.004G005100' => 'pvu', 'Potri.001G343600' => 'ptr', 'Potri.006G066700' => 'ptr', 'Potri.008G186000' => 'ptr', 'Potri.010G046900' => 'ptr', 'Potri.018G127900' => 'ptr', 'Pp3c20_17750' => 'ppa', 'Pp3c24_4380' => 'ppa', 'Prupe.1G245800' => 'ppe', 'Prupe.3G293400' => 'ppe', 'Prupe.7G247400' => 'ppe', 'Psat0s145g0120' => 'psa', 'Psat0s595g0040' => 'psa', 'Psat0s595g0120' => 'psa', 'Psat3g175040' => 'psa', 'Psat7g058120' => 'psa', 'PSO017G0428' => 'pso', 'PSO063G7510' => 'pso', 'PSO067G0046' => 'pso', 'PSO478G1073' => 'pso', 'PSO675G3677' => 'pso', 'PSO675G6558' => 'pso', 'PSO675G7520' => 'pso', 'PSO675G8959' => 'pso', 'QL02p074089' => 'qlo', 'QL02p089614' => 'qlo', 'QL03p057736' => 'qlo', 'RcHm_v2.0_Chr1g0364131' => 'rch', 'RcHm_v2.0_Chr2g0087801' => 'rch', 'RcHm_v2.0_Chr2g0087821' => 'rch', 'RcHm_v2.0_Chr2g0173231' => 'rch', 'RcHm_v2.0_Chr4g0433111' => 'rch', 'Rhsim03G0250300' => 'rsi', 'Rhsim08G0048400' => 'rsi', 'Rhsim10G0014800' => 'rsi', 'Rhsim12G0040100' => 'rsi', 'Rhsim12G0109700' => 'rsi', 'Sabra06G0049600' => 'sbr', 'Sabra08G0141000' => 'sbr', 'Sabra10G0021400' => 'sbr', 'Sabra16G0222900' => 'sbr', 'Sabra18G0108600' => 'sbr', 'SalBow1G0433' => 'sbo', 'SalBow1G2038' => 'sbo', 'SalBow1G5003' => 'sbo', 'SalBow7G1197' => 'sbo', 'SalBow8G3506' => 'sbo', 'Sc03g0007300' => 'sci', 'Sc11g0000950' => 'sci', 'Sc14g0008750' => 'sci', 'Sc18g0000420' => 'sci', 'Sed0006754' => 'sed', 'Sed0008741' => 'sed', 'Sed0017172' => 'sed', 'Sed0018925' => 'sed', 'Sed0023326' => 'sed', 'Sed0025909' => 'sed', 'SEGI_05333' => 'sgi', 'SEGI_10362' => 'sgi', 'SEGI_13380' => 'sgi', 'SEGI_24306' => 'sgi', 'SEGI_29077' => 'sgi', 'SEGI_29095' => 'sgi', 'SEGI_36534' => 'sgi', 'SEGI_37506' => 'sgi', 'SEGI_38321' => 'sgi', 'SGA_v2.0_scaffold307G48031' => 'sas', 'SGA_v2.0_scaffold47G17507' => 'sas', 'SGA_v2.0_scaffold63G21736' => 'sas', 'SGA_v2.0_scaffold87G27070' => 'sas', 'SHI17794' => 'shi', 'SHI28851' => 'shi', 'SMO165G0155' => 'smo', 'SMO340G0217' => 'smo', 'SMO367G1210' => 'smo', 'Solyc02g093430.3' => 'sly', 'Solyc05g013580.4' => 'sly', 'Solyc07g008030.3' => 'sly', 'Solyc12g035470.2' => 'sly', 'Sopen02g038020' => 'spe', 'Sopen05g008490' => 'spe', 'Sopen07g003910' => 'spe', 'Sopen12g015240' => 'spe', 'Sp1g11550' => 'spa', 'Sp2g16710' => 'spa', 'Sp3g00430' => 'spa', 'Sp3g26780' => 'spa', 'Sp5g22900' => 'spa', 'Sp6g29530' => 'spa', 'TAR371G0794' => 'tar', 'TAR374G0164' => 'tar', 'TAR622G0165' => 'tar', 'TAR626G0929' => 'tar', 'TAR629G2155' => 'tar', 'THA.LOC104805282' => 'tha', 'THA.LOC104805363' => 'tha', 'THA.LOC104808968' => 'tha', 'THA.LOC104821093' => 'tha', 'THA.LOC104823953' => 'tha', 'THA.LOC104825562' => 'tha', 'THA.LOC104825665' => 'tha', 'Thecc.02G261400' => 'tca', 'Thecc.04G019200' => 'tca', 'Thecc.09G130400' => 'tca', 'Thhalv10004374m.g' => 'esa', 'Thhalv10007850m.g' => 'esa', 'Thhalv10013782m.g' => 'esa', 'Thhalv10018686m.g' => 'esa', 'Thhalv10020899m.g' => 'esa', 'Thhalv10022755m.g' => 'esa', 'TPR.G23851' => 'tpr', 'TPR.G26500' => 'tpr', 'TPR.G27267' => 'tpr', 'TPR.G32001' => 'tpr', 'TPR.G6251' => 'tpr', 'TPR.G8167' => 'tpr', 'TWI12G1330' => 'twi', 'TWI18G1239' => 'twi', 'TWI34G0979' => 'twi', 'TWI36G0670' => 'twi', 'TWI36G0707' => 'twi', 'TWI56G0233' => 'twi', 'TWI75G1809' => 'twi', 'unitig_21.g20874' => 'ugi', 'unitig_26.g10343' => 'ugi', 'unitig_46.g18392' => 'ugi', 'unitig_52.g17178' => 'ugi', 'unitig_8.g2934' => 'ugi', 'vmacro01122' => 'vma', 'vmacro05875' => 'vma', 'vmacro06147' => 'vma', 'vmacro16191' => 'vma', 'vmacro18293' => 'vma', 'VMungo0251G3707' => 'vmu', 'VMungo0464G1521' => 'vmu', 'VMungo1215G0205' => 'vmu', 'VMungo1383G2484' => 'vmu', 'Zm00001eb079610' => 'zma', 'Zm00001eb135990' => 'zma', 'Zm00001eb183710' => 'zma', 'Zm00001eb246020' => 'zma' ), 'gf_id' => 'HOM05D001124', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001124' ), 'data_identifier' => 'HOM05D001124', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001124', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '548', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02520' => 'bna', 'A03p06630' => 'bna', 'A05p44460' => 'bna', 'A06p08710' => 'bna', 'A06p41090' => 'bna', 'A07p32320' => 'bna', 'A08p32520' => 'bna', 'A09p10360' => 'bna', 'A10p24080' => 'bna', 'Aa31LG11G15250' => 'aar', 'Aa31LG1G1800' => 'aar', 'Aa31LG2G5120' => 'aar', 'Aa31LG2G6070' => 'aar', 'Aa31LG5G10770' => 'aar', 'Aa31sc61G90' => 'aar', 'Actinidia01352' => 'ach', 'Actinidia05983' => 'ach', 'Actinidia08133' => 'ach', 'Actinidia15101' => 'ach', 'Actinidia26379' => 'ach', 'Actinidia35778' => 'ach', 'Actinidia36123' => 'ach', 'Actinidia37436' => 'ach', 'Actinidia38730' => 'ach', 'Ah.02g128210' => 'amhyb', 'Ah.03g132990' => 'amhyb', 'Ah.14g079410' => 'amhyb', 'AL1G24640' => 'aly', 'AL2G26680' => 'aly', 'AL3G10530' => 'aly', 'AL3G45230' => 'aly', 'AL5G15230' => 'aly', 'AL5G16960' => 'aly', 'AL6G25210' => 'aly', 'Aqoxy2G00441' => 'aox', 'Aqoxy3G01236' => 'aox', 'Aqoxy5G03746' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3RQ047' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C7GMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9C8JER' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MBL6KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YXCZ83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZANX40' => 'arhy', 'AT1G12990' => 'ath', 'AT1G67880' => 'ath', 'AT2G13290' => 'ath', 'AT3G01620' => 'ath', 'AT3G26445' => 'ath', 'AT3G27540' => 'ath', 'AT5G14480' => 'ath', 'ATR0824G026' => 'atr', 'ATR1098G019' => 'atr', 'Atru.chr11.2145' => 'acertr', 'Atru.chr2.3636' => 'acertr', 'Atru.chr2.3644' => 'acertr', 'Atru.chr6.2422' => 'acertr', 'Atru.chr7.1112' => 'acertr', 'AUR62005469' => 'cqu', 'AUR62011166' => 'cqu', 'AUR62013319' => 'cqu', 'AUR62024273' => 'cqu', 'AUR62028420' => 'cqu', 'AUR62041942' => 'cqu', 'BcaB01g04969' => 'bca', 'BcaB01g06371' => 'bca', 'BcaB02g11494' => 'bca', 'BcaB03g15382' => 'bca', 'BcaB08g36994' => 'bca', 'BcaC03g13477' => 'bca', 'BcaC03g13478' => 'bca', 'BcaC03g13480' => 'bca', 'BcaC03g13481' => 'bca', 'BcaC03g13486' => 'bca', 'BcaC04g19031' => 'bca', 'BcaC04g23085' => 'bca', 'BcaC05g25094' => 'bca', 'BcaC05g25096' => 'bca', 'BcaC05g25138' => 'bca', 'BcaC05g30416' => 'bca', 'BcaC05g30455' => 'bca', 'BcaC06g30979' => 'bca', 'BcaC06g33805' => 'bca', 'BcaC08g46021' => 'bca', 'BcaNung03154' => 'bca', 'BolC2t06623H' => 'bol', 'BolC2t06632H' => 'bol', 'BolC2t06635H' => 'bol', 'BolC2t06638H' => 'bol', 'BolC3t13266H' => 'bol', 'BolC5t29776H' => 'bol', 'BolC6t38912H' => 'bol', 'BolC7t44183H' => 'bol', 'BolC9t54123H' => 'bol', 'BolC9t59107H' => 'bol', 'BraA02t05221Z' => 'bra', 'BraA03t09996Z' => 'bra', 'BraA05t23210Z' => 'bra', 'BraA06t24068Z' => 'bra', 'BraA06t27032Z' => 'bra', 'BraA08t35176Z' => 'bra', 'BraA09t36680Z' => 'bra', 'BraA10t44471Z' => 'bra', 'C02p06760' => 'bna', 'C02p06890' => 'bna', 'C02p07010' => 'bna', 'C03p07660' => 'bna', 'C05p10300' => 'bna', 'C06p38150' => 'bna', 'C07p36650' => 'bna', 'C08p15770' => 'bna', 'C09p12300' => 'bna', 'C09p62700' => 'bna', 'C09p75040' => 'bna', 'CAN.G13.1' => 'can', 'CAN.G138.4' => 'can', 'CAN.G44.6' => 'can', 'CAN.G473.19' => 'can', 'CANSAT01G0835' => 'cansat', 'CANSAT11G0246' => 'cansat', 'CANSAT11G1766' => 'cansat', 'CANSAT64G1954' => 'cansat', 'CARHR013330' => 'chi', 'CARHR060530' => 'chi', 'CARHR075300' => 'chi', 'CARHR105120' => 'chi', 'CARHR148910' => 'chi', 'CARHR198830' => 'chi', 'Carub.0001s1275' => 'cru', 'Carub.0002s1437' => 'cru', 'Carub.0003s0044' => 'cru', 'Carub.0003s2787' => 'cru', 'Carub.0005s0597' => 'cru', 'Carub.0006s1266' => 'cru', 'Ca_06935_v3' => 'car', 'Ca_13559_v3' => 'car', 'Ca_16941_v3' => 'car', 'Ca_16960_v3' => 'car', 'Ca_17775_v3' => 'car', 'Ca_30464_v3' => 'car', 'Cc06_g08160' => 'ccan', 'Cc07_g01520' => 'ccan', 'Cc11_g15810' => 'ccan', 'CDE02G2840' => 'cde', 'CDE03G0093' => 'cde', 'CDE04G2127' => 'cde', 'CDE07G1857' => 'cde', 'CDE09G1246' => 'cde', 'Cfa003412' => 'cfa', 'Cfa007341' => 'cfa', 'Cfa009220' => 'cfa', 'Ciclev10008737m.g' => 'ccl', 'Ciclev10015565m.g' => 'ccl', 'Ciclev10031761m.g' => 'ccl', 'CiPaw.03G045300' => 'cil', 'CiPaw.03G247200' => 'cil', 'CiPaw.04G029500' => 'cil', 'CiPaw.04G174000' => 'cil', 'CiPaw.05G181200' => 'cil', 'CiPaw.06G067100' => 'cil', 'ClCG05G025800' => 'cla', 'ClCG06G011400' => 'cla', 'ClCG09G019360' => 'cla', 'COL.COLO4_04827' => 'col', 'COL.COLO4_29170' => 'col', 'COL.COLO4_35131' => 'col', 'COL.COLO4_35132' => 'col', 'Cpa.g.sc33.32' => 'cpa', 'Cpa.g.sc46.29' => 'cpa', 'Cpa.g.sc796.1' => 'cpa', 'CsaV3_1G030420' => 'csa', 'CsaV3_5G027050' => 'csa', 'CsaV3_5G031040' => 'csa', 'CsaV3_UNG023130' => 'csa', 'CSS0007726' => 'camsi', 'CSS0016433' => 'camsi', 'CSS0017656' => 'camsi', 'CSS0025364' => 'camsi', 'CSS0027582' => 'camsi', 'CSS0047288' => 'camsi', 'CSS0049950' => 'camsi', 'DCAR_003843' => 'dca', 'DCAR_007052' => 'dca', 'DCAR_020884' => 'dca', 'DCAR_021730' => 'dca', 'DCAR_024423' => 'dca', 'DCAR_026509' => 'dca', 'DCAR_031158' => 'dca', 'Dinv14728' => 'din', 'Dinv15219' => 'din', 'Dinv25728' => 'din', 'Dinv33428' => 'din', 'Dinv36489' => 'din', 'Dinv41486' => 'din', 'Duzib147G0469' => 'dzi', 'Duzib168G0060' => 'dzi', 'Duzib187G1215' => 'dzi', 'Duzib248G0692' => 'dzi', 'Duzib251G0767' => 'dzi', 'Duzib264G0446' => 'dzi', 'Duzib268G0691' => 'dzi', 'ECA232G4767' => 'eca', 'ECA233G2838' => 'eca', 'ECA234G0391' => 'eca', 'ECA234G0857' => 'eca', 'ECA236G1593' => 'eca', 'ECA238G0565' => 'eca', 'ECA246G1027' => 'eca', 'ECA246G3223' => 'eca', 'ECA246G3470' => 'eca', 'EL10Ac6g13829' => 'bvu', 'EL10Ac6g14093' => 'bvu', 'EL10Ac8g18707' => 'bvu', 'Eucgr.C01369' => 'egr', 'Eucgr.H02492' => 'egr', 'Eucgr.I01733' => 'egr', 'Eucgr.J02255' => 'egr', 'Eucgr.J02257' => 'egr', 'Eucgr.J02258' => 'egr', 'FAN02G1601' => 'fan', 'FAN03G1586' => 'fan', 'FAN03G2986' => 'fan', 'FAN05G4837' => 'fan', 'FAN06G0146' => 'fan', 'FAN07G0858' => 'fan', 'FAN09G3179' => 'fan', 'FAN10G0669' => 'fan', 'FAN12G2358' => 'fan', 'FAN14G4198' => 'fan', 'FAN14G5112' => 'fan', 'FAN17G0342' => 'fan', 'FAN19G0342' => 'fan', 'FAN19G0962' => 'fan', 'FAN19G1101' => 'fan', 'FAN19G1872' => 'fan', 'FAN22G0356' => 'fan', 'FAN23G0744' => 'fan', 'FAN23G1914' => 'fan', 'FAN26G0032' => 'fan', 'FAN28G0625' => 'fan', 'FvH4_1g02710' => 'fve', 'FvH4_1g02720' => 'fve', 'FvH4_4g25670' => 'fve', 'FvH4_6g51700' => 'fve', 'FvH4_7g20170' => 'fve', 'Glyma.05G175000' => 'gma', 'Glyma.08G132300' => 'gma', 'Glyma.11G243000' => 'gma', 'Glyma.13G158900' => 'gma', 'Glyma.17G112400' => 'gma', 'Glyma.18G014100' => 'gma', 'Glyma.19G003100' => 'gma', 'Glyma.19G056500' => 'gma', 'Gohir.A01G158900' => 'ghi', 'Gohir.A05G312600' => 'ghi', 'Gohir.A05G354900' => 'ghi', 'Gohir.A07G037200' => 'ghi', 'Gohir.A09G030000' => 'ghi', 'Gohir.A12G145200' => 'ghi', 'Gohir.D01G151500' => 'ghi', 'Gohir.D04G058300' => 'ghi', 'Gohir.D05G314100' => 'ghi', 'Gohir.D07G041400' => 'ghi', 'Gohir.D09G029700' => 'ghi', 'Gohir.D12G149700' => 'ghi', 'Gorai.001G043800' => 'gra', 'Gorai.002G187800' => 'gra', 'Gorai.006G034700' => 'gra', 'Gorai.008G161200' => 'gra', 'Gorai.009G335700' => 'gra', 'Gorai.012G065000' => 'gra', 'GSVIVG01000535001' => 'vvi', 'GSVIVG01015572001' => 'vvi', 'GSVIVG01032386001' => 'vvi', 'HanXRQChr05g0138531' => 'han', 'HanXRQChr06g0174391' => 'han', 'HanXRQChr07g0199021' => 'han', 'HanXRQChr08g0208211' => 'han', 'HanXRQChr09g0255471' => 'han', 'HanXRQChr10g0315791' => 'han', 'HanXRQChr12g0371991' => 'han', 'HanXRQChr15g0475251' => 'han', 'HanXRQChr17g0540001' => 'han', 'HanXRQChr17g0548631' => 'han', 'HanXRQChr17g0569561' => 'han', 'Haze_12256' => 'cav', 'Haze_14756' => 'cav', 'Haze_25528' => 'cav', 'Hma1.2p1_0079F.1_g041020' => 'hma', 'Hma1.2p1_0818F.1_g223260' => 'hma', 'Hma1.2p1_1747F.1_g300530' => 'hma', 'HPP92_004607' => 'vpl', 'HPP92_004608' => 'vpl', 'HPP92_006181' => 'vpl', 'HPP92_012192' => 'vpl', 'HPP92_015680' => 'vpl', 'HPP92_020249' => 'vpl', 'HPP92_021376' => 'vpl', 'HPP92_024275' => 'vpl', 'Hund06031' => 'sun', 'Hund25391' => 'sun', 'Lalb_Chr07g0185371' => 'lal', 'Lalb_Chr07g0185381' => 'lal', 'Lalb_Chr12g0204011' => 'lal', 'Lalb_Chr13g0301671' => 'lal', 'Lalb_Chr14g0362851' => 'lal', 'Lalb_Chr24g0403581' => 'lal', 'Lj1g0000233' => 'lja', 'Lj2g0018120' => 'lja', 'Lj3C621T0' => 'lonja', 'Lj3P1059T14' => 'lonja', 'Lj3P611T9' => 'lonja', 'Lj3P614T13' => 'lonja', 'Lj3P615T5' => 'lonja', 'Lj4g0012315' => 'lja', 'Lj4g0026182' => 'lja', 'Lj6P813T16' => 'lonja', 'Lj7C427T7' => 'lonja', 'Lj7C427T8' => 'lonja', 'Lj7P600T41' => 'lonja', 'Lju41C42G17' => 'lonja', 'Lsat_1_v5_gn_0_47300' => 'lsa', 'Lsat_1_v5_gn_2_91280' => 'lsa', 'Lsat_1_v5_gn_3_30561' => 'lsa', 'Lsat_1_v5_gn_4_184321' => 'lsa', 'Lsat_1_v5_gn_4_4041' => 'lsa', 'Lsat_1_v5_gn_5_92000' => 'lsa', 'Lsat_1_v5_gn_8_152940' => 'lsa', 'Lsat_1_v5_gn_8_62401' => 'lsa', 'Manes.06G055900' => 'mes', 'Manes.12G022200' => 'mes', 'Manes.13G023300' => 'mes', 'Manes.14G115000' => 'mes', 'Manes.15G151700' => 'mes', 'Manes.17G111300' => 'mes', 'Mapoly0226s0009' => 'mpo', 'MBI02_g25363_MAGBIO' => 'mbi', 'MBI06_g00027_MAGBIO' => 'mbi', 'MBI10_g13034_MAGBIO' => 'mbi', 'MD09G1023400' => 'mdo', 'MD13G1100100' => 'mdo', 'MD15G1169200' => 'mdo', 'MD16G1101100' => 'mdo', 'MD17G1022900' => 'mdo', 'Medtr3g096150' => 'mtr', 'Medtr4g115070' => 'mtr', 'Medtr7g033325' => 'mtr', 'Medtr8g089840' => 'mtr', 'MELO3C010319.2' => 'cme', 'MELO3C011944.2' => 'cme', 'MELO3C021589.2' => 'cme', 'Migut.E00207' => 'egut', 'Migut.H00067' => 'egut', 'Migut.K00433' => 'egut', 'Migut.K00606' => 'egut', 'Migut.K01410' => 'egut', 'MSTRG.13347' => 'ama', 'MSTRG.24045' => 'ama', 'MSTRG.2428' => 'ama', 'MSTRG.26410' => 'ama', 'MSTRG.3139' => 'ama', 'MSTRG.3286' => 'ama', 'MSTRG.563' => 'ama', 'MSTRG.7941' => 'ama', 'Nitab4.5_0000028g0060' => 'nta', 'Nitab4.5_0000065g0260' => 'nta', 'Nitab4.5_0000112g0060' => 'nta', 'Nitab4.5_0000489g0120' => 'nta', 'Nitab4.5_0001776g0050' => 'nta', 'Nitab4.5_0001854g0010' => 'nta', 'Nitab4.5_0001860g0020' => 'nta', 'Nitab4.5_0004352g0010' => 'nta', 'Nitab4.5_0008716g0020' => 'nta', 'Nitab4.5_0008922g0010' => 'nta', 'Nn3g16693' => 'nnu', 'Nn4g22596' => 'nnu', 'Nn7g37639' => 'nnu', 'Oeu001701.1' => 'oeu', 'Oeu018149.1' => 'oeu', 'Oeu026220.1' => 'oeu', 'Oeu038635.1' => 'oeu', 'Oeu049176.1' => 'oeu', 'Oeu056706.1' => 'oeu', 'Oeu056937.1' => 'oeu', 'Oeu057540.1' => 'oeu', 'Os02g0594900' => 'osa', 'Os02g0595100' => 'osa', 'Os04g0477500' => 'osa', 'Os12g0611900' => 'osa', 'Peaxi162Scf00076g00020' => 'pax', 'Peaxi162Scf00128g00217' => 'pax', 'Peaxi162Scf00129g01640' => 'pax', 'Peaxi162Scf00669g00007' => 'pax', 'Peaxi162Scf00700g00421' => 'pax', 'Peaxi162Scf00801g00038' => 'pax', 'Peaxi162Scf00891g00025' => 'pax', 'PGR083G0909' => 'pgr', 'PGR119G1005' => 'pgr', 'PGR142G2236' => 'pgr', 'PGR142G3388' => 'pgr', 'PGSC0003DMG400004514' => 'stu', 'PGSC0003DMG400012635' => 'stu', 'PGSC0003DMG400015730' => 'stu', 'PGSC0003DMG400018611' => 'stu', 'PGSC0003DMG400030897' => 'stu', 'Phvul.001G254800' => 'pvu', 'Phvul.002G260100' => 'pvu', 'Phvul.003G167600' => 'pvu', 'Phvul.004G005100' => 'pvu', 'Potri.001G343600' => 'ptr', 'Potri.006G066700' => 'ptr', 'Potri.008G186000' => 'ptr', 'Potri.010G046900' => 'ptr', 'Potri.018G127900' => 'ptr', 'Pp3c20_17750' => 'ppa', 'Pp3c24_4380' => 'ppa', 'Prupe.1G245800' => 'ppe', 'Prupe.3G293400' => 'ppe', 'Prupe.7G247400' => 'ppe', 'Psat0s145g0120' => 'psa', 'Psat0s595g0040' => 'psa', 'Psat0s595g0120' => 'psa', 'Psat3g175040' => 'psa', 'Psat7g058120' => 'psa', 'PSO017G0428' => 'pso', 'PSO063G7510' => 'pso', 'PSO067G0046' => 'pso', 'PSO478G1073' => 'pso', 'PSO675G3677' => 'pso', 'PSO675G6558' => 'pso', 'PSO675G7520' => 'pso', 'PSO675G8959' => 'pso', 'QL02p074089' => 'qlo', 'QL02p089614' => 'qlo', 'QL03p057736' => 'qlo', 'RcHm_v2.0_Chr1g0364131' => 'rch', 'RcHm_v2.0_Chr2g0087801' => 'rch', 'RcHm_v2.0_Chr2g0087821' => 'rch', 'RcHm_v2.0_Chr2g0173231' => 'rch', 'RcHm_v2.0_Chr4g0433111' => 'rch', 'Rhsim03G0250300' => 'rsi', 'Rhsim08G0048400' => 'rsi', 'Rhsim10G0014800' => 'rsi', 'Rhsim12G0040100' => 'rsi', 'Rhsim12G0109700' => 'rsi', 'Sabra06G0049600' => 'sbr', 'Sabra08G0141000' => 'sbr', 'Sabra10G0021400' => 'sbr', 'Sabra16G0222900' => 'sbr', 'Sabra18G0108600' => 'sbr', 'SalBow1G0433' => 'sbo', 'SalBow1G2038' => 'sbo', 'SalBow1G5003' => 'sbo', 'SalBow7G1197' => 'sbo', 'SalBow8G3506' => 'sbo', 'Sc03g0007300' => 'sci', 'Sc11g0000950' => 'sci', 'Sc14g0008750' => 'sci', 'Sc18g0000420' => 'sci', 'Sed0006754' => 'sed', 'Sed0008741' => 'sed', 'Sed0017172' => 'sed', 'Sed0018925' => 'sed', 'Sed0023326' => 'sed', 'Sed0025909' => 'sed', 'SEGI_05333' => 'sgi', 'SEGI_10362' => 'sgi', 'SEGI_13380' => 'sgi', 'SEGI_24306' => 'sgi', 'SEGI_29077' => 'sgi', 'SEGI_29095' => 'sgi', 'SEGI_36534' => 'sgi', 'SEGI_37506' => 'sgi', 'SEGI_38321' => 'sgi', 'SGA_v2.0_scaffold307G48031' => 'sas', 'SGA_v2.0_scaffold47G17507' => 'sas', 'SGA_v2.0_scaffold63G21736' => 'sas', 'SGA_v2.0_scaffold87G27070' => 'sas', 'SHI17794' => 'shi', 'SHI28851' => 'shi', 'SMO165G0155' => 'smo', 'SMO340G0217' => 'smo', 'SMO367G1210' => 'smo', 'Solyc02g093430.3' => 'sly', 'Solyc05g013580.4' => 'sly', 'Solyc07g008030.3' => 'sly', 'Solyc12g035470.2' => 'sly', 'Sopen02g038020' => 'spe', 'Sopen05g008490' => 'spe', 'Sopen07g003910' => 'spe', 'Sopen12g015240' => 'spe', 'Sp1g11550' => 'spa', 'Sp2g16710' => 'spa', 'Sp3g00430' => 'spa', 'Sp3g26780' => 'spa', 'Sp5g22900' => 'spa', 'Sp6g29530' => 'spa', 'TAR371G0794' => 'tar', 'TAR374G0164' => 'tar', 'TAR622G0165' => 'tar', 'TAR626G0929' => 'tar', 'TAR629G2155' => 'tar', 'THA.LOC104805282' => 'tha', 'THA.LOC104805363' => 'tha', 'THA.LOC104808968' => 'tha', 'THA.LOC104821093' => 'tha', 'THA.LOC104823953' => 'tha', 'THA.LOC104825562' => 'tha', 'THA.LOC104825665' => 'tha', 'Thecc.02G261400' => 'tca', 'Thecc.04G019200' => 'tca', 'Thecc.09G130400' => 'tca', 'Thhalv10004374m.g' => 'esa', 'Thhalv10007850m.g' => 'esa', 'Thhalv10013782m.g' => 'esa', 'Thhalv10018686m.g' => 'esa', 'Thhalv10020899m.g' => 'esa', 'Thhalv10022755m.g' => 'esa', 'TPR.G23851' => 'tpr', 'TPR.G26500' => 'tpr', 'TPR.G27267' => 'tpr', 'TPR.G32001' => 'tpr', 'TPR.G6251' => 'tpr', 'TPR.G8167' => 'tpr', 'TWI12G1330' => 'twi', 'TWI18G1239' => 'twi', 'TWI34G0979' => 'twi', 'TWI36G0670' => 'twi', 'TWI36G0707' => 'twi', 'TWI56G0233' => 'twi', 'TWI75G1809' => 'twi', 'unitig_21.g20874' => 'ugi', 'unitig_26.g10343' => 'ugi', 'unitig_46.g18392' => 'ugi', 'unitig_52.g17178' => 'ugi', 'unitig_8.g2934' => 'ugi', 'vmacro01122' => 'vma', 'vmacro05875' => 'vma', 'vmacro06147' => 'vma', 'vmacro16191' => 'vma', 'vmacro18293' => 'vma', 'VMungo0251G3707' => 'vmu', 'VMungo0464G1521' => 'vmu', 'VMungo1215G0205' => 'vmu', 'VMungo1383G2484' => 'vmu', 'Zm00001eb079610' => 'zma', 'Zm00001eb135990' => 'zma', 'Zm00001eb183710' => 'zma', 'Zm00001eb246020' => 'zma' ) $gf_id = 'HOM05D001124' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001124' ) $data_identifier = 'HOM05D001124' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 6, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 7, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 21, 'bol' => (int) 10, 'bra' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 6, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 9, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 21, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 8, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 10, 'lsa' => (int) 8, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 8, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 9, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb246020' $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' => 'HOM05D001124', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '548', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02520' => 'bna', 'A03p06630' => 'bna', 'A05p44460' => 'bna', 'A06p08710' => 'bna', 'A06p41090' => 'bna', 'A07p32320' => 'bna', 'A08p32520' => 'bna', 'A09p10360' => 'bna', 'A10p24080' => 'bna', 'Aa31LG11G15250' => 'aar', 'Aa31LG1G1800' => 'aar', 'Aa31LG2G5120' => 'aar', 'Aa31LG2G6070' => 'aar', 'Aa31LG5G10770' => 'aar', 'Aa31sc61G90' => 'aar', 'Actinidia01352' => 'ach', 'Actinidia05983' => 'ach', 'Actinidia08133' => 'ach', 'Actinidia15101' => 'ach', 'Actinidia26379' => 'ach', 'Actinidia35778' => 'ach', 'Actinidia36123' => 'ach', 'Actinidia37436' => 'ach', 'Actinidia38730' => 'ach', 'Ah.02g128210' => 'amhyb', 'Ah.03g132990' => 'amhyb', 'Ah.14g079410' => 'amhyb', 'AL1G24640' => 'aly', 'AL2G26680' => 'aly', 'AL3G10530' => 'aly', 'AL3G45230' => 'aly', 'AL5G15230' => 'aly', 'AL5G16960' => 'aly', 'AL6G25210' => 'aly', 'Aqoxy2G00441' => 'aox', 'Aqoxy3G01236' => 'aox', 'Aqoxy5G03746' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3RQ047' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C7GMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9C8JER' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MBL6KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YXCZ83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZANX40' => 'arhy', 'AT1G12990' => 'ath', 'AT1G67880' => 'ath', 'AT2G13290' => 'ath', 'AT3G01620' => 'ath', 'AT3G26445' => 'ath', 'AT3G27540' => 'ath', 'AT5G14480' => 'ath', 'ATR0824G026' => 'atr', 'ATR1098G019' => 'atr', 'Atru.chr11.2145' => 'acertr', 'Atru.chr2.3636' => 'acertr', 'Atru.chr2.3644' => 'acertr', 'Atru.chr6.2422' => 'acertr', 'Atru.chr7.1112' => 'acertr', 'AUR62005469' => 'cqu', 'AUR62011166' => 'cqu', 'AUR62013319' => 'cqu', 'AUR62024273' => 'cqu', 'AUR62028420' => 'cqu', 'AUR62041942' => 'cqu', 'BcaB01g04969' => 'bca', 'BcaB01g06371' => 'bca', 'BcaB02g11494' => 'bca', 'BcaB03g15382' => 'bca', 'BcaB08g36994' => 'bca', 'BcaC03g13477' => 'bca', 'BcaC03g13478' => 'bca', 'BcaC03g13480' => 'bca', 'BcaC03g13481' => 'bca', 'BcaC03g13486' => 'bca', 'BcaC04g19031' => 'bca', 'BcaC04g23085' => 'bca', 'BcaC05g25094' => 'bca', 'BcaC05g25096' => 'bca', 'BcaC05g25138' => 'bca', 'BcaC05g30416' => 'bca', 'BcaC05g30455' => 'bca', 'BcaC06g30979' => 'bca', 'BcaC06g33805' => 'bca', 'BcaC08g46021' => 'bca', 'BcaNung03154' => 'bca', 'BolC2t06623H' => 'bol', 'BolC2t06632H' => 'bol', 'BolC2t06635H' => 'bol', 'BolC2t06638H' => 'bol', 'BolC3t13266H' => 'bol', 'BolC5t29776H' => 'bol', 'BolC6t38912H' => 'bol', 'BolC7t44183H' => 'bol', 'BolC9t54123H' => 'bol', 'BolC9t59107H' => 'bol', 'BraA02t05221Z' => 'bra', 'BraA03t09996Z' => 'bra', 'BraA05t23210Z' => 'bra', 'BraA06t24068Z' => 'bra', 'BraA06t27032Z' => 'bra', 'BraA08t35176Z' => 'bra', 'BraA09t36680Z' => 'bra', 'BraA10t44471Z' => 'bra', 'C02p06760' => 'bna', 'C02p06890' => 'bna', 'C02p07010' => 'bna', 'C03p07660' => 'bna', 'C05p10300' => 'bna', 'C06p38150' => 'bna', 'C07p36650' => 'bna', 'C08p15770' => 'bna', 'C09p12300' => 'bna', 'C09p62700' => 'bna', 'C09p75040' => 'bna', 'CAN.G13.1' => 'can', 'CAN.G138.4' => 'can', 'CAN.G44.6' => 'can', 'CAN.G473.19' => 'can', 'CANSAT01G0835' => 'cansat', 'CANSAT11G0246' => 'cansat', 'CANSAT11G1766' => 'cansat', 'CANSAT64G1954' => 'cansat', 'CARHR013330' => 'chi', 'CARHR060530' => 'chi', 'CARHR075300' => 'chi', 'CARHR105120' => 'chi', 'CARHR148910' => 'chi', 'CARHR198830' => 'chi', 'Carub.0001s1275' => 'cru', 'Carub.0002s1437' => 'cru', 'Carub.0003s0044' => 'cru', 'Carub.0003s2787' => 'cru', 'Carub.0005s0597' => 'cru', 'Carub.0006s1266' => 'cru', 'Ca_06935_v3' => 'car', 'Ca_13559_v3' => 'car', 'Ca_16941_v3' => 'car', 'Ca_16960_v3' => 'car', 'Ca_17775_v3' => 'car', 'Ca_30464_v3' => 'car', 'Cc06_g08160' => 'ccan', 'Cc07_g01520' => 'ccan', 'Cc11_g15810' => 'ccan', 'CDE02G2840' => 'cde', 'CDE03G0093' => 'cde', 'CDE04G2127' => 'cde', 'CDE07G1857' => 'cde', 'CDE09G1246' => 'cde', 'Cfa003412' => 'cfa', 'Cfa007341' => 'cfa', 'Cfa009220' => 'cfa', 'Ciclev10008737m.g' => 'ccl', 'Ciclev10015565m.g' => 'ccl', 'Ciclev10031761m.g' => 'ccl', 'CiPaw.03G045300' => 'cil', 'CiPaw.03G247200' => 'cil', 'CiPaw.04G029500' => 'cil', 'CiPaw.04G174000' => 'cil', 'CiPaw.05G181200' => 'cil', 'CiPaw.06G067100' => 'cil', 'ClCG05G025800' => 'cla', 'ClCG06G011400' => 'cla', 'ClCG09G019360' => 'cla', 'COL.COLO4_04827' => 'col', 'COL.COLO4_29170' => 'col', 'COL.COLO4_35131' => 'col', 'COL.COLO4_35132' => 'col', 'Cpa.g.sc33.32' => 'cpa', 'Cpa.g.sc46.29' => 'cpa', 'Cpa.g.sc796.1' => 'cpa', 'CsaV3_1G030420' => 'csa', 'CsaV3_5G027050' => 'csa', 'CsaV3_5G031040' => 'csa', 'CsaV3_UNG023130' => 'csa', 'CSS0007726' => 'camsi', 'CSS0016433' => 'camsi', 'CSS0017656' => 'camsi', 'CSS0025364' => 'camsi', 'CSS0027582' => 'camsi', 'CSS0047288' => 'camsi', 'CSS0049950' => 'camsi', 'DCAR_003843' => 'dca', 'DCAR_007052' => 'dca', 'DCAR_020884' => 'dca', 'DCAR_021730' => 'dca', 'DCAR_024423' => 'dca', 'DCAR_026509' => 'dca', 'DCAR_031158' => 'dca', 'Dinv14728' => 'din', 'Dinv15219' => 'din', 'Dinv25728' => 'din', 'Dinv33428' => 'din', 'Dinv36489' => 'din', 'Dinv41486' => 'din', 'Duzib147G0469' => 'dzi', 'Duzib168G0060' => 'dzi', 'Duzib187G1215' => 'dzi', 'Duzib248G0692' => 'dzi', 'Duzib251G0767' => 'dzi', 'Duzib264G0446' => 'dzi', 'Duzib268G0691' => 'dzi', 'ECA232G4767' => 'eca', 'ECA233G2838' => 'eca', 'ECA234G0391' => 'eca', 'ECA234G0857' => 'eca', 'ECA236G1593' => 'eca', 'ECA238G0565' => 'eca', 'ECA246G1027' => 'eca', 'ECA246G3223' => 'eca', 'ECA246G3470' => 'eca', 'EL10Ac6g13829' => 'bvu', 'EL10Ac6g14093' => 'bvu', 'EL10Ac8g18707' => 'bvu', 'Eucgr.C01369' => 'egr', 'Eucgr.H02492' => 'egr', 'Eucgr.I01733' => 'egr', 'Eucgr.J02255' => 'egr', 'Eucgr.J02257' => 'egr', 'Eucgr.J02258' => 'egr', 'FAN02G1601' => 'fan', 'FAN03G1586' => 'fan', 'FAN03G2986' => 'fan', 'FAN05G4837' => 'fan', 'FAN06G0146' => 'fan', 'FAN07G0858' => 'fan', 'FAN09G3179' => 'fan', 'FAN10G0669' => 'fan', 'FAN12G2358' => 'fan', 'FAN14G4198' => 'fan', 'FAN14G5112' => 'fan', 'FAN17G0342' => 'fan', 'FAN19G0342' => 'fan', 'FAN19G0962' => 'fan', 'FAN19G1101' => 'fan', 'FAN19G1872' => 'fan', 'FAN22G0356' => 'fan', 'FAN23G0744' => 'fan', 'FAN23G1914' => 'fan', 'FAN26G0032' => 'fan', 'FAN28G0625' => 'fan', 'FvH4_1g02710' => 'fve', 'FvH4_1g02720' => 'fve', 'FvH4_4g25670' => 'fve', 'FvH4_6g51700' => 'fve', 'FvH4_7g20170' => 'fve', 'Glyma.05G175000' => 'gma', 'Glyma.08G132300' => 'gma', 'Glyma.11G243000' => 'gma', 'Glyma.13G158900' => 'gma', 'Glyma.17G112400' => 'gma', 'Glyma.18G014100' => 'gma', 'Glyma.19G003100' => 'gma', 'Glyma.19G056500' => 'gma', 'Gohir.A01G158900' => 'ghi', 'Gohir.A05G312600' => 'ghi', 'Gohir.A05G354900' => 'ghi', 'Gohir.A07G037200' => 'ghi', 'Gohir.A09G030000' => 'ghi', 'Gohir.A12G145200' => 'ghi', 'Gohir.D01G151500' => 'ghi', 'Gohir.D04G058300' => 'ghi', 'Gohir.D05G314100' => 'ghi', 'Gohir.D07G041400' => 'ghi', 'Gohir.D09G029700' => 'ghi', 'Gohir.D12G149700' => 'ghi', 'Gorai.001G043800' => 'gra', 'Gorai.002G187800' => 'gra', 'Gorai.006G034700' => 'gra', 'Gorai.008G161200' => 'gra', 'Gorai.009G335700' => 'gra', 'Gorai.012G065000' => 'gra', 'GSVIVG01000535001' => 'vvi', 'GSVIVG01015572001' => 'vvi', 'GSVIVG01032386001' => 'vvi', 'HanXRQChr05g0138531' => 'han', 'HanXRQChr06g0174391' => 'han', 'HanXRQChr07g0199021' => 'han', 'HanXRQChr08g0208211' => 'han', 'HanXRQChr09g0255471' => 'han', 'HanXRQChr10g0315791' => 'han', 'HanXRQChr12g0371991' => 'han', 'HanXRQChr15g0475251' => 'han', 'HanXRQChr17g0540001' => 'han', 'HanXRQChr17g0548631' => 'han', 'HanXRQChr17g0569561' => 'han', 'Haze_12256' => 'cav', 'Haze_14756' => 'cav', 'Haze_25528' => 'cav', 'Hma1.2p1_0079F.1_g041020' => 'hma', 'Hma1.2p1_0818F.1_g223260' => 'hma', 'Hma1.2p1_1747F.1_g300530' => 'hma', 'HPP92_004607' => 'vpl', 'HPP92_004608' => 'vpl', 'HPP92_006181' => 'vpl', 'HPP92_012192' => 'vpl', 'HPP92_015680' => 'vpl', 'HPP92_020249' => 'vpl', 'HPP92_021376' => 'vpl', 'HPP92_024275' => 'vpl', 'Hund06031' => 'sun', 'Hund25391' => 'sun', 'Lalb_Chr07g0185371' => 'lal', 'Lalb_Chr07g0185381' => 'lal', 'Lalb_Chr12g0204011' => 'lal', 'Lalb_Chr13g0301671' => 'lal', 'Lalb_Chr14g0362851' => 'lal', 'Lalb_Chr24g0403581' => 'lal', 'Lj1g0000233' => 'lja', 'Lj2g0018120' => 'lja', 'Lj3C621T0' => 'lonja', 'Lj3P1059T14' => 'lonja', 'Lj3P611T9' => 'lonja', 'Lj3P614T13' => 'lonja', 'Lj3P615T5' => 'lonja', 'Lj4g0012315' => 'lja', 'Lj4g0026182' => 'lja', 'Lj6P813T16' => 'lonja', 'Lj7C427T7' => 'lonja', 'Lj7C427T8' => 'lonja', 'Lj7P600T41' => 'lonja', 'Lju41C42G17' => 'lonja', 'Lsat_1_v5_gn_0_47300' => 'lsa', 'Lsat_1_v5_gn_2_91280' => 'lsa', 'Lsat_1_v5_gn_3_30561' => 'lsa', 'Lsat_1_v5_gn_4_184321' => 'lsa', 'Lsat_1_v5_gn_4_4041' => 'lsa', 'Lsat_1_v5_gn_5_92000' => 'lsa', 'Lsat_1_v5_gn_8_152940' => 'lsa', 'Lsat_1_v5_gn_8_62401' => 'lsa', 'Manes.06G055900' => 'mes', 'Manes.12G022200' => 'mes', 'Manes.13G023300' => 'mes', 'Manes.14G115000' => 'mes', 'Manes.15G151700' => 'mes', 'Manes.17G111300' => 'mes', 'Mapoly0226s0009' => 'mpo', 'MBI02_g25363_MAGBIO' => 'mbi', 'MBI06_g00027_MAGBIO' => 'mbi', 'MBI10_g13034_MAGBIO' => 'mbi', 'MD09G1023400' => 'mdo', 'MD13G1100100' => 'mdo', 'MD15G1169200' => 'mdo', 'MD16G1101100' => 'mdo', 'MD17G1022900' => 'mdo', 'Medtr3g096150' => 'mtr', 'Medtr4g115070' => 'mtr', 'Medtr7g033325' => 'mtr', 'Medtr8g089840' => 'mtr', 'MELO3C010319.2' => 'cme', 'MELO3C011944.2' => 'cme', 'MELO3C021589.2' => 'cme', 'Migut.E00207' => 'egut', 'Migut.H00067' => 'egut', 'Migut.K00433' => 'egut', 'Migut.K00606' => 'egut', 'Migut.K01410' => 'egut', 'MSTRG.13347' => 'ama', 'MSTRG.24045' => 'ama', 'MSTRG.2428' => 'ama', 'MSTRG.26410' => 'ama', 'MSTRG.3139' => 'ama', 'MSTRG.3286' => 'ama', 'MSTRG.563' => 'ama', 'MSTRG.7941' => 'ama', 'Nitab4.5_0000028g0060' => 'nta', 'Nitab4.5_0000065g0260' => 'nta', 'Nitab4.5_0000112g0060' => 'nta', 'Nitab4.5_0000489g0120' => 'nta', 'Nitab4.5_0001776g0050' => 'nta', 'Nitab4.5_0001854g0010' => 'nta', 'Nitab4.5_0001860g0020' => 'nta', 'Nitab4.5_0004352g0010' => 'nta', 'Nitab4.5_0008716g0020' => 'nta', 'Nitab4.5_0008922g0010' => 'nta', 'Nn3g16693' => 'nnu', 'Nn4g22596' => 'nnu', 'Nn7g37639' => 'nnu', 'Oeu001701.1' => 'oeu', 'Oeu018149.1' => 'oeu', 'Oeu026220.1' => 'oeu', 'Oeu038635.1' => 'oeu', 'Oeu049176.1' => 'oeu', 'Oeu056706.1' => 'oeu', 'Oeu056937.1' => 'oeu', 'Oeu057540.1' => 'oeu', 'Os02g0594900' => 'osa', 'Os02g0595100' => 'osa', 'Os04g0477500' => 'osa', 'Os12g0611900' => 'osa', 'Peaxi162Scf00076g00020' => 'pax', 'Peaxi162Scf00128g00217' => 'pax', 'Peaxi162Scf00129g01640' => 'pax', 'Peaxi162Scf00669g00007' => 'pax', 'Peaxi162Scf00700g00421' => 'pax', 'Peaxi162Scf00801g00038' => 'pax', 'Peaxi162Scf00891g00025' => 'pax', 'PGR083G0909' => 'pgr', 'PGR119G1005' => 'pgr', 'PGR142G2236' => 'pgr', 'PGR142G3388' => 'pgr', 'PGSC0003DMG400004514' => 'stu', 'PGSC0003DMG400012635' => 'stu', 'PGSC0003DMG400015730' => 'stu', 'PGSC0003DMG400018611' => 'stu', 'PGSC0003DMG400030897' => 'stu', 'Phvul.001G254800' => 'pvu', 'Phvul.002G260100' => 'pvu', 'Phvul.003G167600' => 'pvu', 'Phvul.004G005100' => 'pvu', 'Potri.001G343600' => 'ptr', 'Potri.006G066700' => 'ptr', 'Potri.008G186000' => 'ptr', 'Potri.010G046900' => 'ptr', 'Potri.018G127900' => 'ptr', 'Pp3c20_17750' => 'ppa', 'Pp3c24_4380' => 'ppa', 'Prupe.1G245800' => 'ppe', 'Prupe.3G293400' => 'ppe', 'Prupe.7G247400' => 'ppe', 'Psat0s145g0120' => 'psa', 'Psat0s595g0040' => 'psa', 'Psat0s595g0120' => 'psa', 'Psat3g175040' => 'psa', 'Psat7g058120' => 'psa', 'PSO017G0428' => 'pso', 'PSO063G7510' => 'pso', 'PSO067G0046' => 'pso', 'PSO478G1073' => 'pso', 'PSO675G3677' => 'pso', 'PSO675G6558' => 'pso', 'PSO675G7520' => 'pso', 'PSO675G8959' => 'pso', 'QL02p074089' => 'qlo', 'QL02p089614' => 'qlo', 'QL03p057736' => 'qlo', 'RcHm_v2.0_Chr1g0364131' => 'rch', 'RcHm_v2.0_Chr2g0087801' => 'rch', 'RcHm_v2.0_Chr2g0087821' => 'rch', 'RcHm_v2.0_Chr2g0173231' => 'rch', 'RcHm_v2.0_Chr4g0433111' => 'rch', 'Rhsim03G0250300' => 'rsi', 'Rhsim08G0048400' => 'rsi', 'Rhsim10G0014800' => 'rsi', 'Rhsim12G0040100' => 'rsi', 'Rhsim12G0109700' => 'rsi', 'Sabra06G0049600' => 'sbr', 'Sabra08G0141000' => 'sbr', 'Sabra10G0021400' => 'sbr', 'Sabra16G0222900' => 'sbr', 'Sabra18G0108600' => 'sbr', 'SalBow1G0433' => 'sbo', 'SalBow1G2038' => 'sbo', 'SalBow1G5003' => 'sbo', 'SalBow7G1197' => 'sbo', 'SalBow8G3506' => 'sbo', 'Sc03g0007300' => 'sci', 'Sc11g0000950' => 'sci', 'Sc14g0008750' => 'sci', 'Sc18g0000420' => 'sci', 'Sed0006754' => 'sed', 'Sed0008741' => 'sed', 'Sed0017172' => 'sed', 'Sed0018925' => 'sed', 'Sed0023326' => 'sed', 'Sed0025909' => 'sed', 'SEGI_05333' => 'sgi', 'SEGI_10362' => 'sgi', 'SEGI_13380' => 'sgi', 'SEGI_24306' => 'sgi', 'SEGI_29077' => 'sgi', 'SEGI_29095' => 'sgi', 'SEGI_36534' => 'sgi', 'SEGI_37506' => 'sgi', 'SEGI_38321' => 'sgi', 'SGA_v2.0_scaffold307G48031' => 'sas', 'SGA_v2.0_scaffold47G17507' => 'sas', 'SGA_v2.0_scaffold63G21736' => 'sas', 'SGA_v2.0_scaffold87G27070' => 'sas', 'SHI17794' => 'shi', 'SHI28851' => 'shi', 'SMO165G0155' => 'smo', 'SMO340G0217' => 'smo', 'SMO367G1210' => 'smo', 'Solyc02g093430.3' => 'sly', 'Solyc05g013580.4' => 'sly', 'Solyc07g008030.3' => 'sly', 'Solyc12g035470.2' => 'sly', 'Sopen02g038020' => 'spe', 'Sopen05g008490' => 'spe', 'Sopen07g003910' => 'spe', 'Sopen12g015240' => 'spe', 'Sp1g11550' => 'spa', 'Sp2g16710' => 'spa', 'Sp3g00430' => 'spa', 'Sp3g26780' => 'spa', 'Sp5g22900' => 'spa', 'Sp6g29530' => 'spa', 'TAR371G0794' => 'tar', 'TAR374G0164' => 'tar', 'TAR622G0165' => 'tar', 'TAR626G0929' => 'tar', 'TAR629G2155' => 'tar', 'THA.LOC104805282' => 'tha', 'THA.LOC104805363' => 'tha', 'THA.LOC104808968' => 'tha', 'THA.LOC104821093' => 'tha', 'THA.LOC104823953' => 'tha', 'THA.LOC104825562' => 'tha', 'THA.LOC104825665' => 'tha', 'Thecc.02G261400' => 'tca', 'Thecc.04G019200' => 'tca', 'Thecc.09G130400' => 'tca', 'Thhalv10004374m.g' => 'esa', 'Thhalv10007850m.g' => 'esa', 'Thhalv10013782m.g' => 'esa', 'Thhalv10018686m.g' => 'esa', 'Thhalv10020899m.g' => 'esa', 'Thhalv10022755m.g' => 'esa', 'TPR.G23851' => 'tpr', 'TPR.G26500' => 'tpr', 'TPR.G27267' => 'tpr', 'TPR.G32001' => 'tpr', 'TPR.G6251' => 'tpr', 'TPR.G8167' => 'tpr', 'TWI12G1330' => 'twi', 'TWI18G1239' => 'twi', 'TWI34G0979' => 'twi', 'TWI36G0670' => 'twi', 'TWI36G0707' => 'twi', 'TWI56G0233' => 'twi', 'TWI75G1809' => 'twi', 'unitig_21.g20874' => 'ugi', 'unitig_26.g10343' => 'ugi', 'unitig_46.g18392' => 'ugi', 'unitig_52.g17178' => 'ugi', 'unitig_8.g2934' => 'ugi', 'vmacro01122' => 'vma', 'vmacro05875' => 'vma', 'vmacro06147' => 'vma', 'vmacro16191' => 'vma', 'vmacro18293' => 'vma', 'VMungo0251G3707' => 'vmu', 'VMungo0464G1521' => 'vmu', 'VMungo1215G0205' => 'vmu', 'VMungo1383G2484' => 'vmu', 'Zm00001eb079610' => 'zma', 'Zm00001eb135990' => 'zma', 'Zm00001eb183710' => 'zma', 'Zm00001eb246020' => 'zma' ), 'gf_id' => 'HOM05D001124', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001124' ), 'data_identifier' => 'HOM05D001124', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001124', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '548', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02520' => 'bna', 'A03p06630' => 'bna', 'A05p44460' => 'bna', 'A06p08710' => 'bna', 'A06p41090' => 'bna', 'A07p32320' => 'bna', 'A08p32520' => 'bna', 'A09p10360' => 'bna', 'A10p24080' => 'bna', 'Aa31LG11G15250' => 'aar', 'Aa31LG1G1800' => 'aar', 'Aa31LG2G5120' => 'aar', 'Aa31LG2G6070' => 'aar', 'Aa31LG5G10770' => 'aar', 'Aa31sc61G90' => 'aar', 'Actinidia01352' => 'ach', 'Actinidia05983' => 'ach', 'Actinidia08133' => 'ach', 'Actinidia15101' => 'ach', 'Actinidia26379' => 'ach', 'Actinidia35778' => 'ach', 'Actinidia36123' => 'ach', 'Actinidia37436' => 'ach', 'Actinidia38730' => 'ach', 'Ah.02g128210' => 'amhyb', 'Ah.03g132990' => 'amhyb', 'Ah.14g079410' => 'amhyb', 'AL1G24640' => 'aly', 'AL2G26680' => 'aly', 'AL3G10530' => 'aly', 'AL3G45230' => 'aly', 'AL5G15230' => 'aly', 'AL5G16960' => 'aly', 'AL6G25210' => 'aly', 'Aqoxy2G00441' => 'aox', 'Aqoxy3G01236' => 'aox', 'Aqoxy5G03746' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3RQ047' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C7GMZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9C8JER' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MBL6KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YXCZ83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZANX40' => 'arhy', 'AT1G12990' => 'ath', 'AT1G67880' => 'ath', 'AT2G13290' => 'ath', 'AT3G01620' => 'ath', 'AT3G26445' => 'ath', 'AT3G27540' => 'ath', 'AT5G14480' => 'ath', 'ATR0824G026' => 'atr', 'ATR1098G019' => 'atr', 'Atru.chr11.2145' => 'acertr', 'Atru.chr2.3636' => 'acertr', 'Atru.chr2.3644' => 'acertr', 'Atru.chr6.2422' => 'acertr', 'Atru.chr7.1112' => 'acertr', 'AUR62005469' => 'cqu', 'AUR62011166' => 'cqu', 'AUR62013319' => 'cqu', 'AUR62024273' => 'cqu', 'AUR62028420' => 'cqu', 'AUR62041942' => 'cqu', 'BcaB01g04969' => 'bca', 'BcaB01g06371' => 'bca', 'BcaB02g11494' => 'bca', 'BcaB03g15382' => 'bca', 'BcaB08g36994' => 'bca', 'BcaC03g13477' => 'bca', 'BcaC03g13478' => 'bca', 'BcaC03g13480' => 'bca', 'BcaC03g13481' => 'bca', 'BcaC03g13486' => 'bca', 'BcaC04g19031' => 'bca', 'BcaC04g23085' => 'bca', 'BcaC05g25094' => 'bca', 'BcaC05g25096' => 'bca', 'BcaC05g25138' => 'bca', 'BcaC05g30416' => 'bca', 'BcaC05g30455' => 'bca', 'BcaC06g30979' => 'bca', 'BcaC06g33805' => 'bca', 'BcaC08g46021' => 'bca', 'BcaNung03154' => 'bca', 'BolC2t06623H' => 'bol', 'BolC2t06632H' => 'bol', 'BolC2t06635H' => 'bol', 'BolC2t06638H' => 'bol', 'BolC3t13266H' => 'bol', 'BolC5t29776H' => 'bol', 'BolC6t38912H' => 'bol', 'BolC7t44183H' => 'bol', 'BolC9t54123H' => 'bol', 'BolC9t59107H' => 'bol', 'BraA02t05221Z' => 'bra', 'BraA03t09996Z' => 'bra', 'BraA05t23210Z' => 'bra', 'BraA06t24068Z' => 'bra', 'BraA06t27032Z' => 'bra', 'BraA08t35176Z' => 'bra', 'BraA09t36680Z' => 'bra', 'BraA10t44471Z' => 'bra', 'C02p06760' => 'bna', 'C02p06890' => 'bna', 'C02p07010' => 'bna', 'C03p07660' => 'bna', 'C05p10300' => 'bna', 'C06p38150' => 'bna', 'C07p36650' => 'bna', 'C08p15770' => 'bna', 'C09p12300' => 'bna', 'C09p62700' => 'bna', 'C09p75040' => 'bna', 'CAN.G13.1' => 'can', 'CAN.G138.4' => 'can', 'CAN.G44.6' => 'can', 'CAN.G473.19' => 'can', 'CANSAT01G0835' => 'cansat', 'CANSAT11G0246' => 'cansat', 'CANSAT11G1766' => 'cansat', 'CANSAT64G1954' => 'cansat', 'CARHR013330' => 'chi', 'CARHR060530' => 'chi', 'CARHR075300' => 'chi', 'CARHR105120' => 'chi', 'CARHR148910' => 'chi', 'CARHR198830' => 'chi', 'Carub.0001s1275' => 'cru', 'Carub.0002s1437' => 'cru', 'Carub.0003s0044' => 'cru', 'Carub.0003s2787' => 'cru', 'Carub.0005s0597' => 'cru', 'Carub.0006s1266' => 'cru', 'Ca_06935_v3' => 'car', 'Ca_13559_v3' => 'car', 'Ca_16941_v3' => 'car', 'Ca_16960_v3' => 'car', 'Ca_17775_v3' => 'car', 'Ca_30464_v3' => 'car', 'Cc06_g08160' => 'ccan', 'Cc07_g01520' => 'ccan', 'Cc11_g15810' => 'ccan', 'CDE02G2840' => 'cde', 'CDE03G0093' => 'cde', 'CDE04G2127' => 'cde', 'CDE07G1857' => 'cde', 'CDE09G1246' => 'cde', 'Cfa003412' => 'cfa', 'Cfa007341' => 'cfa', 'Cfa009220' => 'cfa', 'Ciclev10008737m.g' => 'ccl', 'Ciclev10015565m.g' => 'ccl', 'Ciclev10031761m.g' => 'ccl', 'CiPaw.03G045300' => 'cil', 'CiPaw.03G247200' => 'cil', 'CiPaw.04G029500' => 'cil', 'CiPaw.04G174000' => 'cil', 'CiPaw.05G181200' => 'cil', 'CiPaw.06G067100' => 'cil', 'ClCG05G025800' => 'cla', 'ClCG06G011400' => 'cla', 'ClCG09G019360' => 'cla', 'COL.COLO4_04827' => 'col', 'COL.COLO4_29170' => 'col', 'COL.COLO4_35131' => 'col', 'COL.COLO4_35132' => 'col', 'Cpa.g.sc33.32' => 'cpa', 'Cpa.g.sc46.29' => 'cpa', 'Cpa.g.sc796.1' => 'cpa', 'CsaV3_1G030420' => 'csa', 'CsaV3_5G027050' => 'csa', 'CsaV3_5G031040' => 'csa', 'CsaV3_UNG023130' => 'csa', 'CSS0007726' => 'camsi', 'CSS0016433' => 'camsi', 'CSS0017656' => 'camsi', 'CSS0025364' => 'camsi', 'CSS0027582' => 'camsi', 'CSS0047288' => 'camsi', 'CSS0049950' => 'camsi', 'DCAR_003843' => 'dca', 'DCAR_007052' => 'dca', 'DCAR_020884' => 'dca', 'DCAR_021730' => 'dca', 'DCAR_024423' => 'dca', 'DCAR_026509' => 'dca', 'DCAR_031158' => 'dca', 'Dinv14728' => 'din', 'Dinv15219' => 'din', 'Dinv25728' => 'din', 'Dinv33428' => 'din', 'Dinv36489' => 'din', 'Dinv41486' => 'din', 'Duzib147G0469' => 'dzi', 'Duzib168G0060' => 'dzi', 'Duzib187G1215' => 'dzi', 'Duzib248G0692' => 'dzi', 'Duzib251G0767' => 'dzi', 'Duzib264G0446' => 'dzi', 'Duzib268G0691' => 'dzi', 'ECA232G4767' => 'eca', 'ECA233G2838' => 'eca', 'ECA234G0391' => 'eca', 'ECA234G0857' => 'eca', 'ECA236G1593' => 'eca', 'ECA238G0565' => 'eca', 'ECA246G1027' => 'eca', 'ECA246G3223' => 'eca', 'ECA246G3470' => 'eca', 'EL10Ac6g13829' => 'bvu', 'EL10Ac6g14093' => 'bvu', 'EL10Ac8g18707' => 'bvu', 'Eucgr.C01369' => 'egr', 'Eucgr.H02492' => 'egr', 'Eucgr.I01733' => 'egr', 'Eucgr.J02255' => 'egr', 'Eucgr.J02257' => 'egr', 'Eucgr.J02258' => 'egr', 'FAN02G1601' => 'fan', 'FAN03G1586' => 'fan', 'FAN03G2986' => 'fan', 'FAN05G4837' => 'fan', 'FAN06G0146' => 'fan', 'FAN07G0858' => 'fan', 'FAN09G3179' => 'fan', 'FAN10G0669' => 'fan', 'FAN12G2358' => 'fan', 'FAN14G4198' => 'fan', 'FAN14G5112' => 'fan', 'FAN17G0342' => 'fan', 'FAN19G0342' => 'fan', 'FAN19G0962' => 'fan', 'FAN19G1101' => 'fan', 'FAN19G1872' => 'fan', 'FAN22G0356' => 'fan', 'FAN23G0744' => 'fan', 'FAN23G1914' => 'fan', 'FAN26G0032' => 'fan', 'FAN28G0625' => 'fan', 'FvH4_1g02710' => 'fve', 'FvH4_1g02720' => 'fve', 'FvH4_4g25670' => 'fve', 'FvH4_6g51700' => 'fve', 'FvH4_7g20170' => 'fve', 'Glyma.05G175000' => 'gma', 'Glyma.08G132300' => 'gma', 'Glyma.11G243000' => 'gma', 'Glyma.13G158900' => 'gma', 'Glyma.17G112400' => 'gma', 'Glyma.18G014100' => 'gma', 'Glyma.19G003100' => 'gma', 'Glyma.19G056500' => 'gma', 'Gohir.A01G158900' => 'ghi', 'Gohir.A05G312600' => 'ghi', 'Gohir.A05G354900' => 'ghi', 'Gohir.A07G037200' => 'ghi', 'Gohir.A09G030000' => 'ghi', 'Gohir.A12G145200' => 'ghi', 'Gohir.D01G151500' => 'ghi', 'Gohir.D04G058300' => 'ghi', 'Gohir.D05G314100' => 'ghi', 'Gohir.D07G041400' => 'ghi', 'Gohir.D09G029700' => 'ghi', 'Gohir.D12G149700' => 'ghi', 'Gorai.001G043800' => 'gra', 'Gorai.002G187800' => 'gra', 'Gorai.006G034700' => 'gra', 'Gorai.008G161200' => 'gra', 'Gorai.009G335700' => 'gra', 'Gorai.012G065000' => 'gra', 'GSVIVG01000535001' => 'vvi', 'GSVIVG01015572001' => 'vvi', 'GSVIVG01032386001' => 'vvi', 'HanXRQChr05g0138531' => 'han', 'HanXRQChr06g0174391' => 'han', 'HanXRQChr07g0199021' => 'han', 'HanXRQChr08g0208211' => 'han', 'HanXRQChr09g0255471' => 'han', 'HanXRQChr10g0315791' => 'han', 'HanXRQChr12g0371991' => 'han', 'HanXRQChr15g0475251' => 'han', 'HanXRQChr17g0540001' => 'han', 'HanXRQChr17g0548631' => 'han', 'HanXRQChr17g0569561' => 'han', 'Haze_12256' => 'cav', 'Haze_14756' => 'cav', 'Haze_25528' => 'cav', 'Hma1.2p1_0079F.1_g041020' => 'hma', 'Hma1.2p1_0818F.1_g223260' => 'hma', 'Hma1.2p1_1747F.1_g300530' => 'hma', 'HPP92_004607' => 'vpl', 'HPP92_004608' => 'vpl', 'HPP92_006181' => 'vpl', 'HPP92_012192' => 'vpl', 'HPP92_015680' => 'vpl', 'HPP92_020249' => 'vpl', 'HPP92_021376' => 'vpl', 'HPP92_024275' => 'vpl', 'Hund06031' => 'sun', 'Hund25391' => 'sun', 'Lalb_Chr07g0185371' => 'lal', 'Lalb_Chr07g0185381' => 'lal', 'Lalb_Chr12g0204011' => 'lal', 'Lalb_Chr13g0301671' => 'lal', 'Lalb_Chr14g0362851' => 'lal', 'Lalb_Chr24g0403581' => 'lal', 'Lj1g0000233' => 'lja', 'Lj2g0018120' => 'lja', 'Lj3C621T0' => 'lonja', 'Lj3P1059T14' => 'lonja', 'Lj3P611T9' => 'lonja', 'Lj3P614T13' => 'lonja', 'Lj3P615T5' => 'lonja', 'Lj4g0012315' => 'lja', 'Lj4g0026182' => 'lja', 'Lj6P813T16' => 'lonja', 'Lj7C427T7' => 'lonja', 'Lj7C427T8' => 'lonja', 'Lj7P600T41' => 'lonja', 'Lju41C42G17' => 'lonja', 'Lsat_1_v5_gn_0_47300' => 'lsa', 'Lsat_1_v5_gn_2_91280' => 'lsa', 'Lsat_1_v5_gn_3_30561' => 'lsa', 'Lsat_1_v5_gn_4_184321' => 'lsa', 'Lsat_1_v5_gn_4_4041' => 'lsa', 'Lsat_1_v5_gn_5_92000' => 'lsa', 'Lsat_1_v5_gn_8_152940' => 'lsa', 'Lsat_1_v5_gn_8_62401' => 'lsa', 'Manes.06G055900' => 'mes', 'Manes.12G022200' => 'mes', 'Manes.13G023300' => 'mes', 'Manes.14G115000' => 'mes', 'Manes.15G151700' => 'mes', 'Manes.17G111300' => 'mes', 'Mapoly0226s0009' => 'mpo', 'MBI02_g25363_MAGBIO' => 'mbi', 'MBI06_g00027_MAGBIO' => 'mbi', 'MBI10_g13034_MAGBIO' => 'mbi', 'MD09G1023400' => 'mdo', 'MD13G1100100' => 'mdo', 'MD15G1169200' => 'mdo', 'MD16G1101100' => 'mdo', 'MD17G1022900' => 'mdo', 'Medtr3g096150' => 'mtr', 'Medtr4g115070' => 'mtr', 'Medtr7g033325' => 'mtr', 'Medtr8g089840' => 'mtr', 'MELO3C010319.2' => 'cme', 'MELO3C011944.2' => 'cme', 'MELO3C021589.2' => 'cme', 'Migut.E00207' => 'egut', 'Migut.H00067' => 'egut', 'Migut.K00433' => 'egut', 'Migut.K00606' => 'egut', 'Migut.K01410' => 'egut', 'MSTRG.13347' => 'ama', 'MSTRG.24045' => 'ama', 'MSTRG.2428' => 'ama', 'MSTRG.26410' => 'ama', 'MSTRG.3139' => 'ama', 'MSTRG.3286' => 'ama', 'MSTRG.563' => 'ama', 'MSTRG.7941' => 'ama', 'Nitab4.5_0000028g0060' => 'nta', 'Nitab4.5_0000065g0260' => 'nta', 'Nitab4.5_0000112g0060' => 'nta', 'Nitab4.5_0000489g0120' => 'nta', 'Nitab4.5_0001776g0050' => 'nta', 'Nitab4.5_0001854g0010' => 'nta', 'Nitab4.5_0001860g0020' => 'nta', 'Nitab4.5_0004352g0010' => 'nta', 'Nitab4.5_0008716g0020' => 'nta', 'Nitab4.5_0008922g0010' => 'nta', 'Nn3g16693' => 'nnu', 'Nn4g22596' => 'nnu', 'Nn7g37639' => 'nnu', 'Oeu001701.1' => 'oeu', 'Oeu018149.1' => 'oeu', 'Oeu026220.1' => 'oeu', 'Oeu038635.1' => 'oeu', 'Oeu049176.1' => 'oeu', 'Oeu056706.1' => 'oeu', 'Oeu056937.1' => 'oeu', 'Oeu057540.1' => 'oeu', 'Os02g0594900' => 'osa', 'Os02g0595100' => 'osa', 'Os04g0477500' => 'osa', 'Os12g0611900' => 'osa', 'Peaxi162Scf00076g00020' => 'pax', 'Peaxi162Scf00128g00217' => 'pax', 'Peaxi162Scf00129g01640' => 'pax', 'Peaxi162Scf00669g00007' => 'pax', 'Peaxi162Scf00700g00421' => 'pax', 'Peaxi162Scf00801g00038' => 'pax', 'Peaxi162Scf00891g00025' => 'pax', 'PGR083G0909' => 'pgr', 'PGR119G1005' => 'pgr', 'PGR142G2236' => 'pgr', 'PGR142G3388' => 'pgr', 'PGSC0003DMG400004514' => 'stu', 'PGSC0003DMG400012635' => 'stu', 'PGSC0003DMG400015730' => 'stu', 'PGSC0003DMG400018611' => 'stu', 'PGSC0003DMG400030897' => 'stu', 'Phvul.001G254800' => 'pvu', 'Phvul.002G260100' => 'pvu', 'Phvul.003G167600' => 'pvu', 'Phvul.004G005100' => 'pvu', 'Potri.001G343600' => 'ptr', 'Potri.006G066700' => 'ptr', 'Potri.008G186000' => 'ptr', 'Potri.010G046900' => 'ptr', 'Potri.018G127900' => 'ptr', 'Pp3c20_17750' => 'ppa', 'Pp3c24_4380' => 'ppa', 'Prupe.1G245800' => 'ppe', 'Prupe.3G293400' => 'ppe', 'Prupe.7G247400' => 'ppe', 'Psat0s145g0120' => 'psa', 'Psat0s595g0040' => 'psa', 'Psat0s595g0120' => 'psa', 'Psat3g175040' => 'psa', 'Psat7g058120' => 'psa', 'PSO017G0428' => 'pso', 'PSO063G7510' => 'pso', 'PSO067G0046' => 'pso', 'PSO478G1073' => 'pso', 'PSO675G3677' => 'pso', 'PSO675G6558' => 'pso', 'PSO675G7520' => 'pso', 'PSO675G8959' => 'pso', 'QL02p074089' => 'qlo', 'QL02p089614' => 'qlo', 'QL03p057736' => 'qlo', 'RcHm_v2.0_Chr1g0364131' => 'rch', 'RcHm_v2.0_Chr2g0087801' => 'rch', 'RcHm_v2.0_Chr2g0087821' => 'rch', 'RcHm_v2.0_Chr2g0173231' => 'rch', 'RcHm_v2.0_Chr4g0433111' => 'rch', 'Rhsim03G0250300' => 'rsi', 'Rhsim08G0048400' => 'rsi', 'Rhsim10G0014800' => 'rsi', 'Rhsim12G0040100' => 'rsi', 'Rhsim12G0109700' => 'rsi', 'Sabra06G0049600' => 'sbr', 'Sabra08G0141000' => 'sbr', 'Sabra10G0021400' => 'sbr', 'Sabra16G0222900' => 'sbr', 'Sabra18G0108600' => 'sbr', 'SalBow1G0433' => 'sbo', 'SalBow1G2038' => 'sbo', 'SalBow1G5003' => 'sbo', 'SalBow7G1197' => 'sbo', 'SalBow8G3506' => 'sbo', 'Sc03g0007300' => 'sci', 'Sc11g0000950' => 'sci', 'Sc14g0008750' => 'sci', 'Sc18g0000420' => 'sci', 'Sed0006754' => 'sed', 'Sed0008741' => 'sed', 'Sed0017172' => 'sed', 'Sed0018925' => 'sed', 'Sed0023326' => 'sed', 'Sed0025909' => 'sed', 'SEGI_05333' => 'sgi', 'SEGI_10362' => 'sgi', 'SEGI_13380' => 'sgi', 'SEGI_24306' => 'sgi', 'SEGI_29077' => 'sgi', 'SEGI_29095' => 'sgi', 'SEGI_36534' => 'sgi', 'SEGI_37506' => 'sgi', 'SEGI_38321' => 'sgi', 'SGA_v2.0_scaffold307G48031' => 'sas', 'SGA_v2.0_scaffold47G17507' => 'sas', 'SGA_v2.0_scaffold63G21736' => 'sas', 'SGA_v2.0_scaffold87G27070' => 'sas', 'SHI17794' => 'shi', 'SHI28851' => 'shi', 'SMO165G0155' => 'smo', 'SMO340G0217' => 'smo', 'SMO367G1210' => 'smo', 'Solyc02g093430.3' => 'sly', 'Solyc05g013580.4' => 'sly', 'Solyc07g008030.3' => 'sly', 'Solyc12g035470.2' => 'sly', 'Sopen02g038020' => 'spe', 'Sopen05g008490' => 'spe', 'Sopen07g003910' => 'spe', 'Sopen12g015240' => 'spe', 'Sp1g11550' => 'spa', 'Sp2g16710' => 'spa', 'Sp3g00430' => 'spa', 'Sp3g26780' => 'spa', 'Sp5g22900' => 'spa', 'Sp6g29530' => 'spa', 'TAR371G0794' => 'tar', 'TAR374G0164' => 'tar', 'TAR622G0165' => 'tar', 'TAR626G0929' => 'tar', 'TAR629G2155' => 'tar', 'THA.LOC104805282' => 'tha', 'THA.LOC104805363' => 'tha', 'THA.LOC104808968' => 'tha', 'THA.LOC104821093' => 'tha', 'THA.LOC104823953' => 'tha', 'THA.LOC104825562' => 'tha', 'THA.LOC104825665' => 'tha', 'Thecc.02G261400' => 'tca', 'Thecc.04G019200' => 'tca', 'Thecc.09G130400' => 'tca', 'Thhalv10004374m.g' => 'esa', 'Thhalv10007850m.g' => 'esa', 'Thhalv10013782m.g' => 'esa', 'Thhalv10018686m.g' => 'esa', 'Thhalv10020899m.g' => 'esa', 'Thhalv10022755m.g' => 'esa', 'TPR.G23851' => 'tpr', 'TPR.G26500' => 'tpr', 'TPR.G27267' => 'tpr', 'TPR.G32001' => 'tpr', 'TPR.G6251' => 'tpr', 'TPR.G8167' => 'tpr', 'TWI12G1330' => 'twi', 'TWI18G1239' => 'twi', 'TWI34G0979' => 'twi', 'TWI36G0670' => 'twi', 'TWI36G0707' => 'twi', 'TWI56G0233' => 'twi', 'TWI75G1809' => 'twi', 'unitig_21.g20874' => 'ugi', 'unitig_26.g10343' => 'ugi', 'unitig_46.g18392' => 'ugi', 'unitig_52.g17178' => 'ugi', 'unitig_8.g2934' => 'ugi', 'vmacro01122' => 'vma', 'vmacro05875' => 'vma', 'vmacro06147' => 'vma', 'vmacro16191' => 'vma', 'vmacro18293' => 'vma', 'VMungo0251G3707' => 'vmu', 'VMungo0464G1521' => 'vmu', 'VMungo1215G0205' => 'vmu', 'VMungo1383G2484' => 'vmu', 'Zm00001eb079610' => 'zma', 'Zm00001eb135990' => 'zma', 'Zm00001eb183710' => 'zma', 'Zm00001eb246020' => 'zma' ) $gf_id = 'HOM05D001124' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001124' ) $data_identifier = 'HOM05D001124' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 6, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 7, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 21, 'bol' => (int) 10, 'bra' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 6, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 9, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 21, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 8, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 10, 'lsa' => (int) 8, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 8, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 9, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb246020' $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